Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013980.1 Kokia drynarioides strain JFW-HI SEQ_129011, 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: 20280
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.36
Warning! 120 characters in sequence are not A, C, G, or T
Found at i:627 original size:18 final size:16
Alignment explanation
Indices: 604--647 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
594 TTATAAAATG
*
604 TTTAATATTTACATAAGT
1 TTTAATATGTA-AT-AGT
622 TTTAATATGTAATAGT
1 TTTAATATGTAATAGT
638 TTT-ATATGTA
1 TTTAATATGTA
648 CTTTTATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 2 0.08
18 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (16 bp):
TTTAATATGTAATAGT
Found at i:9478 original size:9 final size:9
Alignment explanation
Indices: 9460--9496 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
9450 TAATTTTATC
*
9460 TTTTACAAA
1 TTTTAAAAA
9469 TTTTAAAAA
1 TTTTAAAAA
9478 TTTTAAAAAA
1 TTTT-AAAAA
9488 TTTTAAAAA
1 TTTTAAAAA
9497 CTTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:9488 original size:10 final size:10
Alignment explanation
Indices: 9466--9496 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
9456 TATCTTTTAC
9466 AAATTTT-AA
1 AAATTTTAAA
9475 AAATTTTAAA
1 AAATTTTAAA
9485 AAATTTTAAA
1 AAATTTTAAA
9495 AA
1 AA
9497 CTTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:12555 original size:29 final size:31
Alignment explanation
Indices: 12503--12590 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 31
12493 TGCTTTAATT
* *
12503 TGCAATCAGATACAT-AAATTTTGATTTG-A-
1 TGCAATCATATACATGAAA-CTTGATTTGTAG
*
12532 TGCAATCATATACATGAAACTTGAATTGTAG
1 TGCAATCATATACATGAAACTTGATTTGTAG
* *
12563 TTCATAT-GTATACATGAAACATTGATTT
1 TGCA-ATCATATACATGAAAC-TTGATTT
12591 TAATTCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 21 0.44
30 4 0.08
31 15 0.31
32 8 0.17
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
TGCAATCATATACATGAAACTTGATTTGTAG
Found at i:15459 original size:23 final size:23
Alignment explanation
Indices: 15414--15526 Score: 124
Period size: 23 Copynumber: 5.0 Consensus size: 23
15404 ACGGAACAAA
* *
15414 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
* *
15435 CAGAGAGCCCACACAGTGCTGAA-
1 CAGAGAGCACACAAAGTGCT-AAT
* * *
15458 CAGAGAGTATACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
15481 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
15504 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
15527 AACAAAGAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
21 8 0.11
22 9 0.12
23 59 0.78
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:15526 original size:46 final size:46
Alignment explanation
Indices: 15412--15526 Score: 146
Period size: 46 Copynumber: 2.5 Consensus size: 46
15402 ATACGGAACA
* *
15412 AACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCCCACACAGTGCTG
1 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTG
*
15456 AACAGAGAGTATACAAAGTACTAATCAGAGAGCACACAAAGTGCT-
1 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTG
* * *
15501 AATCAGAGAGCACACACAGTGCTAAT
1 AA-CAGAGAGTACACAAAGTACTAAT
15527 AACAAAGAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
44 11 0.18
45 13 0.21
46 37 0.61
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (46 bp):
AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTG
Found at i:15538 original size:23 final size:23
Alignment explanation
Indices: 15489--15538 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
15479 ATCAGAGAGC
* * * *
15489 ACACAAAGTGCTAATCAGAGAGC
1 ACACAAAGTGCTAATAACAAAGA
*
15512 ACACACAGTGCTAATAACAAAGA
1 ACACAAAGTGCTAATAACAAAGA
15535 ACAC
1 ACAC
15539 GAGACGTGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (23 bp):
ACACAAAGTGCTAATAACAAAGA
Found at i:18004 original size:6 final size:6
Alignment explanation
Indices: 17995--18020 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17985 ATTCCAATCA
17995 CACTTT CACTTT CACTTT CACTTT CA
1 CACTTT CACTTT CACTTT CACTTT CA
18021 ATTTTGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
CACTTT
Found at i:19414 original size:25 final size:25
Alignment explanation
Indices: 19386--19433 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
19376 AATAAATTAT
*
19386 ATTATATACATACAAATATATTTCA
1 ATTACATACATACAAATATATTTCA
* * *
19411 ATTACATTCGTATAAATATATTT
1 ATTACATACATACAAATATATTT
19434 ATAGTTAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTACATACATACAAATATATTTCA
Found at i:20075 original size:4 final size:4
Alignment explanation
Indices: 20066--20132 Score: 73
Period size: 4 Copynumber: 16.5 Consensus size: 4
20056 CAAATAAACG
* * *
20066 AGAA AGAA AGAA ATGAA AGAA AGAA AGAA AGGA AGAA GGAGA GGAA AGAA
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA
*
20116 AG-A AGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AG
20133 GTAATGTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.06
4 43 0.80
5 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:20088 original size:17 final size:16
Alignment explanation
Indices: 20066--20132 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 16
20056 CAAATAAACG
20066 AGAAAGAAAGAAATGAA
1 AGAAAGAAAGAAA-GAA
*
20083 AGAAAGAAAGAAAGGA
1 AGAAAGAAAGAAAGAA
* *
20099 AGAAGGAGAGGAAAGAA
1 AGAAAGA-AAGAAAGAA
*
20116 AG-AAGAAGGAAAGAA
1 AGAAAGAAAGAAAGAA
20131 AG
1 AG
20133 GTAATGTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
15 11 0.25
16 11 0.25
17 22 0.50
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (16 bp):
AGAAAGAAAGAAAGAA
Found at i:20095 original size:25 final size:24
Alignment explanation
Indices: 20066--20132 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
20056 CAAATAAACG
20066 AGAAAGAAAGAAATGAAAGAAAGAA
1 AGAAAGAAAGAAA-GAAAGAAAGAA
* * *
20091 AGAAAGGAAGAAGGAGAGGAAAGAA
1 AGAAAGAAAGAAAGA-AAGAAAGAA
*
20116 AG-AAGAAGGAAAGAAAG
1 AGAAAGAAAGAAAGAAAG
20133 GTAATGTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 2 0.06
24 11 0.32
25 21 0.62
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (24 bp):
AGAAAGAAAGAAAGAAAGAAAGAA
Done.