Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020493.1 Corchorus olitorius cultivar O-4 contig20526, 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: 14756
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1697 original size:22 final size:22
Alignment explanation
Indices: 1636--1701 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 22
1626 AACGGTGTCG
1636 TTTTGGCCTTGTGATACCTCTTCTTT
1 TTTTGGCCTTGTGATA-C-C-TC-TT
1662 TTTTGGCC--GT--TACCTCTT
1 TTTTGGCCTTGTGATACCTCTT
1680 TTTTGGCCTTGTGATACCTCTT
1 TTTTGGCCTTGTGATACCTCTT
1702 CTTAAACGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
18 10 0.28
19 2 0.06
20 3 0.08
21 1 0.03
22 10 0.28
24 2 0.06
26 8 0.22
ACGTcount: A:0.08, C:0.24, G:0.17, T:0.52
Consensus pattern (22 bp):
TTTTGGCCTTGTGATACCTCTT
Found at i:7288 original size:81 final size:81
Alignment explanation
Indices: 7153--7317 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
7143 AGCAGGTAGC
7153 AATATCAAAGGAAACTGCTTCCGATTGATTTTCTCTGCCACTCACCCAGGCAGGGGCGGCACATG
1 AATATCAAAGGAAACTGCTTCCGATTGATTTTCTCTGCCACTCACCCAGGCAGGGGCGGCACATG
7218 TGGGATTTTTAACAAT
66 TGGGATTTTTAACAAT
7234 AATATCAAAGGAAACTGCTTCCGATTGATTTTCTCTGCCACTCACCCAGGCAGGGGCGGCACATG
1 AATATCAAAGGAAACTGCTTCCGATTGATTTTCTCTGCCACTCACCCAGGCAGGGGCGGCACATG
*
7299 TGGGATTTTTAATAAT
66 TGGGATTTTTAACAAT
7315 AAT
1 AAT
7318 TATTCAATAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (81 bp):
AATATCAAAGGAAACTGCTTCCGATTGATTTTCTCTGCCACTCACCCAGGCAGGGGCGGCACATG
TGGGATTTTTAACAAT
Found at i:7357 original size:19 final size:19
Alignment explanation
Indices: 7307--7357 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
7297 TGTGGGATTT
7307 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
7325 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
7344 TTAATAATTAATTA
1 TTAATAATTAATTA
7358 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:10771 original size:50 final size:50
Alignment explanation
Indices: 10712--10812 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
10702 AACAGTTGCA
10712 GAATCGATGGCACTACAGGAATCTGAAGATATAAGAAAGAGAATAGTCTT
1 GAATCGATGGCACTACAGGAATCTGAAGATATAAGAAAGAGAATAGTCTT
10762 GAATCGATGGCACTACAGGAATCTGAAGATATAAGAAAGAGAATAGTCTT
1 GAATCGATGGCACTACAGGAATCTGAAGATATAAGAAAGAGAATAGTCTT
10812 G
1 G
10813 TGTTGACCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (50 bp):
GAATCGATGGCACTACAGGAATCTGAAGATATAAGAAAGAGAATAGTCTT
Found at i:10923 original size:24 final size:24
Alignment explanation
Indices: 10895--10942 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10885 CAGAACTTAT
10895 AATATTTATTACTAGATTTGTGCC
1 AATATTTATTACTAGATTTGTGCC
10919 AATATTTATTACTAGATTTGTGCC
1 AATATTTATTACTAGATTTGTGCC
10943 CGCGCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (24 bp):
AATATTTATTACTAGATTTGTGCC
Found at i:10980 original size:22 final size:22
Alignment explanation
Indices: 10954--10997 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
10944 GCGCCTAATG
10954 GTGTGGGTGTGCATTTTCAATC
1 GTGTGGGTGTGCATTTTCAATC
10976 GTGTGGGTGTGCATTTTCAATC
1 GTGTGGGTGTGCATTTTCAATC
10998 TTGGGTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.32, T:0.41
Consensus pattern (22 bp):
GTGTGGGTGTGCATTTTCAATC
Found at i:11892 original size:63 final size:63
Alignment explanation
Indices: 11793--11919 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
11783 AAAATAGAGG
11793 AGTTGGCATGAAGTAAACCAATGCCACATCAACCTGAAGAAATCCTTGAGAAACATAAATCCC
1 AGTTGGCATGAAGTAAACCAATGCCACATCAACCTGAAGAAATCCTTGAGAAACATAAATCCC
11856 AGTTGGCATGAAGTAAACCAATGCCACATCAACCTGAAGAAATCCTTGAGAAACATAAATCCC
1 AGTTGGCATGAAGTAAACCAATGCCACATCAACCTGAAGAAATCCTTGAGAAACATAAATCCC
11919 A
1 A
11920 TCTCTCTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.19
Consensus pattern (63 bp):
AGTTGGCATGAAGTAAACCAATGCCACATCAACCTGAAGAAATCCTTGAGAAACATAAATCCC
Found at i:12207 original size:21 final size:21
Alignment explanation
Indices: 12158--12209 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
12148 CGTTTCCCTT
* *
12158 GATGCCAAATCCTTTATCGTC
1 GATGCCAGACCCTTTATCGTC
12179 GATGCCAGACCCTTTATCGTC
1 GATGCCAGACCCTTTATCGTC
12200 GATGCCAGAC
1 GATGCCAGAC
12210 ATAAGACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (21 bp):
GATGCCAGACCCTTTATCGTC
Found at i:14463 original size:43 final size:43
Alignment explanation
Indices: 14415--14737 Score: 426
Period size: 43 Copynumber: 7.7 Consensus size: 43
14405 CCAATAACCA
*
14415 AAAGTCC-CTAAACACATATATAACACAGGGGCACCTTTATTTC
1 AAAGTCCTC-AAACACATATATAACACAGGGGCACCTCTATTTC
* *
14458 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATA-TTC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
* * *
14500 -AAGTCCCCAAACACATATATAATACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
* *
14542 AAAGTCCTCAAACACATATATAACACAGAGGCA--TCTATATC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
* * *
14583 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
* * * *
14626 AAAGTCCTCAAACACATATATAACACA-GAG-ACATTTATATC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
* * *
14667 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
14710 AAAGTCCTCAAACACATATATAACACAG
1 AAAGTCCTCAAACACATATATAACACAG
14738 ATGCATTTCT
Statistics
Matches: 242, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
41 103 0.43
42 9 0.04
43 129 0.53
44 1 0.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTTC
Found at i:14745 original size:84 final size:84
Alignment explanation
Indices: 14415--14743 Score: 552
Period size: 84 Copynumber: 3.9 Consensus size: 84
14405 CCAATAACCA
* * *
14415 AAAGTCCCTAAACACATATATAACACAGGGGCACCTTTATTTCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
14480 ACACAGAGGCACCTATATTC
66 ACACAGAGGCATCTATA-TC
*
14500 -AAGTCCCCAAACACATATATAATACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
14564 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
14583 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
14648 ACACAGAGACATTTATATC
66 ACACAGAGGCATCTATATC
*
14667 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
14732 ACACAGATGCAT
66 ACACAGAGGCAT
14744 TTCTCCTTAT
Statistics
Matches: 231, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
83 2 0.01
84 229 0.99
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.