Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013744.1 Kokia drynarioides strain JFW-HI SEQ_128772, 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: 40999
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:4870 original size:22 final size:22
Alignment explanation
Indices: 4842--4887 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4832 GGGTTCTCGA
4842 TGTTGCGACATCCACTTACCGG
1 TGTTGCGACATCCACTTACCGG
4864 TGTTGCGACATCCACTTACCGG
1 TGTTGCGACATCCACTTACCGG
4886 TG
1 TG
4888 ATCACAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.28
Consensus pattern (22 bp):
TGTTGCGACATCCACTTACCGG
Found at i:5577 original size:291 final size:291
Alignment explanation
Indices: 5053--5637 Score: 1143
Period size: 291 Copynumber: 2.0 Consensus size: 291
5043 CTTGAGATAA
5053 AGAAGCTCGATGTCGTGACATCCTAGCATCAATGTTGCGATACCCATGTCAAATGTAGTTCTCCT
1 AGAAGCTCGATGTCGTGACATCCTAGCATCAATGTTGCGATACCCATGTCAAATGTAGTTCTCCT
5118 CAAAGTCGGGCCATTGTTGTATCCTTACATCAACTCAAGCACACTATTAAGTTCTCTAATGCACC
66 CAAAGTCGGGCCATTGTTGTATCCTTACATCAACTCAAGCACACTATTAAGTTCTCTAATGCACC
* *
5183 ATTTTGCCAAATTGGATCTCAAAAGGAATCAAACTAATCAAAAATGATAATTAATAATAAAAACT
131 ATTTTGCCAAATTGGATCTCAAAAGGAATCAAACTAAGCAAAAATGATAAGTAATAATAAAAACT
5248 AAAAGTCAACAAAAGTATTGAAAAGACTCGTAAGTTACTTGAGAATAAACTCCTCGAGTGTTTTG
196 AAAAGTCAACAAAAGTATTGAAAAGACTCGTAAGTTACTTGAGAATAAACTCCTCGAGTGTTTTG
5313 AAGAACGTAATTTGACGTATCAAATTACAAC
261 AAGAACGTAATTTGACGTATCAAATTACAAC
5344 AGAAGCTCGATGTCGTGACATCCTAGCATCAATGTTGCGATACCCATGTCAAATGTAGTTCTCCT
1 AGAAGCTCGATGTCGTGACATCCTAGCATCAATGTTGCGATACCCATGTCAAATGTAGTTCTCCT
*
5409 CAAAGTCGGGCCATTGTTGTATCCTTACATCAACTCAAGCACACTATTAGGTTCTCTAATGCACC
66 CAAAGTCGGGCCATTGTTGTATCCTTACATCAACTCAAGCACACTATTAAGTTCTCTAATGCACC
5474 ATTTTGCCAAATTGGATCTCAAAAGGAATCAAACTAAGCAAAAATGATAAGTAATAATAAAAACT
131 ATTTTGCCAAATTGGATCTCAAAAGGAATCAAACTAAGCAAAAATGATAAGTAATAATAAAAACT
5539 AAAAGTCAACAAAAGTATTGAAAAGACTCGTAAGTTACTTGAGAATAAACTCCTCGAGTGTTTTG
196 AAAAGTCAACAAAAGTATTGAAAAGACTCGTAAGTTACTTGAGAATAAACTCCTCGAGTGTTTTG
5604 AAGAACGTAATTTGACGTATCAAATTACAAC
261 AAGAACGTAATTTGACGTATCAAATTACAAC
5635 AGA
1 AGA
5638 TTAGTGGAAA
Statistics
Matches: 291, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
291 291 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (291 bp):
AGAAGCTCGATGTCGTGACATCCTAGCATCAATGTTGCGATACCCATGTCAAATGTAGTTCTCCT
CAAAGTCGGGCCATTGTTGTATCCTTACATCAACTCAAGCACACTATTAAGTTCTCTAATGCACC
ATTTTGCCAAATTGGATCTCAAAAGGAATCAAACTAAGCAAAAATGATAAGTAATAATAAAAACT
AAAAGTCAACAAAAGTATTGAAAAGACTCGTAAGTTACTTGAGAATAAACTCCTCGAGTGTTTTG
AAGAACGTAATTTGACGTATCAAATTACAAC
Found at i:6858 original size:22 final size:21
Alignment explanation
Indices: 6806--6858 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
6796 AATTAACCCT
*
6806 TTACAAAAAAAAAAAAACAAAA
1 TTAC-AAATAAAAAAAACAAAA
* * *
6828 TAATAAATAAAAAAAACCAAA
1 TTACAAATAAAAAAAACAAAA
6849 TTACACAATA
1 TTACA-AATA
6859 TGTAAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (21 bp):
TTACAAATAAAAAAAACAAAA
Found at i:12270 original size:21 final size:21
Alignment explanation
Indices: 12246--12298 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
12236 CTCTTAATTT
*
12246 TTTCT-TTACATAATAATAGGA
1 TTTCTGTTA-ATAATAACAGGA
12267 TTTCTGTTAATAATAACAGGA
1 TTTCTGTTAATAATAACAGGA
12288 TTTCTGTTAAT
1 TTTCTGTTAAT
12299 CATCCTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (21 bp):
TTTCTGTTAATAATAACAGGA
Found at i:14490 original size:20 final size:21
Alignment explanation
Indices: 14442--14522 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
14432 ATTTAACACT
14442 AATG-AATCGATTCAAACAGAAA
1 AATGCAATCGATTC-AACAG-AA
*
14464 AAT--AATCAATTCAACAGAA
1 AATGCAATCGATTCAACAGAA
* *
14483 AGT-CAATCGATTTAACA-AA
1 AATGCAATCGATTCAACAGAA
*
14502 AATGCAATCGATTCAAAAGAA
1 AATGCAATCGATTCAACAGAA
14523 CCATATTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.16
20 28 0.57
21 10 0.20
22 3 0.06
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (21 bp):
AATGCAATCGATTCAACAGAA
Found at i:16457 original size:21 final size:21
Alignment explanation
Indices: 16417--16461 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16407 ATGACAGTTT
* *
16417 TACCGAAACAAGTGAAGCTTC
1 TACCGAAACAAATCAAGCTTC
*
16438 TACCGAAACAAATCATGCTTC
1 TACCGAAACAAATCAAGCTTC
16459 TAC
1 TAC
16462 TATTACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (21 bp):
TACCGAAACAAATCAAGCTTC
Found at i:17547 original size:194 final size:194
Alignment explanation
Indices: 17219--17635 Score: 558
Period size: 194 Copynumber: 2.1 Consensus size: 194
17209 ACCAGTACCC
* * * * * *
17219 GATGCTGCTCACACGAGCTGTCGAGGACTTGCAACGTATGCGGTACCCCAGCCTTCGATACGGTG
1 GATGCTGCTCACACGAGCTGTCGAGGACTTGCAACATATGCGGTACCCCAACCATCAATACAGTA
* *
17284 TCTATCTATAAACTGTCCTTTAACGATGCTGCTCACACGAGTTGTCGAGAATATGCATTCAAGCA
66 TCTATCTATAAACTGTCCTCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTCAAGCA
**
17349 TAAATCTCAGCCATCGTAGGGCCTATAATCCATT-TAGGATT-TTATATCTC-TTTTTCAACTCA
131 TAAATCTCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTCTT-TA-CTCATTTCCCAACTCA
17411 T
194 T
* * * *
17412 GATGCTGCTCACACGAGCTATCGAGGACTTGTAACATATGCGGTACCTCAACCATCAATATAGTA
1 GATGCTGCTCACACGAGCTGTCGAGGACTTGCAACATATGCGGTACCCCAACCATCAATACAGTA
* *
17477 TCTATGC-ATATAACTGTTCC-CTGACGATGCTTCTCACACGAGCTGTCGAGAATATGCACTT-A
66 TCTAT-CTATA-AACTG-TCCTCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCA-TTCA
* * * *
17539 TGCATAAATCTCAGCCATCGTAGGGCCTATAATCTATTCTTGGATTCTTTACTCATTTCCCGACT
127 AGCATAAATCTCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTCTTTACTCATTTCCCAACT
17604 CAT
192 CAT
17607 GATGCTGCTCACACGAGCTGTCGAGGACT
1 GATGCTGCTCACACGAGCTGTCGAGGACT
17636 CACAACTCAT
Statistics
Matches: 196, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
193 63 0.32
194 80 0.41
195 51 0.26
196 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (194 bp):
GATGCTGCTCACACGAGCTGTCGAGGACTTGCAACATATGCGGTACCCCAACCATCAATACAGTA
TCTATCTATAAACTGTCCTCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTCAAGCA
TAAATCTCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTCTTTACTCATTTCCCAACTCAT
Found at i:18159 original size:16 final size:16
Alignment explanation
Indices: 18135--18166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18125 TCCTTACAAA
*
18135 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
18151 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
18167 AAATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:23080 original size:6 final size:6
Alignment explanation
Indices: 23069--23125 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
23059 TCAAATTTTC
* * * *
23069 TTTCTT TTTCTT TCTCTT TCTCTT TTTCTT ATTACTTT GTTTTTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT -TTTC-TT -TTTCTT TTTCTT
23120 TTTCTT
1 TTTCTT
23126 GCAAATGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 33 0.79
7 5 0.12
8 4 0.10
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:24766 original size:51 final size:51
Alignment explanation
Indices: 24689--24864 Score: 253
Period size: 51 Copynumber: 3.5 Consensus size: 51
24679 CTATAAACGA
* * *
24689 AAAGGTTTAATGACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
24740 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
24791 AAAGATCTGATGACTAAGTGTCATCGTAAGTAAATGAATCCATGATGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
24842 AAAGGTCCGTTGACTCAGTGTCA
1 AAAGGTCTGATGACTAAGTGTCA
24865 GTATATGAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 113 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:26238 original size:3 final size:3
Alignment explanation
Indices: 26232--26257 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26222 CTCATCATGA
26232 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
26258 GTCCTTACGC
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:36326 original size:20 final size:20
Alignment explanation
Indices: 36301--36368 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
36291 GGACAAGCCA
*
36301 CCAGTAATGCAAATAAACTG
1 CCAGTAATGCAGATAAACTG
* * *
36321 CCAGTAGTGCAGACAAGCTG
1 CCAGTAATGCAGATAAACTG
* *
36341 CCAGTATTACAGATAAACTG
1 CCAGTAATGCAGATAAACTG
36361 CCAGTAAT
1 CCAGTAAT
36369 ACTGTAACAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CCAGTAATGCAGATAAACTG
Found at i:37512 original size:52 final size:52
Alignment explanation
Indices: 37438--37642 Score: 250
Period size: 52 Copynumber: 3.9 Consensus size: 52
37428 CCAAACCTTA
* * **
37438 TAATCCGTAAGGGATTCGTATACTCACGATGACACAGAGTCATCGGACC-TCT
1 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCGT-T
* * * *
37490 TAATTCGTAAAGGATCCATATACTCATGATGACACTTAGTCATCTGACCGTT
1 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCGTT
** * * * *
37542 TAATTTGTAAAGGATTCATATACTCACAATAACACTTAGACATTGGACCGTT
1 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCGTT
* *
37594 TAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCATTGGACC
1 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACC
37643 ACTTCGTTTA
Statistics
Matches: 130, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
52 129 0.99
53 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (52 bp):
TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCGTT
Found at i:40756 original size:25 final size:25
Alignment explanation
Indices: 40716--40771 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
40706 TTTTATTATT
40716 ATTTATATTTACTTATTTATTTTGGC
1 ATTTATATTTACTTATTTA-TTTGGC
* *
40742 ATTTA-ATTTATTTATTTATTTGTC
1 ATTTATATTTACTTATTTATTTGGC
40766 ATTTAT
1 ATTTAT
40772 TTTCATGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 10 0.37
25 12 0.44
26 5 0.19
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.64
Consensus pattern (25 bp):
ATTTATATTTACTTATTTATTTGGC
Done.