Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011180.1 Corchorus olitorius cultivar O-4 contig11213, 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: 43464
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1130 original size:22 final size:23
Alignment explanation
Indices: 1102--1163 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
1092 AATTCTTTGT
1102 GATTATCAAAATTTCATA-TGGA
1 GATTATCAAAATTTCATAGTGGA
*
1124 GATTATCAAAACTTT-ATAGTGTA
1 GATTATCAAAA-TTTCATAGTGGA
*
1147 G-TTATCAAAATTCCATA
1 GATTATCAAAATTTCATA
1164 CAGTCGCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.06
22 26 0.74
23 7 0.20
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGGA
Found at i:1199 original size:22 final size:22
Alignment explanation
Indices: 1174--1295 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
1164 CAGTCGCTAA
*
1174 CAAAATTTCATAAAAAAGTTAT
1 CAAAATTTCATAAAAAGGTTAT
** ***
1196 CAAAATTTTTTAGCGAGGTTAAT
1 CAAAATTTCATAAAAAGGTT-AT
*
1219 -AAAATTTCATACAAAGGTTAT
1 CAAAATTTCATAAAAAGGTTAT
* * ***
1240 CGAAATTTTATAGTGTA-GTTAT
1 CAAAATTTCATA-AAAAGGTTAT
* *
1262 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAAAAAGGTTAT
1284 CAAAATTTCATA
1 CAAAATTTCATA
1296 GGGAGGGCGG
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
21 4 0.05
22 68 0.91
23 3 0.04
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAAAAAGGTTAT
Found at i:1223 original size:44 final size:44
Alignment explanation
Indices: 1174--1296 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
1164 CAGTCGCTAA
* *
1174 CAAAATTTCATAAAAAAGTTATCAAAATTTTTTAGCG-AGGTTAAT
1 CAAAATTTCATAAAAAGGTTATCAAAATTTTATAGCGTA-GTT-AT
* * *
1219 -AAAATTTCATACAAAGGTTATCGAAATTTTATAGTGTAGTTAT
1 CAAAATTTCATAAAAAGGTTATCAAAATTTTATAGCGTAGTTAT
* * *
1262 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAG
1 CAAAATTTCATAAAAAGGTTATCAAAATTTTATAG
1297 GGAGGGCGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 2 0.03
44 63 0.95
45 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAAAAAGGTTATCAAAATTTTATAGCGTAGTTAT
Found at i:1366 original size:23 final size:22
Alignment explanation
Indices: 1340--1391 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1330 ATATCCTAAG
1340 GAGGTTAAAAAAAATTTCATAGA
1 GAGGTTAAAAAAAATTT-ATAGA
*** *
1363 GAGGTTATGGAAAATTTATGGA
1 GAGGTTAAAAAAAATTTATAGA
1385 GAGGTTA
1 GAGGTTA
1392 TCAAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.42, C:0.02, G:0.27, T:0.29
Consensus pattern (22 bp):
GAGGTTAAAAAAAATTTATAGA
Found at i:1389 original size:22 final size:23
Alignment explanation
Indices: 1350--1392 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1340 GAGGTTAAAA
1350 AAAATTTCATAGAGAGGTTATGG
1 AAAATTTCATAGAGAGGTTATGG
*
1373 AAAATTT-ATGGAGAGGTTAT
1 AAAATTTCATAGAGAGGTTAT
1393 CAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (23 bp):
AAAATTTCATAGAGAGGTTATGG
Found at i:1407 original size:20 final size:20
Alignment explanation
Indices: 1350--1414 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 20
1340 GAGGTTAAAA
*
1350 AAAATTTCATAGAGAGGTTATGG
1 AAAATTT-AT-GAGAGGTTAT-C
1373 AAAATTTATGGAGAGGTTATC
1 AAAATTTAT-GAGAGGTTATC
*
1394 AAAATTATAT-AGAGGATATC
1 AAAATT-TATGAGAGGTTATC
1414 A
1 A
1415 CAGTTTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 10 0.26
21 6 0.16
22 15 0.39
23 7 0.18
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.31
Consensus pattern (20 bp):
AAAATTTATGAGAGGTTATC
Found at i:1468 original size:22 final size:22
Alignment explanation
Indices: 1434--1669 Score: 129
Period size: 22 Copynumber: 10.7 Consensus size: 22
1424 TCTCATAAGA
**
1434 AGGTTATTGAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
1456 TGGTTATCAAAATTTTATGAG-G
1 AGGTTATCAAAATTTCAT-AGTG
* *
1478 AGGTCATCAAAATTTTCATAGCG
1 AGGTTATCAAAA-TTTCATAGTG
* * *
1501 CGGTTA-C-CAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
1521 TGGTTATCAAAATTTTATAAG-G
1 AGGTTATCAAAATTTCAT-AGTG
* * * * *
1543 AGATTATCAAAATTTTACACTC
1 AGGTTATCAAAATTTCATAGTG
* *
1565 AGGTTATCAAAATTTCACAATG
1 AGGTTATCAAAATTTCATAGTG
* * * * *
1587 TGATTAACAAATTTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * *
1609 AGATTATCGAAATTTCATATTG
1 AGGTTATCAAAATTTCATAGTG
* *
1631 AGGTTATCAAATTTTTCACAGTG
1 AGGTTATCAAA-ATTTCATAGTG
* * *
1654 TGGTTATTAAGATTTC
1 AGGTTATCAAAATTTC
1670 TATATTGGAA
Statistics
Matches: 161, Mismatches: 45, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
20 13 0.08
21 4 0.02
22 114 0.71
23 30 0.19
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:1622 original size:66 final size:66
Alignment explanation
Indices: 1530--1655 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
1520 GTGGTTATCA
*
1530 AAATTTTATAAGGAGATTATCAAAATTTTACACTCAGGTTATCAAA-ATTTCACAATGTGATTAA
1 AAATTTTATAAGGAGATTATCAAAATTTCACACTCAGGTTATCAAATATTTCACAATGTGATTAA
1594 C
66 C
* * * * * * *
1595 AAATTTTCATAGGGAGATTATCGAAATTTCATATTGAGGTTATCAAATTTTTCACAGTGTG
1 AAATTTT-ATAAGGAGATTATCAAAATTTCACACTCAGGTTATCAAATATTTCACAATGTG
1656 GTTATTAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 7 0.14
66 33 0.65
67 11 0.22
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (66 bp):
AAATTTTATAAGGAGATTATCAAAATTTCACACTCAGGTTATCAAATATTTCACAATGTGATTAA
C
Found at i:11332 original size:39 final size:40
Alignment explanation
Indices: 11276--11356 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
11266 TTTAATTCCT
11276 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
11316 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
11355 AT
1 AT
11357 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:11383 original size:25 final size:24
Alignment explanation
Indices: 11347--11393 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
11337 AATACTTACA
11347 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
11371 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
11394 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:11707 original size:204 final size:205
Alignment explanation
Indices: 11465--11878 Score: 733
Period size: 206 Copynumber: 2.0 Consensus size: 205
11455 TTCCTTAATA
11465 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
11530 ATTTAATAAATCAACCACTAATATTC-AACTAATTTTTTTTGGTATAGTTCTATATAT-ATAATA
66 ATTTAATAAATCAACCACTAATATTCTAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
*
11593 GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAAACTTAAAAAATTAATAACA
131 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAAACTTAAAAAATTAATAACA
11658 TTCACCATTG
196 TTCACCATTG
11668 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * * *
11733 AATTTAATAAATCAACCACTAATGTTCTAACTAATTTTTTTTTGTATCGTTTTATATATAATAAT
65 AATTTAATAAATCAACCACTAATATTCTAACTAATTTTTTTTGGTATAGTTCTATATATAATAAT
* * *
11798 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAT
130 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAAACTTAAAAAATTAATAAC
11863 ATTCACCATTG
195 ATTCACCATTG
11874 ATAAA
1 ATAAA
11879 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
203 16 0.08
204 74 0.37
205 28 0.14
206 82 0.41
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (205 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATATTCTAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAAACTTAAAAAATTAATAACA
TTCACCATTG
Found at i:12453 original size:36 final size:36
Alignment explanation
Indices: 12399--12468 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
12389 GAGATTTTGG
* * *
12399 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA
*
12435 AGAAATATAATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAA
12469 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Found at i:25105 original size:2 final size:2
Alignment explanation
Indices: 25098--25127 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25088 CTAAAACTAG
*
25098 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25128 ATTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:27706 original size:2 final size:2
Alignment explanation
Indices: 27699--27725 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27689 TATTAAATTG
27699 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
27726 GATTATCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38854 original size:14 final size:14
Alignment explanation
Indices: 38835--38865 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38825 TGGAAGCTTT
*
38835 CTTCATTTTTCTTA
1 CTTCATTTTTCTAA
38849 CTTCATTTTTCTAA
1 CTTCATTTTTCTAA
38863 CTT
1 CTT
38866 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTCATTTTTCTAA
Found at i:39052 original size:5 final size:5
Alignment explanation
Indices: 39042--39070 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39032 TTATGGTGGC
39042 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39071 TACTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:39915 original size:7 final size:7
Alignment explanation
Indices: 39903--39944 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
39893 TCTCAGCCTC
39903 AGCCATG
1 AGCCATG
39910 AGCCATG
1 AGCCATG
39917 AGCCATG
1 AGCCATG
39924 AGCCATG
1 AGCCATG
39931 AGCCATG
1 AGCCATG
39938 AGCCATG
1 AGCCATG
39945 GCCTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
AGCCATG
Found at i:42548 original size:13 final size:13
Alignment explanation
Indices: 42530--42556 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42520 AAACAACTAA
42530 AAAGCACTTCTGG
1 AAAGCACTTCTGG
42543 AAAGCACTTCTGG
1 AAAGCACTTCTGG
42556 A
1 A
42557 TTTTTCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Done.