Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012576.1 Kokia drynarioides strain JFW-HI SEQ_127585, 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: 37987
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:37 original size:17 final size:17
Alignment explanation
Indices: 11--80 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
1 ATTGGACATT
11 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
27 ATTTCAAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
44 ATTTAAAATAAACTTAA
1 ATTTAAAATAAATTTAA
*
61 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
78 ATT
1 ATT
81 CTGTTGGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 4 0.08
17 44 0.92
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:52 original size:7 final size:6
Alignment explanation
Indices: 18--80 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
8 ATTATTTAAA
* * *
18 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAATTT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
64 TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT
81 CTGTTGGACC
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 3 0.07
5 9 0.20
6 30 0.67
7 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:2346 original size:22 final size:20
Alignment explanation
Indices: 2318--2408 Score: 50
Period size: 22 Copynumber: 4.5 Consensus size: 20
2308 TAAATTTTAT
2318 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
*
2340 TAATTATCACAATT-TTT-ATTT
1 TAATTAT---AATTATTTAATTA
*
2361 TAATATATAA--ATTTTA-T-
1 TAAT-TATAATTATTTAATTA
2378 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
2400 TAATTATAA
1 TAATTATAA
2409 ATATATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 24
0.68 0.02 0.30
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 9 0.16
19 3 0.05
21 6 0.11
22 20 0.36
23 1 0.02
24 3 0.05
25 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTATAATTATTTAATTA
Found at i:2943 original size:16 final size:16
Alignment explanation
Indices: 2930--2970 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2920 AGTTATTTCG
*
2930 AATTTAAATTATTTAT
1 AATTTAAATTATTTAA
* *
2946 AATTTGAATTATTTTA
1 AATTTAAATTATTTAA
2962 AATTTAAAT
1 AATTTAAAT
2971 CATTCGAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTTAAATTATTTAA
Found at i:3544 original size:23 final size:23
Alignment explanation
Indices: 3501--3545 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3491 AATAATTTTA
*
3501 ATGTATTTAATATTCTTAAAATG
1 ATGTATTTAATATTCTAAAAATG
*
3524 ATGTATTTACCTATT-TAAAAAT
1 ATGTATTTA-ATATTCTAAAAAT
3546 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (23 bp):
ATGTATTTAATATTCTAAAAATG
Found at i:4006 original size:6 final size:6
Alignment explanation
Indices: 3995--4027 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3985 CGTTAGTTCA
*
3995 ACAAAT ACAAAT ACAAAT ATAAAT ACAAAT ACA
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACA
4028 TTGATTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
ACAAAT
Found at i:4689 original size:22 final size:22
Alignment explanation
Indices: 4664--4706 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4654 TTAGTAATAA
* *
4664 TTTTATCTTTAAAGTGTTTTTT
1 TTTTATCTTAAAAGTGCTTTTT
4686 TTTTATCTTAAAAGTGCTTTT
1 TTTTATCTTAAAAGTGCTTTT
4707 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTATCTTAAAAGTGCTTTTT
Found at i:4873 original size:17 final size:18
Alignment explanation
Indices: 4847--4889 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
4837 AATTGTAATT
4847 TTTATAATAGTTT-TATTA
1 TTTATAATAGTTTATA-TA
4865 TTT-TAATAGTTTATATA
1 TTTATAATAGTTTATATA
4882 TTTATAAT
1 TTTATAAT
4890 TTTTAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTATAATAGTTTATATA
Found at i:4894 original size:17 final size:17
Alignment explanation
Indices: 4847--4894 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
4837 AATTGTAATT
4847 TTTATAATAGTTTTATTA
1 TTTATAATA-TTTTATTA
*
4865 TTT-TAATAGTTTATATA
1 TTTATAATATTTTAT-TA
4882 TTTATAAT-TTTTA
1 TTTATAATATTTTA
4895 GAATGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 14 0.54
18 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTATAATATTTTATTA
Found at i:9302 original size:21 final size:22
Alignment explanation
Indices: 9267--9309 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
9257 AATATTATTT
9267 ATTAATTAATTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
*
9289 ATTAATT-TTTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
9310 TTTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTAATTTAATTAAATAA
Found at i:9306 original size:17 final size:17
Alignment explanation
Indices: 9270--9325 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
9260 ATTATTTATT
* *
9270 AATTAATTTAATTAAATA
1 AATTAATTT-TTTAATTA
9288 AATTAATTTTTTAATTA
1 AATTAATTTTTTAATTA
*
9305 AA-TAATTTTTTCAATTC
1 AATTAATTTTTT-AATTA
9322 AATT
1 AATT
9326 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.27
17 14 0.42
18 10 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAATTTTTTAATTA
Found at i:14322 original size:69 final size:68
Alignment explanation
Indices: 14117--14324 Score: 192
Period size: 69 Copynumber: 3.0 Consensus size: 68
14107 GCCTTATATA
* * **
14117 CTTCTTTCTCCATTAAATCAATAACCC-CTTTATCTGTGGCCACCACATCACAAAAGGT-TGTAT
1 CTTCTTGCTCCATTAAATCAAT-ACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGT-TAT
14180 CATGTT
63 CATGTT
* * * * * * *
14186 CTTTTTGC-CTCATTGATTCAATTCACACTTTATCCCTAGACCCCACATCACAAGT-G-GTTATG
1 CTTCTTGCTC-CATTAAATCAATACCCACTTTATCCGT-GGCCCCACATCACAAGTGGTGTTAT-
14248 ACATGTT
63 -CATGTT
* *
14255 CTTCTTGCTCCATTAAAACAATACCCACTTTATCCGTGGCCTTCACATCACAAGTGGTGTTATCA
1 CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGTTATCA
14320 TGTT
65 TGTT
14324 C
1 C
14325 CATCATTGAC
Statistics
Matches: 109, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
67 3 0.03
68 8 0.07
69 88 0.81
70 5 0.05
71 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (68 bp):
CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCCCCACATCACAAGTGGTGTTATCAT
GTT
Found at i:18229 original size:16 final size:16
Alignment explanation
Indices: 18190--18235 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
18180 TGTATTTTTT
18190 ATAATTAAA-TGATTA
1 ATAATTAAATTGATTA
*
18205 A-AATATAAATTTATTA
1 ATAAT-TAAATTGATTA
18221 ATAATTAAA-TGATTA
1 ATAATTAAATTGATTA
18236 TAAGTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 10 0.38
17 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
ATAATTAAATTGATTA
Found at i:18238 original size:14 final size:14
Alignment explanation
Indices: 18188--18238 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
18178 ATTGTATTTT
18188 TTATAATTAAATGA
1 TTATAATTAAATGA
* *
18202 TTAAAATATAAATTTA
1 TTATAAT-TAAA-TGA
18218 TTAATAATTAAATGA
1 TT-ATAATTAAATGA
18233 TTATAA
1 TTATAA
18239 GTGAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
16 8 0.27
17 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (14 bp):
TTATAATTAAATGA
Found at i:18246 original size:31 final size:31
Alignment explanation
Indices: 18161--18248 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
18151 ATCAATTTCG
* * *
18161 AATAATTAAGTGATTAT-ATTG-TATTT-TT
1 AATAATTAAATGATTATAAATGAAATTTATT
* *
18189 TATAATTAAATGATTA-AAATATAAATTTATT
1 AATAATTAAATGATTATAAAT-GAAATTTATT
*
18220 AATAATTAAATGATTATAAGTGAAATTTA
1 AATAATTAAATGATTATAAATGAAATTTA
18249 CCCGTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
28 16 0.34
30 4 0.09
31 24 0.51
32 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (31 bp):
AATAATTAAATGATTATAAATGAAATTTATT
Found at i:29482 original size:24 final size:27
Alignment explanation
Indices: 29453--29517 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 27
29443 AAAAATGTAA
*
29453 TTTTATCATTTTAATA-ATT-TAT-AT
1 TTTTATCATTTTAAAAGATTATATAAT
*
29477 TTTTATAATTTTAAAAGATTATATCAAAT
1 TTTTATCATTTTAAAAGATTATAT--AAT
29506 TTTTATCATTTT
1 TTTTATCATTTT
29518 TTGAGAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 14 0.42
25 3 0.09
26 3 0.09
29 13 0.39
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTATCATTTTAAAAGATTATATAAT
Found at i:29489 original size:16 final size:17
Alignment explanation
Indices: 29450--29489 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
29440 AATAAAAATG
29450 TAATTTTATCATTTTAA
1 TAATTTTATCATTTTAA
*
29467 TAA-TTTAT-ATTTTTA
1 TAATTTTATCATTTTAA
29482 TAATTTTA
1 TAATTTTA
29490 AAAGATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTATCATTTTAA
Found at i:29577 original size:17 final size:17
Alignment explanation
Indices: 29546--29596 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
29536 AATTTTATCA
*
29546 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
29562 TTATAAATTATAAAATT
1 TTATAAATTATAAAATT
* * *
29579 ATCTAAA-TAAAAAATT
1 TTATAAATTATAAAATT
29595 TT
1 TT
29597 CCATTTTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:35418 original size:25 final size:26
Alignment explanation
Indices: 35365--35430 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
35355 GGGATCCTAG
*
35365 TGTGCTTTCCGTTTATTAGCACGTAT
1 TGTGCTCTCCGTTTATTAGCACGTAT
*
35391 TGTGCTCTCCG-TTATTTAGCATGT-T
1 TGTGCTCTCCGTTTA-TTAGCACGTAT
* *
35416 TGTGCTATCTGTTTA
1 TGTGCTCTCCGTTTA
35431 GCACTTCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (26 bp):
TGTGCTCTCCGTTTATTAGCACGTAT
Done.