Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012120.1 Corchorus olitorius cultivar O-4 contig12153, 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: 28824
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Found at i:139 original size:39 final size:38
Alignment explanation
Indices: 8--155 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
1 AGTCTAG
8 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
45 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * *
83 TCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
122 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
156 ATGCACAGCC
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 7 0.07
38 61 0.60
39 33 0.33
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:142 original size:77 final size:75
Alignment explanation
Indices: 9--155 Score: 231
Period size: 77 Copynumber: 1.9 Consensus size: 75
1 AGTCTAGC
9 CAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGT
1 CAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGT
74 CCACTCTTAT
66 CCACTCTTAT
* * * * *
84 CAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACGG
1 CAACAG-TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACGG
149 GTCCACT
64 GTCCACT
156 ATGCACAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 6 0.09
76 24 0.37
77 35 0.54
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (75 bp):
CAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGT
CCACTCTTAT
Found at i:1891 original size:14 final size:14
Alignment explanation
Indices: 1883--1929 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 14
1873 ATAAAACTTG
1883 AAAAATAAAGACAT
1 AAAAATAAAGACAT
*
1897 AAAAATAAAGGAAAAAT
1 AAAAATAAA-G--ACAT
1914 AAAAATAAAG-CAT
1 AAAAATAAAGACAT
1927 AAA
1 AAA
1930 CTAAATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 1 0.04
16 1 0.04
17 12 0.43
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (14 bp):
AAAAATAAAGACAT
Found at i:14344 original size:23 final size:23
Alignment explanation
Indices: 14310--14353 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14300 GACAACCAAG
14310 AACACATCAAACACAGAAAAAAA
1 AACACATCAAACACAGAAAAAAA
* *
14333 AACACATTAAACCCAGAAAAA
1 AACACATCAAACACAGAAAAA
14354 TATAAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.07
Consensus pattern (23 bp):
AACACATCAAACACAGAAAAAAA
Found at i:15672 original size:41 final size:41
Alignment explanation
Indices: 15571--15815 Score: 296
Period size: 41 Copynumber: 5.8 Consensus size: 41
15561 CAATAGCCAA
* *
15571 AAAGTCCCCAAACACATATATAACACAG-GGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-T-C
* *
15613 AAAGTCCTCAAACTCATATATAACACAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
*
15654 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTA-C
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTA-TATC
* * *
15697 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATATT
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
* *
15738 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-T-C
**
15781 AAAAGTCCTGAAACACATATATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT
15816 TTCTCCTTAT
Statistics
Matches: 176, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
40 2 0.01
41 68 0.39
42 30 0.17
43 43 0.24
44 33 0.19
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.21
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
Found at i:15719 original size:84 final size:84
Alignment explanation
Indices: 15571--15815 Score: 402
Period size: 84 Copynumber: 2.9 Consensus size: 84
15561 CAATAGCCAA
* * *
15571 AAAGTCCCCAAACACATATATAACACA-GGGCACCTTTATTACAAAGTCCTCAAACTCATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
15635 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
15654 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
* *
15719 ACACAGAGGCATTTATATT
66 ACACAGAGGCATCTATATC
* *
15738 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTGAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
15803 AACACAGAGGCAT
65 AACACAGAGGCAT
15816 TTCTCCTTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
83 27 0.18
84 91 0.60
85 33 0.22
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:28415 original size:43 final size:41
Alignment explanation
Indices: 28354--28682 Score: 403
Period size: 41 Copynumber: 7.8 Consensus size: 41
28344 CAATAGCCAA
*
28354 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTA-TAC
* *
28397 AAAGTCCTCAAACACATATATAACACAGAGGCA-TCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C
* *
28438 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC
* * *
28481 AAAGTCCTCAAACACATATATAACACAGAGACATCTGTAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTATAC
* *
28522 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC
*
28565 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C
* *
28606 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTT-TA-TAC
*
28649 AAAAGTCCTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
28683 TTTCTCCTTA
Statistics
Matches: 253, Mismatches: 20, Indels: 25
0.85 0.07 0.08
Matches are distributed among these distances:
40 4 0.02
41 103 0.41
42 8 0.03
43 103 0.41
44 35 0.14
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATAC
Found at i:28451 original size:84 final size:84
Alignment explanation
Indices: 28354--28683 Score: 579
Period size: 84 Copynumber: 3.9 Consensus size: 84
28344 CAATAGCCAA
* *
28354 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
28419 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
28438 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
* *
28503 ACACAGAGACATCTGTATC
66 ACACAGAGGCATCTATATC
28522 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
28587 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
**
28606 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
28671 AACACAGAGGCAT
65 AACACAGAGGCAT
28684 TTCTCCTTAT
Statistics
Matches: 234, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
84 200 0.85
85 34 0.15
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:28799 original size:2 final size:2
Alignment explanation
Indices: 28792--28824 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28782 ACCAAATTCC
28792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.