Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016097.1 Corchorus capsularis cultivar CVL-1 contig16118, 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: 23508
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2256 original size:10 final size:9
Alignment explanation
Indices: 2222--2257 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
2212 CTGGTCGAAA
2222 ATTTTTTTT
1 ATTTTTTTT
2231 ATTTTATTTT
1 ATTTT-TTTT
2241 ATTTTTTTT
1 ATTTTTTTT
2250 ATATTTTT
1 AT-TTTTT
2258 CGATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:2358 original size:8 final size:8
Alignment explanation
Indices: 2330--2363 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2320 GAATCGGCTA
2330 TGAATTTT
1 TGAATTTT
*
2338 TGAAGTTTC
1 TGAA-TTTT
2347 TGAATTTT
1 TGAATTTT
2355 TGAATTTT
1 TGAATTTT
2363 T
1 T
2364 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:7165 original size:35 final size:35
Alignment explanation
Indices: 7119--7231 Score: 172
Period size: 35 Copynumber: 3.2 Consensus size: 35
7109 AAAAAGCAAA
* *
7119 TTGGTAATCAACTTAATTCGATGTAATTAAGTAAT
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAT
**
7154 TTGGTAATCAACTTAAACCGGTGCAATTAAGTAAT
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAT
* *
7189 TTGGTAATTAACTTAATTCGGTGCAATTAAGTAAA
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAT
7224 TTGGTAAT
1 TTGGTAAT
7232 TAAAATTAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (35 bp):
TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAT
Found at i:7225 original size:19 final size:18
Alignment explanation
Indices: 7172--7222 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
7162 CAACTTAAAC
7172 CGGTGCAATTAAGTAATT
1 CGGTGCAATTAAGTAATT
* *
7190 TGGT--AATTAACTTAATT
1 CGGTGCAATTAA-GTAATT
7207 CGGTGCAATTAAGTAA
1 CGGTGCAATTAAGTAA
7223 ATTGGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 6 0.23
19 6 0.23
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (18 bp):
CGGTGCAATTAAGTAATT
Found at i:7238 original size:22 final size:22
Alignment explanation
Indices: 7213--7256 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7203 AATTCGGTGC
7213 AATTAAGTAAATTGGTAATTAA
1 AATTAAGTAAATTGGTAATTAA
*
7235 AATTAAGTAATTTGGTAATTAA
1 AATTAAGTAAATTGGTAATTAA
7257 CTCAATTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (22 bp):
AATTAAGTAAATTGGTAATTAA
Found at i:7275 original size:35 final size:35
Alignment explanation
Indices: 7235--7349 Score: 149
Period size: 35 Copynumber: 3.3 Consensus size: 35
7225 TGGTAATTAA
* ** *
7235 AATTAAGTAATTTGGTAATTAACTCAATTTGGTGT
1 AATTAAGTAAATCAGTAATTAACTTAATTTGGTGT
* **
7270 AATTAAGTAAATCAGTAATCAACTTAATTCAGTGT
1 AATTAAGTAAATCAGTAATTAACTTAATTTGGTGT
*
7305 AATTAAGTAAATCAGTAATTAGCTTAATTTGGTGT
1 AATTAAGTAAATCAGTAATTAACTTAATTTGGTGT
*
7340 AGTTAAGTAA
1 AATTAAGTAA
7350 GTAATCAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (35 bp):
AATTAAGTAAATCAGTAATTAACTTAATTTGGTGT
Found at i:7288 original size:57 final size:57
Alignment explanation
Indices: 7178--7288 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
7168 AAACCGGTGC
* **
7178 AATTAAGTAATTTGGTAATTAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAA
1 AATTAAGTAATTTGGTAATTAACTCAATTCGGTGCAATTAAGTAAATCAGTAATTAA
* *
7235 AATTAAGTAATTTGGTAATTAACTCAATTTGGTGTAATTAAGTAAATCAGTAAT
1 AATTAAGTAATTTGGTAATTAACTCAATTCGGTGCAATTAAGTAAATCAGTAAT
7289 CAACTTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (57 bp):
AATTAAGTAATTTGGTAATTAACTCAATTCGGTGCAATTAAGTAAATCAGTAATTAA
Found at i:7309 original size:92 final size:92
Alignment explanation
Indices: 7143--7325 Score: 240
Period size: 92 Copynumber: 2.0 Consensus size: 92
7133 AATTCGATGT
* * ** *
7143 AATTAAGTAATTTGGTAATCAACTTAAACCGGTGCAATTAAGTAATTTGGTAATTAACTTAATTC
1 AATTAAGTAATTTGGTAATCAACTCAAACCGGTGCAATTAAGTAAATCAGTAATCAACTTAATTC
* **
7208 GGTGCAATTAAGTAAATTGGTAATTAA
66 AGTGCAATTAAGTAAATCAGTAATTAA
* *** *
7235 AATTAAGTAATTTGGTAATTAACTCAATTTGGTGTAATTAAGTAAATCAGTAATCAACTTAATTC
1 AATTAAGTAATTTGGTAATCAACTCAAACCGGTGCAATTAAGTAAATCAGTAATCAACTTAATTC
*
7300 AGTGTAATTAAGTAAATCAGTAATTA
66 AGTGCAATTAAGTAAATCAGTAATTA
7326 GCTTAATTTG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (92 bp):
AATTAAGTAATTTGGTAATCAACTCAAACCGGTGCAATTAAGTAAATCAGTAATCAACTTAATTC
AGTGCAATTAAGTAAATCAGTAATTAA
Found at i:7324 original size:16 final size:16
Alignment explanation
Indices: 7268--7325 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
7258 TCAATTTGGT
7268 GTAATTAAGTAAATCA
1 GTAATTAAGTAAATCA
* * *
7284 GTAATCAACTTAATTCA
1 GTAATTAA-GTAAATCA
7301 GTGTAATTAAGTAAATCA
1 --GTAATTAAGTAAATCA
7319 GTAATTA
1 GTAATTA
7326 GCTTAATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 14 0.42
17 6 0.18
18 6 0.18
19 7 0.21
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (16 bp):
GTAATTAAGTAAATCA
Found at i:7346 original size:127 final size:127
Alignment explanation
Indices: 7119--7349 Score: 300
Period size: 127 Copynumber: 1.8 Consensus size: 127
7109 AAAAAGCAAA
* * ** *
7119 TTGGTAATCAACTTAATTCGATGTAATTAAGTAATTTGGTAATCAACTTAAACCGGTGCAATTAA
1 TTGGTAATCAACTCAATTCGATGTAATTAAGTAAATCAGTAATCAACTTAAACCAGTGCAATTAA
* **
7184 GTAATTTGGTAATTAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAAATTAAGTAAT
66 GTAAATCAGTAATTAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAAATTAAGTAAT
* * * ** *
7246 TTGGTAATTAACTCAATTTGGTGTAATTAAGTAAATCAGTAATCAACTTAATTCAGTGTAATTAA
1 TTGGTAATCAACTCAATTCGATGTAATTAAGTAAATCAGTAATCAACTTAAACCAGTGCAATTAA
* * * *
7311 GTAAATCAGTAATTAGCTTAATTTGGTGTAGTTAAGTAA
66 GTAAATCAGTAATTAACTTAATTCGGTGCAATTAAGTAA
7350 GTAATCAAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
127 86 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (127 bp):
TTGGTAATCAACTCAATTCGATGTAATTAAGTAAATCAGTAATCAACTTAAACCAGTGCAATTAA
GTAAATCAGTAATTAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAAATTAAGTAAT
Found at i:9642 original size:41 final size:41
Alignment explanation
Indices: 9580--9815 Score: 217
Period size: 41 Copynumber: 5.7 Consensus size: 41
9570 TTCTCTTTCT
* *
9580 AAAGTCCTCAAGA-ACATTTATAACACAGAGGCACCCATATC
1 AAAGTCCCCAA-ACACATTTATAACACAGAGGCATCCATATC
* * * * *
9621 AAAGTCCCCAAGCACAATTATAACACAGGGGCACCTCTATTTC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCA--TCCATATC
* * **
9664 AAAGTCCTCAAACACATTTATAACACAGAGACATTTATATC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCCATATC
* * **
9705 AAAGTCCCCAAACACATTTATAACATAGGGGCAATCC-TCCC
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-ATCCATATC
* *
9746 TAAGATTCCTCAAACACATTTATAACACAGAGGCATCCATA-C
1 -AA-AGTCCCCAAACACATTTATAACACAGAGGCATCCATATC
* *
9788 TAAAGTCCCTAAACACAATTATAACACA
1 -AAAGTCCCCAAACACATTTATAACACA
9816 AGGGCAATCT
Statistics
Matches: 157, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
41 85 0.54
42 12 0.08
43 60 0.38
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCATCCATATC
Found at i:9822 original size:84 final size:85
Alignment explanation
Indices: 9536--9824 Score: 306
Period size: 84 Copynumber: 3.4 Consensus size: 85
9526 CTCTCTCCCT
* * * * **
9536 AAAGTCCCCAAGA-ACATTTATAGCATAGGGGCAATTCTC-TTTCTAAAGTCCTCAAGA-ACATT
1 AAAGTCCCCAA-ACACAATTATAACACAGGGGCAATCCTCACCTC-AAAGTCCTCAA-ACACATT
*
9598 TATAACACAGAGGCACCCATATC
63 TATAACACAGAGGCATCCATATC
* **
9621 AAAGTCCCCAAGCACAATTATAACACAGGGGC-A-CCTCTATTTCAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTC-ACCTCAAAGTCCTCAAACACATTTA
* **
9684 TAACACAGAGACATTTATATC
65 TAACACAGAGGCATCCATATC
* * *
9705 AAAGTCCCCAAACACATTTATAACATAGGGGCAATCCTC-CCT-AAGATTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTCACCTCAA-AGTCCTCAAACACATTTA
9768 TAACACAGAGGCATCCATA-C
65 TAACACAGAGGCATCCATATC
* *
9788 TAAAGTCCCTAAACACAATTATAACACAAGGGCAATC
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCAATC
9825 TCTATATGGC
Statistics
Matches: 174, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
83 7 0.04
84 131 0.75
85 32 0.18
86 4 0.02
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (85 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTCACCTCAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCCATATC
Found at i:14707 original size:70 final size:70
Alignment explanation
Indices: 14555--14765 Score: 335
Period size: 70 Copynumber: 3.1 Consensus size: 70
14545 ACTTCGAATT
*
14555 CAAAATTTGATG-CATGAACTTAATAATAGAATAGTACAATGGTCTCTC---TAATGTTTATTAA
1 CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAATAA
*
14616 --TAT
66 TGTAA
14619 CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAATAA
1 CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAATAA
14684 TGTAA
66 TGTAA
14689 CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAATTA
1 CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAA-TA
*
14754 ATGGAA
65 ATGTAA
*
14760 CGAAAT
1 CAAAAT
14766 AAAAATCATA
Statistics
Matches: 136, Mismatches: 4, Indels: 7
0.93 0.03 0.05
Matches are distributed among these distances:
64 12 0.09
65 36 0.26
68 12 0.09
70 64 0.47
71 12 0.09
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (70 bp):
CAAAATTTGATGACATGAACTTAATAATAGAATAGTACAATGGTCTCTCAAATAATGTTTAATAA
TGTAA
Found at i:15761 original size:18 final size:18
Alignment explanation
Indices: 15738--15791 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
15728 CACCTTGTAT
*
15738 GTTTTTGAATCCCCATTG
1 GTTTTTGAATCCCCATCG
15756 GTTTTTGAATCCCCATCG
1 GTTTTTGAATCCCCATCG
*
15774 GTTTTTGAATCTCCATCG
1 GTTTTTGAATCCCCATCG
15792 ACATTAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (18 bp):
GTTTTTGAATCCCCATCG
Found at i:19743 original size:14 final size:15
Alignment explanation
Indices: 19716--19749 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19706 CCGCCCGACC
19716 CATATTAGTATAATA
1 CATATTAGTATAATA
*
19731 TATATTA-TATAATA
1 CATATTAGTATAATA
19745 CATAT
1 CATAT
19750 CTTTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
CATATTAGTATAATA
Found at i:20666 original size:452 final size:447
Alignment explanation
Indices: 19957--20855 Score: 1656
Period size: 452 Copynumber: 2.0 Consensus size: 447
19947 TGGACATGAA
*
19957 AACTTAAATATGGGCGAGCTTTGATCGCGGGTTTATGCGAGACTTGGACATGAAAACTTAAATAT
1 AACTTAAATATGGGCGAGCTTTGATCGCGGGTCTATGCGAGACTTGGACATGAAAACTTAAATAT
*
20022 GGGATGGCTTTGGTCAAATTACCAAGCCCAAATAGTCGTGTCGGGCCTAGGCATACAAAATTTCT
66 GGGATGGCTTTGGTCAAATTACCAAGCCCAAATAGTCGGGTCGGGCCTAGGCATACAAAATTTCT
*
20087 ATTATTATTTAGTCAAACCCAGCCCAAACAAGGCCCATGATCAGGTCTCGACGTGAGGAATGAGT
131 ATTATTATCTAGTCAAACCCAGCCCAAACAAGGCCCATGATCAGGTCTCGACGTGAGGAATGAGT
20152 TACACAATTTTTCTAAGATATTTTTAAGTAGAAGAAGACAATCTGAAAATTATTGTAATATCAAT
196 TACACAATTTTTCTAAGATATTTTTAAGTAGAAGAAGACAATCTGAAAATTATTGTAATATCAAT
* *
20217 ATTGAGTTTATGCTTTCGTTTTTATAAATGAAATTTCAATTTGATTTTTTGTAAAAAAAGAAAAA
261 ACTGAGTTTATGCTTTCGTTTTTATAAATGAAAGTTCAATTTGATTTTTTGTAAAAAAAGAAAAA
20282 TCCTTCACTGATGGTATATAGGATTTGATTTGATGCGCTTGCATCAATTGTACACTATTATTATA
326 TCCTTCACTGATGGTATATA-G----GATTTGATGCGCTTGCATCAATTGTACACTATTATTATA
20347 TGGATAATAATACAATACACTTTCAGTGTAAAGTTTTAACTCCACAAGCGGGTTAAGATATT
386 TGGATAATAATACAATACACTTTCAGTGTAAAGTTTTAACTCCACAAGCGGGTTAAGATATT
20409 AACTTAAATATGGGCGAGCTTTGATCGCGGGTCTATGCGAGACTTGGACATGAAAACTTAAATAT
1 AACTTAAATATGGGCGAGCTTTGATCGCGGGTCTATGCGAGACTTGGACATGAAAACTTAAATAT
*
20474 GGGATGGCTTTGGTCAAATTACCAAGCCCAAATAGTCGGGTCGGGCCTAGGCATACAGAATTTCT
66 GGGATGGCTTTGGTCAAATTACCAAGCCCAAATAGTCGGGTCGGGCCTAGGCATACAAAATTTCT
* *
20539 ATTATTATCTAGTGAAACCCAGCCCGAAC-AGGACCCATGATCAGGTCTCGACGTGAGGAATGAG
131 ATTATTATCTAGTCAAACCCAGCCCAAACAAGG-CCCATGATCAGGTCTCGACGTGAGGAATGAG
20603 TTACACAATTTTTCTAAGATATTTTTAAGTAGAAGAAGACAATCTGAAAATTATTGTAATATCAA
195 TTACACAATTTTTCTAAGATATTTTTAAGTAGAAGAAGACAATCTGAAAATTATTGTAATATCAA
20668 TACTGAGTTTATGCTTTCGTTTTTATAAATGAAAGTTCAATTTGATTTTTTGTAAAAAAAGAAAA
260 TACTGAGTTTATGCTTTCGTTTTTATAAATGAAAGTTCAATTTGATTTTTTGTAAAAAAAGAAAA
20733 ATCCTTCACTGATGGTATATAGGATTTGATGCGCTTGCATCAATTGTACACTATTATTATATGGA
325 ATCCTTCACTGATGGTATATAGGATTTGATGCGCTTGCATCAATTGTACACTATTATTATATGGA
*
20798 TAATAATACAATACACTTTCAGTGTAAAGTTTTAACTCCACAAGCGGGTTAAGGTATT
390 TAATAATACAATACACTTTCAGTGTAAAGTTTTAACTCCACAAGCGGGTTAAGATATT
20856 GATATATACC
Statistics
Matches: 437, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
447 100 0.23
451 4 0.01
452 333 0.76
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (447 bp):
AACTTAAATATGGGCGAGCTTTGATCGCGGGTCTATGCGAGACTTGGACATGAAAACTTAAATAT
GGGATGGCTTTGGTCAAATTACCAAGCCCAAATAGTCGGGTCGGGCCTAGGCATACAAAATTTCT
ATTATTATCTAGTCAAACCCAGCCCAAACAAGGCCCATGATCAGGTCTCGACGTGAGGAATGAGT
TACACAATTTTTCTAAGATATTTTTAAGTAGAAGAAGACAATCTGAAAATTATTGTAATATCAAT
ACTGAGTTTATGCTTTCGTTTTTATAAATGAAAGTTCAATTTGATTTTTTGTAAAAAAAGAAAAA
TCCTTCACTGATGGTATATAGGATTTGATGCGCTTGCATCAATTGTACACTATTATTATATGGAT
AATAATACAATACACTTTCAGTGTAAAGTTTTAACTCCACAAGCGGGTTAAGATATT
Done.