Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 105 of 120
Found at i:30515759 original size:29 final size:28
Alignment explanation
Indices: 30515722--30515802 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
30515712 TAATAATTGA
*
30515722 ATTAGATTTTTAAAATTTTAAAATAGTGGG
1 ATTA-ATTTTTAAAATTTTAAAAT-GTAGG
** *
30515752 ATTAATTTTTAAAAAATAAAAATGTAGG
1 ATTAATTTTTAAAATTTTAAAATGTAGG
**
30515780 ATTAAAATTTAAAATTTTGAAAA
1 ATTAATTTTTAAAATTTT-AAAA
30515803 CTACAAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 17 0.41
29 20 0.49
30 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (28 bp):
ATTAATTTTTAAAATTTTAAAATGTAGG
Found at i:30525797 original size:27 final size:26
Alignment explanation
Indices: 30525757--30525808 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
30525747 TGTCAAAATC
* * *
30525757 TTTTCCTTATTTTAACTATAAATTTCT
1 TTTTCATTACTTTAAC-ACAAATTTCT
30525784 TTTTCATTACTTTAACACAAATTTC
1 TTTTCATTACTTTAACACAAATTTC
30525809 AGAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTCATTACTTTAACACAAATTTCT
Found at i:30528279 original size:21 final size:21
Alignment explanation
Indices: 30528230--30528281 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
30528220 GGGAGCCAAG
**
30528230 CTTGAGTAT-CCTAATTCCTGG
1 CTTGAGT-TGCCTAATTCCTAA
*
30528251 CTTAAGTTGCCTAATTCCTAA
1 CTTGAGTTGCCTAATTCCTAA
30528272 CTTGAGTTGC
1 CTTGAGTTGC
30528282 TCGTGAACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
CTTGAGTTGCCTAATTCCTAA
Found at i:30536155 original size:2 final size:2
Alignment explanation
Indices: 30536148--30536176 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30536138 ATGTATCAGC
30536148 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 T
30536177 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30542572 original size:13 final size:14
Alignment explanation
Indices: 30542554--30542601 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
30542544 TTGTATTATG
30542554 TTTAATTTTTAGA-
1 TTTAATTTTTAGAT
*
30542567 TTTAATTTTTATAT
1 TTTAATTTTTAGAT
30542581 TTTAATTTAATTA-AT
1 TTTAATTT--TTAGAT
30542596 TTTAAT
1 TTTAAT
30542602 CATTATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 12 0.39
14 8 0.26
15 8 0.26
16 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTAATTTTTAGAT
Found at i:30542597 original size:23 final size:23
Alignment explanation
Indices: 30542568--30542623 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
30542558 ATTTTTAGAT
* *
30542568 TTAATTTTTAT-ATTTTAATTTAA
1 TTAATTTTAATCATTATAA-TTAA
*
30542591 TTAATTTTAATCATTATAATTAT
1 TTAATTTTAATCATTATAATTAA
30542614 TTAATTTTAA
1 TTAATTTTAA
30542624 ATTTTCAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATTTTAATCATTATAATTAA
Found at i:30545019 original size:21 final size:20
Alignment explanation
Indices: 30544995--30545041 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
30544985 GATTCTCACT
*
30544995 TTATATAATTTATATTTTAAA
1 TTATATAATTT-TACTTTAAA
*
30545016 TTATTCTAATTTTACTTTAAA
1 TTA-TATAATTTTACTTTAAA
30545037 -TATAT
1 TTATAT
30545042 TTTCATCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.09
20 2 0.09
21 11 0.50
22 7 0.32
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATAATTTTACTTTAAA
Found at i:30545026 original size:22 final size:22
Alignment explanation
Indices: 30545000--30545042 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30544990 TCACTTTATA
*
30545000 TAATTTATATTTTAAAT-TATTC
1 TAATTT-TACTTTAAATATATTC
30545022 TAATTTTACTTTAAATATATT
1 TAATTTTACTTTAAATATATT
30545043 TTCATCAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTTTACTTTAAATATATTC
Found at i:30545639 original size:28 final size:26
Alignment explanation
Indices: 30545608--30545674 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
30545598 GTAATGAATT
30545608 TATTTATCAACTTTCAATAAAATAAAAA
1 TATTTATCAA-TTT-AATAAAATAAAAA
* * *
30545636 TATTTTTTAATTTTATAAAATAAAAA
1 TATTTATCAATTTAATAAAATAAAAA
* *
30545662 TATTAATCTATTT
1 TATTTATCAATTT
30545675 TATATATGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 21 0.66
27 3 0.09
28 8 0.25
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTTATCAATTTAATAAAATAAAAA
Found at i:30545674 original size:26 final size:26
Alignment explanation
Indices: 30545624--30545678 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
30545614 TCAACTTTCA
* *
30545624 ATAAAATAAAAATATTTTTTAATTTT
1 ATAAAATAAAAATATTATCTAATTTT
30545650 ATAAAATAAAAATATTAATCT-ATTTT
1 ATAAAATAAAAATATT-ATCTAATTTT
30545676 ATA
1 ATA
30545679 TATGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAAAATAAAAATATTATCTAATTTT
Found at i:30549902 original size:15 final size:15
Alignment explanation
Indices: 30549865--30549914 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30549855 ATGGATGTGC
*
30549865 TTCTTCTTCTTCTTT
1 TTCTTTTTCTTCTTT
*
30549880 TTCATTTTCTT-TTT
1 TTCTTTTTCTTCTTT
*
30549894 GTTCTTTTTGTTCTTT
1 -TTCTTTTTCTTCTTT
30549910 TTCTT
1 TTCTT
30549915 CCACCACCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (15 bp):
TTCTTTTTCTTCTTT
Found at i:30549910 original size:8 final size:9
Alignment explanation
Indices: 30549886--30549911 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30549876 CTTTTTCATT
30549886 TTCTTTTTG
1 TTCTTTTTG
30549895 TTCTTTTTG
1 TTCTTTTTG
30549904 TTCTTTTT
1 TTCTTTTT
30549912 CTTCCACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.81
Consensus pattern (9 bp):
TTCTTTTTG
Found at i:30554906 original size:15 final size:17
Alignment explanation
Indices: 30554885--30554925 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
30554875 TAATCTTTTA
30554885 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
30554901 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
30554917 AAAATTATA
1 AAAATTATA
30554926 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:30556779 original size:18 final size:17
Alignment explanation
Indices: 30556756--30556790 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30556746 CATATAATTT
30556756 AAAATTAAAAAGAAAATA
1 AAAATTAAAAA-AAAATA
*
30556774 AAAATTCAAAAAAAATA
1 AAAATTAAAAAAAAATA
30556791 GCATGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATTAAAAAAAAATA
Found at i:30561474 original size:57 final size:57
Alignment explanation
Indices: 30561391--30561501 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
30561381 CAACTATTGA
* *
30561391 TAATTTTTTTTTATCACTCAACTATGAAA-AGTTACAAAATGATCACTCAACTATCAG
1 TAATTTTTTTTGATCACCCAACTATGAAACA-TTACAAAATGATCACTCAACTATCAG
* * *
30561448 TAATTTTTTTTGGTCACCCAATTATGAAACATTACAAAATGGTCACTCAACTAT
1 TAATTTTTTTTGATCACCCAACTATGAAACATTACAAAATGATCACTCAACTAT
30561502 TCAATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (57 bp):
TAATTTTTTTTGATCACCCAACTATGAAACATTACAAAATGATCACTCAACTATCAG
Found at i:30562044 original size:25 final size:25
Alignment explanation
Indices: 30562010--30562064 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
30562000 TGGGAAAATA
30562010 ATTTTGTGAT-GAATAAAAATAAGAT
1 ATTTTGTGATAG-ATAAAAATAAGAT
* * *
30562035 ATTTTTTGATAGTTAAAAATGAGAT
1 ATTTTGTGATAGATAAAAATAAGAT
30562060 ATTTT
1 ATTTT
30562065 AGCTTAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (25 bp):
ATTTTGTGATAGATAAAAATAAGAT
Found at i:30566833 original size:25 final size:27
Alignment explanation
Indices: 30566785--30566834 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
30566775 AAATTAATAA
*
30566785 AATATTAATATAAAATATATTATTTTC
1 AATATTAATATAAAATACATTATTTTC
*
30566812 AATATTAATA-AAAGTACA-TATTT
1 AATATTAATATAAAATACATTATTT
30566835 AGTTATCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 6 0.29
27 10 0.48
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (27 bp):
AATATTAATATAAAATACATTATTTTC
Found at i:30566977 original size:15 final size:15
Alignment explanation
Indices: 30566957--30567016 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
30566947 AACATTCAAT
30566957 ATAAATATTTTAATA
1 ATAAATATTTTAATA
*
30566972 ATAAATATTGATTACAATT
1 ATAAATATT--TT--AATA
*
30566991 ATAAATATATTAATA
1 ATAAATATTTTAATA
*
30567006 ATAAATGTTTT
1 ATAAATATTTT
30567017 GTAGTATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 21 0.58
17 4 0.11
19 11 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAAATATTTTAATA
Found at i:30568076 original size:3 final size:3
Alignment explanation
Indices: 30568068--30568123 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
30568058 TATAGAGACA
30568068 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30568116 TAT TAT TA
1 TAT TAT TA
30568124 AGTAGTACCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:30568637 original size:2 final size:2
Alignment explanation
Indices: 30568630--30568667 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30568620 TTAATCCTCA
30568630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30568668 TTATCAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30568863 original size:15 final size:16
Alignment explanation
Indices: 30568843--30568872 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30568833 TACTCTTTAT
30568843 ATTTTTTAA-ATTTTG
1 ATTTTTTAATATTTTG
30568858 ATTTTTTAATATTTT
1 ATTTTTTAATATTTT
30568873 TATAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
ATTTTTTAATATTTTG
Found at i:30569556 original size:21 final size:23
Alignment explanation
Indices: 30569506--30569557 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
30569496 GTCATCTATG
30569506 CCAATTTTTAATAGTAAAAATAGA
1 CCAATTTTTAATAG-AAAAATAGA
**
30569530 TTAATTTTTAATA-AAAAA-AGA
1 CCAATTTTTAATAGAAAAATAGA
30569551 CCAATTT
1 CCAATTT
30569558 ACTCTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
24 11 0.46
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (23 bp):
CCAATTTTTAATAGAAAAATAGA
Found at i:30577638 original size:31 final size:31
Alignment explanation
Indices: 30577600--30577738 Score: 126
Period size: 31 Copynumber: 4.5 Consensus size: 31
30577590 ATAATATAAT
*
30577600 ATTTGGTACTTGAACTTGACAC-TTTTTCTTA
1 ATTTGGTACTTAAACTTGACACTTTTTTC-TA
* *
30577631 ATTTGGTACTTAAACTT---ATTTTTTGTCCA
1 ATTTGGTACTTAAACTTGACACTTTTT-TCTA
* * * *
30577660 ATTTGTTACTCAAACTTGATAATTTTTTCTA
1 ATTTGGTACTTAAACTTGACACTTTTTTCTA
* *
30577691 ATTTGGTACCTAAACTTGACACTTTTTT-TT
1 ATTTGGTACTTAAACTTGACACTTTTTTCTA
*
30577721 ATGTTGATACTTAAACTT
1 AT-TTGGTACTTAAACTT
30577739 TTTGGGGTTC
Statistics
Matches: 87, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.01
29 20 0.23
30 5 0.06
31 55 0.63
32 6 0.07
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTTTTTCTA
Found at i:30577790 original size:90 final size:91
Alignment explanation
Indices: 30577600--30577793 Score: 225
Period size: 90 Copynumber: 2.1 Consensus size: 91
30577590 ATAATATAAT
* * * ***
30577600 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTATTTTTTGTCCAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGATACTTAAACTTATTTGGGGTCCAATTTG
* *
30577665 TTACTCAAACTTGATAATTTTTTCTA
66 GTACTCAAACTTGATAATTTTTCCTA
* *
30577691 ATTTGGTACCTAAACTTGACACTTTTT-TTTATGTTGATACTTAAACTT-TTTGGGGTTCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAT-TTGATACTTAAACTTATTTGGGGTCCAATTT
* *
30577754 GGTAC-CTGAACTTGACT-CTTTTTCCTA
65 GGTACTC-AAACTTGA-TAATTTTTCCTA
30577781 ATTTGGTACCTAA
1 ATTTGGTACCTAA
30577794 TCTTTTTAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
89 1 0.01
90 47 0.53
91 40 0.45
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGATACTTAAACTTATTTGGGGTCCAATTTG
GTACTCAAACTTGATAATTTTTCCTA
Found at i:30578064 original size:31 final size:30
Alignment explanation
Indices: 30578023--30578128 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 30
30578013 GGGTCCAAAA
* *
30578023 AAGTTCAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTA-GAAAAAATGTC
* * **
30578054 AAGTTAAGGTACTAAATTGAGTCAAAA----
1 AAGTTTAGGTACCAAATT-AGAAAAAATGTC
30578081 AAGTTTAGGTACCAAATTAGAAAAAAATGTC
1 AAGTTTAGGTACCAAATTAG-AAAAAATGTC
*
30578112 AAGTTTAGGTATCAAAT
1 AAGTTTAGGTACCAAAT
30578129 ATTATATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
26 2 0.03
27 20 0.34
31 36 0.61
32 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (30 bp):
AAGTTTAGGTACCAAATTAGAAAAAATGTC
Found at i:30578091 original size:58 final size:59
Alignment explanation
Indices: 30577959--30578128 Score: 225
Period size: 58 Copynumber: 2.9 Consensus size: 59
30577949 ATGAATCTTA
* * * * *
30577959 AAAAAAGCTTAGGTACCAAACTAGGAAAAAAATGTCAAGTTCATGTACCAAATTGGGTCC
1 AAAAAAGTTTAGGTACCAAATTAGG-AAAAAATGTCAAGTTAAGGTACCAAATTGAGTCC
* * *
30578019 AAAAAAGTTCAGGTACCAAATTAGGAAAAAGTGTCAAGTTAAGGTACTAAATTGAGT-C
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTAAGGTACCAAATTGAGTCC
* * *
30578077 AAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTTAGGTATCAAAT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTAAGGTACCAAAT
30578129 ATTATATTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 47 0.49
59 27 0.28
60 22 0.23
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTAAGGTACCAAATTGAGTCC
Found at i:30578107 original size:27 final size:27
Alignment explanation
Indices: 30578019--30578107 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 27
30578009 AATTGGGTCC
*
30578019 AAAAAAGTTCAGGTACCAAATTAGGAAA
1 AAAAAAGTTAAGGTACCAAATTA-GAAA
** * **
30578047 AAGTGTCAAGTTAAGGTACTAAATT-GAGTC
1 AA---AAAAGTTAAGGTACCAAATTAGA-AA
*
30578077 AAAAAAGTTTAGGTACCAAATTAGAAA
1 AAAAAAGTTAAGGTACCAAATTAGAAA
30578104 AAAA
1 AAAA
30578108 TGTCAAGTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 11
0.66 0.18 0.16
Matches are distributed among these distances:
27 20 0.45
28 4 0.09
29 2 0.05
30 2 0.05
31 16 0.36
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (27 bp):
AAAAAAGTTAAGGTACCAAATTAGAAA
Found at i:30580620 original size:20 final size:21
Alignment explanation
Indices: 30580591--30580636 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
30580581 AAAAATATGT
30580591 AAAA-TATAAAACAT-TAT-TA
1 AAAATTATAAAA-ATATATATA
30580610 AAAATTATAAAAATATATATA
1 AAAATTATAAAAATATATATA
30580631 AAAATT
1 AAAATT
30580637 TCAAGCGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTATAAAAATATATATA
Found at i:30582246 original size:19 final size:19
Alignment explanation
Indices: 30582198--30582248 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
30582188 TATACTTTAA
30582198 TTAATTGTTTTA-AACATT
1 TTAATTGTTTTATAACATT
**
30582216 TATAA-TACTTTATAACATT
1 T-TAATTGTTTTATAACATT
30582235 TTAATTGTTTTATA
1 TTAATTGTTTTATA
30582249 TATTCTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (19 bp):
TTAATTGTTTTATAACATT
Found at i:30583810 original size:19 final size:20
Alignment explanation
Indices: 30583774--30583812 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30583764 TAATTGCACC
*
30583774 ATTTTTTAAAGGATTAAACT
1 ATTTTTTAAAGGAATAAACT
*
30583794 ATTTTTTAAA-TAATAAACT
1 ATTTTTTAAAGGAATAAACT
30583813 GTAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTTTTAAAGGAATAAACT
Found at i:30590957 original size:30 final size:32
Alignment explanation
Indices: 30590901--30590959 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
30590891 TTGAGTTGGA
* *
30590901 TTATTTTTATGAATTCAGTTATTTGAGTTATT
1 TTATATTTATGAATTCAGTTAGTTGAGTTATT
30590933 TTATATTTA-GAATT-AGTTAGTTGAGTT
1 TTATATTTATGAATTCAGTTAGTTGAGTT
30590960 GAGTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
31 5 0.20
32 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (32 bp):
TTATATTTATGAATTCAGTTAGTTGAGTTATT
Found at i:30591477 original size:13 final size:13
Alignment explanation
Indices: 30591459--30591484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30591449 ATAAAAATAT
30591459 ACCATTTAATTTC
1 ACCATTTAATTTC
30591472 ACCATTTAATTTC
1 ACCATTTAATTTC
30591485 CGCCTTCCTA
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ACCATTTAATTTC
Found at i:30596839 original size:140 final size:141
Alignment explanation
Indices: 30596547--30596989 Score: 732
Period size: 140 Copynumber: 3.1 Consensus size: 141
30596537 TTCATTCAAC
30596547 AAATAAAAATTTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTTTACGTTACGACA
1 AAATAAAAA-TTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAA--TTA----ACGACA
*
30596612 AATATTTGTATTTTTTTAATAAGTTTTTAAATTTAATTTATTTTGTTTTTACTTTT-AAAATTTG
59 AATATTTGTATTTTTTT-ATAAG-TTTTAAATTTAATTTA-TTTATTTTTACTTTTAAAAATTTG
30596676 ATCTTTTATTTTTTTGAATTAA
121 ATCTTTTA-TTTTTTGAATTAA
30596698 AAATAAAAATTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTAACGACAAATATTT
1 AAATAAAAATTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTAACGACAAATATTT
30596763 GTATTTTTTTATAAGTTTTAAATTTAATTTATTT-TTTTTACTTTTAAAAATTTGATCTTTTATT
66 GTATTTTTTTATAAGTTTTAAATTTAATTTATTTATTTTTACTTTTAAAAATTTGATCTTTTATT
30596827 TTTTGAATTAA
131 TTTTGAATTAA
*
30596838 AAATAAAAATTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTTACGACAAATATTT
1 AAATAAAAATTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTAACGACAAATATTT
30596903 GTA-TTTTTTATAAGTTTTAAATTTAATTTATTTATTTTTACTTTTAAAAATTTGATC-TTTATT
66 GTATTTTTTTATAAGTTTTAAATTTAATTTATTTATTTTTACTTTTAAAAATTTGATCTTTTATT
30596966 TTTTGAATTAAA
131 TTTTGAATT-AA
30596978 AAATAAAAATTT
1 AAATAAAAATTT
30596990 AATTGTTAAT
Statistics
Matches: 288, Mismatches: 1, Indels: 17
0.94 0.00 0.06
Matches are distributed among these distances:
139 45 0.16
140 128 0.44
141 19 0.07
142 16 0.06
143 5 0.02
144 23 0.08
148 3 0.01
150 40 0.14
151 9 0.03
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (141 bp):
AAATAAAAATTTTCATTACTAATTGTTATAATTCTTTTAAGATTGTAAATTAACGACAAATATTT
GTATTTTTTTATAAGTTTTAAATTTAATTTATTTATTTTTACTTTTAAAAATTTGATCTTTTATT
TTTTGAATTAA
Found at i:30597848 original size:1 final size:1
Alignment explanation
Indices: 30597842--30597873 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
30597832 GACATAGTGT
30597842 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
30597874 CGGGAAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:30599670 original size:58 final size:60
Alignment explanation
Indices: 30599596--30599727 Score: 171
Period size: 58 Copynumber: 2.2 Consensus size: 60
30599586 TTAATATAAC
* *
30599596 ATTTGGTACCTAAACTTGACATTTTT-TCTTAATTTTGTACCTAA-ATTTTTTT-GACCCA
1 ATTTGGTACCTAAACTTGACATTTTTCTC-TAATTTGGCACCTAAGATTTTTTTAGACCCA
* * * **
30599654 ATTTGGTACCTGAACTTGATATTTTTCTCTAATTTGGCACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACCTAAACTTGACATTTTTCTCTAATTTGGCACCTAAGATTTTTTTAGACCCA
30599714 ATTTGGTACCTAAA
1 ATTTGGTACCTAAA
30599728 TGTATTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 37 0.59
59 9 0.14
60 17 0.27
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTCTCTAATTTGGCACCTAAGATTTTTTTAGACCCA
Found at i:30599689 original size:31 final size:30
Alignment explanation
Indices: 30599596--30599697 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 30
30599586 TTAATATAAC
*
30599596 ATTTGGTACCTAAACTTGACATTTTT-TCTTA
1 ATTTGGTACCT-AACTTGATATTTTTCTC-TA
* * * *
30599627 ATTTTGTACCTAAATT--T-TTTTGAC-CCA
1 ATTTGGTACCTAACTTGATATTTT-TCTCTA
30599654 ATTTGGTACCTGAACTTGATATTTTTCTCTA
1 ATTTGGTACCT-AACTTGATATTTTTCTCTA
*
30599685 ATTTGGCACCTAA
1 ATTTGGTACCTAA
30599698 GCTTTTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
27 15 0.28
28 5 0.09
30 8 0.15
31 26 0.48
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCTAACTTGATATTTTTCTCTA
Found at i:30599931 original size:59 final size:60
Alignment explanation
Indices: 30599866--30599978 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 60
30599856 ATTAATATTA
* * * * *
30599866 AAAAAAGATTAGGTACCAA-ATTAGGAAAAAGAG-TCAAGTTTTGGTACCAAATTGCACTC
1 AAAAAAGATTAAGTACCAACATTA-AAAAAAAAGTTCAAGTTTAGATACCAAATTGCACTC
* *
30599925 AAAAAAGTTTAAGTACCAACTTTAAAAAAAAAGTTCAAGTTTAGATACCAAATT
1 AAAAAAGATTAAGTACCAACATTAAAAAAAAAGTTCAAGTTTAGATACCAAATT
30599979 AGAAAAATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 24 0.53
60 21 0.47
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (60 bp):
AAAAAAGATTAAGTACCAACATTAAAAAAAAAGTTCAAGTTTAGATACCAAATTGCACTC
Found at i:30600043 original size:91 final size:91
Alignment explanation
Indices: 30599874--30600043 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 91
30599864 TAAAAAAAGA
* * **
30599874 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTTTGGTACCAAATTGCACTCAAAAAAGTTTAAGT
1 TTAGATACCAAATTAGGAAAAAGAGTCAAGTTTTGGTACCAAATTGCAATCAAAAAAAATTAAGT
* *
30599939 ACCAACTTTAAAAAAAAAGTTCAAGT
66 ACCAAATTAAAAAAAAAAGTTCAAGT
* *
30599965 TTAGATACCAAATTA-GAAAAATGTGTCAAGTTTAT-GTATCAAATTG-AAT-AAAAAAAATTAA
1 TTAGATACCAAATTAGGAAAAA-GAGTCAAGTTT-TGGTACCAAATTGCAATCAAAAAAAATTAA
*
30600026 GTACCAAATTAGAAAAAA
64 GTACCAAATTAAAAAAAA
30600044 TATCAAATTC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
89 25 0.37
90 8 0.12
91 34 0.50
92 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (91 bp):
TTAGATACCAAATTAGGAAAAAGAGTCAAGTTTTGGTACCAAATTGCAATCAAAAAAAATTAAGT
ACCAAATTAAAAAAAAAAGTTCAAGT
Found at i:30601466 original size:30 final size:31
Alignment explanation
Indices: 30601401--30601485 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
30601391 TTAAAAAACG
* * *
30601401 ATTTAAAAAGAGTTGAA-TTGACCCTTAACT
1 ATTTAAAAAAAGTTGAATTTGATCATTAACT
30601431 ATTTAAAAAAAGTTGAATTTGATCATTAAC-
1 ATTTAAAAAAAGTTGAATTTGATCATTAACT
* *
30601461 CTTTAAAAAATAATTGAATTGTGAT
1 ATTTAAAAAA-AGTTGAATT-TGAT
30601486 TTATTTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 25 0.53
31 18 0.38
32 4 0.09
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
ATTTAAAAAAAGTTGAATTTGATCATTAACT
Found at i:30601779 original size:19 final size:21
Alignment explanation
Indices: 30601755--30601797 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
30601745 GAAGGCTAAA
30601755 TTTATCAT-TATACTTTT-AT
1 TTTATCATATATACTTTTAAT
*
30601774 TTTATCATATATATTTTTAAT
1 TTTATCATATATACTTTTAAT
30601795 TTT
1 TTT
30601798 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTATCATATATACTTTTAAT
Found at i:30603323 original size:12 final size:12
Alignment explanation
Indices: 30603306--30603336 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
30603296 AAAAACTACT
30603306 CCACAAGTGACA
1 CCACAAGTGACA
30603318 CCACAAGTGACA
1 CCACAAGTGACA
30603330 CCACAAG
1 CCACAAG
30603337 CAGCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.35, G:0.16, T:0.06
Consensus pattern (12 bp):
CCACAAGTGACA
Found at i:30607098 original size:6 final size:6
Alignment explanation
Indices: 30607080--30607173 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
30607070 TTAAATTGAT
* *
30607080 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAACA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
30607127 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA
30607174 CATTAAGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 47 0.65
7 9 0.12
8 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:30607127 original size:31 final size:31
Alignment explanation
Indices: 30607089--30607149 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
30607079 TTTTAAATTT
*
30607089 ATTTAAATTTAGATTT-ATTTTAAATTTAAAC
1 ATTTAAATTTA-ATTTGAATTTAAATTTAAAC
30607120 ATTTAAATTTAATTTGAATTTAAATTTAAA
1 ATTTAAATTTAATTTGAATTTAAATTTAAA
30607150 TAAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAAATTTAATTTGAATTTAAATTTAAAC
Found at i:30607134 original size:11 final size:11
Alignment explanation
Indices: 30607070--30607148 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 11
30607060 AACTTTTGAG
* *
30607070 TTAAATTGATT
1 TTAAATTTAAT
30607081 TTAAATTT-AT
1 TTAAATTTAAT
30607091 TTAAATTTAGAT
1 TTAAATTTA-AT
*
30607103 TT-ATTTTAAAT
1 TTAAATTT-AAT
30607114 TTAAACATTTAAAT
1 TT-AA-ATTT-AAT
30607128 TT-AATTTGAAT
1 TTAAATTT-AAT
30607139 TTAAATTTAA
1 TTAAATTTAA
30607149 ATAAAAATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
10 9 0.16
11 26 0.46
12 11 0.20
13 1 0.02
14 9 0.16
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:30607147 original size:42 final size:41
Alignment explanation
Indices: 30607080--30607173 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
30607070 TTAAATTGAT
* ** * *
30607080 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAACA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
30607121 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
30607162 TATTAAATTTAA
1 T-TTAAATTTAA
30607174 CATTAAGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:30607442 original size:15 final size:15
Alignment explanation
Indices: 30607422--30607452 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30607412 GCCTATGCTG
30607422 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
30607437 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
30607452 C
1 C
30607453 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:30607919 original size:9 final size:10
Alignment explanation
Indices: 30607885--30607917 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
30607875 AAAGGAGCAA
30607885 TAAATATGTAT
1 TAAATAT-TAT
30607896 TAAATATT-T
1 TAAATATTAT
30607905 TAAATATTAT
1 TAAATATTAT
30607915 TAA
1 TAA
30607918 TAAATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (10 bp):
TAAATATTAT
Found at i:30608227 original size:19 final size:19
Alignment explanation
Indices: 30608191--30608228 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30608181 ATTAAAATCT
30608191 GTCCTAGATCTGGATTTAA
1 GTCCTAGATCTGGATTTAA
*
30608210 GTCC-AGATCGTGGTTTTAA
1 GTCCTAGATC-TGGATTTAA
30608229 AGAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (19 bp):
GTCCTAGATCTGGATTTAA
Found at i:30608909 original size:161 final size:162
Alignment explanation
Indices: 30608717--30609040 Score: 499
Period size: 161 Copynumber: 2.0 Consensus size: 162
30608707 AATTTTAATT
** **
30608717 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCATGCATTGGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGCATTGGAT
30608782 TATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAAC-TTTAT
66 TATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-
* *
30608845 TTTAATTACAAAATTGGCCCAATAATTTTTCAA
130 TTTAATAACAAAATTGGCCCAAAAATTTTTCAA
***
30608878 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTTTTTGGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGCATTGGAT
* * * *
30608943 TATTTCTGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTAT
66 TATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTAT
*
30609008 TTAATAACAAAATTGGTCCAAAAATTTTTCAA
131 TTAATAACAAAATTGGCCCAAAAATTTTTCAA
30609040 G
1 G
30609041 ATTTTCAAAT
Statistics
Matches: 147, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
161 105 0.71
162 38 0.26
163 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (162 bp):
GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGCATTGGAT
TATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTAT
TTAATAACAAAATTGGCCCAAAAATTTTTCAA
Found at i:30609289 original size:59 final size:58
Alignment explanation
Indices: 30609165--30609479 Score: 409
Period size: 59 Copynumber: 5.4 Consensus size: 58
30609155 CAAAACTTTT
* * ** * *
30609165 CCAAAATTA-TATTTTACCCCCCCAAATCTTTTAAAATTCCATTTTTAACCTCGATTACA
1 CCAAAATTACCATTTTA-CCCCCGAAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCA
30609224 CCAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
30609282 CCAAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCGTTTTTAACCCCGATTTCA
1 CC-AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ***
30609341 CAGAAAATTACCATTTTACCCCCGAAACTTCCAAAATTTTGTTTTTAACCCCGATTTCA
1 C-CAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
** * **
30609400 TCGGAAATTACCATTTTA-CCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 -CCAAAATTACCATTTTACCCCCGAAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
30609459 CCAAAATTACCATTTTGCCCC
1 CCAAAATTACCATTTTACCCC
30609480 GGGTATCCAT
Statistics
Matches: 230, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
58 51 0.22
59 172 0.75
60 7 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:30609464 original size:29 final size:30
Alignment explanation
Indices: 30609197--30609474 Score: 165
Period size: 29 Copynumber: 9.5 Consensus size: 30
30609187 CAAATCTTTT
* *
30609197 AAAATT-CCATTTTTAACCTCGATTACACC
1 AAAATTACCATTTTTAACCCCGATTTCACC
* *
30609226 AAAATTACCA-TTTTACCCCCGAAACTT--CC
1 AAAATTACCATTTTTAACCCCG--ATTTCACC
30609255 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTTAACCCCGATTTCACC
* *
30609284 AAAAATTACCA-TTTTACCCCCGAAACTT--CC
1 -AAAATTACCATTTTTAACCCCG--ATTTCACC
* *
30609314 AAAATT-CCGTTTTTAACCCCGATTTCACAG
1 AAAATTACCATTTTTAACCCCGATTTCAC-C
* *
30609344 AAAATTACCA-TTTTACCCCCGAAACTT--CC
1 AAAATTACCATTTTTAACCCCG--ATTTCACC
*** *
30609373 AAAATT-TTGTTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTTAACCCCGATTTCA-CC
* * ** ***
30609403 GAAATTACCA-TTTT-ACCCCTAAATCTTTT
1 AAAATTACCATTTTTAACCCCGATTTC-ACC
30609432 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTTAACCCCGATTTCACC
30609461 AAAATTACCATTTT
1 AAAATTACCATTTT
30609475 GCCCCGGGTA
Statistics
Matches: 184, Mismatches: 39, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
27 9 0.05
28 8 0.04
29 91 0.49
30 63 0.34
31 7 0.04
32 6 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCCGATTTCACC
Found at i:30610809 original size:31 final size:31
Alignment explanation
Indices: 30610763--30610823 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
30610753 TGTGCATGAT
30610763 TAAATCAAAAATAAAATTTCAAGTATATATC
1 TAAATCAAAAATAAAATTTCAAGTATATATC
* * *
30610794 TAAATCACAATTAAAATTTCATGTATATAT
1 TAAATCAAAAATAAAATTTCAAGTATATAT
30610824 TTACGCCAAA
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:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (31 bp):
TAAATCAAAAATAAAATTTCAAGTATATATC
Found at i:30617624 original size:20 final size:20
Alignment explanation
Indices: 30617599--30617660 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
30617589 ACAAAAAGAT
30617599 TCAAAATAATTTTTAAAAAA
1 TCAAAATAATTTTTAAAAAA
* *
30617619 TCAAAAT-ATTTATAAAAATT
1 TCAAAATAATTTTTAAAAA-A
*
30617639 TCAAAATTTATTTTTTAAAAAA
1 TCAAAA--TAATTTTTAAAAAA
30617661 ATTCTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 10 0.30
20 13 0.39
22 1 0.03
23 9 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAAAA
Found at i:30617634 original size:19 final size:20
Alignment explanation
Indices: 30617599--30617636 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30617589 ACAAAAAGAT
*
30617599 TCAAAATAATTTTTAAAAAA
1 TCAAAATAATTTATAAAAAA
30617619 TCAAAAT-ATTTATAAAAA
1 TCAAAATAATTTATAAAAA
30617637 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAA
Found at i:30617670 original size:11 final size:11
Alignment explanation
Indices: 30617654--30617693 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
30617644 ATTTATTTTT
30617654 TAAAAAAATTC
1 TAAAAAAATTC
*
30617665 T-AAAAATTTC
1 TAAAAAAATTC
*
30617675 AAAAAAAATTC
1 TAAAAAAATTC
30617686 TAAAAAAA
1 TAAAAAAA
30617694 ATATTAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAAAATTC
Found at i:30617670 original size:12 final size:12
Alignment explanation
Indices: 30617655--30617695 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
30617645 TTTATTTTTT
30617655 AAAAAAATTCT-
1 AAAAAAATTCTA
*
30617666 -AAAAATTTC-A
1 AAAAAAATTCTA
30617676 AAAAAAATTCTA
1 AAAAAAATTCTA
30617688 AAAAAAAT
1 AAAAAAAT
30617696 ATTAAGAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.32
11 8 0.32
12 9 0.36
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAAATTCTA
Found at i:30621645 original size:31 final size:29
Alignment explanation
Indices: 30621599--30621671 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
30621589 TAAATCTTAA
* *
30621599 AATTATAT--ATGAATTTTGATTGAATGTGT
1 AATTATATACATGAATTTTAATT-AA-GTGC
* *
30621628 AATTGTATACATGAATTTTAATTTAGTGC
1 AATTATATACATGAATTTTAATTAAGTGC
30621657 AATTATATACATGAA
1 AATTATATACATGAA
30621672 ACTCTAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 24 0.65
30 1 0.03
31 12 0.32
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (29 bp):
AATTATATACATGAATTTTAATTAAGTGC
Found at i:30625395 original size:3 final size:3
Alignment explanation
Indices: 30625387--30625415 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30625377 TGACAAAGTT
30625387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30625416 TAAAAACACA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30629382 original size:31 final size:32
Alignment explanation
Indices: 30629344--30629407 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
30629334 AAACTTTAAA
30629344 TTTAATTAAAATTTA-CAATCAACT-TTAATTT
1 TTTAATTAAAATTTACCAATCAA-TATTAATTT
* *
30629375 TTTAATTAAATTTTACCATTCAATATTAATTT
1 TTTAATTAAAATTTACCAATCAATATTAATTT
30629407 T
1 T
30629408 GATGATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTAATTAAAATTTACCAATCAATATTAATTT
Found at i:30629619 original size:17 final size:17
Alignment explanation
Indices: 30629599--30629638 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
30629589 TTACCATTTT
**
30629599 TATTAATTTTAATATTA
1 TATTAATTAAAATATTA
30629616 TATTAATTAAAATATTA
1 TATTAATTAAAATATTA
*
30629633 TTTTAA
1 TATTAA
30629639 AATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAATTAAAATATTA
Found at i:30629650 original size:15 final size:15
Alignment explanation
Indices: 30629601--30629653 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
30629591 ACCATTTTTA
*
30629601 TTAATTTTAATATTAT
1 TTAATTTTAA-AATAT
30629617 ATTAA--TTAAAATA-
1 -TTAATTTTAAAATAT
30629630 TT-ATTTTAAAATAT
1 TTAATTTTAAAATAT
30629644 TTAATTTTAA
1 TTAATTTTAA
30629654 TGTAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
11 1 0.03
12 2 0.06
13 8 0.26
14 5 0.16
15 11 0.35
17 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTTAAAATAT
Found at i:30636345 original size:10 final size:10
Alignment explanation
Indices: 30636330--30636358 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
30636320 TTATTAATTT
30636330 AAAATTTTAA
1 AAAATTTTAA
30636340 AAAA-TTTAA
1 AAAATTTTAA
30636349 AAAATTTTAA
1 AAAATTTTAA
30636359 GGGAGCCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:30647597 original size:20 final size:18
Alignment explanation
Indices: 30647553--30647603 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
30647543 ATGATTAAAT
* *
30647553 TAATTTTTATTATTTTAC
1 TAATTTTTATAATTTTAA
*
30647571 TATTTTTTATAAACTTTTAA
1 TAATTTTTAT-AA-TTTTAA
30647591 TAATTTTT-TAATT
1 TAATTTTTATAATT
30647604 AAATCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 2 0.07
20 12 0.44
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTTATAATTTTAA
Found at i:30652045 original size:73 final size:71
Alignment explanation
Indices: 30651874--30652070 Score: 229
Period size: 75 Copynumber: 2.7 Consensus size: 71
30651864 TTTACAATAA
* * * *
30651874 AAAAATTTAAAATTAATTATAAAAAAGGAAAAAAATAAGTAACTTAAAAAAAT-CAATTATTTTT
1 AAAAA-TTAAAATTAATTATAAAAAATG-AAAAAAT-AG-AAATTAAAAAGATAAAATTATTTTT
30651938 TCTTTTACTG
62 TCTTTTACTG
30651948 AAAAATACTAAAATTAATTATAAAAAATGAAAAAATAGAAATTAAAAAGATAAAATTGATTTTTT
1 AAAAAT--TAAAATTAATTATAAAAAATGAAAAAATAGAAATTAAAAAGATAAAATT-ATTTTTT
**
30652013 CATTTTTTTG
63 C-TTTTACTG
* *
30652023 AAAAATTAAAATTAATTCTAAAAAAT-AAAAAAT-GAAATTTAAAAGATA
1 AAAAATTAAAATTAATTATAAAAAATGAAAAAATAGAAATTAAAAAGATA
30652071 GAATAAGTAA
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
71 14 0.13
72 18 0.16
73 26 0.24
74 20 0.18
75 32 0.29
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.34
Consensus pattern (71 bp):
AAAAATTAAAATTAATTATAAAAAATGAAAAAATAGAAATTAAAAAGATAAAATTATTTTTTCTT
TTACTG
Found at i:30668912 original size:19 final size:18
Alignment explanation
Indices: 30668888--30668928 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
30668878 TATTTAATAA
30668888 ATAAATTAATTAATTTTAT
1 ATAAATTAATT-ATTTTAT
30668907 ATAAATTAATTATTTTAT
1 ATAAATTAATTATTTTAT
30668925 -TAAA
1 ATAAA
30668929 AATTTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAATTAATTATTTTAT
Found at i:30678905 original size:6 final size:6
Alignment explanation
Indices: 30678894--30678919 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30678884 CACACATTTC
30678894 CTACCT CTACCT CTACCT CTACCT CT
1 CTACCT CTACCT CTACCT CTACCT CT
30678920 TCTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
CTACCT
Found at i:30689766 original size:212 final size:212
Alignment explanation
Indices: 30689399--30689825 Score: 721
Period size: 212 Copynumber: 2.0 Consensus size: 212
30689389 ACTCATAATT
*
30689399 TTAGTAATTTTTCATCTTAAACTCAGAACTTTAAATCTCGAATCTTGAATTTTGACTATAAATTT
1 TTAGTAATTTTTCATCTTAAACTCAGAACTTTAAATCTCGAATCCTGAATTTTGACTATAAATTT
*
30689464 TAAATCTTGAACTTTGAATCCAAAACCTTGAATCCCAAAACTTAAATCTTAAATATTGAATTCTA
66 TAAATCTTGAACTTTGAATCCAAAACCTTGAATCCCAAAACTTAAATCTTAAATATTGAACTCTA
* * *
30689529 AATTTGGGGTTCGAGGTCGGGTTGAACT-AAAAATATTACAAAAATTATGTGTAAATGACATGAA
131 AACTTGGGGTTCGAGGTCGGGTTGAACTAAAAAAAATTAC-AAAATTATGTGTAAATAACATGAA
30689593 ATTTTTTTTGAAATGTTA
195 ATTTTTTTTGAAATGTTA
* *
30689611 TTAGTAATTTTTTATCTTAAACTCAGAACTTTATATCTCGAATCCTGAATTTTGACTATAAATTT
1 TTAGTAATTTTTCATCTTAAACTCAGAACTTTAAATCTCGAATCCTGAATTTTGACTATAAATTT
* *
30689676 TAAATCTTGAACTTTGAATTCAAAACCTTGAATCCCAAAACTTAAATCTTAAATCTTGAACTCTA
66 TAAATCTTGAACTTTGAATCCAAAACCTTGAATCCCAAAACTTAAATCTTAAATATTGAACTCTA
* * * *
30689741 AACTTGGGGTTTGAGGTCGGGTTGAACTAAAAAAAATTACAAATTTATGTGTCAATAACATGGAA
131 AACTTGGGGTTCGAGGTCGGGTTGAACTAAAAAAAATTACAAAATTATGTGTAAATAACATGAAA
30689806 TTTTTTTTGAAATGTTA
196 TTTTTTTTGAAATGTTA
30689823 TTA
1 TTA
30689826 AATAATTGGA
Statistics
Matches: 201, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
212 191 0.95
213 10 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (212 bp):
TTAGTAATTTTTCATCTTAAACTCAGAACTTTAAATCTCGAATCCTGAATTTTGACTATAAATTT
TAAATCTTGAACTTTGAATCCAAAACCTTGAATCCCAAAACTTAAATCTTAAATATTGAACTCTA
AACTTGGGGTTCGAGGTCGGGTTGAACTAAAAAAAATTACAAAATTATGTGTAAATAACATGAAA
TTTTTTTTGAAATGTTA
Found at i:30693539 original size:4 final size:4
Alignment explanation
Indices: 30693530--30693571 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
30693520 AAATTTTAAT
30693530 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
30693572 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:30698265 original size:18 final size:19
Alignment explanation
Indices: 30698242--30698280 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
30698232 AGGTTGAAAA
30698242 TATTAAGAAAAT-TT-TATT
1 TATTAA-AAAATATTATATT
30698260 TATTAAAAAATATTATATT
1 TATTAAAAAATATTATATT
30698279 TA
1 TA
30698281 GAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTAAAAAATATTATATT
Found at i:30698275 original size:17 final size:18
Alignment explanation
Indices: 30698242--30698275 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30698232 AGGTTGAAAA
*
30698242 TATTAAGAAAATTTTATT
1 TATTAAGAAAATATTATT
30698260 TATTAA-AAAATATTAT
1 TATTAAGAAAATATTAT
30698276 ATTTAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATTAAGAAAATATTATT
Found at i:30698308 original size:16 final size:17
Alignment explanation
Indices: 30698250--30698310 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
30698240 AATATTAAGA
30698250 AAAT-TTTATTTATTAAA-
1 AAATATTTATTTA--AAAT
*
30698267 AAATATTATATTTAGAAT
1 AAATATT-TATTTAAAAT
30698285 AAATTATTT-TTTAAAAT
1 AAA-TATTTATTTAAAAT
30698302 AAATATTTA
1 AAATATTTA
30698311 AGTTATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.14
17 16 0.43
18 6 0.16
19 10 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATTTATTTAAAAT
Found at i:30698376 original size:12 final size:12
Alignment explanation
Indices: 30698357--30698386 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30698347 ATATTATATC
30698357 AATAAAATTAAA
1 AATAAAATTAAA
*
30698369 ATTAAAATTAAA
1 AATAAAATTAAA
30698381 AATAAA
1 AATAAA
30698387 TAATTTAAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAAATTAAA
Found at i:30698493 original size:15 final size:15
Alignment explanation
Indices: 30698473--30698519 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
30698463 AATTTTTTAA
30698473 TATAAATTCAATATT
1 TATAAATTCAATATT
*
30698488 TATAAAATTTAATA-T
1 TAT-AAATTCAATATT
* *
30698503 TAAAAATTCAACATT
1 TATAAATTCAATATT
30698518 TA
1 TA
30698520 ATTGAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 9 0.35
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAATTCAATATT
Found at i:30698510 original size:14 final size:16
Alignment explanation
Indices: 30698476--30698519 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
30698466 TTTTTAATAT
30698476 AAATTCAATATTTATA
1 AAATTCAATATTTATA
*
30698492 AAATTTAATA-TTA-A
1 AAATTCAATATTTATA
*
30698506 AAATTCAACATTTA
1 AAATTCAATATTTA
30698520 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTCAATATTTATA
Found at i:30699503 original size:13 final size:13
Alignment explanation
Indices: 30699485--30699516 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30699475 TCTGTTTGGG
*
30699485 ATTAATTTTTTTA
1 ATTAATTTTTCTA
30699498 ATTAATTTTTCTA
1 ATTAATTTTTCTA
30699511 ATTAAT
1 ATTAAT
30699517 GATTTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTAATTTTTCTA
Found at i:30714220 original size:27 final size:27
Alignment explanation
Indices: 30714190--30714245 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
30714180 AATACTGAAG
30714190 TTAGGTGTTGAACTTGATGTTGTAACT
1 TTAGGTGTTGAACTTGATGTTGTAACT
30714217 TTAGGTGTTGAACTTGATGTTGTAACT
1 TTAGGTGTTGAACTTGATGTTGTAACT
30714244 TT
1 TT
30714246 GATTCAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (27 bp):
TTAGGTGTTGAACTTGATGTTGTAACT
Found at i:30714248 original size:14 final size:12
Alignment explanation
Indices: 30714195--30714244 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
30714185 TGAAGTTAGG
30714195 TGTTGAACTTGA
1 TGTTGAACTTGA
*
30714207 TGTTGTAACTTTAGG
1 TGTTG-AAC-TT-GA
30714222 TGTTGAACTTGA
1 TGTTGAACTTGA
30714234 TGTTGTAACTT
1 TGTTG-AACTT
30714245 TGATTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 11 0.34
13 10 0.31
14 5 0.16
15 6 0.19
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (12 bp):
TGTTGAACTTGA
Found at i:30714315 original size:15 final size:15
Alignment explanation
Indices: 30714295--30714336 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
30714285 TTTGCCTGGA
30714295 AAACTCTTTAATGGG
1 AAACTCTTTAATGGG
30714310 AAACTCTTTAATGGG
1 AAACTCTTTAATGGG
30714325 AAACTCTTTAAT
1 AAACTCTTTAAT
30714337 AATACCAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (15 bp):
AAACTCTTTAATGGG
Found at i:30717231 original size:58 final size:58
Alignment explanation
Indices: 30717066--30717236 Score: 229
Period size: 58 Copynumber: 2.9 Consensus size: 58
30717056 TCTAATATTA
* *
30717066 TATATCATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAAT
1 TATAT-ATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAAT
* *
30717127 TATATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
* * *
30717184 TATTTATTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
30717237 AACAATAATC
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 22 0.22
58 56 0.57
59 9 0.09
60 7 0.07
61 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:30717379 original size:49 final size:51
Alignment explanation
Indices: 30717318--30717416 Score: 143
Period size: 49 Copynumber: 2.0 Consensus size: 51
30717308 ATTACAGCAT
30717318 CATTCCATTCAACCAAACATA-AGAA-TACT-ATTACAG-CTCTATTCCATTC
1 CATTCCATTCAACCAAACA-ACAGAATTACTAATTACAGTC-CTATTCCATTC
*
30717367 CATTCCATTCAACCAAACAACTGAATTACTAATTACAGTCCTATTCCATT
1 CATTCCATTCAACCAAACAACAGAATTACTAATTACAGTCCTATTCCATT
30717417 ACAGCGAACC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
48 1 0.02
49 22 0.49
50 4 0.09
51 17 0.38
52 1 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (51 bp):
CATTCCATTCAACCAAACAACAGAATTACTAATTACAGTCCTATTCCATTC
Found at i:30719720 original size:24 final size:22
Alignment explanation
Indices: 30719685--30719728 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
30719675 ATATAATATT
30719685 AAAAATTTAAAACTAAATTATC
1 AAAAATTTAAAACTAAATTATC
*
30719707 AAAAACTTCTAAAAGTAAATTA
1 AAAAA-TT-TAAAACTAAATTA
30719729 ACTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATTTAAAACTAAATTATC
Found at i:30724252 original size:21 final size:21
Alignment explanation
Indices: 30724204--30724256 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
30724194 TTAAAGGAAA
*
30724204 ATCTTATTTTTTCTTCTCTTTC
1 ATCTT-TTTTTTCTTCTCTCTC
30724226 AT-TTTTTCTTTCTTCTCTCTC
1 ATCTTTTT-TTTCTTCTCTCTC
30724247 -TCTTTTTTTT
1 ATCTTTTTTTT
30724257 AGATTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.25
21 19 0.68
22 2 0.07
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
ATCTTTTTTTTCTTCTCTCTC
Found at i:30726153 original size:11 final size:10
Alignment explanation
Indices: 30726127--30726152 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30726117 ATAAAATATT
30726127 AAAAAATTCA
1 AAAAAATTCA
30726137 AAAAAATTCA
1 AAAAAATTCA
30726147 AAAAAA
1 AAAAAA
30726153 AAAATCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:30727604 original size:28 final size:27
Alignment explanation
Indices: 30727554--30727665 Score: 107
Period size: 28 Copynumber: 3.8 Consensus size: 27
30727544 TCCAGCATAA
*
30727554 TTGAGTCATCATATATTGGTGATTGTGATT
1 TTGA-TCA-CATATA-TGTTGATTGTGATT
30727584 TTGATCACATATATGCTTGATTGTGATT
1 TTGATCACATATATG-TTGATTGTGATT
*
30727612 TTGATCACATATATTGGTGATGGTGATTGATT
1 TTGATCACATATA-TGTTGAT--TG--TGATT
*
30727644 TTGATTACATATATGTTTGATT
1 TTGATCACATATATG-TTGATT
30727666 TTGGTCACAT
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.03
28 34 0.48
29 5 0.07
30 7 0.10
31 2 0.03
32 21 0.30
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (27 bp):
TTGATCACATATATGTTGATTGTGATT
Found at i:30727664 original size:60 final size:58
Alignment explanation
Indices: 30727554--30727665 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 58
30727544 TCCAGCATAA
30727554 TTGAGTCATCATATATTGGTGATTGTGATTTTGATCACATATATGCTTGATTGTGATT
1 TTGAGTCATCATATATTGGTGATTGTGATTTTGATCACATATATGCTTGATTGTGATT
* *
30727612 TTGA-TCA-CATATATTGGTGATGGTGATTGATTTTGATTACATATATGTTTGATT
1 TTGAGTCATCATATATTGGTGAT--TG--TGATTTTGATCACATATATGCTTGATT
30727666 TTGGTCACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
56 14 0.29
57 3 0.06
58 6 0.12
60 25 0.52
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (58 bp):
TTGAGTCATCATATATTGGTGATTGTGATTTTGATCACATATATGCTTGATTGTGATT
Found at i:30731185 original size:29 final size:29
Alignment explanation
Indices: 30731129--30731318 Score: 111
Period size: 29 Copynumber: 6.5 Consensus size: 29
30731119 GCTCGAGGTT
* * *
30731129 AAAACGGTAATTTTGA-ACACTTCAAGGGC
1 AAAATGGTAATTTTTAGACA-TTCGAGGGC
* *
30731158 AAAATGGTAATTTTTAGACATCCGAGGGT
1 AAAATGGTAATTTTTAGACATTCGAGGGC
* * ** *
30731187 GAAATGGTGATTTTTGAGATTTTTG-GGGTC
1 AAAATGGTAATTTTT-AGACATTCGAGGG-C
* * *
30731217 AAAAATGG-AATTTTTTGATATTCGAGGGT
1 -AAAATGGTAATTTTTAGACATTCGAGGGC
* * * *
30731246 AAAATGGTAATTTTTAAAAATTTTGA-GTC
1 AAAATGGTAATTTTTAGACA-TTCGAGGGC
* *
30731275 AAAAATAG-AATTTTTAGACATTCGAGGGT
1 -AAAATGGTAATTTTTAGACATTCGAGGGC
*
30731304 AAAATAGTAATTTTT
1 AAAATGGTAATTTTT
30731319 TGAAGGTTTG
Statistics
Matches: 121, Mismatches: 30, Indels: 20
0.71 0.18 0.12
Matches are distributed among these distances:
28 18 0.15
29 70 0.58
30 27 0.22
31 6 0.05
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACATTCGAGGGC
Found at i:30731337 original size:58 final size:58
Alignment explanation
Indices: 30731158--30731465 Score: 232
Period size: 58 Copynumber: 5.2 Consensus size: 58
30731148 CTTCAAGGGC
* * * **
30731158 AAAATGGTAATTTTTAGACATCCGAGGGTGAAATGGTGATTTTTGAGATTTTTGGGGTCA
1 AAAATGG-AATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGA-AAATTTGGGGTCA
* * * * *
30731218 AAAATGGAATTTTTTGATATTCGAGGGTAAAATGGTAATTTTTAAAAATTTTGAGTCA
1 AAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAATTTGGGGTCA
* * **
30731276 AAAATAGAATTTTTAGACATTCGAGGGTAAAATAGTAATTTTTTGAAGGTTTGGGGT-A
1 AAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAA-TTTTTGAAAATTTGGGGTCA
* * * * * *
30731334 AAAATGGAA-TTTTGGAAAATT-TAGGGGTAAAAAT-GTGATTTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTTAG-ACATTCGA-GGGT-AAAATGGTAATTTTTGAAAA-TTTGGGGTCA
* * * * * *
30731393 AAAATGCAATTTTTGGAAAGTTCG-GGGACAAAAATGG-AATTTTGGAAAATTTAGGGGTAA
1 AAAATGGAATTTTTAGACA-TTCGAGGG--TAAAATGGTAATTTTTGAAAATTT-GGGGTCA
*
30731453 AAAATGTAATTTT
1 AAAATGGAATTTT
30731466 AAAAAGTTTG
Statistics
Matches: 200, Mismatches: 35, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
57 14 0.07
58 70 0.35
59 68 0.34
60 47 0.23
61 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAATTTGGGGTCA
Found at i:30731338 original size:30 final size:29
Alignment explanation
Indices: 30731300--30731523 Score: 179
Period size: 30 Copynumber: 7.6 Consensus size: 29
30731290 AGACATTCGA
*
30731300 GGGT-AAAATAGTAATTTTTTGAAGGTTT-G
1 GGGTAAAAAT-GTAA-TTTTTGAAAGTTTAG
* * *
30731329 GGGTAAAAATGGAATTTTGGAAAATTTAG
1 GGGTAAAAATGTAATTTTTGAAAGTTTAG
*
30731358 GGGTAAAAATGTGATTTTTGAAAAGTTTAG
1 GGGTAAAAATGTAATTTTTG-AAAGTTTAG
* * *
30731388 GGTTAAAAATGCAATTTTTGGAAAG-TTCG
1 GGGTAAAAATGTAATTTTT-GAAAGTTTAG
* * * *
30731417 GGGACAAAAATGGAATTTTGGAAAATTTAG
1 GGG-TAAAAATGTAATTTTTGAAAGTTTAG
**
30731447 GGGTAAAAAATGTAATTTTAAAAAGTTT-G
1 GGGT-AAAAATGTAATTTTTGAAAGTTTAG
* * *
30731476 GGGTTAAAAATGAAATTTTAGAAAATTTTA-
1 GGG-TAAAAATGTAATTTTTG-AAAGTTTAG
*
30731506 GAGTAAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
30731524 CAATTAATTT
Statistics
Matches: 157, Mismatches: 28, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
28 10 0.06
29 66 0.42
30 80 0.51
31 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTAG
Found at i:30731404 original size:59 final size:58
Alignment explanation
Indices: 30731315--30731523 Score: 178
Period size: 59 Copynumber: 3.6 Consensus size: 58
30731305 AAATAGTAAT
* * *
30731315 TTTTTG-AAGGTTT-GGGGTAAAAATGGAATTTTGGAAAATTTAGGGG-TAAAAATGTGA
1 TTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTTGGAAAATTT-GGGGATAAAAATG-GA
* * * *
30731372 TTTTTGAAAAGTTTAGGGTTAAAAATGCAATTTTTGGAAAGTTCGGGGACAAAAATGGAA
1 TTTTTGAAAAGTTTAGGGTTAAAAATGTAA-TTTTGGAAAATTTGGGGATAAAAATGG-A
* * * * *
30731432 TTTTGGAAAA-TTTAGGGGTAAAAAATGTAATTTT-AAAAAGTTTGGGGTTAAAAATGAAA
1 TTTTTGAAAAGTTTA-GGGTTAAAAATGTAATTTTGGAAAA-TTTGGGGATAAAAATG-GA
* * *
30731491 TTTTAGAAAATTTTAGAG-TAAAAATGTAATTTT
1 TTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTT
30731524 CAATTAATTT
Statistics
Matches: 125, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
57 6 0.05
58 23 0.18
59 51 0.41
60 45 0.36
ACGTcount: A:0.40, C:0.01, G:0.23, T:0.35
Consensus pattern (58 bp):
TTTTTGAAAAGTTTAGGGTTAAAAATGTAATTTTGGAAAATTTGGGGATAAAAATGGA
Found at i:30733203 original size:6 final size:6
Alignment explanation
Indices: 30733194--30733257 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
30733184 TTCCAAATGG
* * **
30733194 ATTTAA ATTT-A ATATAA ATTTAA ATTTAA A-ATGG ATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
30733239 ATATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
30733258 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 10 0.22
6 35 0.78
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:30733204 original size:34 final size:34
Alignment explanation
Indices: 30733173--30733259 Score: 147
Period size: 34 Copynumber: 2.6 Consensus size: 34
30733163 AATATTTATC
*
30733173 ATAAATTTAAATTCCAAATGGATTTAAATTTAAT
1 ATAAATTTAAATTCAAAATGGATTTAAATTTAAT
*
30733207 ATAAATTTAAATTTAAAATGGATTTAAATTTAAT
1 ATAAATTTAAATTCAAAATGGATTTAAATTTAAT
*
30733241 ATAAATTTAAATTTAAAAT
1 ATAAATTTAAATTCAAAAT
30733260 AAATTAAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (34 bp):
ATAAATTTAAATTCAAAATGGATTTAAATTTAAT
Found at i:30733213 original size:11 final size:11
Alignment explanation
Indices: 30733197--30733250 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
30733187 CAAATGGATT
30733197 TAAATTTAATA
1 TAAATTTAATA
*
30733208 TAAATTTAAATT
1 TAAATTT-AATA
* ** *
30733220 TAAAATGGATT
1 TAAATTTAATA
30733231 TAAATTTAATA
1 TAAATTTAATA
30733242 TAAATTTAA
1 TAAATTTAA
30733251 ATTTAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (11 bp):
TAAATTTAATA
Found at i:30733261 original size:17 final size:17
Alignment explanation
Indices: 30733173--30733268 Score: 113
Period size: 17 Copynumber: 5.7 Consensus size: 17
30733163 AATATTTATC
**
30733173 ATAAATTTAAATTCCAA
1 ATAAATTTAAATTTAAA
** *
30733190 ATGGATTTAAATTTAAT
1 ATAAATTTAAATTTAAA
30733207 ATAAATTTAAATTTAAA
1 ATAAATTTAAATTTAAA
** *
30733224 ATGGATTTAAATTTAAT
1 ATAAATTTAAATTTAAA
30733241 ATAAATTTAAATTTAAA
1 ATAAATTTAAATTTAAA
30733258 ATAAA-TTAAAT
1 ATAAATTTAAAT
30733269 CTGTTGGGCC
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
16 6 0.09
17 59 0.91
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
ATAAATTTAAATTTAAA
Found at i:30737496 original size:23 final size:23
Alignment explanation
Indices: 30737470--30737535 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
30737460 TTGTTTATGC
* *
30737470 TTGTCAAATTTGGAGATTTTAGG
1 TTGTCGAATTTGGGGATTTTAGG
* *
30737493 TTGTTGAATTTGGGGATTTTGGG
1 TTGTCGAATTTGGGGATTTTAGG
*
30737516 TGGTCGAATTTGGGGATTTT
1 TTGTCGAATTTGGGGATTTT
30737536 CGGTAAGAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.03, G:0.33, T:0.45
Consensus pattern (23 bp):
TTGTCGAATTTGGGGATTTTAGG
Found at i:30738173 original size:36 final size:37
Alignment explanation
Indices: 30738133--30738203 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
30738123 AAATATATTT
*
30738133 TAATATAAT-ATTTTAATAATTTTATATTTCAAAATA
1 TAATATAATAATTTTAATAATTTTAGATTTCAAAATA
*
30738169 TAATATAATAATTTTAATAATTTTAGATTTTAAAA
1 TAATATAATAATTTTAATAATTTTAGATTTCAAAA
30738204 AAATAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
TAATATAATAATTTTAATAATTTTAGATTTCAAAATA
Found at i:30738217 original size:39 final size:37
Alignment explanation
Indices: 30738133--30738228 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
30738123 AAATATATTT
* * *
30738133 TAATATAAT-ATTTTAATAATTTTATATTTCAAAATA
1 TAATATAATAATTTTAATAATTTTAGATTTAAAAAAA
30738169 TAATATAATAATTTTAATAATTTTAGATTTTAAAAAAA
1 TAATATAATAATTTTAATAATTTTAGA-TTTAAAAAAA
* *
30738207 TAATTTTAATAATCTTAA-AATT
1 TAA-TATAATAATTTTAATAATT
30738229 ATTTGTTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
36 9 0.17
37 16 0.31
38 15 0.29
39 12 0.23
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (37 bp):
TAATATAATAATTTTAATAATTTTAGATTTAAAAAAA
Found at i:30746210 original size:2 final size:2
Alignment explanation
Indices: 30746203--30746247 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
30746193 ACAGAATCTC
30746203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30746245 AT A
1 AT A
30746248 AGATTCATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30748755 original size:403 final size:403
Alignment explanation
Indices: 30748008--30748813 Score: 1490
Period size: 403 Copynumber: 2.0 Consensus size: 403
30747998 ACTACTAAAA
30748008 TTTAAAGTTCATCCAAACTTATCTTGATATTCTTGGACATCCACTTAATAAAATATTCATAACAC
1 TTTAAAGTTCATCCAAACTTATCTTGATATTCTTGGACATCCACTTAATAAAATATTCATAACAC
* * *
30748073 TCCCTTTTGGATGTCCATTGGTTGATAATGTGCCTCCTTAAAATCTTTACTAAGATAAAAAACCC
66 TCCCTCTTGGATGTCCATTGGTTGATAATGTGCCTCCTTAAAACCTTTACTAAGATAAAAAAACC
30748138 TATGAGAAAAAAATTTCCTAGTGAAGGAAAAAAAGTACACATATCTATAATACGCATAACATGTT
131 TATGAGAAAAAAATTTCCTAGTGAAGGAAAAAAAGTACACATATCTATAATACGCATAACATGTT
30748203 GCCCCATTAAAACCTTACCAGAAAAACTCAATGGGACAAAACTTCGATTAAGGGAAAAAGAGTAC
196 GCCCCATTAAAACCTTACCAGAAAAACTCAATGGGACAAAACTTCGATTAAGGGAAAAAGAGTAC
*
30748268 AACGCGTATTTACTCTCCCTCACAAAAATATCACATAATATCTCAAATTCTACGTATTCAATCTT
261 AACGCGTATTTACTCTCCCTCACAAAAATATCACATAATATCTCAAATTCTACATATTCAATCTT
*
30748333 GAATACTAGTATTTCAAAAGACTATTTGAATATATGTACTAAGCATTTATATCACCATTCTTTTG
326 GAATACTAGTATTTCAAAAGACTATTTGAATATATCTACTAAGCATTTATATCACCATTCTTTTG
30748398 AAAGTCACGAGTG
391 AAAGTCACGAGTG
30748411 TTTAAAGTTCATCCAAACTTATCTTGATATTCTTGGACATCCACTTAATAAAATATTCATAACAC
1 TTTAAAGTTCATCCAAACTTATCTTGATATTCTTGGACATCCACTTAATAAAATATTCATAACAC
*
30748476 TCCCTCTTGGATGTCTATTGGTTGATAATGTGCCTCCTTAAAACCTTTACTAAGATAAAAAAAAC
66 TCCCTCTTGGATGTCCATTGGTTGATAATGTGCCTCCTTAAAACCTTTACTAAGAT-AAAAAAAC
*
30748541 CTGTGAGAAAAAAATTTCCTAGTGAAGGAAAAAAAGTACACATATCTATAATACGCATAACATGT
130 CTATGAGAAAAAAATTTCCTAGTGAAGGAAAAAAAGTACACATATCTATAATACGCATAACATGT
30748606 TGCCCCATTAAAAACCTTACCAGAAAAACTCAATGGGACAAAACTTCGATTAAGGG-AAAAGAGT
195 TGCCCCATT-AAAACCTTACCAGAAAAACTCAATGGGACAAAACTTCGATTAAGGGAAAAAGAGT
*
30748670 ACAACGCGTATTTACTCTCCCTCATAAAAATATCACATAATATCTCAAATTCTACATATTCAATC
259 ACAACGCGTATTTACTCTCCCTCACAAAAATATCACATAATATCTCAAATTCTACATATTCAATC
* *
30748735 -TGAATACTAGTATTTCAAAAGGCTATTTGAATGTATCTACTAAGCATTTATATCACCATTCTTT
324 TTGAATACTAGTATTTCAAAAGACTATTTGAATATATCTACTAAGCATTTATATCACCATTCTTT
30748799 TGAAAGTCACGAGTG
389 TGAAAGTCACGAGTG
30748814 AGGGAAAATT
Statistics
Matches: 391, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
403 194 0.50
404 151 0.39
405 46 0.12
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (403 bp):
TTTAAAGTTCATCCAAACTTATCTTGATATTCTTGGACATCCACTTAATAAAATATTCATAACAC
TCCCTCTTGGATGTCCATTGGTTGATAATGTGCCTCCTTAAAACCTTTACTAAGATAAAAAAACC
TATGAGAAAAAAATTTCCTAGTGAAGGAAAAAAAGTACACATATCTATAATACGCATAACATGTT
GCCCCATTAAAACCTTACCAGAAAAACTCAATGGGACAAAACTTCGATTAAGGGAAAAAGAGTAC
AACGCGTATTTACTCTCCCTCACAAAAATATCACATAATATCTCAAATTCTACATATTCAATCTT
GAATACTAGTATTTCAAAAGACTATTTGAATATATCTACTAAGCATTTATATCACCATTCTTTTG
AAAGTCACGAGTG
Found at i:30755265 original size:31 final size:31
Alignment explanation
Indices: 30755230--30755291 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
30755220 TAACAAAATG
*
30755230 ATCATTGAACTATTC-GAAAGTTTTCATTTAA
1 ATCATTGAACTAGTCGGAAA-TTTTCATTTAA
*
30755261 ATCATTGAACTAGTCGGAAATTTTTATTTAA
1 ATCATTGAACTAGTCGGAAATTTTCATTTAA
30755292 GTCACTGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (31 bp):
ATCATTGAACTAGTCGGAAATTTTCATTTAA
Found at i:30768053 original size:16 final size:18
Alignment explanation
Indices: 30768014--30768047 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30768004 TAAATTTATA
30768014 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
30768031 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
30768048 AATTTAGAAC
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:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:30771760 original size:17 final size:17
Alignment explanation
Indices: 30771738--30771782 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
30771728 GTGCAAGTTG
30771738 TGTTTATATGCTAGCTA
1 TGTTTATATGCTAGCTA
*
30771755 TGTTTATATGCTAGTTA
1 TGTTTATATGCTAGCTA
30771772 TGTTTATATGC
1 TGTTTATATGC
30771783 GAACTGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (17 bp):
TGTTTATATGCTAGCTA
Found at i:30771846 original size:35 final size:35
Alignment explanation
Indices: 30771787--30771866 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
30771777 ATATGCGAAC
*
30771787 TGTGTCAATG-TGTGGACCGTGTAAATGTGCAAGT
1 TGTGTCAATGTTGTGGACCGCGTAAATGTGCAAGT
*
30771821 TGTGTCAATGTTGTGGACTGCGTAAATGTGCAAGT
1 TGTGTCAATGTTGTGGACCGCGTAAATGTGCAAGT
30771856 TGTGTCAATGT
1 TGTGTCAATGT
30771867 GTGAATTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 10 0.23
35 33 0.77
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.35
Consensus pattern (35 bp):
TGTGTCAATGTTGTGGACCGCGTAAATGTGCAAGT
Found at i:30775252 original size:12 final size:12
Alignment explanation
Indices: 30775235--30775270 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
30775225 AAATAGAATT
*
30775235 AATTAAATTAAA
1 AATTAATTTAAA
*
30775247 AATTAATTTATA
1 AATTAATTTAAA
30775259 AATTAATTTAAA
1 AATTAATTTAAA
30775271 TATAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATTAATTTAAA
Found at i:30781623 original size:14 final size:14
Alignment explanation
Indices: 30781604--30781630 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30781594 GTAGATGGCA
30781604 TATCAACATTTAAT
1 TATCAACATTTAAT
30781618 TATCAACATTTAA
1 TATCAACATTTAA
30781631 GCAAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
TATCAACATTTAAT
Found at i:30781902 original size:6 final size:6
Alignment explanation
Indices: 30781891--30781923 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30781881 GAAGGGTAAG
*
30781891 AAAA-C AAAAAC AAAACC AAAACC AAAACC AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAA
30781924 GTACCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:30782712 original size:3 final size:3
Alignment explanation
Indices: 30782704--30782739 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
30782694 TATAGATCTT
30782704 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30782740 CAATACACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30783615 original size:6 final size:6
Alignment explanation
Indices: 30783604--30783641 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
30783594 CCACACAAAT
*
30783604 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATCAAA AT
1 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA AT
30783642 GTAGGGATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCCAA
Found at i:30783625 original size:18 final size:18
Alignment explanation
Indices: 30783599--30783641 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
30783589 ATGTTCCACA
30783599 CAAATATCCAAATCCAAAT
1 CAAA-ATCCAAATCCAAAT
*
30783618 CCAAATCCAAATCCAAAT
1 CAAAATCCAAATCCAAAT
30783636 CAAAAT
1 CAAAAT
30783642 GTAGGGATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (18 bp):
CAAAATCCAAATCCAAAT
Found at i:30788529 original size:28 final size:28
Alignment explanation
Indices: 30788466--30788521 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
30788456 TTTGTTTTCA
30788466 AATAAAGAATGGGAGAAAAAATTAGGGT
1 AATAAAGAATGGGAGAAAAAATTAGGGT
30788494 AATAAAGAATGGGA-AATAAAATTAGGGT
1 AATAAAGAATGGGAGAA-AAAATTAGGGT
30788522 CCAAAAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (28 bp):
AATAAAGAATGGGAGAAAAAATTAGGGT
Found at i:30796407 original size:17 final size:17
Alignment explanation
Indices: 30796385--30796426 Score: 75
Period size: 17 Copynumber: 2.4 Consensus size: 17
30796375 TTTATTTGAC
30796385 TTGATATGGTTTTGATT
1 TTGATATGGTTTTGATT
30796402 TTGATATGGTTTTGATT
1 TTGATATGGTTTTGATT
30796419 TTGTATAT
1 TTG-ATAT
30796427 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (17 bp):
TTGATATGGTTTTGATT
Found at i:30796896 original size:22 final size:22
Alignment explanation
Indices: 30796833--30796896 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 22
30796823 AATTTACCCG
* * *
30796833 ATATAAAAACCTATTTTATTAT
1 ATATAAAAATCTATATAATTAT
* * * *
30796855 TTATAAATAT-AAAATAATTAT
1 ATATAAAAATCTATATAATTAT
30796876 ATATAAAAATCTATATAATTA
1 ATATAAAAATCTATATAATTA
30796897 AATTTAATAT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAAAAATCTATATAATTAT
Found at i:30797320 original size:16 final size:16
Alignment explanation
Indices: 30797292--30797361 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
30797282 TTTGGTTCGC
*
30797292 TGTAATAGAATAGAGA
1 TGTAATGGAATAGAGA
* *
30797308 TGCAATGGAATAGAGC
1 TGTAATGGAATAGAGA
30797324 TGTAATGGAATAGA-A
1 TGTAATGGAATAGAGA
30797339 CTGTAATGGAATAG-GA
1 -TGTAATGGAATAGAGA
30797355 CTGTAAT
1 -TGTAAT
30797362 CAATAATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:30797335 original size:32 final size:31
Alignment explanation
Indices: 30797290--30797361 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
30797280 CGTTTGGTTC
30797290 GCTGTAATAGAATAGAGA-TGCAATGGAATAG
1 GCTGTAATAGAATAGA-ACTGCAATGGAATAG
* *
30797321 AGCTGTAATGGAATAGAACTGTAATGGAATAG
1 -GCTGTAATAGAATAGAACTGCAATGGAATAG
30797353 GACTGTAAT
1 G-CTGTAAT
30797362 CAATAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (31 bp):
GCTGTAATAGAATAGAACTGCAATGGAATAG
Found at i:30797601 original size:58 final size:59
Alignment explanation
Indices: 30797539--30797689 Score: 218
Period size: 58 Copynumber: 2.6 Consensus size: 59
30797529 ATTTAATAAG
* *
30797539 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATATTTT-AACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAAACATA
* *
30797597 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATAACATTTTAAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAAACATA
*
30797655 ATTATTATTAAAATATGAA-TTAATAAAAATTATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
30797690 TATATAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
57 25 0.30
58 37 0.45
59 11 0.13
60 10 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAAACATA
Found at i:30800944 original size:9 final size:9
Alignment explanation
Indices: 30800930--30800969 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
30800920 TTTATGTTTT
30800930 TAAAAATTA
1 TAAAAATTA
30800939 TAAAAA-TA
1 TAAAAATTA
30800947 T--AAATTA
1 TAAAAATTA
*
30800954 TTAAAATTA
1 TAAAAATTA
30800963 TAAAAAT
1 TAAAAAT
30800970 ACATTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
6 3 0.11
7 3 0.11
8 3 0.11
9 18 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:30800951 original size:15 final size:16
Alignment explanation
Indices: 30800933--30800966 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30800923 ATGTTTTTAA
30800933 AAATTA-TAAAAATAT
1 AAATTATTAAAAATAT
*
30800948 AAATTATTAAAATTAT
1 AAATTATTAAAAATAT
30800964 AAA
1 AAA
30800967 AATACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATTAAAAATAT
Found at i:30813824 original size:27 final size:29
Alignment explanation
Indices: 30813783--30813843 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
30813773 GCTTTATCCA
*
30813783 CAATGGGTCGAGCTTT-GCATAGAGCCTC
1 CAATGGATCGAGCTTTAGCATAGAGCCTC
* *
30813811 CAATGGAT-GAGCTTTAGGCATTGTGCCTC
1 CAATGGATCGAGCTTTA-GCATAGAGCCTC
30813840 CAAT
1 CAAT
30813844 ACCTTCAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 7 0.25
29 14 0.50
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (29 bp):
CAATGGATCGAGCTTTAGCATAGAGCCTC
Found at i:30817984 original size:31 final size:32
Alignment explanation
Indices: 30817944--30818007 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
30817934 AGTCTTTATC
* *
30817944 TTTATATTTTTTAAAGTATT-AAAT-TAATTT
1 TTTATATTTTTAAAAGAATTAAAATATAATTT
30817974 TTTATCATTTTTAAAAGAATTAAAATATAATTT
1 TTTAT-ATTTTTAAAAGAATTAAAATATAATTT
30818007 T
1 T
30818008 ATAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.17
31 13 0.45
32 4 0.14
33 7 0.24
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTATATTTTTAAAAGAATTAAAATATAATTT
Found at i:30822025 original size:11 final size:11
Alignment explanation
Indices: 30822009--30822037 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
30821999 TTCTGACTTT
30822009 GAAAAATTGTA
1 GAAAAATTGTA
30822020 GAAAAA-TGTA
1 GAAAAATTGTA
30822030 GAAAAATT
1 GAAAAATT
30822038 ATTAGAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (11 bp):
GAAAAATTGTA
Found at i:30822505 original size:23 final size:23
Alignment explanation
Indices: 30822479--30822592 Score: 119
Period size: 23 Copynumber: 5.0 Consensus size: 23
30822469 TTACCGTTCA
*
30822479 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
*
30822502 GCACTTTGTGTGCCTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
30822525 GCACT-TCGTGTGCCTACTGATTTGC
1 GCACTGT-GTGTGCCTACTG-TTT-C
* * *
30822550 GCA--ATGTGCGCCTACTGATT-
1 GCACTGTGTGTGCCTACTGTTTC
*
30822570 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
30822593 CCCAGCACAT
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.04
22 16 0.21
23 49 0.64
24 4 0.05
25 4 0.05
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (23 bp):
GCACTGTGTGTGCCTACTGTTTC
Done.