Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013124.1 Kokia drynarioides strain JFW-HI SEQ_128143, 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: 41904
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:228 original size:6 final size:6
Alignment explanation
Indices: 217--246 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
207 TAAAATAAAT
217 AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
247 TTGGGTTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:2951 original size:15 final size:16
Alignment explanation
Indices: 2924--2953 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2914 ACAATAAAAA
2924 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
2940 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
2954 AATAAGAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:3781 original size:19 final size:19
Alignment explanation
Indices: 3757--3799 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3747 AAACATAAAT
3757 TAAATAGAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
3776 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
3795 TAAAT
1 TAAAT
3800 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3835 original size:29 final size:31
Alignment explanation
Indices: 3770--3838 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3760 ATAGAAATTT
* *
3770 AAATAATAAATAATATCTTAAATATTAAATCC
1 AAATAA-AAATAATATCTTAAATATAAAATCA
* *
3802 TAATAAAAATAATATTTTAAA-ATAAAAT-A
1 AAATAAAAATAATATCTTAAATATAAAATCA
3831 AAATAAAA
1 AAATAAAA
3839 TCAAGTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.22
30 6 0.19
31 14 0.44
32 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (31 bp):
AAATAAAAATAATATCTTAAATATAAAATCA
Found at i:12243 original size:318 final size:316
Alignment explanation
Indices: 11661--12298 Score: 1105
Period size: 318 Copynumber: 2.0 Consensus size: 316
11651 TTTTTGGTCC
11661 AATTTAGTACATATATTTGACAAAAGTTATATATTTTGGTACCCAAAAGTAAATGTGTTAACATT
1 AATTTAGTACATATATTTGACAAAAGTTATATATTTTGGTACCCAAAAGTAAATGTGTTAACATT
*
11726 TTTAGTGTTTAATTCAAGTTTTAGGGTTGATTTGATGAAGTTAATTGCTAATATTATTATGTTTG
66 TTTAGTGTTTAATTCAAGTTCTAGGGTTGATTTGATGAAGTTAATTGCTAATATTATTATGTTTG
*
11791 ATTTTTTATGATTTTTTAATAGAACAAATTTAATTTAATTGTGAATTTGTTTAATTTTGTAATTA
131 ATTTTTCATGATTTTTTAATAGAACAAATTTAATTTAATTGTGAATTTGTTTAATTTTGTAATTA
*
11856 ATTTGTCAAATATAGTCCTATGGATGTGGTTTAATTTGGGTTTTAGGGTTGATTTGATGAAAATT
196 ATTTGTCAAATATAGTCCTATGGATGTGATTTAATTTGGGTTTTAGGGTTGATTTGATGAAAATT
*
11921 AATTGCTAATATTATTAGCTAATTATGAATTCACATCAAATCAACTGTAAAACTTG
261 AATTGCTAATATTATTAGCTAATTATGAATTCACATCAAATCAACTCTAAAACTTG
* * *
11977 AATTTAGTACCTCTATTTGACAAAAGTTATATGTTTTGGTACCCAAAAGTAAATGTGTTAACATT
1 AATTTAGTACATATATTTGACAAAAGTTATATATTTTGGTACCCAAAAGTAAATGTGTTAACATT
**
12042 TTTAGTGTTTAATTTGAGTTCTAGGGTTGATTTGATGAAAGTTAATTGCTAATATTATTATGTTT
66 TTTAGTGTTTAATTCAAGTTCTAGGGTTGATTTGATG-AAGTTAATTGCTAATATTATTATGTTT
* *
12107 GAATTTTTCATTATTTTTTAATAGAATAAATTTAATTTAATTGTGAATTTGTTTAATTTTGTAAT
130 G-ATTTTTCATGATTTTTTAATAGAACAAATTTAATTTAATTGTGAATTTGTTTAATTTTGTAAT
* *
12172 TAATTTGTCAAATATAGTCCTATGGGTGTGATTTAATTTGGGTTTTAGGGTTGATTTGATGAAAG
194 TAATTTGTCAAATATAGTCCTATGGATGTGATTTAATTTGGGTTTTAGGGTTGATTTGATGAAAA
* * * *
12237 TTAATTGTTAATATTGTTAGCTAATTGTGAATTCTCATCAAATCAACTCTAAAACTTG
259 TTAATTGCTAATATTATTAGCTAATTATGAATTCACATCAAATCAACTCTAAAACTTG
12295 AATT
1 AATT
12299 AAACCCTACA
Statistics
Matches: 303, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
316 96 0.32
317 28 0.09
318 179 0.59
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (316 bp):
AATTTAGTACATATATTTGACAAAAGTTATATATTTTGGTACCCAAAAGTAAATGTGTTAACATT
TTTAGTGTTTAATTCAAGTTCTAGGGTTGATTTGATGAAGTTAATTGCTAATATTATTATGTTTG
ATTTTTCATGATTTTTTAATAGAACAAATTTAATTTAATTGTGAATTTGTTTAATTTTGTAATTA
ATTTGTCAAATATAGTCCTATGGATGTGATTTAATTTGGGTTTTAGGGTTGATTTGATGAAAATT
AATTGCTAATATTATTAGCTAATTATGAATTCACATCAAATCAACTCTAAAACTTG
Found at i:16596 original size:30 final size:30
Alignment explanation
Indices: 16560--16621 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
16550 TAACAGGAAC
16560 AAGTCGCGTACTTACAGAGGTGAGACCAAT
1 AAGTCGCGTACTTACAGAGGTGAGACCAAT
16590 AAGTCGCGTACTTACAGAGGTGAGACCAAT
1 AAGTCGCGTACTTACAGAGGTGAGACCAAT
16620 AA
1 AA
16622 CGTGTCGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (30 bp):
AAGTCGCGTACTTACAGAGGTGAGACCAAT
Found at i:16918 original size:7 final size:7
Alignment explanation
Indices: 16906--16943 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
16896 TAGTAGTATC
16906 GTTTGCT
1 GTTTGCT
16913 GTTTGCT
1 GTTTGCT
16920 GTTTGCT
1 GTTTGCT
16927 GTTTGCT
1 GTTTGCT
16934 GTTTGCT
1 GTTTGCT
16941 GTT
1 GTT
16944 ATATGATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.13, G:0.29, T:0.58
Consensus pattern (7 bp):
GTTTGCT
Found at i:23633 original size:3 final size:3
Alignment explanation
Indices: 23627--23659 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
23617 GGGCTGGGAA
23627 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23660 GCTTTTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25290 original size:22 final size:22
Alignment explanation
Indices: 25265--25313 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
25255 TGTTTTCTCT
25265 TTATTTTGCTACAATTTCATTA
1 TTATTTTGCTACAATTTCATTA
* ** *
25287 TTATGTTGCTATTATTTTATTA
1 TTATTTTGCTACAATTTCATTA
25309 TTATT
1 TTATT
25314 ATTTGGATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACAATTTCATTA
Found at i:27308 original size:19 final size:20
Alignment explanation
Indices: 27286--27340 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
27276 TTTATTTACT
27286 AATA-TTATTATTATCAAAA
1 AATATTTATTATTATCAAAA
*
27305 AATATTTATTATTAT-TAAA
1 AATATTTATTATTATCAAAA
27324 AATATTTATTATTATCA
1 AATATTTATTATTATCA
27341 CCATTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTATTATTATCAAAA
Found at i:29538 original size:13 final size:12
Alignment explanation
Indices: 29509--29549 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
29499 AAAGAACCTA
*
29509 TAAAAA-TAAAA
1 TAAAAATTAAAT
29520 TAAAAATTAAAT
1 TAAAAATTAAAT
29532 GTAAAAATTAAAT
1 -TAAAAATTAAAT
29545 TAAAA
1 TAAAA
29550 CAAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
13 12 0.44
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
TAAAAATTAAAT
Found at i:29587 original size:20 final size:17
Alignment explanation
Indices: 29541--29581 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29531 TGTAAAAATT
*
29541 AAATTAAAACAAAAAAA
1 AAATGAAAACAAAAAAA
*
29558 ATATGAAAACAAAAATAA
1 AAATGAAAACAAAAA-AA
29576 AAATGA
1 AAATGA
29582 CTAAACTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (17 bp):
AAATGAAAACAAAAAAA
Found at i:30651 original size:25 final size:23
Alignment explanation
Indices: 30623--30668 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
30613 GTTGGATCCA
30623 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
30648 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
30669 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:37689 original size:28 final size:29
Alignment explanation
Indices: 37657--37713 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
37647 AAACCTTTTT
* *
37657 ACTTTCCTCCAAAATTTTTACTC-CCCCC
1 ACTTTCCCCCAAAACTTTTACTCACCCCC
*
37685 ACTTTCCCCCAAACCTTTTACTCACCCCC
1 ACTTTCCCCCAAAACTTTTACTCACCCCC
37714 CATCTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.21, C:0.47, G:0.00, T:0.32
Consensus pattern (29 bp):
ACTTTCCCCCAAAACTTTTACTCACCCCC
Done.