Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010690.1 Corchorus capsularis cultivar CVL-1 contig10711, 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: 76176
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:25480 original size:25 final size:27
Alignment explanation
Indices: 25452--25510 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
25442 AGTTTCTCCA
25452 ATAATC-A-TATGTATTTTCATAATCT
1 ATAATCAAGTATGTATTTTCATAATCT
25477 ATAATCATAAGTATGTATTTTCATAATCT
1 ATAATC--AAGTATGTATTTTCATAATCT
25506 ATAAT
1 ATAAT
25511 GAAATTATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.20
28 1 0.03
29 23 0.77
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (27 bp):
ATAATCAAGTATGTATTTTCATAATCT
Found at i:26302 original size:25 final size:26
Alignment explanation
Indices: 26250--26302 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
26240 TTACTCAACT
**
26250 AAAAACTCTATTTTTATTTTTCTGTA
1 AAAAACTCTATTTTTATTTTAATGTA
26276 AAAACACTCTATTTTTA-TTTAAT-TA
1 AAAA-ACTCTATTTTTATTTTAATGTA
26301 AA
1 AA
26303 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 8 0.33
27 12 0.50
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAAACTCTATTTTTATTTTAATGTA
Found at i:27645 original size:21 final size:21
Alignment explanation
Indices: 27620--27667 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27610 TATATATAAT
*
27620 ATATATAAT-TAAAATTAAAAA
1 ATATAAAATATAAAA-TAAAAA
*
27641 ATATAAAATATAAAATATAAA
1 ATATAAAATATAAAATAAAAA
27662 ATATAA
1 ATATAA
27668 CTAAACCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATATAAAATATAAAATAAAAA
Found at i:27657 original size:14 final size:14
Alignment explanation
Indices: 27613--27667 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
27603 TTTTGGATAT
* *
27613 ATATAATATATATA
1 ATATAAAATATAAA
*
27627 AT-TAAAATTAAAAA
1 ATATAAAA-TATAAA
27641 ATATAAAATATAAA
1 ATATAAAATATAAA
27655 ATATAAAATATAA
1 ATATAAAATATAA
27668 CTAAACCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 4 0.11
14 26 0.74
15 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAAATATAAA
Found at i:38311 original size:105 final size:105
Alignment explanation
Indices: 38129--38331 Score: 379
Period size: 105 Copynumber: 1.9 Consensus size: 105
38119 TCTTTGTCTT
38129 TAGAATGAATCAAAATCAGTTCTGAGTACTCAAATGTCACTTTATAACCCCCCAACATGCAAAAT
1 TAGAATGAATCAAAATCAGTTCTGAGTACTCAAATGTCACTTTATAACCCCCCAACATGCAAAAT
*
38194 GACTTTCATACTTTTTTCATCAATTTAACCCTCCAACATG
66 GACTTTCATACTTTTTTCATCAATGTAACCCTCCAACATG
* *
38234 TAGAATGAATCAAAATCAGTTCTGAGTACTCAAATGTCATTTTATAACCCCCCAACATGCAGAAT
1 TAGAATGAATCAAAATCAGTTCTGAGTACTCAAATGTCACTTTATAACCCCCCAACATGCAAAAT
38299 GACTTTCATACTTTTTTCATCAATGTAACCCTC
66 GACTTTCATACTTTTTTCATCAATGTAACCCTC
38332 ATATTAGCCA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.32
Consensus pattern (105 bp):
TAGAATGAATCAAAATCAGTTCTGAGTACTCAAATGTCACTTTATAACCCCCCAACATGCAAAAT
GACTTTCATACTTTTTTCATCAATGTAACCCTCCAACATG
Found at i:47609 original size:32 final size:32
Alignment explanation
Indices: 47567--47682 Score: 178
Period size: 32 Copynumber: 3.6 Consensus size: 32
47557 AGCCACGCGG
*
47567 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
47599 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
* *
47631 AGCCGCCCCACTAGGACGGCTATGCCACGTCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
* *
47663 AGCCACCCCACTAGGGCGGC
1 AGCCGCCCCACTAGGACGGC
47683 AAGGCTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.17, C:0.42, G:0.27, T:0.14
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:47805 original size:33 final size:32
Alignment explanation
Indices: 47746--47856 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 32
47736 TAGTACCGGT
* **
47746 GCCGCCCCAGGG-GGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTA-G
47778 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAG
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAG
*
47810 TGCCGCCCCA-GGATGGCGGCTTGGCCATGGCTCA-
1 -GCCGCCCCAGGGA-GGCGGCCTGGCCATGG-T-AG
47844 GCCGCCCCAGGGA
1 GCCGCCCCAGGGA
47857 CGGCACCGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
32 16 0.23
33 48 0.70
34 4 0.06
35 1 0.01
ACGTcount: A:0.13, C:0.35, G:0.40, T:0.13
Consensus pattern (32 bp):
GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAG
Found at i:49294 original size:45 final size:45
Alignment explanation
Indices: 49245--49338 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
49235 GAGCGATTCA
*
49245 AAAGTTTTACAAGTGAACGTACTTTTTAATATAGTATAGATAGAT
1 AAAGTTTTACAAGTGAACATACTTTTTAATATAGTATAGATAGAT
49290 AAAGTTTTACAAGTGAACATACTTTTTAATATAGTATAGATAGAT
1 AAAGTTTTACAAGTGAACATACTTTTTAATATAGTATAGATAGAT
49335 AAAG
1 AAAG
49339 GAGCCCTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (45 bp):
AAAGTTTTACAAGTGAACATACTTTTTAATATAGTATAGATAGAT
Found at i:63356 original size:31 final size:31
Alignment explanation
Indices: 63319--63378 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
63309 GGTCAATTTT
**
63319 TTTTTTTTTGG-TTCAAACCTTCATGGTCAG
1 TTTTTTTTTGGCCACAAACCTTCATGGTCAG
63349 TTTTTTTTTGGCCACAAACCTTCATGGTCA
1 TTTTTTTTTGGCCACAAACCTTCATGGTCA
63379 TTTAGAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (31 bp):
TTTTTTTTTGGCCACAAACCTTCATGGTCAG
Found at i:68201 original size:15 final size:15
Alignment explanation
Indices: 68181--68217 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
68171 TTGGTTAAGG
68181 GATTTGCATTTTCAT
1 GATTTGCATTTTCAT
68196 GATTTGCATTTTCAT
1 GATTTGCATTTTCAT
68211 GATTTGC
1 GATTTGC
68218 TTTCCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (15 bp):
GATTTGCATTTTCAT
Found at i:70035 original size:2 final size:2
Alignment explanation
Indices: 70028--70054 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
70018 CTGATATCTG
70028 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
70055 GTATTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72749 original size:33 final size:33
Alignment explanation
Indices: 72712--72775 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
72702 TTCTTTTGAT
*
72712 TTTCTTGCA-TCTTGGGTTGATGGGTAGTTTCAA
1 TTTCTTGCATTCTTGAG-TGATGGGTAGTTTCAA
*
72745 TTTCTTGCATTTTTGAGTGATGGGTAGTTTC
1 TTTCTTGCATTCTTGAGTGATGGGTAGTTTC
72776 TTGGCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.14, C:0.11, G:0.27, T:0.48
Consensus pattern (33 bp):
TTTCTTGCATTCTTGAGTGATGGGTAGTTTCAA
Done.