Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011463.1 Corchorus olitorius cultivar O-4 contig11496, 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: 2597
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Found at i:292 original size:154 final size:153
Alignment explanation
Indices: 1--406 Score: 580
Period size: 154 Copynumber: 2.6 Consensus size: 153
* *
1 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGTTTTTCTTT
1 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
* * ** *
66 AAGTTGTTTATGGCCTAGTTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
66 CA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
131 TTCGGAACACTTGTTATTTTAAGC
130 TTCGGAACACTTGTTATTTTAAGC
* ** * *
155 CTTTCGGGGCCCATTAGTTCCGATTTGAGTCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
1 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
* * *
220 CCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTGGTCCACTGTGAAGTTTTTAGCTTA
66 -CATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
* ** *
285 TTTGGAACACTTGTTATTTTGGGG
130 TTCGGAACACTTGTTATTTTAAGC
* *
309 CTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACC-CTAATGCTTTTCTT
1 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AATGCTTTTC-T
373 TTCATTGTTTATGGACTAACTATAATCATTTTGG
64 TTCATTGTTTATGGACTAACTATAATCATTTTGG
407 ATTTTGGGCC
Statistics
Matches: 223, Mismatches: 26, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
153 1 0.00
154 218 0.98
155 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (153 bp):
CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
CATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCAT
TCGGAACACTTGTTATTTTAAGC
Found at i:487 original size:107 final size:107
Alignment explanation
Indices: 300--619 Score: 545
Period size: 107 Copynumber: 3.0 Consensus size: 107
290 AACACTTGTT
*
300 ATTTTGGGGCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
365 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
66 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
407 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
* *
472 CTTTTATTTTTATTGTTTATGGACTAACTATAATCATTTTGG
66 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
* * *
514 ATTTTAGGCCTATC-AGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CCTCAA
1 ATTTTGGGCCTATCGA-GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCT-AA
*
577 TGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG
64 TGCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTG
620 ATGAGATTAG
Statistics
Matches: 202, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
106 4 0.02
107 198 0.98
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (107 bp):
ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
Found at i:799 original size:154 final size:153
Alignment explanation
Indices: 514--928 Score: 625
Period size: 154 Copynumber: 2.7 Consensus size: 153
504 ATCATTTTGG
* *
514 ATTTTAGGCCTATCAGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * *
579 CTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTT
66 CTTTTCTTT-CATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTACAATGTGAAGTT
*
644 TTTAGCTCATTTGGAACACTTCTT
130 TTTAGCTCATTCGGAACACTTCTT
* ** *
668 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTCTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * *
733 CTTTTCTCTTCATTATTTATGGACTAACTGTAATCATTTTGGTGAGATTAGTACAATGTGATGTT
66 CTTTTCT-TTCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTACAATGTGAAGTT
*
798 TTTAGCTCATTCGGAACACTTGTT
130 TTTAGCTCATTCGGAACACTTCTT
* * * *
822 ATTTTTGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACC-CTAAT
1 ATTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AAT
886 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
65 GCTTTTC-TTTCATTGTTTATGGACTAACTATAATCATTTTGG
929 ATTTTGGGCC
Statistics
Matches: 235, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
153 1 0.00
154 231 0.98
155 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (153 bp):
ATTTTAGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
CTTTTCTTTCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTACAATGTGAAGTTT
TTAGCTCATTCGGAACACTTCTT
Found at i:991 original size:522 final size:522
Alignment explanation
Indices: 1--1038 Score: 1767
Period size: 522 Copynumber: 2.0 Consensus size: 522
* * *
1 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGTTTTTCTTT
1 CTATCAGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT
* **
66 AAGTTGTTTATGGCCTAGTTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
66 AAGTTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
* * *
131 TTCGGAACACTTGTTATTTTAAGCCTTTCGGGGCCCATTAGTTCCGATTTGAGTCGTCTTCGATT
131 TTCGGAACACTTCTTATTTTAAGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATT
* *
196 TGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTG
196 TGGCAAACCTCAATGCTTTTCTTTCCATTATTTATGGACTAACTATAATCATTTTGGTGAGATTA
* * * * *
261 GTCCACTGTGAAGTTTTTAGCTTATTTGGAACACTTGTTATTTTGGGGCTATCGAGGCCCATTAG
261 GTACAATGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAG
*
326 TGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGACTA
326 TGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGACTA
391 ACTATAATCATTTTGGATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAT
391 ACTATAATCATTTTGGATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAT
*
456 TCGGCAAACCCTAATGCTTTTATTTTTATTGTTTATGGACTAACTATAATCATTTTGGATTTTAG
456 TCGGCAAACCCTAATGCTTTTATTTTCATTGTTTATGGACTAACTATAATCATTTTGGATTTTAG
521 GC
521 GC
*
523 CTATCAGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
1 CTATCAGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT
* * *
588 CCA-TTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTC
66 -AAGTTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTC
* **
652 ATTTGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCG-TTCTGAATCGTCTTCGA
130 ATTCGGAACACTTCTTATTTTAAGCCTATCGGGGCCCATTAGTTCCGATT-TGAATCGTCTTCGA
*
716 TTTGGCAAACCTCAATGCTTTTCTCTT-CATTATTTATGGACTAACTGTAATCATTTTGGTGAGA
194 TTTGGCAAACCTCAATGCTTTTCT-TTCCATTATTTATGGACTAACTATAATCATTTTGGTGAGA
* *
780 TTAGTACAATGTGATGTTTTTAGCTCATTCGGAACACTTGTTATTTTTGGCCTATCGAGGCCCAT
258 TTAGTACAATGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGAGGCCCAT
845 TAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGA
323 TAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGA
910 CTAACTATAATCATTTTGGATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
388 CTAACTATAATCATTTTGGATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
*
975 GATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGGATT
453 GATTCGGCAAACCCTAATGCTTTTATTTTCATTGTTTATGGACTAACTATAATCATTTTGGATT
1039 GTTTATGGAC
Statistics
Matches: 484, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
521 2 0.00
522 479 0.99
523 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (522 bp):
CTATCAGGGCCCATTACTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT
AAGTTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCA
TTCGGAACACTTCTTATTTTAAGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATT
TGGCAAACCTCAATGCTTTTCTTTCCATTATTTATGGACTAACTATAATCATTTTGGTGAGATTA
GTACAATGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAG
TGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATGCTTTTCTTTTCATTGTTTATGGACTA
ACTATAATCATTTTGGATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAT
TCGGCAAACCCTAATGCTTTTATTTTCATTGTTTATGGACTAACTATAATCATTTTGGATTTTAG
GC
Found at i:1008 original size:107 final size:107
Alignment explanation
Indices: 822--1038 Score: 416
Period size: 107 Copynumber: 2.0 Consensus size: 107
812 AACACTTGTT
*
822 ATTTTTGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATG
887 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
66 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
*
929 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCCTAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATG
994 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
66 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
1036 ATT
1 ATT
1039 GTTTATGGAC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (107 bp):
ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATG
CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
Found at i:1397 original size:154 final size:153
Alignment explanation
Indices: 1036--1431 Score: 672
Period size: 153 Copynumber: 2.6 Consensus size: 153
1026 ATCATTTTGG
1036 ATTGTTTATGGACTAAC---AATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
* *
1098 TGGAACATTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
1163 GAAACCTCAATGCTTTTCTTTCC
131 GAAACCTCAATGCTTTTCTTTCC
* * *
1186 ATTGTTTAGGGACTAACTATAATCAATTTGATGAGATTAGTCCATTGTGAAGTTTTTAGGTCATT
1 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
*
1251 TTGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
1316 GCAAACCTCAATGCTTTTCTTTCC
131 G-AAACCTCAATGCTTTTCTTTCC
* * * *
1340 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGTT
1 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
1405 TGGAACACTTGTTATTTTGGGCCTATC
66 TGGAACACTTGTTATTTTGGGCCTATC
1432 TGATACGGGG
Statistics
Matches: 228, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
150 16 0.07
153 106 0.46
154 106 0.46
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (153 bp):
ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
GAAACCTCAATGCTTTTCTTTCC
Done.