Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014485.1 Corchorus capsularis cultivar CVL-1 contig14506, 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: 4899
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:964 original size:323 final size:322
Alignment explanation
Indices: 58--1409 Score: 1481
Period size: 321 Copynumber: 4.2 Consensus size: 322
48 TATATATTAA
* * * * ** * * * *
58 TATTGTGGCAAAAAATT-CAGAAAAATTTTTTTGGTCAGTTTTTAGCTGAAATCTTATACTTATC
1 TATTGAGGCAAAAAATTATAAAAAAAATTTTCAGGTCAGTTTTTAGCCGAAATCGTATACTAACC
* *
122 ATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGTAAGATTTTTGTCAG
66 ATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGCAAGATTTTTGGCAG
* * * * * * * **
187 AAAGACTTCTTGAAGTATATATATTCATCAAACAAAATCTCAACCACATTGGATTTAAATATTTG
131 AAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTGAAGGATTTG
* *
252 TTTTTACGAGCAA-CTGAATCCTGTTTCGATTTAATTATAAATAAATTCGAAAAAAAAGGAGAAA
196 TTTTTACGAG-AATCTGAATCCTGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAAA
* ** *
316 TGATATTCGAAGTATGAAAAAGTCTT-AATTTTTTTTTGCATAGAATAATATATTTTTTCTGAG
260 TGATATTCGAAGCATGAAAAACCCTTCAA-TTTTTTTTGCATAGAATTATATATTTTTTCTGAG
* * * ** * *
379 TAGTGTGGC-AAAAATTATAGAAAAAAATTTTCAGGTCCGTTTTTATTCGAAATCGTAAATTAAC
1 TATTGAGGCAAAAAATTATA-AAAAAAATTTTCAGGTCAGTTTTTAGCCGAAATCGTATACTAAC
* * * *
443 CATCAC-GATTTAAGGCTAAAAACGCGTTTCAGGACCGCAACTCAGTTTTGCAAGATTTTTGGCA
65 CATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGCAAGATTTTTGGCA
* * * *
507 GAAATACTGCTTGAAATATCTATACTCGTCATACCAAATCTCAGCCACATTGGATTGAAGGAATT
130 GAAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTGAAGGATTT
* * * * ** *
572 GTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTATAAATAAATTTGAAAAAAATCTAAGAA
195 GTTTTTACGAGAATCTGAATCCTGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAAA
* * *
637 TGATATTCGAAGCATGAAAAACCCTTCAATCTTTTTTGCATATAATTATATATTTTTTCCGAG
260 TGATATTCGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAGAATTATATATTTTTTCTGAG
* * * *
700 TTTTGAGGCAAAAAAATTCATAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATCGTATAGTAA
1 TATTGAGGC-AAAAAATT-ATAAAAAAAATTTTCAGGTCAGTTTTTAGCCGAAATCGTATACTAA
* **** * * * * *
765 CCATCACAGTTTTTTTATTTAAAACTCGTTTCAGGACCTCGACTCAGTTTTGCAATATTTTTGGT
64 CCATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGCAAGATTTTTGGC
* * *
830 AGAAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGTCACATTGAATTTAAGGATT
129 AGAAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTGAAGGATT
* *
895 TG-TTTTACGAGAATATGAATCCAGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAA
194 TGTTTTTACGAGAATCTGAATCCTGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAA
* * *
959 ATGATATTCAAAGCATCAAAAACCCTTCAATTTTTTTTGAATAGAATTATATATTTTTT-TGAG
259 ATGATATTCGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAGAATTATATATTTTTTCTGAG
* * * *
1022 TATTGGGGCAAAAAA-TATAGAAAAAATTTTCCGATCAGTTTTTAGCCGAAAATCGTATACTAAC
1 TATTGAGGCAAAAAATTATAAAAAAAATTTTCAGGTCAGTTTTTAGCCG-AAATCGTATACTAAC
* * * ** * *
1086 CATCATGGTGTTTAGCCTAAAAACGCGTTTTGGGACCCCGGCTCAATTTTGCAAGATTTTTGGCA
65 CATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGCAAGATTTTTGGCA
* *
1151 GAAATACTGCTTGAAATATCTTTATTTC-TCAAACCAAATCTCAGTCACATTGGATTGAAGGATT
130 GAAATACTGCTTGAAATATCTATA-TTCATCAAACCAAATCTCAGCCACATTGGATTGAAGGATT
* ** * **
1215 TCTTTTTACGAGGCTCTAAATCCTGTTTCGATTTAATTATAAATAAATTCGGGGGAAAAAT-GAA
194 TGTTTTTACGAGAATCTGAATCCTGTTTCGATTTAATTATAAATAAATTC--GAAAAAAATGGAA
* * * * * *
1279 AAACGATATTAGAAG-AGTGAAAAAGAAAAACCCTTCAGTTTTTTTGGCGTTGAATTATATATTT
257 AAATGATATTCGAAGCA-T------GAAAAACCCTTCAATTTTTTTTGCATAGAATTATATATTT
*
1343 TTTCTAAG
315 TTTCTGAG
** * * * *
1351 TATT-ATAACAAAAAAATT-CAGAAAAAATTTTC-GGTTCAGTTGTTAGCCGGAATCGTATA
1 TATTGA-GGC-AAAAAATTATAAAAAAAATTTTCAGG-TCAGTTTTTAGCCGAAATCGTATA
1410 TGTTACATTA
Statistics
Matches: 861, Mismatches: 145, Indels: 42
0.82 0.14 0.04
Matches are distributed among these distances:
319 28 0.03
320 130 0.15
321 278 0.32
322 65 0.08
323 164 0.19
324 108 0.13
328 37 0.04
329 18 0.02
330 32 0.04
331 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (322 bp):
TATTGAGGCAAAAAATTATAAAAAAAATTTTCAGGTCAGTTTTTAGCCGAAATCGTATACTAACC
ATCACGGTTTTTAGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGCAAGATTTTTGGCAG
AAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTGAAGGATTTG
TTTTTACGAGAATCTGAATCCTGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAAAT
GATATTCGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAGAATTATATATTTTTTCTGAG
Found at i:2030 original size:322 final size:320
Alignment explanation
Indices: 1414--4166 Score: 3080
Period size: 323 Copynumber: 8.5 Consensus size: 320
1404 CGTATATGTT
* * * * * *
1414 ACATTAGAGTTTAAAGATTTGTTTTTACTAGCATCTGAATCTTATTTAGATTTAATTATAAAAAA
1 ACATTGGA-TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAA
* * **
1479 ATTCG-AAAAAATGGAAAAATAATATCCGAAGCATGAAAAACCCTTC-ATTGTTTTTTGCATAGA
65 ATTCGAAAAAAATGGGAAAATGATATTAGAAGCATGAAAAACCCTTCAATT-TTTTTTGCATAGA
* * * * * *
1542 ATTATATATTTTTTTGAGTGTTGTGGCAAAAAATACAGAAAAAATATTTCGGGTCATTTTTTATC
129 TTTAT-TTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTAGC
* * * * *
1607 CGAAATCGTAGAGTAACCATAACGGTTTTAAGGCTAAAAACGTGTTTCGGAATCGC-AGCTCAGT
193 CGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGA-CTCAGT
* * *
1671 TTTGCAAGATTTTTGGCAGAAATACTGCTTGAAATATCTATACTCATCATACCAAATCTCAACC
257 TTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
* * * * *
1735 ACATTGAATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
* * * *
1800 TTCAGAAAAAAATGGGAAAATGGTATTAGAAGCGA-GAAAAACCCTTCAAATTTTTTTGGCGTTG
66 TTC-GAAAAAAATGGGAAAATGATATTAGAAGC-ATGAAAAACCCTTC-AATTTTTTTTGCATAG
* * **
1864 -TTTATTTTTTTTTTGGGTATTGTGGCAAAAAAATTCAGAAAAAATTTTTTTGGTCAGTTTTTAG
128 ATTTATTTTTTTTTTGAGTATTGTGGC-AAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTAG
* * * * * *
1928 CTGAAATCGTATACTTACCATCACGGTTTTTAGGCTAAAAACGCATTTCAGAACCCCGACTCAGT
192 CCGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGACTCAGT
** ** * * *
1993 TTTTTAAGATTTTTGGCAGAAAGACTTTTTAAAATATCTATATTCATCAAAGCAAATCTCAATC
257 TTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
* * **
2057 ACATTGTATTTAAGGATTTGTTTCTACGAGCATCTGAATAATGTTTCGATTTAATTATAAATAAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
* *
2122 TTCG-AAAAAATGGAAAAATGATATTCA-AAGCATGAAAAACCCTTAAATTTTTTTTGCATAGAA
66 TTCGAAAAAAATGGGAAAATGATATT-AGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAG-A
* ** * *** * *
2185 TTATATATTTTTCCTGAGTATTGTGGCAAAAAATACAGGAAATTTTTTTTTCAGAGTCAG-TTTT
129 TT-TATTTTTTTTTTGAGTATTGTGGCAAAAAATTCA-GAAA-AAATATTTC-GGGTCAGTTTTT
* * * **
2249 AGACGAAAACATATAGTAACCATCACGGTTTTGGGGCTAAAAACGCGTTTCAGG-ACCCCGACTC
190 AGCCGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTC-GGAACCCCGACTC
* * * *
2313 AGTTTTGTAAGATTTTTAGCAGAAAGACTTCTTAAAATATCTATATTCATCAAACCAAATCTCAA
254 AGTTTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAA
2378 CC
319 CC
* *
2380 ACATTGGATTT-AGGTATTTGTTTTTACGAGAATCTGAATCTTGTTTCAATTTAATTATAAATAA
1 ACATTGGATTTAAGG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAA
* * * * *
2444 ATTCGAAAAAACTGGAAAAATGATATTTGAAGAATGAAAAACCCTTCAATTTTTTTTTTGTATAG
65 ATTCGAAAAAAATGGGAAAATGATATTAGAAGCATGAAAAACCCTTCAA--TTTTTTTTGCATAG
* * * *
2509 AATTATATATTTTTTATGAGTATTGTGGCAAAAATTTCAGAAAAAAAATTTTCGGGTCAG-TTTT
128 -ATT-TATTTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATA-TTTCGGGTCAGTTTTT
* * * *
2573 AGACGAAAACGTATAGTAACCATCACGGTTTT--GGCCTAAAAACGCGTTTC-GACACACCGTCT
190 AGCCGAAATCGTATAGTAACCATCACGGTTTTAAGG-CTAAAAACGCGTTTCGGA-ACCCCGACT
*
2635 CAGTTTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCCATATTCATCAAACCAAATCTCG
253 CAGTTTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTC-
2700 GAA--
317 -AACC
* * ** * * *
2703 ACATTTGAGTTAAGGATTTAATTTTATGAGCATCTGAATCTTATTTAGATTTAATTA-AAATTAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAA-TAA
* * *
2767 ATTCGAAAAAAAT-GGACAAATGATATTCGAAGCATGAAAAACCCTTCAATGTTTGTTGCATAGA
65 ATTCGAAAAAAATGGGA-AAATGATATTAGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAGA
* * * * * *
2831 ATTATATATTTTTTGGAGTGTTGTGGCAAAAAATACAGAAAAAATATTTCGGGTCAGTTTTTATC
129 TTTAT-TTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTAGC
* *
2896 CGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAAACCCGGCTCAGTT
193 CGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGACTCAGTT
* * * * *
2961 TTGCAAGATTTTTGGCAGCAATACTGCTTCAAATATCTATACTCATCATACCAAATCTCAACC
258 TTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
* * *
3024 ACATTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
** * * * * * *
3089 TTCAGATTAAAATGGGAAAATGGTATTAGAAGCGA-CAAAAACCCTTCAATCTTTTTGGCGTTGA
66 TTC-GAAAAAAATGGGAAAATGATATTAGAAGC-ATGAAAAACCCTTCAATTTTTTTTGCATAG-
* * * *
3153 ATTATTATTATTTTTTTGGAGTATTGTGGCGAAAAATTCAGAAAAAAAAAATTTTGGGTCAGTTT
128 A-T-TTATT-TTTTTTTTGAGTATTGTGGCAAAAAATTCAG--AAAAAATATTTCGGGTCAGTTT
* * * * * * *
3218 TTAGCTGAAATCGTATACTTACCATCACGGTTTTTACGCTAAAAACGCATTTCAGAACCCCGACT
188 TTAGCCGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGACT
** *
3283 CAGTTTTTTAAGATTTTTGGCAGAAAGACTTCTTGAAATATCTATATTCATCAAACCAAATCTCA
253 CAGTTTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCA
3348 GA-C
318 -ACC
* ** ** *
3351 ACATTGGAGTTAAGGATTTAATTTTACGAGCATCTGAATCTTGTTTAAATTTAATTAAAAATAAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
*** * *
3416 TTCGAAAAAAATCTAAAAATTATATCAGAAGCATGAAAAACCCTTCAATCTTTTTTCTGCATAGA
66 TTCGAAAAAAATGGGAAAATGATATTAGAAGCATGAAAAACCCTTCAAT-TTTTTT-TGCATAG-
* * * * * * *
3481 ATTATATATATTTTTCTGAGTTTTGTGGAAAAAAATTCA-AAAAAAAAATTCGGGTCAGTTTCTA
128 ATT-TAT-TTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTA
** * *
3545 GCCGAAATCGTATAGTAACCATCACGGTTTTGGGGCTAGAAACGCGTTTCGGGACCCCGACTCAG
191 GCCGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGACTCAG
* * * * * **
3610 TTTT-CAAGTTTTTTGGAAGAAATACTGCTTAAAATATCTATATTTATCAAACCAAATCTCAGTC
256 TTTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
* ** *
3674 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATAATGTTTCGATTTAATTATAAATAAT
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
*
3739 TTCGAAAAAAAT-GGACAAATGATATTCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGA
66 TTCGAAAAAAATGGGA-AAATGATATTAGAAGCATGAAAAACCCTTCAATTT-TTTTTGCATAGA
* * * * * *
3803 ATTATATATTTTTTTGAGTGTTGTGGCAAAAAATACAGAAAAAATATTTCGGGTCATTTTTTATC
129 TTTAT-TTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTAGC
* * *
3868 CGAAATCGTAGAGTAACCATTACGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCC-AGCTCAGT
193 CGAAATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGA-CTCAGT
* * * * *
3932 TTTGCAAGATTTTTGGCAGAAATACTGCCTGAAATATCTGTACTCATCATACCAAATCTCAACC
257 TTTGCAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
* * * * *
3996 ACATTGGATTTAAGGATATGTTTCTACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAA
1 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
* * * *
4061 TTCAGAAAAAAATGGGAAAATGGTATTAGAAGCGA-GAAAAACCCTT-AATCTTTTTGGCGTTGA
66 TTC-GAAAAAAATGGGAAAATGATATTAGAAGC-ATGAAAAACCCTTCAATTTTTTTTGC-AT-A
*
4124 AATTT-TTTTTTTTTT-AG-ATTGTGGCAAAAAAATTCAGAAAAAA
127 GATTTATTTTTTTTTTGAGTATTGTGGC-AAAAAATTCAGAAAAAA
4167 AAATAATTTT
Statistics
Matches: 2059, Mismatches: 308, Indels: 131
0.82 0.12 0.05
Matches are distributed among these distances:
319 37 0.02
320 203 0.10
321 280 0.14
322 444 0.22
323 558 0.27
324 177 0.09
325 42 0.02
326 84 0.04
327 226 0.11
328 8 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (320 bp):
ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA
TTCGAAAAAAATGGGAAAATGATATTAGAAGCATGAAAAACCCTTCAATTTTTTTTGCATAGATT
TATTTTTTTTTTGAGTATTGTGGCAAAAAATTCAGAAAAAATATTTCGGGTCAGTTTTTAGCCGA
AATCGTATAGTAACCATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGACTCAGTTTTG
CAAGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAACC
Found at i:2051 original size:860 final size:862
Alignment explanation
Indices: 570--2125 Score: 2107
Period size: 860 Copynumber: 1.8 Consensus size: 862
560 ATTGAAGGAA
* * * * * *
570 TTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTATAAATAAATTTGAAAAAAATCTAAG
1 TTGTTTTTACGAGCATCCGAATCTTATTTAGATTTAATTATAAAAAAATTCGAAAAAAATCGAAA
* * *
635 AATGATATTCGAAGCATGAAAAACCCTTCAATCTTTTTTGCATATAATTATATATTTTTTCCGAG
66 AATAATATCCGAAGCATGAAAAACCCTTCAATCTTTTTTGCATAGAATTATATATTTTTTCCGAG
* * * *
700 TTTTGAGGCAAAAAAATTCATAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATCGTATAGTAA
131 TGTTGAGGCAAAAAAATACAGAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATCGTAGAGTAA
* *** * * * * *
765 CCATCACAGTTTTTTTATTTAAAACTCGTTTCAGGACCTCGACTCAGTTTTGCAATATTTTTGGT
196 CCATAACAGTTTTAAGACTAAAAACTCGTTTCAGGACATCGACTCAGTTTTGCAAGATTTTTGGC
* ** *
830 AGAAATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCAGTCACATTGAATTTAAGGATT
261 AGAAATACTGCTTGAAATATCTATACTCATCAAACCAAATCTCAACCACATTGAATTTAAGGATA
* *
895 TGTTTTACGAGAATATGAATCCAGTTTCGATTTAATTATAAATAAATTCGAAAAAAATGGAAAAA
326 TGTTTTACGAGAATATGAATCCAGTTTCGATTTAAATAGAAATAAATTCGAAAAAAATGGAAAAA
*
960 TGATATTCAAAGCATCAAAAACCCTTCAATTTTTTTTGAATAGAATTATATATTTTTTTGAGTAT
391 TGATATTCAAAGCATCAAAAACCCTTCAATTTTTTTGGAATAGAATTATATATTTTTTTGAGTAT
1025 TGGGGCAAAAAATATAGAAAAAATTTTCCGATCAGTTTTTAGCCGAAAATCGTATACTAACCATC
456 TGGGGCAAAAAATATAGAAAAAATTTTCCGATCAGTTTTTAGCCGAAAATCGTATACTAACCATC
* * ** * *
1090 ATGGTGTTTAGCCTAAAAACGCGTTTTGGGACCCCGGCTCAATTTTGCAAGATTTTTGGCAGAAA
521 ACGGTGTTTAGCCTAAAAACGCATTTCAGAACCCCGACTCAATTTTGCAAGATTTTTGGCAGAAA
* * * *
1155 TACTGCTTGAAATATCTTTATTTCTCAAACCAAATCTCAGTCACATTGGATTGAAGGATTTCTTT
586 GACTGCTTAAAATATCTATATTTCTCAAACCAAATCTCAATCACATTGGATTGAAGGATTTCTTT
* **
1220 TTACGAGGC-TCTAAATCCTGTTTCGATTTAATTATAAATAAATTCGGGGGAAAAATGAAAAACG
651 CTACGA-GCATCTAAATAATGTTTCGATTTAATTATAAATAAATTCGGGGGAAAAATGAAAAACG
1284 ATATTAGAAGAGTGAAAAAGAAAAACCCTTCAGTTTTTTTGGCGTTGAATTATATATTTTTTCTA
715 ATATTAGAAGAGTGAAAAAGAAAAACCCTTCAGTTTTTTTGGCGTTGAATTATATATTTTTTCTA
1349 AGTATTATAACAAAAAAATTCAGAAAAAATTTTCGGTTCAGTTGTTAGCCGGAATCGTATATGTT
780 AGTATTATAACAAAAAAATTCAGAAAAAATTTTCGGTTCAGTTGTTAGCCGGAATCGTATATGTT
1414 ACATTAGAGTTTAAAGAT
845 ACATTAGAGTTTAAAGAT
* * *
1432 TTGTTTTTACTAGCATCTGAATCTTATTTAGATTTAATTATAAAAAAATTCG-AAAAAATGGAAA
1 TTGTTTTTACGAGCATCCGAATCTTATTTAGATTTAATTATAAAAAAATTCGAAAAAAATCGAAA
* * *
1496 AATAATATCCGAAGCATGAAAAACCCTTCATTGTTTTTTGCATAGAATTATATATTTTTT-TGAG
66 AATAATATCCGAAGCATGAAAAACCCTTCAATCTTTTTTGCATAGAATTATATATTTTTTCCGAG
* * * *
1560 TGTTGTGGC-AAAAAATACAGAAAAAATA-TTTCGGGTCATTTTTTATCCGAAATCGTAGAGTAA
131 TGTTGAGGCAAAAAAATACAGAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATCGTAGAGTAA
* *
1623 CCATAACGGTTTTAAGGCTAAAAACGT-GTTTC-GGA-ATCGCAGCTCAGTTTTGCAAGATTTTT
196 CCATAACAGTTTTAAGACTAAAAAC-TCGTTTCAGGACATCG-A-CTCAGTTTTGCAAGATTTTT
*
1685 GGCAGAAATACTGCTTGAAATATCTATACTCATCATACCAAATCTCAACCACATTGAATTTAAGG
258 GGCAGAAATACTGCTTGAAATATCTATACTCATCAAACCAAATCTCAACCACATTGAATTTAAGG
* * ** *
1750 ATATGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAATTCAGAAAAAAATGG
323 ATATG-TTTTACGAGAATATGAATCCAGTTTCGATTTAAATAGAAATAAATTC-GAAAAAAATGG
* * * ** * * *
1815 GAAAATGGTATT-AGAAGCGA-GAAAAACCCTTCAAATTTTTTTGGCGTTG-TTTAT-TTTTTTT
386 AAAAATGATATTCA-AAGC-ATCAAAAACCCTTC-AATTTTTTTGGAATAGAATTATATATTTTT
* * ** * *
1876 TTGGGTATTGTGGCAAAAAA-ATTCAGAAAAAATTTTTTTGGTCAGTTTTTAGCTG-AAATCGTA
448 TTGAGTATTGGGGCAAAAAATA-T-AGAAAAAA-TTTTCCGATCAGTTTTTAGCCGAAAATCGTA
* * * * **
1939 TACTTACCATCACGGTTTTTAGGCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTTTAAGATT
510 TACTAACCATCACGGTGTTTAGCCTAAAAACGCATTTCAGAACCCCGACTCAATTTTGCAAGATT
** * * *
2004 TTTGGCAGAAAGACTTTTTAAAATATCTATA-TTCATCAAAGCAAATCTCAATCACATTGTATTT
575 TTTGGCAGAAAGACTGCTTAAAATATCTATATTTC-TCAAACCAAATCTCAATCACATTGGATTG
* *
2068 AAGGATTTGTTTCTACGAGCATCTGAATAATGTTTCGATTTAATTATAAATAAATTCG
639 AAGGATTTCTTTCTACGAGCATCTAAATAATGTTTCGATTTAATTATAAATAAATTCG
2126 AAAAAATGGA
Statistics
Matches: 594, Mismatches: 87, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
856 3 0.01
857 4 0.01
858 138 0.23
859 88 0.15
860 220 0.37
861 95 0.16
862 46 0.08
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (862 bp):
TTGTTTTTACGAGCATCCGAATCTTATTTAGATTTAATTATAAAAAAATTCGAAAAAAATCGAAA
AATAATATCCGAAGCATGAAAAACCCTTCAATCTTTTTTGCATAGAATTATATATTTTTTCCGAG
TGTTGAGGCAAAAAAATACAGAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATCGTAGAGTAA
CCATAACAGTTTTAAGACTAAAAACTCGTTTCAGGACATCGACTCAGTTTTGCAAGATTTTTGGC
AGAAATACTGCTTGAAATATCTATACTCATCAAACCAAATCTCAACCACATTGAATTTAAGGATA
TGTTTTACGAGAATATGAATCCAGTTTCGATTTAAATAGAAATAAATTCGAAAAAAATGGAAAAA
TGATATTCAAAGCATCAAAAACCCTTCAATTTTTTTGGAATAGAATTATATATTTTTTTGAGTAT
TGGGGCAAAAAATATAGAAAAAATTTTCCGATCAGTTTTTAGCCGAAAATCGTATACTAACCATC
ACGGTGTTTAGCCTAAAAACGCATTTCAGAACCCCGACTCAATTTTGCAAGATTTTTGGCAGAAA
GACTGCTTAAAATATCTATATTTCTCAAACCAAATCTCAATCACATTGGATTGAAGGATTTCTTT
CTACGAGCATCTAAATAATGTTTCGATTTAATTATAAATAAATTCGGGGGAAAAATGAAAAACGA
TATTAGAAGAGTGAAAAAGAAAAACCCTTCAGTTTTTTTGGCGTTGAATTATATATTTTTTCTAA
GTATTATAACAAAAAAATTCAGAAAAAATTTTCGGTTCAGTTGTTAGCCGGAATCGTATATGTTA
CATTAGAGTTTAAAGAT
Found at i:3456 original size:971 final size:962
Alignment explanation
Indices: 1436--4169 Score: 3528
Period size: 971 Copynumber: 2.8 Consensus size: 962
1426 AAAGATTTGT
* * *
1436 TTTTACTAGCATCTGAATCTTATTTAGATTTAATTATAAAA-AAATTCG-AAAAAATGGAAAAAT
1 TTTTACGAGCATCTGAATCTTGTTTAAATTTAATTA-AAAATAAATTCGAAAAAAATGGAAAAAT
* * *
1499 AATATCCGAAGCATGAAAAACCCTTC-A-TTGTTTTTTGCATAGAATTATATATTTTTTTGAGTG
65 AATATCAGAAGCATGAAAAACCCTTCAATTTTTTTTTTGCATAGAATTATATATTTTTTTGAGTA
* * * * *
1562 TTGTGGCAAAAAATACAGAAAAAATATTTCGGGTCATTTTTTATCCGAAATCGTAGAGTAACCAT
130 TTGTGGCAAAAAATTCAGAAAAAAAATTTCGGGTCA-GTTTTAGCCGAAATCGTATAGTAACCAT
* * * *
1627 AACGGTTTTAAGGCTAAAAACGTGTTTCGGAATCGCAGCTCAGTTTTGCAAGATTTTTGGCAGAA
194 CACGGTTTT-AGGCTAAAAACGCGTTTC-GAA-CACCGCTCAGTTTTGCAAGATTTTTGGCAGAA
* * *
1692 ATACTGCTTGAAATATCTATACTCATCATACCAAATCTC-AACCACA-TTGAATTTAAGGATATG
256 ATACTGCTTGAAATATCTATATTCATCAAACCAAATCTCGAA--ACATTTG-ATTTAAGGATTTG
* *
1755 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAATTCAGAAAAAAATGGGA-AA
318 TTTTTACGAGCATCTGAATCTTGTTTAGATTTAATTAGAAATAAATTC-GAAAAAAAT-GGACAA
* * * * * * * *
1819 ATGGTATTAGAAGCGA-GAAAAACCCTTCAAATTTTTTTGGCGTTG-TTTATTTTTTTTTTGG-G
381 ATGATATTCGAAGC-ATGAAAAACCCTTC-AATGTTTTT-GCATAGAATTATATATTTTTTGGAG
* * * ** * * * *
1881 TATTGTGGCAAAAAAATTCAGAAAAAATTTTTTTGGTCAGTTTTTAGCTGAAATCGTATACTTAC
443 TGTTGTGGC-AAAAAATACAGAAAAAATATTTCGGGTCAGTTTTTATCCGAAATCGTATAGTAAC
* * * * **
1946 CATCACGGTTTTTAGGCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTTTAAGATTTTTGGCA
507 CATCACGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCAAGATTTTTGGCA
* ** * * * * * *
2011 GAAAGACTTTTTAAAATATCTATATTCATCAAAGCAAATCTCAATCACATTGTATTTAAGGATTT
572 GAAATACTGCTTAAAATATCTATACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATAT
** * * *
2076 GTTTCTACGAGCATCTGAATAATGTTTCGATTTAATTATAAATAAATTC-GAAAAAATGGAAAAA
637 GTTTCTACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAGAAAAAATGGGAAAA
* * * * * *
2140 TGATATTCA-AAGC-ATGAAAAACCCTTAAATTTTTTTTGCATAGAATTA-TA-TATTTTTCCTG
702 TGGTATT-AGAAGCGA-GAAAAACCCTT-AATCTTTTTGGCGTTGAATTATTATTATTTTT-TTG
* * ***** *
2201 AGTATTGTGGCAAAAAATACAG-GAAATTTTTTTTTCAGAGTCAGTTTTAGACGAAAACATATAG
763 AGTATTGTGGCAAAAAATTCAGAAAAAAAAAATTTT-AGAGTCAGTTTTAGACGAAAACATATAC
** * *
2265 TAACCATCACGGTTTTGGGGCTAAAAACGCGTTTCAGGACCCCGACTCAGTTTTGTAAGATTTTT
827 TAACCATCACGGTTTTGACGCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTGTAAGATTTTT
*
2330 AGCAGAAAGACTTCTTAAAATATCTATATTCATCAAACCAAATCTCAACCACATTGGATTTAGGT
892 AGCAGAAAGACTTCTTAAAATATCTATATTCATCAAACCAAATCTCAACCACATTGGATTAAGGT
**
2395 ATTTGT
957 ATTTAA
* * * * *
2401 TTTTACGAGAATCTGAATCTTGTTTCAATTTAATTATAAATAAATTCGAAAAAACTGGAAAAATG
1 TTTTACGAGCATCTGAATCTTGTTTAAATTTAATTAAAAATAAATTCGAAAAAAATGGAAAAATA
** * *
2466 ATATTTGAAGAATGAAAAACCCTTCAATTTTTTTTTTGTATAGAATTATATATTTTTTATGAGTA
66 ATATCAGAAGCATGAAAAACCCTTCAATTTTTTTTTTGCATAGAATTATATATTTTTT-TGAGTA
* * *
2531 TTGTGGCAAAAATTTCAGAAAAAAAATTTTCGGGTCAGTTTTAGACGAAAACGTATAGTAACCAT
130 TTGTGGCAAAAAATTCAGAAAAAAAA-TTTCGGGTCAGTTTTAGCCGAAATCGTATAGTAACCAT
2596 CACGGTTTT-GGCCTAAAAACGCGTTTCGACACACCGTCTCAGTTTTGCAAGATTTTTGGCAGAA
194 CACGGTTTTAGG-CTAAAAACGCGTTTCGA-ACACCG-CTCAGTTTTGCAAGATTTTTGGCAGAA
* * * **
2660 AGACTGCTTGAAATATCCATATTCATCAAACCAAATCTCGGAAACATTTGAGTTAAGGATTTAAT
256 ATACTGCTTGAAATATCTATATTCATCAAACCAAATCTC-GAAACATTTGATTTAAGGATTTGTT
* *
2725 TTTATGAGCATCTGAATCTTATTTAGATTTAATTA-AAATTAAATTCGAAAAAAATGGACAAATG
320 TTTACGAGCATCTGAATCTTGTTTAGATTTAATTAGAAA-TAAATTCGAAAAAAATGGACAAATG
2789 ATATTCGAAGCATGAAAAACCCTTCAATGTTTGTTGCATAGAATTATATATTTTTTGGAGTGTTG
384 ATATTCGAAGCATGAAAAACCCTTCAATGTTT-TTGCATAGAATTATATATTTTTTGGAGTGTTG
2854 TGGCAAAAAATACAGAAAAAATATTTCGGGTCAGTTTTTATCCGAAATCGTATAGTAACCATCAC
448 TGGCAAAAAATACAGAAAAAATATTTCGGGTCAGTTTTTATCCGAAATCGTATAGTAACCATCAC
* *
2919 GGTTTTAAGGCTAAAAACGCGTTTCGGAAACCCGGCTCAGTTTTGCAAGATTTTTGGCAGCAATA
513 GGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCAAGATTTTTGGCAGAAATA
* *
2984 CTGCTTCAAATATCTATACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATATGTTTTT
578 CTGCTTAAAATATCTATACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATATGTTTCT
*
3049 ACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAGATTAAAATGGGAAAATGGTA
643 ACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAGA-AAAAATGGGAAAATGGTA
*
3114 TTAGAAGCGACAAAAACCCTTCAATCTTTTTGGCGTTGAATTATTATTATTTTTTTGGAGTATTG
707 TTAGAAGCGAGAAAAACCCTT-AATCTTTTTGGCGTTGAATTATTATTATTTTTTT-GAGTATTG
* * * * *
3179 TGGCGAAAAATTCAGAAAAAAAAAATTTT-GGGTCAGTTTTTAG-CTGAAATCGTATACTTACCA
770 TGGCAAAAAATTCAGAAAAAAAAAATTTTAGAGTCAG-TTTTAGAC-GAAAACATATACTAACCA
* * *
3242 TCACGGTTTTTACGCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTTTAAGATTTTTGGCAGA
833 TCACGGTTTTGACGCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTGTAAGATTTTTAGCAGA
*
3307 AAGACTTCTTGAAATATCTATATTCATCAAACCAAATCTCAGA-CACATTGGAGTTAAGG-ATTT
898 AAGACTTCTTAAAATATCTATATTCATCAAACCAAATCTCA-ACCACATTGGA-TTAAGGTATTT
3370 AA
961 AA
** *
3372 TTTTACGAGCATCTGAATCTTGTTTAAATTTAATTAAAAATAAATTCGAAAAAAATCTAAAAATT
1 TTTTACGAGCATCTGAATCTTGTTTAAATTTAATTAAAAATAAATTCGAAAAAAATGGAAAAATA
* *
3437 ATATCAGAAGCATGAAAAACCCTTCAATCTTTTTTCTGCATAGAATTATATATATTTTTCTGAGT
66 ATATCAGAAGCATGAAAAACCCTTCAATTTTTTTTTTGCATAGAATTATATAT-TTTTT-TGAGT
* * *
3502 TTTGTGGAAAAAAATTCA-AAAAAAAAATTCGGGTCAGTTTCTAGCCGAAATCGTATAGTAACCA
129 ATTGTGGCAAAAAATTCAGAAAAAAAATTTCGGGTCAGTTT-TAGCCGAAATCGTATAGTAACCA
* * * * * *
3566 TCACGGTTTTGGGGCTAGAAACGCGTTTCGGGACCCCGACTCAGTTTT-CAAGTTTTTTGGAAGA
193 TCACGGTTTT-AGGCTAAAAACGCGTTTC-GAACACCG-CTCAGTTTTGCAAGATTTTTGGCAGA
* * ** *
3630 AATACTGCTTAAAATATCTATATTTATCAAACCAAATCTCAGTCACATTGGATTTAAGGATTTGT
255 AATACTGCTTGAAATATCTATATTCATCAAACCAAATCTC-GAAACATTTGATTTAAGGATTTGT
* ** * * *
3695 TTTTACGAGCATCTAAATAATGTTTCGATTTAATTATAAATAATTTCGAAAAAAATGGACAAATG
319 TTTTACGAGCATCTGAATCTTGTTTAGATTTAATTAGAAATAAATTCGAAAAAAATGGACAAATG
*
3760 ATATTCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGAATTATATATTTTTTTGAGTGTT
384 ATATTCGAAGCATGAAAAACCCTTCAA--TGTTTTTGCATAGAATTATATATTTTTTGGAGTGTT
* * *
3825 GTGGCAAAAAATACAGAAAAAATATTTCGGGTCATTTTTTATCCGAAATCGTAGAGTAACCATTA
447 GTGGCAAAAAATACAGAAAAAATATTTCGGGTCAGTTTTTATCCGAAATCGTATAGTAACCATCA
* *
3890 CGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCCAGCTCAGTTTTGCAAGATTTTTGGCAGAAAT
512 CGGTTTTAAGGCTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCAAGATTTTTGGCAGAAAT
* * *
3955 ACTGCCTGAAATATCTGTACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATATGTTTC
577 ACTGCTTAAAATATCTATACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATATGTTTC
*
4020 TACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAATTCAGAAAAAAATGGGAAAATGGT
642 TACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAG-AAAAAATGGGAAAATGGT
4085 ATTAGAAGCGAGAAAAACCCTTAATCTTTTTGGCGTTGAAATT-TT-TT-TTTTTTT-AG-ATTG
706 ATTAGAAGCGAGAAAAACCCTTAATCTTTTTGGCGTTG-AATTATTATTATTTTTTTGAGTATTG
4145 TGGCAAAAAAATTCAGAAAAAAAAA
770 TGGC-AAAAAATTCAGAAAAAAAAA
4170 TAATTTTTGT
Statistics
Matches: 1556, Mismatches: 172, Indels: 80
0.86 0.10 0.04
Matches are distributed among these distances:
964 3 0.00
965 38 0.02
966 58 0.04
967 285 0.18
968 169 0.11
969 117 0.08
970 38 0.02
971 470 0.30
972 369 0.24
973 9 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (962 bp):
TTTTACGAGCATCTGAATCTTGTTTAAATTTAATTAAAAATAAATTCGAAAAAAATGGAAAAATA
ATATCAGAAGCATGAAAAACCCTTCAATTTTTTTTTTGCATAGAATTATATATTTTTTTGAGTAT
TGTGGCAAAAAATTCAGAAAAAAAATTTCGGGTCAGTTTTAGCCGAAATCGTATAGTAACCATCA
CGGTTTTAGGCTAAAAACGCGTTTCGAACACCGCTCAGTTTTGCAAGATTTTTGGCAGAAATACT
GCTTGAAATATCTATATTCATCAAACCAAATCTCGAAACATTTGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTAGATTTAATTAGAAATAAATTCGAAAAAAATGGACAAATGATATTCG
AAGCATGAAAAACCCTTCAATGTTTTTGCATAGAATTATATATTTTTTGGAGTGTTGTGGCAAAA
AATACAGAAAAAATATTTCGGGTCAGTTTTTATCCGAAATCGTATAGTAACCATCACGGTTTTAA
GGCTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCAAGATTTTTGGCAGAAATACTGCTTAA
AATATCTATACTCATCATACCAAATCTCAACCACATTGGATTTAAGGATATGTTTCTACGAGCAT
CTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAGAAAAAATGGGAAAATGGTATTAGAAGCG
AGAAAAACCCTTAATCTTTTTGGCGTTGAATTATTATTATTTTTTTGAGTATTGTGGCAAAAAAT
TCAGAAAAAAAAAATTTTAGAGTCAGTTTTAGACGAAAACATATACTAACCATCACGGTTTTGAC
GCTAAAAACGCATTTCAGAACCCCGACTCAGTTTTGTAAGATTTTTAGCAGAAAGACTTCTTAAA
ATATCTATATTCATCAAACCAAATCTCAACCACATTGGATTAAGGTATTTAA
Found at i:4661 original size:506 final size:504
Alignment explanation
Indices: 3686--4610 Score: 1228
Period size: 506 Copynumber: 1.8 Consensus size: 504
3676 ATTGGATTTA
** * * *
3686 AGGATTTGTTTTTACGAGCATCTAAATAATGTTTCGATTTAATTATAAATAATTTCGAAAAAAAT
1 AGGATTTAATTTTACGAGCATCTAAATAATGTTTAGATTTAATTAAAAATAAATTCGAAAAAAAT
* * *
3751 GGACAAATGATATTCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGAATTATATATTTTT
66 CGAAAAATGATATCCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGAATTATATATTTTT
* * * * * *
3816 TTGAGTGTTGTGGCAAAAAATACAGAAAAAATATTTCGGGTCATTTTTTATCCGAAATCGTAGAG
131 TTGAGTGTTGTGGCAAAAAATACAGAAAAAAAAATTCGGATCAGTTTTTAGCCGAAATCGTAGAA
*
3881 TAACCATTACGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCCAGCTCAGTTTTGCAAGATTTTT
196 TAACCATCACGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCCAGCTCAGTTTTGCAAGATTTTT
* * * * *
3946 GGCAGAAATACTGCCTGAAATATCTGTACTCATCATACCAAATCTCAACCACATTGGATTTAAGG
261 GGCACAAATAATGCCTGAAATAGCTATACTCATCAAACCAAATCTCAACCACATTGGATTTAAGG
** *
4011 ATATGTTTCTACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATAAATTCAGAAAAAAATGG
326 ATATGTTTCTACGAGCATCTGAATAATGTTTCGATTTAAATAGAAATAAATTCAGAAAAAAATGG
* * ** * *
4076 GAAAATGGTATTAGAAGCGAGAAAAACCCTTAATCTTTTTGGCGTTGAAATTTTTTTTTTTTTAG
391 AAAAATGATATTAGAAGCGAGAAAAACCCTTAATCTTTTTGGCGTTGAAATTTTAATGTTTTGAG
4141 ATTGTGGCAAAAAAATTCAGAAAAAAAAATAATTTTTGTGTTAGTTTGC
456 ATTGTGGCAAAAAAATTCAGAAAAAAAAATAATTTTTGTGTTAGTTTGC
** **
4190 AGGATTTAATTTTACGAGCATCTGTATCTTGTTTAGATTTAATTAAAAATAAATTCGAAAAAAAA
1 AGGATTTAATTTTACGAGCATCTAAATAATGTTTAGATTTAATTAAAAATAAATTCG-AAAAAAA
* *
4255 TCTAAAAATGATATCCGAAGCATGAAAAACCCTTCAATTTTTTTTTGCATAGAATTATATATTTT
65 TCGAAAAATGATATCCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGAATTATATATTTT
* ** * *
4320 TTTGAGTTTTGTGGCAAAAAATTTAGAAAAAAAAAATTCTGATCAGTTTTTAGCCGAAATCGTAT
130 TTTGAGTGTTGTGGCAAAAAATACAG-AAAAAAAAATTCGGATCAGTTTTTAGCCGAAATCGTAG
* ** * * * * *
4385 AATAACGATCACGGTTTTGGGGCTAGAAACGCGTTTCGGGATCCCGGCTCAGTTTTGCAAGATTT
194 AATAACCATCACGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCCAGCTCAGTTTTGCAAGATTT
* * * * *** *
4450 TTGGTACAAATAATGCTTGAAATAGCTATATTCATCAAAGCAAATCTCATTTACATTGTATTTAA
259 TTGGCACAAATAATGCCTGAAATAGCTATACTCATCAAACCAAATCTCAACCACATTGGATTTAA
* * * ** *
4515 GGATTTGTTTTTACGAGTATCTGAATAATGTTTCGATTTAGTTATAAATAAATTC-G-AAAAAAT
324 GGATATGTTTCTACGAGCATCTGAATAATGTTTCGATTTAAATAGAAATAAATTCAGAAAAAAAT
4578 GGAAAAATGATATTCA-AAGC-ATGAAAAACCCTT
389 GGAAAAATGATATT-AGAAGCGA-GAAAAACCCTT
4611 CTTTTTTTTC
Statistics
Matches: 359, Mismatches: 58, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
503 1 0.00
504 82 0.23
505 92 0.26
506 184 0.51
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (504 bp):
AGGATTTAATTTTACGAGCATCTAAATAATGTTTAGATTTAATTAAAAATAAATTCGAAAAAAAT
CGAAAAATGATATCCGAAGCATGAAAAACCCTTCAATTTGTTTTTGCATAGAATTATATATTTTT
TTGAGTGTTGTGGCAAAAAATACAGAAAAAAAAATTCGGATCAGTTTTTAGCCGAAATCGTAGAA
TAACCATCACGGTTTTAAGGCTAAAAACGAGTTTCGGAACCCCAGCTCAGTTTTGCAAGATTTTT
GGCACAAATAATGCCTGAAATAGCTATACTCATCAAACCAAATCTCAACCACATTGGATTTAAGG
ATATGTTTCTACGAGCATCTGAATAATGTTTCGATTTAAATAGAAATAAATTCAGAAAAAAATGG
AAAAATGATATTAGAAGCGAGAAAAACCCTTAATCTTTTTGGCGTTGAAATTTTAATGTTTTGAG
ATTGTGGCAAAAAAATTCAGAAAAAAAAATAATTTTTGTGTTAGTTTGC
Found at i:4772 original size:317 final size:318
Alignment explanation
Indices: 4190--4894 Score: 902
Period size: 317 Copynumber: 2.2 Consensus size: 318
4180 GTTAGTTTGC
** * *
4190 AGGATTTAATTTTACGAGCATCTGTATCTTGTTTAGATTTAATTAAAAATAAATTCGAAAAAAAA
1 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCG--AAAAAA
* * * *
4255 TCTAAAAATGATATCCGAAGCATGAAAAACCCTTCAATTTTTTTTTGCATAGAATTATATATTTT
64 TCGAAAAATGATATCCAAAGCATGAAAAACCCTTC-A-TTTTTTTTGCATAGAATTATATAATGT
* *
4320 TTTGAGTTTTGTGGCAAAAAATTTAGAAAAAAAAAATTCTGATCAGTTTTTAGCCGAAATCGTAT
127 TTTGAGTATTGTGGCAAAAAA--TACAAAAAAAAAATTCTGATCAGTTTTTAGCCGAAATCGTAT
* * * *
4385 AATAACGATCACGGTTTTGGGGCTAGAAACGCGTTTCGGGATCCCGGCTCAGTTTTGCAAGATTT
190 AATAACGATCACGCTTTTGGGGCTAAAAACGCGTTTCGGGATCACGGCTCAATTTTGCAAGATTT
* * ** *
4450 TTGGTACAAATAA-TGCTTGAAATAGCTATATTCATCAAAGCAAATCTCATTTACATTGTATTTA
255 TTGGTACAAA-AACTGCTTAAAATAGCTATATTCATCAAACCAAATCTCAGCTACATTGGATTTA
* ** * * *
4514 AGGATTTGTTTTTACGAGTATCTGAATAATGTTTCGATTTAGTTATAAATAAATTCGAAAAAATG
1 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAATC
* *
4579 GAAAAATGATATTCAAAGCATGAAAAACCCTTC-TTTTTTTT-CTTAGAATTATAAATAATGTTT
66 GAAAAATGATATCCAAAGCATGAAAAACCCTTCATTTTTTTTGCATAGAATTAT--ATAATGTTT
* * *
4642 TGAGTATTGTGGCAAAAAA-ACAAAAAAAAATTTC-GTTTCAGTTTTTAGCTGAAATCGTCA-AG
129 TGAGTATTGTGGCAAAAAATACAAAAAAAAAATTCTG-ATCAGTTTTTAGCCGAAATCGT-ATA-
* * *
4704 GTTAC-ATCACGCTTTTGGGGCTAAAAACGCGTTTCGGGATCACGGCTCAATTTTGTAAGATTTT
191 ATAACGATCACGCTTTTGGGGCTAAAAACGCGTTTCGGGATCACGGCTCAATTTTGCAAGATTTT
* *
4768 TGGTAGAAAAACTGCTTAAAATATCTATATTCATCAAACCAAATCTCAGCTACATTGGATTTA
256 TGGTACAAAAACTGCTTAAAATAGCTATATTCATCAAACCAAATCTCAGCTACATTGGATTTA
* * *
4831 AGGATATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAATAGAAATAAATTCAGAAAAAA
1 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTC-GAAAAAA
4895 ATGGG
Statistics
Matches: 332, Mismatches: 42, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
316 3 0.01
317 190 0.57
318 21 0.06
319 8 0.02
320 25 0.08
322 37 0.11
324 48 0.14
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (318 bp):
AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAATC
GAAAAATGATATCCAAAGCATGAAAAACCCTTCATTTTTTTTGCATAGAATTATATAATGTTTTG
AGTATTGTGGCAAAAAATACAAAAAAAAAATTCTGATCAGTTTTTAGCCGAAATCGTATAATAAC
GATCACGCTTTTGGGGCTAAAAACGCGTTTCGGGATCACGGCTCAATTTTGCAAGATTTTTGGTA
CAAAAACTGCTTAAAATAGCTATATTCATCAAACCAAATCTCAGCTACATTGGATTTA
Done.