Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011455.1 Corchorus olitorius cultivar O-4 contig11488, 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: 2473
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1003 original size:154 final size:154
Alignment explanation
Indices: 555--2471 Score: 2728
Period size: 154 Copynumber: 12.4 Consensus size: 154
545 TGGCGCATCA
* *
555 TAGTCCATTGTGAAGTTTTTAACTCATTTTGAACACTTGTTATTTTGGGCC-ATTCGGGGCCCAT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCCAT
*
619 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
65 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
*
684 CTAACTATAATCATTTTGGTAAGAT
130 CTAACTATAATCATTTTGGTGAGAT
*
709 TAGTCCATTGTGAAGTTTTTAGCTCATTTTTGAACACTTGTTATTTTGGGCC-ATTCGGGGCCCA
1 TAGTCCATTGTGAAGTTTTTAGCTCA-TTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCCA
* * *
773 TTAGTTCGGTTTTGAATCATCCTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
64 TTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
*
838 CCTAACTATAATCATTTTGGTAAGAT
129 CCTAACTATAATCATTTTGGTGAGAT
* * *
864 TAGTCGATTGTGAAGTTTTTAGCTCATTTTGAACACTTCTTATTTTGGGCC-ATTCGGGGCCCAT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCCAT
* *
928 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGG
65 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
* * *
993 CTCACCATAATCATTTTGGTAAGAT
130 CTAACTATAATCATTTTGGTGAGAT
*
1018 TAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCC-ATTCGGGGCCCAT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCCAT
* * * * **
1082 TAGTTCGGTTCTGAATCATCTTCGATTTGGTAAACCACAATGCTTTTCTTTCGGTTGTTTATGGC
65 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
* *
1147 CTAACTGTAATCATTTTGGTAAGAT
130 CTAACTATAATCATTTTGGTGAGAT
* *
1172 TAGTCCATTGTGAA-TTTTTATCTTCATTTTGAACACTTGTTATTTTGGGCC-ATTCGGGGCCCA
1 TAGTCCATTGTGAAGTTTTTAGC-TCATTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCCA
* * *
1235 TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
64 TTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
*
1300 CCTAACTATAATCATTTTGGTAAGAT
129 CCTAACTATAATCATTTTGGTGAGAT
*
1326 TAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
*
1391 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
66 AGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
1456 TAACTATAATCATTTTGGTGAGAT
131 TAACTATAATCATTTTGGTGAGAT
* * * ** *
1480 TAGTCCACTCTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGTACCTATCAGGGCCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
* * * *
1545 AGTGAC-GTTTTGAACCGTCTTCGATTTCGCAAACTTCAATGCTTTTCTTTCCATTGTTTATGGC
66 AGT-TCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
* *
1609 CTAACTATAATCATTTTAGTGTGAT
130 CTAACTATAATCATTTTGGTGAGAT
* * * * * *
1634 TAGTCCACTGTGAAGGTTTTAGCTAATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGTCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
* * * *
1699 AGTTCCGTTTTGAATCGTCTTCAATTTGGCAAACCTCAATGCGTTTCTTTCCACTGTTTATGGCC
66 AGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
* *
1764 TAACTATAATCATCTTAGTGAGAT
131 TAACTATAATCATTTTGGTGAGAT
* * * * *
1788 CAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTAACAGGGCCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
* *
1853 AGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGC
66 AGT-TCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
1917 CTAACTATAAAT-ATTTTGGTGAGAT
130 CTAACTAT-AATCATTTTGGTGAGAT
* * *
1942 TAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
** *
2007 ACGAAC-GTTTCGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
66 A-GTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
*
2071 CTAACTATAATCATTTTAGTGAGAT
130 CTAACTATAATCATTTTGGTGAGAT
* * * * * *
2096 TAGCCCACTGTAAAGGTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATT
1 TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
* * * * *
2161 ACTGAC-GTTTTGAATCGTCTTCGATTTGGTAACCCTCGATGCTTTTCTTTCCATTGTTTATGGC
66 AGT-TCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
* *
2225 CTAACTATTATCA-TTTGGTGAGNGT
130 CTAACTATAATCATTTTGGTGAG-AT
* * * *
2250 TAGTCCACTGTGAAGTTTTTAGTCTTATTTGGAACAC-TGTTATTTTGTGCCTATCGAGGCCCAT
1 TAGTCCATTGTGAAGTTTTTAG-CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
** ** *
2314 TAGTTTTGTTTTGAATTATCTTCGATTTGGCAAACCTCAATGC-TTTCTTTTCCATTGTTTATGT
65 TAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTC-TTTCCATTGTTTATGG
2378 CCTAACTATAATCATTTTGGTGAGAT
129 CCTAACTATAATCATTTTGGTGAGAT
2404 TAGTCCACTTGTGAAGTTTTTAGCTTCATTTGGAACTACTTGTTATTTTGGGCCTATCGGGGCCC
1 TAGTCCA-TTGTGAAGTTTTTAGC-TCATTTGGAAC-ACTTGTTATTTTGGGCCTATCGGGGCCC
2469 ATT
63 ATT
2472 CA
Statistics
Matches: 1625, Mismatches: 118, Indels: 37
0.91 0.07 0.02
Matches are distributed among these distances:
153 23 0.01
154 1363 0.84
155 211 0.13
156 2 0.00
157 26 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
AGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
TAACTATAATCATTTTGGTGAGAT
Done.