Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020794.1 Corchorus olitorius cultivar O-4 contig20827, 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: 52078
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:677 original size:336 final size:334
Alignment explanation
Indices: 1--1048 Score: 1177
Period size: 336 Copynumber: 3.1 Consensus size: 334
* *
1 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGAAACGTGTTTTTTTTTTGTCAAAAATCG
1 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACG-GGTTTTTTTTTGTCAAAAATCG
*
66 TGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGATAAGGTTTTCCTCAAT
65 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGATAAGGTTTTCCTCAAT
* * **
131 TTTTTGCCACAATAGTCAGAAAAAATATTTAATTCATTGCCAGAAAAATTGAAGGGGTTTTTTCA
130 TTTTTGCCACAATACTCAGAAAAAAAATTT-ATTCAACGCCAG-AAAATTGAA-GGGTTTTTTCA
* * *
196 CGCTTCTAATATGGTTTTTCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTAA
192 CGCTTCTAATATCGTTTTTCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCA
* ** ** * *
261 TATGCTTGTAAAAAC-AAATTAT-TAACTCCATTGTAGATGAGATTTGGTTAGATGAATATAGAT
257 GATGCACGTAAAAACAAAACCATATAA--CCATTGTGGCTGAGATTTGGTTAGATGAATATAGAT
324 ATTTCAAGGAGTCTT
320 ATTTCAAGGAGTCTT
339 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACGGGTTTTTTTTTGTCAAAAATCGT
1 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACGGGTTTTTTTTTGTCAAAAATCGT
* *
404 TATGGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAACTGACCCGATAAGGTTTTCCTCAATT
66 GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGATAAGGTTTTCCTCAATT
* *
469 TTTTGGCACAATATTCAGAAAAAAAATTTATTCAACGCCAGAATAATTGAAGGGTTTTTTCACGC
131 TTTTGCCACAATACTCAGAAAAAAAATTTATTCAACGCCAGAA-AATTGAAGGGTTTTTTCACGC
*
534 ATCTAATATCGTTTTTCTATATTTTTTCC-AACTTAATTTCTAATTAAATCGAAACAAAATTCAG
195 TTCTAATATCGTTTTTCTAT-TTTTTTCCGAA-TTAATTTCTAATTAAATCGAAACAAAATTCAG
* * * *
598 ATGCACGTAAAAACAAAACCATATAACCATTGTGGCTTAGATTTGGGTCGATGAATATAGCTATT
258 ATGCACGTAAAAACAAAACCATATAACCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATT
*
663 TCAAGGATTCTT
323 TCAAGGAGTCTT
* * * ** * * * * * *
675 TGCACCTAAAATCATGCAAAATTGAGCCGGGGGTCCAGAAC--G-TATTTTTAGCCAGAAACCGT
1 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACGGGTTTTTTTTTGTCAAAAATCGT
* * * * * * *
737 GATGGTTAGTACACAATTTCGCCTAAAATTTTGCCAAAACTTACCCGAAAAGCTTTACCAT-AAT
66 GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGATAAGGTTTTCC-TCAAT
* * *
801 TATTTT-CCATAATACTCAAAATATATATATATATATATATATATAAATTAACGCCA-AAAAGTT
130 T-TTTTGCCACAATACTC---AGA-A-A-A-A-A-A-AT-T-TAT---TCAACGCCAGAAAA--T
* * *
864 TGACGGGCTTTTT-ACGCTTCTAATATCGTTTTTCCT-TTTTTTTCCTCGAATTAATTTCTAATC
177 TGAAGGGTTTTTTCACGCTTCTAATATCGTTTTT-CTATTTTTTT-C-CGAATTAATTTCTAATT
* * * * * * *
927 AAATCAAAACAAAATTCAGATGCACGGAAAAACAAAACCTTATATCCAATGTGCCAGAGATTTGG
239 AAATCGAAACAAAATTCAGATGCACGTAAAAACAAAACCATATAACCATTGTGGCTGAGATTTGG
992 TTAGATGAATATAGATATTTC-AGAGAGTCTT
304 TTAGATGAATATAGATATTTCAAG-GAGTCTT
*
1023 T-CTGCCCAAAATCATGCAAAATTGAG
1 TGC-GCCAAAAATCATGCAAAATTGAG
1049 CCCGGGTCGC
Statistics
Matches: 612, Mismatches: 68, Indels: 50
0.84 0.09 0.07
Matches are distributed among these distances:
333 78 0.13
334 6 0.01
335 35 0.06
336 148 0.24
337 116 0.19
338 45 0.07
339 1 0.00
340 1 0.00
341 1 0.00
342 1 0.00
343 2 0.00
344 1 0.00
345 3 0.00
346 8 0.01
347 26 0.04
348 138 0.23
349 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (334 bp):
TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACGGGTTTTTTTTTGTCAAAAATCGT
GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGATAAGGTTTTCCTCAATT
TTTTGCCACAATACTCAGAAAAAAAATTTATTCAACGCCAGAAAATTGAAGGGTTTTTTCACGCT
TCTAATATCGTTTTTCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATG
CACGTAAAAACAAAACCATATAACCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
AGGAGTCTT
Found at i:828 original size:2 final size:2
Alignment explanation
Indices: 821--845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
811 AATACTCAAA
821 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
846 AATTAACGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1559 original size:303 final size:303
Alignment explanation
Indices: 839--3913 Score: 1059
Period size: 303 Copynumber: 9.8 Consensus size: 303
829 ATATATATAT
* * *
839 ATATATAAATT-AACGCCAAAAAGTTTGACGG-GCTTTTTACGCTTCTAATATCGTTTTTCCTTT
1 ATATAT-AATTCAACGCCAAAAAATTTGATGGAG-TTTTCACGCTTCTAATATCG-TTTTCCTTT
* * * *
902 TTTTTCCTCGAATTAATTTCTAATCAAATCAAAACAAAATTCAGATGCACGGAAAAACAAAACCT
63 TTTTT-C-CGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCT
* *
967 TATATCCAATGT-GCCAGAGATTTGGTTAGATGAATATAGATATTTC-AGAGAGTCTTTCTGCCC
125 TATATCCAATGTGGCTA-AGATTTGGTTAGATGAATATAGATATTTCAAGA-AGTCTTTCTGCCA
* * * *
1030 AAAATCATGCAAAATTGAGCCCGGGTCGCGAAACTCGTTTTTAGCAAAAAACTGTTATGTTTTGG
188 AAAATCATGCAAAATTGAG-CCGGGCCCCGAAACGCGTTTTTAG--AAAAACTG-TA-GTTTCGG
* ** * *
1095 CTAAAAACTGACTCGTGAATTATTTTTCTCGATTTGTTTCCACAATACTCAGAAAA
248 CTAAAAACTGACCCGAAAATTATTTTTCCCAATTTGTTTCCACAATACTCAGAAAA
* * * ** *
1151 ATATTTAATTCAATGCCAAAAAATTTGGTAGGCA--TTTCACGC-TCTAAATATCGTATCACCAT
1 ATATATAATTCAACGCCAAAAAATTTGAT-GG-AGTTTTCACGCTTCT-AATATCGT-TTTCCTT
* * *
1213 TTTTTTCCGAACTAATTTCTAGTTAAATCGAAACAAGATTCAGATTG-TCGTAAAAACAAATCCT
62 TTTTTTCCGAATTAATTTCTA-TTAAATCGAAACAAAATTCAGA-TGCTCGTAAAAACAAAACCT
*
1277 TATATCCAATGTGGCTAAGATTTGGTTAGATGAGTATAGATATTTCAAGAAGTCTTTCTGCCAAA
125 TATATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAA
* * *
1342 AATCATGCAAAACTGAGCCGGGCCCCGAAACGCGCGTTTTTAG-TACAC-G-A-TTTCGGCTAAA
190 AATCATGCAAAATTGAGCCGGGCCCCGAAA--CGCGTTTTTAGAAAAACTGTAGTTTCGGCTAAA
* * *
1403 AACTGGCCCGAAAATT-TTTTTCCCAATTT-TTTGCCATAATAGTCAGAAAAA
253 AACTGACCCGAAAATTATTTTTCCCAATTTGTTT-CCACAATACTCAG-AAAA
*
1454 ATATATAATTCAACGCCAAAAAAATTGATGGAGTTTTCACGCTTCTAATATCGATTTTCCTTTTT
1 ATATATAATTCAACGCCAAAAAATTTGATGGAGTTTTCACGCTTCTAATATCG-TTTTCCTTTTT
1519 TTTCCGAATTAATTTCTGATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTATA
65 TTTCCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTATA
* * * * * * * *
1584 TCCATTGTGGCTGAGATTTGGATCGATGAATATAGATATTTTAAGGATTGTTTGC-GCCAAAAAT
129 TCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTT-CTGCCAAAAAT
* ** *
1648 CATGCAAAATTTAGCCGGGGGTCC-ATAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACAC
193 CATGCAAAATTGAGCC-GGGCCCCGA-AACGCGTTTTTAG--AAAAAC---------T-GT--A-
** * * *
1712 GATTTCGGCTAAAATTTTGCAAAAACTGACCCG-AAA-GGTTTGTCTCAA-TTCTTTCCACAATA
241 G-TTTCGGC--------T--AAAAACTGACCCGAAAATTATTTTTCCCAATTTGTTTCCACAATA
1774 CTCAGAAAAA
295 CTCAG-AAAA
* * * * ** ***
1784 ATACATAATTCAACACCAAAAAAATTGACGG-GCTTGAATT-A-ATTTCTAATTAAATCG--AAA
1 ATATATAATTCAACGCCAAAAAATTTGATGGAG-TT---TTCACGCTTCTAA-T--ATCGTTTTC
**** ** * * * * * * * * ***
1844 C---AAACTCC-AGA-T-GCTTGTA--AAAACAAAACCTTATATCCA-ATG-TGGCTGAGAATTG
59 CTTTTTTTTCCGA-ATTAATTTCTATTAAATCGAAA-C-AAAATTCAGATGCTCG-T-AAAAACA
* * * * * ** ** * *
1899 GATCGATGAATAT--AGATAT-TTTAAGGATTCT--TT-GCACCAA-A-A-ATCA-TGCAAAATT
119 AAAC-CT-TATATCCA-ATGTGGCTAA-GATT-TGGTTAG-ATGAATATAGAT-ATTTCAAGA--
* **** * * ** * * ** *** * * * **
1954 GAGCCGGGGTTCCAGAACGCATTTTTAGTCAAAAACTGTG-ATGG-TTAG-TACACGATTTCGGC
175 -AGTCTTTCTGCCA-AA---AATCAT-G-C-AAAATTGAGCCGGGCCCCGAAACGCGTTTTTAG-
* * * * *
2016 AAAAA---T--TTT--GC-AAAAACTTACCCG-AAATGTTTTTTTCACAATTAT-TTGCCATAAT
231 AAAAACTGTAGTTTCGGCTAAAAACTGACCCGAAAAT-TATTTTTCCCAATT-TGTTTCCACAAT
2071 ACTCAGAAAAA
294 ACTCAG-AAAA
* * * * *
2082 ATATATAATTCAACACCAAAAAAATTGA-CGAGCATTTCACGCTTCTAATATTGTTTTTCCTTTT
1 ATATATAATTCAACGCCAAAAAATTTGATGGAG-TTTTCACGCTTCTAATATCG-TTTTCCTTTT
* *
2146 TTTTCCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCACGTAAAAACAAAACCTTA
64 TTTT-CCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTA
* * * * * * * *
2211 TATCCATTGTGGCTGAGATTTGGATCGATAAATATAGATATTTCAAGGATTTTTTGC-GCCAAAA
127 TATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTT-CTGCC-AAA
* * ** * *
2275 AATCATACAAAATTGAGGCGGGGTCC-AGAACACATTTTTAGCCAAAAATCGAGATGGTTAGTAC
190 AATCATGCAAAATTGAGCCGGGCCCCGA-AACGCGTTTTTAG--AAAAA-C----T-G-TAG---
* * ** *
2339 ACAATTTCGCCTAAAATTTTGCCAAAACTTACCCGAAAA--GCTTTTCCATAATTAT-TTGT-CA
242 ----TTTCGGCT---A-------AAAACTGACCCGAAAATTATTTTTCC-CAATT-TGTT-TCCA
* *
2400 TAACACTCAGAAAAAA
290 CAATACTCAG--AAAA
* * * * * *
2416 AAATATAATTCAACGCCAAAAAAAATT-ACGTG-TTTTTTACGCTTCTAATATCATTTTTCCTTT
1 ATATATAATTCAACGCC-AAAAAATTTGATG-GAGTTTTCACGCTTCTAATATC-GTTTTCCTTT
* * *
2479 TTTCT-CGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGGAAAAAAAAAACCTTA
63 TTTTTCCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTA
* *
2543 TATCCAATGT-GCTAGAGATTTGGTTAGATGAATATAGATATTT-TAGAGAGTCTTTCTGCCCAA
127 TATCCAATGTGGCTA-AGATTTGGTTAGATGAATATAGATATTTCAAGA-AGTCTTTCTGCCAAA
** * * * *
2606 AATCATGCAAAATTGAGCCCAAGTCCCGAAACTCGTTTTTAGGAAAAACCGTTATGTTTTGGCTA
190 AATCATGCAAAATTGAG-CCGGGCCCCGAAACGCGTTTTTA-GAAAAACTG-TA-GTTTCGGCTA
* * * * * *
2671 AAAACTGACTCGAGAATTTTTTTTTCTCAATTT-TTT-----GTACT-AAAAAA
251 AAAACTGACCCGA-AAATTATTTTTCCCAATTTGTTTCCACAATACTCAGAAAA
* * * * **
2718 TATATATAATTCAACACCCAAAAAA-TT-ATGG-GCATTTCACGCTTCTAATATCATTTTATCAA
1 -ATATATAATTCAAC-GCCAAAAAATTTGATGGAG-TTTTCACGCTTCTAATATCGTTTT-CCTT
* * * *
2780 TTTTTTCCGAATTAATTTCTGATTAAATTGAAACAAAAGTCAGATACTCGTAAAAACAAATCCTT
62 TTTTTTCCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTT
* * * * * *
2845 ATAACCAATGAGGTTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAGTCTTTCTGCCAAAA
126 ATATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAA
* * * *
2910 ATCATG-TAAATCTGAGTCGGGGCCTCGAAACGCGTTTTTAGCAAAAAAACTGTGATAATTTCGG
191 ATCATGCAAAAT-TGAG-CCGGGCCCCGAAACGCGTTTTTAG---AAAAAC--TG-TAGTTTCGG
* * * * * * * *
2974 TTAAAAACTGACACAAAAATT-TTTTTCTC-TTTTTTTTGCCATACTACTCAGAAAAA
248 CTAAAAACTGACCCGAAAATTATTTTTCCCAATTTGTTT-CCACAATACTCAG-AAAA
* *
3030 ATTTATAATTCAACGCCAAAAAAATTGATGG-GCTTTTCACGCTTCTAATATCGTTTTTCC--TT
1 ATATATAATTCAACGCCAAAAAATTTGATGGAG-TTTTCACGCTTCTAATATCG-TTTTCCTTTT
* * *
3092 TTTTCTGAATTAATATCTAATTAAATCG-AACAAAAATTCAGATGCTCGTAAACACAAAACCTTA
64 TTTTCCGAATTAATTTCT-ATTAAATCGAAAC-AAAATTCAGATGCTCGTAAAAACAAAACCTTA
* * * * * *
3156 TATCCAATGTGGCTGAGATTTGGATCGAAT-AATATAGATATTTCAAGGATTCTTTGC-ACCAAA
127 TATCCAATGTGGCTAAGATTTGGTTAG-ATGAATATAGATATTTCAAGAAGTCTTT-CTGCCAAA
* * ** * * *
3219 AATCATGCAAACTTGAGCCAAGGGTCTAG-GACACATTTTTAGCCAAAAACTGTGATGATTAGTA
190 AATCATGCAAAATTGAGCC--GGGCCCCGAAACGCGTTTTTAG--AAAAAC---------T-GT-
*
3283 CACGATTTCGGCTATAATTTTGCAAAAACTGACCC-AAAA--AGTTTTTCCTCAATTT-TTGCCA
240 -A-G-TTTCGGC--------T--AAAAACTGACCCGAAAATTA-TTTTTCC-CAATTTGTTTCCA
* *
3344 CTATACTCATAAAAA
290 CAATACTCA-GAAAA
* ** * *
3359 ATATATTATTCAACGCCAAAAAAAATGAAGG-GTTTTTCACGCTTCTAATATCGTTTTTTTCATT
1 ATATATAATTCAACGCCAAAAAATTTGATGGAG-TTTTCACGCTTCTAATATCG---TTTTCCTT
* * * * *
3423 TTTTTTCTGAATT-ATTTCTAATTAAATCTAAACAAGATTCAGATGGTTGTAAAAACAAAACCTT
62 TTTTTTCCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTT
* * * *
3487 ATATCCAATGTGGCTGAGATTTGGATCA-ATGAATATAGATATTTCAAGCAGTCTTTGTGCCAAA
126 ATATCCAATGTGGCTAAGATTTGG-TTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAA
* * ** * *
3551 AATCATGCAAAGTTGAGCCGGGGCTCCGGTACGCATTTTTAGGCAAAAATCGTATACGATTTCGG
190 AATCATGCAAAATTGAGCC-GGGCCCCGAAACGCGTTTTTA-G-AAAAA-C-TGTA-G-TTTCGG
* * * * *
3616 TTAAAATTTTGTAAAAACTGACTCGAAAGTTA--TTTCCTCAATTT-TTAGT-CATAATACTCAT
248 ----------CTAAAAACTGACCCGAAAATTATTTTTCC-CAATTTGTT--TCCACAATACTCAG
3677 AAAA
300 AAAA
* * * * *
3681 ATTATATAATCCAACGCC-AAACATATTG-TAGG-GCTTTCCATGCTTGTAATATCGGTTTTCCT
1 A-TATATAATTCAACGCCAAAAAAT-TTGAT-GGAG-TTTTCACGCTTCTAATATC-GTTTTCCT
* ** * *** *
3743 ATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCC
61 -TTTTTTTCCGAATTAATTTCT-ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACC
* * * * *
3807 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGC-GCCA
124 TTATATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTT-TCTGCCA
* * *
3871 AAAATCATGCAAAATTGACCCGGGGCCCAAAACGCGTTTTTAG
188 AAAATCATGCAAAATTGAGCCGGGCCCCGAAACGCGTTTTTAG
3914 CCCAAAAAAA
Statistics
Matches: 2085, Mismatches: 411, Indels: 526
0.69 0.14 0.17
Matches are distributed among these distances:
294 3 0.00
295 17 0.01
296 2 0.00
297 16 0.01
298 57 0.03
299 4 0.00
300 2 0.00
301 23 0.01
302 85 0.04
303 359 0.17
304 55 0.03
305 25 0.01
306 30 0.01
307 10 0.00
308 6 0.00
309 34 0.02
310 257 0.12
311 59 0.03
312 78 0.04
313 6 0.00
314 1 0.00
316 4 0.00
317 1 0.00
318 1 0.00
319 7 0.00
320 7 0.00
321 26 0.01
322 148 0.07
323 93 0.04
324 10 0.00
325 28 0.01
326 13 0.01
327 14 0.01
328 12 0.01
329 76 0.04
330 67 0.03
331 66 0.03
332 263 0.13
333 41 0.02
334 66 0.03
335 12 0.01
336 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (303 bp):
ATATATAATTCAACGCCAAAAAATTTGATGGAGTTTTCACGCTTCTAATATCGTTTTCCTTTTTT
TTCCGAATTAATTTCTATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTATATC
CAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCAT
GCAAAATTGAGCCGGGCCCCGAAACGCGTTTTTAGAAAAACTGTAGTTTCGGCTAAAAACTGACC
CGAAAATTATTTTTCCCAATTTGTTTCCACAATACTCAGAAAA
Found at i:1890 original size:295 final size:298
Alignment explanation
Indices: 1524--2111 Score: 975
Period size: 295 Copynumber: 2.0 Consensus size: 298
1514 TTTTTTTTCC
* * *
1524 GAATTAATTTCTGATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAAACCTTATATCCAT
1 GAATTAATTTCTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAAACCTTATATCCAA
* * *
1589 TGTGGCTGAGATTTGGATCGATGAATATAGATATTTTAAGGATTGTTTGCGCCAAAAATCATGCA
66 TGTGGCTGAGAATTGGATCGATGAATATAGATATTTTAAGGATTCTTTGCACCAAAAATCATGCA
* *
1654 AAATTTAGCCGGGGGTCCATAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCG
131 AAATTGAGCCGGGGGTCCAGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCG
* * *
1719 GCTAAAATTTTGCAAAAACTGACCCGAAA-G-GTTTGTCTCAATTCTTT-CCACAATACTCAGAA
196 GCAAAAATTTTGCAAAAACTGACCCGAAATGTGTTTGTCACAATTATTTGCCACAATACTCAGAA
1781 AAAATACATAATTCAACACCAAAAAAATTGACGGGCTT
261 AAAATACATAATTCAACACCAAAAAAATTGACGGGCTT
* *
1819 GAATTAATTTCTAATTAAATCGAAACAAACTCCAGATGCTTGTAAAAACAAAACCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAAACCTTATATCCAA
1884 TGTGGCTGAGAATTGGATCGATGAATATAGATATTTTAAGGATTCTTTGCACCAAAAATCATGCA
66 TGTGGCTGAGAATTGGATCGATGAATATAGATATTTTAAGGATTCTTTGCACCAAAAATCATGCA
* *
1949 AAATTGAGCCGGGGTTCCAGAACGCATTTTTAGTCAAAAACTGTGATGGTTAGTACACGATTTCG
131 AAATTGAGCCGGGGGTCCAGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCG
* * * *
2014 GCAAAAATTTTGCAAAAACTTACCCGAAATGTTTTTTTCACAATTATTTGCCATAATACTCAGAA
196 GCAAAAATTTTGCAAAAACTGACCCGAAATGTGTTTGTCACAATTATTTGCCACAATACTCAGAA
*
2079 AAAATATATAATTCAACACCAAAAAAATTGACG
261 AAAATACATAATTCAACACCAAAAAAATTGACG
2112 AGCATTTCAC
Statistics
Matches: 270, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
295 210 0.78
296 1 0.00
297 13 0.05
298 46 0.17
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (298 bp):
GAATTAATTTCTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAAACCTTATATCCAA
TGTGGCTGAGAATTGGATCGATGAATATAGATATTTTAAGGATTCTTTGCACCAAAAATCATGCA
AAATTGAGCCGGGGGTCCAGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCG
GCAAAAATTTTGCAAAAACTGACCCGAAATGTGTTTGTCACAATTATTTGCCACAATACTCAGAA
AAAATACATAATTCAACACCAAAAAAATTGACGGGCTT
Found at i:2428 original size:334 final size:331
Alignment explanation
Indices: 1819--2624 Score: 1079
Period size: 334 Copynumber: 2.4 Consensus size: 331
1809 TGACGGGCTT
* *
1819 GAATTAATTTCTAATTAAATCGAAACAAACTCCAGATGCTTGTAAAAACAAAACCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAA-TTCAGATGCTCGTAAAAACAAAACCTTATATCCAA
* * *
1884 TGTGGCTGAGAATTGGATCGATGAATATAGATATTTTAAGGATTCTTTGCACCAAAAATCATGCA
65 TGTGGCTGAGATTTGGATCGATGAATATAGATATTTCAAGGATTCTTTGCACCAAAAATCATACA
* * * *
1949 AAATTGAGCCGGGGTTCCAGAACGCATTTTTAGTCAAAAACTGTGATGGTTAGTACACGATTTCG
130 AAATTGAGCCGGGGTTCCAGAACACATTTTTAGCCAAAAACTGAGATGGTTAGTACACAATTTCG
* * * * *
2014 GCAAAAATTTTGCAAAAACTTACCCGAAATGTTTTTTTCACAATTATTTGCCATAATACTCAGAA
195 CCAAAAATTTTGCAAAAACTTACCCGAAAAGTCTTTTCCACAATTATTTGCCATAACACTCAGAA
* **
2079 AAAATATATAATTCAACACC-AAAAAAATTGACGAGCATTTCACGCTTCTAATATTGTTTTTCCT
260 AAAAAATATAATTCAACACCAAAAAAAATT-ACGAGCATTTCACGCTTCTAATATCATTTTTCC-
2143 TTTTTTTCCC
323 -TTTTTTCCC
* *
2153 GAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCACGTAAAAACAAAACCTTATATCCAT
1 GAATTAATTTCTAATTAAATCGAAACAA-ATTCAGATGCTCGTAAAAACAAAACCTTATATCCAA
* * *
2218 TGTGGCTGAGATTTGGATCGATAAATATAGATATTTCAAGGATTTTTTGCGCCAAAAAATCATAC
65 TGTGGCTGAGATTTGGATCGATGAATATAGATATTTCAAGGATTCTTTGCACC-AAAAATCATAC
*
2283 AAAATTGAGGCGGGG-TCCAGAACACATTTTTAGCCAAAAA-TCGAGATGGTTAGTACACAATTT
129 AAAATTGAGCCGGGGTTCCAGAACACATTTTTAGCCAAAAACT-GAGATGGTTAGTACACAATTT
* * * *
2346 CGCCTAAAATTTTGCCAAAACTTACCCGAAAAG-CTTTTCCATAATTATTTGTCATAACACTCAG
193 CGCCAAAAATTTTGCAAAAACTTACCCGAAAAGTCTTTTCCACAATTATTTGCCATAACACTCAG
* * ** *
2410 AAAAAAAAATATAATTCAACGCCAAAAAAAATTACGTGTTTTTTACGCTTCTAATATCATTTTTC
258 -AAAAAAAATATAATTCAACACCAAAAAAAATTACGAGCATTTCACGCTTCTAATATCATTTTTC
*
2475 CTTTTTTCTC
322 CTTTTTTCCC
* *
2485 GAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGGAAAAAAAAAACCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAAC-AAATTCAGATGCTCGTAAAAACAAAACCTTATATCCAA
* * * *
2550 TGT-GCTAGAGATTTGGTTAGATGAATATAGATATTT-TAGAGAGTCTTTCTGC-CC-AAAATCA
65 TGTGGCT-GAGATTTGGATCGATGAATATAGATATTTCAAG-GATTC-TT-TGCACCAAAAATCA
*
2611 TGCAAAATTGAGCC
126 TACAAAATTGAGCC
2625 CAAGTCCCGA
Statistics
Matches: 417, Mismatches: 45, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
331 24 0.06
332 98 0.24
333 33 0.08
334 228 0.55
335 34 0.08
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (331 bp):
GAATTAATTTCTAATTAAATCGAAACAAATTCAGATGCTCGTAAAAACAAAACCTTATATCCAAT
GTGGCTGAGATTTGGATCGATGAATATAGATATTTCAAGGATTCTTTGCACCAAAAATCATACAA
AATTGAGCCGGGGTTCCAGAACACATTTTTAGCCAAAAACTGAGATGGTTAGTACACAATTTCGC
CAAAAATTTTGCAAAAACTTACCCGAAAAGTCTTTTCCACAATTATTTGCCATAACACTCAGAAA
AAAAATATAATTCAACACCAAAAAAAATTACGAGCATTTCACGCTTCTAATATCATTTTTCCTTT
TTTCCC
Found at i:3590 original size:332 final size:330
Alignment explanation
Indices: 2976--5175 Score: 1859
Period size: 332 Copynumber: 6.7 Consensus size: 330
2966 AATTTCGGTT
* * * ** * *
2976 AAAAACTGACACAAAAATTTTTTTCTCTTTTTTTTGCCATACTACTCAGAAAAAATTTATAATTC
1 AAAAACTGACCCAAAAAGTTTTTCCTC-AATTTTTGCCATA-TACTCATAAAAAATATATAATTC
* *
3041 AACGCCAAAAAAATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTC--CTTTTTTCTGAATTA
64 AACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTCTGAATTA
* * * * *
3104 ATATCTAATTAAATCG-AACAAAAATTCAGATGCTCGTAAACACAAAACCTTATATCCAATGTGG
129 ATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
3168 CTGAGATTTGGA-TCGAAT-AATATAGATATTTCAAGGATTCTTTGCACCAAAAATCATGCAAAC
193 CTGAGATTT-GATTAG-ATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
* * *
3231 TTGAGCCAAGGG-TCTAGG-ACACATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTTCGG
256 TTGAGCC-GGGGCTC-CGGAACGCATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTTCGG
*
3294 CTATAATTTTGC
319 CTAAAATTTTGC
*
3306 AAAAACTGACCCAAAAAGTTTTTCCTCAATTTTTGCCACTATACTCATAAAAAATATATTATTCA
1 AAAAACTGACCCAAAAAGTTTTTCCTCAATTTTTGCCA-TATACTCATAAAAAATATATAATTCA
* *
3371 ACGCCAAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTTTCATTTTTTTTCTGAATT
65 ACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCG--TTTTTCATTTTTTTTCTGAATT
* * * * *
3436 -ATTTCTAATTAAATCTAAACAAGATTCAGATGGTTGTAAAAACAAAACCTTATATCCAATGTGG
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
3500 CTGAGATTTGGATCA-ATGAATATAGATATTTCAAGCAGTCTTTGTGCCAAAAATCATGCAAAGT
193 CTGAGATTT-GATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
* * * *
3564 TGAGCCGGGGCTCCGGTACGCATTTTTAGGCAAAAA---T--CG--TA-T--ACGATTTCGGTTA
257 TGAGCCGGGGCTCCGGAACGCATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTTCGGCTA
*
3619 AAATTTTGT
322 AAATTTTGC
* * * * *
3628 AAAAACTGACTC-GAAAGTTATTTCCTCAATTTTTAGTCATAATACTCATAAAAATTATATAATC
1 AAAAACTGACCCAAAAAGTT-TTTCCTCAATTTTT-GCCAT-ATACTCATAAAAAATATATAATT
* * * * * * * * * *
3692 CAACGCCAAACATATTGTAGGGCTTTCCATGCTTGTAATATCGGTTTTCCTATTATTTTCCGAAT
63 CAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCAT-TTTTTTTCTGAAT
* * ***
3757 TAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCCAATGTG
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
3821 GCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
192 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
* ** * * *
3886 TGACCCGGGGC-CCAAAACGCGTTTTTAGCCCAAAAAAAAT-TG-TGA-TGGTACACGATTTCGG
257 TGAGCCGGGGCTCCGGAACGCATTTTTAG-CC--AAAAACTGTGATGATTAGTACACGATTTCGG
*
3947 CTAATATTTTGC
319 CTAAAATTTTGC
* * * *
3959 AAAAAATTGACCCGAAAGATA-TTTTT--TCAAATTTTAGCCACAAAACTCATAAAAAATTATAT
1 -AAAAACTGACCC-AAA-A-AGTTTTTCCTC-AATTTTTGCCA-TATACTCATAAAAAA-TATAT
* * * * * * * * * *
4021 AATTAAACACTAAAAAGATTGAATGGC-TTTCACACTTTTAATATTGTTTTTCATATTTTTTCAG
59 AATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTCTG
* * * * *
4085 AATTAATTTCTACTTAAATCGAAACAAGATTCAGATACTCATAAAACCAAATCCTTAAATGCAAT
124 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * *
4150 GTGGTTAAGATTTTATTTGATGAATATAGATATTTCAAGGAGCCTTGGTGCCAAAAATCATGCAA
189 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
** * * * * * * * *
4215 AACTT-AGTTGAGACT-C-GAATCGCGTTTTTAGCCAAAAACCGTGATG-TAAGTATATGATTTT
254 AA-TTGAGCCGGGGCTCCGGAA-CGCATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTTC
*
4276 GGCTAAAATTATGC
317 GGCTAAAATTTTGC
* * * * * * * * *
4290 AAAAAATGACCCAAAAAATTTTTCCTCAATTTTTG-GATAAAGTAATCATAATATATATAATTTA
1 AAAAACTGACCCAAAAAGTTTTTCCTCAATTTTTGCCATATACTCAT-AAAAAATATATAATTCA
* * ** * * * *
4354 ACACCAAAAAGATT-AGAGGATTTTTCACGCTTTTATTATCGTTTTTCATATTTTTTCTTAATTA
65 ACGCCAAAAAAATTGA-AGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTCTGAATTA
* * *
4418 ATTTCTAATT--ATCGAAACAAGATTCAGATGCTCGTAAAAATAAATTCTTAAATCCAATGTAGC
129 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
4481 TGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTGGGCGCCAAAAATCATGCAAAAAAT
194 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC-AAAATT
** * * * *
4546 GAGCCGGGGCCTTGGAAGTTAGAACGCTTTTTTAGCCAAAAACTGTTATGGTTATTACACGATTT
258 GAGCCGGGG-C-T--CCG---GAACGCATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTT
* *
4611 CGGCTAAAATTTAGT
316 CGGCTAAAATTTTGC
* * * * * *
4626 AAAAATTGACTC-AAAAGATATTTCCTCAATTTTTGGCTAAATTACTCATAAAAAAATATATATT
1 AAAAACTGACCCAAAAAG-TTTTTCCTCAATTTTT-GCCATA-TACTCAT-AAAAAATATATAAT
* * * * * * * *
4690 TCAACGCCAAAAAGATTGAAGGGTTTTTGATGTTTCTAATATCGTTTTTC-CTATTTTTCCGAAT
62 TCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTCTGAAT
* *
4754 TAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTA
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * * **
4819 ACTAAAATTTGATTAGATGAATATAGATATTTCAAGTA-TTTTCGGAGTAAAAAATCATGCAAAA
192 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-GGCGCCAAAAATCATGCAAAA
** * * * *
4883 TTGAGGTGGGTCCCCGGAACGCATTTTTAGCGAAAAACCGTGATGGTTAGTTAGTACACGATTTC
256 TTGAGCCGGGGCTCCGGAACGCATTTTTAGCCAAAAACTGTGAT-G--A-TTAGTACACGATTTC
**
4948 GGCTAAAATTTTTA
317 GGCTAAAATTTTGC
* * * * * * * *
4962 AAAAATTGACAC-GAAAGATTTCTCCTAAATTTTTGGCTAAAATACTCAT-AAAAATATTTAATT
1 AAAAACTGACCCAAAAAG-TTTTTCCTCAATTTTT-GC-CATATACTCATAAAAAATATATAATT
** * * * *
5025 CAACGCCAAAAAAGATTGGGGGGCTTTTCATGCTTTTAATATCGTATTTC-TTATTTTTT-AGAA
63 CAACGCCAAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATT-TTTTTTCTG-A
* * * * **
5088 AATAATTTCTTATTAAATCGAAACAAGATTCAGATGCTCATAAAAGC-AATTTTTAAATCCAAT-
125 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * *
5151 T-GCTAAGAATTGCTTAGATG-ATATA
190 TGGCTGAGATTTGATTAGATGAATATA
5176 AAGTATTAAA
Statistics
Matches: 1521, Mismatches: 274, Indels: 148
0.78 0.14 0.08
Matches are distributed among these distances:
321 28 0.02
322 142 0.09
323 92 0.06
324 6 0.00
325 2 0.00
326 98 0.06
327 42 0.03
328 59 0.04
329 86 0.06
330 41 0.03
331 103 0.07
332 300 0.20
333 64 0.04
334 29 0.02
335 76 0.05
336 162 0.11
337 4 0.00
338 23 0.02
339 68 0.04
340 96 0.06
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
AAAAACTGACCCAAAAAGTTTTTCCTCAATTTTTGCCATATACTCATAAAAAATATATAATTCAA
CGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTCTGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATTGAG
CCGGGGCTCCGGAACGCATTTTTAGCCAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:4152 original size:654 final size:645
Alignment explanation
Indices: 2711--5175 Score: 2019
Period size: 654 Copynumber: 3.8 Consensus size: 645
2701 TTTTTTGTAC
* *
2711 TAAAAAATATATATAATTCAACACCCAAAAA-ATT-ATGGG-CATTTCACGCTTCTAATATCATT
1 TAAAAAAT-TATATAATTCAACA-CCAAAAAGATTGAAGGGTC-TTTCACGCTTCTAATATCGTT
* * * *
2773 TTATCA-ATTTTTTCCGAATTAATTTCTGATTAAATTGAAACAAAAGTCAGATACTCGTAAAAAC
63 TT-TCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAC
* * * * *
2837 AAATCCTTATAA-CCAATGAGGTTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAGTCTTT
127 AAATCCTTA-AATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
2901 CTGCCAAAAATCATGTAAATCTGAGTCGGGGC-CTCGAAACGCGTTTTTA-GCAAAAAAACTGTG
191 GTGCCAAAAATCATGCAAAT-TGAGTCGGGGCTC-CGGAACGCGTTTTTAGGCAAAAAATC-GT-
* ** *
2964 ATA-ATTTCGG-------T-TAAAAACTGACACAAAAATTTTTTTCTCTTTTTTTTGCCATACTA
252 ATAGATTTCGGTAAAATTTGTAAAAACTGACACAAAAA-TTTTTCCTC-AATTTTTG-CATAATA
*
3020 CTCAGAAAAAATT-TATAATTCAACGCCAAAAAAATTGATGGGCTTTTCACGCTTCTAATATCGT
314 CTCA-TAAAAATTATATAATTCAACGCCAAAAAAATTGA-GGGCTTTTCACGCTTCTAATATCGT
* * *
3084 TTTTCC--TTTTTTCTGAATTAATATCTAATTAAATCG-AACAAAAATTCAGATGCTCGTAAACA
377 TTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAA
* * * * *
3146 CAAAACCTTATATCCAATGTGGCTGAGATTTGGATCGAAT-AATATAGATATTTCAAGGATTCTT
441 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG-ATGAATATAGATATTTCAAGGAGTCTT
* * * ** * * ** * *
3210 TGCACCAAAAATCATGCAAACTTGAGCCAAGGGTCTAGGACACATTTTTAGCC--AAAAACTGTG
505 GGCGCCAAAAATCATGCAAAATTGA-CCCGGGGCCAAAAACGCATTTTTAGCCAAAAAAAAT-TG
*
3273 ATGATTAGTACACGATTTCGGCT-ATAATTTTGCAAAAACTGACCCAAA-A-AGTTTTTCCTC-A
568 -TGA-TAGTACACGATTTCGGCTAAT-ATTTTGCAAAAATTGACCCAAAGATA-TTTTT--TCAA
* *
3334 ATTTTTGCCACTATACTCA
627 ATTTTAGCCACAATACTCA
* * * * *
3353 TAAAAAA-TATATTATTCAACGCCAAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
1 TAAAAAATTATATAATTCAACACCAAAAAGATTGAAGGGTCTTTCACGCTTCTAATATCG--TTT
* * * ** *
3417 TTCATTTTTTTTCTGAATT-ATTTCTAATTAAATCTAAACAAGATTCAGATGGTTGTAAAAACAA
64 TTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAA
* * * * *
3481 AACCTTATATCCAATGTGGCTGAGATTTGGATCA-ATGAATATAGATATTTCAAGCAGTCTTTGT
129 ATCCTTAAATCCAATGTGGCTAAGATTT-GATTAGATGAATATAGATATTTCAAGGAGTCTTTGT
* * *
3545 GCCAAAAATCATGCAAAGTTGAGCCGGGGCTCCGGTACGCATTTTTAGGC-AAAAATCGTATACG
193 GCCAAAAATCATGCAAA-TTGAGTCGGGGCTCCGGAACGCGTTTTTAGGCAAAAAATCGTATA-G
* * *
3609 ATTTCGGTTAAAATTTTGTAAAAACTGACTCGAAAGTTATTTCCTCAATTTTTAGTCATAATACT
256 ATTTCGG-TAAAA-TTTGTAAAAACTGACACAAAAATT-TTTCCTCAATTTTT-G-CATAATACT
* * * * * * *
3674 CATAAAAATTATATAATCCAACGCCAAACATATTGTAGGGCTTTCCATGCTTGTAATATCGGTTT
316 CATAAAAATTATATAATTCAACGCCAAAAAAATTG-AGGGCTTTTCACGCTTCTAATATCGTTTT
* * * ***
3739 TCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAA
380 TCCTATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
*
3803 ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGCG
444 ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * *
3868 CCAAAAATCATGCAAAATTGACCCGGGGCCCAAAACGCGTTTTTAGCCCAAAAAAAATTGTGATG
509 CCAAAAATCATGCAAAATTGACCCGGGGCCAAAAACGCATTTTTAG-CCAAAAAAAATTGTGATA
3933 GTACACGATTTCGGCTAATATTTTGCAAAAAATTGACCCGAAAGATATTTTTTCAAATTTTAGCC
573 GTACACGATTTCGGCTAATATTTTGC-AAAAATTGACCC-AAAGATATTTTTTCAAATTTTAGCC
*
3998 ACAAAACTCA
636 ACAATACTCA
* * * * * *
4008 TAAAAAATTATATAATTAAACACTAAAAAGATTGAATGG-CTTTCACACTTTTAATATTGTTTTT
1 TAAAAAATTATATAATTCAACACCAAAAAGATTGAAGGGTCTTTCACGCTTCTAATATCGTTTTT
* * * *
4072 CATATTTTTTCAGAATTAATTTCTACTTAAATCGAAACAAGATTCAGATACTCATAAAACCAAAT
66 CATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAAT
* * * * * *
4137 CCTTAAATGCAATGTGGTTAAGATTTTATTTGATGAATATAGATATTTCAAGGAGCCTTGGTGCC
131 CCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCC
* * * * *
4202 AAAAATCATGCAAAACTT-AGTTGAGACT-C-GAATCGCGTTTTTAGCCAAAAACCGTGATGTAA
196 AAAAATCATGC-AAA-TTGAGTCGGGGCTCCGGAA-CGCGTTTTTAGGCAAAAA-----A--T-C
* * * * *
4264 GTATATGATTTTGGCTAAAATTATGCAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGGATA
250 GTATA-GATTTCGG-TAAAATT-TGTAAAAACTGACAC-AAAAATTTTTCCTCAATTTTTGCAT-
* * * * * ** * *
4329 AAGTAATCAT-AATA-TATATAATTTAACACCAAAAAGATTAGAGGATTTTTCACGCTTTTATTA
310 AA-TACTCATAAAAATTATATAATTCAACGCCAAAAAAATT-GAGGGCTTTTCACGCTTCTAATA
* *
4392 TCGTTTTTCATATTTTTTCTTAATTAATTTCTAATT--ATCGAAACAAGATTCAGATGCTCGTAA
373 TCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * * *
4455 AAATAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTC
438 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * *
4520 TGGGCGCCAAAAATCATGCAAAAAATGAGCCGGGGCCTTGGAAGTTAGAACGCTTTTTTAGCCAA
503 TTGGCGCCAAAAATCATGC-AAAATTGACCCGGGGCC----AA---A-AACGCATTTTTAGCCAA
*** * * * * * * * *
4585 AAACTGTTATGGTTATTACACGATTTCGGCTAAAATTTAGTAAAAATTGACTCAAAAGATATTTC
559 AAAAAATTGT-GATAGTACACGATTTCGGCTAATATTTTGCAAAAATTGAC-CCAAAGATATTTT
* * * *
4650 CTCAATTTTTGGCTA-AATTACTCA
622 TTCAAATTTTAGCCACAA-TACTCA
* * * * * * *
4674 TAAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGTTTTTGATGTTTCTAATATCGTTTTT
1 TAAAAAATTATATAATTCAACACCAAAAAGATTGAAGGGTCTTTCACGCTTCTAATATCGTTTTT
* * *
4739 CCTA-TTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
66 CATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAAT
** * * *
4803 CCTTAAATCCAATGTAACTAAAATTTGATTAGATGAATATAGATATTTCAAGTA-T-TTTCGGAG
131 CCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTT--GTG
** * * *
4866 TAAAAAATCATGCAAAATTGAGGT-GGGTCCCCGGAACGCATTTTTA-GCGAAAAACCGTGATGG
194 CCAAAAATCATGC-AAATTGA-GTCGGGGCTCCGGAACGCGTTTTTAGGC-AAAAA-----A---
* * * * * *
4929 TTAGTTAGTACACGATTTCGGCTAAAATTTTTAAAAAATTGACACGAAAGATTTCTCCTAAATTT
248 -TCG-TA-T--A-GATTTCGG-TAAAATTTGT-AAAAACTGACAC-AAAAATTTTTCCTCAATTT
* * * *
4994 TTGGCTAAAATACTCATAAAAA-TATTTAATTCAACGCCAAAAAAGATTGGGGGGCTTTTCATGC
304 TT-GC-ATAATACTCATAAAAATTATATAATTCAACGCCAAAAAA-ATT-GAGGGCTTTTCACGC
* * * * * *
5058 TTTTAATATCGTATTTCTTATTTTTT-AGAAAATAATTTCTTATTAAATCGAAACAAGATTCAGA
365 TTCTAATATCGTTTTTCCTATTTTTTCTG-AATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * ** * * *
5122 TGCTCATAAAAGC-AATTTTTAAATCCAAT-T-GCTAAGAATTGCTTAGATG-ATATA
429 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATA
5176 AAGTATTAAA
Statistics
Matches: 1472, Mismatches: 256, Indels: 160
0.78 0.14 0.08
Matches are distributed among these distances:
639 7 0.00
640 17 0.01
641 25 0.02
642 147 0.10
643 23 0.02
651 15 0.01
652 82 0.06
653 78 0.05
654 212 0.14
655 90 0.06
656 39 0.03
657 24 0.02
658 74 0.05
659 36 0.02
660 50 0.03
661 10 0.01
662 49 0.03
663 6 0.00
664 2 0.00
665 4 0.00
666 202 0.14
667 81 0.06
668 5 0.00
669 3 0.00
670 1 0.00
671 1 0.00
672 54 0.04
673 40 0.03
674 52 0.04
675 15 0.01
676 28 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (645 bp):
TAAAAAATTATATAATTCAACACCAAAAAGATTGAAGGGTCTTTCACGCTTCTAATATCGTTTTT
CATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAAT
CCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCC
AAAAATCATGCAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGGCAAAAAATCGTATAGATTTC
GGTAAAATTTGTAAAAACTGACACAAAAATTTTTCCTCAATTTTTGCATAATACTCATAAAAATT
ATATAATTCAACGCCAAAAAAATTGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTT
CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATG
CAAAATTGACCCGGGGCCAAAAACGCATTTTTAGCCAAAAAAAATTGTGATAGTACACGATTTCG
GCTAATATTTTGCAAAAATTGACCCAAAGATATTTTTTCAAATTTTAGCCACAATACTCA
Found at i:5545 original size:15 final size:17
Alignment explanation
Indices: 5524--5561 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5514 CATGACTATA
*
5524 AATTATAAT-TAAATAT
1 AATTATAATCAAAATAT
5540 -ATTATAATCAAAATAT
1 AATTATAATCAAAATAT
5556 AATTAT
1 AATTAT
5562 TAGAAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTATAATCAAAATAT
Found at i:6925 original size:23 final size:23
Alignment explanation
Indices: 6895--6941 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6885 AATTTTTGAG
*
6895 TTTGTGATTTTATATCGTAGTAA
1 TTTGTGATTTTATATCGTAATAA
*
6918 TTTGTGATTTTATATTGTAATAA
1 TTTGTGATTTTATATCGTAATAA
6941 T
1 T
6942 AGTAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (23 bp):
TTTGTGATTTTATATCGTAATAA
Found at i:8010 original size:15 final size:15
Alignment explanation
Indices: 7986--8022 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
7976 AGTGATTAGT
* *
7986 CTTTGGGAAGATTTG
1 CTTTGTGAAGAATTG
8001 CTTTGTGAAGAATTG
1 CTTTGTGAAGAATTG
8016 CTTTGTG
1 CTTTGTG
8023 CAACGGGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.43
Consensus pattern (15 bp):
CTTTGTGAAGAATTG
Found at i:19912 original size:1 final size:1
Alignment explanation
Indices: 19906--19939 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
19896 AAAACGTGTG
19906 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19940 CAGAAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21030 original size:3 final size:3
Alignment explanation
Indices: 21024--21049 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21014 TTATAAATAA
21024 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
21050 AATGATGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:36098 original size:2 final size:2
Alignment explanation
Indices: 36093--36138 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
36083 AAAAGAAAAA
* *
36093 AG AG AG AG AG AG AG A- AG -G A- AG AG AG AG AG AG CG AG AG CG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36132 AG AG AG A
1 AG AG AG A
36139 AGTGGAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.48, C:0.04, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36108 original size:19 final size:19
Alignment explanation
Indices: 36086--36123 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36076 GAAATAGAAA
36086 AGAAAAAAGAGAGAGAGAG
1 AGAAAAAAGAGAGAGAGAG
**
36105 AGAAGGAAGAGAGAGAGAG
1 AGAAAAAAGAGAGAGAGAG
36124 CGAGAGCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (19 bp):
AGAAAAAAGAGAGAGAGAG
Found at i:36855 original size:43 final size:43
Alignment explanation
Indices: 36794--36879 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
36784 TTCTTTGTAA
36794 TTTATTTATTTGTGTATTTAGTATGTTGATAGTTAATATAGAT
1 TTTATTTATTTGTGTATTTAGTATGTTGATAGTTAATATAGAT
*
36837 TTTATTTGTTTGTGTATTTAGTATGTTGATAGTTAATATAGAT
1 TTTATTTATTTGTGTATTTAGTATGTTGATAGTTAATATAGAT
36880 GAAATTAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (43 bp):
TTTATTTATTTGTGTATTTAGTATGTTGATAGTTAATATAGAT
Found at i:38333 original size:24 final size:24
Alignment explanation
Indices: 38306--38492 Score: 187
Period size: 24 Copynumber: 7.7 Consensus size: 24
38296 AGCAGGAACT
*
38306 GGTGGAGGGCTA-GATGACGTGGCA
1 GGTGGAGAGCTAGGA-GACGTGGCA
* *
38330 GGTGGTGAGCTAGGAGCCGTGGCA
1 GGTGGAGAGCTAGGAGACGTGGCA
* *
38354 GGTGGAGTGCTAGGAGACTTGGCA
1 GGTGGAGAGCTAGGAGACGTGGCA
* * *
38378 GGTGGTGAGCTAGGAGACTTGGCG
1 GGTGGAGAGCTAGGAGACGTGGCA
* * *
38402 GGTGGAGAGCTGGGAGACTTGGCG
1 GGTGGAGAGCTAGGAGACGTGGCA
* * *
38426 GGTGGAGAGCTGGGAGACTTGGCG
1 GGTGGAGAGCTAGGAGACGTGGCA
* *
38450 GGTGGAGAGCTGGCTGGAGACGTGGCG
1 GGTGGAGAGCT---AGGAGACGTGGCA
38477 GGTGGAGAGCTAGGAG
1 GGTGGAGAGCTAGGAG
38493 TGGCCGGAGA
Statistics
Matches: 144, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
24 120 0.83
25 2 0.01
27 22 0.15
ACGTcount: A:0.18, C:0.13, G:0.52, T:0.17
Consensus pattern (24 bp):
GGTGGAGAGCTAGGAGACGTGGCA
Found at i:39194 original size:3 final size:3
Alignment explanation
Indices: 39186--39210 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39176 TTTTTTATTC
39186 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
39211 AATGAATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:39714 original size:48 final size:48
Alignment explanation
Indices: 39643--39742 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
39633 GTTAAGGATT
* * *
39643 AATTAGTAATCCGTTTTAGAAATCGAATGGGTTCAATCTTACTGAAAG
1 AATTAGTAATCCGATTTAGAAATCGAATGAGTTCAATCTTACTGAAAC
* *
39691 AATTAGTAATCCGATTTAGAAATCGAATGAGTTCGATCTTATTGAAAC
1 AATTAGTAATCCGATTTAGAAATCGAATGAGTTCAATCTTACTGAAAC
39739 AATT
1 AATT
39743 GAAACAGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (48 bp):
AATTAGTAATCCGATTTAGAAATCGAATGAGTTCAATCTTACTGAAAC
Found at i:43326 original size:26 final size:26
Alignment explanation
Indices: 43289--43343 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
43279 ATTCAGCATT
*
43289 TACCAGACAACTATTAAAAGGAATGC
1 TACCAGACAACTATTAAAAGGAAAGC
*
43315 TACCAGAGAACTATTAAAAGGAAAGC
1 TACCAGACAACTATTAAAAGGAAAGC
43341 TAC
1 TAC
43344 AATCGGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (26 bp):
TACCAGACAACTATTAAAAGGAAAGC
Found at i:45942 original size:4 final size:4
Alignment explanation
Indices: 45916--45955 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
45906 CAATTAAAAA
* *
45916 AAAC AAA- AAAC AAAA AAAA AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC A
45956 GGAAACTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:45954 original size:12 final size:11
Alignment explanation
Indices: 45911--45955 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
45901 AAACCCAATT
45911 AAAAA-AAACA
1 AAAAACAAACA
*
45921 AAAAACAAAAAA
1 AAAAAC-AAACA
45933 AAAAACAAACA
1 AAAAACAAACA
45944 AACAAACAAACA
1 AA-AAACAAACA
45956 GGAAACTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 5 0.17
11 6 0.20
12 19 0.63
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAACA
Done.