Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_pilon, 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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 27
Found at i:1988463 original size:42 final size:41
Alignment explanation
Indices: 1988409--1988493 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
1988399 ACAACGAATT
*
1988409 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAACCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
1988451 TGGAAAACCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAACCGCAACGCAACTGTCAACTATCGCAACGCGAAA
1988492 TG
1 TG
1988494 CAACGCGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (41 bp):
TGGAAAACCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:1988497 original size:21 final size:21
Alignment explanation
Indices: 1988434--1988497 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
1988424 ACAACTGTAG
*
1988434 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
1988455 A-AACCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1988475 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1988496 AC
1 AC
1988498 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1991382 original size:20 final size:20
Alignment explanation
Indices: 1991337--1991392 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1991327 CGATACTAAG
* **
1991337 CCCTTGAGTATCGGTACTGA
1 CCCTTGAGTATCGATACCCA
*
1991357 CACTTGAGTATCGATACCCA
1 CCCTTGAGTATCGATACCCA
*
1991377 CCCTTG-GTACCGATAC
1 CCCTTGAGTATCGATAC
1991393 TAAAAATGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (20 bp):
CCCTTGAGTATCGATACCCA
Found at i:2002025 original size:21 final size:20
Alignment explanation
Indices: 2001975--2002025 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2001965 AAAAGGATCC
*
2001975 AATTTC-ACATTCTAACATA
1 AATTTCAACACTCTAACATA
* *
2001994 AATTTCAACACTCTAACTTT
1 AATTTCAACACTCTAACATA
2002014 AATTTCCAACAC
1 AATTT-CAACAC
2002026 CTCAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 6 0.22
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTTCAACACTCTAACATA
Found at i:2029306 original size:67 final size:66
Alignment explanation
Indices: 2029186--2029382 Score: 243
Period size: 67 Copynumber: 2.9 Consensus size: 66
2029176 AGTTGGGCAA
* * *
2029186 TGTTTGACTTGTGCTCGTTAA-AATCTTTTGTTGCTCGACTCATTGCTCATTAAGCTCATTAAAA
1 TGTTCGACTCGTGCTCGTTAAGAA-ATTTTGTTGCTCGACTCATTGCT-ATTAAGCTCATTAAAA
2029250 TTT
64 TTT
* * * *
2029253 TGTTCGACTCGTGCTCGTTAAGAAAATTTGTTGCTCGGCTCATTGCATGTTAAGCTCGTTAAAAT
1 TGTTCGACTCGTGCTCGTTAAGAAATTTTGTTGCTCGACTCATTGC-TATTAAGCTCATTAAAAT
2029318 TT
65 TT
* * * * *
2029320 TGATCGACTCATGCTCATTAAGAAATTTTGTTGTTCGACTCATTGCTTATTAAGGTCATTAAA
1 TGTTCGACTCGTGCTCGTTAAGAAATTTTGTTGCTCGACTCATTGC-TATTAAGCTCATTAAA
2029383 CTCTTGCTCA
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 108 0.97
68 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (66 bp):
TGTTCGACTCGTGCTCGTTAAGAAATTTTGTTGCTCGACTCATTGCTATTAAGCTCATTAAAATT
T
Found at i:2029398 original size:67 final size:67
Alignment explanation
Indices: 2029211--2029382 Score: 245
Period size: 67 Copynumber: 2.6 Consensus size: 67
2029201 CGTTAAAATC
* * * *
2029211 TTTTGTTGCTCGACTCATTGCTCATTAAGCTCATTAAAATTTTGTTCGACTCGTGCTCGTTAAGA
1 TTTTGTTGCTCGACTCATTGCTTATTAAGCTCATTAAAATTTTGATCGACTCATGCTCATTAAGA
2029276 AA
66 AA
* * * * *
2029278 ATTTGTTGCTCGGCTCATTGCATGTTAAGCTCGTTAAAATTTTGATCGACTCATGCTCATTAAGA
1 TTTTGTTGCTCGACTCATTGCTTATTAAGCTCATTAAAATTTTGATCGACTCATGCTCATTAAGA
2029343 AA
66 AA
* *
2029345 TTTTGTTGTTCGACTCATTGCTTATTAAGGTCATTAAA
1 TTTTGTTGCTCGACTCATTGCTTATTAAGCTCATTAAA
2029383 CTCTTGCTCA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 89 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (67 bp):
TTTTGTTGCTCGACTCATTGCTTATTAAGCTCATTAAAATTTTGATCGACTCATGCTCATTAAGA
AA
Found at i:2029890 original size:16 final size:16
Alignment explanation
Indices: 2029857--2029891 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2029847 TTGAGTCAAC
**
2029857 TTGAGTCGAGTTTTAG
1 TTGAGTCGAGTTCGAG
2029873 TTGAGTCGAGTTCGAG
1 TTGAGTCGAGTTCGAG
2029889 TTG
1 TTG
2029892 CTCACGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (16 bp):
TTGAGTCGAGTTCGAG
Found at i:2031317 original size:37 final size:38
Alignment explanation
Indices: 2031276--2031409 Score: 116
Period size: 37 Copynumber: 3.6 Consensus size: 38
2031266 CTACAATATC
** *
2031276 ATATTTCAATCTAATATAAATTTGT-ACTAATATATTT
1 ATATTTCAATCTAATATAAATTCATAAATAATATATTT
*
2031313 ATATTTCAAT-TGAATATATATTCATAAATAATATATTT
1 ATATTTCAATCT-AATATAAATTCATAAATAATATATTT
* * * *
2031351 GTATTT-AATCAAATATTAATGT-ATAAATAAGATATTT
1 ATATTTCAATCTAATATAAAT-TCATAAATAATATATTT
* *
2031388 TTATTTTAAT-TGAATATAAATT
1 ATATTTCAATCT-AATATAAATT
2031410 GGTTAACATA
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
36 1 0.01
37 50 0.63
38 28 0.35
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (38 bp):
ATATTTCAATCTAATATAAATTCATAAATAATATATTT
Found at i:2031356 original size:38 final size:38
Alignment explanation
Indices: 2031303--2031405 Score: 113
Period size: 38 Copynumber: 2.7 Consensus size: 38
2031293 AAATTTGTAC
2031303 TAATATATTTATATTTCAATTGAATATAT-AT-TCATAAA
1 TAATATATTTATATTT-AATTGAATATATAATGT-ATAAA
* **
2031341 TAATATATTTGTATTTAATCAAATAT-TAATGTATAAA
1 TAATATATTTATATTTAATTGAATATATAATGTATAAA
* *
2031378 TAAGATATTTTTATTTTAATTGAATATA
1 TAATATATTTATA-TTTAATTGAATATA
2031406 AATTGGTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
36 1 0.02
37 26 0.48
38 27 0.50
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (38 bp):
TAATATATTTATATTTAATTGAATATATAATGTATAAA
Found at i:2033688 original size:87 final size:86
Alignment explanation
Indices: 2033542--2033712 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 86
2033532 TCACCCTAAC
* *
2033542 CCTTTTATTTTCTTATCAAATATCGTTTAGACTATATTTTTTGATTTAATACTTTAACGGTGTAG
1 CCTTTTATTTTCTTATCAAATATCATTTAGACTATATTTTTTGATTTAATACTTTAACGGTGCA-
*
2033607 GGGACGCTCCTTTCTAAACAAT
65 AGGACGCTCCTTTCTAAACAAT
* *
2033629 CCTTTTATTTTCTTATCAGATATCATTTAGATTATATTTTTTGATTTAATA-TCTTAACGGTGCA
1 CCTTTTATTTTCTTATCAAATATCATTTAGACTATATTTTTTGATTTAATACT-TTAACGGTGCA
*
2033693 AGGACGCTCCTTTCTGAACA
65 AGGACGCTCCTTTCTAAACA
2033713 GAATATTAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
86 19 0.25
87 58 0.75
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (86 bp):
CCTTTTATTTTCTTATCAAATATCATTTAGACTATATTTTTTGATTTAATACTTTAACGGTGCAA
GGACGCTCCTTTCTAAACAAT
Found at i:2042464 original size:284 final size:287
Alignment explanation
Indices: 2041768--2043869 Score: 1845
Period size: 288 Copynumber: 7.1 Consensus size: 287
2041758 ATATGAAGCA
*
2041768 GAAGGATTAAATTGTGTTAAAATGACGTAGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
* *
2041833 CATCGCAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAATGAACGTAG
66 CATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
*
2041898 CAAAGACTCGCTGAGCAAT-GATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
131 CAAAGACTCACTGAGC-ATGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
*
2041962 ATTTATTTAAAAAGATTATTTTTTAAACAGAGTATGATTAAAAAGATGATAGAACACGAAAGAAA
195 ATTTATTTAAAAAGATTATTTTTTAAACAGAG-ATGATTAAAAAGATGATTGAACACGAAAGAAA
2042027 TATGAGTTTTGCCAACCTTAAAATGATAT
259 TATGAGTTTTGCCAACCTTAAAATGATAT
*
2042056 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCTCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
* *
2042121 CATCACAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACATAG
66 CATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
* *
2042186 CAAAGACTCACTGAGCATGGATCTCTTAAAAAATGCAAATAATGATAGCTACTAACTATATGAAA
131 CAAAGACTCACTGAGCATGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGAAA
*
2042251 TTTATTTAAAAAGATTATTTTTTAAACAGAG-TGATTGAAAAGATGATTGAACACGAAAGAAATA
196 TTTATTTAAAAAGATTATTTTTTAAACAGAGATGATTAAAAAGATGATTGAACACGAAAGAAATA
2042315 TGAGTTTTGCCAACCTTAAAATGATAT
261 TGAGTTTTGCCAACCTTAAAATGATAT
2042342 GAAGGATTAAATTGTGTT-AAA-GACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
* *
2042405 CATTGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCAATATCGAATTTAACGAACGTAG
66 CATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
*
2042470 CAAAGACTCGA-TGAGCAGGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGA
131 CAAAGACTC-ACTGAGCATGGATCTCTT-AAAAAATGCAAATATTGATAGCTACTAACTAAATGA
*
2042534 AATTTATTTTAAAAAAATTATTTTTTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGA
194 AATTTA-TTTAAAAAGATTATTTTTTAAACAGAG-ATGATTAAAAAGATGATTGAACACGAAAGA
** ** * * *
2042599 AATATGAGTTTTGGAAATGTT-AGATTAAATT
257 AATATGAGTTTTGCCAACCTTAAAATGATA-T
* * * * * * * **
2042630 G--TG-TTAAA-AGTGTATCTATATGAAGCAGAAGG-ATTAAATTGTGTTAA-AATGACGTGGCA
1 GAAGGATTAAATTGTGT-T-AAAATG-A-C-G-TGGCA-T--GTT-T-TTAATCA-GA-GT-AAA
**** ** * * * * * ** * *
2042689 TGTTTTTAATCAGAGTAAATC-CAATTTC-CCGTA-CATTGCAGT-TA-CACCTTAGAATT--AT
52 TCCAATT--TC-CCGTACATCGCAGTTACACCTTAGAATTATA-TCTAGAACCCT--AATTCGAT
** * * *
2042747 ATTTAA---AACCCTAATTCGATATCAAATTTAACGAACGTAGCAAAGACTCGTTGAGCAGGGAT
111 ATCGAATTTAA--CGAA--CG-TAGC--A---AA-G-AC-T--C----A--C--TGAGCATGGAT
*
2042809 CTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAAATTTATTTAAAACGATTA-TTT
153 CTCTT-AAAAAATGCAAATATTGATAGCTACTAACTAAATGAAATTTATTTAAAAAGATTATTTT
2042873 TTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGCCAACCTTAAA
217 TTAAACAGAG-ATGATTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGCCAACCTTAAA
* *
2042938 ATAAAAT
281 ATGATAT
* *
2042945 GTTA-GATTAAATTGTGTTAAAATGACGTGACATGTTTTTAATCAGAGTAAATCCAATTTCCCGT
1 G-AAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGT
*
2043009 ACATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTTGATATCGAATTTAACGAACGTA
65 ACATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTA
*
2043074 GCAAAGACTCGCTGAGC-TGGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGA
130 GCAAAGACTCACTGAGCAT-GGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGA
*
2043138 AATTTATTTAAAAAGATTATTTTTTAGACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAA
194 AATTTATTTAAAAAGATTATTTTTTAAACAGAG-ATGATTAAAAAGATGATTGAACACGAAAGAA
* *
2043203 ATATGAGTTTTGGCAACCTTAAAATGAAAT
258 ATATGAGTTTTGCCAACCTTAAAATGATAT
* * * ** * * *
2043233 GTTA-GATTAAATTGTGTTAAAAGTGTATCTATATGAAGCAGAAGGATTAAAT-TGTGTTAAAAT
1 G-AAGGATTAAATTGTGTTAAAA-TG-A-C---GTG--GC--ATGTTTTTAATCAGAG-T-AAAT
* ** * * * * * * * * *
2043296 GACGTTGCATGTTTTTAATCAGAGTAAATC-CAATTTC-CCGTA-CATCACAGT-TA-CACCTTA
53 --C----CA----ATT--TC-CCGTACATCGCAGTTACACCTTAGAATTATA-TCTAGAACCCT-
** * * ** ** * * ** * * * * *
2043356 GAATTATATTTAGAACCCTAA--TTCGATATCGAA-TTTAAC-GAACGTAGCAAAGA-CTCGCTG
103 -AATTCGATATCGAA-TTTAACGAACG-TAGCAAAGACTCACTGAGCAT-G----GATCTC-TTA
** ** * * * * *
2043416 AGCAATG-ATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACT-AAATTAAATTTATTTAAA
159 AAAAATGCAAATATT---GATA-GC---TACT-A-A-CTA--AA-TGAAATT---TAT--TTAAA
* *
2043479 AAGATTATTTGTTAAACAGAGTATGATTAAAAAGATGATAGAACACGAAAGAAATATGAGTTTTG
206 AAGATTATTTTTTAAACAGAG-ATGATTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTG
*
2043544 CTAACCTTAAAATGATAT
270 CCAACCTTAAAATGATAT
* * * *
2043562 GAAGGATTAAATTGTGTTAAAATGACATGGCTTGTTTTTAATCAGAGTAAATCCAATTTCTCATA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
* *
2043627 CATCACAGTTACACCTTAGAATTATATCTAGAACCCTAATTCAATATCGAATTTAACGAACGTAG
66 CATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
* * *
2043692 CAAAGACTCGCTGAGCAGGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTATATGAAA
131 CAAAGACTCACTGAGCATGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGAAA
2043757 TTTATTTAAAAAGATTATTTTTTAAACAGAG-TGATTAAAAAGATGATTGAACACGAAAGAAATA
196 TTTATTTAAAAAGATTATTTTTTAAACAGAGATGATTAAAAAGATGATTGAACACGAAAGAAATA
*
2043821 TGAGTTTTGCCAACCTTAAAATGATAC
261 TGAGTTTTGCCAACCTTAAAATGATAT
2043848 GAAGGATTAAATTGTGTTAAAA
1 GAAGGATTAAATTGTGTTAAAA
2043870 GTGTATCTAT
Statistics
Matches: 1469, Mismatches: 205, Indels: 282
0.75 0.10 0.14
Matches are distributed among these distances:
284 130 0.09
285 50 0.03
286 182 0.12
287 63 0.04
288 395 0.27
289 3 0.00
290 5 0.00
291 3 0.00
292 4 0.00
293 6 0.00
294 6 0.00
295 5 0.00
296 12 0.01
297 15 0.01
298 24 0.02
299 18 0.01
300 8 0.01
301 11 0.01
302 2 0.00
304 17 0.01
305 22 0.01
306 24 0.02
307 33 0.02
308 32 0.02
309 31 0.02
310 22 0.01
311 14 0.01
312 17 0.01
313 10 0.01
314 2 0.00
315 66 0.04
316 21 0.01
317 64 0.04
318 10 0.01
319 14 0.01
320 3 0.00
321 3 0.00
322 3 0.00
323 3 0.00
324 7 0.00
325 1 0.00
326 1 0.00
327 3 0.00
328 3 0.00
329 101 0.07
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (287 bp):
GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
CATCGCAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
CAAAGACTCACTGAGCATGGATCTCTTAAAAAATGCAAATATTGATAGCTACTAACTAAATGAAA
TTTATTTAAAAAGATTATTTTTTAAACAGAGATGATTAAAAAGATGATTGAACACGAAAGAAATA
TGAGTTTTGCCAACCTTAAAATGATAT
Found at i:2043366 original size:616 final size:616
Alignment explanation
Indices: 2042056--2043891 Score: 3086
Period size: 617 Copynumber: 3.0 Consensus size: 616
2042046 AAAATGATAT
*
2042056 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCTCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
* *
2042121 CATCACAGTTACACCTTAGAATTATATCTAGAACCCTAATTCGATATCGAATTTAACGAACATAG
66 CATCACAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
* * * *
2042186 CAAAGACTCACTGAGCATGGATCTCTT-AAAAAATGCAAATAATGATAGCTACTAACTATATGAA
131 CAAAGACTCGCTGAGCAAGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
*
2042250 ATTTATTTAAAAAGATTATTTTTTAAACAGAG--TGATTGAAAAGATGATTGAACACGAAAGAAA
196 ATTTATTTAAAAAGATTA-TTTTTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAA
2042313 TATGAGTTTTGCCAACCTTAAAATGATATGAAGGATTAAATTGTGTT-AAA-GACGTGGCATGTT
260 TATGAGTTTTGCCAACCTTAAAATGATATGAAGGATTAAATTGTGTTAAAATGACGTGGCATGTT
*
2042376 TTTAATCAGAGTAAATCCAATTTCCCGTACATTGCAGTTACACCTTAGAATTATATCTAGAACCC
325 TTTAATCAGAGTAAATCCAATTTCCCGTACATCGCAGTTACACCTTAGAATTATATCTAGAACCC
*
2042441 TAATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGATGAGCAGGGATCTCTTAAAAAAATG
390 TAATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCAGGGATCTCTT-AAAAAATG
*
2042506 CAAATATTGATAGCTACTAACTAAATGAAATTTATTTTAAAAAAATTATTTTTTAAACAGAGTAT
454 CAAATATTGATAGCTACTAACTAAATGAAATTTA-TTTAAAAAGATTATTTTTTAAACAGAGTAT
2042571 GATTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTT-G------------GAAATGTTAGA
518 GATTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGGCAACCTTAAAATGAAATGTTAGA
2042623 TTAAATTGTGTTAAAAGTGTATCTATATGAAGCA
583 TTAAATTGTGTTAAAAGTGTATCTATATGAAGCA
2042657 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
** * *
2042722 CATTGCAGTTACACCTTAGAATTATATTTAAAACCCTAATTCGATATCAAATTTAACGAACGTAG
66 CATCACAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
* *
2042787 CAAAGACTCGTTGAGCAGGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
131 CAAAGACTCGCTGAGCAAGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
*
2042852 ATTTATTTAAAACGATTATTTTTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAAT
196 ATTTATTTAAAAAGATTATTTTTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAAT
* * * *
2042917 ATGAGTTTTGCCAACCTTAAAATAAAATGTTA-GATTAAATTGTGTTAAAATGACGTGACATGTT
261 ATGAGTTTTGCCAACCTTAAAATGATATG-AAGGATTAAATTGTGTTAAAATGACGTGGCATGTT
2042981 TTTAATCAGAGTAAATCCAATTTCCCGTACATCGCAGTTACACCTTAGAATTATATCTAGAACCC
325 TTTAATCAGAGTAAATCCAATTTCCCGTACATCGCAGTTACACCTTAGAATTATATCTAGAACCC
** *
2043046 TAATTTGATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCTGGGATCTCTTAAAAAATGC
390 TAATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCAGGGATCTCTTAAAAAATGC
*
2043111 AAATATTGATAGCTACTAACTAAATGAAATTTATTTAAAAAGATTATTTTTTAGACAGAGTATGA
455 AAATATTGATAGCTACTAACTAAATGAAATTTATTTAAAAAGATTATTTTTTAAACAGAGTATGA
2043176 TTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGGCAACCTTAAAATGAAATGTTAGATT
520 TTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGGCAACCTTAAAATGAAATGTTAGATT
2043241 AAATTGTGTTAAAAGTGTATCTATATGAAGCA
585 AAATTGTGTTAAAAGTGTATCTATATGAAGCA
*
2043273 GAAGGATTAAATTGTGTTAAAATGACGTTGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
1 GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
2043338 CATCACAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
66 CATCACAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
* *
2043403 CAAAGACTCGCTGAGCAATGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATTAA
131 CAAAGACTCGCTGAGCAAGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
*
2043468 ATTTATTTAAAAAGATTATTTGTTAAACAGAGTATGATTAAAAAGATGATAGAACACGAAAGAAA
196 ATTTATTTAAAAAGATTATTT-TTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAA
* * *
2043533 TATGAGTTTTGCTAACCTTAAAATGATATGAAGGATTAAATTGTGTTAAAATGACATGGCTTGTT
260 TATGAGTTTTGCCAACCTTAAAATGATATGAAGGATTAAATTGTGTTAAAATGACGTGGCATGTT
* * *
2043598 TTTAATCAGAGTAAATCCAATTTCTCATACATCACAGTTACACCTTAGAATTATATCTAGAACCC
325 TTTAATCAGAGTAAATCCAATTTCCCGTACATCGCAGTTACACCTTAGAATTATATCTAGAACCC
2043663 TAATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCAGGGATCTCTTAAAAAATGC
390 TAATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCAGGGATCTCTTAAAAAATGC
*
2043728 AAATATTGATAGCTACTAACTATATGAAATTTATTTAAAAAGATTATTTTTTAAACAGAG--TGA
455 AAATATTGATAGCTACTAACTAAATGAAATTTATTTAAAAAGATTATTTTTTAAACAGAGTATGA
* * * *
2043791 TTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGCCAACCTTAAAATGATACG-AAGGAT
520 TTAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGGCAACCTTAAAATGAAATGTTA-GAT
*
2043855 TAAATTGTGTTAAAAGTGTATCTATACGAAGCA
584 TAAATTGTGTTAAAAGTGTATCTATATGAAGCA
2043888 GAAG
1 GAAG
2043892 AGAAATGAAA
Statistics
Matches: 1157, Mismatches: 56, Indels: 30
0.93 0.05 0.02
Matches are distributed among these distances:
601 160 0.14
602 52 0.04
603 140 0.12
604 47 0.04
605 128 0.11
614 1 0.00
615 97 0.08
616 252 0.22
617 280 0.24
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (616 bp):
GAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTTTTAATCAGAGTAAATCCAATTTCCCGTA
CATCACAGTTACACCTTAGAATTATATTTAGAACCCTAATTCGATATCGAATTTAACGAACGTAG
CAAAGACTCGCTGAGCAAGGATCTCTTAAAAAAATGCAAATATTGATAGCTACTAACTAAATGAA
ATTTATTTAAAAAGATTATTTTTAAACAGAGTATGATTAAAAAGATGATTGAACACGAAAGAAAT
ATGAGTTTTGCCAACCTTAAAATGATATGAAGGATTAAATTGTGTTAAAATGACGTGGCATGTTT
TTAATCAGAGTAAATCCAATTTCCCGTACATCGCAGTTACACCTTAGAATTATATCTAGAACCCT
AATTCAATATCGAATTTAACGAACGTAGCAAAGACTCGCTGAGCAGGGATCTCTTAAAAAATGCA
AATATTGATAGCTACTAACTAAATGAAATTTATTTAAAAAGATTATTTTTTAAACAGAGTATGAT
TAAAAAGATGATTGAACACGAAAGAAATATGAGTTTTGGCAACCTTAAAATGAAATGTTAGATTA
AATTGTGTTAAAAGTGTATCTATATGAAGCA
Found at i:2050218 original size:18 final size:18
Alignment explanation
Indices: 2050180--2050217 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2050170 GTCCTGAAAA
2050180 TTTAAATTTACTATATAT
1 TTTAAATTTACTATATAT
*
2050198 TTTAAATTT-TTATATAT
1 TTTAAATTTACTATATAT
2050215 TTT
1 TTT
2050218 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTTACTATATAT
Found at i:2056661 original size:14 final size:14
Alignment explanation
Indices: 2056642--2056671 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2056632 GGATCAAATG
2056642 AATTATTATTTATT
1 AATTATTATTTATT
*
2056656 AATTATTATTTTTT
1 AATTATTATTTATT
2056670 AA
1 AA
2056672 CAACGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTATTATTTATT
Found at i:2056967 original size:324 final size:330
Alignment explanation
Indices: 2056369--2057026 Score: 967
Period size: 324 Copynumber: 2.0 Consensus size: 330
2056359 AACTCGATAA
* * * * *
2056369 ATTTTAATATTTGCATGAAATTACACAATATGTATAATCTGGTATAAAAAACTTTGAGGGTAAGT
1 ATTTTAATATTTGCATAAAATTACACAATACGTATAATATAGTATAAAAAACTTTGAGGGTAAAT
2056434 ATTTTAAAATATGAATAATTTTATAAAAATTTTATAACTAATATTTCTTTTATAAAATGATGACG
66 ATTTTAAAATATGAATAATTTTATAAAAATTTTATAACTAATATTTCTTTTATAAAA-GAT-A-G
* *
2056499 ATGATAATGATGATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAATATT
128 ATGATAATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTGAAAATATT
*
2056564 AATTGACTTTAAAATTAATTGTTTAAAAATATAAAATAAATCAAAATAAATTTTTAATTACAATT
193 AATTGACTTTAAAATTAATTGTTTAAAAATATAAAATAAATCAAAATAAACTTTTAATTACAATT
* *
2056629 GAAGGATCAAATGAATTATTATTTATTAATTATTATTTTTTAACAACGGTTGATAATATTTATTC
258 GAAGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAAC-ATTGATAATATTTATTC
2056694 ATTTTTAAT
322 ATTTTTAAT
* * * * * *
2056703 ATTTTGATTTTTGCATAAAATTATATAATACGTATAATATAGTATAGGAAAATTTTGAGGGTAAA
1 ATTTTAATATTTGCATAAAATTACACAATACGTATAATATAGTATA-AAAAACTTTGAGGGTAAA
* * *
2056768 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTT-TTTTA-CAAA-AT-GAT
65 TATTTTAAAATATGAATAATTTTATAAAAATTTTATAACTAATATTTCTTTTATAAAAGATAGAT
*
2056829 GATAATGATAATAAAT-TTTTATAA-TTAAAAAATTATAAATTTCATAT-TTTTGAAAAT-TTTA
130 GATAATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTGAAAATATTAA
*
2056890 TTGACTTTTAAAATTAATTGTTTAAAAATATAAAA-AAATTAAAATAAACTTTTAATTACAATTG
195 TTGAC-TTTAAAATTAATTGTTTAAAAATATAAAATAAATCAAAATAAACTTTTAATTACAATTG
* * *
2056954 -AGAGATTAAATGAATTATTATTCATTAATTATTATTTTTTAACAACATTGATAATGTTTATTTA
259 AAG-GATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACATTGATAATATTTATTCA
2057018 TTTTTAAT
323 TTTTTAAT
2057026 A
1 A
2057027 AAATTAATTT
Statistics
Matches: 297, Mismatches: 24, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
323 26 0.09
324 76 0.26
325 38 0.13
326 23 0.08
327 8 0.03
328 18 0.06
331 2 0.01
333 3 0.01
334 43 0.14
335 60 0.20
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (330 bp):
ATTTTAATATTTGCATAAAATTACACAATACGTATAATATAGTATAAAAAACTTTGAGGGTAAAT
ATTTTAAAATATGAATAATTTTATAAAAATTTTATAACTAATATTTCTTTTATAAAAGATAGATG
ATAATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTGAAAATATTAAT
TGACTTTAAAATTAATTGTTTAAAAATATAAAATAAATCAAAATAAACTTTTAATTACAATTGAA
GGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACATTGATAATATTTATTCATTT
TTAAT
Found at i:2057999 original size:11 final size:10
Alignment explanation
Indices: 2057979--2058034 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 10
2057969 ATATTCTAAA
2057979 TATTTTTAAT
1 TATTTTTAAT
2057989 TATTTTATAAT
1 TATTTT-TAAT
*
2058000 TAATGTTTAAT
1 T-ATTTTTAAT
2058011 TATTTTATAAT
1 TATTTT-TAAT
*
2058022 TAATGTTTAAT
1 T-ATTTTTAAT
2058033 TA
1 TA
2058035 CTTTATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 11 0.28
11 20 0.51
12 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (10 bp):
TATTTTTAAT
Found at i:2058008 original size:22 final size:22
Alignment explanation
Indices: 2057983--2058040 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
2057973 TCTAAATATT
2057983 TTTAATTATTTTATAATTAATG
1 TTTAATTATTTTATAATTAATG
2058005 TTTAATTATTTTATAATTAATG
1 TTTAATTATTTTATAATTAATG
*
2058027 TTTAATTACTTTAT
1 TTTAATTATTTTAT
2058041 TTTAACCGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
TTTAATTATTTTATAATTAATG
Found at i:2059546 original size:42 final size:42
Alignment explanation
Indices: 2059500--2059580 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
2059490 TTAATTTCTT
*
2059500 AAATTGAA-TATTTCTGATATAATTAATAAGTTTAATTTTAAG
1 AAATT-AAGTATTTCTGATATAAATAATAAGTTTAATTTTAAG
*
2059542 AAATTAAGTATTTCTGATATAAATAATAATTTTAATTTT
1 AAATTAAGTATTTCTGATATAAATAATAAGTTTAATTTT
2059581 TTATTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (42 bp):
AAATTAAGTATTTCTGATATAAATAATAAGTTTAATTTTAAG
Found at i:2060602 original size:20 final size:20
Alignment explanation
Indices: 2060563--2060611 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
2060553 CGATTTTCCT
2060563 CATTTTTATGAAATTAATTTTA
1 CATTTTTATGAAA-TAA-TTTA
2060585 -ATTTTTATGAAA-ACATTTA
1 CATTTTTATGAAATA-ATTTA
2060604 CATTTTTA
1 CATTTTTA
2060612 AATTCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 12 0.48
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (20 bp):
CATTTTTATGAAATAATTTA
Found at i:2071204 original size:3 final size:3
Alignment explanation
Indices: 2071196--2071243 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2071186 GTGTTGCAGG
2071196 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2071244 TTGCAGGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2072143 original size:128 final size:127
Alignment explanation
Indices: 2071916--2072170 Score: 492
Period size: 128 Copynumber: 2.0 Consensus size: 127
2071906 TACTAAAATG
2071916 AAATAAATACTAAACGTTAGATATGATTTAAAAAAATGAAAGTTTAAGTATTAAACTAGACTAAA
1 AAATAAATACTAAACGTTAGATATGATTTAAAAAAATGAAAGTTTAAGTATTAAACTAGACTAAA
*
2071981 ATTGATAGTTTACGTACTAAACACGAAATTTACCCTTTTTATTGTGCTTATTCTATATATAT
66 ATTGATAGTTTACGTACTAAACACAAAATTTACCCTTTTTATTGTGCTTATTCTATATATAT
2072043 AAATAAATACTAAACGTTAGATATGATTTAAAAAAAATGAAAGTTTAAGTATTAAACTAGACTAA
1 AAATAAATACTAAACGTTAGATATGATTT-AAAAAAATGAAAGTTTAAGTATTAAACTAGACTAA
2072108 AATTGATAGTTTACGTACTAAACACAAAATTTACCCTTTTTATTGTGCTTATTCTATATATAT
65 AATTGATAGTTTACGTACTAAACACAAAATTTACCCTTTTTATTGTGCTTATTCTATATATAT
2072171 TTGGGAGTGG
Statistics
Matches: 126, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
127 29 0.23
128 97 0.77
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (127 bp):
AAATAAATACTAAACGTTAGATATGATTTAAAAAAATGAAAGTTTAAGTATTAAACTAGACTAAA
ATTGATAGTTTACGTACTAAACACAAAATTTACCCTTTTTATTGTGCTTATTCTATATATAT
Found at i:2074484 original size:34 final size:35
Alignment explanation
Indices: 2074444--2074513 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
2074434 CCAAAAAAGG
*
2074444 TATTCTATGACTATACTT-TATGGCAAAAAATTCT
1 TATTCTATGACTATACTTATATGGCAAAAAAATCT
2074478 TATTCTATGACTATACTTATATGGCAAAAAAATCT
1 TATTCTATGACTATACTTATATGGCAAAAAAATCT
2074513 T
1 T
2074514 TATTTTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.53
35 16 0.47
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (35 bp):
TATTCTATGACTATACTTATATGGCAAAAAAATCT
Found at i:2075492 original size:16 final size:16
Alignment explanation
Indices: 2075471--2075502 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2075461 AAAAATAAAT
2075471 GAACATAAACGAACAC
1 GAACATAAACGAACAC
*
2075487 GAACATAAGCGAACAC
1 GAACATAAACGAACAC
2075503 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.25, G:0.16, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:2075592 original size:16 final size:16
Alignment explanation
Indices: 2075571--2075635 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
2075561 TAATAAATAA
**
2075571 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
2075587 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2075603 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2075619 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2075635 A
1 A
2075636 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2075908 original size:12 final size:11
Alignment explanation
Indices: 2075870--2075921 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
2075860 TCGAGACTTG
*
2075870 AGCTCGATTGA
1 AGCTCGATTCA
2075881 AGCTCGATTCA
1 AGCTCGATTCA
*
2075892 AGCTCAATTCTA
1 AGCTCGATTC-A
2075904 AGCTCGATTCA
1 AGCTCGATTCA
2075915 AGCTCGA
1 AGCTCGA
2075922 CATTGCCCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:2076758 original size:14 final size:14
Alignment explanation
Indices: 2076741--2076796 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2076731 AATGAACATA
2076741 AACGAACATAACCG
1 AACGAACATAACCG
2076755 AACGAACAT-A---
1 AACGAACATAACCG
*
2076765 AACGAACATAACAG
1 AACGAACATAACCG
2076779 AACGAACATAACCG
1 AACGAACATAACCG
2076793 AACG
1 AACG
2076797 TTCACAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2076761 original size:24 final size:24
Alignment explanation
Indices: 2076721--2076795 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
2076711 GATTGGGATA
*
2076721 AACATAA-ATGAATGAACATAAACG
1 AACATAACA-GAACGAACATAAACG
*
2076745 AACATAACCGAACGAACATAAACG
1 AACATAACAGAACGAACATAAACG
*
2076769 AACATAACAGAACGAACATAACCG
1 AACATAACAGAACGAACATAAACG
2076793 AAC
1 AAC
2076796 GTTCACAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (24 bp):
AACATAACAGAACGAACATAAACG
Found at i:2079197 original size:7 final size:7
Alignment explanation
Indices: 2079187--2079215 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2079177 TGTTTGGGTA
2079187 AACAATT
1 AACAATT
2079194 AACAATT
1 AACAATT
2079201 AACAATT
1 AACAATT
2079208 AACAATT
1 AACAATT
2079215 A
1 A
2079216 TTTAATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AACAATT
Found at i:2079500 original size:29 final size:28
Alignment explanation
Indices: 2079441--2079518 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 28
2079431 AATTAAATTA
2079441 ATATCTTAACATTAAAAATATATATTTTATT
1 ATATCTTAAC-TT-AAAA-ATATATTTTATT
2079472 ATTATCTTAACTTAAAAATATATTTTATT
1 A-TATCTTAACTTAAAAATATATTTTATT
*
2079501 CATATTTTAACTTAAAAA
1 -ATATCTTAACTTAAAAA
2079519 ATTAAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 27 0.61
30 5 0.11
31 3 0.07
32 9 0.20
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATCTTAACTTAAAAATATATTTTATT
Found at i:2079600 original size:25 final size:25
Alignment explanation
Indices: 2079572--2079634 Score: 63
Period size: 30 Copynumber: 2.3 Consensus size: 25
2079562 AAATAAGGAT
2079572 AAATTATATTTAATAATTTAAGGTA
1 AAATTATATTTAATAATTTAAGGTA
*
2079597 AAATTAGAATATATTTAATAATTTAAGTTA
1 AAA-T----TATATTTAATAATTTAAGGTA
*
2079627 AAAATATA
1 AAATTATA
2079635 ACATATGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
25 7 0.23
26 1 0.03
30 23 0.74
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATTATATTTAATAATTTAAGGTA
Found at i:2079710 original size:29 final size:29
Alignment explanation
Indices: 2079654--2079827 Score: 156
Period size: 29 Copynumber: 6.0 Consensus size: 29
2079644 AGAAGATAAA
**
2079654 ATAAAAATATGATATATTTTTAAAAGTTAAG
1 ATAAAAATAAAATATATTTTT--AAGTTAAG
*
2079685 ATAAAAATAAAATATATTTTTAAGTTATG
1 ATAAAAATAAAATATATTTTTAAGTTAAG
* * * *
2079714 CTAATATTAAAATATA-TTTTAAGTTAAA
1 ATAAAAATAAAATATATTTTTAAGTTAAG
*
2079742 ATAAAAATAAAATATATTTTTAGGTTAAG
1 ATAAAAATAAAATATATTTTTAAGTTAAG
* * * * * *
2079771 ACAATAATAAAATAGATTTCATAATTTAAA
1 ATAAAAATAAAATATATTT-TTAAGTTAAG
*
2079801 AT-AAAA-AATATATATTTTTAATGTTAA
1 ATAAAAATAAAATATATTTTTAA-GTTAA
2079828 TATATGAATT
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
27 3 0.03
28 36 0.32
29 49 0.43
30 7 0.06
31 19 0.17
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (29 bp):
ATAAAAATAAAATATATTTTTAAGTTAAG
Found at i:2079746 original size:57 final size:58
Alignment explanation
Indices: 2079672--2079827 Score: 185
Period size: 57 Copynumber: 2.7 Consensus size: 58
2079662 ATGATATATT
* * * * *
2079672 TTTAAAAGTTAAGATAAAAATAAAATATATTTTTAAGTTATG-CTAATATTAAAATATA
1 TTTATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGAC-AATAATAAAATAGA
*
2079730 TTT-TAAGTTAAAATAAAAATAAAATATATTTTTAGGTTAAGACAATAATAAAATAGA
1 TTTATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGACAATAATAAAATAGA
* *
2079787 TTTCATAATTTAAAAT-AAAA-AATATATATTTTTAATGTTAA
1 TTT-ATAAGTTAAAATAAAAATAAAATATATTTTTAA-GTTAA
2079828 TATATGAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
57 62 0.73
58 13 0.15
59 10 0.12
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (58 bp):
TTTATAAGTTAAAATAAAAATAAAATATATTTTTAAGTTAAGACAATAATAAAATAGA
Found at i:2080620 original size:14 final size:14
Alignment explanation
Indices: 2080596--2080632 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2080586 GTTTATATTT
*
2080596 ATTTATTTTCGTTC
1 ATTTATGTTCGTTC
*
2080610 GTTTATGTTCGTTC
1 ATTTATGTTCGTTC
2080624 ATTTATGTT
1 ATTTATGTT
2080633 TAACATAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.62
Consensus pattern (14 bp):
ATTTATGTTCGTTC
Found at i:2080855 original size:21 final size:21
Alignment explanation
Indices: 2080829--2080881 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2080819 GTTTCCAGAT
2080829 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
2080850 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
2080871 TCGCAATGCGA
1 TCGCAACGCGA
2080882 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:2080919 original size:21 final size:19
Alignment explanation
Indices: 2080885--2081093 Score: 202
Period size: 19 Copynumber: 10.3 Consensus size: 19
2080875 AATGCGATTT
*
2080885 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
2080904 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
2080925 TCGAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
2080944 TCGAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
2080963 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
2080986 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
2081005 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
2081028 TCCAAGTTCATTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
2081047 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
2081070 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
2081089 TCCAA
1 TCCAA
2081094 AATCGCAACG
Statistics
Matches: 161, Mismatches: 15, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
19 70 0.43
21 64 0.40
23 27 0.17
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:2081006 original size:42 final size:42
Alignment explanation
Indices: 2080904--2081090 Score: 301
Period size: 42 Copynumber: 4.5 Consensus size: 42
2080894 GTTGCGATAG
*
2080904 TCCAAGTTCGCGTTGCGATAGTCGAAGTT--CGTTGCGA--TAG
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
2080944 TCGAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
2080986 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
2081028 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
2081070 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
2081091 CAAAATCGCA
Statistics
Matches: 138, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 19 0.14
40 15 0.11
42 104 0.75
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:2082002 original size:42 final size:41
Alignment explanation
Indices: 2081933--2082058 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 41
2081923 CCAGTCGTTG
* *
2081933 CGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAA
1 CGAA-TTGGTATAAATCGCAACGCGAACTTCGACTATCGCAA
2081975 CGAACTTGGTATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAA-TTGGTATAAATCGCAACGCGAACTTCGACTATCGCAA
*
2082017 CGAATTTGTAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTGGT-ATAAATCGCAACGCGAACTTCGACTATCGCAA
2082059 ATCAGTTTCT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 4 0.05
42 75 0.95
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
CGAATTGGTATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:2082099 original size:21 final size:20
Alignment explanation
Indices: 2081947--2082099 Score: 84
Period size: 21 Copynumber: 7.3 Consensus size: 20
2081937 TTTGGAATAA
*
2081947 ATCGCAACACGAACTTCGACT
1 ATCGCAACGC-AACTTCGACT
*
2081968 ATCGCAACG-AACTTGGTA-T
1 ATCGCAACGCAACTTCG-ACT
2081987 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGC-AACTTCGACT
* *
2082010 ATCGCAACG-AA-TTTGTAAT
1 ATCGCAACGCAACTTCG-ACT
2082029 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGC-AACTTCGACT
** **
2082052 ATCGCAAATCAGTTTCTAGA-T
1 ATCGCAACGCAACTTC--GACT
2082073 -TCGCAACGCAAACTTCGACT
1 ATCGCAACGC-AACTTCGACT
2082093 ATCGCAA
1 ATCGCAA
2082100 TGCGAATATG
Statistics
Matches: 100, Mismatches: 15, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
18 3 0.03
19 13 0.13
20 13 0.13
21 54 0.54
22 3 0.03
23 11 0.11
24 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCAACTTCGACT
Found at i:2082118 original size:41 final size:40
Alignment explanation
Indices: 2081933--2082124 Score: 192
Period size: 42 Copynumber: 4.6 Consensus size: 40
2081923 CCAGTCGTTG
*
2081933 CGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAA
1 CGAATTT-G-ATAAATCGCAACGCGAACTTCGACTATCGCAA
*
2081975 CGAACTTGGTATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAA-TTTG-ATAAATCGCAACGCGAACTTCGACTATCGCAA
2082017 CGAATTTGTAATAAATCGCAACGCGAACTTCGACTATCGCAAA
1 CGAATTTG--ATAAATCGCAACGCGAACTTCGACTATCGC-AA
* * * *
2082060 TC-AGTTT-CTAGATTCGCAACGCAAACTTCGACTATCGCAA
1 -CGAATTTGATA-AATCGCAACGCGAACTTCGACTATCGCAA
* *
2082100 TGCGAATATG-TAAATCGCAATGCGA
1 --CGAATTTGATAAATCGCAACGCGA
2082125 TAGTCGAAGT
Statistics
Matches: 127, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.03
41 39 0.31
42 75 0.59
43 8 0.06
44 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (40 bp):
CGAATTTGATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:2083303 original size:22 final size:21
Alignment explanation
Indices: 2083248--2083306 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
2083238 ATTAAATTAA
* *
2083248 AAATAATAATCTAATTAAAAAT
1 AAATTATAAT-TATTTAAAAAT
*
2083270 AAATTATTATTATTTAAATAAT
1 AAATTATAATTATTTAAA-AAT
2083292 AAATT-TCAATTATTT
1 AAATTAT-AATTATTT
2083307 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTATAATTATTTAAAAAT
Found at i:2090822 original size:21 final size:21
Alignment explanation
Indices: 2090792--2090837 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2090782 GTAGCAGTAT
*
2090792 TGTAGTAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
2090813 TGTAGCAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
2090834 TGTA
1 TGTA
2090838 ACACCGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
TGTAGCAGTGCATCGGTACAC
Found at i:2094646 original size:20 final size:20
Alignment explanation
Indices: 2094588--2094646 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
2094578 ATAAAATATC
2094588 ATTTA-AATTAGAA-TTAAAT
1 ATTTATAATTA-AATTTAAAT
* *
2094607 AATTTATAA-T-AGTATAAAT
1 -ATTTATAATTAAATTTAAAT
2094626 ATTTATAATTAAATTTAAAT
1 ATTTATAATTAAATTTAAAT
2094646 A
1 A
2094647 GAAACTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.29
19 6 0.19
20 14 0.45
21 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTATAATTAAATTTAAAT
Found at i:2103605 original size:21 final size:21
Alignment explanation
Indices: 2103581--2103620 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2103571 TTTATTTTAT
2103581 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2103602 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2103621 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2103668 original size:33 final size:33
Alignment explanation
Indices: 2103615--2103713 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2103605 TTTGTTTCAA
2103615 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2103647 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2103680 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2103713 T
1 T
2103714 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2103742 original size:13 final size:13
Alignment explanation
Indices: 2103699--2103753 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2103689 TTGGAAGTAT
2103699 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2103712 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2103726 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2103739 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2103752 TT
1 TT
2103754 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2104201 original size:14 final size:14
Alignment explanation
Indices: 2104149--2104201 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
2104139 ATTTGGAATA
*
2104149 TTAAAATCGGTTTT
1 TTAAAACCGGTTTT
*
2104163 TTATAACCGGTTTT
1 TTAAAACCGGTTTT
2104177 TTAAAAAAACCGGTTTT
1 TT---AAAACCGGTTTT
2104194 TTAAAACC
1 TTAAAACC
2104202 AAAACCGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 20 0.61
17 13 0.39
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (14 bp):
TTAAAACCGGTTTT
Found at i:2104211 original size:20 final size:17
Alignment explanation
Indices: 2104167--2104199 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2104157 GGTTTTTTAT
2104167 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
2104184 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
2104200 CCAAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
AACCGGTTTTTTAAAAA
Found at i:2104317 original size:15 final size:17
Alignment explanation
Indices: 2104291--2104322 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2104281 TTCTATGAGA
2104291 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
2104307 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
2104323 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:2115964 original size:198 final size:197
Alignment explanation
Indices: 2115626--2116001 Score: 526
Period size: 198 Copynumber: 1.9 Consensus size: 197
2115616 TTTAACTTAT
* *** * * * *
2115626 GGTTAACTACATTATTGATCATTTATGTTTGTGTTTTGTCCACTTTTCCTTACTGATTTCAAAAA
1 GGTTAACTACATGATTGATCACCGATGTTCGTGATTTGTCCACTTTTCCTCACTGA-TGCAAAAA
*
2115691 AACATAATATATGGTTACTTTCGTTTTTATTTAATTAAGATTTAGTCACCACAGATCAACTGCCG
65 AACATAATATATGGTTACTTTCGTTTTTATTTAATTAAGATGTAGTCACCACAGATCAACTGCCG
* *
2115756 TTAGACCATTAACGATTTGTTGAA-CTGACATGGTAATTAAATAAAATACTTCATTTCCACGTGG
130 TTAGACCATTAACGATTTGCT-AAGCTGACATAGTAATTAAATAAAATACTTCATTTCCACGTGG
2115820 ATTG
194 ATTG
2115824 GGTTAACTACATGATTGATCACCGATGTTCGT-ATTTGATCCACTTTTCCTCACTGA-GCAGATA
1 GGTTAACTACATGATTGATCACCGATGTTCGTGATTTG-TCCACTTTTCCTCACTGATGCA-A-A
* * *
2115887 AAAACATAATATATGGTTATTTTCGTTTTTATTTAATTAAGATGTGGTCACCAC-GAGTTAACTG
63 AAAACATAATATATGGTTACTTTCGTTTTTATTTAATTAAGATGTAGTCACCACAGA-TCAACTG
* *
2115951 TCGTTAGACCATTAACGATTTGCTAAGTTGACATAGTAATTAAATAAAATA
127 CCGTTAGACCATTAACGATTTGCTAAGCTGACATAGTAATTAAATAAAATA
2116002 GAAAATACAT
Statistics
Matches: 157, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
196 2 0.01
197 9 0.06
198 146 0.93
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (197 bp):
GGTTAACTACATGATTGATCACCGATGTTCGTGATTTGTCCACTTTTCCTCACTGATGCAAAAAA
ACATAATATATGGTTACTTTCGTTTTTATTTAATTAAGATGTAGTCACCACAGATCAACTGCCGT
TAGACCATTAACGATTTGCTAAGCTGACATAGTAATTAAATAAAATACTTCATTTCCACGTGGAT
TG
Found at i:2121803 original size:26 final size:27
Alignment explanation
Indices: 2121748--2121804 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
2121738 AGAGGTGCAC
2121748 AAAAAATCCGAATATCCGATTTTGGTA
1 AAAAAATCCGAATATCCGATTTTGGTA
2121775 AAAAATATCCGAA-A-CCGGATTTTGG-A
1 AAAAA-ATCCGAATATCC-GATTTTGGTA
2121801 AAAA
1 AAAA
2121805 CCGGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.25
27 14 0.50
28 7 0.25
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (27 bp):
AAAAAATCCGAATATCCGATTTTGGTA
Found at i:2121902 original size:24 final size:25
Alignment explanation
Indices: 2121875--2121935 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 25
2121865 AAATTGAACG
*
2121875 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
2121899 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
2121926 ACCGGTTTTT
1 ACCGGTTTTT
2121936 ATCTGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 12 0.36
27 21 0.64
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:2128505 original size:34 final size:30
Alignment explanation
Indices: 2128467--2128535 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
2128457 TTGATATAAA
2128467 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
2128501 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
2128530 AATTTA
1 AATTTA
2128536 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:2128546 original size:29 final size:30
Alignment explanation
Indices: 2128476--2128535 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2128466 AAATTTAAGG
2128476 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2128507 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2128536 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2128642 original size:21 final size:21
Alignment explanation
Indices: 2128615--2128712 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
2128605 AGGGTGTCAA
*
2128615 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
*
2128636 GGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
2128657 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCATCCCTG--C
* *
2128678 TAGTGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
2128699 AGTGCATCCATGCA
1 AGTGCATCCATGCA
2128713 CTCAAACACC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 34 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:2128704 original size:20 final size:20
Alignment explanation
Indices: 2128637--2128809 Score: 69
Period size: 20 Copynumber: 8.8 Consensus size: 20
2128627 CATCCCTGTG
* *
2128637 GTGCATCCATGCATCCCTGCA
1 GTGCATCGATGCAT-CATGCA
* *
2128658 GTGCATCCATGCA-CCTGCACTA
1 GTGCATCGATGCATCATG--C-A
2128680 GTGCATCGATGCATCATGCA
1 GTGCATCGATGCATCATGCA
*
2128700 GTGCATCCATGCA-C-T-CA
1 GTGCATCGATGCATCATGCA
** * *
2128717 -AACACCGAATGCA--AT-TA
1 GTGCATCG-ATGCATCATGCA
* * *
2128734 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCATGCA
*
2128754 GTGCATCGATGCATCAAGGCCA
1 GTGCATCGATGCATC-ATG-CA
* *
2128776 -TGCATCGATGCATCCTTCCA
1 GTGCATCGATGCAT-CATGCA
2128796 -TGCATCGATGCATC
1 GTGCATCGATGCATC
2128810 CTTCCATGCA
Statistics
Matches: 118, Mismatches: 21, Indels: 28
0.71 0.13 0.17
Matches are distributed among these distances:
16 3 0.03
17 14 0.12
18 5 0.04
19 7 0.06
20 43 0.36
21 28 0.24
22 15 0.13
23 3 0.03
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (20 bp):
GTGCATCGATGCATCATGCA
Found at i:2128810 original size:20 final size:20
Alignment explanation
Indices: 2128735--2128829 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
2128725 ATGCAATTAG
**
2128735 TGCATCGATGCATCCTTCTG
1 TGCATCGATGCATCCTTCCA
***
2128755 TGCATCGATGCATCAAGGCCA
1 TGCATCGATGCATC-CTTCCA
2128776 TGCATCGATGCATCCTTCCA
1 TGCATCGATGCATCCTTCCA
2128796 TGCATCGATGCATCCTTCCA
1 TGCATCGATGCATCCTTCCA
*
2128816 TGCATCCATGCATC
1 TGCATCGATGCATC
2128830 AAGGCTGCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 50 0.77
21 15 0.23
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCCTTCCA
Found at i:2129217 original size:34 final size:32
Alignment explanation
Indices: 2129178--2129247 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
2129168 TTTTGTACAG
* * *
2129178 GGGAAATGTTATAGCTTATCCCGTGTAAAATCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
2129212 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
2129244 GGGA
1 GGGA
2129248 GTTGTAAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:2130557 original size:19 final size:18
Alignment explanation
Indices: 2130520--2130571 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
2130510 TAAAGATAAT
2130520 TTGATTTTGAAAGAAAAAA
1 TTGATTTTGAAA-AAAAAA
*
2130539 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAA-AAAAA
2130558 -TGAATTTTGAAAAA
1 TTG-ATTTTGAAAAA
2130572 TGATTTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (18 bp):
TTGATTTTGAAAAAAAAA
Found at i:2131320 original size:184 final size:182
Alignment explanation
Indices: 2130963--2131326 Score: 694
Period size: 184 Copynumber: 2.0 Consensus size: 182
2130953 ACTTAATGCT
2130963 TTAATTTGGTTATTTGGTTGCTCATTTTGATTTTAAGCATGCATGAGTTTTGGTTTTAAATGATT
1 TTAATTTGGTTATTTGGTTGCTCATTTTGATTTTAAGCATGCATGAGTTTTGGTTTTAAATGATT
2131028 ATGCATCATTTTTAATCTCATGTATGTTGAAAAGATTATGATGAACATTTTAAAGTTGTAACGAT
66 ATGCATCATTTTTAATCTCATGTATGTTGAAAAGATTATGATGAACATTTTAAAGTTGTAACGAT
2131093 TTTTCAGAATTTTTAGTTCATCATAATAAAATTTTGGTCAAATTGGTTTTAA
131 TTTTCAGAATTTTTAGTTCATCATAATAAAATTTTGGTCAAATTGGTTTTAA
2131145 TTAATTTGGTTATTTGGTTGCTCA-TTTGATTTTAAGCATGCATGAGTTTTGGTTTTAAATGATT
1 TTAATTTGGTTATTTGGTTGCTCATTTTGATTTTAAGCATGCATGAGTTTTGGTTTTAAATGATT
2131209 ATGCATCATTTTTAATCTCATGTATGTTGAAAAGATGATTATGATGAACATTTTAAAGTTGTAAC
66 ATGCATCATTTTTAATCTCATGTATGTTG-AAA-A-GATTATGATGAACATTTTAAAGTTGTAAC
2131274 GATTTTTCAGAATTTTTAGTTCATCATAATAAAATTTTGGTCAAATTGGTTTT
128 GATTTTTCAGAATTTTTAGTTCATCATAATAAAATTTTGGTCAAATTGGTTTT
2131327 TAATGCAAAT
Statistics
Matches: 179, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
181 69 0.39
182 27 0.15
183 1 0.01
184 82 0.46
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (182 bp):
TTAATTTGGTTATTTGGTTGCTCATTTTGATTTTAAGCATGCATGAGTTTTGGTTTTAAATGATT
ATGCATCATTTTTAATCTCATGTATGTTGAAAAGATTATGATGAACATTTTAAAGTTGTAACGAT
TTTTCAGAATTTTTAGTTCATCATAATAAAATTTTGGTCAAATTGGTTTTAA
Found at i:2131924 original size:34 final size:30
Alignment explanation
Indices: 2131886--2131954 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
2131876 TTGATATAAC
2131886 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
2131920 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
2131949 AATTTA
1 AATTTA
2131955 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:2131965 original size:29 final size:30
Alignment explanation
Indices: 2131895--2131954 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2131885 CAATTTAAGG
2131895 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
2131926 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2131955 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2132063 original size:36 final size:36
Alignment explanation
Indices: 2132016--2132088 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 36
2132006 GAGCCAAAAT
2132016 GCTAAAGGGTGTC-AAGTGCATCCCATGCATCCCTGC
1 GCTAAAGGGTGTCAAAGTGCAT-CCATGCATCCCTGC
2132052 GCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGC
1 GCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGC
2132088 G
1 G
2132089 ATGCATCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 28 0.78
37 8 0.22
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (36 bp):
GCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGC
Found at i:2132095 original size:21 final size:21
Alignment explanation
Indices: 2132067--2132164 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
2132057 AGGGTGTCAA
2132067 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
2132088 -GATGCATCCATGCATCCCTGC
1 AG-TGCATCCATGCATCCCTGC
2132109 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCATCCCTG--C
* *
2132130 TAGTGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
2132151 AGTGCATCCATGCA
1 AGTGCATCCATGCA
2132165 CTCAAACACC
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 33 0.49
22 14 0.21
23 3 0.04
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:2132651 original size:34 final size:32
Alignment explanation
Indices: 2132612--2132681 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2132602 TTTTGTAAAG
* *
2132612 GGGAAAGGTTCTAGCTTATCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
2132646 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2132678 GGGA
1 GGGA
2132682 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2140135 original size:31 final size:31
Alignment explanation
Indices: 2140095--2140159 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2140085 TGCAATATAA
* *
2140095 TCCCCCAACATTTAGTCTATTTTCAATATGG
1 TCCCCCAACATTTAGTCCATTTACAATATGG
* *
2140126 TCCCTCAACATTTATTCCATTTACAATATGG
1 TCCCCCAACATTTAGTCCATTTACAATATGG
2140157 TCC
1 TCC
2140160 GTAACTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTACAATATGG
Found at i:2140263 original size:31 final size:31
Alignment explanation
Indices: 2140215--2140288 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2140205 ACTGTATTGC
* *
2140215 AAGTTTT--AAAAGTTTAGGGACCTAAATGA
1 AAGTTTTAGAAAAGGTTAGGGACCAAAATGA
2140244 AAGTTTTAGAAAAGGTTAGGGACCAAAATGA
1 AAGTTTTAGAAAAGGTTAGGGACCAAAATGA
2140275 AA-TATTTAGAAAAG
1 AAGT-TTTAGAAAAG
2140289 TTCAGTGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 7 0.17
30 1 0.03
31 32 0.80
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (31 bp):
AAGTTTTAGAAAAGGTTAGGGACCAAAATGA
Found at i:2140299 original size:31 final size:30
Alignment explanation
Indices: 2140215--2140299 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
2140205 ACTGTATTGC
*
2140215 AAGTTTT--AAAAGTTTAGGGACCTAAATGA
1 AAGTTTTAGAAAAG-TTAGGGACCAAAATGA
2140244 AAGTTTTAGAAAAGGTTAGGGACCAAAATGA
1 AAGTTTTAGAAAA-GTTAGGGACCAAAATGA
*
2140275 AA-TATTTAGAAAAGTTCAGTGACCA
1 AAGT-TTTAGAAAAGTT-AGGGACCA
2140300 TTACTATACT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
29 7 0.14
30 4 0.08
31 37 0.76
32 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (30 bp):
AAGTTTTAGAAAAGTTAGGGACCAAAATGA
Found at i:2141867 original size:31 final size:30
Alignment explanation
Indices: 2141828--2141891 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 30
2141818 TAATATAATC
2141828 CCCTAACATTTAGTCCATTTGCAATATGGT
1 CCCTAACATTTAGTCCATTTGCAATATGGT
*
2141858 CCCTCAACATTTAGTCCATTTGTAATATGGT
1 CCCT-AACATTTAGTCCATTTGCAATATGGT
2141889 CCC
1 CCC
2141892 CGACGTAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (30 bp):
CCCTAACATTTAGTCCATTTGCAATATGGT
Found at i:2143481 original size:29 final size:29
Alignment explanation
Indices: 2143441--2143544 Score: 104
Period size: 31 Copynumber: 3.6 Consensus size: 29
2143431 CTTTTTCATT
*
2143441 TAAGTACTTAAAGTATTTTTTTGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTGTCAAAA
* *
2143470 TAAGTACCTAAAGTTATCTTTTTGGCCAAAA
1 TAAGTACCTAAAG-TAT-TTTTTTGTCAAAA
* *
2143501 TAGGTA-CTAAAGTA-TTTTATGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTGTCAAAA
* * *
2143528 TAGGTTCCTAAATTATT
1 TAAGTACCTAAAGTATT
2143545 CAAACTTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
27 15 0.24
28 7 0.11
29 15 0.24
30 9 0.15
31 16 0.26
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTTGTCAAAA
Found at i:2143526 original size:27 final size:27
Alignment explanation
Indices: 2143444--2143532 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 27
2143434 TTTCATTTAA
*
2143444 GTACTTAAAGTATTTTTTTGTCAAAATAA
1 GTAC-TAAAGTA-TTTTTTGTCAAAATAG
*
2143473 GTACCTAAAGTTATCTTTTTGGCCAAAATAG
1 GTA-CTAAAG-TAT-TTTTT-GTCAAAATAG
*
2143504 GTACTAAAGTATTTTATGTCAAAATAG
1 GTACTAAAGTATTTTTTGTCAAAATAG
2143531 GT
1 GT
2143533 TCCTAAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 11 0.21
28 4 0.08
29 12 0.23
30 14 0.27
31 11 0.21
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (27 bp):
GTACTAAAGTATTTTTTGTCAAAATAG
Found at i:2143706 original size:31 final size:29
Alignment explanation
Indices: 2143627--2143729 Score: 143
Period size: 29 Copynumber: 3.5 Consensus size: 29
2143617 AAAAAAATTG
* *
2143627 AATACTTTAGGTACCTATTTTGACTAAAA
1 AATACTTTAGATACCTATTTTGACCAAAA
*
2143656 AATACTTTAGGTACCTATTTTGACCAAAA
1 AATACTTTAGATACCTATTTTGACCAAAA
* *
2143685 AGATAACTTTAGATACTTATTTTGATCAAAA
1 A-AT-ACTTTAGATACCTATTTTGACCAAAA
2143716 AATACTTTAGATAC
1 AATACTTTAGATAC
2143730 TTAAAATGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
29 40 0.59
30 4 0.06
31 24 0.35
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (29 bp):
AATACTTTAGATACCTATTTTGACCAAAA
Found at i:2152225 original size:6 final size:6
Alignment explanation
Indices: 2152214--2152239 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2152204 TTCGGATCCA
2152214 GAACCC GAACCC GAACCC GAACCC GA
1 GAACCC GAACCC GAACCC GAACCC GA
2152240 GCCATCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GAACCC
Found at i:2155071 original size:2 final size:2
Alignment explanation
Indices: 2155064--2155092 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2155054 TCAATCTACC
2155064 AT AT 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 AT AT A
2155093 AATGTATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2155920 original size:2 final size:2
Alignment explanation
Indices: 2155913--2155965 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
2155903 ATTGGTCTAC
2155913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2155954 A- AT AT AT AT AT A
1 AT AT AT AT AT AT A
2155966 CAAGTACTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2164758 original size:16 final size:16
Alignment explanation
Indices: 2164737--2164767 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2164727 TCTCATTTTT
2164737 TAATTACAAACTGAAC
1 TAATTACAAACTGAAC
*
2164753 TAATTATAAACTGAA
1 TAATTACAAACTGAA
2164768 GGTTAGCAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TAATTACAAACTGAAC
Found at i:2167717 original size:20 final size:21
Alignment explanation
Indices: 2167692--2167735 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2167682 CCAGAAATGT
* *
2167692 TAAAAA-ATTAATGTTTTAGG
1 TAAAAATAATAATGTTTTAAG
2167712 TAAAAATAATAATGTTTTAAG
1 TAAAAATAATAATGTTTTAAG
2167733 TAA
1 TAA
2167736 TTTTTTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (21 bp):
TAAAAATAATAATGTTTTAAG
Found at i:2168705 original size:12 final size:13
Alignment explanation
Indices: 2168690--2168719 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2168680 TTAAATTCTC
2168690 AAATTAAAAAA-T
1 AAATTAAAAAATT
2168702 AAATTAAAAAATT
1 AAATTAAAAAATT
2168715 AAATT
1 AAATT
2168720 TTCTGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:2170160 original size:48 final size:48
Alignment explanation
Indices: 2170108--2170205 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 48
2170098 TCAAGTCTAA
* * * *
2170108 AACCTTAAATCCTAAACCTTAAAACTCT-TAC-CTCAAATCTTAAATTCT
1 AACCTCAAATCATAAA-CTTAAAACTCTGAACACT-AAATCTTAAACTCT
* *
2170156 AACCTCAAATTATAAACTTTAAACTCTGAACACTAAATCTTAAACTCT
1 AACCTCAAATCATAAACTTAAAACTCTGAACACTAAATCTTAAACTCT
2170204 AA
1 AA
2170206 TCCTAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
47 10 0.24
48 30 0.71
49 2 0.05
ACGTcount: A:0.43, C:0.24, G:0.01, T:0.32
Consensus pattern (48 bp):
AACCTCAAATCATAAACTTAAAACTCTGAACACTAAATCTTAAACTCT
Found at i:2170295 original size:18 final size:17
Alignment explanation
Indices: 2170272--2170305 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2170262 GTTATAATTT
2170272 TTTATTAAATCTAAATCA
1 TTTATTAAAT-TAAATCA
*
2170290 TTTATTTAATTAAATC
1 TTTATTAAATTAAATC
2170306 TAATGACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATTAAATTAAATCA
Found at i:2171345 original size:87 final size:87
Alignment explanation
Indices: 2171199--2171361 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
2171189 TATGTTATAT
2171199 TATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
2171264 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * * *
2171286 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
2171351 AGCGCTTATAT
66 AGCGCTTATAT
2171362 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:2172139 original size:23 final size:23
Alignment explanation
Indices: 2172067--2172139 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2172057 ATACTTTACA
*
2172067 ATATAAGCGCTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2172090 ATAGAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2172113 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2172136 ATAT
1 ATAT
2172140 TTTTATCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2176262 original size:12 final size:12
Alignment explanation
Indices: 2176241--2176286 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2176231 GTTTGGATCA
2176241 TCATCGTCATCT
1 TCATCGTCATCT
* *
2176253 TCATCATCATAT
1 TCATCGTCATCT
*
2176265 TCATCGTCAGCT
1 TCATCGTCATCT
*
2176277 TCATCTTCAT
1 TCATCGTCAT
2176287 TGACAGCTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:2176269 original size:24 final size:24
Alignment explanation
Indices: 2176241--2176286 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2176231 GTTTGGATCA
*
2176241 TCATCGTCATCTTCATCATCATAT
1 TCATCGTCAGCTTCATCATCATAT
*
2176265 TCATCGTCAGCTTCATCTTCAT
1 TCATCGTCAGCTTCATCATCAT
2176287 TGACAGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (24 bp):
TCATCGTCAGCTTCATCATCATAT
Found at i:2178117 original size:200 final size:200
Alignment explanation
Indices: 2177770--2178755 Score: 1654
Period size: 200 Copynumber: 4.9 Consensus size: 200
2177760 ATATTTAAAT
*
2177770 TAGTATCGACACAAAATTAAAAAGTGTCGATACATA-TATTACACCT-ATTCTCTCATAAAACCG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TATACCTAATT-TCTCATAAAACCG
2177833 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
64 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
* *
2177898 TGGGATCGACACCTTTTATATATGGATCGACATTTTATGGTTGCACCCTGTTTGCCATTCATTCT
129 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
2177963 GGACCAA
194 GGACCAA
* * * *
2177970 TAGTATCGACACAAAATTAAACAGTGTCGACACATATTATATACCTACTTTCTCATAAAACTGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATTTCTCATAAAACCGGT
* *
2178035 ATACTTATACCGGTTAGATTGAAAAATTACTTATTACATTATACTTATGGGTTTCGATGTTTATG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* *
2178100 AGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCCTGTTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
2178165 ACCAA
196 ACCAA
*
2178170 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATTTCTCATAAAACCGGT
* * *
2178235 ATACTTATACCGGTTAAATTAAAAAATTACCTATTACATTATACTTATAGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* *
2178300 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCGCCCTGTTTGCCATTCATTCAGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
2178365 ACCAA
196 ACCAA
* * * *
2178370 TAGTATCAACAGAAAATTAAAACGTGTCGATACATA-TATTATACCTATTTTCTCATAAAACCGG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TATACCTAATTTCTCATAAAACCGG
*
2178434 TATACTTATACCGGTTTGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
*
2178499 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
130 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
*
2178564 AACCAA
195 GACCAA
*
2178570 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATTTCTCATAAAACCGGT
* *
2178635 ATACTTATACCGGTTAGATTGAAAAATTGCCTATTACATTATACTTATGGGTTTCGATGTTTATG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
2178700 GGATCGACACTTTTTATATATGGATCGACACGTTATGGTTACACCCTATTTGCCAT
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
2178756 ATTGTAAATT
Statistics
Matches: 732, Mismatches: 50, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
199 2 0.00
200 724 0.99
201 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATTTCTCATAAAACCGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAA
Found at i:2179009 original size:19 final size:19
Alignment explanation
Indices: 2178985--2179032 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2178975 TTACATTCAC
2178985 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
**
2179004 ATACAAAATTATAAATTTT
1 ATACAAAATTATAAATCGT
2179023 ATACAAAATT
1 ATACAAAATT
2179033 CACCCTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2180920 original size:21 final size:21
Alignment explanation
Indices: 2180895--2180959 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2180885 CCCCTTATGC
* *
2180895 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2180916 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
2180937 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2180958 CT
1 CT
2180960 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2181062 original size:15 final size:15
Alignment explanation
Indices: 2181042--2181074 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2181032 ACTCTGTTTT
*
2181042 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
2181057 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
2181072 CCC
1 CCC
2181075 AATACAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.64, G:0.09, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:2185700 original size:16 final size:16
Alignment explanation
Indices: 2185679--2185719 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2185669 CAATGAACAT
*
2185679 CGAGCTTAACGAGTAA
1 CGAGCTTAACGAGCAA
*
2185695 CGAGCTTAATGAGCAA
1 CGAGCTTAACGAGCAA
*
2185711 CGAACTTAA
1 CGAGCTTAA
2185720 TAAATAACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (16 bp):
CGAGCTTAACGAGCAA
Found at i:2187079 original size:18 final size:18
Alignment explanation
Indices: 2187050--2187119 Score: 113
Period size: 18 Copynumber: 3.8 Consensus size: 18
2187040 GTTTGGTTCA
2187050 CGGAATATAAGATTACCGG
1 CGGAA-ATAAGATTACCGG
2187069 CGGAAATAAGATTACCGG
1 CGGAAATAAGATTACCGG
*
2187087 CGGAAATAGGATTACCGG
1 CGGAAATAAGATTACCGG
*
2187105 CGGGAATAAGATTAC
1 CGGAAATAAGATTAC
2187120 TGAGAATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
18 43 0.90
19 5 0.10
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.19
Consensus pattern (18 bp):
CGGAAATAAGATTACCGG
Found at i:2189649 original size:18 final size:18
Alignment explanation
Indices: 2189605--2189650 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2189595 GCTCGATTCT
* *
2189605 TTCGACCGATCTGATCGA
1 TTCGACCGGTCTAATCGA
2189623 TTCGACCGGTCTAATCGA
1 TTCGACCGGTCTAATCGA
2189641 TTCGACCGGT
1 TTCGACCGGT
2189651 TGAACTAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (18 bp):
TTCGACCGGTCTAATCGA
Found at i:2190682 original size:2 final size:2
Alignment explanation
Indices: 2190664--2190737 Score: 130
Period size: 2 Copynumber: 36.5 Consensus size: 2
2190654 ACCATCATAA
*
2190664 AT AT CAT AT AA 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 AT AT AT
2190707 AT AT AT 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 AT AT AT A
2190738 AACTTAACTG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 67 0.97
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2191179 original size:20 final size:20
Alignment explanation
Indices: 2191156--2191207 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2191146 AACGCGATCC
2191156 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2191176 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2191196 CCAAAATCGCAA
1 CCAGAATCGCAA
2191208 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2191224 original size:21 final size:20
Alignment explanation
Indices: 2191197--2191295 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
2191187 AATCAGTTTC
2191197 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2191218 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2191239 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2191259 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2191280 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2191296 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2191324 original size:20 final size:20
Alignment explanation
Indices: 2191262--2191455 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2191252 CGATTTTCCA
* ** *
2191262 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2191282 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2191302 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2191322 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2191342 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2191362 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2191382 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2191402 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2191422 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2191443 AAATCGCAACGCG
1 AAATCGCAACGCG
2191456 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2191346 original size:60 final size:60
Alignment explanation
Indices: 2191262--2191455 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
2191252 CGATTTTCCA
* ** * *
2191262 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
2191322 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
2191382 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
2191443 AAATCGCAACGCG
1 AAATCGCAACGCG
2191456 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:2191876 original size:33 final size:33
Alignment explanation
Indices: 2191837--2191907 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2191827 TTCACTTAGA
*
2191837 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2191870 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2191903 TTTCA
1 TTTCA
2191908 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2192047 original size:14 final size:14
Alignment explanation
Indices: 2192028--2192082 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2192018 AGAATGACTG
2192028 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2192042 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
2192061 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2192075 TCGCAACG
1 TCGCAACG
2192083 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2192095 original size:33 final size:33
Alignment explanation
Indices: 2192028--2192098 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2192018 AGAATGACTG
***
2192028 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2192061 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2192094 TCGCA
1 TCGCA
2192099 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2192116 original size:19 final size:19
Alignment explanation
Indices: 2192094--2192191 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2192084 GAAACCAAAA
*
2192094 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2192113 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2192127 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2192146 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2192160 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2192179 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2192192 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2192135 original size:14 final size:14
Alignment explanation
Indices: 2192116--2192205 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2192106 TTTCATTTCG
2192116 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2192130 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2192149 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2192163 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2192180 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2192196 CGTTGCGATT
1 CGTTGCGATT
2192206 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2192141 original size:33 final size:33
Alignment explanation
Indices: 2192099--2192213 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2192089 CAAAATCGCA
2192099 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2192132 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2192165 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2192198 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2192214 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2194127 original size:92 final size:93
Alignment explanation
Indices: 2193910--2194380 Score: 912
Period size: 92 Copynumber: 5.1 Consensus size: 93
2193900 TAGATTGCTT
2193910 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2193975 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2194003 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
2194067 TTTGTCGTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2194095 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2194160 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2194187 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2194251 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2194279 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2194344 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2194372 AGTAAATTT
1 AGTAAATTT
2194381 ATCCATTCAA
Statistics
Matches: 373, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 36 0.10
92 201 0.54
93 136 0.36
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2194464 original size:19 final size:19
Alignment explanation
Indices: 2194424--2194552 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2194414 TAGTTTACTT
* *
2194424 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2194444 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2194463 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2194482 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2194496 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2194515 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2194529 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2194548 TCGCA
1 TCGCA
2194553 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2194503 original size:33 final size:32
Alignment explanation
Indices: 2194460--2194552 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2194450 CGCGAAACCA
**
2194460 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2194492 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2194525 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2194553 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2194550 original size:52 final size:52
Alignment explanation
Indices: 2194424--2194552 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2194414 TAGTTTACTT
**
2194424 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2194476 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2194529 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2194553 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2194570 original size:19 final size:19
Alignment explanation
Indices: 2194548--2194682 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2194538 GAAACCAAAA
*
2194548 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2194567 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2194583 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2194600 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2194616 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2194633 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2194652 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2194672 TCGTGTTGCGA
1 TCGCGTTGCGA
2194683 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2194589 original size:14 final size:14
Alignment explanation
Indices: 2194570--2194626 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2194560 TTTCATTTCG
2194570 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2194584 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2194601 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2194617 CGTTGCGATT
1 CGTTGCGATT
2194627 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2194595 original size:33 final size:33
Alignment explanation
Indices: 2194553--2194645 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2194543 CAAAATCGCA
*
2194553 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2194586 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2194619 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2194646 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2196604 original size:14 final size:14
Alignment explanation
Indices: 2196585--2196620 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2196575 ATTGTTTAAT
2196585 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2196599 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2196613 TGATTTGT
1 TGATTTGT
2196621 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2196743 original size:19 final size:19
Alignment explanation
Indices: 2196727--2196828 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2196717 AAAAATGACT
2196727 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2196746 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2196765 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2196779 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2196798 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2196818 ATCGCAATGCG
1 ATCGCAATGCG
2196829 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2196877 original size:33 final size:33
Alignment explanation
Indices: 2196835--2197161 Score: 208
Period size: 33 Copynumber: 9.5 Consensus size: 33
2196825 TGCGTTTATA
2196835 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
2196868 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
2196904 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
2196939 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
2196977 ATTTCGCATTGCGATTATGTCGGTT-CGA-TTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
2197009 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
2197049 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
2197080 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* * *
2197113 ATTTCGCGTTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
*
2197146 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2197162 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 20, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 22 0.09
33 108 0.43
34 6 0.02
35 20 0.08
36 18 0.07
37 5 0.02
38 49 0.20
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:2196881 original size:19 final size:19
Alignment explanation
Indices: 2196857--2197161 Score: 347
Period size: 19 Copynumber: 17.4 Consensus size: 19
2196847 GATTATCTCG
2196857 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2196876 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2196895 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2196909 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2196928 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2196947 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
2196966 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
2196985 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
2197000 TT-CGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2197017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2197036 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2197050 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2197069 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2197088 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
2197102 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2197121 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2197135 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2197154 TTGCGATT
1 TTGCGATT
2197162 GTATTTTCCG
Statistics
Matches: 248, Mismatches: 13, Indels: 50
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.13
15 4 0.02
16 34 0.14
17 28 0.11
18 3 0.01
19 147 0.59
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2197161 original size:52 final size:52
Alignment explanation
Indices: 2196857--2197133 Score: 318
Period size: 52 Copynumber: 5.2 Consensus size: 52
2196847 GATTATCTCG
*
2196857 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
2196909 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
2196966 TTGCGATTTTAATTTCGCATTGCGATTAT-GTCGGTT-CGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCG-C-GTTGCGATTTTCATTTCGCA
*
2197017 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
* *
2197069 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
2197121 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2197134 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 8, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
50 3 0.01
51 43 0.21
52 125 0.60
53 2 0.01
54 3 0.01
55 7 0.03
57 24 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
Found at i:2199481 original size:12 final size:12
Alignment explanation
Indices: 2199464--2199488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2199454 TCTTCGGGGA
2199464 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2199476 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2199488 C
1 C
2199489 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2199697 original size:24 final size:24
Alignment explanation
Indices: 2199663--2199709 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2199653 CTGAAACATC
2199663 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2199687 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2199710 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2200411 original size:20 final size:20
Alignment explanation
Indices: 2200383--2200751 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2200373 AAATTTCAGT
* * * *
2200383 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2200403 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2200423 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2200443 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2200463 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2200483 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2200503 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2200523 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2200543 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2200563 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2200583 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2200603 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2200623 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2200643 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2200663 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2200683 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2200703 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2200723 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2200743 GTTGCGATT
1 GTTGCGATT
2200752 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2204938 original size:47 final size:46
Alignment explanation
Indices: 2204885--2205151 Score: 309
Period size: 44 Copynumber: 5.9 Consensus size: 46
2204875 CAAGTCAAAC
*
2204885 AATTAAATAATAAAAATATTAAAAAACAAAATAAATAAAAAGTCAAT
1 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAAGTC-AT
* *
2204932 AATTAAATAATAAAAACATTAAGAAATAAAATAAATAAAAAGTTCAT
1 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAAG-TCAT
* *
2204979 AATTAAATAATAAAAAAATTAAGAAATAAAATAAATAAAAAGT--T
1 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAAGTCAT
* * * *
2205023 CA-TAAATAAAGAAAAATATTAAGAAAGAAAATAAATAAGAAGTCCAT
1 AATTAAAT-AATAAAAATATTAAGAAACAAAATAAATAAAAAGT-CAT
*
2205070 AATT--A-AATAAAAATATTAAGAAACAAAATAAATAAAAAGTTTAT
1 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAAG-TCAT
* * *
2205114 AATT--A-AATAAAAACATTAAAAAACAAAATAGATAAAAA
1 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAA
2205152 CAAGTATATC
Statistics
Matches: 196, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.03
44 101 0.52
45 1 0.01
46 2 0.01
47 84 0.43
48 3 0.02
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (46 bp):
AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAAAAGTCAT
Found at i:2204971 original size:24 final size:22
Alignment explanation
Indices: 2204889--2205019 Score: 100
Period size: 24 Copynumber: 5.5 Consensus size: 22
2204879 TCAAACAATT
*
2204889 AAATAATAAAAATATTAAAAAACA
1 AAATAATAAAAA-ATT-AAAAATA
* * * *
2204913 AAATAAATAAAAAGTCAATAATT
1 AAAT-AATAAAAAATTAAAAATA
2204936 AAATAATAAAAACATTAAGAAATA
1 AAATAATAAAAA-ATTAA-AAATA
* * * *
2204960 AAATAAATAAAAAGTTCATAATT
1 AAAT-AATAAAAAATTAAAAATA
2204983 AAATAATAAAAAAATTAAGAAATA
1 AAATAAT-AAAAAATTAA-AAATA
2205007 AAATAAATAAAAA
1 AAAT-AATAAAAA
2205020 GTTCATAAAT
Statistics
Matches: 83, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
22 11 0.13
23 26 0.31
24 27 0.33
25 19 0.23
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (22 bp):
AAATAATAAAAAATTAAAAATA
Found at i:2205000 original size:16 final size:15
Alignment explanation
Indices: 2204885--2205019 Score: 64
Period size: 16 Copynumber: 8.6 Consensus size: 15
2204875 CAAGTCAAAC
2204885 AATTAAATAATAAAAA
1 AATTAAA-AATAAAAA
*
2204901 TATTAAAAA-ACAAAA
1 AATTAAAAATA-AAAA
* * *
2204916 TAAATAAAAAGT-CAAT
1 -AATTAAAAA-TAAAAA
2204932 AATTAAATAATAAAAA
1 AATTAAA-AATAAAAA
*
2204948 CATTAAGAAATAAAATA
1 AATTAA-AAATAAAA-A
** *
2204965 AA-TAAAAAGT-TCAT
1 AATTAAAAA-TAAAAA
2204979 AATTAAATAATAAAAA
1 AATTAAA-AATAAAAA
2204995 AATTAAGAAATAAAATA
1 AATTAA-AAATAAAA-A
2205012 AA-TAAAAA
1 AATTAAAAA
2205020 GTTCATAAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 29
0.66 0.12 0.22
Matches are distributed among these distances:
14 3 0.03
15 25 0.28
16 54 0.61
17 7 0.08
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AATTAAAAATAAAAA
Found at i:2205029 original size:24 final size:24
Alignment explanation
Indices: 2204912--2205110 Score: 109
Period size: 23 Copynumber: 8.7 Consensus size: 24
2204902 ATTAAAAAAC
2204912 AAAATAAATAAAAAG-TCA-ATAAT
1 AAAATAAATAAAAAGTTCAGA-AAT
* * *
2204935 TAAAT-AATAAAAACATTAAGAAAT
1 AAAATAAATAAAAA-GTTCAGAAAT
*
2204959 AAAATAAATAAAAAGTTCA-TAAT
1 AAAATAAATAAAAAGTTCAGAAAT
* * *
2204982 TAAAT-AATAAAAAAATTAAGAAAT
1 AAAATAAAT-AAAAAGTTCAGAAAT
*
2205006 AAAATAAATAAAAAGTTCATAAAT
1 AAAATAAATAAAAAGTTCAGAAAT
* * * *
2205030 -AAA-GAA-AAATA-TTAAGAAAG
1 AAAATAAATAAAAAGTTCAGAAAT
* * *
2205050 AAAATAAATAAGAAGTCCA-TAAT
1 AAAATAAATAAAAAGTTCAGAAAT
* * * *
2205073 TAAAT-AA-AAATA-TTAAGAAAC
1 AAAATAAATAAAAAGTTCAGAAAT
2205094 AAAATAAATAAAAAGTT
1 AAAATAAATAAAAAGTT
2205111 TATAATTAAA
Statistics
Matches: 125, Mismatches: 36, Indels: 29
0.66 0.19 0.15
Matches are distributed among these distances:
20 8 0.06
21 16 0.13
22 19 0.15
23 35 0.28
24 35 0.28
25 12 0.10
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (24 bp):
AAAATAAATAAAAAGTTCAGAAAT
Done.