Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013957.1 Kokia drynarioides strain JFW-HI SEQ_128987, 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: 41754
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:4268 original size:12 final size:12
Alignment explanation
Indices: 4252--4291 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
4242 TGTTATCCGG
*
4252 CCACCGCCACCG
1 CCACCGCCACCA
4264 CCACCGCCACCA
1 CCACCGCCACCA
*
4276 CCACCACCACCA
1 CCACCGCCACCA
4288 CCAC
1 CCAC
4292 TTTCTCAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.25, C:0.68, G:0.07, T:0.00
Consensus pattern (12 bp):
CCACCGCCACCA
Found at i:4278 original size:3 final size:3
Alignment explanation
Indices: 4252--4291 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
4242 TGTTATCCGG
* * *
4252 CCA CCG CCA CCG CCA CCG CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
4292 TTTCTCAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.25, C:0.68, G:0.07, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:15480 original size:14 final size:14
Alignment explanation
Indices: 15448--15495 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
15438 TCCCTGTACC
15448 TTTTAATTTTTAAA
1 TTTTAATTTTTAAA
* * *
15462 ATTTAGTTTTTATA
1 TTTTAATTTTTAAA
*
15476 TTTTAAATTTTAAA
1 TTTTAATTTTTAAA
*
15490 TATTAA
1 TTTTAA
15496 ACCCCTGTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTTAATTTTTAAA
Found at i:20039 original size:5 final size:5
Alignment explanation
Indices: 20029--20053 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20019 AGGTGCTCAA
20029 GGGTC GGGTC GGGTC GGGTC GGGTC
1 GGGTC GGGTC GGGTC GGGTC GGGTC
20054 TAAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GGGTC
Found at i:33259 original size:6 final size:6
Alignment explanation
Indices: 33248--33318 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
33238 AAGCGGTAGT
* * * * *
33248 AGGAGC AGGAGC AGGAGT AGGGGT AGGAGT AGGAGT AGGAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
* * * *
33296 ACGAGC CGGAGC CGGAGC CGGAG
1 AGGAGC AGGAGC AGGAGC AGGAG
33319 TCGAAACCGG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.51, T:0.06
Consensus pattern (6 bp):
AGGAGC
Found at i:33268 original size:18 final size:18
Alignment explanation
Indices: 33245--33319 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
33235 CCGAAGCGGT
33245 AGTAGGAGCAGGAGCAGG
1 AGTAGGAGCAGGAGCAGG
* * *
33263 AGTAGGGGTAGGAGTAGG
1 AGTAGGAGCAGGAGCAGG
*
33281 AGTAGGAGCAGGAGCACG
1 AGTAGGAGCAGGAGCAGG
** * *
33299 AGCCGGAGCCGGAGCCGG
1 AGTAGGAGCAGGAGCAGG
33317 AGT
1 AGT
33320 CGAAACCGGA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.49, T:0.08
Consensus pattern (18 bp):
AGTAGGAGCAGGAGCAGG
Found at i:34249 original size:23 final size:22
Alignment explanation
Indices: 34199--34249 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
34189 CACATGATAT
*
34199 ATAA-TATAAAATATAAAAATT
1 ATAATTATAAAATATAAAAATC
*
34220 ATAAATTATAAATTATAAAAAATC
1 AT-AATTATAAAATAT-AAAAATC
34244 ATAATT
1 ATAATT
34250 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 13 0.52
24 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATTATAAAATATAAAAATC
Found at i:34473 original size:10 final size:9
Alignment explanation
Indices: 34454--34645 Score: 82
Period size: 9 Copynumber: 21.2 Consensus size: 9
34444 TTTTGATATG
34454 ATAATTTTT
1 ATAATTTTT
34463 ATAATTTTT
1 ATAATTTTT
*
34472 -TACGAATTTT
1 ATA--ATTTTT
34482 AT-ATTTCTT
1 ATAATTT-TT
*
34491 -TACTTTCTT
1 ATAATTT-TT
* *
34500 ATGACTTTAT
1 AT-AATTTTT
* *
34510 AAAATTCTAT
1 ATAATT-TTT
34520 ATA-TTT-T
1 ATAATTTTT
34527 ATAATTTTT
1 ATAATTTTT
34536 -TACGATTTTT
1 ATA--ATTTTT
34546 ATAATTTTT
1 ATAATTTTT
34555 AT-ATTTTT
1 ATAATTTTT
*
34563 AATAAATTTT
1 -ATAATTTTT
*
34573 AAATATTTTT
1 ATA-ATTTTT
34583 AT-ATTTTT
1 ATAATTTTT
* *
34591 ATTAAAATTTA
1 A-T-AATTTTT
34602 ATAATTTTT
1 ATAATTTTT
**
34611 ATAAGATTT
1 ATAATTTTT
34620 AT--TTTTT
1 ATAATTTTT
*
34627 -TATTTTTT
1 ATAATTTTT
34635 ATAATTTTT
1 ATAATTTTT
34644 AT
1 AT
34646 CACATGTCAC
Statistics
Matches: 141, Mismatches: 20, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
6 1 0.01
7 7 0.05
8 30 0.21
9 59 0.42
10 31 0.22
11 13 0.09
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:34570 original size:19 final size:18
Alignment explanation
Indices: 34505--34585 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 18
34495 TTCTTATGAC
* *
34505 TTTATAAAATTCTATATAT
1 TTTATAAATTTTTATAT-T
* *
34524 TTTATAATTTTTTACGATT
1 TTTATAAATTTTTA-TATT
34543 TTTAT-AATTTTTATATT
1 TTTATAAATTTTTATATT
*
34560 TTTAATAAATTTTAAATATT
1 TTT-ATAAATTTT-TATATT
34580 TTTATA
1 TTTATA
34586 TTTTTATTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 6 0.12
18 9 0.18
19 26 0.51
20 10 0.20
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
TTTATAAATTTTTATATT
Found at i:34571 original size:28 final size:27
Alignment explanation
Indices: 34542--34613 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
34532 TTTTTACGAT
34542 TTTTATAATTTTTATATTTTTAATAAA
1 TTTTATAATTTTTATATTTTTAATAAA
* *
34569 TTTTAAATATTTTTATATTTTTATTAAAA
1 TTTTATA-ATTTTTATATTTTTAAT-AAA
*
34598 TTTAATAATTTTTATA
1 TTTTATAATTTTTATA
34614 AGATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 6 0.15
28 25 0.64
29 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTATAATTTTTATATTTTTAATAAA
Found at i:34591 original size:64 final size:63
Alignment explanation
Indices: 34457--34592 Score: 154
Period size: 64 Copynumber: 2.1 Consensus size: 63
34447 TGATATGATA
* *
34457 ATTTTTATAATTTTTTACGAATTTTATATTTCTTTACTTTCTTATGACTTTATAAAATTCTAT
1 ATTTTTATAATTTTTTACGAATTTTATATTTCTTTACTTTCTTATAAATTTATAAAATTCTAT
*
34520 ATATTTTATAATTTTTTACGATTTTTATAATTT-TTATA-TTT-TTAATAAATTT-TAAATATTT
1 AT-TTTTATAATTTTTTACGAATTTTAT-ATTTCTT-TACTTTCTT-ATAAATTTATAAA-A-TT
*
34581 TTAT
60 CTAT
34585 ATTTTTAT
1 ATTTTTAT
34593 TAAAATTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
63 8 0.13
64 42 0.67
65 13 0.21
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (63 bp):
ATTTTTATAATTTTTTACGAATTTTATATTTCTTTACTTTCTTATAAATTTATAAAATTCTAT
Found at i:36013 original size:2 final size:2
Alignment explanation
Indices: 36006--36039 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35996 GTAATACCCC
36006 AT AT AT 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 AT AT AT
36040 GTATGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37937 original size:12 final size:13
Alignment explanation
Indices: 37914--37965 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
37904 AGCTTAGTAT
37914 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
* *
37927 TGTTTTTAAAAAA
1 TGTTTTTGAAAAG
* *
37940 TGCTTTGGAAAAG
1 TGTTTTTGAAAAG
*
37953 TGATTTTGAAAAG
1 TGTTTTTGAAAAG
37966 CTTAGTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:39467 original size:19 final size:17
Alignment explanation
Indices: 39443--39495 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
39433 AAAATGATTA
*
39443 AAAATCATAAATATTATAG
1 AAAATCATAAA-A-TAAAG
*
39462 AAAATCATTAAAATAAAT
1 AAAATCA-TAAAATAAAG
*
39480 AAAATCATAAAGTAAA
1 AAAATCATAAAATAAA
39496 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.27
18 10 0.33
19 8 0.27
20 4 0.13
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATCATAAAATAAAG
Found at i:39495 original size:17 final size:19
Alignment explanation
Indices: 39462--39502 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39452 AATATTATAG
39462 AAAATCATTAAAATAAA-T
1 AAAATCATTAAAATAAATT
*
39480 AAAATCA-TAAAGTAAATT
1 AAAATCATTAAAATAAATT
39498 AAAAT
1 AAAAT
39503 TAAAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATCATTAAAATAAATT
Found at i:39583 original size:10 final size:9
Alignment explanation
Indices: 39561--39647 Score: 61
Period size: 9 Copynumber: 9.2 Consensus size: 9
39551 AAAAACACAT
39561 AAATTATAA
1 AAATTATAA
39570 AAATTATGAA
1 AAATTAT-AA
*
39580 AAATATTTAA
1 AAAT-TATAA
39590 AAA-TATAGA
1 AAATTATA-A
39599 AAATTAATAA
1 AAATT-ATAA
*
39609 AAA-CATTAA
1 AAATTA-TAA
* *
39618 AAATAACAA
1 AAATTATAA
39627 AATATTATAA
1 AA-ATTATAA
*
39637 AAAGTATAA
1 AAATTATAA
39646 AA
1 AA
39648 CAAACTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 4 0.06
9 29 0.47
10 24 0.39
11 5 0.08
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (9 bp):
AAATTATAA
Found at i:39609 original size:19 final size:19
Alignment explanation
Indices: 39561--39611 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
39551 AAAAACACAT
39561 AAATT-ATAAAAATTATGA
1 AAATTAATAAAAATTATGA
* *
39579 AAAATATTTAAAAA-TATAGA
1 AAATTA-ATAAAAATTAT-GA
39599 AAATTAATAAAAA
1 AAATTAATAAAAA
39612 CATTAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 4 0.15
19 9 0.35
20 13 0.50
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AAATTAATAAAAATTATGA
Found at i:39617 original size:28 final size:28
Alignment explanation
Indices: 39586--39639 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
39576 TGAAAAATAT
*
39586 TTAAAAATATAGAAAAT-TAATAAAAACA
1 TTAAAAATA-ACAAAATATAATAAAAACA
*
39614 TTAAAAATAACAAAATATTATAAAAA
1 TTAAAAATAACAAAATATAATAAAAA
39640 GTATAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (28 bp):
TTAAAAATAACAAAATATAATAAAAACA
Found at i:40048 original size:19 final size:20
Alignment explanation
Indices: 40000--40053 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
39990 TTTTCTATAG
40000 TTTTATCATA-TTTTAAATAA
1 TTTT-TCATATTTTTAAATAA
*
40020 TAATTT-ATATTTTTAAAT-A
1 T-TTTTCATATTTTTAAATAA
40039 TTTTTCATATTTTTA
1 TTTTTCATATTTTTA
40054 CAACTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
19 14 0.48
20 10 0.34
21 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTCATATTTTTAAATAA
Found at i:40171 original size:50 final size:46
Alignment explanation
Indices: 40079--40171 Score: 114
Period size: 50 Copynumber: 1.9 Consensus size: 46
40069 AAATTTATAT
* * *
40079 AAAATTTTATTTTATTTTTTTATTTTAATAAGTTTATTTTTTTTGC
1 AAAATTTCATTTAATTTTTTTATTTTAATAAGTTTATATTTTTTGC
*
40125 AAAATTTCATTTAATTTCTTTGTCATTTATAATAATTTTATATTTTT
1 AAAATTTCATTTAATTT-TTT-T-ATTT-TAATAAGTTTATATTTTT
40172 GTAGTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 15 0.38
47 3 0.08
48 1 0.03
49 4 0.10
50 16 0.41
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (46 bp):
AAAATTTCATTTAATTTTTTTATTTTAATAAGTTTATATTTTTTGC
Found at i:40522 original size:2 final size:2
Alignment explanation
Indices: 40515--40557 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
40505 TAAAAATGTA
* * * *
40515 AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT TT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40557 A
1 A
40558 ATTGTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:40684 original size:18 final size:18
Alignment explanation
Indices: 40626--40685 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
40616 AAAATGTAAA
*
40626 AAAAAATATTAGAAATTAT
1 AAAAATTATTAGAAA-TAT
* * * *
40645 AAATATCATAAGAATTAT
1 AAAAATTATTAGAAATAT
*
40663 AAAAATTATTAGAAATAG
1 AAAAATTATTAGAAATAT
40681 AAAAA
1 AAAAA
40686 GATTGTAAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATTATTAGAAATAT
Done.