Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 19 of 26
Found at i:3209079 original size:2 final size:2
Alignment explanation
Indices: 3209022--3209061 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3209012 AATACCTTTA
3209022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3209062 TTCTATGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3209588 original size:40 final size:40
Alignment explanation
Indices: 3209519--3209621 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
3209509 TTTTATAAGT
* * *
3209519 ATTATACATTTA-TTTTTATTAG-TTCATCAAATAAATAT
1 ATTATATATTTATTTTTTAATAGCTTCATCAAATAAATAC
*
3209557 ATTCTATATTTATTTTTTTAATAGCTT-ATCAAATAAATAC
1 ATTATATATTTA-TTTTTTAATAGCTTCATCAAATAAATAC
*
3209597 ATTATATATTTATCTTTTAA-AGCTT
1 ATTATATATTTATTTTTTAATAGCTT
3209622 TTTATCTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 15 0.27
39 7 0.12
40 32 0.57
41 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (40 bp):
ATTATATATTTATTTTTTAATAGCTTCATCAAATAAATAC
Found at i:3209844 original size:15 final size:16
Alignment explanation
Indices: 3209824--3209864 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3209814 TATATGCAAA
3209824 TATAAATTTTAACAT-
1 TATAAATTTTAACATC
*
3209839 TATAAATATTTAATATC
1 TATAAAT-TTTAACATC
3209856 TA-AAATTTT
1 TATAAATTTT
3209865 TAAATGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 11 0.48
17 2 0.09
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAAATTTTAACATC
Found at i:3210650 original size:69 final size:69
Alignment explanation
Indices: 3210536--3210666 Score: 217
Period size: 69 Copynumber: 1.9 Consensus size: 69
3210526 AATGTTTTTC
* * *
3210536 TACCTTCTTTGCTTGTATCGATACATCATGCTACAATGGTCATATTATGTACGTTTAAATGCGTT
1 TACCTTCTTAGCTTGTATCGATACATCATGCTACAATAGTCATATTATGTACATTTAAATGCGTT
3210601 TTGA
66 TTGA
* *
3210605 TACCTTCTTAGCTTGTATCGATACATCATGCTATAATAGTTATATTATGTACATTTAAATGC
1 TACCTTCTTAGCTTGTATCGATACATCATGCTACAATAGTCATATTATGTACATTTAAATGC
3210667 AATGTATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (69 bp):
TACCTTCTTAGCTTGTATCGATACATCATGCTACAATAGTCATATTATGTACATTTAAATGCGTT
TTGA
Found at i:3211845 original size:17 final size:17
Alignment explanation
Indices: 3211796--3211849 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3211786 TTCTTTCTTA
3211796 AAAAATATTTTATATTT
1 AAAAATATTTTATATTT
* *
3211813 AACCCAA-ATTAT-TATTT
1 AA--AAATATTTTATATTT
3211830 AAAAATATTTTATA-TT
1 AAAAATATTTTATATTT
3211846 AAAA
1 AAAA
3211850 CTAGAATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 11 0.38
18 4 0.14
19 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATATTTTATATTT
Found at i:3211866 original size:34 final size:34
Alignment explanation
Indices: 3211796--3211870 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
3211786 TTCTTTCTTA
* * *
3211796 AAAAATATTTTATATTTAACCCAAATTATTATTT
1 AAAAATATTTTATATTAAAACCAAATTACTATTT
*
3211830 AAAAATATTTTATATTAAAACTAGAATTACTA-TT
1 AAAAATATTTTATATTAAAACCA-AATTACTATTT
3211864 AAAAATA
1 AAAAATA
3211871 ATAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (34 bp):
AAAAATATTTTATATTAAAACCAAATTACTATTT
Found at i:3211945 original size:57 final size:54
Alignment explanation
Indices: 3211830--3212410 Score: 414
Period size: 54 Copynumber: 11.3 Consensus size: 54
3211820 ATTATTATTT
*
3211830 AAAAATATTTTATATTAAAACT-AGAATTACTA-TTAAAAATAATAAAAAA-T--
1 AAAAATATTTTATATTAAATCTCA-AATTACTATTTAAAAATAATAAAAAATTAA
3211880 --AAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAAGTTAA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAA-TTAA
* * *
3211933 AAATATATATTTTATACTAAAT-T-ATGAATTACTATGTAAAAAATAATAAAAAA-T-C
1 AAA-A-ATATTTTATATTAAATCTCA--AATTACTAT-TTAAAAATAATAAAAAATTAA
** * * * *
3211988 AAAAATATTTTATATTGCACCTCAAATTACTATTTAAAAATAATAACAATTTTA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
* *
3212042 AAAAATATTTTATATTAAAT-T---A-TA--AATT---AATATTAAAAAATT--
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
* * * **
3212084 AAAAATATATTATATTAAATCTCAAATTACTATTTAAGAATACT-AAAAATTTT
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
** * *
3212137 AAAAATATTACATACTAAATC-CTAAATTACTATTTACAAATAAT-AAAAATTAA
1 AAAAATATTTTATATTAAATCTC-AAATTACTATTTAAAAATAATAAAAAATTAA
* * ** * *
3212190 AAATATATTTTATATAAAATCTTGAATTAATATTT---AA-AAT-----GTT--
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
* *
3212233 AAAAATATTTTATATTAAATCTCAAATTACTATATAAAAATAATAATAAATTAA
1 AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
* * * * * **
3212287 AAATATATTTCATATTAAATCTTAAATTATTATTTAAAAAATAAT-AAAAGTTTT
1 AAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAATAAAAAATTAA
* ** *
3212341 AAAAATATTTTA-AGGTAAATCTTGAATTACTATTTAAAAAATAATAAAAAATT-T
1 AAAAATATTTTATA-TTAAATCTCAAATTACTATTT-AAAAATAATAAAAAATTAA
3212395 AAAAATATTTATATAT
1 AAAAATATTT-TATAT
3212411 GTATTAGCTT
Statistics
Matches: 421, Mismatches: 63, Indels: 89
0.73 0.11 0.16
Matches are distributed among these distances:
42 19 0.05
43 30 0.07
44 11 0.03
45 2 0.00
46 3 0.01
47 8 0.02
48 27 0.06
49 26 0.06
50 3 0.01
51 8 0.02
52 22 0.05
53 92 0.22
54 103 0.24
55 23 0.05
56 4 0.01
57 24 0.06
58 16 0.04
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (54 bp):
AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAAATTAA
Found at i:3212012 original size:110 final size:103
Alignment explanation
Indices: 3211830--3212392 Score: 397
Period size: 96 Copynumber: 5.5 Consensus size: 103
3211820 ATTATTATTT
*
3211830 AAAAATATTTTATATTAAAACTA-GAATTACTATT-AAAAATAATAAAAAATAAATATTTTATAT
1 AAAAATATTTTATATT-AAATTATGAATTACTATTAAAAAATAATAAAAAATAAATATTTTATAT
*
3211893 TAAATCTCAAATTACTATTTAAAAATAATAAAAAAGTTAA
65 TAAACCTCAAATTACTATTTAAAAATAAT-AAAAAGTTAA
*
3211933 AAATATATATTTTATACTAAATTATGAATTACTATGTAAAAAATAATAAAAAATCAAAAATATTT
1 AAA-A-ATATTTTATATTAAATTATGAATTACTAT-TAAAAAATAATAAAAAAT---AAATATTT
** * * *
3211998 TATATTGCACCTCAAATTACTATTTAAAAATAATAACAATTTTA
60 TATATTAAACCTCAAATTACTATTTAAAAATAATAAAAAGTTAA
* *
3212042 AAAAATATTTTATATTAAATTATAAATTAATATTAAAAAAT--T-AAAAAT--ATA--TTATATT
1 AAAAATATTTTATATTAAATTATGAATTACTATTAAAAAATAATAAAAAATAAATATTTTATATT
* * * **
3212100 AAATCTCAAATTACTATTTAAGAATACTAAAAA-TTTT
66 AAACCTCAAATTACTATTTAAAAATAATAAAAAGTTAA
** * ** * * * *
3212137 AAAAATATTACATACTAAATCCTAAATTACTATTTACAAATAATAAAAATTAAAAATATATTTTA
1 AAAAATATTTTATATTAAATTATGAATTACTATTAAAAAATAAT-AAAA--AATAA-ATATTTTA
* * ** *
3212202 TATAAAATCTTGAATTAATATTT---AA-AAT-----GTT--
62 TATTAAACCTCAAATTACTATTTAAAAATAATAAAAAGTTAA
3212233 AAAAATATTTTATATTAAATCTCA--AATTACTATATAAAAATAATAATAAATTAAA-AATATAT
1 AAAAATATTTTATATTAAAT-T-ATGAATTACTAT-T-AAAA-AATAATAAA--AAATAA-ATAT
* * * * **
3212295 TTCATATTAAATCTTAAATTATTATTTAAAAAATAAT-AAAAGTTTT
58 TTTATATTAAACCTCAAATTACTATTT-AAAAATAATAAAAAGTTAA
*
3212341 AAAAATATTTTA-AGGTAAATCT-TGAATTACTATTTAAAAAATAATAAAAAAT
1 AAAAATATTTTATA-TTAAAT-TATGAATTACTA-TTAAAAAATAATAAAAAAT
3212393 TTAAAAATAT
Statistics
Matches: 373, Mismatches: 44, Indels: 84
0.74 0.09 0.17
Matches are distributed among these distances:
95 36 0.10
96 60 0.16
97 32 0.09
98 12 0.03
99 9 0.02
100 1 0.00
101 4 0.01
102 5 0.01
103 11 0.03
104 13 0.03
105 21 0.06
106 43 0.12
107 47 0.13
108 29 0.08
109 11 0.03
110 39 0.10
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (103 bp):
AAAAATATTTTATATTAAATTATGAATTACTATTAAAAAATAATAAAAAATAAATATTTTATATT
AAACCTCAAATTACTATTTAAAAATAATAAAAAGTTAA
Found at i:3212103 original size:21 final size:21
Alignment explanation
Indices: 3212042--3212103 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3212032 AACAATTTTA
*
3212042 AAAAATATTTTATATTAAATT
1 AAAAATATATTATATTAAATT
* *
3212063 ATAAATTAATATTA-A-AAAATT
1 A-AAAAT-ATATTATATTAAATT
3212084 AAAAATATATTATATTAAAT
1 AAAAATATATTATATTAAAT
3212104 CTCAAATTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 11 0.34
22 5 0.16
23 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATATATTATATTAAATT
Found at i:3212112 original size:149 final size:146
Alignment explanation
Indices: 3211959--3212382 Score: 464
Period size: 149 Copynumber: 2.8 Consensus size: 146
3211949 CTAAATTATG
* **
3211959 AATTACTATGTAAAAAATAATAAAAAATCAAAAATATTTTATATTGCACCTCAAATTACTATTTA
1 AATTACTAT-T-AAAAATAATAAAAAATTAAAAATATTTTATATTAAACCT-AAATTACTATTTA
*
3212024 AAAATAATAACAATTTTAAAAAATATTTTATATTAAAT-TATAAATTAATA-TTAAAAAATTAAA
63 AAAATAATAA-AATTTTAAAAAATATTTTATATAAAATCT-TAAATTAATATTTAAAAAATTAAA
3212087 AATATATTATATTAAATCTCA
126 AATATATTATATTAAATCTCA
* * * ** *
3212108 AATTACTATTTAAGAATACTAAAAATTTTAAAAATATTACATACTAAATCCTAAATTACTATTTA
1 AATTACTA-TTAAAAATAATAAAAA-ATTAAAAATATTTTATATTAAA-CCTAAATTACTATTTA
* * * **
3212173 CAAATAATAAAA-ATTAAAAATATATTTTATATAAAATCTTGAATTAATATTTAAAATGTTAAAA
63 AAAATAATAAAATTTTAAAAA-ATATTTTATATAAAATCTTAAATTAATATTTAAAAAATTAAAA
*
3212237 ATATTTTATATTAAATCTCA
127 ATATATTATATTAAATCTCA
* * *
3212257 AATTACTATATAAAAATAATAATAAATTAAAAATATATTTCATATTAAATCTTAAATTATTATTT
1 AATTACTAT-TAAAAATAATAAAAAATTAAAAATAT-TTT-ATATTAAA-CCTAAATTACTATTT
* *
3212322 AAAAAATAATAAAAGTTTT-AAAAATATTTTA-AGGT-AAATCTTGAATTACTATTTAAAAAAT
62 -AAAAATAATAAAA-TTTTAAAAAATATTTTATA--TAAAATCTTAAATTAATATTTAAAAAAT
3212383 AATAAAAAAT
Statistics
Matches: 231, Mismatches: 30, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
147 7 0.03
148 49 0.21
149 99 0.43
150 26 0.11
151 43 0.19
152 5 0.02
153 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (146 bp):
AATTACTATTAAAAATAATAAAAAATTAAAAATATTTTATATTAAACCTAAATTACTATTTAAAA
ATAATAAAATTTTAAAAAATATTTTATATAAAATCTTAAATTAATATTTAAAAAATTAAAAATAT
ATTATATTAAATCTCA
Found at i:3212261 original size:43 final size:44
Alignment explanation
Indices: 3212189--3212271 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
3212179 ATAAAAATTA
** *
3212189 AAAATATATTTTATATAAAATCTTGAATTAATATTTAAAATGTT
1 AAAATATATTTTATATAAAATCTCAAATTAATATATAAAATGTT
* *
3212233 AAAA-ATATTTTATATTAAATCTCAAATTACTATATAAAA
1 AAAATATATTTTATATAAAATCTCAAATTAATATATAAAA
3212272 ATAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 30 0.88
44 4 0.12
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (44 bp):
AAAATATATTTTATATAAAATCTCAAATTAATATATAAAATGTT
Found at i:3212759 original size:22 final size:22
Alignment explanation
Indices: 3212734--3212806 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
3212724 CATTTTTACT
*
3212734 ATATGTATATTTAGTTAAAGTC
1 ATATGTACATTTAGTTAAAGTC
*
3212756 ATATGTACATATT-GTTAAATTC
1 ATATGTACAT-TTAGTTAAAGTC
*
3212778 ATATGTACATATTA-TTATAGTC
1 ATATGTACAT-TTAGTTAAAGTC
3212800 ATATGTA
1 ATATGTA
3212807 AATTCAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 43 0.96
23 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (22 bp):
ATATGTACATTTAGTTAAAGTC
Found at i:3213043 original size:22 final size:22
Alignment explanation
Indices: 3212959--3213045 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
3212949 AAAAATATCA
* *
3212959 TTATTATTATATGTACATATAG
1 TTATAATTATATGTACATTTAG
* *
3212981 TTA-AAGTCATATGTATATATT-G
1 TTATAA-TTATATGTACAT-TTAG
*
3213003 TTATAATTATATTTACATTTAG
1 TTATAATTATATGTACATTTAG
*
3213025 TTATAATTATATATACATTTA
1 TTATAATTATATGTACATTTA
3213046 TATATAGTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 3 0.06
22 47 0.89
23 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TTATAATTATATGTACATTTAG
Found at i:3213058 original size:22 final size:22
Alignment explanation
Indices: 3212967--3213059 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
3212957 CATTATTATT
* *
3212967 ATATGTACATATAGTTA-AAGTC
1 ATATATACATTTAGTTATAA-TC
* * *
3212989 ATATGTATATATT-GTTATAATT
1 ATATATACAT-TTAGTTATAATC
* *
3213011 ATATTTACATTTAGTTATAATT
1 ATATATACATTTAGTTATAATC
*
3213033 ATATATACATTTA-TATATAGTC
1 ATATATACATTTAGT-TATAATC
3213055 ATATA
1 ATATA
3213060 CGTATATAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.05
22 53 0.90
23 3 0.05
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (22 bp):
ATATATACATTTAGTTATAATC
Found at i:3213303 original size:51 final size:51
Alignment explanation
Indices: 3213206--3213343 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 51
3213196 AATATAAAAT
* *
3213206 ATTTAATATAAAAT-TTTCTAA-TTTTTATTATTTTTATATAGTAATTTGA-G
1 ATTTAATATAAAATATTT-TAATTTTTTATTATTTTAAAATAGTAATTT-ATG
*
3213256 ATTTAATATAAAATATTTAAATTTTTTATTATTTTAAAATAGTAATTTATG
1 ATTTAATATAAAATATTTTAATTTTTTATTATTTTAAAATAGTAATTTATG
* *
3213307 ATTTAATATAAAACAATTTTTTATTTTTTATTATTTT
1 ATTTAATATAAAA-TA-TTTTAATTTTTTATTATTTT
3213344 CAATTATATT
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
50 17 0.22
51 41 0.53
52 1 0.01
53 18 0.23
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (51 bp):
ATTTAATATAAAATATTTTAATTTTTTATTATTTTAAAATAGTAATTTATG
Found at i:3217387 original size:52 final size:52
Alignment explanation
Indices: 3217309--3217437 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
3217299 CGAAATATGA
3217309 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
3217361 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
3217413 AAATTTTCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3217438 AAGATTAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3217447 original size:52 final size:52
Alignment explanation
Indices: 3217309--3217457 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 52
3217299 CGAAATATGA
* **
3217309 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
** **
3217361 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* *
3217413 AAATTTTCCTACATGTATCGATACA-AAGATTAGTGTATCGATACA
1 AAATTTGCCTACATGTATCGATACATAACA-TAGTGTATCGATACA
3217458 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.01
52 88 0.99
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:3217464 original size:13 final size:13
Alignment explanation
Indices: 3217446--3217470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3217436 CAAAGATTAG
3217446 TGTATCGATACAA
1 TGTATCGATACAA
3217459 TGTATCGATACA
1 TGTATCGATACA
3217471 TTTGAGTAAT
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:3217557 original size:32 final size:32
Alignment explanation
Indices: 3217515--3217585 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
3217505 AGCTTCGTAG
3217515 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
3217547 CGATATATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
3217579 CGATACA
1 CGATACA
3217586 ACTCGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:3217587 original size:19 final size:19
Alignment explanation
Indices: 3217523--3217587 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
3217513 AGCGATACAT
*
3217523 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
3217542 TGTATCGAT---ATA--T-
1 TGTATCGATACAACACTTA
3217555 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3217574 TGTATCGATACAAC
1 TGTATCGATACAAC
3217588 TCGTTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 4 0.11
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:3222861 original size:21 final size:20
Alignment explanation
Indices: 3222837--3222897 Score: 52
Period size: 25 Copynumber: 2.8 Consensus size: 20
3222827 ATACAATCTC
3222837 ATAAATCTTATTTTATAATTA
1 ATAAATCTTATTTTATAA-TA
3222858 ATAAAATGCATCTATTTTATAATA
1 AT-AAAT-C-T-TATTTTATAATA
3222882 A-AAATTCTTAATTTTA
1 ATAAA-TCTT-ATTTTA
3222898 ATCGGCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 8 0.24
23 2 0.06
24 4 0.12
25 10 0.29
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
ATAAATCTTATTTTATAATA
Found at i:3226847 original size:2 final size:2
Alignment explanation
Indices: 3226835--3226879 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3226825 GAAAAGTAGG
* *
3226835 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3226877 TA T
1 TA T
3226880 GTAAGAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3228880 original size:15 final size:15
Alignment explanation
Indices: 3228822--3228880 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 15
3228812 TAAAATTAAA
3228822 AATAAT-AATAATGAT
1 AATAATAAATAAT-AT
3228837 AATAATAGAATAATTATTTT
1 AATAATA-AATAA-TA---T
3228857 AATAATAAATAATAT
1 AATAATAAATAATAT
3228872 AATAATAAA
1 AATAATAAA
3228881 ATTAAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 16 0.42
17 6 0.16
18 3 0.08
19 5 0.13
20 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAATAAATAATAT
Found at i:3228892 original size:18 final size:18
Alignment explanation
Indices: 3228855--3228900 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3228845 AATAATTATT
*
3228855 TTAATAAT-AAA-TAATA
1 TTAATAATAAAATTAAAA
3228871 -TAATAATAAAATTAAAA
1 TTAATAATAAAATTAAAA
*
3228888 TTAATGATAAAAT
1 TTAATAATAAAAT
3228901 ATATATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 4 0.16
18 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAATAATAAAATTAAAA
Found at i:3229457 original size:15 final size:15
Alignment explanation
Indices: 3229428--3229469 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3229418 AATTTATTGG
*
3229428 ATTTTTAATTA-TAA
1 ATTTTTAAATATTAA
3229442 ATTTTTAAATATTAA
1 ATTTTTAAATATTAA
* *
3229457 ATTATAAAATATT
1 ATTTTTAAATATT
3229470 GGTATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTTAAATATTAA
Found at i:3230065 original size:22 final size:24
Alignment explanation
Indices: 3230035--3230082 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
3230025 TATTTTTGAG
3230035 TTAAGTTTTAATATATTAAT-ATA
1 TTAAGTTTTAATATATTAATAATA
* *
3230058 TTAA-TTTTTATATATTTATAATA
1 TTAAGTTTTAATATATTAATAATA
3230081 TT
1 TT
3230083 TTTATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAAGTTTTAATATATTAATAATA
Found at i:3230068 original size:71 final size:71
Alignment explanation
Indices: 3229949--3230093 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
3229939 ACTAGACGTG
*
3229949 ATAATTATTTTTGAGTTAAGTTTTAATAATAATATGAAAAATAATTTATATATTTAT-TTCATTT
1 ATAATTATTTTTGAGTTAAGTTTTAATAATAATATGAAAAATAATTTATATATTTATAAT-ATTT
3230013 TTATATT
65 TTATATT
** *
3230020 ATAATTATTTTTGAGTTAAGTTTTAATATATTAATAT-ATTAAT-TTTTATATATTTATAATATT
1 ATAATTATTTTTGAGTTAAGTTTTAATA-A-TAATATGAAAAATAATTTATATATTTATAATATT
3230083 TTTATATT
64 TTTATATT
3230091 ATA
1 ATA
3230094 TTTTTTAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 55 0.82
72 6 0.09
73 6 0.09
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.56
Consensus pattern (71 bp):
ATAATTATTTTTGAGTTAAGTTTTAATAATAATATGAAAAATAATTTATATATTTATAATATTTT
TATATT
Found at i:3230099 original size:33 final size:31
Alignment explanation
Indices: 3230054--3230138 Score: 84
Period size: 35 Copynumber: 2.6 Consensus size: 31
3230044 AATATATTAA
3230054 TATATTA-A-TTTTTATATATTTATAATATTTT
1 TATATTATATTTTTTATATATTT-TAAT-TTTT
3230085 TATATTATATTTTTTAAAATAATATTTTAATTTTT
1 TATATTATATTTTTT---AT-ATATTTTAATTTTT
*
3230120 TATATAATATTTTATTATA
1 TATATTATATTTT-TTATA
3230139 GCATATATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
31 7 0.15
32 2 0.04
33 7 0.15
35 16 0.35
36 8 0.17
37 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATATTATATTTTTTATATATTTTAATTTTT
Found at i:3230118 original size:20 final size:20
Alignment explanation
Indices: 3230095--3230133 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3230085 TATATTATAT
3230095 TTTTTAAAATAATATTTTAA
1 TTTTTAAAATAATATTTTAA
* *
3230115 TTTTTTATATAATATTTTA
1 TTTTTAAAATAATATTTTA
3230134 TTATAGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAAATAATATTTTAA
Found at i:3230132 original size:13 final size:12
Alignment explanation
Indices: 3230072--3230138 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
3230062 TTTTTATATA
3230072 TTTATAATATTT
1 TTTATAATATTT
*
3230084 TTATATTATATTT
1 TT-TATAATATTT
* * *
3230097 TTTAAAATAATA
1 TTTATAATATTT
3230109 TTT-TAAT-TTT
1 TTTATAATATTT
3230119 TTATATAATATTT
1 TT-TATAATATTT
3230132 TATTATA
1 T-TTATA
3230139 GCATATATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
10 3 0.07
11 4 0.10
12 15 0.36
13 19 0.45
14 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATAATATTT
Found at i:3235829 original size:78 final size:79
Alignment explanation
Indices: 3235664--3235850 Score: 243
Period size: 78 Copynumber: 2.4 Consensus size: 79
3235654 AGATAACAAA
* **
3235664 GGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGGAAATAAAACCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTCTAAAAATAAAACCGGGGTTGGAGTATC
3235729 CCCTCAAAAATAAC
66 CCCTCAAAAATAAC
* * * * * *
3235743 AGGATTGGAGTATCCCTGATTAT-AGAAAATCTGTATTTTAAAAATAAAA-TGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGA-AAAATCGGTATTCTAAAAATAAAACCGGGGTTGGAGTAT
*
3235806 CCCCTCGAAAATAAC
65 CCCCTCAAAAATAAC
* *
3235821 GGGGTTGGAGTATCCTCGATTGTGAAAAAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAAT
3235851 TGATGCTTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
78 51 0.56
79 40 0.44
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTCTAAAAATAAAACCGGGGTTGGAGTATC
CCCTCAAAAATAAC
Found at i:3235866 original size:78 final size:76
Alignment explanation
Indices: 3235664--3235888 Score: 238
Period size: 78 Copynumber: 2.9 Consensus size: 76
3235654 AGATAACAAA
* * * *
3235664 GGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGGAAATAAAACCGGGGTTGGAGTATC
1 GGGGTTGGAGTAT-CCCGATTATGAAAAATTGATGTT-TAGAAATAAAA-TGGGGTTGGAGTATC
3235729 CCCTCAAAAATAAC
63 CCCTCAAAAATAAC
* * *
3235743 AGGATTGGAGTATCCCTGATTAT-AGAAAATCTGTAT-TTTAAAAATAAAATGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCC-GATTATGA-AAAAT-TG-ATGTTTAGAAATAAAATGGGGTTGGAGTAT
*
3235806 CCCCTCGAAAATAAC
62 CCCCTCAAAAATAAC
* ** *
3235821 GGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGCTTTAGAAATAAGGCTGGGGTTAGAGTATC
1 GGGGTTGGAGTATCC-CGATTATGAAAAATTGATG-TTTAGAAATAA-AATGGGGTTGGAGTATC
3235886 CCC
63 CCC
3235889 GATTGTGAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
76 2 0.02
77 2 0.02
78 64 0.52
79 50 0.41
80 3 0.02
81 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (76 bp):
GGGGTTGGAGTATCCCGATTATGAAAAATTGATGTTTAGAAATAAAATGGGGTTGGAGTATCCCC
TCAAAAATAAC
Found at i:3235916 original size:51 final size:51
Alignment explanation
Indices: 3235820--3235939 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
3235810 TCGAAAATAA
* * *
3235820 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGCTTTAGAAATA-AGG
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATACTTTAGAAATATAGG
* * * * *
3235870 CTGGGGTTAGAGTATCCCCGATTGTGAGAAATTAATATTTTGGAAATATAGT
1 C-GGGGTTGGAGTATCCCCGATTGTGAAAAATTAATACTTTAGAAATATAGG
*
3235922 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
3235940 TCAGAAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.02
51 54 0.93
52 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATACTTTAGAAATATAGG
Found at i:3235982 original size:130 final size:130
Alignment explanation
Indices: 3235750--3236069 Score: 346
Period size: 130 Copynumber: 2.5 Consensus size: 130
3235740 AACAGGATTG
* * * * * **
3235750 GAGTATCCCTGATTATAGAAAATCT-GTATTTTAAAAATAAAA-TGGGGTTGGAGTATCCCCTCG
1 GAGTATCCCCGATTGTGGAAAAT-TAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCG
* * * * ** *
3235813 AAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATG-CTTTAGAAAT-AAGGCTGGGG
65 AAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTCTTGA-AAATAAAATC-GGAG
3235876 TTA
128 TTA
* * **
3235879 GAGTATCCCCGATTGT-GAGAAATTAATATTTTGGAAATATAGTCAGGGTTGGAGTATCCCCTC-
1 GAGTATCCCCGATTGTGGA-AAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCG
*
3235942 AGAAATAATGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTCTTGAAAATAAAATCGGAGT
65 A-AAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTCTTGAAAATAAAATCGGAGT
*
3236007 TG
129 TA
* * *
3236009 GAGTATCTCCGATTGTGGAAAATTGATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GAGTATCCCCGATTGTGGAAAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCC
3236070 GATTGCAGAA
Statistics
Matches: 159, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
128 3 0.02
129 31 0.19
130 116 0.73
131 9 0.06
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (130 bp):
GAGTATCCCCGATTGTGGAAAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGA
AAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTCTTGAAAATAAAATCGGAGTTA
Found at i:3236021 original size:51 final size:49
Alignment explanation
Indices: 3235954--3236119 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 49
3235944 AAATAATGAG
*
3235954 GTTGGAGTATCCCCGATTATGAAAAATTGATGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATT-TGAAAAATTGATGT-TTAAAAATAAAATCGGA
* * * * * *
3236005 GTTGGAGTATCTCCGATTGTGGAAAATTGATATTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-TGAAAAATTGAT-GTTTAAAAATAAAATCGGA
3236056 GTTGGAGTATCCCCGA-TTGCAGAAAATTGATGTTTTAAAAATAAAATC-GA
1 GTTGGAGTATCCCCGATTTG-A-AAAATTGATG-TTTAAAAATAAAATCGGA
3236106 GGTTGGAGTATCCC
1 -GTTGGAGTATCCC
3236120 TAAAAAATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
49 2 0.02
50 2 0.02
51 91 0.95
52 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTTGAAAAATTGATGTTTAAAAATAAAATCGGA
Found at i:3246888 original size:17 final size:16
Alignment explanation
Indices: 3246846--3246897 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
3246836 ACGAAATCAT
*
3246846 ATTATTAAAAATTTAA
1 ATTATTAAAAATGTAA
*
3246862 TTATTTATTATATAATGTAA
1 --A-TTATTA-AAAATGTAA
3246882 ATTATTAAAAATGTAA
1 ATTATTAAAAATGTAA
3246898 TTGGTTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 2 0.07
19 6 0.21
20 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTATTAAAAATGTAA
Found at i:3264694 original size:28 final size:28
Alignment explanation
Indices: 3264654--3264730 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
3264644 TTTTGGAGAT
3264654 AATAACGGGGTTGGAGTATCCCCTTGAA
1 AATAACGGGGTTGGAGTATCCCCTTGAA
3264682 AATAACGGGGTTGGAGTATCCCCTTGAA
1 AATAACGGGGTTGGAGTATCCCCTTGAA
* *
3264710 AATAACGAGGTTGGAATATCC
1 AATAACGGGGTTGGAGTATCC
3264731 TCGAGTGTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCTTGAA
Found at i:3264820 original size:53 final size:52
Alignment explanation
Indices: 3264745--3264939 Score: 243
Period size: 53 Copynumber: 3.8 Consensus size: 52
3264735 GTGTGAAAGA
* *
3264745 TTGGTGTTTT-TAAAATAAAACCGGGGTTGGAGTATCCCCGATCAAAGGAAAT
1 TTGGTGTTTTGAAAAATAAAACCGGGGTTAGAGTATCCCCGAT-AAAGGAAAT
* *
3264797 TTGGCGTTTTGAAAAATAAAACCGGGGTTAAAGTATCCCCGATTAAAGGAAAT
1 TTGGTGTTTTGAAAAATAAAACCGGGGTTAGAGTATCCCCGA-TAAAGGAAAT
* * * * *
3264850 TTGGTGTTTCGAAAAATAAAACCGTGGTTAGAGTATCCCCGAT-ATGAAAAA
1 TTGGTGTTTTGAAAAATAAAACCGGGGTTAGAGTATCCCCGATAAAGGAAAT
* * *
3264901 TTAGTGTTTT-AGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTGGTGTTTTGAAAAATAAAACCGGGGTTAGAGTATCCCC
3264940 TCGGAGGTAA
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 26 0.21
51 13 0.10
52 10 0.08
53 75 0.60
54 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (52 bp):
TTGGTGTTTTGAAAAATAAAACCGGGGTTAGAGTATCCCCGATAAAGGAAAT
Found at i:3264965 original size:28 final size:28
Alignment explanation
Indices: 3264925--3265021 Score: 149
Period size: 28 Copynumber: 3.5 Consensus size: 28
3264915 ATAAAACCGG
3264925 GGTTGGAGTATCCCCTCGGAGGTAACGA
1 GGTTGGAGTATCCCCTCGGAGGTAACGA
3264953 GGTTGGAGTATCCCCTCGGAGGTAACGA
1 GGTTGGAGTATCCCCTCGGAGGTAACGA
*** **
3264981 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCTCGGAGGTAACGA
3265009 GGTTGGAGTATCC
1 GGTTGGAGTATCC
3265022 TCGATTGTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGGAGGTAACGA
Found at i:3265079 original size:52 final size:51
Alignment explanation
Indices: 3265010--3265130 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
3265000 AAATAACGAG
* * * *
3265010 GTTGGAGTATCCTCGATTGTGAA-AAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATT-TAAAGAAATTGGTG-TTTTGAAAATAAAACCGGA
*
3265062 GTTGGAGTATCCCCGA-TTAAAGGAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTTAAA-GAAATTGGTGTTTTGAAAATAAAACCGGA
3265113 GTTGGAGTATCCCCGATT
1 GTTGGAGTATCCCCGATT
3265131 ATGATCAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 3 0.05
51 33 0.54
52 25 0.41
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTTAAAGAAATTGGTGTTTTGAAAATAAAACCGGA
Found at i:3265119 original size:51 final size:52
Alignment explanation
Indices: 3265033--3265131 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 52
3265023 CGATTGTGAA
* *
3265033 AAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
1 AAATTGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATTAAAGG
*
3265085 AAATTGGTG-TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTA
1 AAATTGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATTA
3265132 TGATCAATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 35 0.80
52 9 0.20
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (52 bp):
AAATTGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATTAAAGG
Found at i:3266333 original size:24 final size:27
Alignment explanation
Indices: 3266282--3266339 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 27
3266272 GTTTTCCTCT
*
3266282 TTGCTCGCTGTTCTTCCTTCGTCGATGC
1 TTGCT-GCTGTTCTTCCTTCGTCAATGC
3266310 TTGCTGCTG-TCTT-CTT-GTCAATGC
1 TTGCTGCTGTTCTTCCTTCGTCAATGC
3266334 -TGCTGC
1 TTGCTGC
3266340 CGTTTCTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.21
24 7 0.24
25 3 0.10
26 4 0.14
27 4 0.14
28 5 0.17
ACGTcount: A:0.05, C:0.29, G:0.22, T:0.43
Consensus pattern (27 bp):
TTGCTGCTGTTCTTCCTTCGTCAATGC
Found at i:3266752 original size:50 final size:50
Alignment explanation
Indices: 3266692--3266855 Score: 301
Period size: 50 Copynumber: 3.3 Consensus size: 50
3266682 GCTTTTTTCA
3266692 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
* * *
3266742 TTTCCCATGCATGCCTCCGCATGTTTTGTCTCCAATTGCAATTTTTTTGT
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
3266792 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
3266842 TTTCCCATGCATGC
1 TTTCCCATGCATGC
3266856 ATTTTCTATT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.15, C:0.27, G:0.14, T:0.44
Consensus pattern (50 bp):
TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
Found at i:3267208 original size:3 final size:3
Alignment explanation
Indices: 3267202--3267229 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3267192 AAAAAAATGA
3267202 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3267230 CATAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3268297 original size:18 final size:20
Alignment explanation
Indices: 3268257--3268304 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3268247 TCAACTGAGG
*
3268257 AAAAAAA-AAGAGAAAAGAG
1 AAAAAAATAAGAGAAAAGAC
3268276 AAAAAAATAA-AGAAAA-AC
1 AAAAAAATAAGAGAAAAGAC
*
3268294 AAAAATATAAG
1 AAAAAAATAAG
3268305 GTTTTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
19 13 0.52
20 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (20 bp):
AAAAAAATAAGAGAAAAGAC
Found at i:3268298 original size:19 final size:20
Alignment explanation
Indices: 3268257--3268298 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3268247 TCAACTGAGG
*
3268257 AAAAAAAAAGAGAAAAGAGA
1 AAAAAAAAAGAGAAAACAGA
3268277 AAAAAATAAAGA-AAAACA-A
1 AAAAAA-AAAGAGAAAACAGA
3268296 AAA
1 AAA
3268299 TATAAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAACAGA
Found at i:3269269 original size:20 final size:20
Alignment explanation
Indices: 3269246--3269289 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3269236 TTTTTGGGAC
*
3269246 TTTTATGCAATTTTAGAT-AT
1 TTTTAAGCAATTTTA-ATCAT
*
3269266 TTTTAAGCCATTTTAATCAT
1 TTTTAAGCAATTTTAATCAT
3269286 TTTT
1 TTTT
3269290 TATGATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTAAGCAATTTTAATCAT
Found at i:3271369 original size:54 final size:54
Alignment explanation
Indices: 3271282--3271391 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
3271272 TCAAAAATAA
* * * *
3271282 CAATCTAAATTCTCATTAAGCAAAACATTAATACTTTAGTAATTGACAACCTTT
1 CAATCTAAATTCTCACTAAGCAAAACATCAATACTTTAGTAACTCACAACCTTT
* *
3271336 CAATCTAAATTCTTACTAAGCAAAATATCAATACTTTAGTAACTCACAACCTTT
1 CAATCTAAATTCTCACTAAGCAAAACATCAATACTTTAGTAACTCACAACCTTT
3271390 CA
1 CA
3271392 TTACACCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34
Consensus pattern (54 bp):
CAATCTAAATTCTCACTAAGCAAAACATCAATACTTTAGTAACTCACAACCTTT
Found at i:3273825 original size:28 final size:28
Alignment explanation
Indices: 3273752--3273827 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
3273742 AGTAAAAACA
* *
3273752 TTTTTAATATGTTACTAATAATATTACT
1 TTTTTAATATGTTATTAATAATAATACT
*
3273780 TTTTTAATATTTATATTAATAAAATAATA-T
1 TTTTTAATATGT-TATTAAT--AATAATACT
3273810 TTTTTAA-ATGTTATTAAT
1 TTTTTAATATGTTATTAAT
3273828 TTAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 18 0.44
29 9 0.22
30 8 0.20
31 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTTTAATATGTTATTAATAATAATACT
Found at i:3273881 original size:9 final size:9
Alignment explanation
Indices: 3273869--3273897 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3273859 TTAAAATGTG
3273869 AATATTTTT
1 AATATTTTT
3273878 AATATTTTT
1 AATATTTTT
3273887 AATATTTTT
1 AATATTTTT
3273896 AA
1 AA
3273898 AATCAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
AATATTTTT
Found at i:3278015 original size:20 final size:20
Alignment explanation
Indices: 3277979--3278016 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3277969 ACTTGAAGAG
*
3277979 AAAAATACTAAACTACAAAA
1 AAAAATACGAAACTACAAAA
3277999 AAAAGATACGAAA-TACAA
1 AAAA-ATACGAAACTACAA
3278017 CAAATAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.68, C:0.13, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAAATACGAAACTACAAAA
Found at i:3282831 original size:20 final size:19
Alignment explanation
Indices: 3282763--3282831 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
3282753 TTCCAAAGCC
*
3282763 ATTAAATTT--TTTTAAAT
1 ATTAAATTTAATTTTTAAT
* *
3282780 ACTTAAATTCAATTTTTTAT
1 A-TTAAATTTAATTTTTAAT
3282800 AATT-AATGTTAATTTTTAAT
1 -ATTAAAT-TTAATTTTTAAT
3282820 ATTAAATATTAA
1 ATTAAAT-TTAA
3282832 ATATATTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 1 0.03
18 7 0.17
19 6 0.15
20 25 0.62
21 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (19 bp):
ATTAAATTTAATTTTTAAT
Found at i:3286373 original size:27 final size:27
Alignment explanation
Indices: 3286321--3286390 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
3286311 AATTATTTTT
*
3286321 TATTTATAAATATTTTAAGATATTATC
1 TATTTATAAATATTTTAAAATATTATC
* *
3286348 TATTTATATAA-ATTTTAAAATTTTATA
1 TATTTATA-AATATTTTAAAATATTATC
*
3286375 TAAATT-TAAATATTTT
1 T-ATTTATAAATATTTT
3286391 TATTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.06
27 29 0.81
28 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
TATTTATAAATATTTTAAAATATTATC
Found at i:3286382 original size:18 final size:20
Alignment explanation
Indices: 3286350--3286390 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3286340 ATATTATCTA
3286350 TTTATATAAATTTTAAA-AT
1 TTTATATAAATTTTAAATAT
3286369 TTTATATAAA-TTTAAATAT
1 TTTATATAAATTTTAAATAT
3286388 TTT
1 TTT
3286391 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATAAATTTTAAATAT
Found at i:3286418 original size:19 final size:20
Alignment explanation
Indices: 3286378--3286415 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3286368 TTTTATATAA
3286378 ATTTAAATATTTTTATTTTT
1 ATTTAAATATTTTTATTTTT
3286398 ATTT-AATA-TTTTATTTTT
1 ATTTAAATATTTTTATTTTT
3286416 TATATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTAAATATTTTTATTTTT
Found at i:3286759 original size:11 final size:11
Alignment explanation
Indices: 3286733--3286764 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3286723 TTTTGACATA
3286733 TTAATATT-TT
1 TTAATATTATT
3286743 TT-ATATTATT
1 TTAATATTATT
3286753 TTAATATTATT
1 TTAATATTATT
3286764 T
1 T
3286765 GTGTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.25
10 6 0.30
11 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAATATTATT
Found at i:3287014 original size:14 final size:14
Alignment explanation
Indices: 3286995--3287035 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3286985 ATTATTTTAT
3286995 TTTTATATAATTAA
1 TTTTATATAATTAA
*
3287009 TTTTATATAAAT-A
1 TTTTATATAATTAA
*
3287022 TTTAATA-AATTAA
1 TTTTATATAATTAA
3287035 T
1 T
3287036 GAGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 3 0.13
13 9 0.39
14 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTATATAATTAA
Found at i:3287385 original size:21 final size:21
Alignment explanation
Indices: 3287347--3287386 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3287337 TTTATTAATC
* * *
3287347 AAAAAATTGATTTTAAAAAGA
1 AAAAAATTAATATAAAAAAGA
3287368 AAAAAATTAATATAAAAAA
1 AAAAAATTAATATAAAAAA
3287387 TACTAAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAAATTAATATAAAAAAGA
Found at i:3290560 original size:3 final size:3
Alignment explanation
Indices: 3290552--3290597 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
3290542 TTGAGATCTC
3290552 TTA TTA TTAA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3290598 GTTGTTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3295903 original size:21 final size:18
Alignment explanation
Indices: 3295874--3295918 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
3295864 AATATATATT
3295874 AAATT-AAAATATATTTATA
1 AAATTAAAAATA-ATTT-TA
3295893 ATAATTAAAAATAATTTTA
1 A-AATTAAAAATAATTTTA
3295912 AAATTAA
1 AAATTAA
3295919 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 8 0.33
21 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAAAAATAATTTTA
Found at i:3295924 original size:20 final size:23
Alignment explanation
Indices: 3295853--3295924 Score: 59
Period size: 26 Copynumber: 3.3 Consensus size: 23
3295843 AAAACTAGGT
3295853 TTAAA-ATATTTA-ATATATATTAAA
1 TTAAATATATTTATA-ATA-ATT-AA
3295877 TTAAAATATATTTATAATAATTAA
1 TT-AAATATATTTATAATAATTAA
3295901 --AAATA-ATTT-TAA-AATTAA
1 TTAAATATATTTATAATAATTAA
3295919 TTAAAT
1 TTAAAT
3295925 TTTTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
18 6 0.14
19 3 0.07
20 8 0.19
21 5 0.12
24 4 0.09
25 6 0.14
26 10 0.23
27 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAATATATTTATAATAATTAA
Found at i:3295983 original size:15 final size:16
Alignment explanation
Indices: 3295953--3295989 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3295943 AAATAAATAA
3295953 AAATAAATAGATAATT
1 AAATAAATAGATAATT
*
3295969 AAATAATTA-ATAATT
1 AAATAAATAGATAATT
3295984 -AATAAA
1 AAATAAA
3295990 AATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.26
15 6 0.32
16 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAAATAGATAATT
Found at i:3296478 original size:5 final size:5
Alignment explanation
Indices: 3296470--3296506 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3296460 ATTATATATT
3296470 TTTAA TTTAA TTTAA TTTAA TTT-- TTTAAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT-AA TTTAA TTT
3296507 TTAATCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 23 0.79
6 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTAA
Found at i:3296502 original size:14 final size:13
Alignment explanation
Indices: 3296468--3296508 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
3296458 ATATTATATA
3296468 TTTTTAATTTAA-
1 TTTTTAATTTAAT
3296480 --TTTAATTTAAT
1 TTTTTAATTTAAT
3296491 TTTTTAAATTTAAT
1 TTTTT-AATTTAAT
3296505 TTTT
1 TTTT
3296509 AATCATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
13 3 0.12
14 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:3296612 original size:27 final size:29
Alignment explanation
Indices: 3296556--3296616 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
3296546 ATAACTTAAC
* *
3296556 ATATATTTTAATCTTTATACTATAATATT
1 ATATATTTTAATCTTTATAATATAAAATT
*
3296585 ATATATTTT-ATTTTTATAATA-AAAATT
1 ATATATTTTAATCTTTATAATATAAAATT
3296612 ATATA
1 ATATA
3296617 AAATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.34
28 10 0.34
29 9 0.31
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATATTTTAATCTTTATAATATAAAATT
Found at i:3296631 original size:26 final size:25
Alignment explanation
Indices: 3296602--3296662 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3296592 TTATTTTTAT
3296602 AATAAAAATTATATAAA-ATATATATA
1 AATAAAAATTA-ATAAATAT-TATATA
*
3296628 AATACAAAATTAATATATATTATATA
1 AATA-AAAATTAATAAATATTATATA
*
3296654 ATTAAAAAT
1 AATAAAAAT
3296663 AGATTGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 17 0.55
27 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAAAAATTAATAAATATTATATA
Found at i:3296807 original size:18 final size:18
Alignment explanation
Indices: 3296786--3296832 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
3296776 TAAACTCTCT
3296786 AATAAATTTTTAAACT-TA
1 AATAAATTTTT-AACTATA
*
3296804 AATAAATAATTTAACTCATA
1 AATAAAT-TTTTAACT-ATA
3296824 AATAAATTT
1 AATAAATTT
3296833 ATTGATAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 11 0.46
19 4 0.17
20 9 0.38
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAATTTTTAACTATA
Found at i:3306841 original size:18 final size:16
Alignment explanation
Indices: 3306818--3306863 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
3306808 AAAATTAAAT
3306818 TTTATTAAATTATAATTA
1 TTTATTAAATTAT--TTA
3306836 TTTATTAAATT-TTTA
1 TTTATTAAATTATTTA
3306851 TTT-TTAAATTATT
1 TTTATTAAATTATT
3306864 ATAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
17 1 0.04
18 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATTAAATTATTTA
Found at i:3306859 original size:14 final size:15
Alignment explanation
Indices: 3306818--3306865 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
3306808 AAAATTAAAT
3306818 TTTATTAAATTATAATTA
1 TTTATTAAA-T-T-ATTA
*
3306836 TTTATTAAATTTTTA
1 TTTATTAAATTATTA
3306851 TTT-TTAAATTATTA
1 TTTATTAAATTATTA
3306865 T
1 T
3306866 AATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.39
15 6 0.21
16 1 0.04
17 1 0.04
18 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTAAATTATTA
Found at i:3307674 original size:28 final size:30
Alignment explanation
Indices: 3307621--3307677 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
3307611 AATTTTATTT
*
3307621 ATATAAATATTAAAAGATAATTAAAATATG
1 ATATAAATATTAAAAGATAATAAAAATATG
*
3307651 ATAT-AATA-TAAAAGTTAATAAAAATAT
1 ATATAAATATTAAAAGATAATAAAAATAT
3307678 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.68
29 4 0.16
30 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
ATATAAATATTAAAAGATAATAAAAATATG
Found at i:3308453 original size:14 final size:15
Alignment explanation
Indices: 3308429--3308466 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3308419 ATTTAAAAAT
3308429 AATTATAAATATTAA
1 AATTATAAATATTAA
*
3308444 AATT-TAAATATTAT
1 AATTATAAATATTAA
*
3308458 ATTTATAAA
1 AATTATAAA
3308467 ATTTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:3308853 original size:16 final size:15
Alignment explanation
Indices: 3308814--3308874 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
3308804 AAAAATTAAA
* *
3308814 AATTTAAATTTAAATT
1 AATTTAAA-ATAATTT
*
3308830 AATCTAAAATAATTT
1 AATTTAAAATAATTT
3308845 GAATTTAAAATAATTT
1 -AATTTAAAATAATTT
* *
3308861 AGTTTAAAAAAATT
1 AATTTAAAATAATT
3308875 CGACCACGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 17 0.45
16 21 0.55
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (15 bp):
AATTTAAAATAATTT
Found at i:3308868 original size:15 final size:16
Alignment explanation
Indices: 3308834--3308874 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3308824 TAAATTAATC
3308834 TAAAATAATTTGAATT
1 TAAAATAATTTGAATT
*
3308850 TAAAATAATTT-AGTT
1 TAAAATAATTTGAATT
*
3308865 TAAAAAAATT
1 TAAAATAATT
3308875 CGACCACGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TAAAATAATTTGAATT
Found at i:3309049 original size:18 final size:18
Alignment explanation
Indices: 3309009--3309051 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3308999 TTATAATAAA
* *
3309009 ATTATTTAAAAAATTGAT
1 ATTATATAAAAAATTAAT
* *
3309027 TTTATATAACAAATTAAT
1 ATTATATAAAAAATTAAT
3309045 ATTATAT
1 ATTATAT
3309052 CATTTTATGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTATATAAAAAATTAAT
Found at i:3309674 original size:15 final size:17
Alignment explanation
Indices: 3309646--3309684 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3309636 TAAATTTGAT
3309646 AAATTTATTAACAATAA
1 AAATTTATTAACAATAA
3309663 AAATTT-TT-ACAATAA
1 AAATTTATTAACAATAA
*
3309678 TAATTTA
1 AAATTTA
3309685 AAATTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTATTAACAATAA
Found at i:3310459 original size:16 final size:16
Alignment explanation
Indices: 3310434--3310483 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
3310424 TTAAAACGAC
*
3310434 TTAAACAATTTAAAAT
1 TTAAAAAATTTAAAAT
3310450 TTAAAAAATTATTAAAA-
1 TTAAAAAA-T-TTAAAAT
3310467 TTAAAATAATTTAAAAT
1 TTAAAA-AATTTAAAAT
3310484 AATTAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 13 0.45
17 8 0.28
18 8 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAATTTAAAAT
Found at i:3310466 original size:18 final size:18
Alignment explanation
Indices: 3310443--3310477 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3310433 CTTAAACAAT
3310443 TTAAAATTTAAAA-AATTA
1 TTAAAA-TTAAAATAATTA
3310461 TTAAAATTAAAATAATT
1 TTAAAATTAAAATAATT
3310478 TAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATTAAAATAATTA
Found at i:3310619 original size:1 final size:1
Alignment explanation
Indices: 3310613--3310648 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
3310603 TCATAATGCT
* *
3310613 AAAAAAAAAAAAAAGAAAAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3310649 GGGTTCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:3310789 original size:3 final size:3
Alignment explanation
Indices: 3310783--3310808 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3310773 GTGGAACCCC
3310783 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3310809 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3311370 original size:2 final size:2
Alignment explanation
Indices: 3311363--3311402 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3311353 TCATAAACAT
3311363 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3311403 ACAAAAAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3311962 original size:12 final size:11
Alignment explanation
Indices: 3311945--3312007 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
3311935 TATGCAGTCC
3311945 AAAAAGAAAAAG
1 AAAAAG-AAAAG
3311957 AAAAAG-AAAG
1 AAAAAGAAAAG
*
3311967 AAAAAGAGAAG
1 AAAAAGAAAAG
3311978 -AAAAGAAACA-
1 AAAAAGAAA-AG
3311988 AGAAAAGAAAAG
1 A-AAAAGAAAAG
3312000 ATAAAAGA
1 A-AAAAGA
3312008 CTGCATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 17 0.40
11 5 0.12
12 21 0.49
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:3311968 original size:10 final size:10
Alignment explanation
Indices: 3311953--3311985 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3311943 CCAAAAAGAA
3311953 AAAGAAAAAG
1 AAAGAAAAAG
3311963 AAAGAAAAAG
1 AAAGAAAAAG
3311973 AGAAG-AAAAG
1 A-AAGAAAAAG
3311983 AAA
1 AAA
3311986 CAAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 17 0.77
11 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:3311996 original size:20 final size:20
Alignment explanation
Indices: 3311944--3311988 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
3311934 ATATGCAGTC
*
3311944 CAAAAAGAAAAAGAAAAAGAAA
1 CAAAAAG-AGAAG-AAAAGAAA
*
3311966 GAAAAAGAGAAGAAAAGAAA
1 CAAAAAGAGAAGAAAAGAAA
3311986 CAA
1 CAA
3311989 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (20 bp):
CAAAAAGAGAAGAAAAGAAA
Found at i:3315658 original size:38 final size:38
Alignment explanation
Indices: 3315607--3315695 Score: 169
Period size: 38 Copynumber: 2.3 Consensus size: 38
3315597 AAAATAAAGT
3315607 TTTGTTTCCCTAAAAATTCTCGTTTACTTATTCTATAA
1 TTTGTTTCCCTAAAAATTCTCGTTTACTTATTCTATAA
*
3315645 TTTGTTTCCCTAAAAATTCTTGTTTACTTATTCTATAA
1 TTTGTTTCCCTAAAAATTCTCGTTTACTTATTCTATAA
3315683 TTTGTTTCCCTAA
1 TTTGTTTCCCTAA
3315696 TAGCCATTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.52
Consensus pattern (38 bp):
TTTGTTTCCCTAAAAATTCTCGTTTACTTATTCTATAA
Found at i:3320190 original size:6 final size:6
Alignment explanation
Indices: 3320179--3320234 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
3320169 AATATAAAAA
3320179 AATTTT AATTTT AATTTT -ATTTT ATTATTTT AATTTT -ATTTT -ATTTAAT
1 AATTTT AATTTT AATTTT AATTTT A--ATTTT AATTTT AATTTT AATTT--T
3320228 AATTTT A
1 AATTTT A
3320235 TTAATTAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 14 0.32
6 19 0.43
7 1 0.02
8 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
AATTTT
Found at i:3320210 original size:19 final size:19
Alignment explanation
Indices: 3320186--3320236 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3320176 AAAAATTTTA
3320186 ATTTTAATTTTATTTTATT
1 ATTTTAATTTTATTTTATT
3320205 ATTTTAATTTTATTTTATT
1 ATTTTAATTTTATTTTATT
**
3320224 -TAATAATTTTATT
1 ATTTTAATTTTATT
3320237 AATTAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTTTATTTTATT
Found at i:3320224 original size:24 final size:25
Alignment explanation
Indices: 3320179--3320234 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
3320169 AATATAAAAA
*
3320179 AATTTTAATTTTAATTTTATTTTAT
1 AATTTTAATTTTAATTTTATTTAAT
*
3320204 TATTTTAATTTT-ATTTTATTTAAT
1 AATTTTAATTTTAATTTTATTTAAT
3320228 AATTTTA
1 AATTTTA
3320235 TTAATTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
AATTTTAATTTTAATTTTATTTAAT
Found at i:3320555 original size:2 final size:2
Alignment explanation
Indices: 3320550--3320584 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3320540 TATTAATAAC
*
3320550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3320585 GTCTACATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3322873 original size:22 final size:22
Alignment explanation
Indices: 3322829--3322873 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3322819 AGTCTTGGAG
* *
3322829 TTAATTAGTTTTTATTTATTTT
1 TTAATTAGTTTTTAATTAATTT
3322851 TTAATT-GTTTTTAAATTAATTT
1 TTAATTAGTTTTT-AATTAATTT
3322873 T
1 T
3322874 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTAATTAGTTTTTAATTAATTT
Found at i:3322883 original size:10 final size:10
Alignment explanation
Indices: 3322837--3322889 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
3322827 AGTTAATTAG
3322837 TTTTTATTTA
1 TTTTTATTTA
* *
3322847 TTTTTTAATTG
1 -TTTTTATTTA
*
3322858 TTTTTAAATTA
1 TTTTT-ATTTA
*
3322869 ATTTTATTTA
1 TTTTTATTTA
3322879 TTTTTATTTA
1 TTTTTATTTA
3322889 T
1 T
3322890 ATTAAATTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:3325175 original size:2 final size:2
Alignment explanation
Indices: 3325168--3325207 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3325158 ACTAAGCATT
3325168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3325208 ATTCTATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3325661 original size:2 final size:2
Alignment explanation
Indices: 3325654--3325682 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3325644 AAAATACTGA
3325654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3325683 ATGATATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3327559 original size:14 final size:14
Alignment explanation
Indices: 3327540--3327580 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3327530 TTACCGAATA
*
3327540 TATATATATATATC
1 TATATATACATATC
*
3327554 TATATATACATGTC
1 TATATATACATATC
*
3327568 TATATGTACATAT
1 TATATATACATAT
3327581 AGCTGCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (14 bp):
TATATATACATATC
Found at i:3345424 original size:2 final size:2
Alignment explanation
Indices: 3345419--3345447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3345409 ACTTGTGTGT
3345419 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3345448 ATGGAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3348699 original size:15 final size:14
Alignment explanation
Indices: 3348677--3348712 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
3348667 ACTTGAATGA
3348677 TTTTTTTTTTCTTT
1 TTTTTTTTTTCTTT
3348691 TTGTTTTTTTTCTTT
1 TT-TTTTTTTTCTTT
3348706 TTTTTTT
1 TTTTTTT
3348713 AATTTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.92
Consensus pattern (14 bp):
TTTTTTTTTTCTTT
Found at i:3355879 original size:118 final size:118
Alignment explanation
Indices: 3355666--3355900 Score: 418
Period size: 118 Copynumber: 2.0 Consensus size: 118
3355656 CGCCAAACTA
* *
3355666 TGAGCAATGATGAAGGTTATTGTCTTTCCTTACCATTTTAATTTAGATTTCCATGAAACTAATTT
1 TGAGAAATGATGAAGGTTATTGCCTTTCCTTACCATTTTAATTTAGATTTCCATGAAACTAATTT
3355731 TTTTGAGCAAAAATACATTCTGATGATTTTTAATCATTTTGATGCAAATATGT
66 TTTTGAGCAAAAATACATTCTGATGATTTTTAATCATTTTGATGCAAATATGT
*
3355784 TGAGAAATGATCG-AGGTTATTGCCTTTCTTTACCATTTTAATTTAGATTTCCATGAAACTAATT
1 TGAGAAATGAT-GAAGGTTATTGCCTTTCCTTACCATTTTAATTTAGATTTCCATGAAACTAATT
*
3355848 TTTTTGAGCAAAAATACATTTTGATGATTTTTAATCATTTTGATGCAAATATG
65 TTTTTGAGCAAAAATACATTCTGATGATTTTTAATCATTTTGATGCAAATATG
3355901 CTGGTATGCA
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 111 0.99
119 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (118 bp):
TGAGAAATGATGAAGGTTATTGCCTTTCCTTACCATTTTAATTTAGATTTCCATGAAACTAATTT
TTTTGAGCAAAAATACATTCTGATGATTTTTAATCATTTTGATGCAAATATGT
Found at i:3357519 original size:34 final size:34
Alignment explanation
Indices: 3357481--3357582 Score: 186
Period size: 34 Copynumber: 3.0 Consensus size: 34
3357471 CTTTGTTAAG
*
3357481 TGTATTTGGTGAGAATGATAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
3357515 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
3357549 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
3357583 GAATATTAGG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:3357581 original size:22 final size:22
Alignment explanation
Indices: 3357549--3357604 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3357539 TGTTAGGTGA
* *
3357549 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATATTAGG
3357571 TGTGTTAGGTGAGAATATTAGG
1 TGTGTTAGGTGAGAATATTAGG
3357593 TGTGTTAGGTGA
1 TGTGTTAGGTGA
3357605 TGTATTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATATTAGG
Found at i:3357582 original size:56 final size:56
Alignment explanation
Indices: 3357522--3357633 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
3357512 TGATGTATTT
* *
3357522 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
3357578 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
3357634 ACATGTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (56 bp):
GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
Found at i:3362345 original size:34 final size:34
Alignment explanation
Indices: 3362307--3362442 Score: 263
Period size: 34 Copynumber: 4.0 Consensus size: 34
3362297 CTTTGTTAAG
3362307 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
3362341 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
3362375 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
3362409 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
3362443 GAATATTAGG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 101 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:3362441 original size:22 final size:22
Alignment explanation
Indices: 3362409--3362464 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3362399 TGTTAGGTGA
* *
3362409 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATATTAGG
3362431 TGTGTTAGGTGAGAATATTAGG
1 TGTGTTAGGTGAGAATATTAGG
3362453 TGTGTTAGGTGA
1 TGTGTTAGGTGA
3362465 TGTATTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATATTAGG
Found at i:3362476 original size:68 final size:66
Alignment explanation
Indices: 3362307--3362493 Score: 241
Period size: 68 Copynumber: 2.9 Consensus size: 66
3362297 CTTTGTTAAG
*
3362307 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTAGGT-AG-ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
3362372 TGA
64 TGA
* *
3362375 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTAGGT-AG-ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
3362440 TGA
64 TGA
3362443 -G-A--A--T--A--TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTATTAGGTAGATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
3362494 ACATGTATAT
Statistics
Matches: 116, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
56 45 0.39
58 1 0.01
62 1 0.01
66 1 0.01
67 1 0.01
68 67 0.58
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (66 bp):
TGTATTAGGTAGATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTG
A
Found at i:3363781 original size:12 final size:12
Alignment explanation
Indices: 3363764--3363788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3363754 GGTTTTACAC
3363764 TTTTTTATATAA
1 TTTTTTATATAA
3363776 TTTTTTATATAA
1 TTTTTTATATAA
3363788 T
1 T
3363789 ATGTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTATATAA
Found at i:3363911 original size:20 final size:20
Alignment explanation
Indices: 3363867--3363917 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3363857 TATTTAATAA
*
3363867 TTATTTACTATTAAAATTAT
1 TTATTTAATATTAAAATTAT
* * *
3363887 ATATTTAATATTTAAATTTT
1 TTATTTAATATTAAAATTAT
3363907 TTATTTTAATA
1 TTA-TTTAATA
3363918 CAATTAGCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTAATATTAAAATTAT
Found at i:3365529 original size:13 final size:13
Alignment explanation
Indices: 3365498--3365535 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3365488 CTATATATTA
*
3365498 AATTAAATT-ATT
1 AATTAATTTAATT
3365510 AATTAATTTAATT
1 AATTAATTTAATT
3365523 AATTAATTTAATT
1 AATTAATTTAATT
3365536 TGATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:3366075 original size:18 final size:18
Alignment explanation
Indices: 3366044--3366098 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
3366034 TTTTGTGAAT
3366044 AAGAAAAGAAAGAAAAGAA
1 AAGAAAAG-AAGAAAAGAA
*
3366063 AAG-AAAGATAGAAGA-AA
1 AAGAAAAGA-AGAAAAGAA
3366080 AAGAAAAGAA-AAAAGAA
1 AAGAAAAGAAGAAAAGAA
3366097 AA
1 AA
3366099 CTTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 3 0.10
17 11 0.35
18 14 0.45
19 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAGAAAAGAAGAAAAGAA
Found at i:3366098 original size:5 final size:5
Alignment explanation
Indices: 3366044--3366091 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
3366034 TTTTGTGAAT
3366044 AAGAA AAG-A AAGAA AAGAA AAG-A AAGATA GAAGAAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGA-A -AAG-AA AAGAA AAGAA
3366090 AA
1 AA
3366092 AAGAAAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 8 0.21
5 21 0.55
6 4 0.11
7 4 0.11
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:3369169 original size:32 final size:32
Alignment explanation
Indices: 3369101--3369171 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
3369091 CTAGTTCGAC
* * ****
3369101 TTTTAGCCTATTTAGAAAAATATAAATTGGGT
1 TTTTAACCTATTTAGAAAAATACAAATTCAAA
3369133 TTTTAACCTATTTAGAAAAATACAAATTCAAA
1 TTTTAACCTATTTAGAAAAATACAAATTCAAA
3369165 TTTTAAC
1 TTTTAAC
3369172 TTGTTGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (32 bp):
TTTTAACCTATTTAGAAAAATACAAATTCAAA
Found at i:3369297 original size:32 final size:32
Alignment explanation
Indices: 3369261--3369321 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3369251 CTAGCTGGGC
*
3369261 TTTTGATTTATTCTG-AAAGACACAAGTTTAAA
1 TTTTGACTTATT-TGAAAAGACACAAGTTTAAA
*
3369293 TTTTGACTTATTTGAAAAGATACAAGTTT
1 TTTTGACTTATTTGAAAAGACACAAGTTT
3369322 GGTTCCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (32 bp):
TTTTGACTTATTTGAAAAGACACAAGTTTAAA
Found at i:3369374 original size:63 final size:63
Alignment explanation
Indices: 3369290--3369509 Score: 223
Period size: 61 Copynumber: 3.5 Consensus size: 63
3369280 ACACAAGTTT
* ** *
3369290 AAATTTTGACTTATTTGAAAAGATACAAGTTTGGTTCCTAACCTATTTAGAAA-ATATAGATTC
1 AAATTTTGGCTTATTCAAAAAGATACAAGTTTGGTT-CTAACCTATTTAGAAAGATATAGGTTC
* * * * * * *
3369353 TATTTTTGGCTTATTCAAAAAGATACAAGTTAGGCTTTTAAGCTATTAAAAAAGATATAGGTTC
1 AAATTTTGGCTTATTCAAAAAGATACAAGTTTGG-TTCTAACCTATTTAGAAAGATATAGGTTC
* * *
3369417 AAATTTTGCCTTGTTCAAAAATATACAAGTTTGG--CTAACCTATTTAGAAAGATATAGGTT-
1 AAATTTTGGCTTATTCAAAAAGATACAAGTTTGGTTCTAACCTATTTAGAAAGATATAGGTTC
* * * *
3369477 AAGCTTTTAGCTTGTTCAGAAAGATACAAGTTT
1 AA-ATTTTGGCTTATTCAAAAAGATACAAGTTT
3369510 AACTCCCCTA
Statistics
Matches: 128, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
60 2 0.02
61 47 0.37
63 40 0.31
64 39 0.30
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (63 bp):
AAATTTTGGCTTATTCAAAAAGATACAAGTTTGGTTCTAACCTATTTAGAAAGATATAGGTTC
Found at i:3369437 original size:64 final size:62
Alignment explanation
Indices: 3369307--3369603 Score: 217
Period size: 61 Copynumber: 4.7 Consensus size: 62
3369297 GACTTATTTG
* * * *
3369307 AAAAGATACAAGTTTGG-TTCCTAACCTATTTAGAAA-ATATAGATTCTATTTTTGGCTTATTCA
1 AAAAGATACAAGTTTGGCTT--TAACCTATTTAGAAAGATATAGGTTCAAATTTT-GCTTGTTCA
* * * *
3369370 AAAAGATACAAGTTAGGCTTTTAAGCTATTAAAAAAGATATAGGTTCAAATTTTGCCTTGTTCA
1 AAAAGATACAAGTTTGGC-TTTAACCTATTTAGAAAGATATAGGTTCAAATTTTG-CTTGTTCA
* *
3369434 AAAATATACAAGTTTGGC--TAACCTATTTAGAAAGATATAGGTT-AAGCTTTTAGCTTGTTCA
1 AAAAGATACAAGTTTGGCTTTAACCTATTTAGAAAGATATAGGTTCAA-ATTTT-GCTTGTTCA
* ** * * * * *
3369495 GAAAGATACAAGTTTAACTCCCCTAACCTATTCAGAAAGATACAGGTTTAATTTTTGAACTTGTT
1 AAAAGATACAAGTTTGGCT---TTAACCTATTTAGAAAGATATAGGTTCAAATTTTG--CTTGTT
*
3369560 TA
61 CA
* * * * * *
3369562 GAAAGAAACAAGTTTGACTCCTAGCCTATTCAGAAAGATATA
1 AAAAGATACAAGTTTGGCT-TTAACCTATTTAGAAAGATATA
3369604 AGTTTAGTTT
Statistics
Matches: 194, Mismatches: 26, Indels: 26
0.79 0.11 0.11
Matches are distributed among these distances:
60 2 0.01
61 48 0.25
62 1 0.01
63 29 0.15
64 37 0.19
65 24 0.12
66 27 0.14
67 26 0.13
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (62 bp):
AAAAGATACAAGTTTGGCTTTAACCTATTTAGAAAGATATAGGTTCAAATTTTGCTTGTTCA
Found at i:3369582 original size:67 final size:66
Alignment explanation
Indices: 3369451--3369675 Score: 199
Period size: 67 Copynumber: 3.4 Consensus size: 66
3369441 ACAAGTTTGG
* * * * * * *
3369451 CTAACCTATTTAGAAAGATATAGG-TTAAGCTTTT-AGCTTGTTCAGAAAGATACAAGTTTAACT
1 CTAACCTATTCAGAAAGATACAGGTTTAA-TTTTTGAACTTGTTTAGAAAGAAACAAGTTTGACT
3369514 CCC
65 -CC
3369517 CTAACCTATTCAGAAAGATACAGGTTTAATTTTTGAACTTGTTTAGAAAGAAACAAGTTTGACT-
1 CTAACCTATTCAGAAAGATACAGGTTTAATTTTTGAACTTGTTTAGAAAGAAACAAGTTTGACTC
3369581 C
66 C
* * * * * * * *
3369582 CTAGCCTATTCAGAAAGATATAAGTTTAGTTTTTTG-ACTTGTTTTGAAA-AATGCAAGTTGGAT
1 CTAACCTATTCAGAAAGATACAGGTTTA-ATTTTTGAACTTGTTTAGAAAGAA-ACAAGTTTGAC
3369645 TCTC
64 TC-C
* * * *
3369649 CTAACTTATTCAAAAAAACACAGGTTT
1 CTAACCTATTCAGAAAGATACAGGTTT
3369676 GGTTTTAACA
Statistics
Matches: 131, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
64 2 0.02
65 47 0.36
66 32 0.24
67 50 0.38
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (66 bp):
CTAACCTATTCAGAAAGATACAGGTTTAATTTTTGAACTTGTTTAGAAAGAAACAAGTTTGACTC
C
Found at i:3369615 original size:65 final size:66
Alignment explanation
Indices: 3369451--3369630 Score: 213
Period size: 65 Copynumber: 2.7 Consensus size: 66
3369441 ACAAGTTTGG
* * * * * *
3369451 CTAACCTATTTAGAAAGATATAGGTTAAGCTTTT-AGCTTGTTCAGAAAGATACAAGTTTAACTC
1 CTAACCTATTCAGAAAGATATAGGTTTAGTTTTTGAACTTGTTTAGAAAGAAACAAGTTTAACT-
3369515 CC
65 CC
* * *
3369517 CTAACCTATTCAGAAAGATACAGGTTTAATTTTTGAACTTGTTTAGAAAGAAACAAGTTTGACT-
1 CTAACCTATTCAGAAAGATATAGGTTTAGTTTTTGAACTTGTTTAGAAAGAAACAAGTTTAACTC
3369581 C
66 C
* * *
3369582 CTAGCCTATTCAGAAAGATATAAGTTTAGTTTTTTG-ACTTGTTTTGAAA
1 CTAACCTATTCAGAAAGATATAGGTTTAG-TTTTTGAACTTGTTTAGAAA
3369631 AATGCAAGTT
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 38 0.39
66 35 0.36
67 25 0.26
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (66 bp):
CTAACCTATTCAGAAAGATATAGGTTTAGTTTTTGAACTTGTTTAGAAAGAAACAAGTTTAACTC
C
Found at i:3378187 original size:17 final size:17
Alignment explanation
Indices: 3378161--3378200 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3378151 ATTAAGGATT
3378161 ATGATAATAATTATGAA
1 ATGATAATAATTATGAA
* *
3378178 ATGATTATAATTATGAT
1 ATGATAATAATTATGAA
3378195 ATGATA
1 ATGATA
3378201 GACACTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (17 bp):
ATGATAATAATTATGAA
Found at i:3379474 original size:14 final size:14
Alignment explanation
Indices: 3379455--3379482 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3379445 TGTATTTTTT
3379455 AAAATATATATATA
1 AAAATATATATATA
3379469 AAAATATATATATA
1 AAAATATATATATA
3379483 TTTTTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:3380363 original size:2 final size:2
Alignment explanation
Indices: 3380356--3380382 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3380346 ATACGTGTAC
3380356 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3380383 AGCAGTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3380587 original size:2 final size:2
Alignment explanation
Indices: 3380580--3380609 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3380570 ATATTTGAAA
3380580 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
3380610 TCGGTCAATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3383368 original size:3 final size:3
Alignment explanation
Indices: 3383354--3383410 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
3383344 GAATTCTAAA
*
3383354 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3383402 TAT TAT TAT
1 TAT TAT TAT
3383411 GTGAAACAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3388456 original size:25 final size:26
Alignment explanation
Indices: 3388409--3388457 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3388399 TAACTCTTAA
* **
3388409 TTTATATTTAAATATTTTTTTAATCT
1 TTTATATTTAAATAATTCATTAATCT
3388435 TTTATATTT-AATAATTCATTAAT
1 TTTATATTTAAATAATTCATTAAT
3388458 ATAAACCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATATTTAAATAATTCATTAATCT
Found at i:3389587 original size:79 final size:79
Alignment explanation
Indices: 3389488--3389633 Score: 213
Period size: 79 Copynumber: 1.8 Consensus size: 79
3389478 ATAACAACGA
* * *
3389488 GGCTGGAGTACCCATGATTATGGAAAATCGATGTTCTGGAAATAAAATTGGGATTGGAGTATCCC
1 GGCTGGAGTACCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCCC
3389553 CTTGGAAATAACAG
66 CTTGGAAATAACAG
* * * *
3389567 GGCTGGAGTATCCC-TAATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAGTATCC
1 GGCTGGAGTA-CCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCC
3389631 CCT
65 CCT
3389634 CAAAAATAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 56 0.95
80 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
GGCTGGAGTACCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCCC
CTTGGAAATAACAG
Done.