Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014740.1 Kokia drynarioides strain JFW-HI SEQ_129779, 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: 85270
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:606 original size:23 final size:23
Alignment explanation
Indices: 560--748 Score: 171
Period size: 23 Copynumber: 8.5 Consensus size: 23
550 TAAATGGAAC
* * *
560 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
582 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
605 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
625 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
644 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
667 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* *
692 AAACAGAGAGCACATACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
715 AAACAGAGGGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
738 AAACAGAGAGC
1 AAACAGAGAGC
749 GCGCTAATGT
Statistics
Matches: 136, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 13 0.10
23 87 0.64
24 2 0.01
25 16 0.12
26 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:699 original size:48 final size:46
Alignment explanation
Indices: 628--748 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
618 ACAAAGTACT
* *
628 GAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCT-A-AACAGA
* *
676 GAGCACGAGAC-GTGCTAAACAGAGAGCACATACAGTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAAACAGAGAGCACACACAGTGCTAAACAGA
*
722 GGGCACACACAGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAAACAGAGAGC
749 GCGCTAATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.05
46 27 0.42
47 1 0.02
48 32 0.49
49 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (46 bp):
GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCTAAACAGA
Found at i:6232 original size:23 final size:23
Alignment explanation
Indices: 6186--6374 Score: 171
Period size: 23 Copynumber: 8.5 Consensus size: 23
6176 TAAATGGAAC
* * *
6186 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
6208 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
6231 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
6251 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6270 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6293 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* *
6318 AAACAGAGAGCACATACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6341 AAACAGAGGGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
6364 AAACAGAGAGC
1 AAACAGAGAGC
6375 GCGCTAATGT
Statistics
Matches: 136, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 13 0.10
23 87 0.64
24 2 0.01
25 16 0.12
26 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:6325 original size:48 final size:46
Alignment explanation
Indices: 6254--6374 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
6244 ACAAAGTACT
* *
6254 GAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCT-A-AACAGA
* *
6302 GAGCACGAGAC-GTGCTAAACAGAGAGCACATACAGTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAAACAGAGAGCACACACAGTGCTAAACAGA
*
6348 GGGCACACACAGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAAACAGAGAGC
6375 GCGCTAATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.05
46 27 0.42
47 1 0.02
48 32 0.49
49 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (46 bp):
GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCTAAACAGA
Found at i:11829 original size:618 final size:612
Alignment explanation
Indices: 10544--12841 Score: 3077
Period size: 618 Copynumber: 3.8 Consensus size: 612
10534 TCATCATAAT
* * *
10544 AGAACTGTTGAAGTC-AACCGACTTTTAAAGTCAACATAAAAATTGCAACCAAGAATTTGTATTC
1 AGAA-TGTTGAAGTCAAACCGACTTTCAAAGTCGACATAAAAATTGCAGCCAAGAATTTGTATTC
* * * * *
10608 -AA-TGGCTTCCAACCTTATGGAAACATGGCTTGAAAAGAGTTGCAAAGTGGCAGCCTTAAGCAA
65 AAATTGACTTCCAACTTTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAA
* * * * * *
10671 ATGGAT-ACGTATCAATAAATTAGCTGGAAGATCCATGAAAAATCAAAGGATAAAATAATGATGG
130 ATGGATAAC-CATCAATAAACTGGCTAGAAGGTTCATGAAAAATCAAAGGATAAAATAATGATGG
* * *
10735 CAGCAATGGTTTGAATGGTCTTAGGCAATAAGAATTGCTGAAGTTTAAGTTGATTTAATAATTCT
194 CAGCAATGGTTTGAATGGTCTTAGGCAGTAAGAATTGCTGAAGTTTAAGTCGATTTAATAAGTCT
*
10800 ATAAATATGGTTTATGAGTTAGTGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAATGAGT
259 ATAAATATGGTTTATGAGTTA--GTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGT
* * *
10865 GTTAAAGAAGAAAAGAGAGAAAAAGAGTGAGAGTTGTAAACTAGCAGCAACTAGTAGAG---AAA
322 GTTAAAGAAAAAAAGAGAGAAAAAGAATGAGAGTTGTAAACTACCAGCAACTAGTAGAGAAAAAA
*
10927 AAATAGTTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTCATT
387 AAATAATTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTCATT
* * * * *
10992 GCGCTTCCAATAAGTGGTATTAGAGCAAGTAAAAAAT-AAATATGTGGAGTTAATTTACTACAGA
452 ACGCTTCCAACAAGTGGTATAAGAGCAAGTAAAGAATAAAAAATGTGGAGTTAATTTACTACAGA
* * *
11056 ACAAAAGATCAATTGGTAGAT-TTTTTACGAAACCATTG--AGCGGATGCATTTCATAAACTCAA
517 ACAGAAGATCAATT-GTAGATATTTTTACGAAACCATTGAAAGC-GACGTATTTCATAAACTCAA
11118 AGAAAAGCTTTAAATGAAAGCTCGATTTGAGAG
580 AGAAAAGCTTTAAATGAAAGCTCGATTTGAGAG
* * * * *
11151 AGGATGTTGAAGTCAAATCGACTTTCGAAGTCGACATAAAAGTTGTAGCCAAGAATTTGTATTCA
1 AGAATGTTGAAGTCAAACCGACTTTCAAAGTCGACATAAAAATTGCAGCCAAGAATTTGTATTCA
* *
11216 AATTGACTTCCAACTTTATGAAAACGTGGGTTGAAAAGAGTTGCAAAGTGACAGCCTTGAGCAAA
66 AATTGACTTCCAACTTTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAAA
* *
11281 TGGATAACCATCAATAAACTGGCTAGAAGGGTCATGAAAAATCAAAGGATAAAATAATGATGGTA
131 TGGATAACCATCAATAAACTGGCTAGAAGGTTCATGAAAAATCAAAGGATAAAATAATGATGGCA
* * * *
11346 GCAATGGTTTGAATGGTTTTAGGCGGTAAGAATTGGTTGAAGTTTAAGTCGATTTAAAAAGTCTA
196 GCAATGGTTTGAATGGTCTTAGGCAGTAAGAATT-GCTGAAGTTTAAGTCGATTTAATAAGTCTA
11411 TAAATATGGTTTATGAGTTAGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGTGTT
260 TAAATATGGTTTATGAGTTAGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGTGTT
*
11476 -AAGAAAAAAAGAGAGAAAAAGAATGAGAGTTGTAAACTACCAGCAGCTAGTAGAGAAAAAAAAA
325 AAAGAAAAAAAGAGAGAAAAAGAATGAGAGTTGTAAACTACCAGCAACTAGTAGAG--AAAAAAA
* *
11540 AGATAATTGTATTGTGAGTTATTTTTGTGTAATAAAATTAATATTTTAGCAATTAATTATTCATT
388 A-ATAATTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTCATT
* * *
11605 ATGCTTTCAACAAGTGGTATAAGAGCAAGTAAAGAATAAAAAGAAGTGGAGTTAATTTACTACAG
452 ACGCTTCCAACAAGTGGTATAAGAGCAAGTAAAGAATAAAAA-ATGTGGAGTTAATTTACTACAG
* * * **
11670 AACAGAAGATCAATTAGCAGATATTTTTACGAAGCTATTGAAATTGTACGTATTTCATAAACTCA
516 AACAGAAGATCAATT-GTAGATATTTTTACGAAACCATTGAAAGCG-ACGTATTTCATAAACTCA
**
11735 AAGAAAAGCTTTAAATGAAAGCTCGGCTTGAGAG
579 AAGAAAAGCTTTAAATGAAAGCTCGATTTGAGAG
* * * *
11769 AGAATGTTGAAGTCAAATCGACTTTCGAAGTCGACATAAAAGTTGTAGCCAAGAATTTGTATTCA
1 AGAATGTTGAAGTCAAACCGACTTTCAAAGTCGACATAAAAATTGCAGCCAAGAATTTGTATTCA
* *
11834 AATTAACTTTCAACTTTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAAA
66 AATTGACTTCCAACTTTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAAA
* *
11899 TGGATAACCATCAATAAACTGGCTAGAAGGTTGATGAAAAATCAAAGGATAAAATAATGATGGTA
131 TGGATAACCATCAATAAACTGGCTAGAAGGTTCATGAAAAATCAAAGGATAAAATAATGATGGCA
* * *
11964 GCAATTGTTTGAATGGTCTTAAGCGGTAAGAATTGGCTGAAGTTTAAGTCGATTTAATAAGTCTA
196 GCAATGGTTTGAATGGTCTTAGGCAGTAAGAATT-GCTGAAGTTTAAGTCGATTTAATAAGTCTA
* *
12029 TAAATATGGTTTATGAGTTTGTGTGTGTGTATACAAAAAGTGTGAAAAAGAACAAAGAGTGAGTG
260 TAAATATGGTTTATGAG-TT-AGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGTG
* * * *
12094 TT-AAGAAGAAAAAAAGAGAAAAAGAGT-ATGAGTTGTAAACTAGCC-GTAATTAGTAGAGAGAA
323 TTAAAGAA-AAAAAGAGAGAAAAAGAATGA-GAGTTGTAAACTA-CCAGCAACTAGTAGAGA-AA
* * * * *
12156 AAAAGATAATTGTATTGTGAGATATTTTTGTGTAACAAAATTAGTATTTTAGCAATTAATTATCC
384 AAAAAATAATTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTC
* *
12221 ATTACGCTTCCAACAAGTGGTATTAA-AGCAAGTAAAGAAT-AAAAATGTCGAGTTAATTTATTA
449 ATTACGCTTCCAACAAGTGGTA-TAAGAGCAAGTAAAGAATAAAAAATGTGGAGTTAATTTACTA
* * *
12284 CAGAATAGAAAATCAATTGATAGATATTTTTACGAAACCATTGAAAGCGAGCATATTTCATAAAC
513 CAGAACAGAAGATCAATTG-TAGATATTTTTACGAAACCATTGAAAGCGA-CGTATTTCATAAAC
* * * *
12349 TCAAAGAAAAG-TTCAAAATAAAAGTTTGATTTGAGAG
576 TCAAAGAAAAGCTT-TAAATGAAAGCTCGATTTGAGAG
* * * * *
12386 GGAATGTTGAAGTCAAACCGACTTTCAAAGTTGGCATAAAAATTGCAGCCAATAATTTTTATTCA
1 AGAATGTTGAAGTCAAACCGACTTTCAAAGTCGACATAAAAATTGCAGCCAAGAATTTGTATTCA
* * * ** *
12451 AATTGGCTTCCAA-TCTTATGGAAACGTGACTTGAAAAGAGTTGCAAAGTGATGGTCTTAAGCAA
66 AATTGACTTCCAACT-TTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAA
** * * *
12515 ATGGATAAATATTAATAAACTGGCTAGAAGGTTGATAAAAAATCAAAGGATAAAATAATGATGGC
130 ATGGATAACCATCAATAAACTGGCTAGAAGGTTCATGAAAAATCAAAGGATAAAATAATGATGGC
* * *
12580 AACAATGGTTTGAATGGTCTTAGGCAGTAAGAATTGTTAAAGTTTAAGTCGATTTAATAAGTCTA
195 AGCAATGGTTTGAATGGTCTTAGGCAGTAAGAATTGCTGAAGTTTAAGTCGATTTAATAAGTCTA
* * * *
12645 TAAATATGGTTAATGAATTAGTGCGTGTATGCAAAAAATGTG-AAAA-AA-AAA-A-TGAGTGTT
260 TAAATATGGTTTATGAGTTAGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGTGTT
* * ** * * *
12705 GAA-AAGAAAAGAGAGAAAAAGAATGAGAGTTACAAACTAACAGCAACTA--ATAGAAAAAATAA
325 AAAGAAAAAAAGAGAGAAAAAGAATGAGAGTTGTAAACTACCAGCAACTAGTAGAGAAAAAAAAA
* * * *
12767 TAATTATATTGTGAATTATTTTTATATAATAAAATTAGTATTTTAACAATTAATTA-TCAATTAC
390 TAATTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTC-ATTAC
12831 GCTTCCAACAA
454 GCTTCCAACAA
12842 CAAAATTGTC
Statistics
Matches: 1506, Mismatches: 153, Indels: 66
0.87 0.09 0.04
Matches are distributed among these distances:
604 1 0.00
605 71 0.05
606 14 0.01
607 97 0.06
608 78 0.05
609 151 0.10
610 51 0.03
611 3 0.00
612 7 0.00
613 95 0.06
614 22 0.01
615 42 0.03
616 63 0.04
617 299 0.20
618 318 0.21
619 93 0.06
620 59 0.04
621 40 0.03
622 2 0.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (612 bp):
AGAATGTTGAAGTCAAACCGACTTTCAAAGTCGACATAAAAATTGCAGCCAAGAATTTGTATTCA
AATTGACTTCCAACTTTATGAAAACGTGGCTTGAAAAGAGTTGCAAAGTGACAGCCTTAAGCAAA
TGGATAACCATCAATAAACTGGCTAGAAGGTTCATGAAAAATCAAAGGATAAAATAATGATGGCA
GCAATGGTTTGAATGGTCTTAGGCAGTAAGAATTGCTGAAGTTTAAGTCGATTTAATAAGTCTAT
AAATATGGTTTATGAGTTAGTGTGTGTATGCAAAAAGTGTGAAAAAGAACAAAGAGTGAGTGTTA
AAGAAAAAAAGAGAGAAAAAGAATGAGAGTTGTAAACTACCAGCAACTAGTAGAGAAAAAAAAAT
AATTGTATTGTGAGTTATTTTTGTATAATAAAATTAGTATTTTAGCAATTAATTATTCATTACGC
TTCCAACAAGTGGTATAAGAGCAAGTAAAGAATAAAAAATGTGGAGTTAATTTACTACAGAACAG
AAGATCAATTGTAGATATTTTTACGAAACCATTGAAAGCGACGTATTTCATAAACTCAAAGAAAA
GCTTTAAATGAAAGCTCGATTTGAGAG
Found at i:14243 original size:31 final size:31
Alignment explanation
Indices: 14197--14267 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
14187 TCGGTGTAAT
14197 TATACACATAAAACTTTAATTGTGGTTCAAA
1 TATACACATAAAACTTTAATTGTGGTTCAAA
* * ** * *
14228 TATATACATGAAACTTTCGTTTTGGTTCAAT
1 TATACACATAAAACTTTAATTGTGGTTCAAA
14259 TATACACAT
1 TATACACAT
14268 TTAAAGAACC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (31 bp):
TATACACATAAAACTTTAATTGTGGTTCAAA
Found at i:21428 original size:23 final size:23
Alignment explanation
Indices: 21381--21428 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
21371 ATTACTTTTT
* *
21381 TTTTTTTCTAAATTGATACTTAA
1 TTTTTTTCAAAATTAATACTTAA
21404 TTTTTTT-AAAATTAATACTTGAA
1 TTTTTTTCAAAATTAATACTT-AA
21427 TT
1 TT
21429 ACTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTTTCAAAATTAATACTTAA
Found at i:22023 original size:36 final size:36
Alignment explanation
Indices: 21983--22170 Score: 95
Period size: 36 Copynumber: 5.2 Consensus size: 36
21973 TTTTCTCATA
21983 TTAATTTACTAGTATTTATTCTTCGACTCATGCTTT
1 TTAATTTACTAGTATTTATTCTTCGACTCATGCTTT
* * * ** * *
22019 TTAATCTAATA-TATATATTTGCTT-GTTTTTC-T-CATA
1 TTAATTTACTAGTATTTA-TT-CTTCG--ACTCATGCTTT
*
22055 TTAATTTACTAGTATTTGTTCTTCGACTCATGCTTT
1 TTAATTTACTAGTATTTATTCTTCGACTCATGCTTT
* * * ** * *
22091 TTAATCTAATA-TATATATTTGCTT-GTTTTTC-T-CATA
1 TTAATTTACTAGTATTTA-TT-CTTCG--ACTCATGCTTT
* *
22127 TTAATTTACTAGTATTTGTTCTTCAACTCATGCTTT
1 TTAATTTACTAGTATTTATTCTTCGACTCATGCTTT
22163 TTAATTTA
1 TTAATTTA
22171 ATTATATATA
Statistics
Matches: 104, Mismatches: 32, Indels: 32
0.62 0.19 0.19
Matches are distributed among these distances:
34 4 0.04
35 17 0.16
36 63 0.61
37 16 0.15
38 4 0.04
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.54
Consensus pattern (36 bp):
TTAATTTACTAGTATTTATTCTTCGACTCATGCTTT
Found at i:22071 original size:33 final size:33
Alignment explanation
Indices: 22034--22144 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 33
22024 CTAATATATA
22034 TATTTGCTTGTTTTTCTCATATTAATTTACTAG
1 TATTTGCTTGTTTTTCTCATATTAATTTACTAG
* *
22067 TATTTGTTCTTCGACTCATGCTTT-TTA-ATCTAATATA-TA-
1 TATTTG--CTT-G--T--T--TTTCTCATAT-TAATTTACTAG
22106 TATTTGCTTGTTTTTCTCATATTAATTTACTAG
1 TATTTGCTTGTTTTTCTCATATTAATTTACTAG
22139 TATTTG
1 TATTTG
22145 TTCTTCAACT
Statistics
Matches: 60, Mismatches: 4, Indels: 28
0.65 0.04 0.30
Matches are distributed among these distances:
30 3 0.05
31 8 0.13
32 5 0.08
33 12 0.20
34 1 0.02
35 3 0.05
36 2 0.03
37 3 0.05
38 1 0.02
39 6 0.10
40 5 0.08
41 8 0.13
42 3 0.05
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.56
Consensus pattern (33 bp):
TATTTGCTTGTTTTTCTCATATTAATTTACTAG
Found at i:22078 original size:72 final size:72
Alignment explanation
Indices: 21961--22181 Score: 397
Period size: 72 Copynumber: 3.1 Consensus size: 72
21951 AAATAGATAG
* *
21961 ATATTTGCTTATTTTTCTCATATTAATTTACTAGTATTTATTCTTCGACTCATGCTTTTTAATCT
1 ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCGACTCATGCTTTTTAATCT
22026 AATATAT
66 AATATAT
22033 ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCGACTCATGCTTTTTAATCT
1 ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCGACTCATGCTTTTTAATCT
22098 AATATAT
66 AATATAT
* *
22105 ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCAACTCATGCTTTTTAATTT
1 ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCGACTCATGCTTTTTAATCT
22170 AATTATAT
66 AA-TATAT
22178 ATAT
1 ATAT
22182 ATATATATTT
Statistics
Matches: 144, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
72 135 0.94
73 9 0.06
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (72 bp):
ATATTTGCTTGTTTTTCTCATATTAATTTACTAGTATTTGTTCTTCGACTCATGCTTTTTAATCT
AATATAT
Found at i:27729 original size:60 final size:58
Alignment explanation
Indices: 27630--27744 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 58
27620 AAGTAAATGT
* * *
27630 TCATCCCTTCATAAAGTTATTAAGTAATAACTCTTGAAAGTAAGCATGATTGAAGCGC
1 TCATCCCTTCATAAAGTTATTAAGTAATAACTCTAGAAAGTAAGCAAGATCGAAGCGC
* * *
27688 TCATCCCTTTATAAGGTTATGATAAGTAATAATTCTAGAAAGTAAGCAAGATCGAAG
1 TCATCCCTTCATAAAGTTAT--TAAGTAATAACTCTAGAAAGTAAGCAAGATCGAAG
27745 TGTTTGAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 18 0.37
60 31 0.63
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (58 bp):
TCATCCCTTCATAAAGTTATTAAGTAATAACTCTAGAAAGTAAGCAAGATCGAAGCGC
Found at i:33581 original size:43 final size:43
Alignment explanation
Indices: 33533--33658 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 43
33523 AAAAATACAC
33533 AAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
1 AAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
** * * ** * *
33576 AAATAA--A---AAAAATTATAA-TT-T-A-AGTAGTCA-TGA
1 AAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
33609 CAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
1 -AAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
33653 AAATAA
1 AAATAA
33659 AAAAAATTAT
Statistics
Matches: 56, Mismatches: 16, Indels: 22
0.60 0.17 0.23
Matches are distributed among these distances:
33 2 0.04
34 11 0.20
35 1 0.02
36 2 0.04
37 2 0.04
38 7 0.12
39 7 0.12
40 2 0.04
41 2 0.04
42 1 0.02
43 17 0.30
44 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (43 bp):
AAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTA
Found at i:33693 original size:77 final size:77
Alignment explanation
Indices: 33531--33684 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
33521 ATAAAAATAC
33531 ACAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTAAAATAAAAAAAATTATAATT
1 ACAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTAAAATAAAAAAAATTATAATT
33596 TAAGTAGTCATG
66 TAAGTAGTCATG
33608 ACAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTAAAATAAAAAAAATTATAATT
1 ACAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTAAAATAAAAAAAATTATAATT
33673 TAAGTAGTCATG
66 TAAGTAGTCATG
33685 TTATATAATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (77 bp):
ACAAATAATCACCCAACTATCAAAATTTCTCATTTTAGGCACTTAAAATAAAAAAAATTATAATT
TAAGTAGTCATG
Found at i:40416 original size:60 final size:60
Alignment explanation
Indices: 40335--40469 Score: 189
Period size: 60 Copynumber: 2.2 Consensus size: 60
40325 TCTGTTGACA
* * *
40335 TCATGTATTATTAAAATTTTAAAACATCATTTATAATTATATTTAAAATTTTAAAATATT
1 TCATGTATCATTAAAATTTTAAAACATAATTTATAATTATATTTAAAATTCTAAAATATT
* * * *
40395 TCATGTATCATTACACTTTTAAAATATAATTTATTATTATATTTAAAATTCTAAAATATT
1 TCATGTATCATTAAAATTTTAAAACATAATTTATAATTATATTTAAAATTCTAAAATATT
* *
40455 TTATTTATCATTAAA
1 TCATGTATCATTAAA
40470 TTTATAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (60 bp):
TCATGTATCATTAAAATTTTAAAACATAATTTATAATTATATTTAAAATTCTAAAATATT
Found at i:40453 original size:32 final size:31
Alignment explanation
Indices: 40345--40459 Score: 105
Period size: 32 Copynumber: 3.8 Consensus size: 31
40335 TCATGTATTA
* *
40345 TTAAAATTTTAAAACATCATTTATAATTATAT
1 TTAAAATTTTAAAATAT-ATTTATTATTATAT
* *
40377 TTAAAATTTTAAAATAT-TTCATGTA-T-CA-
1 TTAAAATTTTAAAATATATTTAT-TATTATAT
* *
40405 TTACACTTTTAAAATATAATTTATTATTATAT
1 TTAAAATTTTAAAATAT-ATTTATTATTATAT
*
40437 TTAAAATTCTAAAATAT-TTTATT
1 TTAAAATTTTAAAATATATTTATT
40460 TATCATTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
28 15 0.23
29 3 0.05
30 16 0.24
31 2 0.03
32 30 0.45
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (31 bp):
TTAAAATTTTAAAATATATTTATTATTATAT
Found at i:40468 original size:28 final size:28
Alignment explanation
Indices: 40344--40481 Score: 95
Period size: 32 Copynumber: 4.7 Consensus size: 28
40334 ATCATGTATT
*
40344 ATTAAAATTTTAAAACATCATTTATAATTAT-
1 ATTAAAATTTT-AAA-AT-ATTT-TATTTATC
* *
40375 ATTTAAAATTTTAAAATATTTCATGTATC
1 A-TTAAAATTTTAAAATATTTTATTTATC
* *
40404 ATTACACTTTTAAAATATAATTTATTATTAT-
1 ATTAAAATTTTAAAATAT--TTTA-T-TTATC
*
40435 ATTTAAAATTCTAAAATATTTTATTTATC
1 A-TTAAAATTTTAAAATATTTTATTTATC
*
40464 ATT-AAA-TTTATAATATTT
1 ATTAAAATTTTAAAATATTT
40482 AAAATGTATA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
26 10 0.11
27 3 0.03
28 25 0.29
29 7 0.08
30 9 0.10
31 6 0.07
32 27 0.31
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTAAAATTTTAAAATATTTTATTTATC
Found at i:42182 original size:59 final size:59
Alignment explanation
Indices: 42110--42227 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
42100 CATGTTGCCT
42110 TTAATACTACAAATTCTATAACCCTAATGTTTGACAAAAATACCCTTAGAGAGAATGAA
1 TTAATACTACAAATTCTATAACCCTAATGTTTGACAAAAATACCCTTAGAGAGAATGAA
42169 TTAATACTACAAATTCTATAACCCTAATGTTTGACAAAAATACCCTTAGAGAGAATGAA
1 TTAATACTACAAATTCTATAACCCTAATGTTTGACAAAAATACCCTTAGAGAGAATGAA
42228 GTGACTTTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (59 bp):
TTAATACTACAAATTCTATAACCCTAATGTTTGACAAAAATACCCTTAGAGAGAATGAA
Found at i:51047 original size:34 final size:33
Alignment explanation
Indices: 50979--51048 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
50969 GCCCAAAGAA
**
50979 AAACCAGCAGACCAACCAAAACAAGTCCACAGG
1 AAACCAGCAGACCAACCAAAACAAAACCACAGG
* *
51012 AAACCAGCAGATCCAATCGAAACAAAACCGA-AGG
1 AAACCAGCAGA-CCAACCAAAACAAAACC-ACAGG
51046 AAA
1 AAA
51049 ACAAAATCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 11 0.35
34 19 0.61
35 1 0.03
ACGTcount: A:0.51, C:0.29, G:0.16, T:0.04
Consensus pattern (33 bp):
AAACCAGCAGACCAACCAAAACAAAACCACAGG
Found at i:51513 original size:208 final size:209
Alignment explanation
Indices: 51155--51570 Score: 567
Period size: 208 Copynumber: 2.0 Consensus size: 209
51145 CTCAATTACA
* * **
51155 ACTTAATTAATATATTAGAGTTAATTATATTAATCAATTATTATTTTGAATAATATTTTTTGCAT
1 ACTTAATTAATATATTAAAGTTAATTATATTAATCAATTATTATTTTAAATAATATTACTTGCAT
*
51220 TAATTAAATAAAATAAAAATTATATTGTATGTTGAATATGTTAAAAATATTTTACTATAATTTAT
66 TAATTAAATAAAATAAAAATTATATTGTATGTTGAATATATTAAAAATATTTTACTATAATTTAT
* * *
51285 AAATTTTCTATTATAATATTTGAATT-GATAAGTTAATATA-TTTAATTATGTTCGATAATTCAA
131 AAATTTTCTATTATAATATTTAAATTAG-TAAATTAATATATTTTAATTATATTCGATAATTCAA
51348 A-AAAGAAATATTATC
195 ATAAA-AAATATTATC
* * *
51363 ACTTAATTAATATATTAAAG-TAATTATGTTAATCAATTATTATTTTAAATATTGTTACTTGTCA
1 ACTTAATTAATATATTAAAGTTAATTATATTAATCAATTATTATTTTAAATAATATTACTTG-CA
* * * *
51427 TTAATTAAATAAAGT-AAAATTGTATTGTATGTTGTAA-ATATTAAAAATATTTTAATTATGATT
65 TTAATTAAATAAAATAAAAATTATATTGTATGTTG-AATATATTAAAAATATTTT-ACTATAATT
* *
51490 TGA-AAATTTTCTGTTATAATATTTAAATTAGTAAATTAATATATTTTAATTATATTCGATAGTT
128 T-ATAAATTTTCTATTATAATATTTAAATTAGTAAATTAATATATTTTAATTATATTCGATAATT
*
51554 TAAATAAAAAATATTAT
192 CAAATAAAAAATATTAT
51571 TTAACATTAC
Statistics
Matches: 183, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
207 68 0.37
208 80 0.44
209 32 0.17
210 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (209 bp):
ACTTAATTAATATATTAAAGTTAATTATATTAATCAATTATTATTTTAAATAATATTACTTGCAT
TAATTAAATAAAATAAAAATTATATTGTATGTTGAATATATTAAAAATATTTTACTATAATTTAT
AAATTTTCTATTATAATATTTAAATTAGTAAATTAATATATTTTAATTATATTCGATAATTCAAA
TAAAAAATATTATC
Found at i:61349 original size:33 final size:30
Alignment explanation
Indices: 61299--61360 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 30
61289 TTATAAGTTC
61299 AATTCACATTCTATCAATCTCAATATATCATA
1 AATTCACATTCTATCAAT-TC-ATATATCATA
61331 AATTCATCATT-TCATCAATTCATATATCAT
1 AATTCA-CATTCT-ATCAATTCATATATCAT
61361 GTTTCAGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 9 0.32
32 9 0.32
33 10 0.36
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (30 bp):
AATTCACATTCTATCAATTCATATATCATA
Found at i:66267 original size:2 final size:2
Alignment explanation
Indices: 66262--66292 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66252 TCATGTATTT
*
66262 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66293 TTGCATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68141 original size:33 final size:33
Alignment explanation
Indices: 68064--68145 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
68054 TTTCCCCCAA
* * * *
68064 TACTTAACCTGATTATTGGGGCATCATCGCTGC
1 TACTTAACCTGCTTATAGGGGCACCATCACTGC
68097 TACTTAACCTGCTTATAGGGGCACCATCACTGC
1 TACTTAACCTGCTTATAGGGGCACCATCACTGC
**
68130 TACTTGGCCTGCTTAT
1 TACTTAACCTGCTTAT
68146 TTGAACATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (33 bp):
TACTTAACCTGCTTATAGGGGCACCATCACTGC
Found at i:74576 original size:22 final size:22
Alignment explanation
Indices: 74557--74600 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
74547 AAGTTTTTGT
74557 ACTTTT-ATTTTTAAAATTTTA
1 ACTTTTAATTTTTAAAATTTTA
* *
74578 ATTTTTAATTTTTTAAATTTTA
1 ACTTTTAATTTTTAAAATTTTA
74600 A
1 A
74601 AATTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ACTTTTAATTTTTAAAATTTTA
Found at i:74581 original size:15 final size:15
Alignment explanation
Indices: 74559--74604 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
74549 GTTTTTGTAC
74559 TTTT-ATTTTTAAAA
1 TTTTAATTTTTAAAA
**
74573 TTTTAATTTTTAATT
1 TTTTAATTTTTAAAA
*
74588 TTTTAAATTTTAAAA
1 TTTTAATTTTTAAAA
74603 TT
1 TT
74605 ACAATTAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTAATTTTTAAAA
Done.