Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023179.1 Corchorus olitorius cultivar O-4 contig23212, 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, 607
Length: 1013
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Found at i:917 original size:460 final size:462
Alignment explanation
Indices: 29--1012 Score: 1735
Period size: 460 Copynumber: 2.1 Consensus size: 462
19 TTGGCAACCC
*
29 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCCTCTTCAATTTGACAACCCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCT
94 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT
66 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT
159 TTGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTC
131 TTGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTC
224 TTCGATTTGGCAACTCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGT
196 TTCGATTTGGCAACTCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGT
*
289 GAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGC
261 GAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATGTTGGGCTTATCGGGGC
*
354 CTATTAGTGACGTTTTGAATCGTCATCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA
326 CCATTAGTGACGTTTTGAATCGTCATCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA
419 TTGCCGAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAACAC
391 TTGCCGAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAACAC
484 TTG-TATT
456 TTGTTA-T
491 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCT
556 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-GTTT
66 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT
* * * * * **
620 TTAGCTCATTTGGAACACTTTTTCTTTTGGGCTTATTGGGGCCCATTAGTTCCGTTTTGAATCGT
131 TT-GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGT
*
685 CTTCGATTTGGCAAC-CTCAATGC-TTTC-TTCCATTGTTTAGTGGCCTAACTATAATCATTTTG
195 CTTCGATTTGGCAACTCTCAATGCTTTTCTTTCCATTATTTA-TGGCCTAACTATAATCATTTTG
747 GTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATGTTGGGCTTATCGGG
259 GTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATGTTGGGCTTATCGGG
* * *
812 GCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCATTGCTTTTCTTTTCATTGTT
324 GCCCATTAGTGACGTTTTGAATCGTCATCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTT
*
877 TATTGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAAC
389 TATTGCCGAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAAC
942 ACTTGTTAT
454 ACTTGTTAT
** * *
951 TTTGGGCCTATTAGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTAACAACCTTCAAT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAAT
1013 T
Statistics
Matches: 500, Mismatches: 19, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
459 11 0.02
460 279 0.56
461 16 0.03
462 194 0.39
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (462 bp):
TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCT
TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT
TTGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTC
TTCGATTTGGCAACTCTCAATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGT
GAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATGTTGGGCTTATCGGGGC
CCATTAGTGACGTTTTGAATCGTCATCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA
TTGCCGAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAACAC
TTGTTAT
Found at i:1006 original size:154 final size:154
Alignment explanation
Indices: 29--999 Score: 1565
Period size: 154 Copynumber: 6.3 Consensus size: 154
19 TTGGCAACCC
* * *
29 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCCTCTTCAATTTGACAACCCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
*
94 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT
66 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-GTTT
159 TT-GCTCATTTGGAACACTTGTTAT
130 TTAGCTCATTTGGAACACTTGTTAT
* *
183 TTTGGGCCTATCGGGACCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACTCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
* *
248 TTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCT
66 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
313 TAGCTCATTTGGAACACTTGTTAT
131 TAGCTCATTTGGAACACTTGTTAT
* * *
337 TTTGGGCTTATCGGGGCCTATTAGTGACGTTTTGAATCGTCATCGATTTGGCAACCCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
* * *
402 TTTCTTTCCATTGTTTATTGCCGAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTT
66 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
*
467 TAGCTCATTTAGAACACTTG-TATT
131 TAGCTCATTTGGAACACTTGTTA-T
* *
491 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
*
556 TTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
66 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
* *
621 TAGCTCATTTGGAACACTTTTTCT
131 TAGCTCATTTGGAACACTTGTTAT
* * **
645 TTTGGGCTTATTGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA-CCTCAATGC-
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
*
708 TTTC-TTCCATTGTTTAGTGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTC
66 TTTCTTTCCATTGTTTA-TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
772 TTAGCTCATTTGGAACACTTGTTAT
130 TTAGCTCATTTGGAACACTTGTTAT
* * *
797 GTTGGGCTTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCATTGCT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
* * *
862 TTTCTTTTCATTGTTTATTGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTT
66 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
*
927 TAGCTCATTTAGAACACTTGTTAT
131 TAGCTCATTTGGAACACTTGTTAT
** *
951 TTTGGGCCTATTAGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTT
1 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
1000 AACAACCTTC
Statistics
Matches: 755, Mismatches: 55, Indels: 14
0.92 0.07 0.02
Matches are distributed among these distances:
151 12 0.02
152 123 0.16
153 24 0.03
154 584 0.77
155 12 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
TAGCTCATTTGGAACACTTGTTAT
Done.