Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008559.1 Corchorus capsularis cultivar CVL-1 contig08580, 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: 7937
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:962 original size:8 final size:8
Alignment explanation
Indices: 949--1036 Score: 63
Period size: 8 Copynumber: 10.9 Consensus size: 8
939 AGCTCCGAAA
949 AATTGAAT
1 AATTGAAT
957 AATTGAA-
1 AATTGAAT
964 ACATTGAAT
1 A-ATTGAAT
* **
973 CATTGAGG
1 AATTGAAT
981 AATTGAA-
1 AATTGAAT
*
988 ACACTGAAT
1 A-ATTGAAT
997 AATTGAAT
1 AATTGAAT
*
1005 AATTTGAAG
1 AA-TTGAAT
*
1014 AATTGAAC
1 AATTGAAT
* *
1022 ACTTGAAG
1 AATTGAAT
1030 AATTGAA
1 AATTGAA
1037 GAAAGACCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
7 2 0.03
8 53 0.84
9 8 0.13
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (8 bp):
AATTGAAT
Found at i:964 original size:16 final size:16
Alignment explanation
Indices: 949--1036 Score: 81
Period size: 16 Copynumber: 5.4 Consensus size: 16
939 AGCTCCGAAA
949 AATTGAATAATTGAA-
1 AATTGAATAATTGAAG
* *
964 ACATTGAATCATTGAGG
1 A-ATTGAATAATTGAAG
* *
981 AATTGAA-ACACTGAAT
1 AATTGAATA-ATTGAAG
997 AATTGAATAATTTGAAG
1 AATTGAATAA-TTGAAG
* *
1014 AATTGAACACTTGAAG
1 AATTGAATAATTGAAG
1030 AATTGAA
1 AATTGAA
1037 GAAAGACCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
15 1 0.02
16 43 0.74
17 14 0.24
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (16 bp):
AATTGAATAATTGAAG
Found at i:977 original size:24 final size:24
Alignment explanation
Indices: 950--1036 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
940 GCTCCGAAAA
*
950 ATTGAATAATTGAAACATTGAATC
1 ATTGAAGAATTGAAACATTGAATC
* * *
974 ATTGAGGAATTGAAACACTGAATA
1 ATTGAAGAATTGAAACATTGAATC
*
998 ATTGAATAATTTGAAGA-ATTGAA-C
1 ATTGAAGAA-TTGAA-ACATTGAATC
1022 ACTTGAAGAATTGAA
1 A-TTGAAGAATTGAA
1037 GAAAGACCAC
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 33 0.65
25 17 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (24 bp):
ATTGAAGAATTGAAACATTGAATC
Found at i:1019 original size:33 final size:32
Alignment explanation
Indices: 949--1036 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
939 AGCTCCGAAA
* * * *
949 AATTGAATAATTGAA-ACATTGAATCATTGAGG
1 AATTGAACACTTGAAGA-ATTGAATAATTGAAG
*
981 AATTGAAACAC-TGAATAATTGAATAATTTGAAG
1 AATTG-AACACTTGAAGAATTGAATAA-TTGAAG
1014 AATTGAACACTTGAAGAATTGAA
1 AATTGAACACTTGAAGAATTGAA
1037 GAAAGACCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 22 0.47
33 25 0.53
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (32 bp):
AATTGAACACTTGAAGAATTGAATAATTGAAG
Found at i:1113 original size:14 final size:14
Alignment explanation
Indices: 1095--1371 Score: 72
Period size: 14 Copynumber: 19.4 Consensus size: 14
1085 TAATCGAAAC
*
1095 ATTGAAGGATTGAA
1 ATTGAAGAATTGAA
*
1109 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
* * *
1123 CTCGAAGCATTGAA
1 ATTGAAGAATTGAA
1137 ATTGAAGCGTCAAAGATTTGAA
1 ATTGAA--G----A-A-TTGAA
1159 ATTG-AGACATTGAA
1 ATTGAAGA-ATTGAA
1173 ATTGAA-ATATTGAA
1 ATTGAAGA-ATTGAA
*
1187 GGATTG-A-ATTTGATGA
1 --ATTGAAGAATTGA--A
1203 ATTGAAGAATTCG-A
1 ATTGAAGAATT-GAA
*
1217 ATTGAAGGATTGAA
1 ATTGAAGAATTGAA
*
1231 GTTG-A-AA-T--A
1 ATTGAAGAATTGAA
* *
1240 TTTGAAGAATTGGA
1 ATTGAAGAATTGAA
*
1254 TTTGAAGAATTGAAA
1 ATTGAAGAATTG-AA
1269 CATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
1283 CATT-AAGGAATTGAA
1 -ATTGAA-GAATTGAA
1298 A--GAA-ACATTGAAGA
1 ATTGAAGA-ATTG-A-A
1312 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
1324 GCATTGAAG--TTGAA
1 --ATTGAAGAATTGAA
1338 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
1352 TTTGAAAAATTGAA
1 ATTGAAGAATTGAA
1366 ATTGAA
1 ATTGAA
1372 CAACTGGCAA
Statistics
Matches: 203, Mismatches: 21, Indels: 78
0.67 0.07 0.26
Matches are distributed among these distances:
9 4 0.02
10 1 0.00
11 4 0.02
12 14 0.07
13 6 0.03
14 130 0.64
15 13 0.06
16 18 0.09
17 1 0.00
19 1 0.00
21 2 0.01
22 9 0.04
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:1221 original size:22 final size:22
Alignment explanation
Indices: 1158--1231 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1148 AAAGATTTGA
*
1158 AATTG-AGACATTGAAATTGAA-
1 AATTGAAGA-ATTGAATTTGAAG
* *
1179 ATATTGAAGGATTGAATTTGATG
1 A-ATTGAAGAATTGAATTTGAAG
1202 AATTGAAGAATTCGAA-TTGAAG
1 AATTGAAGAATT-GAATTTGAAG
*
1224 GATTGAAG
1 AATTGAAG
1232 TTGAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
21 1 0.02
22 36 0.84
23 6 0.14
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (22 bp):
AATTGAAGAATTGAATTTGAAG
Found at i:1304 original size:20 final size:20
Alignment explanation
Indices: 1279--1332 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1269 CATTGAAATT
1279 GAAACATT-AAGGAATTGAAA
1 GAAACATTGAA-GAATTGAAA
1299 GAAACATTGAAGAATTGAAA
1 GAAACATTGAAGAATTGAAA
*
1319 TTGAAGCATTGAAG
1 --GAAACATTGAAG
1333 TTGAAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.57
21 2 0.07
22 11 0.37
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (20 bp):
GAAACATTGAAGAATTGAAA
Found at i:1317 original size:8 final size:8
Alignment explanation
Indices: 1196--1351 Score: 60
Period size: 8 Copynumber: 20.6 Consensus size: 8
1186 AGGATTGAAT
*
1196 TTGATGAA
1 TTGAAGAA
1204 TTGAAGAA
1 TTGAAGAA
*
1212 TT--CGAA
1 TTGAAGAA
*
1218 TTGAAGGA
1 TTGAAGAA
1226 TTGAAG--
1 TTGAAGAA
1232 TTGAA-ATA
1 TTGAAGA-A
1240 TTTGAAGAA
1 -TTGAAGAA
*
1249 TTG--GAT
1 TTGAAGAA
1255 TTGAAGAA
1 TTGAAGAA
1263 TTGAA-ACA
1 TTGAAGA-A
1271 TTG-A-AA
1 TTGAAGAA
1277 TTGAA-ACA
1 TTGAAGA-A
1285 TT-AAGGAA
1 TTGAA-GAA
1293 TTGAAAGAAACA
1 TTG-AAG--A-A
1305 TTGAAGAA
1 TTGAAGAA
1313 TTG-A-AA
1 TTGAAGAA
*
1319 TTGAAGCA
1 TTGAAGAA
1327 TTGAAG--
1 TTGAAGAA
1333 TTG-A-AA
1 TTGAAGAA
1339 TTGAAGAA
1 TTGAAGAA
1347 TTGAA
1 TTGAA
1352 TTTGAAAAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 50
0.67 0.04 0.29
Matches are distributed among these distances:
5 1 0.01
6 30 0.26
7 10 0.09
8 55 0.47
9 9 0.08
10 3 0.03
11 4 0.03
12 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.29
Consensus pattern (8 bp):
TTGAAGAA
Found at i:1322 original size:6 final size:6
Alignment explanation
Indices: 1311--1371 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
1301 AACATTGAAG
* *
1311 AATTGA AATTGA AGCATTGA AGTTGA AATTGAA GAATTGA ATTTGAAA
1 AATTGA AATTGA A--ATTGA AATTGA AATTG-A -AATTGA AATTG--A
1359 AATTGA AATTGA A
1 AATTGA AATTGA A
1372 CAACTGGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 27 0.60
7 2 0.04
8 16 0.36
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (6 bp):
AATTGA
Found at i:1330 original size:34 final size:34
Alignment explanation
Indices: 1291--1366 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
1281 AACATTAAGG
*
1291 AATTGAAAG-AAACATTGAAGAATTGAAATTGAAG
1 AATTGAAAGTAAA-ATTGAAGAATTGAAATTGAAA
* * *
1325 CATTG-AAGTTGAAATTGAAGAATTGAATTTGAAA
1 AATTGAAAG-TAAAATTGAAGAATTGAAATTGAAA
1359 AATTGAAA
1 AATTGAAA
1367 TTGAACAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
33 3 0.09
34 27 0.79
35 4 0.12
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.28
Consensus pattern (34 bp):
AATTGAAAGTAAAATTGAAGAATTGAAATTGAAA
Found at i:1336 original size:20 final size:20
Alignment explanation
Indices: 1303--1358 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1293 TTGAAAGAAA
1303 CATTGAAGAATTGAAATTGAAG
1 CATTGAAG--TTGAAATTGAAG
1325 CATTGAAGTTGAAATTGAAG
1 CATTGAAGTTGAAATTGAAG
* *
1345 AATTGAATTTGAAA
1 CATTGAAGTTGAAA
1359 AATTGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 24 0.75
22 8 0.25
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (20 bp):
CATTGAAGTTGAAATTGAAG
Found at i:1371 original size:34 final size:34
Alignment explanation
Indices: 1304--1371 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1294 TGAAAGAAAC
** *
1304 ATTGAAGAATTGAAATTGAAGCATTGAAGTTGAA
1 ATTGAAGAATTGAAATTGAAAAATTGAAATTGAA
*
1338 ATTGAAGAATTGAATTTGAAAAATTGAAATTGAA
1 ATTGAAGAATTGAAATTGAAAAATTGAAATTGAA
1372 CAACTGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.47, C:0.01, G:0.21, T:0.31
Consensus pattern (34 bp):
ATTGAAGAATTGAAATTGAAAAATTGAAATTGAA
Found at i:1822 original size:71 final size:70
Alignment explanation
Indices: 1589--1945 Score: 485
Period size: 71 Copynumber: 5.1 Consensus size: 70
1579 AAGCCAATGT
*
1589 TGCTTGGATGGAACCAATG-CTCGAACT-ATCTCGTATGGAAACGAG-TTGGCTTGTGGAAAAGC
1 TGCTTGGATGGAACCAA-GACTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-
*
1651 CCCTTAAA
63 CCCTTGAA
* * *
1659 TGCTTGGATGGAACCAAAACTTAAACT-ACCTCGTATGGAAACGAGTTTGGTTTGTGGAAAAGCC
1 TGCTTGGATGGAACCAAGACTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
* *
1723 CCTG-C
65 CTTGAA
*
1728 TGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTTGGCTTGTGGAAAAGCC
1 TGCTTGGATGGAACCAAGACTTGAACTGACTCGTATGGAAACGAG-TTTGGCTTGTGGAAAAGCC
1793 CTTGAA
65 CTTGAA
* * *
1799 CGCTTGGATGGGACCAAGACTTGAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAAGCT
1 TGCTTGGATGGAACCAAGACTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAAGC-
1864 CCTTG-A
64 CCTTGAA
*
1870 TGCTTGGATGGAACCAA-AGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 TGCTTGGATGGAACCAAGA-CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1934 CTTGAA
65 CTTGAA
1940 TGCTTG
1 TGCTTG
1946 AAGAGAATAC
Statistics
Matches: 256, Mismatches: 22, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
69 45 0.18
70 92 0.36
71 114 0.45
72 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (70 bp):
TGCTTGGATGGAACCAAGACTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
TTGAA
Found at i:2539 original size:50 final size:50
Alignment explanation
Indices: 2391--2539 Score: 253
Period size: 50 Copynumber: 3.0 Consensus size: 50
2381 AAACGCCCTC
* * * *
2391 TGAAAAGCAAATTTTGATTTTGGACTCACAAATGGAATGCAATCTTATCT
1 TGAAAATCAAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATTT
*
2441 TGAAAATCGAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATTT
1 TGAAAATCAAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATTT
2491 TGAAAATCAAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATT
1 TGAAAATCAAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATT
2540 ATAAAACTTC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (50 bp):
TGAAAATCAAATTTTGATATTGAACTCACAAATGGAATGCAATCTTATTT
Done.