Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006384.1 Kokia drynarioides strain JFW-HI SEQ_120961, 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: 63652
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:1748 original size:22 final size:22
Alignment explanation
Indices: 1723--1766 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1713 CTATTTGAAT
*
1723 TAAAAT-TAAAATTTTAAAAATA
1 TAAAATATAAAA-ATTAAAAATA
1745 TAAAATATAAAAATTAAAAATA
1 TAAAATATAAAAATTAAAAATA
1767 ATTAGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATATAAAAATTAAAAATA
Found at i:1755 original size:15 final size:14
Alignment explanation
Indices: 1724--1767 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1714 TATTTGAATT
*
1724 AAAATTAAAATTTTA
1 AAAATTAAAA-TATA
1739 AAAATATAAAATATA
1 AAAAT-TAAAATATA
1754 AAAATTAAAA-ATA
1 AAAATTAAAATATA
1767 A
1 A
1768 TTAGATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 13 0.48
16 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:2373 original size:20 final size:21
Alignment explanation
Indices: 2350--2388 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2340 TTTTTTAGAT
*
2350 AATT-ACATTTATTTTTTTTA
1 AATTAACAGTTATTTTTTTTA
*
2370 AATTAAGAGTTATTTTTTT
1 AATTAACAGTTATTTTTTT
2389 AATTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (21 bp):
AATTAACAGTTATTTTTTTTA
Found at i:2384 original size:25 final size:25
Alignment explanation
Indices: 2356--2417 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2346 AGATAATTAC
2356 ATTTATTTT-TTTTAAATTAAGAGTT
1 ATTTATTTTATTTT-AATTAAGAGTT
* * *
2381 ATTT-TTTTAATTTTATTTATGATTT
1 ATTTATTTT-ATTTTAATTAAGAGTT
2406 ATTTATTTTATT
1 ATTTATTTTATT
2418 ATTTTCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
26 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (25 bp):
ATTTATTTTATTTTAATTAAGAGTT
Found at i:2557 original size:23 final size:24
Alignment explanation
Indices: 2531--2593 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
2521 AATTTATTAA
2531 AAAAAATAAT-TTGAAAAAAAAAC-
1 AAAAAATAATATT-AAAAAAAAACT
* *
2554 AAAAATTGATATTAAAAAAAAACT
1 AAAAAATAATATTAAAAAAAAACT
2578 AAAAAAT-ATAATTAAA
1 AAAAAATAAT-ATTAAA
2594 TCATTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAAAATAATATTAAAAAAAAACT
Found at i:2591 original size:24 final size:24
Alignment explanation
Indices: 2528--2593 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
2518 TTAAATTTAT
*
2528 TAAAAAAAATAATTTGAAAAAAAAAC
1 TAAAAAATATAA-TT-AAAAAAAAAC
*
2554 -AAAAATTGAT-ATTAAAAAAAAAC
1 TAAAAAAT-ATAATTAAAAAAAAAC
2577 TAAAAAATATAATTAAA
1 TAAAAAATATAATTAAA
2594 TCATTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 12 0.35
24 14 0.41
25 6 0.18
26 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (24 bp):
TAAAAAATATAATTAAAAAAAAAC
Found at i:5852 original size:5 final size:5
Alignment explanation
Indices: 5844--5871 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5834 ACCAAAATAT
5844 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
5872 TCTATCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:8703 original size:55 final size:55
Alignment explanation
Indices: 8619--8730 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
8609 ACTTGTCAAC
8619 CTCTAACCTTATTTGAGGAGTTTAGAAACTCCACTAACAATTTACAAAATATTTT
1 CTCTAACCTTATTTGAGGAGTTTAGAAACTCCACTAACAATTTACAAAATATTTT
8674 CTCTAACCTTATTTGAGGAGTTTAGAAACTCCACTAACAATTTACAAAATATTTT
1 CTCTAACCTTATTTGAGGAGTTTAGAAACTCCACTAACAATTTACAAAATATTTT
8729 CT
1 CT
8731 TCATATATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (55 bp):
CTCTAACCTTATTTGAGGAGTTTAGAAACTCCACTAACAATTTACAAAATATTTT
Found at i:9377 original size:17 final size:17
Alignment explanation
Indices: 9352--9408 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
9342 GGTTTTTTGT
* *
9352 TAAATAATTGATTGAAA
1 TAAAAAATTAATTGAAA
* *
9369 TAAAAAATTAATTGTAT
1 TAAAAAATTAATTGAAA
* **
9386 TAAAAAATAAATAAAAA
1 TAAAAAATTAATTGAAA
9403 TAAAAA
1 TAAAAA
9409 TTGGCATATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
TAAAAAATTAATTGAAA
Found at i:9397 original size:21 final size:22
Alignment explanation
Indices: 9352--9397 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
9342 GGTTTTTTGT
9352 TAAA-TAATTGATTGAAATAAA
1 TAAATTAATTGATTGAAATAAA
9373 -AAATTAATTGTATT-AAA-AAA
1 TAAATTAATTG-ATTGAAATAAA
9393 TAAAT
1 TAAAT
9398 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.27
21 13 0.59
22 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
TAAATTAATTGATTGAAATAAA
Found at i:24080 original size:23 final size:23
Alignment explanation
Indices: 24053--24098 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24043 CTGATCCACT
*
24053 TATAACATGAGTAA-AAAAAATTA
1 TATAAAATGA-TAATAAAAAATTA
*
24076 TATAAAATGATAATAAAACATTA
1 TATAAAATGATAATAAAAAATTA
24099 ATTACAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (23 bp):
TATAAAATGATAATAAAAAATTA
Found at i:31361 original size:106 final size:106
Alignment explanation
Indices: 31176--31393 Score: 427
Period size: 106 Copynumber: 2.0 Consensus size: 106
31166 GAAATTGAGC
31176 TGCCTGTAGATGGATGAAACCCGCTGTGAAAGCAAAGGTATATAATATCCTGAATATCTCTCTCA
1 TGCCTGTAGATGGATGAAACCCGCTGTGAAAGCAAAGGTATATAATATCCTGAATATCTCTCTCA
31241 AGTTTCACCCGCGGCTTTCCAGGTCGATTTGAAAGGAAATA
66 AGTTTCACCCGCGGCTTTCCAGGTCGATTTGAAAGGAAATA
31282 TGCCTGTAGATGGATGAAACCCGCTGTGAAAGCAAAGGTATATAATATCCTGAATATCTCTCTCA
1 TGCCTGTAGATGGATGAAACCCGCTGTGAAAGCAAAGGTATATAATATCCTGAATATCTCTCTCA
31347 AGTTTCACCCGCGGCTTTCCAGGTCGATTTGAAAGGAAATA
66 AGTTTCACCCGCGGCTTTCCAGGTCGATTTGAAAGGAAATA
31388 TAGCCT
1 T-GCCT
31394 TTTTTCCCGT
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 107 0.96
107 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (106 bp):
TGCCTGTAGATGGATGAAACCCGCTGTGAAAGCAAAGGTATATAATATCCTGAATATCTCTCTCA
AGTTTCACCCGCGGCTTTCCAGGTCGATTTGAAAGGAAATA
Found at i:53791 original size:104 final size:104
Alignment explanation
Indices: 53663--53871 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
53653 ATAAATTAAT
* *
53663 TAACATCGACATTAACCAATTCACACACGTAATGATCAAAACATCATCTTATCATATCATACTGT
1 TAACATCGACATTAACCAATTCACACACGTAATGACCAAAACACCATCTTATCATATCATACTGT
53728 TAGATAAATACATAGGTCTATTTGGTAAATCTACATCAA
66 TAGATAAATACATAGGTCTATTTGGTAAATCTACATCAA
53767 TAACATCGACATTAACCAATTCACACACGTAATGACCAAAACACCATCTTATCATATCATACTGT
1 TAACATCGACATTAACCAATTCACACACGTAATGACCAAAACACCATCTTATCATATCATACTGT
53832 TAGATAAATACATAGGTCTATTTGGTAAATCTACATCAA
66 TAGATAAATACATAGGTCTATTTGGTAAATCTACATCAA
53871 T
1 T
53872 CAATAGGTTA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (104 bp):
TAACATCGACATTAACCAATTCACACACGTAATGACCAAAACACCATCTTATCATATCATACTGT
TAGATAAATACATAGGTCTATTTGGTAAATCTACATCAA
Found at i:55330 original size:29 final size:28
Alignment explanation
Indices: 55276--55338 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
55266 ATTTTTCAAA
**
55276 TTTTAAAAATTTAATTTTTATATTTATAT
1 TTTTAAAAATTTAAAATTTATATTTA-AT
*
55305 TTTTAAAATTTTAAAATTTA-AGTTTAAT
1 TTTTAAAAATTTAAAATTTATA-TTTAAT
*
55333 TATTAA
1 TTTTAA
55339 CATCATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTAAAAATTTAAAATTTATATTTAAT
Done.