Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022799.1 Corchorus olitorius cultivar O-4 contig22832, 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: 83289
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:9831 original size:31 final size:31
Alignment explanation
Indices: 9793--9851 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
9783 ATGGTGAGAG
* *
9793 ATCTCTATCCTGATGAATGACAACACAAGAA
1 ATCTCTATCCCGACGAATGACAACACAAGAA
9824 ATCTCTATCCCGACGAATGACAACACAA
1 ATCTCTATCCCGACGAATGACAACACAA
9852 ATTCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (31 bp):
ATCTCTATCCCGACGAATGACAACACAAGAA
Found at i:20359 original size:18 final size:17
Alignment explanation
Indices: 20322--20364 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20312 CAATCGCAAT
**
20322 CGGGAAAAGAAAATTTC
1 CGGGAAAAGAAAATAGC
20339 CGGGAAAACGAAAATAGC
1 CGGGAAAA-GAAAATAGC
20357 C-GGAAAAG
1 CGGGAAAAG
20365 CGTGTCCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.49, C:0.14, G:0.28, T:0.09
Consensus pattern (17 bp):
CGGGAAAAGAAAATAGC
Found at i:22518 original size:24 final size:24
Alignment explanation
Indices: 22486--22538 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
22476 TCCATAGATT
* *
22486 ATATTAGTACAAGTCTATGAAATG
1 ATATCAGTACAAGCCTATGAAATG
*
22510 ATATCAGTACAAGCCTATGAAATT
1 ATATCAGTACAAGCCTATGAAATG
22534 ATATC
1 ATATC
22539 TTGAATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (24 bp):
ATATCAGTACAAGCCTATGAAATG
Found at i:22939 original size:2 final size:2
Alignment explanation
Indices: 22932--22962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22922 AGCATATGCA
22932 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
22963 ACACACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:33161 original size:18 final size:18
Alignment explanation
Indices: 33138--33191 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
33128 TTCCACATCA
33138 GGAAGTTGGGCAAGAGGT
1 GGAAGTTGGGCAAGAGGT
33156 GGAAGTTGGGCAAGAGGT
1 GGAAGTTGGGCAAGAGGT
*
33174 GGAAGTTGCGCAAGAGGT
1 GGAAGTTGGGCAAGAGGT
33192 TGGATTTCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.48, T:0.17
Consensus pattern (18 bp):
GGAAGTTGGGCAAGAGGT
Found at i:33438 original size:54 final size:54
Alignment explanation
Indices: 33373--33479 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
33363 TTACCAATAG
33373 TCTGATCAAGCCGAGGTTTCTTGAGAGGGTTTGGGGTTGGACCATCAACAGAAT
1 TCTGATCAAGCCGAGGTTTCTTGAGAGGGTTTGGGGTTGGACCATCAACAGAAT
* *
33427 TCTGATGAAGCCGAGGTTTCTTGAGAGGGTTTGGGGTTGGATCATCAACAGAA
1 TCTGATCAAGCCGAGGTTTCTTGAGAGGGTTTGGGGTTGGACCATCAACAGAA
33480 ACAGACAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (54 bp):
TCTGATCAAGCCGAGGTTTCTTGAGAGGGTTTGGGGTTGGACCATCAACAGAAT
Found at i:38665 original size:25 final size:25
Alignment explanation
Indices: 38620--38667 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38610 TCCTTTTATG
***
38620 TGCATTCAGTATTTTTTTTGTCCCA
1 TGCATTCAGTATTTCAATTGTCCCA
38645 TGCATTCAGTATTTCAATTGTCC
1 TGCATTCAGTATTTCAATTGTCC
38668 TAGAAATGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (25 bp):
TGCATTCAGTATTTCAATTGTCCCA
Found at i:47028 original size:21 final size:22
Alignment explanation
Indices: 46999--47042 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
46989 TCGTTATTAT
* *
46999 TATATTATAA-TAATAACAAAA
1 TATAGTATAATTAATAAAAAAA
47020 TATAGTATAATTAATAAAAAAA
1 TATAGTATAATTAATAAAAAAA
47042 T
1 T
47043 CAACTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TATAGTATAATTAATAAAAAAA
Found at i:48112 original size:20 final size:20
Alignment explanation
Indices: 48084--48123 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48074 TTCAATGTCA
*
48084 CCGTATATCCGTCGATATAT
1 CCGTATATCCGTCAATATAT
*
48104 CCGTGTATCCGTCAATATAT
1 CCGTATATCCGTCAATATAT
48124 TCTCGATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
CCGTATATCCGTCAATATAT
Found at i:48955 original size:20 final size:22
Alignment explanation
Indices: 48930--48983 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
48920 TTTTGAATCT
48930 CATCGATA-CC-TCGATATATC
1 CATCGATATCCGTCGATATATC
48950 CATCGATATATCCGTCGATATATC
1 CATCG--ATATCCGTCGATATATC
48974 CATTCGATAT
1 CA-TCGATAT
48984 ATCCATGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.17
22 3 0.10
23 6 0.21
24 12 0.41
25 3 0.10
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (22 bp):
CATCGATATCCGTCGATATATC
Found at i:48957 original size:12 final size:12
Alignment explanation
Indices: 48940--48994 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
48930 CATCGATACC
48940 TCGATATATCCA
1 TCGATATATCCA
*
48952 TCGATATATCCG
1 TCGATATATCCA
48964 TCGATATATCCA
1 TCGATATATCCA
48976 TTCGATATATCCA
1 -TCGATATATCCA
*
48989 TGGATA
1 TCGATA
48995 CCTATATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
12 27 0.69
13 12 0.31
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (12 bp):
TCGATATATCCA
Found at i:48994 original size:25 final size:24
Alignment explanation
Indices: 48940--48994 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
48930 CATCGATACC
*
48940 TCGATATATCCATCGATATATCCG
1 TCGATATATCCATCGATATATCCA
48964 TCGATATATCCATTCGATATATCCA
1 TCGATATATCCA-TCGATATATCCA
*
48989 TGGATA
1 TCGATA
48995 CCTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (24 bp):
TCGATATATCCATCGATATATCCA
Found at i:52569 original size:80 final size:80
Alignment explanation
Indices: 52436--52592 Score: 242
Period size: 80 Copynumber: 2.0 Consensus size: 80
52426 CGATAATCAC
* * * * *
52436 ATTGTGCTCCGAACTTGGGTCGAGTCGGAGTCCAAATCAGGTGAAGGAAAGCTCTCCCAATGTCT
1 ATTGTGCTCCAAACTTGAGCCGAGTCGGAGCCCAAATCAGGTGAAGGAAAGCTCTCCCAATGCCT
52501 AATATCTTGTTTCAT
66 AATATCTTGTTTCAT
* **
52516 ATTGTGCTCTAAACTTGAGCCGAGTCGGAGCCCAAATGGGGTGAAGGAAAGCTCTCCCAATGCCT
1 ATTGTGCTCCAAACTTGAGCCGAGTCGGAGCCCAAATCAGGTGAAGGAAAGCTCTCCCAATGCCT
52581 AATATCTTGTTT
66 AATATCTTGTTT
52593 TTAGGCGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (80 bp):
ATTGTGCTCCAAACTTGAGCCGAGTCGGAGCCCAAATCAGGTGAAGGAAAGCTCTCCCAATGCCT
AATATCTTGTTTCAT
Found at i:58160 original size:2 final size:2
Alignment explanation
Indices: 58153--58179 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58143 GTTATTTACT
58153 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
58180 TTTTCTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:58186 original size:16 final size:16
Alignment explanation
Indices: 58153--58201 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
58143 GTTATTTACT
* *
58153 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTTTTTC
58169 TCTCTCTCTCTTTTTC
1 TCTCTCTCTCTTTTTC
*
58185 TCGT-TCACTCTTTTTC
1 TC-TCTCTCTCTTTTTC
58201 T
1 T
58202 GCTTGGGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 28 0.97
17 1 0.03
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.57
Consensus pattern (16 bp):
TCTCTCTCTCTTTTTC
Found at i:68301 original size:15 final size:15
Alignment explanation
Indices: 68283--68315 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
68273 TTTTGCTGGC
68283 TGCAGTATTGCCAGT
1 TGCAGTATTGCCAGT
68298 TGCAGTATTGCCAGT
1 TGCAGTATTGCCAGT
68313 TGC
1 TGC
68316 TAATGTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (15 bp):
TGCAGTATTGCCAGT
Found at i:69821 original size:49 final size:49
Alignment explanation
Indices: 69749--69848 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
69739 CTCAACTTCC
69749 TTACCCTCCTAGTAAGGATGAGATTTTAACCAAAGGTTCATGCTTTAAT
1 TTACCCTCCTAGTAAGGATGAGATTTTAACCAAAGGTTCATGCTTTAAT
* *
69798 TTACCCTCCTTGTAAGGGTGAGATTTTAACCAAAGGTTCATGCTTTAAT
1 TTACCCTCCTAGTAAGGATGAGATTTTAACCAAAGGTTCATGCTTTAAT
69847 TT
1 TT
69849 TCTCAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (49 bp):
TTACCCTCCTAGTAAGGATGAGATTTTAACCAAAGGTTCATGCTTTAAT
Found at i:73254 original size:9 final size:9
Alignment explanation
Indices: 73240--73269 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
73230 GTTTTCTCAA
73240 AAAAAAAAG
1 AAAAAAAAG
73249 AAAAAAAAG
1 AAAAAAAAG
73258 AAAAAAAAG
1 AAAAAAAAG
73267 AAA
1 AAA
73270 TGGATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:79095 original size:26 final size:28
Alignment explanation
Indices: 79047--79098 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
79037 GATAGGAAGA
79047 AGGAAGAATTATCCATCAACCATCTAGG
1 AGGAAGAATTATCCATCAACCATCTAGG
**
79075 AGGAAG-ATT-TCCATCTCCCATCTA
1 AGGAAGAATTATCCATCAACCATCTA
79099 AGAGATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 3 0.14
28 6 0.27
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (28 bp):
AGGAAGAATTATCCATCAACCATCTAGG
Found at i:80537 original size:19 final size:19
Alignment explanation
Indices: 80513--80549 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
80503 GTACAGTACC
*
80513 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGAACAGTG
*
80532 TAATCTCATCTGAACAGT
1 TAATCTAATCTGAACAGT
80550 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (19 bp):
TAATCTAATCTGAACAGTG
Found at i:82370 original size:7 final size:7
Alignment explanation
Indices: 82360--82391 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
82350 AGAATATATT
82360 AAATTTC
1 AAATTTC
82367 AAATTTC
1 AAATTTC
82374 AAATTTC
1 AAATTTC
82381 AAATTTC
1 AAATTTC
82388 AAAT
1 AAAT
82392 CACAAATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTC
Done.