Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:264073 original size:212 final size:212
Alignment explanation
Indices: 263364--264277 Score: 1184
Period size: 213 Copynumber: 4.3 Consensus size: 212
263354 AAAAAAAAAA
*
263364 CAAAAAACAAACAATGAACATCCAAATTTTAAACAAATATGGCCTCTAATCATATCAATTTCACT
1 CAAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACT
* *
263429 ATCTGGAAAACAAGACACAAATAATCAAGCAATTGGCAAAGTCAAT----AAACAACAATCCTTT
66 ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCTCT
* * * *
263490 AATCGTGCTTCCCGGACAACAACCTTGGGAGCCACGGCCGGGAACAGATCGACAATTTAAGTAGC
131 AACCGTGC-TCCCGGACAACAACATCGGGAGCCACGGCCGGGAACAGATCGACAACTTAAGTAGC
* *
263555 TCTACATGTTCCTATAGC
195 TCTACATGCTCCTATACC
* *
263573 AAAAAAACAAACAATGGACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACT
1 CAAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACT
**
263638 ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATAAAGAAACAACAATCCTC-
66 ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCTCT
* * *
263702 -A-CGTGCCTCCCGGACAACAACCTCGGGAGCCATGGCATGGGAACAGATCGACAACTTAAGTAG
131 AACCGTG-CTCCCGGACAACAACATCGGGAGCCACGGC-CGGGAACAGATCGACAACTTAAGTAG
*
263765 CTCTACATGCTCTTATACC
194 CTCTACATGCTCCTATACC
* * * *
263784 AAAAAAAAACAAACAATGAACATCCAGATTTTCAACAAATATTGCTTCTAATCATATCAATTTCA
1 --CAAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCA
* *
263849 CTATCCGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAATAACAATCCT
64 CTATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCT
* * * * * * *
263914 CTAACCATGACTCCCGGACAACAATATCGGGAGACACGGTCGGGAAGATATCGACAACTTGAGTA
129 CTAACCGTG-CTCCCGGACAACAACATCGGGAGCCACGGCCGGGAACAGATCGACAACTTAAGTA
*
263979 GCTCTACATGTTCCTATA-C
193 GCTCTACATGCTCCTATACC
* * * * * *
263998 CAAAAAACTATCAATGAACATCCAGATTTTCAACAAATATGACCTCTAATCATACCATTTTCACT
1 CAAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACT
264063 ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCTCT
66 ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCTCT
* * * * *
264128 AACCGTGTCTTCCGGAAAACAAAGATATTGGGAG--ACGGCCGGGAACAGATCGACAACTTGAGT
131 AACCGTG-CTCCCGGACAAC--A-ACATCGGGAGCCACGGCCGGGAACAGATCGACAACTTAAGT
* *
264191 AGCTCCACATGCTCATATACCC
192 AGCTCTACATGCTCCTATA-CC
* * ** * *
264213 CAAAAAAAACAAGCAATGAA-ATCCACATTTTCAACAAATATGTTCTCTAATCACAGCAATTTCA
1 C--AAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCA
264277 C
64 C
264278 ACGTATAATC
Statistics
Matches: 625, Mismatches: 62, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
209 107 0.17
210 31 0.05
211 42 0.07
212 136 0.22
213 176 0.28
214 2 0.00
215 49 0.08
216 67 0.11
217 15 0.02
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (212 bp):
CAAAAAACAAACAATGAACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACT
ATCTGGAAAACAAGACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAACAACAATCCTCT
AACCGTGCTCCCGGACAACAACATCGGGAGCCACGGCCGGGAACAGATCGACAACTTAAGTAGCT
CTACATGCTCCTATACC
Found at i:264117 original size:425 final size:423
Alignment explanation
Indices: 263257--264277 Score: 1329
Period size: 425 Copynumber: 2.4 Consensus size: 423
263247 AGCCACTTCC
* * *
263257 CAACAGTCCTCTAACCGTGCCTCCCGGACAACAACCTCAGGAGACACGGCCGGGAACAGATCGGC
1 CAACAATCCTC-AACCGTGCCTCCCGGACAACAACCTCGGGAG-CACGGCCGGGAACAGATCGAC
*
263322 AACTTGAGTAGCTCTACATGCTCCTATACCCAAAAAAAAAAACAAAAAACAAACAATGAACATCC
64 AACTTGAGTAGCTCTACATGCTCATATACCC--------AAA-AAAAAACAAACAATGAACATCC
* * * *
263387 AAATTTTAAACAAATATGGCCTCTAATCATATCAATTTCACTATCTGGAAAACAAGACACAAATA
120 AAATTTTCAACAAATATTGCTTCTAATCATATCAATTTCACTATCCGGAAAACAAGACACAAATA
* * * * *
263452 ATCAAGCAATTGGCAAAGTCAATAAACAACAATCCTTTAATCGTGCTTCCCGGACAACAACCTTG
185 ATCAAGCAATTGGCAAAGTCAATAAACAACAATCCTCTAACCATGCTTCCCGGACAACAACATCG
* *
263517 GGAGCCACGGCCGGGAACAGATCGACAATTTAAGTAGCTCTACATGTTCCTATAGCAAAAAAACA
250 GGAGACACGGCCGGGAACAGATCGACAACTTAAGTAGCTCTACATGTTCCTATAGCAAAAAAACA
* * *
263582 AACAATGGACATCCAAATTTTCAACAAATATGGCCTCTAATCATATCAATTTCACTATCTGGAAA
315 AACAATGAACATCCAAATTTTCAACAAATATGACCTCTAATCATACCAATTTCACTATCTGGAAA
263647 ACAAGACACATATAATCAAGCAATTGGCAAAGTCAATAAAGAAA
380 ACAAGACACATATAATCAAGCAATTGGCAAAGTCAATAAAGAAA
* *
263691 CAACAATCCTC-A-CGTGCCTCCCGGACAACAACCTCGGGAGCCATGGCATGGGAACAGATCGAC
1 CAACAATCCTCAACCGTGCCTCCCGGACAACAACCTCGGGAG-CACGGC-CGGGAACAGATCGAC
* * *
263754 AACTTAAGTAGCTCTACATGCTCTTATA-CCAAAAAAAAACAAACAATGAACATCCAGATTTTCA
64 AACTTGAGTAGCTCTACATGCTCATATACCCAAAAAAAAACAAACAATGAACATCCAAATTTTCA
*
263818 ACAAATATTGCTTCTAATCATATCAATTTCACTATCCGGAAAACAAGACACATATAATCAAGCAA
129 ACAAATATTGCTTCTAATCATATCAATTTCACTATCCGGAAAACAAGACACAAATAATCAAGCAA
* *
263883 TTGGCAAAGTCAATGCAGAAATAACAATCCTCTAACCATGAC-TCCCGGACAACAATATCGGGAG
194 TTGGCAAAGTCAAT----AAACAACAATCCTCTAACCATG-CTTCCCGGACAACAACATCGGGAG
* * * * * * *
263947 ACACGGTCGGGAAGATATCGACAACTTGAGTAGCTCTACATGTTCCTATA-CCAAAAAACTATCA
254 ACACGGCCGGGAACAGATCGACAACTTAAGTAGCTCTACATGTTCCTATAGCAAAAAAACAAACA
* *
264011 ATGAACATCCAGATTTTCAACAAATATGACCTCTAATCATACCATTTTCACTATCTGGAAAACAA
319 ATGAACATCCAAATTTTCAACAAATATGACCTCTAATCATACCAATTTCACTATCTGGAAAACAA
**
264076 GACACATATAATCAAGCAATTGGCAAAGTCAATGCAGAAA
384 GACACATATAATCAAGCAATTGGCAAAGTCAATAAAGAAA
* * * ** *
264116 CAACAATCCTCTAACCGTGTCTTCCGGAAAACAAAGATATTGGGAG-ACGGCCGGGAACAGATCG
1 CAACAATCCTC-AACCGTGCCTCCCGGACAAC--A-ACCTCGGGAGCACGGCCGGGAACAGATCG
* * * *
264180 ACAACTTGAGTAGCTCCACATGCTCATATACCCCAAAAAAAACAAGCAATGAA-ATCCACATTTT
62 ACAACTTGAGTAGCTCTACATGCTCATATACCCAAAAAAAAACAAACAATGAACATCCAAATTTT
* * *
264244 CAACAAATA-TGTTCTCTAATCACAGCAATTTCAC
127 CAACAAATATTGCT-TCTAATCATATCAATTTCAC
264278 ACGTATAATC
Statistics
Matches: 519, Mismatches: 54, Indels: 34
0.86 0.09 0.06
Matches are distributed among these distances:
422 104 0.20
423 3 0.01
425 120 0.23
426 81 0.16
427 5 0.01
428 90 0.17
429 24 0.05
430 1 0.00
431 41 0.08
432 40 0.08
434 10 0.02
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (423 bp):
CAACAATCCTCAACCGTGCCTCCCGGACAACAACCTCGGGAGCACGGCCGGGAACAGATCGACAA
CTTGAGTAGCTCTACATGCTCATATACCCAAAAAAAAACAAACAATGAACATCCAAATTTTCAAC
AAATATTGCTTCTAATCATATCAATTTCACTATCCGGAAAACAAGACACAAATAATCAAGCAATT
GGCAAAGTCAATAAACAACAATCCTCTAACCATGCTTCCCGGACAACAACATCGGGAGACACGGC
CGGGAACAGATCGACAACTTAAGTAGCTCTACATGTTCCTATAGCAAAAAAACAAACAATGAACA
TCCAAATTTTCAACAAATATGACCTCTAATCATACCAATTTCACTATCTGGAAAACAAGACACAT
ATAATCAAGCAATTGGCAAAGTCAATAAAGAAA
Found at i:264886 original size:18 final size:21
Alignment explanation
Indices: 264857--264914 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
264847 AAAATTATTT
264857 AAATATTATTATTTTTACTTA
1 AAATATTATTATTTTTACTTA
264878 AAATATTATTATTTTTACTTA
1 AAATATTATTATTTTTACTTA
*
264899 AAATATTAATATTTTT
1 AAATATTATTATTTTT
264915 TTAACATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATATTATTATTTTTACTTA
Found at i:267140 original size:82 final size:83
Alignment explanation
Indices: 267040--267203 Score: 203
Period size: 82 Copynumber: 2.0 Consensus size: 83
267030 AATTTTAGAT
* * * * *
267040 TTTTTTTATCTTTATAATTGAAG-TCCCTAA-TTTTTGTAATCCTACTTTTTATCTTTATAATTG
1 TTTTTTTATCTTTATAATTGAAGAT-CCTAAGTTTTT-CAATCCCACTTTATACCTTTACAATTG
267103 AGGCTC-T-ATTTTTTTCAAA
64 A-GCTCTTGATTTTTTTCAAA
*
267122 TTTTTTTA-CATTTATAATTGATGATCCTAAGTTTTTCAATCCCACTTTATACCTTTACAATTGA
1 TTTTTTTATC-TTTATAATTGAAGATCCTAAGTTTTTCAATCCCACTTTATACCTTTACAATTGA
267186 GCTCTTGATTTTTTTCAA
65 GCTCTTGATTTTTTTCAA
267204 TCTCACTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
81 5 0.07
82 49 0.69
83 17 0.24
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.52
Consensus pattern (83 bp):
TTTTTTTATCTTTATAATTGAAGATCCTAAGTTTTTCAATCCCACTTTATACCTTTACAATTGAG
CTCTTGATTTTTTTCAAA
Found at i:267322 original size:42 final size:43
Alignment explanation
Indices: 267042--267364 Score: 208
Period size: 43 Copynumber: 7.6 Consensus size: 43
267032 TTTTAGATTT
*
267042 TTTTTATCTTTATAATTGAAGT-CCCTAATTTTTGT-AATC-CTAC
1 TTTTTAACTTTATAATTG-AGTCCCCTAATTTTT-TCAATCTC-AC
* * * *
267085 TTTTTATCTTTATAATTGAG-GCTCTATTTTTTTCAAAT-T---
1 TTTTTAACTTTATAATTGAGTCCCCTAATTTTTTC-AATCTCAC
* *
267124 TTTTT-ACATTTATAATTGATGAT--CCTAAGTTTTTCAATCCCAC
1 TTTTTAAC-TTTATAATTGA-G-TCCCCTAATTTTTTCAATCTCAC
* * * * * *
267167 TTTATACCTTTACAATTGAG-CTCTTGATTTTTTTCAATCTCAC
1 TTTTTAACTTTATAATTGAGTCCCCT-AATTTTTTCAATCTCAC
** * * *
267210 TTTTTTCCTTTATAATTGAGACCCCTATTTTTTTTTCAATCCCA-
1 TTTTTAACTTTATAATTGAGTCCCCTA--ATTTTTTCAATCTCAC
* * * *
267254 TTTTTTACTTATATAATTTAGGCCCCTAATTTTGTCAATCTCA-
1 TTTTTAACTT-TATAATTGAGTCCCCTAATTTTTTCAATCTCAC
*
267297 TTTTTAACTTTGA-AATTGAGTCCCCTAATTTTTTTAATCTCAC
1 TTTTTAACTTT-ATAATTGAGTCCCCTAATTTTTTCAATCTCAC
*
267340 TTTTTACCTTTATAATTGAGGTCCC
1 TTTTTAACTTTATAATTGA-GTCCC
267365 TCTGGGATTA
Statistics
Matches: 224, Mismatches: 32, Indels: 47
0.74 0.11 0.16
Matches are distributed among these distances:
38 1 0.00
39 19 0.08
40 10 0.04
41 1 0.00
42 41 0.18
43 105 0.47
44 18 0.08
45 29 0.13
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTTTAACTTTATAATTGAGTCCCCTAATTTTTTCAATCTCAC
Found at i:268480 original size:72 final size:72
Alignment explanation
Indices: 268382--268522 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 72
268372 ATATAGTGGC
* *
268382 GTTTTATCAATAAAACGCCACTATAGATAGACATATTGCGACGTTTTTTCAA-AATACGCCACTA
1 GTTTTATCAATAAAACGCCACTATAGATAGACATATTGCGACG-TTTGTCAAGAAAACGCCACTA
268446 TTATTACG
65 TTATTACG
** * * ** *
268454 GTTTTATTGATAAAACGCCATTATAGATGGATTTATTGCGGCGTTTGTCAAGAAAACGCCACTAT
1 GTTTTATCAATAAAACGCCACTATAGATAGACATATTGCGACGTTTGTCAAGAAAACGCCACTAT
268519 TATT
66 TATT
268523 GCCCCGAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 7 0.12
72 52 0.88
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (72 bp):
GTTTTATCAATAAAACGCCACTATAGATAGACATATTGCGACGTTTGTCAAGAAAACGCCACTAT
TATTACG
Found at i:280058 original size:52 final size:49
Alignment explanation
Indices: 279984--280120 Score: 156
Period size: 45 Copynumber: 2.8 Consensus size: 49
279974 TGTGTGTGTG
* * *
279984 TGTGATTCTTGTTTTGGTTCAAATTTTCAGGTCCAAGTGTTGTGAGTGTGA
1 TGTGATTCTTG-TTTGGCTCAAATTTTCAGATCCAAGTGTTGTG-GTGAGA
* * *
280035 TTTGTGATTCTTGTTTGGCTCAAAATTTCAGATACAA---ATGTGGTGAGA
1 --TGTGATTCTTGTTTGGCTCAAATTTTCAGATCCAAGTGTTGTGGTGAGA
280083 -GTGATTCTTGTTTGGCTCAAATTTTCAGATCCAAGTGT
1 TGTGATTCTTGTTTGGCTCAAATTTTCAGATCCAAGTGT
280121 GATTCTTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
45 32 0.44
48 5 0.07
49 4 0.06
52 20 0.28
53 11 0.15
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (49 bp):
TGTGATTCTTGTTTGGCTCAAATTTTCAGATCCAAGTGTTGTGGTGAGA
Found at i:281323 original size:11 final size:11
Alignment explanation
Indices: 281307--281340 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
281297 ATGTCCACTG
281307 GTCTTTTTCTT
1 GTCTTTTTCTT
281318 GTCTTTTTCTT
1 GTCTTTTTCTT
*
281329 GT-ATTTTCTT
1 GTCTTTTTCTT
281339 GT
1 GT
281341 GCTATGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.03, C:0.15, G:0.12, T:0.71
Consensus pattern (11 bp):
GTCTTTTTCTT
Found at i:284362 original size:16 final size:16
Alignment explanation
Indices: 284319--284365 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
284309 ATGTTAGTTC
* *
284319 GAAATGTTTTTGATTT
1 GAAATATTTTTTATTT
284335 GAAATATTTTTTATTT
1 GAAATATTTTTTATTT
284351 GAAATATTTTTTATT
1 GAAATATTTTTTATT
284366 CGAGTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
GAAATATTTTTTATTT
Found at i:285831 original size:30 final size:30
Alignment explanation
Indices: 285760--285819 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
285750 ACAATTTAAG
*
285760 GCAAAATATTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
285790 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
285820 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:286060 original size:20 final size:21
Alignment explanation
Indices: 286000--286075 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
285990 ATGCAATTAG
286000 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
286021 TACATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
286042 TGCATCGATGCAT-CTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
286062 TGCATCCATGCATC
1 TGCATCGATGCATC
286076 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 19 0.37
21 32 0.63
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:289376 original size:30 final size:30
Alignment explanation
Indices: 289305--289364 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
289295 ACAATTTAAG
289305 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
289335 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
289365 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:289472 original size:21 final size:21
Alignment explanation
Indices: 289446--289503 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
289436 AGGGTGTCAA
* *
289446 AGTGCAGCCACGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
289467 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCATCCCTGC
289488 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
289504 TGTACTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:289542 original size:20 final size:22
Alignment explanation
Indices: 289490--289545 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
289480 ATCCCTGCAG
*
289490 TGCATCCATGCATCTGTACTAA
1 TGCATCCATGCATCAGTACTAA
** *
289512 TGCATATATGCATCAG-GC-AA
1 TGCATCCATGCATCAGTACTAA
289532 TGCATCCATGCATC
1 TGCATCCATGCATC
289546 CAAACAACGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 14 0.50
21 1 0.04
22 13 0.46
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (22 bp):
TGCATCCATGCATCAGTACTAA
Found at i:289592 original size:21 final size:21
Alignment explanation
Indices: 289566--289620 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
289556 ATGCAATTAG
*
289566 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTACCA
289587 TGCATCGATGCAT-CTTACCA
1 TGCATCGATGCATCCTTACCA
*
289607 TGCATCCATGCATC
1 TGCATCGATGCATC
289621 AAGGCTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTACCA
Found at i:290014 original size:34 final size:32
Alignment explanation
Indices: 289975--290044 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
289965 TTTTGTAAAG
* *
289975 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
290009 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
290041 GGGA
1 GGGA
290045 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:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:290816 original size:20 final size:20
Alignment explanation
Indices: 290791--290828 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
290781 TACTGAGTTT
290791 GTATATAAAT-AATTTTTTGA
1 GTATAT-AATGAATTTTTTGA
290811 GTATATAATGAATTTTTT
1 GTATATAATGAATTTTTT
290829 TACACTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
GTATATAATGAATTTTTTGA
Found at i:301837 original size:4 final size:4
Alignment explanation
Indices: 301830--301990 Score: 85
Period size: 4 Copynumber: 39.2 Consensus size: 4
301820 TTGAAATACC
** * * *
301830 TAAA TAAA TAAA TAAA TAAA TTCA -AAA TAAA TAAA TAAA TTTGAG TGGAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA --TAAA T-AAA
* ** * * *
301880 TAAA TAAT TAAA TCTA -AAA TAAA TAAA CAAA TAAA TAAA T-TA GAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
301926 TAAA TGAA TACA TAAA TTCGAAA TAGA TAAA TAAA TAAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA -T--AAA TAAA TAAA TAAA T-AAA TAAA TAAA
* * *
301974 CAAA CAAA TAAA AAAA T
1 TAAA TAAA TAAA TAAA T
301991 TATCTCAAGA
Statistics
Matches: 117, Mismatches: 30, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
3 3 0.03
4 100 0.85
5 8 0.07
6 3 0.03
7 3 0.03
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:301842 original size:23 final size:19
Alignment explanation
Indices: 301788--301825 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
301778 CATGCCCCTT
301788 CAAATAAATAAATTCGAAA
1 CAAATAAATAAATTCGAAA
* *
301807 CAAACAAATAAATTTGAAA
1 CAAATAAATAAATTCGAAA
301826 TACCTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (19 bp):
CAAATAAATAAATTCGAAA
Found at i:301857 original size:19 final size:18
Alignment explanation
Indices: 301835--301973 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 18
301825 ATACCTAAAT
301835 AAATAAATAAATAAATTCA
1 AAATAAATAAATAAATT-A
301854 AAATAAATAAATAAATTTGA
1 AAATAAATAAATAAA-TT-A
* *
301874 GTGGAATAAATAATTAAATCTA
1 ---AAATAAATAAATAAAT-TA
*
301896 AAATAAATAAACAAA-T-
1 AAATAAATAAATAAATTA
* *
301912 AAATAAAT-TAGAAA-T-
1 AAATAAATAAATAAATTA
* * *
301927 AAATGAATACATAAATTCG
1 AAATAAATAAATAAATT-A
*
301946 AAATAGATAAATAAA-TA
1 AAATAAATAAATAAATTA
301963 AAATAAATAAA
1 AAATAAATAAA
301974 CAAACAAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
15 12 0.13
16 12 0.13
17 12 0.13
18 1 0.01
19 39 0.41
20 3 0.03
22 2 0.02
23 14 0.15
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATAAATAAATAAATTA
Found at i:301857 original size:23 final size:22
Alignment explanation
Indices: 301831--301985 Score: 116
Period size: 23 Copynumber: 6.9 Consensus size: 22
301821 TGAAATACCT
*
301831 AAATAAATAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATT-G
** *
301854 AAATAAATAAATAAATTTGAGTG
1 AAATAAATAAATAAA-TAAATTG
* * *
301877 GAATAAATAATTAAATCTAAAAT-
1 AAATAAATAAATAAA--TAAATTG
*
301900 AAATAAACAAATAAATAAATTAG
1 AAATAAATAAATAAATAAATT-G
* *
301923 AAATAAATGAATACATAAATTCG
1 AAATAAATAAATAAATAAATT-G
* *
301946 AAATAGATAAATAAATAAAAT-
1 AAATAAATAAATAAATAAATTG
* *
301967 AAATAAACAAACAAATAAA
1 AAATAAATAAATAAATAAA
301986 AAAATTATCT
Statistics
Matches: 103, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
21 21 0.20
23 76 0.74
24 6 0.06
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (22 bp):
AAATAAATAAATAAATAAATTG
Found at i:301940 original size:27 final size:27
Alignment explanation
Indices: 301877--301942 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
301867 AATTTGAGTG
*
301877 GAATAAATAATTAAATCTAAAATAAAT
1 GAATAAATAAATAAATCTAAAATAAAT
* *
301904 AAACAAATAAATAAAT-TAGAAATAAAT
1 GAATAAATAAATAAATCTA-AAATAAAT
*
301931 GAATACATAAAT
1 GAATAAATAAAT
301943 TCGAAATAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (27 bp):
GAATAAATAAATAAATCTAAAATAAAT
Found at i:304424 original size:24 final size:24
Alignment explanation
Indices: 304396--304447 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
304386 AATTACAAAT
304396 ATTTTTTTATAATTTAATCTTTTA
1 ATTTTTTTATAATTTAATCTTTTA
304420 ATTTTTTTATAATTTAATCTTTTA
1 ATTTTTTTATAATTTAATCTTTTA
304444 ATTT
1 ATTT
304448 GGTCTTGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTTTTATAATTTAATCTTTTA
Found at i:305045 original size:30 final size:31
Alignment explanation
Indices: 304975--305047 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
304965 CGTGGATCTA
*
304975 CCACATCATCATGTACCATGAACTTGACAAG
1 CCACATCATCATGTACCATGAACTCGACAAG
* *
305006 TCA-AGTCATC-TGTACCATGAGCTCGACAAG
1 CCACA-TCATCATGTACCATGAACTCGACAAG
305036 CCACATCATCAT
1 CCACATCATCAT
305048 TTCTGTCCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (31 bp):
CCACATCATCATGTACCATGAACTCGACAAG
Found at i:307725 original size:21 final size:21
Alignment explanation
Indices: 307696--307739 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
307686 ATTCTGACTA
307696 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
307717 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
307738 TC
1 TC
307740 ACAATGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:307801 original size:20 final size:20
Alignment explanation
Indices: 307776--307831 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
307766 CGAATTTGGA
*
307776 AAATCGCAATGTGATTACGT
1 AAATCGCAATGCGATTACGT
*
307796 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGATTACGT
307816 AAATCGCAATGCGATT
1 AAATCGCAATGCGATT
307832 TTCATATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGT
Found at i:309143 original size:13 final size:12
Alignment explanation
Indices: 309125--309168 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
309115 CTTTTCTTCG
309125 ATATTAAAAATAA
1 ATATT-AAAATAA
309138 ATATTAAAATAA
1 ATATTAAAATAA
*
309150 TTTATTTAAAATAA
1 -ATA-TTAAAATAA
309164 ATATT
1 ATATT
309169 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:309169 original size:13 final size:13
Alignment explanation
Indices: 309125--309170 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
309115 CTTTTCTTCG
*
309125 ATATTAAAAATAA
1 ATATTTAAAATAA
309138 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
309150 TTTATTTAAAATAA
1 -ATATTTAAAATAA
309164 ATATTTA
1 ATATTTA
309171 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:310050 original size:15 final size:14
Alignment explanation
Indices: 310026--310067 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
310016 TGACAGTAAG
*
310026 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
310041 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
310055 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
310068 GTCTCTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:310058 original size:20 final size:20
Alignment explanation
Indices: 310026--310073 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
310016 TGACAGTAAG
*
310026 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
310046 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
310066 TTGTCTCT
1 TT-TCTCT
310074 CTCTCTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.12
20 17 0.71
21 3 0.12
22 1 0.04
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:310540 original size:3 final size:3
Alignment explanation
Indices: 310524--310580 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
310514 TGTAATTTTA
*
310524 AAT AAT -AT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
310571 AAT AAT AAT A
1 AAT AAT AAT A
310581 TGAGTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:311229 original size:229 final size:225
Alignment explanation
Indices: 310829--311826 Score: 1258
Period size: 229 Copynumber: 4.4 Consensus size: 225
310819 GCTTTTGATG
* **
310829 AGTTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAATTTCTC
1 AGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTCTC
* * ** * * * * *
310893 TGAAAAAGCTGCTTCATTAAGTGATGGATT-TGAGCAAAAGATTGAACAAATTCTTCTCATTGTG
65 TGGAAAAGATAATCCATCAAGTGATGAATTCAG-GCAAAAGATTGAACAAATTCTTCTCATTATG
* * *
310957 AATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCCCTGGCAATGTTGAT
129 AATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACCTTCCCTGGAAAAGTTGAT
* *
311022 TCATCAAATGATGAATTCAAACAAAAAGTTGAACA
191 CCATCAAATGATGAATTCAAGCAAAAAGTTGAACA
* *
311057 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCGAA
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTC--T
* * ** * *
311121 CTGGAAAA-ACTGATTCATCAAGTGATGGGTT-TGAGCAAAAGATTGAACAAGTTCTTCTCATTA
64 CTGGAAAAGA-TAATCCATCAAGTGATGAATTCAG-GCAAAAGATTGAACAAATTCTTCTCATTA
* * *
311184 TGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAA-CTCTACCTGGAAATGTT
127 TGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACCT-TCCCTGGAAAAGTT
311248 GATCCATCAAATGATGAATTCAAGC-AAAAGATTGAACA
188 GATCCATCAAATGATGAATTCAAGCAAAAAG-TTGAACA
311286 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC-TCTC
* * *
311351 TGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAA-TCTTCTCATTATGA
65 TGGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGATTGAACAAATTCTTCTCATTATGA
* * *
311415 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCAT
130 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCCCTGGAAAAGTTGATCCAT
* * * * *
311480 CAAGTGATGAATTCAGGTAACAGGTTGAACA
195 CAAATGATGAATTCAAGCAAAAAGTTGAACA
* *
311511 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC-TCTC
* * *
311576 TGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAATTCTTCTCATTATGA
65 TGGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGATTGAACAAATTCTTCTCATTATGA
* *
311641 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCAT
130 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCCCTGGAAAAGTTGATCCAT
* * * * *
311706 CAAGTGATGAATTCAGGTAACAGGTTGAACA
195 CAAATGATGAATTCAAGCAAAAAGTTGAACA
* * *
311737 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTCTC
* * *
311802 TTGAAATG-TCAATCCATCAAATGAT
65 TGGAAAAGAT-AATCCATCAAGTGAT
311827 AGATTTGAAT
Statistics
Matches: 710, Mismatches: 45, Indels: 32
0.90 0.06 0.04
Matches are distributed among these distances:
225 171 0.24
226 196 0.28
227 2 0.00
228 97 0.14
229 239 0.34
230 3 0.00
231 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (225 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTCTCT
GGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGATTGAACAAATTCTTCTCATTATGAA
TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCCCTGGAAAAGTTGATCCATC
AAATGATGAATTCAAGCAAAAAGTTGAACA
Found at i:311801 original size:113 final size:113
Alignment explanation
Indices: 310831--311807 Score: 1284
Period size: 113 Copynumber: 8.6 Consensus size: 113
310821 TTTTGATGAG
*
310831 TTCTTCTCATTATGAACTTTC-TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA-TTTCTCT
1 TTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * * * * * *
310894 GAAAAAGCTGCTTCATTAAGTGATGGATT-TGAGCAAAAGATTGAACAAA
65 GGAAAAGATGATCCATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAA
* *
310943 TTCTTCTCATTGTGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT
* * * * * ** * *
311008 CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
63 CTGGAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
* * ****
311059 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* ** * * *
311124 GAAAA-ACTGATTCATCAAGTGATGGGTT-TGAGCAAAAGATTGAACAAG
66 GAAAAGA-TGATCCATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAA
* *
311172 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTC
* * * * * *
311237 -CTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAG
62 TCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
* *
311288 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
311353 GAAAAGATAATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAA
66 GAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
*
311401 -TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
311465 GAAAAGATAATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAA
66 GAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
*
311513 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
311578 GAAAAGATAATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAA
66 GAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
*
311626 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
311691 GAAAAGCTGATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAA
66 GAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
*
311739 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
311804 GAAA
66 GAAA
311808 TGTCAATCCA
Statistics
Matches: 786, Mismatches: 63, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
111 4 0.01
112 143 0.18
113 447 0.57
115 19 0.02
116 173 0.22
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
Found at i:312698 original size:83 final size:83
Alignment explanation
Indices: 312559--313030 Score: 862
Period size: 83 Copynumber: 5.7 Consensus size: 83
312549 GTTCCTACCA
312559 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
312624 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
312642 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
312707 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
312725 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
312790 CAATGATT-GTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
312807 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAC-AATTCATCTTATAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
312870 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
312888 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
312953 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
312971 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCT
313031 TTAAGGATCT
Statistics
Matches: 376, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
80 24 0.06
81 53 0.14
82 55 0.15
83 244 0.65
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
CAATGATTGGTTCTGTCC
Found at i:312995 original size:246 final size:248
Alignment explanation
Indices: 312559--313030 Score: 869
Period size: 246 Copynumber: 1.9 Consensus size: 248
312549 GTTCCTACCA
* *
312559 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTATAAACT
*
312624 CAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
312689 AAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTT
312754 CCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
196 CCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
312807 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAC-AATTCATCTTATAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTATAAACT
312870 CAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
*
312935 AAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTT
*
313000 CCAGAAGATGCTATGAGCACATTCATCTTCT
196 CCAGAAGATGCTATGAGCAAATTCATCTTCT
313031 TTAAGGATCT
Statistics
Matches: 218, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
245 2 0.01
246 171 0.78
247 3 0.01
248 42 0.19
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (248 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTATAAACT
CAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
AAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATGAGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
Found at i:313898 original size:16 final size:16
Alignment explanation
Indices: 313852--313934 Score: 65
Period size: 16 Copynumber: 5.6 Consensus size: 16
313842 CCTTGACCCC
313852 CTTTCTTTTTTC--TT
1 CTTTCTTTTTTCTATT
* *
313866 CTTT-TTTTTCCTCTT
1 CTTTCTTTTTTCTATT
*
313881 TTTTCTTTTTTCTA--
1 CTTTCTTTTTTCTATT
313895 --TT-TTTTTTCTATT
1 CTTTCTTTTTTCTATT
313908 CTTTCTTTTTTCTATTTT
1 CTTTCTTTTTTCTA--TT
313926 CTTTCTTTT
1 CTTTCTTTT
313935 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
11 9 0.16
12 2 0.04
13 6 0.11
14 4 0.07
15 7 0.13
16 16 0.29
18 11 0.20
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTCTTTTTTCTATT
Found at i:313900 original size:18 final size:19
Alignment explanation
Indices: 313852--313918 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
313842 CCTTGACCCC
* *
313852 CTTTCTTTTTTCTTCTTTT
1 CTTTCTTTTTTTTTCTATT
* * *
313871 TTTTCCTCTTTTTTCT-TT
1 CTTTCTTTTTTTTTCTATT
313889 -TTTCTATTTTTTTTCTATT
1 CTTTCT-TTTTTTTTCTATT
313908 CTTTCTTTTTT
1 CTTTCTTTTTT
313919 CTATTTTCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.10
18 11 0.28
19 19 0.49
20 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTCTTTTTTTTTCTATT
Found at i:313920 original size:11 final size:11
Alignment explanation
Indices: 313852--313934 Score: 70
Period size: 11 Copynumber: 7.8 Consensus size: 11
313842 CCTTGACCCC
313852 CTTTCTTTTTT
1 CTTTCTTTTTT
313863 C-TTC-TTTTT
1 CTTTCTTTTTT
* *
313872 -TTTCCTCTTT
1 CTTTCTTTTTT
313882 -TTTCTTTTTT
1 CTTTCTTTTTT
313892 CTATT-TTTTTT
1 CT-TTCTTTTTT
313903 CTATTCTTTCTTT
1 CT-TTCTTT-TTT
*
313916 -TTTCTATTTT
1 CTTTCTTTTTT
313926 CTTTCTTTT
1 CTTTCTTTT
313935 CTTCAAGCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.13
10 18 0.30
11 25 0.42
12 6 0.10
13 3 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTCTTTTTT
Found at i:313927 original size:18 final size:18
Alignment explanation
Indices: 313877--313934 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
313867 TTTTTTTTCC
*
313877 TCTTTTTTCTTTTTTCTAT
1 TCTTTTTTCTATTTTCT-T
313896 T-TTTTTTCTA--TTCTT
1 TCTTTTTTCTATTTTCTT
313911 TCTTTTTTCTATTTTCTT
1 TCTTTTTTCTATTTTCTT
313929 TCTTTT
1 TCTTTT
313935 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 2 0.06
16 13 0.37
18 19 0.54
19 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTTTTCTATTTTCTT
Found at i:313931 original size:27 final size:27
Alignment explanation
Indices: 313852--313937 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
313842 CCTTGACCCC
* *
313852 CTTTCTTTTTTCTTCTTTTTTTTCCTCTT
1 CTTTCTTTTTTC-TATTTTTTTT-CTATT
*
313881 TTTTCTTTTTTCTATTTTTTTTCTATT
1 CTTTCTTTTTTCTATTTTTTTTCTATT
* *
313908 CTTTCTTTTTTCTATTTTCTTTCTTTT
1 CTTTCTTTTTTCTATTTTTTTTCTATT
313935 CTT
1 CTT
313938 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 31 0.61
28 9 0.18
29 11 0.22
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (27 bp):
CTTTCTTTTTTCTATTTTTTTTCTATT
Found at i:324098 original size:154 final size:155
Alignment explanation
Indices: 323859--324167 Score: 611
Period size: 154 Copynumber: 2.0 Consensus size: 155
323849 ATATTTAAAT
323859 AAACATGTAATTTAAACAATAAATTAACAGGAAAGTCAGAATTCATTTCTCCTGTGTGTACACCT
1 AAACATGTAATTTAAACAATAAATTAACAGGAAAGTCAGAATTCATTTCTCCTGTGTGTACACCT
323924 ATTTTGGACAAAATTTCGGCATGACTTCTGATCGGAAGAGTTTCTAAT-TTCTTTATATGCAGAG
66 ATTTTGGACAAAATTTCGGCATGACTTCTGATCGGAAGAGTTTCTAATGTTCTTTATATGCAGAG
323988 TTTCAGATCTAAGAATCAAGGTACC
131 TTTCAGATCTAAGAATCAAGGTACC
324013 AAACATGTAATTTAAACAATAAATTAACAGGAAAGTCAGAATTCATTTCTCCTGTGTGTACACCT
1 AAACATGTAATTTAAACAATAAATTAACAGGAAAGTCAGAATTCATTTCTCCTGTGTGTACACCT
324078 ATTTTGGACAAAATTTCGGCATGACTTCTGATCGGAAGAGTTTCTAATGTTCTTTATATGCAGAG
66 ATTTTGGACAAAATTTCGGCATGACTTCTGATCGGAAGAGTTTCTAATGTTCTTTATATGCAGAG
324143 TTTCAGATCTAAGAATCAAGGTACC
131 TTTCAGATCTAAGAATCAAGGTACC
324168 CGAATTGTCC
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 113 0.73
155 41 0.27
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (155 bp):
AAACATGTAATTTAAACAATAAATTAACAGGAAAGTCAGAATTCATTTCTCCTGTGTGTACACCT
ATTTTGGACAAAATTTCGGCATGACTTCTGATCGGAAGAGTTTCTAATGTTCTTTATATGCAGAG
TTTCAGATCTAAGAATCAAGGTACC
Found at i:324520 original size:28 final size:26
Alignment explanation
Indices: 324489--324565 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 26
324479 AAATACTTAC
324489 AAATAAATAAAACATATAAATATTATGA
1 AAATAAATAAAA-ATATAAATATT-TGA
*
324517 AAAT-AATAAGTAAATATAAAAATTTGA
1 AAATAAATAA--AAATATAAATATTTGA
*
324544 AAAGAAATTAAAAAT-TAAATAT
1 AAATAAA-TAAAAATATAAATAT
324566 ATAACTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
26 6 0.14
27 15 0.36
28 16 0.38
29 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATAAATAAAAATATAAATATTTGA
Found at i:326094 original size:55 final size:55
Alignment explanation
Indices: 326056--326157 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
326046 GGTAGACGTG
326056 GTGGAGG-TGGAACGTTGGTGTGGC-GTGAAGT-TCTCTGGAAGCAGCAGGTAGAC
1 GTGGAGGCTGGAACGTTGGTGTGGCGGTGAAGTCT-TCTGGAAGCAGCAGGTAGAC
326109 GTGGAGGCTGGAACGTTGGTGTGGCGGTGAAGTCTTCTGGAAGCAGCAG
1 GTGGAGGCTGGAACGTTGGTGTGGCGGTGAAGTCTTCTGGAAGCAGCAG
326158 CGGCGGCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
53 7 0.15
54 17 0.37
55 21 0.46
56 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.23
Consensus pattern (55 bp):
GTGGAGGCTGGAACGTTGGTGTGGCGGTGAAGTCTTCTGGAAGCAGCAGGTAGAC
Found at i:326381 original size:3 final size:3
Alignment explanation
Indices: 326373--326420 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
326363 AATATATATT
326373 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
326418 ATA
1 ATA
326421 TGAGTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:327455 original size:20 final size:20
Alignment explanation
Indices: 327430--327496 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
327420 AGAATAATTT
327430 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
327450 ACTATCCCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * **
327470 ACTATCGCGATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
327490 ACTATCG
1 ACTATCG
327497 TAACGAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:327592 original size:20 final size:20
Alignment explanation
Indices: 327544--327592 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
327534 GCGATTCTCT
327544 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
327564 CATTACGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
327584 CGTTGCGAT
1 CGTTGCGAT
327593 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:328325 original size:377 final size:371
Alignment explanation
Indices: 327618--328367 Score: 1383
Period size: 377 Copynumber: 2.0 Consensus size: 371
327608 CTATTCTTCT
327618 TCTGCAAATTGAAACTTGAATGAATTGCATTACTTCAACCAAAAGACAAATACTAACTTCACAGT
1 TCTGCAAATTGAAACTTGAATGAATTGCATTACTTCAACCAAAAGACAAATACTAACTTCACAGT
**
327683 GTTGAAAATTTAAGTTTCAAGAATAAACTACTACTCTTTATGTTGTCATTGAACCTGTACTAAAC
66 GTTGAAAATTTAAGTTTCAAGAATAAACTACTACTCTTTATGTTGTCATTGAACCTACACTAAAC
327748 CTATATGTTGTCCTTTTAAATGTTTATATGCTTACTTCTGGAATTATCTGATGCATTTTGTGAAC
131 CTATATGTTGTCCTTTTAAATGTTTATATGCTTACTTCTGGAATTATCTGATGCATTTTGTGAAC
327813 AATGATATAATAATGACTTGGGTGAATACCGTGCAAGTTTGAAAAATATTTGTCTTTGTTTTCAC
196 AATGATATAATAATGACTTGGGTGAATACCGTGCAAGTTTGAAAAATATTTGTCTTTGTTTTCAC
*
327878 TGTTTGATATCATGTCTGTTTATTTACTGATTTATGTATTAATTTATTTTTAGCGGCCCGCTAAG
261 TGTTTAATATCATGTCTGTTTATTTACTGATTTATGTATTAATTTATTTTTAGCGGCCCGCTAAG
*
327943 GTGGATGCTCTACGTCGGGTTTTTCTTGCAATACGGAGTTCACGCA
326 GTGGATGCTCTACGTCGGGTTTTTCTTGCAAGACGGAGTTCACGCA
*
327989 TCTGCAAATTGAAACTTGAATGAATTGTATTACTTCAACCAAAAGACAAATACTAACTTCACAGT
1 TCTGCAAATTGAAACTTGAATGAATTGCATTACTTCAACCAAAAGACAAATACTAACTTCACAGT
328054 GTTGAAAATTTAAGTTTCAAGAATAAACTACTACTCTTTATGTTGTCATTGAACCTACACTAAAC
66 GTTGAAAATTTAAGTTTCAAGAATAAACTACTACTCTTTATGTTGTCATTGAACCTACACTAAAC
328119 CTATATGTTGTCCTTTTAAATGTTTATATAAGTGCTTACTTCTGGAATGTTATCTGATGCATTTT
131 CTATATGTTGTCCTTTTAAATG-TT-TAT-A-TGCTTACTTCTGGAA--TTATCTGATGCATTTT
*
328184 GTGAACAATGATATAATAATGACTTGGGTGAATAGCGTGCAAGTTTGAAAAATATTTGTCTTTGT
190 GTGAACAATGATATAATAATGACTTGGGTGAATACCGTGCAAGTTTGAAAAATATTTGTCTTTGT
328249 TTTCACTGTTTAATATCATGTCTGTTTATTTACTGATTTATGTATTAATTTATTTTTAGCGGCCC
255 TTTCACTGTTTAATATCATGTCTGTTTATTTACTGATTTATGTATTAATTTATTTTTAGCGGCCC
*
328314 GCTAAGGTGGATGCTCTACGTCGGGTTTTTCTTGTAAGACGGAGTTCACGCA
320 GCTAAGGTGGATGCTCTACGTCGGGTTTTTCTTGCAAGACGGAGTTCACGCA
328366 TC
1 TC
328368 AGACGGCGTG
Statistics
Matches: 366, Mismatches: 7, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
371 149 0.41
372 2 0.01
373 3 0.01
374 1 0.00
375 15 0.04
377 196 0.54
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (371 bp):
TCTGCAAATTGAAACTTGAATGAATTGCATTACTTCAACCAAAAGACAAATACTAACTTCACAGT
GTTGAAAATTTAAGTTTCAAGAATAAACTACTACTCTTTATGTTGTCATTGAACCTACACTAAAC
CTATATGTTGTCCTTTTAAATGTTTATATGCTTACTTCTGGAATTATCTGATGCATTTTGTGAAC
AATGATATAATAATGACTTGGGTGAATACCGTGCAAGTTTGAAAAATATTTGTCTTTGTTTTCAC
TGTTTAATATCATGTCTGTTTATTTACTGATTTATGTATTAATTTATTTTTAGCGGCCCGCTAAG
GTGGATGCTCTACGTCGGGTTTTTCTTGCAAGACGGAGTTCACGCA
Found at i:328538 original size:21 final size:21
Alignment explanation
Indices: 328447--328545 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
328437 GACTCACCTG
*
328447 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
328469 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
328489 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
328510 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
328531 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
328546 TCTCTCCCAA
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 56 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:328544 original size:42 final size:42
Alignment explanation
Indices: 328444--328554 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
328434 CCTGACTCAC
* * *
328444 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
* ** *
328486 CTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGCCA
* * *
328528 CTGTCATCGTTGAAGAGGTCTCTCCCA
1 CTGTCATCGTTCAAGAGGCCTCCCCCA
328555 ACATTCTAGA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:329890 original size:14 final size:14
Alignment explanation
Indices: 329871--329906 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
329861 ATTGTTTAAT
329871 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
329885 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
329899 TGATTTGT
1 TGATTTGT
329907 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:330048 original size:33 final size:34
Alignment explanation
Indices: 330011--330083 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 34
330001 ACAGGCTATT
330011 GCAACGAGAGAATCACAATGCG-AAATGAAAATC
1 GCAACGAGAGAATCACAATGCGAAAATGAAAATC
* *
330044 GCAACGAGTGAATCGCAATGCGAAAATGAAAATC
1 GCAACGAGAGAATCACAATGCGAAAATGAAAATC
330078 GCAACG
1 GCAACG
330084 CGAAATTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (34 bp):
GCAACGAGAGAATCACAATGCGAAAATGAAAATC
Found at i:330118 original size:20 final size:19
Alignment explanation
Indices: 330093--330312 Score: 154
Period size: 19 Copynumber: 11.8 Consensus size: 19
330083 GCGAAATTAG
330093 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
330112 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
330130 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
330146 TTTCGCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
330165 TTTCGCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
330184 TTTCGCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
330203 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* * **
330219 --TCTCGTTACGATAGTCA
1 TTTCGCGTTGCGATTTTCA
**
330236 TTTTCGCGTTGCGATAGTCAA
1 -TTTCGCGTTGCGATTTTC-A
* **
330257 TTCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
* **
330276 TTTCCGTGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
330296 TATTCGCGTTGCAATTT
1 T-TTCGCGTTGCGATTT
330313 CCGTGTTGCA
Statistics
Matches: 168, Mismatches: 18, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.10
16 6 0.04
17 3 0.02
18 4 0.02
19 68 0.40
20 68 0.40
21 3 0.02
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:330158 original size:19 final size:19
Alignment explanation
Indices: 330093--330217 Score: 188
Period size: 19 Copynumber: 6.8 Consensus size: 19
330083 GCGAAATTAG
*
330093 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
330112 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
330130 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
330146 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
330165 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
330184 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
330203 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
330218 CTCTCGTTAC
Statistics
Matches: 97, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 65 0.67
20 12 0.12
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:330272 original size:40 final size:40
Alignment explanation
Indices: 330222--330307 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
330212 GCGATTCTCT
* *
330222 CGTTACGATAGTCATTTTCGCGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CG
*
330262 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
330302 CGTTGC
1 CGTTGC
330308 AATTTCCGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 39 0.93
41 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:332760 original size:24 final size:24
Alignment explanation
Indices: 332726--332779 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
332716 CTGAAAAATC
332726 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
332750 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
332774 ATCAAA
1 ATCAAA
332780 TTTCTAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:333653 original size:20 final size:20
Alignment explanation
Indices: 333633--333846 Score: 259
Period size: 20 Copynumber: 10.7 Consensus size: 20
333623 CGATAGTCAG
*
333633 AATCTCATTGCGATTTACAG-
1 AATCGCATTGCGATTTAC-GT
*
333653 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* * *
333673 ATTTGCAATGCGATTTACGT
1 AATCGCATTGCGATTTACGT
333693 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
333713 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
333733 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
333753 AATCGCATTGCGATTTATGT
1 AATCGCATTGCGATTTACGT
* * *
333773 ATTCGTATTGCGATTTAAGT
1 AATCGCATTGCGATTTACGT
* **
333793 AATCGCATTGCGATTTTCAA
1 AATCGCATTGCGATTTACGT
*
333813 AATTCGCGTTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
333834 ATTCGCATTGCGA
1 AATCGCATTGCGA
333847 ATTAGGAAAA
Statistics
Matches: 167, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
19 1 0.01
20 151 0.90
21 15 0.09
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:333685 original size:40 final size:40
Alignment explanation
Indices: 333638--333846 Score: 285
Period size: 40 Copynumber: 5.2 Consensus size: 40
333628 GTCAGAATCT
*
333638 CATTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTTG
1 CATTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCG
* *
333678 CAATGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
1 CATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
*
333718 CATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCG
1 CATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
* * * *
333758 CATTGCGATTTATGTATTCGTATTGCGATTTAAGTAATCG
1 CATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
* ** *
333798 CATTGCGATTTTCAAAATTCGCGTTGCGATTTACGTATTCG
1 CATTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCG
333839 CATTGCGA
1 CATTGCGA
333847 ATTAGGAAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 120 0.80
41 29 0.19
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
CATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
Found at i:333704 original size:60 final size:60
Alignment explanation
Indices: 333633--333846 Score: 304
Period size: 60 Copynumber: 3.5 Consensus size: 60
333623 CGATAGTCAG
* * *
333633 AATCTCATTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTTGCAATGCGATTTACGT
1 AATCGCATTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
333693 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* * * * * **
333753 AATCGCATTGCGATTTATGTATTCGTATTGCGATTTAAGTAATCGCATTGCGATTTTCAA
1 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
*
333813 AATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 AA-TCGCATTGCGATTTACGTATTCGCATTGCGA
333847 ATTAGGAAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
59 1 0.01
60 110 0.79
61 28 0.20
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (60 bp):
AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:333867 original size:21 final size:21
Alignment explanation
Indices: 333843--333888 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
333833 TATTCGCATT
333843 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
333864 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
333885 GCGA
1 GCGA
333889 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:336121 original size:20 final size:20
Alignment explanation
Indices: 336098--336135 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
336088 TATATAAGAT
336098 TTTAAT-ATTATAAAAATATA
1 TTTAATAATT-TAAAAATATA
336118 TTTAATAATTTAAAAATA
1 TTTAATAATTTAAAAATA
336136 AATAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATAATTTAAAAATATA
Found at i:337207 original size:48 final size:48
Alignment explanation
Indices: 337100--337207 Score: 108
Period size: 48 Copynumber: 2.2 Consensus size: 48
337090 TAAAAAATTG
* * **
337100 TCGAAAAAATTATTATTTATACCGGTTTTGTTATTATTGGACGTTTTA
1 TCGAAAATATTATTATTTATACCAGTTTTGTTATTATTGGACACTTTA
**** * * * *
337148 TCGGTTTTATTATTTTTTTTACCAGTTTTGTTATTGTTTGACACTTTA
1 TCGAAAATATTATTATTTATACCAGTTTTGTTATTATTGGACACTTTA
337196 TCGAAAATATTA
1 TCGAAAATATTA
337208 AAAAACATTA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (48 bp):
TCGAAAATATTATTATTTATACCAGTTTTGTTATTATTGGACACTTTA
Found at i:343308 original size:60 final size:61
Alignment explanation
Indices: 343182--343335 Score: 165
Period size: 60 Copynumber: 2.6 Consensus size: 61
343172 ATACAATAGA
* * * * *
343182 TTGGGGATGAAATT-GAAATACTTAAAAGTTTG-GAGATCAATTTAGAAAGGGGTCATAGTT
1 TTGGGGATGAAATTAG-AATTCTCAAAAGTTTGAGAGATCAATTTAGAAAAGAGTCACAGTT
* *
343242 TGGGGGATGAAATTAGAATTCTCAAAAGTTTGAG-GATCAATTTAGAATAAGATTCACA-TT
1 TTGGGGATGAAATTAGAATTCTCAAAAGTTTGAGAGATCAATTTAGAA-AAGAGTCACAGTT
* *
343302 TTGGGGAT-AAATTTAGAATTTTCAAAAGCTTGAG
1 TTGGGGATGAAA-TTAGAATTCTCAAAAGTTTGAG
343336 TCCTAATTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
59 3 0.04
60 69 0.86
61 8 0.10
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (61 bp):
TTGGGGATGAAATTAGAATTCTCAAAAGTTTGAGAGATCAATTTAGAAAAGAGTCACAGTT
Found at i:344578 original size:41 final size:40
Alignment explanation
Indices: 344496--344578 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
344486 TCAATAAATA
* * *
344496 AATTGTAATAATTTCTTTCTAAAAAAACGCCACAATACATG
1 AATTGTAATAATTTCTTCCT-AAAAAACCCCACAAAACATG
*
344537 AATTGTGATAATTTCTTCCT-AAAAACCCCACTAAAATCATG
1 AATTGTAATAATTTCTTCCTAAAAAACCCCAC-AAAA-CATG
344578 A
1 A
344579 TTTCAGACCG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 10 0.28
40 3 0.08
41 23 0.64
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.31
Consensus pattern (40 bp):
AATTGTAATAATTTCTTCCTAAAAAACCCCACAAAACATG
Found at i:348528 original size:2 final size:2
Alignment explanation
Indices: 348472--348512 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
348462 CCTTCGTGTA
*
348472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
348513 GTATCCGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:348960 original size:6 final size:6
Alignment explanation
Indices: 348936--348988 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
348926 TACACCTGAT
* * *
348936 ATATAC ATATAT ATGTAC ATATAC ATATAC ATATAC ATATAT ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
348984 ATATA
1 ATATA
348989 TGTATGTCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (6 bp):
ATATAC
Found at i:352976 original size:30 final size:30
Alignment explanation
Indices: 352940--353002 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
352930 GTACGCCAAT
** * *
352940 TATATTTTTAATTATTAATATATAAAAATA
1 TATATTTTTAAAAATAAATAAATAAAAATA
352970 TATATTTTTAAAAATAAATAAATAAAAATA
1 TATATTTTTAAAAATAAATAAATAAAAATA
353000 TAT
1 TAT
353003 CATACCCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATATTTTTAAAAATAAATAAATAAAAATA
Found at i:353602 original size:29 final size:27
Alignment explanation
Indices: 353557--353617 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
353547 GAACAAATTT
*
353557 AAAAACTTTATGTACCTATTTTGACTAG
1 AAAAACTTTATGTACCTATTTTGA-TAA
353585 AAAAA-TTTATAGATACCTATTTTGATAA
1 AAAAACTTTAT-G-TACCTATTTTGATAA
353613 AAAAA
1 AAAAA
353618 ATATAAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
28 13 0.43
29 12 0.40
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (27 bp):
AAAAACTTTATGTACCTATTTTGATAA
Found at i:353615 original size:27 final size:26
Alignment explanation
Indices: 353556--353616 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
353546 TGAACAAATT
*
353556 TAAAAACTTTATGTACCTATTTTGAC
1 TAAAAAATTTATGTACCTATTTTGAC
353582 TAGAAAAATTTATAGATACCTATTTTGA-
1 TA-AAAAATTTAT-G-TACCTATTTTGAC
353610 TAAAAAA
1 TAAAAAA
353617 AATATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 2 0.06
27 14 0.45
28 3 0.10
29 12 0.39
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (26 bp):
TAAAAAATTTATGTACCTATTTTGAC
Found at i:353619 original size:29 final size:27
Alignment explanation
Indices: 353557--353617 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
353547 GAACAAATTT
*
353557 AAAAACTTTATGTACCTATTTTGACTA
1 AAAAAATTTATGTACCTATTTTGACTA
*
353584 GAAAAATTTATAGATACCTATTTTGA-TA
1 AAAAAATTTAT-G-TACCTATTTTGACTA
353612 AAAAAA
1 AAAAAA
353618 ATATAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 8 0.28
29 12 0.41
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (27 bp):
AAAAAATTTATGTACCTATTTTGACTA
Found at i:353627 original size:27 final size:29
Alignment explanation
Indices: 353569--353627 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
353559 AAACTTTATG
** *
353569 TACCTATTTTGACTAGAAAAATTTATAGA
1 TACCTATTTTGACTAGAAAAAAATATAAA
353598 TACCTATTTTGA-TA-AAAAAAATATAAA
1 TACCTATTTTGACTAGAAAAAAATATAAA
353625 TAC
1 TAC
353628 AAATTCTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 13 0.48
28 2 0.07
29 12 0.44
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (29 bp):
TACCTATTTTGACTAGAAAAAAATATAAA
Found at i:355725 original size:3 final size:3
Alignment explanation
Indices: 355717--355751 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
355707 GCATGTAAAT
355717 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
355752 TTAAAAGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:355732 original size:13 final size:13
Alignment explanation
Indices: 355714--355755 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
355704 CCTGCATGTA
355714 AATTAATAATAAT
1 AATTAATAATAAT
355727 AATTAATAATAAT
1 AATTAATAATAAT
355740 AA-TAATAA-AAT
1 AATTAATAATAAT
355751 -ATTAA
1 AATTAA
355756 AAGACATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.21
12 6 0.21
13 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:356416 original size:17 final size:17
Alignment explanation
Indices: 356394--356430 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
356384 AACTATAAAG
356394 ACGACGTATAATCAATC
1 ACGACGTATAATCAATC
356411 ACGACGTATAATCAATC
1 ACGACGTATAATCAATC
356428 ACG
1 ACG
356431 GCCTGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (17 bp):
ACGACGTATAATCAATC
Found at i:357304 original size:37 final size:37
Alignment explanation
Indices: 357231--357305 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
357221 GTTGGAAAAT
* *
357231 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
357268 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
357305 A
1 A
357306 AAGGTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:358070 original size:30 final size:29
Alignment explanation
Indices: 358031--358122 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
358021 TAAACACAAT
*
358031 AAATGTAAAGGACTGAAATATAAATACCAG
1 AAATTTAAAGGACTGAAATATAAATA-CAG
* * *
358061 AAATTTAAAGGGCATG-AAT-TAATGTACAT
1 AAATTTAAAGGAC-TGAAATATAA-ATACAG
* *
358090 AAAATTAAAGGACCGAAATATAAATAACAG
1 AAATTTAAAGGACTGAAATATAAAT-ACAG
358120 AAA
1 AAA
358123 AATAAAGTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 20 0.42
30 25 0.52
31 2 0.04
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (29 bp):
AAATTTAAAGGACTGAAATATAAATACAG
Found at i:358129 original size:30 final size:29
Alignment explanation
Indices: 358090--358239 Score: 94
Period size: 30 Copynumber: 5.1 Consensus size: 29
358080 TAATGTACAT
* *
358090 AAAATTAAAGGACCGAAATATAAATAACAG
1 AAAAATAAAGG-CAGAAATATAAATAACAG
* *
358120 AAAAATAAAGTCAGAAATGT-AA-AACA-
1 AAAAATAAAGGCAGAAATATAAATAACAG
* ** * *
358146 TAAAATAAAAGGGTTGAAATATAAATATCAA
1 AAAAAT-AAA-GGCAGAAATATAAATAACAG
* *
358177 AAAAATAAAGG-GGATATATGTAAATAACAG
1 AAAAATAAAGGCAGA-A-ATATAAATAACAG
*
358207 AAAAATAAAGTGCATAGAA-ATAAATAACAG
1 AAAAATAAAG-GCAGA-AATATAAATAACAG
358237 AAA
1 AAA
358240 TGTAAAATCG
Statistics
Matches: 92, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
26 5 0.05
27 7 0.08
28 11 0.12
29 12 0.13
30 48 0.52
31 7 0.08
32 2 0.02
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (29 bp):
AAAAATAAAGGCAGAAATATAAATAACAG
Found at i:358129 original size:59 final size:58
Alignment explanation
Indices: 358031--358188 Score: 160
Period size: 57 Copynumber: 2.7 Consensus size: 58
358021 TAAACACAAT
* ** *
358031 AAATGTAAAGGACTGAAATATAAATACCAGAAATTTAAAGGGCATG-AAT-TAATGTACATA
1 AAAT-TAAAGGACTGAAATATAAATAACAGAAAAATAAAGGGCA-GAAATGTAA--AACATA
* *
358091 AAATTAAAGGACCGAAATATAAATAACAGAAAAATAAA-GTCAGAAATGTAAAACATA
1 AAATTAAAGGACTGAAATATAAATAACAGAAAAATAAAGGGCAGAAATGTAAAACATA
* ** * *
358148 AAATAAAAGGGTTGAAATATAAATATCAAAAAAATAAAGGG
1 AAATTAAAGGACTGAAATATAAATAACAGAAAAATAAAGGG
358189 GATATATGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
57 38 0.46
58 7 0.09
59 33 0.40
60 4 0.05
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (58 bp):
AAATTAAAGGACTGAAATATAAATAACAGAAAAATAAAGGGCAGAAATGTAAAACATA
Found at i:361186 original size:20 final size:20
Alignment explanation
Indices: 361161--361198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
361151 ATAATTGATA
*
361161 AAATTAAAATACTGATAATG
1 AAATTAAAATACTCATAATG
*
361181 AAATTAGAATACTCATAA
1 AAATTAAAATACTCATAA
361199 ATTTTTCGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATTAAAATACTCATAATG
Found at i:373541 original size:2 final size:2
Alignment explanation
Indices: 373534--373574 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
373524 GAATTGCATC
373534 AT AT AT AT AT 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 AT AT AT AT AT A
373575 AGAACTGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:373766 original size:75 final size:75
Alignment explanation
Indices: 373622--373766 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 75
373612 GTGCCCACCA
* *
373622 TGGAATCTGAATTTCTTTATACTAATTATTCATTTTATTGAAGATGCTCACCCTAAAATTTTGTT
1 TGGAATCTGAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCTCACCCTAAAATTTTATT
373687 GTGTCCATCC
66 GTGTCCATCC
* * * *
373697 TGGAAT-TCGAATTTCTTTATATTAGTTATTCATTTTACT-AAGGTG-TCCACCCTGAAATTTTA
1 TGGAATCT-GAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCT-CACCCTAAAATTTTA
373759 TTCGTGTC
64 TT-GTGTC
373767 TGTCCCATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
73 1 0.02
74 21 0.34
75 39 0.64
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (75 bp):
TGGAATCTGAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCTCACCCTAAAATTTTATT
GTGTCCATCC
Found at i:378534 original size:15 final size:15
Alignment explanation
Indices: 378514--378544 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
378504 CATAAATTTT
*
378514 ATTAAAAATATTAAA
1 ATTAAAAATAATAAA
378529 ATTAAAAATAATAAA
1 ATTAAAAATAATAAA
378544 A
1 A
378545 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAAATAATAAA
Found at i:379473 original size:31 final size:30
Alignment explanation
Indices: 379427--379513 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
379417 TTCGATAATA
*
379427 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
379458 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
379489 TAATAAGTATTTTATAAAATTTTAA
1 TAATAA-TATTTTATAATATTTTAA
379514 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:379488 original size:20 final size:21
Alignment explanation
Indices: 379460--379512 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
379450 GATAAATTTA
379460 TTAAT-AATTTTATAA-TATT
1 TTAATAAATTTTATAAGTATT
*
379479 TTAATAAATTTAATAAGTATT
1 TTAATAAATTTTATAAGTATT
379500 TT-ATAAAATTTTA
1 TTAAT-AAATTTTA
379513 AACTTTATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 11 0.38
21 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATAAATTTTATAAGTATT
Found at i:381796 original size:11 final size:11
Alignment explanation
Indices: 381780--381805 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
381770 ACCAGTACGA
381780 CCGGGGTCGGT
1 CCGGGGTCGGT
381791 CCGGGGTCGGT
1 CCGGGGTCGGT
381802 CCGG
1 CCGG
381806 ATTAGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.31, G:0.54, T:0.15
Consensus pattern (11 bp):
CCGGGGTCGGT
Found at i:385793 original size:180 final size:179
Alignment explanation
Indices: 385478--385836 Score: 693
Period size: 180 Copynumber: 2.0 Consensus size: 179
385468 AATGACCAAC
385478 TTTTCTTTAGTTGTTTCTTATTTAAGTTTTACATTCTTAAATGGTGTTATCCCTCTTATTAATAA
1 TTTTCTTTAGTTGTTTCTTATTTAAGTTTTACATTCTTAAATGGTGTTATCCCTCTTATTAATAA
385543 TTGGTTGGGCGTTCAAGAATGTGAAACAAAGCCTCAGTTCTATATGTTGGGTGTTGACTTGGTAT
66 TTGGTTGGGCGTTCAAGAATGTGAAACAAAGCCTCAGTTCTATATGTTGGGTGTTGACTTGGTAT
385608 TAAAAATCCTTGTTTCTTTTCTCTCTATGGTTGATGACTCCAGACCGCT
131 TAAAAATCCTTGTTTCTTTTCTCTCTATGGTTGATGACTCCAGACCGCT
385657 TTTTCTTTAGTTGTTTTCTTATTTAAGTTTTACATTCTTAAATGGTGTTA-CCCTCTTATTAATA
1 TTTTCTTTAGTTG-TTTCTTATTTAAGTTTTACATTCTTAAATGGTGTTATCCCTCTTATTAATA
385721 ATTGGTTGGGCGTTCAAGAATGTGAAACAAAGCCTCAGTTCTATATGTTGGGTGTTTGACTTGGT
65 ATTGGTTGGGCGTTCAAGAATGTGAAACAAAGCCTCAGTTCTATATGTTGGGTG-TTGACTTGGT
385786 ATTAAAAATCCTTGTTTCTTTTCTCTCTATGGTTGATGACTCCAGACCGCT
129 ATTAAAAATCCTTGTTTCTTTTCTCTCTATGGTTGATGACTCCAGACCGCT
385837 GTGCGTTTAC
Statistics
Matches: 178, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
179 81 0.46
180 97 0.54
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (179 bp):
TTTTCTTTAGTTGTTTCTTATTTAAGTTTTACATTCTTAAATGGTGTTATCCCTCTTATTAATAA
TTGGTTGGGCGTTCAAGAATGTGAAACAAAGCCTCAGTTCTATATGTTGGGTGTTGACTTGGTAT
TAAAAATCCTTGTTTCTTTTCTCTCTATGGTTGATGACTCCAGACCGCT
Found at i:392097 original size:28 final size:26
Alignment explanation
Indices: 392066--392130 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
392056 TCTTTGATTA
* *
392066 TTAAAAATATAAAATTATTATATATATT
1 TTAAAAATATAAAA-TATAATA-ATAAT
* *
392094 TTAATAATTTAAAATATAATAATAAT
1 TTAAAAATATAAAATATAATAATAAT
392120 TTAAAATATAT
1 TTAAAA-ATAT
392131 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 9 0.30
27 9 0.30
28 12 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAAAATATAAAATATAATAATAAT
Found at i:392115 original size:15 final size:15
Alignment explanation
Indices: 392095--392148 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
392085 ATATATATTT
392095 TAATAATTTAAAATATAA
1 TAATAATTT-AAA-AT-A
392113 TAATAATTTAAAATA
1 TAATAATTTAAAATA
* *
392128 TATTATTTTAAAATA
1 TAATAATTTAAAATA
392143 TTAATA
1 -TAATA
392149 TATTGGGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 14 0.44
16 6 0.19
17 3 0.09
18 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATTTAAAATA
Found at i:392116 original size:18 final size:18
Alignment explanation
Indices: 392095--392129 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
392085 ATATATATTT
392095 TAATAATTTAAAATATAA
1 TAATAATTTAAAATATAA
392113 TAATAATTTAAAATATA
1 TAATAATTTAAAATATA
392130 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATTTAAAATATAA
Found at i:392436 original size:25 final size:25
Alignment explanation
Indices: 392408--392455 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
392398 TCGTTACAGT
*
392408 GACTTAAAACTTGTCATGTCTAGGC
1 GACTTAAAACTCGTCATGTCTAGGC
* *
392433 GACTTGAAACTCGTTATGTCTAG
1 GACTTAAAACTCGTCATGTCTAG
392456 AATTTTGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
GACTTAAAACTCGTCATGTCTAGGC
Found at i:397526 original size:21 final size:21
Alignment explanation
Indices: 397500--397540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
397490 CTGTAGATCA
397500 ACTGGACACACACACACACAC
1 ACTGGACACACACACACACAC
* * *
397521 ACTGGATAGACATACACACA
1 ACTGGACACACACACACACA
397541 AAAGCACACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.34, G:0.12, T:0.10
Consensus pattern (21 bp):
ACTGGACACACACACACACAC
Found at i:401537 original size:39 final size:36
Alignment explanation
Indices: 401492--401577 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
401482 AACAAGTTGA
* *
401492 AAAATATTTATACATTTTATTTAAAAAATTTAAATTAAT
1 AAAATATTTATACA-TTT-TTTAAAAAATTAAAAAT-AT
* * *
401531 AAAATATATATATATTTTTTACAAAATTAAAAATAT
1 AAAATATTTATACATTTTTTAAAAAATTAAAAATAT
401567 AAAATGATTTA
1 AAAAT-ATTTA
401578 ATGAAATGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 7 0.17
37 18 0.45
38 3 0.08
39 12 0.30
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAATATTTATACATTTTTTAAAAAATTAAAAATAT
Found at i:402096 original size:68 final size:65
Alignment explanation
Indices: 401993--402119 Score: 200
Period size: 68 Copynumber: 1.9 Consensus size: 65
401983 GGTTTAAAAT
* *
401993 AAAAACAAAAAAGATTCTCACAGAGATGACTTGATCACATCAAAATCCTGGATAACTTTTTATTT
1 AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAA-TTTTTATTT
402058 A
65 A
*
402059 AAAAACAAAATAGATTTTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTT
1 AAAAACAAAAAAGA--TTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTT
402120 AAACTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 13 0.23
67 4 0.07
68 39 0.70
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (65 bp):
AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTTTATTTA
Found at i:402128 original size:68 final size:66
Alignment explanation
Indices: 401993--402134 Score: 196
Period size: 68 Copynumber: 2.1 Consensus size: 66
401983 GGTTTAAAAT
* * * *
401993 AAAAACAAAAAAGATTCTCACAGAGATGACTTGATCACATCAAAATCCTGGATAACTTTTTATTT
1 AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTTAACTT
402058 A
66 A
*
402059 AAAAACAAAATAGATTTTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAA-TTTTAAA
1 AAAAACAAAAAAGA--TTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTT-AA
402123 CTTA
63 CTTA
*
402127 AAACACAA
1 AAAAACAA
402135 TTCATGATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 13 0.19
67 4 0.06
68 50 0.75
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (66 bp):
AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTTAACTT
A
Found at i:403429 original size:26 final size:25
Alignment explanation
Indices: 403370--403429 Score: 59
Period size: 26 Copynumber: 2.2 Consensus size: 25
403360 GTTTAATTGT
*
403370 TTTACTTTTTTATTTTATTATTTAAA
1 TTTA-TTTTTTATTTTATGATTTAAA
403396 TATATATTTTTTA-TTTATGATTATAAGA
1 T-T-TATTTTTTATTTTATGATT-TAA-A
403424 TTTATT
1 TTTATT
403430 AAAGATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 13 0.45
27 12 0.41
28 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (25 bp):
TTTATTTTTTATTTTATGATTTAAA
Found at i:414421 original size:21 final size:22
Alignment explanation
Indices: 414385--414425 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
414375 TTAAAATTTA
414385 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
*
414407 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTACCGATACTC
414426 CCTATCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:414483 original size:20 final size:20
Alignment explanation
Indices: 414455--414492 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
414445 TTTTGCAGAA
*
414455 AAATTATCCCCAATGGCTCC
1 AAATCATCCCCAATGGCTCC
414475 AAATCATCCCCAATGGCT
1 AAATCATCCCCAATGGCT
414493 AGAAACGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.24
Consensus pattern (20 bp):
AAATCATCCCCAATGGCTCC
Found at i:416562 original size:26 final size:26
Alignment explanation
Indices: 416538--416622 Score: 125
Period size: 26 Copynumber: 3.3 Consensus size: 26
416528 CCTCGTTTGT
*
416538 CTCTGCGTATCTTCTTCTCCCTTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
* *
416564 CTTTGTGTATCTTCTTCTCCCCTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
**
416590 CTCTTTGTATCTTCTTCTCCCCTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
416616 CTCTGCG
1 CTCTGCG
416623 AAAAATTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.04, C:0.38, G:0.12, T:0.47
Consensus pattern (26 bp):
CTCTGCGTATCTTCTTCTCCCCTTGC
Found at i:420314 original size:2 final size:2
Alignment explanation
Indices: 420307--420344 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
420297 TTAGGTCATT
420307 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
420345 AGAATGTAGA
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:423409 original size:15 final size:15
Alignment explanation
Indices: 423389--423421 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
423379 AACAAATAAT
423389 TTTTTTATATAAATA
1 TTTTTTATATAAATA
*
423404 TTTTTTATTTAAATA
1 TTTTTTATATAAATA
423419 TTT
1 TTT
423422 ATAATTTCAC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTATATAAATA
Found at i:425608 original size:2 final size:2
Alignment explanation
Indices: 425601--425631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
425591 TAATGGTATT
425601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
425632 CATAAGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:426114 original size:58 final size:58
Alignment explanation
Indices: 425999--426184 Score: 162
Period size: 58 Copynumber: 3.2 Consensus size: 58
425989 TGTGGATGAA
* * * * * *
425999 TTTGGGGATAAAAATGGAAATG--CAAAAGTTTAGGGACCATTTTAGAATGATATTCATAG
1 TTTGGGGACAAAAAT-GAAATGTTCAAAAGTTTAAGGACTAATTTAAAATG--AGTCATAG
** * * * *
426058 TTTGGGGATGAAATTGAAATGTTCAAATGTTTAAGGATTAATTTATAATGAGTCATAG
1 TTTGGGGACAAAAATGAAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGTCATAG
* * * *
426116 TTTTGGGACAAAAATGGAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAAGGCCATAG
1 TTTGGGGACAAAAATGAAATGTTCAAAAGTTTAAGGACTAATTTAAAATG-A-GTCATAG
426176 -TTGGGGACA
1 TTTGGGGACA
426185 CATATGATGC
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
58 54 0.52
59 22 0.21
60 27 0.26
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (58 bp):
TTTGGGGACAAAAATGAAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGTCATAG
Found at i:428037 original size:50 final size:50
Alignment explanation
Indices: 427921--428040 Score: 222
Period size: 50 Copynumber: 2.4 Consensus size: 50
427911 ACTCGTTACC
*
427921 TCGACGTGACGAGTTTAAATAAAAAATATTTTTTATTTAAACTCATCATA
1 TCGACGTGACGAGTTTCAATAAAAAATATTTTTTATTTAAACTCATCATA
*
427971 TCGACGTGACGAGTTTCAATAAAAAATATTTTTTATTTAAATTCATCATA
1 TCGACGTGACGAGTTTCAATAAAAAATATTTTTTATTTAAACTCATCATA
428021 TCGACGTGACGAGTTTCAAT
1 TCGACGTGACGAGTTTCAAT
428041 CACCGTAGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (50 bp):
TCGACGTGACGAGTTTCAATAAAAAATATTTTTTATTTAAACTCATCATA
Found at i:437494 original size:142 final size:132
Alignment explanation
Indices: 437238--437565 Score: 334
Period size: 142 Copynumber: 2.4 Consensus size: 132
437228 AGAAAATGAT
* ** * *
437238 ATCTAGTTACTTTAAGACAACCACTTTCTTTAATATTAAAAAATAAATAAATATGATAATTTTTC
1 ATCTAGTTATTTTAAGACCGCCA-GTTC-TTAATATTAAAAAATAAATAAATATGATAAATTTTC
* * *
437303 CTAATAAAATTAGTTAAAATAATTAAATAAGCATGATATTTATTTATTTTTAAAAGACCATAATA
64 CTAATAAAATAAGTTAAAATAATTAAATAAGCAGGATATTTATTTATTTTTAAAAGACCAGAATA
437368 GAAC
129 GAAC
**
437372 ATCTAGTTATTTTAAGATTGCCAGTTCTTAATATTAAAAAATAAATAAATATGATAAATTTTCCT
1 ATCTAGTTATTTTAAGACCGCCAGTTCTTAATATTAAAAAATAAATAAATATGATAAATTTTCC-
* * * *
437437 AAAAATAATAAAAATGAAGTATATATATATATT-TATAAGTAGGATATTTATTTATTTTTAAAAT
65 -----TAAT-AAAAT-AAGT-TA-AAATA-ATTAAATAAGCAGGATATTTATTTATTTTTAAAAG
* * *
437501 ACCCGAATAGGAT
120 ACCAGAATAGAAC
* * * **
437514 GTCTAGTTATTTTAAGACCGTCATTTCTTAATATTTTAAAATAAATAAATAT
1 ATCTAGTTATTTTAAGACCGCCAGTTCTTAATATTAAAAAATAAATAAATAT
437566 TATTATATAT
Statistics
Matches: 160, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
132 36 0.22
133 3 0.02
134 19 0.12
138 4 0.03
139 5 0.03
140 3 0.02
141 2 0.01
142 85 0.53
143 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (132 bp):
ATCTAGTTATTTTAAGACCGCCAGTTCTTAATATTAAAAAATAAATAAATATGATAAATTTTCCT
AATAAAATAAGTTAAAATAATTAAATAAGCAGGATATTTATTTATTTTTAAAAGACCAGAATAGA
AC
Found at i:438924 original size:3 final size:3
Alignment explanation
Indices: 438918--438954 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
438908 ATAATATATT
*
438918 TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
438955 AATTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:438934 original size:16 final size:16
Alignment explanation
Indices: 438906--438947 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
438896 TCCTGGCCTG
438906 TAATAAT-ATATTTAA
1 TAATAATAATATTTAA
438921 TAATAATAATATTTAA
1 TAATAATAATATTTAA
438937 TAATAATAATA
1 TAATAATAATA
438948 ATAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATAATATTTAA
Found at i:442040 original size:14 final size:14
Alignment explanation
Indices: 442029--442058 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
442019 AAAATGAATT
442029 ACATTTTCTGAAAA
1 ACATTTTCTGAAAA
*
442043 ATATTTTCTGAAAA
1 ACATTTTCTGAAAA
442057 AC
1 AC
442059 GTTTCACAAT
Statistics
Matches: 14, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (14 bp):
ACATTTTCTGAAAA
Found at i:442221 original size:28 final size:27
Alignment explanation
Indices: 442168--442223 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 27
442158 TTATTTATCA
442168 TAAAACTAATATTATTATTTTAAATAT
1 TAAAACTAATATTATTATTTTAAATAT
442195 TAAAA-TAAT-TTATTTATTATTAAAATAT
1 TAAAACTAATATTA-TTATT-TT-AAATAT
442223 T
1 T
442224 GTTTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 3 0.12
26 9 0.35
27 7 0.27
28 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAAACTAATATTATTATTTTAAATAT
Found at i:442360 original size:21 final size:22
Alignment explanation
Indices: 442324--442366 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
442314 AGTGTTATAT
442324 TATATTTTAAAAATATTAATTAG
1 TATATTTT-AAAATATTAATTAG
*
442347 TATATTTT-AAATATTTATTA
1 TATATTTTAAAATATTAATTA
442367 AATATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATTTTAAAATATTAATTAG
Found at i:442519 original size:23 final size:23
Alignment explanation
Indices: 442488--442543 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
442478 TATTATTAAA
*
442488 ATAAAAATATAATATC-TTATATT
1 ATAATAATATAAT-TCATTATATT
*
442511 ATAATAATATAATTCATTATTTT
1 ATAATAATATAATTCATTATATT
*
442534 ATTATAATAT
1 ATAATAATAT
442544 TAAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATAATATAATTCATTATATT
Found at i:442561 original size:22 final size:23
Alignment explanation
Indices: 442533--442579 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
442523 TTCATTATTT
442533 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
442555 TATTATATTATTACAAATATTAA
1 TATTATAATATTAAAAATATTAA
442578 TA
1 TA
442580 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:442584 original size:22 final size:22
Alignment explanation
Indices: 442541--442584 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
442531 TTTATTATAA
*
442541 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
442563 TATTACAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
442585 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:443822 original size:13 final size:13
Alignment explanation
Indices: 443804--443828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
443794 TCTCTCTCTC
443804 TATATATATATAA
1 TATATATATATAA
443817 TATATATATATA
1 TATATATATATA
443829 TATTCGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:444607 original size:20 final size:20
Alignment explanation
Indices: 444560--445055 Score: 476
Period size: 20 Copynumber: 24.2 Consensus size: 20
444550 AATGACCAAC
444560 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
444579 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
444599 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
444619 AAGATCGCAATGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
444641 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
* *
444661 AAAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
444681 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
444703 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
444723 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
444743 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
444765 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
444785 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
444805 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
444825 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
444845 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
444865 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
444885 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
444905 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
444927 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
444947 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
444967 TAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
444989 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445009 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
445031 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445051 AAAAT
1 AAAAT
445056 GAGTAAATTC
Statistics
Matches: 403, Mismatches: 40, Indels: 67
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.00
19 32 0.08
20 261 0.65
21 7 0.02
22 92 0.23
23 10 0.02
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:444979 original size:62 final size:60
Alignment explanation
Indices: 444560--445055 Score: 452
Period size: 62 Copynumber: 8.1 Consensus size: 60
444550 AATGACCAAC
** * * * * **
444560 AAAATCGCAACGCGA-TATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTCAG
* * *** * * * *
444619 AAGATCGCAATGCGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
***
444681 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
*** *
444743 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAGAAAATCGCAACGCGATT-CAG
* * *
444805 AGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCAG
*
444865 AAAATCGCAACGCGATTCCAAG--AATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATT--AAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TT-CAG
* *
444927 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGTAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TT-CAG
* * *
444989 AGAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAG
445051 AAAAT
1 AAAAT
445056 GAGTAAATTC
Statistics
Matches: 380, Mismatches: 38, Indels: 35
0.84 0.08 0.08
Matches are distributed among these distances:
59 16 0.04
60 79 0.21
61 12 0.03
62 252 0.66
63 4 0.01
64 15 0.04
65 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (60 bp):
AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
Found at i:444995 original size:42 final size:39
Alignment explanation
Indices: 444622--445048 Score: 404
Period size: 42 Copynumber: 10.4 Consensus size: 39
444612 TGAAAAGAAG
* *
444622 ATCGCAATGCGATCTTCCAAGAATCGCAATGCGA-TTCATAAA
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTTC--AAA
* *
444664 ATCGCAATGCGATT-CATAAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGAT-TT-CAA-A
*
444706 ATCGCAACGCGATT-CAGAAAATCGCAACGCGA-TTCAGAAA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGATTTC--AAA
**
444746 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT-TCAAA
444788 ATCGCAACGCGATTCCAAGAATCGCAACGCGA-TTCAGAAA
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTTC--AAA
444828 ATCGCAACGCGATTCCAAGAATCGCAACGCGA-TTCAGAAA
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTTC--AAA
**
444868 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATT-TCAAA
**
444908 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT-TCAAA
444950 ATCGCAACGCGATT-C-AGTAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATTCCAAG--AATCGCAACGCGAT-TT-CAA-A
*
444992 ATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATTCCA-AGAATCGCAACGCGAT-TT-CAA-A
445034 ATCGCAACGCGATTC
1 ATCGCAACGCGATTC
445049 AGAAAATGAG
Statistics
Matches: 345, Mismatches: 14, Indels: 51
0.84 0.03 0.12
Matches are distributed among these distances:
38 2 0.01
39 5 0.01
40 156 0.45
41 8 0.02
42 169 0.49
43 4 0.01
44 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (39 bp):
ATCGCAACGCGATTCCAAGAATCGCAACGCGATTTCAAA
Found at i:445055 original size:42 final size:39
Alignment explanation
Indices: 444560--445048 Score: 393
Period size: 42 Copynumber: 11.9 Consensus size: 39
444550 AATGACCAAC
* * *
444560 AAAATCGCAACGCGATATCAAAACCGCAACGCGATT-TA
1 AAAATCGCAACGCGATTTCAAAATCGCAACGCGATTCCA
* * **** * *
444598 GAAAAGCGCAACGTTGAAAAGAAGATCGCAATGCGATCTTCCA
1 -AAAATCGCAACG-CGATTTCAAAATCGCAACGCGA--TTCCA
* * *
444641 AGAATCGCAATGCGA-TTCATAAAATCGCAATGCGATT-CA
1 AAAATCGCAACGCGATTTC--AAAATCGCAACGCGATTCCA
444680 TAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CA
1 -AAAATCGCAACGCGAT-TT-CAA-AATCGCAACGCGATTCCA
444722 GAAAATCGCAACGCGA-TTCAGAAAATCGCAACGCGATCTTCCA
1 -AAAATCGCAACGCGATTTC--AAAATCGCAACGCGA--TTCCA
* **
444765 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATT-TCAAAATCGCAACGCGATTCCA
*
444805 AGAATCGCAACGCGA-TTCAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTTC--AAAATCGCAACGCGATTCCA
*
444845 AGAATCGCAACGCGA-TTCAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTTC--AAAATCGCAACGCGATTCCA
* **
444885 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCGATT-TCAAAATCGCAACGCGA--TTCCA
* **
444927 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
1 AAAATCGCAACGCGATT-TCAAAATCGCAACGCGATTCCA
*
444966 GTAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CA
1 -AAAATCGCAACGCGAT-TT-CAA-AATCGCAACGCGATTCCA
445008 GAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 -AAAATCGCAACGCGAT-TT-CAA-AATCGCAACGCGATTC
445049 AGAAAATGAG
Statistics
Matches: 388, Mismatches: 33, Indels: 54
0.82 0.07 0.11
Matches are distributed among these distances:
39 17 0.04
40 171 0.44
41 10 0.03
42 185 0.48
43 5 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (39 bp):
AAAATCGCAACGCGATTTCAAAATCGCAACGCGATTCCA
Found at i:445162 original size:6 final size:6
Alignment explanation
Indices: 445151--445243 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
445141 GACACGTATT
445151 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
445199 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
445244 GACCCGAGAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:445740 original size:5 final size:5
Alignment explanation
Indices: 445732--445791 Score: 102
Period size: 5 Copynumber: 11.6 Consensus size: 5
445722 CCGTCTCGTC
445732 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG
445783 TCGTGG TCG
1 TCG-GG TCG
445792 TGGTAATACG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 43 0.80
6 11 0.20
ACGTcount: A:0.00, C:0.20, G:0.57, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:445941 original size:20 final size:20
Alignment explanation
Indices: 445887--446194 Score: 216
Period size: 20 Copynumber: 15.2 Consensus size: 20
445877 AATTTACTCA
445887 TTTCTTAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
***
445907 TCTTGGAAGATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGAT
445929 TTTCTTAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
*
445949 TTTCTGAATCGCGTTGCGA-
1 TTTCTTAATCGCGTTGCGAT
445968 -TTCTTGGAATCGCGTTGCGAT
1 TTTCTT--AATCGCGTTGCGAT
445989 TTTCTTAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
***
446009 TCTTGGAAGATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGAT
*
446031 TTTCTGAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
*
446051 TTTCTGGAATCGCGTTGCGAT
1 TTTCT-TAATCGCGTTGCGAT
***
446072 TCTTGGAAGAT-GCG-TGCGA-
1 T-TTCTTA-ATCGCGTTGCGAT
* * *
446091 TTTATGAATCGCATTGCGAT
1 TTTCTTAATCGCGTTGCGAT
*** *
446111 TCTTGGAAGATCGTGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGAT
* * * *
446133 CTTCTT-TTCAACGTTGCGCT
1 TTTCTTAATC-GCGTTGCGAT
* *
446153 TTTCTAAATCGCGTTGCGGT
1 TTTCTTAATCGCGTTGCGAT
**
446173 TTTGAT-ATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
446192 TTT
1 TTT
446195 GTTGGTCATT
Statistics
Matches: 227, Mismatches: 43, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.01
18 9 0.04
19 23 0.10
20 106 0.47
21 39 0.17
22 48 0.21
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
TTTCTTAATCGCGTTGCGAT
Found at i:445963 original size:62 final size:60
Alignment explanation
Indices: 445887--446072 Score: 259
Period size: 62 Copynumber: 3.0 Consensus size: 60
445877 AATTTACTCA
*
445887 TTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGAT
1 TTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGAT
445949 TTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGAT
1 TTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGAT
* * *
446009 TCTT-GGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTCTGGAATCGCGTTGCGAT
1 T-TTCTG-A-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCT-TAATCGCGTTGCGAT
446072 T
1 T
446073 CTTGGAAGAT
Statistics
Matches: 115, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
60 35 0.30
61 6 0.05
62 59 0.51
63 15 0.13
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (60 bp):
TTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGAT
Done.