Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 19
Found at i:2176550 original size:19 final size:19
Alignment explanation
Indices: 2176528--2176678 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
2176518 CGAAACTAAA
2176528 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2176547 TTCGCTTTGCGA-TTT--T
1 TTCGCGTTGCGATTTTCAT
*
2176563 GT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2176580 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2176595 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2176613 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2176628 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
2176646 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
2176665 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2176679 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 24 0.24
15 3 0.03
16 8 0.08
17 8 0.08
18 3 0.03
19 42 0.43
20 10 0.10
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2176574 original size:33 final size:33
Alignment explanation
Indices: 2176532--2176658 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
2176522 ACTAAATTCG
* * *
2176532 CGTTGCGATTTTCATTTCGCTTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2176565 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2176598 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2176631 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2176659 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2176677 original size:20 final size:20
Alignment explanation
Indices: 2176631--2176724 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
2176621 GCGATTCTCT
**
2176631 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
2176650 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
2176670 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
2176689 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
2176711 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
2176725 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2179003 original size:12 final size:12
Alignment explanation
Indices: 2178986--2179022 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2178976 TCTTCGAGGA
2178986 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2178998 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2179010 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2179022 C
1 C
2179023 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2179231 original size:24 final size:24
Alignment explanation
Indices: 2179197--2179250 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2179187 CTGAAACATC
*
2179197 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2179221 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2179245 ATCAAA
1 ATCAAA
2179251 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2180111 original size:20 final size:20
Alignment explanation
Indices: 2179985--2180119 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
2179975 GATTCTGTAT
*
2179985 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2180005 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2180025 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2180045 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2180065 TATCGCGTTGCAATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
2180086 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2180106 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2180120 TTACTTATTC
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.82
21 13 0.13
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2180158 original size:21 final size:20
Alignment explanation
Indices: 2180128--2180180 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2180118 ATTTACTTAT
*
2180128 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GAAAAA
*
2180149 TCGCAATGCGAAATTGAAAAA
1 TCGCATTGCG-AATTGAAAAA
2180170 TCGCATTGCGA
1 TCGCATTGCGA
2180181 TAGTCATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGAAAAA
Found at i:2185024 original size:2 final size:2
Alignment explanation
Indices: 2185017--2185060 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2185007 TCAAAGAAGG
2185017 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2185059 CT
1 CT
2185061 TTTCTTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2185453 original size:15 final size:15
Alignment explanation
Indices: 2185433--2185461 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2185423 CTTAGGGGTT
2185433 TATCTGTTATTCATG
1 TATCTGTTATTCATG
2185448 TATCTGTTATTCAT
1 TATCTGTTATTCAT
2185462 ATATACGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (15 bp):
TATCTGTTATTCATG
Found at i:2185800 original size:11 final size:11
Alignment explanation
Indices: 2185768--2185794 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2185758 TTAAATTATA
2185768 AAATAAATATT
1 AAATAAATATT
2185779 AAATAAATATT
1 AAATAAATATT
2185790 AAATA
1 AAATA
2185795 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAAATATT
Found at i:2190443 original size:8 final size:8
Alignment explanation
Indices: 2190430--2190470 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2190420 CTCATTTTCA
2190430 GAGAATTT
1 GAGAATTT
2190438 GAGAATTT
1 GAGAATTT
*
2190446 -AGAGTTT
1 GAGAATTT
*
2190453 GGGAATTT
1 GAGAATTT
2190461 GAGAATTT
1 GAGAATTT
2190469 GA
1 GA
2190471 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2190769 original size:128 final size:128
Alignment explanation
Indices: 2190541--2190913 Score: 640
Period size: 128 Copynumber: 2.9 Consensus size: 128
2190531 TAATCGGAGT
* * *
2190541 ACTATTTACATGAAGGCGTGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2190606 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2190669 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2190734 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
2190797 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
2190861 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2190914 AATCAGGTAA
Statistics
Matches: 233, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 232 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2191289 original size:32 final size:30
Alignment explanation
Indices: 2191235--2191311 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 30
2191225 TTAATAATTC
* *
2191235 TAAATAAATAATAATTATATAAAATTATTTTAA
1 TAAA-AAATAATAATTACAT-AAA-TATATTAA
*
2191268 TAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAATAATAATTACATAAATATATTAA
*
2191298 TATAAAAAAAATAA
1 TA-AAAAATAATAA
2191312 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 9 0.24
31 12 0.32
32 13 0.34
33 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAAAAATAATAATTACATAAATATATTAA
Found at i:2191336 original size:33 final size:34
Alignment explanation
Indices: 2191269--2191343 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
2191259 TTATTTTAAT
* * *
2191269 AAAAAATAATATTTACATAAATATATTAATATAA
1 AAAAAATAATATTTACATAAAAATACTAACATAA
2191303 AAAAAATAACTATTTA-A-AAAAATACTAACATAA
1 AAAAAATAA-TATTTACATAAAAATACTAACATAA
2191336 AAATAAAT
1 AAA-AAAT
2191344 TTCTTACCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 16 0.44
34 14 0.39
35 6 0.17
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (34 bp):
AAAAAATAATATTTACATAAAAATACTAACATAA
Found at i:2192188 original size:26 final size:27
Alignment explanation
Indices: 2192149--2192199 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2192139 ATTTATAATA
**
2192149 ATAAATTTTTTATAATTT-AAAAAATT
1 ATAAATTTCATATAATTTGAAAAAATT
*
2192175 ATAAATTTCATATATTTTGAAAAAA
1 ATAAATTTCATATAATTTGAAAAAA
2192200 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
ATAAATTTCATATAATTTGAAAAAATT
Found at i:2192849 original size:334 final size:337
Alignment explanation
Indices: 2192221--2192968 Score: 1114
Period size: 334 Copynumber: 2.2 Consensus size: 337
2192211 AATTAATTGT
* * * *
2192221 TAAAAAATATATAAAAATAAACTTTTAATTACAATTAAGGGATCAAATAAATTTTTATTCATTAA
1 TAAAAAATAT-T-AAAATAAACTTTTAATTA-AATTGAGGGATCAAATGAATTATTATTCATTAT
* * **
2192286 TTTTTATTTTTTAACAACAGTTAATAATGTTTATTTATTTTTAATAAAATTATTTTTGATTTTTG
63 TTTTTAATTTTTAACAACAGTTAATAATGTTTATTCATTTTTAATAAAATTATTTTAAATTTTTG
* * *
2192351 TATTAAAATTTCACAATACGTATAATCTAGTATAAGAAAACTTTGAGGGTAAGTATTTTAAAATA
128 CATTAAAATTACACAATACATATAATCTAGTATAAGAAAACTTTGAGGGTAAGTATTTTAAAATA
* *
2192416 TGAATAATTTTATAAAATTTTATAACTAGTATTTCTTTTACAAAATGATGATGATGATGATAATA
193 TGAATAATTTTATAAAATTTTATAACTAGTATTTATTTTACAAAATGATGACGATGATG-----A
* * *
2192481 ATAAATATTTTATAATTTTAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTACCTTTTA
253 ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAAATATCACCTTTTA
*
2192546 AAATTAATTGTTTAAAAATA
318 AAATTAATTATTTAAAAATA
*
2192566 TAAAAAATATTAAAATAAACTTTTAATT-AATTGAGGGAT-ATAACGAATTATTATTCATTATTT
1 TAAAAAATATTAAAATAAACTTTTAATTAAATTGAGGGATCA-AATGAATTATTATTCATTA-TT
2192629 TTTTAATTTTTAACAACAGTTAATAAT-TTTATTCATTTTTAATAAAATTA-TTTAAATTTTTGC
64 TTTTAATTTTTAACAACAGTTAATAATGTTTATTCATTTTTAATAAAATTATTTTAAATTTTTGC
* * *
2192692 ATT-AAATTACATAATGCATATAATCTAGTATATA-AAAACTTTGAGGGTATGTATTTTAAAATA
129 ATTAAAATTACACAATACATATAATCTAGTATA-AGAAAACTTTGAGGGTAAGTATTTTAAAATA
2192755 TGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTACAAAATGATGACGATGATG-ATAA
193 TGAATAATTTTATAAAA-TTTTATAACTAGTATTTATTTTACAAAATGATGACGATGATGAATAA
*
2192819 ATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAAATATCGCCTTTTAAAAT
257 ATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAAATATCACCTTTTAAAAT
2192884 TAATTATTTAAAAATA
322 TAATTATTTAAAAATA
*
2192900 TAAAAAATATTAAAATAAACTTTTAATTACAATTGAGGGATCAAATGAATTATTATTCAATAATT
1 TAAAAAATATTAAAATAAACTTTTAATTA-AATTGAGGGATCAAATGAATTATTATTC-ATTATT
2192965 TTTT
64 TTTT
2192969 CAAAATATAT
Statistics
Matches: 371, Mismatches: 24, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
334 108 0.29
336 31 0.08
337 4 0.01
339 70 0.19
340 55 0.15
341 48 0.13
342 27 0.07
343 17 0.05
344 1 0.00
345 10 0.03
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (337 bp):
TAAAAAATATTAAAATAAACTTTTAATTAAATTGAGGGATCAAATGAATTATTATTCATTATTTT
TTAATTTTTAACAACAGTTAATAATGTTTATTCATTTTTAATAAAATTATTTTAAATTTTTGCAT
TAAAATTACACAATACATATAATCTAGTATAAGAAAACTTTGAGGGTAAGTATTTTAAAATATGA
ATAATTTTATAAAATTTTATAACTAGTATTTATTTTACAAAATGATGACGATGATGAATAAATAT
TTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAAATATCACCTTTTAAAATTAAT
TATTTAAAAATA
Found at i:2194982 original size:21 final size:21
Alignment explanation
Indices: 2194953--2194994 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2194943 GGAATTATTA
*
2194953 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
2194974 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
2194995 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:2198617 original size:56 final size:54
Alignment explanation
Indices: 2198514--2198633 Score: 163
Period size: 56 Copynumber: 2.2 Consensus size: 54
2198504 CATGACTTCT
*
2198514 CAGAATGGAT-AGCCATATAAACTCGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAACTCGATAGACAAGAAAAATAAGTGTAGAGATG
* *
2198567 CAGAATGCATAAGCCATATAAAAAGCTGGATAGGCAAG-AAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATAT--AAA-CTCGATAGACAAGAAAAATAAGTGTAGAGATG
*
2198623 CATAATGCATA
1 CAGAATGCATA
2198634 TATGTTCCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
53 9 0.15
54 8 0.14
56 31 0.53
57 11 0.19
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.19
Consensus pattern (54 bp):
CAGAATGCATAAGCCATATAAACTCGATAGACAAGAAAAATAAGTGTAGAGATG
Found at i:2200321 original size:73 final size:73
Alignment explanation
Indices: 2200202--2200339 Score: 276
Period size: 73 Copynumber: 1.9 Consensus size: 73
2200192 AATCAAACTA
2200202 AATCGAGAATCGATTAATGTAGTGGTTGTAAATCATTTATAAATATAAACAAATACAAGAGCATA
1 AATCGAGAATCGATTAATGTAGTGGTTGTAAATCATTTATAAATATAAACAAATACAAGAGCATA
2200267 ACCAATTC
66 ACCAATTC
2200275 AATCGAGAATCGATTAATGTAGTGGTTGTAAATCATTTATAAATATAAACAAATACAAGAGCATA
1 AATCGAGAATCGATTAATGTAGTGGTTGTAAATCATTTATAAATATAAACAAATACAAGAGCATA
2200340 CTTTATCTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (73 bp):
AATCGAGAATCGATTAATGTAGTGGTTGTAAATCATTTATAAATATAAACAAATACAAGAGCATA
ACCAATTC
Found at i:2200963 original size:15 final size:16
Alignment explanation
Indices: 2200943--2200994 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
2200933 ATAATGTAAC
2200943 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
*
2200958 ATTCCCTGGTAATCTTTT
1 ATTCCCTAGTAATC--TT
2200976 ATTCCTACTAGTAATCTT
1 ATTCC--CTAGTAATCTT
2200994 A
1 A
2200995 CATTCCGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 6 0.20
16 6 0.20
18 10 0.33
20 8 0.27
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:2205700 original size:41 final size:41
Alignment explanation
Indices: 2205635--2205889 Score: 375
Period size: 41 Copynumber: 6.2 Consensus size: 41
2205625 AATATTTGGA
*
2205635 CTATCGCAACGAATTTGGAATGAATCGCAACGTGAACTTCGC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
* * * *
2205677 CTGTCGTAACGAATTGGAATGAATCGCAATGCGAACTTCAC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* *
2205718 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* *
2205759 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
2205800 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* * *
2205841 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
2205883 CTATCGC
1 CTATCGC
2205890 GTTGCGAATC
Statistics
Matches: 196, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 153 0.78
42 43 0.22
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
Found at i:2205745 original size:20 final size:20
Alignment explanation
Indices: 2205720--2205830 Score: 86
Period size: 20 Copynumber: 5.5 Consensus size: 20
2205710 AACTTCACCT
2205720 ATCGCAACGATTTGGAATGA
1 ATCGCAACGATTTGGAATGA
* * *
2205740 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CG-ATTTGGAATGA
2205761 ATCGCAACGATTTGGAATGA
1 ATCGCAACGATTTGGAATGA
* * *
2205781 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CG-ATTTGGAATGA
2205802 ATCGCAACGATTTGGAATGA
1 ATCGCAACGATTTGGAATGA
2205822 ATCGCAACG
1 ATCGCAACG
2205831 CGAACTTCGC
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
18 12 0.17
19 4 0.06
20 23 0.33
21 14 0.20
22 4 0.06
23 12 0.17
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (20 bp):
ATCGCAACGATTTGGAATGA
Found at i:2205776 original size:82 final size:82
Alignment explanation
Indices: 2205633--2205889 Score: 417
Period size: 82 Copynumber: 3.1 Consensus size: 82
2205623 GCAATATTTG
* * * *
2205633 GACTATCGCAACGAATTTGGAATGAATCGCAACGTGAACTTCGCCTGTCGTAACGAATTGGAATG
1 GACTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAATG
2205698 AATCGCAATGCGAACTTC
65 AATCGCAATGCGAACTTC
*
2205716 -ACCTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATG
1 GA-CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAATG
*
2205780 AATCGCAACGCGAACTTC
65 AATCGCAATGCGAACTTC
*
2205798 GACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATA
1 GACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACG-ATTTGGAATG
2205863 AATCGCAATGCGAACTTC
65 AATCGCAATGCGAACTTC
2205881 GACTATCGC
1 GACTATCGC
2205890 GTTGCGAATC
Statistics
Matches: 162, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
82 115 0.71
83 47 0.29
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (82 bp):
GACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAATGA
ATCGCAATGCGAACTTC
Found at i:2212115 original size:23 final size:25
Alignment explanation
Indices: 2212057--2212115 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
2212047 TAATGTTTAC
2212057 ATTTAGAT-TTTTAATTAATTTATA
1 ATTTAGATGTTTTAATTAATTTATA
* *
2212081 A-TTATATG-TTTAATT-CTTTATA
1 ATTTAGATGTTTTAATTAATTTATA
2212103 ATTTA-ATGTTTTA
1 ATTTAGATGTTTTA
2212116 TAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (25 bp):
ATTTAGATGTTTTAATTAATTTATA
Found at i:2214918 original size:18 final size:18
Alignment explanation
Indices: 2214897--2214935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2214887 TCACTATCTC
2214897 TTTCTTT-TTCTCCCTCTT
1 TTTCTTTGTTCTCCC-CTT
*
2214915 TTTCTTTGTTTTCCCCTT
1 TTTCTTTGTTCTCCCCTT
2214933 TTT
1 TTT
2214936 TAATCTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTCTTTGTTCTCCCCTT
Found at i:2216776 original size:20 final size:21
Alignment explanation
Indices: 2216727--2216778 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2216717 TAAATTTAAA
*
2216727 TATAT-TATTTTTATAAACAT
1 TATATCTAATTTTATAAACAT
*
2216747 TATTTCTAATTTTATAAA-AT
1 TATATCTAATTTTATAAACAT
2216767 TA-ATCATAATTT
1 TATATC-TAATTT
2216779 AATTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 11 0.41
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATCTAATTTTATAAACAT
Found at i:2225445 original size:183 final size:183
Alignment explanation
Indices: 2225137--2225486 Score: 628
Period size: 183 Copynumber: 1.9 Consensus size: 183
2225127 ATTAAATCCG
2225137 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCACTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCACTGGCTTTATGA
** *
2225202 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
* *
2225267 TTGTCAGGCCAAAGACTTTGTTATGAGATGAACCCTTCAGTGATTTATCCCTC
131 TTGTCAGGCCAAAGACTTTGTGAAGAGATGAACCCTTCAGTGATTTATCCCTC
*
2225320 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCACTGGCTTTATGA
* *
2225385 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
2225450 TTGTCAGGCCAAAGACTTTGTGAAGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGAAGAGATGAACCCTT
2225487 TAATTAAACC
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 159 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCACTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGAAGAGATGAACCCTTCAGTGATTTATCCCTC
Found at i:2226842 original size:37 final size:37
Alignment explanation
Indices: 2226775--2226861 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
2226765 ATTGAAAACA
** * *
2226775 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
2226811 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2226848 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2226862 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2226864 original size:102 final size:105
Alignment explanation
Indices: 2226680--2226927 Score: 369
Period size: 102 Copynumber: 2.4 Consensus size: 105
2226670 TTTTTCTTAA
* * * *
2226680 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
*
2226745 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
2226784 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
2226846 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* *
2226887 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
2226928 TAAACATCGA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 55 0.42
103 40 0.31
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:2226917 original size:66 final size:66
Alignment explanation
Indices: 2226811--2226990 Score: 260
Period size: 66 Copynumber: 2.8 Consensus size: 66
2226801 CTTGAGATAG
* *
2226811 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAAC
2226876 A
66 A
*
2226877 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAAC
2226942 A
66 A
* * * *
2226943 TTTCCCTT-GAA-ATAAA--TTATCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2226991 AAATTTTGTT
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
63 28 0.26
64 1 0.01
65 6 0.06
66 71 0.67
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAAC
A
Found at i:2227020 original size:166 final size:169
Alignment explanation
Indices: 2226707--2227092 Score: 595
Period size: 166 Copynumber: 2.3 Consensus size: 169
2226697 CTTGAGATAG
* * * *
2226707 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATCGAAA
* *
2226772 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
*
2226837 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
2226877 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAA
*
2226941 CATTTCCCTTGAAAT-AA-ATTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTTTCC
66 CATTTCCCTTGAAATGAATATTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
2227004 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
2227043 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
2227093 AATTTTGTCT
Statistics
Matches: 201, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
164 1 0.00
165 36 0.18
166 89 0.44
167 2 0.01
168 58 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAA
CATTTCCCTTGAAATGAATATTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:2227090 original size:36 final size:36
Alignment explanation
Indices: 2227043--2227128 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
2227033 ATTGAAAACA
** *
2227043 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
2227079 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
2227115 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
2227129 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:2227139 original size:101 final size:100
Alignment explanation
Indices: 2226877--2227223 Score: 451
Period size: 100 Copynumber: 3.5 Consensus size: 100
2226867 ATTGAAAACA
* * *
2226877 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATCGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
2226942 ATTTCCCTTGAAATAAATTATCTCTCTTGAGATAG
66 ATTTCCCTTGAAATAAATTATCTCTCTTGAGATAG
* *
2226977 TTTCCCTTGAAACAAAATTTTGTTTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
2227042 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAAT-AA-ATTATCTCTCTTGAGATAG
* * *
2227079 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
2227143 AGTTTCCCTTGAAACAAA--A--TCT-TTGA-ATATG
66 A-TTTCCCTTGAAATAAATTATCTCTCTTGAGATA-G
* * * *
2227174 TTTTACATT-AAAC-AAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 -TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
2227224 AATTTTGTCT
Statistics
Matches: 221, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
94 3 0.01
95 42 0.19
96 9 0.04
100 74 0.33
101 51 0.23
102 42 0.19
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATAAATTATCTCTCTTGAGATAG
Found at i:2227146 original size:30 final size:30
Alignment explanation
Indices: 2227111--2227169 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2227101 CTCCTTTGAG
*
2227111 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
2227141 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
2227170 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:2227234 original size:36 final size:36
Alignment explanation
Indices: 2227183--2227297 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
2227173 GTTTTACATT
*
2227183 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
2227219 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
* *
2227256 AAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2227293 AAACA
1 AAACA
2227298 TCAATCCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 25 0.37
37 24 0.35
38 19 0.28
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2227297 original size:37 final size:37
Alignment explanation
Indices: 2227195--2227297 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2227185 ACAAATTTCG
*
2227195 TCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTA
* * *
2227231 TCTCTCTTAAGACATGTTTTTCTTAAAACAAAATTTTA
1 TCTCTCTTGAGACA-GTTTCTCTTGAAACAAAATTTTA
*
2227269 TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACA
2227298 TCAATCCTTG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 13 0.23
37 25 0.44
38 19 0.33
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTA
Found at i:2227379 original size:36 final size:35
Alignment explanation
Indices: 2227338--2227426 Score: 137
Period size: 33 Copynumber: 2.6 Consensus size: 35
2227328 CCTTGATACA
*
2227338 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAA-AAACCTTTGAAAAT
2227374 GTTTCTCTTGAAACAC--AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
*
2227407 GTTTCTCTTGAAACATAAAA
1 GTTTCTCTTGAAACACAAAA
2227427 CCTTTGAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
33 28 0.57
34 3 0.06
35 2 0.04
36 16 0.33
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:2227402 original size:33 final size:33
Alignment explanation
Indices: 2227338--2227452 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 33
2227328 CCTTGATACA
2227338 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
2227374 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
* *
2227407 GTTTCTCTTG-AA-ACATAAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
2227438 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
2227453 AATTTCGTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
31 25 0.35
32 4 0.06
33 24 0.33
34 3 0.04
36 16 0.22
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.33
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:2227499 original size:67 final size:67
Alignment explanation
Indices: 2227407--2227592 Score: 221
Period size: 67 Copynumber: 2.7 Consensus size: 67
2227397 CTTTGAAAAT
* *
2227407 GTTTCTCTTGAAACATAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
2227472 CA
66 CA
* * * *
2227474 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
2227539 GCC
65 ACA
* * * * *
2227542 GTTT-TCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
2227593 CTGTCTTTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
67 48 0.48
68 30 0.30
69 22 0.22
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:2229549 original size:21 final size:20
Alignment explanation
Indices: 2229517--2229576 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
2229507 TTCCCATCAA
2229517 ATTTACTTTTATTTTTTATTC
1 ATTTA-TTTTATTTTTTATTC
2229538 ATTTATTATTA-TTTTT-TTC
1 ATTTATT-TTATTTTTTATTC
* *
2229557 ATCTAATTTATTATTTTATT
1 ATTTATTTTATT-TTTTATT
2229577 ATTATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 3 0.09
19 9 0.27
20 11 0.33
21 10 0.30
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTATTTTATTTTTTATTC
Found at i:2229586 original size:21 final size:20
Alignment explanation
Indices: 2229525--2229586 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
2229515 AAATTTACTT
2229525 TTATTTTTTATTCATT-TATTA
1 TTATTTTTTATT-ATTAT-TTA
*
2229546 TTATTTTTT-TCATCTAATTTA
1 TTATTTTTTATTAT-T-ATTTA
2229567 TTATTTTATTATTATTATTT
1 TTATTTT-TTATTATTATTT
2229587 TCTTTATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 23 0.68
22 4 0.12
23 3 0.09
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTTTATTATTATTTA
Found at i:2232535 original size:23 final size:24
Alignment explanation
Indices: 2232503--2232550 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2232493 TATCTTGTAA
*
2232503 AAAACTAAATAATACCAATATTAT
1 AAAACTAAATAATACCAACATTAT
*
2232527 AAAA-TAAATAATATCAACATTAT
1 AAAACTAAATAATACCAACATTAT
2232550 A
1 A
2232551 TGCTTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAACTAAATAATACCAACATTAT
Found at i:2233134 original size:2 final size:2
Alignment explanation
Indices: 2233127--2233162 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2233117 ATGATTTTTA
2233127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2233163 CGATATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2239738 original size:455 final size:454
Alignment explanation
Indices: 2238834--2239745 Score: 1725
Period size: 455 Copynumber: 2.0 Consensus size: 454
2238824 AGTAAAACAG
2238834 AAAAAATAACAAACATTAACTCCTAACAATTATAAATATGACCAAAGTACCATTAATACATATGT
1 AAAAAATAACAAACATTAACTCCTAACAATTATAAATATGACCAAAGTACCATTAATACATATGT
2238899 TAAATAACTATTTAACATGTTTAAAAGAGCAACAAACATGTACGAACCAACTTACCTTAGTGGTT
66 TAAATAACTATTTAACATGTTTAAAAGAGCAACAAACATGTACGAACCAACTTACCTTAGTGGTT
* * *
2238964 AAAGGAATCATTATTGTTCCTAGGGGTCATGGGTTTGAACACTAGTGACTGAAAGAGTGATTGAA
131 AAAGGAATCATTATTGTTCCTAGAGGTCATGGGTTTGAACACCAGCGACTGAAAGAGTGATTGAA
* *
2239029 CGTTTATTGTCAATTGGGTCTTAGGTTGTCCTAGTCCTGGGCTAGAAGAGTCACCCTTGACCTAA
196 CGTTTATTGTCAATTGGGTCTTAGGTTGTCCTAGTCCTGGCCTAAAAGAGTCACCCTTGACCTAA
2239094 ACTTTTTGTAACCCAAAAAAAATTTAAACATGAAATGATATTATGTAAATCCCACTTGTTATTCT
261 ACTTTTTGTAACCCAAAAAAAATTTAAACATGAAATGATATTATGTAAATCCCACTTGTTATTCT
2239159 TAAAGGTTGCAGAACACACACATGAATTGATACTTGAAAGAATATGCAAATCCCACTTGTTTCGT
326 TAAAGGTTGCAGAACACACACATGAATTGATACTTGAAAGAATATGCAAATCCCACTTGTTTCGT
2239224 TGTTTGAGTAAAATAGTGGACTAAGAGCTCGCTACGCGTTAATTAACTGAATATATTTGAGGCT
391 TGTTTGAGTAAAATAGTGGACTAAGAGCTCGCTACGCGTTAATTAACTGAATATATTTGAGGCT
*
2239288 AAAAAATAACAAACATTAACTTCTAACAATTATAAATATGACCAAAGTACCATTAATACATATGT
1 AAAAAATAACAAACATTAACTCCTAACAATTATAAATATGACCAAAGTACCATTAATACATATGT
*
2239353 TAAATAACTATTTAACATGTTTAAAAGAGCAACAAACATGTACGAACCAACTTACTTTAGTGGTT
66 TAAATAACTATTTAACATGTTTAAAAGAGCAACAAACATGTACGAACCAACTTACCTTAGTGGTT
2239418 AAAGGAATCATTATTGTTCCTAGAGGTCATGGGTTTGAACACCAGCGACTGAAAGAGTGATTGAA
131 AAAGGAATCATTATTGTTCCTAGAGGTCATGGGTTTGAACACCAGCGACTGAAAGAGTGATTGAA
*
2239483 CGTTTATTGTCAATTGGGTCTTAGGTATGTCCTAGTCCTGGCCTAAAAGAGTCACTCTTGACCTA
196 CGTTTATTGTCAATTGGGTCTTAGGT-TGTCCTAGTCCTGGCCTAAAAGAGTCACCCTTGACCTA
2239548 AACTTTTTGTAACCCAAAAAAAATTTAAACATGAAATGATATTATGTAAATCCCACTTGTTATTC
260 AACTTTTTGTAACCCAAAAAAAATTTAAACATGAAATGATATTATGTAAATCCCACTTGTTATTC
* *
2239613 TTAAAGGTTGCAGAACTCACACATGAATTGATACTTGGAAGAATATGCAAATCCCACTTGTTTCG
325 TTAAAGGTTGCAGAACACACACATGAATTGATACTTGAAAGAATATGCAAATCCCACTTGTTTCG
2239678 TTGTTTGAGTAAAATAGTGGACTAAGAGCTCGCTACGCGTTAATTAACTGAATATATTTGAGGCT
390 TTGTTTGAGTAAAATAGTGGACTAAGAGCTCGCTACGCGTTAATTAACTGAATATATTTGAGGCT
2239743 AAA
1 AAA
2239746 TAATGATTTT
Statistics
Matches: 447, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
454 216 0.48
455 231 0.52
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (454 bp):
AAAAAATAACAAACATTAACTCCTAACAATTATAAATATGACCAAAGTACCATTAATACATATGT
TAAATAACTATTTAACATGTTTAAAAGAGCAACAAACATGTACGAACCAACTTACCTTAGTGGTT
AAAGGAATCATTATTGTTCCTAGAGGTCATGGGTTTGAACACCAGCGACTGAAAGAGTGATTGAA
CGTTTATTGTCAATTGGGTCTTAGGTTGTCCTAGTCCTGGCCTAAAAGAGTCACCCTTGACCTAA
ACTTTTTGTAACCCAAAAAAAATTTAAACATGAAATGATATTATGTAAATCCCACTTGTTATTCT
TAAAGGTTGCAGAACACACACATGAATTGATACTTGAAAGAATATGCAAATCCCACTTGTTTCGT
TGTTTGAGTAAAATAGTGGACTAAGAGCTCGCTACGCGTTAATTAACTGAATATATTTGAGGCT
Found at i:2240545 original size:17 final size:16
Alignment explanation
Indices: 2240505--2240547 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2240495 TTAATAATAT
*
2240505 AAATATTATTTATTTTA
1 AAATATT-TTTATATTA
*
2240522 AATTATTTTTATATTA
1 AAATATTTTTATATTA
2240538 ACAATATTTT
1 A-AATATTTT
2240548 AAAAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATATTTTTATATTA
Found at i:2241846 original size:12 final size:12
Alignment explanation
Indices: 2241829--2241853 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2241819 GAGTCCCAAT
2241829 AAAAAAATTAAA
1 AAAAAAATTAAA
2241841 AAAAAAATTAAA
1 AAAAAAATTAAA
2241853 A
1 A
2241854 GCATTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:2247309 original size:55 final size:55
Alignment explanation
Indices: 2247225--2247981 Score: 912
Period size: 55 Copynumber: 13.7 Consensus size: 55
2247215 TCTTTGAATG
* * *
2247225 ACGGGTCCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCGTCTGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
*
2247280 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTT-TATAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCT-GAAA
* *
2247335 ATGGGTCCGCTCCCTATTCGTTCAGGGAGTATAAAACTCGAACAATCTTCAT-AAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTC-TGAAA
* * * ** *
2247390 ATGAGTTCATTCCCTATTCGTTCAGGGAGTATAGAACTCAAACAATCTTCAT-AAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTC-TGAAA
** *
2247445 ACGGGTTTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTC-TGAAA
* * * * * * *
2247501 ACGAGTTCGCTCCCTATTTGTTCAAGGAGTATAGAACTCAAATAATCTTCTGACA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* * * * *
2247556 ACGGGTTCACTTCCTATTCATTCAGGGAGTATAGAACTTGAACAATCTTCTGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* * * * * *
2247611 ATGGGTTCGCTTCCTATTCATTTAGGGAGTATAGAAATCGAACAATCTTCTGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* * * *
2247666 ACGGGTCCGCTTCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTATGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* * * *
2247721 ACGGGCCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATATTATGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* *
2247776 ACGGGTCCGCTCCCTATTCATTCAGTGAGTATAGAACTCGAACAATCTTCTGAAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
* * *
2247831 ATGGGTCTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTC-TGAAA
* * * * *
2247886 ATGGGTTCACTCCCTATTTGTTCAGGGAGTATAAAACTCGAACAATCTTCAT-AAA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTC-TGAAA
** * * * *
2247941 ACGGGTTTGCTCCGTATTCATTCAGAGAGTATAGGACTCGA
1 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGA
2247982 TCTTCATAAA
Statistics
Matches: 621, Mismatches: 76, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.00
55 571 0.92
56 48 0.08
57 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (55 bp):
ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAA
Found at i:2248105 original size:37 final size:37
Alignment explanation
Indices: 2248002--2248107 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
2247992 ATAAGTTTGT
* *
2248002 TTCACTACTGTTCCGTGAAGGCTTATAGA-TGATTTGC
1 TTCACTACTCTTCCGTGAAGGCTTA-AGATTGAATTGC
*
2248039 TTCACCACTCTTCCGTGAAGGCTTAAGATTGAATTGC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGAATTGC
*
2248076 TTCACTACTCTTTCGTGAAGGCTTAAGATTGA
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGA
2248108 CTTGTTTCGA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 3 0.05
37 60 0.95
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATTGAATTGC
Found at i:2249145 original size:15 final size:16
Alignment explanation
Indices: 2249118--2249147 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2249108 TGTCATATAT
2249118 GTCCCGTAAGGACTAC
1 GTCCCGTAAGGACTAC
2249134 GTCCCG-AAGGACTA
1 GTCCCGTAAGGACTA
2249148 TTATACCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (16 bp):
GTCCCGTAAGGACTAC
Found at i:2249275 original size:29 final size:29
Alignment explanation
Indices: 2249232--2249341 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
2249222 TTTCATATGT
2249232 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2249260 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2249289 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2249318 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
2249342 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:2251503 original size:7 final size:7
Alignment explanation
Indices: 2251491--2251560 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
2251481 CCCCCTTTTA
2251491 TTTCTTT
1 TTTCTTT
2251498 TTTCTTT
1 TTTCTTT
* *
2251505 TTTCATC
1 TTTCTTT
*
2251512 ATTCATTT
1 TTTC-TTT
2251520 TTCTCTTT
1 TT-TCTTT
*
2251528 TCTCTTT
1 TTTCTTT
*
2251535 TTTC-AT
1 TTTCTTT
*
2251541 TTTCTCT
1 TTTCTTT
2251548 TTTCTTT
1 TTTCTTT
2251555 TTTCTT
1 TTTCTT
2251561 CATTTTTTCA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
6 5 0.10
7 36 0.73
8 6 0.12
9 2 0.04
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTTT
Found at i:2251526 original size:23 final size:23
Alignment explanation
Indices: 2251495--2251552 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2251485 CTTTTATTTC
*
2251495 TTTTT-TCTTTTTTCATCATTCA
1 TTTTTCTCTTTTCTCATCATTCA
* **
2251517 TTTTTCTCTTTTCTCTTTTTTCA
1 TTTTTCTCTTTTCTCATCATTCA
2251540 -TTTTCTCTTTTCT
1 TTTTTCTCTTTTCT
2251553 TTTTTCTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTCTCTTTTCTCATCATTCA
Found at i:2251527 original size:30 final size:29
Alignment explanation
Indices: 2251493--2251571 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
2251483 CCCTTTTATT
2251493 TCTTTTTTCTTTTTTCATCATTCAT-TTTTC
1 TCTTTTTTCTTTTTTCAT-ATTC-TCTTTTC
* *
2251523 TCTTTTCTCTTTTTTCATTTTCTCTTTTC
1 TCTTTTTTCTTTTTTCATATTCTCTTTTC
*
2251552 TTTTTTCTTCATTTTTTCAT
1 TCTTTT-TTC-TTTTTTCAT
2251572 TTTTTTCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 13 0.31
30 19 0.45
31 9 0.21
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (29 bp):
TCTTTTTTCTTTTTTCATATTCTCTTTTC
Found at i:2251535 original size:15 final size:15
Alignment explanation
Indices: 2251517--2251559 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2251507 TCATCATTCA
2251517 TTTTTCTCTTTTCTC
1 TTTTTCTCTTTTCTC
2251532 TTTTT-TCATTTTCTC
1 TTTTTCTC-TTTTCTC
*
2251547 -TTTTCTTTTTTCT
1 TTTTTCTCTTTTCT
2251560 TCATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTCTTTTCTC
Found at i:2251536 original size:8 final size:8
Alignment explanation
Indices: 2251517--2251630 Score: 57
Period size: 7 Copynumber: 14.6 Consensus size: 8
2251507 TCATCATTCA
2251517 TTTTTCTC
1 TTTTTCTC
2251525 -TTTTCTC
1 TTTTTCTC
2251532 TTTTT-TC
1 TTTTTCTC
*
2251539 ATTTTCTC
1 TTTTTCTC
2251547 -TTTTCT-
1 TTTTTCTC
2251553 TTTTTCTTC
1 TTTTTC-TC
2251562 ATTTTT-TC
1 -TTTTTCTC
*
2251570 ATTTTTTTC
1 -TTTTTCTC
**
2251579 TTTCAC-C
1 TTTTTCTC
*
2251586 ATTTTTCATT
1 -TTTTTC-TC
2251596 TTTTTCTC
1 TTTTTCTC
2251604 ATTTTTC-C
1 -TTTTTCTC
*
2251612 TTTTCCT-
1 TTTTTCTC
2251619 TTTTTC-C
1 TTTTTCTC
2251626 TTTTT
1 TTTTT
2251631 TTCCTTTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
7 40 0.48
8 24 0.29
9 14 0.17
10 5 0.06
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCTC
Found at i:2251551 original size:22 final size:23
Alignment explanation
Indices: 2251513--2251566 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 23
2251503 TTTTTCATCA
2251513 TTCATTTTTCTCTTTTCTCTTTT-
1 TTCA-TTTTCTCTTTTCTCTTTTC
*
2251536 TTCATTTTCTCTTTTCTTTTTTC
1 TTCATTTTCTCTTTTCTCTTTTC
2251559 TTCATTTT
1 TTCATTTT
2251567 TTCATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCATTTTCTCTTTTCTCTTTTC
Found at i:2251599 original size:32 final size:30
Alignment explanation
Indices: 2251559--2251641 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 30
2251549 TTCTTTTTTC
2251559 TTCA-TTTTTTCATTTTTTTCTTTCACCATTT
1 TTCATTTTTTTC-TTTTTTTCTTT-ACCATTT
* * *
2251590 TTCATTTTTTTCTCATTTTTCCTTTTCCTTTT
1 TTCATTTTTTTCT--TTTTTTCTTTACCATTT
*
2251622 TTCCTTTTTTTCCTTTTTTT
1 TTCATTTTTTT-CTTTTTTT
2251642 TCCCTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 10 0.23
32 22 0.51
33 11 0.26
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (30 bp):
TTCATTTTTTTCTTTTTTTCTTTACCATTT
Found at i:2251621 original size:23 final size:23
Alignment explanation
Indices: 2251588--2251638 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
2251578 CTTTCACCAT
* *
2251588 TTTTCATTTTTTTCTCATTTTTCC
1 TTTTCCTTTTTTCCT-ATTTTTCC
*
2251612 TTTTCCTTTTTTCCTTTTTTTCC
1 TTTTCCTTTTTTCCTATTTTTCC
2251635 TTTT
1 TTTT
2251639 TTTTCCCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTCCTTTTTTCCTATTTTTCC
Found at i:2251632 original size:9 final size:9
Alignment explanation
Indices: 2251612--2251653 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
2251602 TCATTTTTCC
2251612 TTTTCC-TT
1 TTTTCCTTT
2251620 TTTTCCTTT
1 TTTTCCTTT
2251629 TTTTCCTTTT
1 TTTTCC-TTT
2251639 TTTTCCCTTT
1 TTTT-CCTTT
2251649 TTTTC
1 TTTTC
2251654 ATTTCTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.19
9 9 0.29
10 14 0.45
11 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:2251650 original size:8 final size:8
Alignment explanation
Indices: 2251595--2251640 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
2251585 CATTTTTCAT
2251595 TTTTTTCTC
1 TTTTTTC-C
*
2251604 ATTTTTCC
1 TTTTTTCC
2251612 --TTTTCC
1 TTTTTTCC
2251618 TTTTTTCC
1 TTTTTTCC
2251626 TTTTTTTCC
1 -TTTTTTCC
2251635 TTTTTT
1 TTTTTT
2251641 TTCCCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
6 6 0.18
8 13 0.39
9 14 0.42
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2264478 original size:16 final size:16
Alignment explanation
Indices: 2264455--2264508 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 16
2264445 ATGACTGAAT
2264455 TTTTTTAATTAAATT-
1 TTTTTTAATTAAATTA
2264470 TTATTTTAATTAAAAGTTA
1 TT-TTTTAATT-AAA-TTA
2264489 TTTTTTAATTAAA-TA
1 TTTTTTAATTAAATTA
2264504 TTTTT
1 TTTTT
2264509 CATTTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.26
16 8 0.23
17 6 0.17
18 10 0.29
19 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTTTAATTAAATTA
Found at i:2265297 original size:24 final size:24
Alignment explanation
Indices: 2265265--2265317 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2265255 TATAGCATGC
2265265 TTCCTCGGCCAATCTTCGCTATGA
1 TTCCTCGGCCAATCTTCGCTATGA
*
2265289 TTCCTCGGCCAATCTTCGCTATGC
1 TTCCTCGGCCAATCTTCGCTATGA
2265313 TTCCT
1 TTCCT
2265318 ACGTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.36, G:0.15, T:0.36
Consensus pattern (24 bp):
TTCCTCGGCCAATCTTCGCTATGA
Found at i:2276794 original size:18 final size:18
Alignment explanation
Indices: 2276771--2276806 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2276761 CTAACGACAC
2276771 CCATGCAGTTGACTCATA
1 CCATGCAGTTGACTCATA
*
2276789 CCATGCAGTTGAGTCATA
1 CCATGCAGTTGACTCATA
2276807 GCTACAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (18 bp):
CCATGCAGTTGACTCATA
Found at i:2281932 original size:18 final size:17
Alignment explanation
Indices: 2281897--2281942 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
2281887 TTTAATTATT
2281897 TATTTATTTTATCATTA
1 TATTTATTTTATCATTA
*
2281914 TCTTTTATTTTATTC-TTA
1 T-ATTTATTTTA-TCATTA
2281932 TATTTATTTTA
1 TATTTATTTTA
2281943 AAAAAAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTTATCATTA
Found at i:2284984 original size:15 final size:15
Alignment explanation
Indices: 2284960--2285033 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
2284950 GGAGGCAACC
*
2284960 CATTTCATTTTATTT
1 CATTTTATTTTATTT
* *
2284975 CATTTTATTTTTAGTA
1 CATTTTA-TTTTATTT
* *
2284991 CACTTTATTTCATTT
1 CATTTTATTTTATTT
* * * *
2285006 AAATTTATTTCATTC
1 CATTTTATTTTATTT
2285021 CATTTTATTTTAT
1 CATTTTATTTTAT
2285034 CAAATGCTTA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
15 33 0.73
16 12 0.27
ACGTcount: A:0.24, C:0.12, G:0.01, T:0.62
Consensus pattern (15 bp):
CATTTTATTTTATTT
Found at i:2286460 original size:8 final size:8
Alignment explanation
Indices: 2286447--2286477 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2286437 TTTATGTTCT
2286447 TTATTTTA
1 TTATTTTA
*
2286455 TTATTTCA
1 TTATTTTA
2286463 TTATTTTA
1 TTATTTTA
2286471 TTATTTT
1 TTATTTT
2286478 TTTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:2288745 original size:22 final size:22
Alignment explanation
Indices: 2288717--2288762 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2288707 ACCCATTAAA
*
2288717 GAAACTGCATATCCTTGGAGAG
1 GAAACTGCATATCCTTAGAGAG
2288739 GAAACTGCATATCCTTAGAGAG
1 GAAACTGCATATCCTTAGAGAG
2288761 GA
1 GA
2288763 CAGTTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (22 bp):
GAAACTGCATATCCTTAGAGAG
Found at i:2302770 original size:36 final size:36
Alignment explanation
Indices: 2302724--2302989 Score: 263
Period size: 36 Copynumber: 7.4 Consensus size: 36
2302714 AGCAAAGTTA
*
2302724 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGA-ATAGTGAAGCAAACC
* *
2302760 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* *
2302796 ATCCT-AAGCCTTCACCGGAGAATAGTGAAGCTAACC
1 AT-CTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* * *
2302832 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* **
2302868 ATCTGAAGCCTTCACCGGAGAATAGTGAAGTGAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* * *
2302904 ATCAT-AAGTCTTCACC-AGAGAGTAGTGAAGTAAACC
1 ATC-TGAAGCCTTCACCGA-AGAATAGTGAAGCAAACC
* * * *
2302940 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTGAAGCCTTCACCGAAGAA-TAGTGAAGCA-AACC
* *
2302977 ATTTTAAGCCTTC
1 ATCTGAAGCCTTC
2302990 TCAGAAGAGT
Statistics
Matches: 200, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
35 6 0.03
36 177 0.88
37 17 0.09
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
Found at i:2302845 original size:72 final size:72
Alignment explanation
Indices: 2302728--2302955 Score: 293
Period size: 72 Copynumber: 3.2 Consensus size: 72
2302718 AAGTTAATCT
* * *
2302728 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCTGAAGCCTTCACTGGAGAATAGTGAAGCA
1 TAAGCCTTCACCGGAGA-ATAGTGAAGCTAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCA
2302792 AACCATCC
65 AACCATCC
2302800 TAAGCCTTCACCGGAGAATAGTGAAGCTAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAA
1 TAAGCCTTCACCGGAGAATAGTGAAGCTAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAA
* *
2302865 TCAAT-C
66 ACCATCC
* * *
2302871 TGAAGCCTTCACCGGAGAATAGTGAAG-TGAACCATCAT-AAGTCTTCACCAGAGAGTAGTGAAG
1 T-AAGCCTTCACCGGAGAATAGTGAAGCT-AACCATC-TGAAGCCTTCACCGGAGAATAGTGAAG
* *
2302934 TAAACCATCT
63 CAAACCATCC
*
2302944 TAAGTCTTCACC
1 TAAGCCTTCACC
2302956 AAAAAGTAGT
Statistics
Matches: 138, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
71 4 0.03
72 132 0.96
73 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (72 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCTAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAA
ACCATCC
Found at i:2302918 original size:108 final size:108
Alignment explanation
Indices: 2302724--2302971 Score: 329
Period size: 108 Copynumber: 2.3 Consensus size: 108
2302714 AGCAAAGTTA
* *
2302724 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
* *
2302789 GCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCT-AACC
66 GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAG-TAAACC
* * *
2302832 ATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGA
1 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGA
** * *
2302896 AGTGAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGTAAACC
65 AGCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGTAAACC
* * * *
2302940 ATCTTAAGTCTTCACCAAAAAGTAGTGAAGCA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCA
2302972 GATCCATTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
107 2 0.02
108 118 0.98
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGTAAACC
Found at i:2303436 original size:51 final size:51
Alignment explanation
Indices: 2303371--2303720 Score: 450
Period size: 51 Copynumber: 6.7 Consensus size: 51
2303361 AAGATTATTT
* *
2303371 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * * *
2303422 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * * *
2303473 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * *
2303524 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TC
*
2303576 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTC
1 -GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-TGTTC
* * * *
2303629 GAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTC
* *
2303683 GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCG
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG
2303721 ATTGTTGAAG
Statistics
Matches: 265, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.00
51 137 0.52
52 40 0.15
53 44 0.17
54 38 0.14
55 5 0.02
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
Found at i:2303758 original size:106 final size:103
Alignment explanation
Indices: 2303370--2303760 Score: 384
Period size: 102 Copynumber: 3.7 Consensus size: 103
2303360 GAAGATTATT
* * * * * *
2303370 TGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGA-TGTCCGAGTTCCATACT
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTCGAGTTCTATACT
* *
2303434 CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATG-C
66 CCCT--AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTC
* * * * * * * *
2303473 -GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-TGTTCGAGTTCCATACT
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTCGAGTTCTATACT
*
2303536 CCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTC
66 CCCT--AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTC
* *
2303576 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCTATACT
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTCGAGTTCTATACT
* * *
2303641 CCCTAGAGAA-AGAGAGAGCGAACTCGTTTGCAGAAGATAT-
66 CCCTAGA-AAGA-AG-GAGCGAACCCGTTTGAAG-AGATGTC
**
2303681 TCGAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGATTGTTGAAGTTTGTTCGAG-TCTT
1 T-GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCG--T-TTGAAAATTGTTCGAGTTC-T
*
2303745 ATACTCTCT-GAAAGAA
61 ATACTCCCTAGAAAGAA
2303761 TAGGGAGCAG
Statistics
Matches: 250, Mismatches: 25, Indels: 22
0.84 0.08 0.07
Matches are distributed among these distances:
102 91 0.36
103 5 0.02
104 45 0.18
105 36 0.14
106 41 0.16
107 3 0.01
108 6 0.02
109 23 0.09
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (103 bp):
TGAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGTTTGAAAATTGTTCGAGTTCTATACT
CCCTAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTC
Found at i:2303953 original size:55 final size:55
Alignment explanation
Indices: 2303719--2303940 Score: 354
Period size: 55 Copynumber: 4.0 Consensus size: 55
2303709 GGAACGAACC
* * *
2303719 CGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
2303774 CGATTGTTGAAGATTATTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
2303829 CGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACA
*
2303884 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACA
2303939 CG
1 CG
2303941 TTTTCAAAAG
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 159 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:2303986 original size:54 final size:54
Alignment explanation
Indices: 2303361--2304084 Score: 269
Period size: 55 Copynumber: 13.5 Consensus size: 54
2303351 GAAGCAAATG
* * * * *
2303361 AAGATTATTTGAGTTCCATACTCCCT-AGAGAGAGAGGGAGCGAACCCGTTTG---
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * ** * *
2303413 AAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAAGGAGCGAACCCGTGTG---
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * * ** *
2303464 AAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG---
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * * ** *
2303515 AAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-AA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * * *
2303568 GAGA-TGTCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG--A
1 AAGATTTTC-GAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * *
2303620 AA-ATTGTTCGAGTTCTATACTCCCT-AGAGAAAGAGAGAGCGAACTCGTTTGCAG
1 AAGATT-TTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * * * * * ***
2303674 AAGATATTCGAGTTCCATAATCCCT-AGAGAAAGAGGGAACGAACCCGATTGTTG
1 AAGATTTTCGAGTTCTATACTCCCTGA-AGAAAGTGGGAGCGAACACGTTTGCAA
* * * ***
2303728 AAGTTTGTTCGAG-TCTTATACTCTCTGAA-AGAA-TAGGGAGC-AGACACGATTGTTG
1 AAGATT-TTCGAGTTC-TATACTCCCTGAAGA-AAGT-GGGAGCGA-ACACGTTTGCAA
* * ***
2303783 AAGATTATTCGAG-TCTTATACTCTCTGAA-AGAA-TAGGGAGC-AGACACGATTGTTG
1 AAGATT-TTCGAGTTC-TATACTCCCTGAAGA-AAGT-GGGAGCGA-ACACGTTTGCAA
* * * ***
2303838 AAGATTATTCGAG-TCTCATACTCTCTGAA-AGAA-TAGGGAG-TAGACACGATTGTTG
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGA-AAGT-GGGAGCGA-ACACGTTTGCAA
* * *
2303893 AAGATTGTTCGAG-TCTCATACTCTCTGAAGGAA-TAGGGAGC-ATACACGTTTTCAA
1 AAGATT-TTCGAGTTCT-ATACTCCCTGAAGAAAGT-GGGAGCGA-ACACGTTTGCAA
* * *
2303948 AAGATTTTCGAGTTCTATGCTCCCTGAAGAAAGTGGGAGCGAACCCGTTTGCAG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
* * * *
2304002 AAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TAGACAA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTG-CAA
* *
2304056 AAGATTGTACGAGTT-TCTACTCCCTGAAG
1 AAGATT-TTCGAGTTCTATACTCCCTGAAG
2304085 GAATAGGGAG
Statistics
Matches: 581, Mismatches: 66, Indels: 48
0.84 0.09 0.07
Matches are distributed among these distances:
51 133 0.23
52 51 0.09
53 45 0.08
54 150 0.26
55 201 0.35
56 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (54 bp):
AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGTGGGAGCGAACACGTTTGCAA
Found at i:2313556 original size:21 final size:21
Alignment explanation
Indices: 2313530--2313592 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2313520 ATTTTGTGCA
*
2313530 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
2313551 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
2313572 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
2313593 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:2313600 original size:21 final size:21
Alignment explanation
Indices: 2313574--2313613 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2313564 CCCCCTTTGA
*
2313574 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2313595 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2313614 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2318693 original size:2 final size:2
Alignment explanation
Indices: 2318686--2318713 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2318676 ATAAAATTAA
2318686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2318714 TACCTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2320878 original size:62 final size:63
Alignment explanation
Indices: 2320788--2320911 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
2320778 AACCTCGACA
* *
2320788 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAAT-TGCCCATATGTTCATTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAATATGCCCATATGTTCAGTAGAACATAGGTAT
* * * * * *
2320850 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTATGTCTATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAAATATGCCCATATGTTCAGTAGAACATAGGTA
2320912 AACTCTCAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.52
63 24 0.46
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAATATGCCCATATGTTCAGTAGAACATAGGTAT
Found at i:2322854 original size:13 final size:13
Alignment explanation
Indices: 2322836--2322882 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
2322826 TGCGTCATAA
*
2322836 ATTTATGACGCGT
1 ATTTATGACACGT
2322849 ATTTATGACACGT
1 ATTTATGACACGT
* *
2322862 ATTTATGACATGC
1 ATTTATGACACGT
2322875 ATTTATGA
1 ATTTATGA
2322883 TGCACATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
ATTTATGACACGT
Found at i:2322974 original size:85 final size:85
Alignment explanation
Indices: 2322875--2323040 Score: 287
Period size: 85 Copynumber: 2.0 Consensus size: 85
2322865 TATGACATGC
** *
2322875 ATTTATGATGCACATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
2322940 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
*
2322960 ATTTATGACACACATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
2323025 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
2323041 GTGATTGTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:2328902 original size:20 final size:20
Alignment explanation
Indices: 2328877--2328924 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2328867 CTAAATCCTT
*
2328877 TTTCAAAATTTCA-TTTTGAC
1 TTTCAAAATTCCATTTTTG-C
2328897 TTTCAAAA-TCCATTTTTGC
1 TTTCAAAATTCCATTTTTGC
2328916 TTTCAAAAT
1 TTTCAAAAT
2328925 AAAATCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTCAAAATTCCATTTTTGC
Found at i:2328912 original size:19 final size:19
Alignment explanation
Indices: 2328877--2328924 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2328867 CTAAATCCTT
*
2328877 TTTCAAAATTTCA-TTTTGAC
1 TTTCAAAA-TCCATTTTTG-C
2328897 TTTCAAAATCCATTTTTGC
1 TTTCAAAATCCATTTTTGC
2328916 TTTCAAAAT
1 TTTCAAAAT
2328925 AAAATCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTCAAAATCCATTTTTGC
Found at i:2332106 original size:2 final size:2
Alignment explanation
Indices: 2332101--2332125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2332091 TCTCTCCCTC
2332101 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 A
2332126 AGTGTTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2332455 original size:3 final size:3
Alignment explanation
Indices: 2332447--2332472 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2332437 AATAAGGTTT
2332447 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2332473 TAGGTGAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2338415 original size:13 final size:11
Alignment explanation
Indices: 2338390--2338424 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
2338380 TGTGATAATT
2338390 TTTATTTTAAA
1 TTTATTTTAAA
2338401 TTTATTTATACAA
1 TTTATTT-TA-AA
2338414 TTTATTTTAAA
1 TTTATTTTAAA
2338425 ATATTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:2338431 original size:13 final size:12
Alignment explanation
Indices: 2338390--2338431 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2338380 TGTGATAATT
2338390 TTTATTTT-AAA
1 TTTATTTTAAAA
*
2338401 TTTATTTATACAA
1 TTTATTT-TAAAA
2338414 TTTATTTTAAAA
1 TTTATTTTAAAA
2338426 TATTAT
1 T-TTAT
2338432 CAATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 6 0.23
13 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:2339701 original size:98 final size:98
Alignment explanation
Indices: 2339567--2339759 Score: 350
Period size: 98 Copynumber: 2.0 Consensus size: 98
2339557 ACGTACGAAT
**
2339567 GCACACGTGGAATAAAGGTGTATGTATGGATTCATTGCCTGACACCGGAATATGATAAATTTCCA
1 GCACACGTGGAATAAAGGTGTATGTATGGAGGCATTGCCTGACACCGGAATATGATAAATTTCCA
2339632 ACATAAGAACTTTTAGTATCTGTTTGTTTGGGG
66 ACATAAGAACTTTTAGTATCTGTTTGTTTGGGG
*
2339665 GCACACGTGGAATAAAGGTGTATTTATGGAGGCATTGCCTGACACCGGAATATGATAAATTTCCA
1 GCACACGTGGAATAAAGGTGTATGTATGGAGGCATTGCCTGACACCGGAATATGATAAATTTCCA
*
2339730 GCATAAGAACTTTTAGTATCTGTTTGTTTG
66 ACATAAGAACTTTTAGTATCTGTTTGTTTG
2339760 CCGGATTAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (98 bp):
GCACACGTGGAATAAAGGTGTATGTATGGAGGCATTGCCTGACACCGGAATATGATAAATTTCCA
ACATAAGAACTTTTAGTATCTGTTTGTTTGGGG
Found at i:2340101 original size:21 final size:22
Alignment explanation
Indices: 2340060--2340122 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
2340050 AAATATTAAT
*
2340060 TATTAAAATATTTAA-AATATA
1 TATTATAATATTTAATAATATA
2340081 T-TTATAATATTTAATAATATAA
1 TATTATAATATTTAATAATAT-A
*
2340103 TATTAT-AT-TTTAATATTATA
1 TATTATAATATTTAATAATATA
2340123 ATAAAATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 13 0.35
21 16 0.43
22 4 0.11
23 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTATAATATTTAATAATATA
Found at i:2340109 original size:8 final size:8
Alignment explanation
Indices: 2340082--2340125 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
2340072 TAAAATATAT
2340082 TTATAATA
1 TTATAATA
2340090 TT-TAATA
1 TTATAATA
*
2340097 ATATAATA
1 TTATAATA
2340105 TTAT-AT-
1 TTATAATA
2340111 TT-TAATA
1 TTATAATA
2340118 TTATAATA
1 TTATAATA
2340126 AAATTCTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
5 1 0.03
6 4 0.13
7 10 0.33
8 15 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTATAATA
Found at i:2341291 original size:21 final size:21
Alignment explanation
Indices: 2341262--2341314 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2341252 ATTCTGACTA
2341262 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
2341283 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2341304 TCGCAATGCGA
1 TCGCATTGCGA
2341315 ATACATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2341329 original size:20 final size:20
Alignment explanation
Indices: 2341304--2341416 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
2341294 TTTTCCTAAT
*
2341304 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
2341324 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2341344 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
2341364 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2341384 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
2341404 TCGCAACGCGAAT
1 TCGCAATGCGAAT
2341417 CTGACTATCG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2341640 original size:22 final size:21
Alignment explanation
Indices: 2341615--2341677 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
2341605 GACATCTGTC
2341615 CCCATCTCCGACGAAATCAGT
1 CCCATCTCCGACGAAATCAGT
* *
2341636 ACCCATCTCCAACGATATCAGT
1 -CCCATCTCCGACGAAATCAGT
* *
2341658 CTCCATTTCCGGCGAAATCA
1 C-CCATCTCCGACGAAATCA
2341678 TCCACGGTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.22
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCAGT
Found at i:2342090 original size:20 final size:20
Alignment explanation
Indices: 2342048--2342114 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2342038 GATTCTTGCA
** **
2342048 TTGCGATAGTCAAATTCACG
1 TTGCGATAGTCATTTTCGTG
2342068 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
** *
2342088 TTGCGATTTTCATTTTCGTA
1 TTGCGATAGTCATTTTCGTG
2342108 TTGCGAT
1 TTGCGAT
2342115 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:2342124 original size:20 final size:20
Alignment explanation
Indices: 2342081--2342124 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2342071 CGATAGTCAT
* ** *
2342081 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTAAAG
2342101 TTTCGTATTGCGATTTAAAG
1 TTTCGTATTGCGATTTAAAG
2342121 TTTC
1 TTTC
2342125 AGAAACTATT
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:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGATTTAAAG
Found at i:2343991 original size:20 final size:20
Alignment explanation
Indices: 2343966--2344144 Score: 188
Period size: 20 Copynumber: 9.6 Consensus size: 20
2343956 GAATAGGTTT
2343966 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2343986 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2344002 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
2344019 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
2344035 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2344053 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2344073 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2344093 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
**
2344113 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2344133 ACTATCGCAATG
1 ACTATCGCAATG
2344145 AGAGAATCGC
Statistics
Matches: 138, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
14 14 0.10
16 10 0.07
17 8 0.06
18 5 0.04
19 7 0.05
20 94 0.68
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2344026 original size:33 final size:33
Alignment explanation
Indices: 2343969--2344049 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
2343959 TAGGTTTACT
** * * *
2343969 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
2344003 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
2344036 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2344050 ATGACTATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 30 0.73
34 11 0.27
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:2344212 original size:20 final size:20
Alignment explanation
Indices: 2344187--2344274 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
2344177 GCGATTCTCT
2344187 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
2344207 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
*
2344227 CATTGCGATAGTC-ATTTCG
1 CATTGCGATAGTCAAATTCG
**
2344246 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
2344266 CGTTGCGAT
1 CATTGCGAT
2344275 TTTAAGTTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 18 0.28
20 46 0.72
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:2344255 original size:39 final size:40
Alignment explanation
Indices: 2344187--2344274 Score: 133
Period size: 39 Copynumber: 2.2 Consensus size: 40
2344177 GCGATTCTCT
2344187 CATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCG
* **
2344227 CATTGCGATAGTC-ATTTCGCATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCG
*
2344266 CGTTGCGAT
1 CATTGCGAT
2344275 TTTAAGTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (40 bp):
CATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCG
Found at i:2344812 original size:39 final size:40
Alignment explanation
Indices: 2344750--2344845 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 40
2344740 CTGTCATTGT
*
2344750 TCAAGAG-GCCTCCCTATCGTTCAAGAGGCTC-TATCATCCC
1 TCAAGAGTCCCTCCC-ATCGTTCAAGAGGC-CATATCATCCC
* *
2344790 TCAAGAGTCCCTCCCA-CGTTCAAGAGGCCATGTCATCGC
1 TCAAGAGTCCCTCCCATCGTTCAAGAGGCCATATCATCCC
*
2344829 TGAAGAGGTCCCTCCCA
1 TCAAGA-GTCCCTCCCA
2344846 ACATTCTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 1 0.02
39 24 0.49
40 18 0.37
41 6 0.12
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (40 bp):
TCAAGAGTCCCTCCCATCGTTCAAGAGGCCATATCATCCC
Found at i:2345475 original size:202 final size:201
Alignment explanation
Indices: 2345097--2345503 Score: 614
Period size: 202 Copynumber: 2.0 Consensus size: 201
2345087 CAACGATGAT
2345097 ATGCATTTGTTGATTGAACGGTCTTGGTGGGTGTATTAGGGGTGAAGACAACACTATTTCGATGG
1 ATGCATTTGTTGATTGAACGGTCTTGGTGGGTGTATTAGGGGTGAAGACAACACTATTTC-A-GG
2345162 GGGGTAGTCTTATATTCTTCTTATTTTTAGTGATGATTAATTTTTTTTAAAATTTAGGTAATTTA
64 GGGGTAGTCTTATATTCTTCTTATTTTTAGT-ATGATTAA--TTTTTTAAAATTTA-GTAATTTA
2345227 ATAATATATGTCTTTTTTTGTAAAACAACATATTAATGCATGGGTGACACGTCTTCTAATTGTAA
125 ATAATATATGTCTTTTTTTGTAAAACAACATATTAATGCATGGGTGACACGTCTTCTAATTGTAA
2345292 GGAAATTGAATG
190 GGAAATTGAATG
2345304 ATGCATTTGTTGATTGAACGGTCTTGGTGGGGTGTATTATTAGGGGTTGAAGACAACGACTATTT
1 ATGCATTTGTTGATTGAACGGTCTTGGT-GGGTG---TATTAGGGG-TGAAGACAAC-ACTATTT
*
2345369 C-GGGGGGTAAGTCTTATATTTCTTCTTATATTTTAGT-T-TTTAA-TTTTTAAAA-TT-GTAAT
60 CAGGGGGGT-AGTCTTATA-TTCTTCTTAT-TTTTAGTATGATTAATTTTTTAAAATTTAGTAAT
2345428 TTAAT-A-ATATGTCTTTTTTTGTAAAACAACATATTAATGCATGGGTGACACGTCTTCTAATTG
122 TTAATAATATATGTCTTTTTTTGTAAAACAACATATTAATGCATGGGTGACACGTCTTCTAATTG
2345491 TAAGGAAATTGAA
187 TAAGGAAATTGAA
2345504 GAAAAATATA
Statistics
Matches: 190, Mismatches: 1, Indels: 23
0.89 0.00 0.11
Matches are distributed among these distances:
202 70 0.37
203 1 0.01
204 10 0.05
206 2 0.01
207 37 0.19
208 5 0.03
210 11 0.06
211 19 0.10
212 20 0.11
213 15 0.08
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (201 bp):
ATGCATTTGTTGATTGAACGGTCTTGGTGGGTGTATTAGGGGTGAAGACAACACTATTTCAGGGG
GGTAGTCTTATATTCTTCTTATTTTTAGTATGATTAATTTTTTAAAATTTAGTAATTTAATAATA
TATGTCTTTTTTTGTAAAACAACATATTAATGCATGGGTGACACGTCTTCTAATTGTAAGGAAAT
TGAATG
Found at i:2346435 original size:14 final size:14
Alignment explanation
Indices: 2346416--2346451 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2346406 ATTGTTTAAT
2346416 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2346430 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2346444 TGATTTGT
1 TGATTTGT
2346452 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2346618 original size:20 final size:19
Alignment explanation
Indices: 2346593--2346719 Score: 84
Period size: 20 Copynumber: 6.7 Consensus size: 19
2346583 GCGAATTTAG
*
2346593 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATATTCA
*
2346612 TTTTCGCATTGCG--ATTC-
1 -TTTCGCGTTGCGATATTCA
* *
2346629 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATATTCA
* *
2346646 TTTCGCATTGCGATAGTCAA
1 TTTCGCGTTGCGATATTC-A
* *
2346666 TTCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATATTCA
* *
2346685 TTTCTGTGTTGCGATAGTCA
1 TTTC-GCGTTGCGATATTCA
*
2346705 TATTCACGTTGCGAT
1 T-TTCGCGTTGCGAT
2346720 TTTCGCGTTG
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
14 8 0.10
16 3 0.04
18 3 0.04
19 16 0.19
20 51 0.61
21 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATATTCA
Found at i:2346686 original size:39 final size:40
Alignment explanation
Indices: 2346632--2346719 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
2346622 GCGATTCTCT
** *
2346632 CGTTGCGATTTTCATTTC-GCATTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCTGCATTGCGATAGTCATATT-CA
**
2346671 CGTTGCGATAGTCATTTCTGTGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCATTTCTGCATTGCGATAGTCATATTCA
2346711 CGTTGCGAT
1 CGTTGCGAT
2346720 TTTCGCGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 16 0.38
40 23 0.55
41 3 0.07
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCTGCATTGCGATAGTCATATTCA
Found at i:2349117 original size:24 final size:24
Alignment explanation
Indices: 2349083--2349136 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2349073 CTGAAAAATC
2349083 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2349107 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2349131 ATCAAA
1 ATCAAA
2349137 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2349150 original size:24 final size:24
Alignment explanation
Indices: 2349083--2349150 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2349073 CTGAAAAATC
* * *
2349083 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2349107 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2349131 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2349151 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2350002 original size:20 final size:20
Alignment explanation
Indices: 2349977--2350023 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2349967 AAATTCAGTA
*
2349977 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2349997 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
2350017 TTGCGAT
1 TTGCGAT
2350024 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2350033 original size:20 final size:20
Alignment explanation
Indices: 2350010--2350183 Score: 294
Period size: 20 Copynumber: 8.7 Consensus size: 20
2350000 CGATAGTCAG
*
2350010 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350030 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350050 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350070 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350090 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350110 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
2350130 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2350151 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2350171 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2350184 ATTAGGAAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
20 128 0.89
21 16 0.11
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2350204 original size:21 final size:21
Alignment explanation
Indices: 2350180--2350225 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2350170 TATTCGCATT
2350180 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2350201 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2350222 GCGA
1 GCGA
2350226 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2351426 original size:21 final size:20
Alignment explanation
Indices: 2351388--2351452 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
2351378 TTTTAATTTT
2351388 TATTTAAATTTAATTATAAA
1 TATTTAAATTTAATTATAAA
*
2351408 TATTTATAATATT-ATTAT-AT
1 TATTTA-AAT-TTAATTATAAA
* *
2351428 TATTTGATTTTAATT-TAAAA
1 TATTTAAATTTAATTAT-AAA
2351448 TATTT
1 TATTT
2351453 TCTATAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 3 0.08
19 5 0.14
20 18 0.50
21 8 0.22
22 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTAAATTTAATTATAAA
Found at i:2351898 original size:20 final size:20
Alignment explanation
Indices: 2351849--2351925 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
2351839 AAATGACCAA
*
2351849 CAATTTCGCAACGCGAAAGT
1 CAATTTCGCAACGCGAAACT
*
2351869 CAAATTCGCAACGCG-AACT
1 CAATTTCGCAACGCGAAACT
* **
2351888 CAATTTGCGCAAC-CTAATTT
1 CAATTT-CGCAACGCGAAACT
2351908 CCAATTTCGCAACGCGAA
1 -CAATTTCGCAACGCGAA
2351926 TATGTAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
19 9 0.20
20 28 0.61
21 9 0.20
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (20 bp):
CAATTTCGCAACGCGAAACT
Found at i:2351970 original size:21 final size:21
Alignment explanation
Indices: 2351934--2351999 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
2351924 AATATGTAAA
*
2351934 TCGCATTGCG-TTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
2351954 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
* *
2351975 TCACGTTGCGATTTTCTAAAT
1 TCGCGTTGCGATTTTCCAAAT
2351996 TCGC
1 TCGC
2352000 AACGTGAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 9 0.22
21 32 0.78
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:2352039 original size:20 final size:21
Alignment explanation
Indices: 2352016--2352063 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2352006 AATCTGTAAA
2352016 TCGCAACAC-AAAAGTCAAAT
1 TCGCAACACGAAAAGTCAAAT
* **
2352036 TCGCAACGCGAAATTTCAAAT
1 TCGCAACACGAAAAGTCAAAT
2352057 TCGCAAC
1 TCGCAAC
2352064 GTGAATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (21 bp):
TCGCAACACGAAAAGTCAAAT
Found at i:2352086 original size:20 final size:20
Alignment explanation
Indices: 2352061--2352099 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2352051 TCAAATTCGC
2352061 AACGTGAATAGTAAAATCGT
1 AACGTGAATAGTAAAATCGT
2352081 AACGTGAATAGTAAAATCG
1 AACGTGAATAGTAAAATCG
2352100 CAACAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (20 bp):
AACGTGAATAGTAAAATCGT
Found at i:2352422 original size:20 final size:20
Alignment explanation
Indices: 2352376--2352483 Score: 92
Period size: 20 Copynumber: 5.4 Consensus size: 20
2352366 TTCCTGTAAA
* *
2352376 TCGCAACACAGAAGTCAAATT
1 TCGCAACGCAAAAGTCAAA-T
* * *
2352397 TC-CAACGCGATAGTTAAAT
1 TCGCAACGCAAAAGTCAAAT
*
2352416 TCGCAACCCAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*** * *
2352436 TTTTAACGTAATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*
2352456 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
2352476 TCGCAACG
1 TCGCAACG
2352484 TTAATAGTAA
Statistics
Matches: 65, Mismatches: 21, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
19 3 0.05
20 60 0.92
21 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:2352431 original size:40 final size:40
Alignment explanation
Indices: 2352372--2352504 Score: 126
Period size: 40 Copynumber: 3.3 Consensus size: 40
2352362 TTGATTCCTG
* *
2352372 TAAA-TCGCAACACAGAAGTCAAATTTCCAACGCGATAGT
1 TAAATTCGCAACACAAAAGTCAAATTTCCAACGCAATAGT
* ** *
2352411 TAAATTCGCAACCCAAAAGTCAAATTTTTAACGTAATAGT
1 TAAATTCGCAACACAAAAGTCAAATTTCCAACGCAATAGT
* * * *
2352451 CAAATTCGCAACGCGAAAGTCAAA-TTCGCAACGTTAATAGT
1 TAAATTCGCAACACAAAAGTCAAATTTC-CAACG-CAATAGT
* *
2352492 AAAAATCGCAACA
1 TAAATTCGCAACA
2352505 TGAATAGTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.08
40 54 0.70
41 17 0.22
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.23
Consensus pattern (40 bp):
TAAATTCGCAACACAAAAGTCAAATTTCCAACGCAATAGT
Found at i:2352546 original size:20 final size:20
Alignment explanation
Indices: 2352440--2352625 Score: 214
Period size: 20 Copynumber: 9.2 Consensus size: 20
2352430 TCAAATTTTT
*
2352440 AACGT-AATAGTCAAATTCGC
1 AACGTGAATAGT-AAAATCGC
* *
2352460 AACGCGAA-AGTCAAATTCGC
1 AACGTGAATAGT-AAAATCGC
*
2352480 AACGTTAATAGTAAAAATCGC
1 AACGTGAATAGT-AAAATCGC
* *
2352501 AACATGAATAGTAAAAATCAC
1 AACGTGAATAGT-AAAATCGC
* *
2352522 AATGTGAATAGTAAAGTCGC
1 AACGTGAATAGTAAAATCGC
* *
2352542 AATGTGAATAGTAAAATAGC
1 AACGTGAATAGTAAAATCGC
2352562 AACGTGAATAGTAAAATCGC
1 AACGTGAATAGTAAAATCGC
*
2352582 AACGTGAATAGTAAAATTGC
1 AACGTGAATAGTAAAATCGC
*
2352602 AACTTGAATAGTAAAATCGC
1 AACGTGAATAGTAAAATCGC
2352622 AACG
1 AACG
2352626 AATCTATATG
Statistics
Matches: 144, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 104 0.72
21 40 0.28
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.22
Consensus pattern (20 bp):
AACGTGAATAGTAAAATCGC
Found at i:2353048 original size:40 final size:41
Alignment explanation
Indices: 2352998--2353087 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
2352988 ATTCTTCTAA
* * **
2352998 ATTCGCGTTGCAATTTTCCAATTCGTGTTACGA-TTTTACT
1 ATTCACGTTGCAATTTTACAATTCACGTTACGATTTTTACT
* * *
2353038 ATTTACGTTGCGATTTTACTATTCACGTTACGATTTTTACT
1 ATTCACGTTGCAATTTTACAATTCACGTTACGATTTTTACT
2353079 ATTCACGTT
1 ATTCACGTT
2353088 ACGAAATTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 26 0.63
41 15 0.37
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (41 bp):
ATTCACGTTGCAATTTTACAATTCACGTTACGATTTTTACT
Found at i:2353077 original size:21 final size:20
Alignment explanation
Indices: 2353024--2353091 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
2353014 TCCAATTCGT
*
2353024 GTTACGATTTTACTATTTAC
1 GTTACGATTTTACTATTCAC
*
2353044 GTTGCGATTTTACTATTCAC
1 GTTACGATTTTACTATTCAC
2353064 GTTACGATTTTTACTATTCAC
1 GTTACGA-TTTTACTATTCAC
2353085 GTTACGA
1 GTTACGA
2353092 AATTAGAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 24 0.55
21 20 0.45
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GTTACGATTTTACTATTCAC
Found at i:2353143 original size:19 final size:19
Alignment explanation
Indices: 2353105--2353155 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2353095 TAGAAACTGA
* *
2353105 GTTGCGAAATTAGAGTTCGC
1 GTTGCG-AATTTGAGATCGC
2353125 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
*
2353144 GTTGTGAATTTG
1 GTTGCGAATTTG
2353156 TTGGTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:2355650 original size:22 final size:21
Alignment explanation
Indices: 2355617--2355657 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2355607 ATAAACTTTG
2355617 ATTTTTTGCATTGTGCATTTA
1 ATTTTTTGCATTGTGCATTTA
* *
2355638 ATTTTTCTTCATTTTGCATT
1 ATTTTT-TGCATTGTGCATT
2355658 GAACTGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (21 bp):
ATTTTTTGCATTGTGCATTTA
Done.