Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 24
Found at i:1833802 original size:54 final size:54
Alignment explanation
Indices: 1833720--1834183 Score: 700
Period size: 54 Copynumber: 8.6 Consensus size: 54
1833710 GTACTCTACT
* *
1833720 CACTAAGTGTGCAACCCAAGGAATTCATCATATGTTGATGAACGACCGTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
**
1833774 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACTATATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
* **
1833828 TACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAACGACCGTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
1833882 CACTAAGTGTGCAACCCAC-AGAATTCATCATATGTTGATGAACGACCGTATAGG
1 CACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCGTATAGG
* * *
1833936 CACTAAGTGTGCAACCCACGAAATTCATCTTATGTTGATAAACGACCTTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
* * * *
1833990 CACTAACTGTGCAACTCATGGAATTCATCATATGTTGATGAACGACCGTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
* *
1834044 CACTAAGTGTGCAACCCACAAAATTCATCATATGTTAATGAACGACCGTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
** *
1834098 CACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAACAACCGTATAGG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
* *
1834152 CACTATGTGTACTAA-CCACGAAATTCAT-ATAT
1 CACTAAGTGTGC-AACCCACGAAATTCATCATAT
1834184 TTATGATAAG
Statistics
Matches: 373, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.01
54 365 0.98
55 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
Found at i:1849867 original size:12 final size:12
Alignment explanation
Indices: 1849850--1849874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1849840 AAGTTATCTA
1849850 TTTTCTTCTTCT
1 TTTTCTTCTTCT
1849862 TTTTCTTCTTCT
1 TTTTCTTCTTCT
1849874 T
1 T
1849875 CCCCGTGTAG
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:1850138 original size:24 final size:24
Alignment explanation
Indices: 1850106--1850157 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1850096 TGATGAACGA
1850106 CCATATAAGCACTAAGTGTGCAAC
1 CCATATAAGCACTAAGTGTGCAAC
1850130 CCATATAAGCACTAAGTGTGCAAC
1 CCATATAAGCACTAAGTGTGCAAC
1850154 CCAT
1 CCAT
1850158 GAAATTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (24 bp):
CCATATAAGCACTAAGTGTGCAAC
Found at i:1850198 original size:78 final size:78
Alignment explanation
Indices: 1850068--1850215 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 78
1850058 ATGTGTCAAT
* *
1850068 TGTGCAACCCATGGAATTCATCATATGTTGATGAACGACCATATAAGCACTAAGTGTGCAACCCA
1 TGTGCAACCCATGAAATTCATCATATGTTGATGAACGACCATATAAGAACTAAGTGTGCAACCCA
1850133 TATAAGCACTAAG
66 TATAAGCACTAAG
** *
1850146 TGTGCAACCCATGAAATTCATCATATGTTGATGAACGACTGTATATGAACTAAGTGTGCAACCCA
1 TGTGCAACCCATGAAATTCATCATATGTTGATGAACGACCATATAAGAACTAAGTGTGCAACCCA
1850211 TATAA
66 TATAA
1850216 TTCATCATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (78 bp):
TGTGCAACCCATGAAATTCATCATATGTTGATGAACGACCATATAAGAACTAAGTGTGCAACCCA
TATAAGCACTAAG
Found at i:1850204 original size:54 final size:54
Alignment explanation
Indices: 1850133--1850475 Score: 426
Period size: 54 Copynumber: 6.4 Consensus size: 54
1850123 GTGCAACCCA
* * *
1850133 TATAAGCACTAAGTGTGCAACCCATGA-AATTCATCATATGTTGATGAACGACTG
1 TATAGGCACTAAGTGTGCAACCCA-CATAATTCATCATATGTTGATGAACGACCG
* * *
1850187 TATATGAACTAAGTGTGCAACCCATATAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCG
*
1850241 TATAGGCACTAAGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACGACCG
* * * * *
1850295 TATAGGCACTAAGTATGGAACCCACAGAATTTATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCG
* **
1850349 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACAA
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCG
* * * *
1850403 TATAGGCACTATA-TGTGCTAA-CCACGA-AATTCATGATATATTTATGAATGACCG
1 TATAGGCACTA-AGTGTGC-AACCCAC-ATAATTCATCATATGTTGATGAACGACCG
*
1850457 TATAGGCACTATGTGTGCA
1 TATAGGCACTAAGTGTGCA
1850476 TCTCAACGAA
Statistics
Matches: 253, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
53 3 0.01
54 245 0.97
55 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCG
Found at i:1850409 original size:162 final size:162
Alignment explanation
Indices: 1850133--1850467 Score: 469
Period size: 162 Copynumber: 2.1 Consensus size: 162
1850123 GTGCAACCCA
* * * * *
1850133 TATAAGCACTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAACGACTGTATATGAACTA
1 TATAGGCACTAAGTATGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTATAGGAACTA
* * **
1850198 AGTGTGCAACCCATATAATTCATCATATGTTGATGAACGACCGTATAGGCACTA-AGTGTGC-AA
66 AGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACAATATAGGCACTATA-TGTGCTAA
*
1850261 CTCACGAAATTCATCATATGTTGATGAACGACCG
130 C-CACGAAATTCATCATATATTGATGAACGACCG
* * * *
1850295 TATAGGCACTAAGTATGGAACCCACAG-AATTTATCATATGTTGATGAATGACCGTATAGGCACT
1 TATAGGCACTAAGTATGCAACCCA-AGAAATTCATCATATGTTGATGAACGACCGTATAGGAACT
1850359 AAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACAATATAGGCACTATATGTGCTAA
65 AAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACAATATAGGCACTATATGTGCTAA
* * *
1850424 CCACGAAATTCATGATATATTTATGAATGACCG
130 CCACGAAATTCATCATATATTGATGAACGACCG
1850457 TATAGGCACTA
1 TATAGGCACTA
1850468 TGTGTGCATC
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
162 148 0.97
163 5 0.03
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (162 bp):
TATAGGCACTAAGTATGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTATAGGAACTA
AGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACAATATAGGCACTATATGTGCTAAC
CACGAAATTCATCATATATTGATGAACGACCG
Found at i:1853195 original size:23 final size:22
Alignment explanation
Indices: 1853167--1853211 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
1853157 ATCTTAATAC
1853167 AATATAAACATAATTTATTATTT
1 AATATAAACATAATTT-TTATTT
*
1853190 AATATAAATATAATTTTTATTT
1 AATATAAACATAATTTTTATTT
1853212 CTCAGCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATAAACATAATTTTTATTT
Found at i:1854201 original size:15 final size:15
Alignment explanation
Indices: 1854181--1854213 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1854171 CCAGATTTGT
1854181 CACTTGGAGGATCAA
1 CACTTGGAGGATCAA
*
1854196 CACTTGGAGGATCGA
1 CACTTGGAGGATCAA
1854211 CAC
1 CAC
1854214 ATCACTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (15 bp):
CACTTGGAGGATCAA
Found at i:1854818 original size:19 final size:19
Alignment explanation
Indices: 1854789--1854839 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1854779 AAATTTTAAG
* *
1854789 AATTTTAAAAAAATATGACA
1 AATTTT-AAAAAACATGAAA
*
1854809 AATTTTAAAAAACATTAAA
1 AATTTTAAAAAACATGAAA
1854828 AATTATTAAAAA
1 AATT-TTAAAAA
1854840 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AATTTTAAAAAACATGAAA
Found at i:1854844 original size:17 final size:18
Alignment explanation
Indices: 1854817--1854863 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
1854807 CAAATTTTAA
*
1854817 AAAACATTAAAAATT-ATT
1 AAAA-ATTAAAAATTAAGT
1854835 AAAAATT-AAAATTAAGT
1 AAAAATTAAAAATTAAGT
1854852 AAAAATATAAAA
1 AAAAAT-TAAAA
1854864 CTAAAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 5 0.20
19 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATTAAAAATTAAGT
Found at i:1855272 original size:20 final size:20
Alignment explanation
Indices: 1855234--1855277 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1855224 GTGTTCGAAA
*
1855234 ATTTTAATATTTTTATAAAT
1 ATTTTAATATTTCTATAAAT
1855254 ATTTTAATAATTTCT-TAAAT
1 ATTTTAAT-ATTTCTATAAAT
1855274 -TTTT
1 ATTTT
1855278 GTTTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTAATATTTCTATAAAT
Found at i:1857906 original size:21 final size:20
Alignment explanation
Indices: 1857878--1857917 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1857868 CTTCAAATTC
1857878 AAGCTTCCAACAACACATTA
1 AAGCTTCCAACAACACATTA
*
1857898 AAGCATTCCAACAATACATT
1 AAGC-TTCCAACAACACATT
1857918 TAACAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (20 bp):
AAGCTTCCAACAACACATTA
Found at i:1859655 original size:157 final size:157
Alignment explanation
Indices: 1859369--1859682 Score: 610
Period size: 157 Copynumber: 2.0 Consensus size: 157
1859359 AATTGGACCC
1859369 AAAAATAGAATTTTATGAAATTAATAAAGTAGATGGACTAAATAGGTGATTAACCCACTTTATAA
1 AAAAATAGAATTTTATGAAATTAATAAAGTAGATGGACTAAATAGGTGATTAACCCACTTTATAA
*
1859434 TTTTGAATTTTATTTGATGGAAATTTTAGTGAAGTCACTATTAGCCTTATGGGAGAAAAAGCTTA
66 TTTTGAATTTTATTTGAAGGAAATTTTAGTGAAGTCACTATTAGCCTTATGGGAGAAAAAGCTTA
1859499 ACCTTCACCAACATATTCCTCCTTTTT
131 ACCTTCACCAACATATTCCTCCTTTTT
*
1859526 AAAAATAGAATTTTATGAAATTAATAAAGTAGATGGACTAAATAGGTGATTAACCCACTTTATGA
1 AAAAATAGAATTTTATGAAATTAATAAAGTAGATGGACTAAATAGGTGATTAACCCACTTTATAA
1859591 TTTTGAATTTTATTTGAAGGAAATTTTAGTGAAGTCACTATTAGCCTTATGGGAGAAAAAGCTTA
66 TTTTGAATTTTATTTGAAGGAAATTTTAGTGAAGTCACTATTAGCCTTATGGGAGAAAAAGCTTA
1859656 ACCTTCACCAACATATTCCTCCTTTTT
131 ACCTTCACCAACATATTCCTCCTTTTT
1859683 TATATAACAC
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (157 bp):
AAAAATAGAATTTTATGAAATTAATAAAGTAGATGGACTAAATAGGTGATTAACCCACTTTATAA
TTTTGAATTTTATTTGAAGGAAATTTTAGTGAAGTCACTATTAGCCTTATGGGAGAAAAAGCTTA
ACCTTCACCAACATATTCCTCCTTTTT
Found at i:1860154 original size:252 final size:250
Alignment explanation
Indices: 1859685--1860156 Score: 721
Period size: 250 Copynumber: 1.9 Consensus size: 250
1859675 TCCTTTTTTA
* * *
1859685 TATAACACCCTTCTTCTCTATCTTTTCCCTTTTAATTTTAAAGTTTCATTTTAATAATTTCAAGA
1 TATAACACCCTTCTTCTCTATCTTGTCCCTTTTAATTTTAAAGCTTCATATTAATAATTTCAAGA
* *
1859750 AAAACTCTCATCTTCCTCAAGGCAAGAAGCATTACAAGAATCTCACGGCTTCAAATGATATGCAT
66 AAAAATCTCATCTTCCTCAAGGCAAGAAGCATTACAAGAATCTCACGGCTTCAAATGATATACAT
* *
1859815 AGTGATCATTTTGATTTAGGGAGATTTTGATAGGGTTTAGACTTAGAAATCAAATCAAATAGTAT
131 AGTGATCATTTTGATTTAGGGAGATTTTGAGAGGGTTTAGACTTAGAAATCAAATCAAATAATAT
1859880 TTAGGGTACATTCATGTTATTAAATTCTTTTTTAGCTTTTATTTGATTATCTATC
196 TTAGGGTACATTCATGTTATTAAATTCTTTTTTAGCTTTTATTTGATTATCTATC
* * * *
1859935 TATAACACCCTTTTTCTCTCTCTTGTCCTTTTTGATTTTAAAGCTTCATATTAATAATTTCAAGA
1 TATAACACCCTTCTTCTCTATCTTGTCCCTTTTAATTTTAAAGCTTCATATTAATAATTTCAAGA
* * * *
1860000 AAAAATCTCATCTTCCTCAAGGTAAGAATCATTATAAGAATCTCATGGGCTTCAAAATGATATAC
66 AAAAATCTCATCTTCCTCAAGGCAAGAAGCATTACAAGAATCTCA-CGGCTTC-AAATGATATAC
* * * * *
1860065 ATATTG-TCTATTTTTATTTAGGGGGATTTTGAGAGGGTTTAGACTTAGAAGTCAAATTAAATAA
129 ATAGTGATC-ATTTTGATTTAGGGAGATTTTGAGAGGGTTTAGACTTAGAAATCAAATCAAATAA
*
1860129 TATTTAGGGTTCATTCATGTTATTAAAT
193 TATTTAGGGTACATTCATGTTATTAAAT
1860157 ATTCTTTAGA
Statistics
Matches: 198, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
250 99 0.50
251 8 0.04
252 91 0.46
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (250 bp):
TATAACACCCTTCTTCTCTATCTTGTCCCTTTTAATTTTAAAGCTTCATATTAATAATTTCAAGA
AAAAATCTCATCTTCCTCAAGGCAAGAAGCATTACAAGAATCTCACGGCTTCAAATGATATACAT
AGTGATCATTTTGATTTAGGGAGATTTTGAGAGGGTTTAGACTTAGAAATCAAATCAAATAATAT
TTAGGGTACATTCATGTTATTAAATTCTTTTTTAGCTTTTATTTGATTATCTATC
Found at i:1860994 original size:24 final size:24
Alignment explanation
Indices: 1860967--1861021 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1860957 TTATCTCATA
1860967 CTCTCCACTCTTTCATCTTCTTTC
1 CTCTCCACTCTTTCATCTTCTTTC
*
1860991 CTCTTCACTCTTTCATCTTCTTTC
1 CTCTCCACTCTTTCATCTTCTTTC
1861015 CTCTCCA
1 CTCTCCA
1861022 AGAACTAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.09, C:0.42, G:0.00, T:0.49
Consensus pattern (24 bp):
CTCTCCACTCTTTCATCTTCTTTC
Found at i:1865601 original size:2 final size:2
Alignment explanation
Indices: 1865594--1865625 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1865584 GGTGGCTAAT
1865594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1865626 TTCAACCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1867302 original size:18 final size:20
Alignment explanation
Indices: 1867238--1867306 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1867228 CACATGCCGA
1867238 TATCGATACTCTAGGCTGAG
1 TATCGATACTCTAGGCTGAG
* *
1867258 TATCGATACTCTGGTGCTGGGG
1 TATCGATACTCTAG-GCT-GAG
*
1867280 TATCGATACT-T-GCCTGAG
1 TATCGATACTCTAGGCTGAG
1867298 TATCGATAC
1 TATCGATAC
1867307 CAAAATTAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
18 11 0.26
19 2 0.05
20 14 0.33
21 4 0.09
22 12 0.28
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGATACTCTAGGCTGAG
Found at i:1870234 original size:20 final size:21
Alignment explanation
Indices: 1870200--1870253 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1870190 CGAAAAAGGA
*
1870200 TAAATTA-TATGTTTAGTTA-C
1 TAAATTATTAT-TTTAATTACC
1870220 TAAATTATTATTTTAATTACC
1 TAAATTATTATTTTAATTACC
1870241 T-AATTATTATTTT
1 TAAATTATTATTTT
1870254 TTCAAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
TAAATTATTATTTTAATTACC
Found at i:1870293 original size:14 final size:14
Alignment explanation
Indices: 1870274--1870300 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1870264 TCCTAACTAT
1870274 TGGAATATGCATTC
1 TGGAATATGCATTC
1870288 TGGAATATGCATT
1 TGGAATATGCATT
1870301 GTTAACGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (14 bp):
TGGAATATGCATTC
Found at i:1872588 original size:24 final size:24
Alignment explanation
Indices: 1872556--1872601 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1872546 GCTTGCACAA
*
1872556 GCTTATATGCCAATCAAGTTCTGG
1 GCTTATATGCAAATCAAGTTCTGG
1872580 GCTTATATGCAAATCAAGTTCT
1 GCTTATATGCAAATCAAGTTCT
1872602 AAACTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (24 bp):
GCTTATATGCAAATCAAGTTCTGG
Found at i:1872608 original size:24 final size:24
Alignment explanation
Indices: 1872557--1872609 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1872547 CTTGCACAAG
* ***
1872557 CTTATATGCCAATCAAGTTCTGGG
1 CTTATATGCAAATCAAGTTCTAAA
1872581 CTTATATGCAAATCAAGTTCTAAA
1 CTTATATGCAAATCAAGTTCTAAA
1872605 CTTAT
1 CTTAT
1872610 GTTGTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (24 bp):
CTTATATGCAAATCAAGTTCTAAA
Found at i:1874902 original size:20 final size:20
Alignment explanation
Indices: 1874877--1874936 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
1874867 TATTGGAATA
*
1874877 TGCATTCTAGAATATGCATT
1 TGCATTCTGGAATATGCATT
1874897 TGCATTCTGGAATATGCATT
1 TGCATTCTGGAATATGCATT
1874917 TGCATTCTGGAATATGCATT
1 TGCATTCTGGAATATGCATT
1874937 GTTAATGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (20 bp):
TGCATTCTGGAATATGCATT
Found at i:1874954 original size:19 final size:19
Alignment explanation
Indices: 1874930--1875007 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
1874920 ATTCTGGAAT
1874930 ATGCATTGTTAATGTGTGC
1 ATGCATTGTTAATGTGTGC
* ***
1874949 ATGCATTGCATT-CTG-GAAT
1 ATGCATTG--TTAATGTGTGC
* *
1874968 ATGTATTGTTAACGTGTGC
1 ATGCATTGTTAATGTGTGC
*
1874987 ATGCATTGCTAATGTGTGC
1 ATGCATTGTTAATGTGTGC
1875006 AT
1 AT
1875008 TGAGTAAGCT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
17 2 0.05
18 1 0.02
19 35 0.83
20 2 0.05
21 2 0.05
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (19 bp):
ATGCATTGTTAATGTGTGC
Found at i:1874964 original size:38 final size:38
Alignment explanation
Indices: 1874910--1874995 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 38
1874900 ATTCTGGAAT
*
1874910 ATGCATTTGCATTCTGGAATATGCATTGTTAATGTGTGC
1 ATGCA-TTGCATTCTGGAATATGCATTGTTAACGTGTGC
*
1874949 ATGCATTGCATTCTGGAATATGTATTGTTAACGTGTGC
1 ATGCATTGCATTCTGGAATATGCATTGTTAACGTGTGC
1874987 ATGCATTGC
1 ATGCATTGC
1874996 TAATGTGTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 40 0.89
39 5 0.11
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (38 bp):
ATGCATTGCATTCTGGAATATGCATTGTTAACGTGTGC
Found at i:1883984 original size:24 final size:24
Alignment explanation
Indices: 1883948--1883997 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1883938 TGTACTTTAT
1883948 CTTAAAAAACAACAGAGAACTAAA
1 CTTAAAAAACAACAGAGAACTAAA
*
1883972 CTTAAAAATCAACAGAGAACTAAA
1 CTTAAAAAACAACAGAGAACTAAA
1883996 CT
1 CT
1883998 AGTGTCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.16
Consensus pattern (24 bp):
CTTAAAAAACAACAGAGAACTAAA
Found at i:1884397 original size:58 final size:59
Alignment explanation
Indices: 1884279--1884399 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 59
1884269 TAGGATCCTT
* * * * *
1884279 ATTTTTTTTAATTTTATAAAATGGTATCCATTTTTTATCTTTACAATTGAGGACCACTA
1 ATTTATTTTAATTTTATAAAATAGTACCCACTTTCTATCTTTACAATTGAGGACCACTA
* * * *
1884338 ATTTATTTTAATTTTATAAAATAG-ACCCACTTTCTATCTTTATAATTGGGGGCCTCTA
1 ATTTATTTTAATTTTATAAAATAGTACCCACTTTCTATCTTTACAATTGAGGACCACTA
1884396 ATTT
1 ATTT
1884400 GTTTAGTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
58 31 0.58
59 22 0.42
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (59 bp):
ATTTATTTTAATTTTATAAAATAGTACCCACTTTCTATCTTTACAATTGAGGACCACTA
Found at i:1885748 original size:2 final size:2
Alignment explanation
Indices: 1885741--1885765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1885731 TCATTATTAC
1885741 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 T
1885766 TAGTATTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1900447 original size:23 final size:22
Alignment explanation
Indices: 1900412--1900461 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
1900402 GTTAAGCATA
*
1900412 ATTTGTTTATGTTGAATATTTG
1 ATTTCTTTATGTTGAATATTTG
1900434 AGTTTCTTTATGTTGAATATTTG
1 A-TTTCTTTATGTTGAATATTTG
1900457 ATTTC
1 ATTTC
1900462 CCTATTACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (22 bp):
ATTTCTTTATGTTGAATATTTG
Found at i:1903183 original size:24 final size:24
Alignment explanation
Indices: 1903155--1903204 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1903145 TTCGAGATAT
*
1903155 TTCTACGTGGTCCTTAGGGACAAA
1 TTCTACGCGGTCCTTAGGGACAAA
* *
1903179 TTCTACGCGGTTCTTTGGGACAAA
1 TTCTACGCGGTCCTTAGGGACAAA
1903203 TT
1 TT
1903205 TTACATGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (24 bp):
TTCTACGCGGTCCTTAGGGACAAA
Found at i:1905910 original size:45 final size:45
Alignment explanation
Indices: 1905846--1905941 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
1905836 AATGGCTCTA
*
1905846 AAAGAACTAAAGGAGTTAAAAGTTCACTTACAAGAGCTTTTGAAC
1 AAAGAACTAAAGGAGTTAAAAGTTCACTTACAAGAGCGTTTGAAC
*
1905891 AAAGAACTAAAGGAGTTAAAAGTTCAGTTACAAGAGCGTTTGAAC
1 AAAGAACTAAAGGAGTTAAAAGTTCACTTACAAGAGCGTTTGAAC
1905936 AAAGAA
1 AAAGAA
1905942 GTATTTCCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (45 bp):
AAAGAACTAAAGGAGTTAAAAGTTCACTTACAAGAGCGTTTGAAC
Found at i:1908273 original size:12 final size:12
Alignment explanation
Indices: 1908256--1908335 Score: 54
Period size: 12 Copynumber: 6.1 Consensus size: 12
1908246 TATTAATCCT
1908256 AATAAAAAAATA
1 AATAAAAAAATA
**
1908268 AATAAAATTATGA
1 AATAAAAAAAT-A
*
1908281 AATAAATTAAAT-
1 AATAAA-AAAATA
1908293 AATAATAAAAATAA
1 AATAA-AAAAAT-A
1908307 AATAATAAAATAATA
1 AAT-A-AAAA-AATA
1908322 AATAATAAAAATA
1 AATAA-AAAAATA
1908335 A
1 A
1908336 CCAAAACATA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
12 18 0.34
13 14 0.26
14 9 0.17
15 8 0.15
16 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (12 bp):
AATAAAAAAATA
Found at i:1908285 original size:17 final size:16
Alignment explanation
Indices: 1908263--1908330 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 16
1908253 CCTAATAAAA
*
1908263 AAATAAATAAAATTAT
1 AAATAAATAAAATAAT
*
1908279 GAAATAAATTAAATAAT
1 -AAATAAATAAAATAAT
*
1908296 AATAAAAATAAAATAAT
1 AA-ATAAATAAAATAAT
1908313 AAA-ATAAT-AAATAAT
1 AAATA-AATAAAATAAT
1908328 AAA
1 AAA
1908331 AATAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.24
16 6 0.13
17 28 0.62
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (16 bp):
AAATAAATAAAATAAT
Found at i:1908298 original size:3 final size:3
Alignment explanation
Indices: 1908290--1908335 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1908280 AAATAAATTA
* *
1908290 AAT AAT AAT AAA AAT AA- AAT AAT AA- AAT AAT AAAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
1908334 AA
1 AA
1908336 CCAAAACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:1910170 original size:88 final size:81
Alignment explanation
Indices: 1910065--1910235 Score: 234
Period size: 82 Copynumber: 2.0 Consensus size: 81
1910055 TTATGCACTG
1910065 GATTTGAGTGAAATGAAAATATCGATCCACCTCATTCTGTGATGGAGTCGAACGAGATATCGGTG
1 GATTTGAGTGAAATGAAAATATCGATCC-CCTCATTC--TG-T-GA-TCGAACGAGATATCGGTG
1910130 CTGATCTACCTCCTTTTGTGATA
60 CTGATCTACCTCC-TTTGTGATA
* * * * *
1910153 GATTTGAGTGAAATGAAAATGTCGATCCCCTCCTTCTGTGATCGAACGAGATGTTGGTGTTGATC
1 GATTTGAGTGAAATGAAAATATCGATCCCCTCATTCTGTGATCGAACGAGATATCGGTGCTGATC
1910218 TACCTCCTTTGTGATA
66 TACCTCCTTTGTGATA
1910234 GA
1 GA
1910236 ATCAAGCAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
81 11 0.14
82 28 0.36
83 2 0.03
84 1 0.01
85 2 0.03
87 7 0.09
88 27 0.35
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (81 bp):
GATTTGAGTGAAATGAAAATATCGATCCCCTCATTCTGTGATCGAACGAGATATCGGTGCTGATC
TACCTCCTTTGTGATA
Found at i:1911098 original size:21 final size:20
Alignment explanation
Indices: 1911047--1911133 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
1911037 TCTCCTCTCA
* *
1911047 TTTT-TTTTCTCTTTCTCTT
1 TTTTCTTTTCTTTTTCTTTT
1911066 TTTTCTTTTCTTTTTCTTTT
1 TTTTCTTTTCTTTTTCTTTT
*
1911086 TTATTCATTTCTTTTTCTTTTT
1 TT-TTCTTTTCTTTTTC-TTTT
1911108 TCTTTCTTTTC-TTTTCTTTT
1 T-TTTCTTTTCTTTTTCTTTT
*
1911128 TCTTCT
1 TTTTCT
1911134 CAGGCGTAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.14
20 20 0.34
21 18 0.31
22 12 0.20
23 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTCTTTT
Found at i:1911101 original size:27 final size:26
Alignment explanation
Indices: 1911047--1911131 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
1911037 TCTCCTCTCA
*
1911047 TTTTT-TTTCTCTTTCTCTTT--TTTC
1 TTTTTCTTTTTCTTTCT-TTTCATTTC
*
1911071 -TTTTCTTTTTCTTTTTTATTCATTTC
1 TTTTTCTTTTTCTTTCTT-TTCATTTC
*
1911097 TTTTTCTTTTTTCTTTCTTTTCTTTTC
1 TTTTTC-TTTTTCTTTCTTTTCATTTC
1911124 TTTTTCTT
1 TTTTTCTT
1911132 CTCAGGCGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
23 5 0.10
24 11 0.22
26 6 0.12
27 18 0.35
28 11 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTCTTTTTCTTTCTTTTCATTTC
Found at i:1911131 original size:6 final size:6
Alignment explanation
Indices: 1911050--1911131 Score: 64
Period size: 6 Copynumber: 13.3 Consensus size: 6
1911040 CCTCTCATTT
*
1911050 TTTTTC TCTTTCTC TTTTT- TCTTTTC TTTTTC TTTTTTA TTCATTTC
1 TTTTTC T-TTT-TC TTTTTC T-TTTTC TTTTTC -TTTTTC TT--TTTC
*
1911097 TTTTTC TTTTT- TCTTTC -TTTTC -TTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
1911132 CTCAGGCGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
5 14 0.22
6 29 0.46
7 12 0.19
8 8 0.13
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:1914666 original size:12 final size:12
Alignment explanation
Indices: 1914651--1914677 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1914641 ATAATGTAAT
1914651 GAAAAATGTGAA
1 GAAAAATGTGAA
1914663 GAAAAATGTGAA
1 GAAAAATGTGAA
1914675 GAA
1 GAA
1914678 TTTGGAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
GAAAAATGTGAA
Found at i:1924106 original size:29 final size:28
Alignment explanation
Indices: 1924038--1924115 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1924028 ATAGTAATCC
*
1924038 TAATAAAAATAA-AAAATAAAATTATGA
1 TAATAAAAATAATAAAATAAAATTATAA
*
1924065 -AAT-AAATTAAATAATAATAAACATTA-AA
1 TAATAAAAAT-AATAA-AATAAA-ATTATAA
1924093 TAATAAAAATAATAAAAATAAAA
1 TAATAAAAATAAT-AAAATAAAA
1924116 AATAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
25 4 0.10
26 5 0.12
27 2 0.05
28 8 0.20
29 16 0.39
30 6 0.15
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (28 bp):
TAATAAAAATAATAAAATAAAATTATAA
Found at i:1924121 original size:29 final size:30
Alignment explanation
Indices: 1924038--1924126 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 30
1924028 ATAGTAATCC
*
1924038 TAATAAAAATAAAAAATAAAATTATGAAATAA
1 TAATAAAAATAAAAAAT-AAATAAT-AAATAA
*
1924070 -ATTAAATAATAATAAACATTAAATAATAAA-AA
1 TAATAAA-AATAA-AAA-A-TAAATAATAAATAA
1924102 TAATAAAAATAAAAAATAAA-AATAA
1 TAATAAAAATAAAAAATAAATAATAA
1924127 CCAAAACATA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
28 5 0.10
29 4 0.08
30 1 0.02
31 8 0.16
32 12 0.24
33 11 0.22
34 7 0.14
35 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (30 bp):
TAATAAAAATAAAAAATAAATAATAAATAA
Found at i:1924132 original size:22 final size:22
Alignment explanation
Indices: 1924089--1924138 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1924079 TAATAAACAT
* *
1924089 TAAATAATAAAAATAATAAAAA
1 TAAAAAATAAAAATAACAAAAA
1924111 TAAAAAATAAAAATAACCAAAACA
1 TAAAAAATAAAAATAA-CAAAA-A
1924135 TAAA
1 TAAA
1924139 GAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 4 0.17
24 5 0.21
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (22 bp):
TAAAAAATAAAAATAACAAAAA
Found at i:1928135 original size:24 final size:24
Alignment explanation
Indices: 1928107--1928156 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1928097 TTCGAGATAT
* *
1928107 TTCTAAGTGGTCCTTAGGGACAAA
1 TTCTAAGCGGTCCTTAGAGACAAA
* *
1928131 TTCTATGCGGTCCTTCGAGACAAA
1 TTCTAAGCGGTCCTTAGAGACAAA
1928155 TT
1 TT
1928157 TTACATGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (24 bp):
TTCTAAGCGGTCCTTAGAGACAAA
Found at i:1929850 original size:13 final size:13
Alignment explanation
Indices: 1929834--1929867 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1929824 ATATTAAAAA
*
1929834 AAAGATAATTTCT
1 AAAGATAATTCCT
1929847 AAAGATAATTCCT
1 AAAGATAATTCCT
*
1929860 AAAAATAA
1 AAAGATAA
1929868 AAAAAAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (13 bp):
AAAGATAATTCCT
Found at i:1933792 original size:14 final size:14
Alignment explanation
Indices: 1933775--1933805 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1933765 TAAATATTGA
1933775 AAATAAATTAAAAG
1 AAATAAATTAAAAG
*
1933789 AAATGAATTAAAAG
1 AAATAAATTAAAAG
1933803 AAA
1 AAA
1933806 ACGAAATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (14 bp):
AAATAAATTAAAAG
Found at i:1937972 original size:2 final size:2
Alignment explanation
Indices: 1937965--1938024 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1937955 TTAAAAATTA
1937965 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
1938007 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1938025 TACAAATATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1942956 original size:49 final size:49
Alignment explanation
Indices: 1942900--1942997 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1942890 AAGCAAAAAA
1942900 ACAAAGGTAAACACCCAAAGCAAAGCAAAAAAGAAAGTTTTAAACTTTT
1 ACAAAGGTAAACACCCAAAGCAAAGCAAAAAAGAAAGTTTTAAACTTTT
1942949 ACAAAGGTAAACACCCAAAGCAAAGCAAAAAAGAAAGTTTTAAACTTTT
1 ACAAAGGTAAACACCCAAAGCAAAGCAAAAAAGAAAGTTTTAAACTTTT
1942998 TGAAGAGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (49 bp):
ACAAAGGTAAACACCCAAAGCAAAGCAAAAAAGAAAGTTTTAAACTTTT
Found at i:1943225 original size:3 final size:3
Alignment explanation
Indices: 1943217--1943255 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1943207 CCCAGAAACA
1943217 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ACAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AA
1943256 ATATAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1944432 original size:23 final size:26
Alignment explanation
Indices: 1944361--1944453 Score: 70
Period size: 25 Copynumber: 3.7 Consensus size: 26
1944351 TGCTTCTTTA
* *
1944361 TAATATTT-TAA-AAATAATATTATAA
1 TAATATTTATAATGAATAATATTAT-T
* **
1944386 TAATATTTA-AA-AAATGTTATTA-T
1 TAATATTTATAATGAATAATATTATT
* *
1944409 TATTATTTTATGATGAATAATATTATT
1 TAATA-TTTATAATGAATAATATTATT
1944436 TAATATTTATAATGAATA
1 TAATATTTATAATGAATA
1944454 TTTTTAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 4 0.08
24 4 0.08
25 20 0.38
26 20 0.38
27 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TAATATTTATAATGAATAATATTATT
Found at i:1945385 original size:14 final size:14
Alignment explanation
Indices: 1945345--1945385 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1945335 GTTTATTTTA
*
1945345 TGAAAAATAAACTC
1 TGAAAAATAAATTC
* *
1945359 TAAAAAATGAATTC
1 TGAAAAATAAATTC
1945373 TGAAAAATAAATT
1 TGAAAAATAAATT
1945386 ACATTTCTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (14 bp):
TGAAAAATAAATTC
Found at i:1945554 original size:23 final size:25
Alignment explanation
Indices: 1945522--1945567 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1945512 TATTTATTGG
*
1945522 AAAATAATTAATATAA-TTATTTTT
1 AAAATAATTAAAATAATTTATTTTT
1945546 AAAAT-ATTAAAATAATTTATTT
1 AAAATAATTAAAATAATTTATTT
1945568 AATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATAATTAAAATAATTTATTTTT
Found at i:1945576 original size:23 final size:23
Alignment explanation
Indices: 1945522--1945569 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1945512 TATTTATTGG
* *
1945522 AAAATAATTAATATAATTATTTTT
1 AAAAT-ATTAAAATAATTATATTT
1945546 AAAATATTAAAATAATT-TATTT
1 AAAATATTAAAATAATTATATTT
1945568 AA
1 AA
1945570 TATTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATATTAAAATAATTATATTT
Found at i:1946387 original size:50 final size:50
Alignment explanation
Indices: 1946312--1946411 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
1946302 AATTCAATAA
1946312 TATGTAATTTTTATATATTCAATACCAAAATTTTAAGAACGAATCAAGCC
1 TATGTAATTTTTATATATTCAATACCAAAATTTTAAGAACGAATCAAGCC
* *
1946362 TATGTAATTTTTATATATTCAATACCAAAATTTTAAGCACGGATCAAGCC
1 TATGTAATTTTTATATATTCAATACCAAAATTTTAAGAACGAATCAAGCC
1946412 GGGGACGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (50 bp):
TATGTAATTTTTATATATTCAATACCAAAATTTTAAGAACGAATCAAGCC
Found at i:1948703 original size:33 final size:33
Alignment explanation
Indices: 1948666--1948740 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
1948656 TAACATGAAT
*
1948666 CGAAAGCAATTCAAACCGAAAAATAACCTAAAC
1 CGAAAGCAATTCAAACAGAAAAATAACCTAAAC
* * * *
1948699 CGAAAGCAATTCGAATAGAAAAATGACCTGAAC
1 CGAAAGCAATTCAAACAGAAAAATAACCTAAAC
*
1948732 CGATAGCAA
1 CGAAAGCAA
1948741 CTCGAACCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (33 bp):
CGAAAGCAATTCAAACAGAAAAATAACCTAAAC
Found at i:1949623 original size:15 final size:15
Alignment explanation
Indices: 1949603--1949643 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1949593 GTTTGGGTCG
*
1949603 GGTCATTTCGGTTCT
1 GGTCATTTCAGTTCT
1949618 GGTCATTTCAGTTCT
1 GGTCATTTCAGTTCT
*
1949633 AGTCATTTCAG
1 GGTCATTTCAG
1949644 GTCTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (15 bp):
GGTCATTTCAGTTCT
Found at i:1949648 original size:15 final size:15
Alignment explanation
Indices: 1949604--1949648 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1949594 TTTGGGTCGG
*
1949604 GTCATTTC-GGTTCTG
1 GTCATTTCAGG-TCTA
*
1949619 GTCATTTCAGTTCTA
1 GTCATTTCAGGTCTA
1949634 GTCATTTCAGGTCTA
1 GTCATTTCAGGTCTA
1949649 AATTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 25 0.96
16 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (15 bp):
GTCATTTCAGGTCTA
Found at i:1949768 original size:17 final size:17
Alignment explanation
Indices: 1949725--1949768 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1949715 ATAAATCGAG
* *
1949725 TCGGATCAGGTCAATTT
1 TCGGATCGGGTCAAATT
*
1949742 TCGGGT-GGGTCAAATT
1 TCGGATCGGGTCAAATT
1949758 TCGGATCGGGT
1 TCGGATCGGGT
1949769 GATTATCGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (17 bp):
TCGGATCGGGTCAAATT
Found at i:1953242 original size:37 final size:38
Alignment explanation
Indices: 1953175--1953341 Score: 173
Period size: 37 Copynumber: 4.5 Consensus size: 38
1953165 GTCATTCACG
* * *
1953175 AATTTATATTCGATTGAAATATAAACATATTATTTATA
1 AATTTATATTCAATTAAAATATAAATATATTATTTATA
* *
1953213 AATTTATATTTC-ATT-AAATAAAAATATATTATTTATG
1 AATTTATA-TTCAATTAAAATATAAATATATTATTTATA
* *
1953250 AATTTATATTCAATTAAAATATGAATATATTA-GTA-A
1 AATTTATATTCAATTAAAATATAAATATATTATTTATA
* * *
1953286 AAGGTTATATTCAATTAAAATATGAATATATTA-TTACA
1 AA-TTTATATTCAATTAAAATATAAATATATTATTTATA
* *
1953324 AATCTATATTCGATTAAA
1 AATTTATATTCAATTAAA
1953342 TTAAAGTATT
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
36 5 0.04
37 76 0.68
38 28 0.25
39 3 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (38 bp):
AATTTATATTCAATTAAAATATAAATATATTATTTATA
Found at i:1953277 original size:19 final size:19
Alignment explanation
Indices: 1953255--1953314 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1953245 TTATGAATTT
1953255 ATATTCAATTAAAATATGA
1 ATATTCAATTAAAATATGA
* * ** *
1953274 ATATAT-TAGTAAAAGGT-T
1 ATAT-TCAATTAAAATATGA
1953292 ATATTCAATTAAAATATGA
1 ATATTCAATTAAAATATGA
1953311 ATAT
1 ATAT
1953315 ATTATTACAA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
17 1 0.04
18 11 0.39
19 15 0.54
20 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
ATATTCAATTAAAATATGA
Found at i:1953280 original size:21 final size:21
Alignment explanation
Indices: 1953254--1953317 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1953244 TTTATGAATT
1953254 TATATTCAATTAAAATATGAA
1 TATATTCAATTAAAATATGAA
* **
1953275 TATATT--AGT-AAA-A-GGT
1 TATATTCAATTAAAATATGAA
1953291 TATATTCAATTAAAATATGAA
1 TATATTCAATTAAAATATGAA
1953312 TATATT
1 TATATT
1953318 ATTACAAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 7 0.22
17 1 0.03
18 5 0.16
19 5 0.16
20 1 0.03
21 13 0.41
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (21 bp):
TATATTCAATTAAAATATGAA
Found at i:1953307 original size:75 final size:75
Alignment explanation
Indices: 1953174--1953320 Score: 174
Period size: 75 Copynumber: 2.0 Consensus size: 75
1953164 TGTCATTCAC
* * * *
1953174 GAATTTATATTCGATTGAAATATAAACATATTATTTATAAATTTATATTTCATTAAATAAAAATA
1 GAATTTATATTCAATTAAAATATAAACATATTATGTATAAAGTTATATTTCATTAAATAAAAATA
1953239 TATTATTTAT
66 TATTATTTAT
* * **
1953249 GAATTTATATTCAATTAAAATATGAATATATTA-GTA-AAAGGTTATA-TTCAATTAAAATATGA
1 GAATTTATATTCAATTAAAATATAAACATATTATGTATAAA-GTTATATTTC-ATT-AAATAAAA
1953311 ATATATTATT
63 ATATATTATT
1953321 ACAAATCTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
73 6 0.10
74 10 0.16
75 45 0.74
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (75 bp):
GAATTTATATTCAATTAAAATATAAACATATTATGTATAAAGTTATATTTCATTAAATAAAAATA
TATTATTTAT
Found at i:1953321 original size:19 final size:19
Alignment explanation
Indices: 1953262--1953326 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1953252 TTTATATTCA
1953262 ATTAAAATATGAATATATT
1 ATTAAAATATGAATATATT
* **
1953281 AGT-AAA-A-GGTTATATT
1 ATTAAAATATGAATATATT
1953297 CAATTAAAATATGAATATATT
1 --ATTAAAATATGAATATATT
1953318 ATTACAAAT
1 ATTA-AAAT
1953327 CTATATTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 11
0.67 0.12 0.22
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 5 0.15
19 9 0.26
20 5 0.15
21 7 0.21
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
ATTAAAATATGAATATATT
Found at i:1956899 original size:58 final size:58
Alignment explanation
Indices: 1956835--1956950 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1956825 AGGGTTCCCC
1956835 GTGTCCTTGATTCGAGTTTGTTGTGTAAGGGCTCTGCTCATTTTGAGAGTAATACAAT
1 GTGTCCTTGATTCGAGTTTGTTGTGTAAGGGCTCTGCTCATTTTGAGAGTAATACAAT
1956893 GTGTCCTTGATTCGAGTTTGTTGTGTAAGGGCTCTGCTCATTTTGAGAGTAATACAAT
1 GTGTCCTTGATTCGAGTTTGTTGTGTAAGGGCTCTGCTCATTTTGAGAGTAATACAAT
1956951 TTAGTCCAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.40
Consensus pattern (58 bp):
GTGTCCTTGATTCGAGTTTGTTGTGTAAGGGCTCTGCTCATTTTGAGAGTAATACAAT
Found at i:1961232 original size:23 final size:25
Alignment explanation
Indices: 1961192--1961238 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
1961182 GGGGAACCAA
1961192 TTCCCCCTTTGAAGGGGAATCGATT
1 TTCCCCCTTTGAAGGGGAATCGATT
*
1961217 TTCCCCC-TTGGA-GGGAATCGAT
1 TTCCCCCTTTGAAGGGGAATCGAT
1961239 ACCCCCCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (25 bp):
TTCCCCCTTTGAAGGGGAATCGATT
Found at i:1963181 original size:17 final size:18
Alignment explanation
Indices: 1963142--1963185 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1963132 CTTAGAAAGT
* *
1963142 ATTGTTTTAACATTTTGG
1 ATTGTTTGAACATTGTGG
1963160 A-TGTTTGAA-ATTGTGG
1 ATTGTTTGAACATTGTGG
1963176 ATTGTTTGAA
1 ATTGTTTGAA
1963186 TTTGGATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 15 0.65
18 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (18 bp):
ATTGTTTGAACATTGTGG
Found at i:1963187 original size:16 final size:16
Alignment explanation
Indices: 1963155--1963192 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1963145 GTTTTAACAT
1963155 TTTGGA-TGTTTGAAA
1 TTTGGATTGTTTGAAA
1963170 TTGTGGATTGTTTG-AA
1 TT-TGGATTGTTTGAAA
1963186 TTTGGAT
1 TTTGGAT
1963193 GCTTATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (16 bp):
TTTGGATTGTTTGAAA
Found at i:1965957 original size:2 final size:2
Alignment explanation
Indices: 1965950--1965975 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1965940 TTCTTTTGAT
1965950 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1965976 AGATTTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1970357 original size:22 final size:21
Alignment explanation
Indices: 1970315--1970354 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1970305 AAAACTATTT
1970315 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
*
1970336 TCATTTTTTTATTTTGAAA
1 TCATTTTTTAATTTTGAAA
1970355 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:1972723 original size:29 final size:29
Alignment explanation
Indices: 1972646--1972731 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 29
1972636 TTTTGAGATG
1972646 TATATAGAGTCAGAACGGGGAATTAATCC
1 TATATAGAGTCAGAACGGGGAATTAATCC
* ** * * * * *
1972675 CATGCAAAATAATAATGGGGAATTAATCC
1 TATATAGAGTCAGAACGGGGAATTAATCC
1972704 TATATAGAGTCAGAACGGGGAATTAATC
1 TATATAGAGTCAGAACGGGGAATTAATC
1972732 ACATGCAAAA
Statistics
Matches: 41, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (29 bp):
TATATAGAGTCAGAACGGGGAATTAATCC
Found at i:1972737 original size:58 final size:58
Alignment explanation
Indices: 1972646--1972758 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
1972636 TTTTGAGATG
* * *
1972646 TATATAGAGTCAGAACGGGGAATTAATCCCATGCAAAATAATAATGGGGAATTAATCC
1 TATATAGAGTCAGAACGGGGAATTAATCACATGCAAAATAAGAATGGGAAATTAATCC
*
1972704 TATATAGAGTCAGAACGGGGAATTAATCACATGCAAAATTAGAATGGGAAATTAA
1 TATATAGAGTCAGAACGGGGAATTAATCACATGCAAAATAAGAATGGGAAATTAA
1972759 CCCCATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (58 bp):
TATATAGAGTCAGAACGGGGAATTAATCACATGCAAAATAAGAATGGGAAATTAATCC
Found at i:1972747 original size:29 final size:28
Alignment explanation
Indices: 1972655--1972849 Score: 149
Period size: 29 Copynumber: 6.8 Consensus size: 28
1972645 GTATATAGAG
* *
1972655 TCAGAACGGGGAATTAATCCCATGCAAAA
1 TCAGAATGGGAAATTAAT-CCATGCAAAA
* * * ** * *
1972684 TAATAATGGGGAATTAATCCTATATAGAG
1 TCAGAATGGGAAATTAATCC-ATGCAAAA
* *
1972713 TCAGAACGGGGAATTAATCACATGCAAAA
1 TCAGAATGGGAAATTAATC-CATGCAAAA
* * **
1972742 TTAGAATGGGAAATTAACCCCATAAAAAA
1 TCAGAATGGGAAATTAA-TCCATGCAAAA
* * *
1972771 TCATAATGGGAAATTAAGCCTGTGCAAAA
1 TCAGAATGGGAAATTAATCC-ATGCAAAA
*
1972800 TCAGAACT-AGAAATTAATCTCATGCAAAA
1 TCAGAA-TGGGAAATTAATC-CATGCAAAA
1972829 TCAGAATGGGAAATTAATCCA
1 TCAGAATGGGAAATTAATCCA
1972850 ATACAATATC
Statistics
Matches: 128, Mismatches: 31, Indels: 15
0.74 0.18 0.09
Matches are distributed among these distances:
28 7 0.05
29 117 0.91
30 4 0.03
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.23
Consensus pattern (28 bp):
TCAGAATGGGAAATTAATCCATGCAAAA
Found at i:1972786 original size:58 final size:57
Alignment explanation
Indices: 1972655--1972849 Score: 167
Period size: 58 Copynumber: 3.4 Consensus size: 57
1972645 GTATATAGAG
* * * * * * * *
1972655 TCAGAACGGGGAATTAATCCCATGCAAAATAATAATGGGGAATTAATCCTATATAGAG
1 TCAGAATGGGAAATTAAT-CCATGCAAAATAAGAATGGGAAATTAATCCCATAAAAAA
* * * *
1972713 TCAGAACGGGGAATTAATCACATGCAAAATTAGAATGGGAAATTAACCCCATAAAAAA
1 TCAGAATGGGAAATTAATC-CATGCAAAATAAGAATGGGAAATTAATCCCATAAAAAA
* * * * * * **
1972771 TCATAATGGGAAATTAAGCCTGTGCAAAATCAGAACT-AGAAATTAATCTCATGCAAAA
1 TCAGAATGGGAAATTAATCC-ATGCAAAATAAGAA-TGGGAAATTAATCCCATAAAAAA
1972829 TCAGAATGGGAAATTAATCCA
1 TCAGAATGGGAAATTAATCCA
1972850 ATACAATATC
Statistics
Matches: 112, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
57 2 0.02
58 109 0.97
59 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.23
Consensus pattern (57 bp):
TCAGAATGGGAAATTAATCCATGCAAAATAAGAATGGGAAATTAATCCCATAAAAAA
Found at i:1973742 original size:143 final size:143
Alignment explanation
Indices: 1973484--1973761 Score: 477
Period size: 143 Copynumber: 1.9 Consensus size: 143
1973474 GTCGGACACG
*
1973484 GGTAGACTGATTCAGTCAGTTTGATTTAGGGTTAAATTGGTTCAGATAGTTAAAACGGTTTGAAC
1 GGTAGACTGATTCAGTCAGTTTGATTTAGGGTTAAATTGGTTAAGATAGTTAAAACGGTTTGAAC
* * *
1973549 TACTCAGAGAGTCCCACACACGCATGACGGTGCATTGAGCCTTGTGAAAGGCCTTCTGGCGGTAA
66 TACTCAGAGAATCCCACACACGCACGACGGTGCATTGAGCCTTGTGAAAGGCCTTCTGACGGTAA
1973614 AAAAAAATATTTA
131 AAAAAAATATTTA
*
1973627 GGTAGACTGATTCAGTCAGTTTGATTTAGGGTTAAATTGGTTAAG-TCAGTTAAAATGGTTTGAA
1 GGTAGACTGATTCAGTCAGTTTGATTTAGGGTTAAATTGGTTAAGAT-AGTTAAAACGGTTTGAA
* *
1973691 CTGCTCATAGAATCCCACACACGCACGACGGTGCATTGAGCCTTGTGAAAGGCCTTCTGACGGTA
65 CTACTCAGAGAATCCCACACACGCACGACGGTGCATTGAGCCTTGTGAAAGGCCTTCTGACGGTA
1973756 AAAAAA
130 AAAAAA
1973762 TACCAAAATT
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
142 1 0.01
143 126 0.99
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (143 bp):
GGTAGACTGATTCAGTCAGTTTGATTTAGGGTTAAATTGGTTAAGATAGTTAAAACGGTTTGAAC
TACTCAGAGAATCCCACACACGCACGACGGTGCATTGAGCCTTGTGAAAGGCCTTCTGACGGTAA
AAAAAAATATTTA
Found at i:1977195 original size:13 final size:13
Alignment explanation
Indices: 1977159--1977185 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1977149 ATGCATCGGT
1977159 ATAAATAAAATAA
1 ATAAATAAAATAA
1977172 ATAAATAAAATAA
1 ATAAATAAAATAA
1977185 A
1 A
1977186 AATATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:1978556 original size:14 final size:14
Alignment explanation
Indices: 1978537--1978582 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
1978527 AATAAAGTTA
1978537 AATAATAATATAAT
1 AATAATAATATAAT
1978551 AATAATAATA-AAT
1 AATAATAATATAAT
*
1978564 AATATATATTATATAT
1 AATA-ATAATATA-AT
1978580 AAT
1 AAT
1978583 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 7 0.25
14 15 0.54
15 1 0.04
16 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:1978832 original size:151 final size:153
Alignment explanation
Indices: 1978661--1978958 Score: 438
Period size: 151 Copynumber: 2.0 Consensus size: 153
1978651 TGAAAAAATA
*
1978661 ATATAATATATTTTAAAAAAACAATATGTTTTAAAAAATTATATATATTACACACGTTTTCAAAA
1 ATATAATATATTTTAAAAAAACAATATGTTTTAAAAAATTATATATATTACACAAGTTTTCAAAA
* ** * * *
1978726 ACTATTTACATTATATATATTTATTTTCAGTAACTATA-TAT-ATATATATATACACACACACAT
66 ACTATTTACAATATATATATTTATTTTCAACAACTATATTATAACACATATATACACACACACAC
1978789 TACATATTATAAATACACATTAT
131 TACATATTATAAATACACATTAT
* ** * *
1978812 ATATATTATATTTTTCAAAAACAATATGTTTTAAAAAATTATATATATTATACAAGTTTTCAAAG
1 ATATAATATATTTTAAAAAAACAATATGTTTTAAAAAATTATATATATTACACAAGTTTTCAAAA
** *
1978877 ACTATTTACAATATATATATTTATTTTCAACAACTATATTATACACACATATATGTATACACACA
66 ACTATTTACAATATATATATTTATTTTCAACAACTATATTATA-ACACATATATACACACACACA
1978942 CTACATATTATAAATAC
130 CTACATATTATAAATAC
1978959 TATATAATAT
Statistics
Matches: 129, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
151 94 0.73
152 3 0.02
154 32 0.25
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (153 bp):
ATATAATATATTTTAAAAAAACAATATGTTTTAAAAAATTATATATATTACACAAGTTTTCAAAA
ACTATTTACAATATATATATTTATTTTCAACAACTATATTATAACACATATATACACACACACAC
TACATATTATAAATACACATTAT
Found at i:1978937 original size:16 final size:15
Alignment explanation
Indices: 1978911--1978941 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1978901 TTTCAACAAC
1978911 TATATTATACACACA
1 TATATTATACACACA
1978926 TATATGTATACACACA
1 TATAT-TATACACACA
1978942 CTACATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (15 bp):
TATATTATACACACA
Found at i:1991588 original size:180 final size:180
Alignment explanation
Indices: 1991286--1991824 Score: 967
Period size: 180 Copynumber: 3.0 Consensus size: 180
1991276 GCTTCTTCAA
1991286 TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTCTTGAAGAGGTTGGCCA
1 TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTCTTGAAGAGGTTGGCCA
*
1991351 TCTTCTTATCTTTTTCATTGTCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
66 TCTTCTCATCTTTTTCATTGTCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
1991416 GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
131 GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
* *
1991466 TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTATTGAAGAGGATGGCCA
1 TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTCTTGAAGAGGTTGGCCA
* *
1991531 TCTTCTCATCTTTTTCATTGTCATTTTCATCGAAATTGCATTCTTGACGTGTAGATGACCTTAAA
66 TCTTCTCATCTTTTTCATTGTCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
1991596 GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
131 GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
* *
1991646 TTCATGTTTCATCTATTTATCTTTGGATGACATGAATGTTTTGAATCTCTTGAAGAGGTTGGCCA
1 TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTCTTGAAGAGGTTGGCCA
*
1991711 TCTTCTCATCTTTTTCATTATCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
66 TCTTCTCATCTTTTTCATTGTCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
* *
1991776 GCAACACCAACTTGC-TTT-TTTT-TTTCTTCTCTTCTTCTTCCTATTCT
131 GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
1991823 TT
1 TT
1991825 TGGAATTTCA
Statistics
Matches: 345, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
177 25 0.07
178 4 0.01
179 3 0.01
180 313 0.91
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (180 bp):
TTCATGTTTCATCTCTTTATCTTTGGATGACATGAATCTTTTGAATCTCTTGAAGAGGTTGGCCA
TCTTCTCATCTTTTTCATTGTCATTTTCATCAAAATTGCATTCTTTACGTGTAGATGACCTTAAA
GCAACACCAACTTGCTTTTGTTTTCTTTCTTCTCTTATTCTTCCTTTTCT
Found at i:1994480 original size:9 final size:9
Alignment explanation
Indices: 1994466--1994511 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
1994456 GAAAAGGGAA
1994466 AAATAAAAT
1 AAATAAAAT
1994475 AAATAAAAT
1 AAATAAAAT
1994484 AAAT-AAAT
1 AAATAAAAT
*
1994492 AAGATAAAAG
1 AA-ATAAAAT
*
1994502 AAAAAAAAT
1 AAATAAAAT
1994511 A
1 A
1994512 GTAAAGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 6 0.19
9 21 0.66
10 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1994487 original size:13 final size:13
Alignment explanation
Indices: 1994465--1994499 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1994455 GGAAAAGGGA
1994465 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1994479 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1994492 AAGATAAA
1 AAAATAAA
1994500 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1994559 original size:2 final size:2
Alignment explanation
Indices: 1994552--1994612 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1994542 GAAAAAGGAA
1994552 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
1994594 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1994613 CATCAAAGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1994844 original size:2 final size:2
Alignment explanation
Indices: 1994803--1994827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1994793 AAACGAAATA
1994803 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
1994828 AAAGTTATAA
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:1996234 original size:100 final size:100
Alignment explanation
Indices: 1996045--1997516 Score: 2161
Period size: 100 Copynumber: 14.3 Consensus size: 100
1996035 CATTGTTCCA
* * * *
1996045 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA---TGAAA-T-TTTGTTGACAAG
* * * **
1996110 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCA
60 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1996151 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
*
1996216 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
1996251 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTATGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT--GAAT--GAAATT-TTGTTGACAAGC
*
1996316 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
61 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1996356 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1996421 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1996456 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
* *
1996521 TCCCTTCATCGTGAAGTTGAACTTGCATTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1996556 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGC
*
1996621 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
61 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1996661 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
*
1996726 TCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1996761 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
*
1996826 TCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1996861 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT--GAAT--GAAATT-TTGTTGACAAGC
*
1996926 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
61 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1996966 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1997031 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1997066 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGC
*
1997131 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
61 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1997171 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1997236 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1997271 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-T-G-AAA-T-TTTGTTGACAAG
1997336 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
60 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1997377 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAG
* * * * *
1997442 CAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
60 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1997483 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1997517 CGCGGATGGC
Statistics
Matches: 1266, Mismatches: 68, Indels: 61
0.91 0.05 0.04
Matches are distributed among these distances:
100 628 0.50
101 18 0.01
102 21 0.02
103 17 0.01
104 20 0.02
105 356 0.28
106 180 0.14
107 4 0.00
109 22 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (100 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1996398 original size:205 final size:205
Alignment explanation
Indices: 1996045--1997516 Score: 2264
Period size: 205 Copynumber: 7.2 Consensus size: 205
1996035 CATTGTTCCA
* * * ** *
1996045 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTG-TTGTTGACAAG
* * ** **
1996110 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
1996175 TTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
130 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
1996240 GTGTTGTCTGG
195 GCGTTGTCTGG
* * * *
1996251 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTATGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAGC
1996316 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1996381 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1996446 CGTTGTCTGG
196 CGTTGTCTGG
*
1996456 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT--GAAT--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAGC
*
1996516 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1996581 TGAAATTGGCTCTGAGATTGGAAAGTTATTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1996646 ACTTGCATTGTCTGG
191 ACTTGCGTTGTCTGG
* * *
1996661 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCT--GAAT--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAGC
* *
1996721 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
** *
1996786 TGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCATGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1996851 CGTTGTCTGG
196 CGTTGTCTGG
* * *
1996861 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAGC
*
1996926 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1996991 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1997056 CGTTGTCTGG
196 CGTTGTCTGG
*
1997066 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAA-TTGTTGTTGACAAG
*
1997130 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
1997195 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
130 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1997260 GCGTTGTCTGG
195 GCGTTGTCTGG
* * * *
1997271 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTG-TTGTTGACAAG
*
1997336 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * * *
1997401 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTT
130 TTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* *
1997466 GAACTTGTGTTGTCTCG
189 GAACTTGCGTTGTCTGG
* * *
1997483 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1997517 CGCGGATGGC
Statistics
Matches: 1182, Mismatches: 62, Indels: 35
0.92 0.05 0.03
Matches are distributed among these distances:
200 175 0.15
201 8 0.01
202 8 0.01
203 8 0.01
204 12 0.01
205 752 0.64
206 136 0.12
207 2 0.00
208 3 0.00
209 2 0.00
211 1 0.00
212 50 0.04
213 3 0.00
215 22 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAATTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:1996591 original size:305 final size:305
Alignment explanation
Indices: 1996045--1997516 Score: 2270
Period size: 305 Copynumber: 4.8 Consensus size: 305
1996035 CATTGTTCCA
* * * *
1996045 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA---TGAAA-T-TTTGTTGACAAG
* * * **
1996110 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAAGTCCAATATCCTTCGTTGTGAAG
60 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
1996175 TTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
125 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * *
1996240 GTGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTATGGGATTGGGAAGTTGT
190 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGT
1996305 TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
255 TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
1996356 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1996421 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
1996486 TTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTG
131 TTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* * *
1996551 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTATTGTTGA
196 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGA
*
1996616 CAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 CAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
1996661 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
*
1996726 TCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
** *
1996791 TTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTG
131 TTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
1996856 TCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGA
196 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGA
1996921 CAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 CAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
1996966 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
1997031 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1997096 TTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
* * * *
1997161 CATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT--GAAT--GAAATT-TT
191 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTT
* *
1997221 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
256 GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
1997271 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-T-G-AAA-T-TTTGTTGACAAG
1997336 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
60 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * * *
1997401 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTT
125 TTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* * * * *
1997466 GAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
184 GAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1997517 CGCGGATGGC
Statistics
Matches: 1083, Mismatches: 60, Indels: 32
0.92 0.05 0.03
Matches are distributed among these distances:
305 758 0.70
306 8 0.01
307 6 0.01
308 8 0.01
309 5 0.00
310 92 0.08
311 131 0.12
312 50 0.05
313 4 0.00
315 21 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (305 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGA
CAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:1998430 original size:67 final size:67
Alignment explanation
Indices: 1998350--1998499 Score: 223
Period size: 67 Copynumber: 2.2 Consensus size: 67
1998340 GAAACGAAAT
* *
1998350 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATATCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
1998413 AAAA
64 AAAA
* * *
1998417 TTTGTTTCGAGGGAAACAATATCAAAGGTTTTGTGTTTCAAGAGAAGCTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATATCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1998482 AA
66 AA
1998484 TTTGTTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
1998500 TTATCTCAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 70 0.93
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATATCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:1998507 original size:36 final size:36
Alignment explanation
Indices: 1998383--1998859 Score: 237
Period size: 36 Copynumber: 13.9 Consensus size: 36
1998373 AAAGATTTTG
* * *
1998383 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** * **
1998419 TGTTTCGAGGGAAACAATATCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
1998449 GTGTTTCAAGAGAAGCTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
1998486 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
1998522 CATTTCTAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
1998550 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAA-TT
*
1998588 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
1998624 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1998652 ATGTTTCAAGAGAAACCGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
1998690 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
1998726 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
1998754 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
1998792 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1998828 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1998860 TGGTGAGCAT
Statistics
Matches: 319, Mismatches: 79, Indels: 86
0.66 0.16 0.18
Matches are distributed among these distances:
28 8 0.03
29 36 0.11
30 13 0.04
31 17 0.05
32 4 0.01
33 4 0.01
34 4 0.01
35 10 0.03
36 125 0.39
37 89 0.28
38 9 0.03
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1998602 original size:37 final size:37
Alignment explanation
Indices: 1998551--1998859 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
1998541 TCAATGTTTA
*
1998551 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
1998588 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
1998624 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
1998652 ATGTTTCAAGAGAAACCGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1998690 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
1998726 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
1998754 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1998792 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1998828 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1998860 TGGTGAGCAT
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 25 0.12
30 7 0.03
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 65 0.31
37 85 0.41
38 11 0.05
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1998623 original size:102 final size:102
Alignment explanation
Indices: 1998450--1998841 Score: 651
Period size: 102 Copynumber: 3.9 Consensus size: 102
1998440 AAAGGTTTTG
* * *
1998450 TGTTTCAAGAGAAGCTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
1998514 ACGAAATTCATTTCTAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1998551 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1998616 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1998653 TGTTTCAAGAGAAACCGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1998718 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1998755 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* **
1998820 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
1998842 CTGTCTCAAG
Statistics
Matches: 273, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
101 32 0.12
102 241 0.88
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2000383 original size:20 final size:21
Alignment explanation
Indices: 2000357--2000418 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
2000347 CTTTTTGTTC
*
2000357 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
2000378 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
2000398 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
2000419 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:2000429 original size:22 final size:22
Alignment explanation
Indices: 2000375--2000427 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
2000365 ATTTTTGTTC
2000375 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
2000396 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
2000419 TTTCTTTTT
1 TTTCTTTTT
2000428 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:2001585 original size:8 final size:8
Alignment explanation
Indices: 2001572--2001614 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
2001562 GTAGATGAAG
2001572 ATGCAAAA
1 ATGCAAAA
2001580 ATGCAAAA
1 ATGCAAAA
2001588 ATGC-AAA
1 ATGCAAAA
2001595 ATGC-AAA
1 ATGCAAAA
*
2001602 ATGCAAGA
1 ATGCAAAA
2001610 ATGCA
1 ATGCA
2001615 TGAAATGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:2001597 original size:15 final size:15
Alignment explanation
Indices: 2001572--2001614 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
2001562 GTAGATGAAG
2001572 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
2001588 ATGCAAAATGC-AAA
1 ATGCAAAATGCAAAA
2001602 ATGCAAGAATGCA
1 ATGCAA-AATGCA
2001615 TGAAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.36
15 12 0.48
16 4 0.16
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:2003420 original size:9 final size:9
Alignment explanation
Indices: 2003406--2003435 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2003396 TAAAAGGGAA
2003406 AAATAAAAT
1 AAATAAAAT
2003415 AAATAAAAT
1 AAATAAAAT
*
2003424 AAATAAGAT
1 AAATAAAAT
2003433 AAA
1 AAA
2003436 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2003424 original size:14 final size:14
Alignment explanation
Indices: 2003405--2003447 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2003395 GTAAAAGGGA
2003405 AAAATAAAATAAAT
1 AAAATAAAATAAAT
2003419 AAAAT-AAATAAGAT
1 AAAATAAAATAA-AT
* *
2003433 AAAAGAAAAAAAAT
1 AAAATAAAATAAAT
2003447 A
1 A
2003448 GTAAAGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 14 0.56
15 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:2003495 original size:2 final size:2
Alignment explanation
Indices: 2003488--2003518 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2003478 GAAAAAGGAA
2003488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2003519 CATCAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2003935 original size:18 final size:17
Alignment explanation
Indices: 2003914--2003956 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2003904 ATATATACAT
2003914 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
2003932 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
2003949 ATAA-AATA
1 ATAATAATA
2003957 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:2003953 original size:14 final size:13
Alignment explanation
Indices: 2003916--2003954 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2003906 ATATACATAT
2003916 AATAATAATAACATA
1 AATAATAA-AA-ATA
2003931 AATAATAAAAATA
1 AATAATAAAAATA
2003944 AATGAATAAAA
1 AAT-AATAAAA
2003955 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:2004712 original size:34 final size:34
Alignment explanation
Indices: 2004669--2004736 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2004659 AAAGAAACCA
*
2004669 TTGAAATATTCGAGTGGGTTCTGCATAATTTTTT
1 TTGAAATATTCGAGTGGGTTCTACATAATTTTTT
* *
2004703 TTGAAATATTCGAGTGTGTTCTACATCATTTTTT
1 TTGAAATATTCGAGTGGGTTCTACATAATTTTTT
2004737 AGCCCATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGAAATATTCGAGTGGGTTCTACATAATTTTTT
Found at i:2008135 original size:17 final size:17
Alignment explanation
Indices: 2008115--2008166 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
2008105 TAGTATAGCG
2008115 AAAGATACAATACAATA
1 AAAGATACAATACAATA
*
2008132 AAAGATACAGA-ACAGTA
1 AAAGATACA-ATACAATA
2008149 AAAGATACAATACAATA
1 AAAGATACAATACAATA
2008166 A
1 A
2008167 GCAAAATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAGATACAATACAATA
Found at i:2010076 original size:26 final size:26
Alignment explanation
Indices: 2010046--2010096 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2010036 AAAAGTATAA
* *
2010046 GGAATACCTTTTTTTCTCGTGAACTT
1 GGAATACATTCTTTTCTCGTGAACTT
2010072 GGAATACATTCTTTTCTCGTGAACT
1 GGAATACATTCTTTTCTCGTGAACT
2010097 CCTTCGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (26 bp):
GGAATACATTCTTTTCTCGTGAACTT
Found at i:2011001 original size:26 final size:26
Alignment explanation
Indices: 2010971--2011021 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2010961 AAAAGTATAA
*
2010971 GGAATACCTTCTTTTCTCGTGAACTT
1 GGAATACATTCTTTTCTCGTGAACTT
2010997 GGAATACATTCTTTTCTCGTGAACT
1 GGAATACATTCTTTTCTCGTGAACT
2011022 CCTTCGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (26 bp):
GGAATACATTCTTTTCTCGTGAACTT
Found at i:2011221 original size:925 final size:926
Alignment explanation
Indices: 2009624--2011514 Score: 3559
Period size: 925 Copynumber: 2.0 Consensus size: 926
2009614 TTTATATGTT
2009624 CCTTGAGCTTGATGTACATAACCATAACCATTATATTATACGCCTTGCTTAGTTCTTTCCAATCC
1 CCTTGAGCTTGATGTACATAACCATAACCATTATATTATACGCCTTGCTTAGTTCTTTCCAATCC
*
2009689 CCACTCTCAATTACTTCGTCCACAAAATTCACTTCATTTTTAACCCCAACACTGCTACAATTTCC
66 CCACTCTCAATTACTTCGTCCACAAAAGTCACTTCATTTTTAACCCCAACACTGCTACAATTTCC
2009754 TAAACCCCAAAGGAAATGAGTAGCCATTGAACCTAATTCTAGAGTTTTCTATATCAAAATTCTCT
131 TAAACCCCAAAGGAAATGAGTAGCCATTGAACCTAATTCTAGAGTTTTCTATATCAAAATTCTCT
*
2009819 ATCAACTCCAAACATAACTCCCTTCGAATTGGTTGTGCCATTAATCCAATCAAACTATCAAATCC
196 ATCAACTCCAAACATAACTCCCTTCAAATTGGTTGTGCCATTAATCCAATCAAACTATCAAATCC
2009884 CATTTCTTTAACAACATTTCTATCAATTCGTACAACCTTACCAGGCTACATTTTGTAGAGACTTC
261 CATTTCTTTAACAACATTTCTATCAATTCGTACAACCTTACCAGGCTACATTTTGTAGAGACTTC
2009949 CTATATTTATCAAACAAAATAATATAATATTATGTTCTATACAACCTTTATCAAAAAATTTAGAA
326 CTATATTTATCAAACAAAATAATATAATATTATGTTCTATACAACCTTTATCAAAAAATTTAGAA
*
2010014 GTTCAAATACTTATTTAATTGGAAAAGTATAAGGAATACCTTTTTTTCTCGTGAACTTGGAATAC
391 GTTCAAATACTTATTTAATTGGAAAAGTATAAGGAATACCTTCTTTTCTCGTGAACTTGGAATAC
2010079 ATTCTTTTCTCGTGAACTCCTTCGTATAGTGTATTCTTCTTTTTGTTTCTTCGACAATTGTATAT
456 ATTCTTTTCTCGTGAACTCCTTCGTATAGTGTATTCTTCTTTTTGTTTCTTCGACAATTGTATAT
** *
2010144 TAGGTTATTTCTCCTCTTCGGTCATCAACCTCCATTTCGCAGTCGTTTCTTGTCTCACTTGCAAT
521 TAGGTTATTTCAACTCTTCGGTCATCAACCTCCATTTCGCAGTCGTTTCTTGTCTCACCTGCAAT
**
2010209 TAACATTTCTTGCATTATAATGTATTATATTTATAATAGGCATAATGCAAACAAATACCCCTAAC
586 TAACATTTCTTGCACAATAATGTATTATATTTATAATAGGCATAATGCAAACAAATACCCCTAAC
* * *
2010274 GTTTGACAGTTTTTTCAAATTTACCCGTATTGTTTTTTCTTGAAATATTTGACCCCCAAACGTTT
651 GTTTGACAGTATTGTCAAATTTACCCGTATTGTTTTTTCTTGAAACATTTGACCCCCAAACGTTT
2010339 CATTATGGGTCAAAAAGAACCTCTGTTGGATGGAAACCGTTAGTCAACTAACGGTGTAACACCCC
716 CATTATGGGTCAAAAAGAACCTCTGTTGGATGGAAACCGTTAGTCAACTAACGGTGTAACACCCC
2010404 ACTTTAGAGGCTAAATTTTATTAGTTTTAAATTACTGATATAAAGTTGTAAAAAAGAAAAATTTA
781 ACTTTAGAGGCTAAATTTTATTAGTTTTAAATTACTGATATAAAGTTGTAAAAAAGAAAAATTTA
*
2010469 GGACCCAATTGTAAGTTTCTAAAATTTTTGGGCTAATTTAGAAAGTGTTGAAATTTTAGGGACCC
846 GGACCCAATTGTAAGTCTCTAAAATTTTTGGGCTAATTTAGAAAGTGTTGAAATTTTAGGGACCC
* *
2010534 AGTTTTGCTACAATTC
911 AATCTTGCTACAATTC
* *
2010550 CCTTGAGCTTGATGTACATAACCATAACCATTATATTATACGCCTTTCTTAGTTCTTTCCAATCT
1 CCTTGAGCTTGATGTACATAACCATAACCATTATATTATACGCCTTGCTTAGTTCTTTCCAATCC
2010615 CCACTCTCAATTACTTCGTCCACAAAAGTCACTTCATTTTTAACCCCAACACTGCTACAATTTCC
66 CCACTCTCAATTACTTCGTCCACAAAAGTCACTTCATTTTTAACCCCAACACTGCTACAATTTCC
2010680 TAAACCCCAAAGGAAATGAGTAGCCATTGAACCTAATTCTAGAGTTTTCTATATCAAAATTCTCT
131 TAAACCCCAAAGGAAATGAGTAGCCATTGAACCTAATTCTAGAGTTTTCTATATCAAAATTCTCT
2010745 ATCAACTCCAAACATAACTCCCTTCAAATTGGTTGTGCCATTAATCCAATCAAACTATCAAATCC
196 ATCAACTCCAAACATAACTCCCTTCAAATTGGTTGTGCCATTAATCCAATCAAACTATCAAATCC
*
2010810 CATTTCTTTAACAACATTTCTATCAATTCGTATAACCTTACCAGGCTACATTTTGTAGAGACTTC
261 CATTTCTTTAACAACATTTCTATCAATTCGTACAACCTTACCAGGCTACATTTTGTAGAGACTTC
*
2010875 CTATATTTATTAAA-AAAATAATATAATATTATGTTCTATACAACCTTTATCAAAAAATTTAGAA
326 CTATATTTATCAAACAAAATAATATAATATTATGTTCTATACAACCTTTATCAAAAAATTTAGAA
2010939 GTTCAAATACTTATTTAATTGGAAAAGTATAAGGAATACCTTCTTTTCTCGTGAACTTGGAATAC
391 GTTCAAATACTTATTTAATTGGAAAAGTATAAGGAATACCTTCTTTTCTCGTGAACTTGGAATAC
2011004 ATTCTTTTCTCGTGAACTCCTTCGTATAGTGTATTCTTCTTTTTGTTTCTTCGACAATTGTATAT
456 ATTCTTTTCTCGTGAACTCCTTCGTATAGTGTATTCTTCTTTTTGTTTCTTCGACAATTGTATAT
2011069 TAGGTTATTTCAACTCTTCGGTCATCAACCTCCATTTCGCAGTCGTTTCTTGTCTCACCTGCAAT
521 TAGGTTATTTCAACTCTTCGGTCATCAACCTCCATTTCGCAGTCGTTTCTTGTCTCACCTGCAAT
*
2011134 TAACATTTCTTGCACAATAATGTATTATATTTATAATAGGCATAATGTAAACAAATACCCCTAAC
586 TAACATTTCTTGCACAATAATGTATTATATTTATAATAGGCATAATGCAAACAAATACCCCTAAC
*
2011199 GTTTGACAGTATTGTCAAATTTACCCGTATTGTTTTTTCTTGGAACATTTGACCCCCAAACGTTT
651 GTTTGACAGTATTGTCAAATTTACCCGTATTGTTTTTTCTTGAAACATTTGACCCCCAAACGTTT
2011264 CATTATGGGTCAAAAAGAACCTCTGTTGGATGGAAACCGTTAGTCAACTAACGGTGTAACACCCC
716 CATTATGGGTCAAAAAGAACCTCTGTTGGATGGAAACCGTTAGTCAACTAACGGTGTAACACCCC
*
2011329 ACTTTAGGGGCTAAATTTTATTAGTTTTAAATTACTGATATAAAGTTGTAAAAAAGAAAAATTTA
781 ACTTTAGAGGCTAAATTTTATTAGTTTTAAATTACTGATATAAAGTTGTAAAAAAGAAAAATTTA
*
2011394 GGACCCAATTGTAAGTCTCTAAAATTTTTGGGCTAATTTAGAAAGTGTTGGAATTTTAGGGACCC
846 GGACCCAATTGTAAGTCTCTAAAATTTTTGGGCTAATTTAGAAAGTGTTGAAATTTTAGGGACCC
*
2011459 AATCTTGCTACAATTT
911 AATCTTGCTACAATTC
*
2011475 CCTTGAGCTTGATGTACATAACGATAACCATTATATTATA
1 CCTTGAGCTTGATGTACATAACCATAACCATTATATTATA
2011515 AGCCCCAAAG
Statistics
Matches: 941, Mismatches: 24, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
925 608 0.65
926 333 0.35
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (926 bp):
CCTTGAGCTTGATGTACATAACCATAACCATTATATTATACGCCTTGCTTAGTTCTTTCCAATCC
CCACTCTCAATTACTTCGTCCACAAAAGTCACTTCATTTTTAACCCCAACACTGCTACAATTTCC
TAAACCCCAAAGGAAATGAGTAGCCATTGAACCTAATTCTAGAGTTTTCTATATCAAAATTCTCT
ATCAACTCCAAACATAACTCCCTTCAAATTGGTTGTGCCATTAATCCAATCAAACTATCAAATCC
CATTTCTTTAACAACATTTCTATCAATTCGTACAACCTTACCAGGCTACATTTTGTAGAGACTTC
CTATATTTATCAAACAAAATAATATAATATTATGTTCTATACAACCTTTATCAAAAAATTTAGAA
GTTCAAATACTTATTTAATTGGAAAAGTATAAGGAATACCTTCTTTTCTCGTGAACTTGGAATAC
ATTCTTTTCTCGTGAACTCCTTCGTATAGTGTATTCTTCTTTTTGTTTCTTCGACAATTGTATAT
TAGGTTATTTCAACTCTTCGGTCATCAACCTCCATTTCGCAGTCGTTTCTTGTCTCACCTGCAAT
TAACATTTCTTGCACAATAATGTATTATATTTATAATAGGCATAATGCAAACAAATACCCCTAAC
GTTTGACAGTATTGTCAAATTTACCCGTATTGTTTTTTCTTGAAACATTTGACCCCCAAACGTTT
CATTATGGGTCAAAAAGAACCTCTGTTGGATGGAAACCGTTAGTCAACTAACGGTGTAACACCCC
ACTTTAGAGGCTAAATTTTATTAGTTTTAAATTACTGATATAAAGTTGTAAAAAAGAAAAATTTA
GGACCCAATTGTAAGTCTCTAAAATTTTTGGGCTAATTTAGAAAGTGTTGAAATTTTAGGGACCC
AATCTTGCTACAATTC
Found at i:2024595 original size:20 final size:20
Alignment explanation
Indices: 2024545--2024598 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
2024535 AAATGACCAA
2024545 CAAATTCGCAACGCCAACTC
1 CAAATTCGCAACGCCAACTC
* * **
2024565 CAATTTGGCAAC-CCAGTTTC
1 CAAATTCGCAACGCCA-ACTC
2024585 CAAATTCGCAACGC
1 CAAATTCGCAACGC
2024599 GAATATGTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.12
20 22 0.85
21 1 0.04
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCCAACTC
Found at i:2024613 original size:20 final size:20
Alignment explanation
Indices: 2024590--2024677 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
2024580 GTTTCCAAAT
*
2024590 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * **
2024610 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
* *
2024630 TTCGCAACGCGAATCTATAAA
1 -TCGCAACGCGAATTTGTAAA
*
2024651 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
2024671 TCGCAAC
1 TCGCAAC
2024678 ACAGAAGTCA
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:2024694 original size:20 final size:19
Alignment explanation
Indices: 2024671--2024997 Score: 257
Period size: 20 Copynumber: 16.3 Consensus size: 19
2024661 AATTTGTAAA
*
2024671 TCGCAACACAGAAGTCATAT
1 TCGCAACAC-GAAGTCAAAT
*
2024691 TCGCAACATAGAAGTCAAAT
1 TCGCAACA-CGAAGTCAAAT
**
2024711 TCGCAACGTGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
2024731 TCGCAACACGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
2024751 TCGCAA-AGCGATAGTCAAAT
1 TCGCAACA-CGA-AGTCAAAT
* *
2024771 TCACAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
2024791 TCGCAACACATAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
2024811 TCGCAACGCGAAACTGCAAA-
1 TCGCAACACG-AAGT-CAAAT
2024831 TCGCAACACGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
*
2024851 TCGCAACACATAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
2024871 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
2024891 TCGTAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
2024911 TCGCAACACTGAATTTCAAAT
1 TCGCAACAC-GAA-GTCAAAT
*
2024932 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* * *
2024952 GCGCAACGCGATACTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
2024972 TCACAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
2024992 TCGCAA
1 TCGCAA
2024998 AGCGCGTTTA
Statistics
Matches: 254, Mismatches: 35, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.01
19 10 0.04
20 214 0.84
21 27 0.11
22 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:2024735 original size:60 final size:60
Alignment explanation
Indices: 2024671--2024997 Score: 346
Period size: 60 Copynumber: 5.4 Consensus size: 60
2024661 AATTTGTAAA
* * *
2024671 TCGCAACACAGAAGTCATATTCGCAACATAGAAGTCAAATTCGCAACGTGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
*
2024731 TCGCAACAC-GATAGTCAAATTCGCAA-AGC-GATAGTCAAATTCACAACGCGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAATTCGCAACA-CAGA-AGTCAAATTCGCAACGCGATAGTCAAAT
* * * * *
2024791 TCGCAACACATAAGTCAAATTCGCAACGC-GAAACTGCAAA-TCGCAACACGAATTTGT-AAA-
1 TCGCAACACAGAAGTCAAATTCGCAACACAG-AAGT-CAAATTCGCAACGCG-A-TAGTCAAAT
* * *
2024851 TCGCAACACATAAGTCAAATTCGCAACACAAAAGTCAAATTCGTAACGCGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * * *
2024911 TCGCAACACTGAATTTCAAATTCGCAACACAAAAGTCAAATGCGCAACGCGATACTCAAAT
1 TCGCAACACAGAA-GTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
2024972 TCACAACGC-GAAAGTCAAATTCGCAA
1 TCGCAACACAG-AAGTCAAATTCGCAA
2024998 AGCGCGTTTA
Statistics
Matches: 227, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
58 3 0.01
59 13 0.06
60 146 0.64
61 62 0.27
62 3 0.01
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (60 bp):
TCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:2025182 original size:22 final size:22
Alignment explanation
Indices: 2025157--2025207 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2025147 ATACGTCGAC
*
2025157 ATCCGTCCCCATCTCTGACAAA
1 ATCCGTCCCCATCTCCGACAAA
* * *
2025179 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACAAA
2025201 ATCCGTC
1 ATCCGTC
2025208 TATCTCCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:2025589 original size:14 final size:14
Alignment explanation
Indices: 2025572--2025598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2025562 TTTAGTTACG
2025572 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2025586 CGTTGCGATTTTC
1 CGTTGCGATTTTC
2025599 ATTTTCGCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTCT
Found at i:2025624 original size:20 final size:20
Alignment explanation
Indices: 2025581--2025624 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2025571 GCGTTGCGAT
* * * *
2025581 TTTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
2025601 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
2025621 TTTC
1 TTTC
2025625 AGAAACTACT
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:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:2027398 original size:21 final size:21
Alignment explanation
Indices: 2027372--2027414 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2027362 GCGCTATGTT
* * *
2027372 ATGAGGTATCTACTTTACGTG
1 ATGAGGTAGCCACTCTACGTG
2027393 ATGAGGTAGCCACTCTACGTG
1 ATGAGGTAGCCACTCTACGTG
2027414 A
1 A
2027415 GATTGTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
ATGAGGTAGCCACTCTACGTG
Found at i:2027528 original size:12 final size:12
Alignment explanation
Indices: 2027511--2027552 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2027501 TTTTTCGGCA
*
2027511 TTATTTATTTAT
1 TTATTTATTAAT
*
2027523 TTATTTACTAAT
1 TTATTTATTAAT
*
2027535 TTATGTATTAAT
1 TTATTTATTAAT
2027547 TTATTT
1 TTATTT
2027553 TCAGCAGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:2027724 original size:21 final size:20
Alignment explanation
Indices: 2027696--2027814 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 20
2027686 GATTCACCTG
2027696 TCATCGTTCAAGAGGTGCCTC
1 TCATCGTTCAAGAGGT-CCTC
*
2027717 -CTATCGTTCAAGAGACTCCTC
1 TC-ATCGTTCAAGAG-GTCCTC
*
2027738 TCATCGTTCAAGAGGCCCGTC
1 TCATCGTTCAAGAGGTCC-TC
* * * *
2027759 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGG-TCCTC
* *
2027780 TCATCGTTGAATAGGTCACTC
1 TCATCGTTCAAGAGGTC-CTC
* *
2027801 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
2027815 CCCGATTCAC
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.05
21 67 0.88
22 5 0.07
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGTCCTC
Found at i:2027743 original size:42 final size:41
Alignment explanation
Indices: 2027696--2027814 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 41
2027686 GATTCACCTG
* * *
2027696 TCATCGTTCAAGAGGTGCCTCCTATCGTTCAAGAGACTCCTC
1 TCATCGTTCAAGAGGT-CCTCCCACCGTTCAAGAGACCCCTC
* * *
2027738 TCATCGTTCAAGAGGCCCGTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGTCC-TCCCACCGTTCAAGAGACCCCTC
* *
2027780 TCATCGTTGAATAGGTCACTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGTC-CTCCCACCGTTCAAGAG
2027815 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 63 0.95
43 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (41 bp):
TCATCGTTCAAGAGGTCCTCCCACCGTTCAAGAGACCCCTC
Found at i:2029223 original size:68 final size:66
Alignment explanation
Indices: 2029145--2029315 Score: 208
Period size: 65 Copynumber: 2.6 Consensus size: 66
2029135 GGGGTACACT
* *
2029145 TTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGGTTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGCTTAATTTGATGAGGAAATAA
2029208 GAATTA
61 GAATTA
* *
2029214 -TTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGCTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGCTTAATTTGATGAGGAAATAAGAATT
2029277 A
66 A
* *
2029278 TTTTTTCCTTGTTTAATTG-ATTTGTAAAAGTTTATTTG
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTG
2029316 TTGTTTTAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
63 15 0.16
64 19 0.20
65 35 0.38
66 1 0.01
67 4 0.04
68 19 0.20
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (66 bp):
TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGCTTAATTTGATGAGGAAATAAGAATT
A
Found at i:2029278 original size:64 final size:64
Alignment explanation
Indices: 2029176--2029315 Score: 210
Period size: 65 Copynumber: 2.2 Consensus size: 64
2029166 TTTTACATTG
* * *
2029176 AAAGTTGGTTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGCTTAATTGATGAGGAAATAAGAATTATTTTTTCCTTGTTTAATTGATTTGTA
* *
2029239 AAAGTTGATTTGCTTAATTTGATGTGTAAATAAGAATTATTTTTTCCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGCTTAA-TTGATGAGGAAATAAGAATTATTTTTTCCTTGTTTAATTGATTTGTA
*
2029304 AAAGTTTATTTG
1 AAAGTTGATTTG
2029316 TTGTTTTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
63 15 0.22
64 19 0.28
65 35 0.51
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.49
Consensus pattern (64 bp):
AAAGTTGATTTGCTTAATTGATGAGGAAATAAGAATTATTTTTTCCTTGTTTAATTGATTTGTA
Found at i:2029473 original size:20 final size:20
Alignment explanation
Indices: 2029450--2029495 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2029440 AAATAAGCGT
*
2029450 TGCGATAGTGAAATTCGCAA
1 TGCGATAGTCAAATTCGCAA
* *
2029470 TGCGAAAGTCAAATTCGCAT
1 TGCGATAGTCAAATTCGCAA
2029490 TGCGAT
1 TGCGAT
2029496 TTTCGATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGCAA
Found at i:2032094 original size:24 final size:24
Alignment explanation
Indices: 2032043--2032097 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2032033 AAAAACCGAG
***
2032043 TATTGACCAAGATCAAAGTCCGGC
1 TATTGACCAAGATCAAAGTCCAAA
* *
2032067 TATTGACCAAGATCAAATTTCAAA
1 TATTGACCAAGATCAAAGTCCAAA
2032091 TATTGAC
1 TATTGAC
2032098 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCAAA
Found at i:2032230 original size:12 final size:12
Alignment explanation
Indices: 2032209--2032242 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2032199 GGTTGTGGGT
*
2032209 TTTGAGATTGTG
1 TTTGATATTGTG
2032221 TTTGATATTGTG
1 TTTGATATTGTG
*
2032233 TTTGGTATTG
1 TTTGATATTG
2032243 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2033092 original size:19 final size:19
Alignment explanation
Indices: 2033033--2033140 Score: 128
Period size: 19 Copynumber: 5.6 Consensus size: 19
2033023 CTAAAACCTA
* *
2033033 TTGCGAAATT-AAATTCGTG
1 TTGCGAATTTGAAATTC-AG
** *
2033052 TTGCGAATTCAAAAATCGAG
1 TTGCGAATTTGAAATTC-AG
*
2033072 TTGTGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
*
2033091 TTGCGAATTTGAAATTCAT
1 TTGCGAATTTGAAATTCAG
2033110 TTGCGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
2033129 TTGCGAATTTGA
1 TTGCGAATTTGA
2033141 CTATCGCGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
19 57 0.74
20 20 0.26
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGCGAATTTGAAATTCAG
Found at i:2033179 original size:40 final size:40
Alignment explanation
Indices: 2033128--2033214 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
2033118 TTGAAATTCA
*
2033128 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
2033168 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
2033208 GTTGCGA
1 GTTGCGA
2033215 TTTACAGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
Done.