Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005527.1 Kokia drynarioides strain JFW-HI SEQ_119613, 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: 14312
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:189 original size:28 final size:29
Alignment explanation
Indices: 148--221 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
138 AACGGAGTAA
* * *
148 AAAATGAGATTTTTGGATG-CCCGGGGGT
1 AAAATGATAATTTTGGAAGACCCGGGGGT
* **
176 AAAATGATAATTTTTGAAGATTCGGGGGT
1 AAAATGATAATTTTGGAAGACCCGGGGGT
205 AAAAT-AGTAATTTTGGA
1 AAAATGA-TAATTTTGGA
222 CACTTCAGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGATAATTTTGGAAGACCCGGGGGT
Found at i:201 original size:29 final size:28
Alignment explanation
Indices: 169--593 Score: 147
Period size: 29 Copynumber: 14.7 Consensus size: 28
159 TTTGGATGCC
169 CGGGGGTAAAATGATAATTTTTGAAGATT
1 CGGGGGTAAAATG-TAATTTTTGAAGATT
* *
198 CGGGGGTAAAATAGTAATTTTGGACA-CTT
1 CGGGGGTAAAAT-GTAATTTTTGA-AGATT
* * * * * * *
227 CAGCGGCAAAATGGTACTTCTT-AGACACT
1 CGGGGGTAAAAT-GTAATTTTTGA-AGATT
*
256 CGGGGGTAAGAATGCAATTTTTGGAAG-TT
1 CGGGGGTAA-AATGTAATTTTT-GAAGATT
** *
285 TAGGGGTAAAACAGTAATTTTTGGAAG-TT
1 CGGGGGTAAAA-TGTAATTTTT-GAAGATT
* * * *
314 TGGGAGTAAAATGGTAATTTTCAGAAAATT
1 CGGGGGTAAAAT-GTAATTTT-TGAAGATT
* * *
344 C-AGAGTCAAAAATG-ATATTTTTGAAAATT
1 CGGGGGT--AAAATGTA-ATTTTTGAAGATT
*** *
373 AAAGGGTAAAATGGTAATTTTTTAA-AGTT
1 CGGGGGTAAAAT-GTAATTTTTGAAGA-TT
* * *
402 TGGGGGCAAAAATGTGATTTTTTGGAAG-TT
1 CGGGGG-TAAAATGT-AATTTTT-GAAGATT
* *
432 TGGGGGTAAAATGCAATTTTTGAA-AGTT
1 CGGGGGTAAAATGTAATTTTTGAAGA-TT
* *
460 CGAGAGTAAAATGTAATTTTTGGAAG-TT
1 CGGGGGTAAAATGTAATTTTT-GAAGATT
*
488 CAGGGGT-AAATGGTAATTTTTGGAAG-TT
1 CGGGGGTAAAAT-GTAATTTTT-GAAGATT
** * *
516 CAAGGGTAAAATTGCAATTTTTAGAAAATT
1 CGGGGGTAAAA-TGTAATTTTT-GAAGATT
*** *
546 AATGGGTAAAATGTAATTTTGTGAAGTTT
1 CGGGGGTAAAATGTAATTTT-TGAAGATT
* *
575 AGGGGTTAAAATGT-ATTTT
1 CGGGGGTAAAATGTAATTTT
594 AGAAAAGTTT
Statistics
Matches: 303, Mismatches: 63, Indels: 61
0.71 0.15 0.14
Matches are distributed among these distances:
27 7 0.02
28 68 0.22
29 169 0.56
30 51 0.17
31 8 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (28 bp):
CGGGGGTAAAATGTAATTTTTGAAGATT
Found at i:333 original size:58 final size:57
Alignment explanation
Indices: 258--593 Score: 194
Period size: 58 Copynumber: 5.8 Consensus size: 57
248 TAGACACTCG
* *
258 GGGGTAAGAAT-GCAATTTTTGGAAGTTTAGGGGTAAAACAGTAATTTTTGGAAGTT-T
1 GGGGTAA-AATGGTAATTTTTGAAAGTTTAGGGGTAAAA-AGTAATTTTTGGAAGTTAT
* * * * * * *
315 GGGAGTAAAATGGTAATTTTCAGAAAATTCA-GAGTCAAAAA-TGATATTTTTGAAAATTAA
1 GGG-GTAAAATGGTAATTTT-TGAAAGTTTAGGGGT-AAAAAGT-A-ATTTTTGGAAGTTAT
* * * * *
375 AGGGTAAAATGGTAATTTTTTAAAGTTTGGGGGCAAAAATGTGATTTTTTGGAAGTT-T
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAA-GT-AATTTTTGGAAGTTAT
* * * *
433 GGGGGTAAAAT-GCAATTTTTGAAAG-TTCGAGAGTAAAATGTAATTTTTGGAAGTTCA-
1 -GGGGTAAAATGGTAATTTTTGAAAGTTTAG-GGGTAAAAAGTAATTTTTGGAAGTT-AT
* * * * * * *
490 GGGGT-AAATGGTAATTTTTGGAAGTTCAAGGGTAAAATTGCAATTTTTAGAAAATTAAT
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAA-AGTAATTTTT-GGAAGTT-AT
*
549 -GGGTAAAAT-GTAATTTTGTG-AAGTTTAGGGGTTAAAATGT-ATTTT
1 GGGGTAAAATGGTAATTTT-TGAAAGTTTAGGGG-TAAAAAGTAATTTT
594 AGAAAAGTTT
Statistics
Matches: 215, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
55 4 0.02
56 37 0.17
57 27 0.13
58 73 0.34
59 69 0.32
60 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAAGTAATTTTTGGAAGTTAT
Found at i:414 original size:30 final size:28
Alignment explanation
Indices: 380--480 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
370 ATTAAAGGGT
380 AAAATGGTAATTTTTTAAAGTTTGGGGGCA
1 AAAAT-GTAATTTTTTAAAGTTTGGGGG-A
* * *
410 AAAATGTGATTTTTTGGAAGTTTGGGGGT
1 AAAATGTAATTTTTT-AAAGTTTGGGGGA
* * * * * *
439 AAAATGCAATTTTTGAAAGTTCGAGAGT
1 AAAATGTAATTTTTTAAAGTTTGGGGGA
467 AAAATGTAATTTTT
1 AAAATGTAATTTTT
481 GGAAGTTCAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.37
29 21 0.36
30 16 0.27
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTTAAAGTTTGGGGGA
Found at i:593 original size:86 final size:82
Alignment explanation
Indices: 259--593 Score: 257
Period size: 86 Copynumber: 3.9 Consensus size: 82
249 AGACACTCGG
** * *
259 GGGTAAGAATGCAATTTTTGGAAGTTTAGGGGTAAAACAGTAATTTTTGGAAGTTT-GGGAGTAA
1 GGGTAA-AATGCAATTTTT-GAAAATTAAGGGTAAAA-TGTAATTTTT-GAAGTTTAGGG-GTAA
* * *
323 AATGGTAATTTTCAGAAAATTC-A
61 AAT-GTAATTTT-TGGAAGTTCAA
* * * *
346 GAGTCAAAAATG-ATATTTTTGAAAATTAAAGGGTAAAATGGTAATTTTTTAAAGTTTGGGGGCA
1 GGGT--AAAATGCA-ATTTTTGAAAATT-AAGGGTAAAAT-GTAA-TTTTTGAAGTTTAGGGG-T
* ***
410 AAAATGTGATTTTTTGGAAGTTTGG
59 AAAATGT-AATTTTTGGAAGTTCAA
* * * *
435 GGGTAAAATGCAATTTTTGAAAGTTCGAGAGTAAAATGTAATTTTTGGAAGTTCAGGGGT-AAAT
1 GGGTAAAATGCAATTTTTGAAAATT-AAGGGTAAAATGTAATTTTT-GAAGTTTAGGGGTAAAAT
499 GGTAATTTTTGGAAGTTCAA
64 -GTAATTTTTGGAAGTTCAA
519 GGGTAAAATTGCAATTTTTAGAAAATTAATGGGTAAAATGTAATTTTGTGAAGTTTAGGGGTTAA
1 GGGTAAAA-TGCAATTTTT-GAAAATTAA-GGGTAAAATGTAATTTT-TGAAGTTTAGGGG-TAA
584 AATGT-ATTTT
61 AATGTAATTTT
594 AGAAAAGTTT
Statistics
Matches: 199, Mismatches: 30, Indels: 39
0.74 0.11 0.15
Matches are distributed among these distances:
84 25 0.13
85 18 0.09
86 51 0.26
87 40 0.20
88 42 0.21
89 23 0.12
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (82 bp):
GGGTAAAATGCAATTTTTGAAAATTAAGGGTAAAATGTAATTTTTGAAGTTTAGGGGTAAAATGT
AATTTTTGGAAGTTCAA
Found at i:601 original size:29 final size:30
Alignment explanation
Indices: 466--713 Score: 144
Period size: 30 Copynumber: 8.5 Consensus size: 30
456 AGTTCGAGAG
* * *
466 TAAAATGTAATTTTTG-GAAGTTCAGGGG-
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
* * * *
494 T-AAATGGTAATTTTTG-GAAGTTCAAGGG-
1 TAAAAT-GTAATTTTAGAAAAGTTTAGGGGT
* * *
522 TAAAATTGCAATTTTTAGAAAA-TTAATGGG-
1 TAAAA-TGTAA-TTTTAGAAAAGTTTAGGGGT
**
552 TAAAATGTAATTTT-GTGAAGTTTAGGGGT
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
581 TAAAATGT-ATTTTAGAAAAGTTTAGGGGT
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
* * * *
610 TAAAATATTATTTTCA-AAAAATTTAGAGGT
1 TAAAATGTAATTTT-AGAAAAGTTTAGGGGT
* *
640 TAAAATATAATTTTCA-AAAAATTT-GAGGGT
1 TAAAATGTAATTTT-AGAAAAGTTTAG-GGGT
* *
670 TAAAATATAATTTTTAG-AAAGTTTAAGGGT
1 TAAAATGTAA-TTTTAGAAAAGTTTAGGGGT
* *
700 TAAAACGTGATTTT
1 TAAAATGTAATTTT
714 TGGAAAATTC
Statistics
Matches: 183, Mismatches: 23, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
27 7 0.04
28 38 0.21
29 43 0.23
30 88 0.48
31 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
TAAAATGTAATTTTAGAAAAGTTTAGGGGT
Found at i:635 original size:30 final size:30
Alignment explanation
Indices: 572--704 Score: 155
Period size: 30 Copynumber: 4.5 Consensus size: 30
562 TTTTGTGAAG
* *
572 TTTAGGGGTTAAAATGT-ATTTT-AGAAAAG
1 TTTAGGGGTTAAAATATAATTTTCA-AAAAA
*
601 TTTAGGGGTTAAAATATTATTTTCAAAAAA
1 TTTAGGGGTTAAAATATAATTTTCAAAAAA
*
631 TTTAGAGGTTAAAATATAATTTTCAAAAAA
1 TTTAGGGGTTAAAATATAATTTTCAAAAAA
* * *
661 TTT-GAGGGTTAAAATATAATTTTTAGAAAG
1 TTTAG-GGGTTAAAATATAATTTTCAAAAAA
*
691 TTTAAGGGTTAAAA
1 TTTAGGGGTTAAAA
705 CGTGATTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
29 17 0.19
30 73 0.80
31 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATAATTTTCAAAAAA
Found at i:714 original size:30 final size:30
Alignment explanation
Indices: 501--704 Score: 149
Period size: 30 Copynumber: 6.9 Consensus size: 30
491 GGGTAAATGG
* *
501 TAATTTTT-GGAAGTTCAAGGG-TAAAAT-
1 TAATTTTTAGAAAGTTTAAGGGTTAAAATA
* *
528 TGCAATTTTTAGAAA-ATTAATGGG-TAAAATG
1 T--AATTTTTAGAAAGTTTAA-GGGTTAAAATA
* *
559 TAATTTTGT-G-AAGTTTAGGGGTTAAAATG
1 TAATTTT-TAGAAAGTTTAAGGGTTAAAATA
*
588 T-A-TTTTAGAAAAGTTTAGGGGTTAAAATA
1 TAATTTTTAG-AAAGTTTAAGGGTTAAAATA
* * * *
617 TTATTTTCAAAAAATTT-AGAGGTTAAAATA
1 TAATTTTTAGAAAGTTTAAG-GGTTAAAATA
* * * *
647 TAATTTTCAAAAAATTTGAGGGTTAAAATA
1 TAATTTTTAGAAAGTTTAAGGGTTAAAATA
677 TAATTTTTAGAAAGTTTAAGGGTTAAAA
1 TAATTTTTAGAAAGTTTAAGGGTTAAAA
705 CGTGATTTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 6 0.04
29 48 0.33
30 80 0.54
31 7 0.05
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTAAGGGTTAAAATA
Found at i:2560 original size:17 final size:17
Alignment explanation
Indices: 2540--2639 Score: 101
Period size: 17 Copynumber: 5.8 Consensus size: 17
2530 TTTAATTAAT
*
2540 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
2557 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAATAAA
* * * *
2574 TTCAAACTTAAGATAAG
1 TTTAAATTTAAAATAAA
2591 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * *
2608 TTCAAACTTGAAATAAAA
1 TTTAAATTTAAAAT-AAA
*
2626 TTAAAATTTAAAAT
1 TTTAAATTTAAAAT
2640 TTGGACTAAA
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
17 51 0.78
18 14 0.22
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2595 original size:34 final size:34
Alignment explanation
Indices: 2547--2639 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
2537 AATTTTAATT
*
2547 TTAAAATAAATTTAAATTTAAAGTAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
* *
2581 TTAAGATAAGTTTAAATTTAAAATAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
* *
2615 TTGAAATAAAATTAAAATTTAAAAT
1 TTAAAAT-AAATTTAAATTTAAAAT
2640 TTGGACTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 36 0.71
35 15 0.29
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (34 bp):
TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
Found at i:5080 original size:17 final size:17
Alignment explanation
Indices: 5058--5090 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5048 GGGATCTTTT
*
5058 TTTTAAGGTTGTTTTGG
1 TTTTAAGATTGTTTTGG
5075 TTTTAAGATTGTTTTG
1 TTTTAAGATTGTTTTG
5091 AATCTCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (17 bp):
TTTTAAGATTGTTTTGG
Found at i:5598 original size:34 final size:36
Alignment explanation
Indices: 5551--5620 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 36
5541 TCAATTCATC
* *
5551 TAAATTATTATTGATAAGACA-TTA-TTTTATAAAAA
1 TAAATTATGATTGA-AAAACATTTATTTTTATAAAAA
*
5586 TAAA-TATGATTGAAAAATATTTATTTTTATAAAAA
1 TAAATTATGATTGAAAAACATTTATTTTTATAAAAA
5621 GAAGATAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 4 0.13
34 11 0.37
35 15 0.50
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (36 bp):
TAAATTATGATTGAAAAACATTTATTTTTATAAAAA
Found at i:10290 original size:14 final size:14
Alignment explanation
Indices: 10271--10304 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10261 TTATATATCC
10271 AAATAATAACAATA
1 AAATAATAACAATA
*
10285 AAATAATAGCAATA
1 AAATAATAACAATA
*
10299 TAATAA
1 AAATAA
10305 CAAAAGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:11018 original size:29 final size:28
Alignment explanation
Indices: 10968--11027 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
10958 AATTGAAATT
**
10968 ATTTTTAAAAATTTATAAAATTTTAAAG
1 ATTTTTAAAAATACATAAAATTTTAAAG
* *
10996 ATTTTTACAAATACATAGAAATTTTTAAG
1 ATTTTTAAAAATACATA-AAATTTTAAAG
11025 ATT
1 ATT
11028 AAAACATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (28 bp):
ATTTTTAAAAATACATAAAATTTTAAAG
Found at i:13566 original size:17 final size:17
Alignment explanation
Indices: 13544--13622 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
13534 CCAACAGGAT
*
13544 TTAAATTCATTTTAAAA
1 TTAAATTTATTTTAAAA
**
13561 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
* *
13578 TTAAATTTACTTAAAAA
1 TTAAATTTATTTTAAAA
* *
13595 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
13613 TTAAAGTTTA
1 TTAAA-TTTA
13623 AATCTATTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 32 0.65
18 17 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Done.