Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015768.1 Corchorus olitorius cultivar O-4 contig15801, 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: 14524
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:109 original size:42 final size:43
Alignment explanation
Indices: 58--151 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
48 AGTGCATTAC
* * *
58 CTAA-ATTCTA-CTCCATCTCTGGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
99 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
144 CTAATATT
1 CTAATATT
152 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:1177 original size:42 final size:42
Alignment explanation
Indices: 1118--1207 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
1108 TATATAGTAT
* * *
1118 ATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGTAGA
1 ATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGA
1160 ATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGA
1 ATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGA
1202 AT-TTAG
1 ATATTAG
1208 GTAATGCACT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.41
Consensus pattern (42 bp):
ATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGA
Found at i:1346 original size:27 final size:27
Alignment explanation
Indices: 1315--1371 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1305 ACGGCCAATG
* *
1315 CAATATCTACTTTCTAACTGACTTAAA
1 CAATATATACTTTCTAACCGACTTAAA
*
1342 CAATATATTCTTTCTAACCGACTTAAA
1 CAATATATACTTTCTAACCGACTTAAA
1369 CAA
1 CAA
1372 CTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.35
Consensus pattern (27 bp):
CAATATATACTTTCTAACCGACTTAAA
Found at i:7882 original size:350 final size:350
Alignment explanation
Indices: 7239--7936 Score: 1272
Period size: 350 Copynumber: 2.0 Consensus size: 350
7229 AGAGTATTCA
* *
7239 TATACAACTTAGCTTTTGGTTTCTCCTACAATGAAAAAATGAGCATGTGAGTATAAAATATGTAA
1 TATACAACTTAGCTTTCGGTTTCTCCTACAATGAAAAAATAAGCATGTGAGTATAAAATATGTAA
7304 CTAGCAGCATAAGCATAAAAATATATATAAATGTAGCTAACTTTACCTTGATTAACTCATTCCAT
66 CTAGCAGCATAAGCATAAAAATATATATAAATGTAGCTAACTTTACCTTGATTAACTCATTCCAT
* *
7369 ACTTCTGGTTTAGCACTCCTTACTTCTCTTTCCGGATCGAAGGAGAGTCCACTCAAGCTAGTACT
131 ACTTCTGGTTCAGCACTCCTTACTTCTCTTTCCGGATCGAAGAAGAGTCCACTCAAGCTAGTACT
*
7434 GTTAAAGATGTCCCACGCCTCAGCAAAGTGAGCCTTTAAGATCTTACAGCGACCTTGAACTTGAC
196 GTTAAAGATGTCACACGCCTCAGCAAAGTGAGCCTTTAAGATCTTACAGCGACCTTGAACTTGAC
7499 TCTTTTCAATACTAATGTTAAAAGAAATTGAAAGTTCAACGACAACATTGGCAAAAGCCGTGGAA
261 TCTTTTCAATACTAATGTTAAAAGAAATTGAAAGTTCAACGACAACATTGGCAAAAGCCGTGGAA
7564 GTAAAACTGCCATTCACCTTATTTT
326 GTAAAACTGCCATTCACCTTATTTT
*
7589 TATACAACTTAGCTTTCGGTTTCTCCTACAATGAAAAAATAAGCATGTGAGTATACAATATGTAA
1 TATACAACTTAGCTTTCGGTTTCTCCTACAATGAAAAAATAAGCATGTGAGTATAAAATATGTAA
7654 CTAGCAGCATAAGCATAAAAATATATATAAATGTAGCTAACTTTACCTTGATTAACTCATTCCAT
66 CTAGCAGCATAAGCATAAAAATATATATAAATGTAGCTAACTTTACCTTGATTAACTCATTCCAT
*
7719 ACTTCTGGTTCAGCACT-CTATACTTCTCTTTCCGGATCGAAGAAGAGTCCACTCAAGCTAGTAT
131 ACTTCTGGTTCAGCACTCCT-TACTTCTCTTTCCGGATCGAAGAAGAGTCCACTCAAGCTAGTAC
*
7783 TGTTAAAGATGTCACACGCCTTAGCAAAGTGAGCCTTTAAGATCTTACAGCGACCTTGAACTTGA
195 TGTTAAAGATGTCACACGCCTCAGCAAAGTGAGCCTTTAAGATCTTACAGCGACCTTGAACTTGA
*** *
7848 CTCTTTTCAATACTAATGTTAAAAGTCCTTGAAAGTTCAACGACAACATTGGCATAAGCCGTGGA
260 CTCTTTTCAATACTAATGTTAAAAGAAATTGAAAGTTCAACGACAACATTGGCAAAAGCCGTGGA
7913 AGTAAAACTGCCATTCACCTTATT
325 AGTAAAACTGCCATTCACCTTATT
7937 CCCCAAGTTT
Statistics
Matches: 335, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
349 2 0.01
350 333 0.99
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (350 bp):
TATACAACTTAGCTTTCGGTTTCTCCTACAATGAAAAAATAAGCATGTGAGTATAAAATATGTAA
CTAGCAGCATAAGCATAAAAATATATATAAATGTAGCTAACTTTACCTTGATTAACTCATTCCAT
ACTTCTGGTTCAGCACTCCTTACTTCTCTTTCCGGATCGAAGAAGAGTCCACTCAAGCTAGTACT
GTTAAAGATGTCACACGCCTCAGCAAAGTGAGCCTTTAAGATCTTACAGCGACCTTGAACTTGAC
TCTTTTCAATACTAATGTTAAAAGAAATTGAAAGTTCAACGACAACATTGGCAAAAGCCGTGGAA
GTAAAACTGCCATTCACCTTATTTT
Found at i:9370 original size:14 final size:14
Alignment explanation
Indices: 9351--9378 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9341 ATTCTTTGCA
9351 CTATGTGATAATAT
1 CTATGTGATAATAT
9365 CTATGTGATAATAT
1 CTATGTGATAATAT
9379 ATATATATAT
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:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CTATGTGATAATAT
Found at i:9382 original size:2 final size:2
Alignment explanation
Indices: 9375--9401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9365 CTATGTGATA
9375 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9402 AGGTCTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.