Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014955.1 Kokia drynarioides strain JFW-HI SEQ_129999, whole genome shotgun sequence
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: 150147
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 212 characters in sequence are not A, C, G, or T
Found at i:1419 original size:13 final size:14
Alignment explanation
Indices: 1395--1423 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1385 GTTATACTAG
1395 ATTTTATAATTTTT
1 ATTTTATAATTTTT
1409 ATTTT-TAATTTTT
1 ATTTTATAATTTTT
1422 AT
1 AT
1424 GAATTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATAATTTTT
Found at i:10421 original size:58 final size:59
Alignment explanation
Indices: 10350--10471 Score: 203
Period size: 59 Copynumber: 2.1 Consensus size: 59
10340 GAACATAAAT
*
10350 ACCAACTATAACTTTCAATAGGG-AAAAAATAAAGCATGCATATAAGCAAAAACCA-AA
1 ACCAACTATAACTTTCAATAGGGAAAAAAAAAAAGCATGCATATAAGCAAAAACCATAA
*
10407 AGCCAACTATAACTTTCAATAGGGAAAAAAAAAAAGCATGCATATAATCAAAAACCATAA
1 A-CCAACTATAACTTTCAATAGGGAAAAAAAAAAAGCATGCATATAAGCAAAAACCATAA
10467 ACCAA
1 ACCAA
10472 AATTATACTA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 1 0.02
58 22 0.37
59 34 0.57
60 3 0.05
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.17
Consensus pattern (59 bp):
ACCAACTATAACTTTCAATAGGGAAAAAAAAAAAGCATGCATATAAGCAAAAACCATAA
Found at i:14927 original size:16 final size:16
Alignment explanation
Indices: 14905--14959 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
14895 GAAAAATTAT
14905 ATTTTCTATCTTTCCA
1 ATTTTCTATCTTTCCA
* *
14921 TTTTTCTACCCTTT-CA
1 ATTTTCTA-TCTTTCCA
*
14937 ATTTTCTTTCTTTCCA
1 ATTTTCTATCTTTCCA
14953 ATTTTCT
1 ATTTTCT
14960 TTCCTACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 4 0.12
16 24 0.75
17 4 0.12
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTCTATCTTTCCA
Found at i:14969 original size:16 final size:16
Alignment explanation
Indices: 14935--14969 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14925 TCTACCCTTT
* *
14935 CAATTTTCTTTCTTTC
1 CAATTTTCTTTCCTAC
14951 CAATTTTCTTTCCTAC
1 CAATTTTCTTTCCTAC
14967 CAA
1 CAA
14970 GCAAAGCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (16 bp):
CAATTTTCTTTCCTAC
Found at i:22869 original size:60 final size:60
Alignment explanation
Indices: 22735--22870 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 60
22725 TAAAATTCAA
* *
22735 AAAGTACAAGGACT-AAAATCAACCAAATTAAAGTACAATAACTGAATCCACGACTTCCGT
1 AAAGT-CAAGGACTAAAAATCAACCAAATTAAAGTACAATAACTAAATCCACAACTTCCGT
* * * * *
22795 AAAAT-ATAGAGACTAAAAAT-AACCAAATTAAAGTATATTGACTAAATCCACAACTT-TGAT
1 AAAGTCA-AG-GACTAAAAATCAACCAAATTAAAGTACAATAACTAAATCCACAACTTCCG-T
22855 AAAGTGCAAGGACTAA
1 AAAGT-CAAGGACTAA
22871 TAGCAGAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 50 0.81
61 7 0.11
62 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (60 bp):
AAAGTCAAGGACTAAAAATCAACCAAATTAAAGTACAATAACTAAATCCACAACTTCCGT
Found at i:26088 original size:17 final size:16
Alignment explanation
Indices: 26062--26095 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
26052 AGTTACTGTG
*
26062 TTTTAATTTTTATATT
1 TTTTAATTTTTAAATT
26078 TTTTGAATTTTTAAATT
1 TTTT-AATTTTTAAATT
26095 T
1 T
26096 GAGTTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTAAATT
Found at i:28989 original size:20 final size:21
Alignment explanation
Indices: 28964--29006 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
28954 GTATGTGACA
*
28964 TTTTTAATGTG-ATTTTTATT
1 TTTTTAATATGAATTTTTATT
28984 TTTTTAATATGATATTTTTATT
1 TTTTTAATATGA-ATTTTTATT
29006 T
1 T
29007 AATAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTTAATATGAATTTTTATT
Found at i:31375 original size:18 final size:18
Alignment explanation
Indices: 31354--31388 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31344 TTATATGTAC
31354 ATATATATTATAAATTAT
1 ATATATATTATAAATTAT
* *
31372 ATATGTATTATAGATTA
1 ATATATATTATAAATTA
31389 AAGTTACGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATATATTATAAATTAT
Found at i:35033 original size:20 final size:19
Alignment explanation
Indices: 34977--35033 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
34967 AAAATTAAAT
*
34977 TTTTTTTATAATATTTTGAA
1 TTTTTTTAT-ATTTTTTGAA
** *
34997 TTTTTAAATGTTATTTTGAA
1 TTTTTTTATATT-TTTTGAA
35017 TTTCTTTTATATTTTTT
1 TTT-TTTTATATTTTTT
35034 AGAGAGATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.75
21 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTTATATTTTTTGAA
Found at i:35126 original size:24 final size:23
Alignment explanation
Indices: 35099--35153 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
35089 TCAATTTGTT
*
35099 ATTCAAAATTTAAAATTCAACTCG
1 ATTCAAAA-GTAAAATTCAACTCG
* *
35123 ATTCGAACAGTAAAATTCAACTTG
1 ATTC-AAAAGTAAAATTCAACTCG
35147 ATTCAAA
1 ATTCAAA
35154 CTTGAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 21 0.81
25 3 0.12
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (23 bp):
ATTCAAAAGTAAAATTCAACTCG
Found at i:35165 original size:23 final size:24
Alignment explanation
Indices: 35109--35154 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35099 ATTCAAAATT
*
35109 TAAAATTCAACTCGATTCGAACAG
1 TAAAATTCAACTCGATTCAAACAG
*
35133 TAAAATTCAACTTGATTCAAAC
1 TAAAATTCAACTCGATTCAAAC
35155 TTGAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (24 bp):
TAAAATTCAACTCGATTCAAACAG
Found at i:42574 original size:30 final size:30
Alignment explanation
Indices: 42522--42579 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
42512 AATTTTTAAA
42522 TTTTTTTCTATTACATTATTTCTCTTTTTAT
1 TTTTTTTCTATTACATTATTTCT-TTTTTAT
*
42553 TTTTTTTCT-TGTTCATT-TTTCTTTTTT
1 TTTTTTTCTAT-TACATTATTTCTTTTTT
42580 CTTCCTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 6 0.24
31 14 0.56
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (30 bp):
TTTTTTTCTATTACATTATTTCTTTTTTAT
Found at i:47433 original size:29 final size:28
Alignment explanation
Indices: 47365--47440 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
47355 TACTTTTCAA
* *
47365 AAATTTAAAATTTAATATTCGTATTTTT
1 AAATTTAAAATTTAATTTTCATATTTTT
** *
47393 ATTTTTAGAAATTTAATTTTTATATTTTT
1 AAATTTA-AAATTTAATTTTCATATTTTT
47422 AAATTTCAAAATTTCAATT
1 AAATTT-AAAATTT-AATT
47441 CAACTATTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.13
29 28 0.74
30 5 0.13
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (28 bp):
AAATTTAAAATTTAATTTTCATATTTTT
Found at i:47551 original size:17 final size:17
Alignment explanation
Indices: 47529--47563 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47519 CTAAACCCAT
47529 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
47546 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
47563 T
1 T
47564 GTTTTGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:58298 original size:209 final size:208
Alignment explanation
Indices: 57923--58399 Score: 760
Period size: 209 Copynumber: 2.3 Consensus size: 208
57913 TGCGATTATC
* * *
57923 CAAAACAA-TGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAATCA
1 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAATCA
* * *
57987 GGCTCAAAATGAGCAAATCTTCAAACCCAGCTTCCTGATGAGGTATTGAGAAGCAGGTCGAAGCA
66 GGCTCAAAATGAGCAAATCTTCAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGCA
* *
58052 ATAAAGTGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACA
131 ATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACAAGATCCGTCTTCCTGATGAGACA
* *
58117 CAAAGACGTGAAT
196 CAAAGAAGCGAAT
*
58130 CAAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-CT
1 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAATC-
* *
58194 AGGCTCAAAGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAG
65 AGGCTCAAAATGAGCAAATCTTCAAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGATCGAAG
*
58259 CAATAAAGAGGTTACCTTTCTGATGAGATACAGAGAAGTGAACAAGATCCGTCTTCCTGATGAGA
129 CAATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACAAGATCCGTCTTCCTGATGAGA
* *
58324 CACAGAGAAGCGGAT
194 CACAAAGAAGCGAAT
*
58339 CAAAAACAAGTGATGCGGTCATCATCCTGATGAGATACTGAGAAGTAGACCAAATCAATGA
1 C-AAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGA
58400 CACAAAACCA
Statistics
Matches: 248, Mismatches: 18, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
207 9 0.04
208 76 0.31
209 106 0.43
210 57 0.23
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (208 bp):
CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAATCA
GGCTCAAAATGAGCAAATCTTCAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGCA
ATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACAAGATCCGTCTTCCTGATGAGACA
CAAAGAAGCGAAT
Found at i:59414 original size:29 final size:29
Alignment explanation
Indices: 59352--59653 Score: 114
Period size: 29 Copynumber: 10.5 Consensus size: 29
59342 CTAAAGTATC
* *
59352 TAAAAA-TATATTTTGAACCC-CAAACTATC
1 TAAAAATTATATTTTG-ACCCTCGAACT-TT
* *
59381 AAAAAACTATATTTTGACCCTCGAACTTT
1 TAAAAATTATATTTTGACCCTCGAACTTT
* * *
59410 TAAAAATTTTATTTT-TCCCTCGAACTTA
1 TAAAAATTATATTTTGACCCTCGAACTTT
* *
59438 CAAAAATTACACTTTTG-CCCTCGAA-TTT
1 TAAAAATTATA-TTTTGACCCTCGAACTTT
** *
59466 CTAAAAATTCCATTTTGACCC-CAAACTTT
1 -TAAAAATTATATTTTGACCCTCGAACTTT
** * *
59495 CCAAAATTACCATTTT-ACCCTC-AAATTT
1 TAAAAATTA-TATTTTGACCCTCGAACTTT
** * *
59523 CTAAAAATTCCATTTTAACCCT-AAACTTT
1 -TAAAAATTATATTTTGACCCTCGAACTTT
* *
59552 CTAAAAATTACCA-TTT-ACCCTC-AAATTT
1 -TAAAAATTA-TATTTTGACCCTCGAACTTT
* * *
59580 CCAAAAAATT-CATTTT-AACCTCGAACTTT
1 --TAAAAATTATATTTTGACCCTCGAACTTT
* * *
59609 CCAAAAATTACCATTTT-ACCCTTGAA-TTT
1 -TAAAAATTA-TATTTTGACCCTCGAACTTT
*
59638 GTAAAAATTCTATTTT
1 -TAAAAATTATATTTT
59654 TGAGCCTAAA
Statistics
Matches: 219, Mismatches: 35, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
27 2 0.01
28 81 0.37
29 107 0.49
30 29 0.13
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAAAATTATATTTTGACCCTCGAACTTT
Found at i:59471 original size:57 final size:57
Alignment explanation
Indices: 59391--59711 Score: 298
Period size: 57 Copynumber: 5.6 Consensus size: 57
59381 AAAAAACTAT
** * * *
59391 ATTTTGACCCTCGAACTTT-TAAAAATTTTATTTTTCCCTCGAACTTACAAAAATTA-C
1 ATTTT-ACCCTCGAA-TTTCTAAAAATTCCATTTTACCCTCAAACTTTCAAAAATTACC
* *
59448 ACTTTTGCCCTCGAATTTCTAAAAATTCCATTTTGACCC-CAAACTTTCCAAAATTACC
1 A-TTTTACCCTCGAATTTCTAAAAATTCCATTTT-ACCCTCAAACTTTCAAAAATTACC
*
59506 ATTTTACCCTCAAATTTCTAAAAATTCCATTTTAACCCT-AAACTTTCTAAAAATTACC
1 ATTTTACCCTCGAATTTCTAAAAATTCCATTTT-ACCCTCAAACTTTC-AAAAATTACC
* * * *
59564 A-TTTACCCTCAAATTTCCAAAAAATT-CATTTTAACCTCGAACTTTCCAAAAATTACC
1 ATTTTACCCTCGAATTT-CTAAAAATTCCATTTTACCCTCAAACTTT-CAAAAATTACC
* * * * * *
59621 ATTTTACCCTTGAATTTGTAAAAATTCTATTTTTGAGCCT-AAACTTCCCTAAAATTACC
1 ATTTTACCCTCGAATTTCTAAAAATTCCA-TTTT-ACCCTCAAACTT-TCAAAAATTACC
* * *
59680 ATTTTACACTCAAATTTCCAAAAA-TCCATTTT
1 ATTTTACCCTCGAATTTCTAAAAATTCCATTTT
59712 TATCCTCGAG
Statistics
Matches: 221, Mismatches: 29, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
56 7 0.03
57 127 0.57
58 45 0.20
59 38 0.17
60 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (57 bp):
ATTTTACCCTCGAATTTCTAAAAATTCCATTTTACCCTCAAACTTTCAAAAATTACC
Found at i:59652 original size:28 final size:29
Alignment explanation
Indices: 59439--59734 Score: 215
Period size: 29 Copynumber: 10.3 Consensus size: 29
59429 TCGAACTTAC
* *
59439 AAAAATTA-CACTTTTGCCCTCGAATTTCT
1 AAAAATTACCA-TTTTACCCTCAAATTTCT
59468 AAAAATT-CCATTTTGACCC-CAAACTTTC-
1 AAAAATTACCATTTT-ACCCTCAAA-TTTCT
*
59496 CAAAATTACCATTTTACCCTCAAATTTCT
1 AAAAATTACCATTTTACCCTCAAATTTCT
59525 AAAAATT-CCATTTTAACCCT-AAACTTTCT
1 AAAAATTACCATTTT-ACCCTCAAA-TTTCT
*
59554 AAAAATTACCA-TTTACCCTCAAATTTCCA
1 AAAAATTACCATTTTACCCTCAAATTT-CT
* * *
59583 AAAAATT--CATTTTAACCTCGAACTTTCC
1 AAAAATTACCATTTTACCCTC-AAATTTCT
** *
59611 AAAAATTACCATTTTACCCTTGAATTTGT
1 AAAAATTACCATTTTACCCTCAAATTTCT
* * *
59640 AAAAATT-CTATTTTTGAGCCT-AAACTTCCCT
1 AAAAATTACCA-TTTT-ACCCTCAAA-TT-TCT
* *
59671 -AAAATTACCATTTTACACTCAAATTTCC
1 AAAAATTACCATTTTACCCTCAAATTTCT
* * * *
59699 AAAAA-T-CCATTTTTATCCTCGAGTTTCC
1 AAAAATTACCA-TTTTACCCTCAAATTTCT
59727 AAAAATTA
1 AAAAATTA
59735 TAGTTTTACC
Statistics
Matches: 214, Mismatches: 28, Indels: 49
0.74 0.10 0.17
Matches are distributed among these distances:
27 5 0.02
28 78 0.36
29 96 0.45
30 32 0.15
31 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCAAATTTCT
Found at i:59770 original size:116 final size:115
Alignment explanation
Indices: 59461--59734 Score: 297
Period size: 116 Copynumber: 2.4 Consensus size: 115
59451 TTTGCCCTCG
* * * * * ** *
59461 AATTTCTAAAAATTCCATTTTGACCCCAAACTTTCC-AAAATTACCATTTTACCCTCAAATTTCT
1 AATTTCCAAAAAATCCATTTTAACCTCGAACTTTCCAAAAATTACCATTTTACCCTGGAA-TTGT
* * * * * *
59525 AAAAATTCCA-TTTTAACCCTAAACTTTCTAAAAATTACCATTTACCCTCA
65 AAAAAGTCTATTTTTGAGCCTAAACTTCCTAAAAATTACCATTTACACTCA
* *
59575 AATTTCCAAAAAATTCATTTTAACCTCGAACTTTCCAAAAATTACCATTTTACCCTTGAATTTGT
1 AATTTCCAAAAAATCCATTTTAACCTCGAACTTTCCAAAAATTACCATTTTACCCTGGAA-TTGT
*
59640 AAAAATTCTATTTTTGAGCCTAAACTTCCCT-AAAATTACCATTTTACACTCA
65 AAAAAGTCTATTTTTGAGCCTAAACTT-CCTAAAAATTACCA-TTTACACTCA
* *
59692 AATTTCC-AAAAATCCATTTTTATCCTCG-AGTTTCCAAAAATTA
1 AATTTCCAAAAAATCCA-TTTTAACCTCGAACTTTCCAAAAATTA
59735 TAGTTTTACC
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
114 30 0.22
115 34 0.25
116 46 0.33
117 28 0.20
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (115 bp):
AATTTCCAAAAAATCCATTTTAACCTCGAACTTTCCAAAAATTACCATTTTACCCTGGAATTGTA
AAAAGTCTATTTTTGAGCCTAAACTTCCTAAAAATTACCATTTACACTCA
Found at i:63720 original size:7 final size:7
Alignment explanation
Indices: 63708--63759 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
63698 AATGAAACCC
63708 AATTTTA
1 AATTTTA
63715 AATTTTA
1 AATTTTA
63722 AATTTTA
1 AATTTTA
*
63729 AATTATTT
1 AATT-TTA
*
63737 AAGTTTA
1 AATTTTA
63744 AA-TTT-
1 AATTTTA
63749 -ATTTTA
1 AATTTTA
63755 AATTT
1 AATTT
63760 AAACTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 3 0.08
7 26 0.68
8 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:63736 original size:17 final size:18
Alignment explanation
Indices: 63716--63809 Score: 101
Period size: 17 Copynumber: 5.6 Consensus size: 18
63706 CCAATTTTAA
63716 ATTTTAAATTTTAAA-TT
1 ATTTTAAATTTTAAATTT
*
63733 A-TTT-AAGTTTAAATTT
1 ATTTTAAATTTTAAATTT
*
63749 ATTTTAAA-TTTAAACTT
1 ATTTTAAATTTTAAATTT
* * *
63766 ATTTT-GAGTTTGAATTT
1 ATTTTAAATTTTAAATTT
63783 ATTTTAAA-TTTAAATTT
1 ATTTTAAATTTTAAATTT
63800 ATTTTAAATT
1 ATTTTAAATT
63810 AAATATAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
15 8 0.12
16 7 0.11
17 45 0.70
18 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTTTAAATTT
Found at i:63749 original size:6 final size:6
Alignment explanation
Indices: 63711--63821 Score: 58
Period size: 6 Copynumber: 19.5 Consensus size: 6
63701 GAAACCCAAT
* *
63711 TTTAAA TTTTAAA TTTTAAA -TT--A TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
63757 TTTAAA CTT-AT TTTGAG TTTGAA TTT-AT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
63802 TTTAAA -TTAAA TATAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
63822 TAAAAGTCCA
Statistics
Matches: 81, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 22 0.27
6 43 0.53
7 13 0.16
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:63782 original size:34 final size:33
Alignment explanation
Indices: 63716--63806 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 33
63706 CCAATTTTAA
63716 ATTTTAAATTTTAAATTA-TTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTATTTTAAGTTTAAATTT
* *
63749 ATTTTAAATTTAAACTTATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAA-TTATTTTAAGTTTAAATTT
63783 ATTTTAAATTTAAATTTATTTTAA
1 ATTTTAAATTTAAA-TTATTTTAA
63807 ATTAAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 6 0.12
33 11 0.21
34 35 0.67
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTAAGTTTAAATTT
Found at i:63841 original size:22 final size:22
Alignment explanation
Indices: 63816--63876 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
63806 AATTAAATAT
*
63816 AAATTTTAAAAGTCCAAATACA
1 AAATTCTAAAAGTCCAAATACA
* *
63838 AAATTCCAAAAGTCCAAATCCA
1 AAATTCTAAAAGTCCAAATACA
63860 AAA-TCTAAAA-TCCAAAT
1 AAATTCTAAAAGTCCAAAT
63877 TTTACAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.20
21 6 0.17
22 22 0.63
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (22 bp):
AAATTCTAAAAGTCCAAATACA
Found at i:65323 original size:12 final size:12
Alignment explanation
Indices: 65306--65336 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
65296 TTTTGATTAT
65306 TTAATTTCATTC
1 TTAATTTCATTC
*
65318 TTAATTTCATTT
1 TTAATTTCATTC
65330 TTAATTT
1 TTAATTT
65337 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (12 bp):
TTAATTTCATTC
Found at i:65720 original size:30 final size:29
Alignment explanation
Indices: 65643--65720 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 29
65633 ACCCTAAGCT
* *
65643 TTTCCAAAATTATATTATTTTCCCTCGAAC
1 TTTCAAAAATTATATT-TTTCCCCTCGAAC
* *
65673 TTTCAAAAATCACATTTTTACCCCT-GAAC
1 TTTCAAAAATTATATTTTT-CCCCTCGAAC
65702 TCCTT-AAAAATTATATTTT
1 T--TTCAAAAATTATATTTT
65721 AGCCCTTAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 8 0.21
30 29 0.74
31 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTCAAAAATTATATTTTTCCCCTCGAAC
Found at i:65739 original size:29 final size:29
Alignment explanation
Indices: 65707--65772 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
65697 TGAACTCCTT
65707 AAAAATTAT-ATTTTAGCCCT-TAAGCATCC
1 AAAAATTATCATTTT-GCCCTCTAA-CATCC
* *
65736 AAAAAATATCATTTTGCCCTCTAACATCT
1 AAAAATTATCATTTTGCCCTCTAACATCC
*
65765 AAGAATTA
1 AAAAATTA
65773 CTTTTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAAATTATCATTTTGCCCTCTAACATCC
Found at i:65880 original size:30 final size:30
Alignment explanation
Indices: 65853--65940 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
65843 ACGAACTTCA
*
65853 CAAAAATCATATTTTAACCCTTAAACTTTC
1 CAAAAATCATATTTTAACCCCTAAACTTTC
* * *
65883 TAAAAATTATATTTTAACCCCTAAAGTATTC
1 CAAAAATCATATTTTAACCCCTAAACT-TTC
* *
65914 C-AAAATCACATTTTTACCCC-AAACTTT
1 CAAAAATCATATTTTAACCCCTAAACTTT
65941 TTGAAAATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
28 2 0.04
29 4 0.08
30 39 0.81
31 3 0.06
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (30 bp):
CAAAAATCATATTTTAACCCCTAAACTTTC
Found at i:65980 original size:29 final size:30
Alignment explanation
Indices: 65944--66044 Score: 109
Period size: 29 Copynumber: 3.5 Consensus size: 30
65934 AAACTTTTTG
*
65944 AAAATTA-CATTTTTTCCCTCGAACGTCCA
1 AAAATTACCATTTTTTCCCTCGAACATCCA
* * *
65973 AAAGTTACCA-TTTTGCCCTCGAATATCCA
1 AAAATTACCATTTTTTCCCTCGAACATCCA
* * *
66002 AAAATTACTAATTTTT-CCTTGAACATCCA
1 AAAATTACCATTTTTTCCCTCGAACATCCA
*
66031 AAAATTATCATTTT
1 AAAATTACCATTTT
66045 GCCGTCAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
29 52 0.90
30 6 0.10
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTTTCCCTCGAACATCCA
Found at i:66031 original size:58 final size:58
Alignment explanation
Indices: 65944--66072 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 58
65934 AAACTTTTTG
* * * *
65944 AAAATTACATTTTTTCCCTCGAACGTCCAAAAGTTACCATTTTGCCCTCGAATATCCA
1 AAAATTACAATTTTTCCCTCGAACATCCAAAAATTACCATTTTGCCCTCAAATATCCA
* * * *
66002 AAAATTACTAATTTTT-CCTTGAACATCCAAAAATTATCATTTTGCCGTCAAATTTCCA
1 AAAATTAC-AATTTTTCCCTCGAACATCCAAAAATTACCATTTTGCCCTCAAATATCCA
*
66060 AAAATCAC-ATTTT
1 AAAATTACAATTTT
66073 CGACTTCAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
56 5 0.08
58 50 0.82
59 6 0.10
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAATTACAATTTTTCCCTCGAACATCCAAAAATTACCATTTTGCCCTCAAATATCCA
Found at i:66059 original size:29 final size:28
Alignment explanation
Indices: 65969--66072 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 28
65959 CCCTCGAACG
* * *
65969 TCCAAAAGTTACCATTTTGCCCTCGAAT
1 TCCAAAAATTATCATTTTGCCCTCAAAT
* * * *
65997 ATCCAAAAATTACTAATTTTTCCTTGAACA-
1 -TCCAAAAATTA-TCATTTTGCCCTCAA-AT
*
66027 TCCAAAAATTATCATTTTGCCGTCAAATT
1 TCCAAAAATTATCATTTTGCCCTCAAA-T
*
66056 TCCAAAAATCA-CATTTT
1 TCCAAAAATTATCATTTT
66073 CGACTTCAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.02
28 17 0.29
29 31 0.53
30 9 0.15
31 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (28 bp):
TCCAAAAATTATCATTTTGCCCTCAAAT
Found at i:66081 original size:29 final size:29
Alignment explanation
Indices: 66027--66085 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
66017 TCCTTGAACA
* *
66027 TCCAAAAATTATCATTTTGCCGTCAAATT
1 TCCAAAAATCATCATTTTGACGTCAAATT
*
66056 TCCAAAAATCA-CATTTTCGACTTCAAATT
1 TCCAAAAATCATCATTTT-GACGTCAAATT
66085 T
1 T
66086 TTCCAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (29 bp):
TCCAAAAATCATCATTTTGACGTCAAATT
Found at i:71245 original size:15 final size:14
Alignment explanation
Indices: 71227--71268 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
71217 AAAATAAATT
71227 AAAAAAAAGAAGAAA
1 AAAAAAAAGAA-AAA
71242 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
**
71256 AGGAAAAAGAAAA
1 AAAAAAAAGAAAA
71269 TTGGAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:71262 original size:14 final size:12
Alignment explanation
Indices: 71227--71268 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
71217 AAAATAAATT
*
71227 AAAAAAAAGAAG
1 AAAAAAAAAAAG
71239 AAAAAAAAAAAG
1 AAAAAAAAAAAG
71251 AAAAAAGGAAAAAG
1 AAAAAA--AAAAAG
71265 AAAA
1 AAAA
71269 TTGGAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 17 0.63
14 10 0.37
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:72566 original size:41 final size:41
Alignment explanation
Indices: 72509--72673 Score: 208
Period size: 41 Copynumber: 4.0 Consensus size: 41
72499 CATCATCATT
* **
72509 TAGTCTTTTACCCTTAATTAAGAAGGACAGATCAAAGATTC
1 TAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTC
72550 TAGTCTTTTACCCTTAATCAAGAAGGGA-AGATTGAAGATTC
1 TAGTCTTTTACCCTTAATCAAGAA-GGACAGATTGAAGATTC
* * *
72591 CAGTCTTTTACCCTTAATAAAAAAGGACAGATTGAAGATT-
1 TAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTC
* * * *
72631 TCAGTTTTTTAGCCTTAAACAAGAAGGGCAGATTGAAGATTC
1 T-AGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTC
72673 T
1 T
72674 GATCATGGGG
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.03
41 100 0.93
42 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (41 bp):
TAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTC
Found at i:72647 original size:82 final size:82
Alignment explanation
Indices: 72510--72672 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 82
72500 ATCATCATTT
* * *
72510 AGTCTTTTACCCTTAATTAAGAAGGACAGATCAAAGATTCTAGTCTTTTACCCTTAATCAAGAAG
1 AGTCTTTTACCCTTAATAAAAAAGGACAGATCAAAGATTCTAGTCTTTTACCCTTAAACAAGAAG
72575 GGAAGATTGAAGATTCC
66 GGAAGATTGAAGATTCC
** * *
72592 AGTCTTTTACCCTTAATAAAAAAGGACAGATTGAAGATT-TCAGTTTTTTAGCCTTAAACAAGAA
1 AGTCTTTTACCCTTAATAAAAAAGGACAGATCAAAGATTCT-AGTCTTTTACCCTTAAACAAGAA
*
72656 GGGCAGATTGAAGATTC
65 GGGAAGATTGAAGATTC
72673 TGATCATGGG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 1 0.01
82 71 0.99
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (82 bp):
AGTCTTTTACCCTTAATAAAAAAGGACAGATCAAAGATTCTAGTCTTTTACCCTTAAACAAGAAG
GGAAGATTGAAGATTCC
Found at i:72814 original size:78 final size:78
Alignment explanation
Indices: 72700--73272 Score: 623
Period size: 78 Copynumber: 7.4 Consensus size: 78
72690 ATAGTCATCA
* * * * * * *
72700 GATCTTTTACCCTGAGCCTCGAGTAGATCACTATCAGCCAATCTCTTACCTCGAGCTTGAGGCAG
1 GATCTCTTACCCTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
* *
72765 ATTACAACCATTC
66 ATTGCAGCCATTC
* * * * *
72778 GATCTCTTACCCTGAGCTTGGGGTAGATCACCATCAGCCAATCTTTTACCCCGATCATGGGGCAG
1 GATCTCTTACCCTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
*
72843 ATTGCAGCCAGTC
66 ATTGCAGCCATTC
* * ** * * **
72856 GATCTTTTACCCCGAGCCTGGGGCATTTCACCATCAGCCATTCTCTTACCCCGAGCTTGAGGTGG
1 GATCTCTTACCCTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
*
72921 ATTGCAGCCATTT
66 ATTGCAGCCATTC
* * * * *
72934 GATCTTTTACCAC-GAGCTTGGGGTAGATCACCATCAGCCAATCTCTTATCCCGAGCCTGGGGCA
1 GATCTCTTACC-CTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
* **
72998 GATTGTAATCATTC
65 GATTGCAGCCATTC
* * * * * * *
73012 GATCTTTTACCC-GAGCCTAGGGTAGATCNCCATCAGCCAATCTGTTACCTCGAGCTTGGGGAAG
1 GATCTCTTACCCTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
73076 ATTGCAGCCATTC
66 ATTGCAGCCATTC
* * *
73089 GATCTCTTA-CCTCAAGCCTGGGGCAGATCATCATCAGCCAATCTCTTACCTCGAGCTTGGGGCA
1 GATCTCTTACCCT-GAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
73153 GATTGCAGCCATTC
65 GATTGCAGCCATTC
* * * *
73167 GATCTCTTA-CCTCAAGCCTAGGGCAGATCATCATCAGCCAATCTCTTACCCCGAGGTTGGGGCA
1 GATCTCTTACCCT-GAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
* * *
73231 AATTGCAACCATTT
65 GATTGCAGCCATTC
** *
73245 GATCTCTTACCCCAAGCTTGGGGCAGAT
1 GATCTCTTACCCTGAGCCTGGGGCAGAT
73273 TGCAACCATT
Statistics
Matches: 421, Mismatches: 70, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
76 2 0.00
77 63 0.15
78 353 0.84
79 3 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (78 bp):
GATCTCTTACCCTGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAG
ATTGCAGCCATTC
Found at i:73213 original size:117 final size:117
Alignment explanation
Indices: 73090--73335 Score: 302
Period size: 117 Copynumber: 2.1 Consensus size: 117
73080 CAGCCATTCG
* * * *
73090 ATCTCTTACCTCAAGCCTGGGGCAGA-T-C-ATCATCAGCCAATCTCTTACCTCGAGCTTGGGGC
1 ATCTCTTACCTCAAGCCTGGGGCAAATTGCAACCATCAG---ATCTCTTACCCCAAGCTTGGGGC
* * *
73152 AGATTGCAGCCATTCGATCTCTTACCTCAAGCCTAGG-GCAGATCATCATCAGCCA
63 AGATTGCAACCATTCGATCTCTTACCCCAAG-ATAGGTGCAGATCATCATCAGCCA
* * ** **
73207 ATCTCTTACCCCGAGGTTGGGGCAAATTGCAACCATTTGATCTCTTACCCCAAGCTTGGGGCAGA
1 ATCTCTTACCTCAAGCCTGGGGCAAATTGCAACCATCAGATCTCTTACCCCAAGCTTGGGGCAGA
*
73272 TTGCAACCATTCGATCTCTTACCCCAAGATTGGTGCAGATCATCATCAGCCA
66 TTGCAACCATTCGATCTCTTACCCCAAGATAGGTGCAGATCATCATCAGCCA
73324 ATCTCTTACCTC
1 ATCTCTTACCTC
73336 GATCATGGGG
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
116 3 0.03
117 100 0.91
118 1 0.01
119 1 0.01
120 5 0.05
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (117 bp):
ATCTCTTACCTCAAGCCTGGGGCAAATTGCAACCATCAGATCTCTTACCCCAAGCTTGGGGCAGA
TTGCAACCATTCGATCTCTTACCCCAAGATAGGTGCAGATCATCATCAGCCA
Found at i:73230 original size:39 final size:39
Alignment explanation
Indices: 72724--73333 Score: 257
Period size: 39 Copynumber: 15.7 Consensus size: 39
72714 AGCCTCGAGT
* *
72724 AGATCA-CTATCAGCCAATCTCTTACCTCGAGCTTGAGGC
1 AGATCATC-ATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* * ** * * *
72763 AGATTA-CAACCATTCGATCTCTTACCCTGAGCTTGGGGT
1 AGATCATC-ATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* * * *
72802 AGATCACCATCAGCCAATCTTTTACCCCGATCATGGGGC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* * * * *
72841 AGAT--TGCAGCCAGTCGATCTTTTACCCCGAGCCTGGGGC
1 AGATCAT-CA-TCAGCCAATCTCTTACCCCGAGCTTGGGGC
** * * * *
72880 ATTTCACCATCAGCCATTCTCTTACCCCGAGCTTGAGGT
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* * * * *
72919 GGAT--T--GCAGCCATTTGATCTTTTACCACGAGCTTGGGGT
1 AGATCATCATCAGCCA----ATCTCTTACCCCGAGCTTGGGGC
* * *
72958 AGATCACCATCAGCCAATCTCTTATCCCGAGCCTGGGGC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
** * ** * * * * *
72997 AGATTGTAATCATTCGATCTTTTA-CCCGAGCCTAGGGT
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
** * * *
73035 AGATCNCCATCAGCCAATCTGTTACCTCGAGCTTGGGGA
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* ** * * * *
73074 AGAT--TGCAGCCATTCGATCTCTTACCTCAAGCCTGGGGC
1 AGATCAT-CA-TCAGCCAATCTCTTACCCCGAGCTTGGGGC
*
73113 AGATCATCATCAGCCAATCTCTTACCTCGAGCTTGGGGC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* ** * * * * *
73152 AGAT--TGCAGCCATTCGATCTCTTACCTCAAGCCTAGGGC
1 AGATCAT-CA-TCAGCCAATCTCTTACCCCGAGCTTGGGGC
*
73191 AGATCATCATCAGCCAATCTCTTACCCCGAGGTTGGGGC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* * ** *
73230 AAATTGCAACCATTTG---ATCTCTTACCCCAAGCTTGGGGC
1 AGA-T-C-ATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* ** * * * *
73269 AGAT--TGCAACCATTCGATCTCTTACCCCAAGATTGGTGC
1 AGATCAT-C-ATCAGCCAATCTCTTACCCCGAGCTTGGGGC
73308 AGATCATCATCAGCCAATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACC
73334 TCGATCATGG
Statistics
Matches: 414, Mismatches: 125, Indels: 64
0.69 0.21 0.11
Matches are distributed among these distances:
35 7 0.02
36 1 0.00
37 1 0.00
38 35 0.08
39 346 0.84
40 9 0.02
41 4 0.01
42 5 0.01
43 6 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (39 bp):
AGATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
Found at i:73345 original size:117 final size:117
Alignment explanation
Indices: 73129--73345 Score: 328
Period size: 117 Copynumber: 1.9 Consensus size: 117
73119 TCATCAGCCA
* * * * *
73129 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCAAGCCTAGGGCAGA
1 ATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCAAGCATAGGGCAGA
**
73194 TCATCATCAGCCAATCTCTTACCCCGAGGTTGGGGCAAATTGCAACCATTTG
66 TCATCATCAGCCAATCTCTTACCCCGAGCATGGGGCAAATTGCAACCATTTG
*
73246 ATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCAAG-ATTGGTGCAG
1 ATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCAAGCATAGG-GCAG
* *
73310 ATCATCATCAGCCAATCTCTTACCTCGATCATGGGG
65 ATCATCATCAGCCAATCTCTTACCCCGAGCATGGGG
73346 TAGATGGCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 3 0.03
117 86 0.97
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (117 bp):
ATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCAAGCATAGGGCAGA
TCATCATCAGCCAATCTCTTACCCCGAGCATGGGGCAAATTGCAACCATTTG
Found at i:73849 original size:35 final size:35
Alignment explanation
Indices: 73760--73836 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 35
73750 TGGAACCCAA
* * *
73760 TTTTAAATTTTAATTTA-TTTAAGTTTAAATTTAT
1 TTTTAAATTTAAACTTATTTTGAGTTTAAATTTAT
*
73794 TTTTAAATTTAAACTTATTTTGAGTTTGAATTTA-
1 TTTTAAATTTAAACTTATTTTGAGTTTAAATTTAT
73828 TTTTAAATT
1 TTTTAAATT
73837 AAATTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 24 0.63
35 14 0.37
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (35 bp):
TTTTAAATTTAAACTTATTTTGAGTTTAAATTTAT
Found at i:73852 original size:7 final size:6
Alignment explanation
Indices: 73761--73848 Score: 51
Period size: 6 Copynumber: 15.5 Consensus size: 6
73751 GGAACCCAAT
* * **
73761 TTTAAA TTTTAA TTT--A TTTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
73807 CTT-AT TTTGAG TTTGAA TTT-AT TTTAAA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
73849 TAAAAGTCCA
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
4 4 0.06
5 12 0.19
6 47 0.75
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:75941 original size:30 final size:29
Alignment explanation
Indices: 75750--76123 Score: 155
Period size: 29 Copynumber: 12.8 Consensus size: 29
75740 ATTTTTTTCA
* *
75750 TCGAACTTCCAAAAATCACATTTTTACCC
1 TCGAACTTCCAAAAATTACATTTTGACCC
* * *
75779 T-GAACTCCTCAAAAATTTCATTTTGGCCC
1 TCGAACTTC-CAAAAATTACATTTTGACCC
* * *
75808 TCGAACATCAAAAAATTACCATATTG-CCC
1 TCGAACTTCCAAAAATTA-CATTTTGACCC
* * *
75837 TCAAACATCCAAGAATTACCATTTTGACCC
1 TCGAACTTCCAAAAATTA-CATTTTGACCC
* *
75867 T--AAGCTTTTCC-AAAATTACTTTTTTGTCCC
1 TCGAA-C--TTCCAAAAATTAC-ATTTTGACCC
* *
75897 -CAAACATCCAAAAATTACATTTTGACCC
1 TCGAACTTCCAAAAATTACATTTTGACCC
* * *
75925 TCGAACTTCACAAAAATCATATTTTAACCC
1 TCGAACTTC-CAAAAATTACATTTTGACCC
** * *
75955 TTAAACTTTTCC-AAAATCACA-TTTCACCC
1 TCGAAC--TTCCAAAAATTACATTTTGACCC
** *
75984 TAAAATTTTCC-AAAATTACATTTTTG-CCC
1 TCGAA-CTTCCAAAAATTACA-TTTTGACCC
* * * *
76013 CCAAACATCCAAAAGTTACCATTTT-ACCC
1 TCGAACTTCCAAAAATTA-CATTTTGACCC
* * *
76042 TC-AAATATTCAAAAATTGCCA-TTTGACCC
1 TCGAACT-TCCAAAAATT-ACATTTTGACCC
* * * *
76071 CCGAACATACAAAAGTTACCATTTTG-CCC
1 TCGAACTTCCAAAAATTA-CATTTTGACCC
* * *
76100 TCAAATTTCCAAAAATCACATTTT
1 TCGAACTTCCAAAAATTACATTTT
76124 CGACTTCAAA
Statistics
Matches: 260, Mismatches: 58, Indels: 55
0.70 0.16 0.15
Matches are distributed among these distances:
28 45 0.17
29 136 0.52
30 70 0.27
31 6 0.02
32 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
TCGAACTTCCAAAAATTACATTTTGACCC
Found at i:75941 original size:59 final size:59
Alignment explanation
Indices: 75788--75941 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 59
75778 CTGAACTCCT
* * *
75788 CAAAAATTTCATTTTGGCCCTCGAACATCA-AAAAATTACCATATTGCCCTCAAACATC
1 CAAAAATTACATTTTGACCCTCGAACTTCACAAAAATTACCATATTGCCCTCAAACATC
* ** * ** *
75846 CAAGAATTACCATTTTGACCCT--AAGCTTTTCCAAAATTACTTTTTTGTCCC-CAAACATC
1 CAAAAATTA-CATTTTGACCCTCGAA-CTTCACAAAAATTACCATATTG-CCCTCAAACATC
75905 CAAAAATTACATTTTGACCCTCGAACTTCACAAAAAT
1 CAAAAATTACATTTTGACCCTCGAACTTCACAAAAAT
75942 CATATTTTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
57 2 0.03
58 21 0.28
59 48 0.63
60 5 0.07
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (59 bp):
CAAAAATTACATTTTGACCCTCGAACTTCACAAAAATTACCATATTGCCCTCAAACATC
Found at i:75992 original size:28 final size:29
Alignment explanation
Indices: 75937--76006 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
75927 GAACTTCACA
* *
75937 AAAATCATATTTTAACCCTTAAACTTTTCC
1 AAAATCACA-TTTAACCCTTAAAATTTTCC
*
75967 AAAATCACATTTCACCC-TAAAATTTTCC
1 AAAATCACATTTAACCCTTAAAATTTTCC
*
75995 AAAATTACATTT
1 AAAATCACATTT
76007 TTGCCCCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 21 0.58
29 7 0.19
30 8 0.22
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATCACATTTAACCCTTAAAATTTTCC
Found at i:76036 original size:58 final size:57
Alignment explanation
Indices: 75831--76123 Score: 190
Period size: 58 Copynumber: 5.0 Consensus size: 57
75821 AATTACCATA
* * *
75831 TTGCCCTCAAACATCCAAGAATTACCATTTTGACCCT-AAGCTTTTCCAAAATTACTTTT
1 TTGCCCCCAAACATCCAA-AATTACCA-TTTGACCCTCAA-ATTTTCCAAAATTACATTT
* * * *
75890 TTGTCCCCAAACATCCAAAAATTA-CATTTTGACCCTCGAA-CTTCACAAAAAT-CATATT
1 TTGCCCCCAAACATCC-AAAATTACCA-TTTGACCCTCAAATTTTC-CAAAATTACAT-TT
* ** * * * *
75948 TTAACCCTTAAACTTTTCCAAAATCA-CATTTCACCCTAAAATTTTCCAAAATTACATTT
1 TT-GCCCCCAAAC--ATCCAAAATTACCATTTGACCCTCAAATTTTCCAAAATTACATTT
* * * *
76007 TTGCCCCCAAACATCCAAAAGTTACCATTTTACCCTCAAATATTCAAAAATTGCCA--T
1 TTGCCCCCAAACATCCAAAA-TTACCATTTGACCCTCAAATTTTCCAAAATT-ACATTT
* * *
76064 TTGACCCCCGAACATACAAAAGTTACCATTTTG-CCCTCAAA-TTTCCAAAAATCACATTT
1 TTG-CCCCCAAACATCCAAAA-TTACCA-TTTGACCCTCAAATTTTCC-AAAATTACATTT
76123 T
1 T
76124 CGACTTCAAA
Statistics
Matches: 182, Mismatches: 35, Indels: 34
0.73 0.14 0.14
Matches are distributed among these distances:
56 7 0.04
57 16 0.09
58 87 0.48
59 53 0.29
60 16 0.09
61 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (57 bp):
TTGCCCCCAAACATCCAAAATTACCATTTGACCCTCAAATTTTCCAAAATTACATTT
Found at i:88407 original size:30 final size:31
Alignment explanation
Indices: 88303--88415 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 31
88293 TTAATATAAC
* * *
88303 ATTTAGTACCTTAACTTGACACTTTTTTTTGTTCA
1 ATTTGGTACCTAAACTTGACAC---TTTTTCTT-A
*
88338 ATTTGGTA-CTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTCTTA
88369 ATTTGGTACCTAAACTTGACACTTTTT-TTA
1 ATTTGGTACCTAAACTTGACACTTTTTCTTA
* *
88399 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
88416 TTTGGGATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
30 17 0.25
31 25 0.36
32 8 0.12
34 2 0.03
35 17 0.25
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTA
Found at i:88712 original size:58 final size:59
Alignment explanation
Indices: 88621--88746 Score: 175
Period size: 58 Copynumber: 2.2 Consensus size: 59
88611 ATAGATTTAG
*
88621 GTACCAAATTGAATGTAAAAAAAGCTTAGGTACCAAATTA-AGAAAAATGCCAAGTTCAA
1 GTACCAAATTGAATGTAAAAAAAGCTTAGGTACCAAATTAGA-AAAAAAGCCAAGTTCAA
** * * *
88680 GTACCAAATTGGGT-TAAAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTCAAGTTCAG
1 GTACCAAATTGAATGTAAAAAAAGCTTAGGTACCAAATTAGAAAAAAAGCCAAGTTCAA
88738 GTACCAAAT
1 GTACCAAAT
88747 ATTATATTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 47 0.78
59 13 0.22
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.23
Consensus pattern (59 bp):
GTACCAAATTGAATGTAAAAAAAGCTTAGGTACCAAATTAGAAAAAAAGCCAAGTTCAA
Found at i:88740 original size:30 final size:29
Alignment explanation
Indices: 88648--88746 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 29
88638 AAAAAAGCTT
*
88648 AGGTACCAAATTA-AGAAAAATGCCAAGTTC
1 AGGTACCAAATTAGA-AAAAAAG-CAAGTTC
* * ** *
88678 AAGTACCAAATTGGGTTAAAAA--AAGTTT
1 AGGTACCAAATT-AGAAAAAAAGCAAGTTC
88706 AGGTACCAAATTAGAAAAAAAGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAAG-CAAGTTC
88736 AGGTACCAAAT
1 AGGTACCAAAT
88747 ATTATATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
27 6 0.11
28 16 0.30
30 27 0.51
31 4 0.08
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (29 bp):
AGGTACCAAATTAGAAAAAAAGCAAGTTC
Found at i:105537 original size:6 final size:6
Alignment explanation
Indices: 105526--105559 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
105516 TTCTTAAAAC
105526 AGATGA AGATGA AGATGA AGATGA AGATGA AGAT
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGAT
105560 CGAATGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
AGATGA
Found at i:106593 original size:16 final size:16
Alignment explanation
Indices: 106568--106598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
106558 ACTTTCCGCT
*
106568 GTGTTTCGTATTTCCG
1 GTGTTCCGTATTTCCG
106584 GTGTTCCGTATTTCC
1 GTGTTCCGTATTTCC
106599 CACTTTCTTC
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:0.06, C:0.23, G:0.23, T:0.48
Consensus pattern (16 bp):
GTGTTCCGTATTTCCG
Found at i:107886 original size:11 final size:11
Alignment explanation
Indices: 107870--107938 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
107860 GCCCAACAAA
107870 TTTAAATTTAT
1 TTTAAATTTAT
107881 TTTAAA---A-
1 TTTAAATTTAT
*
107888 -TTAAGTTTAT
1 TTTAAATTTAT
107898 TTTAAATTTAT
1 TTTAAATTTAT
*
107909 TATAAATTTAAAT
1 TTTAAATTT--AT
*
107922 TTAAAATTTA-
1 TTTAAATTTAT
107932 TTTAAAT
1 TTTAAAT
107939 AATGCTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 1 0.02
10 6 0.13
11 24 0.53
13 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:107902 original size:28 final size:28
Alignment explanation
Indices: 107870--107924 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
107860 GCCCAACAAA
* *
107870 TTTAAATTTATTTTAAAATTAAGTTTAT
1 TTTAAATTTATTATAAAATTAAATTTAT
*
107898 TTTAAATTTATTATAAATTTAAATTTA
1 TTTAAATTTATTATAAAATTAAATTTA
107925 AAATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAATTTATTATAAAATTAAATTTAT
Found at i:107934 original size:17 final size:17
Alignment explanation
Indices: 107867--107938 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
107857 TGGGCCCAAC
107867 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
107884 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
107901 AAATTT--ATTATAAATTT
1 AAATTTAAATT-T-ATTTT
107918 AAATTTAAAATTTA-TTT
1 AAATTT-AAATTTATTTT
107935 AAAT
1 AAAT
107939 AATGCTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.04
16 1 0.02
17 37 0.82
18 1 0.02
19 1 0.02
20 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:108682 original size:10 final size:10
Alignment explanation
Indices: 108664--108695 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
108654 AATAAATGAC
*
108664 ATTAATAATT
1 ATTATTAATT
108674 ATTATTAATT
1 ATTATTAATT
108684 ATTATTAATT
1 ATTATTAATT
108694 AT
1 AT
108696 AATAATAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTATTAATT
Found at i:109762 original size:59 final size:58
Alignment explanation
Indices: 109661--110101 Score: 343
Period size: 59 Copynumber: 7.5 Consensus size: 58
109651 GAAGGTCCCT
** * * *
109661 AAACTATCCAAAAATTTCGTTTTTACCCTTGAACTTCTAAAAATCTCATTTTTGACCCCA
1 AAACT-TCCAAAAA-TTCCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * * *
109721 AAACTTCTAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * * * * *
109780 AAACTTCTAAAAATTCTATTTTTACCAC-CAAACTTCCAAAAATCCCATTTTTAACCCTG
1 AAACTTCCAAAAATTCCA-TTTTACC-CTCGAACTTCCAAAAATCTCATTTTTGACCCCG
*
109839 AAACTTCCAAAAAATCTCATTTTACCCTCGAACTTCCAAAAAATCTCA-TTTT-ACCCTCG
1 AAACTTCCAAAAATTC-CATTTTACCCTCGAACTTCC-AAAAATCTCATTTTTGACCC-CG
*
109898 -AACTTCCAAAAAATCCATTTTAGCCC-CGAACTTCCAAAAAT-TCCATTTTTG-CCCCG
1 AAACTTCCAAAAATTCCATTTTA-CCCTCGAACTTCCAAAAATCT-CATTTTTGACCCCG
* * * * *
109954 AAACTTCCAAAAATGACCATTTTACCCCCGGA-TGTCCAAAAAT-TCCATTTTCGACCTCG
1 AAACTTCCAAAAAT-TCCATTTTACCCTCGAACT-TCCAAAAATCT-CATTTTTGACCCCG
* * * * *
110013 AAAC-TCTC-AAAATTACCCTTTTACCC-CCAAATCTCTAAAAAT-TCAATTTTTAACCCCG
1 AAACTTC-CAAAAATT-CCATTTTACCCTCGAACT-TCCAAAAATCTC-ATTTTTGACCCCG
* * *
110071 -AATTTTCACAAAATTACCATTTCACCCTCGA
1 AAACTTCCA-AAAATT-CCATTTTACCCTCGA
110102 GAATCCAAAA
Statistics
Matches: 318, Mismatches: 40, Indels: 46
0.79 0.10 0.11
Matches are distributed among these distances:
55 1 0.00
56 10 0.03
57 45 0.14
58 93 0.29
59 151 0.47
60 18 0.06
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
Found at i:109976 original size:30 final size:29
Alignment explanation
Indices: 109661--110092 Score: 236
Period size: 29 Copynumber: 14.7 Consensus size: 29
109651 GAAGGTCCCT
** * *
109661 AAACTATCCAAAAATTTCGTTTTTACCCTTG
1 AAACT-TCCAAAAATACCATTTTTACCC-CG
* *
109692 -AACTTCTAAAAAT-CTCATTTTTGACCCCA
1 AAACTTCCAAAAATAC-CATTTTT-ACCCCG
* *
109721 AAACTTCTAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATACCATTTTTACCC-CG
* * *
109751 -AATTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATACCATTTTT-ACCCCG
* * *
109780 AAACTTCTAAAAATTCTATTTTTACCACC-
1 AAACTTCCAAAAATACCATTTTTACC-CCG
* *
109809 AAACTTCCAAAAATCCCATTTTTAACCCTG
1 AAACTTCCAAAAATACCATTTTT-ACCCCG
109839 AAACTTCCAAAAA-ATCTCA-TTTTACCCTCG
1 AAACTTCCAAAAATA-C-CATTTTTACCC-CG
109869 -AACTTCCAAAAA-ATCTCA-TTTTACCCTCG
1 AAACTTCCAAAAATA-C-CATTTTTACCC-CG
109898 -AACTTCCAAAAA-ATCCA-TTTTAGCCCCG
1 AAACTTCCAAAAATA-CCATTTTTA-CCCCG
* *
109926 -AACTTCCAAAAATTCCATTTTTGCCCCG
1 AAACTTCCAAAAATACCATTTTTACCCCG
109954 AAACTTCCAAAAATGACCA-TTTTACCCCCG
1 AAACTTCCAAAAAT-ACCATTTTTA-CCCCG
* * * *
109984 -GA-TGTCCAAAAATTCCATTTTCGACCTCG
1 AAACT-TCCAAAAATACCATTTT-TACCCCG
* * *
110013 AAAC-TCTCAAAATTACC-CTTTTACCCCC
1 AAACTTC-CAAAAATACCATTTTTACCCCG
* * *
110041 AAA-TCTCTAAAAATTCAATTTTTAACCCCG
1 AAACT-TCCAAAAATACCATTTTT-ACCCCG
** *
110071 AATTTTCACAAAATTACCATTT
1 AAACTTC-CAAAAATACCATTT
110093 CACCCTCGAG
Statistics
Matches: 323, Mismatches: 47, Indels: 62
0.75 0.11 0.14
Matches are distributed among these distances:
28 46 0.14
29 163 0.50
30 100 0.31
31 14 0.04
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATACCATTTTTACCCCG
Found at i:110112 original size:28 final size:28
Alignment explanation
Indices: 110079--110140 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
110069 CGAATTTTCA
*
110079 CAAAATTACCATTTCACCCTCGAGAATC
1 CAAAATTACCATTTCACCCCCGAGAATC
* * *
110107 CAAAATTATCATTTTACCCCCGAGTATC
1 CAAAATTACCATTTCACCCCCGAGAATC
110135 CGAAAA
1 C-AAAA
110141 AGTCTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (28 bp):
CAAAATTACCATTTCACCCCCGAGAATC
Found at i:114293 original size:31 final size:31
Alignment explanation
Indices: 114258--114316 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
114248 TTAATTGATG
114258 TAAAAAATATATATTT-ATTTTGATTTTTAAA
1 TAAAAAATAT-TATTTAATTTTGATTTTTAAA
* *
114289 TAAAATATATTTTTTAATTTTGATTTTT
1 TAAAAAATATTATTTAATTTTGATTTTT
114317 TTTCAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
TAAAAAATATTATTTAATTTTGATTTTTAAA
Found at i:131507 original size:33 final size:33
Alignment explanation
Indices: 131439--131508 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
131429 ATAATAATTT
*
131439 ATATTTAAATAATCTAAAATAATGATAATTGAA
1 ATATTTAAATAATCTAAAATAATGATAATTAAA
*
131472 ATATTTAAATAATTCT-ATATAATGAT-ATATAAA
1 ATATTTAAATAA-TCTAAAATAATGATAAT-TAAA
131505 ATAT
1 ATAT
131509 AAATTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 2 0.06
33 28 0.85
34 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (33 bp):
ATATTTAAATAATCTAAAATAATGATAATTAAA
Found at i:134122 original size:21 final size:19
Alignment explanation
Indices: 134098--134150 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
134088 TTTTCTTGAA
*
134098 TTTTATGAACTTTTGATAAAT
1 TTTTATGAA-ATTTGA-AAAT
* *
134119 TTTTTTGAAATTTGAATAT
1 TTTTATGAAATTTGAAAAT
*
134138 TTTTATAAAATTT
1 TTTTATGAAATTT
134151 AAATTATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.52
20 5 0.19
21 8 0.30
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTTATGAAATTTGAAAAT
Found at i:136785 original size:52 final size:52
Alignment explanation
Indices: 136705--136807 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
136695 AAGGTAAGAG
* * * *
136705 AGTTTGAAAAAAAATATAAATTTAAAAAATAGGGTTAAACTTTAAATAAAAA
1 AGTTTGAAAAAAAATATAAATTCAAAAAATAAGATTAAACCTTAAATAAAAA
* *
136757 AGTTTGAAAAAAAATATAGATTCGAAAAATAAGATTAAACCTTAAATAAAA
1 AGTTTGAAAAAAAATATAAATTCAAAAAATAAGATTAAACCTTAAATAAAA
136808 TATTTTTGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (52 bp):
AGTTTGAAAAAAAATATAAATTCAAAAAATAAGATTAAACCTTAAATAAAAA
Found at i:137342 original size:30 final size:31
Alignment explanation
Indices: 137267--137342 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 31
137257 AAATTTTTTG
137267 AATTTTTTTATTTAAATCATTAAACTATCTAA
1 AATTTTTTT-TTTAAATCATTAAACTATCTAA
* ** * * * *
137299 AAGTTTTAATTTAAGTTATTAAGCTGT-TAA
1 AATTTTTTTTTTAAATCATTAAACTATCTAA
137329 AATTTTTTTTTTAA
1 AATTTTTTTTTTAA
137343 TGTTCCACGC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
30 14 0.41
31 14 0.41
32 6 0.18
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (31 bp):
AATTTTTTTTTTAAATCATTAAACTATCTAA
Found at i:149610 original size:29 final size:29
Alignment explanation
Indices: 149556--149628 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
149546 TATTACATGA
** *
149556 TAAAATTATACTTTTATCTTTAAAAATAT
1 TAAAATTATAAATTCATCTTTAAAAATAT
149585 TAAAATTATAAATTCATCCTTT-AAAATAT
1 TAAAATTATAAATTCAT-CTTTAAAAATAT
*
149614 TAGAAAATATAAATT
1 TA-AAATTATAAATT
149629 ATTAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (29 bp):
TAAAATTATAAATTCATCTTTAAAAATAT
Done.