Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013685.1 Kokia drynarioides strain JFW-HI SEQ_128713, 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: 163382
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:512 original size:29 final size:28
Alignment explanation
Indices: 466--803 Score: 267
Period size: 29 Copynumber: 11.6 Consensus size: 28
456 CCCTAAGCTG
466 TCCAAAAATTCCA-TTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
494 TCCAAAAATTCCATTTTTAGCCCCGAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
*
523 TCCAAAAA-TCCTTTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCG-AACT
* *
552 TCCCAAAATTCCATTTTTAGCCCCCAAACT
1 TCCAAAAATTCCATTTTTA--CCCCGAACT
* * *
582 TCCAAAAATTCAATTTTTAGCACCTAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
* *
611 TCCAAAAATCCCAATTTTGACCCCGAAACT
1 TCCAAAAATTCC-ATTTTTACCCCG-AACT
* *
641 TCC-CAAATTCCATTTTTAGCCTCGAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
* *
669 TCCAGAAATTCCATTTTTGACTCCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCG-AACT
* * *
699 TCCTAAAATTACCA-TTTTACCTTCGGA-T
1 TCCAAAAATT-CCATTTTTACC-CCGAACT
* * *
727 GTCCAAAAACTCCATTTTCGACCTCGTAACT
1 -TCCAAAAATTCCATTTT-TACCCCG-AACT
*
758 TCCTAAAATTACCA-TTTTACCCCCGAA-T
1 TCCAAAAATT-CCATTTTTA-CCCCGAACT
*
786 GTCCAAAAACTCCATTTT
1 -TCCAAAAATTCCATTTT
804 CGACCTCGAA
Statistics
Matches: 250, Mismatches: 37, Indels: 45
0.75 0.11 0.14
Matches are distributed among these distances:
28 47 0.19
29 112 0.45
30 80 0.32
31 11 0.04
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.32
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTTACCCCGAACT
Found at i:615 original size:88 final size:89
Alignment explanation
Indices: 470--686 Score: 327
Period size: 88 Copynumber: 2.5 Consensus size: 89
460 AAGCTGTCCA
*
470 AAAATTCCA-TTTTA-CCCCCGAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAAT-
1 AAAATTCCATTTTTAGCCCCCGAACTTCCAAAAATTCCATTTTTAGCACCGAACTTCCAAAAATC
**
532 CCTTTTTTGACCCCGAAACTTCCC
66 CCAATTTTGACCCCGAAACTTCCC
* * *
556 AAAATTCCATTTTTAGCCCCCAAACTTCCAAAAATTCAATTTTTAGCACCTAACTTCCAAAAATC
1 AAAATTCCATTTTTAGCCCCCGAACTTCCAAAAATTCCATTTTTAGCACCGAACTTCCAAAAATC
621 CCAATTTTGACCCCGAAACTTCCC
66 CCAATTTTGACCCCGAAACTTCCC
* *
645 -AAATTCCATTTTTAG-CCTCGAACTTCCAGAAATTCCATTTTT
1 AAAATTCCATTTTTAGCCCCCGAACTTCCAAAAATTCCATTTTT
687 GACTCCGAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
86 9 0.08
87 28 0.24
88 59 0.50
89 22 0.19
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (89 bp):
AAAATTCCATTTTTAGCCCCCGAACTTCCAAAAATTCCATTTTTAGCACCGAACTTCCAAAAATC
CCAATTTTGACCCCGAAACTTCCC
Found at i:616 original size:58 final size:59
Alignment explanation
Indices: 466--808 Score: 285
Period size: 59 Copynumber: 5.9 Consensus size: 59
456 CCCTAAGCTG
* * *
466 TCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTT-AGCCCCGAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCCAAACT
* *
523 TCCAAAAA-TCC-TTTTTTGACCCCGAAACTTCCCAAAATTCCATTTTT-AGCCCCCAAACT
1 TCCAAAAATTCCATTTTTAG-CCCCG-AACTTCCAAAAATTCCATTTTTGA-CCCCCAAACT
* * * * * *
582 TCCAAAAATTCAATTTTTAGCACCTAACTTCCAAAAATCCCAATTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCCAAACT
* * * * *
641 TCC-CAAATTCCATTTTTAGCCTCGAACTTCCAGAAATTCCATTTTTGACTCCGAAACT
1 TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCCAAACT
* * * * * * **
699 TCCTAAAATTACCA-TTTTA-CCTTCGGA-TGTCCAAAAACTCCATTTTCGACCTCGTAACT
1 TCCAAAAATT-CCATTTTTAGCC-CCGAACT-TCCAAAAATTCCATTTTTGACCCCCAAACT
* * * *
758 TCCTAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCATTTTCGACC
1 TCCAAAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAATTCCATTTTTGACC
809 TCGAAACTCT
Statistics
Matches: 242, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
56 7 0.03
57 13 0.05
58 74 0.31
59 131 0.54
60 11 0.05
61 6 0.02
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTTGACCCCCAAACT
Found at i:860 original size:57 final size:59
Alignment explanation
Indices: 669--860 Score: 192
Period size: 59 Copynumber: 3.3 Consensus size: 59
659 GCCTCGAACT
* * * * ** ** *
669 TCCAGAAATTCCATTTTTGA-CTCCGAAACTTCCTAAAATTACCATTTTACCTTCGGATG
1 TCCAAAAACTCCATTTTCGACCT-CGAAACTTCCTAAAATCACCATTTTACCCCCAAATA
* * * *
728 TCCAAAAACTCCATTTTCGACCTCGTAACTTCCTAAAATTACCATTTTACCCCCGAATG
1 TCCAAAAACTCCATTTTCGACCTCGAAACTTCCTAAAATCACCATTTTACCCCCAAATA
* *
787 TCCAAAAACTCCATTTTCGACCTCGAAAC-T-CTCAAATCACCCTTTTACCCCCAAATA
1 TCCAAAAACTCCATTTTCGACCTCGAAACTTCCTAAAATCACCATTTTACCCCCAAATA
* * *
844 TCTAAAAATTTCATTTT
1 TCCAAAAACTCCATTTT
861 TAACCCCAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
57 36 0.31
58 1 0.01
59 77 0.66
60 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (59 bp):
TCCAAAAACTCCATTTTCGACCTCGAAACTTCCTAAAATCACCATTTTACCCCCAAATA
Found at i:2120 original size:19 final size:20
Alignment explanation
Indices: 2081--2124 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2071 CCGAACCCAA
2081 AATCTTGAACCTCGAACTTG
1 AATCTTGAACCTCGAACTTG
**
2101 AATCTTGAA-CTCGAGTTTG
1 AATCTTGAACCTCGAACTTG
2120 AATCT
1 AATCT
2125 AAAACCCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (20 bp):
AATCTTGAACCTCGAACTTG
Found at i:8191 original size:23 final size:22
Alignment explanation
Indices: 8164--8210 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
8154 CAGTTCTTTT
*
8164 TTTTTTTTTTTTAAATAATTTTAA
1 TTTTTTATTTTT-AA-AATTTTAA
8188 TTTTTTAATTTTTAAAATTTTAA
1 TTTTTT-ATTTTTAAAATTTTAA
8211 AAATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTTATTTTTAAAATTTTAA
Found at i:8860 original size:17 final size:17
Alignment explanation
Indices: 8838--8873 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
8828 TTAATATTGG
8838 ATCAAAATATAGAGTAC
1 ATCAAAATATAGAGTAC
*
8855 ATCAAAATATTGAGTAC
1 ATCAAAATATAGAGTAC
8872 AT
1 AT
8874 ATTTTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (17 bp):
ATCAAAATATAGAGTAC
Found at i:12377 original size:4 final size:4
Alignment explanation
Indices: 12368--12393 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12358 AAGAATAAAA
12368 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
12394 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:12879 original size:32 final size:32
Alignment explanation
Indices: 12829--12891 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
12819 TATAGATATT
*
12829 ATTATCAACGTAGGAGGACAAGAATCCATAAA
1 ATTATCAACGCAGGAGGACAAGAATCCATAAA
* * *
12861 ATTATCAATGCAGTAGGACATGAATCCATAA
1 ATTATCAACGCAGGAGGACAAGAATCCATAA
12892 GTTGTGATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.22
Consensus pattern (32 bp):
ATTATCAACGCAGGAGGACAAGAATCCATAAA
Found at i:30294 original size:25 final size:25
Alignment explanation
Indices: 30241--30286 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
30231 GTTGAATCTA
30241 AATTAAATTCTAAACAGATAATTAG
1 AATTAAATTCTAAACAGATAATTAG
30266 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAACAGATAATT
30287 CCCTAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (25 bp):
AATTAAATTCTAAACAGATAATTAG
Found at i:32636 original size:30 final size:30
Alignment explanation
Indices: 32579--32634 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
32569 ACAATTAAAC
*
32579 TTAAATTTTTAAATTCAAAAGATAAAATTT
1 TTAAATTTTTAAAATCAAAAGATAAAATTT
32609 TTAAATTTTTAAAAAT-AAAA-ATAAAA
1 TTAAATTTTT-AAAATCAAAAGATAAAA
32635 ATAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 6 0.25
30 14 0.58
31 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAATTTTTAAAATCAAAAGATAAAATTT
Found at i:33408 original size:23 final size:23
Alignment explanation
Indices: 33351--33394 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
33341 ATAAAGGAAT
33351 TATTAATTAAAAATATATATTTAA
1 TATTAATT-AAAATATATATTTAA
33375 TATTAATTAAAATATA-ATTT
1 TATTAATTAAAATATATATTT
33395 TTTATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATTAAAATATATATTTAA
Found at i:33453 original size:67 final size:67
Alignment explanation
Indices: 33327--33453 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 67
33317 ATATTTATTA
* * * * *
33327 TTTTATTTATATAAATAAAGGAATTATTAATTAAAAATATATATTTAATATTAATTAAAATATAA
1 TTTTATTTATATAAATAAAGGAATTATTAATTAAAAACATATATTAAAAATAAAATAAAATATAA
33392 TT
66 TT
* *
33394 TTTTATTTATATAAATAAAGGAATTCTTGATTAAAAACATGA-ATTAAAAATAAAATAAAA
1 TTTTATTTATATAAATAAAGGAATTATTAATTAAAAACAT-ATATTAAAAATAAAATAAAA
33454 AATTTGAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
67 51 0.98
68 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (67 bp):
TTTTATTTATATAAATAAAGGAATTATTAATTAAAAACATATATTAAAAATAAAATAAAATATAA
TT
Found at i:41908 original size:9 final size:9
Alignment explanation
Indices: 41894--41925 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
41884 TTCCTCCTCA
41894 TCTTCTTCC
1 TCTTCTTCC
41903 TCTTCTTCC
1 TCTTCTTCC
*
41912 TCCTCTTCC
1 TCTTCTTCC
41921 TCTTC
1 TCTTC
41926 CTCACCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TCTTCTTCC
Found at i:41911 original size:24 final size:24
Alignment explanation
Indices: 41879--41928 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
41869 TGGCTGAAGT
*
41879 TCTTCTTCCTCCTCATCTTCTTCC
1 TCTTCTTCCTCCTCATCCTCTTCC
*
41903 TCTTCTTCCTCCTCTTCCTCTTCC
1 TCTTCTTCCTCCTCATCCTCTTCC
41927 TC
1 TC
41929 ACCCTCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (24 bp):
TCTTCTTCCTCCTCATCCTCTTCC
Found at i:41917 original size:12 final size:12
Alignment explanation
Indices: 41879--41919 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
41869 TGGCTGAAGT
41879 TCTTCTTCCTCC
1 TCTTCTTCCTCC
* *
41891 TCATCTTCTTCC
1 TCTTCTTCCTCC
41903 TCTTCTTCCTCC
1 TCTTCTTCCTCC
41915 TCTTC
1 TCTTC
41920 CTCTTCCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTTCTTCCTCC
Found at i:54136 original size:21 final size:22
Alignment explanation
Indices: 54107--54147 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
54097 TCGGTAGTTG
54107 CATGACTTGTATCAGTAGAAAT
1 CATGACTTGTATCAGTAGAAAT
*
54129 CATG-CTTGTATCGGTAGAA
1 CATGACTTGTATCAGTAGAA
54148 CTAGCACAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (22 bp):
CATGACTTGTATCAGTAGAAAT
Found at i:57239 original size:12 final size:12
Alignment explanation
Indices: 57222--57248 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57212 TTAAATTACC
57222 TGTTTGAGTTCA
1 TGTTTGAGTTCA
57234 TGTTTGAGTTCA
1 TGTTTGAGTTCA
57246 TGT
1 TGT
57249 CTGACACGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (12 bp):
TGTTTGAGTTCA
Found at i:60236 original size:4 final size:4
Alignment explanation
Indices: 60227--60254 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
60217 ACACATGATT
60227 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
60255 TATTTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:68619 original size:17 final size:18
Alignment explanation
Indices: 68583--68617 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
68573 TTTTCAGAAG
*
68583 CACTTTTGAGATAAAAAA
1 CACTTTTGAAATAAAAAA
68601 CACTTTTGAAATAAAAA
1 CACTTTTGAAATAAAAA
68618 CATTGTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
CACTTTTGAAATAAAAAA
Found at i:71432 original size:31 final size:31
Alignment explanation
Indices: 71397--71460 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
71387 CTTAACAATC
*
71397 CAGTGACTTAAATAAAAACTT-TTGAATAGTT
1 CAGTGACTTAAATAAAAA-TTCTTGAATAATT
*
71428 CAGTGACTTAAATGAAAATTCTTGAATAATT
1 CAGTGACTTAAATAAAAATTCTTGAATAATT
71459 CA
1 CA
71461 ATGATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAATTCTTGAATAATT
Found at i:71812 original size:3 final size:3
Alignment explanation
Indices: 71804--71837 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
71794 CACTTCAATA
71804 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
71838 AAGCTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:74974 original size:18 final size:18
Alignment explanation
Indices: 74935--74976 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
74925 TATTAGAAGT
*
74935 ATTAATATATAATTTATG
1 ATTAATATATAATTTATA
74953 ATTAATATA-AATTTATAA
1 ATTAATATATAATTTAT-A
74971 ATTAAT
1 ATTAAT
74977 TTAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTAATATATAATTTATA
Found at i:78171 original size:15 final size:16
Alignment explanation
Indices: 78151--78184 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
78141 GAACTATTAA
*
78151 TTTTTTCTATTAA-TC
1 TTTTTTCTAATAATTC
78166 TTTTTTCTAATAATTC
1 TTTTTTCTAATAATTC
78182 TTT
1 TTT
78185 AATTTGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTCTAATAATTC
Found at i:79696 original size:3 final size:3
Alignment explanation
Indices: 79688--79724 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
79678 TGTCTACCGC
*
79688 TTG TTG TTG CTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
79725 AGAGTCAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:83698 original size:7 final size:7
Alignment explanation
Indices: 83688--83723 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
83678 ATTATGATTA
83688 GGTTTAG
1 GGTTTAG
83695 GGTTTAG
1 GGTTTAG
*
83702 GATTTAG
1 GGTTTAG
83709 GGTTTAG
1 GGTTTAG
83716 GGTTTAG
1 GGTTTAG
83723 G
1 G
83724 AGGTGGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:84876 original size:22 final size:22
Alignment explanation
Indices: 84851--84892 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
84841 CATTACATGA
* *
84851 TATGTCTCGAGGCAAGGTCTTT
1 TATGTCCCAAGGCAAGGTCTTT
*
84873 TATGTCCCAAGGCTAGGTCT
1 TATGTCCCAAGGCAAGGTCT
84893 CGAGACCAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (22 bp):
TATGTCCCAAGGCAAGGTCTTT
Found at i:91410 original size:10 final size:10
Alignment explanation
Indices: 91395--91428 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
91385 TTAGTGTGTG
91395 TGTATATATA
1 TGTATATATA
91405 TGTATATATA
1 TGTATATATA
*
91415 TATATATATA
1 TGTATATATA
91425 -GTAT
1 TGTAT
91429 TTCAAATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.14
10 19 0.86
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
TGTATATATA
Found at i:95037 original size:22 final size:22
Alignment explanation
Indices: 94995--95037 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
94985 AAATCGGTTC
* * *
94995 AATCAATCCATACTAATTCTTA
1 AATCAATCAATACAAAATCTTA
95017 AATCAATCAATACAAAATCTT
1 AATCAATCAATACAAAATCTT
95038 TATTGAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (22 bp):
AATCAATCAATACAAAATCTTA
Found at i:97936 original size:2 final size:2
Alignment explanation
Indices: 97929--97953 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97919 ATATCATTAT
97929 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
97954 TAGCATGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128593 original size:16 final size:17
Alignment explanation
Indices: 128574--128605 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
128564 TGACCAACTA
128574 TAATATAAA-ATTAAAT
1 TAATATAAAGATTAAAT
128590 TAATATAAAGATTAAA
1 TAATATAAAGATTAAA
128606 ATTGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAATATAAAGATTAAAT
Found at i:133152 original size:17 final size:17
Alignment explanation
Indices: 133094--133158 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
133084 TAGTTACAAT
* *
133094 AATATAAAAGGTTGAGG
1 AATATGAAAGGTTAAGG
* *
133111 AAGATGGAAGGTTAAAGG
1 AATATGAAAGGTT-AAGG
*
133129 TCA-ATGAAAGGTTAAGG
1 -AATATGAAAGGTTAAGG
133146 AATATGAAAGGTT
1 AATATGAAAGGTT
133159 GAACATTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 1 0.03
17 24 0.63
18 12 0.32
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.23
Consensus pattern (17 bp):
AATATGAAAGGTTAAGG
Found at i:138291 original size:17 final size:17
Alignment explanation
Indices: 138269--138304 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
138259 AATAATATTC
*
138269 ATAACATTTTCATTTTT
1 ATAACATTGTCATTTTT
*
138286 ATAACATTGTCTTTTTT
1 ATAACATTGTCATTTTT
138303 AT
1 AT
138305 TTCTGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.58
Consensus pattern (17 bp):
ATAACATTGTCATTTTT
Found at i:141436 original size:9 final size:8
Alignment explanation
Indices: 141425--141457 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
141415 ATTGGTTAAT
141425 TTTTAAAA
1 TTTTAAAA
141433 TTTTAAAA
1 TTTTAAAA
141441 TTTTAAAA
1 TTTTAAAA
141449 TATTTAAAA
1 T-TTTAAAA
141458 AGTTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTTAAAA
Found at i:146659 original size:16 final size:17
Alignment explanation
Indices: 146624--146670 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
146614 GAAATTATAC
146624 TTTTATATTTTTAATAA
1 TTTTATATTTTTAATAA
*
146641 TTTTA-ATTTTTAAATAT
1 TTTTATATTTTT-AATAA
146658 TTTTATAATTTTT
1 TTTTAT-ATTTTT
146671 GAATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 14 0.54
19 6 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATTTTTAATAA
Found at i:146675 original size:27 final size:26
Alignment explanation
Indices: 146628--146683 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 26
146618 TTATACTTTT
146628 ATATTTTTAATAATTTTAATTTTTAA
1 ATATTTTTAATAATTTTAATTTTTAA
146654 ATATTTTT-ATAATTTTTGAATTTTTAA
1 ATATTTTTAATAA-TTTT-AATTTTTAA
146681 ATA
1 ATA
146684 AAATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
ATATTTTTAATAATTTTAATTTTTAA
Found at i:150314 original size:3 final size:3
Alignment explanation
Indices: 150306--150338 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
150296 AAATGTTGGC
*
150306 ATG ATG ATG ATG ACG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
150339 GTCTTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:158305 original size:20 final size:21
Alignment explanation
Indices: 158267--158317 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
158257 TCCCTTAAAA
*
158267 ATCGATACCTCAACGAAAT-T
1 ATCGATACCTCAACCAAATGT
**
158287 ATCGATACCTCTTCCAAATGGT
1 ATCGATACCTCAACCAAAT-GT
158309 ATCGATACC
1 ATCGATACC
158318 AGATCGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.62
22 10 0.38
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
ATCGATACCTCAACCAAATGT
Found at i:159239 original size:22 final size:23
Alignment explanation
Indices: 159190--159258 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
159180 ATATTTTTAA
* *
159190 AAAAATATTTAATATATGTATAT
1 AAAAATATTTAATAAATGTAAAT
159213 AAAAATATTTAA-AAATGTAAAAT
1 AAAAATATTTAATAAATGT-AAAT
* * *
159236 AAAAGAAATTAAATAAATTTAAA
1 AAAA-ATATTTAATAAATGTAAA
159259 ATATTTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 5 0.13
23 19 0.50
24 9 0.24
25 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAATATTTAATAAATGTAAAT
Done.