Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 36 of 313
Found at i:12221143 original size:26 final size:26
Alignment explanation
Indices: 12221087--12221143 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
12221077 AAATTAACCC
* *
12221087 TAGGGTATAATGGTAAATTTGCACCT
1 TAGGGTATAATGATAAATTTGCAACT
* *
12221113 AAGGGTATAATGAT-AATTTTCATACT
1 TAGGGTATAATGATAAATTTGCA-ACT
12221139 TAGGG
1 TAGGG
12221144 GTATTTTAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (26 bp):
TAGGGTATAATGATAAATTTGCAACT
Found at i:12222259 original size:25 final size:22
Alignment explanation
Indices: 12222205--12222259 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
12222195 TTTTGGCCAG
12222205 AGAAGAAAAGAAGGAGAAAAGA
1 AGAAGAAAAGAAGGAGAAAAGA
* *
12222227 AAATAGAAGAAGAGAGGAGAAGAGA
1 AGA-AGAA-AAGA-AGGAGAAAAGA
12222252 AGGAAGAA
1 A-GAAGAA
12222260 TTCGGCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 4 0.15
25 15 0.58
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (22 bp):
AGAAGAAAAGAAGGAGAAAAGA
Found at i:12222995 original size:21 final size:22
Alignment explanation
Indices: 12222970--12223013 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
12222960 TAAGAACTTT
12222970 TTTTTA-TTATTATCTTT-TTTA
1 TTTTTACTT-TTATCTTTATTTA
12222991 TTTTTACTTTTATCTTTATTTA
1 TTTTTACTTTTATCTTTATTTA
12223013 T
1 T
12223014 CTTCTGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTACTTTTATCTTTATTTA
Found at i:12227922 original size:22 final size:22
Alignment explanation
Indices: 12227845--12227922 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
12227835 CATGCATATG
*
12227845 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAAGCCGAATGGCCAA
* ***
12227867 TGTGATGAATATGAACAT-GCACATA
1 TGTGATAAAGCCG-A-ATGGC-CA-A
12227892 TGTGATAAAGCCGAATGGCCAA
1 TGTGATAAAGCCGAATGGCCAA
12227914 TGTGATAAA
1 TGTGATAAA
12227923 TGTGAACATG
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
22 18 0.43
23 7 0.17
24 7 0.17
25 10 0.24
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
TGTGATAAAGCCGAATGGCCAA
Found at i:12228003 original size:47 final size:47
Alignment explanation
Indices: 12227004--12227973 Score: 1814
Period size: 47 Copynumber: 20.6 Consensus size: 47
12226994 ATATATGAGC
** *
12227004 TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATTTGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227051 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227098 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227145 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227192 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227239 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227286 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227333 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227380 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227427 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227474 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227521 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227568 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227615 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227662 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227709 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * * *
12227756 TAAGGCCGAATGGCCAATGTGATGAATGAGAACATGTACATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
12227803 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * *
12227850 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGCACATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * *
12227897 TAAAGCCGAATGGCCAATGTGATAAATGTGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
*
12227944 TAAGGCAGAATGGCCAATGTGATGAATGTG
1 TAAGGCCGAATGGCCAATGTGATGAATGTG
12227974 GAAGTGTATA
Statistics
Matches: 902, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 902 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
Found at i:12228036 original size:46 final size:46
Alignment explanation
Indices: 12227983--12228073 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
12227973 GGAAGTGTAT
* * *
12227983 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
12228029 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
12228074 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:12230359 original size:19 final size:20
Alignment explanation
Indices: 12230322--12230359 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12230312 ATAAGGTGGT
12230322 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
12230342 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
12230360 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:12236971 original size:46 final size:46
Alignment explanation
Indices: 12236901--12237073 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
12236891 AAAACGAGTA
* *
12236901 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCC
* * * * *
12236947 GAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CGTCC
* * *
12236994 GAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCC
*
12237040 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12237074 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 60 0.58
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCC
Found at i:12240633 original size:13 final size:13
Alignment explanation
Indices: 12240615--12240639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12240605 TAATGGTATA
12240615 TTGAATCCATGAC
1 TTGAATCCATGAC
12240628 TTGAATCCATGA
1 TTGAATCCATGA
12240640 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:12241220 original size:27 final size:27
Alignment explanation
Indices: 12241185--12241363 Score: 182
Period size: 27 Copynumber: 6.6 Consensus size: 27
12241175 TTAAATTGTA
12241185 TAGCACTAAGTGTGCGATATGACTATG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
12241212 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATATGACTATG
*
12241239 -ATGCACTAAGTGTGCGA-ATTGACCATG
1 TA-GCACTAAGTGTGCGATA-TGACTATG
** *
12241266 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TATGACTATG
* * **
12241294 TAGCACTAAGTGTGCGATTTGATTACA
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
12241321 TAGCACTAAGTGTGCGAGATGATTATA
1 TAGCACTAAGTGTGCGATATGACTATG
*
12241348 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
12241364 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 106 0.82
28 22 0.17
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATATGACTATG
Found at i:12241301 original size:82 final size:81
Alignment explanation
Indices: 12241187--12241337 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
12241177 AAATTGTATA
* *
12241187 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATA-CATAGCACTAAGTG
12241251 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
12241268 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACATAGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACATAGCACTAAGTG
12241333 TGCGA
65 TGCGA
12241338 GATGATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 17 0.27
82 45 0.73
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACATAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12241354 original size:82 final size:81
Alignment explanation
Indices: 12241183--12241363 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 81
12241173 GATTAAATTG
* *
12241183 TATAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATATCATGCACTAA
12241248 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
*** * ** *
12241264 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTA-CATAGCACT
1 TATAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATATCAT-GCACT
**
12241328 AAGTGTGCGAGA-TGATTA
64 AAGTGTGCGA-ATTGACCA
*
12241346 TATAGCACTGAGTGTGCG
1 TATAGCACTAAGTGTGCG
12241364 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 18 0.22
82 63 0.77
83 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATATCATGCACTAA
GTGTGCGAATTGACCA
Found at i:12242538 original size:27 final size:26
Alignment explanation
Indices: 12242500--12242559 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
12242490 ATATATATAT
* *
12242500 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
12242526 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
12242553 ATATCTG
1 ATATCTG
12242560 GCAACTTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:12251360 original size:40 final size:39
Alignment explanation
Indices: 12251164--12251365 Score: 155
Period size: 40 Copynumber: 5.1 Consensus size: 39
12251154 GAATGATGTA
* * * *
12251164 CGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAAC
* *
12251204 CGGACTAAGAT-CCGAAGGCATTTGT-CTGAGATACTA-ATTC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGC-GAG-TACTATA-AC
*
12251244 CAGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA-C
* *
12251283 CGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAAC
* ** *
12251323 CGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAAC
12251363 CGG
1 CGG
12251366 TTAAATTCCA
Statistics
Matches: 134, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
39 35 0.26
40 89 0.66
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAAC
Found at i:12253489 original size:40 final size:40
Alignment explanation
Indices: 12253428--12253828 Score: 581
Period size: 40 Copynumber: 10.1 Consensus size: 40
12253418 AGGTCTCGAC
12253428 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
12253467 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
**
12253507 GATGTATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
12253547 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
12253587 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
12253627 GATGTATCCGGACTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
**
12253667 GATGTATCCGAACTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
12253707 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * * *
12253747 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAGT
* * * * *
12253787 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
12253827 GA
1 GA
12253829 CGTGTATTCG
Statistics
Matches: 329, Mismatches: 30, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
39 5 0.02
40 322 0.98
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:12257322 original size:37 final size:37
Alignment explanation
Indices: 12257272--12257350 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
12257262 TTATTACGAA
* *
12257272 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
12257309 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
12257346 GTCTT
1 GTCTT
12257351 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:12264036 original size:55 final size:54
Alignment explanation
Indices: 12263941--12264090 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
12263931 CTACTTTGTT
* ** * *
12263941 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
12263995 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
12264050 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
12264091 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:12264053 original size:27 final size:27
Alignment explanation
Indices: 12263913--12264090 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
12263903 TAAATTGTAC
12263913 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
12263940 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
12263966 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
12263994 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
12264022 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
12264049 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
12264076 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12264091 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:12264054 original size:82 final size:81
Alignment explanation
Indices: 12263914--12264069 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
12263904 AAATTGTACA
* * * *
12263914 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
12263979 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
12263995 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
12264058 TGTGCGAGTTGA
63 TGTGCGAATTGA
12264070 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:12267521 original size:63 final size:63
Alignment explanation
Indices: 12267451--12267577 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
12267441 AATTTTAATA
*
12267451 TAATAATATCTTGTTTTTTAGCTGAAAATAGTGGGACACGCAGAGGTCGAGGACCTACGTTAC
1 TAATAATATATTGTTTTTTAGCTGAAAATAGTGGGACACGCAGAGGTCGAGGACCTACGTTAC
12267514 TAATAATATATTGTTTTTTAGCTGAAAATAGTGGGACACGCAGAGGTCGAGGACCTACGTTAC
1 TAATAATATATTGTTTTTTAGCTGAAAATAGTGGGACACGCAGAGGTCGAGGACCTACGTTAC
12267577 T
1 T
12267578 TAAAGATTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (63 bp):
TAATAATATATTGTTTTTTAGCTGAAAATAGTGGGACACGCAGAGGTCGAGGACCTACGTTAC
Found at i:12268830 original size:25 final size:25
Alignment explanation
Indices: 12268802--12268871 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
12268792 CTCTTTTAAT
*
12268802 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
12268827 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
12268852 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
12268872 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:12269715 original size:27 final size:25
Alignment explanation
Indices: 12269680--12269752 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
12269670 GGGCATATTC
12269680 GTCATTTTACCATATAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGT-TTACG
* * *
12269707 GTCACTTTACCCTAAAGGGCTTTACG
1 GTCATTTTA-CCTATAGGGGTTTACG
*
12269733 GTCTTTTTACCTATTAGGGG
1 GTCATTTTACCTA-TAGGGG
12269753 AATTTTAGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.11
26 16 0.43
27 15 0.41
28 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (25 bp):
GTCATTTTACCTATAGGGGTTTACG
Found at i:12269741 original size:26 final size:27
Alignment explanation
Indices: 12269668--12269743 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 27
12269658 TACGGAACAT
12269668 AAGGGCATATT-C-GTCATTTTACCATA
1 AAGGGC-TATTACGGTCATTTTACCATA
* * * *
12269694 TAGGGGTATTACGGTCACTTTACCCTA
1 AAGGGCTATTACGGTCATTTTACCATA
*
12269721 AAGGGCT-TTACGGTCTTTTTACC
1 AAGGGCTATTACGGTCATTTTACC
12269744 TATTAGGGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 4 0.10
26 19 0.47
27 17 0.43
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
AAGGGCTATTACGGTCATTTTACCATA
Found at i:12269827 original size:27 final size:27
Alignment explanation
Indices: 12269797--12269904 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
12269787 GTAAATCTAC
12269797 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
12269824 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
** *
12269850 AGAAAGTTAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
12269880 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
12269905 ACAAATTGAG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 40 0.61
28 7 0.11
29 17 0.26
30 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:12269902 original size:56 final size:55
Alignment explanation
Indices: 12269802--12269983 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 55
12269792 TCTACAAACC
* * * *
12269802 AAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTAGAAAGTT
1 AAGGGTATTTCTGTAATTTTGTAAACCAGTGGTATTT-TGGTAATTTTTACAAA-TT
* *
12269858 AAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAA-TTTTACAAATT
1 AAGGGTATTTCTGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTTTACAAATT
* *** *
12269912 GAGGGTATTT-TGGTAATTTCACAAACCAGTGGTATTTTGGTAA-TTTTACAAACT
1 AAGGGTATTTCT-GTAATTTTGTAAACCAGTGGTATTTTGGTAATTTTTACAAATT
*
12269966 AGGGGTATTT-TGGTAATT
1 AAGGGTATTTCT-GTAATT
12269984 CTACCCTATA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 63 0.58
55 9 0.08
56 36 0.33
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (55 bp):
AAGGGTATTTCTGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTTTACAAATT
Found at i:12269910 original size:27 final size:27
Alignment explanation
Indices: 12269860--12269983 Score: 146
Period size: 27 Copynumber: 4.6 Consensus size: 27
12269850 AGAAAGTTAA
**
12269860 GGGTATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAATCAG
*
12269887 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* *
12269913 AGGGTATTTTGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAATCAG
*
12269941 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
12269968 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
12269984 CTACCCTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
26 3 0.04
27 80 0.95
28 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:12270023 original size:27 final size:26
Alignment explanation
Indices: 12269881--12270023 Score: 119
Period size: 27 Copynumber: 5.3 Consensus size: 26
12269871 TAATTTTGTA
*
12269881 AATCAGGGGTATTTTGGTAATTTTAC
1 AATCAGGGGTATTTTGGTAATTTCAC
*
12269907 AAAT-TGAGGGTATTTTGGTAATTTCAC
1 -AATCAG-GGGTATTTTGGTAATTTCAC
* * *
12269934 AAACCAGTGGTATTTTGGTAATTTTAC
1 -AATCAGGGGTATTTTGGTAATTTCAC
* *
12269961 AAACTAGGGGTATTTTGGTAATTCTACCC
1 AATC-AGGGGTATTTTGGTAATT-T-CAC
* **
12269990 TAT-AGGGGTATTTCAGTAATTTCAC
1 AATCAGGGGTATTTTGGTAATTTCAC
12270015 AATCGAGGG
1 AATC-AGGG
12270024 TAAAACGGTA
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 80 0.86
28 2 0.02
29 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (26 bp):
AATCAGGGGTATTTTGGTAATTTCAC
Found at i:12270034 original size:26 final size:26
Alignment explanation
Indices: 12270003--12270106 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 26
12269993 AGGGGTATTT
12270003 CAGTAATTT-CACAATCGAGGGTAAAA
1 CAGTAATTTGCA-AATCGAGGGTAAAA
* *
12270029 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAGGGTAAAA
* *
12270056 CAGTAATTTTGTAAATCAAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAGGGTAAAA
* **
12270083 CAATAATTCTATAAATCGAGGGTA
1 CAGTAATT-TGCAAATCGAGGGTA
12270107 CTTTTAGGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.10
27 60 0.88
28 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (26 bp):
CAGTAATTTGCAAATCGAGGGTAAAA
Found at i:12270045 original size:27 final size:27
Alignment explanation
Indices: 12270015--12270106 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
12270005 GTAATTTCAC
*
12270015 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTA
12270042 AATCGAGGGTAAAACAGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTA
* * * *
12270069 AATCAAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACAGTAATTTTGTA
12270096 AATCGAGGGTA
1 AATCGAGGGTA
12270107 CTTTTAGGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTTTGTA
Found at i:12271848 original size:13 final size:14
Alignment explanation
Indices: 12271832--12271860 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12271822 TTATAAATAT
12271832 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
12271845 TTATAATGGTTTAA
1 TTATAATGGTTTAA
12271859 TT
1 TT
12271861 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:12273413 original size:50 final size:50
Alignment explanation
Indices: 12273352--12273764 Score: 236
Period size: 50 Copynumber: 8.7 Consensus size: 50
12273342 AGAGGTGTCA
* *
12273352 GTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
1 GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTT
* *** * * *
12273402 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATG--AGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTT
* * * * * * * **
12273450 ATGTAAGA-CATGTCCGGGACAT-GCATTGGC-CTCAAGACG-TA-AGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACAC-AAATATGCTAGAGCTT
*
12273496 GTGTAAGA-CATGTCTGGGACAT-GCATCG--AC---TATG--AGAGGTGT
1 GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCT-T
* *
12273538 CAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
1 --GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTT
* ** **
12273590 GTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCA-A-GACATA-AGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATG-C-TAGAGCTT
* * *
12273638 ATGTAAGA-CATGTCTGGGACAT-GCATC-A-AC---TA--CGAGAGGTGT
1 GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCT-T
* * *
12273680 CAGTGTAAGACTATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTT
1 --GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTT
* *
12273732 GTGTAAGACCATGTCTGGAACATGGCGTCGACA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACA
12273765 TTGAGATGAG
Statistics
Matches: 280, Mismatches: 50, Indels: 66
0.71 0.13 0.17
Matches are distributed among these distances:
40 2 0.01
41 7 0.03
43 1 0.00
44 14 0.05
45 28 0.10
46 55 0.20
47 30 0.11
48 27 0.10
49 4 0.01
50 93 0.33
51 6 0.02
52 2 0.01
53 11 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTT
Found at i:12273516 original size:93 final size:93
Alignment explanation
Indices: 12273165--12273664 Score: 391
Period size: 93 Copynumber: 5.3 Consensus size: 93
12273155 GTTATTGTGA
* * * ** *
12273165 GCTATTGTAAGACATGTCTGGGACATCCATCGGCCACATTATG-AGAGCCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGTAGAGCCAGTGTAAGACCATGT
*
12273229 -TGGGATATGGCATCGGCATTGAGACGAGT
66 CTGGGACAT-GCATCGGCATTGAGA-GAGT
* * *
12273258 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGCCAATGTAAGA-CATAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGTAGAGCCAGTGTAAGACCATGT
*
12273321 CTGGGACATGCATCGAC-TATGAGAG-GT
66 CTGGGACATGCATCGGCAT-TGAGAGAGT
* * * * * * **
12273348 G-TCAGTGTAAAACCATGTTTGGGACATGGCATCGACAC-AAATATGCTAGAGCTTGTGTAAGAC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCAAGACG-TAGAGCCAGTGTAAGAC
12273411 CATGTCTGGGACATGGCATCGGCATTGAGATGAGT
61 CATGTCTGGGACAT-GCATCGGCATTGAGA-GAGT
* * *
12273446 GCTAATGTAAGACATGTCCGGGACATGCATTGGCCTCAAGACGTA-AGCCAGTGTAAGA-CATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGTAGAGCCAGTGTAAGACCATGT
*
12273509 CTGGGACATGCATCGAC-TATGAGAG-GT
66 CTGGGACATGCATCGGCAT-TGAGAGAGT
* * * * * * **
12273536 G-TCAGTGTAAAACCATGTTTGGGACATGGCATCGACAC-AAATATGCTAGAGCTTGTGTAAGAC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCAAGACG-TAGAGCCAGTGTAAGAC
* ** *
12273599 CATGTCTGGGACATGGCATCGGCCTCAAGACA-T
61 CATGTCTGGGACAT-GCATCGGCATTGAGAGAGT
* *
12273632 AAGCCAATGTAAGACATGTCTGGGACATGCATC
1 --GCTAGTGTAAGACATGTCTGGGACATGCATC
12273665 AACTACGAGA
Statistics
Matches: 323, Mismatches: 54, Indels: 57
0.74 0.12 0.13
Matches are distributed among these distances:
89 2 0.01
90 21 0.07
91 29 0.09
92 48 0.15
93 75 0.23
94 33 0.10
95 30 0.09
96 38 0.12
97 28 0.09
98 18 0.06
99 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGTAGAGCCAGTGTAAGACCATGT
CTGGGACATGCATCGGCATTGAGAGAGT
Found at i:12273525 original size:142 final size:138
Alignment explanation
Indices: 12273163--12273755 Score: 465
Period size: 142 Copynumber: 4.2 Consensus size: 138
12273153 GTGTTATTGT
* * * * ** *
12273163 GAGCTATTGTAAGACATGTCTGGGACATCCATCGGCCACATTATG-AGAGCCAGTGTAAGACCAT
1 GAGCTAATGTAAGACATGTCTGGGACATGCATTGGCCTCAAGACGTA-AGCCAGTGTAAGA-CAT
* * *
12273227 GT-TGGGATATGGCATCGGC-ATTGAGACGAGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCAT
64 GTCTGGGACAT-GCATCGACTA-TGAGA-G-CTG-TAGTGTAAGACCATGTCTGGGACATGGCAT
* * *
12273288 CGGCCTCGAGACGTA
124 CGGCATAGAGATGTA
* * * * * * *
12273303 -AGCCAATGTAAGACATATCTGGGACATGCA-TCGACT-ATGAGAGGT--GTCAGTGTAAAACCA
1 GAGCTAATGTAAGACATGTCTGGGACATGCATTGGCCTCA--AGACGTAAGCCAGTGTAAGA-CA
*
12273363 TGTTTGGGACATGGCATCGACACAAATATGCTAGAGCT-T-GTGTAAGACCATGTCTGGGACATG
63 TGTCTGGGACAT-GCATCG--AC---TATG--AGAGCTGTAGTGTAAGACCATGTCTGGGACATG
*
12273426 GCATCGGCATTGAGATG-A
120 GCATCGGCATAGAGATGTA
* *
12273444 GTGCTAATGTAAGACATGTCCGGGACATGCATTGGCCTCAAGACGTAAGCCAGTGTAAGACATGT
1 GAGCTAATGTAAGACATGTCTGGGACATGCATTGGCCTCAAGACGTAAGCCAGTGTAAGACATGT
* * * * *
12273509 CTGGGACATGCATCGACTATGAGAGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACAC
66 CTGGGACATGCATCGACTATGAGAGCTGT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* *
12273574 AAATATGCTA
130 AGAGATG-TA
** * * *
12273584 GAGCTTGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGACATAAGCCAATGTAAGACAT
1 GAGCTAATGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCAAGACGTAAGCCAGTGTAAGACAT
* * * * *
12273649 GTCTGGGACATGCATCAACTACGAGAGGTGTCAGTGTAAGACTATGTCTGGGACATGGCATCGAC
64 GTCTGGGACATGCATCGACTATGAGAGCTGT-AGTGTAAGACCATGTCTGGGACATGGCATCGGC
*
12273714 ATAGATATGCTA
128 ATAGAGATG-TA
** *
12273726 GAGCTTGTGTAAGACCATGTCTGGAACATG
1 GAGCTAATGTAAGA-CATGTCTGGGACATG
12273756 GCGTCGACAT
Statistics
Matches: 375, Mismatches: 52, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
135 5 0.01
136 1 0.00
137 21 0.06
138 50 0.13
139 28 0.07
140 23 0.06
141 30 0.08
142 181 0.48
143 20 0.05
144 13 0.03
145 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (138 bp):
GAGCTAATGTAAGACATGTCTGGGACATGCATTGGCCTCAAGACGTAAGCCAGTGTAAGACATGT
CTGGGACATGCATCGACTATGAGAGCTGTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATA
GAGATGTA
Found at i:12273552 original size:188 final size:188
Alignment explanation
Indices: 12273215--12273664 Score: 744
Period size: 188 Copynumber: 2.4 Consensus size: 188
12273205 ATGAGAGCCA
* * *
12273215 GTGTAAGACCATGT-TGGGATATGGCATCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGG
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCTAATGTAAGACATGTCCGG
*
12273279 GACATGCATCGGCCTCGAGACGTAAGCCAATGTAAGACATATCTGGGACATGCATCGACTATGAG
66 GACATGCATCGGCCTCAAGACGTAAGCCAATGTAAGACATATCTGGGACATGCATCGACTATGAG
12273344 AGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
131 AGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
*
12273402 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGTGCTAATGTAAGACATGTCCGG
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCTAATGTAAGACATGTCCGG
* * *
12273467 GACATGCATTGGCCTCAAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTATGAG
66 GACATGCATCGGCCTCAAGACGTAAGCCAATGTAAGACATATCTGGGACATGCATCGACTATGAG
12273532 AGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
131 AGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
* ** * *
12273590 GTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGAC-A-TAAGCCAATGTAAGACATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGT--GCTAATGTAAGACATGTCC
12273653 GGGACATGCATC
64 GGGACATGCATC
12273665 AACTACGAGA
Statistics
Matches: 245, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
186 1 0.00
187 15 0.06
188 229 0.93
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (188 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCTAATGTAAGACATGTCCGG
GACATGCATCGGCCTCAAGACGTAAGCCAATGTAAGACATATCTGGGACATGCATCGACTATGAG
AGGTGTCAGTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTT
Found at i:12273756 original size:142 final size:142
Alignment explanation
Indices: 12273402--12273757 Score: 522
Period size: 142 Copynumber: 2.5 Consensus size: 142
12273392 GCTAGAGCTT
* * * * **
12273402 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATG--AGTGCTAATGTAAGA-CATGTC
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTC
* * * * *
12273464 CGGGACAT-GCATTGGCCTCAAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTA
66 TGGGACATGGCATCGGCCTCAAGACATAAGCCAATGTAAGACATGTCTGGGACATGCATCAACTA
*
12273528 TGAGAGGTGTCA
131 CGAGAGGTGTCA
* * * *
12273540 GTGTAAAACCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTTGTGTAAGACCATGTC
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTC
12273605 TGGGACATGGCATCGGCCTCAAGACATAAGCCAATGTAAGACATGTCTGGGACATGCATCAACTA
66 TGGGACATGGCATCGGCCTCAAGACATAAGCCAATGTAAGACATGTCTGGGACATGCATCAACTA
12273670 CGAGAGGTGTCA
131 CGAGAGGTGTCA
*
12273682 GTGTAAGACTATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTC
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTC
*
12273747 TGGAACATGGC
66 TGGGACATGGC
12273758 GTCGACATTG
Statistics
Matches: 192, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
138 34 0.18
140 12 0.06
141 13 0.07
142 133 0.69
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (142 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTC
TGGGACATGGCATCGGCCTCAAGACATAAGCCAATGTAAGACATGTCTGGGACATGCATCAACTA
CGAGAGGTGTCA
Found at i:12273785 original size:142 final size:141
Alignment explanation
Indices: 12273483--12273808 Score: 456
Period size: 142 Copynumber: 2.3 Consensus size: 141
12273473 CATTGGCCTC
* * *
12273483 AAGACGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTATGAGAGGTGTCAGTGTAAAA
1 AAGACATAAGCCAGTGTAAGACATGTCTGGGACATGCATCAACTACGAGAGGTGTCAGTGTAAAA
* *
12273548 CCATGTTTGGGACATGGCATCGACACAAATATGCTAGAGCTTGTGTAAGACCATGTCTGGGACAT
66 CCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTTGTGTAAGACCATGTCTGGAACAT
* *
12273613 GGCATCGGCCT
131 GGCATCGACAT
* *
12273624 CAAGACATAAGCCAATGTAAGACATGTCTGGGACATGCATCAACTACGAGAGGTGTCAGTGTAAG
1 -AAGACATAAGCCAGTGTAAGACATGTCTGGGACATGCATCAACTACGAGAGGTGTCAGTGTAAA
* * *
12273689 ACTATGTCTGGGACATGGCATCGACATAGATATGCTAGAGCTTGTGTAAGACCATGTCTGGAACA
65 ACCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTTGTGTAAGACCATGTCTGGAACA
*
12273754 TGGCGTCGACAT
130 TGGCATCGACAT
* * * *
12273766 -TGAGATGAGTGCCAGTGTAAGACATTTCTGGGACATGGCATCA
1 AAGACAT-A-AGCCAGTGTAAGACATGTCTGGGACAT-GCATCA
12273809 GCACCTGCAC
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
140 4 0.02
141 1 0.01
142 152 0.93
143 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (141 bp):
AAGACATAAGCCAGTGTAAGACATGTCTGGGACATGCATCAACTACGAGAGGTGTCAGTGTAAAA
CCATGTCTGGGACATGGCATCGACACAAATATGCTAGAGCTTGTGTAAGACCATGTCTGGAACAT
GGCATCGACAT
Found at i:12281645 original size:18 final size:17
Alignment explanation
Indices: 12281618--12281712 Score: 57
Period size: 18 Copynumber: 5.1 Consensus size: 17
12281608 TTTGGTTTGC
*
12281618 TATTTGACTTAGTAGTTT
1 TATTTAACTTAGT-GTTT
12281636 TATTTAACTTAGTGTATT
1 TATTTAACTTAGTGT-TT
** *
12281654 TACTTTTTATTTTAGTTTTGT
1 TA---TTTAACTTAGTGTT-T
12281675 TATTTTAA-TTAGTAGTTT
1 TA-TTTAACTTAGT-GTTT
*
12281693 TATTTAACATAGTGTATT
1 TATTTAACTTAGTGT-TT
12281711 TA
1 TA
12281713 CTTTTTACAG
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
17 9 0.15
18 32 0.52
19 7 0.11
20 1 0.02
21 13 0.21
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTTAACTTAGTGTTT
Found at i:12288462 original size:27 final size:27
Alignment explanation
Indices: 12288423--12288533 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
12288413 CCTGGTTTGT
* * *
12288423 AAATTATCG-AATACCCTTATGGTGTA
1 AAATTACCGAAATACCCTTGTAGTGTA
*
12288449 AAATTACCAAAATACCCTTGTAGTGTA
1 AAATTACCGAAATACCCTTGTAGTGTA
12288476 AAATTACCGAAATGA-CCTTGTAGTGTA
1 AAATTACCGAAAT-ACCCTTGTAGTGTA
*
12288503 AAATTACCGAAATACCAC-TGTAGGGTA
1 AAATTACCGAAATACC-CTTGTAGTGTA
12288530 AAAT
1 AAAT
12288534 GACTGTGCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 8 0.11
27 65 0.87
28 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (27 bp):
AAATTACCGAAATACCCTTGTAGTGTA
Found at i:12288735 original size:32 final size:32
Alignment explanation
Indices: 12288672--12288735 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
12288662 CTAATGGATA
* *
12288672 TGTGCCAAACATAATACAGTTACCGATGGCTT
1 TGTGCCAAACATAATACAGCTACCGAAGGCTT
** * *
12288704 TGTGCCAATTATAATACCGCTACTGAAGGCTT
1 TGTGCCAAACATAATACAGCTACCGAAGGCTT
12288736 AGAGCCGCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (32 bp):
TGTGCCAAACATAATACAGCTACCGAAGGCTT
Found at i:12298630 original size:30 final size:30
Alignment explanation
Indices: 12298596--12298692 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
12298586 AGCTCACTCC
12298596 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
12298626 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
12298656 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
12298686 TAGCTCA
1 TAGCTCA
12298693 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:12300510 original size:30 final size:31
Alignment explanation
Indices: 12300476--12300572 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
12300466 AGCTCACTCC
*
12300476 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
12300506 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
12300536 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
12300566 TAGCTCA
1 TAGCTCA
12300573 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:12301462 original size:22 final size:20
Alignment explanation
Indices: 12301430--12301478 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
12301420 GCCGAATTTA
12301430 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
12301453 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
12301473 TGAACA
1 TGAACA
12301479 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:12312040 original size:10 final size:10
Alignment explanation
Indices: 12312022--12312072 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
12312012 TAAAGGAAAA
*
12312022 GAAATGAGCT
1 GAAACGAGCT
12312032 GAAACGAGCT
1 GAAACGAGCT
*
12312042 AAAATCGAGCT
1 GAAA-CGAGCT
*
12312053 CAAACGAGCT
1 GAAACGAGCT
12312063 GAAACGAGCT
1 GAAACGAGCT
12312073 CAAGTGAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (10 bp):
GAAACGAGCT
Found at i:12312051 original size:21 final size:21
Alignment explanation
Indices: 12312023--12312075 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
12312013 AAAGGAAAAG
*
12312023 AAAT-GAGCTGAAACGAGCTA
1 AAATCGAGCTCAAACGAGCTA
*
12312043 AAATCGAGCTCAAACGAGCTG
1 AAATCGAGCTCAAACGAGCTA
12312064 AAA-CGAGCTCAA
1 AAATCGAGCTCAA
12312076 GTGAGCTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (21 bp):
AAATCGAGCTCAAACGAGCTA
Found at i:12312081 original size:20 final size:21
Alignment explanation
Indices: 12312022--12312084 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
12312012 TAAAGGAAAA
*
12312022 GAAAT-GAGCTGAAACGAGCT
1 GAAATCGAGCTCAAACGAGCT
*
12312042 AAAATCGAGCTCAAACGAGCT
1 GAAATCGAGCTCAAACGAGCT
**
12312063 GAAA-CGAGCTCAAGTGAGCT
1 GAAATCGAGCTCAAACGAGCT
12312083 GA
1 GA
12312085 TTGGAGCTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (21 bp):
GAAATCGAGCTCAAACGAGCT
Found at i:12313166 original size:16 final size:16
Alignment explanation
Indices: 12313140--12313183 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12313130 TACAATACCA
12313140 AAAAAACAAACAAAAGT
1 AAAAAA-AAACAAAAGT
*
12313157 AAAAAAAAAC-CAAGT
1 AAAAAAAAACAAAAGT
*
12313172 TAAAAAAAACAA
1 AAAAAAAAACAA
12313184 CAAAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.57
16 4 0.17
17 6 0.26
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAAAAAAACAAAAGT
Found at i:12313846 original size:14 final size:14
Alignment explanation
Indices: 12313827--12313857 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12313817 GGGATAGTTG
12313827 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
12313841 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
12313855 AAG
1 AAG
12313858 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:12316658 original size:10 final size:10
Alignment explanation
Indices: 12316643--12316680 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
12316633 GCTCGTTTCC
*
12316643 AGCTCACTCG
1 AGCTCAATCG
12316653 AGCTCAAGTC-
1 AGCTCAA-TCG
12316663 AGCTCAATCG
1 AGCTCAATCG
12316673 AGCTCAAT
1 AGCTCAAT
12316681 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:12316667 original size:20 final size:20
Alignment explanation
Indices: 12316642--12316679 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12316632 AGCTCGTTTC
*
12316642 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
12316662 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
12316680 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:12316686 original size:20 final size:20
Alignment explanation
Indices: 12316643--12316703 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
12316633 GCTCGTTTCC
* * *
12316643 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
12316663 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
12316683 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
12316703 A
1 A
12316704 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:12316697 original size:11 final size:10
Alignment explanation
Indices: 12316653--12316699 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
12316643 AGCTCACTCG
*
12316653 AGCTCAAGTC
1 AGCTCAATTC
12316663 AGCTCAA-TC
1 AGCTCAATTC
*
12316672 GAGCTCAATTT
1 -AGCTCAATTC
12316683 AGCTACAATTC
1 AGCT-CAATTC
12316694 AGCTCA
1 AGCTCA
12316700 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:12318117 original size:14 final size:13
Alignment explanation
Indices: 12318098--12318133 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
12318088 AAAGAGTTCG
12318098 AAAAAAAAATTGA
1 AAAAAAAAATTGA
12318111 AAAAAAAAATTGA
1 AAAAAAAAATTGA
12318124 AAAGAAAAAA
1 AAA-AAAAAA
12318134 AAATTGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:12319227 original size:18 final size:18
Alignment explanation
Indices: 12319189--12319230 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12319179 AAATCGAAAG
* **
12319189 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
12319207 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
12319225 AAAAGA
1 AAAAGA
12319231 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:12320940 original size:10 final size:10
Alignment explanation
Indices: 12320925--12320962 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
12320915 GCTCGTTTCC
*
12320925 AGCTCACTCG
1 AGCTCAATCG
12320935 AGCTCAAGTC-
1 AGCTCAA-TCG
12320945 AGCTCAATCG
1 AGCTCAATCG
12320955 AGCTCAAT
1 AGCTCAAT
12320963 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:12320949 original size:20 final size:20
Alignment explanation
Indices: 12320924--12320961 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12320914 AGCTCGTTTC
*
12320924 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
12320944 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
12320962 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:12320968 original size:20 final size:20
Alignment explanation
Indices: 12320925--12320985 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
12320915 GCTCGTTTCC
* * *
12320925 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
12320945 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
12320965 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
12320985 A
1 A
12320986 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:12320979 original size:11 final size:10
Alignment explanation
Indices: 12320935--12320981 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
12320925 AGCTCACTCG
*
12320935 AGCTCAAGTC
1 AGCTCAATTC
12320945 AGCTCAA-TC
1 AGCTCAATTC
*
12320954 GAGCTCAATTT
1 -AGCTCAATTC
12320965 AGCTACAATTC
1 AGCT-CAATTC
12320976 AGCTCA
1 AGCTCA
12320982 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:12321486 original size:13 final size:13
Alignment explanation
Indices: 12321468--12321492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12321458 GTATTGATCA
12321468 TGTGTTCACACCT
1 TGTGTTCACACCT
12321481 TGTGTTCACACC
1 TGTGTTCACACC
12321493 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:12326678 original size:8 final size:7
Alignment explanation
Indices: 12326647--12326677 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
12326637 GCCTATCATA
12326647 TCTCCCT
1 TCTCCCT
12326654 TCTCCCT
1 TCTCCCT
12326661 TCTCCCT
1 TCTCCCT
12326668 TCCTCCCT
1 T-CTCCCT
12326676 TC
1 TC
12326678 CATTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
TCTCCCT
Found at i:12327026 original size:25 final size:25
Alignment explanation
Indices: 12326982--12327029 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12326972 CTTTTTCCCT
*
12326982 TTATTTATTATTCTTATTTCTATTA
1 TTATTTATTATTATTATTTCTATTA
12327007 TTATTTATTATTA-TATTTTCTAT
1 TTATTTATTATTATTA-TTTCTAT
12327030 CATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTTATTATTATTATTTCTATTA
Found at i:12329074 original size:37 final size:37
Alignment explanation
Indices: 12329024--12329102 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
12329014 TTATTACGAA
* * *
12329024 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
12329061 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
12329098 GTCTT
1 GTCTT
12329103 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:12329299 original size:47 final size:47
Alignment explanation
Indices: 12329221--12329633 Score: 691
Period size: 47 Copynumber: 8.7 Consensus size: 47
12329211 CCCTTCGGGA
* * * * * *
12329221 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12329268 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329315 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329362 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
12329456 CTTATCACATATACATACACTTTCACATTCATCATTTCGGCTATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12329505 CTTATTACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329552 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329599 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
12329634 AGAATCCTAA
Statistics
Matches: 344, Mismatches: 20, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
47 302 0.88
49 42 0.12
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12329542 original size:190 final size:188
Alignment explanation
Indices: 12329221--12329633 Score: 691
Period size: 190 Copynumber: 2.2 Consensus size: 188
12329211 CCCTTCGGGA
* * * * * *
12329221 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
12329286 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
12329351 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12329409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATAT--ATAC
** * *
12329474 ACTTTCACATTCATCATTTCGGCTATTAGGCCTTATTACACATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACA
12329539 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12329599 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
12329634 AGAATCCTAA
Statistics
Matches: 210, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
188 51 0.24
190 159 0.76
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12330795 original size:18 final size:18
Alignment explanation
Indices: 12330772--12330813 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
12330762 CATATGCATT
12330772 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
12330790 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
12330808 TTTAAT
1 TTTAAT
12330814 ACAATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
TTTAATCACATCAAGCAA
Found at i:12341401 original size:47 final size:49
Alignment explanation
Indices: 12341176--12341697 Score: 866
Period size: 49 Copynumber: 10.9 Consensus size: 49
12341166 NNNNNNNNNN
*
12341176 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
12341225 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
12341274 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
12341323 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
* * * * * * *
12341371 T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--A
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
12341417 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
12341466 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
12341515 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--A
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
12341562 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--A
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
12341609 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--A
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
12341656 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
12341698 CTATCATTTC
Statistics
Matches: 454, Mismatches: 15, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 212 0.47
48 1 0.00
49 240 0.53
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
Found at i:12341512 original size:192 final size:192
Alignment explanation
Indices: 12341176--12341694 Score: 898
Period size: 192 Copynumber: 2.7 Consensus size: 192
12341166 NNNNNNNNNN
12341176 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATACACTTTCACA
1 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACA
* *
12341241 TTCATCACGTCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACGTCGGCCA
64 TTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCA
*
12341306 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
129 TTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
* * * * * * *
12341370 TTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACTTTCACATT
1 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
*
12341435 CATCACATCGGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATT
66 CATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATT
12341500 AGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
131 AGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
*
12341562 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
1 TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
12341627 CATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATT
66 CATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATT
12341690 AGGCC
131 AGGCC
12341695 TTACTATCAT
Statistics
Matches: 305, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
190 40 0.13
192 226 0.74
194 39 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (192 bp):
TATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
CATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATT
AGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
Found at i:12346191 original size:99 final size:94
Alignment explanation
Indices: 12346062--12346236 Score: 208
Period size: 99 Copynumber: 1.8 Consensus size: 94
12346052 TAAAATGCTG
*
12346062 ATGCCATGTCCCAGACATGGTCTCACACTGACTATCGAAATCG-AGGCCGACGCCATGTCCCAGA
1 ATGCAATGTCCCAGACATGGTCTCACACTGAC-A-C-AAATCGTA-GCCGACG-CATGTCCCAGA
12346126 CATGGTCTTACACTAGCTCTCACATATCCGTGCCA
61 CAT-GTCTTACACTAGCTCTCACATATCCGTGCCA
* * * * ** * *
12346161 ATGCAATGTCCTATACATGGTCTTATACTGACACATCTCGTAGTCGATGCATGTCCCAGACATGT
1 ATGCAATGTCCCAGACATGGTCTCACACTGACACAAATCGTAGCCGACGCATGTCCCAGACATGT
12346226 CTTACACTAGC
66 CTTACACTAGC
12346237 ACACACTATC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
94 13 0.20
95 14 0.21
96 9 0.14
97 2 0.03
98 1 0.02
99 27 0.41
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (94 bp):
ATGCAATGTCCCAGACATGGTCTCACACTGACACAAATCGTAGCCGACGCATGTCCCAGACATGT
CTTACACTAGCTCTCACATATCCGTGCCA
Found at i:12348981 original size:40 final size:40
Alignment explanation
Indices: 12348934--12349012 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
12348924 GCTTACAATT
12348934 CCGGTTTTCACCATTCTGGCAATTTCATCCATAATTCAGA
1 CCGGTTTTCACCATTCTGGCAATTTCATCCATAATTCAGA
12348974 CCGGTTTTCACCATTCTGGCAATTTCATCCATAATTCAG
1 CCGGTTTTCACCATTCTGGCAATTTCATCCATAATTCAG
12349013 GGCAGTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (40 bp):
CCGGTTTTCACCATTCTGGCAATTTCATCCATAATTCAGA
Found at i:12349021 original size:40 final size:40
Alignment explanation
Indices: 12348937--12349021 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
12348927 TACAATTCCG
*
12348937 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCG
1 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
**
12348977 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGGGCA
1 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
12349017 GTTTT
1 GTTTT
12349022 AGTTTTCTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (40 bp):
GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
Found at i:12350758 original size:26 final size:27
Alignment explanation
Indices: 12350720--12350791 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
12350710 TGTAGGGTAG
12350720 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTACAA
*
12350747 AATTACTG-AATACCGTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTACAA
**
12350773 AATTACCAAAATACCCTTG
1 AATTACTGAAATACCCTTG
12350792 ATTAGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 23 0.57
27 17 0.43
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGGTTTACAA
Found at i:12350801 original size:27 final size:27
Alignment explanation
Indices: 12350771--12351007 Score: 226
Period size: 27 Copynumber: 8.8 Consensus size: 27
12350761 GTTGGTTTAC
*
12350771 AAAATTACCAAAATACCCTTGATTAGT
1 AAAATTACCAAAATACCCTTGATTTGT
12350798 AAAATTACCAAAATACCCTCT-ATTTGT
1 AAAATTACCAAAATACCCT-TGATTTGT
12350825 AAAATTACCAAAATACACC-TGATTTGT
1 AAAATTACCAAAATAC-CCTTGATTTGT
* ** * **
12350852 GAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * * **
12350879 AAAATTATCGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* *
12350906 AAAATTACCAAAATACCCCTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
*** * *
12350933 AAAATTATTGAAATACCCTTGGTTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
*
12350960 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * * *
12350987 AGATTTACAAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
12351008 TAGGGTGAAA
Statistics
Matches: 176, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
26 3 0.02
27 170 0.97
28 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGT
Found at i:12351337 original size:40 final size:41
Alignment explanation
Indices: 12351250--12351366 Score: 182
Period size: 40 Copynumber: 2.9 Consensus size: 41
12351240 AAGAAATTGG
* * *
12351250 GGATCACATGGTTGTTTGACGACCGTGGATCCACCGATTGA
1 GGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTAA
* *
12351291 GAATCGCATGGTTGCTTGACGATCGT-GATCCACCGATTAA
1 GGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTAA
12351331 GGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 GGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
12351367 GTGGCTTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 37 0.54
41 31 0.46
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (41 bp):
GGATCGCATGGTTGCTTGACGACCGTGGATCCACCGATTAA
Found at i:12351560 original size:22 final size:22
Alignment explanation
Indices: 12351509--12351572 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
12351499 CCAATTATTT
*
12351509 TGATTATGGCTTTGTGCCAACC
1 TGATTATGGCTATGTGCCAACC
* *
12351531 T-ACATATGGCTCTGTGCCAACC
1 TGA-TTATGGCTATGTGCCAACC
*
12351553 TGATTATGGTTATGTGCCAA
1 TGATTATGGCTATGTGCCAA
12351573 ACGTATTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
TGATTATGGCTATGTGCCAACC
Found at i:12356859 original size:20 final size:20
Alignment explanation
Indices: 12356836--12356881 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12356826 CCAGCTCGAA
*
12356836 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
12356856 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
12356876 TTAGCT
1 TTAGCT
12356882 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:12356863 original size:30 final size:30
Alignment explanation
Indices: 12356828--12356901 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
12356818 AGTTTTTCCC
12356828 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
12356858 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
12356888 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
12356902 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:12359153 original size:12 final size:12
Alignment explanation
Indices: 12359141--12359258 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
12359131 GAAAGAGATT
*
12359141 GAAAAAGAAATT
1 GAAAAAGAAATA
12359153 G--AAAGAAA-A
1 GAAAAAGAAATA
*
12359162 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
12359173 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
12359186 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
12359198 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
12359210 GAAAAAGTGAGA
1 GAAAAAGAAATA
12359222 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
12359233 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
12359249 GAAAAAGAAA
1 GAAAAAGAAA
12359259 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:12359184 original size:18 final size:18
Alignment explanation
Indices: 12359158--12359261 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
12359148 AAATTGAAAG
*
12359158 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
12359176 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
12359194 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
12359212 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
12359230 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
12359251 AAAAGAAAAAG
1 AAAAGAAAAAG
12359262 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:12359186 original size:6 final size:6
Alignment explanation
Indices: 12359154--12359261 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
12359144 AAAGAAATTG
* * ** *
12359154 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
12359201 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
12359252 AAAGAA AAAG
1 AAAGAA AAAG
12359262 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:12359243 original size:14 final size:13
Alignment explanation
Indices: 12359222--12359259 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12359212 AAAAGTGAGA
12359222 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
12359234 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
12359249 GAAAAAGAAAA
1 GAAAAAGAAAA
12359260 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:12359273 original size:21 final size:21
Alignment explanation
Indices: 12359223--12359273 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
12359213 AAAGTGAGAG
*
12359223 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
12359244 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
12359265 AAAAAGAAA
1 AAAAAGAAA
12359274 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:12359313 original size:33 final size:33
Alignment explanation
Indices: 12359276--12359338 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
12359266 AAAAGAAATT
12359276 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
12359309 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
12359339 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:12361138 original size:20 final size:20
Alignment explanation
Indices: 12361115--12361168 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
12361105 AGTTTTTCCC
*
12361115 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
12361135 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
12361155 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
12361169 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:12361150 original size:30 final size:30
Alignment explanation
Indices: 12361115--12361188 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
12361105 AGTTTTTCCC
12361115 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
12361145 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
12361175 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
12361189 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:12361178 original size:20 final size:20
Alignment explanation
Indices: 12361115--12361179 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
12361105 AGTTTTTCCC
* * * *
12361115 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
12361135 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
12361154 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
12361175 AGCTC
1 AGCTC
12361180 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:12362965 original size:100 final size:99
Alignment explanation
Indices: 12362790--12363065 Score: 353
Period size: 100 Copynumber: 2.7 Consensus size: 99
12362780 AGAACACATA
* ** * *
12362790 TGTAGTACTATGTGCAGGCTACTATGTGT-TTAAGATGGTTTTAGGTC-AAGTGTGTAGTACTAA
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAA-AT--TGTTAGGTCGCA-TGTGTAGTACTAA
12362853 GTGCAGGCTACTACATGTACCAAAT-TATTAGGTCCCA-TG
62 GTGCAGGCTACTACATGTACCAAATGT-TTAGG--CCAGTG
*
12362892 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAGTGT
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAGTGC
* *
12362957 AGGCTACTACGTGTATCAAATGTTTAGGCCATGTG
66 AGGCTACTACATGTACCAAATGTTTAGGCCA-GTG
** *
12362992 TGTAGTACTAAGTGCAGGCTACTACATGTACCAAACTGTTAGGTCGCATGTGTAGTACTAAGTGC
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAGTGC
12363057 AGGCTACTA
66 AGGCTACTA
12363066 TGCGTACCAG
Statistics
Matches: 157, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
98 3 0.02
100 120 0.76
101 2 0.01
102 30 0.19
103 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (99 bp):
TGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACTAAGTGC
AGGCTACTACATGTACCAAATGTTTAGGCCAGTG
Found at i:12363012 original size:150 final size:152
Alignment explanation
Indices: 12362790--12363074 Score: 450
Period size: 150 Copynumber: 1.9 Consensus size: 152
12362780 AGAACACATA
* * * *
12362790 TGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGTCAAGTGTGTAGTACTAAGT
1 TGTAGTACTAAGTGCAGGCTACTACGTGTTCAAGATGGTTTTAGGCCAAGTGTGTAGTACTAAGT
* *
12362855 GCAGGCTACTACATGTACCAAATTATTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGTG
66 GCAGGCTACTACATGTACCAAACTATTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGCG
12362920 TACCAAATTGTTAGGTCGCATG
131 TACCAAATTGTTAGGTCGCATG
* *
12362942 TGTAGTACTAAGTGTAGGCTACTACGTGTATCAA-AT-G-TTTAGGCCATGTGTGTAGTACTAAG
1 TGTAGTACTAAGTGCAGGCTACTACGTGT-TCAAGATGGTTTTAGGCCAAGTGTGTAGTACTAAG
* *
12363004 TGCAGGCTACTACATGTACCAAACTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGC
65 TGCAGGCTACTACATGTACCAAACTATTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGC
12363069 GTACCA
130 GTACCA
12363075 GAGAGCTTTG
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
150 90 0.74
151 1 0.01
152 28 0.23
153 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (152 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTTCAAGATGGTTTTAGGCCAAGTGTGTAGTACTAAGT
GCAGGCTACTACATGTACCAAACTATTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGCG
TACCAAATTGTTAGGTCGCATG
Found at i:12363073 original size:50 final size:50
Alignment explanation
Indices: 12362840--12363074 Score: 332
Period size: 50 Copynumber: 4.7 Consensus size: 50
12362830 TTAGGTCAAG
* * *
12362840 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTATTAGGTCCCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
*
12362890 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
* *
12362940 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAAA-TGTTTAGG-C-CA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTG-TTAGGTCGCA
* *
12362988 TGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAACTGTTAGGTCGCA
1 --TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
* *
12363040 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
12363075 GAGAGCTTTG
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
48 2 0.01
49 3 0.02
50 156 0.94
51 3 0.02
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
Found at i:12363926 original size:14 final size:14
Alignment explanation
Indices: 12363907--12363935 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12363897 AATAAATAGA
12363907 AAGAATTTGAAAAT
1 AAGAATTTGAAAAT
12363921 AAGAATTTGAAAAT
1 AAGAATTTGAAAAT
12363935 A
1 A
12363936 GCATGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (14 bp):
AAGAATTTGAAAAT
Found at i:12370772 original size:37 final size:37
Alignment explanation
Indices: 12370719--12370821 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
12370709 CGAATAGTCA
* *
12370719 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCAGACAAAATCT
*
12370756 CCACACGTAGTCATCGGGTCTTACCCAGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCAGACAAAATCT
12370793 CCACACGTAGTCATCGGGTCTTACCCAGA
1 CCACACGTAGTCATCGGGTCTTACCCAGA
12370822 ATATATTTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCAGACAAAATCT
Found at i:12371020 original size:48 final size:48
Alignment explanation
Indices: 12370962--12372305 Score: 2458
Period size: 48 Copynumber: 28.0 Consensus size: 48
12370952 ATATACACAC
* * * *
12370962 ATCTCCTACATATTTCACATTAGCCATTCAGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371010 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371058 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371106 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371154 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371202 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371250 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371298 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371346 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371394 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371442 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371490 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371538 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371586 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371634 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371682 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371730 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371778 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12371826 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12371874 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12371922 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
12371970 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * **
12372018 ATCTCATACATATTTCATATTATCCATTTAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12372066 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12372114 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATAGAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
12372162 ATCTCATGCATA--TGACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12372208 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12372256 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12372304 AT
1 AT
12372306 ATTTATCTTG
Statistics
Matches: 1260, Mismatches: 34, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
46 41 0.03
48 1219 0.97
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:12377248 original size:20 final size:20
Alignment explanation
Indices: 12377211--12377249 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12377201 GCTTGTACGA
*
12377211 GATTGCACTTCGATGCCTCC
1 GATTGCACTTCGAAGCCTCC
12377231 GATTGCACATTC-AAGCCTC
1 GATTGCAC-TTCGAAGCCTC
12377250 TATTCGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (20 bp):
GATTGCACTTCGAAGCCTCC
Found at i:12383107 original size:27 final size:26
Alignment explanation
Indices: 12383060--12383110 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12383050 CGAGGCTACA
*
12383060 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
12383086 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
12383111 TTGCAGTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:12395925 original size:98 final size:98
Alignment explanation
Indices: 12395756--12396019 Score: 458
Period size: 98 Copynumber: 2.7 Consensus size: 98
12395746 CTCCACAGAA
*
12395756 ATTGCAGCGAGGCTACCAGATATTGTGACGAAGTCACCAGATACAAATATTGCGGCTAGGCCACC
1 ATTGCAGCGAGGCTACAAGATATTGTGACGAAGTCACCAGATACAAATATTGCGGCTAGGCCACC
12395821 AGAACAGATATATATAAATGGCAAAGCCACCAG
66 AGAACAGATATATATAAATGGCAAAGCCACCAG
12395854 ATTGCAGCGAGGCTACAAGATATTGTGACGAAGTCACCAGATACAAATATTGCGGCTAGGCCACC
1 ATTGCAGCGAGGCTACAAGATATTGTGACGAAGTCACCAGATACAAATATTGCGGCTAGGCCACC
*
12395919 AGAACAGATATATATATATGGCAAAGCCACCAG
66 AGAACAGATATATATAAATGGCAAAGCCACCAG
* * * *
12395952 ATTGCAGAGAGGCTACAAGATATTGTGACGAAGTCACCAGA-ACAGATATATGTGGCGAGGCCAC
1 ATTGCAGCGAGGCTACAAGATATTGTGACGAAGTCACCAGATACAAATAT-TGCGGCTAGGCCAC
12396016 CAGA
65 CAGA
12396020 TTGCAGCGAG
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
97 7 0.04
98 152 0.96
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (98 bp):
ATTGCAGCGAGGCTACAAGATATTGTGACGAAGTCACCAGATACAAATATTGCGGCTAGGCCACC
AGAACAGATATATATAAATGGCAAAGCCACCAG
Found at i:12396016 original size:27 final size:26
Alignment explanation
Indices: 12395969--12396019 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12395959 AGAGGCTACA
*
12395969 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
12395995 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
12396020 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:12398538 original size:37 final size:37
Alignment explanation
Indices: 12398414--12398538 Score: 142
Period size: 37 Copynumber: 3.4 Consensus size: 37
12398404 CCAACCGAAG
* * * * *
12398414 CATGCCAGATGTTTATAAGATCTAATCCACTTGATAG
1 CATGCCAGATGCTCATAAGAGCTAATCCACCTGATAA
* * **
12398451 CATGCCAAATTCTTTTAAGAGCTAATCCACCTGATAA
1 CATGCCAGATGCTCATAAGAGCTAATCCACCTGATAA
** *
12398488 CACACCAGGTGCTCATAAGAGCTAATCCACCTGATAA
1 CATGCCAGATGCTCATAAGAGCTAATCCACCTGATAA
12398525 CATGCCAGATGCTC
1 CATGCCAGATGCTC
12398539 CGAAAAGCTA
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (37 bp):
CATGCCAGATGCTCATAAGAGCTAATCCACCTGATAA
Found at i:12398548 original size:37 final size:37
Alignment explanation
Indices: 12398470--12398548 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
12398460 TTCTTTTAAG
* * *
12398470 AGCTAATCCACCTGATAACACACCAGGTGCTCATAAG
1 AGCTAATCCACCTGATAACACACCAGATGCTCAGAAA
** *
12398507 AGCTAATCCACCTGATAACATGCCAGATGCTCCGAAA
1 AGCTAATCCACCTGATAACACACCAGATGCTCAGAAA
12398544 AGCTA
1 AGCTA
12398549 GTCTAACAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.19
Consensus pattern (37 bp):
AGCTAATCCACCTGATAACACACCAGATGCTCAGAAA
Found at i:12406144 original size:27 final size:28
Alignment explanation
Indices: 12406103--12406166 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
12406093 GGCATTATCT
12406103 TCATTTTAC-CATAC-AGTGGTATTACGG
1 TCATTTTACACATACAAG-GGTATTACGG
**
12406130 TCATTTTACAC-TACAAGGGTATTTTGG
1 TCATTTTACACATACAAGGGTATTACGG
*
12406157 TGATTTTACA
1 TCATTTTACA
12406167 AACCGGGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (28 bp):
TCATTTTACACATACAAGGGTATTACGG
Found at i:12406427 original size:19 final size:17
Alignment explanation
Indices: 12406385--12406427 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
12406375 AATCCGTGTG
*
12406385 AGGCCCACGAGCCCATT
1 AGGCCCACCAGCCCATT
*
12406402 GGGCCCACACAGCCCATCT
1 AGGCCCAC-CAGCCCAT-T
12406421 AGGCCCA
1 AGGCCCA
12406428 ACGTGGCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.23, C:0.44, G:0.23, T:0.09
Consensus pattern (17 bp):
AGGCCCACCAGCCCATT
Found at i:12409518 original size:46 final size:46
Alignment explanation
Indices: 12409465--12409593 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
12409455 TATTTGGGCA
* *
12409465 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
12409511 TCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
12409557 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12409594 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:12414966 original size:46 final size:46
Alignment explanation
Indices: 12414910--12415085 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
12414900 TATTTGGGCA
* *
12414910 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * *** * * *
12414956 TCTGAACTCGTTGAGTTGTGTCCGAGTTCGAGAGATGTA-ACTAGACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATACGA-ACG
* * *
12415003 TCCGAGCTTGTTGAGTTGAGTCTGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * *
12415049 CCCGAGCTCGTTGATTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12415086 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
46 69 0.68
47 33 0.32
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
Found at i:12415072 original size:93 final size:93
Alignment explanation
Indices: 12414908--12415077 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 93
12414898 GATATTTGGG
* * * *
12414908 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGTT
*
12414973 GTGTCCGAGTTCGAGAGATGTAACTAGA
66 GAGTCCGAGTTCGAGAGATGTAACTAGA
* * * * *
12415001 CATCCGAGCTTGTTGAGTTGAGTCTGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGATTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGTT
12415066 GAGTCCGAGTTC
66 GAGTCCGAGTTC
12415078 ACTTATGGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGAGAGATGTAACTAGA
Found at i:12417440 original size:23 final size:22
Alignment explanation
Indices: 12417413--12417459 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
12417403 TGGAAAACCG
*
12417413 AGGGAAAGAGAAAGTATCGAAT
1 AGGGAAAGAGAAAGTACCGAAT
12417435 ANGGGAAAGAGAAAGTACCGAAT
1 A-GGGAAAGAGAAAGTACCGAAT
12417458 AG
1 AG
12417460 TCCTTGTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.49, C:0.06, G:0.32, T:0.11
Consensus pattern (22 bp):
AGGGAAAGAGAAAGTACCGAAT
Found at i:12418450 original size:23 final size:23
Alignment explanation
Indices: 12418424--12418472 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
12418414 GTGGTAACTG
12418424 ATGAAATGAAAGTAAAATTAATT
1 ATGAAATGAAAGTAAAATTAATT
12418447 ATGAAATGAAAGTAAAATTAATT
1 ATGAAATGAAAGTAAAATTAATT
12418470 ATG
1 ATG
12418473 TATTTGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (23 bp):
ATGAAATGAAAGTAAAATTAATT
Found at i:12430864 original size:32 final size:32
Alignment explanation
Indices: 12430823--12430919 Score: 133
Period size: 32 Copynumber: 3.0 Consensus size: 32
12430813 CGCCGGAGTC
12430823 GAACACGAGGTGTTAACAGACTTAATTCATTA
1 GAACACGAGGTGTTAACAGACTTAATTCATTA
** * *
12430855 GAACACGAGGTGTTAACAGACTT-AGCCGGAGTC
1 GAACACGAGGTGTTAACAGACTTAATTC--ATTA
12430888 GAACACGAGGTGTTAACAGACTTAATTCATTA
1 GAACACGAGGTGTTAACAGACTTAATTCATTA
12430920 CTTAAACAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
31 2 0.04
32 25 0.46
33 25 0.46
34 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (32 bp):
GAACACGAGGTGTTAACAGACTTAATTCATTA
Found at i:12430897 original size:33 final size:33
Alignment explanation
Indices: 12430814--12430911 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
12430804 CGAGACCTTC
12430814 GCCGGAGTCGAACACGAGGTGTTAACAGACTTAA
1 GCCGGAGTCGAACACGAGGTGTTAACAGACTT-A
** * *
12430848 TTC--ATTAGAACACGAGGTGTTAACAGACTTA
1 GCCGGAGTCGAACACGAGGTGTTAACAGACTTA
12430879 GCCGGAGTCGAACACGAGGTGTTAACAGACTTA
1 GCCGGAGTCGAACACGAGGTGTTAACAGACTTA
12430912 ATTCATTACT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.04
32 25 0.46
33 26 0.48
34 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (33 bp):
GCCGGAGTCGAACACGAGGTGTTAACAGACTTA
Found at i:12432298 original size:93 final size:93
Alignment explanation
Indices: 12432172--12432343 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
12432162 GCCCATAAGT
* *
12432172 GAACTCGGACTCAAATCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAAATCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
12432237 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
12432265 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAAATCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
12432330 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
12432344 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAAATCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:12432339 original size:46 final size:46
Alignment explanation
Indices: 12432164--12432339 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
12432154 TGTAACCCGC
* *
12432164 CCATAAGTGAACTCGGACTCAAATCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
12432210 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
12432256 ACATCTCTCGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12432303 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
12432340 TGCCCAAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 67 0.63
47 30 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:12433742 original size:14 final size:15
Alignment explanation
Indices: 12433715--12433744 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12433705 GAACGCAAAC
12433715 AATCATACAATTTCA
1 AATCATACAATTTCA
12433730 AATCATA-AATTTCA
1 AATCATACAATTTCA
12433744 A
1 A
12433745 TCAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCATACAATTTCA
Found at i:12439131 original size:48 final size:47
Alignment explanation
Indices: 12439060--12439391 Score: 333
Period size: 48 Copynumber: 6.9 Consensus size: 47
12439050 TGGGTAAGAT
* * *
12439060 GCCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCACATATTGAG
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCTCACATATTAAG
* * * * * * *
12439108 GCCGATGCCATGTCCTAGACATGGTCCTACACTTGCTCTCTTAATAAT
1 GCCGATGCCATGTCC-AAACATGGTCTTACACTAGCTCACATATTAAG
* * * * *
12439156 ACCGATGTCATGTTCCAAACATGGTCTTACACTGGCCCACATATTGAG
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATATTAAG
* ** *
12439204 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAACAAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCTCACATATTAAG
* * * *
12439252 GCCGATGCCATGTTCCAAACACGGTCTTACACTGGCTTACATATTGAG
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATATTAAG
* * *
12439300 GCCGATGCCATGTCCCAGAA-ATGGTCTTACACTAGCTCTCATAATAAT
1 GCCGATGCCATGT-CCA-AACATGGTCTTACACTAGCTCACATATTAAG
**
12439348 GCTAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATAT
12439392 ACCCCAACGT
Statistics
Matches: 229, Mismatches: 47, Indels: 16
0.78 0.16 0.05
Matches are distributed among these distances:
47 6 0.03
48 216 0.94
49 7 0.03
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCAAACATGGTCTTACACTAGCTCACATATTAAG
Found at i:12439226 original size:96 final size:96
Alignment explanation
Indices: 12439058--12439391 Score: 490
Period size: 96 Copynumber: 3.5 Consensus size: 96
12439048 AATGGGTAAG
* * *
12439058 ATGCCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCACATATTGAGGCCGATGCCATGTCC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCC
* * * * *
12439123 TAGACATGGTCCTACACTTGCTCTCTTAATA
66 CAAACATGGTCTTACACTAGCTCTCATAATA
* * * *
12439154 ATACCGATGTCATGTTCCAAACATGGTCTTACACTGGCCCACATATTGAGGCCGATGCCATGTCC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCC
*
12439219 CAAACATGGTCTTACACTAGCTCTCATAACA
66 CAAACATGGTCTTACACTAGCTCTCATAATA
* * *
12439250 ATGCCGATGCCATGTTCCAAACACGGTCTTACACTGGCTTACATATTGAGGCCGATGCCATGTCC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCC
12439315 CAGAA-ATGGTCTTACACTAGCTCTCATAATA
66 CA-AACATGGTCTTACACTAGCTCTCATAATA
**
12439346 ATGCTAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT
12439392 ACCCCAACGT
Statistics
Matches: 213, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 211 0.99
97 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (96 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCC
CAAACATGGTCTTACACTAGCTCTCATAATA
Found at i:12439324 original size:144 final size:144
Alignment explanation
Indices: 12439060--12439390 Score: 371
Period size: 144 Copynumber: 2.3 Consensus size: 144
12439050 TGGGTAAGAT
* * ***
12439060 GCCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCACATATTGAGGCCGATGCCATGTCCTA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATAACAAGGCCGATGCCATGTCCTA
* * * * * * * *
12439125 GACATGGTCCTACACTTGCTCTCTTAATAATACCGATGTCATGTTCCAAACATGGTCTTACACTG
66 AACACGGTCCTACACTGGCTCTCATAATAAGACCGATGCCATGTCCCAAACATGGTCTTACACTA
* *
12439190 GCCCACATATTGAG
131 GCCCACATAATAAG
* *
12439204 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCC-
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATAACAAGGCCGATGCCATG-TCCT
* * * *
12439268 AAACACGGTCTTACACTGGCT-TACATATTGAGGCCGATGCCATGTCCCAGAA-ATGGTCTTACA
65 AAACACGGTCCTACACTGGCTCT-CATAATAAGACCGATGCCATGTCCCA-AACATGGTCTTACA
* * *
12439331 CTAGCTCTCATAATAAT
128 CTAGCCCACATAATAAG
** *
12439348 GCTAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATA
12439391 TACCCCAACG
Statistics
Matches: 156, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
143 1 0.01
144 150 0.96
145 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (144 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATAACAAGGCCGATGCCATGTCCTA
AACACGGTCCTACACTGGCTCTCATAATAAGACCGATGCCATGTCCCAAACATGGTCTTACACTA
GCCCACATAATAAG
Found at i:12441806 original size:40 final size:40
Alignment explanation
Indices: 12441748--12441968 Score: 295
Period size: 40 Copynumber: 5.6 Consensus size: 40
12441738 AACCCAAGTA
* * *
12441748 CCTTC-GGATTTAG-CCGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* * * * * *
12441786 CCTTCGAGTCTTATCCCGGATATAGTAAATAGCAGAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
12441826 CCTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
12441866 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
12441906 CCTTCGGGACTTAGCCCGGATATAGTCGATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
12441946 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12441969 CATTCGAATA
Statistics
Matches: 158, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
38 5 0.03
39 4 0.03
40 147 0.93
41 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:12448940 original size:40 final size:40
Alignment explanation
Indices: 12448866--12449127 Score: 384
Period size: 40 Copynumber: 6.6 Consensus size: 40
12448856 AACCCAAGTA
* * *
12448866 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* * *
12448905 CCTTCGGGTCTTAGCCCGAATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* * *
12448945 CCTCCAGGACTTAGCCCGGATATAGTCAATAACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
12448985 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
**
12449025 CCTTCTAGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
12449065 CCTTCGGGACTTAGCCCGGATATAGTCGATAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
12449105 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12449128 CATTCGAATA
Statistics
Matches: 200, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
39 12 0.06
40 185 0.93
41 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:12473067 original size:48 final size:48
Alignment explanation
Indices: 12472991--12473318 Score: 365
Period size: 48 Copynumber: 6.8 Consensus size: 48
12472981 TAATATGCCA
**
12472991 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
* * * * *
12473039 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
* * * *
12473087 ATG-C-TGTGCACCAAACATGGTCTTACACTGGCTCACATATTAAGGCCA
1 ATGCCATGT-C-CCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
* * * * *
12473135 ATGCCATGTCTCAGACATGGTCTTACACTAGCTCTTC-TAACAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTC-ACATATCAAGGCCG
* * * **
12473183 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
** * * *
12473231 ATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATAACAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
*
12473279 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATAT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT
12473319 ACCCCAACGT
Statistics
Matches: 227, Mismatches: 47, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
46 3 0.01
47 2 0.01
48 216 0.95
49 3 0.01
50 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCCG
Found at i:12473150 original size:96 final size:95
Alignment explanation
Indices: 12473000--12473318 Score: 464
Period size: 96 Copynumber: 3.3 Consensus size: 95
12472990 AATGCCATGT
* *
12473000 CCCAGACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCTATGTCCCAGACATGGTCTTAC
1 CCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAGACATGGTCTTAC
* *
12473065 ACTAGCTCTCATAACAATGCCAATGCTGTG
66 ACTAGCTCTCATAACAATGTCGATGCTGTG
* * * *
12473095 CACCAAACATGGTCTTACACTGGCTCACATATTAAGGCCAATGCCATGTCTCAGACATGGTCTTA
1 C-CCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAGACATGGTCTTA
12473160 CACTAGCTCTTC-TAACAATGTCGATGCCATGT-
65 CACTAGCTC-TCATAACAATGTCGATG-C-TGTG
* *
12473192 TCCAAACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCCAGACATGGTCTTAC
1 CCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAGACATGGTCTTAC
*
12473257 ACTAGCTTTCATAACAATGTCGATGCCATGT-
66 ACTAGCTCTCATAACAATGTCGATG-C-TGTG
12473288 CCCAAACATGGTCTTACACTAGCTCACATAT
1 CCCAAACATGGTCTTACACTAGCTCACATAT
12473319 ACCCCAACGT
Statistics
Matches: 204, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
95 3 0.01
96 195 0.96
97 3 0.01
98 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (95 bp):
CCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAGACATGGTCTTAC
ACTAGCTCTCATAACAATGTCGATGCTGTG
Found at i:12490208 original size:30 final size:30
Alignment explanation
Indices: 12490167--12490226 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12490157 AGTAGCCGAC
*
12490167 GCTAATTTAAATTGCACACTTAGTGCCAAA
1 GCTAATTTAAATCGCACACTTAGTGCCAAA
*
12490197 GCTAGTTTAAATCGCACACTTAGTGCCAAA
1 GCTAATTTAAATCGCACACTTAGTGCCAAA
12490227 ATTTCCGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (30 bp):
GCTAATTTAAATCGCACACTTAGTGCCAAA
Found at i:12493939 original size:27 final size:26
Alignment explanation
Indices: 12493887--12493946 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
12493877 CCACATATAT
*
12493887 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
12493913 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
12493940 ATATCTG
1 ATATCTG
12493947 GCAGCCTCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:12506660 original size:139 final size:139
Alignment explanation
Indices: 12506410--12507279 Score: 1731
Period size: 139 Copynumber: 6.3 Consensus size: 139
12506400 TGTAACCCGC
12506410 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12506475 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12506540 CATTCGCAT
131 CATTCGCAT
12506549 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12506614 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12506679 CATTCGCAT
131 CATTCGCAT
12506688 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12506753 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12506818 CATTCGCAT
131 CATTCGCAT
12506827 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12506892 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12506957 CATTCGCAT
131 CATTCGCAT
12506966 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12507031 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12507096 CATTCGCAT
131 CATTCGCAT
12507105 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
12507170 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
12507235 CATTCGCAT
131 CATTCGCAT
*
12507244 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
12507280 ATGCCCAAAT
Statistics
Matches: 730, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 730 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (139 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTGGGACT
CAACTCAACGAGTTCGAATGCCTAGTTACATTTCACGAACTCGAACTCAACTCAACGAGTTCGGA
CATTCGCAT
Found at i:12508118 original size:260 final size:260
Alignment explanation
Indices: 12507657--12508175 Score: 1011
Period size: 260 Copynumber: 2.0 Consensus size: 260
12507647 TTTAAAATAT
12507657 AGTCTAATTAGGACTCACATTATTCAAATTGACCCAAAATCATATTTTTGAAAAATTACAATTTT
1 AGTCTAATTAGGACTCACATTATTCAAATTGACCCAAAATCATATTTTTGAAAAATTACAATTTT
12507722 GCCCCTAAACTTTTTCATATTTACACTTTTTCCCCAAAGATCGTAAATTAAACTTTAGCCTATTT
66 GCCCCTAAACTTTTTCATATTTACACTTTTTCCCCAAAGATCGTAAATTAAACTTTAGCCTATTT
12507787 TCTTATGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAAT
131 TCTTATGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAAT
* *
12507852 ATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTTGCTCGTTTTCACTTAAAACCA
196 ATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTCGCTAGTTTTCACTTAAAACCA
12507917 AGTCTAATTAGGACTCACATTATTCAAATTGACCCAAAATCATATTTTTGAAAAATTACAATTTT
1 AGTCTAATTAGGACTCACATTATTCAAATTGACCCAAAATCATATTTTTGAAAAATTACAATTTT
12507982 GCCCCTAAACTTTTTCATATTTACACTTTTTCCCCAAAGATCGTAAATTAAACTTTAGCCTATTT
66 GCCCCTAAACTTTTTCATATTTACACTTTTTCCCCAAAGATCGTAAATTAAACTTTAGCCTATTT
12508047 TCTTATGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAAT
131 TCTTATGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAAT
*
12508112 ATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTCGCTAGTTTTCGCTTAAAACC
196 ATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTCGCTAGTTTTCACTTAAAACC
12508176 GAGTAGCACA
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
260 256 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (260 bp):
AGTCTAATTAGGACTCACATTATTCAAATTGACCCAAAATCATATTTTTGAAAAATTACAATTTT
GCCCCTAAACTTTTTCATATTTACACTTTTTCCCCAAAGATCGTAAATTAAACTTTAGCCTATTT
TCTTATGTTTTATGACATGCTGATCATTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAAT
ATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCCCTTTCGCTAGTTTTCACTTAAAACCA
Found at i:12519253 original size:19 final size:19
Alignment explanation
Indices: 12519207--12519254 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12519197 GTAAATATTT
*
12519207 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAAGTAGA
*
12519225 TAAATCTTATTTAAGTAGA
1 TAAATTTTATTTAAGTAGA
*
12519244 TAAGTTTTATT
1 TAAATTTTATT
12519255 AGAATAAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAAGTAGA
Done.