Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010618.1 Kokia drynarioides strain JFW-HI SEQ_125551, 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: 29894
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:2115 original size:627 final size:612
Alignment explanation
Indices: 927--2116 Score: 2200
Period size: 627 Copynumber: 1.9 Consensus size: 612
917 NNNNNNNNNN
927 GTGAAAGGAGAGAGCTTTTTTGAAGGGTGAATTTGTTTTTCTGAAAAAGAGAAGGGAAAAATGAT
1 GTGAAAGGAGAGAGCTTTTTTGAAGGGTGAATTTGTTTTTCTGAAAAAGAGAAGGGAAAAATGAT
*
992 TTTTTTATTGAAAGTTGGAATTTATAGTAGCATTAAAACGTTGTCGTTTCAAGGGTGATTACTGG
66 TTTTTTAGTGAAAGTTGGAATTTATAGTAGCATTAAAACGTTGTCGTTTCAAGGGTGATTACTGG
*
1057 GTGCCAAAACGACACTGTTTTTAGCCTCTGCCCATGACCCATCTGACCCGACCCGAACCGTCCTT
131 GTGCCAAAACGACACCGTTTTTAGCCTCTGCCCATGACCCATCTGACCCGACCCGAACCGTCCTT
* *
1122 AGGATCCGCGTGTTTTCGTTGAAGGGTATATTTATGCATTTGGTCCTTCCTCTTTTTTTTTATTT
196 AGGATCCACGTGTTTTCGTTGAAGGGTATATTTATGCATTTGGTCCTTCCGCTTTTTTTTTATTT
1187 TTACAATCATATCCTTTTTATACTTTTAATTAATTTTAAATTGACCCAATAATTTTCAATACTTT
261 TTACAATCATATCCTTTTTATACTTTTAATTAATTTTAAATTGACCCAATAATTTTCAATACTTT
1252 TCAATTTAATCCTTTGACCTTTTGAAAGCACCAGGGGCTGCCACATGTCATGATTTTGGTTTATT
326 TCAATTTAATCCTTTGACCTTTTGAAAGCACCAGGGGCTGCCACATGTCATGATTTTGGTTTATT
1317 TATGAAAATGGTCCCTTTTATTTTTAATTTTTTTTAATTTAATCCTCAAATCAAGTTCTGTTTGA
391 TATGAAAATGGTCCCTTTTATTTTTAATTTTTTTTAATTTAATCCTCAAATCAAGTTCTGTTTGA
1382 TTACAAAATTGGTCTAGAAATTTTTCATGGTTTTCAAGTTAGTCCTTTGACTTCAGGAAGCCTGA
456 TTACAAAATTGGTCTAGAAATTTTTCATGGTTTTCAAGTTAGTCCTTTGACTTCAGGAAGCCTGA
1447 GGGGTTGCCACGTGTCACTTATTTTTTGTTTTATTGCCCTAGANNNNNNNNNNACGCGCGGTGGA
521 GGGGTTGCCACGTGTCACTTATTTTTTGTTTTATTGCCCTAGA----------ACGCGCGGTGGA
1512 CGGCAACAAGGTGACCGGCCAGAGCTTGGCCGGCCAT
576 CGGCAACAAGGTGACCGGCCAGAGCTTGGCCGGCCAT
1549 GTGAAAGGAGAGAGCTTTTTTGAAGGGTGAATTTGTTTTTCTGAAAAAGAGAAGGGAAAAATGAT
1 GTGAAAGGAGAGAGCTTTTTTGAAGGGTGAATTTGTTTTTCTGAAAAAGAGAAGGGAAAAATGAT
*
1614 TTTTTTAGTGAAAGTTGGAATTTATAGTAGCATTAAAACGTTGTTGTTTCAAGGGTGATTACTGG
66 TTTTTTAGTGAAAGTTGGAATTTATAGTAGCATTAAAACGTTGTCGTTTCAAGGGTGATTACTGG
1679 GTGCCAAAACGACACCGTTTTTAGCCTCTGCCCATGACCCATCTGACCCGACCCGACCCGAACCG
131 GTGCCAAAACGACACCGTTTTTAGCCTCTGCCCATGACCCATCT-----GACCCGACCCGAACCG
1744 TCCTTAGGATCCACGTGTTTTCGTTGAAGGGTATATTTATGCATTTGGTCCTTCCGCTTTTTTTT
191 TCCTTAGGATCCACGTGTTTTCGTTGAAGGGTATATTTATGCATTTGGTCCTTCCGCTTTTTTTT
1809 TATTTTTACAATCATATCCTTTTTATACTTTTAATTAATTTTAAATTGACCCAATAATTTTCAAT
256 TATTTTTACAATCATATCCTTTTTATACTTTTAATTAATTTTAAATTGACCCAATAATTTTCAAT
1874 ACTTTTCAATTTAATCCTTTGACCTTTTGAAAGCACCAGGGGCTGCCACATGTCATGATTTTGGT
321 ACTTTTCAATTTAATCCTTTGACCTTTTGAAAGCACCAGGGGCTGCCACATGTCATGATTTTGGT
1939 TTATTTATGAAAATGGTCCCTTTTATTTTTAATTTTTTTTAATTTAATCCTCAAATCAAGTTCTG
386 TTATTTATGAAAATGGTCCCTTTTATTTTTAATTTTTTTTAATTTAATCCTCAAATCAAGTTCTG
2004 TTTGATTACAAAATTGGTCTAGAAATTTTTCATGGTTTTCAAGTTAGTCCTTTGACTTCAGGAAG
451 TTTGATTACAAAATTGGTCTAGAAATTTTTCATGGTTTTCAAGTTAGTCCTTTGACTTCAGGAAG
2069 CCTGAGGGGTTGCCACGTGTCACTTATTTTTTGTTTTATTGCCCTAGA
516 CCTGAGGGGTTGCCACGTGTCACTTATTTTTTGTTTTATTGCCCTAGA
2117 GGTCCCTAAA
Statistics
Matches: 558, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
622 171 0.31
627 387 0.69
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (612 bp):
GTGAAAGGAGAGAGCTTTTTTGAAGGGTGAATTTGTTTTTCTGAAAAAGAGAAGGGAAAAATGAT
TTTTTTAGTGAAAGTTGGAATTTATAGTAGCATTAAAACGTTGTCGTTTCAAGGGTGATTACTGG
GTGCCAAAACGACACCGTTTTTAGCCTCTGCCCATGACCCATCTGACCCGACCCGAACCGTCCTT
AGGATCCACGTGTTTTCGTTGAAGGGTATATTTATGCATTTGGTCCTTCCGCTTTTTTTTTATTT
TTACAATCATATCCTTTTTATACTTTTAATTAATTTTAAATTGACCCAATAATTTTCAATACTTT
TCAATTTAATCCTTTGACCTTTTGAAAGCACCAGGGGCTGCCACATGTCATGATTTTGGTTTATT
TATGAAAATGGTCCCTTTTATTTTTAATTTTTTTTAATTTAATCCTCAAATCAAGTTCTGTTTGA
TTACAAAATTGGTCTAGAAATTTTTCATGGTTTTCAAGTTAGTCCTTTGACTTCAGGAAGCCTGA
GGGGTTGCCACGTGTCACTTATTTTTTGTTTTATTGCCCTAGAACGCGCGGTGGACGGCAACAAG
GTGACCGGCCAGAGCTTGGCCGGCCAT
Found at i:2191 original size:30 final size:29
Alignment explanation
Indices: 2136--2471 Score: 342
Period size: 30 Copynumber: 11.4 Consensus size: 29
2126 ACTGTTTGAG
* * **
2136 AATTACATTTTTACCCCCGAACTTCCAAA
1 AATTCCATTTTTACCTCAAAACTTCCAAA
* *
2165 AATTCCATTTTCGACCTCGAAACTTCCAAA
1 AATTCCATTTT-TACCTCAAAACTTCCAAA
*
2195 AATTCCATTTTTACCCTC-AAACTACCAAA
1 AATTCCATTTTTA-CCTCAAAACTTCCAAA
*
2224 AATTCCATTTTTAACC-CTAAAATTTCCAAA
1 AATTCCATTTTT-ACCTC-AAAACTTCCAAA
* *
2254 AATTCCATTTTTACC-CTTAAACTTCAAAA
1 AATTCCATTTTTACCTC-AAAACTTCCAAA
* *
2283 AATTCCAATTTTAACCCCAAAACTTCCAAA
1 AATTCC-ATTTTTACCTCAAAACTTCCAAA
*
2313 AATTCCTTTTTTACCCTC-AAACTTCCAAA
1 AATTCCATTTTTA-CCTCAAAACTTCCAAA
* * *
2342 AATTTCATTTTTGACCTCCAAACTTCTAAA
1 AATTCCATTTTT-ACCTCAAAACTTCCAAA
* *
2372 AATTCCATTTTTACCCCCTAAACTTCCAAA
1 AATTCCATTTTTA-CCTCAAAACTTCCAAA
2402 AATTCCATTTTTGACCTCAAAACTTCCAAA
1 AATTCCATTTTT-ACCTCAAAACTTCCAAA
*
2432 AATTCCATTTTTACCCTC-GAA-TGTCCAAA
1 AATTCCATTTTTA-CCTCAAAACT-TCCAAA
*
2461 AACTCCATTTT
1 AATTCCATTTT
2472 CGACCTCGAA
Statistics
Matches: 264, Mismatches: 29, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.01
29 105 0.40
30 155 0.59
31 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
AATTCCATTTTTACCTCAAAACTTCCAAA
Found at i:2223 original size:59 final size:59
Alignment explanation
Indices: 2136--2531 Score: 462
Period size: 59 Copynumber: 6.7 Consensus size: 59
2126 ACTGTTTGAG
* * * * *
2136 AATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTCGAAACTTCCAAA
1 AATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
* * *
2195 AATTCCATTTTTACCCTCAAACTACCAAAAATTCCATTTTTAACC-CTAAAATTTCCAAA
1 AATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTC-AAAACTTCCAAA
* * * * *
2254 AATTCCATTTTTACCCTTAAACTTCAAAAAATTCCAATTTTAACCCCAAAACTTCCAAA
1 AATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
* * * *
2313 AATTCCTTTTTTACCCTCAAACTTCCAAAAATTTCATTTTTGACCTCCAAACTTCTAAA
1 AATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
*
2372 AATTCCATTTTTACCCCCTAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
1 AATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
* * * *
2432 AATTCCATTTTTACCCTCGAA-TGTCCAAAAACTCCATTTTCGACCTCGAAAC-TCTCAAA
1 AATTCCATTTTTACCCTCAAACT-TCCAAAAATTCCATTTTTGACCTCAAAACTTC-CAAA
* * *
2491 ATTATCC--TTTTACCCTCGAA-TGTCTACAAAATTCCATTTTT
1 AAT-TCCATTTTTACCCTCAAACT-TCCA-AAAATTCCATTTTT
2532 AACCCCGAAC
Statistics
Matches: 294, Mismatches: 36, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
58 22 0.07
59 213 0.72
60 59 0.20
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAA
Found at i:2491 original size:89 final size:87
Alignment explanation
Indices: 2155--2471 Score: 388
Period size: 89 Copynumber: 3.6 Consensus size: 87
2145 TTTACCCCCG
* * *
2155 AACTTCCAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTAC
1 AACTTCCAAAAATTCCATTTT-TACCTC-AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTC
2220 CAAAAATTCCATTTTTAACC-CTAA
64 CAAAAATTCCATTTTTAACCTC-AA
* * * * *
2244 AATTTCCAAAAATTCCATTTTTACCCTTAAACTTCAAAAAATTCCAATTTTAACCCCAAAACTTC
1 AACTTCCAAAAATTCCATTTTTA-CCTCAAACTTCCAAAAATTCC-ATTTTTACCCCCAAACTTC
* *
2309 CAAAAATTCCTTTTTTACCCTC-A
64 CAAAAATTCCATTTTTAACCTCAA
* *
2332 AACTTCCAAAAATTTCATTTTTGACCTCCAAACTTCTAAAAATTCCATTTTTACCCCCTAAACTT
1 AACTTCCAAAAATTCCATTTTT-ACCT-CAAACTTCCAAAAATTCCATTTTTACCCCC-AAACTT
*
2397 CCAAAAATTCCATTTTTGACCTCAA
63 CCAAAAATTCCATTTTTAACCTCAA
* *
2422 AACTTCCAAAAATTCCATTTTTACCCTCGAA-TGTCCAAAAACTCCATTTT
1 AACTTCCAAAAATTCCATTTTTA-CCTCAAACT-TCCAAAAATTCCATTTT
2472 CGACCTCGAA
Statistics
Matches: 196, Mismatches: 23, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
88 52 0.27
89 118 0.60
90 26 0.13
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTACCTCAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCA
AAAATTCCATTTTTAACCTCAA
Found at i:2507 original size:29 final size:30
Alignment explanation
Indices: 2475--2593 Score: 76
Period size: 30 Copynumber: 4.1 Consensus size: 30
2465 CCATTTTCGA
2475 CCTCGAAACTCTCAAAATTATCC-TTTTAC
1 CCTCGAAACTCTCAAAATTATCCATTTTAC
**
2504 CCTCGAATGTCTACAAAA-T-TCCATTTTTAAC
1 CCTCGAAACTCT-CAAAATTATCCA-TTTT-AC
* *
2535 CC-CG-AACTTTCACAAAATTA-CCATTTTGC
1 CCTCGAAAC--TCTCAAAATTATCCATTTTAC
*
2564 CCTCGAGAA-TC-CAAAATTAT-CGTTTTAC
1 CCTCGA-AACTCTCAAAATTATCCATTTTAC
2592 CC
1 CC
2594 CCGGGTATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
28 19 0.27
29 17 0.24
30 22 0.31
31 10 0.14
32 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (30 bp):
CCTCGAAACTCTCAAAATTATCCATTTTAC
Found at i:2579 original size:88 final size:88
Alignment explanation
Indices: 2430--2593 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
2420 AAAACTTCCA
2430 AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATTA
1 AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATTA
2495 TCCTTTTACCCTCGAATGTCTAC
66 TCCTTTTACCCTCGAATGTCTAC
* * *
2518 AAAATTCCATTTTTAACCC-CGAACT-TTCACAAAATTACCATTTT-GCCCTCGAGAA-TC-CAA
1 AAAATTCCATTTTT-ACCCTCGAA-TGTCCA-AAAACT-CCATTTTCGACCTCGA-AACTCTCAA
*
2578 AATTATCGTTTTACCC
61 AATTATCCTTTTACCC
2594 CCGGGTATCC
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
88 39 0.58
89 19 0.28
90 9 0.13
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.33
Consensus pattern (88 bp):
AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATTA
TCCTTTTACCCTCGAATGTCTAC
Found at i:9645 original size:24 final size:24
Alignment explanation
Indices: 9618--9664 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9608 AGAAATAATC
*
9618 TTTCAAATAAATTATGTTTATTTG
1 TTTCAAATAAACTATGTTTATTTG
* *
9642 TTTCAATTAAACTCTGTTTATTT
1 TTTCAAATAAACTATGTTTATTT
9665 ATTTGAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAAATAAACTATGTTTATTTG
Found at i:9677 original size:24 final size:24
Alignment explanation
Indices: 9632--9680 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9622 AAATAAATTA
* *
9632 TGTTTATTTGTTTCAATTAAACTC
1 TGTTTATTTATTTCAATCAAACTC
* *
9656 TGTTTATTTATTTGAGTCAAACTC
1 TGTTTATTTATTTCAATCAAACTC
9680 T
1 T
9681 TATTAGTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
TGTTTATTTATTTCAATCAAACTC
Found at i:11466 original size:15 final size:15
Alignment explanation
Indices: 11446--11478 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11436 CCCCGTGGAG
11446 GGCTTTGGCAAAGAT
1 GGCTTTGGCAAAGAT
11461 GGCTTTGGCAAAGAT
1 GGCTTTGGCAAAGAT
11476 GGC
1 GGC
11479 ATTGTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.24
Consensus pattern (15 bp):
GGCTTTGGCAAAGAT
Found at i:11582 original size:24 final size:24
Alignment explanation
Indices: 11554--11616 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
11544 AGAAATAATC
*
11554 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
* *
11578 TTTCAATTAAACTTTGTTTAGTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
* *
11602 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
11617 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAGTTG
Found at i:22345 original size:17 final size:18
Alignment explanation
Indices: 22323--22358 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
22313 CCTATGCTTA
22323 GTTAATTCA-AATAATTG
1 GTTAATTCAGAATAATTG
22340 GTTAATTCATGAATAATTG
1 GTTAATTCA-GAATAATTG
22359 TTTATTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (18 bp):
GTTAATTCAGAATAATTG
Found at i:23928 original size:18 final size:19
Alignment explanation
Indices: 23905--23947 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
23895 TTGCACTTTA
*
23905 TTAATTAATTTAA-AAATT
1 TTAATTAATATAATAAATT
*
23923 TTAATTAATATAATATATT
1 TTAATTAATATAATAAATT
23942 TTAATT
1 TTAATT
23948 GACATACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATTAATATAATAAATT
Done.