Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001181.1 Kokia drynarioides strain JFW-HI SEQ_112515, 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: 43454
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:6639 original size:15 final size:15
Alignment explanation
Indices: 6604--6636 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6594 AATTTTTATA
6604 AGAATTTTTATTTTT
1 AGAATTTTTATTTTT
*
6619 TGAATTTTT-TTTTT
1 AGAATTTTTATTTTT
6633 AGAA
1 AGAA
6637 ATTATGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
AGAATTTTTATTTTT
Found at i:8097 original size:23 final size:23
Alignment explanation
Indices: 8070--8115 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8060 TCCATAGAAG
8070 CGAGTCAATCGAGTAAAAAATTT
1 CGAGTCAATCGAGTAAAAAATTT
* * * *
8093 CGAGTTAGTCGAGTGACAAATTT
1 CGAGTCAATCGAGTAAAAAATTT
8116 ATTTTAGTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (23 bp):
CGAGTCAATCGAGTAAAAAATTT
Found at i:8410 original size:70 final size:67
Alignment explanation
Indices: 8287--8419 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
8277 ATGAACAATA
* ** * *
8287 TAATGATTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAACGACGTAGTTTTAACTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAAAGTAAACAGTTATCAAAACGACATAGTTTTAACTTTTAA
8352 CT
66 CT
*
8354 TAATGATTTTGACTTTTAACTTTAGAAAAGGTAAACAGTTATCAAAACGACATAGTTTTATCTTT
1 TAATGATTTTGACTTTTAAC-TTA-AAAA-GTAAACAGTTATCAAAACGACATAGTTTTAACTTT
8419 T
63 T
8420 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 2 0.04
70 33 0.58
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAAAGTAAACAGTTATCAAAACGACATAGTTTTAACTTTTAA
CT
Found at i:8542 original size:23 final size:21
Alignment explanation
Indices: 8516--8561 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8506 AATAACTTGA
8516 TTAACTCAAATAATTTGAACTAT
1 TTAACTC-AA-AATTTGAACTAT
* *
8539 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAATTTGAACTAT
8560 TT
1 TT
8562 TCAAGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAATTTGAACTAT
Found at i:8965 original size:21 final size:20
Alignment explanation
Indices: 8931--8975 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
8921 AAAATAATTG
*
8931 TTTTTTTGTTAAAAT-ATAA
1 TTTTTTTGTTAAAATCAAAA
8950 TTTTTTTGCTTCAAAATCAAAA
1 TTTTTTTG-TT-AAAATCAAAA
8972 TTTT
1 TTTT
8976 CAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 5 0.23
22 7 0.32
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTTGTTAAAATCAAAA
Found at i:9139 original size:9 final size:9
Alignment explanation
Indices: 9125--9149 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9115 TATTTAGTTA
9125 TTTATTTTG
1 TTTATTTTG
9134 TTTATTTTG
1 TTTATTTTG
9143 TTTATTT
1 TTTATTT
9150 AATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTATTTTG
Found at i:9204 original size:4 final size:4
Alignment explanation
Indices: 9110--9187 Score: 66
Period size: 4 Copynumber: 19.0 Consensus size: 4
9100 CATCGTAAAA
* * * *
9110 TTAT TTAT TTAG TTAT TTATT TTGT TTATT TTGT TTAT TTAA TTAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T TTAT TTA-T TTAT TTAT TTAT TTAT TTAT
* * * *
9160 TTAC TTAT TTAC ATAC TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
9188 ATCGTAAAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
4 52 0.90
5 6 0.10
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:10090 original size:17 final size:17
Alignment explanation
Indices: 10064--10100 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10054 AAATAAAAAA
* *
10064 TTATATTTTTAAAATTT
1 TTATAATTTTAAAAATT
10081 TTATAATTTTAAAAATT
1 TTATAATTTTAAAAATT
10098 TTA
1 TTA
10101 AATCAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATAATTTTAAAAATT
Found at i:10095 original size:18 final size:17
Alignment explanation
Indices: 10064--10099 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10054 AAATAAAAAA
*
10064 TTATATTTTTAAAATTT
1 TTATATTTTAAAAATTT
10081 TTATAATTTTAAAAATTT
1 TTAT-ATTTTAAAAATTT
10099 T
1 T
10100 AAATCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTTAAAAATTT
Found at i:10533 original size:28 final size:28
Alignment explanation
Indices: 10475--10534 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
10465 TTAATTTCTG
* *
10475 TATTTTTAATTTTAAAAATTTAATTATT
1 TATTTTTAATATTAAAAATTTAATTAAT
10503 TATTTTTAA-ATT-AAAATTTATATTCAAT
1 TATTTTTAATATTAAAAATTTA-ATT-AAT
10531 TATT
1 TATT
10535 AATACTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.29
27 5 0.18
28 15 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTTAATATTAAAAATTTAATTAAT
Found at i:10726 original size:23 final size:23
Alignment explanation
Indices: 10700--10743 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10690 ATTCTTAAAA
*
10700 TTAAAAATATAAAAATTTAAATT
1 TTAAAAATATAAAAAGTTAAATT
**
10723 TTAAATTTATAAAAAGTTAAA
1 TTAAAAATATAAAAAGTTAAA
10744 AAAATATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAAAATATAAAAAGTTAAATT
Found at i:12283 original size:31 final size:29
Alignment explanation
Indices: 12207--12288 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 29
12197 ACAAGAGTGC
12207 TCAAATGAAGG-TCAAACCTTTTAAAATAA
1 TCAAAT-AAGGATCAAACCTTTTAAAATAA
** *
12236 TCAAATAAGGGCCAAACCTTTTCGAAAATAC
1 TCAAATAAGGATCAAACCTTTT--AAAATAA
* * *
12267 TCAACTAATGATCAAACGTTTT
1 TCAAATAAGGATCAAACCTTTT
12289 TGAAGATGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.09
29 16 0.37
31 23 0.53
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (29 bp):
TCAAATAAGGATCAAACCTTTTAAAATAA
Found at i:12746 original size:67 final size:67
Alignment explanation
Indices: 12673--12808 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
12663 GGTCACTTCT
12673 TTGGCACCAAATTAGAAGCAATAAACAAAATTCAACACATAGCTATTGTTTACGCAGTTCGATTT
1 TTGGCACCAAATTAGAAGCAATAAACAAAATTCAACACATAGCTATTGTTTACGCAGTTCGATTT
12738 TC
66 TC
12740 TTGGCACCAAATTAGAAGCAATAAACAAAATTCAACACATAGCTATTGTTTACGCAGTTCGATTT
1 TTGGCACCAAATTAGAAGCAATAAACAAAATTCAACACATAGCTATTGTTTACGCAGTTCGATTT
12805 TC
66 TC
12807 TT
1 TT
12809 ACTTCTGCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (67 bp):
TTGGCACCAAATTAGAAGCAATAAACAAAATTCAACACATAGCTATTGTTTACGCAGTTCGATTT
TC
Found at i:16669 original size:14 final size:14
Alignment explanation
Indices: 16650--16683 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
16640 TTTCAGCAAT
*
16650 TTTTTCTTTTTTTC
1 TTTTTCTTTTCTTC
16664 TTTTTC-TTTCTTC
1 TTTTTCTTTTCTTC
16677 TTTTTCT
1 TTTTTCT
16684 CATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:34656 original size:18 final size:17
Alignment explanation
Indices: 34628--34677 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
34618 GTCGAGATGA
34628 TAAACAATAATAATAATTT
1 TAAACAATAATAATAA--T
34647 TAAA-AATAATAATTAAT
1 TAAACAATAATAA-TAAT
*
34664 TAAAGAATAATAAT
1 TAAACAATAATAAT
34678 TTAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.21
18 16 0.55
19 7 0.24
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAACAATAATAATAAT
Found at i:34678 original size:18 final size:15
Alignment explanation
Indices: 34636--34688 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 15
34626 GATAAACAAT
34636 AATAATAATTTTAAA
1 AATAATAATTTTAAA
34651 AATAATAATTAATTAAA
1 AATAATAATT--TTAAA
34668 GAATAATAA-TTTAATA
1 -AATAATAATTTTAA-A
34684 AATAA
1 AATAA
34689 AAATAAGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 19 0.56
16 1 0.03
17 6 0.18
18 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATAATAATTTTAAA
Found at i:34693 original size:18 final size:20
Alignment explanation
Indices: 34647--34694 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
34637 ATAATAATTT
34647 TAAAAATAATAATTAATTAAA
1 TAAAAATAAT-ATTAATTAAA
* *
34668 GAATAATAAT-TTAA-TAAA
1 TAAAAATAATATTAATTAAA
34686 TAAAAATAA
1 TAAAAATAA
34695 GCTAGAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 11 0.48
19 4 0.17
21 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAATAATATTAATTAAA
Found at i:37287 original size:39 final size:39
Alignment explanation
Indices: 37244--37319 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
37234 TAAGGTATTA
*
37244 CGGTGTTTACAGTGTCACCGTCATTTCATTATAGTATAT
1 CGGTGTTTACAGTGTCACCGTCATTTCAATATAGTATAT
* * *
37283 CGGTGTTTACAGTGTTAGCGTCATTTTAATATAGTAT
1 CGGTGTTTACAGTGTCACCGTCATTTCAATATAGTAT
37320 TGCAATATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (39 bp):
CGGTGTTTACAGTGTCACCGTCATTTCAATATAGTATAT
Done.