Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011924.1 Corchorus olitorius cultivar O-4 contig11957, 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, 606
Length: 1011
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Found at i:493 original size:154 final size:154
Alignment explanation
Indices: 203--1011 Score: 1050
Period size: 154 Copynumber: 5.4 Consensus size: 154
193 GCTTTTCTTT
*
203 CCTAACTATAATCATTCTGGTGAGA-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
* *
267 GTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATAC-TCTTCGATTTGGCAAACCTC
65 GTTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAAT-CGTCTTCGATTTGGCAAACCCC
* *
331 AATTCTTTTTTTTTCAATGTTTATGG
129 AATGCTTTTTTTTCCAATGTTTATGG
* * *
357 CCTAAGTATAATCATTTAGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGTG-ACACAT
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG-GAACACTT
* * * * *
421 ATTAATTTGGGCCTTTCGAGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGCCAAACCCCA
65 GTTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCA
*
486 ATGCTTTTTTTTTCAATTGTTTATGG
130 ATGCTTTTTTTTCCAA-TGTTTATGG
512 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
577 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
66 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
*
642 TG-TTTTTCTTTCCATTGTTTATGG
131 TGCTTTTT-TTTCCAATGTTTATGG
* *
666 CCTAACTATAATCCTTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * * * * * *
731 TTATTTTGGGCCTATCGGGGCCCGTTAGTGAC-GTTTGGAAACGTCTTCGATTTGACAAACCTCA
66 TTATTTTGGGCCTTTCGGGGCCCATTAGT-TCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCA
* *
795 ATGCTTTTCTTTCCATTGTTTATGG
130 ATGCTTTTTTTTCCAATGTTTATGG
* * * * *
820 CATAACTATAATCCTTTTGGTGAGTTTAGCCCACTGTGAAGTTTTTAGCTCATTTGGAACATTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * *** * *
885 TTATTTTTGCCCTTTC---GCCCATTAGTGAAGTTTTGAATCGTCATCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
*
947 AGC----TTTT-C-----TT-T--
131 TGCTTTTTTTTCCAATGTTTATGG
958 CCTAACTATAATCATTTTGGTGAGA-TATGTCCACTGTGAAGTTTTTAGCTCATT
1 CCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATT
Statistics
Matches: 592, Mismatches: 53, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
137 2 0.00
138 47 0.08
140 1 0.00
141 2 0.00
146 1 0.00
147 3 0.01
151 40 0.07
153 1 0.00
154 351 0.59
155 144 0.24
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
TTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
TGCTTTTTTTTCCAATGTTTATGG
Found at i:778 original size:309 final size:308
Alignment explanation
Indices: 203--959 Score: 1071
Period size: 309 Copynumber: 2.5 Consensus size: 308
193 GCTTTTCTTT
*
203 CCTAACTATAATCATTCTGGTGAGA-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
1 CCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
267 GTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATAC-TCTTCGATTTGGCAAACCTC
65 GTTATTTTGGGCCTTTCGGGGCCCATTAGTTCAGTTTTGAAT-CGTCTTCGATTTGGCAAACCTC
* * * *
331 AAT-TCTTTTTTTTTCAATGTTTATGGCCTAAGTATAATCATTTAGGTGAGATTAGTCCACTGTG
129 AATGT-TTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCACTGTG
* * *
395 AAGTTTTTAGCTCATTTGTGACACATATTAATTTGGGCCTTTCGAGGCCCATTAGTTCTGTTTTG
193 AAGTTTTTAGCTCATTTGTGACACATATTAATTTGGGCCTATCGAGGCCCATTAGTACTGTTTGG
* * *
460 AATCGTCTTCAATTTGCCAAACCCCAATGCTTTTTTTTTCAATTGTTTATGG
258 AAACGTCTTCAATTTGACAAACCCCAATGC-TTTTCTTTCAATTGTTTATGG
512 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* *
577 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
66 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCAGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* * *
642 TGTTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGGTAAGATTAGTCCACTGTGAAG
131 TGTTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCACTGTGAAG
* * * * *
707 TTTTTAGCTCATTTG-GAACACTTGTTATTTTGGGCCTATCGGGGCCCGTTAGTGAC-GTTTGGA
196 TTTTTAGCTCATTTGTG-ACACATATTAATTTGGGCCTATCGAGGCCCATTAGT-ACTGTTTGGA
* * *
770 AACGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
259 AACGTCTTCAATTTGACAAACCCCAATGCTTTTCTTTCAATTGTTTATGG
* * * * *
820 CATAACTATAATCCTTTTGGTGAGTTTAGCCCACTGTGAAGTTTTTAGCTCATTTGGAACATTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * ** *
885 TTATTTTTGCCCTTTC---GCCCATTAGTGAAGTTTTGAATCGTCATCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCAGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* *
947 AGCTTTTCTTTCC
131 TGTTTTTCTTTCC
960 TAACTATAAT
Statistics
Matches: 405, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
305 52 0.13
308 95 0.23
309 254 0.63
310 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (308 bp):
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
TTATTTTGGGCCTTTCGGGGCCCATTAGTTCAGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
TGTTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTAGGTAAGATTAGTCCACTGTGAAG
TTTTTAGCTCATTTGTGACACATATTAATTTGGGCCTATCGAGGCCCATTAGTACTGTTTGGAAA
CGTCTTCAATTTGACAAACCCCAATGCTTTTCTTTCAATTGTTTATGG
Found at i:901 original size:463 final size:443
Alignment explanation
Indices: 43--1011 Score: 1185
Period size: 463 Copynumber: 2.2 Consensus size: 443
33 CTCAGAGCTA
* * * *
43 TTTTTTCCATTGTTAATGGTCTAACTATAATCATTTTTGTGAGATATGTCCAATGTGAAGTTTTT
1 TTTTTT-CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTT
*
108 AGCTCATTTGGAACAATTGTAATTTTGGGCCTTTTGGGGCCCATTAGATCCGTTTTGAATCAACT
65 AGCTCATTTGGAACAATTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCAACT
* * *
173 TTGATTTGGCAAACCTCAAAGCTTTTCTTTCCTAACTATAATCATTCTGGTGAGATATGTCCACT
130 TCGATTTGGCAAACCCCAAAGCTTTTCTTTCCTAACTATAATCATTCTGGTAAGATATGTCCACT
* **
238 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTT
195 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTT
* * * * * * *
303 TTGAATACTCTTCGATTTGGCAAACCTCAATTCTTTTTTTTTCAATGTTTATGGCCTAAGTATAA
260 TGGAATACTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCAATGTTTATGGCATAACTATAA
* *
368 TCATTTAGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGTGACACATATTAATTTGGGC
325 TCATTTAGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGTGACACATATTAATTTGGCC
*** * *
433 CTTTCGAGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGCCAAACCCCAATGC
390 CTTTC---GCCCATTAGTGAAGTTTTGAATCGTCATCAATTTGCCAAACCCCAAAGC
490 TTTTTTTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT-TAGTCCACTGTGAAGT
1 ---TTTTTTC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGT
* * * *
554 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCTGTTTTGAATC
61 TTTTAGCTCATTTGGAACAATTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATC
** * * * *
619 GTCTTCGATTTGGCAAACCCCAATGTTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTT
126 AACTTCGATTTGGCAAACCCCAAAG-----C-TT---TT-CTT-T--CCTAACTATAATCATTCT
684 GGTAAGAT-TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
178 GGTAAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* *
748 GGGCCCGTTAGTGACGTTTGGAA-ACGTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATT
242 GGGCCCATTAGTGACGTTTGGAATAC-TCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCAAT
* * *
812 GTTTATGGCATAACTATAATCCTTTTGGTGAGTTTAGCCCACTGTGAAGTTTTTAGCTCATTTG-
306 GTTTATGGCATAACTATAATCATTTAGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGT
* * * * *
876 GA-ACATTTGTTATTTTTGCCCTTTCGCCCATTAGTGAAGTTTTGAATCGTCATCGATTTGGCAA
371 GACACA--TATTAATTTGGCCCTTTCGCCCATTAGTGAAGTTTTGAATCGTCATCAATTTGCCAA
*
940 ACCTCAAAGC
434 ACCCCAAAGC
950 --TTTTC-----TT-T--CCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
1 TTTTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
1005 GCTCATT
66 GCTCATT
Statistics
Matches: 453, Mismatches: 46, Indels: 44
0.83 0.08 0.08
Matches are distributed among these distances:
446 52 0.11
447 1 0.00
448 1 0.00
449 4 0.01
450 133 0.29
455 6 0.01
456 2 0.00
459 2 0.00
460 43 0.09
461 4 0.01
462 5 0.01
463 200 0.44
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (443 bp):
TTTTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
GCTCATTTGGAACAATTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCAACTT
CGATTTGGCAAACCCCAAAGCTTTTCTTTCCTAACTATAATCATTCTGGTAAGATATGTCCACTG
TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
GGAATACTCTTCGATTTGACAAACCTCAATGCTTTTCTTTCCAATGTTTATGGCATAACTATAAT
CATTTAGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGTGACACATATTAATTTGGCCC
TTTCGCCCATTAGTGAAGTTTTGAATCGTCATCAATTTGCCAAACCCCAAAGC
Done.