Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017593.1 Corchorus olitorius cultivar O-4 contig17626, 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: 21914
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:156 original size:29 final size:28
Alignment explanation
Indices: 118--172 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
108 TTATTCCACA
*
118 TTCTTTAGCGTTCTTGAAGATTAGAAATG
1 TTCTTGAGCGTTCTTGAA-ATTAGAAATG
147 TTCTTGAGCGTTCTTGAAATTAGAAA
1 TTCTTGAGCGTTCTTGAAATTAGAAA
173 GTTTGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (28 bp):
TTCTTGAGCGTTCTTGAAATTAGAAATG
Found at i:1171 original size:21 final size:22
Alignment explanation
Indices: 1147--1187 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1137 ACTATTTTTG
1147 TAATTATG-ATTAAGTGTGTTT
1 TAATTATGTATTAAGTGTGTTT
*
1168 TAATTATGTATTAATTGTGT
1 TAATTATGTATTAAGTGTGT
1188 GTGGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (22 bp):
TAATTATGTATTAAGTGTGTTT
Found at i:1520 original size:292 final size:290
Alignment explanation
Indices: 991--1574 Score: 877
Period size: 292 Copynumber: 2.0 Consensus size: 290
981 ATTTTTAGTG
*
991 ACTAAGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGACTTTTTTTGG
1 ACTAAGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTGGACTTTTTTTGG
* *
1056 TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTTGATGAATTTTCTCCCTTACTTTTCCTATT
66 TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTATT
* * **
1121 GCCTTTTTTTTAATTTACTATTTTTGTAATTATGATTAAGTGTGTTTTAATTATGTATTAATTGT
131 GCCTTTTTTTTAATTTACTATTTTTATAATTATGATTAAGTGTGTTTTAAATACATATTAA-T-T
* * *
1186 GTGTGGATATTAGGATTTACTGGTTCAACTAATCTGCCGGAATTCCAAAGGATTGGTGTTATAAA
194 GTGTGGATATTAGGATTTACCGGTTCAACTAATCTGCCGGAATTCCAAAGGATTAGTGCTATAAA
1251 TGTATCTACCCGAGTTCATTAATTCAACAATT
259 TGTATCTACCCGAGTTCATTAATTCAACAATT
* *
1283 ACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTGGGCTTTTTTTTT
1 ACTAAGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTGGAC---TTTTTT
* * *
1348 TTGTCTTTTCTCACTTTTTGGGTGACT-AAAAGGACCCTCGATGAATTTCCTCCCTTACTTTTCT
63 TGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGG-CCCTCGATGAATTTCCTCCCTTACTTTTCC
* *
1412 TGTTGCCTTTTTTTATAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAAATACATATTA
127 TATTGCCTTTTTTT-TAATTTACTATTTTTATAATTATGATTAAGTGTGTTTTAAATACATATTA
** *
1477 A-T-TGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTGT
191 ATTGTGTGGATATTAGGATTTACCGGTTCAACTAATCTGCCGGAATTCCAAAGGATTAGTGCTAT
* * *
1540 AAATGTGTTTACCCGAGTTCATTAATTTAACAATT
256 AAATGTATCTACCCGAGTTCATTAATTCAACAATT
1575 GCAATCAAGA
Statistics
Matches: 264, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
292 140 0.53
293 1 0.00
294 6 0.02
295 71 0.27
296 46 0.17
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (290 bp):
ACTAAGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTGGACTTTTTTTGG
TCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTATT
GCCTTTTTTTTAATTTACTATTTTTATAATTATGATTAAGTGTGTTTTAAATACATATTAATTGT
GTGGATATTAGGATTTACCGGTTCAACTAATCTGCCGGAATTCCAAAGGATTAGTGCTATAAATG
TATCTACCCGAGTTCATTAATTCAACAATT
Found at i:1681 original size:27 final size:27
Alignment explanation
Indices: 1649--1700 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1639 AGCTACAATT
*
1649 AATATTAG-TTTTATTTTGATGAATTAA
1 AATATTAGCTTTT-TATTGATGAATTAA
1676 AATATTAGCTTTTTATTGATGAATT
1 AATATTAGCTTTTTATTGATGAATT
1701 GCCTAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (27 bp):
AATATTAGCTTTTTATTGATGAATTAA
Found at i:3274 original size:87 final size:90
Alignment explanation
Indices: 3117--3316 Score: 361
Period size: 88 Copynumber: 2.3 Consensus size: 90
3107 CCTGTTGGCT
*
3117 GTTTATGGCTATACCAACGCCCCCGCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGT
1 GTTTATGGCTATACCAACGCCACCGCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGT
3182 ATATCTCCAATCATA-CATTTTTTG
66 ATATCTCCAATCATACCATTTTTTG
*
3206 GTTTGTGGCTATACCAACGCCACC-CGCTGTTGGTATACA-TCTATAGCAACGTAAGCCGTAGGT
1 GTTTATGGCTATACCAACGCCACCGCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGT
3269 ATATCTCCAATCATACCATTTTTTG
66 ATATCTCCAATCATACCATTTTTTG
3294 GTTTATGGCTATACCAACGCCAC
1 GTTTATGGCTATACCAACGCCAC
3317 AAGCCGTTTG
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
87 39 0.36
88 46 0.43
89 22 0.21
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (90 bp):
GTTTATGGCTATACCAACGCCACCGCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGT
ATATCTCCAATCATACCATTTTTTG
Found at i:3503 original size:40 final size:40
Alignment explanation
Indices: 3459--3535 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
3449 GTCATTCACA
*
3459 TTAAAAAT-ATAATCCAAAACAATTTGTTCTAATCCACACG
1 TTAAAAATGA-AATCAAAAACAATTTGTTCTAATCCACACG
*
3499 TTAAAAATGAAATTAAAAACAATTTGTTCTAATCCAC
1 TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCAC
3536 TCATGTAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (40 bp):
TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCACACG
Found at i:3742 original size:17 final size:17
Alignment explanation
Indices: 3706--3743 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3696 AAAGCAGTGG
*
3706 GAATATTGAACTTAGGA
1 GAATATTGAACTTAGAA
3723 GAATATTGAA-TTATGAA
1 GAATATTGAACTTA-GAA
3740 GAAT
1 GAAT
3744 GTTTGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (17 bp):
GAATATTGAACTTAGAA
Found at i:6885 original size:18 final size:19
Alignment explanation
Indices: 6847--6886 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6837 TTGAAGATTT
*
6847 ATTGAAGACAATTTGAAGA
1 ATTGAAGACAATTTAAAGA
*
6866 ATTGAAGACCA-TTAAAGA
1 ATTGAAGACAATTTAAAGA
6884 ATT
1 ATT
6887 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (19 bp):
ATTGAAGACAATTTAAAGA
Found at i:9020 original size:13 final size:12
Alignment explanation
Indices: 9002--9051 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
8992 TAAAACTTGA
9002 AAAATAAAGACAT
1 AAAATAAAGA-AT
*
9015 AAAATAAAGGA-
1 AAAATAAAGAAT
9026 AAAATAAA-AAT
1 AAAATAAAGAAT
9037 AAAAATAAAGAAT
1 -AAAATAAAGAAT
9050 AA
1 AA
9052 GCTAAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.03
11 8 0.25
12 11 0.34
13 12 0.38
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (12 bp):
AAAATAAAGAAT
Found at i:9029 original size:24 final size:23
Alignment explanation
Indices: 9000--9046 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
8990 AATAAAACTT
9000 GAAAAATAAAGACAT-AAAATAAAG
1 GAAAAATAAA-A-ATAAAAATAAAG
9024 GAAAAATAAAAATAAAAATAAAG
1 GAAAAATAAAAATAAAAATAAAG
9047 AATAAGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 10 0.45
24 10 0.45
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (23 bp):
GAAAAATAAAAATAAAAATAAAG
Found at i:14617 original size:48 final size:48
Alignment explanation
Indices: 14546--14643 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
14536 AATTGTTAAC
*
14546 TTAAGATCACAAGATCCAGAAACAATCAAGAATTCACAACTTAATTGT
1 TTAAGATCACAAGATCCACAAACAATCAAGAATTCACAACTTAATTGT
* *
14594 TTAAGATCACAAGATTCACAAACAATCAAGAATTCGCAACTTAATTGT
1 TTAAGATCACAAGATCCACAAACAATCAAGAATTCACAACTTAATTGT
14642 TT
1 TT
14644 GCTAAAACTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (48 bp):
TTAAGATCACAAGATCCACAAACAATCAAGAATTCACAACTTAATTGT
Found at i:15100 original size:21 final size:21
Alignment explanation
Indices: 15076--15117 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15066 TCCTTTGCAT
* *
15076 ATGATCTCTAATGCCCTTCAA
1 ATGAACTCCAATGCCCTTCAA
*
15097 ATGAACTCCAATGGCCTTCAA
1 ATGAACTCCAATGCCCTTCAA
15118 CTCTTCAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
ATGAACTCCAATGCCCTTCAA
Done.