Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015281.1 Kokia drynarioides strain JFW-HI SEQ_130326, 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: 648972
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 207 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:546818 original size:21 final size:21
Alignment explanation
Indices: 546792--546863 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
546782 GTTGTTTTAG
546792 TGCTATTTTGGTTGCTATTTT
1 TGCTATTTTGGTTGCTATTTT
*
546813 TGCTATTTTGGTGTTG-TTTTTAT
1 TGCTATTTT-G-GTTGCTATTT-T
* *
546836 TGTTATTTTTGTTGCTATTTT
1 TGCTATTTTGGTTGCTATTTT
*
546857 TTCTATT
1 TGCTATT
546864 ATTTTTACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 19 0.46
22 9 0.22
23 13 0.32
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (21 bp):
TGCTATTTTGGTTGCTATTTT
Found at i:546843 original size:44 final size:43
Alignment explanation
Indices: 546781--546863 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
546771 AAATTTATAT
546781 TGTTGTTTTAGTGCTATTTTGGTTGCTATTTTTGCTATTTTGG
1 TGTTGTTTTAGTGCTATTTTGGTTGCTATTTTTGCTATTTTGG
* * * *
546824 TGTTGTTTTTATTGTTATTTTTGTTGCTATTTTTTCTATT
1 TGTTG-TTTTAGTGCTATTTTGGTTGCTATTTTTGCTATT
546864 ATTTTTACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 5 0.14
44 30 0.86
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.66
Consensus pattern (43 bp):
TGTTGTTTTAGTGCTATTTTGGTTGCTATTTTTGCTATTTTGG
Found at i:546857 original size:12 final size:12
Alignment explanation
Indices: 546792--546857 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
546782 GTTGTTTTAG
*
546792 TGCTATTTTGGT
1 TGCTATTTTTGT
546804 TGCTA--TTT-T
1 TGCTATTTTTGT
*
546813 TGCTA-TTTTGG
1 TGCTATTTTTGT
* * *
546824 TGTTGTTTTTAT
1 TGCTATTTTTGT
*
546836 TGTTATTTTTGT
1 TGCTATTTTTGT
546848 TGCTATTTTT
1 TGCTATTTTT
546858 TCTATTATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 6 0.14
10 5 0.12
11 3 0.07
12 28 0.67
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (12 bp):
TGCTATTTTTGT
Found at i:547877 original size:3 final size:3
Alignment explanation
Indices: 547863--547945 Score: 73
Period size: 3 Copynumber: 28.3 Consensus size: 3
547853 AGAATTTTTC
* * * * *
547863 TCT TCT TTT TCT TCT TCT TCT TC- TCC TCC TCT TCCT CCT CCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT
* *
547907 TCT TCT TTT TCT TCT TCT TC- TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
547946 TTACTATCCA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
2 6 0.09
3 59 0.88
4 2 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:552523 original size:27 final size:27
Alignment explanation
Indices: 552492--552546 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
552482 ACTATCAATG
552492 ACAATAATGTTTGAATTAAGATTTTAA
1 ACAATAATGTTTGAATTAAGATTTTAA
552519 ACAATAATGTTTGAATTAAGATTTTAA
1 ACAATAATGTTTGAATTAAGATTTTAA
552546 A
1 A
552547 TTGAAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (27 bp):
ACAATAATGTTTGAATTAAGATTTTAA
Found at i:552583 original size:28 final size:29
Alignment explanation
Indices: 552533--552620 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
552523 TAATGTTTGA
* *
552533 ATTAAGATTTTAAATT-GAAAAAGTATAGG
1 ATTAA-ATTTTAAATTCTATAAAGTATAGG
*
552562 ATTGAATTTTAAACTT-T-TAAAGTATAGAG
1 ATTAAATTTTAAA-TTCTATAAAGTATAG-G
552591 ATTAAATTTTAAATTCTATACAAGTATAGG
1 ATTAAATTTTAAATTCTATA-AAGTATAGG
552621 GACTACTAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
28 19 0.38
29 20 0.40
30 3 0.06
31 8 0.16
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (29 bp):
ATTAAATTTTAAATTCTATAAAGTATAGG
Found at i:553944 original size:12 final size:12
Alignment explanation
Indices: 553923--553957 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
553913 TATAGAAAAA
553923 CACACACACACG
1 CACACACACACG
*
553935 CACACGCACACG
1 CACACACACACG
553947 CACACACACAC
1 CACACACACAC
553958 CCAGATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.51, G:0.09, T:0.00
Consensus pattern (12 bp):
CACACACACACG
Found at i:560560 original size:2 final size:2
Alignment explanation
Indices: 560553--560580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
560543 ACCTCCATTC
560553 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
560581 ACTCCATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:564900 original size:28 final size:28
Alignment explanation
Indices: 564868--564923 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
564858 ACTCCAAATG
564868 CAAAATTCTTTGCATGACCTAGTCCTAC
1 CAAAATTCTTTGCATGACCTAGTCCTAC
564896 CAAAATTCTTTGCATGACCTAGTCCTAC
1 CAAAATTCTTTGCATGACCTAGTCCTAC
564924 ATAAAACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (28 bp):
CAAAATTCTTTGCATGACCTAGTCCTAC
Found at i:570084 original size:3 final size:3
Alignment explanation
Indices: 570076--570138 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
570066 TTTATAATGT
* * * * * * *
570076 TGC TGC TGC TGT TGT TGT TGC TGC TGT TGT TGA TGC TGT TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
570124 TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC
570139 ATTTTATTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.02, C:0.22, G:0.33, T:0.43
Consensus pattern (3 bp):
TGC
Found at i:570127 original size:15 final size:15
Alignment explanation
Indices: 570073--570134 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
570063 CAATTTATAA
*
570073 TGTTGCTGCTGCTGT
1 TGTTGCTGCTGCTGC
* *
570088 TGTTGTTGCTGCTGT
1 TGTTGCTGCTGCTGC
* *
570103 TGTTGATGCTGTTGC
1 TGTTGCTGCTGCTGC
*
570118 TGCTGCTGCTGCTGC
1 TGTTGCTGCTGCTGC
570133 TG
1 TG
570135 CTGCATTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.02, C:0.19, G:0.34, T:0.45
Consensus pattern (15 bp):
TGTTGCTGCTGCTGC
Found at i:573793 original size:2 final size:2
Alignment explanation
Indices: 573786--573835 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
573776 TTTGTGTTGC
* *
573786 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG ATG -G AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG
573828 AG AG -G AG A
1 AG AG AG AG A
573836 ATTACGGAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.93
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:575840 original size:22 final size:22
Alignment explanation
Indices: 575789--575844 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
575779 AAAAATGATG
575789 AAATTATAATTTAATACATAAT
1 AAATTATAATTTAATACATAAT
* * *
575811 AAACTTATATTTTGATATATGAA-
1 AAA-TTATAATTTAATACAT-AAT
575834 AAATTATAATT
1 AAATTATAATT
575845 AAACTCCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 10 0.36
23 16 0.57
24 2 0.07
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATTATAATTTAATACATAAT
Found at i:584470 original size:172 final size:171
Alignment explanation
Indices: 584183--584502 Score: 405
Period size: 172 Copynumber: 1.9 Consensus size: 171
584173 GGGAGTAAAA
* * *
584183 TTTTGAGGAAGAGTAAATAGGGGACTAAAATTTTGGAGGGAAAATATTCAAAAAAAAATTGAGGG
1 TTTTGAGGAAAAGTAAATAGGGGACTAAAATTTTGAAGGAAAAATATT-AAAAAAAAATTGAGGG
* * * *
584248 AGGGATGAGTTAGAGGTAAATGGGGGTGAAATGAGGGGGGAGTAAAAGTTTTAGTGGGAAAGTGG
65 A-GAATGAGTTAGAGGTAAATGGGAGTGAAATGAGAGGGGAGTAAAAGTTTT-GGGGGAAAGTGG
* *
584313 GATGTAGTAAAAGTTTTGAAAAAAAAATAAAACGTTTTGAGGGT
128 GAAGGAGTAAAAGTTTTGAAAAAAAAATAAAACGTTTTGAGGGT
* *
584357 TTTTG-GGAAAAGTAAATGGGGAGAGTAAAATTTTGAAGGAAAAATATT-AAAAAAAATTAGAGG
1 TTTTGAGGAAAAGTAAATAGGG-GACTAAAATTTTGAAGGAAAAATATTAAAAAAAAATT-GAGG
* * * **
584420 GA-AATGAGGTTGGA-GTAGATAGGGAGTGGAATGAGAGGGGAGTAAAAGTTTTGGGGGAATTTG
64 GAGAATGA-GTTAGAGGTAAAT-GGGAGTGAAATGAGAGGGGAGTAAAAGTTTTGGGGGAAAGTG
584483 GGAAGGAGTAAAAGTTTTGA
127 GGAAGGAGTAAAAGTTTTGA
584503 GGGAAAAGTA
Statistics
Matches: 126, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
171 35 0.28
172 43 0.34
173 20 0.16
174 28 0.22
ACGTcount: A:0.40, C:0.01, G:0.34, T:0.25
Consensus pattern (171 bp):
TTTTGAGGAAAAGTAAATAGGGGACTAAAATTTTGAAGGAAAAATATTAAAAAAAAATTGAGGGA
GAATGAGTTAGAGGTAAATGGGAGTGAAATGAGAGGGGAGTAAAAGTTTTGGGGGAAAGTGGGAA
GGAGTAAAAGTTTTGAAAAAAAAATAAAACGTTTTGAGGGT
Found at i:585451 original size:9 final size:9
Alignment explanation
Indices: 585437--585466 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
585427 TTATTGATTT
585437 AAAATTTTA
1 AAAATTTTA
585446 AAAATTTTA
1 AAAATTTTA
*
585455 AAAAGTTTA
1 AAAATTTTA
585464 AAA
1 AAA
585467 GAAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAATTTTA
Found at i:586131 original size:17 final size:18
Alignment explanation
Indices: 586109--586152 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
586099 TTTAAATAAC
*
586109 TTTAATAATTTTT-AATT
1 TTTAATAATTTTTGAACT
586126 TTTAAT--TTTTTGAACT
1 TTTAATAATTTTTGAACT
586142 TTTAA-AATTTT
1 TTTAATAATTTT
586153 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 10 0.43
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTAATAATTTTTGAACT
Found at i:592437 original size:13 final size:12
Alignment explanation
Indices: 592414--592456 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
592404 CGAATTTTGA
592414 AATTTTTATATT
1 AATTTTTATATT
592426 AATTTTTA-ATAT
1 AATTTTTATAT-T
*
592438 AATTTTTTGTATT
1 AA-TTTTTATATT
592451 AATTTT
1 AATTTT
592457 AAGTGTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 2 0.07
12 15 0.56
13 8 0.30
14 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
AATTTTTATATT
Found at i:592491 original size:18 final size:19
Alignment explanation
Indices: 592470--592513 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
592460 TGTAATAGAA
*
592470 AATTTAAGTTTTGTA-CTT
1 AATTTAAGTTTTATATCTT
* *
592488 AATTTAATTTTTATATTTT
1 AATTTAAGTTTTATATCTT
592507 AATTTAA
1 AATTTAA
592514 TTGTTCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTAAGTTTTATATCTT
Found at i:592770 original size:21 final size:20
Alignment explanation
Indices: 592725--592763 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
592715 AAAAATATAC
592725 AAATAAAAAATGATTAAATTA
1 AAATAAAAAA-GATTAAATTA
592746 AAATAAAAAA-ATTAAATT
1 AAATAAAAAAGATTAAATT
592764 TGTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAATAAAAAAGATTAAATTA
Found at i:593692 original size:13 final size:13
Alignment explanation
Indices: 593674--593700 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
593664 TATATTCGCA
593674 AATTATTTCAAAT
1 AATTATTTCAAAT
593687 AATTATTTCAAAT
1 AATTATTTCAAAT
593700 A
1 A
593701 CACATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATTTCAAAT
Found at i:594001 original size:18 final size:18
Alignment explanation
Indices: 593971--594023 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
593961 TAATATTTAT
593971 AATTT-TTATATAAATAAA
1 AATTTATTA-ATAAATAAA
593989 AATTTATTAAT-AA-AAA
1 AATTTATTAATAAATAAA
**
594005 AATAAATTAA-AAATAAA
1 AATTTATTAATAAATAAA
594022 AA
1 AA
594024 ACTCAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 13 0.43
17 7 0.23
18 7 0.23
19 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTTATTAATAAATAAA
Found at i:594991 original size:23 final size:21
Alignment explanation
Indices: 594963--595007 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
594953 TCCCTTAATG
594963 TTTATA-TTTAGTTCTTATTTTTT
1 TTTATAGTTTA-TT-TT-TTTTTT
594986 TTTATAGTTTATTTTTTTTTT
1 TTTATAGTTTATTTTTTTTTT
595007 T
1 T
595008 AGTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 8 0.38
24 4 0.19
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTATAGTTTATTTTTTTTTT
Found at i:595015 original size:19 final size:19
Alignment explanation
Indices: 594969--595024 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 19
594959 AATGTTTATA
*
594969 TTTAGTTCTTATTTTTTTT
1 TTTAGTTTTTATTTTTTTT
*
594988 TATAG--TTTATTTTTTTT
1 TTTAGTTTTTATTTTTTTT
595005 TTTAGTTTTTATTTGTTTTT
1 TTTAGTTTTTATTT-TTTTT
595025 GTGGAACGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 15 0.48
19 11 0.35
20 5 0.16
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTAGTTTTTATTTTTTTT
Found at i:595705 original size:168 final size:168
Alignment explanation
Indices: 595427--595762 Score: 654
Period size: 168 Copynumber: 2.0 Consensus size: 168
595417 TTAGTTTCCT
595427 TTTGTCTCGTTATTTTTTTACTATATTTTAATTTCGTTTAGAATGTTTATCTATTTTAATTTCTA
1 TTTGTCTCGTTATTTTTTTACTATATTTTAATTTCGTTTAGAATGTTTATCTATTTTAATTTCTA
*
595492 ATAAATTCAATCGACATTTATTCAAAAAGTATAATTTTATTTTTATTAATTTAAAATTTTATAAA
66 ATAAATTCAATCAACATTTATTCAAAAAGTATAATTTTATTTTTATTAATTTAAAATTTTATAAA
*
595557 ATTTAAAAATTAAATAAAAAAAATTTAATTTTAGGGGG
131 ATTTAAAAATTAAATAAAAAAAAATTAATTTTAGGGGG
595595 TTTGTCTCGTTATTTTTTTACTATATTTTAATTTCGTTTAGAATGTTTATCTATTTTAATTTCTA
1 TTTGTCTCGTTATTTTTTTACTATATTTTAATTTCGTTTAGAATGTTTATCTATTTTAATTTCTA
595660 ATAAATTCAATCAACATTTATTCAAAAAGTATAATTTTATTTTTATTAATTTAAAATTTTATAAA
66 ATAAATTCAATCAACATTTATTCAAAAAGTATAATTTTATTTTTATTAATTTAAAATTTTATAAA
595725 ATTTAAAAATTAAATAAAAAAAAATTAATTTTAGGGGG
131 ATTTAAAAATTAAATAAAAAAAAATTAATTTTAGGGGG
595763 AAAAGAACAC
Statistics
Matches: 166, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 166 1.00
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (168 bp):
TTTGTCTCGTTATTTTTTTACTATATTTTAATTTCGTTTAGAATGTTTATCTATTTTAATTTCTA
ATAAATTCAATCAACATTTATTCAAAAAGTATAATTTTATTTTTATTAATTTAAAATTTTATAAA
ATTTAAAAATTAAATAAAAAAAAATTAATTTTAGGGGG
Found at i:597516 original size:2 final size:2
Alignment explanation
Indices: 597509--597542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
597499 TATGGTTTTG
597509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
597543 CTTCGTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:614139 original size:25 final size:25
Alignment explanation
Indices: 614093--614140 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
614083 ACGGGGCTTA
* * *
614093 AATTGATCACATGAGTTGTGAATAT
1 AATTGATCACACGAGCTATGAATAT
*
614118 AATTGCTCACACGAGCTATGAAT
1 AATTGATCACACGAGCTATGAAT
614141 TGAGACTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (25 bp):
AATTGATCACACGAGCTATGAATAT
Found at i:616849 original size:29 final size:29
Alignment explanation
Indices: 616808--616902 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 29
616798 CAATAAATAT
*
616808 TATAAATATTATTAAATTTTAATAAAAAAA
1 TATAAA-AATATTAAATTTTAATAAAAAAA
** *
616838 TATAAAAATATTTTA-TTGAA-ACAAAAAA
1 TATAAAAATATTAAATTTTAATA-AAAAAA
* *
616866 -ATAAAAATATTTAAATTTT-ATTAAAAAT
1 TATAAAAATA-TTAAATTTTAATAAAAAAA
616894 TATAAAAAT
1 TATAAAAAT
616903 CATAGAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
27 10 0.20
28 19 0.37
29 16 0.31
30 6 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
TATAAAAATATTAAATTTTAATAAAAAAA
Found at i:616901 original size:9 final size:9
Alignment explanation
Indices: 616887--616929 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
616877 TAAATTTTAT
616887 TAAAAATTA
1 TAAAAATTA
*
616896 TAAAAATCA
1 TAAAAATTA
616905 TAGAAAATTA
1 TA-AAAATTA
*
616915 TCAAAAATTG
1 T-AAAAATTA
616925 TAAAA
1 TAAAA
616930 TTTTATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 14 0.48
10 14 0.48
11 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (9 bp):
TAAAAATTA
Found at i:616959 original size:20 final size:20
Alignment explanation
Indices: 616888--616960 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
616878 AAATTTTATT
*
616888 AAAAATTAT-AAAAATCATAG
1 AAAATTTATAAAAAATCAT-G
*
616908 AAAA-TTATCAAAAAT--TG
1 AAAATTTATAAAAAATCATG
616925 TAAAATTTTATTAAAAAATCATG
1 -AAAA-TTTA-TAAAAAATCATG
616948 AAAATTTATAAAA
1 AAAATTTATAAAA
616961 TACATCAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
17 1 0.02
18 5 0.11
19 4 0.09
20 18 0.40
21 11 0.24
22 4 0.09
23 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAATTTATAAAAAATCATG
Found at i:617146 original size:9 final size:9
Alignment explanation
Indices: 617132--617330 Score: 63
Period size: 10 Copynumber: 21.0 Consensus size: 9
617122 TTTTGATACG
617132 ATAATTTTT
1 ATAATTTTT
617141 ATAATTTTTT
1 ATAA-TTTTT
* *
617151 ACAAATTTT
1 ATAATTTTT
*
617160 ATATTTCTTT
1 ATAATT-TTT
617170 AT-ATTTTT
1 ATAATTTTT
617178 ATAATTTTCT
1 ATAATTTT-T
*
617188 -TACGACTTTAT
1 ATA--A-TTTTT
* *
617199 AAAATGTTAT
1 ATAAT-TTTT
**
617209 ATTTTTTTTT
1 A-TAATTTTT
*
617219 ATATATTTCT
1 ATA-ATTTTT
617229 AT-ATATTTT
1 ATAAT-TTTT
617238 ATAATTTTT
1 ATAATTTTT
617247 -TGCAATTTTT
1 AT--AATTTTT
617257 ATAA-TTTT
1 ATAATTTTT
*
617265 -TAATATTT
1 ATAATTTTT
617273 ATAATATTTTT
1 AT-A-ATTTTT
*
617284 ATTAAAACTTTT
1 A-T--AATTTTT
617296 ATAATTTTT
1 ATAATTTTT
*
617305 ATTGATTTTT
1 A-TAATTTTT
*
617315 AT-TTTTTT
1 ATAATTTTT
617323 AT-ATTTTT
1 ATAATTTTT
617331 TTGCCACATG
Statistics
Matches: 144, Mismatches: 23, Indels: 47
0.67 0.11 0.22
Matches are distributed among these distances:
7 3 0.02
8 27 0.19
9 42 0.29
10 48 0.33
11 11 0.08
12 11 0.08
13 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:617161 original size:19 final size:19
Alignment explanation
Indices: 617137--617190 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
617127 ATACGATAAT
617137 TTTTATAATTTTTTACAAA
1 TTTTATAATTTTTTACAAA
* *
617156 TTTTAT-ATTTCTTTA-TAT
1 TTTTATAATTT-TTTACAAA
617174 TTTTATAATTTTCTTAC
1 TTTTATAATTTT-TTAC
617191 GACTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAA
Found at i:617272 original size:18 final size:18
Alignment explanation
Indices: 617214--617330 Score: 62
Period size: 19 Copynumber: 6.3 Consensus size: 18
617204 GTTATATTTT
*
617214 TTTTTATATATTTCT-ATA
1 TTTTTATA-ATTTTTAATA
*
617232 TATTTTATAATTTTTTGCA-A
1 T-TTTTATAA-TTTTT-AATA
617252 TTTTTATAATTTTTAATA
1 TTTTTATAATTTTTAATA
* * *
617270 TTTATAATATTTTTATTAAAA
1 TTT-TTATA-ATTT-TTAATA
* *
617291 CTTTTATAATTTTTATTGA
1 TTTTTATAATTTTTAAT-A
*
617310 TTTTTAT--TTTTTTATA
1 TTTTTATAATTTTTAATA
617326 TTTTT
1 TTTTT
617331 TTGCCACATG
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.08
17 7 0.09
18 14 0.18
19 33 0.43
20 9 0.12
21 8 0.10
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATAATTTTTAATA
Found at i:617331 original size:9 final size:9
Alignment explanation
Indices: 617213--617331 Score: 53
Period size: 9 Copynumber: 12.7 Consensus size: 9
617203 TGTTATATTT
617213 TTTTTTATA
1 TTTTTTATA
*
617222 TATTTCTATA
1 T-TTTTTATA
*
617232 TATTTTATAA
1 TTTTTTAT-A
**
617242 TTTTTTGCA
1 TTTTTTATA
*
617251 ATTTTTATAA
1 TTTTTTAT-A
*
617261 TTTTTAATA
1 TTTTTTATA
* *
617270 TTTATAATA
1 TTTTTTATA
*
617279 TTTTTATTAAA
1 -TTTT-TTATA
**
617290 ACTTTTATA
1 TTTTTTATA
*
617299 ATTTTTAT-
1 TTTTTTATA
617307 TGATTTTTAT-
1 T--TTTTTATA
617317 TTTTTTATA
1 TTTTTTATA
617326 TTTTTT
1 TTTTTT
617332 TGCCACATGT
Statistics
Matches: 82, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.09
9 38 0.46
10 34 0.41
11 3 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTTATA
Found at i:636876 original size:15 final size:14
Alignment explanation
Indices: 636848--636889 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
636838 ACGAGAGAGA
636848 CGGA-GGAA-GCGG
1 CGGAGGGAAGGCGG
636860 CGGCAGGGAAGGCGG
1 CGG-AGGGAAGGCGG
636875 CGGAGGCGAAGGCGG
1 CGGAGG-GAAGGCGG
636890 AGAGTAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 7 0.27
15 15 0.58
ACGTcount: A:0.21, C:0.19, G:0.60, T:0.00
Consensus pattern (14 bp):
CGGAGGGAAGGCGG
Found at i:638835 original size:23 final size:25
Alignment explanation
Indices: 638780--638835 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
638770 TCTGGTGTAA
*
638780 ATATTAAAATAATGTTAAAAATAAT
1 ATATTAAAATAATGTTAAAAACAAT
*
638805 -TATATAAAA-AAT-TTAATAACAAT
1 ATAT-TAAAATAATGTTAAAAACAAT
638828 ATATTAAA
1 ATATTAAA
638836 TTATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 13 0.48
24 9 0.33
25 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
ATATTAAAATAATGTTAAAAACAAT
Found at i:640229 original size:13 final size:13
Alignment explanation
Indices: 640206--640238 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
640196 TTTTAATTTT
640206 AATTT-ATTTAAG
1 AATTTAATTTAAG
*
640218 AATTTAATTTAAT
1 AATTTAATTTAAG
640231 AATTTAAT
1 AATTTAAT
640239 CCAAGGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
AATTTAATTTAAG
Found at i:642740 original size:2 final size:2
Alignment explanation
Indices: 642735--642762 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
642725 AAATAAATAA
642735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
642763 TTTAGAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:644605 original size:74 final size:72
Alignment explanation
Indices: 644520--644714 Score: 241
Period size: 72 Copynumber: 2.7 Consensus size: 72
644510 GTAAAATTGG
* *
644520 AAAAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAATATTTTTTGTGCTCAAA
1 AAAAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA-ACTTTTTGTGCACAAA
644585 A-GAAGAA
65 ACGAAGAA
* * * *
644592 GAAGAAGTCCTTCCTTGTCAATTGGAATGTTTTGTGTCCTCTATTG-AAAACTTTTTGTGCACAA
1 -AA-AAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAAACTTTTTGTGCACAA
* *
644656 AATCGGATAA
64 AA-CGAAGAA
* * *
644666 AAAAGCCCTTCCTCGTCAATTGGAACGTTTAATGTCCTCAACTGAAAAA
1 AAAAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAAA
644715 AAAAATCTGT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
72 50 0.49
73 11 0.11
74 42 0.41
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (72 bp):
AAAAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAAACTTTTTGTGCACAAAA
CGAAGAA
Found at i:645578 original size:20 final size:20
Alignment explanation
Indices: 645555--645592 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
645545 ATTTCTAATT
645555 TAAATATA-ATTTATGCATAA
1 TAAATATATATTT-TGCATAA
645575 TAAATATATATTTTGCAT
1 TAAATATATATTTTGCAT
645593 CAATGGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAATATATATTTTGCATAA
Found at i:645976 original size:5 final size:5
Alignment explanation
Indices: 645968--645994 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
645958 GAATTCTTTT
645968 GATTC GATTC GATTC GATTC GATTC GA
1 GATTC GATTC GATTC GATTC GATTC GA
645995 AAAAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (5 bp):
GATTC
Done.