Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011927.1 Corchorus olitorius cultivar O-4 contig11960, 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, 631
Length: 1052
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Found at i:288 original size:156 final size:154
Alignment explanation
Indices: 3--1052 Score: 1558
Period size: 156 Copynumber: 6.8 Consensus size: 154
1 GT
* * * *
3 CCTAACTATAATCATTTTGGTGAGATTAGTCGATTATGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTT
* ** ** * * *
68 TAATTTTGGGCCTTATCGGGTACCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTCA
66 TTATTTTGGGCC-TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCA
133 ATGCTTTTCTTTCCATTGTTTATGG
130 ATGCTTTTCTTTCCATTGTTTATGG
158 CCTAACTATAATCATTTTGGTGACGATTACGT-CACTGTCGAAGTTTTTAGCTCATTTGGAACAC
1 CCTAACTATAATCATTTTGGTGA-GATTA-GTCCACTGT-GAAGTTTTTAGCTCATTTGGAACAC
*
222 TTTTTATTTTGGACTCTATCGGGG-CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
63 TTTTTATTTTGGGC-CTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
286 TCAATGC-TTTCTTTCCATTGTTTATGG
127 TCAATGCTTTTCTTTCCATTGTTTATGG
* * *
313 CCTAACTGTAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTAATTTGGAACACTTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTT
*
378 TTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
443 TGCTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* * * *
467 CGTAACTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTTTTAGCTCATTTGCAACACTTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTT
* * **
532 TTATTTTGGGCCAATCGAGGCCCATTTTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTC
66 TTATTTTGGGCCTATCGGGGCCCA--TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTC
597 AATGCTTTTCTTTCCATTGTTTATGG
129 AATGCTTTTCTTTCCATTGTTTATGG
* * *
623 CTTAACTATAATCATTTTGGTGAGATTAGTCCAGTTTGAAGTTTTTAGCTCATTTGGAACACTTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTT
* *
688 TTA-TTTGGATGCGTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTA
66 TTATTTTGG--GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTC
752 AATGCTTTTCTTTCCATTGTTTATGG
129 AATGCTTTTCTTTCCATTGTTTATGG
* * * *
778 CGTAACTTGTAATCATTTTGGTGAGATTTAGTCCTCTGTTGAAGTTTTTAGCTCATTTGCAACAC
1 CCTAAC-TATAATCATTTTGGTGAGA-TTAGTCCACTG-TGAAGTTTTTAGCTCATTTGGAACAC
* **
843 TTTTTATTTTGGGCCAATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCT
63 TTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCT
908 CAATGCTTTTCTTTCCATTGTTTATGG
128 CAATGCTTTTCTTTCCATTGTTTATGG
* *
935 CCTAACTAT-ATCA-TTTGGTGAG-TTAGTCCAGTTGTGAAG-TTTTAGCTAATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCA-CTGTGAAGTTTTTAGCTCATTTGGAACACTT
* *
996 TCTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
65 TTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
Statistics
Matches: 818, Mismatches: 61, Indels: 36
0.89 0.07 0.04
Matches are distributed among these distances:
151 72 0.09
152 21 0.03
153 87 0.11
154 120 0.15
155 141 0.17
156 195 0.24
157 145 0.18
158 32 0.04
159 5 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (154 bp):
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTT
TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAA
TGCTTTTCTTTCCATTGTTTATGG
Found at i:571 original size:309 final size:308
Alignment explanation
Indices: 3--1052 Score: 1659
Period size: 309 Copynumber: 3.4 Consensus size: 308
1 GT
* * *
3 CCTAACTATAATCATTTTGGTGAGATTAGTCGA-TTATGAAGTTTTTAGCTCATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCAGTTGTGAAGTTTTTAGCTAATTTGGAACACTT
* * * ** ** * * *
67 GTAATTTTGGGCCTTATCGGGTACCATTAGTGACATATTGAATCGTCTTCGATTTGGCAAACCTC
66 TTTATTTTGTGCC-TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTC
* * *
132 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGACGATTACGT-CACTGT
130 AATGCTTTTCTTTCCATTGTTTATGGCGTAACTGTAATCATTTTGGTGA-GATTA-GTCCTCTGT
* * * * **
196 CGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGACTCTATCGGGGCCATTAGTTCCGTTT
193 -GAAGTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGC-CAATCGGGCCCATTAGTGACGTTT
261 TGAATCGTCTTCGATTTGGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGG
256 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
*
313 CCTAACTGTAATCATTTTGGTGAGATTAGTCCA-TTGTGAAGTTTTTAGCTAATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCAGTTGTGAAGTTTTTAGCTAATTTGGAACACTT
377 TTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCA
66 TTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCA
442 ATGCTTTTCTTTCCATTGTTTATGGCGTAACTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAA
131 ATGCTTTTCTTTCCATTGTTTATGGCGTAACTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAA
507 GTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGCCAATCGAGGCCCATTTTAGTGACGTTTTG
196 GTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGCCAATCG-GGCCCA--TTAGTGACGTTTTG
572 AATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
258 AATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
* *
623 CTTAACTATAATCATTTTGGTGAGATTAGTCCAGTT-TGAAGTTTTTAGCTCATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCAGTTGTGAAGTTTTTAGCTAATTTGGAACACTT
* * *
687 TTTATTTGGATGCGTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTA
66 TTTATTTTG-TGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTC
752 AATGCTTTTCTTTCCATTGTTTATGGCGTAACTTGTAATCATTTTGGTGAGATTTAGTCCTCTGT
130 AATGCTTTTCTTTCCATTGTTTATGGCGTAAC-TGTAATCATTTTGGTGAGA-TTAGTCCTCTG-
817 TGAAGTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGCCAATCGGGGCCCATTAGTGACGTTT
192 TGAAGTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGCCAATC-GGGCCCATTAGTGACGTTT
882 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
256 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
935 CCTAACTAT-ATCA-TTTGGTGAG-TTAGTCCAGTTGTGAAG-TTTTAGCTAATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCAGTTGTGAAGTTTTTAGCTAATTTGGAACACTT
*
996 TCTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
66 TTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
Statistics
Matches: 694, Mismatches: 34, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
306 5 0.01
307 44 0.06
308 57 0.08
309 172 0.25
310 170 0.24
311 91 0.13
312 92 0.13
313 11 0.02
314 51 0.07
315 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (308 bp):
CCTAACTATAATCATTTTGGTGAGATTAGTCCAGTTGTGAAGTTTTTAGCTAATTTGGAACACTT
TTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCA
ATGCTTTTCTTTCCATTGTTTATGGCGTAACTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAA
GTTTTTAGCTCATTTGCAACACTTTTTATTTTGGGCCAATCGGGCCCATTAGTGACGTTTTGAAT
CGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGG
Done.