Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011060.1 Corchorus olitorius cultivar O-4 contig11093, 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, 988
Length: 1648
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Found at i:255 original size:21 final size:21
Alignment explanation
Indices: 231--322 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
221 CTTAGGCATT
*
231 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
252 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
273 TCCAATGAACTTGGAACCTGC
1 TCCAATGAGCTTGGAACCTTC
294 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
315 TCCAATGA
1 TCCAATGA
323 ACTTCTAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 2 0.03
21 62 0.97
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:713 original size:154 final size:154
Alignment explanation
Indices: 429--1648 Score: 1691
Period size: 154 Copynumber: 7.9 Consensus size: 154
419 TGGCGCATCA
429 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTT-
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
* * * *
493 CTTTTTGAATCGTCTTCGATTTGGAAACCCTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACT
66 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
558 ATAATCATTTTGGTGAGATTAGTC
131 ATAATCATTTTGGTGAGATTAGTC
* * *
582 CACTATGAAGGTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTC
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
647 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
66 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
*
712 ATAATCATTTTGTTGAGATTAGTC
131 ATAATCATTTTGGTGAGATTAGTC
* * * * * *
736 CACTATGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGTGCCTATCAGGGTCCATTAGTGA
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
* * * * *
801 CGTTTTGAATCGTCTTCGATATGGAAAAAATCCCTCAATGCTTTTCTTTCCATTGTTTTTGGGCT
66 CGTTTTGAATCGTCTTCGATTTGG---CAAT-CCTCGATGCTTTTCTTTCCATTGTTTATGGCCT
* * * *
866 AACTATATTTATTTTAGAGAGA--AGTC
127 AACTATAATCATTTTGGTGAGATTAGTC
* * * * *
892 CACTGTGAAGGTTTTAGCTCATTTGGAACACCTGTTATTTT-TGGCCTATCAGGGCCCATTAGTG
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGT-GCCTTTCGGGGCCCATTAGTT
* * *
956 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTTTCCATTGTTTAAGGCCTAAC
65 ACGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
1020 TATAATCATTTTGTTGAGATTAGTC
130 TATAATCATTTTGGTGAGATTAGTC
1045 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCCTTTCGGGGGCCCCATTAG
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTG-CCTTTC-GGGG-CCCATTAG
* * * *
1110 TGTACGTTTTGAATTCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTTTGACC
63 T-TACGTTTTGAA-TCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCC
* * * *
1175 TAACTATATTTATTTTAGAGAGATTAGTC
126 TAACTATAATCATTTTGGTGAGATTAGTC
1204 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTG-CTTTCGGGGCCCATTTAGTT
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCA-TTAGTT
* * * *
1268 -CTGTTTTAAATCGTCTTCGATTTGG-AAACCATCGATGCATTTCTTTCCATTGTTTAAGGCCTA
65 AC-GTTTTGAATCGTCTTCGATTTGGCAATCC-TCGATGCTTTTCTTTCCATTGTTTATGGCCTA
* *
1331 ACTATTATCATTTTGTTGAGATTAGTC
128 ACTATAATCATTTTGGTGAGATTAGTC
* * *
1358 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTTCCTTTCGGGGTCCATTAGTTC
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
* *
1423 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGCCCTAGCT
66 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
* **
1488 ATAATCATTTTGCTGAGATTAGGG
131 ATAATCATTTTGGTGAGATTAGTC
* * * * *
1512 CTCCGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTGA
1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
* * * * *
1577 CGTTTTGAATCGACTTCAATTTAGCAATCCTCGATGCTTTTCTTTCCATTGTTGATGCCCTAACT
66 CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1642 ATAATCA
131 ATAATCA
Statistics
Matches: 956, Mismatches: 90, Indels: 41
0.88 0.08 0.04
Matches are distributed among these distances:
151 37 0.04
152 9 0.01
153 113 0.12
154 481 0.50
155 33 0.03
156 103 0.11
157 18 0.02
158 75 0.08
159 87 0.09
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (154 bp):
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTA
CGTTTTGAATCGTCTTCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACT
ATAATCATTTTGGTGAGATTAGTC
Done.