Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011928.1 Corchorus olitorius cultivar O-4 contig11961, 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: 2552
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Found at i:2513 original size:154 final size:154
Alignment explanation
Indices: 3--2505 Score: 3607
Period size: 154 Copynumber: 16.3 Consensus size: 154
1 GA
* * * *
3 CCTAACTATAATCTTTTTGGTGAGATAAGGCAACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** ** *
68 TTATTTTGGGCCTATCGGGGCCCATCAGTGACGTTTCT-AATCGTCTTCGATTCAGCAAACCACA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT-TGAATCGTCTTCGATTTGGCAAACCTCA
132 ATGCTTTTCTTTCCATTGTTTATGG
130 ATGCTTTTCTTTCCATTGTTTATGG
* *
157 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGAAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*** * * *
222 TTATTTTGGGCCTATCGGAAACCA-T-G--ACGTCTTGAATCATCTTCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* ** *
283 TACTTTGATTTCCATTGTGTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* *
307 CCTAAATATAATCATTTTGGTGAGATTAGT-CACCGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** * * *
371 TTATTTTGAGCCTATCGGGAACCATTAGATCCGTTTTGAATCGTCTTCGATTTGACAAACCCCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
436 TGCTTTTCCTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* * *
460 CCTAACTATAGTCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAGACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
525 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
590 TGCATTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* * * * * *
614 CATAACTATAATCATTTTGGAGAGGTTAGTCCTCTGTGAAGTTTTTAGCACATTTGCAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
** * *
679 TTATTTTGGGCCTATCGAAGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTTGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* * *
744 TGCTTTTCTTTCAATGGTTTATGA
131 TGCTTTTCTTTCCATTGTTTATGG
* *
768 CCTAAGTATAATC-TCTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCATTTGGAACACTT
1 CCTAACTATAATCAT-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
* ** * **
832 GTTATTTTGGGCCTATCGGGGCCCATCAGTGACGTTTTCAATCGTCTTCGATTCAGCAAACCTCA
65 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
* *
897 GTGCTTTTCTTTCCATTGGTTATGG
130 ATGCTTTTCTTTCCATTGTTTATGG
* * *
922 CCTAACTATAACCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACATG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** * *
987 TTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTTTTCGATTTGGCAAACGTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* *
1052 AGCTTTTCTTT-AAGTTGTTTATGG
131 TGCTTTTCTTTCCA-TTGTTTATGG
* * *
1076 CCTAACTATAATCATTTTGATGAGGTTAATCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
**
1141 TTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
1206 TGCTTTTCTGTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* * * * *
1230 CCTAACAACAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTAGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
1295 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTTAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
1360 AGCTTTTCTTTCCATT-TTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
*
1383 ACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * * * *
1448 TTATTTTGGGCGTATTGTGGCCCATTAGTTCCGTTTTAAATCGTCTTCGATTTGGTAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC-A
* *
1513 AT--TTTTCTCT-AAGTTGTTTATGG
130 ATGCTTTTCTTTCCA-TTGTTTATGG
* * *
1536 CCTAAATATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** *
1601 TTATTTT-GGCCTATCGGGGCCCATCAGTGACGTTTCGAATCGTCTTCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
1665 TGCTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
*
1689 CCTATCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
1754 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGACAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
1819 TGCTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
*
1843 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTGGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** * *
1908 TTATTTTGGGCCTATCGGGGCCCATCAGTGACGTTTCGAATTGTCTTCGATTTGGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
1973 TGCTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
*
1997 CCTATCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * * *
2062 CTATTTTTGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGACAAACCCCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
2127 TGTTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* *
2151 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACATG
1 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* **** * * ** *
2216 TTATTTTGGGCCTTTATTAGACCACTAGTTCCGTTTTGAATCAACTTCGATCTGGCAAACCTCAA
66 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
*
2281 AGCTTTTCTTTCCATTGTTTATGG
131 TGCTTTTCTTTCCATTGTTTATGG
* * *
2305 CCTAACTATAATCATCTTT-GTGAGA-TATGTCCACTGTGAAGTTTTTAACTCTTTTGGAACAAT
1 CCTAACTATAATCAT-TTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
* * * * *
2368 TGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTACGATTTGGCAAACCTC
64 TGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
*
2433 AAAGCTTTTCTTTCCATTGTTTATGG
129 AATGCTTTTCTTTCCATTGTTTATGG
* *
2459 CCTAACTATAATCGTTTTGGTGAGA-TATGTCCACTGTGAAGCTTTTA
1 CCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTA
2506 ACTCTTTTTG
Statistics
Matches: 2105, Mismatches: 224, Indels: 40
0.89 0.09 0.02
Matches are distributed among these distances:
149 54 0.03
150 78 0.04
151 5 0.00
152 56 0.03
153 366 0.17
154 1541 0.73
155 5 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (154 bp):
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
TGCTTTTCTTTCCATTGTTTATGG
Done.