Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 26
Found at i:1644249 original size:20 final size:19
Alignment explanation
Indices: 1644224--1644276 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
1644214 ACCAGACCGT
1644224 GAACCGGTTGAAAACTGGTA
1 GAACCGGTTGAAAAC-GGTA
*
1644244 GAACCGGCTGAGAAACGGTA
1 GAACCGGTTGA-AAACGGTA
*
1644264 AAACCGGTGTGAA
1 GAACCGGT-TGAA
1644277 CCGGCTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.36, C:0.17, G:0.32, T:0.15
Consensus pattern (19 bp):
GAACCGGTTGAAAACGGTA
Found at i:1644725 original size:70 final size:70
Alignment explanation
Indices: 1644641--1644816 Score: 307
Period size: 70 Copynumber: 2.5 Consensus size: 70
1644631 AGTTAGTTGT
1644641 GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCATATTTTTAATCTTTAGACT
1 GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCATATTTTTAATCTTTAGACT
1644706 TTTGG
66 TTTGG
* * * *
1644711 GATGCTCTTTTATGTTTCTTAGCCATGTGGTATTGTTTTGTTCTCATATTTTTACTTTTTAGACT
1 GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCATATTTTTAATCTTTAGACT
1644776 TTTGG
66 TTTGG
*
1644781 AATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGT
1 GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGT
1644817 GTTTTTTTTA
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 99 1.00
ACGTcount: A:0.15, C:0.14, G:0.19, T:0.52
Consensus pattern (70 bp):
GATGCTCTTCTATGTTTCTTAGCCATGTGGGATTGTTTTGTTCTCATATTTTTAATCTTTAGACT
TTTGG
Found at i:1646267 original size:21 final size:23
Alignment explanation
Indices: 1646221--1646268 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1646211 ATCAAGTACA
*
1646221 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
1646244 ATAATATAATATGTAGCGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
1646267 AT
1 AT
1646269 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1646953 original size:159 final size:160
Alignment explanation
Indices: 1646705--1646999 Score: 486
Period size: 159 Copynumber: 1.9 Consensus size: 160
1646695 TTTTACTATC
*
1646705 GGTTTTGTCATTTCAAGACCGATTTTATTATATTTTTACCTGTTATATTGTTAAGGATCGATACA
1 GGTTTTGTCATTTCAAGACCGATTTTATCATATTTTTACCTGTTATATTGTTAAGGATCGATACA
* *
1646770 TTTTTATAAAGTATCGACACTTTATT-GACGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
66 TTTTTATAAAGTATCGACACTTTATTAG-CGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTAT
1646834 CGATACTCAACATATCCGATAGCTCTTTACT
130 CGATACTCAACATATCCGATAGCTCTTTACT
* * * *
1646865 GGTTTTGTCATTTCAAGACCGGTTTTGTCATA-TTTTACCTGTTATATTGTTATGGATCGATATA
1 GGTTTTGTCATTTCAAGACCGATTTTATCATATTTTTACCTGTTATATTGTTAAGGATCGATACA
* *
1646929 TTTTTATAAAGTATCGATATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATC
1646994 GATACT
131 GATACT
1647000 TATAATAAAG
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
159 95 0.76
160 30 0.24
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (160 bp):
GGTTTTGTCATTTCAAGACCGATTTTATCATATTTTTACCTGTTATATTGTTAAGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATC
GATACTCAACATATCCGATAGCTCTTTACT
Found at i:1647123 original size:21 final size:21
Alignment explanation
Indices: 1647099--1647146 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1647089 ATATTGTTAT
1647099 GGATCGATACATTTTTATAAA
1 GGATCGATACATTTTTATAAA
1647120 GGATCGATACATTTTTATAAA
1 GGATCGATACATTTTTATAAA
*
1647141 GTATCG
1 GGATCG
1647147 TCACTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
GGATCGATACATTTTTATAAA
Found at i:1647300 original size:110 final size:112
Alignment explanation
Indices: 1647124--1647370 Score: 396
Period size: 110 Copynumber: 2.2 Consensus size: 112
1647114 TATAAAGGAT
* *
1647124 CGATACATTTTTATAAAGTATCGTCACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCAT
1 CGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACCTGTTTTGTCAT
*
1647189 TTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGAA
66 TTATAGACCGGTTTTGCCA-TTTTTTTACCTGTTATATTGTTATGGAA
1647237 CGATACATTTTTA-AAAGTATCGACACTTTC-A-ATATCCGATAGCGTTTTACCTGTTTTGTCAT
1 CGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACCTGTTTTGTCAT
*
1647299 TTATAGACCGGTTTTGCCATTTTTTTACCTGTTATATTGTTATGGAT
66 TTATAGACCGGTTTTGCCATTTTTTTACCTGTTATATTGTTATGGAA
* *
1647346 C-A-ATATTTTTATAAAATATCGACAC
1 CGATACATTTTTATAAAGTATCGACAC
1647371 AAACCGACAA
Statistics
Matches: 127, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
107 8 0.06
108 13 0.10
109 28 0.22
110 48 0.38
111 1 0.01
112 16 0.13
113 13 0.10
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (112 bp):
CGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACCTGTTTTGTCAT
TTATAGACCGGTTTTGCCATTTTTTTACCTGTTATATTGTTATGGAA
Found at i:1647789 original size:12 final size:12
Alignment explanation
Indices: 1647772--1647810 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1647762 GTTATTTCAT
*
1647772 ATTTATATCTAA
1 ATTTATATTTAA
1647784 ATTTATATTTAA
1 ATTTATATTTAA
*
1647796 ATTTAAATTTAA
1 ATTTATATTTAA
1647808 ATT
1 ATT
1647811 AAACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTATATTTAA
Found at i:1647793 original size:18 final size:18
Alignment explanation
Indices: 1647765--1647806 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1647755 TAATTGAGTT
*
1647765 ATTTCATATTTATATCTAA
1 ATTT-ATATTTAAATCTAA
*
1647784 ATTTATATTTAAATTTAA
1 ATTTATATTTAAATCTAA
1647802 ATTTA
1 ATTTA
1647807 AATTAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATATTTAAATCTAA
Found at i:1647807 original size:6 final size:6
Alignment explanation
Indices: 1647781--1647810 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1647771 TATTTATATC
*
1647781 TAAATT TATATT TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
1647811 AAACTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:1649076 original size:277 final size:280
Alignment explanation
Indices: 1648511--1649078 Score: 811
Period size: 277 Copynumber: 2.0 Consensus size: 280
1648501 TCCACAAGTT
* * *
1648511 TTAATATTTAACTCGGTTGTCATTGCTAGATTTTCAATGCTAAAGCTACACCAGACAGCAGCAAA
1 TTAAGATTCAACTCGGTCGTCATTGCTAGATTTTCAATGCTAAAGCTACACCAGA-AGCAGCAAA
* *
1648576 GAAACTAATCATCTTCAAACACTATTAGCAGCTCAAAGTATCAAATCCAAGTTAATGCATAAATC
65 GAAACTAATCATCTTCAAACACTATTAGCAGCACAAAGTATCAAATCCAAGTTAATGCAGAAATC
* * * *
1648641 GAGCATATTCAGCAAGTTTAAGATTCAACCCATCATTGCTAGATTTGCAATGCCTATGGTAGCAG
130 AAGCACATTCAGCAACTTCAAGATTCAACCCATCATTGCTAGATTTGCAATGCCTATGGTAGCAG
* * * ***
1648706 GGAAGAAACTAATACTTCTCAAACGCCATTCGCAGCTTGAAGTTTCAGACGCCAATTATGTTTAA
195 GGAAGAAACGAATACTTCTCAAACGCCATTAGCAGCTCGAAGTTTCAGACGCCAATTATGCAAAA
** * * * ***
1648771 GTCGAGCACGATCGACAAGTT
260 ACCAAGCACAATCCACAACCC
1648792 TTAAGATTCAACTCGGTCGTCATTGCTAGATTTTCAATGCTAAAGCTACACCAG-AGCAGCAAAG
1 TTAAGATTCAACTCGGTCGTCATTGCTAGATTTTCAATGCTAAAGCTACACCAGAAGCAGCAAAG
* * *
1648856 AAACTAATCATTTTCAAACACTATTAGCGGCACAAAGTATCAAATCCCAGTT-ATGCAGAAATCA
66 AAACTAATCATCTTCAAACACTATTAGCAGCACAAAGTATCAAATCCAAGTTAATGCAGAAATCA
*
1648920 AGCACATTCAGCAACTTCAAGATTCAACCCATCCTTGCTAGATTT-CAATGCCTATGGTAGCAGG
131 AGCACATTCAGCAACTTCAAGATTCAACCCATCATTGCTAGATTTGCAATGCCTATGGTAGCAGG
* * *
1648984 GAAGAAACGAATACTTCTCAAATGCCATTAGCAGCTCGAAGTTTCGGAC-CTCGATTATGCAAAA
196 GAAGAAACGAATACTTCTCAAACGCCATTAGCAGCTCGAAGTTTCAGACGC-CAATTATGCAAAA
*
1649048 ACCAAGCACAATCCATAACCC
260 ACCAAGCACAATCCACAACCC
1649069 TTAAGATTCA
1 TTAAGATTCA
1649079 GCTTACATTG
Statistics
Matches: 255, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
276 1 0.00
277 94 0.37
278 51 0.20
279 58 0.23
281 51 0.20
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (280 bp):
TTAAGATTCAACTCGGTCGTCATTGCTAGATTTTCAATGCTAAAGCTACACCAGAAGCAGCAAAG
AAACTAATCATCTTCAAACACTATTAGCAGCACAAAGTATCAAATCCAAGTTAATGCAGAAATCA
AGCACATTCAGCAACTTCAAGATTCAACCCATCATTGCTAGATTTGCAATGCCTATGGTAGCAGG
GAAGAAACGAATACTTCTCAAACGCCATTAGCAGCTCGAAGTTTCAGACGCCAATTATGCAAAAA
CCAAGCACAATCCACAACCC
Found at i:1655220 original size:16 final size:18
Alignment explanation
Indices: 1655199--1655231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1655189 ACACACTAAA
1655199 TCGGTT-TC-GTTTTTTT
1 TCGGTTATCGGTTTTTTT
1655215 TCGGTTATCGGTTTTTT
1 TCGGTTATCGGTTTTTT
1655232 GGATCGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.03, C:0.12, G:0.21, T:0.64
Consensus pattern (18 bp):
TCGGTTATCGGTTTTTTT
Found at i:1659189 original size:31 final size:31
Alignment explanation
Indices: 1659125--1659243 Score: 129
Period size: 30 Copynumber: 3.9 Consensus size: 31
1659115 CCTTGGCAAC
* * * *
1659125 TCCATAGGTTCCGAAGAACCTA-GTAAACTG
1 TCCATATGTTCCGTAGAACATAGGTATACTG
*
1659155 TCCATATGTTCCTTAGAACATAGGTATACTG
1 TCCATATGTTCCGTAGAACATAGGTATACTG
* * *
1659186 TCCATATG-T-CG-AAAACATAGGTAATTCTA
1 TCCATATGTTCCGTAGAACATAGGT-ATACTG
1659215 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
1659244 CCTCGACTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.14
29 13 0.18
30 20 0.27
31 20 0.27
32 10 0.14
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (31 bp):
TCCATATGTTCCGTAGAACATAGGTATACTG
Found at i:1668296 original size:16 final size:17
Alignment explanation
Indices: 1668265--1668313 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1668255 ATCATAAATG
* *
1668265 ATTTATAATATATATTT
1 ATTTAAAATTTATATTT
*
1668282 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
1668297 ATTTAAAATTTATATTT
1 ATTTAAAATTTATATTT
1668314 TATCATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.23
16 14 0.54
17 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:1668917 original size:2 final size:2
Alignment explanation
Indices: 1668904--1668936 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1668894 TCTCTTTTCC
*
1668904 TA TA TA TT TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1668937 AACACACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1668927 original size:11 final size:11
Alignment explanation
Indices: 1668904--1668933 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1668894 TCTCTTTTCC
1668904 TATATAT-TTA
1 TATATATATTA
1668914 TATATATATTA
1 TATATATATTA
1668925 TATATATAT
1 TATATATAT
1668934 ATAAACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATATATTA
Found at i:1672386 original size:32 final size:33
Alignment explanation
Indices: 1672320--1672388 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1672310 AGCTTGTGCC
*
1672320 TTAATTTTTGACCACAAAAGAGGATTTTGACTT
1 TTAACTTTTGACCACAAAAGAGGATTTTGACTT
1672353 TTAACTTTTGACCACAAAAGAGGA-TTTGACTT
1 TTAACTTTTGACCACAAAAGAGGATTTTGACTT
1672385 TTAA
1 TTAA
1672389 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (33 bp):
TTAACTTTTGACCACAAAAGAGGATTTTGACTT
Found at i:1672395 original size:2 final size:2
Alignment explanation
Indices: 1672388--1672424 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1672378 TTGACTTTTA
* *
1672388 AT AT AT AT AT AT AT TT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1672425 ATGTGTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1674809 original size:23 final size:23
Alignment explanation
Indices: 1674783--1674831 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1674773 CACATACAAT
*
1674783 AACATGTTAGTGAAGACTAAACG
1 AACATGTTAGTAAAGACTAAACG
* * *
1674806 AACATGTTCGTAAATATTAAACG
1 AACATGTTAGTAAAGACTAAACG
1674829 AAC
1 AAC
1674832 TAAACATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.24
Consensus pattern (23 bp):
AACATGTTAGTAAAGACTAAACG
Found at i:1677548 original size:106 final size:106
Alignment explanation
Indices: 1677420--1677681 Score: 328
Period size: 106 Copynumber: 2.5 Consensus size: 106
1677410 GTATTGTTCC
* * * * * * *
1677420 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTTACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAACTGGGAAATTATTTATTGACAA
* * * * *
1677485 TCAGCCGCCCCTTC-TCTGTGAAGTTGAGCTTGTGATGTCTT
66 CCAGCCGCCCATTCGTC-GTGAAGTTGAACTTGCGATGTCTG
* * *
1677526 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAACTGGGAAATTATTTATTGACAA
* * * *
1677591 CCAGCGGTCTATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCCGCCCATTCGTCGTGAAGTTGAACTTGCGATGTCTG
*
1677632 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGATCTGAAACTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAACTGGGAA
1677682 GCCCCTTCGT
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
106 131 0.98
107 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAACTGGGAAATTATTTATTGACAA
CCAGCCGCCCATTCGTCGTGAAGTTGAACTTGCGATGTCTG
Found at i:1678468 original size:66 final size:66
Alignment explanation
Indices: 1678362--1678581 Score: 336
Period size: 66 Copynumber: 3.3 Consensus size: 66
1678352 AAGTATTTTG
* * * *
1678362 TGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCCCAAGTGAAACAAAATT
1 TGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1678427 C
66 C
* *
1678428 TGTTTCAAGGGTAACGTTTTCAAAGTTTATGTTTCGAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1678493 C
66 C
* *
1678494 -ATTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
*
1678558 T
66 C
1678559 TGTTTCAAGGGAAAC-TATTTCAA
1 TGTTTCAAGGGAAACGT-TTTCAA
1678582 GAGAGACAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
65 61 0.44
66 78 0.56
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (66 bp):
TGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
C
Found at i:1678618 original size:37 final size:37
Alignment explanation
Indices: 1678519--1678614 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
1678509 TTTTCAAAGT
* * *
1678519 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TTATGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAA
* *
1678556 TTTTGTTTCAAGGGAAACTATTTCAAGAGAGACAAAA
1 TTATGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAA
1678593 TTCAT-TTTCAAGGGAAA-TGTTT
1 TT-ATGTTTCAAGGGAAACTGTTT
1678615 TCAATGTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.08
37 46 0.90
38 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (37 bp):
TTATGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAA
Found at i:1678672 original size:22 final size:22
Alignment explanation
Indices: 1678644--1678695 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1678634 AGAAACTATC
1678644 TCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAGACAAAATTTTGTT
1678666 TCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAGACAAAATTTTGTT
1678688 TCAAGGGA
1 TCAAGGGA
1678696 AACTAGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (22 bp):
TCAAGGGAGACAAAATTTTGTT
Found at i:1678781 original size:92 final size:92
Alignment explanation
Indices: 1678666--1679262 Score: 939
Period size: 92 Copynumber: 6.4 Consensus size: 92
1678656 AAATTTTGTT
1678666 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
1678731 AATGTTTATGTTTCAAGAGAAACTGTC
66 AATGTTTATGTTTCAAGAGAAACTGTC
*
1678758 TCAAGGAAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
* *
1678823 AATGTTTATGTTTTAAAAGAAACTGTC
66 AATGTTTATGTTTCAAGAGAAACTGTC
* * *
1678850 TCAATGGAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGG-AA--A-CT------AGACAAAATTCATTTCAAGAG
* *
1678915 AAATATTTTCAATGTTTATGTTTCAAGAGACA-TCGTC
56 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACT-GTC
* *
1678952 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATACATTTCAAGGGAAATGTTTTC
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
*
1679017 AATGTTTATGCTTCAAGAGAAACTGTC
66 AATGTTTATGTTTCAAGAGAAACTGTC
1679044 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
*
1679109 AATGTTTACGTTTCAAGAGAAA-TCGTC
66 AATGTTTATGTTTCAAGAGAAACT-GTC
*
1679136 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGGGAAATGTTTTC
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
1679201 AATGTTTATGTTTCAAGAGAAAAC-GTC
66 AATGTTTATGTTTCAAGAG-AAACTGTC
1679228 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTA
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTA
1679263 TATCAAGCGG
Statistics
Matches: 467, Mismatches: 23, Indels: 30
0.90 0.04 0.06
Matches are distributed among these distances:
91 1 0.00
92 373 0.80
93 6 0.01
95 1 0.00
96 2 0.00
98 2 0.00
99 1 0.00
101 3 0.01
102 78 0.17
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (92 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAGACAAAATTCATTTCAAGAGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTGTC
Found at i:1679269 original size:37 final size:37
Alignment explanation
Indices: 1679228--1679319 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 37
1679218 AGAAAACGTC
*
1679228 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATA
1 TCAAGGGAGATAAAATTTTGTTTCAAGGGAAACTATA
*
1679265 TCAAGCGG-GATAAAATCTTTTGTTTCAAGGGAAACTATC
1 TCAAG-GGAGATAAAA--TTTTGTTTCAAGGGAAACTATA
*
1679304 TCAAGCGAGATAAAAT
1 TCAAGGGAGATAAAAT
1679320 CTTCTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
37 12 0.25
38 3 0.06
39 33 0.69
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (37 bp):
TCAAGGGAGATAAAATTTTGTTTCAAGGGAAACTATA
Found at i:1679291 original size:39 final size:39
Alignment explanation
Indices: 1679243--1679322 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1679233 GGAGACAAAA
*
1679243 TTTTGTTTCAAGGGAAACTATATCAAGCGGGATAAAATC
1 TTTTGTTTCAAGGGAAACTATATCAAGCGAGATAAAATC
*
1679282 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATATCAAGCGAGATAAAATC
1679321 TT
1 TT
1679323 CTTTAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (39 bp):
TTTTGTTTCAAGGGAAACTATATCAAGCGAGATAAAATC
Found at i:1680921 original size:183 final size:183
Alignment explanation
Indices: 1680606--1680959 Score: 618
Period size: 183 Copynumber: 1.9 Consensus size: 183
1680596 ATCAGGTTTA
*
1680606 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
* ** *
1680671 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCAAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCAAGTT
*
1680736 TCCTCTATAACCAATTGCTTTAGCGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGCGGAATAGCTCAGCTTTAGAGGGACAAATC
*
1680789 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
* *
1680854 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCAAGTT
*
1680919 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGCGGAATAGCTCAGCTTTA
1680960 CGGATTTAAT
Statistics
Matches: 161, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCAAGTT
TCCTCTATAACCAATTGCCTTAGCGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1686036 original size:20 final size:20
Alignment explanation
Indices: 1686011--1686055 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1686001 TTATCCGGAA
*
1686011 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTAGGGTTT
1686031 AAAAATCCGGTCTAGGGTTT
1 AAAAATCCGGTCTAGGGTTT
1686051 AAAAA
1 AAAAA
1686056 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTAGGGTTT
Found at i:1697125 original size:35 final size:35
Alignment explanation
Indices: 1697086--1697160 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1697076 AAAATACTTT
* *
1697086 AATTTAGGGTTTAGAATATAATTAAAGTATTTTAG
1 AATTTAGGGTTTAAAATATAATCAAAGTATTTTAG
* * * *
1697121 AATTTAGGGTTTAAAATGTAATCGAAGTGTTTTGG
1 AATTTAGGGTTTAAAATATAATCAAAGTATTTTAG
1697156 AATTT
1 AATTT
1697161 TGAACATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (35 bp):
AATTTAGGGTTTAAAATATAATCAAAGTATTTTAG
Found at i:1698790 original size:3 final size:3
Alignment explanation
Indices: 1698782--1698815 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1698772 TATTTATATA
1698782 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1698816 TTTACATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1700807 original size:23 final size:23
Alignment explanation
Indices: 1700781--1700844 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1700771 CAGCTCATAT
1700781 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1700804 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1700827 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1700845 TATAATACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1701032 original size:103 final size:103
Alignment explanation
Indices: 1700863--1701180 Score: 573
Period size: 103 Copynumber: 3.1 Consensus size: 103
1700853 TGTCCATAAG
* * * *
1700863 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1700928 TTCACACATGTTCCAGAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
1700966 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1701031 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
1701069 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1701134 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
1701172 GACCACATA
1 GACCACATA
1701181 GACCCTTGAC
Statistics
Matches: 207, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:1705178 original size:18 final size:18
Alignment explanation
Indices: 1705155--1705225 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
1705145 AGGGATTATA
**
1705155 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCAGGACAT
1705173 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
1705191 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
1705209 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
1705226 AATTTTTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1726131 original size:120 final size:120
Alignment explanation
Indices: 1725913--1726274 Score: 652
Period size: 120 Copynumber: 3.0 Consensus size: 120
1725903 CATTAAATCA
*
1725913 TTGGTAAGTTAATTCAACGATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
1 TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
*
1725978 TTGAAACGGTCATATCTTTCGGAAATTTCAAATTTTCACGTAATTTTAATAAATT
66 TTGAAACGGCCATATCTTTCGGAAATTTCAAATTTTCACGTAATTTTAATAAATT
1726033 TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
1 TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
* * *
1726098 TTGAAACGGCCATATCTTTCGGAAATTTTAAATTTTAACGTAATTTTGATAAATT
66 TTGAAACGGCCATATCTTTCGGAAATTTCAAATTTTCACGTAATTTTAATAAATT
*
1726153 TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGTGTAT
1 TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
**
1726218 TTGAAACGGCCATATCTTTCAAAAATTTCAAATTTTCACGTAATTTTAATAAATT
66 TTGAAACGGCCATATCTTTCGGAAATTTCAAATTTTCACGTAATTTTAATAAATT
1726273 TT
1 TT
1726275 CACATTTATA
Statistics
Matches: 231, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 231 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (120 bp):
TTGGTAAGTTAATTCAACAATTAGGGTTTTAGTAGGGTATTAATTTAGGATGAATTCAGGAGTAT
TTGAAACGGCCATATCTTTCGGAAATTTCAAATTTTCACGTAATTTTAATAAATT
Found at i:1733134 original size:31 final size:31
Alignment explanation
Indices: 1733099--1733160 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1733089 CTCCTGTTAT
*
1733099 TTACTCGGGCTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
1733130 TTACTCGGACTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
1733161 GAGCAGTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
TTACTCGGACTGAGCAGCACTTACTGAATCA
Found at i:1734662 original size:30 final size:31
Alignment explanation
Indices: 1734604--1734662 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1734594 ATTTCAAAAT
1734604 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATATATTAATTTATA
* * * *
1734635 TATATTTAT-AAAAATATTTATTTATTTA
1 TATAATTATGAAAAAAATATATTAATTTA
1734663 GAAATATCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
TATAATTATGAAAAAAATATATTAATTTATA
Found at i:1735037 original size:2 final size:2
Alignment explanation
Indices: 1735030--1735071 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1735020 ATTTAAACCA
*
1735030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1735071 A
1 A
1735072 ATAATGAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1736466 original size:13 final size:14
Alignment explanation
Indices: 1736448--1736489 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1736438 TATATATATT
1736448 TAATAATAATA-AA
1 TAATAATAATATAA
*
1736461 TAATAAT-ATATAT
1 TAATAATAATATAA
1736474 TAATAATAATTATAA
1 TAATAATAA-TATAA
1736489 T
1 T
1736490 TATTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.12
13 15 0.62
14 1 0.04
15 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:1736694 original size:46 final size:46
Alignment explanation
Indices: 1736619--1736722 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
1736609 GATGAAAATG
*
1736619 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
1736665 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1736710 TTTAAAAACATCA
1 TTTGAAAACATCA
1736723 AAAAGCTCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 12 0.23
46 40 0.77
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:1736806 original size:75 final size:76
Alignment explanation
Indices: 1736655--1737379 Score: 1280
Period size: 76 Copynumber: 9.6 Consensus size: 76
1736645 TTACAGATGA
* *
1736655 CCCGAAGG-TTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1736719 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1736730 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATAACCCGAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1736794 ATCAAAAAGCT
66 ATCAAAAAGCT
1736805 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1736870 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1736881 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1736945 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1736956 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1737020 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1737031 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1737095 ATCAAAAAGCT
66 ATCAAAAAGCT
1737106 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1737171 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1737182 CCCGAAGGCTTTTTAGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1737247 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1737258 CCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1737323 ATCAAAAATCT
66 ATCAAAAAGCT
* *
1737334 CCCGAAGGCTTTTTGGAAACATCATGCACTACAAGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1737380 TGGGAAATAG
Statistics
Matches: 629, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
75 303 0.48
76 326 0.52
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:1736937 original size:151 final size:151
Alignment explanation
Indices: 1736655--1737379 Score: 1310
Period size: 151 Copynumber: 4.8 Consensus size: 151
1736645 TTACAGATGA
* *
1736655 CCCGAAGG-TTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1736719 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATAACCCGAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
1736784 GTTTGAAAACATCAAAAAGCT
131 GTTTGAAAACATCAAAAAGCT
1736805 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1736870 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
1736935 GTTTGAAAACATCAAAAAGCT
131 GTTTGAAAACATCAAAAAGCT
* *
1736956 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1737020 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
1737085 GTTTGAAAACATCAAAAAGCT
131 GTTTGAAAACATCAAAAAGCT
1737106 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
* *
1737171 ATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
1737236 GCTTTGAAAACATCAAAAAGCT
131 G-TTTGAAAACATCAAAAAGCT
* *
1737258 CCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
* * *
1737323 ATCAAAAATCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAAGACTTACAGATG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1737380 TGGGAAATAG
Statistics
Matches: 555, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
150 155 0.28
151 264 0.48
152 136 0.25
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (151 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAG
GTTTGAAAACATCAAAAAGCT
Found at i:1738254 original size:22 final size:22
Alignment explanation
Indices: 1738226--1738280 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1738216 CATAAAGCTT
1738226 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1738248 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1738270 TCATCTTTGAA
1 TCATCTTTGAA
1738281 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1742966 original size:9 final size:9
Alignment explanation
Indices: 1742952--1743002 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
1742942 TCCCTTTTTC
1742952 TTTTTCCCT
1 TTTTTCCCT
1742961 TTTTTCCCT
1 TTTTTCCCT
*
1742970 TTTTTCTCATT
1 TTTTTC-C-CT
*
1742981 TTTTTCATCT
1 TTTTTC-CCT
1742991 TTTTT-CCT
1 TTTTTCCCT
1742999 TTTT
1 TTTT
1743003 CCTCATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.17
9 15 0.43
10 7 0.20
11 7 0.20
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCCCT
Found at i:1743002 original size:20 final size:21
Alignment explanation
Indices: 1742968--1743017 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1742958 CCTTTTTTCC
**
1742968 CTTTTTTCTCATTTTTTTCAT
1 CTTTTTTCTCATTTTCCTCAT
*
1742989 CTTTTTTC-CTTTTTCCTCAT
1 CTTTTTTCTCATTTTCCTCAT
*
1743009 TTTTTTTCT
1 CTTTTTTCT
1743018 TTGTTAGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTTCTCATTTTCCTCAT
Found at i:1750065 original size:22 final size:22
Alignment explanation
Indices: 1750034--1750088 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1750024 GGGAAACCTC
*
1750034 GGTGAGTCACCAAAGCTAGGCT
1 GGTGACTCACCAAAGCTAGGCT
1750056 GGTGACTCACCAAAGCTAGGCT
1 GGTGACTCACCAAAGCTAGGCT
1750078 GGTGACTCACC
1 GGTGACTCACC
1750089 GTAGGGAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.18
Consensus pattern (22 bp):
GGTGACTCACCAAAGCTAGGCT
Found at i:1750401 original size:3 final size:3
Alignment explanation
Indices: 1750393--1750440 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1750383 TATATATATT
* * *
1750393 TAA TAA TAAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
1750440 T
1 T
1750441 TATTATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1750417 original size:28 final size:29
Alignment explanation
Indices: 1750372--1750449 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 29
1750362 ATGTAATTTG
1750372 TAATATATATATATATATATT-TAATAATAAA
1 TAATA-ATA-ATATATATATTATAATAAT-AA
*
1750403 TAATAATAATA-ATATATTATATTAATAA
1 TAATAATAATATATATATTATAATAATAA
*
1750431 TAATTATAAT-TAT-TATTAT
1 TAATAATAATATATATATTAT
1750450 GAAAAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.14
28 20 0.47
29 9 0.21
30 3 0.07
31 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATAATAATATATATATTATAATAATAA
Found at i:1750431 original size:22 final size:22
Alignment explanation
Indices: 1750403--1750448 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1750393 TAATAATAAA
1750403 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
1750425 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
1750447 TA
1 TA
1750449 TGAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:1750442 original size:16 final size:16
Alignment explanation
Indices: 1750387--1750442 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1750377 TATATATATA
*
1750387 TATATTTAATAATAAAT
1 TATAATTAATAAT-AAT
*
1750404 AATAA-TAATAATATAT
1 TATAATTAATAATA-AT
1750420 TAT-ATTAATAATAAT
1 TATAATTAATAATAAT
1750435 TATAATTA
1 TATAATTA
1750443 TTATTATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 7 0.21
16 23 0.70
17 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATTAATAATAAT
Found at i:1754991 original size:16 final size:16
Alignment explanation
Indices: 1754972--1755024 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1754962 CCATAGCCCC
1754972 TATCACACATATATCA
1 TATCACACATATATCA
** * *
1754988 TATCATGCACACATCA
1 TATCACACATATATCA
1755004 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1755022 TAT
1 TAT
1755025 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1755223 original size:23 final size:23
Alignment explanation
Indices: 1755197--1755265 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1755187 CACCACAGCT
*
1755197 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1755220 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
1755243 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1755266 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1755593 original size:103 final size:103
Alignment explanation
Indices: 1755281--1755596 Score: 569
Period size: 103 Copynumber: 3.1 Consensus size: 103
1755271 TAATGTCCAT
* * * * *
1755281 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTTTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1755346 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1755384 AAGAACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1755449 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1755487 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1755552 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1755590 AAGGACC
1 AAGGACC
1755597 GCGTAGACCC
Statistics
Matches: 204, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 204 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1757303 original size:21 final size:21
Alignment explanation
Indices: 1757279--1757323 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1757269 TTTTGTTCGT
* *
1757279 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1757300 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1757321 TTG
1 TTG
1757324 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1761142 original size:25 final size:25
Alignment explanation
Indices: 1761110--1761183 Score: 148
Period size: 25 Copynumber: 3.0 Consensus size: 25
1761100 CAATTATGTT
1761110 TTATTATTGTTTTGTTTTCACTTTG
1 TTATTATTGTTTTGTTTTCACTTTG
1761135 TTATTATTGTTTTGTTTTCACTTTG
1 TTATTATTGTTTTGTTTTCACTTTG
1761160 TTATTATTGTTTTGTTTTCACTTT
1 TTATTATTGTTTTGTTTTCACTTT
1761184 TCTGTATCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.12, C:0.08, G:0.11, T:0.69
Consensus pattern (25 bp):
TTATTATTGTTTTGTTTTCACTTTG
Found at i:1766201 original size:26 final size:27
Alignment explanation
Indices: 1766151--1766201 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1766141 TATGTGAGAT
***
1766151 CTAAGGAGATAACCATTTTTTTAATAG
1 CTAAGGAGATAACCATTTAAATAATAG
1766178 CTAAGGAGATAA-CATTTAAATAAT
1 CTAAGGAGATAACCATTTAAATAAT
1766202 CTATTTTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (27 bp):
CTAAGGAGATAACCATTTAAATAATAG
Found at i:1773559 original size:41 final size:41
Alignment explanation
Indices: 1773521--1773618 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
1773511 CGTTTTTTCG
* *
1773521 ACAAATGCCGCTATAGAGTAGTAATTTAGCAGCATTTTTAA
1 ACAAACGCCGCAATAGAGTAGTAATTTAGCAGCATTTTTAA
* * * *
1773562 ACAAACGCCGCAATAGATTAGTACTTTAGCAGCCTTTTTAT
1 ACAAACGCCGCAATAGAGTAGTAATTTAGCAGCATTTTTAA
*
1773603 ACAAACACCGCAATAG
1 ACAAACGCCGCAATAG
1773619 GATTCACCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (41 bp):
ACAAACGCCGCAATAGAGTAGTAATTTAGCAGCATTTTTAA
Found at i:1780044 original size:51 final size:53
Alignment explanation
Indices: 1779948--1780051 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 53
1779938 GAATCGCTCA
1779948 AATAAATTTAAGAATTTTTCCAGATTTTTATGCAGACGGAAGGGG-CCACGCG
1 AATAAATTTAAGAATTTTTCCAGATTTTTATGCAGACGGAAGGGGCCCACGCG
*
1780000 AATAAATTTAAGAATTTTTCCA-ATTTTTATGCAGCCGGAAGGGGCCCACGCG
1 AATAAATTTAAGAATTTTTCCAGATTTTTATGCAGACGGAAGGGGCCCACGCG
1780052 CCCCCACTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 21 0.42
52 29 0.58
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (53 bp):
AATAAATTTAAGAATTTTTCCAGATTTTTATGCAGACGGAAGGGGCCCACGCG
Found at i:1785610 original size:41 final size:41
Alignment explanation
Indices: 1785560--1785981 Score: 340
Period size: 41 Copynumber: 10.2 Consensus size: 41
1785550 AAGGTAATTA
* *
1785560 GCGGTGTTTGTAT-CAAAACGCCGCTATAGATCTAACCTTTT
1 GCGGCGTTTGT-TCCAAAACGCCGCTATAGATCTGACCTTTT
* ** ** *
1785601 GTGGCGTTTGTTCCAAAA-AACATTATAGATCTCGATCTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATCT-GACCTTTT
* * * *
1785642 GCGG-GTTTGTTCAAAAATGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATCTGACCTTTT
* * * *
1785682 ACGGCGTTTGTTCCAAAAACACCGCTATAGATCTAACTTTTT
1 GCGGCGTTTGTTCC-AAAACGCCGCTATAGATCTGACCTTTT
*
1785724 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCT-ACCTTTT
1 GCGGCGTTTGTTCC-AAAACGCCGCTATAGATCTGACCTTTT
* ** * * *
1785765 GCGGAGTTAATTCCAAAACGTCGCCATAGATTTGACCTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATCTGACCTTTT
** * * *
1785806 GCGGTATTTATTCCAAAATGCCGCTATAAATCTTGACCTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATC-TGACCTTTT
* *
1785848 GCGGCGTTTGTTCC--AATGCCGCTATA-ATCTCGACTTTTT
1 GCGGCGTTTGTTCCAAAACGCCGCTATAGATCT-GACCTTTT
*** * * *
1785887 GCGGCGTTTGTT-CAAAATTATCGCTTTAGGTGTCGACCTTTT
1 GCGGCGTTTGTTCCAAAA-CGCCGCTATAGATCT-GACCTTTT
*
1785929 GCGGCGTTTGTTACAAAAACGCCGCTATAGGTAT-TGACCTTTTT
1 GCGGCGTTTGTT-CCAAAACGCCGCTATA-G-ATCTGACC-TTTT
1785973 GCGGCGTTT
1 GCGGCGTTT
1785982 ATAGAGCTTG
Statistics
Matches: 307, Mismatches: 57, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.01
39 22 0.07
40 63 0.21
41 96 0.31
42 94 0.31
43 10 0.03
44 19 0.06
45 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
GCGGCGTTTGTTCCAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1785700 original size:81 final size:82
Alignment explanation
Indices: 1785560--1785947 Score: 351
Period size: 81 Copynumber: 4.7 Consensus size: 82
1785550 AAGGTAATTA
* * * **
1785560 GCGGTGTTTGTATC-AAAACGCCGCTATAGATCTAACCTTTTGTGGCGTTTGTTCCAAAAAACAT
1 GCGGTGTTTGT-TCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAACGC
1785624 TATAGATCTCGA-TCTTTT
65 TATAGATCTCGACT-TTTT
* * *
1785642 GCGG-GTTTGTTCAAAAATGCCGTTATAGGTCTGACCTTTTACGGCGTTTGTTCCAAAAACACCG
1 GCGGTGTTTGTTCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAA-A-CG
*
1785706 CTATAGATCT-AACTTTTT
64 CTATAGATCTCGACTTTTT
* * ** **
1785724 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCT-ACCTTTTGCGGAGTTAATTCCAAAACGTCG
1 GCGGTGTTTGTT-CAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAA-AACG
* * *
1785788 CCATAGAT-TTGACCTTTT
64 CTATAGATCTCGACTTTTT
* * * * ***
1785806 GCGGTATTTATTCCAAAATGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC-AATGCCGC
1 GCGGTGTTTGTTCAAAAATGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAAACGC
1785870 TATA-ATCTCGACTTTTT
65 TATAGATCTCGACTTTTT
* * ** * * * *
1785887 GCGGCGTTTGTTCAAAATTATCGCTTTAGGTGTCGACCTTTTGCGGCGTTTGTTACAAAAA
1 GCGGTGTTTGTTCAAAAATGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAA
1785948 CGCCGCTATA
Statistics
Matches: 245, Mismatches: 48, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
80 5 0.02
81 121 0.49
82 44 0.18
83 57 0.23
84 18 0.07
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (82 bp):
GCGGTGTTTGTTCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAACGCT
ATAGATCTCGACTTTTT
Found at i:1785711 original size:42 final size:42
Alignment explanation
Indices: 1785574--1785981 Score: 347
Period size: 42 Copynumber: 9.9 Consensus size: 42
1785564 TGTTTGTATC
* *
1785574 AAAACGCCGCTATAGATCTAACCTTTTGTGGCGTTTGTTCCA
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
* ** *
1785616 AAAA--ACATTATAGATCTCGATCTTTTGCGG-GTTTGTT-CA
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCA
* * * *
1785655 AAAATGCCGTTATAGGTCTGACCTTTTACGGCGTTTGTTCCA
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
* * * *
1785697 AAAACACCGCTATAGATCTAACTTTTTGCGGTGTTTGTTCCA
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
* **
1785739 AAAACGCCGCTATAGATCT-ACCTTTTGCGGAGTTAATTCC-
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
* * * ** *
1785779 AAAACGTCGCCATAGATTTGACCTTTTGCGGTATTTATTCC-
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
* *
1785820 AAAATGCCGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC-
1 AAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCA
* *
1785862 --AATGCCGCTATA-ATCTCGACTTTTTGCGGCGTTTGTT-CA
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCA
**** * * * *
1785901 AAATTATCGCTTTAGGTGTCGACCTTTTGCGGCGTTTGTTACA
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCA
1785944 AAAACGCCGCTATAGGTAT-TGACCTTTTTGCGGCGTTT
1 AAAACGCCGCTATA-G-ATCTGACC-TTTTGCGGCGTTT
1785982 ATAGAGCTTG
Statistics
Matches: 298, Mismatches: 52, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.01
39 28 0.09
40 55 0.18
41 82 0.28
42 100 0.34
43 15 0.05
44 15 0.05
45 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (42 bp):
AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA
Found at i:1786148 original size:20 final size:21
Alignment explanation
Indices: 1786104--1786155 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1786094 GGCGCTTAGG
1786104 AAACGCCGCTATAGGACTAAA
1 AAACGCCGCTATAGGACTAAA
*
1786125 AAACACCGCTATAGGACT-AA
1 AAACGCCGCTATAGGACTAAA
1786145 AAACGCCGCTA
1 AAACGCCGCTA
1786156 AAAGCCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.13
Consensus pattern (21 bp):
AAACGCCGCTATAGGACTAAA
Found at i:1790513 original size:29 final size:29
Alignment explanation
Indices: 1790470--1790580 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1790460 CCCGACCCGG
*
1790470 TGACATTTTGAGAATTATTTTGAAAAATA
1 TGACATTTTGGGAATTATTTTGAAAAATA
1790499 TGACATTTTGGGAATTATTTTGAAAAATA
1 TGACATTTTGGGAATTATTTTGAAAAATA
* * *
1790528 TGACATTCTGGGAATTATTTTAAAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAATA
1790557 TGACATTTTGGGAATTATTTTGAA
1 TGACATTTTGGGAATTATTTTGAA
1790581 TGTAGACTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTGAAAAATA
Found at i:1791498 original size:31 final size:31
Alignment explanation
Indices: 1791463--1791530 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
1791453 AGGTAGCTCT
* * *
1791463 GGCCCTGAGATCA-TTCTCGGGTAGGCCCTAC
1 GGCCCTAAGAT-AGTTCTCAGGTAGGCCCCAC
*
1791494 GGCCCTAAGATATGTTCTTAGGTAGGCCCCAC
1 GGCCCTAAGATA-GTTCTCAGGTAGGCCCCAC
1791526 GGCCC
1 GGCCC
1791531 CGAAATCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.03
31 10 0.32
32 20 0.65
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (31 bp):
GGCCCTAAGATAGTTCTCAGGTAGGCCCCAC
Found at i:1791950 original size:9 final size:9
Alignment explanation
Indices: 1791893--1791949 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
1791883 GGTTTATCGT
1791893 AAATTATTAA
1 AAATT-TTAA
1791903 AAATTTT-A
1 AAATTTTAA
1791911 AAATTTTAA
1 AAATTTTAA
*
1791920 AACATTTGAA
1 AA-ATTTTAA
*
1791930 AAATATTAA
1 AAATTTTAA
*
1791939 AATTTTTAA
1 AAATTTTAA
1791948 AA
1 AA
1791950 TATACAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 8 0.20
9 19 0.47
10 13 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATTTTAA
Found at i:1791951 original size:17 final size:17
Alignment explanation
Indices: 1791892--1791952 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1791882 TGGTTTATCG
* *
1791892 TAAATTATTAAAAATTT
1 TAAAATATTAAAATTTT
* *
1791909 TAAAATTTTAAAACATTTG
1 TAAAATATT-AAA-ATTTT
*
1791928 AAAAATATTAAAATTTT
1 TAAAATATTAAAATTTT
1791945 TAAAATAT
1 TAAAATAT
1791953 ACAAATATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 18 0.53
18 6 0.18
19 10 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAATATTAAAATTTT
Found at i:1792054 original size:18 final size:17
Alignment explanation
Indices: 1792017--1792059 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1792007 TATAAATTTC
1792017 TAAAAAATAGTAAGACT
1 TAAAAAATAGTAAGACT
*
1792034 TAATAAAATATTAA-ACAT
1 TAA-AAAATAGTAAGAC-T
1792052 TAAAAAAT
1 TAAAAAAT
1792060 CAAACTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAAATAGTAAGACT
Found at i:1798901 original size:23 final size:21
Alignment explanation
Indices: 1798858--1798920 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
1798848 GACCGAAACG
* * *
1798858 AGCTCGATTGAAACTCAATTCC
1 AGCTCGTTTG-AACTCGATTCA
1798880 AGCTCGACTTTGAACTCGATTCA
1 AGCTCG--TTTGAACTCGATTCA
1798903 AGCTCGTTTGAAGCTCGA
1 AGCTCGTTTGAA-CTCGA
1798921 AGAGGGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 15 0.43
24 3 0.09
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (21 bp):
AGCTCGTTTGAACTCGATTCA
Found at i:1800304 original size:7 final size:7
Alignment explanation
Indices: 1800280--1800326 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
1800270 GGATTTAGGT
*
1800280 TTTAGGG
1 TTTATGG
1800287 TTTA-GG
1 TTTATGG
*
1800293 TTTTATGA
1 -TTTATGG
1800301 TTTATGG
1 TTTATGG
*
1800308 TTTGTGG
1 TTTATGG
1800315 TTTATGG
1 TTTATGG
1800322 TTTAT
1 TTTAT
1800327 TGCAAAGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 31 0.91
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.57
Consensus pattern (7 bp):
TTTATGG
Found at i:1800304 original size:14 final size:14
Alignment explanation
Indices: 1800270--1800310 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1800260 TCACATAATT
1800270 GGATTTAGGTTTTA
1 GGATTTAGGTTTTA
*
1800284 GGGTTTAGGTTTTA
1 GGATTTAGGTTTTA
*
1800298 TGATTTATGGTTT
1 GGATTTA-GGTTT
1800311 GTGGTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (14 bp):
GGATTTAGGTTTTA
Found at i:1804485 original size:32 final size:34
Alignment explanation
Indices: 1804444--1804506 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
1804434 ATGTTGATGC
* *
1804444 AAAATTTAATA-TATTTTTAAAT-AAATAATGTA
1 AAAAATTAATACTATTTATAAATAAAATAATGTA
*
1804476 AAAAATTAATACTATTTATAATTAAAATAAT
1 AAAAATTAATACTATTTATAAATAAAATAAT
1804507 ACACGATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 10 0.38
33 9 0.35
34 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (34 bp):
AAAAATTAATACTATTTATAAATAAAATAATGTA
Found at i:1817539 original size:14 final size:15
Alignment explanation
Indices: 1817520--1817548 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1817510 TGACCAGCAT
1817520 AATAAA-ATTTTTTA
1 AATAAACATTTTTTA
1817534 AATAAACATTTTTTA
1 AATAAACATTTTTTA
1817549 TGAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAACATTTTTTA
Found at i:1819099 original size:21 final size:22
Alignment explanation
Indices: 1819075--1819117 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1819065 TGTTATTTTT
* *
1819075 ATATTT-AATTATTTTATGATA
1 ATATTTGAATAATTTAATGATA
1819096 ATATTTGAATAATTTAATGATA
1 ATATTTGAATAATTTAATGATA
1819118 GAGATCTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATTTGAATAATTTAATGATA
Found at i:1825613 original size:21 final size:22
Alignment explanation
Indices: 1825589--1825631 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
1825579 AATGGAACAT
1825589 TATAC-TTAAATAAATGATAAC
1 TATACTTTAAATAAATGATAAC
1825610 TATACTTATTAAATAAATGATA
1 TATAC-T-TTAAATAAATGATA
1825632 TAAAGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
TATACTTTAAATAAATGATAAC
Found at i:1825862 original size:2 final size:2
Alignment explanation
Indices: 1825855--1825894 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1825845 ATTAAATAAA
*
1825855 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1825895 GAACAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1825968 original size:76 final size:77
Alignment explanation
Indices: 1825803--1825954 Score: 202
Period size: 76 Copynumber: 2.0 Consensus size: 77
1825793 TGTTAAACAA
* *
1825803 ATATATATATATATGAACAAAAAAAATCAGTTTCCAAGACACATTAAATAAAATATATATATATA
1 ATATAGATATATATGAAC-AAAAAAATCAGTTTCCAAGACACATTAAATAAAATATATATATACA
* *
1825868 TCTATATATATAT
65 TCTATACAAATAT
* * *
1825881 ATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAAT-AACTATATATATACGT
1 ATATAGATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAATATATATATACAT
*
1825944 TTA-ACAAATAT
66 CTATACAAATAT
1825955 CCAACTAGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
74 6 0.09
75 15 0.22
76 29 0.43
78 18 0.26
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.34
Consensus pattern (77 bp):
ATATAGATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAATATATATATACAT
CTATACAAATAT
Found at i:1825998 original size:31 final size:31
Alignment explanation
Indices: 1825963--1826054 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 31
1825953 ATCCAACTAG
1825963 CTATATGTTAAACAAATAAATAATGGCTATT
1 CTATATGTTAAACAAATAAATAATGGCTATT
* *** **
1825994 CTATATACGTT--TCAAATATCCAA---CTAAG
1 CTATAT--GTTAAACAAATAAATAATGGCTATT
1826022 CTATATGTTAAACAAATAAATAATGGCTATT
1 CTATATGTTAAACAAATAAATAATGGCTATT
1826053 CT
1 CT
1826055 TCCTAAGACA
Statistics
Matches: 42, Mismatches: 12, Indels: 14
0.62 0.18 0.21
Matches are distributed among these distances:
26 3 0.07
28 17 0.40
31 19 0.45
33 3 0.07
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (31 bp):
CTATATGTTAAACAAATAAATAATGGCTATT
Found at i:1826016 original size:58 final size:60
Alignment explanation
Indices: 1825935--1826054 Score: 217
Period size: 59 Copynumber: 2.0 Consensus size: 60
1825925 AATAACTATA
1825935 TATATACGTTTAACAAATATCCAACT-AGCTATATGTTAAACAAATAAATAATGGCTATTC
1 TATATACGTTT-ACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTC
1825995 TATATACGTTT-CAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTC
1 TATATACGTTTACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTC
1826054 T
1 T
1826055 TCCTAAGACA
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 13 0.22
59 35 0.59
60 11 0.19
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (60 bp):
TATATACGTTTACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTC
Found at i:1826152 original size:47 final size:48
Alignment explanation
Indices: 1826054--1826184 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 48
1826044 ATGGCTATTC
* *
1826054 TTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAAC-AATATATATATATATGAACAAAGAATAAGT
**
1826104 TTCCAAGACATGTTTAAACAATATATATATATATGAACAAA-AA-AAGT
1 TTCCAAGACA-CATTAAACAATATATATATATATGAACAAAGAATAAGT
*
1826151 TTCCAAGACACATTAAATATATATATATATATAT
1 TTCCAAGACACATTAAACA-ATATATATATATAT
1826185 ATATATATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
46 6 0.08
47 27 0.38
48 2 0.03
49 27 0.38
50 10 0.14
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (48 bp):
TTCCAAGACACATTAAACAATATATATATATATGAACAAAGAATAAGT
Found at i:1826174 original size:2 final size:2
Alignment explanation
Indices: 1826167--1826229 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1826157 GACACATTAA
1826167 AT AT AT 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 AT AT AT
1826209 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1826230 CACGTTTAAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1826311 original size:232 final size:236
Alignment explanation
Indices: 1826006--1826439 Score: 763
Period size: 232 Copynumber: 1.8 Consensus size: 236
1825996 ATATACGTTT
1826006 CAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAA
1 CAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAA
*
1826071 ACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTTAAAC-A-ATATATATAT
66 ACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACA-GGTTAAACAATATATATATAT
1826134 ATATGAAC-AAAAAA-AG-TTTCCAAGACACATTAAATATATATATATATATATATATATATATA
130 ATATGAACAAAAAAACAGTTTTCCAAGACACATTAAATATATATATATATATATATATATATATA
1826196 TATATATATATATATATATATATATATATATATACACGTTTAA
195 -ATATATATATATATATATATATATATATATATACACGTTTAA
1826239 CAAATATCCAACTAAGCTATATGTTAAAC-AATAAATAATGGCTATTCTTCCTAAGACACATTAA
1 CAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAA
*
1826303 ACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGATAGGTTAAACAAATATATATATAT
66 ACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACAGGTTAAAC-AATATATATATAT
1826368 ATATGAACAAAAAAAATCAGTTTTCCAAGACACATTAAATATATATATATATATATATATATATA
130 ATATGAAC-AAAAAAA-CAGTTTTCCAAGACACATTAAATATATATATATATATATATATATATA
1826433 TAATATA
193 TAATATA
1826440 CGTTTAACAA
Statistics
Matches: 191, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
231 7 0.04
232 77 0.40
233 30 0.16
234 18 0.09
236 6 0.03
238 7 0.04
239 46 0.24
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (236 bp):
CAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAA
ACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACAGGTTAAACAATATATATATATA
TATGAACAAAAAAACAGTTTTCCAAGACACATTAAATATATATATATATATATATATATATATAA
TATATATATATATATATATATATATATATATACACGTTTAA
Found at i:1826413 original size:2 final size:2
Alignment explanation
Indices: 1826406--1826439 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1826396 GACACATTAA
1826406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1826440 CGTTTAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1826415 original size:54 final size:50
Alignment explanation
Indices: 1826286--1826628 Score: 191
Period size: 54 Copynumber: 6.7 Consensus size: 50
1826276 ATGGCTATTC
* *
1826286 TTCCTAAGACACATTAAACAA-ATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAACAATATATATATATATATGAACAAAAAATCAGT
* **
1826336 TTCCAAGATAGGTTAAACAAATATATATATATATATGAACAAAAAAAATCAGTT
1 TTCCAAGACACATTAAAC-AATATATATATATATATGAAC--AAAAAATCAG-T
* * *
1826390 TTCCAAGACACATTAAATATATATATATATATATAT-ATATATATAATAT-ACGT
1 TTCCAAGACACATTAAACA-ATATATATATATATATGA-ACA-A-AAAATCA-GT
* * * ** ** * * ** * * * *
1826443 TT--AACAAATATCCAACTAAGCTATATGT-TAAACAAATAAACAATGGTATT
1 TTCCAAGACACATTAAAC-AATATATATATATATATGAACAAAAAAT--CAGT
* * * * *
1826493 CTTCCTAAGACACGTTAAACAA-ATATATATGTATACGAACAAAGAATCAAT
1 -TTCC-AAGACACATTAAACAATATATATATATATATGAACAAAAAATCAGT
**
1826544 TTCCAAGACATGTT-AACAA-ATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAATATATATATATATATGAAC-AAAAAATCAGT
*
1826593 TTCCAAGACACATTAAATATATATATATATATATAT
1 TTCCAAGACACATTAAACA-ATATATATATATATAT
1826629 ATTATATATA
Statistics
Matches: 222, Mismatches: 47, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
48 24 0.11
49 42 0.19
50 20 0.09
51 39 0.18
52 22 0.10
53 30 0.14
54 45 0.20
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (50 bp):
TTCCAAGACACATTAAACAATATATATATATATATGAACAAAAAATCAGT
Found at i:1826581 original size:48 final size:49
Alignment explanation
Indices: 1826494--1826624 Score: 167
Period size: 48 Copynumber: 2.7 Consensus size: 49
1826484 AATGGTATTC
* * *
1826494 TTCCTAAGACACGTTAAACAAATATATATGTATACGAAC-AAAGAATCAAT
1 TTCC-AAGACACGTT-AACAAATATATATATATATGAACAAAAAAATCAAT
* *
1826544 TTCCAAGACATGTTAACAAATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACGTTAACAAATATATATATATATGAACAAAAAAATCAAT
* *
1826593 TTCCAAGACACATTAA-ATATATATATATATAT
1 TTCCAAGACACGTTAACAAATATATATATATAT
1826625 ATATATTATA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
48 36 0.50
49 32 0.44
50 4 0.06
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (49 bp):
TTCCAAGACACGTTAACAAATATATATATATATGAACAAAAAAATCAAT
Found at i:1826616 original size:2 final size:2
Alignment explanation
Indices: 1826609--1826650 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1826599 GACACATTAA
1826609 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1826650 A
1 A
1826651 CACGTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826637 original size:208 final size:213
Alignment explanation
Indices: 1826190--1826759 Score: 893
Period size: 208 Copynumber: 2.7 Consensus size: 213
1826180 TATATATATA
*
1826190 TATATATATATATATATATATATATATATATATATATATACACGTTTAACAAATATCCAACTAAG
1 TATATATATATATATATATATATATATATATATATATATATACGTTTAACAAATATCCAACTAAG
* *
1826255 CTATATGTTAAACAATAAATAATGGCTATTCTTCCTAAGACACATTAAACAAATATATATGTATA
66 CTATATGTTAAACAATAAACAATGGCTATTCTTCCTAAGACACGTTAAACAAATATATATGTATA
* *
1826320 TGAACAAAGAATCAGTTTCCAAGATAGGTTAAACAAATATATATATATATATGAACAAAAAAAAT
131 TGAACAAAGAATCAATTTCCAAGACAGGTTAAACAAATATATATATATATATGAACAAAAAAAAT
1826385 CAGTTTTCCAAGACACA-
196 CAGTTTTCCAAGACACAT
1826402 T-TA-A-ATATATATATATATATATATATATATATA-ATATACGTTTAACAAATATCCAACTAAG
1 TATATATATATATATATATATATATATATATATATATATATACGTTTAACAAATATCCAACTAAG
1826463 CTATATGTTAAACAAATAAACAATGG-TATTCTTCCTAAGACACGTTAAACAAATATATATGTAT
66 CTATATGTTAAAC-AATAAACAATGGCTATTCTTCCTAAGACACGTTAAACAAATATATATGTAT
* *
1826527 ACGAACAAAGAATCAATTTCCAAGACATGTT-AAC-AA-ATATATATATATATGAAC-AAAAAAA
130 ATGAACAAAGAATCAATTTCCAAGACAGGTTAAACAAATATATATATATATATGAACAAAAAAAA
1826588 TCAG-TTTCCAAGACACAT
195 TCAGTTTTCCAAGACACAT
1826606 TAAATATATATATATATATATATATTATATATATATATATATATACACGTTTAACAAATATCCAA
1 T--ATATATATATATATATATATA-TATATATATATATATATAT--ACGTTTAACAAATATCCAA
*
1826671 CTAAGCTATATGTTAAACAA-AAACAATGGTTATTCTTCCTAAGACACGTTTAAAC--A-ATATA
61 CTAAGCTATATGTTAAACAATAAACAATGGCTATTCTTCCTAAGACACG-TTAAACAAATATATA
1826732 TGTATATGAAC-AAGAATCAATTTCCAAG
125 TGTATATGAACAAAGAATCAATTTCCAAG
1826760 GTAAATGTAC
Statistics
Matches: 337, Mismatches: 8, Indels: 29
0.90 0.02 0.08
Matches are distributed among these distances:
203 13 0.04
204 12 0.04
205 18 0.05
206 2 0.01
207 5 0.01
208 105 0.31
209 72 0.21
210 30 0.09
211 16 0.05
212 21 0.06
213 43 0.13
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (213 bp):
TATATATATATATATATATATATATATATATATATATATATACGTTTAACAAATATCCAACTAAG
CTATATGTTAAACAATAAACAATGGCTATTCTTCCTAAGACACGTTAAACAAATATATATGTATA
TGAACAAAGAATCAATTTCCAAGACAGGTTAAACAAATATATATATATATATGAACAAAAAAAAT
CAGTTTTCCAAGACACAT
Found at i:1827894 original size:3 final size:3
Alignment explanation
Indices: 1827881--1827931 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
1827871 AAATATAAAC
*
1827881 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- TTA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1827926 ATA ATA
1 ATA ATA
1827932 TTTTTTAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.91
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1828651 original size:136 final size:135
Alignment explanation
Indices: 1828171--1828650 Score: 645
Period size: 136 Copynumber: 3.6 Consensus size: 135
1828161 ACTTGAAAGG
* * *
1828171 AACAAGTTCTTCTCATTATGAAC-T-TTCT-CCTT-TAGGACGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTCATTATGAACTCT
* *
1828232 TAATTGGAAATGTCAATCCC-CAAGTGAGGTGTCA-TGATTCG-AATACCGTGAATCGAGTGATA
66 TAATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATA
1828294 GGTCA
131 GGTCA
* * *
1828299 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTGTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTC-TCCCTTGTCGGATGAGTTCTTCTCATTATGAACTC
* * ** *
1828364 TCAATTGAAAAT-TTCAATCCCTCAAGTGAGGTGTCACTGATTTAAAATGCTGTGAATCGAGTGA
65 TTAATTGGAAATGTT-AATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGA
*
1828428 TAGGTCG
129 TAGGTCA
1828435 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TGTCGGATGAGTTCTTCTCATTATGAACTC
* * * * ***
1828500 TTCACTGGAAATGTTGATCCCTCAAGCGAGACATCACTGATTCGAAATGCCGTGAATCGAGTGAT
65 TTAATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGAT
1828565 AGGTCA
130 AGGTCA
* *
1828571 AAAAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TGTCGGATGAGTTCTTCTCATTATGAACTC
1828636 TCT-ATTGGAAATGTT
65 T-TAATTGGAAATGTT
1828651 GGTTCACCTC
Statistics
Matches: 306, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
128 22 0.07
129 1 0.00
130 3 0.01
131 1 0.00
132 4 0.01
133 40 0.13
134 14 0.05
135 9 0.03
136 209 0.68
137 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (135 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTCATTATGAACTCT
TAATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATA
GGTCA
Found at i:1829533 original size:8 final size:8
Alignment explanation
Indices: 1829522--1829600 Score: 55
Period size: 8 Copynumber: 10.5 Consensus size: 8
1829512 CCTTTTTCTC
1829522 TTTTCATT
1 TTTTCATT
1829530 TTTTCA--
1 TTTTCATT
*
1829536 -TTTCTTT
1 TTTTCATT
1829543 TTTTCA-T
1 TTTTCATT
1829550 TTTTCATT
1 TTTTCATT
1829558 TTTT--TT
1 TTTTCATT
*
1829564 CATTTCATT
1 -TTTTCATT
1829573 TTTTCATCT
1 TTTTCAT-T
1829582 TTTT-ATT
1 TTTTCATT
* *
1829589 TGTTCCTT
1 TTTTCATT
1829597 TTTT
1 TTTT
1829601 TTCTTCAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.07
6 2 0.04
7 14 0.25
8 28 0.51
9 7 0.13
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:1829539 original size:13 final size:13
Alignment explanation
Indices: 1829523--1829579 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 13
1829513 CTTTTTCTCT
1829523 TTTCATTTTTTCA
1 TTTCATTTTTTCA
*
1829536 TTTCTTTTTTTCA
1 TTTCATTTTTTCA
1829549 TTTTTCATTTTTTTTCA
1 --TTTCA--TTTTTTCA
1829566 TTTCATTTTTTCA
1 TTTCATTTTTTCA
1829579 T
1 T
1829580 CTTTTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 21 0.55
15 9 0.24
17 8 0.21
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:1829545 original size:20 final size:20
Alignment explanation
Indices: 1829516--1829568 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1829506 AACCCTCCTT
*
1829516 TTTCTCTTTTCATTTTTTCA
1 TTTCTTTTTTCATTTTTTCA
1829536 TTTCTTTTTTTCA-TTTTTCA
1 TTTC-TTTTTTCATTTTTTCA
1829556 -TT-TTTTTTCATTT
1 TTTCTTTTTTCATTT
1829569 CATTTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.27
18 2 0.07
19 2 0.07
20 11 0.37
21 7 0.23
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTCTTTTTTCATTTTTTCA
Found at i:1829562 original size:17 final size:15
Alignment explanation
Indices: 1829528--1829576 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1829518 TCTCTTTTCA
1829528 TTTTTTCATTTC--T
1 TTTTTTCATTTCATT
1829541 TTTTTTCATTTTTCATT
1 TTTTTTCA--TTTCATT
1829558 TTTTTTCATTTCATT
1 TTTTTTCATTTCATT
1829573 TTTT
1 TTTT
1829577 CATCTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.25
15 15 0.47
17 9 0.28
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCATTTCATT
Found at i:1829564 original size:30 final size:31
Alignment explanation
Indices: 1829514--1829589 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 31
1829504 CAAACCCTCC
*
1829514 TTTTTC-TCTTTTCA--TTTTTTCATTTCTT
1 TTTTTCATCTTTTCATTTTTTTTCATTTCAT
1829542 TTTTTCAT-TTTTCATTTTTTTTCATTTCAT
1 TTTTTCATCTTTTCATTTTTTTTCATTTCAT
*
1829572 TTTTTCATCTTTTTATTT
1 TTTTTCATCTTTTCATTT
1829590 GTTCCTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 12 0.29
29 1 0.02
30 21 0.50
31 8 0.19
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTTCATCTTTTCATTTTTTTTCATTTCAT
Found at i:1833393 original size:7 final size:7
Alignment explanation
Indices: 1833381--1833416 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
1833371 GAAATGACTG
1833381 TAAAGAA
1 TAAAGAA
1833388 TAAAGAA
1 TAAAGAA
1833395 TAAAGAA
1 TAAAGAA
1833402 TAAAGAA
1 TAAAGAA
1833409 TAAAGAA
1 TAAAGAA
1833416 T
1 T
1833417 GAAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (7 bp):
TAAAGAA
Found at i:1841438 original size:22 final size:23
Alignment explanation
Indices: 1841412--1841455 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1841402 AATGGAACAT
1841412 TATACTTATTAAA-AATGATAAC
1 TATACTTATTAAATAATGATAAC
1841434 TATACTTATTAAATAATGATAA
1 TATACTTATTAAATAATGATAA
1841456 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (23 bp):
TATACTTATTAAATAATGATAAC
Found at i:1841724 original size:53 final size:54
Alignment explanation
Indices: 1841629--1841742 Score: 212
Period size: 53 Copynumber: 2.1 Consensus size: 54
1841619 TGTTAAACAA
*
1841629 ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAT
1 ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
1841683 ATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
1 ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
1841736 ATATATA
1 ATATATA
1841743 CGTTTAACAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
53 41 0.69
54 18 0.31
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (54 bp):
ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
Found at i:1841857 original size:40 final size:44
Alignment explanation
Indices: 1841808--1841891 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
1841798 TAAGACACAT
* *
1841808 TAAAC-AA-ATATATGTAT-AACAAAGAATCA-TTTCCAAGACA
1 TAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACA
1841848 TAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACA
1 TAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACA
1841892 CATTAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 5 0.13
41 2 0.05
42 9 0.24
43 11 0.29
44 11 0.29
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (44 bp):
TAAACAAATATATATATATGAACAAAAAATCAGTTTCCAAGACA
Found at i:1841908 original size:2 final size:2
Alignment explanation
Indices: 1841897--1841952 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1841887 AGACACATTA
1841897 AT AT -T 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 AT AT AT
1841938 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1841953 CGTTTAACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1842084 original size:54 final size:55
Alignment explanation
Indices: 1842025--1842144 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 55
1842015 ACATTAAACA
* * **
1842025 ATATATGTATATGAAC-AAAGAATCAG-TTCCAAGATAGGTTAAACAAATATATAT
1 ATATAT-TATATGAACAAAAAAATCAGTTTCCAAGACACATTAAACAAATATATAT
* *
1842079 ATATA-TATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATATATATATAT
1 ATATATTATATGAACAAAAAAATCAGTTTCCAAGACACATTAAACAAATATATAT
1842133 ATATATATATAT
1 ATATAT-TATAT
1842145 ATACACGTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
52 9 0.16
53 9 0.16
54 33 0.59
56 5 0.09
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (55 bp):
ATATATTATATGAACAAAAAAATCAGTTTCCAAGACACATTAAACAAATATATAT
Found at i:1842128 original size:2 final size:2
Alignment explanation
Indices: 1842121--1842147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1842111 GACACATTAA
1842121 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1842148 CACGTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1842283 original size:46 final size:46
Alignment explanation
Indices: 1842202--1842326 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
1842192 ATGGTTATTC
* * * *
1842202 TTCCTAAGA-ACGTTAAACAAAATATATGTATATGAACAAGAATCAAT
1 TTCC-AAGACACGTTAAA-AATATATATATATATGAAAAAAAATCAAT
* *
1842249 TTCCAAGACATGTTAAAAATATATATATATATGAAAAAAAATCAGT
1 TTCCAAGACACGTTAAAAATATATATATATATGAAAAAAAATCAAT
* * *
1842295 TTCCAAGACACATTATATATATATATATATAT
1 TTCCAAGACACGTTAAAAATATATATATATAT
1842327 ATATATATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 56 0.84
47 11 0.16
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (46 bp):
TTCCAAGACACGTTAAAAATATATATATATATGAAAAAAAATCAAT
Found at i:1842315 original size:2 final size:2
Alignment explanation
Indices: 1842308--1842368 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1842298 CAAGACACAT
1842308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1842349 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1842369 CGTTTAACAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1843603 original size:3 final size:3
Alignment explanation
Indices: 1843595--1843652 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
1843585 AAATATAAAC
1843595 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1843643 ATTA ATA ATA
1 A-TA ATA ATA
1843653 TTTTTTAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1843813 original size:2 final size:2
Alignment explanation
Indices: 1843806--1843837 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1843796 ATATTAAATC
1843806 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
1843838 TGATGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1847104 original size:60 final size:60
Alignment explanation
Indices: 1847038--1847174 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
1847028 ATAGTCTGGC
* * * *
1847038 GACCATTTTATAAGTTTTAATAGTCGAATGACTCAACAAAGCATCACCCTATAGTCGAA-T
1 GACCATTTTATAACTTTTAATAGTCGAAGGACTCAACAAAACATCACCCTATAGTC-AAGG
* * *
1847098 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAACATCACCCTATAGTCAAGG
1 GACCATTTTATAACTTTTAATAGTCGAAGGACTCAACAAAACATCACCCTATAGTCAAGG
1847158 GACCATTTGTAT-ACTTT
1 GACCATTT-TATAACTTT
1847175 ACCAAAATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 63 0.94
61 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCGAAGGACTCAACAAAACATCACCCTATAGTCAAGG
Found at i:1851051 original size:13 final size:13
Alignment explanation
Indices: 1851033--1851058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1851023 ACATATTTGA
1851033 ACAGTCTTCATAT
1 ACAGTCTTCATAT
1851046 ACAGTCTTCATAT
1 ACAGTCTTCATAT
1851059 GCGCGTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:1860203 original size:2 final size:2
Alignment explanation
Indices: 1860196--1860229 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1860186 ACTACAAAAT
1860196 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1860230 AAACAAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1861230 original size:27 final size:27
Alignment explanation
Indices: 1861192--1861264 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
1861182 TGATGGTCAC
1861192 TGGATCATTGGTTTCAATAAGACTTGT
1 TGGATCATTGGTTTCAATAAGACTTGT
1861219 TGGATCATTGGTTTCAATAAGACTTGT
1 TGGATCATTGGTTTCAATAAGACTTGT
*
1861246 TGGATCATTGGGTTCAATA
1 TGGATCATTGGTTTCAATA
1861265 TCTTTTAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (27 bp):
TGGATCATTGGTTTCAATAAGACTTGT
Found at i:1861376 original size:2 final size:2
Alignment explanation
Indices: 1861333--1861359 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1861323 TCTTTATGAC
1861333 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1861360 CTATGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1869170 original size:2 final size:2
Alignment explanation
Indices: 1869158--1869192 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1869148 ATAAGTGAAC
*
1869158 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1869193 GTATGTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1874637 original size:15 final size:16
Alignment explanation
Indices: 1874619--1874653 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1874609 AAAATAATTA
1874619 AAAATTT-TAATTTTC
1 AAAATTTCTAATTTTC
*
1874634 AAAATTTCTAATTTTT
1 AAAATTTCTAATTTTC
1874650 AAAA
1 AAAA
1874654 ATCTTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTCTAATTTTC
Found at i:1886689 original size:41 final size:41
Alignment explanation
Indices: 1886636--1886797 Score: 132
Period size: 41 Copynumber: 3.9 Consensus size: 41
1886626 AATGTCGATG
* *
1886636 AAACCTAGTACTTTATTGGCGTTTTCCAATAAACGCCGCTA
1 AAACGTAGTACTTTAGTGGCGTTTTCCAATAAACGCCGCTA
* * * **
1886677 AAACGTAATACTTTAATGGCGTTTTAAGCAA-AAACGCTACTA
1 AAACGTAGTACTTTAGTGGCGTTTT--CCAATAAACGCCGCTA
* * * * *
1886719 AATAC-TCGTATTTTAGTGGCGTTTCCCAACAAACGCTGCTA
1 AA-ACGTAGTACTTTAGTGGCGTTTTCCAATAAACGCCGCTA
* * *
1886760 AAACGTAGTATTTTAGCGGCGTGTTT-GAATAAACGCCG
1 AAACGTAGTACTTTAGTGGCGT-TTTCCAATAAACGCCG
1886798 TAATTTATTA
Statistics
Matches: 96, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
40 5 0.05
41 58 0.60
42 28 0.29
43 5 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
AAACGTAGTACTTTAGTGGCGTTTTCCAATAAACGCCGCTA
Found at i:1888520 original size:33 final size:33
Alignment explanation
Indices: 1888476--1888540 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1888466 CACTGTTGGT
* *
1888476 GCTTTACATGGATGTGTATACCTGTTGGTGCTC
1 GCTTTACATGGATCTCTATACCTGTTGGTGCTC
* *
1888509 GCTTTATATGGATCTCTGTACCTGTTGGTGCT
1 GCTTTACATGGATCTCTATACCTGTTGGTGCT
1888541 TAGTCTTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (33 bp):
GCTTTACATGGATCTCTATACCTGTTGGTGCTC
Found at i:1891237 original size:21 final size:21
Alignment explanation
Indices: 1891213--1891267 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1891203 GATTTATTAA
**
1891213 TATGGATTTCATTTTTCTTGT
1 TATGGATTTCAAGTTTCTTGT
* *
1891234 TATGGATTTTAAGTTTGTTGT
1 TATGGATTTCAAGTTTCTTGT
*
1891255 TATGGATGTCAAG
1 TATGGATTTCAAG
1891268 CTAATTGGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (21 bp):
TATGGATTTCAAGTTTCTTGT
Found at i:1891467 original size:43 final size:43
Alignment explanation
Indices: 1891383--1891478 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 43
1891373 AGGTAATTAG
* * *
1891383 CGGCGTTTGTATCTTAAAACGCCGCTATAGATATGACCTTTTG
1 CGGCGTTTGTATCTAAAAACGCCGCTATAGACATGACCTTTTA
* * *
1891426 TGGCGTTTGT-TCTAAAAAACGCCGCTATATACCA-GATCTTTTA
1 CGGCGTTTGTATCT-AAAAACGCCGCTATAGA-CATGACCTTTTA
1891469 CGGCGTTTGT
1 CGGCGTTTGT
1891479 GGGAAAAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 3 0.07
43 40 0.91
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
CGGCGTTTGTATCTAAAAACGCCGCTATAGACATGACCTTTTA
Found at i:1891594 original size:43 final size:43
Alignment explanation
Indices: 1891469--1891605 Score: 202
Period size: 43 Copynumber: 3.2 Consensus size: 43
1891459 AGATCTTTTA
1891469 CGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTG
1 CGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTG
*
1891512 CGGCGTTTGTGGGAAAAACTCCGCTAAATCTCAACACCTATTG
1 CGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTG
* * * * ***
1891555 CGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTG
1 CGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTG
1891598 CGGCGTTT
1 CGGCGTTT
1891606 TTTGTTACCA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (43 bp):
CGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTG
Found at i:1893415 original size:16 final size:15
Alignment explanation
Indices: 1893367--1893417 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
1893357 GATTTAAATA
*
1893367 ATTTTAAAATA-TTT
1 ATTTTAAATTATTTT
1893381 ATTTT-AATTATTTT
1 ATTTTAAATTATTTT
1893395 AATTTTAAATTGATTTT
1 -ATTTTAAATT-ATTTT
1893412 ATTTTA
1 ATTTTA
1893418 GAACTGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 5 0.16
16 10 0.31
17 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTTAAATTATTTT
Found at i:1894210 original size:27 final size:28
Alignment explanation
Indices: 1894149--1894211 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
1894139 CCTAAAACCG
1894149 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
1894177 ACCCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
1894204 ACCCGACC
1 ACCCGACC
1894212 TGAACAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 13 0.37
28 22 0.63
ACGTcount: A:0.43, C:0.37, G:0.08, T:0.13
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:1896614 original size:30 final size:29
Alignment explanation
Indices: 1896579--1896636 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1896569 ATTAACGACA
*
1896579 GGTGGTTTGATTGAATT-AATTAAATAGTTT
1 GGTGGTCTGATTG-ATTCAATTAAA-AGTTT
1896609 GGTGGTCTGATTGATTCAATTAAAAGTT
1 GGTGGTCTGATTGATTCAATTAAAAGTT
1896637 CGATGGTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGGTCTGATTGATTCAATTAAAAGTTT
Found at i:1898856 original size:2 final size:2
Alignment explanation
Indices: 1898840--1898880 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1898830 AGTTGCCTGG
* *
1898840 TC TC TC CC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1898881 GTATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:1908220 original size:21 final size:21
Alignment explanation
Indices: 1908168--1908220 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
1908158 GTTTTTATGA
* * *
1908168 TACATTTTTTTTTATCTTTAT
1 TACATGTTTTTTTACCTTCAT
* *
1908189 GACACGCTTTTTTTACCTTCAT
1 TACATG-TTTTTTTACCTTCAT
1908211 TACATGTTTT
1 TACATGTTTT
1908221 CGATTGTTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.58
Consensus pattern (21 bp):
TACATGTTTTTTTACCTTCAT
Found at i:1913323 original size:25 final size:25
Alignment explanation
Indices: 1913295--1913343 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1913285 ATATATCAGT
1913295 TTTAATTTGACTGGACTCGAATTAC
1 TTTAATTTGACTGGACTCGAATTAC
*
1913320 TTTAATTTGACTTGACTCGAATTA
1 TTTAATTTGACTGGACTCGAATTA
1913344 TTTTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (25 bp):
TTTAATTTGACTGGACTCGAATTAC
Done.