Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010853.1 Corchorus olitorius cultivar O-4 contig10885, 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: 1781
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Found at i:383 original size:154 final size:154
Alignment explanation
Indices: 1--749 Score: 1239
Period size: 154 Copynumber: 4.9 Consensus size: 154
* * *
1 ATAATCATTTTGGTGAGACTAGTCCACTGGGAAGTTTTTAACCCATTTGGAACACTTGTTATTTT
1 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
* ** * *
66 GGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAATCTCAATGTTTTT
66 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
131 CTTTCCATTGTTTATGGCCT-ACT
131 CTTTCCATTGTTTATGGCCTAACT
**
154 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCAAATTTGGAACACTTGTTATTTT
1 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
219 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
66 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
284 CTTTCCATTGTTTATGGCCTAACT
131 CTTTCCATTGTTTATGGCCTAACT
*
308 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
1 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
* *
373 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTCCGATTTGGCAACTCTCAATGCTTTT
66 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
438 CTTTCCATTGTTTATGGCCTAACT
131 CTTTCCATTGTTTATGGCCTAACT
* *
462 ATAATCATTTTGGTGAGATTAGTCCACTGAGAAGTTTTTAGCCCATTTGGAACATTTGTTATTTT
1 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
* ** * **
527 GGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAATCTCAATATTTTT
66 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
592 CTTTCCATTGTTTATGGCCTAACT
131 CTTTCCATTGTTTATGGCCTAACT
* *
616 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAGTTT
1 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
* * * * *
681 GGGTCTGTCGGGGCCTATTAGTTCCGTTTTGAATCGTCTCCGATTTGGCAACTCCCAATGCTTTT
66 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
746 CTTT
131 CTTT
750 TTTTTAGAAA
Statistics
Matches: 555, Mismatches: 40, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
153 140 0.25
154 415 0.75
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (154 bp):
ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTT
GGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCTTTT
CTTTCCATTGTTTATGGCCTAACT
Found at i:1293 original size:21 final size:21
Alignment explanation
Indices: 1267--1379 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
1257 TGCTAGAAGT
1267 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
1288 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
1309 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
1330 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
1351 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
1372 TCATTGGA
1 TCATTGGA
1380 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.