Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009274.1 Kokia drynarioides strain JFW-HI SEQ_123979, 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: 74761
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1942 original size:44 final size:44
Alignment explanation
Indices: 1892--1980 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1882 CAAAGAATGG
1892 TCTAATCTAATCATGAAGCAGCATCATAATTATGAACATAACTA
1 TCTAATCTAATCATGAAGCAGCATCATAATTATGAACATAACTA
1936 TCTAATCTAATCATGAAGCAGCATCATAATTATGAACATAACTA
1 TCTAATCTAATCATGAAGCAGCATCATAATTATGAACATAACTA
1980 T
1 T
1981 TTTATAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (44 bp):
TCTAATCTAATCATGAAGCAGCATCATAATTATGAACATAACTA
Found at i:9329 original size:16 final size:16
Alignment explanation
Indices: 9308--9339 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9298 TTCACAAGTT
9308 TCTAATTAAATCAGAA
1 TCTAATTAAATCAGAA
9324 TCTAATTAAATCAGAA
1 TCTAATTAAATCAGAA
9340 CTGAGTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
TCTAATTAAATCAGAA
Found at i:10076 original size:24 final size:25
Alignment explanation
Indices: 10049--10107 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
10039 CACCGGCAAA
*
10049 AAAGAGGGAGAAACGGA-GGATCCG
1 AAAGAGGGAGAAACCGAGGGATCCG
*
10073 AAAGTGGGAGAAACCGAGGGATCCG
1 AAAGAGGGAGAAACCGAGGGATCCG
10098 AACAGAGGGA
1 AA-AGAGGGA
10108 TTCGGGTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 15 0.50
25 9 0.30
26 6 0.20
ACGTcount: A:0.41, C:0.14, G:0.41, T:0.05
Consensus pattern (25 bp):
AAAGAGGGAGAAACCGAGGGATCCG
Found at i:10411 original size:17 final size:19
Alignment explanation
Indices: 10374--10412 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
10364 AAATTGAGAT
*
10374 AAATATATAAAAATTTAAG
1 AAATATATAAAAATCTAAG
10393 AAATATAT-AAAATCT-AG
1 AAATATATAAAAATCTAAG
10410 AAA
1 AAA
10413 AAATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATATATAAAAATCTAAG
Found at i:25429 original size:17 final size:17
Alignment explanation
Indices: 25403--25435 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25393 AATTATCCTA
25403 TTTTTCATAATTTTTAT
1 TTTTTCATAATTTTTAT
*
25420 TTTTTTATAATTTTTA
1 TTTTTCATAATTTTTA
25436 CATTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTCATAATTTTTAT
Found at i:25515 original size:30 final size:31
Alignment explanation
Indices: 25441--25517 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
25431 TTTTACATTT
25441 AAATAATTTAAAAAATCAATTAAACCCTCATA
1 AAATAA-TTAAAAAATCAATTAAACCCTCATA
* * *
25473 AAATTAA--AAAAAAACAATTAAATCCTCGTA
1 AAA-TAATTAAAAAATCAATTAAACCCTCATA
25503 AAATAATTAAAAAAT
1 AAATAATTAAAAAAT
25518 TATTAAGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 3 0.08
30 23 0.61
31 6 0.16
32 3 0.08
33 3 0.08
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.26
Consensus pattern (31 bp):
AAATAATTAAAAAATCAATTAAACCCTCATA
Found at i:25898 original size:19 final size:17
Alignment explanation
Indices: 25876--25933 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 17
25866 CATAAATTTA
25876 AATATTTTTATTAATTTTT
1 AATATTTTTA-T-ATTTTT
25895 AATAGTTTCTTATATTTTT
1 AATA-TTT-TTATATTTTT
25914 AATAATTTTCTATAGTTTTT
1 AAT-ATTTT-TATA-TTTTT
25934 GAAAAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 10 0.29
21 3 0.09
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
AATATTTTTATATTTTT
Found at i:26598 original size:19 final size:19
Alignment explanation
Indices: 26558--26601 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
26548 TGCTTAAAGC
26558 TTAATAAAAACAAATTAAGT
1 TTAATAAAAACAAA-TAAGT
*
26578 TTAATAAAAAGCAAA-ATGT
1 TTAATAAAAA-CAAATAAGT
26597 TTAAT
1 TTAAT
26602 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 10 0.45
21 4 0.18
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (19 bp):
TTAATAAAAACAAATAAGT
Found at i:42669 original size:22 final size:24
Alignment explanation
Indices: 42644--42688 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
42634 GTTGATAAGG
42644 TTCTTAGTCATTC-G-ATATATAT
1 TTCTTAGTCATTCAGTATATATAT
42666 TTCTTAGTCATTCAGTATATATA
1 TTCTTAGTCATTCAGTATATATA
42689 AGCTTAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (24 bp):
TTCTTAGTCATTCAGTATATATAT
Found at i:43018 original size:21 final size:21
Alignment explanation
Indices: 42994--43095 Score: 91
Period size: 21 Copynumber: 4.7 Consensus size: 21
42984 TTTTTGCTAT
*
42994 TTTTGTGTTATTTTTTTACTG
1 TTTTGTGCTATTTTTTTACTG
*
43015 TTTTGATGCT-TTTTTTTACTA
1 TTTTG-TGCTATTTTTTTACTG
* *
43036 TTTTG-GTTTTTTTTTTACTG
1 TTTTGTGCTATTTTTTTACTG
**
43056 TTTTAGTGCTATTTTTGTTGTTG
1 TTTT-GTGCTATTTTT-TTACTG
43079 TTTTTGTTGCTATTTTT
1 -TTTTG-TGCTATTTTT
43096 GTTGTTGTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 21 0.32
22 10 0.15
23 5 0.08
24 14 0.21
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.71
Consensus pattern (21 bp):
TTTTGTGCTATTTTTTTACTG
Found at i:43046 original size:19 final size:20
Alignment explanation
Indices: 42978--43050 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
42968 AAAATTATTT
* *
42978 TGTTGTTTTTTGCTATTTTTG
1 TGTTTTTTTTTACTA-TTTTG
*
42999 TGTTATTTTTTTACTGTTTTG
1 TGTT-TTTTTTTACTATTTTG
*
43020 ATGCTTTTTTTTACTATTTTG
1 -TGTTTTTTTTTACTATTTTG
43041 -GTTTTTTTTT
1 TGTTTTTTTTT
43051 TACTGTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.20
21 24 0.55
22 11 0.25
ACGTcount: A:0.08, C:0.05, G:0.14, T:0.73
Consensus pattern (20 bp):
TGTTTTTTTTTACTATTTTG
Found at i:43070 original size:20 final size:19
Alignment explanation
Indices: 43004--43071 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
42994 TTTTGTGTTA
43004 TTTTTTTACTGTTTTGATGC
1 TTTTTTTACTGTTTTG-TGC
* **
43024 TTTTTTTTACTATTTTGGTTT
1 -TTTTTTTACTGTTTT-GTGC
43045 TTTTTTTACTGTTTTAGTGC
1 TTTTTTTACTGTTTT-GTGC
*
43065 TATTTTT
1 TTTTTTT
43072 GTTGTTGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 22 0.58
21 15 0.39
22 1 0.03
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (19 bp):
TTTTTTTACTGTTTTGTGC
Found at i:43071 original size:41 final size:43
Alignment explanation
Indices: 42983--43071 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 43
42973 TATTTTGTTG
* *
42983 TTTTTTGCTATTTTTGTGTTATTTTTTTACTGTTTTGATGCTT
1 TTTTTTACTATTTTTGTGTTATTTTTTTACTGTTTTGATGCTA
*
43026 TTTTTTACTA-TTTTG-GTTTTTTTTTTACTGTTTT-AGTGCTA
1 TTTTTTACTATTTTTGTGTTATTTTTTTACTGTTTTGA-TGCTA
43067 TTTTT
1 TTTTT
43072 GTTGTTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 1 0.02
41 27 0.64
42 5 0.12
43 9 0.21
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (43 bp):
TTTTTTACTATTTTTGTGTTATTTTTTTACTGTTTTGATGCTA
Found at i:43082 original size:12 final size:12
Alignment explanation
Indices: 43067--43104 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43057 TTTAGTGCTA
43067 TTTTTGTTGTTG
1 TTTTTGTTGTTG
* *
43079 TTTTTGTTGCTA
1 TTTTTGTTGTTG
43091 TTTTTGTTGTTG
1 TTTTTGTTGTTG
43103 TT
1 TT
43105 GTATAGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.03, G:0.21, T:0.74
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:43083 original size:24 final size:24
Alignment explanation
Indices: 43054--43148 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
43044 TTTTTTTTAC
*
43054 TGTTTTAG-TGCTATTTTTGTTGT
1 TGTTTTTGTTGCTATTTTTGTTGT
43077 TGTTTTTGTTGCTATTTTTGTTGT
1 TGTTTTTGTTGCTATTTTTGTTGT
* * * * ** **
43101 TG-TTGTATAGTTATTTTTACTAC
1 TGTTTTTGTTGCTATTTTTGTTGT
*
43124 TGTTTTTGTTGTTATTTTTGTTGT
1 TGTTTTTGTTGCTATTTTTGTTGT
43148 T
1 T
43149 TGGATGTTAT
Statistics
Matches: 54, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
23 22 0.41
24 32 0.59
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.67
Consensus pattern (24 bp):
TGTTTTTGTTGCTATTTTTGTTGT
Found at i:43160 original size:44 final size:47
Alignment explanation
Indices: 43077--43163 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
43067 TTTTTGTTGT
*
43077 TGTTTTTGTTGCTATTTTTGTTGTTGTTGTATAGTTATTTTTACTAC
1 TGTTTTTGTTGCTATTTTTGTTGTTGTTGGATAGTTATTTTTACTAC
*
43124 TGTTTTTGTTGTTATTTTTGTTG-T-TTGGAT-GTTATTTTTA
1 TGTTTTTGTTGCTATTTTTGTTGTTGTTGGATAGTTATTTTTA
43164 TGCGTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 10 0.26
45 5 0.13
46 1 0.03
47 22 0.58
ACGTcount: A:0.11, C:0.03, G:0.18, T:0.67
Consensus pattern (47 bp):
TGTTTTTGTTGCTATTTTTGTTGTTGTTGGATAGTTATTTTTACTAC
Found at i:44290 original size:21 final size:20
Alignment explanation
Indices: 44261--44301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44251 TTAATTTTTT
44261 AAAATTTTTAAAATATTTAA
1 AAAATTTTTAAAATATTTAA
* *
44281 AAAATATTTTTATATATTTAA
1 AAAAT-TTTTAAAATATTTAA
44302 TAATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTTTTAAAATATTTAA
Found at i:44334 original size:28 final size:28
Alignment explanation
Indices: 44254--44339 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 28
44244 TATTTAATTA
44254 ATTTTTTAAAATTTTTAAAATATTTAAAAAAT
1 ATTTTTT--AATTTTTAAAA-A-TTAAAAAAT
* *
44286 A-TTTTTATATATTTAATAATTAAAAAAT
1 ATTTTTTA-ATTTTTAAAAATTAAAAAAT
*
44314 ATTTTTTGAATTTTTAAAATTTAAAA
1 ATTTTTT-AATTTTTAAAAATTAAAA
44340 GAACTAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.22
29 21 0.46
30 9 0.20
31 5 0.11
32 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTTTTAATTTTTAAAAATTAAAAAAT
Found at i:49701 original size:18 final size:17
Alignment explanation
Indices: 49678--49712 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49668 AATATGATTT
*
49678 TATTATTTTAATATTTTA
1 TATTATTATAAT-TTTTA
49696 TATTATTATAATTTTTA
1 TATTATTATAATTTTTA
49713 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATAATTTTTA
Found at i:58840 original size:140 final size:141
Alignment explanation
Indices: 58588--58869 Score: 404
Period size: 140 Copynumber: 2.0 Consensus size: 141
58578 GGGCTCTGGT
* * *
58588 TTAGATTTGATCCTAGGTTGACTCCTTTCATCTAAACTTTTGGACTGGTAGAGAAGGCTATGAAA
1 TTAGATTTGATCCCAGGTTGACTCCTTTCACCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
* * * *
58653 AGTCTGAGAGCTGAATAAGGATACATGGATATCATAATATTATAGGACAATAC-AAAATTGAAAT
66 AGTATGAGAGCTGAATAAGGATACATAGATACCATAATATTATAGGACAACACAAAAATTGAAAT
*
58717 TTCAGAATTAA
131 TTCAGAACTAA
* * * * *
58728 TTAGATTTGATCCCAGGTTGACTTCTTTCACCTCAACTTTTGGACTAGTAGAGTAGGCTGTGAAG
1 TTAGATTTGATCCCAGGTTGACTCCTTTCACCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
* * * *
58793 AGTATGAGAGCTGGATATGGATACATAGATACCATAATATTATAGGACTACGCAAAAATTGAAAT
66 AGTATGAGAGCTGAATAAGGATACATAGATACCATAATATTATAGGACAACACAAAAATTGAAAT
58858 TTCAGAACTAA
131 TTCAGAACTAA
58869 T
1 T
58870 GAAAATTCCA
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
140 102 0.82
141 22 0.18
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (141 bp):
TTAGATTTGATCCCAGGTTGACTCCTTTCACCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
AGTATGAGAGCTGAATAAGGATACATAGATACCATAATATTATAGGACAACACAAAAATTGAAAT
TTCAGAACTAA
Found at i:63741 original size:17 final size:17
Alignment explanation
Indices: 63715--63748 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63705 AGCATATTTG
*
63715 TATTTTCTTAGTTTCTT
1 TATTTGCTTAGTTTCTT
*
63732 TATTTGCTTATTTTCTT
1 TATTTGCTTAGTTTCTT
63749 ATACAAGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTGCTTAGTTTCTT
Found at i:70688 original size:6 final size:6
Alignment explanation
Indices: 70677--70720 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
70667 AGTGGGTTGC
70677 CACCCA CACCCA CACCCA CACCCA CACCCA CACCCA CACCCA CA
1 CACCCA CACCCA CACCCA CACCCA CACCCA CACCCA CACCCA CA
70721 TGCTTAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCA
Found at i:72028 original size:3 final size:3
Alignment explanation
Indices: 72020--72057 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
72010 CACTCAATTC
72020 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
72058 TGTGCCAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.