Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003724.1 Kokia drynarioides strain JFW-HI SEQ_116679, 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: 24905
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:566 original size:60 final size:58
Alignment explanation
Indices: 462--643 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 58
452 TAATTTTAAG
462 AGTTTTAGGGGTAAAAATGGAA-TTTGGAAGTTTCGGGGGCAAAAATG-GAATTTTTGGA
1 AGTTTT-GGGGTAAAAATGGAATTTTGGAAGTTTCGGGGGCAAAAATGAG-ATTTTTGGA
* * *
520 AGTTTTGGGGTAAAAAATGGAATCTTTGGAAGTTTTGTGGTCAAAAATGAGATTTTTGGA
1 AGTTTTGGGGT-AAAAATGGAAT-TTTGGAAGTTTCGGGGGCAAAAATGAGATTTTTGGA
* * * **
580 AG-TTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGTTAAAATGAGATTTTTGGA
1 AGTTTTGGGGT-AAAAAT-GGAATTTTGGAAGTTTCGGGGGCAAAAATGAGATTTTTGGA
638 CAGTTT
1 -AGTTT
644 AGGGACCCCT
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
57 5 0.05
58 38 0.36
59 22 0.21
60 39 0.37
61 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (58 bp):
AGTTTTGGGGTAAAAATGGAATTTTGGAAGTTTCGGGGGCAAAAATGAGATTTTTGGA
Found at i:591 original size:29 final size:29
Alignment explanation
Indices: 469--643 Score: 171
Period size: 30 Copynumber: 6.0 Consensus size: 29
459 AAGAGTTTTA
*
469 GGGGT-AAAAATGGA-ATTTGGAAGTTTC
1 GGGGTCAAAAATGGATTTTTGGAAGTTTC
* *
496 GGGGGCAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTCAAAAATGG-ATTTTTGGAAGTTTC
* * *
526 GGGGTAAAAAATGGAATCTTTGGAAGTTTT
1 GGGGTCAAAAATGG-ATTTTTGGAAGTTTC
*
556 GTGGTCAAAAATGAGATTTTTGGAAG-TTC
1 GGGGTCAAAAATG-GATTTTTGGAAGTTTC
*
585 GAGGTCAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTCAAAAAT-GGATTTTTGGAAGTTTC
*
614 GGGGGT-TAAAATGAGATTTTTGGACAGTTT
1 -GGGGTCAAAAATG-GATTTTTGGA-AGTTT
644 AGGGACCCCT
Statistics
Matches: 126, Mismatches: 13, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
27 4 0.03
28 9 0.07
29 44 0.35
30 66 0.52
31 3 0.02
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (29 bp):
GGGGTCAAAAATGGATTTTTGGAAGTTTC
Found at i:1674 original size:3 final size:3
Alignment explanation
Indices: 1666--1745 Score: 61
Period size: 3 Copynumber: 25.0 Consensus size: 3
1656 GTTTTCCTTT
* * * * **
1666 TTA TTA TTAA TGA TTA ATA TTA TTA TCA TTA TTA TTAA TGA GGCA ATTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA -TTA
1715 TTA CTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1746 GCACATTTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
3 52 0.85
4 9 0.15
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:1722 original size:25 final size:28
Alignment explanation
Indices: 1666--1733 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
1656 GTTTTCCTTT
**
1666 TTATTATTAATGATTAATATTATTATCA
1 TTATTATTAATGAGGAATATTATTATCA
*
1694 TTATTATTAATGAGGCAATTATTACTTATTA
1 TTATTATTAATGAGG-AA-TATTA-TTATCA
1725 TTATTATTA
1 TTATTATTA
1734 TTATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 13 0.38
29 2 0.06
30 5 0.15
31 14 0.41
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (28 bp):
TTATTATTAATGAGGAATATTATTATCA
Found at i:1756 original size:40 final size:39
Alignment explanation
Indices: 1678--1770 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 39
1668 ATTATTAATG
1678 ATTAATATTATTATCATTATTATTAATGAGGCAATTATT
1 ATTAATATTATTATCATTATTATTAATGAGGCAATTATT
* * *
1717 ACTTATTATTATTATTATTATTATT-ATTA-GCACATTTATT
1 A-TTAATATTATTATCATTATTATTAATGAGGCA-A-TTATT
1757 ATTAATAGTTATTA
1 ATTAATA-TTATTA
1771 AATAAATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
38 3 0.07
39 10 0.22
40 33 0.72
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (39 bp):
ATTAATATTATTATCATTATTATTAATGAGGCAATTATT
Found at i:2524 original size:6 final size:6
Alignment explanation
Indices: 2514--2588 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
2504 TAATGGACTT
* *
2514 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
*
2562 -TT-AA TTTAAA -TTAAA ATTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2589 ATAAATTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
4 1 0.02
5 13 0.22
6 45 0.75
7 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:2546 original size:17 final size:17
Alignment explanation
Indices: 2514--2588 Score: 107
Period size: 17 Copynumber: 4.4 Consensus size: 17
2504 TAATGGACTT
*
2514 TTTAATTTTAAAATTAAA
1 TTTAAATTT-AAATTAAA
2532 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
2549 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
2566 TTTAAATTAAAATTAAA
1 TTTAAATTTAAATTAAA
2583 TTTAAA
1 TTTAAA
2589 ATAAATTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
16 3 0.06
17 39 0.74
18 11 0.21
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:2547 original size:11 final size:11
Alignment explanation
Indices: 2521--2600 Score: 81
Period size: 11 Copynumber: 7.0 Consensus size: 11
2511 CTTTTTAATT
*
2521 TTAAAATTAAA
1 TTAAATTTAAA
2532 TTTAAATTTAAA
1 -TTAAATTTAAA
2544 TTAAATTTAAA
1 TTAAATTTAAA
*
2555 TTTAAGA-TTAAT
1 -TTAA-ATTTAAA
*
2567 TTAAATTAAAA
1 TTAAATTTAAA
2578 TTAAATTTAAA
1 TTAAATTTAAA
*
2589 ATAAATTATAAA
1 TTAAATT-TAAA
2601 GGGGCCCGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
10 1 0.02
11 34 0.59
12 22 0.38
13 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:13442 original size:94 final size:93
Alignment explanation
Indices: 13313--13504 Score: 267
Period size: 94 Copynumber: 2.1 Consensus size: 93
13303 ATTGTTAGGG
* * ** * * *
13313 AACAATTATATGTACAGATCTATATCGATGGCTGAGGTACCGTATATGTTGCGAGTCTTCATCAG
1 AACAGTTATATGTACAGATCCATATCGATGGCTGAGGTACCACATATGTTACGAGTCCTCATCAA
* *
13378 CTTAGTGTGAGTAGCATCGTATACTGGT
66 CTTAGTGTGAGCAGCATCGTATACTAGT
* *
13406 AACAGTTATATGTATAGATACCGTATCGATGGCTGAGGTACCACATATGTTACGAGTCCTCATCA
1 AACAGTTATATGTACAGAT-CCATATCGATGGCTGAGGTACCACATATGTTACGAGTCCTCATCA
*
13471 ACTTAGTGTGAGCAGCTTCGTATACTAGT
65 ACTTAGTGTGAGCAGCATCGTATACTAGT
13500 AACAG
1 AACAG
13505 AGACAATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 17 0.20
94 69 0.80
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (93 bp):
AACAGTTATATGTACAGATCCATATCGATGGCTGAGGTACCACATATGTTACGAGTCCTCATCAA
CTTAGTGTGAGCAGCATCGTATACTAGT
Found at i:20105 original size:8 final size:8
Alignment explanation
Indices: 20091--20140 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
20081 TTCTAGTGTG
20091 GTTTT-TT
1 GTTTTGTT
*
20098 GTTTTTTT
1 GTTTTGTT
20106 GTTTT-TT
1 GTTTTGTT
*
20113 GTTTTGAT
1 GTTTTGTT
20121 GTTGTTGTT
1 GTT-TTGTT
20130 GTTTTGTT
1 GTTTTGTT
20138 GTT
1 GTT
20141 ACTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
7 12 0.32
8 19 0.50
9 7 0.18
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.76
Consensus pattern (8 bp):
GTTTTGTT
Found at i:20117 original size:14 final size:15
Alignment explanation
Indices: 20091--20140 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
20081 TTCTAGTGTG
*
20091 GTTTTTTGTTTTTTT
1 GTTTTTTGTTTTGTT
*
20106 GTTTTTTGTTTTGAT
1 GTTTTTTGTTTTGTT
20121 GTTGTTGTTGTTTTGTT
1 GTT-TT-TTGTTTTGTT
20138 GTT
1 GTT
20141 ACTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 12 0.40
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.76
Consensus pattern (15 bp):
GTTTTTTGTTTTGTT
Found at i:23517 original size:59 final size:58
Alignment explanation
Indices: 23416--23725 Score: 453
Period size: 59 Copynumber: 5.3 Consensus size: 58
23406 GCACGAGGGC
* * * *
23416 AAAATGGT-AGTTTTAGAGGGTTC-GAGTCAAAAATTGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGT
* *
23473 AAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAATTGGGATTTTTGGAAGTTCGGAGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAA-TGGGATTTTTGGAAGTTCGGGGGT
* * **
23532 AAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAATGAGATTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
23590 AAAATGGTAACTTTTAGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGG-TCAAAATGGGATTTTTGGAAGTTCGGGGGT
*
23649 AAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGGT
23707 AAAATGGTAATTTTTAGAA
1 AAAATGGTAATTTTTAGAA
23726 AGTTTATGGA
Statistics
Matches: 228, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
57 8 0.04
58 109 0.48
59 111 0.49
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:23632 original size:117 final size:117
Alignment explanation
Indices: 23452--23725 Score: 449
Period size: 117 Copynumber: 2.3 Consensus size: 117
23442 TCAAAAATTG
* *
23452 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAATTGGGATTTT
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAAATGAGATTTT
23517 TGGAAGTTCGGAGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAATGA
66 TGGAAGTTCGGAGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAATGA
** * * *
23569 GATTTTTGGAAGTTTAGGGGTAAAATGGTAACTTTTAGAAGGTTCGGGGTTAAAAATGAGATTTT
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAAATGAGATTTT
* * * *
23634 TGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAATGG
66 TGGAAGTTCGGAGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAATGA
23686 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA
23726 AGTTTATGGA
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 143 1.00
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (117 bp):
GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAAATGAGATTTT
TGGAAGTTCGGAGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAATGA
Done.