Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011836.1 Corchorus olitorius cultivar O-4 contig11869, 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: 22810
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:698 original size:50 final size:51
Alignment explanation
Indices: 617--765 Score: 187
Period size: 50 Copynumber: 2.9 Consensus size: 51
607 GAAGTTTTAT
*
617 AATAAGATTGCATTTCATTTGTGAGGT-CAAGATCAAAATTCGCTTTTC-AA
1 AATAAGATTGCATTCCATTTGTGA-GTCCAAGATCAAAATTCGCTTTTCAAA
* *
667 AATGAA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTGTCAAA
1 AAT-AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
* * * *
718 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCTCGCTTTT
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAA-TTCGCTTTT
766 TCGAAAGGCA
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
49 2 0.02
50 41 0.48
51 36 0.42
52 6 0.07
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (51 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
Found at i:1360 original size:91 final size:91
Alignment explanation
Indices: 1190--1368 Score: 288
Period size: 92 Copynumber: 2.0 Consensus size: 91
1180 ACCAGAGTTA
***
1190 TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACAT
1 TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACAT
*
1255 CAGACTCAGAGTTATTTTTCAAATTG
66 CAGACTCAGAGTTATTTTCCAAATTG
*
1281 TTTTTCAAAGTTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAG-TTTCAACCACAACA
1 TTTTTC-AAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACA
*
1345 TCAGATTCAGAGTTATTTTCCAAA
65 TCAGACTCAGAGTTATTTTCCAAA
1369 GGTATTTTCT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 39 0.48
92 42 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (91 bp):
TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACAT
CAGACTCAGAGTTATTTTCCAAATTG
Found at i:1377 original size:91 final size:91
Alignment explanation
Indices: 1190--1377 Score: 281
Period size: 91 Copynumber: 2.1 Consensus size: 91
1180 ACCAGAGTTA
***
1190 TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACAT
1 TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACAT
* *
1255 CAGACTCAGAGTTATTTTTCAAATTG
66 CAGACTCAGAGTTATTTTCCAAATGG
*
1281 TTTTTCAAAGTTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAG-TTTCAACCACAACA
1 TTTTTC-AAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACA
*
1345 TCAGATTCAGAGTTATTTTCCAAA-GG
65 TCAGACTCAGAGTTATTTTCCAAATGG
1371 TATTTTC
1 T-TTTTC
1378 TTCCAAAATC
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
90 2 0.02
91 44 0.50
92 42 0.48
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (91 bp):
TTTTTCAAGTTGACCACACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAACCACAACAT
CAGACTCAGAGTTATTTTCCAAATGG
Found at i:1577 original size:51 final size:50
Alignment explanation
Indices: 1450--1586 Score: 247
Period size: 50 Copynumber: 2.7 Consensus size: 50
1440 AATGCTTTGA
1450 CTTTTTCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAACATAGG
1 CTTTTTCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAACATAGG
* *
1500 CTTTTCCATAGGTCAAACTCGTTTCCATACGAGTCAATTAGCAACATAGG
1 CTTTTTCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAACATAGG
1550 CTTTTTCATCAAGTCAAACTCGTTTCCATACGAGTCA
1 CTTTTTCAT-AAGTCAAACTCGTTTCCATACGAGTCA
1587 GTTTAAGCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 56 0.68
51 26 0.32
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (50 bp):
CTTTTTCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAACATAGG
Found at i:1647 original size:69 final size:69
Alignment explanation
Indices: 1543--1980 Score: 655
Period size: 69 Copynumber: 6.3 Consensus size: 69
1533 TCAATTAGCA
* *
1543 ACATAGGCTTTTTCATCAAGTCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCC
1 ACATAGGCTTTTCCA-CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCC
*
1608 AAGTC
65 AAGCC
*
1613 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTTAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1678 AGCC
66 AGCC
1682 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1747 AGCC
66 AGCC
* * *
1751 ATATAGGCTTTTCCATAAGCCAAATTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1816 AGCC
66 AGCC
* * *
1820 ACATAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGATTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1885 AGCC
66 AGCC
* * * * * * * *
1889 ATATAGACTTTTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTTTAAACATTGGGTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1954 TA--C
66 -AGCC
* *
1957 AGCAGAGGCTTTTCCATAAGCCAA
1 A-CATAGGCTTTTCCACAAGCCAA
1981 GTTTATGAGG
Statistics
Matches: 337, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
68 2 0.01
69 320 0.95
70 15 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (69 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
AGCC
Found at i:2211 original size:103 final size:102
Alignment explanation
Indices: 2071--2316 Score: 384
Period size: 103 Copynumber: 2.4 Consensus size: 102
2061 TCCATGTAAG
* *
2071 TTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGTTAAAACCTCCAGGTACCATCTCC
1 TTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGTTAAAACCTCCAGGTACCATCTCA
*
2136 TTCCATTAAGTTTTTCATCAAAGATTCATGTTTAAGAT
66 TTCCATTAAGTTTTTCATCAAAGACTCATGTTTAA-AT
* *
2174 TTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGTTAAAACCTCCGGGTACCATTTCA
1 TTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGTTAAAACCTCCAGGTACCATCTCA
*
2239 TTTCATTAAGTTTTTCATCAAAGACTCATGTTTAAAT
66 TTCCATTAAGTTTTTCATCAAAGACTCATGTTTAAAT
* * * *
2276 TTAATATCCTTGGTCAAGGCCTCTATTTTAAAGTTTGCATT
1 TTAAAATCCTTGGTCAAGGTCTCTA-TTCAGAGTTTGCATT
2317 TGTAAGTCCT
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
102 25 0.19
103 107 0.81
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (102 bp):
TTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGTTAAAACCTCCAGGTACCATCTCA
TTCCATTAAGTTTTTCATCAAAGACTCATGTTTAAAT
Found at i:10225 original size:33 final size:33
Alignment explanation
Indices: 10174--10295 Score: 118
Period size: 33 Copynumber: 3.7 Consensus size: 33
10164 TCCTCTACAC
* * *
10174 ATCCGTCACCCACTATCACACCTCCATCCACAT
1 ATCCCTCACCAACCATCACACCTCCATCCACAT
* * **
10207 ATCCCTCATCAACCATCACACCTTCATCCAGTT
1 ATCCCTCACCAACCATCACACCTCCATCCACAT
* ** * * * *
10240 CTCATTCCCCCACTATCACACCTCCATCCACAC
1 ATCCCTCACCAACCATCACACCTCCATCCACAT
10273 ATCCCTCACCAACCATCACACCT
1 ATCCCTCACCAACCATCACACCT
10296 TCACCCACTC
Statistics
Matches: 65, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.27, C:0.49, G:0.02, T:0.22
Consensus pattern (33 bp):
ATCCCTCACCAACCATCACACCTCCATCCACAT
Found at i:10267 original size:66 final size:66
Alignment explanation
Indices: 10182--10318 Score: 220
Period size: 66 Copynumber: 2.1 Consensus size: 66
10172 ACATCCGTCA
* * * * *
10182 CCCACTATCACACCTCCATCCACATATCCCTCATCAACCATCACACCTTCATCCAGTTCTCATTC
1 CCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCACACCTTCACCCACTCCTCATTC
10247 C
66 C
*
10248 CCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCACACCTTCACCCACTCCTCCTTC
1 CCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCACACCTTCACCCACTCCTCATTC
10313 C
66 C
10314 CCCAC
1 CCCAC
10319 ACATCCTACC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.25, C:0.53, G:0.01, T:0.22
Consensus pattern (66 bp):
CCCACTATCACACCTCCATCCACACATCCCTCACCAACCATCACACCTTCACCCACTCCTCATTC
C
Found at i:12570 original size:2 final size:2
Alignment explanation
Indices: 12565--12617 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
12555 TCTCTCTCTC
* *
12565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12607 TA TC TA TA TA T
1 TA TA TA TA TA T
12618 GTCTTTTGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14400 original size:16 final size:16
Alignment explanation
Indices: 14379--14413 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
14369 ACAATTCAGA
14379 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
14395 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
14411 AAG
1 AAG
14414 TATTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:14566 original size:41 final size:41
Alignment explanation
Indices: 14509--14832 Score: 429
Period size: 41 Copynumber: 7.9 Consensus size: 41
14499 TTTTCGTTTG
*
14509 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
14550 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
14591 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
14632 TTCAAGAGTT-AGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGA-TTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
14673 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
14714 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
** * * * * *
14758 TTCAAGACCAAGTCGTCAAGACCTTTGAATTAGATTGTCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
14799 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATTAAGTCA-TCGAGACCCTTGAATTAAAT
14833 CAAATCAAAC
Statistics
Matches: 260, Mismatches: 17, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
40 15 0.06
41 204 0.78
42 6 0.02
43 1 0.00
44 34 0.13
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (41 bp):
TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
Done.