Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020333.1 Corchorus olitorius cultivar O-4 contig20366, 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: 29801
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2166 original size:2 final size:2
Alignment explanation
Indices: 2159--2198 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2149 GAATTAAGGG
2159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2199 CAAGTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22161 original size:68 final size:67
Alignment explanation
Indices: 21867--22373 Score: 559
Period size: 67 Copynumber: 7.6 Consensus size: 67
21857 AAAGCTCTAC
* * *
21867 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTCTCGTCTTTTGCATTTAAGTATAGT
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGT
*
21932 AC
66 AT
* *
21934 TTTCTATTTCCAAAAATACCCTTTCCGTCGAAGGATCATTTTCGTCTTTTGCATTTAAGTTTAGT
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGT
21999 AT
66 AT
*
22001 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTGGT
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGT
22066 AT
66 AT
* * * *
22068 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGATCGTTTTTGTCTTCTTGCATTTAATTTTAG
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTT-TTGCATTTAAGTTTAG
22133 TAT
65 TAT
* * * *
22136 TTTCTATTTTCAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAG
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAG
22201 ---
65 TAT
* ** * * * **
22201 ----TGTTTCCAAAAATGTCTTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTTTAG
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAG
*
22262 TAC
65 TAT
* * * * ** * *
22265 TTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCATATCCAAG-TTA
1 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCAT-T-TAAGTTTA
22329 --AT
64 GTAT
* * *
22331 TTACT-TTTCCCAAAATACCCTTTCGGTCAAAAGGGTCAATTTT
1 TTTCTATTTCCAAAAATACCCTTTCGGTC-GAAGGGTC-ATTTT
22374 GTGATTCTTG
Statistics
Matches: 375, Mismatches: 52, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
61 51 0.14
65 21 0.06
66 11 0.03
67 179 0.48
68 108 0.29
69 5 0.01
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.43
Consensus pattern (67 bp):
TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGT
AT
Found at i:22259 original size:61 final size:61
Alignment explanation
Indices: 22146--22262 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
22136 TTTCTATTTT
*** *
22146 CAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAGTGTTTC
1 CAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAGTGTTTC
** * *
22207 CAAAAATGTCTTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTTTAGT
1 CAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAGT
22263 ACTTTCTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (61 bp):
CAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAGTGTTTC
Found at i:22488 original size:264 final size:262
Alignment explanation
Indices: 21867--22488 Score: 584
Period size: 264 Copynumber: 2.3 Consensus size: 262
21857 AAAGCTCTAC
* * * *
21867 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-GTTCTCGTCTTT-TGCATTTAAGTATA
1 TTTCGATTTACAAAAATACCCTTTCGGTCGAAAGGTCAGTT-TCATCTTTCTGCA-TT---T-TA
* * **
21930 GTACTTTCTA-TTTCCAAAAATACCCTTTCCGTCGAAGGATCATTTTCGTCTTTTGCATTTAAGT
60 GT--TTTCTAGTTTCCAAAAATGCCCTTTCGGTCGAAGGATCATTTTCGTCTTTTGCACCTAAGT
* * * ** * *
21994 TTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAA
123 TTAGTACTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCATTCAA
* * * ** *
22059 GTTTGGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGATCGTTTTTGTCTTCTTGCATT
188 GTTT-GAATTTACTATTTCCAAAAATACCCTTTCGGTCAAAGGATCAATTTTGTATTCTTGCATT
*
22124 TAATTTTAGTAT
252 TAAGTTTAG-AT
* * * * * * * * **
22136 TTTCTATTTTCAAAAATACCTTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAG
1 TTTCGATTTACAAAAATACCCTTTCGGTCGAAAGGTCAGTTTCATCTTTCTGCATTTTAGTTTTC
* * * * *
22201 T-GTTTCCAAAAATGTCTTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTTTAGTAC
66 TAGTTTCCAAAAATGCCCTTTCGGTCGAAGGATCATTTTCGTC-TTTTGCACCTAAGTTTAGTAC
* *
22265 TTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCATATCCAAG-TT-
130 TTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCAT-T-CAAGTTTG
* *
22328 AATTTACT-TTTCCCAAAATACCCTTTCGGTCAAAAGGGTCAATTTTGTGATTCTTGCA-TTAGA
193 AATTTACTATTTCCAAAAATACCCTTTCGGTC-AAAGGATCAATTTTGT-ATTCTTGCATTTA-A
*
22391 GTTTA-CT
255 GTTTAGAT
*
22398 TTT-GA-TTACCAAAATACCCTTTCGGT-GAAAAGGTCAGTTTCATCATTTCTGCATTTTAGGTT
1 TTTCGATTTACAAAAATACCCTTTCGGTCG-AAAGGTCAGTTTCATC-TTTCTGCATTTTA-GTT
*
22460 ATTCTAGTTTCCAAAAACGCCCTTTCGGT
63 -TTCTAGTTTCCAAAAATGCCCTTTCGGT
22489 GAAAGGGAAA
Statistics
Matches: 291, Mismatches: 48, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
259 1 0.00
260 31 0.11
261 12 0.04
262 29 0.10
263 60 0.21
264 97 0.33
265 7 0.02
266 4 0.01
269 45 0.15
270 5 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (262 bp):
TTTCGATTTACAAAAATACCCTTTCGGTCGAAAGGTCAGTTTCATCTTTCTGCATTTTAGTTTTC
TAGTTTCCAAAAATGCCCTTTCGGTCGAAGGATCATTTTCGTCTTTTGCACCTAAGTTTAGTACT
TTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCATTCAAGTTTGAAT
TTACTATTTCCAAAAATACCCTTTCGGTCAAAGGATCAATTTTGTATTCTTGCATTTAAGTTTAG
AT
Found at i:23581 original size:44 final size:45
Alignment explanation
Indices: 23507--23598 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 45
23497 ATTTTTCAAA
23507 GGAGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACC
1 GGAGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACC
* *
23552 GGAGTTGAATTTTT-AACGTATAATCATACTATAAGAGCTAAATC
1 GGAGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACC
23596 GGA
1 GGA
23599 TTAGATTGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 31 0.69
45 14 0.31
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (45 bp):
GGAGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACC
Found at i:23868 original size:22 final size:22
Alignment explanation
Indices: 23842--23898 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
23832 TACTATAGTT
*
23842 ACAAAAAATTATAGAGAGATTA
1 ACAAAAAATCATAGAGAGATTA
** *
23864 ACAAAATCTCATAGAGAGGTTA
1 ACAAAAAATCATAGAGAGATTA
*
23886 TC-AAAAATCATAG
1 ACAAAAAATCATAG
23899 GAAGGTTACA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (22 bp):
ACAAAAAATCATAGAGAGATTA
Found at i:23898 original size:21 final size:20
Alignment explanation
Indices: 23839--23911 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
23829 TCATACTATA
*
23839 GTTACAAAAAATTATAGAGAG
1 GTTAC-AAAAATCATAGAGAG
* *
23860 ATTAACAAAATCTCATAGAGAG
1 GTT-ACAAAA-ATCATAGAGAG
23882 GTTATCAAAAATCATAG-GAAG
1 GTTA-CAAAAATCATAGAG-AG
23903 GTTACAAAA
1 GTTACAAAA
23912 TTTTGTAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 6 0.14
21 19 0.44
22 18 0.42
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (20 bp):
GTTACAAAAATCATAGAGAG
Found at i:24021 original size:22 final size:21
Alignment explanation
Indices: 23926--24050 Score: 83
Period size: 22 Copynumber: 5.8 Consensus size: 21
23916 GTAGGAAGGT
*
23926 TTATTAAAATTTCATA-GTTA
1 TTATCAAAATTTCATAGGTTA
* * *
23946 GGTAATCATAATTTCATATGGAGT-
1 --TTATCAAAATTTCATA-GG-TTA
* *
23970 TTATCACAATTTCATAGGTAA
1 TTATCAAAATTTCATAGGTTA
**
23991 CAATCAAAATTTCATAGCGTTA
1 TTATCAAAATTTCATAG-GTTA
* * *
24013 TTATCAAAATTTAATGGGGTA
1 TTATCAAAATTTCATAGGTTA
24034 GTTATCAAAATTTCATA
1 -TTATCAAAATTTCATA
24051 AAATTATTCA
Statistics
Matches: 78, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 19 0.24
22 57 0.73
24 1 0.01
25 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTTA
Done.