Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003960.1 Kokia drynarioides strain JFW-HI SEQ_117051, 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: 52977
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 154 characters in sequence are not A, C, G, or T
Found at i:1370 original size:150 final size:149
Alignment explanation
Indices: 1105--1379 Score: 453
Period size: 150 Copynumber: 1.8 Consensus size: 149
1095 TCAAGCCTAC
* *
1105 GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCTTGATGAAACACTGAGAAGTAGGTGGAGCT
1 GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCCTGATGAAACACTGAGAAGCAGGTGGAGCT
*
1170 AAAAGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGACACTG
66 AAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGACACTG
1235 AGGAGAAGACCCAAGCGAG
131 AGGAGAAGACCCAAGCGAG
** *
1254 GCTCAAAGTGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAAACACTGAGAAGCAGGTGGGAGC
1 GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCCTGATGAAACACTGAGAAGCAGGT-GGAGC
* *
1319 TAAAAGGTTAGCTTCCTGATGAGATA-TAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
65 TAAAAGGTTAGCTTCCTGATGAGATACT-GAGAAGTGAACCAAATCCATCTTCCTGATGAGA
1380 TACAGAGAAG
Statistics
Matches: 116, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
149 55 0.47
150 61 0.53
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (149 bp):
GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCCTGATGAAACACTGAGAAGCAGGTGGAGCT
AAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGACACTG
AGGAGAAGACCCAAGCGAG
Found at i:1526 original size:126 final size:128
Alignment explanation
Indices: 1285--1517 Score: 366
Period size: 126 Copynumber: 1.8 Consensus size: 128
1275 TGAACCCCAG
* *
1285 CTTCCTGATGAAACACTGAGAAGCAGGTGGGAGCTAAAAGGTTAGCTTCCTGATGAGATATAGAG
1 CTTCCTGATGAAACACTGAGAAGCAGGAGGAAGCT-AAA-GTTAGCTTCCTGATGAGATATAGAG
1350 AAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAGTGAAACGATGATGGGACCAT
64 AAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAGTGAAACGATGATGGGACCAT
*
1415 CTTCCTGATGAGACACTGAGAAGCAGGAGGAAGCT-AA-TTAGCTTCCTGATGAGATACT-GAGA
1 CTTCCTGATGAAACACTGAGAAGCAGGAGGAAGCTAAAGTTAGCTTCCTGATGAGATA-TAGAGA
*
1477 AGTGAACCAAATTTGTCTTCCTGAT-AGGATACAGAGAAGCG
65 AGTGAACCAAATTCGTCTTCCTGATGA-GATACAGAGAAGCG
1518 GATCGAAACA
Statistics
Matches: 97, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
125 1 0.01
126 61 0.63
127 1 0.01
128 2 0.02
130 32 0.33
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (128 bp):
CTTCCTGATGAAACACTGAGAAGCAGGAGGAAGCTAAAGTTAGCTTCCTGATGAGATATAGAGAA
GTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAGTGAAACGATGATGGGACCAT
Found at i:2999 original size:18 final size:19
Alignment explanation
Indices: 2965--3006 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
2955 AAAACGTTTC
*
2965 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
2984 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
3002 AATAA
1 AATAA
3007 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:3220 original size:7 final size:7
Alignment explanation
Indices: 3197--3231 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3187 ATATTAATGA
3197 TAATAAT
1 TAATAAT
3204 ATAATAAT
1 -TAATAAT
*
3212 TATTAAT
1 TAATAAT
3219 TAATAAT
1 TAATAAT
3226 TAATAA
1 TAATAA
3232 AAAAGGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATAAT
Found at i:4428 original size:59 final size:58
Alignment explanation
Indices: 4337--4796 Score: 593
Period size: 59 Copynumber: 7.8 Consensus size: 58
4327 TTAAACTTTC
* ** *
4337 CAAAAATTACCTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACTCT
1 CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
* * ** *
4395 CAAAAAATTACTATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTCAACCTCGAACTCT
1 C-AAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
** * *
4454 CAAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCAAACTCT
1 C-AAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
**
4513 CCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCTAAACTCT
1 -CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
* ** *
4572 CTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTTACCCTAAACTTT
1 C-AAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
*
4631 CCAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCCGAAC-CTT
1 CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGA-CCCCGAACTC-T
* * *
4690 CTAAAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTAACCCCGAACCTTT
1 C-AAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAA-CTCT
*
4750 CAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGA
4797 TTCCAAACCT
Statistics
Matches: 362, Mismatches: 29, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
58 53 0.15
59 259 0.72
60 50 0.14
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.31
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACTCT
Found at i:6113 original size:126 final size:127
Alignment explanation
Indices: 5886--6126 Score: 306
Period size: 126 Copynumber: 1.9 Consensus size: 127
5876 TAAGTGCAAA
* ** * * *
5886 CAAGCTGTCGTTTGGTTTGAGGATCCACAATCCCTCGCAAATAAAAGCTGTCATAGAAATTTGTG
1 CAAGCTGTCGTATGGTTTGAAAATCCACAACCCCTCGCAAATAAAAGCTGTCAAAGAAATTCGTG
* * *
5951 GATGATTCATTCGTTTAGTCGTAGTTGGAATTTGCTAAGCTATGAGTACATAAAGGGTGCAG
66 GATGATTCATTCGTATAGTCGCAGTTGGAATATGCTAAGCTATGAGTACATAAAGGGTGCAG
* * *
6013 CAAGCTGTCGTATGG-TTGAAAATCCACAACCCCTCGCAGATAAAAGTTGTTAAAGGAAA-TCGT
1 CAAGCTGTCGTATGGTTTGAAAATCCACAACCCCTCGCAAATAAAAGCTGTCAAA-GAAATTCGT
* * * * *
6076 GGATGCTTCGTTCGTATAGTTGCAGTTGGAATATGCTAAGCTGTGGGTACA
65 GGATGATTCATTCGTATAGTCGCAGTTGGAATATGCTAAGCTATGAGTACA
6127 CAACGAACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
126 78 0.81
127 18 0.19
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (127 bp):
CAAGCTGTCGTATGGTTTGAAAATCCACAACCCCTCGCAAATAAAAGCTGTCAAAGAAATTCGTG
GATGATTCATTCGTATAGTCGCAGTTGGAATATGCTAAGCTATGAGTACATAAAGGGTGCAG
Found at i:7094 original size:18 final size:19
Alignment explanation
Indices: 7062--7098 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
7052 GATTAAATAA
*
7062 TTTTTTTTATTCTTTAAAG
1 TTTTTTTTATACTTTAAAG
7081 TTTTTTTTA-ACTTTAAAG
1 TTTTTTTTATACTTTAAAG
7099 AATCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTTTTATACTTTAAAG
Found at i:13111 original size:30 final size:30
Alignment explanation
Indices: 13060--13120 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
13050 TTAATATCTA
*
13060 AATTATTTAAAAAATTTTATTTAAGTCATTG
1 AATTATTTAAAAAA-TATATTTAAGTCATTG
13091 AATTATTTTAAAAAA-ATATTTAAGTCATTG
1 AATTA-TTTAAAAAATATATTTAAGTCATTG
13121 GGTTGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 14 0.50
31 5 0.18
32 9 0.32
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (30 bp):
AATTATTTAAAAAATATATTTAAGTCATTG
Found at i:21391 original size:70 final size:70
Alignment explanation
Indices: 21278--21414 Score: 238
Period size: 70 Copynumber: 2.0 Consensus size: 70
21268 AAAAAATATA
* * * *
21278 ATTTTGCTTAGTTCTATTTTTATTTCTCTGTTTTTGGTTTATACAAATATTTCTAAGATCTTTTC
1 ATTTTGCTTAGTTCTATTTCTATTCCTCTGTTTCTGGTTTATACAAATATTTCTAAGAGCTTTTC
21343 ATGGT
66 ATGGT
21348 ATTTTGCTTAGTTCTATTTCTATTCCTCTGTTTCTGGTTTATACAAATATTTCTAAGAGCTTTTC
1 ATTTTGCTTAGTTCTATTTCTATTCCTCTGTTTCTGGTTTATACAAATATTTCTAAGAGCTTTTC
21413 AT
66 AT
21415 AAATGTATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (70 bp):
ATTTTGCTTAGTTCTATTTCTATTCCTCTGTTTCTGGTTTATACAAATATTTCTAAGAGCTTTTC
ATGGT
Found at i:21505 original size:5 final size:5
Alignment explanation
Indices: 21495--21520 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21485 AGGCTGCAGT
21495 TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG T
21521 ACTTCAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:21557 original size:29 final size:30
Alignment explanation
Indices: 21516--21586 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 30
21506 TTTGTTTTGT
* *
21516 TTTGTACTTCAATACCC-TGAATTTTAGTA
1 TTTGAACTGCAATACCCATGAATTTTAGTA
21545 TTTGAACTGCAATACCCAAAGTTGAATTTTAGTA
1 TTTGAACTGCAATACCC--A--TGAATTTTAGTA
21579 TTTGAACT
1 TTTGAACT
21587 AGCAGCTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 15 0.43
34 20 0.57
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTGAACTGCAATACCCATGAATTTTAGTA
Found at i:37560 original size:56 final size:57
Alignment explanation
Indices: 37493--37601 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
37483 TTAATAGTCA
* *
37493 CCCAACAATTAG-TGATTTTTTTTGTCAT-TCAATTAT-AAAAAGTTACAAAATGGCCT
1 CCCAACAATTAGTTGATTTTTTTTATCATCT-AACTATGAAAAA-TTACAAAATGGCCT
* **
37549 CCCAACTATTAGTTTTTTTTTTTTATCATCTAACTATGAAAAATTACAAAATG
1 CCCAACAATTAGTTGATTTTTTTTATCATCTAACTATGAAAAATTACAAAATG
37602 ATCACTCAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 11 0.24
57 28 0.62
58 6 0.13
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (57 bp):
CCCAACAATTAGTTGATTTTTTTTATCATCTAACTATGAAAAATTACAAAATGGCCT
Found at i:39059 original size:12 final size:13
Alignment explanation
Indices: 39042--39072 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
39032 GATATCCAAG
39042 TTTTTATTAT-TA
1 TTTTTATTATATA
39054 TTTTTATTATATA
1 TTTTTATTATATA
39067 TTTTTA
1 TTTTTA
39073 AATGGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTATATA
Found at i:40197 original size:18 final size:19
Alignment explanation
Indices: 40174--40212 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40164 TAATTCAATC
* *
40174 ATTAAAATATTTATT-TAA
1 ATTAAAAAATATATTATAA
40192 ATTAAAAAATATATTATAA
1 ATTAAAAAATATATTATAA
40211 AT
1 AT
40213 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAAAAATATATTATAA
Found at i:40514 original size:24 final size:24
Alignment explanation
Indices: 40487--40537 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
40477 TTGTCGTTTT
40487 TTGAA-ATTTCTTTATTGGTCCCCA
1 TTGAATATTTCTTTATTGGT-CCCA
*
40511 TTGAATTTTTCTTTATTGGTCCCA
1 TTGAATATTTCTTTATTGGTCCCA
40535 TTG
1 TTG
40538 TTAGCCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.51
Consensus pattern (24 bp):
TTGAATATTTCTTTATTGGTCCCA
Found at i:47398 original size:29 final size:30
Alignment explanation
Indices: 47343--47401 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
47333 CATAGTTCCT
*
47343 TATGCTCTTTATAATTTTGAAATTTAGTCTC
1 TATGCTCTTTAT-ATTTTAAAATTTAGTCTC
47374 TATGCT-TTTAT-TTTTAAAATTTTAGTCT
1 TATGCTCTTTATATTTTAAAA-TTTAGTCT
47402 TTTTACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
30 5 0.19
31 6 0.23
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.56
Consensus pattern (30 bp):
TATGCTCTTTATATTTTAAAATTTAGTCTC
Found at i:48128 original size:15 final size:15
Alignment explanation
Indices: 48110--48138 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48100 ATTTTTTTAT
48110 AATTAATATTTTAAC
1 AATTAATATTTTAAC
48125 AATTAATATTTTAA
1 AATTAATATTTTAA
48139 ATACTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATATTTTAAC
Found at i:50660 original size:27 final size:25
Alignment explanation
Indices: 50620--50676 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
50610 GTTGTTATTA
**
50620 TTATTATTTTTTATAATAAAAAAGTTG
1 TTATTATTGATTATAA-AAAAAA-TTG
*
50647 TTATTATTGATTATGAAAAAAATTG
1 TTATTATTGATTATAAAAAAAATTG
50672 TTATT
1 TTATT
50677 TTTGGAGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 8 0.30
26 6 0.22
27 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (25 bp):
TTATTATTGATTATAAAAAAAATTG
Done.