Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 104 of 328
Found at i:28982542 original size:21 final size:20
Alignment explanation
Indices: 28982516--28982569 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
28982506 CCTTCCACAA
*
28982516 TTTTTTTTTTGTCTTTTTTGT
1 TTTTTTTTTTGAC-TTTTTGT
*
28982537 TTTTTTTTTTCACTTTTTGT
1 TTTTTTTTTTGACTTTTTGT
28982557 TTCTTTCTTTTTG
1 TT-TTT-TTTTTG
28982570 GCTGCCTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 14 0.50
22 5 0.18
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTTGACTTTTTGT
Found at i:28985314 original size:19 final size:19
Alignment explanation
Indices: 28985290--28985335 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28985280 TGTAAAGTTT
* *
28985290 AATGCACATG-ATGCAATG
1 AATGCAAATGCATGAAATG
28985308 CAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
28985328 AATGCAAA
1 AATGCAAA
28985336 AGAAAGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:28985779 original size:32 final size:32
Alignment explanation
Indices: 28985743--28985809 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
28985733 TTTCTTATGA
*
28985743 CAAACTGTTCTATTTAGCAATCAAATATGAAT
1 CAAACTATTCTATTTAGCAATCAAATATGAAT
28985775 CAAACTATTCTATTTAGCAATCAAATATGAAT
1 CAAACTATTCTATTTAGCAATCAAATATGAAT
28985807 CAA
1 CAA
28985810 CACCTCCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.33
Consensus pattern (32 bp):
CAAACTATTCTATTTAGCAATCAAATATGAAT
Found at i:28988209 original size:16 final size:15
Alignment explanation
Indices: 28988189--28988256 Score: 91
Period size: 16 Copynumber: 4.3 Consensus size: 15
28988179 GGGAGGAATG
28988189 GAATAGAGCTGTAAT
1 GAATAGAGCTGTAAT
*
28988204 GTAATAGAGTTGTAAT
1 G-AATAGAGCTGTAAT
28988220 GGAATAGAGCTGTAAT
1 -GAATAGAGCTGTAAT
*
28988236 AGAATAGACCTGTAAT
1 -GAATAGAGCTGTAAT
28988252 GAATA
1 GAATA
28988257 ATTCAGTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.13
16 40 0.85
17 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (15 bp):
GAATAGAGCTGTAAT
Found at i:28988226 original size:32 final size:32
Alignment explanation
Indices: 28988185--28988256 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
28988175 GGTTGGGAGG
**
28988185 AATGGAATAGAGCTGTAAT-GTAATAGAGTTGT
1 AATGGAATAGAGCTGTAATAG-AATAGACCTGT
28988217 AATGGAATAGAGCTGTAATAGAATAGACCTGT
1 AATGGAATAGAGCTGTAATAGAATAGACCTGT
28988249 AAT-GAATA
1 AATGGAATA
28988257 ATTCAGTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 5 0.14
32 31 0.84
33 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (32 bp):
AATGGAATAGAGCTGTAATAGAATAGACCTGT
Found at i:28988472 original size:26 final size:26
Alignment explanation
Indices: 28988417--28988472 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
28988407 TTTTAAATTT
* * * *
28988417 TAATAAAATTATTATTAAATATAATT
1 TAATAAAAATAATAATAAATATAATA
28988443 TAATAAAAATAATAATAAATAATAA-A
1 TAATAAAAATAATAATAAAT-ATAATA
28988469 TAAT
1 TAAT
28988473 TTAATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAAAAATAATAATAAATATAATA
Found at i:29006627 original size:46 final size:44
Alignment explanation
Indices: 29006568--29006682 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
29006558 ACAGGACAGA
* *
29006568 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
29006614 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
29006658 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
29006683 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:29006663 original size:44 final size:45
Alignment explanation
Indices: 29006568--29006701 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
29006558 ACAGGACAGA
* *
29006568 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
29006614 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
29006658 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29006702 CAGATATTGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:29010950 original size:17 final size:18
Alignment explanation
Indices: 29010928--29010961 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29010918 AGTCATATTG
29010928 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
*
29010945 AAATTGTGAAAATTAAA
1 AAATTGCGAAAATTAAA
29010962 ATGGAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:29011711 original size:20 final size:20
Alignment explanation
Indices: 29011682--29011733 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
29011672 AATTAAATTC
29011682 TAAAAGATAAATACAA-ATAAA
1 TAAAA-ATAAATA-AATATAAA
*
29011703 TAAAAATAATTAAATATAAA
1 TAAAAATAAATAAATATAAA
*
29011723 TAAAATTAAAT
1 TAAAAATAAAT
29011734 CCTAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAATAAATAAATATAAA
Found at i:29011721 original size:16 final size:16
Alignment explanation
Indices: 29011688--29011733 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29011678 ATTCTAAAAG
29011688 ATAAATACAAA-TAAAT
1 ATAAATA-AAATTAAAT
*
29011704 A-AAA-ATAATTAAAT
1 ATAAATAAAATTAAAT
29011718 ATAAATAAAATTAAAT
1 ATAAATAAAATTAAAT
29011734 CCTAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 7 0.28
15 6 0.24
16 10 0.40
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATAAAATTAAAT
Found at i:29013465 original size:21 final size:21
Alignment explanation
Indices: 29013439--29013487 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
29013429 AATAATTAAC
*
29013439 TAATAAATAATTAAGATAAAA
1 TAATAAATAATTAAAATAAAA
29013460 TAATAAATAATTAAAATAAAA
1 TAATAAATAATTAAAATAAAA
29013481 TAATAAA
1 TAATAAA
29013488 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATAAATAATTAAAATAAAA
Found at i:29017249 original size:10 final size:10
Alignment explanation
Indices: 29017230--29017279 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
29017220 TTAAATTCTA
29017230 AAAGATAAAT
1 AAAGATAAAT
29017240 ACAA-ATAAAT
1 A-AAGATAAAT
*
29017250 AAAGATAATT
1 AAAGATAAAT
29017260 AAAGATAAAT
1 AAAGATAAAT
29017270 GAAA-ATAAAT
1 -AAAGATAAAT
29017280 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:29020723 original size:15 final size:16
Alignment explanation
Indices: 29020681--29020733 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29020671 AAAAGTGACT
*
29020681 AAAATAGAAACAATCA
1 AAAATAGAAATAATCA
*
29020697 AAAATATG-AATAA-CC
1 AAAATA-GAAATAATCA
*
29020712 AAAATAGAAATAATCT
1 AAAATAGAAATAATCA
29020728 AAAATA
1 AAAATA
29020734 TTAGTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 17 0.55
17 1 0.03
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAATAGAAATAATCA
Found at i:29032484 original size:2 final size:2
Alignment explanation
Indices: 29032472--29032519 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
29032462 GATATTTCTT
*
29032472 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29032514 TA TA TA
1 TA TA TA
29032520 AGCATTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29032814 original size:33 final size:33
Alignment explanation
Indices: 29032772--29032844 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
29032762 TTTGTAATTT
*
29032772 TTTTGTAAAGAATGTTAGCTATGATTTTCATTG
1 TTTTCTAAAGAATGTTAGCTATGATTTTCATTG
29032805 TTTTCTAAAGAATGTTAGCTATGATTTTCATTG
1 TTTTCTAAAGAATGTTAGCTATGATTTTCATTG
29032838 TTTTCTA
1 TTTTCTA
29032845 TTATAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTCTAAAGAATGTTAGCTATGATTTTCATTG
Found at i:29033145 original size:22 final size:22
Alignment explanation
Indices: 29033110--29033152 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29033100 TATTAGTTAC
*
29033110 ATTTTAATTTTTAAT-AATTAT
1 ATTTTAAGTTTTAATGAATTAT
29033131 ATTTTACAGTTTTAATGAATTA
1 ATTTTA-AGTTTTAATGAATTA
29033153 GTTGAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTTAAGTTTTAATGAATTAT
Found at i:29048398 original size:12 final size:13
Alignment explanation
Indices: 29048376--29048408 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29048366 TTATTACAAA
*
29048376 TATTTTAATTAAT
1 TATTATAATTAAT
29048389 TA-TATAATTAAT
1 TATTATAATTAAT
29048401 TATTATAA
1 TATTATAA
29048409 AAATCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATAATTAAT
Found at i:29057055 original size:25 final size:25
Alignment explanation
Indices: 29057018--29057068 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29057008 TTCCTTATAA
* **
29057018 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAAGTAGGAATTAGATTAGG
29057043 ACTTTAAAGTAGGAATTAGATTAGG
1 ACTTTAAAGTAGGAATTAGATTAGG
29057068 A
1 A
29057069 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
ACTTTAAAGTAGGAATTAGATTAGG
Found at i:29061733 original size:25 final size:25
Alignment explanation
Indices: 29061686--29061733 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29061676 TTCCTTATAA
**
29061686 ACTTTAAATTAAGAATTCTATTAAG
1 ACTTTAAATTAAGAATTAGATTAAG
*
29061711 ACTTTAAATTAGGAATTAGATTA
1 ACTTTAAATTAAGAATTAGATTA
29061734 GGATTTTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTAGATTAAG
Found at i:29065558 original size:18 final size:18
Alignment explanation
Indices: 29065499--29065559 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
29065489 TCATTTCCTT
29065499 AAAAAATAAAAGAAATTA
1 AAAAAATAAAAGAAATTA
* **
29065517 AAAATATAAAATG-AATGG
1 AAAAAATAAAA-GAAATTA
29065535 AAAAAATAAAA-AAACTTA
1 AAAAAATAAAAGAAA-TTA
29065553 AAAAAAT
1 AAAAAAT
29065560 TGGTTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 31 0.91
19 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (18 bp):
AAAAAATAAAAGAAATTA
Found at i:29068837 original size:18 final size:18
Alignment explanation
Indices: 29068816--29068875 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
29068806 GCAGTCATGA
* *
29068816 GTGAGCTTGCAGTTTTGG
1 GTGAGCTCGCAGCTTTGG
29068834 GTGAGCTCGCAGCTTT--
1 GTGAGCTCGCAGCTTTGG
* *
29068850 GTAGAGCTCG-AACTTTTG
1 GT-GAGCTCGCAGCTTTGG
29068868 GTGAGCTC
1 GTGAGCTC
29068876 ATAGTCTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 7 0.19
17 13 0.36
18 16 0.44
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (18 bp):
GTGAGCTCGCAGCTTTGG
Found at i:29071729 original size:35 final size:35
Alignment explanation
Indices: 29071685--29071756 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
29071675 GTTTTAGACA
*
29071685 TTACAAATTGGTAAGTCAAAATTTGAACTGTTTTT
1 TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
*
29071720 TTACGAATTGGTAAGTCAAAATTTGAACTATTTTT
1 TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
29071755 TT
1 TT
29071757 CTCTGATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (35 bp):
TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
Found at i:29079269 original size:24 final size:24
Alignment explanation
Indices: 29079241--29079287 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29079231 CGTTTGCTAC
29079241 AAAAATAAATACCGAAATAGGTTTT
1 AAAAA-AAATACCGAAATAGGTTTT
*
29079266 AAAAAAAATACCGAAATGGGTT
1 AAAAAAAATACCGAAATAGGTT
29079288 ATTTGCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (24 bp):
AAAAAAAATACCGAAATAGGTTTT
Found at i:29080711 original size:26 final size:25
Alignment explanation
Indices: 29080681--29080750 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 25
29080671 ATATTCAGTA
29080681 CATGTTATTAATTGTGTTACTACCTT
1 CATGTTATTAATTGTGTTACTACC-T
* *
29080707 CATGTTATTTTAATCGTGTTACTATCT
1 CATGTTA--TTAATTGTGTTACTACCT
*
29080734 CTATGGTATTAATTGTG
1 C-ATGTTATTAATTGTG
29080751 CAGTTCATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 15 0.41
27 2 0.05
28 20 0.54
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.50
Consensus pattern (25 bp):
CATGTTATTAATTGTGTTACTACCT
Found at i:29081997 original size:40 final size:41
Alignment explanation
Indices: 29081953--29082054 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 41
29081943 GCCTGGAGCA
*
29081953 ATTTTGACTTGTTTGAAAATTATTTTGA-TGTG-TTAAAATG
1 ATTTTGACTTGTTTGAAAATTATTTTGACT-TGATTAAAATC
* *
29081993 ATTTTAACTTGGTTG-AAATTATTTTGACTTGATTAAAATC
1 ATTTTGACTTGTTTGAAAATTATTTTGACTTGATTAAAATC
*
29082033 ATTTTGACTTGATTTTAAAATT
1 ATTTTGACTTG-TTTGAAAATT
29082055 GTTTCAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
39 14 0.27
40 31 0.60
41 2 0.04
42 5 0.10
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (41 bp):
ATTTTGACTTGTTTGAAAATTATTTTGACTTGATTAAAATC
Found at i:29082044 original size:20 final size:20
Alignment explanation
Indices: 29081953--29082046 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
29081943 GCCTGGAGCA
*
29081953 ATTTTGACTTGTTTGAAAATT
1 ATTTTGACTTGATT-AAAATT
*
29081974 ATTTTGA-TGTG-TTAAAATG
1 ATTTTGACT-TGATTAAAATT
* * *
29081993 ATTTTAACTTGGTTGAAATT
1 ATTTTGACTTGATTAAAATT
*
29082013 ATTTTGACTTGATTAAAATC
1 ATTTTGACTTGATTAAAATT
29082033 ATTTTGACTTGATT
1 ATTTTGACTTGATT
29082047 TTAAAATTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
19 13 0.21
20 40 0.65
21 9 0.15
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
ATTTTGACTTGATTAAAATT
Found at i:29084455 original size:5 final size:5
Alignment explanation
Indices: 29084445--29084502 Score: 66
Period size: 5 Copynumber: 11.4 Consensus size: 5
29084435 CAAGCTAATT
29084445 AATAA AATAAA AATAA AA-AA AATAA AA-AA AATAAA AATAA AAGTAA
1 AATAA AAT-AA AATAA AATAA AATAA AATAA AAT-AA AATAA AA-TAA
*
29084491 AAGAA AATAA AA
1 AATAA AATAA AA
29084503 ATATTAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 8 0.17
5 23 0.50
6 15 0.33
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:29084459 original size:6 final size:6
Alignment explanation
Indices: 29084448--29084505 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
29084438 GCTAATTAAT
* * *
29084448 AAAATA AAAATA AAAA-A AATAAAA AAAATA AAAATA AAAGT- AAAA-G
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA AAAATA
29084494 AAAATA AAAATA
1 AAAATA AAAATA
29084506 TTAAACAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 10 0.23
6 31 0.70
7 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:29084467 original size:9 final size:9
Alignment explanation
Indices: 29084453--29084503 Score: 66
Period size: 9 Copynumber: 5.2 Consensus size: 9
29084443 TTAATAAAAT
29084453 AAAAATAAA
1 AAAAATAAA
29084462 AAAAATAAA
1 AAAAATAAA
29084471 AAAAATAAAA
1 AAAAAT-AAA
29084481 ATAAAAGTAAA
1 A-AAAA-TAAA
29084492 AGAAAATAAA
1 A-AAAATAAA
29084502 AA
1 AA
29084504 TATTAAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
9 16 0.42
10 9 0.24
11 12 0.32
12 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:29084504 original size:22 final size:20
Alignment explanation
Indices: 29084453--29084505 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
29084443 TTAATAAAAT
29084453 AAAAAT-AAAA-AAAATAAA
1 AAAAATAAAAATAAAATAAA
29084471 AAAAATAAAAATAAAAGTAAA
1 AAAAATAAAAATAAAA-TAAA
29084492 AGAAAATAAAAATA
1 A-AAAATAAAAATA
29084506 TTAAACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.19
19 4 0.13
20 4 0.13
21 5 0.16
22 12 0.39
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAATAAAATAAA
Found at i:29085075 original size:2 final size:2
Alignment explanation
Indices: 29085068--29085097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29085058 TCATTTAACT
29085068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29085098 ACTCATATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29086232 original size:51 final size:51
Alignment explanation
Indices: 29086156--29086274 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
29086146 TCCCAAACTT
* * *
29086156 ACTTCATATTTCATCCGGAATTATTACTTTGTTGTTCTGGCTTCAACAAGA
1 ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
*
29086207 ACTTCATATTTCATCCGG-ATATATTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGAAT-TATTACTTTATTGCTCTAGCTTCAACAAGA
*
29086258 GCTTCATATTTCATCCG
1 ACTTCATATTTCATCCG
29086275 ATTAACTTAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (51 bp):
ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
Found at i:29087195 original size:16 final size:16
Alignment explanation
Indices: 29087157--29087206 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
29087147 TCTATAATTC
*
29087157 ATATTATAACTTAAATA
1 ATATAATAA-TTAAATA
* *
29087174 AAATAATAATTATATA
1 ATATAATAATTAAATA
*
29087190 ATATAATAATTTAATA
1 ATATAATAATTAAATA
29087206 A
1 A
29087207 AGTAAGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATAATTAAATA
Found at i:29096834 original size:46 final size:46
Alignment explanation
Indices: 29096782--29097141 Score: 506
Period size: 46 Copynumber: 7.8 Consensus size: 46
29096772 AGTGTGCTCT
*
29096782 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
29096828 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
29096874 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29096920 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
29096966 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
29097012 GTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGCCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
29097058 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
29097105 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
29097142 TATGACATCA
Statistics
Matches: 296, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 255 0.86
47 41 0.14
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:29098406 original size:16 final size:16
Alignment explanation
Indices: 29098361--29098411 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
29098351 TTATTTATCT
*
29098361 ATAATT-TATATTATA
1 ATAATTATATAATATA
* *
29098376 AT--TTAAATAAAATA
1 ATAATTATATAATATA
29098390 ATAATTATATAATATA
1 ATAATTATATAATATA
29098406 ATAATT
1 ATAATT
29098412 TAGTAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 2 0.07
16 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTATATAATATA
Found at i:29098711 original size:3 final size:3
Alignment explanation
Indices: 29098703--29098823 Score: 77
Period size: 3 Copynumber: 40.3 Consensus size: 3
29098693 GGGTCATTAC
* * **
29098703 AAT AAT AAT AAAT AA- AAT AAT AGT AAC AAT AAT GCT AAT AAAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* * * ** *
29098749 AAT AGT AA- AAA AAT AAT AGT AAT AAT AAT AGG AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
29098796 AAAT AA- AAT ATT GAT AAT AAA AAT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29098824 CAAATAAGTA
Statistics
Matches: 87, Mismatches: 25, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
2 6 0.07
3 72 0.83
4 9 0.10
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:29098830 original size:54 final size:51
Alignment explanation
Indices: 29098703--29098830 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 51
29098693 GGGTCATTAC
* * *
29098703 AATAATAATAAATAAAATAATAGTAACAATAATGCTAATAAATAATAATAGT
1 AATAAAAAT-AATAAAATAATAGGAACAATAATGATAATAAATAATAATAGT
*
29098755 AA-AAAAATAATAGTAATAATAATAGGAATAATAATGATAATAAATAA-AATATTGAT
1 AATAAAAAT-A-A-TAA-AATAATAGGAACAATAATGATAATAAATAATAATA--G-T
29098811 AATAAAAATAATACAAATAA
1 AATAAAAATAATA-AAATAA
29098831 GTATTATGTA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
51 7 0.11
52 3 0.05
53 7 0.11
54 34 0.53
55 3 0.05
56 4 0.06
57 6 0.09
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.27
Consensus pattern (51 bp):
AATAAAAATAATAAAATAATAGGAACAATAATGATAATAAATAATAATAGT
Found at i:29099223 original size:17 final size:15
Alignment explanation
Indices: 29099161--29099228 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 15
29099151 TTAATACATA
29099161 AATATATATAGAGATAT
1 AATATATATA-A-ATAT
29099178 AATATATA-AAATAT
1 AATATATATAAATAT
*
29099192 AATATTAATAGAAATAT
1 AATA-T-ATATAAATAT
29099209 AAATATATAATAAATA-
1 -AATATAT-ATAAATAT
29099225 AATA
1 AATA
29099229 AATAAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
14 8 0.18
15 6 0.13
16 6 0.13
17 21 0.47
18 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (15 bp):
AATATATATAAATAT
Found at i:29099282 original size:3 final size:3
Alignment explanation
Indices: 29099274--29099483 Score: 107
Period size: 3 Copynumber: 72.0 Consensus size: 3
29099264 AGATGAAAAT
* * * * * *
29099274 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ATA ATA ATA ACA AAA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
29099321 AGTA ATA ATA ATA AT- ATG TTAA ATA A-A AAA ATA ACA GTA ACA ATA
1 A-TA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
29099366 AT- TTA A-A AAA GATA ATA ATA A-A AAA ATA A-G ATA ATA ATA AGA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
29099408 ATA AGA ATA A-A ATA ATA AAA ATA ATA AAA ATA ATA AAA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
29099454 AGGA ATA ATA ATA ATA GTA A-A ATA ATA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29099484 GTATATTAAA
Statistics
Matches: 155, Mismatches: 38, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
2 17 0.11
3 131 0.85
4 7 0.05
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:29099296 original size:14 final size:14
Alignment explanation
Indices: 29099279--29099305 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29099269 AAAATATAAT
29099279 AATAGTAATAATAC
1 AATAGTAATAATAC
29099293 AATAGTAATAATA
1 AATAGTAATAATA
29099306 ATAATAACAA
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:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:29099296 original size:17 final size:17
Alignment explanation
Indices: 29099271--29099483 Score: 51
Period size: 17 Copynumber: 13.1 Consensus size: 17
29099261 TATAGATGAA
* *
29099271 AATATAATAATAGTAAT
1 AATACAATAATAATAAT
*
29099288 AATACAATAGTAATAAT
1 AATACAATAATAATAAT
*
29099305 AAT--AATAACAA-AA-
1 AATACAATAATAATAAT
*
29099318 AA-A-AGTAATAATAAT
1 AATACAATAATAATAAT
*** *
29099333 AATATGTTAAATAA-AAA
1 AATACAAT-AATAATAAT
* *
29099350 AATAACAGTAACAATAAT
1 AAT-ACAATAATAATAAT
* * *
29099368 -TTAAAAAAGATAATAAT
1 AATACAATA-ATAATAAT
*
29099385 AA-A-AA-AATAA-GAT
1 AATACAATAATAATAAT
* *
29099398 AATA--ATAAGAATAAG
1 AATACAATAATAATAAT
* *
29099413 AATAAAATAATAAAAAT
1 AATACAATAATAATAAT
* *
29099430 AATAAAAATAATAAAAAT
1 AAT-ACAATAATAATAAT
* *
29099448 AATAAAAGGAATAATAAT
1 AATACAA-TAATAATAAT
*
29099466 AATAGTAA-AATAATAAT
1 AATA-CAATAATAATAAT
29099483 A
1 A
29099484 GTATATTAAA
Statistics
Matches: 147, Mismatches: 31, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
13 13 0.09
14 13 0.09
15 14 0.10
16 6 0.04
17 61 0.41
18 38 0.26
19 2 0.01
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (17 bp):
AATACAATAATAATAAT
Found at i:29099446 original size:71 final size:73
Alignment explanation
Indices: 29099303--29099446 Score: 163
Period size: 74 Copynumber: 2.0 Consensus size: 73
29099293 AATAGTAATA
* * * *
29099303 ATAATAATAACAAAAAAAAGTAATAATAATAATATGTTAAATAAAAAAATAACAGTAACAATAAT
1 ATAATAATAACAAAAAAAAGTAATAATAAGAATAAGTAAAATAAAAAAATAACAGTAAAAATAA-
29099368 TTAAAAAAG
65 TTAAAAAAG
*
29099377 ATAATAATAA-AAAAATAAGATAATAATAAGAATAAGAATAAAATAATAAAAAT-A-A-TAAAAA
1 ATAATAATAACAAAAAAAAG-TAATAATAAGAATAAG--TAAAATAA-AAAAATAACAGTAAAAA
29099438 TAA-TAAAAA
62 TAATTAAAAA
29099447 TAATAAAAGG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
72 6 0.10
73 8 0.13
74 32 0.52
75 1 0.02
76 8 0.13
77 6 0.10
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (73 bp):
ATAATAATAACAAAAAAAAGTAATAATAAGAATAAGTAAAATAAAAAAATAACAGTAAAAATAAT
TAAAAAAG
Found at i:29100201 original size:13 final size:14
Alignment explanation
Indices: 29100177--29100206 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29100167 AGATTCGAAA
29100177 AAAATAAAATAAAG
1 AAAATAAAATAAAG
29100191 AAAAT-AAATAAAG
1 AAAATAAAATAAAG
29100204 AAA
1 AAA
29100207 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAATAAAATAAAG
Found at i:29100207 original size:17 final size:17
Alignment explanation
Indices: 29100173--29100212 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29100163 AAGTAGATTC
*
29100173 GAAAAAAATAAAATAAA
1 GAAAAAAATAAAAGAAA
29100190 GAAAATAAAT-AAAGAAA
1 GAAAA-AAATAAAAGAAA
29100207 GAAAAA
1 GAAAAA
29100213 GAAAAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
GAAAAAAATAAAAGAAA
Found at i:29100670 original size:26 final size:26
Alignment explanation
Indices: 29100647--29100698 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29100637 GGTTGTTTGG
*
29100647 GTTT-GTTTGGGGTTTAGTTGGTTTA
1 GTTTGGTTTGGGGTGTAGTTGGTTTA
*
29100672 GTTTGGTTTTGGGTGTAGTTGGGTTTA
1 GTTTGGTTTGGGGTGTAGTT-GGTTTA
29100699 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 13 0.57
27 6 0.26
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (26 bp):
GTTTGGTTTGGGGTGTAGTTGGTTTA
Found at i:29100705 original size:5 final size:5
Alignment explanation
Indices: 29100695--29100720 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29100685 TGTAGTTGGG
29100695 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
29100721 GGGCCGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:29100707 original size:26 final size:26
Alignment explanation
Indices: 29100647--29100707 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
29100637 GGTTGTTTGG
* *
29100647 GTTTG-TTTGGGGTTTAGTTGGTTTA
1 GTTTGATTTTGGGTGTAGTTGGTTTA
*
29100672 GTTTGGTTTTGGGTGTAGTTGGGTTTA
1 GTTTGATTTTGGGTGTAGTT-GGTTTA
*
29100699 -TTTTATTTT
1 GTTTGATTTT
29100708 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 19 0.63
27 6 0.20
ACGTcount: A:0.08, C:0.00, G:0.33, T:0.59
Consensus pattern (26 bp):
GTTTGATTTTGGGTGTAGTTGGTTTA
Found at i:29103391 original size:21 final size:21
Alignment explanation
Indices: 29103365--29103406 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29103355 TAAATACCTA
*
29103365 GAGTTACTTTCTCTTCATCTT
1 GAGTTACTCTCTCTTCATCTT
*
29103386 GAGTTACTCTCTTTTCATCTT
1 GAGTTACTCTCTCTTCATCTT
29103407 AACTCTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (21 bp):
GAGTTACTCTCTCTTCATCTT
Found at i:29104603 original size:31 final size:31
Alignment explanation
Indices: 29104565--29104627 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29104555 TAAAGTAATA
29104565 AAGTATGTCATCTTTTTCAATTCTTTCTTTC
1 AAGTATGTCATCTTTTTCAATTCTTTCTTTC
29104596 AAGTATGTCATCTTTTTCAATTCTTTCTTTC
1 AAGTATGTCATCTTTTTCAATTCTTTCTTTC
29104627 A
1 A
29104628 CAAGCTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (31 bp):
AAGTATGTCATCTTTTTCAATTCTTTCTTTC
Found at i:29110522 original size:46 final size:45
Alignment explanation
Indices: 29110469--29110591 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 45
29110459 GGGATAGGGT
29110469 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGCA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCGCAG
* *
29110515 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTCG-AG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGAC--ACATCTCGCAG
*
29110561 GCCTATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
29110592 AGCTCTTGTC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
44 12 0.17
45 14 0.20
46 44 0.63
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACACATCTCGCAG
Found at i:29112656 original size:75 final size:76
Alignment explanation
Indices: 29112489--29112656 Score: 200
Period size: 75 Copynumber: 2.2 Consensus size: 76
29112479 CCGTTGGTTG
*
29112489 ACCTGACTAGCGCTGGGTGCAATTTACCGTTGGTATATCCAACTAGAGCTAGGCCTACAATTATT
1 ACCTGACTAGCGCTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCCTACAATTATT
*
29112554 ATCGTCGGTTA
66 ATCGTCGATTA
* ** * *
29112565 ACCTGACTAGCACTGGGTGCAA-ATATTGTTGGTTTATCCAACTAGAGCT-GGGCT-CACATTCA
1 ACCTGACTAGCGCTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCCTACA-ATT-A
29112627 TTA-CTGTCGATTA
64 TTATC-GTCGATTA
* *
29112640 ATCTGACTAACGCTGGG
1 ACCTGACTAGCGCTGGG
29112657 CGTAGCCTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
73 2 0.03
74 8 0.10
75 48 0.61
76 21 0.27
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (76 bp):
ACCTGACTAGCGCTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCCTACAATTATT
ATCGTCGATTA
Found at i:29112861 original size:2 final size:2
Alignment explanation
Indices: 29112854--29112890 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29112844 TACAGGTTAG
29112854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29112891 GTAGAATTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29114636 original size:21 final size:22
Alignment explanation
Indices: 29114612--29114655 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29114602 ATTTAACATC
* *
29114612 AATTTAATCCATTTCATA-CTT
1 AATTCAATCCAATTCATATCTT
29114633 AATTCAATCCAATTCATATCTT
1 AATTCAATCCAATTCATATCTT
29114655 A
1 A
29114656 GGCAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCAATCCAATTCATATCTT
Found at i:29131835 original size:18 final size:18
Alignment explanation
Indices: 29131812--29131846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29131802 TTCATTGCTT
*
29131812 TTCAAAAACATTTCTGGC
1 TTCAAAAACACTTCTGGC
*
29131830 TTCAAAAGCACTTCTGG
1 TTCAAAAACACTTCTGG
29131847 AAGAAAAGCT
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:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (18 bp):
TTCAAAAACACTTCTGGC
Found at i:29132412 original size:13 final size:13
Alignment explanation
Indices: 29132396--29132459 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
29132386 TTTAAACTAA
29132396 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
29132409 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
29132422 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
29132435 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
29132448 ACTTTTCAAAAG
1 ACTTTTCAAAAG
29132460 TAACGAAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:29132435 original size:26 final size:26
Alignment explanation
Indices: 29132396--29132459 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
29132386 TTTAAACTAA
29132396 ACTTTTCAAAAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
* *
29132422 ACTTTTCCACAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
29132448 ACTTTTCAAAAG
1 ACTTTTCAAAAG
29132460 TAACGAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:29135033 original size:45 final size:45
Alignment explanation
Indices: 29134971--29135058 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
29134961 TTAGTTTAAT
* *
29134971 AGATTTCTAGATCTTTTAGCTGAATTAAGTTTTAAGTTTAAATTA
1 AGATTTCTACATCTTTTAGCTCAATTAAGTTTTAAGTTTAAATTA
*
29135016 AGATTT-TACATCTTTTTATCTCAATTAAGTTTTAAGTTTAAAT
1 AGATTTCTACATC-TTTTAGCTCAATTAAGTTTTAAGTTTAAAT
29135059 CTTTAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 5 0.13
45 34 0.87
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (45 bp):
AGATTTCTACATCTTTTAGCTCAATTAAGTTTTAAGTTTAAATTA
Found at i:29138034 original size:18 final size:17
Alignment explanation
Indices: 29138011--29138057 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
29138001 ATGGTAAGGG
*
29138011 TTAATTTTTTAATATTAT
1 TTAATTTTTTAAT-TTAA
29138029 TTAATTTTTATAATTTAA
1 TTAATTTTT-TAATTTAA
29138047 TTAATATTTTT
1 TTAAT-TTTTT
29138058 TATGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTAATTTAA
Found at i:29140128 original size:59 final size:58
Alignment explanation
Indices: 29139989--29140184 Score: 274
Period size: 59 Copynumber: 3.4 Consensus size: 58
29139979 ATTGGTTTAT
*
29139989 TTTTGAATATTTTTGTACAAATTGTTTTTATATTGTTCCATTTAATAAAAT---AGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTT-CATTTAATAAAATAGAAGTTC
*
29140045 TTTTGAATATTTTTGTACAAATTATTTTAATATTGCTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTG-TTCATTTAATAAAATAGAAGTTC
** *
29140104 TTTTGAATATTTTCATACATATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTG-TTCATTTAATAAAATAGAAGTTC
*
29140163 TTTGGAATATTTTT-TAACAAAT
1 TTTTGAATATTTTTGT-ACAAAT
29140185 ATACTACTAA
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
56 46 0.37
57 2 0.02
58 1 0.01
59 76 0.61
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.52
Consensus pattern (58 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTCATTTAATAAAATAGAAGTTC
Found at i:29140502 original size:67 final size:64
Alignment explanation
Indices: 29140362--29140503 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 64
29140352 TTTAAACTGT
*
29140362 AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
1 AAAACCCTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
* * * *
29140426 AAAATCCTAAACAATTAAAAACTTGATACCTTAATTTAAT-TTTTTTTCTAAATCCTAATCAAAC
1 AAAACCCTAAACAATTAAAAAC-TAATACCCT-ATTT--TGTTTTTTTCTAAACCCTAATCAAAC
*
29140490 ATC-
62 -CCA
29140493 AAAACCCTAAA
1 AAAACCCTAAA
29140504 TCTAGGCCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
64 20 0.30
65 7 0.11
66 4 0.06
67 33 0.50
68 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.33
Consensus pattern (64 bp):
AAAACCCTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
Found at i:29142287 original size:3 final size:3
Alignment explanation
Indices: 29142281--29142333 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
29142271 AAGAAAGGGA
29142281 AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29142328 AAG AAG
1 AAG AAG
29142334 GAGGAGGAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29142906 original size:16 final size:15
Alignment explanation
Indices: 29142887--29142929 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29142877 ATATCTTAAT
*
29142887 GAAAAAATAAAATAC
1 GAAAAAATAAAACAC
29142902 GGAAAGAAATAAAACAC
1 -GAAA-AAATAAAACAC
29142919 GAAAATAATAA
1 GAAAA-AATAA
29142930 CTTTTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 10 0.42
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.12
Consensus pattern (15 bp):
GAAAAAATAAAACAC
Found at i:29143137 original size:25 final size:25
Alignment explanation
Indices: 29143109--29143184 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 25
29143099 ATTATGTACT
29143109 AAAATAATATAAAAAATAAAATACG
1 AAAATAATATAAAAAATAAAATACG
*
29143134 AAAATAGCATATTTTAAAAAATAAAATCCG
1 AAAATA--ATA---TAAAAAATAAAATACG
* *
29143164 AAAATAAAATAAATAATAAAA
1 AAAATAATATAAAAAATAAAA
29143185 ACAAAGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 17 0.40
27 3 0.07
28 2 0.05
30 21 0.49
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.22
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATACG
Found at i:29143339 original size:152 final size:155
Alignment explanation
Indices: 29142961--29143618 Score: 969
Period size: 152 Copynumber: 4.4 Consensus size: 155
29142951 TGGCGGTTTT
* ** *
29142961 TACTAAAATAATAT--AAAATAAAATACAAAAATAGTTTATTTTAAAAAATAAAATACGAAAAT-
1 TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
*
29143023 --A-AAA-AAT-AAAA-AAA-GGCCAAAACCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
66 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
*
29143081 AAATAATACATTT-AAAACATTATG
131 AAATAATACATTTGAAACCATTATG
**
29143105 TACTAAAATAATATAAAAAATAAAATACGAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
1 TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
* *
29143170 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTAC-AAATTTATATAAAAAATACTA
66 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
29143234 AAATAATACATTTGAAACCATTATG
131 AAATAATACATTTGAAACCATTATG
* * *
29143259 TACTAAAATAATAT-AAAAATAAAA-AAAAAAATAACATATTTTAAAAAATAAAATCTGAAAATA
1 TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
29143322 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAAACAC
66 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATAT--AAAAAACAC
*
29143387 TAAAATAATACATTCG-AACCATTATG
129 TAAAATAATACATTTGAAACCATTATG
* * * *
29143413 TACTAAAATAATATAAAAAATAAAATATGAAGATAGTATATTTTAAAAAATAAAATCCAAAAATA
1 TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
29143478 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAACACTA
66 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
29143542 AAATAATACATTTGAAA--ATTATG
131 AAATAATACATTTGAAACCATTATG
* * *
29143565 TATTAAAATAATATAAAAAATAATAT-TAAAAA-AGTATATTTTAAAAAATAAAAT
1 TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAAT
29143619 AAATACCAAA
Statistics
Matches: 470, Mismatches: 27, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
144 14 0.03
146 44 0.09
149 1 0.00
150 25 0.05
151 7 0.01
152 112 0.24
153 77 0.16
154 71 0.15
155 33 0.07
156 86 0.18
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (155 bp):
TACTAAAATAATATAAAAAATAAAATATAAAAATAGCATATTTTAAAAAATAAAATCCGAAAATA
AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
AAATAATACATTTGAAACCATTATG
Found at i:29143509 original size:308 final size:301
Alignment explanation
Indices: 29143018--29143618 Score: 954
Period size: 308 Copynumber: 2.0 Consensus size: 301
29143008 ATAAAATACG
29143018 AAAATAAAAAATAAAAAAAGGCCAAAACCAGAGTTTTTTACTAAATTAATATAAAAAACACTAAA
1 AAAATAAAAAATAAAAAAAGGCCAAAACCAGAGTTTTTTACTAAATTAATATAAAAAACACTAAA
*
29143083 ATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGCATATTT
66 ATAATACATTCAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGCATATTT
*
29143148 TAAAAAATAAAATCCGAAAATAAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTAC
131 TAAAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTAC
* *
29143213 -AAATTTATATAAAAAATACTAAAATAATACATTTGAAACCATTATGTACTAAAATAATAT-AAA
196 TAAATTAATAT-AAAAACACTAAAATAATACATTTGAAA--ATTATGTACTAAAATAATATAAAA
29143276 AATAAAAAAAAAAATAACATATTTTAAAAAATAAAATCTGAAAAT
258 AATAAAAAAAAAAA-AACATATTTTAAAAAATAAAATCTGAAAAT
* *
29143321 AAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAAACA
1 AAAATAAAAAAT-AAAA-AAA-GGCCAAAACCAGAGTTTTTTACTAAATTAATAT--AAAAAACA
* * * * *
29143386 CTAAAATAATACATTCGAACCATTATGTACTAAAATAATATAAAAAATAAAATATGAAGATAGTA
61 CTAAAATAATACATTCAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGCA
29143451 TATTTTAAAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTT
126 TATTTTAAAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTT
*
29143516 TTTACTAAATTAATATAAAAACACTAAAATAATACATTTGAAAATTATGTATTAAAATAATATAA
191 TTTACTAAATTAATATAAAAACACTAAAATAATACATTTGAAAATTATGTACTAAAATAATATAA
* ** **
29143581 AAAATAATATTAAAAAAGTATATTTTAAAAAATAAAAT
256 AAAATAAAAAAAAAAAAACATATTTTAAAAAATAAAAT
29143619 AAATACCAAA
Statistics
Matches: 274, Mismatches: 17, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
303 11 0.04
304 4 0.01
305 3 0.01
306 71 0.26
307 14 0.05
308 162 0.59
309 9 0.03
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (301 bp):
AAAATAAAAAATAAAAAAAGGCCAAAACCAGAGTTTTTTACTAAATTAATATAAAAAACACTAAA
ATAATACATTCAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGCATATTT
TAAAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTAC
TAAATTAATATAAAAACACTAAAATAATACATTTGAAAATTATGTACTAAAATAATATAAAAAAT
AAAAAAAAAAAAACATATTTTAAAAAATAAAATCTGAAAAT
Found at i:29143586 original size:12 final size:12
Alignment explanation
Indices: 29143569--29143621 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
29143559 ATTATGTATT
29143569 AAAATAATATAA
1 AAAATAATATAA
29143581 AAAATAATATTAA
1 AAAATAATA-TAA
*
29143594 AAAAGTATATTTTAA
1 AAAA-TA-A-TATAA
*
29143609 AAAATAAAATAA
1 AAAATAATATAA
29143621 A
1 A
29143622 TACCAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
12 13 0.38
13 8 0.24
14 4 0.12
15 8 0.24
16 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:29143608 original size:15 final size:13
Alignment explanation
Indices: 29143569--29143615 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 13
29143559 ATTATGTATT
29143569 AAAATAATA-TAA
1 AAAATAATATTAA
29143581 AAAATAATATTAA
1 AAAATAATATTAA
*
29143594 AAAAGTATATTTTAA
1 AAAA-TA-ATATTAA
29143609 AAAATAA
1 AAAATAA
29143616 AATAAATACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 9 0.29
13 8 0.26
14 4 0.13
15 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
AAAATAATATTAA
Found at i:29150155 original size:27 final size:27
Alignment explanation
Indices: 29150103--29150156 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
29150093 GCCCACCGTT
*
29150103 GGTGCCGCCTATGATTATCCCACAACC
1 GGTGCCGCCTATGATGATCCCACAACC
*
29150130 GGTGCCGCCTATGA-GATGCCCTCAACC
1 GGTGCCGCCTATGATGAT-CCCACAACC
29150157 CATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTATGATGATCCCACAACC
Found at i:29153720 original size:45 final size:45
Alignment explanation
Indices: 29153645--29153763 Score: 152
Period size: 45 Copynumber: 2.7 Consensus size: 45
29153635 GGAATTAAGA
* *
29153645 AATCCGAGCTCGTTGAG-TGGTCCGAGTTCGTGATATATGTG-AG
1 AATCCGAACTCATTGAGTTGGTCCGAGTTCGTGATATATGTGAAG
* * *
29153688 AAATCTGAACTTATTGAGTTGGTCCAAGTTCGTGATATATGTGAAG
1 -AATCCGAACTCATTGAGTTGGTCCGAGTTCGTGATATATGTGAAG
* *
29153734 CATCCGAACTCGTTGAGTTGGTCCGAGTTC
1 AATCCGAACTCATTGAGTTGGTCCGAGTTC
29153764 ATTATGGATG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 13 0.21
45 48 0.76
46 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (45 bp):
AATCCGAACTCATTGAGTTGGTCCGAGTTCGTGATATATGTGAAG
Found at i:29155167 original size:28 final size:29
Alignment explanation
Indices: 29155127--29155181 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
29155117 CATGGGCGAT
29155127 GACACGGGCGTGT-CTAGGCAGTGTGAGG
1 GACACGGGCGTGTGCTAGGCAGTGTGAGG
* * *
29155155 GACACGGTCGTGTGCTCGGCCGTGTGA
1 GACACGGGCGTGTGCTAGGCAGTGTGA
29155182 AAACCTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.15, C:0.22, G:0.44, T:0.20
Consensus pattern (29 bp):
GACACGGGCGTGTGCTAGGCAGTGTGAGG
Found at i:29164353 original size:14 final size:15
Alignment explanation
Indices: 29164331--29164417 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
29164321 CGTCACTCTA
29164331 CTAGCAGAGTGA-G-G
1 CTAG-AGAGTGACGAG
29164345 CTAGTAGAGTGACGAG
1 CTAG-AGAGTGACGAG
*
29164361 CTAGAGAGTGGCGAG
1 CTAGAGAGTGACGAG
* *
29164376 TTAGCGAG-GAGGCGAG
1 CTAGAGAGTGA--CGAG
* *
29164392 CTAGCAGAGTGGCAAG
1 CTAG-AGAGTGACGAG
*
29164408 CTAGAAAGTG
1 CTAGAGAGTG
29164418 GTGAGCTAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
14 12 0.21
15 22 0.39
16 19 0.33
17 3 0.05
18 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.41, T:0.15
Consensus pattern (15 bp):
CTAGAGAGTGACGAG
Found at i:29164409 original size:16 final size:16
Alignment explanation
Indices: 29164331--29164592 Score: 144
Period size: 16 Copynumber: 16.4 Consensus size: 16
29164321 CGTCACTCTA
*
29164331 CTAGCAGAGT-GAG-G
1 CTAGCAGAGTGGCGAG
* *
29164345 CTAGTAGAGTGACGAG
1 CTAGCAGAGTGGCGAG
29164361 CTAG-AGAGTGGCGAG
1 CTAGCAGAGTGGCGAG
* *
29164376 TTAGC-GAGGAGGCGAG
1 CTAGCAGA-GTGGCGAG
*
29164392 CTAGCAGAGTGGCAAG
1 CTAGCAGAGTGGCGAG
* *
29164408 CTAG-AAAGTGGTGAG
1 CTAGCAGAGTGGCGAG
* * *
29164423 CTAACAGGGTAGCGAG
1 CTAGCAGAGTGGCGAG
* ***
29164439 CTAGCAGACAATTATGAG
1 CTAGCAG--AGTGGCGAG
* **
29164457 CTAGTAGAGTGGTAAG
1 CTAGCAGAGTGGCGAG
*
29164473 CTAGCAGACAGTGACGAG
1 CTAGCAG--AGTGGCGAG
*
29164491 CTAGTAGAGTGGCGAG
1 CTAGCAGAGTGGCGAG
* *
29164507 CTAGC-GAGGAGGTGAG
1 CTAGCAGA-GTGGCGAG
*
29164523 CTAGCAGAGTGGTGAG
1 CTAGCAGAGTGGCGAG
* *
29164539 CTAG-TGAGGAGGCGAG
1 CTAGCAGA-GTGGCGAG
* *
29164555 CTAGCA-ATGAGGTGAG
1 CTAGCAGA-GTGGCGAG
*
29164571 CTAGCAGGGTGGCGAG
1 CTAGCAGAGTGGCGAG
29164587 CTAGCA
1 CTAGCA
29164593 AAGCGTCGCA
Statistics
Matches: 186, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
14 9 0.05
15 31 0.17
16 120 0.65
17 4 0.02
18 22 0.12
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.16
Consensus pattern (16 bp):
CTAGCAGAGTGGCGAG
Found at i:29164475 original size:34 final size:34
Alignment explanation
Indices: 29164437--29164511 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
29164427 CAGGGTAGCG
* * *
29164437 AGCTAGCAGACAATTATGAGCTAGTAGAGTGGTA
1 AGCTAGCAGACAATGACGAGCTAGTAGAGTGGCA
* *
29164471 AGCTAGCAGACAGTGACGAGCTAGTAGAGTGGCG
1 AGCTAGCAGACAATGACGAGCTAGTAGAGTGGCA
29164505 AGCTAGC
1 AGCTAGC
29164512 GAGGAGGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (34 bp):
AGCTAGCAGACAATGACGAGCTAGTAGAGTGGCA
Found at i:29166019 original size:18 final size:18
Alignment explanation
Indices: 29165977--29166079 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 18
29165967 GAAAAAAATC
*
29165977 TTTAGAAAAATA-TAAAA
1 TTTATAAAAATATTAAAA
* * *
29165994 ATTGTAAAAATATTTAAA
1 TTTATAAAAATATTAAAA
29166012 -TTATTAAAAATATTAAAA
1 TTTA-TAAAAATATTAAAA
*
29166030 TTTATAAAAATA--AATA
1 TTTATAAAAATATTAAAA
29166046 TTT-TAAATAATAATTAAATA
1 TTTATAAA-AAT-ATTAAA-A
* *
29166066 TTTTTAAGAATATT
1 TTTATAAAAATATT
29166080 TTAAAATTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
15 4 0.06
16 9 0.13
17 12 0.18
18 25 0.37
19 8 0.12
20 7 0.10
21 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTATAAAAATATTAAAA
Found at i:29166077 original size:20 final size:20
Alignment explanation
Indices: 29166040--29166077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29166030 TTTATAAAAA
*
29166040 TAAATATTTTAAATAATAAT
1 TAAATATTTTAAAGAATAAT
*
29166060 TAAATATTTTTAAGAATA
1 TAAATATTTTAAAGAATA
29166078 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAATATTTTAAAGAATAAT
Found at i:29166153 original size:20 final size:21
Alignment explanation
Indices: 29166128--29166171 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29166118 TTTTTAAAAT
29166128 TTATT-AAAAACTGCAAATAA
1 TTATTAAAAAACTGCAAATAA
* *
29166148 TTATTAAAAAATTGTAAATAA
1 TTATTAAAAAACTGCAAATAA
29166169 TTA
1 TTA
29166172 ACTAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
TTATTAAAAAACTGCAAATAA
Found at i:29166445 original size:19 final size:19
Alignment explanation
Indices: 29166401--29166531 Score: 100
Period size: 19 Copynumber: 6.6 Consensus size: 19
29166391 TTAAATAATT
*
29166401 TTTTAATAATTATTTACAAT
1 TTTTAATAATT-TTTACAAA
**
29166421 TTTTAATAATTTTCCCAAA
1 TTTTAATAATTTTTACAAA
29166440 TTTTAATAATTTTTACAAA
1 TTTTAATAATTTTTACAAA
* ** *
29166459 TTTTAAAAAATGTTTTGTAAT
1 TTTT-AATAAT-TTTTACAAA
**
29166480 TTTTAATAATTTTTTTAAGA
1 TTTTAATAATTTTTACAA-A
* * *
29166500 TTTTAAGTTATTTTCAAAAA
1 TTTTAA-TAATTTTTACAAA
29166520 TATTTAATAATT
1 T-TTTAATAATT
29166532 ATTTGAAATA
Statistics
Matches: 89, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
19 33 0.37
20 33 0.37
21 23 0.26
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAATAATTTTTACAAA
Found at i:29166491 original size:10 final size:10
Alignment explanation
Indices: 29166386--29166577 Score: 75
Period size: 10 Copynumber: 19.5 Consensus size: 10
29166376 CCACCAATTC
29166386 AATTTTTAAAT
1 AATTTTT-AAT
29166397 AATTTTTTAAT
1 AA-TTTTTAAT
*
29166408 AATTATTT-AC
1 AATT-TTTAAT
29166418 AATTTTTAAT
1 AATTTTTAAT
**
29166428 AATTTTCCCA-
1 AATTTT-TAAT
29166438 AA-TTTTAAT
1 AATTTTTAAT
29166447 AATTTTTACA-
1 AATTTTTA-AT
* *
29166457 AATTTTAAAA
1 AATTTTTAAT
*
29166467 AATGTTTT-GT
1 AAT-TTTTAAT
29166477 AATTTTTAAT
1 AATTTTTAAT
*
29166487 AATTTTT-TT
1 AATTTTTAAT
*
29166496 AAGATTTTAAGT
1 AA-TTTTTAA-T
* * *
29166508 TATTTTCAAA
1 AATTTTTAAT
*
29166518 AATATTTAAT
1 AATTTTTAAT
*
29166528 AATTATTTGA-
1 AATT-TTTAAT
*
29166538 AA-TATT--T
1 AATTTTTAAT
29166545 AATTTTT-AT
1 AATTTTTAAT
*
29166554 AATTTTTTAT
1 AATTTTTAAT
*
29166564 -TTTTTTAAT
1 AATTTTTAAT
29166573 AATTT
1 AATTT
29166578 AAATATTTTT
Statistics
Matches: 133, Mismatches: 29, Indels: 39
0.66 0.14 0.19
Matches are distributed among these distances:
7 2 0.02
8 6 0.05
9 32 0.24
10 62 0.47
11 24 0.18
12 7 0.05
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:29168153 original size:27 final size:28
Alignment explanation
Indices: 29168123--29168175 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
29168113 AAAAAACCTT
29168123 AAAAACCT-TTAAAAATA-AAAAAAATA
1 AAAAACCTATTAAAAATAGAAAAAAATA
**
29168149 AAAAATTTATTAAAAATAGAAAAAAAT
1 AAAAACCTATTAAAAATAGAAAAAAAT
29168176 GAAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAAACCTATTAAAAATAGAAAAAAATA
Found at i:29171198 original size:62 final size:58
Alignment explanation
Indices: 29171132--29171291 Score: 175
Period size: 57 Copynumber: 2.7 Consensus size: 58
29171122 TTTTAATAAG
* * *
29171132 ATTATTATTAAATATAATTTAATAATAAATAATAATAAATAATTTAATCATATTTTAACAT
1 ATTATTATTAAATATAATTTAATAA-AAATAATAAT-AATAATTTAATAACATTCTAA-AT
* *
29171193 AATTATTATTAAATACAATTTAAT-AAAATAAT-AT-ATAATTTAATAACATTCTCAAT
1 -ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
*
29171249 ATTATTATTAAAATATGAA-TTAATAAAAATCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAATA-ATAAT
29171292 ATTATAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
55 9 0.11
56 12 0.14
57 25 0.29
58 2 0.02
59 2 0.02
60 12 0.14
61 1 0.01
62 22 0.26
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
Found at i:29171288 original size:24 final size:23
Alignment explanation
Indices: 29171261--29171310 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
29171251 TATTATTAAA
*
29171261 ATATGAAT-TAATAAAAATCATAAT
1 ATAT-AATATAATAAAAATAAT-AT
*
29171285 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
29171308 ATA
1 ATA
29171311 ACTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:29172346 original size:43 final size:43
Alignment explanation
Indices: 29172286--29172441 Score: 224
Period size: 43 Copynumber: 3.7 Consensus size: 43
29172276 AAAAAAAACT
* *
29172286 CCGCT-AAAGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCA
1 CCGCTAAAAGTCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
* *
29172328 CCGCTAAAAGTCATGGCTTTTAGTGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAAGTCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
* * * *
29172371 CCGCTAAAAATCACGGCTTTTAGCAGCATTTATGGGAAAAGCG
1 CCGCTAAAAGTCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
*
29172414 CCGCTAAAAGTCACGTCTTTTAGCGGCG
1 CCGCTAAAAGTCACGGCTTTTAGCGGCG
29172442 CTTTTTCTAC
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 5 0.05
43 95 0.95
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (43 bp):
CCGCTAAAAGTCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
Found at i:29172550 original size:31 final size:31
Alignment explanation
Indices: 29172515--29172581 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
29172505 CTTCCTACAT
* *
29172515 TAAAATCCAACTAAATACAACAAATATAGTA
1 TAAAATCCAACTAAAAACAACAAATATAGCA
* * * *
29172546 TAAAATGCAGCTAAAAACAGCAAATTTAGCA
1 TAAAATCCAACTAAAAACAACAAATATAGCA
29172577 TAAAA
1 TAAAA
29172582 ATACAACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.21
Consensus pattern (31 bp):
TAAAATCCAACTAAAAACAACAAATATAGCA
Found at i:29173350 original size:46 final size:46
Alignment explanation
Indices: 29173297--29173391 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
29173287 TGATGAATTG
29173297 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATAAATCA
1 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATAAATCA
*
29173343 AATTAAACAATTATCATTAAAGATTATAAATATTTAGAATAAATCA
1 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATAAATCA
29173389 AAT
1 AAT
29173392 ATTATTAAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (46 bp):
AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATAAATCA
Found at i:29178517 original size:9 final size:9
Alignment explanation
Indices: 29178505--29178563 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
29178495 TCCGTAAGTT
*
29178505 GTTATGTAC
1 GTTATGTAA
*
29178514 GTTATGTGA
1 GTTATGTAA
29178523 GTTATGTAA
1 GTTATGTAA
*
29178532 ATTATGTAA
1 GTTATGTAA
*
29178541 GTTATGTGA
1 GTTATGTAA
29178550 GTTATGTAA
1 GTTATGTAA
29178559 GTTAT
1 GTTAT
29178564 TTTTTAAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:29178537 original size:27 final size:27
Alignment explanation
Indices: 29178506--29178563 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
29178496 CCGTAAGTTG
*
29178506 TTATGTACGTTATGTGAGTTATGTAAA
1 TTATGTAAGTTATGTGAGTTATGTAAA
*
29178533 TTATGTAAGTTATGTGAGTTATGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAAA
29178560 TTAT
1 TTAT
29178564 TTTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATGTGAGTTATGTAAA
Found at i:29178985 original size:241 final size:241
Alignment explanation
Indices: 29178562--29178995 Score: 789
Period size: 241 Copynumber: 1.8 Consensus size: 241
29178552 TATGTAAGTT
*
29178562 ATTTTTTAAGATTCATCATACGTGGCATTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
1 ATTTTTTAAGATTCATCATACGTGGCATTGTTACACCTAGGGAGGATCCATTATATCTTACAACT
29178627 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
66 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
*
29178692 GGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATGGTAATAAATA
131 GGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATAGTAATAAATA
29178757 TTCAATAGTAAATGAGCTCAATAGAACTTTTTTCAAGTCTTTTGGA
196 TTCAATAGTAAATGAGCTCAATAGAACTTTTTTCAAGTCTTTTGGA
* *
29178803 ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACTTAAGGG-GGATCCATTATATCTTACAAC
1 ATTTTTTAAGATTCATCATACGTGGCATTGTTACACCT-AGGGAGGATCCATTATATCTTACAAC
29178867 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAA
65 TCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAA
* * *
29178932 AGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGTAAGCTACATAGTAATAAA
130 AGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATAGTAATAAA
29178996 ATTAATTCAT
Statistics
Matches: 185, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
241 181 0.98
242 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (241 bp):
ATTTTTTAAGATTCATCATACGTGGCATTGTTACACCTAGGGAGGATCCATTATATCTTACAACT
CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
GGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTAATAGACAAGCAAGCTACATAGTAATAAATA
TTCAATAGTAAATGAGCTCAATAGAACTTTTTTCAAGTCTTTTGGA
Found at i:29179062 original size:33 final size:33
Alignment explanation
Indices: 29179020--29179086 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
29179010 ATTCATACTT
*
29179020 AAGAACATACGCATTGGAACCAGTAGCAATGAG
1 AAGAACATACGCATTGGAACCAGTAGCAAAGAG
*
29179053 AAGAACATACGCATTGGAACTAGTAGCAAAGAG
1 AAGAACATACGCATTGGAACCAGTAGCAAAGAG
29179086 A
1 A
29179087 TCCAAAGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (33 bp):
AAGAACATACGCATTGGAACCAGTAGCAAAGAG
Found at i:29182074 original size:18 final size:18
Alignment explanation
Indices: 29182033--29182074 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29182023 GAAAGGCTGA
*
29182033 GAAAGAAAAGAGAATTGG
1 GAAAGAAAAGAGAATCGG
*
29182051 GAAAGAAAAGGGAATCGG
1 GAAAGAAAAGAGAATCGG
*
29182069 GGAAGA
1 GAAAGA
29182075 GAAATAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.07
Consensus pattern (18 bp):
GAAAGAAAAGAGAATCGG
Found at i:29182319 original size:40 final size:40
Alignment explanation
Indices: 29182236--29182319 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
29182226 TAAATTATTT
* *
29182236 TTTTGCGGCATTTTTATCATAAACGCCGCTATTGCTTGCC
1 TTTTGCGGCATTTTTATCATAAACGCCGCTAATGCTTGAC
* *
29182276 TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGTTTGAC
1 TTTTGCGGCATTTTTATCATAAACGCCGCTAATGCTTGAC
29182316 TTTT
1 TTTT
29182320 TTATAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (40 bp):
TTTTGCGGCATTTTTATCATAAACGCCGCTAATGCTTGAC
Found at i:29182345 original size:22 final size:20
Alignment explanation
Indices: 29182318--29182374 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
29182308 TGTTTGACTT
29182318 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
29182339 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
29182360 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
29182375 TTGAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Found at i:29182754 original size:14 final size:14
Alignment explanation
Indices: 29182724--29182869 Score: 102
Period size: 14 Copynumber: 10.4 Consensus size: 14
29182714 AATCATACAA
*
29182724 CATAACCCTTAAACC
1 CATAACCCAT-AACC
29182739 CATAACCCATAACC
1 CATAACCCATAACC
29182753 CATAACCCATAACC
1 CATAACCCATAACC
29182767 C-TAACCCATAA-C
1 CATAACCCATAACC
*
29182779 CACTAACCCCTAACAC
1 CA-TAACCCATAAC-C
* *
29182795 C-TAAACCTTAAACC
1 CATAACCCAT-AACC
* * *
29182809 C-CAACCCTTAAAC
1 CATAACCCATAACC
* * *
29182822 CATAAACTATAAAC
1 CATAACCCATAACC
*
29182836 CATAATCCATAAACC
1 CATAACCCAT-AACC
* *
29182851 CATAATCCATAATC
1 CATAACCCATAACC
29182865 CATAA
1 CATAA
29182870 ACCTTAAAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.02
13 14 0.13
14 66 0.61
15 25 0.23
16 2 0.02
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CATAACCCATAACC
Found at i:29182761 original size:21 final size:21
Alignment explanation
Indices: 29182724--29182869 Score: 111
Period size: 22 Copynumber: 6.9 Consensus size: 21
29182714 AATCATACAA
*
29182724 CATAACCCTTAAACCCATAACC
1 CATAACCCATAAA-CCATAACC
*
29182746 CATAACCCATAACCCATAACC
1 CATAACCCATAAACCATAACC
29182767 C-TAACCCAT-AACCACTAACC
1 CATAACCCATAAACCA-TAACC
* *
29182787 CCTAACACC-TAAACCTTAAACC
1 CATAAC-CCATAAACCAT-AACC
* * *
29182809 C-CAACCCTTAAACCATAAAC
1 CATAACCCATAAACCATAACC
* * *
29182829 TATAAACCATAATCCATAAACC
1 CATAACCCATAAACCAT-AACC
* *
29182851 CATAATCCATAATCCATAA
1 CATAACCCATAAACCATAA
29182870 ACCTTAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.04
20 19 0.19
21 38 0.38
22 40 0.40
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (21 bp):
CATAACCCATAAACCATAACC
Found at i:29182877 original size:7 final size:7
Alignment explanation
Indices: 29182705--29182877 Score: 84
Period size: 7 Copynumber: 24.6 Consensus size: 7
29182695 TTTTATCCCC
*
29182705 TAAACCC
1 TAAACCA
*
29182712 TAAATCA
1 TAAACCA
29182719 TACAA-CA
1 TA-AACCA
* *
29182726 TAACCCT
1 TAAACCA
29182733 TAAACCCA
1 TAAA-CCA
*
29182741 TAACCCA
1 TAAACCA
*
29182748 TAACCCA
1 TAAACCA
*
29182755 TAACCCA
1 TAAACCA
*
29182762 T-AACCC
1 TAAACCA
*
29182768 TAACCCA
1 TAAACCA
29182775 T-AACCA
1 TAAACCA
* *
29182781 CTAACCCC
1 -TAAACCA
29182789 TAACACC-
1 TAA-ACCA
*
29182796 TAAACCT
1 TAAACCA
*
29182803 TAAACCC
1 TAAACCA
* * *
29182810 CAACCCT
1 TAAACCA
29182817 TAAACCA
1 TAAACCA
*
29182824 TAAACTA
1 TAAACCA
29182831 TAAACCA
1 TAAACCA
*
29182838 TAATCCA
1 TAAACCA
29182845 TAAACCCA
1 TAAA-CCA
*
29182853 TAATCCA
1 TAAACCA
*
29182860 TAATCCA
1 TAAACCA
*
29182867 TAAACCT
1 TAAACCA
29182874 TAAA
1 TAAA
29182878 ATAGTAACTC
Statistics
Matches: 128, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
6 12 0.09
7 98 0.77
8 18 0.14
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:29183188 original size:24 final size:24
Alignment explanation
Indices: 29183160--29183208 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
29183150 CCAAAATAAC
*
29183160 AATTAATTTTTATATAGACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29183184 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29183208 A
1 A
29183209 TAAATATACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:29183874 original size:41 final size:41
Alignment explanation
Indices: 29183817--29183982 Score: 187
Period size: 41 Copynumber: 4.1 Consensus size: 41
29183807 GAGTTTATGA
* *
29183817 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTACTGCTTTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * *
29183858 CTTTTACCGGCATTTTACCAAAAGCGCCGCTAAAGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * * *
29183899 CTTTTAGCGGTGTTTTACCAAAAGCGCCTCTATTGCTCAGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * *
29183940 -TTTTAGTGGCG-TTT--CAAAAACGCCGCTATTGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
*
29183977 GTTTTA
1 CTTTTA
29183983 CAATTTTTGT
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
37 20 0.19
38 5 0.05
39 3 0.03
40 9 0.08
41 70 0.65
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (41 bp):
CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
Found at i:29186317 original size:19 final size:19
Alignment explanation
Indices: 29186290--29186328 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29186280 TAGTTTCTTG
29186290 TATCCTATGATACTTCATA
1 TATCCTATGATACTTCATA
* *
29186309 TATCTTATGATATTTCATA
1 TATCCTATGATACTTCATA
29186328 T
1 T
29186329 TAATATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (19 bp):
TATCCTATGATACTTCATA
Found at i:29187784 original size:20 final size:20
Alignment explanation
Indices: 29187759--29187824 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
29187749 TAGGTGCTCT
29187759 TGATAGTACTTTCATACTCC
1 TGATAGTACTTTCATACTCC
* * ** **
29187779 TGATAGCACTATGGTGTTCC
1 TGATAGTACTTTCATACTCC
* *
29187799 TAATAGTACTTTCATACTCT
1 TGATAGTACTTTCATACTCC
29187819 TGATAG
1 TGATAG
29187825 CACTACAATG
Statistics
Matches: 31, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (20 bp):
TGATAGTACTTTCATACTCC
Found at i:29187816 original size:40 final size:40
Alignment explanation
Indices: 29187751--29187964 Score: 223
Period size: 40 Copynumber: 5.3 Consensus size: 40
29187741 TTCTTGAATA
* * *
29187751 GGTGCTCTTGATAGTACTTTCATACTCCTGATAGCACTAT
1 GGTGCTCCTAATAGTACTTTCATACTCCTGATAGCACTAC
* *
29187791 GGTGTTCCTAATAGTACTTTCATACTCTTGATAGCACTAC
1 GGTGCTCCTAATAGTACTTTCATACTCCTGATAGCACTAC
** * * * * *
29187831 AATGCTTCTAAGAGTATTTTCCTACTCCTGATAACACTAC
1 GGTGCTCCTAATAGTACTTTCATACTCCTGATAGCACTAC
* * *
29187871 GGAGCTCCTAACAGTACTTTCCTACTCCT-ATTAGCACTAC
1 GGTGCTCCTAATAGTACTTTCATACTCCTGA-TAGCACTAC
* * * *
29187911 GGTGCTCCTGATAGTACTTTCGTACTCTTGTTAGCACTAC
1 GGTGCTCCTAATAGTACTTTCATACTCCTGATAGCACTAC
* *
29187951 AGTGCTCCTGATAG
1 GGTGCTCCTAATAG
29187965 CATATGCATG
Statistics
Matches: 144, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 143 0.99
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (40 bp):
GGTGCTCCTAATAGTACTTTCATACTCCTGATAGCACTAC
Found at i:29189129 original size:40 final size:40
Alignment explanation
Indices: 29189074--29189153 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
29189064 ATGTAGTTGG
29189074 TAATTCTAGAGAATTCATCATTTTTCTTCATCTTCATCAA
1 TAATTCTAGAGAATTCATCATTTTTCTTCATCTTCATCAA
29189114 TAATTCTAGAGAATTCATCATTTTTCTTCATCTTCATCAA
1 TAATTCTAGAGAATTCATCATTTTTCTTCATCTTCATCAA
29189154 CTAAAAACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (40 bp):
TAATTCTAGAGAATTCATCATTTTTCTTCATCTTCATCAA
Found at i:29191835 original size:42 final size:42
Alignment explanation
Indices: 29191788--29191905 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
29191778 CAACGTTTCA
* *
29191788 ATGCCATATCCCCGATATGGTCTTACATGAAAT-ATCATATCG
1 ATGCCATATCCCCGATATGGTCTTACACGAAATCA-CATACCG
* * *
29191830 ATGCCATGTCCCCGACATGGTCTTATACGAAATCACATACCG
1 ATGCCATATCCCCGATATGGTCTTACACGAAATCACATACCG
* * * *
29191872 AGGCCATATCCCAGATATGGTCTTATACGGAATC
1 ATGCCATATCCCCGATATGGTCTTACACGAAATC
29191906 TTAATAACCT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (42 bp):
ATGCCATATCCCCGATATGGTCTTACACGAAATCACATACCG
Found at i:29193484 original size:53 final size:52
Alignment explanation
Indices: 29193354--29193484 Score: 154
Period size: 52 Copynumber: 2.5 Consensus size: 52
29193344 GGAAAAGAAG
* *
29193354 TGATATGTGCACCCGTATAAAACCATAACTGGGCTATGGCATCGGTGCAATA
1 TGATATGTGCTCCCGTATAAAACCATAACAGGGCTATGGCATCGGTGCAATA
* * * ** *
29193406 TGATATGTGCTCCCGTATAAGACCATAGCAGGGTTATGGCATCGGTGTGATG
1 TGATATGTGCTCCCGTATAAAACCATAACAGGGCTATGGCATCGGTGCAATA
** *
29193458 TGATAATGTGCTTTCGTATAATACCAT
1 TGAT-ATGTGCTCCCGTATAAAACCAT
29193485 GTCTTGGACA
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 48 0.72
53 19 0.28
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (52 bp):
TGATATGTGCTCCCGTATAAAACCATAACAGGGCTATGGCATCGGTGCAATA
Found at i:29198247 original size:5 final size:5
Alignment explanation
Indices: 29198237--29198270 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
29198227 CTATGTGTTC
29198237 TTTAT TTTAT TTTAT TTTAT TTT-T ATTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA
29198271 AAAAATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:29206819 original size:36 final size:37
Alignment explanation
Indices: 29206736--29206820 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
29206726 CGTAGTAGTG
29206736 TGTAAGACCATAGCTCGGCTATGGCATCGTGATGACA
1 TGTAAGACCATAGCTCGGCTATGGCATCGTGATGACA
* * * *
29206773 TGCAAAACCATAGCTGGGCTATGGCATTGTGAT-ACA
1 TGTAAGACCATAGCTCGGCTATGGCATCGTGATGACA
29206809 TGTAAGACCATA
1 TGTAAGACCATA
29206821 TCTAGGACGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 13 0.31
37 29 0.69
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (37 bp):
TGTAAGACCATAGCTCGGCTATGGCATCGTGATGACA
Found at i:29206932 original size:42 final size:42
Alignment explanation
Indices: 29206809--29207004 Score: 171
Period size: 42 Copynumber: 4.7 Consensus size: 42
29206799 TTGTGATACA
* ***
29206809 TGTAAGACCATATCTAGGACGTGGCATCGATATGAGATCACG
1 TGTAAGACCATATCTAGGACATGGCATCGATATGAGATTTTG
* * * * *
29206851 TGTAAGACCATATCTGGGATATGGCTTTGGTATGAGATTTTG
1 TGTAAGACCATATCTAGGACATGGCATCGATATGAGATTTTG
* * * ** *
29206893 TGTAAGACCGTGTCTGGGATGTGGCATCGATATGTGATTTTG
1 TGTAAGACCATATCTAGGACATGGCATCGATATGAGATTTTG
* * * * * *
29206935 TATAAGACCATGTTTAGGACATGGCAACGATGTGAGACTTTG
1 TGTAAGACCATATCTAGGACATGGCATCGATATGAGATTTTG
29206977 TGTAAGACCATAGT-T-GGACTATGGCATC
1 TGTAAGACCATA-TCTAGGAC-ATGGCATC
29207005 AAGTAAATGA
Statistics
Matches: 123, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
41 4 0.03
42 118 0.96
43 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTAGGACATGGCATCGATATGAGATTTTG
Found at i:29211551 original size:54 final size:54
Alignment explanation
Indices: 29211469--29211598 Score: 251
Period size: 54 Copynumber: 2.4 Consensus size: 54
29211459 TCATTGCAAG
29211469 GGATTTAGCCTGGATTGGTAATCCCGACATCACCTTATGAGTTCACTATACGGA
1 GGATTTAGCCTGGATTGGTAATCCCGACATCACCTTATGAGTTCACTATACGGA
29211523 GGATTTAGCCTGGATTGGTAATCCCGACATCACCTTATGAGTTCACTATACGGA
1 GGATTTAGCCTGGATTGGTAATCCCGACATCACCTTATGAGTTCACTATACGGA
*
29211577 GGATTTAGCCTGGACTGGTAAT
1 GGATTTAGCCTGGATTGGTAAT
29211599 TCCACCTTAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (54 bp):
GGATTTAGCCTGGATTGGTAATCCCGACATCACCTTATGAGTTCACTATACGGA
Found at i:29216512 original size:18 final size:18
Alignment explanation
Indices: 29216489--29216526 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29216479 TGAGAATTTC
*
29216489 TGATACCGTGACTGAATG
1 TGATACCATGACTGAATG
*
29216507 TGATACTATGACTGAATG
1 TGATACCATGACTGAATG
29216525 TG
1 TG
29216527 TTACTGATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (18 bp):
TGATACCATGACTGAATG
Found at i:29216531 original size:18 final size:18
Alignment explanation
Indices: 29216497--29216531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29216487 TCTGATACCG
29216497 TGACTGAATGTGATACTA
1 TGACTGAATGTGATACTA
*
29216515 TGACTGAATGTGTTACT
1 TGACTGAATGTGATACT
29216532 GATCGACTAA
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:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
TGACTGAATGTGATACTA
Found at i:29229962 original size:46 final size:46
Alignment explanation
Indices: 29229909--29230084 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
29229899 TATTTGGGCA
29229909 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29229955 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29230000 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
29230048 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29230085 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29230064 original size:93 final size:93
Alignment explanation
Indices: 29229905--29230076 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29229895 GGGATATTTG
* *
29229905 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29229970 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
29229998 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29230063 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29230077 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29233046 original size:15 final size:15
Alignment explanation
Indices: 29233026--29233094 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
29233016 GTATCTTGGG
29233026 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
29233041 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
29233056 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
29233071 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
29233086 TTTCTTTAT
1 TTTCTTTAT
29233095 TCGGTTTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:29233095 original size:30 final size:30
Alignment explanation
Indices: 29233017--29233103 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
29233007 CATAGTATCG
* * * * *
29233017 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGGTTTCTC
29233047 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGGTTTCTC
29233077 TATCTTGGATTTCTTTATTC--GGTTTCT
1 TATCTTGGATTTCTTTATTCTGGGTTTCT
29233104 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.14
29 1 0.02
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGGTTTCTC
Found at i:29235626 original size:46 final size:46
Alignment explanation
Indices: 29235464--29235635 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
29235454 ATTTGGGCAT
*
29235464 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A--T
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
29235507 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
29235552 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
29235600 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29235636 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
40 5 0.05
42 2 0.02
43 28 0.26
46 34 0.31
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:29239659 original size:17 final size:17
Alignment explanation
Indices: 29239637--29239688 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
29239627 ACTAAACCGA
29239637 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
29239654 CCACTAA----ATCACC
1 CCACTAACTCCATCACC
*
29239667 CCACTAACTCCACCACC
1 CCACTAACTCCATCACC
29239684 CCACT
1 CCACT
29239689 TGCCACTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 13 0.43
17 17 0.57
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:29239666 original size:13 final size:13
Alignment explanation
Indices: 29239648--29239673 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29239638 CACTAACTCC
29239648 ATCACCCCACTAA
1 ATCACCCCACTAA
29239661 ATCACCCCACTAA
1 ATCACCCCACTAA
29239674 CTCCACCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:29239673 original size:30 final size:29
Alignment explanation
Indices: 29239621--29239727 Score: 109
Period size: 30 Copynumber: 3.8 Consensus size: 29
29239611 ATCCAATTAG
*
29239621 CACCCCACTAAA-CCGACCACTAACTCCAT
1 CACCCCACTAAATCC-CCCACTAACTCCAT
*
29239650 CACCCCACTAAATCACCCCACTAACTCCAC
1 CACCCCACTAAATC-CCCCACTAACTCCAT
* *
29239680 CACCCCACT---T--GCCACTAACTCTAT
1 CACCCCACTAAATCCCCCACTAACTCCAT
29239704 CACCCCACTAAATCACCCCACTAA
1 CACCCCACTAAATC-CCCCACTAA
29239728 ACTTGCAACT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
24 20 0.31
27 2 0.03
29 12 0.19
30 29 0.45
31 1 0.02
ACGTcount: A:0.33, C:0.50, G:0.02, T:0.16
Consensus pattern (29 bp):
CACCCCACTAAATCCCCCACTAACTCCAT
Found at i:29239694 original size:24 final size:24
Alignment explanation
Indices: 29239667--29239712 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29239657 CTAAATCACC
29239667 CCACTAACTCCACCACCCCACTTG
1 CCACTAACTCCACCACCCCACTTG
* *
29239691 CCACTAACTCTATCACCCCACT
1 CCACTAACTCCACCACCCCACT
29239713 AAATCACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.52, G:0.02, T:0.20
Consensus pattern (24 bp):
CCACTAACTCCACCACCCCACTTG
Found at i:29239720 original size:13 final size:13
Alignment explanation
Indices: 29239702--29239728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29239692 CACTAACTCT
29239702 ATCACCCCACTAA
1 ATCACCCCACTAA
29239715 ATCACCCCACTAA
1 ATCACCCCACTAA
29239728 A
1 A
29239729 CTTGCAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:29239741 original size:42 final size:40
Alignment explanation
Indices: 29239686--29239767 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 40
29239676 CCACCACCCC
* *
29239686 ACTTGCCACTAACTCTATCACCCCACTAAATCACCCCACTAA
1 ACTTGCAACTAACTCCATCA-CCCACTAAATCA-CCCACTAA
29239728 ACTTGCAACTAACTCCATCACCCACTAAATCACCCACTAA
1 ACTTGCAACTAACTCCATCACCCACTAAATCACCCACTAA
29239768 CTCCATTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 8 0.21
41 12 0.32
42 18 0.47
ACGTcount: A:0.35, C:0.41, G:0.02, T:0.21
Consensus pattern (40 bp):
ACTTGCAACTAACTCCATCACCCACTAAATCACCCACTAA
Done.