Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009892.1 Kokia drynarioides strain JFW-HI SEQ_124628, 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: 63720
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:805 original size:23 final size:23
Alignment explanation
Indices: 777--926 Score: 176
Period size: 23 Copynumber: 6.4 Consensus size: 23
767 ACACTAGTGC
*
777 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
800 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
825 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * * * *
848 GCTCTCTGATTAGTATTTTGTAT
1 GCTCTCTGTTTAGCACTGTGTGT
*
871 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
894 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
917 GCTCTCTGTT
1 GCTCTCTGTT
927 GCCCAACATT
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
23 89 0.82
24 1 0.01
25 16 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:6478 original size:91 final size:91
Alignment explanation
Indices: 6298--6515 Score: 237
Period size: 91 Copynumber: 2.4 Consensus size: 91
6288 TGGAAACCTT
* * * *
6298 AAAGTTCAAGCCTTAATATG-GAAACAATTGCCAAGTTCAGGCCTCATGTAAGAACAGTTGTCAA
1 AAAGTTCAAGCCCTAATATGAGAAA-AATTGCCAAATCCAGGCCTCATGTAAGAACAGTTGCCAA
*
6362 GTTTAGGACCTAACTTGGATAAAAAA-
65 GTTTAGGACCTAACTTGGACAAAAAAG
* * * * *
6388 AAATTTCAAGCCCTAATGTGAGAAAATTTGCCAAATCCAGGTCTCAATGTGAGAACAAG-TGCCA
1 AAAGTTCAAGCCCTAATATGAGAAAAATTGCCAAATCCAGGCCTC-ATGTAAGAAC-AGTTGCCA
* *
6452 AGTTTAGGACCTAACTTGTACCAAAAAG
64 AGTTTAGGACCTAACTTGGACAAAAAAG
* * *
6480 AAAGTTC-AGACCCCAAAATGAGAAAAGTTGCCAAAT
1 AAAGTTCAAG-CCCTAATATGAGAAAAATTGCCAAAT
6516 TCAAGTCCCA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
90 33 0.31
91 43 0.41
92 30 0.28
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (91 bp):
AAAGTTCAAGCCCTAATATGAGAAAAATTGCCAAATCCAGGCCTCATGTAAGAACAGTTGCCAAG
TTTAGGACCTAACTTGGACAAAAAAG
Found at i:8808 original size:7 final size:7
Alignment explanation
Indices: 8798--8832 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
8788 GGTACATGGT
8798 AGCCTTG
1 AGCCTTG
8805 AGCCTTG
1 AGCCTTG
8812 AGCCTTG
1 AGCCTTG
*
8819 AGCCTTA
1 AGCCTTG
8826 AGCCTTG
1 AGCCTTG
8833 TTGACATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (7 bp):
AGCCTTG
Found at i:11321 original size:31 final size:30
Alignment explanation
Indices: 11281--11353 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
11271 ATTGAAAATT
*
11281 AAAATTATTTAATAATTTTAT-TCTTTCAAAA
1 AAAAATATTTAATAATTTTATAT-TTT-AAAA
11312 AAAAATATTTTAATAATTTTATATTTTAAAA
1 AAAAATA-TTTAATAATTTTATATTTTAAAA
*
11343 AATAAT-TTTAA
1 AAAAATATTTAA
11354 ATCATTTGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 5 0.13
31 15 0.39
32 17 0.45
33 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAAATATTTAATAATTTTATATTTTAAAA
Found at i:12426 original size:23 final size:23
Alignment explanation
Indices: 12375--12437 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
12365 CATTGTTCGT
* *
12375 GAACATGTTCAATTATATGTTCAT
1 GAACATGTTCATTTA-ATGTTCAC
* *
12399 AAACATGTTCGTTTAATGTTCAC
1 GAACATGTTCATTTAATGTTCAC
12422 GAACATGTTCATTTAA
1 GAACATGTTCATTTAA
12438 CTTAAATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (23 bp):
GAACATGTTCATTTAATGTTCAC
Found at i:12465 original size:23 final size:23
Alignment explanation
Indices: 12422--12466 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12412 TAATGTTCAC
* *
12422 GAACATGTTCATTTAACTTAAAT
1 GAACATGTTCAGTGAACTTAAAT
12445 GAACATGTTC-GTGAACATTAAA
1 GAACATGTTCAGTGAAC-TTAAA
12467 CAAACGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
GAACATGTTCAGTGAACTTAAAT
Found at i:13640 original size:29 final size:30
Alignment explanation
Indices: 13607--13685 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
13597 TTTGTGGATT
* *
13607 TAGTCCCTGTACTTTT-ATTTGAACAATTA
1 TAGTCCCTATACTTTTCAATTGAACAATTA
* * *
13636 TAGTCTCTATACTTTTCGAATTGATCAATTT
1 TAGTCCCTATACTTTTC-AATTGAACAATTA
*
13667 TAGTCCCTATTCTTTTCAA
1 TAGTCCCTATACTTTTCAA
13686 ATTTTGAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 14 0.34
30 2 0.05
31 25 0.61
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (30 bp):
TAGTCCCTATACTTTTCAATTGAACAATTA
Found at i:17174 original size:21 final size:21
Alignment explanation
Indices: 17145--17185 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17135 AAAAAATATG
*
17145 AATACTAAAATGGGAAAAACA
1 AATACTAAAATGGAAAAAACA
* *
17166 AATATTAAAATTGAAAAAAC
1 AATACTAAAATGGAAAAAAC
17186 GAACATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (21 bp):
AATACTAAAATGGAAAAAACA
Found at i:25797 original size:21 final size:21
Alignment explanation
Indices: 25773--25812 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25763 CAATTCATTA
*
25773 TTATAAATAATCATAATTTTT
1 TTATAAATAATCAAAATTTTT
*
25794 TTATTAATAATCAAAATTT
1 TTATAAATAATCAAAATTT
25813 ATAATTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAAATAATCAAAATTTTT
Found at i:34289 original size:9 final size:9
Alignment explanation
Indices: 34275--34339 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
34265 TTGATAAGTC
*
34275 ATTCGGGTA
1 ATTCGGATA
*
34284 ATTCGGATG
1 ATTCGGATA
* *
34293 ATTCAGTTA
1 ATTCGGATA
*
34302 ATTCGAATA
1 ATTCGGATA
34311 ATTC--ATTA
1 ATTCGGA-TA
*
34319 ATTCGGGTA
1 ATTCGGATA
34328 ATTCGGATA
1 ATTCGGATA
34337 ATT
1 ATT
34340 TTTATACAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
7 1 0.02
8 6 0.14
9 36 0.84
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (9 bp):
ATTCGGATA
Found at i:34321 original size:17 final size:18
Alignment explanation
Indices: 34282--34323 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34272 GTCATTCGGG
* *
34282 TAATTCGGATGATTCAGT
1 TAATTCGAATAATTCAGT
34300 TAATTCGAATAATTCA-T
1 TAATTCGAATAATTCAGT
34317 TAATTCG
1 TAATTCG
34324 GGTAATTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (18 bp):
TAATTCGAATAATTCAGT
Found at i:34329 original size:17 final size:18
Alignment explanation
Indices: 34282--34331 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
34272 GTCATTCGGG
*
34282 TAATTCGGATGATTCAGT
1 TAATTCGGATAATTCAGT
*
34300 TAATTCGAATAATTCA-T
1 TAATTCGGATAATTCAGT
*
34317 TAATTCGGGTAATTC
1 TAATTCGGATAATTC
34332 GGATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (18 bp):
TAATTCGGATAATTCAGT
Found at i:52389 original size:23 final size:23
Alignment explanation
Indices: 52328--52389 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
52318 TATTGAAAAT
* *
52328 TATTTCAAATATATAAT-ATTATA
1 TATTT-AAATGTAAAATGATTATA
* *
52351 TATTTAAATTTGAAATGATTATA
1 TATTTAAATGTAAAATGATTATA
52374 T-TTTAATATGTAAAAT
1 TATTTAA-ATGTAAAAT
52390 ATAGTTTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
TATTTAAATGTAAAATGATTATA
Found at i:56913 original size:44 final size:46
Alignment explanation
Indices: 56825--56913 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 46
56815 TAGGATTTAA
*
56825 ATAATATATTTTTTGTTATAATTTATAAAATAAAAAAATTATTTCT
1 ATAATATATTTTTTGTTATAATTTATAAAATAAAAAAATAATTTCT
*
56871 ATAATATA-TTTTT-TTA-AGATTTATAATATAAGAAAAA-AATTTC
1 ATAATATATTTTTTGTTATA-ATTTATAAAATAA-AAAAATAATTTC
56914 ATAGCCATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 1 0.03
44 20 0.51
45 10 0.26
46 8 0.21
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (46 bp):
ATAATATATTTTTTGTTATAATTTATAAAATAAAAAAATAATTTCT
Done.