Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 9 of 47
Found at i:1188219 original size:17 final size:15
Alignment explanation
Indices: 1188199--1188249 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1188189 TTAAGCAAAA
1188199 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1188216 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
* *
1188230 AA-AAAGAAAAAAAA
1 AAGAAAGAAAGAAAG
1188244 AAGAAA
1 AAGAAA
1188250 AAATATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1188250 original size:17 final size:17
Alignment explanation
Indices: 1188196--1188251 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1188186 AAGTTAAGCA
* *
1188196 AAAAAGAAAGAAAGAAG
1 AAAAAGAAAAAAAAAAG
** * *
1188213 ATGAAGAAGAAAGAAAG
1 AAAAAGAAAAAAAAAAG
1188230 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
1188247 AAAAA
1 AAAAA
1188252 ATATGAAATA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:1190992 original size:17 final size:17
Alignment explanation
Indices: 1190944--1190995 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1190934 ATCTGTAATT
* *
1190944 ATTTAAATTTAATATAA
1 ATTTATATTTAATTTAA
* *
1190961 GTTTAT-TTATTATTTAA
1 ATTTATATT-TAATTTAA
1190978 ATTTATATTTAATTTAA
1 ATTTATATTTAATTTAA
1190995 A
1 A
1190996 AAATAATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTATATTTAATTTAA
Found at i:1191940 original size:27 final size:27
Alignment explanation
Indices: 1191907--1191974 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1191897 AGCCACCCTT
*
1191907 TGTTTGTAAAAAATGGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
1191934 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
1191961 TATTTGTCAAAAAT
1 TGTTTGTCAAAAAT
1191975 AATGGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:1193858 original size:27 final size:28
Alignment explanation
Indices: 1193780--1193868 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 28
1193770 CATTCATCAC
*
1193780 CCTTCAAAAGCCCACAAGTCAGTGGCATTT
1 CCTTCAAAAGCCCACAAGTCAGTGGCA--A
** *
1193810 TTTTCGAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1193838 CCTTC-AAAGCCCACAAATCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1193865 CCTT
1 CCTT
1193869 TTTCGAAGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 24 0.47
28 3 0.06
30 24 0.47
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1194063 original size:58 final size:58
Alignment explanation
Indices: 1193782--1194222 Score: 312
Period size: 58 Copynumber: 7.5 Consensus size: 58
1193772 TTCATCACCC
*** * *
1193782 TTCAAAAGCCCACAAGTCAGTGGCATTTTTTTCGAAAGCCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAAGCCCACAAGTCAGTGGCAACTT
* * * * *
1193840 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTTC-GAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC--TTTCAAAAGCCCACAAGTCAGTGGCAACTT
* * * * ** * * *
1193898 TTCCAAAGTCCACAACTCCGTGGC-ACTCTTTTTCTTTTGTAAGCTCACAACTCTA-TAGC-ACT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C--TTTC----AAAAGCCCACAAGTC-AGTGGCAACT
1193960 T
58 T
*** * * *
1193961 TT-TTCAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAGTCAGTGGCA-ACTT
* * *
1194020 TTCAAAAGCCCACAAGTCAGTGGCAACCTTT-AAAAGCCCACAAGTTAGTGGCACCCTG
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCA-ACTT
** *
1194078 TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAAGCCCACAAGTCAGTGGCAACTT
* *
1194137 TT-AAAAGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCA-ACTT
** * * *
1194193 TTCCGAAGACCACAAATCGGTGGC-ACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTT
1194223 TCCATCTTTA
Statistics
Matches: 304, Mismatches: 58, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
55 20 0.07
56 11 0.04
57 73 0.24
58 80 0.26
59 39 0.13
60 41 0.13
61 5 0.02
62 15 0.05
63 6 0.02
64 14 0.05
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (58 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAGTCAGTGGCAACTT
Found at i:1194071 original size:88 final size:87
Alignment explanation
Indices: 1193966--1194187 Score: 385
Period size: 88 Copynumber: 2.6 Consensus size: 87
1193956 CACTTTTTTC
1193966 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1194031 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
1194054 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCT-TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1194119 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
* * *
1194142 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCACAAATCAGTGGCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCA
1194188 CCCTTTTCCG
Statistics
Matches: 130, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
85 20 0.15
86 3 0.02
87 1 0.01
88 106 0.82
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.20
Consensus pattern (87 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
CAAGTCAGTGGCAACCTTTAAA
Found at i:1194208 original size:30 final size:30
Alignment explanation
Indices: 1193782--1194224 Score: 343
Period size: 30 Copynumber: 15.1 Consensus size: 30
1193772 TTCATCACCC
***
1193782 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
*
1193812 TTCGAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
* *
1193840 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-TT
* * *
1193870 TTC-GAAGCCCACAAGTCGGTGGC-ATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
* * * *
1193898 TTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C-TT
** * * * *
1193929 TTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTTTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCAAC-CTT
* *
1193963 TTC---AGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
*
1193990 TTCAAAAGCCCACAAGTCAGTGGCATA-TTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTT
1194020 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
* * *
1194049 TT-AAAAGCCCACAAGTTAGTGGCACCCTG
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
*
1194078 TTCAAAAGCCCACAAGTCAGTGGCATA-TTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTT
1194108 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
1194137 TT-AAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
* *
1194164 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
** * * *
1194193 TTCCGAAGACCACAAATCGGTGGC-ACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
1194222 TTC
1 TTC
1194225 CATCTTTAAG
Statistics
Matches: 340, Mismatches: 47, Indels: 53
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.00
27 63 0.19
28 57 0.17
29 38 0.11
30 154 0.45
31 5 0.01
34 5 0.01
35 17 0.05
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:1194296 original size:43 final size:43
Alignment explanation
Indices: 1194228--1194317 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1194218 CCTTTTCCAT
*
1194228 CTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
* * *
1194271 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
1194314 CTTT
1 CTTT
1194318 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
Found at i:1194349 original size:52 final size:53
Alignment explanation
Indices: 1194271--1194424 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
1194261 ACATTGGCAC
*
1194271 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
* * * *
1194323 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAG
* * * * * *
1194378 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1194425 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 35 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
Found at i:1195274 original size:13 final size:13
Alignment explanation
Indices: 1195256--1195280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195246 CATAAAGTGT
1195256 TGTATCGATACAA
1 TGTATCGATACAA
1195269 TGTATCGATACA
1 TGTATCGATACA
1195281 TATTTTTTTG
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:1195278 original size:33 final size:33
Alignment explanation
Indices: 1195236--1195302 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1195226 TTCAACGATT
1195236 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1195269 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1195302 T
1 T
1195303 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1195362 original size:13 final size:13
Alignment explanation
Indices: 1195344--1195368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195334 ATCACTTAAA
1195344 TGTATCGATACAT
1 TGTATCGATACAT
1195357 TGTATCGATACA
1 TGTATCGATACA
1195369 CTGATCTTTG
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):
TGTATCGATACAT
Found at i:1195433 original size:52 final size:52
Alignment explanation
Indices: 1195377--1195557 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
1195367 CACTGATCTT
*
1195377 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1195429 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1195481 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1195533 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1195558 TCATATTTTG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1202522 original size:27 final size:27
Alignment explanation
Indices: 1202492--1202556 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1202482 TTTGTTTATA
*
1202492 AAAAATGGTGGTTACTTTGTGTTTGTC
1 AAAAATGGTGGTTACTTTGTATTTGTC
* *
1202519 AAAAATGGTGGTTTCTTTTTATTTGTC
1 AAAAATGGTGGTTACTTTGTATTTGTC
*
1202546 AAAAATTGTGG
1 AAAAATGGTGG
1202557 CATGTTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (27 bp):
AAAAATGGTGGTTACTTTGTATTTGTC
Found at i:1203944 original size:13 final size:14
Alignment explanation
Indices: 1203909--1203964 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
1203899 TATTAAAATT
*
1203909 TTAAATATACT-TA
1 TTAAATATATTATA
1203922 TTATAA-ATA-TATA
1 TTA-AATATATTATA
1203935 TTAAATATATTATA
1 TTAAATATATTATA
*
1203949 TTATAT-TATTATA
1 TTAAATATATTATA
1203962 TTA
1 TTA
1203965 TTTTCATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 3 0.08
13 24 0.63
14 11 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATATATTATA
Found at i:1203965 original size:13 final size:14
Alignment explanation
Indices: 1203920--1203965 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
1203910 TAAATATACT
*
1203920 TATTATAAATA-TA
1 TATTATATATATTA
*
1203933 TATTAAATATATTA
1 TATTATATATATTA
1203947 TATTATAT-TATTA
1 TATTATATATATTA
1203960 TATTAT
1 TATTAT
1203966 TTTCATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATATATATTA
Found at i:1204243 original size:15 final size:14
Alignment explanation
Indices: 1204203--1204231 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1204193 TATTAATAAT
1204203 TTATTATTTAAATA
1 TTATTATTTAAATA
1204217 TTATTATTTAAATA
1 TTATTATTTAAATA
1204231 T
1 T
1204232 ATTTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTATTTAAATA
Found at i:1204330 original size:18 final size:19
Alignment explanation
Indices: 1204307--1204355 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1204297 AATTTTTTAA
1204307 AAATAAAAATATAAA-AT-T
1 AAATAAAAAT-TAAATATAT
1204325 AAATAAAAATTAAATATAT
1 AAATAAAAATTAAATATAT
*
1204344 AAATAAATATTA
1 AAATAAAAATTA
1204356 CATTTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 12 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAAAAATTAAATATAT
Found at i:1204335 original size:11 final size:12
Alignment explanation
Indices: 1204313--1204353 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1204303 TTAAAAATAA
1204313 AAATATAAAATT
1 AAATATAAAATT
1204325 AAATA-AAAATT
1 AAATATAAAATT
1204336 AAATATATAAA-T
1 AAATATA-AAATT
1204348 AAATAT
1 AAATAT
1204354 TACATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.41
12 13 0.48
13 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:1204339 original size:23 final size:24
Alignment explanation
Indices: 1204304--1204352 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1204294 TATAATTTTT
1204304 TAAAAATAAAAATATA-AAATTAAA
1 TAAAAATAAAAATATATAAA-TAAA
*
1204328 TAAAAAT-TAAATATATAAATAAA
1 TAAAAATAAAAATATATAAATAAA
1204351 TA
1 TA
1204353 TTACATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAAAATAAAAATATATAAATAAA
Found at i:1204985 original size:49 final size:49
Alignment explanation
Indices: 1204866--1204988 Score: 210
Period size: 49 Copynumber: 2.5 Consensus size: 49
1204856 ATATGCGGCT
* * * *
1204866 AGCGATATTGGGCTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCT
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1204915 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1204964 AGCGACATTGGACTTAAAGATGAAG
1 AGCGACATTGGACTTAAAGATGAAG
1204989 ATGAGAAAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:1205176 original size:43 final size:43
Alignment explanation
Indices: 1205111--1205573 Score: 548
Period size: 43 Copynumber: 10.1 Consensus size: 43
1205101 TAAAGATGGA
* *
1205111 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205154 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205197 AAAGATGAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -AA-A-G---GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205246 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1205289 AAAGAAGAAGTTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-AAG--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205338 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205381 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205430 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* *
1205479 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1205525 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1205568 AGAAGG
1 A-AAGG
1205574 GTTACCACCG
Statistics
Matches: 368, Mismatches: 24, Indels: 55
0.82 0.05 0.12
Matches are distributed among these distances:
43 190 0.52
44 9 0.02
45 2 0.01
46 9 0.02
47 2 0.01
48 4 0.01
49 113 0.31
51 1 0.00
52 38 0.10
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1205246 original size:92 final size:92
Alignment explanation
Indices: 1205067--1205568 Score: 851
Period size: 92 Copynumber: 5.4 Consensus size: 92
1205057 AAAAAGATGT
** * *
1205067 CAATGTGCTGATTCAAGGTTAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTAATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
1205132 CAAGGCCAGCTATATTGGACTTAAAGGTGC
63 CAAGGCCAGCTATATTGGACTTAAAGGTGC
*
1205162 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAATGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1205227 GGCCAGCTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
* *
1205254 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
1205319 GGCCAGCGATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
*
1205346 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1205411 GGCCAGCTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
1205438 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
*
1205503 CAAGGCCAACTATATTGGACTTAAAGGTGC
63 CAAGGCCAGCTATATTGGACTTAAAGGTGC
*
1205533 CAATGTGCTGATTCAAGGCCAGCTACATTAGACTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1205569 GAAGGGTTAC
Statistics
Matches: 390, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
92 266 0.68
93 1 0.00
94 1 0.00
95 122 0.31
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGC
Found at i:1205639 original size:27 final size:27
Alignment explanation
Indices: 1205609--1205664 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1205599 AGAAGAGGAG
*
1205609 AAAGATGCCACAGAGTTGTAGACTTAA
1 AAAGATGCCACAGAATTGTAGACTTAA
* * *
1205636 AAAGGTGCCACGGAATTGTGGACTTAA
1 AAAGATGCCACAGAATTGTAGACTTAA
1205663 AA
1 AA
1205665 GGGAAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (27 bp):
AAAGATGCCACAGAATTGTAGACTTAA
Found at i:1205721 original size:34 final size:34
Alignment explanation
Indices: 1205634--1206232 Score: 631
Period size: 34 Copynumber: 17.8 Consensus size: 34
1205624 TTGTAGACTT
* * *
1205634 AAAAAGGTGCCACGGAATTGTGGAC-TTAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AG
* * *
1205668 AAAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
1205703 AAAAAGGTGCCACGGAGTTATGGGCTTT-GAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
1205736 --GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-G
* **
1205769 AAAAAGGTACCACGGAGTTGTGGG-TTTTGAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
1205802 --GAAGGTGCCACGGAGTTATGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
1205834 GAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG
* *
1205870 AAAAAAAGTGCCACGAAGTTGTGGGCTTTAAAAAG
1 -AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1205905 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
1205939 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* ** *
1205973 AACAAGGTGCCAC-GAGGTCATGGAC-TTAAAAAG
1 AAAAAGGTGCCACGGA-GTTGTGGGCTTTAAAAAG
* *
1206006 -AAAATGTGCCACGGAGTGGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
** *
1206039 AAAAAGGTGCCACGGAGTTGTGCACTTTGAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG
1206075 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
* * * *
1206110 -AAAATGTGCCACGGAGTGGTGGGCTTTGAGAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
1206143 AAAAAGGTTGCCACGGAATTGTGAGCTTT-AAAAG
1 AAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAAG
* * *
1206177 -----GGTGCCACAGAGTTGTGGAC-TTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
1206205 AACAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT
1206233 GAAGAAAAAA
Statistics
Matches: 473, Mismatches: 64, Indels: 56
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.00
28 18 0.04
29 2 0.00
31 43 0.09
32 26 0.05
33 68 0.14
34 178 0.38
35 70 0.15
36 21 0.04
37 45 0.10
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:1205787 original size:100 final size:101
Alignment explanation
Indices: 1205635--1206232 Score: 661
Period size: 100 Copynumber: 5.9 Consensus size: 101
1205625 TGTAGACTTA
* * * * *
1205635 AAAAGGTGCCACGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAGAGTTATGGGCTTTGA
1 AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
* *
1205699 AAAGAAAAAGGTGCCACGGAGTTATGGGCTTT-GAAAG
65 AAAG-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* * * **
1205736 -GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTACCACGGAGTTGTGGG-TTTTGA
1 AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* *
1205799 AAG-GAAGGTGCCACGGAGTTATGGGCTTTAAAAAGG
66 AAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-G
* *
1205835 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGAAGTTGTGGGCTTTA
1 AAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTA
1205900 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
64 AAAAG-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* ** *
1205939 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAACAAGGTGCCAC-GAGGTCATGGAC-TTA
1 -AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGA-GTTGTGGGCTTTA
* *
1206001 AAAAGAAAATGTGCCACGGAGTGGTGGGCTTTAAAAAG
64 AAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
**
1206039 AAAAAGGTGCCACGGAGTTGTGCACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 -AAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
* * * *
1206104 AAAAAGAAAATGTGCCACGGAGTGGTGGGCTTTGAGAAG
63 AAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* * * *
1206143 AAAAAGGTTGCCACGGAATTGTGAGCTTTAAAA--G-----GGTGCCACAGAGTTGTGGAC-TTA
1 -AAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
*
1206200 AAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
64 AAAAGAA-AAGGTGCCACGGAGTTGTGGGCTTT
1206233 GAAGAAAAAA
Statistics
Matches: 435, Mismatches: 44, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
95 9 0.02
96 40 0.09
97 26 0.06
98 3 0.01
99 8 0.02
100 117 0.27
101 33 0.08
102 46 0.11
103 22 0.05
104 57 0.13
105 74 0.17
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (101 bp):
AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
AAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:1205799 original size:66 final size:65
Alignment explanation
Indices: 1205634--1206232 Score: 543
Period size: 66 Copynumber: 8.9 Consensus size: 65
1205624 TTGTAGACTT
* * * * * *
1205634 AAAAAGGTGCCACGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAGAGTTATGGGCTTTG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA-GG---AAG-GTGCCACGGAGTTGTGGGCTTTA
1205698 AAAAG
61 AAAAG
*
1205703 AAAAAGGTGCCACGGAGTTATGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-
1205768 G
65 G
* * *
1205769 AAAAAGGTACCACGGAGTTGTGGGTTTTGAAAGGAAGGTGCCACGGAGTTATGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* * *
1205834 GAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTG-AAA-GG----AAGGTGCCACGGAGTTGTGGGCTTT
1205899 AAAAAG
60 AAAAAG
* *
1205905 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-GAAAG--GAAGGTGCCACGGAGTTGTGGGCTTTAAA
*
1205970 AGG
63 AAG
* ** * ** * * *
1205973 AACAAGGTGCCAC-GAGGTCATGGACTTAAAAAGAAAATGTGCCACGGAGTGGTGGGCTTTAAAA
1 AAAAAGGTGCCACGGA-GTTGTGGGCTTTGAAAG-GAAGGTGCCACGGAGTTGTGGGCTTTAAAA
1206037 AG
64 AG
**
1206039 AAAAAGGTGCCACGGAGTTGTGCACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTG-AAA-GG---AAG-GTGCCACGGAGTTGTGGGCTTT
1206104 AAAAAG
60 AAAAAG
* * * * *
1206110 -AAAATGTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAAGGTTGCCACGGAATTGTGAGCTTT-A
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGA-AAG--GAAGG-TGCCACGGAGTTGTGGGCTTTAA
1206173 AAAG
62 AAAG
* * *
1206177 -----GGTGCCACAGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGG---AAGGTGCCACGGAGTTGTGGGCTTT
1206233 GAAGAAAAAA
Statistics
Matches: 449, Mismatches: 55, Indels: 60
0.80 0.10 0.11
Matches are distributed among these distances:
61 22 0.05
62 7 0.02
63 16 0.04
65 51 0.11
66 117 0.26
67 20 0.04
68 71 0.16
69 26 0.06
70 34 0.08
71 85 0.19
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (65 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:1206046 original size:205 final size:203
Alignment explanation
Indices: 1205634--1206177 Score: 724
Period size: 205 Copynumber: 2.7 Consensus size: 203
1205624 TTGTAGACTT
* *
1205634 AAAAAGGTGCCACGGAATTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCAC-AGAGTTATGGGCTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGA-AGTTGTGGGCTT
* * * *
1205696 TGAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAG--GAAGGTGCCACGGAGTTGTGGGC
65 TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGC
** ** ** * *
1205759 TTTAAAAAGGAAAAAGGTACCACGGAGTTGTGGGTTTTGAAAGGAAGGTGCCACGGAGTTATGGG
130 TTT-AAAAGGAAAAAGGTACCACGGAGTCATGGACTTAAAAAGAAAGGTGCCACGGAGTGATGGG
1205824 CTTTAAAAAG
194 CTTTAAAAAG
* * *
1205834 GAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT
1205899 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC
66 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGC
* * * *
1205964 TTTAAAAGGAACAAGGTGCCAC-GAGGTCATGGACTTAAAAAGAAAATGTGCCACGGAGTGGTGG
130 TTTAAAAGGAAAAAGGTACCACGGA-GTCATGGACTTAAAAAG-AAAGGTGCCACGGAGTGATGG
1206028 GCTTTAAAAAG
193 GCTTTAAAAAG
* *
1206039 AAAAAGGTGCCACGGAGTTGTGCACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT
* * * * *
1206104 AAAAAG-AAAATGTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAAGGTTGCCACGGAATTGTGAG
66 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGG-TGCCACGGAGTTGTGGG
1206168 CTTTAAAAGG
129 CTTTAAAAGG
1206178 GTGCCACAGA
Statistics
Matches: 303, Mismatches: 32, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
200 22 0.07
201 2 0.01
202 64 0.21
203 7 0.02
204 64 0.21
205 144 0.48
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (203 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT
AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCT
TTAAAAGGAAAAAGGTACCACGGAGTCATGGACTTAAAAAGAAAGGTGCCACGGAGTGATGGGCT
TTAAAAAG
Found at i:1206265 original size:31 final size:31
Alignment explanation
Indices: 1206212--1206385 Score: 203
Period size: 31 Copynumber: 5.7 Consensus size: 31
1206202 AGGAACAAGG
* * *
1206212 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAA
* *
1206243 TGCCACTGAGTCGTGGAATTTG-AGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAA
*
1206273 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAA-AA
* * *
1206305 TGCCACTGAGTCGTGGACTTTG-AGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAG-AAAAAA
* *
1206336 TGCCACTGAGTCGTGGACTTTGAAG--AGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAA
1206365 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1206386 AAAAAGGTAT
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
29 25 0.20
30 28 0.22
31 47 0.37
32 27 0.21
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAAA
Found at i:1207348 original size:1 final size:1
Alignment explanation
Indices: 1207339--1207395 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1207329 TTTTTCCTTC
* * * * * * *
1207339 TTTTGTTTTTTTTTGTTTGTTTTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1207396 AAGGTGAGCC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:1207367 original size:6 final size:6
Alignment explanation
Indices: 1207339--1207392 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
1207329 TTTTTCCTTC
* *
1207339 TTTTGTT TTTTTT TGTTTGT TTTTTT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTG-T TTTTGT T-TTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1207389 TTTT
1 TTTT
1207393 TTTAAGGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
6 33 0.79
7 9 0.21
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:1213753 original size:24 final size:22
Alignment explanation
Indices: 1213697--1213745 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1213687 TGGACATGTT
*
1213697 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAAAAA
1213719 AAAAATGCATGAAACATAAAAA
1 AAAAATGCATGAAACATAAAAA
1213741 AAAAA
1 AAAAA
1213746 AATGCATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAATGCATGAAACATAAAAA
Found at i:1214711 original size:20 final size:20
Alignment explanation
Indices: 1214664--1214738 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1214654 AAAAAGACAT
*
1214664 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1214683 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1214704 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1214724 AATGTATCGATACAT
1 AATGTATCGATACAT
1214739 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1214732 original size:40 final size:39
Alignment explanation
Indices: 1214661--1214738 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1214651 GGTAAAAAGA
* *
1214661 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1214700 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1214739 CAGGGTATGA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1218287 original size:52 final size:52
Alignment explanation
Indices: 1218209--1218337 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1218199 CGAAATATGA
* *
1218209 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
1218261 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1218313 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1218338 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1218350 original size:52 final size:51
Alignment explanation
Indices: 1218209--1218357 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
1218199 CGAAATATGA
*
1218209 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
1218261 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1218313 AAATTTGCCTACATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1218358 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1218364 original size:13 final size:13
Alignment explanation
Indices: 1218346--1218383 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1218336 CAAAGATCAG
1218346 TGTATCGATACAA
1 TGTATCGATACAA
1218359 TGTATCGATACAA
1 TGTATCGATACAA
1218372 TGTATCGATACA
1 TGTATCGATACA
1218384 TTTGAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1218465 original size:13 final size:13
Alignment explanation
Indices: 1218447--1218471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1218437 CAAAAAGATA
1218447 TGTATCGATACAT
1 TGTATCGATACAT
1218460 TGTATCGATACA
1 TGTATCGATACA
1218472 ACACTTTATG
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):
TGTATCGATACAT
Found at i:1218467 original size:33 final size:33
Alignment explanation
Indices: 1218425--1218491 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1218415 AGTAGCTTAA
1218425 ATTGTATCGATACAAAAAGATATGTATCGATAC
1 ATTGTATCGATACAAAAAGATATGTATCGATAC
* ***
1218458 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAGATATGTATCGATAC
1218491 A
1 A
1218492 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAGATATGTATCGATAC
Found at i:1220950 original size:24 final size:22
Alignment explanation
Indices: 1220928--1220977 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
1220918 CATATAATAG
1220928 ATAAAATATAATATATTTAAAT
1 ATAAAATATAATATATTTAAAT
*
1220950 ATAATTACTATAATATATTTAATAT
1 ATAA--AATATAATATATTTAA-AT
1220975 ATA
1 ATA
1220978 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAATATAATATATTTAAAT
Found at i:1220975 original size:14 final size:14
Alignment explanation
Indices: 1220932--1220975 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1220922 TAATAGATAA
1220932 AATATAATATATTT
1 AATATAATATATTT
1220946 AA-AT-ATA-A-TT
1 AATATAATATATTT
*
1220956 ACTATAATATATTT
1 AATATAATATATTT
1220970 AATATA
1 AATATA
1220976 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 3 0.12
11 3 0.12
12 6 0.25
13 3 0.12
14 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATAATATATTT
Found at i:1221014 original size:19 final size:17
Alignment explanation
Indices: 1220973--1221017 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1220963 TATATTTAAT
1220973 ATATATTTAAAATTTTA
1 ATATATTTAAAATTTTA
*
1220990 ACATATTTAATAATTTTTA
1 ATATATTTAA-AA-TTTTA
*
1221009 TTATATTTA
1 ATATATTTA
1221018 CGTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTTAAAATTTTA
Found at i:1222280 original size:17 final size:17
Alignment explanation
Indices: 1222255--1222287 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1222245 ATAAAAATTT
*
1222255 AAATTTATTTTATTTTA
1 AAATATATTTTATTTTA
1222272 AAATATATTTTATTTT
1 AAATATATTTTATTTT
1222288 TATTTGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AAATATATTTTATTTTA
Found at i:1222286 original size:22 final size:23
Alignment explanation
Indices: 1222258--1222303 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1222248 AAAATTTAAA
1222258 TTTA-TTTTATTT-TAAAATATAT
1 TTTATTTTTATTTGTAAAAT-TAT
1222280 TTTATTTTTATTTGTAAAATTAT
1 TTTATTTTTATTTGTAAAATTAT
1222303 T
1 T
1222304 GTGATTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATTTTTATTTGTAAAATTAT
Found at i:1222816 original size:72 final size:72
Alignment explanation
Indices: 1222470--1223295 Score: 719
Period size: 72 Copynumber: 11.5 Consensus size: 72
1222460 ATAATTTATT
* * *
1222470 TTTATTTTTATTTTTAAAAGTTTAAATTTATATTTTTA-TTTGATTATACATG--TTTAAATATT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTAT-TTTTTAGTATGATTAT--ATGAATTTAAATTTT
* *
1222532 TAAGTTATTA
63 TAAGGTATAA
* ** * **
1222542 TTTATTTTTATTTGTAGAAGTTTAAATTCGTTTTTTGAGTGTGATTATACAAATTTAAATGTTTT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-AGTATGATTATATGAATTTAAAT-TTTT
**
1222607 AATCTATAA
64 AAGGTATAA
* * * * * * *
1222616 TTTATTTTCATTTGTAGAAGTTTAAATTTGTTTTTTAGTTTAATTATATGAGTTTAAATATTTAA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAATTTAAATTTTTAA
* *
1222681 GTTATTA
66 GGTATAA
* * * *
1222688 TTTA-TTTT-TTTGTAAAAATTTAAATTAATTTTTTACTATGATTATATGAGTTTAAATTTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAATTTAAA-TTTTTA
1222751 AGGTATAA
65 AGGTATAA
* * * * *
1222759 TGTATTTTTAGTTATAAAAGTTTAAATTTATTTTTT-GTTTGATTATATGAATATAAATTTTTAA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAATTTAAATTTTTAA
* *
1222823 AGTATTA
66 GGTATAA
* * *
1222830 TTTATTTTTATTTTTAAAAATTTAAATTTATTTTTT--TATGATTATA-CAACTTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAA-TTTAAATTTTTA
1222892 AGGTATAA
65 AGGTATAA
* * * * * *
1222900 TTTATTTTTATTTGCAGAAGTTTAAATTTGTTTTTTAGTTTAATTATA-AAAGTTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAA-TTTAAATTTTTA
*
1222964 AGGTATTA
65 AGGTATAA
* * * *
1222972 TCTATCTTTATCTGTAAAAGTTTAAATTTATTTTTTAGCTATGATTATATGAGTTTAAATTTTTT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAG-TATGATTATATGAATTTAAA-TTTTT
*
1223037 AATGTATAA
64 AAGGTATAA
* * * * * * * *
1223046 TATATTTTTATTTGTAGAAGTTTTAATTTGTTTTTTGGGTACGATTATACGAGTTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-AGTATGATTATATGAATTTAAATTTTTA
* *
1223111 AGATATGA
65 AGGTATAA
* * * * * * * * * *
1223119 TTTATTTTTATTTATAAAACTTTAAATTTGTTCTCTGGTTTGATTATATGAGTTTAATTTTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAATTTAAATTTTTAA
* *
1223184 TG-ATATT
66 GGTATA-A
* *
1223191 TTTATTTTTATTTGT-AAAGTTTAAA--TATTTTTTGGGTATGATTATACGAATTTAAATTTTTT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-AGTATGATTATATGAATTTAAA-TTTTT
* *
1223253 AAGATATGA
64 AAGGTATAA
* * *
1223262 TATATTTTTATTTGTAGAA-TTCTAAATTTGTTTT
1 TTTATTTTTATTTGTAAAAGTT-TAAATTTATTTT
1223296 CTGGTTTAAT
Statistics
Matches: 611, Mismatches: 120, Indels: 44
0.79 0.15 0.06
Matches are distributed among these distances:
69 7 0.01
70 116 0.19
71 100 0.16
72 169 0.28
73 109 0.18
74 109 0.18
75 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (72 bp):
TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTATGATTATATGAATTTAAATTTTTAA
GGTATAA
Found at i:1222884 original size:142 final size:144
Alignment explanation
Indices: 1222470--1223295 Score: 782
Period size: 142 Copynumber: 5.7 Consensus size: 144
1222460 ATAATTTATT
* * *
1222470 TTTATTTTTATTTTTAAAAGTTTAAATTTATATTTTT-ATTTGATTATACATG--TTTAAATATT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTAT-TTTTTGGTTTGATTAT--ATGAATTTAAATTTT
* * * ** * ** *
1222532 TAAGTTATTATTTATTTTTATTTGTAGAAGTTTAAATTCGTTTTTTGAGTGTGATTATACAAATT
63 TAAGATATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTT-A-TATGATTATATGAGTT
* **
1222597 TAAATGTTTTAATCTATAA
126 TAAATTTTTTAAGGTATAA
* * * * * * *
1222616 TTTATTTTCATTTGTAGAAGTTTAAATTTGTTTTTTAGTTTAATTATATGAGTTTAAATATTTAA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTGATTATATGAATTTAAATTTTTAA
* *
1222681 GTTATTATTTA-TTTT-TTTGTAAAAATTTAAATTAATTTTTTACTATGATTATATGAGTTTAAA
66 GATATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTA-TATGATTATATGAGTTTAAA
1222744 TTTTTTAAGGTATAA
130 TTTTTTAAGGTATAA
* * * *
1222759 TGTATTTTTAGTTATAAAAGTTTAAATTTATTTTTT-GTTTGATTATATGAATATAAATTTTTAA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTGATTATATGAATTTAAATTTTTAA
* ** *
1222823 -AGTATTATTTATTTTTATTTTTAAAAATTTAAATTTATTTTTT-TATGATTATACAACTTTAAA
66 GA-TATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTATATGATTATATGAGTTTAAA
1222886 -TTTTTAAGGTATAA
130 TTTTTTAAGGTATAA
* * * * * *
1222900 TTTATTTTTATTTGCAGAAGTTTAAATTTGTTTTTTAGTTTAATTATA-AAAGTTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTGATTATATGAA-TTTAAATTTTTA
* * * * *
1222964 AGGTATTATCTATCTTTATCTGTAAAAGTTTAAATTTATTTTTTAGCTATGATTATATGAGTTTA
65 AGATATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTA--TATGATTATATGAGTTTA
*
1223029 AATTTTTTAATGTATAA
128 AATTTTTTAAGGTATAA
* * * * ** * *
1223046 TATATTTTTATTTGTAGAAGTTTTAATTTGTTTTTTGGGTACGATTATACGAGTTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTTTGATTATATGAATTTAAATTTTTA
* * * * * ** *
1223111 AGATATGATTTATTTTTATTTATAAAACTTTAAATTTGTTCTCTGGTTTGATTATATGAGTTTAA
65 AGATATTATTTATTTTTATTTGTAAAAATTTAAATTTATT-TTTTATATGATTATATGAGTTTAA
* * * *
1223176 TTTTTTTATGATAT-T
129 ATTTTTTAAGGTATAA
* *
1223191 TTTATTTTTATTTGT-AAAGTTTAAA--TATTTTTTGGGTATGATTATACGAATTTAAATTTTTT
1 TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTTTGATTATATGAATTTAAA-TTTTT
* * * *
1223253 AAGATATGATATATTTTTATTTGT-AGAATTCTAAATTTGTTTT
64 AAGATATTATTTATTTTTATTTGTAAAAATT-TAAATTTATTTT
1223296 CTGGTTTAAT
Statistics
Matches: 572, Mismatches: 90, Indels: 40
0.81 0.13 0.06
Matches are distributed among these distances:
141 46 0.08
142 141 0.25
143 100 0.17
144 57 0.10
145 40 0.07
146 133 0.23
147 52 0.09
148 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (144 bp):
TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTGATTATATGAATTTAAATTTTTAA
GATATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTATATGATTATATGAGTTTAAAT
TTTTTAAGGTATAA
Found at i:1223031 original size:430 final size:433
Alignment explanation
Indices: 1222434--1223274 Score: 1020
Period size: 430 Copynumber: 1.9 Consensus size: 433
1222424 TTTTGGTATA
* **
1222434 ATTATACAAGTTTAAATTTTTAAGATATAATTTATTTTTATTTTTATTTTTAAAAGTTTAAATTT
1 ATTATACAACTTTAAATTTTTAAGATATAA--TA-TTTTATTTTTATTTGCAAAAGTTTAAATTT
* * * * * * * *
1222499 ATATTTTTATTTGATTATACATGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAGAAGTT
63 ATATTTTTATTTAATTATAAAAGTTTAAATATTTAAGGTATTATCTATCTTTATCTGTAAAAGTT
* * *
1222564 TAAATTCGTTTTTTGAGTGTGATTATACAAATTTAAATGTTTTAATCTATAATTTATTTTCATTT
128 TAAATTCATTTTTTGAGTATGATTATACAAATTTAAATGTTTTAATCTATAATATATTTTCATTT
** * * *
1222629 GTAGAAGTTTAAATTTGTTTTTTAGTTTA-ATTATATGAGTTTAAATATTTAAGTTATTATTTAT
193 GTAGAAGTTTAAATTTGTTTTTT-GGGTACATTATACGAGTTTAAATATTTAAGATATGATTTAT
* * *
1222693 TTTT-TTGTA-AAAA-TTTAAATTAATTTTTTACTATGATTATATGAGTTTAAATTTTTTAAGGT
257 TTTTATT-TATAAAACTTTAAATTAATTCTCTACTATGATTATATGAGTTTAAATTTTTTAAGAT
* *
1222755 ATAATGTATTTTTAGTTATAAAAGTTTAAATTTATTTTTT-GTTTGATTATATGAATATAAATTT
321 AT-ATGTATTTTTAGTTAT-AAAGTTTAAA--TATTTTTTGGTATGATTATACGAATATAAATTT
* *
1222819 TTAAAG-TATTATTTATTTTTATTTTTAAAAATTTAAATTTATTTTTTTATG
382 TTAAAGATATGATATATTTTTATTTTTAAAAATTTAAATTTATTTTTTTATG
* * *
1222870 ATTATACAACTTTAAATTTTTAAGGTAT-A-A-TTTATTTTTATTTGCAGAAGTTTAAATTTGT-
1 ATTATACAACTTTAAATTTTTAAGATATAATATTTTATTTTTATTTGCAAAAGTTTAAATTTATA
*
1222931 TTTTTAGTTTAATTATAAAAGTTTAAATTTTTAAGGTATTATCTATCTTTATCTGTAAAAGTTTA
66 TTTTTA-TTTAATTATAAAAGTTTAAATATTTAAGGTATTATCTATCTTTATCTGTAAAAGTTTA
* ** * * * *
1222996 AATTTATTTTTT-AGCTATGATTATATGAGTTTAAATTTTTTAATGTATAATATATTTTTATTTG
130 AATTCATTTTTTGAG-TATGATTATACAAATTTAAATGTTTTAATCTATAATATATTTTCATTTG
* *
1223060 TAGAAGTTTTAATTTGTTTTTTGGGTACGATTATACGAGTTTAAATTTTTAAGATATGATTTATT
194 TAGAAGTTTAAATTTGTTTTTTGGGTAC-ATTATACGAGTTTAAATATTTAAGATATGATTTATT
** ** * * *
1223125 TTTATTTATAAAACTTTAAATTTGTTCTCTGGTTTGATTATATGAGTTTAATTTTTTTATGATAT
258 TTTATTTATAAAACTTTAAATTAATTCTCTACTATGATTATATGAGTTTAAATTTTTTAAGATAT
* * * * * *
1223190 TTTTATTTTTATTTGTAAAGTTTAAATATTTTTTGGGTATGATTATACGAATTTAAATTTTTTAA
323 ATGTATTTTTAGTTATAAAGTTTAAATATTTTTT-GGTATGATTATACGAATATAAATTTTTAAA
1223255 GATATGATATATTTTTATTT
387 GATATGATATATTTTTATTT
1223275 GTAGAATTCT
Statistics
Matches: 343, Mismatches: 52, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
429 19 0.06
430 148 0.43
431 73 0.21
432 35 0.10
433 41 0.12
435 1 0.00
436 26 0.08
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (433 bp):
ATTATACAACTTTAAATTTTTAAGATATAATATTTTATTTTTATTTGCAAAAGTTTAAATTTATA
TTTTTATTTAATTATAAAAGTTTAAATATTTAAGGTATTATCTATCTTTATCTGTAAAAGTTTAA
ATTCATTTTTTGAGTATGATTATACAAATTTAAATGTTTTAATCTATAATATATTTTCATTTGTA
GAAGTTTAAATTTGTTTTTTGGGTACATTATACGAGTTTAAATATTTAAGATATGATTTATTTTT
ATTTATAAAACTTTAAATTAATTCTCTACTATGATTATATGAGTTTAAATTTTTTAAGATATATG
TATTTTTAGTTATAAAGTTTAAATATTTTTTGGTATGATTATACGAATATAAATTTTTAAAGATA
TGATATATTTTTATTTTTAAAAATTTAAATTTATTTTTTTATG
Found at i:1223366 original size:143 final size:141
Alignment explanation
Indices: 1223076--1223367 Score: 331
Period size: 143 Copynumber: 2.0 Consensus size: 141
1223066 TTTTAATTTG
* *
1223076 TTTTTTGGGTACGATTATACGAGTTTAAATTTTTAAGATATGATTTATTTTTATTTATAAAACTT
1 TTTTTTGGGTACGATTATACGAATTTAAATTTTTAAGATATGATATATTTTTATTTATAAAACTT
* * * ** * *
1223141 TAAATTTGTTCTCTGGTTTGATTATATGAGTTTAATTTTTTTATGATATTTTTATTTTTATTTGT
66 TAAATTTGTTCTCTGGTTTAATTATACGAGTTTAATTTTTCTAAAATATTTTTA-TTTAATTTAT
*
1223206 AAAGTTTAAATA
130 AAAGTGTAAATA
* * *
1223218 TTTTTTGGGTATGATTATACGAATTTAAATTTTTTAAGATATGATATATTTTTATTTGTAGAA-T
1 TTTTTTGGGTACGATTATACGAATTTAAA-TTTTTAAGATATGATATATTTTTATTTATAAAACT
* * *
1223282 TCTAAATTTGTTTTCTGGTTTAATTATACGATTTTAATCTTGTGTCTAAAATCTTGTTTA-TTAA
65 T-TAAATTTGTTCTCTGGTTTAATTATACGAGTTTAAT-TT-T-TCTAAAATATT-TTTATTTAA
*
1223346 TGTTATAAA-TGT-ATTA
125 T-TTATAAAGTGTAAATA
1223362 TTTTTT
1 TTTTTT
1223368 TATTACTTTA
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
142 29 0.23
143 62 0.49
144 11 0.09
145 7 0.06
146 13 0.10
147 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (141 bp):
TTTTTTGGGTACGATTATACGAATTTAAATTTTTAAGATATGATATATTTTTATTTATAAAACTT
TAAATTTGTTCTCTGGTTTAATTATACGAGTTTAATTTTTCTAAAATATTTTTATTTAATTTATA
AAGTGTAAATA
Found at i:1226863 original size:91 final size:90
Alignment explanation
Indices: 1226756--1227037 Score: 270
Period size: 90 Copynumber: 3.1 Consensus size: 90
1226746 TTACAATGTG
* *
1226756 ACATTTACAATAAATCAACTTTC-TTCTTTTCTACCAAAAAGAATTCGATTTTTAAATATAATCT
1 ACATTTACAATAAATCAAATTTCTTTC-TTTCTACCAAAAAGAATTCGATTTTTAAAAATAATCT
* *
1226820 ATGCATTAGTCTAATCCTTATAATTT
65 ATACATTAGTCTAATCATTATAATTT
* * * * *
1226846 ATCATTTACAATTAATCAAATTTTATTTCTTTCTACC-AAAAG-ATCCAATTCTTAAAAATAATC
1 A-CATTTACAATAAATCAAA-TTTCTTTCTTTCTACCAAAAAGAATTCGATTTTTAAAAATAATC
* * *
1226909 TATAAATTAGCCTAATCTTTATAATTT
64 TATACATTAGTCTAATCATTATAATTT
* * * **
1226936 GACATTTACAATCAATC--TTTTCTTTCTTTCGACCAAAAAGAACTT-GATTCTCAAAAAATAAT
1 -ACATTTACAATAAATCAAATTTCTTTCTTTCTACCAAAAAGAA-TTCGATT-TTTAAAAATAAT
* * * *
1226998 CTATACATTAGTTTAATTATTATAGTCTA
63 CTATACATTAGTCTAATCATTATAAT-TT
1227027 ACATTTACAAT
1 ACATTTACAAT
1227038 CCATGCATTA
Statistics
Matches: 156, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
87 14 0.09
88 5 0.03
89 4 0.03
90 96 0.62
91 23 0.15
92 11 0.07
93 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.41
Consensus pattern (90 bp):
ACATTTACAATAAATCAAATTTCTTTCTTTCTACCAAAAAGAATTCGATTTTTAAAAATAATCTA
TACATTAGTCTAATCATTATAATTT
Found at i:1227903 original size:2 final size:2
Alignment explanation
Indices: 1227896--1227929 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1227886 TGCAATTTGA
1227896 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
1227930 CTTCATTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228221 original size:17 final size:17
Alignment explanation
Indices: 1228192--1228224 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1228182 TAAAGTATTA
1228192 TAAATTTATATAATTTT
1 TAAATTTATATAATTTT
1228209 TAAATATTA-ATAATTT
1 TAAAT-TTATATAATTT
1228225 ATTTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTTATATAATTTT
Found at i:1228704 original size:16 final size:17
Alignment explanation
Indices: 1228664--1228719 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1228654 AACGATAAAA
* *
1228664 ATTTATTTTATTTAAAT
1 ATTTATATTATTTATAT
1228681 -TTTGATA-TATTTATAT
1 ATTT-ATATTATTTATAT
1228697 ATTTATATTATTT-TAT
1 ATTTATATTATTTATAT
1228713 ATGTTAT
1 AT-TTAT
1228720 GTTTGATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTATATTATTTATAT
Found at i:1228748 original size:20 final size:21
Alignment explanation
Indices: 1228725--1228800 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 21
1228715 GTTATGTTTG
*
1228725 ATAAATATAAAAATTATATA-
1 ATAAATATAAAAATAATATAT
*
1228745 ATAAATA-AAATATAATATAT
1 ATAAATATAAAAATAATATAT
*
1228765 TTAAATATAATTAAAATAATATAT
1 ATAAATAT-A--AAAATAATATAT
*
1228789 TTAATATATAAA
1 ATAA-ATATAAA
1228801 TATTTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
19 10 0.22
20 13 0.28
22 3 0.07
24 16 0.35
25 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATATAAAAATAATATAT
Found at i:1228772 original size:15 final size:14
Alignment explanation
Indices: 1228756--1228810 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
1228746 TAAATAAAAT
1228756 ATAATATATTT-AA
1 ATAATATATTTAAA
1228769 AT-ATA-A-TTAAA
1 ATAATATATTTAAA
1228780 ATAATATATTTAATA
1 ATAATATATTTAA-A
1228795 TATAA-ATATTTAAA
1 -ATAATATATTTAAA
1228809 AT
1 AT
1228811 TTTAATACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 6 0.17
13 5 0.14
14 5 0.14
15 9 0.25
16 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATATTTAAA
Found at i:1228774 original size:29 final size:27
Alignment explanation
Indices: 1228740--1228802 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 27
1228730 TATAAAAATT
1228740 ATATAATAAATAAAATATAATATATTTA
1 ATATAATAAATAAAA-ATAATATATTTA
*
1228768 A-AT-AT-AATTAAAATAATATATTTA
1 ATATAATAAATAAAAATAATATATTTA
1228792 ATAT-ATAAATA
1 ATATAATAAATA
1228803 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 13 0.42
25 10 0.32
26 5 0.16
27 2 0.06
28 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAATAAATAAAAATAATATATTTA
Found at i:1230065 original size:20 final size:20
Alignment explanation
Indices: 1230020--1230076 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1230010 TTATAAATAA
* **
1230020 TAAAAAATAAAAATACTTTAT
1 TAAAAAATAAAAA-AATAAAT
1230041 T-AAAAATAAAAAAATAAAT
1 TAAAAAATAAAAAAATAAAT
*
1230060 TAAAAATTTAAAAAAAT
1 TAAAAA-ATAAAAAAAT
1230077 TCTTAGCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.17
20 15 0.50
21 10 0.33
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAATAAAAAAATAAAT
Found at i:1230350 original size:114 final size:115
Alignment explanation
Indices: 1230104--1230368 Score: 345
Period size: 114 Copynumber: 2.3 Consensus size: 115
1230094 TAATTAATTT
***
1230104 CTAATAAATTTTCAAAGGTGGCCAAGAATCTCCTTATTGATGGAGACCGAAAAGAAAAGGCTAAA
1 CTAATAAATTTTCAAAGGTGGCCAAGAATCTCC-TATTGACAAAGACCGAAAAGAAAAGGCTAAA
1230169 TTAACAAATAAAAAAAAATTATTCGTCCTTATTAATAAAATATAATAATAA
65 TTAACAAATAAAAAAAAATTATTCGTCCTTATTAATAAAATATAATAATAA
* * *
1230220 CTAATAAATTTTCAAAGGTGGCCAAGAGTCTCCTATTGACAAAGACCGACAAGAAAAGGTTAAAT
1 CTAATAAATTTTCAAAGGTGGCCAAGAATCTCCTATTGACAAAGACCGAAAAGAAAAGGCTAAAT
* * * * * * * *
1230285 TAAGAATTAAAAAAATA-TATTCGTCGTTATTAGTACAATATAATGATAC
66 TAACAAATAAAAAAAAATTATTCGTCCTTATTAATAAAATATAATAATAA
** *
1230334 CTGCTAGATTTTCAAA-GTCGGCCAAGAATCTCCTA
1 CTAATAAATTTTCAAAGGT-GGCCAAGAATCTCCTA
1230369 AAATAAGGGG
Statistics
Matches: 130, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
113 2 0.02
114 55 0.42
115 41 0.32
116 32 0.25
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (115 bp):
CTAATAAATTTTCAAAGGTGGCCAAGAATCTCCTATTGACAAAGACCGAAAAGAAAAGGCTAAAT
TAACAAATAAAAAAAAATTATTCGTCCTTATTAATAAAATATAATAATAA
Found at i:1235354 original size:29 final size:28
Alignment explanation
Indices: 1235318--1235377 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
1235308 TTTTAATATT
1235318 AAAATAATAATAATTTAATAAATTATTTA
1 AAAATAATAATAATTTAAT-AATTATTTA
* * *
1235347 AAAATAATTATATTTTAATAATTTTTTA
1 AAAATAATAATAATTTAATAATTATTTA
1235375 AAA
1 AAA
1235378 TTTTAACTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATAATAATAATTTAATAATTATTTA
Found at i:1235576 original size:20 final size:21
Alignment explanation
Indices: 1235553--1235596 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1235543 TATTATATTT
1235553 ATTATTTATTTAATA-TTAAA
1 ATTATTTATTTAATATTTAAA
*
1235573 ATTATTTTTTTAATATTTAAA
1 ATTATTTATTTAATATTTAAA
1235594 ATT
1 ATT
1235597 CTAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTTATTTAATATTTAAA
Found at i:1237353 original size:32 final size:28
Alignment explanation
Indices: 1237324--1237383 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
1237314 TATAAAATTT
*
1237324 TTTA-TTAAATAATATTATAATTAATAAAA
1 TTTATTTAAA-AATATT-TAATAAATAAAA
1237353 TTTATTTAAAAATATTTAATAAAT-AAA
1 TTTATTTAAAAATATTTAATAAATAAAA
1237380 TTTA
1 TTTA
1237384 AAGTCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.24
28 7 0.24
29 10 0.34
30 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTATTTAAAAATATTTAATAAATAAAA
Found at i:1237382 original size:13 final size:14
Alignment explanation
Indices: 1237307--1237384 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
1237297 TTTTCTGTTT
1237307 TAATATTT-ATAAA
1 TAATATTTAATAAA
* * *
1237320 -ATTTTTTATTAAA
1 TAATATTTAATAAA
*
1237333 TAATATTATAATTAA
1 TAATATT-TAATAAA
* *
1237348 TAAAATTTATTTAAA
1 TAATATTTA-ATAAA
1237363 -AATATTTAATAAA
1 TAATATTTAATAAA
1237376 TAA-ATTTAA
1 TAATATTTAA
1237385 AGTCAAAATT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
12 5 0.10
13 14 0.29
14 15 0.31
15 14 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:1237431 original size:11 final size:12
Alignment explanation
Indices: 1237418--1237478 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 12
1237408 AATTATATAA
1237418 AATATAAGATA-
1 AATATAAGATAT
1237429 AAT-TAAGATAT
1 AATATAAGATAT
*
1237440 GATATAA-ATAT
1 AATATAAGATAT
* *
1237451 AATATAAAAAAT
1 AATATAAGATAT
*
1237463 AAT-TAAAATAT
1 AATATAAGATAT
1237474 AATAT
1 AATAT
1237479 GATAGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 7 0.17
11 25 0.60
12 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
AATATAAGATAT
Found at i:1237587 original size:32 final size:31
Alignment explanation
Indices: 1237516--1237590 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
1237506 GAATATAAGA
*
1237516 ATATTTAAATATTTATATAAAATAAATTATT
1 ATATATAAATATTTATATAAAATAAATTATT
* * *
1237547 AATGTATAAATATTTATATAAATTTATATTACTT
1 -ATATATAAATATTTATATAAA-ATAAATTA-TT
1237581 -TATATAAATA
1 ATATATAAATA
1237591 AAAATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 28 0.78
33 6 0.17
34 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
ATATATAAATATTTATATAAAATAAATTATT
Found at i:1238522 original size:19 final size:19
Alignment explanation
Indices: 1238461--1238534 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
1238451 TGAACACACA
1238461 CTTTT-TTTCTTTAC-CTCT
1 CTTTTCTTTCTTT-CTCTCT
* * *
1238479 CTTTTTTTTATTTCTCTTT
1 CTTTTCTTTCTTTCTCTCT
1238498 CTTTTCTTTCTTTCTCTCT
1 CTTTTCTTTCTTTCTCTCT
* * *
1238517 CATTTCCTTCGTTCTCTC
1 CTTTTCTTTCTTTCTCTC
1238535 CCTTCATGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
18 6 0.13
19 40 0.87
ACGTcount: A:0.04, C:0.28, G:0.01, T:0.66
Consensus pattern (19 bp):
CTTTTCTTTCTTTCTCTCT
Found at i:1239085 original size:20 final size:22
Alignment explanation
Indices: 1239051--1239107 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
1239041 ACATATAAAA
* *
1239051 ATATACATAAAATAAAATAAATT
1 ATATA-ATAATATAAAAAAAATT
1239074 AT-TAAT-ATATAAAAAAAATT
1 ATATAATAATATAAAAAAAATT
1239094 ATATAATAATATAA
1 ATATAATAATATAA
1239108 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 14 0.47
21 6 0.20
22 8 0.27
23 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAATAATATAAAAAAAATT
Found at i:1239179 original size:17 final size:16
Alignment explanation
Indices: 1239153--1239194 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1239143 TATAAAAAAA
1239153 TTTC-TCTTTTTTTTCT
1 TTTCTTCTTTTTTTT-T
1239169 TTTCTTCTTTTTTTTT
1 TTTCTTCTTTTTTTTT
*
1239185 TTTCTCCTTT
1 TTTCTTCTTT
1239195 ACCTTACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTCTTTTTTTTT
Found at i:1239514 original size:19 final size:18
Alignment explanation
Indices: 1239478--1239529 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1239468 ATAAAAATTT
*
1239478 AATTTAATTATATTAAATA
1 AATTTATTTAT-TTAAATA
*
1239497 ATTATTATTTATTTAAATA
1 AAT-TTATTTATTTAAATA
1239516 AATTTATTT-TTTAA
1 AATTTATTTATTTAA
1239530 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 11 0.38
20 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTATTTATTTAAATA
Found at i:1239517 original size:23 final size:25
Alignment explanation
Indices: 1239491--1239543 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
1239481 TTAATTATAT
1239491 TAAATAATTATTATTT-A-TTTAAA
1 TAAATAATTATTATTTAATTTTAAA
*
1239514 TAAAT--TTATTTTTTAATTTTAAA
1 TAAATAATTATTATTTAATTTTAAA
1239537 TAAATAA
1 TAAATAA
1239544 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAATAATTATTATTTAATTTTAAA
Found at i:1239590 original size:24 final size:22
Alignment explanation
Indices: 1239528--1239587 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
1239518 TTTATTTTTT
* *
1239528 AATTTTAAATAAATAAATTTAA
1 AATTTTAAATAATTAAATATAA
*
1239550 AA-TTAAAATTAAATTAATATATAA
1 AATTTTAAA-T-AATTAA-ATATAA
1239574 AATTTTAAATAATT
1 AATTTTAAATAATT
1239588 TAAAATATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 9 0.30
24 8 0.27
25 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTTAAATAATTAAATATAA
Found at i:1239595 original size:24 final size:23
Alignment explanation
Indices: 1239528--1239595 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
1239518 TTTATTTTTT
* *
1239528 AATTTTAAATAAAT-AAATTTAA
1 AATTTTAAATAATTAAAATATAA
* *
1239550 AA-TTAAAATTAAATTAATATATAA
1 AATTTTAAA-T-AATTAAAATATAA
1239574 AATTTTAAATAATTTAAAATAT
1 AATTTTAAATAA-TTAAAATAT
1239596 CATCATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 3 0.09
23 5 0.14
24 17 0.49
25 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTTTAAATAATTAAAATATAA
Found at i:1239620 original size:11 final size:11
Alignment explanation
Indices: 1239580--1239665 Score: 60
Period size: 11 Copynumber: 8.2 Consensus size: 11
1239570 ATAAAATTTT
*
1239580 AAATAATTTAA
1 AAATAATATAA
*
1239591 AATATCATCATAA
1 AA-ATAAT-ATAA
*
1239604 ATATAATATAA
1 AAATAATATAA
1239615 AAATAAT-T-A
1 AAATAATATAA
1239624 AAAT-ATAT--
1 AAATAATATAA
*
1239632 -TATAATATAA
1 AAATAATATAA
1239642 AAATAATATAA
1 AAATAATATAA
1239653 ATAA-AATATAA
1 A-AATAATATAA
1239664 AA
1 AA
1239666 TTAAAAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
7 2 0.03
8 6 0.10
9 6 0.10
10 2 0.03
11 30 0.50
12 10 0.17
13 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATAA
Found at i:1239635 original size:27 final size:26
Alignment explanation
Indices: 1239604--1239697 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 26
1239594 ATCATCATAA
*
1239604 ATATAATATAAAAATAATTAAAATAT
1 ATATAAAATAAAAATAATTAAAATAT
* *
1239630 ATTATAATATAAAAATAA-TATAAATAAA
1 A-TATAAAATAAAAATAATTA-AAAT-AT
*
1239658 ATATAAAATTAAAAATAAATTAAAATTT
1 ATATAAAA-TAAAAAT-AATTAAAATAT
1239686 ATATAAAATAAA
1 ATATAAAATAAA
1239698 TTATTAACTT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.05
27 30 0.52
28 17 0.29
29 6 0.10
30 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATATAAAATAAAAATAATTAAAATAT
Found at i:1239689 original size:28 final size:27
Alignment explanation
Indices: 1239604--1239694 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 27
1239594 ATCATCATAA
*
1239604 ATATAATA-TAAAAATAATTAAAATAT
1 ATATAAAATTAAAAATAATTAAAATAT
* *
1239630 AT-TATAATATAAAAATAA-TATAAATAAA
1 ATATAAAAT-TAAAAATAATTA-AAAT-AT
*
1239658 ATATAAAATTAAAAATAAATTAAAATTT
1 ATATAAAATTAAAAAT-AATTAAAATAT
1239686 ATATAAAAT
1 ATATAAAAT
1239695 AAATTATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 13 0.25
28 19 0.37
29 11 0.21
30 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATAAAATTAAAAATAATTAAAATAT
Found at i:1248058 original size:41 final size:41
Alignment explanation
Indices: 1248006--1248086 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
1247996 AAGTTTTAAA
* * * *
1248006 ATTTATTTATATTTTTAAATAGATAATTTAAATTTTTTTAG
1 ATTTATCTATATTTATAAATAGATAATTCAAATTTATTTAG
*
1248047 ATTTATCTATATTTATAAATGGATAATTCAAATTTATTTA
1 ATTTATCTATATTTATAAATAGATAATTCAAATTTATTTA
1248087 TATCTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.54
Consensus pattern (41 bp):
ATTTATCTATATTTATAAATAGATAATTCAAATTTATTTAG
Found at i:1248111 original size:15 final size:16
Alignment explanation
Indices: 1248093--1248130 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1248083 TTTATATCTT
1248093 ATTTTTTAA-AATTTA
1 ATTTTTTAATAATTTA
1248108 A-TTTTTAATAATTTA
1 ATTTTTTAATAATTTA
*
1248123 ATATTTTA
1 ATTTTTTA
1248131 TATTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 8 0.40
16 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTTAATAATTTA
Found at i:1248240 original size:54 final size:49
Alignment explanation
Indices: 1248182--1248284 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 49
1248172 ATTTATGCTA
* *
1248182 TAATATTATATATATTTATTTTTTATATAATAAAAATTATATAACATATAAAAT
1 TAATATTATAT-TATATAATTTTTA-A-AA-AAAAATTATATAA-ATATAAAAT
*
1248236 TAATATTATATTATATAATTTTTAAAAAAATATTATATAAATATAAAAT
1 TAATATTATATTATATAATTTTTAAAAAAAAATTATATAAATATAAAAT
1248285 ATATCAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
49 9 0.20
50 12 0.26
51 2 0.04
52 1 0.02
53 11 0.24
54 11 0.24
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (49 bp):
TAATATTATATTATATAATTTTTAAAAAAAAATTATATAAATATAAAAT
Found at i:1248308 original size:49 final size:49
Alignment explanation
Indices: 1248213--1248310 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 49
1248203 TTTATATAAT
* * * *
1248213 AAAAATTATATAACATATAAAATTAATATTATATTATATAATTTTTAAA
1 AAAAATTATATAACATATAAAATTAATATCAAATTAAATAAATTTTAAA
1248262 AAAATATTATATAA-ATATAAAA-T-ATATCAAATTAAATTCAAATTTTAAA
1 AAAA-ATTATATAACATATAAAATTAATATCAAATTAAA-T-AAATTTTAAA
1248311 TATTAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
47 10 0.24
48 2 0.05
49 21 0.50
50 9 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (49 bp):
AAAAATTATATAACATATAAAATTAATATCAAATTAAATAAATTTTAAA
Found at i:1254081 original size:3 final size:3
Alignment explanation
Indices: 1254073--1254112 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1254063 TGAATAAATC
1254073 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1254113 AAAAAATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1254545 original size:2 final size:2
Alignment explanation
Indices: 1254540--1254567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1254530 ACACACACAC
1254540 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
1254568 GCTCAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1256948 original size:3 final size:3
Alignment explanation
Indices: 1256940--1256973 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1256930 ACTATACCTC
1256940 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1256974 TCATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1258184 original size:32 final size:32
Alignment explanation
Indices: 1258130--1258216 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
1258120 TAGCCCCTTA
* * * * * *
1258130 GCTAAGGTATGAACTATATTTTTTTGTATAAG
1 GCTAAGGTGTGAATTGTGTTTTTTCGCATAAG
*
1258162 GCTAAGGTGTGAATTGTGTTTTTTCGCATAGG
1 GCTAAGGTGTGAATTGTGTTTTTTCGCATAAG
* * *
1258194 GCTAGGGTGAGGATTGTGTTTTT
1 GCTAAGGTGTGAATTGTGTTTTT
1258217 CTGCACGAGG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.43
Consensus pattern (32 bp):
GCTAAGGTGTGAATTGTGTTTTTTCGCATAAG
Found at i:1259409 original size:29 final size:28
Alignment explanation
Indices: 1259359--1259414 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1259349 ATACTTTATA
* *
1259359 TTTTATAATTAAAATTAAAATTTAATTT
1 TTTTATAATTAAAATAAAAATTAAATTT
* *
1259387 TTTTATTATTTAAATAATAAATTAAATT
1 TTTTATAATTAAAATAA-AAATTAAATT
1259415 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTATAATTAAAATAAAAATTAAATTT
Found at i:1259723 original size:16 final size:17
Alignment explanation
Indices: 1259699--1259775 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 17
1259689 AAAATTAATA
*
1259699 AAATATATATTATA-TG
1 AAATTTATATTATATTG
*
1259715 AAATTTATATTAATATTT
1 AAATTTATATT-ATATTG
* *
1259733 AAATTTATTTTATGTATG
1 AAATTTATATTATAT-TG
* *
1259751 -AATATAAATTATATT-
1 AAATTTATATTATATTG
*
1259766 AAATTAATAT
1 AAATTTATAT
1259776 CAGTTATTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
16 17 0.38
17 16 0.36
18 12 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTTATATTATATTG
Found at i:1259807 original size:23 final size:21
Alignment explanation
Indices: 1259751--1259807 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
1259741 TTTATGTATG
1259751 AATATA-AATTATATTAAATT
1 AATATATAATTATATTAAATT
* *
1259771 AATATCAGTTATTATTTTTAATATT
1 AATAT-A-TAATTA-TATTAA-ATT
1259796 AATATATAATTA
1 AATATATAATTA
1259808 AAATGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
23 9 0.31
24 6 0.21
25 8 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATATAATTATATTAAATT
Found at i:1259932 original size:21 final size:20
Alignment explanation
Indices: 1259901--1259939 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1259891 TAAAATGATG
1259901 AATTTTTTATTTATTAAATA
1 AATTTTTTATTTATTAAATA
*
1259921 AATTTATTTATTTTTTAAA
1 AATTT-TTTATTTATTAAA
1259940 ATTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTTTTATTTATTAAATA
Found at i:1260088 original size:16 final size:16
Alignment explanation
Indices: 1260019--1260091 Score: 66
Period size: 15 Copynumber: 4.7 Consensus size: 16
1260009 AAAAACTCAT
1260019 TAAATAAAAAATTTTATA
1 TAAAT-AAAAATTTTA-A
1260037 TAAAT--AAATTTT-A
1 TAAATAAAAATTTTAA
* *
1260050 TTAATAATAAA-TATAA
1 TAAATAA-AAATTTTAA
1260066 T-AATAAAAATTTTAA
1 TAAATAAAAATTTTAA
1260081 TAAATAAAAAT
1 TAAATAAAAAT
1260092 AACTATTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
13 5 0.11
14 3 0.07
15 19 0.41
16 14 0.30
18 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATAAAAATTTTAA
Found at i:1261426 original size:2 final size:2
Alignment explanation
Indices: 1261419--1261448 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1261409 CATACGGGAA
1261419 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1261449 TTATTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1263013 original size:2 final size:2
Alignment explanation
Indices: 1263006--1263036 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1262996 ATAATGAATT
1263006 TA TA TA 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 TA TA TA T
1263037 CTTACCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1269111 original size:3 final size:3
Alignment explanation
Indices: 1269103--1269134 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1269093 ATCCTTTAAT
1269103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1269135 CAATATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1269683 original size:11 final size:11
Alignment explanation
Indices: 1269669--1269751 Score: 100
Period size: 11 Copynumber: 7.5 Consensus size: 11
1269659 TAATTATATG
1269669 TTAAAATTATA
1 TTAAAATTATA
1269680 TTAAAATATAATTA
1 TTAAAAT-T-A-TA
*
1269694 TTAAAATCATA
1 TTAAAATTATA
1269705 TTAAAATTA-A
1 TTAAAATTATA
1269715 -TAAAATTATA
1 TTAAAATTATA
*
1269725 TTAAAAAT-TA
1 TTAAAATTATA
1269735 TTAAAATTATA
1 TTAAAATTATA
1269746 TTAAAA
1 TTAAAA
1269752 GATATAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
9 8 0.13
10 11 0.18
11 31 0.50
12 2 0.03
13 1 0.02
14 9 0.15
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAATTATA
Found at i:1269718 original size:20 final size:20
Alignment explanation
Indices: 1269689--1269751 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1269679 ATTAAAATAT
*
1269689 AATTATTAAAATCATATTAA
1 AATTATTAAAATTATATTAA
*
1269709 AATTAATAAAATTATATTAAA
1 AATTATTAAAATTATATT-AA
1269730 AATTATTAAAATTATATTAA
1 AATTATTAAAATTATATTAA
1269750 AA
1 AA
1269752 GATATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 20 0.51
21 19 0.49
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTATTAAAATTATATTAA
Found at i:1269744 original size:9 final size:9
Alignment explanation
Indices: 1269689--1269744 Score: 58
Period size: 9 Copynumber: 5.7 Consensus size: 9
1269679 ATTAAAATAT
1269689 AATTATTAA
1 AATTATTAA
1269698 AATCATATTAA
1 AAT--TATTAA
*
1269709 AATTAATAA
1 AATTATTAA
1269718 AATTATATTAAA
1 AA-T-TATT-AA
1269730 AATTATTAA
1 AATTATTAA
1269739 AATTAT
1 AATTAT
1269745 ATTAAAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 18 0.45
10 5 0.12
11 13 0.32
12 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTATTAA
Found at i:1269759 original size:41 final size:44
Alignment explanation
Indices: 1269670--1269760 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 44
1269660 AATTATATGT
*
1269670 TAAAATTATATTAAAATATAATTATTAAAATCATATTAAAATTAA
1 TAAAATTATATT-AAATATAATTATTAAAATCATATTAAAAATAA
*
1269715 TAAAATTATATT-AA-A-AATTATTAAAATTATATTAAAAGAT-A
1 TAAAATTATATTAAATATAATTATTAAAATCATATTAAAA-ATAA
1269756 TAAAA
1 TAAAA
1269761 AATATAAGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 27 0.63
42 2 0.05
43 2 0.05
45 12 0.28
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (44 bp):
TAAAATTATATTAAATATAATTATTAAAATCATATTAAAAATAA
Found at i:1269761 original size:21 final size:21
Alignment explanation
Indices: 1269670--1269763 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 21
1269660 AATTATATGT
1269670 TAAAATTATATTAAAATATAATTA
1 TAAAATTATATTAAAA-AT-A-TA
* *
1269694 TTAAAATCATATTAAAATTA-A
1 -TAAAATTATATTAAAAATATA
1269715 TAAAATTATATTAAAAAT-TA
1 TAAAATTATATTAAAAATATA
1269735 TTAAAATTATATTAAAAGATATA
1 -TAAAATTATATTAAAA-ATATA
*
1269758 AAAAAT
1 TAAAAT
1269764 ATAAGTGTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.28
21 17 0.28
22 7 0.12
23 3 0.05
24 1 0.02
25 15 0.25
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
TAAAATTATATTAAAAATATA
Found at i:1269766 original size:21 final size:20
Alignment explanation
Indices: 1269696--1269766 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
1269686 TATAATTATT
1269696 AAAATCATATT-AAAAT-TAA
1 AAAAT-ATATTAAAAATATAA
*
1269715 TAAAATTATATTAAAAATTATTA
1 -AAAA-TATATTAAAAA-TATAA
*
1269738 AAATTATATTAAAAGATATAA
1 AAAATATATTAAAA-ATATAA
1269759 AAAATATA
1 AAAATATA
1269767 AGTGTAAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 9 0.21
21 26 0.62
22 5 0.12
23 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAATATATTAAAAATATAA
Found at i:1273007 original size:6 final size:6
Alignment explanation
Indices: 1272996--1273027 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1272986 TCTCAAGATA
1272996 TATATT TATATT TATATT TATATT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TA
1273028 CTGGAGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:1273265 original size:16 final size:16
Alignment explanation
Indices: 1273246--1273312 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
1273236 TCATTAAGTT
*
1273246 AATAATTTGAATTTAA
1 AATAATTTAAATTTAA
1273262 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
1273278 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
* * *
1273294 AGTAAATTAAGTTTAA
1 AATAATTTAAATTTAA
1273310 AAT
1 AAT
1273313 GATACGAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:1273308 original size:22 final size:22
Alignment explanation
Indices: 1273265--1273310 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1273255 AATTTAAAAT
*
1273265 AATTTAAATTTAAAATAATTTA
1 AATTTAAATGTAAAATAATTTA
*
1273287 AATTTAAA-GTAAATTAAGTTTA
1 AATTTAAATGTAAAATAA-TTTA
1273309 AA
1 AA
1273311 ATGATACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
AATTTAAATGTAAAATAATTTA
Found at i:1278313 original size:21 final size:21
Alignment explanation
Indices: 1278289--1278333 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1278279 TCGATATATG
*
1278289 TTTGTTAACCTTTAAAA-TAAT
1 TTTGATAA-CTTTAAAATTAAT
*
1278310 TTTGATAATTTTAAAATTAAT
1 TTTGATAACTTTAAAATTAAT
1278331 TTT
1 TTT
1278334 AGTAATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTGATAACTTTAAAATTAAT
Found at i:1282671 original size:2 final size:2
Alignment explanation
Indices: 1282666--1282703 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1282656 GACACACGCG
*
1282666 CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1282704 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1282727 original size:2 final size:2
Alignment explanation
Indices: 1282722--1282746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1282712 TATATATATA
1282722 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1282747 TATTATAAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1284722 original size:2 final size:2
Alignment explanation
Indices: 1284715--1284755 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1284705 CTGATTAAGC
1284715 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
1284756 GATGTAACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1287002 original size:18 final size:18
Alignment explanation
Indices: 1286979--1287033 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
1286969 ATGATCATAT
* *
1286979 AAATATATGATTCTTAAA
1 AAATATATAATTTTTAAA
*
1286997 AAATATGTAATTTTTAAA
1 AAATATATAATTTTTAAA
* *
1287015 AAATTTATCATTTTTAAA
1 AAATATATAATTTTTAAA
1287033 A
1 A
1287034 TCTGTAAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (18 bp):
AAATATATAATTTTTAAA
Found at i:1287101 original size:84 final size:84
Alignment explanation
Indices: 1286960--1287123 Score: 249
Period size: 84 Copynumber: 1.9 Consensus size: 84
1286950 ATTTATTATA
* *
1286960 TGAAAATCTATGATCATATAAATATATGATTCTTAAAAAATATGTAATTTTTAAAAAATTTATCA
1 TGAAAATCTATAATCATATAAATATATGATTCTTAAAAAATATCTAATTTTTAAAAAATTTATCA
*
1287025 TTTTTAAAATCTGTAAAGT
66 TTTATAAAATCTGTAAAGT
* *
1287044 TGAAAATCTATAATTATATAAATTTATGATTCTTAAAAAA-ATCTAAAATTTTTAAAAAATTTAT
1 TGAAAATCTATAATCATATAAATATATGATTCTTAAAAAATATCT--AATTTTTAAAAAATTTAT
*
1287108 GATTTATAAAATCTGT
64 CATTTATAAAATCTGT
1287124 GATTTATATT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
83 3 0.04
84 37 0.51
85 32 0.44
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (84 bp):
TGAAAATCTATAATCATATAAATATATGATTCTTAAAAAATATCTAATTTTTAAAAAATTTATCA
TTTATAAAATCTGTAAAGT
Found at i:1287112 original size:18 final size:18
Alignment explanation
Indices: 1287063--1287118 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1287053 ATAATTATAT
*
1287063 AAATTTATGATTCTTAAAA
1 AAATTTATGATT-TTTAAA
* **
1287082 AAATCTAAAATTTTTAAA
1 AAATTTATGATTTTTAAA
*
1287100 AAATTTATGATTTATAAA
1 AAATTTATGATTTTTAAA
1287118 A
1 A
1287119 TCTGTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
AAATTTATGATTTTTAAA
Found at i:1289683 original size:18 final size:18
Alignment explanation
Indices: 1289660--1289733 Score: 96
Period size: 18 Copynumber: 4.1 Consensus size: 18
1289650 ATTGGGGTTG
1289660 AAAATCTATAATTCTTAA
1 AAAATCTATAATTCTTAA
* *
1289678 AAAATCTGTGATTCTTAA
1 AAAATCTATAATTCTTAA
1289696 AAAATCTA-AGATTCTTAA
1 AAAATCTATA-ATTCTTAA
* *
1289714 AAAATCTATGATTTTTAA
1 AAAATCTATAATTCTTAA
1289732 AA
1 AA
1289734 TCTGTAAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATCTATAATTCTTAA
Found at i:1289700 original size:36 final size:36
Alignment explanation
Indices: 1289660--1289827 Score: 122
Period size: 36 Copynumber: 4.9 Consensus size: 36
1289650 ATTGGGGTTG
*
1289660 AAAATCTATA-ATTCTTAAAAAATCTGTGATTCTTAA
1 AAAATCTA-AGATTCTTAAAAAATCTATGATTCTTAA
*
1289696 AAAATCTAAGATTCTTAAAAAATCTATGATTTTTAA
1 AAAATCTAAGATTCTTAAAAAATCTATGATTCTTAA
** * * *
1289732 AATCTGTAAG-GT-TT--GAAATCTATGA---TTACA
1 AAAATCTAAGATTCTTAAAAAATCTATGATTCTTA-A
* * * * *
1289762 GAAATCTATGATTCTT-AAAAATTTGTGATTCCTAA
1 AAAATCTAAGATTCTTAAAAAATCTATGATTCTTAA
*
1289797 AAAATCTAAGATT-TCTATAAAATCTATGATT
1 AAAATCTAAGATTCT-TAAAAAATCTATGATT
1289828 TATAAAATTT
Statistics
Matches: 100, Mismatches: 22, Indels: 20
0.70 0.15 0.14
Matches are distributed among these distances:
29 3 0.03
30 6 0.06
31 1 0.01
32 12 0.12
33 8 0.08
34 3 0.03
35 15 0.15
36 52 0.52
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (36 bp):
AAAATCTAAGATTCTTAAAAAATCTATGATTCTTAA
Found at i:1289828 original size:18 final size:18
Alignment explanation
Indices: 1289763--1289828 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
1289753 ATGATTACAG
1289763 AAATCTATGA-TTCT-TAA
1 AAATCTATGATTTCTAT-A
* * * *
1289780 AAATTTGTGATTCCTAAA
1 AAATCTATGATTTCTATA
*
1289798 AAATCTAAGATTTCTATA
1 AAATCTATGATTTCTATA
1289816 AAATCTATGATTT
1 AAATCTATGATTT
1289829 ATAAAATTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
17 8 0.22
18 29 0.78
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (18 bp):
AAATCTATGATTTCTATA
Found at i:1289833 original size:16 final size:16
Alignment explanation
Indices: 1289714--1289835 Score: 61
Period size: 16 Copynumber: 7.3 Consensus size: 16
1289704 AGATTCTTAA
*
1289714 AAAATCTATGATTTTT
1 AAAATCTATGATTTAT
* * *
1289730 AAAATCTGTAAGGTT-T
1 AAAATCTATGA-TTTAT
* *
1289746 GAAATCTATGA-TTAC
1 AAAATCTATGATTTAT
1289761 AGAAATCTATGATTCT-T
1 A-AAATCTATGATT-TAT
* * *
1289778 AAAAATTTGTGATTCCTAA
1 -AAAATCTATGATT--TAT
*
1289797 AAAATCTAAGATTTCTAT
1 AAAATCTATGA-TT-TAT
1289815 AAAATCTATGATTTAT
1 AAAATCTATGATTTAT
1289831 AAAAT
1 AAAAT
1289836 TTGGGATTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
14 2 0.03
16 36 0.45
17 15 0.19
18 25 0.31
19 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (16 bp):
AAAATCTATGATTTAT
Found at i:1291301 original size:20 final size:20
Alignment explanation
Indices: 1291276--1291347 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1291266 TACCCTGATG
1291276 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
1291296 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATA
* * *
1291316 TATCGATATATTCTACAATA
1 TATCGATACATTTTTCAATA
1291336 TATCGATACATT
1 TATCGATACATT
1291348 ATGTCTTTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:1291335 original size:40 final size:39
Alignment explanation
Indices: 1291273--1291350 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1291263 TCATACCCTG
* *
1291273 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
*
1291313 ATGTATCGATATATTCTACAATATATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1291351 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:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1292285 original size:23 final size:23
Alignment explanation
Indices: 1292258--1292313 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
1292248 AGCCTTTGAC
1292258 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1292281 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1292303 CATGCATTTTT
1 CATGCATTTTT
1292314 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1292320 original size:20 final size:21
Alignment explanation
Indices: 1292266--1292320 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1292256 ACCATGCATT
**
1292266 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
1292287 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
1292309 -TTTTTAACATGT
1 TTTTTTAACATGT
1292321 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:1305396 original size:12 final size:12
Alignment explanation
Indices: 1305379--1305434 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
1305369 CTTTACACCC
1305379 AAAAAAAAAC--
1 AAAAAAAAACAA
*
1305389 AAAAAAAAACAC
1 AAAAAAAAACAA
1305401 AAAAAAAAACAA
1 AAAAAAAAACAA
*
1305413 AACAAAAAACAA
1 AAAAAAAAACAA
1305425 AAAAAGAAAA
1 AAAAA-AAAA
1305435 AATAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.25
12 26 0.65
13 4 0.10
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:1305436 original size:22 final size:22
Alignment explanation
Indices: 1305378--1305429 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1305368 CCTTTACACC
1305378 CAAAAAAAAACAAAAAAAAACA
1 CAAAAAAAAACAAAAAAAAACA
1305400 CAAAAAAAAACAAAACAAAAA-A
1 CAAAAAAAAACAAAA-AAAAACA
1305422 CAAAAAAA
1 CAAAAAAA
1305430 GAAAAAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAACAAAAAAAAACA
Found at i:1305449 original size:1 final size:1
Alignment explanation
Indices: 1305379--1305436 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
1305369 CTTTACACCC
* * * * * * *
1305379 AAAAAAAAACAAAAAAAAACACAAAAAAAAACAAAACAAAAAACAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1305437 TAGCAAAAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1305449 original size:22 final size:20
Alignment explanation
Indices: 1305381--1305436 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
1305371 TTACACCCAA
*
1305381 AAAAAAACAAAAAAAAACACAA
1 AAAAAAACAAAAAAAAA-A-AC
*
1305403 AAAAAAACAAAACAAAAAAC
1 AAAAAAACAAAAAAAAAAAC
*
1305423 AAAAAAAGAAAAAA
1 AAAAAAACAAAAAA
1305437 TAGCAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 16 0.53
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAAAAC
Found at i:1306710 original size:29 final size:29
Alignment explanation
Indices: 1306668--1307612 Score: 1314
Period size: 28 Copynumber: 32.9 Consensus size: 29
1306658 AATGTTCATC
1306668 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1306697 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1306726 CTTTTCAAAGCCCACAAGTCATTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1306754 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1306782 CCTTTCAAAGCCCACAAATCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1306811 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1306839 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1306868 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1306896 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1306925 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1306954 CCTTTCAAATCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1306983 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307011 CCTTTCAAAGCCCATAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307039 CCTTTCAAAGCTCACAAGTCAATGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1307068 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307097 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307126 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1307154 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307183 CCTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307212 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1307241 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307269 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307297 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307325 CTTTTCGAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1307353 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307382 -CTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307409 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * * *
1307440 CCTTTTAAAGCTCACGCAAGTTAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
1307470 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1307499 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1307526 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1307554 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
1307584 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
1307613 ACCCTTTTCA
Statistics
Matches: 825, Mismatches: 74, Indels: 33
0.89 0.08 0.04
Matches are distributed among these distances:
27 1 0.00
28 388 0.47
29 349 0.42
30 62 0.08
31 25 0.03
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1306932 original size:86 final size:86
Alignment explanation
Indices: 1306668--1307612 Score: 1302
Period size: 86 Copynumber: 11.0 Consensus size: 86
1306658 AATGTTCATC
* *
1306668 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
*
1306733 AAGCCCACAAGTCATTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * *
1306754 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCATTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCA
1306818 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
*
1306839 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1306904 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* * *
1306925 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAATCCCACAAATCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
*
1306990 AAGCCCACAAGTTAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * * *
1307011 CCTTTCAAAGCCCATAACTCAGTGGCAC-CCTTTCAAAGCTCACAAGTCAATGGCACTCCTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
1307075 AAGCCCACAAGTCAGTGGCACT
65 AAGCCCACAAGTCAGTGGCACT
* * * *
1307097 CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1307162 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* * *
1307183 CCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCACAAATCAGTGGCACTCCTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
1307248 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * * *
1307269 CCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTCAGTGGCACCTTTTCGA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1307333 AGCCCACAAGTCAGTGGCA-T
66 AGCCCACAAGTCAGTGGCACT
* * * * * *
1307353 CATTGCGAAGCCCACAATTCAGTGGCACT-CTTTTAAAGCCCACAAGTCAGTGGCACCCTTTTAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1307417 AGCCCACACAAGTCAGTGGCACT
66 AG-CC-CACAAGTCAGTGGCACT
* * * * * *
1307440 CCTTTTAAAGCTCACGCAAGTTAGTGGTAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTC
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
1307504 AAAGCCCACAAGTCAGTGGCA-T
64 AAAGCCCACAAGTCAGTGGCACT
* * * *
1307526 CCTTTCAAAGCCCACGAGTTAGTGGCA-TTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTC
*
1307590 AAAGCCCATGCAAGTCAATGGCA
64 AAAGCCCA--CAAGTCAGTGGCA
1307613 ACCCTTTTCA
Statistics
Matches: 770, Mismatches: 69, Indels: 38
0.88 0.08 0.04
Matches are distributed among these distances:
84 104 0.14
85 188 0.24
86 317 0.41
87 101 0.13
88 15 0.02
89 45 0.06
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (86 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACT
Done.