Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4418299
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 127125 characters in sequence are not A, C, G, or T
File 8 of 28
Found at i:1107991 original size:23 final size:23
Alignment explanation
Indices: 1107956--1107999 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1107946 TTTTTTCTAA
*
1107956 ATTTTAAAATTTTTTTATTTTTG
1 ATTTTAAAATTTTTTCATTTTTG
* *
1107979 ATTTTTAATTTTTTTCATTTT
1 ATTTTAAAATTTTTTCATTTT
1108000 ATTATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTAAAATTTTTTCATTTTTG
Found at i:1116300 original size:19 final size:18
Alignment explanation
Indices: 1116276--1116343 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
1116266 ATTTTTTTCC
1116276 AAAAAACAAAAAAAAATTA
1 AAAAAACAAAAAAAAA-TA
*
1116295 AAAAAATAAAAACAAAATA
1 AAAAAACAAAAA-AAAATA
*
1116314 AAAAAAGAGAAAAAAAA-A
1 AAAAAACA-AAAAAAAATA
*
1116332 AAGAAAAGAAAA
1 AA-AAAACAAAA
1116344 GAACCTACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.14
19 30 0.68
20 8 0.18
ACGTcount: A:0.85, C:0.03, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAACAAAAAAAAATA
Found at i:1116311 original size:14 final size:13
Alignment explanation
Indices: 1116283--1116343 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
1116273 TCCAAAAAAC
**
1116283 AAAAAAAAATTAA
1 AAAAAAAAAAGAA
*
1116296 AAAAATAAAAACAA
1 AAAAA-AAAAAGAA
*
1116310 AATAAAAAAAGAGA
1 AAAAAAAAAAGA-A
1116324 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
1116337 AAGAAAA
1 AA-AAAA
1116344 GAACCTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 14 0.35
14 26 0.65
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:1116328 original size:17 final size:17
Alignment explanation
Indices: 1116294--1116343 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1116284 AAAAAAAATT
*
1116294 AAAAAAATAAAA-ACAAA
1 AAAAAAAGAAAAGA-AAA
* *
1116311 ATAAAAA-AAGAGAAAA
1 AAAAAAAGAAAAGAAAA
1116327 AAAAAAAGAAAAGAAAA
1 AAAAAAAGAAAAGAAAA
1116344 GAACCTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.86, C:0.02, G:0.08, T:0.04
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAAA
Found at i:1117414 original size:61 final size:61
Alignment explanation
Indices: 1117309--1118178 Score: 823
Period size: 61 Copynumber: 14.3 Consensus size: 61
1117299 AACCTTTTAT
* * * * * * **
1117309 CCTTTCAGTCCTCAAAGAGTAAGAC-AC-TTTCCTTTCAAAACCCACACAAGTTGGTGATA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1117368 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** * *
1117429 -TTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCGTACAAATTGGCGGCA
1 CCTTTT-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** *
1117490 -CTTTCTAGTCCTCAAAGAGCAAAACGCCTTTTCCTTTTAAAGCCCACGCAAGTTGGTGGCA
1 CCTTT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** * * * * *
1117551 -TTTTTCAGTCCTCAAAGAGTAGGACGTTTTTTCCTTTCAAAGTCCATATAAATTGGTGGCA
1 CCTTTT-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
1117612 CCTTTCAATCCTCAAAGAGCATGATGTCTTTTCCTTTTAAAACCCACA-AAGTTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1117672 -CTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGATGGCA
1 CCTTT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1117733 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1117794 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCTTTTTAAAACCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * * * *
1117855 CCTTCCAATCCTCAAAAAACAAGACG-C-TTTCCTTTCAAAGCCTACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
1117914 CCTTTTAATCCTCAAAGAGCAGGACGCCTTTTTATTTTAAAGCCTACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * * *
1117975 CCTTCTAGTCCTCAAAGAGCAAGATG-C-TTT-CTTTCCAAAGCTCACACAAGTTGATCGTA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT-TAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1118034 CCTTCTAGTCCTCAAAGAGCAAGAC-AC-TTTCTTTTTGCAAAGCCCACGCGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT--AAAGCCCACACAAGTTGGTGGCA
* * * * * * *
1118095 CCTTCTAGTCCCCAAAAAGCAGGACACTTTCCTTTTTCTTTTTAAAGCCCACACAAGTTAGTAGC
1 CCTTTTAGTCCTCAAAGAGCAGG--AC--GCC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
1118160 A
61 A
*
1118161 CCTTTTAGTTCTCAAAGA
1 CCTTTTAGTCCTCAAAGA
1118179 AAAGGATCCA
Statistics
Matches: 671, Mismatches: 117, Indels: 39
0.81 0.14 0.05
Matches are distributed among these distances:
58 3 0.00
59 122 0.18
60 58 0.09
61 435 0.65
62 8 0.01
63 2 0.00
66 34 0.05
68 9 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (61 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1117745 original size:243 final size:243
Alignment explanation
Indices: 1117309--1118178 Score: 875
Period size: 243 Copynumber: 3.6 Consensus size: 243
1117299 AACCTTTTAT
* * * ** *
1117309 CCTTTCAGTCCTCAAAGAGTAAGAC-AC-TTTCCTTTCAAAACCCACACAAGTTGGTGATACTTT
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTCAAAACCCACACAAATTGGTGGCACCTT
** * * *
1117372 TTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCATTTTTCAG
66 CCAATCCTCAAAGAGCAAGATG-CTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTT-AG
** * *
1117437 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCGTACAAATTGGCGGCA-CTTTCTAGTCC
129 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGGTGGCACCTTTCTAGTCC
* *
1117501 TCAAAGAGCAAAACGCCTTTTCCTTTTAAAGCCCACGCAAGTTGGTGGCA
194 TCAAAGAGCAAAACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * ** ** * *
1117551 TTTTTCAGTCCTCAAAGAGTAGGACGTTTTTTCCTTTCAAAGTCCATATAAATTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTCAAAACCCACACAAATTGGTGGCACCTT
* * *
1117616 TCAATCCTCAAAGAGCATGATGTCTTTTCCTTTTAAAACCCACA-AAGTTAGTGGCACTTTCTAG
66 CCAATCCTCAAAGAGCAAGATG-CTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTT-TAG
*
1117680 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGATGGCACCTTTC-AGTCC
129 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGGTGGCACCTTTCTAGTCC
** *
1117744 TCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCA
194 TCAAAGAGCAAAACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1117794 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTCAAAACCCACACAAATTGGTGGCACCTT
* * * * * * *
1117859 CCAATCCTCAAAAAACAAGACGC-TTTCCTTTCAAAGCCTACACAAGTTGGTGGCACCTTTTAAT
66 CCAATCCTCAAAGAGCAAGATGCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA-CTTTTAGT
** *
1117923 CCTCAAAGAGCAGGACGCCTTTTTATTTTAAAGCCTACACAAGTTGGTGGCACC-TTCTAGTCCT
130 CCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGGTGGCACCTTTCTAGTCCT
* ** * * * * *
1117987 CAAAGAGCAAGA-TGC-TTT-CTTTCCAAAGCTCACACAAGTTGATCGTA
195 CAAAGAGCAAAACACCTTTTCCTTT-TAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1118034 CC-TTCTAGTCCTCAAAGAGCAAGAC-AC-TTTCTTTTTGCAAAGCCCACGCGAGTTGGTGGCAC
1 CCTTTC-AGTCCTCAAAGAGCAAGACGCCTTTTC-CTTT-CAAAACCCACACAAATTGGTGGCAC
* * * * * * * *
1118096 CTTCTAGTCCCCAAAAAGCAGGACACTTTCCTTTTTCTTTTTAAAGCCCACACAAGTTAGTAGCA
63 CTTCCAATCCTCAAAGAGCA--AGA---TGC-TTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
*
1118161 CCTTTTAGTTCTCAAAGA
122 -CTTTTAGTCCTCAAAGA
1118179 AAAGGATCCA
Statistics
Matches: 526, Mismatches: 84, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
238 4 0.01
239 12 0.02
240 79 0.15
241 20 0.04
242 106 0.20
243 188 0.36
244 73 0.14
245 1 0.00
247 43 0.08
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (243 bp):
CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTCAAAACCCACACAAATTGGTGGCACCTT
CCAATCCTCAAAGAGCAAGATGCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTAGTC
CTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCTATACAAGTTGGTGGCACCTTTCTAGTCCTC
AAAGAGCAAAACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1118287 original size:82 final size:81
Alignment explanation
Indices: 1118198--1118598 Score: 436
Period size: 82 Copynumber: 4.9 Consensus size: 81
1118188 ACTTCATTTC
*
1118198 TTTCCTTTCTCTTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTTTTTCCCTTTGTCCTCAAA
1 TTTCCTTT-TCTTTTGTCCTCAAAGAGCAGGACATATTTTATTTCTTTTTCCCTTTGTCCTCAAA
*
1118263 GAGTATGACGCATTTTA
65 GAGTAGGACGCATTTTA
* * *
1118280 TTTCCTTTTCTCTTTGTCCTCAAAGAGTAGGAAATATTTTATTTCTTTTTCCATTTGTCCTCAAA
1 TTTCCTTTTCT-TTTGTCCTCAAAGAGCAGGACATATTTTATTTCTTTTTCCCTTTGTCCTCAAA
*
1118345 GAGTATGACGCATTTTA
65 GAGTAGGACGCATTTTA
* * *
1118362 TTTTCTTTTCTCTTTGTCCTCAAATAGCAGGACATACTTTATTTCTTTTTCTCCTTTGTCCTCAA
1 TTTCCTTTTCT-TTTGTCCTCAAAGAGCAGGACATATTTTATTTCTTTTTC-CCTTTGTCCTCAA
* *
1118427 AGAGTAGGACACACTTAATTT
64 AGAGTAGGACGCA-TT--TTA
* * ** ** *
1118448 TTTTCTTTTCCTTTGTCCTCAAAGAGCAGGATGTATTTTATTTCCTTTTTTTCTTTGTCCTCGAA
1 TTTCCTTTTCTTTTGTCCTCAAAGAGCAGGACATATTTTATTT-CTTTTTCCCTTTGTCCTCAAA
* * *
1118513 GAGTAGGATGCA-CTCA
65 GAGTAGGACGCATTTTA
* * ** *
1118529 -TT--TTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCA-TTCTCTTTT-CCTTTGTCCTCAAA
1 TTTCCTTTTCTTTTGTCCTCAAAGAGCAGGACATATTTTATTTCT-TTTTCCCTTTGTCCTCAAA
*
1118589 AAGTAGGACG
65 GAGTAGGACG
1118599 TACTCATTTT
Statistics
Matches: 279, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
76 22 0.08
77 6 0.02
78 30 0.11
80 2 0.01
81 4 0.01
82 122 0.44
83 23 0.08
84 2 0.01
85 50 0.18
86 18 0.06
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (81 bp):
TTTCCTTTTCTTTTGTCCTCAAAGAGCAGGACATATTTTATTTCTTTTTCCCTTTGTCCTCAAAG
AGTAGGACGCATTTTA
Found at i:1118436 original size:42 final size:42
Alignment explanation
Indices: 1118203--1118520 Score: 360
Period size: 41 Copynumber: 7.6 Consensus size: 42
1118193 ATTTCTTTCC
*
1118203 TTTCTCTTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
* ** *
1118245 TTTC-CCTTTGTCCTCAAAGAGTATGACGCATTTTATTTCCT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
*
1118286 TTTCT-CTTTGTCCTCAAAGAGTAGGAAATATTTTATTTCTT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
* * **
1118327 TTTC-CATTTGTCCTCAAAGAGTATGACGCATTTTATTT-TCT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCT-T
* * *
1118368 TTTCT-CTTTGTCCTCAAATAGCAGGACATACTTTATTTCTT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
* * * *
1118409 TTTCTCCTTTGTCCTCAAAGAGTAGGACACACTTAATTTTTT
1 TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
* * **
1118451 TCTTTTCCTTTGTCCTCAAAGAGCAGGATGTATTTTATTTCCTT
1 T-TTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTT-CTT
* *
1118495 TTT-TTCTTTGTCCTCGAAGAGTAGGA
1 TTTCTCCTTTGTCCTCAAAGAGTAGGA
1118521 TGCACTCATT
Statistics
Matches: 230, Mismatches: 38, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.00
41 136 0.59
42 57 0.25
43 33 0.14
44 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.46
Consensus pattern (42 bp):
TTTCTCCTTTGTCCTCAAAGAGTAGGACATATTTTATTTCTT
Found at i:1118533 original size:36 final size:35
Alignment explanation
Indices: 1118493--1118621 Score: 109
Period size: 36 Copynumber: 3.5 Consensus size: 35
1118483 TTTTATTTCC
*
1118493 TTTTTTTCTTTGTCCTCGAAGAGTAGGATGCACTCA
1 TTTTTTTCTTTGTCCTC-AAGAGTAGGACGCACTCA
* * * *
1118529 TTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCA
1 TTTTTTTCTTTGTCCTCAA-GAGTAGGACGCA-CTCA
* *
1118566 TTCTCTTTTCCTTTGTCCTCAAAAAGTAGGACGTACTCA
1 TT-T-TTTT-CTTTGTCCTC-AAGAGTAGGACGCACTCA
*
1118605 --TTTTCCTTTGTCCTCAA
1 TTTTTTTCTTTGTCCTCAA
1118622 AAAAGCAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
33 2 0.03
34 10 0.13
35 5 0.07
36 26 0.35
37 5 0.07
38 1 0.01
39 6 0.08
40 18 0.24
41 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (35 bp):
TTTTTTTCTTTGTCCTCAAGAGTAGGACGCACTCA
Found at i:1118539 original size:78 final size:74
Alignment explanation
Indices: 1118453--1118622 Score: 205
Period size: 76 Copynumber: 2.2 Consensus size: 74
1118443 AATTTTTTTC
*** * * * * *
1118453 TTTTCCTTTGTCCTCAAAGAGCAGGATGTATTTTATTTCCTTTTTTTCTTTGTCCTCGAAGAGTA
1 TTTTCCTTTGTCCTCAAAGAGCAGGACCCATTTCA-TT-CTCTTTTCCTTTGTCCTCAAAAAGTA
*
1118518 GGATGCACTCA
64 GGACGCACTCA
*
1118529 TTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTA
1 --TTTTCCTTTGTCCTCAAAGAGCAGGACCCATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTA
*
1118594 GGACGTACTCA
64 GGACGCACTCA
1118605 TTTTCCTTTGTCCTCAAA
1 TTTTCCTTTGTCCTCAAA
1118623 AAAGCAAGAC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
74 17 0.21
76 31 0.39
77 2 0.03
78 30 0.38
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (74 bp):
TTTTCCTTTGTCCTCAAAGAGCAGGACCCATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTAGG
ACGCACTCA
Found at i:1119278 original size:30 final size:30
Alignment explanation
Indices: 1119204--1119279 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
1119194 CATTCTTCAT
* *
1119204 TGTATCGATACATCCTGGGTTTTACCCAGA
1 TGTATCGATACATTCTAGGTTTTACCCAGA
*
1119234 TGTATCGATGCATTCTAGGTTTTACCCAGA
1 TGTATCGATACATTCTAGGTTTTACCCAGA
*
1119264 TGTATCGGTACATTCT
1 TGTATCGATACATTCT
1119280 TCATTATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (30 bp):
TGTATCGATACATTCTAGGTTTTACCCAGA
Found at i:1119344 original size:50 final size:50
Alignment explanation
Indices: 1119233--1119348 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
1119223 TTTTACCCAG
* *
1119233 ATGTATCGATGCATTCTAGGTTTTACCCAGATGTATCGGTACATTCTTCA
1 ATGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTCTTCA
* * * * *
1119283 TTATATTGATACATTCTGGGTTTTACCTAGATGTATCGATACATT-TCTCA
1 ATGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTCT-TCA
1119333 ATGTATCGATACATTC
1 ATGTATCGATACATTC
1119349 AGGCATTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 54 0.98
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (50 bp):
ATGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTCTTCA
Found at i:1121777 original size:79 final size:78
Alignment explanation
Indices: 1121670--1122025 Score: 387
Period size: 79 Copynumber: 4.5 Consensus size: 78
1121660 CATGTTTTCA
* * * *
1121670 TTTCTAAAACATTGATTTTCCACC-TCGGGGATACTCCAGCCTCGTTATTTTTG-AGGGAATACT
1 TTTC-AAAACATCGATTTTTCACCATCGGGGATACTCCAACCTCATTATTTTTGAAGGG-ATACT
* *
1121733 TCAATCTCGGTTTTAT
64 CCAA-CTCAGTTTTAT
* * * *
1121749 TTTTAAAACATCGATTTTTCACCATCGGGAATACTCCAACCTCGTTATTTTTGAGGGGATACTCC
1 TTTCAAAACATCGATTTTTCACCATCGGGGATACTCCAACCTCATTATTTTTGAAGGGATACTCC
1121814 AACTCCAGTTTTAT
66 AACT-CAGTTTTAT
** * * *
1121828 TTTCAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTCTGAAGGGATACTTC
1 TTTCAAAACATCGATTTTTCACCATCGGGGATACTCCAACCTCATTATTTTTGAAGGGATACTCC
*
1121893 AAC-CTTGATTTTAT
66 AACTC-AG-TTTTAT
* * * * * * *
1121907 TTTCAAAACA-CTAATTTTCCACAACCAGAGATACTCCTACCTCATTATTTTTGAAGGGATACTC
1 TTTCAAAACATC-GATTTTTCACCATCGGGGATACTCCAACCTCATTATTTTTGAAGGGATACTC
*
1121971 CAACCCAGTTTTAT
65 CAACTCAGTTTTAT
* *
1121985 TTCCAAAACACCGATTTTTCACCATCGGGGATACTCCAACC
1 TTTCAAAACATCGATTTTTCACCATCGGGGATACTCCAACC
1122026 CCGATTTTTA
Statistics
Matches: 232, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 58 0.25
79 169 0.73
80 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (78 bp):
TTTCAAAACATCGATTTTTCACCATCGGGGATACTCCAACCTCATTATTTTTGAAGGGATACTCC
AACTCAGTTTTAT
Found at i:1121955 original size:158 final size:157
Alignment explanation
Indices: 1121663--1122027 Score: 432
Period size: 158 Copynumber: 2.3 Consensus size: 157
1121653 TTTCATTCAT
* ** * * * * * *
1121663 GTTTTCATTTCTAAAACATTGATTTTCCAC-CTCGGGGATACTCCAGCCTCGTTATTTTTGAGGG
1 GTTTT-ATTTCCAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCTGAGGG
* * * * * * * *
1121727 AATACTTCAATCTCGGTTTTATTTTTAAAACATCGATTTTTCACCATCGGGAATACTCCAACCTC
65 AATACTTCAACCTCGATTTTATTTTCAAAACATCAATTTTCCACAACCGAGAATACTCCAACCTC
* *
1121792 GTTATTTTTGAGGGGATACTCCAACTCCA
130 ATTATTTTTGAAGGGATACTCCAAC-CCA
* * *
1121821 GTTTTATTTTCAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTCTGAAGGG
1 GTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCTG-AGGG
* *
1121886 -ATACTTCAACCTTGATTTTATTTTCAAAACA-CTAATTTTCCACAACC-AGAGATACTCCTACC
65 AATACTTCAACCTCGATTTTATTTTCAAAACATC-AATTTTCCACAACCGAGA-ATACTCCAACC
1121948 TCATTATTTTTGAAGGGATACTCCAACCCA
128 TCATTATTTTTGAAGGGATACTCCAACCCA
*
1121978 GTTTTATTTCCAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCC
1 GTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCC
1122028 GATTTTTATT
Statistics
Matches: 177, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
157 71 0.40
158 102 0.58
159 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (157 bp):
GTTTTATTTCCAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCTGAGGGA
ATACTTCAACCTCGATTTTATTTTCAAAACATCAATTTTCCACAACCGAGAATACTCCAACCTCA
TTATTTTTGAAGGGATACTCCAACCCA
Found at i:1122047 original size:52 final size:51
Alignment explanation
Indices: 1121962--1122079 Score: 150
Period size: 52 Copynumber: 2.3 Consensus size: 51
1121952 TATTTTTGAA
*
1121962 GGGATACTCCAA-CCC-AGTTTTATTTCCAAAACACCGATTTTTCACCATCG
1 GGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCGATTTTTCA-AATCG
* ** *
1122012 GGGATACTCCAACCCCGATTTTTATTTTTAAAACACCTATTTTTCAAATCG
1 GGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCGATTTTTCAAATCG
* *
1122063 GGGATATTCTAACCCCG
1 GGGATACTCCAACCCCG
1122080 TTACTTCCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 12 0.20
51 22 0.37
52 25 0.42
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCGATTTTTCAAATCG
Found at i:1122161 original size:208 final size:209
Alignment explanation
Indices: 1121803--1122220 Score: 499
Period size: 208 Copynumber: 2.0 Consensus size: 209
1121793 TTATTTTTGA
* *
1121803 GGGGATACTCCAACTCCAGTTTTATTTTCAAAACATCGATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCGATTTTTCATAATCGGGGATACTCCAAC
* * ** * *
1121868 CCCATTATTTCTGAAGGGATACTTCAACCTTGATTTTATTTTCAAAACACTAATTTTCCACAACC
66 CCCATTACTTCCGAAGGGATACTTCAACCCCGACTTTATTTTCAAAACACTAATTTTCCACAACA
*
1121933 AGAGATACTCCTACCTCATTATTTTTGAAGGGATACTCCAACCC-AGTTTTATTTCCAAAACACC
131 AGAGATACTCCTACCTCATTATTTCTGAAGGGATACTCCAACCCTAGTTTTATTTCCAAAACACC
* *
1121997 GATTTTTCACCATC
196 AATTTTCCACCATC
* * * * *
1122011 GGGGATACTCCAACCCCGATTTTTATTTTTAAAACACCTATTTTTCA-AATCGGGGATATTCTAA
1 GGGGATACTCCAACCCC-AGTTTTATTTTCAAAACACCGATTTTTCATAATCGGGGATACTCCAA
* * * * * *
1122075 CCCCGTTACTTCCGAGGGGATGC-TCTAACCCCGGCTTTATTTAT-AAAACA-TCGATTTTTCAC
65 CCCCATTACTTCCGAAGGGATACTTC-AACCCCGACTTTATTT-TCAAAACACT-AATTTTCCAC
* * *
1122137 AATCAAG-GATACTCC-AGCCTCATTATTTCTGAGGGGATACTTCAACCCTGGTTTTATTTCCAA
127 AA-CAAGAGATACTCCTA-CCTCATTATTTCTGAAGGGATACTCCAACCCTAGTTTTATTTCCAA
*
1122200 AACATCAATTTTCCACCATC
190 AACACCAATTTTCCACCATC
1122220 G
1 G
1122221 AGAAATGCAC
Statistics
Matches: 177, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
207 4 0.02
208 113 0.64
209 60 0.34
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (209 bp):
GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCGATTTTTCATAATCGGGGATACTCCAAC
CCCATTACTTCCGAAGGGATACTTCAACCCCGACTTTATTTTCAAAACACTAATTTTCCACAACA
AGAGATACTCCTACCTCATTATTTCTGAAGGGATACTCCAACCCTAGTTTTATTTCCAAAACACC
AATTTTCCACCATC
Found at i:1123666 original size:2 final size:2
Alignment explanation
Indices: 1123659--1123696 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1123649 GTTTACAATT
1123659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1123697 ATCTATCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1127317 original size:5 final size:5
Alignment explanation
Indices: 1127302--1127341 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
1127292 ACTCATAATT
1127302 ATTTAA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
1127342 TTAGCATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:1127486 original size:21 final size:22
Alignment explanation
Indices: 1127462--1127507 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1127452 TTAATAAAAA
1127462 TTTAGATTAAAAT-AATTTAAT
1 TTTAGATTAAAATCAATTTAAT
* * *
1127483 TTTATATTATATTCAATTTAAT
1 TTTAGATTAAAATCAATTTAAT
1127505 TTT
1 TTT
1127508 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAGATTAAAATCAATTTAAT
Found at i:1131845 original size:16 final size:15
Alignment explanation
Indices: 1131810--1131843 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1131800 ATAAATATCA
*
1131810 TAAATAAAATTATAT
1 TAAATAAAAATATAT
1131825 TAAATAAAAATATAT
1 TAAATAAAAATATAT
1131840 TAAA
1 TAAA
1131844 ATTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAAAAATATAT
Found at i:1135757 original size:20 final size:20
Alignment explanation
Indices: 1135732--1135769 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1135722 GTAAAAAGAT
1135732 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
1135752 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
1135770 TGGGTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1138409 original size:2 final size:2
Alignment explanation
Indices: 1138402--1138445 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1138392 TTATGGTGTC
1138402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1138444 AT
1 AT
1138446 TGATCAAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1138698 original size:15 final size:15
Alignment explanation
Indices: 1138678--1138713 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1138668 TATTTAAATT
1138678 TAAATATATAATA-TA
1 TAAATAT-TAATATTA
1138693 TAAATATTAATATTA
1 TAAATATTAATATTA
1138708 TAAATA
1 TAAATA
1138714 AATTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATATTAATATTA
Found at i:1139064 original size:19 final size:20
Alignment explanation
Indices: 1139026--1139072 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1139016 ATTTTAAATA
1139026 TAATATAAATATTATATATT
1 TAATATAAATATTATATATT
1139046 TAATAATAAATATTATAT-TT
1 TAAT-ATAAATATTATATATT
*
1139066 AAATATA
1 TAATATA
1139073 GTTATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 9 0.36
21 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATAAATATTATATATT
Found at i:1139138 original size:9 final size:9
Alignment explanation
Indices: 1139118--1139152 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1139108 ATTTTAATTT
1139118 ATTTA-ATA
1 ATTTATATA
*
1139126 ATTTATATT
1 ATTTATATA
1139135 ATTTATATA
1 ATTTATATA
1139144 ATTTATATA
1 ATTTATATA
1139153 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.21
9 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTATATA
Found at i:1139144 original size:18 final size:17
Alignment explanation
Indices: 1139094--1139151 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 17
1139084 TAATATAAAA
1139094 TATATTTATTTAA-AATT
1 TATA-TTATTTAATAATT
1139111 T-TAATTTATTTAATAATT
1 TAT-A-TTATTTAATAATT
1139129 TATATTATTTATATAATT
1 TATATTATTTA-ATAATT
1139147 TATAT
1 TATAT
1139152 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.03
17 18 0.49
18 17 0.46
19 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATTTAATAATT
Found at i:1140486 original size:2 final size:2
Alignment explanation
Indices: 1140479--1140503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1140469 AATTTAGTTT
1140479 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1140504 GTATTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1140621 original size:7 final size:7
Alignment explanation
Indices: 1140610--1140643 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1140600 TCTCCTCCCT
*
1140610 TTTTCTT
1 TTTTCTC
1140617 TTTTCTC
1 TTTTCTC
1140624 TTTTCTC
1 TTTTCTC
1140631 TTTTCTC
1 TTTTCTC
1140638 TTTTCT
1 TTTTCT
1140644 ATATTCATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTC
Found at i:1141695 original size:6 final size:6
Alignment explanation
Indices: 1141686--1141723 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1141676 TATTATATTT
* *
1141686 ATTATA ATTATA AATATA ATTATA ATTATA TTTATA AT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA AT
1141724 AAAATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATA
Found at i:1142219 original size:34 final size:33
Alignment explanation
Indices: 1142171--1142391 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
1142161 TGGTAAAAAC
* *
1142171 CACCATTTAATCAACAATGGCAACCTATCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
1142204 CTACAATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1142238 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1142272 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1142306 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1142340 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1142374 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1142392 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 130 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1142315 original size:102 final size:101
Alignment explanation
Indices: 1142171--1142391 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
1142161 TGGTAAAAAC
* * *
1142171 CACCATTTAATCAACAATGGCAACCTATCAAATCTACAATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCAA
* *
1142236 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
1142272 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCA
1142337 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1142374 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1142392 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACAATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1146846 original size:34 final size:33
Alignment explanation
Indices: 1146798--1147017 Score: 237
Period size: 34 Copynumber: 6.5 Consensus size: 33
1146788 TGGTAAAAAC
*
1146798 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1146831 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * * *
1146865 CACCCATTTAATCAATAATAGTAAGCTACCGAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1146899 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
1146933 CTCCCACTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1146967 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1147001 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1147018 CGATGAATCA
Statistics
Matches: 155, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
33 22 0.14
34 127 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1146914 original size:68 final size:67
Alignment explanation
Indices: 1146800--1147017 Score: 267
Period size: 68 Copynumber: 3.2 Consensus size: 67
1146790 GTAAAAACCA
* * *
1146800 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1146865 CAC
65 CAC
* * * * * *
1146868 CCATTTAATCAATAATAGTAAGCTACCGAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1146933 CTC
65 CAC
* * * * *
1146936 CCACTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1147001 CA-
65 CAC
1147003 CCATTTAATCAACAA
1 CCATTTAATCAACAA
1147018 CGATGAATCA
Statistics
Matches: 125, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
67 15 0.12
68 109 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1146977 original size:102 final size:101
Alignment explanation
Indices: 1146798--1147017 Score: 323
Period size: 102 Copynumber: 2.2 Consensus size: 101
1146788 TGGTAAAAAC
* * *
1146798 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCACTTAGTCAACAATGGCAAACCACCAA
* * *
1146863 ATCACCCATTTAATCAATAATAGTAAGCTACCGAAT
66 ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
** * * *
1146899 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCACTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCACTTAGTCAACAATGGCAAACCACCA
*
1146964 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATAGTAAACTACCAAAT
1147001 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1147018 CGATGAATCA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 15 0.14
102 89 0.86
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCACTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
Found at i:1147896 original size:22 final size:21
Alignment explanation
Indices: 1147871--1147925 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
1147861 AAAATTACAG
1147871 TTTTTCATCCAAAAAAAGCATT
1 TTTTTCATCCAAAAAAAGCA-T
1147893 TTTTTCATCCAAAAAAAGCAT
1 TTTTTCATCCAAAAAAAGCAT
*
1147914 TCTTTCATCCAA
1 TTTTTCATCCAA
1147926 CCAATGCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (21 bp):
TTTTTCATCCAAAAAAAGCAT
Found at i:1151423 original size:21 final size:21
Alignment explanation
Indices: 1151377--1151436 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1151367 TATTAAAAGT
*
1151377 TGCATTTTTTCATCCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
* **
1151398 AGCATTCTTTCATCCAACTAA
1 TGCATTCTTTCATCCAAAAAA
*
1151419 TGCA-TCATTTCATTCAAA
1 TGCATTC-TTTCATCCAAA
1151437 GATATCTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:1152503 original size:17 final size:19
Alignment explanation
Indices: 1152462--1152505 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1152452 ATTTTAAAAT
1152462 TATTATATCATCATATTTA
1 TATTATATCATCATATTTA
* *
1152481 TATTATATTAT-AT-TTTG
1 TATTATATCATCATATTTA
1152498 TATTATAT
1 TATTATAT
1152506 ATTCGAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.48
18 2 0.09
19 10 0.43
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTATATCATCATATTTA
Found at i:1152984 original size:27 final size:27
Alignment explanation
Indices: 1152954--1153005 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1152944 ACTTAAATAA
* *
1152954 AATATATTTAATTTATTTA-TATTTACT
1 AATAAATTT-ATTTATATATTATTTACT
1152981 AATAAATTTATTTATATATTATTTA
1 AATAAATTTATTTATATATTATTTA
1153006 AATTCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
AATAAATTTATTTATATATTATTTACT
Found at i:1153115 original size:16 final size:16
Alignment explanation
Indices: 1153094--1153127 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1153084 ATTATTTTAC
1153094 ATTTAATAATAATTAA
1 ATTTAATAATAATTAA
*
1153110 ATTTAATAATATTTAA
1 ATTTAATAATAATTAA
1153126 AT
1 AT
1153128 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAATAATAATTAA
Found at i:1153285 original size:18 final size:19
Alignment explanation
Indices: 1153249--1153289 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1153239 CTAATATTTA
**
1153249 TAAATAAATTTATTTAATT
1 TAAATAAATTTATAAAATT
1153268 TAAATAAA-TTATAAAATT
1 TAAATAAATTTATAAAATT
1153286 TAAA
1 TAAA
1153290 CACATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATAAATTTATAAAATT
Found at i:1153296 original size:18 final size:18
Alignment explanation
Indices: 1153264--1153298 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1153254 AAATTTATTT
*
1153264 AATTTAAATAAATTATAA
1 AATTTAAACAAATTATAA
*
1153282 AATTTAAACACATTATA
1 AATTTAAACAAATTATA
1153299 TTTTAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTTAAACAAATTATAA
Found at i:1153795 original size:8 final size:8
Alignment explanation
Indices: 1153782--1153825 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1153772 TAAATCTTAC
1153782 TATTTATA
1 TATTTATA
1153790 TATTTATATTA
1 TA-TT-TA-TA
1153801 TATTTATA
1 TATTTATA
1153809 TATTTA-A
1 TATTTATA
1153816 TATTTATA
1 TATTTATA
1153824 TA
1 TA
1153826 AATTTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.22
8 13 0.41
9 4 0.12
10 4 0.12
11 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:1153806 original size:19 final size:19
Alignment explanation
Indices: 1153782--1153856 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 19
1153772 TAAATCTTAC
1153782 TATTTATATATTTATATTA
1 TATTTATATATTTATATTA
1153801 TATTTATATATTTA-A-TA
1 TATTTATATATTTATATTA
* *
1153818 T-TTATATAAATTT-TAATA
1 TATT-TATATATTTATATTA
* *
1153836 TATTAATA-ATTTTTATTA
1 TATTTATATATTTATATTA
1153854 TAT
1 TAT
1153857 ACATTTTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.04
17 16 0.33
18 14 0.29
19 16 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTATATATTTATATTA
Found at i:1153846 original size:17 final size:18
Alignment explanation
Indices: 1153800--1153850 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1153790 TATTTATATT
1153800 ATATTTATAT--A-TTTA
1 ATATTTATATAAATTTTA
1153815 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
*
1153833 ATATATTA-ATAATTTTTA
1 ATAT-TTATATAAATTTTA
1153851 TTATATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 10 0.32
17 1 0.03
18 17 0.55
19 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:1153855 original size:18 final size:18
Alignment explanation
Indices: 1153811--1153856 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1153801 TATTTATATA
*
1153811 TTTAATAT-TTATATAAAT
1 TTTAATATATTA-ATAATT
1153829 TTTAATATATTAATAATT
1 TTTAATATATTAATAATT
*
1153847 TTTATTATAT
1 TTTAATATAT
1153857 ACATTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATATATTAATAATT
Found at i:1154299 original size:33 final size:34
Alignment explanation
Indices: 1154236--1154313 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 34
1154226 TTTATATTAT
*
1154236 AAAT-TAATTAAAATATAAAATTTAATTCAAA-A
1 AAATATAATTAAAATATAAAAATTAATTCAAATA
*
1154268 AAATATAATTATAAAT-TAAAAATT-ATATCAAATT
1 AAATATAATTA-AAATATAAAAATTAAT-TCAAATA
*
1154302 AAATATATTTAA
1 AAATATAATTAA
1154314 TTATTACTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 6 0.15
33 19 0.49
34 14 0.36
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (34 bp):
AAATATAATTAAAATATAAAAATTAATTCAAATA
Found at i:1155741 original size:49 final size:50
Alignment explanation
Indices: 1155624--1155754 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
1155614 AGTTGTTGTC
* * * * *
1155624 ATTGTTGACTATTTTTCACTAACTTTTGATAATAGAAAGAGGTGATCGTA
1 ATTGTTGACGATTTTTCACCAACTTTTGACAATAGAAAGAGGTGAGCATA
* * *
1155674 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-AAGAGAGGTG-GCATT
1 ATTGTTGACGATTTTTCACCAACTTTTGACAATAGAA-AGAGGTGAGCATA
1155723 ATTGTTGACGATTTTTCACCAACTTTTGACAA
1 ATTGTTGACGATTTTTCACCAACTTTTGACAA
1155755 ATGTGGTCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 34 0.49
50 36 0.51
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (50 bp):
ATTGTTGACGATTTTTCACCAACTTTTGACAATAGAAAGAGGTGAGCATA
Found at i:1155801 original size:21 final size:23
Alignment explanation
Indices: 1155771--1155813 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1155761 TCATAATTGT
*
1155771 TGACTCTAAATA-T-ATCAAGTA
1 TGACTATAAATAGTCATCAAGTA
1155792 TGACTATAAATAGTCATCAAGT
1 TGACTATAAATAGTCATCAAGT
1155814 TCATTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (23 bp):
TGACTATAAATAGTCATCAAGTA
Found at i:1161187 original size:58 final size:58
Alignment explanation
Indices: 1161101--1161217 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
1161091 TATAAAAGCA
*
1161101 TATTTATATATCAAGTAATTAGGTAGCCTTTAGACATTTAGTTAGATTAAAATTTATT
1 TATTTATATATAAAGTAATTAGGTAGCCTTTAGACATTTAGTTAGATTAAAATTTATT
**
1161159 TATTTATATATAAAGTAATTAGGTAGCCTTTAGATTTTTAGTTAGATTAAAATTTATT
1 TATTTATATATAAAGTAATTAGGTAGCCTTTAGACATTTAGTTAGATTAAAATTTATT
1161217 T
1 T
1161218 TACTCTCACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (58 bp):
TATTTATATATAAAGTAATTAGGTAGCCTTTAGACATTTAGTTAGATTAAAATTTATT
Found at i:1161275 original size:62 final size:62
Alignment explanation
Indices: 1161204--1161331 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 62
1161194 TTTTAGTTAG
1161204 ATTAAAATTTATTTTACTCTCACATAAAATAAAAATCTTTGACCACCTATCATAGTGCAAAT
1 ATTAAAATTTATTTTACTCTCACATAAAATAAAAATCTTTGACCACCTATCATAGTGCAAAT
* *
1161266 ATTAAAATTTATTTTACTCTCACATAAAATAAAAATCTTTGACCGCCTATCATAGTGCAGAT
1 ATTAAAATTTATTTTACTCTCACATAAAATAAAAATCTTTGACCACCTATCATAGTGCAAAT
1161328 ATTA
1 ATTA
1161332 TTTAGGTCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (62 bp):
ATTAAAATTTATTTTACTCTCACATAAAATAAAAATCTTTGACCACCTATCATAGTGCAAAT
Found at i:1165416 original size:163 final size:165
Alignment explanation
Indices: 1165096--1165472 Score: 485
Period size: 163 Copynumber: 2.3 Consensus size: 165
1165086 TAACTGCCAT
* *
1165096 TAAATCAGTTTTGAAAAATTCATTTATTTTCAT-ATGTTTTTCATTTTTTTCTTAAAATTTTCTT
1 TAAATCAGTTTTGAAAAATTCATTTATTTTCATGA-G-TTTTCATTTTTTCCTTAAAATTATCTT
** * * *
1165160 GTTTATGAAAAATTGAGTTTTCTATTTCATAAACATATTCGGGGGGATTTTTCTCAGTTTAAAAT
64 GTTTATGAAAAATCAAGTTTTCTATTTCATAAACATATTCGAGAGAATTTTTCTCAGTTTAAAAT
1165225 TTTTAAAATTCATCTAATAATATCATTAAATTTACAC
129 TTTTAAAATTCATCTAATAATATCATTAAATTTACAC
1165262 TAAATCAGTTTTGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTTCCTTAAAATTCAT-TTG
1 TAAATCAGTTTTGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTTCCTTAAAATT-ATCTTG
* ** * *
1165326 TTTCT--AAAATACAAGTTTTCTATTTCATAAATGTTTTCGAGAGAATTTTT-TCGGTTTAAAAT
65 TTTATGAAAAAT-CAAGTTTTCTATTTCATAAACATATTCGAGAGAATTTTTCTCAGTTTAAAAT
* * * *
1165388 TTTTAAAATTCATCTAATATTGTCATTAAATTTTCAT
129 TTTTAAAATTCATCTAATAATATCATTAAATTTACAC
* * * * * *
1165425 TAAATTAGTTTTGAAAAATTTAATTAATTTCATGAATTTTGATTTTTT
1 TAAATCAGTTTTGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTT
1165473 TGTATATGTT
Statistics
Matches: 186, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
163 91 0.49
164 31 0.17
165 28 0.15
166 35 0.19
167 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (165 bp):
TAAATCAGTTTTGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTTCCTTAAAATTATCTTGT
TTATGAAAAATCAAGTTTTCTATTTCATAAACATATTCGAGAGAATTTTTCTCAGTTTAAAATTT
TTAAAATTCATCTAATAATATCATTAAATTTACAC
Found at i:1165733 original size:20 final size:20
Alignment explanation
Indices: 1165708--1165754 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1165698 CATTATATGT
*
1165708 GTTGATCAGCCTCATCATGA
1 GTTGATCAACCTCATCATGA
* *
1165728 GTTGATCAACTTTATCATGA
1 GTTGATCAACCTCATCATGA
1165748 GCTTGAT
1 G-TTGAT
1165755 AATAGGGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
GTTGATCAACCTCATCATGA
Found at i:1165974 original size:10 final size:10
Alignment explanation
Indices: 1165961--1166004 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
1165951 GTGGAGAGGA
*
1165961 AAAAAGAGAG
1 AAAAAGAAAG
1165971 AAAAAGAAAG
1 AAAAAGAAAG
1165981 AAAAAGAAAG
1 AAAAAGAAAG
1165991 AAAAA-AAGAG
1 AAAAAGAA-AG
1166001 AAAA
1 AAAA
1166005 TAGGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 2 0.06
10 30 0.94
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1167800 original size:20 final size:21
Alignment explanation
Indices: 1167775--1167813 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1167765 TCTTAACGGC
1167775 CCATGTTC-ATGCATTTTGTG
1 CCATGTTCTATGCATTTTGTG
1167795 CCATGTTCTATGCATTTTG
1 CCATGTTCTATGCATTTTG
1167814 ACATGTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (21 bp):
CCATGTTCTATGCATTTTGTG
Found at i:1169867 original size:23 final size:24
Alignment explanation
Indices: 1169825--1169870 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1169815 AGATTAAAAC
1169825 TTTTATCAAAACTTAGATTTATTT
1 TTTTATCAAAACTTAGATTTATTT
1169849 TTTTATACAAAA-TTA-ATTTATT
1 TTTTAT-CAAAACTTAGATTTATT
1169871 CAAGGCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTATCAAAACTTAGATTTATTT
Found at i:1170984 original size:17 final size:17
Alignment explanation
Indices: 1170947--1170985 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1170937 CAATTTTTCA
* *
1170947 AAATAAATATTAATAAT
1 AAATAAATATAAATAAC
*
1170964 AAATAAATATAAATACC
1 AAATAAATATAAATAAC
1170981 AAATA
1 AAATA
1170986 TTATTTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAATATAAATAAC
Found at i:1179346 original size:16 final size:16
Alignment explanation
Indices: 1179325--1179357 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1179315 TAAATTTTTA
1179325 TATATACTTTCTTCTT
1 TATATACTTTCTTCTT
1179341 TATATACTTTCTTCTT
1 TATATACTTTCTTCTT
1179357 T
1 T
1179358 CCTAATGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATACTTTCTTCTT
Found at i:1182341 original size:20 final size:20
Alignment explanation
Indices: 1182313--1182387 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1182303 TTTTACCCAG
1182313 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1182333 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1182353 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
1182373 ATGTATCGATACATT
1 ATGTATCGATACATT
1182388 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1182373 original size:40 final size:39
Alignment explanation
Indices: 1182313--1182390 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1182303 TTTTACCCAG
*
1182313 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
1182353 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
1182391 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:1196407 original size:9 final size:9
Alignment explanation
Indices: 1196393--1196452 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
1196383 TTACACCAAA
1196393 AAAAAAAAC
1 AAAAAAAAC
1196402 AAAAAAAA-
1 AAAAAAAAC
*
1196410 AAACAAAAC
1 AAAAAAAAC
1196419 -AAAAAAAC
1 AAAAAAAAC
1196427 AAAAAAAA-
1 AAAAAAAAC
1196435 AGAAAAAATAGC
1 A-AAAAAA-A-C
1196447 AAAAAA
1 AAAAAA
1196453 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 15 0.35
9 21 0.49
10 1 0.02
11 5 0.12
12 1 0.02
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1196408 original size:13 final size:13
Alignment explanation
Indices: 1196390--1196435 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1196380 CCTTTACACC
1196390 AAAAAAAAAAAC-
1 AAAAAAAAAAACA
1196402 AAAAAAAAAAACA
1 AAAAAAAAAAACA
*
1196415 AAACAAAAAAACA
1 AAAAAAAAAAACA
1196428 AAAAAAAA
1 AAAAAAAA
1196436 GAAAAAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 12 0.39
13 19 0.61
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:1196412 original size:17 final size:17
Alignment explanation
Indices: 1196390--1196442 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
1196380 CCTTTACACC
1196390 AAAAAAAAAAACAAAAA
1 AAAAAAAAAAACAAAAA
*
1196407 AAAAAACAAAACAAAAA
1 AAAAAAAAAAACAAAAA
*
1196424 AACAAAAAAAAAGAAAAA
1 AA-AAAAAAAAACAAAAA
1196442 A
1 A
1196443 TAGCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.91, C:0.08, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAACAAAAA
Found at i:1196450 original size:25 final size:25
Alignment explanation
Indices: 1196389--1196435 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1196379 TCCTTTACAC
1196389 CAAAA-AAAAAAACAAAAAAAAAAA
1 CAAAACAAAAAAACAAAAAAAAAAA
1196413 CAAAACAAAAAAACAAAAAAAAA
1 CAAAACAAAAAAACAAAAAAAAA
1196436 GAAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (25 bp):
CAAAACAAAAAAACAAAAAAAAAAA
Found at i:1196452 original size:1 final size:1
Alignment explanation
Indices: 1196390--1196442 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
1196380 CCTTTACACC
* * * * *
1196390 AAAAAAAAAAACAAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1196443 TAGCAAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1196452 original size:12 final size:12
Alignment explanation
Indices: 1196389--1196435 Score: 85
Period size: 12 Copynumber: 3.8 Consensus size: 12
1196379 TCCTTTACAC
1196389 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1196401 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1196413 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
1196426 CAAAAAAAAA
1 CAAAAAAAAA
1196436 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 22 0.65
13 12 0.35
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1197740 original size:28 final size:28
Alignment explanation
Indices: 1197670--1198497 Score: 976
Period size: 29 Copynumber: 28.2 Consensus size: 28
1197660 GAACGTTCAA
*
1197670 ACCCTTTCAAAGCCCATAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
*
1197698 ACCCCTTTCAAAGCCCACAAGTCAATGGC
1 A-CCCTTTCAAAGCCCACAAGTCAGTGGC
1197727 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1197755 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1197783 ACTCTTTTCAAAGCCCACACGAGTCGGTGGC
1 AC-CCTTTCAAAGCCCACA--AGTCAGTGGC
*
1197814 AACTCTTTTTCAAAGCCCACAAGTCAGTGGC
1 -AC-C-CTTTCAAAGCCCACAAGTCAGTGGC
*
1197845 ACCCTTTCAAAGCCCACACAAGTCAGTGGT
1 ACCCTTTCAAAG-CC-CACAAGTCAGTGGC
*
1197875 ACCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1197903 ACCCCTTTCAAAGCCCACGAAAGTCAGTGGC
1 A-CCCTTTCAAAGCCCAC--AAGTCAGTGGC
*
1197934 ACCCTTTTAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1197962 ACTCTTTCCAAAGCCCACAAGACAGTGGC
1 ACCCTTT-CAAAGCCCACAAGTCAGTGGC
*
1197991 ACCCCTTTCAAAGCCCACAAGTAAGTGGC
1 A-CCCTTTCAAAGCCCACAAGTCAGTGGC
1198020 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
*
1198048 ACTCTTTTCAAAGCCCACAAGTCAGTGGC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
1198077 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
*
1198105 ACCCCTTTCAAAGCCCACGCAAGTTAGTGGC
1 A-CCCTTTCAAAGCCCA--CAAGTCAGTGGC
*
1198136 ACCCTTTCAAAGCCCACAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* * **
1198164 ACTCTTTTCAAAGCCCATAAGAAAGTGGC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
*
1198193 ACCCCTTTCGAAGCCCACAAGTCAGTGGC
1 A-CCCTTTCAAAGCCCACAAGTCAGTGGC
*
1198222 ACCCCTTTCAAAGCTCACAAGTCAGTGGC
1 A-CCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1198251 ACCTTTTCAAAACCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1198279 ACTCTTTTCAAAGCCCACAAGTCAGTGAC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
* * *
1198308 ACTCTTTTTAAAGCCCACACAAGTCAGTAGC
1 AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC
* *
1198339 AACTCTTTTCAAAGCCCACACAAATCAGTGGC
1 -AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC
1198371 ACCC-TTCTAAAGCCCACAAGTCAGTGGC
1 ACCCTTTC-AAAGCCCACAAGTCAGTGGC
* * * *
1198399 ACCCTTTTAAAGCCCACAAGCCAATGGTA
1 ACCCTTTCAAAGCCCACAAGTCAGTGG-C
*
1198428 ACTCTTTTCAAAGCCCACACGAGTCAGTGGC
1 AC-CCTTTCAAAGCCCACA--AGTCAGTGGC
*
1198459 AACCCTTTTC-AAGTCCCACATAAGTTAGTGGC
1 -ACCC-TTTCAAAG-CCCAC--AAGTCAGTGGC
1198491 ACCCTTT
1 ACCCTTT
1198498 TTTTAAAAAA
Statistics
Matches: 709, Mismatches: 57, Indels: 66
0.85 0.07 0.08
Matches are distributed among these distances:
28 224 0.32
29 260 0.37
30 86 0.12
31 64 0.09
32 59 0.08
33 15 0.02
34 1 0.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:1197758 original size:57 final size:57
Alignment explanation
Indices: 1197670--1198497 Score: 984
Period size: 57 Copynumber: 14.1 Consensus size: 57
1197660 GAACGTTCAA
* *
1197670 ACCCTTTCAAAGCCCATAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAATGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
1197727 ACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* * **
1197783 ACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTTCAAAGCCCACAAGTCAGTGGC
1 AC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1197845 ACCCTTTCAAAGCCCACACAAGTCAGTGGTA-CCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
*
1197903 ACCCCTTTCAAAGCCCACGAAAGTCAGTGGCA-CCCTTTTAAAGCCCACAAGTCAGTGGC
1 A-CCCTTTCAAAGCCCAC--AAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
1197962 ACTCTTTCCAAAGCCCACAAGACAGTGGCACCCCTTTCAAAGCCCACAAGTAAGTGGC
1 ACCCTTT-CAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1198020 ACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
*
1198077 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACGCAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCA--CAAGTCAGTGGC
* * * * **
1198136 ACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCATAAGAAAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1198193 ACCCCTTTCGAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCTCACAAGTCAGTGGC
1 A-CCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * *
1198251 ACCTTTTCAAAACCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGAC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * * *
1198308 ACTCTTTTTAAAGCCCACACAAGTCAGTAGCAACTCTTTTCAAAGCCCACACAAATCAGTGGC
1 AC-CCTTTCAAAG-CC-CACAAGTCAGTGGC-ACCCCTTTCAAAG-CC-CACAAGTCAGTGGC
* * * *
1198371 ACCC-TTCTAAAGCCCACAAGTCAGTGGCA-CCCTTTTAAAGCCCACAAGCCAATGGTA
1 ACCCTTTC-AAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGG-C
* * *
1198428 ACTCTTTTCAAAGCCCACACGAGTCAGTGGCAACCCTTTTC-AAGTCCCACATAAGTTAGTGGC
1 AC-CCTTTCAAAGCCCACA--AGTCAGTGGC-ACCCCTTTCAAAG-CCCAC--AAGTCAGTGGC
1198491 ACCCTTT
1 ACCCTTT
1198498 TTTTAAAAAA
Statistics
Matches: 669, Mismatches: 69, Indels: 61
0.84 0.09 0.08
Matches are distributed among these distances:
56 38 0.06
57 211 0.32
58 141 0.21
59 126 0.19
60 38 0.06
61 38 0.06
62 50 0.07
63 20 0.03
64 7 0.01
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (57 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:1199082 original size:20 final size:20
Alignment explanation
Indices: 1199054--1199128 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1199044 TTTTTACCCG
1199054 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1199074 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1199094 ATGTATAGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
1199114 ATGTATCGATACATT
1 ATGTATCGATACATT
1199129 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1199114 original size:40 final size:39
Alignment explanation
Indices: 1199054--1199131 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1199044 TTTTTACCCG
* *
1199054 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATAGATACATTCTTCAATATATCGATACAT-TATGA
* *
1199094 ATGTATAGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATAGATACATTCTTCAATATATCGATACATTATG
1199132 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATAGATACATTCTTCAATATATCGATACATTATGA
Found at i:1199176 original size:20 final size:20
Alignment explanation
Indices: 1199148--1199198 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1199138 TACCTAGATT
*
1199148 TATCAATACATTGAATAATG
1 TATCGATACATTGAATAATG
1199168 TATCGATACATTGAATAATG
1 TATCGATACATTGAATAATG
1199188 TATCGATACAT
1 TATCGATACAT
1199199 CTAGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTGAATAATG
Found at i:1203804 original size:19 final size:19
Alignment explanation
Indices: 1203780--1203843 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1203770 TTTCAGCGAT
1203780 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1203799 TTGTATTGATAC--AA---
1 TTGTATCGATACATAAGTG
1203813 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1203831 TTGTATCGATACA
1 TTGTATCGATACA
1203844 GTGTATCGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 10 0.27
15 2 0.05
17 2 0.05
19 23 0.62
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1203822 original size:32 final size:32
Alignment explanation
Indices: 1203781--1203856 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
1203771 TTCAGCGATT
*
1203781 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1203813 TGTATCGATACATAAGTGTTGTATCGATACAG
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1203845 TGTATCGCTACA
1 TGTATCGATACA
1203857 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1206296 original size:51 final size:50
Alignment explanation
Indices: 1206241--1206583 Score: 210
Period size: 52 Copynumber: 6.6 Consensus size: 50
1206231 TTAAGTTTCT
*
1206241 CAATTGTTCATAATCGGGAATACTCCAACCCCGGTTTTATTTCCAAAACAC
1 CAATT-TTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * *
1206292 CAATTCTCCTTTAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
1 CAATT-TTC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACAC
* * * * *
1206345 CAATTTTTCACAATTGAGGATACTCCAACCTC-G--TTATTTCATCAGGAATACTC
1 CAA-TTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTC--CA--AA-ACAC
*** * * * * *
1206398 CAA-CCCCATTACCTCTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATAT
1 CAATTTTCA-TA-ATC---GGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
** ** *
1206452 TGATTTCTCATAATCGGGGATACTCCAACCCTAGTTTTATTTCTAAAACAC
1 CAATTT-TCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * * *
1206503 TAATTTTCCACAATC-GGGATACTCCAACCCCGATTTTATTTCCAAAAACATT
1 CAATTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACA-C
* * * *
1206555 GATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCATAATCGGGGATACTCCAACC
1206584 TCGTTATTTC
Statistics
Matches: 224, Mismatches: 46, Indels: 43
0.72 0.15 0.14
Matches are distributed among these distances:
49 7 0.03
50 26 0.12
51 65 0.29
52 71 0.32
53 19 0.08
54 6 0.03
55 4 0.02
56 17 0.08
57 2 0.01
59 7 0.03
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (50 bp):
CAATTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
Found at i:1206366 original size:52 final size:52
Alignment explanation
Indices: 1206241--1206583 Score: 204
Period size: 51 Copynumber: 6.6 Consensus size: 52
1206231 TTAAGTTTCT
* * *
1206241 CAATTGTTCATAATCG-GGAATACTCCAACCCCGGTTTTATTTCC-AAAACAC
1 CAATTTTTCACAATCGAGG-ATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * ** *
1206292 CAATTCTCCTTTAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * * *
1206345 CAATTTTTCACAATTGAGGATACTCCAACCTCG---TTATTTCATCAGGAATACTC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTC--CA--AAAACAC
*** * ** * * *
1206398 CAACCCCATT-AC-CTCTGAGGGGATACTCCAACCCCGGCTTTATTT-CTAAAATAT
1 CAA--TTTTTCACAATC-GA--GGATACTCCAACCCCGATTTTATTTCCAAAAACAC
** * * * * *
1206452 TGATTTCTCATAATCGGGGATACTCCAA-CCCTAGTTTTATTT-CTAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGA-TTTTATTTCCAAAAACAC
* * *
1206503 TAATTTTCCACAATCG-GGATACTCCAACCCCGATTTTATTTCCAAAAACAT
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
**
1206554 TGATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTTCACAATCGAGGATACTCCAACC
1206584 TCGTTATTTC
Statistics
Matches: 224, Mismatches: 47, Indels: 41
0.72 0.15 0.13
Matches are distributed among these distances:
49 7 0.03
50 22 0.10
51 71 0.32
52 63 0.28
53 27 0.12
54 10 0.04
55 2 0.01
56 16 0.07
59 6 0.03
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:1206431 original size:108 final size:107
Alignment explanation
Indices: 1206308--1206699 Score: 360
Period size: 107 Copynumber: 3.7 Consensus size: 107
1206298 TCCTTTAATC
* *** *
1206308 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCAA
1206373 CCTCGTTATTTCATCAGGAATACTCCAACCCCATTACCTCTGA
66 CCTCGTTATTTCATCAGGAATACTCCAACCCCATTACCTC-GA
* * * * * *
1206416 GGGGATACTCCAACCCCGGCTTTATTT-CTAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCAA
* * * * * * *
1206480 CCCTAGTTTTATTTC-T-A--AA-ACACTAA----TTTTCCACAA
66 -CCTCG--TTATTTCATCAGGAATACTCCAACCCCATTACCTCGA
* *
1206516 TCGGGATACTCCAACCCCGATTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCA
1 -GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCA
* * *
1206581 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
65 ACCTCGTTATTTCATCAGGAATACTCCAACCCCATTACCT-CGA
* * * *
1206625 GGGGATACTCCAACCCC-AGCTTTATTTCC-AAAATATTGATTTCTCATAAT-TAGGGATACTCC
1 GGGGATACTCCAACCCCGA-CTTTATTTCCAAAAACATTGATTTTTCACAATCGA-GGATACTCC
* *
1206687 AACCCCATTATTT
64 AACCTCGTTATTT
1206700 TTGAGAGGAT
Statistics
Matches: 224, Mismatches: 43, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
99 7 0.03
100 2 0.01
101 33 0.15
102 32 0.14
103 1 0.00
104 5 0.02
105 5 0.02
106 3 0.01
107 67 0.30
108 59 0.26
109 3 0.01
110 7 0.03
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCAA
CCTCGTTATTTCATCAGGAATACTCCAACCCCATTACCTCGA
Found at i:1206610 original size:209 final size:211
Alignment explanation
Indices: 1206248--1206693 Score: 698
Period size: 209 Copynumber: 2.1 Consensus size: 211
1206238 TCTCAATTGT
* * **
1206248 TCATAATCGGGAATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTCTCCTTTAATCGGGGA
1 TCATAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGA
*
1206313 TACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAACCTCG
66 TACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCG
* *
1206378 TTATTTCATCAGGAATACTCCAACCCCATTACCTCTGAGGGGATACTCCAACCCCGGCTTTATTT
131 TTATTTCATCAGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTT
*
1206443 CTAAAATATTGATTTC
196 CCAAAATATTGATTTC
* * * *
1206459 TCATAATCGGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCC-ACAATC-GGGA
1 TCATAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGA
***
1206522 TACTCCAACCCCGATTTTATTTCCAAAAACATTGATTTTTCACAATCGAGGATACTCCAACCTCG
66 TACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCG
* * *
1206587 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTT
131 TTATTTCATCAGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTT
1206652 CCAAAATATTGATTTC
196 CCAAAATATTGATTTC
**
1206668 TCATAATTAGGGATACTCCAACCCCA
1 TCATAATCGGGGATACTCCAACCCCA
1206694 TTATTTTTGA
Statistics
Matches: 214, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
209 163 0.76
210 4 0.02
211 47 0.22
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (211 bp):
TCATAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGA
TACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCG
TTATTTCATCAGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTT
CCAAAATATTGATTTC
Found at i:1206710 original size:79 final size:78
Alignment explanation
Indices: 1206598--1206830 Score: 220
Period size: 79 Copynumber: 2.9 Consensus size: 78
1206588 TATTTCATCG
* ** * *
1206598 GGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTG
1 GGGATACTCCAACCCCGTTA-TTTTGAGAGGATACTCCAACCCCAGTTTTATTTCCAAAATATTG
*
1206663 ATTTCTCATAATTA
65 ATTTCTCATAACTA
* * * * *
1206677 GGGATACTCCAACCCCATTATTTTTGAGAGGATACTCCAATCCCAATTTTATTTCC-TAATCATC
1 GGGATACTCCAACCCCGTTA-TTTTGAGAGGATACTCCAACCCCAGTTTTATTTCCAAAAT-ATT
* *
1206741 GATCTT-TCACAACTG
64 GAT-TTCTCATAACTA
* * * *
1206756 GGGATACTCTAACCCCGTTATTTTCAAAGGGATACTCCAACCCC-GTTATTATCTCCAAAATATT
1 GGGATACTCCAACCCCGTTATTTTGAGA-GGATACTCCAACCCCAGTT-TTATTTCCAAAATATT
*
1206820 AAATTTCTCAT
64 -GATTTCTCAT
1206831 CGGGACATAT
Statistics
Matches: 122, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
78 11 0.09
79 101 0.83
80 10 0.08
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTTGAGAGGATACTCCAACCCCAGTTTTATTTCCAAAATATTGA
TTTCTCATAACTA
Found at i:1217144 original size:13 final size:13
Alignment explanation
Indices: 1217126--1217150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1217116 TTCAACGATT
1217126 TGTATCGATACAA
1 TGTATCGATACAA
1217139 TGTATCGATACA
1 TGTATCGATACA
1217151 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1217299 original size:52 final size:52
Alignment explanation
Indices: 1217255--1217354 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
1217245 CACTGATCTT
* *
1217255 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1217307 TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTAT
1 TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTAT
1217355 TGTAGATACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1218230 original size:19 final size:19
Alignment explanation
Indices: 1218206--1218271 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
1218196 TGTCAACGAT
1218206 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1218225 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1218239 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1218257 TTGTATCGATACATA
1 TTGTATCGATACATA
1218272 TGAAGCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1218243 original size:32 final size:32
Alignment explanation
Indices: 1218207--1218269 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1218197 GTCAACGATT
1218207 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1218239 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1218270 TATGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1218244 original size:13 final size:13
Alignment explanation
Indices: 1218226--1218250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1218216 ACATAAGTGT
1218226 TGTATCGATACAA
1 TGTATCGATACAA
1218239 TGTATCGATACA
1 TGTATCGATACA
1218251 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1218327 original size:13 final size:13
Alignment explanation
Indices: 1218309--1218336 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1218299 ATACATTACT
1218309 CATTGTATCGATA
1 CATTGTATCGATA
1218322 CATTGTATCGATA
1 CATTGTATCGATA
1218335 CA
1 CA
1218337 CTGATCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1218334 original size:33 final size:33
Alignment explanation
Indices: 1218292--1218357 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1218282 GCTAAGAAAA
*
1218292 TGTATCGATACA-TTACTCATTGTATCGATACAT
1 TGTATCGATACACTGA-TCATTGTATCGATACAT
*
1218325 TGTATCGATACACTGATCTTTGTATCGATACAT
1 TGTATCGATACACTGATCATTGTATCGATACAT
1218358 GCAGGTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTGATCATTGTATCGATACAT
Found at i:1219317 original size:20 final size:20
Alignment explanation
Indices: 1219280--1219318 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1219270 ACAACCTTGA
*
1219280 TCATGCATTTTTACCATGTT
1 TCATGCATTTATACCATGTT
*
1219300 TCATGCATTTATAGCATGT
1 TCATGCATTTATACCATGT
1219319 CCAGCACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
TCATGCATTTATACCATGTT
Found at i:1222425 original size:20 final size:20
Alignment explanation
Indices: 1222388--1222426 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1222378 ACAACCCTGA
*
1222388 TCATGCATTTTTACCATGTT
1 TCATGCATTTATACCATGTT
*
1222408 TCATGCATTTATAGCATGT
1 TCATGCATTTATACCATGT
1222427 CCAGCACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
TCATGCATTTATACCATGTT
Found at i:1227200 original size:8 final size:7
Alignment explanation
Indices: 1227187--1227252 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
1227177 TTCTTTTTCA
1227187 AAAAAACC
1 AAAAAA-C
1227195 AAAAAA-
1 AAAAAAC
* *
1227201 AATAACC
1 AAAAAAC
1227208 AAAAAA-
1 AAAAAAC
1227214 AACAAAA-
1 AA-AAAAC
1227221 AAAAAAC
1 AAAAAAC
1227228 AAAAAAAC
1 -AAAAAAC
1227236 AAAAAA-
1 AAAAAAC
*
1227242 ACAAAAC
1 AAAAAAC
1227249 AAAA
1 AAAA
1227253 CAAAGAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
6 15 0.32
7 19 0.40
8 13 0.28
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:1227201 original size:10 final size:9
Alignment explanation
Indices: 1227197--1227271 Score: 73
Period size: 10 Copynumber: 7.9 Consensus size: 9
1227187 AAAAAACCAA
1227197 AAAAAATAACC
1 AAAAAA-AA-C
1227208 AAAAAAAAC
1 AAAAAAAAC
*
1227217 AAAAAAAAA
1 AAAAAAAAC
1227226 ACAAAAAAAC
1 A-AAAAAAAC
1227236 -AAAAAAAC
1 AAAAAAAAC
1227244 AAAACAAAAC
1 AAAA-AAAAC
1227254 AAAGAAAAA-
1 AAA-AAAAAC
1227263 AGAAAAAAA
1 A-AAAAAAA
1227272 AAGAAGAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.14
9 19 0.33
10 23 0.40
11 7 0.12
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1227207 original size:13 final size:12
Alignment explanation
Indices: 1227186--1227273 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 12
1227176 ATTCTTTTTC
1227186 AAAAAAACCAAA
1 AAAAAAACCAAA
1227198 AAAAATAACC--A
1 AAAAA-AACCAAA
1227209 AAAAAAA-CAAA
1 AAAAAAACCAAA
1227220 AAAAAAA-CAAA
1 AAAAAAACCAAA
*
1227231 AAAACAAA-AAAA
1 AAAA-AAACCAAA
*
1227243 CAAAACAAAACAAA
1 -AAAA-AAACCAAA
* *
1227257 GAAAAAA-GAAA
1 AAAAAAACCAAA
1227268 AAAAAA
1 AAAAAA
1227274 GAAGAAGAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
9 1 0.02
10 2 0.03
11 30 0.46
12 14 0.22
13 15 0.23
14 3 0.05
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (12 bp):
AAAAAAACCAAA
Found at i:1227212 original size:1 final size:1
Alignment explanation
Indices: 1227208--1227273 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
1227198 AAAAATAACC
* * * * * * * *
1227208 AAAAAAAACAAAAAAAAAACAAAAAAACAAAAAAACAAAACAAAACAAAGAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1227273 A
1 A
1227274 GAAGAAGAAT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1227220 original size:20 final size:19
Alignment explanation
Indices: 1227185--1227271 Score: 95
Period size: 19 Copynumber: 4.4 Consensus size: 19
1227175 CATTCTTTTT
1227185 CAAAAAAACCAAAAAAAATAA
1 CAAAAAAA-CAAAAAAAA-AA
1227206 CCAAAAAAAACAAAAAAAAAA
1 -C-AAAAAAACAAAAAAAAAA
*
1227227 CAAAAAAACAAAAAAACAA
1 CAAAAAAACAAAAAAAAAA
* *
1227246 -AACAAAACAAAGAAAAAA
1 CAAAAAAACAAAAAAAAAA
*
1227264 GAAAAAAA
1 CAAAAAAA
1227272 AAGAAGAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.26
19 23 0.40
20 1 0.02
21 2 0.03
22 10 0.17
23 7 0.12
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.01
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAAA
Found at i:1227247 original size:21 final size:20
Alignment explanation
Indices: 1227185--1227273 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 20
1227175 CATTCTTTTT
*
1227185 CAAAAAAACCAAAAAAAATAAC
1 CAAAAAAA-CAAAAAAAA-AAA
1227207 CAAAAAAA-ACAAAAAAAAAA
1 CAAAAAAACA-AAAAAAAAAA
1227227 CAAAAAAACAAAAAAACAAAA
1 CAAAAAAACAAAAAAA-AAAA
*
1227248 CAAAACAAAGAAAAAAGAAAAA
1 CAAAA-AAACAAAAAA-AAAAA
1227270 -AAAA
1 CAAAA
1227274 GAAGAAGAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
20 17 0.28
21 21 0.35
22 21 0.35
23 1 0.02
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAAA
Found at i:1227247 original size:22 final size:21
Alignment explanation
Indices: 1227185--1227270 Score: 93
Period size: 20 Copynumber: 4.0 Consensus size: 21
1227175 CATTCTTTTT
* *
1227185 CAAAAAAACCAAAAAAAATAAC
1 CAAAAAAA-CAAAAAAAAAAAA
*
1227207 CAAAAAAA-ACAAAAAAAAAA
1 CAAAAAAACAAAAAAAAAAAA
*
1227227 CAAAAAAACAAAAAAACAAAA
1 CAAAAAAACAAAAAAAAAAAA
*
1227248 CAAAACAAAGAAAAAAGAAAAAA
1 CAAAA-AAACAAAAAA-AAAAAA
1227271 AAAGAAGAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 17 0.31
21 15 0.28
22 17 0.31
23 5 0.09
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.01
Consensus pattern (21 bp):
CAAAAAAACAAAAAAAAAAAA
Found at i:1227262 original size:37 final size:38
Alignment explanation
Indices: 1227198--1227271 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
1227188 AAAAACCAAA
1227198 AAAAATAACCAAAAAAAACAAAAAAAAAACAAAAAAAC
1 AAAAATAACCAAAAAAAACAAAAAAAAAACAAAAAAAC
* *
1227236 AAAAA-AA-CAAAACAAAACAAAGAAAAAAGAAAAAAA
1 AAAAATAACCAAAA-AAAACAAAAAAAAAACAAAAAAA
1227272 AAGAAGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 5 0.15
37 23 0.70
38 5 0.15
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (38 bp):
AAAAATAACCAAAAAAAACAAAAAAAAAACAAAAAAAC
Found at i:1228325 original size:55 final size:54
Alignment explanation
Indices: 1228241--1229219 Score: 1085
Period size: 55 Copynumber: 17.3 Consensus size: 54
1228231 ACTTTTTAGC
1228241 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGT
*
1228296 CCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGT
* * *
1228351 CCTCAAAGATCAGGACGCCTTTCAAAGCCCACACAAATTGGTGGCACCCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGT
1228406 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCA-T
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGT
1228460 CCTCAAAGAGCAGGACGCCTTTT-AAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGT
* *
1228514 CCTCAAAAAACAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGT
*
1228569 CCTTAAAGAGCAGGACGCCTTTT-AAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGT
** * * * *
1228623 CCTCAAAGTTCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCTCCCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGC-ACCTTCAGT
*
1228678 CCTCAAAGAGCAGGACGCATTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGT
* *
1228733 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGT
*
1228788 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTGGTGGCA-CTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* * **
1228842 CCTCAAAGAGTAGGACGCCTTGCCTTTAAAAGCTCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCC-T---TTT-AAAGCCCACACAAGTTGGTGGCACCTT-CAGT
*
1228902 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGT
1 CCTCAAAGAGCAGGACGC---CT-TTT--AAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* **
1228963 CCTCAAAGAGCAGGACCCCTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGA-----CGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* *
1229023 CCTCAAAGAGCAGGATGCTTTCTTTCTGCAAAGCCCACATAAGTT-GTGGCACCTTCTAGT
1 CCTCAAAGAGCAGGACGC---CTTT-T--AAAGCCCACACAAGTTGGTGGCACCTTC-AGT
*
1229083 CATCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGT
1 CCTCAAAGAGCAGGACGCC--T--TTT--AAAGCCCACACAAGTTGGTGGCACCTTC-AGT
* * * ** * *
1229144 CCCCAAAAAGCAAGACGCCTTTCCGTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGT
1 CCTCAAAGAGCAGGACGCC--T---TTT-AAAGCCCACACAAGTTGGTGGCAC-CTTCAGT
1229205 CCTCAAAGAGCAGGA
1 CCTCAAAGAGCAGGA
1229220 TGCACCTTAT
Statistics
Matches: 808, Mismatches: 67, Indels: 92
0.84 0.07 0.10
Matches are distributed among these distances:
51 3 0.00
52 3 0.00
53 32 0.04
54 113 0.14
55 351 0.43
56 1 0.00
57 12 0.01
58 7 0.01
59 23 0.03
60 117 0.14
61 132 0.16
62 9 0.01
63 3 0.00
66 2 0.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (54 bp):
CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
Found at i:1232456 original size:52 final size:51
Alignment explanation
Indices: 1232397--1232697 Score: 207
Period size: 52 Copynumber: 5.8 Consensus size: 51
1232387 CTCAATTGTT
*
1232397 CATAATCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACCAATTCTC
1 CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTCTC
* * * *
1232448 CTTTAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAAATT-TT
1 C-ATAATCGGGGATACTCCAACCCCGGTTTTA-TTTCCAAAACACC-AATTCTC
* * * * **** * * *
1232501 CACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGAATACTCCAA--CCC
1 CATAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCCAAAACACCAATTCTC
* * * ***
1232552 CATTACCTCTGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATT-TC
1 CA-TA-ATC---GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTCTC
* * * * *
1232607 TCATAATCGGGGATACTCTAA-CCCAGTTTTATTTCTAAAACACTAATTTTC
1 -CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTCTC
* *
1232658 CACAATCGGGGATACTTCAACCCCGGTTTTATTTCCAAAA
1 CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAA
1232698 ATACCGATTT
Statistics
Matches: 186, Mismatches: 48, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
50 38 0.20
51 34 0.18
52 51 0.27
53 26 0.14
54 13 0.07
55 6 0.03
56 18 0.10
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTCTC
Found at i:1232588 original size:108 final size:108
Alignment explanation
Indices: 1232456--1232805 Score: 330
Period size: 108 Copynumber: 3.3 Consensus size: 108
1232446 TCCTTTAATC
* *
1232456 GGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAAATTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAATACCAAATTTTCACAATCGAGGATACTCCAA
1232521 CCTCGTTATTTCATCGGGAATACTCCAACCCCATTACCTCTGA
66 CCTCGTTATTTCATCGGGAATACTCCAACCCCATTACCTCTGA
** *** * * *
1232564 GGGGATACTCCAACCCCGGCTTTATTTCC-AAAATA-TTGATTTCTCATAATCGGGGATACTCTA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAATACCAAATTT-TCACAATCGAGGATACTCCA
* * * * * * *
1232627 ACC-CAGTTTTATTTC-T----AAAACACTAA----TTTTCCACAAT-C
65 ACCTC-G--TTATTTCATCGGGAATACTCCAACCCCATTACCTC--TGA
* * * * *
1232665 GGGGATACTTCAACCCCGGTTTTATTTCCAAAAATACCGATTTTTCACAATCGAGGATACTTCAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAATACCAAATTTTCACAATCGAGGATACTCCAA
* * *
1232730 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCTCGTTATTTCATCGGGAATACTCCAACCCCATTACCTCTGA
1232773 GGGGATACTCCAACCCCGATTTTATTTCCAAAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAA
1232806 TATTGATTTC
Statistics
Matches: 185, Mismatches: 38, Indels: 38
0.71 0.15 0.15
Matches are distributed among these distances:
100 12 0.06
101 28 0.15
102 27 0.15
103 4 0.02
104 7 0.04
105 6 0.03
106 5 0.03
107 26 0.14
108 58 0.31
109 12 0.06
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAATACCAAATTTTCACAATCGAGGATACTCCAA
CCTCGTTATTTCATCGGGAATACTCCAACCCCATTACCTCTGA
Found at i:1232667 original size:50 final size:52
Alignment explanation
Indices: 1232611--1232731 Score: 149
Period size: 52 Copynumber: 2.4 Consensus size: 52
1232601 GATTTCTCAT
* *
1232611 AATCGGGGATAC-TCTAA-CCCAGTTTTATTT-CTAAAACACTAATTTTCCAC
1 AATCGGGGATACTTC-AACCCCAGTTTTATTTCCAAAAACACCAATTTTCCAC
* * * *
1232661 AATCGGGGATACTTCAACCCCGGTTTTATTTCCAAAAATACCGATTTTTCAC
1 AATCGGGGATACTTCAACCCCAGTTTTATTTCCAAAAACACCAATTTTCCAC
*
1232713 AATCGAGGATACTTCAACC
1 AATCGGGGATACTTCAACC
1232732 TCGTTATTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
50 14 0.23
51 14 0.23
52 33 0.54
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (52 bp):
AATCGGGGATACTTCAACCCCAGTTTTATTTCCAAAAACACCAATTTTCCAC
Found at i:1232723 original size:52 final size:51
Alignment explanation
Indices: 1232564--1232731 Score: 196
Period size: 50 Copynumber: 3.3 Consensus size: 51
1232554 TTACCTCTGA
* * * * *
1232564 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATC
1 GGGGATACTTCAACCCCGGTTTTATTTCCAAAATACTGATTTTTCACAATC
* * * * *
1232615 GGGGATAC-TCTAA-CCCAGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTTC-AACCCCGGTTTTATTTCCAAAATACTGATTTTTCACAATC
*
1232665 GGGGATACTTCAACCCCGGTTTTATTTCCAAAAATACCGATTTTTCACAATC
1 GGGGATACTTCAACCCCGGTTTTATTTCC-AAAATACTGATTTTTCACAATC
*
1232717 GAGGATACTTCAACC
1 GGGGATACTTCAACC
1232732 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
50 39 0.41
51 25 0.26
52 32 0.33
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTTCAACCCCGGTTTTATTTCCAAAATACTGATTTTTCACAATC
Found at i:1232812 original size:209 final size:210
Alignment explanation
Indices: 1232396--1232839 Score: 692
Period size: 209 Copynumber: 2.1 Consensus size: 210
1232386 TCTCAATTGT
* **
1232396 TCATAATCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACCAATTCTCCTTTAATCGGGGA
1 TCATAATCGGGGATACTCCAACC-CAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGA
*
1232461 TACTCCAACCCCGATTTTATTTTCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCG
65 TACTCCAACCCCGATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCG
* *
1232526 TTATTTCATCGGGAATACTCCAACCCCATTACCTCTGAGGGGATACTCCAACCCCGGCTTTATTT
130 TTATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGACTTTATTT
1232591 CCAAAATATTGATTTC
195 CCAAAATATTGATTTC
* * * *
1232607 TCATAATCGGGGATACTCTAACCCAGTTTTATTTCTAAAACACTAATTTTCC-ACAATCGGGGAT
1 TCATAATCGGGGATACTCCAACCCAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGAT
* * * * * *
1232671 ACTTCAACCCCGGTTTTATTTCCAAAAATACCGATTTTTCACAATCGAGGATACTTCAACCTCGT
66 ACTCCAACCCCGATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCGT
* * *
1232736 TATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGATTTTATTTC
131 TATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTC
1232801 CAAAATATTGATTTC
196 CAAAATATTGATTTC
*
1232816 TCATAATTGGGGATACTCCAACCC
1 TCATAATCGGGGATACTCCAACCC
1232840 CGTTATTTTC
Statistics
Matches: 212, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
209 165 0.78
210 25 0.12
211 22 0.10
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (210 bp):
TCATAATCGGGGATACTCCAACCCAGTTTTATTTCCAAAACACCAATTCTCCTACAATCGGGGAT
ACTCCAACCCCGATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCGT
TATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTC
CAAAATATTGATTTC
Found at i:1232838 original size:79 final size:79
Alignment explanation
Indices: 1232744--1232967 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 79
1232734 GTTATTTCAT
** *
1232744 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATAT
* *
1232809 TGAT-TTCTCATAAT
66 TGATCTT-TCACAAC
* ** * *
1232823 TGGGGATACTCCAACCCCGTTATTTTCGAGAAGATACTCCAATCCCGATTTTATTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAT-A
*
1232887 TCGATCTTTCACAAC
65 TTGATCTTTCACAAC
* * * * * *
1232902 CGGGAATACTCTAATCCCGTTATTTTCAAAGGGATACTCCAACCCCG-TTATTATCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATT-TTATTTCCAAAATA
1232966 TT
65 TT
1232968 AAATTTCACA
Statistics
Matches: 118, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
78 5 0.04
79 108 0.92
80 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATAT
TGATCTTTCACAAC
Found at i:1232859 original size:107 final size:106
Alignment explanation
Indices: 1232456--1232869 Score: 344
Period size: 107 Copynumber: 3.9 Consensus size: 106
1232446 TCCTTTAATC
* * **
1232456 GGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAAATTT-TCACAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTA-TTTCCAAAATA-CTGATTTCTCACAATCGAGGATACTCCA
* * * *
1232520 ACCTCGTTATTTCATCGGGAATACTCCAACCCCATTACCTCTGA
64 ACCCCGTTATTT-ATCGGAAATACTCCAACCCCGTTACCTCCGA
** * * * *
1232564 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACTGATTTCTCACAATCGAGGATACTCCAAC
* * * * * * * * *
1232629 CCAGTT-TTATTTC-TAAA-ACACTAA----TTTTCC-ACAA
66 CCCGTTATT-TATCGGAAATACTCCAACCCCGTTACCTCCGA
* * * * *
1232663 TCGGGGATACTTCAACCCCGGTTTTATTTCCAAAAATACCGATTTTTCACAATCGAGGATACTTC
1 --GGGGATACTCCAACCCCGATTTTATTTCC-AAAATACTGATTTCTCACAATCGAGGATACTCC
* **
1232728 AACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
63 AACCCCGTTATTT-ATCGGAAATACTCCAACCCCGTTACCTCCGA
* * * *
1232773 GGGGATACTCCAACCCCGATTTTATTTCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACTGATTTCTCACAATCGAGGATACTCCAAC
*
1232838 CCCGTTATTT-TCGAGAAGATACTCCAATCCCG
66 CCCGTTATTTATCG-GAA-ATACTCCAACCCCG
1232870 ATTTTATTTC
Statistics
Matches: 234, Mismatches: 56, Indels: 33
0.72 0.17 0.10
Matches are distributed among these distances:
99 1 0.00
100 4 0.02
101 27 0.12
102 34 0.15
103 4 0.02
104 6 0.03
105 10 0.04
106 9 0.04
107 84 0.36
108 49 0.21
109 4 0.02
110 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACTGATTTCTCACAATCGAGGATACTCCAAC
CCCGTTATTTATCGGAAATACTCCAACCCCGTTACCTCCGA
Found at i:1234503 original size:92 final size:92
Alignment explanation
Indices: 1234339--1234675 Score: 417
Period size: 92 Copynumber: 3.7 Consensus size: 92
1234329 GGAAAGTGCA
* *
1234339 AACCACACATTCCTAATCATATCCCCTTCATCCAAACACTAAATGGTATTGATGCATCACAAAGC
1 AACCACACATTCCCAATCATATCCCCTTCATCCAACCACTAAATGGTATTGATGCATCACAAAGC
* * *
1234404 TTAATTTCCTTAGGGCAAGGATAT-CC
66 CTGATTTCCTTAGGGTAAGGATATCCC
* *
1234430 ACACCACACATTCCCAATCATATCCTCTTCATCCAACCACTAGATGGTATTGATGCATCACAAAG
1 A-ACCACACATTCCCAATCATATCCCCTTCATCCAACCACTAAATGGTATTGATGCATCACAAAG
* *
1234495 CCTGATTTCTTTCA-GGTAAGGGTATCCC
65 CCTGATTTCCTT-AGGGTAAGGATATCCC
* * * *
1234523 AACTACACATTCTCAATCATATCCCCTTTATCCAACCACTAAATGGTATTGATGCGTCACAAAGC
1 AACCACACATTCCCAATCATATCCCCTTCATCCAACCACTAAATGGTATTGATGCATCACAAAGC
1234588 CTGATTTCCTTAGGGTAAGGATATCCC
66 CTGATTTCCTTAGGGTAAGGATATCCC
** ** ** * * ** * *
1234615 AACCACTTATTCTTAATCATATATCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACA
1 AACCACACATTCCCAATCATATCCCCTTCATCCAACCACTAAATGGTATTGATGCATCACA
1234676 TGACCACAAA
Statistics
Matches: 211, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
91 2 0.01
92 205 0.97
93 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (92 bp):
AACCACACATTCCCAATCATATCCCCTTCATCCAACCACTAAATGGTATTGATGCATCACAAAGC
CTGATTTCCTTAGGGTAAGGATATCCC
Found at i:1234656 original size:184 final size:184
Alignment explanation
Indices: 1234343--1234675 Score: 483
Period size: 184 Copynumber: 1.8 Consensus size: 184
1234333 AGTGCAAACC
*
1234343 ACACATTCCTAATCATATCCCCTTCATCCAAACACTAAATGGTATTGATGCATCACAAAGCTTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAAACACTAAATGGTATTGATGCATCACAAAGCCTAA
1234408 TTTCCTTAGGGCAAGGATATCCACACCACACATTCCCAATCATATCCTCTTCATCCAACCACTAG
66 TTTCCTTAGGGCAAGGATATCCACACCACACATTCCCAATCATATCCTCTTCATCCAACCACTAG
1234473 ATGGTATTGATGCATCACAAAGCCTGATTTCTTTCAGGTAAGGGTATCCCAACT
131 ATGGTATTGATGCATCACAAAGCCTGATTTCTTTCAGGTAAGGGTATCCCAACT
* * * *
1234527 ACACATT-CTCAATCATATCCCCTTTATCCAACCACTAAATGGTATTGATGCGTCACAAAGCCTG
1 ACACATTCCT-AATCATATCCCCTTCATCCAAACACTAAATGGTATTGATGCATCACAAAGCCTA
* ** ** * * ** *
1234591 ATTTCCTTAGGGTAAGGATATCC-CAACCACTTATTCTTAATCATAT-ATCTTTCTTTTAGCCAC
65 ATTTCCTTAGGGCAAGGATATCCAC-ACCACACATTCCCAATCATATCCTC-TTCATCCAACCAC
1234654 TAGATGGTATTGATGCATCACA
128 TAGATGGTATTGATGCATCACA
1234676 TGACCACAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
183 5 0.04
184 126 0.96
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (184 bp):
ACACATTCCTAATCATATCCCCTTCATCCAAACACTAAATGGTATTGATGCATCACAAAGCCTAA
TTTCCTTAGGGCAAGGATATCCACACCACACATTCCCAATCATATCCTCTTCATCCAACCACTAG
ATGGTATTGATGCATCACAAAGCCTGATTTCTTTCAGGTAAGGGTATCCCAACT
Found at i:1234959 original size:18 final size:19
Alignment explanation
Indices: 1234925--1234970 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1234915 CGAATGAATG
*
1234925 AAAA-ATGAATAAAAAAT-
1 AAAACATGAAGAAAAAATC
*
1234942 AAAACATGAAGAATAAATC
1 AAAACATGAAGAAAAAATC
*
1234961 AAATCATGAA
1 AAAACATGAA
1234971 ATTTCATGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (19 bp):
AAAACATGAAGAAAAAATC
Found at i:1235340 original size:85 final size:84
Alignment explanation
Indices: 1235192--1236906 Score: 1264
Period size: 85 Copynumber: 20.3 Consensus size: 84
1235182 GCTATACTCG
* * * * *
1235192 GTCAACCTCTTTATCCTTTATTTACCTGTTGGCTTAGTCC-CAGGTAAATCTTTTTATCCTTTGT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGA-GTAAATCCTTTTATCCTTTGT
*
1235256 TAACTTGTCGATTCAATCCCT
65 TGACTTGTCGATTCAAT-CCT
* ** * * * *
1235277 GTCAACCTTTTGATCCTTTGTTTATTTTTTAGCTTAGTCTTGGGTAAATCCTTTTATCTTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
* * * *
1235342 GACTTATCGGTTTAATCTT
66 GACTTGTCGATTCAATCCT
* * * *
1235361 GATCAACCTTTTTATCCTTTGTTTACCT-ATCGACTTAGTCCCGGGTAAATCCTTTTATCCTTTG
1 G-TCAACCTTTTTATCCTTTGTTTACCTGTTAG-CTTAGTCCTGAGTAAATCCTTTTATCCTTTG
* * *
1235425 TTGAATTGTCGATTTAATCTT
64 TTGACTTGTCGATTCAATCCT
* * * *
1235446 AGTCAACCTTTTTATCTTTTATTTAACTGTT-GCCTCAGTCCT-AGATAAATCCTTTTATCCTTT
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAG-CTTAGTCCTGAG-TAAATCCTTTTATCCTTT
* *
1235509 GTTAACTTGTC-AGTTCAATCTT
63 GTTGACTTGTCGA-TTCAATCCT
* * * * *
1235531 GGTCAA-CTTTTTATCCTTTATTTAGCT-ATGGACTCAGTCCTTG-GTAAATCCTTTTATCCTTT
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAG-CTTAGTCC-TGAGTAAATCCTTTTATCCTTT
* * *
1235593 GTTGACTTATCGATTTAATCTCA
63 GTTGACTTGTCGATTCAATC-CT
* ** ** *
1235616 GTCAGCC-TTTTATGATTTGTTTAGTTGTCAGCTTAGTCCTG-GTAAATCCTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
*
1235679 GACTTGTCGATTCAATCTT
66 GACTTGTCGATTCAATCCT
* * * * * * **
1235698 GGCCAACCTTTTTTTCCTTTGTTTACCTGTCAGCTCAGTCTTAAGTAAATCCTTTTAAGCTTTGT
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGT
* * *
1235763 TCACTTGTTTG-TTCAATCCCA
65 TGACTTG-TCGATTCAAT-CCT
* * * * * * *
1235784 GTTAACCTTTTTATCCTTCGTTTACCTGTCAACTTAGTCCCGGGTAAATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
*
1235849 GACTTGTC-AGTTCAATCCCA
66 GACTTGTCGA-TTCAAT-CCT
* * * * * * *
1235869 ATCAACC-TTTTATCCTTTGTTCACCAGTCAACTCAGT-CTGGGGTAAATCCTTTTATCCTTT-T
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCT-GAGTAAATCCTTTTATCCTTTGT
*
1235931 CTGACTTATCGATTCAATCCT
65 -TGACTTGTCGATTCAATCCT
* * * *
1235952 AGTGAACCTTTTTATCTTTTGTTTACTTGTTGGCTTAGTCCT-AGATAAATCCTTTTATCCTTTG
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAG-TAAATCCTTTTATCCTTTG
* *
1236016 TTGACTTGTCGGTACAATCCT
64 TTGACTTGTCGATTCAATCCT
* * * * * * *
1236037 GGTCAACTTTTTTACCCTTTGTTTACCTATCA-ATTCAGTCCTAAGTAAGTCCTTTTATCCTTTG
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTT-AGTCCTGAGTAAATCCTTTTATCCTTTG
*
1236101 TTGACTTGTC-ATTTCAATCTTT
64 TTGACTTGTCGA-TTCAATC-CT
** * * * *
1236123 GTCGTCCTTTTTATCCGTTGTTTACCT-ATAGGCTCAGTCACT-AGTAAATCCTTTTATCGTTTG
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTA-GCTTAGTC-CTGAGTAAATCCTTTTATCCTTTG
* * * * *
1236186 TTAACTTATCAATTTAATCTT
64 TTGACTTGTCGATTCAATCCT
* * * * * * *
1236207 GGTTAACC-TTTAATGCTTTGTTTACCTG-TCGACTCAGTCCTAAGT-AATCTTTTTATCCTTTG
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAG-CTTAGTCCTGAGTAAATCCTTTTATCCTTTG
* * *
1236269 TTCACTTGTC-AATCTAATCCCG
64 TTGACTTGTCGATTC-AAT-CCT
* * * * * * * *
1236291 GTCATCCTTTTTATTCTTTGTTTACCTATTAGCTTAATCCCGACTAAATCATTTTAACCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
* *
1236356 GACTTCTCGATTCAATCCCA
66 GACTTGTCGATTCAAT-CCT
* * * *
1236376 GTCAACCTTTTTATCCTTTGTTTA-CT-TATCGACTTAGTCCTAAGTAAATCTTTTTATCCTTTA
1 GTCAACCTTTTTATCCTTTGTTTACCTGT-TAG-CTTAGTCCTGAGTAAATCCTTTTATCCTTTG
*
1236439 TTGACTTGTCGGTTCAATCCT
64 TTGACTTGTCGATTCAATCCT
* * * * * *
1236460 GGTCAACCTTTTTATCCTTTGTTTACTTGTTGGCTCAATCCCGAGTAAATCTTTTTATCCTTTGT
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGT
* * *
1236525 TGACTTGTTGGTTCAATCTCA
65 TGACTTGTCGATTCAATC-CT
* * ** * *
1236546 ATTAACC-TTTTATCCTTTGTTTACCT-TTCAGCTTAGTCCCAACTTAATCCTTTTATCCTTTGT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTT-AGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGT
* * *
1236609 TAACTTGTCGGTTCAATCCCG
65 TGACTTGTCGATTCAAT-CCT
* * ** * * * * *
1236630 GTCAGCCTTTATATCCTTTGTTTATTTGTCAGCTTAGTCTTGGGTAAATACTTTTATCCTTTCTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
* *
1236695 GACTTGT-TAGTTTAATCCT
66 GACTTGTCGA-TTCAATCCT
* * * * *
1236714 AGTCAACC-ATTTATCCTTTGTTTACTTG-TCGACTTAGTCCTTAGTAAATCCTTTTATCTTTTG
1 -GTCAACCTTTTTATCCTTTGTTTACCTGTTAG-CTTAGTCCTGAGTAAATCCTTTTATCCTTTG
* * *
1236777 TTGACTTGTCGGTTCAGTCCC
64 TTGACTTGTCGATTCAATCCT
* ** * ** *
1236798 GATCAA-CTTTTGTATTCTTTGTTTAATTATCGGCTTAGTCCTGAGTAAATTCTTTTATCCTTTG
1 G-TCAACCTTTT-TATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTG
* * *
1236862 TTGACTTTTCAATTCAATCTT
64 TTGACTTGTCGATTCAATCCT
*
1236883 AGTCAA-CTTTTGTATCTTTTGTTT
1 -GTCAACCTTTT-TATCCTTTGTTT
1236907 GCCTATCGGC
Statistics
Matches: 1298, Mismatches: 266, Indels: 132
0.77 0.16 0.08
Matches are distributed among these distances:
82 2 0.00
83 89 0.07
84 381 0.29
85 800 0.62
86 25 0.02
87 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (84 bp):
GTCAACCTTTTTATCCTTTGTTTACCTGTTAGCTTAGTCCTGAGTAAATCCTTTTATCCTTTGTT
GACTTGTCGATTCAATCCT
Found at i:1235361 original size:43 final size:43
Alignment explanation
Indices: 1235314--1235699 Score: 154
Period size: 42 Copynumber: 9.1 Consensus size: 43
1235304 TTTAGCTTAG
* *
1235314 TCTTGGGTAAATCCTTTTATCTTTTGTTGACTTATCGGTTTAA
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
* * * * * *
1235357 TCTT-GATCAA-CCTTTTTATCCTTTGTTTACCTATCGACTTAG
1 TCTTGGGTAAATCC-TTTTATCCTTTGTTGACTTATCGATTTAA
** * *
1235399 TCCCGGGTAAATCCTTTTATCCTTTGTTGAATTGTCGATTTAA
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
* * * * * ** * *
1235442 TCTT-AGTCAA-CCTTTTTATCTTTTATTTAACTGT-T-GCCTCAG
1 TCTTGGGTAAATCC-TTTTATCCTTT-GTTGACT-TATCGATTTAA
* * * * * *
1235484 TCCTAGATAAATCCTTTTATCCTTTGTTAACTTGTC-AGTTCAA
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGA-TTTAA
* * * * * * * *
1235527 TCTT-GGTCAA-CTTTTTATCCTTTATTTAGC-TATGGACTCAG
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGA-CTTATCGATTTAA
1235568 TCCTT-GGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
1 T-CTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
** * * ** * * * * *
1235611 TC-TCAGT-CAGCCTTTTATGATTTGTTTAGTTGTC-AGCTTAG
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGA-TTTAA
* * *
1235652 TCCT-GGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAA
1 TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
1235694 TCTTGG
1 TCTTGG
1235700 CCAACCTTTT
Statistics
Matches: 243, Mismatches: 78, Indels: 44
0.67 0.21 0.12
Matches are distributed among these distances:
40 1 0.00
41 54 0.22
42 101 0.42
43 82 0.34
44 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (43 bp):
TCTTGGGTAAATCCTTTTATCCTTTGTTGACTTATCGATTTAA
Found at i:1235382 original size:42 final size:42
Alignment explanation
Indices: 1235241--1235720 Score: 119
Period size: 42 Copynumber: 11.4 Consensus size: 42
1235231 CCAGGTAAAT
* * * *
1235241 CTTTTTATCCTTTGTTAACTTGTCGATTCAATCCCTG-TCAAC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAAT-CTTGATCAAC
* * * ** * * * *
1235283 CTTTTGATCCTTTGTTTA-TTTTTTAGCTTAGTCTTGGGTAAATC
1 CTTTTTATCCTTTGTTGACTTATCGA-TTTAATCTT-GATCAA-C
* *
1235327 C-TTTTATCTTTTGTTGACTTATCGGTTTAATCTTGATCAAC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAATCTTGATCAAC
* * * * ** * *
1235368 CTTTTTATCCTTTGTTTACCTATCGACTTAGTCCCGGGTAAATC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAAT-CTTGATCAA-C
* *
1235412 C-TTTTATCCTTTGTTGAATTGTCGATTTAATCTT-AGTCAAC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAATCTTGA-TCAAC
* * * ** * * * *
1235453 CTTTTTATCTTTTATTTAACTGT-T-GCCTCAGTCCTAGATAAATC
1 CTTTTTATCCTTT-GTTGACT-TATCGATTTAAT-CTTGATCAA-C
* * * *
1235497 C-TTTTATCCTTTGTTAACTTGTC-AGTTCAATCTTGGTCAA-
1 CTTTTTATCCTTTGTTGACTTATCGA-TTTAATCTTGATCAAC
* * * * * * * *
1235537 CTTTTTATCCTTTATTTAGC-TATGGACTCAGTCCTTGGTAAATC
1 CTTTTTATCCTTTGTTGA-CTTATCGATTTAAT-CTTGATCAA-C
* *
1235581 C-TTTTATCCTTTGTTGACTTATCGATTTAATC-TCAGTCAGC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAATCTTGA-TCAAC
** * * * * * * * *
1235622 C-TTTTATGATTTGTTTAGTTGTC-AGCTTAGTCCTGGTAAATC
1 CTTTTTATCCTTTGTTGACTTATCGA-TTTAATCTTGATCAA-C
* * **
1235664 C-TTTTATCCTTTGTTGACTTGTCGATTCAATCTTGGCCAAC
1 CTTTTTATCCTTTGTTGACTTATCGATTTAATCTTGATCAAC
*
1235705 CTTTTTTTCCTTTGTT
1 CTTTTTATCCTTTGTT
1235721 TACCTGTCAG
Statistics
Matches: 309, Mismatches: 98, Indels: 62
0.66 0.21 0.13
Matches are distributed among these distances:
40 2 0.01
41 60 0.19
42 136 0.44
43 99 0.32
44 12 0.04
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (42 bp):
CTTTTTATCCTTTGTTGACTTATCGATTTAATCTTGATCAAC
Found at i:1235608 original size:169 final size:168
Alignment explanation
Indices: 1235191--1236923 Score: 1357
Period size: 169 Copynumber: 10.2 Consensus size: 168
1235181 AGCTATACTC
* * * * * * * * *
1235191 GGTCAACCTCTTTATCCTTTATTTACCTGTTGGCTTAGTCCCAGGTAAATCTTTTTATCCTTTGT
1 GGTCAA-CTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGT
* * * ** * * * *
1235256 TAACTTGTCGATTCAATCCCTGTCAACCTTTTGATCCTTTGTTTATTTTTTAGCTTAGTCTTGGG
65 TGACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGTT-GCTTAGTCCTAGA
* * * *
1235321 TAAATCCTTTTATCTTTTGTTGACTTATCGGTTTAATCTT
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* * ***
1235361 GATCAACCTTTTTATCCTTTGTTTACCTATCGACTTAGTCCCGGGTAAATCCTTTTATCCTTTGT
1 GGTCAA-CTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGT
* * ** * * *
1235426 TGAATTGTCGATTTAATCTTAGTCAACCTTTTTATCTTTTATTTAACTGTTGCCTCAGTCCTAGA
65 TGACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGTTG-CTTAGTCCTAGA
*
1235491 TAAATCCTTTTATCCTTTGTTAACTTGTCAGTTCAATCTT
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* * * **
1235531 GGTCAACTTTTTATCCTTTATTTAGCTATGGACTCAGTCCTTGGTAAATCCTTTTATCCTTTGTT
1 GGTCAACTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGTT
* * * * ** ** * *
1235596 GACTTATCGATTTAATCTCAGTCAGCC-TTTTATGATTTGTTTAGTTGTCAGCTTAGTCCT-GGT
66 GACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGT-TGCTTAGTCCTAGAT
1235659 AAATCCTTTTATCCTTTGTTGACTTGTC-GATTCAATCTT
130 AAATCCTTTTATCCTTTGTTGACTTGTCAG-TTCAATCTT
* * * * **
1235698 GGCCAACCTTTTTTTCCTTTGTTTACCTGTC-AGCTCAGTCTTAAGTAAATCCTTTTAAGCTTTG
1 GGTCAA-CTTTTTATCCTTTGTTTACCTATCGA-CTCAGTCCTAAGTAAATCCTTTTATCCTTTG
* * * * * ** **
1235762 TTCACTTGTTTG-TTCAATCCCAGTTAACCTTTTTATCCTTCGTTTACCTGTCAACTTAGTCCCG
64 TTGACTTG-TCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGT-TGCTTAGTCCTA
* * **
1235826 GGTAAATCTTTTTATCCTTTGTTGACTTGTCAGTTCAATCCC
127 GATAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
** * * * **
1235868 AATCAACCTTTTATCCTTTGTTCACC-AGTCAACTCAGT-CTGGGGTAAATCCTTTTATCCTTT-
1 GGTCAACTTTTTATCCTTTGTTTACCTA-TCGACTCAGTCCT-AAGTAAATCCTTTTATCCTTTG
* * * *
1235930 TCTGACTTATCGATTCAATCCTAGTGAACCTTTTTATCTTTTGTTT-ACTTGTTGGCTTAGTCCT
64 T-TGACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAAC-TGTT-GCTTAGTCCT
* * *
1235994 AGATAAATCCTTTTATCCTTTGTTGACTTGTCGGTACAATCCT
126 AGATAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* * * *
1236037 GGTCAACTTTTTTACCCTTTGTTTACCTATCAATTCAGTCCTAAGTAAGTCCTTTTATCCTTTGT
1 GGTCAAC-TTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGT
*** ** * * * * *
1236102 TGACTTGTC-ATTTCAATCTTTGTCGTCCTTTTTATCCGTTGTTTACCTATAGGCTCAGTCACTA
65 TGACTTGTCGA-TTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGT-TGCTTAGTC-CTA
* * * * *
1236166 G-TAAATCCTTTTATCGTTTGTTAACTTATCAATTTAATCTT
127 GATAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* * * * * *
1236207 GGTTAACCTTTAATGCTTTGTTTACCTGTCGACTCAGTCCTAAGT-AATCTTTTTATCCTTTGTT
1 GGTCAACTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGTT
* * * * * * * * *
1236271 CACTTGTC-AATCTAATCCCGGTCATCCTTTTTATTCTTTGTTTACCTATTAGCTTAATCC-CGA
66 GACTTGTCGATTC-AATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGTT-GCTTAGTCCTAGA
* * * **
1236334 CTAAATCATTTTAACCTTTGTTGACTTCTC-GATTCAATCCC
129 -TAAATCCTTTTATCCTTTGTTGACTTGTCAG-TTCAATCTT
* * * * *
1236375 AGTCAACCTTTTTATCCTTTGTTTACTTATCGACTTAGTCCTAAGTAAATCTTTTTATCCTTTAT
1 GGTCAA-CTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGT
* ** * * *
1236440 TGACTTGTCGGTTCAATCCTGGTCAACCTTTTTATCCTTTGTTT-ACTTGTTGGCTCAATCC-CG
65 TGACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAAC-TGTT-GCTTAGTCCTAG
* ** *
1236503 AGTAAATCTTTTTATCCTTTGTTGACTTGTTGGTTCAATCTC
128 A-TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
** * * * * * * *
1236545 AATTAACCTTTTATCCTTTGTTTACCTTTC-AGCTTAGTCCCAACTTAATCCTTTTATCCTTTGT
1 GGTCAACTTTTTATCCTTTGTTTACCTATCGA-CTCAGTCCTAAGTAAATCCTTTTATCCTTTGT
* * * * * ** * * * *
1236609 TAACTTGTCGGTTCAATCCCGGTCAGCCTTTATATCCTTTGTTTATTTGTCAGCTTAGTCTTGGG
65 TGACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGT-TGCTTAGTCCTAGA
* * * * *
1236674 TAAATACTTTTATCCTTTCTTGACTTGTTAGTTTAATCCT
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* ** * * * * *
1236714 AGTCAACCATTTATCCTTTGTTTACTTGTCGACTTAGTCCTTAGTAAATCCTTTTATCTTTTGTT
1 GGTCAACTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGTT
* * * * * *
1236779 GACTTGTCGGTTCAGTCCC-GATCAA-CTTTTGTATTCTTTGTTTAATTATCGGCTTAGTCCT-G
66 GACTTGTCGATTCAATCCCAG-TCAACCTTTT-TATCCTTTGTTTAACTGT-TGCTTAGTCCTAG
* * *
1236841 AGTAAATTCTTTTATCCTTTGTTGACTTTTCAATTCAATCTT
128 A-TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
* * * * *
1236883 AGTCAACTTTTGTATCTTTTGTTTGCCTATCGGCTTAGTCC
1 GGTCAACTTTT-TATCCTTTGTTTACCTATCGACTCAGTCC
1236924 CAGGTAACAC
Statistics
Matches: 1266, Mismatches: 254, Indels: 86
0.79 0.16 0.05
Matches are distributed among these distances:
166 2 0.00
167 47 0.04
168 195 0.15
169 571 0.45
170 438 0.35
171 13 0.01
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (168 bp):
GGTCAACTTTTTATCCTTTGTTTACCTATCGACTCAGTCCTAAGTAAATCCTTTTATCCTTTGTT
GACTTGTCGATTCAATCCCAGTCAACCTTTTTATCCTTTGTTTAACTGTTGCTTAGTCCTAGATA
AATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCTT
Found at i:1235857 original size:43 final size:43
Alignment explanation
Indices: 1235792--1236873 Score: 129
Period size: 43 Copynumber: 25.6 Consensus size: 43
1235782 CAGTTAACCT
* * * *
1235792 TTTTATCCTTCGTTTACCTGTCAACTTAGTCCCGGGTAAATCT
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * ** *
1235835 TTTTATCCTTTGTTGACTTGTC-AGTTCAATCCC-AATCAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* ** * **
1235876 TTTTATCCTTTGTTCACCAGTCAACTCAGTCTGGGGTAAATCC
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * * ** *
1235919 TTTTATCCTTT-TCTGACTTATCGA-TTCAAT-CCTAGTGAA-CC
1 TTTTATCCTTTGT-TGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * *** ** *
1235960 TTTTTATCTTTTGTTTACTTGTTGGCTTAGTCCTAGATAAATCC
1 -TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * * * *
1236004 TTTTATCCTTTGTTGACTTGTCGGTAC--AAT-CCTGGTCAA-CTT
1 TTTTATCCTTTGTTGACTTGTC--AACTTAGTCCCGGGTAAATC-C
* * * * *** *
1236046 TTTTACCCTTTGTTTACCTATCAA-TTCAGTCCTAAGTAAGTCC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * *** **
1236089 TTTTATCCTTTGTTGACTTGTC-ATTTCAAT-CTTTGT-CGTCC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * * * * * * **
1236130 TTTTTATCCGTTGTTTACCTAT-AGGCTCAGTCACTAGTAAATCC
1 -TTTTATCCTTTGTTGACTTGTCA-ACTTAGTCCCGGGTAAATCC
* * * * * ** *
1236174 TTTTATCGTTTGTTAACTTATCAATTTAAT-CTTGGTTAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * * * * * *** *
1236215 TTTAATGCTTTGTTTACCTGTCGACTCAGTCCTAAGT-AATCT
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * *
1236257 TTTTATCCTTTGTTCACTTGTCAA-TCTAATCCC-GGT-CATCC
1 TTTTATCCTTTGTTGACTTGTCAACT-TAGTCCCGGGTAAATCC
* * * * * * * ** *
1236298 TTTTTATTCTTTGTTTACCTATTAGCTTAATCCCGACTAAATCA
1 -TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * * * * *
1236342 TTTTAACCTTTGTTGACTTCTCGA-TTCAATCCC-AGTCAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * * *** *
1236383 TTTTTATCCTTTGTTTACTTATCGACTTAGTCCTAAGTAAATCT
1 -TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* ** * * *
1236427 TTTTATCCTTTATTGACTTGTC-GGTTCAAT-CCTGGTCAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* *** * * * *
1236468 TTTTTATCCTTTGTTTACTTGTTGGCTCAATCCCGAGTAAATCT
1 -TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
*** * * ** *
1236512 TTTTATCCTTTGTTGACTTGT-TGGTTCAATCTC-AATTAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * *** *
1236553 TTTTATCCTTTGTTTACCTT-TCAGCTTAGTCCCAACTTAATCC
1 TTTTATCCTTTGTTGA-CTTGTCAACTTAGTCCCGGGTAAATCC
* ** * * *
1236596 TTTTATCCTTTGTTAACTTGTC-GGTTCAATCCC-GGT-CAGCC
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * * ** *
1236637 TTTATATCCTTTGTTTATTTGTCAGCTTAGTCTTGGGTAAATAC
1 TTT-TATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * ** * ** *
1236681 TTTTATCCTTTCTTGACTTGTTAGTTTAAT-CCTAGTCAA-CC
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* * * ***
1236722 ATTTATCCTTTGTTTACTTGTCGACTTAGTCCTTAGTAAATCC
1 TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
* ** * * *
1236765 TTTTATCTTTTGTTGACTTGTC-GGTTCAGTCCC-GATCAA-CT
1 TTTTATCCTTTGTTGACTTGTCAACTT-AGTCCCGGGTAAATCC
* * * * ** * * *
1236806 TTTGTATTCTTTGTTTAATTATCGGCTTAGTCCTGAGTAAATTC
1 TTT-TATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
*
1236850 TTTTATCCTTTGTTGACTTTTCAA
1 TTTTATCCTTTGTTGACTTGTCAA
1236874 TTCAATCTTA
Statistics
Matches: 727, Mismatches: 251, Indels: 122
0.66 0.23 0.11
Matches are distributed among these distances:
40 1 0.00
41 116 0.16
42 282 0.39
43 307 0.42
44 20 0.03
45 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (43 bp):
TTTTATCCTTTGTTGACTTGTCAACTTAGTCCCGGGTAAATCC
Found at i:1235975 original size:254 final size:252
Alignment explanation
Indices: 1235192--1236906 Score: 1404
Period size: 254 Copynumber: 6.8 Consensus size: 252
1235182 GCTATACTCG
* * * * * * *
1235192 GTCAACCTCTTTATCCTTTATTTACCTGTTGGCTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCCTA-GTAAATCCTTTTATCCTTTGTT
* * * * * ** * * * *
1235257 AACTTGTCGATTCAATCCCTGTCAACCTTTTGATCCTTTGTTTATTTTTTAGCTTAGTCTTGGGT
65 GACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTTAGTCCTGAGT
* * * * **
1235322 AAATCCTTTTATCTTTTGTTGACTTATCGGTTTAAT-CTTGATCAACCTTTTTATCCTTTGTTTA
130 AAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAG-TCAACCTTTTTATCCTTTGTTTA
* * * * *
1235386 CCTATCGACTTAGTCCCGGGTAAATCCTTTTATCCTTTGTTGAATTGTCGATTTAATCTTA
194 CC-ATCAACTTAGT-CTGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCCTA
* * * * *
1235447 GTCAACCTTTTTATCTTTTATTTAACTGTTGCCTCAGTCCTAGATAAATCCTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCCTAG-TAAATCCTTTTATCCTTTGTT
* ** ** * * * *
1235512 AACTTGTCAGTTCAATCTTGGTCAA-CTTTTTATCCTTTATTTAGCTAT-GGACTCAGTCCTTG-
65 GACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAG-CTTAGTCC-TGA
* * * * **
1235574 GTAAATCCTTTTATCCTTTGTTGACTTATC-GATTTAATCTCAGTCAGCC-TTTTATGATTTGTT
128 GTAAATCCTTTTATCCTTTGTTGACTTGTCAG-TTCAATCCCAGTCAACCTTTTTATCCTTTGTT
*** * * *
1235637 TAGTTGTCAGCTTAGTCCT-GGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCTTG
192 TA-CCATCAACTTAGT-CTGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCCTA
* * * **
1235699 GCCAACCTTTTTTTCCTTTGTTTACCTGTC-AGCTCAGTCTTAAGTAAATCCTTTTAAGCTTTGT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGA-CTCAGTCCT-AGTAAATCCTTTTATCCTTTGT
* * * * * * * * *
1235763 TCACTTGTTTGTTCAATCCCAGTTAACCTTTTTATCCTTCGTTTACCTGTCAACTTAGTCCCGGG
64 TGACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTTAGTCCTGAG
* * *
1235828 TAAATCTTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAATCAACC-TTTTATCCTTTGTTCA
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACCTTTTTATCCTTTGTTTA
* *
1235892 CCAGTCAACTCAGTCTGGGGTAAATCCTTTTATCCTTT-TCTGACTTATCGATTCAATCCTA
194 CCA-TCAACTTAGTCT-GGGTAAATCCTTTTATCCTTTGT-TGACTTGTCGATTCAATCCTA
* * * * * *
1235953 GTGAACCTTTTTATCTTTTGTTTACTTGTTGGCTTAGTCCTAGATAAATCCTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCCTAG-TAAATCCTTTTATCCTTTGTT
* * * * * * *
1236018 GACTTGTCGGTACAATCCTGGTCAACTTTTTTACCCTTTGTTTACCTATCA-ATTCAGTCCTAAG
65 GACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTT-AGTCCTGAG
* * *** ** *
1236082 TAAGTCCTTTTATCCTTTGTTGACTTGTCATTTCAATCTTTGTCGTCCTTTTTATCCGTTGTTTA
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACCTTTTTATCCTTTGTTTA
* * * * * * * * * *
1236147 CCTAT-AGGCTCAGTCACT-AGTAAATCCTTTTATCGTTTGTTAACTTATCAATTTAATCTTG
194 CC-ATCA-ACTTAGT--CTGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCCTA
* * * *
1236208 GTTAACC-TTTAATGCTTTGTTTACCTGTCGACTCAGTCCTAAGT-AATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCCT-AGTAAATCCTTTTATCCTTTGTT
* *** * * * * * *
1236271 CACTTG-TCAATCTAATCCCGGTCATCCTTTTTATTCTTTGTTTACCTATTAGCTTAATCCCGAC
65 GACTTGTTGGTTC-AATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTTAGTCCTGAG
* * *
1236335 TAAATCATTTTAACCTTTGTTGACTTCTC-GATTCAATCCCAGTCAACCTTTTTATCCTTTGTTT
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAG-TTCAATCCCAGTCAACCTTTTTATCCTTTGTTT
* * ** * * * *
1236399 ACTTATCGACTTAGTCCTAAGTAAATCTTTTTATCCTTTATTGACTTGTCGGTTCAATCCTG
193 AC-CATCAACTTAGT-CTGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCCTA
* * * * * *
1236461 GTCAACCTTTTTATCCTTTGTTTACTTGTTGGCTCAATCCCGAGTAAATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGT-CCTAGTAAATCCTTTTATCCTTTGTT
* ** * * ** *
1236526 GACTTGTTGGTTCAATCTCAATTAACC-TTTTATCCTTTGTTTACCTTTCAGCTTAGTCCCAACT
65 GACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTTAGTCCTGAGT
* * * * * *
1236590 TAATCCTTTTATCCTTTGTTAACTTGTCGGTTCAATCCCGGTCAGCCTTTATATCCTTTGTTTAT
130 AAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACCTTTTTATCCTTTGTTTA-
*** * * * * *
1236655 TTGTCAGCTTAGTCTTGGGTAAATACTTTTATCCTTTCTTGACTTGT-TAGTTTAATCCTA
194 CCATCAACTTAGTC-TGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGA-TTCAATCCTA
* * * *
1236715 GTCAACC-ATTTATCCTTTGTTTACTTGTCGACTTAGTCCTTAGTAAATCCTTTTATCTTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCC-TAGTAAATCCTTTTATCCTTTGTT
* * * * ** *
1236779 GACTTGTCGGTTCAGTCCCGATCAA-CTTTTGTATTCTTTGTTTAATTATCGGCTTAGTCCTGAG
65 GACTTGTTGGTTCAATCCCGGTCAACCTTTT-TATCCTTTGTTTACCTATCAGCTTAGTCCTGAG
* * * ** *
1236843 TAAATTCTTTTATCCTTTGTTGACTTTTCAATTCAATCTTAGTCAA-CTTTTGTATCTTTTGTTT
129 TAAATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACCTTTT-TATCCTTTGTTT
1236907 GCCTATCGGC
Statistics
Matches: 1166, Mismatches: 250, Indels: 89
0.77 0.17 0.06
Matches are distributed among these distances:
252 118 0.10
253 356 0.31
254 505 0.43
255 180 0.15
256 5 0.00
257 2 0.00
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (252 bp):
GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTCAGTCCTAGTAAATCCTTTTATCCTTTGTTG
ACTTGTTGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACCTATCAGCTTAGTCCTGAGTA
AATCCTTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACCTTTTTATCCTTTGTTTACC
ATCAACTTAGTCTGGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCCTA
Found at i:1236820 original size:592 final size:588
Alignment explanation
Indices: 1235192--1236880 Score: 1720
Period size: 592 Copynumber: 2.9 Consensus size: 588
1235182 GCTATACTCG
* * * *
1235192 GTCAACCTCTTTATCCTTTATTTACCTGTTGGCTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
* * * * * * *
1235257 AACTTGTCGATTCAATCCCTGTCAACCTTTTGATCCTTTGTTTATTTTTTAGCTTAGTCTTGGGT
66 GACTTGTCGGTTCAAT-CCTGTCAACCTTTTTATCCTTTGTTTACTTGTTAGCTCAGTCTCGGGT
* * **
1235322 AAATCCTTTTATCTTTTGTTGACTTATCGGTTTAATCTTGATCAACCTTTTTATCCTTTGTTTAC
130 AAATCCTTTTATCCTTTGTTGACTTATCGGTTCAATCTCAATCAACCTTTTTATCCTTTGTTTAC
* ** * * * *
1235387 CTATCGACTTAGTCCCGGGTAAATCCTTTTATCCTTTGTTGAA-TTGTCGATTTAATCTTAGTCA
195 CTTTCG-CTTAGTCCC-AATAAATCCTTTTATCCTTTGTT-AACTTGTCGGTTCAATCCTGGTCA
* * * * * *
1235451 ACCTTTTTATCTTTTATTTAACTGT-TGCCTCAGTCCTAGATAAATCCTTTTATCCTTTGTTAAC
257 ACCTTTTTATCCTTTGTTTAACTGTCAG-CTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGAC
* * * * *
1235515 TTGTCAGTTCAATCTTGGTCAACTTTTTATCCTTTATTTAGCTATG-GACTCAGTCCTTGGTAAA
321 TTGTCAGTTTAATCTTAGTCAACCTTTTATCCTTTGTTTA-CT-TGTGACTCAGTCCTTAGTAAA
* * *
1235579 TCCTTTTATCCTTTGTTGACTTATCGATTTAATCTC-AGTCAGCCTTTTATGATTTGTTTAGTTG
384 TCCTTTTATCCTTTGTTGACTTATCGATTTAATCTCGA-TCAACCTTTTATGCTTTGTTTAATTG
* * * **
1235643 TC-AGCTTAGTCCTGGTAAATCCTTTTATCCTTTGTTGACTTGTCGATTCAATCTTGGCCAACCT
448 TCGA-CTTAGTCCTAGTAAATCTTTTTATCCTTTGTTGACTTGTCAATTCAATCCCGGCCAACCT
* * ** * * * *
1235707 TTTTTTCCTTTGTTTACCTGTCAGCTCAGTCTTAAGTAAATCCTTTTAAGCTTTGTTCACTTGTT
512 TTTTTTCCTTTGTTTACCTATCAGCTCAATCCCAACTAAATCATTTTAACCTTTGTTCACTTGCT
*
1235772 TGTTCAATCCCA
577 CGTTCAATCCCA
* * * *
1235784 GTTAACCTTTTTATCCTTCGTTTACCTGTCAACTTAGTCCCGGGTAAATCTTTTTATCCTTTGTT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
* ** * ** * * *
1235849 GACTTGTCAGTTCAATCCCAATCAACC-TTTTATCCTTTGTTCACCAGTCAACTCAGTCTGGGGT
66 GACTTGTCGGTTCAAT-CCTGTCAACCTTTTTATCCTTTGTTTACTTGTTAGCTCAGTCTCGGGT
* * * *
1235913 AAATCCTTTTATCCTTT-TCTGACTTATCGATTCAATC-CTAGTGAACCTTTTTATCTTTTGTTT
130 AAATCCTTTTATCCTTTGT-TGACTTATCGGTTCAATCTC-AATCAACCTTTTTATCCTTTGTTT
* * * * *
1235976 ACTTGTTGGCTTAGTCCTAGATAAATCCTTTTATCCTTTGTTGACTTGTCGGTACAATCCTGGTC
193 ACCT-TTCGCTTAGTCCCA-ATAAATCCTTTTATCCTTTGTTAACTTGTCGGTTCAATCCTGGTC
* * * * * * *
1236041 AACTTTTTTACCCTTTGTTTACCTATCA-ATTCAGTCCTAAGTAAGTCCTTTTATCCTTTGTTGA
256 AACCTTTTTATCCTTTGTTTAACTGTCAGCTT-AGTCCTAGGTAAATCCTTTTATCCTTTGTTGA
* ** * * * *
1236105 CTTGTCA-TTTCAATCTTTGTCGTCCTTTTTATCCGTTGTTTACCTATAGGCTCAGTCAC-TAGT
320 CTTGTCAGTTT-AATCTTAGTCAACC-TTTTATCCTTTGTTTACTTGT-GACTCAGTC-CTTAGT
* * * * * * * **
1236168 AAATCCTTTTATCGTTTGTTAACTTATCAATTTAATCTTGGTTAACCTTTAATGCTTTGTTTACC
381 AAATCCTTTTATCCTTTGTTGACTTATCGATTTAATCTCGATCAACCTTTTATGCTTTGTTTAAT
* * * *
1236233 TGTCGACTCAGTCCTAAGT-AATCTTTTTATCCTTTGTTCACTTGTCAA-TCTAATCCCGGTCAT
446 TGTCGACTTAGTCCT-AGTAAATCTTTTTATCCTTTGTTGACTTGTCAATTC-AATCCCGGCCAA
* * * *
1236296 CCTTTTTATT-CTTTGTTTACCTATTAGCTTAATCCCGACTAAATCATTTTAACCTTTGTTGACT
509 CCTTTTT-TTCCTTTGTTTACCTATCAGCTCAATCCCAACTAAATCATTTTAACCTTTGTTCACT
1236360 T-CTCGATTCAATCCCA
573 TGCTCG-TTCAATCCCA
* * * * *
1236376 GTCAACCTTTTTATCCTTTGTTTACTTATCGACTTAGTCCTAAGTAAATCTTTTTATCCTTTATT
1 GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
* * * *
1236441 GACTTGTCGGTTCAATCCTGGTCAACCTTTTTATCCTTTGTTTACTTGTTGGCTCAATCCCGAGT
66 GACTTGTCGGTTCAATCCT-GTCAACCTTTTTATCCTTTGTTTACTTGTTAGCTCAGTCTCGGGT
* * * *
1236506 AAATCTTTTTATCCTTTGTTGACTTGTTGGTTCAATCTCAATTAACC-TTTTATCCTTTGTTTAC
130 AAATCCTTTTATCCTTTGTTGACTTATCGGTTCAATCTCAATCAACCTTTTTATCCTTTGTTTAC
* * *
1236570 CTTTCAGCTTAGTCCCAACTTAATCCTTTTATCCTTTGTTAACTTGTCGGTTCAATCCCGGTCAG
195 CTTTC-GCTTAGTCCCAA-TAAATCCTTTTATCCTTTGTTAACTTGTCGGTTCAATCCTGGTCAA
* ** * * * *
1236635 CCTTTATATCCTTTGTTTATTTGTCAGCTTAGTCTTGGGTAAATACTTTTATCCTTTCTTGACTT
258 CCTTTTTATCCTTTGTTTAACTGTCAGCTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGACTT
* * * *
1236700 GTTAGTTTAATCCTAGTCAACCATTTATCCTTTGTTTACTTGTCGACTTAGTCCTTAGTAAATCC
323 GTCAGTTTAATCTTAGTCAACCTTTTATCCTTTGTTTACTTGT-GACTCAGTCCTTAGTAAATCC
* * * * * * * * *
1236765 TTTTATCTTTTGTTGACTTGTCGGTTCAGTCCCGATCAACTTTTGTATTCTTTGTTTAATTATCG
387 TTTTATCCTTTGTTGACTTATCGATTTAATCTCGATCAACCTTT-TATGCTTTGTTTAATTGTCG
* *
1236830 GCTTAGTCCTGAGTAAAT-TCTTTTATCCTTTGTTGACTTTTCAATTCAATC
451 ACTTAGTCCT-AGTAAATCT-TTTTATCCTTTGTTGACTTGTCAATTCAATC
1236881 TTAGTCAACT
Statistics
Matches: 882, Mismatches: 184, Indels: 61
0.78 0.16 0.05
Matches are distributed among these distances:
590 7 0.01
591 267 0.30
592 500 0.57
593 104 0.12
594 4 0.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (588 bp):
GTCAACCTTTTTATCCTTTGTTTACCTGTCGACTTAGTCCCAGGTAAATCTTTTTATCCTTTGTT
GACTTGTCGGTTCAATCCTGTCAACCTTTTTATCCTTTGTTTACTTGTTAGCTCAGTCTCGGGTA
AATCCTTTTATCCTTTGTTGACTTATCGGTTCAATCTCAATCAACCTTTTTATCCTTTGTTTACC
TTTCGCTTAGTCCCAATAAATCCTTTTATCCTTTGTTAACTTGTCGGTTCAATCCTGGTCAACCT
TTTTATCCTTTGTTTAACTGTCAGCTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGACTTGTC
AGTTTAATCTTAGTCAACCTTTTATCCTTTGTTTACTTGTGACTCAGTCCTTAGTAAATCCTTTT
ATCCTTTGTTGACTTATCGATTTAATCTCGATCAACCTTTTATGCTTTGTTTAATTGTCGACTTA
GTCCTAGTAAATCTTTTTATCCTTTGTTGACTTGTCAATTCAATCCCGGCCAACCTTTTTTTCCT
TTGTTTACCTATCAGCTCAATCCCAACTAAATCATTTTAACCTTTGTTCACTTGCTCGTTCAATC
CCA
Found at i:1239203 original size:19 final size:19
Alignment explanation
Indices: 1239179--1239233 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1239169 CAAATAGTAA
1239179 ATGTATCGATACATAAGCC
1 ATGTATCGATACATAAGCC
* **
1239198 ATGTATCGATGCATAAGTT
1 ATGTATCGATACATAAGCC
*
1239217 TTGTATCGATACA-AAGC
1 ATGTATCGATACATAAGC
1239234 TGCCCTGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 3 0.10
19 27 0.90
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACATAAGCC
Found at i:1241030 original size:16 final size:16
Alignment explanation
Indices: 1241001--1241033 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1240991 CGAATTTGGC
1241001 AAATTATTTCTTCTAG
1 AAATTATTTCTTCTAG
1241017 AAATTGATTT-TTCTAG
1 AAATT-ATTTCTTCTAG
1241033 A
1 A
1241034 TTTTTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (16 bp):
AAATTATTTCTTCTAG
Found at i:1258693 original size:8 final size:8
Alignment explanation
Indices: 1258680--1258705 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1258670 ATTTGATTAA
1258680 ATTTTGTG
1 ATTTTGTG
1258688 ATTTTGTG
1 ATTTTGTG
1258696 ATTTTGTG
1 ATTTTGTG
1258704 AT
1 AT
1258706 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1258878 original size:13 final size:13
Alignment explanation
Indices: 1258860--1258898 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1258850 ACAGCATTCT
1258860 TTGTATCGATACA
1 TTGTATCGATACA
*
1258873 TTGTATCGATACG
1 TTGTATCGATACA
*
1258886 GTGTATCGATACA
1 TTGTATCGATACA
1258899 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1261382 original size:13 final size:13
Alignment explanation
Indices: 1261364--1261388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1261354 AGATTGCACA
1261364 GTATCGATACATT
1 GTATCGATACATT
1261377 GTATCGATACAT
1 GTATCGATACAT
1261389 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1261401 original size:20 final size:21
Alignment explanation
Indices: 1261376--1261428 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1261366 ATCGATACAT
*
1261376 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1261396 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1261417 TGTATCGATACA
1 TGTATCGATACA
1261429 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1261506 original size:13 final size:13
Alignment explanation
Indices: 1261488--1261513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1261478 TACACACAAG
1261488 ATGTATCGATACA
1 ATGTATCGATACA
1261501 ATGTATCGATACA
1 ATGTATCGATACA
1261514 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1261530 original size:33 final size:32
Alignment explanation
Indices: 1261470--1261533 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1261460 CTTAACTATT
*
1261470 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1261502 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1261534 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Done.