Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012058.1 Kokia drynarioides strain JFW-HI SEQ_127056, 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: 48895
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1582 original size:16 final size:16
Alignment explanation
Indices: 1561--1609 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1551 TGATGGAGAT
1561 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1577 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
1591 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
1606 ATTA
1 ATTA
1610 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 4 0.14
16 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:2462 original size:23 final size:23
Alignment explanation
Indices: 2436--2513 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
2426 CTATAATAAC
*
2436 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATAAATTAAAA
*
2459 ATTAAATTAA-AAA-AAATAAAAA
1 ATTAAA-TAACAAATAAATTAAAA
* *
2481 ACTTAAAATAATCAAATTAACTAACAA
1 A-TT-AAATAA-CAAATAAATTAA-AA
2508 ATTAAA
1 ATTAAA
2514 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 8 0.19
23 14 0.33
24 6 0.14
25 6 0.14
26 6 0.14
27 3 0.07
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
ATTAAATAACAAATAAATTAAAA
Found at i:2695 original size:13 final size:13
Alignment explanation
Indices: 2674--2709 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2664 AAATTAAAAT
*
2674 ATTTTAAAATTAA
1 ATTTAAAAATTAA
2687 ATTTAAAAATTAA
1 ATTTAAAAATTAA
2700 ATTTAAAAAT
1 ATTTAAAAAT
2710 AAACACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAAAAATTAA
Found at i:4588 original size:29 final size:29
Alignment explanation
Indices: 4533--4589 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4523 TTTTAACCTG
* * *
4533 TATTATTTTGAAAATAATTTCTTATTTTA
1 TATTATTTTGAAAATAATATATAATTTTA
4562 TATTATTTTGATAAA-AATATATAATTTT
1 TATTATTTTGA-AAATAATATATAATTTT
4590 TAAACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (29 bp):
TATTATTTTGAAAATAATATATAATTTTA
Found at i:5015 original size:14 final size:15
Alignment explanation
Indices: 4980--5018 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
4970 ATAGTAAAAA
4980 TATAATTTTATCATTT
1 TATAA-TTTATCATTT
4996 TAATAATTTAT-ATTT
1 T-ATAATTTATCATTT
5011 TATAATTT
1 TATAATTT
5019 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 6 0.27
17 4 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TATAATTTATCATTT
Found at i:5105 original size:8 final size:9
Alignment explanation
Indices: 5080--5112 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5070 TACATTTATT
5080 AATTT-AAA
1 AATTTAAAA
*
5088 ATTTTAAAA
1 AATTTAAAA
5097 AATTTAAAA
1 AATTTAAAA
5106 AATTTAA
1 AATTTAA
5113 TTGAAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTTAAAA
Found at i:9812 original size:26 final size:26
Alignment explanation
Indices: 9725--9814 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 26
9715 AGTCGTTCTA
* * *
9725 AAAGTTTAGCTCATAC-AATCCCAAAC
1 AAAGTTTAGCTCTTACGAA-CCCAGAT
* *
9751 AGAA-TTTAGATCTTACGAACCTAGAT
1 A-AAGTTTAGCTCTTACGAACCCAGAT
* *
9777 AAAGTTTAGCTCTTTCGAGCCCAGAT
1 AAAGTTTAGCTCTTACGAACCCAGAT
*
9803 AGAGTTTAGCTC
1 AAAGTTTAGCTC
9815 ATGTGAGTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 2 0.04
26 45 0.88
27 4 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (26 bp):
AAAGTTTAGCTCTTACGAACCCAGAT
Found at i:11864 original size:34 final size:34
Alignment explanation
Indices: 11820--11896 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
11810 TTTATATCTA
*
11820 ACCAATTAAGCTCCAAATCATACATGACCACGAT
1 ACCAAGTAAGCTCCAAATCATACATGACCACGAT
11854 ACCAAGTAAGCTCCAAATCATACATGACCACGAT
1 ACCAAGTAAGCTCCAAATCATACATGACCACGAT
*
11888 ACCATGTAA
1 ACCAAGTAA
11897 AACCCTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (34 bp):
ACCAAGTAAGCTCCAAATCATACATGACCACGAT
Found at i:20098 original size:24 final size:24
Alignment explanation
Indices: 20071--20121 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
20061 AATTTGACTC
* *
20071 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
20095 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
20119 AAA
1 AAA
20122 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:25336 original size:16 final size:16
Alignment explanation
Indices: 25315--25350 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
25305 ATATATATAT
25315 GCATTACTTTGTCATA
1 GCATTACTTTGTCATA
25331 GCATTACTTTGTCATA
1 GCATTACTTTGTCATA
25347 GCAT
1 GCAT
25351 AGTATTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (16 bp):
GCATTACTTTGTCATA
Found at i:26834 original size:152 final size:152
Alignment explanation
Indices: 26558--26848 Score: 494
Period size: 152 Copynumber: 1.9 Consensus size: 152
26548 CTGACACCTT
26558 AGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGTAACACATAGTGGAGGCAAT
1 AGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGTAACACATAGTGGAGGCAAT
* * **
26623 CACGAGTTGGAAAAATGCCATTTGAATCTTGAACTCGTGTGTTACGTAAAAAACTTCAATCGTAA
66 CACGAGTTGGAAAAATGCCATTTGAATCTTGAACCCATGTGTTACGTAAAAAACTTCAATCACAA
26688 CAACAACCCTTAACATGGGTTC
131 CAACAACCCTTAACATGGGTTC
* * *
26710 AGGTATCCTCTCTAGCCAATATGATTAAAAATATGCAAAGATTCGTAACATATCGTGGAGGCAAT
1 AGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGTAACACATAGTGGAGGCAAT
*
26775 CACGAGTTGGAAGAATGCCATTTGAATCTTGAACCCATGTGTTACGTGAAAAAA-TTCAATCACA
66 CACGAGTTGGAAAAATGCCATTTGAATCTTGAACCCATGTGTTACGT-AAAAAACTTCAATCACA
26839 ACAACAACCC
130 ACAACAACCC
26849 ATACTCAAAC
Statistics
Matches: 130, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
152 124 0.95
153 6 0.05
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (152 bp):
AGGTATCCTCTCTAGCCAACATGATTAAAAATATGCAAAGATTCGTAACACATAGTGGAGGCAAT
CACGAGTTGGAAAAATGCCATTTGAATCTTGAACCCATGTGTTACGTAAAAAACTTCAATCACAA
CAACAACCCTTAACATGGGTTC
Found at i:28141 original size:15 final size:15
Alignment explanation
Indices: 28123--28156 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28113 TTTTATTTTC
*
28123 TTTTATTGCATGTGA
1 TTTTATTGCAGGTGA
*
28138 TTTTATTTCAGGTGA
1 TTTTATTGCAGGTGA
28153 TTTT
1 TTTT
28157 TTCTTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (15 bp):
TTTTATTGCAGGTGA
Found at i:42166 original size:21 final size:21
Alignment explanation
Indices: 42142--42193 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
42132 TGTAAAAAAC
*
42142 ATGATATGTGTTATGTGATCT
1 ATGATATGTGTTACGTGATCT
* * *
42163 ATGAAAAGTGTTACGTGATGT
1 ATGATATGTGTTACGTGATCT
*
42184 ATGATTTGTG
1 ATGATATGTG
42194 ATTTCATCTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.42
Consensus pattern (21 bp):
ATGATATGTGTTACGTGATCT
Found at i:42777 original size:8 final size:8
Alignment explanation
Indices: 42749--42782 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
42739 TGTTTTAAAC
42749 ATGTGATT
1 ATGTGATT
42757 ATTGTGA-T
1 A-TGTGATT
42765 ATGTGATT
1 ATGTGATT
42773 ATGTGATT
1 ATGTGATT
42781 AT
1 AT
42783 CTAGATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 5 0.21
8 14 0.58
9 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (8 bp):
ATGTGATT
Found at i:42881 original size:107 final size:108
Alignment explanation
Indices: 42760--42962 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 108
42750 TGTGATTATT
* * * * * *
42760 GTGATATGTGATTATGTGATTATCTAGATCTATGATCTAATATGAAA-AGCATGTTAAGCATGTT
1 GTGATAAGTGATTATGTCATTACCAAGATCTATGATCTAACATGAAATA-CATGTTAAACATG-T
42824 AA-AAGCT-AAATA-AGTGATTATGTGAGCATATCTATATGCCTAA
64 AATAAG-TGAAATATAGTGATTATGTGAGCATATCTATATGCCTAA
* *
42867 GTGATAAGTGATTATGTCATTACCAAGATCTATGATCTAACGTGAAATACATGTTAAATATGTAA
1 GTGATAAGTGATTATGTCATTACCAAGATCTATGATCTAACATGAAATACATGTTAAACATGTAA
* *
42932 TAAGTGATATATTGTGATTATGTGAGCATAT
66 TAAGTGAAATATAGTGATTATGTGAGCATAT
42963 TCATATGTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
106 4 0.05
107 59 0.72
108 19 0.23
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (108 bp):
GTGATAAGTGATTATGTCATTACCAAGATCTATGATCTAACATGAAATACATGTTAAACATGTAA
TAAGTGAAATATAGTGATTATGTGAGCATATCTATATGCCTAA
Found at i:43504 original size:19 final size:19
Alignment explanation
Indices: 43462--43559 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
43452 GAGATATGAA
*
43462 AATATGTGGAATT--TGTG
1 AATATGTGAAATTGATGTG
43479 -ATCATGTGAAATTGATGTG
1 AAT-ATGTGAAATTGATGTG
**
43498 AATATGTGAAATTGATGCC
1 AATATGTGAAATTGATGTG
* *
43517 AATATGTGACATTGATGTT
1 AATATGTGAAATTGATGTG
*
43536 AATATGTGAAATAGATGTG
1 AATATGTGAAATTGATGTG
43555 AATAT
1 AATAT
43560 CAAATGTGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.03
17 9 0.13
19 55 0.81
20 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (19 bp):
AATATGTGAAATTGATGTG
Found at i:46849 original size:20 final size:19
Alignment explanation
Indices: 46824--46863 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
46814 CGTTTCTCAC
46824 TTCTTT-TTTCTCTTTAGTTT
1 TTCTTTCTTTCT-TTTA-TTT
46844 TTCTTTCTTTCTTTTATTT
1 TTCTTTCTTTCTTTTATTT
46863 T
1 T
46864 CAAAAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (19 bp):
TTCTTTCTTTCTTTTATTT
Found at i:48515 original size:3 final size:3
Alignment explanation
Indices: 48441--48498 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
48431 TACAATTTAC
*
48441 ATT ATT -TT A-T ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48487 ATT ATT ATT ATT
1 ATT ATT ATT ATT
48499 TAGATTTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:48598 original size:14 final size:13
Alignment explanation
Indices: 48581--48616 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
48571 CTTTTGGTAC
48581 TTTATTTTTTTAGT
1 TTTATTTTTTTA-T
*
48595 TTTATTTATTTAT
1 TTTATTTTTTTAT
48608 TTTATTTTT
1 TTTATTTTT
48617 AGTTATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:48616 original size:19 final size:18
Alignment explanation
Indices: 48581--48622 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
48571 CTTTTGGTAC
48581 TTTATTTTTTTAGTTTTA
1 TTTATTTTTTTAGTTTTA
*
48599 TTTATTTATTTTATTTTTA
1 TTTATTT-TTTTAGTTTTA
*
48618 GTTAT
1 TTTAT
48623 AAGTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTATTTTTTTAGTTTTA
Done.