Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001165.1 Corchorus capsularis cultivar CVL-1 contig01165, 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: 2517
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Found at i:272 original size:22 final size:22
Alignment explanation
Indices: 222--273 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
212 TCACATTTTG
222 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
243 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
265 AAAATTTTG
1 AAAATTTTG
274 TTGACCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:291 original size:22 final size:22
Alignment explanation
Indices: 220--343 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 22
210 AATCACATTT
* * *
220 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
242 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
264 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* * * *
286 TGAAATTCTAATAATCACAT-TA
1 TGAAATTTTGATAA-CCCCTCTA
** * * *
308 TTTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCCCTCTA
330 TGAAATTTTGATAA
1 TGAAATTTTGATAA
344 TAACACCATG
Statistics
Matches: 76, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
21 1 0.01
22 72 0.95
23 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:344 original size:44 final size:43
Alignment explanation
Indices: 198--365 Score: 126
Period size: 44 Copynumber: 3.8 Consensus size: 43
188 AATACCATTA
* *
198 TGAAATTTTTG-TAATCACATT-TTGAAAATTTGATAACCTCTTT
1 TGAAA-TTTTGATAATCACATTATT-AAATTTTGATAACCTCCTT
* * * * * *
241 ATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACC-CCTCT
1 -TGAAATTTTGATAATCACATTATTAAATTTTGATAACCTCCT-T
* * *
285 ATGAAATTCTAATAATCACATTATTTAATTTTGATAACCTCGCTT
1 -TGAAATTTTGATAATCACATTATTAAATTTTGATAACCTC-CTT
* ** *
330 TGAAATTTTGATAATAACACCATGAAATTTTGATAA
1 TGAAATTTTGATAATCACATTATTAAATTTTGATAA
366 TCTGATCACA
Statistics
Matches: 95, Mismatches: 24, Indels: 10
0.74 0.19 0.08
Matches are distributed among these distances:
43 7 0.07
44 83 0.87
45 3 0.03
46 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (43 bp):
TGAAATTTTGATAATCACATTATTAAATTTTGATAACCTCCTT
Found at i:490 original size:22 final size:22
Alignment explanation
Indices: 464--555 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 22
454 TATAACCTTC
*
464 ATAACCACACTATAAAATTTTG
1 ATAACCACACTATGAAATTTTG
*
486 ATAACCTC-CTAATGAAATTTTG
1 ATAACCACACT-ATGAAATTTTG
*
508 TTAACCACACTATGAAATTCTT-
1 ATAACCACACTATGAAATT-TTG
* * *
530 ATAACCTCGCTATGACATTTTG
1 ATAACCACACTATGAAATTTTG
552 ATAA
1 ATAA
556 TCTCTTTGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.07
22 50 0.86
23 4 0.07
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:534 original size:44 final size:44
Alignment explanation
Indices: 465--551 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
455 ATAACCTTCA
465 TAACCACACTATAAAATTTTGATAACCTC-CTAATGAAATTTTGT
1 TAACCACACTATAAAATTTTGATAACCTCGCT-ATGAAATTTTGT
* *
509 TAACCACACTATGAAATTCTT-ATAACCTCGCTATGACATTTTG
1 TAACCACACTATAAAATT-TTGATAACCTCGCTATGAAATTTTG
552 ATAATCTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (44 bp):
TAACCACACTATAAAATTTTGATAACCTCGCTATGAAATTTTGT
Found at i:698 original size:22 final size:21
Alignment explanation
Indices: 620--729 Score: 85
Period size: 22 Copynumber: 5.0 Consensus size: 21
610 CAATAATCAA
* *
620 CCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACC---T
* *
644 CCTATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAACCT
*
665 CACTATGGAATTTTGATAACCT
1 C-CTATGAAATTTTGATAACCT
* * *
687 CCTCATGAAATTATAATAACTAT
1 CCT-ATGAAATTTTGATAAC-CT
*
710 CTTATGAAATTTTGATAACC
1 CCTATGAAATTTTGATAACC
730 ACATAGAGAC
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.04
22 45 0.66
23 3 0.04
24 17 0.25
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCT
Found at i:926 original size:19 final size:20
Alignment explanation
Indices: 895--932 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
885 TATTGACATT
895 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
914 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
933 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:1213 original size:13 final size:13
Alignment explanation
Indices: 1175--1213 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
1165 GTCTAAATTG
1175 AAATTTTAA-AAT
1 AAATTTTAATAAT
*
1187 TAATTTTAAATAAT
1 AAATTTT-AATAAT
1201 AAATTTTAATAAT
1 AAATTTTAATAAT
1214 GTCAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 8 0.35
14 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTTAATAAT
Found at i:1224 original size:168 final size:165
Alignment explanation
Indices: 947--1249 Score: 425
Period size: 168 Copynumber: 1.8 Consensus size: 165
937 AATAGTAAAG
* *
947 GAAATTTACATGTTCATCAACTAAAATCAGTTTGACAAACTTATAATTTGGTCTAAATTGAAATT
1 GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
*
1012 TTTAATTAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTTGGAAAAAAGG
66 TTAAATTAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATA-TTT-GAAAAAAGG
*
1077 GTGCAATCAAAAAACATAAAGTTTCCTATTATTTGTA
129 GTACAATCAAAAAACATAAAGTTTCCTATTATTTGTA
* * *
1114 GAAATTTGCGTGTTCATCAA-TGAAAATCAATTTTACAAAACTTATAATTCGGTCTAAATTGAAA
1 GAAATTTACATGTTCATCAACT-AAAATCAATTTGAC-AAACTTATAATTCGGTCTAAATTGAAA
* **
1178 TTTTAAAATTAATTTTAAA-TA-A-TAAATTTTAATAATGTCAATTTAGAAATATATTTGAAAAA
64 TTTT-AAATTAA--TAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGAAAAA
1240 AGGGTACAAT
126 AGGGTACAAT
1250 AAGAGACAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
166 16 0.13
167 33 0.27
168 59 0.49
169 7 0.06
170 2 0.02
171 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (165 bp):
GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
TTAAATTAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGAAAAAAGGGT
ACAATCAAAAAACATAAAGTTTCCTATTATTTGTA
Found at i:1328 original size:37 final size:38
Alignment explanation
Indices: 1255--1334 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
1245 ACAATAAGAG
* *
1255 ACAAAGACAAAAAGCAAAATTACATACAATGATTGGAA
1 ACAAAGACAAAAAGCAAAATTAAATACAACGATTGGAA
* *
1293 ACAAAGACAAAAGGCAAAATTAAATAGAACG-TTGGAA
1 ACAAAGACAAAAAGCAAAATTAAATACAACGATTGGAA
1330 ACAAA
1 ACAAA
1335 AAGTCAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 11 0.29
38 27 0.71
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.14
Consensus pattern (38 bp):
ACAAAGACAAAAAGCAAAATTAAATACAACGATTGGAA
Found at i:1490 original size:31 final size:31
Alignment explanation
Indices: 1449--1516 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1439 TTTAGTAATG
1449 ACAATTTAGAAATATGTTTTAGAAAA-AAGAGT
1 ACAA-TTAGAAATATGTTTTA-AAAATAAGAGT
*
1481 ACAATTAGAAATATGTTTTAAAAATAAGGGT
1 ACAATTAGAAATATGTTTTAAAAATAAGAGT
1512 ACAAT
1 ACAAT
1517 CGGAAAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 26 0.76
32 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (31 bp):
ACAATTAGAAATATGTTTTAAAAATAAGAGT
Done.