Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011348.1 Kokia drynarioides strain JFW-HI SEQ_126328, 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: 24299
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:114 original size:17 final size:17
Alignment explanation
Indices: 71--167 Score: 122
Period size: 17 Copynumber: 5.6 Consensus size: 17
61 GGTTTTATTT
71 TAAATTTTAAATTTTAAAA
1 TAAA-TTTAAA-TTTAAAA
* * *
90 TAACTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
107 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
124 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
* *
141 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
158 TAAATTTAAA
1 TAAATTTAAA
168 GGGAGTATGG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 57 0.86
18 6 0.09
19 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5776 original size:21 final size:22
Alignment explanation
Indices: 5751--5801 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
5741 CAAAACCATG
* *
5751 AAAACCCAAT-ACTCAAACCCT
1 AAAACCAAATCACCCAAACCCT
*
5772 AAAACCAAATCACCCAAACCTT
1 AAAACCAAATCACCCAAACCCT
*
5794 AAATCCAA
1 AAAACCAA
5802 TTCGATTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAACCAAATCACCCAAACCCT
Found at i:10230 original size:14 final size:16
Alignment explanation
Indices: 10197--10229 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10187 ACAATGTTTC
10197 TTTCTCTCTCGAAATT
1 TTTCTCTCTCGAAATT
*
10213 TTTCTCTGT-GAAATT
1 TTTCTCTCTCGAAATT
10228 TT
1 TT
10230 CATACGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (16 bp):
TTTCTCTCTCGAAATT
Found at i:13135 original size:30 final size:30
Alignment explanation
Indices: 13094--13171 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
13084 TTACGTTAAC
*
13094 AAGATACCCCTCACATTTTCAAGTGGTTCT
1 AAGACACCCCTCACATTTTCAAGTGGTTCT
*
13124 AAGACACCCCTCACATTTTCAAGTGTTTCT
1 AAGACACCCCTCACATTTTCAAGTGGTTCT
*
13154 AAGACACCCCTCATATTT
1 AAGACACCCCTCACATTT
13172 CCAAATGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.32
Consensus pattern (30 bp):
AAGACACCCCTCACATTTTCAAGTGGTTCT
Found at i:17500 original size:29 final size:29
Alignment explanation
Indices: 17467--17522 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
17457 TCTTTCAATA
* *
17467 TGATATTTTTACTTTAAAAAAGTTTATTT
1 TGATACTTATACTTTAAAAAAGTTTATTT
* *
17496 TGATACTTATACTTTAAACATGTTTAT
1 TGATACTTATACTTTAAAAAAGTTTAT
17523 CAATGTAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (29 bp):
TGATACTTATACTTTAAAAAAGTTTATTT
Found at i:18097 original size:21 final size:19
Alignment explanation
Indices: 18054--18126 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
18044 TTATAAAAAA
* **
18054 AAAAATCAATAAAAGTTAT
1 AAAAATTAATAAATTTTAT
18073 AAAAATTAATAAATTTTAAT
1 AAAAATTAATAAATTTT-AT
*
18093 AAAAATATATTTAAATTTTATT
1 AAAAAT-TA-ATAAATTTTA-T
18115 AAAAATT-ATAAA
1 AAAAATTAATAAA
18127 AATCGTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 18 0.40
20 8 0.18
21 4 0.09
22 15 0.33
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTAATAAATTTTAT
Found at i:18129 original size:21 final size:21
Alignment explanation
Indices: 18071--18147 Score: 79
Period size: 22 Copynumber: 3.8 Consensus size: 21
18061 AATAAAAGTT
18071 ATAAAAATTA-ATAAATTTTA
1 ATAAAAATTATATAAATTTTA
*
18091 ATAAAAATATATTTAAATTTTA
1 ATAAAAAT-TATATAAATTTTA
* * **
18113 TTAAAAATTATAAAAATCGTA
1 ATAAAAATTATATAAATTTTA
18134 A-AAAAATT-TATAAA
1 ATAAAAATTATATAAA
18148 ATGCATCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
19 5 0.11
20 15 0.32
21 11 0.23
22 16 0.34
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAAAAATTATATAAATTTTA
Found at i:18294 original size:21 final size:20
Alignment explanation
Indices: 18258--18323 Score: 87
Period size: 21 Copynumber: 3.2 Consensus size: 20
18248 ATATGTAGCG
*
18258 AAAAATGATAAAAAATAAAT
1 AAAAATTATAAAAAATAAAT
* *
18278 AAAATTTATAGAAAAATCAAT
1 AAAAATTATA-AAAAATAAAT
18299 AAAAATTATAAAAAATAAAAT
1 AAAAATTATAAAAAAT-AAAT
18320 AAAA
1 AAAA
18324 GTTAACGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAATTATAAAAAATAAAT
Found at i:18490 original size:87 final size:88
Alignment explanation
Indices: 18360--18528 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 88
18350 ATGCATCAGG
* *
18360 CCCTCAAACTTTAAAAAAAAAAACAATTAACCCCTACTTTTTTTGCACTGAATTAAATACTTAAA
1 CCCTCAAACTTT-AAAAAAAAAACAATTAACCCCTACTTTTTTTACACTCAATTAAATACTTAAA
18425 CTT-TCAAAATGCATAAAGAAAAAA
65 -TTGTCAAAATGCATAAAGAAAAAA
* * * * *
18449 CCCTCAAACTTT-AAAAAAAAACAATTAA-GCCTATTTTTTTTTACACTCAATTGAGTACTTGAA
1 CCCTCAAACTTTAAAAAAAAAACAATTAACCCCTA-CTTTTTTTACACTCAATTAAATACTTAAA
*
18512 TTGTTAAAATGCATAAA
65 TTGTCAAAATGCATAAA
18529 AAAGACTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
86 6 0.09
87 52 0.74
89 12 0.17
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (88 bp):
CCCTCAAACTTTAAAAAAAAAACAATTAACCCCTACTTTTTTTACACTCAATTAAATACTTAAAT
TGTCAAAATGCATAAAGAAAAAA
Found at i:18755 original size:20 final size:20
Alignment explanation
Indices: 18730--18793 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
18720 TTAAAAATAG
18730 AAAATTTATAAAAATCGTAA
1 AAAATTTATAAAAATCGTAA
*
18750 AAAATTTATAAAAAAACTGT-A
1 AAAATTTAT-AAAAATC-GTAA
* *
18771 AAATTTTATAAAAATCATAA
1 AAAATTTATAAAAATCGTAA
18791 AAA
1 AAA
18794 TTATAAATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 15 0.41
22 2 0.05
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAATTTATAAAAATCGTAA
Found at i:18773 original size:21 final size:21
Alignment explanation
Indices: 18730--18784 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
18720 TTAAAAATAG
*
18730 AAAATTTAT-AAAAATCGTAA
1 AAAATTTATAAAAAAACGTAA
18750 AAAATTTATAAAAAAACTGT-A
1 AAAATTTATAAAAAAAC-GTAA
*
18771 AAATTTTATAAAAA
1 AAAATTTATAAAAA
18785 TCATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 9 0.29
21 20 0.65
22 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATTTATAAAAAAACGTAA
Found at i:18939 original size:17 final size:17
Alignment explanation
Indices: 18917--18958 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
18907 CATATAGTAA
18917 AAAAATAATAAAAAAAT
1 AAAAATAATAAAAAAAT
* *
18934 AAAAATTATAAAAAATT
1 AAAAATAATAAAAAAAT
18951 ATAAAATA
1 A-AAAATA
18959 CCTCTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATAATAAAAAAAT
Found at i:18998 original size:27 final size:27
Alignment explanation
Indices: 18968--19023 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
18958 ACCTCTTTTG
18968 TTATGATTT-TTT-TATTTTTTACAAATT
1 TTAT-ATTTCTTTATATTTTTTAC-AATT
18995 TTATATTTCTTTATATTTTTTACAATT
1 TTATATTTCTTTATATTTTTTACAATT
19022 TT
1 TT
19024 CTTACGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.15
27 13 0.48
28 10 0.37
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (27 bp):
TTATATTTCTTTATATTTTTTACAATT
Found at i:19007 original size:10 final size:9
Alignment explanation
Indices: 18963--19083 Score: 50
Period size: 10 Copynumber: 12.8 Consensus size: 9
18953 AAAATACCTC
18963 TTTTGTTATGA
1 TTTT-TTAT-A
18974 TTTTTT-TA
1 TTTTTTATA
*
18982 TTTTTTACA
1 TTTTTTATA
**
18991 AATTTTATA
1 TTTTTTATA
19000 TTTCTTTATA
1 TTT-TTTATA
*
19010 TTTTTTACAA
1 TTTTTTA-TA
*
19020 TTTTCTTACGA
1 TTTT-TTA-TA
*
19031 TTTTATA-A
1 TTTTTTATA
**
19039 AATTTTATAA
1 TTTTTTAT-A
19049 TTTTTTACTA
1 TTTTTTA-TA
19059 -TTTTTATTA
1 TTTTTTA-TA
*
19068 TTTTTTCTA
1 TTTTTTATA
*
19077 ATTTTTA
1 TTTTTTA
19084 AGAAATTTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
8 12 0.14
9 28 0.33
10 30 0.36
11 14 0.17
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTTTATA
Found at i:19063 original size:19 final size:19
Alignment explanation
Indices: 19041--19083 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19031 TTTTATAAAA
19041 TTTTATAATTTTTTACT-AT
1 TTTTATAATTTTTT-CTAAT
*
19060 TTTTATTATTTTTTCTAAT
1 TTTTATAATTTTTTCTAAT
19079 TTTTA
1 TTTTA
19084 AGAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATAATTTTTTCTAAT
Found at i:21507 original size:20 final size:20
Alignment explanation
Indices: 21482--21565 Score: 109
Period size: 20 Copynumber: 4.3 Consensus size: 20
21472 ATTATATTGT
21482 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
* *
21502 TGTTTT-G-ATATTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
* *
21520 TGTTTTGATGTTTTTTTTGC
1 TGTTTTGGTGTTTTTTTTAC
*
21540 TGTTTTGGTTTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
21560 TGTTTT
1 TGTTTT
21566 TGCTGTCATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
18 15 0.28
19 1 0.02
20 37 0.70
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:21517 original size:18 final size:18
Alignment explanation
Indices: 21494--21535 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21484 TTTTGGTGTT
21494 TTTTTTACTGTTTTGATA
1 TTTTTTACTGTTTTGATA
*
21512 TTTTTTACTGTTTTGATG
1 TTTTTTACTGTTTTGATA
21530 TTTTTT
1 TTTTTT
21536 TTGCTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.71
Consensus pattern (18 bp):
TTTTTTACTGTTTTGATA
Found at i:21532 original size:38 final size:40
Alignment explanation
Indices: 21482--21565 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 40
21472 ATTATATTGT
*
21482 TGTTTTGGTGTTTTTTTTACTGTTTT-G-ATATTTTTTAC
1 TGTTTTGATGTTTTTTTTACTGTTTTGGTATATTTTTTAC
* * *
21520 TGTTTTGATGTTTTTTTTGCTGTTTTGGTTTTTTTTTTAC
1 TGTTTTGATGTTTTTTTTACTGTTTTGGTATATTTTTTAC
21560 TGTTTT
1 TGTTTT
21566 TGCTGTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 24 0.60
39 1 0.03
40 15 0.38
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (40 bp):
TGTTTTGATGTTTTTTTTACTGTTTTGGTATATTTTTTAC
Found at i:21602 original size:36 final size:36
Alignment explanation
Indices: 21562--21635 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
21552 TTTTTTACTG
21562 TTTTTGCTGTCATTTTTGTTGTTGTTTTTGTTGCTA
1 TTTTTGCTGTCATTTTTGTTGTTGTTTTTGTTGCTA
** *
21598 TTTTTGCTGTTTTTTTTGTTGTTGTTTTTGTTGTTA
1 TTTTTGCTGTCATTTTTGTTGTTGTTTTTGTTGCTA
21634 TT
1 TT
21636 ATTGTTTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.04, C:0.05, G:0.19, T:0.72
Consensus pattern (36 bp):
TTTTTGCTGTCATTTTTGTTGTTGTTTTTGTTGCTA
Found at i:21610 original size:21 final size:21
Alignment explanation
Indices: 21512--21611 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 21
21502 TGTTTTGATA
* * *
21512 TTTTTTACTG-TTTTGATGTT
1 TTTTTTGCTGTTTTTGTTGCT
* *
21532 TTTTTTGCTGTTTTGGTT-TT
1 TTTTTTGCTGTTTTTGTTGCT
* *
21552 TTTTTTACTGTTTTTGCTGTCAT
1 TTTTTTGCTGTTTTTGTTG-C-T
*
21575 TTTTGTTGTTGTTTTTGTTGCT
1 TTTT-TTGCTGTTTTTGTTGCT
*
21597 ATTTTTGCTGTTTTT
1 TTTTTTGCTGTTTTT
21612 TTTGTTGTTG
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 26 0.41
21 15 0.24
22 4 0.06
23 6 0.10
24 12 0.19
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (21 bp):
TTTTTTGCTGTTTTTGTTGCT
Found at i:21640 original size:12 final size:12
Alignment explanation
Indices: 21562--21641 Score: 88
Period size: 12 Copynumber: 6.7 Consensus size: 12
21552 TTTTTTACTG
* *
21562 TTTTTGCTGTCA
1 TTTTTGTTGTTA
*
21574 TTTTTGTTGTTG
1 TTTTTGTTGTTA
*
21586 TTTTTGTTGCTA
1 TTTTTGTTGTTA
* *
21598 TTTTTGCTGTTT
1 TTTTTGTTGTTA
*
21610 TTTTTGTTGTTG
1 TTTTTGTTGTTA
21622 TTTTTGTTGTTA
1 TTTTTGTTGTTA
*
21634 TTATTGTT
1 TTTTTGTT
21642 TTACTATTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 56 1.00
ACGTcount: A:0.05, C:0.05, G:0.19, T:0.71
Consensus pattern (12 bp):
TTTTTGTTGTTA
Done.