Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005386.1 Corchorus capsularis cultivar CVL-1 contig05404, 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: 13502
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:215 original size:19 final size:21
Alignment explanation
Indices: 183--225 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
173 TTCTTTACTA
183 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
204 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
223 TTA
1 TTA
226 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:419 original size:22 final size:22
Alignment explanation
Indices: 391--493 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
381 TGTCTCTATG
391 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
413 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
436 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
457 TGGTTACCGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
479 TCAGGTTATTAAAAT
1 T--GGTTATCAAAAT
494 CTCTTAGGTT
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.02
22 45 0.76
23 4 0.07
24 9 0.15
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:527 original size:26 final size:26
Alignment explanation
Indices: 465--532 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
455 TGTGGTTACC
*
465 GAAATTTCATAGGAT--CAGGTTATT
1 GAAATTTCATAGGATGGTAGGTTATT
* * * *
489 AAAATCTCTTAGGTTGGTAGGTTATT
1 GAAATTTCATAGGATGGTAGGTTATT
*
515 GAAATTTCATAGGGTGGT
1 GAAATTTCATAGGATGGT
533 TAATTATCAC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.33
26 22 0.67
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
GAAATTTCATAGGATGGTAGGTTATT
Found at i:693 original size:22 final size:21
Alignment explanation
Indices: 645--929 Score: 98
Period size: 22 Copynumber: 12.8 Consensus size: 21
635 TTTCATGGGG
*
645 AGGTTATCAAAATTTTATA-A
1 AGGTTATCAAAATTTCATAGA
*
665 TGTGGTTATCAAAATTTCATATGA
1 --AGGTTATCAAAATTTCATA-GA
* *
689 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
714 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
736 AGGTTATC-AAATCTCATA-A
1 AGGTTATCAAAATTTCATAGA
*
755 AGTGATTATCGAAATTTCATAGAGA
1 AG-G-TTATCAAAATTTCAT--AGA
*
780 TCAGATTATCAAAATTT-ATAGAA
1 --AGGTTATCAAAATTTCATAG-A
* *
803 AGATTATCAAAATTCCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
823 CGTTGTTATCAAAATTACATA-A
1 AG--GTTATCAAAATTTCATAGA
* * *
845 TGTGATTATCAGAATTTCATTGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
868 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
890 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
912 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
930 AAATGTGATT
Statistics
Matches: 201, Mismatches: 37, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.01
20 10 0.05
21 28 0.14
22 121 0.60
23 5 0.02
24 5 0.02
25 18 0.09
26 5 0.02
27 6 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:794 original size:25 final size:22
Alignment explanation
Indices: 722--822 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 22
712 TAAGGAGTAC
* *
722 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* *
743 C-AAATCTCATA-AAGTGATTAT
1 CAAAATTTCATAGAA-AGATTAT
*
764 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGA-A--AGATTAT
789 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
*
810 CAAAATTCCATAG
1 CAAAATTTCATAG
823 CGTTGTTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
20 9 0.14
21 21 0.33
22 13 0.20
23 2 0.03
24 6 0.09
25 13 0.20
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:1085 original size:20 final size:20
Alignment explanation
Indices: 1035--1085 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1025 TCATGGAGTA
* *
1035 ATCAAGATTTCAATGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
1055 AT-AAAAATTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
1074 ATCAAAATTTCA
1 ATCAAAATTTCA
1086 TACGAACGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:1167 original size:44 final size:42
Alignment explanation
Indices: 1094--1196 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 42
1084 CATACGAACG
*
1094 TTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCACAAGAG-GA
1 TTATCAAAATTTCATAGTTTAG-TATC-AAATTTCA-AAGAGAGA
* *
1138 TTATCAAAATTTCATAGTATGTAG-ATCAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGT-T-TAGTATCAAATTTCAAAGAGAGA
*
1181 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
1197 ATGAGGTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.06
43 25 0.48
44 20 0.38
45 1 0.02
46 3 0.06
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (42 bp):
TTATCAAAATTTCATAGTTTAGTATCAAATTTCAAAGAGAGA
Found at i:1193 original size:22 final size:22
Alignment explanation
Indices: 1065--1569 Score: 197
Period size: 22 Copynumber: 23.5 Consensus size: 22
1055 ATAAAAATTC
*
1065 AGGGAGGATATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * *
1087 ACGAACGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * *
1109 AGTTTA-GTTTTCAAAATTTCAC
1 AG-GGAGGTTATCAAAATTTCAT
*
1131 A-AGAGGATTATCAAAATTTCAT
1 AGGGAGG-TTATCAAAATTTCAT
* * *
1153 A-GTATGTAGATC-AAATTTCAT
1 AGGGAGGT-TATCAAAATTTCAT
* *
1174 AGGGAGATTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** **
1196 AATGAGGTTATCAAAAAATCAT
1 AGGGAGGTTATCAAAATTTCAT
1218 AGGGAGGTTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* *
1237 --GTA-GTTATCAAGAA-ATCAT
1 AGGGAGGTTATCAA-AATTTCAT
1256 AGGGAGGTTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* *
1275 --GTA-GTTATCAAGATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
1294 AAGAAAGTTATCAAAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
*
1316 AGGGAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
** ** *
1339 AGAAATATTTATCAAAATTTCGT
1 AGGGA-GGTTATCAAAATTTCAT
* * *
1362 AGCGAGGTTATCACAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
1384 AGTGTGATTATCAAAATTTCAG
1 AGGGAGGTTATCAAAATTTCAT
* * *
1406 AGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGGTTATC-AA-AATTTCAT
* * * *
1428 ATGGAGATT-TTAAATTTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * * *
1449 AACGTGGTTATCAATATATCAT
1 AGGGAGGTTATCAAAATTTCAT
* *
1471 ATGGAGGTTATCAACATCTT-AT
1 AGGGAGGTTATCAAAAT-TTCAT
**
1493 AGTGTTGGTTATCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* * * * *
1516 TGGGAAGTTGTCAAAATTCCTT
1 AGGGAGGTTATCAAAATTTCAT
* *
1538 AGGGAGGTTAACCAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* *
1560 AAGAAGGTTA
1 AGGGAGGTTA
1570 AAAAAAATTT
Statistics
Matches: 354, Mismatches: 101, Indels: 56
0.69 0.20 0.11
Matches are distributed among these distances:
16 17 0.05
17 9 0.03
19 4 0.01
20 2 0.01
21 35 0.10
22 234 0.66
23 53 0.15
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:1245 original size:16 final size:16
Alignment explanation
Indices: 1224--1290 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 16
1214 TCATAGGGAG
1224 GTTATCAAAATTTGTA
1 GTTATCAAAATTTGTA
* *
1240 GTTATCAAGAAATCATAGGGA
1 GTTATC-A-AAAT--T-TGTA
1261 GGTTATCAAAATTTGTA
1 -GTTATCAAAATTTGTA
*
1278 GTTATCAAGATTT
1 GTTATCAAAATTT
1291 CATAAGAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 18 0.45
17 3 0.08
18 5 0.12
20 5 0.12
21 3 0.08
22 6 0.15
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (16 bp):
GTTATCAAAATTTGTA
Found at i:1253 original size:38 final size:38
Alignment explanation
Indices: 1202--1312 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
1192 TCATAATGAG
*
1202 GTTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 GTTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTA
1240 GTTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTA
1 GTTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTA
** * * *
1278 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 GTTATCAAGAAATCATAGGGAGGTTATCAAAATTT
1313 TATAGGGAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.33
Consensus pattern (38 bp):
GTTATCAAGAAATCATAGGGAGGTTATCAAAATTTGTA
Found at i:1329 original size:23 final size:23
Alignment explanation
Indices: 1301--1402 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
1291 CATAAGAAAG
*
1301 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGAGGT
* **
1324 TTATCAAAATTTTATAGAAATAT
1 TTATCAAAATTTTATAGAGAGGT
** *
1347 TTATCAAAATTTCGTAGCGAGG-
1 TTATCAAAATTTTATAGAGAGGT
* * * *
1369 TTATCACAATTTTATAGTG-TGA
1 TTATCAAAATTTTATAGAGAGGT
1391 TTATCAAAATTT
1 TTATCAAAATTT
1403 CAGAGTGTGA
Statistics
Matches: 62, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
21 1 0.02
22 26 0.42
23 35 0.56
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGAGGT
Found at i:2873 original size:16 final size:16
Alignment explanation
Indices: 2849--2884 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2839 CACAATTCAG
* *
2849 AAAGTAGAAAAGCTCT
1 AAAGCAGAAAAACTCT
2865 AAAGCAGAAAAACTCT
1 AAAGCAGAAAAACTCT
2881 AAAG
1 AAAG
2885 TATTTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAGCAGAAAAACTCT
Found at i:3073 original size:91 final size:91
Alignment explanation
Indices: 2918--3094 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 91
2908 GCTTAAGAAG
* * * **
2918 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAATATTTAATTATTGGAGAATT
1 ATTGAAAGAAAATCCACGTATGTGGAAAATTCTTCTTTAAAAGAAGATCCAATTATTGGAGAATT
*
2983 ATTGAAGACCCAGTTATTGGGGAGTT
66 ACTGAAGACCCAGTTATTGGGGAGTT
* **
3009 ATTGAAAGAAAATCCATGTATGTGGAGTATTCTTCTTTAAAAGAAGATCCAATTATTGGAGAATT
1 ATTGAAAGAAAATCCACGTATGTGGAAAATTCTTCTTTAAAAGAAGATCCAATTATTGGAGAATT
3074 ACTGAAGACCCAGTTATTGGG
66 ACTGAAGACCCAGTTATTGGG
3095 AAAGAAGATC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (91 bp):
ATTGAAAGAAAATCCACGTATGTGGAAAATTCTTCTTTAAAAGAAGATCCAATTATTGGAGAATT
ACTGAAGACCCAGTTATTGGGGAGTT
Found at i:7792 original size:1 final size:1
Alignment explanation
Indices: 7786--7818 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
7776 TTTTATTGCC
7786 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7819 CTCTGCACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8229 original size:14 final size:14
Alignment explanation
Indices: 8210--8239 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
8200 AATATATACT
8210 ATATAGATATATAG
1 ATATAGATATATAG
8224 ATATAGATATATAG
1 ATATAGATATATAG
8238 AT
1 AT
8240 TGTATGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (14 bp):
ATATAGATATATAG
Found at i:10918 original size:15 final size:15
Alignment explanation
Indices: 10898--10934 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
10888 TTATTATATC
10898 ATTATTA-AACTTATT
1 ATTATTATAA-TTATT
10913 ATTATTATAATTATT
1 ATTATTATAATTATT
10928 ATTATTA
1 ATTATTA
10935 GTGGTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATAATTATT
Found at i:10919 original size:18 final size:17
Alignment explanation
Indices: 10887--10957 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 17
10877 CATCTTATAT
10887 ATTATTATATCATTATTAA
1 ATTATTAT-T-ATTATTAA
10906 ACTTATTATTATTA-T-A
1 A-TTATTATTATTATTAA
10922 ATTATTATTATTAGTGGTAAA
1 ATTATTATTATTA-T--T-AA
10943 ATTATTATTAGTTAT
1 ATTATTATTA-TTAT
10958 ATGATCATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
15 12 0.27
16 2 0.05
17 1 0.02
18 4 0.09
19 3 0.07
20 7 0.16
21 12 0.27
22 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTATTATTATTATTAA
Found at i:12352 original size:20 final size:19
Alignment explanation
Indices: 12327--12376 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
12317 AGCAAAAAAA
12327 AATAATAATATAGTTTTTAG
1 AATAATAAT-TAGTTTTTAG
* *
12347 AATAATCACTTATTTTTTAG
1 AATAAT-AATTAGTTTTTAG
*
12367 AACAATAATT
1 AATAATAATT
12377 GAAGCTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 20 0.80
21 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (19 bp):
AATAATAATTAGTTTTTAG
Done.