Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017661.1 Corchorus olitorius cultivar O-4 contig17694, 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: 52678
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1737 original size:72 final size:72
Alignment explanation
Indices: 1620--1760 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
1610 TTGAACGGTT
1620 AAGTTCTCTTAATGAACTACAAACTGGTACAGGTATGAACGAAGTGGGCACTTTACAGCGTCCTG
1 AAGTTCTCTTAATGAACTACAAACTGGTACAGGTATGAACGAAGTGGGCACTTTACAGCGTCCTG
1685 GTGATTC
66 GTGATTC
*
1692 AAGTTCTCTTAATGAACTACAAACTGGTACATGTATGAACGAAGTGGGCACTTTACAGCGTCCTG
1 AAGTTCTCTTAATGAACTACAAACTGGTACAGGTATGAACGAAGTGGGCACTTTACAGCGTCCTG
1757 GTGA
66 GTGA
1761 AACTCGATGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (72 bp):
AAGTTCTCTTAATGAACTACAAACTGGTACAGGTATGAACGAAGTGGGCACTTTACAGCGTCCTG
GTGATTC
Found at i:11451 original size:15 final size:16
Alignment explanation
Indices: 11421--11454 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
11411 TCGAACCTGA
11421 AATAATTTGAATAAAAT
1 AATAATTT-AATAAAAT
11438 AATAATTT-ATAAAAT
1 AATAATTTAATAAAAT
11453 AA
1 AA
11455 AAGATTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AATAATTTAATAAAAT
Found at i:15549 original size:80 final size:80
Alignment explanation
Indices: 15451--15608 Score: 253
Period size: 80 Copynumber: 2.0 Consensus size: 80
15441 CCAGCCAAAG
**
15451 CCAAATTTAATTATTGGTACAAGAAATTCAATTTTCAATTTTGCTGATGTTAAATATGTCATGGC
1 CCAAATTTAATTATTGGTACAAGAAATTCAATTTTCAATTTTGCTGATGCCAAATATGTCATGGC
15516 CAATTTTGAGATTCA
66 CAATTTTGAGATTCA
* ** * *
15531 CCAAATTTGATTATTGGTACAAGAAATTCAATTTTTTATTTTGTTGATGCCAAATATGTCATGGT
1 CCAAATTTAATTATTGGTACAAGAAATTCAATTTTCAATTTTGCTGATGCCAAATATGTCATGGC
15596 CAATTTTGAGATT
66 CAATTTTGAGATT
15609 AATAATTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (80 bp):
CCAAATTTAATTATTGGTACAAGAAATTCAATTTTCAATTTTGCTGATGCCAAATATGTCATGGC
CAATTTTGAGATTCA
Found at i:23878 original size:1 final size:1
Alignment explanation
Indices: 23872--23901 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
23862 CTGATATAGG
23872 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23902 GCATATGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27739 original size:14 final size:13
Alignment explanation
Indices: 27720--27756 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
27710 AAGACTTATA
27720 AAAAATAATAATAT
1 AAAAATAATAAT-T
27734 AAAAATAATAATT
1 AAAAATAATAATT
27747 AAAAGATAAT
1 AAAA-ATAAT
27757 TTTAGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAAATAATAATT
Found at i:30268 original size:6 final size:6
Alignment explanation
Indices: 30259--30286 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30249 CAAGGACAAG
30259 TAGCCA TAGCCA TAGCCA TAGCCA TAGC
1 TAGCCA TAGCCA TAGCCA TAGCCA TAGC
30287 TGGTCTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (6 bp):
TAGCCA
Found at i:30650 original size:36 final size:36
Alignment explanation
Indices: 30576--30653 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
30566 CATAAGAAAT
** * *
30576 GCCCAAATACATAATTAAGTTGGCTTAGTTCTATTG
1 GCCCAAATACATAATTAAGTTGGCCAACTTCTACTG
30612 GCCCAAATACATAATTAAGTTGGCCCAACTT-TACTG
1 GCCCAAATACATAATTAAGTTGG-CCAACTTCTACTG
30648 GCCCAA
1 GCCCAA
30654 TACTACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 33 0.89
37 4 0.11
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (36 bp):
GCCCAAATACATAATTAAGTTGGCCAACTTCTACTG
Found at i:30863 original size:37 final size:36
Alignment explanation
Indices: 30813--30946 Score: 207
Period size: 36 Copynumber: 3.7 Consensus size: 36
30803 ATCCAAACTT
30813 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTC
1 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTC
*
30849 TTCACCAAAGTTATTCATCAAAGTTCTTCAACAAGTC
1 TTCACC-AAGTTATTCATCAAAATTCTTCAACAAGTC
* *
30886 TTCACCAAGTTATTCATCAAAGTTCTTCAACAAGTT
1 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTC
* *
30922 TTCACCCAGTTCTTCATC-AAATTCT
1 TTCACCAAGTTATTCATCAAAATTCT
30947 CCACCAATCT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.07
36 51 0.55
37 35 0.38
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (36 bp):
TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTC
Found at i:30870 original size:13 final size:13
Alignment explanation
Indices: 30819--30946 Score: 94
Period size: 13 Copynumber: 10.5 Consensus size: 13
30809 ACTTTTCACC
*
30819 AAGTTATTCATCA
1 AAGTTCTTCATCA
* *
30832 AAATTCTTCAAC-
1 AAGTTCTTCATCA
*
30844 AAG-TCTTCACCA
1 AAGTTCTTCATCA
*
30856 AAGTTATTCATCA
1 AAGTTCTTCATCA
*
30869 AAGTTCTTCAAC-
1 AAGTTCTTCATCA
*
30881 AAG-TCTTCA-CC
1 AAGTTCTTCATCA
*
30892 AAGTTATTCATCA
1 AAGTTCTTCATCA
*
30905 AAGTTCTTCAAC-
1 AAGTTCTTCATCA
*
30917 AAGTT-TTCA-CC
1 AAGTTCTTCATCA
*
30928 CAGTTCTTCATCA
1 AAGTTCTTCATCA
30941 AA-TTCT
1 AAGTTCT
30947 CCACCAATCT
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
10 2 0.02
11 24 0.26
12 26 0.29
13 39 0.43
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (13 bp):
AAGTTCTTCATCA
Found at i:30898 original size:73 final size:71
Alignment explanation
Indices: 30813--30946 Score: 214
Period size: 73 Copynumber: 1.9 Consensus size: 71
30803 ATCCAAACTT
30813 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTCTTCACCAAAGTTATTCATCAAAGTTCTTC
1 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTCTTCACC-AAGTTATTCATCAAA-TTCTTC
30878 AACAAGTC
64 AACAAGTC
* * * *
30886 TTCACCAAGTTATTCATCAAAGTTCTTCAACAAGTTTTCACCCAGTTCTTCATCAAATTCT
1 TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTCTTCACCAAGTTATTCATCAAATTCT
30947 CCACCAATCT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
71 4 0.07
72 13 0.23
73 40 0.70
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (71 bp):
TTCACCAAGTTATTCATCAAAATTCTTCAACAAGTCTTCACCAAGTTATTCATCAAATTCTTCAA
CAAGTC
Found at i:38855 original size:52 final size:52
Alignment explanation
Indices: 38773--38926 Score: 229
Period size: 52 Copynumber: 3.0 Consensus size: 52
38763 AAAAAAAAAT
* *
38773 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAG
1 GCCTGCTAAGTTGAAAACCCCATCGGGGCGGCTTAGGCAAAAGTTAAGGCAA
*
38825 GCCTGCTAAGTTGAAAACCCCATCGAGGCGGCTTAGGCAAAAGTTAAGGCAA
1 GCCTGCTAAGTTGAAAACCCCATCGGGGCGGCTTAGGCAAAAGTTAAGGCAA
* * * *
38877 GCCTGCTAGGTTGAAAGCCCCA-CTGGGGCAGCCTAGGCAAAAGTTAAGGC
1 GCCTGCTAAGTTGAAAACCCCATC-GGGGCGGCTTAGGCAAAAGTTAAGGC
38927 TAAAAAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 1 0.01
52 92 0.99
ACGTcount: A:0.29, C:0.23, G:0.30, T:0.18
Consensus pattern (52 bp):
GCCTGCTAAGTTGAAAACCCCATCGGGGCGGCTTAGGCAAAAGTTAAGGCAA
Found at i:42628 original size:15 final size:16
Alignment explanation
Indices: 42604--42643 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
42594 AAAGGTTGAA
*
42604 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
42619 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
42635 AGAAAACAA
1 AGAAAACAA
42644 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:48238 original size:16 final size:15
Alignment explanation
Indices: 48200--48241 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
48190 ACAGAGATTG
*
48200 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
48215 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
48230 ACTAGAAAACAA
1 AC-AGAAAACAA
48242 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:50389 original size:46 final size:48
Alignment explanation
Indices: 50316--50406 Score: 125
Period size: 46 Copynumber: 1.9 Consensus size: 48
50306 TTTTTCAAAA
50316 ACGCAACACAAAAAATTTAAAAAACGCAAAAATCAAAAAAAATTTTATG
1 ACGCAACACAAAAAATTTAAAAAACGCAAAAA-CAAAAAAAATTTTATG
* * *
50365 ACGCAA-ACACAAAA-TT-AAAAACGCAAAAACAACAAAATTTTT
1 ACGCAACACAAAAAATTTAAAAAACGCAAAAACAAAAAAAATTTT
50407 TTTTAGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 11 0.28
46 13 0.33
47 2 0.05
48 7 0.18
49 6 0.15
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.18
Consensus pattern (48 bp):
ACGCAACACAAAAAATTTAAAAAACGCAAAAACAAAAAAAATTTTATG
Found at i:50722 original size:15 final size:16
Alignment explanation
Indices: 50698--50737 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
50688 AGAGGTTGAA
*
50698 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
50713 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
50729 AGAAAACAA
1 AGAAAACAA
50738 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:52449 original size:45 final size:45
Alignment explanation
Indices: 52400--52677 Score: 493
Period size: 45 Copynumber: 6.2 Consensus size: 45
52390 TGGCTCAATC
* *
52400 AGAGGGCGATAAAAATCAACCCCGCCGAGAGTCTGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
* *
52445 AGAGGGCGATAAACATCAACCCCGCCAAGAGTCCTATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
*
52490 AGAGGGCGATAAAAATCAACCCCGACAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
*
52535 AGAGGGCGATAAAGATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
*
52580 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGAAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
52625 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
1 AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
52670 AGAGGGCG
1 AGAGGGCG
52678 G
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 221 1.00
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (45 bp):
AGAGGGCGATAAAAATCAACCCCGCCAAGAGTCCGATGCAGAGGT
Done.