Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 9 of 132
Found at i:2362595 original size:15 final size:15
Alignment explanation
Indices: 2362577--2362627 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2362567 TTGATGTTGG
2362577 CAATTTGTTATTATT
1 CAATTTGTTATTATT
* *
2362592 CAATTT-ATATGT-TGG
1 CAATTTGTTAT-TAT-T
2362607 CAATTTGTTATTATT
1 CAATTTGTTATTATT
2362622 CAATTT
1 CAATTT
2362628 ATGCATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (15 bp):
CAATTTGTTATTATT
Found at i:2362606 original size:30 final size:30
Alignment explanation
Indices: 2362570--2362629 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2362560 ATAGATTTTG
2362570 ATGTTGGCAATTTGTTATTATTCAATTTAT
1 ATGTTGGCAATTTGTTATTATTCAATTTAT
2362600 ATGTTGGCAATTTGTTATTATTCAATTTAT
1 ATGTTGGCAATTTGTTATTATTCAATTTAT
2362630 GCATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (30 bp):
ATGTTGGCAATTTGTTATTATTCAATTTAT
Found at i:2363913 original size:30 final size:30
Alignment explanation
Indices: 2363873--2363949 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
2363863 GACATAAATG
* *
2363873 GGGTTACCGTGTTCGTCAGTGAGTTGAACC
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
2363903 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
2363933 GGGTTGCCGTGTTCGTC
1 GGGTTGCCGTGTTCGTC
2363950 TCTCAAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.13, C:0.19, G:0.36, T:0.31
Consensus pattern (30 bp):
GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
Found at i:2365013 original size:31 final size:31
Alignment explanation
Indices: 2364977--2365043 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
2364967 ATAACACCAG
*
2364977 AGTGACTTAAATAAAAATTTTCAAATAATTT
1 AGTGACTTAAATAAAAACTTTCAAATAATTT
* *
2365008 AGTGACTTACATAAAAACTTTCTAATAATTT
1 AGTGACTTAAATAAAAACTTTCAAATAATTT
2365039 AGTGA
1 AGTGA
2365044 TCATTTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTCAAATAATTT
Found at i:2369794 original size:15 final size:15
Alignment explanation
Indices: 2369774--2369802 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2369764 TTAAATTCAA
2369774 TACTTAATTTTTTAG
1 TACTTAATTTTTTAG
2369789 TACTTAATTTTTTA
1 TACTTAATTTTTTA
2369803 ATTTATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (15 bp):
TACTTAATTTTTTAG
Found at i:2371316 original size:2 final size:2
Alignment explanation
Indices: 2371309--2371344 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2371299 GGTAGGGCTC
2371309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2371345 TCAAATTGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2374443 original size:19 final size:20
Alignment explanation
Indices: 2374406--2374448 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2374396 TTTGATAAAG
*
2374406 TTTTAAATTTAATTCATT-A
1 TTTTAAATTTAATTAATTAA
2374425 TTTTAAATATTAA-TAATTAA
1 TTTTAAAT-TTAATTAATTAA
2374445 TTTT
1 TTTT
2374449 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAATTTAATTAATTAA
Found at i:2380711 original size:4 final size:4
Alignment explanation
Indices: 2380704--2380728 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2380694 GCATGTACGA
2380704 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
2380729 CCCTTTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:2380715 original size:16 final size:16
Alignment explanation
Indices: 2380686--2380728 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2380676 AGCAAACAAT
* *
2380686 GAATGCATGCATGTAC
1 GAATGTATGTATGTAC
*
2380702 GAATGTATGTATGTAT
1 GAATGTATGTATGTAC
*
2380718 GTATGTATGTA
1 GAATGTATGTA
2380729 CCCTTTTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (16 bp):
GAATGTATGTATGTAC
Found at i:2397614 original size:58 final size:57
Alignment explanation
Indices: 2397440--2397617 Score: 277
Period size: 58 Copynumber: 3.1 Consensus size: 57
2397430 AAAAGAAGTT
*
2397440 GTTTATGAGTGTTATTT-AAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATA-TGGGGTTTAAAAATATTTGGGTTTA
* *
2397498 ATTTATGAGTGTTTTTGAAGAATGAAATTATATTGGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATA-TGGGGTTTAAAAATATTTGGGTTTA
*
2397556 GTTTATGAGTGTTTTTGAAGAATAAAATTATATGCGAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATG-GGGTTTAAAAATATTTGGGTTTA
2397614 GTTT
1 GTTT
2397618 GTTGATGAGT
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
57 5 0.04
58 107 0.96
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.46
Consensus pattern (57 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATGGGGTTTAAAAATATTTGGGTTTA
Found at i:2403106 original size:17 final size:18
Alignment explanation
Indices: 2403084--2403119 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2403074 TCATGTATAA
2403084 ATAAATATA-AAAAATGT
1 ATAAATATATAAAAATGT
*
2403101 ATAAATTTATAAAAATGT
1 ATAAATATATAAAAATGT
2403119 A
1 A
2403120 AAAAGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAAATATATAAAAATGT
Found at i:2408602 original size:15 final size:15
Alignment explanation
Indices: 2408582--2408614 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2408572 CTCAATTATT
*
2408582 AATTTTTTTAAATTA
1 AATTTTTTGAAATTA
2408597 AATTTTTTGAAATTA
1 AATTTTTTGAAATTA
2408612 AAT
1 AAT
2408615 GTTGATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTTTTGAAATTA
Found at i:2416502 original size:17 final size:18
Alignment explanation
Indices: 2416463--2416507 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2416453 TAAAATGGTT
* *
2416463 TTTAAGTTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
2416481 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
2416498 TTTAAATTTA
1 TTTAAATTTA
2416508 AATTATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:2416526 original size:22 final size:23
Alignment explanation
Indices: 2416477--2416526 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 23
2416467 AGTTTATTTC
*
2416477 TAAAATTAAATTTACTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
2416500 TAAATTTAAA-TTA-TTTAAATT
1 TAAATTTAAATTTACTTTAAATT
2416521 TGAAAT
1 T-AAAT
2416527 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TAAATTTAAATTTACTTTAAATT
Found at i:2416531 original size:16 final size:15
Alignment explanation
Indices: 2416496--2416541 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
2416486 ATTTACTTTA
2416496 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
*
2416511 TATTTAAATTTGAAAT
1 AATTTAAATTT-AAAT
*
2416527 AATTTTAAAATTAAA
1 AA-TTTAAATTTAAA
2416542 ATTAAAAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 10 0.38
16 8 0.31
17 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATTTAAATTTAAAT
Found at i:2418326 original size:162 final size:162
Alignment explanation
Indices: 2418136--2418481 Score: 586
Period size: 162 Copynumber: 2.1 Consensus size: 162
2418126 TTTTAATTGG
2418136 TTTTTAAATTAGTCCTTTGACTGTTTGACTACACCAGAGGCTGCCACATGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTACACCAGAGGCTGCCACATGTCACTTTTTGGTTTA
* *
2418201 TTTATGTATCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGCTT
66 TTTATGTATCTAGTCCCTGTCATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTCTACTT
*
2418266 AATTACAAAATCGACCCAAGAATCTTTT-GAGA
131 AATTACAAAATCGACCCAAGAAT-TTTTCAAGA
* *
2418298 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTACACCAGAGGCTGCCACATGTCACTTTTTGGTTTA
2418363 TTTATGTATCTAGTCCCTGTCATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTCTACTT
66 TTTATGTATCTAGTCCCTGTCATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTCTACTT
* *
2418428 AATTACAAAATTGGCCCAAGAATTTTTCAAGA
131 AATTACAAAATCGACCCAAGAATTTTTCAAGA
** *
2418460 TTTAAAAATTCGTCCTTTGACT
1 TTTTTAAATTAGTCCTTTGACT
2418482 TCTGGATGCC
Statistics
Matches: 173, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 4 0.02
162 169 0.98
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (162 bp):
TTTTTAAATTAGTCCTTTGACTGTTTGACTACACCAGAGGCTGCCACATGTCACTTTTTGGTTTA
TTTATGTATCTAGTCCCTGTCATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTCTACTT
AATTACAAAATCGACCCAAGAATTTTTCAAGA
Found at i:2418645 original size:29 final size:28
Alignment explanation
Indices: 2418555--2418654 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 28
2418545 GGACTGTCCG
*
2418555 AAAATTGCCATTTTACCC-CTAAACTTTCC
1 AAAATT-CCATTTTACCCTC-AAACTCTCC
* *** *
2418584 AAAATTCTATTTTAACCCT-AGTTTCATCA
1 AAAATTCCATTTT-ACCCTCAAACTC-TCC
2418613 AAAATTACCATTTTACCCTCAAACTCTCC
1 AAAATT-CCATTTTACCCTCAAACTCTCC
2418642 AAAATTCCATTTT
1 AAAATTCCATTTT
2418655 TAACCCCGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
28 15 0.27
29 31 0.56
30 9 0.16
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTACCCTCAAACTCTCC
Found at i:2418979 original size:235 final size:235
Alignment explanation
Indices: 2418555--2419096 Score: 817
Period size: 235 Copynumber: 2.3 Consensus size: 235
2418545 GGACTGTCCG
* *
2418555 AAAATTGCCATTTTACCCCTAAACTTTCCAAAATTCTATTTTAA-CCCTAGTTTCA-TCAAAAAT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCTA-TTTCACT-AAAAAT
*
2418618 TACCATTTTACCCTCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTTATTAAAAATTACCAT
64 TACCATTTTACCCTCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCATTAAAAATTACCAT
* * *
2418683 TTTACCCCCGAACTTCCCAAAGTTCCATTTTTAATCCCAGTTTCATTAAAAATTGCCATTTTACT
129 TTTACCCCCGAACTTCCCAAAATTCCATTTTTAATCCCAGTTTCATCAAAAATTACCATTTTAC-
* * *
2418748 CCC-GAACTTCCCAAAGTTCCATTTTTAATCCCGATTTCATCA
193 CCCTAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATCA
* *
2418790 AAAATTACCATTTTACCCCTAAACATTCCAAAATTCCATTTTAACCCCGATTTCACTAAAAATTA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCTATTTCACTAAAAATTA
*
2418855 CCATTTTACCC-CTAAACTCTCCAAAATTCTATTTTTAACCCCGATTTCATTAAAAATTACCATT
66 CCATTTTACCCTC-AAACTCTCCAAAATTCCATTTTTAACCCCGATTTCATTAAAAATTACCATT
*
2418919 TTACCCCCGAACTTCCCAAAATTTCATTTTTAA-CCTC-GATTTCATCAAAAATTACCATTTTAC
130 TTACCCCCGAACTTCCCAAAATTCCATTTTTAATCC-CAG-TTTCATCAAAAATTACCATTTTAC
*
2418982 CCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
193 CCCTAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATCA
** * * *
2419025 AAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTACCCCTATTTCACCAAAAATTA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCTATTTCACTAAAAATTA
2419090 CCATTTT
66 CCATTTT
2419097 GCCCGTCGCG
Statistics
Matches: 280, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
234 7 0.03
235 268 0.96
236 5 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (235 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCTATTTCACTAAAAATTA
CCATTTTACCCTCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCATTAAAAATTACCATTT
TACCCCCGAACTTCCCAAAATTCCATTTTTAATCCCAGTTTCATCAAAAATTACCATTTTACCCC
TAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:2419115 original size:29 final size:28
Alignment explanation
Indices: 2419083--2419142 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
2419073 TATTTCACCA
2419083 AAAATTACCATTTTGCCCGTCGCGCATCC
1 AAAATTACCATTTTGCCC-TCGCGCATCC
* *
2419112 AAAATTACCATTTTGCCCTCGGGTATCC
1 AAAATTACCATTTTGCCCTCGCGCATCC
2419140 AAA
1 AAA
2419143 GTCCCGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCGCGCATCC
Found at i:2419125 original size:59 final size:59
Alignment explanation
Indices: 2418555--2419096 Score: 664
Period size: 59 Copynumber: 9.2 Consensus size: 59
2418545 GGACTGTCCG
* * *
2418555 AAAATTGCCATTTTACCCCT-AAACTTTCCAAAATTCTA-TTTTAA-CCCTAGTTTCATCA
1 AAAATTACCATTTTACCCCTCAAAC-TTCCAAAATTCCATTTTTAACCCCGA-TTTCATCA
* *
2418613 AAAATTACCATTTTA-CCCTCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTTATTA
1 AAAATTACCATTTTACCCCTCAAACT-TCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * *
2418672 AAAATTACCATTTTACCCC-CGAACTTCCCAAAGTTCCATTTTTAATCCC-AGTTTCATTA
1 AAAATTACCATTTTACCCCTCAAACTT-CCAAAATTCCATTTTTAACCCCGA-TTTCATCA
* * * * *
2418731 AAAATTGCCATTTTACTCC-CGAACTTCCCAAAGTTCCATTTTTAATCCCGATTTCATCA
1 AAAATTACCATTTTACCCCTCAAACTT-CCAAAATTCCATTTTTAACCCCGATTTCATCA
2418790 AAAATTACCATTTTACCCCT-AAACATTCCAAAATTCCA-TTTTAACCCCGATTTCA-CTA
1 AAAATTACCATTTTACCCCTCAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCATC-A
* *
2418848 AAAATTACCATTTTACCCCT-AAACTCTCCAAAATTCTATTTTTAACCCCGATTTCATTA
1 AAAATTACCATTTTACCCCTCAAACT-TCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
2418907 AAAATTACCATTTTACCCC-CGAACTTCCCAAAATTTCATTTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCCTCAAACTT-CCAAAATTCCATTTTTAACCCCGATTTCATCA
2418966 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCTCAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * *
2419025 AAAATTACCATTTTACCCC-CGAACTTTCTAAAATTCCATTTTT-ACCCCTATTTCACCA
1 AAAATTACCATTTTACCCCTCAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCATCA
2419083 AAAATTACCATTTT
1 AAAATTACCATTTT
2419097 GCCCGTCGCG
Statistics
Matches: 434, Mismatches: 31, Indels: 38
0.86 0.06 0.08
Matches are distributed among these distances:
57 7 0.02
58 111 0.26
59 304 0.70
60 12 0.03
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTCAAACTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:2425256 original size:16 final size:16
Alignment explanation
Indices: 2425235--2425305 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 16
2425225 AATATAATAA
2425235 AATAATTTAATTATAT
1 AATAATTTAATTATAT
2425251 AATAATTTATATTATTAT
1 AATAATTTA-ATTA-TAT
*
2425269 ATTCTAATATTAATTA-AT
1 A--ATAAT-TTAATTATAT
*
2425287 AATAACTTAAATTATAT
1 AATAA-TTTAATTATAT
2425304 AA
1 AA
2425306 AAAAAATCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 18 0.40
17 9 0.20
18 7 0.16
20 8 0.18
21 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAATTTAATTATAT
Found at i:2428103 original size:18 final size:18
Alignment explanation
Indices: 2428076--2428111 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2428066 AAGCTCTTTA
*
2428076 TAACTAATAATTGTAATT
1 TAACTAATAATTATAATT
*
2428094 TAACTTATAATTATAATT
1 TAACTAATAATTATAATT
2428112 ATTACAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
TAACTAATAATTATAATT
Found at i:2428569 original size:47 final size:48
Alignment explanation
Indices: 2428450--2428575 Score: 130
Period size: 47 Copynumber: 2.6 Consensus size: 48
2428440 ATCTTAATTA
* * * *
2428450 GAACTTAATTAGAATTAC-AAAAGTTATATTTTATAAATATATATTAGTTT
1 GAACTGAATTAGAATTACGAAAA-TTATA-TTTAT-AATAAATATTAGCTG
* * * *
2428500 GAATTGAATTAGGATTATGAAAATTATATTTAT-ATAAATCTTAGCTG
1 GAACTGAATTAGAATTACGAAAATTATATTTATAATAAATATTAGCTG
*
2428547 GAACTGAATTAGAATCACGAAAATTATAT
1 GAACTGAATTAGAATTACGAAAATTATAT
2428576 ATTTATAGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
47 35 0.56
49 5 0.08
50 19 0.30
51 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (48 bp):
GAACTGAATTAGAATTACGAAAATTATATTTATAATAAATATTAGCTG
Found at i:2433156 original size:12 final size:12
Alignment explanation
Indices: 2433139--2433173 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2433129 AAAAAATTAT
2433139 TAATTATTTTTA
1 TAATTATTTTTA
2433151 TAATTATTTTTA
1 TAATTATTTTTA
2433163 TAATTATTTTT
1 TAATTATTTTT
2433174 TACTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TAATTATTTTTA
Found at i:2436261 original size:13 final size:14
Alignment explanation
Indices: 2436226--2436254 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2436216 TCATATTCAA
2436226 TAATATAATATTAT
1 TAATATAATATTAT
2436240 TAATATAAT-TTAT
1 TAATATAATATTAT
2436253 TA
1 TA
2436255 TTTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATAATATTAT
Found at i:2443071 original size:11 final size:11
Alignment explanation
Indices: 2443052--2443134 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
2443042 CATTTAGAAA
* *
2443052 TTAAATTTATT
1 TTAATTTTAAT
2443063 TTAATTTTAAAT
1 TTAATTTT-AAT
2443075 TT-ATTTTAAAT
1 TTAATTTT-AAT
*
2443086 TCAATTTTAAAT
1 TTAATTTT-AAT
* *
2443098 TAAATTTGAAT
1 TTAATTTTAAT
*
2443109 TTAATTTAAAT
1 TTAATTTTAAT
* *
2443120 TTAATATTATT
1 TTAATTTTAAT
2443131 TTAA
1 TTAA
2443135 ATTCAAAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
11 41 0.68
12 19 0.32
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TTAATTTTAAT
Found at i:2443072 original size:17 final size:17
Alignment explanation
Indices: 2443052--2443137 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
2443042 CATTTAGAAA
*
2443052 TTAAATTTATTTTAATT
1 TTAAATTTATTTTAAAT
2443069 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* * **
2443086 TCAATTTTAAATTAAAT
1 TTAAATTTATTTTAAAT
* *
2443103 TTGAATTTAATTTAAAT
1 TTAAATTTATTTTAAAT
2443120 TT-AATATTATTTTAAAT
1 TTAAAT-TTATTTTAAAT
2443137 T
1 T
2443138 CAAAAAGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 3 0.05
17 55 0.95
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:2443091 original size:23 final size:23
Alignment explanation
Indices: 2443065--2443124 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2443055 AATTTATTTT
*
2443065 AATTTTAAATTTATTTTAAATTC
1 AATTTTAAATTTAATTTAAATTC
* * *
2443088 AATTTTAAATTAAATTTGAATTT
1 AATTTTAAATTTAATTTAAATTC
2443111 AA-TTTAAATTTAAT
1 AATTTTAAATTTAAT
2443125 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTTTAAATTTAATTTAAATTC
Found at i:2443092 original size:12 final size:11
Alignment explanation
Indices: 2443049--2443120 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
2443039 AACCATTTAG
*
2443049 AAATTAAATTT
1 AAATTAATTTT
**
2443060 ATTTTAATTTT
1 AAATTAATTTT
*
2443071 AAATTTATTTT
1 AAATTAATTTT
2443082 AAATTCAATTTT
1 AAATT-AATTTT
*
2443094 AAATTAAATTTG
1 AAATT-AATTTT
*
2443106 AATTTAA-TTT
1 AAATTAATTTT
2443116 AAATT
1 AAATT
2443121 TAATATTATT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
10 6 0.12
11 23 0.48
12 19 0.40
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:2443934 original size:29 final size:30
Alignment explanation
Indices: 2443881--2443962 Score: 78
Period size: 32 Copynumber: 2.7 Consensus size: 30
2443871 TTGAATGTAT
* *
2443881 ATTAATAGTAATTAATAA-CTATTTT-CAAC
1 ATTAATAGTAA-TAATAATTTTTTTTACAAC
* * *
2443910 ATTAATATTATTAATAATTTTTTTTAAATAAC
1 ATTAATAGTAATAATAATTTTTTTT--ACAAC
2443942 ATTAATAGTAATAATAATTTT
1 ATTAATAGTAATAATAATTTT
2443963 AATAATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.14
29 14 0.33
32 22 0.52
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTAATAGTAATAATAATTTTTTTTACAAC
Found at i:2443965 original size:12 final size:12
Alignment explanation
Indices: 2443950--2443974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2443940 ACATTAATAG
2443950 TAATAATAATTT
1 TAATAATAATTT
2443962 TAATAATAATTT
1 TAATAATAATTT
2443974 T
1 T
2443975 TATTAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:2444627 original size:18 final size:18
Alignment explanation
Indices: 2444604--2444641 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2444594 GCGTGTTTTC
2444604 GCTTAATGGTCTAATTGT
1 GCTTAATGGTCTAATTGT
2444622 GCTTAATGGTCTAATTGT
1 GCTTAATGGTCTAATTGT
2444640 GC
1 GC
2444642 GTTTGGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (18 bp):
GCTTAATGGTCTAATTGT
Found at i:2445021 original size:30 final size:28
Alignment explanation
Indices: 2444987--2445214 Score: 204
Period size: 30 Copynumber: 7.6 Consensus size: 28
2444977 AAACTGTCCA
*
2444987 AAAATTAAATTTTAACCTCAAAACTTTTT
1 AAAATTACATTTTAACC-CAAAACTTTTT
2445016 GAAAATTACATTTTAACCCTAAAACTTTTCT
1 -AAAATTACATTTTAACCC-AAAACTTTT-T
*
2445047 AAAATTACATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTAACCC-AAAACTTTT-T
* * * *
2445077 AAAATTATATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTAACC-CAAAACTTTT-T
* *
2445107 AAAATTACATTTTAACCCTAAAAATTTTCC
1 AAAATTACATTTTAACCC-AAAACTTTT-T
* *
2445137 AATATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTT-AACCCAAAACTTTT-T
* * * *
2445167 AATATTATATTTTGACCTTAAAACTTTTT
1 AAAATTACATTTTAACC-CAAAACTTTTT
2445196 CAAAATTACATTTTAACCC
1 -AAAATTACATTTTAACCC
2445215 CCAAACCTTC
Statistics
Matches: 170, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.02
30 161 0.95
31 5 0.03
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTAACCCAAAACTTTTT
Found at i:2445051 original size:60 final size:60
Alignment explanation
Indices: 2444987--2445214 Score: 280
Period size: 60 Copynumber: 3.8 Consensus size: 60
2444977 AAACTGTCCA
* *
2444987 AAAATTAAATTTTAA-CCTCAAAACTTTTTGAAAATTACATTTTAACCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCT-AAAACTTTTTCAAAATTACATTTTAACCCTAAAACTTTTCT
* * * * *
2445047 AAAATTACATTTTGACCCTAAAAC-TTTTCTAAAATTATATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTTC-AAAATTACATTTTAACCCTAAAACTTTTCT
* * * * *
2445107 AAAATTACATTTTAACCCTAAAAATTTTCCAATATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTAACCCTAAAACTTTTTCAAAATTACATTTTAACCCTAAAACTTTTCT
* * * *
2445167 AATATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCC
1 AAAATTACATTTTAACCCTAAAACTTTTTCAAAATTACATTTTAACCC
2445215 CCAAACCTTC
Statistics
Matches: 142, Mismatches: 23, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.03
60 131 0.92
61 7 0.05
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTAAAACTTTTTCAAAATTACATTTTAACCCTAAAACTTTTCT
Found at i:2445135 original size:90 final size:90
Alignment explanation
Indices: 2444987--2445214 Score: 366
Period size: 90 Copynumber: 2.5 Consensus size: 90
2444977 AAACTGTCCA
* * * * * *
2444987 AAAATTAAATTTTAACCTCAAAACTTTTTGAAAATTACATTTTAACCCTAAAACTTTTCTAAAAT
1 AAAATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCCTAAAAATTTTCCAAAAT
*
2445052 TACATTTTGACCCTAAAACTTTTCT
66 TACATTTTGACCCCAAAACTTTTCT
* *
2445077 AAAATTATATTTTGACCTTAAAACTTTTCCAAAATTACATTTTAACCCTAAAAATTTTCCAATAT
1 AAAATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCCTAAAAATTTTCCAAAAT
2445142 TACATTTTGACCCCAAAACTTTTCT
66 TACATTTTGACCCCAAAACTTTTCT
*
2445167 AATATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCC
1 AAAATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCC
2445215 CCAAACCTTC
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 127 1.00
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (90 bp):
AAAATTATATTTTGACCTTAAAACTTTTTCAAAATTACATTTTAACCCTAAAAATTTTCCAAAAT
TACATTTTGACCCCAAAACTTTTCT
Found at i:2450556 original size:26 final size:28
Alignment explanation
Indices: 2450499--2450557 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
2450489 ATGATAATAT
* *
2450499 CCCACCACATGTCGAATATTCCTAATGCC
1 CCCACCACATGTCGAATATGCCT-ATGAC
*
2450528 CCCACCACATGTCGAATCTGCCT-T-AC
1 CCCACCACATGTCGAATATGCCTATGAC
2450554 CCCA
1 CCCA
2450558 AAATGCTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 1 0.04
29 21 0.78
ACGTcount: A:0.25, C:0.42, G:0.10, T:0.22
Consensus pattern (28 bp):
CCCACCACATGTCGAATATGCCTATGAC
Found at i:2453821 original size:24 final size:24
Alignment explanation
Indices: 2453788--2453838 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2453778 AGAAATAATT
* *
2453788 TTTCAGTTAAATTTTATTTATTTG
1 TTTCAATTAAATTCTATTTATTTG
2453812 TTTCAATTAAATTCTATTTATTTG
1 TTTCAATTAAATTCTATTTATTTG
2453836 TTT
1 TTT
2453839 TAGTGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (24 bp):
TTTCAATTAAATTCTATTTATTTG
Found at i:2458429 original size:30 final size:30
Alignment explanation
Indices: 2458393--2458456 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2458383 TTAGTAAAAG
* *
2458393 TAAAATTATATTTTGA-CCTCTTAAAAATAA
1 TAAAATTATAATTTAACCCT-TTAAAAATAA
* *
2458423 TAAAATTTTAATTTAACCCTTTAAAAATTA
1 TAAAATTATAATTTAACCCTTTAAAAATAA
2458453 TAAA
1 TAAA
2458457 CATATAGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (30 bp):
TAAAATTATAATTTAACCCTTTAAAAATAA
Found at i:2458848 original size:221 final size:223
Alignment explanation
Indices: 2458463--2458902 Score: 731
Period size: 221 Copynumber: 2.0 Consensus size: 223
2458453 TAAACATATA
*
2458463 GACTATTAAAATAGTAAAATTACACTTTTACTATCGTAAAAATTACAATTTAATTTTCACCCTCT
1 GACTATTAAAATAGTAAAATTACACTTTTACTATCGCAAAAATTACAATTTAATTTTCACCCTCT
*
2458528 TTAAAATTTTTTTTTTTGACTTCCACCTGATTCTTTTATATATATCCTGTAGACCTGCAAAGTAT
66 CTAAAATTTTTTTTTTTGACTTCCACCTGATTCTTTTATATATATCCTGTAGACCTGCAAAGTAT
* * * *
2458593 TCTCCCTGTCTGTATTGACAGTCAACATGGAATAATTGTTACAATAATAGTTTATTTGATGTTAT
131 TCTCCCTGTCTGTAATGACAATCAACATGGAATAATTGTTACAATAATAATTTATTTGATGTTAC
2458658 AAAAGAGTTAACATCACAAATATCTATG
196 AAAAGAGTTAACATCACAAATATCTATG
* * * *
2458686 GACTATTAAAATAGTGAAATTACATTTTTACTATCGCAAAAATTATATTTTAATTTTCACCCTCT
1 GACTATTAAAATAGTAAAATTACACTTTTACTATCGCAAAAATTACAATTTAATTTTCACCCTCT
* *
2458751 CT-GAA-TTTTTTTTTTGACTTCCACCTGATTCTTTTATATATATCTTGTAGACCTGCAAAGTAT
66 CTAAAATTTTTTTTTTTGACTTCCACCTGATTCTTTTATATATATCCTGTAGACCTGCAAAGTAT
** *
2458814 TCTTTCTGTCTGTAATGACAATCAACATGGAATAATTGTTACAATAATAATTTATTTGATGTTCC
131 TCTCCCTGTCTGTAATGACAATCAACATGGAATAATTGTTACAATAATAATTTATTTGATGTTAC
2458879 AAAAGAGTTAACATCACAAATATC
196 AAAAGAGTTAACATCACAAATATC
2458903 CCAACAGTTC
Statistics
Matches: 202, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
221 139 0.69
222 2 0.01
223 61 0.30
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (223 bp):
GACTATTAAAATAGTAAAATTACACTTTTACTATCGCAAAAATTACAATTTAATTTTCACCCTCT
CTAAAATTTTTTTTTTTGACTTCCACCTGATTCTTTTATATATATCCTGTAGACCTGCAAAGTAT
TCTCCCTGTCTGTAATGACAATCAACATGGAATAATTGTTACAATAATAATTTATTTGATGTTAC
AAAAGAGTTAACATCACAAATATCTATG
Found at i:2460017 original size:25 final size:23
Alignment explanation
Indices: 2459986--2460050 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
2459976 TAAATAATAT
2459986 ATATATATATTAAAAATTTCGCTG
1 ATATATATATTAAAAATTTC-CTG
*
2460010 ATA-ATATATTAAATATTTTCCTG
1 ATATATATATTAAA-AATTTCCTG
2460033 ATAGTATA-ATTATAAAAT
1 ATA-TATATATTA-AAAAT
2460051 GTTTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 16 0.46
24 14 0.40
25 5 0.14
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATATATATTAAAAATTTCCTG
Found at i:2468740 original size:30 final size:29
Alignment explanation
Indices: 2468685--2469087 Score: 326
Period size: 30 Copynumber: 13.6 Consensus size: 29
2468675 GAAGAATACG
* * *
2468685 GGGTCAAAACGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-A
* * *
2468715 GGGTAAAAATGTATTTTTTGAAAAGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
* * * * *
2468744 AGGTTAAAATATGATTTTAGAGAAGTTTG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
* * * * *
2468773 GGGTCAAAATGTGATTTTGGGAAGGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
* *
2468802 GGGTTTAAAATGTGATTTTA-AAGAAGTTTG
1 GGG-TTAAAATGTAATTTTAGAA-AAGTTTA
* *
2468832 GGAGTTAAAATGTAATTTTGGAGAAGTTTA
1 GG-GTTAAAATGTAATTTTAGAAAAGTTTA
* *
2468862 GGGATCAAAATGCT-ATTTTGGAAAAGTTTA
1 GGG-TTAAAATG-TAATTTTAGAAAAGTTTA
* * *
2468892 GGAGTTAAAATATAATTTTTGAGAAGTTTAA
1 GG-GTTAAAATGTAATTTTAGAAAAGTTT-A
* * *
2468923 GGG-TCAAATGCAATTTTAAAAAAGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
*
2468951 GGGGTTAAAATGTAATTTTAGAGAAGTTTA
1 -GGGTTAAAATGTAATTTTAGAAAAGTTTA
* ** * *
2468981 GGCATTAAAATACAATTATGGAAAAGTTTA
1 GG-GTTAAAATGTAATTTTAGAAAAGTTTA
*
2469011 GGGTTAAAATGTAATTTTAAAAAAGTTTGA
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-A
* * *
2469041 GGGTCAAAATGTAATTTTAGAAAATTTTGG
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-A
*
2469071 GGGTTAAAATGTGATTT
1 GGGTTAAAATGTAATTT
2469088 ATAAAAATTT
Statistics
Matches: 297, Mismatches: 63, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.00
29 92 0.31
30 197 0.66
31 7 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTA
Found at i:2468770 original size:59 final size:58
Alignment explanation
Indices: 2468696--2469087 Score: 286
Period size: 59 Copynumber: 6.6 Consensus size: 58
2468686 GGTCAAAACG
* * * *
2468696 TAATTTTGGAAAAGTTTAAGGGTAAAAATGTATTTTTTGAAAAGTTTAAGGTTAAAATA
1 TAATTTTAGAAAAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGTTAAAATA
* * * * * * * * * *
2468755 TGATTTTAGAGAAGTTTGGGGTCAAAATGTGATTTTGGGAAGGTTTAGGGTTTAAAATG
1 TAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGG-TTAAAATA
* * * * * * *
2468814 TGATTTTA-AAGAAGTTTGGGAGTTAAAATGTAATTTTGGAGAAGTTTAGGGATCAAAATGC
1 TAATTTTAGAA-AAGTTTAGG-GTTAAAATGTAATTTTAGAAAAGTTTAAGG-TTAAAAT-A
* * * * * * *
2468875 T-ATTTTGGAAAAGTTTAGGAGTTAAAATATAATTTTTGAGAAGTTTAAGGGTCAAATG
1 TAATTTTAGAAAAGTTTAGG-GTTAAAATGTAATTTTAGAAAAGTTTAAGGTTAAAATA
* * *
2468933 CAATTTTAAAAAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTT-AGGCATTAAAATA
1 TAATTTTAGAAAAGTTTA-GGGTTAAAATGTAATTTTAGAAAAGTTTAAGG--TTAAAATA
* * * * * * *
2468993 CAATTATGGAAAAGTTTAGGGTTAAAATGTAATTTTAAAAAAGTTTGAGGGTCAAAATG
1 TAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTT-AAGGTTAAAATA
* * *
2469052 TAATTTTAGAAAATTTTGGGGGTTAAAATGTGATTT
1 TAATTTTAGAAAAGTTT-AGGGTTAAAATGTAATTT
2469088 ATAAAAATTT
Statistics
Matches: 269, Mismatches: 52, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
58 29 0.11
59 125 0.46
60 110 0.41
61 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (58 bp):
TAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGTTAAAATA
Found at i:2468978 original size:89 final size:87
Alignment explanation
Indices: 2468684--2469080 Score: 359
Period size: 89 Copynumber: 4.5 Consensus size: 87
2468674 CGAAGAATAC
* * * * * *
2468684 GGGGTCAAAACGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTATTTTTTGAAAAGTTTAAGGTT
1 GGGGTCAAAATGTAATTTTAGAAAAGTTT-AGGGTTAAAATATAATTTTTGAAAAGTTTAGGGTT
* * * *
2468749 AAAATATGATTTTAGAGAAGTTT
65 AAAATGTAATTTTAAAAAAGTTT
* * * * * * * *
2468772 GGGGTCAAAATGTGATTTTGGGAAGGTTTAGGGTTTAAAATGTGA-TTTTAAAGAAGTTTGGGAG
1 GGGGTCAAAATGTAATTTTAGAAAAGTTTAGGG-TTAAAATATAATTTTTGAA-AAGTTTAGG-G
** *
2468836 TTAAAATGTAATTTTGGAGAAGTTT
63 TTAAAATGTAATTTTAAAAAAGTTT
* * *
2468861 AGGGATCAAAATGCT-ATTTTGGAAAAGTTTAGGAGTTAAAATATAATTTTTGAGAAGTTTAAGG
1 -GGGGTCAAAATG-TAATTTTAGAAAAGTTTAGG-GTTAAAATATAATTTTTGAAAAGTTT-AGG
* *
2468925 G-TCAAATGCAATTTTAAAAAAGTTT
62 GTTAAAATGTAATTTTAAAAAAGTTT
* * * * * *
2468950 AGGGGTTAAAATGTAATTTTAGAGAAGTTTAGGCATTAAAATACAATTATGGAAAAGTTTAGGGT
1 -GGGGTCAAAATGTAATTTTAGAAAAGTTTAGG-GTTAAAATATAATTTTTGAAAAGTTTAGGGT
2469015 TAAAATGTAATTTTAAAAAAGTTT
64 TAAAATGTAATTTTAAAAAAGTTT
* *
2469039 GAGGGTCAAAATGTAATTTTAGAAAATTTTGGGGGTTAAAAT
1 G-GGGTCAAAATGTAATTTTAGAAAAGTTT-AGGGTTAAAAT
2469081 GTGATTTATA
Statistics
Matches: 254, Mismatches: 43, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
87 10 0.04
88 46 0.18
89 144 0.57
90 45 0.18
91 9 0.04
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (87 bp):
GGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATATAATTTTTGAAAAGTTTAGGGTTA
AAATGTAATTTTAAAAAAGTTT
Found at i:2469900 original size:26 final size:26
Alignment explanation
Indices: 2469843--2469900 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2469833 TAAAATCTTC
* * *
2469843 TTTTTTTTTTCTGTTATTATTGTTTA
1 TTTTTTTTTTCTGTTATTAATATATA
*
2469869 TATTTTTTATT-TGTTATTAATATATA
1 T-TTTTTTTTTCTGTTATTAATATATA
2469895 TTTTTT
1 TTTTTT
2469901 GATCTGCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.19
26 14 0.52
27 8 0.30
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (26 bp):
TTTTTTTTTTCTGTTATTAATATATA
Found at i:2470054 original size:18 final size:17
Alignment explanation
Indices: 2470031--2470066 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2470021 ATCTTCTTTT
*
2470031 TATTAATTTATTATATTA
1 TATTAATTAATTAT-TTA
2470049 TATTAATTAATTATTTA
1 TATTAATTAATTATTTA
2470066 T
1 T
2470067 TAAAACGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTAATTAATTATTTA
Found at i:2471322 original size:85 final size:85
Alignment explanation
Indices: 2471178--2471336 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 85
2471168 GCTTCATTTA
** * * *
2471178 ATTTGGTCTGCTTCTCTGTATCTCATCAGGAAGACGATCGCTTCATTATTGTGATCCACTTCTCC
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTCATTATTGTGACCCACTTCTCA
2471243 GTATCTCATAAGGAAAATGG
66 GTATCTCATAAGGAAAATGG
* * * *
2471263 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCA
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTCATTATTGTGACCCACTTCTCA
*
2471328 GTGTCTCAT
66 GTATCTCAT
2471337 CTATAAGATA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTCATTATTGTGACCCACTTCTCA
GTATCTCATAAGGAAAATGG
Found at i:2471459 original size:210 final size:209
Alignment explanation
Indices: 2471055--2471730 Score: 795
Period size: 210 Copynumber: 3.2 Consensus size: 209
2471045 ACTTCATCTC
* * * * * *
2471055 TTGGTCTACTTCTCTGTATCTCATCAGAAAGATGATCGCTTTATCGTTTCGACCCACTTCTTTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTAGT
* * * * * ** *
2471120 ATCTCATCAGGAAGATAAGGGTTTGGAGTTTCACTCGCATTGAACTTTGCTTCATTTAATTTGGT
66 ATCTCATCAGAAAGATAAGGGTTAGAAGTTTCACTCACATTGAGCTTCACTTCA-TTGATTTGGT
* * * * * ** *
2471185 CTGCTTCTCTGTATCTCATCAGGAAGACGATCGCTT-CATTATTGTGATCCACTTCTCCGTATCT
130 CTACTTCTCTGTATCTCATCAGGAAGATGATCGATTAC-TTATTTTAATCTGCTTCTCTGTATCT
* *
2471249 CAT-AAGGAAAATGGAT
194 CATCAA-GAAGACGGAT
*
2471265 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCAGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTAGT
* * * * *
2471330 GTCTCATCTA-TAAGAT-AGGTGTTCGAAGTTTCACTCACATTGAGCTTCACTTCATCGATTTAG
66 ATCTCATC-AGAAAGATAAGG-GTTAGAAGTTTCACTCACATTGAGCTTCACTTCATTGATTTGG
* * ** *
2471393 TCTACTTCTCTATATCTCATCAAGAAGATGGCCGTATTACTTGTTTTAATCTGCTTCTCTGTATC
129 TCTACTTCTCTGTATCTCATCAGGAAGATGATCG-ATTACTTATTTTAATCTGCTTCTCTGTATC
2471458 TCATCAAGAAGACGGAT
193 TCATCAAGAAGACGGAT
* * * * * *
2471475 TTGGTTCACTTCTCTGTATCTTATCAAGAAGAAGACCGCTTTATTGCTTTGACCCATTTCTTAGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTAGT
* * * * *
2471540 ATCTCATCAGAAAGATGACGGTTAGAAGTTTCACTTACATTGAGCTTCACTTCATTGTTTTGGTT
66 ATCTCATCAGAAAGATAAGGGTTAGAAGTTTCACTCACATTGAGCTTCACTTCATTGATTTGGTC
* *
2471605 TACTTCTCTGTATCTCATTAGGAAGATGATCGCATCACTTATTTTAATCTGCTTCTCTGTATCTC
131 TACTTCTCTGTATCTCATCAGGAAGATGATCG-ATTACTTATTTTAATCTGCTTCTCTGTATCTC
*
2471670 ATCAAGAAGACAGAT
195 ATCAAGAAGACGGAT
* *
2471685 TTGGTCCACTTCTCTCTATCTCATCAGGAAGATGACTGCTTT-TTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGT
2471731 CATAAGCTTT
Statistics
Matches: 394, Mismatches: 65, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
209 41 0.10
210 347 0.88
211 6 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (209 bp):
TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTAGT
ATCTCATCAGAAAGATAAGGGTTAGAAGTTTCACTCACATTGAGCTTCACTTCATTGATTTGGTC
TACTTCTCTGTATCTCATCAGGAAGATGATCGATTACTTATTTTAATCTGCTTCTCTGTATCTCA
TCAAGAAGACGGAT
Found at i:2478310 original size:17 final size:19
Alignment explanation
Indices: 2478283--2478321 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2478273 ATACGAGACC
*
2478283 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
2478301 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
2478319 AAA
1 AAA
2478322 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:2478459 original size:27 final size:27
Alignment explanation
Indices: 2478429--2478493 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
2478419 CTAATTCCCA
2478429 GAGGGTCGTGGGCAGTCCCAATTCCTT
1 GAGGGTCGTGGGCAGTCCCAATTCCTT
*
2478456 GAGGGTCGTGGGCAGTCTCAATTCCTT
1 GAGGGTCGTGGGCAGTCCCAATTCCTT
2478483 GAGGGTCGTGG
1 GAGGGTCGTGG
2478494 ACTACTCTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.14, C:0.22, G:0.38, T:0.26
Consensus pattern (27 bp):
GAGGGTCGTGGGCAGTCCCAATTCCTT
Found at i:2485679 original size:145 final size:145
Alignment explanation
Indices: 2485382--2485650 Score: 425
Period size: 145 Copynumber: 1.9 Consensus size: 145
2485372 ATGCAAATTG
2485382 AGTGATGGACTTGGGCGGCTATCTACTTATTTGGCTAAATTTTAAAATTGGAGGAAAGGACAAAG
1 AGTGATGGACTTGGGCGGCTATCTACTTATTTGGCTAAATTTTAAAATTGGAGGAAAGGACAAAG
** * * * *
2485447 ATTTTGTCGCATTCCATGCCATAATTGTCATCATAAGATTATTTTTTTTATTATGATTGAATATA
66 ATTTTGTCGCATTCCATGCCATAATTGTCATCATAAGATTATTAATTCTATCATAATAGAATATA
* *
2485512 ATACGTGGCAAATTG
131 ATACGTGGCAAACTC
* *
2485527 AGTGATGGACTTGGGCTGCTATCTATTTATTTGGCTAAATTTTAAAATTGGAGGAAAGGACAAAG
1 AGTGATGGACTTGGGCGGCTATCTACTTATTTGGCTAAATTTTAAAATTGGAGGAAAGGACAAAG
*
2485592 ATTTTGTCGCATTCCATGCCATAATTGTCATCATAATATTATTAATTCT-TCA-AATAGAA
66 ATTTTGTCGCATTCCATGCCATAATTGTCATCATAAGATTATTAATTCTATCATAATAGAA
2485651 AGGGTAATTG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
143 5 0.04
144 2 0.02
145 108 0.94
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (145 bp):
AGTGATGGACTTGGGCGGCTATCTACTTATTTGGCTAAATTTTAAAATTGGAGGAAAGGACAAAG
ATTTTGTCGCATTCCATGCCATAATTGTCATCATAAGATTATTAATTCTATCATAATAGAATATA
ATACGTGGCAAACTC
Found at i:2489994 original size:45 final size:44
Alignment explanation
Indices: 2489928--2490024 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 44
2489918 TGGATCCAGC
* *
2489928 AGTTAAGATTTAATCGTCTTTAATATTATTTTTAAATTTATGAAG
1 AGTTATGATTTAATCGACTTTAATATTATTTTTAAA-TTATGAAG
2489973 AGTTATGATTTAATCGACTTTAATATTATTTTTAAATTATGAAG
1 AGTTATGATTTAATCGACTTTAATATTATTTTTAAATTATGAAG
2490017 AGTTATGA
1 AGTTATGA
2490025 GACTTAAGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 16 0.32
45 34 0.68
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (44 bp):
AGTTATGATTTAATCGACTTTAATATTATTTTTAAATTATGAAG
Found at i:2500503 original size:3 final size:3
Alignment explanation
Indices: 2500495--2500551 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2500485 AACAGAAATT
2500495 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2500543 TGA TGA TGA
1 TGA TGA TGA
2500552 AGGAAACATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:2505440 original size:22 final size:23
Alignment explanation
Indices: 2505399--2505442 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2505389 TTGATGGATA
*
2505399 TTTTGAAAATTTTAATTTAATAG
1 TTTTGAAAATTTTAAATTAATAG
*
2505422 TTTTG-AATTTTTAAATTAATA
1 TTTTGAAAATTTTAAATTAATA
2505443 TATATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTTGAAAATTTTAAATTAATAG
Found at i:2510349 original size:99 final size:99
Alignment explanation
Indices: 2510173--2510404 Score: 333
Period size: 99 Copynumber: 2.3 Consensus size: 99
2510163 TCCACTGGAA
* *
2510173 TTTGAGGGCAGTTTGGGTCGAAATCCTTGACAAAAGATTTATCAGTTTCTACAGGTTCCTCAGCC
1 TTTGAGGGCGGTTTGGGTCGAAATCCTTGACAAAAGATATATCAGTTTCTACAGGTTCCTCAGCC
* * * *
2510238 TGATCACTTTTTTTGTACGTAGAAT-AATGAAAAAG
66 TGATCACCTTTTTT-CAAGTA-AATGAAGGAAAAAG
2510273 -TTGAGGGCGGTTTGGGTCGAAATCCTTGACAAAAGATATATCAGTTTCTACAGGTTCCTCAGCC
1 TTTGAGGGCGGTTTGGGTCGAAATCCTTGACAAAAGATATATCAGTTTCTACAGGTTCCTCAGCC
* * **
2510337 TGGTCACCTTTTTTCAAGTAAATGACGGAAGGAG
66 TGATCACCTTTTTTCAAGTAAATGAAGGAAAAAG
*
2510371 TTTGAGGGCGGTTTGGCTCGAAATCCTTGACAAA
1 TTTGAGGGCGGTTTGGGTCGAAATCCTTGACAAA
2510405 GGATTCATGT
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
97 3 0.03
98 10 0.08
99 106 0.89
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (99 bp):
TTTGAGGGCGGTTTGGGTCGAAATCCTTGACAAAAGATATATCAGTTTCTACAGGTTCCTCAGCC
TGATCACCTTTTTTCAAGTAAATGAAGGAAAAAG
Found at i:2510920 original size:60 final size:61
Alignment explanation
Indices: 2510849--2510999 Score: 157
Period size: 61 Copynumber: 2.5 Consensus size: 61
2510839 TTTGTTTACT
* * * *
2510849 AATAAAATTAGTCTTTAATATTTAC-ATATTTTATCATTTT-GATCCTAA-TATAAAAAAATC
1 AATAAATTTAGTCCTCAATATTTACAAAATTTT-TCATTTTAG-TCCTAATTATAAAAAAATC
* * * *
2510909 AATAAATTTAGTCCTCAATGTTTACAAAATTTTTTATTTTAGTTCTAATTTTAAAAAAATC
1 AATAAATTTAGTCCTCAATATTTACAAAATTTTTCATTTTAGTCCTAATTATAAAAAAATC
* *
2510970 AATAAATAT-GATTCTCAATATTTACAAAAT
1 AATAAATTTAG-TCCTCAATATTTACAAAAT
2511000 ATGTCAATGT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
60 33 0.43
61 43 0.57
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (61 bp):
AATAAATTTAGTCCTCAATATTTACAAAATTTTTCATTTTAGTCCTAATTATAAAAAAATC
Found at i:2511023 original size:61 final size:61
Alignment explanation
Indices: 2510891--2511026 Score: 143
Period size: 61 Copynumber: 2.2 Consensus size: 61
2510881 ATCATTTTGA
* * * * * * * *
2510891 TCCTAATATAAAAAAATCAATAAATTTAGTCCTCAATGTTTACAAAATTTTTTATTTTAGT
1 TCCTAATTTAAAAAAATCAATAAATTGAGTCCTCAATATTTACAAAATATGTCAATGTAGT
*
2510952 T-CTAATTTTAAAAAAATCAATAAATATGA-TTCTCAATATTTACAAAATATGTCAATGTA-T
1 TCCTAA-TTTAAAAAAATCAATAAAT-TGAGTCCTCAATATTTACAAAATATGTCAATGTAGT
2511012 TCCTAACTTTAAAAA
1 TCCTAA-TTTAAAAA
2511027 TTTAAAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
60 6 0.10
61 54 0.87
62 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (61 bp):
TCCTAATTTAAAAAAATCAATAAATTGAGTCCTCAATATTTACAAAATATGTCAATGTAGT
Found at i:2520435 original size:27 final size:27
Alignment explanation
Indices: 2520405--2520463 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
2520395 GCTCTCCCAA
*
2520405 ACTTGGGTTTTTGGTTTAAATTAGTGT
1 ACTTGGGTTTTTGATTTAAATTAGTGT
*
2520432 ACTTGGGTTTTTTATTTAAATTAGTGT
1 ACTTGGGTTTTTGATTTAAATTAGTGT
2520459 ACTTG
1 ACTTG
2520464 AACTTGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (27 bp):
ACTTGGGTTTTTGATTTAAATTAGTGT
Found at i:2521158 original size:17 final size:18
Alignment explanation
Indices: 2521120--2521158 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2521110 TAAATTGACA
2521120 TTAAATAATTAAGTTGTT
1 TTAAATAATTAAGTTGTT
2521138 TTAAATAA-TAGAGTT-TT
1 TTAAATAATTA-AGTTGTT
2521155 TTAA
1 TTAA
2521159 GAACAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
TTAAATAATTAAGTTGTT
Found at i:2521925 original size:25 final size:23
Alignment explanation
Indices: 2521790--2521937 Score: 163
Period size: 23 Copynumber: 6.3 Consensus size: 23
2521780 TGCTGGGCAA
*
2521790 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACACAGTGCTAAT
* ** * * *
2521813 CAGAAAATACACAAAGTACTGAT
1 CAGAGAGCACACACAGTGCTAAT
*
2521836 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
2521859 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
*
2521882 CAGAGAGCACATACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* *
2521905 AACAGAGAGCACGAGAC-GTGCTAAA
1 --CAGAGAGCAC-ACACAGTGCTAAT
2521930 CAGAGAGC
1 CAGAGAGC
2521938 GCGCTAGTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
23 86 0.81
25 17 0.16
26 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACACAGTGCTAAT
Found at i:2528200 original size:23 final size:23
Alignment explanation
Indices: 2528169--2528318 Score: 176
Period size: 23 Copynumber: 6.4 Consensus size: 23
2528159 AGTGCTGGGC
2528169 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * * * *
2528192 AACAAAGAGTACACAAAGTACTG
1 AACAGAGAGCACACACAGTGCTA
* *
2528215 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2528238 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2528261 ACCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
2528285 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
2528309 AACAGAGAGC
1 AACAGAGAGC
2528319 GCGCTAGTGT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
23 89 0.81
24 2 0.02
25 16 0.15
26 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:2537696 original size:2 final size:2
Alignment explanation
Indices: 2537689--2537717 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2537679 ACTAATCAGG
2537689 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2537718 TACAATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2541359 original size:16 final size:18
Alignment explanation
Indices: 2541338--2541373 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2541328 AAATTAATCG
2541338 TAAAATTAA-AC-AAATT
1 TAAAATTAACACTAAATT
2541354 TAAAATTAACACTAAATT
1 TAAAATTAACACTAAATT
2541372 TA
1 TA
2541374 TTCTGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAACACTAAATT
Found at i:2553030 original size:21 final size:18
Alignment explanation
Indices: 2552991--2553026 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2552981 ATTATTTTTA
*
2552991 ATATGATTATTAGATTTC
1 ATATGACTATTAGATTTC
2553009 ATATGACTATTAGATTTC
1 ATATGACTATTAGATTTC
2553027 TTCACGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (18 bp):
ATATGACTATTAGATTTC
Found at i:2557226 original size:3 final size:3
Alignment explanation
Indices: 2557212--2557246 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2557202 GATCGACTAC
*
2557212 CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
2557247 CCTGAGACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:2563171 original size:183 final size:183
Alignment explanation
Indices: 2562863--2563233 Score: 733
Period size: 183 Copynumber: 2.0 Consensus size: 183
2562853 TATTTAACTC
2562863 TTTAATTGTACAAAAATAAATCATTTTAATCTTTAAATTTGCGTTATTATCAAATCACTCAAAAA
1 TTTAATTGTACAAAAATAAATCATTTTAATCTTTAAATTTGCGTTATTATCAAATCACTCAAAAA
2562928 TAGATGGAAAAGTTAACCTCTACTAATTTTGTTGACATGACATACACATGGATTACTTTATGGAT
66 TAGATGGAAAAGTTAACCTCTACTAATTTTGTTGACATGACATACACATGGATTACTTTATGGAT
2562993 TTCACGTTAATAATTAATTTTTTTAGATTTAAAAATTCAAAAAATTATAATTT
131 TTCACGTTAATAATTAATTTTTTTAGATTTAAAAATTCAAAAAATTATAATTT
*
2563046 TTTAATTGTACAAAAATAAATCATTTTAGTCTTTAAATTTGCGTTATTATCAAATCACTCAAAAA
1 TTTAATTGTACAAAAATAAATCATTTTAATCTTTAAATTTGCGTTATTATCAAATCACTCAAAAA
2563111 TAGATGGAAAAGTTAACCTCTACTAATTTTGTTGACATGACATACACATGGATTACTTTATGGAT
66 TAGATGGAAAAGTTAACCTCTACTAATTTTGTTGACATGACATACACATGGATTACTTTATGGAT
2563176 TTCACGTTAATAATTAATTTTTTTAGATTTAAAAATTCAAAAAATTATAATTT
131 TTCACGTTAATAATTAATTTTTTTAGATTTAAAAATTCAAAAAATTATAATTT
2563229 TTTAA
1 TTTAA
2563234 AAAACTAAAA
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 187 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (183 bp):
TTTAATTGTACAAAAATAAATCATTTTAATCTTTAAATTTGCGTTATTATCAAATCACTCAAAAA
TAGATGGAAAAGTTAACCTCTACTAATTTTGTTGACATGACATACACATGGATTACTTTATGGAT
TTCACGTTAATAATTAATTTTTTTAGATTTAAAAATTCAAAAAATTATAATTT
Found at i:2563334 original size:10 final size:10
Alignment explanation
Indices: 2563319--2563343 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2563309 CGTAGATGTG
2563319 AACATCAGCA
1 AACATCAGCA
2563329 AACATCAGCA
1 AACATCAGCA
2563339 AACAT
1 AACAT
2563344 TAATTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.08, T:0.12
Consensus pattern (10 bp):
AACATCAGCA
Found at i:2563602 original size:18 final size:17
Alignment explanation
Indices: 2563570--2563603 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2563560 TAATATATCG
2563570 ATAAAATACAAAAAAAA
1 ATAAAATACAAAAAAAA
*
2563587 ATAAAGATATAAAAAAA
1 ATAAA-ATACAAAAAAA
2563604 GTGGTCTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAAATACAAAAAAAA
Found at i:2576782 original size:24 final size:24
Alignment explanation
Indices: 2576764--2576811 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2576754 GTTTTAATTA
2576764 TTAATTAATATTTTCTTTTTGTAT
1 TTAATTAATATTTTCTTTTTGTAT
2576788 TTAATTAATATTTTCTTTTTGTAT
1 TTAATTAATATTTTCTTTTTGTAT
2576812 GATGATGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTAATTAATATTTTCTTTTTGTAT
Found at i:2579160 original size:23 final size:23
Alignment explanation
Indices: 2579117--2579161 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2579107 AAAAAAATTC
**
2579117 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
2579140 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
2579162 ATTCGAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:2585911 original size:27 final size:27
Alignment explanation
Indices: 2585873--2585925 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2585863 TGTTTTCAAG
*
2585873 CCATCGATGCTAGACCATCAGTAAGTA
1 CCATCAATGCTAGACCATCAGTAAGTA
*
2585900 CCATCAATGCTAGGCCATCAGTAAGT
1 CCATCAATGCTAGACCATCAGTAAGT
2585926 TTATTACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (27 bp):
CCATCAATGCTAGACCATCAGTAAGTA
Found at i:2597111 original size:29 final size:30
Alignment explanation
Indices: 2597076--2597132 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
2597066 GCATTTTGAT
2597076 AAATTTAAGATTT-AAT-TTTTATATTTTAA
1 AAATTTAA-ATTTAAATCTTTTATATTTTAA
*
2597105 AAATTTAAATTTAAATCTTTTTTATTTT
1 AAATTTAAATTTAAATCTTTTATATTTT
2597133 TCTATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 11 0.44
30 10 0.40
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
AAATTTAAATTTAAATCTTTTATATTTTAA
Found at i:2597870 original size:32 final size:32
Alignment explanation
Indices: 2597834--2597895 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
2597824 TAGTGTTTCC
2597834 ATAATCA-AGGTTGTTTAAATTAAAACTAGTCG
1 ATAATCATA-GTTGTTTAAATTAAAACTAGTCG
* *
2597866 ATAATCATAGTTGTTTGAATTAGAACTAGT
1 ATAATCATAGTTGTTTAAATTAAAACTAGT
2597896 TGATGGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (32 bp):
ATAATCATAGTTGTTTAAATTAAAACTAGTCG
Found at i:2599547 original size:26 final size:26
Alignment explanation
Indices: 2599498--2599548 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2599488 TTGAACTGGT
*
2599498 TTTTTTAATAATTTTTTATTTTTGAG
1 TTTTTTAATAATTTTTTACTTTTGAG
2599524 TTTTTTAATAATTTATTT-CTTTTGA
1 TTTTTTAATAATTT-TTTACTTTTGA
2599549 ACTGCCCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTTTTAATAATTTTTTACTTTTGAG
Found at i:2606723 original size:31 final size:29
Alignment explanation
Indices: 2606688--2606759 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2606678 AATTATATTA
* * * *
2606688 TTGATCATTAAATTACGGGTAAATTTTCATT
1 TTGATCATTAAATTA-GAGT-AAGTTACAAT
*
2606719 TTGATCATTTAATTAGAGTAAGTTACAAT
1 TTGATCATTAAATTAGAGTAAGTTACAAT
2606748 TTGATCATTAAA
1 TTGATCATTAAA
2606760 ATTTTCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 18 0.51
30 3 0.09
31 14 0.40
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (29 bp):
TTGATCATTAAATTAGAGTAAGTTACAAT
Found at i:2608649 original size:18 final size:18
Alignment explanation
Indices: 2608626--2608689 Score: 128
Period size: 18 Copynumber: 3.6 Consensus size: 18
2608616 TAAATAGTTT
2608626 GAGTTATTCGATTTAATC
1 GAGTTATTCGATTTAATC
2608644 GAGTTATTCGATTTAATC
1 GAGTTATTCGATTTAATC
2608662 GAGTTATTCGATTTAATC
1 GAGTTATTCGATTTAATC
2608680 GAGTTATTCG
1 GAGTTATTCG
2608690 GATCAACTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.44
Consensus pattern (18 bp):
GAGTTATTCGATTTAATC
Found at i:2608654 original size:9 final size:9
Alignment explanation
Indices: 2608626--2608689 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
2608616 TAAATAGTTT
2608626 GAGTTATTC
1 GAGTTATTC
* *
2608635 GATTTAATC
1 GAGTTATTC
2608644 GAGTTATTC
1 GAGTTATTC
* *
2608653 GATTTAATC
1 GAGTTATTC
2608662 GAGTTATTC
1 GAGTTATTC
* *
2608671 GATTTAATC
1 GAGTTATTC
2608680 GAGTTATTC
1 GAGTTATTC
2608689 G
1 G
2608690 GATCAACTCG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.44
Consensus pattern (9 bp):
GAGTTATTC
Found at i:2614529 original size:20 final size:21
Alignment explanation
Indices: 2614489--2614530 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2614479 AAGATTTGGT
2614489 ATTTGAATGACGTATTGATTG
1 ATTTGAATGACGTATTGATTG
*
2614510 ATTTGGATGACGTA-TGATTG
1 ATTTGAATGACGTATTGATTG
2614530 A
1 A
2614531 AAGCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (21 bp):
ATTTGAATGACGTATTGATTG
Found at i:2615813 original size:15 final size:15
Alignment explanation
Indices: 2615781--2615831 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2615771 TTATCCATTT
*
2615781 ATTTATTAAA-TAATA
1 ATTT-TTAAATTAAAA
2615796 ATTTTTAAATTAAAA
1 ATTTTTAAATTAAAA
*
2615811 ATTTTT--ATTCAAA
1 ATTTTTAAATTAAAA
2615824 ATTTTTAA
1 ATTTTTAA
2615832 TTTTTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 12 0.39
14 5 0.16
15 14 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTTAAATTAAAA
Found at i:2617254 original size:31 final size:33
Alignment explanation
Indices: 2617186--2617254 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 33
2617176 GAATTATAAA
* *
2617186 TTTTAAAGAGAGAGTAAAATATAATTTTATCAG
1 TTTTAAAGAGAGAGTAAAATATAAATTTACCAG
* * *
2617219 TTTTAAAGAG-G-TTAAATTATAAATTTACCAT
1 TTTTAAAGAGAGAGTAAAATATAAATTTACCAG
2617250 TTTTA
1 TTTTA
2617255 GTATCAAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 20 0.65
32 1 0.03
33 10 0.32
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (33 bp):
TTTTAAAGAGAGAGTAAAATATAAATTTACCAG
Found at i:2618882 original size:23 final size:24
Alignment explanation
Indices: 2618835--2618882 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2618825 TTTCAGATTT
**
2618835 AAAAATGCAACTCCAATTTCTTTAA
1 AAAAATGCAACTCCAA-TTAGTTAA
2618860 AAAAATGCAACTCCAA-TAGTTAA
1 AAAAATGCAACTCCAATTAGTTAA
2618883 TACTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAAATGCAACTCCAATTAGTTAA
Found at i:2620271 original size:18 final size:19
Alignment explanation
Indices: 2620250--2620303 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
2620240 TATTTATTTT
2620250 ATATATTATAAATTA-TAA
1 ATATATTATAAATTATTAA
* *
2620268 ATATATTTTAAATAATTAA
1 ATATATTATAAATTATTAA
*
2620287 AAATATATATTAAATTA
1 ATATAT-TA-TAAATTA
2620304 AGTAGATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 13 0.46
19 8 0.29
20 1 0.04
21 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATTATAAATTATTAA
Found at i:2620290 original size:21 final size:21
Alignment explanation
Indices: 2620249--2620301 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2620239 ATATTTATTT
* *
2620249 TATATATTATA-AATTATAAA
1 TATATATTAAATAATTAAAAA
*
2620269 TATATTTTAAATAATTAAAAA
1 TATATATTAAATAATTAAAAA
2620290 TATATATTAAAT
1 TATATATTAAAT
2620302 TAAGTAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATTAAATAATTAAAAA
Found at i:2620873 original size:12 final size:12
Alignment explanation
Indices: 2620856--2620880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2620846 ACTGAATTAG
2620856 ATCGATTAACCA
1 ATCGATTAACCA
2620868 ATCGATTAACCA
1 ATCGATTAACCA
2620880 A
1 A
2620881 ATTAAATCGA
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:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCGATTAACCA
Found at i:2623234 original size:19 final size:20
Alignment explanation
Indices: 2623192--2623244 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2623182 ATTACAAAAG
2623192 AAAAATTCAAAATAATCTTA
1 AAAAATTCAAAATAATCTTA
2623212 AAAAATTCAAAAT-AT-TTA
1 AAAAATTCAAAATAATCTTA
2623230 TAAAAATTTCAAAAT
1 -AAAAA-TTCAAAAT
2623245 TTATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.10
19 7 0.23
20 21 0.68
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATCTTA
Found at i:2623302 original size:19 final size:19
Alignment explanation
Indices: 2623278--2623314 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2623268 AATTTTAAAA
2623278 AAAAATCTAAAAAATATAT
1 AAAAATCTAAAAAATATAT
* *
2623297 AAAAATGTTAAAAATATA
1 AAAAATCTAAAAAATATA
2623315 AATTTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAATCTAAAAAATATAT
Found at i:2623970 original size:17 final size:17
Alignment explanation
Indices: 2623940--2624016 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
2623930 TTAAATTGAT
2623940 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
2623956 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
2623973 TTTTAAATTAAATATTTAAA
1 -TTTAAATT-TAT-TTTAAA
*
2623993 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
2624010 TTTAAAT
1 TTTAAAT
2624017 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 15 0.30
18 15 0.30
19 5 0.10
20 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2623994 original size:37 final size:34
Alignment explanation
Indices: 2623948--2624039 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 34
2623938 ATTTTAAATT
*
2623948 TATTTAAATTTAGATTTATTTTAAATTTTAAATTAAA
1 TATTTAAATTTA-ATTTAATTTAAA-TTTAAA-TAAA
2623985 TATTTAAATTTAATTTGAATTTAAATTTAAATAAA
1 TATTTAAATTTAATTT-AATTTAAATTTAAATAAA
* *
2624020 AATTAAAATATTAAATTTAA
1 TATTTAAAT-TT-AATTTAA
2624040 CATTTAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 11 0.22
36 14 0.29
37 24 0.49
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (34 bp):
TATTTAAATTTAATTTAATTTAAATTTAAATAAA
Found at i:2624005 original size:11 final size:11
Alignment explanation
Indices: 2623930--2624016 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
2623920 GACTCTTGAG
* *
2623930 TTAAATTGATT
1 TTAAATTTAAT
2623941 TTAAATTT-AT
1 TTAAATTTAAT
2623951 TTAAATTTAGAT
1 TTAAATTTA-AT
*
2623963 TT-ATTTTAAATT
1 TTAAATTT-AA-T
*
2623975 TTAAATTAAATAT
1 TTAAATT-TA-AT
2623988 TTAAATTTAAT
1 TTAAATTTAAT
*
2623999 TTGAATTTAAAT
1 TTAAATTT-AAT
2624011 TTAAAT
1 TTAAAT
2624017 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 21 0.35
12 17 0.28
13 12 0.20
14 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2624044 original size:7 final size:6
Alignment explanation
Indices: 2623940--2624047 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
2623930 TTAAATTGAT
* * *
2623940 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTTAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAA-A
* ** *
2623987 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
2624035 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
2624048 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.59
7 22 0.27
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:2624097 original size:14 final size:14
Alignment explanation
Indices: 2624078--2624115 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
2624068 TGGCCCACGA
2624078 CCCAATTACAATGG
1 CCCAATTACAATGG
*
2624092 CCCAATT--AAGGG
1 CCCAATTACAATGG
2624104 CCCAATTACAAT
1 CCCAATTACAAT
2624116 AGTCCAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (14 bp):
CCCAATTACAATGG
Found at i:2624735 original size:15 final size:15
Alignment explanation
Indices: 2624715--2624751 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2624705 AATGACGGTT
*
2624715 ATAATATCAATAATA
1 ATAATAACAATAATA
*
2624730 ATAATAACAGTAATA
1 ATAATAACAATAATA
2624745 ATAATAA
1 ATAATAA
2624752 ATATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATAACAATAATA
Found at i:2625255 original size:12 final size:12
Alignment explanation
Indices: 2625235--2625264 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2625225 GGGAGTTTGA
2625235 GAGAAAAAAGGG
1 GAGAAAAAAGGG
*
2625247 GAGAGAAAAGGG
1 GAGAAAAAAGGG
2625259 GAGAAA
1 GAGAAA
2625265 TTTCAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAGGG
Found at i:2625777 original size:30 final size:30
Alignment explanation
Indices: 2625741--2626000 Score: 394
Period size: 30 Copynumber: 8.7 Consensus size: 30
2625731 TAAATTGTCT
* *
2625741 CAAAATTATATTTCGACCCTAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
**
2625771 CAAAATTACCTTTTGACCCCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
** *
2625801 CAAAATTACCTTTTGACCCTAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
**
2625831 CAAAATTACCTTTTGACCCCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
* *
2625861 CAAAATTACATTTTGACGCCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
*
2625891 CAAAATTATATTTTGACTCCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
2625921 CAAAATTATATTTTGACCCCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
*
2625951 CAAAATTATATTTTGACCTCAAAACTTTTC
1 CAAAATTATATTTTGACCCCAAAACTTTTC
*
2625981 CAAAATTATATTTTAACCCC
1 CAAAATTATATTTTGACCCC
2626001 CGAAGCTTCT
Statistics
Matches: 216, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 216 1.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
CAAAATTATATTTTGACCCCAAAACTTTTC
Found at i:2626058 original size:29 final size:30
Alignment explanation
Indices: 2626021--2626118 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 30
2626011 AAAATTCCGT
2626021 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACCAAAAATTACCA
** ** * *
2626051 TTTT-ACCCTCGA-AGCTTCTAAAATT-CTA
1 TTTTAACCC-CGATTTCACCAAAAATTACCA
* *
2626079 TTTTTAACCCTGATTTTACCAAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAAATTACCA
2626110 TTTT-ACCCC
1 TTTTAACCCC
2626119 TGAAGCTTCT
Statistics
Matches: 48, Mismatches: 15, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
28 2 0.04
29 22 0.46
30 22 0.46
31 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:2626064 original size:59 final size:59
Alignment explanation
Indices: 2625982--2626235 Score: 307
Period size: 59 Copynumber: 4.3 Consensus size: 59
2625972 AAACTTTTCC
* * *
2625982 AAAATTA-TATTTTAACCCCCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTT-ACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
2626041 AAAATTACCATTTTA-CCCTCGAAGCTTCTAAAATTCTATTTTTAACCCTGATTTTACCA
1 AAAATTACCATTTTACCCCT-GAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* ** *
2626100 AAAATTACCATTTTACCCCTGAAGCTTCTAAAATTGCATTTTTAACCCTAATTTCACCG
1 AAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * * * * * *
2626159 AAGATTGCCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCTCGATTACACC-
1 AAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*
2626217 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
2626236 CCGGGTATCC
Statistics
Matches: 168, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
58 19 0.11
59 140 0.83
60 9 0.05
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:2626120 original size:30 final size:30
Alignment explanation
Indices: 2626021--2626121 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 30
2626011 AAAATTCCGT
*
2626021 TTTTAACCCC-GATTTCACCAAAAATTACCA
1 TTTT-ACCCCTGATTTTACCAAAAATTACCA
** * *
2626051 TTTTA-CCCTCGAAGCTT--CTAAAATT-CTA
1 TTTTACCCCT-G-ATTTTACCAAAAATTACCA
*
2626079 TTTTTAACCCTGATTTTACCAAAAATTACCA
1 -TTTTACCCCTGATTTTACCAAAAATTACCA
2626110 TTTTACCCCTGA
1 TTTTACCCCTGA
2626122 AGCTTCTAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
28 8 0.15
29 14 0.26
30 27 0.51
31 4 0.08
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTTACCCCTGATTTTACCAAAAATTACCA
Found at i:2626133 original size:29 final size:28
Alignment explanation
Indices: 2626041--2626134 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 28
2626031 GATTTCACCA
2626041 AAAATTACCATTTTACCCTCGAAGCTTCT
1 AAAATTACCATTTTACCCT-GAAGCTTCT
* ** *
2626070 AAAATT-CTATTTTTAACCCTG-ATTTTACCA
1 AAAATTACCA-TTTT-ACCCTGAAGCTT--CT
2626100 AAAATTACCATTTTACCCCTGAAGCTTCT
1 AAAATTACCATTTTA-CCCTGAAGCTTCT
2626129 AAAATT
1 AAAATT
2626135 GCATTTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
28 5 0.10
29 19 0.38
30 21 0.42
31 5 0.10
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTGAAGCTTCT
Found at i:2626142 original size:29 final size:28
Alignment explanation
Indices: 2626051--2626148 Score: 76
Period size: 30 Copynumber: 3.4 Consensus size: 28
2626041 AAAATTACCA
2626051 TTTT-ACCCTCGAAGCTTCTAAAATTCTAT
1 TTTTAACCCT-GAAGCTTCTAAAATTC-AT
** *
2626080 TTTTAACCCTG-ATTTTACCAAAAATTACCA-
1 TTTTAACCCTGAAGCTT--CTAAAATT--CAT
*
2626110 TTTTACCCCTGAAGCTTCTAAAATTGCAT
1 TTTTAACCCTGAAGCTTCTAAAATT-CAT
2626139 TTTTAACCCT
1 TTTTAACCCT
2626149 AATTTCACCG
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
28 5 0.09
29 21 0.40
30 22 0.42
31 4 0.08
32 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (28 bp):
TTTTAACCCTGAAGCTTCTAAAATTCAT
Found at i:2638029 original size:68 final size:68
Alignment explanation
Indices: 2637920--2638704 Score: 1444
Period size: 68 Copynumber: 11.5 Consensus size: 68
2637910 CTGCAGGTCT
*
2637920 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAGTTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2637985 GAG
66 GAG
2637988 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638053 GAG
66 GAG
2638056 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638121 GAG
66 GAG
*
2638124 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638189 GAG
66 GAG
*
2638192 CAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638257 GAG
66 GAG
*
2638260 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638325 GAG
66 GAG
*
2638328 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638393 GAG
66 GAG
* *
2638396 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGAATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638461 GAG
66 GAG
2638464 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638529 GAG
66 GAG
*
2638532 CAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638597 GAG
66 GAG
* * *
2638600 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
2638665 GAG
66 GAG
* *
2638668 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATA
2638705 GCAAAGTCTT
Statistics
Matches: 700, Mismatches: 16, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
68 694 0.99
69 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:2639025 original size:6 final size:6
Alignment explanation
Indices: 2639007--2639114 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
2638997 TTAAATTGAT
* * *
2639007 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
2639054 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
2639102 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
2639115 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 21 0.25
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:2639037 original size:17 final size:17
Alignment explanation
Indices: 2639007--2639083 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
2638997 TTAAATTGAT
2639007 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
2639023 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
2639040 TTTAAAATTAAATATTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
2639060 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
2639077 TTTAAAT
1 TTTAAAT
2639084 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2639072 original size:11 final size:11
Alignment explanation
Indices: 2638997--2639083 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
2638987 GACTCTTGAG
* *
2638997 TTAAATTGATT
1 TTAAATTTAAT
2639008 TTAAATTT-AT
1 TTAAATTTAAT
2639018 TTAAATTTAGAT
1 TTAAATTTA-AT
*
2639030 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
2639041 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
2639055 TTAAATTTAAT
1 TTAAATTTAAT
*
2639066 TTGAATTTAAAT
1 TTAAATTT-AAT
2639078 TTAAAT
1 TTAAAT
2639084 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 14 0.23
13 9 0.15
14 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2639104 original size:31 final size:30
Alignment explanation
Indices: 2639034--2639114 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
2639024 TTAGATTTAT
* * *
2639034 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAATTTAAATA-TAAAATTAAA
*
2639065 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAATTTAAATATAAAATT-AAA
2639095 TATTAAATTTAACATTTAAA
1 T-TTAAATTTAA-ATTTAAA
2639115 AGTCCAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 3 0.07
31 27 0.64
32 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAATTTAAATATAAAATTAAA
Found at i:2639162 original size:14 final size:14
Alignment explanation
Indices: 2639143--2639181 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
2639133 CATGGCCCAC
2639143 GGCCCAATTACAAA
1 GGCCCAATTACAAA
*
2639157 GGCCCAATT--AAG
1 GGCCCAATTACAAA
2639169 GGCCCAATTACAA
1 GGCCCAATTACAA
2639182 TAGTCCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:2639249 original size:20 final size:20
Alignment explanation
Indices: 2639224--2639264 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2639214 GTGCCTACTG
* *
2639224 CTGCTGGCCACCGGCTCCAT
1 CTGCTGACCACCAGCTCCAT
*
2639244 CTGCTGACCACTAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
2639264 C
1 C
2639265 CACCAGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.44, G:0.20, T:0.22
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:2639802 original size:15 final size:15
Alignment explanation
Indices: 2639782--2639818 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2639772 AATGACGGTT
*
2639782 ATAATATCAATAATA
1 ATAATAACAATAATA
*
2639797 ATAATAACAGTAATA
1 ATAATAACAATAATA
2639812 ATAATAA
1 ATAATAA
2639819 ATATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATAACAATAATA
Found at i:2640038 original size:15 final size:15
Alignment explanation
Indices: 2640018--2640050 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2640008 ATTTGAGAAG
2640018 TTTCCAGATCTGGAT
1 TTTCCAGATCTGGAT
2640033 TTTCCAGATCTGGAT
1 TTTCCAGATCTGGAT
2640048 TTT
1 TTT
2640051 GAAAAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (15 bp):
TTTCCAGATCTGGAT
Found at i:2640320 original size:12 final size:12
Alignment explanation
Indices: 2640300--2640329 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2640290 GGGAGTTTGA
2640300 GAGAAAAAAGGG
1 GAGAAAAAAGGG
*
2640312 GAGAGAAAAGGG
1 GAGAAAAAAGGG
2640324 GAGAAA
1 GAGAAA
2640330 TTTCAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAGGG
Found at i:2640843 original size:30 final size:30
Alignment explanation
Indices: 2640807--2640885 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
2640797 AAATTATCTA
*
2640807 AAAATTATATTTCGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
2640837 AAAATTATATTTTGACCCCGAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
2640867 AAAATTACATTTTGACCCC
1 AAAATTATATTTTGACCCC
2640886 CGAAGCTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:2640933 original size:59 final size:58
Alignment explanation
Indices: 2640865--2641062 Score: 272
Period size: 59 Copynumber: 3.4 Consensus size: 58
2640855 CGAAACTTTT
** *
2640865 CCAAAATTA-CATTTTGACCCCCGAAGCTTCTAAAATTCTGTTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTT-ACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCA
*
2640923 CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCA
1 CC-AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCA
* * * * *
2640982 CCGAAGATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTACA
1 CC-AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCA
*
2641041 CCAAAATTACCATTTTGCCCCC
1 CCAAAATTACCATTTTACCCCC
2641063 CGGGTATCCA
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 19 0.15
59 99 0.80
60 6 0.05
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCA
Found at i:2640940 original size:30 final size:29
Alignment explanation
Indices: 2640906--2641056 Score: 83
Period size: 29 Copynumber: 5.1 Consensus size: 29
2640896 AAAATTCTGT
*
2640906 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACCTAAAATT-CCA
* ** **
2640936 TTTTACCCCCGA-AGCTTCTAAAATTCCA
1 TTTTAACCCCGATTTCACCTAAAATTCCA
** * *
2640964 TTTTTAACCCTAATTTCACCGAAGATTGCCA
1 -TTTTAACCCCGATTTCACCTAAAATT-CCA
* * ***
2640995 TTTTACCCCCGA-ATCTTTTAAAATTCCA
1 TTTTAACCCCGATTTCACCTAAAATTCCA
* *
2641023 TTTTTAACCCCAATTACACC-AAAATTACCA
1 -TTTTAACCCCGATTTCACCTAAAATT-CCA
2641053 TTTT
1 TTTT
2641057 GCCCCCCGGG
Statistics
Matches: 84, Mismatches: 31, Indels: 13
0.66 0.24 0.10
Matches are distributed among these distances:
28 6 0.07
29 44 0.52
30 31 0.37
31 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCTAAAATTCCA
Found at i:2640958 original size:29 final size:28
Alignment explanation
Indices: 2640867--2640967 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 28
2640857 AAACTTTTCC
*
2640867 AAAATTACATTTTGACCCCCGAAGCTTCT
1 AAAATTCCATTTT-ACCCCCGAAGCTTCT
** * ** ** *
2640896 AAAATTCTGTTTTTAACCCCGATTTCACCA
1 AAAATTC-CATTTTACCCCCGA-AGCTTCT
2640926 AAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATT-CCATTTTACCCCCGAAGCTTCT
2640955 AAAATTCCATTTT
1 AAAATTCCATTTT
2640968 TAACCCTAAT
Statistics
Matches: 52, Mismatches: 17, Indels: 7
0.68 0.22 0.09
Matches are distributed among these distances:
28 7 0.13
29 21 0.40
30 23 0.44
31 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCCGAAGCTTCT
Found at i:2640968 original size:29 final size:29
Alignment explanation
Indices: 2640867--2641033 Score: 92
Period size: 29 Copynumber: 5.7 Consensus size: 29
2640857 AAACTTTTCC
* *
2640867 AAAATTACATTTTGACCCCCGAAGCTTCT
1 AAAATTCCATTTTTACCCCCGAAGCTTCT
** * ** ** *
2640896 AAAATTCTGTTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTACCCCCGA-AGCTTCT
2640926 AAAATTACCA-TTTTACCCCCGAAGCTTCT
1 AAAATT-CCATTTTTACCCCCGAAGCTTCT
* * *
2640955 AAAATTCCATTTTTA-ACCCTAA-TTTC-
1 AAAATTCCATTTTTACCCCCGAAGCTTCT
* *
2640981 ACCGAAGATTGCCA-TTTTACCCCCGAATCTTTT
1 A---AA-ATT-CCATTTTTACCCCCGAAGCTTCT
*
2641014 AAAATTCCATTTTTAACCCC
1 AAAATTCCATTTTTACCCCC
2641034 AATTACACCA
Statistics
Matches: 100, Mismatches: 26, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
26 1 0.01
27 3 0.03
28 11 0.11
29 44 0.44
30 29 0.29
31 9 0.09
32 2 0.02
33 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCGAAGCTTCT
Found at i:2644370 original size:11 final size:11
Alignment explanation
Indices: 2644311--2644372 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
2644301 TATTTATATT
2644311 ATATTATTTTA
1 ATATTATTTTA
2644322 ATATTTAATTTT-
1 ATA-TT-ATTTTA
2644334 ATATT-TTTTA
1 ATATTATTTTA
* *
2644344 TATAGTCATCTTA
1 -ATA-TTATTTTA
2644357 ATATTATTTTA
1 ATATTATTTTA
2644368 ATATT
1 ATATT
2644373 TACATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
11 19 0.46
12 9 0.22
13 9 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:2644380 original size:23 final size:23
Alignment explanation
Indices: 2644300--2644380 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
2644290 TTTAAAATAT
*
2644300 ATATTTATATT-ATATTATTTTA
1 ATATTTACATTAATATTATTTTA
*
2644322 ATATTTA-ATTTTATATT-TTTTA
1 ATATTTACA-TTAATATTATTTTA
* *
2644344 TATAGTCATC-TTAATATTATTTTA
1 -ATATTTA-CATTAATATTATTTTA
2644368 ATATTTACATTAA
1 ATATTTACATTAA
2644381 AACAATATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.02
22 15 0.32
23 26 0.55
24 5 0.11
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
ATATTTACATTAATATTATTTTA
Found at i:2646093 original size:31 final size:31
Alignment explanation
Indices: 2646058--2646118 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2646048 ATGATCATTG
* *
2646058 AACTATTTTAAAGTTTTCGTTTAAGTTATTA
1 AACTATTTGAAAGTTTTCATTTAAGTTATTA
*
2646089 AACTATTTGAAAGTTTTTATTTAAGTTATT
1 AACTATTTGAAAGTTTTCATTTAAGTTATT
2646119 GGGTTGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (31 bp):
AACTATTTGAAAGTTTTCATTTAAGTTATTA
Found at i:2646447 original size:12 final size:12
Alignment explanation
Indices: 2646430--2646469 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2646420 TCAGACCAAC
*
2646430 AATAATTAAATA
1 AATAATTAAAAA
2646442 AATAATTAAAAA
1 AATAATTAAAAA
2646454 AATAA-TAAAAA
1 AATAATTAAAAA
*
2646465 TATAA
1 AATAA
2646470 AAATCCAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAATTAAAAA
Found at i:2653504 original size:10 final size:9
Alignment explanation
Indices: 2653488--2653543 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
2653478 CTTCATGCTA
2653488 TTTTTTAAT
1 TTTTTTAAT
2653497 TCTTTTTAAT
1 T-TTTTTAAT
2653507 TTTTTTGAAT
1 TTTTTT-AAT
*
2653517 ATTTTTAAT
1 TTTTTTAAT
**
2653526 TTTTAAATAT
1 TTTTTTA-AT
2653536 TTTTTTAA
1 TTTTTTAA
2653544 ATTATTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 14 0.37
10 24 0.63
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:2653688 original size:64 final size:64
Alignment explanation
Indices: 2653587--2653714 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
2653577 TATCTTTTTA
* *
2653587 GCATGAAGTAAACTTGCTCATGGGTCGGGCCACCCACCCAGGCCCGAAGGCTTGCCCTAAAATG
1 GCATGAAGTAAACCTGCTCATGGGTCGGGCCACCCACCCAGGCCCGAAGGCTTGCCCGAAAATG
* *
2653651 GCATGAAGTAAACCTGCTCATGGGTTGGGCCACCCACCCAGGCCCGAAGGCTTGTCCGAAAATG
1 GCATGAAGTAAACCTGCTCATGGGTCGGGCCACCCACCCAGGCCCGAAGGCTTGCCCGAAAATG
2653715 AAAGGGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.17
Consensus pattern (64 bp):
GCATGAAGTAAACCTGCTCATGGGTCGGGCCACCCACCCAGGCCCGAAGGCTTGCCCGAAAATG
Found at i:2653896 original size:29 final size:29
Alignment explanation
Indices: 2653845--2653907 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2653835 CGACCCAAAT
*
2653845 TTATA-ATGTTAAAAAAATTATTATATTAA
1 TTATATATGTTAAAAAAATAATTATA-TAA
* *
2653874 TTATATATGTT-AAATAATAATTATATAT
1 TTATATATGTTAAAAAAATAATTATATAA
2653902 TTATAT
1 TTATAT
2653908 TTATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 17 0.57
30 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATATGTTAAAAAAATAATTATATAA
Done.