Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 33 of 33
Found at i:5604037 original size:77 final size:77
Alignment explanation
Indices: 5603883--5604038 Score: 199
Period size: 77 Copynumber: 2.0 Consensus size: 77
5603873 AACTCAAAAT
*
5603883 AAAAATACTTATGATAATTAAATAATTATGTTCAGTAACACAAACAAAGCTAGAATAAAACCTAT
1 AAAAATACTTATGATAATTAAATAATTATGTTCAATAACACAAACAAAGCTAGAATAAAACCTAT
* **
5603948 TATAATCGTTAA
66 TACAATAATTAA
* * * * *
5603960 AAAAATATTTATGGTAATTAAATAATTA-GATTCAATAACATAAACATAGCTAGAAT-AAAGCTC
1 AAAAATACTTATGATAATTAAATAATTATG-TTCAATAACACAAACAAAGCTAGAATAAAACCT-
5604023 ATTACAATAATTAA
64 ATTACAATAATTAA
5604037 AA
1 AA
5604039 GTTCATCTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 6 0.09
77 62 0.91
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (77 bp):
AAAAATACTTATGATAATTAAATAATTATGTTCAATAACACAAACAAAGCTAGAATAAAACCTAT
TACAATAATTAA
Found at i:5604528 original size:253 final size:259
Alignment explanation
Indices: 5603960--5604550 Score: 834
Period size: 253 Copynumber: 2.3 Consensus size: 259
5603950 TAATCGTTAA
* * * *
5603960 AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACATAAACATAGCTAGAATAAAGCTCAT
1 AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACACAAACAAAGTTAGAATAAGGCTCAT
* *
5604025 TACAATAATTAAAAGTTCATCTATTTTAATCACAAGCTTAAGATTTGATAAACTTTTAACCAATA
66 TACAATCATTAAAAATTCATCTATTTTAATCACAAGCTTAAGATTTGATAAACTTTTAACCAATA
* * *
5604090 TATTATTATGAAAATAACTAAATTTAAAGTAAAAAAATACAAAGAAAAATTAGACGTTAAGAGTT
131 TATTATTATGAAAATAACTAAATTT--A-TAAAAAAAGACAAAGAAAAATTAAACGTTAAGACTT
* * *
5604155 GAGAACTGAGATTTAATAGAAGATTTATATATAAAACCAATATACTTTATGAATCACAACCCAAA
193 GAAAACTGAGATTTAATAGAAAATTTATATATAAAACCAACATACTTTATGAATCACAACCCAAA
*
5604220 AT
258 AC
*
5604222 AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACACAAACAGAGTTAGAATAAGGCTCAT
1 AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACACAAACAAAGTTAGAATAAGGCTCAT
* * * * *
5604287 TATAATCATTAAAAATTCATTTATTTTAATCTCAAGCTTAGGATTTGATAAAC-TTTAATCAATA
66 TACAATCATTAAAAATTCATCTATTTTAATCACAAGCTTAAGATTTGATAAACTTTTAACCAATA
* *
5604351 TATTATTATGAAAATAACTAAA-TT-TAAAATAAGA-AAA-AAAAATTAAACGTTGAGACTTGAA
131 TATTATTATGAAAATAACTAAATTTATAAAAAAAGACAAAGAAAAATTAAACGTTAAGACTTGAA
* * *
5604412 AACTGAGATTTGATA-AAAATTTATATATAAAACCAACATAGTTTATGAATTACAACCCAAAAC
196 AACTGAGATTTAATAGAAAATTTATATATAAAACCAACATACTTTATGAATCACAACCCAAAAC
* * * * * * *
5604475 AAAAATACTTACGATAATTAAATAATTAAATTTAATATCACAAACAAAGTTAGAATAAGTCTCAT
1 AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACACAAACAAAGTTAGAATAAGGCTCAT
5604540 TACAATCATTA
66 TACAATCATTA
5604551 CTTAAGCTTA
Statistics
Matches: 297, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
253 110 0.37
254 34 0.11
255 3 0.01
256 8 0.03
260 2 0.01
261 32 0.11
262 108 0.36
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (259 bp):
AAAAATATTTATGGTAATTAAATAATTAGATTCAATAACACAAACAAAGTTAGAATAAGGCTCAT
TACAATCATTAAAAATTCATCTATTTTAATCACAAGCTTAAGATTTGATAAACTTTTAACCAATA
TATTATTATGAAAATAACTAAATTTATAAAAAAAGACAAAGAAAAATTAAACGTTAAGACTTGAA
AACTGAGATTTAATAGAAAATTTATATATAAAACCAACATACTTTATGAATCACAACCCAAAAC
Found at i:5605591 original size:239 final size:237
Alignment explanation
Indices: 5605164--5606116 Score: 785
Period size: 256 Copynumber: 3.9 Consensus size: 237
5605154 TTATTATAGA
* * * * *
5605164 AATAACTAAATTTAAAATAATAAAAAAACAAAGAAAATTTAAACGCTGAGAGTTGATAACTGAGT
1 AATAACTAAATTTAAAATAAAAAAAAAACAAA-AAAAATTAAACGTTAAGAGTTGATAACTGAGA
* * * *
5605229 TTTAATGGAAGATTTATTTACAAAATCAACAGTAGTTTATGAGT-AGCAA-CTCAAAACGAAAAT
65 TTTGATGAAAGATTTATTTACAAAACCAACA-TAATTTATG-GTCA-CAACCT-AAAACGAAAAT
* * *
5605292 ACTTATAGTAATTAAATAATTAGGTTCAATAACACAAATAGAACTAAAATAAAGCTCATTACAAT
126 ACTTAGA-TAATTAAATAATTAGATTCAATAACACAAATAGAGCTAAAATAAAGCTCATTACAAT
5605357 CATTAAAAATTCA-CTTATTTTAATCTCAAGCTTAAGATTTGATAAATT
190 CATTAAAAATTCATC-TATTTTAATCTCAAGCTTAAGATTTGATAAATT
* * * *
5605405 AATAACTAAATTTAAAATAAGAAAGAAACCAACAAAATTAAACGTTAAGAGTTGATAACTGAGAT
1 AATAACTAAATTTAAAATAAAAAAAAAACAAAAAAAATTAAACGTTAAGAGTTGATAACTGAGAT
** * *
5605470 TTGACAAAAGATTTATTAACAAAACCAACATAATTTATAGGTCACAACCTAAAACGAAAATACCT
66 TTGATGAAAGATTTATTTACAAAACCAACATAATTTAT-GGTCACAACCTAAAACGAAAATACTT
* * *
5605535 ACGATAATTAAATAACTAGATTCTATAACACAAATAGAGCTAAAAT-AAGACTCATTACAATCAA
130 A-GATAATTAAATAATTAGATTCAATAACACAAATAGAGCTAAAATAAAG-CTCATTACAATCAT
*
5605599 TAAAAGTTCATCTATTTTAATCTCATA-CTTAAGATTTGATAAATT
193 TAAAAATTCATCTATTTTAATCTCA-AGCTTAAGATTTGATAAATT
* * *
5605644 -TTAACTATTATATTTTTATGAAAATAACTAATTTTAAAATAAAAAAATAAAAAATTAAACATTA
1 AATAACTA--A-A---TT-T---AA-AA-TAA----AAAA-AAAACAA-AAAAAATTAAACGTTA
* * * * * *
5605708 AGAGTTAAAAATTAAGATTTGATGAAAGATTTATTTATAAAACCAATATAATTTATGGGTCACAA
48 AGAGTTGATAACTGAGATTTGATGAAAGATTTATTTACAAAACCAACATAATTTAT-GGTCACAA
* * * * *
5605773 CCCAAAACGAAAATACTTATGATAATTAAATAATTAAATTAAATAAAACAAACAGAGCTAAAATA
112 CCTAAAACGAAAATACTTA-GATAATTAAATAATTAGATTCAATAACACAAATAGAGCTAAAATA
* * * * * *
5605838 AAGCTTATTGCAATCCTTGAAAATTCATCTATTTTTATCCCAAGCTTAAGATTTGATAAAATTT
176 AAGCTCATTACAATCATTAAAAATTCATCTATTTTAATCTCAAGCTTAAGATTTGAT-AAA-TT
* * * ** * ** ** * *
5605902 AATCAGTATATTATTATTATAAAACTAACTACATTTAAAATAAA--AAAAATT-AGACATTGAGA
1 AATAACTA-AAT-TTAAAATAAAA-AAAAAACA---AAAA-AAATTAAACGTTAAGA-GTTGATA
* * * * * * *
5605964 ACTAAGATTTAATAGAAA-ATTTATTTGCACAACCAACATAATTTATGAGTTACAACCCAAAATG
58 ACTGAGATTTGAT-GAAAGATTTATTTACAAAACCAACATAATTTATG-GTCACAACCTAAAACG
* * * * * *
5606028 AAAATACTTACGATAATTAAATAATTAAATTCGATAACATAAACAGAGCTAGAATAAGACCT-AT
121 AAAATACTTA-GATAATTAAATAATTAGATTCAATAACACAAATAGAGCTAAAATAA-AGCTCAT
* *
5606092 TATAATCATTAAAAATTTATCTATT
184 TACAATCATTAAAAATTCATCTATT
5606117 CTTAGGATTT
Statistics
Matches: 581, Mismatches: 91, Indels: 75
0.78 0.12 0.10
Matches are distributed among these distances:
238 9 0.02
239 118 0.20
240 60 0.10
241 30 0.05
244 2 0.00
245 10 0.02
246 133 0.23
247 10 0.02
248 6 0.01
249 5 0.01
250 4 0.01
251 1 0.00
254 5 0.01
255 6 0.01
256 168 0.29
257 6 0.01
258 4 0.01
259 4 0.01
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (237 bp):
AATAACTAAATTTAAAATAAAAAAAAAACAAAAAAAATTAAACGTTAAGAGTTGATAACTGAGAT
TTGATGAAAGATTTATTTACAAAACCAACATAATTTATGGTCACAACCTAAAACGAAAATACTTA
GATAATTAAATAATTAGATTCAATAACACAAATAGAGCTAAAATAAAGCTCATTACAATCATTAA
AAATTCATCTATTTTAATCTCAAGCTTAAGATTTGATAAATT
Found at i:5606185 original size:495 final size:491
Alignment explanation
Indices: 5605112--5606205 Score: 1135
Period size: 502 Copynumber: 2.2 Consensus size: 491
5605102 AATCATTTAC
* *
5605112 TTTAATCTCA-AGCTTACGATTTGATAAATTTTAACCAATATATTATTAT-AGAAATAACTAAAT
1 TTTAATCTCATA-CTTAAGATTTGATAAATTTTAACAAATATATTATTATGA-AAATAACTAAAT
* * * * * * *
5605175 TTAAAATAATAAAAAAACAAAGAAAATTTAAACGCTGAGAGTTGATAACTGAGTTTTAATGGAAG
64 TT--AA-AATAAAAAAA-AAA-AAAA-TTAAACGTTAAGAGTTAAAAACTAAGATTTAATGAAAG
* * *
5605240 ATTTATTTACAAAATCAACAGTAGTTTATGAGTAGCAACTCAAAACGAAAATACTTATAGTAATT
123 ATTTATTTACAAAACCAACAGTAATTTATGAGTAGCAACCCAAAACGAAAATACTTATAGTAATT
** * * *
5605305 AAATAATTAGGTTCAATAACACAAATAGAACTAAAATAAAGCTCATTACAATCATTAAAAATTCA
188 AAATAATTAAATTAAATAAAACAAACAGAACTAAAATAAAGCTCATTACAATCATTAAAAATTCA
*
5605370 CTTATTTTAATCTCAAGCTTAAGATTTGATAAATTAATAACTAAATTTAAAATAAGAAAGAAACC
253 CTTATTTTAATCCCAAGCTTAAGATTTGATAAATTAATAACTAAATTTAAAATAAGAAAGAAACC
* ** * * * *
5605435 AACAAAATTAAACGTTAAGAGTTGATAACTGAGATTTGACAAAAGATTTATTAACAAAACCAACA
318 AACAAAATAAAAAATTAAGAATTGAGAACTAAGATTTAACAAAAGATTTATTAACAAAACCAACA
* * *
5605500 TAATTTATAGGTCACAACCTAAAACGAAAATACCTACGATAATTAAATAACTAGATTCTATAACA
383 TAATTTATAGGTCACAACCCAAAACGAAAATACCTACGATAATTAAATAACTAAATTCGATAACA
*
5605565 CAAATAGAGCTAAAATAAGACTCATTACAATCAATAAAAGTTCATCTAT
448 CAAACAGAGCTAAAATAAGACTCATTACAATCAATAAAA--T-A--TAT
* * * *
5605614 TTTAATCTCATACTTAAGATTTGATAAATTTTAACTATTATATTTTTATGAAAATAACTAATTTT
1 TTTAATCTCATACTTAAGATTTGATAAATTTTAACAAATATATTATTATGAAAATAACTAAATTT
* * * *
5605679 AAAATAAAAAAATAAAAAATTAAACATTAAGAGTTAAAAATTAAGATTTGATGAAAGATTTATTT
66 AAAATAAAAAAAAAAAAAATTAAACGTTAAGAGTTAAAAACTAAGATTTAATGAAAGATTTATTT
* * *
5605744 ATAAAACCAATA-TAATTTATGGGTCA-CAACCCAAAACGAAAATACTTAT-GATAATTAAATAA
131 ACAAAACCAACAGTAATTTATGAGT-AGCAACCCAAAACGAAAATACTTATAG-TAATTAAATAA
* * * * *
5605806 TTAAATTAAATAAAACAAACAGAGCTAAAATAAAGCTTATTGCAATCCTTGAAAATTCA-TCTAT
194 TTAAATTAAATAAAACAAACAGAACTAAAATAAAGCTCATTACAATCATTAAAAATTCACT-TAT
* * * * * * **
5605870 TTTTATCCCAAGCTTAAGATTTGATAAAATTTAATCAGTATA-TTATTATTATA-AAACTAACTA
258 TTTAATCCCAAGCTTAAGATTTGAT-AAA-TTAATAACTAAATTTA-AAATA-AGAAAGAAAC--
** * ** *
5605933 CATTTAAAATAAAAAAAATT-AGACATTGAGAACTAAGATTTAATAGAAA-ATTTATTTGCACAA
317 CA-ACAAAAT--AAAAAATTAAGA-ATTGAGAACTAAGATTTAACA-AAAGATTTATTAACAAAA
* * * *
5605996 CCAACATAATTTAT-GAGTTACAACCCAAAATGAAAATACTTACGATAATTAAATAATTAAATTC
377 CCAACATAATTTATAG-GTCACAACCCAAAACGAAAATACCTACGATAATTAAATAACTAAATTC
* * * *
5606060 GATAACATAAACAGAGCTAGAATAAGAC-CTATTATAATC-ATTAAA-A-A-
441 GATAACACAAACAGAGCTAAAATAAGACTC-ATTACAATCAATAAAATATAT
* *
5606107 TTT-ATCT-ATTCTTAGGATTTGATAAATTTTAACAAATATATTATTATGAAAATAACTAAATTT
1 TTTAATCTCATACTTAAGATTTGATAAATTTTAACAAATATATTATTATGAAAATAACTAAATTT
* *
5606170 AAAATTAGCAAAAAAAGAAAAATTAAATGTTAAGAG
66 AAAA-TA--AAAAAAAAAAAAATTAAACGTTAAGAG
5606206 AGATTTGATG
Statistics
Matches: 495, Mismatches: 76, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
491 54 0.11
492 6 0.01
493 3 0.01
494 26 0.05
495 118 0.24
496 52 0.11
497 23 0.05
498 3 0.01
499 12 0.02
500 7 0.01
501 10 0.02
502 176 0.36
503 5 0.01
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (491 bp):
TTTAATCTCATACTTAAGATTTGATAAATTTTAACAAATATATTATTATGAAAATAACTAAATTT
AAAATAAAAAAAAAAAAAATTAAACGTTAAGAGTTAAAAACTAAGATTTAATGAAAGATTTATTT
ACAAAACCAACAGTAATTTATGAGTAGCAACCCAAAACGAAAATACTTATAGTAATTAAATAATT
AAATTAAATAAAACAAACAGAACTAAAATAAAGCTCATTACAATCATTAAAAATTCACTTATTTT
AATCCCAAGCTTAAGATTTGATAAATTAATAACTAAATTTAAAATAAGAAAGAAACCAACAAAAT
AAAAAATTAAGAATTGAGAACTAAGATTTAACAAAAGATTTATTAACAAAACCAACATAATTTAT
AGGTCACAACCCAAAACGAAAATACCTACGATAATTAAATAACTAAATTCGATAACACAAACAGA
GCTAAAATAAGACTCATTACAATCAATAAAATATAT
Found at i:5610564 original size:227 final size:227
Alignment explanation
Indices: 5610156--5610838 Score: 870
Period size: 227 Copynumber: 2.9 Consensus size: 227
5610146 GCAAAATCCA
*
5610156 TTGCTTCATTGTCTTCCGCTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGAATACACTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAG-----ACTATA
** * *
5610221 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCTGGAACACCAAGTCCAAACCCAGCACC
61 AAAAAGAAA-CTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCACC
* *
5610286 TTGCCTACTTAA-TCTAAATCGATTGGGTTCAAAAAAAGAACAGCTTGGAAATGGACGAATCATT
125 TTGCCTAC-TAACTCTAAATCAATTGGGTTCAAAAAAAGAACAGCCTGGAAATGGACGAATCATT
5610350 CAAAAAAACTCTTTCACCAGTATACTTTCCAGAACTGGT
189 CAAAAAAACTCTTTCACCAGTATACTTTCCAGAACTGGT
*
5610389 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGA-TATAAAAAT
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGACTATAAAAAA
*
5610453 GAAACTTTTTAAAATTAAAATAAAAAAGAAATCCAGAACGCCAAGGCCAAATCCAGCACCTTGCC
66 GAAAC-TTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCACCTTGCC
* * * * *
5610518 TGCTAACTCTAAATCAATTGGGTTCATATAAAGAATAGCCTGGAAATGGAAGAATCATTCAAAAA
130 TACTAACTCTAAATCAATTGGGTTCAAAAAAAGAACAGCCTGGAAATGGACGAATCATTCAAAAA
** * *
5610583 AACTCTTTCATGAGTATCCTTTCTAGAACTGGT
195 AACTCTTTCACCAGTATACTTTCCAGAACTGGT
*
5610616 TTGCTTCATTGTCTTCCACTTGGCGGCCTATCTAACAAACTACAAGAAGGCAAGCAAAACTACAT
1 TTGCTTCATTGTCTTCCACTT---GGCCTATCTAACAAACTACAAGAAGGCAAGC---A-GAC--
* *
5610681 TATAAAAAAAAAAAAAAACTTTTAAAATTAAAATAAAAAAGAAATCCAAAACACCAAGGCCAAAT
57 TAT-----AAAAAAGAAACTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAAT
** * * *
5610746 CCATAACCTTGACTAC-ATACTCTAAATCAATTGGGTTCAGAAAAAGAACAG-CTCGGAAAAGGA
117 CCAGCACCTTGCCTACTA-ACTCTAAATCAATTGGGTTCAAAAAAAGAACAGCCT-GGAAATGGA
* *
5610809 CAAATCATTCAAAAACACTCTTTCACCAGT
180 CGAATCATTCAAAAAAACTCTTTCACCAGT
5610839 TTCCTTTCTT
Statistics
Matches: 395, Mismatches: 36, Indels: 30
0.86 0.08 0.07
Matches are distributed among these distances:
226 4 0.01
227 170 0.43
228 1 0.00
230 31 0.08
233 54 0.14
234 1 0.00
237 3 0.01
240 3 0.01
241 119 0.30
242 9 0.02
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (227 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGACTATAAAAAA
GAAACTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCAGCACCTTGCCT
ACTAACTCTAAATCAATTGGGTTCAAAAAAAGAACAGCCTGGAAATGGACGAATCATTCAAAAAA
ACTCTTTCACCAGTATACTTTCCAGAACTGGT
Found at i:5617385 original size:12 final size:12
Alignment explanation
Indices: 5617368--5617394 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5617358 GGTCACTTAA
5617368 AAATCTTTGACT
1 AAATCTTTGACT
5617380 AAATCTTTGACT
1 AAATCTTTGACT
5617392 AAA
1 AAA
5617395 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:5618235 original size:18 final size:16
Alignment explanation
Indices: 5618221--5618267 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
5618211 AATTATATCA
5618221 TTTTATTTAAATATAT
1 TTTTATTTAAATATAT
*
5618237 TTTTATTTTTAAAT-TAA
1 TTTTA--TTTAAATATAT
5618254 TTTT-TTTAAATATA
1 TTTTATTTAAATATA
5618268 AATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.26
15 2 0.07
16 5 0.19
17 6 0.22
18 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATTTAAATATAT
Found at i:5618240 original size:16 final size:16
Alignment explanation
Indices: 5618215--5618268 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5618205 ATTTTTAATT
*
5618215 ATATCATTTTATTTAA
1 ATATAATTTTATTTAA
*
5618231 ATATATTTTTATTTTTAA
1 ATATAATTTTA--TTTAA
5618249 AT-TAATTTT-TTTAA
1 ATATAATTTTATTTAA
5618263 ATATAA
1 ATATAA
5618269 ATAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.22
15 3 0.09
16 9 0.28
17 6 0.19
18 7 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATAATTTTATTTAA
Found at i:5618299 original size:29 final size:29
Alignment explanation
Indices: 5618252--5618336 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
5618242 TTTTTAAATT
*
5618252 AATTTTTTTAAATATAAATAAAAATTAAAA
1 AATTATTTT-AATATAAATAAAAATTAAAA
* *
5618282 AATTATTTTAATATAAATTCAAAATTAAAT
1 AATTATTTTAATATAAA-TAAAAATTAAAA
* * *
5618312 ATTTA-TTTAATTTAAATTAAAATTA
1 AATTATTTTAATATAAATAAAAATTA
5618337 TTAACTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.17
29 18 0.38
30 22 0.46
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTATTTTAATATAAATAAAAATTAAAA
Found at i:5618306 original size:30 final size:29
Alignment explanation
Indices: 5618252--5618336 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
5618242 TTTTTAAATT
* *
5618252 AATTTTTTTAAATATAAATAAAAATTAAAA
1 AATTATTTT-AATATAAATTAAAATTAAAA
*
5618282 AATTATTTTAATATAAATTCAAAATTAAAT
1 AATTATTTTAATATAAATT-AAAATTAAAA
* *
5618312 ATTTA-TTTAATTTAAATTAAAATTA
1 AATTATTTTAATATAAATTAAAATTA
5618337 TTAACTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 7 0.14
29 21 0.43
30 21 0.43
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTATTTTAATATAAATTAAAATTAAAA
Found at i:5618334 original size:23 final size:22
Alignment explanation
Indices: 5618303--5618351 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
5618293 TATAAATTCA
* *
5618303 AAATTAAA-TATTTATTTAATTT
1 AAATTAAATTATTAACTT-ATTT
5618325 AAATTAAAATTATTAACTTATTT
1 AAATT-AAATTATTAACTTATTT
5618348 AAAT
1 AAAT
5618352 ATTATCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 11 0.48
24 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTAAATTATTAACTTATTT
Found at i:5618345 original size:28 final size:29
Alignment explanation
Indices: 5618262--5618349 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
5618252 AATTTTTTTA
* * *
5618262 AATATAAA-TAAAAATTAAAAAATTATTTT
1 AATATAAATTCAAAATTAAATACTTA-TTT
*
5618291 AATATAAATTCAAAATTAAATATTTATTT
1 AATATAAATTCAAAATTAAATACTTATTT
* *
5618320 AATTTAAATT-AAAATT-ATTAACTTATTT
1 AATATAAATTCAAAATTAAAT-ACTTATTT
5618348 AA
1 AA
5618350 ATATTATCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.04
28 15 0.29
29 20 0.39
30 14 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AATATAAATTCAAAATTAAATACTTATTT
Found at i:5619984 original size:2 final size:2
Alignment explanation
Indices: 5619977--5620003 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5619967 AGTCAAACAA
5619977 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
5620004 AAAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5625299 original size:2 final size:2
Alignment explanation
Indices: 5625292--5625342 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
5625282 CTGCAGAAAT
*
5625292 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5625334 TA TA CA TA T
1 TA TA TA TA T
5625343 CAAGAAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5625565 original size:2 final size:2
Alignment explanation
Indices: 5625558--5625583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5625548 CAGAATACAA
5625558 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
5625584 TCTTGTCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5630344 original size:26 final size:26
Alignment explanation
Indices: 5630310--5630362 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5630300 CTAGGGTTTA
5630310 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
5630336 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
5630362 T
1 T
5630363 CAGAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTATTACTTTATTATAACAAGT
Found at i:5634059 original size:12 final size:12
Alignment explanation
Indices: 5634042--5634068 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5634032 GGTCACTTAA
5634042 AAATCTTTGACT
1 AAATCTTTGACT
5634054 AAATCTTTGACT
1 AAATCTTTGACT
5634066 AAA
1 AAA
5634069 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:5634902 original size:18 final size:18
Alignment explanation
Indices: 5634875--5634937 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
5634865 TTTAAATATC
*
5634875 TTTAATTATATTATTTTA
1 TTTAAATATATTATTTTA
5634893 TTTAAATATATT-TTTATA
1 TTTAAATATATTATTT-TA
**
5634911 TTTAAAT-TAAAATTTTA
1 TTTAAATATATTATTTTA
5634928 TTTAAATATA
1 TTTAAATATA
5634938 AATAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.36
18 25 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAAATATATTATTTTA
Found at i:5634940 original size:17 final size:17
Alignment explanation
Indices: 5634887--5634940 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
5634877 TAATTATATT
*
5634887 ATTTTATTTAAATATAT
1 ATTTTATTTAAATATAA
*
5634904 TTTTATATTTAAAT-TAAA
1 ATTT-TATTTAAATAT-AA
5634922 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
5634939 AT
1 AT
5634941 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:5634985 original size:45 final size:44
Alignment explanation
Indices: 5634903--5634991 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
5634893 TTTAAATATA
*
5634903 TTTTTATATTTAAATTAAAATTTTATTTAAATATAAATA-AATTT
1 TTTTTATATTTAAATTAAAATTTTACTT-AATATAAATATAATTT
* *
5634947 TTTTTATTTTTTAAATTAAAATTATTGACTT-ATTTAAATATAATT
1 TTTTTA-TATTTAAATTAAAATT-TT-ACTTAATATAAATATAATT
5634992 ATAAAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
44 6 0.16
45 23 0.61
46 6 0.16
47 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (44 bp):
TTTTTATATTTAAATTAAAATTTTACTTAATATAAATATAATTT
Found at i:5634997 original size:30 final size:30
Alignment explanation
Indices: 5634975--5635033 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
5634965 AAATTATTGA
* *
5634975 CTTATTTAAATATAATTATAAAA-TATAAAT
1 CTTAATTAAATA-AATAATAAAATTATAAAT
5635005 CTTAATTAAATAAATAATAAAATTA-AAAT
1 CTTAATTAAATAAATAATAAAATTATAAAT
5635034 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
CTTAATTAAATAAATAATAAAATTATAAAT
Found at i:5635033 original size:29 final size:30
Alignment explanation
Indices: 5634975--5635031 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5634965 AAATTATTGA
* *
5634975 CTTATTTAAATATAATTATAAAATATAAAT
1 CTTAATTAAATATAATAATAAAATATAAAT
5635005 CTTAATTAAATA-AATAATAAAAT-TAAA
1 CTTAATTAAATATAATAATAAAATATAAA
5635032 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 11 0.44
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (30 bp):
CTTAATTAAATATAATAATAAAATATAAAT
Found at i:5635138 original size:27 final size:27
Alignment explanation
Indices: 5635056--5635139 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
5635046 TATTTCAAAT
*
5635056 AAAATTTTTAAAAGTT-T-AAAA-TAT-
1 AAAATTTTT-AAATTTATAAAAATTATA
* * * *
5635080 AAATTTTTTTAATTTATAAAAATAACA
1 AAAATTTTTAAATTTATAAAAATTATA
*
5635107 TAAATTTTTAAATTTATAAAAATTATA
1 AAAATTTTTAAATTTATAAAAATTATA
5635134 AAAATT
1 AAAATT
5635140 AAGCCTTCAA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
23 4 0.09
24 9 0.20
25 4 0.09
26 1 0.02
27 27 0.60
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
AAAATTTTTAAATTTATAAAAATTATA
Found at i:5635314 original size:18 final size:20
Alignment explanation
Indices: 5635289--5635338 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
5635279 TGATATATTT
5635289 TATTTTATATTA-TTAATAA
1 TATTTTATATTATTTAATAA
*
5635308 T-TTTTATA-TATTTTATAA
1 TATTTTATATTATTTAATAA
5635326 TATATTTATATTA
1 TAT-TTTATATTA
5635339 CATAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 14 0.54
19 2 0.08
20 6 0.23
21 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATATTATTTAATAA
Found at i:5635319 original size:20 final size:20
Alignment explanation
Indices: 5635289--5635336 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5635279 TGATATATTT
5635289 TATTT-TATATTATTAATAAT-
1 TATTTATATATT-TT-ATAATA
5635309 T-TTTATATATTTTATAATA
1 TATTTATATATTTTATAATA
5635328 TATTTATAT
1 TATTTATAT
5635337 TACATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.20
19 6 0.24
20 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATATATTTTATAATA
Found at i:5635832 original size:19 final size:19
Alignment explanation
Indices: 5635808--5635844 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5635798 AGCTTTATTA
5635808 TTGATTAAGATTTTTGATG
1 TTGATTAAGATTTTTGATG
5635827 TTGATTAAGATTTTTGAT
1 TTGATTAAGATTTTTGAT
5635845 ATTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (19 bp):
TTGATTAAGATTTTTGATG
Found at i:5637030 original size:35 final size:33
Alignment explanation
Indices: 5636974--5637043 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
5636964 AATATGCAAT
*
5636974 AGAGTGTGTGACGAGTAAAACACAAAAAAAAGAAC
1 AGAGTGAGTGACGAGT-AAA-ACAAAAAAAAGAAC
* *
5637009 AGAGTGAGTGATGAGTCAAACAAAAAAAAGAAC
1 AGAGTGAGTGACGAGTAAAACAAAAAAAAGAAC
5637042 AG
1 AG
5637044 TGTTCCAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 16 0.50
34 2 0.06
35 14 0.44
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.11
Consensus pattern (33 bp):
AGAGTGAGTGACGAGTAAAACAAAAAAAAGAAC
Found at i:5642808 original size:102 final size:102
Alignment explanation
Indices: 5642628--5642818 Score: 292
Period size: 102 Copynumber: 1.9 Consensus size: 102
5642618 GATGACTACG
* * *
5642628 CTGCAACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
* * *
5642693 GATGGACTCTTTTAACCAAAAAATCTGAAAAAATATC
66 AATAGACTATTTTAACCAAAAAATCTGAAAAAATATC
* * *
5642730 CTGCAACCAAACATATTTGAGACACTAGTCATTATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
*
5642795 AATATACTATTTTAACCAAAAAAT
66 AATAGACTATTTTAACCAAAAAAT
5642819 ACTAACAAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
AATAGACTATTTTAACCAAAAAATCTGAAAAAATATC
Found at i:5644140 original size:2 final size:2
Alignment explanation
Indices: 5644135--5644201 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
5644125 CACATACACA
* *
5644135 TG TG TG TG TT TG TG TG TG TG TT TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5644177 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5644202 ATATATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:5647181 original size:2 final size:2
Alignment explanation
Indices: 5647119--5647168 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
5647109 CAGAACGCAA
5647119 AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5647160 AG AG AG AG A
1 AG AG AG AG A
5647169 CGTTGGAGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5647446 original size:28 final size:30
Alignment explanation
Indices: 5647414--5647469 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5647404 AAATAAAAAA
* *
5647414 TTTATTTAA-TACAATTTAAATT-TTAAAT
1 TTTATTTAATTAAAATTAAAATTATTAAAT
5647442 TTTATTTAATTAAAATTAAAATTATTAA
1 TTTATTTAATTAAAATTAAAATTATTAA
5647470 CTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 11 0.46
30 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATTTAATTAAAATTAAAATTATTAAAT
Found at i:5647475 original size:56 final size:56
Alignment explanation
Indices: 5647371--5647478 Score: 128
Period size: 56 Copynumber: 1.9 Consensus size: 56
5647361 ATATTTTTAT
*
5647371 ATTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAAATTTATTTAATACA
1 ATTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAAACTTATTTAATACA
* * * * * **
5647427 ATTTAAATTTTAAATTTTATTTAATTA-AAATTAAAATTATTAACTTATTTAA
1 ATTTAAA-TTAAAAATTTATTTAAATATAAATAAAAATAAAAAACTTATTTAA
5647479 ATATTATCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 27 0.63
57 16 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (56 bp):
ATTTAAATTAAAAATTTATTTAAATATAAATAAAAATAAAAAACTTATTTAATACA
Found at i:5647760 original size:21 final size:21
Alignment explanation
Indices: 5647704--5647789 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
5647694 TTCCCTTTAC
* *
5647704 TTTATTT-TACATAATTTTTA
1 TTTATTTATAAATAATTTATA
* * *
5647724 ATTA-TGATATATAATTTAT-
1 TTTATTTATAAATAATTTATA
* *
5647743 TTTATATTATTAATAATTTTTA
1 TTTAT-TTATAAATAATTTATA
5647765 TTTATTTATAAATAATATTTATA
1 TTTATTTATAAAT-A-ATTTATA
5647788 TT
1 TT
5647790 ACATAATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.08
20 13 0.27
21 18 0.37
22 6 0.12
23 8 0.16
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (21 bp):
TTTATTTATAAATAATTTATA
Found at i:5647789 original size:23 final size:24
Alignment explanation
Indices: 5647737--5647789 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 24
5647727 ATGATATATA
*
5647737 ATTTAT-TTTATATTATTAATAAT
1 ATTTATATTTATATTATAAATAAT
5647760 -TTT-TATTTAT-TTATAAATAAT
1 ATTTATATTTATATTATAAATAAT
5647781 ATTTATATT
1 ATTTATATT
5647790 ACATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATATTTATATTATAAATAAT
Found at i:5647829 original size:14 final size:16
Alignment explanation
Indices: 5647795--5647829 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5647785 ATATTACATA
5647795 ATTTTAATATATATAT
1 ATTTTAATATATATAT
5647811 ATTTTAATA-ATAT-T
1 ATTTTAATATATATAT
5647825 ATTTT
1 ATTTT
5647830 TATTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 4 0.21
16 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATATATATAT
Found at i:5648107 original size:54 final size:54
Alignment explanation
Indices: 5647994--5648121 Score: 128
Period size: 53 Copynumber: 2.4 Consensus size: 54
5647984 TATTACTATC
5647994 ATTTTAT-ATTTTAAAAAATAATTTAATAAAAAAATGATACTTCAAAATTTATTA
1 ATTTTATAATTTTAAAAAATAATTTAATAAAAAAATGATACTT-AAAATTTATTA
*
5648048 A--TTATAATTATTAATAAATACATTTAATAATAAAAAT-ATA--TATAAATTT-TTA
1 ATTTTATAATT-TTAAAAAATA-ATTTAATAA-AAAAATGATACTTA-AAATTTATTA
*
5648100 ATTTTAT-ATTTTATAATAATAA
1 ATTTTATAATTTTA-AAAAATAA
5648122 AAAAATATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
52 13 0.21
53 18 0.29
54 14 0.22
55 12 0.19
56 6 0.10
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (54 bp):
ATTTTATAATTTTAAAAAATAATTTAATAAAAAAATGATACTTAAAATTTATTA
Found at i:5650648 original size:32 final size:32
Alignment explanation
Indices: 5650607--5650671 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5650597 AACACAAATT
*
5650607 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
5650639 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
1 AGCAGAACCAAGATAAAACAAAACAGGTCCAC
5650671 A
1 A
5650672 AATCCTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (32 bp):
AGCAGAACCAAGATAAAACAAAACAGGTCCAC
Found at i:5653057 original size:2 final size:2
Alignment explanation
Indices: 5653050--5653087 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5653040 ACGAAGAAAT
5653050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5653088 AAGAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5658017 original size:46 final size:46
Alignment explanation
Indices: 5657950--5658041 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
5657940 TAAAGTAAGT
5657950 AGACTTTTTTTAGCATGGAAGATCCTGTCAAATTGTTCATAAATTG
1 AGACTTTTTTTAGCATGGAAGATCCTGTCAAATTGTTCATAAATTG
5657996 AGACTTTTTTTAGCATGGAAGATCCTGTCAAATTGTTCATAAATTG
1 AGACTTTTTTTAGCATGGAAGATCCTGTCAAATTGTTCATAAATTG
5658042 TAAATTAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (46 bp):
AGACTTTTTTTAGCATGGAAGATCCTGTCAAATTGTTCATAAATTG
Found at i:5661863 original size:12 final size:12
Alignment explanation
Indices: 5661846--5661872 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5661836 GGTCACTTAA
5661846 AAATCTTTGACT
1 AAATCTTTGACT
5661858 AAATCTTTGACT
1 AAATCTTTGACT
5661870 AAA
1 AAA
5661873 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:5662696 original size:18 final size:18
Alignment explanation
Indices: 5662669--5662726 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
5662659 TTTAAATATC
*
5662669 TTTAATTATATTATTTTA
1 TTTAAATATATTATTTTA
**
5662687 TTTAAATATATT-TCAATA
1 TTTAAATATATTAT-TTTA
5662705 TTT-AA-AT-TTATTTTA
1 TTTAAATATATTATTTTA
5662720 TTTAAAT
1 TTTAAAT
5662727 TAAAGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 3 0.10
18 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAATATATTATTTTA
Found at i:5662714 original size:28 final size:28
Alignment explanation
Indices: 5662657--5662717 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5662647 ATGTTTAAAA
* *
5662657 TATTTAAATATCTTTAATTATATTATTT
1 TATTTAAATATATTTAATTATATTAATT
5662685 TATTTAAATATATTTCAA-TAT-TTAAATT
1 TATTTAAATATATTT-AATTATATT-AATT
5662713 TATTT
1 TATTT
5662718 TATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 25 0.86
29 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTTAAATATATTTAATTATATTAATT
Found at i:5662723 original size:15 final size:15
Alignment explanation
Indices: 5662679--5662727 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
5662669 TTTAATTATA
5662679 TTATTTTATTTAAAT
1 TTATTTTATTTAAAT
*
5662694 ATATTTCAATATTTAAAT
1 TTATTT---TATTTAAAT
5662712 TTATTTTATTTAAAT
1 TTATTTTATTTAAAT
5662727 T
1 T
5662728 AAAGTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 15 0.52
18 14 0.48
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTTATTTAAAT
Found at i:5662730 original size:38 final size:37
Alignment explanation
Indices: 5662651--5662730 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 37
5662641 ATTTTTATGT
* * *
5662651 TTAAAATATTTAAATATCTTTAATTATATTATTTTAT
1 TTAAAATATTTAAATATCTTAAATTATATTATTTAAA
* *
5662688 TTAAATATATTTCAATAT-TTAAATTTATTTTATTTAAA
1 TTAAA-ATATTTAAATATCTTAAA-TTATATTATTTAAA
5662726 TTAAA
1 TTAAA
5662731 GTTATTAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 9 0.25
38 27 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (37 bp):
TTAAAATATTTAAATATCTTAAATTATATTATTTAAA
Found at i:5663370 original size:2 final size:2
Alignment explanation
Indices: 5663365--5663394 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5663355 ATTGATCAAA
*
5663365 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5663395 GATTATGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5665131 original size:102 final size:102
Alignment explanation
Indices: 5664955--5665142 Score: 268
Period size: 102 Copynumber: 1.8 Consensus size: 102
5664945 GATGACTACG
* * * * *
5664955 CTGCAAGCAGACATATTTGAGACGCTAGTTATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAAACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
* * *
5665020 GATGGACTATTTTAACCAAAAAATCTGAAAAAATATC
66 AATAGACTATTTGAACCAAAAAATCTGAAAAAATATC
* * *
5665057 CTGCAACCAAACATATTTGAAACGCTAGTCATTATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAAACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
*
5665122 AATATACTATTTGAACCAAAA
66 AATAGACTATTTGAACCAAAA
5665143 TATACTAACA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAAACGCTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
AATAGACTATTTGAACCAAAAAATCTGAAAAAATATC
Found at i:5666461 original size:2 final size:2
Alignment explanation
Indices: 5666456--5666485 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5666446 ACACATACAC
*
5666456 GT GT GT GT GT GT GT GT GT AT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5666486 ATATAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:5669679 original size:15 final size:15
Alignment explanation
Indices: 5669643--5669684 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
5669633 CCCACCACTA
* *
5669643 AAAGCCCAACTCTTC
1 AAAGCCTAACTCTGC
5669658 AAAGCCTAACTCTGC
1 AAAGCCTAACTCTGC
5669673 AAAGCCT-ACTCT
1 AAAGCCTAACTCT
5669685 AAAAGCCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.33, C:0.36, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAGCCTAACTCTGC
Found at i:5669701 original size:32 final size:33
Alignment explanation
Indices: 5669664--5669728 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
5669654 CTTCAAAGCC
*
5669664 TAACTCTGCAAAGCCTACTCTAAAAGCC-AACA
1 TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
* * *
5669696 TAACTCTTCAAAGCCCATTTTAAAAGCCGAACA
1 TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
5669729 CAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (33 bp):
TAACTCTGCAAAGCCCACTCTAAAAGCCGAACA
Found at i:5669864 original size:3 final size:3
Alignment explanation
Indices: 5669856--5669900 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5669846 ATTTATCTTA
*
5669856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5669901 AAAGATGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5673241 original size:32 final size:32
Alignment explanation
Indices: 5673200--5673264 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5673190 AACACAAATT
5673200 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCATGATAAAACAAAACAGGTCCAC
5673232 AGCAGAACCATGATAAAACAAAACAGGTCCAC
1 AGCAGAACCATGATAAAACAAAACAGGTCCAC
5673264 A
1 A
5673265 AATCCTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.09
Consensus pattern (32 bp):
AGCAGAACCATGATAAAACAAAACAGGTCCAC
Found at i:5677370 original size:19 final size:19
Alignment explanation
Indices: 5677346--5677383 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5677336 GATAGTTGCC
5677346 TCATAAAGTTGCTCCCGAA
1 TCATAAAGTTGCTCCCGAA
*
5677365 TCATAAAGTTTCTCCCGAA
1 TCATAAAGTTGCTCCCGAA
5677384 GTACATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (19 bp):
TCATAAAGTTGCTCCCGAA
Found at i:5677737 original size:2 final size:2
Alignment explanation
Indices: 5677730--5677778 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
5677720 ATGCAGAAAT
* * ** *
5677730 TA TA TA TA TA TA TA TA TG TA TG TA TA TA CG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5677772 TA TA TA T
1 TA TA TA T
5677779 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5677842 original size:8 final size:8
Alignment explanation
Indices: 5677730--5677842 Score: 73
Period size: 8 Copynumber: 13.6 Consensus size: 8
5677720 ATGCAGAAAT
*
5677730 TATATATA
1 TATATGTA
*
5677738 TATATATA
1 TATATGTA
*
5677746 TGTATGTA
1 TATATGTA
5677754 TATACGTGTATA
1 TATA--TG--TA
*
5677766 TATATATA
1 TATATGTA
*
5677774 TATATGTG
1 TATATGTA
* * *
5677782 TGTGTGTG
1 TATATGTA
* *
5677790 TGTGTGTA
1 TATATGTA
*
5677798 TATACGTA
1 TATATGTA
* *
5677806 TATATCTG
1 TATATGTA
5677814 TATATGTA
1 TATATGTA
5677822 TATATGTA
1 TATATGTA
5677830 TATATGTA
1 TATATGTA
5677838 TATAT
1 TATAT
5677843 CTACATACAT
Statistics
Matches: 84, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
8 75 0.89
10 3 0.04
12 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.49
Consensus pattern (8 bp):
TATATGTA
Found at i:5681542 original size:2 final size:2
Alignment explanation
Indices: 5681535--5681568 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5681525 TCATTGATCA
5681535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5681569 GATTATTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5683299 original size:102 final size:102
Alignment explanation
Indices: 5683123--5683310 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
5683113 GATGACTACG
* * * *
5683123 CTGCAACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
* **
5683188 GATGGACTATTTAAACCAAAAAATCTGAAAAAATATC
66 AATACACTATTTAAACCAAAAAATCTGAAAAAATATC
* * *
5683225 CTGCAACCAAACATATTTGAGACACTAGTCATAATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
*
5683290 AATACACTATTTTAACCAAAA
66 AATACACTATTTAAACCAAAA
5683311 TATACTAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
AATACACTATTTAAACCAAAAAATCTGAAAAAATATC
Found at i:5684319 original size:304 final size:305
Alignment explanation
Indices: 5683767--5684374 Score: 1173
Period size: 304 Copynumber: 2.0 Consensus size: 305
5683757 GAAAAATTAA
5683767 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAAAGCATTTTTCTTCACAGTT
1 TATCAACCATGAACGGTAGTTATGGCTCTAAC--AAAAAAAAAAAAAGCATTTTTCTTCACAGTT
5683832 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
64 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
*
5683897 TCTTATCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAAT
129 TCTTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAAT
5683962 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
194 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
5684027 TTTGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
259 TTTGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
5684074 TATCAACCATGAACGGTAGTTATGGCTCTAAC-AAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
1 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
5684138 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
66 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
*
5684203 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAATAT
131 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAATAT
5684268 GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
196 GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
5684333 TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAA
261 TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAA
5684375 ATGTTGACAT
Statistics
Matches: 299, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
304 267 0.89
307 32 0.11
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (305 bp):
TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAATAT
GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
Found at i:5691146 original size:12 final size:12
Alignment explanation
Indices: 5691129--5691155 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5691119 GGTCACTTAA
5691129 AAATCTTTGACT
1 AAATCTTTGACT
5691141 AAATCTTTGACT
1 AAATCTTTGACT
5691153 AAA
1 AAA
5691156 GTCTACGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:5691742 original size:1 final size:1
Alignment explanation
Indices: 5691697--5691724 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5691687 GGAAGGGGAC
5691697 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
5691725 GGAAAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5691994 original size:18 final size:17
Alignment explanation
Indices: 5691942--5692010 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
5691932 TCAAAAATTT
* *
5691942 TATTTTTATGTTTAAAA
1 TATTTTTATTTTTAATA
* *
5691959 TATTTAAATATCTTTAATTA
1 TATTT--TTATTTTTAA-TA
5691979 TATTATTT-TTTTTAATA
1 TATT-TTTATTTTTAATA
5691996 TATTTTTATTTTTAA
1 TATTTTTATTTTTAA
5692011 ATTAAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
16 3 0.07
17 18 0.43
18 6 0.14
19 9 0.21
20 5 0.12
21 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (17 bp):
TATTTTTATTTTTAATA
Found at i:5691999 original size:17 final size:18
Alignment explanation
Indices: 5691971--5692024 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
5691961 TTTAAATATC
5691971 TTTAATTATATTATTT-TT
1 TTTAATTATATT-TTTATT
5691989 TTTAA-TATATTTTTATT
1 TTTAATTATATTTTTATT
*
5692006 TTTAAATTA-AATTTTATT
1 TTT-AATTATATTTTTATT
5692024 T
1 T
5692025 AAATATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 16 0.50
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAATTATATTTTTATT
Found at i:5692100 original size:25 final size:25
Alignment explanation
Indices: 5692071--5692120 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5692061 TATTAACTTA
* *
5692071 TTTAAATATATTATAAAATAAAAAT
1 TTTAAATAAAATATAAAATAAAAAT
*
5692096 TTTAAATAAAATATAAAATTAAAAT
1 TTTAAATAAAATATAAAATAAAAAT
5692121 AATTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAAATAAAATATAAAATAAAAAT
Found at i:5692120 original size:18 final size:18
Alignment explanation
Indices: 5692083--5692122 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5692073 TAAATATATT
*
5692083 ATAAAATAAAAATTTTAA
1 ATAAAATAAAAATTTAAA
5692101 ATAAAATATAAAA-TTAAA
1 ATAAAATA-AAAATTTAAA
5692119 ATAA
1 ATAA
5692123 TTTTTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAATAAAAATTTAAA
Found at i:5692203 original size:27 final size:29
Alignment explanation
Indices: 5692157--5692212 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
5692147 TTTACAAGTT
**
5692157 TAAAATATAATTTTTGAA-TTTATAAAAA
1 TAAAATATAATTTTCAAATTTTATAAAAA
5692185 TAAAATA-AATTTTCAAATTTTATAAAAA
1 TAAAATATAATTTTCAAATTTTATAAAAA
5692213 ATTTAAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TAAAATATAATTTTCAAATTTTATAAAAA
Found at i:5694932 original size:102 final size:102
Alignment explanation
Indices: 5694756--5694943 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
5694746 GATGACTACG
* * * *
5694756 CTGCAACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
* **
5694821 GATGGACTATTTAAACCAAAAAATCTGAAAAAATATC
66 AATACACTATTTAAACCAAAAAATCTGAAAAAATATC
* * *
5694858 CTGCAACCAAACATATTTGAGACACTAGTCATAATTTTACAGGAAATGGAATAAGATAAGATGCC
1 CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
*
5694923 AATACACTATTTTAACCAAAA
66 AATACACTATTTAAACCAAAA
5694944 TATACTAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATAATCTTACAGGAAATAGAATAAGATAAGATACC
AATACACTATTTAAACCAAAAAATCTGAAAAAATATC
Found at i:5695952 original size:304 final size:305
Alignment explanation
Indices: 5695400--5696007 Score: 1164
Period size: 304 Copynumber: 2.0 Consensus size: 305
5695390 GAAAAATTAA
5695400 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAAAGCATTTTTCTTCACAGTT
1 TATCAACCATGAACGGTAGTTATGGCTCTAAC--AAAAAAAAAAAAAGCATTTTTCTTCACAGTT
5695465 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
64 GTTAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACA
*
5695530 TCTTATCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAAT
129 TCTTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAAT
5695595 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
194 ATGAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAG
5695660 TTTGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
259 TTTGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
5695707 TATCAACCATGAACGGTAGTTATGGCTCTAAC-AAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
1 TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
5695771 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
66 TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
*
5695836 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCATTTTTGAAGTTAAAATAT
131 TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAATAT
*
5695901 GAGGTATCAATACCATCTATACATAAATTTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
196 GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
5695966 TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAA
261 TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAA
5696008 ATGTTGACAT
Statistics
Matches: 298, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
304 266 0.89
307 32 0.11
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (305 bp):
TATCAACCATGAACGGTAGTTATGGCTCTAACAAAAAAAAAAAAAGCATTTTTCTTCACAGTTGT
TAATGTCAATATTATCAAGAGAATACTATCATATTCAACGCATCTTTTTAAGGTAGCGCAACATC
TTACCATACAACGTGACAAACAGCAGCTATCACATGAATGTTTTCCAGTTTTGAAGTTAAAATAT
GAGGTATCAATACCATCTATACATAAAATTTAATATATTTATTGAGAGAAAATTTCCGGCAAGTT
TGGGCCAATGTCATTTTATAACGGCCAAAAACTGAGTGACAATAT
Found at i:5697931 original size:2 final size:2
Alignment explanation
Indices: 5697924--5697951 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5697914 TCATTGATCA
5697924 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
5697952 GATTATTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5699686 original size:102 final size:102
Alignment explanation
Indices: 5699510--5699693 Score: 278
Period size: 102 Copynumber: 1.8 Consensus size: 102
5699500 ACTACGCTGG
* * * * * *
5699510 AACCAGACATATTTGAGACGCTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACCGATG
1 AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
5699575 GACTATTTTAACCAAAAAATCTGAAAAAATATCCTGC
66 GACTATTTTAACCAAAAAATCTGAAAAAATATCCTGC
* * *
5699612 AACCAAACATATTTGAGACACTAGTCATTATTTTACAGGAAATGGAATAAGATAAAATGCCAATA
1 AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
*
5699677 TACTATTTTAACCAAAA
66 GACTATTTTAACCAAAA
5699694 TATACTAACA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 72 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (102 bp):
AACCAAACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAAATACCAATA
GACTATTTTAACCAAAAAATCTGAAAAAATATCCTGC
Found at i:5703286 original size:96 final size:96
Alignment explanation
Indices: 5703179--5703373 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
5703169 GACAAAAGAG
5703179 ACGTTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTT
1 ACGTTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTT
5703244 TAAGGCGGTTTGAGAGTACAGCTAAGCACTA
66 TAAGGCGGTTTGAGAGTACAGCTAAGCACTA
*
5703275 ACGTTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATGAAAAGAGAAAGGAGGAAAGTT
1 ACGTTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTT
5703340 TAAGGCGGTTTGAGAGTACAGCTAAGCACTA
66 TAAGGCGGTTTGAGAGTACAGCTAAGCACTA
5703371 ACG
1 ACG
5703374 GTCACTTAAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (96 bp):
ACGTTAGAATTCAGAAGAACAAAATGAGGTTGGAAATCGGTATAAAAAGAGAAAGGAGGAAAGTT
TAAGGCGGTTTGAGAGTACAGCTAAGCACTA
Found at i:5710283 original size:28 final size:28
Alignment explanation
Indices: 5710251--5710307 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5710241 ATGGCCAAAA
5710251 TATAAGAGGTTATGGCCGTAGCCAGTTC
1 TATAAGAGGTTATGGCCGTAGCCAGTTC
5710279 TATAAGAGGTTATGGCCGTAGCCAGTTC
1 TATAAGAGGTTATGGCCGTAGCCAGTTC
5710307 T
1 T
5710308 TCAGTTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (28 bp):
TATAAGAGGTTATGGCCGTAGCCAGTTC
Found at i:5718492 original size:12 final size:12
Alignment explanation
Indices: 5718475--5718501 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5718465 GGTCACTTAA
5718475 AAATCTTTGACT
1 AAATCTTTGACT
5718487 AAATCTTTGACT
1 AAATCTTTGACT
5718499 AAA
1 AAA
5718502 GTTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATCTTTGACT
Found at i:5719185 original size:2 final size:2
Alignment explanation
Indices: 5719148--5719172 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5719138 CAGTACGTAA
5719148 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5719173 CGTTGGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5719350 original size:18 final size:18
Alignment explanation
Indices: 5719323--5719365 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5719313 TTAAAATATC
*
5719323 TTTAATTATATCATTT-TA
1 TTTAAATATAT-ATTTATA
*
5719341 TTTAAATATATTTTTATA
1 TTTAAATATATATTTATA
5719359 TTTAAAT
1 TTTAAAT
5719366 TAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAATATATATTTATA
Found at i:5719376 original size:15 final size:16
Alignment explanation
Indices: 5719356--5719385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5719346 ATATATTTTT
5719356 ATATTTAAAT-TAAAA
1 ATATTTAAATATAAAA
5719371 ATATTTAAATATAAA
1 ATATTTAAATATAAA
5719386 TAAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTTAAATATAAAA
Found at i:5720842 original size:21 final size:21
Alignment explanation
Indices: 5720800--5720844 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5720790 GCTTTGAATG
* *
5720800 TAATAAAGATTTCTGCTCTAA
1 TAATAAAGATTTATGATCTAA
* *
5720821 TAATACAGATTTATGATGTAA
1 TAATAAAGATTTATGATCTAA
5720842 TAA
1 TAA
5720845 AGCAATCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
TAATAAAGATTTATGATCTAA
Found at i:5723843 original size:2 final size:2
Alignment explanation
Indices: 5723792--5723831 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5723782 CAGTCCGTAA
*
5723792 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5723832 GTTGGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5724034 original size:18 final size:17
Alignment explanation
Indices: 5724007--5724069 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
5723997 TTAAAATATC
*
5724007 TTTAATTATATCATTTTA
1 TTTAAATATAT-ATTTTA
*
5724025 TTTAAATATATTTTTATA
1 TTTAAATATATATTT-TA
*
5724043 TTTAAAT-TAAAATTTTA
1 TTTAAATAT-ATATTTTA
5724060 TTTAAATATA
1 TTTAAATATA
5724070 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 14 0.37
18 24 0.63
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATATATATTTTA
Found at i:5724072 original size:17 final size:17
Alignment explanation
Indices: 5724019--5724072 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
5724009 TAATTATATC
*
5724019 ATTTTATTTAAATATAT
1 ATTTTATTTAAATATAA
*
5724036 TTTTATATTTAAAT-TAAA
1 ATTT-TATTTAAATAT-AA
5724054 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
5724071 AT
1 AT
5724073 AAAAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:5724101 original size:24 final size:23
Alignment explanation
Indices: 5724046--5724103 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
5724036 TTTTATATTT
* *
5724046 AAATTAAAATTTTATTTAAATAT
1 AAATTAAAAATTTATTTAAATAC
* *
5724069 AAATAAAAAATTTATTTTAATAC
1 AAATTAAAAATTTATTTAAATAC
*
5724092 AAATTCAAAATT
1 AAATTAAAAATT
5724104 AAGTGTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTAAAAATTTATTTAAATAC
Found at i:5724429 original size:40 final size:39
Alignment explanation
Indices: 5724385--5724478 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 39
5724375 TAAAAAAAAA
*
5724385 ATATTACTAATTTTTTTA-ATTATGATAT-ATATTTTATTTT
1 ATATTACTAATTTTTTTATA-TATGATATGA-ATATTA-TTT
* ** *
5724425 ATATTATTAATAATTTTATATATTATATGAATATTATTT
1 ATATTACTAATTTTTTTATATATGATATGAATATTATTT
5724464 ATATTACATAATTTT
1 ATATTAC-TAATTTT
5724479 AATACATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
39 9 0.21
40 32 0.74
41 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (39 bp):
ATATTACTAATTTTTTTATATATGATATGAATATTATTT
Found at i:5724430 original size:24 final size:22
Alignment explanation
Indices: 5724398--5724452 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
5724388 TTACTAATTT
5724398 TTTTA-ATTATGATATATATTTTA
1 TTTTATATTATGA-ATA-ATTTTA
*
5724421 TTTTATATTATTAATAATTTTA
1 TTTTATATTATGAATAATTTTA
5724443 TATATTATAT
1 T-T-TTATAT
5724453 GAATATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.25
23 9 0.32
24 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATATTATGAATAATTTTA
Found at i:5724464 original size:22 final size:20
Alignment explanation
Indices: 5724418--5724467 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5724408 GATATATATT
5724418 TTATTT-TATATTATTAATA
1 TTATTTATATATTATTAATA
*
5724437 AT-TTTATATATTATATGAATA
1 TTATTTATATATTAT-T-AATA
5724458 TTATTTATAT
1 TTATTTATAT
5724468 TACATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 9 0.36
20 1 0.04
21 5 0.20
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTTATATATTATTAATA
Found at i:5727886 original size:48 final size:48
Alignment explanation
Indices: 5727811--5727907 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
5727801 AGCAAATGTC
*
5727811 AGACTTTTCGTCCTTTTATCTGTCTTCCTTCGACCCAAGAGCATGTTT
1 AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
*
5727859 AGACTTTTCGTCTTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
1 AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
5727907 A
1 A
5727908 ACGTAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (48 bp):
AGACTTTTCGTCCTTTTATCTGCCTTCCTTCGACCCAAGAGCATGTTT
Found at i:5728065 original size:17 final size:17
Alignment explanation
Indices: 5728045--5728080 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5728035 TTATTTAAAT
5728045 AATAAAAATAATTTTTA
1 AATAAAAATAATTTTTA
* *
5728062 AATATAAATTATTTTTA
1 AATAAAAATAATTTTTA
5728079 AA
1 AA
5728081 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAAAATAATTTTTA
Found at i:5728775 original size:15 final size:16
Alignment explanation
Indices: 5728748--5728780 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5728738 AAATTCCAAT
5728748 TTATTACAAAATTTAC
1 TTATTACAAAATTTAC
5728764 TTATTA-AAAATTTAC
1 TTATTACAAAATTTAC
5728779 TT
1 TT
5728781 TGTACAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTACAAAATTTAC
Found at i:5728895 original size:211 final size:203
Alignment explanation
Indices: 5728597--5728992 Score: 544
Period size: 211 Copynumber: 1.9 Consensus size: 203
5728587 ATATTATTTT
** *
5728597 TTTATGTCATAATCGTATTTAAAATATTATATATTTTATATAAATTTTAACATATAAAAATTTAT
1 TTTATGTCATAATCGTATGCAAAATATTATATATTTTATACAAATTTTAACATATAAAAATTTAT
* * *
5728662 AATTTATAAATTTTACCATATTTATCTATTCTTATTATATAATTAAATTTATATGATAATATAGT
66 AATTTATAAATTTTACCATATTTATCTATTCTTATTATATAATTAAATTTAGATGATAATACACT
5728727 AAAATATAATAAAATTCCAATTTATTACAAAATTTACTTATTAAAAA-TTTACTTTGTACAATAA
131 -AAATATAATAAAATT--AATTTATT--AAAATTTA-TTATTAAAAATTTTACTTT-TACAATAA
5728791 CACATAAATTATCTA
189 CACATAAATTATCTA
* * *
5728806 TTTATGTCATAATTGTATGCAAAATATTATATATTTTATACAATTTTTTAACATGTTAAAAATTT
1 TTTATGTCATAATCGTATGCAAAATATTATATATTTTATACAA-ATTTTAACAT-ATAAAAATTT
* * * *
5728871 ATTATTTATAAATTTTGA-CATATTTATTTATTCTTATTATATCATTAAATTTAGATTATAATAC
64 ATAATTTATAAATTTT-ACCATATTTATCTATTCTTATTATATAATTAAATTTAGATGATAATAC
* * *
5728935 ACTAAATATAATAAAATTATTTTGTTAAATTTTATTATTAAAAATTTTACTTTTACAA
128 ACTAAATATAATAAAATTAATTTATTAAAATTTATTATTAAAAATTTTACTTTTACAA
5728993 CAACGCACAA
Statistics
Matches: 167, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
205 15 0.09
206 15 0.09
208 6 0.04
209 39 0.23
210 24 0.14
211 67 0.40
212 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (203 bp):
TTTATGTCATAATCGTATGCAAAATATTATATATTTTATACAAATTTTAACATATAAAAATTTAT
AATTTATAAATTTTACCATATTTATCTATTCTTATTATATAATTAAATTTAGATGATAATACACT
AAATATAATAAAATTAATTTATTAAAATTTATTATTAAAAATTTTACTTTTACAATAACACATAA
ATTATCTA
Found at i:5729937 original size:54 final size:54
Alignment explanation
Indices: 5729877--5729987 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
5729867 TAAAATTAAC
*
5729877 ATAATGAAATTGAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
1 ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
*
5729931 ATAATGAAATTAAAATTATATAGCAATCCAATATTCAATAAAATTTAACATGAA
1 ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
5729985 ATA
1 ATA
5729988 TAGACAATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (54 bp):
ATAATGAAATTAAAATTATATAGCAATCAAATATTCAATAAAATTTAACATGAA
Found at i:5732180 original size:17 final size:18
Alignment explanation
Indices: 5732158--5732191 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5732148 AAATAAGAAC
5732158 CATCAAAGA-AATTTATT
1 CATCAAAGATAATTTATT
*
5732175 CATCAATGATAATTTAT
1 CATCAAAGATAATTTAT
5732192 CAAAATCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
CATCAAAGATAATTTATT
Found at i:5739107 original size:13 final size:13
Alignment explanation
Indices: 5739089--5739115 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5739079 GACAGTTTAG
5739089 GCTCTTCTGGAAA
1 GCTCTTCTGGAAA
5739102 GCTCTTCTGGAAA
1 GCTCTTCTGGAAA
5739115 G
1 G
5739116 AAGATGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (13 bp):
GCTCTTCTGGAAA
Done.