Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004886.1 Corchorus capsularis cultivar CVL-1 contig04904, 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: 8548
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--45 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
***
1 TTTTTTTTTTTTTTTTTGCCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46 CTGTCTGTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.04, G:0.02, T:0.93
Consensus pattern (1 bp):
T
Found at i:72 original size:20 final size:21
Alignment explanation
Indices: 43--81 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33 TTTTTTTTTT
*
43 TTTCTGTCTG-TTATCTTCTG
1 TTTCTCTCTGTTTATCTTCTG
63 TTTCTCTCTGTTTATCTTC
1 TTTCTCTCTGTTTATCTTC
82 AACTTCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.05, C:0.23, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTCTCTCTGTTTATCTTCTG
Found at i:4292 original size:22 final size:21
Alignment explanation
Indices: 4266--4321 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
4256 AAGAAATAGG
4266 AAGGAAAGGAAGTAGCAAGGGA
1 AAGGAAAGGAAGTAGCAA-GGA
* *
4288 AAGGAAAGGAAATAGGAAGGA
1 AAGGAAAGGAAGTAGCAAGGA
* *
4309 AGGGAGAGGAAGT
1 AAGGAAAGGAAGT
4322 CATATTTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.43, T:0.05
Consensus pattern (21 bp):
AAGGAAAGGAAGTAGCAAGGA
Found at i:6789 original size:22 final size:21
Alignment explanation
Indices: 6758--6921 Score: 102
Period size: 22 Copynumber: 7.6 Consensus size: 21
6748 AATCACTATC
*
6758 AAATTGTGATAACCTCATTATA
1 AAATTTTGATAACCTC-TTATA
*
6780 AAATTTTGATAAACCTCTCTGTA
1 AAATTTTGAT-AACCTCT-TATA
*
6803 AAATTTTGATAATCCTCTTTTGA
1 AAATTTTGATAA-CCTCTTAT-A
* *
6826 AAA-TTTGATAA--TCTCATG
1 AAATTTTGATAACCTCTTATA
** * *
6844 AAATTTCAATAACCACCTCATA
1 AAATTTTGATAACC-TCTTATA
*
6866 AAATTTTGATAA-CTACCTTATG
1 AAATTTTGATAACCT--CTTATA
* *
6888 AAATTTTGATAACCTCCTATG
1 AAATTTTGATAACCTCTTATA
* *
6909 AATTTTTTATAAC
1 AAATTTTGATAAC
6922 ATCCTTACGG
Statistics
Matches: 113, Mismatches: 18, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.03
19 10 0.09
21 17 0.15
22 53 0.47
23 30 0.27
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAACCTCTTATA
Found at i:6804 original size:23 final size:22
Alignment explanation
Indices: 6758--6836 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
6748 AATCACTATC
* *
6758 AAATTGTGAT-AACCTCATTATA
1 AAATTTTGATAAACCTC-TTGTA
6780 AAATTTTGATAAACCTCTCTGTA
1 AAATTTTGATAAACCTCT-TGTA
* *
6803 AAATTTTGATAATCCTCTTTTGA
1 AAATTTTGATAAACCTCTTGT-A
6826 AAA-TTTGATAA
1 AAATTTTGATAA
6837 TCTCATGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 20 0.40
23 30 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAAACCTCTTGTA
Found at i:7001 original size:22 final size:22
Alignment explanation
Indices: 6954--7031 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
6944 CTCCCTACGA
* *
6954 AATTTTGAAAACTGTACTAT-T
1 AATTTTGATAACTCTACTATGT
6975 AAATTTTGATAACTCTACTATGT
1 -AATTTTGATAACTCTACTATGT
** * *
6998 AATTACGATAAC-CTCCTTGTGT
1 AATTTTGATAACTCTAC-TATGT
7020 AATTTTGATAAC
1 AATTTTGATAAC
7032 CAAACTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.07
22 42 0.91
23 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
AATTTTGATAACTCTACTATGT
Found at i:7032 original size:22 final size:21
Alignment explanation
Indices: 6867--7032 Score: 68
Period size: 22 Copynumber: 7.6 Consensus size: 21
6857 CACCTCATAA
*
6867 AATTTTGATAA-CTACCTTATGA
1 AATTTTGATAACCTA-C-TATGT
*
6889 AATTTTGATAACCTCCTATG-
1 AATTTTGATAACCTACTATGT
* * * * *
6909 AATTTTTTATAACATCCTTACGG
1 AA-TTTTGATAACCTAC-TATGT
* * * * *
6932 AATTTTGTTAATCTCCCTACGA
1 AATTTTGATAACCT-ACTATGT
* *
6954 AATTTTGAAAACTGTACTAT-T
1 AATTTTGATAAC-CTACTATGT
6975 AAATTTTGATAACTCTACTATGT
1 -AATTTTGATAAC-CTACTATGT
** * *
6998 AATTACGATAACCTCCTTGTGT
1 AATTTTGATAACCTAC-TATGT
7020 AATTTTGATAACC
1 AATTTTGATAACC
7033 AAACTATCAA
Statistics
Matches: 111, Mismatches: 24, Indels: 18
0.73 0.16 0.12
Matches are distributed among these distances:
20 2 0.02
21 19 0.17
22 82 0.74
23 8 0.07
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (21 bp):
AATTTTGATAACCTACTATGT
Found at i:7053 original size:22 final size:22
Alignment explanation
Indices: 7028--7069 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7018 GTAATTTTGA
*
7028 TAACCAAACTATCAAATTTATT
1 TAACCAAACTAACAAATTTATT
* *
7050 TAACCATACTAAGAAATTTA
1 TAACCAAACTAACAAATTTA
7070 GATTACCCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (22 bp):
TAACCAAACTAACAAATTTATT
Found at i:7135 original size:22 final size:22
Alignment explanation
Indices: 7103--7161 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
7093 ATAACATCCC
*
7103 TCTTAAAAACCACACTATGAAA
1 TCTTAATAACCACACTATGAAA
* *
7125 TCTTAATAACCATATTATGAAA
1 TCTTAATAACCACACTATGAAA
* * *
7147 TTTTGATAATCACAC
1 TCTTAATAACCACAC
7162 AATAAAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (22 bp):
TCTTAATAACCACACTATGAAA
Found at i:8171 original size:21 final size:22
Alignment explanation
Indices: 8147--8194 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8137 GAATTTCGAG
* *
8147 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATGAAATTTTGTT
*
8168 AACCTTCTTGTGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
8190 AACCT
1 AACCT
8195 CTAAGGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:8533 original size:22 final size:22
Alignment explanation
Indices: 8178--8533 Score: 111
Period size: 22 Copynumber: 16.4 Consensus size: 22
8168 AACCTTCTTG
*
8178 TGAAATTTTGTTAACCT--CTA
1 TGAAATTTTGATAACCTCACTA
* * * *
8198 AGGAATTTTGA-AGATCTCAATA
1 TGAAATTTTGATA-ACCTCACTA
**
8220 TGAAATTTTGATAATTTGC-C-A
1 TGAAATTTTGATAACCT-CACTA
*
8241 CTGAAATTTTGATAACCAACACTA
1 -TGAAATTTTGATAACC-TCACTA
*
8265 T-AAGATGTTGATAACCTC-CATA
1 TGAA-ATTTTGATAACCTCAC-TA
* * **
8287 TGACATTTTGATAACCACGTTA
1 TGAAATTTTGATAACCTCACTA
** * * *
8309 CAAAAATTTAAAAACCTTCA-TA
1 TGAAATTTTGATAACC-TCACTA
* * *
8331 TG-AATTGTT-AGTAATCACACTC
1 TGAAATT-TTGA-TAACCTCACTA
* *
8353 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCACTA
* * *
8375 TGAAATTGTGATAATCTCGCTA
1 TGAAATTTTGATAACCTCACTA
*
8397 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AA-CCTCACTA
* *
8420 T-AAGATTTTAATAAACCTCCCTA
1 TGAA-ATTTTGAT-AACCTCACTA
* * *
8443 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAAC-CTCACTA
*
8465 TGAAATCTTGATAA-CT-AC--
1 TGAAATTTTGATAACCTCACTA
*
8483 --AAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCACTA
** * *
8503 TGATTTTTTGATAACCTTATTA
1 TGAAATTTTGATAACCTCACTA
8525 TGAAATTTT
1 TGAAATTTT
8534 TTAATCTCCA
Statistics
Matches: 246, Mismatches: 58, Indels: 62
0.67 0.16 0.17
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
19 1 0.00
20 12 0.05
21 8 0.03
22 155 0.63
23 51 0.21
24 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Done.