Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002711.1 Kokia drynarioides strain JFW-HI SEQ_115001, 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: 78942
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 145 characters in sequence are not A, C, G, or T
Found at i:77 original size:3 final size:3
Alignment explanation
Indices: 12--65 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2 TAATATTTAT
* * *
12 ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATG ACA CTA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58 ATA ATA AT
1 ATA ATA AT
66 TTTTAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1269 original size:29 final size:29
Alignment explanation
Indices: 1210--1621 Score: 301
Period size: 29 Copynumber: 14.1 Consensus size: 29
1200 CCCCGAAGGT
*
1210 CCCCGAA-CTTCCAAAAA-TCCCATTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTT-A
*
1238 CCCCGAACCTTTCAAAAATTACCATTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTA
*
1267 CCCTCGAA-CTTCCAAAAATCA-CATTTTTGA
1 CCC-CGAACCTTCCAAAAATTACCA-TTTT-A
* * *
1297 CCCCGAACCTTTCGANAATTACCATTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTA
* *
1326 CCCCCGAA-CTTCCAAAAA-TCCCATTTTT
1 -CCCCGAACCTTCCAAAAATTACCATTTTA
** * *
1354 GACCAAACCTTCTAAAAATTACCATTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTA
* * *
1383 CCCCCAAACTTCCAAAAA-TCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCA-TTTT-A
** * *
1413 CCCCGAATATTCTAAAAATTACCATTTTG
1 CCCCGAACCTTCCAAAAATTACCATTTTA
* * *
1442 CCCCTAAACTTCCAAGAA-T-CCTATTTTTGA
1 CCCCGAACCTTCCAAAAATTACC-A-TTTT-A
* *
1472 CCCCAAACCTTCTAAAAATTACCATTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTA
* * *
1501 CCCCAAAACTTCCAAAAA-TCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCA-TTTT-A
* *
1531 CCCCGAACCTTTCGAAAATTACCATTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTA
*
1560 CCCTCGAA-CTTCCAAAAA-TCCCATTTTTGA
1 CCC-CGAACCTTCCAAAAATTACCA-TTTT-A
* * *
1590 CTCCGAACCTTCC-AAAACTACCATTTTG
1 CCCCGAACCTTCCAAAAATTACCATTTTA
1618 CCCC
1 CCCC
1622 CGTGCATCCG
Statistics
Matches: 302, Mismatches: 56, Indels: 52
0.74 0.14 0.13
Matches are distributed among these distances:
27 6 0.02
28 43 0.14
29 131 0.43
30 108 0.36
31 12 0.04
32 2 0.01
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.30
Consensus pattern (29 bp):
CCCCGAACCTTCCAAAAATTACCATTTTA
Found at i:1303 original size:59 final size:58
Alignment explanation
Indices: 1210--1621 Score: 534
Period size: 59 Copynumber: 7.1 Consensus size: 58
1200 CCCCGAAGGT
1210 CCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
* * *
1267 CCCTCGAACTTCCAAAAATCACATTTTTGACCCCGAACCTTTCGANAATTACCATTTTA
1 CCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
*
1326 CCCCCGAACTTCCAAAAATCCCATTTTTGA--CCAAACC-TTCTAAAAATTACCATTTTA
1 -CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTC-AAAAATTACCATTTTA
* *
1383 CCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAA--TATTCTAAAAATTACCATTTTG
1 -CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT-TTC-AAAAATTACCATTTTA
* * * *
1442 CCCCTAAACTTCCAAGAATCCTATTTTTGACCCCAAACC-TTCTAAAAATTACCATTTTA
1 CCCC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTC-AAAAATTACCATTTTA
* *
1501 CCCCAAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCGAAAATTACCATTTTA
1 CCCC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
* * * *
1560 CCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC-TTCCAAAACTACCATTTTG
1 CCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
1618 CCCC
1 CCCC
1622 CGTGCATCCG
Statistics
Matches: 318, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
56 3 0.01
57 53 0.17
58 41 0.13
59 214 0.67
60 7 0.02
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.30
Consensus pattern (58 bp):
CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTA
Found at i:10644 original size:15 final size:16
Alignment explanation
Indices: 10624--10653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10614 TCATACTTGC
10624 TTTTTTTCTT-AATTT
1 TTTTTTTCTTGAATTT
10639 TTTTTTTCTTGAATT
1 TTTTTTTCTTGAATT
10654 ACATGACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTTGAATTT
Found at i:11386 original size:38 final size:37
Alignment explanation
Indices: 11331--11405 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
11321 GTTAGTCTTT
*
11331 TATAAACCACAACAAAGCACAATGGACCAACAACCAG
1 TATAAACCACAACAAAGCACAACGGACCAACAACCAG
11368 TATACAACCACAACAAAGCACAACGGACCAACAACCAG
1 TATA-AACCACAACAAAGCACAACGGACCAACAACCAG
11406 CAACTGTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.51, C:0.32, G:0.11, T:0.07
Consensus pattern (37 bp):
TATAAACCACAACAAAGCACAACGGACCAACAACCAG
Found at i:11407 original size:20 final size:20
Alignment explanation
Indices: 11346--11407 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
11336 ACCACAACAA
*
11346 AGCACAATGGACCAACAACC
1 AGCACAACGGACCAACAACC
* *
11366 AGTATACAAC-CA-CAACAA--
1 AG--CACAACGGACCAACAACC
11384 AGCACAACGGACCAACAACC
1 AGCACAACGGACCAACAACC
11404 AGCA
1 AGCA
11408 ACTGTTGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
16 5 0.16
17 1 0.03
18 8 0.26
20 12 0.39
21 1 0.03
22 4 0.13
ACGTcount: A:0.48, C:0.34, G:0.13, T:0.05
Consensus pattern (20 bp):
AGCACAACGGACCAACAACC
Found at i:18518 original size:18 final size:17
Alignment explanation
Indices: 18482--18522 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
18472 TTTTTGAAAG
18482 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
18499 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
18514 ATAATTTTA
1 ATAATTTTA
18523 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 12 0.55
17 4 0.18
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:23658 original size:6 final size:6
Alignment explanation
Indices: 23647--23721 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
23637 TGATTCAATA
23647 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
23695 TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TAT
23722 GTTTTCTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:26687 original size:16 final size:18
Alignment explanation
Indices: 26661--26695 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
26651 ATTACCTATG
26661 TTTATATAAAAAAT-ATA
1 TTTATATAAAAAATCATA
26678 TTTA-ATAAAAAATCATA
1 TTTATATAAAAAATCATA
26695 T
1 T
26696 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTATATAAAAAATCATA
Found at i:33375 original size:2 final size:2
Alignment explanation
Indices: 33368--33402 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33358 CTAGTAAGAT
33368 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
33403 TCATTATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:33821 original size:2 final size:2
Alignment explanation
Indices: 33816--33843 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33806 ACATGCATAC
33816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33844 TAAGAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35483 original size:21 final size:23
Alignment explanation
Indices: 35459--35500 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35449 TTATTTCAAC
35459 AAAATAT-TT-AAATTTTATATA
1 AAAATATATTCAAATTTTATATA
*
35480 AAAATATATTCAGATTTTATA
1 AAAATATATTCAAATTTTATA
35501 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAATATATTCAAATTTTATATA
Found at i:35518 original size:13 final size:13
Alignment explanation
Indices: 35502--35527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35492 GATTTTATAA
35502 AATAAAAATAATT
1 AATAAAAATAATT
35515 AATAAAAATAATT
1 AATAAAAATAATT
35528 TACATTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAAAATAATT
Found at i:41956 original size:22 final size:23
Alignment explanation
Indices: 41914--41956 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41904 TGTTAAAGAT
* *
41914 TAATTTTGATATTATGCTTTTTC
1 TAATTTTAATAATATGCTTTTTC
41937 TAATTTTAATAAT-TGCTTTT
1 TAATTTTAATAATATGCTTTT
41957 CAAAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (23 bp):
TAATTTTAATAATATGCTTTTTC
Found at i:42479 original size:16 final size:16
Alignment explanation
Indices: 42452--42496 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
42442 AAATTTAGCA
42452 ATCATAT-T-ATATAT
1 ATCATATATAATATAT
42466 ATCATATATAATATAAT
1 ATCATATATAATAT-AT
*
42483 AT-ATAAATAATATA
1 ATCATATATAATATA
42497 ATAAGCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 2 0.07
16 14 0.52
17 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
ATCATATATAATATAT
Found at i:42497 original size:16 final size:17
Alignment explanation
Indices: 42459--42499 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
42449 GCAATCATAT
*
42459 TATATATATCATATATAA
1 TATA-ATATCATAAATAA
42477 TATAATAT-ATAAATAA
1 TATAATATCATAAATAA
42493 TATAATA
1 TATAATA
42500 AGCTACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
17 4 0.18
18 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATATCATAAATAA
Found at i:42500 original size:12 final size:12
Alignment explanation
Indices: 42459--42496 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
42449 GCAATCATAT
*
42459 TATAT-ATATCA
1 TATATAATATAA
42470 TATATAATATAA
1 TATATAATATAA
42482 TATATAA-ATAA
1 TATATAATATAA
42493 TATA
1 TATA
42497 ATAAGCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATAATATAA
Found at i:56773 original size:2 final size:2
Alignment explanation
Indices: 56768--56803 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
56758 GTGTGTATGT
*
56768 GA GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
56804 AGCTCACAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:64195 original size:3 final size:3
Alignment explanation
Indices: 64182--64216 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
64172 ATTTTTCTAA
*
64182 AAT AA- AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
64217 TCAACAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:70643 original size:20 final size:20
Alignment explanation
Indices: 70620--70665 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
70610 AATTTAAAGT
*
70620 AAATGACAAAAAAGGAAACA
1 AAATAACAAAAAAGGAAACA
70640 AAATAACAAAAAAGGAAACA
1 AAATAACAAAAAAGGAAACA
*
70660 ACATAA
1 AAATAA
70666 TTTCTTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.07
Consensus pattern (20 bp):
AAATAACAAAAAAGGAAACA
Found at i:74828 original size:12 final size:10
Alignment explanation
Indices: 74822--74880 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
74812 TTTTTGGTTG
74822 TTTTTTTTGTT
1 TTTTTTTTG-T
74833 TTTGTTTTTGT
1 TTT-TTTTTGT
*
74844 TTTTTTATGT
1 TTTTTTTTGT
74854 TTTTGTTTT-T
1 TTTT-TTTTGT
*
74864 GTTTTTTTGT
1 TTTTTTTTGT
*
74874 TTGTTTT
1 TTTTTTT
74881 GATAACACGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 4 0.10
10 20 0.50
11 10 0.25
12 6 0.15
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:74836 original size:6 final size:6
Alignment explanation
Indices: 74812--74880 Score: 74
Period size: 6 Copynumber: 11.7 Consensus size: 6
74802 TCTTCTCTCT
*
74812 TTTTTGG TTGTTT- TTTTTG TTTTTG TTTTTG -TTTT- TTTATG TTTTTG
1 TTTTT-G TT-TTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
74859 TTTTTG TTTTT- TTGTTTG TTTT
1 TTTTTG TTTTTG TT-TTTG TTTT
74881 GATAACACGT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
5 12 0.22
6 35 0.65
7 4 0.07
8 3 0.06
ACGTcount: A:0.01, C:0.00, G:0.16, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:74854 original size:22 final size:21
Alignment explanation
Indices: 74819--74875 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
74809 TCTTTTTTGG
74819 TTGTTTTTTTTGTTTTTGTTT
1 TTGTTTTTTTTGTTTTTGTTT
74840 TTGTTTTTTTATGTTTTTGTTT
1 TTGTTTTTTT-TGTTTTTGTTT
74862 TTG-TTTTTTTGTTT
1 TTGTTTTTTTTGTTT
74876 GTTTTGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.14
21 16 0.46
22 14 0.40
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (21 bp):
TTGTTTTTTTTGTTTTTGTTT
Done.