Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012326.1 Corchorus olitorius cultivar O-4 contig12359, 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: 36889
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:874 original size:20 final size:18
Alignment explanation
Indices: 841--877 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
831 TTGAAATAAT
841 TCTTCAATAGTCTTCAAG
1 TCTTCAATAGTCTTCAAG
859 TCTTCAAATAAGTCTTCAA
1 TCTTC-AAT-AGTCTTCAA
878 ATGGTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAG
Found at i:875 original size:30 final size:31
Alignment explanation
Indices: 829--888 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
819 CAATTATTCC
* *
829 TCTTGAAATAATTCTTC-AATAGTCTTCAAG
1 TCTTCAAATAAGTCTTCAAATAGTCTTCAAG
*
859 TCTTCAAATAAGTCTTCAAATGGTCTTCAA
1 TCTTCAAATAAGTCTTCAAATAGTCTTCAA
889 ACACGAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (31 bp):
TCTTCAAATAAGTCTTCAAATAGTCTTCAAG
Found at i:886 original size:11 final size:12
Alignment explanation
Indices: 856--889 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
846 AATAGTCTTC
856 AAGTCTTCAAAT
1 AAGTCTTCAAAT
868 AAGTCTTCAAAT
1 AAGTCTTCAAAT
*
880 -GGTCTTCAAA
1 AAGTCTTCAAA
890 CACGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (12 bp):
AAGTCTTCAAAT
Found at i:6596 original size:11 final size:10
Alignment explanation
Indices: 6580--6626 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
6570 AAACTCGTGT
6580 TTGAAGACTCA
1 TTGAAGA-TCA
*
6591 TTGAAGATAA
1 TTGAAGATCA
6601 TTTGAAGAT--
1 -TTGAAGATCA
6610 TTGAAGATCA
1 TTGAAGATCA
6620 TTGAAGA
1 TTGAAGA
6627 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:6615 original size:19 final size:18
Alignment explanation
Indices: 6591--6626 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6581 TGAAGACTCA
6591 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
6610 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
6627 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:14304 original size:14 final size:14
Alignment explanation
Indices: 14287--14314 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14277 CATGCAAAGG
14287 TTAGAGCTCAAATT
1 TTAGAGCTCAAATT
14301 TTAGAGCTCAAATT
1 TTAGAGCTCAAATT
14315 GAGAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TTAGAGCTCAAATT
Found at i:20125 original size:578 final size:577
Alignment explanation
Indices: 19005--20132 Score: 1837
Period size: 578 Copynumber: 2.0 Consensus size: 577
18995 GAGTAAGCTT
19005 CTCCAAGGTAGTATCCTCACTTGAATCCTAGAGAAACTTGTGAAGTCAGGTACCTTGTATCCTAT
1 CTCCAAGGTAGTATCCTCACTTGAATCCTAGAGAAACTTGTGAAGTCAGGTACCTTGTATCCTAT
* ** * *
19070 TCGAAGGGGATGAACTTGGTCATATTCTTCAGGGTAAGGTTTGTGAAAGGATGGTCGGCCAACTC
66 TCGAAGAGGATGAACTCAGTCATATTATTCAGGGTAAGGTTTGTGAAAGGATGGTCGACCAACTC
* *
19135 TTCTAAAAGCAGGACCGATCATGTCTTTAATTATCTCCCTGATGTGATTTTGGTTGACCTGACCA
131 TTCTAAAAGCAGGACCGATCATGTCTTCAATTATCTCCCTGATGTGATTTTGGTTCACCTGACCA
* *
19200 AGTACCTCAGCAACACAGGTAGGTTTATAGCATTTGGGAGAGGTGCAACGACTTGAGGTGGAGGT
196 AGTACCTCAGCAACACAGCTAGGTTCATAGCATTTGGGAGAGGTGCAACGACTTGAGGTGGAGGT
* * * * ** * *
19265 CGTGGCATAGGATGGCGTGGATTGCCATACCTAGCGCCATAACCATTCGCATTGTTGCCATTTCG
261 CGTGGAATAGGATGACATGGATTGCCATACCTAGCGCCATAACCATTCGCATCGTTAACAGTTCC
* *
19330 ATTTCCGTTTCCATTCCCATTATTGTTTCTGACATGAGGTGGAACATAAGCCACAGCTCGAGGTT
326 ATTTCCGTTTCCATTCCCATTACTGTTTCGGACATGAGGTGGAACATAAGCCACAGCTCGAGGTT
* * *
19395 CAACATAATTGACTTCCTCTTCAATGTTGTCGGCAACATTTTCCACAGCATCTTGGTGTGCAAGT
391 CAACATAATTGACCTCCTCTTCAACGTTGCCGGCAACATTTTCCACAGCATCTTGGTGTGCAAGT
19460 ATGAGCTCGACCCCATTCTCTTCCCTTGCTACTCCGTTTCTAGGAGGTGGTACATTATTGTTACC
456 ATGAGCTCGACCCCATTCTCTTCCCTTGCTACTCCGTTTCTAGGAGGTGGTACATTATTGTTACC
19525 AACAACATCGACTTGAGGCTGACCTCGTCCACACTGTACTGTGAAACGCGCAATGTG
521 AACAACATCGACTTGAGGCTGACCTCGTCCACACTGTACTGTGAAACGCGCAATGTG
* * *
19582 CTCCAAGGTAGTCTGCTCACTTGAAGTCCTAGAGAAACTTGTGAAGTCAGGTACCTTGTATCCTC
1 CTCCAAGGTAGTATCCTCACTTGAA-TCCTAGAGAAACTTGTGAAGTCAGGTACCTTGTATCCTA
19647 TTCGAAGAGGATGAACTCAGTCATATTATTCAGGGTAAGGTTTGTGAAAGGATGGAT-GACCAAC
65 TTCGAAGAGGATGAACTCAGTCATATTATTCAGGGTAAGGTTTGTGAAAGGATGG-TCGACCAAC
* * *
19711 TCTTCTAAAAGCAGGACCGATCATGTCTTCAATTTTCTCCCTGGTGTGATTTTGGTTCAGCTGAC
129 TCTTCTAAAAGCAGGACCGATCATGTCTTCAATTATCTCCCTGATGTGATTTTGGTTCACCTGAC
** * * *
19776 CTTGTGCCTCAGCAGGCGCAGCTAGGTTCATAGCATTTGGGAGAGGTGCAACGACTTGAGGTGGA
194 CAAGTACCTCAGCA-ACACAGCTAGGTTCATAGCATTTGGGAGAGGTGCAACGACTTGAGGTGGA
* *
19841 GGTCGTGGAATAGGATGACATGGA-TGCCATTCCTAGCGCCATAACCATTTGCATCGTTAACAGT
258 GGTCGTGGAATAGGATGACATGGATTGCCATACCTAGCGCCATAACCATTCGCATCGTTAACAGT
* * *
19905 TCCATTTCTGTTTCCATTCCCATTGCTGTTTCGGACATGAGTTGGAACATAAGCCACAGCTCGAG
323 TCCATTTCCGTTTCCATTCCCATTACTGTTTCGGACATGAGGTGGAACATAAGCCACAGCTCGAG
*
19970 GTTCAACATAGTTGACCTCCTCTTCAACGTTGCCGGCAACATTTTCCACAGCATCTTGGTGTGCA
388 GTTCAACATAATTGACCTCCTCTTCAACGTTGCCGGCAACATTTTCCACAGCATCTTGGTGTGCA
* * *
20035 AGTATGAGCTCGACGCCATTCTCTTCCCTTGCTGCTCCGTTTCTAGGAGGTGGTATATTATTGTT
453 AGTATGAGCTCGACCCCATTCTCTTCCCTTGCTACTCCGTTTCTAGGAGGTGGTACATTATTGTT
20100 ACCAACAACATCGACTTGAGGCTGACCTCGTCC
518 ACCAACAACATCGACTTGAGGCTGACCTCGTCC
20133 GTGATTGGCA
Statistics
Matches: 506, Mismatches: 42, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
577 23 0.05
578 415 0.82
579 68 0.13
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (577 bp):
CTCCAAGGTAGTATCCTCACTTGAATCCTAGAGAAACTTGTGAAGTCAGGTACCTTGTATCCTAT
TCGAAGAGGATGAACTCAGTCATATTATTCAGGGTAAGGTTTGTGAAAGGATGGTCGACCAACTC
TTCTAAAAGCAGGACCGATCATGTCTTCAATTATCTCCCTGATGTGATTTTGGTTCACCTGACCA
AGTACCTCAGCAACACAGCTAGGTTCATAGCATTTGGGAGAGGTGCAACGACTTGAGGTGGAGGT
CGTGGAATAGGATGACATGGATTGCCATACCTAGCGCCATAACCATTCGCATCGTTAACAGTTCC
ATTTCCGTTTCCATTCCCATTACTGTTTCGGACATGAGGTGGAACATAAGCCACAGCTCGAGGTT
CAACATAATTGACCTCCTCTTCAACGTTGCCGGCAACATTTTCCACAGCATCTTGGTGTGCAAGT
ATGAGCTCGACCCCATTCTCTTCCCTTGCTACTCCGTTTCTAGGAGGTGGTACATTATTGTTACC
AACAACATCGACTTGAGGCTGACCTCGTCCACACTGTACTGTGAAACGCGCAATGTG
Found at i:31192 original size:31 final size:30
Alignment explanation
Indices: 31150--31222 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
31140 GCTTAAATAC
*
31150 CAAAT-AATCCCTTATCTTTTTATTTTGGGA
1 CAAATAAATCCCTGATCTTTTT-TTTTGGGA
*
31180 CAAATAAATCCCTGATCTTTTTTTTTGGGC
1 CAAATAAATCCCTGATCTTTTTTTTTGGGA
31210 CAAATAAATCCCT
1 CAAATAAATCCCT
31223 CAACTTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (30 bp):
CAAATAAATCCCTGATCTTTTTTTTTGGGA
Found at i:31314 original size:13 final size:13
Alignment explanation
Indices: 31298--31333 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
31288 ACTCATAATT
31298 TCATAATTTTAAC
1 TCATAATTTTAAC
31311 TCATAAATTTTAAC
1 TCAT-AATTTTAAC
*
31325 GCATAATTT
1 TCATAATTT
31334 CATATTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (13 bp):
TCATAATTTTAAC
Done.