Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019493.1 Corchorus olitorius cultivar O-4 contig19526, 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: 33451
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:211 original size:21 final size:24
Alignment explanation
Indices: 182--232 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
172 TTTTGAACTC
182 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
205 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
228 ATTAT
1 ATTAT
233 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:227 original size:25 final size:25
Alignment explanation
Indices: 182--230 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
172 TTTTGAACTC
*
182 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
207 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
231 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:5335 original size:13 final size:13
Alignment explanation
Indices: 5309--5344 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5299 AAAAGCTTGG
5309 TTTTGAAGAAGTGC
1 TTTTGAA-AAGTGC
5323 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
5336 TTTTTAAAA
1 TTTTGAAAA
5345 TTGGGGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:5875 original size:21 final size:22
Alignment explanation
Indices: 5831--5909 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
5821 TATTTTTATG
5831 AAATTTTGATAACCACCATATA
1 AAATTTTGATAACCACCATATA
* **
5853 AACTTTTGATAATTACC-TATA
1 AAATTTTGATAACCACCATATA
* * *
5874 AAATTGTGATAAACTCCATA-A
1 AAATTTTGATAACCACCATATA
*
5895 AAGACTTTGATAACC
1 AA-ATTTTGATAACC
5910 TAACTATGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 19 0.43
22 25 0.57
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCACCATATA
Found at i:8280 original size:19 final size:18
Alignment explanation
Indices: 8256--8293 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
8246 GTTCGTATGG
8256 AAGTCCAAAGAAGGAGTTC
1 AAGTCCAAAGAAGG-GTTC
8275 AAGTCCAAAGAAGGGTTC
1 AAGTCCAAAGAAGGGTTC
8293 A
1 A
8294 GGATGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (18 bp):
AAGTCCAAAGAAGGGTTC
Found at i:9971 original size:22 final size:22
Alignment explanation
Indices: 9896--10063 Score: 96
Period size: 22 Copynumber: 7.5 Consensus size: 22
9886 AGGAGATTAA
* *
9896 CAAAATCTCATAGGGAAAGTTA-
1 CAAAATTTCATA-GGAAGGTTAT
9918 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
9941 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
9963 CAAAGTTTCATATGGAA-TTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
9985 CACAATTTTATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
* *
10006 CAAAAAATTTTATAGTG-TGGTTAT
1 C--AAAATTTCATAG-GAAGGTTAT
* * *
10030 CAAAATTTAATA-TAATAGTTAT
1 CAAAATTTCATAGGAA-GGTTAT
10052 CAAAATTTCATA
1 CAAAATTTCATA
10064 AAAATATTCA
Statistics
Matches: 115, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
21 12 0.10
22 69 0.60
23 28 0.24
24 6 0.05
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:10034 original size:24 final size:23
Alignment explanation
Indices: 9988--10034 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
9978 AATTTATCAC
9988 AATTTTATAGGTAATTATCAAAA
1 AATTTTATAGGTAATTATCAAAA
**
10011 AATTTTATAGTGTGGTTATCAAAA
1 AATTTTATAG-GTAATTATCAAAA
10035 TTTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (23 bp):
AATTTTATAGGTAATTATCAAAA
Found at i:10808 original size:13 final size:13
Alignment explanation
Indices: 10775--10808 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10765 TAGCCTTGGT
*
10775 CATTATTACACAC
1 CATTATTGCACAC
*
10788 TATTATTGCACAC
1 CATTATTGCACAC
10801 CATTATTG
1 CATTATTG
10809 TATAATGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (13 bp):
CATTATTGCACAC
Found at i:10858 original size:10 final size:11
Alignment explanation
Indices: 10834--10864 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
10824 ATGACATCAT
10834 CATGTCTACAA
1 CATGTCTACAA
10845 CATGTCTA-AA
1 CATGTCTACAA
10855 CATGTCTACA
1 CATGTCTACA
10865 TAAGTCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (11 bp):
CATGTCTACAA
Found at i:28530 original size:332 final size:334
Alignment explanation
Indices: 27871--28594 Score: 903
Period size: 332 Copynumber: 2.2 Consensus size: 334
27861 AAAAGGTATG
* * * *
27871 AAAAGCAATATTAGAAGCATGAAAAGCCCTTCAGTCTTTTTGGCATTGAGTTATATATTTTTTAT
1 AAAATCAATATTAGAAGCATG-AAAGCCTTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTAT
* * * * *
27936 TAGTATTGTGGCCCAAAATTGAGGAGAAATTTCTTGGGTCAATTTTTGCAACATTTTAGCTGAAA
65 GAGTATCGTGGCCCAAAATTGAGGAGAAATTTCTTAGGTCAATTTTTACAAAATTTTAGCTGAAA
* *
28001 TCGTGTATTAATCATCACGGTTTTTGACTAAAAACGCGTTCCGGAACCTCGCCTCAGTTTTGCAC
130 TCGTGTACTAATCATCACGGTGTTTGACTAAAAACGCGTTCCGGAACCTCGCCTCAGTTTTGCAC
* * *
28066 GATTTTTGGCACCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTACCCACATTGGA
195 GATTTTTGGCACCAAGACTCATTGAAATATCTATATCCATCTAACAAAATCTCACCCACATTGGA
* * *
28131 TTTAAGTATTTGTTTTTACGAGCATATGAATCATGTTTCGATTCAATCAGGAATTAATACGG-AA
260 TTTAAGAATTTGTTTTTACGAGCATATCAATCATGTTTCGATTCAATCAGAAATTAATACGGAAA
*
28195 AAAATAG-GA
325 AAAATAGAAA
* * * *
28204 AAAA-CGATATTAGAAGCATGAATAGCCTTTCAATCTTTTTAGTGTTGAATTATATATTTTTTAT
1 AAAATCAATATTAGAAGCATGAA-AGCCTTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTAT
* *
28268 GAGTATCGTGGCCCAAAATTTAGGA-AAA-TTCTTTCAGGTCAATTTTTATAAAATTTTAG-TCG
65 GAGTATCGTGGCCCAAAATTGAGGAGAAATTTC-TT-AGGTCAATTTTTACAAAATTTTAGCT-G
* * **
28330 AAATCGTGTACTAA-CTATCACGGTGTTTGGCTAAAAACGCGTTCTGGGTCCCCTCG-CTCAGTT
127 AAATCGTGTACTAATC-ATCACGGTGTTTGACTAAAAACGCGTTC-CGG-AACCTCGCCTCAGTT
* * * ** *
28393 TTGCATGATTTTTGGCGCCAAGACTCATTGTAATATCTATATTTATCTAACAAAATCTCAGCCAC
189 TTGCACGATTTTTGGCACCAAGACTCATTGAAATATCTATATCCATCTAACAAAATCTCACCCAC
* * *
28458 ATTGGATTTAAGAATTTGTTTTTAC-AGGCATCTCAATCCA-GTTTCGATTTAATTAGAAATTAA
254 ATTGGATTTAAGAATTTGTTTTTACGA-GCATATCAAT-CATGTTTCGATTCAATCAGAAATTAA
* *
28521 TTC-GAAAAAAATTGAAA
317 TACGGAAAAAAATAGAAA
* *
28538 AAAATCAATATTAGAATCGTGAGAAGCCTTTCAATCTTTTTGGCGTTGAGTTATATA
1 AAAATCAATATTAGAAGCATGA-AAGCCTTTCAATCTTTTTGGCGTTGAGTTATATA
28595 CTCCCTCTGT
Statistics
Matches: 334, Mismatches: 44, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
330 3 0.01
331 9 0.03
332 134 0.40
333 131 0.39
334 12 0.04
335 44 0.13
336 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (334 bp):
AAAATCAATATTAGAAGCATGAAAGCCTTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATG
AGTATCGTGGCCCAAAATTGAGGAGAAATTTCTTAGGTCAATTTTTACAAAATTTTAGCTGAAAT
CGTGTACTAATCATCACGGTGTTTGACTAAAAACGCGTTCCGGAACCTCGCCTCAGTTTTGCACG
ATTTTTGGCACCAAGACTCATTGAAATATCTATATCCATCTAACAAAATCTCACCCACATTGGAT
TTAAGAATTTGTTTTTACGAGCATATCAATCATGTTTCGATTCAATCAGAAATTAATACGGAAAA
AAATAGAAA
Done.