Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01003439.1 Corchorus olitorius cultivar O-4 contig03446, 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: 2320
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Found at i:678 original size:57 final size:57
Alignment explanation
Indices: 503--678 Score: 130
Period size: 57 Copynumber: 3.1 Consensus size: 57
493 ATGGTAAAAA
* * *
503 TAAAATAGATATAAGAATATTAGATTTAATTACATAAAAATAGAGTTTTTAGTTGAG
1 TAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAG
* * * * * ** * * *
560 TAAAATTA-TAAAAAGTATATTTAAAATTT-CTT-AATAAAAAT--A-TTAAAATGGTAAAAA
1 TAAAA-TAGTTATAAGAATA-TT-AGATTTAATTAAATAAAAATAGAGTT--TTTAGT-TAAG
*
617 TAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAG
1 TAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAG
674 TAAAA
1 TAAAA
679 CTATAAAAGT
Statistics
Matches: 84, Mismatches: 23, Indels: 24
0.64 0.18 0.18
Matches are distributed among these distances:
54 2 0.02
55 6 0.07
56 9 0.11
57 50 0.60
58 9 0.11
59 6 0.07
60 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (57 bp):
TAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAG
Found at i:1096 original size:22 final size:22
Alignment explanation
Indices: 1066--1145 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
1056 TGTTATCTCT
1066 GTGTGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
1088 GTGTTGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
1110 GTGTGGTTATCAAAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
* *
1132 GCGAGGTTATCAAA
1 GTGTGGTTATCAAA
1146 GGAAGTTATC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:1141 original size:44 final size:44
Alignment explanation
Indices: 1066--1661 Score: 212
Period size: 44 Copynumber: 13.4 Consensus size: 44
1056 TGTTATCTCT
* **
1066 GTGTGGTTATCAAAATTTCATAGTGTTGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
*
1110 GTGTGGTTATCAAAATTTTATAGCGAGGTTATC---A----A-A
1 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
** ** * * * *
1146 G-GAAGTTATCACGATTTCACAGTGTGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
* * * *
1189 GTGTTGTTA-CAAAAATTTCATAGGGAGGTTATCAAAATTTTATA
1 GTGTGGTTATC-AAAATTTTATAGTGAGGTTATCAAAATTTCATA
** ** ** * *
1233 -TGAAAGTTATCCGAATTAAATAGTGTA-GTTATTAAATTTTCATAA
1 GTG-TGGTTATCAAAATTTTATAGTG-AGGTTATCAAAATTTCAT-A
* * * * *
1278 G-GAGGTTATCAAAATTTCATAGTGAGATTATCAAAATTTTATT
1 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
* * *
1321 GCGTGGTTATCAAAACTTTATAGGGAGGTTATCAAAATTTCATTA
1 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCA-TA
** * * *
1366 GAAT-GTTA-CTAAAATTTCCCATTTCCCATTGTGGTTATCAAAATTTCATA
1 GTGTGGTTATC-AAAATTT----TAT---AGTGAGGTTATCAAAATTTCATA
* * * * ** * *
1416 GAGAT-GTTA-CCAAATTTCATAGGGAGGTTATTGAAATTTTATG
1 GTG-TGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
* * * * * *
1459 GGGAGGTTATCAAAAATTTTATATTGTGGTTACCAAAATTTCATC
1 GTGTGGTTATC-AAAATTTTATAGTGAGGTTATCAAAATTTCATA
* * * * *
1504 GGGAGGTCATCAAAATAATTTCATAGTGTGGTTATCAAAGTTTCATA
1 GTGTGGTTATCAAAAT--TTT-ATAGTGAGGTTATCAAAATTTCATA
* * * *
1551 G-GAAGGTTATC-AAATTTTCA-AATAGAGGTTATCGAAATTTCATG
1 GTG-TGGTTATCAAAATTTT-ATAGT-GAGGTTATCAAAATTTCATA
* *
1595 GTGTACTGGTTATCAAAATTTCT-T-TTAGAGGTTATCAAAATTTCACA
1 GTG---TGGTTATCAAAATTT-TATAGT-GAGGTTATCAAAATTTCATA
*
1642 TTGATGG-TATCAAAAATTTT
1 GTG-TGGTTATC-AAAATTTT
1662 GAAATTTCAT
Statistics
Matches: 413, Mismatches: 97, Indels: 84
0.70 0.16 0.14
Matches are distributed among these distances:
35 23 0.06
36 2 0.00
37 1 0.00
38 1 0.00
41 1 0.00
42 1 0.00
43 32 0.08
44 192 0.46
45 51 0.12
46 9 0.02
47 57 0.14
48 8 0.02
49 1 0.00
50 10 0.02
51 24 0.06
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (44 bp):
GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATA
Found at i:1191 original size:22 final size:22
Alignment explanation
Indices: 1150--1656 Score: 237
Period size: 22 Copynumber: 22.5 Consensus size: 22
1140 ATCAAAGGAA
** * *
1150 GTTATCACGATTTCACAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* **
1172 GTTATCAAAATTCCATAGTGTT
1 GTTATCAAAATTTCATAGTGAG
*
1194 GTTA-CAAAAATTTCATAGGGAG
1 GTTATC-AAAATTTCATAGTGAG
* *
1216 GTTATCAAAATTTTATA-TGAAA
1 GTTATCAAAATTTCATAGTG-AG
** **
1238 GTTATCCGAATTAAATAGTGTA-
1 GTTATCAAAATTTCATAGTG-AG
* *
1260 GTTATTAAATTTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGAG
1282 GTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
* * * * *
1304 ATTATCAAAATTTTATTGCGTG
1 GTTATCAAAATTTCATAGTGAG
*
1326 GTTATCAAAACTTT-ATAGGGAG
1 GTTATCAAAA-TTTCATAGTGAG
* *
1348 GTTATCAAAATTTCATTAG-AAT
1 GTTATCAAAATTTCA-TAGTGAG
* *
1370 GTTA-CTAAAATTTCCCATTTCCCATTGTG
1 GTTATC-AAAATTT--CA--T---AGTGAG
* *
1399 GTTATCAAAATTTCATAGAGAT
1 GTTATCAAAATTTCATAGTGAG
* *
1421 GTTA-CCAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
** * * *
1442 GTTATTGAAATTTTATGGGGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
1464 GTTATCAAAAATTTTATATTGTG
1 GTTATC-AAAATTTCATAGTGAG
* * *
1487 GTTACCAAAATTTCATCGGGAG
1 GTTATCAAAATTTCATAGTGAG
* *
1509 GTCATCAAAATAATTTCATAGTGTG
1 GTTATC--AA-AATTTCATAGTGAG
*
1534 GTTATCAAAGTTTCATAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
* *
1556 GTTATCAAATTTTCA-AATAGAG
1 GTTATCAAAATTTCATAGT-GAG
* *
1578 GTTATCGAAATTTCATGGTGTACTG
1 GTTATCAAAATTTCATAGTG-A--G
**
1603 GTTATCAAAATTTC-TTTTAGAG
1 GTTATCAAAATTTCATAGT-GAG
* *
1625 GTTATCAAAATTTCACATTGATG
1 GTTATCAAAATTTCATAGTGA-G
1648 G-TATCAAAA
1 GTTATCAAAA
1657 ATTTTGAAAT
Statistics
Matches: 369, Mismatches: 82, Indels: 68
0.71 0.16 0.13
Matches are distributed among these distances:
21 29 0.08
22 247 0.67
23 37 0.10
24 7 0.02
25 34 0.09
27 2 0.01
28 1 0.00
29 11 0.03
30 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:1204 original size:79 final size:79
Alignment explanation
Indices: 1071--1224 Score: 220
Period size: 79 Copynumber: 1.9 Consensus size: 79
1061 TCTCTGTGTG
* * * *
1071 GTTATCAAAATTTCATAGTGTTGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGCGA
1 GTTATCAAAATTTCACAGTGTGGTTATCAAAATTCCATAGTGTGGTTATCAAAATTTCATAGCGA
1136 GGTTATCAAAGGAA
66 GGTTATCAAAGGAA
** * *
1150 GTTATCACGATTTCACAGTGTGGTTATCAAAATTCCATAGTGTTGTTA-CAAAAATTTCATAGGG
1 GTTATCAAAATTTCACAGTGTGGTTATCAAAATTCCATAGTGTGGTTATC-AAAATTTCATAGCG
1214 AGGTTATCAAA
65 AGGTTATCAAA
1225 ATTTTATATG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
78 1 0.02
79 65 0.98
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (79 bp):
GTTATCAAAATTTCACAGTGTGGTTATCAAAATTCCATAGTGTGGTTATCAAAATTTCATAGCGA
GGTTATCAAAGGAA
Found at i:1497 original size:117 final size:116
Alignment explanation
Indices: 1281--1500 Score: 257
Period size: 117 Copynumber: 1.9 Consensus size: 116
1271 TTCATAAGGA
* * * *
1281 GGTTATCAAAATTTCATAGTGAGATTATCAAAATTTTATTGCGTGGTTATCAAAACTTTATAGGG
1 GGTTATCAAAATTTCATAGAGAGATTATCAAAATTTCATAGCGAGGTTATCAAAACTTTATAGGG
*
1346 AGGTTATCAAAATTTCATTAGAATGTTACTAAAATTTCCCATTTCCCATTGT
66 AGGTTATCAAAATTTCATTAG-ATGTTACCAAAATTTCCCATTTCCCATTGT
* * ** * *
1398 GGTTATCAAAATTTCATAGAGATG-TTA-CCAAATTTCATAGGGAGGTTATTGAAATTTTATGGG
1 GGTTATCAAAATTTCATAGAGA-GATTATCAAAATTTCATAGCGAGGTTATCAAAACTTTATAGG
* *
1461 GAGGTTATCAAAAATTTTATATTG-TGGTTACCAAAATTTC
65 GAGGTTATC-AAAATTTCAT-TAGAT-GTTACCAAAATTTC
1501 ATCGGGAGGT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
116 37 0.43
117 46 0.53
118 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (116 bp):
GGTTATCAAAATTTCATAGAGAGATTATCAAAATTTCATAGCGAGGTTATCAAAACTTTATAGGG
AGGTTATCAAAATTTCATTAGATGTTACCAAAATTTCCCATTTCCCATTGT
Found at i:1548 original size:47 final size:45
Alignment explanation
Indices: 1395--1564 Score: 141
Period size: 47 Copynumber: 3.8 Consensus size: 45
1385 CATTTCCCAT
* * *
1395 TGTGGTTATCAAAATTTCATAGAGATGTTA-C--CAAATTTCATAG
1 TGTGGTTATC-AAATTTCATAGGGAGGTTATCAAAAAATTTCATAG
* * * * * * *
1438 GGAGGTTATTGAAATTTTATGGGGAGGTTATC-AAAAATTTTATAT
1 TGTGGTTA-TCAAATTTCATAGGGAGGTTATCAAAAAATTTCATAG
* * *
1483 TGTGGTTACCAAAATTTCATCGGGAGGTCATCAAAATAATTTCATAG
1 TGTGGTTATC-AAATTTCATAGGGAGGTTATCAAAA-AATTTCATAG
*
1530 TGTGGTTATCAAAGTTTCATAGGAAGGTTATCAAA
1 TGTGGTTATCAAA-TTTCATAGGGAGGTTATCAAA
1565 TTTTCAAATA
Statistics
Matches: 97, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
43 21 0.22
44 2 0.02
45 33 0.34
46 6 0.06
47 35 0.36
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (45 bp):
TGTGGTTATCAAATTTCATAGGGAGGTTATCAAAAAATTTCATAG
Done.