Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016518.1 Corchorus olitorius cultivar O-4 contig16551, 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: 34980
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:1408 original size:323 final size:322
Alignment explanation
Indices: 744--6441 Score: 4138
Period size: 323 Copynumber: 17.5 Consensus size: 322
734 TTAAATATTA
* *
744 CACGCTTCTAATATCGTTTTCCCA-TTTTTT-CGAATTAATTTATAATTAAATCGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * ** * * * * * *
807 CAGATACTCGTAAATACAAATTATTAAATCGAATGTGACTGGGATTTTGTTCGATGAATATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* ** * * *
872 ATTTCAAGGAATCTTTACACCAAAAATCATGCAAAACTGAATC-ATGCCCC-AGAACGCGTTTTT
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGA-AACGCGTTTTT
* * *
935 AGC--CAAAAACCATGA-TGAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCC-AAAA-
195 AGCAAAAAAAACCGTGAGT-AGTACACGATTTCGGC--------T---AAAACTGACCCGAAAAT
* * * **
995 ATTTTTCCTCAATTCTTTGCCAAAATACTCAGAAAAAAGGTATAATTCAACG-CAAATAAAATT-
248 TTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAA-AAAATTG
* *
1058 CAAGGATTGTTT
312 GACGGATT-TTT
* * * * *
1070 CACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAATTGATTTCTAATTAAATTGAACCAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * * *
1135 CAAATTCTCGTAAAAAATCAAATCCTTAAATCCAATGGGGATGAGATTCGATTTGATGATTATAG
66 CAGATGCTCGT-AAAAA-CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAG
* * * * *
1200 ATATTTCAATGAGTCTTTATACCAAAAAACCAAGCAAAACTGAGTAGAAGCCCCGAAACGCGTTT
129 ATATTTCAAGGAGTCTTTATGCC-AAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTT
*
1265 TTAGCAAAAAAAAAAACCGTGA-TA-TACACGA-TTCGGCTAAAACTGACCTG-AAATTTTTTTC
193 TTAGC---AAAAAAAACCGTGAGTAGTACACGATTTCGGCTAAAACTGACCCGAAAATTTTTTTC
* * * *
1326 TTCAATTTTTTGTCACAATACTCACAAAAAAAATATAATTCAACGCCAAAAAAATTGGA-GGATT
255 CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGACGGATT
1390 TTT
320 TTT
*
1393 CACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGAT
1 CACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * *
1458 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATAAATATAAA
65 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGA
* * * * * * * *
1523 TATTTCAAGGAGTCTTTGTGCAAAAAATCATGCAAAACTAAGTTGGGGACCTCAAAACGCGTTTT
130 TATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGG-CCCCGAAACGCGTTTT
* * * *
1588 TAGC--CAAAAACCGTGATGGTAAGTACACGATTT-GGCTAAAAATATACCCGAAAACTTTTTT-
194 TAGCAAAAAAAACCGTGA--GT-AGTACACGATTTCGGCTAAAACT-GACCCGAAAATTTTTTTC
* * * * * *
1649 CTCAA-TTTTTGCCCCAATTCTCTGAAAAAAAATATAATTCAACTCCAAAAAGATT-GACGGGA-
255 CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGAC-GGAT
1711 TTTT
319 TTTT
* * *
1715 CACACTTCTAATATCATTTTT-C-TTTTATTCTCTGAATTAATTTCTAATTAAATCGAAACAAGA
1 CACGCTTCTAATATCGTTTTTCCATTTT-TT-TCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * * *
1778 TTCAGACGCTCGTAAAAA-AATAT--TTATATCAAATATGGCTGTGATTTGGTTCGATGAATCAT
64 TTCAGATGCTCGTAAAAACAA-ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG-AT--T
* ** * * * *
1840 GCAAAATTCGTATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAATGAG-CTGGGGCTCC
125 -----A-TAG-ATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTC-GAGGCCCC
* * * *
1904 GGAACGCGTTTTTAGC--CAAAAACTGTGA-T-GTACACGATTTCGGCTAAAATTTTGCAAGAAC
182 GAAACGCGTTTTTAGCAAAAAAAACCGTGAGTAGTACACGATTTCGGCTAAAA-----C-TG-AC
* ** * * * *
1965 TTACCCAAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGGAAAAACATATAATTCAACGAC
240 ---CCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
*
2030 AAAAAAATT-GAAGG-TTTTT
302 AAAAAAATTGGACGGATTTTT
* * * * * * * * *
2049 TACGATCCTAATATCGGTTTTCCA-TGTTTTCTGAATTCATTTATAATTAAATCGAAACAAAATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
** *
2113 CAGATTTATCGTAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGAGCTT-GATGATTATA
66 CAGA-TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG-G-TTAGATGATTATA
* *
2177 GATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGCCGAGGCCCCGAAACGCTTTT
128 GATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTT
* * * * * * *
2242 TTAAC-CAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAATATTGACCTGAAAACTTTCTT
193 TTAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGCTAAA-ACTGACCCGAAAATTTTTTT
* * ** *
2306 -CTCAATTTATTGCCACAATACT-ATGAAAAAATATGTAATTCAACGATAAAAAGATT-GACGTG
254 CCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATTCAACGCCAAAAAAATTGGACG-G
2368 A-TTTT
317 ATTTTT
* *
2373 CACGCTTCTAATATCGTTCTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * *
2438 CAGATGTTCGTAAAAACAAATCTTTATATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* * *** * * * * *
2503 ATTTCAAGGAATATTTGCACCAAAAAATCATACAAAATTGAG-CTGGGGCTCC-ATAACGCGTTT
131 ATTTCAAGGAGTCTTTATGCC-AAAAACCATGCAAAACTGAGTC-GAGGCCCCGA-AACGCGTTT
**
2566 TTAG--TTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAACTGACCCGA
193 TTAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGC--------T---AAAACTGACCCGA
** * *
2629 AAAGATTATT-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAA
244 AAATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACG-C-CAAAAA
* *
2693 AATTGAATGG-TTTTT
307 AATTGGACGGATTTTT
* * * * *
2708 CACGATTCTAATA------TT---GTTTTTT-CGAATTTATTTTTAATTAAATCGAAACTAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * *
2763 CATATGCTCGTAAAAACAAATCCTTAAATGCAATGTAGCTGAGATTTGGTTAGATGATTAAATAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* *
2828 ATTTCAAGGAGTCTATATGCCAAAAACCATGCAAAACTGAGTCGAGACCCCGAAACGCGTTTTTA
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTA
* * * **
2893 GCCAAAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGGCCCTAAAATTTTTTTTG
196 G-CAAAAAAAACCGTGA--G-TAGTACACGATTTCGGCT-AAAACTGACCCGAAAATTTTTTTCC
** ** * * * *
2958 TCAACCTTTTGCCATGATACTCTG-AAAAATAAATAAGTCAACGCCAAAAAGATT-GACTGGA-T
256 TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGAC-GGATT
3020 TTT
320 TTT
** * * * * ***
3023 CTTGCTTATAATATCG-ATTTCC-TTTTTTTCCGAATTAATATCTATTTAGGGCGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * *
3086 CAGATGCACGTAAAAA-AAATACTTATATCCAATGTGGCTGAGATTTGGTTTGATAAATATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
** ** * * * * * **
3150 ATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGCCGGGGCTCTGCGACGCGTTTTTA
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTA
* *
3215 GC--CAAAAACCGTGATGGTTAGTACACGATTTCGATAAAAATTTTG-TGAAAACTGACCCGAAT
196 GCAAAAAAAACCGTGA--G-TAGTACACGATTTCG-----------GCT-AAAACTGACCCGAAA
* * * * * * * *
3277 A-GTTTTTCCACAATTTTCTACCACAATACTCAGAAAAAATATTTATTTCAACGACAAAAATATT
246 ATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATT
* *
3341 -GAAGGGTTTTT
311 GGACGGATTTTT
* * * ** ** *
3352 TACGCTTCTAATATCGCTTTACCATGATTTTCCTTATTTATTTCTAATTAAATCGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * *
3417 TAGATGATCGTAAAAACAAATTCTTAAATCTAATGTGCCTGAGATTTGGTTAGATCATTATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* * * * * * *
3482 ATTTCAAAGAGTATTTATGCCAAAAAGGAAAAAAACCATTCATAACTGAGTTGAGGGCCCAAAAC
131 ATTTCAAGGAGTCTTTATGCC---------AAAAACCATGCAAAACTGAGTCGAGGCCCCGAAAC
3547 GCGTTTTTAGCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTGACCCGAAAATT
187 GCGTTTTTAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGCTAAAACTGACCCGAAAA-T
* * * *
3612 TTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAACATATAATTCAACGCCCAAAAGATT-G
248 TTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGG
3676 ACGAGA-TTTT
313 ACG-GATTTTT
** * * *
3686 CTTGCTTTTAATATCGTTTTTCCATTTTTTTTCCGAATCAATTGCTAATTAAATCGAAACAAGAT
1 CACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * *
3751 TCAGATGCAT-GTAAAAA-AAATCCTTATATCCAACGTGGCTGAGATTTGGTTCGATGAATATAG
65 TCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAG
** ** * * * *** *
3814 ATATTTCAAGGGAGTCTTTGCGCCAAAATTCATGCATAATTGA-TCTG-GGACTCCGGGTCACGT
129 ATATTTCAA-GGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTC-GAGG-CCCCGAAACGCGT
* * * * *
3877 TTTTAGC--CAAAAACCGTGAGTACGCGAAATCGGCTTAAATTT-TGCAAAAACTGA-CC-AAAG
191 TTTTAGCAAAAAAAACCGTGAGTA-G-TACA-C-G-----ATTTCGGCTAAAACTGACCCGAAA-
*** * * *
3937 AAGATTTTCCTCAATTATTTGCGACAATACTCAG-AAAAATATATAATTCAACGACAAAAAAATT
246 ATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATT
* * *
4001 GAAGGGTTTTTTT
311 GGACGG-ATTTTT
* * * * * *
4014 CA--ATTCTAATATAGTTTTTCCA-TGTTTTCAGAATTCATTTCTAATTAAATCGAAACAAAATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * *
4076 CAGATGATCGTAAGAACAAATCCTTAAATTCAATGTGGCTGAAATTTGGTTAGATGATTATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* * * *
4141 ATTTCAAGGAGT-TTCTATGCCAAAAACCATGCAAAATTGAGTCAAGGCCCCGAAATGTGTTTTT
131 ATTTCAAGGAGTCTT-TATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTT
* * * * * * *
4205 AG-AAAATAAACTGTGATGGTTAATACACGAATTCGGCTAAAACTGAACAGAAAAATTTTTT-CT
195 AGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGCTAAAACTGACCCGAAAATTTTTTTCCT
* * * * * *
4268 CAATTCTTTGTCACAATACTCA-AAAAAATATATAATTCAACACCAAAAAATTTGAAAGG-TTTT
257 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGACGGATTTT
4331 T
322 T
* * * *
4332 CACGCTTCAAATATCGTTTTTCCCA-TTCTTTCTGAAGTT-ATTTCTAA-TAAATCGGAACAAGA
1 CACGCTTCTAATATCGTTTTT-CCATTTTTTTCCGAA-TTAATTTCTAATTAAATCGAAACAAGA
* * * * * *
4394 TTCGGATGCTTGT-AAAA-AAATTCTTAAATCCAATATGGCTGAGATTTGGTTAGATGATTAAAT
64 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAG
* * *
4457 ATATTTAAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGATGCCCCGAAACGCGTTTT
129 ATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTT
* ** * * * *
4522 TAGC--TAAAAACTATGATGGTTAGTACACGATTTCGGCTTAATATTGTCCCGAAAACTTTTTT-
194 TAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGC-TAAAACTGACCCGAAAATTTTTTTC
* * * *
4584 CTCAATTTTTTGCCACAATACTCTGAAAAAATATGTAATTCAACGCCAAAAAGA-TAGACGGGA-
255 CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGAC-GGAT
4647 TTTT
319 TTTT
* *
4651 CACGCTTCTAATATCGTTCTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
*** *
4716 CAGATGCTCGTAAAAACAAATCCTTGTGTCCAATGTGGCTGAGATTTGGTTAGGTGATTATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
* * *
4781 TTTTCAAGCAGTCTTTATGCCAAAAACCATGCAAAACTAAGTCGAGTG-CCCGAAACGCGTTTTT
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAG-GCCCCGAAACGCGTTTTT
* * *
4845 AGC--AAAAAACTGTGGTGGTTAGTACACGATTTCGGCTAAAACCGACCC-AAAAGTTTTTTTTC
195 AGCAAAAAAAACCGT-G-AG-TAGTACACGATTTCGGCTAAAACTGACCCGAAAA--TTTTTTTC
* * *
4907 CTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATT-GACGAGA-
255 CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGACG-GAT
4970 TTTT
319 TTTT
** * * * * *
4974 CTTGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATCAATTGCTGATTAAATGGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
** * * *
5039 CAGATGCAAGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
** ** * * * * ** *
5104 ATTTCAAGGAGTCTTTGCGCCAAAATTCATG-AATAATTGAGCCG-GGACTCTGGGACACGTTTT
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA-AACTGAGTCGAGG-CCCCGAAACGCGTTTT
* * *
5167 TAGC--CAAAAACCGTGATGGTTAGTACGCGAATTCGGCTTAAATTTTGCAAAAACTGGA-CCGA
194 TAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGC--------T---AAAACT-GACCCGA
* * * * *
5229 GAA-GTTTTTCCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTTAACGAC-AAAAAA
244 AAATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAA
* *
5292 TT-GAAGGGTTTTT
309 TTGGACGGATTTTT
* * *
5305 TACGCTTCTAATATCGTTTTTCCA-TATTTTCCCAA-TATATTTCTAATTAAATCGAAACAAGAT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTA-ATTTCTAATTAAATCGAAACAAGAT
* * * * * *
5368 TCAGATGATCATAAAAACAAATTCTTAAATCCAGTGTGTCTGATATTTGGTTAGATGATTATAGA
65 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGA
* * * * ***
5433 TATTTCAAGAAGTCTCTATGCAAAAAAACCAAGCAAAACTGAGTCTTTGCCCCGAAACGCGTTTT
130 TATTTCAAGGAGTCTTTATGC-CAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTT
* * * * * **
5498 TAGC---AAAAACCGTGATATTTAGTGCACGATTTTGGTTAAAACTGAACCGAAAAGATTTTTCC
194 TAGCAAAAAAAACCGTG--A-GTAGTACACGATTTCGGCTAAAACTGACCCGAAAATTTTTTTCC
* * *
5560 TCAATTCTTTGCCATAATACTCAGAAAAAA-ATATAATTCAACGCCAAAAAGATT-GACGGGA-T
256 TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGAC-GGATT
5622 TTT
320 TTT
** **
5625 CTTGCTTCTTGTATCGTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAAT-GATAACAAGAT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA-AACAAGAT
* * * * * * *
5688 TCAGATGCACGTAATAACAAATCCTTATATTCCAATATGGCTGAGATTTGGTTCGATGAATATAA
65 TCAGATGCTCGTAAAAACAAATCCTTA-AATCCAATGTGGCTGAGATTTGGTTAGATGATTATAG
** ** * * * * * * *
5753 ATATTTCAAGGAGTCTTTGCGCCAAAATTCATTCATAATTGAGCCG-GGACTCC-AAGACACGGT
129 ATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGG-CCCCGAA-ACGCGTT
* *
5816 TTTAGC---AGAAACCGTGATGGTTAGTACACGAATTCGGCTTAAATTTTGCAAAAACTTGA-CC
192 TTTAGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGC--------T---AAAAC-TGACCC
* * * *
5877 GAGAA-GTTTTTCTTCAATTTTTTGCCACAATACTCAGATAAAATATATAATTCAACGCCAAAAA
242 GAAAATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
*
5941 GATT-GACAGGA-TTTT
307 AATTGGAC-GGATTTTT
** *
5956 CTTGCTTCT--TA-------T--A------TCCGAATTAATTTCTAATTAAATAGAAACAAGATT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * *
6004 CAGATACACGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTTGTTCGATGAATATAGAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
** * ** ** * * * * ** *
6069 ATTTCAAGGAGTCTTTGCGTCAAAATTCATGCATGATTAAGCCG-GGACTCCGGGACACGTTTTT
131 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGG-CCCCGAAACGCGTTTTT
* * * * *
6133 AGC---CAAAACCGTGATGGTTAGTACGCGAATTCGGCTTAAATTTTGCAAAAACTGAACCGAGA
195 AGCAAAAAAAACCGTGA--G-TAGTACACGATTTCGGC--------T---AAAACTGACCCGAAA
* * * **
6195 A-GTTTTTCCTCAATTTTTTGCCACAATACTCA-AAAAAATACATAATTCAACACCAAAATGATT
246 ATTTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATT
6258 -GACGAGA-TTTT
311 GGACG-GATTTTT
** * *
6269 CTTGCTTCTAATATCGTTTTTCC-TTTTTTTCCGAATCAATTGT-TGATTAAATCGAAACAAGAT
1 CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATT-TCTAATTAAATCGAAACAAGAT
* * *
6332 TCAGATGATCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCA-ATGAATATAG
65 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGATTATAG
* * *
6396 ATATTTCAAGGAGTCTCTATGCAAAAAACCATACAAAATCTGAGTC
129 ATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAA-CTGAGTC
6442 TTGGCCTCGA
Statistics
Matches: 4342, Mismatches: 759, Indels: 538
0.77 0.13 0.10
Matches are distributed among these distances:
312 1 0.00
313 48 0.01
314 177 0.04
315 81 0.02
316 3 0.00
317 74 0.02
318 173 0.04
319 166 0.04
320 308 0.07
321 167 0.04
322 406 0.09
323 469 0.11
324 356 0.08
325 216 0.05
326 104 0.02
327 132 0.03
328 114 0.03
329 234 0.05
330 229 0.05
331 181 0.04
332 150 0.03
333 124 0.03
334 181 0.04
335 141 0.03
336 27 0.01
337 16 0.00
338 2 0.00
341 32 0.01
343 30 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
CACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGAT
ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTA
GCAAAAAAAACCGTGAGTAGTACACGATTTCGGCTAAAACTGACCCGAAAATTTTTTTCCTCAAT
TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGGACGGATTTTT
Found at i:3303 original size:979 final size:959
Alignment explanation
Indices: 768--6411 Score: 4587
Period size: 979 Copynumber: 5.8 Consensus size: 959
758 CGTTTTCCCA
* * * **
768 TTTTTTCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAATACAAATTATTA
1 TTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * * * *
833 AATCGAATGTGACTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAATCTTTACACCAAAAA
66 TATCCAATGTGGCTGAGATTTGGTTCGATGATTAAAGATATTTCAAGGAGTCTTTGCGCCAAAAA
* ** * ** *
898 TCATGCAAAACTGAATCATG-C-CCCAGAACGCGTTTTTAGCCAAAAACCATGAT-G--AGTAAA
131 TCATGCAAAACTGAGTCGGGACTCCGA-AACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACA
* * *
958 CGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAAA-TTTTTCCTCAATTCTTTGCCAAAATA
195 CGATTTCGGC--------T--AAAAACTGGCCCAAAAATTTTTTTCTCAATT-TTTGCCACAATA
* * **
1022 CTCAGAAAAA-AGGTATAATTCAACG-CAAATAAAATTCA-AGGATTGTTTCACGCTTCTAATAT
249 CTCAGAAAAATA--TATAATTCAACGCCAAA-AAGATTGACAGGA-T-TTTCTTGCTTCTAATAT
* * * * * * * * *
1084 CGTTTTTTCATTTTTTTCTGAATTGATTTCTAATTAAATTGAACCAAGATTCAAATTCTCGTAAA
309 CG-TTTTCCA-TGTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGT-AA
* * * * * * * *
1149 AAATCAAATCCTTAAATCCAATGGGGATGAGATTCGATTTGATGATTATAGATATTTCAATGAGT
371 AAA--AAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT
*** ** * * ** ** * * *
1214 CTTTATACCAAAAAACCAAGCAAAACTGAGTAGAAGCCCCGAAACGCGTTTTTAGCAAAAAAAAA
434 CTTTGCGCC-AAAATTCATGCAAAATTGAGCCGGGGCTCCGAGACGCGTTTTTAGC-----CAAA
* *
1279 AACCGTGA----TA-TACACG-ATTCGGC---------T-AAAACTGACCTGAAATTTTTTTCTT
493 AACCGTGATGGTTAGTACACGAATTCGGCTAAATTTTGTAAAAACTGACC-GAAA-GTTTTTCCT
* * * * * *
1328 CAATTTTTTGTCACAATACTCACAAAAAAAATATAATTCAACGCCAAAAAAATTGGAGGATTTTT
556 CAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGAC-AAAAAATTGAAGGGTTTTT
1393 CACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGAT
619 CACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGAT
* * * *
1458 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATAAATATAAA
683 TCAGATGATCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAA
** * * *
1523 TATTTCAAGGAGTCTTTG-TGCAAAAAATCATGCAAAACTAAGTTGGGGACCTCAAAACGCGTTT
748 TATTTCAAGGAGTCTTTGCACCAAAAAATCATACAAAACTGAGCTGGGG-CC-C-AAACGCGTTT
*
1587 TTAGCCAAAAACCGTGATGGTAAGTACACGATTT-GGCTAA--AAATA-T-ACCCGAAAACTTTT
810 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAATTAAA-ACTGACCCGAAAACTTTT
* * * * *
1647 TTCTCAA-TTTTTGCCCCAATTCTCTGAAAAAAAATATAATTCAACTCCAAAAAGATTGACGGGA
874 TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGA
1711 TTTTCAC-ACTTCTAATATCATTTTTCT
939 TTTTCACGA-TTCT-A-AT-A---TTCT
*
1738 TTTATTCTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGACGCTCGTAAAAA-AATAT-
1 TTT-TT-TC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA-ATC
* * *
1801 -TTATATCAAATATGGCTGTGATTTGGTTCGATGAATCATGCAAAATTCGTATATTTCAAGGAGT
62 CTTATATCCAATGTGGCTGAGATTTGGTTCGATG-AT--T---AAA---G-ATATTTCAAGGAGT
* * *
1865 CTTTGCGCCAAAAATCATGCAAAAATGAG-CTGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTG
117 CTTTGCGCCAAAAATCATGCAAAACTGAGTC-GGGACTCCGAAACGCGTTTTTAGCCAAAAACTG
** * *
1929 TGA----T-GTACACGATTTCGGCTAAAATTTTGCAAGAACTTACCCAAAAAGTTTTTCCTCAAT
181 TGATGGTTAGTACACGATTTCGGCT---A------AA-AACTGGCCCAAAAATTTTTTTCTCAA-
* * * *
1989 TTTTTGCCATAATACTCAGGAAAAACATATAATTCAACGACAAAAAAATTGA-AGG-TTTT-TTA
235 TTTTTGCCACAATACTCA-GAAAAATATATAATTCAACGCCAAAAAGATTGACAGGATTTTCTT-
* * * * * *
2051 CGATCCTAATATCGGTTTTCCATGTTTTCTGAATTCATTTATAATTAAATCGAAACAAAATTCAG
298 -GCTTCTAATATC-GTTTTCCATGTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
** * * *
2116 ATTTATCGTAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGAGCTT-GATGATTATAGAT
361 ATGCA-CGTAAAA-AAAATCCTTATATCCAATGTGGCTGAGATTTG-G-TTCGATGAATATAGAT
** ** * * * * *
2180 ATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGCCGAGGCCCCGAAACGCTTTTTTA
422 ATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGCCGGGGCTCCGAGACGCGTTTTTA
* * * * * *
2245 ACCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAATATTG----ACCTGA---AAACTTT
487 GCC-AAAAACCGTGATGGTTAGTACACGAATTCGGCTAAATTTTGTAAAAACTGACCGAAAGTTT
* * *
2303 CTT-CTCAATTTATTGCCACAATACT-ATGAAAAAATATGTAATTCAACGATAAAAAGATTGACG
551 -TTCCTCAATTT-TTGCCACAATACTCA-GAAAAAATATATAATTCAACGACAAAAA-ATTGAAG
* * *
2366 TGATTTTCACGCTTCTAATATCGTTCTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAA
612 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAA
* *
2431 CAAGATTCAGATGTTCGTAAAAACAAATCTTTATATCCAATGTGGCTGAGATTTGGTTAGATGAA
677 CAAGATTCAGATGATCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAA
* * *
2496 TATAAATATTTCAAGGAATATTTGCACCAAAAAATCATACAAAATTGAGCTGGGGCTCCATAACG
742 TATAAATATTTCAAGGAGTCTTTGCACCAAAAAATCATACAAAACTGAGCTGGGGC-CCA-AACG
**
2561 CGTTTTTAGTTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAACTGACC
805 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT--AA--TT---AAAACTGACC
** * *
2626 CGAAAAGATTATTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGACAAAAA
863 CGAAAACTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACG-C-CAAA
* ** * *
2691 AAAATTGAATGGTTTTTCACGATTCTAATATT-G
926 AAGATTGACGGGATTTTCACGATTCTAATATTCT
* * * *
2724 TTTTTTCGAATTTATTTTTAATTAAATCGAAACTAGATTCATATGCTCGTAAAAACAAATCCTTA
1 TTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * **
2789 AATGCAATGTAGCTGAGATTTGGTTAGATGATTAAATATATTTCAAGGAGTCTATATGCCAAAAA
66 TATCCAATGTGGCTGAGATTTGGTTCGATGATTAAAGATATTTCAAGGAGTCTTTGCGCCAAAAA
* * *
2854 CCATGCAAAACTGAGTCGAGACCCCGAAACGCGTTTTTAGCCAAAAAAAACTGTGATGGTTAGTA
131 TCATGCAAAACTGAGTCGGGACTCCGAAACGCGTTTTTAGCC---AAAAACTGTGATGGTTAGTA
* * * ** *
2919 CACGATTTCGGCTAAAAACTGGCCCTAAAATTTTTTTTGTCAACCTTTTGCCATGATACTCTGAA
193 CACGATTTCGGCTAAAAACTGGCCC-AAAAATTTTTTTCTCAA-TTTTTGCCACAATACTCAGAA
* * * * * * *
2984 AAATAAATAAGTCAACGCCAAAAAGATTGACTGGATTTTCTTGCTTATAATATCGATTTCCTTTT
256 AAATATATAATTCAACGCCAAAAAGATTGACAGGATTTTCTTGCTTCTAATATCGTTTTCCATGT
* * *** *
3049 TTTCCGAATTAATATCTATTTAGGGCGAAACAAGATTCAGATGCACGTAAAAAAAATACTTATAT
321 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAAAAATCCTTATAT
* *
3114 CCAATGTGGCTGAGATTTGGTTTGATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAATTCA
386 CCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAATTCA
* * *
3179 TGCAAAATTGAGCCGGGGCTCTGCGACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
451 TGCAAAATTGAGCCGGGGCTCCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAA
* * * *
3244 TTC-GATAAAAATTTTGTGAAAACTGACCCGAATAGTTTTTCCACAATTTTCTACCACAATACTC
516 TTCGGCT--AAATTTTGTAAAAACTGA-CCGAA-AGTTTTTCCTCAATTTT-TGCCACAATACTC
* * * * *
3308 AGAAAAAATATTTATTTCAACGACAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCGCTTTA
576 AGAAAAAATATATAATTCAACGACAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
** ** *
3373 CCATGATTTTCCTTATTTATTTCTAATTAAATCGAAACAAGATTTAGATGATCGTAAAAACAAAT
640 CCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAAT
* * * * * * *
3438 -TCTTAAATCTAATGTGCCTGAGATTTGGTTAGATCATTATAGATATTTCAAAGAGTATTTATGC
705 CT-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGT-CTT-TG-
** * * * * *
3502 CAAAAAGGAAAAAAACCATTCATAACTGAGTTGAGGGCCCAAAACGCGTTTTTAGCAAAAAAAAC
766 C----A-CCAAAAAATCATACAAAACTGAGCTG-GGGCCC-AAACGCGTTTTTAGC--CAAAAAC
* *
3567 CGTGATGGTTAGTACACGATTTCGGC----TAAAACTGACCCGAAAATTTTTTTTCCTCAATTCT
822 CGTGATGGTTAGTACACGATTTCGGCTAATTAAAACTGACCCGAAAA-CTTTTTT-CTCAATTTT
* * * ** *
3628 TTGCCACAATACTCAGAAAAAACATATAATTCAACGCCCAAAAGATTGACGAGATTTTCTTGCTT
885 TTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGATT
*
3693 TTAATATCGTTTTTCCATT
950 CTAATA------TT-C--T
* *
3712 TTTTTTCCGAATCAATTGCTAATTAAATCGAAACAAGATTCAGATGCAT-GTAAAAA-AAATCCT
1 TTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCT
* * *
3775 TATATCCAACGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGGAGTCTTTGCGCCAA
64 TATATCCAATGTGGCTGAGATTTGGTTCGATGATTAAAGATATTTCAA-GGAGTCTTTGCGCCAA
* * * *** * *
3840 AATTCATGCATAATTGA-TCTGGGACTCCGGGTCACGTTTTTAGCCAAAAACCGTGA--G-TACG
128 AAATCATGCAAAACTGAGTC-GGGACTCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTA-G
* * * * ** * *
3901 CGAAATCGGCTTAAATTT-TGC-AAAAACT-GACCAAAGAAGATTTTCCTCAATTATTTGCGACA
191 -TACA-C-G-----ATTTCGGCTAAAAACTGGCCCAAA-AATTTTTTTCTCAATT-TTTGCCACA
* * * *
3963 ATACTCAGAAAAATATATAATTCAACGACAAAAAAATTGA-AGGGTTTT-TTTCAATTCTAATAT
246 ATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTGACAGGATTTTCTTGC--TTCTAATAT
* * * *
4026 AGTTTTTCCATGTTTTCAGAATTCATTTCTAATTAAATCGAAACAAAATTCAGATG-ATCGTAAG
309 CG-TTTTCCATGTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCA-CGTAA-
* * * * * *
4090 AACAAATCCTTAAATTCAATGTGGCTGAAATTTGGTTAGATGATTATAGATATTTCAAGGAGT-T
371 AAAAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
** ** * ** * * * * ** *
4154 TCTATGCCAAAAACCATGCAAAATTGAGTCAAGGCCCCGAAATGTGTTTTTAGAAAATAAACTGT
436 T-TGCGCCAAAATTCATGCAAAATTGAGCCGGGGCTCCGAGACGCGTTTTTAGCCAA-AAACCGT
* ** * * *
4219 GATGGTTAATACACGAATTCGGCTAAA-ACTG----AACAGA---AAAATTTTTTCTCAATTCTT
499 GATGGTTAGTACACGAATTCGGCTAAATTTTGTAAAAACTGACCGAAAGTTTTTCCTCAATT-TT
* *
4276 TGTCACAATACTCA-AAAAAATATATAATTCAAC-ACCAAAAAATTTGAAAGGTTTTTCACGCTT
563 TGCCACAATACTCAGAAAAAATATATAATTCAACGA-CAAAAAA-TTGAAGGGTTTTTCACGCTT
* * * * * *
4339 CAAATATCGTTTTTCCCA-TTCTTTCTGAAGTTATTTCTAA-TAAATCGGAACAAGATTCGGATG
626 CTAATATCGTTTTT-CCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATG
* * * * * *
4402 CTTGTAAAAA-AATTC-TTAAATCCAATATGGCTGAGATTTGGTTAGATGATTA-AATATATTTA
690 ATCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAA-ATATTTC
*** * * * *
4464 AAGGAGTCTTTATGCC-AAAAATCATGCAAAACTGAG-TCGATGCCCCGAAACGCGTTTTTAGCT
754 AAGGAGTCTTTGCACCAAAAAATCATACAAAACTGAGCT-G-GGGCCC-AAACGCGTTTTTAGCC
** * * *
4527 AAAAACTATGATGGTTAGTACACGATTTCGGC---TTAATATTGTCCCGAAAACTTTTTTCTCAA
816 AAAAACCGTGATGGTTAGTACACGATTTCGGCTAATTAAAACTGACCCGAAAACTTTTTTCTCAA
* * *
4589 TTTTTTGCCACAATACTCTGAAAAAATATGTAATTCAACGCCAAAAAGATAGACGGGATTTTCAC
881 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCAC
*
4654 GCTTCTAATATCGTTCTTCCAT
946 GATTCTAATA------TT-C-T
*
4676 TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * * * **
4741 GTGTCCAATGTGGCTGAGATTTGGTTAGGTGATTATAGATTTTTCAAGCAGTCTTTATGCCAAAA
65 ATATCCAATGTGGCTGAGATTTGGTTCGATGATTAAAGATATTTCAAGGAGTCTTTGCGCCAAAA
* * * *
4806 ACCATGCAAAACTAAGTCGAGTG-C-CCGAAACGCGTTTTTAGCAAAAAACTGTGGTGGTTAGTA
130 ATCATGCAAAACTGAGTCG-G-GACTCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTA
* * *
4869 CACGATTTCGGCT-AAAACCGACCCAAAAGTTTTTTTTCCTCAATTCTTTGCCACAATACTCAGA
193 CACGATTTCGGCTAAAAACTGGCCCAAAA-ATTTTTTT-CTCAATT-TTTGCCACAATACTCAG-
*
4933 AAAAATATATAATTCAAAGCCAAAAAGATTGAC-GAGATTTTCTTGCTTCTAATATCGTTTTTCC
254 AAAAATATATAATTCAACGCCAAAAAGATTGACAG-GATTTTCTTGCTTCTAATATCG-TTTTCC
* * * * * * *
4997 TTTTTTTTCCGAATCAATTGCTGATTAAATGGAAACAAGATTCAGATGCAAGTAAAAACAAATCC
317 -ATGTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAA-AAATCC
5062 TTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAA
380 TTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAA
* * * *
5127 AATTCATG-AATAATTGAGCCGGGACTCTGGGACACGTTTTTAGCCAAAAACCGTGATGGTTAGT
445 AATTCATGCAA-AATTGAGCCGGGGCTCCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
* *
5191 ACGCGAATTCGGCTTAAATTTTGCAAAAACTGGACCGAGAAGTTTTTCCTCAATTTTTTGCCACA
509 ACACGAATTCGGC-TAAATTTTGTAAAAACT-GACCGA-AAGTTTTTCCTCAA-TTTTTGCCACA
* * *
5256 ATACTTAGAAAAAATATATAATTTAACGACAAAAAATTGAAGGGTTTTTTACGCTTCTAATATCG
570 ATACTCAGAAAAAATATATAATTCAACGACAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
* * * *
5321 TTTTTCCA-TATTTTCCCAATATATTTCTAATTAAATCGAAACAAGATTCAGATGATCATAAAAA
635 TTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAA
* * * * * *
5385 CAAAT-TCTTAAATCCAGTGTGTCTGATATTTGGTTAGATGATTATAGATATTTCAAGAAGTCTC
700 CAAATCT-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCT-
* ** *
5449 TATGCA--AAAAAACCA-AGCAAAACTGAGTCTTTGCCCCGAAACGCGTTTTTAG-CAAAAACCG
763 T-TGCACCAAAAAATCATA-CAAAACTGAG-CTGGGGCCC-AAACGCGTTTTTAGCCAAAAACCG
** * * * * * *
5510 TGATATTTAGTGCACGATTTTGG----TTAAAACTGAACCGAAAAGATTTTTCCTCAATTCTTTG
824 TGATGGTTAGTACACGATTTCGGCTAATTAAAACTGACCCGAAAA-CTTTTTTCTCAATTTTTTG
* ** *
5571 CCATAATACTCAGAAAAAA-ATATAATTCAACGCCAAAAAGATTGACGGGATTTTCTTGCTTCTT
888 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGATTC--
* *
5635 GTATCGTTTTTCCAT
951 -TA---ATATT-C-T
* * *
5650 TTTTTCCGAATTAATTTCTAATTAAAT-GATAACAAGATTCAGATGCACGTAATAACAAATCCTT
1 TTTTTTCGAATTAATTTCTAATTAAATCGA-AACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* *
5714 ATATTCCAATATGGCTGAGATTTGGTTCGATGAATATAA-ATATTTCAAGGAGTCTTTGCGCCAA
65 ATA-TCCAATGTGGCTGAGATTTGGTTCGATGATTA-AAGATATTTCAAGGAGTCTTTGCGCCAA
* * * * * * * * *
5778 AATTCATTCATAATTGAGCCGGGACTCC-AAGACACGGTTTTAG-CAGAAACCGTGATGGTTAGT
128 AAATCATGCAAAACTGAGTCGGGACTCCGAA-ACGCGTTTTTAGCCAAAAACTGTGATGGTTAGT
* * * * * *
5841 ACACGAATTCGGCTTAAATTTTGCAAAAACTTGACCGAGAA-GTTTTTCTTCAATTTTTTGCCAC
192 ACACGATTTCGGC--------T--AAAAACTGGCCCAAAAATTTTTTTC-TCAA-TTTTTGCCAC
5905 AATACTCAGATAAAATATATAATTCAACGCCAAAAAGATTGACAGGATTTTCTTGCTTCT--TA-
245 AATACTCAGA-AAAATATATAATTCAACGCCAAAAAGATTGACAGGATTTTCTTGCTTCTAATAT
* *
5967 -----T--A-----TCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATACACGTAAAAA
309 CGTTTTCCATGTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAA
*
6020 CAAATCCTTATATCCAATGTGGCTGAGATTTTGTTCGATGAATATAGATATTTCAAGGAGTCTTT
374 -AAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* ** * * * *
6085 GCGTCAAAATTCATGCATGATTAAGCCGGGACTCCGGGACACGTTTTTAGCC-AAAACCGTGATG
438 GCGCCAAAATTCATGCAAAATTGAGCCGGGGCTCCGAGACGCGTTTTTAGCCAAAAACCGTGATG
* *
6149 GTTAGTACGCGAATTCGGCTTAAATTTTGCAAAAACTGAACCGAGAAGTTTTTCCTCAATTTTTT
503 GTTAGTACACGAATTCGGC-TAAATTTTGTAAAAACTG-ACCGA-AAGTTTTTCCTCAA-TTTTT
* * * * * **
6214 GCCACAATACTCA-AAAAAATACATAATTCAAC-ACCAAAATGATTGACGAGATTTTCTTGCTTC
564 GCCACAATACTCAGAAAAAATATATAATTCAACGA-CAAAA-AATTGAAGGGTTTTTCACGCTTC
** *
6277 TAATATCGTTTTTCC-TTTTTTTCCGAATCAATTGT-TGATTAAATCGAAACAAGATTCAGATGA
627 TAATATCGTTTTTCCATTTTTTTCCGAATTTATT-TCTAATTAAATCGAAACAAGATTCAGATGA
* * *
6340 TCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCA-ATGAATATAGATATTTCA
691 TCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAAATATTTCA
6404 AGGAGTCT
755 AGGAGTCT
6412 CTATGCAAAA
Statistics
Matches: 3826, Mismatches: 601, Indels: 500
0.78 0.12 0.10
Matches are distributed among these distances:
958 4 0.00
959 8 0.00
960 9 0.00
961 23 0.01
962 79 0.02
963 166 0.04
964 329 0.09
965 289 0.08
966 40 0.01
967 17 0.00
968 43 0.01
969 32 0.01
970 78 0.02
971 58 0.02
972 36 0.01
973 305 0.08
974 216 0.06
975 171 0.04
976 46 0.01
977 120 0.03
978 145 0.04
979 415 0.11
980 245 0.06
981 125 0.03
982 118 0.03
983 69 0.02
984 19 0.00
985 35 0.01
986 20 0.01
987 40 0.01
988 71 0.02
989 185 0.05
990 78 0.02
991 136 0.04
992 30 0.01
993 25 0.01
994 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (959 bp):
TTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
TATCCAATGTGGCTGAGATTTGGTTCGATGATTAAAGATATTTCAAGGAGTCTTTGCGCCAAAAA
TCATGCAAAACTGAGTCGGGACTCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACAC
GATTTCGGCTAAAAACTGGCCCAAAAATTTTTTTCTCAATTTTTGCCACAATACTCAGAAAAATA
TATAATTCAACGCCAAAAAGATTGACAGGATTTTCTTGCTTCTAATATCGTTTTCCATGTTTTCC
GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAAAAATCCTTATATCCAAT
GTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAA
AATTGAGCCGGGGCTCCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAATTCGG
CTAAATTTTGTAAAAACTGACCGAAAGTTTTTCCTCAATTTTTGCCACAATACTCAGAAAAAATA
TATAATTCAACGACAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTC
CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCTTTAAATCCA
ATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTTGCACCAAAAAATCATA
CAAAACTGAGCTGGGGCCCAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
GCTAATTAAAACTGACCCGAAAACTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATA
TAATTCAACGCCAAAAAGATTGACGGGATTTTCACGATTCTAATATTCT
Found at i:6515 original size:32 final size:33
Alignment explanation
Indices: 6456--6529 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 33
6446 CCTCGAAATG
*
6456 TATCTCATAGTATCAATTTTTTTTTTTTGGCAA
1 TATCTCATAGTATCAATGTTTTTTTTTTGGCAA
6489 TATCTCATAGTATC-ATGTTTTTTTTTTGGCAA
1 TATCTCATAGTATCAATGTTTTTTTTTTGGCAA
6521 TA-CT-ATAGT
1 TATCTCATAGT
6530 GCAATACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 5 0.12
31 2 0.05
32 19 0.47
33 14 0.35
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (33 bp):
TATCTCATAGTATCAATGTTTTTTTTTTGGCAA
Found at i:16131 original size:36 final size:36
Alignment explanation
Indices: 16090--16162 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
16080 AATTGAACGC
16090 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
1 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
*
16126 ATGGGTTCTTCAGCTTAAATACTCAAATCAGGATTA
1 ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
16162 A
1 A
16163 AATTTTGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (36 bp):
ATGGGTTCCTCAGCTTAAATACTCAAATCAGGATTA
Found at i:17879 original size:16 final size:16
Alignment explanation
Indices: 17858--17890 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17848 TGATTACATC
17858 TGAGTCGGAATAATAT
1 TGAGTCGGAATAATAT
17874 TGAGTCGGAATAATAT
1 TGAGTCGGAATAATAT
17890 T
1 T
17891 TTGTAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (16 bp):
TGAGTCGGAATAATAT
Found at i:23496 original size:24 final size:24
Alignment explanation
Indices: 23450--23496 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23440 GTTTGATTTA
* *
23450 ATTAATTAATAGTAATAATAATTC
1 ATTAATTAATAGTAACAAAAATTC
23474 ATTAATTAAT-GTTAACAAAAATT
1 ATTAATTAATAG-TAACAAAAATT
23497 TTCATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTAATTAATAGTAACAAAAATTC
Found at i:31533 original size:17 final size:17
Alignment explanation
Indices: 31511--31544 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31501 AAACAGAGGA
31511 AGAATCCAATTCCAAGG
1 AGAATCCAATTCCAAGG
31528 AGAATCCAATTCCAAGG
1 AGAATCCAATTCCAAGG
31545 GGTATATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (17 bp):
AGAATCCAATTCCAAGG
Done.