Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019884.1 Corchorus olitorius cultivar O-4 contig19917, 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: 1982
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Found at i:617 original size:154 final size:153
Alignment explanation
Indices: 18--1980 Score: 2671
Period size: 154 Copynumber: 12.8 Consensus size: 153
8 GTGACATATG
* *
18 GAATCCTCTTCGATTTGGCAAACCTCAA-TTCTTTC-TTCCATTGTTTATGGACTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCAAGCT-TTTCTTTCCATTGTTTATGGACTAACTATAATC
* * * *
81 -TTTTGGGTGAGATTACTCCTCTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTT-GGTC
65 ATTTT-GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* *
144 T-T-GGGGCCCATTAGTTCTGTTAT
129 TATCGGGGCCCATTAGTTCCGTTTT
* * * *
167 GAATAGTCCTCGATTTGGCAAACCTCAAAGCTTCTCTTTCCATAT-TTTATGGACTAAATATAAT
1 GAATCGTCTTCGATTTGGCAAACCTC-AAGCTTTTCTTTCCAT-TGTTTATGGACTAACTATAAT
* * *
231 CATTTTGGTGACATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACGC-TGTTATTTTGGGCC
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
** * *
295 TATCGGGGCCCATTAGTGACATATT
129 TATCGGGGCCCATTAGTTCCGTTTT
* ** *
320 GAATCCTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATACTTTATGGACTAAATATAATC
1 GAATCGTCTTCGATTTGGCAAACCTC-AAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * * * *
385 ATTTTGGTGACATTAGTCCACTATGAAGTTCTTAGCTCATTTGGAATAC-TGTTATTCTGGGCCT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
449 ATCGGGGCCCATTAGTTCCATTTT
130 ATCGGGGCCCATTAGTTCCGTTTT
* * *
473 GAATCTTGTTCGATTTGGCAAACCTCAGAGCTTTTCTTTCCATTTTTTTATGGACTAACTATAAT
1 GAATCGTCTTCGATTTGGCAAACCTCA-AGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAAT
* * *
538 CAATTTGGTGAGATTAGTCCACTGT-AAATTTTTAGCTCATTTGTAACACTTGTTATTTTGGGCC
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
** *
602 TATCGGGGCCCATTAGTGACGTCTT
129 TATCGGGGCCCATTAGTTCCGTTTT
* * *
627 GGATCGTGTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCAA-GCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * *
692 AATTTGGTGACATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
**
757 ATCGGGGCGTATTAGTTCCGTTTT
130 ATCGGGGCCCATTAGTTCCGTTTT
* * * *
781 GAATCGTTTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTTGTTTATGGCCTAACAATAAT
1 GAATCGTCTTCGATTTGGCAAACCTC-AAGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAAT
* * * *
845 CATTTTGATGAGATTGGTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
*
910 GATCGGGGCCCATTAGTTCCGTTTT
129 TATCGGGGCCCATTAGTTCCGTTTT
* * * *
935 CAATCGTCTTCGATTTCGCAAACCTCAGAGCATTTCTTTCCATTTTTTATGGACTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCA-AGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* *
1000 ATTTTGGTGAGATCAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
1065 ATCGGGGCCTATTAGTTCCGTTTT
130 ATCGGGGCCCATTAGTTCCGTTTT
* * * * *
1089 GAATCGTTTTCGATTTGGCAAACCTTAAAGATTTTCTTT-AAGTTGTTTATGGCCTAACTATAAT
1 GAATCGTCTTCGATTTGGCAAACC-TCAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAAT
* * * *
1153 CATTTTGATGAGATTGGTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* *
1218 TATCGAGGCCTATTAGTTCCGTTTT
129 TATCGGGGCCCATTAGTTCCGTTTT
* * *
1243 GAATCGTCTTCGAATTGGCAAACCTCAGAGCATTT-TTTCCATTTTTTATGGACTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCA-AGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * *
1307 ATTTTGGTGAGATTAGTCCACTGT-AAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGACAT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* ** *
1371 ATCGGGGCCAATTAGTGACGTTCT
130 ATCGGGGCCCATTAGTTCCGTTTT
* *
1395 GAATCGTTTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCAA-GCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
* * * * *
1460 AATTTGGTGAGATTAATCCACTGTGAAGTTCTTAACTCATTTGGAACATTTGTTATTTTGGGCCT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
1525 ATCGGGGCCCATTAGTTCCATTTT
130 ATCGGGGCCCATTAGTTCCGTTTT
* * *
1549 GAATTGTCTTCGATTTGCCAAACCTCAAAGATTTTCTTTCCATTGTTTATGGACTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTC-AAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
1614 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
65 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
** *
1679 ATCGGGGCCCATTAGTGACGTATT
130 ATCGGGGCCCATTAGTTCCGTTTT
*
1703 GAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG-CATAACTATAAT
1 GAATCGTCTTCGATTTGGCAAACCTCAA-GCTTTTCTTTCCATTGTTTATGGAC-TAACTATAAT
* *
1767 CATTTTGATCAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
*
1832 TTTCGGGGCCCATTAGTTCCGTTTT
129 TATCGGGGCCCATTAGTTCCGTTTT
* *
1857 GAATCGTCTTCG-TGTTGGCAAACCTCAATGCTTTTCTTTCCATTGGTTAGGGACTAACTATAAT
1 GAATCGTCTTCGAT-TTGGCAAACCTCAA-GCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
* * **
1921 CATTTTGGTAAGATTAGTCCACTGTAAAGTTTTTAGCTTGTTTGGAACACTTGTTATTTT
64 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
1981 CG
Statistics
Matches: 1605, Mismatches: 179, Indels: 55
0.87 0.10 0.03
Matches are distributed among these distances:
149 23 0.01
150 14 0.01
151 69 0.04
152 92 0.06
153 358 0.22
154 1041 0.65
155 8 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (153 bp):
GAATCGTCTTCGATTTGGCAAACCTCAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCA
TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
TCGGGGCCCATTAGTTCCGTTTT
Found at i:1627 original size:768 final size:767
Alignment explanation
Indices: 18--1980 Score: 2885
Period size: 768 Copynumber: 2.6 Consensus size: 767
8 GTGACATATG
* *
18 GAATCCTCTTCGATTTGGCAAACCTC-AA-TTCTTTC-TTCCATTGTTTATGGACTAACTATAAT
1 GAATCGTCTTCGATTTGGCAAACCTCAAAGAT-TTTCTTTCCATTGTTTATGGACTAACTATAAT
* * * *
80 C-TTTTGGGTGAGATTACTCCTCTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTT-GGT
65 CATTTT-GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
* * * * *
143 C-TTGGGGCCCATTAGTTCTGTTATGAATAGTCCTCGATTTGGCAAACCTCAAAGCTTCTCTTTC
129 CATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AAGCTT-TCTTTC
* * *
207 CATATTTTATGGACTAAATATAATCATTTTGGTGACATTAGTCCACTGTGAAGTTTTTACCTCAT
192 CATTTTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCAT
* ** * * *
272 TTGGAACGC-TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAATCCTCTTCGATTT
257 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT
** * *
336 GGCAAACCTCAAAGCTTTTCTTTCCATACTTTATGGACTAAATATAATCATTTTGGTGACATTAG
322 GGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAG
* * *
401 TCCACTATGAAGTTCTTAGCTCATTTGGAATAC-TGTTATTCTGGGCCTATCGGGGCCCATTAGT
387 TCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGT
* * * *
465 TCCATTTTGAATCTTGTTCGATTTGGCAAACCTCAGAGCTTTTCTTTCCATTTTTTTATGGACTA
452 TCCATTTTGAATCGTCTTCGAATTGGCAAACCTCAGAGCATTTCTTTCCATTTTTTTATGGACTA
*
530 ACTATAATCAATTTGGTGAGATTAGTCCACTGTAAATTTTTAGCTCATTTGTAACACTTGTTATT
517 ACTATAATCAATTTGGTGAGATTAGTCCACTGTAAATTTTTAGCTCATTTGGAACACTTGTTATT
* * * *
595 TTGGGCCTATCGGGGCCCATTAGTGACGTCTTGGATCGTGTTCGATTTGGCAAACCTCAATGCTT
582 TTGGACATATCGGGGCCAATTAGTGACGTCTTGAATCGTGTTCGATTTGGCAAACCTCAATGCTT
* *
660 TTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGACATCAGTCCACTGTGAAGTTTTT
647 TTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGACATCAATCCACTGTGAAGTTCTT
* ** *
725 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCGTATTAGTTCCGTTTT
712 AACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTT
* * * * *
781 GAATCGTTTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTTGTTTATGGCCTAACAATAAT
1 GAATCGTCTTCGATTTGGCAAACCTCAAAGATTTTCTTTCCA-TTGTTTATGGACTAACTATAAT
* * * *
845 CATTTTGATGAGATTGGTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
65 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* *
910 GATCGGGGCCCATTAGTTCCGTTTTCAATCGTCTTCGATTTCGCAAACCTCAGAGCATTTCTTTC
130 -ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA-AGC-TTTCTTTC
*
975 CATTTTTTATGGACTAACTATAATCATTTTGGTGAGATCAGTCCACTGTGAAGTTTTTACCTCAT
192 CATTTTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCAT
* *
1040 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCGTTTTCGATTT
257 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT
* * * * * *
1105 GGCAAACCTTAAAGATTTTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGAGATTG
322 GGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTA
*
1169 GTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCTATTAG
386 GTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAG
*
1234 TTCCGTTTTGAATCGTCTTCGAATTGGCAAACCTCAGAGCATTT-TTTCCA-TTTTTTATGGACT
451 TTCCATTTTGAATCGTCTTCGAATTGGCAAACCTCAGAGCATTTCTTTCCATTTTTTTATGGACT
*
1297 AACTATAATCATTTTGGTGAGATTAGTCCACTGTAAATTTTTAGCTCATTTGGAACACTTGTTAT
516 AACTATAATCAATTTGGTGAGATTAGTCCACTGTAAATTTTTAGCTCATTTGGAACACTTGTTAT
*
1362 TTTGGACATATCGGGGCCAATTAGTGACGT-TCTGAATCGTTTTCGATTTGGCAAACCTCAATGC
581 TTTGGACATATCGGGGCCAATTAGTGACGTCT-TGAATCGTGTTCGATTTGGCAAACCTCAATGC
* *
1426 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAGATTAATCCACTGTGAAGTTC
645 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGACATCAATCCACTGTGAAGTTC
*
1491 TTAACTCATTTGGAACATTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTT
710 TTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTT
* *
1549 GAATTGTCTTCGATTTGCCAAACCTCAAAGATTTTCTTTCCATTGTTTATGGACTAACTATAATC
1 GAATCGTCTTCGATTTGGCAAACCTCAAAGATTTTCTTTCCATTGTTTATGGACTAACTATAATC
1614 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
66 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC-
** * *
1679 ATCGGGGCCCATTAGTGACGTATTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
130 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA-GC-TTTCTTTCC
* * * *
1744 ATTGTTTATGG-CATAACTATAATCATTTTGATCAGATTAGTCCACTGTGAAGTTTTTAGCTCAT
193 ATTTTTTATGGAC-TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCAT
*
1808 TTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG-TGT
257 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT-T
* * * *
1872 TGGCAAACCTCAATGCTTTTCTTTCCATTGGTTAGGGACTAACTATAATCATTTTGGTAAGATTA
321 TGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTA
* * * **
1937 GTCCACTGTAAAGTTTTTAGCTTGTTTGGAACACTTGTTATTTT
386 GTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTT
1981 CG
Statistics
Matches: 1071, Mismatches: 110, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
763 24 0.02
764 7 0.01
765 71 0.07
766 7 0.01
767 5 0.00
768 748 0.70
769 143 0.13
770 66 0.06
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (767 bp):
GAATCGTCTTCGATTTGGCAAACCTCAAAGATTTTCTTTCCATTGTTTATGGACTAACTATAATC
ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCA
TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAGCTTTCTTTCCATT
TTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCATTTGG
AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
AACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCA
CTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCA
TTTTGAATCGTCTTCGAATTGGCAAACCTCAGAGCATTTCTTTCCATTTTTTTATGGACTAACTA
TAATCAATTTGGTGAGATTAGTCCACTGTAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGG
ACATATCGGGGCCAATTAGTGACGTCTTGAATCGTGTTCGATTTGGCAAACCTCAATGCTTTTCT
TTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGACATCAATCCACTGTGAAGTTCTTAACT
CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTT
Done.