Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 141 of 214
Found at i:42519354 original size:9 final size:9
Alignment explanation
Indices: 42519326--42519366 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
42519316 TGTTTTTTAT
42519326 ATATAA-TA
1 ATATAATTA
42519334 ATATAA-TA
1 ATATAATTA
42519342 ATATAATTA
1 ATATAATTA
42519351 ATATAATTA
1 ATATAATTA
42519360 ATATAAT
1 ATATAAT
42519367 ACTTATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATAATTA
Found at i:42520893 original size:23 final size:23
Alignment explanation
Indices: 42520850--42520895 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42520840 CTTTCTTTCT
* *
42520850 GTAGTATTTTTCGGGGGATTACA
1 GTAGTAATTTTCGGGAGATTACA
*
42520873 GTAGTAATTTTCGGGATATTACA
1 GTAGTAATTTTCGGGAGATTACA
42520896 ATAACCCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
GTAGTAATTTTCGGGAGATTACA
Found at i:42521063 original size:43 final size:43
Alignment explanation
Indices: 42521016--42521115 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
42521006 ATATTGGCAT
* *
42521016 ACACAGTGCATCATCAGG-CAAGCCAAAACAATTATACTGACAC
1 ACACAGTACATCATC-GGACAAGCCAAAACAATTATACTAACAC
** **
42521059 ACACAGTACATCATCGGACAAGCCGGAGTAATTATACTAACAC
1 ACACAGTACATCATCGGACAAGCCAAAACAATTATACTAACAC
*
42521102 ACACAATACATCAT
1 ACACAGTACATCAT
42521116 TGGATAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 2 0.04
43 47 0.96
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (43 bp):
ACACAGTACATCATCGGACAAGCCAAAACAATTATACTAACAC
Found at i:42525983 original size:28 final size:28
Alignment explanation
Indices: 42525951--42526009 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
42525941 GCCTGACCCT
* *
42525951 ATACAACAATAGTGTG-GGCTTCAGCCCA
1 ATACAACAACAGTGTGAGCCTT-AGCCCA
**
42525979 ATACAGTAACAGTGTGAGCCTTAGCCCA
1 ATACAACAACAGTGTGAGCCTTAGCCCA
42526007 ATA
1 ATA
42526010 TAGAAACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (28 bp):
ATACAACAACAGTGTGAGCCTTAGCCCA
Found at i:42526501 original size:27 final size:27
Alignment explanation
Indices: 42526372--42526689 Score: 284
Period size: 27 Copynumber: 11.8 Consensus size: 27
42526362 CCCTATGAAC
* * * * *
42526372 GTATTTCGGTTATTTTACCCTTTGGGG
1 GTATTTCAGTCATTTTACCCATCGAGG
* *
42526399 GTATTTC-GATCATTTTACCCTTCGGGG
1 GTATTTCAG-TCATTTTACCCATCGAGG
* *
42526426 GTATTTCAGTCATTTTACCCTTTGAGG
1 GTATTTCAGTCATTTTACCCATCGAGG
*
42526453 GTATTTCAGTCATTTTACCCATCGGGG
1 GTATTTCAGTCATTTTACCCATCGAGG
* * **
42526480 GTATTTCAGTCATTTTATCCATCAAAT
1 GTATTTCAGTCATTTTACCCATCGAGG
* * *
42526507 GTATTT-TGATCTTTTTACCTATCGAGG
1 GTATTTCAG-TCATTTTACCCATCGAGG
42526534 GTATTTCAGTCATTTTACCCATCGAGG
1 GTATTTCAGTCATTTTACCCATCGAGG
* * * *
42526561 GTATTTCAATCATTTTATCCATCAAAG
1 GTATTTCAGTCATTTTACCCATCGAGG
* * *
42526588 GTATTTCAGTCTTTTTACCCATCAAAG
1 GTATTTCAGTCATTTTACCCATCGAGG
* * *
42526615 TTATTTCGGTCATTTTACCCTTCGAAGG
1 GTATTTCAGTCATTTTACCCATCG-AGG
** *
42526643 GTATTTC-GATCATTTTACTTATTGAGG
1 GTATTTCAG-TCATTTTACCCATCGAGG
**
42526670 GTATTTTGGTCATTTT-CCCA
1 GTATTTCAGTCATTTTACCCA
42526690 CGAATCGCAA
Statistics
Matches: 241, Mismatches: 43, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.02
27 215 0.89
28 22 0.09
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (27 bp):
GTATTTCAGTCATTTTACCCATCGAGG
Found at i:42531925 original size:17 final size:18
Alignment explanation
Indices: 42531891--42531926 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42531881 CAAGAGTCTC
*
42531891 CCTACAGTTTCTAGTTTT
1 CCTACAGTCTCTAGTTTT
42531909 CCTACAGTCTC-AGTTTT
1 CCTACAGTCTCTAGTTTT
42531926 C
1 C
42531927 TCTAATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (18 bp):
CCTACAGTCTCTAGTTTT
Found at i:42532729 original size:28 final size:28
Alignment explanation
Indices: 42532697--42532807 Score: 141
Period size: 28 Copynumber: 4.0 Consensus size: 28
42532687 AGTAGCAGCT
* * *
42532697 TGGGCCTGAGCCCTATACAGCAACAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGTG
* *
42532725 TGGGCCTTAGCCCAATACAGTAACAATA
1 TGGGCCTTAGCCCAATACAGTAACAGTG
*
42532753 TGGGCCTTATCCCAATACAGTAACAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGTG
* * *
42532781 TAGGCATTAGCCCAATACAGAAACAGT
1 TGGGCCTTAGCCCAATACAGTAACAGT
42532808 ACAATGCAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAGTAACAGTG
Found at i:42533212 original size:54 final size:54
Alignment explanation
Indices: 42533138--42533388 Score: 247
Period size: 54 Copynumber: 4.6 Consensus size: 54
42533128 GGTATAACAG
* * * *
42533138 TCATTTTACCCTAT-GGGGGTATTTCAATTATTTTACCCTTCAGGGGTATTTCGA
1 TCATTTTACCCT-TCGAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTCGA
** *
42533192 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTCGA
* * * * *
42533246 TCATTTTATCCATCGAGGGTATTT-AGATCTTTTTACCAATCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCA-ATCATTTTACCCATCAAGGGTATTTCGA
* * **
42533300 TAATTTTACCCTTCGGGGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTC-A
1 TCATTTTACCCTTC-GAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTCGA
* * * ** *
42533354 GTTATTTTATCCATAAAGGGTATTTCGATCATTTT
1 -TCATTTTACCCTTCGAGGGTATTTCAATCATTTT
42533389 TCTACGAATC
Statistics
Matches: 161, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 119 0.74
55 41 0.25
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (54 bp):
TCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCATCAAGGGTATTTCGA
Found at i:42533361 original size:109 final size:109
Alignment explanation
Indices: 42533181--42533389 Score: 339
Period size: 109 Copynumber: 1.9 Consensus size: 109
42533171 TACCCTTCAG
* *
42533181 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCGG
1 GGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCAG
**
42533246 TCATTTTATCCATCGAGGGTATTTAGATC-TTTTTACCAATCGA
66 TCATTTTATCCATAAAGGGTATTTAGATCATTTTTACCAATCGA
*
42533289 GGGTATTTCGATAATTTTACCCTTCGGGGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCA
1 GGGTATTTCGATAATTTTACCCTTC-GAGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCA
* *
42533354 GTTATTTTATCCATAAAGGGTATTTCGATCATTTTT
65 GTCATTTTATCCATAAAGGGTATTTAGATCATTTTT
42533390 CTACGAATCA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 24 0.26
109 63 0.68
110 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (109 bp):
GGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCAG
TCATTTTATCCATAAAGGGTATTTAGATCATTTTTACCAATCGA
Found at i:42533367 original size:27 final size:27
Alignment explanation
Indices: 42533135--42533388 Score: 212
Period size: 27 Copynumber: 9.4 Consensus size: 27
42533125 AGGGGTATAA
**
42533135 CAGTCATTTTACCCTAT-GGGGGTATTT
1 CAGTCATTTTACCC-ATCAAGGGTATTT
* * * *
42533162 CAATTATTTTACCCTTCAGGGGTATTT
1 CAGTCATTTTACCCATCAAGGGTATTT
* *
42533189 C-GATCATTTTACCCTTCGAGGGTATTT
1 CAG-TCATTTTACCCATCAAGGGTATTT
*
42533216 CGGTCATTTTACCCATCAAGGGTATTT
1 CAGTCATTTTACCCATCAAGGGTATTT
* * *
42533243 CGGTCATTTTATCCATCGAGGGTATTT
1 CAGTCATTTTACCCATCAAGGGTATTT
* * *
42533270 -AGATCTTTTTACCAATCGAGGGTATTT
1 CAG-TCATTTTACCCATCAAGGGTATTT
* * **
42533297 C-GATAATTTTACCCTTCGGGGGGTATTT
1 CAG-TCATTTTACCCATC-AAGGGTATTT
*
42533325 CGGTCATTTTACCCATCAAGGGTATTT
1 CAGTCATTTTACCCATCAAGGGTATTT
* * *
42533352 CAGTTATTTTATCCATAAAGGGTATTT
1 CAGTCATTTTACCCATCAAGGGTATTT
42533379 C-GATCATTTT
1 CAG-TCATTTT
42533389 TCTACGAATC
Statistics
Matches: 189, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
26 3 0.02
27 162 0.86
28 23 0.12
29 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCATCAAGGGTATTT
Found at i:42536604 original size:3 final size:3
Alignment explanation
Indices: 42536596--42536629 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
42536586 AGCAAGTTGG
*
42536596 AAT AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42536630 GCTAATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:42541241 original size:21 final size:20
Alignment explanation
Indices: 42541205--42541246 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42541195 CTGAATATAC
42541205 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAAC-TTTT
**
42541226 GTCTGTTTGTGTGAACTTTT
1 GTCTGTTTGTCAGAACTTTT
42541246 G
1 G
42541247 GTTATTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
GTCTGTTTGTCAGAACTTTT
Found at i:42546075 original size:21 final size:21
Alignment explanation
Indices: 42546049--42546092 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42546039 AAATATATAT
*
42546049 AATATGTACATGTATTTACAA
1 AATATGTACATATATTTACAA
* *
42546070 AATATGTATATATATTTATAA
1 AATATGTACATATATTTACAA
42546091 AA
1 AA
42546093 AAATAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
AATATGTACATATATTTACAA
Found at i:42546164 original size:24 final size:26
Alignment explanation
Indices: 42546137--42546194 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
42546127 ACAGATATGT
*
42546137 AAATTAT-TAAATATATATATA-AAA
1 AAATTATGAAAATATATATATACAAA
*
42546161 AAA-TATGAAAATATGTATATACAAA
1 AAATTATGAAAATATATATATACAAA
42546186 AAATGTATG
1 AAAT-TATG
42546195 TATATAGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 3 0.11
24 15 0.54
25 6 0.21
27 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (26 bp):
AAATTATGAAAATATATATATACAAA
Found at i:42548176 original size:44 final size:44
Alignment explanation
Indices: 42548084--42548338 Score: 169
Period size: 44 Copynumber: 5.8 Consensus size: 44
42548074 GATAAGATTG
* * * * *
42548084 TCTTCAATGTACTCCACT-GTAACCTCAGGGAGATAAAATCTGTCA
1 TCTTCAATCTACTCCACTACT-GCCT-AGGGAGATAAGATCTGTAA
* *
42548129 TCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATTTGTAA
1 TCTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAA
* ** * *
42548173 TCTTCAATCTATTCCACTACAACCTAGGGAGAT-AGA-AT-TAC
1 TCTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAA
* * * * * * ***
42548214 TGGCCTCAATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCTACCA
1 T--CTTCAATCTACTCCACTACT-GCCT-AGGGAGATAAGATCTGTAA
** * *
42548261 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAA
* * *
42548305 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATA
1 TCTTCAATCTACTCCACTACTGCCTAGGGAGATA
42548339 GAATTACTGG
Statistics
Matches: 157, Mismatches: 44, Indels: 19
0.71 0.20 0.09
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
43 21 0.13
44 93 0.59
45 35 0.22
46 3 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
TCTTCAATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAA
Found at i:42548235 original size:132 final size:131
Alignment explanation
Indices: 42548087--42548434 Score: 534
Period size: 132 Copynumber: 2.6 Consensus size: 131
42548077 AAGATTGTCT
* *
42548087 TCAATGTACTCCACTGTAACCTCAGGGAGATAAAATCTGTCATCTTCGATCTACTCCACTACTGC
1 TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTG-CATCTTCGATCTGCTCCACTACTGC
* *
42548152 CTAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTACAACCTAGGGAGATAGAATTACTGG
65 TTAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTACAACCCAGGGAGATAGAATTACTGG
42548217 CC
130 CC
* *
42548219 TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGC
1 TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCT-GCATCTTCGATCTGCTCCACTACTGC
* * **
42548284 TTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGG
65 TTAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTACAACCCAGGGAGATAGAATTACTGG
*
42548349 CT
130 CC
* *
42548351 TCAATGTACACCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTCCACTACTGC
1 TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGC-ATCTTCGATCTGCTCCACTACTGC
* *
42548416 TTAAGGAGATAAGACTTGT
65 TTAGGGAGATAAGATTTGT
42548435 GGTTTTAATC
Statistics
Matches: 196, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
131 1 0.01
132 195 0.99
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (131 bp):
TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCATCTTCGATCTGCTCCACTACTGCT
TAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTACAACCCAGGGAGATAGAATTACTGGC
C
Found at i:42548470 original size:132 final size:133
Alignment explanation
Indices: 42548003--42548429 Score: 510
Period size: 132 Copynumber: 3.2 Consensus size: 133
42547993 AAATCTGAAG
* ** * ** * * * *
42548003 CGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCACTCCATTGCAACT
1 CGATCTGCTCCACTACTGCTTAAG-GAGATAAGATCTGTAATCTTCAATCCATTCCACTGCAACC
* * *
42548067 TCAAGGAGATA-AGA-T--TGTCTTCAATGTACTCCACTGTAACCTCAGGGAGATAAAATCTG-T
65 TCAGGGAGATAGA-ATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCT
42548127 CATCTT
129 -ATCTT
* * * * * *
42548133 CGATCTACTCCACTACTGCCTAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTACAACCT
1 CGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCCATTCCACTGCAACCT
* * *
42548198 -AGGGAGATAGAATTACTGGCCTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCAT
66 CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCTAT
42548262 CTT
131 CTT
* * * **
42548265 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCC-
1 CGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCCATTCCACTGCAACCT
* *
42548329 CAGGGAGATAGAATTACTGGCTTCAATGTACACCACTGTAACCTCAGGGAGGTAAAATCCGCTAT
66 CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCTAT
42548394 CTT
131 CTT
42548397 CGATCTGCTCCACTACTGCTTAAGGAGATAAGA
1 CGATCTGCTCCACTACTGCTTAAGGAGATAAGA
42548430 CTTGTGGTTT
Statistics
Matches: 254, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
129 23 0.09
130 36 0.14
132 195 0.77
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (133 bp):
CGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCCATTCCACTGCAACCT
CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCTAT
CTT
Found at i:42548606 original size:89 final size:89
Alignment explanation
Indices: 42548485--42548920 Score: 696
Period size: 89 Copynumber: 4.9 Consensus size: 89
42548475 TTGTATTTTT
*
42548485 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTT-TCCTTGATCTACTTCACGCCAGTA
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTCACGCCAGTA
42548549 CATGAAGACAAGATCTGCTTTCTTC
65 CATGAAGACAAGATCTGCTTTCTTC
* * *
42548574 GATCCACTTCGCCACCAGTATAGGAAGACAAGATCTGTTCTCTTTGATCTACTTCACGCCAGTAC
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTAC
42548639 ATGAAGACAAGATCTGCTTTCTTC
66 ATGAAGACAAGATCTGCTTTCTTC
* * *
42548663 GATCTGCTTCACCACTAGTATGGGAAGGA-AAGATCTGTTATCTTTGATCTACTTCACGCCAGTA
1 GATCTACTTCGCCACCAGTATGGGAA-GACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTA
42548727 CATGAAGACAAGATCTGCTTTCTTC
65 CATGAAGACAAGATCTGCTTTCTTC
* * ** * *
42548752 GATCTGCTTCGCCACCAGTATAGGAAGGTAAGATCTGTTATCTTTGATCTAATTCACACCAGTAC
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTAC
*
42548817 ATGAAGACAAGATCTGTTTTCTTC
66 ATGAAGACAAGATCTGCTTTCTTC
* *
42548841 GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTAC
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTAC
42548906 ATGAAGACAAGATCT
66 ATGAAGACAAGATCT
42548921 ACTGTTACTC
Statistics
Matches: 320, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
88 3 0.01
89 315 0.98
90 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (89 bp):
GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTAC
ATGAAGACAAGATCTGCTTTCTTC
Found at i:42549065 original size:44 final size:44
Alignment explanation
Indices: 42549011--42549214 Score: 148
Period size: 44 Copynumber: 4.6 Consensus size: 44
42549001 GCCATCCTTG
*
42549011 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * * *
42549055 ATCTATTCCACTACTGCCTAGGGAGAT-AGA-AT-TATTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * **** **
42549098 ATGTACTCCACTGTAAC--CTCAGGGAGGTAAAATCCACCATCTTTG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTGTAATCTTCA
*
42549143 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * **
42549187 ATCTATTCCACTGCTGCCCAGGGAGATA
1 ATCTACTCCACTACTGCTTAGGGAGATA
42549215 GAATTACTGG
Statistics
Matches: 116, Mismatches: 34, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
41 3 0.03
42 3 0.03
43 18 0.16
44 74 0.64
45 15 0.13
46 2 0.02
47 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
Found at i:42549126 original size:132 final size:132
Alignment explanation
Indices: 42548941--42549270 Score: 588
Period size: 132 Copynumber: 2.5 Consensus size: 132
42548931 CACTGTTGCT
*
42548941 CAGGAAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
1 CAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
42549006 CCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
66 CCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
42549071 CC
131 CC
* *
42549073 TAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
1 CAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
* *
42549138 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG
66 CCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
42549203 CC
131 CC
* * *
42549205 CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGGGAGGTAAAATCCGCCAT
1 CAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
42549270 C
66 C
42549271 AACCTGCTCC
Statistics
Matches: 188, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 188 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (132 bp):
CAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
CCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
CC
Found at i:42549551 original size:44 final size:44
Alignment explanation
Indices: 42549484--42549687 Score: 137
Period size: 44 Copynumber: 4.6 Consensus size: 44
42549474 GCCATCCTTG
* * **
42549484 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTAATCTTCA
* * * *
42549528 ATCTATTCTACTGCTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTAAT--CTTCA
* * * * **** **
42549571 ATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACCATCTTTG
1 ATCTACTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAATCTTCA
* * **
42549616 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTAATCTTCA
*
42549660 ATCTATTCCACTGCTGCCCAGGGAGATA
1 ATCTACTCCACTGCTGCCCAGGGAGATA
42549688 GAATTACTGG
Statistics
Matches: 112, Mismatches: 40, Indels: 16
0.67 0.24 0.10
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 20 0.18
44 69 0.62
45 16 0.14
46 1 0.01
47 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTAATCTTCA
Found at i:42549599 original size:132 final size:132
Alignment explanation
Indices: 42549402--42549743 Score: 612
Period size: 132 Copynumber: 2.6 Consensus size: 132
42549392 CTACTGCTAC
* *
42549402 TCCACTGTTGCTCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
1 TCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
42549467 AAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
66 AAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
42549532 AT
131 AT
*
42549534 TCTACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
1 TCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
* *
42549599 AAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
66 AAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
42549664 AT
131 AT
* *
42549666 TCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGGGAGGT
1 TCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
*
42549731 AAAATCTGCCATC
66 AAAATCCGCCATC
42549744 AACCTGCTCC
Statistics
Matches: 200, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 200 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGT
AAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
AT
Found at i:42549715 original size:43 final size:44
Alignment explanation
Indices: 42549398--42549715 Score: 131
Period size: 44 Copynumber: 7.2 Consensus size: 44
42549388 AGATCTACTG
* *
42549398 CTACTCCACTGTTGCTCAGGGAGATAGAAT-TACTGGCTTCAAT
1 CTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAAT
* * * * ** * *
42549441 GTACTCCACTG-TAACCTCAGGGAGGTAAAATCCGCCAT-CCTT-GAT
1 CTACTCCACTGCT-GCC-CAGGGAGATAGAAT-CTAC-TGGCTTCAAT
* * ** *
42549486 CTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT--CTTCAAT
1 CTACTCCACTGCTGCCCAGGGAGATAGA-ATC--TACTGGCTTCAAT
* *
42549530 CTATTCTACTGCTGCCCAGGGAGATAGAAT-TACTGGCTTCAAT
1 CTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAAT
* * * * * *** **
42549573 GTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACCATCTTTGAT
1 CTACTCCACTGCT-GCC-CAGGGAGATAGAATCTACTGGCTTCAAT
* * ** *
42549618 CTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT--CTTCAAT
1 CTACTCCACTGCTGCCCAGGGAGATAGA-ATC--TACTGGCTTCAAT
*
42549662 CTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGGCTTCAAT
1 CTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAAT
*
42549705 GTACTCCACTG
1 CTACTCCACTG
42549716 TAAGCTTAGG
Statistics
Matches: 193, Mismatches: 59, Indels: 46
0.65 0.20 0.15
Matches are distributed among these distances:
41 6 0.03
42 2 0.01
43 50 0.26
44 98 0.51
45 29 0.15
46 7 0.04
47 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
CTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAAT
Found at i:42549721 original size:473 final size:473
Alignment explanation
Indices: 42548863--42549831 Score: 1778
Period size: 473 Copynumber: 2.0 Consensus size: 473
42548853 CACCAGTATG
* * *
42548863 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTGTTA
1 GGAAGGCAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTGCTA
*
42548928 CTCCACTGTTGCTCAGGAAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
66 CTCCACTGTTGCTCAGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
42548993 TAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
131 TAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
* *
42549058 TATTCCACTACTGCCTAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
196 TATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
42549123 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
261 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
42549188 TCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGG
326 TCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGG
*
42549253 GAGGTAAAATCCGCCATCAACCTGCTCCACTGA-AACCGAGGGAGGTAAGGCTGGTATCTTCGAT
391 GAGGTAAAATCCGCCATCAACCTGCTCCACT-ACAACCGAGGGAGGTAAGGCTAGTATCTTCGAT
* *
42549317 CTGCTTTGCTGTCAATACA
455 CTGCTTCGCTATCAATACA
*
42549336 GGAAGGCAAGATCTGCTCTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTGCTA
1 GGAAGGCAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTGCTA
*
42549401 CTCCACTGTTGCTCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
66 CTCCACTGTTGCTCAGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
42549466 TAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
131 TAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
* *
42549531 TATTCTACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
196 TATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
42549596 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
261 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
42549661 TCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGG
326 TCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGG
*
42549726 GAGGTAAAATCTGCCATCAACCTGCTCCACTACAACCGAGGGAGGTAAGGCTAGTATCTTCGATC
391 GAGGTAAAATCCGCCATCAACCTGCTCCACTACAACCGAGGGAGGTAAGGCTAGTATCTTCGATC
* *
42549791 TGCTTCGCTATTAATGCA
456 TGCTTCGCTATCAATACA
42549809 GGAAGGCAAGATCTGCTATCTTT
1 GGAAGGCAAGATCTGCTATCTTT
42549832 AACCTGCTCC
Statistics
Matches: 478, Mismatches: 17, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
472 1 0.00
473 477 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (473 bp):
GGAAGGCAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTGCTA
CTCCACTGTTGCTCAGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
TAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
TATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
TCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAGCTTAGG
GAGGTAAAATCCGCCATCAACCTGCTCCACTACAACCGAGGGAGGTAAGGCTAGTATCTTCGATC
TGCTTCGCTATCAATACA
Found at i:42551002 original size:14 final size:13
Alignment explanation
Indices: 42550983--42551023 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
42550973 TTAGCCTCTC
*
42550983 CATTTTTACCTTTT
1 CATTTTT-CATTTT
42550997 CATTTTTCATTTT
1 CATTTTTCATTTT
42551010 CATCTTTTCATTTT
1 CAT-TTTTCATTTT
42551024 TCACATCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:42551007 original size:21 final size:21
Alignment explanation
Indices: 42550983--42551026 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42550973 TTAGCCTCTC
*
42550983 CATTTTTACCTTTTCATTTTT
1 CATTTTCACCTTTTCATTTTT
*
42551004 CATTTTCATCTTTTCATTTTT
1 CATTTTCACCTTTTCATTTTT
42551025 CA
1 CA
42551027 CATCACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (21 bp):
CATTTTCACCTTTTCATTTTT
Found at i:42551009 original size:6 final size:7
Alignment explanation
Indices: 42550993--42551026 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
42550983 CATTTTTACC
42550993 TTTTCAT
1 TTTTCAT
42551000 TTTTCA-
1 TTTTCAT
42551006 TTTTCAT
1 TTTTCAT
42551013 CTTTTCAT
1 -TTTTCAT
42551021 TTTTCA
1 TTTTCA
42551027 CATCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTCAT
Found at i:42553830 original size:19 final size:20
Alignment explanation
Indices: 42553806--42553845 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42553796 AACTGTGTTT
* *
42553806 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
42553825 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
42553845 A
1 A
42553846 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:42553896 original size:13 final size:13
Alignment explanation
Indices: 42553878--42553903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42553868 TGTTTAATTT
42553878 TTTACTAGAAAAC
1 TTTACTAGAAAAC
42553891 TTTACTAGAAAAC
1 TTTACTAGAAAAC
42553904 AAATCTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:42555793 original size:28 final size:29
Alignment explanation
Indices: 42555762--42555827 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
42555752 AATTATTAAA
*
42555762 TATATATATAAAAAA-ATATGAAAATATG
1 TATATATATAAAAAATATATGAAAATAGG
* * * *
42555790 TATATACA-AAAAAATGTATGTATATAGG
1 TATATATATAAAAAATATATGAAAATAGG
42555818 TATATATATA
1 TATATATATA
42555828 TGTACGTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 6 0.20
28 23 0.77
29 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (29 bp):
TATATATATAAAAAATATATGAAAATAGG
Found at i:42556151 original size:23 final size:26
Alignment explanation
Indices: 42556108--42556160 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
42556098 TTATGAACAC
*
42556108 ATATATATTATATAAAGAAAT-ATGT
1 ATATATACTATATAAAGAAATCATGT
42556133 ATATATACTATAT-AA-AAATGCATGT
1 ATATATACTATATAAAGAAAT-CATGT
42556158 ATA
1 ATA
42556161 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 2 0.08
25 19 0.76
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (26 bp):
ATATATACTATATAAAGAAATCATGT
Found at i:42557085 original size:44 final size:44
Alignment explanation
Indices: 42556980--42557286 Score: 216
Period size: 44 Copynumber: 7.1 Consensus size: 44
42556970 ATTTTCTCAG
* * * *
42556980 TCTGCTCCACTGCAACCTCAGGGAGATAAGA-CT-TGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAA
** ** * *
42557021 TCCACTCTGCTGCAACTTCAGAGAGATAAGATCTATTACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAA
* * *
42557065 TCTGCTCCACTACAACTTCAGGGAGATAGGAT-TATCAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAA
* * * *
42557109 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGTCATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAA
* * * * * * * *
42557154 TCTGCCCCACTGCAGCTTCAGGGGGATAA-AAC--CTGCTGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAA
** * * * *
42557195 TCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAA
* * * *
42557239 TCCGCTCCACTACAACTTCAGGGAGATAGGAT-TATCGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAA
42557283 TCTG
1 TCTG
42557287 GTTCCTTACA
Statistics
Matches: 198, Mismatches: 58, Indels: 17
0.73 0.21 0.06
Matches are distributed among these distances:
41 50 0.25
42 4 0.02
43 8 0.04
44 103 0.52
45 33 0.17
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAA
Found at i:42557413 original size:128 final size:128
Alignment explanation
Indices: 42557281--42557872 Score: 941
Period size: 128 Copynumber: 4.6 Consensus size: 128
42557271 TATCGACTTC
* * *
42557281 AATCTGGTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTGCTCCGCAACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
* * *
42557346 AGACAAGATCTGCAATTTCCAGCCTATTCCACTGCTGGTCAGGGACATAGGACTTGCGGCTTA
66 AGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTTA
* * * *
42557409 AATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTA
1 AATCTGCTTCCTTAC-ACT--TGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTA
* * * *
42557474 GGGAGATAAGATCTGTAATTTCCAACCTATTCCACTACTGGTTAGGGACATATGACTTGTGGCTT
63 GGGAGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTT
42557539 A
128 A
* * *
42557540 GATCTGCTTCCTTACACTTGAAGATAACATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGAG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
42557605 AGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTTA
66 AGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTTA
* * * *
42557668 AATCTGCTTCCTTACATTTGAAGATAAGATTCACCGTCTTCGATCTGCTTCACTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
* * *
42557733 AGACAAGATATGCAAATTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTA
66 AGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTTA
42557796 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
42557861 AGACAAGATCTG
66 AGACAAGATCTG
42557873 GAATATTCAC
Statistics
Matches: 422, Mismatches: 39, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
128 306 0.73
129 2 0.00
130 2 0.00
131 112 0.27
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (128 bp):
AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
AGACAAGATCTGCAATTTCCAACCTATTCCACTACTGGTCAGGGACATAGGACTTGTGGCTTA
Found at i:42558823 original size:15 final size:15
Alignment explanation
Indices: 42558803--42558835 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
42558793 AAATAATATG
42558803 AGAATCGGGTGCCCC
1 AGAATCGGGTGCCCC
42558818 AGAATCGGGTGCCCC
1 AGAATCGGGTGCCCC
42558833 AGA
1 AGA
42558836 TATCAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.30, G:0.33, T:0.12
Consensus pattern (15 bp):
AGAATCGGGTGCCCC
Found at i:42559098 original size:7 final size:7
Alignment explanation
Indices: 42559086--42559119 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
42559076 CCGTCATTAC
42559086 TTTTCAT
1 TTTTCAT
42559093 TTTTCA-
1 TTTTCAT
*
42559099 ATTTCAT
1 TTTTCAT
42559106 TTTTCAT
1 TTTTCAT
42559113 TTTTCAT
1 TTTTCAT
42559120 CCCTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTCAT
Found at i:42559105 original size:13 final size:13
Alignment explanation
Indices: 42559087--42559111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42559077 CGTCATTACT
42559087 TTTCATTTTTCAA
1 TTTCATTTTTCAA
42559100 TTTCATTTTTCA
1 TTTCATTTTTCA
42559112 TTTTTCATCC
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:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCATTTTTCAA
Found at i:42574997 original size:12 final size:12
Alignment explanation
Indices: 42574982--42575012 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42574972 TTTTAGTTAG
42574982 TTTCTTTTAGGT
1 TTTCTTTTAGGT
*
42574994 TTTCTTTTAGTT
1 TTTCTTTTAGGT
42575006 TTTCTTT
1 TTTCTTT
42575013 GCACTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTCTTTTAGGT
Found at i:42576977 original size:29 final size:30
Alignment explanation
Indices: 42576937--42577014 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
42576927 ATTTTACGAT
42576937 ACTTTT-GAAAATTTTAATTAA-CCCTCAA
1 ACTTTTAGAAAATTTTAATTAAGCCCTCAA
* *
42576965 ACTTTTAGAAAATTTTTATTAAGCCTTCAA
1 ACTTTTAGAAAATTTTAATTAAGCCCTCAA
* *
42576995 ATTTTTA-AAGATTTTAATTA
1 ACTTTTAGAAAATTTTAATTA
42577015 TGCTCTTCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.14
29 25 0.58
30 12 0.28
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
ACTTTTAGAAAATTTTAATTAAGCCCTCAA
Found at i:42579105 original size:75 final size:77
Alignment explanation
Indices: 42578975--42579148 Score: 216
Period size: 75 Copynumber: 2.3 Consensus size: 77
42578965 GGGATCTAAG
*
42578975 GATAATTGTTCAATACCTAATATAATCGACCACTTTCTCTGAGTCTTCTGTCATTATACCAT-AG
1 GATAATAGTTCAATACCTAATATAATCGACCACTTTCTCTGAGTCTTCTGTCATTATACCATAAG
42579039 A-TAGGTG-ACA
66 ACTAGGTGAACA
* * * * *
42579049 GATATTAGTTCAATA-CTAATATAATCGA-TATTTTTTCATCTGAAGT-TTTTGTCATTATACCG
1 GATAATAGTTCAATACCTAATATAATCGACCA--CTTTC-TCTG-AGTCTTCTGTCATTATACCA
42579111 TAAGACTAGGTGAACA
62 TAAGACTAGGTGAACA
42579127 GATAATAGTTCAATACCTAATA
1 GATAATAGTTCAATACCTAATA
42579149 AATGTAAACC
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
72 1 0.01
73 13 0.15
74 17 0.20
75 19 0.22
76 6 0.07
77 6 0.07
78 17 0.20
79 6 0.07
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (77 bp):
GATAATAGTTCAATACCTAATATAATCGACCACTTTCTCTGAGTCTTCTGTCATTATACCATAAG
ACTAGGTGAACA
Found at i:42589665 original size:17 final size:17
Alignment explanation
Indices: 42589640--42589673 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42589630 TTTCATCTAG
* *
42589640 ATTTTTTCTTTTTTCTT
1 ATTTCTTCTTTCTTCTT
42589657 ATTTCTTCTTTCTTCTT
1 ATTTCTTCTTTCTTCTT
42589674 TCTCTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTCTTCTTTCTTCTT
Found at i:42594563 original size:17 final size:17
Alignment explanation
Indices: 42594543--42594575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42594533 TTTCAAAACG
42594543 AAAAGAAAAAGAAAAAT
1 AAAAGAAAAAGAAAAAT
*
42594560 AAAAGAAAAATAAAAA
1 AAAAGAAAAAGAAAAA
42594576 ATAGAGAGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAT
Found at i:42604544 original size:12 final size:12
Alignment explanation
Indices: 42604529--42604559 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42604519 TTTTAGTTAG
42604529 TTTCTTTTAGGT
1 TTTCTTTTAGGT
*
42604541 TTTCTTTTAGTT
1 TTTCTTTTAGGT
42604553 TTTCTTT
1 TTTCTTT
42604560 GCACTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTCTTTTAGGT
Found at i:42606597 original size:32 final size:32
Alignment explanation
Indices: 42606507--42606632 Score: 104
Period size: 32 Copynumber: 4.1 Consensus size: 32
42606497 TTTACGATAC
* *
42606507 TTTT-GAAAATTTTAATTAA-CCCT-C-AAAC
1 TTTTAGAAAATTTTAATTAAGCCTTCCAAAAT
* *
42606535 TTTTAGAAAATTTTTATTAAGCCTTTCAAAAT
1 TTTTAGAAAATTTTAATTAAGCCTTCCAAAAT
* *
42606567 TTTTA-AAGATTTTAATTATGCTCTTCCAAAAT
1 TTTTAGAAAATTTTAATTAAGC-CTTCCAAAAT
* * *
42606599 TTTT-GTAAATTTTTATTAAGTC-TCCAAATAT
1 TTTTAGAAAATTTTAATTAAGCCTTCCAAA-AT
42606630 TTT
1 TTT
42606633 AAAAGTTTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.05
29 14 0.18
30 9 0.11
31 20 0.25
32 32 0.41
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.48
Consensus pattern (32 bp):
TTTTAGAAAATTTTAATTAAGCCTTCCAAAAT
Found at i:42607062 original size:13 final size:13
Alignment explanation
Indices: 42607008--42607060 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
42606998 CTAGTTTGAT
42607008 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
42607021 AATGCTGTGGAAA
1 AATGCTTTTGAAA
** *
42607034 AATATTTTTGAGA
1 AATGCTTTTGAAA
*
42607047 AGTGCTTTTGAAA
1 AATGCTTTTGAAA
42607060 A
1 A
42607061 GTTTGGTATA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.36
Consensus pattern (13 bp):
AATGCTTTTGAAA
Found at i:42608933 original size:82 final size:78
Alignment explanation
Indices: 42608776--42608963 Score: 304
Period size: 82 Copynumber: 2.4 Consensus size: 78
42608766 GGATCTAAGC
42608776 GATAATTAGTTCAATACCTAATATTAATCGACACTTTCTCTGAAGTCTTCTGTCATTATACCATA
1 GATAATTAGTTCAATACCTAATATTAATCGACACTTTCTCTGAAGTCTTCTGTCATTATACCATA
42608841 GACTAGGTTGACA
66 GACTAGGTTGACA
* * *
42608854 GATAATTAGTTCAATACCTAATATTAATCGATATTTTCTTCATCTGAAGTCTTTTGTCATTATAC
1 GATAATTAGTTCAATACCTAATATTAATCGACA--CT-TTC-TCTGAAGTCTTCTGTCATTATAC
*
42608919 CGTAGACTAGGTTGACA
62 CATAGACTAGGTTGACA
42608936 GATAATTAGTTCAATACCTAATATTAAT
1 GATAATTAGTTCAATACCTAATATTAAT
42608964 GTAACATCCT
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
78 32 0.31
80 1 0.01
81 3 0.03
82 66 0.65
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (78 bp):
GATAATTAGTTCAATACCTAATATTAATCGACACTTTCTCTGAAGTCTTCTGTCATTATACCATA
GACTAGGTTGACA
Found at i:42609866 original size:18 final size:18
Alignment explanation
Indices: 42609845--42609884 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
42609835 GAAGAGATAA
42609845 GAAATATTGTAGAGAAAG
1 GAAATATTGTAGAGAAAG
42609863 GAAATATTGTAGAGAAAG
1 GAAATATTGTAGAGAAAG
42609881 GAAA
1 GAAA
42609885 GGAGAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.20
Consensus pattern (18 bp):
GAAATATTGTAGAGAAAG
Found at i:42615797 original size:21 final size:20
Alignment explanation
Indices: 42615768--42615816 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
42615758 GATAATGTGG
*
42615768 ATTTAGATTTTGTGAATATTTA
1 ATTT-GATTTTATGAAT-TTTA
*
42615790 ATTTGATTTTATGAATTTTG
1 ATTTGATTTTATGAATTTTA
42615810 ATTTGAT
1 ATTTGAT
42615817 AAATATGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 11 0.44
22 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (20 bp):
ATTTGATTTTATGAATTTTA
Found at i:42617298 original size:19 final size:19
Alignment explanation
Indices: 42617274--42617311 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42617264 TATGCGCCAA
42617274 GATGCACTTCGTGTGCTAG
1 GATGCACTTCGTGTGCTAG
*
42617293 GATGCACTTCGTGTTCTAG
1 GATGCACTTCGTGTGCTAG
42617312 TATACGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
GATGCACTTCGTGTGCTAG
Found at i:42617676 original size:8 final size:8
Alignment explanation
Indices: 42617657--42617688 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
42617647 TAATGGTAAG
42617657 TGTAATTAA
1 TGTAA-TAA
42617666 TGTAATAA
1 TGTAATAA
42617674 TGTAATAA
1 TGTAATAA
42617682 TGTAATA
1 TGTAATA
42617689 TTATTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (8 bp):
TGTAATAA
Found at i:42624266 original size:10 final size:11
Alignment explanation
Indices: 42624251--42624279 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
42624241 TCCAAAGATG
42624251 TGAATTGAAT-
1 TGAATTGAATA
42624261 TGAATTGAATA
1 TGAATTGAATA
42624272 TGAATTGA
1 TGAATTGA
42624280 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:42624620 original size:24 final size:24
Alignment explanation
Indices: 42624593--42624657 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 24
42624583 CACAGCTCGA
*
42624593 ATGAGCGTCCCGTTATTAGCTCTC
1 ATGAGCATCCCGTTATTAGCTCTC
** * *
42624617 ATGAGCATCCCAATATTTGGCTTTC
1 ATGAGCATCCCGTTA-TTAGCTCTC
*
42624642 ATGAGCTTCCCGTTAT
1 ATGAGCATCCCGTTAT
42624658 ACGGTTCTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (24 bp):
ATGAGCATCCCGTTATTAGCTCTC
Found at i:42624812 original size:27 final size:25
Alignment explanation
Indices: 42624765--42624837 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
42624755 CCCGATATAT
42624765 GGCTCTTTGGAGCTTCCTGATTAAA
1 GGCTCTTTGGAGCTTCCTGATTAAA
* **
42624790 GGCTCTTTCGTGAGCTTCTTGATTAGT
1 GGCTCTTT-G-GAGCTTCCTGATTAAA
***
42624817 GGCTCTCCAGAGCTTCCTGAT
1 GGCTCTTTGGAGCTTCCTGAT
42624838 ATTGGCTCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 19 0.49
26 1 0.03
27 19 0.49
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCTGATTAAA
Found at i:42624945 original size:25 final size:25
Alignment explanation
Indices: 42624898--42624945 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42624888 ACAACTTGAA
* *
42624898 TGAGCTTCCCTTTACATGGCTCACT
1 TGAGCTTCCCGTTACATGACTCACT
* *
42624923 TGAGCTTCTCGTTATATGACTCA
1 TGAGCTTCCCGTTACATGACTCA
42624946 AGAGAGAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.38
Consensus pattern (25 bp):
TGAGCTTCCCGTTACATGACTCACT
Found at i:42626380 original size:16 final size:16
Alignment explanation
Indices: 42626359--42626397 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42626349 TTATGATTGT
* *
42626359 ATATGATTGATTACTG
1 ATATGAATGATTAATG
*
42626375 ATATGAATGTTTAATG
1 ATATGAATGATTAATG
42626391 ATATGAA
1 ATATGAA
42626398 AATGTCTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (16 bp):
ATATGAATGATTAATG
Found at i:42627217 original size:47 final size:46
Alignment explanation
Indices: 42627135--42627224 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 46
42627125 TTCAGCCCAA
42627135 CTATTTAGTTTGTAGGCCCATTTTATGTTTCATTTTGATTTTGGGG
1 CTATTTAGTTTGTAGGCCCATTTTATGTTTCATTTTGATTTTGGGG
* *
42627181 CTATTTAGTTTGTGGGCCTACA-TTTATGTTTTATTTTGATTTTG
1 CTATTTAGTTTGTAGGCC--CATTTTATGTTTCATTTTGATTTTG
42627225 AGCAAATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 17 0.43
47 21 0.52
48 2 0.05
ACGTcount: A:0.16, C:0.10, G:0.20, T:0.54
Consensus pattern (46 bp):
CTATTTAGTTTGTAGGCCCATTTTATGTTTCATTTTGATTTTGGGG
Found at i:42631006 original size:18 final size:18
Alignment explanation
Indices: 42630983--42631020 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
42630973 TCATTTTTAT
42630983 TTTCTCTTTTCCTATTTC
1 TTTCTCTTTTCCTATTTC
*
42631001 TTTCTCTTTTGCTATTTC
1 TTTCTCTTTTCCTATTTC
42631019 TT
1 TT
42631021 CTGTTCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTCTCTTTTCCTATTTC
Found at i:42631030 original size:17 final size:18
Alignment explanation
Indices: 42630983--42631030 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
42630973 TCATTTTTAT
* *
42630983 TTTCTCTTTTCCTATTTC
1 TTTCTCTTCTGCTATTTC
*
42631001 TTTCTCTTTTGCTATTTC
1 TTTCTCTTCTGCTATTTC
*
42631019 -TTCTGTTCTGCT
1 TTTCTCTTCTGCT
42631031 TTCTGTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.04, C:0.25, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTCTCTTCTGCTATTTC
Found at i:42632045 original size:138 final size:135
Alignment explanation
Indices: 42631753--42632560 Score: 646
Period size: 138 Copynumber: 6.0 Consensus size: 135
42631743 TTCATCTTAT
* * * * * *
42631753 TCCACTACAAATTCAAGGAGATAAGACTTGTAGCTTTAATCTGTTCCACTACAACTTCAGTGAGA
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
* * * * * * *
42631818 TAAG---ACTTGTAGCTTAAATCTGCTTCACTACAACTTTAGGGAGATAATATTTGTAGCTTCGA
66 TAAGATTACTTGTAGATTCAATCAGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAA
42631880 TCTGC
131 TCTGC
* * * *
42631885 TCCACTACAACTTCAGTGAGATAAGACTTGTAGCTTAAATCTGTTCCACTGCAACTTCTGGGAGA
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
* * * *
42631950 TAAGATTCACTATGGTAGATTCAATCAGAC-CCACTACAACTTTAAGGATAT-GGTATTTGTAGC
66 TAAGATT-ACT-T-GTAGATTCAATCAG-CTCCACTACAACTTCAGGGAGATAAG-ATTTGTAGC
42632013 TTCAATCTGC
126 TTCAATCTGC
* * * * *
42632023 TACATTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGTAACTTCAAGGAGA
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
* * * * * *
42632088 TAAGATTCGCTATGGTAGACTCAATCCAAC-CTACTACAACTTCATGGG-TATAGGATTTGTAGC
66 TAAGATT-ACT-T-GTAGATTCAAT-CAGCTCCACTACAACTTCA-GGGAGATAAGATTTGTAGC
42632151 TTCAATCTGC
126 TTCAATCTGC
* * * * * ** *
42632161 TCCACTGCAAATTTAGAGAGATAAGATTTGTAGATTCAATCTACTCTACTGCAACTTCAGGGAGA
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
* * *
42632226 TGAGATT-C--GTAGCTTCAAT-ATGCTCCACTACAACTTCAGGGAGATAAGATTCGTAGCTTCA
66 TAAGATTACTTGTAGATTCAATCA-GCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCA
*
42632287 ATCTAC
130 ATCTGC
* * * ** *
42632293 TCTACTACAACTTCAGGGAGATAAGATTTGTAACTTTAATCTACTCCACTACAACTTCAGGGAGA
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
* * * * * *
42632358 TAAGA-T--TTGTAGCTTTAATCAGCTCCACTGCAAATTCAGGAAGATAAGATTCACTAGTAGAT
66 TAAGATTACTTGTAGATTCAATCAGCTCCACTACAACTTCAGGGAGATAAGATT---T-GTAGCT
42632420 TCAATCTG-
127 TCAATCTGC
** * * * * * * * *
42632428 TCCCACTGTAACTTTAGGG-GTGTAGGATCTGTAGCTTAAATCTGCTCCACTGCAACTTTAGAGA
1 T-CCACTACAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGA
* * *
42632492 GATAAGATTCGCTATGGT-GATTTCAATCTGAC-CCACTACAACTTCAGGG-GTATAGGATTTGT
64 GATAAGATT-ACT-T-GTAGA-TTCAATCAG-CTCCACTACAACTTCAGGGAG-ATAAGATTTGT
*
42632554 AGTTTCA
123 AGCTTCA
42632561 CTAATCTGTT
Statistics
Matches: 554, Mismatches: 90, Indels: 58
0.79 0.13 0.08
Matches are distributed among these distances:
130 1 0.00
131 5 0.01
132 201 0.36
133 1 0.00
135 2 0.00
136 70 0.13
137 2 0.00
138 229 0.41
139 8 0.01
140 1 0.00
141 3 0.01
142 30 0.05
143 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (135 bp):
TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGA
TAAGATTACTTGTAGATTCAATCAGCTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAA
TCTGC
Found at i:42632407 original size:44 final size:44
Alignment explanation
Indices: 42631753--42632408 Score: 538
Period size: 44 Copynumber: 14.6 Consensus size: 44
42631743 TTCATCTTAT
* * * * * *
42631753 TCCACTACAAATTCAAGGAGATAAGACTTGTAGCTTTAATCTGT
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
* * * *
42631797 TCCACTACAACTTCAGTGAGATAAGACTTGTAGCTTAAATCTGC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
* * * * *
42631841 TTCACTACAACTTTAGGGAGATAATATTTGTAGCTTCGATCTGC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
* * * * *
42631885 TCCACTACAACTTCAGTGAGATAAGACTTGTAGCTTAAATCTGT
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
* * *
42631929 TCCACTGCAACTTCTGGGAGATAAGATTCACTATGGTAGATTCAATCAGAC
1 TCCACTACAACTTCAGGGAGATAAGA-T---T-T-GTAGCTTCAATCAG-C
* * * * *
42631980 -CCACTACAACTTTAAGGATAT-GGTATTTGTAGCTTCAATCTGC
1 TCCACTACAACTTCAGGGAGATAAG-ATTTGTAGCTTCAATCAGC
* * * * *
42632023 TACATTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGT
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
** * *
42632067 TCCACTGTAACTTCAAGGAGATAAGATTCGCTATGGTAGAC-TCAATCCAAC
1 TCCACTACAACTTCAGGGAGATAAGA-T---T-T-GTAG-CTTCAAT-CAGC
* * * *
42632118 -CTACTACAACTTCATGGG-TATAGGATTTGTAGCTTCAATCTGC
1 TCCACTACAACTTCA-GGGAGATAAGATTTGTAGCTTCAATCAGC
* * * * *
42632161 TCCACTGCAAATTTAGAGAGATAAGATTTGTAGATTCAATCTA-C
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-AGC
* * * *
42632205 TCTACTGCAACTTCAGGGAGATGAGATTCGTAGCTTCAAT-ATGC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCA-GC
*
42632249 TCCACTACAACTTCAGGGAGATAAGATTCGTAGCTTCAATCTA-C
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-AGC
* * *
42632293 TCTACTACAACTTCAGGGAGATAAGATTTGTAACTTTAATCTA-C
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-AGC
*
42632337 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTTAATCAGC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
* * *
42632381 TCCACTGCAAATTCAGGAAGATAAGATT
1 TCCACTACAACTTCAGGGAGATAAGATT
42632409 CACTAGTAGA
Statistics
Matches: 497, Mismatches: 87, Indels: 56
0.78 0.14 0.09
Matches are distributed among these distances:
42 1 0.00
43 7 0.01
44 418 0.84
45 4 0.01
46 3 0.01
48 2 0.00
49 5 0.01
50 53 0.11
51 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (44 bp):
TCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTCAATCAGC
Found at i:42632461 original size:92 final size:93
Alignment explanation
Indices: 42632330--42632555 Score: 255
Period size: 92 Copynumber: 2.4 Consensus size: 93
42632320 TTGTAACTTT
* * *
42632330 AATCT-ACTCCACTACAACTTCAGGGAG-ATAAGATTTGTAGCTTTAATCAGCTCCACTGCAAAT
1 AATCTGAC-CCACTACAACTTCAGGG-GTATAGGATCTGTAGCTTAAATCAGCTCCACTGCAAAT
42632393 TCAG-GAAGATAAGATTCACTA-GTAGA-TTC
64 TCAGAG-AGATAAGATTCACTAGGT-GATTTC
* ** * * * * *
42632422 AATCTGTCCCACTGTAACTTTAGGGGTGTAGGATCTGTAGCTTAAATCTGCTCCACTGCAACTTT
1 AATCTGACCCACTACAACTTCAGGGGTATAGGATCTGTAGCTTAAATCAGCTCCACTGCAAATTC
*
42632487 AGAGAGATAAGATTCGCTATGGTGATTTC
66 AGAGAGATAAGATTCACTA-GGTGATTTC
*
42632516 AATCTGACCCACTACAACTTCAGGGGTATAGGATTTGTAG
1 AATCTGACCCACTACAACTTCAGGGGTATAGGATCTGTAG
42632556 TTTCACTAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
91 1 0.01
92 66 0.60
93 4 0.04
94 39 0.35
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (93 bp):
AATCTGACCCACTACAACTTCAGGGGTATAGGATCTGTAGCTTAAATCAGCTCCACTGCAAATTC
AGAGAGATAAGATTCACTAGGTGATTTC
Found at i:42640988 original size:19 final size:20
Alignment explanation
Indices: 42640966--42641006 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
42640956 TATTTGTATT
42640966 TTTATTATTAAAAT-TAAAA
1 TTTATTATTAAAATATAAAA
42640985 TTTATTATTAAAATATAAAA
1 TTTATTATTAAAATATAAAA
42641005 TT
1 TT
42641007 GAAATGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATTATTAAAATATAAAA
Found at i:42641188 original size:33 final size:32
Alignment explanation
Indices: 42641112--42641271 Score: 108
Period size: 33 Copynumber: 4.8 Consensus size: 32
42641102 CATTGTTTAT
* *
42641112 ATGTAAGACCATAGTTGGGCTT-TGGCATTTTA
1 ATGTAAGACCATAGCTGGG-TTATGGCATTTGA
* *
42641144 ATGAAAGACCATAACTGGGTTATGGCACTTTGA
1 ATGTAAGACCATAGCTGGGTTATGGCA-TTTGA
* * * * * *
42641177 ATGTAAGACCATGGTTGGATCATGACAGTATTTA
1 ATGTAAGACCATAGCTGGGTTATGGCA-T-TTGA
* * * *
42641211 TAAGTAAAACCATAGCTGGGCTATGACATTGTG-
1 -ATGTAAGACCATAGCTGGGTTATGGCATT-TGA
*
42641244 ATGATAAGACCATAACTGGGTTATGGCA
1 ATG-TAAGACCATAGCTGGGTTATGGCA
42641272 CTACAAATGT
Statistics
Matches: 96, Mismatches: 26, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
31 2 0.02
32 23 0.24
33 46 0.48
34 5 0.05
35 20 0.21
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGTTATGGCATTTGA
Found at i:42641291 original size:101 final size:100
Alignment explanation
Indices: 42641080--42641291 Score: 280
Period size: 100 Copynumber: 2.1 Consensus size: 100
42641070 AATTGACGGA
* * * * * * * * *
42641080 TAAGACCATGGTTGGACCATGGCATTGTTTATATGTAAGACCATAGTTGGGCTTTGGCATTTTAA
1 TAAGACCATGGTTGGACCATGACAGTATTTATAAGTAAAACCATAGCTGGGCTATGACATTGTAA
***
42641145 TGAAAGACCATAACTGGGTTATGGCACTTTGAATG
66 TGAAAGACCATAACTGGGTTATGGCACTACAAATG
* *
42641180 TAAGACCATGGTTGGATCATGACAGTATTTATAAGTAAAACCATAGCTGGGCTATGACATTGTGA
1 TAAGACCATGGTTGGACCATGACAGTATTTATAAGTAAAACCATAGCTGGGCTATGACATTGTAA
42641245 TGATAAGACCATAACTGGGTTATGGCACTACAAATG
66 TGA-AAGACCATAACTGGGTTATGGCACTACAAATG
*
42641281 TAAGATCATGG
1 TAAGACCATGG
42641292 CTGGGTCGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 57 0.59
101 39 0.41
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGACAGTATTTATAAGTAAAACCATAGCTGGGCTATGACATTGTAA
TGAAAGACCATAACTGGGTTATGGCACTACAAATG
Found at i:42645501 original size:19 final size:20
Alignment explanation
Indices: 42645477--42645523 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
42645467 GGTTTTTTTT
*
42645477 ATGAAATTTAATGCAT-ATG-
1 ATGAAATGTAATGC-TGATGA
42645496 ATGAAATGTAATGCTGATGA
1 ATGAAATGTAATGCTGATGA
42645516 ATGAAATG
1 ATGAAATG
42645524 AAAGCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGAAATGTAATGCTGATGA
Found at i:42650569 original size:18 final size:18
Alignment explanation
Indices: 42650524--42650561 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
42650514 TCGTTTTTAT
*
42650524 TTTCTCTTTTGTTATTTC
1 TTTCTCTTTTGCTATTTC
42650542 TTTCTCTTTTGCTATTTC
1 TTTCTCTTTTGCTATTTC
42650560 TT
1 TT
42650562 CTGTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTCTCTTTTGCTATTTC
Found at i:42651508 original size:20 final size:20
Alignment explanation
Indices: 42651480--42651517 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42651470 TAGTGAGCAA
42651480 AAACAAATACAATAATAATC
1 AAACAAATACAATAATAATC
* *
42651500 AAACCAATATAATAATAA
1 AAACAAATACAATAATAA
42651518 AATACAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACAAATACAATAATAATC
Found at i:42652572 original size:21 final size:21
Alignment explanation
Indices: 42652546--42652586 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42652536 TGTGTTACCT
42652546 CAATTGTATTGTATGGAAAAA
1 CAATTGTATTGTATGGAAAAA
*
42652567 CAATTGTGTTGTATGGAAAA
1 CAATTGTATTGTATGGAAAA
42652587 TTTCATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (21 bp):
CAATTGTATTGTATGGAAAAA
Found at i:42656078 original size:5 final size:5
Alignment explanation
Indices: 42656068--42656099 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
42656058 TTAAATTTGA
42656068 TATTT TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TATTT TA
42656100 ACTTTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:42656219 original size:8 final size:8
Alignment explanation
Indices: 42656206--42656237 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
42656196 TTTATTTCAC
42656206 TTTTTTAT
1 TTTTTTAT
42656214 TTTTTTAT
1 TTTTTTAT
*
42656222 TTTTTAAT
1 TTTTTTAT
42656230 TTTTTTAT
1 TTTTTTAT
42656238 ATATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:42657722 original size:25 final size:24
Alignment explanation
Indices: 42657694--42657749 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
42657684 CTTATGACAA
**
42657694 TCCCGTTATATGGCTCTCACGAGCT
1 TCCCGTTA-ATGAATCTCACGAGCT
**
42657719 TCCCGATTAATGAATCTCTTGAGCT
1 TCCCG-TTAATGAATCTCACGAGCT
42657744 TCCCGT
1 TCCCGT
42657750 GTATGACTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.85
26 3 0.12
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (24 bp):
TCCCGTTAATGAATCTCACGAGCT
Found at i:42657844 original size:25 final size:25
Alignment explanation
Indices: 42657763--42657847 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
42657753 TGACTCTTAT
* *
42657763 GAGCTTCTAGATTAATGGCTTTTTG
1 GAGCTTCTAGATTAATGGCTCTTCG
* * * * *
42657788 GAGCATCCCA-ATAAAAAGGCTCTCTCAT
1 GAGC-TTCTAGAT-TAATGGCTCT-TC-G
42657816 GAGCTTCTAGATTAATGGCTCTTCG
1 GAGCTTCTAGATTAATGGCTCTTCG
42657841 GAGCTTC
1 GAGCTTC
42657848 CTCATATTGG
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 13 0.30
26 12 0.28
27 12 0.28
28 6 0.14
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (25 bp):
GAGCTTCTAGATTAATGGCTCTTCG
Found at i:42663852 original size:22 final size:21
Alignment explanation
Indices: 42663812--42663858 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
42663802 GGAAAAATAA
42663812 TAAAATAAAACCAAATGAAAT
1 TAAAATAAAACCAAATGAAAT
42663833 TAAAACTAAAA-CAAATTGAAAT
1 TAAAA-TAAAACCAAA-TGAAAT
42663855 TAAA
1 TAAA
42663859 GGTTTCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (21 bp):
TAAAATAAAACCAAATGAAAT
Found at i:42664768 original size:25 final size:25
Alignment explanation
Indices: 42664692--42664825 Score: 75
Period size: 25 Copynumber: 5.3 Consensus size: 25
42664682 GGCTCTCACA
* *
42664692 AGCTTCCTGATTAATGACTC-TCTTG
1 AGCTTCC-GATTAATGGCTCTTCTGG
* *
42664717 AGCTTCCCG-TGT-ATGGCTCGTAT-G
1 AGCTT-CCGAT-TAATGGCTCTTCTGG
42664741 AGCTTCCAGATTAATGGCT-TTCTGG
1 AGCTTCC-GATTAATGGCTCTTCTGG
* *
42664766 AGCATTCCGATAAAAAGGCTCTCTCAT-G
1 AGC-TTCCGAT-TAATGGCTCT-TC-TGG
*
42664794 AGCTTCCCGATTAATAGCTCTT-TGG
1 AGCTT-CCGATTAATGGCTCTTCTGG
42664819 AGCTTCC
1 AGCTTCC
42664826 CAATATTGGC
Statistics
Matches: 86, Mismatches: 9, Indels: 29
0.69 0.07 0.23
Matches are distributed among these distances:
23 2 0.02
24 20 0.23
25 29 0.34
26 13 0.15
27 10 0.12
28 11 0.13
29 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTTCCGATTAATGGCTCTTCTGG
Found at i:42664867 original size:24 final size:24
Alignment explanation
Indices: 42664786--42664875 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 24
42664776 TAAAAAGGCT
* * *
42664786 CTCTCATGAGCTTCCCGATTAATAG
1 CTCTTATGAGCTTCCCGATT-TTGG
* *
42664811 CTCTT-TGGAGCTTCCCAATATTGG
1 CTCTTAT-GAGCTTCCCGATTTTGG
** *
42664835 CTCCAATGAGCTTCTCGATTTTGG
1 CTCTTATGAGCTTCCCGATTTTGG
*
42664859 CTCTTATGATCTTCCCG
1 CTCTTATGAGCTTCCCG
42664876 TTATAGCTCG
Statistics
Matches: 49, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
24 33 0.67
25 16 0.33
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (24 bp):
CTCTTATGAGCTTCCCGATTTTGG
Found at i:42667812 original size:21 final size:21
Alignment explanation
Indices: 42667775--42667820 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
42667765 ATATAAAAAT
*
42667775 TAAATTAAAAACAAAAAT-AC
1 TAAAATAAAAACAAAAATAAC
*
42667795 TAAAATAAAAATAGAAAATAAC
1 TAAAATAAAAACA-AAAATAAC
42667817 TAAA
1 TAAA
42667821 TTAATAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAAATAAAAACAAAAATAAC
Found at i:42671229 original size:25 final size:24
Alignment explanation
Indices: 42671151--42671245 Score: 70
Period size: 25 Copynumber: 3.9 Consensus size: 24
42671141 TAACTTGCAT
* *
42671151 GAGCTTCCTGAT-TATGGCTCTCAT
1 GAGCTTCCTGTTATATGGCTC-CAA
**
42671175 GAGCTTCCTGTTATACAG-TCCAGA
1 GAGCTTCCTGTTATATGGCTCCA-A
*
42671199 TAAGCTTCCTGTTATATGGCTCACAA
1 -GAGCTTCCTGTTATATGGCTC-CAA
*
42671225 GAGCTTCTTGTTACT-TGGCTC
1 GAGCTTCCTGTTA-TATGGCTC
42671246 GAGAGAGGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.04
24 13 0.23
25 35 0.62
26 4 0.07
27 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (24 bp):
GAGCTTCCTGTTATATGGCTCCAA
Found at i:42672289 original size:11 final size:11
Alignment explanation
Indices: 42672273--42672298 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42672263 ACATGGGCGT
42672273 GTGTCTTGGCC
1 GTGTCTTGGCC
42672284 GTGTCTTGGCC
1 GTGTCTTGGCC
42672295 GTGT
1 GTGT
42672299 GTGACACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.38, T:0.38
Consensus pattern (11 bp):
GTGTCTTGGCC
Found at i:42675596 original size:27 final size:27
Alignment explanation
Indices: 42675539--42676286 Score: 530
Period size: 27 Copynumber: 27.9 Consensus size: 27
42675529 ATATCTGCAT
* * *
42675539 CGAAATATCCTCATAGGGT-AAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
*
42675565 CGAAATACCCCCATAGGATAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
42675592 CGAAATACCCTC--AGGGTAGAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * * *
42675617 TGAAATACCCCTATAGGGTAGAATGGC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
42675644 CGAAATACCCCCATAGGGTAGAATGGC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
42675671 CAAAATACCCCCATAGGGTAGAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
** * ** *
42675698 TAAAATACCCCTATAGAATAATATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
42675725 CGAAATAACCCTATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * * *
42675752 TGAAATACCCCCATAGGATAAAATAAG
1 CGAAATACCCCCATAGGGTAAAATGAC
* * *
42675779 TGAAATACCCTCATGGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * *
42675806 TGGAATACCCCCATAGGGTAAAATAAC
1 CGAAATACCCCCATAGGGTAAAATGAC
**
42675833 TAAAATACCCCCATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * * *
42675860 TG-AATTCCCACACAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* ** * *
42675886 CGAATTACCCCCACCGAGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
* * * *
42675913 CGAATTCCCCCCACAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
*** *
42675940 CGAAATACTCGTGA-AAGGTAAAATGAC
1 CGAAATAC-CCCCATAGGGTAAAATGAC
* *
42675967 TGAAATACCCTCATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
** *** * *
42675994 TAAAATATTGCCAAAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
42676021 CGAAATACCCTCGA-AGGGTAAAATGAT
1 CGAAATACCC-CCATAGGGTAAAATGAC
* *
42676048 CGAAATACCCCCGA-ACGATAAAATGAC
1 CGAAATACCCCC-ATAGGGTAAAATGAC
** * * * *
42676075 TAAAATACCCCAAAAGGGTAAAATAAT
1 CGAAATACCCCCATAGGGTAAAATGAC
*
42676102 CGAAATACCCTCGA-AGGGTAAAATGAC
1 CGAAATACCC-CCATAGGGTAAAATGAC
* *
42676129 TGAAATACCCTCATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
** *
42676156 TAAAATACCCCTGA-AGGGTAAAATGA-
1 CGAAATACCCC-CATAGGGTAAAATGAC
** * *
42676182 TTAAATACCCTCGA-AGGGTAAAATGAT
1 CGAAATACCC-CCATAGGGTAAAATGAC
* **
42676209 CAAAATACCCTTGA-AGGGTAAAATGAC
1 CGAAATACCC-CCATAGGGTAAAATGAC
** ** *
42676236 TAAAATACCCTGAAAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
** *
42676263 TAAAATACCCTCATAGGGTAAAAT
1 CGAAATACCCCCATAGGGTAAAAT
42676287 AACTTTTATA
Statistics
Matches: 594, Mismatches: 113, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.03
26 70 0.12
27 497 0.84
28 7 0.01
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATGAC
Found at i:42676686 original size:28 final size:28
Alignment explanation
Indices: 42676654--42676743 Score: 144
Period size: 28 Copynumber: 3.1 Consensus size: 28
42676644 TACTGCATTG
42676654 CACTGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTTACTGTATTAGGCTAAGGCCCA
*
42676682 CACTGTTACTGTATTGGGCTAAGGTCCACA
1 CACTGTTACTGTATTAGGCTAAGG-CC-CA
*
42676712 CACTGTTACTGTAATAGGCTAAGGCCCA
1 CACTGTTACTGTATTAGGCTAAGGCCCA
42676740 CACT
1 CACT
42676744 ATACTGCTAC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 29 0.51
29 4 0.07
30 24 0.42
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (28 bp):
CACTGTTACTGTATTAGGCTAAGGCCCA
Found at i:42677060 original size:32 final size:32
Alignment explanation
Indices: 42677024--42677092 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
42677014 GCTTTTTCCT
*
42677024 TGAATATTTCAAACTGCTAAATTAGGAGATGA
1 TGAATATTTCAAACTGCTAAATTAGGAGATAA
* *
42677056 TGAATATTTTAAACTGCTAGATTAGGAGATAA
1 TGAATATTTCAAACTGCTAAATTAGGAGATAA
42677088 TGAAT
1 TGAAT
42677093 TTTAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (32 bp):
TGAATATTTCAAACTGCTAAATTAGGAGATAA
Found at i:42679676 original size:21 final size:20
Alignment explanation
Indices: 42679646--42679687 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42679636 GAGTTCTTGG
42679646 GGTAATCTCACAGCCTCACA
1 GGTAATCTCACAGCCTCACA
* *
42679666 GGTAACTCTCACTGTCTCACA
1 GGTAA-TCTCACAGCCTCACA
42679687 G
1 G
42679688 CTCCCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (20 bp):
GGTAATCTCACAGCCTCACA
Found at i:42682674 original size:20 final size:20
Alignment explanation
Indices: 42682649--42682706 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
42682639 ATCAGAAGTA
*
42682649 TTAATTA-AGCTTAAGTTTAG
1 TTAATTATAGCTTAA-TTAAG
*
42682669 TTAATTATAGGTTAATTAAG
1 TTAATTATAGCTTAATTAAG
*
42682689 TTAATTATA-ATTAATTAA
1 TTAATTATAGCTTAATTAA
42682707 TAAACTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.24
20 20 0.59
21 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (20 bp):
TTAATTATAGCTTAATTAAG
Found at i:42682684 original size:11 final size:10
Alignment explanation
Indices: 42682649--42682705 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
42682639 ATCAGAAGTA
42682649 TTAATTA-AG
1 TTAATTATAG
42682658 CTTAAGTT-TAG
1 -TTAA-TTATAG
42682669 TTAATTATAGG
1 TTAATTATA-G
42682680 TTAATTA-AG
1 TTAATTATAG
*
42682689 TTAATTATAA
1 TTAATTATAG
42682699 TTAATTA
1 TTAATTA
42682706 ATAAACTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
9 10 0.24
10 19 0.46
11 12 0.29
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (10 bp):
TTAATTATAG
Found at i:42685168 original size:24 final size:24
Alignment explanation
Indices: 42685141--42685192 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42685131 TTCGTAGGTC
* *
42685141 AAATAAATCATGCTAATAAATGCT
1 AAATAAATCATACTAATAAATACT
* *
42685165 AAATATATTATACTAATAAATACT
1 AAATAAATCATACTAATAAATACT
42685189 AAAT
1 AAAT
42685193 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATCATACTAATAAATACT
Found at i:42689084 original size:23 final size:23
Alignment explanation
Indices: 42689058--42689105 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
42689048 ACGGCCTAAC
*
42689058 TGACCCAACTTATGTGGCCCACA
1 TGACCCAAATTATGTGGCCCACA
* *
42689081 TGACCCAAATTGTGTGGTCCACA
1 TGACCCAAATTATGTGGCCCACA
42689104 TG
1 TG
42689106 GCCGTGTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (23 bp):
TGACCCAAATTATGTGGCCCACA
Found at i:42694712 original size:32 final size:32
Alignment explanation
Indices: 42694675--42694753 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
42694665 GGCCGCTAAT
42694675 AAATGTCACATCATCATCAATTGCTAATGTGG
1 AAATGTCACATCATCATCAATTGCTAATGTGG
**
42694707 AAATGTCATGTCATCATCAATTGCTAATGTGG
1 AAATGTCACATCATCATCAATTGCTAATGTGG
* * *
42694739 CATTGCCACATCATC
1 AAATGTCACATCATC
42694754 GCCTATTGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (32 bp):
AAATGTCACATCATCATCAATTGCTAATGTGG
Found at i:42694955 original size:29 final size:28
Alignment explanation
Indices: 42694923--42694978 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
42694913 ATTAAAATTT
42694923 ATAATATTATTA-AAAATTAATTAAAAACC
1 ATAAT-TTATTATAAAATTAA-TAAAAACC
* *
42694952 ATAATTTTTTATAAAATTTATAAAAAC
1 ATAATTTATTATAAAATTAATAAAAAC
42694979 ATTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAATTTATTATAAAATTAATAAAAACC
Found at i:42694963 original size:39 final size:41
Alignment explanation
Indices: 42694920--42694996 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
42694910 AACATTAAAA
* * *
42694920 TTTATAATA-TTATTAAAA-ATTAATTAAAAACCATAATTT
1 TTTATAAAATTTATAAAAACATTAATTAAAAACAATAATTT
*
42694959 TTTATAAAATTTATAAAAACATTTATTAAAAACAATAA
1 TTTATAAAATTTATAAAAACATTAATTAAAAACAATAA
42694997 AAAGTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.25
40 8 0.25
41 16 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (41 bp):
TTTATAAAATTTATAAAAACATTAATTAAAAACAATAATTT
Found at i:42695858 original size:45 final size:46
Alignment explanation
Indices: 42695782--42695871 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
42695772 TGGGGTTGGA
* *
42695782 AGTGATACTTTTAAAGAAAAATTCATCTCATAATTATTTTGATTAT
1 AGTGATACTTTTAAAGAAAAATACATCTCATAACTATTTTGATTAT
*
42695828 AGTGATACTTTT-AAGAAAAATACATTTCATAACTATTTTGATTA
1 AGTGATACTTTTAAAGAAAAATACATCTCATAACTATTTTGATTA
42695872 GGTAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 29 0.71
46 12 0.29
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (46 bp):
AGTGATACTTTTAAAGAAAAATACATCTCATAACTATTTTGATTAT
Found at i:42706558 original size:26 final size:26
Alignment explanation
Indices: 42706507--42706559 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
42706497 ATTAGATATT
* * *
42706507 TTTTTTAAATTGTAAAAATATTAATA
1 TTTTTCAAATTATAAAAATATAAATA
42706533 TTTTTCAAATTATATAAAAT-TAAATA
1 TTTTTCAAATTATA-AAAATATAAATA
42706559 T
1 T
42706560 AATAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTCAAATTATAAAAATATAAATA
Found at i:42706577 original size:15 final size:15
Alignment explanation
Indices: 42706539--42706579 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42706529 AATATTTTTC
42706539 AAATTATATAA-AATT
1 AAATT-TATAATAATT
42706554 AAA--TATAATAATT
1 AAATTTATAATAATT
42706567 AAATTTATAATAA
1 AAATTTATAATAA
42706580 ACTTTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 7 0.30
15 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTTATAATAATT
Found at i:42707354 original size:7 final size:7
Alignment explanation
Indices: 42707342--42707367 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42707332 ACTTCTCAAT
42707342 TCATCCC
1 TCATCCC
42707349 TCATCCC
1 TCATCCC
42707356 TCATCCC
1 TCATCCC
42707363 TCATC
1 TCATC
42707368 TCTCTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:42713316 original size:46 final size:46
Alignment explanation
Indices: 42713181--42713318 Score: 240
Period size: 46 Copynumber: 3.0 Consensus size: 46
42713171 CCATGACAAA
*
42713181 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
42713227 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
42713273 TTGTGAAAAATAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
42713319 CTATAGCATT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:42719344 original size:20 final size:20
Alignment explanation
Indices: 42719319--42719361 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42719309 AATATAAAAG
*
42719319 TATAAATATGTACATATATA
1 TATAAATAAGTACATATATA
* *
42719339 TATAAATAAGTATATATGTA
1 TATAAATAAGTACATATATA
42719359 TAT
1 TAT
42719362 GTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
TATAAATAAGTACATATATA
Found at i:42721140 original size:41 final size:41
Alignment explanation
Indices: 42721089--42721280 Score: 125
Period size: 41 Copynumber: 4.5 Consensus size: 41
42721079 TCAACCTGCC
*
42721089 CTACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTACT
1 CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
* * * * * * **
42721130 CTACTACAACTTCAGAGAGATAAGATCGGTGATTTTAATCCGCT
1 CTACTGCAACTTCAGGGAGATAAGGT--TTGA-TATGATCTACT
* * * * * * * *
42721174 CCATTACATCTTCAGGGAGAT-AGGATTGGTATGTTCAACCT
1 CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTA-CT
* * *
42721215 GCCCCACTGCAACTTTAGGGGGATAAGGTTTGATATGATCTACT
1 ---CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
*
42721259 CTACTGCAACTTCAGAGAGATA
1 CTACTGCAACTTCAGGGAGATA
42721281 GGATTGGCTT
Statistics
Matches: 108, Mismatches: 35, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
40 4 0.04
41 44 0.41
43 5 0.05
44 42 0.39
45 13 0.12
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
CTACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTACT
Found at i:42721147 original size:129 final size:129
Alignment explanation
Indices: 42720999--42721280 Score: 483
Period size: 129 Copynumber: 2.2 Consensus size: 129
42720989 GTGTGATCCG
** *
42720999 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTGTATCTTCAGGGAT
1 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
*
42721064 ATAGGATTGGTATGTTCAACCTGCCCTACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
66 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
* * * *
42721128 CTCTACTACAACTTCAGAGAGATAAGATCGGTGATTTTAATCCGCTCCATTACATCTTCAGGGAG
1 CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
*
42721193 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTTAGGGGGATAAGGTTTGATATGATCTA
66 ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
42721257 CTCTACTGCAACTTCAGAGAGATA
1 CTCTACTGCAACTTCAGAGAGATA
42721281 GGATTGGCTT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 143 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (129 bp):
CTCTACTGCAACTTCAGAGAGATAAGATCGATGATTTTAATCCACTCCACTACATCTTCAGGGAG
ATAGGATTGGTATGTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGATATGATCTA
Found at i:42721419 original size:100 final size:99
Alignment explanation
Indices: 42721291--42721699 Score: 520
Period size: 100 Copynumber: 4.1 Consensus size: 99
42721281 GGATTGGCTT
* ** * * * *
42721291 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTCTA
1 CTTCAATCT-TTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
* * * *
42721356 CTACACCATCAGGAAAAGTAAGATTCGTCGTTGTGG
65 CTGCACC-TCTGGGAAAGTAAGATTCGCCGTTGTGG
* *
42721392 CCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
* *
42721457 TGCACCGCCTGGGAAAGTAAGATCCGCCGTTGTGG
66 TGCACC-TCTGGGAAAGTAAGATTCGCCGTTGTGG
*
42721492 CTTCAATCTTTTAATTGCAATGTCGGGGAAACGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
*
42721557 TGCA-CTGCTTGGGAAAGTAA-AATCTGCCGTTGTGG
66 TGCACCT-C-TGGGAAAGTAAGATTC-GCCGTTGTGG
* * **
42721592 CTTCAATCTTTTAATTGCAATG-CCGGAAAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
*
42721656 TGCA-CTGCTTGGGAAAGTAAGATTCGCCGTTGTAG
66 TGCACCT-C-TGGGAAAGTAAGATTCGCCGTTGTGG
42721691 CTTCAATCT
1 CTTCAATCT
42721700 GTTCCACTGC
Statistics
Matches: 275, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
99 79 0.29
100 188 0.68
101 8 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (99 bp):
CTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
TGCACCTCTGGGAAAGTAAGATTCGCCGTTGTGG
Found at i:42721497 original size:51 final size:51
Alignment explanation
Indices: 42721291--42721810 Score: 371
Period size: 50 Copynumber: 10.4 Consensus size: 51
42721281 GGATTGGCTT
** * * * * *
42721291 CTTCAATCTGTTTAACTGCAATGTC-GGGGAAGTAAGATTCGTCGTCGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
* * * *** * * * *
42721341 CTTCAATCTATTCTACTACACCATCAGGAAAAGTAAGATTCGTCGTTGTGG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
* ** * * * * ** *
42721392 CCTCAATCT-TTTAATTGCAATGTC-GGGGAAGCGAGATTCGCCATTGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
* * *
42721441 CTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
** * * * *
42721492 CTTCAATCT-TTTAATTGCAATGTCGGGGAAACG--AGATTCGCCGTTGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAA-GTAAGATTCGCCGTTGTAG
* * *
42721541 CTTCAATCTGTTCCACTGCACTGCTTGGGAAAGTAA-AATCTGCCGTTGTGG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTC-GCCGTTGTAG
** * * ** **
42721592 CTTCAATCT-TTTAATTGCAATGCC--GGAAAGCGAGATTTACCGTTGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
*
42721640 CTTCAATCTGTTCCACTGCACTGCTTGGGAAAGTAAGATTCGCCGTTGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
** *
42721691 CTTCAATCTGTTCCACTGCACCACCTGGG-AAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
* ** * * ** * * *
42721741 CTTCAATCTTTTTAATTGCAATATC-GGGGAAGTGAGATTCGCTGTTGTAG
1 CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
* *
42721791 CTTCAATCTATTCTACTGCA
1 CTTCAATCTGTTCCACTGCA
42721811 TCGCAAGAGA
Statistics
Matches: 362, Mismatches: 95, Indels: 26
0.75 0.20 0.05
Matches are distributed among these distances:
48 24 0.07
49 65 0.18
50 150 0.41
51 123 0.34
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (51 bp):
CTTCAATCTGTTCCACTGCACTGCCTGGGAAAGTAAGATTCGCCGTTGTAG
Found at i:42721733 original size:200 final size:200
Alignment explanation
Indices: 42721291--42721749 Score: 530
Period size: 200 Copynumber: 2.3 Consensus size: 200
42721281 GGATTGGCTT
* *** * * *
42721291 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTCTA
1 CTTCAATCT-TTCAACTGCAACACCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* * * *
42721356 CTACACCATCAGGAAAAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAATTGCAATGTCGGGGA
65 CTACACCATCAGGAAAAGTAAAATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCCGGAA
*
42721421 AGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATCCGCCG
130 AGCGAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATCCGCCG
*
42721486 TTGTGG
195 TTGTAG
* * *** *** *
42721492 CTTCAATCTTTTAATTGCAATGTCGGGGAAACGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTCAACTGCAACACCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
* * * *
42721557 TGCA-C-TGCTTGGGAAAGTAAAA-TCTGCCGTTGTGGCTTCAATCTTTTAATTGCAATG-CCGG
66 TACACCAT-C-AGGAAAAGTAAAATTC-GCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCCGG
* * * * *
42721618 AAAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTTGGGAAAGTAAGATTCGC
128 AAAGCGAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATCCGC
42721683 CGTTGTAG
193 CGTTGTAG
* * * *
42721691 CTTCAATCTGTTCCACTGCACCACCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 CTTCAATCT-TTCAACTGCAACACCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
42721750 TTTTAATTGC
Statistics
Matches: 219, Mismatches: 35, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
198 1 0.00
199 81 0.37
200 128 0.58
201 9 0.04
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (200 bp):
CTTCAATCTTTCAACTGCAACACCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
TACACCATCAGGAAAAGTAAAATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCCGGAAA
GCGAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATCCGCCGT
TGTAG
Found at i:42721809 original size:100 final size:100
Alignment explanation
Indices: 42721670--42721861 Score: 276
Period size: 100 Copynumber: 1.9 Consensus size: 100
42721660 CTGCTTGGGA
* ** * * *
42721670 AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGGAAGTAAGATTCGCCG
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCACAAGAGAAGTAAGATTCACCA
42721735 TTGTGGCTTCAATCTTTTTAATTGCAATATCGGGG
66 TTGTGGCTTCAATCTTTTTAATTGCAATATCGGGG
* * * * * *
42721770 AAGTGAGATTCGCTGTTGTAGCTTCAATCTATTCTACTGCATCGCAAGAGAAGTAAGATTTACCA
1 AAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCACAAGAGAAGTAAGATTCACCA
42721835 TTGTGGCTTCAATCTTTTTAATTGCAA
66 TTGTGGCTTCAATCTTTTTAATTGCAA
42721862 ACTATGGTGT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCACAAGAGAAGTAAGATTCACCA
TTGTGGCTTCAATCTTTTTAATTGCAATATCGGGG
Found at i:42721824 original size:150 final size:150
Alignment explanation
Indices: 42721525--42721849 Score: 406
Period size: 150 Copynumber: 2.2 Consensus size: 150
42721515 CGGGGAAACG
** *
42721525 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTTGGGAAAGTAAAATCTGCCGTTGT
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGGAAAGTAAAATCTGCCGTTGT
* *
42721590 GGCTTCAATCTTTTAATTGCAATGCCGGAAAGCGAGATTTACCGTTGTAGCTTCAATCTGTTCCA
66 GGCTTCAATCTTTTAATTGCAATGCCGGAAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCA
** *
42721655 CTGCACTGCTTGGGAAAGTA
131 CTGCACTGCAAGAGAAAGTA
*
42721675 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGG-AAGTAAGAT-TCGCCGTTG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGGAAAGTAAAATCT-GCCGTTG
* * * * * *
42721738 TGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTATT
65 TGGCTTCAATC-TTTTAATTGCAAT-GCCGGAAAGCGAGATTCACCGTTGTAGCTTCAATCTATT
*
42721803 CTACTGCA-TCGCAAGAG-AAGTA
128 CCACTGCACT-GCAAGAGAAAGTA
** * *
42721825 AGATTTACCATTGTGGCTTCAATCT
1 AGATTCGCCGTTGTAGCTTCAATCT
42721850 TTTTAATTGC
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
148 1 0.01
149 26 0.17
150 82 0.54
151 42 0.28
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (150 bp):
AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTGGGAAAGTAAAATCTGCCGTTGT
GGCTTCAATCTTTTAATTGCAATGCCGGAAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCA
CTGCACTGCAAGAGAAAGTA
Found at i:42728371 original size:15 final size:15
Alignment explanation
Indices: 42728351--42728388 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
42728341 ACATATATAT
42728351 GTATGTATAACAAAC
1 GTATGTATAACAAAC
42728366 GTATGTATAACAAAC
1 GTATGTATAACAAAC
42728381 GTATGTAT
1 GTATGTAT
42728389 GTATATAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (15 bp):
GTATGTATAACAAAC
Found at i:42728372 original size:19 final size:18
Alignment explanation
Indices: 42728348--42728393 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 18
42728338 TAGACATATA
42728348 TATGTATGTATAACAAAC
1 TATGTATGTATAACAAAC
42728366 ---GTATGTATAACAAAC
1 TATGTATGTATAACAAAC
42728381 GTATGTATGTATA
1 -TATGTATGTATA
42728394 TAGGTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 15 0.62
19 9 0.38
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
TATGTATGTATAACAAAC
Found at i:42728457 original size:12 final size:12
Alignment explanation
Indices: 42728442--42728472 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42728432 ATATAATAAG
42728442 ATATAAAGATAT
1 ATATAAAGATAT
42728454 ATATAAAGATAT
1 ATATAAAGATAT
42728466 ATATAAA
1 ATATAAA
42728473 TAGTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
ATATAAAGATAT
Found at i:42737598 original size:30 final size:30
Alignment explanation
Indices: 42737564--42737625 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
42737554 ACTTATTTTA
*
42737564 TTGTTTATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
42737594 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
42737624 TT
1 TT
42737626 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:42737779 original size:12 final size:12
Alignment explanation
Indices: 42737749--42737781 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
42737739 TATATATTTT
42737749 AAAATT-ATATA
1 AAAATTAATATA
42737760 AAAA-TAATATA
1 AAAATTAATATA
42737771 AAAATTAATAT
1 AAAATTAATAT
42737782 GGGTGGGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:42739190 original size:24 final size:24
Alignment explanation
Indices: 42739146--42739191 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42739136 TATGAGAATT
* *
42739146 ATATATAAAAAAATACTAAAAACG
1 ATATATAAAAAAAGACAAAAAACG
42739170 ATAT-TAAAATAAAGACAAAAAA
1 ATATATAAAA-AAAGACAAAAAA
42739192 ATTATACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (24 bp):
ATATATAAAAAAAGACAAAAAACG
Found at i:42746338 original size:3 final size:3
Alignment explanation
Indices: 42746332--42746356 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42746322 ATTGATGATG
42746332 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
42746357 TTTGTGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:42749232 original size:72 final size:73
Alignment explanation
Indices: 42749096--42749243 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 73
42749086 TATAGGGAAC
42749096 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACACAAAGTTCTTTCGCAAGTTTGCA
1 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACAC-AAGTTCTTTCGCAAGTTTGCA
42749161 TCAGAACAG
65 TCAGAACAG
*
42749170 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACAC-AGTTTTTTCGCAAGTTTGCAT
1 AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACACAAGTTCTTTCGCAAGTTTGCAT
42749234 CAGAACAG
66 CAGAACAG
42749242 AG
1 AG
42749244 TAGAAAGAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 30 0.41
74 43 0.59
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (73 bp):
AGAGAGCTAAAGCTAATTGGTTGAAGAATGGAGATCGCAACACAAGTTCTTTCGCAAGTTTGCAT
CAGAACAG
Found at i:42750458 original size:19 final size:19
Alignment explanation
Indices: 42750430--42750482 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
42750420 ATCTTCAAGT
42750430 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
42750449 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
42750468 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
42750483 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:42750733 original size:23 final size:23
Alignment explanation
Indices: 42750689--42750733 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42750679 TTTTATTTCG
* *
42750689 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
42750712 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
42750734 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:42750967 original size:3 final size:3
Alignment explanation
Indices: 42750959--42751000 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
42750949 ATCTTGTATC
* *
42750959 ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT TTT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT AT
42751001 ATTCATGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:42750984 original size:19 final size:18
Alignment explanation
Indices: 42750960--42751000 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
42750950 TCTTGTATCA
42750960 TTATTATTATTATTATTAT
1 TTATTATTATTATTATT-T
*
42750979 TTATTATTATTTTTATTT
1 TTATTATTATTATTATTT
42750997 TTAT
1 TTAT
42751001 ATTCATGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTATTATTATTATTT
Found at i:42750987 original size:22 final size:22
Alignment explanation
Indices: 42750959--42751000 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42750949 ATCTTGTATC
42750959 ATTATTATTATTATTATTATTT
1 ATTATTATTATTATTATTATTT
* *
42750981 ATTATTATTTTTATTTTTAT
1 ATTATTATTATTATTATTAT
42751001 ATTCATGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTATTATTATTATTATTATTT
Found at i:42756295 original size:20 final size:19
Alignment explanation
Indices: 42756272--42756316 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
42756262 TCAAAATATA
42756272 AAAAAAATAAGAAG-AAAAAG
1 AAAAAAA-AAG-AGTAAAAAG
*
42756292 AAAAAAAAAGAGTGAAAAG
1 AAAAAAAAAGAGTAAAAAG
42756311 AAAAAA
1 AAAAAA
42756317 GAAAATGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAGAGTAAAAAG
Found at i:42757558 original size:44 final size:44
Alignment explanation
Indices: 42757510--42757740 Score: 124
Period size: 44 Copynumber: 5.2 Consensus size: 44
42757500 GACACTAGCA
*
42757510 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATACCAGATC
* ** * * * * ** * * *
42757554 TTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGACACCAG-CC
1 TTGCCTCCCTGGGT-TACAGCGGAGCAGGTTAAAAATACCAGATC
* * **
42757598 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAGTTGCAGATC
1 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATACCAGATC
* **** * * ** * * *
42757642 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCT-
1 TTGCCTCCCTG-GGTTACAGCGGAGCAGGTTAAAAATACCAGATC
* ** *
42757686 TTGCCTCCCTAGGTTGTAGCGGAGCAGGTTAAAAATAACAGATC
1 TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATACCAGATC
*
42757730 TTGCCTTCCTG
1 TTGCCTCCCTG
42757741 CACCGACAGC
Statistics
Matches: 120, Mismatches: 63, Indels: 8
0.63 0.33 0.04
Matches are distributed among these distances:
43 33 0.28
44 52 0.43
45 35 0.29
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.23
Consensus pattern (44 bp):
TTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATACCAGATC
Found at i:42757590 original size:88 final size:88
Alignment explanation
Indices: 42757371--42757950 Score: 820
Period size: 88 Copynumber: 6.6 Consensus size: 88
42757361 GTGAAGATAA
* * *
42757371 CAGATCTTGCCTTCCTGCACAC-ACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGT
1 CAGATCTTGCCTTCCTGCAC-CGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
* *
42757435 TGTAGCAGAGCAGGTTAAAAAATAG
65 TGCAGCGGAGCAGGTT-AAAAATAG
* * * * * * *
42757460 CATATCTTGTCTTCATGCACCGACAACGAAGCAGATCAAAGACACTAGCATTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
42757525 ACAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
42757548 CAGATCTTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
42757613 GCAGCGGAGCAGGTTAAAAGTTG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
42757636 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
42757701 GTAGCGGAGCAGGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
42757724 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAACCTTGCTTCCCTCGGTA
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
42757789 GTAGCGGAGCAAGTTAAAAAATAG
66 GCAGCGGAGCAGGTT-AAAAATAG
* *
42757813 TAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
42757878 GCAGCAGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
42757901 CAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
42757951 CTATCTCTCT
Statistics
Matches: 433, Mismatches: 56, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
88 291 0.67
89 142 0.33
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:42757851 original size:265 final size:265
Alignment explanation
Indices: 42757371--42757950 Score: 842
Period size: 265 Copynumber: 2.2 Consensus size: 265
42757361 GTGAAGATAA
* * * *
42757371 CAGATCTTGCCTTCCTGCACAC-ACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCTGGGT
1 CAGATCTTGCCTTCCTGCAC-CGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
* * *
42757435 TGTAGCAGAGCAGGTTAAAAAATAGCATATCTTGTCTTCATGCACCGACAACGAAGCAGATCAAA
65 TGTAGCAGAGCAGGTTAAAAAATAACAGATCTTGCCTTCATGCACCGACAACGAAGCAGATCAAA
* * * *
42757500 GACACTAGCATTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTG
130 GACACCAACATTGCCTCCCTCGGTTACAGCGGAGCAAGTTAAAAATAGCAGATCTTGCCTTCCTG
* * *
42757565 CATCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAA
195 CACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAA
* *
42757630 AAGTTG
260 AAATAG
*
42757636 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
* * * * *
42757701 GTAGCGGAGCAGGTT-AAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGG
66 GTAGCAGAGCAGGTTAAAAAATAACAGATCTTGCCTTCATGCACCGACAACGAAGCAGATCAAAG
* * * *
42757765 ACACCAACCTTGCTTCCCTCGG-TAGTAGCGGAGCAAGTTAAAAAATAGTAGATCTTGCCTTCCT
131 ACACCAACATTGCCTCCCTCGGTTA-CAGCGGAGCAAGTT-AAAAATAGCAGATCTTGCCTTCCT
*
42757829 GCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTA
194 GCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTA
42757894 AAAATAG
259 AAAATAG
* * *
42757901 CAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
42757951 CTATCTCTCT
Statistics
Matches: 281, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
263 2 0.01
264 72 0.26
265 207 0.74
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (265 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
GTAGCAGAGCAGGTTAAAAAATAACAGATCTTGCCTTCATGCACCGACAACGAAGCAGATCAAAG
ACACCAACATTGCCTCCCTCGGTTACAGCGGAGCAAGTTAAAAATAGCAGATCTTGCCTTCCTGC
ACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAA
AATAG
Found at i:42757898 original size:177 final size:177
Alignment explanation
Indices: 42757367--42757939 Score: 862
Period size: 177 Copynumber: 3.2 Consensus size: 177
42757357 ATCAGTGAAG
*
42757367 ATAACAGATCTTGCCTTCCTGCACAC-ACAGCGAAGTAGATCGAAGACACCAACCTTGCTTCCCT
1 ATAACAGATCTTGCCTTCCTGCAC-CGACAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCT
* * * * *
42757431 GGGTTGTAGCAGAGCAGGTTAAAAAATAGCATATCTTGTCTTCATGCACCGACAACGAAGCAGAT
65 GGGTTGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
* *
42757496 CAAAGACACTAGCATTGCCTCCCTGGGTTACAGCGGAGCAGGTTAAAA
130 CGAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* * * * *
42757544 ATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTG
* * *
42757609 GGTTGCAGCGGAGCAGGTT-AAAAGTTGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
66 GGTTGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
* * * *
42757673 GAAGACACCAGCTTTGCCTCCCTAGGTTGTAGCGGAGCAGGTTAAAA
131 GAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* *
42757720 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAACCTTGCTTCCCTC
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTG
* * *
42757785 GGTAGTAGCGGAGCAAGTTAAAAAATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
66 GGTTGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
* *
42757850 GAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAA
131 GAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
* *
42757897 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCGA
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
42757940 TGACCCCAGC
Statistics
Matches: 356, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
176 155 0.44
177 201 0.56
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (177 bp):
ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTG
GGTTGTAGCGGAGCAGGTTAAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
GAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
Found at i:42757997 original size:44 final size:45
Alignment explanation
Indices: 42757947--42758046 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 45
42757937 CGATGACCCC
42757947 AGCCCTATCTCTCTAGACAGTAGTGGAATAGGTTGAAGATTGT-A
1 AGCCCTATCTCTCTAGACAGTAGTGGAATAGGTTGAAGATTGTGA
* * *
42757991 AGCCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGA
1 AGCCCTATCTCTCTAGACAGTAGTGGAATAGGTTGAAGATTGTGA
*
42758036 A-TCCTATCTCT
1 AGCCCTATCTCT
42758047 TTAAGCAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 48 0.96
45 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
AGCCCTATCTCTCTAGACAGTAGTGGAATAGGTTGAAGATTGTGA
Done.