Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 14 of 24
Found at i:1879335 original size:15 final size:15
Alignment explanation
Indices: 1879317--1879353 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1879307 AAAAAATTTT
1879317 ATTTTAAATAATAAA
1 ATTTTAAATAATAAA
*
1879332 ATTTAAAATAATAAA
1 ATTTTAAATAATAAA
1879347 ACTTTTA
1 A-TTTTA
1879354 GGACTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:1882367 original size:21 final size:21
Alignment explanation
Indices: 1882341--1882383 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1882331 TTTTAGATTT
1882341 TAGCTTAAATCGTTAATATTA
1 TAGCTTAAATCGTTAATATTA
1882362 TAGCTTAAATCGTTAATATTA
1 TAGCTTAAATCGTTAATATTA
1882383 T
1 T
1882384 GTTGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TAGCTTAAATCGTTAATATTA
Found at i:1884360 original size:13 final size:13
Alignment explanation
Indices: 1884342--1884368 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1884332 TAATAAATCA
1884342 TTTTGGTTCATAG
1 TTTTGGTTCATAG
1884355 TTTTGGTTCATAG
1 TTTTGGTTCATAG
1884368 T
1 T
1884369 GTTTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TTTTGGTTCATAG
Found at i:1884580 original size:18 final size:18
Alignment explanation
Indices: 1884557--1884594 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1884547 GCTTTGAGTA
1884557 TTATTTATTATTTATTAT
1 TTATTTATTATTTATTAT
* *
1884575 TTATTTTTTATTTTTTAT
1 TTATTTATTATTTATTAT
1884593 TT
1 TT
1884595 TAGATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTTATTATTTATTAT
Found at i:1884595 original size:7 final size:7
Alignment explanation
Indices: 1884555--1884593 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1884545 TTGCTTTGAG
1884555 TATTATT
1 TATTATT
1884562 TATTATT
1 TATTATT
1884569 TATTATT
1 TATTATT
*
1884576 TATTTTT
1 TATTATT
*
1884583 TATTTTT
1 TATTATT
1884590 TATT
1 TATT
1884594 TTAGATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TATTATT
Found at i:1885913 original size:57 final size:57
Alignment explanation
Indices: 1885841--1885954 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 57
1885831 AAATTATAAA
* * **
1885841 CAATACTTTTTCGAAAA-GAGAATTTCGTATACTTTTTGAGAAAAATATTTAAAAAAT
1 CAATACCTCTTCGAAAAGGA-AATTTCGTATACTTTTCAAGAAAAATATTTAAAAAAT
* *
1885898 CAATACCTCTTCGAAAAGGAAATTTTGTGTACTTTTCAAGAAAAATATTTAAAAAAT
1 CAATACCTCTTCGAAAAGGAAATTTCGTATACTTTTCAAGAAAAATATTTAAAAAAT
1885955 ATTAAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 48 0.96
58 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (57 bp):
CAATACCTCTTCGAAAAGGAAATTTCGTATACTTTTCAAGAAAAATATTTAAAAAAT
Found at i:1886541 original size:4 final size:4
Alignment explanation
Indices: 1886532--1886565 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
1886522 TTTTATTTTT
1886532 TTAA TTAA TTAA TTAA TTAAA CTTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TT-AA -TTAA TTAA TTAA
1886566 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.79
5 4 0.14
6 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:1888672 original size:2 final size:2
Alignment explanation
Indices: 1888665--1888697 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1888655 AGATTTCCAC
1888665 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 T
1888698 GATACTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1889294 original size:30 final size:30
Alignment explanation
Indices: 1889259--1889318 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1889249 TAAATTCTAG
1889259 TAAGTTAAAAACTTTAAGACGGGGCAAAAC
1 TAAGTTAAAAACTTTAAGACGGGGCAAAAC
*
1889289 TAAGTTGAAAACTTTAAGACGGGGCAAAAC
1 TAAGTTAAAAACTTTAAGACGGGGCAAAAC
1889319 GAAGGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (30 bp):
TAAGTTAAAAACTTTAAGACGGGGCAAAAC
Found at i:1900407 original size:10 final size:10
Alignment explanation
Indices: 1900392--1900455 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
1900382 TATCGTATTT
1900392 ATATATTTTA
1 ATATATTTTA
*
1900402 ATATATTATA
1 ATATATTTTA
1900412 AT-TATATTTA
1 ATATAT-TTTA
*
1900422 AAATATTTT-
1 ATATATTTTA
*
1900431 ATAT-TTAT-
1 ATATATTTTA
*
1900439 ATAAATTTTA
1 ATATATTTTA
1900449 ATATATT
1 ATATATT
1900456 ATAAATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 6 0.14
9 9 0.21
10 24 0.57
11 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATATTTTA
Found at i:1900432 original size:22 final size:21
Alignment explanation
Indices: 1900393--1900440 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1900383 ATCGTATTTA
*
1900393 TATATTTTAATATATTATAAT
1 TATATTTAAATATATTATAAT
* *
1900414 TATATTTAAAATATTTTATATT
1 TATATTT-AAATATATTATAAT
1900436 TATAT
1 TATAT
1900441 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTAAATATATTATAAT
Found at i:1900434 original size:16 final size:17
Alignment explanation
Indices: 1900413--1900467 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
1900403 TATATTATAA
1900413 TTATATTTA-AAATATT
1 TTATATTTATAAATATT
1900429 TTATATTTATATAA-ATT
1 TTATATTTATA-AATATT
1900446 TTAATATATTATAAAT-TT
1 TT-ATAT-TTATAAATATT
1900464 TTAT
1 TTAT
1900468 TATGTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.26
17 8 0.24
18 12 0.35
19 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTATAAATATT
Found at i:1900448 original size:17 final size:17
Alignment explanation
Indices: 1900413--1900468 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1900403 TATATTATAA
1900413 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
1900429 TTATATTTATATAAATT
1 TTATATTTATATAAATT
*
1900446 TTA-ATATATTATAAATT
1 TTATATTTA-TATAAATT
1900463 TT-TATT
1 TTATATT
1900469 ATGTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:1900482 original size:32 final size:35
Alignment explanation
Indices: 1900426--1900491 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 35
1900416 TATTTAAAAT
*
1900426 ATTTTATATTTATATAAATTTTAATATA-TTATAA
1 ATTTTATATTTATATAAAATTTAATATAGTTATAA
*
1900460 ATTTT-TA-TTATGTAAAATTTAATATAGTTATA
1 ATTTTATATTTATATAAAATTTAATATAGTTATA
1900492 TCATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 17 0.59
33 7 0.24
34 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
ATTTTATATTTATATAAAATTTAATATAGTTATAA
Found at i:1900526 original size:13 final size:13
Alignment explanation
Indices: 1900510--1900547 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1900500 TTATATTACT
1900510 TTTTAAATTTATA
1 TTTTAAATTTATA
*
1900523 TTTTAAATTTTTA
1 TTTTAAATTTATA
*
1900536 TATTAAATTTAT
1 TTTTAAATTTAT
1900548 CTAATATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAAATTTATA
Found at i:1900700 original size:18 final size:18
Alignment explanation
Indices: 1900640--1900700 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
1900630 ATAGTTAAAT
1900640 TTTTAAAATAA-ATAGATAA
1 TTTTAAAA-AATATA-ATAA
1900659 TTTTAAAAAATTATAA-AA
1 TTTTAAAAAA-TATAATAA
* *
1900677 TATTAAAAAATATAATTA
1 TTTTAAAAAATATAATAA
1900695 TTTTAA
1 TTTTAA
1900701 TTTAATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.14
18 19 0.53
19 9 0.25
20 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTTAAAAAATATAATAA
Found at i:1901377 original size:12 final size:11
Alignment explanation
Indices: 1901362--1901402 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1901352 GTAAATAAAT
1901362 TTATTTACAAAA
1 TTATTTA-AAAA
*
1901374 TTATTTAAAAT
1 TTATTTAAAAA
*
1901385 TTATTCAAAAA
1 TTATTTAAAAA
1901396 TTATTTA
1 TTATTTA
1901403 CTATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (11 bp):
TTATTTAAAAA
Found at i:1901382 original size:22 final size:21
Alignment explanation
Indices: 1901357--1901402 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1901347 TATTTGTAAA
*
1901357 TAAATTTATTTACAAAATTATT
1 TAAATTTATTCA-AAAATTATT
1901379 TAAAATTTATTCAAAAATTATT
1 T-AAATTTATTCAAAAATTATT
1901401 TA
1 TA
1901403 CTATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.50
23 10 0.45
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTATTCAAAAATTATT
Found at i:1901770 original size:15 final size:15
Alignment explanation
Indices: 1901749--1901789 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1901739 AATAAAAATA
*
1901749 TATTTATTTA-AGTT
1 TATTTATTTATAATT
1901763 TGATTTATTTATAATT
1 T-ATTTATTTATAATT
1901779 TATTTATTTAT
1 TATTTATTTAT
1901790 TTTTTTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 19 0.79
16 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TATTTATTTATAATT
Found at i:1902074 original size:23 final size:23
Alignment explanation
Indices: 1902013--1902075 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
1902003 AATACTAGTT
1902013 AAATTTACTCACTTTTTATTAGAAA
1 AAATTT-C-CACTTTTTATTAGAAA
* *
1902038 AAACTATCTA-TTTTTATATA-AAA
1 AAA-TTTCCACTTTTTAT-TAGAAA
1902061 AAATTTCCACTTTTT
1 AAATTTCCACTTTTT
1902076 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.13
23 18 0.58
24 3 0.10
25 4 0.13
26 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTCCACTTTTTATTAGAAA
Found at i:1902814 original size:16 final size:17
Alignment explanation
Indices: 1902795--1902827 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1902785 TAATGTTAAG
1902795 TTTAA-TTAAATTAAAT
1 TTTAATTTAAATTAAAT
*
1902811 TTTAATTTAATTTAAAT
1 TTTAATTTAAATTAAAT
1902828 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATTAAAT
Found at i:1902825 original size:22 final size:22
Alignment explanation
Indices: 1902790--1902832 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1902780 TCTGTTAATG
*
1902790 TTAAGTTTAATTAAATTAAATT
1 TTAAGTTTAATTAAATAAAATT
1902812 TTAA-TTTAATTTAAATAAAAT
1 TTAAGTTTAA-TTAAATAAAAT
1902833 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAAGTTTAATTAAATAAAATT
Found at i:1902891 original size:27 final size:25
Alignment explanation
Indices: 1902852--1902920 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 25
1902842 TGATAATATA
1902852 ATTTTAAATTTTAAAAAAATTATCTT
1 ATTTTAAATTTTAAAAAAATTAT-TT
*
1902878 ATTTTAAAATTTTAAAAATATTATTT
1 ATTTT-AAATTTTAAAAAAATTATTT
1902904 AGTTTTTAAATTTTAAA
1 A--TTTTAAATTTTAAA
1902921 TCAGGATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 8 0.21
27 27 0.69
28 4 0.10
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTTTAAATTTTAAAAAAATTATTT
Found at i:1903915 original size:18 final size:19
Alignment explanation
Indices: 1903889--1903931 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1903879 TTGTATGTTT
*
1903889 ATATCTTTTAAATTT-TTA
1 ATATATTTTAAATTTATTA
* *
1903907 ATATATTTTATATTTATTT
1 ATATATTTTAAATTTATTA
1903926 ATATAT
1 ATATAT
1903932 ATTATTGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATTTTAAATTTATTA
Found at i:1907415 original size:26 final size:26
Alignment explanation
Indices: 1907358--1907426 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
1907348 TTTAATAAGA
* *
1907358 TAGTTTTAAATTTTGAAAAGTTATCT
1 TAGTTTTAAATTTTAAAAAATTATCT
*
1907384 TA-TTTTGAATTTTAAAAATATTAT-T
1 TAGTTTTAAATTTTAAAAA-ATTATCT
1907409 TAGTTTTTAAATTTTAAA
1 TAG-TTTTAAATTTTAAA
1907427 TTAAGATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 17 0.47
26 6 0.17
27 13 0.36
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (26 bp):
TAGTTTTAAATTTTAAAAAATTATCT
Found at i:1907999 original size:20 final size:19
Alignment explanation
Indices: 1907976--1908024 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1907966 GTTTTATTGA
**
1907976 TTTTATTTTGTTTTTAAAAT
1 TTTTATTTTAATTTT-AAAT
*
1907996 TTTTAATTTTAATTTTAATT
1 TTTT-ATTTTAATTTTAAAT
1908016 TTTTATTTT
1 TTTTATTTT
1908025 TAACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTTAATTTTAAAT
Found at i:1908135 original size:3 final size:3
Alignment explanation
Indices: 1908127--1908167 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1908117 TTACACAATC
1908127 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1908168 TATTATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1908172 original size:3 final size:3
Alignment explanation
Indices: 1908166--1908204 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1908156 AATAATAATA
1908166 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1908205 TTTAACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1909118 original size:27 final size:27
Alignment explanation
Indices: 1909088--1909143 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1909078 TAATTAAAAT
1909088 ATGATAT-AACATAAAAATAATATGTAA
1 ATGATATGAACATAAAAAT-ATATGTAA
* * *
1909115 ATGATATGAATATATAAATATATTTAA
1 ATGATATGAACATAAAAATATATGTAA
1909142 AT
1 AT
1909144 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (27 bp):
ATGATATGAACATAAAAATATATGTAA
Found at i:1910018 original size:24 final size:24
Alignment explanation
Indices: 1909991--1910067 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
1909981 TTTAAATATA
1909991 ATTTTAATTTTAATTAATATAAAT
1 ATTTTAATTTTAATTAATATAAAT
* *
1910015 A-TTTATTTTTAATATAA-ATATAT
1 ATTTTAATTTTAAT-TAATATAAAT
* * *
1910038 TTTTTATTTTTAATAAATAT-AAT
1 ATTTTAATTTTAATTAATATAAAT
1910061 -TTTTAAT
1 ATTTTAAT
1910068 ATTTTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 6 0.14
23 20 0.45
24 18 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTAATTTTAATTAATATAAAT
Found at i:1910038 original size:17 final size:18
Alignment explanation
Indices: 1910004--1910041 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1909994 TTAATTTTAA
1910004 TTAATATAAATATTTATTT
1 TTAATATAAATA-TTATTT
1910023 TTAATATAAATA-TATTT
1 TTAATATAAATATTATTT
1910040 TT
1 TT
1910042 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATATAAATATTATTT
Found at i:1910043 original size:41 final size:40
Alignment explanation
Indices: 1909974--1910069 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
1909964 ATATTTGTTA
* *
1909974 ATTTATTTTTAAATATAATTTTAATTTTAATTAAT-ATAAAT
1 ATTTATTTTT-AATATAAATATAATTTT-ATTAATAATAAAT
* **
1910015 ATTTATTTTTAATATAAATATATTTTTTATTTTTAATAAAT
1 ATTTATTTTTAATATAAATATA-ATTTTATTAATAATAAAT
*
1910056 A-TAATTTTTAATAT
1 ATTTATTTTTAATAT
1910070 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 26 0.55
41 21 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (40 bp):
ATTTATTTTTAATATAAATATAATTTTATTAATAATAAAT
Found at i:1910064 original size:22 final size:22
Alignment explanation
Indices: 1909983--1910065 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
1909973 AATTTATTTT
*
1909983 TAAATATAA-TTTTAATTTTAA
1 TAAATATAATTTTTATTTTTAA
* *
1910004 TTAATATAAATATTTATTTTTAATA
1 TAAATAT-AATTTTTATTTTT-A-A
*
1910029 TAAATATATTTTTTATTTTTAA
1 TAAATATAATTTTTATTTTTAA
1910051 TAAATATAATTTTTA
1 TAAATATAATTTTTA
1910066 ATATTTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.12
22 17 0.33
23 9 0.18
24 12 0.24
25 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAAATATAATTTTTATTTTTAA
Found at i:1910078 original size:16 final size:16
Alignment explanation
Indices: 1910034--1910082 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
1910024 TAATATAAAT
1910034 ATATTTTTTATTTTTA
1 ATATTTTTTATTTTTA
** * *
1910050 ATAAATATAATTTTTA
1 ATATTTTTTATTTTTA
1910066 ATATTTTTTATTTTTA
1 ATATTTTTTATTTTTA
1910082 A
1 A
1910083 ATATATTTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTTTTATTTTTA
Found at i:1910118 original size:29 final size:28
Alignment explanation
Indices: 1910077--1910206 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 28
1910067 TATTTTTTAT
* * *
1910077 TTTTAAATATATTTGACATA-AAATATAT
1 TTTTAATTATATTTTA-ATATAAATATAA
*
1910105 TTTTAATTTATATTTTATTATAAATATAA
1 TTTTAA-TTATATTTTAATATAAATATAA
* *
1910134 TTTTAATAATTTTTTAATATAAATATAAA
1 TTTTAATTATATTTTAATATAAATAT-AA
1910163 TTTTAATTAT-TATTTAACT-TAAATATAA
1 TTTTAATTATAT-TTTAA-TATAAATATAA
*
1910191 TTTTATTTATATTTTA
1 TTTTAATTATATTTTA
1910207 TGATTTAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
28 41 0.47
29 45 0.52
30 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (28 bp):
TTTTAATTATATTTTAATATAAATATAA
Found at i:1910138 original size:57 final size:57
Alignment explanation
Indices: 1910077--1910204 Score: 129
Period size: 57 Copynumber: 2.2 Consensus size: 57
1910067 TATTTTTTAT
* * *
1910077 TTTTAAATATATTTGACATA-AAATAT-ATTTTTAATT-TATATTTTATTATAAATATAA
1 TTTTAAATATATTTGA-ATATAAATATAAATTTTAATTAT-TATTTAACT-TAAATATAA
* *
1910134 TTTT-AATAATTTTTTAATATAAATATAAATTTTAATTATTATTTAACTTAAATATAA
1 TTTTAAAT-ATATTTGAATATAAATATAAATTTTAATTATTATTTAACTTAAATATAA
**
1910191 TTTTATTTATATTT
1 TTTTAAATATATTT
1910205 TATGATTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
56 6 0.10
57 34 0.59
58 17 0.29
59 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (57 bp):
TTTTAAATATATTTGAATATAAATATAAATTTTAATTATTATTTAACTTAAATATAA
Found at i:1910213 original size:35 final size:35
Alignment explanation
Indices: 1910169--1910297 Score: 138
Period size: 35 Copynumber: 3.6 Consensus size: 35
1910159 TAAATTTTAA
1910169 TTATTATTTAACT-TAAATATAATTTTATTTATATT
1 TTATTATTTAA-TATAAATATAATTTTATTTATATT
* * * * *
1910204 TTATGATTTAATATTATTATAATTTTAATAAT-TT
1 TTATTATTTAATATAAATATAATTTTATTTATATT
*
1910238 TTAATTACTATTTAATA-AAATATTATTTTATTTATATT
1 TT-A-T--TATTTAATATAAATATAATTTTATTTATATT
1910276 TTATTATTTAATATAAATATAA
1 TTATTATTTAATATAAATATAA
1910298 ATATAATTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
34 14 0.19
35 33 0.44
36 2 0.03
37 14 0.19
38 12 0.16
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (35 bp):
TTATTATTTAATATAAATATAATTTTATTTATATT
Found at i:1910297 original size:72 final size:73
Alignment explanation
Indices: 1910158--1910297 Score: 210
Period size: 72 Copynumber: 1.9 Consensus size: 73
1910148 TAATATAAAT
* * * *
1910158 ATAAATTTTAATTATTATTTAACTTAAATATAATTTTATTTATATTTTATGATTTAATATTATTA
1 ATAAATTTTAATTACTATTTAACTAAAATATAATTTTATTTATATTTTATGATTTAATATAAATA
1910223 TAATTTTA
66 TAATTTTA
* * *
1910231 ATAATTTTTAATTACTATTTAA-TAAAATATTATTTTATTTATATTTTATTATTTAATATAAATA
1 ATAAATTTTAATTACTATTTAACTAAAATATAATTTTATTTATATTTTATGATTTAATATAAATA
1910295 TAA
66 TAA
1910298 ATATAATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 40 0.67
73 20 0.33
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (73 bp):
ATAAATTTTAATTACTATTTAACTAAAATATAATTTTATTTATATTTTATGATTTAATATAAATA
TAATTTTA
Found at i:1910346 original size:14 final size:16
Alignment explanation
Indices: 1910312--1910344 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1910302 AATTTAATTA
*
1910312 TTTATTATATATATTT
1 TTTAATATATATATTT
1910328 TTTAATATA-ATATTT
1 TTTAATATATATATTT
1910343 TT
1 TT
1910345 AACGATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAATATATATATTT
Found at i:1912567 original size:1 final size:1
Alignment explanation
Indices: 1912563--1912593 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1912553 GGATTATTAA
1912563 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1912594 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1918864 original size:17 final size:16
Alignment explanation
Indices: 1918826--1918866 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1918816 ACTAAATTTT
1918826 TAAATTATT-ATTATAA
1 TAAATT-TTAATTATAA
1918842 -AAATTTTAATTATAAA
1 TAAATTTTAATTAT-AA
1918858 TAAATTTTA
1 TAAATTTTA
1918867 TTGAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 10 0.45
16 2 0.09
17 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTTAATTATAA
Found at i:1919747 original size:21 final size:20
Alignment explanation
Indices: 1919714--1919760 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1919704 CAATATATAG
1919714 TTTTTTAAATTTTTCTATT-
1 TTTTTTAAATTTTTCTATTA
*
1919733 TTTTTATATAATTTTTTTATTA
1 TTTTT-TA-AATTTTTCTATTA
1919755 TTTTTT
1 TTTTTT
1919761 TCAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 12 0.50
22 5 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTAAATTTTTCTATTA
Found at i:1919760 original size:11 final size:12
Alignment explanation
Indices: 1919729--1919761 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1919719 TAAATTTTTC
1919729 TATTTTTTTATA
1 TATTTTTTTATA
1919741 TAATTTTTTTAT-
1 T-ATTTTTTTATA
1919753 TATTTTTTT
1 TATTTTTTT
1919762 CAATTATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 2 0.10
13 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATTTTTTTATA
Found at i:1919766 original size:21 final size:19
Alignment explanation
Indices: 1919714--1919766 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1919704 CAATATATAG
*
1919714 TTTTTTAAATTTTTCTATT
1 TTTTTTTAATTTTTCTATT
*
1919733 TTTTTATATAATTTTTTTATT
1 TTTTT-T-TAATTTTTCTATT
1919754 ATTTTTTTCAATT
1 -TTTTTTT-AATT
1919767 ATATCGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 5 0.18
20 2 0.07
21 16 0.57
22 5 0.18
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTAATTTTTCTATT
Found at i:1920076 original size:4 final size:4
Alignment explanation
Indices: 1920067--1920093 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1920057 GTAGTCCATA
1920067 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1920094 GCTATGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1920360 original size:14 final size:16
Alignment explanation
Indices: 1920332--1920383 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1920322 GTATTCTATA
1920332 TATATAAAATAAAATT
1 TATATAAAATAAAATT
*
1920348 TATAT-AAATAAATTAT
1 TATATAAAATAAAAT-T
* *
1920364 TA-ATATATTAAAATT
1 TATATAAAATAAAATT
1920379 TATAT
1 TATAT
1920384 TATTATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATATAAAATAAAATT
Found at i:1920475 original size:27 final size:29
Alignment explanation
Indices: 1920409--1920477 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
1920399 TTAATATAAT
1920409 TATTATATATAAAAATAAAAAATTTTATTTA
1 TATTAT-TATAAAAATAAAAAATTTTA-TTA
* *
1920440 TATTATTATAAAATTAAATAATTTTA-TA
1 TATTATTATAAAAATAAAAAATTTTATTA
1920468 TATT-TTATAA
1 TATTATTATAA
1920478 TTTTTATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 6 0.17
28 6 0.17
30 18 0.50
31 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTATTATAAAAATAAAAAATTTTATTA
Found at i:1920614 original size:17 final size:17
Alignment explanation
Indices: 1920569--1920616 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1920559 TTTAAATTAA
1920569 AATATTTAAATATTTATT
1 AATA-TTAAATATTTATT
*
1920587 AATATAAAAATATTT-TT
1 AATAT-TAAATATTTATT
1920604 AATCATTAAATAT
1 AAT-ATTAAATAT
1920617 ATATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTAAATATTTATT
Found at i:1920625 original size:29 final size:28
Alignment explanation
Indices: 1920588--1920654 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1920578 ATATTTATTA
1920588 ATATAAAAAT-AT-TTTTAATCATTAAATAT
1 ATATAAAAATAATATTTTAA--ATT-AATAT
1920617 ATATAAAAAATAATATTTTAAATTAATAT
1 ATAT-AAAAATAATATTTTAAATTAATAT
1920646 A-ATAAAAAT
1 ATATAAAAAT
1920655 TAATTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 10 0.29
30 9 0.26
31 2 0.06
32 6 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAAAATAATATTTTAAATTAATAT
Found at i:1920651 original size:28 final size:29
Alignment explanation
Indices: 1920569--1920658 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 29
1920559 TTTAAATTAA
* *
1920569 AATATTTAAATATTTAT-TAATATAAAAAT
1 AATATTTTAATATTAATATAATA-AAAAAT
1920598 -AT-TTTTAATCATTAAATATATATAAAAAAT
1 AATATTTTAAT-ATT-AATATA-ATAAAAAAT
*
1920628 AATATTTTAA-ATTAATATAATAAAAATT
1 AATATTTTAATATTAATATAATAAAAAAT
1920656 AAT
1 AAT
1920659 TTAAAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
27 6 0.12
28 16 0.31
29 8 0.15
30 11 0.21
31 5 0.10
32 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
AATATTTTAATATTAATATAATAAAAAAT
Found at i:1921333 original size:21 final size:22
Alignment explanation
Indices: 1921309--1921350 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1921299 ATGATAATTT
1921309 ATATAATTAATT-TTTAAAAAA
1 ATATAATTAATTATTTAAAAAA
*
1921330 ATATATTTAATTAATTTAAAA
1 ATATAATTAATT-ATTTAAAA
1921351 TTCAGATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTAATTATTTAAAAAA
Found at i:1922007 original size:35 final size:36
Alignment explanation
Indices: 1921940--1922009 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
1921930 AATTAATTTT
* **
1921940 AAAATAATTTATAAATTTTATAATTTTTATTTATAAA
1 AAAATAATTTATAAA-TTTATAAATTAAATTTATAAA
*
1921977 AAAATTATTTATAAA-TTATAAATTAAATTTATA
1 AAAATAATTTATAAATTTATAAATTAAATTTATA
1922010 TACTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.52
37 14 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATAATTTATAAATTTATAAATTAAATTTATAAA
Found at i:1922523 original size:14 final size:14
Alignment explanation
Indices: 1922506--1922582 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
1922496 AATAAGTGAC
*
1922506 GATAATTAATATAT
1 GATAGTTAATATAT
1922520 GATAGTTAATATAT
1 GATAGTTAATATAT
1922534 GATAGTTAA-AT-T
1 GATAGTTAATATAT
* * *
1922546 AAT-TTTAAAAATAT
1 GATAGTT-AATATAT
* *
1922560 TATAATTAATATAT
1 GATAGTTAATATAT
1922574 GATAGTTAA
1 GATAGTTAA
1922583 ATTTTTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 4 0.08
14 38 0.75
15 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
GATAGTTAATATAT
Found at i:1922574 original size:40 final size:38
Alignment explanation
Indices: 1922516--1922593 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
1922506 GATAATTAAT
*
1922516 ATATGATAGTTAATATATGATAGTTAAATTAATTTTAAAA
1 ATATGATAATTAATATATGATAGTTAAATT--TTTTAAAA
*
1922556 ATATTATAATTAATATATGATAGTTAAATTTTTTAAAA
1 ATATGATAATTAATATATGATAGTTAAATTTTTTAAAA
1922594 TTAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 8 0.22
40 28 0.78
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (38 bp):
ATATGATAATTAATATATGATAGTTAAATTTTTTAAAA
Found at i:1922714 original size:11 final size:11
Alignment explanation
Indices: 1922698--1922726 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1922688 TTAAAATATA
1922698 TATTTTTAAAG
1 TATTTTTAAAG
1922709 TATTTTT-AAG
1 TATTTTTAAAG
1922719 TATTTTTA
1 TATTTTTA
1922727 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAG
Found at i:1922797 original size:22 final size:21
Alignment explanation
Indices: 1922764--1922884 Score: 89
Period size: 22 Copynumber: 5.3 Consensus size: 21
1922754 TATATTATAA
1922764 AAATAAAAAATTAATTAAAATTT
1 AAAT-AAAAATTAATT-AAATTT
*
1922787 AAATAAAAATTAAATTACATTT
1 AAATAAAAATT-AATTAAATTT
** * * *
1922809 AAATAATTATGATTTTAATTTAT
1 AAATAAAAATTA-ATTAAATT-T
*
1922832 AAAAAATTTAAATTAATTAAGATTT
1 AAATAA---AAATTAATTAA-ATTT
1922857 AAATAAAAATTAAATTAAATTT
1 AAATAAAAATT-AATTAAATTT
1922879 AAATAA
1 AAATAA
1922885 TTATGGTTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.01
22 40 0.53
23 20 0.26
25 10 0.13
26 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATAAAAATTAATTAAATTT
Found at i:1922909 original size:37 final size:35
Alignment explanation
Indices: 1922798--1922921 Score: 96
Period size: 37 Copynumber: 3.5 Consensus size: 35
1922788 AATAAAAATT
*
1922798 AAATTACATTTAAATAATTATGATTTTAATTTAT--
1 AAATTAAATTTAAATAATTATG-TTTTAATTTATAA
* * * * *
1922832 AAA--AAATTTAAATTAATTAAGATTTAAATAAAAA
1 AAATTAAATTTAAA-TAATTATGTTTTAATTTATAA
1922866 TTAAATTAAATTTAAATAATTATGGTTTTTAATTTATAA
1 --AAATTAAATTTAAATAATTAT-G-TTTTAATTTATAA
1922905 AAATTTAAA-TTAAATAA
1 AAA-TTAAATTTAAATAA
1922922 AATTTAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
32 15 0.22
33 7 0.10
34 3 0.04
36 3 0.04
37 17 0.25
38 15 0.22
39 9 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (35 bp):
AAATTAAATTTAAATAATTATGTTTTAATTTATAA
Found at i:1922945 original size:27 final size:27
Alignment explanation
Indices: 1922896--1922952 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1922886 TATGGTTTTT
*
1922896 AATTTATAAAAATTTAAATTAAAT-AA
1 AATTTATAAAAATTTAAACTAAATCAA
1922922 AATTTAATAAAAA-TTAAACCTAAATCAA
1 AATTT-ATAAAAATTTAAA-CTAAATCAA
1922950 AAT
1 AAT
1922953 CCAATCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 10 0.37
27 12 0.44
28 5 0.19
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (27 bp):
AATTTATAAAAATTTAAACTAAATCAA
Found at i:1922946 original size:70 final size:70
Alignment explanation
Indices: 1922771--1922939 Score: 279
Period size: 70 Copynumber: 2.4 Consensus size: 70
1922761 TAAAAATAAA
*
1922771 AAATTAATTAAAATTTAAATAAAAATTAAATTACATTTAAATAATTATGATTTTAATTTATAAAA
1 AAATTAATTAAAATTTAAATAAAAATTAAATTAAATTTAAATAATTATGATTTTAATTTATAAAA
1922836 AATTT
66 AATTT
* *
1922841 AAATTAATTAAGATTTAAATAAAAATTAAATTAAATTTAAATAATTATGGTTTTTAATTTAT-AA
1 AAATTAATTAAAATTTAAATAAAAATTAAATTAAATTTAAATAATTAT-GATTTTAATTTATAAA
1922905 AAATTT
65 AAATTT
*
1922911 AAATTAAATAAAATTT-AATAAAAATTAAA
1 AAATTAATTAAAATTTAAATAAAAATTAAA
1922940 CCTAAATCAA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
69 13 0.14
70 68 0.73
71 12 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (70 bp):
AAATTAATTAAAATTTAAATAAAAATTAAATTAAATTTAAATAATTATGATTTTAATTTATAAAA
AATTT
Found at i:1923543 original size:33 final size:32
Alignment explanation
Indices: 1923440--1923543 Score: 127
Period size: 33 Copynumber: 3.2 Consensus size: 32
1923430 GCCACCTAAG
*
1923440 CCTCCTGTTGTTAAGCCTCCTTATGTACCCAAA
1 CCTCCTGTTG-TAAGCCTCCCTATGTACCCAAA
* * *
1923473 CCACCAGTTGTGAAGCCTCCCTATGTACCCAAG
1 CCTCCTGTTGT-AAGCCTCCCTATGTACCCAAA
* *
1923506 CCTCCTGTTGTAACGCCACCCTACGTACCCAAA
1 CCTCCTGTTGTAA-GCCTCCCTATGTACCCAAA
1923539 CCTCC
1 CCTCC
1923544 CGTCATCCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 3 0.05
33 57 0.95
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.25
Consensus pattern (32 bp):
CCTCCTGTTGTAAGCCTCCCTATGTACCCAAA
Found at i:1923661 original size:63 final size:63
Alignment explanation
Indices: 1923591--1923777 Score: 232
Period size: 63 Copynumber: 3.0 Consensus size: 63
1923581 CCAGTCATTT
* * * * *
1923591 CACCACCAAATCTGCCTCCAAAGCCTCCCGTCTATCCTAGCCCTCCAATTGTGAATCCGCCTA
1 CACCACCAAATCTGCCTCCAAAGCCTCCCGTCTATCCAAGTCCTCCAATTGTGAAGCCACCAA
* * * ** *
1923654 CCCCACCAATTCGGCCTCCAACTCCTCCCGTCTATCCAAGTCCTCCAACTGTGAAGCCACCAA
1 CACCACCAAATCTGCCTCCAAAGCCTCCCGTCTATCCAAGTCCTCCAATTGTGAAGCCACCAA
* * *
1923717 CACCACCAACTCTGCCTCCAAAGCC-CCCTGTATATCCAAGTCCTCCCATTGTGAAGCCACC
1 CACCACCAAATCTGCCTCCAAAGCCTCCC-GTCTATCCAAGTCCTCCAATTGTGAAGCCACC
1923778 TCCAGTCGAG
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
62 3 0.03
63 101 0.97
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.20
Consensus pattern (63 bp):
CACCACCAAATCTGCCTCCAAAGCCTCCCGTCTATCCAAGTCCTCCAATTGTGAAGCCACCAA
Found at i:1924889 original size:17 final size:18
Alignment explanation
Indices: 1924861--1924894 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1924851 TATCCATCGA
1924861 TAAATAAATATTTTTTTT
1 TAAATAAATATTTTTTTT
1924879 TAAAT-AATATTTTTTT
1 TAAATAAATATTTTTTT
1924895 AATCTAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATAAATATTTTTTTT
Found at i:1925172 original size:20 final size:20
Alignment explanation
Indices: 1925120--1925172 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1925110 TATATATTTT
*
1925120 TATAATTTAATTTAAATAAA
1 TATAATTTAAATTAAATAAA
**
1925140 TAT-ATTTTTATTAAA-AAA
1 TATAATTTAAATTAAATAAA
1925158 TAATAATTTAAATTA
1 T-ATAATTTAAATTA
1925173 GATCAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAATTTAAATTAAATAAA
Found at i:1927199 original size:23 final size:23
Alignment explanation
Indices: 1927171--1927214 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1927161 TATAATTATT
1927171 TTTAAAAGTT-AATATTTAATAAA
1 TTTAAAAGTTAAATA-TTAATAAA
*
1927194 TTTAAAATTTAAATATTAATA
1 TTTAAAAGTTAAATATTAATA
1927215 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAAAAGTTAAATATTAATAAA
Found at i:1928075 original size:16 final size:15
Alignment explanation
Indices: 1928054--1928089 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
1928044 TTAATTATTT
1928054 TAATATTAAAATTAAA
1 TAATATTAAAATT-AA
1928070 TAATATTAAAATTAA
1 TAATATTAAAATTAA
1928085 TAATA
1 TAATA
1928090 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATATTAAAATTAA
Found at i:1928083 original size:22 final size:21
Alignment explanation
Indices: 1928039--1928097 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
1928029 ATAATAACAG
* * *
1928039 TAAAATTAATTATTTTAATAT
1 TAAAATTAATAATATTAAAAT
1928060 TAAAATTAAATAATATTAAAAT
1 TAAAATT-AATAATATTAAAAT
1928082 TAATAA-TAATATATAT
1 TAA-AATTAATA-ATAT
1928098 ATTTAGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 11 0.34
22 19 0.59
23 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTAATAATATTAAAAT
Found at i:1928233 original size:27 final size:26
Alignment explanation
Indices: 1928192--1928274 Score: 89
Period size: 26 Copynumber: 3.1 Consensus size: 26
1928182 AAATAAAATA
*
1928192 AAATATATATAAAAATTATATTTATGTT
1 AAATA-AT-TAAAAATTATATTTATATT
1928220 AATAATAATT-AAAATTA-ATTTATATT
1 -A-AATAATTAAAAATTATATTTATATT
* *
1928246 AAATAATTAAAAATTTTATTTACATT
1 AAATAATTAAAAATTATATTTATATT
1928272 AAA
1 AAA
1928275 AAATAATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 7 0.15
25 7 0.15
26 19 0.40
27 7 0.15
28 1 0.02
29 3 0.06
30 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATAATTAAAAATTATATTTATATT
Found at i:1928316 original size:14 final size:15
Alignment explanation
Indices: 1928274--1928315 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1928264 TTTACATTAA
*
1928274 AAAATAATTTAACAT
1 AAAATAATTTAAAAT
1928289 AAAATAATTTAAAAT
1 AAAATAATTTAAAAT
1928304 -AAATAA-TTAAAA
1 AAAATAATTTAAAA
1928316 AAAGTGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
15 14 0.54
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAATTTAAAAT
Found at i:1931826 original size:29 final size:29
Alignment explanation
Indices: 1931770--1931826 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1931760 GAAGTGATGA
*
1931770 TTTTAATTTATGTATTATTAAATTTAATT
1 TTTTAATTTATATATTATTAAATTTAATT
*
1931799 TTTTAATTT-TATATTTTTAAATTATAAT
1 TTTTAATTTATATATTATTAAATT-TAAT
1931827 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTAATTTATATATTATTAAATTTAATT
Found at i:1932075 original size:14 final size:15
Alignment explanation
Indices: 1932047--1932097 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 15
1932037 TTTTTTATTT
1932047 ATTATAATTTAAAAAA
1 ATTA-AATTTAAAAAA
*
1932063 ATTAAATTT-AAAAT
1 ATTAAATTTAAAAAA
1932077 ATTAAATATTTTAAAAAA
1 ATT-AA-A-TTTAAAAAA
1932095 ATT
1 ATT
1932098 TCATTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 7 0.24
15 7 0.24
16 5 0.17
17 3 0.10
18 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATTTAAAAAA
Found at i:1932517 original size:11 final size:11
Alignment explanation
Indices: 1932455--1932522 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
1932445 GATCATATTG
* *
1932455 AATATCATATT
1 AATATAATATA
*
1932466 AATAAAATATA
1 AATATAATATA
*
1932477 AAAATAAT-TAA
1 AATATAATAT-A
*
1932488 AATTTAATATA
1 AATATAATATA
*
1932499 TA-ATAATATA
1 AATATAATATA
1932509 AATATAATATA
1 AATATAATATA
1932520 AAT
1 AAT
1932523 TTTTTATAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 9 0.20
11 34 0.77
12 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAATATA
Found at i:1932517 original size:48 final size:45
Alignment explanation
Indices: 1932463--1932589 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 45
1932453 TGAATATCAT
1932463 ATTAATAAAATATAAAAATAATTAAAATTTAATATATAATAATATAA
1 ATTAATAAAATAT-AAAATAATTAAAATTTAATATATAATAATA-AA
* *** *
1932510 ATATAATATAAATTTTTTATAA-TAAAATTTATTA-AT-ATAATAAA
1 AT-TAATA-AAATATAAAATAATTAAAATTTAATATATAATAATAAA
* * *
1932554 ATTTATAAAATATAAAATATTTAAAATATAAT-TATA
1 ATTAATAAAATATAAAATAATTAAAATTTAATATATA
1932590 CGACATAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
42 8 0.13
43 15 0.24
44 4 0.06
45 6 0.10
46 2 0.03
47 13 0.21
48 9 0.15
49 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (45 bp):
ATTAATAAAATATAAAATAATTAAAATTTAATATATAATAATAAA
Found at i:1932523 original size:32 final size:32
Alignment explanation
Indices: 1932465--1932558 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
1932455 AATATCATAT
*
1932465 TAATAAAATATAAAAATAAT-TAAAATTTAATA
1 TAATAAAATATAAATATAATAT-AAATTTAATA
**
1932497 T-ATAATAATATAAATATAATATAAATTTTTTA
1 TAATAA-AATATAAATATAATATAAATTTAATA
*
1932529 TAATAAAATTTATTAATATAATA-AAATTTA
1 TAATAAAA--TATAAATATAATATAAATTTA
1932559 TAAAATATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
31 4 0.08
32 25 0.48
33 11 0.21
34 12 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATAAAATATAAATATAATATAAATTTAATA
Found at i:1932530 original size:16 final size:16
Alignment explanation
Indices: 1932511--1932584 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
1932501 ATAATATAAA
1932511 TATAATATAAATTTTT
1 TATAATATAAATTTTT
1932527 TATAATA-AAATTTATT
1 TATAATATAAATTT-TT
*
1932543 AATATAATA-AAA-TTTA
1 --TATAATATAAATTTTT
* * *
1932559 TAAAATATAAAATATT
1 TATAATATAAATTTTT
*
1932575 TAAAATATAA
1 TATAATATAA
1932585 TTATACGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.12
15 9 0.18
16 22 0.45
17 2 0.04
18 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATATAAATTTTT
Found at i:1932550 original size:18 final size:18
Alignment explanation
Indices: 1932465--1932585 Score: 86
Period size: 18 Copynumber: 7.2 Consensus size: 18
1932455 AATATCATAT
*
1932465 TAATAAAA--TATAAAAA
1 TAATAAAATTTATAAATA
*
1932481 TAATTAAAATTTA-ATATA
1 TAA-TAAAATTTATAAATA
1932499 TAAT--AA--TATAAATA
1 TAATAAAATTTATAAATA
*
1932513 TAATATAAATTT-T--TTA
1 TAATA-AAATTTATAAATA
*
1932529 TAATAAAATTTATTAATA
1 TAATAAAATTTATAAATA
1932547 TAATAAAATTTATAAAATA
1 TAATAAAATTTAT-AAATA
*
1932566 TAA-AATATTTA-AAATA
1 TAATAAAATTTATAAATA
1932582 TAAT
1 TAAT
1932586 TATACGACAT
Statistics
Matches: 84, Mismatches: 7, Indels: 27
0.71 0.06 0.23
Matches are distributed among these distances:
13 2 0.02
14 8 0.10
15 8 0.10
16 19 0.23
17 8 0.10
18 29 0.35
19 10 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAAAATTTATAAATA
Found at i:1932806 original size:15 final size:17
Alignment explanation
Indices: 1932774--1932951 Score: 55
Period size: 16 Copynumber: 11.0 Consensus size: 17
1932764 ATTAATATAA
*
1932774 ATATATTTATTGTATTT
1 ATATATTTATTATATTT
1932791 ATATATTT-TTAT-TTT
1 ATATATTTATTATATTT
* *
1932806 AT-T-GTAATTATATTT
1 ATATATTTATTATATTT
*
1932821 A-A-ATTATTTTATATTT
1 ATATATT-TATTATATTT
*
1932837 ATATA--AATT-T-TTT
1 ATATATTTATTATATTT
*
1932850 -TATA-TTAATA-ATTT
1 ATATATTTATTATATTT
* *
1932864 ATAT-TATATTAATTTTT
1 ATATATTTATT-ATATTT
* * *
1932881 AAATATTAATTTTATTT
1 ATATATTTATTATATTT
*
1932898 -TATTTTTATTAT-TTT
1 ATATATTTATTATATTT
*
1932913 TTATATTATATTCATATTAT
1 ATATATT-TATT-ATATT-T
*
1932933 ATATAATATTATCATATTT
1 ATAT-AT-TTATTATATTT
1932952 TAACCCAAAA
Statistics
Matches: 114, Mismatches: 25, Indels: 42
0.63 0.14 0.23
Matches are distributed among these distances:
12 4 0.04
13 6 0.05
14 9 0.08
15 21 0.18
16 26 0.23
17 23 0.20
18 7 0.06
19 3 0.03
20 9 0.08
21 5 0.04
22 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (17 bp):
ATATATTTATTATATTT
Found at i:1932843 original size:20 final size:19
Alignment explanation
Indices: 1932820--1932873 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1932810 TAATTATATT
1932820 TAAATTATTTTATATTTATA
1 TAAATTATTTTATATTTA-A
*
1932840 TAAATTTTTTTATA-TTAA
1 TAAATTATTTTATATTTAA
* *
1932858 TAATTTATATTATATT
1 TAAATTATTTTATATT
1932874 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 12 0.41
19 4 0.14
20 13 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAAATTATTTTATATTTAA
Found at i:1932860 original size:18 final size:18
Alignment explanation
Indices: 1932820--1932876 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1932810 TAATTATATT
*
1932820 TAAATTATTTTATATTTATA
1 TAAATTTTTTTATA-TTA-A
1932840 TAAATTTTTTTATATTAA
1 TAAATTTTTTTATATTAA
*
1932858 T-AATTTATATTATATTAA
1 TAAATTT-TTTTATATTAA
1932876 T
1 T
1932877 TTTTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.15
18 13 0.38
19 3 0.09
20 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTTTTTATATTAA
Found at i:1932878 original size:32 final size:31
Alignment explanation
Indices: 1932828--1932939 Score: 102
Period size: 32 Copynumber: 3.5 Consensus size: 31
1932818 TTTAAATTAT
*
1932828 TTTATATTTATATAAATTTTTTTATATTAATAA
1 TTTATA-TTATATTAATTTTTTTATATTAAT-A
**
1932861 TTTATATTATATTAATTTTTAAATATTAAT-
1 TTTATATTATATTAATTTTTTTATATTAATA
* * *
1932891 TTTATTTTATTTTTATTATTTTTTATATT-ATA
1 TTTATATTA-TATTAAT-TTTTTTATATTAATA
*
1932923 TTCATATTATATATAAT
1 TTTATATTATAT-TAAT
1932940 ATTATCATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
30 8 0.13
31 9 0.14
32 40 0.63
33 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTATATTATATTAATTTTTTTATATTAATA
Found at i:1932913 original size:10 final size:11
Alignment explanation
Indices: 1932788--1932934 Score: 50
Period size: 11 Copynumber: 12.9 Consensus size: 11
1932778 ATTTATTGTA
1932788 TTTA-TATATT
1 TTTATTATATT
*
1932798 TTTATTTTATT
1 TTTATTATATT
* *
1932809 GTAATTATATT
1 TTTATTATATT
* *
1932820 TAAATTATTTTATA
1 T---TTATTATATT
*
1932834 TTTATATAAATT
1 TTTAT-TATATT
1932846 TTT-TTATATT
1 TTTATTATATT
* *
1932856 AATAATT-TATAT
1 -TTTATTATAT-T
*
1932868 TATATTA-ATT
1 TTTATTATATT
* *
1932878 TTTAAATATTAAT
1 TTT-ATTA-TATT
*
1932891 TTTATTTTATT
1 TTTATTATATT
*
1932902 TTTATTATTTT
1 TTTATTATATT
1932913 TTATATTATATT
1 TT-TATTATATT
**
1932925 CATATTATAT
1 TTTATTATAT
1932935 ATAATATTAT
Statistics
Matches: 96, Mismatches: 28, Indels: 25
0.64 0.19 0.17
Matches are distributed among these distances:
10 12 0.12
11 52 0.54
12 19 0.20
13 5 0.05
14 8 0.08
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.65
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1932930 original size:20 final size:20
Alignment explanation
Indices: 1932911--1932953 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1932901 TTTTATTATT
*
1932911 TTTTATATTATA-T-TCATA
1 TTTTATATAATATTATCATA
*
1932929 TTATATATAATATTATCATA
1 TTTTATATAATATTATCATA
1932949 TTTTA
1 TTTTA
1932954 ACCCAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.50
19 1 0.05
20 9 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATATAATATTATCATA
Found at i:1933543 original size:16 final size:17
Alignment explanation
Indices: 1933518--1933550 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1933508 TAATAATTTA
*
1933518 TTTTATTTTATATATAT
1 TTTTATTTTATACATAT
1933535 TTTTA-TTTATACATAT
1 TTTTATTTTATACATAT
1933551 AATCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTTTATACATAT
Found at i:1935006 original size:19 final size:18
Alignment explanation
Indices: 1934991--1935027 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1934981 TATTATTTTT
1934991 ATTTATATAAAATATTATAA
1 ATTTATAT-AAATATT-TAA
1935011 ATTTATATAAATATTTA
1 ATTTATATAAATATTTA
1935028 TACATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 7 0.41
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATATAAATATTTAA
Found at i:1935239 original size:28 final size:25
Alignment explanation
Indices: 1935197--1935247 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
1935187 ATTTTAACTT
*
1935197 TAAATTTATTTATTAAATAATTTTAAA
1 TAAATTTATTAATT--ATAATTTTAAA
1935224 TAAATTTTATTAATTATAATTTTA
1 TAAA-TTTATTAATTATAATTTTA
1935248 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 4 0.18
28 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAATTTATTAATTATAATTTTAAA
Found at i:1935246 original size:15 final size:16
Alignment explanation
Indices: 1935225--1935285 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
1935215 AATTTTAAAT
1935225 AAATTTTATTAATT-A
1 AAATTTTATTAATTAA
*
1935240 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATTAA
* *
1935257 AAATTTTATAAATATTA
1 AAATTTTATTAAT-TAA
1935274 AAATTTT-TTAAT
1 AAATTTTATTAAT
1935286 AAACAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.18
16 14 0.37
17 17 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTTTATTAATTAA
Found at i:1935566 original size:6 final size:6
Alignment explanation
Indices: 1935555--1935618 Score: 92
Period size: 6 Copynumber: 10.5 Consensus size: 6
1935545 TTAAAAATTT
* *
1935555 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTTAAT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
*
1935603 TTAATAA TTTAAA TTA
1 TTAA-AA TTAAAA TTA
1935619 TTATTTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
6 47 0.92
7 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAA
Found at i:1935611 original size:13 final size:12
Alignment explanation
Indices: 1935541--1935614 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 12
1935531 AGGTAGATTA
*
1935541 TAATTTAAAAAT
1 TAATTTAAAATT
1935553 T--TTTAAAATT
1 TAATTTAAAATT
* *
1935563 AAAATTAAAATT
1 TAATTTAAAATT
* *
1935575 AAAATTAAAATT
1 TAATTTAAAATT
* *
1935587 AAAATTAAAATT
1 TAATTTAAAATT
1935599 TAATTTAATAATT
1 TAATTTAA-AATT
1935612 TAA
1 TAA
1935615 ATTATTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
10 8 0.15
12 39 0.72
13 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATTTAAAATT
Found at i:1936265 original size:18 final size:18
Alignment explanation
Indices: 1936242--1936282 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1936232 TGCACTCATG
1936242 TTATGATAA-ATCTATTTT
1 TTATGATAATAT-TATTTT
1936260 TTATGATAATATTATTTT
1 TTATGATAATATTATTTT
1936278 TTATG
1 TTATG
1936283 TTGTGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (18 bp):
TTATGATAATATTATTTT
Found at i:1936419 original size:20 final size:19
Alignment explanation
Indices: 1936394--1936433 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1936384 TTTAATATGT
1936394 TTATTTGTATCATGATTATA
1 TTATTTGTATCATG-TTATA
* *
1936414 TTATTTTTTTCATGTTATA
1 TTATTTGTATCATGTTATA
1936433 T
1 T
1936434 CAGATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATTTGTATCATGTTATA
Found at i:1936669 original size:24 final size:24
Alignment explanation
Indices: 1936638--1936692 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1936628 ATATTAAATA
1936638 AAAAATTATAACAATTAAAAAGAT
1 AAAAATTATAACAATTAAAAAGAT
1936662 AAAAATTATAACAATTAAAAAGAT
1 AAAAATTATAACAATTAAAAAGAT
1936686 AAAAATT
1 AAAAATT
1936693 TATGTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAAATTATAACAATTAAAAAGAT
Found at i:1936881 original size:11 final size:11
Alignment explanation
Indices: 1936865--1936900 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
1936855 TATATATTAG
1936865 TATTATTTTTA
1 TATTATTTTTA
1936876 TATTATTTTTA
1 TATTATTTTTA
1936887 TAATTATATTTTA
1 T-ATTAT-TTTTA
1936900 T
1 T
1936901 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 5 0.22
13 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:1937554 original size:22 final size:22
Alignment explanation
Indices: 1937529--1937570 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1937519 ATAATTATTT
1937529 TTTAAAAATAATATTTAATAAA
1 TTTAAAAATAATATTTAATAAA
* *
1937551 TTTAAAATTAATTTTTAATA
1 TTTAAAAATAATATTTAATA
1937571 TTTGTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAAAATAATATTTAATAAA
Found at i:1938336 original size:17 final size:20
Alignment explanation
Indices: 1938314--1938357 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1938304 TTGGTGCATT
1938314 ATTTTTTTAA-A-AT-GATA
1 ATTTTTTTAAGATATGGATA
*
1938331 ATTTTTATAAGATATGGATA
1 ATTTTTTTAAGATATGGATA
1938351 ATTTTTT
1 ATTTTTT
1938358 ACACAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 2 0.09
20 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
ATTTTTTTAAGATATGGATA
Found at i:1939560 original size:2 final size:2
Alignment explanation
Indices: 1939553--1939580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1939543 CATCTTCTTC
1939553 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
1939581 TCCTTCTCAA
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:1939822 original size:23 final size:24
Alignment explanation
Indices: 1939769--1939823 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1939759 GATTAACATG
*
1939769 ATAAAGAAGTACCTTATTTTGATAA
1 ATAAA-AAATACCTTATTTTGATAA
*
1939794 ATAAAAAATACCTTATTTTTA-AA
1 ATAAAAAATACCTTATTTTGATAA
1939817 ATAAAAA
1 ATAAAAA
1939824 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.32
24 14 0.50
25 5 0.18
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (24 bp):
ATAAAAAATACCTTATTTTGATAA
Found at i:1940560 original size:2 final size:2
Alignment explanation
Indices: 1940543--1940587 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
1940533 TAAATAAATT
1940543 TA TA -A TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
1940585 TA T
1 TA T
1940588 TTACTCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 2 0.05
2 34 0.87
3 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1941021 original size:32 final size:33
Alignment explanation
Indices: 1940975--1941122 Score: 101
Period size: 32 Copynumber: 4.4 Consensus size: 33
1940965 CATTTATATA
*
1940975 TTTATAT-TACATTTAAATTATTATTATTATTAT
1 TTTATATATATATTTAAATTA-TATTATTATTAT
*
1941008 TTTA-AT-TATATTTAAAATATTATATATTTATATAAAT
1 TTTATATATATATTTAAATTA-TAT-TA-TTAT-T--AT
* *
1941045 TTTGATATAT-T-TTTAATTTATATTA-TATTAA
1 TTT-ATATATATATTTAAATTATATTATTATTAT
* * *
1941076 TTTATATATATATTTATATTATATTATTTTTTAA
1 TTTATATATATATTTAAATTATATTA-TTATTAT
*
1941110 ATTATATATATAT
1 TTTATATATATAT
1941123 ATTTTCGTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
30 6 0.06
31 5 0.05
32 29 0.31
33 7 0.07
34 24 0.26
35 1 0.01
36 2 0.02
37 8 0.09
38 8 0.09
39 3 0.03
40 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (33 bp):
TTTATATATATATTTAAATTATATTATTATTAT
Found at i:1941104 original size:48 final size:49
Alignment explanation
Indices: 1940974--1941122 Score: 133
Period size: 50 Copynumber: 2.9 Consensus size: 49
1940964 CCATTTATAT
* * *
1940974 ATTTATAT-TACATTTAAATTATTATTATTATTATTTTA-ATTATATTTAAA
1 ATTTATATATATATTTAAATTA-TATTATTTTTAATTTATATTATA-TT-AA
* * *
1941024 ATATTATATATTTATATAAATTTTGATATATTTTTAATTTATATTATATT-A
1 AT-TTATATATATATTTAAATTAT-AT-TATTTTTAATTTATATTATATTAA
* *
1941075 ATTTATATATATATTTATATTATATTATTTTTTAAATTATATATATAT
1 ATTTATATATATATTTAAATTATATTA-TTTTTAATTTATAT-TATAT
1941123 ATTTTCGTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
48 2 0.02
49 15 0.19
50 24 0.30
51 10 0.12
52 11 0.14
53 13 0.16
54 6 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (49 bp):
ATTTATATATATATTTAAATTATATTATTTTTAATTTATATTATATTAA
Found at i:1942650 original size:14 final size:14
Alignment explanation
Indices: 1942615--1942663 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1942605 ATTTTCCTAT
*
1942615 TTTATTTTTTAAAA
1 TTTAATTTTTAAAA
*
1942629 -ATATATTTTTAAAA
1 TTTA-ATTTTTAAAA
1942643 TTTAATTTTTAATAA
1 TTTAATTTTTAA-AA
1942658 TTTAAT
1 TTTAAT
1942664 ACATTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.59
15 10 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATTTTTAAAA
Found at i:1942703 original size:21 final size:21
Alignment explanation
Indices: 1942648--1942714 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
1942638 TAAAATTTAA
*
1942648 TTTTTAATAATTTAATACAT-T
1 TTTTTAAT-ATTTAATAAATAT
*
1942669 TTTATTAAGATTTAATAAATAT
1 TTT-TTAATATTTAATAAATAT
*
1942691 TTTTTAATCTTTACATTAAATAT
1 TTTTTAATATTTA-A-TAAATAT
1942714 T
1 T
1942715 AAATATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 21 0.55
22 9 0.24
23 8 0.21
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTTTAATATTTAATAAATAT
Found at i:1942890 original size:18 final size:16
Alignment explanation
Indices: 1942868--1942962 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 16
1942858 TCAAATTTAT
1942868 TTTTTGAATTTAAAATA
1 TTTTT-AATTTAAAATA
*
1942885 TATTTTTATTT-AAATA
1 T-TTTTAATTTAAAATA
1942901 TTTTTTAATATTAATCAA-A
1 -TTTTTAAT-TTAA--AATA
*
1942920 TTTTTAAATTTAAATAAA
1 TTTTT-AATTTAAA-ATA
*
1942938 TAATTTAATTTATAAATA
1 T-TTTTAATTTA-AAATA
1942956 TTTTTAA
1 TTTTTAA
1942963 ATTAGATGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
16 12 0.19
17 14 0.23
18 25 0.40
19 9 0.15
20 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTTTAATTTAAAATA
Found at i:1942897 original size:17 final size:15
Alignment explanation
Indices: 1942838--1942907 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 15
1942828 ATCAAACCTA
*
1942838 TTTTTAATT-AAT-T
1 TTTTTATTTAAATAT
*
1942851 TTTTTATTCAAATTTAT
1 TTTTTATTTAAA--TAT
1942868 TTTTTGAATTTAAAATAT
1 TTTTT--ATTT-AAATAT
1942886 ATTTTTATTTAAATAT
1 -TTTTTATTTAAATAT
1942902 TTTTTA
1 TTTTTA
1942908 ATATTAATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.15
14 2 0.04
15 6 0.13
16 7 0.15
17 10 0.22
18 3 0.07
19 8 0.17
20 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (15 bp):
TTTTTATTTAAATAT
Found at i:1942914 original size:17 final size:16
Alignment explanation
Indices: 1942865--1942935 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 16
1942855 TATTCAAATT
1942865 TATTTTTTGAATTTAAAA
1 TATTTTTT-AATTT-AAA
1942883 TATATTTTT-ATTTAAA
1 TAT-TTTTTAATTTAAA
1942899 TATTTTTTAATATTAATCA
1 TATTTTTTAAT-TTAA--A
* *
1942918 AATTTTTAAATTTAAA
1 TATTTTTTAATTTAAA
1942934 TA
1 TA
1942936 AATAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 5 0.11
16 10 0.22
17 8 0.18
18 7 0.16
19 15 0.33
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
TATTTTTTAATTTAAA
Found at i:1942984 original size:2 final size:2
Alignment explanation
Indices: 1942977--1943008 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1942967 GATGAATCAA
*
1942977 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1943009 GCACGCGCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1943200 original size:16 final size:16
Alignment explanation
Indices: 1943168--1943201 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1943158 ATTAAATTTC
* *
1943168 AAAATTTAAGTTTAAA
1 AAAATTTAAATTCAAA
1943184 AAAATTTAAATTCAAA
1 AAAATTTAAATTCAAA
1943200 AA
1 AA
1943202 TTTTGAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAATTTAAATTCAAA
Found at i:1944835 original size:18 final size:19
Alignment explanation
Indices: 1944793--1944836 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1944783 ATTTACGTTA
*
1944793 AATTTAATTTATATTAAGT
1 AATTTAAATTATATTAAGT
**
1944812 GTTTTAAATTATA-TAAGT
1 AATTTAAATTATATTAAGT
1944830 AATTTAA
1 AATTTAA
1944837 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
AATTTAAATTATATTAAGT
Found at i:1945017 original size:30 final size:26
Alignment explanation
Indices: 1944975--1945044 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 26
1944965 AATTTAATAA
* *
1944975 AAATTATATTTATATATGATATATTATT
1 AAATTAAATTTATATAT-AT-TATTAGT
1945003 AATATATAAATTTATATATATTATTAGT
1 AA-AT-TAAATTTATATATATTATTAGT
1945031 AAATTAAA-TTATAT
1 AAATTAAATTTATAT
1945045 TATCTCATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.16
26 4 0.11
27 2 0.05
28 10 0.26
29 4 0.11
30 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (26 bp):
AAATTAAATTTATATATATTATTAGT
Found at i:1945042 original size:25 final size:25
Alignment explanation
Indices: 1944993--1945060 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
1944983 TTTATATATG
*
1944993 ATATATTATTAATATATAAATTTAT
1 ATATATTATTAATAAATAAATTTAT
*
1945018 ATATATTATTAGTAAATTAAA-TTAT
1 ATATATTATTAATAAA-TAAATTTAT
1945043 AT-TATCTCATTAA-AAATA
1 ATATAT-T-ATTAATAAATA
1945061 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.14
25 24 0.65
26 8 0.22
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATATTATTAATAAATAAATTTAT
Found at i:1945108 original size:19 final size:21
Alignment explanation
Indices: 1945070--1945108 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1945060 ATTAAAAATA
*
1945070 AATATAAATAATTTTTATTTT
1 AATATAAATAATTTTAATTTT
1945091 AATA-AAATAA-TTTAATTT
1 AATATAAATAATTTTAATTT
1945109 GATACATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATTTTAATTTT
Found at i:1947821 original size:10 final size:10
Alignment explanation
Indices: 1947794--1947835 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1947784 AATTTCAAAT
1947794 ATATATATTAA
1 ATATATA-TAA
*
1947805 AAATATATAA
1 ATATATATAA
*
1947815 ATTTATATAA
1 ATATATATAA
1947825 ATATATA-AA
1 ATATATATAA
1947834 AT
1 AT
1947836 GTCATTCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 4 0.15
10 17 0.63
11 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATATAA
Found at i:1948619 original size:23 final size:21
Alignment explanation
Indices: 1948567--1948620 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
1948557 TACGAATATT
*
1948567 TTAAAATTTATATAATATAAA
1 TTAAAATATATATAATATAAA
* *
1948588 TTATTAATATATATTTATATAAA
1 TTA-AAATATATA-TAATATAAA
1948611 TATAAAATAT
1 T-TAAAATAT
1948621 CTTAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 7 0.27
23 14 0.54
24 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAATATATATAATATAAA
Found at i:1948833 original size:14 final size:13
Alignment explanation
Indices: 1948814--1948874 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
1948804 CATTAAATAT
1948814 TTAAATTTATTAAA
1 TTAAATTTA-TAAA
1948828 TTAAATATTATAAA
1 TTAAAT-TTATAAA
* *
1948842 ATAAA-ATATAAAA
1 TTAAATTTAT-AAA
*
1948855 TTAAATATATAAA
1 TTAAATTTATAAA
1948868 -TAAATTT
1 TTAAATTT
1948875 CAAATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 9 0.22
13 10 0.25
14 18 0.45
15 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATTTATAAA
Found at i:1948851 original size:12 final size:12
Alignment explanation
Indices: 1948836--1948871 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1948826 AATTAAATAT
1948836 TATAAAATAAAA
1 TATAAAATAAAA
*
1948848 TATAAAATTAAA
1 TATAAAATAAAA
1948860 TATATAAATAAA
1 TATA-AAATAAA
1948872 TTTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TATAAAATAAAA
Found at i:1948872 original size:12 final size:14
Alignment explanation
Indices: 1948814--1948867 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1948804 CATTAAATAT
* *
1948814 TTAAATTTATTAAA
1 TTAAATATATAAAA
1948828 TTAAATATTATAAAA
1 TTAAATA-TATAAAA
1948843 -TAAA-ATATAAAA
1 TTAAATATATAAAA
1948855 TTAAATATATAAA
1 TTAAATATATAAA
1948868 TAAATTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.20
13 5 0.14
14 17 0.49
15 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATATATAAAA
Found at i:1950648 original size:22 final size:22
Alignment explanation
Indices: 1950619--1950680 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
1950609 GATAGATGTT
*
1950619 TATTTTTCCTCTTTATTTGAC-
1 TATTTTTCCTCTTTATTTAACA
1950640 T-TTGATTTCCTCTTTATTTAACA
1 TATT--TTTCCTCTTTATTTAACA
1950663 TATTTTTCCTCTTTATTT
1 TATTTTTCCTCTTTATTT
1950681 CATTTCAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 30 0.83
23 1 0.03
24 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTTTTCCTCTTTATTTAACA
Found at i:1952216 original size:25 final size:26
Alignment explanation
Indices: 1952161--1952238 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 26
1952151 TATAAATATT
* ***
1952161 AAATATAAATATATATTTAATTTATTT
1 AAATAT-ATTATATATTTAATTTAAAA
* *
1952188 AAATTTTTTATATA-TTAATTTAAAA
1 AAATATATTATATATTTAATTTAAAA
1952213 AAATATATTATATATTTATATTTAAA
1 AAATATATTATATATTTA-ATTTAAA
1952239 TATAAGTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 20 0.49
26 9 0.22
27 12 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATATATTATATATTTAATTTAAAA
Found at i:1955602 original size:27 final size:27
Alignment explanation
Indices: 1955572--1955625 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1955562 GTTCGACCAA
*
1955572 AACCTAATTACGCATAATGTTAGCTGT
1 AACCTAAATACGCATAATGTTAGCTGT
1955599 AACCTAAATACGCATAATGTTAGCTGT
1 AACCTAAATACGCATAATGTTAGCTGT
1955626 TGGGCCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (27 bp):
AACCTAAATACGCATAATGTTAGCTGT
Found at i:1959700 original size:13 final size:13
Alignment explanation
Indices: 1959682--1959707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1959672 ACAAAGATCC
1959682 ATGTATCGATACA
1 ATGTATCGATACA
1959695 ATGTATCGATACA
1 ATGTATCGATACA
1959708 TTTGAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1959784 original size:19 final size:18
Alignment explanation
Indices: 1959760--1959822 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1959750 AGCGATACAT
1959760 TGTATCGATACAACATTTA
1 TGTATCGATACAACA-TTA
1959779 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
1959792 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
*
1959811 TATATCGATACA
1 TGTATCGATACA
1959823 GTTACTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:1959791 original size:16 final size:13
Alignment explanation
Indices: 1959746--1959803 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1959736 AGCAGTAGCT
*
1959746 TTGTAGCGATACA
1 TTGTATCGATACA
1959759 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1959775 TTTATGTATCGATACA
1 --T-TGTATCGATACA
1959791 TTGTATCGATACA
1 TTGTATCGATACA
1959804 ACACTTATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Done.