Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016195.1 Corchorus olitorius cultivar O-4 contig16228, 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: 23907
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3291 original size:21 final size:21
Alignment explanation
Indices: 3242--3291 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3232 CTACATTATG
*
3242 AAATTATGATAACCTCCCTAT
1 AAATTTTGATAACCTCCCTAT
* * *
3263 AAAATTTGATAACCTCTCTGT
1 AAATTTTGATAACCTCCCTAT
3284 AAATTTTG
1 AAATTTTG
3292 TTTTCTTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACCTCCCTAT
Found at i:13924 original size:21 final size:19
Alignment explanation
Indices: 13898--13955 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
13888 GTTGTTTTAA
13898 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
13919 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
13938 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
13956 TGCTAAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:14994 original size:28 final size:28
Alignment explanation
Indices: 14962--15015 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
14952 ACTTGAGATT
14962 AATATTGATGCAGAACAGGTTATCAAAA
1 AATATTGATGCAGAACAGGTTATCAAAA
14990 AATATTGATGCAGAACAGGTTATCAA
1 AATATTGATGCAGAACAGGTTATCAA
15016 GCTTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
AATATTGATGCAGAACAGGTTATCAAAA
Found at i:18778 original size:6 final size:6
Alignment explanation
Indices: 18767--18793 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18757 AACATCATGA
18767 TGATTC TGATTC TGATTC TGATTC TGA
1 TGATTC TGATTC TGATTC TGATTC TGA
18794 CCATAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (6 bp):
TGATTC
Found at i:22438 original size:95 final size:97
Alignment explanation
Indices: 22324--22520 Score: 274
Period size: 97 Copynumber: 2.1 Consensus size: 97
22314 AAATTTTATA
* *
22324 TTTTT-CGATTATACCATTTTTTAAAAATATATTTCTAAATTACCATTATT-ATA-ATATTTTAA
1 TTTTTCCGATTATACCATTTTTTAAAAACATATTTCTAAATTACCATTATTAAAATATATTTTAA
* *
22386 TTATGTCATTATTAAAATATAATTTTATGTAT
66 CTATGCCATTATTAAAATATAATTTTATGTAT
* * ** * *
22418 TTTTTCCGATTGTACTATTTTTTTCAAACATATTTTTAAATTATCATTATTAAAATATATTTTAA
1 TTTTTCCGATTATACCATTTTTTAAAAACATATTTCTAAATTACCATTATTAAAATATATTTTAA
*
22483 CTATGCCATTATTAAAATATAATTTTGTGTAT
66 CTATGCCATTATTAAAATATAATTTTATGTAT
22515 TTTTTC
1 TTTTTC
22521 AAATATATTT
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 5 0.06
95 38 0.43
96 2 0.02
97 44 0.49
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (97 bp):
TTTTTCCGATTATACCATTTTTTAAAAACATATTTCTAAATTACCATTATTAAAATATATTTTAA
CTATGCCATTATTAAAATATAATTTTATGTAT
Found at i:23491 original size:332 final size:330
Alignment explanation
Indices: 22563--23749 Score: 1412
Period size: 332 Copynumber: 3.6 Consensus size: 330
22553 ATATAATTTT
*
22563 TTTAATTAGAAATTAATTTGGAAAAAGGTAGGAAAAACGATATTAGAAGCGTG-AGAAGCCCTTC
1 TTTAATTAGAAATTAATTCGGAAAAA-GTAGGAAAAACGATATTAGAAGCGTGAAGAAGCCCTTC
** * * *
22627 TGTCTTTTTAGCGTTGAGTTATATATTTTTTATTAGTATTTTCAATTGTGGTCC--AAATTGAGG
65 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA---TC----GTGG-CCAAAAATTGAGG
* * * * *
22690 AGAAATTTCTCGCGTCAATTTTTGTAAAATTTTAGTTGAAATCGTGTAATAACCATCACGGTTTT
122 A-AAATTT-TCGAGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTATTAACCATCACAGTTTT
* * * *
22755 TGACTAAAAACGCGTTCCGGAGCCCGGCTCTGTTTTGCATGATTTTTTGCGTCAAGTCTCATTGA
185 TGACTAAAAACGCGTTTCGGGGCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGA
* *
22820 AATATCTATATCCATCTAACCAAATACT-ACCCACATTGAATTTAAGGATTTGTTTTTACGAGCA
250 AATATCTATATCCATCTAACCAAAT-CTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCA
*
22884 TATGAATCATGTTTCGA
314 TCTGAATCATGTTTCGA
* * * * * *
22901 TTCAATTAGGAATCAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAATAA-CCTTTCA
1 TTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGTGAAGAAGCCCTTCA
* * *
22965 ATCGTTTTGGTGTTGAATTATA-AATTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTT
66 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATT-TT
** * * * * *
23029 TAAGTCAATTTTTACAAAATTTTAGCTGAAATTGTGTATTAACTATCACGGTTTTTGGCTAAAAA
130 CGAGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTATTAACCATCACAGTTTTTGACTAAAAA
* * * *
23094 CGCG-TTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAACATCTA
195 CGCGTTTC-GGGG-CCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTA
** * * * * *
23158 TATTTATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTCGTTTTTACGAGCATCTCAATCC
258 TATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCA
*
23223 GGTTTCGA
323 TGTTTCGA
* **
23231 TTTAATCT-GAAATTAATTCGAGAAAAA-TAGAAAAAATAATATTAGAAGCGT-AAGAAGCCCTT
1 TTTAAT-TAGAAATTAATTCG-GAAAAAGTAGGAAAAACGATATTAGAAGCGTGAAGAAGCCCTT
* ** * * **
23293 CAATATTTTTGGCGTTGGGTTATATATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAATG
64 CAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAAT-
* * *
23358 TTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAA
127 TTTCGAGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTATTAACCATCACAGTTTTTGACTAA
*
23423 AAACGCGTTTCGGGGTCCCGGTTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATC
192 AAACGCGTTTCGGGG-CCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATC
*
23488 TATATCCATCTAACCAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
256 TATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
23553 CATGTTTCGA
321 CATGTTTCGA
* *
23563 TTTAATTAGAAATTAATTTGGAAAAAGTAGG-AAAACTGATATTAGAAGCGTGAA-AAGCCTTTC
1 TTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAAC-GATATTAGAAGCGTGAAGAAGCCCTTC
* * * *
23626 AATCTTTTTGGTGTTTAATTATATATATTTTTATGAGTATCGTGG-CAAAAATTTAAGAAAATTC
65 AATCTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAA-T-
* * * *
23690 TTTCGGGTAAATTGTTGCAAAATTTTA-ATAGAAATCGTGTATTAACCATCACAGTTTTTG
127 TTTCGAGTCAATTTTTGCAAAATTTTAGCT-GAAATCGTGTATTAACCATCACAGTTTTTG
23750 GTAACAAAGG
Statistics
Matches: 719, Mismatches: 109, Indels: 48
0.82 0.12 0.05
Matches are distributed among these distances:
328 4 0.01
329 78 0.11
330 175 0.24
331 50 0.07
332 304 0.42
333 24 0.03
336 12 0.02
337 47 0.07
338 25 0.03
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (330 bp):
TTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGTGAAGAAGCCCTTCA
ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTTTC
GAGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTATTAACCATCACAGTTTTTGACTAAAAAC
GCGTTTCGGGGCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATAT
CCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGT
TTCGA
Done.