Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014465.1 Kokia drynarioides strain JFW-HI SEQ_129504, 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: 45893
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:579 original size:21 final size:21
Alignment explanation
Indices: 554--606 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
544 ACGGTTTCAA
*
554 ATTTAGGGTTTTAAATTTAAGG
1 ATTTAAGGTTTTAAATTT-AGG
576 -TTTAAGGTTTTAAATTTAGG
1 ATTTAAGGTTTTAAATTTAGG
*
596 ATTTATGGTTT
1 ATTTAAGGTTT
607 ATGGTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (21 bp):
ATTTAAGGTTTTAAATTTAGG
Found at i:581 original size:7 final size:7
Alignment explanation
Indices: 569--672 Score: 63
Period size: 7 Copynumber: 14.6 Consensus size: 7
559 GGGTTTTAAA
569 TTTAAGG
1 TTTAAGG
576 TTTAAGG
1 TTTAAGG
*
583 TTTTAA-A
1 -TTTAAGG
590 TTT-AGG
1 TTTAAGG
*
596 ATTTATGG
1 -TTTAAGG
*
604 TTTATGG
1 TTTAAGG
611 TTTAAGG
1 TTTAAGG
*
618 ATTTATGG
1 -TTTAAGG
*
626 TTTATGG
1 TTTAAGG
633 TTTAAGG
1 TTTAAGG
640 TTTGATA-G
1 TTT-A-AGG
648 TTT-AGG
1 TTTAAGG
*
654 ATTTATGG
1 -TTTAAGG
*
662 TTTAGGG
1 TTTAAGG
669 TTTA
1 TTTA
673 TAAGTATGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
5 2 0.03
6 4 0.05
7 52 0.66
8 20 0.25
9 1 0.01
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:613 original size:35 final size:35
Alignment explanation
Indices: 526--622 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 35
516 AAGGTTTCCA
* * *
526 ATTTAAGG-TTATGGGTTTACGGTTTCAAATTTAGG
1 ATTTATGGTTTAT-GGTTTAAGGTTTTAAATTTAGG
* ** *
561 GTTT-TAAATTTAAGGTTTAAGGTTTTAAATTTAGG
1 ATTTAT-GGTTTATGGTTTAAGGTTTTAAATTTAGG
*
596 ATTTATGGTTTATGGTTTAAGGATTTA
1 ATTTATGGTTTATGGTTTAAGGTTTTA
623 TGGTTTATGG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
35 43 0.91
36 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (35 bp):
ATTTATGGTTTATGGTTTAAGGTTTTAAATTTAGG
Found at i:621 original size:22 final size:21
Alignment explanation
Indices: 597--673 Score: 93
Period size: 22 Copynumber: 3.6 Consensus size: 21
587 AAATTTAGGA
597 TTTATGGTTTATGGTTTAAGG
1 TTTATGGTTTATGGTTTAAGG
618 ATTTATGGTTTATGGTTTAAGG
1 -TTTATGGTTTATGGTTTAAGG
* *
640 TTTGATAGTTTA-GGATTTATGG
1 TTT-ATGGTTTATGG-TTTAAGG
*
662 TTTAGGGTTTAT
1 TTTATGGTTTAT
674 AAGTATGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.23
22 37 0.77
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTTATGGTTTATGGTTTAAGG
Found at i:631 original size:29 final size:29
Alignment explanation
Indices: 568--674 Score: 123
Period size: 29 Copynumber: 3.7 Consensus size: 29
558 AGGGTTTTAA
* *
568 ATTTAAGGTTTAAGGTTT-TAAATTTAGG
1 ATTTATGGTTTAAGGTTTATAGATTTAGG
*
596 ATTTATGGTTTATGGTTTA-AGGATTTATGG
1 ATTTATGGTTTAAGGTTTATA-GATTTA-GG
626 -TTTATGGTTTAAGGTTTGATAG-TTTAGG
1 ATTTATGGTTTAAGGTTT-ATAGATTTAGG
*
654 ATTTATGGTTTAGGGTTTATA
1 ATTTATGGTTTAAGGTTTATA
675 AGTATGAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
28 22 0.32
29 41 0.60
30 4 0.06
31 1 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (29 bp):
ATTTATGGTTTAAGGTTTATAGATTTAGG
Found at i:1264 original size:136 final size:138
Alignment explanation
Indices: 999--1276 Score: 499
Period size: 136 Copynumber: 2.0 Consensus size: 138
989 TAGGCATATG
999 TGACGATCCTGCAAAATCTAGACGATAAGAATCATTGTCATCCAATGCCTCTTCCTCTTCCTCTT
1 TGACGATCCTGCAAAATCTAGACGATAAGAATCATTGTCATCCAATGCCTCTTCCTCTT-CTC-T
1064 GCTCTTGCTCTGGCTTTGGCTTTAGGGCAGGAGCTACATGATAAGGGTGACCTTGTTGAGACGTG
64 -CTCTTGCTCTGGCTTTGGCTTTAGGGCAGGAGCTACATGATAAGGGTGACCTTGTTGAGACGTG
1129 TGGGGGAATTA
128 TGGGGGAATTA
1140 TNGACGATCCTGCAAAATCTAGACGATAAGAATCATTGTCATCCAATGCCTCTTCCTC-T-TC-C
1 T-GACGATCCTGCAAAATCTAGACGATAAGAATCATTGTCATCCAATGCCTCTTCCTCTTCTCTC
1202 TCTTGCTCTGGCTTTGGCTTTAGGGCAGGAGCTACATGATAAGGGTGACCTTGTTGAGACGTGTG
65 TCTTGCTCTGGCTTTGGCTTTAGGGCAGGAGCTACATGATAAGGGTGACCTTGTTGAGACGTGTG
1267 GGGGAATTA
130 GGGGAATTA
1276 T
1 T
1277 CGTTGATTGT
Statistics
Matches: 136, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
136 76 0.56
139 2 0.01
141 2 0.01
142 56 0.41
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (138 bp):
TGACGATCCTGCAAAATCTAGACGATAAGAATCATTGTCATCCAATGCCTCTTCCTCTTCTCTCT
CTTGCTCTGGCTTTGGCTTTAGGGCAGGAGCTACATGATAAGGGTGACCTTGTTGAGACGTGTGG
GGGAATTA
Found at i:2546 original size:84 final size:83
Alignment explanation
Indices: 2405--2571 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 83
2395 ACGCCGGTGA
*
2405 CCGGTAGACCATTGATTGGGAGCCCGAGTTGGAGCGCAATATCCTCCAATGTCACAGTGCACTCC
1 CCGGTAGACCATTGATTGGGAGCCCGAGTTGGAGCGCAACATCCTCCAATGTCACAGTGCACTCC
*
2470 CCACAAGGCAGATGAAAT
66 CCACAAGGAAGATGAAAT
2488 NCCGGTAGACCATTGATTGGGAGCCCGAGTTGGAGCGCAACATCCTCCAATGTCACAGTGCACTC
1 -CCGGTAGACCATTGATTGGGAGCCCGAGTTGGAGCGCAACATCCTCCAATGTCACAGTGCACTC
2553 CCCACAAGGAAGATGAAAT
65 CCCACAAGGAAGATGAAAT
2572 GTGTGGGTCT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (83 bp):
CCGGTAGACCATTGATTGGGAGCCCGAGTTGGAGCGCAACATCCTCCAATGTCACAGTGCACTCC
CCACAAGGAAGATGAAAT
Found at i:3114 original size:29 final size:29
Alignment explanation
Indices: 3023--3116 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
3013 CCAAAATAGA
*
3023 TTATTTACTAAAATGGTACAAAATAAGTAT
1 TTATTTACCAAAATGGTACAAAATAA-TAT
* *** * **
3053 TTATATACCAAAATGGTATCCGCACACCA-
1 TTATTTACCAAAATGGTA-CAAAATAATAT
3082 TTATTTACCAAAATGGTACAAAATAATAT
1 TTATTTACCAAAATGGTACAAAATAATAT
3111 TTATTT
1 TTATTT
3117 TGTACCATTT
Statistics
Matches: 47, Mismatches: 15, Indels: 5
0.70 0.22 0.07
Matches are distributed among these distances:
28 4 0.09
29 23 0.49
30 17 0.36
31 3 0.06
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
TTATTTACCAAAATGGTACAAAATAATAT
Found at i:3170 original size:16 final size:15
Alignment explanation
Indices: 3149--3197 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
3139 GGATGAAAAT
3149 ATTATTTTGGTAATTA
1 ATTATTTT-GTAATTA
3165 ATTATTTT-TATATT-
1 ATTATTTTGTA-ATTA
3179 A-TATTTTGATAATTA
1 ATTATTTTG-TAATTA
3194 ATTA
1 ATTA
3198 ACTAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTATTTTGTAATTA
Found at i:3853 original size:21 final size:21
Alignment explanation
Indices: 3828--3867 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3818 TACTTACTAC
3828 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
*
3849 TACTAACAAAATTAAATTA
1 TACTAACAAAATAAAATTA
3868 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:8128 original size:4 final size:4
Alignment explanation
Indices: 8121--8154 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
8111 TCATTCTTCC
* *
8121 TTCT TTCT TTCT TTTT TTCT TTCT TTTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
8155 GTTCTGCCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTCT
Found at i:8141 original size:12 final size:12
Alignment explanation
Indices: 8124--8154 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8114 TTCTTCCTTC
8124 TTTCTTTCTTTT
1 TTTCTTTCTTTT
8136 TTTCTTTCTTTT
1 TTTCTTTCTTTT
8148 TTTCTTT
1 TTTCTTT
8155 GTTCTGCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:9224 original size:19 final size:20
Alignment explanation
Indices: 9196--9238 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
9186 CATGCTCAGG
*
9196 AAACAGACCA-AAAAGCAAT-
1 AAACAAACCATAAAA-CAATC
9215 AAACAAACCATAAAACAATC
1 AAACAAACCATAAAACAATC
9235 AAAC
1 AAAC
9239 CCTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.65, C:0.23, G:0.05, T:0.07
Consensus pattern (20 bp):
AAACAAACCATAAAACAATC
Found at i:15379 original size:12 final size:12
Alignment explanation
Indices: 15359--15445 Score: 95
Period size: 12 Copynumber: 7.2 Consensus size: 12
15349 TTATTTTTGC
* *
15359 TCTTCCTTCACT
1 TCTTTCTTCTCT
*
15371 TCTTTCTTCTCC
1 TCTTTCTTCTCT
15383 TCGTTT-TTCTCT
1 TC-TTTCTTCTCT
*
15395 TCTTTCTTCTCC
1 TCTTTCTTCTCT
*
15407 TCTTTCTTTTCT
1 TCTTTCTTCTCT
*
15419 TCCTTCTTCTCT
1 TCTTTCTTCTCT
*
15431 TCCTTCTTCTCT
1 TCTTTCTTCTCT
15443 TCT
1 TCT
15446 ATTGCAGGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
11 3 0.05
12 57 0.90
13 3 0.05
ACGTcount: A:0.01, C:0.37, G:0.01, T:0.61
Consensus pattern (12 bp):
TCTTTCTTCTCT
Found at i:15395 original size:21 final size:21
Alignment explanation
Indices: 15371--15420 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
15361 TTCCTTCACT
* *
15371 TCTTTCTTCTCCTCGTTTTTC
1 TCTTTCTTCTCCTCCTCTTTC
*
15392 TC-TTCTTTCTTCTCCTCTTTC
1 TCTTTC-TTCTCCTCCTCTTTC
15413 T-TTTCTTC
1 TCTTTCTTC
15421 CTTCTTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (21 bp):
TCTTTCTTCTCCTCCTCTTTC
Found at i:25241 original size:11 final size:11
Alignment explanation
Indices: 25219--25260 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
25209 ACCCTAAACT
25219 AAAAATGAAAAG
1 AAAAA-GAAAAG
*
25231 AAAAAGGAAAG
1 AAAAAGAAAAG
*
25242 GAAAAGAAAAG
1 AAAAAGAAAAG
25253 -AAAAGAAA
1 AAAAAGAAA
25261 GCCTAACCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
11 14 0.52
12 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:45475 original size:29 final size:30
Alignment explanation
Indices: 45410--45475 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
45400 ATTTTCGAGG
* * *
45410 AATTTAGGGATCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATCAAAATTCAAACTTTAGGAA
*
45441 AATTTGGGATTAAAA-TCAAACTTTAGGAA
1 AATTTGGGATCAAAATTCAAACTTTAGGAA
45470 AATTTG
1 AATTTG
45476 AAGTTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.55
30 9 0.29
31 5 0.16
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
AATTTGGGATCAAAATTCAAACTTTAGGAA
Found at i:45573 original size:30 final size:29
Alignment explanation
Indices: 45537--45610 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
45527 TGTTCGGGGG
45537 CAAAATGGTAATTTTGGAGAATTTTAGGGT
1 CAAAAT-GTAATTTTGGAGAATTTTAGGGT
* *
45567 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTGGAGAATTTTA-GGGT
*
45597 TAAAATGTAATTTT
1 CAAAATGTAATTTT
45611 AGAAAAGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (29 bp):
CAAAATGTAATTTTGGAGAATTTTAGGGT
Found at i:45616 original size:30 final size:29
Alignment explanation
Indices: 45537--45673 Score: 125
Period size: 29 Copynumber: 4.7 Consensus size: 29
45527 TGTTCGGGGG
* * *
45537 CAAAATGGTAATTTTGGAGAATTTTAGGGT
1 CAAAAT-GTAATTTTAGAAAAGTTTAGGGT
*
45567 CAAAATGTAATTTTGGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTAGAAAAGTTTA-GGGT
* *
45597 TAAAATGTAATTTTAGAAAAG-TTAGATGT
1 CAAAATGTAATTTTAGAAAAGTTTAG-GGT
* * * * * *
45626 TAGAATGTGATTTTATAAAAATCTAGGGT
1 CAAAATGTAATTTTAGAAAAGTTTAGGGT
45655 CAAAATGTAATTTTA-AAAA
1 CAAAATGTAATTTTAGAAAA
45674 TCTAAGGACC
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
28 5 0.06
29 53 0.59
30 32 0.36
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAAGTTTAGGGT
Found at i:45665 original size:146 final size:146
Alignment explanation
Indices: 45392--45668 Score: 309
Period size: 146 Copynumber: 1.9 Consensus size: 146
45382 ATTCGGGATG
45392 AAAATGTAATTTTCGAGGAATTTAGGGATCAAAATTGAAATTTTTGGAAAATTTGGGATTAAAAT
1 AAAATGTAATTTTCGAGGAATTTAGGGATCAAAATTGAAATTTTTGGAAAATTTGGGATTAAAAT
* * * * *
45457 CAAACTTTAGGAAAATTTGAAGTTGAAAATGTGATTTTTGAAAATTTGGAGGTATATGGTAATTT
66 CAAACTTTAGGAAAATTAGAAGTTGAAAATGTGATTTTTAAAAATCTAGAGGTAAATGGTAATTT
45522 TGGGATGTTCGGGGGC
131 TGGGATGTTCGGGGGC
* * *
45538 AAAATGGTAATTTTGGA-GAATTTTAGGG-TCAAAA-TGTAA-TTTTGGAAAAGTTTAGGGGTTA
1 AAAAT-GTAATTTTCGAGGAA-TTTAGGGATCAAAATTGAAATTTTTGGAAAA-TTT-GGGATTA
** * * *
45599 AAATGTAATTTTA-GAAAAGTTAGATGTT-AGAATGTGATTTTATAAAAATCTAG-GGTCAAAAT
62 AAATCAAACTTTAGGAAAA-TTAGAAGTTGAAAATGTGATTTT-TAAAAATCTAGAGGT--AAAT
45661 -GTAATTTT
123 GGTAATTTT
45669 AAAAATCTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
144 10 0.09
145 27 0.25
146 53 0.48
147 20 0.18
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (146 bp):
AAAATGTAATTTTCGAGGAATTTAGGGATCAAAATTGAAATTTTTGGAAAATTTGGGATTAAAAT
CAAACTTTAGGAAAATTAGAAGTTGAAAATGTGATTTTTAAAAATCTAGAGGTAAATGGTAATTT
TGGGATGTTCGGGGGC
Done.