Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017827.1 Corchorus olitorius cultivar O-4 contig17860, 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: 6768
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1044 original size:7 final size:7
Alignment explanation
Indices: 1032--1068 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1022 AAAAAATGCA
1032 AATTTTG
1 AATTTTG
1039 AATTTTG
1 AATTTTG
1046 AATTTTG
1 AATTTTG
*
1053 ACTTTTG
1 AATTTTG
*
1060 ACTTTTG
1 AATTTTG
1067 AA
1 AA
1069 GAATGCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (7 bp):
AATTTTG
Found at i:1125 original size:7 final size:7
Alignment explanation
Indices: 1119--1482 Score: 539
Period size: 7 Copynumber: 52.0 Consensus size: 7
1109 GAGCCATGAA
*
1119 TTTTGAA
1 TTTTGAG
1126 TTTTGAG
1 TTTTGAG
1133 TTTTGAG
1 TTTTGAG
1140 TTTTGAG
1 TTTTGAG
1147 TTTTGAG
1 TTTTGAG
1154 TTTTGAG
1 TTTTGAG
1161 TTTTGAG
1 TTTTGAG
1168 TTTTGAG
1 TTTTGAG
1175 TTTTGAG
1 TTTTGAG
1182 TTTTGAG
1 TTTTGAG
1189 TTTTGAG
1 TTTTGAG
1196 TTTTGAG
1 TTTTGAG
1203 TTTTGAG
1 TTTTGAG
1210 TTTTGAG
1 TTTTGAG
1217 TTTTGAG
1 TTTTGAG
1224 TTTTGAG
1 TTTTGAG
1231 TTTTGAG
1 TTTTGAG
1238 TTTTGAG
1 TTTTGAG
1245 TTTTGAG
1 TTTTGAG
1252 TTTTGAG
1 TTTTGAG
1259 TTTTGAG
1 TTTTGAG
1266 TTTTGAG
1 TTTTGAG
1273 TTTTGAG
1 TTTTGAG
1280 TTTTGAG
1 TTTTGAG
1287 TTTTGAG
1 TTTTGAG
1294 TTTTGAG
1 TTTTGAG
1301 TTTTGAG
1 TTTTGAG
1308 TTTTGAG
1 TTTTGAG
1315 TTTTGAG
1 TTTTGAG
1322 TTTTGAG
1 TTTTGAG
*
1329 TTTTGAC
1 TTTTGAG
1336 TTTTGAG
1 TTTTGAG
*
1343 TTTTGAC
1 TTTTGAG
*
1350 TTTTGAA
1 TTTTGAG
*
1357 TTTTGAA
1 TTTTGAG
*
1364 TTTTGAA
1 TTTTGAG
*
1371 TTTTGAA
1 TTTTGAG
*
1378 TTTTGAA
1 TTTTGAG
*
1385 TTTTGAA
1 TTTTGAG
*
1392 TTTTGAA
1 TTTTGAG
*
1399 TTTTGAA
1 TTTTGAG
*
1406 TTTTGAA
1 TTTTGAG
*
1413 TTTTGAA
1 TTTTGAG
*
1420 TTTTGAA
1 TTTTGAG
*
1427 TTTTGAA
1 TTTTGAG
*
1434 TTTTGAA
1 TTTTGAG
*
1441 TTTTGAA
1 TTTTGAG
*
1448 TTTTGAA
1 TTTTGAG
*
1455 TTTTGAA
1 TTTTGAG
*
1462 TTTTGAA
1 TTTTGAG
*
1469 TTTTGAA
1 TTTTGAG
1476 TTTTGAG
1 TTTTGAG
1483 CAATGAAATG
Statistics
Matches: 351, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 351 1.00
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.57
Consensus pattern (7 bp):
TTTTGAG
Found at i:1688 original size:33 final size:33
Alignment explanation
Indices: 1618--1691 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1608 GAAATTATGG
* * * * *
1618 ATTTTGAACTTTGAGTTTTGATATAATATGTAG
1 ATTTTGAAATTTGAATTTTGAAATAATATGCAA
1651 ATTTTGAAATTTGAATTTTGAAATGAA-ATGCAA
1 ATTTTGAAATTTGAATTTTGAAAT-AATATGCAA
1684 ATTTTGAA
1 ATTTTGAA
1692 CTTCTTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (33 bp):
ATTTTGAAATTTGAATTTTGAAATAATATGCAA
Found at i:1892 original size:54 final size:54
Alignment explanation
Indices: 1798--2014 Score: 242
Period size: 54 Copynumber: 4.0 Consensus size: 54
1788 TGATCATCGT
* * * * * * *
1798 AAACTTCT-TGGAATGACCACACTA-GATCAACTTAAGATCAACTAAAATTTTTGA
1 AAACTTCTAT-GAAAGACCACAC-AGGGTCATCTTAAGATCAACTTAGATCTCTGA
* * * *
1852 AAACTTCTATGGAAGACCACACAGGGTCATCTGAAAATCAACTTAGACCTCT-A
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
1905 AAACCTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAA-CTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
* * * *
1960 AAACGTCTATGAAAGACCACACTGGGTCATCTTAAGATCAATTTAGATATCTGA
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
2014 A
1 A
2015 CACAGGGTCA
Statistics
Matches: 140, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
53 5 0.04
54 130 0.93
55 5 0.04
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
Found at i:1928 original size:108 final size:108
Alignment explanation
Indices: 1812--2006 Score: 273
Period size: 108 Copynumber: 1.8 Consensus size: 108
1802 TTCTTGGAAT
* * * *
1812 GACCACACTAGATCAACTTAAGATCAACTAAAATTTTTGAAAACTTCTATGGAAGACCACACAGG
1 GACCACACTAGATCAACTTAAGATCAACTAAAATCTCTGAAAACGTCTATGAAAGACCACACAGG
1877 GTCATCTGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAA
66 GTCATCTGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAA
* * * * * *
1920 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACGTCTATGAAAGACCACACTGG
1 GACCACACTAGATCAACTTAAGATCAACTAAAATCTCTGAAAACGTCTATGAAAGACCACACAGG
* * *
1985 GTCATCTTAAGATCAATTTAGA
66 GTCATCTGAAAATCAACTTAGA
2007 TATCTGAACA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 74 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (108 bp):
GACCACACTAGATCAACTTAAGATCAACTAAAATCTCTGAAAACGTCTATGAAAGACCACACAGG
GTCATCTGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAA
Found at i:2086 original size:53 final size:53
Alignment explanation
Indices: 2020--2137 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
2010 CTGAACACAG
*
2020 GGTCATATGAAGATCAACTTAGACCTCT-AAAAGCTTCTATG-AAGAACCACACT
1 GGTCATATTAAGATCAACTTAGACCTCTGAAAA-CTTCTATGAAAG-ACCACACT
* *
2073 GGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACT
1 GGTCATATTAAGATCAACTTAGACCTCTGAAAACTTCTATGAAAGACCACACT
*
2126 GGATCATTTTAA
1 GG-TCATATTAA
2138 ACACAAAACA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
53 43 0.74
54 15 0.26
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (53 bp):
GGTCATATTAAGATCAACTTAGACCTCTGAAAACTTCTATGAAAGACCACACT
Found at i:2160 original size:144 final size:144
Alignment explanation
Indices: 1870--2148 Score: 429
Period size: 143 Copynumber: 1.9 Consensus size: 144
1860 ATGGAAGACC
*
1870 ACACAGGGTCATCTGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAAGACCACACTGGGTCA
1 ACACAGGGTCATATGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAAGACCACACTGGGTCA
* *
1935 TCTTAAGATCAACTTAGATCTCTGAAAACGTCTATGAAAGACCACACTGGGTCATCTTAAGATCA
66 TCTTAAGATCAACTTAGATCTCTGAAAACGTCTATGAAAGACCACACTGGATCATCTTAAGAACA
***
2000 ATTTAGATATCTGA
131 AAACAGATATCTGA
* *
2014 ACACAGGGTCATATGAAGATCAACTTAGACCTCTAAAAGCTTCTATG-AAGAACCACACT-GGTC
1 ACACAGGGTCATATGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAAG-ACCACACTGGGTC
* *
2077 ATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGATCATTTTAA-ACA
65 ATCTTAAGATCAACTTAGATCTCTGAAAACGTCTATGAAAGACCACACTGGATCATCTTAAGA-A
2141 CAAAACAG
129 CAAAACAG
2149 GAATTTTGAA
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
142 1 0.01
143 70 0.57
144 52 0.42
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (144 bp):
ACACAGGGTCATATGAAAATCAACTTAGACCTCTAAAACCTTCTATGAAAGACCACACTGGGTCA
TCTTAAGATCAACTTAGATCTCTGAAAACGTCTATGAAAGACCACACTGGATCATCTTAAGAACA
AAACAGATATCTGA
Found at i:2300 original size:37 final size:37
Alignment explanation
Indices: 2275--2512 Score: 252
Period size: 37 Copynumber: 6.5 Consensus size: 37
2265 ATGAATTTTG
* * *
2275 AACAAGATTTTGATGAGACACCTAAACAGCGACCTTA
1 AACAAGATTTTGATAAGACACCTAAACAGGGATCTTA
* * * *
2312 AATAAGGA-TTCGATAAGAAACCTAAACAGGGATTTTA
1 AACAA-GATTTTGATAAGACACCTAAACAGGGATCTTA
* * * *
2349 AACAAAATTTTGATGAGACACCTAAATAGGGACCTTA
1 AACAAGATTTTGATAAGACACCTAAACAGGGATCTTA
* *
2386 AATAAGGA-TTTGATAAGAAACCTAAACAGGGATCTTA
1 AACAA-GATTTTGATAAGACACCTAAACAGGGATCTTA
2423 AACAAGATTTTGAT--GACACCTAAACAGGGATCTTA
1 AACAAGATTTTGATAAGACACCTAAACAGGGATCTTA
* * * *
2458 AACAAGA-TTTGATAAGAAACCTAAACAAGAATCTTG
1 AACAAGATTTTGATAAGACACCTAAACAGGGATCTTA
* *
2494 AACAAGGTTTTGATGAGAC
1 AACAAGATTTTGATAAGAC
2513 TGAATTTTGT
Statistics
Matches: 164, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
34 6 0.04
35 27 0.16
36 26 0.16
37 102 0.62
38 3 0.02
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (37 bp):
AACAAGATTTTGATAAGACACCTAAACAGGGATCTTA
Found at i:2347 original size:74 final size:74
Alignment explanation
Indices: 2205--2512 Score: 397
Period size: 74 Copynumber: 4.2 Consensus size: 74
2195 CCTAAACTGG
* * * * * * *
2205 GATTTTGAAGAGACACCAAAACAAGTACCTTAAAATAAGGATTTAATAAGAAAGCTAAACATGAA
1 GATTTTGATGAGACACCTAAACAGGGACCTT-AAATAAGGATTTGATAAGAAACCTAAACAGGAA
* *
2270 TTTTGAACAA
65 TCTTAAACAA
* * *
2280 GATTTTGATGAGACACCTAAACAGCGACCTTAAATAAGGATTCGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
*
2345 TTTAAACAA
66 CTTAAACAA
* * *
2354 AATTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
2419 CTTAAACAA
66 CTTAAACAA
* * *
2428 GATTTTGAT--GACACCTAAACAGGGATCTTAAACAA-GATTTGATAAGAAACCTAAACAAGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
*
2490 CTTGAACAA
66 CTTAAACAA
*
2499 GGTTTTGATGAGAC
1 GATTTTGATGAGAC
2513 TGAATTTTGT
Statistics
Matches: 207, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
71 41 0.20
72 23 0.11
73 3 0.01
74 114 0.55
75 26 0.13
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
CTTAAACAA
Found at i:3584 original size:8 final size:8
Alignment explanation
Indices: 3557--3587 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3547 CCTTTTGATT
3557 TTTTTTTC
1 TTTTTTTC
*
3565 TTTCTTTC
1 TTTTTTTC
3573 TTTTTTTC
1 TTTTTTTC
3581 TTTTTTT
1 TTTTTTT
3588 TCTCACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3608 original size:25 final size:25
Alignment explanation
Indices: 3556--3608 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3546 TCCTTTTGAT
** *
3556 TTTTTTTTCTTTCTTTCTTTTTTTC
1 TTTTTTTTCTCACTTTCTTTTTTGC
3581 TTTTTTTTCTCACTTT-TTTATTTGC
1 TTTTTTTTCTCACTTTCTTT-TTTGC
3606 TTT
1 TTT
3609 CTCTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTTTCTCACTTTCTTTTTTGC
Found at i:3617 original size:20 final size:18
Alignment explanation
Indices: 3556--3617 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
3546 TCCTTTTGAT
3556 TTTTTTTTCTTTCTTTCT-
1 TTTTTTTT-TTTCTTTCTC
3574 TTTTTTCTTTTT-TTTCTCAC
1 TTTTTT-TTTTTCTTTCT--C
* *
3594 TTTTTTATTTGCTTTCTC
1 TTTTTTTTTTTCTTTCTC
3612 TTTTTT
1 TTTTTT
3618 CTTTAGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.14
18 16 0.43
19 5 0.14
20 11 0.30
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTTCTTTCTC
Found at i:4302 original size:28 final size:27
Alignment explanation
Indices: 4261--4331 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
4251 TTGAAAACTC
* *
4261 AAATCCTTTTTGAAAACTGATTT-TTGA
1 AAATCATTTTTGAAAACAG-TTTATTGA
*
4288 AAATCATTTCTTGAAAGCAGTTTATTGA
1 AAATCATTT-TTGAAAACAGTTTATTGA
4316 AAATCATTTTTGAAAA
1 AAATCATTTTTGAAAA
4332 ATGTTCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (27 bp):
AAATCATTTTTGAAAACAGTTTATTGA
Found at i:4333 original size:14 final size:13
Alignment explanation
Indices: 4261--4331 Score: 72
Period size: 14 Copynumber: 5.2 Consensus size: 13
4251 TTGAAAACTC
*
4261 AAATCCTTTTTGA
1 AAATCATTTTTGA
*
4274 AAACTGATTTTTGA
1 AAA-TCATTTTTGA
4288 AAATCATTTCTTG-
1 AAATCATTT-TTGA
*
4301 AAAGCAGTTTATTGA
1 AAATCA-TTT-TTGA
4316 AAATCATTTTTGA
1 AAATCATTTTTGA
4329 AAA
1 AAA
4332 ATGTTCTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
13 20 0.42
14 23 0.48
15 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (13 bp):
AAATCATTTTTGA
Done.