Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010570.1 Corchorus capsularis cultivar CVL-1 contig10591, 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: 105224
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2210 original size:323 final size:313
Alignment explanation
Indices: 1181--3506 Score: 1718
Period size: 323 Copynumber: 7.1 Consensus size: 313
1171 ACTTAAGGAT
* * * * * * * *
1181 TTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTATTTAGAAATTAATT-GAGAAAAA-ATGAA
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAA
* * * * *
1244 AAACGATATTAAAAGCGTGAAAAGCCCTTTAATATTTTTGGCA-TTTAATTATATATTTTTTTTA
66 AAACGATATTTAAAGCGTGAAAAG-CCTTCAATCTTTTTCG-AGTTGAATTATATA--TTTTTTA
* *
1308 TTAGTATTATGGCTAAAAATAGAGGAAATCTCTTTCGGGT-ACATTTTTGCAAAATTTTAGCCGA
127 TGAGTATTATGGCTAAAAATTGAGGAAAT-TCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGA
* * * * *
1372 AATCGTGTACTAATCATCATGGTTTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGACCCGA-TTT
190 AATCGTGTAATAATCATCA-CG------TTTTTTTTGCTAAAAACGCGTTCCGGG-CCCTAGTTC
* * * *
1436 AATTTTGAATATTTTTGGC-GTCGAGACTACTTGAAATATCTATATTTATCTAACCAAATCCCAG
247 AATTTTGAATGTTTTTGGCACT-GAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAG
1500 CAA
311 CAA
* * * * * *
1503 CTGTTTTGACAAACATCTGAATCATGATTCGTTTTAATTAGAAATTAATTCGTTAAAAAAATAGG
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC--AAAAAAAATATG
* * * * * * * *
1568 GAGAACAATA-TTAGAAGCATGAAAAGCCATTCAATGTTTTTGGCGTTGAATTATATATTTTGTA
64 AAAAACGATATTTA-AAGCGTGAAAAGCC-TTCAATCTTTTTCGAGTTGAATTATATATTTTTTA
* * * ** *
1632 TGAGTATTGTGGCTAAAAATTTAGGAAAATTTTTTCTAGTCATTTTTTGCAAAATTTTTAGCCGA
127 TGAGTATTATGGCTAAAAATTGAGG-AAATTCTTTCGGGTCAATTTTTGCAAAA-TTTTAGCCGA
* * * * * * * * *
1697 AATCATGTACTAACCATCACG-GTTTTTTGCTATAAACGCGTTTCGGGGCCAC-GGCTCAGTTTT
190 AATCGTGTAATAATCATCACGTTTTTTTTGCTAAAAACGCG-TTCCGGGCC-CTAGTTCAATTTT
* * * * * ***
1760 GCATGGTTTTGTGCACCGACACTCCTTGAAATATCTATTTTCATCTAGTAAAATCTTTGCCACAT
253 GAATGTTTTTG-GCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAA----T-CC-CA-
1825 TGCACTTAAGGA
310 -G--C---A--A
** * * * *
1837 TTTGTTTTTATGAGCATC-CAGATCTTGTTTCGATTTAATTAGAAATTAATTCATAAAAAATATG
1 -TTGTTTTTACAAACATCTGA-ATCATGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATG
* * * **
1901 AAAAACGATATTTAAAGCATTAAAAGCTCTTTAATCTTTTTTTAGTTGAATTATATATTTTTTTA
64 AAAAACGATATTTAAAGCGTGAAAAGC-CTTCAATCTTTTTCGAGTTGAATTATATA-TTTTTTA
* * *
1966 TGTGTATTATGACTAAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTGGCCGAA
127 TGAGTATTATGGCTAAAAATTGAGGAAAT-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
*
2031 ATCGTGTAATAATCATC-CTAGTTTTTTTTTTTTGGCTAAAAACGCGTTCCGGGGCCTAGTTCAA
191 ATCGTGTAATAATCATCAC--G----TTTTTTTT-GCTAAAAACGCGTTCCGGGCCCTAGTTCAA
* *
2095 TTTTGAATTGATTTTGGCACTGAGACTCCTTGAAATATCTATATTCATTTAACCAAATCCCAGCA
249 TTTTGAA-TGTTTTTGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCA
2160 A
313 A
* *
2161 TTGTTTTTACAAACATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAAT-TGG
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC-AAAAAAAATAT-G
* * * * *
2225 GAAAATGATA-TTAGAATCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTA
64 AAAAACGATATTTA-AAGCGTGAAAAGCC-TTCAATCTTTTTCGAGTTGAATTATATATTTTTTA
* * * * ** * *
2289 TGAATATTGTGGCTAATAATTGAGGGAAAATT-TTTCTGGTCTTTTTTTGCAAAATTTTAACTGA
127 TGAGTATTATGGCTAAAAATTGA-GG-AAATTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* * * * * * * * * *
2353 AATCGTTTACTAACCATCACGTTTTTTTTGTTAAAAACACGTTCGGGGTCTCGACTT-AGTTTT-
190 AATCGTGTAATAATCATCACGTTTTTTTTGCTAAAAACGCGTTCCGGG-CCCTAGTTCAATTTTG
* * **
2416 ACATGATTTTAT-GCATTGAGACTCATTGAAATATCTATATTCATCTAATAAAATCTTAACCACA
254 A-ATG-TTTT-TGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAA---T--CC-CA
2480 TTGCATTTAAGCA
310 --GC-----A--A
* * * * * * * *
2493 TTTTTTTTACAATCATTTAAATCTTGTTTCAATTTAATTAGAAATTAATTGAGAAAAAAATTTGA
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCA-AAAAAAATATGA
* * * *
2558 AAAACGATATTAAAACCGTGAAAAGCCCTCCAATCTTTTTCGCGTTGAATTATATATTTTTTATG
65 AAAACGATATTTAAAGCGTGAAAAG-CCTTCAATCTTTTTCGAGTTGAATTATATATTTTTTATG
*
2623 CGTATTATGGCTAAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
129 AGTATTATGGCTAAAAATTGAGGAAAT-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * *
2688 CGTGTAATAATCATCACGGTTTTTTTTTTACTAAAAACGCGTTCCGGGCCCTGGTTTAATTTTGA
193 CGTGTAATAATCATCAC-G--TTTTTTTTGCTAAAAACGCGTTCCGGGCCCTAGTTCAATTTTGA
* * * * *
2753 ATGTTTTTTGGCACCGAGACTCCTTGAAAAATCTATATTCACCTAACCAAATCGCAGCCA
255 ATG-TTTTTGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAA
*
2813 TTGTTTTTACAAACATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAAAAATA
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC----AAAAAAAATA
* * * * * * * * *
2878 GGGAAAACGATA-TTAGAAGTGTGAAAAGCCATTCAATATTTTTGGTGTTAAATTATAAATTTTG
62 TGAAAAACGATATTTA-AAGCGTGAAAAGCC-TTCAATCTTTTTCGAGTTGAATTATATATTTTT
* * * **
2942 CATGAGTATTGTGGCTAAAAATTGAGGGAAATTTTTTTTGGTC-ATTTGTTGCAAAATTTTAGCC
125 TATGAGTATTATGGCTAAAAATTGA-GGAAATTCTTTCGGGTCAATTT-TTGCAAAATTTTAGCC
* * * * * * * *
3006 GAAATTGTGTACTAA-CTATCACG-GTTTTTTGCTATAAACGCGTTTCGCGGCCCCAGCTCAGTT
188 GAAATCGTGTAATAATC-ATCACGTTTTTTTTGCTAAAAACGCGTTCCG-GGCCCTAGTTCAATT
* ** ** * * *
3069 TTGCATGTTTTTGGTGCCAACACTCCTTGAAATATCTATATTTATCTAGTA-AAATCTTATCCAC
251 TTGAATGTTTTTGGCACTGAGACTCCTTGAAATATCTATATTCATCTA--ACCAA----ATCC-C
3133 ATTGCACTTAAGGA
309 A--G--C---A--A
* * ** * *
3147 TTTGTTTTTACGAGCATCCAAATCTTGTTTCGATTAAATTAGAAATTAATTCGGAAAAAAAATAT
1 -TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC--AAAAAAAATAT
* * *
3212 GAAAAACGATATTTAAAGCATGAAAAACTCTTCAATCTTTTTTGAGTTGAATTATATATTTCTTT
63 GAAAAACGATATTTAAAGCGTGAAAAGC-CTTCAATCTTTTTCGAGTTGAATTATATATTT-TTT
* * * *
3277 ATGTGTATTATGACTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGTAAAATTTTGGCCGA
126 ATGAGTATTATGGCTAAAAATTGAGGAAAT-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
** * * *
3342 AATCGTGTAATAATCATCACG-GGTTTTGGCTGAAAACGCGTTCCGGGACCT-GATTCAATTTTG
190 AATCGTGTAATAATCATCACGTTTTTTTTGCTAAAAACGCGTTCCGGGCCCTAG-TTCAATTTTG
* * * * * *
3405 AATGTTATTTGACGA-TGAGACTCCTAGAAATTTCTATA-T-ATCTAACCAAATCGCAACCA
254 AATGTT-TTTGGC-ACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAA
* * *
3464 TTGTTTTTACAAACATTTGAATCATGTTTTGTTTTAATTAGAA
1 TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAA
3507 GTCATCACAG
Statistics
Matches: 1575, Mismatches: 307, Indels: 250
0.74 0.14 0.12
Matches are distributed among these distances:
316 37 0.02
317 81 0.05
318 33 0.02
319 85 0.05
320 63 0.04
321 1 0.00
322 54 0.03
323 234 0.15
324 114 0.07
325 52 0.03
326 46 0.03
327 7 0.00
329 5 0.00
330 7 0.00
331 6 0.00
332 177 0.11
333 167 0.11
334 170 0.11
335 159 0.10
336 1 0.00
338 1 0.00
339 57 0.04
340 18 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (313 bp):
TTGTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAA
AAACGATATTTAAAGCGTGAAAAGCCTTCAATCTTTTTCGAGTTGAATTATATATTTTTTATGAG
TATTATGGCTAAAAATTGAGGAAATTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
GTAATAATCATCACGTTTTTTTTGCTAAAAACGCGTTCCGGGCCCTAGTTCAATTTTGAATGTTT
TTGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAA
Found at i:2580 original size:332 final size:325
Alignment explanation
Indices: 545--3362 Score: 1776
Period size: 332 Copynumber: 8.6 Consensus size: 325
535 TATCTATATT
** * **
545 CATCTAAATTTTGTTTCGATTTAATTAGAAATTAATT-GAGAAAACAATTTTGAAAAACGATATT
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCG-GAAAA-AAATAGGAAAAACGATATT
* * * * * ** * *
609 AAAAGAGTGTAAAGCCCTTCTATTTTTTTAACGTTAAATTATATATTTTTTTATGAGTATTATGG
64 AAAAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATA-TTTTGTATGAGTATTATGG
* * ** * *
674 CTAAAAATTGTGG-AAA--TCTC-ATTC-ATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAAT
128 CTAAAAATTGAGGAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC
* * * * * *
734 CATCACGGTTTTTTTTTTTGCTAAAAACGAGTTCTGTGGCCTG-GTTCAATTTTGA-ATGATTTT
193 CATCAC-G---TTTTTTTTGTTAAAAACGCGTTC-GGGGCCCGACTT-AGTTTT-ACATG--TTT
** *
797 TAGTGCCA-AGACTCCTTGAAATATCTATATTCATCTA-ACCA-C--ATCC-CA--GC------C
249 TA-TG-CAGAGACTCCTTGAAATATCTATATTCATCTATAAAATCTTAACCACATTGCATTAAGC
*
848 ATTGTTTTTACAAA
312 ATTTTTTTTACAAA
* ** *
862 CATCTAAATCATGTTTCGTTTTAATTAGAAATTAATTCATAAAAAAATAGGGAAAA--ATATTAG
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTA-
** * * * * * * *
925 AAA-AATTAAAAGCAATTC-ATTTTTCTTGGCGTCGAATTATATATTTTATATGAGTATTGTGGC
65 AAAGCGTGAAAAGCCATTCAATCTTT-TTCGCGTTGAATTATATATTTTGTATGAGTATTATGGC
* * * * *
988 TAAAAATTTAGGAAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCGGAAATCGTGTACTAA
129 TAAAAATTGAGG-AAAATTTTTCGGGTCAATTTTTGCAAAA-TTTTAGCCGAAATCGTGTAATAA
* * * * * * * * * * *
1053 CCATCACG-GTTTTTAGCTATAAATGCGTTTTGCGGCCCCGGCTCAGTTTTGCATGGTTTTTTGC
192 CCATCACGTTTTTTTTGTTAAAAACGCG-TTCG-GGGCCCGACTTAGTTTTACAT-GTTTTAT--
* * * * * *
1117 GCCGATACTCGTTGAAATATCTAT-TTCCATGTAGTAAAATCTTTACCACATTGCACTTAAGGAT
252 GCAGAGACTCCTTGAAATATCTATATT-CATCTA-TAAAATCTTAACCACATTGCA-TTAAGCAT
* *
1181 TTGTTTTTACGAG
314 TT-TTTTTACAAA
* * *
1194 CATCTAAATCTTGTTTCAATTTATTTAGAAATTAATT--GAGAAAAAAT--GAAAAACGATATTA
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGA-AAAAAATAGGAAAAACGATATTA
* * * * * * * *
1255 AAAGCGTGAAAAGCCCTTTAATATTTTTGGCATTTAATTATATATTTTTTTTATTAGTATTATGG
65 AAAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATA--TTTTGTATGAGTATTATGG
* *
1320 CTAAAAATAGAGG-AAATCTCTTTCGGGT-ACATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
128 CTAAAAATTGAGGAAAAT-T-TTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
* * * * * * *
1383 AATCATCATGGTTTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGACCCGATTTAATTTTGA-ATA
190 AACCATCA-CG------TTTTTTTTGTTAAAAACGCG-TTCGGGGCCCGACTTAGTTTT-ACATG
* * *
1447 TTTT-TGGCGTCGAGACTACTTGAAATATCTATATTTATCTA-ACCAAA---T--CC-CA--GC-
246 TTTTAT-GC--AGAGACTCCTTGAAATATCTATATTCATCTATA--AAATCTTAACCACATTGCA
* *
1501 --AA-C--TGTTTTGACAAA
306 TTAAGCATTTTTTTTACAAA
* * * * * * *
1516 CATCTGAATCATGATTCGTTTTAATTAGAAATTAATTCGTTAAAAAAATAGGGAGAACAATATTA
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAAATAGGAAAAACGATATTA
* * * * *
1581 GAAGCATGAAAAGCCATTCAATGTTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTGGCT
65 AAAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAGTATTATGGCT
* ** * * *
1646 AAAAATTTAGGAAAATTTTTTCTAGTCATTTTTTGCAAAATTTTTAGCCGAAATCATGTACTAAC
130 AAAAATTGAGGAAAA-TTTTTCGGGTCAATTTTTGCAAAA-TTTTAGCCGAAATCGTGTAATAAC
* * * * * * *
1711 CATCACG-GTTTTTTGCTATAAACGCGTTTCGGGGCCACGGCTCAGTTTTGCATGGTTTTGTGCA
193 CATCACGTTTTTTTTGTTAAAAACGCG-TTCGGGGCC-CGACTTAGTTTTACAT-GTTTTATGCA
* * ** *
1775 CCGACACTCCTTGAAATATCTATTTTCATCTAGTAAAATCTTTGCCACATTGCACTTAAGGATTT
255 --GAGACTCCTTGAAATATCTATATTCATCTA-TAAAATCTTAACCACATTGCA-TTAAGCATTT
** *
1840 GTTTTTATGAG
316 -TTTTTACAAA
* * * * *
1851 CATCCAGATCTTGTTTCGATTTAATTAGAAATTAATTC--ATAAAAAATATGAAAAACGATATTT
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGA-AAAAAATAGGAAAAACGATATTA
* * * *** * * *
1914 AAAGCATTAAAAGCTC-TTTAATCTTTTTTTAGTTGAATTATATATTTTTTTATGTGTATTATGA
65 AAAGCGTGAAAAGC-CATTCAATCTTTTTCGCGTTGAATTATATA-TTTTGTATGAGTATTATGG
*
1978 CTAAAAATTGAGG-AAATCTCTTTCGGGTCAATTTTTGCAAAATTTTGGCCGAAATCGTGTAATA
128 CTAAAAATTGAGGAAAAT-T-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATA
* * * * *
2042 ATCATC-CTAGTTTTTTTTTTTTGGCTAAAAACGCGTTCCGGGG-CCTAGTTCAATTTTGA-ATT
191 ACCATCAC--G----TTTTTTTT-GTTAAAAACGCGTT-CGGGGCCCGACTT-AGTTTT-ACA-T
* **
2104 GATTTT-GGCACTGAGACTCCTTGAAATATCTATATTCAT-T-T--AA-CCAAATCC-CA--GC-
245 G-TTTTATGCA--GAGACTCCTTGAAATATCTATATTCATCTATAAAATCTTAA-CCACATTGCA
*
2159 ---A--ATTGTTTTTACAAA
306 TTAAGCATTTTTTTTACAAA
* * * * * * *
2174 CATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAATTGGGAAAATGATATTAG
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAA
* * *
2239 AATCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAATATTGTGGCTA
66 AAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAGTATTATGGCTA
* * ** * * * *
2304 ATAATTGAGGGAAAATTTTTCTGGTCTTTTTTTGCAAAATTTTAACTGAAATCGTTTACTAACCA
131 AAAATTGA-GGAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCA
* *
2369 TCACGTTTTTTTTGTTAAAAACACGTTCGGGGTCTCGACTTAGTTTTACATGATTTTATGCATTG
195 TCACGTTTTTTTTGTTAAAAACGCGTTCGGGG-CCCGACTTAGTTTTACATG-TTTTATGCA--G
*
2434 AGACTCATTGAAATATCTATATTCATCTAATAAAATCTTAACCACATTGCATTTAAGCATTTTTT
256 AGACTCCTTGAAATATCTATATTCATCT-ATAAAATCTTAACCACATTGCA-TTAAGCATTTTTT
*
2499 TTACAAT
319 TTACAAA
* * * **
2506 CATTTAAATCTTGTTTCAATTTAATTAGAAATTAATT-GAGAAAAAAATTTGAAAAACGATATTA
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAAATAGGAAAAACGATATTA
* * * * *
2570 AAACCGTGAAAAGCCCTCCAATCTTTTTCGCGTTGAATTATATATTTTTTATGCGTATTATGGCT
65 AAAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAGTATTATGGCT
*
2635 AAAAATTGAGG-AAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAT
130 AAAAATTGAGGAAAAT-T-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC
* * ** * *
2699 CATCACGGTTTTTTTTTTACTAAAAACGCGTTCCGGGCCCTGGTTTAATTTTGA-ATGTTTTTTG
193 CATCAC-GTTTTTTTTGT--TAAAAACGCGTTCGGGGCCC-GACTTAGTTTT-ACATGTTTTAT-
* * *
2763 GCACCGAGACTCCTTGAAAAATCTATATTCA-C--------C-TAACCAAATCGC----AGCCAT
252 GCA--GAGACTCCTTGAAATATCTATATTCATCTATAAAATCTTAACCACATTGCATTAAG-CAT
*
2814 TGTTTTTACAAA
314 TTTTTTTACAAA
* * * *
2826 CATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAAAAATAGGGAAAACGATAT
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCG---GAAAAAAATAGGAAAAACGATAT
* * * * * * * * *
2891 TAGAAGTGTGAAAAGCCATTCAATATTTTTGGTGTTAAATTATAAATTTTGCATGAGTATTGTGG
63 TAAAAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAGTATTATGG
* ** * *
2956 CTAAAAATTGAGGGAAATTTTTTTTGGTC-ATTTGTTGCAAAATTTTAGCCGAAATTGTGTACTA
128 CTAAAAATTGA-GGAAAATTTTTCGGGTCAATTT-TTGCAAAATTTTAGCCGAAATCGTGTAATA
* * * * * * * * *
3020 ACTATCACG-GTTTTTTGCTATAAACGCGTTTCGCGGCCCCAGCTCAGTTTTGCATGTTTTTGGT
191 ACCATCACGTTTTTTTTGTTAAAAACGCG-TTCGGGGCCCGA-CTTAGTTTTACATG-TTTT-AT
* * * *
3084 GCCA-ACACTCCTTGAAATATCTATATTTATCTAGTAAAATCTTATCCACATTGCACTTAAGGAT
252 G-CAGAGACTCCTTGAAATATCTATATTCATCTA-TAAAATCTTAACCACATTGCA-TTAAGCAT
* *
3148 TTGTTTTTACGAG
314 TT-TTTTTACAAA
* * * * *
3161 CATCCAAATCTTGTTTCGATTAAATTAGAAATTAATTCGGAAAAAAAATATGAAAAACGATATTT
1 CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATAGGAAAAACGATATTA
* * * * * * *
3226 AAAGCATGAAAAACTC-TTCAATCTTTTTTGAGTTGAATTATATATTTCTTTATGTGTATTATGA
65 AAAGCGTGAAAAGC-CATTCAATCTTTTTCGCGTTGAATTATATATTT-TGTATGAGTATTATGG
* * *
3290 CTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGTAAAATTTTGGCCGAAATCGTGTAATAA
128 CTAAAAATTGAGGAAA-ATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
*
3355 TCATCACG
192 CCATCACG
3363 GGTTTTGGCT
Statistics
Matches: 1943, Mismatches: 377, Indels: 345
0.73 0.14 0.13
Matches are distributed among these distances:
313 34 0.02
314 31 0.02
315 28 0.01
316 58 0.03
317 117 0.06
318 27 0.01
319 81 0.04
320 91 0.05
321 15 0.01
322 54 0.03
323 235 0.12
324 128 0.07
325 46 0.02
326 52 0.03
327 2 0.00
329 6 0.00
330 20 0.01
331 52 0.03
332 254 0.13
333 204 0.10
334 128 0.07
335 140 0.07
336 5 0.00
337 1 0.00
338 33 0.02
339 61 0.03
340 40 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (325 bp):
CATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAA
AAGCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAGTATTATGGCTA
AAAATTGAGGAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCAT
CACGTTTTTTTTGTTAAAAACGCGTTCGGGGCCCGACTTAGTTTTACATGTTTTATGCAGAGACT
CCTTGAAATATCTATATTCATCTATAAAATCTTAACCACATTGCATTAAGCATTTTTTTTACAAA
Found at i:2712 original size:655 final size:655
Alignment explanation
Indices: 545--3506 Score: 3740
Period size: 657 Copynumber: 4.5 Consensus size: 655
535 TATCTATATT
* * *
545 CATCTAAATTTTGTTTCGATTTAATTAGAAATTAATTGAGAAAACAATTTTGAAAAACGATATTA
1 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTGAGAAAA-AAATATGAAAAACGATATTA
* * * * *
610 AAAGAGTGTAAAGCCCTTCTAT-TTTTTTAACGTTAAATTATATATTTTTTTATGAGTATTATGG
65 AAAGCGTGAAAAGCCCTTCAATCTTTTTT-GCGTTGAATTATATATTTTTTTATGAGTATTATGG
* * *
674 CTAAAAATTGTGGAAATCTC-AT----TC-ATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAA
129 CTAAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* *
733 TCATCACGGTTTTTTTTTTTGCTAAAAACGAGTTCTGTGG-CCTGGTTCAATTTTGAATGATTTT
194 TCATCACGGTTTTTTTTTTTGCTAAAAACGCGTTCCG-GGACCTGGTTCAATTTTGAATGA-TTT
* *
797 TAGTGC-C-AAGACTCCTTGAAATATCTATATTCATCTAACCACATCCCAGCCATTGTTTTTACA
257 T-G-GCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTACA
* *
860 AACATCTAAATCATGTTTCGTTTTAATTAGAAATTAATTCATAAAAAAATAGGGAAAA--ATATT
320 AACATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAATAGGGAAAACGATATT
** * * * * *
923 AGAAAAATTAAAAGCAATTC-ATTTTTCTTGGCGTCGAATTATATATTTTATATGAGTATTGTGG
385 AGAATCATGAAAAGCCATTCAATATTT-TTGGCGTTGAATTATATATTTTGTATGAGTATTGTGG
* * *
987 CTAAAAATTTAGGAAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCGGAAATCGTGTACTA
449 CTAAAAATTGAGGGAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCCGAAATCGTGTACTA
* * * * *
1052 ACCATCACGGTTTTTAGCTATAAATGCGTTTTGCGGCCCCGGCTCAGTTTTGCATGGTTTTTTGC
514 ACCATCACGGTTTTTTGCTATAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATGGTTTTGTGC
* * * * *
1117 GCCGATACTCGTTGAAATATCTAT-TTCCATGTAGTAAAATCTTTACCACATTGCACTTAAGGAT
579 ACCGACACTCCTTGAAATATCTATATT-CATCTAGTAAAATCTTAACCACATTGCACTTAAGGAT
1181 TTGTTTTTACGAG
643 TTGTTTTTACGAG
* *
1194 CATCTAAATCTTGTTTCAATTTATTTAGAAATTAATTGAG--AAAAA-ATGAAAAACGATATTAA
1 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTGAGAAAAAAATATGAAAAACGATATTAA
* * * * * *
1256 AAGCGTGAAAAGCCCTTTAATATTTTTGGCATTTAATTATATATTTTTTTTATTAGTATTATGGC
66 AAGCGTGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATA-TTTTTTTATGAGTATTATGGC
* *
1321 TAAAAATAGAGGAAATCTCTTTCGGGT-ACATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
130 TAAAAATTGAGGAAATCTCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * *
1385 TCATCATGGTTTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGACCCGATTTAATTTTGAAT-ATT
194 TCATCACGG---TTTTTTTTTTTGCTAAAAACGCGTTCCGGGACCTGGTTCAATTTTGAATGA-T
* * * * * *
1449 TTTGGC-GTCGAGACTACTTGAAATATCTATATTTATCTAACCAAATCCCAGCAACTGTTTTGAC
255 TTTGGCACT-GAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTAC
* * *
1513 AAACATCTGAATCATGATTCGTTTTAATTAGAAATTAATTCGTTAAAAAAATAGGGAGAACAATA
319 AAACATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCG-TAAAAAAATAGGGAAAACGATA
* *
1578 TTAGAAGCATGAAAAGCCATTCAATGTTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTG
383 TTAGAATCATGAAAAGCCATTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTG
* * *
1643 GCTAAAAATTTA-GGAAAATTTTTTCTAGTCATTTTTTGCAAAATTTTTAGCCGAAATCATGTAC
448 GCTAAAAATTGAGGGAAAA-TTTTTCTGGTCATTTTTTGCAAAATTTTTAGCCGAAATCGTGTAC
* * *
1707 TAACCATCACGGTTTTTTGCTATAAACGCGTTTCGGGGCCACGGCTCAGTTTTGCATGGTTTTGT
512 TAACCATCACGGTTTTTTGCTATAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATGGTTTTGT
* **
1772 GCACCGACACTCCTTGAAATATCTATTTTCATCTAGTAAAATCTTTGCCACATTGCACTTAAGGA
577 GCACCGACACTCCTTGAAATATCTATATTCATCTAGTAAAATCTTAACCACATTGCACTTAAGGA
*
1837 TTTGTTTTTATGAG
642 TTTGTTTTTACGAG
* * * * *
1851 CATCCAGATCTTGTTTCGATTTAATTAGAAATTAATTCA-TAAAAAATATGAAAAACGATATTTA
1 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTGAGAAAAAAATATGAAAAACGATATTAA
* * * * ** * *
1915 AAGCATTAAAAGCTCTTTAATCTTTTTTTAGTTGAATTATATATTTTTTTATGTGTATTATGACT
66 AAGCGTGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTTATGAGTATTATGGCT
*
1980 AAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTGGCCGAAATCGTGTAATAATC
131 AAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
* * *
2045 ATC-CTAGTTTTTTTTTTTTGGCTAAAAACGCGTTCCGGGGCCTAGTTCAATTTTGAATTGATTT
196 ATCAC--GGTTTTTTTTTTT-GCTAAAAACGCGTTCCGGGACCTGGTTCAATTTTGAA-TGATTT
* *
2109 TGGCACTGAGACTCCTTGAAATATCTATATTCATTTAACCAAATCCCAGCAATTGTTTTTACAAA
257 TGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTACAAA
* *
2174 CATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAATTGGGAAAATGATATTAG
322 CATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAATAGGGAAAACGATATTAG
* * * *
2239 AATCGTGAAAAGCCATTCAATCTTTTTCGCGTTGAATTATATATTTTGTATGAATATTGTGGCTA
387 AATCATGAAAAGCCATTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTGGCTA
* * * * *
2304 ATAATTGAGGGAAAATTTTTCTGGTCTTTTTTTGCAAAA-TTTTAACTGAAATCGTTTACTAACC
452 AAAATTGAGGGAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCCGAAATCGTGTACTAACC
* * * * * * * * * * * *
2368 ATCACGTTTTTTTTGTTAAAAACACG-TTCGGGGTCTCGACTTAGTTTTACATGATTTTATGCAT
517 ATCACG-GTTTTTTGCTATAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATGGTTTTGTGCAC
* * * * * *
2432 TGAGACTCATTGAAATATCTATATTCATCTAATAAAATCTTAACCACATTGCATTTAAGCATTT-
581 CGACACTCCTTGAAATATCTATATTCATCTAGTAAAATCTTAACCACATTGCACTTAAGGATTTG
* *
2496 TTTTTACAAT
646 TTTTTACGAG
* * *
2506 CATTTAAATCTTGTTTCAATTTAATTAGAAATTAATTGAGAAAAAAATTTGAAAAACGATATTAA
1 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTGAGAAAAAAATATGAAAAACGATATTAA
* * * *
2571 AACCGTGAAAAGCCCTCCAATCTTTTTCGCGTTGAATTATATA-TTTTTTATGCGTATTATGGCT
66 AAGCGTGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTTATGAGTATTATGGCT
2635 AAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
131 AAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
* * * *
2700 ATCACGG-TTTTTTTTTTACTAAAAACGCGTTCCGGGCCCTGGTTTAATTTTGAATGTTTTTTGG
196 ATCACGGTTTTTTTTTTTGCTAAAAACGCGTTCCGGGACCTGGTTCAATTTTGAATG-ATTTTGG
* * * *
2764 CACCGAGACTCCTTGAAAAATCTATATTCACCTAACCAAATCGCAGCCATTGTTTTTACAAACAT
260 CACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTACAAACAT
2829 CTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAAAAATAGGGAAAACGATATTAG
325 CTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGT---AAAAAAATAGGGAAAACGATATTAG
* * * * *
2894 AAGT-GTGAAAAGCCATTCAATATTTTTGGTGTTAAATTATAAATTTTGCATGAGTATTGTGGCT
387 AA-TCATGAAAAGCCATTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTGGCT
* * * *
2958 AAAAATTGAGGGAAATTTTTTTTGGTCATTTGTTGCAAAA-TTTTAGCCGAAATTGTGTACTAAC
451 AAAAATTGAGGGAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCCGAAATCGTGTACTAAC
* *
3022 TATCACGGTTTTTTGCTATAAACGCGTTTCGCGGCCCC-AGCTCAGTTTTGCATGTTTTTGGTG-
516 CATCACGGTTTTTTGCTATAAACGCGTTTCGCGGCCCCGA-CTCAGTTTTGCATGGTTTT-GTGC
* * *
3085 -CCAACACTCCTTGAAATATCTATATTTATCTAGTAAAATCTTATCCACATTGCACTTAAGGATT
579 ACCGACACTCCTTGAAATATCTATATTCATCTAGTAAAATCTTAACCACATTGCACTTAAGGATT
3149 TGTTTTTACGAG
644 TGTTTTTACGAG
* *
3161 CATCCAAATCTTGTTTCGATTAAATTAGAAATTAATTCG-GAAAAAAAATATGAAAAACGATATT
1 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATT-GAG-AAAAAAATATGAAAAACGATATT
* * * * * * * *
3225 TAAAGCATGAAAAACTCTTCAATCTTTTTTGAGTTGAATTATATATTTCTTTATGTGTATTATGA
64 AAAAGCGTGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTTATGAGTATTATGG
* * *
3290 CTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGTAAAATTTTGGCCGAAATCGTGTAATAA
129 CTAAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * *
3355 TCATCACGG-----GTTTTGGCTGAAAACGCGTTCCGGGACCTGATTCAATTTTGAATGTTATTT
194 TCATCACGGTTTTTTTTTTTGCTAAAAACGCGTTCCGGGACCTGGTTCAATTTTGAATGAT-TTT
* * * * *
3415 GACGA-TGAGACTCCTAGAAATTTCTATA-T-ATCTAACCAAATCGCAACCATTGTTTTTACAAA
258 GGC-ACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTACAAA
* *
3477 CATTTGAATCATGTTTTGTTTTAATTAGAA
322 CATCTGAATCATGTTTCGTTTTAATTAGAA
3507 GTCATCACAG
Statistics
Matches: 2017, Mismatches: 247, Indels: 96
0.85 0.10 0.04
Matches are distributed among these distances:
645 45 0.02
646 44 0.02
647 3 0.00
649 37 0.02
651 62 0.03
652 181 0.09
653 73 0.04
654 168 0.08
655 388 0.19
656 248 0.12
657 515 0.26
658 199 0.10
659 54 0.03
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (655 bp):
CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTGAGAAAAAAATATGAAAAACGATATTAA
AAGCGTGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTTATGAGTATTATGGCT
AAAAATTGAGGAAATCTCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
ATCACGGTTTTTTTTTTTGCTAAAAACGCGTTCCGGGACCTGGTTCAATTTTGAATGATTTTGGC
ACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCATTGTTTTTACAAACATC
TGAATCATGTTTCGTTTTAATTAGAAATTAATTCGTAAAAAAATAGGGAAAACGATATTAGAATC
ATGAAAAGCCATTCAATATTTTTGGCGTTGAATTATATATTTTGTATGAGTATTGTGGCTAAAAA
TTGAGGGAAAATTTTTCTGGTCATTTTTTGCAAAATTTTTAGCCGAAATCGTGTACTAACCATCA
CGGTTTTTTGCTATAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATGGTTTTGTGCACCGACA
CTCCTTGAAATATCTATATTCATCTAGTAAAATCTTAACCACATTGCACTTAAGGATTTGTTTTT
ACGAG
Found at i:5113 original size:330 final size:327
Alignment explanation
Indices: 4235--5694 Score: 1524
Period size: 330 Copynumber: 4.5 Consensus size: 327
4225 ATCTTATTCA
* ** * *
4235 TGTTTCGATTTAATTAGAAATT-ATTCAGAAAATAATAGGAAAAATTATATTAGAAGCATGAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAAAAGCGTGAAAA
* * * *
4299 GCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTCG-GG
64 G-CCTTCAATCTTTTTGGTGTTGAATTATAT-ATTTTTATGAGTATTTTAGCCAAAAA-TCGAGG
* * * * * *
4363 AAATAA-CTTTCGAGTCAA-TTTTGCAAAATTCTAGTCGAAATCTTGTAATAATCATCACAGTTT
126 AAA-AATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GGTT
* * * * * *
4426 TTTGCTAAAAACACGTTCCGAGG-CCCGGCTAAGTTTTGCT-TGATTTTTGGCGCCAAGACTCTT
189 TTCGCTAAAAACGCGTTCTG-GGCCCCGACTCAGTTTTG-TATGATTTTTGGCGCCAAGACTCCT
* * * * * * * *
4489 TGAGATAT-TCATATTCATTTAAACAAATTTCAGCAACATTGGATTTCAGAATTTGTTTTTACGA
252 TGAAATATCT-ATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGA
4553 GCATCTGAATCT
316 GCATCTGAATCT
* *
4565 TGTTTTGATTTAATTAGAAATTAATCCAGAAAAATATG---AA--A-ATTAAAAGCGTGAAAAGT
1 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG-
* * * * *
4624 CCTCCAATCTTTTTGGTGTTAAATTATATA-TATTATGAGTATTTTAACCAAAAATTGATGGAAA
65 CCTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATCGA-GGAAA
* * * * * *
4688 AATATTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACAGTTTTCGG
129 AATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGC
* ** * *
4753 TGGAAAACGCGTTCTGGGGTCCGACTCAGTTTTGTATGATTTTTGGTGCCGAGACTCCTTGAAAT
194 T-AAAAACGCGTTCTGGGCCCCGACTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * *
4818 ATATATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTT
258 ATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTG
4883 AATCT
323 AATCT
*
4888 TGTTTCGA-TTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAAG
1 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTG-AAAA-
* * * * *
4952 GCTTTCAAATTTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTCGCTAGAAATCGAGGAA
64 GCCTTC-AATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATCGAGGAA
* * ** * *
5017 AAATCTTTTGAGTCAATTTTTGCAAAATTTTAGCTGAAATTATGTACTAACCATTACGGGTTTCG
128 AAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCG
* * * *
5082 ACTAAAAACGTGTTTCTGGGCCCCG-CTCAGTTTTGCATTATTTTTGGTGCCAAGACTCCTTGAA
193 -CTAAAAACGCG-TTCTGGGCCCCGACTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGAA
* * *
5146 ATATCTATATTCATCTAACCAATTCTCAGCCACATT-AGATTTAAGGATTTGTTTTTACTAGCAT
256 ATATCTATATTCATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCAT
*
5210 CTGAATTT
320 CTGAATCT
** * * *** *
5218 TGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACAATATTAGTTGCGTTAAAAG
1 TGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAG
* ** * *
5283 CCCTTCAATATTTTTAATGTCGAATTATATATTTTT-TGAGTATTTTAGCCAAAAATTGAGGAAA
65 -CCTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATCGAGGAAA
* * * *
5347 TATCTTTCGAGTCAATTTTTGTAAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
129 AATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTCG
** * * * *
5412 CTAAAAACGCGTTCCAAGGCCACGACTCTGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAA
193 CTAAAAACGCGTT-CTGGGCCCCGACTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGAAA
* * * * * * *
5477 TATCTTTATTCATCTAATCAAATCTCTGGCACATTGGATTTAAGGATTTATTTTTATGTGCATCT
257 TATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCT
5542 GAATCT
322 GAATCT
* * * * ** *
5548 TGTTTCGATTTAATTA-AAATAAATTAAAAAAAATATGAAAAACGGTATTAAAATAGTGAAAAGT
1 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGC
** *
5612 CTTCCAATCTTTTTGACGTTGAATTATATATATTTT-TGAGTATTTTTGCCAAAAAAT-GAGGAA
66 CTT-CAATCTTTTTGGTGTTGAATTATATAT-TTTTATGAGTATTTTAGCC-AAAAATCGAGGAA
* *
5675 AAATATTTCGGGTC-ATTTTT
128 AAATCTTTCGAGTCAATTTTT
5695 ACCATCATGG
Statistics
Matches: 947, Mismatches: 151, Indels: 66
0.81 0.13 0.06
Matches are distributed among these distances:
320 2 0.00
321 21 0.02
322 52 0.05
323 191 0.20
324 2 0.00
325 2 0.00
326 2 0.00
327 4 0.00
328 69 0.07
329 146 0.15
330 369 0.39
331 64 0.07
332 23 0.02
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (327 bp):
TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGC
CTTCAATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATCGAGGAAAAA
TCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGCTA
AAAACGCGTTCTGGGCCCCGACTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGAAATATC
TATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CT
Found at i:5582 original size:660 final size:649
Alignment explanation
Indices: 4235--5666 Score: 1677
Period size: 660 Copynumber: 2.2 Consensus size: 649
4225 ATCTTATTCA
* * * * * *
4235 TGTTTCGATTTAATTAGAAATTATTCAGAAAATAATAGGAAAAATTATATTAGAAGCATGAAAAG
1 TGTTTCGATTTAATTAGAAATAATT-A-AAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAG
* *
4300 CCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTCGGGAA
64 -CCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGTATTTTCGCTAAAAATTCGGGAA
* ** *
4365 ATAACTTTCGAGTCAATTTTGCAAAATTCTAGTCGAAATCTTGTAATAATCATCACAGTTTTTTG
127 ATAACTTTCGAGTCAATTTTGCAAAATTCTAGTCGAAATCTTGTAATAACCATCACAGGGTTTCG
* * *
4430 CTAAAAACACGTTCCGAGGCCCGGCTAAGTTTTGCTTGATTTTTGGCGCCAAGACTCTTTGAGAT
192 CTAAAAACACGTTCCGAGGCCCCGCTAAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAAT
* * *
4495 ATTCATATTCATTTAAACAAATTTCAGCAACATTGGATTTCAGAATTTGTTTTTACGAGCATCTG
257 ATTCATATTCATCTAAACAAATTTCAGCAACATTAGATTTAAGAATTTGTTTTTACGAGCATCTG
* * ** *
4560 AATCTTGTTTTGATTTAATTAGAAATTAATCCAGAAAAATATGAAAATTAAAAGCGTGAAAAGTC
322 AATCTTGTTTCGATTTAATTAGAAATTAATCCAGAAAAATAGGAAAAACAAAAGCGTGAAAAGCC
* ** *
4625 CTCCAATCTTTTTGGTGTTAAATTATATATATTATGAGTATTTTAACCAAAAATTGATGGAAAAA
387 CTCCAATATTTTTAATGTCAAATTATATATATTATGAGTATTTTAACCAAAAATTGATGGAAAAA
* * *
4690 TATTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACAGTTTTCGGTG
452 TATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGTG
* *** * * *
4755 GAAAACGCGTTCTGGGGTCCGACTCAGTTTTGTATGATTTTTGGTGCCGAGACTCCTTGAAATAT
517 AAAAACGCGTTCCAAGGCCCGACTCAGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATAT
* * *
4820 ATATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTTAA
582 ATATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTACGAGCATCTGAA
4885 TCT
647 TCT
* *
4888 TGTTTCGA-TTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAAG
1 TGTTTCGATTTAATTAGAAA-TAATTAAAAAAAATATGAAAAATGATATTAAAAGCGTG-AAAA-
* * * *
4952 GCTTTCAAATTTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTCGCTAGAAA-TCGAGGA
63 GCCTTC-AATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTCGCTAAAAATTCG-GGA
* * * *
5016 AA-AATCTTTTGAGTCAATTTTTGCAAAATTTTAG-CTGAAAT-TATGTACTAACCATTAC-GGG
126 AATAA-CTTTCGAGTCAA-TTTTGCAAAATTCTAGTC-GAAATCT-TGTAATAACCATCACAGGG
** * * *
5077 TTTCGACTAAAAACGTGTTTCTG-GGCCCCGCTCAGTTTTGCATT-ATTTTTGGTGCCAAGACTC
187 TTTCG-CTAAAAACACG-TTCCGAGGCCCCGCTAAGTTTTGC-TTGATTTTTGGCGCCAAGACTC
* * *
5140 CTTGAAATA-TCTATATTCATCT-AACCAATTCTCAGCCACATTAGATTTAAGGATTTGTTTTTA
249 CTTGAAATATTC-ATATTCATCTAAACAAATT-TCAGCAACATTAGATTTAAGAATTTGTTTTTA
* * ***
5203 CTAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACAATAT
312 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATCCAG-AAAAATAGGAAAAACAA-A-
* * * * * *
5268 TAGTTGCGTTAAAAGCCCTTCAATATTTTTAATGTCGAATTATATATTTTTTGAGTATTTTAGCC
374 -A---GCGTGAAAAGCCCTCCAATATTTTTAATGTCAAATTATATATATTATGAGTATTTTAACC
* * * *
5333 AAAAATTGA-GGAAATATCTTTCGAGTCAATTTTTGTAAATTTTTAGCCGAAATCGTGTACTAAC
435 AAAAATTGATGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * *
5397 CATCACGGTTTTTGGCT-AAAAACGCGTTCCAAGGCCACGACTCTGTTTTGAATGATTTTTGGCG
500 CATCACAGTTTTCGG-TGAAAAACGCGTTCCAAGGCC-CGACTCAGTTTTGAATGATTTTTGGCG
* * * * *
5461 CCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCTGGCACATTGGATTTAAGGATTT
563 CCGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTT
* *
5526 ATTTTTATGTGCATCTGAATCT
628 ATTTTTACGAGCATCTGAATCT
* * ** *
5548 TGTTTCGATTTAATTA-AAATAAATTAAAAAAAATATGAAAAACGGTATTAAAATAGTGAAAAGT
1 TGTTTCGATTTAATTAGAAAT-AATTAAAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGC
* * *
5612 CTTCCAATCTTTTTGACGTTGAATTATATATATTTT-TGAGTATTTTTGCCAAAAA
65 CTT-CAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTCGCTAAAAA
5667 ATGAGGAAAA
Statistics
Matches: 655, Mismatches: 97, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
651 31 0.05
652 74 0.11
653 192 0.29
654 20 0.03
655 1 0.00
657 1 0.00
658 42 0.06
659 85 0.13
660 202 0.31
661 7 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (649 bp):
TGTTTCGATTTAATTAGAAATAATTAAAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGCC
TTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTCGCTAAAAATTCGGGAAATAA
CTTTCGAGTCAATTTTGCAAAATTCTAGTCGAAATCTTGTAATAACCATCACAGGGTTTCGCTAA
AAACACGTTCCGAGGCCCCGCTAAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAATATTC
ATATTCATCTAAACAAATTTCAGCAACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATC
TTGTTTCGATTTAATTAGAAATTAATCCAGAAAAATAGGAAAAACAAAAGCGTGAAAAGCCCTCC
AATATTTTTAATGTCAAATTATATATATTATGAGTATTTTAACCAAAAATTGATGGAAAAATATT
TCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGTGAAAA
ACGCGTTCCAAGGCCCGACTCAGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATATATAT
ATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTACGAGCATCTGAATCT
Found at i:6347 original size:2 final size:2
Alignment explanation
Indices: 6340--6373 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6330 GAACTAGGTC
6340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6374 GTAGCAGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7784 original size:39 final size:39
Alignment explanation
Indices: 7730--7879 Score: 186
Period size: 39 Copynumber: 3.9 Consensus size: 39
7720 TCCTCATTCG
* *
7730 CTTGCTGCACTGGTTCCTCTTTCTC-ATCTTCATTCATCA
1 CTTGTTGCAGTGGTTCCTCTTTCTCAAT-TTCATTCATCA
*
7769 CTTGTTGCAGTGGTTCCTCTTCCTCAATTTCA---ATCA
1 CTTGTTGCAGTGGTTCCTCTTTCTCAATTTCATTCATCA
* *
7805 CTTGTTGCAGTGGTTCCTCTTTCTCAATATCAATCAGT-A
1 CTTGTTGCAGTGGTTCCTCTTTCTCAATTTCATTCA-TCA
7844 CTTGTTGCAGTGGTTCCTCTTTCTC-ATTTCCATTCA
1 CTTGTTGCAGTGGTTCCTCTTTCTCAATTT-CATTCA
7880 ATGGCGAAGC
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
36 34 0.35
38 3 0.03
39 58 0.59
40 3 0.03
ACGTcount: A:0.15, C:0.28, G:0.13, T:0.43
Consensus pattern (39 bp):
CTTGTTGCAGTGGTTCCTCTTTCTCAATTTCATTCATCA
Found at i:7832 original size:30 final size:32
Alignment explanation
Indices: 7765--7870 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 32
7755 ATCTTCATTC
7765 ATCACTTGTTGCAGTGGTTCCTCTTCCTCAATTTCA
1 ATCACTTGTTGCAGTGGTTCCTCTT-CTC-A--TCA
7801 ATCACTTGTTGCAGTGGTTCCTCTTTCTCAATATCA
1 ATCACTTGTTGCAGTGGTTCCTC-TTCTC---ATCA
7837 ATCAGTACTTGTTGCAGTGGTTCCTCTTTCTCAT
1 ATC---ACTTGTTGCAGTGGTTCCTC-TTCTCAT
7871 TTCCATTCAA
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
36 34 0.54
37 2 0.03
38 1 0.02
39 26 0.41
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (32 bp):
ATCACTTGTTGCAGTGGTTCCTCTTCTCATCA
Found at i:7861 original size:75 final size:74
Alignment explanation
Indices: 7730--7873 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 74
7720 TCCTCATTCG
* *
7730 CTTGCTGCACTGGTTCCTCTTTCTCATCTTCATTCATCACTTGTTGCAGTGGTTCCTCTTCCTCA
1 CTTGCTGCACTGGTTCCTCTTTCTCATCATCAATCATCACTTGTTGCAGTGGTTCCTCTTCCTC-
7795 ATTTCAATCA
65 ATTTCAATCA
* * *
7805 CTTGTTGCAGTGGTTCCTCTTTCTCAAT-ATCAATCAGT-ACTTGTTGCAGTGGTTCCTCTTTCT
1 CTTGCTGCACTGGTTCCTCTTTCTC-ATCATCAATCA-TCACTTGTTGCAGTGGTTCCTCTTCCT
7868 CATTTC
64 CATTTC
7874 CATTCAATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
74 5 0.08
75 54 0.87
76 3 0.05
ACGTcount: A:0.15, C:0.28, G:0.14, T:0.44
Consensus pattern (74 bp):
CTTGCTGCACTGGTTCCTCTTTCTCATCATCAATCATCACTTGTTGCAGTGGTTCCTCTTCCTCA
TTTCAATCA
Found at i:8422 original size:35 final size:36
Alignment explanation
Indices: 8381--8488 Score: 164
Period size: 37 Copynumber: 3.0 Consensus size: 36
8371 ACCGTTAATT
*
8381 GGCGCGCAAATAAACAACCGTTAATCAAATAATCAG
1 GGCGCGCAAATAATCAACCGTTAATCAAATAATCAG
*
8417 GCGCGCGCAAATAATCAACCGTTAATTAAATAATCA-
1 G-GCGCGCAAATAATCAACCGTTAATCAAATAATCAG
*
8453 GGCACGCAAATAATCAACCGTTAATCAAAATAATCA
1 GGCGCGCAAATAATCAACCGTTAATC-AAATAATCA
8489 AACCATTAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
35 23 0.35
36 11 0.17
37 32 0.48
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (36 bp):
GGCGCGCAAATAATCAACCGTTAATCAAATAATCAG
Found at i:10256 original size:31 final size:29
Alignment explanation
Indices: 10220--10416 Score: 145
Period size: 31 Copynumber: 6.5 Consensus size: 29
10210 TTTGGCTAAT
10220 TGCTCAAATAAGGGCCTAACGT-TTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTATT---AAAA
* * **
10251 TGCTCAAATAAGGGCCTGATC-TTTTAATT
1 TGCTCAAATAAGGGCCT-AACGTATTAAAA
* *
10280 TGGC-CAAATAAGGGCCTAATGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACG-TAT-TAAAA
* **
10311 TGCTCAAATAAGGGCCCAATC-T-TCTAATT
1 TGCTCAAATAAGGGCCTAA-CGTAT-TAAAA
10340 TGGC-CAAATAAGGGCCTAACGTTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACG-TATT-AAAA
10371 TGCTCAAATAAGGGCCTAACGTTATTGAAAA
1 TGCTCAAATAAGGGCCTAACG-TATT-AAAA
10402 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
10417 TTGATTTCAG
Statistics
Matches: 135, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.01
29 35 0.26
30 13 0.10
31 81 0.60
32 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACGTATTAAAA
Found at i:10292 original size:60 final size:59
Alignment explanation
Indices: 10224--10389 Score: 237
Period size: 60 Copynumber: 2.8 Consensus size: 59
10214 GCTAATTGCT
* *
10224 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTG-CAAAATGCTCAAATAAGGGCCTAATCTTCTAATTTGGC
* *
10284 CAAATAAGGGCCTAATGTTAT-CGAAAATGCTCAAATAAGGGCCCAATCTTCTAATTTGGC
1 CAAATAAGGGCCTAACGTT-TGC-AAAATGCTCAAATAAGGGCCTAATCTTCTAATTTGGC
10344 CAAATAAGGGCCTAACGTTATTG-AAAATGCTCAAATAAGGGCCTAA
1 CAAATAAGGGCCTAACG-T-TTGCAAAATGCTCAAATAAGGGCCTAA
10390 CGTTATTGAA
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
59 1 0.01
60 90 0.95
61 3 0.03
62 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTGCAAAATGCTCAAATAAGGGCCTAATCTTCTAATTTGGC
Found at i:10355 original size:29 final size:29
Alignment explanation
Indices: 10255--10358 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 29
10245 CCAAAATGCT
* *
10255 CAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATCTTCTAATTTGGC
* * **
10284 CAAATAAGGGCCTAATGTTATCGAAAAT-GC
1 CAAATAAGGGCCTAAT-CT-TCTAATTTGGC
*
10314 TCAAATAAGGGCCCAATCTTCTAATTTGGC
1 -CAAATAAGGGCCTAATCTTCTAATTTGGC
10344 CAAATAAGGGCCTAA
1 CAAATAAGGGCCTAA
10359 CGTTATTGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 34 0.58
30 6 0.10
31 19 0.32
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTCTAATTTGGC
Found at i:10484 original size:31 final size:30
Alignment explanation
Indices: 10449--10613 Score: 117
Period size: 31 Copynumber: 5.5 Consensus size: 30
10439 ATGAGATAGA
10449 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** ***
10480 CCCTTATTTG-GCCAAATT-CAAA-GACCGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
10509 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * * *
10540 CCCTTATTT-AGCCAAATT--AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
* *
10569 CCCTTATTTGAGTATTTTGACAAACGTTAGA
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGG
10600 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
10614 ATTAGCCAAA
Statistics
Matches: 101, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.35
30 6 0.06
31 50 0.50
32 5 0.05
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:10513 original size:60 final size:60
Alignment explanation
Indices: 10446--10609 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
10436 CGTATGAGAT
*
10446 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGACC
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * * *
10506 GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATC
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * *
10566 AGACCCTTATTTGAGTATTTTGACAAACGTTAGACCCTTATTTG
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
10610 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
Found at i:17060 original size:29 final size:29
Alignment explanation
Indices: 17000--17075 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
16990 TTTCAACATT
17000 AAGGACATGAGGATTTC----A-AAAAAA
1 AAGGACATGAGGATTTCAAAAAGAAAAAA
17024 AAGGACATGAGGATTTCAAAAAGAAAAAA
1 AAGGACATGAGGATTTCAAAAAGAAAAAA
17053 AAGGACATGAGGATTTCAAAAAG
1 AAGGACATGAGGATTTCAAAAAG
17076 CTTTTAGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
24 17 0.36
28 1 0.02
29 29 0.62
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (29 bp):
AAGGACATGAGGATTTCAAAAAGAAAAAA
Found at i:35740 original size:15 final size:16
Alignment explanation
Indices: 35720--35749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35710 GGGAGTAGAT
35720 TAAAAT-ATTTAAAAC
1 TAAAATAATTTAAAAC
35735 TAAAATAATTTAAAA
1 TAAAATAATTTAAAA
35750 AATGAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTAAAAC
Found at i:36408 original size:21 final size:21
Alignment explanation
Indices: 36382--36426 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
36372 ATATTCTGGA
36382 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
36403 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
36424 TTG
1 TTG
36427 ACGCTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:36827 original size:33 final size:33
Alignment explanation
Indices: 36790--36886 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 33
36780 GGCGGCTGAG
36790 CCATGGCCAAGCCGCC-CTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCTC-CCTGGGGCGGCACTA
* * *
36823 CCATGGCCAGGCCGCCTCCCTGGGGCGACCCTA
1 CCATGGCCAAGCCGCCTCCCTGGGGCGGCACTA
36856 CCATGG--ATAGACCGCCTCCCTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCTCCCTGGGGCGGCAC
36887 CGGTACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 52 0.95
34 1 0.02
ACGTcount: A:0.14, C:0.42, G:0.31, T:0.12
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCTCCCTGGGGCGGCACTA
Found at i:37510 original size:31 final size:31
Alignment explanation
Indices: 37454--37520 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
37444 CAATTTCAGA
**
37454 CTAAACCTTTAAAAAGTTGTTCAATTTAAAG
1 CTAAACCTTTAAAAAGTTGACCAATTTAAAG
* * * *
37485 CTAAATCTTTCAAAAGTTGACCAATTTGAGG
1 CTAAACCTTTAAAAAGTTGACCAATTTAAAG
37516 CTAAA
1 CTAAA
37521 AACATAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (31 bp):
CTAAACCTTTAAAAAGTTGACCAATTTAAAG
Found at i:38394 original size:32 final size:32
Alignment explanation
Indices: 38285--38398 Score: 117
Period size: 33 Copynumber: 3.5 Consensus size: 32
38275 CTGGTGCCGT
*
38285 CCCCCTGGGGCGG--CTGAGCCATGGCCA-AGCCG
1 CCCCCTGGGGCGGCACT-A-CCATGGACAGA-CCG
* *
38317 CCCTCCTGGGGCGGCACTACCATGGCCAGGCCG
1 CCC-CCTGGGGCGGCACTACCATGGACAGACCG
* *
38350 CCTCCCTGGGGCGGCCCTACCATGGATAGACCG
1 CC-CCCTGGGGCGGCACTACCATGGACAGACCG
38383 CCCCCTGGGGCGGCAC
1 CCCCCTGGGGCGGCAC
38399 CGGTACTAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
32 16 0.23
33 51 0.72
34 2 0.03
35 2 0.03
ACGTcount: A:0.12, C:0.42, G:0.34, T:0.11
Consensus pattern (32 bp):
CCCCCTGGGGCGGCACTACCATGGACAGACCG
Found at i:57602 original size:3 final size:3
Alignment explanation
Indices: 57594--57620 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
57584 CTATTACTAT
57594 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
57621 CTTATATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:64080 original size:18 final size:18
Alignment explanation
Indices: 64053--64088 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
64043 ATTGGTAGTA
*
64053 AATAATTTAAGAGTAATT
1 AATAAATTAAGAGTAATT
*
64071 AATAAATTAATAGTAATT
1 AATAAATTAAGAGTAATT
64089 GAGCAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AATAAATTAAGAGTAATT
Found at i:67726 original size:2 final size:2
Alignment explanation
Indices: 67719--67746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
67709 AGAAAATAGC
67719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67747 AATGACTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72218 original size:1 final size:1
Alignment explanation
Indices: 72212--72239 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
72202 ATAATTAAAG
72212 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
72240 GCAATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:77737 original size:33 final size:33
Alignment explanation
Indices: 77695--77759 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
77685 TTGCCCTCAT
77695 TTTTGTTACTTCAACAGAAAGCAGCAGCTTCAG
1 TTTTGTTACTTCAACAGAAAGCAGCAGCTTCAG
77728 TTTTGTTACTTCAACAGAAAGCAGCAGCTTCA
1 TTTTGTTACTTCAACAGAAAGCAGCAGCTTCA
77760 ACTGAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (33 bp):
TTTTGTTACTTCAACAGAAAGCAGCAGCTTCAG
Found at i:82984 original size:21 final size:21
Alignment explanation
Indices: 82958--83001 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
82948 TTCACCCATA
*
82958 CAACAATTAA-CAACTCAAAAT
1 CAACAAGTAATCAA-TCAAAAT
*
82979 CAACAAGTAATTAATCAAAAT
1 CAACAAGTAATCAATCAAAAT
83000 CA
1 CA
83002 TTAATGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.20
Consensus pattern (21 bp):
CAACAAGTAATCAATCAAAAT
Found at i:93436 original size:6 final size:6
Alignment explanation
Indices: 93425--93456 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
93415 TTCGAGGTTT
93425 TTTTTG TTTTTG -TTTTG TTTTTG TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
93457 CAAAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:93442 original size:11 final size:11
Alignment explanation
Indices: 93422--93456 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
93412 GGATTCGAGG
93422 TTTT-TTTTGT
1 TTTTGTTTTGT
93432 TTTTGTTTTGT
1 TTTTGTTTTGT
93443 TTTTGTTTT-T
1 TTTTGTTTTGT
93453 TTTT
1 TTTT
93457 CAAAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTGTTTTGT
Found at i:93447 original size:17 final size:16
Alignment explanation
Indices: 93425--93456 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
93415 TTCGAGGTTT
93425 TTTTTGTTTTTGTTTTG
1 TTTTTGTTTTT-TTTTG
93442 TTTTTGTTTTTTTTT
1 TTTTTGTTTTTTTTT
93457 CAAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTGTTTTTTTTTG
Found at i:95876 original size:68 final size:64
Alignment explanation
Indices: 95771--95902 Score: 219
Period size: 68 Copynumber: 2.0 Consensus size: 64
95761 AACAAGAAAA
*
95771 AGGATGTGGTTACAACTTATACAACATCCCCATTTAAAGAATTTAATGTTTTGTTCAAATGCAT
1 AGGATGTGGGTACAACTTATACAACATCCCCATTTAAAGAATTTAATGTTTTGTTCAAATGCAT
95835 AGGATGTGGGTACAACTTACAAGTACAACATCCCCATTTAAAGAATTTAATGTTTTGTTCAAATG
1 AGGATGTGGGTACAACTT---A-TACAACATCCCCATTTAAAGAATTTAATGTTTTGTTCAAATG
95900 CAT
62 CAT
95903 TAAAATGCCC
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
64 17 0.27
67 1 0.02
68 45 0.71
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (64 bp):
AGGATGTGGGTACAACTTATACAACATCCCCATTTAAAGAATTTAATGTTTTGTTCAAATGCAT
Found at i:102149 original size:2 final size:2
Alignment explanation
Indices: 102142--102177 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
102132 TGGCCTTCTG
102142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102178 GACTTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104781 original size:28 final size:26
Alignment explanation
Indices: 104750--104810 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
104740 TTATTTTAGA
*
104750 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTCAATCTCAAC
104778 CAAACTC--ACAATTTCAATCTCAAC
1 CAAACTCTTACAATTTCAATCTCAAC
*
104802 CAACCTCTT
1 CAAACTCTT
104811 CAAGATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 21 0.72
25 1 0.03
28 7 0.24
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.30
Consensus pattern (26 bp):
CAAACTCTTACAATTTCAATCTCAAC
Found at i:104937 original size:26 final size:26
Alignment explanation
Indices: 104887--104937 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
104877 ACCCGTAATA
*
104887 TATAATTGGAATTGGACTACGAAAAC
1 TATAATTGGAATTGGACTAAGAAAAC
* *
104913 TATAATTTGAATTGGACTAATAAAA
1 TATAATTGGAATTGGACTAAGAAAA
104938 TTCAACCCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (26 bp):
TATAATTGGAATTGGACTAAGAAAAC
Done.