Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010211.1 Kokia drynarioides strain JFW-HI SEQ_125031, 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: 76567
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:2017 original size:19 final size:19
Alignment explanation
Indices: 1974--2024 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1964 GTTGTTTTCT
* *
1974 CACTATTTTGTTATTATTT
1 CACTATTTTGTTATCATTC
1993 CACTATTTTGTTATCATTC
1 CACTATTTTGTTATCATTC
* *
2012 CGCTATTATGTTA
1 CACTATTTTGTTA
2025 CTACTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.55
Consensus pattern (19 bp):
CACTATTTTGTTATCATTC
Found at i:2723 original size:14 final size:14
Alignment explanation
Indices: 2687--2724 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2677 CCAAATTTAA
2687 AATTTAATTTTTTT
1 AATTTAATTTTTTT
*
2701 ACTTTAATTTTTTT
1 AATTTAATTTTTTT
*
2715 AATTAAATTT
1 AATTTAATTT
2725 AGTACTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTAATTTTTTT
Found at i:3693 original size:31 final size:30
Alignment explanation
Indices: 3634--3693 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3624 TACAAATATA
* *
3634 ATTTTTAAAAAATTAAATTAAAATTTTATC
1 ATTTTTAAAAAATCAAAATAAAATTTTATC
*
3664 ATTTTTAAAATAATCAAAATATAATTTTAT
1 ATTTTTAAAA-AATCAAAATAAAATTTTAT
3694 TTAAGTTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTTTAAAAAATCAAAATAAAATTTTATC
Found at i:5454 original size:2 final size:2
Alignment explanation
Indices: 5447--5476 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5437 ATTAGAAATT
5447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5477 AAAGCATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9044 original size:39 final size:39
Alignment explanation
Indices: 9001--9128 Score: 157
Period size: 39 Copynumber: 3.3 Consensus size: 39
8991 ACCGTCGATG
* * *
9001 CAGTATCGCAATACGGTATTTTCAGTGTTACTGTCAGTT
1 CAGTATTGCATTACGGTATTTACAGTGTTACTGTCAGTT
* * *
9040 CAGTATTACGTTACGGTATTTACAGTGTTACTGTTAGTT
1 CAGTATTGCATTACGGTATTTACAGTGTTACTGTCAGTT
* * * *
9079 CAGTATTGCATTACGATATTTACAATATTACCGTCAGTT
1 CAGTATTGCATTACGGTATTTACAGTGTTACTGTCAGTT
*
9118 CGGTATTGCAT
1 CAGTATTGCAT
9129 CGCAGTGTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (39 bp):
CAGTATTGCATTACGGTATTTACAGTGTTACTGTCAGTT
Found at i:16648 original size:28 final size:28
Alignment explanation
Indices: 16574--16659 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
16564 TTATAAATCT
* * *
16574 TAAAATTATACATGAATTTTGTTTTAATGTG
1 TAAATTTATACATGAATTTTG-ATT--TGTA
*
16605 TAAATTTATGCATGAATTTTGATTTGTA
1 TAAATTTATACATGAATTTTGATTTGTA
* *
16633 TAATTTTATACATGAAATCTTGATTTG
1 TAAATTTATACATG-AATTTTGATTTG
16660 ATGCAATTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 15 0.32
29 11 0.23
30 2 0.04
31 19 0.40
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.49
Consensus pattern (28 bp):
TAAATTTATACATGAATTTTGATTTGTA
Found at i:32088 original size:23 final size:22
Alignment explanation
Indices: 32033--32090 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
32023 CCATTTTAAT
32033 AATATAAA-TTATAATTATATA
1 AATATAAATTTATAATTATATA
* * *
32054 ATTACATAATTTATATTTAATATA
1 AATATA-AATTTATAATT-ATATA
32078 AATATAAATTTAT
1 AATATAAATTTAT
32091 TTTCTAACGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 14 0.48
24 9 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATAAATTTATAATTATATA
Found at i:33289 original size:23 final size:20
Alignment explanation
Indices: 33261--33315 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
33251 ATAACATTTC
33261 TTATAAATAATATAATTTTTT
1 TTATAAATAA-ATAATTTTTT
* *
33282 TATCATAACTTAATAATTTTTT
1 T-T-ATAAATAAATAATTTTTT
33304 TTATAAATAAAT
1 TTATAAATAAAT
33316 TATGATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 12 0.43
23 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAAATAAATAATTTTTT
Found at i:33313 original size:24 final size:20
Alignment explanation
Indices: 33261--33313 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
33251 ATAACATTTC
33261 TTATAAATAATATAATTTTT
1 TTATAAATAATATAATTTTT
*
33281 TTATCATAACTTAATA-ATTTTTT
1 TTAT-A-AA--TAATATAATTTTT
33304 TTATAAATAA
1 TTATAAATAA
33314 ATTATGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
19 3 0.11
20 4 0.14
21 3 0.11
22 3 0.11
23 10 0.36
24 5 0.18
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAAATAATATAATTTTT
Found at i:33477 original size:16 final size:16
Alignment explanation
Indices: 33446--33478 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33436 TATTTTTGTA
33446 ATATGTAAATTATTTT
1 ATATGTAAATTATTTT
33462 ATATGATAAATT-TTTT
1 ATATG-TAAATTATTTT
33478 A
1 A
33479 GTCCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
ATATGTAAATTATTTT
Found at i:37199 original size:29 final size:29
Alignment explanation
Indices: 37168--37223 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
37158 TTTCTCGGAT
*
37168 TTTTTTTATCAAA-CA-AATTAATTTAATG
1 TTTTTTTAT-AAAGCATAAATAATTTAATG
37196 TTTTTTTATAAAGCATAAATAATTTAAT
1 TTTTTTTATAAAGCATAAATAATTTAAT
37224 TGTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 11 0.44
29 11 0.44
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (29 bp):
TTTTTTTATAAAGCATAAATAATTTAATG
Found at i:38198 original size:47 final size:47
Alignment explanation
Indices: 38144--38237 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
38134 ACCAAACCCA
38144 CTTAAATTTATCTTTCAATTTTACAGATGGAGTCCCTCAATAATTAT
1 CTTAAATTTATCTTTCAATTTTACAGATGGAGTCCCTCAATAATTAT
38191 CTTAAATTTATCTTTCAATTTTACAGATGGAGTCCCTCAATAATTAT
1 CTTAAATTTATCTTTCAATTTTACAGATGGAGTCCCTCAATAATTAT
38238 TAAATTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (47 bp):
CTTAAATTTATCTTTCAATTTTACAGATGGAGTCCCTCAATAATTAT
Found at i:39084 original size:19 final size:21
Alignment explanation
Indices: 39060--39108 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
39050 ATTCGAGCTG
39060 AATTAAATTAAAT-AAA-TAT
1 AATTAAATTAAATAAAATTAT
* *
39079 AATTAAAATAATTAAAATTAT
1 AATTAAATTAAATAAAATTAT
*
39100 GATTAAATT
1 AATTAAATT
39109 TTAAGAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 11 0.46
20 3 0.12
21 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTAAATTAAATAAAATTAT
Found at i:43309 original size:15 final size:14
Alignment explanation
Indices: 43291--43320 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
43281 AAATAAAAAA
43291 TTAAAAAATATTAAT
1 TTAAAAAA-ATTAAT
43306 TTAAAAAAATTAAT
1 TTAAAAAAATTAAT
43320 T
1 T
43321 GATTGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAAAATTAAT
Found at i:44424 original size:16 final size:16
Alignment explanation
Indices: 44403--44445 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
44393 ATAAAATGGG
*
44403 CTCACTCGTTCGTCTC
1 CTCACTCATTCGTCTC
*
44419 CTCACTCATTCTTCTC
1 CTCACTCATTCGTCTC
44435 CTCACTCATTC
1 CTCACTCATTC
44446 CCGTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.44, G:0.05, T:0.40
Consensus pattern (16 bp):
CTCACTCATTCGTCTC
Found at i:44540 original size:27 final size:27
Alignment explanation
Indices: 44520--44622 Score: 188
Period size: 27 Copynumber: 3.8 Consensus size: 27
44510 GGACGTGGTG
44520 GAGGTCGGGGTGATGGTGGACGAGGCA
1 GAGGTCGGGGTGATGGTGGACGAGGCA
44547 GAGGTCGGGGTGATGGTGGACGAGGCA
1 GAGGTCGGGGTGATGGTGGACGAGGCA
44574 GAGGTCGGGGTGATGGTGGACGAGGCA
1 GAGGTCGGGGTGATGGTGGACGAGGCA
* *
44601 GAGGCCGGGGTGGTGGTGGACG
1 GAGGTCGGGGTGATGGTGGACG
44623 TGGCCGGGGG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.17, C:0.12, G:0.57, T:0.15
Consensus pattern (27 bp):
GAGGTCGGGGTGATGGTGGACGAGGCA
Found at i:70376 original size:23 final size:23
Alignment explanation
Indices: 70350--70398 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
70340 TTGGAGGATT
70350 ATTCGTTGAATTTCTCGATTTCA
1 ATTCGTTGAATTTCTCGATTTCA
*
70373 ATTCGTTGAATTTGTCGATTTCA
1 ATTCGTTGAATTTCTCGATTTCA
70396 ATT
1 ATT
70399 ATTATCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (23 bp):
ATTCGTTGAATTTCTCGATTTCA
Done.