Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008242.1 Corchorus capsularis cultivar CVL-1 contig08263, 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: 19406
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:173 original size:20 final size:20
Alignment explanation
Indices: 144--192 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
134 CTTCAAAAGG
*
144 TATAAAATTATTAA-AAATGT
1 TATAATATTATTAATAAAT-T
164 TATAATATTATTAATAAATT
1 TATAATATTATTAATAAATT
184 TAGTAATAT
1 TA-TAATAT
193 CTTACATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAATATTATTAATAAATT
Found at i:1201 original size:6 final size:6
Alignment explanation
Indices: 1190--1224 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1180 GTTTAGACTT
1190 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1225 TTGTGCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:6874 original size:31 final size:31
Alignment explanation
Indices: 6828--6898 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
6818 GGGGAAACAT
*
6828 TATATTTTCCGATTGTACCCTTACTTTTAAAA
1 TATA-TTTCCAATTGTACCCTTACTTTTAAAA
* **
6860 TATATTTCCAATTGTACCTTTTTTTTTAAAA
1 TATATTTCCAATTGTACCCTTACTTTTAAAA
*
6891 CATATTTC
1 TATATTTC
6899 TAAATTGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (31 bp):
TATATTTCCAATTGTACCCTTACTTTTAAAA
Found at i:6957 original size:18 final size:19
Alignment explanation
Indices: 6908--6960 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
6898 CTAAATTGCT
*
6908 ATTACTAAATAATATTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
6928 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
6947 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
6961 CATTACATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:7035 original size:22 final size:22
Alignment explanation
Indices: 7010--7094 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
7000 TCCATGAGGA
* *
7010 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
7032 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
7054 AGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
7076 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
7095 GATCAAGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:7125 original size:46 final size:44
Alignment explanation
Indices: 7011--7148 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
7001 CCATGAGGAG
* * *
7011 GTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGTG-TA
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG-GATA
7055 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATCAA
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGAT--A
** * *** *
7101 GTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCATAGGATG
1 GTTACCAAAATTTCATAGAG-TGGTTACCAAAATTTCATAGGATA
7145 GTTA
1 GTTA
7149 ATTATCACAA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 42 0.52
45 1 0.01
46 36 0.45
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATA
Found at i:7133 original size:22 final size:22
Alignment explanation
Indices: 6987--7148 Score: 107
Period size: 22 Copynumber: 7.3 Consensus size: 22
6977 TATTTTACTT
* *
6987 TGGTTATTATAATTCCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
* *
7010 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
7031 TGGTTACCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
* **
7053 TAGTTACCAAAATTTCATA-GA
1 TGGTTATTAAAATTTCATAGGA
**
7074 GTGGTTACCAAAATTTCATAGGA
1 -TGGTTATTAAAATTTCATAGGA
* * *
7097 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGA
*
7121 TGGTTATTGAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
7143 TGGTTA
1 TGGTTA
7149 ATTATCACAA
Statistics
Matches: 117, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 95 0.81
23 2 0.02
24 17 0.15
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:7284 original size:19 final size:19
Alignment explanation
Indices: 7262--7317 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
7252 TTAAAATTTT
*
7262 AGGGAGGATACCAAAATTC
1 AGGGAGGATATCAAAATTC
7281 AGGGAGGATATCAAAATTC
1 AGGGAGGATATCAAAATTC
*
7300 AGTGAGGATATCAAAATT
1 AGGGAGGATATCAAAATT
7318 TCATATGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (19 bp):
AGGGAGGATATCAAAATTC
Found at i:7336 original size:22 final size:22
Alignment explanation
Indices: 7308--7935 Score: 174
Period size: 22 Copynumber: 28.7 Consensus size: 22
7298 TCAGTGAGGA
7308 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
7330 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7352 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
7374 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
7395 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
7418 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
7440 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
7462 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
7478 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
7500 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
7523 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* *
7546 TATCGAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
7568 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7590 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
7613 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* *
7636 TATCGAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
7658 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
7680 TATCAAAATTTTAAAATG-TGAT
1 TATCAAAA-TTTCATATGAAGGT
*
7702 TA-CTAACAA-TTCATATGTAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
7724 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
7746 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
7768 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
7791 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
7813 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
7835 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
7857 T-TAAAAATTTTATA-AAAGGAT
1 TATCAAAATTTCATATGAAGG-T
* ** * **
7878 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
7900 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
7921 TATCAAAATTTCATA
1 TATCAAAATTTCATA
7936 ATGGGGTCAT
Statistics
Matches: 443, Mismatches: 123, Indels: 81
0.68 0.19 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.00
18 2 0.00
20 11 0.02
21 49 0.11
22 257 0.58
23 108 0.24
24 6 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:7530 original size:23 final size:23
Alignment explanation
Indices: 7499--7692 Score: 144
Period size: 23 Copynumber: 8.6 Consensus size: 23
7489 CATAAGAAAG
7499 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* ** *
7522 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * *
7545 TTATCGAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
7567 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
7589 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* ** *
7612 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * *
7635 TTATCGAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
7657 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
7679 TTATCAAAATTTTA
1 TTATCAAAATTTTA
7693 AAATGTGATT
Statistics
Matches: 133, Mismatches: 35, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
21 2 0.02
22 60 0.45
23 71 0.53
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:7608 original size:90 final size:90
Alignment explanation
Indices: 7499--7692 Score: 388
Period size: 90 Copynumber: 2.2 Consensus size: 90
7489 CATAAGAAAG
7499 TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATTTATCGAAATTTCATAGCG
1 TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATTTATCGAAATTTCATAGCG
7564 AGGTTATCACAATTTCATAGTGTGA
66 AGGTTATCACAATTTCATAGTGTGA
7589 TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATTTATCGAAATTTCATAGCG
1 TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATTTATCGAAATTTCATAGCG
7654 AGGTTATCACAATTTCATAGTGTGA
66 AGGTTATCACAATTTCATAGTGTGA
7679 TTATCAAAATTTTA
1 TTATCAAAATTTTA
7693 AAATGTGATT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 104 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (90 bp):
TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATTTATCGAAATTTCATAGCG
AGGTTATCACAATTTCATAGTGTGA
Found at i:8099 original size:15 final size:15
Alignment explanation
Indices: 8079--8110 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8069 ATGATTAGTA
8079 AATGTGGTTTAAAAT
1 AATGTGGTTTAAAAT
8094 AATGTGGTTTAAAAT
1 AATGTGGTTTAAAAT
8109 AA
1 AA
8111 GTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (15 bp):
AATGTGGTTTAAAAT
Found at i:12115 original size:29 final size:30
Alignment explanation
Indices: 12073--12132 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
12063 TAATCCTCTC
12073 GCCTGATTATTTAGAACG-TATGATTTTCT
1 GCCTGATTATTTAGAACGCTATGATTTTCT
12102 GCCTGATTATTTAGAACGTCTATGATTTTCT
1 GCCTGATTATTTAGAACG-CTATGATTTTCT
12133 TCAACGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 18 0.62
31 11 0.38
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (30 bp):
GCCTGATTATTTAGAACGCTATGATTTTCT
Found at i:12623 original size:21 final size:21
Alignment explanation
Indices: 12599--12643 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
12589 TGTTTTCTGT
12599 AGATCGGCTGGAATTTGATGA
1 AGATCGGCTGGAATTTGATGA
12620 AGATCGGCTGGAATTTGATGA
1 AGATCGGCTGGAATTTGATGA
12641 AGA
1 AGA
12644 GAAAACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.27
Consensus pattern (21 bp):
AGATCGGCTGGAATTTGATGA
Found at i:16788 original size:2 final size:2
Alignment explanation
Indices: 16771--16810 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
16761 CAACAAGTTC
*
16771 AT AT -T AT AT A- AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16811 CTTCAGTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18101 original size:6 final size:6
Alignment explanation
Indices: 18090--18114 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18080 CCAATGGAAG
18090 ACTAGT ACTAGT ACTAGT ACTAGT A
1 ACTAGT ACTAGT ACTAGT ACTAGT A
18115 TTTATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ACTAGT
Found at i:19358 original size:2 final size:2
Alignment explanation
Indices: 19351--19379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19341 TTGTAGTTAT
19351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19380 TACTAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.