Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014481.1 Corchorus olitorius cultivar O-4 contig14514, 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: 18735
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1796 original size:333 final size:331
Alignment explanation
Indices: 1111--4506 Score: 2986
Period size: 333 Copynumber: 10.2 Consensus size: 331
1101 TTTAATACTT
* * ** *
1111 TATA-TCATCTAACCAAATCTCAGCCACATTGCATTTAAAAATTTGTTTTTACGAGCATCTGACT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * **
1175 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATGCGATATTAAAAGCGTGAAA
66 CTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * * *
1240 GGCCCCCCCAATCTTTTTTGGCGTTGAATTATATAT-TTTTATGAGTTTTTTAGCCAAAAATTGA
130 AG-TCCTCCAATC-TTTTTGGCGTTGAAATATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * * * *
1304 GGAAAAATCTTTCGTGTCAATTTTTGCAAAAATTTAGCCGAAATAGTGTACTAACTAACCATAAC
193 AGAAAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-TAACCATCAC
* * * * * * * *
1369 GGTTTTTGGCTAAAAATGCGTTCCGGGGACCCGCCTTAATTTTGCATGATTTTTGACTCCAAGAC
254 AGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGAC
*
1434 TACTTGAAATATC
319 TCCTTGAAATATC
* * * *
1447 TATATTCATCTAATCAAATATCAACCACATAGGATTTAAGGATTTGTTTTTACGAGCATCTTAAT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * * *
1512 CTTGTTTCGATTTGATTATAAATTAATTCGGAAAAA-ATAGAAAAAATGATATTAGAAA-CGTCA
66 CTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATAT-G-AAAAACGATATTA-AAAGCGTGA
* *
1575 AAAGCCCTTCAATCTTTTTGGCGTTGAAATATATAT-TTTTATGAGTATTTTAGCCAAAAATT-A
128 AAAGTCCTCCAATCTTTTTGGCGTTGAAATATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * *
1638 AGAAAATATCTTTCGGGCCCCTTTTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACA
193 AGAAAA-ATCTTTCGGG--TCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACA
* * * * *
1703 ATTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACT
255 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACT
*
1768 CCTTGAGATATC
320 CCTTGAAATATC
* * * * *
1780 CATATTCATTTAATCAAATCTCAGA-TACATTGGATTTAAGAATTT-TTTTTACGAGCATCTGAA
1 TATATTCATCTAATCAAATCTCA-ACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * * *
1843 TCTTGTTTCGATTTATTTAAAAATTAATTCA-AAAAATAAGAAAAAACGATATTAAAAGCGTGAA
65 TCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATG-AAAAACGATATTAAAAGCGTGAA
* *
1907 AAGTCCTCCAATCTTTTTGGTGTT-AAATTATATATATTTTATGAGTATTTTATCCAAAAATTGA
129 AAGTCCTCCAATCTTTTTGGCGTTGAAA-TATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * * *
1971 GGAAAAATTTTTCAGGTCATATTTTTTTTCAAAATTTTAGCCAAAAAATCGTGTACTATAACCAT
193 AGAAAAATCTTTCGGGTC--A-TTTTTTGCAAAATTTTAGCC--GAAATCGTGTA--ATAACCAT
* * ** *
2036 CACGGTTTTTTTTTTTTTTGGCTAAAAAGGCGTTTTGGGGCCCCGGCTTAGTTTTGCGTGATTTT
251 CACAG---------TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTT
* * * *
2101 TGGCGTCGAGATTTCTTGAAAAATC
307 TGGCGCCGAGACTCCTTGAAATATC
* * * *
2126 TATATTCATCTAATAAAATATTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
2191 CTTGTTTTGATTTAATTAGAAATTAATTCTGAAAAAAAATATGAAAAACGATATTAAAAACGTGA
66 CTTGTTTTGATTTAATTAGAAATTAATTC---AGAAAAATATGAAAAACGATATTAAAAGCGTGA
* * * * * * * * *
2256 AAAGCCCTTCAATCTTTTTGGTGTAGAATTATATAT-TTTGTATGAGTATTATGGCTAAAATTTG
128 AAAGTCCTCCAATCTTTTTGGCGTTGAAATATATATATTT-TATGAGTATTTTAGCCAAAAATTG
* * * * *
2320 AGGAAATATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAAATCGTAG-AATAATCATCACA
192 AAGAAAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCG-AAATCGT-GTAATAACCATCACA
** *
2384 GTTTTTGGCTAAAAACGAATTCCGGGG-CCCGGTTTAGTTTTGCATGATTTTTGGCGCCGAGACT
255 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACT
2448 CCTTGAAATATC
320 CCTTGAAATATC
* * * * * *
2460 TTTATTTATCTAACCAAA--T----CACA--GC---T----A-TTATTTTTACAAGCATCTAAAT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * *
2509 CATGTTTTGATTTAATTAGAAATTAGTTCGGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
66 CTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * * * * * *
2574 AGCCCTTCGATCTTCTTGGCGTTGAATTATAAATTTTTTTATGAAAATTATGGCTAAACATTGAG
130 AGTCCTCCAATCTTTTTGGCGTTGAAATATATA-TATTTTATG---AGTAT---T-----TT-AG
** * * * * * *
2639 GAAAAATATTTCGCCAAAATTGAGGGATAATTTTTCGGGTCATTTTCTGCAAAATTTAAGCTGGA
182 CCAAAA-A-TT-G----AA--GA---AAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAA
* * * *
2704 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCA
235 ATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCA
** *
2769 TGATTTTTGATGCCGAGACTCCTTGAAATGTC
300 TGATTTTTGGCGCCGAGACTCCTTGAAATATC
* * * * * *
2801 TATATTCATCTAA-CAAAATCTCAGCTACATTTGAATTTAAGGATTTATTTTTATGAGCATCTCA
1 TATATTCATCTAATC-AAATCTCAACCACA-TTGCATTTAAGGATTTGTTTTTACGAGCATCTGA
* * *
2865 ATCTTGTTTTGATTTAATTAAAAATTAATTCAGAAAAATATAAAAAACGATATGAAAAGC-TCGA
64 ATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT-GA
* * * * *
2929 AAAGTCCTTCAACCTTTTTGGTGTT-AAATTATATATATTTCATGAGTATTTTAGCCAAAAATTT
128 AAAGTCCTCCAATCTTTTTGGCGTTGAAA-TATATATATTTTATGAGTATTTTAGCCAAAAATTG
*
2993 AAGATAAAT-TTTCCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG-AACTAACAGCATCA
192 AAGAAAAATCTTT-CGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAA-TAAC--CATCA
* * * * * ** * * ** *
3056 CGGTTTTTTGCTAAAAAACGCGTTTCGAGGCTCCAACTCATTTTTGCATGATTTTTGGCGTTGAT
253 CAGTTTTTGGCT-AAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAG
3121 ACTCCTTGAAATATC
317 ACTCCTTGAAATATC
* * * *
3136 TATATTCATCAAATCAAATCTC-AGCACATTGCATTTAAGGATTTGTTTATACGAGCATTTGAAT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
3200 CTTGTTTAGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGCGAAAA
66 CTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* * * * *
3265 GTCCTCCAATCTTTTTGGCGTT-AAATTATATATTTTTTATGACTATTTTATCAAAAAATTGAGG
131 GTCCTCCAATCTTTTTGGCGTTGAAA-TATATATATTTTATGAGTATTTTAGCCAAAAATTGAAG
* * * * * *** *
3329 AGAAATGTTTCGGGCCA--TTTTCCAAAATTTAAG-C----T-G-G-AAT-AGTGT-ACGGTTTT
195 AAAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTT
* *
3382 TGGCTAAAAACGCGTTTCC-GGGCCTCGGC-TATGTTTTGCATGATTTTTGGCGCCGGGACTCCT
260 TGGCTAAAAACGCG-TTCCGGGGCCCCGGCTTA-GTTTTGCATGATTTTTGGCGCCGAGACTCCT
3445 TGAAATATC
323 TGAAATATC
* *
3454 TATACTT-ATCTAATCAAATCTCAACCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGA
1 TATA-TTCATCTAATCAAATCTCAACCACA-TTGCATTTAAGGATTTGTTTTTACGAGCATCTGA
* * * * *
3518 ATCTTGTTTTGATTTAAGTACAAGTTAATTCAGAAAACTATGAAAAACGATATCAAAAGC-TCGA
64 ATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT-GA
** * * *
3582 AAAGTCCTTAAACCATTTTGGCGTT-AAATTATATATATTTCATGAAGTATTTTAGCCAAAAATT
128 AAAGTCCTCCAATCTTTTTGGCGTTGAAA-TATATATATTTTATG-AGTATTTTAGCCAAAAATT
* * *
3646 GAAGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGTCGAAATC--GT-AT-A-CATCACAG
191 GAAGAAAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG
* * * * * * * *
3706 TTTTTCTGCTAAAAACGCGTTTCAGGGCTCCGACTCAGTTTTGCGTGATTTTTGGCGTCGAGACT
256 TTTTT-GGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACT
3771 -CTTGAAATATC
320 CCTTGAAATATC
* * * * * * *
3782 TATATTCATTTAATCAAATCTCAGCCATATTGCATTTAAAGATTT-TTTATACGAGTATTTGAAT
1 TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * ** *
3846 CTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGGTAAGCGATATTAAAAGCGTGAAAA
66 CTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* * * * *
3911 ATCCTCCAACCTTTTTGGCGTTAAATTTATATATATATATATATATTATGAGTATGTTAGCTAAA
131 GTCCTCCAATCTTTTTGGCG-----TTGA-A-ATATATATAT-T-TTATGAGTATTTTAGCCAAA
* * * * * * * * * *
3976 AATTGAGGAAAAGT-TTGTTGGGTCATTTTTTGCAAAAGTTAAGCTGGAATCGTATACTAACTAT
187 AATTGAAGAAAAATCTT-TCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCAT
* *
4040 CACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCCGA
251 CACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGA
**
4105 GACTTTTTGAAATATC
316 GACTCCTTGAAATATC
* * * * * * * *
4121 TATACTCATGTAATCAAATCCCAGCCACATTTGAATTTAATGCTTTGTTTTTACGAGCATCTTAA
1 TATATTCATCTAATCAAATCTCAACCACA-TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAA
* *
4186 TCTTGTTTTGATTTAATTAGAAATTGATTCAGAAAAATATGGAAAACGATATTAAAAGCGTGAAA
65 TCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * * * *
4251 AGTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGT-TTGTGGCTAAAAATTGAGG
130 AGTCCTCCAATCTTTTTGGCGTTGAAATATATATATTTTATGAGTATTTTAGCCAAAAATTGAAG
* ** *
4315 AAAAATATTTCATGTC-TATTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACCATCACGATTT
195 AAAAATCTTTCGGGTCAT-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAC-AGTT
* ** * * * * * * *
4375 TTTGGCTAAAAACGCATTCCGGGATCCCGGATCAGTTTTGCATGATTTTATTGTGGCAAAACTCC
258 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTT-TGGCGCCGAGACTCC
*
4440 TTTAAATATC
322 TTGAAATATC
* * * * * *
4450 TATACTCATCTAACCTAATCTTAGCCACATTAG-ATTTAAGGATTTTTTTTTACGAGC
1 TATATTCATCTAATCAAATCTCAACCACATT-GCATTTAAGGATTTGTTTTTACGAGC
4507 TGTAGAGCAA
Statistics
Matches: 2515, Mismatches: 403, Indels: 292
0.78 0.13 0.09
Matches are distributed among these distances:
316 59 0.02
317 6 0.00
318 116 0.05
319 23 0.01
320 129 0.05
321 33 0.01
322 1 0.00
323 17 0.01
324 4 0.00
325 1 0.00
326 88 0.03
327 25 0.01
328 124 0.05
329 91 0.04
330 10 0.00
331 122 0.05
332 130 0.05
333 305 0.12
334 152 0.06
335 168 0.07
336 24 0.01
337 134 0.05
338 59 0.02
339 48 0.02
340 55 0.02
341 180 0.07
342 2 0.00
343 2 0.00
344 17 0.01
345 2 0.00
346 107 0.04
347 67 0.03
348 1 0.00
349 3 0.00
350 87 0.03
351 10 0.00
353 5 0.00
356 10 0.00
357 52 0.02
358 46 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (331 bp):
TATATTCATCTAATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
GTCCTCCAATCTTTTTGGCGTTGAAATATATATATTTTATGAGTATTTTAGCCAAAAATTGAAGA
AAAATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTT
GGCTAAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGA
AATATC
Found at i:4170 original size:667 final size:661
Alignment explanation
Indices: 1111--4506 Score: 3205
Period size: 667 Copynumber: 5.1 Consensus size: 661
1101 TTTAATACTT
* * * *
1111 TATA-TCATCTAACCAAATCTCAGCCACATTGCATTTAAAAATTTGTTTTTACGAGCATCTGACT
1 TATATTCATCTAATCAAATCTCAG-CACATTGCATTTAAAGATTT-TTTATACGAGCATCTGAAT
* * *
1175 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAA-ATAAGAAATGCGATATTAAAAGCGTGAA
64 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT-GGAAA-ACGATATTAAAAGCGTGAA
* * * * *
1239 AGGCCCCCCCAATCTTTTTTGGCG-T--TGAATTATATAT-TTTTATGAGTTTTTTAGCCAAAAA
127 AAG-TCCTCCAATC-TTTTTGGCGTTAATTAATTATATATATTTTATGAGTATTTTAGCCAAAAA
* * * * * *
1300 TTGAGGAAAAATCTTTCGTGTCAATTTTTGCAAAAATTT-AGCCGAAATAGTGTACTAACTAACC
190 TTGAGG-AAAAT-TTTTGGGTCATTTTTTGC-AAAATTTAAGCTGGAAT--CGTA-T-ACTAACC
* * * * * * * *
1364 ATAACGGTTTTTGGCTAAAAATGCGTTCCGGGGACCCGCCTTAATTTTGCATGATTTTTGACTCC
248 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCC
* * * * * *
1429 AAGACTACTTGAAATATCTATATTCATCTAATCAAATATCAACCACA-TAGGATTTAAGGATTTG
313 GAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTG
* * * * *
1493 TTTTTACGAGCATCTTAATCTTGTTTCGATTTGATTATAAATTAATTCGGAAAAA-ATAGAAAAA
378 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATAT-G-AAAA
* *
1557 ATGATATTAGAAA-CGTC-AAAAGCCCTTCAATCTTTTTGGCGTTGAAA-TATATAT-TTTTATG
441 ACGATATTA-AAAGCGTCGAAAAGTCCTTCAATCTTTTTGGCGTT-AAATTATATATATTTTATG
* * * * *
1618 AGTATTTTAGCCAAAAATT-AAGAAAATATCTTTCGGGCCCCTTTTTTTACAAAATTTTAGCCAA
504 AGTATTTTAGCCAAAAATTGAAGAAAA-ATTTTTCGGG--TCATTTTTTGCAAAATTTTAGCCGA
* * * * * *
1682 AATCGTGTAATAACCATCACAATTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGC
566 AATC--GTAATAACCATCACAGTTTTTTGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGC
* * *
1747 ATGATTTTTGGCACCAAGACTCCTTGAGATATC
629 ATGATTTTTGGCGCCGAGACTCCTTGAAATATC
* * * * *
1780 CATATTCATTTAATCAAATCTCAGATACATTGGATTT-AAGAATTTTTTTTACGAGCATCTGAAT
1 TATATTCATCTAATCAAATCTCAG-CACATTGCATTTAAAG-ATTTTTTATACGAGCATCTGAAT
* * * *
1844 CTTGTTTCGATTTATTTAAAAATTAATTCA-AAAAATAAGAAAAAACGATATTAAAAGCGTGAAA
64 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATG-GAAAACGATATTAAAAGCGTGAAA
* *
1908 AGTCCTCCAATCTTTTTGGTGTT-A--AATTATATATATTTTATGAGTATTTTATCCAAAAATTG
128 AGTCCTCCAATCTTTTTGGCGTTAATTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
* * * *** *
1970 AGGAAAAATTTTTCAGGTCATATTTTTTTTCAAAATTTTAGCCAAAAAATCGTGTACTATAACCA
193 AGG-AAAATTTTT-GGGTC--A-TTTTTTGCAAAATTTAAG-C-TGGAATCGTATAC--TAACCA
* * *
2035 TCACGGTTTTTTTTTTTTTTGGCTAAAAAGGCGTTTTGGGGCCCCGGCTTAGTTTTGCGTGATTT
249 TCACGG---------TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTT
* * * * * * * *
2100 TTGGCGTCGAGATTTCTTGAAAAATCTATATTCATCTAATAAAATATTAGCCACA-TTGCATTTA
305 TTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTTGAATTTA
*
2164 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCTGAAAAAAA
370 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTC---AGAAAA
* * *
2229 ATATGAAAAACGATATTAAAAACGT-GAAAAGCCCTTCAATCTTTTTGGTG-TAGAATTATATAT
432 ATATGAAAAACGATATTAAAAGCGTCGAAAAGTCCTTCAATCTTTTTGGCGTTA-AATTATATAT
* * * * * * *
2292 -TTTGTATGAGTATTATGGCTAAAATTTGAGGAAATATCTTTT-GGGTCAATTTTTGCAAAATTT
496 ATTT-TATGAGTATTTTAGCCAAAAATTGAAGAAAAAT-TTTTCGGGTCATTTTTTGCAAAATTT
* * ** * ** *
2355 TAGCCGAAAATCGTAGAATAATCATCACAGTTTTTGGCTAAAAACGAATTCCGGGGC-CCGGTTT
559 TAGCCG-AAATCGT--AATAACCATCACAGTTTTTTGCTAAAAACGCGTTTCGGGGCTCCGACTC
2419 AGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
621 AGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
* * * * * * *
2460 TTTATTTATCTAACCAAATCACAG--C--T--A-TT----A--TTTT-TACAAGCATCTAAATCA
1 TATATTCATCTAATCAAATCTCAGCACATTGCATTTAAAGATTTTTTATACGAGCATCTGAATCT
* * *
2511 TGTTTTGATTTAATTAGAAATTAGTTCGGAAAAA-ATAGGAAAAACGATATTAAAAGCGTGAAAA
66 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT-GG-AAAACGATATTAAAAGCGTGAAAA
* * * * * *
2575 GCCCTTCGATCTTCTTGGCGTTGAATTATAAATTTTTTTATGAAAATTATGGCTAAACATTGAGG
129 GTCCTCCAATCTTTTTGGCGTT-AA-T-T-AA---TTATAT--ATATT-T---T----A-TGA-G
* * * *
2640 AAAAATATTTCGCC-AAAATTGAGGGATAATTTTTCGGGTCATTTTCTGCAAAATTTAAGCTGGA
175 ---TAT-TTTAGCCAAAAATTGA-GGAAAATTTTT-GGGTCATTTTTTGCAAAATTTAAGCTGGA
* *
2704 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCA
234 ATCGTATACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCA
** * *
2769 TGATTTTTGATGCCGAGACTCCTTGAAATGTCTATATTCATCTAA-CAAAATCTCAGCTACATTT
299 TGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTT
* * * *
2833 GAATTTAAGGATTTATTTTTATGAGCATCTCAATCTTGTTTTGATTTAATTAAAAATTAATTCAG
363 GAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAG
* * * *
2898 AAAAATATAAAAAACGATATGAAAAGC-TCGAAAAGTCCTTCAACCTTTTTGGTGTTAAATTATA
428 AAAAATATGAAAAACGATATTAAAAGCGTCGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATA
* * * *
2962 TATATTTCATGAGTATTTTAGCCAAAAATTTAAGATAAATTTTCCGGGTCATTTTTTGCAAAATT
493 TATATTTTATGAGTATTTTAGCCAAAAATTGAAGAAAAATTTTTCGGGTCATTTTTTGCAAAATT
* * *
3027 TTAGCCGAAATCGTGAACTAACAGCATCACGGTTTTTTGCTAAAAAACGCGTTTCGAGGCTCCAA
558 TTAGCCGAAATCGT-AA-TAAC--CATCACAGTTTTTTGCT-AAAAACGCGTTTCGGGGCTCCGA
* ** *
3092 CTCATTTTTGCATGATTTTTGGCGTTGATACTCCTTGAAATATC
618 CTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
* * *
3136 TATATTCATCAAATCAAATCTCAGCACATTGCATTTAAGGATTTGTTTATACGAGCATTTGAATC
1 TATATTCATCTAATCAAATCTCAGCACATTGCATTTAAAGATTT-TTTATACGAGCATCTGAATC
* * *
3201 TTGTTTAGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGCGAAAAG
65 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAAAAGCGTGAAAAG
* * * *
3266 TCCTCCAATCTTTTTGGCGTT-A--AATTATATATTTTTTATGACTATTTTATCAAAAAATTGAG
130 TCCTCCAATCTTTTTGGCGTTAATTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAG
* * * * *
3328 GAGAAATGTTTCGGGCCA--TTTTCCAAAATTTAAGCTGG-A----ATAGT----GT-ACGGTTT
195 GA-AAAT-TTTTGGGTCATTTTTTGCAAAATTTAAGCTGGAATCGTATACTAACCATCACGGTTT
* * *
3381 TTGGCTAAAAACGCGTTTCCGGGCCTCGGC-TATGTTTTGCATGATTTTTGGCGCCGGGACTCCT
258 TTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTA-GTTTTGCATGATTTTTGGCGCCGAGACTCCT
* *
3445 TGAAATATCTATACTT-ATCTAATCAAATCTCAACCACATTTGAATTTAATGATTTGTTTTTACG
322 TGAAATATCTATA-TTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACG
* * * * *
3509 AGCATCTGAATCTTGTTTTGATTTAAGTACAAGTTAATTCAGAAAACTATGAAAAACGATATCAA
386 AGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAA
* * * *
3574 AAGC-TCGAAAAGTCCTTAAACCATTTTGGCGTTAAATTATATATATTTCATGAAGTATTTTAGC
451 AAGCGTCGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATATATATTTTATG-AGTATTTTAGC
* *
3638 CAAAAATTGAAGAAAAATTTTTCGGGTCATTTTTTACAAAATTTTAGTCGAAATCGT-AT-A-CA
515 CAAAAATTGAAGAAAAATTTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTAATAACCA
* * *
3700 TCACAGTTTTTCTGCTAAAAACGCGTTTCAGGGCTCCGACTCAGTTTTGCGTGATTTTTGGCGTC
580 TCACAGTTTTT-TGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGCGCC
3765 GAGACT-CTTGAAATATC
644 GAGACTCCTTGAAATATC
* * * *
3782 TATATTCATTTAATCAAATCTCAGCCATATTGCATTTAAAGATTTTTTATACGAGTATTTGAATC
1 TATATTCATCTAATCAAATCTCAG-CACATTGCATTTAAAGATTTTTTATACGAGCATCTGAATC
* * * *
3847 TTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGGTAAGCGATATTAAAAGCGTGAAAAA
65 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAAAAGCGTGAAAAG
* * *
3912 TCCTCCAACCTTTTTGGCGTTAAATTTATATATATATATATATATTATGAGTATGTTAGCTAAAA
130 TCCTCCAATCTTTTTGGCGTT-AA-TTA-AT-TATATATAT-T-TTATGAGTATTTTAGCCAAAA
* *
3977 ATTGAGGAAAAGTTTGTTGGGTCATTTTTTGCAAAAGTTAAGCTGGAATCGTATACTAACTATCA
189 ATTGAGGAAAA-TTT-TTGGGTCATTTTTTGCAAAATTTAAGCTGGAATCGTATACTAACCATCA
* *
4042 CAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCCGAGA
252 CGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGA
** * * * * *
4107 CTTTTTGAAATATCTATACTCATGTAATCAAATCCCAGCCACATTTGAATTTAATGCTTTGTTTT
317 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTT
* * *
4172 TACGAGCATCTTAATCTTGTTTTGATTTAATTAGAAATTGATTCAGAAAAATATGGAAAACGATA
382 TACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATA
* * * *
4237 TTAAAAGCGT-GAAAAGTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGT-TTGT
447 TTAAAAGCGTCGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTT
* * * * ** *
4300 GGCTAAAAATTGAGGAAAAATATTTCATGTC-TATTTTTGCAAAATTTTAGCCGAAATCGT-GT-
512 AGCCAAAAATTGAAGAAAAATTTTTCGGGTCAT-TTTTTGCAAAATTTTAGCCGAAATCGTAATA
* * *
4362 ACCATCAC-GATTTTTTGGCTAAAAACGC-ATTCCGGGATCCCGGA-TCAGTTTTGCATGATTTT
576 ACCATCACAG-TTTTTT-GCTAAAAACGCGTTTCGGGGCT-CC-GACTCAGTTTTGCATGATTTT
* * * * * *
4424 ATTGTGGCAAAACTCCTTTAAATATC
637 -TGGCGCCGAGACTCCTTGAAATATC
* * * * * *
4450 TATACTCATCTAACCTAATCTTAGCCACATTAG-ATTTAAGGATTTTTTTTTACGAGC
1 TATATTCATCTAATCAAATCTCAG-CACATT-GCATTTAAAGA-TTTTTTATACGAGC
4507 TGTAGAGCAA
Statistics
Matches: 2271, Mismatches: 315, Indels: 282
0.79 0.11 0.10
Matches are distributed among these distances:
646 130 0.06
647 78 0.03
648 5 0.00
650 1 0.00
651 2 0.00
652 5 0.00
653 230 0.10
654 73 0.03
655 32 0.01
657 18 0.01
658 4 0.00
662 5 0.00
663 18 0.01
664 8 0.00
665 120 0.05
666 121 0.05
667 274 0.12
668 75 0.03
669 79 0.03
670 53 0.02
671 4 0.00
672 20 0.01
673 111 0.05
674 21 0.01
675 104 0.05
676 124 0.05
677 2 0.00
678 8 0.00
679 151 0.07
680 92 0.04
681 89 0.04
682 32 0.01
683 14 0.01
684 12 0.01
686 11 0.00
687 5 0.00
688 17 0.01
689 2 0.00
690 44 0.02
691 68 0.03
692 9 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (661 bp):
TATATTCATCTAATCAAATCTCAGCACATTGCATTTAAAGATTTTTTATACGAGCATCTGAATCT
TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAAAAGCGTGAAAAGT
CCTCCAATCTTTTTGGCGTTAATTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGG
AAAATTTTTGGGTCATTTTTTGCAAAATTTAAGCTGGAATCGTATACTAACCATCACGGTTTTTG
GCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
ATATCTATATTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCAT
CTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG
TCGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAA
TTGAAGAAAAATTTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTAATAACCATCACAG
TTTTTTGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTC
CTTGAAATATC
Found at i:4984 original size:40 final size:37
Alignment explanation
Indices: 4905--4976 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
4895 ATTATTGAAA
*
4905 GAAGATCCACCTATGTGGAGGATTATTTTCAAAGATT
1 GAAGATCCACCTATGTGGAGGATTATTATCAAAGATT
* *
4942 GAAGATCCACGTATGTGGGGGATTATTATCAAAGA
1 GAAGATCCACCTATGTGGAGGATTATTATCAAAGA
4977 AGATTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (37 bp):
GAAGATCCACCTATGTGGAGGATTATTATCAAAGATT
Found at i:5302 original size:62 final size:58
Alignment explanation
Indices: 5195--5318 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 58
5185 AAGACCCTTG
* * *
5195 AATCAAATCAAACTCCCAAGTCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA
1 AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCA
* *
5253 AATCAAATCAAACTCTCAAATTATCATCAAGTTCAATATCAAGTTATTCGACCCTTGAAGCA
1 AATCAAATCAAACTC-CAAA--ATCATCAA-TTCAAGATCAAGTCATTCGACCCTTGAAGCA
5315 AATC
1 AATC
5319 TTGAAGCATA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 15 0.26
59 3 0.05
61 7 0.12
62 32 0.56
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (58 bp):
AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCA
Found at i:6162 original size:323 final size:328
Alignment explanation
Indices: 5504--6275 Score: 852
Period size: 323 Copynumber: 2.4 Consensus size: 328
5494 ATGTTTCGAT
* ** *
5504 TTAA-TTAGAAATAAAATAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTT-CAACCTTTTTGG
1 TTAATTTAGAAATAAAATAGAAAAAACGATATTAGAAGCGTGAAAAG-GTTTCCAATCTTTTTGG
* * * * * * *
5567 CATTGAATTATATGTTTTTTATGAGTATTGTGGGTAAAAATTGA-GATAAATATTTAGGGCCAAT
65 CATTGAATTATAT-ATTTTTATGAGTATTTTCGCT-AAAATTGAGGAAAAATCTTTAGGACCAAT
**
5631 TTTTGCAAAAACTTTAGCCGAAATCGTGTACCATCACGGTTTTTTGGCTAAAAACGCGTTTTGGG
128 TTTTGCAAAAACTTTAGCCGAAATCGTG----ATCACGGTTTTTTGGCTAAAAACGCGTTCCGGG
* * * *
5696 GCCCCAGGTCAGTTTTGCATGATTTTTTACGCCAAGACTCCTTAAAATATATCTTTATTCATGTA
189 GCCACAGCTCAGTTTTGCATGATTTTTTACACCAAGACTCCTTAAAATATATCTTTATTCATCTA
*** *
5761 ACCAAATCTCAGCCACATTTTTTTTAAGAATTTGTTTTTATGAGCATCTAAATCTTGTTCTGAAT
254 ACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTCTGAAT
5826 TAATCAGAAA
319 TAATCAGAAA
* * *
5836 TTAATTTATAAATAAAATAGAAAAAACGATATTAGAAGTGTGAAAAGGTTTCCAATTTTTTTGGT
1 TTAATTTAGAAATAAAATAGAAAAAACGATATTAGAAGCGTGAAAAGGTTTCCAATCTTTTTGG-
* * * *
5901 C-TTGATTTATATATTTTTATGAATATTTTCGCTAGAAATTGAGGAAAAATCTTTTGGATCAATT
65 CATTGAATTATATATTTTTATGAGTATTTTCGCTA-AAATTGAGGAAAAATCTTTAGGACCAATT
* *
5965 TTTGC-AAAATTTTAGCTGAAATCGTG-T-ACGG-TTTTTGGCTAAAAACGCGTTCCGGGGCCAC
129 TTTGCAAAAACTTTAGCCGAAATCGTGATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCAC
** * * **
6026 AGCTTTGTTTTGCATGATTTTTTGCACCAAGACTCCTT-CAA-ATATCTTTATTCATCTAATTAA
194 AGCTCAGTTTTGCATGATTTTTTACACCAAGACTCCTTAAAATATATCTTTATTCATCTAACCAA
* * * * * * * *
6089 ATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGTGCATTTGAATCTTGTTTTGATTTAATT
259 ATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTCTGAATTAATC
*
6154 ATAAA
324 AGAAA
* * * *
6159 TTAATTCAGAAA-AAAATATG-AAAAACGATATTAAAAGCGTGAAAA-GTACTCCAGTCTTTTTG
1 TTAATTTAGAAATAAAATA-GAAAAAACGATATTAGAAGCGTGAAAAGGT-TTCCAATCTTTTTG
* * * * *
6221 GCGTTGAACTATATA-TTTTATGAGTATTTTTGCCAAAATTTGAGAAAAAATCTTT
64 GCATTGAATTATATATTTTTATGAGTATTTTCGCTAAAA-TTGAGGAAAAATCTTT
6276 CCGGTCATTT
Statistics
Matches: 373, Mismatches: 58, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
320 3 0.01
321 35 0.09
322 51 0.14
323 87 0.23
324 2 0.01
325 60 0.16
326 4 0.01
327 1 0.00
331 1 0.00
332 48 0.13
333 80 0.21
334 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (328 bp):
TTAATTTAGAAATAAAATAGAAAAAACGATATTAGAAGCGTGAAAAGGTTTCCAATCTTTTTGGC
ATTGAATTATATATTTTTATGAGTATTTTCGCTAAAATTGAGGAAAAATCTTTAGGACCAATTTT
TGCAAAAACTTTAGCCGAAATCGTGATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCACAG
CTCAGTTTTGCATGATTTTTTACACCAAGACTCCTTAAAATATATCTTTATTCATCTAACCAAAT
CTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTCTGAATTAATCAG
AAA
Found at i:11972 original size:23 final size:22
Alignment explanation
Indices: 11939--11983 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11929 CCACCCAAGT
11939 AGAAATCTTTTTCCCACCTCTA
1 AGAAATCTTTTTCCCACCTCTA
11961 AGAAATCTTTTTCCCACCTCTA
1 AGAAATCTTTTTCCCACCTCTA
11983 A
1 A
11984 CCAGCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (22 bp):
AGAAATCTTTTTCCCACCTCTA
Found at i:12896 original size:29 final size:31
Alignment explanation
Indices: 12834--13000 Score: 116
Period size: 31 Copynumber: 5.5 Consensus size: 31
12824 CGATGCCGGA
* *
12834 CCTTATTTGAGCATTTTTA-ATAACG-TTAGGC
1 CCTTATTTGAGCAATTTGACA-AA-GATTAGGC
*
12865 CCTTATTTG-GCCAAATT-A-AAAGATTAGGC
1 CCTTATTTGAG-CAATTTGACAAAGATTAGGC
* * *
12894 CCTTATTTGAGCATTTTCGATAATG-TTAGGC
1 CCTTATTTGAGCAATTT-GACAAAGATTAGGC
** * * *
12925 CCTTATTTGCCCAAGTT-A-AAAGATCAGGA
1 CCTTATTTGAGCAATTTGACAAAGATTAGGC
* *
12954 CCTTATTTGAGCATTTTGACAAACATTAGGC
1 CCTTATTTGAGCAATTTGACAAAGATTAGGC
*
12985 CCTTATTTGAACAATT
1 CCTTATTTGAGCAATT
13001 AGCCATGTTT
Statistics
Matches: 106, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
28 4 0.04
29 39 0.37
30 5 0.05
31 55 0.52
32 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (31 bp):
CCTTATTTGAGCAATTTGACAAAGATTAGGC
Found at i:12927 original size:60 final size:59
Alignment explanation
Indices: 12831--12993 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 59
12821 TGTCGATGCC
* * *
12831 GGACCTTATTTGAGCATTTTTAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTA
1 GGACCTTATTTGAGCA-TTTTGATAACGTTAGGCCCTTATTTGCCCAAATTAAAAGATCA
* * *
12891 GGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGCCCAAGTTAAAAGATCA
1 GGACCTTATTTGAGCATTTT-GATAACGTTAGGCCCTTATTTGCCCAAATTAAAAGATCA
* *
12951 GGACCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTG
1 GGACCTTATTTGAGCATTTTGA-TAACGTTAGGCCCTTATTTG
12994 AACAATTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
59 6 0.07
60 85 0.93
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (59 bp):
GGACCTTATTTGAGCATTTTGATAACGTTAGGCCCTTATTTGCCCAAATTAAAAGATCA
Found at i:14933 original size:11 final size:11
Alignment explanation
Indices: 14917--14942 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14907 AGATAATTTC
14917 TTTTCTTCTAG
1 TTTTCTTCTAG
14928 TTTTCTTCTAG
1 TTTTCTTCTAG
14939 TTTT
1 TTTT
14943 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:15732 original size:15 final size:15
Alignment explanation
Indices: 15702--15743 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
15692 TTACTTTGCT
15702 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
15718 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
15733 TTGCTTTCTGT
1 TTGTTTTCTGT
15744 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:16109 original size:22 final size:20
Alignment explanation
Indices: 16083--16155 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 20
16073 TTGTTTTGTG
16083 TTTTGCGTCGAAAAAAAAATAT
1 TTTTGCGTC-AAAAAAAAAT-T
16105 TTTTGCGTCATAAAAAAAAATT
1 TTTTGCGTC--AAAAAAAAATT
*
16127 GTTTCTGCGTCATAAAAAAAAGT
1 -TTT-TGCGTCA-AAAAAAAATT
16150 TTTTGC
1 TTTTGC
16156 ATTTTTCTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.07
22 14 0.31
23 22 0.49
24 6 0.13
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTGCGTCAAAAAAAAATT
Found at i:16135 original size:24 final size:24
Alignment explanation
Indices: 16081--16147 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
16071 CCTTGTTTTG
*
16081 TGTTTTGCGTC-GAAAAAAAAATA
1 TGTTTTGCGTCATAAAAAAAAATA
16104 T-TTTTGCGTCATAAAAAAAAAT-
1 TGTTTTGCGTCATAAAAAAAAATA
16126 TGTTTCTGCGTCATAAAAAAAA
1 TGTTT-TGCGTCATAAAAAAAA
16148 GTTTTTGCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 10 0.25
23 14 0.35
24 16 0.40
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (24 bp):
TGTTTTGCGTCATAAAAAAAAATA
Done.