Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008254.1 Kokia drynarioides strain JFW-HI SEQ_122919, 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: 33706
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:747 original size:31 final size:31
Alignment explanation
Indices: 712--775 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
702 TATAAGAGTA
712 AATGACAAAACAACCACTCAACTTT-AATCTC
1 AATGACAAAACAACCACTCAACTTTCAAT-TC
* * *
743 AATGATAAAACAATCATTCAACTTTCAATTC
1 AATGACAAAACAACCACTCAACTTTCAATTC
774 AA
1 AA
776 CAACTTAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (31 bp):
AATGACAAAACAACCACTCAACTTTCAATTC
Found at i:2611 original size:16 final size:16
Alignment explanation
Indices: 2590--2624 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2580 TTTACAGCAT
2590 ACAGAAATAACATAAC
1 ACAGAAATAACATAAC
2606 ACAGAAATAACATAAC
1 ACAGAAATAACATAAC
2622 ACA
1 ACA
2625 AAGGAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.11
Consensus pattern (16 bp):
ACAGAAATAACATAAC
Found at i:7731 original size:21 final size:22
Alignment explanation
Indices: 7705--7750 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
7695 ATATGATTAT
* * *
7705 AAAATTTTATAAAATTGT-AAG
1 AAAATTATAAAAAAATGTAAAG
7726 AAAATTATAAAAAAATGTAAAG
1 AAAATTATAAAAAAATGTAAAG
7748 AAA
1 AAA
7751 TATAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (22 bp):
AAAATTATAAAAAAATGTAAAG
Found at i:7735 original size:19 final size:18
Alignment explanation
Indices: 7711--7776 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
7701 TTATAAAATT
7711 TTATAAAATTGTAAGAAAA
1 TTATAAAATTGTAA-AAAA
*
7730 TTATAAAAAAATGTAAAGAAA
1 TTAT--AAAATTGTAAA-AAA
*
7751 -TATAAATTTTGTAAAAAA
1 TTATAAA-ATTGTAAAAAA
7769 TTATAAAA
1 TTATAAAA
7777 ATTATCATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 6 0.16
19 16 0.42
20 4 0.11
21 12 0.32
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
TTATAAAATTGTAAAAAA
Found at i:8011 original size:9 final size:9
Alignment explanation
Indices: 7963--8118 Score: 75
Period size: 9 Copynumber: 16.4 Consensus size: 9
7953 TTTTGATGTA
*
7963 TTTTATAAA
1 TTTTATAAT
*
7972 TTTTATTAT
1 TTTTATAAT
*
7981 TTTTATAAAA
1 TTTTAT-AAT
7991 TTTTAT-AT
1 TTTTATAAT
7999 TTTTATAAT
1 TTTTATAAT
*
8008 TTTT-TACGGT
1 TTTTATA--AT
*
8018 TTTTATATTTT
1 TTTTATA--AT
* *
8029 TTTTCTTAT
1 TTTTATAAT
8038 TTTTAATAAAT
1 TTTT-AT-AAT
* **
8049 TTTAAGTTTT
1 TTTTA-TAAT
8059 TTTTATATAT
1 TTTTATA-AT
8069 TTTTATTAAT
1 TTTTA-TAAT
* *
8079 ACTTAATAAT
1 -TTTTATAAT
8089 TTTTATAAT
1 TTTTATAAT
*
8098 TTTTAT-TT
1 TTTTATAAT
8106 TTTTATAAT
1 TTTTATAAT
8115 TTTT
1 TTTT
8119 TTTTCACATG
Statistics
Matches: 109, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
8 16 0.15
9 43 0.39
10 31 0.28
11 19 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:8401 original size:85 final size:86
Alignment explanation
Indices: 8304--8481 Score: 252
Period size: 85 Copynumber: 2.1 Consensus size: 86
8294 AGTTTGAAAG
* *
8304 TTTTTTTGATGTATTTTAAAAGTTCAAGTTTCTAATTGAGTG-AAAAAAAACAGGAGCTTAATT-
1 TTTTTTTGATGTATTTTAAAAGTTCAAGTATCTAATTGAATGCAAAAAAAACAGGAGCTTAATTA
* *
8367 GGTTTTTTTTTAATTTAAGGAT
66 CGTTTTTTTTTAA-TTAAGGAC
* * *
8389 TTTTTTTTATGTATTTTAAAAGTTTAAGTATCTAATTGAATGCAAAAAAAATAGGAGCTTAATTA
1 TTTTTTTGATGTATTTTAAAAGTTCAAGTATCTAATTGAATGCAAAAAAAACAGGAGCTTAATTA
* *
8454 CTTTTTTTTTTAATTAAGGGC
66 CGTTTTTTTTTAATTAAGGAC
8475 TTTTTTT
1 TTTTTTT
8482 CACCATTAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 38 0.46
86 33 0.40
87 11 0.13
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (86 bp):
TTTTTTTGATGTATTTTAAAAGTTCAAGTATCTAATTGAATGCAAAAAAAACAGGAGCTTAATTA
CGTTTTTTTTTAATTAAGGAC
Found at i:14298 original size:33 final size:33
Alignment explanation
Indices: 14254--14319 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
14244 GTAACATTCA
* *
14254 ATTTAAACATATAAACAATTGATTCAAAAGAAG
1 ATTTAAACATATAAAAAATCGATTCAAAAGAAG
*
14287 ATTTAAGCATATAAAAAATCGATTCAAAAGAAG
1 ATTTAAACATATAAAAAATCGATTCAAAAGAAG
14320 TAATATTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (33 bp):
ATTTAAACATATAAAAAATCGATTCAAAAGAAG
Found at i:15687 original size:2 final size:2
Alignment explanation
Indices: 15682--15716 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15672 CTTTTCCTTT
15682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15717 TACTTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18400 original size:26 final size:26
Alignment explanation
Indices: 18368--18435 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
18358 AGAATAAATT
18368 TTTTAATATTATTTTTTTAGTGAAAA
1 TTTTAATATTATTTTTTTAGTGAAAA
18394 TTTTAATATTATTTTTTTAGTGAAAA
1 TTTTAATATTATTTTTTTAGTGAAAA
18420 TTTTAATATTATTTTT
1 TTTTAATATTATTTTT
18436 AATCCTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTTAATATTATTTTTTTAGTGAAAA
Found at i:18636 original size:42 final size:42
Alignment explanation
Indices: 18577--18660 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
18567 TTATAAAAAA
*
18577 ACTAAATTGAAAAAAATTAATCTTTGGAGAGGCCATGACTAC
1 ACTAAATTGAAAAAAATTAATCTTTGGAGAGACCATGACTAC
18619 ACTAAATTGAAAAAAATTAATCTTTGGAGAGACCATGACTAC
1 ACTAAATTGAAAAAAATTAATCTTTGGAGAGACCATGACTAC
18661 CACCGAACAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (42 bp):
ACTAAATTGAAAAAAATTAATCTTTGGAGAGACCATGACTAC
Found at i:26656 original size:18 final size:18
Alignment explanation
Indices: 26633--26689 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
26623 TGAGAAGAAG
26633 AAATGGTGTTAGATGGAA
1 AAATGGTGTTAGATGGAA
26651 AAATGGTG--AG--GAGAA
1 AAATGGTGTTAGATG-GAA
*
26666 GAAGTGGTGTTAGATGGAA
1 -AAATGGTGTTAGATGGAA
26685 AAATG
1 AAATG
26690 AGGAAGAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 3 0.10
16 9 0.29
18 14 0.45
19 3 0.10
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (18 bp):
AAATGGTGTTAGATGGAA
Found at i:26674 original size:34 final size:34
Alignment explanation
Indices: 26623--26689 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
26613 ACTTGGACAA
26623 TGAGAAGAAGAAATGGTGTTAGATGGAAAAATGG
1 TGAGAAGAAGAAATGGTGTTAGATGGAAAAATGG
* *
26657 TGAGGAGAAGAAGTGGTGTTAGATGGAAAAATG
1 TGAGAAGAAGAAATGGTGTTAGATGGAAAAATG
26690 AGGAAGAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.21
Consensus pattern (34 bp):
TGAGAAGAAGAAATGGTGTTAGATGGAAAAATGG
Found at i:32639 original size:6 final size:6
Alignment explanation
Indices: 32607--32670 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
32597 TATTTTAAGG
* * *
32607 TTAAAT TT-ATT TTGAAT TTAAATT TTAAAT TTAACA- -TAAAT TTAGAT
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT
*
32654 TTATAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
32671 ACTTATTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 1 0.02
5 7 0.15
6 32 0.68
7 7 0.15
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:33506 original size:24 final size:24
Alignment explanation
Indices: 33475--33520 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
33465 TTATATATTA
*
33475 AATAATTTCATTAATGATAATAGT
1 AATAATTTCATTAAAGATAATAGT
*
33499 AATAATTTTATTAAAGATAATA
1 AATAATTTCATTAAAGATAATA
33521 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (24 bp):
AATAATTTCATTAAAGATAATAGT
Found at i:33518 original size:15 final size:16
Alignment explanation
Indices: 33500--33529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33490 GATAATAGTA
33500 ATAAT-TTTATTAAAG
1 ATAATATTTATTAAAG
33515 ATAATATTTATTAAA
1 ATAATATTTATTAAA
33530 TAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATATTTATTAAAG
Done.