Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011026.1 Corchorus olitorius cultivar O-4 contig11059, 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, 724
Length: 1208
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1208 Score: 1793
Period size: 154 Copynumber: 7.9 Consensus size: 154
* * * *
1 GAATCGACTTCGATTTAGCAAACCT-AAAGCTTTTCTTTCCACTGTTGATGGGCTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * *
65 ATTTTTGCTGAGAT-TAGTGCACTGTGAAATTTTTAGCTGATTTGGAACACTTGTTATTTTGGGC
66 A-TTTTGGTGAGATAT-GTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
* ** *
129 CTTTCGTGGATCATTGGTACCGTTTT
129 CTTTCGGGGCCCATTAGTACCGTTTT
*
155 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTT-TTATCCATTGTTTATGGCCTAACTATAAT
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTT-TCCATTGTTTATGGACTAACTATAAT
* * * *
219 CATTTTGGTGAGATATGTCCACTGTGCAGTTTTTAGCTCGTTTGGAACACATGTTATTTTGGGCC
65 CATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
*
284 TTTCGGGGCCCATTAG-ATCCGTTAT
130 TTTCGGGGCCCATTAGTA-CCGTTTT
* *
309 GAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * *
374 ATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTTATTTGGAACAATTGTTATTTTGGGCCT
66 ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
439 TTCGAGGCCCATTAGTACCGTTTT
131 TTCGGGGCCCATTAGTACCGTTTT
* * * *
463 GAATCGACTTCGATTTAGCAAACCT-AAAGCTTTTCTTTCCACTGTTGATGGGCTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * *
527 ATTTTGCTGAGAT-TAGTGCACTGTGAAATTTTTAGCTGATTTGGAACACTTGTTATTTTGGGCC
66 ATTTTGGTGAGATAT-GTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* ** *
591 TTTCGTGGATCATTGGTACCGTTTT
130 TTTCGGGGCCCATTAGTACCGTTTT
* * *
616 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATGGCCTAACTGTAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * * * *
681 ATTTTGGAGAAATATGTGCACTGTGAAATTTTTATCTCATTTGGAACACTTGTCATTTTGGGCCT
66 ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
746 TTCGGGGCCCATTAGTACCGTTTT
131 TTCGGGGCCCATTAGTACCGTTTT
* * * *
770 GAATCGACTTCGATTTAGCAAACCTAAAAGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* *
835 ATTTTGCTGAGAT-TAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTAGGCC
66 ATTTTGGTGAGATAT-GTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
*
899 TTTCGGGGCTCATTAGTACCGTTTT
130 TTTCGGGGCCCATTAGTACCGTTTT
* * *
924 GAATCGACTTCGATATGGCAAACCTCAAAGCTTTTCTTTACATTGTTTATGAACTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
989 ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
66 ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* *
1054 TTCGTGGCCCATTAGTTCCGTTTT
131 TTCGGGGCCCATTAGTACCGTTTT
*
1078 AAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
1 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* *
1143 ATTTTGGTGAGATA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTAATTTTGGGCCT
66 ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
1207 TT
131 TT
Statistics
Matches: 955, Mismatches: 88, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
152 1 0.00
153 188 0.20
154 726 0.76
155 40 0.04
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
ATTTTGGTGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
TTCGGGGCCCATTAGTACCGTTTT
Found at i:1176 original size:615 final size:614
Alignment explanation
Indices: 1--1208 Score: 1915
Period size: 615 Copynumber: 2.0 Consensus size: 614
* *
1 GAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTTTCCACTGTTGATGGGCTAACTATAATCA
1 GAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTATCCACTGTTGATGGCCTAACTATAATCA
* * *
66 TTTTTGCTGAGATTAGTGCACTGTGAAATTTTTAGCTGATTTGGAACACTTGTTATTTTGGGCCT
66 TTTTTGC-GAGAATAGTGCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTCATTTTGGGCCT
* * * * * *
131 TTCGTGGATCATTGGTACCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTTTATCC
130 TTCGGGGACCATTAGTACCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAAGCTTTTGTATCC
* * * *
196 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGCAGTTTTTAGCTCGTT
195 ATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATATGTCCACTGTGAAATTTTTAGCTCATT
* *
261 TGGAACACATGTTATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTATGAATCGACTTCGATTTG
260 TGGAACACATGTTATTTTAGGCCTTTCGGGGCCCATTAGATCCGTTATGAATCGACTTCGATATG
*
326 GCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTATAATCATTTTGGTGAGATATGT
325 GCAAACCTCAAAACTTTTCTTTACATTGTTTATGAACTAACTATAATCATTTTGGTGAGATATGT
* *
391 CCACTGTGAAGTTTTTAGCTTATTTGGAACAATTGTTATTTTGGGCCTTTCGAGGCCCATTAGTA
390 CCACTGTGAAATTTTTAGCTCATTTGGAACAATTGTTATTTTGGGCCTTTCGAGGCCCATTAGTA
* *
456 CCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTTTCCACTGTTGATGGGCTAACT
455 CCGTTTTAAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTTTCCACTGTTGATGGACTAACT
* * *
521 ATAATCATTTTGCTGAGATTAGTGCACTGTGAAATTTTTAGCTGATTTGGAACACTTGTTATTTT
520 ATAATCATTTTGCTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTAATTTT
586 GGGCCTTTCGTGGATCATTGGTACCGTTTT
585 GGGCCTTTCGTGGATCATTGGTACCGTTTT
* * * *
616 GAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATGGCCTAACTGTAATC
1 GAATCGACTTCGATTTAGCAAACCT-AAAGCTTTTCTATCCACTGTTGATGGCCTAACTATAATC
*
681 A-TTTTG-GAGAAATATGTGCACTGTGAAATTTTTATCTCATTTGGAACACTTGTCATTTTGGGC
65 ATTTTTGCGAG-AATA-GTGCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTCATTTTGGGC
*
744 CTTTCGGGGCCCATTAGTACCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAAGCTTTTCGT-
128 CTTTCGGGGACCATTAGTACCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAAGCTTTT-GTA
808 TCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGAT-TAGTCCACTGTGAAATTTTTAGCT
192 TCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATAT-GTCCACTGTGAAATTTTTAGCT
* * *
872 CATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCTCATTAG-TACCGTTTTGAATCGACTTCG
256 CATTTGGAACACATGTTATTTTAGGCCTTTCGGGGCCCATTAGAT-CCGTTATGAATCGACTTCG
*
936 ATATGGCAAACCTCAAAGCTTTTCTTTACATTGTTTATGAACTAACTATAATCATTTTGGTGAGA
320 ATATGGCAAACCTCAAAACTTTTCTTTACATTGTTTATGAACTAACTATAATCATTTTGGTGAGA
* *
1001 TATGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGTGGCCCAT
385 TATGTCCACTGTGAAATTTTTAGCTCATTTGGAACAATTGTTATTTTGGGCCTTTCGAGGCCCAT
* * * *
1066 TAGTTCCGTTTTAAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGA
450 TAGTACCGTTTTAAATCGACTTCGATTTAGCAAACCT-AAAGCTTTTCTTTCCACTGTTGATGGA
* *
1131 CTAACTATAATCATTTTGGTGAGA-TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
514 CTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGT
1195 AATTTTGGGCCTTT
579 AATTTTGGGCCTTT
Statistics
Matches: 543, Mismatches: 43, Indels: 14
0.90 0.07 0.02
Matches are distributed among these distances:
613 3 0.01
614 5 0.01
615 452 0.83
616 83 0.15
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (614 bp):
GAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTATCCACTGTTGATGGCCTAACTATAATCA
TTTTTGCGAGAATAGTGCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTCATTTTGGGCCTT
TCGGGGACCATTAGTACCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAAGCTTTTGTATCCA
TTGTTTATGGCCTAACTATAATCATTTTGCTGAGATATGTCCACTGTGAAATTTTTAGCTCATTT
GGAACACATGTTATTTTAGGCCTTTCGGGGCCCATTAGATCCGTTATGAATCGACTTCGATATGG
CAAACCTCAAAACTTTTCTTTACATTGTTTATGAACTAACTATAATCATTTTGGTGAGATATGTC
CACTGTGAAATTTTTAGCTCATTTGGAACAATTGTTATTTTGGGCCTTTCGAGGCCCATTAGTAC
CGTTTTAAATCGACTTCGATTTAGCAAACCTAAAGCTTTTCTTTCCACTGTTGATGGACTAACTA
TAATCATTTTGCTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTAATTTTG
GGCCTTTCGTGGATCATTGGTACCGTTTT
Done.