Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009584.1 Hibiscus syriacus cultivar Beakdansim tig00116961_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: 2003061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:223094 original size:12 final size:12
Alignment explanation
Indices: 223077--223114 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
223067 CAATTAGATC
223077 CAAAATCAAGTT
1 CAAAATCAAGTT
*
223089 CAAAATCAAATT
1 CAAAATCAAGTT
*
223101 CATAATCAAGTT
1 CAAAATCAAGTT
223113 CA
1 CA
223115 GGAAAATCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (12 bp):
CAAAATCAAGTT
Found at i:241705 original size:21 final size:19
Alignment explanation
Indices: 241672--241712 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
241662 TGCATCAAGG
241672 TCTTTGTAGAGGCCATGAAA
1 TCTTTGTAGAGGCCAT-AAA
*
241692 TCTTTCGTCGAGGCCATAAA
1 TCTTT-GTAGAGGCCATAAA
241712 T
1 T
241713 TCCTACAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (19 bp):
TCTTTGTAGAGGCCATAAA
Found at i:245113 original size:16 final size:17
Alignment explanation
Indices: 245092--245124 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
245082 ATAAAATTTA
245092 AATTTTAAATAA-AAGG
1 AATTTTAAATAAGAAGG
*
245108 AATTTTATATAAGAAGG
1 AATTTTAAATAAGAAGG
245125 GATACTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
AATTTTAAATAAGAAGG
Found at i:249318 original size:270 final size:277
Alignment explanation
Indices: 248782--249318 Score: 725
Period size: 270 Copynumber: 1.9 Consensus size: 277
248772 TAATATTTAT
* * *
248782 ATTAGTTATATAACAGTTTGTGACGTAATATCTAAAAATGATTTAAATATAAAATATTAAGCATT
1 ATTAGTTATATAACAGTTTGTGACGTAATATCTAAAAATCATTTAAATAGAAAATATTAAGCACT
248847 ATAAATAATATATATGAATAGTACAATATAAATTTATGTTTTTAAATATTACATTATGGTTTTAT
66 ATAAATAATATATATGAATAGTACAATATAAATTTATG--TTT--ATATTACATTATGGTTTTAT
* * * *
248912 TTGATTATTAATTAAAATAAATAAATAAATGCATTTTATGATTTTTAAAGAAACAAAATTTTATT
127 GTGATTATTAATTAAAATAAATAAAGAAATACATTTTAAGATTTTTAAAGAAACAAAATTTTATT
* * *
248977 GGTTTTCAAATAAAAAACGTTTTATACGTTTGGTGTGACATCTTTAACTCATATGTGGTGACGTA
192 GGTTTTCAAATAAAAAACGTTTTATACGATTGGTGTGACATATTTAACTCATATGCGGTGACGTA
249042 TATGGGTGGAAACTTCAACAA
257 TATGGGTGGAAACTTCAACAA
* * * * *
249063 ATTAGTTATATAATAGTTTGTGATGTAATATCTAAAATTCTTTTAAAATAGAAAATATTAAGTAC
1 ATTAGTTATATAACAGTTTGTGACGTAATATCTAAAAATCATTT-AAATAGAAAATATTAAGCAC
* *
249128 TATAAATAATATATATGCATAGTAGAATATTAAA-TTATG-TT-T-TTA-A-TATGGTTTTATGT
65 TATAAATAATATATATGAATAGTACAATA-TAAATTTATGTTTATATTACATTATGGTTTTATGT
* *
249187 GATTATTAGCTT-AAA-AAATAAAGAAATATATTTTAAGA-TTTTAAAGAAACAAAATTTTATTG
129 GATTATTA-ATTAAAATAAATAAAGAAATACATTTTAAGATTTTTAAAGAAACAAAATTTTATTG
* * * * *
249249 GTTTTCAAA-AAAAAATGTTTTATACGATTGGTGTTATATATTTAACTCGTATGCGGTGATGTAT
193 GTTTTCAAATAAAAAACGTTTTATACGATTGGTGTGACATATTTAACTCATATGCGGTGACGTAT
249313 ATGGGT
258 ATGGGT
249319 TAAGGTTGTT
Statistics
Matches: 229, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
270 53 0.23
271 33 0.14
272 19 0.08
273 23 0.10
274 3 0.01
275 3 0.01
276 1 0.00
279 2 0.01
281 39 0.17
282 49 0.21
283 4 0.02
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (277 bp):
ATTAGTTATATAACAGTTTGTGACGTAATATCTAAAAATCATTTAAATAGAAAATATTAAGCACT
ATAAATAATATATATGAATAGTACAATATAAATTTATGTTTATATTACATTATGGTTTTATGTGA
TTATTAATTAAAATAAATAAAGAAATACATTTTAAGATTTTTAAAGAAACAAAATTTTATTGGTT
TTCAAATAAAAAACGTTTTATACGATTGGTGTGACATATTTAACTCATATGCGGTGACGTATATG
GGTGGAAACTTCAACAA
Found at i:250752 original size:23 final size:23
Alignment explanation
Indices: 250678--250778 Score: 105
Period size: 23 Copynumber: 4.4 Consensus size: 23
250668 AGCGTTCACT
* *
250678 AACATATTCATTTAACATTCACG
1 AACATGTTCATTTAACATTCATG
* * * *
250701 AATATGTT-ATTTAATACTCATC
1 AACATGTTCATTTAACATTCATG
* *
250723 AATATGTTCATTTAACATTCGTG
1 AACATGTTCATTTAACATTCATG
* *
250746 AACATGTTCGTTTAACGTTCATG
1 AACATGTTCATTTAACATTCATG
250769 AACATGTTCA
1 AACATGTTCA
250779 AAAATGGTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 18 0.29
23 44 0.71
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (23 bp):
AACATGTTCATTTAACATTCATG
Found at i:254636 original size:60 final size:61
Alignment explanation
Indices: 254524--254645 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 61
254514 TATAGGGTGA
* *
254524 TGCTTTATTGAATCCCTCGATTATTAAAAGTTACAAAATGATCCCTCAACTA-TAATACGT
1 TGCTTTATTGAATCCCTCGACTATTAAAAGTTACAAAATGATCACTCAACTATTAATACGT
* * * * ** *
254584 TGCTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCACTTGACTATTCATACGT
1 TGCTTTATTGAATCCCTCGACTATTAAAAGTTACAAAATGATCACTCAACTATTAATACGT
254645 T
1 T
254646 CTAAACTCGT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 44 0.85
61 8 0.15
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (61 bp):
TGCTTTATTGAATCCCTCGACTATTAAAAGTTACAAAATGATCACTCAACTATTAATACGT
Found at i:260482 original size:5 final size:5
Alignment explanation
Indices: 260474--260499 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
260464 GGGGTTTCTC
260474 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
260500 TGTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:261162 original size:3 final size:3
Alignment explanation
Indices: 261147--261247 Score: 175
Period size: 3 Copynumber: 33.7 Consensus size: 3
261137 ATATTGTTAA
* * *
261147 AAT AAT AAC AAT AAT AAT AAT AAT AGT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
261195 AAT AAT AAT AAT 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
261243 AAT AA
1 AAT AA
261248 CCCGGACATA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:261812 original size:140 final size:140
Alignment explanation
Indices: 261556--261968 Score: 693
Period size: 140 Copynumber: 3.0 Consensus size: 140
261546 AAATTTGGAG
* * * * *
261556 ACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTACCTAAGGGTGACA-GTGCTCCTACGTGAT
1 ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGA-ATCTGCTCCTACGTGAT
* * * * *
261620 GAGGAAATATGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGGA
65 GAGGAGATCTGGTCGGTGGATGAAATTGTTCCTACGTAATGAGGACGTCTAGCCATCTTTAGGGA
261685 TAATATGGGAC
130 TAATATGGGAC
261696 ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGAATCTGCTCCTACGTGATG
1 ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGAATCTGCTCCTACGTGATG
* *
261761 AGGAGATCTGGTCGGTGGATGATATTGTTCCTACGTAATGAGGAAGTCTAGCCATCTTTAGGGAT
66 AGGAGATCTGGTCGGTGGATGAAATTGTTCCTACGTAATGAGGACGTCTAGCCATCTTTAGGGAT
261826 AATATGGGAC
131 AATATGGGAC
261836 ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGAATCTGCTCCTACGTGATG
1 ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGAATCTGCTCCTACGTGATG
*
261901 AGGAGATCTGGTCGGTGGATGAAATTGTTCGTACGTAATGAGGACGTCTAGCCATCTTTAGGGAT
66 AGGAGATCTGGTCGGTGGATGAAATTGTTCCTACGTAATGAGGACGTCTAGCCATCTTTAGGGAT
261966 AAT
131 AAT
261969 TTGTTTCAAT
Statistics
Matches: 258, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
139 1 0.00
140 257 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (140 bp):
ACAACATGGTTCATACGTGATGAGGAAGTCTGGTTATCTAAGGATGAATCTGCTCCTACGTGATG
AGGAGATCTGGTCGGTGGATGAAATTGTTCCTACGTAATGAGGACGTCTAGCCATCTTTAGGGAT
AATATGGGAC
Found at i:262211 original size:65 final size:65
Alignment explanation
Indices: 261987--262426 Score: 686
Period size: 65 Copynumber: 6.8 Consensus size: 65
261977 ATAGGAACCA
* * *
261987 TCTCAAGCGAGACAAAATCTGTTTCAAGAGAAACTATCTCAAAGGTTTATGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAA-GTTTATGTTTCAAGAGAAACT
262052 G
65 G
* * * *
262053 TCTCAATAGAGACAAAATTTGATTCAAGAGAAACAATCTCAAGGGTTATGTTTCAAGAG-AACTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
*
262117 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAAAGTTTATGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
* * * *
262182 TCTCAAGAGAGACAAAATTTGTTTAAAGAGAAATAATCTCAAAGTTTATATTTCAAGTGAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
* * * *
262247 TCTCAAGCGAGACAAAATTTGTTTTAAGAGAAACAATCTCAAATTTTATGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
262312 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
*
262377 TCTCAAGCGAGA-AAAAGTTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAA-GTTTAT
262427 CAATTTTGTT
Statistics
Matches: 342, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
64 63 0.18
65 236 0.69
66 43 0.13
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTCAAGAGAAACTG
Found at i:262287 original size:36 final size:35
Alignment explanation
Indices: 262165--262418 Score: 136
Period size: 36 Copynumber: 7.7 Consensus size: 35
262155 TAAAAGTTTA
** *
262165 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAAGCGAGA-AAAATT
* * *
262201 TGTTTAAAGAGAAATAATCTCAA---AG----TTT
1 TGTTTCAAGAGAAACAATCTCAAGCGAGAAAAATT
* * **
262229 ATATTTCAAGTGAAACTGTCTCAAGCGAGACAAAATT
1 -TGTTTCAAGAGAAACAATCTCAAGCGAGA-AAAATT
* **
262266 TGTTTTAAGAGAAACAATCT----C---AAATTTT
1 TGTTTCAAGAGAAACAATCTCAAGCGAGAAAAATT
* *
262294 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 -TGTTTCAAGAGAAACAATCTCAAGCGAGA-AAAATT
*
262331 TGTTTCAAGAGAAACAATCTCAA---AG----TTT
1 TGTTTCAAGAGAAACAATCTCAAGCGAGAAAAATT
**
262359 ATGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAGTT
1 -TGTTTCAAGAGAAACAATCTCAAGCGAGAAAAA-TT
262396 TGTTTCAAGAGAAACAATCTCAA
1 TGTTTCAAGAGAAACAATCTCAA
262419 AGGTTTATCA
Statistics
Matches: 160, Mismatches: 31, Indels: 54
0.65 0.13 0.22
Matches are distributed among these distances:
28 8 0.05
29 57 0.36
32 5 0.03
33 4 0.03
36 78 0.49
37 8 0.05
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATCTCAAGCGAGAAAAATT
Found at i:262304 original size:29 final size:29
Alignment explanation
Indices: 262259--262374 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 29
262249 TCAAGCGAGA
*
262259 CAAAA-TT-TGTTTTAAGAGAAACAATCT
1 CAAAATTTATGTTTCAAGAGAAACAATCT
* *
262286 CAAATTTTATGTTTCAAGAGAAACTATCT
1 CAAAATTTATGTTTCAAGAGAAACAATCT
*
262315 CAAGAGAGACAAAATT-TGTTTCAAGAGAAACAATCT
1 C-------A-AAATTTATGTTTCAAGAGAAACAATCT
*
262351 CAAAGTTTATGTTTCAAGAGAAAC
1 CAAAATTTATGTTTCAAGAGAAAC
262375 TGTCTCAAGC
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
27 4 0.06
28 6 0.09
29 35 0.50
36 21 0.30
37 4 0.06
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (29 bp):
CAAAATTTATGTTTCAAGAGAAACAATCT
Found at i:263348 original size:176 final size:177
Alignment explanation
Indices: 263054--263411 Score: 709
Period size: 176 Copynumber: 2.0 Consensus size: 177
263044 AATGTATGAT
263054 TCAAAGGTGAAAATTTCATATAACATGTATGTATATGTTGATGTATGTTTTATCGATCTGTGAAG
1 TCAAAGGTGAAAATTTCATATAACATGTATGTATATGTTGATGTATGTTTTATCGATCTGTGAAG
263119 GGAATGGTTGCGTGAGCAATCTTCATTCTATTCCTGATTCAGTTGTCTTCATTTTCCACCAGGGT
66 GGAATGGTTGCGTGAGCAATCTTCATTCTATTCCTGATTCAGTTGTCTTCATTTTCCACCAGGGT
263184 GTACCCTTGTGAACTACGACTTGCGGCAATTTGTC-TTCTTGCCCCA
131 GTACCCTTGTGAACTACGACTTGCGGCAATTTGTCTTTCTTGCCCCA
263230 TCAAAGGTGAAAATTTCATATAACATGTATGTATATGTTGATGTATGTTTTATCGATCTGTGAAG
1 TCAAAGGTGAAAATTTCATATAACATGTATGTATATGTTGATGTATGTTTTATCGATCTGTGAAG
263295 GGAATGGTTGCGTGAGCAATCTTCATTCTATTCCTGATTCAGTTGTCTTCATTTTCCACCAGGGT
66 GGAATGGTTGCGTGAGCAATCTTCATTCTATTCCTGATTCAGTTGTCTTCATTTTCCACCAGGGT
263360 GTACCCTTGTGAACTACGACTTGCGGCAATTTGTCTTTCTTGCCCCA
131 GTACCCTTGTGAACTACGACTTGCGGCAATTTGTCTTTCTTGCCCCA
263407 TCAAA
1 TCAAA
263412 TTTTCCCCCA
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 165 0.91
177 16 0.09
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (177 bp):
TCAAAGGTGAAAATTTCATATAACATGTATGTATATGTTGATGTATGTTTTATCGATCTGTGAAG
GGAATGGTTGCGTGAGCAATCTTCATTCTATTCCTGATTCAGTTGTCTTCATTTTCCACCAGGGT
GTACCCTTGTGAACTACGACTTGCGGCAATTTGTCTTTCTTGCCCCA
Found at i:263872 original size:14 final size:16
Alignment explanation
Indices: 263842--263874 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
263832 ATGACTCAAC
263842 TAGCATAGTCAATTGT
1 TAGCATAGTCAATTGT
263858 TAGCATAG-C-ATTGT
1 TAGCATAGTCAATTGT
263872 TAG
1 TAG
263875 AACACTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (16 bp):
TAGCATAGTCAATTGT
Found at i:272581 original size:31 final size:31
Alignment explanation
Indices: 272497--272582 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
272487 GGGCCTGAGA
* *
272497 GCCTACCCAAGAAAGTTACTCGGGGCCACGGG
1 GCCTACCCAAGAAAGATA-TCGGGGCCACAGG
* **
272529 GCCTA-CCAAG-AAGAATCTCGGGGCCGTAGG
1 GCCTACCCAAGAAAG-ATATCGGGGCCACAGG
272559 GCCTACCCAAGAAAGATATCGGGG
1 GCCTACCCAAGAAAGATATCGGGG
272583 ACTCAAATCC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 18 0.40
31 19 0.42
32 8 0.18
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.13
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATATCGGGGCCACAGG
Found at i:274450 original size:13 final size:14
Alignment explanation
Indices: 274432--274465 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
274422 GACTTTTTGT
274432 TCAAAGTTAACG-G
1 TCAAAGTTAACGAG
274445 TCAAAGTTAACGAG
1 TCAAAGTTAACGAG
274459 TCAAAGT
1 TCAAAGT
274466 CATATGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (14 bp):
TCAAAGTTAACGAG
Found at i:294568 original size:20 final size:21
Alignment explanation
Indices: 294543--294594 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
294533 ATAGGTTTGG
294543 GATCGATCCTTTAAGT-AAGA-
1 GATCGATCCTTTAAGTGAA-AT
*
294563 GATCGAAT-CTTTCAGTGAAAT
1 GATCG-ATCCTTTAAGTGAAAT
294584 GATCGATCCTT
1 GATCGATCCTT
294595 CCACCCACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (21 bp):
GATCGATCCTTTAAGTGAAAT
Found at i:301509 original size:21 final size:20
Alignment explanation
Indices: 301484--301522 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
301474 CATCAGGGTC
301484 TTTGTAGAAGCCATGAAATCT
1 TTTGTAGAAGCCAT-AAATCT
* *
301505 TTTGTTGAGGCCATAAAT
1 TTTGTAGAAGCCATAAAT
301523 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTAGAAGCCATAAATCT
Found at i:305172 original size:36 final size:36
Alignment explanation
Indices: 305051--305326 Score: 168
Period size: 36 Copynumber: 7.6 Consensus size: 36
305041 CCCTGAAACT
*
305051 AACCTAGTCTTCCTTAAGACTATTTCCCTTTAAATC
1 AACCTAGTCTTCCTTAAGACTATTTCCCTATAAATC
** * * * *
305087 AACCTACCCTTTCTTAAGACTATTTTCATAAAAATC
1 AACCTAGTCTTCCTTAAGACTATTTCCCTATAAATC
*
305123 AACCTAGTATTCCTTAAGACTATTTCCCTATAAATC
1 AACCTAGTCTTCCTTAAGACTATTTCCCTATAAATC
** * *
305159 AATTTAGTCTTCCTTATGA-T-TGTTCCCTAGAAA-C
1 AACCTAGTCTTCCTTAAGACTAT-TTCCCTATAAATC
* * * * * *
305193 TAACCCAGTCTT-CTCTAGGAATGTTTCCCTAAAAACCTT
1 -AACCTAGTCTTCCT-TAAGACTATTTCCCTATAAA--TC
* * * * *
305232 ATCTTAGTCTTTCTTAA-AATATTTCCCCTAGAAA-C
1 AACCTAGTCTTCCTTAAGACTATTT-CCCTATAAATC
* * * * *
305267 AAACCTAATATTCCTTAAGATTGTTTCCCTATAAACCTA
1 -AACCTAGTCTTCCTTAAGACTATTTCCCTATAAA--TC
*
305306 AACTTAGTCTTCCTTAAGACT
1 AACCTAGTCTTCCTTAAGACT
305327 TTCTCTTGAA
Statistics
Matches: 180, Mismatches: 45, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
34 4 0.02
35 23 0.13
36 104 0.58
37 12 0.07
38 35 0.19
39 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (36 bp):
AACCTAGTCTTCCTTAAGACTATTTCCCTATAAATC
Found at i:305696 original size:71 final size:70
Alignment explanation
Indices: 305572--305943 Score: 248
Period size: 71 Copynumber: 5.3 Consensus size: 70
305562 GCATCAGGAA
* * * * *
305572 TTAGTA-AGTGAACCCTCTG-CATGGAGGAAGTCAAACACAACCCTGAACCTCAGTCATGGAGGA
1 TTAGTAGA-TGAACCCTCAGTCATGGA-GAAATCAAACGCAACCCCGAGCCTCAGTCATGGAGGA
305635 CACCCCG
64 CACCCCG
* * * * **
305642 TTAGCAGAAGAACCCTCAG-CAATTGAGAAATCCAAACGTAACCCCGAGCCTCAGTCATATAGGA
1 TTAGTAGATGAACCCTCAGTC-ATGGAGAAAT-CAAACGCAACCCCGAGCCTCAGTCATGGAGGA
* *
305706 CAACCTG
64 CACCCCG
* * * * * * * *
305713 TTAGTAGGTGAACCCTTAGTCATGGAGGAAGTCAAACGCAACACTGAGCCTAAATCATAGGGGGA
1 TTAGTAGATGAACCCTCAGTCATGGA-GAAATCAAACGCAACCCCGAGCCTCAGTCAT-GGAGGA
*
305778 AACCCC-
64 CACCCCG
* * * * * * * * *
305784 TTAGTAGATGAACCTTCAGCCATGGAAAAAGTTAAACGTAACCCCGAGCCTCATTCATAGAGAAA
1 TTAGTAGATGAACCCTCAGTCATGGAGAAA-TCAAACGCAACCCCGAGCCTCAGTCATGGAGGAC
** *
305849 AAACTG
65 ACCCCG
* * * * ** * *
305855 TTAATAGGTGAACCCTTAGTCATAGAGGAAGCCGAACGCAACCCCGAGCCTTAGTCATGGAGGAC
1 TTAGTAGATGAACCCTCAGTCATGGA-GAAATCAAACGCAACCCCGAGCCTCAGTCATGGAGGAC
*
305920 ACCCCA
65 ACCCCG
*
305926 TTAGTAGACGAACCCTCA
1 TTAGTAGATGAACCCTCA
305944 ACTATAGAGG
Statistics
Matches: 220, Mismatches: 73, Indels: 17
0.71 0.24 0.05
Matches are distributed among these distances:
70 27 0.12
71 180 0.82
72 13 0.06
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (70 bp):
TTAGTAGATGAACCCTCAGTCATGGAGAAATCAAACGCAACCCCGAGCCTCAGTCATGGAGGACA
CCCCG
Found at i:305827 original size:142 final size:142
Alignment explanation
Indices: 305572--305943 Score: 437
Period size: 142 Copynumber: 2.6 Consensus size: 142
305562 GCATCAGGAA
* * * *
305572 TTAGTAAGTGAACCCTCT-G-CATGGAGGAAGTCAAACACAACCCTGAACCTCAGTCATGGAGGA
1 TTAGTAGGTGAACCCT-TAGTCATGGAGGAAGTCAAACGCAACCCTGAGCCTAAGTCATGGAGGA
* * * *
305635 CACCCCGTTAGCAGAAGAACCCTCAGCAATTGAGAAATCCAAACGTAACCCCGAGCCTCAGTCAT
65 CACCCCATTAGTAGAAGAACCCTCAGCAATGGAAAAATCCAAACGTAACCCCGAGCCTCAGTCAT
* * * *
305700 ATAGGACAACCTG
130 AGAGAAAAAACTG
* * *
305713 TTAGTAGGTGAACCCTTAGTCATGGAGGAAGTCAAACGCAACACTGAGCCTAAATCATAGGGGGA
1 TTAGTAGGTGAACCCTTAGTCATGGAGGAAGTCAAACGCAACCCTGAGCCTAAGTCAT-GGAGGA
* * * * * *
305778 AACCCC-TTAGTAGATGAACCTTCAGCCATGGAAAAAGT-TAAACGTAACCCCGAGCCTCATTCA
65 CACCCCATTAGTAGAAGAACCCTCAGCAATGGAAAAA-TCCAAACGTAACCCCGAGCCTCAGTCA
305841 TAGAGAAAAAACTG
129 TAGAGAAAAAACTG
* * * * * *
305855 TTAATAGGTGAACCCTTAGTCATAGAGGAAGCCGAACGCAACCCCGAGCCTTAGTCATGGAGGAC
1 TTAGTAGGTGAACCCTTAGTCATGGAGGAAGTCAAACGCAACCCTGAGCCTAAGTCATGGAGGAC
*
305920 ACCCCATTAGTAGACGAACCCTCA
66 ACCCCATTAGTAGAAGAACCCTCA
305944 ACTATAGAGG
Statistics
Matches: 194, Mismatches: 32, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
140 1 0.01
141 26 0.13
142 156 0.80
143 11 0.06
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (142 bp):
TTAGTAGGTGAACCCTTAGTCATGGAGGAAGTCAAACGCAACCCTGAGCCTAAGTCATGGAGGAC
ACCCCATTAGTAGAAGAACCCTCAGCAATGGAAAAATCCAAACGTAACCCCGAGCCTCAGTCATA
GAGAAAAAACTG
Found at i:315858 original size:14 final size:15
Alignment explanation
Indices: 315841--315871 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
315831 TTAACTCAAT
315841 AAAAA-TAAAAGATA
1 AAAAATTAAAAGATA
315855 AAAAATTAAAAGATA
1 AAAAATTAAAAGATA
315870 AA
1 AA
315872 TTGTAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAAATTAAAAGATA
Found at i:318508 original size:23 final size:24
Alignment explanation
Indices: 318463--318508 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
318453 CTCACCTTAA
*
318463 AAATATTTATAACTACTAGATCAT
1 AAATATTTATAACTACTACATCAT
318487 AAATA-TTATAAC-ACCTACATCA
1 AAATATTTATAACTA-CTACATCA
318509 CTCAGAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 14 0.70
24 5 0.25
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATATTTATAACTACTACATCAT
Found at i:322257 original size:20 final size:20
Alignment explanation
Indices: 322219--322262 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
322209 GTTAACCCAA
* *
322219 CTGAGTCAACTTGAACCGAC
1 CTGAGTAAACCTGAACCGAC
* *
322239 CTGAGTAAACCTGAGCCGAT
1 CTGAGTAAACCTGAACCGAC
322259 CTGA
1 CTGA
322263 CCTGTTAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (20 bp):
CTGAGTAAACCTGAACCGAC
Found at i:328210 original size:48 final size:46
Alignment explanation
Indices: 328099--328220 Score: 138
Period size: 48 Copynumber: 2.6 Consensus size: 46
328089 GTAACCATGC
*
328099 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG-AAAAA
* * * **
328146 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAAA
*
328194 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
328221 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.03
46 1 0.02
47 22 0.34
48 24 0.38
49 1 0.02
50 14 0.22
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:331073 original size:17 final size:17
Alignment explanation
Indices: 331051--331117 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
331041 TATTATAAGA
331051 AGAAGAA-AAAAACAAAC
1 AGAAGAAGAAAAA-AAAC
*
331068 AGAAGAAGAAAAAAAAT
1 AGAAGAAGAAAAAAAAC
*
331085 AGAAAAAGAAAAAGAAA-
1 AGAAGAAGAAAAA-AAAC
331102 ACGAAGAAGAAAAAAA
1 A-GAAGAAGAAAAAAA
331118 TGAAAATGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
17 25 0.57
18 19 0.43
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (17 bp):
AGAAGAAGAAAAAAAAC
Found at i:331073 original size:20 final size:19
Alignment explanation
Indices: 331048--331117 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
331038 ATATATTATA
331048 AGAAGAAGAAAAAAACAAAC
1 AGAAGAAGAAAAAAA-AAAC
*
331068 AGAAGAAG--AAAAAAAAT
1 AGAAGAAGAAAAAAAAAAC
* *
331085 AGAAAAAGAAAAAGAAAAC
1 AGAAGAAGAAAAAAAAAAC
331104 -GAAGAAGAAAAAAA
1 AGAAGAAGAAAAAAA
331118 TGAAAATGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.24
18 17 0.40
19 7 0.17
20 8 0.19
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.01
Consensus pattern (19 bp):
AGAAGAAGAAAAAAAAAAC
Found at i:331094 original size:6 final size:6
Alignment explanation
Indices: 331047--331115 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
331037 CATATATTAT
* * * *
331047 AAGAAG AAGAAA AAAACAA ACAGAAG AAGAAA AA-AAA TAGAAA AAGAAA
1 AAGAAA AAGAAA AAGA-AA A-AGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
331096 AAGAAA ACGAAG AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AA
331116 AATGAAAATG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
5 4 0.08
6 38 0.78
7 5 0.10
8 2 0.04
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:331094 original size:23 final size:22
Alignment explanation
Indices: 331047--331102 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
331037 CATATATTAT
*
331047 AAGAAGAAGAAAAAAACAAACAG
1 AAGAAGAA-AAAAAAACAAAAAG
*
331070 AAGAAGAAAAAAAATAGAAAAAG
1 AAGAAGAAAAAAAA-ACAAAAAG
*
331093 AAAAAGAAAA
1 AAGAAGAAAA
331103 CGAAGAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (22 bp):
AAGAAGAAAAAAAAACAAAAAG
Found at i:331129 original size:17 final size:16
Alignment explanation
Indices: 331109--331153 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
331099 AAAACGAAGA
331109 AGAAAAAAATGAAA-ATG
1 AGAAAAAAAT-AAATA-G
331126 AGAAAGAAAATAAATAG
1 AGAAA-AAAATAAATAG
331143 AGAAAAAAATA
1 AGAAAAAAATA
331154 TTTCACTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.23
17 14 0.54
18 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (16 bp):
AGAAAAAAATAAATAG
Found at i:331132 original size:21 final size:21
Alignment explanation
Indices: 331080--331140 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
331070 AAGAAGAAAA
331080 AAAAT-AGAAA-AAGAAAAA-G
1 AAAATGAGAAAGAA-AAAAATG
*
331099 AAAACGA-AGAAGAAAAAAATG
1 AAAATGAGA-AAGAAAAAAATG
331120 AAAATGAGAAAGAAAATAAAT
1 AAAATGAGAAAGAAAA-AAAT
331141 AGAGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 16 0.47
22 5 0.15
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (21 bp):
AAAATGAGAAAGAAAAAAATG
Found at i:331149 original size:33 final size:34
Alignment explanation
Indices: 331048--331153 Score: 106
Period size: 33 Copynumber: 3.0 Consensus size: 34
331038 ATATATTATA
* *
331048 AGAAGAAGAAAAAAACAAACAGAAGAAGAAAAAAAAT
1 AGAAAAAGAAAAAGA-AAAC-GAAGAAG-AAAAAAAT
331085 AGAAAAAGAAAAAGAAAACGAAGAAGAAAAAAAT
1 AGAAAAAGAAAAAGAAAACGAAGAAGAAAAAAAT
* * ** *
331119 -GAAAATGAGAAAGAAAATAAATAGAGAAAAAAAT
1 AGAAAAAGAAAAAGAAAACGAAGA-AGAAAAAAAT
331153 A
1 A
331154 TTTCACTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 18 0.30
34 18 0.30
35 7 0.12
36 4 0.07
37 13 0.22
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (34 bp):
AGAAAAAGAAAAAGAAAACGAAGAAGAAAAAAAT
Found at i:336703 original size:14 final size:14
Alignment explanation
Indices: 336686--336727 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
336676 TTAACGAGGA
336686 AAAGTCAATGGGTC
1 AAAGTCAATGGGTC
*
336700 AAAGTCAACGGGT-
1 AAAGTCAATGGGTC
* *
336713 TAGGTCAATGGGTC
1 AAAGTCAATGGGTC
336727 A
1 A
336728 GGTTTGGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (14 bp):
AAAGTCAATGGGTC
Found at i:336726 original size:27 final size:28
Alignment explanation
Indices: 336661--336727 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
336651 ACGATCGACT
* *
336661 GTCAATGGGTTAAAGTTAACGAGGAAAA
1 GTCAATGGGTCAAAGTCAACGAGGAAAA
** *
336689 GTCAATGGGTCAAAGTCAACG-GGTTAG
1 GTCAATGGGTCAAAGTCAACGAGGAAAA
336716 GTCAATGGGTCA
1 GTCAATGGGTCA
336728 GGTTTGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (28 bp):
GTCAATGGGTCAAAGTCAACGAGGAAAA
Found at i:339697 original size:37 final size:36
Alignment explanation
Indices: 339640--339747 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 36
339630 CATTATTGTG
* * *
339640 TTTATCATCCCAAGGCATGAACCAGTCGGTAATTGGA
1 TTTATCATCCTAAGG-ATGAACTAGTCAGTAATTGGA
* * *
339677 TTTATCATCCTAATGGATGAACTAGTTAATAATTGGG
1 TTTATCATCCTAA-GGATGAACTAGTCAGTAATTGGA
339714 TTTATCATCCTGAAGGATGAACTAGTCAGTAATT
1 TTTATCATCCT-AAGGATGAACTAGTCAGTAATT
339748 CGGCCACCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 57 0.93
38 4 0.07
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (36 bp):
TTTATCATCCTAAGGATGAACTAGTCAGTAATTGGA
Found at i:342510 original size:36 final size:36
Alignment explanation
Indices: 342463--342631 Score: 302
Period size: 36 Copynumber: 4.7 Consensus size: 36
342453 CAAAAGTTTA
* *
342463 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
342499 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
342535 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
342571 TTCCGATTCAAGTCAAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
342607 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
342632 TGTGTCTTAC
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:349591 original size:222 final size:222
Alignment explanation
Indices: 349205--349648 Score: 888
Period size: 222 Copynumber: 2.0 Consensus size: 222
349195 TAACATCACA
349205 CCTTAATAAAGAAAAACTTCAAGGATTTCAAATGGACCAGACCATCGAGATCGAAGCTTCCCATG
1 CCTTAATAAAGAAAAACTTCAAGGATTTCAAATGGACCAGACCATCGAGATCGAAGCTTCCCATG
349270 AAATAGTTTCAAATGAGAGTTAAATAACAAAACATGTTGTCCAACATAAATTTGTCATGGCAAAA
66 AAATAGTTTCAAATGAGAGTTAAATAACAAAACATGTTGTCCAACATAAATTTGTCATGGCAAAA
349335 TGTGTTTTTCGTGTCATTTCTTGTTATGGTCTTTGTAAATTCGGGCATTGTCGTATGCATCATTT
131 TGTGTTTTTCGTGTCATTTCTTGTTATGGTCTTTGTAAATTCGGGCATTGTCGTATGCATCATTT
349400 TGAAGTTCTTCTATTTCATTAATGTCC
196 TGAAGTTCTTCTATTTCATTAATGTCC
349427 CCTTAATAAAGAAAAACTTCAAGGATTTCAAATGGACCAGACCATCGAGATCGAAGCTTCCCATG
1 CCTTAATAAAGAAAAACTTCAAGGATTTCAAATGGACCAGACCATCGAGATCGAAGCTTCCCATG
349492 AAATAGTTTCAAATGAGAGTTAAATAACAAAACATGTTGTCCAACATAAATTTGTCATGGCAAAA
66 AAATAGTTTCAAATGAGAGTTAAATAACAAAACATGTTGTCCAACATAAATTTGTCATGGCAAAA
349557 TGTGTTTTTCGTGTCATTTCTTGTTATGGTCTTTGTAAATTCGGGCATTGTCGTATGCATCATTT
131 TGTGTTTTTCGTGTCATTTCTTGTTATGGTCTTTGTAAATTCGGGCATTGTCGTATGCATCATTT
349622 TGAAGTTCTTCTATTTCATTAATGTCC
196 TGAAGTTCTTCTATTTCATTAATGTCC
349649 AACATTCTTT
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 222 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (222 bp):
CCTTAATAAAGAAAAACTTCAAGGATTTCAAATGGACCAGACCATCGAGATCGAAGCTTCCCATG
AAATAGTTTCAAATGAGAGTTAAATAACAAAACATGTTGTCCAACATAAATTTGTCATGGCAAAA
TGTGTTTTTCGTGTCATTTCTTGTTATGGTCTTTGTAAATTCGGGCATTGTCGTATGCATCATTT
TGAAGTTCTTCTATTTCATTAATGTCC
Found at i:356851 original size:20 final size:21
Alignment explanation
Indices: 356823--356877 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
356813 ACATATATAT
*
356823 AATAATAATATA-AAAAATAA
1 AATAGTAATATATAAAAATAA
* *
356843 AATAGTAATA-ATTAATATAA
1 AATAGTAATATATAAAAATAA
356863 AATAGTATATATATA
1 AATAGTA-ATATATA
356878 TATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.79
21 3 0.11
22 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
AATAGTAATATATAAAAATAA
Found at i:356875 original size:2 final size:2
Alignment explanation
Indices: 356868--356903 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
356858 TATAAAATAG
356868 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
356904 ATAATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:356880 original size:20 final size:21
Alignment explanation
Indices: 356839--356909 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 21
356829 AATATAAAAA
356839 ATAAAATAGTA-ATA-ATTAAT
1 ATAAAATAGTATATATA-TAAT
356859 ATAAAATAGTATATATAT-AT
1 ATAAAATAGTATATATATAAT
*
356879 ATATATATA-TATATATCATAAT
1 ATA-AAATAGTATATAT-ATAAT
356901 ATAATAATA
1 ATAA-AATA
356910 AATTAAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 23 0.53
21 11 0.26
22 9 0.21
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAAAATAGTATATATATAAT
Found at i:356907 original size:8 final size:8
Alignment explanation
Indices: 356824--356909 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
356814 CATATATATA
356824 ATAATAAT
1 ATAATAAT
*
356832 ATAA-AAA
1 ATAATAAT
356839 ATAA-AAT
1 ATAATAAT
356846 AGTAATAAT
1 A-TAATAAT
356855 -TAAT-AT
1 ATAATAAT
* *
356861 AAAATAGT
1 ATAATAAT
356869 AT-AT-AT
1 ATAATAAT
356875 AT-ATATAT
1 ATAATA-AT
356883 ATATATATAT
1 ATA-ATA-AT
*
356893 ATCATAAT
1 ATAATAAT
356901 ATAATAAT
1 ATAATAAT
356909 A
1 A
356910 AATTAAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
6 7 0.11
7 18 0.29
8 23 0.37
9 6 0.10
10 8 0.13
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:357098 original size:17 final size:16
Alignment explanation
Indices: 357076--357114 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
357066 AATAATTATT
357076 TAAAAATATACTAATAA
1 TAAAAATATA-TAATAA
357093 TAAAAAATATATAATAA
1 T-AAAAATATATAATAA
357110 TAAAA
1 TAAAA
357115 TGGTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATATATAATAA
Found at i:360345 original size:24 final size:23
Alignment explanation
Indices: 360313--360368 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
360303 TTTATGAATA
360313 AAAAATAAAATTCATCATTATTT
1 AAAAATAAAATTCATCATTATTT
* *
360336 AAAAATTAAATTTATCATTATTT
1 AAAAATAAAATTCATCATTATTT
*
360359 AGAAATAAAA
1 AAAAATAAAA
360369 CAGATTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAATAAAATTCATCATTATTT
Found at i:360957 original size:45 final size:45
Alignment explanation
Indices: 360867--361291 Score: 550
Period size: 45 Copynumber: 9.5 Consensus size: 45
360857 TATAAACCCG
* * *
360867 GTAAGGGCTTACCCTGTGCACA-AAGCAGAGGAGCCTGGGGAAAACT
1 GTAAGGTCTTACCCT-TGCACACAA-CAAAGGAACCTGGGGAAAACT
* * *
360913 ATAAGGTCTTACCCTTTCACACATCAAAGGAACCTGGGGAAAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
** * *
360958 GTAAGGTCTTATACTTACACACAGCAAAGGAACCTGGGGAAAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
* **
361003 GTAAGGTCTTACCCTTGTACACAACAAAGGAACCTAAGG-AAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
* *
361047 GTAAGGTCTTACCCTTGCACACAACAAATGAACATGGGGAAAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
*
361092 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTAGGGAAAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
* * * *
361137 GTAACGTCTTACCATTGCACACAACAAAGGAACATGGGTAAAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
* * *
361182 CTAAGGTCTTACCCTTGCACACAACAAAGAAACCTGGGGAAAATT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
* * * **
361227 TTAAGGTCTTTCCCTTGCCCACAGTAAAGGAACCTGGGG-AAACT
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
*
361271 GTAAGGACTTACCCTTGCACA
1 GTAAGGTCTTACCCTTGCACA
361292 TAGCAGAGGA
Statistics
Matches: 328, Mismatches: 49, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
44 60 0.18
45 254 0.77
46 14 0.04
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (45 bp):
GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACT
Found at i:361206 original size:179 final size:180
Alignment explanation
Indices: 360867--361291 Score: 552
Period size: 179 Copynumber: 2.4 Consensus size: 180
360857 TATAAACCCG
* * * * *
360867 GTAAGGGCTTACCCTGTGCACA-AAGCAGAGGAGCCTGGGGAAAACTATAAGGTCTTACCCTTTC
1 GTAAGGTCTTACCCT-TGCACACAA-CAAAGGAACCTGGGGAAAACTGTAAGGTCTTACCCTTGC
* * * * * *
360931 ACACATCAAAGGAACCTGGGGAAAACTGTAAGGTCTTATACTTACACACAGCAAAGGAACCTGGG
64 ACACAACAAAGGAACCTAGGGAAAACTGTAACGTCTTACACTTACACACAACAAAGGAACATGGG
* * *
360996 GAAAACTGTAAGGTCTTACCCTTGTACACAACAAAGGAACCTAAGG-AAACT
129 GAAAACTCTAAGGTCTTACCCTTGCACACAACAAAGAAACCTAAGGAAAACT
* *
361047 GTAAGGTCTTACCCTTGCACACAACAAATGAACATGGGGAAAACTGTAAGGTCTTACCCTTGCAC
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACTGTAAGGTCTTACCCTTGCAC
* *
361112 ACAACAAAGGAACCTAGGGAAAACTGTAACGTCTTAC-CATTGCACACAACAAAGGAACATGGGT
66 ACAACAAAGGAACCTAGGGAAAACTGTAACGTCTTACAC-TTACACACAACAAAGGAACATGGGG
** *
361176 AAAACTCTAAGGTCTTACCCTTGCACACAACAAAGAAACCTGGGGAAAATT
130 AAAACTCTAAGGTCTTACCCTTGCACACAACAAAGAAACCTAAGGAAAACT
* * * ** *
361227 TTAAGGTCTTTCCCTTGCCCACAGTAAAGGAACCTGGGG-AAACTGTAAGGACTTACCCTTGCAC
1 GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACTGTAAGGTCTTACCCTTGCAC
361291 A
66 A
361292 TAGCAGAGGA
Statistics
Matches: 213, Mismatches: 29, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
178 1 0.00
179 160 0.75
180 52 0.24
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (180 bp):
GTAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAAACTGTAAGGTCTTACCCTTGCAC
ACAACAAAGGAACCTAGGGAAAACTGTAACGTCTTACACTTACACACAACAAAGGAACATGGGGA
AAACTCTAAGGTCTTACCCTTGCACACAACAAAGAAACCTAAGGAAAACT
Found at i:367822 original size:20 final size:20
Alignment explanation
Indices: 367797--367836 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
367787 ATTAGCCTAA
*
367797 TGGGTTAACCCAAACCCACT
1 TGGGTTAACCCAAAACCACT
*
367817 TGGGTTACCCCAAAACCACT
1 TGGGTTAACCCAAAACCACT
367837 AACCCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (20 bp):
TGGGTTAACCCAAAACCACT
Found at i:382189 original size:90 final size:89
Alignment explanation
Indices: 382077--382244 Score: 264
Period size: 90 Copynumber: 1.9 Consensus size: 89
382067 ACGAATATGT
* * * * *
382077 AATTTCAATTAATTAATTATAGATTTAATTAATTTCAACTAATAAAATCCCTAATATGATTAGGG
1 AATTCCAATTAATTAAATATAGATTTAATTAATATCAAATAATAAAA-CCCTAATATGAGTAGGG
382142 TAACTTGGATATAAGAGGATTATTA
65 TAACTTGGATATAAGAGGATTATTA
*
382167 AATTCCAATTAATTAAATATAGATTTAATTAATATGAAATAATAAAACCCTAATATGAGTAGGGT
1 AATTCCAATTAATTAAATATAGATTTAATTAATATCAAATAATAAAACCCTAATATGAGTAGGGT
*
382232 AACTTGGCTATAA
66 AACTTGGATATAA
382245 AAGGGTGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 29 0.41
90 42 0.59
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (89 bp):
AATTCCAATTAATTAAATATAGATTTAATTAATATCAAATAATAAAACCCTAATATGAGTAGGGT
AACTTGGATATAAGAGGATTATTA
Found at i:399908 original size:20 final size:18
Alignment explanation
Indices: 399871--399910 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
399861 ATTGATTCAT
*
399871 ATTTATTTATATTTTTTA
1 ATTTATTTATAATTTTTA
399889 ATTTAGTTTAATAATTTTTA
1 ATTTA-TTT-ATAATTTTTA
399909 AT
1 AT
399911 ATGTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTATTTATAATTTTTA
Found at i:400266 original size:14 final size:15
Alignment explanation
Indices: 400247--400276 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
400237 AAAAACATAA
400247 AAAAATA-TTTTTTT
1 AAAAATACTTTTTTT
400261 AAAAATACTTTTTTT
1 AAAAATACTTTTTTT
400276 A
1 A
400277 GAATTATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAAATACTTTTTTT
Found at i:401468 original size:2 final size:2
Alignment explanation
Indices: 401461--401494 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
401451 AGACTATAAC
401461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
401495 ATTAGACGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406091 original size:3 final size:3
Alignment explanation
Indices: 406079--406125 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
406069 TGTAATTATT
406079 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
406126 CGGGAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:406630 original size:135 final size:134
Alignment explanation
Indices: 406336--406651 Score: 456
Period size: 134 Copynumber: 2.4 Consensus size: 134
406326 TGAATCGAGG
* * *
406336 TTGATTTGCTTCGCTGCTCTTCAGGAATACCAAATCTGAAAGAAGAATAATATGCTCCACTACTC
1 TTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACTC
* * * * * *
406401 TTTAGGGGAGATCAAACTCGATAAATCTTTGATTCACTTCGTTGTTCTTCAAGGAAGTTTGAATT
66 TTTAGGGGAGATCAAACTCGAAAAATCTTTGATCCACTTCGCTGCTCTTCAAGGAAGATTGAATC
*
406466 GAAC
131 CAAC
* * * *
406470 ATGATTTGCTTCGATGCTCTTCAGGAAGACCAAATCTGAAAGAAGGAGAATCTACTCCACTACTC
1 TTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACTC
*
406535 TTTAGGGGAGATCAGACTCGAGAAAAAT-TTTGATCCACTTCGCTGCTCTTC-AGAGAAGATTGA
66 TTTAGGGGAGATCAAACTC--GAAAAATCTTTGATCCACTTCGCTGCTCTTCAAG-GAAGATTGA
406598 ATCCAAC
128 ATCCAAC
406605 TTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA
1 TTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA
406652 AACTCTGAGT
Statistics
Matches: 161, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
134 78 0.48
135 77 0.48
136 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (134 bp):
TTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACTC
TTTAGGGGAGATCAAACTCGAAAAATCTTTGATCCACTTCGCTGCTCTTCAAGGAAGATTGAATC
CAAC
Found at i:415725 original size:9 final size:9
Alignment explanation
Indices: 415687--415730 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
415677 TTCTGTTACA
415687 TTTATATTTT
1 TTTAT-TTTT
415697 TTTATTTTT
1 TTTATTTTT
* * *
415706 TATACTGTT
1 TTTATTTTT
415715 TTTATTTTT
1 TTTATTTTT
415724 TTTATTT
1 TTTATTT
415731 CGATTGAGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 23 0.82
10 5 0.18
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTATTTTT
Found at i:418143 original size:20 final size:20
Alignment explanation
Indices: 418118--418165 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
418108 TATGTGTTGG
418118 TTGGATTTGCGAAATTTTCA
1 TTGGATTTGCGAAATTTTCA
418138 TTGGATTTGCGAAATTTTCA
1 TTGGATTTGCGAAATTTTCA
*
418158 TTGAATTT
1 TTGGATTT
418166 CTTTGTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (20 bp):
TTGGATTTGCGAAATTTTCA
Found at i:418712 original size:13 final size:14
Alignment explanation
Indices: 418694--418723 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
418684 CAACAGTTCG
418694 AAAAG-AAAAGAAA
1 AAAAGAAAAAGAAA
418707 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
418721 AAA
1 AAA
418724 GTTGTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:420413 original size:147 final size:146
Alignment explanation
Indices: 420211--420480 Score: 402
Period size: 147 Copynumber: 1.8 Consensus size: 146
420201 GAATTTTAAG
* *
420211 AAAATATATTAATATATATATATTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAATG
1 AAAATAAATTAATATATATATATTTATAAAAAAGATATTTATTTACTTAGAAATATCAGAAAATG
* * *
420276 ACTTCTAGGTGTTTTAAGAC-AGCCTATTTCTTAATATTAAAAAAGAAATAAATATTAATAAAAA
66 ACTTCTAGGTGCTTTAAGACAAGAC-ATTTCTTAATATTAAAAAACAAATAAATATTAATAAAAA
420340 ATTTCTCAAAAATAAAT
130 ATTTCTCAAAAATAAAT
*
420357 AAAATAAATTAATATATATA-ATTTATAAAAATAGCATATTTATTTATTTA-AGAATATCAGAAA
1 AAAATAAATTAATATATATATATTTATAAAAA-AG-ATATTTATTTACTTAGA-AATATCAGAAA
* * *
420420 ATGACTTCTTGGTGCTTTAAGACAATACATTTCTTAATGTTAAAAAACAAATAAATATTAA
63 ATGACTTCTAGGTGCTTTAAGACAAGACATTTCTTAATATTAAAAAACAAATAAATATTAA
420481 AATATGATTA
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
145 10 0.09
146 22 0.20
147 77 0.69
148 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (146 bp):
AAAATAAATTAATATATATATATTTATAAAAAAGATATTTATTTACTTAGAAATATCAGAAAATG
ACTTCTAGGTGCTTTAAGACAAGACATTTCTTAATATTAAAAAACAAATAAATATTAATAAAAAA
TTTCTCAAAAATAAAT
Found at i:420651 original size:21 final size:22
Alignment explanation
Indices: 420610--420654 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
420600 TAATAATAAT
420610 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
420632 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
420653 AA
1 AA
420655 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:422106 original size:3 final size:3
Alignment explanation
Indices: 422098--422183 Score: 127
Period size: 3 Copynumber: 28.0 Consensus size: 3
422088 AATATTTATT
* *
422098 TAA TAA TAA TAA TAAA TAA TAT TAA TAA TAA TGTA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
422145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
422184 AAGCAAACTG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
3 70 0.93
4 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:422360 original size:45 final size:45
Alignment explanation
Indices: 422309--422477 Score: 286
Period size: 45 Copynumber: 3.8 Consensus size: 45
422299 GATGGAAATG
422309 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTT
* *
422354 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGATA-GTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGA-AGGTT
* *
422399 TTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTT
422444 TTGAAAACATCATGCACTGAAGGGCTTACAGATA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATA
422478 TGGGAAATAG
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.01
45 114 0.98
46 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTT
Found at i:422462 original size:90 final size:90
Alignment explanation
Indices: 422309--422476 Score: 318
Period size: 90 Copynumber: 1.9 Consensus size: 90
422299 GATGGAAATG
422309 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTTTTGAAAACATCATGCACTGA
422374 AGGGCTTACAGATGACCTGATAGTT
66 AGGGCTTACAGATGACCTGATAGTT
* *
422399 TTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTTTTGAAAACATCATGCACTGA
422464 AGGGCTTACAGAT
66 AGGGCTTACAGAT
422477 ATGGGAAATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (90 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGTTTTGAAAACATCATGCACTGA
AGGGCTTACAGATGACCTGATAGTT
Found at i:423141 original size:22 final size:22
Alignment explanation
Indices: 423089--423145 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
423079 AATAAAGCTT
* *
423089 TCATCTTTCAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
423111 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
423133 TCATCTTTGAAGA
1 TCATCTTTGAAGA
423146 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:424379 original size:243 final size:245
Alignment explanation
Indices: 423944--424441 Score: 948
Period size: 243 Copynumber: 2.0 Consensus size: 245
423934 GACACACAGA
*
423944 ATACAAAATTCAAAGATAAAATTTTAAGGAACTGAGCCCTAGATTGAATGGCCTGCCAGGGGACT
1 ATACAACATTCAAAGATAAAATTTTAAGGAACTGAGCCCTAGATTGAATGGCCTGCCAGGGGACT
424009 ATCTTAATTCCTGCAACCGTGATATCTCTTAACAAAGAACATGCTATCATGTGACACATGGTTAA
66 ATCTTAATTCCTGCAACCGTGATATCTCTTAACAAAGAACATGCTATCATGTGACACATGGTTAA
424074 GAAGATTGGGTATTTAAAACCATTTACTGAACCAATTTATGTGAACAATAATCTTATTTTGATGC
131 GAAGATTGGGTATTTAAAACCATTTACTGAACCAATTTATGTGAACAATAATCTTATTTTGATGC
424139 -ATAGCAAGACTA-ATAT-AGTGGTACAGGCTCTTAAAAAAATCCGCACCC
196 AATAGCAAGACTACATATAAGTGGTACAGGCTCTT-AAAAAATCCGCACCC
424187 ATACAACATTCAAAGATAAAATTTTAAGGAACTGAGCCCTAGATTGAATGGCCTGCCAGGGGACT
1 ATACAACATTCAAAGATAAAATTTTAAGGAACTGAGCCCTAGATTGAATGGCCTGCCAGGGGACT
424252 ATCTTAATTCCTGCAACCGTGATATCTCTTAACAAAGAACATGCTATCATGTGACACATGGTTAA
66 ATCTTAATTCCTGCAACCGTGATATCTCTTAACAAAGAACATGCTATCATGTGACACATGGTTAA
424317 GAAGATTGGGTATTTAAAACCATTTACTGAACCAATTTATGTGAACAATAATCTTATTTTGATGC
131 GAAGATTGGGTATTTAAAACCATTTACTGAACCAATTTATGTGAACAATAATCTTATTTTGATGC
424382 AATAGCAAGACTACATATACAGTGGTACAGGCTCTTAAAAAATCCGCACCC
196 AATAGCAAGACTACATATA-AGTGGTACAGGCTCTTAAAAAATCCGCACCC
424433 ATACAACAT
1 ATACAACAT
424442 GTTGATTCTG
Statistics
Matches: 250, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
243 194 0.78
244 12 0.05
245 4 0.02
246 24 0.10
247 16 0.06
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (245 bp):
ATACAACATTCAAAGATAAAATTTTAAGGAACTGAGCCCTAGATTGAATGGCCTGCCAGGGGACT
ATCTTAATTCCTGCAACCGTGATATCTCTTAACAAAGAACATGCTATCATGTGACACATGGTTAA
GAAGATTGGGTATTTAAAACCATTTACTGAACCAATTTATGTGAACAATAATCTTATTTTGATGC
AATAGCAAGACTACATATAAGTGGTACAGGCTCTTAAAAAATCCGCACCC
Found at i:426817 original size:21 final size:21
Alignment explanation
Indices: 426791--426843 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
426781 TATAACAGGT
*
426791 GTTTCTTAGCATCCTTAGTCC
1 GTTTCTTAACATCCTTAGTCC
426812 GTTTCTTAACATCCTTAGTCC
1 GTTTCTTAACATCCTTAGTCC
*
426833 ATTTCTTAACA
1 GTTTCTTAACA
426844 CATTTTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.43
Consensus pattern (21 bp):
GTTTCTTAACATCCTTAGTCC
Found at i:431293 original size:2 final size:2
Alignment explanation
Indices: 431286--431314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
431276 ATAAAGAAGA
431286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
431315 AACTATAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:432058 original size:148 final size:150
Alignment explanation
Indices: 431844--432126 Score: 398
Period size: 148 Copynumber: 1.9 Consensus size: 150
431834 TAATTTTAAG
* * * * *
431844 AAAATATATTAATATATATATATATATATTTATATTTATAAATAAGATATTTATTTACTTAGAAA
1 AAAATATATTAAAATAAATATATATATATATATATTTATAAATAAGATATTTATATACTTAAAAA
* * *
431909 TATCAGAAAA-GGACTTTTAGGTGCTTTAAGA-TAGCTCATTTCTTAATATTAAAAAATAAATAA
66 TATCA-AAAAGGGACTTCTAGGTGCTTTAAGACAATCT-ATTTCTTAATATTAAAAAATAAATAA
431972 ATATTAATAAAATATTTCTCTA
129 ATATTAATAAAATATTTCTCTA
* *
431994 AAAATA-ATTAAAATAAAT-TA-ATATATATA-ATTTATAAAAATAGGATATTTATATATTTAAA
1 AAAATATATTAAAATAAATATATATATATATATATTTAT--AAATAAGATATTTATATACTTAAA
432055 AATATCAAAAAGGGACTTCTAGGTGCTTTAAGACAATCTATTTCTTAATATTAAAAAATAAATAA
64 AATATCAAAAAGGGACTTCTAGGTGCTTTAAGACAATCTATTTCTTAATATTAAAAAATAAATAA
432120 ATATTAA
129 ATATTAA
432127 AATATGATTA
Statistics
Matches: 119, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
146 6 0.05
147 12 0.10
148 82 0.69
149 13 0.11
150 6 0.05
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (150 bp):
AAAATATATTAAAATAAATATATATATATATATATTTATAAATAAGATATTTATATACTTAAAAA
TATCAAAAAGGGACTTCTAGGTGCTTTAAGACAATCTATTTCTTAATATTAAAAAATAAATAAAT
ATTAATAAAATATTTCTCTA
Found at i:435434 original size:39 final size:39
Alignment explanation
Indices: 435374--435449 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
435364 CCTGGCAGTG
*
435374 CTGGAAGCTGCTGCAACTGATGCGTGGACGGGCTGCTCA
1 CTGGAAGCTGCTGCAAATGATGCGTGGACGGGCTGCTCA
* * *
435413 CTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 CTGGAAGCTGCTGCAAATGATGCGTGGACGGGCTGCT
435450 GGATGGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.18, C:0.20, G:0.39, T:0.22
Consensus pattern (39 bp):
CTGGAAGCTGCTGCAAATGATGCGTGGACGGGCTGCTCA
Found at i:436053 original size:139 final size:137
Alignment explanation
Indices: 435701--436053 Score: 456
Period size: 139 Copynumber: 2.5 Consensus size: 137
435691 CAAAAAGTTA
* * * * * *
435701 AACAAATTATTCTCATTATAAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCC
1 AACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * * *
435766 TTCTGGAAATGCTGATCTTCAAAAGAGGGATTTGTTGATTCAACTCCATATGTGATGAATTAAGG
66 -TCTGGAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAATTAAGG
*
435831 TAAGGTTG
130 CAAGGTTG
*
435839 AACAAATTCTTCTTATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 AACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TT
* * * * *
435904 CTCTGAAAATATTGATCCTCAAATGAGGTTATTCT-TTCATTCAATTCCATAGGAGATGAATTAA
65 CTCTGGAAATACTGATCCTCAAAAGAGG-GATT-TGTTCATTCAACTCCATAGGAGATGAATTAA
*
435968 TGCAAGGTTG
128 GGCAAGGTTG
* *
435978 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 AACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
*
436043 ACCTGGAAATA
66 -TCTGGAAATA
436054 GCTCTGCTGC
Statistics
Matches: 187, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
138 81 0.43
139 105 0.56
140 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (137 bp):
AACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTC
TCTGGAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAATTAAGGC
AAGGTTG
Found at i:436133 original size:124 final size:122
Alignment explanation
Indices: 435971--436399 Score: 381
Period size: 124 Copynumber: 3.6 Consensus size: 122
435961 GAATTAATGC
* *
435971 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
436036 GAACTTCACCTGGAAATAGCT-CTGCTGCTCTAT-CTCTT-TTTGGAAATGGAGTCCA-GCAA
66 GAACTTC-CCTGGAAA-AGCTGCTGCTGATCTATATTCTTCTGT-G--ATGGAGT-CATGAAA
* *
436095 AAGGTTGAATAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * *
436160 AAACTTTCTCTGGAAAAGTTGGTGTTGATCTATATTCTTCTGTGATTGAGTCATGAAA
66 GAAC-TTCCCTGGAAAAGCTGCTGCTGATCTATATTCTTCTGTGATGGAGTCATGAAA
* * * *
436218 AAGGTTGAACAAGCTCATCTCATTATGAAC-TTCTTTTTCCTCTTCAGATAAATTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTC-TCTTCCTCTTCAGATAAGTTCTTCTCATTA
* * * ** * *
436282 TGAACTTTCTCTGG-CAA-C-G-T--TGATC--CA-TC--GGGTGAT-GAAT-TTGAGCAA
65 TGAAC-TTCCCTGGAAAAGCTGCTGCTGATCTATATTCTTCTGTGATGGAGTCATGA--AA
* * *
436330 AAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
436395 GAACT
66 GAACT
436400 CTTCTGGAAA
Statistics
Matches: 261, Mismatches: 35, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
110 3 0.01
111 4 0.02
112 66 0.25
113 2 0.01
114 2 0.01
115 1 0.00
117 5 0.02
119 1 0.00
120 1 0.00
122 7 0.03
123 79 0.30
124 80 0.31
125 8 0.03
126 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTCCCTGGAAAAGCTGCTGCTGATCTATATTCTTCTGTGATGGAGTCATGAAA
Found at i:436274 original size:123 final size:122
Alignment explanation
Indices: 435971--436411 Score: 403
Period size: 123 Copynumber: 3.7 Consensus size: 122
435961 GAATTAATGC
*
435971 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTT-TTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
436036 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCCAGCAA
65 GAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCTTTGTGG-AATGGAGTCCAGAAA
* * *
436095 AAGGTTGAATAAGTTCTTCTCATTATGAACTTTCTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTT-TTTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * *
436160 AAACTTTCTCTGGAAA-AGTTGGTGTTGATCTATATTCTTCTGT-G-ATTGAGT-CATGAAA
65 GAACTTTCTCTGGAAATAGCT-CTGCTGATCTAT-CTCTT-TGTGGAATGGAGTCCA-GAAA
* * *
436218 AAGGTTGAACAAGCTCATCTCATTATGAACTTCTTTTTCCTCTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTTTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * ** * * ** *
436283 GAACTTTCTCTGG-CA-A---C-GTTGATCCA--TC-GGGT-G-ATGAATTTGAGCAA
65 GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCTTTGTGGAATGGAGTCCAGAAA
* *
436330 AAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTT-TTCCTCTTCAGATAAGTTCTTCTCATTAT
*
436395 GAACTCT-TCTGGAAATA
65 GAACTTTCTCTGGAAATA
436412 TTGACAACAT
Statistics
Matches: 268, Mismatches: 38, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
111 8 0.03
112 73 0.27
113 2 0.01
114 2 0.01
117 8 0.03
122 4 0.01
123 81 0.30
124 79 0.29
125 9 0.03
126 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTTTCCTCTTCAGATAAGTTCTTCTCATTATG
AACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCTTTGTGGAATGGAGTCCAGAAA
Found at i:436594 original size:73 final size:73
Alignment explanation
Indices: 436460--436766 Score: 436
Period size: 73 Copynumber: 4.2 Consensus size: 73
436450 GAGGTCTTAT
* *
436460 CATCTTGCACTGTATGG-CTTACAGATGACCCTGAGGCTTTAAGATCAAAAAACTCCCGAAGGCT
1 CATCATGCACTGTA-GGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCT
436524 TTTTGAAAA
65 TTTTGAAAA
* * * * *
436533 CATCATGCACTGTAGGTCTTACATATGACCCTGAGGCTATAAGATCAAAAGGCTTCTGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
436598 TTTGAGAA
66 TTTGAAAA
436606 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
436671 TTTGAAAA
66 TTTGAAAA
* * * * *
436679 CATCATGCACTGTAGGTCTTACAGTTGACCCTAAGGGTTTTGAAAACATCAAAAAACTCCCGAAG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGA-GGCTTT---AAGATCAAAAAGCTCCCGAAG
436744 GCTTTTTGAAAA
62 GCTTTTTGAAAA
*
436756 CATCCTGCACT
1 CATCATGCACT
436767 ACAGGGCTTA
Statistics
Matches: 209, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
72 2 0.01
73 161 0.77
74 5 0.02
77 41 0.20
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:437490 original size:22 final size:22
Alignment explanation
Indices: 437453--437510 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
437443 GATAAAGCTT
* *
437453 TCATATTCGAAAAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
437475 TCATCTTTGAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
437497 TCATATTTGAAGAG
1 TCATATTTGAAGAG
437511 TGTAGATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATATTTGAAGAGAGAATCTA
Found at i:437899 original size:54 final size:54
Alignment explanation
Indices: 437817--437971 Score: 148
Period size: 55 Copynumber: 2.9 Consensus size: 54
437807 AATTATTGGT
* ** * *
437817 TCGTAAAACACTTGACAATGCATTCATCATTTCTTGTGGCTTATGCTCAGAGGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGCCCAGAGGC
* * * * * * *
437871 TCGTAAAACATTTGACAACACGTTCATCATTCTCACGCGGTTTCTGCCCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCATT-TCATGTGGCTTATGCCCAGAGGC
* * * * *
437926 TCATAAAACATTTAATAACACATTCATCTTTTCCTGTGGCTTATGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGC
437972 ATAAATTTAT
Statistics
Matches: 78, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
54 37 0.47
55 41 0.53
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGCCCAGAGGC
Found at i:444343 original size:38 final size:39
Alignment explanation
Indices: 444270--444343 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
444260 TGCATCAAAC
* *
444270 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTATCT
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
* * *
444309 AAAAC-TTTACATATAGGGGATAATTTTCCCTCCTA
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTA
444344 AATTCTCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 25 0.83
39 5 0.17
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (39 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
Found at i:446207 original size:20 final size:22
Alignment explanation
Indices: 446184--446225 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
446174 TTCAAAAATA
446184 TATTT-AA-TTTATAATATTAT
1 TATTTAAATTTTATAATATTAT
*
446204 TATTTAAATTTTATAATTTTAT
1 TATTTAAATTTTATAATATTAT
446226 GAAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTAAATTTTATAATATTAT
Found at i:446382 original size:18 final size:19
Alignment explanation
Indices: 446347--446395 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
446337 ATATTAAAGC
446347 ATTTATTAAAATAGATATA
1 ATTTATTAAAATAGATATA
446366 ATTTA-TAAAAGTA-ATAT-
1 ATTTATTAAAA-TAGATATA
446383 A-TTATTTAAAATA
1 ATTTA-TTAAAATA
446396 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 3 0.11
18 14 0.52
19 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
ATTTATTAAAATAGATATA
Found at i:446659 original size:12 final size:12
Alignment explanation
Indices: 446645--446683 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
446635 GAATAAGATA
446645 AAAACAATAA-T
1 AAAACAATAATT
*
446656 AAAATAATAATT
1 AAAACAATAATT
*
446668 AAAGCAATAATT
1 AAAACAATAATT
446680 AAAA
1 AAAA
446684 TATAAAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (12 bp):
AAAACAATAATT
Found at i:446691 original size:20 final size:19
Alignment explanation
Indices: 446642--446704 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 19
446632 TATGAATAAG
*
446642 ATAAAAACAATAATAAAAT
1 ATAAAAGCAATAATAAAAT
446661 AATAATTAAAGCAATAATTAAAAT
1 -AT-A--AAAGCAATAA-TAAAAT
* *
446685 ATAAAAGTAATGATAAAAT
1 ATAAAAGCAATAATAAAAT
446704 A
1 A
446705 ATATTGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 7 0.19
20 10 0.28
21 1 0.03
22 1 0.03
23 11 0.31
24 6 0.17
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (19 bp):
ATAAAAGCAATAATAAAAT
Found at i:449020 original size:3 final size:3
Alignment explanation
Indices: 449012--449051 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
449002 AATATTTATT
*
449012 TAA TAA TAA TTA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
449052 AGGCAAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:449036 original size:19 final size:19
Alignment explanation
Indices: 449012--449048 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
449002 AATATTTATT
*
449012 TAATAATAATTATAATAAA
1 TAATAATAATAATAATAAA
449031 TAATAATAATAATAATAA
1 TAATAATAATAATAATAA
449049 TAAAGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAATAATAATAATAAA
Found at i:455897 original size:53 final size:55
Alignment explanation
Indices: 455817--455936 Score: 208
Period size: 53 Copynumber: 2.2 Consensus size: 55
455807 CGGTTCTTGC
455817 AAAATAAAAATAGAAATTAAATTAAACATGCTTAATGAAAC-AAAA-AAAAAGTA
1 AAAATAAAAATAGAAATTAAATTAAACATGCTTAATGAAACAAAAACAAAAAGTA
*
455870 AAAATAAAAATAGAAATTAAATTAAACATGCTTGATGAAACAAAAACAAAAAGTA
1 AAAATAAAAATAGAAATTAAATTAAACATGCTTAATGAAACAAAAACAAAAAGTA
*
455925 AAAATTAAAATA
1 AAAATAAAAATA
455937 TAGCGGAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 40 0.63
54 4 0.06
55 19 0.30
ACGTcount: A:0.66, C:0.06, G:0.07, T:0.21
Consensus pattern (55 bp):
AAAATAAAAATAGAAATTAAATTAAACATGCTTAATGAAACAAAAACAAAAAGTA
Found at i:458645 original size:94 final size:94
Alignment explanation
Indices: 458484--458671 Score: 324
Period size: 94 Copynumber: 2.0 Consensus size: 94
458474 TTGGTTCAAG
458484 TTTTCCCTCAGAATTTTTTATCACAGTAACTCCTTTTTTTAGGAACTACGTGTATCGGACTTACC
1 TTTTCCCTCAGAATTTTTTATCACAGTAACTCCTTTTTTTAGGAACTACGTGTATCGGACTTACC
* *
458549 CATTTGCTATCCGAAATTGGATATATAAT
66 CATTCGCTATCCGAAATTGGAAATATAAT
* *
458578 TTTTCCTTCAGAATTTTTTTATCATAGTAACT-CTTTTTTTAGGAACTACGTGTATCGGACTTAC
1 TTTTCCCTCAGAA-TTTTTTATCACAGTAACTCCTTTTTTTAGGAACTACGTGTATCGGACTTAC
458642 CCATTCGCTATCCGAAATTGGAAATATAAT
65 CCATTCGCTATCCGAAATTGGAAATATAAT
458672 ATCTGCATCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 72 0.81
95 17 0.19
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (94 bp):
TTTTCCCTCAGAATTTTTTATCACAGTAACTCCTTTTTTTAGGAACTACGTGTATCGGACTTACC
CATTCGCTATCCGAAATTGGAAATATAAT
Found at i:461558 original size:19 final size:19
Alignment explanation
Indices: 461517--461563 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
461507 GTAATGAGAT
* *
461517 ATTTAAAT-AATAAAAGCG
1 ATTTAAATAAATAAAAACA
461535 A-TTAAATAAATAAAAACA
1 ATTTAAATAAATAAAAACA
461553 ATTTAAATAAA
1 ATTTAAATAAA
461564 AATAATAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAACA
Found at i:466326 original size:24 final size:24
Alignment explanation
Indices: 466295--466340 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
466285 AAACACAATA
*
466295 ATTTG-AAAATTAACATTTTTTTT
1 ATTTGAAAAATTAAAATTTTTTTT
466318 ATTTCGAAAAATTAAAATTTTTT
1 ATTT-GAAAAATTAAAATTTTTT
466341 GGAAAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 1 0.05
25 15 0.75
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTGAAAAATTAAAATTTTTTTT
Found at i:466738 original size:21 final size:21
Alignment explanation
Indices: 466712--466751 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
466702 AGAACCCCAG
*
466712 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
466733 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
466752 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:466786 original size:20 final size:21
Alignment explanation
Indices: 466732--466794 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
466722 GATTCCCCTG
466732 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
466756 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
466776 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
466795 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:474967 original size:15 final size:15
Alignment explanation
Indices: 474947--474989 Score: 77
Period size: 15 Copynumber: 2.8 Consensus size: 15
474937 CTTTGAAAAA
474947 ATCCATCTCTTTATC
1 ATCCATCTCTTTATC
474962 ATCCATCTCTTTATC
1 ATCCATCTCTTTATC
474977 ATCCATCATCTTT
1 ATCCATC-TCTTT
474990 TGTACCAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.47
Consensus pattern (15 bp):
ATCCATCTCTTTATC
Found at i:476150 original size:18 final size:18
Alignment explanation
Indices: 476129--476167 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
476119 AACTTTGAAC
476129 TTAGGAGGAAACACCAAA
1 TTAGGAGGAAACACCAAA
476147 TT---AGGAAACACCAAA
1 TTAGGAGGAAACACCAAA
476162 TTAGGA
1 TTAGGA
476168 ACCAAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 6
0.75 0.00 0.25
Matches are distributed among these distances:
15 15 0.83
18 3 0.17
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (18 bp):
TTAGGAGGAAACACCAAA
Found at i:476154 original size:15 final size:15
Alignment explanation
Indices: 476134--476168 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
476124 TGAACTTAGG
476134 AGGAAACACCAAATT
1 AGGAAACACCAAATT
476149 AGGAAACACCAAATT
1 AGGAAACACCAAATT
476164 AGGAA
1 AGGAA
476169 CCAAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.11
Consensus pattern (15 bp):
AGGAAACACCAAATT
Found at i:482702 original size:3 final size:3
Alignment explanation
Indices: 482690--482736 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
482680 TGTAATTATT
482690 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
482737 GAACAACAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:484192 original size:26 final size:26
Alignment explanation
Indices: 484158--484216 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
484148 TTTTCTCCCA
*
484158 TAAAATTTTATAAATTTATCATCTCC
1 TAAAATTTTATAAATTTATCACCTCC
* *
484184 TAAAATTTTATAAATTTGTCCCCTCC
1 TAAAATTTTATAAATTTATCACCTCC
484210 TAAAATT
1 TAAAATT
484217 CTAGAGATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAATTTTATAAATTTATCACCTCC
Found at i:484230 original size:26 final size:25
Alignment explanation
Indices: 484180--484237 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
484170 AATTTATCAT
* * *
484180 CTCCTAAAATTTTATAAATTTGTCCC
1 CTCCTAAAATTCTAGAAATTCGT-CC
*
484206 CTCCTAAAATTCTAGAGATTCGTCC
1 CTCCTAAAATTCTAGAAATTCGTCC
484231 CTCCTAA
1 CTCCTAA
484238 CTTAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (25 bp):
CTCCTAAAATTCTAGAAATTCGTCC
Found at i:485392 original size:32 final size:32
Alignment explanation
Indices: 485351--485411 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
485341 AATAAAACTC
*
485351 TTCGATTACTGTCTGCCCCGTCTATTAACCTG
1 TTCGATTACTCTCTGCCCCGTCTATTAACCTG
485383 TTCGATTACTCTCTGCCCCGTCTATTAAC
1 TTCGATTACTCTCTGCCCCGTCTATTAAC
485412 AACCCTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.13, T:0.38
Consensus pattern (32 bp):
TTCGATTACTCTCTGCCCCGTCTATTAACCTG
Found at i:493341 original size:15 final size:14
Alignment explanation
Indices: 493304--493364 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
493294 CCTATGTAGA
*
493304 AAAAAGAGGGGAGG
1 AAAAAGAGAGGAGG
493318 AAAAAGAGAGGAGG
1 AAAAAGAGAGGAGG
493332 AAAAATGAGA-GA--
1 AAAAA-GAGAGGAGG
493344 AAAAA-AGAGGA-G
1 AAAAAGAGAGGAGG
493356 -AAAAGAGAG
1 AAAAAGAGAG
493365 AAAATGGAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 9 0.21
14 20 0.48
15 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.02
Consensus pattern (14 bp):
AAAAAGAGAGGAGG
Found at i:493363 original size:22 final size:25
Alignment explanation
Indices: 493317--493368 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
493307 AAGAGGGGAG
*
493317 GAAAAAGAGAGGAGGAAAAATGAGA
1 GAAAAAAAGAGGAGGAAAAATGAGA
493342 GAAAAAAAGAGGA-G-AAAA-GAGA
1 GAAAAAAAGAGGAGGAAAAATGAGA
493364 GAAAA
1 GAAAA
493369 TGGAGAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 4 0.15
24 1 0.04
25 12 0.46
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (25 bp):
GAAAAAAAGAGGAGGAAAAATGAGA
Found at i:493621 original size:6 final size:6
Alignment explanation
Indices: 493610--493667 Score: 71
Period size: 6 Copynumber: 9.5 Consensus size: 6
493600 TAAAGGCAAC
* * *
493610 ATTTTT ATTTTT ATTTTT ATTTTC ATTTTC ATTTTT ATCTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
493658 GAGTTTT ATT
1 -ATTTTT ATT
493668 GTTTCGGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 40 0.89
7 5 0.11
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:495031 original size:45 final size:45
Alignment explanation
Indices: 494982--495432 Score: 582
Period size: 45 Copynumber: 10.2 Consensus size: 45
494972 TATTCATTAT
* * *
494982 TTTCATTTATGGTATCCTTTCATGCCCTTAATGCACAGTTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
** * * *
495027 TTTCATTTATGGTGTCTTTTCATGCCTTTAATGCATAGTTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
*
495072 TTTCATTTATGGCGTCCTTTCATGCCTTTAATGCATC-GTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCA-CAGTTATGCA
* *
495117 TTTCATTTATGGCATCCTTTTATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
*
495162 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
*
495207 TTTCATTTATGGCATCCTTTCATGCCTTTAATACACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
* * * *
495252 TTTCGTTTATAGCATCATTTCATG-CTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
* * *
495296 TTCCATTTATGGCA-----T-AT---TTTCATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
* * *
495332 TTTCATTGATGGCATCTTTTCATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
* *
495377 TTTCATTTATGACATCCTTTCATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
*
495422 TTTTATTTATG
1 TTTCATTTATG
495433 TAATGAAAAC
Statistics
Matches: 364, Mismatches: 31, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
36 30 0.08
38 2 0.01
39 1 0.00
41 1 0.00
42 2 0.01
44 30 0.08
45 298 0.82
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCA
Found at i:495321 original size:36 final size:36
Alignment explanation
Indices: 495281--495356 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
495271 TCATGCTTTA
*
495281 ATGCACCGTTATGCATTCCATTTATGGCATATTTTC
1 ATGCACCGTTATGCATTCCATTGATGGCATATTTTC
* *
495317 ATGCACCGTTATGCATTTCATTGATGGCATCTTTTC
1 ATGCACCGTTATGCATTCCATTGATGGCATATTTTC
495353 ATGC
1 ATGC
495357 CTTTAATGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (36 bp):
ATGCACCGTTATGCATTCCATTGATGGCATATTTTC
Found at i:495338 original size:125 final size:126
Alignment explanation
Indices: 495192--495432 Score: 369
Period size: 125 Copynumber: 1.9 Consensus size: 126
495182 CATGCCTTTA
* * *
495192 ATGCACTGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATACACAGTTATGCATTTCG
1 ATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATGCCTTTAATACACAGTTATGCATTTCA
495257 TTTAT-AGCATCATTTCATG-CTTTAATGCACCGTTATGCATTCCATTTATGGCATATTTTC
66 TTTATGA-CATCATTTCATGCCTTTAATGCACCGTTATGCATTCCATTTATGGCATATTTTC
* * *
495317 ATGCACCGTTATGCATTTCATTGATGGCATCTTTTCATGCCTTTAATGCACTGTTATGCATTTCA
1 ATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATGCCTTTAATACACAGTTATGCATTTCA
* * **
495382 TTTATGACATCCTTTCATGCCTTTAATGCACTGTTATGCATTTTATTTATG
66 TTTATGACATCATTTCATGCCTTTAATGCACCGTTATGCATTCCATTTATG
495433 TAATGAAAAC
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
125 75 0.72
126 29 0.28
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (126 bp):
ATGCACCGTTATGCATTTCATTGATGGCATCCTTTCATGCCTTTAATACACAGTTATGCATTTCA
TTTATGACATCATTTCATGCCTTTAATGCACCGTTATGCATTCCATTTATGGCATATTTTC
Found at i:495384 original size:81 final size:80
Alignment explanation
Indices: 495244--495401 Score: 226
Period size: 81 Copynumber: 2.0 Consensus size: 80
495234 TTAATACACA
* * *
495244 GTTATGCATTTCGTTTATAGCATCATTTCATGCTTTAATGCACCGTTATGCATTCCATTTATGGC
1 GTTATGCATTTCATTGATAGCATCATTTCATGCTTTAATGCACCGTTATGCATTCCATTTATGAC
*
495309 ATATTTTCATGCACC
66 ATACTTTCATGCACC
* * * *
495324 GTTATGCATTTCATTGATGGCATCTTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGA
1 GTTATGCATTTCATTGATAGCATCATTTCATG-CTTTAATGCACCGTTATGCATTCCATTTATGA
*
495389 CATCCTTTCATGC
65 CATACTTTCATGC
495402 CTTTAATGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 28 0.41
81 40 0.59
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.44
Consensus pattern (80 bp):
GTTATGCATTTCATTGATAGCATCATTTCATGCTTTAATGCACCGTTATGCATTCCATTTATGAC
ATACTTTCATGCACC
Found at i:495909 original size:95 final size:96
Alignment explanation
Indices: 495766--495966 Score: 237
Period size: 95 Copynumber: 2.1 Consensus size: 96
495756 CCCGACCATG
* * * *
495766 GTATCGATACTTCTATACTATGGTATCGATACGCCCTTCTAGTATCGATACCATTTCTATATTAT
1 GTATCGATACTTCTATACTAAGGTATCGATACGCCCTTCTACTATCGATACCATTTCGACATTAT
* * * *
495831 -GTAATTCATGGTATCGATACCTTTGTCTTA
66 GGAAATCCATGGTATCGATACATTTCTCTTA
** *
495861 GTATCGATACTTCTATTA-TAAGGTATTTATACTCCCTT-TCACTATCGATACCATTTCGACATT
1 GTATCGATACTTCTA-TACTAAGGTATCGATACGCCCTTCT-ACTATCGATACCATTTCGACATT
* * *
495924 CTGGAAATCCCTGGTATCGATACATTTCTCTTG
64 ATGGAAATCCATGGTATCGATACATTTCTCTTA
495957 GTATCGATAC
1 GTATCGATAC
495967 CCACAGCAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
94 1 0.01
95 52 0.58
96 36 0.40
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (96 bp):
GTATCGATACTTCTATACTAAGGTATCGATACGCCCTTCTACTATCGATACCATTTCGACATTAT
GGAAATCCATGGTATCGATACATTTCTCTTA
Found at i:501232 original size:135 final size:134
Alignment explanation
Indices: 500890--501660 Score: 947
Period size: 135 Copynumber: 5.7 Consensus size: 134
500880 GTGATGGAAA
* * * * * *
500890 CGAGCTAAGGTTGAACAAGTACTTCACATTATGAACTTCTTCTTCATC-ATCGGATGAGTTCTTC
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
* * * * *
500954 TCATTATGAACTCTCTATTGAAAATATTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATA
66 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAA----A-A
501019 TTCGATGAAT
126 TTC-ATGAAT
* * * * * * **
501029 CGAGCTAAGGTTGAACAAGTTTTTTTTATTATGAACTTTTTTCTCCCTC-ATCAAATGAGTTCTT
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAAC-TTCTTCTCCCTCTATCGGATGAGTTCTT
* * * * * *
501093 CTCATTATGAATTCTCCAATGGAAATGTTGATCCCTCAAGTGAGGTATTGCTAATTCAAAATTCT
65 CTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAAAATTC-
*
501158 GTGAAT
129 ATGAAT
* * * *
501164 CGAGAAAAGGTTGAACAAGTTCTTCTCGTTACGAACTTCTTTTCCCTCTATTGGATGAGTTCTTC
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
* * * *
501229 TCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGG-CTCGCTAATTCAAAATGACA
66 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAAAAT-TCA
501293 TGAAT
130 TGAAT
* *
501298 CAAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCCCTATCGGATGAGTTCTTC
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
* **
501363 TCATTATAAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCATTGATTCAAAATGTCA
66 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAAAAT-TCA
501428 TGAAT
130 TGAAT
* * * *
501433 CGAGCAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCTATCTGATGTGTTCTTC
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
* *
501498 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCT-TCACTGATTCAAAATGCC
66 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGG-TGTCGCTGATTCAAAAT-TC
501562 ATGAAT
129 ATGAAT
* * * *
501568 CGAGCAAAGATTGAACAAGTTCTTCTCATTACTAACTTATTCTCCCTCTATCGGATGAGTTTTTC
1 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
* *
501633 TCATTATGAACTCTCAATTAGAAATGTT
66 TCATTATGAACTCTCCATTGGAAATGTT
501661 GATTGGTTTA
Statistics
Matches: 554, Mismatches: 73, Indels: 14
0.86 0.11 0.02
Matches are distributed among these distances:
134 130 0.23
135 319 0.58
136 2 0.00
139 31 0.06
140 72 0.13
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (134 bp):
CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAAAATTCAT
GAAT
Found at i:501387 original size:269 final size:268
Alignment explanation
Indices: 500896--501663 Score: 961
Period size: 269 Copynumber: 2.8 Consensus size: 268
500886 GAAACGAGCT
* * * *
500896 AAGGTTGAACAAGTACTTCACATTATGAACTTCTTCTT-CATC-ATCGGATGAGTTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCCTCTATTGGATGAGTTCTTCTCATT
* * * * * *
500959 ATGAACTCTCTATTGAAAATATTGATCCCTCGAGTGAGGTGTCGCTGATTCAACTCCATAT-TCG
65 ATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGG-CTCGCTGATTCAA----A-ATGAC-
* * * * * * * **
501023 ATGAATCGAGCTAAGGTTGAACAAGTTTTTTTTATTATGAACTTTTTTCTCCCTCATCAAATGAG
123 ATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTTTCTCCCCCT-ATCGGATGAG
* * **
501088 TTCTTCTCATTATGAATTCTCCAATGGAAATGTTGATCCCTCAAGTGAGGTATTGCTAATTCAAA
187 TTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGTGAGGTATCACTAATTCAAA
*
501153 AT-TCTGTGAATCGAGAA
252 ATGTC-ATGAATCGAGAA
* *
501170 AAGGTTGAACAAGTTCTTCTCGTTACGAACTTCTTTTCCCTCTATTGGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCTATTGGATGAGTTCTTCTCATTA
* *
501235 TGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGCTCGCTAATTCAAAATGACATGAATCA
66 TGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGCTCGCTGATTCAAAATGACATGAATCG
501300 AGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCCCTATCGGATGAGTTCTTCTC
131 AGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTT-TTCTCCCCCTATCGGATGAGTTCTTCTC
* * * * *
501365 ATTATAAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCATTGATTCAAAATGTCATG
195 ATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGTGAGGTATCACTAATTCAAAATGTCATG
*
501430 AATCGAGCA
260 AATCGAGAA
* * *
501439 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCTATCT-GATGTGTTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCTAT-TGGATGAGTTCTTCTCATT
* * *
501503 ATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCTTCACTGATTCAAAATGCCATGAAT
65 ATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC-TCGCTGATTCAAAATGACATGAAT
* * * *
501568 CGAGCAAAGATTGAACAAGTTCTTCTCATTACTAACTTATTCTCCCTCTATCGGATGAGTTTTTC
129 CGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTT-TTCTCCCCCTATCGGATGAGTTCTTC
* *
501633 TCATTATGAACTCTCAATTAGAAATGTTGAT
193 TCATTATGAACTCTCCATTGGAAATGTTGAT
501664 TGGTTTATAT
Statistics
Matches: 434, Mismatches: 53, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
269 212 0.49
270 120 0.28
273 2 0.00
274 45 0.10
275 55 0.13
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (268 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCTATTGGATGAGTTCTTCTCATTA
TGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGCTCGCTGATTCAAAATGACATGAATCG
AGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTTTCTCCCCCTATCGGATGAGTTCTTCTCA
TTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGTGAGGTATCACTAATTCAAAATGTCATGA
ATCGAGAA
Found at i:503015 original size:54 final size:54
Alignment explanation
Indices: 502903--503068 Score: 172
Period size: 54 Copynumber: 3.1 Consensus size: 54
502893 TATGGCTATT
* * * * * * ** ***
502903 ATCAAGAAATCCCAAAAAATTAGGCTTAGCTTCTTTAAAAATTCATCGGAAGTG
1 ATCAAGAAACCCCTAAAAATTAGGCTAAGTTTCTTTCAAAACTCATTTGAAAAC
* *
502957 ATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTGCAAACCT-ATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATTAGGCTAAGTTTCTTT-CAAAACTCATTTGAAAAC
* * *
503011 ATCAAGAAGCCCCTAAAAATTGGGCTAAGTTTCTTTCAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATTAGGCTAAGTTTCTTTCAAAACTCATTTGAAAAC
503065 ATCA
1 ATCA
503069 CACTATTTGG
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
53 5 0.05
54 85 0.90
55 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (54 bp):
ATCAAGAAACCCCTAAAAATTAGGCTAAGTTTCTTTCAAAACTCATTTGAAAAC
Found at i:505445 original size:26 final size:26
Alignment explanation
Indices: 505406--505456 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
505396 AAATACTTTA
505406 GGTCATTTTACACTTTAGGGGCATTTT
1 GGTCATTTTACACTTTA-GGGCATTTT
505433 GGTCA-TTTACACTTTAGGGCATTT
1 GGTCATTTTACACTTTAGGGCATTT
505457 CTATGAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 8 0.33
26 11 0.46
27 5 0.21
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (26 bp):
GGTCATTTTACACTTTAGGGCATTTT
Found at i:506379 original size:14 final size:14
Alignment explanation
Indices: 506357--506426 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
506347 CTGAACGCTC
*
506357 AACGGGTTGACTCA
1 AACGAGTTGACTCA
506371 AACGAGTTGACTCA
1 AACGAGTTGACTCA
* * *
506385 GATGGGTTGACTCA
1 AACGAGTTGACTCA
* *
506399 GACGAGTTGAATCA
1 AACGAGTTGACTCA
*
506413 GAATGAGTTGACTC
1 -AACGAGTTGACTC
506427 GGTTACTGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
14 35 0.78
15 10 0.22
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (14 bp):
AACGAGTTGACTCA
Found at i:506393 original size:28 final size:29
Alignment explanation
Indices: 506360--506426 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
506350 AACGCTCAAC
*
506360 GGGTTGACTCAAACGAGTTGACTCAG-AT
1 GGGTTGACTCAAACGAGTTGAATCAGAAT
*
506388 GGGTTGACTCAGACGAGTTGAATCAGAAT
1 GGGTTGACTCAAACGAGTTGAATCAGAAT
*
506417 GAGTTGACTC
1 GGGTTGACTC
506427 GGTTACTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (29 bp):
GGGTTGACTCAAACGAGTTGAATCAGAAT
Found at i:509832 original size:30 final size:29
Alignment explanation
Indices: 509775--509846 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
509765 AAATTTTGTC
* **
509775 TAGTGACTAAAATATAACTTTTGAAAGTT
1 TAGTGGCTAAAATATAACTTTAAAAAGTT
*
509804 TAGTGGCTAAAGTATAAACTTTAAAAAGTT
1 TAGTGGCTAAAATAT-AACTTTAAAAAGTT
509834 TAAG-GGCTAAAAT
1 T-AGTGGCTAAAAT
509847 TGTAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.36
30 21 0.58
31 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (29 bp):
TAGTGGCTAAAATATAACTTTAAAAAGTT
Found at i:511548 original size:15 final size:15
Alignment explanation
Indices: 511530--511561 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
511520 TTTAGTTGAT
511530 ATCTATTTAATCTCA
1 ATCTATTTAATCTCA
511545 ATCTATTTAATCTCA
1 ATCTATTTAATCTCA
511560 AT
1 AT
511562 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (15 bp):
ATCTATTTAATCTCA
Found at i:518784 original size:22 final size:21
Alignment explanation
Indices: 518744--518877 Score: 114
Period size: 22 Copynumber: 6.1 Consensus size: 21
518734 AACAAAGAGT
*
518744 AAAAAGAAAAA-AATGAAGAAA
1 AAAAAGAAAAAGAA-AAAGAAA
*
518765 AAAAATGAAACAGAAAAAGAAA
1 AAAAA-GAAAAAGAAAAAGAAA
*
518787 GAAATAGAAAAAGAAAAA-AACA
1 -AAAAAGAAAAAGAAAAAGAA-A
518809 GAAAAAGAAAAAGAAAAA-AAGA
1 -AAAAAGAAAAAGAAAAAGAA-A
518831 GTAAAAAGAAAAAGAAAAAGAAA
1 --AAAAAGAAAAAGAAAAAGAAA
*
518854 ATGAAA-AAAAGAGAAAAAGAAA
1 A-AAAAGAAAA-AGAAAAAGAAA
518876 AA
1 AA
518878 GTGAAAAAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
21 12 0.12
22 58 0.60
23 24 0.25
24 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAGAAA
Found at i:518813 original size:7 final size:6
Alignment explanation
Indices: 518744--518878 Score: 103
Period size: 6 Copynumber: 24.0 Consensus size: 6
518734 AACAAAGAGT
* * *
518744 AAAAAG AAAAA- AATGAAG -AAAA- AAAATG AAACAG AAAAAG --AAAG
1 AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * *
518788 AAATAG AAAAAG -AAAA- AAACAG AAAAAG AAAAAG -AAAA- AAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
518832 TAAAAAG AAAAAG AAAAAG AAAATG -AAAA- AAAGAG AAAAAG AAAAAG
1 -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
518879 TGAAAAAATG
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
4 4 0.04
5 27 0.27
6 64 0.64
7 5 0.05
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:518819 original size:16 final size:15
Alignment explanation
Indices: 518744--518877 Score: 114
Period size: 16 Copynumber: 8.7 Consensus size: 15
518734 AACAAAGAGT
*
518744 AAAAAGAAAAAAATG
1 AAAAAGAAAAAAAAG
*
518759 AAGAAAAAAAATGAAACAG
1 AA-AAAGAAAA--AAA-AG
*
518778 AAAAAGAAAGAAATAG
1 AAAAAGAAA-AAAAAG
518794 AAAAAGAAAAAAACAG
1 AAAAAGAAAAAAA-AG
*
518810 AAAAAGAAAAAGAA-
1 AAAAAGAAAAAAAAG
**
518824 AAAAAGAGTAAAAAG
1 AAAAAGAAAAAAAAG
518839 AAAAAG---AAAAAG
1 AAAAAGAAAAAAAAG
*
518851 AAAATGAAAAAAAGAG
1 AAAAAGAAAAAAA-AG
518867 AAAAAGAAAAA
1 AAAAAGAAAAA
518878 GTGAAAAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
12 11 0.11
14 11 0.11
15 16 0.16
16 44 0.45
17 2 0.02
18 9 0.09
19 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:523362 original size:3 final size:3
Alignment explanation
Indices: 523356--523393 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
523346 TAGTAATCTT
523356 TAA TAA TAA TAA TAA TAA TAA TAA TAA CTTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA
523394 CGGGACGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 30 0.91
5 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:530799 original size:110 final size:111
Alignment explanation
Indices: 530667--530892 Score: 330
Period size: 111 Copynumber: 2.0 Consensus size: 111
530657 TTAATGAATT
* *
530667 TCATCTTTATTCACTTTCCCTTAATATCATTGATTAATGTTGCTTGA-TTTTATTTTTGGCTTGT
1 TCATGTTTATTCACTTTCCCTTAATATCAATGATTAATGTTGCTTGATTTTTATTTTTGGCTTGT
* * *
530731 TT-TCAGAGATATAAACTGCCTAGTAATGCTGCGAGAGTAGGTTACA
66 TTGT-AGAGATATAAACTACCCAGTAATGCTACGAGAGTAGGTTACA
* * **
530777 TCATGTTTATTCACTTTTCCTTAGTATCAATGATTGGTGTTGCTTGATTTTTATTTTTGGCTTGT
1 TCATGTTTATTCACTTTCCCTTAATATCAATGATTAATGTTGCTTGATTTTTATTTTTGGCTTGT
* *
530842 TTGTAGAGATATAAATTACCCAGTAATGCTATGAGAGTAGGTTACA
66 TTGTAGAGATATAAACTACCCAGTAATGCTACGAGAGTAGGTTACA
530888 TCATG
1 TCATG
530893 AATAACATCA
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
110 41 0.40
111 61 0.59
112 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (111 bp):
TCATGTTTATTCACTTTCCCTTAATATCAATGATTAATGTTGCTTGATTTTTATTTTTGGCTTGT
TTGTAGAGATATAAACTACCCAGTAATGCTACGAGAGTAGGTTACA
Found at i:532513 original size:15 final size:15
Alignment explanation
Indices: 532472--532518 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
532462 GACTTTGGGA
*
532472 ATACACAACAACACT
1 ATACACAACAACAAT
532487 ATCAACAGCAACAACAAT
1 AT--ACA-CAACAACAAT
532505 ATACACAACAACAA
1 ATACACAACAACAA
532519 CCAATGTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 3 0.11
18 11 0.39
ACGTcount: A:0.57, C:0.30, G:0.02, T:0.11
Consensus pattern (15 bp):
ATACACAACAACAAT
Found at i:532516 original size:18 final size:18
Alignment explanation
Indices: 532476--532519 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
532466 TTGGGAATAC
*
532476 ACAACAACACTATCAACA
1 ACAACAACAATATCAACA
*
532494 GCAACAACAATAT-ACACA
1 ACAACAACAATATCA-ACA
532512 ACAACAAC
1 ACAACAAC
532520 CAATGTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.57, C:0.32, G:0.02, T:0.09
Consensus pattern (18 bp):
ACAACAACAATATCAACA
Found at i:534213 original size:23 final size:23
Alignment explanation
Indices: 534154--534206 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
534144 CTCGTATAAA
534154 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
534177 TGTACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
534200 TGCACCG
1 TGCACCG
534207 TACTGCCCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:541068 original size:23 final size:23
Alignment explanation
Indices: 541042--541094 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
541032 CTCGTATAAA
*
541042 TGCAGCGAAATACCACGTAGAAT
1 TGCACCGAAATACCACGTAGAAT
* * *
541065 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAATACCACGTAGAAT
541088 TGCACCG
1 TGCACCG
541095 TAGTGCCCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
TGCACCGAAATACCACGTAGAAT
Found at i:541099 original size:23 final size:23
Alignment explanation
Indices: 541057--541101 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
541047 CGAAATACCA
541057 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
541080 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
541102 CTATAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:554826 original size:22 final size:22
Alignment explanation
Indices: 554778--554828 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
554768 TTCAACTTTT
* *
554778 ATAACTCCCGGAATTATATCAT
1 ATAACTCCCGGAATTAAATCAA
*
554800 GTAAC-CCCTGGAATTAAATCAA
1 ATAACTCCC-GGAATTAAATCAA
554822 ATAACTC
1 ATAACTC
554829 ATGTAACTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.13
22 19 0.83
23 1 0.04
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (22 bp):
ATAACTCCCGGAATTAAATCAA
Found at i:556641 original size:19 final size:19
Alignment explanation
Indices: 556612--556648 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
556602 ACAAAAAATC
556612 GAGGAAGAATTTTTCTTAAG
1 GAGGAAGAATTTTT-TTAAG
556632 GAGG-AGAATTTTTTTAA
1 GAGGAAGAATTTTTTTAA
556649 TACCAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (19 bp):
GAGGAAGAATTTTTTTAAG
Done.