Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021048.1 Corchorus olitorius cultivar O-4 contig21081, 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: 47800
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:69 original size:25 final size:24
Alignment explanation
Indices: 35--81 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
25 ACGTTTGCAC
35 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
60 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
82 TATAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:122 original size:34 final size:36
Alignment explanation
Indices: 78--147 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
68 AAGAATTTAA
* *
78 TTAATATAAGTATTTCAGTTATTATA-GTATTACAT
1 TTAATATAAGTATTTCAGTGATTATATATATTACAT
*
113 TTAAT-TAAGTATTTTAGTGATTATATATATTACAT
1 TTAATATAAGTATTTCAGTGATTATATATATTACAT
148 AGGAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (36 bp):
TTAATATAAGTATTTCAGTGATTATATATATTACAT
Found at i:376 original size:2 final size:2
Alignment explanation
Indices: 364--421 Score: 64
Period size: 2 Copynumber: 28.0 Consensus size: 2
354 AGTTTAGACT
* *
364 TA TA TA GTA TA TA GA TA TA TA TA GTA TA TA GA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
408 TA TA T- TA TA CTA TA
1 TA TA TA TA TA -TA TA
422 CTTACAATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
1 1 0.02
2 41 0.85
3 6 0.12
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:416 original size:17 final size:17
Alignment explanation
Indices: 364--409 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
354 AGTTTAGACT
364 TATATAGTATATAGATA
1 TATATAGTATATAGATA
381 TATATAGTATATAGATA
1 TATATAGTATATAGATA
398 TATATA-TATATA
1 TATATAGTATATA
410 TATTATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATAGTATATAGATA
Found at i:4102 original size:14 final size:15
Alignment explanation
Indices: 4072--4104 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4062 GCTGTCGATT
*
4072 TTTTTTTCTTCTCTC
1 TTTTTTTCTTCTATC
4087 TTTTTTTCTTC-ATC
1 TTTTTTTCTTCTATC
4101 TTTT
1 TTTT
4105 GTCTGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTCTATC
Found at i:8729 original size:37 final size:37
Alignment explanation
Indices: 8687--8761 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
8677 TTATTCATTA
*
8687 TTTATTTTATTTAAGAGAGATTTATTCATTATTGGAG
1 TTTATTTTATTTAAGAGAGATATATTCATTATTGGAG
* * *
8724 TTTATTTTGTTTAGGAGAGATATATTCCTTATTGGAG
1 TTTATTTTATTTAAGAGAGATATATTCATTATTGGAG
8761 T
1 T
8762 GGAAGGCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.51
Consensus pattern (37 bp):
TTTATTTTATTTAAGAGAGATATATTCATTATTGGAG
Found at i:17273 original size:16 final size:16
Alignment explanation
Indices: 17240--17273 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17230 GACCTGAAAA
*
17240 ACCCAAAACTCGAATG
1 ACCCAAAACCCGAATG
*
17256 ACCCAAAACCCGAGTG
1 ACCCAAAACCCGAATG
17272 AC
1 AC
17274 ATGAGGCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.35, G:0.15, T:0.09
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:18076 original size:93 final size:88
Alignment explanation
Indices: 17927--18102 Score: 239
Period size: 93 Copynumber: 1.9 Consensus size: 88
17917 TAATTAAATT
*
17927 AGTAATATGGTAAAAATAAAAATAAGTATAAGGATATTAATCAAATAAAAATAGAGTTTTTAGTT
1 AGTAAAATGGTAAAAATAAAAATAAGTATAAGGATATTAATCAAATAAAAATAGAGTTTTTAGTT
*
17992 GAGTAAAACTATAAAAGTAAAAC
66 GACTAAAACTATAAAAGTAAAAC
* *
18015 AGTAAAATGGTAAAAAT-AAAAT-AGTTATAAGGATATTAGATTTAATTAAATAAATTAAGAGTT
1 AGTAAAATGGTAAAAATAAAAATAAG-TATAAGGATATTA-A-TCAAAT-AA-AAA-T-AGAGTT
18078 TTTAGTTGACTAAAACTATAAAAGT
59 TTTAGTTGACTAAAACTATAAAAGT
18103 TTAAACAATG
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
86 2 0.03
87 18 0.23
88 17 0.22
89 4 0.05
90 2 0.03
91 3 0.04
92 1 0.01
93 30 0.39
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.31
Consensus pattern (88 bp):
AGTAAAATGGTAAAAATAAAAATAAGTATAAGGATATTAATCAAATAAAAATAGAGTTTTTAGTT
GACTAAAACTATAAAAGTAAAAC
Found at i:27057 original size:13 final size:13
Alignment explanation
Indices: 27013--27058 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
27003 TAGAGGGGAA
27013 AGAAGGGAAGGAG
1 AGAAGGGAAGGAG
27026 AG-AGGGAAGGA-
1 AGAAGGGAAGGAG
* *
27037 AAACAGGGGAGGAG
1 AGA-AGGGAAGGAG
27051 AGAAGGGA
1 AGAAGGGA
27059 GAGCATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 14 0.54
14 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.52, T:0.00
Consensus pattern (13 bp):
AGAAGGGAAGGAG
Found at i:27907 original size:20 final size:20
Alignment explanation
Indices: 27882--27932 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
27872 AGGTTTTGTA
27882 TGATATTTCTTCTAAGTGAG
1 TGATATTTCTTCTAAGTGAG
27902 TGATATTTCTTCTAAGTGAG
1 TGATATTTCTTCTAAGTGAG
27922 TGATATTTCTT
1 TGATATTTCTT
27933 GAAGGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.49
Consensus pattern (20 bp):
TGATATTTCTTCTAAGTGAG
Found at i:36204 original size:21 final size:21
Alignment explanation
Indices: 36141--36204 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
36131 AGCAATAATT
36141 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
* ** ** * *
36162 -A-ATTATCTAGAGATAGAAG
1 AATATTAGCTTTATTTTGATG
36181 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
36202 AAT
1 AAT
36205 TACTAGAGAT
Statistics
Matches: 27, Mismatches: 14, Indels: 4
0.60 0.31 0.09
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 14 0.52
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
AATATTAGCTTTATTTTGATG
Found at i:36270 original size:45 final size:45
Alignment explanation
Indices: 36219--36309 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
36209 AGAGATGAAA
* * *
36219 TAGAATTTAGATAATGCACTTTTAGAATGAAAGAGAGGTCATGTG
1 TAGAATTTAGATAATGCACTTTTAAAATGAAAGAGAGATAATGTG
36264 TAGAATTTAGATAATGCACTTTTAAAATGAAAGAGAGATAATGTG
1 TAGAATTTAGATAATGCACTTTTAAAATGAAAGAGAGATAATGTG
36309 T
1 T
36310 TTTGCTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (45 bp):
TAGAATTTAGATAATGCACTTTTAAAATGAAAGAGAGATAATGTG
Found at i:41279 original size:17 final size:18
Alignment explanation
Indices: 41254--41300 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
41244 ATTGAGGTTT
*
41254 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
41271 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
41290 -AAAATTTGAAG
1 GAAAATTTGAAG
41301 TTTAAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 10 0.37
19 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:41880 original size:31 final size:29
Alignment explanation
Indices: 41834--41914 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
41824 AGCCACTAAA
41834 ATATATATAATATTTT-ATATATAATATAT
1 ATATATATAATATTTTAATAT-TAATATAT
41863 ATATATATTAATAATTTTAATATTAAT-T-T
1 ATATATA-TAAT-ATTTTAATATTAATATAT
*
41892 ATATATA-AAT-TTTTAGTATTAAT
1 ATATATATAATATTTTAATATTAAT
41915 GTTTTATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
25 12 0.25
27 3 0.06
29 15 0.31
30 5 0.10
31 9 0.19
32 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATATATAATATTTTAATATTAATATAT
Found at i:41894 original size:25 final size:26
Alignment explanation
Indices: 41866--41938 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
41856 AATATATATA
41866 TATATTAATAATTTTAATATTAAT-T
1 TATATTAATAATTTTAATATTAATGT
* *
41891 TATATATAA-ATTTTTAGTATTAATGT
1 TATAT-TAATAATTTTAATATTAATGT
*
41917 TTTA-TAATAA-TTTATATATTAA
1 TATATTAATAATTTTA-ATATTAA
41939 CATTTAGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.18
25 25 0.64
26 7 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (26 bp):
TATATTAATAATTTTAATATTAATGT
Found at i:41945 original size:38 final size:40
Alignment explanation
Indices: 41840--41954 Score: 101
Period size: 38 Copynumber: 2.9 Consensus size: 40
41830 TAAAATATAT
* *
41840 ATAATATTTTATATATAATATATATATA-TATTAATAATTTTA
1 ATAATAATTTATATATAA-ACAT-T-TAGTATTAATAATTTTA
* ** *
41882 ATATTAATTTATATATAAATTTTTAGTATTAAT-GTTTT-
1 ATAATAATTTATATATAAACATTTAGTATTAATAATTTTA
* * *
41920 ATAATAATTTATATATTAACATTTAGAAATAATAA
1 ATAATAATTTATATATAAACATTTAGTATTAATAA
41955 AATTAATTAG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
38 27 0.45
39 6 0.10
40 8 0.13
41 3 0.05
42 16 0.27
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (40 bp):
ATAATAATTTATATATAAACATTTAGTATTAATAATTTTA
Found at i:42215 original size:110 final size:111
Alignment explanation
Indices: 42016--42245 Score: 383
Period size: 110 Copynumber: 2.1 Consensus size: 111
42006 ATTCAAAATC
*
42016 GACCGAAACTGATAGTAACCGACCAAAATCGATTTAGTCGGTTTCTTATATATCTCTGTTGGTTT
1 GACCGAAACTGATAGTAACCGACCAAAATCGATTTAGTCGGTTTCTTATATATCTCTATTGGTTT
*
42081 CGGTTTTGGTTATCTCACAATTCAAAACCGAAAAAAACGACGAA-AA
66 CAGTTTTGGTTATCTCACAATTCAAAACCGAAAAAAACGAC-AAGAA
* *
42127 GACCG-AACTGATCGTAACTGACCAAAATCGATTTAGTCGGTTTCTTATATATCTCTATTGGTTT
1 GACCGAAACTGATAGTAACCGACCAAAATCGATTTAGTCGGTTTCTTATATATCTCTATTGGTTT
*
42191 CAGTTTTGGTTATCTCACAATTCAAAATCGAAAAAAACGACAAGAA
66 CAGTTTTGGTTATCTCACAATTCAAAACCGAAAAAAACGACAAGAA
*
42237 GACTGAAAC
1 GACCGAAAC
42246 CGACCGATGC
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
109 2 0.02
110 101 0.91
111 8 0.07
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (111 bp):
GACCGAAACTGATAGTAACCGACCAAAATCGATTTAGTCGGTTTCTTATATATCTCTATTGGTTT
CAGTTTTGGTTATCTCACAATTCAAAACCGAAAAAAACGACAAGAA
Found at i:44041 original size:6 final size:6
Alignment explanation
Indices: 44020--44065 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
44010 GCAGCCCAAA
* *
44020 CCCGA- CCCGAG ACCGAG CCCGAG CCCGAG CCCGAG CCCGAA CCCGA
1 CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGA
44066 AATAGTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (6 bp):
CCCGAG
Found at i:44503 original size:13 final size:12
Alignment explanation
Indices: 44467--44513 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
44457 TCAATCTTTA
*
44467 TATATATTGATAA
1 TATATATT-ATAT
*
44480 TA-ATGTTATAT
1 TATATATTATAT
44491 TATATTATTATAT
1 TATA-TATTATAT
44504 TATATATTAT
1 TATATATTAT
44514 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:44659 original size:23 final size:23
Alignment explanation
Indices: 44633--44680 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
44623 ATCGAATCGA
* *
44633 AATCAAACTCGAGCCCGAACCCG
1 AATCAAACCCGAGACCGAACCCG
**
44656 AATCCTACCCGAGACCGAACCCG
1 AATCAAACCCGAGACCGAACCCG
44679 AA
1 AA
44681 AATACCCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.40, G:0.17, T:0.08
Consensus pattern (23 bp):
AATCAAACCCGAGACCGAACCCG
Found at i:44691 original size:16 final size:16
Alignment explanation
Indices: 44670--44760 Score: 87
Period size: 16 Copynumber: 5.7 Consensus size: 16
44660 CTACCCGAGA
44670 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
44686 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
44702 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
**
44718 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
* * *
44734 CTGAGCTCGAAAATAC
1 CCGAACCCGAAAATAC
44750 CCGAACCCGAA
1 CCGAACCCGAA
44761 CCCTCCCAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
15 5 0.09
16 47 0.82
17 5 0.09
ACGTcount: A:0.37, C:0.38, G:0.15, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:44713 original size:32 final size:32
Alignment explanation
Indices: 44670--44759 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
44660 CTACCCGAGA
*
44670 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
*
44702 CCGAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
* *
44734 CTGAGCTCGAAAATACCCGAACCCGA
1 CCGAGCCCGAAAATACCCGAACCCGA
44760 ACCCTCCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.09
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACATAAC
Done.