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 106 of 120
Found at i:30825755 original size:24 final size:24
Alignment explanation
Indices: 30825704--30825758 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
30825694 TCTTTTAGTT
*
30825704 AAACTCTGTATATTTGTTTCAATT
1 AAACTCTGTATATTTGTTTCAATC
* * *
30825728 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTATATTTGTTTCAATC
30825752 AAACTCT
1 AAACTCT
30825759 TGTTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTATATTTGTTTCAATC
Found at i:30826571 original size:15 final size:15
Alignment explanation
Indices: 30826522--30826576 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
30826512 ATATCATCAC
*
30826522 TTAATTAATTAACTA
1 TTAATTAATTATCTA
* *
30826537 GTAA-TAA-TATATA
1 TTAATTAATTATCTA
* *
30826550 TTTATTATTTATCTA
1 TTAATTAATTATCTA
30826565 TTAATTAATTAT
1 TTAATTAATTAT
30826577 AATGAATACG
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 18 0.62
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (15 bp):
TTAATTAATTATCTA
Found at i:30832585 original size:18 final size:18
Alignment explanation
Indices: 30832562--30832596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30832552 ACATATATAT
*
30832562 ATATAATCTAGAAAAAAC
1 ATATAAACTAGAAAAAAC
*
30832580 ATATAAACTATAAAAAA
1 ATATAAACTAGAAAAAA
30832597 TTTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAAACTAGAAAAAAC
Found at i:30832833 original size:21 final size:20
Alignment explanation
Indices: 30832788--30832849 Score: 85
Period size: 19 Copynumber: 3.2 Consensus size: 20
30832778 TTACTTGAAA
30832788 TTTA-AATATTTTTTGAATT
1 TTTATAATATTTTTTGAATT
30832807 TTTATAATATTTTTT-AATT
1 TTTATAATATTTTTTGAATT
*
30832826 TTTAT-ATATTATTTTGACTT
1 TTTATAATATT-TTTTGAATT
30832846 TTTA
1 TTTA
30832850 AAATTTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 5 0.13
19 17 0.44
20 17 0.44
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTATAATATTTTTTGAATT
Found at i:30833049 original size:11 final size:11
Alignment explanation
Indices: 30833022--30833055 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30833012 ATTAACTCTC
30833022 AATCAAC-ATT
1 AATCAACAATT
*
30833032 GATCAACAATT
1 AATCAACAATT
30833043 AATCAACAATT
1 AATCAACAATT
30833054 AA
1 AA
30833056 GTAAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (11 bp):
AATCAACAATT
Found at i:30841205 original size:3 final size:3
Alignment explanation
Indices: 30841145--30841188 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
30841135 TGTTATTGAG
30841145 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G-T GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
30841189 TAGTGTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:30846750 original size:19 final size:19
Alignment explanation
Indices: 30846710--30846754 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30846700 TAAATCACAT
* *
30846710 TTTTAAATTATTATTCAGA
1 TTTTAAATTATTATTAAAA
30846729 TTTTAAATTGATT-TTAAAA
1 TTTTAAATT-ATTATTAAAA
30846748 TTTTAAA
1 TTTTAAA
30846755 AATTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTAAATTATTATTAAAA
Found at i:30846784 original size:20 final size:20
Alignment explanation
Indices: 30846746--30846784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30846736 TTGATTTTAA
* *
30846746 AATTTTAAAAATTTTAATTG
1 AATTTTAAAAATATCAATTG
*
30846766 AATTTTTAAAATATCAATT
1 AATTTTAAAAATATCAATT
30846785 AGGGTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
AATTTTAAAAATATCAATTG
Found at i:30847089 original size:46 final size:46
Alignment explanation
Indices: 30847022--30847117 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
30847012 TAAGAACTTT
* *
30847022 TTTGAAGTTTGGATCAATTTAGATTTTACAATATTCTTTAAAGACG
1 TTTGAAGTTCGGATCAATTTAGATTCTACAATATTCTTTAAAGACG
* * *
30847068 TTTGAAGTTCGGATCAATTTAGATTCTATAATATTCTTTAAGGATG
1 TTTGAAGTTCGGATCAATTTAGATTCTACAATATTCTTTAAAGACG
30847114 TTTG
1 TTTG
30847118 TTGAAACTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (46 bp):
TTTGAAGTTCGGATCAATTTAGATTCTACAATATTCTTTAAAGACG
Found at i:30851016 original size:31 final size:31
Alignment explanation
Indices: 30850948--30851018 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
30850938 CAAGTTAGTC
* * * **
30850948 CTTGAACTTGGCAATTGTTTCCATATTGGGG
1 CTTGAACTTGACAATTGTTCCCACATTGGAA
* *
30850979 CCTGAACTTGACAATTGTTCCCACGTTGGAA
1 CTTGAACTTGACAATTGTTCCCACATTGGAA
30851010 CTTGAACTT
1 CTTGAACTT
30851019 TAGGGTTTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (31 bp):
CTTGAACTTGACAATTGTTCCCACATTGGAA
Found at i:30851136 original size:58 final size:57
Alignment explanation
Indices: 30851045--30851212 Score: 185
Period size: 58 Copynumber: 2.9 Consensus size: 57
30851035 ATATCAAGGA
* *
30851045 CTAACTTCGACAAATAAAAGTTCAAGCCCCAATGTGAAAATAATTGCCAAGTTCAGGGT
1 CTAACTTGGAC-AA-AAAAGTTCAAGCCCCAATGTGAAAATAATTGCCAAGTTCAGGGC
* * * * *
30851104 CTAACTTGGGCAAAAAGAGTTCAGGCCCCAATGTGGAAACAATTGCCAAGTTTAGGGC
1 CTAACTTGGACAAAAA-AGTTCAAGCCCCAATGTGAAAATAATTGCCAAGTTCAGGGC
* * * * *
30851162 CTAATTTGAACAAAAAACTTCACA-CCCCAATATGAAAATAGTTGCCAAGTT
1 CTAACTTGGACAAAAAAGTTCA-AGCCCCAATGTGAAAATAATTGCCAAGTT
30851213 TAAGCCCCCA
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
57 31 0.34
58 51 0.56
59 9 0.10
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (57 bp):
CTAACTTGGACAAAAAAGTTCAAGCCCCAATGTGAAAATAATTGCCAAGTTCAGGGC
Found at i:30853899 original size:21 final size:21
Alignment explanation
Indices: 30853874--30853915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30853864 GATGAAATTA
* *
30853874 TTAATTTTTAATATAATTTAT
1 TTAATTATTAAGATAATTTAT
*
30853895 TTAATTATTGAGATAATTTAT
1 TTAATTATTAAGATAATTTAT
30853916 ATATCACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTAATTATTAAGATAATTTAT
Found at i:30855365 original size:29 final size:28
Alignment explanation
Indices: 30855333--30855439 Score: 65
Period size: 29 Copynumber: 3.6 Consensus size: 28
30855323 TGTAATTTCA
30855333 AGAAAATTCAGGGTTAAAAATGGGATTTT
1 AGAAAATTCAGGG-TAAAAATGGGATTTT
* * * *
30855362 AGAAGATTTAAGGGT-AAAGTGGTAATTTTT
1 AGAA-AATTCAGGGTAAAAATGG-GA-TTTT
* *
30855392 TGTGAAATT-AGGGTTAAAAATGGGATTTT
1 AG-AAAATTCAGGG-TAAAAATGGGATTTT
* *
30855421 GGAAAGTTCATGGGTAAAA
1 AGAAAATTCA-GGGTAAAA
30855440 TGGTAATTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
28 10 0.17
29 21 0.36
30 20 0.34
31 7 0.12
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (28 bp):
AGAAAATTCAGGGTAAAAATGGGATTTT
Found at i:30855405 original size:59 final size:59
Alignment explanation
Indices: 30855343--30855686 Score: 437
Period size: 59 Copynumber: 5.9 Consensus size: 59
30855333 AGAAAATTCA
* * ** * * *
30855343 GGGTTAAAAATGGGATTTTAG-AAGATTTAAGGGTAAAGTGGTAATTTTTTGTGAAATTA
1 GGGTTAAAAATGGAATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGGTGAAATTG
* *
30855402 GGGTTAAAAATGGGATTTTGGAAAGTTC-ATGGGTAAAATGGTAATTTTTGATGAAATTG
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATTG
* * *
30855461 GGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTG
* * *
30855519 GGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGATAATTTTTGGTGAAATCG
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTG
* * * * * *
30855578 AGGTT-AAAATGAAATTTTAGAAAGTTCG-GGAGTAAAATGGTAATTTTCGATGAAATCG
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGG-GTAAAATGGTAATTTTTGGTGAAATTG
30855636 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
30855687 AAGTTTTAGG
Statistics
Matches: 251, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.01
58 101 0.40
59 143 0.57
60 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTG
Found at i:30855494 original size:117 final size:117
Alignment explanation
Indices: 30855373--30855685 Score: 459
Period size: 117 Copynumber: 2.7 Consensus size: 117
30855363 GAAGATTTAA
* * ** *
30855373 GGGTAAAGTGGTAATTTTTTGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTC-ATGGGTA
1 GGGTAAAATGGTAATTTTTCGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTA
* * * * *
30855437 AAATGGTAATTTTTGATGAAATTGGGGTTAAAATGGAATTTTGGAAAGTTTGG
65 AAATGGTAATTTTTGATGAAATCGAGGTTAAAATGAAATTTTAGAAAGTTCGG
* *
30855490 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAA
1 GGGTAAAATGGTAATTTTTCGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAA
* *
30855555 AATGATAATTTTTGGTGAAATCGAGGTTAAAATGAAATTTTAGAAAGTTCGG
66 AATGGTAATTTTTGATGAAATCGAGGTTAAAATGAAATTTTAGAAAGTTCGG
*
30855607 GAGTAAAATGGTAA-TTTTCGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTA
1 GGGTAAAATGGTAATTTTTCG-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTA
30855671 AAATGGTAATTTTTG
65 AAATGGTAATTTTTG
30855686 GAAGTTTTAG
Statistics
Matches: 177, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 5 0.03
117 171 0.97
118 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTTCGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAA
AATGGTAATTTTTGATGAAATCGAGGTTAAAATGAAATTTTAGAAAGTTCGG
Found at i:30855713 original size:29 final size:29
Alignment explanation
Indices: 30855417--30855713 Score: 173
Period size: 30 Copynumber: 10.1 Consensus size: 29
30855407 AAAAATGGGA
30855417 TTTTGGAAAGTTC-ATGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGA-GGGTAAAAT-GTAAT
*
30855447 TTTTGATGAAA-TT-G-GGGTTAAAATGGAA-
1 TTTTG--GAAAGTTCGAGGG-TAAAATGTAAT
* *
30855475 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAAT-GTAAT
30855505 TTTTGGTGAAA--TCG-GGGTTAAAAATAG-AA-
1 TTTT-G-GAAAGTTCGAGGG-T-AAAAT-GTAAT
30855534 TTTTGGAAAGTTCGAGGGTAAAATGATAAT
1 TTTTGGAAAGTTCGAGGGTAAAATG-TAAT
* *
30855564 TTTTGGTGAAA--TCGAGGTTAAAATG-AAA
1 TTTT-G-GAAAGTTCGAGGGTAAAATGTAAT
*
30855592 TTTTAGAAAGTTCG-GGAGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGG-GTAAAAT-GTAAT
* *
30855622 TTTCGATGAAA--TCG-GGGTTAAAAATGGAA-
1 TTTTG--GAAAGTTCGAGGG-T-AAAATGTAAT
30855651 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAAT-GTAAT
**
30855681 TTTTGG-AAGTTTTAGGGTCAAAATGTAAT
1 TTTTGGAAAGTTCGAGGGT-AAAATGTAAT
30855710 TTTT
1 TTTT
30855714 TTTGAAATTT
Statistics
Matches: 215, Mismatches: 16, Indels: 73
0.71 0.05 0.24
Matches are distributed among these distances:
26 8 0.04
27 13 0.06
28 38 0.18
29 57 0.27
30 68 0.32
31 15 0.07
32 16 0.07
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTCGAGGGTAAAATGTAAT
Found at i:30855714 original size:30 final size:30
Alignment explanation
Indices: 30855651--30855743 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
30855641 AAAAATGGAA
**
30855651 TTTTGGAAAGTTCGAGGGT-AAAATGGTAA-T
1 TTTTGG-AAGTTTTAGGGTCAAAAT-GTAATT
30855681 TTTTGGAAGTTTTAGGGTCAAAATGTAATTT
1 TTTTGGAAGTTTTAGGGTCAAAATGTAA-TT
* * * *
30855712 TTTTTGAAATTTTGGGGTCACAAATATAATT
1 TTTTGGAAGTTTTAGGGTCA-AAATGTAATT
30855743 T
1 T
30855744 ATGAACAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
29 14 0.26
30 11 0.21
31 21 0.40
32 7 0.13
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (30 bp):
TTTTGGAAGTTTTAGGGTCAAAATGTAATT
Found at i:30855730 original size:31 final size:32
Alignment explanation
Indices: 30855680--30855743 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
30855670 AAAATGGTAA
* *
30855680 TTTTTGGAAGTTTTAGGGTCA-AAATGTAATT
1 TTTTTGGAAATTTTAGGGTCACAAATATAATT
* *
30855711 TTTTTTGAAATTTTGGGGTCACAAATATAATT
1 TTTTTGGAAATTTTAGGGTCACAAATATAATT
30855743 T
1 T
30855744 ATGAACAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (32 bp):
TTTTTGGAAATTTTAGGGTCACAAATATAATT
Found at i:30855748 original size:117 final size:113
Alignment explanation
Indices: 30855337--30855712 Score: 391
Period size: 117 Copynumber: 3.2 Consensus size: 113
30855327 ATTTCAAGAA
* * ** * *
30855337 AATTCAGGGTTAAAAATGGGATTTTAGAAGATTTAAGGGTAAAGTGGTAATTTTTTG-TGAAATT
1 AATTTAGGGTT-AAAAT-GAATTTTAGAA-ATTTCGGGGTAAAATGGTAA--TTTTGATGAAATC
* *
30855401 AGGGTTAAAAATGGGATTTTGGAAAGTTC-ATGGGTAAAATGGTAATTTTTGATG
61 GGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTG-TG
* * * * *
30855455 AAATTGGGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGG
1 AATTTAGGGTTAAAAT-GAATTTTAGAAA-TTTCGGGGTAAAATGGTAA-TTTTGATGAAATCGG
* *
30855520 GGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGATAATTTTTGGTG
63 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT-GTG
* * *
30855572 AA-ATCGAGGTTAAAATGAAATTTTAGAAAGTTCGGGAGTAAAATGGTAATTTTCGATGAAATCG
1 AATTTAG-GGTTAAAATG-AATTTTAGAAATTTCGGG-GTAAAATGGTAATTTT-GATGAAATCG
30855636 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTG-G
62 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGTG
*
30855687 AAGTTTTAGGGTCAAAATGTAATTTT
1 AA--TTTAGGGTTAAAATG-AATTTT
30855713 TTTTGAAATT
Statistics
Matches: 222, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
115 3 0.01
116 20 0.09
117 187 0.84
118 12 0.05
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (113 bp):
AATTTAGGGTTAAAATGAATTTTAGAAATTTCGGGGTAAAATGGTAATTTTGATGAAATCGGGGT
TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGTG
Found at i:30857580 original size:26 final size:27
Alignment explanation
Indices: 30857530--30857580 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
30857520 CATTGGGCCT
30857530 ATTTGGGCCATTGTAATTGGGCCTTCA
1 ATTTGGGCCATTGTAATTGGGCCTTCA
30857557 ATTTGGGCC-TT-TAATTTGGGCCTT
1 ATTTGGGCCATTGTAA-TTGGGCCTT
30857581 TGTAAATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 11 0.48
27 9 0.39
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (27 bp):
ATTTGGGCCATTGTAATTGGGCCTTCA
Found at i:30857581 original size:13 final size:13
Alignment explanation
Indices: 30857530--30857581 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
30857520 CATTGGGCCT
30857530 ATTTGGGCCATTGTA
1 ATTTGGGCC-TT-TA
*
30857545 A-TTGGGCCTTCA
1 ATTTGGGCCTTTA
30857557 ATTTGGGCCTTTA
1 ATTTGGGCCTTTA
30857570 ATTTGGGCCTTT
1 ATTTGGGCCTTT
30857582 GTAAATGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 2 0.06
13 24 0.71
14 7 0.21
15 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (13 bp):
ATTTGGGCCTTTA
Found at i:30857697 original size:18 final size:18
Alignment explanation
Indices: 30857643--30857708 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
30857633 TTTGATATTG
* *
30857643 ATTTAAATTTTA-ATTAA
1 ATTTAAATTTAACAATAA
*
30857660 ATTTAGATTTAAAGCAATAA
1 ATTTAAATTT-AA-CAATAA
30857680 ATTTAAATTTAACAATAA
1 ATTTAAATTTAACAATAA
30857698 ATTTAAATTTA
1 ATTTAAATTTA
30857709 TTTAAACCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.21
18 18 0.43
19 2 0.05
20 13 0.31
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTTAAATTTAACAATAA
Found at i:30858901 original size:364 final size:364
Alignment explanation
Indices: 30858232--30858961 Score: 1397
Period size: 364 Copynumber: 2.0 Consensus size: 364
30858222 GTGCTGTTCC
30858232 GGTCACTGCTTCTTCTCCGGCGGTGTCTGCTACGACTTCATTGCGATCATCTAATGAAGAAAATT
1 GGTCACTGCTTCTTCTCCGGCGGTGTCTGCTACGACTTCATTGCGATCATCTAATGAAGAAAATT
30858297 TTTACAGAATGATGCAGGCGTTTCCAATGCATGGTCTTCGTGCAGACAATTTTGTGCAATGGCAG
66 TTTACAGAATGATGCAGGCGTTTCCAATGCATGGTCTTCGTGCAGACAATTTTGTGCAATGGCAG
30858362 TACCAGTTGAGTTTACTTTTGGAGGCTTATGATTTAGTTGGTTTTGCTGATGGCACGGCTGTGGC
131 TACCAGTTGAGTTTACTTTTGGAGGCTTATGATTTAGTTGGTTTTGCTGATGGCACGGCTGTGGC
*
30858427 TCCAGTGCAGTTCATCGATGATTCTGAAGGCAGGTCTATCCCTAATCCTGCTTATTTGTTTTTTT
196 TCCAGTGCAGTTCATCGATGATTCTGAAGGCAGATCTATCCCTAATCCTGCTTATTTGTTTTTTT
30858492 ATTAAACAGAGCAAGTTAATTCTTTCTTGGTTGATATCCACTATAAGTGGCGAGTTATTACCAAA
261 ATTAAACAGAGCAAGTTAATTCTTTCTTGGTTGATATCCACTATAAGTGGCGAGTTATTACCAAA
* *
30858557 GTTTGTTAGATCCACGACGGTAAGCCAGATCTGGACGAA
326 GTTTGTTAGATCCACGACGGTAAGCCAAATCTGAACGAA
30858596 GGTCACTGCTTCTTCTCCGGCGGTGTCTGCTACGACTTCATTGCGATCATCTAATGAAGAAAATT
1 GGTCACTGCTTCTTCTCCGGCGGTGTCTGCTACGACTTCATTGCGATCATCTAATGAAGAAAATT
*
30858661 TTTATAGAATGATGCAGGCGTTTCCAATGCATGGTCTTCGTGCAGACAATTTTGTGCAATGGCAG
66 TTTACAGAATGATGCAGGCGTTTCCAATGCATGGTCTTCGTGCAGACAATTTTGTGCAATGGCAG
*
30858726 TACCAGTTGAGTTTACTTTTGGAGGCTTATGATTTAGTTGGTTTTGTTGATGGCACGGCTGTGGC
131 TACCAGTTGAGTTTACTTTTGGAGGCTTATGATTTAGTTGGTTTTGCTGATGGCACGGCTGTGGC
* *
30858791 TCTAGTGCAGTTCATCGATGATTCTGAAGGCAGATCTATCCTTAATCCTGCTTATTTGTTTTTTT
196 TCCAGTGCAGTTCATCGATGATTCTGAAGGCAGATCTATCCCTAATCCTGCTTATTTGTTTTTTT
30858856 ATTAAACAGAGCAAGTTAATTCTTTCTTGGTTGATATCCACTATAAGTGGCGAGTTATTACCAAA
261 ATTAAACAGAGCAAGTTAATTCTTTCTTGGTTGATATCCACTATAAGTGGCGAGTTATTACCAAA
30858921 GTTTGTTAGATCCACGACGGTAAGCCAAATCTGAACGAA
326 GTTTGTTAGATCCACGACGGTAAGCCAAATCTGAACGAA
30858960 GG
1 GG
30858962 CTTCGAGGTT
Statistics
Matches: 359, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
364 359 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (364 bp):
GGTCACTGCTTCTTCTCCGGCGGTGTCTGCTACGACTTCATTGCGATCATCTAATGAAGAAAATT
TTTACAGAATGATGCAGGCGTTTCCAATGCATGGTCTTCGTGCAGACAATTTTGTGCAATGGCAG
TACCAGTTGAGTTTACTTTTGGAGGCTTATGATTTAGTTGGTTTTGCTGATGGCACGGCTGTGGC
TCCAGTGCAGTTCATCGATGATTCTGAAGGCAGATCTATCCCTAATCCTGCTTATTTGTTTTTTT
ATTAAACAGAGCAAGTTAATTCTTTCTTGGTTGATATCCACTATAAGTGGCGAGTTATTACCAAA
GTTTGTTAGATCCACGACGGTAAGCCAAATCTGAACGAA
Found at i:30864758 original size:24 final size:24
Alignment explanation
Indices: 30864726--30864776 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
30864716 ATTGGGATAC
30864726 GTTCAATTTGATGCTCCGGTGATG
1 GTTCAATTTGATGCTCCGGTGATG
*
30864750 GTTCAATTTGATGCTCTGGTGATG
1 GTTCAATTTGATGCTCCGGTGATG
30864774 GTT
1 GTT
30864777 TTTACAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (24 bp):
GTTCAATTTGATGCTCCGGTGATG
Found at i:30867446 original size:29 final size:30
Alignment explanation
Indices: 30867413--30867470 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
30867403 AAATAAAAAT
30867413 TTTAACGAAAAGATA-AATTTACTCTTTAA
1 TTTAACGAAAAGATATAATTTACTCTTTAA
** *
30867442 TTTAACTTACAGATATTAATTTACTCTTT
1 TTTAACGAAAAGATA-TAATTTACTCTTT
30867471 TTTAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
31 12 0.50
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTAACGAAAAGATATAATTTACTCTTTAA
Found at i:30872302 original size:61 final size:57
Alignment explanation
Indices: 30872133--30872308 Score: 165
Period size: 58 Copynumber: 3.0 Consensus size: 57
30872123 ATATCAGGGA
* * * *
30872133 CTAACTTGGACAAATAAAAGTTCAAGCCCCAATGTGAAAATAATTGCCAAGTTCAAGGT
1 CTAACTTGAACAAA-AAAAGTTCAA-CCCCAATATGAAAATAATTGCCAAGTTTAAGGC
* * * * * *
30872192 CTAACTTGAGCAAAAAGAGTTCAGGCCCCAATACGTAAACAATAT-CCAAGTTTAAGGC
1 CTAACTTGAACAAAAAAAGTTCA-ACCCCAATATGAAAATAAT-TGCCAAGTTTAAGGC
* *
30872250 CTAATTTGAACAAAAAAACAAGTTCACACCCCAATATGAAAATAGTTGCCAAGTTTAAG
1 CTAACTTGAAC--AAAAA-AAGTTCA-ACCCCAATATGAAAATAATTGCCAAGTTTAAG
30872309 CCCCAAAAAG
Statistics
Matches: 92, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
58 42 0.46
59 13 0.14
60 6 0.07
61 31 0.34
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (57 bp):
CTAACTTGAACAAAAAAAGTTCAACCCCAATATGAAAATAATTGCCAAGTTTAAGGC
Found at i:30880570 original size:28 final size:30
Alignment explanation
Indices: 30880510--30880574 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
30880500 TATATAAATA
*
30880510 AAAATATATCAAATTTAATCATAATACAAT
1 AAAATATATCAAATATAATCATAATACAAT
*
30880540 AAAATATAT-AAATATGAT-ATGAATAC-AT
1 AAAATATATCAAATATAATCAT-AATACAAT
30880568 AAAATAT
1 AAAATAT
30880575 CGAATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.34
29 12 0.38
30 9 0.28
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATATATCAAATATAATCATAATACAAT
Found at i:30884366 original size:29 final size:30
Alignment explanation
Indices: 30884312--30884371 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
30884302 TGAACTTGAA
*
30884312 TTTTGAAATTTAAAAATAATGAAACTAAATT
1 TTTTGAAA-TTAAAAATAAAGAAACTAAATT
30884343 TTTTGAAA-TAAAAATAAA-AGAACTAAATT
1 TTTTGAAATTAAAAATAAAGA-AACTAAATT
30884372 CCAAATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 18 0.67
31 8 0.30
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (30 bp):
TTTTGAAATTAAAAATAAAGAAACTAAATT
Found at i:30887645 original size:18 final size:18
Alignment explanation
Indices: 30887622--30887658 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30887612 GAAAATTAGA
30887622 TTACCAAAGTTTTAAAAT
1 TTACCAAAGTTTTAAAAT
30887640 TTACCAAAGTTTTAAAAT
1 TTACCAAAGTTTTAAAAT
30887658 T
1 T
30887659 ATAAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (18 bp):
TTACCAAAGTTTTAAAAT
Found at i:30889029 original size:11 final size:11
Alignment explanation
Indices: 30889007--30889106 Score: 103
Period size: 11 Copynumber: 8.9 Consensus size: 11
30888997 TACTTTGAAA
* *
30889007 TTAAATTAAAT
1 TTAATTTAATT
30889018 TTAATTTTAA-T
1 TTAA-TTTAATT
30889029 TTAATTTAAATT
1 TTAATTT-AATT
*
30889041 TAAATTTAATT
1 TTAATTTAATT
30889052 TTAATTTAATT
1 TTAATTTAATT
* *
30889063 TAAATTTAAAT
1 TTAATTTAATT
30889074 TTAATTTAAGTT
1 TTAATTTAA-TT
*
30889086 TGAATTTAATT
1 TTAATTTAATT
*
30889097 TAAATTTAAT
1 TTAATTTAAT
30889107 ATTATTTGTA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
10 3 0.04
11 53 0.70
12 20 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
TTAATTTAATT
Found at i:30889032 original size:17 final size:17
Alignment explanation
Indices: 30889007--30889123 Score: 123
Period size: 17 Copynumber: 6.9 Consensus size: 17
30888997 TACTTTGAAA
*
30889007 TTAAATTAAATTTAATT
1 TTAATTTAAATTTAATT
30889024 TTAATTT-AATTTAAATT
1 TTAATTTAAATTT-AATT
* *
30889041 TAAATTTAATTTTAA-T
1 TTAATTTAAATTTAATT
*
30889057 TTAATTTAAATTTAAAT
1 TTAATTTAAATTTAATT
*
30889074 TTAATTTAAGTTTGAA-T
1 TTAATTTAAATTT-AATT
*
30889091 TTAATTTAAATTTAATA
1 TTAATTTAAATTTAATT
*
30889108 TTATTTGTAAATTTAA
1 TTAATT-TAAATTTAA
30889124 AATGTTCAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
16 21 0.25
17 49 0.58
18 15 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAATTTAAATTTAATT
Found at i:30889046 original size:28 final size:29
Alignment explanation
Indices: 30889007--30889124 Score: 156
Period size: 28 Copynumber: 4.2 Consensus size: 29
30888997 TACTTTGAAA
30889007 TTAAA-TTAAATTTAATTTTAATTT-AAT
1 TTAAATTTAAATTTAATTTTAATTTAAAT
30889034 TTAAATTTAAATTTAATTTTAATTT-AAT
1 TTAAATTTAAATTTAATTTTAATTTAAAT
*
30889062 TTAAATTTAAATTTAA-TTTAAGTTTGAAT
1 TTAAATTTAAATTTAATTTTAA-TTTAAAT
* *
30889091 TT-AATTTAAATTTAATATTATTTGTAAAT
1 TTAAATTTAAATTTAATTTTAATT-TAAAT
30889120 TTAAA
1 TTAAA
30889125 ATGTTCAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.12
28 56 0.68
29 14 0.17
30 2 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
TTAAATTTAAATTTAATTTTAATTTAAAT
Found at i:30891858 original size:22 final size:23
Alignment explanation
Indices: 30891831--30891874 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
30891821 ATCACTTTTT
30891831 CTACTATTTTATTATT-ATGTTA
1 CTACTATTTTATTATTAATGTTA
*
30891853 CTACTATTTTATTGTTAATGTT
1 CTACTATTTTATTATTAATGTT
30891875 TGGATATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (23 bp):
CTACTATTTTATTATTAATGTTA
Found at i:30892014 original size:25 final size:27
Alignment explanation
Indices: 30891986--30892036 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
30891976 CTTTTTTAAA
*
30891986 ATTTATTTTCA-ATTTGTTA-AAAAAT
1 ATTTATTTTAATATTTGTTAGAAAAAT
30892011 ATTTATTTTAATATTTGTTAGAAAAA
1 ATTTATTTTAATATTTGTTAGAAAAA
30892037 GAGGATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 8 0.35
27 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (27 bp):
ATTTATTTTAATATTTGTTAGAAAAAT
Found at i:30894051 original size:16 final size:16
Alignment explanation
Indices: 30894032--30894073 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30894022 ATTATGCTTA
*
30894032 AAAATAAACATAATAT
1 AAAATAAACATAAAAT
30894048 AAAATAAATC-TAAAAT
1 AAAATAAA-CATAAAAT
*
30894064 AAAACAAACA
1 AAAATAAACA
30894074 CTCAAGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAACATAAAAT
Found at i:30898568 original size:29 final size:30
Alignment explanation
Indices: 30898517--30898929 Score: 417
Period size: 30 Copynumber: 13.9 Consensus size: 30
30898507 CTCAAGAGGT
* * *
30898517 CCCTAGACTTTTCCAAAAATACAATTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
*
30898547 CTCTAAACTTTT-CAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
*
30898576 CCCTAAACTTTTACC-AAATCACATTTTAAC
1 CCCTAAACTTTT-CCAAAATTACATTTTAAC
* *
30898606 CCC-AAAATTTTCCAAAATTAGATTTT-AC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898634 CCCTAAAATTTTCTAAAATTACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
30898664 CCCTAAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898694 TCCTAAACTTTTCCAAAATTACTTTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
30898724 ACCTAAACTTTTCCAAAATTAAATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898754 TCCTAAACTTTTCCAAAATTACTTTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * ** *
30898784 ACCC-ACACTTTTCTAAAATTATTTTTTGAC
1 -CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898814 CCCT-AACTTTTCCAAAATCATATTTTAGC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898843 CCCTAATCTTTTTCAAAATCACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* ** * *
30898873 CCTTAAACTTTTTTAAAATCATATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
30898903 CTCC-AAACTTCTCTAAAATTTCATTTT
1 C-CCTAAACTTTTCCAAAATTACATTTT
30898930 CATCCCGAGT
Statistics
Matches: 325, Mismatches: 49, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.02
29 90 0.28
30 224 0.69
31 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:30908126 original size:19 final size:20
Alignment explanation
Indices: 30908099--30908138 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
30908089 TGTTTAGTTA
30908099 TTTGTTTTTAATTTA-TTTTT
1 TTTGTTTTT-ATTTACTTTTT
30908119 TTTG-TTTTATTTACTTTTT
1 TTTGTTTTTATTTACTTTTT
30908138 T
1 T
30908139 ATATAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTGTTTTTATTTACTTTTT
Found at i:30908136 original size:18 final size:20
Alignment explanation
Indices: 30908099--30908138 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
30908089 TGTTTAGTTA
*
30908099 TTTGTTTTTAATTTATTTTT
1 TTTGTTTTTAATTTACTTTT
30908119 TTTG-TTTT-ATTTACTTTT
1 TTTGTTTTTAATTTACTTTT
30908137 TT
1 TT
30908139 ATATAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTGTTTTTAATTTACTTTT
Found at i:30916165 original size:14 final size:14
Alignment explanation
Indices: 30916148--30916195 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
30916138 TGGGTTCACT
*
30916148 TATAGGAGTTCGCA
1 TATAGGAGCTCGCA
30916162 TATA-GAGGCTCGCA
1 TATAGGA-GCTCGCA
* *
30916176 TATAGGGGCTCGCC
1 TATAGGAGCTCGCA
30916190 TATAGG
1 TATAGG
30916196 GTTCGCGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 26 0.90
15 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (14 bp):
TATAGGAGCTCGCA
Found at i:30916196 original size:14 final size:14
Alignment explanation
Indices: 30916157--30916196 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
30916147 TTATAGGAGT
*
30916157 TCGCATATAGAGGC
1 TCGCATATAGGGGC
30916171 TCGCATATAGGGGC
1 TCGCATATAGGGGC
*
30916185 TCGCCTATAGGG
1 TCGCATATAGGG
30916197 TTCGCGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.23
Consensus pattern (14 bp):
TCGCATATAGGGGC
Found at i:30919266 original size:14 final size:14
Alignment explanation
Indices: 30919243--30919280 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
30919233 TTGTTCATTG
30919243 AAAATGATTTTTGA
1 AAAATGATTTTTGA
* *
30919257 AAAATAATTTTTGG
1 AAAATGATTTTTGA
30919271 AAAATGATTT
1 AAAATGATTT
30919281 ATTTTCTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:30919737 original size:19 final size:19
Alignment explanation
Indices: 30919713--30919749 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30919703 AATTATTAAT
*
30919713 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
30919732 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
30919750 TTAATATGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:30932146 original size:30 final size:30
Alignment explanation
Indices: 30932105--30932347 Score: 339
Period size: 30 Copynumber: 8.1 Consensus size: 30
30932095 AATTGTCTAG
30932105 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCTAAAACTTTTCCA
* * *
30932135 AAATTATATTTTGACCCCAAAACTTTACCA
1 AAATTACATTTTGACCCTAAAACTTTTCCA
*
30932165 AAATTACATTTTGA-CCTCAAAACTTTACCA
1 AAATTACATTTTGACCCT-AAAACTTTTCCA
* **
30932195 AAATTATATTTTGACCCCGAAACTTTAT-CA
1 AAATTACATTTTGACCCTAAAACTTT-TCCA
*
30932225 AAATTACATTTTGACCCTGAAACTTTTCCA
1 AAATTACATTTTGACCCTAAAACTTTTCCA
30932255 AAATTACATTTTGACCCTAAAACTTTTCCCA
1 AAATTACATTTTGACCCTAAAACTTTT-CCA
* *
30932286 AAATTACATTTTGACCCAAAAACCTTTCCA
1 AAATTACATTTTGACCCTAAAACTTTTCCA
30932316 AAATTACATTTTGA-CCTCAAAACTTTTCCA
1 AAATTACATTTTGACCCT-AAAACTTTTCCA
30932346 AA
1 AA
30932348 TTCCATTCTT
Statistics
Matches: 191, Mismatches: 16, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
29 5 0.03
30 156 0.82
31 30 0.16
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCTAAAACTTTTCCA
Found at i:30939032 original size:16 final size:18
Alignment explanation
Indices: 30939001--30939033 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
30938991 GCAGGAGATG
30939001 TATTAGTATCATGTGTAA
1 TATTAGTATCATGTGTAA
30939019 TATTAGT-T-ATGTGTA
1 TATTAGTATCATGTGTA
30939034 TTACATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (18 bp):
TATTAGTATCATGTGTAA
Found at i:30943385 original size:37 final size:37
Alignment explanation
Indices: 30943335--30943405 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
30943325 TTTTAAGCAC
30943335 ATAATTGGTTGGATTAGTTTTTAACGTCTAAAGGCAT
1 ATAATTGGTTGGATTAGTTTTTAACGTCTAAAGGCAT
30943372 ATAATTGGTTGGATTAGTTTTTAACGTCTAAAGG
1 ATAATTGGTTGGATTAGTTTTTAACGTCTAAAGG
30943406 ACTAATTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (37 bp):
ATAATTGGTTGGATTAGTTTTTAACGTCTAAAGGCAT
Found at i:30946587 original size:18 final size:20
Alignment explanation
Indices: 30946566--30946606 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30946556 AGAAAACTAT
*
30946566 TAATAG-TTTAT-TTTTTAA
1 TAATAGTTTTATAATTTTAA
30946584 TAATAGTTTTATAATTTTAA
1 TAATAGTTTTATAATTTTAA
30946604 TAA
1 TAA
30946607 AATAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATAGTTTTATAATTTTAA
Found at i:30955812 original size:59 final size:59
Alignment explanation
Indices: 30955711--30955963 Score: 334
Period size: 58 Copynumber: 4.3 Consensus size: 59
30955701 TTTGACCTTC
*
30955711 GGGGTAAAACT-GTAATTTTTGGTGAAACCGAGGTTAAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAA-TGGTAATTTTTGGTGAAATCGAGGTT-AAAAATGGGATTTTGGAAAGTTTA
* * * * *
30955771 AGGGTAAAATGGTAATTTTGGGTGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * *
30955830 GGGGTAAATTGGTATTTTTTGGTAAAATCGAGGTT-AAAATAGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
* *
30955888 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
*
30955946 CGGGTCAAAAT-GTAATTT
1 GGGGT-AAAATGGTAATTT
30955964 CTGGACAGTT
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
57 17 0.10
58 63 0.38
59 59 0.35
60 28 0.17
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTA
Found at i:30955897 original size:117 final size:117
Alignment explanation
Indices: 30955726--30955943 Score: 366
Period size: 117 Copynumber: 1.9 Consensus size: 117
30955716 AAAACTGTAA
* *
30955726 TTTTTGGTGAAACCGAGGTTAAAAAATGGGATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTG
1 TTTTTGGTAAAACCGAGGTT-AAAAATAGGATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTT-
30955791 GGTGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTAAATTGGTAT
64 GGTGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTAAATTGGTAT
* *
30955845 TTTTTGGTAAAATCGAGGTT-AAAATAGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGG
1 TTTTTGGTAAAACCGAGGTTAAAAATAGGATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGG
*
30955909 TGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
66 TGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTT
30955944 CACGGGTCAA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
116 36 0.38
117 40 0.43
119 18 0.19
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (117 bp):
TTTTTGGTAAAACCGAGGTTAAAAATAGGATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGG
TGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTAAATTGGTAT
Found at i:30956305 original size:32 final size:33
Alignment explanation
Indices: 30956246--30956307 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
30956236 ATCGGGTCAG
* *
30956246 ATTAAGAATAATTAAAAGTATGAAAAGGACTAA
1 ATTAAGAATAATTAAAAATACGAAAAGGACTAA
30956279 ATTAA-AATAATTAAAAAATACG-AAAGGAC
1 ATTAAGAATAATT-AAAAATACGAAAAGGAC
30956308 CAAACGCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.23
Consensus pattern (33 bp):
ATTAAGAATAATTAAAAATACGAAAAGGACTAA
Found at i:30957830 original size:6 final size:6
Alignment explanation
Indices: 30957810--30957864 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
30957800 TTAATACTAT
* *
30957810 TTTAAA TTT-AA -TTAAA TTTAAA CTTAAA -GTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
30957855 --TAAA TTTAAA
1 TTTAAA TTTAAA
30957865 ATCAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
4 6 0.15
5 8 0.20
6 27 0.66
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:30957858 original size:27 final size:27
Alignment explanation
Indices: 30957812--30957875 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
30957802 AATACTATTT
*
30957812 TAAATTT-AATTAAATTTAAACTTAAAG
1 TAAATTTAAATTAAA-TTAAACTTAAAA
*
30957839 TAAATTTAAATTTAAA-TAAATTTAAAA
1 TAAATTTAAA-TTAAATTAAACTTAAAA
*
30957866 TCAATTTAAA
1 TAAATTTAAA
30957876 CCTCAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 25 0.78
28 2 0.06
29 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAATTTAAATTAAATTAAACTTAAAA
Found at i:30957866 original size:17 final size:16
Alignment explanation
Indices: 30957810--30957864 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
30957800 TTAATACTAT
*
30957810 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
*
30957826 TTTAAACTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
30957843 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
30957859 TTTAAA
1 TTTAAA
30957865 ATCAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 20 0.57
17 15 0.43
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:30960275 original size:17 final size:17
Alignment explanation
Indices: 30960233--30960347 Score: 60
Period size: 17 Copynumber: 6.8 Consensus size: 17
30960223 TTATATTATA
30960233 TAAAA-AATATATAATAT
1 TAAAATAATATA-AATAT
***
30960250 TATTCTAATATAAATAT
1 TAAAATAATATAAATAT
30960267 TAAAATAATATTAAAATGAT
1 TAAAATAATA-T-AAAT-AT
* * *
30960287 T-ATATAAAACAAAT-T
1 TAAAATAATATAAATAT
* * *
30960302 CAATA-AATAAAAATAT
1 TAAAATAATATAAATAT
*
30960318 ATAAAATTAT-TAAATAT
1 -TAAAATAATATAAATAT
30960335 TAAAATAATATAA
1 TAAAATAATATAA
30960348 TATAAATATT
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
15 8 0.11
16 12 0.17
17 30 0.42
18 9 0.12
19 10 0.14
20 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAAATAATATAAATAT
Found at i:30966145 original size:4 final size:4
Alignment explanation
Indices: 30966138--30966163 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30966128 AATAAATAAT
30966138 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
30966164 TACATACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:30971123 original size:2 final size:2
Alignment explanation
Indices: 30971116--30971168 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
30971106 ACTGAAACTA
30971116 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
30971158 AT AT AT -T AT AT
1 AT AT AT AT AT AT
30971169 TCCCATTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30973819 original size:17 final size:17
Alignment explanation
Indices: 30973796--30973834 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
30973786 TTAAATTATT
30973796 ATAAAATATAAGACAAC
1 ATAAAATATAAGACAAC
* *
30973813 TTAAAATATAATACAAC
1 ATAAAATATAAGACAAC
30973830 ATAAA
1 ATAAA
30973835 CATAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (17 bp):
ATAAAATATAAGACAAC
Found at i:30975042 original size:52 final size:52
Alignment explanation
Indices: 30974985--30975084 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
30974975 TCAATACAAT
* * * *
30974985 ATTTAAAAAATTAATC-TTTTTGGATGTTGGGATATTGATGGCCGACACTAAA
1 ATTTAAAAAATTAATCTTTTTTGG-TGTTAGGACACTGATGACCGACACTAAA
30975037 ATTTAAAAAATTAATCTTTTTTGGTGTTAGGACACTGATGACCGACAC
1 ATTTAAAAAATTAATCTTTTTTGGTGTTAGGACACTGATGACCGACAC
30975085 CTTTGTACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 36 0.84
53 7 0.16
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (52 bp):
ATTTAAAAAATTAATCTTTTTTGGTGTTAGGACACTGATGACCGACACTAAA
Found at i:30975263 original size:15 final size:15
Alignment explanation
Indices: 30975243--30975285 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
30975233 TCATTGGATA
30975243 AAAAAAGAAATAATT
1 AAAAAAGAAATAATT
*
30975258 AAAAAAGAAATATTT
1 AAAAAAGAAATAATT
* *
30975273 AAAGAATAAATAA
1 AAAAAAGAAATAA
30975286 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAAAAGAAATAATT
Found at i:30978662 original size:59 final size:57
Alignment explanation
Indices: 30978466--30978662 Score: 191
Period size: 59 Copynumber: 3.4 Consensus size: 57
30978456 TGGTTTTTTA
*
30978466 GGGGTAAAATGGTAATTTTT-GTGAAATCGGGGCTAAAAATGGAATTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTGGAAAGTTTG
* * * * * * *
30978523 GGGAGTAAAATGGTAAATTTTGGTAAAAACAAGGTGAAAAATGAAATTTTGGAAAGTTCG
1 GGG-GTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAA-TTTGGAAAGTTTG
* * * * * *
30978583 GAGGCAAAACGGTGAGTTTTGGTGAAATCGGGATTAAAAATGGGATTTAAGG-AAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGG-TTAAAAATGGAATTT--GGAAAGTTTG
30978642 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
30978663 AAAGTTTCGA
Statistics
Matches: 108, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
57 3 0.03
58 21 0.19
59 68 0.63
60 16 0.15
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTGGAAAGTTTG
Found at i:30978697 original size:30 final size:30
Alignment explanation
Indices: 30978647--30978897 Score: 314
Period size: 30 Copynumber: 8.4 Consensus size: 30
30978637 GTTTGGGGGT
* *
30978647 AAAATGGTAATTTTTG-AAAGTTTCGAGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTTGAGGTC
* *
30978677 AAAATGTAATTTTAGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
30978707 AAAATGTAATTTTGGAAAAGTTTTG-GGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
* *
30978736 AAAATGTAATTTTGAAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
*
30978766 AAAATATAATTTTGGAAAAGTTTTG-GCGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAG-GTC
* *
30978796 AAAATGCAATTTTGG-AAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
*
30978825 -AAATGCAATTTTGGAAAAGTTTTGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
* * *
30978854 AAACTATAATTTTGGAAAAGTTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGA-GGTC
*
30978885 AAAATATAATTTT
1 AAAATGTAATTTT
30978898 TGGACAATTT
Statistics
Matches: 199, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
28 14 0.07
29 63 0.32
30 106 0.53
31 16 0.08
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGAGGTC
Found at i:30978698 original size:59 final size:58
Alignment explanation
Indices: 30978635--30978897 Score: 334
Period size: 59 Copynumber: 4.4 Consensus size: 58
30978625 GGATTTAAGG
* * *
30978635 AAGTTTGGGGGT-AAAATGGTAATTTTTG-AAAGTTTCGAGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAAAAGTTTTG-GGTCAAAATGTAATTTT-GAA
30978694 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGTCAAAATGTAATTTTGAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGTCAAAATGTAATTTTG-AA
* * *
30978753 AAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGCGTCAAAATGCAATTTTGGA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGG-GTCAAAATGTAATTTTGAA
* * *
30978812 AAGTTTTGGGGTC-AAATGCAATTTTGGAAAAGTTTTGAGGTCAAACTATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTG-GGTCAAAATGTAATTTT-GAA
* *
30978871 AAGTTTTTAGGGTCAAAATATAATTTT
1 AAG-TTTTGGGGTCAAAATGTAATTTT
30978898 TGGACAATTT
Statistics
Matches: 181, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
58 36 0.20
59 97 0.54
60 38 0.21
61 10 0.06
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (58 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGTCAAAATGTAATTTTGAA
Found at i:30979800 original size:26 final size:26
Alignment explanation
Indices: 30979747--30979803 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
30979737 TATTATTATC
* * *
30979747 TTTTTAATCTTTTGATTGTTTTTTTT
1 TTTTTAAACTTTTGATTGTTTCTCTT
30979773 TTTTTAAACTTTTGATT-TTTCCTCTT
1 TTTTTAAACTTTTGATTGTTT-CTCTT
30979799 TTTTT
1 TTTTT
30979804 TGAAAGCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (26 bp):
TTTTTAAACTTTTGATTGTTTCTCTT
Found at i:30980485 original size:7 final size:7
Alignment explanation
Indices: 30980473--30980501 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
30980463 TAATGCTTGT
30980473 CTTGTTG
1 CTTGTTG
30980480 CTTGTTG
1 CTTGTTG
30980487 CTTGTTG
1 CTTGTTG
30980494 CTTGTTG
1 CTTGTTG
30980501 C
1 C
30980502 AGGTACCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.28, T:0.55
Consensus pattern (7 bp):
CTTGTTG
Found at i:30980755 original size:6 final size:6
Alignment explanation
Indices: 30980746--30980819 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
30980736 ATTTTTAATG
* * ** * *
30980746 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
30980794 TTAAAT AATTAAAT TTAAAT TTAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT
30980820 AAAATTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.06
6 41 0.76
7 4 0.07
8 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:30980792 original size:17 final size:15
Alignment explanation
Indices: 30980772--30980828 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
30980762 AATTTTTATT
30980772 TAAATTTAAATTCAAA
1 TAAATTTAAATT-AAA
*
30980788 GTAAATTTAAA-TAAT
1 -TAAATTTAAATTAAA
30980803 TAAATTTAAATTTAAA
1 TAAATTTAAA-TTAAA
*
30980819 TAAAATTAAA
1 TAAATTTAAA
30980829 AATCAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 13 0.37
17 10 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
TAAATTTAAATTAAA
Found at i:30980806 original size:31 final size:30
Alignment explanation
Indices: 30980771--30980828 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
30980761 TAATTTTTAT
*
30980771 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAA-TAAAATTAAATAA
*
30980802 TTAAATTTAAATTTAAATAAAATTAAA
1 TTAAATTTAAATTCAAATAAAATTAAA
30980829 AATCAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TTAAATTTAAATTCAAATAAAATTAAATAA
Found at i:30983093 original size:6 final size:6
Alignment explanation
Indices: 30983072--30983145 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
30983062 GCTTAAATTG
* * * *
30983072 ATTTAA ATTT-A TTTTAA ATTTAA ATTTATCT TTTTAA ATTTAA ATTT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA--A ATTTAA ATTTAA ATTTAA
*
30983120 CTTTAA ATTTAA ATTT-A A-TTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
30983146 GAATCAATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.21
6 35 0.67
8 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:30983094 original size:17 final size:17
Alignment explanation
Indices: 30983072--30983145 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
30983062 GCTTAAATTG
30983072 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
30983089 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTA---TTTTAA
**
30983109 ATTTAAATTTGCTTTAA
1 ATTTAAATTTATTTTAA
*
30983126 ATTTAAATTTA-ATTAA
1 ATTTAAATTTATTTTAA
30983142 ATTT
1 ATTT
30983146 GAATCAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.16
17 26 0.52
20 16 0.32
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:30985044 original size:30 final size:30
Alignment explanation
Indices: 30985001--30985152 Score: 148
Period size: 30 Copynumber: 5.0 Consensus size: 30
30984991 AAAAGTCCTT
* * *
30985001 AAACTATCCAAAAATAATATTTTGACCCCA
1 AAACTTTCTAAAAATTATATTTTGACCCCA
30985031 AAACTTTCTAAAAATT-TCATTTTGACCCTC-
1 AAACTTTCTAAAAATTAT-ATTTTGACCC-CA
* *
30985061 AAAC-TTCTCCAAAATTATTTTTTGACCCCA
1 AAACTTTCT-AAAAATTATATTTTGACCCCA
* * * *
30985091 CAACTTTTTGAAAATTATATTTTGACTCCA
1 AAACTTTCTAAAAATTATATTTTGACCCCA
* *
30985121 AAACTTTCTAAAAATTACATTTTTATCCCCA
1 AAACTTTCTAAAAATTATATTTTGA-CCCCA
30985152 A
1 A
30985153 GTTTTCCAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
29 6 0.06
30 83 0.84
31 10 0.10
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
AAACTTTCTAAAAATTATATTTTGACCCCA
Found at i:30985190 original size:29 final size:29
Alignment explanation
Indices: 30985131--30985321 Score: 114
Period size: 29 Copynumber: 6.7 Consensus size: 29
30985121 AAACTTTCTA
* *
30985131 AAAATTA-CATTTTTATCCCC-AAGTTTTCC
1 AAAATTACCATTTTTA-CCCCTGA-TTTACC
*
30985160 AAAATT-CCATTTTTGCCCCTGATTTCACC
1 AAAATTACCATTTTTACCCCTGATTT-ACC
* * **
30985189 AAAATTACC-CTTTTACCCTCAGACTTT-TT
1 AAAATTACCATTTTTACCC-CTGA-TTTACC
* *
30985218 AAAATT-CTATTTTTAACCCTGATTTTACC
1 AAAATTACCATTTTTACCCCTGA-TTTACC
** *
30985247 AAAATTACCA-TTTTACCTTTGAACTTACC
1 AAAATTACCATTTTTACCCCTG-ATTTACC
* *
30985276 AAAATT-CCATTTTGA-CCCTAATTTTACC
1 AAAATTACCATTTTTACCCCTGA-TTTACC
30985304 AAAATTACCA-TTTTACCC
1 AAAATTACCATTTTTACCC
30985322 TCGAACTTTC
Statistics
Matches: 122, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
27 1 0.01
28 34 0.28
29 76 0.62
30 8 0.07
31 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAATTACCATTTTTACCCCTGATTTACC
Found at i:30985203 original size:58 final size:56
Alignment explanation
Indices: 30985131--30985373 Score: 191
Period size: 58 Copynumber: 4.3 Consensus size: 56
30985121 AAACTTTCTA
* *
30985131 AAAATTA-CATTTTTATCCCCAAGTTTTCCAAAATTCCATTTTTGCCCCTGATTTCACC
1 AAAATTACCA-TTTTA-CCCCAA-TTTTCCAAAATTCCATTTTTGACCCTGATTTTACC
* * * *
30985189 AAAATTACCCTTTTACCCTCAGACTTTT-TAAAATTCTATTTTTAACCCTGATTTTACC
1 AAAATTACCATTTTACCC-CA-A-TTTTCCAAAATTCCATTTTTGACCCTGATTTTACC
** * * *
30985247 AAAATTACCATTTTACCTTTGAACTTACCAAAATTCCA-TTTTGACCCTAATTTTACC
1 AAAATTACCATTTTACC--CCAATTTTCCAAAATTCCATTTTTGACCCTGATTTTACC
* * *
30985304 AAAATTACCATTTTACCCTCGAACTTTCC---A--CC-TTTTTGACCC-AATTTCAACC
1 AAAATTACCATTTTACCC-C-AATTTTCCAAAATTCCATTTTTGACCCTGATTT-TACC
30985356 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
30985374 TCGAGTATCC
Statistics
Matches: 155, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
51 5 0.03
52 32 0.21
54 1 0.01
57 46 0.30
58 64 0.41
59 7 0.05
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (56 bp):
AAAATTACCATTTTACCCCAATTTTCCAAAATTCCATTTTTGACCCTGATTTTACC
Found at i:30985313 original size:57 final size:57
Alignment explanation
Indices: 30985155--30985372 Score: 218
Period size: 58 Copynumber: 3.9 Consensus size: 57
30985145 ATCCCCAAGT
* * * * * *
30985155 TTTCCAAAATTCCATTTTTGCCCCTGATTTCACCAAAATTACCCTTTTACCCTCAGAC
1 TTTCCAAAATTCCATTTTTGACCCTAATTTTACCAAAATTACCATTTTACCTTGA-AC
** * * *
30985213 TTTTTAAAATTCTATTTTTAACCCTGATTTTACCAAAATTACCATTTTACCTTTGAAC
1 TTTCCAAAATTCCATTTTTGACCCTAATTTTACCAAAATTACCATTTTACC-TTGAAC
* *
30985271 TTACCAAAATTCCA-TTTTGACCCTAATTTTACCAAAATTACCATTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTGACCCTAATTTTACCAAAATTACCATTTTA-CCTTGAAC
*
30985328 TTTCC---A--CC-TTTTTGACCC-AATTTCAACCAAAATTACCATTTTACC
1 TTTCCAAAATTCCATTTTTGACCCTAATTT-TACCAAAATTACCATTTTACC
30985373 CTCGAGTATC
Statistics
Matches: 138, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
51 7 0.05
52 29 0.21
54 1 0.01
57 41 0.30
58 58 0.42
59 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.39
Consensus pattern (57 bp):
TTTCCAAAATTCCATTTTTGACCCTAATTTTACCAAAATTACCATTTTACCTTGAAC
Found at i:30991508 original size:13 final size:13
Alignment explanation
Indices: 30991492--30991516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30991482 TGTTTCTATT
30991492 TTCTTCTTCTTTC
1 TTCTTCTTCTTTC
30991505 TTCTTCTTCTTT
1 TTCTTCTTCTTT
30991517 TTTTTTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTCTTTC
Found at i:30999515 original size:3 final size:3
Alignment explanation
Indices: 30999507--30999533 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30999497 TAAATAAATA
30999507 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
30999534 GTACATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31037652 original size:13 final size:13
Alignment explanation
Indices: 31037626--31037670 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
31037616 TCCACTATTA
*
31037626 AATTTATTTT-TT
1 AATTTTTTTTCTT
31037638 AATTTTTTTTCTT
1 AATTTTTTTTCTT
*
31037651 AATCTTTTTTCTT
1 AATTTTTTTTCTT
31037664 -ATTTTTT
1 AATTTTTT
31037671 CAACTTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTCTT
Found at i:31039974 original size:26 final size:26
Alignment explanation
Indices: 31039953--31040002 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31039943 TTCAATTTTA
*
31039953 TAACACCATTACTTAGTCCAATTAGT
1 TAACACCATTAATTAGTCCAATTAGT
*
31039979 TAACACCATTAATTATTCCAATTA
1 TAACACCATTAATTAGTCCAATTA
31040003 TCAGGGGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (26 bp):
TAACACCATTAATTAGTCCAATTAGT
Found at i:31048656 original size:20 final size:20
Alignment explanation
Indices: 31048604--31048657 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
31048594 AAAATTGACT
*
31048604 TATTTTAT-AT-TATTTTTA
1 TATTTTATAATATATATTTA
* *
31048622 -ATTTTTTTAAAATATATTTA
1 TA-TTTTATAATATATATTTA
31048642 TATTTTATAATATATA
1 TATTTTATAATATATA
31048658 ATAAATAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 1 0.04
20 19 0.70
21 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATAATATATATTTA
Found at i:31052877 original size:12 final size:12
Alignment explanation
Indices: 31052860--31052884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31052850 GCTTTCACTT
31052860 CCACTTCCGCTA
1 CCACTTCCGCTA
31052872 CCACTTCCGCTA
1 CCACTTCCGCTA
31052884 C
1 C
31052885 TTTCACTACC
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:0.16, C:0.52, G:0.08, T:0.24
Consensus pattern (12 bp):
CCACTTCCGCTA
Found at i:31052886 original size:27 final size:27
Alignment explanation
Indices: 31052856--31052926 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
31052846 CAGTGCTTTC
* *
31052856 ACTTCCACTTCCGCTACCACTTCCGCT
1 ACTTCCACTTCCACTACCACTTCCACT
* * *
31052883 ACTTTCACTACCACTACCGCTTCCACT
1 ACTTCCACTTCCACTACCACTTCCACT
31052910 AC-TCTCACTTCCACTAC
1 ACTTC-CACTTCCACTAC
31052927 TACTACTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.20, C:0.46, G:0.04, T:0.30
Consensus pattern (27 bp):
ACTTCCACTTCCACTACCACTTCCACT
Found at i:31052922 original size:15 final size:15
Alignment explanation
Indices: 31052873--31052927 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
31052863 CTTCCGCTAC
* *
31052873 CACTTCCGCTACTTT
1 CACTTCCACTACTCT
*
31052888 CACTACCACTA--C-
1 CACTTCCACTACTCT
*
31052900 CGCTTCCACTACTCT
1 CACTTCCACTACTCT
31052915 CACTTCCACTACT
1 CACTTCCACTACT
31052928 ACTACTACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 9 0.29
14 1 0.03
15 21 0.68
ACGTcount: A:0.20, C:0.45, G:0.04, T:0.31
Consensus pattern (15 bp):
CACTTCCACTACTCT
Found at i:31062767 original size:43 final size:43
Alignment explanation
Indices: 31062706--31062793 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 43
31062696 GATATCAAAT
*
31062706 TTTCTTTGGTCATTACATCCTAACATATTGTCG-TAAGTAAAAG
1 TTTCTTTGGTCATTACATCCCAACATATTGT-GTTAAGTAAAAG
31062749 TTTCTTTGGTCATTACATCCCAACATATTGTGTTAAGTAAAAG
1 TTTCTTTGGTCATTACATCCCAACATATTGTGTTAAGTAAAAG
31062792 TT
1 TT
31062794 AAAAGTCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (43 bp):
TTTCTTTGGTCATTACATCCCAACATATTGTGTTAAGTAAAAG
Found at i:31066809 original size:29 final size:30
Alignment explanation
Indices: 31066768--31066855 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
31066758 AAATAAAAAA
*
31066768 GGGTTAAAAATGTAA-ATTTGGAAAGTTTAG
1 GGGTT-AAAATGTAATATTTAGAAAGTTTAG
*
31066798 GGGTTAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTTAAAATGTAATATTTAGAAAGTTTAG
* * * *
31066828 GGGTCAAAATATAATTTTTAGGAAGTTT
1 GGGTTAAAATGTAATATTTAGAAAGTTT
31066856 GGAGGCTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 9 0.17
30 43 0.83
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGTTAAAATGTAATATTTAGAAAGTTTAG
Found at i:31067439 original size:10 final size:9
Alignment explanation
Indices: 31067419--31067443 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31067409 CGAAAGGTCA
31067419 TTTTTTATT
1 TTTTTTATT
31067428 TTTTTTATT
1 TTTTTTATT
31067437 TTTTTTA
1 TTTTTTA
31067444 GAAAACTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:31071804 original size:22 final size:22
Alignment explanation
Indices: 31071763--31071824 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
31071753 TATCATTTGT
*
31071763 ATTTGA-ATTTTATAATTTTTTTA
1 ATTTGATA-TTTA-AATTTTTTCA
*
31071786 ATTTGGTATTTAAATTTTTTCA
1 ATTTGATATTTAAATTTTTTCA
*
31071808 ATTTGATATTTTAATTT
1 ATTTGATATTTAAATTT
31071825 AATATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.71
23 9 0.26
24 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (22 bp):
ATTTGATATTTAAATTTTTTCA
Found at i:31071858 original size:53 final size:51
Alignment explanation
Indices: 31071757--31071861 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 51
31071747 TTAATATATC
* * *
31071757 ATTTGTATTTGAATTTTATAATTTTTTTAATTTGGTATTTAAATTTTTTCA
1 ATTTGTATTTGAATTTAATAATTTTTTTAATTTGGTAATGAAATTTTTTCA
* * *
31071808 ATTTGATATTTTAATTTAATATTTTTTTTTAATTTGGTACATGATATTTTTTCA
1 ATTTG-TATTTGAATTTAATA-ATTTTTTTAATTTGGTA-ATGAAATTTTTTCA
31071862 GTTTAATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 5 0.11
52 13 0.29
53 16 0.36
54 11 0.24
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (51 bp):
ATTTGTATTTGAATTTAATAATTTTTTTAATTTGGTAATGAAATTTTTTCA
Found at i:31071878 original size:54 final size:53
Alignment explanation
Indices: 31071778--31071880 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 53
31071768 AATTTTATAA
* * * * *
31071778 TTTTTTTAATTTGGTATTTAAATTTTTTCAATTTGATATTTTAATTTAATATT
1 TTTTTTTAATTTGGTAATGAAATTTTTTCAATTTAATACTTAAATTTAATATT
* *
31071831 TTTTTTTAATTTGGTACATGATATTTTTTCAGTTTAATACTTAAATTTAA
1 TTTTTTTAATTTGGTA-ATGAAATTTTTTCAATTTAATACTTAAATTTAA
31071881 CACCTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 16 0.38
54 26 0.62
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (53 bp):
TTTTTTTAATTTGGTAATGAAATTTTTTCAATTTAATACTTAAATTTAATATT
Found at i:31071889 original size:54 final size:53
Alignment explanation
Indices: 31071778--31071901 Score: 131
Period size: 54 Copynumber: 2.3 Consensus size: 53
31071768 AATTTTATAA
* * * * * * **
31071778 TTTTTTTAATTTGGTATTTAAATTTTTTCAATTTGATATTTTAATTTAATATT
1 TTTTTTTAATTTGGTAATGAAATTTTTTCAATTTAATACTTAAATTTAACACC
* *
31071831 TTTTTTTAATTTGGTACATGATATTTTTTCAGTTTAATACTTAAATTTAACACC
1 TTTTTTTAATTTGGTA-ATGAAATTTTTTCAATTTAATACTTAAATTTAACACC
*
31071885 TTTTTTAAAATTTGGTA
1 TTTTTT-TAATTTGGTA
31071902 TCTAAGTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 16 0.28
54 33 0.57
55 9 0.16
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (53 bp):
TTTTTTTAATTTGGTAATGAAATTTTTTCAATTTAATACTTAAATTTAACACC
Found at i:31072352 original size:23 final size:23
Alignment explanation
Indices: 31072326--31072383 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31072316 AAATTTGATA
*
31072326 AATTAAAAAATTAAATTAAAA-G
1 AATTAAAAAATTAAAATAAAATG
* *
31072348 TAATTAAACATTTAAAATAAAATG
1 -AATTAAAAAATTAAAATAAAATG
*
31072372 AAATAAAAAATT
1 AATTAAAAAATT
31072384 CTATGCTATC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (23 bp):
AATTAAAAAATTAAAATAAAATG
Found at i:31072566 original size:16 final size:15
Alignment explanation
Indices: 31072543--31072595 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
31072533 AATATTTATT
31072543 TAAATAAATATATAC
1 TAAATAAATATATAC
31072558 TAAATTAAATA-A-A-
1 TAAA-TAAATATATAC
31072571 TAAA-AAATATATAC
1 TAAATAAATATATAC
31072585 TAAATTAAATA
1 TAAA-TAAATA
31072596 AATGTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
11 5 0.16
12 1 0.03
13 5 0.16
14 5 0.16
15 5 0.16
16 11 0.34
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAATAAATATATAC
Found at i:31072582 original size:27 final size:28
Alignment explanation
Indices: 31072543--31072598 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
31072533 AATATTTATT
31072543 TAAATAAATATATACTAAATTAAATAAA
1 TAAATAAATATATACTAAATTAAATAAA
31072571 TAAA-AAATATATACTAAATTAAATAAA
1 TAAATAAATATATACTAAATTAAATAAA
31072598 T
1 T
31072599 GTTAAATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAATAAATATATACTAAATTAAATAAA
Found at i:31082278 original size:12 final size:12
Alignment explanation
Indices: 31082263--31082296 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
31082253 AAAATTTACA
31082263 AAAAAAAATTAT
1 AAAAAAAATTAT
31082275 AAAAAAAA-T-T
1 AAAAAAAATTAT
31082285 AAAAAAAATTAT
1 AAAAAAAATTAT
31082297 TAAACAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:31088970 original size:14 final size:14
Alignment explanation
Indices: 31088951--31088992 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
31088941 TCATTTGAAG
*
31088951 AAACAACTAAAACA
1 AAACAACAAAAACA
31088965 AAACAACAAAAACA
1 AAACAACAAAAACA
31088979 AAA-AA-AAAAA-A
1 AAACAACAAAAACA
31088990 AAA
1 AAA
31088993 AAAAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 2 0.07
14 16 0.59
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (14 bp):
AAACAACAAAAACA
Found at i:31093530 original size:20 final size:21
Alignment explanation
Indices: 31093505--31093546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31093495 CAAGCCCATC
*
31093505 TCATTTTA-AAATTTAATAAT
1 TCATTTTAGAAAGTTAATAAT
*
31093525 TCATTTTAGCAAGTTAATAAT
1 TCATTTTAGAAAGTTAATAAT
31093546 T
1 T
31093547 AAGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (21 bp):
TCATTTTAGAAAGTTAATAAT
Found at i:31094978 original size:17 final size:17
Alignment explanation
Indices: 31094948--31094981 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31094938 AATAACCTAA
31094948 ATCTCTTTAATTATATT
1 ATCTCTTTAATTATATT
31094965 ATCT-TTTAAGTTATATT
1 ATCTCTTTAA-TTATATT
31094982 TTTCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (17 bp):
ATCTCTTTAATTATATT
Found at i:31095046 original size:2 final size:2
Alignment explanation
Indices: 31095039--31095066 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31095029 TTAAATCTAC
31095039 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
31095067 TTCGAGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31097428 original size:17 final size:17
Alignment explanation
Indices: 31097384--31097424 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
31097374 TAAAATTTTA
31097384 ATAAA-TAAA-AAATAT
1 ATAAATTAAATAAATAT
*
31097399 ATAAATTTAATAAATAT
1 ATAAATTAAATAAATAT
31097416 -TAAATTAAA
1 ATAAATTAAA
31097425 ATAATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAATTAAATAAATAT
Found at i:31110121 original size:14 final size:15
Alignment explanation
Indices: 31110099--31110127 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31110089 CAAATCCTAC
31110099 ATGACAAAATTTAAA
1 ATGACAAAATTTAAA
31110114 ATGA-AAAATTTAAA
1 ATGACAAAATTTAAA
31110128 TAAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
ATGACAAAATTTAAA
Found at i:31115258 original size:32 final size:31
Alignment explanation
Indices: 31115221--31115314 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 31
31115211 TTTTAAATTT
*
31115221 TTTGGTAGGTCTAATTAAAAATGTTAAAAAAA
1 TTTGGTAGGTCTAATTGAAAAT-TTAAAAAAA
* *
31115253 TTTGGT-GGTTTAA-TGAAAATTTACAAAACA
1 TTTGGTAGGTCTAATTGAAAATTTA-AAAAAA
* *
31115283 TTTTGAAGAGTCTAATTGAAAATTTAAAAAAA
1 TTTGGTAG-GTCTAATTGAAAATTTAAAAAAA
31115315 AAGTCAAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 3 0.06
30 15 0.29
31 7 0.14
32 16 0.31
33 10 0.20
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (31 bp):
TTTGGTAGGTCTAATTGAAAATTTAAAAAAA
Found at i:31128884 original size:15 final size:15
Alignment explanation
Indices: 31128861--31128894 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31128851 CATTGATATC
* *
31128861 TTAATTTTAAGATTT
1 TTAACTTTAAAATTT
31128876 TTAACTTTAAAATTT
1 TTAACTTTAAAATTT
31128891 TTAA
1 TTAA
31128895 GGAGATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAACTTTAAAATTT
Found at i:31129565 original size:31 final size:31
Alignment explanation
Indices: 31129529--31129587 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
31129519 TTAAACATGA
31129529 TAATTATTTTTACATT-GGGACTTGAACTAAG
1 TAATTATTTTTACATTAGGG-CTTGAACTAAG
31129560 TAATTATTTTTACATTAGGGCTTGAACT
1 TAATTATTTTTACATTAGGGCTTGAACT
31129588 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
TAATTATTTTTACATTAGGGCTTGAACTAAG
Found at i:31129753 original size:112 final size:113
Alignment explanation
Indices: 31129553--31129776 Score: 281
Period size: 112 Copynumber: 2.0 Consensus size: 113
31129543 TTGGGACTTG
* * * * * * *
31129553 AACTAAGTAATTATTTTTACATTAGGGCTTGAACTTTTTTTTTTTGTCTAAATTAATCCTTAAAC
1 AACTAAGTAATTATTCTCACATTAAGACTTAAAC--TTTTTCTTTGTCGAAATTAATCCTTAAAC
* *
31129618 TTGACAATTATTATCATATTAGAACCTAAATTTGACAACTGTTCTCACAT
64 TTGACAATTATTACCATATTAGAACCTAAATTTGACAACTATTCTCACAT
*
31129668 AACTAAGTAATTATTCTCACATTAAGACTTAAAC-TTTTCTTTGTCGAAATTAATCCTTAAATTT
1 AACTAAGTAATTATTCTCACATTAAGACTTAAACTTTTTCTTTGTCGAAATTAATCCTTAAACTT
* * * *
31129732 GATAATTGA-TCCCATATTAGAACCTAAGTTTGACAATTATTCTCA
66 GACAATT-ATTACCATATTAGAACCTAAATTTGACAACTATTCTCA
31129777 TATTGTGTGG
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
112 64 0.68
113 1 0.01
115 29 0.31
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (113 bp):
AACTAAGTAATTATTCTCACATTAAGACTTAAACTTTTTCTTTGTCGAAATTAATCCTTAAACTT
GACAATTATTACCATATTAGAACCTAAATTTGACAACTATTCTCACAT
Found at i:31130208 original size:17 final size:17
Alignment explanation
Indices: 31130180--31130223 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
31130170 ATTTCTTCTC
*
31130180 AAAAGTATTTTTGAGAT
1 AAAAATATTTTTGAGAT
31130197 AAAAAATATTTTTGAGAT
1 -AAAAATATTTTTGAGAT
31130215 AAAAATATT
1 AAAAATATT
31130224 ACTAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
AAAAATATTTTTGAGAT
Found at i:31131682 original size:19 final size:21
Alignment explanation
Indices: 31131655--31131702 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
31131645 ATAAAATTAA
31131655 TTTTATAAAAAA-TGTTT-TT
1 TTTTATAAAAAACTGTTTATT
*
31131674 TTTTCTAAAAAACTGTTTATT
1 TTTTATAAAAAACTGTTTATT
31131695 TTTTATAA
1 TTTTATAA
31131703 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 5 0.20
21 9 0.36
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTATAAAAAACTGTTTATT
Found at i:31138402 original size:16 final size:16
Alignment explanation
Indices: 31138383--31138438 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
31138373 AAAGATGGAA
31138383 TTGGTTCGTAAAAGAT
1 TTGGTTCGTAAAAGAT
** *
31138399 TTGGTTTTC-TCAATGGAA
1 TTGG--TTCGT-AAAAGAT
31138417 TTGGTTCGTAAAAGAT
1 TTGGTTCGTAAAAGAT
31138433 TTGGTT
1 TTGGTT
31138439 TTCTCAATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 17 0.57
17 2 0.07
18 11 0.37
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (16 bp):
TTGGTTCGTAAAAGAT
Found at i:31138420 original size:34 final size:34
Alignment explanation
Indices: 31138377--31138453 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
31138367 TAATAAAAAG
31138377 ATGGAATTGGTTCGTAAAAGATTTGGTTTTCTCA
1 ATGGAATTGGTTCGTAAAAGATTTGGTTTTCTCA
31138411 ATGGAATTGGTTCGTAAAAGATTTGGTTTTCTCA
1 ATGGAATTGGTTCGTAAAAGATTTGGTTTTCTCA
31138445 ATGGAATTG
1 ATGGAATTG
31138454 ATATTTCGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
ATGGAATTGGTTCGTAAAAGATTTGGTTTTCTCA
Found at i:31138422 original size:18 final size:18
Alignment explanation
Indices: 31138399--31138453 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
31138389 CGTAAAAGAT
31138399 TTGGTTTTCTCAATGGAA
1 TTGGTTTTCTCAATGGAA
** *
31138417 TTGG--TTCGT-AAAAGAT
1 TTGGTTTTC-TCAATGGAA
31138433 TTGGTTTTCTCAATGGAA
1 TTGGTTTTCTCAATGGAA
31138451 TTG
1 TTG
31138454 ATATTTCGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (18 bp):
TTGGTTTTCTCAATGGAA
Found at i:31143285 original size:23 final size:23
Alignment explanation
Indices: 31143223--31143287 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
31143213 CGACAAATTA
* *
31143223 AAAATATATTAAAA-AATATTAATT
1 AAAATA-ATTAAAAGAA-ATAAATG
**
31143247 AAAATTAATTTTAAGAAATAAATG
1 AAAA-TAATTAAAAGAAATAAATG
31143271 AAAATAATTAAAAGAAA
1 AAAATAATTAAAAGAAA
31143288 AGAACACTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 11 0.33
24 18 0.55
25 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (23 bp):
AAAATAATTAAAAGAAATAAATG
Found at i:31145413 original size:14 final size:12
Alignment explanation
Indices: 31145381--31145406 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31145371 AAATTTCTCA
31145381 AATTATTGATAT
1 AATTATTGATAT
31145393 AATTATTGATAT
1 AATTATTGATAT
31145405 AA
1 AA
31145407 CATTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTATTGATAT
Found at i:31145559 original size:20 final size:20
Alignment explanation
Indices: 31145526--31145563 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31145516 ATAGATTTGA
31145526 ATCACAATTAAATTTTAAAT
1 ATCACAATTAAATTTTAAAT
31145546 ATCA-AATTACAATTTTAA
1 ATCACAATTA-AATTTTAA
31145564 TCAAAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
ATCACAATTAAATTTTAAAT
Found at i:31147301 original size:18 final size:18
Alignment explanation
Indices: 31147278--31147312 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31147268 ATTTGGTACA
31147278 GCAGCATCTGGTGTAACC
1 GCAGCATCTGGTGTAACC
*
31147296 GCAGCATTTGGTGTAAC
1 GCAGCATCTGGTGTAAC
31147313 AACAGCAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (18 bp):
GCAGCATCTGGTGTAACC
Found at i:31147320 original size:21 final size:20
Alignment explanation
Indices: 31147275--31147320 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
31147265 AACATTTGGT
31147275 ACAGCAGCATCTGGTGTAAC
1 ACAGCAGCATCTGGTGTAAC
*
31147295 -C-GCAGCATTTGGTGTAAC
1 ACAGCAGCATCTGGTGTAAC
31147313 AACAGCAG
1 -ACAGCAG
31147321 TTGGCACCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 16 0.73
19 1 0.05
20 1 0.05
21 4 0.18
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (20 bp):
ACAGCAGCATCTGGTGTAAC
Found at i:31147363 original size:63 final size:63
Alignment explanation
Indices: 31147296--31147424 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
31147286 TGGTGTAACC
* *
31147296 GCAGCATTTGGTGTAACAACAGCAGTTGGCACCCTAACATTTGGCACAACAACATTTGGTACA
1 GCAGCATCTGGTGTAACAACAGCAGTTGGCACCCCAACATTTGGCACAACAACATTTGGTACA
* * * * * *
31147359 GCAGCATCTGGTGTAACAGCAGCATTTGGTACCCCAGCATTTGGCACAGCAGCATTTGGTACA
1 GCAGCATCTGGTGTAACAACAGCAGTTGGCACCCCAACATTTGGCACAACAACATTTGGTACA
31147422 GCA
1 GCA
31147425 ACATAGGGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (63 bp):
GCAGCATCTGGTGTAACAACAGCAGTTGGCACCCCAACATTTGGCACAACAACATTTGGTACA
Found at i:31147370 original size:15 final size:15
Alignment explanation
Indices: 31147252--31147424 Score: 96
Period size: 15 Copynumber: 10.9 Consensus size: 15
31147242 AGAACCCCAA
* * *
31147252 CATTTGGCACAACAA
1 CATTTGGTACAGCAG
31147267 CATTTGGTACAGCAG
1 CATTTGGTACAGCAG
* *
31147282 CATCTGGTGTAACCGCAG
1 CAT-TTG-GT-ACAGCAG
*
31147300 CATTTGGTGTAACAACAG
1 CATTT-G-GT-ACAGCAG
* * * *
31147318 CAGTTGGCAC-CCTAA
1 CATTTGGTACAGC-AG
* * *
31147333 CATTTGGCACAACAA
1 CATTTGGTACAGCAG
31147348 CATTTGGTACAGCAG
1 CATTTGGTACAGCAG
*
31147363 CATCTGGTGTAACAGCAG
1 CAT-TTG-GT-ACAGCAG
**
31147381 CATTTGGTACCCCAG
1 CATTTGGTACAGCAG
*
31147396 CATTTGGCACAGCAG
1 CATTTGGTACAGCAG
31147411 CATTTGGTACAGCA
1 CATTTGGTACAGCA
31147425 ACATAGGGTA
Statistics
Matches: 124, Mismatches: 25, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
14 1 0.01
15 74 0.60
16 8 0.06
17 8 0.06
18 33 0.27
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (15 bp):
CATTTGGTACAGCAG
Found at i:31147427 original size:81 final size:81
Alignment explanation
Indices: 31147219--31147388 Score: 279
Period size: 81 Copynumber: 2.1 Consensus size: 81
31147209 GGTACTGCAA
* * * *
31147219 CATTTGGTGTAA-AAGCAGCATTTAGAACCCCAACATTTGGCACAACAACATTTGGTACAGCAGC
1 CATTTGGTGTAACAA-CAGCAGTTGGCACCCTAACATTTGGCACAACAACATTTGGTACAGCAGC
*
31147283 ATCTGGTGTAACCGCAG
65 ATCTGGTGTAACAGCAG
31147300 CATTTGGTGTAACAACAGCAGTTGGCACCCTAACATTTGGCACAACAACATTTGGTACAGCAGCA
1 CATTTGGTGTAACAACAGCAGTTGGCACCCTAACATTTGGCACAACAACATTTGGTACAGCAGCA
31147365 TCTGGTGTAACAGCAG
66 TCTGGTGTAACAGCAG
31147381 CATTTGGT
1 CATTTGGT
31147389 ACCCCAGCAT
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 81 0.98
82 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (81 bp):
CATTTGGTGTAACAACAGCAGTTGGCACCCTAACATTTGGCACAACAACATTTGGTACAGCAGCA
TCTGGTGTAACAGCAG
Found at i:31147601 original size:2 final size:2
Alignment explanation
Indices: 31147594--31147621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31147584 TCATTTTCTA
31147594 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
31147622 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31147626 original size:2 final size:2
Alignment explanation
Indices: 31147621--31147658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31147611 TATATATATA
31147621 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31147659 AAGATGATGA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:31149902 original size:21 final size:21
Alignment explanation
Indices: 31149864--31149903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31149854 AACCTAAAAA
* * *
31149864 GTCAACGGTTAACGGTCAATT
1 GTCAACGATCAACAGTCAATT
31149885 GTCAACGATCAACAGTCAA
1 GTCAACGATCAACAGTCAA
31149904 CAGTAAACGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GTCAACGATCAACAGTCAATT
Found at i:31149913 original size:35 final size:35
Alignment explanation
Indices: 31149863--31149932 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
31149853 CAACCTAAAA
* * * *
31149863 AGTCAACGGTTAACGGTCAATTGTCAACGATCAAC
1 AGTCAACAGTAAACGGTCAACTATCAACGATCAAC
*
31149898 AGTCAACAGTAAACGGTCAACTATCATCGATCAAC
1 AGTCAACAGTAAACGGTCAACTATCAACGATCAAC
31149933 GATCAACGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (35 bp):
AGTCAACAGTAAACGGTCAACTATCAACGATCAAC
Found at i:31150053 original size:24 final size:24
Alignment explanation
Indices: 31149950--31150077 Score: 107
Period size: 24 Copynumber: 5.3 Consensus size: 24
31149940 GGGTCCGGGT
*
31149950 CAGGTTCGGGTC-GAGTTCGATCAA
1 CAGGTTCAGGTCAG-GTTCGATCAA
* * * *
31149974 C-GATTTCAGGTCAAGTTCAATCTA
1 CAG-GTTCAGGTCAGGTTCGATCAA
* * *
31149998 CAGGTTCGGGTCGGGTTCGGTCAA
1 CAGGTTCAGGTCAGGTTCGATCAA
31150022 CAGGTTCAGGTCAGGTTCGATCAA
1 CAGGTTCAGGTCAGGTTCGATCAA
** * * *
31150046 CATATTCAGGCCGGGTTCGATCTA
1 CAGGTTCAGGTCAGGTTCGATCAA
31150070 CAGGTTCA
1 CAGGTTCA
31150078 CTTGATTTGG
Statistics
Matches: 79, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (24 bp):
CAGGTTCAGGTCAGGTTCGATCAA
Found at i:31150797 original size:20 final size:20
Alignment explanation
Indices: 31150761--31150802 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
31150751 TCAAATCCCC
31150761 TAAACTTCTCAAATTTATGAAT
1 TAAACTTCT-AAATTTAT-AAT
31150783 TAAACTTCT-AATTTATAAT
1 TAAACTTCTAAATTTATAAT
31150802 T
1 T
31150803 TCCACAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
22 9 0.45
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAACTTCTAAATTTATAAT
Done.