Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011301.1 Corchorus olitorius cultivar O-4 contig11334, 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, 885
Length: 1475
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Found at i:347 original size:154 final size:154
Alignment explanation
Indices: 1--566 Score: 841
Period size: 154 Copynumber: 3.6 Consensus size: 154
* *
1 TATGGCCTAACA-ATAATCCATTTTTAGTGAGATTGGTCCACTGTGAAGTTTTTTAGCTCATTTA
1 TATGGCCTAA-ATATAAT-CA-TTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTA
* *
65 GAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGT-CCGTTTTAAATCGTCTTCGATTTTGG
62 GAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGA-TTT-G
129 GCAAAACCTTCAATGCTTTTCTTTCCATTGTT
125 GC-AAACC-TCAATGCTTTTCTTTCCATTGTT
* *
161 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTAGAAC
1 TATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
* * * * *
226 GCTTGTTATTTTGGGCTTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAAC
291 CTCAATGCTTTTCTTTCCATTGTT
131 CTCAATGCTTTTCTTTCCATTGTT
* * * *
315 TATGGCCTAAATATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTTTCTAGCTCATTTGGAAC
1 TATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
380 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAAC
*
445 CTCAATGCTTTTCTTTCCACTGTT
131 CTCAATGCTTTTCTTTCCATTGTT
* * * *
469 TATGGCCTAACTATAATCGTTTTGGTGAGATTAGTCCACAGTGAAGTTATTAGCTCATTTAGAAC
1 TATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
* *
534 ACTTGTCATTTTGGGCCTATCGGGG-TCATTAGT
66 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
567 TCTGTTTTGA
Statistics
Matches: 371, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
153 7 0.02
154 246 0.66
155 5 0.01
156 3 0.01
157 53 0.14
158 40 0.11
159 2 0.01
160 15 0.04
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAAC
CTCAATGCTTTTCTTTCCATTGTT
Found at i:812 original size:279 final size:280
Alignment explanation
Indices: 312--846 Score: 876
Period size: 279 Copynumber: 1.9 Consensus size: 280
302 TCTTTCCATT
* * **
312 GTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTTTCTAGCTCATTTGG
1 GTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCAACTGTGAAATTTCTAGCTCATTTAA
377 AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCA
66 AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCA
*
442 AACCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCGTTTTGGTGAGATTAGTCCA
131 AACCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
*
507 CAGTGAAGTTATTAGCTCATTTAGAACACTTGTCATTTTGGGCCTATCGGGGTC-ATTAGTTCTG
196 CAGTGAAGTTATTAGCTCATTTAGAACACTTGTCATTTTGGGCCTATCGGGGCCTATTAGTTCTG
571 TTTTGACTCGTCTTCGAATG
261 TTTTGACTCGTCTTCGAATG
* *
591 GTTTATGGCCTAACA-ATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTA
1 GTTTATGGCCTAA-ATATAATCATTTTGGTGAGATTAGTCAACTGTGAAATTTCTAGCTCATTTA
* * ** *
655 AAACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
65 AAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGC
*
720 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
130 AAACCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
* * * * *
785 ACTGTGATGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCTTATCGGGGCCTATTAGT
195 ACAGTGAAGTTATTAGCTCATTTAGAACACTTGTCATTTTGGGCCTATCGGGGCCTATTAGT
847 GACGTATTGA
Statistics
Matches: 235, Mismatches: 19, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
279 228 0.97
280 7 0.03
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (280 bp):
GTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCAACTGTGAAATTTCTAGCTCATTTAA
AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
CAGTGAAGTTATTAGCTCATTTAGAACACTTGTCATTTTGGGCCTATCGGGGCCTATTAGTTCTG
TTTTGACTCGTCTTCGAATG
Found at i:871 original size:154 final size:154
Alignment explanation
Indices: 591--929 Score: 565
Period size: 154 Copynumber: 2.2 Consensus size: 154
581 TCTTCGAATG
*
591 GTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTAA
1 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTAA
** *
656 AACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
66 AACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCA
721 AACCTCAATGCTTTTCTTTCCATT
131 AACCTCAATGCTTTTCTTTCCATT
** *
745 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTAG
1 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTAA
*
810 AACACTTGTTATTTTGGG-CTTATCGGGG-CCTATTAGTGACGTATTGAATCTTCTTCGATTTGG
66 AACACTTGTTATTTTGGGTC-TATCGGGGTCC-ATTAGTGACGTATTGAATCGTCTTCGATTTGG
873 CAAACCTCAATGCTTTTCTTTCCATT
129 CAAACCTCAATGCTTTTCTTTCCATT
*
899 GTTTATGGCCTAAATATAATCATTTTGGTGA
1 GTTTATGGCCTAACTATAATCATTTTGGTGA
930 ACCATCTCCA
Statistics
Matches: 174, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
153 3 0.02
154 171 0.98
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (154 bp):
GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTAA
AACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCATT
Done.