Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 127 of 333
Found at i:41006328 original size:67 final size:67
Alignment explanation
Indices: 41006220--41006373 Score: 299
Period size: 67 Copynumber: 2.3 Consensus size: 67
41006210 CACCACAGAA
*
41006220 ATTGCAGCGAGGCTGCCAGATATTTTGACGAAGTCACCAGAACAGATATATGTGGCGAAGCCACC
1 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAAGCCACC
41006285 AG
66 AG
41006287 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAAGCCACC
1 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAAGCCACC
41006352 AG
66 AG
41006354 ATTGCAGCGAGGCTGCCAGA
1 ATTGCAGCGAGGCTGCCAGA
41006374 ACGCTTCCTC
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 86 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAAGCCACC
AG
Found at i:41006345 original size:27 final size:26
Alignment explanation
Indices: 41006303--41006354 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
41006293 GCGAGGCTGC
*
41006303 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
41006329 CAGATATATGTGGCGAAGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41006355 TTGCAGCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41006656 original size:27 final size:27
Alignment explanation
Indices: 41006600--41006872 Score: 243
Period size: 27 Copynumber: 10.2 Consensus size: 27
41006590 GGGCAAAATG
* * * * *
41006600 GTAATTTTACCCCACA-AGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41006626 GTAATTCCACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41006653 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41006680 GTAATTCTACCCTATAGGGGTATTGC-
1 GTAATTCTACCCTACAGGGGTATTTCA
*
41006706 GATAATTCTACCCTACAGGGGTATTTCG
1 G-TAATTCTACCCTACAGGGGTATTTCA
* *
41006734 GTAATTCTATCCTACA-GGGTA-TTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41006759 GTAATTCTACCTTACTA-GGGTATTTTA
1 GTAATTCTACCCTAC-AGGGGTATTTCA
* * *
41006786 GTAATTCTACCTTACAAGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* ** * **
41006813 GTAATTTTA-CAAACTAGGGGTGTTTTG
1 GTAATTCTACCCTAC-AGGGGTATTTCA
*
41006840 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
41006867 GTAATT
1 GTAATT
41006873 TCACAATCGA
Statistics
Matches: 207, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
25 17 0.08
26 29 0.14
27 158 0.76
28 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:41006692 original size:54 final size:55
Alignment explanation
Indices: 41006617--41006872 Score: 283
Period size: 54 Copynumber: 4.8 Consensus size: 55
41006607 TACCCCACAA
* * *
41006617 GGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACCCTA-TAGG
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACTAGG
* *
41006671 GGTATTTCGGTAATTCTACCCTATAGGGGTATTGC-GATAATTCTACCCTAC-AGG
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAG-TAATTCTACCCTACTAGG
* * *
41006725 GGTATTTCGGTAATTCTATCCTACA-GGGTA-TTCGGTAATTCTACCTTACTA-G
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACTAGG
** * * * * **
41006777 GGTATTTTAGTAATTCTACCTTACAAGGGTATTTTAGTAATTTTA-CAAACTAGG
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACTAGG
* * *
41006831 GGTGTTTTGGTAATTCTACCCTATAGGGGTATTTCAGTAATT
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATT
41006873 TCACAATCGA
Statistics
Matches: 171, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
52 37 0.22
53 18 0.11
54 116 0.68
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (55 bp):
GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACTAGG
Found at i:41006794 original size:79 final size:80
Alignment explanation
Indices: 41006626--41006872 Score: 268
Period size: 81 Copynumber: 3.1 Consensus size: 80
41006616 AGGTATCTCG
* * *
41006626 GTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
*
41006691 CTATAGGGGTATTGC
66 CTATAGGGGTATTGA
* *
41006706 GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTATCCTACA-GGGTA-TTCGGTAATTCTAC
1 G-TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
* *
41006769 CTTACTA-GGGTATTTTA
65 CCTA-TAGGGGTA-TTGA
* * * * ** * *
41006786 GTAATTCTACCTTACAAGGGTATTTTAGTAATTTTA-CAAACTAGGGGTGTTTTGGTAATTCTAC
1 GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTAC-AGGGGTATTTCGGTAATTCTAC
*
41006850 CCTATAGGGGTATTTCA
65 CCTATAGGGGTA-TTGA
41006867 GTAATT
1 GTAATT
41006873 TCACAATCGA
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
78 3 0.02
79 53 0.38
80 17 0.12
81 68 0.48
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (80 bp):
GTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
CTATAGGGGTATTGA
Found at i:41006831 original size:133 final size:134
Alignment explanation
Indices: 41006599--41006872 Score: 329
Period size: 133 Copynumber: 2.1 Consensus size: 134
41006589 GGGGCAAAAT
*
41006599 GGTAATTTTACCCCACAAGGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACC
1 GGTAATTCTACCCCACAAGGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACC
* * * **
41006664 CTATAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTGCGATAATTCTACCCTACAGGGGTA
66 CTACAAGGGTATTTCAGTAATTCTACCAAATAGGGGTATTGCGATAATTCTACCCTACAGGGGTA
41006729 TTTC
131 TTTC
* * * * *
41006733 GGTAATTCTATCCTACAGGGTAT-TCGGTAATTCTACCTTACTA-GGGTATTTTAGTAATTCTAC
1 GGTAATTCTACCCCACAAGGTATCTCGGTAATTCCACCCTAC-AGGGGTATTTTAGTAATTCTAC
* * * * ** * *
41006796 CTTACAAGGGTATTTTAGTAATTTTA-CAAACTAGGGGTGTTTTGGTAATTCTACCCTATAGGGG
65 CCTACAAGGGTATTTCAGTAATTCTACCAAA-TAGGGGTATTGCGATAATTCTACCCTACAGGGG
41006860 TATTTC
129 TATTTC
*
41006866 AGTAATT
1 GGTAATT
41006873 TCACAATCGA
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
132 2 0.02
133 96 0.81
134 20 0.17
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (134 bp):
GGTAATTCTACCCCACAAGGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACC
CTACAAGGGTATTTCAGTAATTCTACCAAATAGGGGTATTGCGATAATTCTACCCTACAGGGGTA
TTTC
Found at i:41006907 original size:27 final size:27
Alignment explanation
Indices: 41006877--41007292 Score: 338
Period size: 27 Copynumber: 15.4 Consensus size: 27
41006867 GTAATTTCAC
**
41006877 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* * * *
41006904 AATCAAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* * *
41006931 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTTTGTA
*** *
41006958 AATCGAGGGTACTTTGGTAATTTT-TA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* ** **
41006984 CCAGTCGAGGGT-ATTTCAGTAATTTTACA
1 --AATCGAGGGTAAAAT-AGTAATTTTGTA
* *** **
41007013 AATCAGGGGGTATTTTAGTAATTTTACA
1 AATC-GAGGGTAAAATAGTAATTTTGTA
* *** *
41007041 AA-CTAGGGGTATTTTAGTAATTTTCTA
1 AATCGA-GGGTAAAATAGTAATTTTGTA
* * *
41007068 AAT-GAGGGTAAAATGGTAATTCTCTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* * **
41007094 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* ** *
41007121 AATCGAGGGTAGAACGGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
41007148 AATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
* * * *
41007175 ATTCAAGGGTAAAACA-TAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
41007201 AATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
*
41007228 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
*
41007255 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTTTGTA
41007282 AATCGAGGGTA
1 AATCGAGGGTA
41007293 CTTTGATAAT
Statistics
Matches: 330, Mismatches: 49, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
26 43 0.13
27 247 0.75
28 36 0.11
29 4 0.01
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTTTGTA
Found at i:41006941 original size:80 final size:80
Alignment explanation
Indices: 41006864--41007267 Score: 293
Period size: 80 Copynumber: 5.0 Consensus size: 80
41006854 TAGGGGTATT
* * *
41006864 TCAGTAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTA
1 TCAGTAATTTCACAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTA
41006929 TAAATCGAGGGTAAA
66 TAAATCGAGGGTAAA
* * *** * **
41006944 ACAGTAA-TTCTATAAATCGAGGGTACTTTGGTAATTTT-TACCAGTCGAGGGT-ATTTCAGTAA
1 TCAGTAATTTC-A-CAATCGAGGGTAAAATGGTAATTTTGTA--AATCGAGGGTAAAAT-AGTAA
* * * **
41007006 TTTTACAAATCAGGGGGTATT
61 TTCTATAAATC-GAGGGTAAA
* * * * *** * * *
41007027 TTAGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTCTAAAT-GAGGGTAAAATGGTAATTCT
1 TCAGTAATTTCACAATCGA-GGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCT
*
41007091 CTAAATCGAGGGTAAAA
65 ATAAATCGAGGGT-AAA
* * * * *
41007108 T-GGTAA-TTCTACAAATCGAGGGTAGAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTT
1 TCAGTAATTTC-AC-AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATAGTAATTC
* * *
41007171 TGTAATTCAAGGGTAAA
64 TATAAATCGAGGGTAAA
* * *
41007188 ACA-TAATTCTGTA-AATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATAGTAATTC
1 TCAGTAATT-T-CACAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATAGTAATTC
*
41007251 TGTAAATCGAGGGTAAA
64 TATAAATCGAGGGTAAA
41007268 ATGGTAATTT
Statistics
Matches: 246, Mismatches: 60, Indels: 36
0.72 0.18 0.11
Matches are distributed among these distances:
79 5 0.02
80 103 0.42
81 74 0.30
82 32 0.13
83 28 0.11
84 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (80 bp):
TCAGTAATTTCACAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTA
TAAATCGAGGGTAAA
Found at i:41006968 original size:107 final size:106
Alignment explanation
Indices: 41006857--41007345 Score: 326
Period size: 107 Copynumber: 4.5 Consensus size: 106
41006847 TACCCTATAG
* * **
41006857 GGGTATTTCAGTAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGT
1 GGGTATTT-AGTAATTTTACAATCGAGGGTAAAACAGTAATTTTACAAATCAAGGGTAAAACAGT
* * *
41006922 AATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGA
65 AATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGA
* * *** * ****
41006964 GGGTACTTTGGTAATTTTTACCAGTCGAGGGTATTTCAGTAATTTTACAAATCAGGGGGTATTTT
1 GGGTA-TTTAGTAA-TTTTA-CAATCGAGGGTAAAACAGTAATTTTACAAATCA-AGGGTAAAAC
* * * *** *
41007029 AGTAATTTTACAAA-CTAGGGGTATTTTAGTAATTTTCTAAAT-GA
62 AGTAATTCTATAAATCGA-GGGTAAAATAGTAATTTTGTAAATCGA
** * ** * * * *
41007073 GGGTAAAATGGTAATTCTCTA-AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGGTAGAACG
1 GGGT-ATTTAGTAATT-T-TACAATCGAGGGTAAAACAGTAATTTTACAAATCAAGGGTAAAACA
* * *
41007137 GTAATTCTGTAAATCGAGGGTAAAATAGTAATTTTGTAATTCAA
63 GTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGA
** * * ** * *
41007181 GGGTA-AAACATAATTCTGTA-AATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATA
1 GGGTATTTA-GTAATT-T-TACAATCGAGGGTAAAACAGTAATTTTACAAATCAAGGGTAAAACA
* *
41007244 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGA
63 GTAATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGA
* *** * *
41007288 GGGTACTTT-GATAATTTTACATGTCGAGGGTATTTCAATAATTTTGCAAAT-AAGGGTA
1 GGGTA-TTTAG-TAATTTTACA-ATCGAGGGTAAAACAGTAATTTTACAAATCAAGGGTA
41007346 TTTCGATAAT
Statistics
Matches: 292, Mismatches: 74, Indels: 32
0.73 0.19 0.08
Matches are distributed among these distances:
106 3 0.01
107 143 0.49
108 67 0.23
109 41 0.14
110 38 0.13
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (106 bp):
GGGTATTTAGTAATTTTACAATCGAGGGTAAAACAGTAATTTTACAAATCAAGGGTAAAACAGTA
ATTCTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCGA
Found at i:41007023 original size:28 final size:27
Alignment explanation
Indices: 41006992--41007064 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
41006982 TACCAGTCGA
*
41006992 GGGTATTTCAGTAATTTTACAAA-TCAGG
1 GGGTATTTTAGTAATTTTACAAACT-A-G
41007020 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTAGTAATTTTACAAACTAG
41007047 GGGTATTTTAGTAATTTT
1 GGGTATTTTAGTAATTTT
41007065 CTAAATGAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
27 19 0.44
28 23 0.53
29 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAACTAG
Found at i:41007077 original size:190 final size:189
Alignment explanation
Indices: 41006802--41007158 Score: 488
Period size: 190 Copynumber: 1.9 Consensus size: 189
41006792 CTACCTTACA
* * * **
41006802 AGGGTATTTTAGTAATTTTACAAACTAGGGGTGTTTTGGTAATTCTACCCTATAGGGGTATTTCA
1 AGGGTATTTCAGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACCAAATAGGGGTATTTCA
* * *
41006867 GTAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAA
66 GTAATTTCACAATCGAGGGTAAAACGGTAATTCTCTAAATCAAGGGTAAAACAGTAATTCTACAA
41006932 ATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACCAGTCG
131 ATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACCAGTCG
*
41006991 AGGGTATTTCAGTAATTTTACAAA-TCAGGGGGTATTTTAGTAATTTTA-CAAACTAGGGGTATT
1 AGGGTATTTCAGTAATTTTACAAACT-A-GGGGTATTTTAGTAATTCTACCAAA-TAGGGGTATT
* * * **
41007054 TTAGTAATTTTCTA-AAT-GAGGGTAAAATGGTAATTCTCTAAATCGAGGGTAAAATGGTAATTC
63 TCAGTAA-TTTC-ACAATCGAGGGTAAAACGGTAATTCTCTAAATCAAGGGTAAAACAGTAATTC
* * *
41007117 TACAAATCGAGGGTAGAACGGTAATTCTGTAAATCGAGGGTA
126 TACAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTA
41007159 AAATAGTAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
188 1 0.01
189 26 0.18
190 111 0.76
191 7 0.05
192 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (189 bp):
AGGGTATTTCAGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACCAAATAGGGGTATTTCA
GTAATTTCACAATCGAGGGTAAAACGGTAATTCTCTAAATCAAGGGTAAAACAGTAATTCTACAA
ATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACCAGTCG
Found at i:41007302 original size:27 final size:26
Alignment explanation
Indices: 41007190--41007411 Score: 119
Period size: 27 Copynumber: 8.3 Consensus size: 26
41007180 AGGGTAAAAC
* **
41007190 ATAATTCTGTAAATCGAGGGTAAAAT-
1 ATAATTTTGTAAATCGAGGGT-ATTTG
**
41007216 AGTAATTTTGTAAATCGAGGGTAAAAT-
1 A-TAATTTTGTAAATCGAGGGT-ATTTG
* **
41007243 AGTAATTCTGTAAATCGAGGGTAAAATG
1 A-TAATTTTGTAAATCGAGGGT-ATTTG
*
41007271 GTAATTTTGTAAATCGAGGGTACTTTG
1 ATAATTTTGTAAATCGAGGGTA-TTTG
** ** *
41007298 ATAATTTTACATGTCGAGGGTATTTCA
1 ATAATTTTGTAAATCGAGGGTATTT-G
* *
41007325 ATAATTTTGCAAAT-AAGGGTATTTCG
1 ATAATTTTGTAAATCGAGGGTATTT-G
** *
41007351 ATAATTTTACAAATCGAGGATATTTGG
1 ATAATTTTGTAAATCGAGGGTATTT-G
* * *
41007378 GTAATTTTATAAACCG-GGGTACTTTG
1 ATAATTTTGTAAATCGAGGGTA-TTTG
*
41007404 GTAATTTT
1 ATAATTTT
41007412 ACAACTTAGG
Statistics
Matches: 165, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
26 41 0.25
27 124 0.75
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAATTTTGTAAATCGAGGGTATTTG
Found at i:41007315 original size:54 final size:53
Alignment explanation
Indices: 41006868--41007415 Score: 203
Period size: 54 Copynumber: 10.2 Consensus size: 53
41006858 GGTATTTCAG
* * * * ****
41006868 TAATTTCACAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTA-AAACA
1 TAATTTTACAATCGAGGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
* * * *
41006920 GTAATTCTATA-AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTGG
1 -TAATT-T-TACAATCGAGGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
* ** ** * *
41006975 TAATTTTTACCAGTCGAGGGTATTTCAGTAATTTTACAAATCAGGGGGTA-TTTTA
1 TAA-TTTTA-CAATCGAGGGTAAATCAGTAATTTTGTAAATC-GAGGGTACTTTGA
* * ** * * *** *
41007030 GTAATTTTACAAACTAGGGGTATTTTAGTAATTTTCTAAAT-GAGGGTAAAATGG
1 -TAATTTTACAATCGA-GGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
* * ** **** *
41007084 TAATTCTCTA-AATCGAGGGTAAAAT-GGTAATTCTACAAATCGAGGGTAGAACGG
1 TAATT-T-TACAATCGAGGGT-AAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
* * ****
41007138 TAATTCTGTA-AATCGAGGGTAAAAT-AGTAATTTTGTAATTCAAGGGTA-AAACA
1 TAATT-T-TACAATCGAGGGT-AAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
***
41007191 TAATTCTGTA-AATCGAGGGTAAAAT-AGTAATTTTGTAAATCGAGGGTAAAAT-A
1 TAATT-T-TACAATCGAGGGT-AAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
*
41007244 GTAATTCTGTA-AATCGAGGGTAAAAT-GGTAATTTTGTAAATCGAGGGTACTTTGA
1 -TAATT-T-TACAATCGAGGGT-AAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
* ** * * *
41007299 TAATTTTACATGTCGAGGGTATTTCAATAATTTTGCAAAT-AAGGGTA-TTTCGA
1 TAATTTTACA-ATCGAGGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTT-GA
* ** ** * * *
41007352 TAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAACCG-GGGTACTTTGG
1 TAATTTTAC-AATCGAGGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
41007405 TAATTTTACAA
1 TAATTTTACAA
41007416 CTTAGGATAT
Statistics
Matches: 397, Mismatches: 74, Indels: 49
0.76 0.14 0.09
Matches are distributed among these distances:
52 7 0.02
53 139 0.35
54 182 0.46
55 60 0.15
56 9 0.02
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (53 bp):
TAATTTTACAATCGAGGGTAAATCAGTAATTTTGTAAATCGAGGGTACTTTGA
Found at i:41007347 original size:26 final size:26
Alignment explanation
Indices: 41007314--41007364 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
41007304 TTACATGTCG
*
41007314 AGGGTATTTCAATAATTTTGCAAATA
1 AGGGTATTTCAATAATTTTACAAATA
*
41007340 AGGGTATTTCGATAATTTTACAAAT
1 AGGGTATTTCAATAATTTTACAAAT
41007365 CGAGGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (26 bp):
AGGGTATTTCAATAATTTTACAAATA
Found at i:41007360 original size:53 final size:54
Alignment explanation
Indices: 41007272--41007436 Score: 149
Period size: 53 Copynumber: 3.1 Consensus size: 54
41007262 GGTAAAATGG
* * ** *
41007272 TAATTTTGTAAATCGAGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAA
1 TAATTTTGCAAATCAAGGGTACTTTGATAATTTTACAAATCGAGGATATTTCAA
***
41007326 TAATTTTGCAAAT-AAGGGTA-TTTCGATAATTTTACAAATCGAGGATATTTGGG
1 TAATTTTGCAAATCAAGGGTACTTT-GATAATTTTACAAATCGAGGATATTTCAA
** ** * * * *
41007379 TAATTTTATAAA-CCGGGGTACTTTGGTAATTTTACAACT-TAGGATATTTCAG
1 TAATTTTGCAAATCAAGGGTACTTTGATAATTTTACAAATCGAGGATATTTCAA
41007431 TAATTT
1 TAATTT
41007437 GGTAAACTAA
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
52 19 0.21
53 57 0.63
54 15 0.16
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
TAATTTTGCAAATCAAGGGTACTTTGATAATTTTACAAATCGAGGATATTTCAA
Found at i:41008433 original size:48 final size:47
Alignment explanation
Indices: 41008328--41008457 Score: 136
Period size: 48 Copynumber: 2.7 Consensus size: 47
41008318 CATATATCGG
* * **
41008328 GGCCGATGCCATGTTCCAAACATGGTCTTACACTAGTCCACATGTCGA
1 GGCCGATGCCATGTT-CAGACATGGTCTTACACTAGTCCACATATAAA
* * *
41008376 GGCCAATGCCATGTCTCAGACATGGTCTTACATTAG-CTCTCATATAAA
1 GGCCGATGCCATGT-TCAGACATGGTCTTACACTAGTC-CACATATAAA
* *
41008424 TGCCGATGCCATGTTCCGAACATGGTCTTACACT
1 GGCCGATGCCATGTTCAG-ACATGGTCTTACACT
41008458 GGCTCACATA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.06
48 63 0.93
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
GGCCGATGCCATGTTCAGACATGGTCTTACACTAGTCCACATATAAA
Found at i:41016855 original size:40 final size:40
Alignment explanation
Indices: 41016781--41017000 Score: 304
Period size: 40 Copynumber: 5.6 Consensus size: 40
41016771 AACCCAAGTA
* * *
41016781 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
41016820 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41016860 CCTT-GGGACTTAGCCCAGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
41016899 -CTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41016938 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
41016978 CCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41017001 CATTCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
38 3 0.02
39 75 0.47
40 80 0.50
41 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:41016954 original size:79 final size:80
Alignment explanation
Indices: 41016781--41017000 Score: 322
Period size: 79 Copynumber: 2.8 Consensus size: 80
41016771 AACCCAAGTA
* * * *
41016781 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
41016844 GTCAATAGCACAAAAG
65 ATCAATAGCACAAAAG
*
41016860 CCTT-GGGACTTAGCCCAGATATAATCACTAGCACAAATG-CTTCGGGACTTAGCCCGGATATAA
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
*
41016923 TCAATAGCACAAATG
66 TCAATAGCACAAAAG
* *
41016938 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
41017001 CATTCGAATA
Statistics
Matches: 127, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
78 48 0.38
79 56 0.44
80 23 0.18
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
TCAATAGCACAAAAG
Found at i:41025328 original size:40 final size:40
Alignment explanation
Indices: 41025254--41025475 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
41025244 AACCCAAGTA
* * *
41025254 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
41025293 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41025333 CCTTCGGGACTTAGCCCAGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
41025373 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
41025413 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
41025453 CCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41025476 CATTCGAATA
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 12 0.07
40 150 0.91
41 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:41035460 original size:24 final size:24
Alignment explanation
Indices: 41035428--41035516 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
41035418 CTGTCAGGAG
*
41035428 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCTGATAAGGGAT
*
41035452 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCTGATAAGGGAT
*
41035476 AGGATTTAGGAGCTGATAAGGGAG
1 AGGATTTAGGAGCTGATAAGGGAT
41035500 AGGATTTAGGAGCTGAT
1 AGGATTTAGGAGCTGAT
41035517 TGGGAGAACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.27
Consensus pattern (24 bp):
AGGATTTAGGAGCTGATAAGGGAT
Found at i:41036502 original size:16 final size:15
Alignment explanation
Indices: 41036477--41036506 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41036467 CTAGATCGGC
41036477 AAAAGCCGAAAAGCT
1 AAAAGCCGAAAAGCT
41036492 AAAATGCCGAAAAGC
1 AAAA-GCCGAAAAGC
41036507 CGATATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGCCGAAAAGCT
Found at i:41036982 original size:26 final size:27
Alignment explanation
Indices: 41036920--41037029 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
41036910 AGGAAGCGTC
* * * *
41036920 CTGGTGGCTATGCCACATTTATTTGAT
1 CTGGTGGCTCTGCCACATATATCTGTT
41036947 CTGGTGGCTCTGCCACATATAT-TGTT
1 CTGGTGGCTCTGCCACATATATCTGTT
41036973 CTGGTGGCTCTGCCACA-ATTATCTGTT
1 CTGGTGGCTCTGCCACATA-TATCTGTT
* *
41037000 CTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGTT
41037026 CTGG
1 CTGG
41037030 CAGCAATGCT
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.01
26 35 0.47
27 39 0.52
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGTT
Found at i:41037003 original size:53 final size:53
Alignment explanation
Indices: 41036920--41037029 Score: 150
Period size: 53 Copynumber: 2.1 Consensus size: 53
41036910 AGGAAGCGTC
* * *
41036920 CTGGTGGCTATGCCACATTTATTTGATCTGGTGGCTCTGCCACATATAT-TGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * *
41036973 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
41037026 CTGG
1 CTGG
41037030 CAGCAATGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
52 3 0.06
53 47 0.94
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:41042702 original size:45 final size:48
Alignment explanation
Indices: 41042637--41042732 Score: 144
Period size: 45 Copynumber: 2.1 Consensus size: 48
41042627 ACAGGAAAGA
*
41042637 AATGAGCCATGTAAGTCCATA-T-CAGATATATGGC-TTGGAGACAGG
1 AATGAGCCATGTAAGCCCATAGTACAGATATATGGCATTGGAGACAGG
* *
41042682 AATGAGCCATGTAAGCCCATAGTATATATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGCCCATAGTACAGATATATGGCATTGGAGACAGG
41042730 AAT
1 AAT
41042733 AATTCATGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 20 0.44
46 1 0.02
47 10 0.22
48 14 0.31
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (48 bp):
AATGAGCCATGTAAGCCCATAGTACAGATATATGGCATTGGAGACAGG
Found at i:41047033 original size:45 final size:48
Alignment explanation
Indices: 41046962--41047080 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 48
41046952 GACAGGACAG
* * *
41046962 GACAGAAATGAGCCATGTAAGTCCATA-T-CAGATATAT-GCTTTGGA
1 GACAGGAATGATCCATGTAAGTCCATAGTACAGATATATGGCATTGGA
* * * *
41047007 GATAGGAATGATCCATGTAAGCCCATAGTATATATATATGGCATTGGA
1 GACAGGAATGATCCATGTAAGTCCATAGTACAGATATATGGCATTGGA
* *
41047055 GACAGGAATAATTCATGTAAGTCCAT
1 GACAGGAATGATCCATGTAAGTCCAT
41047081 GTCGAAGACA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
45 23 0.38
46 1 0.02
47 7 0.12
48 29 0.48
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
GACAGGAATGATCCATGTAAGTCCATAGTACAGATATATGGCATTGGA
Found at i:41051394 original size:45 final size:46
Alignment explanation
Indices: 41051305--41051398 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 46
41051295 ACAGGACAAA
* *
41051305 AATGAGCCATGTAAGTCCATATCAGATATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATCAGATATATGGCATTGGAGACAGG
*
41051351 AATGAGCCATGTAAGCCCATAT-ATATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATCAGATATATGGCATTGGAGACAGG
41051396 AAT
1 AAT
41051399 AATTCATGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 24 0.53
46 21 0.47
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (46 bp):
AATGAGCCATGTAAGCCCATATCAGATATATGGCATTGGAGACAGG
Found at i:41051407 original size:45 final size:46
Alignment explanation
Indices: 41051309--41051415 Score: 153
Period size: 45 Copynumber: 2.3 Consensus size: 46
41051299 GACAAAAATG
* *
41051309 AGCCATGTAAGTCCATATCAGATATATGGCTTTGGAGACAGGAATG
1 AGCCATGTAAGTCCATATCAGATATATGGCATTGGAGACAGGAATA
* *
41051355 AGCCATGTAAGCCCATAT-ATATATATGGCATTGGAGACAGGAATA
1 AGCCATGTAAGTCCATATCAGATATATGGCATTGGAGACAGGAATA
**
41051400 ATTCATGTAAGTCCAT
1 AGCCATGTAAGTCCAT
41051416 GTCGAAGACA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 37 0.69
46 17 0.31
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (46 bp):
AGCCATGTAAGTCCATATCAGATATATGGCATTGGAGACAGGAATA
Found at i:41053579 original size:46 final size:46
Alignment explanation
Indices: 41053523--41053689 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 46
41053513 TGGTTGAGCA
* *
41053523 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
* * * * *
41053569 TCCGAACTCGTTGAATTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAA--A--CG
* *
41053616 TCCGAACTCGTTGAGTTGAG-CCGAGTTCACTCATGGATGCGAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
* * * *
41053661 CCCGAGCTCATTGAGTTGAGTCCAAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
41053690 GCTGATGGGC
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 22 0.22
46 43 0.44
47 22 0.22
49 5 0.05
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
Found at i:41053680 original size:92 final size:93
Alignment explanation
Indices: 41053520--41053690 Score: 254
Period size: 92 Copynumber: 1.8 Consensus size: 93
41053510 GGATGGTTGA
* *** *
41053520 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAAT
*
41053585 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* * *
41053613 GCATCCGAACTCGTTGAGTTGAG-CCGAGTTCACTCATGGATGCGAACACCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAAT
41053677 TGAGTCCAAGTTCG
66 TGAGTCCAAGTTCG
41053691 CTGATGGGCG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
92 46 0.67
93 23 0.33
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAAT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:41056755 original size:24 final size:24
Alignment explanation
Indices: 41056657--41056756 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
41056647 AGTCTGTCAA
*
41056657 GAGAGGATTTAGGAGTTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
* *
41056681 GATAGGATTTAGGAGTTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
41056705 GATAGGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
41056729 GAGAGGATTTAGGAGCTGATTAGG
1 GAGAGGATTTAGGAGCTGATAAGG
41056753 GAGA
1 GAGA
41056757 ACAGTGTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.33, C:0.02, G:0.40, T:0.25
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:41058193 original size:27 final size:27
Alignment explanation
Indices: 41058153--41058263 Score: 152
Period size: 27 Copynumber: 4.1 Consensus size: 27
41058143 AGGAAGCGTC
* *
41058153 CTGGTGGCTATGCCACATTTATCTGAT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
41058180 CTGGTGGCTCTGCCACATATATCTGTC
1 CTGGTGGCTCTGCCACATTTATCTGTT
*
41058207 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
41058234 CTGGTGACTCTGTCACA-TTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
41058260 CTGG
1 CTGG
41058264 CAGCAATGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 13 0.17
27 62 0.83
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTTATCTGTT
Found at i:41060597 original size:29 final size:29
Alignment explanation
Indices: 41060552--41060670 Score: 143
Period size: 29 Copynumber: 4.2 Consensus size: 29
41060542 GTGAGCATAA
*
41060552 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
* *
41060580 ATATGAATGTGAATTGGGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
* * *
41060609 ATAAGAATATGAACTGGGCCAAATGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
* * *
41060638 ATTTGAATAAG-ATTGGGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
41060666 ATATG
1 ATATG
41060671 CATGTATGTA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
28 22 0.29
29 53 0.71
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCTAATGGGCC
Found at i:41061733 original size:17 final size:18
Alignment explanation
Indices: 41061701--41061734 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41061691 TTTAAGAAGG
41061701 GTTTTCAATGAAAACACA
1 GTTTTCAATGAAAACACA
*
41061719 GTTTTCACT-AAAACAC
1 GTTTTCAATGAAAACAC
41061735 TTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (18 bp):
GTTTTCAATGAAAACACA
Found at i:41066648 original size:37 final size:37
Alignment explanation
Indices: 41066598--41066676 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41066588 TTATTACGAA
* * *
41066598 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41066635 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41066672 GTCTT
1 GTCTT
41066677 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:41066875 original size:49 final size:49
Alignment explanation
Indices: 41066795--41067176 Score: 531
Period size: 49 Copynumber: 8.1 Consensus size: 49
41066785 CCCTTCGGGA
* * * * *
41066795 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
41066842 CCTGTCACATATATATACATTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41066891 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41066940 CTTATCTC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41066987 CTTATCAC--GTATAT--A----CACATTCATCACATCGACCGTTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41067028 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41067077 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41067126 CTTATCAC--ATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41067173 CTTA
1 CTTA
41067177 CTATCATTTC
Statistics
Matches: 303, Mismatches: 22, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
41 32 0.11
43 5 0.02
45 2 0.01
47 101 0.33
48 1 0.00
49 162 0.53
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41067049 original size:137 final size:138
Alignment explanation
Indices: 41066869--41067148 Score: 490
Period size: 137 Copynumber: 2.0 Consensus size: 138
41066859 CATTTTCACG
*
41066869 TTCATCACATCGGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCA
1 TTCATCACATCGACCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCA
* *
41066934 TTAGGCCTTATCTC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTA
66 TTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
41066998 TATACACA
131 TATACACA
* *
41067006 TTCATCACATCGACCGTTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCA
1 TTCATCACATCGACCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCA
41067071 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
66 TTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
41067136 ATATACACT
130 ATATACACA
41067145 TTCA
1 TTCA
41067149 CGTTCATCAC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
137 75 0.56
139 60 0.44
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (138 bp):
TTCATCACATCGACCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
TATACACA
Found at i:41074210 original size:49 final size:49
Alignment explanation
Indices: 41074138--41074281 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 49
41074128 GCCGAAGCTA
41074138 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAG
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAG
* * * * * **
41074187 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATAG
* *
41074238 TCGGGAACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
41074282 TCACAATAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
49 39 0.49
50 2 0.03
51 39 0.49
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (49 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAG
Found at i:41074274 original size:51 final size:49
Alignment explanation
Indices: 41074144--41074281 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 49
41074134 GCTATCTGGT
* * *
41074144 ACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAGTCTGGT
1 ACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAATAGTCGGGA
* * * * **
41074193 ACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGA
1 ACGCATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAATAGTCGGGA
*
41074244 ACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
41074282 TCACAATAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
49 33 0.45
50 2 0.03
51 39 0.53
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (49 bp):
ACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAATAGTCGGGA
Found at i:41080146 original size:55 final size:54
Alignment explanation
Indices: 41080012--41080416 Score: 347
Period size: 55 Copynumber: 7.6 Consensus size: 54
41080002 GGCATTTGGT
* * * *
41080012 AGGATAAGGATATCATGTAAGACCATGCCAAGGCAT-GCAATTGATAAGTTCTATA
1 AGGA-AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGATGAGTTCTATA
* * *
41080067 AGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATA
1 AGGAAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATA
* * * *
41080122 AGGAAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATA
1 AGG-AAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATA
* * *** *
41080175 A-AAAAGGATGCCATGTAAGACCATGTTTGGAACAAGGCATT--TG-G-----TA
1 AGGAAAGGATACCATGTAAGACCATGTCAAG-ACATGGCATTGATGAGTTCTATA
* * * *
41080221 A-GATAAGGATATCATGTAAGACCATG-CAAGGCATGGCATTGATAAGTTCTATG
1 AGGA-AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATA
* * *
41080274 AGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATA
1 AGGAAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATA
* * * * *
41080329 AGGCAAAGG-TCCCATATAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATA
1 AGG-AAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATA
* *
41080382 AGGCAAGGATACCACGTAAGACCATGTCAAGACAT
1 AGGAAAGGATACCATGTAAGACCATGTCAAGACAT
41080417 TGCAATGGTA
Statistics
Matches: 282, Mismatches: 49, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
45 8 0.03
46 5 0.02
47 21 0.07
48 1 0.00
50 1 0.00
51 7 0.02
52 21 0.07
53 62 0.22
54 61 0.22
55 87 0.31
56 8 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
AGGAAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATA
Found at i:41080339 original size:207 final size:209
Alignment explanation
Indices: 41079979--41080408 Score: 749
Period size: 207 Copynumber: 2.1 Consensus size: 209
41079969 TATAATTTAT
* *
41079979 ATGTAAGACCATGTTTGGAACATGGCATTTGGTAGGATAAGGATATCATGTAAGACCATGCCAAG
1 ATGTAAGACCATGTTTGGAACAAGGCATTTGGTAAGATAAGGATATCATGTAAGACCATGCCAAG
41080044 GCATGCAATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTG
66 GCATGCAATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTG
*
41080109 ATGAGTTACTATAAGGAAAAGGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCAT
131 ATGAGTTACTATAAGGAAAAGGTCCCATATAAGACCATGCCAAGGCATGGCATTGGTGAGTTCAT
*
41080174 AA-AAAAGGATGCC
196 AAGAAAAGGATACC
41080187 ATGTAAGACCATGTTTGGAACAAGGCATTTGGTAAGATAAGGATATCATGTAAGACCATG-CAAG
1 ATGTAAGACCATGTTTGGAACAAGGCATTTGGTAAGATAAGGATATCATGTAAGACCATGCCAAG
*
41080251 GCATGGC-ATTGATAAGTTCTATGAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATT
66 GCAT-GCAATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATT
*
41080315 GATGAGTTACTATAAGGCAAAGGTCCCATATAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
130 GATGAGTTACTATAAGGAAAAGGTCCCATATAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
**
41080380 TAAGGCAAGGATACC
195 TAAGAAAAGGATACC
*
41080395 ACGTAAGACCATGT
1 ATGTAAGACCATGT
41080409 CAAGACATTG
Statistics
Matches: 211, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
207 130 0.62
208 81 0.38
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (209 bp):
ATGTAAGACCATGTTTGGAACAAGGCATTTGGTAAGATAAGGATATCATGTAAGACCATGCCAAG
GCATGCAATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTG
ATGAGTTACTATAAGGAAAAGGTCCCATATAAGACCATGCCAAGGCATGGCATTGGTGAGTTCAT
AAGAAAAGGATACC
Found at i:41080553 original size:16 final size:17
Alignment explanation
Indices: 41080534--41080566 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41080524 CTTATTTAAT
41080534 ATTGAGATTAT-AAGTA
1 ATTGAGATTATCAAGTA
*
41080550 ATTGAGGTTATCAAGTA
1 ATTGAGATTATCAAGTA
41080567 TTAAGTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.36
Consensus pattern (17 bp):
ATTGAGATTATCAAGTA
Found at i:41084813 original size:46 final size:48
Alignment explanation
Indices: 41084711--41085028 Score: 250
Period size: 46 Copynumber: 6.7 Consensus size: 48
41084701 ACATTATTAG
* * * *
41084711 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAAATG-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTTGAGATGTA
* *
41084758 GAGCTAGTGTAAGA-TATGTCTGGGACAT-GCATCAGCCTTGAGATGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTTGAGATGTA
41084805 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CTATGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-TGAGATGTA
* * * * * *
41084850 -GTCAATGTAAGACCATGTCTGGGACATGGCATCGGCATGTATAGAGGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-T-GAGATGTA
** * * * * * *
41084898 -GTTAGTGTAAGACCATGTCTAGGACATTGTATCGGCAC-GGATATGTGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTTGAGATGT-A
* *
41084946 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGATGGATGT-
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTTGA--GATGTA
*
41084995 -GCCAGTGTAAGACCATGTCTGGGACATTGCATCA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCA
41085029 ACACTATTCC
Statistics
Matches: 221, Mismatches: 34, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
44 10 0.05
45 16 0.07
46 64 0.29
47 46 0.21
48 49 0.22
49 3 0.01
50 29 0.13
51 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTTGAGATGTA
Found at i:41084887 original size:138 final size:144
Alignment explanation
Indices: 41084712--41085027 Score: 366
Period size: 138 Copynumber: 2.2 Consensus size: 144
41084702 CATTATTAGA
* * *
41084712 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAA-ATGA-GAGCTAGTGTAAGA-TA
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCA-TGAATA-GAGGAGCTAGTGTAAGACCA
* *
41084774 TGTCTGGGACA-TGCATCAGC-CTTGAGATGT-A-AGCCAGTGTAAGA-CATGTCTGGGACAT-G
64 TGTCTAGGACATTGCATCAGCAC-GGAGATGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGG
41084833 CATC-AGCTATGA-GATGT
128 CATCGA-CT-TGAGGATGT
* * * *
41084850 GTCAATGTAAGACCATGTCTGGGACATGGCATCGGCATGTATAGAGGTGTTAGTGTAAGACCATG
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATGAATAGAGGAGCTAGTGTAAGACCATG
* * * *
41084915 TCTAGGACATTGTATCGGCACGGATATGTGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
66 TCTAGGACATTGCATCAGCACGGAGATGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
41084980 CGACTTGATGGATGT
131 CGACTTGA-GGATGT
* *
41084995 GCCAGTGTAAGACCATGTCTGGGACATTGCATC
1 GCCAATGTAAGACCATGTCTGGGACATGGCATC
41085028 AACACTATTC
Statistics
Matches: 150, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
137 5 0.03
138 47 0.31
139 11 0.07
140 13 0.09
141 2 0.01
142 12 0.08
143 17 0.11
144 7 0.05
145 36 0.24
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (144 bp):
GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATGAATAGAGGAGCTAGTGTAAGACCATG
TCTAGGACATTGCATCAGCACGGAGATGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
CGACTTGAGGATGT
Found at i:41084965 original size:50 final size:48
Alignment explanation
Indices: 41084664--41085027 Score: 199
Period size: 48 Copynumber: 7.7 Consensus size: 48
41084654 TTATTTGTGT
* * *
41084664 GCTAGTGTAAGAGACATGTCTGGGACAT-GCATCGACCAC--ATTATTA-GA
1 GCTAGTGTAAGA-CCATGTCTGGGACATGGCATCG-GCACGGA-TA-GAGGA
* * ** *
41084712 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAAATGA-GA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATA-GAGGA
* *
41084760 GCTAGTGTAAGA-TATGTCTGGGACAT-GCATCAGC-CTTGAGAT-GTA--A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--G-GATAG-AGGA
* * * * *
41084806 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG--C-TATGAGATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGAT-AGAGGA
* * * *
41084850 G-TCAATGTAAGACCATGTCTGGGACATGGCATCGGCATGTATAGAGGT
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATAGAGGA
* * * * *
41084898 GTTAGTGTAAGACCATGTCTAGGACATTGTATCGGCACGGATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATA-GAG-GA
* * * *
41084948 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGATGGATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGATAGAGGA
* *
41084995 GCCAGTGTAAGACCATGTCTGGGACATTGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
41085028 AACACTATTC
Statistics
Matches: 253, Mismatches: 42, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
41 2 0.01
42 1 0.00
43 1 0.00
44 9 0.04
45 15 0.06
46 46 0.18
47 60 0.24
48 78 0.31
49 11 0.04
50 30 0.12
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATAGAGGA
Found at i:41093807 original size:25 final size:25
Alignment explanation
Indices: 41093763--41093811 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41093753 TTAAAGTATG
* * *
41093763 AAAAATGACTATTTTGCCCCTAGGT
1 AAAAATGACCATTATACCCCTAGGT
41093788 AAAAATGACCATTATACCCCTAGG
1 AAAAATGACCATTATACCCCTAGG
41093812 GTTTGATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (25 bp):
AAAAATGACCATTATACCCCTAGGT
Found at i:41093861 original size:10 final size:10
Alignment explanation
Indices: 41093842--41093887 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
41093832 CATGAAACAT
41093842 TGATAT-ACA
1 TGATATGACA
41093851 TGATATGACA
1 TGATATGACA
41093861 TGATATGCACA
1 TGATATG-ACA
41093872 TGATATG-CTA
1 TGATATGAC-A
41093882 TGATAT
1 TGATAT
41093888 ATTCACTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.21
10 17 0.50
11 10 0.29
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:41093874 original size:11 final size:11
Alignment explanation
Indices: 41093848--41093879 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
41093838 ACATTGATAT
41093848 ACATGATATG-
1 ACATGATATGC
41093858 ACATGATATGC
1 ACATGATATGC
41093869 ACATGATATGC
1 ACATGATATGC
41093880 TATGATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (11 bp):
ACATGATATGC
Found at i:41093874 original size:21 final size:21
Alignment explanation
Indices: 41093848--41093887 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41093838 ACATTGATAT
41093848 ACATGATATGAC-ATGATATGC
1 ACATGATATG-CTATGATATGC
41093869 ACATGATATGCTATGATAT
1 ACATGATATGCTATGATAT
41093888 ATTCACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (21 bp):
ACATGATATGCTATGATATGC
Found at i:41093992 original size:24 final size:24
Alignment explanation
Indices: 41093961--41094006 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41093951 AATTTATCGA
**
41093961 AAAGGGCTTTGCC-CCAGTTATTT
1 AAAGGGCTAGGCCTCCAGTTATTT
41093984 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
41094007 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTT
Found at i:41096817 original size:13 final size:13
Alignment explanation
Indices: 41096799--41096832 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
41096789 CGGCTAACCT
41096799 ACATAATTAAATA
1 ACATAATTAAATA
41096812 ACATAATTAAATA
1 ACATAATTAAATA
*
41096825 AAATAATT
1 ACATAATT
41096833 TTTCATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:41097091 original size:20 final size:21
Alignment explanation
Indices: 41097057--41097102 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
41097047 GAACTGAAAT
41097057 GAGCTAAATTCGAGCTCAAGC
1 GAGCTAAATTCGAGCTCAAGC
*
41097078 GAGCTAAA-TCGAGCTCAAGT
1 GAGCTAAATTCGAGCTCAAGC
41097098 GAGCT
1 GAGCT
41097103 GATTGGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGCTAAATTCGAGCTCAAGC
Found at i:41097409 original size:22 final size:21
Alignment explanation
Indices: 41097370--41097410 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41097360 CCAGTCCCAT
41097370 GCATCAGAAAATAATAACATG
1 GCATCAGAAAATAATAACATG
* *
41097391 GCATGCAGTAAATAGTAACA
1 GCAT-CAGAAAATAATAACA
41097411 GTCAAACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (21 bp):
GCATCAGAAAATAATAACATG
Found at i:41102301 original size:39 final size:40
Alignment explanation
Indices: 41102193--41102377 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
41102183 TCAAATGATG
* * *
41102193 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
41102232 ATCCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
41102273 TCCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41102312 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41102351 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41102378 AATGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41102391 original size:40 final size:40
Alignment explanation
Indices: 41102194--41102410 Score: 133
Period size: 40 Copynumber: 5.5 Consensus size: 40
41102184 CAAATGATGT
** * * * *
41102194 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAAC-GAGTTACTATAA
* * ** *
41102234 CCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGAACGAGTTACTATA-A
* * **
41102274 CCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATAA
* **
41102312 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATAA
* * *
41102353 CCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CTATAA
* *
41102393 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41102411 TACGTGATTC
Statistics
Matches: 147, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
39 48 0.33
40 89 0.61
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATAA
Found at i:41102408 original size:79 final size:78
Alignment explanation
Indices: 41102230--41102410 Score: 188
Period size: 79 Copynumber: 2.3 Consensus size: 78
41102220 CTAAGTGACC
*
41102230 ATATCCGGACTAAGATT-CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCAAAGGCA
1 ATATCCGG-CTAA-ATTCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCA
**
41102294 TTGGTGCGAGTTACT
64 TTGGAACGAGTTACT
* * * * * *
41102309 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGC
1 ATATCC-GGCTAAATTCCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAGGC
* *
41102373 ATTTGAATGAG-TAGCT
63 ATTGGAACGAGTTA-CT
41102389 ATATCCGGCTAAATTCCGAAGG
1 ATATCCGGCTAAATTCCGAAGG
41102411 TACGTGATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
78 3 0.04
79 55 0.67
80 24 0.29
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
ATATCCGGCTAAATTCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATT
GGAACGAGTTACT
Found at i:41119396 original size:22 final size:22
Alignment explanation
Indices: 41119366--41119409 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41119356 TTTGGTATTT
41119366 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
41119388 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
41119410 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:41124170 original size:39 final size:39
Alignment explanation
Indices: 41124114--41124198 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
41124104 CTCACTTTCA
* *
41124114 TTTTC-TTTTTCTGCTTCTCTTGATTCTCGCTCATCATC
1 TTTTCTTTTTTCTACTTCTCTTGATTCTAGCTCATCATC
41124152 TTTTCTTTTTTCTACTTCTCTTGATTCTAGCTCATCATC
1 TTTTCTTTTTTCTACTTCTCTTGATTCTAGCTCATCATC
41124191 TTTTCTTT
1 TTTTCTTT
41124199 CTTCAGTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 5 0.11
39 39 0.89
ACGTcount: A:0.09, C:0.26, G:0.06, T:0.59
Consensus pattern (39 bp):
TTTTCTTTTTTCTACTTCTCTTGATTCTAGCTCATCATC
Found at i:41124306 original size:17 final size:18
Alignment explanation
Indices: 41124284--41124319 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41124274 TCTCACACTC
*
41124284 TTTTTCTTT-AATTTCTT
1 TTTTTCTTTCAAATTCTT
41124301 TTTTTCTTTCAAATTCTT
1 TTTTTCTTTCAAATTCTT
41124319 T
1 T
41124320 CTTACATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTCTTTCAAATTCTT
Found at i:41126130 original size:22 final size:23
Alignment explanation
Indices: 41126105--41126164 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
41126095 TGGACTGAAT
41126105 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
41126127 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
41126149 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
41126165 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:41126132 original size:4 final size:4
Alignment explanation
Indices: 41126114--41126147 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
41126104 TATAAAAATT
41126114 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
41126148 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:41127553 original size:23 final size:22
Alignment explanation
Indices: 41127502--41127553 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41127492 CCTCGTCTTT
*
41127502 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41127524 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41127547 TTCTTTT
1 TTCTTTT
41127554 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41127568 original size:18 final size:18
Alignment explanation
Indices: 41127547--41127585 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41127537 TTTCTTCAAC
* *
41127547 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
41127565 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
41127583 TTC
1 TTC
41127586 GCTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:41129942 original size:22 final size:23
Alignment explanation
Indices: 41129917--41129976 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
41129907 TGGACTGAAT
41129917 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
41129939 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
41129961 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
41129977 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:41129944 original size:4 final size:4
Alignment explanation
Indices: 41129926--41129959 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
41129916 TATAAAAATT
41129926 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
41129960 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:41132643 original size:20 final size:20
Alignment explanation
Indices: 41132618--41132657 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41132608 CTGAGTACTT
41132618 ATGCTGAAAGTATTCAATGG
1 ATGCTGAAAGTATTCAATGG
41132638 ATGCTGAAAGTATTCAATGG
1 ATGCTGAAAGTATTCAATGG
41132658 TTGAACCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
ATGCTGAAAGTATTCAATGG
Found at i:41137043 original size:30 final size:28
Alignment explanation
Indices: 41136982--41137053 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
41136972 AAAAAAATTC
*
41136982 AAAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAGTGAAAAAAAAATCAAGCAA
* **
41137010 AAAAAAAAGGTGACCAAAAAAATCAAG-TT
1 AAAAAAAA-GTGA-AAAAAAAATCAAGCAA
41137039 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
41137054 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 2 0.05
28 12 0.32
29 12 0.32
30 11 0.30
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:41137917 original size:18 final size:18
Alignment explanation
Indices: 41137896--41137930 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41137886 AGAAAAGAAA
41137896 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41137914 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41137931 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41149805 original size:39 final size:39
Alignment explanation
Indices: 41149771--41149847 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
41149761 TTTAGTTTAT
*
41149771 GTCTTTAATTATGTTATAGTTTGAACATCATTAGTATGA
1 GTCTTTAATTATGTTATAGTTTGAACAACATTAGTATGA
*
41149810 GTCTTTAATTATGTTATAGTTTGAATAACATTAGTATG
1 GTCTTTAATTATGTTATAGTTTGAACAACATTAGTATG
41149848 TGTTCTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (39 bp):
GTCTTTAATTATGTTATAGTTTGAACAACATTAGTATGA
Found at i:41149984 original size:52 final size:50
Alignment explanation
Indices: 41149864--41149986 Score: 165
Period size: 50 Copynumber: 2.4 Consensus size: 50
41149854 GTATTTAATA
* *
41149864 AAGTCATGCATTATGTAATTCTCATGTAAGTTAAGTTTGCATCATAAATT
1 AAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATT
* * * *
41149914 ATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGTATCATTAAATT
1 AAGTCATGCATTATGTAACTCCCATGTAAGTT-AAGTTTGCATCA-TAAATT
*
41149966 AAGTCATGCATTAAGTAACTC
1 AAGTCATGCATTATGTAACTC
41149987 ATTTGTTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 27 0.44
51 11 0.18
52 24 0.39
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (50 bp):
AAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATT
Found at i:41152516 original size:16 final size:16
Alignment explanation
Indices: 41152486--41152538 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
41152476 AAAAAAAATC
41152486 AAAAAAAAATT---TG
1 AAAAAAAAATTGAGTG
41152499 AAAAAAAAATTGAGTG
1 AAAAAAAAATTGAGTG
* *
41152515 AAAAAAAAATCGAG-C
1 AAAAAAAAATTGAGTG
41152530 AAAAAAAAA
1 AAAAAAAAA
41152539 GAAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 11 0.31
15 9 0.26
16 15 0.43
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATTGAGTG
Found at i:41153481 original size:18 final size:18
Alignment explanation
Indices: 41153460--41153494 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41153450 AGAAAAGAAA
41153460 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41153478 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41153495 AAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41158564 original size:8 final size:8
Alignment explanation
Indices: 41158551--41158588 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
41158541 GAAGTGAGCA
*
41158551 AAAAAAAG
1 AAAAAAAC
41158559 AAAAAAA-
1 AAAAAAAC
*
41158566 AGAAAAAC
1 AAAAAAAC
41158574 AAAAAAAC
1 AAAAAAAC
41158582 AAAAAAA
1 AAAAAAA
41158589 AGTGAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:41159638 original size:18 final size:17
Alignment explanation
Indices: 41159555--41159683 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
41159545 GGAACAAGAA
*
41159555 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AATGAG
*
41159573 ATTGAAGAAAGAAACGAG
1 ATTGAA-AAAGAAATGAG
* * *
41159591 AGTGTAAAAGAAACGAGTG
1 ATTGAAAAAGAAATGA--G
*
41159610 TCATGGAAAAAGAAATTGAG
1 --ATTGAAAAAGAAA-TGAG
*
41159630 ATTGAAAAAG-GAT--G
1 ATTGAAAAAGAAATGAG
*
41159644 --TGAAAAAGAGAATGAA
1 ATTGAAAAAGA-AATGAG
*
41159660 ATCGAAAAAGAAATTGAG
1 ATTGAAAAAGAAA-TGAG
41159678 ATTGAA
1 ATTGAA
41159684 CAAAAGTGTG
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
12 8 0.10
14 3 0.04
16 1 0.01
17 13 0.16
18 39 0.47
19 6 0.07
20 1 0.01
21 10 0.12
22 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAATGAG
Found at i:41159715 original size:48 final size:47
Alignment explanation
Indices: 41159615--41159720 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
41159605 GAGTGTCATG
*
41159615 GAAAAAGAAATTGAGATTGAAAAAGGATGTGAAAAAGAGAATGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAA-GAAATC
*
41159663 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAGAAAGAG-A-AAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA--A-AAAGAGAAGAAATC
41159711 GAAAAAGAAA
1 GAAAAAGAAA
41159721 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 40 0.77
49 4 0.08
50 2 0.04
51 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAGAAATC
Found at i:41164527 original size:9 final size:9
Alignment explanation
Indices: 41164513--41164557 Score: 63
Period size: 9 Copynumber: 4.7 Consensus size: 9
41164503 AGTATTTGAA
41164513 AAAAAATTC
1 AAAAAATTC
41164522 AAAAAATTC
1 AAAAAATTC
41164531 TAAAAAAATTC
1 --AAAAAATTC
41164542 AAAACAATTC
1 AAAA-AATTC
41164552 AAAAAA
1 AAAAAA
41164558 ATATTCGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 15 0.45
10 9 0.27
11 9 0.27
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTC
Found at i:41164527 original size:10 final size:10
Alignment explanation
Indices: 41164512--41164559 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
41164502 AAGTATTTGA
41164512 AAAAAAATTC
1 AAAAAAATTC
41164522 -AAAAAATTC
1 AAAAAAATTC
41164531 TAAAAAAATTC
1 -AAAAAAATTC
*
41164542 AAAACAATTC
1 AAAAAAATTC
41164552 AAAAAAAT
1 AAAAAAAT
41164560 ATTCGTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
11 9 0.26
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:41164537 original size:21 final size:21
Alignment explanation
Indices: 41164511--41164563 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
41164501 TAAGTATTTG
41164511 AAAAAAAATTCAAAA-AATTC
1 AAAAAAAATTCAAAACAATTC
*
41164531 TAAAAAAATTCAAAACAATTC
1 AAAAAAAATTCAAAACAATTC
41164552 AAAAAAATATTC
1 AAAAAAA-ATTC
41164564 GTGAATGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.48
21 11 0.38
22 4 0.14
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAAAATTCAAAACAATTC
Found at i:41176723 original size:19 final size:19
Alignment explanation
Indices: 41176699--41176738 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41176689 AGCTCCCATG
41176699 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
41176718 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
41176737 TA
1 TA
41176739 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:41178002 original size:14 final size:14
Alignment explanation
Indices: 41177980--41178027 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
41177970 ACCTAAACCG
* *
41177980 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
41177994 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
41178008 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
41178022 ACCATT
1 ACCATT
41178028 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:41178305 original size:14 final size:15
Alignment explanation
Indices: 41178286--41178319 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41178276 TACAAGTTTG
41178286 AAAAAAA-AATCGAA
1 AAAAAAAGAATCGAA
*
41178300 AAAAAAAGATTCGAA
1 AAAAAAAGAATCGAA
41178315 AAAAA
1 AAAAA
41178320 TTCGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAAAAAGAATCGAA
Found at i:41178327 original size:22 final size:22
Alignment explanation
Indices: 41178300--41178352 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
41178290 AAAAATCGAA
41178300 AAAAAAAGATTCGAAAAA-AATTC
1 AAAAAAA-ATTC-AAAAACAATTC
*
41178323 GAAAAAAATTCAAAAACAATTC
1 AAAAAAAATTCAAAAACAATTC
41178345 AAAAAAAA
1 AAAAAAAA
41178353 AGTGATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 16 0.59
23 6 0.22
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAAAAATTCAAAAACAATTC
Found at i:41179276 original size:9 final size:10
Alignment explanation
Indices: 41179269--41179325 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
41179259 AAGAGAAAAT
41179269 AAAGAAAAGA
1 AAAGAAAAGA
41179279 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
41179291 AAAGAAGA-A
1 AAAGAAAAGA
41179300 AAAGAAAATGA
1 AAAGAAAA-GA
41179311 AATA-AAAAGA
1 AA-AGAAAAGA
41179321 AAAGA
1 AAAGA
41179326 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:41179293 original size:6 final size:5
Alignment explanation
Indices: 41179269--41179325 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
41179259 AAGAGAAAAT
*
41179269 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
41179316 AAAGA AAAGA
1 AAAGA AAAGA
41179326 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:41179300 original size:15 final size:14
Alignment explanation
Indices: 41179269--41179325 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
41179259 AAGAGAAAAT
41179269 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
41179285 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
41179300 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
41179316 AAAGAAAAGA
1 AAAGAAAAGA
41179326 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:41181934 original size:22 final size:22
Alignment explanation
Indices: 41181883--41181948 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
41181873 GGTATTTGGG
* *
41181883 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
41181904 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
41181926 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
41181949 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:41188764 original size:18 final size:17
Alignment explanation
Indices: 41188742--41188775 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41188732 ACCTCTTCTT
41188742 TTTTTTTTAATTCTGAA
1 TTTTTTTTAATTCTGAA
*
41188759 TTTTTTTTACTTCTGAA
1 TTTTTTTTAATTCTGAA
41188776 ACTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTTTAATTCTGAA
Found at i:41188876 original size:11 final size:11
Alignment explanation
Indices: 41188860--41188891 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41188850 AAATTGAATA
41188860 CAATTTTTTTT
1 CAATTTTTTTT
41188871 CAATTTTTTTT
1 CAATTTTTTTT
*
41188882 TAATTTTTTT
1 CAATTTTTTT
41188892 CCCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:41191448 original size:11 final size:12
Alignment explanation
Indices: 41191434--41191470 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
41191424 TTTTTTTTCC
41191434 TTTTTTTCG-AT
1 TTTTTTTCGAAT
41191445 TTTTTTT-GAAT
1 TTTTTTTCGAAT
41191456 TTTTTTTCTGAAT
1 TTTTTTTC-GAAT
41191469 TT
1 TT
41191471 CTTCTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 16 0.70
13 6 0.26
ACGTcount: A:0.14, C:0.05, G:0.08, T:0.73
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:41193215 original size:30 final size:30
Alignment explanation
Indices: 41193181--41193277 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
41193171 TAAACTAAAA
*
41193181 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
41193211 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
41193241 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
41193270 ATGAGCTA
1 -TGAGCTA
41193278 GGAGTGAGCT
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:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:41195475 original size:23 final size:22
Alignment explanation
Indices: 41195424--41195475 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41195414 TCCTCGTCTT
*
41195424 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41195446 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41195469 TTCTTTT
1 TTCTTTT
41195476 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41203984 original size:10 final size:10
Alignment explanation
Indices: 41203969--41204012 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
41203959 TATACAAGTT
41203969 AAAAAAATAA
1 AAAAAAATAA
*
41203979 AAAAAAATCA
1 AAAAAAATAA
41203989 AAAAAAAT-A
1 AAAAAAATAA
41203998 AAAAAAATAA
1 AAAAAAATAA
41204008 AAAAA
1 AAAAA
41204013 GAGTGATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.89, C:0.02, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:41211909 original size:14 final size:14
Alignment explanation
Indices: 41211887--41211934 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
41211877 ACCTAAACCG
* *
41211887 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
41211901 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
41211915 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
41211929 ACCATT
1 ACCATT
41211935 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:41213838 original size:20 final size:20
Alignment explanation
Indices: 41213815--41213862 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41213805 TCCAGCTCAA
*
41213815 TTTATCTCATTTGAGCTTGT
1 TTTAGCTCATTTGAGCTTGT
* *
41213835 TTTAGCTCGTTTGAGTTTGT
1 TTTAGCTCATTTGAGCTTGT
*
41213855 TTCAGCTC
1 TTTAGCTC
41213863 GTTCTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTAGCTCATTTGAGCTTGT
Found at i:41213863 original size:20 final size:20
Alignment explanation
Indices: 41213824--41213865 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
41213814 ATTTATCTCA
*
41213824 TTTGAGCTTGTTTTAGCTCG
1 TTTGAGCTTGTTTCAGCTCG
*
41213844 TTTGAGTTTGTTTCAGCTCG
1 TTTGAGCTTGTTTCAGCTCG
41213864 TT
1 TT
41213866 CTTTATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (20 bp):
TTTGAGCTTGTTTCAGCTCG
Found at i:41219187 original size:56 final size:55
Alignment explanation
Indices: 41219071--41219188 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
41219061 TGCATGCTTT
* * * *
41219071 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
41219125 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
41219181 CATTAAAT
1 CATTAAAT
41219189 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:41219837 original size:20 final size:20
Alignment explanation
Indices: 41219812--41219866 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
41219802 ACGAGTTAAA
* *
41219812 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
41219832 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
41219852 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
41219867 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:41221385 original size:17 final size:15
Alignment explanation
Indices: 41221348--41221386 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
41221338 TATCTCCCAC
41221348 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
41221364 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
41221381 TCATTT
1 TCATTT
41221387 TCTCGCGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:41223896 original size:28 final size:30
Alignment explanation
Indices: 41223853--41223920 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
41223843 TTTCAATCAC
41223853 TCTTTTTTTTTCAATTTCG-ATTTTTTTCT
1 TCTTTTTTTTTCAATTTCGAATTTTTTTCT
41223882 TCTTTTTTTTT-AATTTCGAATTTTTTTCT
1 TCTTTTTTTTTCAATTTCGAATTTTTTTCT
41223911 TCTTTTTTTT
1 TCTTTTTTTT
41223921 CCTTCAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (30 bp):
TCTTTTTTTTTCAATTTCGAATTTTTTTCT
Found at i:41224004 original size:13 final size:12
Alignment explanation
Indices: 41223965--41224016 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
41223955 GAATACAAAC
41223965 TTTTTTTTGAAT
1 TTTTTTTTGAAT
41223977 TTTTTTTTGAAT
1 TTTTTTTTGAAT
* *
41223989 TTTTTTTTCAAG
1 TTTTTTTTGAAT
41224001 TTTTTTTT--AT
1 TTTTTTTTGAAT
41224011 TTTTTT
1 TTTTTT
41224017 ACAATACCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 7 0.19
12 30 0.81
ACGTcount: A:0.13, C:0.02, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:41225381 original size:56 final size:55
Alignment explanation
Indices: 41225265--41225382 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
41225255 TGCATGCTTT
* * * *
41225265 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
41225319 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
41225375 CATTAAAT
1 CATTAAAT
41225383 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:41226030 original size:20 final size:20
Alignment explanation
Indices: 41226005--41226059 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
41225995 ACGAGTTAAA
* *
41226005 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
41226025 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
41226045 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
41226060 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:41228834 original size:14 final size:14
Alignment explanation
Indices: 41228815--41228859 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
41228805 AACTCATCTT
*
41228815 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
41228829 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
41228842 AATTTAATTTAATG
1 AGTTTAATTTAATG
41228856 AGTT
1 AGTT
41228860 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:41230114 original size:12 final size:11
Alignment explanation
Indices: 41230060--41230116 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
41230050 TCAAGTAAGT
41230060 TTCAAAAAAAA
1 TTCAAAAAAAA
*
41230071 AT-AAAAAAAA
1 TTCAAAAAAAA
**
41230081 TGAAAAAAAAA
1 TTCAAAAAAAA
41230092 TTCAAACAAAAA
1 TTCAAA-AAAAA
41230104 TTCTGAAAAAAAA
1 TTC--AAAAAAAA
41230117 ACAAAATCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
10 8 0.22
11 13 0.35
12 8 0.22
13 5 0.14
14 3 0.08
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:41233628 original size:14 final size:14
Alignment explanation
Indices: 41233609--41233653 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
41233599 AACTCATCTT
*
41233609 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
41233623 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
41233636 AATTTAATTTAATG
1 AGTTTAATTTAATG
41233650 AGTT
1 AGTT
41233654 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:41236840 original size:22 final size:22
Alignment explanation
Indices: 41236812--41236855 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41236802 TTTTGAAGCA
41236812 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41236834 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41236856 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41237712 original size:12 final size:12
Alignment explanation
Indices: 41237697--41237730 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41237687 CTTGAAAGAG
*
41237697 ATTGAAAAAGTC
1 ATTGAAAAAGCC
41237709 ATTGAAAAAGCC
1 ATTGAAAAAGCC
*
41237721 TTTGAAAAAG
1 ATTGAAAAAG
41237731 AAAAAGGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.24
Consensus pattern (12 bp):
ATTGAAAAAGCC
Found at i:41237863 original size:18 final size:19
Alignment explanation
Indices: 41237820--41237865 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41237810 CGAGAGAAGC
*
41237820 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
41237838 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
41237856 GAAAAAGAAA
1 GAAAAAGAAA
41237866 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:41239847 original size:20 final size:20
Alignment explanation
Indices: 41239824--41239877 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
41239814 AGCTAAAGTA
41239824 AGCTAAATTGAGCTCAAACG
1 AGCTAAATTGAGCTCAAACG
* * *
41239844 AGCTAAATTAAGCTCATATG
1 AGCTAAATTGAGCTCAAACG
*
41239864 AGCTAAATCGAGCT
1 AGCTAAATTGAGCT
41239878 GGGAAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
AGCTAAATTGAGCTCAAACG
Found at i:41250614 original size:18 final size:18
Alignment explanation
Indices: 41250593--41250652 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
41250583 GACCTCACTC
41250593 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
41250611 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
41250629 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
41250650 TCT
1 TCT
41250653 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:41264364 original size:12 final size:12
Alignment explanation
Indices: 41264333--41264403 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
41264323 TAGGAGCAAC
41264333 AAAAAAAA-TCA
1 AAAAAAAATTCA
41264344 AAAAAAAATTCGA
1 AAAAAAAATTC-A
*
41264357 AAAAAAATTTGATTGA
1 AAAAAAA----ATTCA
41264373 AAAAAAAATTCA
1 AAAAAAAATTCA
* * *
41264385 TAAAAAAAGTGA
1 AAAAAAAATTCA
41264397 AAAAAAA
1 AAAAAAA
41264404 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 8 0.17
12 21 0.44
13 8 0.17
16 8 0.17
17 3 0.06
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:41265511 original size:6 final size:6
Alignment explanation
Indices: 41265481--41265588 Score: 60
Period size: 6 Copynumber: 17.7 Consensus size: 6
41265471 AAAGAAATTG
* ** *
41265481 AAAG-A AAACAA AAAGAA AACA-AA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
41265528 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
41265579 AAAGAA AAAG
1 AAAGAA AAAG
41265589 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 20, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
5 5 0.07
6 57 0.76
7 9 0.12
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:41265511 original size:18 final size:18
Alignment explanation
Indices: 41265485--41265543 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
41265475 AAATTGAAAG
* *
41265485 AAAACAAAAAGAAAACAA
1 AAAAGAAAAAGAAATCAA
***
41265503 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCAA
41265521 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCAA
41265539 AAAAG
1 AAAAG
41265544 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.76, C:0.07, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCAA
Found at i:41265568 original size:14 final size:13
Alignment explanation
Indices: 41265549--41265586 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
41265539 AAAAGTGAGA
41265549 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
41265561 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
41265576 GAAAAAGAAAA
1 GAAAAAGAAAA
41265587 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:41265583 original size:13 final size:12
Alignment explanation
Indices: 41265467--41265586 Score: 54
Period size: 12 Copynumber: 10.0 Consensus size: 12
41265457 AGAAAGAGAT
*
41265467 TGAAAAAGAAAT
1 TGAAAAAGAAAA
41265479 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
41265489 -CAAAAAGAAAA
1 TGAAAAAGAAAA
**
41265500 CAAAAAAGAAAA
1 TGAAAAAGAAAA
* **
41265512 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
41265525 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
41265535 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
41265549 -GAAAAAGAAAA
1 TGAAAAAGAAAA
41265560 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
41265574 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
41265587 AGCGAAAAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 34 0.41
13 14 0.17
14 12 0.15
15 2 0.02
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:41265600 original size:21 final size:21
Alignment explanation
Indices: 41265550--41265600 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
41265540 AAAGTGAGAG
*
41265550 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
41265571 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
41265592 AAAAAGAAA
1 AAAAAGAAA
41265601 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:41267690 original size:20 final size:20
Alignment explanation
Indices: 41267644--41267690 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41267634 AGCTCGTTTC
*
41267644 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41267664 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41267684 CAGCTCA
1 CAGCTCA
41267691 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41269255 original size:22 final size:21
Alignment explanation
Indices: 41269219--41269263 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
41269209 AGAAGTGAGC
*
41269219 AAAAAAAGAAAAAAAAGTAAA
1 AAAAAAACAAAAAAAAGTAAA
*
41269240 AAAAAGAACAAAAAAAAGTGAA
1 AAAAA-AACAAAAAAAAGTAAA
41269262 AA
1 AA
41269264 GTCTTGTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAGTAAA
Found at i:41269263 original size:10 final size:9
Alignment explanation
Indices: 41269219--41269254 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
41269209 AGAAGTGAGC
41269219 AAAAAAAGA
1 AAAAAAAGA
41269228 AAAAAAAGTA
1 AAAAAAAG-A
41269238 AAAAAAAGA
1 AAAAAAAGA
41269247 ACAAAAAA
1 A-AAAAAA
41269255 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:41270362 original size:48 final size:47
Alignment explanation
Indices: 41270283--41270388 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
41270273 GAGTGTCATG
*
41270283 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
41270331 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
41270379 GAAAAAGAAA
1 GAAAAAGAAA
41270389 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:41272105 original size:20 final size:20
Alignment explanation
Indices: 41272059--41272105 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41272049 AGCTCGTTTC
*
41272059 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41272079 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41272099 CAGCTCA
1 CAGCTCA
41272106 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.