Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010575.1 Kokia drynarioides strain JFW-HI SEQ_125500, 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: 55394
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3907 original size:3 final size:3
Alignment explanation
Indices: 3899--3932 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3889 CTGTCTCATA
3899 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3933 CATTTGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:8514 original size:19 final size:19
Alignment explanation
Indices: 8461--8519 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
8451 AGTTTTCCAT
* *
8461 ATTTTTTTGAATTTTCTAA
1 ATTTTTTTTAATTTTTTAA
* **
8480 ATTTTTTTATGA-TTTTTGG
1 ATTTTTTT-TAATTTTTTAA
8499 ATTTTTTTTAATTTTTTAA
1 ATTTTTTTTAATTTTTTAA
8518 AT
1 AT
8520 AGTTCATAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
18 2 0.07
19 27 0.90
20 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.68
Consensus pattern (19 bp):
ATTTTTTTTAATTTTTTAA
Found at i:9010 original size:19 final size:20
Alignment explanation
Indices: 8986--9038 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
8976 GGTATAATTA
8986 TAAAATATATTAT-ATTTTT
1 TAAAATATATTATAATTTTT
*
9005 TAAAATTTAATT-TAATTTTT
1 TAAAATAT-ATTATAATTTTT
*
9025 GAAAATAATATTAT
1 TAAAAT-ATATTAT
9039 TGAAAGGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.30
20 17 0.63
21 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAAATATATTATAATTTTT
Found at i:21989 original size:21 final size:19
Alignment explanation
Indices: 21953--21991 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
21943 ATTATGAATT
*
21953 TTTTATAAAAATTTATTTA
1 TTTTACAAAAATTTATTTA
21972 TTTTACAATAAATATTATTT
1 TTTTACAA-AAAT-TTATTT
21992 TGAGAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTACAAAAATTTATTTA
Found at i:22057 original size:23 final size:22
Alignment explanation
Indices: 22024--22066 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22014 CAATTTGCTA
* *
22024 AATATAGAAAAATACATACATGT
1 AATATA-AAAAAAAAATACATGT
22047 AATATAAAAAAAAAATACAT
1 AATATAAAAAAAAAATACAT
22067 TAAACCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (22 bp):
AATATAAAAAAAAAATACATGT
Found at i:24693 original size:22 final size:22
Alignment explanation
Indices: 24665--24709 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24655 TGTATTATTT
24665 TAGTAAATAACACATTTTAGTA
1 TAGTAAATAACACATTTTAGTA
*
24687 TAGTAAATAACACATTTTGGTA
1 TAGTAAATAACACATTTTAGTA
24709 T
1 T
24710 TTAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (22 bp):
TAGTAAATAACACATTTTAGTA
Found at i:25944 original size:43 final size:43
Alignment explanation
Indices: 25862--25946 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
25852 ATTAACATGT
* *
25862 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
25905 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
25947 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:26586 original size:45 final size:45
Alignment explanation
Indices: 26513--26649 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 45
26503 GCATAGCTCA
* * *
26513 TCAAGCCAAGGATATCAGCCTCTGTTTGACGAGCCACCATAATAC
1 TCAAGCCAAGGATATCAGTCTCAGTTTGACGAGCCACCACAATAC
* * * *
26558 TCAAGCTAAGGATATCAGTCTCAATTTGACGAGCCATCGCAATAC
1 TCAAGCCAAGGATATCAGTCTCAGTTTGACGAGCCACCACAATAC
** * * * *
26603 TCAAGAGAAAGATATCATGT-TGAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATCA-GTCTCAGTTTGACGAGCCACCACAATAC
26648 TC
1 TC
26650 TATTCCTCCC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 75 0.97
46 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGTCTCAGTTTGACGAGCCACCACAATAC
Found at i:29959 original size:20 final size:19
Alignment explanation
Indices: 29932--29977 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
29922 AATAAATCTG
*
29932 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
*
29951 TTAATAAATAAAATACAATT
1 TTAA-AAATAAAATAAAATT
29971 TTAAAAA
1 TTAAAAA
29978 GATATCATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:30037 original size:4 final size:4
Alignment explanation
Indices: 30018--30128 Score: 71
Period size: 4 Copynumber: 27.0 Consensus size: 4
30008 ACACATTATA
* * * * * *
30018 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TATC TTTCC TCTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTT-C TTTC
* * * * * *
30067 CTTC TTCC TATC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC TTTTC TTTC
1 TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC
30117 TTTC TTTC TTTC
1 TTTC TTTC TTTC
30129 CTGTTTATTT
Statistics
Matches: 79, Mismatches: 23, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
3 3 0.04
4 63 0.80
5 13 0.16
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (4 bp):
TTTC
Found at i:30061 original size:21 final size:21
Alignment explanation
Indices: 30024--30103 Score: 135
Period size: 21 Copynumber: 3.9 Consensus size: 21
30014 TATATTTCTT
*
30024 TCCTTCTT-CTTTCTTTCCTC
1 TCCTTCTTCCTATCTTTCCTC
30044 TCCTTCTTCCTATCTTTCCTC
1 TCCTTCTTCCTATCTTTCCTC
30065 TCCTTCTTCCTATCTTTCCTC
1 TCCTTCTTCCTATCTTTCCTC
*
30086 TCCTTCTTCCTTTCTTTC
1 TCCTTCTTCCTATCTTTC
30104 TTTCTTTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
20 8 0.14
21 49 0.86
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (21 bp):
TCCTTCTTCCTATCTTTCCTC
Found at i:30113 original size:21 final size:21
Alignment explanation
Indices: 30089--30128 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30079 TTTCCTCTCC
30089 TTCTTCCTTTCTTTCTTTCTT
1 TTCTTCCTTTCTTTCTTTCTT
*
30110 TTCTTTCTTTCTTTCTTTC
1 TTCTTCCTTTCTTTCTTTC
30129 CTGTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTCCTTTCTTTCTTTCTT
Found at i:34002 original size:47 final size:48
Alignment explanation
Indices: 33937--34033 Score: 187
Period size: 47 Copynumber: 2.0 Consensus size: 48
33927 TTGTGCCATC
33937 TTTGCATCTCTCAACAATGTGCTTCTTGGCTATGGTAAG-TTTTTCTT
1 TTTGCATCTCTCAACAATGTGCTTCTTGGCTATGGTAAGTTTTTTCTT
33984 TTTGCATCTCTCAACAATGTGCTTCTTGGCTATGGTAAGTTTTTTCTT
1 TTTGCATCTCTCAACAATGTGCTTCTTGGCTATGGTAAGTTTTTTCTT
34032 TT
1 TT
34034 CTCTCTTCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 39 0.80
48 10 0.20
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (48 bp):
TTTGCATCTCTCAACAATGTGCTTCTTGGCTATGGTAAGTTTTTTCTT
Found at i:34075 original size:3 final size:3
Alignment explanation
Indices: 34067--34091 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34057 TTATGACTGC
34067 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
34092 TCTATGTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39937 original size:15 final size:15
Alignment explanation
Indices: 39917--39954 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
39907 AAAAACACGC
*
39917 CTTTTTTTCAT-TTTT
1 CTTTTTTT-ATATATT
39932 CTTTTTTTATATATT
1 CTTTTTTTATATATT
39947 CTTTTTTT
1 CTTTTTTT
39955 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTTATATATT
Found at i:40477 original size:51 final size:51
Alignment explanation
Indices: 40417--40517 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
40407 TTACAGTTGA
*
40417 GCTCTCCTAGATCTAATGGTACAAGTTGAATTACATCAATGGTTGAGATTT
1 GCTCTCCTAGATCTAATGGTACAAGTTGAATTACATCAATGGCTGAGATTT
40468 GCTCTCCTAGATCTAATGGTACAAGTTGAATTACATCAATGGCTGAGATT
1 GCTCTCCTAGATCTAATGGTACAAGTTGAATTACATCAATGGCTGAGATT
40518 AATGTCTATC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (51 bp):
GCTCTCCTAGATCTAATGGTACAAGTTGAATTACATCAATGGCTGAGATTT
Found at i:41375 original size:18 final size:18
Alignment explanation
Indices: 41366--41400 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41356 ATTTTGAATA
41366 TTCTAAAAATTTTAAAAG
1 TTCTAAAAATTTTAAAAG
*
41384 TTCTTAAAATTTTAAAA
1 TTCTAAAAATTTTAAAA
41401 TTAGGACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TTCTAAAAATTTTAAAAG
Found at i:50724 original size:18 final size:19
Alignment explanation
Indices: 50691--50742 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 19
50681 ATTGAATTAC
50691 AAAAAA-TAAAAA--AATA
1 AAAAAATTAAAAATTAATA
*
50707 AAAAAATT-TAAATTAAT-
1 AAAAAATTAAAAATTAATA
*
50724 ACAAAATTAAAAATTAATA
1 AAAAAATTAAAAATTAATA
50743 TATTTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 11 0.39
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAATTAAAAATTAATA
Found at i:50730 original size:33 final size:32
Alignment explanation
Indices: 50693--50758 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
50683 TGAATTACAA
50693 AAAATAAAAAAATAAAAAAATTTAAATTAATAC
1 AAAAT-AAAAAATAAAAAAATTTAAATTAATAC
* * * * *
50726 AAAATTAAAAATTAATATATTTTAATTAATAC
1 AAAATAAAAAATAAAAAAATTTAAATTAATAC
50758 A
1 A
50759 TATAATCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAATAAAAAATAAAAAAATTTAAATTAATAC
Found at i:51941 original size:19 final size:19
Alignment explanation
Indices: 51892--51941 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
51882 TTTTTGTGTA
*
51892 TTTTT-TATTTTTAATTAT
1 TTTTTATATTTTTAAATAT
* *
51910 ATTTTAGATTTTTAAATAT
1 TTTTTATATTTTTAAATAT
51929 TTTTTATATTTTT
1 TTTTTATATTTTT
51942 TTTATCAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTATATTTTTAAATAT
Found at i:55199 original size:29 final size:30
Alignment explanation
Indices: 55134--55210 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
55124 ATACCAAAAC
* *
55134 TATACATGAACTATGGTTTAATGTACAATTG
1 TATACATGAACTTTGATTT-ATGTACAATTG
* *
55165 CATACATGAACTTTGATTT-TGTGCAATTG
1 TATACATGAACTTTGATTTATGTACAATTG
55194 TATACATGAA--TTGATTT
1 TATACATGAACTTTGATTT
55211 GATTCAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.17
29 18 0.44
31 16 0.39
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTACAATTG
Done.