Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009639.1 Kokia drynarioides strain JFW-HI SEQ_124356, 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: 45598
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33 TCTTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:726 original size:21 final size:21
Alignment explanation
Indices: 701--767 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
691 GAGAAAAGTA
*
701 AAATGCAATGACATTTATATG
1 AAATGCAATGACATCTATATG
* *
722 AAATGC-ATG-CAACTAAACT-
1 AAATGCAATGACATCTATA-TG
741 -AATGCAATGACATCTATATG
1 AAATGCAATGACATCTATATG
761 AAATGCA
1 AAATGCA
768 TGCAACTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
18 5 0.14
19 9 0.25
20 10 0.28
21 12 0.33
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (21 bp):
AAATGCAATGACATCTATATG
Found at i:747 original size:39 final size:39
Alignment explanation
Indices: 702--781 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
692 AGAAAAGTAA
*
702 AATGCAATGACATTTATATGAAATGCATGCAACTAAACT
1 AATGCAATGACATCTATATGAAATGCATGCAACTAAACT
741 AATGCAATGACATCTATATGAAATGCATGCAACTAAACT
1 AATGCAATGACATCTATATGAAATGCATGCAACTAAACT
780 AA
1 AA
782 GTAATGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (39 bp):
AATGCAATGACATCTATATGAAATGCATGCAACTAAACT
Found at i:6300 original size:47 final size:47
Alignment explanation
Indices: 6199--6319 Score: 152
Period size: 47 Copynumber: 2.6 Consensus size: 47
6189 ATCACATTAA
*
6199 TGTAGATAAACTACCACATAATTAAATTATGGACAAGCCACCAAAAT
1 TGTAGATAAACTACCACATAATCAAATTATGGACAAGCCACCAAAAT
* * * * * *
6246 CGCAGATATACTACCACATAATCAAATTGTGGACAAGCCACCACATT
1 TGTAGATAAACTACCACATAATCAAATTATGGACAAGCCACCAAAAT
* * *
6293 TGTAGATAAACTTCTACATTATCAAAT
1 TGTAGATAAACTACCACATAATCAAAT
6320 CGTGAACATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (47 bp):
TGTAGATAAACTACCACATAATCAAATTATGGACAAGCCACCAAAAT
Found at i:13225 original size:17 final size:17
Alignment explanation
Indices: 13203--13249 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
13193 TCGTTAGCAT
*
13203 TGTGAAAACTATAGATC
1 TGTGAAAACTATAGATA
*
13220 TGTGAAAGCTATAGATA
1 TGTGAAAACTATAGATA
*
13237 AGTG-AAACTATAG
1 TGTGAAAACTATAG
13250 GAAACTTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (17 bp):
TGTGAAAACTATAGATA
Found at i:16971 original size:24 final size:21
Alignment explanation
Indices: 16925--16964 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16915 GGCAAGTTCT
16925 TTTCCTTCTTTCTCTTCTTCC
1 TTTCCTTCTTTCTCTTCTTCC
*
16946 TTTCCTTCTTTTTCTTCTT
1 TTTCCTTCTTTCTCTTCTT
16965 GATCCTTCTC
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:0.33, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCCTTCTTTCTCTTCTTCC
Found at i:28423 original size:21 final size:21
Alignment explanation
Indices: 28399--28449 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28389 TGGGAAGGTT
28399 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * * *
28420 CTACCGATACAATTATTATTT
1 CTACCGATACAAGTATGACTA
28441 CTACCGATA
1 CTACCGATA
28450 TGATAAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:29548 original size:16 final size:16
Alignment explanation
Indices: 29524--29555 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29514 TCCTTACAAA
*
29524 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
29540 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
29556 AAAAATTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:39647 original size:21 final size:23
Alignment explanation
Indices: 39618--39668 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
39608 TTTTGTCCCA
39618 CTCCATCTCAC-C-TCCTTATTT
1 CTCCATCTCACGCTTCCTTATTT
* *
39639 CTCCTTCTCTCGTCTTCCTTATTT
1 CTCCATCTCACG-CTTCCTTATTT
39663 CTCCAT
1 CTCCAT
39669 ATTTAGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
23 1 0.04
24 14 0.58
ACGTcount: A:0.10, C:0.41, G:0.02, T:0.47
Consensus pattern (23 bp):
CTCCATCTCACGCTTCCTTATTT
Found at i:43976 original size:26 final size:26
Alignment explanation
Indices: 43947--44030 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
43937 ATCTTATACA
* *
43947 AGCCCAGACAGAGTTTAGCCCTTACG
1 AGCCCAGACAGAATTTAGCTCTTACG
* * *
43973 AGCCCAAACAGAATTTAGTTCTTATG
1 AGCCCAGACAGAATTTAGCTCTTACG
* *
43999 TGCCCAGATAGAATTTAGCTCTTACG
1 AGCCCAGACAGAATTTAGCTCTTACG
44025 AGCCCA
1 AGCCCA
44031 AACAAAATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (26 bp):
AGCCCAGACAGAATTTAGCTCTTACG
Found at i:44048 original size:52 final size:52
Alignment explanation
Indices: 43948--44048 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
43938 TCTTATACAA
* * * *
43948 GCCCAGACAGAGTTTAGCCCTTACGAGCCCAAACAGAATTTAGTTCTTATGT
1 GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATAGCTCTTATGT
* *
44000 GCCCAGATAGAATTTAGCTCTTACGAGCCCAAACAAAATA-ATGCTCTTA
1 GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATA-GCTCTTA
44049 CAAGTCTGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 1 0.02
52 41 0.98
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (52 bp):
GCCCAGACAGAATTTAGCCCTTACGAGCCCAAACAAAATATAGCTCTTATGT
Found at i:44070 original size:25 final size:25
Alignment explanation
Indices: 44036--44097 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
44026 GCCCAAACAA
* *
44036 AATAATGCTCTTACAAGTCT-GACAG
1 AATAACGCTCTTACAA-ACTAGACAG
44061 AATAACGCTC-TACAAACTAGACAG
1 AATAACGCTCTTACAAACTAGACAG
44085 AATAACGCTCTTA
1 AATAACGCTCTTA
44098 TGTGCCAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 20 0.61
25 11 0.33
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (25 bp):
AATAACGCTCTTACAAACTAGACAG
Found at i:44573 original size:154 final size:154
Alignment explanation
Indices: 44320--44613 Score: 518
Period size: 154 Copynumber: 1.9 Consensus size: 154
44310 CACGATCCTA
* * *
44320 ATCTATCACAACAAAGCATTCAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTGCATTT
1 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
* *
44385 AAGTTATTTTGGGGAAATTTACAAAGTTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
66 AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
44450 -AACCTTAAATTTAGCATGATCTTG
131 GAA-CTTAAATTTAGCATGATCTTG
44474 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
1 ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
*
44539 AAGTCATTTTGGGGAAATTTACAAAATTATCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
66 AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
44604 GAACTTAAAT
131 GAACTTAAAT
44614 ATGCAAAATA
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
154 131 0.98
155 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (154 bp):
ATCTATCACAACAAAGCATACAAATTTCTTATTAAAGTATGAAATTCAAATCATTTATTCCATTA
AAGTCATTTTGGGGAAATTTACAAAATTACCCCTAACATTTCATTTTTATTCAATTTAGTCCTTA
GAACTTAAATTTAGCATGATCTTG
Done.