Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011425.1 Corchorus olitorius cultivar O-4 contig11458, 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: 14574
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:999 original size:303 final size:303
Alignment explanation
Indices: 447--1034 Score: 891
Period size: 303 Copynumber: 1.9 Consensus size: 303
437 TGTTTCTCAA
* * *
447 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAAGTGTTCCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAAGTGTCCCACGTTTTTATACTATTCTT
* * *
512 TGCAATTGCTGACTCACTTAAGTTTTTATATATAGGGTCTTCAAGAGTCTTCTTAACAAATGCAT
66 CGCAATTGCTGACTCACTTAAGTCTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* *
577 CGTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACAATTCTTAGTGACGACTCCGGTTTTG
131 CGTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACAATTCTTAGTGACGACTCCGGTATAG
* * * * *
642 AATATACTTGTGAAAACTTCCCTGGCACATGGCAGTTCCATTTTTGTTTTGCAATTGTTTTCCTT
196 AATATACTTGTGAAAACTTCCCTAGAACATGGCAGTACCATTTTTGTCTTGCAATTATTTTCCTT
707 AAGT-ATCAAGTCTGGGTTTTCTGCAGGTGAAATGACCTCGCTT
261 AA-TAATCAAGTCTGGGTTTTCTGCAGGTGAAATGACCTCGCTT
* *
750 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTCCCATGTTTTTATACTATTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAAGTGTCCCACGTTTTTATACTATTCTT
* * *
815 CGCAATTGTTGACTCGCTTAAGTCTTTATATA-ACGGATCTTCATGAGTCTTCTTAACAAATGCA
66 CGCAATTGCTGACTCACTTAAGTCTTTATATATA-GGATCTTCAAGAGTCTTCTTAACAAATGCA
* *
879 TCGTGACAAACTTTACCCAATTCCATT-AGTTCACCGCAACACTTCTTAGTGAC-AGCTCCGGTA
130 TCGTGACAAACTTTACCCAATACC-TTGAGTTCACCGCAACAATTCTTAGTGACGA-CTCCGGTA
942 TAGAATATACTTGTGAAAACTTCCCTAGAACA-GGTCAG-ACCTATTTTTGTCTTGCAATTATTT
193 TAGAATATACTTGTGAAAACTTCCCTAGAACATGG-CAGTACC-ATTTTTGTCTTGCAATTATTT
*
1005 TGCTTAATAATCAAGTCTGGGTTTTCTGCA
256 TCCTTAATAATCAAGTCTGGGTTTTCTGCA
1035 CCTGAAACGA
Statistics
Matches: 258, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
302 7 0.03
303 249 0.97
304 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACAAGTGTCCCACGTTTTTATACTATTCTT
CGCAATTGCTGACTCACTTAAGTCTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACAATTCTTAGTGACGACTCCGGTATAG
AATATACTTGTGAAAACTTCCCTAGAACATGGCAGTACCATTTTTGTCTTGCAATTATTTTCCTT
AATAATCAAGTCTGGGTTTTCTGCAGGTGAAATGACCTCGCTT
Found at i:3061 original size:303 final size:303
Alignment explanation
Indices: 2509--3115 Score: 878
Period size: 303 Copynumber: 2.0 Consensus size: 303
2499 TGCTTCTCAA
* * *
2509 GCAGAAGAAGATGGTGAAACGTCGATGACTGAGGCACAAATGTTCCACGTTTTTGTACTCTTTTT
1 GCAGAAGAAGATGGTGAAACGTCGATGACTGAGGCACAAATGTCCCACGTTTTTATACTCTTCTT
* * *
2574 TGCAATTGCTGACTCACTTAAGTTTTTATATATAAGGTCTTCAAGAGTCTTGTTAACAAATGCAT
66 CGCAATTGCTGACTCACTTAAGTCTTTATATATAAGGTCTTCAAGAGTCTTCTTAACAAATGCAT
* * *
2639 CGTCACAAACTTTACCCAATACCTTGAGTTCACCGCAACAATTCTTAGTGACAGCTCCGGTTTTG
131 CGTCACAAACTTTACCCAATACCATGAGTTCACCGCAACAATTCTTAGTGACAGCTCCGGTATAG
* ** * *
2704 AATATACTTGTGAAAACTTCCCTGGCACATGGCAGTTCCATTTTTGTTTTGCAATTGTTTTCCTT
196 AATATACTTGTGAAAACTTCCCTGGAACATGGCAGACCCATTTTTGTCTTGCAATTATTTTCCTT
* *
2769 AATAATCGAA-TCCGGGTTTTCCGCAGGTGAAATGACTCCGCTT
261 AATAATC-AAGTCCGGGTTTTCCGCAGCTGAAACGACTCCGCTT
* * ** *
2812 GCAGAAGAAGATGGTGAAATGTTGATGACTGAGGCACATGTGTCCCATGTTTTTATACTCTTCTT
1 GCAGAAGAAGATGGTGAAACGTCGATGACTGAGGCACAAATGTCCCACGTTTTTATACTCTTCTT
* * * *
2877 CGCAATTGTTGACTCGCTTAAGTCTTTATATA-ATGGATCTTCATGAGTCTTCTTAACAAATGCA
66 CGCAATTGCTGACTCACTTAAGTCTTTATATATAAGG-TCTTCAAGAGTCTTCTTAACAAATGCA
* * * *
2941 TCGTGACAAACTTTACCCAATTCCATGAGTTCACCGCAACACTTCTTAGTTACAGCTCCGGTATA
130 TCGTCACAAACTTTACCCAATACCATGAGTTCACCGCAACAATTCTTAGTGACAGCTCCGGTATA
*
3006 GAATATACTTGTGAAAACTTCCCTGGAACA-GGCCAGACCCATTTTTGTCTTGCAATTATTTTGC
195 GAATATACTTGTGAAAACTTCCCTGGAACATGG-CAGACCCATTTTTGTCTTGCAATTATTTTCC
* *
3070 TTAATAATCAAGTCTGGGTTTTCTGCAGCTGAAACGACTCCGCTT
259 TTAATAATCAAGTCCGGGTTTTCCGCAGCTGAAACGACTCCGCTT
3115 G
1 G
3116 GTAAAACAAA
Statistics
Matches: 269, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
302 7 0.03
303 262 0.97
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAACGTCGATGACTGAGGCACAAATGTCCCACGTTTTTATACTCTTCTT
CGCAATTGCTGACTCACTTAAGTCTTTATATATAAGGTCTTCAAGAGTCTTCTTAACAAATGCAT
CGTCACAAACTTTACCCAATACCATGAGTTCACCGCAACAATTCTTAGTGACAGCTCCGGTATAG
AATATACTTGTGAAAACTTCCCTGGAACATGGCAGACCCATTTTTGTCTTGCAATTATTTTCCTT
AATAATCAAGTCCGGGTTTTCCGCAGCTGAAACGACTCCGCTT
Found at i:5475 original size:11 final size:11
Alignment explanation
Indices: 5441--5488 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5431 TTGAAATAAT
5441 TCTTC-AATAG
1 TCTTCAAATAG
5451 TCTTC--A-AG
1 TCTTCAAATAG
5459 TCTTCAAATTA-
1 TCTTCAAA-TAG
5470 TCTTCAAATAG
1 TCTTCAAATAG
5481 TCTTCAAA
1 TCTTCAAA
5489 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:14240 original size:16 final size:17
Alignment explanation
Indices: 14207--14240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14197 TCCTCTTGCA
*
14207 TGAAAGCACTTCTTTTT
1 TGAAAGCAATTCTTTTT
14224 TGAAAGCAATT-TTTTT
1 TGAAAGCAATTCTTTTT
14240 T
1 T
14241 AACTACCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (17 bp):
TGAAAGCAATTCTTTTT
Done.