Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021983.1 Corchorus olitorius cultivar O-4 contig22016, 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: 2882
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Found at i:2429 original size:154 final size:154
Alignment explanation
Indices: 1933--2882 Score: 1387
Period size: 154 Copynumber: 6.1 Consensus size: 154
1923 ATTCGTATCA
* *
1933 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAGATTTGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * *
1998 CACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGGGCCTTTCGGAGCCCATTAGTTC
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
* *
2063 CATTTTGAATCATCTTCGATTTGG
131 CGTTTTGAATCGTCTTCGATTTGG
* * *
2087 GAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * * *
2152 CACTGTGAAATGTTTAGCTCATTTGGAACACTTGTTAATTTTTTGGGCCTATTGAGGCCCATTAG
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT-A--TTTTGGGCCTATCGGGGCCCATTAG
* * *
2217 TGCTGTTTTGAATTGTCTTCGATTTGG
128 TTCCGTTTTGAATCGTCTTCGATTTGG
* *
2244 CAAACCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGTGAAATTAGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * * ***
2309 CACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTTTTTTGGGCCTATCGGGGACCATTAGGGA
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
2374 CGTTTTGAATCGTCTTCGATTTGG
131 CGTTTTGAATCGTCTTCGATTTGG
* *
2398 CAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGGGAGATTAGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * * *
2463 CACTGTGAAGTTTTTAGCTCAATTCGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTATTTC
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
* *
2528 CGTTTTAAAATCGTCTTTGATTTGG
131 CGTTTT-GAATCGTCTTCGATTTGG
* * **
2553 CAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCATTTTGGTGAGATTAGAA
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* *
2618 CACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
* *
2683 CATTTTGAATCATCTTCGATTTGG
131 CGTTTTGAATCGTCTTCGATTTGG
*
2707 CAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * *
2772 CACTGTGAAGTATTTAGCTCATTTGGAACACTTGTTATTTTTTTGGGCCTATTGAGGCCCATTAG
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA---TTTTGGGCCTATCGGGGCCCATTAG
** *
2837 TTTTGTTTTGAATTGTCTTCGATTTGG
128 TTCCGTTTTGAATCGTCTTCGATTTGG
*
2864 CTAAACCTCAAAGCTTTTC
1 C-AAACCTCAATGCTTTTC
Statistics
Matches: 710, Mismatches: 78, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
154 372 0.52
155 142 0.20
157 181 0.25
158 15 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC
CGTTTTGAATCGTCTTCGATTTGG
Found at i:2679 original size:309 final size:309
Alignment explanation
Indices: 1933--2882 Score: 1465
Period size: 309 Copynumber: 3.1 Consensus size: 309
1923 ATTCGTATCA
* *
1933 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAGATTTGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* *
1998 CACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGGGCCTTTCGGAGCCCATTAGTTC
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
*
2063 CATTTTGAATCATCTTCGATTTGGGAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
131 CATTTTGAATCATCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
* * *
2128 ATAATCATTTTAGTGAGATTAGTCCACTGTGAAATGTTTAGCTCATTTGGAACACTTGTTAATTT
196 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACACTTGTT-A-TT
* *
2193 TTTGGGCCTATTGAGGCCCATTAGTGCTGTTTTGAATTGTCTTCGATTTGG
259 TTTGGGCCTATTGAGGCCCATTATTTCTGTTTTGAATTGTCTTCGATTTGG
* *
2244 CAAACCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGTGAAATTAGTC
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* * * * ***
2309 CACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTTTTTTGGGCCTATCGGGGACCATTAGGGA
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
* * * *
2374 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACT
131 CATTTTGAATCATCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
* * * *
2439 ATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTCGAACACTTGTTA-TTT
196 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACACTTGTTATTTT
* * * * *
2503 TGGGCCT-TTCGGGGCCCATTATTTCCGTTTTAAAATCGTCTTTGATTTGG
261 TGGGCCTATT-GAGGCCCATTATTTCTGTTTT-GAATTGTCTTCGATTTGG
* * **
2553 CAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCATTTTGGTGAGATTAGAA
1 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
*
2618 CACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
66 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
2683 CATTTTGAATCATCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
131 CATTTTGAATCATCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
2748 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACACTTGTTATTTT
196 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACACTTGTTA--TT
2813 TTTGGGCCTATTGAGGCCCATTAGTTT-TGTTTTGAATTGTCTTCGATTTGG
259 TTTGGGCCTATTGAGGCCCATTA-TTTCTGTTTTGAATTGTCTTCGATTTGG
*
2864 CTAAACCTCAAAGCTTTTC
1 C-AAACCTCAATGCTTTTC
Statistics
Matches: 571, Mismatches: 60, Indels: 15
0.88 0.09 0.02
Matches are distributed among these distances:
307 2 0.00
308 27 0.05
309 249 0.44
310 1 0.00
311 247 0.43
312 40 0.07
313 5 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (309 bp):
CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTC
CATTTTGAATCATCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACACTTGTTATTTT
TGGGCCTATTGAGGCCCATTATTTCTGTTTTGAATTGTCTTCGATTTGG
Done.