Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008203.1 Corchorus capsularis cultivar CVL-1 contig08224, 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: 12672
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1222 original size:20 final size:20
Alignment explanation
Indices: 1194--1232 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1184 TTGTTTTCAA
*
1194 AAAATAAAAATGGCAACAAG
1 AAAACAAAAATGGCAACAAG
1214 AAAACAAAAATGGCAACAA
1 AAAACAAAAATGGCAACAA
1233 TGCCAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.67, C:0.13, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAACAAAAATGGCAACAAG
Found at i:2752 original size:6 final size:6
Alignment explanation
Indices: 2741--2766 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2731 ATAATTGCTA
2741 TAGATT TAGATT TAGATT TAGATT TA
1 TAGATT TAGATT TAGATT TAGATT TA
2767 CTTTGCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TAGATT
Found at i:3166 original size:21 final size:21
Alignment explanation
Indices: 3140--3204 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
3130 AACCTACAGA
3140 GAACAAAACACACAAGCATGG
1 GAACAAAACACACAAGCATGG
*
3161 GAAC---A-A-ATAAGCGATGG
1 GAACAAAACACACAAGC-ATGG
3178 GAACAAAACACACAAGCATGG
1 GAACAAAACACACAAGCATGG
3199 GAACAA
1 GAACAA
3205 GAAAAACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
16 5 0.14
17 9 0.25
18 1 0.03
20 1 0.03
21 15 0.42
22 5 0.14
ACGTcount: A:0.52, C:0.20, G:0.22, T:0.06
Consensus pattern (21 bp):
GAACAAAACACACAAGCATGG
Found at i:3172 original size:16 final size:17
Alignment explanation
Indices: 3153--3184 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3143 CAAAACACAC
3153 AAGC-ATGGGAACAAAT
1 AAGCGATGGGAACAAAT
3169 AAGCGATGGGAACAAA
1 AAGCGATGGGAACAAA
3185 ACACACAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.12, G:0.28, T:0.09
Consensus pattern (17 bp):
AAGCGATGGGAACAAAT
Found at i:4118 original size:234 final size:234
Alignment explanation
Indices: 3691--4148 Score: 778
Period size: 233 Copynumber: 2.0 Consensus size: 234
3681 ACACGTACCC
*
3691 AGACGCCGCCATATATAAGAAATTAAAAAAATTATATTAATAATTAGAAATTAGAAAGCCTAACT
1 AGACGCCGCCATATATAAGAAATTAAAAAAATTATATTAATAATTAGAAATTAGAAAGCCCAACT
* *
3756 GGGGGCCCGGTTAGGGGTCAACTGGGCGCCCACTCAAGACAGACCTTAAACCAAAATTAAAGTCC
66 GGGGGCCCGGTTAGGGGTCAACTGGGCGCCCACTCAAGACAGACCCTAAACCAAAATTAAAATCC
* * * *
3821 TCAACCGGGCTCCAGTTAAGTGGCAATCGGCCTCTCGCTTTGACTCCACCAAATAGCGGCGTCTA
131 TCAACCGAGCTCCAGTTAAGTGGCAACCGGCCTCCCACTTTGACTCCACCAAATAGCGGCGTCTA
*
3886 CCTT-ATCAGACGCCGCCAAATAGTGGCGTCTAGTATTCA
196 -CTTCATCAGACGCCGCCAAATAGCGGCGTCTAGTATTCA
* *
3925 AGACGCTGCCATATATAAGAAATTAAAAATA-TATATTAATAATTAGAAATTAGAAAGCCCAACT
1 AGACGCCGCCATATATAAGAAATTAAAAAAATTATATTAATAATTAGAAATTAGAAAGCCCAACT
3989 GGGGGCCCGGTTAGGGGTCAACTGGGCGCCCACTC-AGAACAGACCCTAAACCAAAATTAAAATC
66 GGGGGCCCGGTTAGGGGTCAACTGGGCGCCCACTCAAG-ACAGACCCTAAACCAAAATTAAAATC
4053 CTCAACCGAGCTCCCAGTTAAGTGGCAACCGGCCTCCCACTTTGACTCCACCAAATAGCGGCGTC
130 CTCAACCGAGCT-CCAGTTAAGTGGCAACCGGCCTCCCACTTTGACTCCACCAAATAGCGGCGTC
4118 TACTTCATCAGACGCCGCCAAATAGCGGCGT
194 TACTTCATCAGACGCCGCCAAATAGCGGCGT
4149 TTTCTTCATT
Statistics
Matches: 211, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
232 2 0.01
233 105 0.50
234 104 0.49
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (234 bp):
AGACGCCGCCATATATAAGAAATTAAAAAAATTATATTAATAATTAGAAATTAGAAAGCCCAACT
GGGGGCCCGGTTAGGGGTCAACTGGGCGCCCACTCAAGACAGACCCTAAACCAAAATTAAAATCC
TCAACCGAGCTCCAGTTAAGTGGCAACCGGCCTCCCACTTTGACTCCACCAAATAGCGGCGTCTA
CTTCATCAGACGCCGCCAAATAGCGGCGTCTAGTATTCA
Found at i:4139 original size:32 final size:32
Alignment explanation
Indices: 4103--4199 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
4093 TTTGACTCCA
* *
4103 CCAAATAGCGGCGTCTACTTCATCAGACGCCG
1 CCAAATAGCGGCGTTTACTTCATTAGACGCCG
* * *
4135 CCAAATAGCGGCGTTTTCTTCATTAGGCGCCA
1 CCAAATAGCGGCGTTTACTTCATTAGACGCCG
* * *
4167 CTAAATGGTGGCGTTTACTTCATTAGACGCCG
1 CCAAATAGCGGCGTTTACTTCATTAGACGCCG
4199 C
1 C
4200 TATCCTGGTG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (32 bp):
CCAAATAGCGGCGTTTACTTCATTAGACGCCG
Found at i:10214 original size:20 final size:21
Alignment explanation
Indices: 10189--10227 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10179 TAAAAGTGTA
10189 AAAAGG-GGGCGGTATTTAGC
1 AAAAGGAGGGCGGTATTTAGC
10209 AAAAGGAGGGCGGTATTTA
1 AAAAGGAGGGCGGTATTTA
10228 ACAATCCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.08, G:0.38, T:0.21
Consensus pattern (21 bp):
AAAAGGAGGGCGGTATTTAGC
Found at i:12400 original size:40 final size:39
Alignment explanation
Indices: 12356--12445 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
12346 CTCCTCCTTC
*
12356 AATCATATTTTTAATTT-AATTTTTCCTTGATTTGTATGCT
1 AATCA-ATTTTTAATTTAAATTTTT-CTTGATTCGTATGCT
* **
12396 AATCAGTTTTTCCTTTAAATTTTTCTTGATTCGTATGCT
1 AATCAATTTTTAATTTAAATTTTTCTTGATTCGTATGCT
12435 AATCAATTTTT
1 AATCAATTTTT
12446 TCCTTTAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
39 32 0.73
40 12 0.27
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (39 bp):
AATCAATTTTTAATTTAAATTTTTCTTGATTCGTATGCT
Found at i:12413 original size:39 final size:39
Alignment explanation
Indices: 12370--12454 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
12360 ATATTTTTAA
*
12370 TTTAATTTTTCCTTGATTTGTATGCTAATC-AGTTTTTCC
1 TTTAATTTTT-CTTGATTCGTATGCTAATCAAGTTTTTCC
*
12409 TTTAAATTTTTCTTGATTCGTATGCTAATCAATTTTTTCC
1 TTT-AATTTTTCTTGATTCGTATGCTAATCAAGTTTTTCC
12449 TTTAAT
1 TTTAAT
12455 GAACAAGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
39 24 0.57
40 18 0.43
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.56
Consensus pattern (39 bp):
TTTAATTTTTCTTGATTCGTATGCTAATCAAGTTTTTCC
Found at i:12446 original size:40 final size:40
Alignment explanation
Indices: 12373--12453 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
12363 TTTTTAATTT
*
12373 AATTTTTCCTTGATTTGTATGCTAATCAGTTTTTCCTTTA
1 AATTTTTCCTTGATTCGTATGCTAATCAGTTTTTCCTTTA
*
12413 AATTTTT-CTTGATTCGTATGCTAATCAATTTTTTCCTTTA
1 AATTTTTCCTTGATTCGTATGCTAATC-AGTTTTTCCTTTA
12453 A
1 A
12454 TGAACAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 18 0.47
40 20 0.53
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (40 bp):
AATTTTTCCTTGATTCGTATGCTAATCAGTTTTTCCTTTA
Done.