Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008679.1 Corchorus capsularis cultivar CVL-1 contig08700, 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: 33684
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:3127 original size:31 final size:29
Alignment explanation
Indices: 3063--3127 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
3053 TGTGGGGCTT
* *
3063 ATTTATCCCAAAAAATAGATAAGGGGCAG
1 ATTTGTCCCAAAAAATAGATAAGGGCCAG
*
3092 ATTTGTCCCAAAATCAATAGTTAGAGGGCCA-
1 ATTTGTCCCAAAA--AATAGATA-AGGGCCAG
3123 ATTTG
1 ATTTG
3128 GGCATTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 12 0.40
31 12 0.40
32 6 0.20
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (29 bp):
ATTTGTCCCAAAAAATAGATAAGGGCCAG
Found at i:7499 original size:29 final size:29
Alignment explanation
Indices: 7453--7509 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
7443 GGATCAAATG
* *
7453 GCATCTTCATGAGGCTTTGCGATTCCATA
1 GCATCTCCATGAGACTTTGCGATTCCATA
7482 GCATCTCCATGAGACTTTGCGATTCCAT
1 GCATCTCCATGAGACTTTGCGATTCCAT
7510 CCTCTCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (29 bp):
GCATCTCCATGAGACTTTGCGATTCCATA
Found at i:11334 original size:487 final size:487
Alignment explanation
Indices: 10421--11398 Score: 1938
Period size: 487 Copynumber: 2.0 Consensus size: 487
10411 AGTCAATCCA
10421 TTCAATAAATGTGACAGCTAGAGTCAAACTTATCATCATACAACTTGCAAAATAGCAGGCACCAC
1 TTCAATAAATGTGACAGCTAGAGTCAAACTTATCATCATACAACTTGCAAAATAGCAGGCACCAC
10486 AGCATGACTCCCTTAATTGTCCGCATTTGATAGCAACAGTAGGATATAAGCTAATGAATTGCTGA
66 AGCATGACTCCCTTAATTGTCCGCATTTGATAGCAACAGTAGGATATAAGCTAATGAATTGCTGA
10551 AAATTTATAATAACATCATTTGTTCATTAAATTCTAAAAGAAACCGACTTATCATATATACTCAA
131 AAATTTATAATAACATCATTTGTTCATTAAATTCTAAAAGAAACCGACTTATCATATATACTCAA
10616 GAAACTATTTTAACATGCATGCTTTTATGATCCTATTATGTACAAATTTACACTGTTCACTTAGT
196 GAAACTATTTTAACATGCATGCTTTTATGATCCTATTATGTACAAATTTACACTGTTCACTTAGT
10681 AGGATCTGCACAAGAAAAAGCATAGCTGGAACACTTCCAGTCAAGTGATACAGTACCATGAGTAA
261 AGGATCTGCACAAGAAAAAGCATAGCTGGAACACTTCCAGTCAAGTGATACAGTACCATGAGTAA
*
10746 TGCACATGTTTGATGCAAATAAGACTAGCATATACAATTGGTTATATGATTGTCTCTATATTTCA
326 TGCACATGTTTGATGCAAATAAGACTAGCATATACAATTGGTTATATGATTGTCTATATATTTCA
10811 ATATAAGTCAAAATCTAACTATATACATTCATATATGAATTAATGTTAAGGAAAAAATAGCATAT
391 ATATAAGTCAAAATCTAACTATATACATTCATATATGAATTAATGTTAAGGAAAAAATAGCATAT
10876 CATAGACTAATATATAATGTATACAAAGAAAT
456 CATAGACTAATATATAATGTATACAAAGAAAT
*
10908 TTCAATAAATGTGACAGCTAGAGTCAAACTTATCATCATACAACTTGCAAAATAGCAGGCACCAT
1 TTCAATAAATGTGACAGCTAGAGTCAAACTTATCATCATACAACTTGCAAAATAGCAGGCACCAC
10973 AGCATGACTCCCTTAATTGTCCGCATTTGATAGCAACAGTAGGATATAAGCTAATGAATTGCTGA
66 AGCATGACTCCCTTAATTGTCCGCATTTGATAGCAACAGTAGGATATAAGCTAATGAATTGCTGA
11038 AAATTTATAATAACATCATTTGTTCATTAAATTCTAAAAGAAACCGACTTATCATATATACTCAA
131 AAATTTATAATAACATCATTTGTTCATTAAATTCTAAAAGAAACCGACTTATCATATATACTCAA
11103 GAAACTATTTTAACATGCATGCTTTTATGATCCTATTATGTACAAATTTACACTGTTCACTTAGT
196 GAAACTATTTTAACATGCATGCTTTTATGATCCTATTATGTACAAATTTACACTGTTCACTTAGT
11168 AGGATCTGCACAAGAAAAAGCATAGCTGGAACACTTCCAGTCAAGTGATACAGTACCATGAGTAA
261 AGGATCTGCACAAGAAAAAGCATAGCTGGAACACTTCCAGTCAAGTGATACAGTACCATGAGTAA
11233 TGCACATGTTTGATGCAAATAAGACTAGCATATACAATTGGTTATATGATTGTCTATATATTTCA
326 TGCACATGTTTGATGCAAATAAGACTAGCATATACAATTGGTTATATGATTGTCTATATATTTCA
11298 ATATAAGTCAAAATCTAACTATATACATTCATATATGAATTAATGTTAAGGAAAAAATAGCATAT
391 ATATAAGTCAAAATCTAACTATATACATTCATATATGAATTAATGTTAAGGAAAAAATAGCATAT
11363 CATAGACTAATATATAATGTATACAAAGAAAT
456 CATAGACTAATATATAATGTATACAAAGAAAT
11395 TTCA
1 TTCA
11399 TGTAATGAGT
Statistics
Matches: 489, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
487 489 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (487 bp):
TTCAATAAATGTGACAGCTAGAGTCAAACTTATCATCATACAACTTGCAAAATAGCAGGCACCAC
AGCATGACTCCCTTAATTGTCCGCATTTGATAGCAACAGTAGGATATAAGCTAATGAATTGCTGA
AAATTTATAATAACATCATTTGTTCATTAAATTCTAAAAGAAACCGACTTATCATATATACTCAA
GAAACTATTTTAACATGCATGCTTTTATGATCCTATTATGTACAAATTTACACTGTTCACTTAGT
AGGATCTGCACAAGAAAAAGCATAGCTGGAACACTTCCAGTCAAGTGATACAGTACCATGAGTAA
TGCACATGTTTGATGCAAATAAGACTAGCATATACAATTGGTTATATGATTGTCTATATATTTCA
ATATAAGTCAAAATCTAACTATATACATTCATATATGAATTAATGTTAAGGAAAAAATAGCATAT
CATAGACTAATATATAATGTATACAAAGAAAT
Found at i:17236 original size:2 final size:2
Alignment explanation
Indices: 17214--17254 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
17204 AGATGCGATT
17214 TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA 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
17253 TA
1 TA
17255 CCTAATGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:18979 original size:22 final size:23
Alignment explanation
Indices: 18891--18983 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 23
18881 AACCCTAAAC
*
18891 ATAACGTTAAGAATTTAATATAT
1 ATAACATTAAGAATTTAATATAT
*
18914 ATAATC-TTAAGAATTAAATATAACATTAT
1 ATAA-CATTAAGAA-T---T-TAATA-TAT
18943 ATAACATTAAGAATTTAATATAT
1 ATAACATTAAGAATTTAATATAT
18966 ATAACATT-AGAATTTAAT
1 ATAACATTAAGAATTTAAT
18984 TTACATAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
22 10 0.17
23 22 0.37
24 6 0.10
25 1 0.02
27 1 0.02
28 6 0.10
29 14 0.23
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (23 bp):
ATAACATTAAGAATTTAATATAT
Found at i:19033 original size:15 final size:15
Alignment explanation
Indices: 18998--19036 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
18988 ATAATGTTAA
*
18998 AAATAAATAACAATT
1 AAATATATAACAATT
19013 AAATATATAAC-ATT
1 AAATATATAACAATT
19027 -AATATATAAC
1 AAATATATAAC
19037 GTCAGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATATAACAATT
Found at i:19218 original size:2 final size:2
Alignment explanation
Indices: 19211--19257 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
19201 CCAAAAATAC
* *
19211 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AG AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19252 AT AT AT
1 AT AT AT
19258 TGTCTTCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20852 original size:23 final size:23
Alignment explanation
Indices: 20822--20865 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20812 CACTTGAATG
20822 GTGCATTCTTCTTCATCACACTT
1 GTGCATTCTTCTTCATCACACTT
*
20845 GTGCATTCTTCTTCATTACAC
1 GTGCATTCTTCTTCATCACAC
20866 CACAAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.43
Consensus pattern (23 bp):
GTGCATTCTTCTTCATCACACTT
Found at i:22136 original size:182 final size:182
Alignment explanation
Indices: 21829--22195 Score: 725
Period size: 182 Copynumber: 2.0 Consensus size: 182
21819 AAATCCTCTT
21829 TCAATTTCAATTGATCTTTTAAAGCTTCTTGAGGTGATAAAGGAATCAAAGTAATAAGATGCTTA
1 TCAATTTCAATTGATCTTTTAAAGCTTCTTGAGGTGATAAAGGAATCAAAGTAATAAGATGCTTA
21894 CCATAAACAAAAGAATACTTATTTGTCTCACCATCATGATGGACCTTGTTGTCATATTGCCATGG
66 CCATAAACAAAAGAATACTTATTTGTCTCACCATCATGATGGACCTTGTTGTCATATTGCCATGG
21959 TCGACCAAGTAAAACATGGCATGCTTGCATTGGAAGAACATCACATAGCACC
131 TCGACCAAGTAAAACATGGCATGCTTGCATTGGAAGAACATCACATAGCACC
22011 TCAATTTCAATTGATCTTTTAAAGCTTCTTGAGGTGATAAAGGAATCAAAGTAATAAGATGCTTA
1 TCAATTTCAATTGATCTTTTAAAGCTTCTTGAGGTGATAAAGGAATCAAAGTAATAAGATGCTTA
*
22076 CCATAAACAAAAGAATACTTGTTTGTCTCACCATCATGATGGACCTTGTTGTCATATTGCCATGG
66 CCATAAACAAAAGAATACTTATTTGTCTCACCATCATGATGGACCTTGTTGTCATATTGCCATGG
22141 TCGACCAAGTAAAACATGGCATGCTTGCATTGGAAGAACATCACATAGCACC
131 TCGACCAAGTAAAACATGGCATGCTTGCATTGGAAGAACATCACATAGCACC
22193 TCA
1 TCA
22196 TCCTTGTACC
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 184 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (182 bp):
TCAATTTCAATTGATCTTTTAAAGCTTCTTGAGGTGATAAAGGAATCAAAGTAATAAGATGCTTA
CCATAAACAAAAGAATACTTATTTGTCTCACCATCATGATGGACCTTGTTGTCATATTGCCATGG
TCGACCAAGTAAAACATGGCATGCTTGCATTGGAAGAACATCACATAGCACC
Found at i:26168 original size:126 final size:120
Alignment explanation
Indices: 25931--26172 Score: 324
Period size: 126 Copynumber: 1.9 Consensus size: 120
25921 CTCTTATTAG
* *
25931 GCCTATTGAAGCTAGTAAAAGGCATAATCTTGTGAGATCATTAAGAGAGTAGTGGATCGCCAATC
1 GCCTATTGAAGCTAGTAAAAGGCATAATCTTGTGAGATCATCAAGAGAGTAGTGGACCGCCAATC
*
25996 CATAGGTTGAGTGTAAACACGAGAGCACAAAGGTATACACACACACACACACACTTGTGA
66 CATAGGTTGAGTGAAAACACGAGAGCACAAAGGTAT----A-ACACACACACACTTGTGA
*
26056 GCCTATTGAAAGCTAGTAAAAGGCATAATCTTGTGAGATCATCAAGAGAGTAGTGGACCGCCATT
1 GCCTATTG-AAGCTAGTAAAAGGCATAATCTTGTGAGATCATCAAGAGAGTAGTGGACCGCCAAT
*
26121 CCATAAGATTTGAGTGCAAAACACGAGAGCACAATCAAGGTAT-ACACACACA
65 CCAT-AG-GTTGAGTG-AAAACACGAGAGCAC-A--AAGGTATAACACACACA
26173 GTATTTGTGA
Statistics
Matches: 105, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
125 8 0.08
126 66 0.63
127 2 0.02
128 7 0.07
129 14 0.13
130 1 0.01
132 7 0.07
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (120 bp):
GCCTATTGAAGCTAGTAAAAGGCATAATCTTGTGAGATCATCAAGAGAGTAGTGGACCGCCAATC
CATAGGTTGAGTGAAAACACGAGAGCACAAAGGTATAACACACACACACTTGTGA
Found at i:30236 original size:33 final size:33
Alignment explanation
Indices: 30194--30272 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
30184 AGCACTTGTG
30194 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
*
30227 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
*
30260 ATCGGCCACGCGA
1 ACCGGCCACGCGA
30273 AATGACCATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.39, G:0.29, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGACCATC
Found at i:30284 original size:33 final size:33
Alignment explanation
Indices: 30194--30290 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
30184 AGCACTTGTG
** * *
30194 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
1 ACCGGCCACGCGAAATGGACATGCCCGGCCATC
** *
30227 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGAAATGGACATGCCCGGCCATC
*
30260 ATCGGCCACGCGAAAT-GACCATGCCCGGCCA
1 ACCGGCCACGCGAAATGGA-CATGCCCGGCCA
30291 CAATCGGTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 2 0.03
33 56 0.97
ACGTcount: A:0.22, C:0.39, G:0.28, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGAAATGGACATGCCCGGCCATC
Done.