Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019518.1 Corchorus olitorius cultivar O-4 contig19551, 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: 9372
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29 GAGTTGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1238 original size:15 final size:15
Alignment explanation
Indices: 1218--1250 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1208 AAAATTCAAA
1218 AAAATGA-GAAAAGAT
1 AAAATGATGAAAAG-T
1233 AAAATGATGAAAAGT
1 AAAATGATGAAAAGT
1248 AAA
1 AAA
1251 GCTCTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (15 bp):
AAAATGATGAAAAGT
Found at i:1336 original size:68 final size:67
Alignment explanation
Indices: 1256--1637 Score: 441
Period size: 68 Copynumber: 5.7 Consensus size: 67
1246 GTAAAGCTCT
* *
1256 ATTTTCTATTTCCAAAAATACCCTTTTGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTT
1 ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTCTTGCATTTAAGTTT
1321 AG
66 AG
* * * * * *
1323 CATTTTCTATTTCCAAAAATACCCTTTCGGTCCAATGGTCATTTTCATCTTTTTTCATTTAAGTT
1 -ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTCTTGCATTTAAGTT
1388 TAG
65 TAG
* *
1391 TGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
1 -ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTCTTGCATTTAAGTT
1456 TAG
65 TAG
* * * ** *
1459 TATTTTC-GTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCTTCTTGTGTTTAGGTT
1 -ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTCTTGCATTTAAGTT
1523 TAG
65 TAG
* * * * *
1526 -TTTT-TCTTTCCAAAAATATCCTTCCGGTCGAAGGGTCAGTTTCGTCAGGATATTGCATTTAAG
1 ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTC---TTCTTGCATTTAAG
*
1589 TCTAG
63 TTTAG
* * *
1594 --TCTCTCTTTCCAAAGAATACCCTTTCGGTCGAAAGGTCAGTTTC
1 ATTTTCTATTTCCAAA-AATACCCTTTCGGTCGAAGGGTCAGTTTC
1638 ATCATTTTCG
Statistics
Matches: 274, Mismatches: 34, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
65 42 0.15
67 55 0.20
68 151 0.55
69 26 0.09
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (67 bp):
ATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTCTTGCATTTAAGTTT
AG
Found at i:1582 original size:135 final size:133
Alignment explanation
Indices: 1257--1645 Score: 489
Period size: 136 Copynumber: 2.9 Consensus size: 133
1247 TAAAGCTCTA
*
1257 TTTTCTATTTCCAAAAATACCCTTTTGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTTA
1 TTTTC-ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTTA
* * * * *
1322 GCATTTTCTATTTCCAAAAATACCCTTTCGGTCCAATGGTCATTTTCATCTTTTTTCATTTAAGT
65 GTATTTTC--TTTCCAAAAATACCCTTTCGGTCGAAAGGTCAGTTTCATCTTTTGTCATTTAAGT
1387 TTAGTG
128 TTAGTG
1393 TTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTTA
1 TTTTC-ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTTA
* * * *
1458 GTATTTTCGTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCTTCTTGT-GTTTAGGT
65 GTATTTTC-TTTCCAAAAATACCCTTTCGGTCGAAAGGTCAGTTTCATCTT-TTGTCATTTAAGT
1522 TTAGT-
128 TTAGTG
* * * * * *
1527 TTTTC-TTTCCAAAAATATCCTTCCGGTCGAAGGGTCAGTTTCGTCAGGATATTGCATTTAAGTC
1 TTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC---TTCTTGCATTTAAGTT
* *
1591 TAGT-CTCTCTTTCCAAAGAATACCCTTTCGGTCGAAAGGTCAGTTTCATCATTTT
63 TAGTATTTTCTTTCCAAA-AATACCCTTTCGGTCGAAAGGTCAGTTTCATC-TTTT
1646 CGCACTTCCG
Statistics
Matches: 227, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
132 37 0.16
133 8 0.04
134 40 0.18
135 68 0.30
136 74 0.33
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (133 bp):
TTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTTTAG
TATTTTCTTTCCAAAAATACCCTTTCGGTCGAAAGGTCAGTTTCATCTTTTGTCATTTAAGTTTA
GTG
Found at i:4605 original size:145 final size:145
Alignment explanation
Indices: 4342--4605 Score: 474
Period size: 145 Copynumber: 1.8 Consensus size: 145
4332 CCTATTTTGA
*
4342 CTAGGATTTCAACTCTAGGAAGACTTTTAAGCTAACGCGGAGTCTAAGTTAACCTCAAAAACGTC
1 CTAGGATTTCAACTCTAGGAAGACTTTTAAGCTAACGCGGAGTCTAAGTTAACCTAAAAAACGTC
* *
4407 CTAGACTCCTTTCCTACTTAGAATTGGATTTTCTAGAGTTTTTTCCACTATAAACGTCCTATAGT
66 CTAGACTCCTTTCCTACTTAGAATTGGATTTTCTAGAGCTATTTCCACTATAAACGTCCTATAGT
4472 GGAGTCTAAGTTAAG
131 GGAGTCTAAGTTAAG
* *
4487 CTAGGATTTCAACTCTAGGAAGACTTTTAAGTTAACGCGGAGTCTAAGTTAGCCTAAAAAACGTC
1 CTAGGATTTCAACTCTAGGAAGACTTTTAAGCTAACGCGGAGTCTAAGTTAACCTAAAAAACGTC
*
4552 CTAGACTCCTTTCCTACTTAGAATTGGATTTTCTAGGGCTATTTCCACTATAAA
66 CTAGACTCCTTTCCTACTTAGAATTGGATTTTCTAGAGCTATTTCCACTATAAA
4606 TAGCCATCTT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 113 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (145 bp):
CTAGGATTTCAACTCTAGGAAGACTTTTAAGCTAACGCGGAGTCTAAGTTAACCTAAAAAACGTC
CTAGACTCCTTTCCTACTTAGAATTGGATTTTCTAGAGCTATTTCCACTATAAACGTCCTATAGT
GGAGTCTAAGTTAAG
Found at i:6300 original size:14 final size:15
Alignment explanation
Indices: 6281--6309 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6271 AATTATTGAA
6281 TTTAA-TTTTTAATT
1 TTTAATTTTTTAATT
6295 TTTAATTTTTTAATT
1 TTTAATTTTTTAATT
6310 AATTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATTTTTTAATT
Found at i:7150 original size:19 final size:19
Alignment explanation
Indices: 7123--7180 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
7113 GCTCGGCCAG
*
7123 CCGGCTTGGCCGGTCCGAA
1 CCGGTTTGGCCGGTCCGAA
* * *
7142 CCGGTTTGGTCGGACCGGA
1 CCGGTTTGGCCGGTCCGAA
* *
7161 CCAGTTTGACCCGGTCCGAA
1 CCGGTTTG-GCCGGTCCGAA
7181 AAAAAGTTTG
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.14, C:0.33, G:0.34, T:0.19
Consensus pattern (19 bp):
CCGGTTTGGCCGGTCCGAA
Found at i:7933 original size:13 final size:13
Alignment explanation
Indices: 7915--7961 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
7905 TCTTCTCTTT
7915 ATTTCATTTCTCA
1 ATTTCATTTCTCA
7928 ATTTCATTT-T-A
1 ATTTCATTTCTCA
7939 ATTTTCATTTCTCA
1 A-TTTCATTTCTCA
7953 ATTTCATTT
1 ATTTCATTT
7962 TAGTGGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 18 0.58
14 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTCATTTCTCA
Found at i:7944 original size:25 final size:25
Alignment explanation
Indices: 7916--7963 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
7906 CTTCTCTTTA
7916 TTTCATTTCTCAATTTCATTTTAAT
1 TTTCATTTCTCAATTTCATTTTAAT
7941 TTTCATTTCTCAATTTCATTTTA
1 TTTCATTTCTCAATTTCATTTTA
7964 GTGGTCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTCATTTCTCAATTTCATTTTAAT
Done.