Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010170.1 Kokia drynarioides strain JFW-HI SEQ_124975, 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: 126516
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:6649 original size:27 final size:28
Alignment explanation
Indices: 6618--6675 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
6608 TTTTATATAA
*
6618 AAATAAATTTAAAA-AATATAAT-ACATT
1 AAATAAA-TTAAAATAATAAAATAACATT
* *
6645 AAATATATTAAAATACTAAAATAACATT
1 AAATAAATTAAAATAATAAAATAACATT
6673 AAA
1 AAA
6676 ATAAGTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.23
27 12 0.46
28 8 0.31
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAAATTAAAATAATAAAATAACATT
Found at i:7109 original size:21 final size:22
Alignment explanation
Indices: 7069--7113 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
7059 AATACAATAC
7069 ATTATTTAGAATAATAAAGAAA
1 ATTATTTAGAATAATAAAGAAA
7091 ATTATTTA-AA-AATTAAAGAAA
1 ATTATTTAGAATAA-TAAAGAAA
7112 AT
1 AT
7114 AATTATCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 12 0.55
22 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
ATTATTTAGAATAATAAAGAAA
Found at i:14136 original size:21 final size:21
Alignment explanation
Indices: 14110--14174 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
14100 TAGAGAAAAG
14110 AAAGAAAATTTCTATGCTTAA
1 AAAGAAAATTTCTATGCTTAA
14131 AAAGAAAATTTCTATGCTTAA
1 AAAGAAAATTTCTATGCTTAA
14152 AAAGAAAATTTCTATGCTTAA
1 AAAGAAAATTTCTATGCTTAA
14173 AA
1 AA
14175 TTTATCAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (21 bp):
AAAGAAAATTTCTATGCTTAA
Found at i:23427 original size:13 final size:14
Alignment explanation
Indices: 23409--23441 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23399 CAAATCTATT
23409 TTTTTACTT-AATA
1 TTTTTACTTAAATA
*
23422 TTTTTATTTAAATA
1 TTTTTACTTAAATA
23436 TTTTTA
1 TTTTTA
23442 AAATTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTACTTAAATA
Found at i:26110 original size:17 final size:17
Alignment explanation
Indices: 26069--26109 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
26059 TTCAATGTTA
26069 AAATTTTTATAATATTT
1 AAATTTTTATAATATTT
*
26086 ACATTTTTATAAT-TTT
1 AAATTTTTATAATATTT
26102 AAATTTTT
1 AAATTTTT
26110 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATTTTTATAATATTT
Found at i:27363 original size:31 final size:29
Alignment explanation
Indices: 27325--27394 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
27315 ATATCAAAAC
* *
27325 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TATGCAATTA
* * *
27356 TATACATGCACTTTTATTTTATGCAATTA
1 TATACATGAACTATGATTTTATGCAATTA
27385 TATACATGAA
1 TATACATGAA
27395 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (29 bp):
TATACATGAACTATGATTTTATGCAATTA
Found at i:27399 original size:29 final size:30
Alignment explanation
Indices: 27348--27404 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
27338 TGATTTAATG
* * *
27348 TGCAATTGTATACATGCACTTTT-ATTTTA
1 TGCAATTATATACATGAAATTTTGATTTTA
27377 TGCAATTATATACATGAAATTTTGATTT
1 TGCAATTATATACATGAAATTTTGATTT
27405 GATCAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (30 bp):
TGCAATTATATACATGAAATTTTGATTTTA
Found at i:35139 original size:2 final size:2
Alignment explanation
Indices: 35132--35176 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35122 ATGATTCATA
35132 AT AT AT AT AT 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 AT AT AT AT AT
35174 AT A
1 AT A
35177 AAAGTCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44431 original size:31 final size:30
Alignment explanation
Indices: 44396--44459 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
44386 TACAAAATTA
44396 TCACTGAA-TGATTCAAAAGATTTTATTTAAG
1 TCACTGAACT-ATTCAAAAGATTTT-TTTAAG
* *
44427 TCACTTAACTATTCAAAATATTTTTTTAAG
1 TCACTGAACTATTCAAAAGATTTTTTTAAG
44457 TCA
1 TCA
44460 ATCAAGTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 9 0.30
31 20 0.67
32 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (30 bp):
TCACTGAACTATTCAAAAGATTTTTTTAAG
Found at i:45380 original size:26 final size:27
Alignment explanation
Indices: 45334--45384 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
45324 TTCGAAATTG
*
45334 ATAGAGATTAAATTATTTTAATTTTTT
1 ATAGAGATTAAATTATCTTAATTTTTT
45361 ATAGAGATT-AATT-TGCTTAATTTT
1 ATAGAGATTAAATTAT-CTTAATTTT
45385 CTAAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 12 0.55
27 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (27 bp):
ATAGAGATTAAATTATCTTAATTTTTT
Found at i:49132 original size:4 final size:4
Alignment explanation
Indices: 49125--49154 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
49115 AGCTCTTTCT
49125 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TT
1 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TT
49155 TTTCTCGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (4 bp):
TTCC
Found at i:52442 original size:31 final size:31
Alignment explanation
Indices: 52406--52464 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
52396 AGATTAAGTT
52406 TCAATATGAAAACAATTGTCAAGTTTAATCC
1 TCAATATGAAAACAATTGTCAAGTTTAATCC
* **
52437 TCAATATGAGAATTATTGTCAAGTTTAA
1 TCAATATGAAAACAATTGTCAAGTTTAA
52465 GGATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
TCAATATGAAAACAATTGTCAAGTTTAATCC
Found at i:64937 original size:27 final size:27
Alignment explanation
Indices: 64887--64938 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
64877 AAAAAACTCA
* *
64887 ATGCGTGAAAGATGAAATACCAAAGGC
1 ATGCATGAAAGAGGAAATACCAAAGGC
* *
64914 ATGCATGAAAGAGGAGATATCAAAG
1 ATGCATGAAAGAGGAAATACCAAAG
64939 TCATAAGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.15
Consensus pattern (27 bp):
ATGCATGAAAGAGGAAATACCAAAGGC
Found at i:73491 original size:199 final size:200
Alignment explanation
Indices: 73151--73549 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 200
73141 GCGCACAAAG
*
73151 AATCGATGGTACCTTCAATGTTATCAGCAGATTGATTCGAAACAATATTGTTCTGAACTTGCCGA
1 AATCGATGCTACCTTCAATGTTATCAGCAGATTGATTCGAAACAATATTGTTCTGAACTTGCCGA
* *
73216 TTATCTGGCATCGGTGGATGCGGCACGAAATTTTTGTTAAACCGTATCTTACTTTTGATCGAAAC
66 TTATCTGGCATCGGTGGATGCGGCACGAAATTTTTGTAAAACCGTACCTTACTTTTGATCGAAAC
73281 AATCAAAACCCAAGCAACAAGAGA-TTTAAAAAAAAATCAATTGCAGGGCATAAATCAACGCAAA
131 AATCAAAACCCAAGCAACAAGAGATTTTAAAAAAAAATCAATTGCAGGGCATAAATCAACGCAAA
73345 TTCGT
196 TTCGT
73350 AATCGATGCTACCTTCAATGTTATCAGCAGATTGATTCGAAACAATATTGTTCTGAACTTGCCGA
1 AATCGATGCTACCTTCAATGTTATCAGCAGATTGATTCGAAACAATATTGTTCTGAACTTGCCGA
*
73415 TTATCTGGCATCGGTGGATGCGGCACGAAATTTTTGTAAAACTGTACCTTACTTTTGATCGAAAC
66 TTATCTGGCATCGGTGGATGCGGCACGAAATTTTTGTAAAACCGTACCTTACTTTTGATCGAAAC
*
73480 AATCAAAACCCAAGCAACAAGAGATTTTAAAAAAAAATCAATTGCAGGGCATAAATCAAGGCAAA
131 AATCAAAACCCAAGCAACAAGAGATTTTAAAAAAAAATCAATTGCAGGGCATAAATCAACGCAAA
73545 TTCGT
196 TTCGT
73550 CTGGTTTTCC
Statistics
Matches: 194, Mismatches: 5, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
199 150 0.77
200 44 0.23
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (200 bp):
AATCGATGCTACCTTCAATGTTATCAGCAGATTGATTCGAAACAATATTGTTCTGAACTTGCCGA
TTATCTGGCATCGGTGGATGCGGCACGAAATTTTTGTAAAACCGTACCTTACTTTTGATCGAAAC
AATCAAAACCCAAGCAACAAGAGATTTTAAAAAAAAATCAATTGCAGGGCATAAATCAACGCAAA
TTCGT
Found at i:73716 original size:5 final size:5
Alignment explanation
Indices: 73706--73732 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
73696 AAATATTCCA
73706 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
73733 GTTTGTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:84327 original size:2 final size:2
Alignment explanation
Indices: 84320--84351 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
84310 ATAAAAATTA
84320 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
84352 CCTATCTGAT
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:85130 original size:3 final size:3
Alignment explanation
Indices: 85122--85158 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
85112 TATCAATATC
* *
85122 TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
85159 GGATAAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:103116 original size:13 final size:13
Alignment explanation
Indices: 103098--103122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
103088 ATAATAATAT
103098 ATGTTCTGATAAA
1 ATGTTCTGATAAA
103111 ATGTTCTGATAA
1 ATGTTCTGATAA
103123 TTATTCTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTTCTGATAAA
Found at i:103268 original size:6 final size:6
Alignment explanation
Indices: 103257--103290 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
103247 TACATACCAC
*
103257 GTATAT GTATAT GTATAT GTACAT GTATAT GTAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTAT
103291 GTTTAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (6 bp):
GTATAT
Found at i:103813 original size:42 final size:42
Alignment explanation
Indices: 103729--103820 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
103719 ATGATCCAAG
* * *
103729 GGAAAGCTAACGGTGTTTGGAGGCCTCGGCGTCATCCAAAAT
1 GGAAAGCTAACGGTGTTTGGAGGCCGCGCCGCCATCCAAAAT
* ***
103771 GGAAAGCTAACGGTGTTTGGAGGTCGCGCCGCCATTGGAAAT
1 GGAAAGCTAACGGTGTTTGGAGGCCGCGCCGCCATCCAAAAT
103813 GGAAAGCT
1 GGAAAGCT
103821 GCTGAGTGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
GGAAAGCTAACGGTGTTTGGAGGCCGCGCCGCCATCCAAAAT
Found at i:110155 original size:21 final size:21
Alignment explanation
Indices: 110130--110170 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
110120 AGTAATATGG
* *
110130 TTTTTAGATTACTTATAATTT
1 TTTTTAAAATACTTATAATTT
*
110151 TTTTTAAAATAGTTATAATT
1 TTTTTAAAATACTTATAATT
110171 ATTATTGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTAAAATACTTATAATTT
Found at i:110207 original size:26 final size:28
Alignment explanation
Indices: 110151--110207 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
110141 CTTATAATTT
* *
110151 TTTTTAAAATAGTTATAATTATTATTGA
1 TTTTTAAAATAATTATAATTATTATTAA
*
110179 TTTTTAAATTAATTAT-A-TATTATTAA
1 TTTTTAAAATAATTATAATTATTATTAA
110205 TTT
1 TTT
110208 GATATTATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 11 0.42
27 1 0.04
28 14 0.54
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTTAAAATAATTATAATTATTATTAA
Found at i:111875 original size:30 final size:30
Alignment explanation
Indices: 111809--111885 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
111799 ATCTTAAAAT
111809 TATATATGAAATTTAATTTAATGTGTAATTTA
1 TATATAT-AAATTTAATTTAA-GTGTAATTTA
*
111841 -ATATATAATTTTAATTTAA-TGTAA-TTA
1 TATATATAAATTTAATTTAAGTGTAATTTA
* *
111868 TATATATATATATAATTT
1 TATATATAAATTTAATTT
111886 TGATTACGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 19 0.47
30 12 0.30
31 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
TATATATAAATTTAATTTAAGTGTAATTTA
Found at i:112284 original size:29 final size:29
Alignment explanation
Indices: 112247--112306 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
112237 TATGGTTTAA
112247 TGTGTAATTATATACAT-AAATTTTGACTT
1 TGTGTAATTATATACATGAAATTTTGA-TT
*
112276 TGTGTAATTTTATACATGAAATTTTGATT
1 TGTGTAATTATATACATGAAATTTTGATT
112305 TG
1 TG
112307 ATCCAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (29 bp):
TGTGTAATTATATACATGAAATTTTGATT
Found at i:115697 original size:18 final size:20
Alignment explanation
Indices: 115671--115709 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
115661 AATGTGTTTT
*
115671 AAATTACATA-AT-ATATAA
1 AAATAACATATATAATATAA
115689 AAATAACATATATAATATAA
1 AAATAACATATATAATATAA
115709 A
1 A
115710 GTATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAACATATATAATATAA
Done.