Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014245.1 Corchorus olitorius cultivar O-4 contig14278, 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: 91236
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:763 original size:320 final size:323
Alignment explanation
Indices: 1--859 Score: 1375
Period size: 320 Copynumber: 2.7 Consensus size: 323
* *
1 AAAAGAAATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACATTGTAGACAATACACATCACA
1 AAAAGAGATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACGTTGTAGACAATACACATCACA
** *
66 TATGTCACGCGTAGCTAGTAACGTATGCTGCATTTCAGACATTTGTATGACATTTCAGTTACTTG
66 TATGTCACGTATAGCTAGTAACGTACGCTGCATTTCAGACATTTGTATGACATTTCAGTTACTTG
*
131 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTATATTACTTCAACCTCAAGCAA
131 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTCTATTACTTCAACCTCAAGCAA
* *
196 GTTGAGTCTCAATTCCGGTATCAATGTCCTGCTTCAGAGAAATACAGCGTGGATTACGCTGGTTC
196 TTTGAGTCTCAATTCCGG-ATCAATGTCCTGCTTCAGAGAAATACAACGTGGATTACGCTGGTTC
* *
261 TGCCAACCTATATTGTTCAAAAAAAATTAATGGCATACAAAAGGTAAGAAACTGAAACTGAAACC
260 TGCCAACCTATATTGCTCAAAAAAAATTAATGGCACACAAAAGGTAAG--A--GAAACTGAAACC
*
326 AAT
321 AAC
* *
329 ATAAGAGATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACGTTATAGACAATACACATCACA
1 AAAAGAGATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACGTTGTAGACAATACACATCACA
*
394 TATGTCACGTATAGCTAGTAACGTACGCTGCATTTCAGACATCTGTATGACATTTCAGTTACTTG
66 TATGTCACGTATAGCTAGTAACGTACGCTGCATTTCAGACATTTGTATGACATTTCAGTTACTTG
459 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTCTATTACTTCAACCTCAAGCAA
131 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTCTATTACTTCAACCTCAAGCAA
* * *
524 TTTGAGTCTCAATTCCGG-TCAAT-TTCTGCTTCAGGGAAGTACAACGTGGATTACGCTGGTTCT
196 TTTGAGTCTCAATTCCGGATCAATGTCCTGCTTCAGAGAAATACAACGTGGATTACGCTGGTTCT
* * *
587 GCCAACCTATATTGCTCAAAAGGAAATTAATGGCACATAAAAGGTAAG-G-AATTGAAACCAAC
261 GCCAACCTATATTGCTCAAAA-AAAATTAATGGCACACAAAAGGTAAGAGAAACTGAAACCAAC
*
649 AAAAGAGATAAGTATGGTAAAAGCATATGGTTGTGGCCTTTACGTTGTAGACAATACACATCACA
1 AAAAGAGATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACGTTGTAGACAATACACATCACA
* * * * *
714 TTTGTCACGTAAAGCTAGTAACGTACGCTGCATTTCAGACATTTGTATGAAATTTCGGTTACTTC
66 TATGTCACGTATAGCTAGTAACGTACGCTGCATTTCAGACATTTGTATGACATTTCAGTTACTTG
* *
779 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTTCTATACTCTATTAGTTCAACCTCAAGCAA
131 ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTCTATTACTTCAACCTCAAGCAA
*
844 TTTGAGTCTCAGTTCC
196 TTTGAGTCTCAATTCC
860 TCTAAACAGT
Statistics
Matches: 498, Mismatches: 32, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
320 210 0.42
321 1 0.00
325 56 0.11
326 28 0.06
328 203 0.41
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (323 bp):
AAAAGAGATAAGTATGGTAAAGGCATATGGTTGTGGCCTTTACGTTGTAGACAATACACATCACA
TATGTCACGTATAGCTAGTAACGTACGCTGCATTTCAGACATTTGTATGACATTTCAGTTACTTG
ATTCCCTTTAAGTTCATCGTTTCTTCCGCCCCTCTCCTATACTCTATTACTTCAACCTCAAGCAA
TTTGAGTCTCAATTCCGGATCAATGTCCTGCTTCAGAGAAATACAACGTGGATTACGCTGGTTCT
GCCAACCTATATTGCTCAAAAAAAATTAATGGCACACAAAAGGTAAGAGAAACTGAAACCAAC
Found at i:1361 original size:160 final size:160
Alignment explanation
Indices: 1097--1419 Score: 646
Period size: 160 Copynumber: 2.0 Consensus size: 160
1087 TAGTTCTGAT
1097 ATGGCATTTATGTCTTGCTTGTGCTTGATGTAGAAAGAATCAATTATTAAAGTTTTAACAAGAAT
1 ATGGCATTTATGTCTTGCTTGTGCTTGATGTAGAAAGAATCAATTATTAAAGTTTTAACAAGAAT
1162 TGAAAATCCAAGCTTGATCAGACGATTAATCTATGAAATCTTCCTATAGATCTCCTACAAGATTA
66 TGAAAATCCAAGCTTGATCAGACGATTAATCTATGAAATCTTCCTATAGATCTCCTACAAGATTA
1227 GTGTTTCAGGAATTCATAATGAGAAAATGA
131 GTGTTTCAGGAATTCATAATGAGAAAATGA
1257 ATGGCATTTATGTCTTGCTTGTGCTTGATGTAGAAAGAATCAATTATTAAAGTTTTAACAAGAAT
1 ATGGCATTTATGTCTTGCTTGTGCTTGATGTAGAAAGAATCAATTATTAAAGTTTTAACAAGAAT
1322 TGAAAATCCAAGCTTGATCAGACGATTAATCTATGAAATCTTCCTATAGATCTCCTACAAGATTA
66 TGAAAATCCAAGCTTGATCAGACGATTAATCTATGAAATCTTCCTATAGATCTCCTACAAGATTA
1387 GTGTTTCAGGAATTCATAATGAGAAAATGA
131 GTGTTTCAGGAATTCATAATGAGAAAATGA
1417 ATG
1 ATG
1420 CATGTATCTT
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (160 bp):
ATGGCATTTATGTCTTGCTTGTGCTTGATGTAGAAAGAATCAATTATTAAAGTTTTAACAAGAAT
TGAAAATCCAAGCTTGATCAGACGATTAATCTATGAAATCTTCCTATAGATCTCCTACAAGATTA
GTGTTTCAGGAATTCATAATGAGAAAATGA
Found at i:4194 original size:97 final size:98
Alignment explanation
Indices: 4027--4223 Score: 369
Period size: 97 Copynumber: 2.0 Consensus size: 98
4017 ATTTGTCGAA
* *
4027 TGTTGTTGTCTATGTAGTCTAAGTGTCTGCTAAACTTTCTAGTTCATGTTTTAAGTAAGGGGGTC
1 TGTTGTGGTCTATGTAGTCTAAGTGTCTGCTAAACTTTCTAGTTCATGTTTTAAGTAAGGGAGTC
4092 TATCAATAATGTGGACAAGTTCTAGGTTTTTTC
66 TATCAATAATGTGGACAAGTTCTAGGTTTTTTC
4125 TGTTGTGGTCTATGTAGTC-AAGTGTCTGCTAAACTTTCTAGTTCATGTTTTAAGTAAGGGAGTC
1 TGTTGTGGTCTATGTAGTCTAAGTGTCTGCTAAACTTTCTAGTTCATGTTTTAAGTAAGGGAGTC
4189 TATCAATAATGTGGACAAGTTCTAGGTTTTTTC
66 TATCAATAATGTGGACAAGTTCTAGGTTTTTTC
4222 TG
1 TG
4224 CTTTAATAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 79 0.81
98 18 0.19
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (98 bp):
TGTTGTGGTCTATGTAGTCTAAGTGTCTGCTAAACTTTCTAGTTCATGTTTTAAGTAAGGGAGTC
TATCAATAATGTGGACAAGTTCTAGGTTTTTTC
Found at i:8363 original size:6 final size:6
Alignment explanation
Indices: 8352--8377 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8342 ATACTACTTC
8352 ACCCAA ACCCAA ACCCAA ACCCAA AC
1 ACCCAA ACCCAA ACCCAA ACCCAA AC
8378 AGAGCATACT
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:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCAA
Found at i:8878 original size:27 final size:28
Alignment explanation
Indices: 8831--8885 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
8821 ATAATTAGGG
8831 CTCTATAGTTTTTTAATTCTTTAATTCT
1 CTCTATAGTTTTTTAATTCTTTAATTCT
8859 CTCTATAG-TTTTTAATTCTTTAATTCT
1 CTCTATAGTTTTTTAATTCTTTAATTCT
8886 TCTTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.22, C:0.15, G:0.04, T:0.60
Consensus pattern (28 bp):
CTCTATAGTTTTTTAATTCTTTAATTCT
Found at i:8900 original size:27 final size:27
Alignment explanation
Indices: 8831--8902 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 27
8821 ATAATTAGGG
*
8831 CTCTATAGTTTTTTAATTCTTTAATTCT
1 CTCTATAG-TTGTTAATTCTTTAATTCT
*
8859 CTCTATAGTTTTTAATTCTTTAATTCTT
1 CTCTATAGTTGTTAATTCTTTAATTC-T
8887 CTTCT-TA-TTGTTAATT
1 C-TCTATAGTTGTTAATT
8903 GTTCTCTAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 26 0.63
28 12 0.29
29 3 0.07
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.61
Consensus pattern (27 bp):
CTCTATAGTTGTTAATTCTTTAATTCT
Found at i:34298 original size:6 final size:6
Alignment explanation
Indices: 34289--34315 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34279 AAAGTAAAAA
34289 ACTCCT ACTCCT ACTCCT ACTCCT ACT
1 ACTCCT ACTCCT ACTCCT ACTCCT ACT
34316 TATACTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
ACTCCT
Found at i:34853 original size:44 final size:43
Alignment explanation
Indices: 34775--34859 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
34765 CCTCCTCACC
*
34775 TTTTGGGTCTCATGAGTTGCTGAACTTCTGGCTTTGGTCTAAA
1 TTTTGGGTCTCATGAGTTGCTAAACTTCTGGCTTTGGTCTAAA
* *
34818 TTTTGGGTCTTATGA-TCTGCTAAATTTTCTGGCTTTGGTCTA
1 TTTTGGGTCTCATGAGT-TGCTAAA-CTTCTGGCTTTGGTCTA
34860 TTTGATTGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 1 0.03
43 20 0.54
44 16 0.43
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (43 bp):
TTTTGGGTCTCATGAGTTGCTAAACTTCTGGCTTTGGTCTAAA
Found at i:51635 original size:18 final size:18
Alignment explanation
Indices: 51612--51647 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51602 TAGCATTGTG
51612 TAAATTACATAGGAATTA
1 TAAATTACATAGGAATTA
*
51630 TAAATTACATGGGAATTA
1 TAAATTACATAGGAATTA
51648 CTATATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (18 bp):
TAAATTACATAGGAATTA
Found at i:72315 original size:10 final size:10
Alignment explanation
Indices: 72300--72328 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
72290 GGAATCCCCT
72300 CCCCGTCCCG
1 CCCCGTCCCG
72310 CCCCGTCCCG
1 CCCCGTCCCG
72320 CCCCGTCCC
1 CCCCGTCCC
72329 TGAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.72, G:0.17, T:0.10
Consensus pattern (10 bp):
CCCCGTCCCG
Found at i:80571 original size:24 final size:24
Alignment explanation
Indices: 80542--80614 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
80532 TTGGTATCAC
*
80542 AATCAAATTGTGTTGAAAAAGGCG
1 AATCAAATTGAGTTGAAAAAGGCG
* * *
80566 AATCAAATTGAGTGGAAAAGGGTG
1 AATCAAATTGAGTTGAAAAAGGCG
*
80590 AATCAAACTGAGTTGAAAAAGGCG
1 AATCAAATTGAGTTGAAAAAGGCG
80614 A
1 A
80615 GTTCGGTGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.27, T:0.21
Consensus pattern (24 bp):
AATCAAATTGAGTTGAAAAAGGCG
Done.