Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 19
Found at i:1893016 original size:13 final size:11
Alignment explanation
Indices: 1893001--1893057 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 11
1892991 TTAAAATATT
1893001 TTTTGAAATCAA
1 TTTTGAAAT-AA
*
1893013 TTTTGAAAATTA
1 TTTTG-AAATAA
1893025 TCTTTGAAAATAA
1 T-TTTG-AAATAA
1893038 TTTTGAAATCAA
1 TTTTGAAAT-AA
1893050 TTTTGAAA
1 TTTTGAAA
1893058 ATTACTCCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 4 0.10
12 21 0.52
13 15 0.38
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (11 bp):
TTTTGAAATAA
Found at i:1893044 original size:12 final size:13
Alignment explanation
Indices: 1893001--1893059 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1892991 TTAAAATATT
1893001 TTTTG-AAATCAA
1 TTTTGAAAATCAA
*
1893013 TTTTGAAAAT-TA
1 TTTTGAAAATCAA
1893025 TCTTTGAAAAT-AA
1 T-TTTGAAAATCAA
1893038 TTTTG-AAATCAA
1 TTTTGAAAATCAA
1893050 TTTTGAAAAT
1 TTTTGAAAAT
1893060 TACTCCCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 4 0.10
12 18 0.44
13 19 0.46
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAATCAA
Found at i:1893871 original size:24 final size:24
Alignment explanation
Indices: 1893844--1893894 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1893834 CCCATTGACC
1893844 CTTGTCCTGGGACCATCCCGATTT
1 CTTGTCCTGGGACCATCCCGATTT
*
1893868 CTTGTCCTGGGACCATCCTGATTT
1 CTTGTCCTGGGACCATCCCGATTT
1893892 CTT
1 CTT
1893895 TAAGGAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (24 bp):
CTTGTCCTGGGACCATCCCGATTT
Found at i:1894861 original size:12 final size:13
Alignment explanation
Indices: 1894823--1894859 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1894813 TCCTAATGGG
1894823 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
1894836 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
1894848 CAATGTTTGAAA
1 CAATGTTTGAAA
1894860 CATCATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1895015 original size:12 final size:13
Alignment explanation
Indices: 1894977--1895013 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1894967 TCCTAATGGG
1894977 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
1894990 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
1895002 CAATGTTTGAAA
1 CAATGTTTGAAA
1895014 CATCATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1895036 original size:154 final size:154
Alignment explanation
Indices: 1894756--1895064 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
1894746 TGTATGCAAT
1894756 ATAATCAATCCCAAAACTCAATAAGAGTCTGCAATATTCAAGGTTCTCTAAACCGAATCCTAATG
1 ATAATCAATCCCAAAACTCAATAAGAGTCTGCAATATTCAAGGTTCTCTAAACCGAATCCTAATG
1894821 GGCAATGTTTGAAAATAATTTTGAAAACAATGTTTGAAACATCATAATACGTATAGTTTTTCATG
66 GGCAATGTTTGAAAATAATTTTGAAAACAATGTTTGAAACATCATAATACGTATAGTTTTTCATG
1894886 AAAACAACATAATTAAATCAAAAA
131 AAAACAACATAATTAAATCAAAAA
1894910 ATAATCAATCCCAAAACTCAATAAGAGTCTGCAATATTCAAGGTTCTCTAAACCGAATCCTAATG
1 ATAATCAATCCCAAAACTCAATAAGAGTCTGCAATATTCAAGGTTCTCTAAACCGAATCCTAATG
1894975 GGCAATGTTTGAAAATAATTTTGAAAACAATGTTTGAAACATCATAATACGTATAGTTTTTCATG
66 GGCAATGTTTGAAAATAATTTTGAAAACAATGTTTGAAACATCATAATACGTATAGTTTTTCATG
1895040 AAAACAACATAATTAAATCAAAAA
131 AAAACAACATAATTAAATCAAAAA
1895064 A
1 A
1895065 CATTAATAAA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (154 bp):
ATAATCAATCCCAAAACTCAATAAGAGTCTGCAATATTCAAGGTTCTCTAAACCGAATCCTAATG
GGCAATGTTTGAAAATAATTTTGAAAACAATGTTTGAAACATCATAATACGTATAGTTTTTCATG
AAAACAACATAATTAAATCAAAAA
Found at i:1899286 original size:117 final size:117
Alignment explanation
Indices: 1899067--1899286 Score: 309
Period size: 117 Copynumber: 1.9 Consensus size: 117
1899057 TTTCAAATCA
* *
1899067 AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAGAGCTCTAGATCCTTCTTCAATATTTC
1 AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAGATCCTTCTTCAAAATTTC
* * *
1899132 ATTTTGATTTTCAAAATCCATTTTAGTTCTTAGAAGAATATTGTTTAATTTG
66 ATTTTGATATTCAAAATCCATTTTAGTTCTCAAAAGAATATTGTTTAATTTG
* * *
1899184 AAATTTTCTTTTTCAAAGTTTTCAGATTTCATTTTTGAAAGCTCTA-ACTCCTTTTTCAAAATTT
1 AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAGA-TCCTTCTTCAAAATTT
* * *
1899248 CATTTTGATATTCCAAATCTATTTTGGCTT-TCAAAAGAA
65 CATTTTGATATTCAAAATCCATTTTAG-TTCTCAAAAGAA
1899287 GATCATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
116 1 0.01
117 87 0.97
118 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAGATCCTTCTTCAAAATTTC
ATTTTGATATTCAAAATCCATTTTAGTTCTCAAAAGAATATTGTTTAATTTG
Found at i:1900977 original size:18 final size:17
Alignment explanation
Indices: 1900923--1900971 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1900913 TTGAACCCTT
* *
1900923 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1900941 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1900959 AGTGCATTCGATG
1 AGTGCA-TCGATG
1900972 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1901083 original size:65 final size:65
Alignment explanation
Indices: 1900943--1901152 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 65
1900933 TGCACTAAGA
* * *
1900943 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGTATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
1901007 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATTGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
1901070 AT
65 -G
* * ** ** ** *
1901072 GTGCATTGATGCATGAAATGCATTCGATG--TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT-AGCCACAGTGCATCGATGCATGG-C
1901135 TG
64 TG
1901137 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
1901153 CTTTGATAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.39
65 63 0.53
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:1902974 original size:628 final size:627
Alignment explanation
Indices: 1902117--1903369 Score: 2344
Period size: 628 Copynumber: 2.0 Consensus size: 627
1902107 GTTGAAACTC
*
1902117 ATGTTTATGACATCACTAGTTGACTGAAGATAATGTGGGGTAGATTGATTTTGATCTTATTCTTG
1 ATGTTTATGACATCACTAGTTGACTGAAGATAATATGGGGTAGATTGATTTTGATCTTATTCTTG
*
1902182 AGACAGTGCATCCACCACAAATCCCTAATACGAAGAGTGGAGTATCTACCTCCGGATGGTCTAAA
66 AGACAATGCATCCACCACAAATCCCTAATACGAAGAGTGGAGTATCTACCTCCGGATGGTCTAAA
*
1902247 CCACCAAGAGATCATCAGATGAAGAAAACGATCGTGATGAGATTGTAGAGTACTAACACTAGCAT
131 CCACCAAGAGATCATCAGATGAAGAAAACGATCGTGATGAGATCGTAGAGTACTAACACTAGCAT
*
1902312 TTGGAACATAGGGATAATCTACAGTTTCATTCTCATTATATAACCCATAATCATCTAATCCAAAA
196 TTGGAACATAGAGATAATCTACAGTTTCATTCTCATTATATAACCCATAATCATCTAATCCAAAA
* * *
1902377 CGTGAAGCTATAATCGCGGGGTTAATATTAATATATTGGCCTAAAAGATATGATCTAATGGTTAT
261 CGTGAAGCTATAATCGCAGGGTCAATATTAATATATTGGCCTAAAAGATATGATCTAATGGCTAT
*
1902442 AGTCCCACATTGAGTTTCGTTTTGAATACATGCCGCATTGGAATAGAAAATGCGGACTAACTGTT
326 AGTCCCACATTGAGTTTCGTTTTGAATACATACCGCATTGGAATAGAAAATGCGGACTAACTGTT
*
1902507 GATAAACGATAGGTTTTAGCTGAAACATTTTATCAAACTTCCAAGCTTTAAGAATCGAAAGGTAT
391 GATAAACGATAGGTTTGAGCTGAAACATTTTATCAAACTTCCAAGCTTTAAGAATCGAAAGGTAT
1902572 TCAAAGTCAATATCTATCATAGGTTGAAGAGAAGGATTACGCTCTTCCCGGATTCTATAAGTTTG
456 TCAAAGTCAATATCTATCATAGGTTGAAGAGAAGGATTACGCTCTTCCCGGATTCTATAAGTTTG
1902637 AAAAGAATTTCTGTACCTATAGTACAATTTGTCTCTACGATGCTCAGGCATGTTAAAACAAGATC
521 AAAAGAATTTCTGTACCTATAGTACAATTTGTCTCTACGATGCTCAGGCATGTTAAAACAAGATC
*
1902702 CTAATAGGCTATTAGGAGGTTGAGGAACGGGATTAGGAGGCA
586 CTAATAGGCTATTAGGAGGTTGAGGAACGAGATTAGGAGGCA
1902744 ATGTTTATGACATCAACTAGTTGACTGAAGATAATATGGGGTAGATTGATTTTGATCTTATTCTT
1 ATGTTTATGACATC-ACTAGTTGACTGAAGATAATATGGGGTAGATTGATTTTGATCTTATTCTT
1902809 GAGACAATGCATCCACCACAAATCCCTAATACGAAGAGTGGAGTATCTACCTCCGGATGGTCTAA
65 GAGACAATGCATCCACCACAAATCCCTAATACGAAGAGTGGAGTATCTACCTCCGGATGGTCTAA
* *
1902874 ACCACCAAGAGATCATCAGATGAAGAAAACGATCGTGATGAGATCGTAGAGTACTTACACTAGCG
130 ACCACCAAGAGATCATCAGATGAAGAAAACGATCGTGATGAGATCGTAGAGTACTAACACTAGCA
*
1902939 TTTGGAACATAGAGATAATCTACAGTTTCATTCTCATTATATAACCCATCATCATCTAATCCAAA
195 TTTGGAACATAGAGATAATCTACAGTTTCATTCTCATTATATAACCCATAATCATCTAATCCAAA
1903004 ACGTGAAGCTATAATCGCAGGGTCAATATTAATATATTGGCCTAAAAGATATGATCTAATGGCTA
260 ACGTGAAGCTATAATCGCAGGGTCAATATTAATATATTGGCCTAAAAGATATGATCTAATGGCTA
* *
1903069 TAGTCCCGCATTGAGTTTCGTTTTGAATACATACTGCATTGGAATAGAAAATGCGGACTAACTGT
325 TAGTCCCACATTGAGTTTCGTTTTGAATACATACCGCATTGGAATAGAAAATGCGGACTAACTGT
*
1903134 TGATAAACGATAGGTTTGAGCTGAAACATTTTATCAAACTTCCAAGCTTTAAGAATCGGAAGGTA
390 TGATAAACGATAGGTTTGAGCTGAAACATTTTATCAAACTTCCAAGCTTTAAGAATCGAAAGGTA
1903199 TTCAAAGTCAATATCTATCATAGGTTGAAGAGAAGGATTACGCTCTTCCCGGATTCTATAAGTTT
455 TTCAAAGTCAATATCTATCATAGGTTGAAGAGAAGGATTACGCTCTTCCCGGATTCTATAAGTTT
1903264 GAAAAGAATTTCTGTACCTATAGTACAATTTGTCTCTACGATGCTCAGGCATGTTAAAACAAGAT
520 GAAAAGAATTTCTGTACCTATAGTACAATTTGTCTCTACGATGCTCAGGCATGTTAAAACAAGAT
*
1903329 CCTAATAGGCTATTAGGAGGTTGAGGAATGAGATTAGGAGG
585 CCTAATAGGCTATTAGGAGGTTGAGGAACGAGATTAGGAGG
1903370 TTGGTTTGAA
Statistics
Matches: 608, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
627 14 0.02
628 594 0.98
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (627 bp):
ATGTTTATGACATCACTAGTTGACTGAAGATAATATGGGGTAGATTGATTTTGATCTTATTCTTG
AGACAATGCATCCACCACAAATCCCTAATACGAAGAGTGGAGTATCTACCTCCGGATGGTCTAAA
CCACCAAGAGATCATCAGATGAAGAAAACGATCGTGATGAGATCGTAGAGTACTAACACTAGCAT
TTGGAACATAGAGATAATCTACAGTTTCATTCTCATTATATAACCCATAATCATCTAATCCAAAA
CGTGAAGCTATAATCGCAGGGTCAATATTAATATATTGGCCTAAAAGATATGATCTAATGGCTAT
AGTCCCACATTGAGTTTCGTTTTGAATACATACCGCATTGGAATAGAAAATGCGGACTAACTGTT
GATAAACGATAGGTTTGAGCTGAAACATTTTATCAAACTTCCAAGCTTTAAGAATCGAAAGGTAT
TCAAAGTCAATATCTATCATAGGTTGAAGAGAAGGATTACGCTCTTCCCGGATTCTATAAGTTTG
AAAAGAATTTCTGTACCTATAGTACAATTTGTCTCTACGATGCTCAGGCATGTTAAAACAAGATC
CTAATAGGCTATTAGGAGGTTGAGGAACGAGATTAGGAGGCA
Found at i:1904102 original size:23 final size:22
Alignment explanation
Indices: 1904074--1904153 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
1904064 GCATGGCCTT
*
1904074 GTGCATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1904096 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1904118 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1904140 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1904154 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 16 0.35
23 15 0.33
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1904131 original size:44 final size:42
Alignment explanation
Indices: 1904081--1904172 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 42
1904071 CTTGTGCATT
* *
1904081 GATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGTATC
1 GATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGTATC
*
1904125 GATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGTATC
1 GATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGTATC
1904167 GATGCA
1 GATGCA
1904173 TAAAGCACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 16 0.36
43 13 0.30
44 15 0.34
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (42 bp):
GATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGTATC
Found at i:1904169 original size:20 final size:21
Alignment explanation
Indices: 1904081--1904172 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
1904071 CTTGTGCATT
*
1904081 GATGCACATTCAAGGCGTGCATC
1 GATGCACATTCAA-G-GTGTATC
* * *
1904104 GGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGTGTATC
*
1904125 GATGCACATTCAAGGATGCATC
1 GATGCACATTCAAGG-TGTATC
*
1904147 GATGCAC-TGT-TAGGTGTATC
1 GATGCACAT-TCAAGGTGTATC
1904167 GATGCA
1 GATGCA
1904173 TAAAGCACAA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 11 0.19
21 22 0.39
22 14 0.25
23 10 0.18
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
GATGCACATTCAAGGTGTATC
Found at i:1904944 original size:23 final size:23
Alignment explanation
Indices: 1904914--1905018 Score: 122
Period size: 23 Copynumber: 4.6 Consensus size: 23
1904904 CTCGAGGGTT
*
1904914 CTATGTGGTCATTAGGGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
* *
1904937 CTATGTGGTCCTTTGAGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
**
1904960 CTATGTGGTCCTTCA-TAACAAAA
1 CTATGTGGTCCTT-AGGGACAAAA
* *
1904983 CTATGTAGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
*
1905006 ATATGTGGTCCTT
1 CTATGTGGTCCTT
1905019 GAGTGCAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTAGGGACAAAA
Found at i:1904981 original size:46 final size:46
Alignment explanation
Indices: 1904931--1905018 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
1904921 GTCATTAGGG
* * *
1904931 ACAAAACTATGTGGTCCTTTGAGACAAAACTATGTGGTCCTTCATA
1 ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTTCATA
*
1904977 ACAAAACTATGTAGTCCTTCGGGACAAAAATATGTGGTCCTT
1 ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTT
1905019 GAGTGCAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (46 bp):
ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTTCATA
Found at i:1905265 original size:23 final size:23
Alignment explanation
Indices: 1905235--1905339 Score: 122
Period size: 23 Copynumber: 4.6 Consensus size: 23
1905225 CTCGAGGGTT
*
1905235 CTATGTGGTCATTAGGGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
* *
1905258 CTATGTGGTCCTTTGAGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
**
1905281 CTATGTGGTCCTTCA-TAACAAAA
1 CTATGTGGTCCTT-AGGGACAAAA
* *
1905304 CTATGTAGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTAGGGACAAAA
*
1905327 ATATGTGGTCCTT
1 CTATGTGGTCCTT
1905340 GAGTGCAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTAGGGACAAAA
Found at i:1905302 original size:46 final size:46
Alignment explanation
Indices: 1905252--1905339 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
1905242 GTCATTAGGG
* * *
1905252 ACAAAACTATGTGGTCCTTTGAGACAAAACTATGTGGTCCTTCATA
1 ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTTCATA
*
1905298 ACAAAACTATGTAGTCCTTCGGGACAAAAATATGTGGTCCTT
1 ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTT
1905340 GAGTGCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (46 bp):
ACAAAACTATGTAGTCCTTCGAGACAAAAATATGTGGTCCTTCATA
Found at i:1910408 original size:13 final size:13
Alignment explanation
Indices: 1910390--1910444 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
1910380 TGCGTCCTAA
1910390 ATTTATGACGTGC
1 ATTTATGACGTGC
*
1910403 ATTTATGAC-TCAC
1 ATTTATGACGT-GC
*
1910416 ATTTATGACGCGC
1 ATTTATGACGTGC
*
1910429 ATTTATGACGTTC
1 ATTTATGACGTGC
1910442 ATT
1 ATT
1910445 GAGCATCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.03
13 34 0.97
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTTATGACGTGC
Found at i:1910515 original size:85 final size:85
Alignment explanation
Indices: 1910416--1910581 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
1910406 TATGACTCAC
* * * * **
1910416 ATTTATGACGCGCATTTATGACGTT-CATTGAGCATCATTGAAGCCCCCGTCA-TAAATTAA-GA
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCATCATTGAAGCACACACCATTAAA--AATGA
1910478 TGACACACATTTGTGTGTCATAA
63 TGACACACATTTGTGTGTCATAA
* **
1910501 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACACCATTAAAAATGATGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCATCATTGAAGCACACACCATTAAAAATGATGA
1910566 CACACATTTGTGTGTC
66 CACACATTTGTGTGTC
1910582 TTGATTGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 4 0.06
85 61 0.88
86 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCATCATTGAAGCACACACCATTAAAAATGATGA
CACACATTTGTGTGTCATAA
Found at i:1927284 original size:19 final size:19
Alignment explanation
Indices: 1927260--1927299 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1927250 TACAAGAGAG
1927260 ATTGAGTG-GTAAAATGCAA
1 ATTGAGTGAGTAAAAT-CAA
*
1927279 ATTGAGTGAGTGAAATCAA
1 ATTGAGTGAGTAAAATCAA
1927298 AT
1 AT
1927300 GGGAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (19 bp):
ATTGAGTGAGTAAAATCAA
Found at i:1932323 original size:2 final size:2
Alignment explanation
Indices: 1932316--1932374 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1932306 TATGGTCATG
1932316 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
1932358 AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
1932375 TTTCTTTGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1939812 original size:37 final size:38
Alignment explanation
Indices: 1939746--1939821 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
1939736 ATCACCTAAC
1939746 TATTTAGTCCTTTTATTTTTTCCATTAATATTTCAATT
1 TATTTAGTCCTTTTATTTTTTCCATTAATATTTCAATT
1939784 TATTTAGTCCTTTTA-TTTTTCCATTAATATTTCAATT
1 TATTTAGTCCTTTTATTTTTTCCATTAATATTTCAATT
1939821 T
1 T
1939822 TGTCAATCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 23 0.61
38 15 0.39
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (38 bp):
TATTTAGTCCTTTTATTTTTTCCATTAATATTTCAATT
Found at i:1940674 original size:49 final size:50
Alignment explanation
Indices: 1940552--1940677 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
1940542 AAAATGTTTA
* * * * * *
1940552 ACTTAACACATATTTACACCAGTATAAGTGAATAAAATAAAAAGTGTAAC
1 ACTTAACACATACTTACATCGGTGTAAATGAATAAAATAAAAAGTATAAC
* * *
1940602 ACTTAACAGATACTTACATCGGTGTAAATGAATAACATAAAAAGTATAGC
1 ACTTAACACATACTTACATCGGTGTAAATGAATAAAATAAAAAGTATAAC
1940652 AC-TAACACATACTTA-ATCCGGTGTAA
1 ACTTAACACATACTTACAT-CGGTGTAA
1940678 GTATCTACAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.03
49 20 0.31
50 43 0.66
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (50 bp):
ACTTAACACATACTTACATCGGTGTAAATGAATAAAATAAAAAGTATAAC
Found at i:1941649 original size:24 final size:25
Alignment explanation
Indices: 1941617--1941671 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
1941607 TTAATTTTTT
1941617 TTTTATTTTAATTTTA-AAAATATA
1 TTTTATTTTAATTTTATAAAATATA
*
1941641 TTTTATTTTAATTTTATTAAATATA
1 TTTTATTTTAATTTTATAAAATATA
1941666 TATTTA
1 T-TTTA
1941672 AGACTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 16 0.57
25 8 0.29
26 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTATTTTAATTTTATAAAATATA
Found at i:1941762 original size:31 final size:31
Alignment explanation
Indices: 1941727--1941790 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1941717 TAACCATACA
* *
1941727 ATATATATTTAAGCTAAGATAGGAATAAAAT
1 ATATATATTTAAACTAAAATAGGAATAAAAT
* * *
1941758 ATATATTTTTAAATTAAAATAGTAATAAAAT
1 ATATATATTTAAACTAAAATAGGAATAAAAT
1941789 AT
1 AT
1941791 TCTTATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.38
Consensus pattern (31 bp):
ATATATATTTAAACTAAAATAGGAATAAAAT
Found at i:1941834 original size:32 final size:30
Alignment explanation
Indices: 1941750--1941855 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 30
1941740 CTAAGATAGG
* *
1941750 AATAA-AATATATATTTTTA-AATTAAAAT
1 AATAATAAAATATATTTTTATAATTAAGAT
* * *
1941778 AGTAAT-AAA-ATATTCTTAT-ATTAAGTT
1 AATAATAAAATATATTTTTATAATTAAGAT
*
1941805 AATAATAAAATTTATATTTTATAATTTAAGAT
1 AATAATAAAATATAT-TTTTATAA-TTAAGAT
*
1941837 AAAAATAAAATATATTTTT
1 AATAATAAAATATATTTTT
1941856 CAAGATATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
27 19 0.32
28 9 0.15
29 3 0.05
30 5 0.08
31 5 0.08
32 19 0.32
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
AATAATAAAATATATTTTTATAATTAAGAT
Found at i:1942355 original size:208 final size:208
Alignment explanation
Indices: 1942111--1942526 Score: 832
Period size: 208 Copynumber: 2.0 Consensus size: 208
1942101 ACCTGATATA
1942111 AATTAAAGATTTAATTAAAAATAATAAAAATTTCAAGGAAATTACATTATTATCCTCGAGTCGGG
1 AATTAAAGATTTAATTAAAAATAATAAAAATTTCAAGGAAATTACATTATTATCCTCGAGTCGGG
1942176 TCGGAATTTTTCACCCTCCACCAAAAATTGACCCAACCCGACTTCACCCTTTAAAAAATTCGAAC
66 TCGGAATTTTTCACCCTCCACCAAAAATTGACCCAACCCGACTTCACCCTTTAAAAAATTCGAAC
1942241 CAACCCAATTAAATCCAAAATTTTTAAAAAAATCGATCCTATCAGGTCAAATTGAGTCAGAACCC
131 CAACCCAATTAAATCCAAAATTTTTAAAAAAATCGATCCTATCAGGTCAAATTGAGTCAGAACCC
1942306 GTCAGATGCTGGT
196 GTCAGATGCTGGT
1942319 AATTAAAGATTTAATTAAAAATAATAAAAATTTCAAGGAAATTACATTATTATCCTCGAGTCGGG
1 AATTAAAGATTTAATTAAAAATAATAAAAATTTCAAGGAAATTACATTATTATCCTCGAGTCGGG
1942384 TCGGAATTTTTCACCCTCCACCAAAAATTGACCCAACCCGACTTCACCCTTTAAAAAATTCGAAC
66 TCGGAATTTTTCACCCTCCACCAAAAATTGACCCAACCCGACTTCACCCTTTAAAAAATTCGAAC
1942449 CAACCCAATTAAATCCAAAATTTTTAAAAAAATCGATCCTATCAGGTCAAATTGAGTCAGAACCC
131 CAACCCAATTAAATCCAAAATTTTTAAAAAAATCGATCCTATCAGGTCAAATTGAGTCAGAACCC
1942514 GTCAGATGCTGGT
196 GTCAGATGCTGGT
1942527 GAAATTGCCA
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 208 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (208 bp):
AATTAAAGATTTAATTAAAAATAATAAAAATTTCAAGGAAATTACATTATTATCCTCGAGTCGGG
TCGGAATTTTTCACCCTCCACCAAAAATTGACCCAACCCGACTTCACCCTTTAAAAAATTCGAAC
CAACCCAATTAAATCCAAAATTTTTAAAAAAATCGATCCTATCAGGTCAAATTGAGTCAGAACCC
GTCAGATGCTGGT
Found at i:1956867 original size:16 final size:16
Alignment explanation
Indices: 1956825--1956875 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1956815 TTTTGATGGA
1956825 TTTGTGTTTTGAATAT
1 TTTGTGTTTTGAATAT
* *
1956841 TTCGT-TGTTTGGATAT
1 TTTGTGT-TTTGAATAT
*
1956857 TTTGTGTTTTGAATGT
1 TTTGTGTTTTGAATAT
1956873 TTT
1 TTT
1956876 ATTTTGAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.14, C:0.02, G:0.22, T:0.63
Consensus pattern (16 bp):
TTTGTGTTTTGAATAT
Found at i:1956882 original size:14 final size:15
Alignment explanation
Indices: 1956863--1956899 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1956853 ATATTTTGTG
1956863 TTTTGAATG-TTTTA
1 TTTTGAATGATTTTA
1956877 TTTTGAATGATTTTTA
1 TTTTGAATGA-TTTTA
1956893 TTTTGAA
1 TTTTGAA
1956900 CTTTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTTGAATGATTTTA
Found at i:1958001 original size:44 final size:44
Alignment explanation
Indices: 1957942--1958028 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
1957932 TCCATTCAAT
1957942 ATTCATTTTGCTTTCAAGAACACAATTTGTGCTCAATCGTATTC
1 ATTCATTTTGCTTTCAAGAACACAATTTGTGCTCAATCGTATTC
*
1957986 ATTCATTTTGTTTTCAAGAACACAATTTGTGCTCAATCGTATT
1 ATTCATTTTGCTTTCAAGAACACAATTTGTGCTCAATCGTATT
1958029 TATTTTTTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (44 bp):
ATTCATTTTGCTTTCAAGAACACAATTTGTGCTCAATCGTATTC
Found at i:1959490 original size:16 final size:16
Alignment explanation
Indices: 1959469--1959502 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1959459 AAATTAATCT
1959469 AAAAAATCGATAACCGA
1 AAAAAATCGA-AACCGA
1959486 AAAAAATCGAAACCGA
1 AAAAAATCGAAACCGA
1959502 A
1 A
1959503 TTAGTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.62, C:0.18, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAAAATCGAAACCGA
Found at i:1963501 original size:12 final size:12
Alignment explanation
Indices: 1963484--1963509 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1963474 TTATTGAAAA
1963484 TAAAATATTTTT
1 TAAAATATTTTT
1963496 TAAAATATTTTT
1 TAAAATATTTTT
1963508 TA
1 TA
1963510 GAAAGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:1968958 original size:46 final size:46
Alignment explanation
Indices: 1968888--1969053 Score: 219
Period size: 46 Copynumber: 3.6 Consensus size: 46
1968878 TTTATGTCGT
** * *
1968888 TAATGCACTATTATGAATTTTCATTTGTGACATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTGTGACATCCTTTCATGCCGA
* * * *
1968934 TAATGCACCGTTATACATTCTCATTTGT-AGCATACTTTTATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGA-CATCCTTTCATGCCGA
*
1968980 TAATGCACCGTTATGCATTTTCATTTGTGGA-ATCCTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTGT-GACATCCTTTCATGCCGA
1969026 TAATGCACCGTTATGCATTTTCATTTGT
1 TAATGCACCGTTATGCATTTTCATTTGT
1969054 TCATTCATTT
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
45 1 0.01
46 102 0.98
48 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTGTGACATCCTTTCATGCCGA
Found at i:1969065 original size:92 final size:92
Alignment explanation
Indices: 1968877--1969053 Score: 257
Period size: 92 Copynumber: 1.9 Consensus size: 92
1968867 GAGTGGCACT
* * *
1968877 TTTTATGTCGTTAATGCACTATTATGAATTTTCATTTGTGACATCCTTTCATGCCAATAATGCAC
1 TTTTATGCCGATAATGCACCATTATGAATTTTCATTTGTGACATCCTTTCATGCCAATAATGCAC
1968942 CGTTATACATTCTCATTTGTAGCATAC
66 CGTTATACATTCTCATTTGTAGCATAC
* * **
1968969 TTTTATGCCGATAATGCACCGTTATGCATTTTCATTTGTGGA-ATCCTTTCATGCTGATAATGCA
1 TTTTATGCCGATAATGCACCATTATGAATTTTCATTTGT-GACATCCTTTCATGCCAATAATGCA
* *
1969033 CCGTTATGCATTTTCATTTGT
65 CCGTTATACATTCTCATTTGT
1969054 TCATTCATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
92 73 0.97
93 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (92 bp):
TTTTATGCCGATAATGCACCATTATGAATTTTCATTTGTGACATCCTTTCATGCCAATAATGCAC
CGTTATACATTCTCATTTGTAGCATAC
Found at i:1975602 original size:46 final size:46
Alignment explanation
Indices: 1975533--1975809 Score: 448
Period size: 46 Copynumber: 6.0 Consensus size: 46
1975523 AATATCATGA
* * **
1975533 GTGGCA-CCTTTTATGCCGTTAATGCACTATTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1975578 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
* ** *
1975624 GTTGCATCCTTTCATATCGATAATGTACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
*
1975670 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
* *
1975716 GTGGCATCCTTTCATGCCGATAATGCACTGTTATGTATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1975762 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1975808 GT
1 GT
1975810 TCATTCAATT
Statistics
Matches: 215, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 6 0.03
46 209 0.97
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (46 bp):
GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
Found at i:1976335 original size:21 final size:21
Alignment explanation
Indices: 1976309--1976364 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1976299 TCGATACTCA
*
1976309 CATCAGTATCGATACTAATTG
1 CATCAGTATTGATACTAATTG
1976330 CATCAGTATTGATACTAATTG
1 CATCAGTATTGATACTAATTG
1976351 CATCAGTATTGATA
1 CATCAGTATTGATA
1976365 TTGTTCATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (21 bp):
CATCAGTATTGATACTAATTG
Found at i:1978766 original size:130 final size:130
Alignment explanation
Indices: 1978599--1978867 Score: 396
Period size: 130 Copynumber: 2.1 Consensus size: 130
1978589 TTGATATTGA
* *
1978599 AAATAGTAATATCTTTTCATTTCGATTGGAGTAATAAACGACTGCTTTAAGGCATAAGAGGTCAT
1 AAATAGTAATATCTCTTCATTTCAATTGGAGTAATAAACGACTGCTTTAAGGCATAAGAGGTCAT
* * * **
1978664 TTATTATCGGTTGTAAATAATTAGATATTATGGTTTTCTTTCGAAACAATATTG-ATTTTAAGAT
66 TTATTATCGATTGGAAATAATTAGATATTAT-CTTTTCACTCGAAACAATATTGAATTTTAAGAT
1978728 G
130 G
* * *
1978729 AAATAGTAATATCTCTTCATTTCAATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTAATATCTCTTCATTTCAATTGGAGTAATAAACGACTGCTTTAAGGCATAAGAGGTCAT
* * *
1978794 TTATTCTCGATTGGAAATCATTAGATATTATCTTTTCACTCGAATCAATATTGAATTTTAAGATG
66 TTATTATCGATTGGAAATAATTAGATATTATCTTTTCACTCGAAACAATATTGAATTTTAAGATG
*
1978859 AAATTGTAA
1 AAATAGTAA
1978868 CACCCATCTC
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 18 0.15
130 106 0.85
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (130 bp):
AAATAGTAATATCTCTTCATTTCAATTGGAGTAATAAACGACTGCTTTAAGGCATAAGAGGTCAT
TTATTATCGATTGGAAATAATTAGATATTATCTTTTCACTCGAAACAATATTGAATTTTAAGATG
Found at i:1980203 original size:45 final size:45
Alignment explanation
Indices: 1980145--1980259 Score: 194
Period size: 45 Copynumber: 2.6 Consensus size: 45
1980135 TTCGTTTATA
*
1980145 CATCCTTTTATGCCTTTTATACACCATGATACATTTCATTTATGG
1 CATCCTTTCATGCCTTTTATACACCATGATACATTTCATTTATGG
*
1980190 CATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGG
1 CATCCTTTCATGCCTTTTATACACCATGATACATTTCATTTATGG
* *
1980235 AATCCTTTCATGTCTTTTATACACC
1 CATCCTTTCATGCCTTTTATACACC
1980260 GTTTTGCATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (45 bp):
CATCCTTTCATGCCTTTTATACACCATGATACATTTCATTTATGG
Found at i:1980578 original size:55 final size:55
Alignment explanation
Indices: 1980509--1981109 Score: 880
Period size: 55 Copynumber: 10.9 Consensus size: 55
1980499 TTTATTAAGA
* *
1980509 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCCGTGGGTT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGGTT
* * *
1980564 TACACATATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
*
1980619 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * * * *
1980674 TGTACACATAGTGTCTGTATGGTTATTCATCAACTTATGATGAATTCCATGGGTT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * *
1980729 TGCACACATAGTGCATGAATGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
*
1980784 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * *
1980839 TGCACACAAAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCATGGGTT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * *
1980894 TACACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* *
1980949 TGTACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * * *
1981004 TGCACATATATTGCATGTACGGTTATTCATCAACTCATGATGAATTACGTGGGTT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
* * ** * * *
1981059 TTCACATATAGTTTCTGTACGGTTATTGATCAACTCAGGATGGATTCCGTG
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTG
1981110 AAATGCACAC
Statistics
Matches: 496, Mismatches: 49, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
55 494 1.00
56 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
Found at i:1981549 original size:22 final size:22
Alignment explanation
Indices: 1981518--1981560 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1981508 TATCGATACC
*
1981518 CATACCATGGTATCAATACTAA
1 CATACCATGGTACCAATACTAA
* *
1981540 CATACTATGGTACCGATACTA
1 CATACCATGGTACCAATACTA
1981561 TGCTATGGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (22 bp):
CATACCATGGTACCAATACTAA
Found at i:1984416 original size:98 final size:98
Alignment explanation
Indices: 1984295--1984491 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
1984285 GACATCTTGT
**
1984295 ATCTCTTAGATGTTCCGATTGACTGAAATTTGTTTAGCGCTATTGTGCAGTTTTGGAATCCTGCT
1 ATCTCTTAGATGTTCCGATTGACTGAAATTTGTTTAGCGCTATTCCGCAGTTTTGGAATCCTGCT
1984360 TATAGTTGCTTTACTTTTGGCCGAGCAGACATG
66 TATAGTTGCTTTACTTTTGGCCGAGCAGACATG
* *
1984393 ATCTCTTAGATGTTCCGATTGACTGAAATTTGTTTAGCGCTATTCCGTAGTTTTGGAATCCTTCT
1 ATCTCTTAGATGTTCCGATTGACTGAAATTTGTTTAGCGCTATTCCGCAGTTTTGGAATCCTGCT
1984458 TATAGTTGCTTTACTTTTGGCCGAGCAGACATG
66 TATAGTTGCTTTACTTTTGGCCGAGCAGACATG
1984491 A
1 A
1984492 CGCCTACCAT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (98 bp):
ATCTCTTAGATGTTCCGATTGACTGAAATTTGTTTAGCGCTATTCCGCAGTTTTGGAATCCTGCT
TATAGTTGCTTTACTTTTGGCCGAGCAGACATG
Found at i:1990825 original size:13 final size:13
Alignment explanation
Indices: 1990807--1990841 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1990797 TATATGAATC
1990807 AGCTACAATTTCA
1 AGCTACAATTTCA
1990820 AGCTACAATTTCA
1 AGCTACAATTTCA
*
1990833 AGCAACAAT
1 AGCTACAAT
1990842 ATAGGAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
AGCTACAATTTCA
Found at i:1995972 original size:19 final size:19
Alignment explanation
Indices: 1995948--1995997 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1995938 ATCTAATTTT
1995948 GGTATCGATACCGGTAAGG
1 GGTATCGATACCGGTAAGG
1995967 GGTATCGATACCGGTAAGG
1 GGTATCGATACCGGTAAGG
1995986 GGTATCGATACC
1 GGTATCGATACC
1995998 CTATTAGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCGGTAAGG
Found at i:1996548 original size:59 final size:58
Alignment explanation
Indices: 1996454--1996621 Score: 203
Period size: 59 Copynumber: 2.9 Consensus size: 58
1996444 ATTACCAAAT
* *
1996454 GGCACTTCGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
* * *** *
1996512 GGTACTTCATGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATTG
1 GGCACTTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
* * **
1996571 GGCACCTT-GTGTGCTAAAGGATAAGGAATTCATACTAAGTCCATGAATTTC
1 GGCA-CTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
1996622 TTTATGGGAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
58 43 0.46
59 47 0.51
60 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (58 bp):
GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
Found at i:1997132 original size:81 final size:80
Alignment explanation
Indices: 1996993--1997314 Score: 373
Period size: 81 Copynumber: 4.0 Consensus size: 80
1996983 ATAAAAGATC
* * * ** *
1996993 AAAA-GGCCTAACTGTGTAATTGGAAGAAATACGTCAATTATGCCAGTTCGATGAACGATTAAGT
1 AAAATGGCCTAGCTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGT
1997057 ACCGTTGAGTAAAAG
66 ACCGTTGAGTAAAAG
* * *
1997072 AAAATTGGCCTAGCTGTGCAATAGGCAGTAATGTGTCAATTATGCCAGTTAGATGAACGATTATG
1 AAAA-TGGCCTAGCTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAG
*
1997137 TACCGTTGAGTAAATG
65 TACCGTTGAGTAAAAG
*
1997153 AAAAATGGCCTAGCTGTGCAATTGGCAGAAAAT-TGTCAATTATGCCAGTTAGATGAACGGTTAA
1 -AAAATGGCCTAGCTGTGCAATTGGCAG-AAATGTGTCAATTATGCCAGTTAGATGAACGATTAA
*
1997217 GTACTGTTGAGTAAAAG
64 GTACCGTTGAGTAAAAG
** * * * * ** *
1997234 AATAATGGCCTAATTATG-AATTGGCACAAAGGTGTCAATTATGCCAGTTAAACAAACG-TTAAA
1 AA-AATGGCCTAGCTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAG
* *
1997297 TACTGTTGAGTAAGAG
65 TACCGTTGAGTAAAAG
1997313 AA
1 AA
1997315 TAAAGAAATT
Statistics
Matches: 211, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
79 28 0.13
80 33 0.16
81 143 0.68
82 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (80 bp):
AAAATGGCCTAGCTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGT
ACCGTTGAGTAAAAG
Found at i:2007639 original size:14 final size:13
Alignment explanation
Indices: 2007617--2007680 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
2007607 GAAGAAAGAA
*
2007617 AAAATGAAAAAAG
1 AAAATGAAAAAAC
2007630 AAAATGGAAAAAAC
1 AAAAT-GAAAAAAC
*
2007644 AAAA-AACAAAAAGC
1 AAAATGA-AAAAA-C
2007658 AAAA-GAAAAATAC
1 AAAATGAAAAA-AC
*
2007671 AAAAGGAAAA
1 AAAATGAAAA
2007681 GAAAAGAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.02
13 19 0.44
14 23 0.53
ACGTcount: A:0.77, C:0.06, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAATGAAAAAAC
Found at i:2007675 original size:19 final size:19
Alignment explanation
Indices: 2007639--2007685 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2007629 GAAAATGGAA
*
2007639 AAAACAAAAAACAAAAAGC
1 AAAAGAAAAAACAAAAAGC
*
2007658 AAAAGAAAAATAC-AAAAGG
1 AAAAGAAAAA-ACAAAAAGC
2007677 AAAAGAAAA
1 AAAAGAAAA
2007686 GAGAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.79, C:0.09, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAACAAAAAGC
Found at i:2010171 original size:23 final size:23
Alignment explanation
Indices: 2010141--2010188 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2010131 ATTGTTGAGG
2010141 TGTGTGGATGCCAAAACAATCAT
1 TGTGTGGATGCCAAAACAATCAT
2010164 TGTGTGGATGCCAAAACAATCAT
1 TGTGTGGATGCCAAAACAATCAT
2010187 TG
1 TG
2010189 AAGAAGTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (23 bp):
TGTGTGGATGCCAAAACAATCAT
Found at i:2011267 original size:22 final size:22
Alignment explanation
Indices: 2011248--2011289 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2011238 AGAAAAAATG
2011248 AAAAAAC-AAAAACAAAAAAAC
1 AAAAAACAAAAAACAAAAAAAC
2011269 AAAAAACAAAAAACAAAAAAA
1 AAAAAACAAAAAACAAAAAAA
2011290 ATACAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAAAACAAAAAAAC
Found at i:2011297 original size:8 final size:7
Alignment explanation
Indices: 2011248--2011288 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
2011238 AGAAAAAATG
2011248 AAAAAAC
1 AAAAAAC
2011255 -AAAAAC
1 AAAAAAC
2011261 AAAAAAAC
1 -AAAAAAC
2011269 AAAAAAC
1 AAAAAAC
2011276 AAAAAAC
1 AAAAAAC
2011283 AAAAAA
1 AAAAAA
2011289 AATACAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:2012441 original size:135 final size:134
Alignment explanation
Indices: 2012093--2012461 Score: 391
Period size: 135 Copynumber: 2.7 Consensus size: 134
2012083 TAACCAATTC
* * * * * * * * *
2012093 AGATCCCCTATCTTTCCA-AATTCGATCTTTCCTGAGTAGCAGTGGAATAAGTCTACCTTGATTC
1 AGATCCCATCTCTTTCCAGACTT-GATCTTCCCTGAGTAGCAGTGGAACAACTATGCCTCGATTC
** * *
2012157 AATCTTCCCTGAAGAGAAGTAGAATGAATCAACATCTCGAGATCTGATTTTCCCTAAAGAAGCTC
65 AATCTTCCCTGAAGA-AAGTAGAATGAATCAATGTCTCGAGATCTAATTTTCCCTAAAGAAGCAC
2012222 TGGAAA
129 TGGAAA
* * * * *
2012228 AGATCCCATCTCTTTCTAGATTTGATCTTCCTTGAGTAGCAATGGAACAACTTTGCCTCGATTCA
1 AGATCCCATCTCTTTCCAGACTTGATCTTCCCTGAGTAGCAGTGGAACAACTATGCCTCGATTCA
* * * * * *
2012293 ATCTT-TCTCGAAGAACACTCGAATGAATCAATGTCTCTAGATCTAATTTTCCCTGAAGAAGCAG
66 ATCTTCCCT-GAAGAA-AGTAGAATGAATCAATGTCTCGAGATCTAATTTTCCCTAAAGAAGCAC
*
2012357 TGGAAC
129 TGGAAA
* * * * *
2012363 ATATCCCCTTTTTTTCCAGACTTGATCTTCCCTGAGTAGCAGTGGAACAACTATGCCTCGGTTCA
1 AGATCCCATCTCTTTCCAGACTTGATCTTCCCTGAGTAGCAGTGGAACAACTATGCCTCGATTCA
* *
2012428 ATCTTCCCTGAAGAATAGTGGAGTGAATCAATGT
66 ATCTTCCCTGAAGAA-AGTAGAATGAATCAATGT
2012462 TTCCAGATTT
Statistics
Matches: 192, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
134 3 0.02
135 184 0.96
136 5 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (134 bp):
AGATCCCATCTCTTTCCAGACTTGATCTTCCCTGAGTAGCAGTGGAACAACTATGCCTCGATTCA
ATCTTCCCTGAAGAAAGTAGAATGAATCAATGTCTCGAGATCTAATTTTCCCTAAAGAAGCACTG
GAAA
Found at i:2015014 original size:131 final size:131
Alignment explanation
Indices: 2014766--2015131 Score: 459
Period size: 131 Copynumber: 2.8 Consensus size: 131
2014756 ATTAATATTG
* * * * * *
2014766 AAAATAGTAATATCTTTTCATTTTGGTTGGAGTAATAAACGATTGCTTTAAGGCATGAGAGGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCA
** ** * *
2014831 TTTATTC-ATGATTGGAAATAATTAGATATTATGGTTTTCTTTCGAATCAATATTG-ATTTTTAA
66 TTTATTCTA-GATTGGAAATAATTAGATATTATAATTTTCACTCAAATAAATATTGTA-TTTTAA
2014894 CAC
129 CAC
* * * *
2014897 AGAATAGTGATATATCTTCATTTCGATTAGAGTAATAAATGAATGATTTAAGGCATGAGAGGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCA
* * * *
2014962 TTTATTCTAGATTGGAAATCATTAGAGATTATCATTTTCACTCAAATAAATATTGTATTTTAATA
66 TTTATTCTAGATTGGAAATAATTAGATATTATAATTTTCACTCAAATAAATATTGTATTTTAACA
2015027 C
131 C
* *
2015028 AAAATA-TAGATATCTCTTCATTTCGATTGGAGTAATAAATGACTTCTTTAAGGCATGAGAGGTC
1 AAAATAGT-GATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTC
* **
2015092 ATTTATTCTCGATTCAAAATAATTAGATATTATAATTTTC
65 ATTTATTCTAGATTGGAAATAATTAGATATTATAATTTTC
2015132 TCTCTTATAA
Statistics
Matches: 201, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
130 1 0.00
131 198 0.99
132 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (131 bp):
AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCA
TTTATTCTAGATTGGAAATAATTAGATATTATAATTTTCACTCAAATAAATATTGTATTTTAACA
C
Found at i:2020857 original size:22 final size:22
Alignment explanation
Indices: 2020829--2020873 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2020819 ACCCGAAATA
2020829 ACATTCAAAATAAACATCATAT
1 ACATTCAAAATAAACATCATAT
** *
2020851 ACATTCATGATAAACATTATAT
1 ACATTCAAAATAAACATCATAT
2020873 A
1 A
2020874 TAATAAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (22 bp):
ACATTCAAAATAAACATCATAT
Found at i:2020938 original size:16 final size:16
Alignment explanation
Indices: 2020917--2020952 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2020907 CCCAAGGATC
2020917 AACATCATATATAATA
1 AACATCATATATAATA
2020933 AACATCATATATAATA
1 AACATCATATATAATA
2020949 AACA
1 AACA
2020953 ATGATCAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (16 bp):
AACATCATATATAATA
Found at i:2024827 original size:62 final size:62
Alignment explanation
Indices: 2024747--2024880 Score: 196
Period size: 62 Copynumber: 2.2 Consensus size: 62
2024737 ATTCGATTCG
* *
2024747 AATTAGTGACGTTACAAATTTGTCACTGAAATATTTTATTCGCAACAATGTGATTTTTCACT
1 AATTAGTGACGTTACAAATTTGTCACTGAAATATTTTATTCACAACAATGTGATTTGTCACT
* * * * *
2024809 AATTAGTGACGTTGCAAATTTTTCACTGATATATTTTATTCACTACAATTTGATTTGTCACT
1 AATTAGTGACGTTACAAATTTGTCACTGAAATATTTTATTCACAACAATGTGATTTGTCACT
*
2024871 ATTTAGTGAC
1 AATTAGTGAC
2024881 TGATATATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (62 bp):
AATTAGTGACGTTACAAATTTGTCACTGAAATATTTTATTCACAACAATGTGATTTGTCACT
Found at i:2024885 original size:46 final size:46
Alignment explanation
Indices: 2024833--2024926 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
2024823 CAAATTTTTC
2024833 ACTGATATATTTTATTCACTACAATTTGATTTGTCACTATTTAGTG
1 ACTGATATATTTTATTCACTACAATTTGATTTGTCACTATTTAGTG
2024879 ACTGATATATTTTATTCACTACAATTTGATTTGTCACTATTTAGTG
1 ACTGATATATTTTATTCACTACAATTTGATTTGTCACTATTTAGTG
2024925 AC
1 AC
2024927 GTTGCAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (46 bp):
ACTGATATATTTTATTCACTACAATTTGATTTGTCACTATTTAGTG
Found at i:2025048 original size:21 final size:21
Alignment explanation
Indices: 2024985--2025048 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
2024975 GTTTTATATG
*
2024985 TTTATGTATTTATATAAAACTT
1 TTTATGTGTTTA-ATAAAACTT
*
2025007 TTT-T-TCG-TTAATACATA-TT
1 TTTATGT-GTTTAATA-AAACTT
2025026 TTTATGTGTTTAATAAAACTT
1 TTTATGTGTTTAATAAAACTT
2025047 TT
1 TT
2025049 CTGGTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 13
0.67 0.06 0.27
Matches are distributed among these distances:
19 8 0.24
20 10 0.30
21 12 0.36
22 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTATGTGTTTAATAAAACTT
Found at i:2025066 original size:41 final size:41
Alignment explanation
Indices: 2024979--2025075 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
2024969 TTGTGTGTTT
* *
2024979 TATATGTTTATGTATTTATATAAAACTTTTTTTCGTTAATA
1 TATATTTTTATGTATTTATATAAAACTTTTTCTCGTTAATA
* * *
2025020 CATATTTTTATGTGTTTA-ATAAAAC-TTTTCTGGTTAATA
1 TATATTTTTATGTATTTATATAAAACTTTTTCTCGTTAATA
2025059 TATATATTTGTATGTAT
1 TATAT-TTT-TATGTAT
2025076 ATTTAATACA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 16 0.34
40 10 0.21
41 21 0.45
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (41 bp):
TATATTTTTATGTATTTATATAAAACTTTTTCTCGTTAATA
Found at i:2025409 original size:11 final size:10
Alignment explanation
Indices: 2025390--2025448 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
2025380 AAAATATGAT
2025390 GGAAATTAGA
1 GGAAATTAGA
2025400 GGAAATTTAGA
1 GGAAA-TTAGA
**
2025411 CTAAATTAGA
1 GGAAATTAGA
2025421 GGAAATTTAGA
1 GGAAA-TTAGA
**
2025432 CTAAATTAGA
1 GGAAATTAGA
2025442 GGAAATT
1 GGAAATT
2025449 TTGAATTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 23 0.59
11 16 0.41
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (10 bp):
GGAAATTAGA
Found at i:2025416 original size:21 final size:21
Alignment explanation
Indices: 2025392--2025449 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
2025382 AATATGATGG
2025392 AAATTAGAGGAAATTTAGACT
1 AAATTAGAGGAAATTTAGACT
2025413 AAATTAGAGGAAATTTAGACT
1 AAATTAGAGGAAATTTAGACT
2025434 AAATTAGAGGAAATTT
1 AAATTAGAGGAAATTT
2025450 TGAATTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (21 bp):
AAATTAGAGGAAATTTAGACT
Found at i:2027213 original size:21 final size:21
Alignment explanation
Indices: 2027187--2027236 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2027177 TTTATTTTCA
2027187 TTAGTTATAACATTTTATCAT
1 TTAGTTATAACATTTTATCAT
2027208 TTAGTTATAACATTTTATCAT
1 TTAGTTATAACATTTTATCAT
2027229 TTAGTTAT
1 TTAGTTAT
2027237 TAATTTCGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (21 bp):
TTAGTTATAACATTTTATCAT
Found at i:2027532 original size:30 final size:29
Alignment explanation
Indices: 2027491--2027554 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2027481 TTTTAATTTG
**
2027491 TAAAAAGATTTGTGTTTTGATTGTAAATT-A
1 TAAAAAGATTTGT-CCTTGATTGT-AATTCA
*
2027521 TAAAAATATTTGTCCTTGATTGTAATTCA
1 TAAAAAGATTTGTCCTTGATTGTAATTCA
2027550 TAAAA
1 TAAAA
2027555 TAAAATATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 14 0.47
30 12 0.40
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (29 bp):
TAAAAAGATTTGTCCTTGATTGTAATTCA
Found at i:2027625 original size:22 final size:22
Alignment explanation
Indices: 2027581--2027625 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2027571 ATAATTTATG
*
2027581 AAAAGATTTATCCTATATTACA
1 AAAAGATTTATCCTATATCACA
2027603 AAAAGATTTATCCGT-TATCACA
1 AAAAGATTTATCC-TATATCACA
2027625 A
1 A
2027626 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAGATTTATCCTATATCACA
Found at i:2029216 original size:17 final size:17
Alignment explanation
Indices: 2029177--2029248 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
2029167 ATTCATGCAT
2029177 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
*
2029194 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* * * *
2029212 CTAGTCCCTTGATCAAA
1 CTAGTTCATTAATTAAA
*
2029229 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
2029246 CTA
1 CTA
2029249 ACTCTAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 32 0.74
18 11 0.26
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:2031164 original size:29 final size:30
Alignment explanation
Indices: 2031128--2031185 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2031118 TTAGAAAATT
* *
2031128 TTGGGGACCACTTGGAA-ATTTTTGAAAAG
1 TTGGGGACCAATTGAAATATTTTTGAAAAG
*
2031157 TTGGGGACCAATTTAAATATTTTTGAAAA
1 TTGGGGACCAATTGAAATATTTTTGAAAA
2031186 ATGATCGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (30 bp):
TTGGGGACCAATTGAAATATTTTTGAAAAG
Found at i:2048213 original size:18 final size:19
Alignment explanation
Indices: 2048185--2048220 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2048175 TTATTTTATT
2048185 AATATATAATTTAAAATTA
1 AATATATAATTTAAAATTA
*
2048204 AATATA-AATTTAGAATT
1 AATATATAATTTAAAATT
2048221 TAGAATTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATATAATTTAAAATTA
Found at i:2056390 original size:2 final size:2
Alignment explanation
Indices: 2056373--2056427 Score: 92
Period size: 2 Copynumber: 26.5 Consensus size: 2
2056363 CAAAACAAAC
2056373 AT AT CAT AT CAT 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
2056417 AT AT AT AT AT A
1 AT AT AT AT AT A
2056428 CACGTTGTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 47 0.92
3 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2058291 original size:12 final size:12
Alignment explanation
Indices: 2058274--2058298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2058264 ATGGACTTTA
2058274 TTATCTTCCAGT
1 TTATCTTCCAGT
2058286 TTATCTTCCAGT
1 TTATCTTCCAGT
2058298 T
1 T
2058299 AATGCCTTGA
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:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATCTTCCAGT
Found at i:2058368 original size:3 final size:3
Alignment explanation
Indices: 2058360--2058412 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
2058350 ATTTTGATTT
* *
2058360 TTA TTA TTAA TTA ATA TTA TTTA TTA TTA TCA TTA TTA TTA -TA TTA
1 TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2058406 TTA TTA T
1 TTA TTA T
2058413 ACCAACACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2058384 original size:20 final size:21
Alignment explanation
Indices: 2058359--2058411 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2058349 TATTTTGATT
2058359 TTTATTATTA-ATTAATATTA
1 TTTATTATTACATTAATATTA
*
2058379 TTTATTATTATCATTATTATTA
1 TTTATTATTA-CATTAATATTA
2058401 TATTATTATTA
1 T-TTATTATTA
2058412 TACCAACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.34
22 10 0.34
23 9 0.31
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATTACATTAATATTA
Found at i:2062336 original size:21 final size:21
Alignment explanation
Indices: 2062307--2062346 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2062297 AAAGTGTGAT
2062307 CCTCATATAGTCCATGTCTGG
1 CCTCATATAGTCCATGTCTGG
*
2062328 CCTCCTATAGTCCATGTCT
1 CCTCATATAGTCCATGTCT
2062347 AACTACAACC
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:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (21 bp):
CCTCATATAGTCCATGTCTGG
Found at i:2062931 original size:7 final size:7
Alignment explanation
Indices: 2062915--2062952 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
2062905 TTTCTTTATA
2062915 TTTT-TT
1 TTTTGTT
2062921 TTTTGTT
1 TTTTGTT
2062928 TTTTGTT
1 TTTTGTT
2062935 TTTTGTT
1 TTTTGTT
2062942 TTTTGTT
1 TTTTGTT
2062949 TTTT
1 TTTT
2062953 TCATTTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTGTT
Found at i:2062972 original size:22 final size:22
Alignment explanation
Indices: 2062947--2063007 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
2062937 TTGTTTTTTG
2062947 TTTTTTTCATTTTTCA-TTTTCC
1 TTTTTTT-ATTTTTCAGTTTTCC
*
2062969 TTTTTTTAATTTTT-AGTTTTTC
1 TTTTTTT-ATTTTTCAGTTTTCC
2062991 TTTCTATTTATTTTTCA
1 TTT-T-TTTATTTTTCA
2063008 AGAATAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 21 0.64
23 7 0.21
24 4 0.12
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTATTTTTCAGTTTTCC
Found at i:2063739 original size:18 final size:18
Alignment explanation
Indices: 2063716--2063758 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2063706 TTCATGAACT
*
2063716 TCTTCAAGTACTTTCTTG
1 TCTTCAAGTACTTTATTG
2063734 TCTTCAAGTACTTTATTG
1 TCTTCAAGTACTTTATTG
*
2063752 GCTTCAA
1 TCTTCAA
2063759 CGTTTTCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (18 bp):
TCTTCAAGTACTTTATTG
Found at i:2067707 original size:20 final size:20
Alignment explanation
Indices: 2067684--2067732 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2067674 TGATCGTTGT
2067684 TGTTGACCATTGACTGTCAC
1 TGTTGACCATTGACTGTCAC
*
2067704 TGTTGACCATTGATTGTCAC
1 TGTTGACCATTGACTGTCAC
2067724 TGTTGACCA
1 TGTTGACCA
2067733 CTGTTGCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (20 bp):
TGTTGACCATTGACTGTCAC
Found at i:2067745 original size:20 final size:20
Alignment explanation
Indices: 2067684--2067748 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
2067674 TGATCGTTGT
* *
2067684 TGTTGACCATTGACTGTCAC
1 TGTTGACCACTGATTGTCAC
*
2067704 TGTTGACCATTGATTGTCAC
1 TGTTGACCACTGATTGTCAC
*
2067724 TGTTGACCACTG-TTGCTGAC
1 TGTTGACCACTGATTG-TCAC
2067744 TGTTG
1 TGTTG
2067749 GTCAATGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 3 0.07
20 38 0.93
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (20 bp):
TGTTGACCACTGATTGTCAC
Found at i:2069483 original size:2 final size:2
Alignment explanation
Indices: 2069476--2069506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2069466 TCATACAAAT
2069476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2069507 TTAGGATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2083517 original size:40 final size:40
Alignment explanation
Indices: 2083459--2083538 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
2083449 ATGATGTATA
* * * *
2083459 AGGTGGGCAAGGCCCGACCTCAGCGCTACGGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAACACTACGGTGCAATATT
*
2083499 AGGTGAGCAAGGCTCGACCTCAACACTACGGTGCAATATT
1 AGGTGAGCAAGGCCCGACCTCAACACTACGGTGCAATATT
2083539 TGATTCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (40 bp):
AGGTGAGCAAGGCCCGACCTCAACACTACGGTGCAATATT
Found at i:2099040 original size:20 final size:20
Alignment explanation
Indices: 2099003--2099046 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2098993 TTGATTCAAT
*
2099003 ATACTGAAGAGGGAGTATCG
1 ATACTGAAGAGGAAGTATCG
*
2099023 ATACTGAAG-GGAAGGTATTG
1 ATACTGAAGAGGAA-GTATCG
2099043 ATAC
1 ATAC
2099047 CATTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (20 bp):
ATACTGAAGAGGAAGTATCG
Found at i:2099525 original size:55 final size:55
Alignment explanation
Indices: 2099461--2099668 Score: 328
Period size: 55 Copynumber: 3.8 Consensus size: 55
2099451 TAAGTGTGTA
2099461 AAAACCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
*
2099517 AAAACTAAGAAATTCATACTAAGTGTATGGATTTCCGTATGGGCACTTTGTGTGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
* * * *
2099572 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCTTATGGGTACTATATGTGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
* * *
2099627 -AAACTAGGAAATTCATACTAAGTGTATGAAGTTCTGTATGGG
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
2099669 AAATATATGT
Statistics
Matches: 142, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
54 38 0.27
55 100 0.70
56 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGC
Found at i:2100098 original size:68 final size:68
Alignment explanation
Indices: 2099886--2100247 Score: 480
Period size: 67 Copynumber: 5.4 Consensus size: 68
2099876 TAACAGAAAT
* * * * *
2099886 GTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTCAGGCCTAACTGT-CATTTGATAGA
1 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATA
2099950 AAG
66 AAG
* * * *
2099953 GTGTCAATTATGACAGTTAGATGAAAGGCTAAGTTCC-TTGAGGACTAATTGTGCATATT-ACAT
1 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCAT-TTGACAT
2100016 AAAG
65 AAAG
* * *
2100020 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTAAAATA
1 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATA
2100085 AAG
66 AAG
* * * * *
2100088 GTGTCAATTATTCCAGTTAGATGAAAGGCTAAATGCCTTTGCGGCCTAACTGTGAATTTTACATA
1 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATA
2100153 AAG
66 AAG
** * *
2100156 GTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGTATTTGATGCCTAACTGTGCATTTGACAGA
1 GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATA
*
2100220 AAT
66 AAG
*
2100223 GTGTCAATTATGCCGGTTAGATGAA
1 GTGTCAATTATGCCAGTTAGATGAA
2100248 CGATTAAATA
Statistics
Matches: 257, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
66 12 0.05
67 137 0.53
68 108 0.42
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (68 bp):
GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATA
AAG
Found at i:2100256 original size:135 final size:135
Alignment explanation
Indices: 2099870--2100247 Score: 517
Period size: 135 Copynumber: 2.8 Consensus size: 135
2099860 TCTAAAATAA
* * * * *
2099870 TGAATTTAACAGAAATGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTCAGGCCTAA
1 TGAATTTTACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAA
* * * *
2099935 CTGT-CATTTGATAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGTTCCTTGAGGACT
66 CTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTGAGGACT
*
2099999 AATTG
131 AACTG
* * *
2100004 TGCATATTACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAA
1 TGAATTTTACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAA
* * * * * *
2100069 CTATGCATTTAAAATAAAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAATGCCTTTGCGGCC
66 CTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCC-TTGAGGAC
2100134 TAACTG
130 TAACTG
* *
2100140 TGAATTTTACATAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGTATTTGATGCCTAA
1 TGAATTTTACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAA
* * *
2100204 CTGTGCATTTGACAGAAATGTGTCAATTATGCCGGTTAGATGAA
66 CTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2100248 CGATTAAATA
Statistics
Matches: 211, Mismatches: 31, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
134 60 0.28
135 114 0.54
136 37 0.18
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (135 bp):
TGAATTTTACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAA
CTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTGAGGACT
AACTG
Found at i:2100335 original size:80 final size:81
Alignment explanation
Indices: 2100198--2100391 Score: 239
Period size: 80 Copynumber: 2.4 Consensus size: 81
2100188 TGTATTTGAT
* * *
2100198 GCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCGGTTAGATGAACGATTAAATA-CGTT
1 GCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCGGTTAGATGAACGATTAAATACCATT
* *
2100262 GAGTAAAAGATTAATA
66 AAGTAAAAGATGAATA
* * ** * *
2100278 GCCTAGTTGTGCATTTGGCAGAAATGTGTCGATTATGCTTGTTAGATGAATGGTTAAATACCATT
1 GCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCGGTTAGATGAACGATTAAATACCATT
*
2100343 AAGTAAAAGATGAATG
66 AAGTAAAAGATGAATA
* *
2100359 GCCTAGCTGTGTATTTGG-AGTAAAGGTGTCAAT
1 GCCTAGCTGTGCATTTGGCAG-AAATGTGTCAAT
2100392 GTTGAGTGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
80 54 0.56
81 42 0.44
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (81 bp):
GCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCGGTTAGATGAACGATTAAATACCATT
AAGTAAAAGATGAATA
Found at i:2106754 original size:21 final size:21
Alignment explanation
Indices: 2106730--2106772 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2106720 AAATACAAGG
2106730 AAAATAAC-AAGTAAAACTAAA
1 AAAATAACGAAGTAAAAC-AAA
*
2106751 AAAATGACGAAGTAAAACAAA
1 AAAATAACGAAGTAAAACAAA
2106772 A
1 A
2106773 TAGCTATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (21 bp):
AAAATAACGAAGTAAAACAAA
Found at i:2108373 original size:22 final size:21
Alignment explanation
Indices: 2108347--2108399 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
2108337 TGTTACAATA
2108347 TTTTTCTTGATTTAGATG-CCT
1 TTTTTCTTGA-TTAGATGCCCT
*
2108368 TTTTTTTACTGATTAGATGCCCT
1 TTTTTCT--TGATTAGATGCCCT
*
2108391 TTTTACTTG
1 TTTTTCTTG
2108400 TCGCAGCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 8 0.31
22 7 0.27
23 11 0.42
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTTTCTTGATTAGATGCCCT
Found at i:2114753 original size:22 final size:21
Alignment explanation
Indices: 2114725--2114769 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
2114715 GTAGATATTC
2114725 AAGAGGAATTCCCTGATGAGAA
1 AAGAGGAATTCCCTGATGA-AA
2114747 AAGAGGAATTCCCTGATGAAA
1 AAGAGGAATTCCCTGATGAAA
2114768 AA
1 AA
2114770 TTTTTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.18
Consensus pattern (21 bp):
AAGAGGAATTCCCTGATGAAA
Found at i:2126473 original size:25 final size:23
Alignment explanation
Indices: 2126443--2126498 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
2126433 ACCCACTTTA
* *
2126443 TTCTTTTCTCTCTCACTGTTTCTCT
1 TTCTTTTCTCT-TCA-TCTTTATCT
*
2126468 TTCTTTCCTCTTCATCTTTATCT
1 TTCTTTTCTCTTCATCTTTATCT
2126491 TT-TTTTCT
1 TTCTTTTCT
2126499 TCCTTTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 3 0.11
25 10 0.37
ACGTcount: A:0.05, C:0.29, G:0.02, T:0.64
Consensus pattern (23 bp):
TTCTTTTCTCTTCATCTTTATCT
Found at i:2135123 original size:21 final size:20
Alignment explanation
Indices: 2135095--2135133 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2135085 CATTGCATGA
*
2135095 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
2135115 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
2135134 GACTTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:2145883 original size:14 final size:14
Alignment explanation
Indices: 2145859--2145892 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2145849 TTGATCAAAT
*
2145859 ATATAATATTTTAAA
1 ATAT-ATATTTGAAA
2145874 ATATATATTTGAAA
1 ATATATATTTGAAA
2145888 ATATA
1 ATATA
2145893 ATAATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
ATATATATTTGAAA
Found at i:2147522 original size:15 final size:16
Alignment explanation
Indices: 2147504--2147542 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
2147494 AAAACAAAAG
2147504 AAATTAAATTAAATT-
1 AAATTAAATTAAATTA
2147519 AAATTAAATTAAATTA
1 AAATTAAATTAAATTA
2147535 AAATTAAA
1 AAATTAAA
2147543 ACATTACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTAAATTAAATTA
Found at i:2156372 original size:2 final size:2
Alignment explanation
Indices: 2156365--2156446 Score: 64
Period size: 2 Copynumber: 42.5 Consensus size: 2
2156355 ATTAACCCAA
* * * *
2156365 AT AT AT AT AT AT AT AT AT AC GT A- AT AT GT ACT -T AT AT GT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
2156405 AT AT AC AC AC A- 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
2156446 A
1 A
2156447 CACAAGTGCA
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
1 4 0.06
2 61 0.92
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2156572 original size:13 final size:13
Alignment explanation
Indices: 2156541--2156579 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2156531 GTCATATCTT
2156541 TTAATATT-TT-A
1 TTAATATTATTAA
*
2156552 TTATTATTATTAA
1 TTAATATTATTAA
2156565 TTAATATTATTAA
1 TTAATATTATTAA
2156578 TT
1 TT
2156580 TACAAGCAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 7 0.29
12 2 0.08
13 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATATTATTAA
Found at i:2159543 original size:2 final size:2
Alignment explanation
Indices: 2159531--2159575 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
2159521 ATAAATAATA
2159531 AT AT GAT 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
2159574 AT
1 AT
2159576 GCCTATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2161573 original size:29 final size:30
Alignment explanation
Indices: 2161540--2161603 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
2161530 ATTATGATAC
* *
2161540 TATAATGTACATTATGCTTATGCAT-TATA
1 TATAATGCACATTATACTTATGCATATATA
2161569 TATAATGCACATTATACTTATGCATATATA
1 TATAATGCACATTATACTTATGCATATATA
2161599 TATAA
1 TATAA
2161604 GTGGCAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (30 bp):
TATAATGCACATTATACTTATGCATATATA
Found at i:2161600 original size:16 final size:16
Alignment explanation
Indices: 2161556--2161600 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
2161546 GTACATTATG
2161556 CTTATGCAT-TATATA
1 CTTATGCATATATATA
* *
2161571 -TAATGCACAT-TATA
1 CTTATGCATATATATA
2161585 CTTATGCATATATATA
1 CTTATGCATATATATA
2161601 TAAGTGGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.43
15 9 0.39
16 4 0.17
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (16 bp):
CTTATGCATATATATA
Found at i:2161752 original size:2 final size:2
Alignment explanation
Indices: 2161747--2161885 Score: 63
Period size: 2 Copynumber: 67.0 Consensus size: 2
2161737 ATAAAGTGTG
* * * *
2161747 TA TA TA TA TA TA AA CTA TA TA TA TA AA CTA TA AA GTA TT TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
2161790 TG TA AA GTA TA T- TA TA TA TA TA TA TA TA TA TA -A AA GTA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
2161832 AA GTA TA -A GTA TA AA GTA TA TA TA TA AA GTA TA -A GTA TA TA TA
1 TA -TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA
2161875 TA TA TA -A TA TA
1 TA TA TA TA TA TA
2161886 AGTGGCAAAG
Statistics
Matches: 103, Mismatches: 19, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
1 5 0.05
2 88 0.85
3 10 0.10
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (2 bp):
TA
Found at i:2161765 original size:13 final size:13
Alignment explanation
Indices: 2161749--2161778 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2161739 AAAGTGTGTA
2161749 TATATATATAAAC
1 TATATATATAAAC
2161762 TATATATATAAAC
1 TATATATATAAAC
2161775 TATA
1 TATA
2161779 AAGTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2161797 original size:15 final size:16
Alignment explanation
Indices: 2161777--2161806 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2161767 ATATAAACTA
2161777 TAAAGTAT-TTATATG
1 TAAAGTATATTATATG
2161792 TAAAGTATATTATAT
1 TAAAGTATATTATAT
2161807 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
TAAAGTATATTATATG
Found at i:2161811 original size:44 final size:42
Alignment explanation
Indices: 2161806--2161886 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
2161796 GTATATTATA
* *
2161806 TATATATATATATATAAAAGTATATA-AAGTATAAGTATAAAG
1 TATATATATAAATAT-AAAGTATATATATGTATAAGTATAAAG
*
2161848 TATATATATAAAGTAT-AAGTATATATATATATAA-TATAA
1 TATATATATAAA-TATAAAGTATATATATGTATAAGTATAA
2161887 GTGGCAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 14 0.41
42 17 0.50
43 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.38
Consensus pattern (42 bp):
TATATATATAAATATAAAGTATATATATGTATAAGTATAAAG
Found at i:2161843 original size:15 final size:15
Alignment explanation
Indices: 2161823--2161872 Score: 72
Period size: 13 Copynumber: 3.6 Consensus size: 15
2161813 ATATATATAA
2161823 AAGTATATAAAGTAT
1 AAGTATATAAAGTAT
2161838 AAG--TATAAAGTAT
1 AAGTATATAAAGTAT
2161851 -A-TATATAAAGTAT
1 AAGTATATAAAGTAT
2161864 AAGTATATA
1 AAGTATATA
2161873 TATATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 20 0.65
14 1 0.03
15 9 0.29
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (15 bp):
AAGTATATAAAGTAT
Found at i:2161884 original size:13 final size:13
Alignment explanation
Indices: 2161747--2161885 Score: 51
Period size: 13 Copynumber: 10.3 Consensus size: 13
2161737 ATAAAGTGTG
2161747 TATATATATATAA
1 TATATATATATAA
2161760 -ACTATATATATAA
1 TA-TATATATATAA
2161773 -ACTATA-A-AGT-A
1 TA-TATATATA-TAA
* *
2161784 TTTATATGTA-AA
1 TATATATATATAA
2161796 GTATATTATATATATA
1 -TATA-TATATATA-A
*
2161812 TATATATATAAAA
1 TATATATATATAA
*
2161825 GTATATAAAGTATAA
1 -TATATATA-TATAA
*
2161840 GTATAAAGTATAT-A
1 -TATATA-TATATAA
*
2161854 TATAAAGTATA-AGTA
1 TATATA-TATATA--A
2161869 TATATATATATAA
1 TATATATATATAA
2161882 TATA
1 TATA
2161886 AGTGGCAAAG
Statistics
Matches: 99, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
11 6 0.06
12 4 0.04
13 38 0.38
14 24 0.24
15 25 0.25
16 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (13 bp):
TATATATATATAA
Found at i:2162441 original size:2 final size:2
Alignment explanation
Indices: 2162424--2162465 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2162414 TCATCTTATT
*
2162424 TA TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2162465 T
1 T
2162466 TAAATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2164398 original size:25 final size:25
Alignment explanation
Indices: 2164370--2164420 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2164360 TTTTGTCTTC
2164370 TTATTAATATAGTAGAAACTCAATT
1 TTATTAATATAGTAGAAACTCAATT
2164395 TTATTAATATAGTAGAAACTCAATT
1 TTATTAATATAGTAGAAACTCAATT
2164420 T
1 T
2164421 AAACATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (25 bp):
TTATTAATATAGTAGAAACTCAATT
Found at i:2167082 original size:22 final size:22
Alignment explanation
Indices: 2167056--2167106 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2167046 TTGGTCAGAG
2167056 TTGACCGGTCAGACCGTTGACC
1 TTGACCGGTCAGACCGTTGACC
* * * *
2167078 TTGACCAGTCTGATCGTTGACT
1 TTGACCGGTCAGACCGTTGACC
2167100 TTGACCG
1 TTGACCG
2167107 AAAAAGTTAA
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:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (22 bp):
TTGACCGGTCAGACCGTTGACC
Found at i:2169174 original size:27 final size:30
Alignment explanation
Indices: 2169143--2169203 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2169133 ATTTCTTTAA
*
2169143 AGAGCG-CTTC-AGGA-AGCGTTTTCTAGG
1 AGAGCGTCTTCTAGGAGAGCGTTATCTAGG
* *
2169170 AGAGCGTTTTCTAGGAGAGCGTTATCTAGT
1 AGAGCGTCTTCTAGGAGAGCGTTATCTAGG
2169200 AGAG
1 AGAG
2169204 AGACAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 3 0.11
29 4 0.14
30 15 0.54
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (30 bp):
AGAGCGTCTTCTAGGAGAGCGTTATCTAGG
Found at i:2169177 original size:15 final size:15
Alignment explanation
Indices: 2169153--2169203 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
2169143 AGAGCGCTTC
2169153 AGGA-AGCGTTTTCT
1 AGGAGAGCGTTTTCT
2169167 AGGAGAGCGTTTTCT
1 AGGAGAGCGTTTTCT
*
2169182 AGGAGAGCGTTATCT
1 AGGAGAGCGTTTTCT
*
2169197 AGTAGAG
1 AGGAGAG
2169204 AGACAACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 4 0.12
15 30 0.88
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (15 bp):
AGGAGAGCGTTTTCT
Found at i:2173883 original size:23 final size:24
Alignment explanation
Indices: 2173853--2173904 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2173843 GTAAGTTACC
2173853 GATTGGTTCATTGGTGAT-A-ATTG
1 GATTGGTTCATTGGT-ATAACATTG
*
2173876 GATTGGTTTATTGGTATAACATTG
1 GATTGGTTCATTGGTATAACATTG
2173900 GATTG
1 GATTG
2173905 ATTTAGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.08
23 15 0.58
24 9 0.35
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.44
Consensus pattern (24 bp):
GATTGGTTCATTGGTATAACATTG
Found at i:2178010 original size:35 final size:36
Alignment explanation
Indices: 2177960--2178079 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 36
2177950 TGGCAACTAA
*
2177960 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATATTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGATAAAT-TTTT
*
2177998 -TTT-TAAAATGGTTTTCAAAGTTTGATAAATTTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGATAAATTTTT
* * * *
2178032 CTTTGAAAAATAGTTTTTCAAAGCTTGATAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGATAAATTTTT
*
2178069 -GTTGAAAAATG
1 CTTTGAAAAATG
2178080 ATAATGGGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
34 4 0.06
35 25 0.35
36 18 0.25
37 24 0.34
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGATAAATTTTT
Found at i:2178074 original size:36 final size:37
Alignment explanation
Indices: 2178009--2178078 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
2177999 TTTAAAATGG
* * *
2178009 TTTTCAAAGTTTGATAAATTTTTCTTTGAAAAATAGT
1 TTTTCAAAGCTTGATAAATGTTTCGTTGAAAAATAGT
*
2178046 TTTTCAAAGCTTGATAGATGTTT-GTTGAAAAAT
1 TTTTCAAAGCTTGATAAATGTTTCGTTGAAAAAT
2178079 GATAATGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 9 0.31
37 20 0.69
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (37 bp):
TTTTCAAAGCTTGATAAATGTTTCGTTGAAAAATAGT
Found at i:2179267 original size:15 final size:15
Alignment explanation
Indices: 2179243--2179274 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2179233 TGGCAGATCC
*
2179243 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
2179258 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
2179273 AA
1 AA
2179275 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:2182691 original size:36 final size:36
Alignment explanation
Indices: 2182577--2182696 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
2182567 TGGCAACCAA
2182577 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
* *
2182614 CTTTG-AAAATGGTTTTCAAAGTTTGATAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
2182649 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
2182686 -GTTGAAAAATG
1 CTTTGAAAAATG
2182697 ATAACGGGAT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 30 0.41
36 18 0.24
37 26 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2183475 original size:18 final size:17
Alignment explanation
Indices: 2183448--2183482 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2183438 GCACCAAGTG
2183448 TGCATCGATGTATGAAA
1 TGCATCGATGTATGAAA
*
2183465 TGCATTCGATGTTTGAAA
1 TGCA-TCGATGTATGAAA
2183483 AAAGCCTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
TGCATCGATGTATGAAA
Found at i:2183577 original size:19 final size:19
Alignment explanation
Indices: 2183553--2183591 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2183543 GAAAATATTC
2183553 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2183572 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2183591 A
1 A
2183592 ATGCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2183588 original size:65 final size:64
Alignment explanation
Indices: 2183447--2183605 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 64
2183437 TGCACCAAGT
* * ***
2183447 GTGCATCGATGTATGAAATGCATTCGATG-TTTGAAAAAAGCCTGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAAGCCAGGTGCATCGATGCATGGAGA
* * **
2183510 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAAGCCAG-GTGCATCGATGCATGGAGA
* * *
2183575 GTGCATCGGTGCATGGAATGCATTTGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
2183606 CAATTAATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 27 0.33
64 11 0.14
65 43 0.53
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAAGCCAGGTGCATCGATGCATGGAGA
Found at i:2184629 original size:21 final size:21
Alignment explanation
Indices: 2184595--2184638 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2184585 CTGGAGGAGG
*
2184595 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
*
2184616 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
2184637 AG
1 AG
2184639 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:2185468 original size:21 final size:23
Alignment explanation
Indices: 2185444--2185489 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2185434 TTAGGAGCTT
*
2185444 GAGGATCAGGATTAGG-T-TGAG
1 GAGGAACAGGATTAGGATGTGAG
*
2185465 GAGGAACGGGATTAGGATGTGAG
1 GAGGAACAGGATTAGGATGTGAG
2185488 GA
1 GA
2185490 ACGGGAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 1 0.05
23 6 0.29
ACGTcount: A:0.30, C:0.04, G:0.46, T:0.20
Consensus pattern (23 bp):
GAGGAACAGGATTAGGATGTGAG
Found at i:2190051 original size:22 final size:21
Alignment explanation
Indices: 2190009--2190048 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2189999 GAGTTTGTTT
*
2190009 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2190030 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2190049 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2192007 original size:19 final size:19
Alignment explanation
Indices: 2191983--2192034 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2191973 AAATAGCCTG
2191983 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
2192002 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
2192021 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2192035 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:2192026 original size:83 final size:84
Alignment explanation
Indices: 2191937--2192101 Score: 235
Period size: 83 Copynumber: 2.0 Consensus size: 84
2191927 GTGCACCAAG
* * *
2191937 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATGGC
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATAGCCAGAGTGCATCGATGCATGGA
**
2192000 TTGTGCATCGATGCATGGCT
65 GAGTGCATCGATGCATGGCT
**
2192020 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAG
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAG
*
2192085 AGTGCATCGGTGCATGG
66 AGTGCATCGATGCATGG
2192102 AATGCATTCG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
83 37 0.51
84 35 0.49
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (84 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAG
AGTGCATCGATGCATGGCT
Found at i:2192088 original size:19 final size:19
Alignment explanation
Indices: 2192064--2192114 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2192054 GAAAATATTC
2192064 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2192083 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2192102 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2192115 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Done.