Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014420.1 Corchorus olitorius cultivar O-4 contig14453, 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: 7330
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Found at i:105 original size:22 final size:22
Alignment explanation
Indices: 73--143 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
63 ATAACATCCC
*
73 TCTTAAAAACCACACTATAAAA
1 TCTTAATAACCACACTATAAAA
* *
95 TCTTAATAACCACATTATGAAA
1 TCTTAATAACCACACTATAAAA
* * *
117 TCTTGATAATCACACAATAAAA
1 TCTTAATAACCACACTATAAAA
139 T-TTAA
1 TCTTAA
144 ATAATCTCCC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (22 bp):
TCTTAATAACCACACTATAAAA
Found at i:778 original size:2 final size:2
Alignment explanation
Indices: 771--802 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
761 TTCCGTAAAG
771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
803 ATCCGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1205 original size:22 final size:20
Alignment explanation
Indices: 1165--1229 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
1155 TTTTATGAAA
1165 TTTGATAATCACTATAAAAT
1 TTTGATAATCACTATAAAAT
*
1185 TTTGATAATCTCCATATAAAAT
1 TTTGATAATC-AC-TATAAAAT
* *
1207 TTTTATAATTAC-ACTAAAAT
1 TTTGATAATCACTA-TAAAAT
1227 TTT
1 TTT
1230 TATGACGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.50
21 2 0.05
22 16 0.42
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTGATAATCACTATAAAAT
Found at i:1352 original size:21 final size:23
Alignment explanation
Indices: 1317--1363 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1307 GATCCCTATA
1317 AAAATTTTAATAACC-ACCAATG
1 AAAATTTTAATAACCTACCAATG
* *
1339 AAAA-TTTGATAACCTCCCAATG
1 AAAATTTTAATAACCTACCAATG
1361 AAA
1 AAA
1364 TGTTGGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (23 bp):
AAAATTTTAATAACCTACCAATG
Found at i:1496 original size:44 final size:45
Alignment explanation
Indices: 1425--1569 Score: 128
Period size: 41 Copynumber: 3.4 Consensus size: 45
1415 GTAATCACAT
1425 TATGAAATTTTGAT-AACCATACCATAAAATTGTGAT-ACCT-CA
1 TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
* * *
1467 CTATGAAATTTTTATAAACC-TTCCTATAAAATTTTGATAACCTCCA
1 -TATGAAATTTTGATAAACCATACC-ATAAAATTGTGATAACCTCCA
* * * * *
1513 TTTGAAATTTTGAT-AACC-T--CATGAAATTTTGAAAACCACC-
1 TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
1553 TCATGAAATTTTGATAA
1 T-ATGAAATTTTGATAA
1570 CATCCCTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
40 1 0.01
41 29 0.33
42 2 0.02
43 16 0.18
44 21 0.24
45 16 0.18
46 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (45 bp):
TATGAAATTTTGATAAACCATACCATAAAATTGTGATAACCTCCA
Found at i:1508 original size:22 final size:21
Alignment explanation
Indices: 1429--1787 Score: 167
Period size: 22 Copynumber: 16.6 Consensus size: 21
1419 TCACATTATG
1429 AAATTTTGATAACCATACC-ATA
1 AAATTTTGATAACC-T-CCTATA
* *
1451 AAATTGTGAT-ACCTCACTATG
1 AAATTTTGATAACCTC-CTATA
*
1472 AAATTTTTATAAACCTTCCTATA
1 AAATTTTGAT-AACC-TCCTATA
* *
1495 AAATTTTGATAACCTCCATTTG
1 AAATTTTGATAACCTCC-TATA
*
1517 AAATTTTGATAACCT-C-ATG
1 AAATTTTGATAACCTCCTATA
* * *
1536 AAATTTTGAAAACCACCTCATG
1 AAATTTTGATAACCTCCT-ATA
*
1558 AAATTTTGATAACATCCCTATA
1 AAATTTTGATAACCT-CCTATA
* * *
1580 AATTTTTTATAACCT-C-AAA
1 AAATTTTGATAACCTCCTATA
* **
1599 AAATTTTGTTAACCTCCTACG
1 AAATTTTGATAACCTCCTATA
*** *
1620 AAATTTTGATAAGAACACTATT
1 AAATTTTGATAACCTC-CTATA
* * *
1642 AAATTTTGATAACCCCCAATG
1 AAATTTTGATAACCTCCTATA
** *
1663 AAATTTTGATAATTAATTACACCAT-
1 AAATTTTGAT-A--ACCT-C-CTATA
* *
1688 AAATTTACGATAACTTACCTATA
1 AAATTT-TGATAACCT-CCTATA
* *
1711 AAATTTTGTTAATCTCCCTATA
1 AAATTTTGATAACCT-CCTATA
* * * *
1733 AAATTTTGAGAACCACAATATC
1 AAATTTTGATAACCTC-CTATA
* *
1755 AAATTTTGTTAATCTCGCTAT-
1 AAATTTTGATAACCTC-CTATA
1776 AAATTTTGATAA
1 AAATTTTGATAA
1788 ACTCATCATG
Statistics
Matches: 256, Mismatches: 60, Indels: 43
0.71 0.17 0.12
Matches are distributed among these distances:
19 30 0.12
20 5 0.02
21 55 0.21
22 119 0.46
23 30 0.12
24 3 0.01
25 8 0.03
26 6 0.02
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATA
Found at i:1592 original size:63 final size:62
Alignment explanation
Indices: 1425--1671 Score: 214
Period size: 63 Copynumber: 3.9 Consensus size: 62
1415 GTAATCACAT
* * *
1425 TATGAAATTTTGATAACCATACC-ATAAAATTGTGAT-ACCTCACTATGAAATTTTTATAAACCT
1 TATGAAATTTTGATAA-CATCCCTAT-AAATTTTGATAACCTCA--ATGAAATTTTGA-AAACC-
1488 TCC
60 TCC
* * * * *
1491 TATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTC-ATGAAATTTTGAAAACCACC
1 TATGAAATTTTGATAACATCCCTAT-AAATTTTGATAACCTCAATGAAATTTTGAAAACCTCC
* * **
1553 TCATGAAATTTTGATAACATCCCTATAAATTTTTTATAACCTCAA-AAAATTTTGTTAACCTCC
1 T-ATGAAATTTTGATAACATCCCTATAAA-TTTTGATAACCTCAATGAAATTTTGAAAACCTCC
* * * * *
1616 TACGAAATTTTGATAAGAACACTATTAAATTTTGATAACCCCCAATGAAATTTTGA
1 TATGAAATTTTGATAACATCCCTA-TAAATTTTGATAA-CCTCAATGAAATTTTGA
1672 TAATTAATTA
Statistics
Matches: 147, Mismatches: 26, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
62 33 0.22
63 61 0.41
64 20 0.14
65 3 0.02
66 25 0.17
67 5 0.03
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (62 bp):
TATGAAATTTTGATAACATCCCTATAAATTTTGATAACCTCAATGAAATTTTGAAAACCTCC
Found at i:2004 original size:21 final size:22
Alignment explanation
Indices: 1920--1997 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
1910 TTACCTACCC
* *
1920 ATGAAATTTTGTTAAC--CTCT
1 ATGAAATTTTGATAACAACACT
* * **
1940 ATGAAATTGTGATTATTACACT
1 ATGAAATTTTGATAACAACACT
*
1962 ATGAAATTTTGGTAACAACACT
1 ATGAAATTTTGATAACAACACT
1984 -TGAAATTTTGATAA
1 ATGAAATTTTGATAA
1998 GCTCACTCTA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 12 0.27
21 13 0.29
22 20 0.44
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (22 bp):
ATGAAATTTTGATAACAACACT
Found at i:2051 original size:22 final size:21
Alignment explanation
Indices: 2013--2387 Score: 149
Period size: 22 Copynumber: 17.0 Consensus size: 21
2003 CTCTATCTCA
* *
2013 CTATGTAATTTCT-ATAAGCAC
1 CTATGAAATTT-TGATAACCAC
**
2034 ACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAA-CCAC
* *
2057 CTATGAAATTTTAATAACCTC
1 CTATGAAATTTTGATAACCAC
*
2078 CATAT-AAGATTTCGATAATCGC-C
1 C-TATGAA-ATTTTGATAA-C-CAC
*
2101 CTATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAACCA-C
* *
2123 GTATGAAATTTT-AGTAACCTCC
1 CTATGAAATTTTGA-TAACC-AC
* * *
2145 CTGTGAAATTTTGACAACCTTC
1 CTATGAAATTTTGATAACC-AC
* * *
2167 CCATG-AATTTCGATAACCTC
1 CTATGAAATTTTGATAACCAC
*
2187 CTTATGAAATTTTGATAACCTC
1 C-TATGAAATTTTGATAACCAC
*
2209 TATATGAAATTTTGATAA-CATC
1 -CTATGAAATTTTGATAACCA-C
* *
2231 CTTATGAAATTTTATTTTAATAACCTC
1 C-TATG-AA----ATTTTGATAACCAC
2258 CTTATGAAATTTTGATAA-CATC
1 C-TATGAAATTTTGATAACCA-C
* * *
2280 CCATGGAATTTTGATAACTAC
1 CTATGAAATTTTGATAACCAC
* * * * *
2301 ACTATAAAATTTTAACATGCTAC
1 -CTATGAAATTTTGATA-ACCAC
*
2324 CTATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACCAC
*
2345 ACTAT-AAGA-TTTGAGAACCAC
1 -CTATGAA-ATTTTGATAACCAC
*
2366 ACTATAAAATTTT-AGTAACCAC
1 -CTATGAAATTTTGA-TAACCAC
2388 ACAATAATCC
Statistics
Matches: 273, Mismatches: 48, Indels: 64
0.71 0.12 0.17
Matches are distributed among these distances:
20 4 0.01
21 62 0.23
22 174 0.64
23 13 0.05
24 1 0.00
26 2 0.01
27 16 0.06
28 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCAC
Found at i:2235 original size:44 final size:43
Alignment explanation
Indices: 2036--2297 Score: 185
Period size: 44 Copynumber: 5.9 Consensus size: 43
2026 ATAAGCACAC
* * *
2036 TATGAAATTTTGATAATCTTCCTATGAAATTTTAATAACCTCCA
1 TATGAAATTTTGATAA-CATCCTATGAAATTTTGATAACCTCTA
* ** **
2080 TAT-AAGATTTCGATAATCGCCCTATGAAATTTTGATAACC-AGA
1 TATGAA-ATTTTGATAA-CATCCTATGAAATTTTGATAACCTCTA
* * * *
2123 GTATGAAATTTT-AGTAACCTCCCTGTGAAATTTTGACAACCT-TCC
1 -TATGAAATTTTGA-TAACAT-CCTATGAAATTTTGATAACCTCT-A
* * *
2168 CATG-AATTTCGATAACCTCCTTATGAAATTTTGATAACCTCTA
1 TATGAAATTTTGATAACATCC-TATGAAATTTTGATAACCTCTA
*
2211 TATGAAATTTTGATAACATCCTTATGAAATTTTATTTTAATAACCTCCT-
1 TATGAAATTTTGATAACATCC-TATG-AA----ATTTTGATAACCT-CTA
* *
2260 TATGAAATTTTGATAACATCCCATGGAATTTTGATAAC
1 TATGAAATTTTGATAACATCCTATGAAATTTTGATAAC
2298 TACACTATAA
Statistics
Matches: 176, Mismatches: 25, Indels: 35
0.75 0.11 0.15
Matches are distributed among these distances:
42 2 0.01
43 46 0.26
44 85 0.48
45 4 0.02
47 1 0.01
48 3 0.02
49 33 0.19
50 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACATCCTATGAAATTTTGATAACCTCTA
Found at i:2259 original size:27 final size:27
Alignment explanation
Indices: 2217--2270 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2207 TCTATATGAA
*
2217 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
*
2244 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
2271 GATAACATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTTTAATAACATCCTTATGAAATTTT
Found at i:2363 original size:21 final size:22
Alignment explanation
Indices: 2324--2394 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 22
2314 AACATGCTAC
*
2324 CTATGAAATTTTG-GTAACCACA
1 CTAT-AAAATTTGAGTAACCACA
*
2346 CTATAAGATTTGAG-AACCACA
1 CTATAAAATTTGAGTAACCACA
*
2367 CTATAAAATTTTAGTAACCACA
1 CTATAAAATTTGAGTAACCACA
*
2389 CAATAA
1 CTATAA
2395 TCCTTTTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 25 0.60
22 17 0.40
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (22 bp):
CTATAAAATTTGAGTAACCACA
Found at i:3439 original size:2 final size:2
Alignment explanation
Indices: 3432--3468 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3422 TATTCGTACT
3432 TA TA TA TA TA TA TA TA TA TA -A TA -A TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3469 GTGCGTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5294 original size:25 final size:26
Alignment explanation
Indices: 5259--5309 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5249 TAATAAATTA
*
5259 ATAATGGCAATTT-AAATATATTTTG
1 ATAATGACAATTTAAAATATATTTTG
5284 ATAATGACAATTTAGAAATATATTTT
1 ATAATGACAATTTA-AAATATATTTT
5310 TAGAAGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (26 bp):
ATAATGACAATTTAAAATATATTTTG
Found at i:6147 original size:21 final size:21
Alignment explanation
Indices: 6122--6179 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
6112 GCTGCTCTAA
6122 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* * **
6143 TAATCTAATCTATACA--ATG
1 TAATCTCATCTGTACAGTACC
6162 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
6180 TGCTAAACAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Done.