Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009882.1 Kokia drynarioides strain JFW-HI SEQ_124617, 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: 123948
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1383 original size:43 final size:43
Alignment explanation
Indices: 1320--1592 Score: 305
Period size: 43 Copynumber: 6.3 Consensus size: 43
1310 TTTGTTAATG
* * *
1320 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAACCACGTTCA
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
1363 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTCTTAAAGACCACGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCG--C-TAAAGACCACGTTCT
* * * * *
1409 TTAGCGGCATTTGTGATAAAAGCGCCGATAAAGACTATGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
* * * * *
1452 ATAGCAGCGTTTGAGAAAAAAGCGCCGCTAAAGACAACGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
* * * * *
1495 TTAGCGGCATTTGTGGGGAAAGCTCCGCTAAAGATCACGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
* * *
1538 TTAGCGGTGTTTGTGGGGAAAGCGCCGCTAAAGACCACGTT-T
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
*
1580 TATAGCGACGTTT
1 T-TAGCGGCGTTT
1593 TCCCTCGTAA
Statistics
Matches: 194, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.01
43 153 0.79
45 1 0.01
46 38 0.20
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCT
Found at i:5155 original size:51 final size:51
Alignment explanation
Indices: 5100--5216 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
5090 AGTATATCAA
* **
5100 TAGTCACTTAATTTTGAAGTAGTTGACAAAACAGTTATTCTGATTTCAATT
1 TAGTCACTTAATTTTAAAGTAACTGACAAAACAGTTATTCTGATTTCAATT
* *
5151 TAGTCACTTAATTTTAAAGTAACTGACAAAACAGTTATTTTGATTTTAATT
1 TAGTCACTTAATTTTAAAGTAACTGACAAAACAGTTATTCTGATTTCAATT
* *
5202 TAATCACTCAATTTT
1 TAGTCACTTAATTTT
5217 CGAAAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (51 bp):
TAGTCACTTAATTTTAAAGTAACTGACAAAACAGTTATTCTGATTTCAATT
Found at i:11330 original size:56 final size:56
Alignment explanation
Indices: 11244--11353 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
11234 GGTACTCTTG
*
11244 TTGCAAGAATTTGATTTATGAATTATGGATCAGAAAGAGACTAAAAATCAAATTGC
1 TTGCAAGAATTTGATTTATGAATTATGGATCAGAAAGAAACTAAAAATCAAATTGC
* *
11300 TTGCAATAATTTGATTTATGAATTATGGATCAGAAAGAAACTGAAAATCAAATT
1 TTGCAAGAATTTGATTTATGAATTATGGATCAGAAAGAAACTAAAAATCAAATT
11354 ACATCTTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (56 bp):
TTGCAAGAATTTGATTTATGAATTATGGATCAGAAAGAAACTAAAAATCAAATTGC
Found at i:14095 original size:40 final size:40
Alignment explanation
Indices: 14035--14116 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
14025 ATGTAGGTAT
* * *
14035 TTATACTTTAGGTTTTCTTTAGGATTAGGTTATAATTTTC
1 TTATACTTTAGGTTTCCTTTAGAACTAGGTTATAATTTTC
* *
14075 TTATACTTTATGTTTCCTTTAGAACTAGGTTTTAATTTTC
1 TTATACTTTAGGTTTCCTTTAGAACTAGGTTATAATTTTC
14115 TT
1 TT
14117 TATTAGGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (40 bp):
TTATACTTTAGGTTTCCTTTAGAACTAGGTTATAATTTTC
Found at i:15111 original size:24 final size:23
Alignment explanation
Indices: 15084--15128 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
15074 TTTCCTAAGT
15084 GGAGAGAA-AAGGAAGGTAAGAGAA
1 GGAGA-AATAAGG-AGGTAAGAGAA
*
15108 GGAGAAATAAGGAGGTGAGAG
1 GGAGAAATAAGGAGGTAAGAG
15129 GGAATGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (23 bp):
GGAGAAATAAGGAGGTAAGAGAA
Found at i:16759 original size:23 final size:23
Alignment explanation
Indices: 16733--16865 Score: 151
Period size: 23 Copynumber: 5.7 Consensus size: 23
16723 TAATGTTCAC
**
16733 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-CGAACATTAATT
* *
16756 GAACATGTTCTCGAACATTAATC
1 GAACATGTTCACGAACATTAATT
* * *
16779 GACCATGTTCACAAACATTAATC
1 GAACATGTTCACGAACATTAATT
*
16802 GAACATGTTCACGAACATTAAAT
1 GAACATGTTCACGAACATTAATT
* *
16825 GGACATGTTCATGAACATATAATT
1 GAACATGTTCACGAACAT-TAATT
16849 GAACATGTTCACGAACA
1 GAACATGTTCACGAACA
16866 ATGTTAATGA
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
22 3 0.03
23 70 0.76
24 19 0.21
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (23 bp):
GAACATGTTCACGAACATTAATT
Found at i:16788 original size:46 final size:46
Alignment explanation
Indices: 16735--16865 Score: 167
Period size: 46 Copynumber: 2.8 Consensus size: 46
16725 ATGTTCACGA
* *
16735 ACATGTTCATTTAAC-TTAATTGAACATGTTCTCGAACATT-AATCG
1 ACATGTTCA-TAAACATTAATTGAACATGTTCACGAACATTAAATCG
* * *
16780 ACCATGTTCACAAACATTAATCGAACATGTTCACGAACATTAAATGG
1 A-CATGTTCATAAACATTAATTGAACATGTTCACGAACATTAAATCG
*
16827 ACATGTTCATGAACATATAATTGAACATGTTCACGAACA
1 ACATGTTCATAAACAT-TAATTGAACATGTTCACGAACA
16866 ATGTTAATGA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 4 0.05
46 44 0.59
47 26 0.35
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (46 bp):
ACATGTTCATAAACATTAATTGAACATGTTCACGAACATTAAATCG
Found at i:16895 original size:4 final size:4
Alignment explanation
Indices: 16881--16910 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
16871 AATGAATAAT
*
16881 AAAC TAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
16911 TGAAAACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.23, G:0.00, T:0.03
Consensus pattern (4 bp):
AAAC
Found at i:19815 original size:128 final size:128
Alignment explanation
Indices: 19587--19840 Score: 402
Period size: 128 Copynumber: 2.0 Consensus size: 128
19577 TTTAAAGCAA
* *
19587 CATAAAATTATTGGACTACTAGAACAACTGCAGGCTCTGTGGAGATTGTCCAAAATCGTTCCCAC
1 CATAAAATTACTGGACTACTAGAACAACTGCAAGCTCTGTGGAGATTGTCCAAAATCGTTCCCAC
* *
19652 CTAGGGTACCTAACTAGAGGCCAGATTTCCTTGCATAGAACCATTAAAGGGTCAAAACCCCAT
66 CTAGGGTACCTAACTAGAGGCCAGATTTCCTTGCATAGAACAATCAAAGGGTCAAAACCCCAT
* * *
19715 CATAAAATTCCTGGACTACTGGAATAACTGCAAGCTCTGT-GAGGATTGTCCAAAATCGTTCCCA
1 CATAAAATTACTGGACTACTAGAACAACTGCAAGCTCTGTGGA-GATTGTCCAAAATCGTTCCCA
* * *
19779 CCTATGGTACCTAACTAGATGCCAGATTTCCTTGCATAGAATAATCAAAGGGTCAAAACCCC
65 CCTAGGGTACCTAACTAGAGGCCAGATTTCCTTGCATAGAACAATCAAAGGGTCAAAACCCC
19841 TCTCTTGAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
127 2 0.02
128 113 0.98
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (128 bp):
CATAAAATTACTGGACTACTAGAACAACTGCAAGCTCTGTGGAGATTGTCCAAAATCGTTCCCAC
CTAGGGTACCTAACTAGAGGCCAGATTTCCTTGCATAGAACAATCAAAGGGTCAAAACCCCAT
Found at i:20563 original size:17 final size:16
Alignment explanation
Indices: 20529--20569 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
20519 CAATTAAAAT
*
20529 TAATAAAATAAATGAA
1 TAATAAAATAAATAAA
*
20545 TAATAAAGTAAAATAAA
1 TAATAAAAT-AAATAAA
20562 TAATAAAA
1 TAATAAAA
20570 ACTAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
TAATAAAATAAATAAA
Found at i:40623 original size:24 final size:24
Alignment explanation
Indices: 40596--40641 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40586 TAAATAATAA
40596 TATTA-TTATAATATAATAATATTT
1 TATTATTTATAATATAA-AATATTT
*
40620 TATTATTTATAATTTAAAATAT
1 TATTATTTATAATATAAAATAT
40642 AAAAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATTTATAATATAAAATATTT
Found at i:53964 original size:23 final size:23
Alignment explanation
Indices: 53937--53981 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
53927 AGTGAAAAGA
53937 ACAAAACA-AAAATGAGT-AGAAAT
1 ACAAAA-AGAAAA-GAGTAAGAAAT
53960 ACAAAAAGAAAAGAGTAAGAAA
1 ACAAAAAGAAAAGAGTAAGAAA
53982 AGTGTGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.69, C:0.07, G:0.16, T:0.09
Consensus pattern (23 bp):
ACAAAAAGAAAAGAGTAAGAAAT
Found at i:54128 original size:24 final size:24
Alignment explanation
Indices: 54101--54156 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
54091 GATTTCCTAA
54101 AAGGGGAAATAAGGAAGGTGAGA-G
1 AAGGGGAAATAAGG-AGGTGAGATG
*
54125 AAGGAGAAATAAGGAGGTGAGATG
1 AAGGGGAAATAAGGAGGTGAGATG
54149 AAGTGGGA
1 AAG-GGGA
54157 CGGAAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.29
24 17 0.61
25 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.11
Consensus pattern (24 bp):
AAGGGGAAATAAGGAGGTGAGATG
Found at i:73880 original size:18 final size:18
Alignment explanation
Indices: 73857--73891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73847 GATAATATGC
*
73857 GATCACATAACCAAATGT
1 GATCACAAAACCAAATGT
*
73875 GATCACAAAATCAAATG
1 GATCACAAAACCAAATG
73892 CATTCATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (18 bp):
GATCACAAAACCAAATGT
Found at i:83544 original size:13 final size:13
Alignment explanation
Indices: 83526--83550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83516 GGGGGTGTTA
83526 GGATATTATTTTG
1 GGATATTATTTTG
83539 GGATATTATTTT
1 GGATATTATTTT
83551 TAGGAACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
GGATATTATTTTG
Found at i:86678 original size:23 final size:22
Alignment explanation
Indices: 86646--86696 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
86636 GTTGAAGAAG
*
86646 GAGAGGTTAAGAAGAAGAAATA-A
1 GAGAGATTAAGAAG-AGAAA-AGA
86669 GAGAGATTAAGAAGAGAAAAGA
1 GAGAGATTAAGAAGAGAAAAGA
86691 GAGAGA
1 GAGAGA
86697 AGGCTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
23 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (22 bp):
GAGAGATTAAGAAGAGAAAAGA
Found at i:91426 original size:23 final size:23
Alignment explanation
Indices: 91388--91446 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
91378 GAAAAGGTTG
*
91388 AAGAAGGAGAGGTTAAGAAGA-AGA
1 AAGAA-GAGAGATTAAGAAGAGA-A
91412 AAGAAGAGAGATTAAGAAGAGAA
1 AAGAAGAGAGATTAAGAAGAGAA
91435 AAGAGAGAGAGA
1 AAGA-AGAGAGA
91447 AGACTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAGAGAGATTAAGAAGAGAA
Found at i:100571 original size:40 final size:40
Alignment explanation
Indices: 100498--100737 Score: 248
Period size: 40 Copynumber: 6.0 Consensus size: 40
100488 TGATCTAACG
* * * **
100498 GTGTTTACAGTGTCACCT-CCAGTTTAGTTGTAATGTCGTA
1 GTGTTTACAGTGTCA-CTACCAGTTCAGTAGTAATATCACA
* *
100538 GTGTTTACAGTGTCACCACCAGTTCATTAGTAATATCACA
1 GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
* * * *
100578 GAGCTTACAGTGTCACTGCCAATTCAGTAGTAATATCACA
1 GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
* * * *
100618 GCGTTTATAGTGTCACTGCCAGTTCAGTAGTAATATCGCA
1 GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
* * * *
100658 GTGTTTAAAATGTCACTACCAGTTCAATAGTAATATCTCA
1 GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
* * * * *
100698 ATGTTTATAGTGTCATTGCCAGTTTAGTAGTAATATCACA
1 GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
100738 ATGTGGTTAT
Statistics
Matches: 167, Mismatches: 32, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.01
40 166 0.99
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (40 bp):
GTGTTTACAGTGTCACTACCAGTTCAGTAGTAATATCACA
Found at i:100693 original size:120 final size:120
Alignment explanation
Indices: 100500--100737 Score: 309
Period size: 120 Copynumber: 2.0 Consensus size: 120
100490 ATCTAACGGT
* * * * * * *
100500 GTTTACAGTGTCACCTCCAGTTTAGTTGTAATGTCGTAGTGTTTACAGTGTCACCACCAGTTCAT
1 GTTTACAGTGTCACCTCCAGTTCAGTAGTAATATCGCAGTGTTTAAAATGTCACCACCAGTTCAA
100565 TAGTAATATCACAGA-GCTTACAGTGTCACTGCCAATTCAGTAGTAATATCACAGC
66 TAGTAATATCACA-ATGCTTACAGTGTCACTGCCAATTCAGTAGTAATATCACAGC
* *
100620 GTTTATAGTGTCA-CTGCCAGTTCAGTAGTAATATCGCAGTGTTTAAAATGTCACTACCAGTTCA
1 GTTTACAGTGTCACCT-CCAGTTCAGTAGTAATATCGCAGTGTTTAAAATGTCACCACCAGTTCA
* * * * * *
100684 ATAGTAATATCTCAATGTTTATAGTGTCATTGCCAGTTTAGTAGTAATATCACA
65 ATAGTAATATCACAATGCTTACAGTGTCACTGCCAATTCAGTAGTAATATCACA
100738 ATGTGGTTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
119 3 0.03
120 98 0.97
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (120 bp):
GTTTACAGTGTCACCTCCAGTTCAGTAGTAATATCGCAGTGTTTAAAATGTCACCACCAGTTCAA
TAGTAATATCACAATGCTTACAGTGTCACTGCCAATTCAGTAGTAATATCACAGC
Found at i:105330 original size:31 final size:31
Alignment explanation
Indices: 105292--105353 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
105282 ACTCCCTTTG
105292 GGAAGCTATCAATACCCTAAGTTCATACTGT
1 GGAAGCTATCAATACCCTAAGTTCATACTGT
105323 GGAAGCTATCAATACCCTAAGTTCATACTGT
1 GGAAGCTATCAATACCCTAAGTTCATACTGT
105354 AAACCTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (31 bp):
GGAAGCTATCAATACCCTAAGTTCATACTGT
Found at i:106773 original size:40 final size:40
Alignment explanation
Indices: 106725--106917 Score: 197
Period size: 40 Copynumber: 4.8 Consensus size: 40
106715 TACCGTAGTT
* ** *
106725 TTTACAGTGTCACCGCCAGTTCAATTTTAATGTCACAATG
1 TTTACAGTGTCACTGCCAGTTCAATAGTAATATCACAATG
* * * *
106765 TTTACAGTGTCAGTGCCAATTCAATAGTAATATCGCAGTG
1 TTTACAGTGTCACTGCCAGTTCAATAGTAATATCACAATG
* * * ** ***
106805 TTTACAGTGTCACTACCAGTTCAGTAATAATATTGCAGCA
1 TTTACAGTGTCACTGCCAGTTCAATAGTAATATCACAATG
* * *
106845 TTTATAGTGTCACTGCCAGTTTAGTAGTAATATCACAATG
1 TTTACAGTGTCACTGCCAGTTCAATAGTAATATCACAATG
* *
106885 TTTACAGTGTCACTGTCAGTTCAGTAGTAATAT
1 TTTACAGTGTCACTGCCAGTTCAATAGTAATAT
106918 TGCAGTATAG
Statistics
Matches: 125, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 125 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (40 bp):
TTTACAGTGTCACTGCCAGTTCAATAGTAATATCACAATG
Found at i:106862 original size:80 final size:80
Alignment explanation
Indices: 106765--106922 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 80
106755 TGTCACAATG
* * *
106765 TTTACAGTGTCAGTGCCAATTCAATAGTAATATCGCAGTGTTTACAGTGTCACTACCAGTTCAGT
1 TTTACAGTGTCACTGCCAATTCAATAGTAATATCACAATGTTTACAGTGTCACTACCAGTTCAGT
106830 AATAATATTGCAGCA
66 AATAATATTGCAGCA
* * * * **
106845 TTTATAGTGTCACTGCCAGTTTAGTAGTAATATCACAATGTTTACAGTGTCACTGTCAGTTCAGT
1 TTTACAGTGTCACTGCCAATTCAATAGTAATATCACAATGTTTACAGTGTCACTACCAGTTCAGT
*
106910 AGTAATATTGCAG
66 AATAATATTGCAG
106923 TATAGTTTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (80 bp):
TTTACAGTGTCACTGCCAATTCAATAGTAATATCACAATGTTTACAGTGTCACTACCAGTTCAGT
AATAATATTGCAGCA
Found at i:108594 original size:11 final size:11
Alignment explanation
Indices: 108578--108607 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
108568 TTTTAATTTT
108578 TTATTTAACAA
1 TTATTTAACAA
*
108589 TTATTTTACAA
1 TTATTTAACAA
108600 TTATTTAA
1 TTATTTAA
108608 GACTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTTAACAA
Found at i:109020 original size:20 final size:20
Alignment explanation
Indices: 108995--109063 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
108985 TTTATTTTTA
108995 TTTTTTCATGTTGTTTCAAGT
1 TTTTTTCATGTTGTTTCAA-T
* * * **
109016 TTTTTTCTTTTATTTTTTTAT
1 TTTTTTCATGT-TGTTTCAAT
109037 TTTTTTCATGTTGTTTCAAT
1 TTTTTTCATGTTGTTTCAAT
109057 TTTTTTC
1 TTTTTTC
109064 TCCTTCTCTT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 13 0.35
21 19 0.51
22 5 0.14
ACGTcount: A:0.12, C:0.09, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTTTCATGTTGTTTCAAT
Found at i:109076 original size:41 final size:41
Alignment explanation
Indices: 108990--109076 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
108980 CATTTTTTAT
* * *
108990 TTTTATTTTTTCATGTTGTTTCAAGTTTTTTTCTTTTATTT
1 TTTTATTTTTTCATGTTGTTTCAAGTTTTTTTCTCTTACTC
109031 TTTTATTTTTTTCATGTTGTTTCAA-TTTTTTTCTCCTT-CTC
1 TTTTA-TTTTTTCATGTTGTTTCAAGTTTTTTTCT-CTTACTC
109072 TTTTA
1 TTTTA
109077 AATTTTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
41 20 0.49
42 21 0.51
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (41 bp):
TTTTATTTTTTCATGTTGTTTCAAGTTTTTTTCTCTTACTC
Found at i:116640 original size:16 final size:17
Alignment explanation
Indices: 116619--116650 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
116609 TTCCTAAGTG
116619 GAGAGAAA-AGAAATAT
1 GAGAGAAAGAGAAATAT
116635 GAGAGAAAGAGAAATA
1 GAGAGAAAGAGAAATA
116651 AGGAGGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.09
Consensus pattern (17 bp):
GAGAGAAAGAGAAATAT
Found at i:117725 original size:39 final size:37
Alignment explanation
Indices: 117621--117732 Score: 124
Period size: 39 Copynumber: 3.0 Consensus size: 37
117611 TGATAGTCTA
*
117621 GTAGTGTTTACAGTGTCACT-TC---AGTATAGCATT
1 GTAGTGTTTACAGTGTCACTGTCAGTAGTATATCATT
* * *
117654 GTAGTGTTTAAAGTGTCATTGCCAGCTCAGTATATCATT
1 GTAGTGTTTACAGTGTCACTGTCAG-T-AGTATATCATT
117693 GTAGTGTTTACAGTGTCACTGTCAGTTTAGTATATCATT
1 GTAGTGTTTACAGTGTCACTGTCAG--TAGTATATCATT
117732 G
1 G
117733 CAAAATACTC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
33 18 0.28
34 1 0.02
39 44 0.69
40 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (37 bp):
GTAGTGTTTACAGTGTCACTGTCAGTAGTATATCATT
Found at i:120149 original size:29 final size:29
Alignment explanation
Indices: 120117--120180 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
120107 TAGTCATGCC
*
120117 ACAGATATAGTCACGTCACAA-ATACAATT
1 ACAGATACAGTCACGTCA-AAGATACAATT
* * *
120146 ACAGATACAGTCATGTCAAAGATATAGTT
1 ACAGATACAGTCACGTCAAAGATACAATT
120175 ACAGAT
1 ACAGAT
120181 GCAGACATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (29 bp):
ACAGATACAGTCACGTCAAAGATACAATT
Found at i:120189 original size:29 final size:29
Alignment explanation
Indices: 120142--120218 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
120132 TCACAAATAC
* *
120142 AATTACAGATACAGTCATG-TCAAAGATAT
1 AATTACAGATGCAGACATGCT-AAAGATAT
* *
120171 AGTTACAGATGCAGACATGCTACAGATAT
1 AATTACAGATGCAGACATGCTAAAGATAT
120200 AATTACAGATGCAGACATG
1 AATTACAGATGCAGACATG
120219 ATACCTCCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 41 0.98
30 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (29 bp):
AATTACAGATGCAGACATGCTAAAGATAT
Found at i:120363 original size:40 final size:40
Alignment explanation
Indices: 120308--120415 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
120298 ACACGTCGCT
* * * *
120308 GTGTTTACAATGTCACTGTCAGTTTAGTTGTAATCTTGCA
1 GTGTTTATAATGTCACTGCCAGTTCAGTTGAAATCTTGCA
* *
120348 GTGTTTATAATGTCACTACCGGTTCAGTTGAAATCTTGCA
1 GTGTTTATAATGTCACTGCCAGTTCAGTTGAAATCTTGCA
* * *
120388 GTGTTAATAGTGTCATTGCCAGTTCAGT
1 GTGTTTATAATGTCACTGCCAGTTCAGT
120416 AAATATTCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (40 bp):
GTGTTTATAATGTCACTGCCAGTTCAGTTGAAATCTTGCA
Found at i:121013 original size:53 final size:52
Alignment explanation
Indices: 120956--121065 Score: 139
Period size: 53 Copynumber: 2.1 Consensus size: 52
120946 TATACACACA
* *
120956 CATGTATCAACCCATGTTCCCCAGAACAATATACACACACCCTAACACATGAC
1 CATGTATCAACCCATGTGCCCCAGAACAATATACACACACCCTAACACACG-C
* * * * * *
121009 CATGTGTCAGCCCGTGTGCTCTAGAACAGTATACACACACCCTAACACACGC
1 CATGTATCAACCCATGTGCCCCAGAACAATATACACACACCCTAACACACGC
121061 CATGT
1 CATGT
121066 GTTAGACCGT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 6 0.12
53 43 0.88
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.20
Consensus pattern (52 bp):
CATGTATCAACCCATGTGCCCCAGAACAATATACACACACCCTAACACACGC
Found at i:121092 original size:52 final size:52
Alignment explanation
Indices: 120976--121114 Score: 163
Period size: 53 Copynumber: 2.6 Consensus size: 52
120966 CCCATGTTCC
* * *
120976 CCAGAACAATATACACACACCCTAACACATGACCATGTGTCAGCCCGTGTGCT
1 CCAGAACAGTATACACACACCCTAACACACG-CCATGTGTCAGACCGTGTGCT
* *
121029 CTAGAACAGTATACACACACCCTAACACACGCCATGTGTTAGACCGTGTGCCT
1 CCAGAACAGTATACACACACCCTAACACACGCCATGTGTCAGACCGTGTG-CT
* * *
121082 CCA-AATAGTATAAACACATACCCTGACACACGC
1 CCAGAACAGTAT--ACACACACCCTAACACACGC
121115 TCGTGTGCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 24 0.32
53 32 0.43
54 18 0.24
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (52 bp):
CCAGAACAGTATACACACACCCTAACACACGCCATGTGTCAGACCGTGTGCT
Found at i:121121 original size:43 final size:43
Alignment explanation
Indices: 121072--121210 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 43
121062 ATGTGTTAGA
* *
121072 CCGTGTGCCTCCAAATAGTATAA-ACACATACCCTGACACACGC
1 CCGTGTGCCTCCAAATAGTA-AAGACACACACCCTGACACACCC
* *
121115 TCGTGTGCCTCCAAATAGTAAAGACACACACCTTGACACACCC
1 CCGTGTGCCTCCAAATAGTAAAGACACACACCCTGACACACCC
* * * * ** *
121158 CCATGTGCCTCCAAACAATATAGATGCACACCTTAGACACACCC
1 CCGTGTGCCTCCAAATAGTAAAGACACACACCCT-GACACACCC
*
121202 CTGTGTGCC
1 CCGTGTGCC
121211 AGCCCATGTG
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 2 0.02
43 63 0.78
44 16 0.20
ACGTcount: A:0.31, C:0.35, G:0.14, T:0.19
Consensus pattern (43 bp):
CCGTGTGCCTCCAAATAGTAAAGACACACACCCTGACACACCC
Done.