Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021642.1 Corchorus olitorius cultivar O-4 contig21675, 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: 3399
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Found at i:187 original size:105 final size:105
Alignment explanation
Indices: 1--190 Score: 362
Period size: 105 Copynumber: 1.8 Consensus size: 105
1 CATGAGCCAAGTTCATTTCCATCTAAATTCAGTCTTCCAAGACTAAACTCATTTCCATACGAATC
1 CATGAGCCAAGTTCATTTCCATCTAAATTCAGTCTTCCAAGACTAAACTCATTTCCATACGAATC
* *
66 AGTTTAAGCCTTGGTTCCATCCAAGCAGCATAGGCTATTC
66 AGTTCAAGCCTCGGTTCCATCCAAGCAGCATAGGCTATTC
106 CATGAGCCAAGTTCATTTCCATCTAAATTCAGTCTTCCAAGACTAAACTCATTTCCATACGAATC
1 CATGAGCCAAGTTCATTTCCATCTAAATTCAGTCTTCCAAGACTAAACTCATTTCCATACGAATC
171 AGTTCAAGCCTCGGTTCCAT
66 AGTTCAAGCCTCGGTTCCAT
191 ACATGCGGTA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 83 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (105 bp):
CATGAGCCAAGTTCATTTCCATCTAAATTCAGTCTTCCAAGACTAAACTCATTTCCATACGAATC
AGTTCAAGCCTCGGTTCCATCCAAGCAGCATAGGCTATTC
Found at i:228 original size:68 final size:69
Alignment explanation
Indices: 150--287 Score: 197
Period size: 68 Copynumber: 2.0 Consensus size: 69
140 TTCCAAGACT
* * ***
150 AAACTCATTTCCATACGAATCAGTTCAAGCCTCGGTTCCATACATGCGGTAAGGGCTTTTCCA-A
1 AAACTCATTTCCATACGAATCAGTTCAAGCATCGGTTCCATACAAGCAACAAGGGCTTTTCCATA
214 AGCC
66 AGCC
* * *
218 AAACTCATTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCAACAAGGGCTTTTCCATA
1 AAACTCATTTCCATACGAATCAGTTCAAGCATCGGTTCCATACAAGCAACAAGGGCTTTTCCATA
283 AGCC
66 AGCC
287 A
1 A
288 GGTCCCATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
68 55 0.90
69 6 0.10
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (69 bp):
AAACTCATTTCCATACGAATCAGTTCAAGCATCGGTTCCATACAAGCAACAAGGGCTTTTCCATA
AGCC
Found at i:563 original size:47 final size:46
Alignment explanation
Indices: 399--565 Score: 219
Period size: 47 Copynumber: 3.6 Consensus size: 46
389 ATCCAGGTAA
*
399 TCTTTTCTCGCTTCCATGCGAGT-TTGCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTTG--ATTTAGTGACCAAAGTTGG
* * *
446 TCTTTTCTCGCTTCCACACGAGTCTGCGATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTCT-TGATTTAGTGACCAAAGTTGG
**
493 TCTTTTCTCGCTTCCACGCGAGTCTATGATTGGGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCT-TGATTTAGTGACCAAAGTTGG
* *
540 TCTTTTCTCGCTTCCATGTGAGTCTT
1 TCTTTTCTCGCTTCCACGCGAGTCTT
566 CAATTTCAGA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.01
47 103 0.97
48 1 0.01
49 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (46 bp):
TCTTTTCTCGCTTCCACGCGAGTCTTGATTTAGTGACCAAAGTTGG
Found at i:1008 original size:141 final size:141
Alignment explanation
Indices: 578--995 Score: 705
Period size: 141 Copynumber: 3.0 Consensus size: 141
568 ATTTCAGAAA
* *
578 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGATGTGTTTAAGTTCCAATAAACCT
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGATGTATTTAAGTTTCAATAAACCT
*
643 TGCTCAAGTTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTA-CTA
66 TGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATC-A
707 ATTCTGATAAAT
130 ATTCTGATAAAT
*
719 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGTTGTATTTAAGTTTCAATAAACCT
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGATGTATTTAAGTTTCAATAAACCT
* * *
784 TGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGTCACCATTTCAGAAACCTCCGTGTATTAA
66 TGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATCAA
849 TTCTGATAAAT
131 TTCTGATAAAT
*
860 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTATTTAAGTTTCAATAAACCT
1 CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGATGTATTTAAGTTTCAATAAACCT
* * *
925 TGCTCAAGGTCGAGTTTGCATTTGTGAGACCAT-CGGGCACAATTTCAGAAACCTCCGGGTATCA
66 TGCTCAAGGTTGAGTTTGCATTTGTAAGACC-TCCGGGCACCATTTCAGAAACCTCCGGGTATCA
989 ATTCTGA
130 ATTCTGA
996 CTTGTCCTCC
Statistics
Matches: 261, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
141 260 1.00
142 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (141 bp):
CCTCCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGATGTATTTAAGTTTCAATAAACCT
TGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAACCTCCGGGTATCAA
TTCTGATAAAT
Found at i:1101 original size:39 final size:37
Alignment explanation
Indices: 1058--1161 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 37
1048 TATGTGTTTT
* * * * *
1058 AATCCTATTCATGATCATTGCTTTATTAGTCGATTCCAG
1 AATCCTACTCAAGATCATTGCTTTATCAGTC-AAT-CAC
* * * * *
1097 AATCCTGCTCAGGATAATTTCTTTACCAGTCAATCAC
1 AATCCTACTCAAGATCATTGCTTTATCAGTCAATCAC
1134 AATCCTACTCAAGATCATTGCTTTATCA
1 AATCCTACTCAAGATCATTGCTTTATCA
1162 AATTAATTTC
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
37 25 0.49
38 2 0.04
39 24 0.47
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (37 bp):
AATCCTACTCAAGATCATTGCTTTATCAGTCAATCAC
Found at i:1158 original size:37 final size:39
Alignment explanation
Indices: 1058--1158 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 39
1048 TATGTGTTTT
* * ** * *
1058 AATCCTATTCATGATCATTGCTTTATTAGTCGATTCCAG
1 AATCCTACTCAAGATCATTGCTTTACCAGTCGAATCCAC
* * * *
1097 AATCCTGCTCAGGATAATTTCTTTACCAGTC-AAT-CAC
1 AATCCTACTCAAGATCATTGCTTTACCAGTCGAATCCAC
1134 AATCCTACTCAAGATCATTGCTTTA
1 AATCCTACTCAAGATCATTGCTTTA
1159 TCAAATTAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
37 23 0.47
38 2 0.04
39 24 0.49
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (39 bp):
AATCCTACTCAAGATCATTGCTTTACCAGTCGAATCCAC
Found at i:1190 original size:40 final size:40
Alignment explanation
Indices: 1141--1649 Score: 641
Period size: 40 Copynumber: 12.8 Consensus size: 40
1131 CACAATCCTA
*
1141 CTCAAGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
*
1181 CTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
1221 CTCAGGATCATTGCTTTATCAAATCAATTTCAGAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
1261 CTCAGAATCATTGTTTTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
1301 CTCAGGATCATTG-TTCTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCATTGCTT-TATCAAATTAATTTCAAAACCCTG
*
1341 CTCAGGATCATTGTTTTATCAAATTAATTTCAAAACCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
1381 CTCAGGATCATTGCTTTATCAAATTAATTTCAGAATCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* *
1421 CTCAGGATCATCT-TTTTATCAAATTGATTTCAAAACCCTG
1 CTCAGGATCAT-TGCTTTATCAAATTAATTTCAAAACCCTG
* * *
1461 CTCAGGATCATTGCTTTATCTAATTAATTTCAAAATCCTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* * * *
1501 CTCAGGGTCATTGCTTT-TCAAGTGAATTTCAAAATCCTG
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* ** * *
1540 TTCAGGATCATTTTTGTTATC-AATTAATTTCCAAACCCTA
1 CTCAGGATCATTGCT-TTATCAAATTAATTTCAAAACCCTG
* * * * * * * *
1580 TTCAGGATCGTTGCCTCATCAAGTCAATTTCAAAATCCTA
1 CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
* * * *
1620 TTCAGGATCATGGC-TTATCAAGTTGATTTC
1 CTCAGGATCATTGCTTTATCAAATTAATTTC
1650 GGCATCCAAA
Statistics
Matches: 412, Mismatches: 50, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
39 49 0.12
40 358 0.87
41 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (40 bp):
CTCAGGATCATTGCTTTATCAAATTAATTTCAAAACCCTG
Found at i:2313 original size:21 final size:21
Alignment explanation
Indices: 2287--2329 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2277 ATCCTTACAT
2287 TTCACTTACTCTCATAGGTAA
1 TTCACTTACTCTCATAGGTAA
2308 TTCACTTACTCTCATAGGTAA
1 TTCACTTACTCTCATAGGTAA
2329 T
1 T
2330 CTAATATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (21 bp):
TTCACTTACTCTCATAGGTAA
Done.