Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010105.1 Corchorus olitorius cultivar O-4 contig10137, 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: 2356
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Found at i:397 original size:138 final size:139
Alignment explanation
Indices: 4--539 Score: 862
Period size: 138 Copynumber: 3.8 Consensus size: 139
1 TTT
*
4 ATTTCATCAAGTTTTAATCAAAGCTGCG-TTAAGTTTCAAAAACCTTGCTCAAGGTTGAGTTTGC
1 ATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGC
68 ATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
66 ATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
133 TATCATTTC
131 TATCATTTC
* * *
142 ATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAAATTTCAAAAACCTTGCTCAA-GATGGGTTT
1 ATTTCATCAAG-TTTTAATCAAAGCTGCGTTT-AAATTTCAAAAACCTTGCTCAAGGTTGAGTTT
* *
206 GCATTTATAAGACCTCCGGGCACATTTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCG
64 GCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCG
271 GGTATCATTTC
129 GGTATCATTTC
282 ATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTC-AAAACCTTGCTCAAGGTTGAGTTTGC
1 ATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGC
*
346 ATTTGTAAGACCTCCAGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
66 ATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
*
411 TATCATCTC
131 TATCATTTC
* ** *
420 ATTTCATCATGTTGTTAATCAAATTTGCGTTTAAATTTCAAATAAACCTTGCTCAAGGTCGAGTT
1 ATTTCATCAAGTT-TTAATCAAAGCTGCGTTTAAATTTC-AA-AAACCTTGCTCAAGGTTGAGTT
* * * *
485 TGCATTTGTGAGACCACTGGGCACAATTTCAGAAACCTCCGGGTATCAATTCTGA
63 TGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGA
540 CTTGTCCTCC
Statistics
Matches: 368, Mismatches: 22, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
137 14 0.04
138 109 0.30
139 58 0.16
140 94 0.26
141 22 0.06
142 71 0.19
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (139 bp):
ATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGC
ATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
TATCATTTC
Found at i:753 original size:40 final size:40
Alignment explanation
Indices: 695--1109 Score: 468
Period size: 40 Copynumber: 10.3 Consensus size: 40
685 CACAATCCTA
* *
695 CTCAGGATCATTGCTTTATTAAATTAATTTCAGAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
735 CTCAGGATCATTGTTTTATCAAATTAATTTCAAAACTCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* * * * *
775 CTCAAGATCATTGCTTTGTCAAATCAATTTCAGAATCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
*
815 CTCAGGATCATCT-TTTTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCAT-TGCTTTATCAAATTAATTTCAAAACCCTG
* * * *
855 CTCAGGATCATTTCTTTA-CCAGTTAATTTC--AATCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* * *
892 CTCAGGATCATTGCTTTATCAAATTAATTTTAAAATCCTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
932 CTCAGGATCATCT-TTTTATCAAATTAATTTC-AAATCCTG
1 CTCAGGATCAT-TGCTTTATCAAATTAATTTCAAAACCCTG
*
971 CTCAGGATCAGGATCAT-CTTTTTATCAAATTAGTTTTC-AAACCCTG
1 CTCAGGATC---AT--TGC--TTTATCAAATTA-ATTTCAAAACCCTG
*
1017 CTCTAGGATCATTACTTTATCAAATTAATTTCAAAACCCTG
1 CTC-AGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
1058 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
1098 CTCAGGATCATT
1 CTCAGGATCATT
1110 ATATTCAGAA
Statistics
Matches: 322, Mismatches: 37, Indels: 32
0.82 0.09 0.08
Matches are distributed among these distances:
37 23 0.07
38 9 0.03
39 27 0.08
40 199 0.62
41 25 0.08
42 3 0.01
43 2 0.01
44 2 0.01
45 12 0.04
46 14 0.04
47 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (40 bp):
CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
Found at i:833 original size:80 final size:79
Alignment explanation
Indices: 695--1566 Score: 574
Period size: 80 Copynumber: 11.4 Consensus size: 79
685 CACAATCCTA
* *
695 CTCAGGATCATTGCTTTATTAAATTAATTTCAGAACCCTGCTCAGGATCATTGTTTTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCA-AATCCTGCTCAGGATCATTGTTTTATCAAATT
760 AATTTCAAAACTCTG
65 AATTTCAAAACTCTG
* * *
775 CTCAAGATCATTGCTTTGTCAAATCAATTTCAGAATCCTGCTCAGGATCATCT-TTTTATCAAAT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCA-AATCCTGCTCAGGATCAT-TGTTTTATCAAAT
*
839 TAATTTCAAAACCCTG
64 TAATTTCAAAACTCTG
* * * *
855 CTCAGGATCATTTCTTTA-CCAGTTAATTTC-AATCCTGCTCAGGATCATTGCTTTATCAAATTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCATTGTTTTATCAAATTA
* *
918 ATTTTAAAA-TCCTA
66 ATTTCAAAACT-CTG
* *
932 CTCAGGATCATCT-TTTTATCAAATTAATTTCAAATCCTGCTCAGGATCAGGATCATCTTTTTAT
1 CTCAGGATCAT-TGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATC---AT--T-GTTTTAT
* *
996 CAAATTAGTTTTC-AAACCCTG
59 CAAATTA-ATTTCAAAACTCTG
* * *
1017 CTCTAGGATCATTACTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAAT
1 CTC-AGGATCATTGCTTTATCAAATTAATTTC-AAATCCTGCTCAGGATCATTGTTTTATCAAAT
*
1082 TAATTTCAAAA-TCCTA
64 TAATTTCAAAACT-CTG
* * * * *
1098 CTCAGGATCATT-ATAT-TC--A-GAA--TC--A-CAT--TCATGATCATCT-TTTTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCAT-TGTTTTATCAAATT
* *
1150 AATTTCAGAA-TCCTA
65 AATTTCAAAACT-CTG
* * *** * ** * ***
1165 CTTAGGATCATTGCTTTATCGAGCCACTTTTCAAAATCCTATTTAGGATCATT-TCTTTAT-TGG
1 CTCAGGATCATTGCTTTATCAAATTA-ATTTC-AAATCCTGCTCAGGATCATTGT-TTTATCAAA
* * *
1228 TCAATTTCAGAA-TCCTA
63 TTAATTTCAAAACT-CTG
* * * ** * *
1245 CTTAGGATCA------T-T-AAATTCA----GAATCCTATTCAGGATCATAGCTTTATCAAATTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCATTGTTTTATCAAATTA
*
1298 ATTTCAGAA-TCCTG
66 ATTTCAAAACT-CTG
* * * *
1312 CTCATGATCATTGCTTTATC--A--AA-TT--AATCCTACTCGGGATCATTGATTTATCAAATTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCATTGTTTTATCAAATTA
*
1370 ATTTCAGAA-TCCTG
66 ATTTCAAAACT-CTG
* * *
1384 CTCAGGATCATTGCTTTATC--A--AA-TT--AATCCTACTCGGGATCATTGCTTTATCAAATTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCATTGTTTTATCAAATTA
* *
1442 ATTTCAGAATTCTG
66 ATTTCAAAACTCTG
* * *
1456 CTCAGGATCATTGCTTTTTCAAATTAATTTCAGAATTCTGCTCAGGATCATTGCTTTATCAAATT
1 CTCAGGATCATTGCTTTATCAAATTAATTTCA-AATCCTGCTCAGGATCATTGTTTTATCAAATT
1521 AA-TTCAAAA-TCCTG
65 AATTTCAAAACT-CTG
1535 CTCAGGATCATTGCTTTATCAAATTAATTTCA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCA
1567 GTTAATTTTA
Statistics
Matches: 653, Mismatches: 82, Indels: 115
0.77 0.10 0.14
Matches are distributed among these distances:
66 22 0.03
67 68 0.10
68 3 0.00
69 4 0.01
70 1 0.00
71 1 0.00
72 132 0.20
73 6 0.01
74 3 0.00
75 4 0.01
76 4 0.01
77 57 0.09
78 15 0.02
79 69 0.11
80 159 0.24
81 34 0.05
82 3 0.00
84 3 0.00
85 21 0.03
86 28 0.04
87 16 0.02
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (79 bp):
CTCAGGATCATTGCTTTATCAAATTAATTTCAAATCCTGCTCAGGATCATTGTTTTATCAAATTA
ATTTCAAAACTCTG
Found at i:1205 original size:41 final size:39
Alignment explanation
Indices: 1150--1256 Score: 142
Period size: 41 Copynumber: 2.7 Consensus size: 39
1140 TTATCAAATT
1150 AATTTCAGAATCCTACTTAGGATCATTGCTTTATCGAGCC
1 AATTTCAGAATCCTACTTAGGATCATTGCTTTATCG-GCC
* * * * * *
1190 ACTTTTCAAAATCCTATTTAGGATCATTTCTTTATTGGTC
1 A-ATTTCAGAATCCTACTTAGGATCATTGCTTTATCGGCC
1230 AATTTCAGAATCCTACTTAGGATCATT
1 AATTTCAGAATCCTACTTAGGATCATT
1257 AAATTCAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 23 0.40
40 4 0.07
41 30 0.53
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (39 bp):
AATTTCAGAATCCTACTTAGGATCATTGCTTTATCGGCC
Found at i:1309 original size:40 final size:40
Alignment explanation
Indices: 1254--1411 Score: 188
Period size: 40 Copynumber: 4.2 Consensus size: 40
1244 ACTTAGGATC
* ** *
1254 ATTAAATTCAGAATCCTATTCAGGATCATAGCTTTATCAA
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
*
1294 ATTAATTTCAGAATCCTGCTCATGATCATTGCTTTATC--
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
* * *
1332 A--AA-TT---AATCCTACTCGGGATCATTGATTTATCAA
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
1366 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
1 ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
1406 ATTAAT
1 ATTAAT
1412 CCTACTCGGG
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
32 23 0.23
34 1 0.01
35 2 0.02
36 4 0.04
37 2 0.02
38 1 0.01
40 65 0.66
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (40 bp):
ATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAA
Found at i:1341 original size:32 final size:32
Alignment explanation
Indices: 1305--1443 Score: 152
Period size: 32 Copynumber: 4.1 Consensus size: 32
1295 TTAATTTCAG
* *
1305 AATCCTGCTCATGATCATTGCTTTATCAAATT
1 AATCCTACTCAGGATCATTGCTTTATCAAATT
* *
1337 AATCCTACTCGGGATCATTGATTTATCAAATTAATTT
1 AATCCTACTCAGGATCATTGCTTTATC--A--AA-TT
*
1374 CAGAATCCTGCTCAGGATCATTGCTTTATCAAATT
1 ---AATCCTACTCAGGATCATTGCTTTATCAAATT
*
1409 AATCCTACTCGGGATCATTGCTTTATCAAATT
1 AATCCTACTCAGGATCATTGCTTTATCAAATT
1441 AAT
1 AAT
1444 TTCAGAATTC
Statistics
Matches: 90, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
32 56 0.62
34 1 0.01
35 2 0.02
36 4 0.04
37 2 0.02
38 1 0.01
40 24 0.27
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (32 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATT
Found at i:1364 original size:72 final size:72
Alignment explanation
Indices: 1265--1562 Score: 427
Period size: 72 Copynumber: 4.0 Consensus size: 72
1255 TTAAATTCAG
* * *
1265 AATCCTATTCAGGATCATAGCTTTATCAAATTAATTTCAGAATCCTGCTCATGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
1330 TCAAATT
66 TCAAATT
* *
1337 AATCCTACTCGGGATCATTGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
1402 TCAAATT
66 TCAAATT
* * *
1409 AATCCTACTCGGGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCAGGATCATTGCTTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
1474 TCAAATT
66 TCAAATT
* *
1481 AATTTCAGAATTCTGCTCAGGATCATTGCTTTATCAAATTAA-TTCAAAATCCTGCTCAGGATCA
1 AA--TC------CTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCA
1545 TTGCTTTATCAAATT
58 TTGCTTTATCAAATT
1560 AAT
1 AAT
1563 TTCAGTTAAT
Statistics
Matches: 205, Mismatches: 13, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
72 138 0.67
74 2 0.01
77 1 0.00
79 36 0.18
80 28 0.14
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (72 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
TCAAATT
Found at i:1392 original size:112 final size:111
Alignment explanation
Indices: 1021--1562 Score: 387
Period size: 112 Copynumber: 4.9 Consensus size: 111
1011 ACCCTGCTCT
* *
1021 AGGATCATT-ACTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAA
1 AGGATCATTGA-TTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAA
* * * * *
1085 TTTCAAAATCCTACTCAGGATCATT-ATAT-TC--A-GAATCAC-ATTC
65 -TTC-AAATCCTGCTCAGGATCATTGCTTTATCAAATTAATCACTACTC
* * * * *
1128 ATGATCATCT-TTTTATCAAATTAATTTCAGAATCCTACTTAGGATCATTGCTTTATCGAGCCAC
1 AGGATCAT-TGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATC-A---AA
** * * ** * *
1192 TT--TTCAAAATCCTATTTAGGATCATTTC-TT-T---ATTGGTCAAT-TTC
61 TTAATTC-AAATCCTGCTCAGGATCATTGCTTTATCAAATTAATCACTACTC
* * * ** * * ** *
1236 AGAATC-CT-ACTTAGGATCATTAAATTCAGAATCCTATTCAGGATCATAGCTTTATCAAATTAA
1 AGGATCATTGATTTATCA-AATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAA
*
1299 TTTCAGAATCCTGCTCATGATCATTGCTTTATCAAATTAATC-CTACTC
65 -TTCA-AATCCTGCTCAGGATCATTGCTTTATCAAATTAATCACTACTC
*
1347 GGGATCATTGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATC--A--AAT
1 AGGATCATTGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
* * *
1408 T--AATCCTACTCGGGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTC
66 TCAAATCCTGCTCAGGATCATTGCTTTATCAAATTAA--TC---A--CTACTC
* * *
1459 AGGATCATTGCTTTTTCAAATTAATTTCAGAATTCTGCTCAGGATCATTGCTTTATCAAATTAAT
1 AGGATCATTGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
1524 TCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
66 TC-AAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
1563 TTCAGTTAAT
Statistics
Matches: 341, Mismatches: 58, Indels: 62
0.74 0.13 0.13
Matches are distributed among these distances:
103 3 0.01
104 31 0.09
105 1 0.00
106 27 0.08
107 88 0.26
108 39 0.11
110 2 0.01
111 14 0.04
112 93 0.27
113 5 0.01
114 1 0.00
116 4 0.01
117 1 0.00
119 32 0.09
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (111 bp):
AGGATCATTGATTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
TCAAATCCTGCTCAGGATCATTGCTTTATCAAATTAATCACTACTC
Found at i:1478 original size:40 final size:40
Alignment explanation
Indices: 1420--1567 Score: 262
Period size: 40 Copynumber: 3.7 Consensus size: 40
1410 ATCCTACTCG
1420 GGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCA
1 GGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCA
*
1460 GGATCATTGCTTTTTCAAATTAATTTCAGAATTCTGCTCA
1 GGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCA
* *
1500 GGATCATTGCTTTATCAAATTAA-TTCAAAATCCTGCTCA
1 GGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCA
1539 GGATCATTGCTTTATCAAATTAATTTCAG
1 GGATCATTGCTTTATCAAATTAATTTCAG
1568 TTAATTTTAG
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
39 37 0.36
40 65 0.64
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (40 bp):
GGATCATTGCTTTATCAAATTAATTTCAGAATTCTGCTCA
Done.