Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024782.1 Corchorus olitorius cultivar O-4 contig24815, 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: 28524
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:356 original size:6 final size:6
Alignment explanation
Indices: 325--355 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
315 TGGTTGTGCA
*
325 GTCGGG GTCGGG GTCGGG GTCGGG GACGGG G
1 GTCGGG GTCGGG GTCGGG GTCGGG GTCGGG G
356 AATACACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.68, T:0.13
Consensus pattern (6 bp):
GTCGGG
Found at i:989 original size:167 final size:172
Alignment explanation
Indices: 704--1041 Score: 447
Period size: 168 Copynumber: 2.0 Consensus size: 172
694 CGTACGCAAC
* * *
704 TGTCTCGTTGGTAGACTCACCCAACAAAACCAAATGAGCGATATGGGTCAGATCCGGATTAGTTA
1 TGTCCCGTTGGTAGACTCACCCAACAAAACCAAATGAGCGATACGGGTCAGATCCGAATTAGTTA
* * *
769 AGGGAACAACGTGGTTTGAAACCATGCATCTAGTGATTATGATTTCAAATATTAATAAT-TAA-T
66 AGGGAACAACATGATTTGAAACCATGCATCTAGTGATTATGATTTCAAATATTAACAATGTAATT
*
832 TTTTTT-TT-CATTA-CGTGCTTTTTATATTTTAATTGATACA
131 TTTTTTATTGCA-TAGCGTGCTTTTTACATTTTAATTGATACA
* ** * * * *
872 TGTCCCGTTGGTAGACTCACCCACCAAAATTAGATGAGCGATGCGGGTCGGATCTGAATTAGTT-
1 TGTCCCGTTGGTAGACTCACCCAACAAAACCAAATGAGCGATACGGGTCAGATCCGAATTAGTTA
* *
936 AGGGAACATCATGATTT-AAATCCATGTATCTAGTGATTATGATTTCAAATATTAACAATGTAAT
66 AGGGAACAACATGATTTGAAA-CCATGCATCTAGTGATTATGATTTCAAATATTAACAATGTAAT
*
1000 TTTTTTTATTGCATAGTTGTGCTTTTTACATTTTAATTGATA
130 TTTTTTTATTGCATAG-CGTGCTTTTTACATTTTAATTGATA
1042 TTTGAAGGTT
Statistics
Matches: 146, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
166 3 0.02
167 50 0.34
168 57 0.39
169 7 0.05
170 4 0.03
171 2 0.01
172 23 0.16
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (172 bp):
TGTCCCGTTGGTAGACTCACCCAACAAAACCAAATGAGCGATACGGGTCAGATCCGAATTAGTTA
AGGGAACAACATGATTTGAAACCATGCATCTAGTGATTATGATTTCAAATATTAACAATGTAATT
TTTTTTATTGCATAGCGTGCTTTTTACATTTTAATTGATACA
Found at i:1459 original size:54 final size:56
Alignment explanation
Indices: 1380--1484 Score: 178
Period size: 54 Copynumber: 1.9 Consensus size: 56
1370 TAAAAAAAAA
1380 AAAAAACAAAACAAAACAAGCACAACACTAACCCTTTAAAAGATTTTGTAAAAACC
1 AAAAAACAAAACAAAACAAGCACAACACTAACCCTTTAAAAGATTTTGTAAAAACC
* *
1436 AAAAAA-AAAA-AAAACAAGTACAACACTAACCCTTTCAAAGATTTTGTAA
1 AAAAAACAAAACAAAACAAGCACAACACTAACCCTTTAAAAGATTTTGTAA
1485 TTTGTCATCG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 37 0.79
55 4 0.09
56 6 0.13
ACGTcount: A:0.57, C:0.19, G:0.06, T:0.18
Consensus pattern (56 bp):
AAAAAACAAAACAAAACAAGCACAACACTAACCCTTTAAAAGATTTTGTAAAAACC
Found at i:1621 original size:13 final size:13
Alignment explanation
Indices: 1603--1634 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1593 TAATTTGTTT
1603 GTTTGTTTATTTG
1 GTTTGTTTATTTG
1616 GTTTGTTTATTTG
1 GTTTGTTTATTTG
1629 GTTTGT
1 GTTTGT
1635 AGGTAGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.25, T:0.69
Consensus pattern (13 bp):
GTTTGTTTATTTG
Found at i:1789 original size:78 final size:78
Alignment explanation
Indices: 1699--1850 Score: 286
Period size: 78 Copynumber: 1.9 Consensus size: 78
1689 ATTGTATTTG
*
1699 TTGGGAAGGGGTTTGTTGGCTCATAGATTAGCGAATAAGTTTGTTGGCTTATAGATTAGCGTTTC
1 TTGGGAAAGGGTTTGTTGGCTCATAGATTAGCGAATAAGTTTGTTGGCTTATAGATTAGCGTTTC
1764 AATAATGTAGCTA
66 AATAATGTAGCTA
*
1777 TTGGGAAAGGGTTTGTTGGCTCATAGATTAGCGAATGAGTTTGTTGGCTTATAGATTAGCGTTTC
1 TTGGGAAAGGGTTTGTTGGCTCATAGATTAGCGAATAAGTTTGTTGGCTTATAGATTAGCGTTTC
1842 AATAATGTA
66 AATAATGTA
1851 ACTAATTATG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.38
Consensus pattern (78 bp):
TTGGGAAAGGGTTTGTTGGCTCATAGATTAGCGAATAAGTTTGTTGGCTTATAGATTAGCGTTTC
AATAATGTAGCTA
Found at i:2013 original size:66 final size:62
Alignment explanation
Indices: 1911--2038 Score: 211
Period size: 66 Copynumber: 2.0 Consensus size: 62
1901 CTCATTAATC
*
1911 AAAAATTTTATTTTTAAAAAAAAAAGTTTTTGTAATTTGAGAGGACTCAAGCCTTAGCTCGT
1 AAAAAGTTTATTTTTAAAAAAAAAAGTTTTTGTAATTTGAGAGGACTCAAGCCTTAGCTCGT
1973 AAAAAGTTTATTTCTTAAAAACAAAAAGAGTTTTTGTAATTTGAGAGGACTCAAGCCTTAGCTCG
1 AAAAAGTTTATTT-TT-AAAA-AAAAA-AGTTTTTGTAATTTGAGAGGACTCAAGCCTTAGCTCG
2038 T
62 T
2039 GGCCTCAGTC
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
62 12 0.20
63 2 0.03
64 4 0.07
65 5 0.08
66 38 0.62
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (62 bp):
AAAAAGTTTATTTTTAAAAAAAAAAGTTTTTGTAATTTGAGAGGACTCAAGCCTTAGCTCGT
Found at i:3121 original size:31 final size:31
Alignment explanation
Indices: 3086--3192 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 31
3076 GTGTCCGACG
* *
3086 TGACATGCCACGTGTACCAAAAAGCGACATA
1 TGACATGCCACGTGTACCAAAAAGTGACACA
*
3117 TGACACGCCACGTGTACCAAAAAGTGACACA
1 TGACATGCCACGTGTACCAAAAAGTGACACA
* * ** *
3148 TGGCATGCCATGTGTTTCAAAAAGTGACACG
1 TGACATGCCACGTGTACCAAAAAGTGACACA
*
3179 TGGCATGCCACGTG
1 TGACATGCCACGTG
3193 CACACAGGGA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (31 bp):
TGACATGCCACGTGTACCAAAAAGTGACACA
Found at i:5900 original size:13 final size:13
Alignment explanation
Indices: 5882--5907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5872 AAGTTAACAA
5882 CAAAAATCATCAC
1 CAAAAATCATCAC
5895 CAAAAATCATCAC
1 CAAAAATCATCAC
5908 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:7464 original size:22 final size:22
Alignment explanation
Indices: 7415--7465 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
7405 AAATATCACC
* **
7415 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
7437 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
7460 A-AATTA
1 ATAATTA
7466 GGCAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:24587 original size:211 final size:210
Alignment explanation
Indices: 24178--24603 Score: 672
Period size: 211 Copynumber: 2.0 Consensus size: 210
24168 TCTGTCAACC
* * * *
24178 TGTAAAGACATATGTACGACCTCATCGGAAGTAATATCGAGTCTTCTGGAACGACTGCCATAAGT
1 TGTAAACACATATGTACGACCTCATCGGAAGTAATATCGAGTCTGCTGGAACGACTACCATAAGC
* * *
24243 ATATGATGTTCCTCCGCAATAACCTCCCATATCATGTCTCTAACTTTGATTGCCTCGTCCCCAAA
66 ATATGATGCTCCTCCGCAATAACCTCCCATATCATGTCTCTAACTCTAATTGCCTCGTCCCCAAA
* * *
24308 CCCATTTCTAATGCTAGGCAAGTCGAGTAGATGTAGAGGCCCTAAATAATTATTATCGAGATAAC
131 CCCATCTCTAATGCTAAGCAAGTCGAGTAGATGTAGAGGCCCTAAAGAATTATTATCGAGATAAC
24373 AAATCCTCATCTGAA
196 AAATCCTCATCTGAA
* ** * *
24388 TGTAAACACATCTGTACGGTCTCATTGGAAGTAATATTGGAGTCTGCTGGAACGACTACCATAAG
1 TGTAAACACATATGTACGACCTCATCGGAAGTAATA-TCGAGTCTGCTGGAACGACTACCATAAG
* *
24453 CATATGTTGCTCCTTCGCAATAACCTCCCATATCATGTCTCTAACTCTAATTGCCTCGTCCCCAA
65 CATATGATGCTCCTCCGCAATAACCTCCCATATCATGTCTCTAACTCTAATTGCCTCGTCCCCAA
* *
24518 ACCCATCTCTAATGCTAAGCAAGTCGAGTAGATGTAGAGGTCCTAAAGAATTATTATCGGGATAA
130 ACCCATCTCTAATGCTAAGCAAGTCGAGTAGATGTAGAGGCCCTAAAGAATTATTATCGAGATAA
24583 CAAATCCTCATCTGAA
195 CAAATCCTCATCTGAA
24599 TGTAA
1 TGTAA
24604 GTCCCCCACG
Statistics
Matches: 196, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
210 31 0.16
211 165 0.84
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (210 bp):
TGTAAACACATATGTACGACCTCATCGGAAGTAATATCGAGTCTGCTGGAACGACTACCATAAGC
ATATGATGCTCCTCCGCAATAACCTCCCATATCATGTCTCTAACTCTAATTGCCTCGTCCCCAAA
CCCATCTCTAATGCTAAGCAAGTCGAGTAGATGTAGAGGCCCTAAAGAATTATTATCGAGATAAC
AAATCCTCATCTGAA
Done.