Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009509.1 Kokia drynarioides strain JFW-HI SEQ_124220, 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: 198024
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:35184 original size:21 final size:23
Alignment explanation
Indices: 35142--35200 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 23
35132 ATAAAATTTT
*
35142 ATAAATATGTAAAATATATAAATAA
1 ATAAAT-TATAAAATATATAAA-AA
*
35167 A-AAATTCTAAAA-AT-TAAAAA
1 ATAAATTATAAAATATATAAAAA
35187 ATAAATTATAAAAT
1 ATAAATTATAAAAT
35201 TACAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 3 0.10
21 14 0.47
22 2 0.07
23 6 0.20
24 4 0.13
25 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAAATTATAAAATATATAAAAA
Found at i:36472 original size:131 final size:130
Alignment explanation
Indices: 36259--36605 Score: 426
Period size: 131 Copynumber: 2.6 Consensus size: 130
36249 AATTGTTATT
*
36259 ATTAAGGTTCGTTGATTTAAGATCACAGCTTAAGTTCATTCAATTTAATATCATGAACAATTTTA
1 ATTAAAGTTCGTTGATTTAAGATCACAGC-TAAGTTCATTCAATTTAATATCATGAACAATTTTA
* * * * * * * ** *
36324 TTTGAGTT-GATTGATTTAATATTGTTGCTTCAAATAACTCGTTAATTTAAGATCACATTTGATG
65 TCTGAGTTAGCTT-ATTTAATATCGCTGCTCCAAACAACTCGCTAATTTAAGATCACAACTGATA
36388 TC
129 TC
* * *
36390 ATTAAAGTTCGTTGATTTAATATCACAGTCTAAGTTCAGTCAATTTAATATCATGAATAATTTTA
1 ATTAAAGTTCGTTGATTTAAGATCACAG-CTAAGTTCATTCAATTTAATATCATGAACAATTTTA
* * *
36455 CCTGAGTTAGCTTATTTAATATCGCTGCTCCAAACAACTCGCTAATTTATGATCGCAACTGATAT
65 TCTGAGTTAGCTTATTTAATATCGCTGCTCCAAACAACTCGCTAATTTAAGATCACAACTGATAT
36520 C
130 C
* * * * * *
36521 ATTAAAGCTCGTTGATTTAAGATCGCAACCTAAGTTTATTCGATTTAATATCATTAACAATTTTA
1 ATTAAAGTTCGTTGATTTAAGATCAC-AGCTAAGTTCATTCAATTTAATATCATGAACAATTTTA
* *
36586 TCTGAATTAGCTAATTTAAT
65 TCTGAGTTAGCTTATTTAAT
36606 GTTCCTACTC
Statistics
Matches: 184, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
131 179 0.97
132 5 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (130 bp):
ATTAAAGTTCGTTGATTTAAGATCACAGCTAAGTTCATTCAATTTAATATCATGAACAATTTTAT
CTGAGTTAGCTTATTTAATATCGCTGCTCCAAACAACTCGCTAATTTAAGATCACAACTGATATC
Found at i:36963 original size:131 final size:131
Alignment explanation
Indices: 36711--36953 Score: 335
Period size: 131 Copynumber: 1.9 Consensus size: 131
36701 CTCTCGTAGC
* * * * * * *
36711 CTAAGTTCATTCGATTTAATATCATGAACAATTTTATTTGAGTTAGGTGATTTAATATTGCTGCT
1 CTAAGTTCATTCGATTTAATACCATAAACAATTTTATCTGAATTAAGTGATTTAACATCGCTGCT
*
36776 CCAAACAACTCGTTGATTTAAAATCGCAACTGATATCATTAAAACTCATTGATTTAATATAGTGG
66 CCAAACAACTCATTGATTTAAAATCGCAACTGATATCATTAAAACTCATTGATTTAATATAGTGG
36841 T
131 T
* * *
36842 CTAAGTTCATTCGATTTAATACCATAAATAATTTTATCTGAATTAATTGATTTAACGTCGCTGCT
1 CTAAGTTCATTCGATTTAATACCATAAACAATTTTATCTGAATTAAGTGATTTAACATCGCTGCT
* * * *
36907 CCAAATAACTTATTGATTTAATATCGCAA-TCGATATCGTTAAAACTC
66 CCAAACAACTCATTGATTTAAAATCGCAACT-GATATCATTAAAACTC
36954 GCTTATTTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
130 1 0.01
131 95 0.99
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (131 bp):
CTAAGTTCATTCGATTTAATACCATAAACAATTTTATCTGAATTAAGTGATTTAACATCGCTGCT
CCAAACAACTCATTGATTTAAAATCGCAACTGATATCATTAAAACTCATTGATTTAATATAGTGG
T
Found at i:42683 original size:36 final size:36
Alignment explanation
Indices: 42633--42703 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
42623 TTTTATCAGA
*
42633 AATTTATATAATATAAATAGTATAAAATATGAAATTT
1 AATTTATATAATATAAATAATAT-AAATATGAAATTT
*
42670 AATTTA-ATAATATAAATAATATATATATGAAATT
1 AATTTATATAATATAAATAATATAAATATGAAATT
42704 ATTACTATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 11 0.34
36 15 0.47
37 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (36 bp):
AATTTATATAATATAAATAATATAAATATGAAATTT
Found at i:53501 original size:21 final size:19
Alignment explanation
Indices: 53461--53503 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
53451 TTCTCTCTGT
53461 TTCTCTCTTAAATTTCTTC
1 TTCTCTCTTAAATTTCTTC
*
53480 TTCTCTTCTTTAATTTCATTC
1 TTCTC-TCTTAAATTTC-TTC
53501 TTC
1 TTC
53504 CAATCTGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (19 bp):
TTCTCTCTTAAATTTCTTC
Found at i:54517 original size:29 final size:29
Alignment explanation
Indices: 54484--54793 Score: 169
Period size: 29 Copynumber: 10.6 Consensus size: 29
54474 CCCTAAATTA
* *
54484 TTCAAAAATTACATTTTTACCCTCGAATT
1 TTCAAAAATTACATTTTTACCCTCAAACT
* *
54513 TTCAAAAATCT-CATTTTTGTCTCC-AAAACT
1 TTCAAAAAT-TACATTTTT-AC-CCTCAAACT
* *
54543 TCCAAAAATTATATTTTTA-CCTCAAACT
1 TTCAAAAATTACATTTTTACCCTCAAACT
* *
54571 TTCAAAAATCACATTTTTAACCTCAAAAC-
1 TTCAAAAATTACATTTTTACCCTC-AAACT
**
54600 TTCTAAAAATTTTATTTTTATCCC-CAAACT
1 TTC-AAAAATTACATTTTTA-CCCTCAAACT
* ** *
54630 TCCAAAAATTTTATTTTGA-CCTCGAAAC-
1 TTCAAAAATTACATTTTTACCCTC-AAACT
* * *
54658 TTCTAAAAATTTCATATTTACCCTCGAAC-
1 TTC-AAAAATTACATTTTTACCCTCAAACT
* **
54687 TTCTAAAAATT-CTATTTTCAATCTCGAAACT
1 TTC-AAAAATTAC-ATTTTTACCCTC-AAACT
*
54718 TCCAAAAATT-CTATTTTTACCC-CAAAC-
1 TTCAAAAATTAC-ATTTTTACCCTCAAACT
* * *
54745 CTCCAAAATTTCAATTTTTGACCC-CGAAACT
1 TTCAAAAATTAC-ATTTTT-ACCCTC-AAACT
54776 TTCAAAAATTACCATTTT
1 TTCAAAAATTA-CATTTT
54794 ACCTTCGGAT
Statistics
Matches: 221, Mismatches: 38, Indels: 42
0.73 0.13 0.14
Matches are distributed among these distances:
27 11 0.05
28 36 0.16
29 88 0.40
30 66 0.30
31 19 0.09
32 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
TTCAAAAATTACATTTTTACCCTCAAACT
Found at i:54559 original size:59 final size:59
Alignment explanation
Indices: 54486--54786 Score: 242
Period size: 58 Copynumber: 5.2 Consensus size: 59
54476 CTAAATTATT
* * * **
54486 CAAAAATTACATTTTTACCCTCGAATTTTCAAAAATCTCATTTTT-GTCTCCAAAACTTC
1 CAAAAATTATATTTTTACCCTCAAACTTTCAAAAATCTCATTTTTAACCT-CAAAACTTC
*
54545 CAAAAATTATATTTTTA-CCTCAAACTTTCAAAAATCACATTTTTAACCTCAAAACTTC
1 CAAAAATTATATTTTTACCCTCAAACTTTCAAAAATCTCATTTTTAACCTCAAAACTTC
* * * * * * *
54603 TAAAAATTTTATTTTTATCCC-CAAACTTCCAAAAATTTTA-TTTTGACCTCGAAACTTC
1 CAAAAATTATATTTTTA-CCCTCAAACTTTCAAAAATCTCATTTTTAACCTCAAAACTTC
* * * * * *
54661 TAAAAATT-TCATATTTACCCTCGAAC-TTCTAAAAAT-TCTATTTTCAATCTCGAAACTTC
1 CAAAAATTAT-ATTTTTACCCTCAAACTTTC-AAAAATCTC-ATTTTTAACCTCAAAACTTC
* * * * * * * *
54720 CAAAAATTCTATTTTTACCC-CAAAC-CTCCAAAATTTCAATTTTTGACCCCGAAACTTT
1 CAAAAATTATATTTTTACCCTCAAACTTTCAAAAATCTC-ATTTTTAACCTCAAAACTTC
54778 CAAAAATTA
1 CAAAAATTA
54787 CCATTTTACC
Statistics
Matches: 199, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
57 12 0.06
58 120 0.60
59 64 0.32
60 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
CAAAAATTATATTTTTACCCTCAAACTTTCAAAAATCTCATTTTTAACCTCAAAACTTC
Found at i:54630 original size:87 final size:85
Alignment explanation
Indices: 54484--54785 Score: 286
Period size: 87 Copynumber: 3.5 Consensus size: 85
54474 CCCTAAATTA
* * * * *
54484 TTCAAAAATTACATTTTTACCCTCGAA-TTTTCAAAAATCTCATTTTTGTCTCCAAAACTTCCAA
1 TTCAAAAATTACATTTTTACCCTCAAACTTCT-AAAAATTTTATTTTTATC-CCAAAACTTCCAA
54548 AAATTATATTTTTACCTCAAAC
64 AAATTATATTTTTACCTCAAAC
* * *
54570 TTTCAAAAATCACATTTTTAACCTCAAAACTTCTAAAAATTTTATTTTTATCCCCAAACTTCCAA
1 -TTCAAAAATTACATTTTTACCCTC-AAACTTCTAAAAATTTTATTTTTATCCCAAAACTTCCAA
* *
54635 AAATTTTATTTTGACCTCGAAAC
64 AAATTATATTTTTACCTC-AAAC
* * * * * * *
54658 TTCTAAAAATTTCATATTTACCCTCGAACTTCTAAAAATTCTATTTTCAATCTCGAAACTTCCAA
1 TTC-AAAAATTACATTTTTACCCTCAAACTTCTAAAAATTTTATTTT-TATCCCAAAACTTCCAA
* *
54723 AAATTCTATTTTTACCCCAAAC
64 AAATTATATTTTTACCTCAAAC
* * *
54745 CTCCAAAATTTCAATTTTTGACCC-CGAAACTT-TCAAAAATT
1 TTCAAAAATTAC-ATTTTT-ACCCTC-AAACTTCT-AAAAATT
54786 ACCATTTTAC
Statistics
Matches: 180, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
86 8 0.04
87 86 0.48
88 83 0.46
89 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (85 bp):
TTCAAAAATTACATTTTTACCCTCAAACTTCTAAAAATTTTATTTTTATCCCAAAACTTCCAAAA
ATTATATTTTTACCTCAAAC
Found at i:54795 original size:117 final size:117
Alignment explanation
Indices: 54574--54834 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 117
54564 TCAAACTTTC
* * * * *
54574 AAAAA-TCACATTTTTAACCTCAAAACTTCTAAAAATTTTATTTTTATCCCCAAACTTCCAAAAA
1 AAAAACTC-CATTTTCAACCTCGAAACTTCCAAAAATTCTATTTTTATCCCCAAACCTCCAAAAA
* * *
54638 TTTTATTTTGACCTCGAAACTTCTAAAAATTTCATATTTACCCTCGAACT-TCT
65 TTTAATTTTGACCCCGAAACTTCTAAAAATTCCATATTTACCCTCGAA-TGTCT
* * *
54691 AAAAATTCTATTTTCAATCTCGAAACTTCCAAAAATTCTATTTTTA-CCCCAAACCTCC-AAAAT
1 AAAAACTCCATTTTCAACCTCGAAACTTCCAAAAATTCTATTTTTATCCCCAAACCTCCAAAAAT
* *
54754 TTCAATTTTTGACCCCGAAACTT-TCAAAAATTACCAT-TTTACCTTCGGATGTCT
66 TT-AA-TTTTGACCCCGAAACTTCT-AAAAATT-CCATATTTACCCTCGAATGTCT
*
54808 AAAAACTCCATTTTCGACCTCGAAACT
1 AAAAACTCCATTTTCAACCTCGAAACT
54835 CTCGAAATTA
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
115 7 0.06
116 14 0.11
117 96 0.79
118 5 0.04
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (117 bp):
AAAAACTCCATTTTCAACCTCGAAACTTCCAAAAATTCTATTTTTATCCCCAAACCTCCAAAAAT
TTAATTTTGACCCCGAAACTTCTAAAAATTCCATATTTACCCTCGAATGTCT
Found at i:54870 original size:29 final size:31
Alignment explanation
Indices: 54834--54916 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 31
54824 ACCTCGAAAC
54834 TCTC-GAAATTACCTTTTTACCCTCAAA-TG
1 TCTCAGAAATTACCTTTTTACCCTCAAATTG
* * *
54863 TCT-AGAAATTTCATTTTTAACCCT-AAATTT
1 TCTCAGAAATTACCTTTTT-ACCCTCAAATTG
* *
54893 TCTCA-AAATTACCATTCTACCCTC
1 TCTCAGAAATTACCTTTTTACCCTC
54917 GGGTATCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
29 23 0.55
30 18 0.43
31 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.40
Consensus pattern (31 bp):
TCTCAGAAATTACCTTTTTACCCTCAAATTG
Found at i:54878 original size:58 final size:59
Alignment explanation
Indices: 54633--54879 Score: 163
Period size: 58 Copynumber: 4.2 Consensus size: 59
54623 CCAAACTTCC
* * * *
54633 AAAAATTTTATTTT-GACCTCGAAACT-TCTAAAAATT-TCATATTTACCCTCGAACT-TCT
1 AAAAATTTCATTTTCGACCCCGAAACTCTC-AAAAATTACCAT-TTTACCCTC-AAATGTCT
* * * * **
54691 AAAAA-TTCTATTTTCAATCTCGAAACT-TCCAAAAATT-CTATTTTTACCC-CAAACCTC-
1 AAAAATTTC-ATTTTCGACCCCGAAACTCT-CAAAAATTACCA-TTTTACCCTCAAATGTCT
* * * * **
54748 CAAAATTTCAATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCTTCGGATGTCT
1 AAAAATTTC-ATTTTCGACCCCGAAACTCTCAAAAATTACCATTTTACCCTCAAATGTCT
* * * * *
54808 AAAAACTCCATTTTCGACCTCGAAACTCTC-GAAATTACCTTTTTACCCTCAAATGTCT
1 AAAAATTTCATTTTCGACCCCGAAACTCTCAAAAATTACCATTTTACCCTCAAATGTCT
*
54866 AGAAATTTCATTTT
1 AAAAATTTCATTTT
54880 TAACCCTAAA
Statistics
Matches: 146, Mismatches: 33, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
57 8 0.05
58 79 0.54
59 51 0.35
60 8 0.05
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.37
Consensus pattern (59 bp):
AAAAATTTCATTTTCGACCCCGAAACTCTCAAAAATTACCATTTTACCCTCAAATGTCT
Found at i:57733 original size:56 final size:58
Alignment explanation
Indices: 57606--57748 Score: 173
Period size: 56 Copynumber: 2.5 Consensus size: 58
57596 TATATTATGA
* * * * *
57606 TTTTTATTAATTTATATTTTAATAATAATTAAATTAAGAATGTTATTAAATTATATACT
1 TTTTTATTAAATTATA-TTTAATAATAATCAAATTAAGAATATGATTAAAATATATACT
* * * * *
57665 ATTTTATTAAATTGTATTTAATAATAATCAAGTTCA-AATATGATTAAAATATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCAAATTAAGAATATGATTAAAATATATACT
57721 TTTTTATTAAATTATATTTAATAATAAT
1 TTTTTATTAAATTATATTTAATAATAAT
57749 TTTATTAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
56 27 0.38
57 15 0.21
58 17 0.24
59 13 0.18
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTTATTAAATTATATTTAATAATAATCAAATTAAGAATATGATTAAAATATATACT
Found at i:61952 original size:96 final size:95
Alignment explanation
Indices: 61841--62030 Score: 236
Period size: 96 Copynumber: 2.0 Consensus size: 95
61831 GTAAGGGTAT
* * *** ** **
61841 AAAAAACTCTTAAACTTTTTCAAAAAAAACAATTAAACTTTTTTTTTTTTTCCTGTACTCAATTG
1 AAAAAACTCTCAAACTTCTTCAAAAAAAACAATTAAACCCCTACTTTTTTT-CTCCACTCAATTG
* *
61906 AGCATTTGAACTTTCAAAATGCATAAAAAAA
65 AGCACTTCAACTTTCAAAATGCATAAAAAAA
* *
61937 AAAAAAGTCTCAAACTTCTTCAAAAAAAGCAATTAAACCCCTACTTTTTTTCTCCACTCAATTGA
1 AAAAAACTCTCAAACTTCTTCAAAAAAAACAATTAAACCCCTACTTTTTTTCTCCACTCAATTGA
* *
62002 GTACTTCAACTTTCAAAATGCATCAAAAA
66 GCACTTCAACTTTCAAAATGCATAAAAAA
62031 GACCTTCAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
95 37 0.47
96 42 0.53
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (95 bp):
AAAAAACTCTCAAACTTCTTCAAAAAAAACAATTAAACCCCTACTTTTTTTCTCCACTCAATTGA
GCACTTCAACTTTCAAAATGCATAAAAAAA
Found at i:62127 original size:19 final size:21
Alignment explanation
Indices: 62105--62151 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
62095 ATAAAAAAAA
62105 TAAATTTT-AGAAAAAT-TAT
1 TAAATTTTAAGAAAAATATAT
*
62124 TAAATTTTAATAAAAATATAT
1 TAAATTTTAAGAAAAATATAT
*
62145 AAAATTT
1 TAAATTT
62152 AAAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 7 0.29
21 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATTTTAAGAAAAATATAT
Found at i:62152 original size:20 final size:20
Alignment explanation
Indices: 62115--62153 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
62105 TAAATTTTAG
*
62115 AAAAATTATTAAATTTTAAT
1 AAAAATTATTAAAATTTAAT
62135 AAAAA-TATATAAAATTTAA
1 AAAAATTAT-TAAAATTTAA
62154 AATTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTATTAAAATTTAAT
Found at i:62501 original size:10 final size:10
Alignment explanation
Indices: 62440--62571 Score: 71
Period size: 10 Copynumber: 13.6 Consensus size: 10
62430 TTTTTACGAA
*
62440 TTTTATATTT
1 TTTTATAATT
62450 TTTTAT-ATT
1 TTTTATAATT
*
62459 TTGTATAATT
1 TTTTATAATT
* *
62469 TTATTATGACT
1 TT-TTATAATT
* *
62480 TTATAGAA--
1 TTTTATAATT
62488 TTTTATAA-T
1 TTTTATAATT
62497 TTTT-TAATAT
1 TTTTATAAT-T
* *
62507 TTCTAT-ATA
1 TTTTATAATT
62516 TTTTATAATT
1 TTTTATAATT
*
62526 TTTTACAA-T
1 TTTTATAATT
*
62535 TTTTATATTTT
1 TTTTATA-ATT
*
62546 TTTTCTAATT
1 TTTTATAATT
* *
62556 TTTAATAATA
1 TTTTATAATT
62566 TTTTAT
1 TTTTAT
62572 TAAAATTTAA
Statistics
Matches: 90, Mismatches: 23, Indels: 18
0.69 0.18 0.14
Matches are distributed among these distances:
8 9 0.10
9 23 0.26
10 43 0.48
11 15 0.17
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:62527 original size:28 final size:28
Alignment explanation
Indices: 62487--62547 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
62477 ACTTTATAGA
62487 ATTTTATAATTTTTTA-ATATTTCTATAT
1 ATTTTATAATTTTTTACA-ATTTCTATAT
*
62515 ATTTTATAATTTTTTACAATTTTTATAT
1 ATTTTATAATTTTTTACAATTTCTATAT
*
62543 TTTTT
1 ATTTT
62548 TTCTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTTTATAATTTTTTACAATTTCTATAT
Found at i:62557 original size:19 final size:18
Alignment explanation
Indices: 62425--62561 Score: 71
Period size: 19 Copynumber: 7.3 Consensus size: 18
62415 TTTTGGTACA
62425 ATAATTTTTTACGAATTTT
1 ATAATTTTTTAC-AATTTT
* * *
62444 ATATTTTTTTATATTTTGT
1 ATAATTTTTTACAATTT-T
** *
62463 ATAATTTTATTATGACTTT
1 ATAATTTT-TTACAATTTT
* *
62482 ATAGA-ATTTTATAATTTT
1 ATA-ATTTTTTACAATTTT
* * *
62500 TTAATATTTCTATATATTTT
1 ATAAT-TTTTTACA-ATTTT
62520 ATAATTTTTTACAATTTTT
1 ATAATTTTTTACAA-TTTT
* *
62539 ATATTTTTTTTCTAATTTT
1 ATAATTTTTTAC-AATTTT
62558 -TAAT
1 ATAAT
62562 AATATTTTAT
Statistics
Matches: 91, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.01
18 18 0.20
19 54 0.59
20 18 0.20
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (18 bp):
ATAATTTTTTACAATTTT
Found at i:62724 original size:91 final size:94
Alignment explanation
Indices: 62629--62837 Score: 252
Period size: 91 Copynumber: 2.3 Consensus size: 94
62619 ATTTTTTAGT
***
62629 AAAAGCAGGGGCTTAATTGTTTTTTTTTTTTTTAA-GTTTGA-GG-ATCTTTTTGATGCATTTTA
1 AAAAG-AGGGGCTTAATTGTTTTTTTTTTTGAAAAGGTTTGAGGGCATCTTTTTGATGCATTTTA
* *
62691 AAAGTTCAAGTATTCAATTGAGTGC-AAAA
65 AAAGTTCAAGTACTCAAATGAGTGCAAAAA
* * * *
62720 AAAAGTAGGGGTTTAATTG---CTTTTTTTGAAAAGGTTTGAGGGCCTTTTTTTGATGCATTTTA
1 AAAAG-AGGGGCTTAATTGTTTTTTTTTTTGAAAAGGTTTGAGGGCATCTTTTTGATGCATTTTA
62782 AAAGTTCAAGTACTCAAATGAGTGCAAAAA
65 AAAGTTCAAGTACTCAAATGAGTGCAAAAA
*
62812 AATAAGAGGGACTTAATTGTTTTTTT
1 AA-AAGAGGGGCTTAATTGTTTTTTT
62838 GAAAAAGTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
88 9 0.09
89 6 0.06
90 2 0.02
91 57 0.59
92 17 0.18
93 3 0.03
95 3 0.03
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (94 bp):
AAAAGAGGGGCTTAATTGTTTTTTTTTTTGAAAAGGTTTGAGGGCATCTTTTTGATGCATTTTAA
AAGTTCAAGTACTCAAATGAGTGCAAAAA
Found at i:62838 original size:91 final size:91
Alignment explanation
Indices: 62675--62849 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 91
62665 TTTGAGGATC
* * **
62675 TTTTTGATGCATTTTAAAAGTTCAAGTATTCAATTGAGTGCAAAAAAAAGTAGGGGTTTAATTGC
1 TTTTTGATGCATTTTAAAAGTTCAAGTACTCAAATGAGTGCAAAAAAAAGTAGGGACTTAATTGC
*
62740 TTTTTTTGAAAAGGTTTGAGGGCCTT
66 TTTTTTTGAAAAAGTTTGAGGGCCTT
62766 TTTTTGATGCATTTTAAAAGTTCAAGTACTCAAATGAGTGCAAAAAAATAAG-AGGGACTTAATT
1 TTTTTGATGCATTTTAAAAGTTCAAGTACTCAAATGAGTGC-AAAAAA-AAGTAGGGACTTAATT
62830 G-TTTTTTTGAAAAAGTTTGA
64 GCTTTTTTTGAAAAAGTTTGA
62850 AGGTTTTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
91 57 0.74
92 17 0.22
93 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.38
Consensus pattern (91 bp):
TTTTTGATGCATTTTAAAAGTTCAAGTACTCAAATGAGTGCAAAAAAAAGTAGGGACTTAATTGC
TTTTTTTGAAAAAGTTTGAGGGCCTT
Found at i:62926 original size:34 final size:34
Alignment explanation
Indices: 62883--62951 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
62873 AATTTTTTAG
62883 ACTGAACTAATCGATTAATCACTCCTAGACATCA
1 ACTGAACTAATCGATTAATCACTCCTAGACATCA
62917 ACTGAACTAATCGATTAATCACTCCTAGACATCA
1 ACTGAACTAATCGATTAATCACTCCTAGACATCA
62951 A
1 A
62952 TTTAGTATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (34 bp):
ACTGAACTAATCGATTAATCACTCCTAGACATCA
Found at i:63441 original size:56 final size:56
Alignment explanation
Indices: 63332--63629 Score: 287
Period size: 56 Copynumber: 5.2 Consensus size: 56
63322 TACTAATAAA
* * * * *
63332 AAAAATATTTTTTTAAGTGTTTGTCACCCAATGGTCTACAAC-ACATTTCTCAAATTT
1 AAAAATATTTTTTTAA-TGTTTGTCATCCAATAGTTTACATCAAC-TTTTTCAAATTT
* * *
63389 AAAAATATTTTTTTAATGCTTGTCATTCAGTAGTTTACATCAACTTTTTCAAATTT
1 AAAAATATTTTTTTAATGTTTGTCATCCAATAGTTTACATCAACTTTTTCAAATTT
* * * * * *
63445 AAAAATATTTTTTTGATGTTTATCATCTAAT-GATTTACATCACCTTTTTCAGATAT
1 AAAAATATTTTTTTAATGTTTGTCATCCAATAG-TTTACATCAACTTTTTCAAATTT
* *
63501 AAAAATATTTTCTTTAGATGTTTGTTATCCAATAGCTTACATCAACTTTTTCAAATTT
1 AAAAATATTTT-TTTA-ATGTTTGTCATCCAATAGTTTACATCAACTTTTTCAAATTT
* * * * * * * * *
63559 AAAAATATTTTTTTTGATGTTTGCCA-CTTAATGGTTTACACCATCTTTTTTAGATAT
1 AAAAATA-TTTTTTTAATGTTTGTCATC-CAATAGTTTACATCAACTTTTTCAAATTT
63616 AAAAATATTTTTTT
1 AAAAATATTTTTTT
63630 TGATGTTTAC
Statistics
Matches: 198, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
55 1 0.01
56 93 0.47
57 57 0.29
58 42 0.21
59 5 0.03
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (56 bp):
AAAAATATTTTTTTAATGTTTGTCATCCAATAGTTTACATCAACTTTTTCAAATTT
Found at i:63548 original size:114 final size:112
Alignment explanation
Indices: 63332--63637 Score: 371
Period size: 114 Copynumber: 2.7 Consensus size: 112
63322 TACTAATAAA
* * * * * * *
63332 AAAAATATTTTTTTAAGTGTTTGTCACCCAATGGTCTACAACACATTTCTCAAATTTAAAAATAT
1 AAAAATATTTTTTTGA-TGTTTGTCA-CTAATGGTTTACAACACCTTTTTCAGATATAAAAATAT
* * * *
63397 TTTTTTA-ATGCTTGTCATTCAGTAGTTTACATCAACTTTTTCAAATTT
64 TTTTTTAGATGTTTGTCATCCAATAGCTTACATCAACTTTTTCAAATTT
* * *
63445 AAAAATATTTTTTTGATGTTTATCATCTAATGATTTACATCACCTTTTTCAGATATAAAAATATT
1 AAAAATATTTTTTTGATGTTTGTCA-CTAATGGTTTACAACACCTTTTTCAGATATAAAAATATT
*
63510 TTCTTTAGATGTTTGTTATCCAATAGCTTACATCAACTTTTTCAAATTT
65 TT-TTTAGATGTTTGTCATCCAATAGCTTACATCAACTTTTTCAAATTT
* * * *
63559 AAAAATATTTTTTTTGATGTTTGCCACTTAATGGTTTACACCATCTTTTTTAGATATAAAAATAT
1 AAAAATA-TTTTTTTGATGTTTGTCAC-TAATGGTTTACAACACCTTTTTCAGATATAAAAATAT
*
63624 TTTTTTTGATGTTT
64 TTTTTTAGATGTTT
63638 ACTATTCAAT
Statistics
Matches: 166, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
112 41 0.25
113 19 0.11
114 54 0.33
115 52 0.31
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (112 bp):
AAAAATATTTTTTTGATGTTTGTCACTAATGGTTTACAACACCTTTTTCAGATATAAAAATATTT
TTTTAGATGTTTGTCATCCAATAGCTTACATCAACTTTTTCAAATTT
Found at i:63675 original size:115 final size:114
Alignment explanation
Indices: 63424--63678 Score: 282
Period size: 115 Copynumber: 2.2 Consensus size: 114
63414 TTCAGTAGTT
* * * * *
63424 TACATCAACTTTTTCAAATTTAAAAATATTTTTTTGATGTTTATCATCTAATGATTTACATCACC
1 TACATCAACATCTCCAAATTTAAAAATATTTTTTTGATGTTTACCATCTAATGATTTACACCACC
** *
63489 TTTTTCAGATATAAAAATATTTTCTTTAGATGTTTGTTATCCAATAGCT
66 TTTTTCAGATATAAAAATATTTTCTTTAGATGTTTACTATCCAATAGCC
* * * * *
63538 TACATCAACTTTTTCAAATTTAAAAATATTTTTTTTGATGTTTGCCA-CTTAATGGTTTACACCA
1 TACATCAACATCTCCAAATTTAAAAATA-TTTTTTTGATGTTTACCATC-TAATGATTTACACCA
* * * *
63602 TCTTTTTTAGATATAAAAATATTTT-TTTTGATGTTTACTATTCAATAGCC
64 CCTTTTTCAGATATAAAAATATTTTCTTTAGATGTTTACTATCCAATAGCC
* *
63652 TATA-CCACATCTCCAAAATTTTAAAAA
1 TACATCAACATCTCC-AAA-TTTAAAAA
63679 AATAATTAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
113 6 0.05
114 55 0.45
115 60 0.50
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (114 bp):
TACATCAACATCTCCAAATTTAAAAATATTTTTTTGATGTTTACCATCTAATGATTTACACCACC
TTTTTCAGATATAAAAATATTTTCTTTAGATGTTTACTATCCAATAGCC
Found at i:63729 original size:26 final size:25
Alignment explanation
Indices: 63672--63731 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
63662 CTCCAAAATT
*
63672 TTAAAAAAATAATTAAAACATAATT
1 TTAAAAAAATAATTAAAACATAATA
**
63697 TTAAAAAACATAATTAAATTATAATAA
1 TTAAAAAA-ATAATTAAAACATAAT-A
63724 TTAAAAAA
1 TTAAAAAA
63732 TGATTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 8 0.27
26 14 0.47
27 8 0.27
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
TTAAAAAAATAATTAAAACATAATA
Found at i:63913 original size:56 final size:57
Alignment explanation
Indices: 63832--64122 Score: 167
Period size: 57 Copynumber: 5.3 Consensus size: 57
63822 AATTTTAAAA
* * ** * * *
63832 TTTTAAATTTGAGAAAGGTGGTGTAGGTCATTAGATGATAAACACT-TAAAAAATAT
1 TTTTAAATTTGAAAAAGATAATGTAGGTCATTAGATAACAAACACTCAAAAAAATAT
* *
63888 TTTTAAATTTGAAAAAGATTATGTAGATCATTAGATAACAAACACTCAAAAAAATAT
1 TTTTAAATTTGAAAAAGATAATGTAGGTCATTAGATAACAAACACTCAAAAAAATAT
* * * * * ** * *
63945 TTTTAAATCTAAAAAAAATAATGTAGG-CTATTGGGTGTCAAACACTCAAAAAAAAAA
1 TTTTAAATTTGAAAAAGATAATGTAGGTC-ATTAGATAACAAACACTCAAAAAAATAT
* * * ** * ** * *
64002 ATTT-AATTTG-GAAATATGGTGTAAGTCATT-GAGTGGCAAATA-TCTAAAAAATAT
1 TTTTAAATTTGAAAAAGATAATGTAGGTCATTAGA-TAACAAACACTCAAAAAAATAT
* ** *
64056 TTTTAAATATAGAAAAA-ATGGTGTA-G--A-TAG-TGACAAACACTC-AAAAAATAT
1 TTTTAAAT-TTGAAAAAGATAATGTAGGTCATTAGATAACAAACACTCAAAAAAATAT
*
64107 TTTTAAATTTGGAAAA
1 TTTTAAATTTGAAAAA
64123 TGTGGTGTAA
Statistics
Matches: 186, Mismatches: 40, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
50 6 0.03
51 24 0.13
52 3 0.02
53 2 0.01
54 13 0.07
55 24 0.13
56 55 0.30
57 59 0.32
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (57 bp):
TTTTAAATTTGAAAAAGATAATGTAGGTCATTAGATAACAAACACTCAAAAAAATAT
Found at i:64167 original size:57 final size:56
Alignment explanation
Indices: 63879--64224 Score: 217
Period size: 57 Copynumber: 6.2 Consensus size: 56
63869 ATAAACACTT
* ** * * *
63879 AAAAAATATTTTTAAAT-TTGAAAAAGATTATGTAGATCATT-AGATAACAAACACTCA
1 AAAAAATATTTTTAAATATGGAAAAA-ATGGTGTAAACCATTGAG-TGACAAACAC-CA
* ** ** ** * * *
63936 AAAAAATATTTTTAAATCTAAAAAAAATAATGTAGGCTATTGGGTGTCAAACACTCA
1 AAAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACAC-CA
* ** * * ** * * * *
63993 AAAAAAAAAATTT-AATTTGG-AAATATGGTGTAAGTCATTGAGTGGCAAATATCT
1 AAAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACACCA
* *
64047 AAAAAATATTTTTAAATATAGAAAAAATGGTGT--A-GA-T-AGTGACAAACACTC-
1 AAAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACAC-CA
* ** *
64098 AAAAAATATTTTTAAATTTGGAAAATGTGGTGTAAACTATTGAGTGACAAACACCA
1 AAAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACACCA
** * *
64154 AGAAAAATATTTTTAAATATGGAAAAAATGGTGTAGGCCATTGGGTGGCAAACATCCA
1 A-AAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACA-CCA
*
64212 ACAAAATATTTTT
1 AAAAAATATTTTT
64225 TATTCGTATT
Statistics
Matches: 225, Mismatches: 51, Indels: 26
0.75 0.17 0.09
Matches are distributed among these distances:
51 38 0.17
52 2 0.01
53 2 0.01
54 12 0.05
55 29 0.13
56 27 0.12
57 104 0.46
58 11 0.05
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.30
Consensus pattern (56 bp):
AAAAAATATTTTTAAATATGGAAAAAATGGTGTAAACCATTGAGTGACAAACACCA
Found at i:64182 original size:108 final size:106
Alignment explanation
Indices: 63925--64189 Score: 282
Period size: 108 Copynumber: 2.4 Consensus size: 106
63915 TCATTAGATA
* * ** * *
63925 ACAAACACTCAAAAAAATATTTTTAAATCTAAAAAAAATAATGTAGGCTATTGGGTGTCAAACAC
1 ACAAACAC-CAAAAAAATATTTTTAAATATAGAAAAAATGGTGTA-G--A-T-AGTGACAAACAC
*
63990 TCAAAAAAAAAAATTTAATTTGGAAATATGGTGTAAGTCATTGAGTG
60 TCAAAAAAAAAAATTTAATTTGGAAATATGGTGTAACTCATTGAGTG
* * * *
64037 GCAAATATCTAAAAAATATTTTTAAATATAGAAAAAATGGTGTAGATAGTGACAAACACTC-AAA
1 ACAAACACCAAAAAAATATTTTTAAATATAGAAAAAATGGTGTAGATAGTGACAAACACTCAAAA
* ** *
64101 AAATATTTTTAAATTTGGAAAATGTGGTGTAAACT-ATTGAGTG
66 AAAAAAATTT-AATTTGG-AAATATGGTGT-AACTCATTGAGTG
*
64144 ACAAACACCAAGAAAAATATTTTTAAATATGGAAAAAATGGTGTAG
1 ACAAACACCAA-AAAAATATTTTTAAATATAGAAAAAATGGTGTAG
64190 GCCATTGGGT
Statistics
Matches: 129, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
105 10 0.08
106 19 0.15
107 26 0.20
108 37 0.29
110 1 0.01
111 31 0.24
112 5 0.04
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (106 bp):
ACAAACACCAAAAAAATATTTTTAAATATAGAAAAAATGGTGTAGATAGTGACAAACACTCAAAA
AAAAAAATTTAATTTGGAAATATGGTGTAACTCATTGAGTG
Found at i:67555 original size:2 final size:2
Alignment explanation
Indices: 67548--67584 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
67538 CAAATCAGCG
67548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
67585 TAATCCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:74588 original size:42 final size:40
Alignment explanation
Indices: 74515--74593 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
74505 AAATCTAGTT
* *
74515 ATTATAAATTTAAGATTATTTTCTATAAATTTGAAAATAA
1 ATTATAAATTTAAAATTATTTTCTATAAATTTAAAAATAA
* * *
74555 ATTATAATTTTAAAATATAATTTTCTGTTAATTTAAAAA
1 ATTATAAATTTAAAAT-T-ATTTTCTATAAATTTAAAAA
74594 ATGATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.44
41 1 0.03
42 17 0.53
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (40 bp):
ATTATAAATTTAAAATTATTTTCTATAAATTTAAAAATAA
Found at i:77560 original size:22 final size:22
Alignment explanation
Indices: 77491--77561 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
77481 TTAAATTTTA
77491 TTTTACTCATAATTTTAATTAT
1 TTTTACTCATAATTTTAATTAT
* * *** *
77513 TTTTATTTAT-ATGAAAATTTT
1 TTTTACTCATAATTTTAATTAT
77534 ATTTTACTCATAATTTTAATTAT
1 -TTTTACTCATAATTTTAATTAT
77557 TTTTA
1 TTTTA
77562 TTTTAATTTC
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
21 7 0.20
22 21 0.60
23 7 0.20
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (22 bp):
TTTTACTCATAATTTTAATTAT
Found at i:77570 original size:38 final size:38
Alignment explanation
Indices: 77478--77570 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 38
77468 TGTATTTACC
*
77478 TATTTAAATTTTATTTTACTCATAATTTTAATTATTTT
1 TATTTTAATTTTATTTTACTCATAATTTTAATTATTTT
77516 TATTTATATGAAAATTTTATTTTACTCATAATTTTAATTATTTT
1 TA-TT-T-T---AATTTTATTTTACTCATAATTTTAATTATTTT
77560 TATTTTAATTT
1 TATTTTAATTT
77571 CATACATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
38 7 0.15
39 2 0.04
40 1 0.02
41 1 0.02
42 1 0.02
43 2 0.04
44 34 0.71
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (38 bp):
TATTTTAATTTTATTTTACTCATAATTTTAATTATTTT
Found at i:81385 original size:31 final size:31
Alignment explanation
Indices: 81331--81396 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
81321 TTTATTTAAT
* *
81331 TTTTAAGGGCTCAAAATTTTTTTTAT-CAAC
1 TTTTAAGGGCTCAAAAATATTTTTATCCAAC
* *
81361 TTTTAAGGGACTTAAAAATATTTTTCTCCAAC
1 TTTTAAGGG-CTCAAAAATATTTTTATCCAAC
81393 TTTT
1 TTTT
81397 GAGAAATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.30
31 13 0.43
32 8 0.27
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (31 bp):
TTTTAAGGGCTCAAAAATATTTTTATCCAAC
Found at i:84369 original size:18 final size:18
Alignment explanation
Indices: 84340--84410 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
84330 TTTTTAGTAA
*
84340 TTATATATATTTATACAT
1 TTATATAAATTTATACAT
* *
84358 TTCTATAAA-TT-TACAG
1 TTATATAAATTTATACAT
* **
84374 TTATATATATTTATATGT
1 TTATATAAATTTATACAT
*
84392 TTTTATAAATTTATA-AT
1 TTATATAAATTTATACAT
84409 TT
1 TT
84411 GTTTATAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
16 11 0.28
17 7 0.17
18 22 0.55
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATATAAATTTATACAT
Found at i:84380 original size:34 final size:34
Alignment explanation
Indices: 84340--84404 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
84330 TTTTTAGTAA
84340 TTATATATATTTATACATTTCTATAAATTTACAG
1 TTATATATATTTATACATTTCTATAAATTTACAG
** *
84374 TTATATATATTTATATGTTTTTATAAATTTA
1 TTATATATATTTATACATTTCTATAAATTTA
84405 TAATTTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (34 bp):
TTATATATATTTATACATTTCTATAAATTTACAG
Found at i:85921 original size:24 final size:24
Alignment explanation
Indices: 85889--85951 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
85879 AAACTTTTAG
85889 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
85913 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
85937 TTAAACTCTATTTAT
1 TTAAACTCTATTTAT
85952 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.54
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:85962 original size:24 final size:24
Alignment explanation
Indices: 85911--85962 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
85901 TATTTGTTTC
* *** *
85911 AATTAAACTCTATTTATTTGTTTC
1 AATTAAACTCTATTTATATAAATA
85935 AATTAAACTCTATTTATATAAATA
1 AATTAAACTCTATTTATATAAATA
85959 AATT
1 AATT
85963 TTTTTACTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTAAACTCTATTTATATAAATA
Found at i:90266 original size:32 final size:32
Alignment explanation
Indices: 90213--90275 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
90203 AAAGGGTTCA
*
90213 AAAAAATATTTATCAACTTTTAAGAGACTTAC
1 AAAAAATATTTATCAACTTTTAAGAAACTTAC
* *
90245 AAAAAA-ATTTCTCAAATTTTTAAGAAACTTA
1 AAAAAATATTTATC-AACTTTTAAGAAACTTA
90276 AAATCCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (32 bp):
AAAAAATATTTATCAACTTTTAAGAAACTTAC
Found at i:93581 original size:22 final size:23
Alignment explanation
Indices: 93555--93599 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
93545 TCATTAATAT
*
93555 TGTTCATGAACATGTTCG-TTAA
1 TGTTCATGAACATGCTCGATTAA
*
93577 TGTTCGTGAACATGCTCGATTAA
1 TGTTCATGAACATGCTCGATTAA
93600 GTTAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (23 bp):
TGTTCATGAACATGCTCGATTAA
Found at i:115951 original size:297 final size:300
Alignment explanation
Indices: 115542--116340 Score: 775
Period size: 306 Copynumber: 2.7 Consensus size: 300
115532 AAATTTAAAA
* * * * * * *
115542 AAAAAAATCCTTCCGTAATTAAAATATGTTAAATTAATCGAGAATATTTTAGTATTTTTATTTCT
1 AAAAATATCCTTCCGTAATTAAAATAAGTTATATTATTTGTGGATATTTTAGTATTTTTATTTCT
* * * * * *
115607 -TAAAAATAAATAAAAAATTTAAATGTAACTAGATTTGAACCTATGCTATATATATTAATAAAAC
66 AAAAAAATAAA-AAAAAATTTATATGTGATTAGATTTGAACTTATGCTATATACATTAATAAAAC
* * *
115671 AAATATTTTACCACTAATCC-A-A-AGCTTTATTTT-A-AT-AT-T-TATATTTTAA-TTATATT
130 --A-ATTTTACCACTAAACCAAGATAGATTTATTTTAATATAATATCTACATTTTAATTTATATT
* * * *
115727 ATACCT-ACTTTATTATCTCTATCAACTGTATATATATACTCTATACTATTACTTGAAC-CC-TT
192 ATACATGACTTTATCATCTCCATCAA-T-TATATATATA-T-T-TACTATTACTTAAACTCCATT
* *
115789 GAGTTGGTGTCATGAGTCAACCGAATACCAACTCAGTTAGAGAAA-TTTC
252 AAGTTGGTGTCATGAGTCAACCGAACACCAACTCAGTTAGA-AAATTTTC
*
115838 AAAAATATCATTCCGTAATTAAAATAAGTTATATTATTTGTGGATATTTTAGT-TTTTTAATTTC
1 AAAAATATCCTTCCGTAATTAAAATAAGTTATATTATTTGTGGATATTTTAGTATTTTT-ATTTC
* *
115902 TAAAAACAATAAAAAAAAATTTGTATGTGATTAGATTTGAACTTATGCTATTTACATTAATAAAA
65 TAAAAA-AATAAAAAAAAATTTATATGTGATTAGATTTGAACTTATGCTATATACATTAATAAAA
*
115967 CAATTTTACCACTAAACCAAAGATTTAGATTTATTTTAATATAATATCTACATTTTAATTTGTAT
129 CAATTTTACCACTAAACC-AAGA--TAGATTTATTTTAATATAATATCTACATTTTAATTTATAT
* ** * *
116032 TATGCATGTTTTTATCATCTCCATCAATTATATATTTATTTACTATTATTTAAACTCCTGATTAA
191 TATACATGACTTTATCATCTCCATCAATTATATATATATTTACTATTACTTAAACTCC--ATTAA
*
116097 GTTGGTGTCATGAGTCAATCGAACACCAACTCAGTTAGAAAATTTTC
254 GTTGGTGTCATGAGTCAACCGAACACCAACTCAGTTAGAAAATTTTC
* * * *
116144 AAAAATATCCTTTCATAATTAAAATAAGTTATATT-TTT-TAGAGTA-TTTAGTCTTTTTATTTC
1 AAAAATATCCTTCCGTAATTAAAATAAGTTATATTATTTGTGGA-TATTTTAGTATTTTTATTTC
* * * * * * * * *
116206 TAAAAAAACAATAAAAAA-TTATATGTGATTGGATTTTAACTCAAGTTAT-TGACAATAATTAAA
65 TAAAAAAATAAAAAAAAATTTATATGTGATTAGATTTGAACTTATGCTATAT-ACATTAATAAAA
* * * * * * *
116269 CAAATTTACCACTAAACCACG--A-CTTTAATTTAATATAAGATTTACATTTTAA-TTGTATTAT
129 CAATTTTACCACTAAACCAAGATAGATTTATTTTAATATAATATCTACATTTTAATTTATATTAT
*
116330 GCAT-ACTTTAT
194 ACATGACTTTAT
116341 TAACAATTAA
Statistics
Matches: 425, Mismatches: 54, Indels: 50
0.80 0.10 0.09
Matches are distributed among these distances:
294 20 0.05
295 19 0.04
296 78 0.18
297 51 0.12
298 6 0.01
300 10 0.02
301 4 0.01
302 67 0.16
303 15 0.04
304 22 0.05
305 31 0.07
306 87 0.20
307 15 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (300 bp):
AAAAATATCCTTCCGTAATTAAAATAAGTTATATTATTTGTGGATATTTTAGTATTTTTATTTCT
AAAAAAATAAAAAAAAATTTATATGTGATTAGATTTGAACTTATGCTATATACATTAATAAAACA
ATTTTACCACTAAACCAAGATAGATTTATTTTAATATAATATCTACATTTTAATTTATATTATAC
ATGACTTTATCATCTCCATCAATTATATATATATTTACTATTACTTAAACTCCATTAAGTTGGTG
TCATGAGTCAACCGAACACCAACTCAGTTAGAAAATTTTC
Found at i:124617 original size:29 final size:29
Alignment explanation
Indices: 124576--124634 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
124566 AATTGAATTT
*
124576 TTTTTTTCATGTTATATATATTATAAATA
1 TTTTTTTCATGTTATACATATTATAAATA
124605 TTTTTTTCATGTTATACATATTATAAATA
1 TTTTTTTCATGTTATACATATTATAAATA
124634 T
1 T
124635 ATGTACTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTTTTCATGTTATACATATTATAAATA
Found at i:132557 original size:18 final size:18
Alignment explanation
Indices: 132534--132573 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
132524 AAGTTGAACC
132534 AAAAGAA-AGTAACTCTAA
1 AAAAGAACA-TAACTCTAA
*
132552 AAAAGAACATAACTTTAA
1 AAAAGAACATAACTCTAA
132570 AAAA
1 AAAA
132574 TTAATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.65, C:0.10, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAAGAACATAACTCTAA
Found at i:134634 original size:12 final size:12
Alignment explanation
Indices: 134617--134688 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
134607 AGTTAGTTTA
134617 ATGTTCACGAAC
1 ATGTTCACGAAC
**
134629 ATGTTCATTTAAC
1 ATGTTCA-CGAAC
134642 ---TTCATCGAAC
1 ATGTTCA-CGAAC
134652 ATGTTCACGAAC
1 ATGTTCACGAAC
**
134664 AT-TAAACGAAC
1 ATGTTCACGAAC
*
134675 ATGTTCATGAAC
1 ATGTTCACGAAC
134687 AT
1 AT
134689 ATAATTAAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 8 0.17
11 9 0.20
12 22 0.48
13 7 0.15
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (12 bp):
ATGTTCACGAAC
Found at i:134673 original size:23 final size:24
Alignment explanation
Indices: 134647--134711 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 24
134637 TTAACTTCAT
134647 CGAACATGTTCACGAACAT-TAAA
1 CGAACATGTTCACGAACATATAAA
* *
134670 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACATATAAA
**
134694 TAAACATGTTCACGAACA
1 CGAACATGTTCACGAACA
134712 ATGTTAATGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
CGAACATGTTCACGAACATATAAA
Found at i:139399 original size:57 final size:57
Alignment explanation
Indices: 139338--139492 Score: 141
Period size: 59 Copynumber: 2.7 Consensus size: 57
139328 TTTTATTAAA
*
139338 ATTTAATAACA-ATAACAATAATTATATTAAAAATATTATTAAATTATATATTATTTT
1 ATTTAATAACATATAACAATAATTATATT-AAAATATAATTAAATTATATATTATTTT
*** * * * *
139395 ATTTAATTGTATTTAATAATAATTATATTAAAATGTAATTAAATTATTTATTATTTATT
1 ATTTAATAACATATAACAATAATTATATTAAAATATAATTAAATTATATATTA-TT-TT
* * * * * * *
139454 ATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 ATTTAATAACATATAACAATAATTATATTAAAATATAAT
139493 AATAATAATA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 29 0.35
58 17 0.20
59 37 0.45
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (57 bp):
ATTTAATAACATATAACAATAATTATATTAAAATATAATTAAATTATATATTATTTT
Found at i:139483 original size:59 final size:57
Alignment explanation
Indices: 139354--139492 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 57
139344 TAACAATAAC
* * *
139354 AATAATTATATTAAAAATATTATTAAATTATATATTATTTTATTTAATTGTATTTAAT
1 AATAATTATATT-AAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAAT
* *
139412 AATAATTATATTAAAATGTAATTAAATTATTTATTATTTATTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATAATTAAATTATATATTA-TT-TTATTAAATTATATTTAAT
* *
139471 AATAATTTTATTAAAATTTAAT
1 AATAATTATATTAAAATATAAT
139493 AATAATAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
57 21 0.29
58 14 0.19
59 37 0.51
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (57 bp):
AATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAAT
Found at i:139660 original size:16 final size:16
Alignment explanation
Indices: 139639--139678 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
139629 CGAATTATTG
*
139639 ATTACAACTCTATTCT
1 ATTACAACTCTATTCC
* *
139655 ATTACAATTTTATTCC
1 ATTACAACTCTATTCC
139671 ATTACAAC
1 ATTACAAC
139679 GAACTAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:150116 original size:13 final size:13
Alignment explanation
Indices: 150098--150123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150088 GTCTGTATTT
150098 TTTTAATTTTTAA
1 TTTTAATTTTTAA
150111 TTTTAATTTTTAA
1 TTTTAATTTTTAA
150124 AAATTTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:151194 original size:23 final size:24
Alignment explanation
Indices: 151164--151220 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
151154 CAACAACCAA
* *
151164 AACAACAAAAATGACCGC-AAAAC
1 AACAACAAAAATAACAGCAAAAAC
*
151187 AACAACAAAAATAATAGCAAAAAC
1 AACAACAAAAATAACAGCAAAAAC
151211 AAC-ACAAAAA
1 AACAACAAAAA
151221 CAGTATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.68, C:0.21, G:0.05, T:0.05
Consensus pattern (24 bp):
AACAACAAAAATAACAGCAAAAAC
Found at i:151230 original size:22 final size:23
Alignment explanation
Indices: 151182--151245 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
151172 AAATGACCGC
*
151182 AAAACAACAACAAAAATAATAGCA
1 AAAACAAC-ACAAAAACAATAGCA
* *
151206 AAAACAACACAAAAACAGTA-TA
1 AAAACAACACAAAAACAATAGCA
* *
151228 AAAGCAGCACAAAAACAA
1 AAAACAACACAAAAACAA
151246 CAAAAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 16 0.47
23 10 0.29
24 8 0.24
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (23 bp):
AAAACAACACAAAAACAATAGCA
Found at i:151252 original size:22 final size:21
Alignment explanation
Indices: 151147--151252 Score: 54
Period size: 22 Copynumber: 4.8 Consensus size: 21
151137 TAACACTCAA
151147 ACAAAAACAACAACCAAAACAAC
1 ACAAAAACAACAA--AAAACAAC
**
151170 A-AAAATGACCGCAAAACAACAAC
1 ACAAAA--ACAACAAAA-AACAAC
* * *
151193 AAAAATAATAGC-AAAAACAAC
1 ACAAA-AACAACAAAAAACAAC
** * *
151214 ACAAAAACAGTATAAAAGCAGC
1 ACAAAAACAACA-AAAAACAAC
151236 ACAAAAACAACAAAAAA
1 ACAAAAACAACAAAAAA
151253 ATAGTAATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.06
21 14 0.22
22 26 0.41
23 11 0.17
24 8 0.12
25 1 0.02
ACGTcount: A:0.68, C:0.22, G:0.06, T:0.05
Consensus pattern (21 bp):
ACAAAAACAACAAAAAACAAC
Found at i:153863 original size:167 final size:171
Alignment explanation
Indices: 153553--153888 Score: 406
Period size: 167 Copynumber: 2.0 Consensus size: 171
153543 GGAAGTAAAA
*
153553 TTTTGAGGGAAAGTAAATAGAGGAAGAAAATTTTGGAGGAAAAATATTCAAAAAAAATAGAGAGA
1 TTTTGAGGGAAAGTAAATAGAGAAAGAAAATTTTGGAGGAAAAATATT-AAAAAAAATA-AGAGA
* * *
153618 GGGAATTGGTTTGGGGTAGATGGGGGTGAGATGGGAGGAGAGTAAAAGTTTTAGGCGGAAAGTGA
64 GGGAAATGGTTTAGGGTAGATGGGGGTGAGATGGGAGGAGAGT-AAAGTTTTAGGAGGAAAGTGA
* *
153683 GAGGAAGTAAAAGTTTTG-GGG-AAATTAAAAAATTTTGAAGGT
128 GAGGAAGTAAAAGTTTTGAGGGAAAAGTAAAAAAGTTTGAAGGT
* * *
153725 TTTTGA-GGAAAGTAAATGGTGAAAGTAAAATTTTGGA-GAGAAAATATT-AAAAAAAT-TG-GA
1 TTTTGAGGGAAAGTAAATAGAGAAAG-AAAATTTTGGAGGA-AAAATATTAAAAAAAATAAGAGA
* *
153785 GGGAAATGAGTTTAGGGTAGATGGGGGGTGGGATGGGA-GAGGAGT-AAGTTTTGGGAGGAAAGT
64 GGGAAATG-GTTTAGGGTAGAT-GGGGGTGAGATGGGAGGA-GAGTAAAGTTTTAGGAGGAAAGT
153848 -AGGAAGGAA-TAAAAGTTTTGAGGGAAAAGTAAAAAAGTTTG
126 GA-G-AGGAAGTAAAAGTTTTGAGGGAAAAGTAAAAAAGTTTG
153889 GGGTTTGGGG
Statistics
Matches: 144, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
166 1 0.01
167 37 0.26
168 23 0.16
169 32 0.22
170 8 0.06
171 18 0.12
172 25 0.17
ACGTcount: A:0.40, C:0.01, G:0.35, T:0.24
Consensus pattern (171 bp):
TTTTGAGGGAAAGTAAATAGAGAAAGAAAATTTTGGAGGAAAAATATTAAAAAAAATAAGAGAGG
GAAATGGTTTAGGGTAGATGGGGGTGAGATGGGAGGAGAGTAAAGTTTTAGGAGGAAAGTGAGAG
GAAGTAAAAGTTTTGAGGGAAAAGTAAAAAAGTTTGAAGGT
Found at i:153894 original size:7 final size:7
Alignment explanation
Indices: 153884--153909 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
153874 AAGTAAAAAA
153884 GTTTGGG
1 GTTTGGG
153891 GTTTGGG
1 GTTTGGG
153898 GTTTGGG
1 GTTTGGG
153905 GTTTG
1 GTTTG
153910 AGGTAAAAAT
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:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:156004 original size:23 final size:24
Alignment explanation
Indices: 155978--156022 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
155968 CCAATTAGGG
155978 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCT-TTTAGAATTTAATTCA
156001 AATTATCTTTTAGAATTTAATT
1 AATTATCTTTTAGAATTTAATT
156023 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (24 bp):
AATTATCTTTTAGAATTTAATTCA
Found at i:157102 original size:10 final size:11
Alignment explanation
Indices: 157084--157116 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
157074 TTACTTTAGC
157084 TATTTTATTAT
1 TATTTTATTAT
*
157095 TA-TTTATTTT
1 TATTTTATTAT
157105 TATTTTATTAT
1 TATTTTATTAT
157116 T
1 T
157117 TGTATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:157110 original size:21 final size:20
Alignment explanation
Indices: 157084--157131 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
157074 TTACTTTAGC
*
157084 TATTTTATTATTATTTATTTT
1 TATTTTATTATT-TGTATTTT
157105 TATTTTATTATTTGTATTTT
1 TATTTTATTATTTGTATTTT
*
157125 TAATTTA
1 TATTTTA
157132 ATTTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTATTATTTGTATTTT
Found at i:157117 original size:14 final size:15
Alignment explanation
Indices: 157086--157124 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
157076 ACTTTAGCTA
157086 TTTTATTATTATTTAT
1 TTTTATT-TTATTTAT
157102 TTTTATTTTA-TTAT
1 TTTTATTTTATTTAT
*
157116 TTGTATTTT
1 TTTTATTTT
157125 TAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
16 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTATTTAT
Found at i:157142 original size:14 final size:13
Alignment explanation
Indices: 157121--157152 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
157111 ATTATTTGTA
157121 TTTTTAATTTAAT
1 TTTTTAATTTAAT
157134 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
157148 TTTTT
1 TTTTT
157153 TTCCCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:165039 original size:6 final size:6
Alignment explanation
Indices: 165028--165072 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
165018 TGATCAAAAT
* * * *
165028 TGAAAG TGAAAG TGAAAG TGAAAG TAAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
165073 TATGAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:170716 original size:6 final size:6
Alignment explanation
Indices: 170693--170746 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
170683 AAATAGTATA
* * *
170693 TTTATT TTCATA TTTATT TTTATT TTTA-T TTTA-T TTTATT TTTAAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
170739 TTTATT TT
1 TTTATT TT
170747 AATTATGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:170716 original size:22 final size:21
Alignment explanation
Indices: 170693--170747 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 21
170683 AAATAGTATA
170693 TTTATTTTCATATTTATTTTTATT
1 TTTATTTT-AT-TTTATTTTTA-T
170717 TTTATTTTATTTTATTTTTAAT
1 TTTATTTTATTTTATTTTT-AT
170739 TTTATTTTA
1 TTTATTTTA
170748 ATTATGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 19 0.63
23 3 0.10
24 8 0.27
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTTATTTTATTTTTAT
Found at i:170727 original size:17 final size:17
Alignment explanation
Indices: 170693--170746 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
170683 AAATAGTATA
*
170693 TTTATTTTCATATTTATT
1 TTTATTTTTAT-TTTATT
170711 TTTATTTTTATTTTA-T
1 TTTATTTTTATTTTATT
170727 TTTATTTTTAATTTTATT
1 TTTATTTTT-ATTTTATT
170745 TT
1 TT
170747 AATTATGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 10 0.30
17 10 0.30
18 13 0.39
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTTATTTTATT
Found at i:171714 original size:7 final size:6
Alignment explanation
Indices: 171700--171799 Score: 71
Period size: 6 Copynumber: 15.7 Consensus size: 6
171690 TATTGTTTAG
* * *
171700 AAAGAA AAAGAA AAA-AA TAAAAAA AAAGTCGA AAAGAA AAATTGAA AAAAAA
1 AAAGAA AAAGAA AAAGAA -AAAGAA AAAG--AA AAAGAA AAA--GAA AAAGAA
171752 AAAGAA AATTGAGAA AAA-AA AAAGAA AAAGAA AAA-AA AAAGATA AAAG
1 AAAGAA AA---AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A AAAG
171800 TGTGTTTGAG
Statistics
Matches: 77, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
5 12 0.16
6 41 0.53
7 7 0.09
8 11 0.14
9 6 0.08
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:171753 original size:19 final size:20
Alignment explanation
Indices: 171731--171798 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
171721 AAAAAAGTCG
171731 AAAAGA-AAAATTGAAAAAA
1 AAAAGAGAAAATTGAAAAAA
171750 AAAA-AGAAAATTGAGAAAAA
1 AAAAGAGAAAATTGA-AAAAA
*
171770 AAAA-AGAAAA-AGAAAAAA
1 AAAAGAGAAAATTGAAAAAA
*
171788 AAAAGATAAAA
1 AAAAGAGAAAA
171799 GTGTGTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.23
19 19 0.43
20 15 0.34
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAGAGAAAATTGAAAAAA
Found at i:171756 original size:20 final size:20
Alignment explanation
Indices: 171731--171791 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
171721 AAAAAAGTCG
171731 AAAAGAAAAATTGAAAAAAA
1 AAAAGAAAAATTGAAAAAAA
171751 AAAAG-AAAATTGAGAAAAAA
1 AAAAGAAAAATTGA-AAAAAA
171771 AAAAGAAAAA--GAAAAAAA
1 AAAAGAAAAATTGAAAAAAA
171789 AAA
1 AAA
171792 GATAAAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.23
19 10 0.26
20 16 0.41
21 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAATTGAAAAAAA
Found at i:172836 original size:23 final size:25
Alignment explanation
Indices: 172810--172855 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
172800 CCAATTAGGG
172810 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
172833 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
172856 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:174895 original size:24 final size:25
Alignment explanation
Indices: 174860--174907 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
174850 ATGTTTTTCA
*
174860 ATTTTTTTAAAAT-AATAAAAAATC
1 ATTTTTTAAAAATAAATAAAAAATC
174884 ATTTTTTAAAAATAAAATAAAAAA
1 ATTTTTTAAAAAT-AAATAAAAAA
174908 ATATTTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTTTTAAAAATAAATAAAAAATC
Found at i:187290 original size:13 final size:15
Alignment explanation
Indices: 187274--187305 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
187264 ATAATAATAA
187274 AAAATAAA-CAA-TT
1 AAAATAAAGCAATTT
187287 AAAATAAAGCAATTT
1 AAAATAAAGCAATTT
187302 AAAA
1 AAAA
187306 CTGTGTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAATAAAGCAATTT
Found at i:192951 original size:15 final size:15
Alignment explanation
Indices: 192930--192971 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
192920 CCTAAACATA
192930 ATATTAACATATTATT
1 ATATTAACAT-TTATT
*
192946 -TATTAAAATTTATT
1 ATATTAACATTTATT
*
192960 ATATAAACATTT
1 ATATTAACATTT
192972 TAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAACATTTATT
Found at i:196020 original size:2 final size:2
Alignment explanation
Indices: 196013--196044 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
196003 TGTTGCAAGT
196013 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
196045 ATGGATATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:197834 original size:18 final size:18
Alignment explanation
Indices: 197811--197896 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
197801 CATACTCCCT
197811 TTAAATTTATTTTAAAAA
1 TTAAATTTATTTTAAAAA
**
197829 TTAAATTT-GCTTAAAAA
1 TTAAATTTATTTTAAAAA
*
197846 TTTAAATTTATTTT-AAAT
1 -TTAAATTTATTTTAAAAA
* *
197864 TTAAATTTATTTCAAAAT
1 TTAAATTTATTTTAAAAA
*
197882 TTAAATTTAATTTAA
1 TTAAATTTATTTTAA
197897 GTTTAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
17 19 0.33
18 36 0.63
19 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (18 bp):
TTAAATTTATTTTAAAAA
Found at i:197854 original size:6 final size:6
Alignment explanation
Indices: 197843--197928 Score: 65
Period size: 6 Copynumber: 14.5 Consensus size: 6
197833 ATTTGCTTAA
*
197843 AAATTT AAATTT -ATTTT AAATTT AAATTT --ATTT CAAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT --AAATTT AAATTT
* * *
197890 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAAGTTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA-TTT AAA
197929 ATAAATAGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.06
5 12 0.19
6 33 0.52
7 10 0.16
8 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:197871 original size:53 final size:53
Alignment explanation
Indices: 197810--197926 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
197800 CCATACTCCC
* ** *
197810 TTTAAATTTATTTTAAAAATTAAATTTGCTTAAAAATTTAAATTTATTTT-AAA
1 TTTAAATTTATTTCAAAAATTAAATTTAATT-AAAATTTAAAATTATTTTCAAA
* * *
197863 TTTAAATTTATTTCAAAATTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTCAAAAATTAAATTTAATTAAAATTTAAAATTATTTTCAAA
197916 TTTAAAGTTTA
1 TTTAAA-TTTA
197927 AAATAAATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
52 15 0.27
53 36 0.65
54 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (53 bp):
TTTAAATTTATTTCAAAAATTAAATTTAATTAAAATTTAAAATTATTTTCAAA
Found at i:197881 original size:35 final size:35
Alignment explanation
Indices: 197810--197926 Score: 137
Period size: 35 Copynumber: 3.3 Consensus size: 35
197800 CCATACTCCC
* ** *
197810 TTTAAATTTATTTTAAAAATTAAATTTGCTTAAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTCAAAA
197846 TTTAAATTTATTTTAAATTTAAATTTATTTCAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTCAAAA
* * *
197881 TTTAAATTTAATTTAAGTTTAAAATTATTTTC-AAA
1 TTTAAATTTATTTTAAATTTAAATTTA-TTTCAAAA
197916 TTTAAAGTTTA
1 TTTAAA-TTTA
197927 AAATAAATAG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 50 0.69
36 22 0.31
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTCAAAA
Found at i:197905 original size:18 final size:17
Alignment explanation
Indices: 197810--197927 Score: 94
Period size: 18 Copynumber: 6.6 Consensus size: 17
197800 CCATACTCCC
*
197810 TTTAAATTTATTTTAAAA
1 TTTAAATTTAATTT-AAA
* ** *
197828 ATTAAATTTGCTTAAAAA
1 TTTAAATTTAATT-TAAA
*
197846 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
197863 TTTAAATTT-ATTTCAAAA
1 TTTAAATTTAATTT--AAA
*
197881 TTTAAATTTAATTTAAG
1 TTTAAATTTAATTTAAA
* *
197898 TTTAAAATTATTTTCAAA
1 TTTAAATTTAATTT-AAA
197916 TTTAAAGTTTAA
1 TTTAAA-TTTAA
197928 AATAAATAGA
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
16 3 0.04
17 26 0.33
18 43 0.54
19 7 0.09
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Done.