Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 10 of 24
Found at i:1960744 original size:23 final size:22
Alignment explanation
Indices: 1960687--1960747 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
1960677 ATTTTAACCA
1960687 ATTTTAAATAATTT-TATAATTT
1 ATTTTAAA-AATTTATATAATTT
* *
1960709 AATTTAATTAATTTATATAATTAT
1 ATTTTAA-AAATTTATATAATT-T
*
1960733 TTTTTAAAAATTTAT
1 ATTTTAAAAATTTAT
1960748 TTTTAACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 11 0.35
23 14 0.45
24 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTAAAAATTTATATAATTT
Found at i:1961229 original size:31 final size:33
Alignment explanation
Indices: 1961171--1961247 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 33
1961161 CCTGGTCAAA
1961171 TAATTATTAATTTAATTAAAATTAAAA-T-TTT
1 TAATTATTAATTTAATTAAAATTAAAATTATTT
1961202 TAATTATTAATTTAA-TAAAATTAAAAATTATTT
1 TAATTATTAATTTAATTAAAATT-AAAATTATTT
1961235 TAA--ATTAATTTAA
1 TAATTATTAATTTAA
1961248 CTTAGATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.16
31 29 0.67
32 1 0.02
33 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TAATTATTAATTTAATTAAAATTAAAATTATTT
Found at i:1963362 original size:11 final size:11
Alignment explanation
Indices: 1963346--1963394 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1963336 ATATAACACA
1963346 AATAAATTATT
1 AATAAATTATT
1963357 AATAAATTATTT
1 AATAAATTA-TT
*
1963369 AAT-ATTTATT
1 AATAAATTATT
1963379 AA-AAA-TA-T
1 AATAAATTATT
1963387 AATAAATT
1 AATAAATT
1963395 TTTAGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 6 0.19
11 13 0.41
12 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAAATTATT
Found at i:1964023 original size:3 final size:3
Alignment explanation
Indices: 1964015--1964058 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
1964005 GCAAGAACAA
*
1964015 AAT AAT AAT TAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1964059 GAAAGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1965292 original size:2 final size:2
Alignment explanation
Indices: 1965285--1965317 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1965275 TTTGAGAGGT
1965285 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
1965318 TGTTTTATTA
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:1971706 original size:7 final size:7
Alignment explanation
Indices: 1971694--1971720 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1971684 GTTTTTGTTG
1971694 AAATTTA
1 AAATTTA
1971701 AAATTTA
1 AAATTTA
1971708 AAATTTA
1 AAATTTA
1971715 AAATTT
1 AAATTT
1971721 TGATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:1971756 original size:21 final size:20
Alignment explanation
Indices: 1971732--1971781 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
1971722 GATTAAATTT
1971732 ATTTATATTTA-TAAATTAATA
1 ATTTATATTTATTAAA--AATA
*
1971753 ATTTAAATTTATTTAAAAATA
1 ATTTATATTTA-TTAAAAATA
1971774 ATTTATAT
1 ATTTATAT
1971782 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 21 0.84
23 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTATATTTATTAAAAATA
Found at i:1971882 original size:19 final size:20
Alignment explanation
Indices: 1971858--1971898 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1971848 ATTTTTTATG
*
1971858 TTTATTTTA-ATATTATAAA
1 TTTATTTTATATAATATAAA
1971877 TTTATTTTATATAATATAAA
1 TTTATTTTATATAATATAAA
1971897 TT
1 TT
1971899 ATATAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTTTATATAATATAAA
Found at i:1971886 original size:37 final size:38
Alignment explanation
Indices: 1971802--1971886 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
1971792 GTATATTATT
*
1971802 TTTATTTAATTTTTTATTATATTTTAAAATATAAATAA
1 TTTATTTTATTTTTTATTATATTTTAAAATATAAATAA
* * * *
1971840 TTTAATTTATTTTTTATGTTTATTTTAATAT-TATA-AA
1 TTTATTTTATTTTTTAT-TATATTTTAAAATATAAATAA
1971877 TTTATTTTAT
1 TTTATTTTAT
1971887 ATAATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 11 0.28
38 18 0.45
39 11 0.28
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (38 bp):
TTTATTTTATTTTTTATTATATTTTAAAATATAAATAA
Found at i:1974549 original size:2 final size:2
Alignment explanation
Indices: 1974542--1974576 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1974532 TTTACGTATG
1974542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1974577 TCGGGAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1976504 original size:27 final size:31
Alignment explanation
Indices: 1976424--1976507 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 31
1976414 CTAAAAATTA
* *
1976424 TAAACTAAAATTTAATTTTTTATAATTATTTT
1 TAAA-TAATATTTAATATTTTATAATTATTTT
*
1976456 TAAAAATAATATTTAATTTTTTATAATTATTTT
1 T--AAATAATATTTAATATTTTATAATTATTTT
1976489 T-AA-AAT-TTTAA-ATTTTATA
1 TAAATAATATTTAATATTTTATA
1976508 CTCTTGATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
27 7 0.15
28 5 0.10
29 3 0.06
30 2 0.04
32 1 0.02
33 27 0.56
34 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TAAATAATATTTAATATTTTATAATTATTTT
Found at i:1982854 original size:14 final size:15
Alignment explanation
Indices: 1982814--1982856 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
1982804 TTATTAAAAT
*
1982814 ATTAATTTTATATTA
1 ATTAATTTTTTATTA
1982829 ATATATATTTTTTA-TA
1 AT-TA-ATTTTTTATTA
1982845 ATTAATTTTTTA
1 ATTAATTTTTTA
1982857 AAAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 6 0.24
17 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTAATTTTTTATTA
Found at i:1985528 original size:6 final size:6
Alignment explanation
Indices: 1985517--1985545 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1985507 GTTATTTAAA
1985517 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1985546 TCAATAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1985942 original size:31 final size:33
Alignment explanation
Indices: 1985871--1985943 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
1985861 TTATTATTTT
*
1985871 ATAATAAAAATAATAATTTTAATTTAATTAAAAA
1 ATAAT-AAAATAATAATTTTAATATAATTAAAAA
*
1985905 AT-ATAAAATAAT-ATTTTAATCAT-A-TAATAA
1 ATAATAAAATAATAATTTTAAT-ATAATTAAAAA
1985935 ATAATAAAA
1 ATAATAAAA
1985944 AAAACTTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 7 0.20
31 15 0.43
32 9 0.26
33 2 0.06
34 2 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (33 bp):
ATAATAAAATAATAATTTTAATATAATTAAAAA
Found at i:1986388 original size:7 final size:7
Alignment explanation
Indices: 1986376--1986400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1986366 ACCCTGTAAT
1986376 AAATTTA
1 AAATTTA
1986383 AAATTTA
1 AAATTTA
1986390 AAATTTA
1 AAATTTA
1986397 AAAT
1 AAAT
1986401 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:1986507 original size:32 final size:30
Alignment explanation
Indices: 1986448--1986507 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1986438 TAAAAATAAA
* * *
1986448 AAATTATATTTTTATATTTAAATATTTATT
1 AAATTATATTTTTAAAATTAAAAATTTATT
1986478 AAATATATATTTTTAAAAATTAAAAATTTA
1 AAAT-TATATTTTT-AAAATTAAAAATTTA
1986508 ACATGTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 9 0.36
32 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AAATTATATTTTTAAAATTAAAAATTTATT
Found at i:1986718 original size:6 final size:6
Alignment explanation
Indices: 1986709--1986739 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1986699 GGGTTGCTGT
*
1986709 TGCATC TGCATC TGCATC TGCGTC TGCATC T
1 TGCATC TGCATC TGCATC TGCATC TGCATC T
1986740 ATCTTAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.19, T:0.35
Consensus pattern (6 bp):
TGCATC
Found at i:1987503 original size:2 final size:2
Alignment explanation
Indices: 1987487--1987533 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1987477 AGTTTCATTC
* * *
1987487 AT AT AC AT A- AT AT AT AT AT TT AA AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1987527 AT AT AT A
1 AT AT AT A
1987534 CTTTTGAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1987532 original size:19 final size:19
Alignment explanation
Indices: 1987487--1987533 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1987477 AGTTTCATTC
*
1987487 ATATACATAATATATATAT
1 ATATATATAATATATATAT
* *
1987506 TTAAATATAATATATATAT
1 ATATATATAATATATATAT
1987525 ATATATATA
1 ATATATATA
1987534 CTTTTGAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATATAATATATATAT
Found at i:1987815 original size:22 final size:21
Alignment explanation
Indices: 1987774--1987830 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1987764 TATTTTTACT
1987774 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1987795 TAAATATT-ATTATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
*
1987815 T---TTTAATAATAAAATA
1 TAAATTTAATTATAAAATA
1987831 AAATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 2 0.06
17 9 0.28
18 1 0.03
20 4 0.12
21 14 0.44
22 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1988181 original size:16 final size:16
Alignment explanation
Indices: 1988157--1988225 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
1988147 AAAAAAAGTG
**
1988157 TTTTAATAAAATTATTA
1 TTTT-ATAAAATTAAAA
1988174 TTTTATAAAATTAAAA
1 TTTTATAAAATTAAAA
*
1988190 TTTAATAAAA-TAAAA
1 TTTTATAAAATTAAAA
*
1988205 TATTATAAAATTTAAAA
1 TTTTATAAAA-TTAAAA
1988222 TTTT
1 TTTT
1988226 GATTAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.30
16 19 0.43
17 12 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTATAAAATTAAAA
Found at i:1988199 original size:32 final size:32
Alignment explanation
Indices: 1988158--1988224 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1988148 AAAAAAGTGT
** *
1988158 TTTAATAAAATTATTATTTTATAAAA-TTAAAA
1 TTTAATAAAA-TAAAATATTATAAAATTTAAAA
1988190 TTTAATAAAATAAAATATTATAAAATTTAAAA
1 TTTAATAAAATAAAATATTATAAAATTTAAAA
1988222 TTT
1 TTT
1988225 TGATTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTAATAAAATAAAATATTATAAAATTTAAAA
Found at i:1994006 original size:13 final size:13
Alignment explanation
Indices: 1993988--1994013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1993978 GCAAATAGTC
1993988 ACAATAATTTTTT
1 ACAATAATTTTTT
1994001 ACAATAATTTTTT
1 ACAATAATTTTTT
1994014 TTTGGATAAG
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ACAATAATTTTTT
Found at i:2004657 original size:36 final size:35
Alignment explanation
Indices: 2004599--2004684 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
2004589 ATTTGAGACG
* * * *
2004599 AATTAATTTAGTTTTTAATTAATTAAT-TAAATTT
1 AATTAATTTAATTATTAATTAATAAATAAAAATTT
*
2004633 AATTTAAATTTAATTATTATTTAATAAATAAAAAATTT
1 AA-TT-AATTTAATTATTAATTAATAAAT-AAAAATTT
2004671 AATTAATTTAATTA
1 AATTAATTTAATTA
2004685 AAAATATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 2 0.05
35 2 0.05
36 29 0.67
37 2 0.05
38 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
AATTAATTTAATTATTAATTAATAAATAAAAATTT
Found at i:2013785 original size:56 final size:56
Alignment explanation
Indices: 2013699--2013814 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
2013689 ATGATTATTT
2013699 TACACTTTCACATACTGAAGATTACTCATATATAATGTCATACCTCATTCGCAAAA
1 TACACTTTCACATACTGAAGATTACTCATATATAATGTCATACCTCATTCGCAAAA
*
2013755 TACACTTTCACATACTGAAGATTACTCATATATAATGTCATACCTTATTCGCAAAA
1 TACACTTTCACATACTGAAGATTACTCATATATAATGTCATACCTCATTCGCAAAA
2013811 TACA
1 TACA
2013815 AGTCGGAAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (56 bp):
TACACTTTCACATACTGAAGATTACTCATATATAATGTCATACCTCATTCGCAAAA
Found at i:2017593 original size:118 final size:118
Alignment explanation
Indices: 2017384--2017622 Score: 433
Period size: 118 Copynumber: 2.0 Consensus size: 118
2017374 AATCAATAAA
2017384 TTCAAGAGATCATCTGCAGCATGAACAAATATTAAGAAACAGCTCTAAGACAGTGAGGAGGGCTC
1 TTCAAGAGATCATCTGCAGCATGAACAAATATTAAGAAACAGCTCTAAGACAGTGAGGAGGGCTC
*
2017449 CTCTGCCAAAATTACAAGATTCATGGATATTCTTATGGTACTAAGGTTGTAAT
66 CTCTGCCAAAATTACAAGATTAATGGATATTCTTATGGTACTAAGGTTGTAAT
* *
2017502 TTCAAGAGATCATCTGCAGCATTAACTAATATTAAGAAACAGCTCTAAGACAGTGAGGAGGGCTC
1 TTCAAGAGATCATCTGCAGCATGAACAAATATTAAGAAACAGCTCTAAGACAGTGAGGAGGGCTC
**
2017567 CTCTGCCAATGTTACAAGATTAATGGATATTCTTATGGTACTAAGGTTGTAAT
66 CTCTGCCAAAATTACAAGATTAATGGATATTCTTATGGTACTAAGGTTGTAAT
2017620 TTC
1 TTC
2017623 TAAACGCACA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (118 bp):
TTCAAGAGATCATCTGCAGCATGAACAAATATTAAGAAACAGCTCTAAGACAGTGAGGAGGGCTC
CTCTGCCAAAATTACAAGATTAATGGATATTCTTATGGTACTAAGGTTGTAAT
Found at i:2021766 original size:19 final size:18
Alignment explanation
Indices: 2021728--2021781 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
2021718 TAAACTAAAC
2021728 AAAACAAAGGAAGGAA-AAA
1 AAAACAAA-GAA-GAAGAAA
2021747 AAAACAAAGAGAGAAGAAA
1 AAAACAAAGA-AGAAGAAA
**
2021766 AACCCAAAGAAGAAGA
1 AAAACAAAGAAGAAGA
2021782 TTGGTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.70, C:0.09, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAACAAAGAAGAAGAAA
Found at i:2022704 original size:17 final size:17
Alignment explanation
Indices: 2022682--2022719 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2022672 CCAAATAATC
2022682 ATATTTATATAACAATA
1 ATATTTATATAACAATA
*
2022699 ATATTTATATAACAGTA
1 ATATTTATATAACAATA
2022716 ATAT
1 ATAT
2022720 GATATAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTTATATAACAATA
Found at i:2024680 original size:102 final size:101
Alignment explanation
Indices: 2024501--2024688 Score: 268
Period size: 102 Copynumber: 1.9 Consensus size: 101
2024491 AAGTATGAAT
* * * *
2024501 CTGCAACCAGACATATTTGAGACACTAGTCATTATCTTATACGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGCCATTATCTTACACGAAATAGAATAAGCTAACATACC
2024566 GACAAACCATTTTAACCCAAAAATCTGAAAAAATATC
66 GACAAACCATTTTAA-CCAAAAATCTGAAAAAATATC
* * *
2024603 CTGCAACCAAACGTATTTGAGACACTAGCCATTATCTTACAGGAAATAGAATAAGCTAACATGCC
1 CTGCAACCAAACATATTTGAGACACTAGCCATTATCTTACACGAAATAGAATAAGCTAACATACC
* * * *
2024668 GATAGACTATTTTGACCAAAA
66 GACAAACCATTTTAACCAAAA
2024689 TATACTGACA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
101 6 0.08
102 69 0.92
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (101 bp):
CTGCAACCAAACATATTTGAGACACTAGCCATTATCTTACACGAAATAGAATAAGCTAACATACC
GACAAACCATTTTAACCAAAAATCTGAAAAAATATC
Found at i:2026139 original size:2 final size:2
Alignment explanation
Indices: 2026132--2026159 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2026122 CGAGTTGTTA
2026132 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
2026160 TCTCCCCAAA
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:2026958 original size:14 final size:15
Alignment explanation
Indices: 2026939--2026972 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2026929 GTCACCCTAA
*
2026939 AAAAAAT-ACAAAAT
1 AAAAAATAAAAAAAT
2026953 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
2026968 AAAAA
1 AAAAA
2026973 CAAGAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:2026965 original size:7 final size:7
Alignment explanation
Indices: 2026939--2026972 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2026929 GTCACCCTAA
2026939 AAAAAAT
1 AAAAAAT
*
2026946 ACAAAAT
1 AAAAAAT
2026953 AAAAAAT
1 AAAAAAT
2026960 AAAAAAAT
1 -AAAAAAT
2026968 AAAAA
1 AAAAA
2026973 CAAGAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:2027109 original size:12 final size:12
Alignment explanation
Indices: 2027092--2027116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2027082 GACAGGTACG
2027092 AAACTTGCTTGT
1 AAACTTGCTTGT
2027104 AAACTTGCTTGT
1 AAACTTGCTTGT
2027116 A
1 A
2027117 TATCACTGCT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AAACTTGCTTGT
Found at i:2031006 original size:2 final size:2
Alignment explanation
Indices: 2030999--2031038 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2030989 ACACAAACAC
2030999 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2031039 AACAAGCCAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2031619 original size:67 final size:67
Alignment explanation
Indices: 2031540--2031671 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
2031530 GTCTCTTAAG
*
2031540 ATAATGAACTATAGACAACCAAGAAACAAAGCAGTTTAACTGTTAAACACGGACATAGCTCCCTT
1 ATAATGAACTATAGACAACCAAGAAACAAAGCAGTTTAACTGTTAAACAAGGACATAGCTCCCTT
2031605 CA
66 CA
*
2031607 ATAATGAACTATAGATAACCAAGAAACAAAGCAGTTTAACTGTTAAACAAGGACATAGCTCCCTT
1 ATAATGAACTATAGACAACCAAGAAACAAAGCAGTTTAACTGTTAAACAAGGACATAGCTCCCTT
2031672 TAAAAGAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (67 bp):
ATAATGAACTATAGACAACCAAGAAACAAAGCAGTTTAACTGTTAAACAAGGACATAGCTCCCTT
CA
Found at i:2038669 original size:2 final size:2
Alignment explanation
Indices: 2038658--2038700 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2038648 GAAATAGAAT
2038658 TA TA -A 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 TA
2038699 TA
1 TA
2038701 AAGAACTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2040306 original size:17 final size:18
Alignment explanation
Indices: 2040281--2040318 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2040271 ACCTTGAGAA
* *
2040281 AAATTAAGTGAACC-AAG
1 AAATCAAGTAAACCAAAG
2040298 AAATCAAGTAAACCAAAG
1 AAATCAAGTAAACCAAAG
2040316 AAA
1 AAA
2040319 ATAAAGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (18 bp):
AAATCAAGTAAACCAAAG
Found at i:2048008 original size:21 final size:20
Alignment explanation
Indices: 2047984--2048031 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2047974 GGAGTCGGAG
2047984 AAAATTTTAACAAAAGATGTC
1 AAAATTTT-ACAAAAGATGTC
**
2048005 AAAATTTTAGTAAAGATGTC
1 AAAATTTTACAAAAGATGTC
*
2048025 AGAATTT
1 AAAATTT
2048032 AGAAGAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAATTTTACAAAAGATGTC
Found at i:2048148 original size:12 final size:12
Alignment explanation
Indices: 2048131--2048155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2048121 CATATAAATT
2048131 ATCTTTGACTAA
1 ATCTTTGACTAA
2048143 ATCTTTGACTAA
1 ATCTTTGACTAA
2048155 A
1 A
2048156 GTATAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2048824 original size:2 final size:2
Alignment explanation
Indices: 2048784--2048809 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2048774 CAGCACGTAA
2048784 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2048810 GGGTTGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2049273 original size:17 final size:16
Alignment explanation
Indices: 2049248--2049295 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2049238 AATTATATTA
2049248 TTTTATTTAAATATAT
1 TTTTATTTAAATATAT
* *
2049264 TTTATATTTAAATAAAAA
1 TTT-TATTTAAAT-ATAT
2049282 TTTTATTTAAATAT
1 TTTTATTTAAATAT
2049296 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.67
18 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTATTTAAATATAT
Found at i:2049349 original size:22 final size:21
Alignment explanation
Indices: 2049295--2049353 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
2049285 TATTTAAATA
*
2049295 TTAATAAAAATTTAAAATGAT
1 TTAATAAAAATTAAAAATGAT
*
2049316 TTAGATAAAAATTAAAAATTTAT
1 TTA-ATAAAAATTAAAAA-TGAT
*
2049339 TTAATATAAATTAAA
1 TTAATAAAAATTAAA
2049354 GTTATTGACT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 24 0.73
23 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
TTAATAAAAATTAAAAATGAT
Found at i:2049399 original size:22 final size:22
Alignment explanation
Indices: 2049369--2049420 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2049359 TGACTTATTT
*
2049369 AAATATAATCACAA-AATATAAAA
1 AAAT-TAATCA-AATAAAATAAAA
*
2049392 AAATTAATTAAATAAAATAAAA
1 AAATTAATCAAATAAAATAAAA
2049414 AAATTAA
1 AAATTAA
2049421 AAGAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 4 0.15
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATTAATCAAATAAAATAAAA
Found at i:2055101 original size:81 final size:81
Alignment explanation
Indices: 2055000--2055162 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
2054990 ATTTTCTTGA
2055000 GGGGTGTTGGGGAGCTACGGGAATGGATTTTTGCTGAGCTTTATGCTAGTTTTTGGCTAAGATAT
1 GGGGTGTTGGGGAGCTACGGGAATGGATTTTTGCTGAGCTTTATGCTAGTTTTTGGCTAAGATAT
2055065 GGCTGATAATGTGATT
66 GGCTGATAATGTGATT
2055081 GGGGTGTTGGGGAGCTACGGGAATGGATTTTTGCTGAGCTTTATGCTAGTTTTTGGCTAAGATAT
1 GGGGTGTTGGGGAGCTACGGGAATGGATTTTTGCTGAGCTTTATGCTAGTTTTTGGCTAAGATAT
2055146 GGCTGATAATGTGATT
66 GGCTGATAATGTGATT
2055162 G
1 G
2055163 AAAATGTGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.20, C:0.09, G:0.35, T:0.37
Consensus pattern (81 bp):
GGGGTGTTGGGGAGCTACGGGAATGGATTTTTGCTGAGCTTTATGCTAGTTTTTGGCTAAGATAT
GGCTGATAATGTGATT
Found at i:2055612 original size:30 final size:28
Alignment explanation
Indices: 2055564--2055620 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
2055554 GCTCAAAATT
*
2055564 AACTAAATGTATTAATACATCTGATAAAAA
1 AACTAAATGTATCAATACAT-TGA-AAAAA
* *
2055594 AACTGAATGTATCGATACATTGAAAAA
1 AACTAAATGTATCAATACATTGAAAAA
2055621 TGTATCCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 3 0.12
30 17 0.71
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (28 bp):
AACTAAATGTATCAATACATTGAAAAAA
Found at i:2056496 original size:61 final size:61
Alignment explanation
Indices: 2056379--2056496 Score: 132
Period size: 61 Copynumber: 1.9 Consensus size: 61
2056369 AAATGCGAAA
* * * * * *
2056379 AATGATAAAGGTTCCAATTTGTTGATTTCCGGCCAGCGATATCGATCTTGAAGATGAGTAG
1 AATGATAAAGGTGCCAATATGCTGATTTCCGACCAGCAATATCGAGCTTGAAGATGAGTAG
* *
2056440 AATGATAAAGGTGCCAATATGCTGA-TTCACGACCATCAATATTGAGCTT-AACGATGA
1 AATGATAAAGGTGCCAATATGCTGATTTC-CGACCAGCAATATCGAGCTTGAA-GATGA
2056497 CAAAGGTGCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
60 5 0.11
61 42 0.89
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (61 bp):
AATGATAAAGGTGCCAATATGCTGATTTCCGACCAGCAATATCGAGCTTGAAGATGAGTAG
Found at i:2056812 original size:64 final size:64
Alignment explanation
Indices: 2056716--2056838 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 64
2056706 AAAATGGTTG
* * *
2056716 CCACCGAATTGTATGGGCTTTAGAGAAAGTTGCCACCAACTTATATGGGCTTTAGAAGGAGATA
1 CCACCGAATTATATGAGCTTTAGAGAAAGTTGCCACCAACTTATATAGGCTTTAGAAGGAGATA
* * ** ** * *
2056780 CCACCGACTTATATGAGCTTTTGAGAGGGTTGCCACTGACTTATGTAGGCTTTTGAAGG
1 CCACCGAATTATATGAGCTTTAGAGAAAGTTGCCACCAACTTATATAGGCTTTAGAAGG
2056839 GGGTTGCCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (64 bp):
CCACCGAATTATATGAGCTTTAGAGAAAGTTGCCACCAACTTATATAGGCTTTAGAAGGAGATA
Found at i:2056821 original size:32 final size:32
Alignment explanation
Indices: 2056711--2056823 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
2056701 GCTTAAAAAT
* * * *
2056711 GGTTGCCACCGAATTGTATGGGCTTTAGAGAA
1 GGTTGCCACCGACTTATATGAGCTTTAGAGAG
* * *
2056743 AGTTGCCACCAACTTATATGGGCTTTAGA-AG
1 GGTTGCCACCGACTTATATGAGCTTTAGAGAG
* * *
2056774 GAGATACCACCGACTTATATGAGCTTTTGAGAG
1 G-GTTGCCACCGACTTATATGAGCTTTAGAGAG
*
2056807 GGTTGCCACTGACTTAT
1 GGTTGCCACCGACTTAT
2056824 GTAGGCTTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
31 1 0.02
32 61 0.94
33 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (32 bp):
GGTTGCCACCGACTTATATGAGCTTTAGAGAG
Found at i:2056899 original size:33 final size:33
Alignment explanation
Indices: 2056852--2057038 Score: 193
Period size: 33 Copynumber: 5.8 Consensus size: 33
2056842 TTGCCATAAG
* * *
2056852 GTTACCACCAACTTGTGTGGGCTTTTGAAGATA
1 GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
* * **
2056885 GTTACCACCGACTTGTGTGGACTTTTGAAGAGG
1 GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
* *
2056918 GTTGCCACCAACTTGTGTGGGCTTTAGAA-AAA
1 GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
* * *
2056950 ATTGCCACCGACTTGTTTGGGCTTTAG-AGAAA
1 GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
* * *
2056982 ATTACCACCGACTTGTGTGGGCTTTAAAAG-GA
1 GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
**
2057014 GTT-TTACCGACTTGTGTGGGCTTTA
1 GTTACCACCGACTTGTGTGGGCTTTA
2057039 AAAAGATGCC
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
31 21 0.16
32 55 0.42
33 56 0.42
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (33 bp):
GTTACCACCGACTTGTGTGGGCTTTAGAAGAAA
Found at i:2056964 original size:32 final size:32
Alignment explanation
Indices: 2056856--2057118 Score: 190
Period size: 33 Copynumber: 8.3 Consensus size: 32
2056846 CATAAGGTTA
* * * *
2056856 CCACCAACTTGTGTGGGCTTTTGAAGATAGTTA
1 CCACCGACTTGTGTGGGCTTTAGAA-AAAGTTG
* * **
2056889 CCACCGACTTGTGTGGACTTTTGAAGAGGGTTG
1 CCACCGACTTGTGTGGGCTTTAGAA-AAAGTTG
* *
2056922 CCACCAACTTGTGTGGGCTTTAGAAAAAATTG
1 CCACCGACTTGTGTGGGCTTTAGAAAAAGTTG
* *
2056954 CCACCGACTTGTTTGGGCTTTAGAGAAAA-TTA
1 CCACCGACTTGTGTGGGCTTTAGA-AAAAGTTG
*
2056986 CCACCGACTTGTGTGGGCTTTA-AAAGGAGTT-
1 CCACCGACTTGTGTGGGCTTTAGAAA-AAGTTG
** *
2057017 TTACCGACTTGTGTGGGCTTT--AAAAAGATG
1 CCACCGACTTGTGTGGGCTTTAGAAAAAGTTG
** *
2057047 CCACTAAC-T-TGTGAGCTTT-GAAAAAGGGTTG
1 CCACCGACTTGTGTGGGCTTTAGAAAAA--GTTG
2057078 CCACC-AGCTTGTGTGGGCTTT-G--AAAGTATG
1 CCACCGA-CTTGTGTGGGCTTTAGAAAAAGT-TG
*
2057108 CCACTGACTTG
1 CCACCGACTTG
2057119 AAGGCTTTGA
Statistics
Matches: 189, Mismatches: 29, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.05
29 11 0.06
30 20 0.11
31 33 0.17
32 52 0.28
33 64 0.34
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (32 bp):
CCACCGACTTGTGTGGGCTTTAGAAAAAGTTG
Found at i:2057152 original size:28 final size:27
Alignment explanation
Indices: 2057090--2057154 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
2057080 ACCAGCTTGT
*
2057090 GTGGGCTTTGAAAGTATGCCACTGACTT
1 GTGGGCTTTGAAAGTAT-CCACTGACTC
**
2057118 GAAGGCTTTGAAAGGGTAT-CACTGACTC
1 GTGGGCTTTGAAA--GTATCCACTGACTC
2057146 GTGGGCTTT
1 GTGGGCTTT
2057155 TGAGAGGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 26 0.87
30 4 0.13
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (27 bp):
GTGGGCTTTGAAAGTATCCACTGACTC
Found at i:2058887 original size:26 final size:26
Alignment explanation
Indices: 2058858--2058940 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
2058848 TCTGAAGGAG
2058858 TGTGAGCATGAACGACATTGACAAAA
1 TGTGAGCATGAACGACATTGACAAAA
* * *
2058884 TGTGATGACA--AA-AACATCTGA-AGGAG
1 TGTGA-G-CATGAACGACAT-TGACA-AAA
2058910 TGTGAGCATGAACGACATTGACAAAA
1 TGTGAGCATGAACGACATTGACAAAA
2058936 TGTGA
1 TGTGA
2058941 TGACAAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
24 2 0.05
25 6 0.14
26 27 0.63
27 6 0.14
28 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.20
Consensus pattern (26 bp):
TGTGAGCATGAACGACATTGACAAAA
Found at i:2058923 original size:52 final size:52
Alignment explanation
Indices: 2058845--2058952 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
2058835 TTTTACCAGT
2058845 ACATCTGAAGGAGTGTGAGCATGAACGACATTGACAAAATGTGATGACAAAA
1 ACATCTGAAGGAGTGTGAGCATGAACGACATTGACAAAATGTGATGACAAAA
2058897 ACATCTGAAGGAGTGTGAGCATGAACGACATTGACAAAATGTGATGACAAAA
1 ACATCTGAAGGAGTGTGAGCATGAACGACATTGACAAAATGTGATGACAAAA
2058949 ACAT
1 ACAT
2058953 GTATGGACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (52 bp):
ACATCTGAAGGAGTGTGAGCATGAACGACATTGACAAAATGTGATGACAAAA
Found at i:2064876 original size:51 final size:51
Alignment explanation
Indices: 2064821--2064918 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
2064811 AAAATGTATC
* * *
2064821 TAGGTAAAAATACAGAATGTTTCGATA-CATTGAAAAATGTATCGATACATT
1 TAGGTAAAAAAACAAAATGTATCGA-AGCATTGAAAAATGTATCGATACATT
*
2064872 TAGGTAAAAAAATAAAATGTATCGAAGCATTGAAAAATGTATCGATA
1 TAGGTAAAAAAACAAAATGTATCGAAGCATTGAAAAATGTATCGATA
2064919 TATTCACACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (51 bp):
TAGGTAAAAAAACAAAATGTATCGAAGCATTGAAAAATGTATCGATACATT
Found at i:2066070 original size:65 final size:65
Alignment explanation
Indices: 2065959--2066080 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
2065949 AAATAGTTGC
* *
2065959 CACCGACTTGTATGGGTTTTAGAGAAAGTTGCCACCGACTTGTATGGACTTT-AGAATGAGATAT
1 CACCGACTTGTATGGCTTTTAGAGAAAGTTGCCACCGACTTATATGGACTTTGAGAATGAGATAT
* * * *
2066023 CACCGACTTGTGTAGGCTTTT-GAAGGAAGTTGCCACCGATTTATATGGGCTTTGAGAA
1 CACCGACTTGTAT-GGCTTTTAG-AGAAAGTTGCCACCGACTTATATGGACTTTGAGAA
2066081 CGGTTGCCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 13 0.27
65 32 0.65
66 4 0.08
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
CACCGACTTGTATGGCTTTTAGAGAAAGTTGCCACCGACTTATATGGACTTTGAGAATGAGATAT
Found at i:2066174 original size:33 final size:33
Alignment explanation
Indices: 2065953--2066174 Score: 134
Period size: 32 Copynumber: 6.8 Consensus size: 33
2065943 GTTTAAAAAT
* * *
2065953 AGTTGCCACCGACTTGTATGGG-TTTT-AGAGAA
1 AGTTGCCACCAACTTGTGTGGGCTTTTGA-AGGA
* * * * *
2065985 AGTTGCCACCGACTTGTATGGACTTTAGAATG-
1 AGTTGCCACCAACTTGTGTGGGCTTTTGAAGGA
* ** * *
2066017 AGATATCACCGACTTGTGTAGGCTTTTGAAGGA
1 AGTTGCCACCAACTTGTGTGGGCTTTTGAAGGA
* * * *
2066050 AGTTGCCACCGATTTATATGGGC-TTTG-A-GA
1 AGTTGCCACCAACTTGTGTGGGCTTTTGAAGGA
* * *
2066080 ACGGTTGCCACCAGCTTGTGTGGGCTTTAAGAAAG-
1 A--GTTGCCACCAACTTGTGTGGGCTTT-TGAAGGA
* * *
2066115 AGTTGCCAGCAGCTTGTGTGAGCTTTTGAAGGA
1 AGTTGCCACCAACTTGTGTGGGCTTTTGAAGGA
* *
2066148 AGTTGCTAGCAACTTGTGTGGGCTTTT
1 AGTTGCCACCAACTTGTGTGGGCTTTT
2066175 AAAGAGGATT
Statistics
Matches: 148, Mismatches: 32, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
30 3 0.02
31 1 0.01
32 70 0.47
33 69 0.47
34 2 0.01
35 2 0.01
36 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (33 bp):
AGTTGCCACCAACTTGTGTGGGCTTTTGAAGGA
Found at i:2066202 original size:30 final size:28
Alignment explanation
Indices: 2066167--2066247 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
2066157 CAACTTGTGT
*
2066167 GGGCTTTTAAAGAGGATTGCCACCGACTGC
1 GGGCTTTAAAAGA-GA-TGCCACCGACTGC
* *
2066197 GGGCTTTAAAAGAGATGTCACCGACTTGTGT
1 GGGCTTTAAAAGAGATGCCACCGAC---TGC
2066228 GGGCTTTAAAAGAG-TGCCAC
1 GGGCTTTAAAAGAGATGCCAC
2066248 TGAGTTGTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 9 0.20
29 2 0.05
30 17 0.39
31 16 0.36
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (28 bp):
GGGCTTTAAAAGAGATGCCACCGACTGC
Found at i:2066235 original size:31 final size:32
Alignment explanation
Indices: 2065955--2066241 Score: 136
Period size: 33 Copynumber: 9.0 Consensus size: 32
2065945 TTAAAAATAG
* *
2065955 TTGCCACCGACTTGTATGGGTTTTAGAGAA-AG-
1 TTGCCACCGACTTGTGTGGGCTTTA-A-AAGAGA
* * *
2065987 TTGCCACCGACTTGTATGGACTTTAGAATGAGA
1 TTGCCACCGACTTGTGTGGGCTTTA-AAAGAGA
* **
2066020 TAT--CACCGACTTGTGTAGGCTTTTGAAG-GAA
1 T-TGCCACCGACTTGTGTGGGCTTTAAAAGAG-A
* * * *
2066051 GTTGCCACCGATTTATATGGGCTTTGAGAACG-G-
1 -TTGCCACCGACTTGTGTGGGCTTT-A-AAAGAGA
2066084 TTGCCACC-AGCTTGTGTGGGCTTTAAGAA-AGA
1 TTGCCACCGA-CTTGTGTGGGCTTTAA-AAGAGA
* * **
2066116 GTTGCCAGC-AGCTTGTGTGAGCTTTTGAAG-GAA
1 -TTGCCACCGA-CTTGTGTGGGCTTTAAAAGAG-A
* * * *
2066149 GTTGCTAGCAACTTGTGTGGGCTTTTAAAGAGGA
1 -TTGCCACCGACTTGTGTGGGCTTTAAAAGA-GA
*
2066183 TTGCCACCGAC---TGCGGGCTTTAAAAGAGA
1 TTGCCACCGACTTGTGTGGGCTTTAAAAGAGA
*
2066212 -TGTCACCGACTTGTGTGGGCTTTAAAAGAG
1 TTGCCACCGACTTGTGTGGGCTTTAAAAGAG
2066242 TGCCACTGAG
Statistics
Matches: 199, Mismatches: 34, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
28 9 0.05
29 2 0.01
30 16 0.08
31 25 0.13
32 67 0.34
33 73 0.37
34 3 0.02
35 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (32 bp):
TTGCCACCGACTTGTGTGGGCTTTAAAAGAGA
Found at i:2066362 original size:28 final size:28
Alignment explanation
Indices: 2066291--2066380 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
2066281 GCTTATGTAG
* **
2066291 GCTTTGAAAGGATGCCACTGACTTATAGA
1 GCTTTGAAAGGGTGCCACTGACTCGT-GA
** *
2066320 TTTTTGAAAGAGTGCCACTGACTCGTGA
1 GCTTTGAAAGGGTGCCACTGACTCGTGA
* *
2066348 GCTTTGAAAGGGTGCCACTAACTCGTGG
1 GCTTTGAAAGGGTGCCACTGACTCGTGA
2066376 GCTTT
1 GCTTT
2066381 TGAGAGAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
28 30 0.60
29 20 0.40
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (28 bp):
GCTTTGAAAGGGTGCCACTGACTCGTGA
Found at i:2067931 original size:22 final size:22
Alignment explanation
Indices: 2067903--2067949 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2067893 AAGATCAAAA
2067903 TATAATAATGGTGTCATAAGGT
1 TATAATAATGGTGTCATAAGGT
*
2067925 TATAATAATGGTGTCATAGGGT
1 TATAATAATGGTGTCATAAGGT
2067947 TAT
1 TAT
2067950 CATACGACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (22 bp):
TATAATAATGGTGTCATAAGGT
Found at i:2078638 original size:13 final size:13
Alignment explanation
Indices: 2078620--2078644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2078610 AGGAAGACGA
2078620 GAAAAGAAAAAAG
1 GAAAAGAAAAAAG
2078633 GAAAAGAAAAAA
1 GAAAAGAAAAAA
2078645 AAAGGTCTAA
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAAG
Found at i:2079056 original size:14 final size:15
Alignment explanation
Indices: 2079037--2079065 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2079027 TTAAATTATT
2079037 TTTAAA-AAAAATAA
1 TTTAAATAAAAATAA
2079051 TTTAAATAAAAATAA
1 TTTAAATAAAAATAA
2079066 ATAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTTAAATAAAAATAA
Found at i:2082852 original size:14 final size:14
Alignment explanation
Indices: 2082833--2082861 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2082823 AAATAATTAA
2082833 ATAGAACATAATGT
1 ATAGAACATAATGT
2082847 ATAGAACATAATGT
1 ATAGAACATAATGT
2082861 A
1 A
2082862 AAGGATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAGAACATAATGT
Found at i:2090684 original size:24 final size:24
Alignment explanation
Indices: 2090639--2090685 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2090629 ACATCAAATT
**
2090639 AAATACAAAGGAAAAAGTTAAAAA
1 AAATACAAAGGAAAAAAATAAAAA
2090663 AAAT-CAAAGGAAAAAAAATAAAA
1 AAATACAAAGG-AAAAAAATAAAA
2090686 CATACCTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (24 bp):
AAATACAAAGGAAAAAAATAAAAA
Found at i:2093945 original size:9 final size:9
Alignment explanation
Indices: 2093917--2093951 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2093907 ATGAAATTTA
2093917 TCATAAATT
1 TCATAAATT
**
2093926 TCATATGTT
1 TCATAAATT
2093935 TCATAAATT
1 TCATAAATT
2093944 TCATAAAT
1 TCATAAAT
2093952 CACCTCTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
TCATAAATT
Found at i:2094800 original size:12 final size:12
Alignment explanation
Indices: 2094783--2094807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2094773 TCATATAAAC
2094783 ATCTTTGACTAA
1 ATCTTTGACTAA
2094795 ATCTTTGACTAA
1 ATCTTTGACTAA
2094807 A
1 A
2094808 GTTTAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2095472 original size:2 final size:2
Alignment explanation
Indices: 2095465--2095490 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2095455 CAGCACGTAA
2095465 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2095491 GTTGGAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2095718 original size:18 final size:18
Alignment explanation
Indices: 2095691--2095753 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
2095681 ATTAAAGTTT
*
2095691 TTTAATTATATTATTTTA
1 TTTAAATATATTATTTTA
*
2095709 TTTAAATATATT-TTTATG
1 TTTAAATATATTATTT-TA
** *
2095727 TTTAAA-ATAAAAATTTA
1 TTTAAATATATTATTTTA
2095744 TTTAAATATA
1 TTTAAATATA
2095754 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 13 0.36
18 23 0.64
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATATATTATTTTA
Found at i:2095770 original size:30 final size:29
Alignment explanation
Indices: 2095727--2095832 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 29
2095717 TATTTTTATG
2095727 TTTAAAA-TAAAAATTTATTTAAATATAA
1 TTTAAAATTAAAAATTTATTTAAATATAA
*
2095755 TTTAAAAATTAAAAATTTATTT-AATGTAA
1 TTT-AAAATTAAAAATTTATTTAAATATAA
* *** * *
2095784 ATTAAAATTATTGACTTATTTAAATACAA
1 TTTAAAATTAAAAATTTATTTAAATATAA
*
2095813 TCTCAAAATATAAAAATTTA
1 T-TTAAAAT-TAAAAATTTA
2095833 AATAAATAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
28 17 0.29
29 17 0.29
30 19 0.32
31 6 0.10
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (29 bp):
TTTAAAATTAAAAATTTATTTAAATATAA
Found at i:2095788 original size:29 final size:29
Alignment explanation
Indices: 2095730--2095790 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2095720 TTTTATGTTT
*
2095730 AAAATAAAAATTTATTTAAATATAATTTA
1 AAAATAAAAATTTATTTAAATATAAATTA
*
2095759 AAAATTAAAAATTTATTT-AATGTAAATTA
1 AAAA-TAAAAATTTATTTAAATATAAATTA
2095788 AAA
1 AAA
2095791 TTATTGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAATAAAAATTTATTTAAATATAAATTA
Found at i:2095950 original size:28 final size:28
Alignment explanation
Indices: 2095899--2095953 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2095889 AAAAATTTAA
*
2095899 AAAATAAAATTTCATATCTAATAAAAAT
1 AAAATAAAATTTCAAATCTAATAAAAAT
* * *
2095927 AAAATAAATTTTCAAATTTTATAAAAA
1 AAAATAAAATTTCAAATCTAATAAAAA
2095954 ATTTCAGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATAAAATTTCAAATCTAATAAAAAT
Found at i:2098217 original size:37 final size:37
Alignment explanation
Indices: 2098175--2098247 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
2098165 TAATAATAGA
*
2098175 CGTTCAATTAAAGATCTTTGATTCACAGATATTAAAC
1 CGTTCAATTAAAAATCTTTGATTCACAGATATTAAAC
*
2098212 CGTTCAATTAAAAATCTTTGATTCACAGATGTTAAA
1 CGTTCAATTAAAAATCTTTGATTCACAGATATTAAA
2098248 ACAGTTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (37 bp):
CGTTCAATTAAAAATCTTTGATTCACAGATATTAAAC
Found at i:2098480 original size:23 final size:22
Alignment explanation
Indices: 2098436--2098480 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2098426 AGATATGTTT
**
2098436 AAAAAATTAAAAATTTAATAAA
1 AAAAAATTAAAAAAATAATAAA
*
2098458 AAAAAATGTAAAAAAATATTAAA
1 AAAAAAT-TAAAAAAATAATAAA
2098481 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAAATTAAAAAAATAATAAA
Found at i:2099555 original size:82 final size:83
Alignment explanation
Indices: 2099456--2099620 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
2099446 ATTATTAAAA
2099456 GATTTATAAATTCATAAATAAAAAGACAAATTTTGGAGAC-TTAAAATTTTTCTTTCTTTTATTT
1 GATTTATAAATTCATAAATAAAAAGACAAATTTTGGAGACTTTAAAATTTTTCTTTCTTTTATTT
2099520 TAAACTCACTCAAAAACT
66 TAAACTCACTCAAAAACT
*
2099538 GATTTATAAATTCATAAATAAAAAGATAAATTTTGGAGACTTTAAAATTTTTCTTTCTTTTATTT
1 GATTTATAAATTCATAAATAAAAAGACAAATTTTGGAGACTTTAAAATTTTTCTTTCTTTTATTT
2099603 TAAACTCACTCAAAAACT
66 TAAACTCACTCAAAAACT
2099621 AATGTATGTA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 39 0.48
83 42 0.52
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (83 bp):
GATTTATAAATTCATAAATAAAAAGACAAATTTTGGAGACTTTAAAATTTTTCTTTCTTTTATTT
TAAACTCACTCAAAAACT
Found at i:2100013 original size:24 final size:23
Alignment explanation
Indices: 2099973--2100018 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2099963 ATTCATTTAA
*
2099973 ATTAAATGAAATTATTTTATAAAC
1 ATTAAATGAAATCA-TTTATAAAC
2099997 ATTAAATG-AATACATTTATAAA
1 ATTAAATGAAAT-CATTTATAAA
2100019 TGTATAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
ATTAAATGAAATCATTTATAAAC
Found at i:2101939 original size:24 final size:24
Alignment explanation
Indices: 2101900--2101948 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2101890 CTGTAACTGT
*
2101900 ATAAGGATGTCATATAATCAAAAA
1 ATAAGGATATCATATAATCAAAAA
*
2101924 ATAAGGATATCGTATAATCAAAAA
1 ATAAGGATATCATATAATCAAAAA
2101948 A
1 A
2101949 AAAAATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
ATAAGGATATCATATAATCAAAAA
Found at i:2102472 original size:102 final size:102
Alignment explanation
Indices: 2102293--2102480 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
2102283 ATGAATATCC
* * * **
2102293 TGCAACCAGACATATTTGAGACACTAGTCATTATCTTATAGGAAATAGAATAAGCCAAAATACTG
1 TGCAACCAAACATACTTGAGACACTAGTCATTATCTTAGAGGAAATAGAATAAGCCAAAATACCA
*
2102358 ACGGACTATTTTAACCAAAATTTCTGAAAAAATATAT
66 ACAGACTATTTTAACCAAAATTTCTGAAAAAATATAT
* * *
2102395 TGCAACCAAACATACTTGAGACACTAGTCATTATCTTAGAGGAAATAGAATAAGCTAAGATGCCA
1 TGCAACCAAACATACTTGAGACACTAGTCATTATCTTAGAGGAAATAGAATAAGCCAAAATACCA
* *
2102460 ATAGACTTTTTTAACCAAAAT
66 ACAGACTATTTTAACCAAAAT
2102481 ATACTGACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 75 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (102 bp):
TGCAACCAAACATACTTGAGACACTAGTCATTATCTTAGAGGAAATAGAATAAGCCAAAATACCA
ACAGACTATTTTAACCAAAATTTCTGAAAAAATATAT
Found at i:2103748 original size:488 final size:485
Alignment explanation
Indices: 2102835--2103751 Score: 1514
Period size: 488 Copynumber: 1.9 Consensus size: 485
2102825 ATATAAATAA
* *
2102835 AATTTTTACTAAGATCAACGACCTTAGTCAGTGCCTCTTTCTTCAAAGCTGGCATTTAACTTCAG
1 AATTTTTACTAAGATCAACAACCTTAGTCAGTGCCTCTTTCTTCAAAACTGGCATTTAACTTCAG
*
2102900 ATGAGTGACAACAGCTAATAAGAAAAAAGCAAAACCCCAAAAACAGCAGACAATTCAGAGTACTG
66 ATGAGTGACAACAGCTAATAAGAAAAAAGCAAAACCCCAAAAAAAGCAGACAATTCAGAGTACTG
* * *
2102965 GTGACAATTCGAAATATGTATATTGAACCCCAAAGCAATACTCAGTACCTGGCACATTTTAGTCT
131 GTGACAATTCAAAATATGTAAATTGAACCCCAAAGCAATACTCAGTAACTGGCACATTTTAGTCT
* *
2103030 TCTCACCACCTGTTTCACCGACAAGGAGCAGCAGCTCATGAAACTTATAGCAACTTCAGACAAGG
196 TCCCACCACCTGTTTCACCAACAAGGAGCAGCAGCTCATGAAACTTATAGCAACTTCAGACAAGG
* *
2103095 AAGTTCAATCTTCTCACCCTCTATTTAAGATCACATGGCAATAAAGAAGATCATTAGGAGTAAAA
261 AAGTACAATCTTCTCACCCTCTAGTTAAGATCACATGGCAATAAAGAAGATCATTAGGAGTAAAA
*
2103160 TGAAACATACCACAAATTAGCAGAACCATGATAAAACAAAACAGGTCCACAAATCCTTGCTTTCT
326 TGAAACATACCACAAATTAGCAGAACCATGATAAAACAAAACAGGTCCACAAATCCTTACTTTCT
* * *
2103225 GAGACTCTCTCTGGAACAGAGTCCTCTCCAATCAATTCCTCAAGAATGAAAAACAAGATAGCAAA
391 AAGACTATCTCTGGAACAGAGTCCCCTCCAATCAATTCCTCAAGAATGAAAAACAAGATAGCAAA
2103290 AAAAAGACACGGCATGCTGGCACGGGAGTG
456 AAAAAGACACGGCATGCTGGCACGGGAGTG
* *
2103320 AATTTTTACTAAGATCAACAACCTTAGTCAGTGTCTC-TTCTTCAAAACTGGCGTTTAACTTTCA
1 AATTTTTACTAAGATCAACAACCTTAGTCAGTGCCTCTTTCTTCAAAACTGGCATTTAAC-TTCA
* * * * *
2103384 GATGAGTGGCAACAGCTAATGAGAAAAAAGTAAACAAAACCCCAAAAAAAGCTGAGACTTCAGAG
65 GATGAGTGACAACAGCTAATAAGAAAAAAG----CAAAACCCCAAAAAAAGCAGACAATTCAGAG
2103449 TACTGGTGACAATTCAAAATATGTAAATTGAACCCCAAAGCAATACTCAGTAACTGGCACATTTT
126 TACTGGTGACAATTCAAAATATGTAAATTGAACCCCAAAGCAATACTCAGTAACTGGCACATTTT
* * * * *
2103514 AGTTTTCCCATCATCTGTTTCGCCAACAAGGAGCAGCGGCTCATGAAACTT-TAGCAACTTCAGA
191 AGTCTTCCCACCACCTGTTTCACCAACAAGGAGCAGCAGCTCATGAAACTTATAGCAACTTCAGA
*
2103578 CAAGGAAGTACAATCTTCTCACCTTCTAGTTAAGATCACATGGCAATAAAGAAGATCATTAGGAG
256 CAAGGAAGTACAATCTTCTCACCCTCTAGTTAAGATCACATGGCAATAAAGAAGATCATTAGGAG
*
2103643 TAAAATGAAACATACCACAAATTAGCAGAACCATGATAAAACAAAACAGGTCCACAAGTCCTTAC
321 TAAAATGAAACATACCACAAATTAGCAGAACCATGATAAAACAAAACAGGTCCACAAATCCTTAC
*
2103708 TTTCTAAGACTATCTCTGGAACAGGGTCCCCTCCAATCAATTCC
386 TTTCTAAGACTATCTCTGGAACAGAGTCCCCTCCAATCAATTCC
2103752 GTGAGAATTA
Statistics
Matches: 398, Mismatches: 29, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
484 20 0.05
485 67 0.17
488 178 0.45
489 133 0.33
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24
Consensus pattern (485 bp):
AATTTTTACTAAGATCAACAACCTTAGTCAGTGCCTCTTTCTTCAAAACTGGCATTTAACTTCAG
ATGAGTGACAACAGCTAATAAGAAAAAAGCAAAACCCCAAAAAAAGCAGACAATTCAGAGTACTG
GTGACAATTCAAAATATGTAAATTGAACCCCAAAGCAATACTCAGTAACTGGCACATTTTAGTCT
TCCCACCACCTGTTTCACCAACAAGGAGCAGCAGCTCATGAAACTTATAGCAACTTCAGACAAGG
AAGTACAATCTTCTCACCCTCTAGTTAAGATCACATGGCAATAAAGAAGATCATTAGGAGTAAAA
TGAAACATACCACAAATTAGCAGAACCATGATAAAACAAAACAGGTCCACAAATCCTTACTTTCT
AAGACTATCTCTGGAACAGAGTCCCCTCCAATCAATTCCTCAAGAATGAAAAACAAGATAGCAAA
AAAAAGACACGGCATGCTGGCACGGGAGTG
Found at i:2107905 original size:2 final size:2
Alignment explanation
Indices: 2107894--2107932 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2107884 GAAATAGAAT
2107894 TA TA TA -A 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
2107933 AAGAACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2110415 original size:228 final size:229
Alignment explanation
Indices: 2109996--2110692 Score: 1056
Period size: 228 Copynumber: 3.0 Consensus size: 229
2109986 GCAAAATCCA
* * *
2109996 TTGCTTCATTGTCTACCACTTGGCTTATCTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCT----AACTACAAGAAGGCAAGCAGAATACATTATA
*
2110061 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACTAAGGCCAAATCCAGCACC
62 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACAAAGGCCAAATCCAGCACC
*
2110126 TTGCCTATTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTC
127 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTC
2110191 AAAAAAACTCTTTCACCACTATCCTTTCTAGAACTGGT
192 AAAAAAACTCTTTCACCACTATCCTTTCTAGAACTGGT
*
2110229 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACTACAAGAAGGCAAGCCGAATACATTATAAAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACTACAAGAAGGCAAGCAGAATACATTATAAAAA
* * * *
2110294 AGAAACCTTCTAAAATTAAAATAAAAGAGAAATCCGGAACACCAA-GCCCAATCCAGCACCTTGC
66 AGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACAAAGGCCAAATCCAGCACCTTGC
* * *
2110358 CTACTTACTCTAAGTCAATTGGGCTCATAAAAAGAATAGCTTGGAAATTGACGAATCATTCAAAA
131 CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAAA
2110423 AAACTCTTTCACCACTATCCTTTCTAGAACTGGT
196 AAACTCTTTCACCACTATCCTTTCTAGAACTGGT
*
2110457 TTGCTTCATTGTCTTCCACTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT----CTAACTACAAGAAGGCAAGCAGAATACATTATA
* * *
2110522 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACAAAGGCCAAACCCATCACC
62 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACAAAGGCCAAATCCAGCACC
* * *
2110587 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCGT
127 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATC-A
* * * * *
2110652 TTC-GAAAACCTCTTTAACCAGTTTCCTTTCTAGAACTGGT
189 TTCAAAAAAACTCTTTCACCACTATCCTTTCTAGAACTGGT
2110692 T
1 T
2110693 GTCAATGCCT
Statistics
Matches: 424, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
228 141 0.33
229 75 0.18
232 76 0.18
233 85 0.20
235 44 0.10
236 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (229 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATCTAACTACAAGAAGGCAAGCAGAATACATTATAAAAA
AGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACAAAGGCCAAATCCAGCACCTTGC
CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAAA
AAACTCTTTCACCACTATCCTTTCTAGAACTGGT
Found at i:2114806 original size:274 final size:275
Alignment explanation
Indices: 2114316--2114869 Score: 1092
Period size: 274 Copynumber: 2.0 Consensus size: 275
2114306 TTATGCGGTA
2114316 GCAAAGAATAAAAATAATTACCATAACAAGTTTAAATTAGTCAATGGTATATATTGAACCTCAAA
1 GCAAAGAATAAAAATAATTACCATAACAAGTTTAAATTAGTCAATGGTATATATTGAACCTCAAA
2114381 CTTTTTTTTCGCCCCATGCGATTGATATTTCGGAAAATATTGAAGACAAAAACACAAAAACACTG
66 CTTTTTTTTCGCCCCATGCGATTGATATTTCGGAAAATATTGAAGACAAAAACACAAAAACACTG
2114446 GAATAATGTCAAGAGAAGAAAACTACAGAGAAATCATCAATTTTACATCTAATAAATAGTCAAAC
131 GAATAATGTCAAGAGAAGAAAACTACAGAGAAATCATCAATTTTACATCTAATAAATAGTCAAAC
2114511 ATGCAACCATAAAAAGGATATTGTAAATATCAAACCCATAAATTGCTCAAAAAATGAAAGGATTA
196 ATGCAACCATAAAAAGGATATTGTAAATATCAAACCCATAAATTGCTCAAAAAATGAAAGGATTA
2114576 AAAGTTGTATAACCT
261 AAAGTTGTATAACCT
2114591 -CAAAGAATAAAAATAATTACCATAACAAGTTTAAATTAGTCAATGGTATATATTGAACCTCAAA
1 GCAAAGAATAAAAATAATTACCATAACAAGTTTAAATTAGTCAATGGTATATATTGAACCTCAAA
*
2114655 CTTTTTTTTCGCCCCATGCGATTGATGTTTCGGAAAATATTGAAGACAAAAACACAAAAACACTG
66 CTTTTTTTTCGCCCCATGCGATTGATATTTCGGAAAATATTGAAGACAAAAACACAAAAACACTG
2114720 GAATAATGTCAAGAGAAGAAAACTACAGAGAAATCATCAATTTTACATCTAATAAATAGTCAAAC
131 GAATAATGTCAAGAGAAGAAAACTACAGAGAAATCATCAATTTTACATCTAATAAATAGTCAAAC
2114785 ATGCAACCATAAAAAGGATATTGTAAATATCAAACCCATAAATTGCTCAAAAAATGAAAGGATTA
196 ATGCAACCATAAAAAGGATATTGTAAATATCAAACCCATAAATTGCTCAAAAAATGAAAGGATTA
2114850 AAAGTTGTATAACCT
261 AAAGTTGTATAACCT
2114865 GCAAA
1 GCAAA
2114870 ACAAATTACA
Statistics
Matches: 277, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
274 273 0.99
275 4 0.01
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (275 bp):
GCAAAGAATAAAAATAATTACCATAACAAGTTTAAATTAGTCAATGGTATATATTGAACCTCAAA
CTTTTTTTTCGCCCCATGCGATTGATATTTCGGAAAATATTGAAGACAAAAACACAAAAACACTG
GAATAATGTCAAGAGAAGAAAACTACAGAGAAATCATCAATTTTACATCTAATAAATAGTCAAAC
ATGCAACCATAAAAAGGATATTGTAAATATCAAACCCATAAATTGCTCAAAAAATGAAAGGATTA
AAAGTTGTATAACCT
Found at i:2122054 original size:9 final size:9
Alignment explanation
Indices: 2122026--2122060 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2122016 ATGAAATTTA
2122026 TCATAAATT
1 TCATAAATT
**
2122035 TCATATGTT
1 TCATAAATT
2122044 TCATAAATT
1 TCATAAATT
2122053 TCATAAAT
1 TCATAAAT
2122061 CACCTCTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
TCATAAATT
Found at i:2122905 original size:12 final size:12
Alignment explanation
Indices: 2122888--2122912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2122878 TCATATAAAC
2122888 ATCTTTGACTAA
1 ATCTTTGACTAA
2122900 ATCTTTGACTAA
1 ATCTTTGACTAA
2122912 A
1 A
2122913 GTATAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2124177 original size:29 final size:29
Alignment explanation
Indices: 2124136--2124196 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2124126 TTTATTTTTG
*
2124136 TTAAAAATATATTTAAATATAAATAAAAA
1 TTAAAAATTTATTTAAATATAAATAAAAA
* * *
2124165 TTAAGAATTTATTTTAATAAAAATTAAAAA
1 TTAAAAATTTATTTAAATATAAA-TAAAAA
2124195 TT
1 TT
2124197 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
TTAAAAATTTATTTAAATATAAATAAAAA
Found at i:2124202 original size:19 final size:19
Alignment explanation
Indices: 2124150--2124211 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
2124140 AAATATATTT
*
2124150 AAATATAAATAAAAATTAA
1 AAATTTAAATAAAAATTAA
*
2124169 GAATTTATTTTAATAAAAATTAA
1 -AA---ATTTAAATAAAAATTAA
*
2124192 AAATTTAAATAAAATTTAA
1 AAATTTAAATAAAAATTAA
2124211 A
1 A
2124212 TAAAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 16 0.46
20 2 0.06
22 2 0.06
23 15 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTTAAATAAAAATTAA
Found at i:2124207 original size:11 final size:11
Alignment explanation
Indices: 2124191--2124222 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2124181 ATAAAAATTA
2124191 AAAATTTAAAT
1 AAAATTTAAAT
2124202 AAAATTTAAAT
1 AAAATTTAAAT
2124213 AAAATTTAAA
1 AAAATTTAAA
2124223 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTTAAAT
Found at i:2124275 original size:80 final size:80
Alignment explanation
Indices: 2124136--2124293 Score: 178
Period size: 80 Copynumber: 2.0 Consensus size: 80
2124126 TTTATTTTTG
* * * *
2124136 TTAAAAATATATTTAAATATAAATAAAAATTAAGAATTTATTTTAATAAAAATTAAAAATTTAAA
1 TTAAAAATATATTTAAATATAAATAAAAATTAACAATTTATTTAAATAAAAATCAAAAATATAAA
*
2124201 TAAAATTTAAATAAAAT
66 -AAAA-GTAAATAAAAT
* * * * *
2124218 TTAAAATTA-ATTT-AATGTAAATTAAAATTATCAATTTATTTAAAT-ATAATCATAAAATATAA
1 TTAAAAATATATTTAAATATAAATAAAAATTAACAATTTATTTAAATAAAAATCA-AAAATATAA
2124280 AAAAAGTAAATAAA
65 AAAAAGTAAATAAA
2124294 TAAAATAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
78 8 0.12
79 9 0.14
80 36 0.55
81 4 0.06
82 8 0.12
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (80 bp):
TTAAAAATATATTTAAATATAAATAAAAATTAACAATTTATTTAAATAAAAATCAAAAATATAAA
AAAAGTAAATAAAAT
Found at i:2124601 original size:23 final size:23
Alignment explanation
Indices: 2124555--2124621 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
2124545 TTTTTAATAA
* *
2124555 TAATAAATGTTTTATTTATATTAT
1 TAAT-AATATTTTATATATATTAT
* *
2124579 TAATAATTTTTTATATATTTTAT
1 TAATAATATTTTATATATATTAT
* *
2124602 GAATAATATTTAATATATAT
1 TAATAATATTTTATATATAT
2124622 ATGTTATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
TAATAATATTTTATATATATTAT
Found at i:2129001 original size:39 final size:39
Alignment explanation
Indices: 2128947--2129024 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2128937 ATGTGAAGCA
2128947 ATGAAAAACAGCATGATTAAAATTCCAAACTGCTATCTG
1 ATGAAAAACAGCATGATTAAAATTCCAAACTGCTATCTG
2128986 ATGAAAAACAGCATGATTAAAATTCCAAACTGCTATCTG
1 ATGAAAAACAGCATGATTAAAATTCCAAACTGCTATCTG
2129025 GTCTTATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (39 bp):
ATGAAAAACAGCATGATTAAAATTCCAAACTGCTATCTG
Found at i:2132958 original size:122 final size:122
Alignment explanation
Indices: 2132741--2132986 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
2132731 CCACCAGCAT
2132741 TTTCATGCTTTTGCTGTGACATTGGAAAGCAAACTTACACTCCAAACTGTGGCATGAGAGGCCTT
1 TTTCATGCTTTTGCTGTGACATTGGAAAGCAAACTTACACTCCAAACTGTGGCATGAGAGGCCTT
2132806 TAGATCCAACCTATGCATCAAGGAAGCCAAAAATGCAGATGAAGAGAGCATAGTTAA
66 TAGATCCAACCTATGCATCAAGGAAGCCAAAAATGCAGATGAAGAGAGCATAGTTAA
2132863 TTTCATGCTTTTGCTGTGACATTGGAAAGCAAACTTACACTCCAAACTGTGGCATGAGAGGCCTT
1 TTTCATGCTTTTGCTGTGACATTGGAAAGCAAACTTACACTCCAAACTGTGGCATGAGAGGCCTT
2132928 TAGATCCAACCTATGCATCAAGGAAGCCAAAAATGCAGATGAAGAGAGCATAGTTAA
66 TAGATCCAACCTATGCATCAAGGAAGCCAAAAATGCAGATGAAGAGAGCATAGTTAA
2132985 TT
1 TT
2132987 CAAACCTACA
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (122 bp):
TTTCATGCTTTTGCTGTGACATTGGAAAGCAAACTTACACTCCAAACTGTGGCATGAGAGGCCTT
TAGATCCAACCTATGCATCAAGGAAGCCAAAAATGCAGATGAAGAGAGCATAGTTAA
Found at i:2134436 original size:32 final size:32
Alignment explanation
Indices: 2134395--2134458 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2134385 CACAAATTAG
2134395 CAGAACCATGATAAAACAAAACAGGTCCACAA
1 CAGAACCATGATAAAACAAAACAGGTCCACAA
2134427 CAGAACCATGATAAAACAAAACAGGTCCACAA
1 CAGAACCATGATAAAACAAAACAGGTCCACAA
2134459 ATCCTTACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.09
Consensus pattern (32 bp):
CAGAACCATGATAAAACAAAACAGGTCCACAA
Found at i:2135056 original size:23 final size:23
Alignment explanation
Indices: 2135002--2135056 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2134992 TGCAATCCTA
* *
2135002 GAGAAACAAAAATAAAGAGCAAT
1 GAGAAACAAAAACAAAGAGCAAG
* *
2135025 GAGAGACAAAAACAATGA-CAAG
1 GAGAAACAAAAACAAAGAGCAAG
2135047 GATGAAACAA
1 GA-GAAACAA
2135057 GGTAATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.62, C:0.11, G:0.20, T:0.07
Consensus pattern (23 bp):
GAGAAACAAAAACAAAGAGCAAG
Found at i:2139077 original size:6 final size:6
Alignment explanation
Indices: 2139063--2139114 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
2139053 CAATACCAGA
* * * *
2139063 ACACAC ACACGC ACACGC ACACGC ACACTC ACACTC ACACTC ACACGC
1 ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC
2139111 ACAC
1 ACAC
2139115 TTGTCCAGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.37, C:0.50, G:0.08, T:0.06
Consensus pattern (6 bp):
ACACGC
Found at i:2139083 original size:12 final size:12
Alignment explanation
Indices: 2139063--2139115 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
2139053 CAATACCAGA
*
2139063 ACACACACACGC
1 ACACTCACACGC
*
2139075 ACACGCACACGC
1 ACACTCACACGC
*
2139087 ACACTCACACTC
1 ACACTCACACGC
2139099 ACACTCACACGC
1 ACACTCACACGC
2139111 ACACT
1 ACACT
2139116 TGTCCAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.36, C:0.49, G:0.08, T:0.08
Consensus pattern (12 bp):
ACACTCACACGC
Found at i:2143898 original size:17 final size:17
Alignment explanation
Indices: 2143876--2143908 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2143866 ATGCTTAAGA
*
2143876 AAAAAATAAGTAAAATG
1 AAAAAATAAATAAAATG
2143893 AAAAAATAAATAAAAT
1 AAAAAATAAATAAAAT
2143909 TAAGTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAAATAAATAAAATG
Found at i:2148131 original size:38 final size:38
Alignment explanation
Indices: 2148080--2148156 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2148070 AAAAAAAAAA
2148080 AAAAGAAACTTTATCCATCCAGGGAAACATGGAAACAC
1 AAAAGAAACTTTATCCATCCAGGGAAACATGGAAACAC
2148118 AAAAGAAACTTTATCCATCCAGGGAAACATGGAAACAC
1 AAAAGAAACTTTATCCATCCAGGGAAACATGGAAACAC
2148156 A
1 A
2148157 TGGGTGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.16
Consensus pattern (38 bp):
AAAAGAAACTTTATCCATCCAGGGAAACATGGAAACAC
Found at i:2148884 original size:9 final size:9
Alignment explanation
Indices: 2148856--2148890 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2148846 ATGAAATTTA
2148856 TCATAAATT
1 TCATAAATT
**
2148865 TCATATGTT
1 TCATAAATT
2148874 TCATAAATT
1 TCATAAATT
2148883 TCATAAAT
1 TCATAAAT
2148891 CACCTCTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
TCATAAATT
Found at i:2149619 original size:20 final size:20
Alignment explanation
Indices: 2149563--2149619 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
2149553 GGAGTCGGAG
*
2149563 AAAATTTTGACAAAAGATGTC
1 AAAATTTT-AGAAAAGATGTC
*
2149584 AAAATTTTAGTAAAGATGTC
1 AAAATTTTAGAAAAGATGTC
*
2149604 AGAA-TTTAGAAGAAGA
1 AAAATTTTAGAA-AAGA
2149620 AAATGAGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 6 0.19
20 17 0.55
21 8 0.26
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (20 bp):
AAAATTTTAGAAAAGATGTC
Found at i:2149726 original size:12 final size:12
Alignment explanation
Indices: 2149709--2149733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2149699 TCATATAAGC
2149709 ATCTTTGACTAA
1 ATCTTTGACTAA
2149721 ATCTTTGACTAA
1 ATCTTTGACTAA
2149733 A
1 A
2149734 GTTTAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2150838 original size:19 final size:18
Alignment explanation
Indices: 2150804--2150859 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2150794 TTAATTATAT
2150804 TATTTTATTT-AAATAAA
1 TATTTTATTTAAAATAAA
*
2150821 TTTTTATATTTAAAATAAA
1 TATTT-TATTTAAAATAAA
2150840 -ATTTTATTTAAATATAAA
1 TATTTTATTTAAA-ATAAA
2150858 TA
1 TA
2150860 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 12 0.36
18 13 0.39
19 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTTATTTAAAATAAA
Found at i:2150858 original size:17 final size:17
Alignment explanation
Indices: 2150805--2150858 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
2150795 TAATTATATT
2150805 ATTTTATTTAAATA-AA
1 ATTTTATTTAAATATAA
*
2150821 TTTTTATATTTAAA-ATAAA
1 -ATTT-TATTTAAATAT-AA
2150840 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
2150857 AT
1 AT
2150859 AAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 16 0.52
18 13 0.42
19 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:2150905 original size:28 final size:27
Alignment explanation
Indices: 2150874--2150954 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
2150864 TAAAAAATTT
2150874 ATTTTTTATAAAAATTAAATATTTTAAA
1 ATTTTTTATAAAAATTAAA-ATTTTAAA
** * * *
2150902 ATTTTAAATATAAATTAAAAATTAAAA
1 ATTTTTTATAAAAATTAAAATTTTAAA
2150929 ATTTATTTA-AGATAAATTAAAATTTT
1 ATTT-TTTATA-A-AAATTAAAATTTT
2150955 TGACTTTTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
27 11 0.28
28 18 0.45
29 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
ATTTTTTATAAAAATTAAAATTTTAAA
Found at i:2150969 original size:58 final size:57
Alignment explanation
Indices: 2150846--2150954 Score: 150
Period size: 59 Copynumber: 1.9 Consensus size: 57
2150836 TAAAATTTTA
* *
2150846 TTTAAATATAAATAAAAATAAAAAATTTATTTTTTATAAAAATTAAATATTTTAAAAT
1 TTTAAATATAAATAAAAATAAAAAATTTA-TTTTAAGAAAAATTAAATATTTTAAAAT
* *
2150904 TTTAAATATAAATTAAAAATTAAAAATTTA-TTTAAGATAAATTAAA-ATTTT
1 TTTAAATATAAA-TAAAAATAAAAAATTTATTTTAAGAAAAATTAAATATTTT
2150955 TGACTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
56 5 0.11
57 13 0.28
58 12 0.26
59 16 0.35
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (57 bp):
TTTAAATATAAATAAAAATAAAAAATTTATTTTAAGAAAAATTAAATATTTTAAAAT
Found at i:2152335 original size:21 final size:23
Alignment explanation
Indices: 2152311--2152356 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2152301 AAACCACAAG
*
2152311 TAAAAAACTATTTA-T-ATATTT
1 TAAAAAACTAATTACTAATATTT
*
2152332 TAAAAAATTAATTACTAATATTT
1 TAAAAAACTAATTACTAATATTT
2152355 TA
1 TA
2152357 TTTGATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 1 0.05
23 8 0.38
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAAACTAATTACTAATATTT
Found at i:2152506 original size:14 final size:15
Alignment explanation
Indices: 2152481--2152509 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2152471 ATCAAACAGT
2152481 TAAAAAAGGAATTTA
1 TAAAAAAGGAATTTA
2152496 TAAAAAA-GAATTTA
1 TAAAAAAGGAATTTA
2152510 CAAACGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
TAAAAAAGGAATTTA
Found at i:2157774 original size:62 final size:62
Alignment explanation
Indices: 2157609--2158272 Score: 657
Period size: 62 Copynumber: 10.8 Consensus size: 62
2157599 ACACAAGTTG
* * * * *
2157609 GAGCAAGATGCCTTTTTCTTTTAAAGCCCACATAAGTTGTTGGCACTCGTTCAGTCCTCAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * *
2157671 GAGCAGGACG-TTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACCCGTTCAGTCCTCAAC
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * * * * * *
2157732 GAACATGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATCCATTTAGTCCTCAAC
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
** * *
2157794 GAATAGGA--CTTTTTTCTTTTAAAGCCCACACAAGTTGGTGACACCCGTTCAGTCCTCAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* *
2157854 GAGCAAGACGCCTTTTT-TTTAAAAGCCCACAC-A----GTGGCACCCGTTCAGTCCTCAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * ** * * *
2157910 TAGCATGACGTTTTTTTCTTTTAAAGCTCACACAAGTTGGTAGCACTCGTTCAGTCCTCAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * *** *
2157972 AAGCAGGACGCCTTTTTCTTTTAAAGCCCACATAAGTTGGCAACACCCGCTCAGTCCTCAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * * *
2158034 GAGCAGGACG-CTTGCTTCTTTTAAAACCCATACAAGTTGGTGGCACCCATTCAGTCCTCAAA
1 GAGCAGGACGCCTT-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * * * * * * * * *
2158096 GAGTAAGACGCCTTTTTATTTTAAAGCTCACACAAGTTGATAGTACCTGTTCAATCCTTAAA
1 GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
* * * *
2158158 GAGCAGTACGCCTTTTT-TTTATAAAAAAAAACCTACACAAGTTGGTGGCACCTGTTCAGTCCTC
1 GAGCAGGACGCCTTTTTCTTT-T-----AAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTC
2158222 AAA
60 AAA
* * * * * *
2158225 GAGCAAGACACTTTTTTTCGTTTAAAGACCACACAAGTCGGTGGCACC
1 GAGCAGGACGC-CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
2158273 TCTTTTCAAA
Statistics
Matches: 492, Mismatches: 91, Indels: 37
0.79 0.15 0.06
Matches are distributed among these distances:
56 35 0.07
57 13 0.03
58 1 0.00
60 51 0.10
61 75 0.15
62 245 0.50
63 24 0.05
67 40 0.08
68 6 0.01
69 2 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (62 bp):
GAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAA
Found at i:2159957 original size:60 final size:60
Alignment explanation
Indices: 2159864--2159986 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
2159854 CCCACACAAC
2159864 TCATGTTGAAGGAGAAGCAACCAGCCACTTGGCCATGCCCATTTTTTTAAACAAAAAATG
1 TCATGTTGAAGGAGAAGCAACCAGCCACTTGGCCATGCCCATTTTTTTAAACAAAAAATG
2159924 TCATGTTGAAGGAGAAGCAACCAGCCACTTGGCCATGCCCATTTTTTTAAACAAAAAATG
1 TCATGTTGAAGGAGAAGCAACCAGCCACTTGGCCATGCCCATTTTTTTAAACAAAAAATG
2159984 TCA
1 TCA
2159987 GAATATTTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (60 bp):
TCATGTTGAAGGAGAAGCAACCAGCCACTTGGCCATGCCCATTTTTTTAAACAAAAAATG
Found at i:2160313 original size:10 final size:10
Alignment explanation
Indices: 2160293--2160350 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 10
2160283 TGATTTTCAC
2160293 AAAAA-AAAT
1 AAAAATAAAT
*
2160302 AAAAATATAT
1 AAAAATAAAT
2160312 -AAAATAAAT
1 AAAAATAAAT
*
2160321 AAAAAGAAAGT
1 AAAAATAAA-T
2160332 ATAAAA-AAAT
1 A-AAAATAAAT
*
2160342 AATAATAAA
1 AAAAATAAA
2160351 AAGTGTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 16 0.40
10 15 0.38
11 5 0.12
12 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:2164669 original size:22 final size:21
Alignment explanation
Indices: 2164620--2164674 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2164610 ATCTCTTTAC
2164620 AATAATAAAATATAAAAATTA
1 AATAATAAAATATAAAAATTA
* * * *
2164641 AAGAATAAATTGATAAAATTTT
1 AATAATAAAAT-ATAAAAATTA
2164663 AATAATAAAATA
1 AATAATAAAATA
2164675 ATTGTTGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AATAATAAAATATAAAAATTA
Found at i:2168152 original size:188 final size:188
Alignment explanation
Indices: 2167826--2168184 Score: 583
Period size: 188 Copynumber: 1.9 Consensus size: 188
2167816 TGTTGAAAGG
*
2167826 TGCAAAGGCTTACAAGCTGAAATTTTGCGAGCATTGTATTCTGGGAAAGCAGAAGAGATTAAAGT
1 TGCAAAGGCTTACAAGCTAAAATTTTGCGAGCATTGTATTCTGGGAAAGCAGAAGAGATTAAAGT
* *
2167891 TTGGCACCGCTATCCATAATACTAAAGGTATTTTGGATTATATTCACTCAGATGTGTGGGATCCT
66 TTGGCACCACTATCCATAATACGAAAGGTATTTTGGATTATATTCACTCAGATGTGTGGGATCCT
* *
2167956 TTCAAGACAACTTCGTTGGGAGAAAAACACTATTTTGTAACATTGGGAGGAAAACACT
131 TCCAAGACAACTTCGTTAGGAGAAAAACACTATTTTGTAACATTGGGAGGAAAACACT
** * *
2168014 TGCAAAGGCTTGTAAGCTAAAATTTTTCGAGCATTGTATTCTGGGAAAGCAGAAGAGATTGAAGT
1 TGCAAAGGCTTACAAGCTAAAATTTTGCGAGCATTGTATTCTGGGAAAGCAGAAGAGATTAAAGT
* * * *
2168079 TTGGTACCACTATCCATAATACGAAAGGTATTTTGGATTTTATTCACTTAGATGTGTGGGGTCCT
66 TTGGCACCACTATCCATAATACGAAAGGTATTTTGGATTATATTCACTCAGATGTGTGGGATCCT
* *
2168144 TCCAAGACAACTTTGTTAGGAGGAAAACACTATTTTGTAAC
131 TCCAAGACAACTTCGTTAGGAGAAAAACACTATTTTGTAAC
2168185 GTTTGTTGAT
Statistics
Matches: 156, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
188 156 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (188 bp):
TGCAAAGGCTTACAAGCTAAAATTTTGCGAGCATTGTATTCTGGGAAAGCAGAAGAGATTAAAGT
TTGGCACCACTATCCATAATACGAAAGGTATTTTGGATTATATTCACTCAGATGTGTGGGATCCT
TCCAAGACAACTTCGTTAGGAGAAAAACACTATTTTGTAACATTGGGAGGAAAACACT
Found at i:2177096 original size:21 final size:22
Alignment explanation
Indices: 2177072--2177120 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2177062 ATAATTATTT
2177072 TATTTTAT-TTAATTATAA-AAA
1 TATTTTATATTAA-TATAACAAA
*
2177093 TA-TTAATATTAATATAACAAA
1 TATTTTATATTAATATAACAAA
2177114 TATTTTA
1 TATTTTA
2177121 ATATCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 9 0.39
21 11 0.48
22 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTTATATTAATATAACAAA
Found at i:2177100 original size:36 final size:37
Alignment explanation
Indices: 2177027--2177105 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 37
2177017 TTAAAATTTG
* **
2177027 AATTAATTTTATTTTATTTAAATTATTATTTAATAAT
1 AATTAATTTTATTTTATTTAAATTATAAAATAATAAT
*
2177064 AATT-ATTTTATTTTATTT-AATTATAAAAATATTAAT
1 AATTAATTTTATTTTATTTAAATTAT-AAAATAATAAT
2177100 -ATTAAT
1 AATTAAT
2177106 ATAACAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 9 0.25
36 23 0.64
37 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (37 bp):
AATTAATTTTATTTTATTTAAATTATAAAATAATAAT
Found at i:2177745 original size:46 final size:47
Alignment explanation
Indices: 2177695--2177801 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 47
2177685 TATAATATTT
*
2177695 TAAATATAATTATAACATAAATAATAAT-TA-A-TAATTTTTTATTTTA
1 TAAATATAATT-TAAAAT-AATAATAATGTATATTAATTTTTTATTTTA
* * * *
2177741 TAAATA-AATTTAAAATATTTATAATGTATATTATTTTTTTATTTTT
1 TAAATATAATTTAAAATAATAATAATGTATATTAATTTTTTATTTTA
*
2177787 TAAATATAATCTAAA
1 TAAATATAATTTAAA
2177802 TTGTAGAGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 7 0.14
44 7 0.14
45 5 0.10
46 25 0.49
47 7 0.14
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (47 bp):
TAAATATAATTTAAAATAATAATAATGTATATTAATTTTTTATTTTA
Found at i:2180094 original size:2 final size:2
Alignment explanation
Indices: 2180087--2180112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2180077 TGTGAAAAAC
2180087 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
2180113 ACGTTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2185967 original size:19 final size:19
Alignment explanation
Indices: 2185940--2186002 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2185930 TCACGTGTAC
* *
2185940 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2185959 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2185978 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2185997 AGTACC
1 AGTACC
2186003 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2191447 original size:16 final size:16
Alignment explanation
Indices: 2191423--2191473 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
2191413 TTTACATTTT
*
2191423 TTTACTTAATTTTAAA
1 TTTAATTAATTTTAAA
2191439 TTTAATTAAATTTATAAA
1 TTTAATT-AATTT-TAAA
*
2191457 TTTAAGTAATTATTAAA
1 TTTAATTAATT-TTAAA
2191474 AATATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 13 0.43
18 11 0.37
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTAATTAATTTTAAA
Found at i:2191493 original size:23 final size:23
Alignment explanation
Indices: 2191467--2191526 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
2191457 TTTAAGTAAT
*
2191467 TATTAAAAATATTTTTAAATTAA
1 TATTAAATATATTTTTAAATTAA
*
2191490 TATT-TATATATTTTT-AATTAA
1 TATTAAATATATTTTTAAATTAA
*
2191511 -ATTAATTATATTTTTA
1 TATTAAATATATTTTTA
2191527 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 3 0.10
21 15 0.48
22 9 0.29
23 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTAAATATATTTTTAAATTAA
Found at i:2191539 original size:23 final size:22
Alignment explanation
Indices: 2191475--2191539 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
2191465 ATTATTAAAA
*
2191475 ATATTTTTAAATT-AATATTTAT
1 ATATTTTT-AATTAAATAATTAT
2191497 ATATTTTTAATTAAATTAATTAT
1 ATATTTTTAATTAAA-TAATTAT
* *
2191520 ATTTTTATTTATTAAATAAT
1 ATATTT-TTAATTAAATAAT
2191540 AATTTAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.11
22 10 0.27
23 15 0.41
24 8 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTAATTAAATAATTAT
Found at i:2200220 original size:3 final size:3
Alignment explanation
Indices: 2200214--2200242 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2200204 TTTAATTTTG
2200214 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2200243 CGCAATTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2201061 original size:12 final size:12
Alignment explanation
Indices: 2201044--2201068 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2201034 AGCCTTATAC
2201044 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2201056 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2201068 T
1 T
2201069 GTTTATATGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Done.