Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015376.1 Corchorus capsularis cultivar CVL-1 contig15397, 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: 71339
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8215 original size:3 final size:3
Alignment explanation
Indices: 8153--8200 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
8143 CTACACACGA
8153 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8201 ATTCTACATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9279 original size:3 final size:3
Alignment explanation
Indices: 9271--9304 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9261 CCCCTCTCGC
9271 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9305 TTGGCTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11155 original size:66 final size:66
Alignment explanation
Indices: 11049--11179 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
11039 CTCTTGGATC
*
11049 AATATGATCAAATCTTTTGATTGGTTTTTTGGTTATTTCATTTCTTCCTATTATTGTTTTGTATA
1 AATATGATCAAATCTTTTGATTGGTTTTTTGGTTAATTCATTTCTTCCTATTATTGTTTTGTATA
11114 T
66 T
*
11115 AATATTATCAAATCTTTTGATTGGTTTTTTGG-TAGATTCATTTCTTCCTATTATTGTTTTGTAT
1 AATATGATCAAATCTTTTGATTGGTTTTTTGGTTA-ATTCATTTCTTCCTATTATTGTTTTGTAT
11179 A
65 A
11180 ATAAATGCCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 60 0.97
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.56
Consensus pattern (66 bp):
AATATGATCAAATCTTTTGATTGGTTTTTTGGTTAATTCATTTCTTCCTATTATTGTTTTGTATA
T
Found at i:12181 original size:20 final size:20
Alignment explanation
Indices: 12148--12186 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12138 AGAATAAGGA
*
12148 AAATAAATCTAATTTATAAG
1 AAATAAATCTAATTCATAAG
12168 AAATCAAATC-AATTCATAA
1 AAAT-AAATCTAATTCATAA
12187 ATCAAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATAAATCTAATTCATAAG
Found at i:13223 original size:75 final size:75
Alignment explanation
Indices: 12947--13212 Score: 462
Period size: 75 Copynumber: 3.5 Consensus size: 75
12937 TTGATATTTT
* *
12947 CTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCA-ACTTTATTATTAT-TTTATTT
13011 CTTAAAATATCTC
63 CTTAAAATATCTC
* *
13024 CTAAATCTCCCACAAATTGGCAAGATTTAAAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
13089 AAAATATCTC
66 AAAATATCTC
13099 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
13164 AAAATATCTC
66 AAAATATCTC
13174 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
13213 CCATTATTAT
Statistics
Matches: 182, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
75 142 0.78
76 12 0.07
77 28 0.15
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (75 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
AAAATATCTC
Found at i:26776 original size:118 final size:117
Alignment explanation
Indices: 26569--26788 Score: 395
Period size: 118 Copynumber: 1.9 Consensus size: 117
26559 TTTCCTACCA
*
26569 GACAAGAGGCTCCTTCAAATAACGATGGATTAACCCCCCAACGTAGCTTGTAAGAAACTTGAATT
1 GACAAGAGGCTCCTCCAAATAACGATGGATTAACCCCCCAACGTAGCTTGTAAGAAACTTGAATT
*
26634 GTTAAAATATTTTGCTTTTAACAATTTGAAACAGAGAGTCAGAGAACCTTGT
66 GTTAAAATAGTTTGCTTTTAACAATTTGAAACAGAGAGTCAGAGAACCTTGT
26686 GACAAGAGGCTCCTCCAAATAAACGATGGATTAACCCCCCAACGTAGCTTGTAAGAAACTTGAAT
1 GACAAGAGGCTCCTCCAAAT-AACGATGGATTAACCCCCCAACGTAGCTTGTAAGAAACTTGAAT
* *
26751 TGTTACAATAGTTTGCTTTTAACAATTTGAAACGGAGA
65 TGTTAAAATAGTTTGCTTTTAACAATTTGAAACAGAGA
26789 ATTCTGATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 19 0.19
118 79 0.81
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (117 bp):
GACAAGAGGCTCCTCCAAATAACGATGGATTAACCCCCCAACGTAGCTTGTAAGAAACTTGAATT
GTTAAAATAGTTTGCTTTTAACAATTTGAAACAGAGAGTCAGAGAACCTTGT
Found at i:32028 original size:15 final size:15
Alignment explanation
Indices: 31979--32027 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
31969 TCATCAGTAT
*
31979 AAATGCTATCATTTTG
1 AAATGCT-TCATTTTA
* *
31995 AAATGATGCATTTTA
1 AAATGCTTCATTTTA
32010 AAATGCTTCATTTCTA
1 AAATGCTTCATTT-TA
32026 AA
1 AA
32028 TTCTTCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (15 bp):
AAATGCTTCATTTTA
Found at i:36228 original size:3 final size:3
Alignment explanation
Indices: 36220--36251 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
36210 AGTAGAAAAG
36220 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
36252 CACTTGGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:36510 original size:15 final size:15
Alignment explanation
Indices: 36490--36528 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
36480 CAAACCCCTC
*
36490 CCCCTCCCTACCCCA
1 CCCCTCCCCACCCCA
*
36505 CCCCTCCCCACTCCA
1 CCCCTCCCCACCCCA
36520 CCCCTCCCC
1 CCCCTCCCC
36529 CATTTGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.77, G:0.00, T:0.13
Consensus pattern (15 bp):
CCCCTCCCCACCCCA
Found at i:36857 original size:38 final size:38
Alignment explanation
Indices: 36815--36891 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
36805 GAACCGAGAC
36815 AATCCGATTCCTCTTTCTCTTCCCAAAAGAACAATCCA
1 AATCCGATTCCTCTTTCTCTTCCCAAAAGAACAATCCA
36853 AATCCGATTCCTCTTTCTCTTCCCAAAAGAACAATCCA
1 AATCCGATTCCTCTTTCTCTTCCCAAAAGAACAATCCA
36891 A
1 A
36892 TTTCACTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (38 bp):
AATCCGATTCCTCTTTCTCTTCCCAAAAGAACAATCCA
Found at i:45813 original size:72 final size:72
Alignment explanation
Indices: 45720--45948 Score: 275
Period size: 72 Copynumber: 3.2 Consensus size: 72
45710 TCATCACCTG
* ** *
45720 TACAACTTTCGGT-ATTCAAAACTTTTTCCCCTTT-ATTAGTGTCAGCTTCACATGCATCAGATT
1 TACAACTTTCTGTCATT-AAAACTTTTTCTTCTTTGCTT-GTGTCAGCTTCACATGCATCAGATT
* *
45783 CGCCTTCCA
64 CACCTTCAA
* * * *
45792 CACAACTTTCTGTCATTAAAACTCTTTCTTCTTTGCTTGTGTTAGCTTCACATGCATCAGAGTCA
1 TACAACTTTCTGTCATTAAAACTTTTTCTTCTTTGCTTGTGTCAGCTTCACATGCATCAGATTCA
45857 CCTTCAA
66 CCTTCAA
* * * **
45864 TACCA-TGTTCTGTCATCAAAACTTTTTCTTCTTTGCTTGTTTCAGCTTCACAAACATCAGATTC
1 TACAACT-TTCTGTCATTAAAACTTTTTCTTCTTTGCTTGTGTCAGCTTCACATGCATCAGATTC
45928 ACCTTCAA
65 ACCTTCAA
45936 TACAACTTTCTGT
1 TACAACTTTCTGT
45949 TCTCACAACT
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
71 1 0.01
72 126 0.95
73 6 0.05
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (72 bp):
TACAACTTTCTGTCATTAAAACTTTTTCTTCTTTGCTTGTGTCAGCTTCACATGCATCAGATTCA
CCTTCAA
Found at i:46832 original size:15 final size:15
Alignment explanation
Indices: 46809--46838 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46799 AATTTTAATG
46809 CTTTGTTTCTTTTTC
1 CTTTGTTTCTTTTTC
*
46824 CTTTTTTTCTTTTTC
1 CTTTGTTTCTTTTTC
46839 TAGTTATACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
CTTTGTTTCTTTTTC
Found at i:48529 original size:12 final size:12
Alignment explanation
Indices: 48512--48537 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48502 GGCTCCTAAG
48512 ATATTTCTATCT
1 ATATTTCTATCT
48524 ATATTTCTATCT
1 ATATTTCTATCT
48536 AT
1 AT
48538 CTATCTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTTCTATCT
Found at i:54081 original size:20 final size:21
Alignment explanation
Indices: 54056--54097 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
54046 TCTTGGGTTC
54056 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
54076 TACTCTCACGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
54097 T
1 T
54098 TTCTCTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Found at i:68355 original size:37 final size:37
Alignment explanation
Indices: 68305--68376 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
68295 TCAATACAAC
68305 CAATAATTCTACTTTGTACTATTGACATAATTGGAAT
1 CAATAATTCTACTTTGTACTATTGACATAATTGGAAT
68342 CAATAATTCTACTTTGTACTATTGACATAATTGGA
1 CAATAATTCTACTTTGTACTATTGACATAATTGGA
68377 GACAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (37 bp):
CAATAATTCTACTTTGTACTATTGACATAATTGGAAT
Found at i:68612 original size:21 final size:21
Alignment explanation
Indices: 68588--68633 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
68578 ATTGGGATAA
68588 CTTTGCAGACAATTATTTTTC
1 CTTTGCAGACAATTATTTTTC
*
68609 CTTTGCAGACCATTATTTTTC
1 CTTTGCAGACAATTATTTTTC
68630 CTTT
1 CTTT
68634 TTTTTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.50
Consensus pattern (21 bp):
CTTTGCAGACAATTATTTTTC
Done.