Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011704.1 Corchorus olitorius cultivar O-4 contig11737, 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: 1800
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Found at i:1067 original size:155 final size:154
Alignment explanation
Indices: 576--1205 Score: 1023
Period size: 154 Copynumber: 4.1 Consensus size: 154
566 TGGCGCATCA
*
576 CTATCGGGGTCCATTTGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
1 CTATCGGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
* * *
641 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAAATTAGTCAACTTTGAAGTTTCTAGCTCA
66 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTAGCTCA
*
706 TTTGGAACACTTGTAATTTTGGGC
131 TTTGGAACACTTGTTATTTTGGGC
*
730 CTATCGGGGTCCATTTGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
1 CTATCGGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
* * *
795 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAACTCA
66 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTAGCTCA
*
860 TTTGTAACACTTGTTATTTTGGGC
131 TTTGGAACACTTGTTATTTTGGGC
* * * * *
884 CTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTTAATGCTTTTCTTT
1 CTATCGGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
* * *
949 CCATTGTTTATGGCCTAACAATAATAATTTTGGTGTAGATTAGTCCACTGTGAAGTTTTTAGCTC
66 CCATTGTTTATGGCCTAACTATAATCATTTTGGTG-AGATTAGTCAACTGTGAAGTTTTTAGCTC
*
1014 ATTTAGAACACTTGTTATTTTGGGC
130 ATTTGGAACACTTGTTATTTTGGGC
** *
1039 CTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTTT
1 CTATCGGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
1103 CCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCAACT-TGAAGTTTCTTAGCTC
66 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTT-TTAGCTC
1166 ATTTGGAACACTTGTTATTTTGGGC
130 ATTTGGAACACTTGTTATTTTGGGC
1191 CTATCGGGGTCCATT
1 CTATCGGGGTCCATT
1206 GTTTATGGCC
Statistics
Matches: 444, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
151 8 0.02
152 58 0.13
153 7 0.02
154 270 0.61
155 101 0.23
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (154 bp):
CTATCGGGGTCCATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAATGCTTTTCTTT
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGC
Found at i:1272 original size:99 final size:98
Alignment explanation
Indices: 1102--1297 Score: 340
Period size: 99 Copynumber: 2.0 Consensus size: 98
1092 ATGCTTTCTT
*
1102 TCCATTGTTTATGGCCTAACTATAATCATTTGGTGAGATTAGTCAACTTGAAGTTTCTTAGCTCA
1 TCCATTGTTTATGGCCTAACTATAATCATTTGGTGAGATTAGTCAACGTGAAGTTTCTTAGCTCA
*
1167 TTTGGAACACTTGTTATTTTGGGCCTATCGGGG
66 TTTGGAACACTTGTTATTTTGGGCCAATCGGGG
*
1200 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTT-TTAGCT
1 TCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGT-CAACGTGAAGTTTCTTAGCT
1264 CATTTGGAACACTTGTTATTTTGGGCCAATCGGG
64 CATTTGGAACACTTGTTATTTTGGGCCAATCGGG
1298 ACCCATTAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 28 0.30
99 54 0.58
100 11 0.12
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.39
Consensus pattern (98 bp):
TCCATTGTTTATGGCCTAACTATAATCATTTGGTGAGATTAGTCAACGTGAAGTTTCTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCAATCGGGG
Found at i:1655 original size:155 final size:154
Alignment explanation
Indices: 1200--1800 Score: 968
Period size: 155 Copynumber: 3.9 Consensus size: 154
1190 CCTATCGGGG
* *
1200 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTC
1 TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* * * * *
1265 ATTTGGAACACTTGTTATTTTGGGCCAATCGGGACCCATTAATGACGTATTGAATCTTCTTCGAT
66 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGAT
1330 TTGGCAAACCTCAATGCTTTTCTT
131 TTGGCAAACCTCAATGCTTTTCTT
*
1354 TCCATTGTTTATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
1 TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* ** *
1419 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGAT
66 ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGAT
1484 TTGGCAAACCTCAATGCTTTTCTT
131 TTGGCAAACCTCAATGCTTTTCTT
1508 TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCT
1 TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCT
* * ** *
1573 CATTTAGAACATTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGA
65 CATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGA
1638 TTTGGCAAACCTCAATGCTTTTCTT
130 TTTGGCAAACCTCAATGCTTTTCTT
* * ** *
1663 TCCACTGTTTATGGACTAATTATAATCATTTTGGTTGAGATTAGTCCACTCTGAAGTTTTTAGCT
1 TCCATTGTTTATGGCCTAACAATAATCATTTTGG-TGAGATTAGTCCACTGTGAAGTTTTTAGCT
* *
1728 CATTTAGAACACATGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGA
65 CATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGA
1793 TTTGGCAA
130 TTTGGCAA
Statistics
Matches: 419, Mismatches: 26, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
154 196 0.47
155 203 0.48
156 20 0.05
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TCCATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
ATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGAT
TTGGCAAACCTCAATGCTTTTCTT
Done.