Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007381.1 Corchorus capsularis cultivar CVL-1 contig07402, 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: 6723
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:708 original size:15 final size:15
Alignment explanation
Indices: 661--711 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
651 TAGTAATATT
661 TTAATTATTTCATTA
1 TTAATTATTTCATTA
*
676 TT--TT-TTTAATTA
1 TTAATTATTTCATTA
*
688 TAAATTATTTCATTA
1 TTAATTATTTCATTA
703 TTAATTATT
1 TTAATTATT
712 AGATTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 8 0.28
13 2 0.07
14 2 0.07
15 17 0.59
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTATTTCATTA
Found at i:904 original size:22 final size:22
Alignment explanation
Indices: 835--1026 Score: 101
Period size: 22 Copynumber: 8.6 Consensus size: 22
825 TAAAAGTCTC
* *
835 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
855 AATTTAATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
875 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
897 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
922 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
943 AATTTCATATATAGTGTTGTTATCAA
1 AATTTC--ATAGAGTG--ATTATCAA
* * * * *
969 AAATTCAAAGCGAAGGTTATCAA
1 AATTTCATAGAG-TGATTATCAA
* *
992 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
1014 AATTTCATAGAGT
1 AATTTCATAGAGT
1027 AGTCAACAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.02
20 18 0.14
21 22 0.17
22 32 0.25
23 17 0.13
24 13 0.10
25 14 0.11
26 12 0.09
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:938 original size:21 final size:22
Alignment explanation
Indices: 852--947 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 22
842 TAAGGAGTAC
*
852 CAAAATTTAATAG-AAGGTTAT
1 CAAAATTTAATAGAAAGATTAT
* * **
873 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTAATAGAAAGATTAT
* * *
894 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTAATAGA-A--AGATTAT
919 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTAATAGAAAGATTAT
940 CAAAATTT
1 CAAAATTT
948 CATATATAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
20 9 0.15
21 21 0.35
22 11 0.18
23 1 0.02
24 5 0.08
25 13 0.22
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTAATAGAAAGATTAT
Found at i:1232 original size:22 final size:22
Alignment explanation
Indices: 1164--1415 Score: 116
Period size: 22 Copynumber: 11.8 Consensus size: 22
1154 TTTTATTATG
* *
1164 GAGTAATCAAAATTTCA-AGGA
1 GAGTTATCAAAATTTCATAAGA
* * ***
1185 G-GATAACAAAATTTCATACTT
1 GAGTTATCAAAATTTCATAAGA
* *
1206 TAGTTTTCAAAATTTCATAAGA
1 GAGTTATCAAAATTTCATAAGA
*
1228 GAGTTATCAAAATTTCATAGGGA
1 GAGTTATCAAAATTTCATA-AGA
*
1251 GAG-TAACAAAATTTCATAATGA
1 GAGTTATCAAAATTTCATAA-GA
** *
1273 -AGTTATCAAAAAATCAT-AGG
1 GAGTTATCAAAATTTCATAAGA
*
1293 GAGGTTATTAAAA-TT--T--G-
1 GA-GTTATCAAAATTTCATAAGA
* * *
1310 TAGTTTTCAAGATTTCATAAGA
1 GAGTTATCAAAATTTCATAAGA
* * *
1332 AAGTTATCAAAATTTTATAGGAA
1 GAGTTATCAAAATTTCATAAG-A
* * *
1355 GATTTATTAAAATTTCAT-AGC
1 GAGTTATCAAAATTTCATAAGA
* *
1376 GAGGTTATCACAATTTCAT-AGT
1 GA-GTTATCAAAATTTCATAAGA
*
1398 GTGATTATCAAAATTTCA
1 GAG-TTATCAAAATTTCA
1416 GAGTGTGATT
Statistics
Matches: 170, Mismatches: 45, Indels: 31
0.69 0.18 0.13
Matches are distributed among these distances:
16 7 0.04
17 3 0.02
18 1 0.01
19 2 0.01
20 13 0.08
21 11 0.06
22 113 0.66
23 20 0.12
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
GAGTTATCAAAATTTCATAAGA
Found at i:1290 original size:66 final size:63
Alignment explanation
Indices: 1164--1308 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 63
1154 TTTTATTATG
* * ** * **
1164 GAGTAATCAAAATTTCAAGGAGGATAACAAAATTTCATACTTTAGTTTTCAAAATTTCATAAGA
1 GAGTTATCAAAATTTCAAGGAGGATAACAAAATTTCATAATGAAGTTATCAAAAAATCAT-AGA
1228 GAGTTATCAAAATTTCATAGG-GAGAGTAACAAAATTTCATAATGAAGTTATCAAAAAATCATAG
1 GAGTTATCAAAATTTCA-AGGAG-GA-TAACAAAATTTCATAATGAAGTTATCAAAAAATCATAG
*
1292 G
63 A
*
1293 GAGGTTATTAAAATTT
1 GA-GTTATCAAAATTT
1309 GTAGTTTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 17 0.25
65 9 0.13
66 42 0.62
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (63 bp):
GAGTTATCAAAATTTCAAGGAGGATAACAAAATTTCATAATGAAGTTATCAAAAAATCATAGA
Found at i:1420 original size:22 final size:22
Alignment explanation
Indices: 1380--1426 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1370 CATAGCGAGG
* *
1380 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
1402 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
1424 TTA
1 TTA
1427 CTAACAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:1437 original size:22 final size:23
Alignment explanation
Indices: 1380--1435 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
1370 CATAGCGAGG
*
1380 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
1402 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
1424 TTA-CTAACAATT
1 TTATC-AACAATT
1436 CATATGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 24 0.80
23 5 0.17
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATCAACAATTTCAGAGTGTGA
Found at i:1579 original size:22 final size:22
Alignment explanation
Indices: 1511--1661 Score: 78
Period size: 22 Copynumber: 6.9 Consensus size: 22
1501 TCATAGTGTT
*
1511 GGTTATCAAAATTTCATATTG-A
1 GGTTATCAAAATTTCATA-AGAA
* * * *
1533 GGTCT-TCAAAATTACTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
1555 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
**
1577 GGTTAAAAAACATTT-ATAA-AA
1 GGTTATCAAA-ATTTCATAAGAA
* * * *
1598 TGGTTTTCGAAATTCCAT-AGTAT
1 -GGTTATCAAAATTTCATAAG-AA
** * *
1621 CCTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
1643 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
1662 TGGGATTATA
Statistics
Matches: 93, Mismatches: 27, Indels: 18
0.67 0.20 0.13
Matches are distributed among these distances:
21 8 0.09
22 78 0.84
23 7 0.08
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:5178 original size:51 final size:51
Alignment explanation
Indices: 5118--5249 Score: 219
Period size: 51 Copynumber: 2.6 Consensus size: 51
5108 GATTGATTGC
5118 ACAGAGTTATGGCATCGCAGATTGGATCACGCAGAGTTATTTGGGCATCGT
1 ACAGAGTTATGGCATCGCAGATTGGATCACGCAGAGTTATTTGGGCATCGT
* *
5169 ACAGAGTTATGGCATCACAGATTGGATCACGTAGAGTTATTTGGGCATCGT
1 ACAGAGTTATGGCATCGCAGATTGGATCACGCAGAGTTATTTGGGCATCGT
* * *
5220 ACAGAGTTATGACATTGCAGATTGGGTCAC
1 ACAGAGTTATGGCATCGCAGATTGGATCAC
5250 ACAAATTTGG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (51 bp):
ACAGAGTTATGGCATCGCAGATTGGATCACGCAGAGTTATTTGGGCATCGT
Found at i:5753 original size:6 final size:6
Alignment explanation
Indices: 5744--5776 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5734 AAAACAAAGC
*
5744 AAATCA AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
5777 GCAGATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATCT
Done.