Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001848.1 Kokia drynarioides strain JFW-HI SEQ_113602, 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: 39315
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:2118 original size:4 final size:4
Alignment explanation
Indices: 2111--2148 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
2101 TTTTATTTAT
*
2111 TAAA TAAA TAAA TAAA TAAA TAATA TAAT TAAA -AAA TA
1 TAAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TA
2149 TACAAACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:2143 original size:13 final size:13
Alignment explanation
Indices: 2111--2150 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2101 TTTTATTTAT
2111 TAAATAAATAA-A
1 TAAATAAATAATA
2123 TAAATAAATAATA
1 TAAATAAATAATA
* *
2136 TAATTAAAAAATA
1 TAAATAAATAATA
2149 TA
1 TA
2151 CAAACCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:5239 original size:31 final size:28
Alignment explanation
Indices: 5167--5286 Score: 109
Period size: 28 Copynumber: 4.2 Consensus size: 28
5157 ATAAAAAAAA
* *
5167 TAAAAGAAACAAAACAAAAGGG-TAATTT
1 TAAAA-AAATAAAATAAAAGGGTTAATTT
5195 TAAAAAAATAAAATAAAAGGGTTAAATTT
1 TAAAAAAATAAAATAAAAGGGTT-AATTT
*
5224 TAACAAAAATAAAAATAAAAGGATTTAA-TT
1 TAA-AAAAAT-AAAATAAAAGG-GTTAATTT
* * * * *
5254 TAAAAAAACAGAATAAATGGGTAAAATT
1 TAAAAAAATAAAATAAAAGGGTTAATTT
5282 TAAAA
1 TAAAA
5287 GAGAGAATCG
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
27 17 0.22
28 22 0.28
29 13 0.17
30 11 0.14
31 13 0.17
32 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.23
Consensus pattern (28 bp):
TAAAAAAATAAAATAAAAGGGTTAATTT
Found at i:6818 original size:29 final size:29
Alignment explanation
Indices: 6715--6818 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 29
6705 ATACAATTCT
* **
6715 AAATACAGATATAATACGTATACAGTTAC
1 AAATGCAGATATAATACAAATACAGTTAC
* * * *
6744 ACATGTAGATATAATATAGATACAGTTAC
1 AAATGCAGATATAATACAAATACAGTTAC
* * * * **
6773 AGATGCAAACATGATACAAATATTGTTAC
1 AAATGCAGATATAATACAAATACAGTTAC
6802 AAATGCAGATATAATAC
1 AAATGCAGATATAATAC
6819 CCCATTTGCT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (29 bp):
AAATGCAGATATAATACAAATACAGTTAC
Found at i:10829 original size:15 final size:16
Alignment explanation
Indices: 10809--10847 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
10799 TTCGTCACTG
10809 AACTTTTCAACA-TTT
1 AACTTTTCAACACTTT
*
10824 AACTTTTCAATACTTT
1 AACTTTTCAACACTTT
10840 AA-TTTTCA
1 AACTTTTCA
10848 GTTTAGCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (16 bp):
AACTTTTCAACACTTT
Found at i:13312 original size:22 final size:21
Alignment explanation
Indices: 13264--13312 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
13254 CTTTACTTTG
13264 TAATTA-TTATTTTTTCAATA
1 TAATTATTTATTTTTTCAATA
*
13284 TAA--ATTTATTTTTTCTATAA
1 TAATTATTTATTTTTTCAAT-A
13304 TAATTATTT
1 TAATTATTT
13313 GTTTGCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 12 0.50
20 7 0.29
22 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATTATTTATTTTTTCAATA
Found at i:14283 original size:60 final size:59
Alignment explanation
Indices: 14208--14350 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 59
14198 GTTTTTTTTC
*
14208 TCGAGTCTTGAAAAAGGTGGCAT-CGATCATAC-ATAGGCCAAAATACTAGAAAAAAAAATT
1 TCGAGTCTTGAAAAAGGT-G-ATCCGATCAT-CTATAGGCCAAAACACTAGAAAAAAAAATT
14268 TCGAGT-TTCGAAAAAGGTGATGCCGATCATCTATAGGCCAAAACACTAGAAAAAAAAAATTCT
1 TCGAGTCTT-GAAAAAGGTGAT-CCGATCATCTATAGGCCAAAACACTAG-AAAAAAAAA-T-T
*
14331 TCGA-TCCTGAAAAAGGTGAT
1 TCGAGTCTTGAAAAAGGTGAT
14351 GTCAACCATC
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 38 0.52
61 9 0.12
62 14 0.19
63 6 0.08
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (59 bp):
TCGAGTCTTGAAAAAGGTGATCCGATCATCTATAGGCCAAAACACTAGAAAAAAAAATT
Found at i:14361 original size:62 final size:60
Alignment explanation
Indices: 14240--14362 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 60
14230 TCGATCATAC
* * * *
14240 ATAGGCCAAAATACTAGAAAAAAAAATTTCGAGTTTCGAAAAAGGTGATGCCGATCATCT
1 ATAGGCCAAAACACTAGAAAAAAAAATTTCGAGTCTCGAAAAAGGTGATGCCAACCATCT
*
14300 ATAGGCCAAAACACTAGAAAAAAAAAATTCTTCGA-TC-CTGAAAAAGGTGATGTCAACCATCT
1 ATAGGCCAAAACACTAG-AAAAAAAAA-T-TTCGAGTCTC-GAAAAAGGTGATGCCAACCATCT
14362 A
1 A
14363 ATGACCAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
60 16 0.30
61 10 0.19
62 23 0.43
63 5 0.09
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (60 bp):
ATAGGCCAAAACACTAGAAAAAAAAATTTCGAGTCTCGAAAAAGGTGATGCCAACCATCT
Found at i:15613 original size:22 final size:22
Alignment explanation
Indices: 15583--15624 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15573 TATATTTAAG
15583 TCAACTGAAACAATTTTAAAAA
1 TCAACTGAAACAATTTTAAAAA
* *
15605 TCAAGTGAAACAGTTTTAAA
1 TCAACTGAAACAATTTTAAA
15625 TCGAGCTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (22 bp):
TCAACTGAAACAATTTTAAAAA
Found at i:35394 original size:16 final size:16
Alignment explanation
Indices: 35375--35418 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
35365 ATATATCAAA
35375 TACACTTAAAAACATT
1 TACACTTAAAAACATT
*
35391 TACAC--AAAAA-A-A
1 TACACTTAAAAACATT
35403 TACACTTAAAAACATT
1 TACACTTAAAAACATT
35419 AAAACAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 8
0.69 0.06 0.25
Matches are distributed among these distances:
12 5 0.23
13 1 0.05
14 10 0.45
15 1 0.05
16 5 0.23
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACTTAAAAACATT
Found at i:35425 original size:28 final size:28
Alignment explanation
Indices: 35372--35426 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
35362 ATAATATATC
* *
35372 AAATACACTTAAAAACATTTACACAAAA
1 AAATACACTTAAAAACATTAAAACAAAA
35400 AAATACACTTAAAAACATTAAAACAAA
1 AAATACACTTAAAAACATTAAAACAAA
35427 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (28 bp):
AAATACACTTAAAAACATTAAAACAAAA
Found at i:35610 original size:11 final size:10
Alignment explanation
Indices: 35593--35644 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
35583 AATAACACCC
35593 AAACAACAAA
1 AAACAACAAA
35603 AAAGCAACAACA
1 AAA-CAACAA-A
35615 AAACAAC-AA
1 AAACAACAAA
* **
35624 AAATAACACC
1 AAACAACAAA
35634 AAACAACAAA
1 AAACAACAAA
35644 A
1 A
35645 CACTAGAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 7 0.21
10 12 0.36
11 10 0.30
12 4 0.12
ACGTcount: A:0.73, C:0.23, G:0.02, T:0.02
Consensus pattern (10 bp):
AAACAACAAA
Found at i:35611 original size:22 final size:20
Alignment explanation
Indices: 35579--35644 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
35569 AAAACATATA
*
35579 AAAAAATAACACCCAAACAAC
1 AAAAAACAACA-CCAAACAAC
*
35600 AAAAAAGCAACAACAAAACAAC
1 AAAAAA-CAAC-ACCAAACAAC
*
35622 -AAAAATAACACCAAACAAC
1 AAAAAACAACACCAAACAAC
35641 AAAA
1 AAAA
35645 CACTAGAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.24
20 6 0.16
21 11 0.29
22 11 0.29
23 1 0.03
ACGTcount: A:0.71, C:0.24, G:0.02, T:0.03
Consensus pattern (20 bp):
AAAAAACAACACCAAACAAC
Found at i:35637 original size:19 final size:19
Alignment explanation
Indices: 35580--35644 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
35570 AAACATATAA
35580 AAAAATAACACCCAAACAAC
1 AAAAATAACA-CCAAACAAC
* *
35600 AAAAAAGCAACAACAAAACAAC
1 -AAAAA-TAAC-ACCAAACAAC
35622 AAAAATAACACCAAACAAC
1 AAAAATAACACCAAACAAC
35641 AAAA
1 AAAA
35645 CACTAGAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 13 0.34
20 3 0.08
21 10 0.26
22 11 0.29
23 1 0.03
ACGTcount: A:0.71, C:0.25, G:0.02, T:0.03
Consensus pattern (19 bp):
AAAAATAACACCAAACAAC
Found at i:36043 original size:25 final size:25
Alignment explanation
Indices: 36009--36057 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
35999 TTCATAAATA
36009 ATCATTTTCTTAAT-TAAAAGTCACG
1 ATCATTTTCTTAATCT-AAAGTCACG
36034 ATCATTTTCTTAATCTAAAGTCAC
1 ATCATTTTCTTAATCTAAAGTCAC
36058 CAAAATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (25 bp):
ATCATTTTCTTAATCTAAAGTCACG
Found at i:36541 original size:16 final size:16
Alignment explanation
Indices: 36515--36553 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
36505 ATGAATTCAA
36515 ATAATTTTAAAT-TTT
1 ATAATTTTAAATATTT
36530 ATAATTTATAAATATTT
1 ATAATTT-TAAATATTT
36547 -TAATTTT
1 ATAATTTT
36554 GATGTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATAATTTTAAATATTT
Done.