Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011629.1 Corchorus olitorius cultivar O-4 contig11662, 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: 1770
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:735 original size:154 final size:153
Alignment explanation
Indices: 1--1770 Score: 2309
Period size: 154 Copynumber: 11.5 Consensus size: 153
* * * * * *
1 TTGGAACACTTGTTATTTTTAGCCTATCGTGGCCCATTAGTAACGTTTTGAATCATCTTCGCTTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
* * * *
66 GGTAACCCTTAATGCCTTTCTTTACATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
131 TCCACTGTGAAGTTTTTATTCTCAT
130 TCCACTGTGAAGTTTTTA-GCTCAT
* * *
156 TTGCAACACATT-TTATTTTGGGCCTATCT--GGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
1 TTGGAACAC-TTGTTATTTTGAGCCTAT-TGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* *
218 TAGGCAAACCTCAATGCTTTTCTATCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
64 TTGGC-AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
283 AGTCCACTGTGAAGTTTTTAGCTCAT
128 AGTCCACTGTGAAGTTTTTAGCTCAT
* * * *
309 TTGGAACACTTG-----TTGAGCCTATCGGGACCCATTAGTGACGTTTTGAATCCTCTTCGATTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
* *
369 -GTAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* *
433 TCCAATGTGAAGTGTTTAGCTCAT
130 TCCACTGTGAAGTTTTTAGCTCAT
* * * *
457 TTGGAACACATT-TTATTTTG-GCCAATCT-AGGCCCATTAGTTCCGTTTTGAATCGTATTCGAT
1 TTGGAACAC-TTGTTATTTTGAGCCTAT-TGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* * * *
519 TAGACAAACCTCAATGCTTTTCTCTCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATT
64 TTGGC-AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
*
584 AGTCCAATGTGAAGTTTTTAGCTCAT
128 AGTCCACTGTGAAGTTTTTAGCTCAT
* * * ** * *
610 TTGGAACACTTGTTATTTTGAGTCTATTAGGGCCCATTAGTGAATTTTTGTATCGTCTTCGCTTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
* *
675 GGCAACCGTCAATGCCTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* *
740 TCCACTGTGAAGTTTTAAGCTTAT
130 TCCACTGTGAAGTTTTTAGCTCAT
* * * * * * *
764 TTTGAGCACTTGTTATTTTGGGCTTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTTCGATTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
* *
829 GGCAACCCTCAATGCTTTTCTTTCCATTGTTCATGGCCTAACTATAATCATTTTGGTGAGATTCG
66 GGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * *
894 TACACTGTGAAGTTTTTATCACAT
130 TCCACTGTGAAGTTTTTAGCTCAT
* * *
918 TTGGAACACTTGTTATTTTAAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
*
983 -GCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* *
1047 TCCACTATGAAGTTTTTAACTCAT
130 TCCACTGTGAAGTTTTTAGCTCAT
* * * *
1071 ATGGAACACATT-TTATTTTGGGCCTATCT-GGGCCCATGAGTTCCGTTTTGAATCGTCTTCGAT
1 TTGGAACAC-TTGTTATTTTGAGCCTAT-TGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* *
1134 TAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATT
64 TTGGC-AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
1199 AGTCCACTGTGAAGTTTTTAGCTCAT
128 AGTCCACTGTGAAGTTTTTAGCTCAT
* * **
1225 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CTGTTCCGAATCGTCTTCGATT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTAC-GTTTTGAATCGTCTTCGATT
*
1289 TGGCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
65 TGGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
*
1354 GACCACTGTGAAGTTTTTAGCTCAT
129 GTCCACTGTGAAGTTTTTAGCTCAT
* * * * * *
1379 TTGGAACACTTGTTATTTTGAGCCTATCGGGACCCATTAGTGACTTTTTTGAATCCTCTTCGAGT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTAC-GTTTTGAATCGTCTTCGATT
* * *
1444 T-GCAATCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGCGATAA
65 TGGCAA-CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
*
1508 GTCGACTGTGAAGTTTTTAGCTCAT
129 GTCCACTGTGAAGTTTTTAGCTCAT
* * * * * *
1533 TTGGAATAGATT-TTATTTTGGGCCTATCT-AGGCCCATTAGTTCCGTTTTGAATCGTATTCGAT
1 TTGGAACA-CTTGTTATTTTGAGCCTAT-TGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* * *
1596 TAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAATTATAATCATTTTGGTGAGATT
64 TTGGC-AACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
*
1661 AATCCACTGTGAAGTTTTTAGCTCAT
128 AGTCCACTGTGAAGTTTTTAGCTCAT
* * * * *
1687 TTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCACTAGTTTCGTTTTGATTCGTCTTCAATTT
1 TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
1752 GGCAACCCTCAATGCTTTT
66 GGCAA-CCTCAATGCTTTT
Statistics
Matches: 1414, Mismatches: 164, Indels: 75
0.86 0.10 0.05
Matches are distributed among these distances:
147 2 0.00
148 98 0.07
149 32 0.02
152 38 0.03
153 277 0.20
154 916 0.65
155 49 0.03
156 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (153 bp):
TTGGAACACTTGTTATTTTGAGCCTATTGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTT
GGCAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
CCACTGTGAAGTTTTTAGCTCAT
Found at i:1044 original size:461 final size:459
Alignment explanation
Indices: 1--1770 Score: 2583
Period size: 461 Copynumber: 3.8 Consensus size: 459
* * * *
1 TTGGAACACTTGTTATTTTTAGCCTATCGTGGCCCATTAGTAACGTTTTGAATCATCTTCGCTTT
1 TTGGAACACTTGTTA-TTTTAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
* * *
66 GGTAACCCTTAATGCCTTTCTTTACATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
65 -GCAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* *
131 TCCACTGTGAAGTTTTTATTCTCATTTGCAACACATTTTATTTTGGGCCTATCTGGCCCATTAGT
129 TCCACTGTGAAGTTTTTA-GCTCATTTGGAACACATTTTATTTTGGGCCTATCTGGCCCATTAGT
* *
196 TCCGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTATCCATTGTTTATGGCCTAA
193 TCCGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAA
261 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG-----
258 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
* * ** * * *
321 TTGAGCCTATCGGGACCCATTAGTGACGTTTTGAATCCTCTTCGATTT-GTAACCCTCAATGCCT
323 TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTT
* * *
385 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTGTTT
388 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTT
450 AGCTCAT
453 AGCTCAT
* * ** ** * *
457 TTGGAACACATT-TTATTTTGGCCAATCTAGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTA
1 TTGGAACAC-TTGTTATTTTAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
* * * *
521 GACAAACCTCAATGCTTTTCTCTCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAG
65 G-CAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * *
586 TCCAATGTGAAGTTTTTAGCTCATTTGGAACAC-TTGTTATTTTGAGTCTAT-TAGGGCCCATTA
129 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACATT-TTATTTTGGGCCTATCT--GGCCCATTA
**** * * * *
649 GTGAATTTTTGTATCGTCTTCGCTTTGGC-AACCGTCAATGCCTTTCTTTCCATTGTTTAT-GAC
191 GTTCCGTTTTGAATCGTCTTCGATTAGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATAG-C
* * * *
712 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAAGCTTATTTTGAGCACTTGT
254 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
777 TATTTTGGGCTTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTTCGATTTGGCAACCCTCAAT
319 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
* *
842 GCTTTTCTTTCCATTGTTCATGGCCTAACTATAATCATTTTGGTGAGATTCGTACACTGTGAAGT
384 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGT
* *
907 TTTTATCACAT
449 TTTTAGCTCAT
918 TTGGAACACTTGTTATTTTAAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
1 TTGGAACACTTGTTATTTT-AGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
*
983 GCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
65 GCAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* * * *
1048 CCACTATGAAGTTTTTAACTCATATGGAACACATTTTATTTTGGGCCTATCTGGGCCCATGAGTT
130 CCACTGTGAAGTTTTTAGCTCATTTGGAACACATTTTATTTTGGGCCTATCT-GGCCCATTAGTT
1113 CCGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAAC
194 CCGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAAC
1178 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
259 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* ** *
1243 TGGGCCTATCGGGGCCCATTAGTTCTGTTCCGAATCGTCTTCGATTTGGCAACCCTCAATGCATT
324 TGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTT
1308 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG-ACCACTGTGAAGTTTTT
389 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTA-CACTGTGAAGTTTTT
1372 AGCTCAT
453 AGCTCAT
* * * *
1379 TTGGAACACTTGTTATTTTGAGCCTATCGGGACCCATTAGTGACTTTTTTGAATCCTCTTCGAGT
1 TTGGAACACTTGTTATTTT-AGCCTATCGGGGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATT
* * *
1444 TGCAATCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGCGATAAG
64 TGCAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * *
1509 TCGACTGTGAAGTTTTTAGCTCATTTGGAATAGATTTTATTTTGGGCCTATCTAGGCCCATTAGT
129 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACATTTTATTTTGGGCCTATCT-GGCCCATTAGT
*
1574 TCCGTTTTGAATCGTATTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAA
193 TCCGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAA
* *
1639 TTATAATCATTTTGGTGAGATTAATCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
258 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
* * * * *
1704 TTGGGCCTATTGGGGCCCACTAGTTTCGTTTTGATTCGTCTTCAATTTGGCAACCCTCAATGCTT
323 TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTT
1769 TT
388 TT
Statistics
Matches: 1172, Mismatches: 121, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
453 3 0.00
454 32 0.03
455 228 0.19
456 12 0.01
457 2 0.00
460 44 0.04
461 485 0.41
462 366 0.31
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (459 bp):
TTGGAACACTTGTTATTTTAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
CAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
CACTGTGAAGTTTTTAGCTCATTTGGAACACATTTTATTTTGGGCCTATCTGGCCCATTAGTTCC
GTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTA
TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
GGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTC
TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGC
TCAT
Done.