Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012775.1 Corchorus capsularis cultivar CVL-1 contig12796, 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: 26263
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Found at i:2225 original size:27 final size:27
Alignment explanation
Indices: 2143--2225 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
2133 ATGAAAAGAC
* *
2143 ATTAATGAATAATGTGATTAATCATGA
1 ATTAATTAATAATGTGATTATTCATGA
** *
2170 ACCAATTAATAGTGTGATTATTCATGA
1 ATTAATTAATAATGTGATTATTCATGA
* *
2197 ATTAATTAATATTGTAATTATTCATGA
1 ATTAATTAATAATGTGATTATTCATGA
2224 AT
1 AT
2226 CAAGAGTTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (27 bp):
ATTAATTAATAATGTGATTATTCATGA
Found at i:7054 original size:27 final size:27
Alignment explanation
Indices: 7023--7080 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
7013 TACATTAATG
7023 AATAATGTGATTATTCATGAATCAATT
1 AATAATGTGATTATTCATGAATCAATT
*
7050 AATAATGTGATTATTCATGAATTAATT
1 AATAATGTGATTATTCATGAATCAATT
7077 AATA
1 AATA
7081 TTGTTGGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (27 bp):
AATAATGTGATTATTCATGAATCAATT
Found at i:7157 original size:135 final size:135
Alignment explanation
Indices: 6947--7219 Score: 528
Period size: 135 Copynumber: 2.0 Consensus size: 135
6937 TAGTGGGGAC
6947 TGTTGGTAGTTTAGAATGTTGGTAAGTAAATATGATATTTACCAATGATAATTTAGTTGATGAAA
1 TGTTGGTAGTTTAGAATGTTGGTAAGTAAATATGATATTTACCAATGATAATTTAGTTGATGAAA
* *
7012 ATACATTAATGAATAATGTGATTATTCATGAATCAATTAATAATGTGATTATTCATGAATTAATT
66 AGACATTAATGAATAATGTGATTATTCATGAATCAATTAATAATGTGATTATTCATGAATTAATA
7077 AATAT
131 AATAT
7082 TGTTGGTAGTTTAGAATGTTGGTAAGTAAATATGATATTTACCAATGATAATTTAGTTGATGAAA
1 TGTTGGTAGTTTAGAATGTTGGTAAGTAAATATGATATTTACCAATGATAATTTAGTTGATGAAA
7147 AGACATTAATGAATAATGTGATTATTCATGAATCAATTAATAATGTGATTATTCATGAATTAATA
66 AGACATTAATGAATAATGTGATTATTCATGAATCAATTAATAATGTGATTATTCATGAATTAATA
7212 AATAT
131 AATAT
7217 TGT
1 TGT
7220 AATTATTCAT
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.40
Consensus pattern (135 bp):
TGTTGGTAGTTTAGAATGTTGGTAAGTAAATATGATATTTACCAATGATAATTTAGTTGATGAAA
AGACATTAATGAATAATGTGATTATTCATGAATCAATTAATAATGTGATTATTCATGAATTAATA
AATAT
Found at i:7189 original size:27 final size:27
Alignment explanation
Indices: 7158--7236 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
7148 GACATTAATG
*
7158 AATAATGTGATTATTCATGAATCAATT
1 AATAATGTGATTATTCATGAATCAATA
*
7185 AATAATGTGATTATTCATGAATTAATA
1 AATAATGTGATTATTCATGAATCAATA
* *
7212 AATATTGTAATTATTCATGAATCAA
1 AATAATGTGATTATTCATGAATCAA
7237 GAGTTGTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (27 bp):
AATAATGTGATTATTCATGAATCAATA
Found at i:10550 original size:16 final size:16
Alignment explanation
Indices: 10520--10560 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
10510 AGTTATATCG
* *
10520 AAAAATATAAAAAATA
1 AAAAAAATAAAAATTA
10536 AAATAAAATAAAAATTA
1 AAA-AAAATAAAAATTA
10553 AAAAAAAT
1 AAAAAAAT
10561 TCGTGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAAATAAAAATTA
Found at i:20482 original size:18 final size:18
Alignment explanation
Indices: 20461--20497 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20451 AATTTCTGAA
20461 TTTTT-TTTAAAACTTTT
1 TTTTTCTTTAAAACTTTT
*
20478 TTTTTCTTTAAACCTTTT
1 TTTTTCTTTAAAACTTTT
20496 TT
1 TT
20498 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTCTTTAAAACTTTT
Found at i:22249 original size:16 final size:17
Alignment explanation
Indices: 22220--22252 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22210 TTAAATATTC
*
22220 TTTTATTATTTTTTTAA
1 TTTTATTATATTTTTAA
22237 TTTT-TTATATTTTTAA
1 TTTTATTATATTTTTAA
22253 ACCGGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTATATTTTTAA
Found at i:22294 original size:31 final size:31
Alignment explanation
Indices: 22256--22324 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
22246 TTTTTAAACC
22256 GGCTCAAATAGGTACTAAAAGTTTCAAAATT
1 GGCTCAAATAGGTACTAAAAGTTTCAAAATT
* *
22287 GGCTCAAATAGGTACTGAATGTTTCAAAATT
1 GGCTCAAATAGGTACTAAAAGTTTCAAAATT
*
22318 GGATCAA
1 GGCTCAA
22325 TTCAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (31 bp):
GGCTCAAATAGGTACTAAAAGTTTCAAAATT
Found at i:25768 original size:429 final size:434
Alignment explanation
Indices: 24994--26016 Score: 1131
Period size: 429 Copynumber: 2.3 Consensus size: 434
24984 TTGCCTTTTA
* * *
24994 TTTTTGTTTT-TTTTTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTTAA-AT
1 TTTTTATTTTCTTTCTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGG-TAATTT
* * * * * *
25057 CATGATCTA-CGATTTTCATTAAGAACTCAAAAGTCAATTTTAATATCTTGATTCTAAAAAATGC
65 CATGATCTATAG-CTTTCATGAAG-ACTCAAAAG-CAATTTTTATAT-TTCAATCTAAAAAATGC
* * * * **
25121 TTCCGAAATTTTGTGGTTTTGATTGCCGGTTTATTTAATATCGTATAATTTTTTTTCCACATGTC
126 TTCCGAAATTTTGTCGTTTCGATTGCCGGTCTATTTAATATAGTATAATTTTCGTTCCACATGTC
* * * * * * * * * * *
25186 CGATTGAAGTTATTGAAGTGTTGGTTAAAAGATTATTGCATGATTTACGACTTTCATGAAGGATC
191 CAATTAAAGTTATTCAAGTGTCGATTAAAAGATTACTGCATAATCTACGACATTCATGAAGAACC
* *
25251 CAAAAGTTAAATTTGATCTATGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT
256 CAAAAGTTAAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTCTTATGTTTCAAGAT
* ** * *
25316 ATCCATTAACAAACATATTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTA
321 ATCCATTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTCCTACTTTA
25381 TACTACTCAGTCCTTAACAAATTCTATCTTA-ATCT-A-A-TGT-TTAAG
386 TACTACTCAGTCCTTAACAAATTCTATCTTAGATCTAACACT-TATTAAG
* * * *
25426 TTTTT-TTTTCTTTGTTCTATTTGTCTGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTC
1 TTTTTATTTTCTTTCTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTC
*
25490 ATGATCTATAGCTTTCATGAATGACGCAAAAGCAAATTTTTATATTTCAAT-TAAAAAATGCTTC
66 ATGATCTATAGCTTTCATGAA-GACTCAAAAGC-AATTTTTATATTTCAATCTAAAAAATGCTTC
* **
25554 CTAAA-TTTGTTCGTTTCGATTGTTGGTCTATTTAATA-AGATATAATTTTCGTTCCACATGTCC
129 CGAAATTTTG-TCGTTTCGATTGCCGGTCTATTTAATATAG-TATAATTTTCGTTCCACATGTCC
* *
25617 AATTAAAGTTATTCTAGTGTCGATTAAAATG-TTACTGTATAATCTACGACATTCATGAAGAACC
192 AATTAAAGTTATTCAAGTGTCGATTAAAA-GATTACTGCATAATCTACGACATTCATGAAGAACC
*
25681 CCAAAGTT-AATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTCTTATGTTTCAAGAT
256 CAAAAGTTAAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTCTTATGTTTCAAGAT
* * * * *
25745 TTCCATTAACATATATTTTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTCCTATTTTA
321 ATCCATTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTCCTACTTTA
* * * ** * ***
25810 TGCTACTTATTCCTTGCCAAATTCTATCTTAGTCGATTTAACACTTCATTTTT
386 TACTACTCAGTCCTTAACAAATTCTATCTTA---GATCTAACACTT-ATTAAG
* * * * *
25863 TTTTTAATTTTCTTTCTTCTATTTGTCCAATTATGGTAATTCAAGTGTTTATTAAAAGGTAATTT
1 TTTTT-ATTTTCTTTCTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTT
* * * * *
25928 TAAGATCTATAACTCTCATGAAAGACTCAAATGCTAATTTTTATATTTCAATTCTAAAAAATGCT
65 CATGATCTATAGCTTTCATG-AAGACTCAAAAGC-AATTTTTATATTTCAA-TCTAAAAAATGCT
**
25993 TTTGAAATTTTGT-GATTTCGATTG
127 TCCGAAATTTTGTCG-TTTCGATTG
26017 ACAATTTATT
Statistics
Matches: 493, Mismatches: 74, Indels: 39
0.81 0.12 0.06
Matches are distributed among these distances:
429 140 0.28
430 116 0.24
431 13 0.03
432 84 0.17
433 5 0.01
434 1 0.00
435 2 0.00
436 1 0.00
437 7 0.01
439 91 0.18
440 4 0.01
441 25 0.05
442 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (434 bp):
TTTTTATTTTCTTTCTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTC
ATGATCTATAGCTTTCATGAAGACTCAAAAGCAATTTTTATATTTCAATCTAAAAAATGCTTCCG
AAATTTTGTCGTTTCGATTGCCGGTCTATTTAATATAGTATAATTTTCGTTCCACATGTCCAATT
AAAGTTATTCAAGTGTCGATTAAAAGATTACTGCATAATCTACGACATTCATGAAGAACCCAAAA
GTTAAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTCTTATGTTTCAAGATATCCA
TTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTCCTACTTTATACTA
CTCAGTCCTTAACAAATTCTATCTTAGATCTAACACTTATTAAG
Done.