Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000420.1 Kokia drynarioides strain JFW-HI SEQ_111249, 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: 60191
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2328 original size:7 final size:7
Alignment explanation
Indices: 2316--2341 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2306 ATTAAATTAA
2316 TTAATGT
1 TTAATGT
2323 TTAATGT
1 TTAATGT
2330 TTAATGT
1 TTAATGT
2337 TTAAT
1 TTAAT
2342 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
TTAATGT
Found at i:13974 original size:30 final size:30
Alignment explanation
Indices: 13938--13998 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
13928 GTAAACCTTT
13938 AGTCCTAGCCGAGTGGCTCAACCGATAGAC
1 AGTCCTAGCCGAGTGGCTCAACCGATAGAC
*
13968 AGTCCTAGCTGAGTGGCTCAACCGATAGAC
1 AGTCCTAGCCGAGTGGCTCAACCGATAGAC
13998 A
1 A
13999 ACTCTAGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (30 bp):
AGTCCTAGCCGAGTGGCTCAACCGATAGAC
Found at i:14006 original size:30 final size:30
Alignment explanation
Indices: 13940--14007 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
13930 AAACCTTTAG
*
13940 TCCTAGCCGAGTGGCTCAACCGATAGACAG
1 TCCTAGCCGAGTGGCTCAACCGATAGACAC
*
13970 TCCTAGCTGAGTGGCTCAACCGATAGACAAC
1 TCCTAGCCGAGTGGCTCAACCGATAGAC-AC
14001 T-CTAGCC
1 TCCTAGCC
14008 AGCCCCTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (30 bp):
TCCTAGCCGAGTGGCTCAACCGATAGACAC
Found at i:22691 original size:2 final size:2
Alignment explanation
Indices: 22684--22711 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22674 AAAATTCAGC
22684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22712 CAGTTAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23580 original size:38 final size:39
Alignment explanation
Indices: 23502--23581 Score: 90
Period size: 40 Copynumber: 2.1 Consensus size: 39
23492 TTATGAGTAA
* *
23502 AATTTTGAAAAAAATATATTATAAAAGTTTTTTATGAATT
1 AATTTTGAAAAAAATATATTATAAAAG-ATTTAATGAATT
* * * *
23542 AATTTTTAAAAATATATTTTATAAAA-ATTTAATTAATT
1 AATTTTGAAAAAAATATATTATAAAAGATTTAATGAATT
23580 AA
1 AA
23582 AATATTTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.32
40 23 0.68
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (39 bp):
AATTTTGAAAAAAATATATTATAAAAGATTTAATGAATT
Found at i:24145 original size:16 final size:16
Alignment explanation
Indices: 24126--24159 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24116 TTCATTTTAG
24126 ACCACATAAATTTGAA
1 ACCACATAAATTTGAA
* *
24142 ACCATATATATTTGAA
1 ACCACATAAATTTGAA
24158 AC
1 AC
24160 TCTTTCAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (16 bp):
ACCACATAAATTTGAA
Found at i:24352 original size:28 final size:28
Alignment explanation
Indices: 24319--24376 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
24309 TAATTTTTTT
24319 AATTTTTATTTAAAAA-TAT-AAATTTTGA
1 AATTTTTA--TAAAAATTATAAAATTTTGA
*
24347 AATTTTTATAAAAATTTTAAAATTTTGA
1 AATTTTTATAAAAATTATAAAATTTTGA
24375 AA
1 AA
24377 ATTATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
AATTTTTATAAAAATTATAAAATTTTGA
Found at i:28094 original size:22 final size:22
Alignment explanation
Indices: 28069--28128 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
28059 TATAAATATT
28069 TAAATTATAAATTAATACATAA
1 TAAATTATAAATTAATACATAA
** **
28091 TAAATTTATATTTTAATTTATAA
1 TAAA-TTATAAATTAATACATAA
*
28114 AAAATTAT-AATTAAT
1 TAAATTATAAATTAAT
28129 CCCGACCTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 5 0.17
22 8 0.27
23 17 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTATAAATTAATACATAA
Found at i:30725 original size:99 final size:101
Alignment explanation
Indices: 30613--30818 Score: 285
Period size: 107 Copynumber: 2.0 Consensus size: 101
30603 CTACAAATAG
*
30613 ATGTGAGGTATAATAATAAGA-CCAATTACAGTCTAAAA-AGAAAAATAG-AGTTCG-AAACTTA
1 ATGTGAGGTATAATAATAAGATCC-ATTACACTCTAAAAGAGAAAAAT-GCAGTTCGAAAACTTA
*
30674 AAAGAGGATATTGTTAAAAGTAATAAATAAATAATGAA
64 AAAGAGGATATTATTAAAAGTAATAAATAAATAATGAA
*
30712 ATGTGAGGTATAATAATAAGATCCATTATACTCTAAAAGAGAAAAATGCAGTTCGAAACTTAAAA
1 ATGTGAGGTATAATAATAAGATCCATTACACTCTAAAAGAGAAAAATGCAGTTCG------AAAA
30777 CTTAAAAGAGGATATTATTAAAAGTAATAAATAAATAATGAA
60 CTTAAAAGAGGATATTATTAAAAGTAATAAATAAATAATGAA
30819 TACTTTTGGT
Statistics
Matches: 94, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
99 34 0.36
100 16 0.17
107 44 0.47
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (101 bp):
ATGTGAGGTATAATAATAAGATCCATTACACTCTAAAAGAGAAAAATGCAGTTCGAAAACTTAAA
AGAGGATATTATTAAAAGTAATAAATAAATAATGAA
Found at i:31612 original size:25 final size:25
Alignment explanation
Indices: 31583--31633 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
31573 AATTTTTTGA
*
31583 ATTTTTTA-ATTTTAAATATT-TTT
1 ATTTTTTATATTTTAAAAATTATTT
31606 ATTTTTTATATTTTAAAAATTATTT
1 ATTTTTTATATTTTAAAAATTATTT
31631 ATT
1 ATT
31634 AACATGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.32
24 11 0.44
25 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
ATTTTTTATATTTTAAAAATTATTT
Found at i:36622 original size:21 final size:21
Alignment explanation
Indices: 36597--36639 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36587 ATTACTGCAA
*
36597 ACACTCCATTCTTGCAAGAAC
1 ACACTCCATTCTTACAAGAAC
*
36618 ACACTCCATTCTTATAAGAAC
1 ACACTCCATTCTTACAAGAAC
36639 A
1 A
36640 TTGGTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (21 bp):
ACACTCCATTCTTACAAGAAC
Found at i:39032 original size:127 final size:127
Alignment explanation
Indices: 38806--39060 Score: 431
Period size: 127 Copynumber: 2.0 Consensus size: 127
38796 ATACACAAGG
* * *
38806 TTTCTATATGACTGTAAAACTACGAATTAAGCCACACAAGGCTACGAGGTCTTCAATAAATAATA
1 TTTCTATATGAATGTAAAACTACAAATTAAACCACACAAGGCTACGAGGTCTTCAATAAATAATA
* *
38871 CATTTACTAAAAAACTTAATTCAAAACAAGCTTAGAGATCTTTCTCATACTTGATTGGTGAT
66 CATTTACTAAAAAACTTAATTCAAAACAAACTTAGAGATCTTTCTCATACTCGATTGGTGAT
* *
38933 TTTCTATATGAATGTAAAACTACAAATTAAACCACACAATGCTACGAGGTTTTCAA-AAAGTAAT
1 TTTCTATATGAATGTAAAACTACAAATTAAACCACACAAGGCTACGAGGTCTTCAATAAA-TAAT
38997 ACATTTACTAAAAAACTTAATTCAAAACAAACTTAGAGATCTTTCTCATACTCGATTGGTGAT
65 ACATTTACTAAAAAACTTAATTCAAAACAAACTTAGAGATCTTTCTCATACTCGATTGGTGAT
39060 T
1 T
39061 CTTCGGGCCC
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 3 0.03
127 117 0.98
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (127 bp):
TTTCTATATGAATGTAAAACTACAAATTAAACCACACAAGGCTACGAGGTCTTCAATAAATAATA
CATTTACTAAAAAACTTAATTCAAAACAAACTTAGAGATCTTTCTCATACTCGATTGGTGAT
Found at i:39855 original size:24 final size:24
Alignment explanation
Indices: 39825--39884 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 24
39815 ACTAAAAACA
39825 AAAGAAACATAGTTTTCCAGCCAC
1 AAAGAAACATAGTTTTCCAGCCAC
39849 AAAGAAACATAATAGTTTTCCAGCCAC
1 AAAGAAAC---ATAGTTTTCCAGCCAC
39876 AAAGAAACA
1 AAAGAAACA
39885 AACTTCCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.27
27 24 0.73
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (24 bp):
AAAGAAACATAGTTTTCCAGCCAC
Found at i:39870 original size:27 final size:27
Alignment explanation
Indices: 39833--39884 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
39823 CAAAAGAAAC
39833 ATAGTTTTCCAGCCACAAAGAAACATA
1 ATAGTTTTCCAGCCACAAAGAAACATA
39860 ATAGTTTTCCAGCCACAAAGAAACA
1 ATAGTTTTCCAGCCACAAAGAAACA
39885 AACTTCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (27 bp):
ATAGTTTTCCAGCCACAAAGAAACATA
Found at i:49145 original size:87 final size:87
Alignment explanation
Indices: 48997--49342 Score: 464
Period size: 87 Copynumber: 4.0 Consensus size: 87
48987 GGCAACAGTA
* * *
48997 TTTCGGGCTTGGGCTCATTTGTAAATTTATAAACATGATGTAATTAACGCACGCCAAGAAGAAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCATGCCACGAAGAAAA
49062 TCA-TTCTAAAAATGGAAATCCC
66 TCATTTC-AAAAATGGAAATCCC
* *
49084 TTTCGGGCTTTGGCTCATTCGTAAATTTATAAACATGATGTACTTAACGCACT-CCACGAAGAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCA-TGCCACGAAGAAA
** *
49148 ATCATTTTGAAAATGGATATCCC
65 ATCATTTCAAAAATGGAAATCCC
* * *
49171 TTTCGGGCTTGGGCTCGTTCGT-AATTTATAAACATGATGTAATTAATGCATGGCACGAAGAAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCATGCCACGAAGAAAA
* *
49235 TCATTTCAAAAATGGAAATTCT
66 TCATTTCAAAAATGGAAATCCC
** ** * * *
49257 TTTCAAGCTTGGGCTTGTTTGTAAATTTATAAACATGATGTAATCAACACATGCCACGAAGAAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCATGCCACGAAGAAAA
*
49322 TCATTTCAAAAATCGAAATCC
66 TCATTTCAAAAATGGAAATCC
49343 AATTCATAGG
Statistics
Matches: 227, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.00
86 72 0.32
87 152 0.67
88 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (87 bp):
TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCATGCCACGAAGAAAA
TCATTTCAAAAATGGAAATCCC
Found at i:49287 original size:173 final size:174
Alignment explanation
Indices: 48997--49327 Score: 470
Period size: 173 Copynumber: 1.9 Consensus size: 174
48987 GGCAACAGTA
*
48997 TTTCGGGCTTGGGCTCATTTGTAAATTTATAAACATGATGTAATTAACGCACGCCAAGAAGAAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCAAGAAGAAAA
** * *
49062 TCATTCTAAAAATGGAAATCCCTTTCGGGCTTTGGCTCATTCGTAAATTTATAAACATGATGTAC
66 TCATTCTAAAAATGGAAATCCCTTTCAAGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAA
* *
49127 TTAACGCACT-CCACGAAGAAAATCATTTTGAAAATGGATATCCC
131 TCAACACA-TGCCACGAAGAAAATCATTTTGAAAATGGATATCCC
* * * * *
49171 TTTCGGGCTTGGGCTCGTTCGT-AATTTATAAACATGATGTAATTAATGCATGGCACGAAGAAAA
1 TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCAAGAAGAAAA
* * ** *
49235 TCATT-TCAAAAATGGAAATTCTTTTCAAGCTTGGGCTTGTTTGTAAATTTATAAACATGATGTA
66 TCATTCT-AAAAATGGAAATCCCTTTCAAGCTTGGGCTCATTCGTAAATTTATAAACATGATGTA
49299 ATCAACACATGCCACGAAGAAAATCATTT
130 ATCAACACATGCCACGAAGAAAATCATTT
49328 CAAAAATCGA
Statistics
Matches: 138, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
172 2 0.01
173 116 0.84
174 20 0.14
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (174 bp):
TTTCGGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCAAGAAGAAAA
TCATTCTAAAAATGGAAATCCCTTTCAAGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAA
TCAACACATGCCACGAAGAAAATCATTTTGAAAATGGATATCCC
Found at i:51649 original size:31 final size:30
Alignment explanation
Indices: 51613--51685 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
51603 GATTAAATTA
51613 AAATTAAAGTTTTAAGTATAT-ATTTGAACC
1 AAATTAAAGTTTTAAGTATATGA-TTGAACC
* * * * *
51643 ATAATTAAAATCTTACGTGTATGATTGTACC
1 A-AATTAAAGTTTTAAGTATATGATTGAACC
51674 AAATTAAAGTTT
1 AAATTAAAGTTT
51686 ATGTATACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
30 10 0.29
31 23 0.68
32 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
AAATTAAAGTTTTAAGTATATGATTGAACC
Found at i:56560 original size:9 final size:9
Alignment explanation
Indices: 56542--56592 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
56532 TTTTGGTACG
56542 ATAA-TTTT
1 ATAATTTTT
56550 ATAATTTTT
1 ATAATTTTT
*
56559 ATACAAATTTT
1 AT--AATTTTT
56570 ATATATTTTT
1 ATA-ATTTTT
*
56580 ATATTTTTT
1 ATAATTTTT
56589 ATAA
1 ATAA
56593 AATCATTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 4 0.11
9 15 0.43
10 8 0.23
11 8 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:56569 original size:20 final size:21
Alignment explanation
Indices: 56544--56582 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
56534 TTGGTACGAT
56544 AATTTTATA-ATTTTTATACA
1 AATTTTATATATTTTTATACA
56564 AATTTTATATATTTTTATA
1 AATTTTATATATTTTTATA
56583 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTATATATTTTTATACA
Found at i:56664 original size:30 final size:30
Alignment explanation
Indices: 56613--56689 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
56603 ACTTTATAAA
*
56613 ATTTTATAATTTTTT-CTATATTTCTATAT
1 ATTTTATAATTTTTTACAATATTTCTATAT
56642 ATTTTATAATTTTTTACAATATTTCTATAT
1 ATTTTATAATTTTTTACAATATTTCTATAT
*
56672 ACTTTATAAATTTTTTAC
1 ATTTTAT-AATTTTTTAC
56690 TATTTTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 15 0.34
30 19 0.43
31 10 0.23
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTTATAATTTTTTACAATATTTCTATAT
Found at i:56716 original size:20 final size:20
Alignment explanation
Indices: 56614--56714 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
56604 CTTTATAAAA
*
56614 TTTTAT-AAT-TTTTTCTAT
1 TTTTATAAATATTTTACTAT
* * *
56632 ATTTCTATATATTTTA-TAAT
1 TTTTATAAATATTTTACT-AT
56652 TTTT-TACAATATTTCTA-TAT
1 TTTTATA-AATATTT-TACTAT
* *
56672 ACTTTATAAATTTTTTACTAT
1 -TTTTATAAATATTTTACTAT
56693 TTTTATAAA-ATTTTAC-AT
1 TTTTATAAATATTTTACTAT
56711 TTTT
1 TTTT
56715 TTCTAACTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
18 10 0.15
19 11 0.17
20 27 0.42
21 15 0.23
22 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATAAATATTTTACTAT
Found at i:58136 original size:15 final size:15
Alignment explanation
Indices: 58116--58146 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58106 ATTGAATTAT
58116 CATTGAAGAACAGTG
1 CATTGAAGAACAGTG
58131 CATTGAAGAACAGTG
1 CATTGAAGAACAGTG
58146 C
1 C
58147 CGTCGGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (15 bp):
CATTGAAGAACAGTG
Done.