Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013986.1 Kokia drynarioides strain JFW-HI SEQ_129017, 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: 184687
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:11730 original size:29 final size:30
Alignment explanation
Indices: 11694--11797 Score: 120
Period size: 29 Copynumber: 3.4 Consensus size: 30
11684 ATTTTAAGTA
* *
11694 TAACTTTTTAATTTCATAAAAATGTTATTT
1 TAACTTTTTAATTTTATAAAAATATTATTT
*
11724 TAA-TTTTTTATTTTATAAAAATATTATTT
1 TAACTTTTTAATTTTATAAAAATATTATTT
11753 TAACTCTTTATTAAATTTTATAAAAATATTATTT
1 TAA--CTTT-TT-AATTTTATAAAAATATTATTT
* *
11787 TAGCTCTTTAA
1 TAACTTTTTAA
11798 ATAGGTTAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
29 26 0.41
30 5 0.08
31 2 0.03
32 6 0.10
33 2 0.03
34 22 0.35
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (30 bp):
TAACTTTTTAATTTTATAAAAATATTATTT
Found at i:11771 original size:34 final size:33
Alignment explanation
Indices: 11697--11796 Score: 129
Period size: 34 Copynumber: 3.2 Consensus size: 33
11687 TTAAGTATAA
* *
11697 CTTT-TTAATTTCATAAAAATGTTATTTTAA-T
1 CTTTATTAATTTTATAAAAATATTATTTTAACT
11728 -TTT-TT-ATTTTATAAAAATATTATTTTAACT
1 CTTTATTAATTTTATAAAAATATTATTTTAACT
*
11758 CTTTATTAAATTTTATAAAAATATTATTTTAGCT
1 CTTTATT-AATTTTATAAAAATATTATTTTAACT
11792 CTTTA
1 CTTTA
11797 AATAGGTTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
29 21 0.34
30 6 0.10
31 3 0.05
32 2 0.03
34 29 0.48
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (33 bp):
CTTTATTAATTTTATAAAAATATTATTTTAACT
Found at i:17601 original size:6 final size:5
Alignment explanation
Indices: 17574--17607 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
17564 GTCTTGATAT
*
17574 AAAA- AAAAG AAAAG AAAAG AAAAG GAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
17608 GTAGTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:26610 original size:98 final size:98
Alignment explanation
Indices: 26441--26638 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
26431 TGATGCAACA
26441 ATGGTTAAATCAGGCCAACCCAAGTCAATCCACTGAAAGCTCCAGTGAATAGTTTATGAATGACT
1 ATGGTTAAATCAGGCCAACCCAAGTCAATCCACTGAAAGCTCCAGTGAATAGTTTATGAATGACT
26506 TAACTAACATACATATACACAACCATCATGTGG
66 TAACTAACATACATATACACAACCATCATGTGG
26539 ATGGTTAAATCAGGCCAACCCAAGTCAATCCACTGAAAGCTCCAGTGAATAGTTTATGAATGACT
1 ATGGTTAAATCAGGCCAACCCAAGTCAATCCACTGAAAGCTCCAGTGAATAGTTTATGAATGACT
26604 TAACTAACATACATATACACAACCATCATGTGG
66 TAACTAACATACATATACACAACCATCATGTGG
26637 AT
1 AT
26639 CGACCAAATT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (98 bp):
ATGGTTAAATCAGGCCAACCCAAGTCAATCCACTGAAAGCTCCAGTGAATAGTTTATGAATGACT
TAACTAACATACATATACACAACCATCATGTGG
Found at i:43512 original size:30 final size:30
Alignment explanation
Indices: 43476--43536 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
43466 CATTCAACCC
43476 TACCAAGTCTTTTAAAAAGTTCCAAAAAGT
1 TACCAAGTCTTTTAAAAAGTTCCAAAAAGT
43506 TACCAAGTCTTTTAAAAAGTTCCAAAAAGT
1 TACCAAGTCTTTTAAAAAGTTCCAAAAAGT
43536 T
1 T
43537 TTCTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (30 bp):
TACCAAGTCTTTTAAAAAGTTCCAAAAAGT
Found at i:47372 original size:3 final size:3
Alignment explanation
Indices: 47364--47414 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
47354 ATTGGAGGAA
* * *
47364 CTG CTG CTG CTG CTG CTG CTG CTG CTG TTG CTG TTG TTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
47412 CTG
1 CTG
47415 AAAAAGCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.27, G:0.33, T:0.39
Consensus pattern (3 bp):
CTG
Found at i:56167 original size:18 final size:18
Alignment explanation
Indices: 56144--56218 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 18
56134 TCTCCTTTAA
56144 TTTTTCTCATTTAATTATT
1 TTTTTCTCATTTAATTA-T
**
56163 TTTTCTCCTTCAATTTTTCTTAT
1 TTTT-T-C-TC-A-TTTAATTAT
56186 TTTTTCTCATTTAATTAAT
1 TTTTTCTCATTTAATT-AT
*
56205 CTTTTCTCATTTAA
1 TTTTTCTCATTTAA
56219 AAATTTGTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 5 0.11
19 20 0.44
20 3 0.07
21 2 0.04
22 3 0.07
23 6 0.13
24 6 0.13
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTCTCATTTAATTAT
Found at i:56207 original size:24 final size:24
Alignment explanation
Indices: 56158--56207 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
56148 TCTCATTTAA
* **
56158 TTATTTTTTCTCCTTCAATTTTTC
1 TTATTTTTTCTCATTCAATTAATC
*
56182 TTATTTTTTCTCATTTAATTAATC
1 TTATTTTTTCTCATTCAATTAATC
56206 TT
1 TT
56208 TTCTCATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTTTTTCTCATTCAATTAATC
Found at i:58297 original size:14 final size:14
Alignment explanation
Indices: 58265--58298 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58255 TTTTAAATAT
58265 TTTTTATTTTTAAA
1 TTTTTATTTTTAAA
* *
58279 GTTTTATTTTTGAA
1 TTTTTATTTTTAAA
58293 TTTTTA
1 TTTTTA
58299 AGAATCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTATTTTTAAA
Found at i:59001 original size:23 final size:22
Alignment explanation
Indices: 58953--59005 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
58943 CTTCAGATCT
*
58953 TTTCATTTTTGTTTTCAGGTAAA
1 TTTC-TTTTTGTTTCCAGGTAAA
* *
58976 TTTCTTTTTGTTTCCGAGTTAGA
1 TTTCTTTTTGTTTCC-AGGTAAA
58999 TTTCTTT
1 TTTCTTT
59006 GATTTTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.60
Consensus pattern (22 bp):
TTTCTTTTTGTTTCCAGGTAAA
Found at i:59388 original size:47 final size:47
Alignment explanation
Indices: 59319--59413 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
59309 TTACTATAAG
59319 TGGATTTATTTGAATTTCTTAGATATGTTGCATTTTTCAATGATGTA
1 TGGATTTATTTGAATTTCTTAGATATGTTGCATTTTTCAATGATGTA
59366 TGGATTTATTTGAATTTCTTAGATATGTTGCATTTTTCAATGATGTA
1 TGGATTTATTTGAATTTCTTAGATATGTTGCATTTTTCAATGATGTA
59413 T
1 T
59414 TAGCCTAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (47 bp):
TGGATTTATTTGAATTTCTTAGATATGTTGCATTTTTCAATGATGTA
Found at i:60189 original size:72 final size:72
Alignment explanation
Indices: 60095--60327 Score: 430
Period size: 72 Copynumber: 3.2 Consensus size: 72
60085 AACGCTCAGC
*
60095 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGACTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
60160 GCTTTGA
66 GCTTTGA
*
60167 TGATCAGGTAAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
60232 GCTTTGA
66 GCTTTGA
* *
60239 TGATCAGGTGAAAAAGAAGAGTTCAAATGACGATTCCCCGAAAGGAGATAAGGTGTTTGATAAAA
1 TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
60304 GCTTTGA
66 GCTTTGA
60311 TGATCAGGTGAAAAAGA
1 TGATCAGGTGAAAAAGA
60328 GCTCAAATGA
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 156 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (72 bp):
TGATCAGGTGAAAAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAA
GCTTTGA
Found at i:65784 original size:10 final size:11
Alignment explanation
Indices: 65769--65802 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
65759 CTTTTATTAA
65769 TTTTCTC-CTT
1 TTTTCTCTCTT
*
65779 TTTTCTCTTTT
1 TTTTCTCTCTT
65790 TTTTCTCTCTT
1 TTTTCTCTCTT
65801 TT
1 TT
65803 CTGTTTCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:67261 original size:24 final size:25
Alignment explanation
Indices: 67205--67267 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
67195 TCGGAGTATG
*
67205 AACAA-AATA-TAGTATTCAACAGC
1 AACAACAATACTAATATTCAACAGC
* *
67228 AACAACAATATTAATATT-AACAGT
1 AACAACAATACTAATATTCAACAGC
67252 AAC-ACTAATACTAATA
1 AACAAC-AATACTAATA
67268 ACAATGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 21 0.62
25 6 0.18
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (25 bp):
AACAACAATACTAATATTCAACAGC
Found at i:69076 original size:3 final size:3
Alignment explanation
Indices: 69065--69093 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
69055 AGTGTAAAAA
69065 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69094 TAAGAAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:69168 original size:29 final size:29
Alignment explanation
Indices: 69122--69185 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
69112 ATATTGATTT
69122 AAAAGTAAAGACTAAATCGTAAATATGTG
1 AAAAGTAAAGACTAAATCGTAAATATGTG
*
69151 AAAAGTAAAGACTGAATCGTAAATATGTG
1 AAAAGTAAAGACTAAATCGTAAATATGTG
69180 AAAAGT
1 AAAAGT
69186 TTTTGGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (29 bp):
AAAAGTAAAGACTAAATCGTAAATATGTG
Found at i:71860 original size:17 final size:17
Alignment explanation
Indices: 71824--71865 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
71814 TAATATTAAA
71824 TAAATAA-AAAATTATT
1 TAAATAATAAAATTATT
* *
71840 TAAATAATAAATTTTTT
1 TAAATAATAAAATTATT
*
71857 TAAAAAATA
1 TAAATAATA
71866 CTTATACGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATAATAAAATTATT
Found at i:72314 original size:17 final size:17
Alignment explanation
Indices: 72294--72327 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
72284 AAAAAAATTT
*
72294 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
72311 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
72328 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:78213 original size:27 final size:26
Alignment explanation
Indices: 78153--78219 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
78143 ATAGTTTTGA
78153 CAAAGGCACCACTAGTGCCGCCTACC
1 CAAAGGCACCACTAGTGCCGCCTACC
* * * *
78179 CAGTAGGCACCATTGGTGCCGTCTACC
1 CA-AAGGCACCACTAGTGCCGCCTACC
78206 CTAAAGGCACCACT
1 C-AAAGGCACCACT
78220 TGTCAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.06
27 30 0.91
28 1 0.03
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.16
Consensus pattern (26 bp):
CAAAGGCACCACTAGTGCCGCCTACC
Found at i:94655 original size:16 final size:17
Alignment explanation
Indices: 94636--94673 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
94626 TTAGTAATGT
94636 TTTTATG-TCAAAAGTA
1 TTTTATGCTCAAAAGTA
*
94652 TTTTTTGTCTCAAAAGTA
1 TTTTATG-CTCAAAAGTA
94670 TTTT
1 TTTT
94674 TGAAAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (17 bp):
TTTTATGCTCAAAAGTA
Found at i:99901 original size:23 final size:23
Alignment explanation
Indices: 99869--99993 Score: 71
Period size: 23 Copynumber: 5.3 Consensus size: 23
99859 ACGCTAGCGC
*
99869 GCTTATTGTTTCGCA-CTTCGTGT
1 GCTTACTGTTTCGCACCTT-GTGT
99892 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
* * * *
99915 GCCTATTGATTT-GC-GCTATGTGC
1 GCTTACTG-TTTCGCACCT-TGTGT
* *
99938 GCCTACTAGATT-GCA-CTGTGTGT
1 GCTTACT-GTTTCGCACCT-TGTGT
*
99961 GCTTACTGTTTCCTCAGCACTTGTGT
1 GCTTACTGTTT-CGCA-C-CTTGTGT
99987 GCTTACT
1 GCTTACT
99994 ATTAAGTACT
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.06
23 52 0.65
24 9 0.11
26 12 0.15
27 2 0.03
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTTGTGT
Found at i:103217 original size:30 final size:30
Alignment explanation
Indices: 103182--103240 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
103172 TATTTTATTG
103182 TTAATTTTGTTATTATTTTAGAGGCATTTA
1 TTAATTTTGTTATTATTTTAGAGGCATTTA
*
103212 TTAATTTTGTTATTATTTTAGATGCATTT
1 TTAATTTTGTTATTATTTTAGAGGCATTT
103241 GTTTATTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAGAGGCATTTA
Found at i:103322 original size:25 final size:24
Alignment explanation
Indices: 103288--103338 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
103278 ATATATTTTT
103288 TAAAATTTATTTTCAAT-TTGTTAG
1 TAAAATTTATTTT-AATGTTGTTAG
*
103312 TAAATATTTATTTTAATGTTTTTAG
1 TAAA-ATTTATTTTAATGTTGTTAG
103337 TA
1 TA
103339 TTTTTAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
TAAAATTTATTTTAATGTTGTTAG
Found at i:103392 original size:23 final size:23
Alignment explanation
Indices: 103349--103394 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
103339 TTTTTAATGT
* *
103349 ATTATATATATATATATTTAAAA
1 ATTATATAAAAATATATTTAAAA
103372 ATTATATAAAAATA-ATATTAAAA
1 ATTATATAAAAATATAT-TTAAAA
103395 GTTAATATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTATATAAAAATATATTTAAAA
Found at i:104015 original size:21 final size:21
Alignment explanation
Indices: 103991--104031 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
103981 CAATTAATTT
103991 TAAA-ATTTTATCATATAAAAA
1 TAAATATTTTAT-ATATAAAAA
*
104012 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATATAAAA
104032 TGGTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATATTTTATATATAAAAA
Found at i:104949 original size:18 final size:19
Alignment explanation
Indices: 104926--104968 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
104916 GAATAAAATT
104926 TTAATTAAATAAATTT-AA
1 TTAATTAAATAAATTTAAA
* *
104944 TTAATT-GATAATTTTAAA
1 TTAATTAAATAAATTTAAA
104962 TTAATTA
1 TTAATTA
104969 CAATTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATTAAATAAATTTAAA
Found at i:109632 original size:22 final size:22
Alignment explanation
Indices: 109604--109648 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
109594 TTATGCTGAT
*
109604 TCATAGAGCCGATTTGTAGGGA
1 TCATAGAACCGATTTGTAGGGA
*
109626 TCATAGAACTGATTTGTAGGGA
1 TCATAGAACCGATTTGTAGGGA
109648 T
1 T
109649 TTGTTTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (22 bp):
TCATAGAACCGATTTGTAGGGA
Found at i:130954 original size:241 final size:241
Alignment explanation
Indices: 130531--131250 Score: 1350
Period size: 241 Copynumber: 3.0 Consensus size: 241
130521 GCGTGGGGGG
*
130531 ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTAAA
1 ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
* *
130596 ATAAAGGGGCCCTTCCACCTATACCAAGCAATTTTAGGATGGGAACCTCATAATAATTTTTGACA
66 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
130661 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
131 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
130726 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
196 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
*
130772 ACTGTGAGCAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
1 ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
130837 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
66 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
*
130902 ATAGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
131 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
130967 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
196 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
* * *
131013 ACTGTGAATAGTGATAAGAGAACAAATACCATATCAACTCAAAATGGGTTATCATAAGTCCTTAA
1 ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
*
131078 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTTACA
66 ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
131143 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
131 ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
*
131208 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAATAGCTA
196 ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTA
131251 AAATACTGGA
Statistics
Matches: 467, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 467 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (241 bp):
ACTGTGAGTAGTGATGAGAGAACAAATACCATATCAACTAAAAATGGGTTATCATAAGTCCTTAA
ATAAAGGGGCCTTTCCACCTATACCAAGCAGTTTTAGGATGGGAACCTCATAATAATTTTTGACA
ATGGCTCCATATGGGCTTTTATAGTGCAAGCCACTGCATAACCTCAGAATAAATCAAGTAAATTC
ATTGAAGTAATGCCATAAAAGCAACTCGAGTTACTAGTAGCTACAA
Found at i:138727 original size:11 final size:11
Alignment explanation
Indices: 138711--138735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
138701 TCAATATCAT
138711 AAAAAAATAAA
1 AAAAAAATAAA
138722 AAAAAAATAAA
1 AAAAAAATAAA
138733 AAA
1 AAA
138736 CTACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:138733 original size:19 final size:20
Alignment explanation
Indices: 138709--138746 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
138699 TCTCAATATC
138709 ATAAAAAAATA-AAAAAAAA
1 ATAAAAAAATACAAAAAAAA
*
138728 ATAAAAAACTACAAAAAAA
1 ATAAAAAAATACAAAAAAA
138747 CTTAAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (20 bp):
ATAAAAAAATACAAAAAAAA
Found at i:140376 original size:24 final size:24
Alignment explanation
Indices: 140344--140389 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
140334 ATAATAAAAA
140344 TATAATTTTAT-TATTTTAATAATT
1 TATAATTTTATAT-TTTTAATAATT
*
140368 TATATTTTTATATTTTTAATAA
1 TATAATTTTATATTTTTAATAA
140390 AATAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATAATTTTATATTTTTAATAATT
Found at i:146072 original size:15 final size:15
Alignment explanation
Indices: 146054--146084 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
146044 ATTGAAGCAT
*
146054 AATATTTTAAATATA
1 AATATTTAAAATATA
146069 AATATTTAAAATATA
1 AATATTTAAAATATA
146084 A
1 A
146085 CTTGATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATTTAAAATATA
Found at i:148114 original size:20 final size:21
Alignment explanation
Indices: 148089--148134 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
148079 AAAACCAAAT
* *
148089 TAAAATTAAAAT-TTATAAAA
1 TAAAATAAAAATATTAAAAAA
148109 TAAAATAAAAATATTAAAAAA
1 TAAAATAAAAATATTAAAAAA
148130 TAAAA
1 TAAAA
148135 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAATAAAAATATTAAAAAA
Found at i:155750 original size:23 final size:23
Alignment explanation
Indices: 155724--155770 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
155714 TTTTTGGGGG
155724 AGACTAAAGTGTAATTTTATTTT
1 AGACTAAAGTGTAATTTTATTTT
155747 AGACTAAAGTGTAATTTTATTTT
1 AGACTAAAGTGTAATTTTATTTT
155770 A
1 A
155771 TTAATTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (23 bp):
AGACTAAAGTGTAATTTTATTTT
Found at i:157257 original size:125 final size:125
Alignment explanation
Indices: 157009--157259 Score: 414
Period size: 125 Copynumber: 2.0 Consensus size: 125
156999 ATCTGGATTA
* *
157009 TCTATAATCATCAAACATTAGGCTTTGGGTTTAACCCTTGGACCAAGTATATGAGTTTACATTGT
1 TCTATAATCATCAAACATTAGGCTTTGGGTTTAACCCTTGGACAAAGTATATGAGTTTACATAGT
* * *
157074 GGGTTGAACTAAGGTGACTATTGGAATTTACTAAAAGTTTAGCTTAATTAAAATGTATGT
66 GGGCTGAACTAAGGTGACCATTGGAATATACTAAAAGTTTAGCTTAATTAAAATGTATGT
* *
157134 TCTATAATCATCACACATTAGGCTTTGGGTTTAACCCTTGGACAAAGTGTATGAGTTTACATAGT
1 TCTATAATCATCAAACATTAGGCTTTGGGTTTAACCCTTGGACAAAGTATATGAGTTTACATAGT
*
157199 GGGCTGAACCTAAGGTGACCATTGGAATATAGTAAAAGTTTAGCTTAATTAAAA-GTATGT
66 GGGCTGAA-CTAAGGTGACCATTGGAATATACTAAAAGTTTAGCTTAATTAAAATGTATGT
157259 T
1 T
157260 TTATGGTTTT
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 75 0.64
126 42 0.36
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (125 bp):
TCTATAATCATCAAACATTAGGCTTTGGGTTTAACCCTTGGACAAAGTATATGAGTTTACATAGT
GGGCTGAACTAAGGTGACCATTGGAATATACTAAAAGTTTAGCTTAATTAAAATGTATGT
Found at i:163099 original size:20 final size:21
Alignment explanation
Indices: 163074--163115 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
163064 AAAAAAAATC
163074 AAATTCAA-ATGAAATTGTTG
1 AAATTCAAGATGAAATTGTTG
163094 AAATTCAAGATGAAATTGTTG
1 AAATTCAAGATGAAATTGTTG
163115 A
1 A
163116 TGTGGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATTCAAGATGAAATTGTTG
Found at i:171085 original size:3 final size:3
Alignment explanation
Indices: 171070--171111 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
171060 CCATATGCAA
*
171070 ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
171112 CAGTACAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:178571 original size:3 final size:3
Alignment explanation
Indices: 178563--178588 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
178553 CTACGATTCA
178563 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
178589 AACCTGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:182323 original size:20 final size:20
Alignment explanation
Indices: 182281--182325 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
182271 TAAAATATAA
*
182281 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTGATAAAT
182301 ATTTTGAAATTTTGA-AAATT
1 ATTTTGAAATTTTGATAAA-T
182321 ATTTT
1 ATTTT
182326 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTTGAAATTTTGATAAAT
Done.