Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010909.1 Kokia drynarioides strain JFW-HI SEQ_125877, 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: 20866
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:3366 original size:17 final size:17
Alignment explanation
Indices: 3346--3420 Score: 114
Period size: 17 Copynumber: 4.4 Consensus size: 17
3336 TCAATTTTAA
*
3346 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
3363 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
3380 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
3397 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
3414 ATTTTAA
1 ATTTTAA
3421 TTGATTTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:3385 original size:11 final size:12
Alignment explanation
Indices: 3345--3420 Score: 54
Period size: 11 Copynumber: 6.7 Consensus size: 12
3335 TTCAATTTTA
3345 AATTTTAAATTTT
1 AATTTTAAA-TTT
*
3358 AA-TTT-ATTTT
1 AATTTTAAATTT
*
3368 AAGTTTAAATTT
1 AATTTTAAATTT
3380 -ATTTTAAATTT
1 AATTTTAAATTT
* *
3391 AAATTT-ATTTT
1 AATTTTAAATTT
* *
3402 GAGTTTAAATTT
1 AATTTTAAATTT
3414 -ATTTTAA
1 AATTTTAA
3421 TTGATTTGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
10 5 0.10
11 28 0.56
12 15 0.30
13 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:3389 original size:34 final size:34
Alignment explanation
Indices: 3346--3420 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
3336 TCAATTTTAA
*
3346 ATTTTAAATTTTAATTTATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
*
3380 ATTTTAAATTTAAATTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
3414 ATTTTAA
1 ATTTTAA
3421 TTGATTTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
Found at i:3414 original size:6 final size:6
Alignment explanation
Indices: 3317--3397 Score: 60
Period size: 6 Copynumber: 13.8 Consensus size: 6
3307 CGGATCTAAC
* * * * *
3317 ATTTAA A-TTAA AATTGA ATTCAA TTTTAA ATTTTAA ATTTTA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA
* * *
3364 TTTTAA GTTTAA ATTT-A TTTTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
3398 TTTTGAGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
5 13 0.22
6 39 0.67
7 6 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:3453 original size:142 final size:142
Alignment explanation
Indices: 3280--3559 Score: 434
Period size: 142 Copynumber: 2.0 Consensus size: 142
3270 TTTATGTAAG
* * * * * **
3280 TGATTTGTGTTGGAGTTCAATTTTGATCGGATCTAACATTTAAATTAAAATTGAATTCAATTTTA
1 TGATTTGTATTGGAGTTCAATTTTAACCGGATCCAACATTTAAACTAAAATTGAACCCAATTTTA
* * *
3345 AATTTTAAATTTTAATTTATTTTAAGTTTAAATTTATTTTAAATTTAAATTTATTTTGAGTTTAA
66 AATTTTAAATTTTAATTTATTTTAAATTTAAATTTATTCTAAATTTAAATTTATTTTAAGTTTAA
3410 ATTTATTTTAAT
131 ATTTATTTTAAT
*
3422 TGATTTGTATTGGAGTTTAATTTTAACCGGATCCAACATTTAAACTAAAATTGAACCCAATTTTA
1 TGATTTGTATTGGAGTTCAATTTTAACCGGATCCAACATTTAAACTAAAATTGAACCCAATTTTA
* * *
3487 AATTTTAAATTTTAATTTATTTTAAATTTAAATTTATTCTGAGTTTAAATTTATTTTAATTTTAA
66 AATTTTAAATTTTAATTTATTTTAAATTTAAATTTATTCTAAATTTAAATTTATTTTAAGTTTAA
3552 ATTTATTT
131 ATTTATTT
3560 CGAATTCAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
142 124 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (142 bp):
TGATTTGTATTGGAGTTCAATTTTAACCGGATCCAACATTTAAACTAAAATTGAACCCAATTTTA
AATTTTAAATTTTAATTTATTTTAAATTTAAATTTATTCTAAATTTAAATTTATTTTAAGTTTAA
ATTTATTTTAAT
Found at i:3492 original size:7 final size:7
Alignment explanation
Indices: 3480--3521 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
3470 AATTGAACCC
3480 AATTTTA
1 AATTTTA
3487 AATTTTA
1 AATTTTA
3494 AATTTTA
1 AATTTTA
3501 ATTTATTTTA
1 A---ATTTTA
3511 AA-TTTA
1 AATTTTA
3517 AATTT
1 AATTT
3522 ATTCTGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
10 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
AATTTTA
Found at i:3508 original size:17 final size:17
Alignment explanation
Indices: 3488--3573 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 17
3478 CCAATTTTAA
*
3488 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
3505 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* * *
3522 ATTCTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
3539 ATTTTAATTTTAAATTT
1 ATTTTAAATTTAAATTT
** *
3556 ATTTCGAATTCAAATTT
1 ATTTTAAATTTAAATTT
3573 A
1 A
3574 AAGTTTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:3516 original size:6 final size:6
Alignment explanation
Indices: 3483--3584 Score: 54
Period size: 6 Copynumber: 17.3 Consensus size: 6
3473 TGAACCCAAT
* * * *
3483 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAA TTTAAA TTT--A TTCTGAG
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
* * * *
3530 TTTAAA TTT-AT TTTAAT TTTAAA TTT--A TTTCGAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
3576 GTTTAAA TT
1 -TTTAAA TT
3585 AAAAGTCCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
4 7 0.09
5 9 0.12
6 42 0.56
7 17 0.23
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5350 original size:29 final size:30
Alignment explanation
Indices: 5294--5437 Score: 129
Period size: 30 Copynumber: 4.9 Consensus size: 30
5284 AAACTCCTTG
* *
5294 AACTTTCCAAAAATT-CATGTTTTGACCCTTA
1 AACTTTTCAAAAATTACAT-TTTT-ACCCCTA
*
5325 AACTTTT-TAAAATTACATTTTTACCCCTA
1 AACTTTTCAAAAATTACATTTTTACCCCTA
** *
5354 AACTTTTCAAAAAAAACATTTTCACCCCTA
1 AACTTTTCAAAAATTACATTTTTACCCCTA
*
5384 AA-TTTATCCAAAATTACATTTTTACCCC-A
1 AACTTT-TCAAAAATTACATTTTTACCCCTA
* * *
5413 AAC--TCCCAAAATCACATTTTTACCC
1 AACTTTTCAAAAATTACATTTTTACCC
5438 TCGAACTTCT
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
27 19 0.20
28 1 0.01
29 19 0.20
30 48 0.50
31 9 0.09
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (30 bp):
AACTTTTCAAAAATTACATTTTTACCCCTA
Found at i:5430 original size:87 final size:88
Alignment explanation
Indices: 5333--5539 Score: 219
Period size: 87 Copynumber: 2.4 Consensus size: 88
5323 TAAACTTTTT
* *
5333 AAAATTACATTTTTACCCCTAAACTTTTCAAAAA-AAACATTTTCACCC-CTAAATTTATCCAAA
1 AAAATCACATTTTTACCCCTAAACTTCT-AAAAAGAAACATTTT-ACCCTC-AAATTTATCCAAA
*
5396 ATTACATTTTTACC-CCAAAC-TCCC
63 ATTACATTTTTACCTCCAAACTTCCA
* ** * *
5420 AAAATCACATTTTTA-CCCTCGAACTTCTAAAAAGTCACATTTTACCCTCGAATTTCTCCAAAAT
1 AAAATCACATTTTTACCCCT-AAACTTCTAAAAAGAAACATTTTACCCTCAAATTTATCCAAAAT
* * *
5484 TACCTTTTTTCCTCCATACTTCCA
65 TACATTTTTACCTCCAAACTTCCA
* *
5508 AAAATCACA-TTTTACTCCTAAACTTCCAAAAA
1 AAAATCACATTTTTACCCCTAAACTTCTAAAAA
5540 TCACATTTTG
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
86 36 0.36
87 49 0.49
88 15 0.15
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (88 bp):
AAAATCACATTTTTACCCCTAAACTTCTAAAAAGAAACATTTTACCCTCAAATTTATCCAAAATT
ACATTTTTACCTCCAAACTTCCA
Found at i:5463 original size:29 final size:28
Alignment explanation
Indices: 5393--5664 Score: 133
Period size: 29 Copynumber: 9.5 Consensus size: 28
5383 AAATTTATCC
* * *
5393 AAAATTACATTTTTACCC-CAAAC-TCCC
1 AAAATCACA-TTTTACCCTCGAACTTCCA
*
5420 AAAATCACATTTTTACCCTCGAACTTCTA
1 AAAATCACA-TTTTACCCTCGAACTTCCA
* *
5449 AAAAGTCACATTTTACCCTCGAATTTCTCC
1 AAAA-TCACATTTTACCCTCGAACTTC-CA
* * ** *
5479 AAAATTACCTTTTTTCCTCCATACTTCCA
1 AAAATCACATTTTACCCTCGA-ACTTCCA
*
5508 AAAATCACATTTTACTCCT-AAACTTCCA
1 AAAATCACATTTTAC-CCTCGAACTTCCA
* * *
5536 AAAATCACATTTTGA-CCTTGAACATTTCT
1 AAAATCACATTTT-ACCCTCGAAC-TTCCA
* *** * *
5565 AAAATTACCATTCCGCCCCCGAACCTCGCA
1 AAAATCA-CATTTTACCCTCGAACTTC-CA
* *
5595 AAAATTACATTTTGGCCC-CGAACATT-CA
1 AAAATCACATTTT-ACCCTCGAAC-TTCCA
* * *
5623 AAAATTACCATTTTACCCTCAAATTTCCA
1 AAAATCA-CATTTTACCCTCGAACTTCCA
* *
5652 AAAGTCACGTTTT
1 AAAATCACATTTT
5665 CAACTTCAAA
Statistics
Matches: 188, Mismatches: 40, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
27 20 0.11
28 46 0.24
29 83 0.44
30 39 0.21
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATCACATTTTACCCTCGAACTTCCA
Found at i:5569 original size:86 final size:85
Alignment explanation
Indices: 5392--5573 Score: 203
Period size: 86 Copynumber: 2.1 Consensus size: 85
5382 TAAATTTATC
* * * *
5392 CAAAATTACATTTTTACCCCAAACTCCCAAAATCACATTTTTACCCTCGAACTTCTAAAAAGTCA
1 CAAAATTACCTTTTTACCCCAAACTCCAAAAATCACATTTTTACCCTCAAACTTCCAAAAAGTCA
5457 CATTTTACCCTCGAATTTCT
66 CATTTTACCCTCGAATTTCT
* *
5477 CCAAAATTACCTTTTTTCCTCCATACTTCCAAAAATCACA-TTTTACTCCT-AAACTTCCAAAAA
1 -CAAAATTACCTTTTTACC-CCAAAC-TCCAAAAATCACATTTTTAC-CCTCAAACTTCCAAAAA
*
5540 -TCACATTTTGA-CCTTGAACATTTCT
62 GTCACATTTT-ACCCTCG-A-ATTTCT
5565 -AAAATTACC
1 CAAAATTACC
5574 ATTCCGCCCC
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
86 38 0.46
87 24 0.29
88 21 0.25
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (85 bp):
CAAAATTACCTTTTTACCCCAAACTCCAAAAATCACATTTTTACCCTCAAACTTCCAAAAAGTCA
CATTTTACCCTCGAATTTCT
Found at i:5703 original size:29 final size:31
Alignment explanation
Indices: 5670--5736 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
5660 GTTTTCAACT
*
5670 TCAAATTTTCCAAAAGTTT-AATTTTAATCC
1 TCAAATTTTCCAAAAATTTCAATTTTAATCC
* *
5700 -CAAATTTTCCAAAAATTTCGATTTTGATCC
1 TCAAATTTTCCAAAAATTTCAATTTTAATCC
5730 TCAAATT
1 TCAAATT
5737 CCTTGAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.53
30 9 0.28
31 6 0.19
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (31 bp):
TCAAATTTTCCAAAAATTTCAATTTTAATCC
Found at i:13698 original size:6 final size:6
Alignment explanation
Indices: 13687--13734 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
13677 TTTGACGAAT
*
13687 ATACTC ATACTC ATACTC ATACTC ATACTC ATACTA ATACTC ATACTC
1 ATACTC ATACTC ATACTC ATACTC ATACTC ATACTC ATACTC ATACTC
13735 GTACCATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACTC
Found at i:18093 original size:39 final size:39
Alignment explanation
Indices: 18050--18196 Score: 186
Period size: 39 Copynumber: 3.8 Consensus size: 39
18040 AGCCTGCGGT
*
18050 AGATCACCACTAGTCAATCTCTTACCCCGAGCTTGGGGC
1 AGATCACCACCAGTCAATCTCTTACCCCGAGCTTGGGGC
* *
18089 AGATCACCACCAGTTAATCTTTTACCCCGAGCTTGGGGC
1 AGATCACCACCAGTCAATCTCTTACCCCGAGCTTGGGGC
* * * * * * *
18128 AGATTACAACCATTCGATCTTTTACCCCGAGCCTGGGAC
1 AGATCACCACCAGTCAATCTCTTACCCCGAGCTTGGGGC
* *
18167 AGATCACCATCAGCCAATCTCTTACCCCGA
1 AGATCACCACCAGTCAATCTCTTACCCCGA
18197 TCATGGGCAG
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (39 bp):
AGATCACCACCAGTCAATCTCTTACCCCGAGCTTGGGGC
Found at i:18699 original size:17 final size:17
Alignment explanation
Indices: 18631--18699 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
18621 CCAATTTTAA
* *
18631 ATTTTAAATTTTAATTT
1 ATTTTGAATTTAAATTT
*
18648 ATTTT-AAGTTTAAACTT
1 ATTTTGAA-TTTAAATTT
* * *
18665 ATTCTGAGTTTAATTTT
1 ATTTTGAATTTAAATTT
*
18682 ATTTTGAATTCAAATTT
1 ATTTTGAATTTAAATTT
18699 A
1 A
18700 AAGTTTAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 2 0.05
17 37 0.93
18 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTTTGAATTTAAATTT
Done.