Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009373.1 Kokia drynarioides strain JFW-HI SEQ_124080, 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: 73257
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:1024 original size:23 final size:23
Alignment explanation
Indices: 994--1048 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
984 AATGCTAGTT
* *
994 TGCTTACTGTTTCGCACTTCATG
1 TGCTTACTGCTTCGCACCTCATG
*
1017 TGCTTACTGCTTCGCACCTCGTG
1 TGCTTACTGCTTCGCACCTCATG
*
1040 TGCCTACTG
1 TGCTTACTG
1049 ATTTGCGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.11, C:0.31, G:0.20, T:0.38
Consensus pattern (23 bp):
TGCTTACTGCTTCGCACCTCATG
Found at i:1063 original size:23 final size:23
Alignment explanation
Indices: 1037--1117 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
1027 TTCGCACCTC
* *
1037 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGATTTGCACTGT
*
1060 GTGTGCCTACTGATTTGCATTGT
1 GTGTGCCTACTGATTTGCACTGT
1083 GTGTGCCTACTAGA-TTGCACTGT
1 GTGTGCCTACT-GATTTGCACTGT
*
1106 GTGTGCTTACTG
1 GTGTGCCTACTG
1118 TTTCCCCAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.02
23 49 0.94
24 2 0.04
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.40
Consensus pattern (23 bp):
GTGTGCCTACTGATTTGCACTGT
Found at i:1065 original size:46 final size:46
Alignment explanation
Indices: 1015--1117 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 46
1005 TCGCACTTCA
* *
1015 TGTGCTTACTGCTTCGCACCT-CGTGTGCCTACT-GATTTGCGCTATG
1 TGTGCTTACTGATTCGCA-CTGCGTGTGCCTACTAGA-TTGCACTATG
* * * * *
1061 TGTGCCTACTGATTTGCATTGTGTGTGCCTACTAGATTGCACTGTG
1 TGTGCTTACTGATTCGCACTGCGTGTGCCTACTAGATTGCACTATG
1107 TGTGCTTACTG
1 TGTGCTTACTG
1118 TTTCCCCAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
45 1 0.02
46 44 0.94
47 2 0.04
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (46 bp):
TGTGCTTACTGATTCGCACTGCGTGTGCCTACTAGATTGCACTATG
Found at i:9481 original size:2 final size:2
Alignment explanation
Indices: 9474--9509 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9464 ATTTATTGAG
9474 AT 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 AT
9510 TAAATAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9749 original size:29 final size:28
Alignment explanation
Indices: 9674--9751 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
9664 GATCGCTTAC
* * *
9674 TTTTAAATATAAGTAAATTTGACACTAAA
1 TTTTAAATTTAA-TTAATTTTACACTAAA
*
9703 -TTTATATGTT-ATTGAATTTTATCACTAAA
1 TTTTAAAT-TTAATT-AATTTTA-CACTAAA
9732 TTTTAAATTTAATTAATTTT
1 TTTTAAATTTAATTAATTTT
9752 TGCCATCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.03
28 13 0.33
29 16 0.41
30 9 0.23
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (28 bp):
TTTTAAATTTAATTAATTTTACACTAAA
Found at i:10300 original size:21 final size:21
Alignment explanation
Indices: 10275--10315 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10265 ACACGTAAAA
*
10275 ATAAAATTTAAAAAACTATAT
1 ATAAAATTTAAAAAAATATAT
10296 ATAAAATTTAAAAAAATATA
1 ATAAAATTTAAAAAAATATA
10316 CGTAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAATTTAAAAAAATATAT
Found at i:10706 original size:22 final size:21
Alignment explanation
Indices: 10676--10716 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
10666 AGTATTCAAG
10676 AAGTTGA-TTAGAATTAAAATT
1 AAGTTGATTTA-AATTAAAATT
10697 AAGTTGGATTTAAATTAAAA
1 AAGTT-GATTTAAATTAAAA
10717 GCAACTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (21 bp):
AAGTTGATTTAAATTAAAATT
Found at i:14337 original size:22 final size:23
Alignment explanation
Indices: 14312--14361 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
14302 AACAAGCTCA
14312 TTTA-AAAGCTCGTTTA-AGCTTG
1 TTTATAAA-CTCGTTTATAGCTTG
*
14334 TTTATTAACTCGTTTATAGCTTG
1 TTTATAAACTCGTTTATAGCTTG
14357 TTTAT
1 TTTAT
14362 CTATTAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (23 bp):
TTTATAAACTCGTTTATAGCTTG
Found at i:14428 original size:4 final size:4
Alignment explanation
Indices: 14419--14444 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
14409 TATGTTTTTA
14419 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
14445 ATTATTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:14505 original size:24 final size:23
Alignment explanation
Indices: 14457--14522 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
14447 TATTCATTAC
*
14457 ATTGTTCATGAACGTGTTCAATT
1 ATTGTTCATGAACATGTTCAATT
* **
14480 ATATGTTCATGACCATGTTCGTTT
1 AT-TGTTCATGAACATGTTCAATT
**
14504 ATTGTTTGTGAACATGTTC
1 ATTGTTCATGAACATGTTC
14523 TATCAAGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (23 bp):
ATTGTTCATGAACATGTTCAATT
Found at i:18137 original size:16 final size:16
Alignment explanation
Indices: 18116--18152 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
18106 TAATTTAATA
18116 ACTTTAAGTGGAATTT
1 ACTTTAAGTGGAATTT
18132 ACTTT-AGTGGAATTT
1 ACTTTAAGTGGAATTT
18147 ACTTTA
1 ACTTTA
18153 TAAGGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (16 bp):
ACTTTAAGTGGAATTT
Found at i:28449 original size:6 final size:6
Alignment explanation
Indices: 28438--28476 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
28428 TTCTCGTCAA
28438 CCATCC CCATCC CCATCC CCATCC CCATCC CCATCC CCA
1 CCATCC CCATCC CCATCC CCATCC CCATCC CCATCC CCA
28477 CCCAACCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.67, G:0.00, T:0.15
Consensus pattern (6 bp):
CCATCC
Found at i:31775 original size:15 final size:15
Alignment explanation
Indices: 31743--31772 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
31733 TAATATGCTT
31743 ATAAAAATAATTAAA
1 ATAAAAATAATTAAA
31758 ATAAAAA-AATTAAA
1 ATAAAAATAATTAAA
31772 A
1 A
31773 ATATCATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAAATAATTAAA
Found at i:32162 original size:141 final size:138
Alignment explanation
Indices: 31939--32271 Score: 413
Period size: 141 Copynumber: 2.4 Consensus size: 138
31929 TAAAAAATTT
* * * *
31939 TTGAAGCAACATGAAATAAAAAATACAAATGT-AAGTAGTATAGAAATTAAACTTGAGACTCAAG
1 TTGAAGCAACATGAAATAAAAAATACAAATGTGAA-TAGAAGAGGAATTAAACTCGAGACTCAAG
* * *
32003 GATGTAATGAAAATTATCTAACCATCTAACGACAA-AACTAATACGTTAAAAAACATTAATTAAA
65 GATGTAATGAAAACTATCTAACCATCTAAC-AAAAGAACTAAAACGTTAAAAAA-A-TAATTAAA
32067 AATTTA-AAATGA
127 AATTTAGAAA-GA
* * * * *
32079 TTGAAGCAACATGAATTAAAAAAATACAAATGTGAATAGGAGAGGAATCAAACTCGATACTCGAG
1 TTGAAGCAACATGAAAT-AAAAAATACAAATGTGAATAGAAGAGGAATTAAACTCGAGACTCAAG
* * *
32144 GATGTAATTG-TAACTATCTAACCATCTAACAAAAGAACTAAAATGTTAAAAAAATAATTAAAGA
65 GATGTAA-TGAAAACTATCTAACCATCTAACAAAAGAACTAAAACGTTAAAAAAATAATTAAAAA
*
32208 TTTAGAAAGC
129 TTTAGAAAGA
* *
32218 TTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAAGAATTAAACTC
1 TTGAAGCAACATGAAATAAAAAATACAAATGTGAATAGAAGAGGAATTAAACTC
32272 AGGATTTAAC
Statistics
Matches: 168, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
138 33 0.20
139 30 0.18
140 23 0.14
141 78 0.46
142 4 0.02
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (138 bp):
TTGAAGCAACATGAAATAAAAAATACAAATGTGAATAGAAGAGGAATTAAACTCGAGACTCAAGG
ATGTAATGAAAACTATCTAACCATCTAACAAAAGAACTAAAACGTTAAAAAAATAATTAAAAATT
TAGAAAGA
Found at i:32305 original size:138 final size:140
Alignment explanation
Indices: 32017--32306 Score: 306
Period size: 138 Copynumber: 2.1 Consensus size: 140
32007 TAATGAAAAT
* *
32017 TATCTAACCATCTAACGACAAAACTAATACGTTAAAAAACATTAATTAAAAATTTAAAATGATTG
1 TATCTAACCATCTAACGAAAAAACTAAAACGTTAAAAAACATTAATTAAAAATTTAAAATGATTG
* * * * *
32082 AAGCAACATGAATTAAAAAAATACAAATGTGAATAGGAGAGGAATCAAACTCGATACTCGAGGAT
66 AAGCAACATGAAATAAAAAAATACAAATGTGAATAGAAGAAGAATCAAACTCGATA-TCAACGAT
** ***
32147 GTAATTGTAAC
130 AAAACACTAAC
* * *
32158 TATCTAACCATCTAAC-AAAAGAACTAAAATGTTAAAAAA-A-TAATTAAAGATTTAGAAA-GCT
1 TATCTAACCATCTAACGAAAA-AACTAAAACGTTAAAAAACATTAATTAAAAATTTA-AAATGAT
* * *
32219 TGAAGCAACATGAAAT-AAAAAATACAAATGTGAGTAGAAGAAGAATTAAACTCAGGAT-TTAAC
64 TGAAGCAACATGAAATAAAAAAATACAAATGTGAATAGAAGAAGAATCAAACTC--GATATCAAC
32282 GATAAAAGCACTAAC
127 GATAAAA-CACTAAC
*
32297 -ATTTAACCAT
1 TATCTAACCAT
32307 TTGACCAAAG
Statistics
Matches: 125, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
138 49 0.39
139 34 0.27
140 10 0.08
141 32 0.26
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (140 bp):
TATCTAACCATCTAACGAAAAAACTAAAACGTTAAAAAACATTAATTAAAAATTTAAAATGATTG
AAGCAACATGAAATAAAAAAATACAAATGTGAATAGAAGAAGAATCAAACTCGATATCAACGATA
AAACACTAAC
Found at i:37304 original size:2 final size:2
Alignment explanation
Indices: 37297--37325 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37287 GGTTTAATCA
37297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37326 ATTTTAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39615 original size:30 final size:31
Alignment explanation
Indices: 39574--39636 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
39564 TTAGACTATG
* *
39574 AAGCCAAGTTCA-GTACTAAATTGAACCAAA
1 AAGCCAAGTTCATATACCAAATTGAACCAAA
* *
39604 AAGCCAGGTTCATATACCCAATTGAACCAAA
1 AAGCCAAGTTCATATACCAAATTGAACCAAA
39635 AA
1 AA
39637 AGGTTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.19
Consensus pattern (31 bp):
AAGCCAAGTTCATATACCAAATTGAACCAAA
Found at i:39653 original size:27 final size:29
Alignment explanation
Indices: 39581--39658 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
39571 ATGAAGCCAA
*
39581 GTTCA-GTACTAAATTGAACCAAAAAGCCAG
1 GTTCAGGTACCAAATTGAACCAAAAA--CAG
** *
39611 GTTCATATACCCAATTGAACCAAAAA-AG
1 GTTCAGGTACCAAATTGAACCAAAAACAG
39639 GTT-AGGTACCAAATTGAACC
1 GTTCAGGTACCAAATTGAACC
39659 TTGAGGCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 14 0.34
28 5 0.12
30 5 0.12
31 17 0.41
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (29 bp):
GTTCAGGTACCAAATTGAACCAAAAACAG
Found at i:44579 original size:14 final size:14
Alignment explanation
Indices: 44557--44590 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
44547 TCGAGTTCGA
*
44557 GTTTTGGATTTAGG
1 GTTTAGGATTTAGG
44571 GTTTAGGATTTAGG
1 GTTTAGGATTTAGG
44585 GTTTAG
1 GTTTAG
44591 TGAATTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (14 bp):
GTTTAGGATTTAGG
Found at i:44654 original size:7 final size:7
Alignment explanation
Indices: 44642--44696 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
44632 AGGGGTACAA
44642 GTTTAAG
1 GTTTAAG
44649 GTTTAAG
1 GTTTAAG
44656 GTTTAAG
1 GTTTAAG
*
44663 ATTTAAG
1 GTTTAAG
**
44670 GATTTGGG
1 G-TTTAAG
*
44678 GTTTTAG
1 GTTTAAG
*
44685 GTTTAGG
1 GTTTAAG
44692 GTTTA
1 GTTTA
44697 GGATTTTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (7 bp):
GTTTAAG
Found at i:44711 original size:36 final size:36
Alignment explanation
Indices: 44642--44722 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
44632 AGGGGTACAA
*
44642 GTTTAAGGTTTAAGGTTTAAGATTTAAGGATTTGGG
1 GTTTAAGGTTTAAGGTTTAAGATTTAAGAATTTGGG
* * * * *
44678 GTTTTAGGTTTAGGGTTTAGGATTTTATAATTT-GG
1 GTTTAAGGTTTAAGGTTTAAGATTTAAGAATTTGGG
*
44713 GTTTACGGTT
1 GTTTAAGGTT
44723 CGGGATTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
35 10 0.27
36 27 0.73
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (36 bp):
GTTTAAGGTTTAAGGTTTAAGATTTAAGAATTTGGG
Found at i:54645 original size:2 final size:2
Alignment explanation
Indices: 54638--54662 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54628 CTTCGATTTT
54638 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
54663 TTGTTGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54674 original size:6 final size:6
Alignment explanation
Indices: 54668--54698 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54658 AGAGATTGTT
*
54668 GGAGTT GGAGTC GGAGTC GGAGTC GGAGTC G
1 GGAGTC GGAGTC GGAGTC GGAGTC GGAGTC G
54699 ATGTCTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.52, T:0.19
Consensus pattern (6 bp):
GGAGTC
Found at i:70410 original size:21 final size:21
Alignment explanation
Indices: 70385--70424 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
70375 CATCTCAACA
70385 ATATTAATCCAAATTAAGAAT
1 ATATTAATCCAAATTAAGAAT
* * *
70406 ATATTGATCTAGATTAAGA
1 ATATTAATCCAAATTAAGA
70425 TAGAAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
ATATTAATCCAAATTAAGAAT
Done.