Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010045.1 Corchorus olitorius cultivar O-4 contig10077, 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: 10853
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1375 original size:16 final size:16
Alignment explanation
Indices: 1354--1385 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1344 AATATAATCC
1354 TGGGTCAGAATTTGCA
1 TGGGTCAGAATTTGCA
1370 TGGGTCAGAATTTGCA
1 TGGGTCAGAATTTGCA
1386 CCAATAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (16 bp):
TGGGTCAGAATTTGCA
Found at i:3035 original size:50 final size:50
Alignment explanation
Indices: 2975--3130 Score: 312
Period size: 50 Copynumber: 3.1 Consensus size: 50
2965 AGCCTAACAA
2975 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
1 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
3025 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
1 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
3075 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
1 ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
3125 ATTTAG
1 ATTTAG
3131 GCAAATCCAC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 106 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (50 bp):
ATTTAGTTTCATATTTGCTGCAACAATAGCCTGCATTGTTCCATATAGGC
Found at i:3354 original size:28 final size:28
Alignment explanation
Indices: 3314--3374 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
3304 TTAGTATTTA
*
3314 CATAATCTAACCCTGCCTAAACAGAGAG
1 CATAATCTAACCCTCCCTAAACAGAGAG
* *
3342 CATAATCTAACCCTCCCTACATAGAGAG
1 CATAATCTAACCCTCCCTAAACAGAGAG
3370 CATAA
1 CATAA
3375 AGCCCCTACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (28 bp):
CATAATCTAACCCTCCCTAAACAGAGAG
Found at i:6593 original size:33 final size:33
Alignment explanation
Indices: 6523--6593 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
6513 TCTCAGACGT
* * * *
6523 TTGGAATTGAGGCCTTGAAGCTGCTGATCGTGG
1 TTGGAACTGAGGCCGTGAAGCTGCTGATCGCGC
*
6556 TTGGAACTGTGGCCGTGAAGCTGCTGATAC-CGC
1 TTGGAACTGAGGCCGTGAAGCTGCTGAT-CGCGC
6589 TTGGA
1 TTGGA
6594 GCCGTAGTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (33 bp):
TTGGAACTGAGGCCGTGAAGCTGCTGATCGCGC
Found at i:8597 original size:129 final size:132
Alignment explanation
Indices: 8427--8752 Score: 392
Period size: 132 Copynumber: 2.5 Consensus size: 132
8417 AAGTACTTTT
* *
8427 GATGGTATTTAACACAACAACATTTTTAGTCGTTGTTAATGTTTATAATTTTCGTAACAACAAAA
1 GATGGTATTTTACACAAC-ACATTTTTAGTCGTTGTCAATGTTTATAATTTTCGTAACAACAAAA
* * *
8492 ATAAAAACGTTGC-AAATC-CATAATC-TATTCGTAACAACTTTAAAAAATTGTTGTCTAAGTGA
65 ACAAAAACGTTGCGAAATCGCATAA-CATATTCGTAACAACTTTAAAAAATCGTTGGCTAAGTGA
8554 TTTG
129 TTTG
* *
8558 GATGGTATTTTACA-AACACTTTTTTAGTCGTTGTCAATGTTT-TCAATTTTCATAACAACAAAA
1 GATGGTATTTTACACAACACATTTTTAGTCGTTGTCAATGTTTAT-AATTTTCGTAACAACAAAA
** * * * *
8621 ACAAAGTCGTTGCGAAATCGTGATAACATATTCGTAGCAATTTTATAAAATCGTTGGCTAAGTGA
65 ACAAAAACGTTGCGAAATCG-CATAACATATTCGTAACAACTTTAAAAAATCGTTGGCTAAGTGA
*
8686 TTTT
129 TTTG
* * * * * * *
8690 GATGATATTTTACATACCACATTTTTAGTCGTTGTCAATGGTTACAATATTCGTAATAACAAA
1 GATGGTATTTTACACAACACATTTTTAGTCGTTGTCAATGTTTATAATTTTCGTAACAACAAA
8753 TTTTTAAGTT
Statistics
Matches: 166, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
128 1 0.01
129 51 0.31
130 8 0.05
131 14 0.08
132 52 0.31
133 40 0.24
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (132 bp):
GATGGTATTTTACACAACACATTTTTAGTCGTTGTCAATGTTTATAATTTTCGTAACAACAAAAA
CAAAAACGTTGCGAAATCGCATAACATATTCGTAACAACTTTAAAAAATCGTTGGCTAAGTGATT
TG
Found at i:9060 original size:24 final size:24
Alignment explanation
Indices: 9032--9087 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
9022 TTGGTAAGAT
9032 TGGAGCCGACGTATAAGTTGGCCG
1 TGGAGCCGACGTATAAGTTGGCCG
9056 TGGAGCCGACGTATAAGTTGGCCG
1 TGGAGCCGACGTATAAGTTGGCCG
9080 TGGAGCCG
1 TGGAGCCG
9088 CTTATTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.20, C:0.21, G:0.39, T:0.20
Consensus pattern (24 bp):
TGGAGCCGACGTATAAGTTGGCCG
Found at i:9208 original size:87 final size:86
Alignment explanation
Indices: 9096--9515 Score: 477
Period size: 87 Copynumber: 5.0 Consensus size: 86
9086 CGCTTATTGT
* * * * * *
9096 GGTTGGGACTGTGGTAGGTAAGATTGGAGCCGATGTATAAGTTTAGTTTTAGAGATTTGGAATTG
1 GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACTG
* *
9161 TAGCCGTGAAGCTGCTAATGGA
66 TGGCCGTGAAGCTGCTGAT-GA
* * *
9183 GGTTGGGACTATGGTTGGTAAGATTGGAGCCGCCGTATAAGTTCAGTCTCAGAGATTTGGAACCG
1 GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACTG
* *
9248 TGGCGGTGAAGCTGCTGATCGT
66 TGGCCGTGAAGCTGCTGAT-GA
* * * * * *
9270 GGTTGGGACTGCGATAGGTAAGATTGAAGCCTACGTATAAGTTCAGTCTCAGAGGTTTGGAACTG
1 GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACTG
*
9335 TGGCCATGAAGCTGC---TGA
66 TGGCCGTGAAGCTGCTGATGA
*
9353 ---T----C-GTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGGTTTGGAACTG
1 GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACTG
* *
9410 TGGCCGTGAATCTGCTGATTGT
66 TGGCCGTGAAGCTGCTGA-TGA
* * *
9432 GGTCGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAATTTCAGTCTTAGAGGA-TTGGAACT
1 GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGA-GATTTGGAACT
*
9496 GTGGCCGTGAAGCTGTTGAT
65 GTGGCCGTGAAGCTGCTGAT
9516 TGTTGTGAAG
Statistics
Matches: 280, Mismatches: 40, Indels: 27
0.81 0.12 0.08
Matches are distributed among these distances:
75 63 0.22
76 1 0.00
79 2 0.01
80 1 0.00
83 1 0.00
84 1 0.00
86 2 0.01
87 208 0.74
88 1 0.00
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.30
Consensus pattern (86 bp):
GGTTGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACTG
TGGCCGTGAAGCTGCTGATGA
Found at i:9470 original size:162 final size:162
Alignment explanation
Indices: 9194--9515 Score: 491
Period size: 162 Copynumber: 2.0 Consensus size: 162
9184 GTTGGGACTA
* *
9194 TGGTTGGTAAGATTGGAGCCGCCGTATAAGTTCAGTCTCAGAGATTTGGAACCGTGGCGGTGAAG
1 TGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACCGTGGCCGTGAAG
* *
9259 CTGCTGATCGTGGTTGGGACTGCGATAGGTAAGATTGAAGCCTACGTATAAGTTCAGTCTCAGAG
66 CTGCTGATCGTGGTCGGGACTGCGATAGGTAAGATTGAAGCCGACGTATAAGTTCAGTCTCAGAG
*
9324 GTTTGGAACTGTGGCCATGAAGCTGCTGATCG
131 GATTGGAACTGTGGCCATGAAGCTGCTGATCG
* * *
9356 TGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGGTTTGGAACTGTGGCCGTGAAT
1 TGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACCGTGGCCGTGAAG
* * * * * * *
9421 CTGCTGATTGTGGTCGGGACTGTGGTTGGTAAGATTGGAGCCGACGTATAATTTCAGTCTTAGAG
66 CTGCTGATCGTGGTCGGGACTGCGATAGGTAAGATTGAAGCCGACGTATAAGTTCAGTCTCAGAG
* *
9486 GATTGGAACTGTGGCCGTGAAGCTGTTGAT
131 GATTGGAACTGTGGCCATGAAGCTGCTGAT
9516 TGTTGTGAAG
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 143 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (162 bp):
TGGTTGGTAAGATTGGAGCCGACGTATAAGTTCAGTCTCAGAGATTTGGAACCGTGGCCGTGAAG
CTGCTGATCGTGGTCGGGACTGCGATAGGTAAGATTGAAGCCGACGTATAAGTTCAGTCTCAGAG
GATTGGAACTGTGGCCATGAAGCTGCTGATCG
Done.