Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014109.1 Kokia drynarioides strain JFW-HI SEQ_129140, 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: 23561
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1378 original size:29 final size:28
Alignment explanation
Indices: 1287--1698 Score: 256
Period size: 29 Copynumber: 14.1 Consensus size: 28
1277 CCTAGAAGGT
* *
1287 CCTTAAACTATCTAAAAATCATATTTTGAC
1 CCTTAAACT-TCTAAAAATTACATTTT-AC
**
1317 CCTCGAACATTCTAAAAATTACATTTTAAC
1 CCTTAAAC-TTCTAAAAATTACATTTT-AC
*
1347 CCTTAAACATCGTAAAAATTACATTTTAC
1 CCTTAAACTTC-TAAAAATTACATTTTAC
* *
1376 CC-TAAACTCCACAAAAATTACATTTTTAC
1 CCTTAAACTTC-TAAAAATTACA-TTTTAC
*
1405 CCTTGAACTTCCTAAAAATTACATTTTTAC
1 CCTTAAACTT-CTAAAAATTACA-TTTTAC
* * *
1435 CCCTGAACTTTTAAAAATTACACTTTTAC
1 CCTTAAACTTCTAAAAATTACA-TTTTAC
* *
1464 CCTTAAATTTCTAAAAATTCCATTTTGA-
1 CCTTAAACTTCTAAAAATTACATTTT-AC
* *
1492 CCTTAAACTTTCCAAAAATTACCATTTTAT
1 CCTTAAAC-TTCTAAAAATTA-CATTTTAC
* *
1522 CCTTAAATTTCTAAAAATTCCATTTTAAC
1 CCTTAAACTTCTAAAAATTACATTTT-AC
* * *
1551 CC-TGATCTTTCCAAAAATTACCATTTTAC
1 CCTTAAAC-TTCTAAAAATTA-CATTTTAC
** * * *
1580 CCTCGAATTTCCAAAAATTTCATTTTTAAC
1 CCTTAAACTTCTAAAAATTACA-TTTT-AC
* * * * *
1610 CC-TGACCTTCCCAAAATTTATCATTTTGC
1 CCTTAAACTT-CTAAAAATTA-CATTTTAC
* * *
1639 CCTTAAATTTCCAAAAATTCCATTTTTAC
1 CCTTAAACTTCTAAAAATTACA-TTTTAC
* ** **
1668 TCTCGAGTTTCTAAAAATTACCATTTTAC
1 CCTTAAACTTCTAAAAATTA-CATTTTAC
1697 CC
1 CC
1699 CTCGAGCATC
Statistics
Matches: 304, Mismatches: 58, Indels: 41
0.75 0.14 0.10
Matches are distributed among these distances:
28 39 0.13
29 143 0.47
30 118 0.39
31 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
CCTTAAACTTCTAAAAATTACATTTTAC
Found at i:1685 original size:59 final size:57
Alignment explanation
Indices: 1330--1698 Score: 327
Period size: 58 Copynumber: 6.3 Consensus size: 57
1320 CGAACATTCT
** * * * *
1330 AAAAATTA-CATTTTAACCCTTAAACATCGTAAAAATTACA-TTTTACCCTAAAC-TCCAC
1 AAAAATTACCATTTT-ACCCTTAAATTTC-CAAAAATTCCATTTTTACCCT-GACTTTC-C
* * * *
1388 AAAAATTA-CATTTTTACCCTTGAACTTCCTAAAAATTACATTTTTACCCCTGAACTTT-T
1 AAAAATTACCA-TTTTACCCTTAAATTTCC-AAAAATTCCATTTTTA-CCCTG-ACTTTCC
* * * *
1447 AAAAATTA-CACTTTTACCCTTAAATTTCTAAAAATTCCATTTTGACCTTAAACTTTCC
1 AAAAATTACCA-TTTTACCCTTAAATTTCCAAAAATTCCATTTTTACCCT-GACTTTCC
* * *
1505 AAAAATTACCATTTTATCCTTAAATTTCTAAAAATTCCATTTTAACCCTGATCTTTCC
1 AAAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTACCCTGA-CTTTCC
** * *
1563 AAAAATTACCATTTTACCCTCGAATTTCCAAAAATTTCATTTTTAACCCTGACCTTCCC
1 AAAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTT-ACCCTGA-CTTTCC
* * * * * *
1622 AAAATTTATCATTTTGCCCTTAAATTTCCAAAAATTCCATTTTTACTCTCGAGTTTCT
1 AAAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTACCCT-GACTTTCC
1680 AAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
1699 CTCGAGCATC
Statistics
Matches: 259, Mismatches: 40, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
57 9 0.03
58 155 0.60
59 88 0.34
60 6 0.02
61 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCTTAAATTTCCAAAAATTCCATTTTTACCCTGACTTTCC
Found at i:9954 original size:96 final size:96
Alignment explanation
Indices: 9770--9961 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
9760 TTTTTGGGAA
** * *
9770 AAGGATATTCGATTATCTCGATTTAAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAATATTTCA
*
9835 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * **
9866 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGCTAAGGCGCAA-ATTTTT
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAATATTTCA
*
9930 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
66 G-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
9962 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 6 0.07
96 70 0.86
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:10427 original size:117 final size:113
Alignment explanation
Indices: 10306--10676 Score: 374
Period size: 117 Copynumber: 3.2 Consensus size: 113
10296 TTCGAGGTCG
* * * *
10306 AAAATGGAGTTTTTGGATA-TTCGGGGGT-AAAATGGTAATTTTTGGAGGTTTTGGGGTTAAAAA
1 AAAATGAAATTTTTGGA-AGTTC-GGGGTCAAAATGG-AATTTTTGGAAG-TTTAGGG-TAAAAA
10369 TAGAATTTTT-TAA-TGTTCGAGGCTAAAAATGAGATTTTTGGAAGTTCGTGGGTA
61 TAGAATTTTTGTAAGT-TTCGAGG-TAAAAATGAGATTTTTGGAAGTTCG-GGGTA
* * * * *
10423 AAAATAAAATTTTTGGAAGTTTTGGGGTCAAAATTGAGATTTTTGGAAGTTCAGAGTAAAAATAG
1 AAAATGAAATTTTTGGAAG-TTCGGGGTCAAAATGGA-ATTTTTGGAAGTTTAGGGTAAAAATAG
* * *
10488 AATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAGTTTCGGGGTA
64 AATTTTTGTAAGTTTCGAGG-TAAAAATGAGATTTTTGGAAG-TTCGGGGTA
* * * * *
10540 AAAATGAAATTTTTGGAAGTTTCGGAGTCAAAAACGGGATTTTTGGAAG-TTCGGGATAAAAATG
1 AAAATGAAATTTTTGGAAG-TTCGGGGTC-AAAATGGAATTTTTGGAAGTTTAGGG-TAAAAATA
* * *
10604 GAATTTTTGTAAGTTTCGAGGTCAAAATGAGATTTTTGGAAATTTGGGGTA
63 GAATTTTTGTAAGTTTCGAGGTAAAAATGAGATTTTTGGAAGTTCGGGGTA
*
10655 AAAACGAAATTTTTTGGAAGTT
1 AAAATGAAA-TTTTTGGAAGTT
10677 TCAGGGTCTC
Statistics
Matches: 214, Mismatches: 30, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
115 18 0.08
116 48 0.22
117 120 0.56
118 28 0.13
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (113 bp):
AAAATGAAATTTTTGGAAGTTCGGGGTCAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATAGAA
TTTTTGTAAGTTTCGAGGTAAAAATGAGATTTTTGGAAGTTCGGGGTA
Found at i:10456 original size:58 final size:57
Alignment explanation
Indices: 10394--10684 Score: 348
Period size: 58 Copynumber: 5.0 Consensus size: 57
10384 TTCGAGGCTA
*
10394 AAAATGAGATTTTTGGAAGTTCGTGGGTAAAAATAAAATTTTTGGAAGTTTTGGGGTC
1 AAAATGAGATTTTTGGAAGTTCG-GGGTAAAAATAAAATTTTTGGAAGTTTCGGGGTC
* * * *
10452 AAAATTGAGATTTTTGGAAGTTCAGAGTAAAAATAGAATTTTTGGAAGTTTCGGGGTTA
1 AAAA-TGAGATTTTTGGAAGTTCGGGGTAAAAATAAAATTTTTGGAAGTTTCGGGG-TC
* * *
10511 AAAATGGGATTTTTGGAAGTTTCGGGGTAAAAATGAAATTTTTGGAAGTTTCGGAGTC
1 AAAATGAGATTTTTGGAAG-TTCGGGGTAAAAATAAAATTTTTGGAAGTTTCGGGGTC
* * * ** * *
10569 AAAAACGGGATTTTTGGAAGTTCGGGATAAAAATGGAATTTTTGTAAGTTTCGAGGTC
1 -AAAATGAGATTTTTGGAAGTTCGGGGTAAAAATAAAATTTTTGGAAGTTTCGGGGTC
* * * * *
10627 AAAATGAGATTTTTGGAAATTTGGGGTAAAAACGAAATTTTTTGGAAGTTTCAGGGTC
1 AAAATGAGATTTTTGGAAGTTCGGGGTAAAAA-TAAAATTTTTGGAAGTTTCGGGGTC
10685 TCTAAGGCAA
Statistics
Matches: 198, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
57 27 0.14
58 99 0.50
59 72 0.36
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (57 bp):
AAAATGAGATTTTTGGAAGTTCGGGGTAAAAATAAAATTTTTGGAAGTTTCGGGGTC
Found at i:10668 original size:29 final size:29
Alignment explanation
Indices: 10217--10683 Score: 314
Period size: 29 Copynumber: 16.0 Consensus size: 29
10207 TTATGGGGGC
10217 AAAATGAAAATTTTTGGAAAGTTT-GGGGTTA
1 AAAATG-AAATTTTTGG-AAGTTTCGGGG-TA
* * **
10248 AAAATGAAATTGTT-AAACATTCAGGGGTA
1 AAAATGAAATTTTTGGAAGTTTC-GGGGTA
** * ** * *
10277 AAAGGGTAATTTTAAG-AGTTTCGAGGTCG
1 AAAATGAAATTTTTGGAAGTTTCGGGGT-A
* *
10306 AAAATGGAGTTTTTGG-A-TATTCGGGGGT-
1 AAAATGAAATTTTTGGAAGT-TTC-GGGGTA
* * *
10334 AAAATGGTAATTTTTGGAGGTTTTGGGGTTA
1 AAAAT-GAAATTTTTGGAAGTTTCGGGG-TA
* *
10365 AAAAT-AGAATTTTT-TAA-TGTTCGAGGCTA
1 AAAATGA-AATTTTTGGAAGT-TTCG-GGGTA
*
10394 AAAATGAGATTTTTGGAAG-TTCGTGGGTA
1 AAAATGAAATTTTTGGAAGTTTCG-GGGTA
* *
10423 AAAATAAAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGAAATTTTTGGAAGTTTCGGGGT-A
* * * *
10453 AAATTGAGATTTTTGGAAG-TTCAGAGTA
1 AAAATGAAATTTTTGGAAGTTTCGGGGTA
10481 AAAAT-AGAATTTTTGGAAGTTTCGGGGTTA
1 AAAATGA-AATTTTTGGAAGTTTCGGGG-TA
**
10511 AAAATGGGATTTTTGGAAGTTTCGGGGTA
1 AAAATGAAATTTTTGGAAGTTTCGGGGTA
*
10540 AAAATGAAATTTTTGGAAGTTTCGGAGTCA
1 AAAATGAAATTTTTGGAAGTTTCGGGGT-A
* ** *
10570 AAAACGGGATTTTTGGAAG-TTCGGGATA
1 AAAATGAAATTTTTGGAAGTTTCGGGGTA
* * * *
10598 AAAATGGAATTTTTGTAAGTTTCGAGGTC
1 AAAATGAAATTTTTGGAAGTTTCGGGGTA
* *
10627 AAAATGAGATTTTTGGAAATTT-GGGGTA
1 AAAATGAAATTTTTGGAAGTTTCGGGGTA
* *
10655 AAAACGAAATTTTTTGGAAGTTTCAGGGT
1 AAAATGAAA-TTTTTGGAAGTTTCGGGGT
10684 CTCTAAGGCA
Statistics
Matches: 336, Mismatches: 73, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.00
28 59 0.18
29 167 0.50
30 97 0.29
31 12 0.04
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGAAATTTTTGGAAGTTTCGGGGTA
Found at i:11474 original size:26 final size:27
Alignment explanation
Indices: 11421--11511 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 27
11411 AAATTGAAGG
*
11421 TAAAAAAAACCTTCCCTTTTTCCCTTTTT
1 TAAAAAAAA-CTTCTC-TTTTCCCTTTTT
11450 TAAAAAAAACTTCTCTTTT--CTTTTT
1 TAAAAAAAACTTCTCTTTTCCCTTTTT
****
11475 TCGTTTAAAACTTCTCTTTTCCCTTTTT
1 T-AAAAAAAACTTCTCTTTTCCCTTTTT
11503 TAAAAAAAA
1 TAAAAAAAA
11512 AACTTATCAG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
25 7 0.14
26 14 0.28
27 8 0.16
28 12 0.24
29 9 0.18
ACGTcount: A:0.31, C:0.21, G:0.01, T:0.47
Consensus pattern (27 bp):
TAAAAAAAACTTCTCTTTTCCCTTTTT
Found at i:11512 original size:28 final size:28
Alignment explanation
Indices: 11421--11512 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
11411 AAATTGAAGG
* *
11421 TAAAAAAAACCTTCCCTTTTTCCCTTTTT
1 TAAAAAAAAACTTCTC-TTTTCCCTTTTT
11450 T-AAAAAAAACTTCTCTTTT--CTTTTT
1 TAAAAAAAAACTTCTCTTTTCCCTTTTT
*****
11475 TCGTTTAAAACTTCTCTTTTCCCTTTTT
1 TAAAAAAAAACTTCTCTTTTCCCTTTTT
11503 TAAAAAAAAA
1 TAAAAAAAAA
11513 ACTTATCAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
25 7 0.14
26 14 0.29
27 4 0.08
28 23 0.47
29 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.01, T:0.47
Consensus pattern (28 bp):
TAAAAAAAAACTTCTCTTTTCCCTTTTT
Found at i:12510 original size:17 final size:17
Alignment explanation
Indices: 12490--12572 Score: 87
Period size: 17 Copynumber: 4.9 Consensus size: 17
12480 AAATAAATTT
12490 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
**
12507 TAAATTTAAATTTCA-GC
1 TAAATTTAAATTT-ATAA
*
12524 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
12541 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
12558 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
12573 TGGGCCCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 1 0.02
17 52 0.96
18 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:12530 original size:34 final size:34
Alignment explanation
Indices: 12490--12572 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
12480 AAATAAATTT
* * **
12490 TAAATTTAAATTTATAATAAATTTAAATTTCAGC
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
* *
12524 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
12558 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
12573 TGGGCCCAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:14084 original size:27 final size:27
Alignment explanation
Indices: 14046--14105 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
14036 TCAAAAATTC
* *
14046 TATTAAGAAGAGGATGAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
14073 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
14100 TCATTA
1 T-ATTA
14106 GTTGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Found at i:14385 original size:44 final size:44
Alignment explanation
Indices: 14337--14425 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
14327 TTGGTTCCAG
* * *
14337 GACGCCCTTTGCGAGTTTTCATCCTGAACT-CCCTTTTTTTTTTA
1 GACGCCCTTTACGAGTTTTCAT-CTCAACTCCCCTTTTGTTTTTA
* *
14381 GACGCCCTTTACGGGTTTTCATCTCAATTCCCCTTTTGTTTTTA
1 GACGCCCTTTACGAGTTTTCATCTCAACTCCCCTTTTGTTTTTA
14425 G
1 G
14426 GCGAAGTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 5 0.13
44 34 0.87
ACGTcount: A:0.13, C:0.27, G:0.15, T:0.45
Consensus pattern (44 bp):
GACGCCCTTTACGAGTTTTCATCTCAACTCCCCTTTTGTTTTTA
Found at i:20692 original size:11 final size:11
Alignment explanation
Indices: 20668--20701 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
20658 TACTTGGGTT
20668 GCCACCTC-GC
1 GCCACCTCTGC
20678 GCCACCTCTGC
1 GCCACCTCTGC
20689 GCCACCTCTGC
1 GCCACCTCTGC
20700 GC
1 GC
20702 ATATGTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.09, C:0.56, G:0.21, T:0.15
Consensus pattern (11 bp):
GCCACCTCTGC
Found at i:22988 original size:29 final size:30
Alignment explanation
Indices: 22934--23015 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
22924 GTCTTTGAGA
22934 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
* *
22964 GATTTTTGGAAG-TTCGGGGGT-AAAAATGG
1 AATTTTTGGAAGTTTC-GAGGTCAAAAATGG
*
22993 AATTTTTTTGAAGTTTCGAGGTC
1 AA-TTTTTGGAAGTTTCGAGGTC
23016 TCCAGGGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 12 0.28
30 28 0.65
31 3 0.07
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.37
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCGAGGTCAAAAATGG
Done.