Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 120 of 208
Found at i:36625859 original size:16 final size:16
Alignment explanation
Indices: 36625838--36625868 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36625828 ACACTCTTCT
36625838 CAATAGGGATCAAACC
1 CAATAGGGATCAAACC
36625854 CAATAGGGATCAAAC
1 CAATAGGGATCAAAC
36625869 TAGCCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (16 bp):
CAATAGGGATCAAACC
Found at i:36635209 original size:60 final size:60
Alignment explanation
Indices: 36635152--36635335 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 60
36635142 AAGGGCATTC
* * * *
36635152 TTTACATTCAGTACTTGCCACAAAGGCTTTCCTATCCAAAGTTTTACTACAAAGGCATCT
1 TTTACATTCAGTACTCGCCACAAAGGCTTTCCTATCCAAAGTTTTTCCACAAAGGCATCA
* ** * *
36635212 TTTACATTCAGTACTCACCACAAATGG-TTTTATGTCTAGAA-TTTTTCCACAAAGGCATCA
1 TTTACATTCAGTACTCGCCACAAA-GGCTTTCCTATCCA-AAGTTTTTCCACAAAGGCATCA
* * * * * *
36635272 TTTATATTTAGCACTCGCCACAAAGGCTTTCCCATCCAGAGTTTTTCCACAAAGGCATCC
1 TTTACATTCAGTACTCGCCACAAAGGCTTTCCTATCCAAAGTTTTTCCACAAAGGCATCA
36635332 TTTA
1 TTTA
36635336 ACTAGTGTTT
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
59 3 0.03
60 93 0.93
61 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (60 bp):
TTTACATTCAGTACTCGCCACAAAGGCTTTCCTATCCAAAGTTTTTCCACAAAGGCATCA
Found at i:36642015 original size:17 final size:18
Alignment explanation
Indices: 36641975--36642017 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
36641965 TTAAAAAACC
*
36641975 ATAAAATTTATAAAAATT
1 ATAAAAGTTATAAAAATT
*
36641993 -TTAAAGTTAT-AAAATT
1 ATAAAAGTTATAAAAATT
36642009 ATAAAAGTT
1 ATAAAAGTT
36642018 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAAAGTTATAAAAATT
Found at i:36648165 original size:25 final size:25
Alignment explanation
Indices: 36648136--36648188 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
36648126 TCATTCATAT
*
36648136 ATAACTAGAAACATTATTAATCACA
1 ATAACTAGAAACATCATTAATCACA
36648161 ATAACTAGAAACATCATTAATCACA
1 ATAACTAGAAACATCATTAATCACA
36648186 ATA
1 ATA
36648189 CAATGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (25 bp):
ATAACTAGAAACATCATTAATCACA
Found at i:36651379 original size:53 final size:53
Alignment explanation
Indices: 36651296--36651452 Score: 260
Period size: 53 Copynumber: 3.0 Consensus size: 53
36651286 AAGAAAGAAT
* *
36651296 AATGTTTGTCAATGCTAGAAAAGACGAAGGTGATGAAATAAAAAGTAATGCAG
1 AATGTTTGTCAATGCTAGAGAAGACGAAGGTGATGAAATACAAAGTAATGCAG
* * *
36651349 AATGTTTCTCAATGCTAGAGAAGACAAAGGTGATGAAATACAAAGTAATGTAG
1 AATGTTTGTCAATGCTAGAGAAGACGAAGGTGATGAAATACAAAGTAATGCAG
*
36651402 AATATTTGTCAATGCTAGAGAAGACGAAGGTGATGAAATACAAAGTAATGC
1 AATGTTTGTCAATGCTAGAGAAGACGAAGGTGATGAAATACAAAGTAATGC
36651453 TCTTCCACAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 95 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (53 bp):
AATGTTTGTCAATGCTAGAGAAGACGAAGGTGATGAAATACAAAGTAATGCAG
Found at i:36652773 original size:23 final size:23
Alignment explanation
Indices: 36652743--36652799 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
36652733 ACGAGTTTTC
* * *
36652743 GATAGATCTTGCATATATGCATT
1 GATAGATCCTGAATATATGAATT
36652766 GATAGATCCTGAATATATGAATT
1 GATAGATCCTGAATATATGAATT
*
36652789 AATAGATCCTG
1 GATAGATCCTG
36652800 GATCTACCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (23 bp):
GATAGATCCTGAATATATGAATT
Found at i:36661099 original size:104 final size:104
Alignment explanation
Indices: 36660914--36661121 Score: 398
Period size: 104 Copynumber: 2.0 Consensus size: 104
36660904 ATATCCTTAA
* *
36660914 GTACTTGTGAAGGACTAAGGATACATTCCTTATATATGGAGGGTAGGAAGAGCTGAGTGTAAAAG
1 GTACCTGTGAAGGACTAAGGATACATTCCTCATATATGGAGGGTAGGAAGAGCTGAGTGTAAAAG
36660979 GTTACACTGATGCCAACTTCTAAACCTACAAGGATGATT
66 GTTACACTGATGCCAACTTCTAAACCTACAAGGATGATT
36661018 GTACCTGTGAAGGACTAAGGATACATTCCTCATATATGGAGGGTAGGAAGAGCTGAGTGTAAAAG
1 GTACCTGTGAAGGACTAAGGATACATTCCTCATATATGGAGGGTAGGAAGAGCTGAGTGTAAAAG
36661083 GTTACACTGATGCCAACTTCTAAACCTACAAGGATGATT
66 GTTACACTGATGCCAACTTCTAAACCTACAAGGATGATT
36661122 CACGATCGCA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (104 bp):
GTACCTGTGAAGGACTAAGGATACATTCCTCATATATGGAGGGTAGGAAGAGCTGAGTGTAAAAG
GTTACACTGATGCCAACTTCTAAACCTACAAGGATGATT
Found at i:36677101 original size:29 final size:29
Alignment explanation
Indices: 36677060--36677166 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
36677050 ACAAACCATT
* *
36677060 CATTTAGCTGAGATAGCCACAAAGGCATC
1 CATTTAACAGAGATAGCCACAAAGGCATC
36677089 CATTTAACAGAGATCA-CCACAAAGGCATC
1 CATTTAACAGAGAT-AGCCACAAAGGCATC
* * * *
36677118 CATCTAACAGAGATAGGCACAAAGACATT
1 CATTTAACAGAGATAGCCACAAAGGCATC
*
36677147 CATTTAACTGAGATAGCCAC
1 CATTTAACAGAGATAGCCAC
36677167 TGTAATACCC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.01
29 65 0.97
30 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (29 bp):
CATTTAACAGAGATAGCCACAAAGGCATC
Found at i:36680532 original size:22 final size:22
Alignment explanation
Indices: 36680468--36680532 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
36680458 TGCCTGTAAC
*
36680468 CAGAATGGCTACCAGCCGTAAA
1 CAGAATGGCTACCAGCCATAAA
* * * * *
36680490 TAGGATAGCTA-TAACCTATAAA
1 CAGAATGGCTACCAGCC-ATAAA
36680512 CAGAATGGCTACCAGCCATAA
1 CAGAATGGCTACCAGCCATAA
36680533 GTACAGTAAT
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
21 3 0.10
22 24 0.80
23 3 0.10
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTACCAGCCATAAA
Found at i:36680597 original size:32 final size:32
Alignment explanation
Indices: 36680525--36680725 Score: 219
Period size: 32 Copynumber: 6.3 Consensus size: 32
36680515 AATGGCTACC
* * *
36680525 AGCCATAAGT-ACAGTAATATCATTGGCACAA
1 AGCCATCAGTAACAGTAATATGATCGGCACAA
* * * *
36680556 AGCCATCAGTAGCAGTGATATGATCGACACAC
1 AGCCATCAGTAACAGTAATATGATCGGCACAA
* * *
36680588 AGCCATCAGTAACGGTAATATGATCGGTACAT
1 AGCCATCAGTAACAGTAATATGATCGGCACAA
* * *
36680620 AGCTATCAG-AACGGTAATATGATCAGCACAA
1 AGCCATCAGTAACAGTAATATGATCGGCACAA
* *
36680651 AGCCATCAGTAACAATAATATGATCGGTACAA
1 AGCCATCAGTAACAGTAATATGATCGGCACAA
* *
36680683 AGCCATCAGTAAC-GATAACATGATCGGTACAA
1 AGCCATCAGTAACAG-TAATATGATCGGCACAA
36680715 AGCCATCAGTA
1 AGCCATCAGTA
36680726 GCATTGCAGC
Statistics
Matches: 143, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
31 36 0.25
32 107 0.75
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
AGCCATCAGTAACAGTAATATGATCGGCACAA
Found at i:36680640 original size:63 final size:64
Alignment explanation
Indices: 36680525--36680725 Score: 212
Period size: 63 Copynumber: 3.2 Consensus size: 64
36680515 AATGGCTACC
* * * * * * * *
36680525 AGCCATAAGT-ACAGTAATATCATTGGCACAAAGCCATCAGTAGC-AGTGATATGATCGACACAC
1 AGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGA-TAATATGATCGACACAA
** * * *
36680588 AGCCATCAGTAACGGTAATATGATCGGTACATAGCTATCAG-AACGGTAATATGATC-AGCACAA
1 AGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGA-CACAA
* **
36680651 AGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGATAACATGATCGGTACAA
1 AGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGACACAA
36680715 AGCCATCAGTA
1 AGCCATCAGTA
36680726 GCATTGCAGC
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
62 1 0.01
63 61 0.54
64 52 0.46
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (64 bp):
AGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGACACAA
Found at i:36680706 original size:95 final size:95
Alignment explanation
Indices: 36680550--36680723 Score: 258
Period size: 95 Copynumber: 1.8 Consensus size: 95
36680540 AATATCATTG
* * * * * *
36680550 GCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATCAGTAACGGTAATATGATCGG
1 GCACAAAGCCATCAGTAACAATAATATGATCGACACAAAGCCATCAGTAACGATAACATGATCGG
* *
36680615 TACATAGCTATCAGAACGGTAATATGATCA
66 TACAAAGCCATCAGAACGGTAATATGATCA
**
36680645 GCACAAAGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAACGATAACATGATCGG
1 GCACAAAGCCATCAGTAACAATAATATGATCGACACAAAGCCATCAGTAACGATAACATGATCGG
36680710 TACAAAGCCATCAG
66 TACAAAGCCATCAG
36680724 TAGCATTGCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 69 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (95 bp):
GCACAAAGCCATCAGTAACAATAATATGATCGACACAAAGCCATCAGTAACGATAACATGATCGG
TACAAAGCCATCAGAACGGTAATATGATCA
Found at i:36680896 original size:11 final size:11
Alignment explanation
Indices: 36680880--36680922 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
36680870 AATCAGTCAT
36680880 ACAAATCATAG
1 ACAAATCATAG
*
36680891 ACAAATCAGTCAT
1 ACAAATCA-T-AG
*
36680904 ACCAATCATAG
1 ACAAATCATAG
36680915 ACAAATCA
1 ACAAATCA
36680923 ATCATTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 16 0.62
12 2 0.08
13 8 0.31
ACGTcount: A:0.51, C:0.23, G:0.07, T:0.19
Consensus pattern (11 bp):
ACAAATCATAG
Found at i:36680902 original size:24 final size:24
Alignment explanation
Indices: 36680870--36680927 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
36680860 CCATGCTCAG
36680870 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
*
36680894 AATCAGTCATACCAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
*
36680918 AATCAATCAT
1 AATCAGTCAT
36680928 TTACACTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:36680951 original size:26 final size:27
Alignment explanation
Indices: 36680917--36680969 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
36680907 AATCATAGAC
36680917 AAATCAATCATTTACACTCGAGGGGCA
1 AAATCAATCATTTACACTCGAGGGGCA
* *
36680944 AAAT-AATCATTTACCCTCTAGGGGCA
1 AAATCAATCATTTACACTCGAGGGGCA
36680970 TTACGATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (27 bp):
AAATCAATCATTTACACTCGAGGGGCA
Found at i:36681188 original size:54 final size:54
Alignment explanation
Indices: 36680953--36681289 Score: 317
Period size: 54 Copynumber: 6.3 Consensus size: 54
36680943 AAAATAATCA
* * * ** * *
36680953 TTTACCCT-CTAGGGGCATTACGATCATTTTACCCTA-TGGAGATATTTCAGTCAT
1 TTTACCCTAC-AGGGGCATTACGGTCATTTTACCTTACAGG-GGCATTACGGTCAT
* * *
36681007 TTTACCCTACAAGGGTATTATGGTCATTTTACCTTACAGGGGCATTACGGTCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCAT
* * * * * *
36681061 TTTACCTTACA-GGGCATTGCGGTCATTTTACCCTA-TGAGGG-TTTTCGGTCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAG-GGGCATTACGGTCAT
* * * *
36681113 TTTACTCTACAGGGGAATTACGGTCATTTTACCTTACAGGGGCGTTACGGTTAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCAT
** * ** * *
36681167 TTTACCCTATGGGGGCATTACGGTCATTTTATCC-TATAGGGGGTTTTCGATCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTA-CCTTACAGGGGCATTACGGTCAT
* * *
36681221 TTTACCCTACAGGGGCATTACGGTCATTCTACCTTACGGGGGCATTACGATCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCAT
36681275 TTTACCCTACGAGGG
1 TTTACCCTAC-AGGG
36681290 CGTAACAGTC
Statistics
Matches: 229, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
52 19 0.08
53 49 0.21
54 152 0.66
55 9 0.04
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (54 bp):
TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGCATTACGGTCAT
Found at i:36681225 original size:81 final size:80
Alignment explanation
Indices: 36681002--36681289 Score: 310
Period size: 81 Copynumber: 3.6 Consensus size: 80
36680992 AGATATTTCA
*** * * * *
36681002 GTCATTTTACCCTACAAGGGTATTATGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTACC
1 GTCATTTTACCCTATGGGGGCATTACGGTCATTTTACC-TACAGGGGAATTACGATCATTTTACC
*
36681067 TTACA-GGGCATTGCG
65 TTACAGGGGCATTACG
* * * *
36681082 GTCATTTTACCCTATGAGGG-TTTTCGGTCATTTTACTCTACAGGGGAATTACGGTCATTTTACC
1 GTCATTTTACCCTATGGGGGCATTACGGTCATTTTAC-CTACAGGGGAATTACGATCATTTTACC
*
36681146 TTACAGGGGCGTTACG
65 TTACAGGGGCATTACG
* * ** *
36681162 GTTATTTTACCCTATGGGGGCATTACGGTCATTTTATCCTATAGGGGGTTTTCGATCATTTTACC
1 GTCATTTTACCCTATGGGGGCATTACGGTCATTTTA-CCTACAGGGGAATTACGATCATTTTACC
*
36681227 CTACAGGGGCATTACG
65 TTACAGGGGCATTACG
* * * *
36681243 GTCATTCTACCTTACGGGGGCATTACGATCATTTTACCCTACGAGGG
1 GTCATTTTACCCTATGGGGGCATTACGGTCATTTTA-CCTAC-AGGG
36681290 CGTAACAGTC
Statistics
Matches: 177, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 43 0.24
80 45 0.25
81 84 0.47
82 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (80 bp):
GTCATTTTACCCTATGGGGGCATTACGGTCATTTTACCTACAGGGGAATTACGATCATTTTACCT
TACAGGGGCATTACG
Found at i:36681290 original size:27 final size:26
Alignment explanation
Indices: 36680965--36681308 Score: 260
Period size: 27 Copynumber: 12.8 Consensus size: 26
36680955 TACCCTCTAG
* *
36680965 GGGCATTACGATCATTTTACCCTA-T
1 GGGCATTACGGTCATTTTACCCTACA
* * *
36680990 GGAGATATTTCAGTCATTTTACCCTACAA
1 GG-G-CATTACGGTCATTTTACCCTAC-A
* * *
36681019 GGGTATTATGGTCATTTTACCTTACA
1 GGGCATTACGGTCATTTTACCCTACA
*
36681045 GGGGCATTACGGTCATTTTACCTTACA
1 -GGGCATTACGGTCATTTTACCCTACA
* *
36681072 GGGCATTGCGGTCATTTTACCCTATGA
1 GGGCATTACGGTCATTTTACCCTA-CA
* * *
36681099 GGG-TTTTCGGTCATTTTACTCTACA
1 GGGCATTACGGTCATTTTACCCTACA
* *
36681124 GGGGAATTACGGTCATTTTACCTTACA
1 -GGGCATTACGGTCATTTTACCCTACA
* * **
36681151 GGGGCGTTACGGTTATTTTACCCTATGG
1 -GGGCATTACGGTCATTTTACCCTA-CA
* *
36681179 GGGCATTACGGTCATTTTATCCTATA
1 GGGCATTACGGTCATTTTACCCTACA
** * *
36681205 GGGGGTTTTCGATCATTTTACCCTACA
1 -GGGCATTACGGTCATTTTACCCTACA
* * *
36681232 GGGGCATTACGGTCATTCTACCTTACGG
1 -GGGCATTACGGTCATTTTACCCTAC-A
*
36681260 GGGCATTACGATCATTTTACCCTACGA
1 GGGCATTACGGTCATTTTACCCTAC-A
* * * *
36681287 GGGCGTAACAGTCATTATACCC
1 GGGCATTACGGTCATTTTACCC
36681309 CATCACATAC
Statistics
Matches: 253, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
25 3 0.01
26 44 0.17
27 203 0.80
28 1 0.00
29 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (26 bp):
GGGCATTACGGTCATTTTACCCTACA
Found at i:36688399 original size:18 final size:19
Alignment explanation
Indices: 36688378--36688417 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
36688368 TAAATTATTT
36688378 AAATTAATTTAAT-AAATA
1 AAATTAATTTAATGAAATA
* *
36688396 AAATTGATTTTATGAAATA
1 AAATTAATTTAATGAAATA
36688415 AAA
1 AAA
36688418 ACATGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATTAATTTAATGAAATA
Found at i:36689575 original size:13 final size:13
Alignment explanation
Indices: 36689557--36689595 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
36689547 ATAAACTCTA
36689557 TTTCCAAGTTATG
1 TTTCCAAGTTATG
*
36689570 TTTCCAAGATATG
1 TTTCCAAGTTATG
*
36689583 TTTTCAAGTTATG
1 TTTCCAAGTTATG
36689596 CTGTATACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTCCAAGTTATG
Found at i:36691003 original size:25 final size:25
Alignment explanation
Indices: 36690969--36691047 Score: 140
Period size: 25 Copynumber: 3.2 Consensus size: 25
36690959 TAGGGTTACT
36690969 GATTTATGGCTCGTGAGAGCATACC
1 GATTTATGGCTCGTGAGAGCATACC
*
36690994 GATTTATGGCTCGTGAGAGCCTACC
1 GATTTATGGCTCGTGAGAGCATACC
*
36691019 GATTTATAGCTCGTGAGAGCATACC
1 GATTTATGGCTCGTGAGAGCATACC
36691044 GATT
1 GATT
36691048 CACAACTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (25 bp):
GATTTATGGCTCGTGAGAGCATACC
Found at i:36700207 original size:20 final size:20
Alignment explanation
Indices: 36700179--36700225 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
36700169 ATTATTCGAG
*
36700179 CCTTTGAGGACTTAGAAACA
1 CCTTAGAGGACTTAGAAACA
*
36700199 CCTTAGAGGCCTTAGAAACA
1 CCTTAGAGGACTTAGAAACA
36700219 CCTTAGA
1 CCTTAGA
36700226 AATGATTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
CCTTAGAGGACTTAGAAACA
Found at i:36704556 original size:43 final size:43
Alignment explanation
Indices: 36704495--36704674 Score: 202
Period size: 43 Copynumber: 4.2 Consensus size: 43
36704485 GGAGGAAGAG
36704495 TTGGTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAAT
1 TTGGTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAAT
* * * * *
36704538 TTGGTGGTTTACCCACAACTTACATGGCAGCTTGTCTGCAAAAT
1 TTGGTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGC-GAAT
* * * *
36704582 TT-GTGGTTTATTCACAACCTACATGGTAGCTTGTCTGTGCAT
1 TTGGTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAAT
* * * *
36704624 TTGGTGGTTTGTCCACAACCTACAAGGCT-GCTTGTTTGCGATT
1 TTGGTGGTTTATCCACAACCTAC-AGGGTAGCTTGTCTGCGAAT
36704667 ATTGGTGG
1 -TTGGTGG
36704675 CTTCATCTAC
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
42 4 0.04
43 94 0.83
44 15 0.13
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (43 bp):
TTGGTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAAT
Found at i:36704657 original size:86 final size:86
Alignment explanation
Indices: 36704498--36704658 Score: 241
Period size: 86 Copynumber: 1.9 Consensus size: 86
36704488 GGAAGAGTTG
* *
36704498 GTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAATTTGGTGGTTTACCCACAACTTACAT
1 GTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAATTTGGTGGTTTACCCACAACCTACAA
36704563 GGCAGCTTGTCTGCAAAATTT
66 GGCAGCTTGTCTGCAAAATTT
* * * * **
36704584 GTGGTTTATTCACAACCTACATGGTAGCTTGTCTGTGCATTTGGTGGTTTGTCCACAACCTACAA
1 GTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAATTTGGTGGTTTACCCACAACCTACAA
*
36704649 GGCTGCTTGT
66 GGCAGCTTGT
36704659 TTGCGATTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (86 bp):
GTGGTTTATCCACAACCTACAGGGTAGCTTGTCTGCGAATTTGGTGGTTTACCCACAACCTACAA
GGCAGCTTGTCTGCAAAATTT
Found at i:36708572 original size:43 final size:43
Alignment explanation
Indices: 36708448--36708574 Score: 182
Period size: 43 Copynumber: 3.0 Consensus size: 43
36708438 AAGGAGGAAG
* *
36708448 AATTGTTGGTTTATCCACAACCTACATGGCAACTTGTCCGCAA
1 AATTGGTGGTTTATCCACAACCTACATGGCAACTTGTCTGCAA
36708491 AATTGGTGGTTTATCCACAACCTACATGGCAACTTGTCTGCAA
1 AATTGGTGGTTTATCCACAACCTACATGGCAACTTGTCTGCAA
* ** * * *
36708534 ATTTGGTGGTTTATGTACAACCAACATAGCAGCTTGTCTGC
1 AATTGGTGGTTTATCCACAACCTACATGGCAACTTGTCTGC
36708575 GATTATTGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
AATTGGTGGTTTATCCACAACCTACATGGCAACTTGTCTGCAA
Found at i:36709687 original size:38 final size:38
Alignment explanation
Indices: 36709636--36709712 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
36709626 TTTTATCGTC
* *
36709636 ATATGAGTTTGTTCTACGGCGACCCTTGTATGTTTGCA
1 ATATGAGTTTGTTCTACAGCAACCCTTGTATGTTTGCA
*
36709674 ATATGAGTTTGTTCTACAGCAATCCTTGTATGTTTGCA
1 ATATGAGTTTGTTCTACAGCAACCCTTGTATGTTTGCA
36709712 A
1 A
36709713 CCCTATTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (38 bp):
ATATGAGTTTGTTCTACAGCAACCCTTGTATGTTTGCA
Found at i:36710969 original size:40 final size:40
Alignment explanation
Indices: 36710911--36711099 Score: 272
Period size: 40 Copynumber: 4.8 Consensus size: 40
36710901 AATTATTGTA
36710911 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
* **
36710951 TGAATGCACACACATGCCCCTGTTTGTACTTCGGTACCCT
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
* *
36710991 TGAATGCACATATGTGCCCCTATTTGTACTTCGGTGCCCT
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
* * *
36711031 TGAATGCACATGTGTGCCGCTGTTTGTACTTCGGTATCC-
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
* * *
36711070 TGAATGCACTTTTGTGCCCCTGTTTATACT
1 TGAATGCACATATGTGCCCCTGTTTGTACT
36711100 CCAGTAACTC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 26 0.20
40 106 0.80
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (40 bp):
TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCT
Found at i:36722850 original size:45 final size:45
Alignment explanation
Indices: 36722791--36722883 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
36722781 AAGGACACAA
36722791 CTTAGCCTGTTGAATGATGCATCCGTGTATACTCTATACTCAACT
1 CTTAGCCTGTTGAATGATGCATCCGTGTATACTCTATACTCAACT
36722836 CTTAGCCTGTTGAATGATGCATCCGTGTATACTCTATACTCAACT
1 CTTAGCCTGTTGAATGATGCATCCGTGTATACTCTATACTCAACT
36722881 CTT
1 CTT
36722884 GGCTCGGGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (45 bp):
CTTAGCCTGTTGAATGATGCATCCGTGTATACTCTATACTCAACT
Found at i:36727720 original size:28 final size:27
Alignment explanation
Indices: 36727680--36727737 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
36727670 GTACTGATAT
* *
36727680 TGTATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTAGGCTAAGGCCCACACTG-TAC
36727708 TGTATTAGGCTAAGGCCCACACTGTAC
1 TGTATTAGGCTAAGGCCCACACTGTAC
36727735 TGT
1 TGT
36727738 TACTGAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (27 bp):
TGTATTAGGCTAAGGCCCACACTGTAC
Found at i:36727739 original size:33 final size:33
Alignment explanation
Indices: 36727666--36727765 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
36727656 TGCATTATTT
* * *
36727666 CACTGTACTGATATTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTAGGCTAAGGCCCA
36727699 CA---T--TGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTAGGCTAAGGCCCA
* *
36727727 CACTGTACTGTTACTG-AATAGGGCTCAGGCCCA
1 CACTGTACTGTTACTGTATTA-GGCTAAGGCCCA
*
36727760 GACTGT
1 CACTGT
36727766 TATAACATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
28 24 0.44
30 1 0.02
31 1 0.02
32 3 0.05
33 26 0.47
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTAGGCTAAGGCCCA
Found at i:36737254 original size:20 final size:22
Alignment explanation
Indices: 36737215--36737254 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36737205 GAAAAATATT
*
36737215 AAATATATATATTTTATTTTTA
1 AAATATATATAGTTTATTTTTA
36737237 AAATATA-ATAGTTT-TTTT
1 AAATATATATAGTTTATTTT
36737255 ATTTTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
AAATATATATAGTTTATTTTTA
Found at i:36737389 original size:59 final size:59
Alignment explanation
Indices: 36737326--36737495 Score: 286
Period size: 59 Copynumber: 2.9 Consensus size: 59
36737316 TCAAGTTTGT
* *
36737326 TTTACTAATCAAATGTTAGATTTTGTGACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
36737385 TTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* * *
36737444 TTTACTAATCAAATATTAGATTTTATTACAACAATTAATAAAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
36737496 AGTAATTTGA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 104 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:36737527 original size:16 final size:16
Alignment explanation
Indices: 36737506--36737547 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
36737496 AGTAATTTGA
*
36737506 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
36737522 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
36737538 TAGTTTTAAT
1 TAATTTTAAT
36737548 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:36737531 original size:22 final size:23
Alignment explanation
Indices: 36737523--36737582 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
36737513 ACTAACAATT
* * *
36737523 AATTTTA-ATAACAATTAGTTTT
1 AATTTTATATAAAAAATAATTTT
*
36737545 AATTTTATTTAAAAAATAATTTT
1 AATTTTATATAAAAAATAATTTT
*
36737568 AATTTTA-ATTAAAAA
1 AATTTTATATAAAAAA
36737583 CGGACCGGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTTTATATAAAAAATAATTTT
Found at i:36738185 original size:27 final size:27
Alignment explanation
Indices: 36738153--36738285 Score: 205
Period size: 27 Copynumber: 5.0 Consensus size: 27
36738143 CAATAAATGA
36738153 GAAATACCCCCATAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
*
36738180 GAAATACCCCTATAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
* **
36738207 GAAATACCCCCATAGAGTAAAATGATT
1 GAAATACCCCCATAGGGTAAAATGACC
*
36738234 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
*
36738261 GAAATA-CCCCATAAGGTAAAATGAC
1 GAAATACCCCCATAGGGTAAAATGAC
36738286 TGTTATACCC
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 18 0.18
27 80 0.82
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACC
Found at i:36738524 original size:26 final size:26
Alignment explanation
Indices: 36738476--36738529 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
36738466 TTGCCACATT
* *
36738476 TACTGTTACTGGCAGCTTCGCTGTGA
1 TACTATTACTGGCAGCTTCGCTGCGA
* *
36738502 TACTATTACTGGCAGTTTTGCTGCGA
1 TACTATTACTGGCAGCTTCGCTGCGA
36738528 TA
1 TA
36738530 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTCGCTGCGA
Found at i:36745439 original size:27 final size:27
Alignment explanation
Indices: 36745409--36745464 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
36745399 AATAAATGAT
* *
36745409 TGAAATACCCCCATAGTGTAAAACGAC
1 TGAAATACCCACATAGGGTAAAACGAC
*
36745436 TGAAATACCCACATAGGGTAAAATGAC
1 TGAAATACCCACATAGGGTAAAACGAC
36745463 TG
1 TG
36745465 TTATACTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (27 bp):
TGAAATACCCACATAGGGTAAAACGAC
Found at i:36745470 original size:27 final size:26
Alignment explanation
Indices: 36745417--36745495 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
36745407 ATTGAAATAC
* * **
36745417 CCCCATAGTGTAAAACGACTGAAATA
1 CCCCATAGGGTAAAATGACTGTTATA
36745443 CCCACATAGGGTAAAATGACTGTTATA
1 CCC-CATAGGGTAAAATGACTGTTATA
* *
36745470 CTCC-TAGGAGATGAAATGACTGTTAT
1 CCCCATAGG-G-TAAAATGACTGTTAT
36745496 GGCCTTATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.09
26 5 0.11
27 35 0.80
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (26 bp):
CCCCATAGGGTAAAATGACTGTTATA
Found at i:36745705 original size:26 final size:26
Alignment explanation
Indices: 36745652--36745705 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
36745642 TTGCCACATT
* *
36745652 TACTGTTACTGACAGCTTCACTGTGA
1 TACTATTACTGACAGCTTCACTGCGA
*
36745678 TACTATTACTGGCAGCTTTC-CTGCGA
1 TACTATTACTGACAGC-TTCACTGCGA
36745704 TA
1 TA
36745706 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (26 bp):
TACTATTACTGACAGCTTCACTGCGA
Found at i:36745855 original size:28 final size:27
Alignment explanation
Indices: 36745808--36745873 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
36745798 ATTGCACGGT
36745808 ACTGATACTGTATTGAGCTAAGGCCCAC
1 ACTG-TACTGTATTGAGCTAAGGCCCAC
* *
36745836 ATTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTG-TACTGTATTGAGCTAAGGCCCAC
36745864 ACTGTACTGT
1 ACTGTACTGT
36745874 TACTGAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (27 bp):
ACTGTACTGTATTGAGCTAAGGCCCAC
Found at i:36745875 original size:33 final size:31
Alignment explanation
Indices: 36745806--36745895 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 31
36745796 TCATTGCACG
* *
36745806 GTACTGATACTGTATTGAGCTAAGGCCCACA
1 GTACTGTTACTGTATTGGGCTAAGGCCCACA
36745837 -T--TGTTACTGTATTGGGCTAAGGCCCACA
1 GTACTGTTACTGTATTGGGCTAAGGCCCACA
* *
36745865 CTGTACTGTTACTGAATAGGGCTCAA-GCCCA
1 --GTACTGTTACTGTATTGGGCT-AAGGCCCA
36745896 AAATGTCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
28 25 0.51
30 1 0.02
31 1 0.02
33 20 0.41
34 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (31 bp):
GTACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:36746993 original size:3 final size:3
Alignment explanation
Indices: 36746985--36747019 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
36746975 TAGAGTATAG
*
36746985 GTT GTT GTT GTT GTT GTT GTT GTT GTA GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
36747020 GAATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.34, T:0.63
Consensus pattern (3 bp):
GTT
Found at i:36748789 original size:14 final size:15
Alignment explanation
Indices: 36748763--36748800 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
36748753 ATGTTTCACA
*
36748763 TCCTTCGTTCTCTTT
1 TCCTTCTTTCTCTTT
36748778 TCC-TCTTTCTCTTT
1 TCCTTCTTTCTCTTT
36748792 TCCTTCTTT
1 TCCTTCTTT
36748801 TTTCCTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (15 bp):
TCCTTCTTTCTCTTT
Found at i:36753747 original size:7 final size:7
Alignment explanation
Indices: 36753735--36753762 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
36753725 GATAAATCTT
36753735 TTGGTCA
1 TTGGTCA
36753742 TTGGTCA
1 TTGGTCA
36753749 TTGGTCA
1 TTGGTCA
36753756 TTGGTCA
1 TTGGTCA
36753763 AAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (7 bp):
TTGGTCA
Found at i:36769484 original size:22 final size:22
Alignment explanation
Indices: 36769434--36769484 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
36769424 CGCAATGTAA
36769434 TATATTTATAAATAATGAAAAT
1 TATATTTATAAATAATGAAAAT
* *
36769456 T-TAATTTAATATATAGT-AAAAT
1 TAT-ATTT-ATAAATAATGAAAAT
36769478 TATATTT
1 TATATTT
36769485 CGGTTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATTTATAAATAATGAAAAT
Found at i:36771970 original size:2 final size:2
Alignment explanation
Indices: 36771963--36771994 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36771953 ATAATTATTC
36771963 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
36771995 CTTTGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36773064 original size:23 final size:23
Alignment explanation
Indices: 36773012--36773066 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
36773002 AATTTTAATA
*
36773012 ATATTATTTATTAATTCAATTTT
1 ATATTATTTATTAACTCAATTTT
*
36773035 ATTTTATTTAATT-ACTCAATATTT
1 ATATTATTT-ATTAACTCAAT-TTT
36773059 -TATTATTT
1 ATATTATTT
36773067 CTTTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTATTTATTAACTCAATTTT
Found at i:36776734 original size:20 final size:20
Alignment explanation
Indices: 36776709--36776750 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
36776699 CAGAAAATAA
36776709 TTTTTGGAAAAT-TAATTATT
1 TTTTTGGAAAATCTAA-TATT
36776729 TTTTTGGAAAATCTAATATT
1 TTTTTGGAAAATCTAATATT
36776749 TT
1 TT
36776751 CTGGCGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTTTGGAAAATCTAATATT
Found at i:36778980 original size:43 final size:42
Alignment explanation
Indices: 36778933--36779077 Score: 166
Period size: 43 Copynumber: 3.4 Consensus size: 42
36778923 AGACTAAGAG
* * *
36778933 CTTTAACGGCGTTTTTAATATAACCGCCGCTATAGAT-TGGTGT
1 CTTTAGCGGCGTTTTT-ATATAAGCGCCGCTATAGATCAGG-GT
* *
36778976 CTTTAGTGGCGTTTTCTAGATAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTT-TATATAAGCGCCGCTATAGATCAGGGT
* * *
36779019 CTTTAGCGGCGTTTTTTCTATAAGCGCCGCTATAGATCATGGC
1 CTTTAGCGGCG-TTTTTATATAAGCGCCGCTATAGATCAGGGT
*
36779062 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
36779078 GCCAAAAACG
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
42 4 0.05
43 77 0.88
44 7 0.08
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTATATAAGCGCCGCTATAGATCAGGGT
Found at i:36779090 original size:43 final size:42
Alignment explanation
Indices: 36778957--36779267 Score: 155
Period size: 43 Copynumber: 7.2 Consensus size: 42
36778947 TTAATATAAC
* * *
36778957 CGCCGCTATAGAT--TGGTGTCTTTAGTGGCG-TTTTCTAGATAAG
1 CGCCGCTATAGATCAT-G-GTCTTTAGCGGCGCTTTTCCA-A-AAA
* * * * *
36779000 CGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTTTTCTATAAG
1 CGCCGCTATAGATCATGGTCTTTAGCGGCG-CTTTTCCAAAAA
*
36779043 CGCCGCTATAGATCATGGCCTTTAGCGGCGCTTTTGCCAAAAA
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTT-CCAAAAA
* * * * *
36779086 CGCCG-TAATAGACCCTGATCTATAGCGGCGCTTATCCAGAAAA
1 CGCCGCT-ATAGATCATGGTCTTTAGCGGCGCTTTTCCA-AAAA
* * * * * * *
36779129 CGCCGCAATAGACCCTGATCTATAGCAGCGCTTATCCAGAAAA
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCA-AAAA
* * * * * **
36779172 CGCCGCTAAATACCCTTTGTCTATATAGCGGCGCTTCGCGCAAAAA
1 CGCCGCTATAGA-TCATGGTCT-T-TAGCGGCGCTTTTC-CAAAAA
* * ** * *
36779218 CGCCGCTAAAGA-CCTAATCTATAACGGCGCTTTTACCAAAAA
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTT-CCAAAAA
36779260 CGCCGCTA
1 CGCCGCTA
36779268 AATTTGGCAG
Statistics
Matches: 220, Mismatches: 35, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
42 32 0.15
43 141 0.64
44 12 0.05
45 7 0.03
46 26 0.12
47 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (42 bp):
CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCAAAAA
Found at i:36779231 original size:89 final size:88
Alignment explanation
Indices: 36779106--36779270 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 88
36779096 GACCCTGATC
* * *
36779106 TATAGCGGCGCTTATCCAGAAAACGCCGCAATAGACCCTGATCTATAGCAGCGCTTAT-CCAGAA
1 TATAGCGGCGCTTAGCCAGAAAACGCCGCAATAGA-CCTAATCTATAACAGCGCTTATACCA-AA
36779170 AACGCCGCTAAATACCCTTTGTCTA
64 AACGCCGCTAAATACCCTTTGTCTA
* * *
36779195 TATAGCGGCGCTTCGCGCA-AAAACGCCGCTAA-AGACCTAATCTATAACGGCGCTTTTACCAAA
1 TATAGCGGCGCTTAGC-CAGAAAACGCCGC-AATAGACCTAATCTATAACAGCGCTTATACCAAA
36779258 AACGCCGCTAAAT
64 AACGCCGCTAAAT
36779271 TTGGCAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
88 33 0.49
89 30 0.45
90 4 0.06
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (88 bp):
TATAGCGGCGCTTAGCCAGAAAACGCCGCAATAGACCTAATCTATAACAGCGCTTATACCAAAAA
CGCCGCTAAATACCCTTTGTCTA
Found at i:36779270 original size:88 final size:85
Alignment explanation
Indices: 36779068--36779270 Score: 218
Period size: 88 Copynumber: 2.3 Consensus size: 85
36779058 TGGCCTTTAG
* *
36779068 CGGCGCTTTTGCCAAAAACGCCG-TAATAGACCCTGATCTATAGCGGCGCTTATCCAGAAAACGC
1 CGGCGCTTTT-CCAAAAACGCCGCTAA-ATACCCTGATCTATAGCGGCGCTTAGCCAGAAAACGC
* *
36779132 CGCAATAGACCCTGATCTATAG
64 CGCAATAGACCCTAATCTATAA
* * *
36779154 CAGCGCTTATCCAGAAAACGCCGCTAAATACCCTTTG-TCTATATAGCGGCGCTTCGCGCA-AAA
1 CGGCGCTTTTCCA-AAAACGCCGCTAAATACCC--TGATC--TATAGCGGCGCTTAGC-CAGAAA
36779217 ACGCCGCTAA-AGA-CCTAATCTATAA
60 ACGCCGC-AATAGACCCTAATCTATAA
36779242 CGGCGCTTTTACCAAAAACGCCGCTAAAT
1 CGGCGCTTTT-CCAAAAACGCCGCTAAAT
36779271 TTGGCAGATT
Statistics
Matches: 99, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
85 3 0.03
86 22 0.22
87 5 0.05
88 35 0.35
89 30 0.30
90 4 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.21
Consensus pattern (85 bp):
CGGCGCTTTTCCAAAAACGCCGCTAAATACCCTGATCTATAGCGGCGCTTAGCCAGAAAACGCCG
CAATAGACCCTAATCTATAA
Found at i:36779724 original size:21 final size:21
Alignment explanation
Indices: 36779700--36779744 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
36779690 GCAGCCTGTT
* *
36779700 CTTCT-TTCGCTGGCGCCTCTG
1 CTTCTCTT-GCTGCCGCATCTG
36779721 CTTCTCTTGCTGCCGCATCTG
1 CTTCTCTTGCTGCCGCATCTG
36779742 CTT
1 CTT
36779745 TAAGCTGCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.02, C:0.38, G:0.20, T:0.40
Consensus pattern (21 bp):
CTTCTCTTGCTGCCGCATCTG
Found at i:36779805 original size:66 final size:66
Alignment explanation
Indices: 36779715--36779880 Score: 201
Period size: 66 Copynumber: 2.5 Consensus size: 66
36779705 TTCGCTGGCG
* * *
36779715 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
36779778 GAA
64 GAA
* * *
36779781 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGTTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
36779846 A
66 A
* * * * *
36779847 CATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
36779881 TTGTGTAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 82 0.94
67 4 0.05
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:36784738 original size:17 final size:17
Alignment explanation
Indices: 36784718--36784755 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
36784708 TTAAAGTTCA
36784718 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
*
36784735 CAAGGAAGTAGAGGCTG
1 CAAGGAAGTAAAGGCTG
36784752 CAAG
1 CAAG
36784756 TTCCTGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.37, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:36785043 original size:33 final size:33
Alignment explanation
Indices: 36784996--36785063 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
36784986 ATATACATAT
*
36784996 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
36785029 ATTCATACCCAACACTCATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
36785062 AT
1 AT
36785064 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:36785304 original size:14 final size:15
Alignment explanation
Indices: 36785285--36785323 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
36785275 AATTGGGAAA
36785285 TTGGGGAAAAT-ACT
1 TTGGGGAAAATAACT
36785299 TTGGGGAAGAATAACT
1 TTGGGGAA-AATAACT
*
36785315 TGGGGGAAA
1 TTGGGGAAA
36785324 TTGGGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (15 bp):
TTGGGGAAAATAACT
Found at i:36785328 original size:25 final size:22
Alignment explanation
Indices: 36785299--36785355 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
36785289 GGAAAATACT
*
36785299 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
36785324 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
36785347 TTGGGGAAA
1 TTGGGGAAA
36785356 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:36789191 original size:42 final size:41
Alignment explanation
Indices: 36789106--36789407 Score: 424
Period size: 41 Copynumber: 7.3 Consensus size: 41
36789096 CGCATATATA
* * *
36789106 AAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGGCG
1 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACG
* * *
36789147 AAAACGCCGCTATAGACACAGAGCATTATCAGCGCTTAGACG
1 AAAACGCCGCTATAGAC-CCGAGCATTAGCGGCGCTTAGACG
* * *
36789189 AAAACGCCGCTAAAGACTCGGAGCATTAGCGGTGCTTAGACG
1 AAAACGCCGCTATAGAC-CCGAGCATTAGCGGCGCTTAGACG
** * * *
36789231 AAAGTGCCGCTAAAGACTCGGAGCATTAGCGGCGCTTATACG
1 AAAACGCCGCTATAGAC-CCGAGCATTAGCGGCGCTTAGACG
*
36789273 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACA
1 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACG
*
36789314 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACA
1 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACG
*
36789355 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACA
1 AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACG
36789396 AAAACGCCGCTA
1 AAAACGCCGCTA
36789408 AATGTTTAAA
Statistics
Matches: 238, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 131 0.55
42 107 0.45
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.15
Consensus pattern (41 bp):
AAAACGCCGCTATAGACCCGAGCATTAGCGGCGCTTAGACG
Found at i:36789311 original size:23 final size:24
Alignment explanation
Indices: 36789280--36789394 Score: 71
Period size: 24 Copynumber: 5.4 Consensus size: 24
36789270 ACGAAAACGC
36789280 CGCTATAGACCCGAGCATTAGCGG
1 CGCTATAGACCCGAGCATTAGCGG
* * *
36789304 CGCT-TAGA--C-A--A-AAACGC
1 CGCTATAGACCCGAGCATTAGCGG
36789321 CGCTATAGACCCGAGCATTAGCGG
1 CGCTATAGACCCGAGCATTAGCGG
* * *
36789345 CGCT-TAGA--C-A--A-AAACGC
1 CGCTATAGACCCGAGCATTAGCGG
36789362 CGCTATAGACCCGAGCATTAGCGG
1 CGCTATAGACCCGAGCATTAGCGG
36789386 CGCT-TAGAC
1 CGCTATAGAC
36789395 AAAAACGCCG
Statistics
Matches: 65, Mismatches: 12, Indels: 29
0.61 0.11 0.27
Matches are distributed among these distances:
17 14 0.22
18 10 0.15
20 4 0.06
21 4 0.06
23 15 0.23
24 18 0.28
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.16
Consensus pattern (24 bp):
CGCTATAGACCCGAGCATTAGCGG
Found at i:36789557 original size:40 final size:40
Alignment explanation
Indices: 36789491--36789568 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
36789481 AATTCCTATT
*
36789491 TTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACC
1 TTTAGCGGCGCTTCCGTATAAACGCCGCTAATGCTCTACC
** *
36789531 TTTAGCGGCGCTTTGGCTA-AATCGCCGCTAATGCTCTA
1 TTTAGCGGCGCTTCCG-TATAAACGCCGCTAATGCTCTA
36789569 TTTTTTGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGCTTCCGTATAAACGCCGCTAATGCTCTACC
Found at i:36790432 original size:18 final size:18
Alignment explanation
Indices: 36790396--36790434 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36790386 AAGAAATATA
*
36790396 AAAAATACATAATATTTT
1 AAAAATACATAATAATTT
36790414 AAAAATA-ATAATAAATTT
1 AAAAATACATAAT-AATTT
36790432 AAA
1 AAA
36790435 TTTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATACATAATAATTT
Found at i:36790465 original size:24 final size:23
Alignment explanation
Indices: 36790438--36790487 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
36790428 ATTTAAATTT
* *
36790438 TATATTAATATTAAATACATATAA
1 TATATCAATATTAAATAAATA-AA
*
36790462 TATATCAATATTACATAAATAAA
1 TATATCAATATTAAATAAATAAA
36790485 TAT
1 TAT
36790488 CTTCCATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATCAATATTAAATAAATAAA
Found at i:36791141 original size:25 final size:24
Alignment explanation
Indices: 36791091--36791169 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
36791081 AATTATATTG
* * *
36791091 ATTTAATATTAATATAAAATTT-AA
1 ATTT-ATATTTATATATATTTTAAA
36791115 ATTTATGA-TTATATATATTTTAAAA
1 ATTTAT-ATTTATATATATTTT-AAA
*
36791140 ATATT-TATTTTTATATATTTTAAA
1 AT-TTATATTTATATATATTTTAAA
36791164 ATTTAT
1 ATTTAT
36791170 TCCTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
23 14 0.31
24 12 0.27
25 17 0.38
26 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
ATTTATATTTATATATATTTTAAA
Found at i:36792697 original size:21 final size:21
Alignment explanation
Indices: 36792658--36792697 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36792648 TGAATAAAAT
**
36792658 AACTAAAAAAGGGCTAAATTG
1 AACTAAAAAAGGGAAAAATTG
*
36792679 AACTTAAAAAGGGAAAAAT
1 AACTAAAAAAGGGAAAAAT
36792698 GGGGCAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (21 bp):
AACTAAAAAAGGGAAAAATTG
Found at i:36794359 original size:44 final size:44
Alignment explanation
Indices: 36794286--36794788 Score: 209
Period size: 44 Copynumber: 11.4 Consensus size: 44
36794276 GAATTACTGG
* * * *
36794286 CTTCAATATACTCCACT-GTAACCTCAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTACT-ACCT-AGGGAGATAAAATCTGCAAT
* * * *
36794331 TTTCGATCTACTCCACTACTACCTAGGGAGATAAGATCTGTAAT
1 CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
* * * * * ***
36794375 CTTCAATCTATTCCACTACTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
* * * * *
36794418 CTTCAATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTACT-ACCT-AGGGAGATAAAATCTGCAAT
* * * * * * * *
36794463 CCTT-GATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGAAAT
1 -CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
* * * * * **
36794507 CTTCAATCTATTCCACTGCTGACC-AGAGAGATAGAAT-TAC-GG
1 CTTCAATCTACTCCACTACT-ACCTAGGGAGATAAAATCTGCAAT
* * * * * *
36794549 CTTCAATGTACTCCAGT-GTAACCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTACT-ACC-TAGGGAGATAAAATCTGCAAT
* * * * * *
36794594 CTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
* * * ***
36794638 CTTCAATCTATTCCACTGACTGGACC-AGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACT-ACT--ACCTAGGGAGATAAAATCTGCAAT
* * * * *
36794683 CTTCAATGTACTCCACT-GTAACCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTACT-ACC-TAGGGAGATAAAATCTGCAAT
* * * * * * *
36794728 CTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATTTGAAAT
1 CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
*
36794772 CTTCAATCTATTCCACT
1 CTTCAATCTACTCCACT
36794789 GCCAACCAGG
Statistics
Matches: 320, Mismatches: 118, Indels: 41
0.67 0.25 0.09
Matches are distributed among these distances:
41 4 0.01
42 18 0.06
43 33 0.10
44 163 0.51
45 82 0.26
46 18 0.06
47 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTACTACCTAGGGAGATAAAATCTGCAAT
Found at i:36794430 original size:132 final size:132
Alignment explanation
Indices: 36794263--36794860 Score: 930
Period size: 132 Copynumber: 4.5 Consensus size: 132
36794253 TTCCTCTGCC
* * *
36794263 GACCGGGGAGGTAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
1 GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
* * * * *
36794328 CATTTTCGATCTACTCCACTACTACCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTA
66 CATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTA
36794393 CT
131 CT
* *
36794395 GCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGC
1 GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
* * * *
36794460 CATCCTT-GATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACT
66 CAT-CTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
*
36794524 GCT
130 ACT
* * *
36794527 GACCAGAGAGATAGAATTAC-GGCTTCAATGTACTCCAGTGTAACCACAGGGAGGTAAAATCTGC
1 GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
36794591 CATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG
66 CATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT-
36794656 ACT
130 ACT
*
36794659 GGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
1 -GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTG
*
36794724 CCATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATTTGAAATCTTCAATCTATTCCACT
65 CCATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
* *
36794789 GCC
130 ACT
* * *
36794792 AACCAGGGAGATAGAATTACTGGATTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGC
1 GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
36794857 CATC
66 CATC
36794861 AACCTACTCC
Statistics
Matches: 429, Mismatches: 32, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
130 3 0.01
131 97 0.23
132 201 0.47
133 22 0.05
134 106 0.25
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (132 bp):
GACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC
CATCTTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTA
CT
Found at i:36794742 original size:45 final size:45
Alignment explanation
Indices: 36794286--36794860 Score: 178
Period size: 44 Copynumber: 13.0 Consensus size: 45
36794276 GAATTACTGG
* * *
36794286 CTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
* * * * * **
36794331 TTTCGATCTACTCCACTACT-ACC-TAGGGAGATAAGATCTGTAAT
1 CTTCAATCTACTCCACT-GTAACCACAGGGAGATAAAATCTGCCAT
* * * * * ***
36794375 CTTCAATCTATTCCACTACT-GCC-CAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACT-GTAACCACAGGGAGATAAAATCTGCCAT
* * * *
36794418 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
* * * ** * * **
36794463 CCTT-GATCTGCTCTAC--T-ACTGCTTAGGGAGACAAGATCTGAAAT
1 -CTTCAATCTACTCCACTGTAAC--CACAGGGAGATAAAATCTGCCAT
* * * * * **
36794507 CTTCAATCTATTCCACTGCTGA-C-CAGAGAGATAGAAT-T-ACGG
1 CTTCAATCTACTCCACTG-TAACCACAGGGAGATAAAATCTGCCAT
* * *
36794549 CTTCAATGTACTCCAGTGTAACCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
* * * * **
36794594 CTTCGATCTGCTCCAC--TAATGCC-TAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTGTAA--CCACAGGGAGATAAAATCTGCCAT
* * * * ***
36794638 CTTCAATCTATTCCACTG--ACTGGACCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTAAC--CA-CAGGGAGATAAAATCTGCCAT
* *
36794683 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
* * * * * **
36794728 CTTCGATCTGCTCCAC--TAATGCC-TAGGGAGATAAGATTTGAAAT
1 CTTCAATCTACTCCACTGTAA--CCACAGGGAGATAAAATCTGCCAT
* * * *
36794772 CTTCAATCTATTCCACTGCCAA-C-CAGGGAGATAGAATTACTG-GA-
1 CTTCAATCTACTCCACTG-TAACCACAGGGAGATA-AAAT-CTGCCAT
* * * *
36794816 -TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
36794860 C
1 C
36794861 AACCTACTCC
Statistics
Matches: 371, Mismatches: 120, Indels: 78
0.65 0.21 0.14
Matches are distributed among these distances:
41 2 0.01
42 25 0.07
43 60 0.16
44 181 0.49
45 80 0.22
46 17 0.05
47 5 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGTAACCACAGGGAGATAAAATCTGCCAT
Found at i:36795678 original size:13 final size:13
Alignment explanation
Indices: 36795660--36795684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36795650 AAATTGTCGA
36795660 GGATAACAAAGAT
1 GGATAACAAAGAT
36795673 GGATAACAAAGA
1 GGATAACAAAGA
36795685 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:36797049 original size:20 final size:20
Alignment explanation
Indices: 36797024--36797064 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
36797014 AATTTGGCAG
36797024 AAAAAATC-TGAAAGAATGAA
1 AAAAAATCGT-AAAGAATGAA
36797044 AAAAAATCGTAAAGAATGAA
1 AAAAAATCGTAAAGAATGAA
36797064 A
1 A
36797065 GAACATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAAATCGTAAAGAATGAA
Found at i:36811699 original size:25 final size:25
Alignment explanation
Indices: 36811647--36811700 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
36811637 CTCAGTACAG
* *
36811647 TTTCAAAAAGTACTAACTATAGTGT
1 TTTCAAAAAGTACTAACTATAATAT
* *
36811672 TTTCAGAAAGTTCTAACTATAATAT
1 TTTCAAAAAGTACTAACTATAATAT
36811697 TTTC
1 TTTC
36811701 TAAATTCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (25 bp):
TTTCAAAAAGTACTAACTATAATAT
Found at i:36815427 original size:35 final size:36
Alignment explanation
Indices: 36815383--36815451 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
36815373 ATTATAATCA
*
36815383 TTGTAACATGGTATGAA-AACATACCCACATATTTG
1 TTGTAACATGGCATGAATAACATACCCACATATTTG
* *
36815418 TTGTCACATGGCATGAATAACATGCCCACATATT
1 TTGTAACATGGCATGAATAACATACCCACATATT
36815452 CTCTTTCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (36 bp):
TTGTAACATGGCATGAATAACATACCCACATATTTG
Found at i:36815461 original size:36 final size:35
Alignment explanation
Indices: 36815383--36815461 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
36815373 ATTATAATCA
* * *
36815383 TTGTAACATGGTATGAAAACATACCCACATATTTG
1 TTGTCACATGGCATGAAAACATACCCACATATTTC
*
36815418 TTGTCACATGGCATGAATAACATGCCCACATATTCTC
1 TTGTCACATGGCATGAA-AACATACCCACATATT-TC
36815455 TT-TCACA
1 TTGTCACA
36815462 ACAGTCATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 15 0.39
36 20 0.53
37 3 0.08
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (35 bp):
TTGTCACATGGCATGAAAACATACCCACATATTTC
Found at i:36816876 original size:17 final size:18
Alignment explanation
Indices: 36816850--36816884 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36816840 TTAGAATTGG
*
36816850 ATTGAGAAAATT-ATTTA
1 ATTGAAAAAATTAATTTA
36816867 ATTGAAAAAATTAATTTA
1 ATTGAAAAAATTAATTTA
36816885 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
ATTGAAAAAATTAATTTA
Found at i:36819386 original size:18 final size:18
Alignment explanation
Indices: 36819363--36819398 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36819353 GTTGATATAC
36819363 ATTTTCGTTTTACTATTT
1 ATTTTCGTTTTACTATTT
* *
36819381 ATTTTCTTTTTATTATTT
1 ATTTTCGTTTTACTATTT
36819399 TTTATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (18 bp):
ATTTTCGTTTTACTATTT
Found at i:36819749 original size:12 final size:11
Alignment explanation
Indices: 36819721--36819748 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
36819711 GGGGGAGAAC
36819721 TTTTTTGAAGT
1 TTTTTTGAAGT
36819732 TTTTTTGAAGT
1 TTTTTTGAAGT
36819743 TTTTTT
1 TTTTTT
36819749 TAAAAAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (11 bp):
TTTTTTGAAGT
Found at i:36820210 original size:18 final size:18
Alignment explanation
Indices: 36820168--36820213 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
36820158 TTTTTTATAT
* **
36820168 ATATGTATATTTATTTTT
1 ATATATATATTTATTTCC
*
36820186 ATGTATATATTTATTTCC
1 ATATATATATTTATTTCC
36820204 ATATATATAT
1 ATATATATAT
36820214 GCATATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
ATATATATATTTATTTCC
Found at i:36820242 original size:42 final size:42
Alignment explanation
Indices: 36820163--36820242 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
36820153 TTTTCTTTTT
* * * *
36820163 TATATATATGTATATTTATTTTTATGTATATATTTATTTCCA
1 TATATATATGCATATTTATTTTAATATATATAATTATTTCCA
*
36820205 TATATATATGCATATTT-TTTTAATATAATGTAATTATT
1 TATATATATGCATATTTATTTTAATAT-ATATAATTATT
36820243 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 7 0.22
42 25 0.78
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (42 bp):
TATATATATGCATATTTATTTTAATATATATAATTATTTCCA
Found at i:36820678 original size:19 final size:20
Alignment explanation
Indices: 36820650--36820695 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36820640 CATGTCCGCG
*
36820650 TTTATCTATTTA-TGTTAAT
1 TTTATTTATTTATTGTTAAT
*
36820669 TTTATTTATTTATTGTTTAT
1 TTTATTTATTTATTGTTAAT
*
36820689 ATTATTT
1 TTTATTT
36820696 CTATACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTATTGTTAAT
Found at i:36824068 original size:2 final size:2
Alignment explanation
Indices: 36824061--36824103 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
36824051 NNNNNNTTAT
36824061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36824102 TA
1 TA
36824104 CTTCTTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36832868 original size:13 final size:14
Alignment explanation
Indices: 36832850--36832878 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36832840 TCTACTCGTA
36832850 TGGATTTT-CTTTT
1 TGGATTTTCCTTTT
36832863 TGGATTTTCCTTTT
1 TGGATTTTCCTTTT
36832877 TG
1 TG
36832879 TTTTGTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.66
Consensus pattern (14 bp):
TGGATTTTCCTTTT
Found at i:36840643 original size:19 final size:19
Alignment explanation
Indices: 36840610--36840662 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
36840600 TTCAGAATAG
36840610 TAATTCATCAA-CATTTAAC
1 TAATT-ATCAATCATTTAAC
* *
36840629 TAA-TATCATATCATTTCAG
1 TAATTATCA-ATCATTTAAC
36840648 TAATTATCAATCATT
1 TAATTATCAATCATT
36840663 CATATTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 18 0.62
20 5 0.17
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATTATCAATCATTTAAC
Found at i:36851645 original size:20 final size:20
Alignment explanation
Indices: 36851622--36851670 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
36851612 AATAAAGTGC
*
36851622 AAATGATTTTAACCAAGTCA
1 AAATGATTTCAACCAAGTCA
* *
36851642 AAATGATTTCAATCAAGTTA
1 AAATGATTTCAACCAAGTCA
*
36851662 AAATAATTT
1 AAATGATTT
36851671 ATAAATGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (20 bp):
AAATGATTTCAACCAAGTCA
Found at i:36851677 original size:31 final size:31
Alignment explanation
Indices: 36851642--36851722 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
36851632 AACCAAGTCA
36851642 AAATGATTTCAATCAAGTTAAAATAATTTAT
1 AAATGATTTCAATCAAGTTAAAATAATTTAT
* *
36851673 AAATGATTTCAATCAAGCTAAAATCATTTAT
1 AAATGATTTCAATCAAGTTAAAATAATTTAT
*
36851704 AAATGATTTTCAAACAAGT
1 AAATGA-TTTCAATCAAGT
36851723 CAAATTTACT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 35 0.78
32 10 0.22
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
AAATGATTTCAATCAAGTTAAAATAATTTAT
Found at i:36855575 original size:149 final size:148
Alignment explanation
Indices: 36855367--36855658 Score: 521
Period size: 149 Copynumber: 2.0 Consensus size: 148
36855357 TGACTCAAGA
* * **
36855367 CTCTCTTTATATAGGGAGAGTTTAAAGAGCTCAACTATGATTAAACTTAATTACTTTAATATTAA
1 CTCTATTTATATAGGGAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
36855432 ATTAATATAATATTTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
66 ATTAATATAATA-TTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
36855497 AGAATGTTTATCTATAAGG
130 AGAATGTTTATCTATAAGG
*
36855516 CTCTATTTATATAGGGAGAGTTTAGAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
1 CTCTATTTATATAGGGAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
*
36855581 ATTAATATAATATTATCAAGACAAATATTAGATTAAATTTAATATAAAATCTTATTAAAATAATA
66 ATTAATATAATATTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAATA
36855646 GAATGTTTATCTA
131 GAATGTTTATCTA
36855659 CAATATAAAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
148 65 0.47
149 72 0.53
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (148 bp):
CTCTATTTATATAGGGAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
ATTAATATAATATTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAATA
GAATGTTTATCTATAAGG
Found at i:36863464 original size:34 final size:34
Alignment explanation
Indices: 36863426--36863494 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
36863416 TAGCTCTCAT
*
36863426 ATACGGTCTGCAACGAGATACTCCTGTCATACAG
1 ATACGGTCTGCAACGAGATACTCCTGTCACACAG
*
36863460 ATACGGTCTGCAACGAGATGCTCCTGTCACACAG
1 ATACGGTCTGCAACGAGATACTCCTGTCACACAG
36863494 A
1 A
36863495 CTTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (34 bp):
ATACGGTCTGCAACGAGATACTCCTGTCACACAG
Found at i:36863478 original size:17 final size:17
Alignment explanation
Indices: 36863426--36863478 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
36863416 TAGCTCTCAT
36863426 ATACGGTCTGCAACGAG
1 ATACGGTCTGCAACGAG
36863443 ATAC--TCCTGTCATAC-AG
1 ATACGGT-CTG-CA-ACGAG
36863460 ATACGGTCTGCAACGAG
1 ATACGGTCTGCAACGAG
36863477 AT
1 AT
36863479 GCTCCTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
15 1 0.03
16 5 0.17
17 18 0.60
18 5 0.17
19 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (17 bp):
ATACGGTCTGCAACGAG
Found at i:36865522 original size:24 final size:24
Alignment explanation
Indices: 36865482--36865535 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
36865472 TATATACACA
*
36865482 ATTATAAAATTACATAATATAAAT
1 ATTATAAAATTACATAAAATAAAT
* *
36865506 ATTATAAACATT-TATAAAATAGAT
1 ATTATAAA-ATTACATAAAATAAAT
36865530 A-TATAA
1 ATTATAA
36865536 TGAGATAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATAAAATTACATAAAATAAAT
Found at i:36867162 original size:318 final size:318
Alignment explanation
Indices: 36866585--36867209 Score: 959
Period size: 318 Copynumber: 2.0 Consensus size: 318
36866575 CAAATTAACA
* *
36866585 AAATTTTCTGTTAAAGTCCCTATGGGAGTGTAACTCTTCCACTACTCAACCACCGAATATCAACC
1 AAATTTTCTGGTAAAGTCCCTATAGGAGTGTAACTCTTCCACTACTCAACCACCGAATATCAACC
* * *
36866650 ACTGCCAACCACTGGAACGCCGTCGTCGCAGTCGCCGCGTCTAGTGATACAGGTGCAACACTTTT
66 ACCGCCAACCACTGGAACGCCGTCATCGCAGCCGCCGCGTCTAGTGATACAGGTGCAACACTTTT
* * * *
36866715 ACGGTACCCCAAACCAGTTCAATTACTATCGATTCGGTCCGGGTCAGTGATGACCCAATCGGTCC
131 ACGGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTCC
* ** * *
36866780 GGTCTAGCCACCGGTTGGATTGTCGACTCAATTTCACATACAGGACCTGATTTAATCAGTTTTTG
196 GGTCTAACCACCGGTTGGATTGTCGACTCAATTTCACATACAGGACCCAATTCAACCAGTTTTTG
* * *
36866845 GGTCTTGGTCTTAGTTTTAGGCTCTCGTGCCCAATTTATGATCTCAATTCCATTTTTC
261 GGTCTTGGTCTCAATTTTAGGCTCTCGTACCCAATTTATGATCTCAATTCCATTTTTC
* *
36866903 AAATTTTCTGGTAGAGTCCCTATAGGAGTGTAACTCTTCCACTGCTCAACCACCGAATATCAACC
1 AAATTTTCTGGTAAAGTCCCTATAGGAGTGTAACTCTTCCACTACTCAACCACCGAATATCAACC
* * * * *
36866968 ACCGCCAGCCACTGGAATGCCGTCATCGCAGCCGCTGTGTCTAGTGATACAGGTGTGAA-ACTTT
66 ACCGCCAACCACTGGAACGCCGTCATCGCAGCCGCCGCGTCTAGTGATACAGGTG-CAACACTTT
*
36867032 TACGGCACCCCAAACAAGTTCAATTACTATCGATTTGGTACGGGTCAGTGACGACCCAATCGGTC
130 TACGGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTC
* *
36867097 CGGTCTAACCACTGGTTGGATTGTCGAC-CTGATTTCACATACCAGG-CCCAATTCAACCAGTTT
195 CGGTCTAACCACCGGTTGGATTGTCGACTC-AATTTCACATA-CAGGACCCAATTCAACCAGTTT
36867160 TTGGGTCTTGGTCTCAATTTTAGGCTCTCGTACCCAATTTATGATCTCAA
258 TTGGGTCTTGGTCTCAATTTTAGGCTCTCGTACCCAATTTATGATCTCAA
36867210 GTCTAATTTT
Statistics
Matches: 277, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
317 1 0.00
318 270 0.97
319 6 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (318 bp):
AAATTTTCTGGTAAAGTCCCTATAGGAGTGTAACTCTTCCACTACTCAACCACCGAATATCAACC
ACCGCCAACCACTGGAACGCCGTCATCGCAGCCGCCGCGTCTAGTGATACAGGTGCAACACTTTT
ACGGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTCC
GGTCTAACCACCGGTTGGATTGTCGACTCAATTTCACATACAGGACCCAATTCAACCAGTTTTTG
GGTCTTGGTCTCAATTTTAGGCTCTCGTACCCAATTTATGATCTCAATTCCATTTTTC
Found at i:36872223 original size:3 final size:3
Alignment explanation
Indices: 36872215--36872255 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
36872205 AAGTTAAAAT
36872215 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
36872256 GGAAGAGCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:36876348 original size:16 final size:16
Alignment explanation
Indices: 36876327--36876357 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36876317 ATCGGGTTGA
*
36876327 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
36876343 GAAAATTAATTAATT
1 GAAAATTAATTAATT
36876358 TATGATGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:36876685 original size:19 final size:20
Alignment explanation
Indices: 36876627--36876680 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
36876617 AAATAGTGAG
36876627 AATT-TATTTTCTGAGTATA
1 AATTCTATTTTCTGAGTATA
36876646 AATTCTATTTT-TCGAGTATA
1 AATTCTATTTTCT-GAGTATA
36876666 AATTCTATTTTCTGA
1 AATTCTATTTTCTGA
36876681 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 26 0.81
21 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
AATTCTATTTTCTGAGTATA
Found at i:36877401 original size:46 final size:46
Alignment explanation
Indices: 36877348--36877438 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
36877338 GATTAAATAA
36877348 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
1 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
*
36877394 TTTATTTAACTTTGATTTAATTTTATTTCAAAATTAAGAAAACTA
1 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTA
36877439 ACTTTTATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (46 bp):
TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
Found at i:36877605 original size:23 final size:23
Alignment explanation
Indices: 36877563--36877606 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
36877553 CTATATCTCG
*
36877563 AAATGACCTGACCCTCAAATTTA
1 AAATGACCTGAACCTCAAATTTA
* *
36877586 AAATGACCTGAATCTGAAATT
1 AAATGACCTGAACCTCAAATT
36877607 AACTGAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (23 bp):
AAATGACCTGAACCTCAAATTTA
Found at i:36886421 original size:2 final size:2
Alignment explanation
Indices: 36886414--36886454 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
36886404 GAGTTAAGAA
*
36886414 AT AT AT AT AT GT 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 AT AT AT AT AT A
36886455 GGTGAAAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36887095 original size:20 final size:20
Alignment explanation
Indices: 36887047--36887095 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
36887037 CGGAAAAGTT
* *
36887047 ATTTTTACATATATTAATAA
1 ATTTTTATACATATTAATAA
* *
36887067 ATCTATATACATATTAATAA
1 ATTTTTATACATATTAATAA
36887087 ATTTTTATA
1 ATTTTTATA
36887096 TTTTAAATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTTATACATATTAATAA
Found at i:36888357 original size:32 final size:32
Alignment explanation
Indices: 36888311--36888371 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
36888301 TGTCAATCAT
36888311 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
36888343 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
36888372 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:36888378 original size:27 final size:30
Alignment explanation
Indices: 36888311--36888384 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
36888301 TGTCAATCAT
*
36888311 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
36888343 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
36888371 -TCAATATCTAACAA
1 TTCAATATCTAACAA
36888385 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 14 0.34
28 2 0.05
29 2 0.05
32 23 0.56
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:36888395 original size:27 final size:27
Alignment explanation
Indices: 36888312--36888398 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 27
36888302 GTCAATCATT
* *
36888312 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
36888343 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
36888371 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
36888398 T
1 T
36888399 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:36907020 original size:31 final size:30
Alignment explanation
Indices: 36906985--36907053 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
36906975 ATTGAACAGC
*
36906985 TCAATGACTTAAATAAAAACTTTTGAATATT
1 TCAATGACTTAAATAAAAACTTTCGAATA-T
* *
36907016 TCAATTACTTGAATAAAAACTTTCGAATAT
1 TCAATGACTTAAATAAAAACTTTCGAATAT
36907046 TCAATGAC
1 TCAATGAC
36907054 CATTTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (30 bp):
TCAATGACTTAAATAAAAACTTTCGAATAT
Found at i:36920222 original size:22 final size:23
Alignment explanation
Indices: 36920173--36920224 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
36920163 AAATGGTTAG
* *
36920173 ATTTTAATTTTAATTTCTTTGAA
1 ATTTTAATTTTAATATCTTTAAA
*
36920196 A-TTTAATTTTTATAT-TTTAAA
1 ATTTTAATTTTAATATCTTTAAA
36920217 ATTTTAAT
1 ATTTTAAT
36920225 ATAATTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTAATTTTAATATCTTTAAA
Found at i:36930151 original size:17 final size:17
Alignment explanation
Indices: 36930129--36930162 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
36930119 TGGATTGTCT
36930129 AGAAGCTCACACTATCC
1 AGAAGCTCACACTATCC
36930146 AGAAGCTCACACTATCC
1 AGAAGCTCACACTATCC
36930163 CATTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.12, T:0.18
Consensus pattern (17 bp):
AGAAGCTCACACTATCC
Found at i:36933486 original size:15 final size:15
Alignment explanation
Indices: 36933468--36933501 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
36933458 ATTTATTTTA
36933468 ATATTATTTTATGGT
1 ATATTATTTTATGGT
36933483 ATATTATTTTATGGT
1 ATATTATTTTATGGT
36933498 ATAT
1 ATAT
36933502 AGTATCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (15 bp):
ATATTATTTTATGGT
Found at i:36937105 original size:25 final size:25
Alignment explanation
Indices: 36937071--36937181 Score: 127
Period size: 25 Copynumber: 4.4 Consensus size: 25
36937061 ACAACTCTCT
36937071 TGAGCTTCCCGATATTTAGCTCATA
1 TGAGCTTCCCGATATTTAGCTCATA
36937096 TGAGCTTCCCGAT-TTCTAGCTCATA
1 TGAGCTTCCCGATATT-TAGCTCATA
* *
36937121 TGAGCTTCCCGATATAT-GACTCGTA
1 TGAGCTTCCCGATATTTAG-CTCATA
* * **
36937146 TGAGCTTCTCGTTGCTTAGCTCATA
1 TGAGCTTCCCGATATTTAGCTCATA
*
36937171 TGAGCATCCCG
1 TGAGCTTCCCG
36937182 TTATATGGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.04
25 67 0.93
26 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
TGAGCTTCCCGATATTTAGCTCATA
Found at i:36937148 original size:50 final size:50
Alignment explanation
Indices: 36937071--36937208 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
36937061 ACAACTCTCT
* * *
36937071 TGAGCTTCCCGATAT-TTAGCTCATATGAGCTTCCCGATTTC-TAGCTCATA
1 TGAGCTTCCCGATATATGA-CTCGTATGAGCTTCCCG-TTGCTTAGCTCATA
*
36937121 TGAGCTTCCCGATATATGACTCGTATGAGCTTCTCGTTGCTTAGCTCATA
1 TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTTGCTTAGCTCATA
* * * * *
36937171 TGAGCATCCCGTTATATGGCTCGGAAGAGCTTCCCGTT
1 TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTT
36937209 TACATGCTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
49 3 0.04
50 71 0.93
51 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (50 bp):
TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTTGCTTAGCTCATA
Found at i:36937192 original size:25 final size:25
Alignment explanation
Indices: 36937071--36937208 Score: 120
Period size: 25 Copynumber: 5.5 Consensus size: 25
36937061 ACAACTCTCT
* *
36937071 TGAGCTTCCCGATATTTAGCTCATA
1 TGAGCTTCCCGTTATATAGCTCATA
*
36937096 TGAGCTTCCCGATT-TCTAGCTCATA
1 TGAGCTTCCCG-TTATATAGCTCATA
* *
36937121 TGAGCTTCCCGATATAT-GACTCGTA
1 TGAGCTTCCCGTTATATAG-CTCATA
* *
36937146 TGAGCTTCTCGTTGCT-TAGCTCATA
1 TGAGCTTCCCGTT-ATATAGCTCATA
* * **
36937171 TGAGCATCCCGTTATATGGCTCGGA
1 TGAGCTTCCCGTTATATAGCTCATA
*
36937196 AGAGCTTCCCGTT
1 TGAGCTTCCCGTT
36937209 TACATGCTTG
Statistics
Matches: 90, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
24 3 0.03
25 84 0.93
26 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
TGAGCTTCCCGTTATATAGCTCATA
Found at i:36937359 original size:19 final size:19
Alignment explanation
Indices: 36937335--36937373 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
36937325 ATACGAAACA
36937335 ATATGAGTTCGAAATGAAT
1 ATATGAGTTCGAAATGAAT
36937354 ATATGAGTTCGAAATGAAT
1 ATATGAGTTCGAAATGAAT
36937373 A
1 A
36937374 ATCATGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (19 bp):
ATATGAGTTCGAAATGAAT
Found at i:36945675 original size:21 final size:21
Alignment explanation
Indices: 36945608--36945676 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
36945598 GCATTAAAGA
* *
36945608 GTGTTGTGGTTGCATCTGATT
1 GTGTTGTGGATGCATCTGAGT
* *
36945629 CTGATGTGGATGCATCT-AGCT
1 GTGTTGTGGATGCATCTGAG-T
* *
36945650 TTGTTGTGGATGAATCTGAGT
1 GTGTTGTGGATGCATCTGAGT
36945671 GTGTTG
1 GTGTTG
36945677 ATTGCAGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.42
Consensus pattern (21 bp):
GTGTTGTGGATGCATCTGAGT
Found at i:36948608 original size:22 final size:22
Alignment explanation
Indices: 36948446--36948600 Score: 229
Period size: 22 Copynumber: 7.0 Consensus size: 22
36948436 TTTATTGTTC
*
36948446 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
36948468 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
36948490 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
36948512 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
36948534 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
36948556 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
36948578 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
36948600 A
1 A
36948601 TATTTGAGTT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 120 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:36952762 original size:36 final size:40
Alignment explanation
Indices: 36952680--36952765 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
36952670 ATGTAGTACG
* *
36952680 TATATATTTTATTATCATATCATTTTATTTTTATAGTTTA
1 TATATATTTTATTATCATATCATATTATTTTTATAGTATA
36952720 TATATATTTTA-TATACAT-TCATATT-TTTTTAT-G-ATA
1 TATATATTTTATTAT-CATATCATATTATTTTTATAGTATA
*
36952756 TTTATATTTT
1 TATATATTTT
36952766 CATGTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 7 0.17
39 9 0.21
40 14 0.33
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (40 bp):
TATATATTTTATTATCATATCATATTATTTTTATAGTATA
Found at i:36954317 original size:16 final size:16
Alignment explanation
Indices: 36954296--36954330 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36954286 TTGTGTTTTG
36954296 TTTTGAATGCATGACA
1 TTTTGAATGCATGACA
* *
36954312 TTTTGACTGCATGGCA
1 TTTTGAATGCATGACA
36954328 TTT
1 TTT
36954331 CATTATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGAATGCATGACA
Found at i:36957518 original size:7 final size:7
Alignment explanation
Indices: 36957508--36957549 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
36957498 AAAGATGTGA
36957508 AAAAATG
1 AAAAATG
36957515 -AAAATG
1 AAAAATG
36957521 AAAAATG
1 AAAAATG
36957528 AAAAATGG
1 AAAAAT-G
36957536 AAAAA-G
1 AAAAATG
36957542 TAAAAATG
1 -AAAAATG
36957550 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.23
7 17 0.55
8 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:36957538 original size:15 final size:15
Alignment explanation
Indices: 36957508--36957551 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
36957498 AAAGATGTGA
36957508 AAAAATG-AAAAT-G
1 AAAAATGAAAAATGG
36957521 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
36957536 AAAAA-GTAAAAATGG
1 AAAAATG-AAAAATGG
36957551 A
1 A
36957552 GAGGCTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 6 0.21
15 15 0.54
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:36959089 original size:100 final size:100
Alignment explanation
Indices: 36958909--36960310 Score: 2111
Period size: 100 Copynumber: 14.1 Consensus size: 100
36958899 GCGTTGTAGC
*
36958909 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
*
36958974 CACAATGGCGGATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* **
36959009 GGAGCAGATTGAAGTCACAACGGCGGTTCTGGTTTCTTCGACAGCGCAATTAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* *
36959074 CACAACGGTGAATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
*
36959109 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* * * ** *
36959174 CACAACGTCAGATCTTACTTCCCTAGTAGTGTAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* ** *
36959209 GGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCTTCGACAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* *
36959274 CACAATGGCGGATCTTACTTCCTTGGC---G--GT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
**
36959304 ---GCAGATTGAAGTCACAACGGCGGATCTGGTTTCTTCGACAGCGCAATTAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* * * * *
36959366 CACAATGGCGGATCTTA-TTTCCTGGGCGTTGTAGC
66 CACAACGGCGGATCTTACTTCCCT-GGCGGTGCAGT
*
36959401 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
*
36959466 CACAATGGCGGATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
**
36959501 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTTCGACAGCGCAATTAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
*
36959566 CACAACGGCAGATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* *
36959601 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCTCGACAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* *
36959666 CACAACGGCAGATCTTACTTCCCTGGCGGTGTAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* ** *
36959701 GGAGCAGATTGAAGTTACAACGGCGGATCTGGTTTCTTCGACAGCGTAATTAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
36959766 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* * *
36959801 GGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTTAAAAGATTAAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* * * *
36959866 CACAACGGCGGATCTTAGTTCTCTGGCGGTGTATT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
**
36959901 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTTCGACAGCGCAATTAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
*
36959966 CACAACGGCAGATCTTACTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* *
36960001 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGATAGCGCAATTTAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
*
36960066 CACAACGGCGGATCTTATTTCCCTGGCGGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* * *
36960101 GGAGTAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAGGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* ** *
36960166 CACAGCGATGGATCTTACTTCCCTGGCAGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* * *
36960201 GGAGCAGATTGAAGTCACAGCGGCAGATCTGGTTTCCCCGACAGCGCAATCAAAAAGATTGAAGC
1 GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
* * * *
36960266 CACAACGGCGGATCTTACCTCCTTAGCAGTGCAGT
66 CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
* *
36960301 TGAACAGATT
1 GGAGCAGATT
36960311 TCAACGACGA
Statistics
Matches: 1189, Mismatches: 103, Indels: 20
0.91 0.08 0.02
Matches are distributed among these distances:
91 4 0.00
92 80 0.07
95 3 0.00
97 2 0.00
100 1095 0.92
101 5 0.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (100 bp):
GGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGC
CACAACGGCGGATCTTACTTCCCTGGCGGTGCAGT
Found at i:36962040 original size:36 final size:40
Alignment explanation
Indices: 36961958--36962043 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
36961948 ATGTAGTACG
* *
36961958 TATATATTTTATTATCATATCATTTTATTTTTATAGTTTA
1 TATATATTTTATTATCATATCATATTATTTTTATAGTATA
36961998 TATATATTTTA-TATACAT-TCATATT-TTTTTAT-G-ATA
1 TATATATTTTATTAT-CATATCATATTATTTTTATAGTATA
*
36962034 TTTATATTTT
1 TATATATTTT
36962044 CATGTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 7 0.17
39 9 0.21
40 14 0.33
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (40 bp):
TATATATTTTATTATCATATCATATTATTTTTATAGTATA
Found at i:36964214 original size:9 final size:9
Alignment explanation
Indices: 36964200--36964247 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
36964190 GAAAGATAGT
36964200 GGTAATGTG
1 GGTAATGTG
36964209 GGTAATAGT-
1 GGTAAT-GTG
*
36964218 TG-AA-GT-
1 GGTAATGTG
36964224 GGTAATGTG
1 GGTAATGTG
36964233 GGTAATGTG
1 GGTAATGTG
36964242 GGTAAT
1 GGTAAT
36964248 AGTTGAAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 3 0.09
7 2 0.06
8 4 0.12
9 22 0.67
10 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (9 bp):
GGTAATGTG
Found at i:36964237 original size:33 final size:32
Alignment explanation
Indices: 36964200--36964262 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 32
36964190 GAAAGATAGT
36964200 GGTAATGTGGGTAATAGTTGAAGTGGTAATGTG
1 GGTAATGTGGGTAATAGTTGAAGTGG-AATGTG
36964233 GGTAATGTGGGTAATAGTTGAAGTGGAATG
1 GGTAATGTGGGTAATAGTTGAAGTGGAATG
36964263 AAAGAGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.32
Consensus pattern (32 bp):
GGTAATGTGGGTAATAGTTGAAGTGGAATGTG
Found at i:36972601 original size:25 final size:23
Alignment explanation
Indices: 36972553--36972601 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
36972543 TTTGATTGAG
*
36972553 ATTAATTTATTTAATGTTATGGT
1 ATTAATTTATTTAATGTTACGGT
36972576 ATTAATATTATTCTAATTGTT-CGGT
1 ATTAAT-TTATT-TAA-TGTTACGGT
36972601 A
1 A
36972602 ATGCTCTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 6 0.27
24 5 0.23
25 7 0.32
26 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (23 bp):
ATTAATTTATTTAATGTTACGGT
Found at i:36981195 original size:21 final size:21
Alignment explanation
Indices: 36981156--36981197 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36981146 GAAATTAAAA
*
36981156 TGTTTTAATTTCACTTTAATT
1 TGTTTTAATTTCACGTTAATT
36981177 TGTTTTAATTTCTA-GTTAATT
1 TGTTTTAATTTC-ACGTTAATT
36981198 ACAAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCACGTTAATT
Found at i:36984172 original size:4 final size:4
Alignment explanation
Indices: 36984163--36984222 Score: 111
Period size: 4 Copynumber: 15.0 Consensus size: 4
36984153 TATTAAATCA
36984163 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
36984211 GTAT ATAT GTAT
1 GTAT GTAT GTAT
36984223 ATTGTATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
GTAT
Done.