Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012505.1 Corchorus olitorius cultivar O-4 contig12538, 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: 27341
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:76 original size:50 final size:50
Alignment explanation
Indices: 1--202 Score: 350
Period size: 50 Copynumber: 4.0 Consensus size: 50
1 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
51 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
101 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
1 AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
* * * **
151 AGTCAATTATCAACATGGGATTTTCCATAAACCACAGTTCGTTTCCATACG
1 AGTCAATTATCAACATGGGCTTTTCCACAAGCCA-AACTCGTTTCCATACG
202 A
1 A
203 TACATTACCA
Statistics
Matches: 146, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 131 0.90
51 15 0.10
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
AGTCAATTATCAACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG
Found at i:267 original size:35 final size:33
Alignment explanation
Indices: 221--697 Score: 402
Period size: 35 Copynumber: 13.7 Consensus size: 33
211 CATCTTCTCA
*
221 GATGACTCGGTGTAGCATCTTCAAAGTTATATTCG
1 GATGACTCGGTGTAGCATCTTCAAA--AATATTCG
* * *
256 GATGACTCGGTGTAGCATCTTCAAAGATGAATCA
1 GATGACTCGGTGTAGCATCTTCAAAAAT-ATTCG
* *
290 GATGACTCGGTGTAGCATCTTCAAAAATGACCTCA
1 GATGACTCGGTGTAGCATCTTCAAAAAT-A-TTCG
325 GATGACTCGGTGTAGCATCTTCAAAAATGATCTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT-AT-TCG
*
360 GATGACTCGGTGTAGCATCTTCAAAAATGACCTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT-A-TTCG
* *
395 GATGACGCGGTGTAGCATCTTCAAAGATAATCTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT-AT-TCG
* *
430 GATGACTCGGTGTAGCATCTTCAAAGATGAATTCA
1 GATGACTCGGTGTAGCATCTTCAAAAAT--ATTCG
* *
465 GATGACTCGGTGTAGCATCTTC-AATATGAACTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT--ATTCG
* * * * * * *
499 G-TGAGCTCGGTGCAACAAACCTTCAAATAGATCCA
1 GATGA-CTCGGTGTAGC--ATCTTCAAAAATATTCG
534 GATGACTCGGTGTAGCATCTTCAAAAATGATCTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT-AT-TCG
* * * * * * *
569 GATGGCTCGGTGCAGCAAACCTTCAAATAGATCCA
1 GATGACTCGGTGTAGC--ATCTTCAAAAATATTCG
604 GATGACTCGGTGTAGCATCTTCAAAAATGATCTCG
1 GATGACTCGGTGTAGCATCTTCAAAAAT-AT-TCG
* * * *
639 GATGGCTCGGTGCAGCAAATCTTCAAATAGA-TCAG
1 GATGACTCGGTGTAGC--ATCTTCAAAAATATTC-G
*
674 GATGACTCGGTGCAGCATCTTCAA
1 GATGACTCGGTGTAGCATCTTCAA
698 TATGGACTCA
Statistics
Matches: 372, Mismatches: 50, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
33 31 0.08
34 57 0.15
35 247 0.66
36 14 0.04
37 23 0.06
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (33 bp):
GATGACTCGGTGTAGCATCTTCAAAAATATTCG
Found at i:384 original size:70 final size:69
Alignment explanation
Indices: 216--697 Score: 534
Period size: 70 Copynumber: 6.9 Consensus size: 69
206 ATTACCATCT
* * *
216 TCTCAGATGACTCGGTGTAGCATCTTCAAAGTTAT-ATTCGGATGACTCGGTGTAGCATCTTCAA
1 TCTCGGATGACTCGGTGTAGCATCTTCAAA--TATGACTCAGATGACTCGGTGTAGCATCTTCAA
*
280 AGATGA
64 AAATGA
* * *
286 -ATCAGATGACTCGGTGTAGCATCTTCAAAAATGACCTCAGATGACTCGGTGTAGCATCTTCAAA
1 TCTCGGATGACTCGGTGTAGCATCTTCAAATATGA-CTCAGATGACTCGGTGTAGCATCTTCAAA
350 AATGA
65 AATGA
* * *
355 TCTCGGATGACTCGGTGTAGCATCTTCAAAAATGACCTCGGATGACGCGGTGTAGCATCTTCAAA
1 TCTCGGATGACTCGGTGTAGCATCTTCAAATATGA-CTCAGATGACTCGGTGTAGCATCTTCAAA
* *
420 GATAA
65 AATGA
* *
425 TCTCGGATGACTCGGTGTAGCATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTC-AA
1 TCTCGGATGACTCGGTGTAGCATCTTCAAATATG-ACTCAGATGACTCGGTGTAGCATCTTCAAA
*
489 TATGA
65 AATGA
* * * *
494 ACTCGG-TGAGCTCGGTGCAACAAACCTTCAAATA-GA-TCCAGATGACTCGGTGTAGCATCTTC
1 TCTCGGATGA-CTCGGTGTAGC--ATCTTCAAATATGACT-CAGATGACTCGGTGTAGCATCTTC
556 AAAAATGA
62 AAAAATGA
* * *
564 TCTCGGATGGCTCGGTGCAGCAAACCTTCAAATA-GA-TCCAGATGACTCGGTGTAGCATCTTCA
1 TCTCGGATGACTCGGTGTAGC--ATCTTCAAATATGACT-CAGATGACTCGGTGTAGCATCTTCA
627 AAAATGA
63 AAAATGA
* * *
634 TCTCGGATGGCTCGGTGCAGCAAATCTTCAAATA-GA-TCAGGATGACTCGGTGCAGCATCTTCA
1 TCTCGGATGACTCGGTGTAGC--ATCTTCAAATATGACTCA-GATGACTCGGTGTAGCATCTTCA
697 A
63 A
698 TATGGACTCA
Statistics
Matches: 373, Mismatches: 28, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
67 2 0.01
68 5 0.01
69 105 0.28
70 249 0.67
71 12 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (69 bp):
TCTCGGATGACTCGGTGTAGCATCTTCAAATATGACTCAGATGACTCGGTGTAGCATCTTCAAAA
ATGA
Found at i:540 original size:174 final size:175
Alignment explanation
Indices: 221--697 Score: 566
Period size: 174 Copynumber: 2.7 Consensus size: 175
211 CATCTTCTCA
* *
221 GATGACTCGGTGTAGCATCTTCAAAGTTATAT-TCGGATGACTCGGTGTAGCATCTTCAAAGATG
1 GATGACTCGGTGTAGCATCTTCAAAGATAGATCTCGGATGACTCGGTGTAGCATCTTCAAAGATG
* * * *
285 AA-TCAGATGACTCGGTGTAGCATCTTCAAAAATGACCTCAGATGACTCGGTGTAGCATCTTCAA
66 AATTCAGATGACTCGGTGTAGCATCTTC-AAAATGAACTCAGATGACTCGGTGCAACACCTTCAA
*
349 AAATGATCTCGGATGACTCGGTGTAGCATCTTCAAAAATGACCTCG
130 AAATGATCTCAGATGACTCGGTGTAGCATCTTCAAAAATGACCTCG
*
395 GATGACGCGGTGTAGCATCTTCAAAGATA-ATCTCGGATGACTCGGTGTAGCATCTTCAAAGATG
1 GATGACTCGGTGTAGCATCTTCAAAGATAGATCTCGGATGACTCGGTGTAGCATCTTCAAAGATG
* *
459 AATTCAGATGACTCGGTGTAGCATCTTCAATATGAACTC-GGTGAGCTCGGTGCAACAAACCTTC
66 AATTCAGATGACTCGGTGTAGCATCTTCAAAATGAACTCAGATGA-CTCGGTGCAAC--ACCTTC
* *
523 AAATA-GATC-CAGATGACTCGGTGTAGCATCTTCAAAAATGATCTCG
128 AAAAATGATCTCAGATGACTCGGTGTAGCATCTTCAAAAATGACCTCG
* * * * *
569 GATGGCTCGGTGCAGCAAACCTTC-AA-ATAGATC-CAGATGACTCGGTGTAGCATCTTCAAAAA
1 GATGACTCGGTGTAGC--ATCTTCAAAGATAGATCTCGGATGACTCGGTGTAGCATCTTCAAAGA
* * * * *
631 TG-ATCTCGGATGGCTCGGTGCAGCAAATCTTC-AAAT-AGA-TCAGGATGACTCGGTGCAGCAT
64 TGAAT-TCAGATGACTCGGTGTAGC--ATCTTCAAAATGA-ACTCA-GATGACTCGGTGCAACAC
692 CTTCAA
124 CTTCAA
698 TATGGACTCA
Statistics
Matches: 265, Mismatches: 24, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
173 15 0.06
174 178 0.67
175 48 0.18
176 24 0.09
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (175 bp):
GATGACTCGGTGTAGCATCTTCAAAGATAGATCTCGGATGACTCGGTGTAGCATCTTCAAAGATG
AATTCAGATGACTCGGTGTAGCATCTTCAAAATGAACTCAGATGACTCGGTGCAACACCTTCAAA
AATGATCTCAGATGACTCGGTGTAGCATCTTCAAAAATGACCTCG
Found at i:617 original size:209 final size:210
Alignment explanation
Indices: 216--739 Score: 656
Period size: 209 Copynumber: 2.5 Consensus size: 210
206 ATTACCATCT
* * *
216 TCTCAGATGACTCGGTGTAGCATCTTCAAAG-TTATATTCGGATGACTCGGTGTAGCATCTTCAA
1 TCTCGGATGACTCGGTGTAGCATCTTCAAAGATGA-ATTCAGATGACTCGGTGTAGCATCTTC-A
* * * * *
280 AGATGAA-TCAGATGA-CTCGGTGTAGC--ATCTTCAAAAATGACCTCAGATGACTCGGTGTAGC
64 ATATGAACTC-GGTGAGCTCGGTGCAGCAAATCTTCAAATA-GATCTCAGATGACTCGGTGTAGC
* * *
341 ATCTTCAAAAATGATCTCGGATGACTCGGTGTAGCATCTTCAAAAATGACCTCGGATGACGCGGT
127 ATCTTCAAAAATGATCTCGGATGACTCGGTGCAGCACCTTCAAAAATGACCTCAGATGACGCGGT
*
406 GTAGCATCTTCAAAGATAA
192 GTAGCATCTTCAAAAATAA
425 TCTCGGATGACTCGGTGTAGCATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTCAAT
1 TCTCGGATGACTCGGTGTAGCATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTCAAT
* *
490 ATGAACTCGGTGAGCTCGGTGCAACAAACCTTCAAATAGATC-CAGATGACTCGGTGTAGCATCT
66 ATGAACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCTCAGATGACTCGGTGTAGCATCT
* * * *
554 TCAAAAATGATCTCGGATGGCTCGGTGCAGCAAACCTTCAAATA-GATC-CAGATGACTCGGTGT
131 TCAAAAATGATCTCGGATGACTCGGTGCAGC--ACCTTCAAAAATGACCTCAGATGACGCGGTGT
*
617 AGCATCTTCAAAAATGA
194 AGCATCTTCAAAAATAA
* * * *
634 TCTCGGATGGCTCGGTGCAGCAAATCTTCAAATA-G-A-TCAGGATGACTCGGTGCAGCATCTTC
1 TCTCGGATGACTCGGTGTAGC--ATCTTCAAAGATGAATTCA-GATGACTCGGTGTAGCATCTTC
* * *
696 AATATGGACTCAGTGGGCTCGGTGCAGCAAATCTTCAAATAGAT
63 AATATGAACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGAT
740 TAGGGGTGAT
Statistics
Matches: 277, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
208 14 0.05
209 226 0.82
210 9 0.03
211 28 0.10
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (210 bp):
TCTCGGATGACTCGGTGTAGCATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTCAAT
ATGAACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCTCAGATGACTCGGTGTAGCATCT
TCAAAAATGATCTCGGATGACTCGGTGCAGCACCTTCAAAAATGACCTCAGATGACGCGGTGTAG
CATCTTCAAAAATAA
Found at i:1161 original size:27 final size:28
Alignment explanation
Indices: 1095--1169 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
1085 AGGATCACCT
*
1095 AGGGGCATTTTGGTCATTTTCAAAAATCC
1 AGGGGCATTTTGGTCATTTGC-AAAATCC
* * *
1124 AGGGGTATTTTGGTCATTTGC-ACATTC
1 AGGGGCATTTTGGTCATTTGCAAAATCC
*
1151 AGGGGCATTTTTGTCATTT
1 AGGGGCATTTTGGTCATTT
1170 TAAGTTAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 21 0.52
29 19 0.47
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTGCAAAATCC
Found at i:6895 original size:1 final size:1
Alignment explanation
Indices: 6879--6923 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
6869 ATGTATTGGG
* * * *
6879 TTTTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6924 CATGTTTTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:6907 original size:23 final size:23
Alignment explanation
Indices: 6880--6923 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
6870 TGTATTGGGT
6880 TTTTTGTTTTGTTTTTTTTTTTG
1 TTTTTGTTTTGTTTTTTTTTTTG
*
6903 TTTTTTTTTTGTTTTTTTTTT
1 TTTTTGTTTTGTTTTTTTTTT
6924 CATGTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (23 bp):
TTTTTGTTTTGTTTTTTTTTTTG
Found at i:6931 original size:12 final size:11
Alignment explanation
Indices: 6878--6923 Score: 74
Period size: 11 Copynumber: 4.0 Consensus size: 11
6868 AATGTATTGG
6878 GTTTTTTGTTTT
1 GTTTTTT-TTTT
6890 GTTTTTTTTTTT
1 G-TTTTTTTTTT
6902 GTTTTTTTTTT
1 GTTTTTTTTTT
6913 GTTTTTTTTTT
1 GTTTTTTTTTT
6924 CATGTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.64
12 6 0.18
13 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:6931 original size:23 final size:24
Alignment explanation
Indices: 6881--6931 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
6871 GTATTGGGTT
6881 TTTTGTTTTGTTTTTTTTTT--TG
1 TTTTGTTTTGTTTTTTTTTTCATG
*
6903 TTTTTTTTTTGTTTTTTTTTTCATG
1 -TTTTGTTTTGTTTTTTTTTTCATG
6928 TTTT
1 TTTT
6932 CTATGGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 19 0.76
24 4 0.16
25 2 0.08
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (24 bp):
TTTTGTTTTGTTTTTTTTTTCATG
Found at i:9145 original size:15 final size:16
Alignment explanation
Indices: 9119--9154 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
9109 TTTGTTTTGA
*
9119 TTTCTAGTTTAATTGT
1 TTTCTAGTTTAATTGC
9135 TTTCT-GTTTAATTGC
1 TTTCTAGTTTAATTGC
9150 TTTCT
1 TTTCT
9155 TTCAACCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (16 bp):
TTTCTAGTTTAATTGC
Found at i:9588 original size:21 final size:23
Alignment explanation
Indices: 9563--9605 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
9553 GAGTTTTCGG
9563 TTTTGCG-ATA-AAAAAAAAAGT
1 TTTTGCGCATATAAAAAAAAAGT
9584 TTTTGCGTCATATAAAAAAAAA
1 TTTTGCG-CATATAAAAAAAAA
9606 TATTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (23 bp):
TTTTGCGCATATAAAAAAAAAGT
Found at i:14638 original size:19 final size:17
Alignment explanation
Indices: 14614--14649 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
14604 GAAGTTCGTG
14614 TTTGAAGACCATTTGAAGA
1 TTTGAAGA-CA-TTGAAGA
14633 TTTGAAGACATTGAAGA
1 TTTGAAGACATTGAAGA
14650 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (17 bp):
TTTGAAGACATTGAAGA
Found at i:16063 original size:15 final size:16
Alignment explanation
Indices: 16033--16072 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
16023 TTGCTTTGTT
16033 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
16049 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
16064 TTGCTTTCT
1 TTGTTTTCT
16073 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:16610 original size:21 final size:21
Alignment explanation
Indices: 16586--16629 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16576 CTAGCTCTTG
16586 TCAAAGGACC-AATAGGCATCT
1 TCAAAGGACCAAAT-GGCATCT
* *
16607 TCAATGGATCAAATGGCATCT
1 TCAAAGGACCAAATGGCATCT
16628 TC
1 TC
16630 TTGGTGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (21 bp):
TCAAAGGACCAAATGGCATCT
Done.