Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013671.1 Kokia drynarioides strain JFW-HI SEQ_128699, 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: 13403
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:1186 original size:29 final size:29
Alignment explanation
Indices: 1152--1579 Score: 214
Period size: 29 Copynumber: 14.6 Consensus size: 29
1142 TAAACTGTCC
*
1152 AAAAATTACCATTTTATCCTCGAACTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCT
*
1181 AAAAA-TCCCATTTTAACCC-CGAAACTTCCT
1 AAAAATTACCATTTT-ACCCTCG-AACTT-CT
* *
1211 -ATAATTACCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCT
*
1239 AAAAA-TCCCATTTTTTA-CCTCGAAACTTCT
1 AAAAATTACCA--TTTTACCCTCG-AACTTCT
*
1269 TAAAATTACCATTTTACCCCTC-AACATTC-
1 AAAAATTACCATTTTA-CCCTCGAAC-TTCT
* * *
1298 AAAAA-TCCCGTTTTTGACCCT-GAAACTTCC
1 AAAAATTACC-ATTTT-ACCCTCG-AACTTCT
* *
1328 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCT
* * *
1357 AAAAATT-CTATTTTAACCTCGAACCTTTT
1 AAAAATTACCATTTTACCCTCGAA-CTTCT
* * * *
1386 AAAAATTACCATTTTACCCCCAAACTCCC
1 AAAAATTACCATTTTACCCTCGAACTTCT
*
1415 AAAAA-T-CCTATTTTTGACCC-CAAAACTTCT
1 AAAAATTACC-A-TTTT-ACCCTC-GAACTTCT
* * *
1445 AAAAATTACCATTTTGCCC-CTAAAC-TCAC
1 AAAAATTACCATTTTACCCTC-GAACTTC-T
*
1474 AAAAATCTTA--TTTTTGA-CCTCGAAACATT-T
1 AAAAA--TTACCATTTT-ACCCTCG-AAC-TTCT
*
1504 AAAAATTACCATTTTACCCTCAAACTTC-
1 AAAAATTACCATTTTACCCTCGAACTTCT
* * * *
1532 AAAAAATCCCATTTTTGACCC-CGAAACATCC
1 AAAAATTACCA-TTTT-ACCCTCG-AACTTCT
*
1563 AAAAATTACTATTTTAC
1 AAAAATTACCATTTTAC
1580 TCCCGAATGT
Statistics
Matches: 309, Mismatches: 46, Indels: 88
0.70 0.10 0.20
Matches are distributed among these distances:
27 2 0.01
28 49 0.16
29 126 0.41
30 105 0.34
31 24 0.08
32 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAACTTCT
Found at i:1287 original size:59 final size:59
Alignment explanation
Indices: 1143--1579 Score: 458
Period size: 59 Copynumber: 7.4 Consensus size: 59
1133 GGAGGTCCCT
* * * * *
1143 AAACTGTCCAAAAATTACCATTTTATCCTCGAACTTCTAAAAATCCCA-TTTTAACCCCG
1 AAACT-TCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
1202 AAACTTCCT-ATAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCTCG
1 AAACTT-CTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
1261 AAACTTCTTAAAATTACCATTTTACCCCTC-AACATT-CAAAAATCCCGTTTTTGACCCTG
1 AAACTTCTAAAAATTACCATTTTA-CCCTCAAAC-TTCCAAAAATCCCATTTTTGACCCCG
* * * * * * *
1320 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCTA-TTTTAACCTCG
1 AAACTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * *
1378 AACCTTTTAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTTTGACCCCA
1 AAACTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* ** *
1437 AAACTTCTAAAAATTACCATTTTGCCC-CTAAAC-TCACAAAAATCTTATTTTTGACCTCG
1 AAACTTCTAAAAATTACCATTTTACCCTC-AAACTTC-CAAAAATCCCATTTTTGACCCCG
*
1496 AAACATT-TAAAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCG
1 AAAC-TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
1555 AAACATCCAAAAATTACTATTTTAC
1 AAACTTCTAAAAATTACCATTTTAC
1580 TCCCGAATGT
Statistics
Matches: 320, Mismatches: 44, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
58 96 0.30
59 212 0.66
60 12 0.04
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:1352 original size:118 final size:117
Alignment explanation
Indices: 1153--1586 Score: 527
Period size: 118 Copynumber: 3.7 Consensus size: 117
1143 AAACTGTCCA
* * * * * *
1153 AAAATTACCATTTTATCCTCGAACTTCTAAAAATCCCA-TTTTAACCCCGAAACTTCCTATAATT
1 AAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATT
* * *
1217 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCTT
66 ACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTAACCTCGAAACTT-TT
* *
1270 AAAATTACCATTTTACCCCTC-AACATTC-AAAAATCCCGTTTTTGACCCTGAAACTTCCAAAAA
1 AAAATTACCATTTTA-CCCTCAAAC-TTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAA
* *
1333 TTACCATTTTACCCCCGAACTTCCAAAAATTCTA-TTTTAACCTCGAACCTTTT
64 TTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTAACCTCGAAACTTTT
* * * * * *
1386 AAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTTTGACCCCAAAACTTCTAAAAAT
1 -AAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAT
* ** * * *
1451 TACCATTTTGCCCCTAAAC-TCACAAAAATCTTATTTTTGACCTCGAAACATTTA
65 TACCATTTTACCCCCGAACTTC-CAAAAATCCTATTTTTAACCTCGAAAC-TTTT
*
1505 AAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAAACATCCAAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATT
* *
1570 ACTATTTTACTCCCGAA
66 ACCATTTTACCCCCGAA
1587 TGTCCGAAGA
Statistics
Matches: 270, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
116 10 0.04
117 116 0.43
118 141 0.52
119 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (117 bp):
AAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATT
ACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTAACCTCGAAACTTTT
Found at i:1443 original size:176 final size:176
Alignment explanation
Indices: 1139--1579 Score: 523
Period size: 176 Copynumber: 2.5 Consensus size: 176
1129 CCTCGGAGGT
* *
1139 CCCT-AAACTGTCCAAAAATTACCATTTTATCCTCGAACTTCTAAAAATCCCATTTTAACCCCGA
1 CCCTGAAACT-TCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTAACCCCGA
* * * * * * *
1203 AACTTCCTATAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTC
65 AACTTCCTAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTC
* * * *
1268 TTAAAATTACCATTTTACCCCTCAACAT-TCAAAAATCCCGTTTTTGA
130 TAAAAATTACCATTTTACCCCTAAAC-TCACAAAAATCCCATTTTTGA
* * * * *
1315 CCCTGAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCTATTTTAACCTCGAA
1 CCCTGAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTAACCCCGAA
* * *
1380 CCTT-TTAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTTTGACCCCAAAACTTC
66 ACTTCCT-AAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTC
* **
1444 TAAAAATTACCATTTTGCCCCTAAACTCACAAAAATCTTATTTTTGA
130 TAAAAATTACCATTTTACCCCTAAACTCACAAAAATCCCATTTTTGA
* * *
1491 -CCTCGAAACATT-TAAAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTGACCCC
1 CCCT-GAAAC-TTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCA-TTTTAACCCC
* * *
1554 GAAACATCCAAAAATTACTATTTTAC
63 GAAACTTCCTAAAATTACCATTTTAC
1580 TCCCGAATGT
Statistics
Matches: 222, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
175 5 0.02
176 182 0.82
177 35 0.16
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (176 bp):
CCCTGAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTAACCCCGAA
ACTTCCTAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCT
AAAAATTACCATTTTACCCCTAAACTCACAAAAATCCCATTTTTGA
Found at i:7171 original size:12 final size:12
Alignment explanation
Indices: 7156--7182 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7146 TCCAAACAAT
7156 AAAAATAACAGC
1 AAAAATAACAGC
7168 AAAAATAACAGC
1 AAAAATAACAGC
7180 AAA
1 AAA
7183 CAACGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAACAGC
Found at i:7237 original size:24 final size:24
Alignment explanation
Indices: 7196--7262 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
7186 CGTTAAAAAT
** *
7196 AACAAAAATAGCAACAAAAGCAAC
1 AACAAAAATAATAACAAAAACAAC
*
7220 AACAAAAATAATAGCAAAAACAAC
1 AACAAAAATAATAACAAAAACAAC
*
7244 -ACGAAAATAATAATCAAAA
1 AACAAAAATAATAA-CAAAA
7263 CAGTAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.09
Consensus pattern (24 bp):
AACAAAAATAATAACAAAAACAAC
Found at i:8827 original size:5 final size:5
Alignment explanation
Indices: 8817--8841 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8807 ATCTTTTCGT
8817 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
8842 TTTGAGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:10922 original size:18 final size:17
Alignment explanation
Indices: 10899--10937 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
10889 TGTGGATAAT
10899 ATAATAATATGCGAAAAG
1 ATAATAA-ATGCGAAAAG
*
10917 ATAATAAGTGCGAAAAG
1 ATAATAAATGCGAAAAG
10934 ATAA
1 ATAA
10938 AAAAAATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (17 bp):
ATAATAAATGCGAAAAG
Found at i:11709 original size:96 final size:96
Alignment explanation
Indices: 11535--11726 Score: 250
Period size: 96 Copynumber: 2.0 Consensus size: 96
11525 ATTTTTGCAA
** *
11535 AAGGATATTCGATTTTCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTTTCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
11600 GAATCGAAGATAAACA-AACATTGCCTCGATT
66 GAATCGAAGATAAA-AGAACATTGCCTCGATT
* *
11631 AAGGGTATTCGATTATT-TCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATT-TTCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
11694 C-GAAACTCGAA-ATAAAAGAATATTGCCTCGATT
64 CAG-AA-TCGAAGATAAAAGAACATTGCCTCGATT
11727 TTTTTAAAGC
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
95 3 0.04
96 75 0.88
97 7 0.08
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTTTCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTGCCTCGATT
Found at i:12111 original size:29 final size:29
Alignment explanation
Indices: 12078--12281 Score: 161
Period size: 29 Copynumber: 7.0 Consensus size: 29
12068 CGGACATCCG
12078 GGGGT-AAAAGGGTAATTTTTGGAAGTTTC
1 GGGGTAAAAAGGG-AATTTTTGGAAGTTTC
12107 GGGGTCAAAAATGGG-ATTTTTGGAAG-TTC
1 GGGGT-AAAAA-GGGAATTTTTGGAAGTTTC
* *
12136 GCGGGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAAGGGAATTTTTGGAAGTTTC
** *
12166 GGGGTTAAAAA-TTAGATTTTTGGAAGTTTT
1 GGGG-TAAAAAGGGA-ATTTTTGGAAGTTTC
* *
12196 GGGGTAAAAATGGAATTTTTGAAAGTTTC
1 GGGGTAAAAAGGGAATTTTTGGAAGTTTC
* ** *
12225 GAGGTAAAAAATGAGATTATTGGAAG-TTC
1 GGGGTAAAAAGGGA-ATTTTTGGAAGTTTC
* *
12254 -GAG-AGAAAATGGAATTTTTGGACAGTTT
1 GGGGTA-AAAAGGGAATTTTTGGA-AGTTT
12282 AGGGACCTCT
Statistics
Matches: 144, Mismatches: 18, Indels: 26
0.77 0.10 0.14
Matches are distributed among these distances:
27 9 0.06
28 11 0.08
29 64 0.44
30 53 0.37
31 4 0.03
32 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAAGGGAATTTTTGGAAGTTTC
Found at i:12144 original size:59 final size:58
Alignment explanation
Indices: 12078--12281 Score: 243
Period size: 59 Copynumber: 3.5 Consensus size: 58
12068 CGGACATCCG
* * *
12078 GGGGT-AAAAGGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGTAAAAAATGAGATTTTTGGAAGTTC
* * * *
12136 GCGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATTAGATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATGAGATTTTTGGAAG-TTC
* * *
12196 GGGGTAAAAATGGAATTTTTGAAAGTTTCGAGGTAAAAAATGAGATTATTGGAAGTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATGAGATTTTTGGAAGTTC
*
12254 -GAG-AGAAAATGGAATTTTTGGACAGTTT
1 GGGGTA-AAAATGGAATTTTTGGA-AGTTT
12282 AGGGACCTCT
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 18 0.14
58 8 0.06
59 90 0.71
60 9 0.07
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATGAGATTTTTGGAAGTTC
Done.