Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011923.1 Corchorus olitorius cultivar O-4 contig11956, 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: 3218
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Found at i:139 original size:73 final size:73
Alignment explanation
Indices: 13--159 Score: 210
Period size: 73 Copynumber: 2.0 Consensus size: 73
3 GCTAGAGTAG
**
13 TACTAGGATGGGTGACCTCCTGGGAAGTCGCTTTTGTTGCACCCCTTTATTCATTTATATTTTCT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCGCTCGTGTTGCACCCCTTTATTCATTTATATTTTCT
78 TTTCTTCT
66 TTTCTTCT
* *
86 TACTAGGATGGGTGACCTCTTGGGAACGTTC-CGTCGTGTTGCA-CCCTTT-TTCATTTTTATTT
1 TACTAGGATGGGTGACCTCCTGGGAA-G-TCGC-TCGTGTTGCACCCCTTTATTCATTTATATTT
148 TCTTTTCTTCT
63 TCTTTTCTTCT
159 T
1 T
160 CTTTCGAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
73 49 0.73
74 8 0.12
75 10 0.15
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (73 bp):
TACTAGGATGGGTGACCTCCTGGGAAGTCGCTCGTGTTGCACCCCTTTATTCATTTATATTTTCT
TTTCTTCT
Found at i:797 original size:72 final size:72
Alignment explanation
Indices: 665--809 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
655 GCGAGACTAG
* *
665 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGTACCCCTTTATTCATTTATATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTCCTT
730 TTCTTCT
66 TTCTTCT
* * * * *
737 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCGTTTTTATTTCCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTCCTT
802 TTCTTCT
66 TTCTTCT
809 T
1 T
810 CTTTCGAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (72 bp):
TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTCCTT
TTCTTCT
Found at i:1109 original size:360 final size:361
Alignment explanation
Indices: 376--1458 Score: 1927
Period size: 360 Copynumber: 3.0 Consensus size: 361
366 GCGAGAGTAG
* * * * *
376 TACTAGGATGGGTGACATCCTAGGAAGTCC-CCTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
*
440 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTGAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
* *
505 TATGGCGTGAATGATCATATTTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
*
570 TTATTATGCGAAGACTAGATGGGTGCGATCATACCAGCACTAATCCACCGGATCCCATCAGAACT
196 TTATTATGCGAAGACT-GATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACT
* *
635 CCGCAGTTAAACGTGCTTGGGCGAGACTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
260 CCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
*
700 TTGTACCCCTTTATTCATTTATATTTTCTTTTCTTCT
325 TTGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
* *
737 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCGTTTTTATTTCCTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
*
802 TTCTTCTTCTTTCGAAATTTCTTATGTTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
* * *
867 TATGGCGTGTATGATCATATGTCTGCAACAATGCACCGGATCCAATGAGATGTGCTTATACATA-
131 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
* *
931 TTATTATGCGAAGACTGATGGGTGCGATCATACCAACACTAATGCACCGGTTCCCATCAGAACTC
196 TTATTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
*
996 CGCAATTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
1061 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
326 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
1097 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1162 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
1227 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
*
1292 TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
196 TTATTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
1357 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
* *
1422 TGCACCCCTTTTTTCATTTTTATTTTCTTTTCTTCT
326 TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
1458 T
1 T
1459 CTTTCGAAAT
Statistics
Matches: 687, Mismatches: 33, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
360 331 0.48
361 204 0.30
362 152 0.22
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (361 bp):
TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
TTATTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
CGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
TGCACCCCTTTATTCATTTATATTTTCTTTTCTTCT
Found at i:1149 original size:72 final size:72
Alignment explanation
Indices: 1025--1169 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
1015 GCGAGAGTAG
1025 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTTCTT
1090 TTCTTCT
66 TTCTTCT
* * * *
1097 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTTCTT
1162 TTCTTCT
66 TTCTTCT
1169 T
1 T
1170 CTTTCGAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTATTCATTTATATTTTCTT
TTCTTCT
Found at i:1807 original size:291 final size:289
Alignment explanation
Indices: 1097--2297 Score: 2179
Period size: 289 Copynumber: 4.1 Consensus size: 289
1087 CTTTTCTTCT
* *
1097 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCTTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
1162 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
* *
1227 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATAT
1292 TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
196 TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
1357 CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
1386 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
1451 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
1516 TATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATAT
* *
1581 TTATTATGCGAAGACCGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCTATCAGAACTC
196 TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
1646 CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
*
1675 TACTATGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCTTTTTTCATTTTTATTTTC
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA-CCC-CTTTTTTCATTTTTATTTTC
1740 TTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAA
64 TTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAA
1805 CGTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATAT
129 CGTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATAT
* * * *
1870 ATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCATCGGATCCCATCAAAAC
194 ATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
* *
1935 TCCGCAGTTAAGCGTGTTTGGGCGAGAGTAC
259 TCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
*
1966 TTCTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCA-TTTTATTTTCTT
1 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
*
2030 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTTTTCAAACG
66 TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
* * *
2095 TATGGCGTGTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATAT
131 TATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATAT
*
2160 TTATTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
196 TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
*
2225 CGTAGTTAAGCGTGCTTGGGCGAGAGTAG
261 CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
*
2254 TACTAGGATGGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCC
1 TACTAGGAT-GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
2298 GCGTGTATGA
Statistics
Matches: 878, Mismatches: 31, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
288 232 0.26
289 364 0.41
290 6 0.01
291 276 0.31
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (289 bp):
TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTT
TTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACG
TATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATAT
TTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
CGCAGTTAAGCGTGCTTGGGCGAGAGTAG
Found at i:2270 original size:580 final size:579
Alignment explanation
Indices: 1097--2297 Score: 2208
Period size: 580 Copynumber: 2.1 Consensus size: 579
1087 CTTTTCTTCT
1097 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCA-CCCTTTTTTTCATTTTTATTTTCT
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTTTCATTTTTATTTTCT
1161 TTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAAC
66 TTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAAC
* *
1226 GTATGGCGTGTATGATCATATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATA
131 GTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATA
* * *
1291 TTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACT
196 TTTATTATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAACT
*
1356 CCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
261 CCGCAGTTAAGCGTGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
1421 TTGCACCCCTTTTTTCATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAAT
326 TTGCACCCCTTTTTTCATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAAT
1486 CGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAAAATACA
391 CGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAAAATACA
*
1551 CCGTATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACCGATGGGTGCGATCATACCA
456 CCGAATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACCGATGGGTGCGATCATACCA
*
1616 GCACTAATGCACCGGATCCTATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
521 GCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
* *
1675 TACTATGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCTTTTTTCATTTTTATTTTC
1 TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCT-TTTTTTCATTTTTATTTTC
1740 TTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAA
65 TTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAA
1805 CGTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATAT
130 CGTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATAT
*
1870 ATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCATCGGATCCCATCAAAAC
195 ATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAAC
* *
1935 TCCGCAGTTAAGCGTGTTTGGGCGAGAGTACTTCTAGGATGGGTGACCTCCTGGGAAGTCCTCGT
260 TCCGCAGTTAAGCGTGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGT
2000 GTTGCACCCCTTTTTTCA-TTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAA
325 GTTGCACCCCTTTTTTCATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAA
* * *
2064 TCGTTTCAAGTAAGCATTAAGTTTTCAAACGTATGGCGTGTATGATCATATGTCGGCAACAATGC
390 TCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAAAATAC
*
2129 ACCGAATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACTGATGGGTGCGATCATACC
455 ACCGAATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACCGATGGGTGCGATCATACC
*
2194 AGCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGAGAGTAG
520 AGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
2254 TACTAGGATGGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCC
1 TACTAGGAT-GGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCC
2298 GCGTGTATGA
Statistics
Matches: 600, Mismatches: 20, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
578 38 0.06
579 241 0.40
580 321 0.54
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (579 bp):
TACTAGGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTTTCATTTTTATTTTCT
TTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAAC
GTATGGCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATA
TTTATTATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAACT
CCGCAGTTAAGCGTGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
TTGCACCCCTTTTTTCATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAAT
CGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAAAATACA
CCGAATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACCGATGGGTGCGATCATACCA
GCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAG
Found at i:2442 original size:199 final size:198
Alignment explanation
Indices: 2099--2495 Score: 713
Period size: 199 Copynumber: 2.0 Consensus size: 198
2089 CAAACGTATG
*
2099 GCGTGTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATATTTAT
1 GCGTGTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTACATATATTTAT
*
2164 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGTA
66 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
* * * *
2229 GTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGGTGACCTCTTGGGAAGTCCTCGTGTTGC
131 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGAT-GGGTGACCTCCTGGGAAGTCATCGTGTTGC
2294 ACCC
195 ACCC
* *
2298 GCGTGTATGATCATCTGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTACATATATTTAT
1 GCGTGTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTACATATATTTAT
2363 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
66 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
2428 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
131 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
2493 CCC
196 CCC
2496 CCTTTTATCA
Statistics
Matches: 190, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
198 32 0.17
199 158 0.83
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (198 bp):
GCGTGTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTACATATATTTAT
TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
CCC
Found at i:2771 original size:487 final size:487
Alignment explanation
Indices: 1811--2784 Score: 1664
Period size: 488 Copynumber: 2.0 Consensus size: 487
1801 CAAACGTATG
* *
1811 GCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATATTTAT
1 GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
*
1876 TATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCATCGGATCCCATCAAAACTCCGCA
66 TATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAACTCCGCA
* * * * *
1941 GTTAAGCGTGTTTGGGCGAGAGTACTTCTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
131 CTTAAGCATGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
* *
2006 CCCCTTTTTTCATTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTTTC
196 CCCCTTTTATCATTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGTTTC
* *
2071 AAGTAAGCATTAAGTTTTCAAACGTATGGCGTGTATGATCATATGTCGGCAACAATGCACCGAAT
261 AAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAACAATGCACCGAAT
*
2136 CCAATGAGATGTGCTTATATATATTTATTATGCGAAGACTGATGGGTGCGATCATACCAGCACTA
326 CCAATGAGATGTGCTTATATATATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTA
* *
2201 ATGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGG
391 ATGCACCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTGGGCGAGAGTAGTACTAGGATGGG
*
2266 GTGACCTCTTGGGAAGTCCTCGTGTTGCACCC
456 GTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
* * *
2298 GCGTGTATGATCATCTGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTACATATATTTAT
1 GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
* * * *
2363 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
66 TATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAACTCCGCA
*
2428 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
131 CTTAAGCATGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
2493 CCCCCTTTTATCATTTTTATTTTCTTTTCTTCTTC-ATCGAAATTTCTTATGGTAGACAATCGTT
196 -CCCCTTTTATCA-TTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGTT
*
2557 TCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAACAATGCACCGT
259 TCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAACAATGCACCGA
2622 ATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCAC
324 ATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCAC
* *
2687 TAATGCATCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTTGGCGAGAGTAGTACTAGGAT-
389 TAATGCACCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTGGGCGAGAGTAGTACTAGGATG
*
2751 GGGTGACCTCCTGTGAAGTCCTCGTGTTGCACCC
454 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
2785 CTCTTTTTCA
Statistics
Matches: 457, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
487 211 0.46
488 225 0.49
489 21 0.05
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (487 bp):
GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
TATGCGAACACAGATGGCTGCGATCATACCAGCACTAATGCACCGGATCCCATCAAAACTCCGCA
CTTAAGCATGCTTGGGCGAGAGTACTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
CCCCTTTTATCATTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGTTTC
AAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAACAATGCACCGAAT
CCAATGAGATGTGCTTATATATATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCACTA
ATGCACCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTGGGCGAGAGTAGTACTAGGATGGG
GTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
Found at i:2824 original size:289 final size:289
Alignment explanation
Indices: 2298--3105 Score: 1424
Period size: 289 Copynumber: 2.8 Consensus size: 289
2288 TGTTGCACCC
* *
2298 GCGTGTATGATCATC-TGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTACATATATTTA
1 GCGTGTATGATCA-CATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTA
2362 TTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGC
65 TTATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGC
* * *
2427 ACTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGC
130 AGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
2492 ACCCC-CTTTTATCATTTTTATTTTCTTTTCTTCTTCATCGAAATTTCTTATGGTAGACAATCGT
195 ACCCCTCTTTT-TCATTTTTATTTTCTTTTCTTCTTCATCGAAATTTCTTATGGTAGACAATCGT
2556 TTCAAGTAAGCATTAAGTCTTCAAACGTATG
259 TTCAAGTAAGCATTAAGTCTTCAAACGTATG
2587 GCGTGTATGATCACATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTAT
1 GCGTGTATGATCACATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTAT
* *
2652 TATGCGAAGACAGATGGGTGCGATCATACCAGCACTAATGCATCGGATCCCATCAGAACTCCGCA
66 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
* * *
2717 GTTAAACGTGCTTTGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGTGAAGTCCTCGTGTTGCA
131 GTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
* *
2782 CCCCTCTTTTTCA-TTTTATTTTATTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGTT
196 CCCCTCTTTTTCATTTTTATTTTCTTTTCTTCTTC-ATCGAAATTTCTTATGGTAGACAATCGTT
2846 TCAAGTAAGCATTAAGTCTTCAAACGTATG
260 TCAAGTAAGCATTAAGTCTTCAAACGTATG
* *
2876 GCGTGTATGATCATATGTCTGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTAT
1 GCGTGTATGATCACATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTAT
*
2941 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCT
66 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
3006 GTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
131 GTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
3071 CCCCTCTTTATTCATTTTTATTTTCTTTTCTTCTT
196 CCCCTCTTT-TTCATTTTTATTTTCTTTTCTTCTT
3106 ACTAGGATGG
Statistics
Matches: 493, Mismatches: 21, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
288 21 0.04
289 444 0.90
290 9 0.02
291 19 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (289 bp):
GCGTGTATGATCACATGTCGGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTAT
TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
GTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
CCCCTCTTTTTCATTTTTATTTTCTTTTCTTCTTCATCGAAATTTCTTATGGTAGACAATCGTTT
CAAGTAAGCATTAAGTCTTCAAACGTATG
Found at i:3015 original size:777 final size:777
Alignment explanation
Indices: 1520--3073 Score: 2792
Period size: 777 Copynumber: 2.0 Consensus size: 777
1510 CAAACGTATG
* *
1520 GCGTGTATGATCATATGTCGGCAAAAATACACCGTATCCAATGAGATGTGCTTATATATATTTAT
1 GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
*
1585 TATGCGAAGACCGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCTATCAGAACTCCGCA
66 TATGCGAAGACCGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
* * * *
1650 GTTAAGCGTGCTTGGGCGAGAGTAGTACTATGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCA
131 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
* *
1715 CCCCTCTTTTTTCATTTTTATTTTCTTTTCTTCTTCTTTCGAAATTTCTTATGGTAGACAATCGT
196 CCCCTCTTTTATCATTTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGT
*
1780 TTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAAAAATACACCG
261 TTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAAAAATACACCG
1845 TATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCA
326 TATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCA
* *
1910 CTAATGCATCGGATCCCATCAAAACTCCGCAGTTAAGCGTGTTTGGGCGAGAGTACTTCTAGGAT
391 CTAATGCATCGGATCCCATCAAAACTCCGCAGTTAAACGTGTTTGGGCGAGAGTACTACTAGGAT
*
1975 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTATTTTCTTTTCTTCTTCT
456 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTATTTTATTTTCTTCTTCT
*
2040 TTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTTTTCAAACGTATGGCGTGT
521 TTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGT
2105 ATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATATTTATTATGCG
586 ATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATATTTATTATGCG
2170 AAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAG
651 AAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAG
*
2235 CGTGCTTGGGCGAGAGTAGTACTAGGATGGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCC
716 CGTGCTTGGGCGAGAGTAGTACTAGGAT-GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
* * *
2298 GCGTGTATGATCATCTGTCGGCAACAATGCACCGGATCCAATGAGATGTGCTTACATATATTTAT
1 GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
*
2363 TATGCGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
66 TATGCGAAGACCGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
2428 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
131 CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
2493 CCCC-CTTTTATCATTTTTATTTTCTTTTCTTCTTC-ATCGAAATTTCTTATGGTAGACAATCGT
196 CCCCTCTTTTATCATTTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGT
* *
2556 TTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAACAATGCACCG
261 TTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAAAAATACACCG
* *
2621 TATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACAGATGGGTGCGATCATACCAGCA
326 TATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCA
* *
2686 CTAATGCATCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTT-GGCGAGAGTAGTACTAGGA
391 CTAATGCATCGGATCCCATCAAAACTCCGCAGTTAAACGTG-TTTGGGCGAGAGTACTACTAGGA
*
2750 TGGGTGACCTCCTGTGAAGTCCTCGTGTTGCACCCCTCTTTTTCATTTTATTTTATTTTCTTCTT
455 TGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCT-TTTTTCATTTTATTTTATTTTCTTCTT
2815 CTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGT
519 CTTTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGT
* *
2880 GTATGATCATATGTCTGCAACAATGCACCGTATCCAATGAGATGTGCTTATATATATTTATTATG
584 GTATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATATTTATTATG
2945 CGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCT-GTT
649 CGAAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCG-TAGTT
3009 AAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
713 AAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
3074 CTCTTTATTC
Statistics
Matches: 745, Mismatches: 28, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
776 277 0.37
777 279 0.37
778 189 0.25
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (777 bp):
GCGTGTATGATCATATGTCGGCAAAAATACACCGGATCCAATGAGATGTGCTTACATATATTTAT
TATGCGAAGACCGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCA
CTTAAGCATGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCATCGTGTTGCA
CCCCTCTTTTATCATTTTTATTTTCTTTTCTTCTTCTATCGAAATTTCTTATGGTAGACAATCGT
TTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCACATGTCGGCAAAAATACACCG
TATCCAATGAGATGTGCTTATATATATTTATTATGCGAACACAGATGGCTGCGATCATACCAGCA
CTAATGCATCGGATCCCATCAAAACTCCGCAGTTAAACGTGTTTGGGCGAGAGTACTACTAGGAT
GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTATTTTATTTTCTTCTTCT
TTCGAAATTTCTTATGGTAGACAATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGT
ATGATCATATGTCGGCAACAATGCACCGAATCCAATGAGATGTGCTTATATATATTTATTATGCG
AAGACTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAG
CGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCC
Done.