Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 83 of 208
Found at i:29098751 original size:18 final size:18
Alignment explanation
Indices: 29098728--29098779 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
29098718 CCTTGGCCTC
29098728 TCCTTTTTCTTTTTATTT
1 TCCTTTTTCTTTTTATTT
*
29098746 TCC-TTTTCTTCTTTTCTTT
1 TCCTTTTTC-T-TTTTATTT
*
29098765 TCTTTTCTTCTTTTT
1 TCCTTT-TTCTTTTT
29098780 TTTGTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 13 0.46
20 3 0.11
21 3 0.11
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TCCTTTTTCTTTTTATTT
Found at i:29098766 original size:13 final size:12
Alignment explanation
Indices: 29098731--29098782 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
29098721 TGGCCTCTCC
29098731 TTTTTCTTTT-T
1 TTTTTCTTTTCT
*
29098742 ATTTTCCTTTTCT
1 -TTTTTCTTTTCT
29098755 TCTTTTCTTTTCT
1 T-TTTTCTTTTCT
29098768 TTTCTTCTTTT-T
1 TTT-TTCTTTTCT
29098780 TTT
1 TTT
29098783 GTTTGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 16 0.46
13 19 0.54
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:29103810 original size:3 final size:3
Alignment explanation
Indices: 29103797--29103850 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
29103787 CAAATAAAAC
*
29103797 TAA TAA T-A TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29103842 TGA TAA TAA
1 TAA TAA TAA
29103851 ATGCTAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29116398 original size:28 final size:28
Alignment explanation
Indices: 29116343--29116399 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
29116333 TTCTTTTTAA
* * *
29116343 AAAATTTAAAAGATCTAAAAATACATAG
1 AAAATTTAAAAAAACTAAAAATAAATAG
29116371 AAAATTTAAAAAAACTAAATAA-AAATAG
1 AAAATTTAAAAAAACTAAA-AATAAATAG
29116399 A
1 A
29116400 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAATTTAAAAAAACTAAAAATAAATAG
Found at i:29116433 original size:19 final size:19
Alignment explanation
Indices: 29116392--29116434 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
29116382 AAACTAAATA
**
29116392 AAAATAGATAAAAAAATTC
1 AAAATAGATAAAAAAAGAC
* *
29116411 AAAATAGATAAAATAAGAG
1 AAAATAGATAAAAAAAGAC
29116430 AAAAT
1 AAAAT
29116435 TATTTTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (19 bp):
AAAATAGATAAAAAAAGAC
Found at i:29130533 original size:44 final size:44
Alignment explanation
Indices: 29130424--29131062 Score: 302
Period size: 44 Copynumber: 14.8 Consensus size: 44
29130414 ATTATACATG
* * * * * *
29130424 TCTTATTTCCCTGAGACTACAGTGGAACAGATCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATA-GT-A-A
*
29130470 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
* * * *
29130514 TCCTATCTCCCTGATATTACAGTGGAGCGGATT-AA-A-ACGAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATA-GTA--A
* * * * * *
29130558 TCTTATCTCTCTGA-AGTTATAGTAGAGTAGATCG--TTTCAG--A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATAT-AGTAA
* *
29130599 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
* * *
29130643 TCCTATCTCCCTG-GTATTATAGTGGAGCAGATT-AA-A-ACGAAGGA
1 TCTTATCTCCCTGAG-ATTACAGTGGAGCAGATTGAATATA-GTA--A
* * * * *
29130687 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG--TTTCAG--A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATAT-AGTAA
* * *
29130728 TCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
* * * *
29130772 TCCTATCTCCCTGATATTACAGTGGAGCGGATT-AA-A-ACGAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATA-GTA--A
* * * * *
29130816 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG--TTTCAG--A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATAT-AGTAA
* *
29130857 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
* * * *
29130901 TCCTATCTCCCTGATATTACAGTGGAGCGGATT-AA-A-ACGAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATA-GTA--A
* * * * *
29130945 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG--TGTCAG--A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAATAT-AGTAA
** * **
29130986 TCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
* * *
29131030 TCCTATCTCCTTGAGATTACAGTGGAGCGGATT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATT
29131063 AAAATGAAGG
Statistics
Matches: 447, Mismatches: 91, Indels: 112
0.69 0.14 0.17
Matches are distributed among these distances:
41 114 0.26
42 24 0.05
43 17 0.04
44 249 0.56
45 5 0.01
46 37 0.08
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAA
Found at i:29130618 original size:85 final size:85
Alignment explanation
Indices: 29130468--29131140 Score: 313
Period size: 85 Copynumber: 7.8 Consensus size: 85
29130458 AAGAATTTCA
** * * *
29130468 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAATAT-AGTAATCCTATCTCCCTGATAT
1 GATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCG--TATCAG--ATCTTATCTCCCTGAGAT
*
29130531 TACAGTGGAGCGGATTAAAACGAAG
61 TACAGTGGAGCAGATTAAAACGAAG
* * * *
29130556 GATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGTTTCAGATCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGTATCAGATCTTATCTCCCTGAGATTACAG
* *
29130621 CGGAGCAGATT-GAA-GATAG
66 TGGAGCAGATTAAAACGA-AG
* * * * * *** * *
29130640 TAATCCTATCTCCCTGGTA-TTATAGTGGAGCAGATTAAAACGAAGGATCTTATCTCTCTGA-AG
1 -GATCTTATCTCCCT-GAAGTTACAGTAGAGCAGATCGTATC--A-GATCTTATCTCCCTGAGA-
* * *****
29130703 TTACAGTAGAGTAGATCGTTTC--A-
60 TTACAGTGGAGCAGATTAAAACGAAG
** * * * *
29130726 GATCTTATCTCCCT-AAGATTACAGCGGAGCAGATTGAAGAT-AGTAATCCTATCTCCCTGATAT
1 GATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCG--TATCAG--ATCTTATCTCCCTGAGAT
*
29130789 TACAGTGGAGCGGATTAAAACGAAG
61 TACAGTGGAGCAGATTAAAACGAAG
* * *
29130814 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTCAGATCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGTATCAGATCTTATCTCCCTGAGATTACAG
* *
29130879 CGGAGCAGATT-GAA-GATAG
66 TGGAGCAGATTAAAACGA-AG
* * * * *** * *
29130898 TAATCCTATCTCCCTGATA-TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGA-AG
1 -GATCTTATCTCCCTGA-AGTTACAGTAGAGCAGATCGTATC--A-GATCTTATCTCCCTGAGA-
* * *****
29130961 TTACAGTAGAGTAGATCGTGTC--A-
60 TTACAGTGGAGCAGATTAAAACGAAG
* *** * * *
29130984 GATCTTATCTCCCTG-AGATTACAGCAGAGCAGATTAAAGCTAGTAATCCTATCTCCTTGAGATT
1 GATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGTATC-AG--ATCTTATCTCCCTGAGATT
* *
29131048 ACAGTGGAGCGGATTAAAATGAAG
62 ACAGTGGAGCAGATTAAAACGAAG
* * * * * *
29131072 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTGTCAGGTCTTATTTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGTATCAGATCTTATCTCCCTGAGATTACAG
29131137 TGGA
66 TGGA
29131141 ATAGACTGAA
Statistics
Matches: 434, Mismatches: 110, Indels: 85
0.69 0.17 0.14
Matches are distributed among these distances:
83 8 0.02
84 10 0.02
85 246 0.57
86 8 0.02
87 15 0.03
88 140 0.32
89 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (85 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGTATCAGATCTTATCTCCCTGAGATTACAG
TGGAGCAGATTAAAACGAAG
Found at i:29130693 original size:129 final size:129
Alignment explanation
Indices: 29130463--29131136 Score: 1195
Period size: 129 Copynumber: 5.2 Consensus size: 129
29130453 GATCGAAGAA
*
29130463 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGA
1 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
*
29130528 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCG
66 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
*
29130592 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGG
1 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
* *
29130657 TATTATAGTGGAGCAGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
66 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
*
29130721 TTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
1 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
29130786 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
66 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
29130850 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
1 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
29130915 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
66 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
* * * * *
29130979 TGTCAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGCTAGTAATCCTATCTCCTTGA
1 TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
* * *
29131044 GATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCG
66 TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
* * *
29131108 TGTCAGGTCTTATTTCCCTGAGATTACAG
1 TTTCAGATCTTATCTCCCTGAGATTACAG
29131137 TGGAATAGAC
Statistics
Matches: 525, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 525 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (129 bp):
TTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
TATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
Found at i:29132886 original size:14 final size:16
Alignment explanation
Indices: 29132857--29132888 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
29132847 TTACTTATTT
29132857 TATATACCCTTGTATA
1 TATATACCCTTGTATA
29132873 TATATA-CCTT-TATA
1 TATATACCCTTGTATA
29132887 TA
1 TA
29132889 CTTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATACCCTTGTATA
Found at i:29138969 original size:45 final size:45
Alignment explanation
Indices: 29138914--29139001 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
29138904 TATACCTTAC
29138914 ATAAAAGATTACATCCATAACCATAATCTAAATCATTTATTAGAA
1 ATAAAAGATTACATCCATAACCATAATCTAAATCATTTATTAGAA
*
29138959 ATAAAAGATTACATCCGTAACCATAATCTAAATCATTTATTAG
1 ATAAAAGATTACATCCATAACCATAATCTAAATCATTTATTAG
29139002 CATTCTACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.32
Consensus pattern (45 bp):
ATAAAAGATTACATCCATAACCATAATCTAAATCATTTATTAGAA
Found at i:29144679 original size:50 final size:50
Alignment explanation
Indices: 29144604--29144705 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
29144594 AGATTACAGC
29144604 ACTGAAGTGTAGTCAGATAGTCAACCAACAACATATAATGTTGCCAAGAT
1 ACTGAAGTGTAGTCAGATAGTCAACCAACAACATATAATGTTGCCAAGAT
29144654 ACTGAAGTGTAGTCAGATAGTCAACCAACAACATATAATGTTGCCAAGAT
1 ACTGAAGTGTAGTCAGATAGTCAACCAACAACATATAATGTTGCCAAGAT
29144704 AC
1 AC
29144706 AAGGATTAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (50 bp):
ACTGAAGTGTAGTCAGATAGTCAACCAACAACATATAATGTTGCCAAGAT
Found at i:29148556 original size:365 final size:365
Alignment explanation
Indices: 29147885--29148618 Score: 1443
Period size: 365 Copynumber: 2.0 Consensus size: 365
29147875 AACAGCAATC
*
29147885 ACTACCATAGTAAGTCTTTACTATGTTAGGAATATTTCAGTCAATCAATCAAAAAATACATATCA
1 ACTACCATAGTAAGTCTTTACTATGTTAGGAATATTTCAGTCAATCAATCAAAAAATACATACCA
29147950 GGCTTTAATTAATTGCTGCTTCTGTTATTTTTCTTTATGAGAAGAAAAGAAGGGTGATACAAAAC
66 GGCTTTAATTAATTGCTGCTTCTGTTATTTTTCTTTATGAGAAGAAAAGAAGGGTGATACAAAAC
29148015 CAAACAAGTTTTTAAATAATTAAAAGAATTCTTTAGAAAATGATAAAAGGAATAACTTTCTTTCC
131 CAAACAAGTTTTTAAATAATTAAAAGAATTCTTTAGAAAATGATAAAAGGAATAACTTTCTTTCC
29148080 TTTAATACCGAACAGTTAACTGCAATTACTTTTAGACAATTTTTAATAAAAAATGTCATGTTGAA
196 TTTAATACCGAACAGTTAACTGCAATTACTTTTAGACAATTTTTAATAAAAAATGTCATGTTGAA
29148145 ATCATATGATTTTGTGCTTTAATTAATACACTACATATTCTTTCTTAAAAATTTTGCGAGCAAAA
261 ATCATATGATTTTGTGCTTTAATTAATACACTACATATTCTTTCTTAAAAATTTTGCGAGCAAAA
29148210 AACAGCAACCAAACAAAATCTGAATGACATCACCGGAACA
326 AACAGCAACCAAACAAAATCTGAATGACATCACCGGAACA
29148250 ACTACCATAGTAAGTCTTTACTATGTTAGGAATATTTCAGTCAATCAATCAAAAAATACATACCA
1 ACTACCATAGTAAGTCTTTACTATGTTAGGAATATTTCAGTCAATCAATCAAAAAATACATACCA
29148315 GGCTTTAATTAATTGCTGCTTCTGTTATTTTTCTTTATGAGAAGAAAAGAAGGGTGATACAAAAC
66 GGCTTTAATTAATTGCTGCTTCTGTTATTTTTCTTTATGAGAAGAAAAGAAGGGTGATACAAAAC
29148380 CAAACAAGTTTTTAAATAATTAAAAGAATTCTTTAGAAAATGATAAAAGGAATAACTTTCTTTCC
131 CAAACAAGTTTTTAAATAATTAAAAGAATTCTTTAGAAAATGATAAAAGGAATAACTTTCTTTCC
29148445 TTTAATACCGAACAGTTAACTGCAATTACTTTTAGACAATTTTTAAT-AAAAATGTCATGTTGAA
196 TTTAATACCGAACAGTTAACTGCAATTACTTTTAGACAATTTTTAATAAAAAATGTCATGTTGAA
29148509 ATCATATGATTTTGTGCTTTAATTAATACACTACATATTCTTTTCTTAAAAATTTTGCGAGCAAA
261 ATCATATGATTTTGTGCTTTAATTAATACACTACATATTC-TTTCTTAAAAATTTTGCGAGCAAA
29148574 AAACAGCAACCAAACAAAATCTGAATGACATCACCGGAACA
325 AAACAGCAACCAAACAAAATCTGAATGACATCACCGGAACA
29148615 ACTA
1 ACTA
29148619 AGTATAGGAA
Statistics
Matches: 367, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
364 57 0.16
365 310 0.84
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (365 bp):
ACTACCATAGTAAGTCTTTACTATGTTAGGAATATTTCAGTCAATCAATCAAAAAATACATACCA
GGCTTTAATTAATTGCTGCTTCTGTTATTTTTCTTTATGAGAAGAAAAGAAGGGTGATACAAAAC
CAAACAAGTTTTTAAATAATTAAAAGAATTCTTTAGAAAATGATAAAAGGAATAACTTTCTTTCC
TTTAATACCGAACAGTTAACTGCAATTACTTTTAGACAATTTTTAATAAAAAATGTCATGTTGAA
ATCATATGATTTTGTGCTTTAATTAATACACTACATATTCTTTCTTAAAAATTTTGCGAGCAAAA
AACAGCAACCAAACAAAATCTGAATGACATCACCGGAACA
Found at i:29154401 original size:13 final size:12
Alignment explanation
Indices: 29154383--29154415 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29154373 CATGGGAGTA
29154383 TTTCTTTTTCTTT
1 TTTCTTTTT-TTT
29154396 TTTCTTTTTTTT
1 TTTCTTTTTTTT
29154408 TTT-TTTTT
1 TTTCTTTTT
29154416 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
13 9 0.45
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:29157217 original size:333 final size:334
Alignment explanation
Indices: 29156237--29157245 Score: 1876
Period size: 334 Copynumber: 3.0 Consensus size: 334
29156227 AAGAAGTAAG
* *
29156237 ATAGATTATATTATTACATTTTATTCATATCAAACATCTTTATTTTCCAAAAATGGGTCACTCCA
1 ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
29156302 AATAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
66 AATAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
* *
29156367 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCATAATTCTTTCAACAAAACTGT
131 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCACACTTCTTTCAACAAAACTGT
*
29156432 AGCCATTATTTTAGATCATGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
196 AGCCATTATTTTAGATCACGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
29156497 ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
261 ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
29156562 CTTGTCAGT
326 CTTGTCAGT
29156571 ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
1 ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
*
29156636 ATTAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
66 AATAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
29156701 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCACACTTCTTTCAACAAAACTGT
131 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCACACTTCTTTCAACAAAACTGT
29156766 AGCCATTATTTTAGATCACGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
196 AGCCATTATTTTAGATCACGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
29156831 ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
261 ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
29156896 CTTGTCAGT
326 CTTGTCAGT
29156905 ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
1 ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
29156970 AATAGCAAATGAATATGGTCCCA-TTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
66 AATAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
* * **
29157034 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTTTCCACACTTGTTTCAACAAAACACT
131 AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCACACTTCTTTCAACAAAACTGT
* *
29157099 AGCCATTATTTTAGATCACGAATACCATGTTTACCTCAATCTTAAACTTGAATACCCTAGATCAA
196 AGCCATTATTTTAGATCACGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
* *
29157164 ACTCCAAGCCAAGGCTCATCTTGGTGCTACTTACTAATTTCCTATTTGCGTTCTGCTCCCTAAAA
261 ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
*
29157229 CTTGTTAGT
326 CTTGTCAGT
29157238 ATAGATTA
1 ATAGATTA
29157246 ACAAAAAATG
Statistics
Matches: 659, Mismatches: 16, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
333 244 0.37
334 415 0.63
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (334 bp):
ATAGATTATATTATTATATTTTATTCATATCAAACATCTTTACTTTCCAAAAATGGGTCACTCCA
AATAGCAAATGAATATGGTCCCATTTTTAATCAAAATATTGACAAATGGAGTAAACCAACAAATG
AAGAAACTAGTAGCAAAATCAATGCATGCCCTTGTGTCTGTCCACACTTCTTTCAACAAAACTGT
AGCCATTATTTTAGATCACGAATACCATGTTTGCCTCGATCTTAAACTTGAATACCCTAGATCAA
ACTCCAAGCCAAGGCTCATCTTGTTGCTACTTACTAATTTCCTATTCGCGTTCTGCTCCCTAAAA
CTTGTCAGT
Found at i:29158742 original size:30 final size:30
Alignment explanation
Indices: 29158699--29158771 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
29158689 AAATAAAAAA
* * * * *
29158699 TAAAATTGGTAAAATTATATTTTAACCTTT
1 TAAAAATGATAAAATTATAATTTAACCATC
* *
29158729 TAAAAATGATAAAATTTTAATTTAATCATC
1 TAAAAATGATAAAATTATAATTTAACCATC
*
29158759 TAAAAATTATAAA
1 TAAAAATGATAAA
29158772 GATATAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAAATGATAAAATTATAATTTAACCATC
Found at i:29160779 original size:18 final size:18
Alignment explanation
Indices: 29160750--29160791 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29160740 TTACATATAT
29160750 AATATA-TTTTATTAAAA
1 AATATATTTTTATTAAAA
* *
29160767 AATATATTTTTATTTATA
1 AATATATTTTTATTAAAA
29160785 AATATAT
1 AATATAT
29160792 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATATTTTTATTAAAA
Found at i:29160804 original size:18 final size:19
Alignment explanation
Indices: 29160783--29160824 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29160773 TTTTTATTTA
29160783 TAAATATAT-AAAAAAATT
1 TAAATATATCAAAAAAATT
*
29160801 TAAA-ATATCAACAAAATT
1 TAAATATATCAAAAAAATT
*
29160819 AAAATA
1 TAAATA
29160825 GAGCACGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 15 0.75
19 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAATATATCAAAAAAATT
Found at i:29171948 original size:58 final size:58
Alignment explanation
Indices: 29171826--29171960 Score: 141
Period size: 58 Copynumber: 2.3 Consensus size: 58
29171816 CCACATAACC
** *
29171826 CTTTTTTTATCTGTTTTAGTACCTGGACTTGACACTTTTTTCTAATTTAGTAACAAAT
1 CTTTTTTTATCTAATTTGGTACCTGGACTTGACACTTTTTTCTAATTTAGTAACAAAT
* * * *
29171884 -TATTTTTTTTCTAATTTGGTACCT-GATCTTGACACTTTTTTGCCTAATTTGGTACCTAA-
1 CT-TTTTTTATCTAATTTGGTACCTGGA-CTTGACACTTTTTT--CTAATTTAGTAACAAAT
*
29171943 CTTTTTTTATCCAATTTG
1 CTTTTTTTATCTAATTTG
29171961 ACGCCTAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
57 3 0.05
58 32 0.51
59 14 0.22
60 14 0.22
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.52
Consensus pattern (58 bp):
CTTTTTTTATCTAATTTGGTACCTGGACTTGACACTTTTTTCTAATTTAGTAACAAAT
Found at i:29173809 original size:14 final size:14
Alignment explanation
Indices: 29173790--29173820 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29173780 TTTTGATTTG
29173790 ATGCAATTATATAC
1 ATGCAATTATATAC
*
29173804 ATGCAATTATATTC
1 ATGCAATTATATAC
29173818 ATG
1 ATG
29173821 TACCTTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (14 bp):
ATGCAATTATATAC
Found at i:29174868 original size:21 final size:21
Alignment explanation
Indices: 29174844--29174883 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29174834 ATTCCATACT
29174844 TACCCTTTATCACTTAACAGG
1 TACCCTTTATCACTTAACAGG
29174865 TACCCTTTATCACTTAACA
1 TACCCTTTATCACTTAACA
29174884 CGAACTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (21 bp):
TACCCTTTATCACTTAACAGG
Found at i:29179159 original size:23 final size:23
Alignment explanation
Indices: 29179132--29179242 Score: 101
Period size: 23 Copynumber: 5.0 Consensus size: 23
29179122 GGCTTTGTCG
*
29179132 ATCAGACACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
29179155 ATCAGGCACTTTATGTGTCGTACT
1 ATCAGGCACTTTATGTGTCGTA-T
29179179 -TCAGGCACTTCT-TGTGTCG--T
1 ATCAGGCACTT-TATGTGTCGTAT
* **
29179199 ATCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACTTTATGTGTCGTAT
* *
29179221 -TCAAGCAC-TTACGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
29179242 A
1 A
29179243 CTGATCTGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
20 9 0.12
21 24 0.32
22 1 0.01
23 38 0.51
24 2 0.03
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:29179597 original size:23 final size:24
Alignment explanation
Indices: 29179556--29179600 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
29179546 AGAAATGAGA
29179556 AGTGAAAATAAAATGATTTGAAAT
1 AGTGAAAATAAAATGATTTGAAAT
29179580 AGTG-AAATAATAAT-ATTTGAA
1 AGTGAAAATAA-AATGATTTGAA
29179601 TTTAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (24 bp):
AGTGAAAATAAAATGATTTGAAAT
Found at i:29189512 original size:42 final size:42
Alignment explanation
Indices: 29189447--29189602 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 42
29189437 AAATCGTACA
*
29189447 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
29189489 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * * *
29189531 ATGTCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
29189575 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
29189603 CGATAACATA
Statistics
Matches: 94, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
41 2 0.02
42 50 0.53
43 14 0.15
44 26 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:29195381 original size:15 final size:14
Alignment explanation
Indices: 29195361--29195403 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
29195351 TAATTGAGAT
29195361 TTTTTATTTTAGAAC
1 TTTTTATTTTA-AAC
*
29195376 TTTTTATTTTAAAT
1 TTTTTATTTTAAAC
29195390 TTTTTATATTTAAA
1 TTTTTAT-TTTAAA
29195404 GTTTGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTTTATTTTAAAC
Found at i:29200862 original size:7 final size:7
Alignment explanation
Indices: 29200850--29200875 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29200840 AAGTTGGAAA
29200850 AAAAAAC
1 AAAAAAC
29200857 AAAAAAC
1 AAAAAAC
29200864 AAAAAAC
1 AAAAAAC
29200871 AAAAA
1 AAAAA
29200876 GCCAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:29201430 original size:8 final size:8
Alignment explanation
Indices: 29201417--29201442 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29201407 GTATGGTGCC
29201417 TGCATGTA
1 TGCATGTA
29201425 TGCATGTA
1 TGCATGTA
29201433 TGCATGTA
1 TGCATGTA
29201441 TG
1 TG
29201443 TGTTGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (8 bp):
TGCATGTA
Found at i:29207542 original size:30 final size:30
Alignment explanation
Indices: 29207466--29207542 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
29207456 GTTACCACTA
* * *
29207466 ACCATTTTTCATTACAAAAGTAACGGAGTT
1 ACCATTTTTCGTTACAGAAGTAACGGAGCT
* *
29207496 ACCATTTTCCGTTACAGACGTAACGGAGCT
1 ACCATTTTTCGTTACAGAAGTAACGGAGCT
*
29207526 ATCATTTTTCGTTACAG
1 ACCATTTTTCGTTACAG
29207543 TTCCACTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (30 bp):
ACCATTTTTCGTTACAGAAGTAACGGAGCT
Found at i:29207621 original size:71 final size:71
Alignment explanation
Indices: 29207495--29207647 Score: 243
Period size: 71 Copynumber: 2.2 Consensus size: 71
29207485 GTAACGGAGT
* * *
29207495 TACCATTTTCCGTTACAGACGTAACGGAGCTATCATTTTTCGTTACAGTTCCACTACATACTTAA
1 TACCATTTTCCGTTACAGACGTAACGGAGCTACCATTTTCCGTTACAGTTCCACTACAGACTTAA
29207560 CCAAAC
66 CCAAAC
* * *
29207566 TACCATTTTCCGTTACAGACGTAATGGAGCTACCATTTTCCGTTATAGTTTCACTACAGACTTAA
1 TACCATTTTCCGTTACAGACGTAACGGAGCTACCATTTTCCGTTACAGTTCCACTACAGACTTAA
*
29207631 CTAAAC
66 CCAAAC
29207637 TACCATTTTCC
1 TACCATTTTCC
29207648 ATCCCCCTCC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (71 bp):
TACCATTTTCCGTTACAGACGTAACGGAGCTACCATTTTCCGTTACAGTTCCACTACAGACTTAA
CCAAAC
Found at i:29207726 original size:45 final size:46
Alignment explanation
Indices: 29207668--29207758 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 46
29207658 CATCCCTCAC
29207668 CCTCTTCCCCACCAT-C-CC-CCTACTCTGATTCTCTCTCCCTCTCCG
1 CCTCTTCCCCACCATCCTCCTCCTACTCTGATTCT-T-TCCCTCTCCG
*
29207713 CCTCTTCCTCACCATCCTTCCTCCTACTCTGATTCTTTCCCTCTCC
1 CCTCTTCCCCACCATCC-TCCTCCTACTCTGATTCTTTCCCTCTCC
29207759 CCCACCATCC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 14 0.34
46 1 0.02
47 9 0.22
48 3 0.07
49 14 0.34
ACGTcount: A:0.09, C:0.53, G:0.03, T:0.35
Consensus pattern (46 bp):
CCTCTTCCCCACCATCCTCCTCCTACTCTGATTCTTTCCCTCTCCG
Found at i:29213272 original size:75 final size:75
Alignment explanation
Indices: 29213179--29213322 Score: 270
Period size: 75 Copynumber: 1.9 Consensus size: 75
29213169 ATCTAAAGGG
29213179 TAATTACTTCATCATGTTTCTGAACATTTTATATAATCACACTTCAGTCCAATGTCATCACTAAA
1 TAATTACTTCATCATGTTTCTGAACATTTTATATAATCACACTTCAGTCCAATGTCATCACTAAA
29213244 AATTTAAATT
66 AATTTAAATT
* *
29213254 TAATTACTTCATCATGTTTCTGAACGTTTTATATAATCACACTTCAGTCCAATGTCATCACTAAG
1 TAATTACTTCATCATGTTTCTGAACATTTTATATAATCACACTTCAGTCCAATGTCATCACTAAA
29213319 AATT
66 AATT
29213323 GTTTTTTTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (75 bp):
TAATTACTTCATCATGTTTCTGAACATTTTATATAATCACACTTCAGTCCAATGTCATCACTAAA
AATTTAAATT
Found at i:29214115 original size:13 final size:15
Alignment explanation
Indices: 29214099--29214135 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
29214089 GACAAACACA
29214099 AAAAAAAAC-TGAT-
1 AAAAAAAACTTGATG
29214112 AAAAAAAACTTGATG
1 AAAAAAAACTTGATG
29214127 AAAACAAAA
1 AAAA-AAAA
29214136 ATTAAACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 4 0.19
16 4 0.19
ACGTcount: A:0.70, C:0.08, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAAAAACTTGATG
Found at i:29214350 original size:16 final size:16
Alignment explanation
Indices: 29214303--29214350 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
29214293 AAAATAGCAG
* * *
29214303 GAGAAGATAGGGAGAA
1 GAGAAGAAAGAGAAAA
29214319 GAGAAGAAAGAAAGAAAA
1 GAGAAGAAAG--AGAAAA
29214337 GAGAAGAAAGAGAA
1 GAGAAGAAAGAGAA
29214351 TGTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.02
Consensus pattern (16 bp):
GAGAAGAAAGAGAAAA
Found at i:29217635 original size:65 final size:62
Alignment explanation
Indices: 29217480--29217646 Score: 205
Period size: 62 Copynumber: 2.7 Consensus size: 62
29217470 TCCAATGTAC
* * * *
29217480 CTAATTTAT-ATTACAAAGTTTATTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTA
1 CTAATTTATGATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATGTAATTTAAATTA
* *
29217541 CAAAATTTATG-TTACAAAGTCTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTACAATTA
1 C-TAATTTATGATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATGTAAT-TTA-AATT-
29217604 A
62 A
*
29217605 TCTAATTTATGACTACAAAGTTTGTTCCAAGTTTTAATGTTG
1 -CTAATTTATGATTACAAAGTTTGTTCCAAGTTTTAATGTTG
29217647 CAATTAATCT
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
61 6 0.07
62 43 0.48
63 3 0.03
64 9 0.10
65 29 0.32
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (62 bp):
CTAATTTATGATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATGTAATTTAAATTA
Found at i:29218077 original size:6 final size:6
Alignment explanation
Indices: 29218058--29218097 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
29218048 GTATGCGACC
* * *
29218058 GCTCGA GCTCGG GCTTGG GCTCTG GCTCGG GCTCGG GCTC
1 GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTC
29218098 TGACTCTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.33, G:0.42, T:0.23
Consensus pattern (6 bp):
GCTCGG
Found at i:29218085 original size:18 final size:18
Alignment explanation
Indices: 29218064--29218109 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
29218054 GACCGCTCGA
*
29218064 GCTCGGGCTTGGGCTCTG
1 GCTCGGGCTCGGGCTCTG
29218082 GCTCGGGCTCGGGCTCTG
1 GCTCGGGCTCGGGCTCTG
* *
29218100 ACTCTGGCTC
1 GCTCGGGCTC
29218110 ATCTTCTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.33, G:0.39, T:0.26
Consensus pattern (18 bp):
GCTCGGGCTCGGGCTCTG
Found at i:29218774 original size:14 final size:14
Alignment explanation
Indices: 29218755--29218789 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29218745 TAAATTACAT
29218755 GTTAGAATAGAATC
1 GTTAGAATAGAATC
*
29218769 GTTAGAATAGTATC
1 GTTAGAATAGAATC
*
29218783 ATTAGAA
1 GTTAGAA
29218790 AAAATGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (14 bp):
GTTAGAATAGAATC
Found at i:29221529 original size:9 final size:9
Alignment explanation
Indices: 29221515--29221539 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29221505 TTACTAATTT
29221515 AAAATTTTA
1 AAAATTTTA
29221524 AAAATTTTA
1 AAAATTTTA
29221533 AAAATTT
1 AAAATTT
29221540 AAGGATGTAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTA
Found at i:29225254 original size:37 final size:36
Alignment explanation
Indices: 29225200--29225269 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
29225190 TTCTTTTTCC
*
29225200 TTTTTTTGAAACCGTTTATACATACAAATATTTCTT
1 TTTTTTTAAAACCGTTTATACATACAAATATTTCTT
* * *
29225236 TTTTTTTAAATACTGTTTATACATATATATATTT
1 TTTTTTTAAA-ACCGTTTATACATACAAATATTT
29225270 ATTTCAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 9 0.31
37 20 0.69
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (36 bp):
TTTTTTTAAAACCGTTTATACATACAAATATTTCTT
Found at i:29225832 original size:23 final size:23
Alignment explanation
Indices: 29225789--29225834 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29225779 TTTCTGTAAA
* *
29225789 TATATTTATTTTTATCATTTTAT
1 TATATTTACTTATATCATTTTAT
29225812 TATATTTACTTATATTC-TTTTAT
1 TATATTTACTTATA-TCATTTTAT
29225835 AATTTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (23 bp):
TATATTTACTTATATCATTTTAT
Found at i:29230012 original size:24 final size:25
Alignment explanation
Indices: 29229961--29230016 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
29229951 TAATTTTAAT
**
29229961 TAATTAGGTGACTAAAAAATAATGA
1 TAATTAGGTGACTAAAAAATAACCA
* *
29229986 TAATTGGGTGATTAAAAAA-AACCA
1 TAATTAGGTGACTAAAAAATAACCA
29230010 TAATTAG
1 TAATTAG
29230017 ATCAACAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (25 bp):
TAATTAGGTGACTAAAAAATAACCA
Found at i:29233306 original size:15 final size:15
Alignment explanation
Indices: 29233286--29233318 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29233276 CCAGTACTTC
29233286 TGAAAAAATATAGCA
1 TGAAAAAATATAGCA
29233301 TGAAAAAATATAGCA
1 TGAAAAAATATAGCA
29233316 TGA
1 TGA
29233319 TACCCATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (15 bp):
TGAAAAAATATAGCA
Found at i:29233360 original size:21 final size:21
Alignment explanation
Indices: 29233334--29233375 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29233324 ATCCACTCCG
29233334 GGTGCTTTCAATGGTGCCATC
1 GGTGCTTTCAATGGTGCCATC
29233355 GGTGCTTTCAATGGTGCCATC
1 GGTGCTTTCAATGGTGCCATC
29233376 TGCTTAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.29, T:0.33
Consensus pattern (21 bp):
GGTGCTTTCAATGGTGCCATC
Found at i:29240428 original size:11 final size:11
Alignment explanation
Indices: 29240414--29240439 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29240404 AAAATAAAAA
29240414 TAAAAGTATTT
1 TAAAAGTATTT
29240425 TAAAAGTATTT
1 TAAAAGTATTT
29240436 TAAA
1 TAAA
29240440 TTTTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (11 bp):
TAAAAGTATTT
Found at i:29246563 original size:26 final size:25
Alignment explanation
Indices: 29246503--29246563 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
29246493 ACTTGAAATC
29246503 TTTGTTATATATATACATATACATG
1 TTTGTTATATATATACATATACATG
*
29246528 TGTT-TATATATATATACACATATGCAT-
1 T-TTGT-TATATATAT--ACATATACATG
29246555 TTTGTTATA
1 TTTGTTATA
29246564 ATTTATCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
25 2 0.07
26 17 0.57
27 2 0.07
28 9 0.30
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (25 bp):
TTTGTTATATATATACATATACATG
Found at i:29247673 original size:143 final size:143
Alignment explanation
Indices: 29247415--29247699 Score: 534
Period size: 143 Copynumber: 2.0 Consensus size: 143
29247405 TGCCCTAATA
29247415 TATTGGGCTGCAATTTTTTCATCTGACATAAACAATTGAATATCTTTTTAAATTTTATTGCACGA
1 TATTGGGCTGCAATTTTTTCATCTGACATAAACAATTGAATATCTTTTTAAATTTTATTGCACGA
* * *
29247480 GTTTTTAGATAAAGCTCATTTTTGAGGAGGTGAAAAGTCATGCCCTAACTCATTGGGTATGATAT
66 GTTTTTAGACAAAGCTCATTTTTGAAGAGGTGAAAAATCATGCCCTAACTCATTGGGTATGATAT
29247545 TTTCTCTCTCTAT
131 TTTCTCTCTCTAT
29247558 TATTGGGCTGCAATTTTTTCATCTGACATAAACAATTGAATATCTTTTTAAATTTTATTGCACGA
1 TATTGGGCTGCAATTTTTTCATCTGACATAAACAATTGAATATCTTTTTAAATTTTATTGCACGA
*
29247623 GTTTTTAGACAAAGCTCATTTTTGAAGAGGTGAAAAATCATGCCTTAACTCATTGGGTATGATAT
66 GTTTTTAGACAAAGCTCATTTTTGAAGAGGTGAAAAATCATGCCCTAACTCATTGGGTATGATAT
29247688 TTTCTCTCTCTA
131 TTTCTCTCTCTA
29247700 AAAGGAGAAG
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (143 bp):
TATTGGGCTGCAATTTTTTCATCTGACATAAACAATTGAATATCTTTTTAAATTTTATTGCACGA
GTTTTTAGACAAAGCTCATTTTTGAAGAGGTGAAAAATCATGCCCTAACTCATTGGGTATGATAT
TTTCTCTCTCTAT
Found at i:29251876 original size:5 final size:5
Alignment explanation
Indices: 29251866--29251923 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
29251856 ATATATATAT
* * * *
29251866 ATTCC ATTCC ACTCC ATTCC ATACT ATTCC ATTTC ATAT-C ATTCC ATTCC
1 ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC AT-TCC ATTCC ATTCC
29251916 ATTCC ATT
1 ATTCC ATT
29251924 TCATCAAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
4 1 0.02
5 42 0.95
6 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCC
Found at i:29252957 original size:51 final size:51
Alignment explanation
Indices: 29252823--29253220 Score: 283
Period size: 51 Copynumber: 7.8 Consensus size: 51
29252813 ACTATTATTA
* * * *
29252823 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-TCAA-TTT
1 TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTAAAGCTT
* * * * *
29252872 TTACGGTTCACGTTGTAGCTTTCACATAGTACTACATACGTGACTAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTAAAGCTT
* * * * *
29252924 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTAAC--CATCATT
1 TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTAAAGC-TT
** * ** *
29252974 TATCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTAAAGCTT
* ** * * * * * *
29253026 CTCGGTACATATTGTAGACGTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTA-AAGCTT
* * *
29253076 TATCGATTCACGTAGTAGCCTTCACTCAGTACTACACACGTGA-TCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACT-AAAGCTT
* * * * ** *
29253128 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCT--TTCGT
1 TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGA-CTAAAGCTT
* * * *
29253178 TCCAGTACACGTAGTAGCCTACACATAGTACTACACACGTGAC
1 TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGAC
29253221 CATCACTTTC
Statistics
Matches: 265, Mismatches: 70, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
49 5 0.02
50 77 0.29
51 171 0.65
52 9 0.03
53 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTTCACTTAGTACTACACACGTGACTAAAGCTT
Found at i:29252959 original size:26 final size:26
Alignment explanation
Indices: 29252929--29253011 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
29252919 AGCTTTTCGG
29252929 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
* * * *
29252955 TACACAT-GTAACCATCATTTA-TCAA
1 TACACATAGTAGCCTTCACTTAGT-AC
* * **
29252980 TTCACGTAGTAGCCTTCACACAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
29253006 TACACA
1 TACACA
29253012 CGTGACCAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.29
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:29253015 original size:102 final size:102
Alignment explanation
Indices: 29252828--29253220 Score: 463
Period size: 102 Copynumber: 3.9 Consensus size: 102
29252818 TATTATTCGA
* * * * * ** *
29252828 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA--ATTTTTACGGTTCACGTTGTAGC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTAT-CAATTCACGTAGTAGC
* * * *
29252891 TTTCACATAGTACTACATACGTGACTAAAGCTTTTCGG
65 CTTCACACAGTACTACACACGTGACTAAAGCTTCTCGG
*
29252929 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATCATTTATCAATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATTCACGTAGTAGCC
*
29252994 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
66 TTCACACAGTACTACACACGTGACTAAAGCTTCTCGG
* * * * * *
29253031 TACATATTGTAGACGTCACTTAGTACTACACATGTGACCATTATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATTCACGTAGTAGCC
*
29253096 TTCACTCAGTACTACACACGTGA-TCAAAGCTTCTCGG
66 TTCACACAGTACTACACACGTGACT-AAAGCTTCTCGG
* * * * * *
29253133 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCTTTC-GTT-CCAGTACACGTAGTAGC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCAATTCACGTAGTAGC
* *
29253196 CTACACATAGTACTACACACGTGAC
65 CTTCACACAGTACTACACACGTGAC
29253221 CATCACTTTC
Statistics
Matches: 251, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
101 69 0.27
102 176 0.70
103 6 0.02
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACTAAAGCTTCTCGG
Found at i:29256380 original size:44 final size:44
Alignment explanation
Indices: 29256332--29256438 Score: 153
Period size: 44 Copynumber: 2.5 Consensus size: 44
29256322 TCCCAGATAG
29256332 GGTCTTACACGAAAGTCTCAAATCAATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAGTCTCAAATCAATGCCAACGTCCCAGACGT
* * * *
29256376 GGTCTTACATGAAAGTCTCAAATCGATGCTAACGTCCTAGACGT
1 GGTCTTACACGAAAGTCTCAAATCAATGCCAACGTCCCAGACGT
* *
29256420 AGTCTTACAC-AAAATCTCA
1 GGTCTTACACGAAAGTCTCA
29256439 TACCGGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 8 0.14
44 48 0.86
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (44 bp):
GGTCTTACACGAAAGTCTCAAATCAATGCCAACGTCCCAGACGT
Found at i:29260111 original size:21 final size:21
Alignment explanation
Indices: 29260087--29260138 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
29260077 GCAGTGGCGA
* * *
29260087 TGAGATTAGTTACTGTTGCGG
1 TGAGATTAGATACTGTAGCAG
* *
29260108 TGAGATTGGATATTGTAGCAG
1 TGAGATTAGATACTGTAGCAG
29260129 TGAGATTAGA
1 TGAGATTAGA
29260139 AACAATGGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCAG
Found at i:29262220 original size:16 final size:16
Alignment explanation
Indices: 29262180--29262220 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29262170 GGCTTTTACT
29262180 TATATATTTTCAAAAA
1 TATATATTTTCAAAAA
*
29262196 TATAAATTTTCAATAAA
1 TATATATTTTCAA-AAA
29262213 T-TATATTT
1 TATATATTT
29262221 AAAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATTTTCAAAAA
Found at i:29268054 original size:16 final size:17
Alignment explanation
Indices: 29268033--29268067 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29268023 TTATCTTATG
29268033 TTAAAA-TGTTTTGTAT
1 TTAAAACTGTTTTGTAT
29268049 TTAAAACTGTTTTGTAT
1 TTAAAACTGTTTTGTAT
29268066 TT
1 TT
29268068 TTTTTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (17 bp):
TTAAAACTGTTTTGTAT
Found at i:29269643 original size:20 final size:20
Alignment explanation
Indices: 29269615--29269665 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29269605 TTTTTCAAAT
* *
29269615 AATTATTAAAAGTTA-TAGAA
1 AATTTTTAAAAATTATTA-AA
29269635 AATTTTTAAAAATTATTAAA
1 AATTTTTAAAAATTATTAAA
*
29269655 ATTTTTTAAAA
1 AATTTTTAAAA
29269666 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
AATTTTTAAAAATTATTAAA
Found at i:29273649 original size:43 final size:43
Alignment explanation
Indices: 29273600--29273779 Score: 161
Period size: 43 Copynumber: 4.2 Consensus size: 43
29273590 GCGTCGCTAA
*
29273600 CTTTAGCGGCG-TTTATAGAAAAAAAGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTT-TACAAAAAAAGCCGCTAAAGACCAAGAC
* * * * * * *
29273643 ATTTAGCGACGCTTTTCTCACAAACA-CTGTTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTT-ACAAAAAAAGCCGCTAAAGACCAAGAC
* * *
29273686 CTTTAGCGGCGCTTATT-C-CACAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTT-TTACAAAAAAAGCCGCTAAAGACCAAGAC
* * * *
29273728 CTTTAGCGGCGCCTTTTACCACAAACGCCGCTAAAGATCAAGAC
1 CTTTAGCGGCG-CTTTTACAAAAAAAGCCGCTAAAGACCAAGAC
29273772 CTTTAGCG
1 CTTTAGCG
29273780 ACGCGTCTAT
Statistics
Matches: 110, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
41 3 0.03
42 29 0.26
43 41 0.37
44 37 0.34
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACAAAAAAAGCCGCTAAAGACCAAGAC
Found at i:29273696 original size:86 final size:86
Alignment explanation
Indices: 29273600--29273779 Score: 220
Period size: 86 Copynumber: 2.1 Consensus size: 86
29273590 GCGTCGCTAA
*
29273600 CTTTAGCGGCGTTTATAGAAAAAAAGCCGCTAAAGACCAAGACATTTAGCGACG-CTTTT-CTCA
1 CTTTAGCGGCGCTTAT-GAAAAAAAGCCGCTAAAGACCAAGACATTTAGCGACGCCTTTTAC-CA
* *
29273663 CAAACACTGTTAAAGACCAAGAC
64 CAAACACCGCTAAAGACCAAGAC
*** * * * *
29273686 CTTTAGCGGCGCTTATTCCACAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCCTTTTACCACA
1 CTTTAGCGGCGCTTATGAAAAAAAGCCGCTAAAGACCAAGACATTTAGCGACGCCTTTTACCACA
* *
29273751 AACGCCGCTAAAGATCAAGAC
66 AACACCGCTAAAGACCAAGAC
29273772 CTTTAGCG
1 CTTTAGCG
29273780 ACGCGTCTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
85 30 0.38
86 49 0.61
87 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (86 bp):
CTTTAGCGGCGCTTATGAAAAAAAGCCGCTAAAGACCAAGACATTTAGCGACGCCTTTTACCACA
AACACCGCTAAAGACCAAGAC
Found at i:29273819 original size:86 final size:83
Alignment explanation
Indices: 29273625--29273846 Score: 223
Period size: 86 Copynumber: 2.6 Consensus size: 83
29273615 TAGAAAAAAA
* * * *
29273625 GCCGCTAAAGACCAAGACATTTAGCGACGCTTTTCTCACAAACACTGTTAAAGACCAAGACCTTT
1 GCCGCTAAAGA-CAAGACCTTTAGCGACGCTTTTC-CACAAACGCCGCTAAAGACCAAGACCTTT
* * *
29273690 AGCGGCGCTTATTCCACAAT
64 AGCGACGCTTATTACACAAC
* *
29273710 GCCGCTAAAGACCAAGACCTTTAGCGGCGCCTTTTACCACAAACGCCGCTAAAGATCAAGACCTT
1 GCCGCTAAAGA-CAAGACCTTTAGCGACG-CTTTT-CCACAAACGCCGCTAAAGACCAAGACCTT
29273775 TAGCGACGCGTCTATTACA-AAC
63 TAGCGACGC-T-TATTACACAAC
** * ** *
29273797 GCCGCTATAAGA-TTGACTTTTAGCGACGCTTTTTTAGAAACGCCGCTAAA
1 GCCGCTA-AAGACAAGACCTTTAGCGACGCTTTTCCACAAACGCCGCTAAA
29273847 AACATAACTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
84 14 0.12
85 32 0.28
86 49 0.42
87 11 0.09
88 10 0.09
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (83 bp):
GCCGCTAAAGACAAGACCTTTAGCGACGCTTTTCCACAAACGCCGCTAAAGACCAAGACCTTTAG
CGACGCTTATTACACAAC
Found at i:29273857 original size:41 final size:42
Alignment explanation
Indices: 29273748--29273857 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 42
29273738 GCCTTTTACC
* *
29273748 ACAAACGCCGCTAAAGATCA-AGACCTTTAGCGACGCGTCTATT
1 ACAAACGCCGCTAAA-AACATA-ACTTTTAGCGACGCGTCTATT
* * * * *
29273791 ACAAACGCCGCTATAAGA-TTGACTTTTAGCGACGC-TTTTTT
1 ACAAACGCCGCTA-AAAACATAACTTTTAGCGACGCGTCTATT
*
29273832 AGAAACGCCGCTAAAAACATAACTTT
1 ACAAACGCCGCTAAAAACATAACTTT
29273858 AAAAAAAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
40 3 0.06
41 22 0.42
42 13 0.25
43 13 0.25
44 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
ACAAACGCCGCTAAAAACATAACTTTTAGCGACGCGTCTATT
Found at i:29277437 original size:147 final size:148
Alignment explanation
Indices: 29277236--29277590 Score: 561
Period size: 148 Copynumber: 2.4 Consensus size: 148
29277226 CTATTTCTCA
* * *
29277236 AAAAAAGCCAC-AAAAATTATTTCGTTTGGAATAAAAGGACACTGTTTTGCTATGCTAAAAGGGC
1 AAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAAGGGC
* * *
29277300 GCTATTTTTTTAAAGTAAAATTA-TTTTTGTGGCGTTTTTTATAAAAATGCTGCTATTGCTTATC
66 GCTATTTTTTTAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACC
*
29277364 TTTTGCGGTGTTTTTCAT
131 TTTTGCGGCGTTTTTCAT
* * *
29277382 AAAAACGCCGCAAAAAATTATTTCATTTGGAATAAAACAACACTGTTTTGCTATGCTAAAAGGGT
1 AAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAAGGGC
*
29277447 GCTATTTTTTTAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTGCC
66 GCTATTTTTTTAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACC
29277512 TTTTGCGGCGTTTTTCAT
131 TTTTGCGGCGTTTTTCAT
* * * *
29277530 AAAAACGGCACAAAAAATTATTTCATTTAGAATAAAATGACACTGTTTTGCTATGCAAAAA
1 AAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAA
29277591 ATCTTTTATT
Statistics
Matches: 190, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
146 9 0.05
147 72 0.38
148 109 0.57
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (148 bp):
AAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAAGGGC
GCTATTTTTTTAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACC
TTTTGCGGCGTTTTTCAT
Found at i:29278468 original size:21 final size:22
Alignment explanation
Indices: 29278401--29278468 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 22
29278391 ACCGAATCCA
*
29278401 TAAACCTTAAATCCCTAACTCT
1 TAAACCTTAAATCCCTAACCCT
* * *
29278423 T-AACCTTTAACCCCTAACCCA
1 TAAACCTTAAATCCCTAACCCT
*
29278444 TAAACCTTAAATCAC-AACCCT
1 TAAACCTTAAATCCCTAACCCT
29278465 TAAA
1 TAAA
29278469 TCAGAATCCC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAACCTTAAATCCCTAACCCT
Found at i:29278975 original size:41 final size:41
Alignment explanation
Indices: 29278909--29279142 Score: 326
Period size: 41 Copynumber: 5.7 Consensus size: 41
29278899 AAATGTTTTT
* * ** *
29278909 GCGGCGC-TTTTAAAAAACACCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
29278949 GCGGCACTTTTTCAAAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
29278990 GCGGTGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
29279031 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGGGCATTC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
29279072 GCGACGCTTTTTCAAAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
29279113 GCGGCGCTTTTTTAAAGAACGCCGCTAAAG
1 GCGGCGCTTTTTCAAA-AACGCCGCTAAAG
29279143 CCCCGAAAGG
Statistics
Matches: 172, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 6 0.03
41 154 0.90
42 12 0.07
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:29284649 original size:25 final size:25
Alignment explanation
Indices: 29284622--29284669 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
29284612 TTATATAATT
*
29284622 TTTTTTTA-TCAATTTGACTTTTTA
1 TTTTTTTAGTAAATTTGACTTTTTA
29284646 TTTTTTTAGTTAAATTTGACTTTT
1 TTTTTTTAG-TAAATTTGACTTTT
29284670 AACTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTTTTTAGTAAATTTGACTTTTTA
Found at i:29285854 original size:16 final size:17
Alignment explanation
Indices: 29285833--29285876 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
29285823 TTTGGTTCGC
29285833 TGTAAT-GTAATAGAGG
1 TGTAATAGTAATAGAGG
29285849 TGTAATAG-AATAGAGG
1 TGTAATAGTAATAGAGG
*
29285865 CGTAATAGTAAT
1 TGTAATAGTAAT
29285877 TCAATTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.30
Consensus pattern (17 bp):
TGTAATAGTAATAGAGG
Found at i:29286584 original size:10 final size:11
Alignment explanation
Indices: 29286569--29286598 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
29286559 TTATATATAT
29286569 TTTTATTTTC-
1 TTTTATTTTCA
29286579 TTTTATTTTCA
1 TTTTATTTTCA
29286590 TTTTATTTT
1 TTTTATTTT
29286599 TCCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:29287201 original size:3 final size:3
Alignment explanation
Indices: 29287195--29287251 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
29287185 GTTTTTTTAA
* * *
29287195 ATT ATT ATT ATT ATT ATC ATTT ATT ATC ATT ATT ATAT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T ATT ATT ATT
*
29287242 ATT ACT ATT A
1 ATT ATT ATT A
29287252 CTATCTCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:29287220 original size:13 final size:12
Alignment explanation
Indices: 29287195--29287245 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
29287185 GTTTTTTTAA
*
29287195 ATTATTATTATT
1 ATTATCATTATT
29287207 ATTATCATTTATT
1 ATTATCA-TTATT
* *
29287220 ATCATTATTATAT
1 ATTATCATTAT-T
29287233 ATTATCATTATT
1 ATTATCATTATT
29287245 A
1 A
29287246 CTATTACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATCATTATT
Found at i:29287220 original size:19 final size:19
Alignment explanation
Indices: 29287195--29287245 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29287185 GTTTTTTTAA
29287195 ATTATTATTATTATTATCAT
1 ATTATTATTATTATTAT-AT
*
29287215 -TTATTATCATTATTATAT
1 ATTATTATTATTATTATAT
*
29287233 ATTATCATTATTA
1 ATTATTATTATTA
29287246 CTATTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATTATTATTATTATAT
Found at i:29287244 original size:16 final size:15
Alignment explanation
Indices: 29287195--29287251 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
29287185 GTTTTTTTAA
*
29287195 ATTATTATTATTATT
1 ATTATTATTATCATT
*
29287210 ATCATTTATTATCATT
1 ATTA-TTATTATCATT
29287226 ATTATATATTATCATT
1 ATTAT-TATTATCATT
*
29287242 ATTACTATTA
1 ATTATTATTA
29287252 CTATCTCTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.25
16 27 0.75
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATCATT
Found at i:29287406 original size:22 final size:21
Alignment explanation
Indices: 29287359--29287401 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
29287349 CATATATATA
*
29287359 TATATACATTTTTTTGAATTAT
1 TATAAACATTTTTTT-AATTAT
29287381 TATAAACATTTTTTT-ATTAT
1 TATAAACATTTTTTTAATTAT
29287401 T
1 T
29287402 CTATATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TATAAACATTTTTTTAATTAT
Found at i:29292091 original size:49 final size:49
Alignment explanation
Indices: 29292038--29292148 Score: 161
Period size: 49 Copynumber: 2.3 Consensus size: 49
29292028 TAAAAGGTGG
* *
29292038 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAA-AGAGA
1 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGT-AAAAAAAATAGAGA
*
29292087 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAATGGAGA
1 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAATAGAGA
* *
29292136 GGCTAAGGTGAAA
1 GACCAAGGTGAAA
29292149 ACTCGCAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 8 0.14
49 48 0.86
ACGTcount: A:0.44, C:0.14, G:0.29, T:0.13
Consensus pattern (49 bp):
GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAATAGAGA
Found at i:29292158 original size:49 final size:49
Alignment explanation
Indices: 29292038--29292166 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
29292028 TAAAAGGTGG
* *
29292038 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAGAGA
1 GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTCAAAAAAAAAGAGA
* * *
29292087 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGT-AAAAAAAATGGAGA
1 GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTCAAAAAAAA-AGAGA
* * *
29292136 GGCTAAGGTGAAAA-CTCGCAAAGGGCGCCTT
1 GACCAAGGTGAAAACCT-ACAAAGGGCGCCTT
29292167 AGACCAAAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
48 10 0.14
49 60 0.86
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.13
Consensus pattern (49 bp):
GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTCAAAAAAAAAGAGA
Found at i:29293527 original size:89 final size:88
Alignment explanation
Indices: 29293431--29294153 Score: 524
Period size: 89 Copynumber: 8.1 Consensus size: 88
29293421 ATCGAAGACC
* * *
29293431 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
29293496 GGCGTGAAGTAGATCAAAGTCAAA
66 GGCGTGAAGTAGATCAAAGT-AAA
* * * * *
29293520 AAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATGTAT
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGTAT
* * **
29293584 TGGCGTGAAGTAGATCAGAGATACT
65 CGGCGTGAAGTAGATCAAAG-TAAA
* * *
29293609 AGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTA-C
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
* * **
29293673 TGACGTGAAGTAGATCAGAGATACT
66 -GGCGTGAAGTAGATCAAAG-TAAA
*** * * * * * * *
29293698 AGATCTTGTCTTCATGTACT-G-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCTATA-C
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
* * *
29293760 TGGTGGTGGAGTAGATCGAAG-AAA
66 -GG-CGTGAAGTAGATCAAAGTAAA
*** * * * * * * *
29293784 GTAGATCTTGTCTTCATGTA-TCGG-CGTGAAGTAGATCAAAGTCAA-CAAATCTTGCCTTCCTA
1 --AGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCGAAG-AAAGCAGATCTTGTCTTCATG
* * * *
29293846 TACTAGTG-GCGAAGTAGATCGAAGAAAA
62 TA-TCG-GCGTGAAGTAGATCAAAGTAAA
* **** * * *
29293874 CAGATCTTTTCTTTATGTACTGG-CGTGAAGTAGATC-AGAGATA-CTAGATCTAGTCTTCATGT
1 -AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGA-AGAAAGC-AGATCTTGTCTTCATGT
**
29293936 A-CTGGCGTGAAGTAGATCAAAGATACC
63 ATC-GGCGTGAAGTAGATCAAAG-TAAA
* * *
29293963 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
29294028 GGCGTGAAGTAGATCAAAGTCAACA
66 GGCGTGAAGTAGATCAAAGT-AA-A
* * * *
29294053 A-ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATGTAT
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGTAT
* * ** *
29294116 TGGTGTGAAGTAGATTGAAGAAAA
65 CGGCGTGAAGTAGATCAAAGTAAA
29294140 CAGATCTTGTCTTC
1 -AGATCTTGTCTTC
29294154 ATGTATTGGC
Statistics
Matches: 515, Mismatches: 90, Indels: 58
0.78 0.14 0.09
Matches are distributed among these distances:
86 1 0.00
87 38 0.07
88 74 0.14
89 389 0.76
90 12 0.02
91 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (88 bp):
AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
GGCGTGAAGTAGATCAAAGTAAA
Found at i:29293997 original size:310 final size:310
Alignment explanation
Indices: 29293428--29294130 Score: 914
Period size: 310 Copynumber: 2.3 Consensus size: 310
29293418 TGGATCGAAG
29293428 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
1 ACCAGATCTTGTCT-CCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
* * *
29293493 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGA
65 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCGA
** * * *
29293558 AAATGGCAAATCTTATATTCATGTATTGGCGTGAAGTAGATCAGAGATACTAGATCTTGCCTTCC
130 AAATAACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTCA
* * * **
29293623 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGAT
195 CATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACTGACGTGAAGTAGAT
* *
29293688 C-AGAGATACTAGATCTTGTCTTCATGTA-CTGCGTGAAGTAGATCAAAGAT-
260 CGA-AGAAACTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAG-TC
29293738 ACCAGATCTTGTCTCCCTATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
1 ACCAGATCTTGTCTCCC-ATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
* *
29293803 ATCGGCGTGAAGTAGATCAAAGTCAACAAATCTTGCCTTCCTATACTAGTGGCGAAGTAGATCGA
65 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCGA
* * * * *
29293868 AGAA-AACAGATCTTTTCTTTATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGTCTTC
130 A-AATAACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTC
** * * * * ** *
29293932 ATGTACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAG
194 ACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACT-GACGTGAAGTAG
*
29293996 ATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
258 ATCGAAGAAACTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
* * * * * * * *
29294049 AACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATG
1 ACCAGATCTTGTC-TCCCATACTGGTGGTGGAGTAGATCGAAGAA-AGTAGATCTTGTCTTCATG
* *
29294113 TATTGGTGTGAAGTAGAT
64 TATCGGCGTGAAGTAGAT
29294131 TGAAGAAAAC
Statistics
Matches: 343, Mismatches: 42, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
309 36 0.10
310 217 0.63
311 86 0.25
312 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (310 bp):
ACCAGATCTTGTCTCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTA
TCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCGAA
AATAACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTCAC
ATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACTGACGTGAAGTAGATC
GAAGAAACTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
Found at i:29294042 original size:222 final size:222
Alignment explanation
Indices: 29293475--29294177 Score: 974
Period size: 222 Copynumber: 3.2 Consensus size: 222
29293465 TCGAAGAAAG
** * *
29293475 TAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAAG-TCAAAAAATCTTGTCTTCCCATA
1 TAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAGAT-ACCAGATCTTGTCTCCCCATA
* * * * * * * *
29293538 CTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATGTATTGGCGTGAAGTAGATCAG
64 CTGGTGGTGGAGTAGATCGAAGAA-AGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAA
* *
29293602 AG--ATACTAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
128 AGTCA-AC-AAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTATCT
*
29293665 TCATGTACTGACGTGAAGTAGATCAGAGATAC
191 TCATGTACTGGCGTGAAGTAGATCAGAGATAC
*
29293697 TAGATCTTGTCTTCATGTACT-GCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCTATACT
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
29293761 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
66 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
* * * *
29293826 CAACAAATCTTGCCTTCCTATACTAGTGGCGAAGTAGATCGAAGAAAACAGATCTTTTCTTTATG
131 CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTATCTTCATG
29293891 TACTGGCGTGAAGTAGATCAGAGATAC
196 TACTGGCGTGAAGTAGATCAGAGATAC
*
29293918 TAGATCTAGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
29293983 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
66 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
* * ** * *
29294048 CAACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCAT
131 CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA-AACAGATCTTATCTTCAT
* * * *
29294112 GTATTGGTGTGAAGTAGAT-TGAAGAAAAC
195 GTACTGGCGTGAAGTAGATCAG-AG-ATAC
* *
29294141 -AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAA
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
29294178 GAACGGTAGA
Statistics
Matches: 434, Mismatches: 38, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
221 194 0.45
222 235 0.54
223 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (222 bp):
TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTATCTTCATG
TACTGGCGTGAAGTAGATCAGAGATAC
Found at i:29294177 original size:133 final size:131
Alignment explanation
Indices: 29293447--29294177 Score: 562
Period size: 133 Copynumber: 5.5 Consensus size: 131
29293437 TGTCTCCCCA
* ** *
29293447 TACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
* *** * ** * *
29293512 AAGTCAAA-AAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAAATGGCAAATCTTATAT
66 AAG--AAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAATAACAAATCTTGTCT
29293576 TCATG
127 TCATG
* * * * *** * * *
29293581 TATTGG-CGTGAAGTAGATC--AGAGATACTAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGA
1 TACTGGTGGTGAAGTAGATCGAAGA-AAAC-AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGA
* * * *
29293643 TCGAAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAGAGAT-ACTAGATCTTGT
63 TCAAAG-AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA-AAATAAC-AAATCTTGT
29293707 CTTCATG
125 CTTCATG
* * * * * * * * * *
29293714 TACT-G-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCTATACTGGTGGTGGAGTAGATC
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
* * * *
29293777 GAAGAAAGTAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAAGTCAACAAATCTTGCCT
65 AAAGAAA-CAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAAT-AACAAATCTTGTCT
* *
29293841 TCCTA
127 TCATG
* * * * *
29293846 TACTAGTGGCGAAGTAGATCGAAGAAAACAGATCTTTTCTTTATGTACTGGCGTGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
* * * * * *
29293911 GAGATACTAGATCTAGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCC
66 AAGAAAC-AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA-ATAACAAATCTTGTCTTC
***
29293976 CCA
129 ATG
* ** *
29293979 TACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
* * *** * ** * *
29294044 AAGTCAACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAAATGGCAAATCTTATATT
66 AAG-AAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAATAACAAATCTTGTCTT
29294109 CATG
128 CATG
* * *
29294113 TATTGGT-GTGAAGTAGATTGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
29294177 A
66 A
29294178 GAACGGTAGA
Statistics
Matches: 476, Mismatches: 101, Indels: 41
0.77 0.16 0.07
Matches are distributed among these distances:
131 9 0.02
132 101 0.21
133 256 0.54
134 107 0.22
135 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (131 bp):
TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
AAGAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAATAACAAATCTTGTCTTCAT
G
Found at i:29295128 original size:10 final size:11
Alignment explanation
Indices: 29295113--29295142 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
29295103 TATATATATT
29295113 TTTTATTTTC-
1 TTTTATTTTCA
29295123 TTTTATTTTCA
1 TTTTATTTTCA
29295134 TTTTATTTT
1 TTTTATTTT
29295143 TCCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:29295743 original size:3 final size:3
Alignment explanation
Indices: 29295737--29295793 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
29295727 GTTTTTTTAA
* * *
29295737 ATT ATT ATT ATT ATT ATC ATTT ATT ATC ATT ATT ATAT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T ATT ATT ATT
*
29295784 ATT ACT ATT A
1 ATT ATT ATT A
29295794 CTATCTCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:29295762 original size:13 final size:12
Alignment explanation
Indices: 29295737--29295787 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
29295727 GTTTTTTTAA
*
29295737 ATTATTATTATT
1 ATTATCATTATT
29295749 ATTATCATTTATT
1 ATTATCA-TTATT
* *
29295762 ATCATTATTATAT
1 ATTATCATTAT-T
29295775 ATTATCATTATT
1 ATTATCATTATT
29295787 A
1 A
29295788 CTATTACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATCATTATT
Found at i:29295762 original size:19 final size:19
Alignment explanation
Indices: 29295737--29295787 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29295727 GTTTTTTTAA
29295737 ATTATTATTATTATTATCAT
1 ATTATTATTATTATTAT-AT
*
29295757 -TTATTATCATTATTATAT
1 ATTATTATTATTATTATAT
*
29295775 ATTATCATTATTA
1 ATTATTATTATTA
29295788 CTATTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATTATTATTATTATAT
Found at i:29295786 original size:16 final size:15
Alignment explanation
Indices: 29295737--29295793 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
29295727 GTTTTTTTAA
*
29295737 ATTATTATTATTATT
1 ATTATTATTATCATT
*
29295752 ATCATTTATTATCATT
1 ATTA-TTATTATCATT
29295768 ATTATATATTATCATT
1 ATTAT-TATTATCATT
*
29295784 ATTACTATTA
1 ATTATTATTA
29295794 CTATCTCTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.25
16 27 0.75
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATCATT
Found at i:29297000 original size:18 final size:18
Alignment explanation
Indices: 29296977--29297014 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29296967 TTATTATTAA
*
29296977 ATATAATTTAATCAAAAT
1 ATATAATTTAATAAAAAT
29296995 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
29297013 AT
1 AT
29297015 TCTTATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:29297113 original size:27 final size:26
Alignment explanation
Indices: 29297054--29297118 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
29297044 TATAATACTA
* *
29297054 TAAATATAATTTTAACATAATTATTAT
1 TAAATATAA-TTTAACAAAATTATAAT
*
29297081 TAAATATAATTTAATAAAATATATAAT
1 TAAATATAATTTAACAAAAT-TATAAT
* *
29297108 TTAATAAAATT
1 TAAATATAATT
29297119 ATTAATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAATATAATTTAACAAAATTATAAT
Found at i:29297124 original size:17 final size:17
Alignment explanation
Indices: 29297084--29297117 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29297074 TTATTATTAA
29297084 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29297101 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29297118 TATTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29297126 original size:22 final size:21
Alignment explanation
Indices: 29297076--29297126 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 21
29297066 TAACATAATT
29297076 ATTATTAAATATAATTTAATAA
1 ATTATT-AATATAATTTAATAA
29297098 A--A-T-ATATAATTTAATAAA
1 ATTATTAATATAATTTAAT-AA
29297116 ATTATTAATAT
1 ATTATTAATAT
29297127 TAAATATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
17 12 0.50
18 3 0.12
19 1 0.04
20 2 0.08
21 1 0.04
22 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTATTAATATAATTTAATAA
Found at i:29297682 original size:119 final size:121
Alignment explanation
Indices: 29297009--29297658 Score: 1182
Period size: 121 Copynumber: 5.4 Consensus size: 121
29296999 AATTTAATAA
29297009 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTAT-AAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
*
29297073 ATTATTATTAAATATAATTTAAT-AAAATATATAATTTAATAAAATTATTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
29297128 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATATTTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
*
29297193 ATTATTATTAAATATAATTTAAAAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
29297249 AAATATTCTGATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
*
29297314 ATTACTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
29297370 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
29297435 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
29297491 AAATATTCTTATAAGAATTTACTAAAATCATAATATATAATGCTATAAAATATAA-TTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
* *
29297555 A-TATTATTAAATATAATTTAATAAAAATATATAATTTTATAAAATTCTTAAAATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
29297610 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
29297659 GATAATGTAT
Statistics
Matches: 514, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 145 0.28
120 49 0.10
121 320 0.62
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (121 bp):
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
Found at i:29307267 original size:26 final size:27
Alignment explanation
Indices: 29307215--29307267 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
29307205 CCATTTACAA
* *
29307215 AAATATACAGGCCCAAATACATTACCC
1 AAATATACAAGCCCAAATACATAACCC
29307242 AAAT-TACAAGCCCAAACTAC-TAACCC
1 AAATATACAAGCCCAAA-TACATAACCC
29307268 TAGTCCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.17
Consensus pattern (27 bp):
AAATATACAAGCCCAAATACATAACCC
Found at i:29319901 original size:44 final size:44
Alignment explanation
Indices: 29319838--29320273 Score: 368
Period size: 44 Copynumber: 9.6 Consensus size: 44
29319828 TACCATAGCG
* *
29319838 AATCTTATCTTCTTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
29319882 AATCTCATCTTCCTGAAGTTGTAGTGGAGCAGATTAAAACTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
29319926 AATCTTATC-TCCTTGAAGTTGCAGTGGAGCAGATTGAAA-CTACA
1 AATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* * *
29319970 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
29320014 AATCTTATC-TCACTGAAGTTGTAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
29320058 AATCTTATCTTGCTGAAGTTGCAGTGGAGAAGATTGAAG-TGACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-ACA
* * *
29320102 AATCTTATGCCT-CTGAAGTTACAGTGG-GTC-GAATTAAATCTACCA
1 AATCTTAT-CTTCCTGAAGTTGCAGTGGAG-CAG-ATTAAAGCTA-CA
* * * *
29320147 TAGCGAGTTTTAT-TTCCCTGAAGTTGCAGTGGAATAGATTAAATCTACAAGTTACA
1 -A---A-TCTTATCTT-CCTGAAGTTGCAGTGG---AG--CAGAT-TA-AAGCTACA
* * *
29320203 AATCTTATCTCCCTGAACTTGCAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
29320247 AGTCCTATC-ACCTTAAAGTTGCAGTGG
1 AATCTTATCTTCC-TGAAGTTGCAGTGG
29320274 GTTAGAATGA
Statistics
Matches: 321, Mismatches: 42, Indels: 58
0.76 0.10 0.14
Matches are distributed among these distances:
43 12 0.04
44 235 0.73
45 12 0.04
46 4 0.01
48 3 0.01
49 1 0.00
50 19 0.06
51 20 0.06
52 2 0.01
54 1 0.00
55 4 0.01
56 4 0.01
57 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:29320139 original size:132 final size:132
Alignment explanation
Indices: 29319838--29320128 Score: 419
Period size: 132 Copynumber: 2.2 Consensus size: 132
29319828 TACCATAGCG
* * *
29319838 AATCTTATCTTCTTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTG
*
29319903 TAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTA
66 TAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAACTA
29319968 CA
131 CA
*
29319970 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATC-TCACTGAAGTT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTCATCTTC-CTGAAGTT
* * * *
29320034 GTAGTGGAGCAGATTGAAGCTACAAATCTTATCTTGC-TGAAGTTGCAGTGGAGAAGATTG-AAG
65 GTAGTGGAGCAGATTAAAACTACAAATCTTATC-TCCTTGAAGTTGCAGTGGAGAAGATTGAAAC
29320097 TGACA
129 T-ACA
* *
29320102 AATCTTATGC-CTCTGAAGTTACAGTGG
1 AATCTTAT-CTCCCTAAAGTTACAGTGG
29320129 GTCGAATTAA
Statistics
Matches: 144, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
131 5 0.03
132 136 0.94
133 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (132 bp):
AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTG
TAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAACTA
CA
Found at i:29321921 original size:3 final size:3
Alignment explanation
Indices: 29321905--29321953 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
29321895 TTGTTGCCCC
* * *
29321905 TAT TAT TAC CAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29321953 T
1 T
29321954 TATTTTACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:29326128 original size:33 final size:33
Alignment explanation
Indices: 29326086--29326148 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
29326076 GGAAAGATAC
29326086 AAAGAATTATTACGGAAGCGCCCTCATCACAGA
1 AAAGAATTATTACGGAAGCGCCCTCATCACAGA
* * *
29326119 AAAGAATTATTATGGAAGTGCCCTTATCAC
1 AAAGAATTATTACGGAAGCGCCCTCATCAC
29326149 GGAATCCCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (33 bp):
AAAGAATTATTACGGAAGCGCCCTCATCACAGA
Found at i:29330461 original size:22 final size:23
Alignment explanation
Indices: 29330428--29330471 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
29330418 GAACATGTTG
29330428 AATTTTACTTAATTTT-ATAATA
1 AATTTTACTTAATTTTGATAATA
29330450 AATTTTGA-TTAATTTTGATAAT
1 AATTTT-ACTTAATTTTGATAAT
29330472 TTTCAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTACTTAATTTTGATAATA
Found at i:29334207 original size:21 final size:21
Alignment explanation
Indices: 29334169--29334208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29334159 CTAAAGTTTG
**
29334169 GTTTCTTGCAAATTAAGTCAA
1 GTTTCTTGCAAAACAAGTCAA
29334190 GTTTCTTGCAAAACAAGTC
1 GTTTCTTGCAAAACAAGTC
29334209 GCTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTTCTTGCAAAACAAGTCAA
Found at i:29340876 original size:17 final size:16
Alignment explanation
Indices: 29340842--29340872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29340832 AATTAATTTA
*
29340842 AATTAACTAATTTTTC
1 AATTAAATAATTTTTC
29340858 AATTAAATAATTTTT
1 AATTAAATAATTTTT
29340873 TCAACCCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAATAATTTTTC
Found at i:29341011 original size:4 final size:4
Alignment explanation
Indices: 29341002--29341034 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
29340992 TATTCAAACT
29341002 TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
29341035 TAAAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:29344812 original size:17 final size:17
Alignment explanation
Indices: 29344781--29344825 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
29344771 TATATTTTAT
29344781 ATGTTATTA-TTATTAC
1 ATGTTATTATTTATTAC
* *
29344797 ATTTTATTATTTATTAT
1 ATGTTATTATTTATTAC
29344814 ATGTTATT-TTTA
1 ATGTTATTATTTA
29344826 AATACAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (17 bp):
ATGTTATTATTTATTAC
Found at i:29345820 original size:2 final size:2
Alignment explanation
Indices: 29345813--29345838 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29345803 TTGTACTATT
29345813 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
29345839 GCATCTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29346795 original size:2 final size:2
Alignment explanation
Indices: 29346788--29346832 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29346778 TAATCTAACA
29346788 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29346830 TC T
1 TC T
29346833 AACCTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29356038 original size:18 final size:18
Alignment explanation
Indices: 29356013--29356053 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
29356003 CAACCCAATT
*
29356013 TTTA-TTTTTATCATTA-
1 TTTATTTTTTTTCATTAC
*
29356029 TTTATTTTTTTTCTTTAC
1 TTTATTTTTTTTCATTAC
29356047 TTTATTT
1 TTTATTT
29356054 ATTACTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTTTTCATTAC
Found at i:29363828 original size:42 final size:42
Alignment explanation
Indices: 29363797--29363891 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
29363787 GGCCAGGAAT
29363797 ATGGGCGTGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
1 ATGGGCGTGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
* ** * *
29363839 ATGGGCGTGTGCCCAAGCCCTGTGAGTTACACGGGCAAAGAC
1 ATGGGCGTGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
*
29363881 ATGGGCATGTG
1 ATGGGCGTGTG
29363892 TCCAGGTCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (42 bp):
ATGGGCGTGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
Found at i:29365580 original size:813 final size:813
Alignment explanation
Indices: 29364014--29365646 Score: 3221
Period size: 813 Copynumber: 2.0 Consensus size: 813
29364004 GAATAGGATC
29364014 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
1 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
29364079 TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
66 TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
29364144 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
131 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
*
29364209 AACCTAAGTGAGTAGGACCTGTCAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
196 AACCTAAGTGAGTAGGACCTGTCAAAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
*
29364274 ACGATATCTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
261 ACGATATCTATTCTATTAAGTTTGTTGGTACACCTCTACATTGCTTTGTTAATGAAGAATATGTG
29364339 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
326 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
29364404 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
391 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
*
29364469 TGTTATTTAGAGATGGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
456 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
29364534 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
521 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
29364599 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
586 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
29364664 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
651 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
29364729 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
716 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
29364794 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
781 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
29364827 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
1 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
29364892 TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
66 TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
29364957 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
131 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
*
29365022 AACCTAAGTGAGTAGGACCTGTCAAAATGTAATGTCCTATTGTCTATGTGTGCGAATTATCAGGT
196 AACCTAAGTGAGTAGGACCTGTCAAAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
29365087 ACGATATCTATTCTATTAAGTTTGTTGGTACACCTCTACATTGCTTTGTTAATGAAGAATATGTG
261 ACGATATCTATTCTATTAAGTTTGTTGGTACACCTCTACATTGCTTTGTTAATGAAGAATATGTG
29365152 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
326 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
29365217 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
391 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
29365282 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
456 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
29365347 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
521 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
29365412 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
586 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
29365477 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
651 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
29365542 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
716 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
29365607 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
781 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
*
29365640 TGCATCT
1 TGAATCT
29365647 GCATAAACAT
Statistics
Matches: 815, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
813 815 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (813 bp):
TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
AACCTAAGTGAGTAGGACCTGTCAAAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
ACGATATCTATTCTATTAAGTTTGTTGGTACACCTCTACATTGCTTTGTTAATGAAGAATATGTG
AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
Found at i:29367468 original size:5 final size:5
Alignment explanation
Indices: 29367458--29367490 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
29367448 TAATAAGCAG
29367458 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29367491 CATGTTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:29369297 original size:44 final size:44
Alignment explanation
Indices: 29369224--29369582 Score: 260
Period size: 44 Copynumber: 8.0 Consensus size: 44
29369214 ACTCTCTGTG
* * *
29369224 GTAGATTTAATCTGAC-CCACTGCAACTTCAGAGG-TATAGGATTT
1 GTAGCTTTAATCT-ACTCCACTGCAACTTCAG-GGAGATAAGATTT
* * *
29369268 GTCGCTTTAATCTACTCCACTGCAGCTTCAGCGAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * *
29369312 GTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATTAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * *
29369356 GTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * * *
29369400 GTAGCTTTAA-CTTGCTCCACTACAACTTCAAGGAAATAAGATTCGCCAT
1 GTAGCTTTAATC-TACTCCACTGCAACTTCAGGGAGATAAGATT-----T
* * * * *
29369449 GGTAACTTTAATCCGACT-CACTGCAACTTTAGGG-TATAGGATATT
1 -GTAGCTTTAAT-CTACTCCACTGCAACTTCAGGGAGATAAGAT-TT
* * * ** * * * *
29369494 TTAGCTTCAATTTGTTCTACTACAACTTCAAGAAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
* * * ** *
29369538 GTGGCTTTAATCTGCTCTACTATAGCTTCAGGGAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
29369582 G
1 G
29369583 CCTTGGTAAC
Statistics
Matches: 249, Mismatches: 52, Indels: 28
0.76 0.16 0.09
Matches are distributed among these distances:
43 4 0.02
44 205 0.82
45 7 0.03
49 7 0.03
50 23 0.09
51 2 0.01
52 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (44 bp):
GTAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
Found at i:29369442 original size:88 final size:87
Alignment explanation
Indices: 29369240--29369582 Score: 289
Period size: 88 Copynumber: 3.8 Consensus size: 87
29369230 TTAATCTGAC
* * * * * * *
29369240 CCACTGCAACTTCAGAGG-TATAGGATTTGTCGCTTTAATCTACTCCACTGCAGCTTCAGCGAGA
1 CCACTACAACTTCA-AGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
*
29369304 TAAGATTTGTAGTTTTAATCTGCT
65 TAAGATTTGTAGCTTTAAT-TGCT
* * * * * *
29369328 CCACTGCAACTTCAGGGAGATTAGATTTGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGAT
1 CCACTACAACTTCAAGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
29369393 AAGATTTGTAGCTTTAACTTGCT
66 AAGATTTGTAGCTTTAA-TTGCT
* * *
29369416 CCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTTAATCCGACT-CACTGCAACTTTA
1 CCACTACAACTTCAAGGAAATAAGATT-----T-GTAGCTTTAATCTG-CTCCACTGCAACTTCA
* * * * *
29369480 GGG-TATAGGATATTTTAGCTTCAATTTGTT
59 GGGAGATAAGAT-TTGTAGCTTTAA-TTGCT
* * * ** *
29369510 CTACTACAACTTCAA-GAAGATAAGATTTGTGGCTTTAATCTGCTCTACTATAGCTTCAGGGAGA
1 CCACTACAACTTCAAGGAA-ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
29369574 TAAGATTTG
65 TAAGATTTG
29369583 CCTTGGTAAC
Statistics
Matches: 204, Mismatches: 38, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
87 4 0.02
88 119 0.58
89 8 0.04
93 10 0.05
94 61 0.30
95 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (87 bp):
CCACTACAACTTCAAGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTTGTAGCTTTAATTGCT
Found at i:29369667 original size:138 final size:138
Alignment explanation
Indices: 29369329--29369633 Score: 337
Period size: 138 Copynumber: 2.2 Consensus size: 138
29369319 TAATCTGCTC
* * * * * * * ** * *
29369329 CACTGCAACTTCAGGGAGATTAGAT-TTGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGAT
1 CACTGCAACTTCAGGG-TATAAGATATTATAGCTTCAATCTGATCTACTACAACTTCAAGAAGAT
*
29369393 AAGATTTGTAGCTTTAACTTGCTCCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTT
65 AAGATTTGTAGCTTTAACTTGCTCCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTC
29369458 AATCCGACT
130 AATCCGACT
* * * * *
29369467 CACTGCAACTTTAGGGTATAGGATATTTTAGCTTCAATTTGTTCTACTACAACTTCAAGAAGATA
1 CACTGCAACTTCAGGGTATAAGATATTATAGCTTCAATCTGATCTACTACAACTTCAAGAAGATA
* * * * * * * *
29369532 AGATTTGTGGCTTTAA-TCTGCTCTACTATAGCTTCAGGGAGATAAGATTTGCCTTGGTAACTTC
66 AGATTTGTAGCTTTAACT-TGCTCCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTC
29369596 AATCCGACT
130 AATCCGACT
29369605 CACTGCAACTTCAGGGGTATAAGAT-TTAT
1 CACTGCAACTTCA-GGGTATAAGATATTAT
29369634 GGTCTCACTG
Statistics
Matches: 139, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
137 6 0.04
138 123 0.88
139 10 0.07
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (138 bp):
CACTGCAACTTCAGGGTATAAGATATTATAGCTTCAATCTGATCTACTACAACTTCAAGAAGATA
AGATTTGTAGCTTTAACTTGCTCCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTCA
ATCCGACT
Found at i:29381125 original size:5 final size:5
Alignment explanation
Indices: 29381115--29381143 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29381105 TAATAAGCAG
29381115 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
29381144 GAAACATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:29384843 original size:16 final size:16
Alignment explanation
Indices: 29384822--29384871 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 16
29384812 GTATTCTCTC
29384822 ATAATTAACTTTAATT
1 ATAATTAACTTTAATT
29384838 ATAATT-A-TTT-ATT
1 ATAATTAACTTTAATT
29384851 A-AA--AACTTTAATT
1 ATAATTAACTTTAATT
29384864 ATAATTAA
1 ATAATTAA
29384872 ATAAACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 1 0.04
12 5 0.18
13 8 0.29
14 5 0.18
15 1 0.04
16 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATTAACTTTAATT
Found at i:29392666 original size:21 final size:21
Alignment explanation
Indices: 29392627--29392666 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29392617 ACGTTATCGA
* **
29392627 TTTTTAATTTAATTGATTAAT
1 TTTTTAATTAAATAAATTAAT
29392648 TTTTTAATTAAATAAATTA
1 TTTTTAATTAAATAAATTA
29392667 CTAAAAATAA
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTTAATTAAATAAATTAAT
Found at i:29395482 original size:16 final size:15
Alignment explanation
Indices: 29395461--29395490 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29395451 AATTAAATAC
29395461 AACAACATTCATTAAT
1 AACAACATT-ATTAAT
29395477 AACAACATTATTAA
1 AACAACATTATTAA
29395491 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AACAACATTATTAAT
Found at i:29401819 original size:8 final size:8
Alignment explanation
Indices: 29401795--29401837 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
29401785 AAATATTGTA
29401795 TTTATTAT
1 TTTATTAT
29401803 CTCTTATTAT
1 -T-TTATTAT
29401813 TTTATTAT
1 TTTATTAT
29401821 TTTATTAT
1 TTTATTAT
29401829 TTTATTAT
1 TTTATTAT
29401837 T
1 T
29401838 ACGAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 24 0.73
9 2 0.06
10 7 0.21
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTATTAT
Found at i:29406246 original size:4 final size:4
Alignment explanation
Indices: 29406237--29406265 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
29406227 AATACAGATA
29406237 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
29406266 TCAGTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:29408361 original size:21 final size:21
Alignment explanation
Indices: 29408337--29408378 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29408327 ATTTTCAAAT
*
29408337 TAATTGCACATTGATTTGTAA
1 TAATTGCACATTAATTTGTAA
*
29408358 TAATTGCATATTAATTTGTAA
1 TAATTGCACATTAATTTGTAA
29408379 ATTTTTGTGT
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:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATTGCACATTAATTTGTAA
Found at i:29409854 original size:32 final size:32
Alignment explanation
Indices: 29409818--29409888 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
29409808 TTGTTGGATT
29409818 TTGAAATTATTATGTTTTAAA-TTTGTTAGACA
1 TTGAAATTATTATGTTTTAAACTTT-TTAGACA
* * *
29409850 TTGAATTTATTATGTTTTAAACTTTTTGGATA
1 TTGAAATTATTATGTTTTAAACTTTTTAGACA
29409882 TTGAAAT
1 TTGAAAT
29409889 GATTGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (32 bp):
TTGAAATTATTATGTTTTAAACTTTTTAGACA
Found at i:29412780 original size:19 final size:19
Alignment explanation
Indices: 29412744--29412791 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29412734 TTAGTAAAAT
*
29412744 ATTTAATATTACAATTTAA
1 ATTTAATAATACAATTTAA
*
29412763 TTTTAATAATA-AATTTTAA
1 ATTTAATAATACAA-TTTAA
*
29412782 AATTAATAAT
1 ATTTAATAAT
29412792 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAATAATACAATTTAA
Found at i:29413542 original size:15 final size:15
Alignment explanation
Indices: 29413520--29413558 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
29413510 GTTCGTTTCA
29413520 CAAAAAAAATAATTT
1 CAAAAAAAATAATTT
**
29413535 -TTAAAAAATAATTT
1 CAAAAAAAATAATTT
29413549 CAAAAAAAAT
1 CAAAAAAAAT
29413559 TACTAAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
CAAAAAAAATAATTT
Found at i:29422832 original size:23 final size:24
Alignment explanation
Indices: 29422783--29422840 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
29422773 ATAAAATATT
29422783 TAAAATATTTTAATATAATTTTAATA
1 TAAAATA--TTAATATAATTTTAATA
*
29422809 TAAAATATTAATTTAA-TTTAATA
1 TAAAATATTAATATAATTTTAATA
29422832 TAAAATATT
1 TAAAATATT
29422841 TTATTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 16 0.52
24 8 0.26
26 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATATTAATATAATTTTAATA
Found at i:29422846 original size:24 final size:24
Alignment explanation
Indices: 29422783--29422920 Score: 93
Period size: 24 Copynumber: 5.3 Consensus size: 24
29422773 ATAAAATATT
*
29422783 TAAAATATTTTAATATAATTTTAATA
1 TAAAATATTTT-ATTTAA-TTTAATA
*
29422809 TAAAATA-TTAATTTAATTTAATA
1 TAAAATATTTTATTTAATTTAATA
*
29422832 TAAAATATTTTATTTCAAAATATAATTTGAAA
1 TAAAATATTTTATTT---AATTTAA--T---A
*
29422864 TAAAATATTTTATATAATTTAATA
1 TAAAATATTTTATTTAATTTAATA
*
29422888 TAAAA-ATAATTATATT-ATTTAATAA
1 TAAAATAT-TTTAT-TTAATTTAAT-A
29422913 TAAAATAT
1 TAAAATAT
29422921 GATTAAATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
23 16 0.18
24 28 0.31
25 9 0.10
26 9 0.10
27 7 0.08
29 7 0.08
32 15 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TAAAATATTTTATTTAATTTAATA
Found at i:29422932 original size:26 final size:25
Alignment explanation
Indices: 29422862--29422934 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 25
29422852 TATAATTTGA
* *
29422862 AATAAAATATTTTATATAATTTAAT
1 AATAAAATATATTATATTATTTAAT
29422887 -ATAAAA-ATAATTATATTATTTAAT
1 AATAAAATAT-ATTATATTATTTAAT
*
29422911 AATAAAATATGATTAAATTATTTA
1 AATAAAATAT-ATTATATTATTTA
29422935 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 6 0.15
26 14 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
AATAAAATATATTATATTATTTAAT
Found at i:29423952 original size:32 final size:32
Alignment explanation
Indices: 29423916--29423980 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29423906 CACCCAAGTA
29423916 AGATTTATTTAAATTAGATTGTATATCCACAC
1 AGATTTATTTAAATTAGATTGTATATCCACAC
29423948 AGATTTATTTAAATTAGATTGTATATCCACAC
1 AGATTTATTTAAATTAGATTGTATATCCACAC
29423980 A
1 A
29423981 ACATTGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (32 bp):
AGATTTATTTAAATTAGATTGTATATCCACAC
Found at i:29425730 original size:13 final size:13
Alignment explanation
Indices: 29425712--29425736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29425702 TGTCAAATAA
29425712 TAAAAAATATTTT
1 TAAAAAATATTTT
29425725 TAAAAAATATTT
1 TAAAAAATATTT
29425737 CAAGCAATAC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAAAATATTTT
Found at i:29425780 original size:19 final size:19
Alignment explanation
Indices: 29425756--29425802 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29425746 CAATATATAT
29425756 ATCAATTTTTTTTCAAAA-A
1 ATCAATTTTTTTT-AAAAGA
*
29425775 ATCAATTCATTTTTAAAAGA
1 ATCAATT-TTTTTTAAAAGA
29425795 ATC-ATTTT
1 ATCAATTTT
29425803 CCGAATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 9 0.38
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (19 bp):
ATCAATTTTTTTTAAAAGA
Done.