Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021716.1 Corchorus olitorius cultivar O-4 contig21749, 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: 16531
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:358 original size:54 final size:55
Alignment explanation
Indices: 281--423 Score: 243
Period size: 54 Copynumber: 2.6 Consensus size: 55
271 TTTTAGAAGA
*
281 ACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGATTGGAAGACAAT-
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATC
*
335 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATC
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATC
* *
390 TCATCGGAAGACGGTTTGCTAGAAAGAATTTTCA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCA
424 GGAGTTGATC
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
54 52 0.62
55 32 0.38
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (55 bp):
ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATC
Found at i:423 original size:55 final size:55
Alignment explanation
Indices: 282--445 Score: 242
Period size: 54 Copynumber: 3.0 Consensus size: 55
272 TTTAGAAGAA
* * *
282 CACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGATTGGAAGACAAT-A
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCT
336 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCT
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCT
* * * *
391 CATCGGAAGACGGTTTGCTAGAAAGAATTTTCAGGA-GTTGATCGGAAGACGATCT
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCT
446 TGTCAAGAAG
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 51 0.50
55 49 0.49
56 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (55 bp):
CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCT
Found at i:500 original size:64 final size:64
Alignment explanation
Indices: 416--773 Score: 475
Period size: 64 Copynumber: 5.6 Consensus size: 64
406 TGCTAGAAAG
*
416 AATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
**
480 AATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
** * *
544 AATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGTTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * * **
608 AGTTTTCAGAAGTAGATCGGAAGATGATCTTGTCAAAAAGTACATCAGAAGATGGACTCTC-AA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * * *
671 AATTTTCAAAAGTCGATCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTTCTCGAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAA
** * * *
736 AGGTTTCAGAAGTGGGTCGGAAGACGATCTTGTTAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
774 GATGCACCGG
Statistics
Matches: 260, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
63 52 0.20
64 174 0.67
65 34 0.13
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:1293 original size:50 final size:50
Alignment explanation
Indices: 1003--1284 Score: 483
Period size: 50 Copynumber: 5.6 Consensus size: 50
993 GATTTTCTCG
* *
1003 AGATTGAATTGGAAGACGGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1053 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
*
1103 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
1153 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCAGAAGACGGTTCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
1203 AGATTGTATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
1253 AGATTGAATTGGAAGACAGTTCAAGGGATAAG
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAG
1285 TAGGAGACGA
Statistics
Matches: 219, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 219 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (50 bp):
AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
Found at i:1589 original size:27 final size:28
Alignment explanation
Indices: 1516--1595 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
1506 TTAGGATCAC
1516 CTAGGGGCATTTTGGTCATTTTCAAAAAT
1 CTAGGGGCATTTTGGTCATTTT-AAAAAT
* * *
1545 CTAGGGGCATTTTAGTCATTTGT-ATATT
1 CTAGGGGCATTTTGGTCATTT-TAAAAAT
1573 C-AGGGGCATTTTGGTCATTTTAA
1 CTAGGGGCATTTTGGTCATTTTAA
1596 GGTCACGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.02
27 19 0.42
28 4 0.09
29 20 0.44
30 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTAAAAAT
Found at i:1751 original size:22 final size:22
Alignment explanation
Indices: 1717--1771 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1707 TGATTTAGCT
* *
1717 TCATTTAGTTTTTGCACTTTGA
1 TCATATAGCTTTTGCACTTTGA
1739 TCATATAGCTTTTGCACTTTGA
1 TCATATAGCTTTTGCACTTTGA
1761 TCATATAGCTT
1 TCATATAGCTT
1772 AAGCCCTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (22 bp):
TCATATAGCTTTTGCACTTTGA
Found at i:2881 original size:34 final size:34
Alignment explanation
Indices: 2838--2906 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2828 TTTTGAATTT
2838 AGTCAATATATATTAAAATCGGTCAACCGGACCA
1 AGTCAATATATATTAAAATCGGTCAACCGGACCA
2872 AGTCAATATATATTAAAATCGGTCAACCGGACCA
1 AGTCAATATATATTAAAATCGGTCAACCGGACCA
2906 A
1 A
2907 TTGAACCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (34 bp):
AGTCAATATATATTAAAATCGGTCAACCGGACCA
Found at i:3731 original size:28 final size:28
Alignment explanation
Indices: 3699--3753 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3689 TCCAAGGAAA
*
3699 ATACAGTTCTTCAGGTGCAAAAAGTAAG
1 ATACAGTTCTTCAGATGCAAAAAGTAAG
3727 ATACAGTTCTTCAGATGCAAAAAGTAA
1 ATACAGTTCTTCAGATGCAAAAAGTAA
3754 TCGATTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (28 bp):
ATACAGTTCTTCAGATGCAAAAAGTAAG
Found at i:8018 original size:27 final size:27
Alignment explanation
Indices: 7974--8026 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7964 TTTCTCAAAT
*
7974 ATATTTTTAAATTATCATTTTTAAAAA
1 ATATTTTTAAATTATCATTATTAAAAA
*
8001 ATATTTTTATTATT-TCATTATTAAAA
1 ATATTTTTA-AATTATCATTATTAAAA
8027 TAATGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTTTTAAATTATCATTATTAAAAA
Found at i:10856 original size:8 final size:8
Alignment explanation
Indices: 10838--10869 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
10828 CTTTTATATT
10838 TTATATATA
1 TTAT-TATA
10847 TTATTATA
1 TTATTATA
10855 TTATTATA
1 TTATTATA
10863 TTATTAT
1 TTATTAT
10870 TGGCCAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:12775 original size:21 final size:21
Alignment explanation
Indices: 12728--12825 Score: 99
Period size: 22 Copynumber: 4.6 Consensus size: 21
12718 CCATTGTTAG
* * *
12728 GTTATCAAAGTTTTTTATGGAA
1 GTTATCAAAATTTTATA-GGTA
* *
12750 TTTATCACAATTTTATAGGTA
1 GTTATCAAAATTTTATAGGTA
* *
12771 ATTATCAAAATTTCATATGGTA
1 GTTATCAAAATTTTATA-GGTA
*
12793 GTTATCAAAATTTTA-GGGTA
1 GTTATCAAAATTTTATAGGTA
12813 GTTATCAAAATTT
1 GTTATCAAAATTT
12826 CATAAAAATA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.27
21 17 0.27
22 30 0.47
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (21 bp):
GTTATCAAAATTTTATAGGTA
Found at i:12778 original size:43 final size:42
Alignment explanation
Indices: 12729--12829 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
12719 CATTGTTAGG
* ** * *
12729 TTATCAAAGTTTTTTATGGAATTTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTTA-AGGTAA
* * *
12772 TTATCAAAATTTCATATGGTAGTTATCAAAATTTTAGGGTAG
1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTTAAGGTAA
12814 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
12830 AAAATATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
42 20 0.40
43 30 0.60
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (42 bp):
TTATCAAAATTTCATATGGAAGTTATCAAAATTTTAAGGTAA
Found at i:12814 original size:20 final size:20
Alignment explanation
Indices: 12751--12825 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
12741 TTTATGGAAT
* *
12751 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTA-AGGTAG
*
12772 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTT--TAAGGTAG
*
12794 TTATCAAAATTTTAGGGTAG
1 TTATCAAAATTTTAAGGTAG
12814 TTATCAAAATTT
1 TTATCAAAATTT
12826 CATAAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 19 0.40
21 11 0.23
22 16 0.33
23 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (20 bp):
TTATCAAAATTTTAAGGTAG
Found at i:13165 original size:25 final size:26
Alignment explanation
Indices: 13137--13186 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
13127 ATTATTAAAA
*
13137 TATTTTATTTAG-AAAATTCAATTTT
1 TATTTTATTTAGAAAAAATCAATTTT
*
13162 TATTTTGTTTAGAAAAAATCAATTT
1 TATTTTATTTAGAAAAAATCAATTT
13187 CTATAATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (26 bp):
TATTTTATTTAGAAAAAATCAATTTT
Found at i:16417 original size:27 final size:26
Alignment explanation
Indices: 16379--16436 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
16369 GCTGTCGGTC
* * *
16379 ATGAAGCTGCTGGTGTTGGGGATGAAA
1 ATGATGCTGCTGATGGTGGGGATG-AA
*
16406 ATGATGCTGCTGATGGTGGTGATGAA
1 ATGATGCTGCTGATGGTGGGGATGAA
16432 ATGAT
1 ATGAT
16437 TGATGGGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (26 bp):
ATGATGCTGCTGATGGTGGGGATGAA
Done.