Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 1 of 8
Found at i:7643 original size:74 final size:73
Alignment explanation
Indices: 7522--8444 Score: 767
Period size: 85 Copynumber: 12.0 Consensus size: 73
7512 CTTTTCAAGG
* * *
7522 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-TTTTCAATTTC
7587 TGTTTTTCA
65 TGTTTTTCA
* *
7596 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
*
7661 GTTTGTCA
66 GTTTTTCA
* * * *
7669 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGCTGAGGTATTTTCAATTT
***
7734 CTGTTCGTAAAAAA
64 CTGTT--T--TTCA
* * * *
7748 AAAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACGCTGAAGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-TTTTCAATTTC
7813 TGTTTTTCA
65 TGTTTTTCA
* *
7822 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA--TTT
*
7887 GTGTTTTAATTTATTTTTCA
64 CTG----------TTTTTCA
* *
7907 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA--TTT
*
7972 GTGTTTTAATTTATTTTTCA
64 CTG----------TTTTTCA
* *
7992 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA--TTT
*
8057 GTGTTTTAATTTATTTTTCA
64 CTG----------TTTTTCA
** * *** *
8077 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCATATTGAGGTATTTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
** ***
8142 -CATCAAA
66 GTTTTTCA
** *
8149 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACGTTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG--GGACACGCTGAGGTATTTTCAATTT
*
8214 CTGTCTTTTAAAA
64 CTGT-TTTT--CA
* * * * * * *
8227 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTC--AAGACGCTGAGGTAATTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
*
8290 GTTTGTCA
66 GTTTTTCA
* * ** **
8298 AAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
*
8363 GTCTTTCAAA
66 GTTTTTC--A
* * * * * * *
8373 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTC--AAGACGCTGAGGTGTTTTCCATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
*
8436 GTTCTTCA
66 GTTTTTCA
8444 A
1 A
8445 TTTCTGTTTT
Statistics
Matches: 727, Mismatches: 93, Indels: 61
0.83 0.11 0.07
Matches are distributed among these distances:
71 35 0.05
72 39 0.05
73 111 0.15
74 144 0.20
75 64 0.09
76 2 0.00
77 11 0.02
78 50 0.07
79 37 0.05
83 4 0.01
85 230 0.32
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTCA
Found at i:8097 original size:170 final size:159
Alignment explanation
Indices: 7815--8932 Score: 898
Period size: 170 Copynumber: 7.0 Consensus size: 159
7805 TAAATTTCTG
* *
7815 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
*
7880 AATTTTTGTGTTTTAATTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
66 AATTTCTGT-TTTTAA--TA------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-
* * *
7945 GGGCACGCTGAGGTATTGTCAATTTTTGTGTTTTAATTTA
121 AGGCACGCTGAGGTATTTTCAATTTTTGT-TTTCAATTTA
* *
7985 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
*
8050 AATTTTTGTGTTTTAATTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
66 AATTTCTGT-TTTTAA--TA------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-
* *** * *
8115 AGTCATATTGAGGTATTTTCAA----T-TTATC-A-TCA
121 AGGCACGCTGAGGTATTTTCAATTTTTGTTTTCAATTTA
* ** *
8147 -----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACGTTGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG--GGACACGCTGAGGTATTT
* * * *
8207 TCAATTTCTGTCTTTTAA-AAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG-ACG
64 TCAATTTCTGT-TTTTAATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACG
*
8270 CTGAGGTAATTTCAATTTTTG-----------
128 CTGAGGTATTTTCAATTTTTGTTTTCAATTTA
* * * ** **
8291 TTTGTCAAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACATTGAGGTATTTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
* * * * *
8356 AATTTCTGTCTTTCA-AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG-ACGCTG
66 AATTTCTGTTTTTAATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTG
* * *
8419 AGGTGTTTTCCATTTTTGTTCTTCAATTTCTG
131 AGGTATTTTCAATTTTTGTT-TTCAA-TT-TA
8451 TTTTTCAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTT
1 TTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTT
* * * *
8516 TCAAATTCTATTTTT-ATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACA
64 TCAATTTCTGTTTTTAAT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CA
* *
8580 CACTGAGGTATTTTCAATTTCTGCTTTTCAATTTCTA
126 CGCTGAGGTATTTTCAATTTTTG-TTTTCAA-TT-TA
* * **
8617 CTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGCGT
1 TTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTAT
* * *
8682 TTTCAATTTCTGCTTTTAA-AAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
62 TTTCAATTTCTGTTTTTAATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---
* ** *
8746 CACACTGAGGCGTTTTCAATTTCTGCTTTT-AA---A
124 CACGCTGAGGTATTTTCAATTTTTG-TTTTCAATTTA
* *
8779 ------AAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGCATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTT
* * * * *
8838 TCAATTTCTG-CTTT--TCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACA
64 TCAATTTCTGTTTTTAATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---CA
* * * * *
8900 CACTGAGGTCTTTTCAAATTCTGTTTTTAATTT
126 CGCTGAGGTATTTTCAATTTTTGTTTTCAATTT
8933 CTGCTTTTCA
Statistics
Matches: 820, Mismatches: 83, Indels: 105
0.81 0.08 0.10
Matches are distributed among these distances:
146 66 0.08
147 26 0.03
148 14 0.02
149 37 0.05
150 35 0.04
151 4 0.00
152 65 0.08
153 3 0.00
154 64 0.08
155 2 0.00
156 1 0.00
157 39 0.05
159 29 0.04
160 5 0.01
161 5 0.01
162 62 0.08
163 1 0.00
164 39 0.05
165 1 0.00
166 117 0.14
167 5 0.01
168 54 0.07
169 1 0.00
170 145 0.18
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (159 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
AATTTCTGTTTTTAATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTG
AGGTATTTTCAATTTTTGTTTTCAATTTA
Found at i:8421 original size:73 final size:73
Alignment explanation
Indices: 8076--8433 Score: 395
Period size: 75 Copynumber: 4.8 Consensus size: 73
8066 TTTATTTTTC
***
8076 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCATATTGAGGTATTTTCAA-TT-
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACGCTGAGGTATTTTCAATTTC
* *
8139 TATC-ATCAA
64 TGTCTTTCAA
* * *
8148 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACGTTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC----AAGACGCTGAGGTATTTTCAATT
*
8213 TCTGTCTTTTAAA
62 TCTGTC-TTTCAA
* * * * *
8226 AAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCAATTTTTG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCTG
8291 T-TTGTC--
66 TCTT-TCAA
* * *
8297 AAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGC--TGAGGTATTTTCAATTTC
8362 TGTCTTTCAA
64 TGTCTTTCAA
* * * *
8372 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTT
8434 TTGTTCTTCA
Statistics
Matches: 241, Mismatches: 31, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
71 39 0.16
72 40 0.17
73 37 0.15
74 41 0.17
75 42 0.17
76 4 0.02
78 38 0.16
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCTGAGGTATTTTCAATTTCTG
TCTTTCAA
Found at i:8565 original size:77 final size:78
Alignment explanation
Indices: 8440--8928 Score: 563
Period size: 77 Copynumber: 6.2 Consensus size: 78
8430 ATTTTTGTTC
*
8440 TTCAATTTCTG-TTTT-TCAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-AC
1 TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
* *
8502 ACGCTGAGGTATT
66 ACACTGAGGCATT
* * *
8515 TTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGG-AC
1 TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
8579 ACACTGAGGTATT
66 ACACTGAGGCATT
*
8592 TTCAATTTCTGCTTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
1 TTCAATTTCTG----T---TTT-TA----TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
8657 AGCCTCGGGTCACACACTGAGGCGTT
54 AGCCTCGGG-CACACACTGAGGCATT
* *
8683 TTCAATTTCTGCTTTTA--AAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
*
8746 CACACTGAGGCGTT
65 CACACTGAGGCATT
* *
8760 TTCAATTTCTGCTTTTA--AAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
*
8823 CACGCTGAGGCATT
65 CACACTGAGGCATT
* * *
8837 TTCAATTTCTG-CTTT-TC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGTCTCGGGCCA
1 TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
8898 CACACTGAGGTC-TT
65 CACACTGAGG-CATT
*
8912 TTCAAATTCTGTTTTTA
1 TTCAATTTCTGTTTTTA
8929 ATTTCTGCTT
Statistics
Matches: 371, Mismatches: 22, Indels: 40
0.86 0.05 0.09
Matches are distributed among these distances:
75 70 0.19
76 11 0.03
77 212 0.57
81 1 0.00
83 2 0.01
84 6 0.02
85 2 0.01
89 43 0.12
91 24 0.06
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (78 bp):
TTCAATTTCTGTTTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
ACACTGAGGCATT
Found at i:8609 original size:14 final size:14
Alignment explanation
Indices: 8590--8624 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
8580 CACTGAGGTA
*
8590 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
8604 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
8618 TTTTCAA
1 TTTTCAA
8625 AAGAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:8644 original size:166 final size:164
Alignment explanation
Indices: 8279--8943 Score: 750
Period size: 166 Copynumber: 4.1 Consensus size: 164
8269 GCTGAGGTAA
* * * **
8279 TTTCAATTTTTG-TTTGTC-AAA-AATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAG-AC
1 TTTCAATTTCTGCTTT-TCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
* * * *
8340 ACATTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGA
65 ACACTGAGGCATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * * * * *
8405 ACCTC---AAGACGCTGAGGTGTTTTCCATTTTTGT
130 GCCTCGGGCACACACTGAGGT-TTTTCAATTTCTGT
*
8438 TCTTCAATTTCTGTTTTTCAAAA-ACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-A
1 T-TTCAATTTCTGCTTTTCAAAAGA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCA
* * * * *
8501 CACGCTGAGGTATTTTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGT
64 CACACTGAGGCATTTTCAATTTCT-GTTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
8566 TGAGCCTCGGG-ACACACTGAGGTATTTTCAATTTCTGCT
127 TGAGCCTCGGGCACACACTGAGGT-TTTTCAATTTCTG-T
*
8605 TTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* *
8670 ACACTGAGGCGTTTTCAATTTCTGCTTTT-AAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
65 ACACTGAGGCATTTTCAATTTCTGTTTTTCAAAAA-AATCAACTCATATTGCGAGAGGTGAGTTG
8734 AGCCTCGGGTCACACACTGAGG-----------C-GT
129 AGCCTCGGG-CACACACTGAGGTTTTTCAATTTCTGT
*
8759 TTTCAATTTCTGCTTTTAAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* * *
8824 ACGCTGAGGCATTTTCAATTTCTGCTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGA
65 ACACTGAGGCATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
8887 GTCTCGGGCCACACACTGAGGTCTTTTCAAATTCTGT
130 GCCTCGGG-CACACACTGAGGT-TTTTCAATTTCTGT
*
8924 TTTTAATTTCTGCTTTTCAA
1 TTTCAATTTCTGCTTTTCAA
8944 TTTCTATTTT
Statistics
Matches: 440, Mismatches: 36, Indels: 54
0.83 0.07 0.10
Matches are distributed among these distances:
152 48 0.11
153 3 0.01
154 91 0.21
155 1 0.00
156 1 0.00
159 1 0.00
160 12 0.03
161 7 0.02
162 55 0.12
163 3 0.01
164 40 0.09
165 25 0.06
166 115 0.26
167 6 0.01
168 32 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (164 bp):
TTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACA
CACTGAGGCATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGGGCACACACTGAGGTTTTTCAATTTCTGT
Found at i:8691 original size:91 final size:91
Alignment explanation
Indices: 8513--8698 Score: 286
Period size: 89 Copynumber: 2.0 Consensus size: 91
8503 CGCTGAGGTA
*
8513 TTTTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
1 TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
*
8578 CACACTGAGGTATTTTCAATTTCTGC
66 CACACTGAGGCATTTTCAATTTCTGC
* * *
8604 TTTTCAATTTCTA-CTTT-TCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGG-
*
8667 CACACACTGAGGCGTTTTCAATTTCTGC
65 -ACACACTGAGGCATTTTCAATTTCTGC
8695 TTTT
1 TTTT
8699 AAAAAGAATC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
89 43 0.49
90 3 0.03
91 41 0.47
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (91 bp):
TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
CACACTGAGGCATTTTCAATTTCTGC
Found at i:8940 original size:14 final size:13
Alignment explanation
Indices: 8910--8953 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
8900 CACTGAGGTC
*
8910 TTTTCAAATTCTG
1 TTTTCAATTTCTG
*
8923 TTTTTAATTTCTG
1 TTTTCAATTTCTG
*
8936 CTTTTCAATTTCTA
1 -TTTTCAATTTCTG
8950 TTTT
1 TTTT
8954 TTCAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:8954 original size:14 final size:14
Alignment explanation
Indices: 8910--8972 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
8900 CACTGAGGTC
* *
8910 TTTTCAAATTCTGT
1 TTTTCAATTTCTAT
**
8924 TTTT-AATTTCTGC
1 TTTTCAATTTCTAT
8937 TTTTCAATTTCTATT
1 TTTTCAATTTCTA-T
*
8952 TTTTCAATTTATAT
1 TTTTCAATTTCTAT
8966 TTTTCAA
1 TTTTCAA
8973 AAATTAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.22, C:0.13, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTTCAATTTCTAT
Found at i:8957 original size:15 final size:15
Alignment explanation
Indices: 8937--8969 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8927 TAATTTCTGC
*
8937 TTTTCAATTTCTATT
1 TTTTCAATTTATATT
8952 TTTTCAATTTATATT
1 TTTTCAATTTATATT
8967 TTT
1 TTT
8970 CAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:9156 original size:14 final size:14
Alignment explanation
Indices: 9133--9167 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9123 CGCTGAGGTG
* *
9133 TTTTCCATTTCTGT
1 TTTTCAATTTCTGC
9147 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
9161 TTTTCAA
1 TTTTCAA
9168 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:9185 original size:85 final size:87
Alignment explanation
Indices: 9062--9254 Score: 257
Period size: 85 Copynumber: 2.2 Consensus size: 87
9052 GAGTTGAGCC
* *
9062 TTTTAATTTCTGTTTTTCAAAAAACAAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG-ACGC
1 TTTTAATTTCTGCTTTTCAAAAAACAAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGCACAC
* * *
9126 -TGAGGTGTTTTCCATTTCTGT
66 GTGAGGTCTTTTCAAATTCTGT
* ** **
9147 TTTTCAATTTCTGCTTTTCAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCAC
1 TTTT-AATTTCTGCTTTTCAAAAAACAAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG-CAC
9211 ACGTGAGGTCTTTTCAAATTCTGT
64 ACGTGAGGTCTTTTCAAATTCTGT
9235 TTTTAATTTCTGCTTTTCAA
1 TTTTAATTTCTGCTTTTCAA
9255 TTTCTGTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
85 34 0.36
86 19 0.20
87 19 0.20
88 22 0.23
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (87 bp):
TTTTAATTTCTGCTTTTCAAAAAACAAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGCACAC
GTGAGGTCTTTTCAAATTCTGT
Found at i:9266 original size:14 final size:14
Alignment explanation
Indices: 9221--9283 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
9211 ACGTGAGGTC
*
9221 TTTTCAAATTCTGT
1 TTTTCAATTTCTGT
*
9235 TTTT-AATTTCTGC
1 TTTTCAATTTCTGT
9248 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
* *
9262 TTTTCCAATTTATAT
1 TTTT-CAATTTCTGT
9277 TTTTCAA
1 TTTTCAA
9284 AAATCAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:14523 original size:18 final size:18
Alignment explanation
Indices: 14496--14535 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14486 CAGGTGCGTT
*
14496 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
14514 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
14532 TCCT
1 TCCT
14536 TTTTCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:15159 original size:32 final size:33
Alignment explanation
Indices: 15115--15396 Score: 134
Period size: 33 Copynumber: 8.4 Consensus size: 33
15105 ACCCCTAAAC
* *
15115 TAAAAACTCTAACCCTAATCATAACCCATAACT
1 TAAAAACCCTAACCCTAATCCTAACCCATAACT
*
15148 T-AGAACCCTAACCCTAATCCTAA-CCATTAACT
1 TAAAAACCCTAACCCTAATCCTAACCCA-TAACT
*
15180 TAAAAAACCCTAACCCTAACCCTAACCC-TAACACT
1 T-AAAAACCCTAACCCTAATCCTAACCCAT-A-ACT
*
15215 TAACATAA---AAACCCTAATCCTAACCC-TAAACT
1 TAA-A-AACCCTAACCCTAATCCTAACCCAT-AACT
* * * * *
15247 TAAAAACCCTAAAACTTAAAACACTAAACCTTAAACT
1 TAAAAACCCT-AACCCT-AATC-CTAACCCAT-AACT
* * *** *
15284 TAAAAA-CCTAAACCTTAAACCTAAAAATATAAACCC
1 TAAAAACCCT-AACCCTAATCCT-AACCCAT-AA-CT
* * * *
15320 T--AAACCTTAAACCCAAATTCTAACCCTTAACT
1 TAAAAACCCT-AACCCTAATCCTAACCCATAACT
* * *
15352 TAAAAATCCTAACCCTAATCTTAACCCTTAACT
1 TAAAAACCCTAACCCTAATCCTAACCCATAACT
*
15385 TAAAAACACTAA
1 TAAAAACCCTAA
15397 AATCTAAACC
Statistics
Matches: 195, Mismatches: 34, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
30 2 0.01
31 4 0.02
32 33 0.17
33 53 0.27
34 40 0.21
35 32 0.16
36 19 0.10
37 12 0.06
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.23
Consensus pattern (33 bp):
TAAAAACCCTAACCCTAATCCTAACCCATAACT
Found at i:15196 original size:6 final size:6
Alignment explanation
Indices: 15185--15211 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15175 TAACTTAAAA
15185 AACCCT AACCCT AACCCT AACCCT AAC
1 AACCCT AACCCT AACCCT AACCCT AAC
15212 ACTTAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:15196 original size:40 final size:39
Alignment explanation
Indices: 15151--15243 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 39
15141 CATAACTTAG
* *
15151 AACCCTAACCCTAATCCTAAC-CATTAACTTAAAAAACCCT
1 AACCCTAACCCTAACCCTAACAC-TTAACAT-AAAAACCCT
15191 AACCCTAACCCTAACCCTAACACTTAACATAAAAACCCT
1 AACCCTAACCCTAACCCTAACACTTAACATAAAAACCCT
*
15230 AATCCTAACCCTAA
1 AACCCTAACCCTAA
15244 ACTTAAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 22 0.45
40 26 0.53
41 1 0.02
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (39 bp):
AACCCTAACCCTAACCCTAACACTTAACATAAAAACCCT
Found at i:15227 original size:27 final size:27
Alignment explanation
Indices: 15197--15258 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
15187 CCCTAACCCT
*
15197 AACCCTAACCCTAACACTTAACATAAA
1 AACCCTAACCCTAACACTAAACATAAA
* * *
15224 AACCCTAATCCTAACCCTAAACTTAAA
1 AACCCTAACCCTAACACTAAACATAAA
15251 AACCCTAA
1 AACCCTAA
15259 AACTTAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (27 bp):
AACCCTAACCCTAACACTAAACATAAA
Found at i:15256 original size:15 final size:15
Alignment explanation
Indices: 15236--15281 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
15226 CCCTAATCCT
15236 AACCCTAAACTTAAA
1 AACCCTAAACTTAAA
15251 AACCCTAAAACTT-AA
1 AACCCT-AAACTTAAA
*
15266 AACACTAAACCTTAAA
1 AACCCTAAA-CTTAAA
15282 CTTAAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 8 0.30
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (15 bp):
AACCCTAAACTTAAA
Found at i:15257 original size:21 final size:20
Alignment explanation
Indices: 15233--15375 Score: 64
Period size: 21 Copynumber: 6.8 Consensus size: 20
15223 AAACCCTAAT
15233 CCTAACCCTAAACTT--AAA
1 CCTAACCCTAAACTTAAAAA
15251 ---AACCCTAAAACTT-AAAA
1 CCTAACCCT-AAACTTAAAAA
*
15268 CACTAAACCTTAAACTTAAAAA
1 C-CT-AACCCTAAACTTAAAAA
* *
15290 CCTAAACCTTAAACCTAAAAA
1 CCT-AACCCTAAACTTAAAAA
**
15311 TATAAACCCTAAACCTTAAACCCAAA
1 CCT-AACCCTAAA-CTT-AA---AAA
* *
15337 TTCTAACCCTTAACTTAAAAA
1 -CCTAACCCTAAACTTAAAAA
*
15358 TCCTAACCCTAATCTTAA
1 -CCTAACCCTAAACTTAA
15376 CCCTTAACTT
Statistics
Matches: 100, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.06
16 6 0.06
17 3 0.03
21 53 0.53
22 12 0.12
23 2 0.02
24 2 0.02
25 3 0.03
26 11 0.11
27 2 0.02
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (20 bp):
CCTAACCCTAAACTTAAAAA
Found at i:15434 original size:22 final size:22
Alignment explanation
Indices: 15409--15490 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
15399 TCTAAACCCC
15409 TAAACCTTAAACTTAAAAACCA
1 TAAACCTTAAACTTAAAAACCA
*
15431 TAAA-CTCTAAACCTAAAAAACC-
1 TAAACCT-TAAA-CTTAAAAACCA
* * * *
15453 TAAACCCTAAAC-CATAAATCA
1 TAAACCTTAAACTTAAAAACCA
*
15474 TAACCCTT-AACTTAAAA
1 TAAACCTTAAACTTAAAA
15491 CCCCAAACTC
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
20 8 0.17
21 12 0.26
22 16 0.35
23 10 0.22
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCTTAAACTTAAAAACCA
Found at i:15455 original size:15 final size:17
Alignment explanation
Indices: 15432--15463 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15422 TAAAAACCAT
15432 AAACTCTAAA-CCTAAA
1 AAACTCTAAACCCTAAA
15448 AAAC-CTAAACCCTAAA
1 AAACTCTAAACCCTAAA
15464 CCATAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (17 bp):
AAACTCTAAACCCTAAA
Found at i:15563 original size:14 final size:14
Alignment explanation
Indices: 15425--15568 Score: 56
Period size: 14 Copynumber: 10.7 Consensus size: 14
15415 TTAAACTTAA
*
15425 AAACCATAAACTCT
1 AAACCATAAACCCT
* *
15439 AAACCTAAAAAACCT
1 AAACC-ATAAACCCT
* *
15454 AAACCCTAAACCAT
1 AAACCATAAACCCT
*
15468 AAATCAT-AACCCT
1 AAACCATAAACCCT
* * *
15481 TAA-CTTAAAACCCC
1 AAACCAT-AAACCCT
15495 AAACTC-TAAACCCT
1 AAAC-CATAAACCCT
* *
15509 AAA-CACTAAGCCAT
1 AAACCA-TAAACCCT
* *
15523 AAACTATAAACCTT
1 AAACCATAAACCCT
*
15537 AAA-CATTAA----
1 AAACCATAAACCCT
15546 AAACCATAAACCCT
1 AAACCATAAACCCT
15560 AAACC-TAAA
1 AAACCATAAA
15569 AACCATAACC
Statistics
Matches: 94, Mismatches: 23, Indels: 27
0.65 0.16 0.19
Matches are distributed among these distances:
9 3 0.03
10 5 0.05
12 3 0.03
13 15 0.16
14 54 0.57
15 13 0.14
16 1 0.01
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.19
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:15571 original size:22 final size:22
Alignment explanation
Indices: 15523--15591 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 22
15513 ACTAAGCCAT
* *
15523 AAACTATAAACCTTAAACATTAA
1 AAACCATAAACCCTAAAC-TTAA
*
15546 AAACCATAAACCCTAAACCTAA
1 AAACCATAAACCCTAAACTTAA
*
15568 AAACCAT-AACCCTTAACTTAA
1 AAACCATAAACCCTAAACTTAA
15589 AAA
1 AAA
15592 TACTAACCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 15 0.37
22 10 0.24
23 16 0.39
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACCATAAACCCTAAACTTAA
Found at i:15578 original size:21 final size:21
Alignment explanation
Indices: 15543--15609 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
15533 CCTTAAACAT
15543 TAAAAACCATAAACCCTAAACC
1 TAAAAACCAT-AACCCTAAACC
* *
15565 TAAAAACCATAACCCTTAACT
1 TAAAAACCATAACCCTAAACC
* *
15586 TAAAAA-TACTAACCCTAATCC
1 TAAAAACCA-TAACCCTAAACC
15607 TAA
1 TAA
15610 TCCTTAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.03
21 27 0.71
22 10 0.26
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAAAACCATAACCCTAAACC
Found at i:15615 original size:33 final size:33
Alignment explanation
Indices: 15574--15658 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
15564 CTAAAAACCA
*
15574 TAACCCTTAACTTAAAAATACTAACCCTAATCC
1 TAACCCTTAACTTAAAAACACTAACCCTAATCC
* *
15607 TAATCCTTAACTTAAAAACACTAACCCTCATCC
1 TAACCCTTAACTTAAAAACACTAACCCTAATCC
*
15640 TAACCCTTAACTAAAAAAC
1 TAACCCTTAACTTAAAAAC
15659 CATAAACCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (33 bp):
TAACCCTTAACTTAAAAACACTAACCCTAATCC
Found at i:15692 original size:22 final size:23
Alignment explanation
Indices: 15666--15738 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
15656 AACCATAAAC
15666 CCTAAACTC-TAAACTTTAAAAT
1 CCTAAACTCATAAACTTTAAAAT
* **
15688 TCTAAA-TCATAAACCCT-AAAT
1 CCTAAACTCATAAACTTTAAAAT
* *
15709 CCTAAACCCTTAAACTTTAAAA-
1 CCTAAACTCATAAACTTTAAAAT
15731 CCTTAAAC
1 CC-TAAAC
15739 CCCAAACCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
21 11 0.28
22 20 0.51
23 8 0.21
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAAACTCATAAACTTTAAAAT
Found at i:15708 original size:14 final size:14
Alignment explanation
Indices: 15689--15718 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15679 CTTTAAAATT
15689 CTAAATCATAAACC
1 CTAAATCATAAACC
*
15703 CTAAATCCTAAACC
1 CTAAATCATAAACC
15717 CT
1 CT
15719 TAAACTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAATCATAAACC
Found at i:15738 original size:7 final size:7
Alignment explanation
Indices: 15697--15851 Score: 86
Period size: 7 Copynumber: 21.7 Consensus size: 7
15687 TTCTAAATCA
*
15697 TAAACCC
1 TAAACCT
15704 TAAATCC-
1 TAAA-CCT
15711 TAAACCCT
1 TAAA-CCT
*
15719 TAAACTT
1 TAAACCT
15726 TAAAACCT
1 T-AAACCT
*
15734 TAAACCC
1 TAAACCT
*
15741 CAAACCT
1 TAAACCT
* * *
15748 AAAAACA
1 TAAACCT
15755 T-AACCT
1 TAAACCT
*
15761 CAAAACCT
1 -TAAACCT
15769 TAAACCT
1 TAAACCT
15776 T-AA-CT
1 TAAACCT
*
15781 TAAAAACCA
1 T--AAACCT
15790 TAAACCT
1 TAAACCT
15797 TAAACCT
1 TAAACCT
15804 TAAA-CT
1 TAAACCT
*
15810 ATAAACCA
1 -TAAACCT
*
15818 TAAACCC
1 TAAACCT
*
15825 TAAACAT
1 TAAACCT
*
15832 AAAACCCT
1 TAAA-CCT
15840 TAAACCT
1 TAAACCT
15847 TAAAC
1 TAAAC
15852 ACTAACCATT
Statistics
Matches: 113, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
5 3 0.03
6 7 0.06
7 76 0.67
8 25 0.22
9 2 0.02
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCT
Found at i:15767 original size:35 final size:36
Alignment explanation
Indices: 15726--15845 Score: 104
Period size: 35 Copynumber: 3.4 Consensus size: 36
15716 CCTTAAACTT
15726 TAAAACCTTAAACCCCAAACCTAAAAA-CAT-AACC
1 TAAAACCTTAAACCCCAAACCTAAAAACCATAAACC
** *
15760 TCAAAACCTTAAA-CCTTAACTTAAAAACCATAAACC
1 T-AAAACCTTAAACCCCAAACCTAAAAACCATAAACC
* *** * * *
15796 TTAAACCTTAAACTATAAACC-ATAAACCCTAAACA
1 TAAAACCTTAAACCCCAAACCTAAAAACCATAAACC
15831 TAAAACCCTTAAACC
1 TAAAA-CCTTAAACC
15846 TTAAACACTA
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 12 0.18
35 39 0.57
36 17 0.25
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (36 bp):
TAAAACCTTAAACCCCAAACCTAAAAACCATAAACC
Found at i:15851 original size:29 final size:30
Alignment explanation
Indices: 15784--15880 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 30
15774 CTTAACTTAA
* *
15784 AAACCATAAAC-CTTAAACCTT--AAACTAT
1 AAACCATAAACAC-TAAACATTAAAAACCAT
* * *
15812 AAACCATAAACCCTAAACA-TAAAACCCTT
1 AAACCATAAACACTAAACATTAAAAACCAT
* *
15841 AAACCTTAAACACTAACCATTAAAAACCAT
1 AAACCATAAACACTAAACATTAAAAACCAT
15871 AAACCATAAA
1 AAACCATAAA
15881 ATTAAAAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
27 1 0.02
28 16 0.29
29 21 0.38
30 17 0.31
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.20
Consensus pattern (30 bp):
AAACCATAAACACTAAACATTAAAAACCAT
Found at i:15863 original size:21 final size:21
Alignment explanation
Indices: 15788--15864 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
15778 ACTTAAAAAC
15788 CATAAACC-TTAAACCTTAAA
1 CATAAACCATTAAACCTTAAA
*
15808 CTATAAACCA-TAAACCCTAAA
1 C-ATAAACCATTAAACCTTAAA
*
15829 CATAAAACCCTTAAACCTTAAA
1 CAT-AAACCATTAAACCTTAAA
15851 CACT-AACCATTAAA
1 CA-TAAACCATTAAA
15865 AACCATAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 3 0.06
21 32 0.67
22 12 0.25
23 1 0.02
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
CATAAACCATTAAACCTTAAA
Found at i:15876 original size:7 final size:7
Alignment explanation
Indices: 15784--15880 Score: 65
Period size: 7 Copynumber: 13.4 Consensus size: 7
15774 CTTAACTTAA
15784 AAACCAT
1 AAACCAT
*
15791 AAACCTT
1 AAACCAT
*
15798 AAACCTT
1 AAACCAT
*
15805 AAACTAT
1 AAACCAT
15812 AAACCAT
1 AAACCAT
*
15819 AAACCCT
1 AAACCAT
15826 AAA-CAT
1 AAACCAT
*
15832 AAAACCCTT
1 -AAA-CCAT
*
15841 AAACCTT
1 AAACCAT
15848 AAA-CACT
1 AAACCA-T
15855 -AACCATT
1 AAACCA-T
15862 AAAAACCAT
1 --AAACCAT
15871 AAACCAT
1 AAACCAT
15878 AAA
1 AAA
15881 ATTAAAAAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
6 5 0.07
7 57 0.78
8 3 0.04
9 3 0.04
10 5 0.07
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCAT
Found at i:15960 original size:14 final size:14
Alignment explanation
Indices: 15941--15998 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
15931 CCCTAATCCT
*
15941 AACCCTTAACTTAA
1 AACCCTAAACTTAA
*
15955 AACCCTAAAACCTAA
1 AACCCT-AAACTTAA
*
15970 AACCATAAACTTAA
1 AACCCTAAACTTAA
15984 AACCC-AAACCTTAA
1 AACCCTAAA-CTTAA
15998 A
1 A
15999 CCTAAACCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 3 0.08
14 23 0.62
15 11 0.30
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCTAAACTTAA
Found at i:15969 original size:33 final size:33
Alignment explanation
Indices: 15885--15969 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
15875 CATAAAATTA
*
15885 AAAAACC-TAAACCTAAAAACCATAACCCTTAACTT
1 AAAAACCATAAACCT--AATCC-TAACCCTTAACTT
*
15920 AAAAACCATAACCCTAATCCTAACCCTTAACTT
1 AAAAACCATAAACCTAATCCTAACCCTTAACTT
*
15953 -AAAACCCTAAAACCTAA
1 AAAAACCAT-AAACCTAA
15970 AACCATAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
32 7 0.16
33 20 0.45
34 4 0.09
35 7 0.16
36 6 0.14
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (33 bp):
AAAAACCATAAACCTAATCCTAACCCTTAACTT
Found at i:16086 original size:15 final size:15
Alignment explanation
Indices: 16068--16139 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
16058 CTTTAACTTA
16068 AAAACCATAAACCCT
1 AAAACCATAAACCCT
* *
16083 AAAACCCTAAAACCT
1 AAAACCATAAACCCT
* * *
16098 TAAACCTTAAA-CTT
1 AAAACCATAAACCCT
* *
16112 AAAAACTATAAACTCT
1 -AAAACCATAAACCCT
16128 -AAACCATAAACC
1 AAAACCATAAACC
16140 ATAACCCTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
14 12 0.28
15 30 0.70
16 1 0.02
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAACCATAAACCCT
Found at i:16162 original size:15 final size:16
Alignment explanation
Indices: 16062--16172 Score: 55
Period size: 15 Copynumber: 7.6 Consensus size: 16
16052 CTTAACCTTT
*
16062 AACT-TAAAAACCATA
1 AACTCTAAAAACCCTA
*
16077 AACCCT-AAAACCCTAA
1 AACTCTAAAAACCCT-A
* *
16093 AAC-CT-TAAACCTTA
1 AACTCTAAAAACCCTA
**
16107 AACT-TAAAAACTATA
1 AACTCTAAAAACCCTA
*
16122 AACTCT--AAACCATA
1 AACTCTAAAAACCCTA
* *
16136 AAC-C--ATAACCCTT
1 AACTCTAAAAACCCTA
16149 AACT-TAAAAACCCTA
1 AACTCTAAAAACCCTA
16164 AACTCTAAA
1 AACTCTAAA
16173 TCTTAAACCC
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
13 9 0.12
14 15 0.21
15 39 0.53
16 10 0.14
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
AACTCTAAAAACCCTA
Found at i:16193 original size:14 final size:14
Alignment explanation
Indices: 16120--16207 Score: 65
Period size: 14 Copynumber: 6.3 Consensus size: 14
16110 TTAAAAACTA
*
16120 TAAACTCTAAACCA
1 TAAACTCTAAACCC
16134 TAAAC-C-ATAACCC
1 TAAACTCTA-AACCC
*
16147 TTAACT-TAAAAACCC
1 TAAACTCT--AAACCC
* *
16162 TAAACTCTAAATCT
1 TAAACTCTAAACCC
*
16176 TAAACCCTAAACCC
1 TAAACTCTAAACCC
* *
16190 TAAATTGTAAACCC
1 TAAACTCTAAACCC
16204 TAAA
1 TAAA
16208 TATTAAAAAC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.02
13 9 0.16
14 35 0.61
15 10 0.18
16 2 0.04
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:16194 original size:21 final size:21
Alignment explanation
Indices: 16156--16207 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
16146 CTTAACTTAA
*
16156 AAACCCTAAACTCTAAATCT-T
1 AAACCCTAAACCCTAAAT-TGT
16177 AAACCCTAAACCCTAAATTGT
1 AAACCCTAAACCCTAAATTGT
16198 AAACCCTAAA
1 AAACCCTAAA
16208 TATTAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACCCTAAACCCTAAATTGT
Found at i:16225 original size:7 final size:7
Alignment explanation
Indices: 16156--16207 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
16146 CTTAACTTAA
16156 AAACCCT
1 AAACCCT
*
16163 AAACTCT
1 AAACCCT
* *
16170 AAATCTT
1 AAACCCT
16177 AAACCCT
1 AAACCCT
16184 AAACCCT
1 AAACCCT
***
16191 AAATTGT
1 AAACCCT
16198 AAACCCT
1 AAACCCT
16205 AAA
1 AAA
16208 TATTAAAAAC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (7 bp):
AAACCCT
Found at i:16237 original size:22 final size:22
Alignment explanation
Indices: 16197--16282 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
16187 CCCTAAATTG
*
16197 TAAACCCTAAATATTAAAAACCT
1 TAAACCCTAAA-ATTAAAAACCA
*
16220 TAAACCCTAAAATTAAAAGCCA
1 TAAACCCTAAAATTAAAAACCA
* **
16242 TAAACCATAAACCTAAAAACCA
1 TAAACCCTAAAATTAAAAACCA
* *
16264 T-AACCCTTAACTTAAAAAC
1 TAAACCCTAAAATTAAAAAC
16283 ACTAACTCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.28
22 28 0.52
23 11 0.20
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAAATTAAAAACCA
Found at i:16301 original size:33 final size:33
Alignment explanation
Indices: 16264--16348 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
16254 CTAAAAACCA
16264 TAACCCTTAACTTAAAAACACTAACTC-TAATCC
1 TAACCCTTAACTTAAAAACACTAAC-CATAATCC
*
16297 TAACCCTTAACTTAAAAACACTAACCATAATCT
1 TAACCCTTAACTTAAAAACACTAACCATAATCC
*
16330 TAACCCTTAACTAAAAAAC
1 TAACCCTTAACTTAAAAAC
16349 CTTAAACATT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (33 bp):
TAACCCTTAACTTAAAAACACTAACCATAATCC
Found at i:16355 original size:7 final size:7
Alignment explanation
Indices: 16345--16548 Score: 62
Period size: 7 Copynumber: 28.4 Consensus size: 7
16335 CTTAACTAAA
16345 AAACCTT
1 AAACCTT
*
16352 AAACATT
1 AAACCTT
*
16359 AAACCAT
1 AAACCTT
16366 AAA-CTCT
1 AAACCT-T
*
16373 AAACTCTA
1 AAAC-CTT
*
16381 AAACCAT
1 AAACCTT
* *
16388 AAATCAT
1 AAACCTT
*
16395 AAACCCT
1 AAACCTT
*
16402 AAATCTT
1 AAACCTT
16409 AAACACTT
1 AAAC-CTT
*
16417 AAACTTT
1 AAACCTT
*
16424 AAAACCAT
1 -AAACCTT
**
16432 AAACCCC
1 AAACCTT
16439 AAA-CTT
1 AAACCTT
* *
16445 AAAAAACAT
1 --AAACCTT
*
16454 -AGCCTCT
1 AAACCT-T
16461 AAACCTT
1 AAACCTT
*
16468 AAACCCT
1 AAACCTT
16475 -AA-CTT
1 AAACCTT
*
16480 AAAAACCCT
1 --AAACCTT
16489 AAACAC-T
1 AAAC-CTT
*
16496 AAACATT
1 AAACCTT
16503 AAACCTT
1 AAACCTT
*
16510 AAACCTAA
1 AAACCT-T
*
16518 AAATCTT
1 AAACCTT
16525 AAACCTT
1 AAACCTT
16532 AAACAC-T
1 AAAC-CTT
*
16539 AAACATT
1 AAACCTT
16546 AAA
1 AAA
16549 AACCCTAAAC
Statistics
Matches: 143, Mismatches: 35, Indels: 38
0.66 0.16 0.18
Matches are distributed among these distances:
5 2 0.01
6 6 0.04
7 97 0.68
8 32 0.22
9 6 0.04
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCTT
Found at i:16387 original size:22 final size:23
Alignment explanation
Indices: 16359--16435 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 23
16349 CTTAAACATT
16359 AAACCATAAACTC-TAAACTCTA
1 AAACCATAAACTCATAAACTCTA
*
16381 AAACCATAAA-TCATAAACCCT-
1 AAACCATAAACTCATAAACTCTA
* * * * *
16402 AAATCTTAAACACTTAAACTTTA
1 AAACCATAAACTCATAAACTCTA
16425 AAACCATAAAC
1 AAACCATAAAC
16436 CCCAAACTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 10 0.23
22 24 0.56
23 9 0.21
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (23 bp):
AAACCATAAACTCATAAACTCTA
Found at i:16528 original size:22 final size:21
Alignment explanation
Indices: 16482--16564 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
16472 CCTAACTTAA
* *
16482 AAACCCTAAACACTAAACA-TT
1 AAACCTTAAAC-CTAAAAATTT
16503 AAACCTTAAACCTAAAAATCTT
1 AAACCTTAAACCTAAAAAT-TT
* *
16525 AAACCTTAAACACTAAACATTAA
1 AAACCTTAAAC-CTAAAAATT-T
*
16548 AAACCCTAAACCTAAAA
1 AAACCTTAAACCTAAAA
16565 CACATAACCC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.12
21 10 0.19
22 19 0.37
23 17 0.33
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCTTAAACCTAAAAATTT
Found at i:16612 original size:33 final size:33
Alignment explanation
Indices: 16540--16672 Score: 149
Period size: 33 Copynumber: 3.9 Consensus size: 33
16530 TTAAACACTA
* *
16540 AACATTAAAAACCCTAAACCTAAAACACATAACCCTT
1 AACA-TAAAAACCCTAATCCT-AATC-C-TAACCCTT
*
16577 AACATAAAAACCCTAATCCTAATCCTAACCGTT
1 AACATAAAAACCCTAATCCTAATCCTAACCCTT
* **
16610 AACTTAAAAACCCTAATCCTAATTTTAACCCTT
1 AACATAAAAACCCTAATCCTAATCCTAACCCTT
* * *
16643 AACTTAAAAACACTAACCCTAATCCTAACC
1 AACATAAAAACCCTAATCCTAATCCTAACC
16673 TTTACTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
33 62 0.73
34 1 0.01
35 3 0.04
36 15 0.18
37 4 0.05
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (33 bp):
AACATAAAAACCCTAATCCTAATCCTAACCCTT
Found at i:16683 original size:33 final size:32
Alignment explanation
Indices: 16573--16687 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 32
16563 AACACATAAC
* *
16573 CCTTAACATAAAAACCCTAATCCTAATCCTAA
1 CCTTAACTTAAAAACACTAATCCTAATCCTAA
* **
16605 CCGTTAACTTAAAAACCCTAATCCTAATTTTAA
1 CC-TTAACTTAAAAACACTAATCCTAATCCTAA
*
16638 CCCTTAACTTAAAAACACTAACCCTAATCCTAA
1 -CCTTAACTTAAAAACACTAATCCTAATCCTAA
*
16671 CCTTTACTTTAAAAACA
1 CCTTAAC-TTAAAAACA
16688 TTAAATCATA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.11
33 62 0.86
34 2 0.03
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.29
Consensus pattern (32 bp):
CCTTAACTTAAAAACACTAATCCTAATCCTAA
Found at i:16766 original size:22 final size:23
Alignment explanation
Indices: 16741--16786 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
16731 TTTAGATTTT
* *
16741 AAAACCTAAACCCTAAAC-CTAA
1 AAAAACTAAACACTAAACACTAA
*
16763 AAAAATTAAACACTAAACACTAA
1 AAAAACTAAACACTAAACACTAA
16786 A
1 A
16787 CCCTATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAACTAAACACTAAACACTAA
Found at i:16771 original size:29 final size:29
Alignment explanation
Indices: 16739--16823 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
16729 CCTTTAGATT
16739 TTAAAACCTAAACCCTAAACCTAAAAAAA
1 TTAAAACCTAAACCCTAAACCTAAAAAAA
* *
16768 TT-AAACACTAAACACTAAACCCT---ATAA
1 TTAAAAC-CTAAACCCTAAA-CCTAAAAAAA
16795 TTAAAAACCATAAACCCTAAA-CTAAAAAA
1 TT-AAAACC-TAAACCCTAAACCTAAAAAA
16824 CCATAACCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
27 7 0.16
28 5 0.11
29 27 0.61
30 5 0.11
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.19
Consensus pattern (29 bp):
TTAAAACCTAAACCCTAAACCTAAAAAAA
Found at i:16808 original size:22 final size:21
Alignment explanation
Indices: 16783--16845 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
16773 CACTAAACAC
16783 TAAACCCTATAATTAAAAACCA
1 TAAACCCTA-AATTAAAAACCA
*
16805 TAAACCCTAAACTAAAAAACCA
1 TAAACCCTAAA-TTAAAAACCA
*
16827 T-AACCACTAACTTAAAAAC
1 TAAACC-CTAAATTAAAAAC
16846 ACTAACCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCCTAAATTAAAAACCA
Found at i:16864 original size:33 final size:34
Alignment explanation
Indices: 16827--16890 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
16817 TAAAAAACCA
16827 TAACCACTAACTTAAAAA-CACT-AACCTTAATCC
1 TAACCACTAACTTAAAAATC-CTAAACCTTAATCC
**
16860 TAACCTTTAACTTAAAAATCCTAAACCTTAA
1 TAACCACTAACTTAAAAATCCTAAACCTTAA
16891 ACTCTAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (34 bp):
TAACCACTAACTTAAAAATCCTAAACCTTAATCC
Found at i:16880 original size:21 final size:23
Alignment explanation
Indices: 16855--16912 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
16845 CACTAACCTT
*
16855 AATCCT-AACCTTTAACT-TAAA
1 AATCCTAAACCTTAAACTCTAAA
16876 AATCCTAAACCTTAAACTCT--A
1 AATCCTAAACCTTAAACTCTAAA
*
16897 AATCCTAAACCCTAAA
1 AATCCTAAACCTTAAA
16913 ATCCTAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 22 0.67
22 10 0.30
23 1 0.03
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (23 bp):
AATCCTAAACCTTAAACTCTAAA
Found at i:16917 original size:36 final size:35
Alignment explanation
Indices: 16868--17007 Score: 124
Period size: 36 Copynumber: 3.9 Consensus size: 35
16858 CCTAACCTTT
*
16868 AACTTAAAAATCC-TAAACCTTAAACTCTAAATCCTA
1 AACTTTAAAA-CCATAAACCTTAAAC-CTAAATCCTA
** * *
16904 AACCCTAAAATCC-TAAACTTTTAAAACCCTAAACCCTA
1 AACTTTAAAA-CCATAAAC-CTT-AAA-CCTAAATCCTA
*
16942 AACTTTAAAACCATAAACC-TAAACACTAAATCTTTA
1 AACTTTAAAACCATAAACCTTAAAC-CTAAATC-CTA
*
16978 AACTTTAAAACCATAAACCCTAAACCTAAA
1 AACTTTAAAACCATAAACCTTAAACCTAAA
17008 AACCCTAAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
34 1 0.01
35 9 0.10
36 42 0.48
37 9 0.10
38 25 0.29
39 1 0.01
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (35 bp):
AACTTTAAAACCATAAACCTTAAACCTAAATCCTA
Found at i:16951 original size:22 final size:22
Alignment explanation
Indices: 16903--16965 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
16893 TCTAAATCCT
16903 AAACCCTAAAATCCTAAACTTTTA
1 AAACCCT-AAA-CCTAAACTTTTA
16927 AAACCCTAAACCCTAAAC-TTTA
1 AAACCCTAAA-CCTAAACTTTTA
*
16949 AAACCATAAACCTAAAC
1 AAACCCTAAACCTAAAC
16966 ACTAAATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 7 0.19
22 13 0.35
23 10 0.27
24 7 0.19
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (22 bp):
AAACCCTAAACCTAAACTTTTA
Found at i:16952 original size:15 final size:14
Alignment explanation
Indices: 16879--17032 Score: 89
Period size: 15 Copynumber: 10.6 Consensus size: 14
16869 ACTTAAAAAT
16879 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
*
16893 TCTAAATCC-TAAAC
1 CCTAAA-CCTTAAAC
16907 CCTAAAATCC-TAAAC
1 CCT-AAA-CCTTAAAC
** *
16922 TTTTAAAACCCTAAAC
1 -CCT-AAACCTTAAAC
*
16938 CCTAAACTTTAAAAC
1 CCTAAACCTT-AAAC
*
16953 CATAAACC-TAAAC
1 CCTAAACCTTAAAC
* *
16966 ACTAAATCTTTAAAC
1 CCTAAA-CCTTAAAC
** *
16981 TTTAAAACCATAAAC
1 CCT-AAACCTTAAAC
*
16996 CCTAAACCTAAAAAC
1 CCTAAACCT-TAAAC
*
17011 CCTAAACCATAAAC
1 CCTAAACCTTAAAC
17025 CCTAAACC
1 CCTAAACC
17033 CTAATTCTGA
Statistics
Matches: 108, Mismatches: 23, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
13 8 0.07
14 36 0.33
15 51 0.47
16 13 0.12
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:16971 original size:21 final size:22
Alignment explanation
Indices: 16925--17036 Score: 61
Period size: 22 Copynumber: 5.1 Consensus size: 22
16915 CCTAAACTTT
* **
16925 TAAAACCCTAAACCCTAAACTT
1 TAAAACCATAAACCCTAAACAC
16947 TAAAACCATAAA-CCTAAACAC
1 TAAAACCATAAACCCTAAACAC
* ** **
16968 TAAATCTTTAAACTTTAAA-AC
1 TAAAACCATAAACCCTAAACAC
* * *
16989 CATAAACCCTAAA-CCTAAAAACCC
1 TA-AAACCATAAACCCT--AAACAC
*
17013 T-AAACCATAAACCCTAAACCC
1 TAAAACCATAAACCCTAAACAC
17034 TAA
1 TAA
17037 TTCTGACCCT
Statistics
Matches: 66, Mismatches: 17, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
21 27 0.41
22 32 0.48
23 6 0.09
24 1 0.02
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAACCATAAACCCTAAACAC
Found at i:17001 original size:22 final size:22
Alignment explanation
Indices: 16984--17030 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16974 TTTAAACTTT
*
16984 AAAACCATAAACCCTAAACCTA
1 AAAACCATAAACCATAAACCTA
*
17006 AAAACCCTAAACCATAAACCCTA
1 AAAACCATAAACCATAAA-CCTA
17029 AA
1 AA
17031 CCCTAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAACCATAAACCATAAACCTA
Found at i:17017 original size:7 final size:7
Alignment explanation
Indices: 16879--17036 Score: 86
Period size: 7 Copynumber: 21.7 Consensus size: 7
16869 ACTTAAAAAT
16879 CCTAAAC
1 CCTAAAC
*
16886 CTTAAAC
1 CCTAAAC
* *
16893 TCTAAAT
1 CCTAAAC
16900 CCTAAAC
1 CCTAAAC
*
16907 CCTAAAAT
1 CCT-AAAC
16915 CCTAAAC
1 CCTAAAC
**
16922 TTTTAAAAC
1 -CCT-AAAC
16931 CCTAAAC
1 CCTAAAC
16938 CCTAAAC
1 CCTAAAC
**
16945 TTTAAAAC
1 CCT-AAAC
*
16953 CATAAA-
1 CCTAAAC
16959 CCTAAAC
1 CCTAAAC
*
16966 ACTAAATC
1 CCTAAA-C
**
16974 TTTAAAC
1 CCTAAAC
**
16981 TTTAAAAC
1 CCT-AAAC
*
16989 CATAAAC
1 CCTAAAC
16996 CCTAAA-
1 CCTAAAC
17002 CCTAAAAAC
1 CCT--AAAC
17011 CCTAAAC
1 CCTAAAC
*
17018 CATAAAC
1 CCTAAAC
17025 CCTAAAC
1 CCTAAAC
17032 CCTAA
1 CCTAA
17037 TTCTGACCCT
Statistics
Matches: 116, Mismatches: 25, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
6 8 0.07
7 75 0.65
8 26 0.22
9 7 0.06
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:17017 original size:29 final size:29
Alignment explanation
Indices: 16927--17032 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
16917 TAAACTTTTA
* *
16927 AAACCCTAAACCCTAAACTTTAAAACCAT
1 AAACCATAAACCCTAAACCTTAAAACCAT
* * * **
16956 AAACC-TAAACACTAAATCTTTAAACTTT
1 AAACCATAAACCCTAAACCTTAAAACCAT
* *
16984 AAAACCATAAACCCTAAACCTAAAAACCCT
1 -AAACCATAAACCCTAAACCTTAAAACCAT
17014 AAACCATAAACCCTAAACC
1 AAACCATAAACCCTAAACC
17033 CTAATTCTGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 17 0.27
29 29 0.46
30 17 0.27
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (29 bp):
AAACCATAAACCCTAAACCTTAAAACCAT
Found at i:17099 original size:33 final size:33
Alignment explanation
Indices: 17025--17102 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
17015 AACCATAAAC
* *
17025 CCTAAACCCTAATTCTGACCCTTAACTTAAAAA
1 CCTAAACCCTAATTCTAACCATTAACTTAAAAA
17058 TCCT-AACCCTAA-TCATAACCATTAACTT-AAAA
1 -CCTAAACCCTAATTC-TAACCATTAACTTAAAAA
17090 CCTTAAACCCTAA
1 CC-TAAACCCTAA
17103 AATATAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 2 0.05
32 7 0.18
33 27 0.69
34 3 0.08
ACGTcount: A:0.41, C:0.31, G:0.01, T:0.27
Consensus pattern (33 bp):
CCTAAACCCTAATTCTAACCATTAACTTAAAAA
Found at i:17164 original size:15 final size:17
Alignment explanation
Indices: 17138--17169 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17128 TAAAAACCAC
17138 AAACCTTAAA-CCTAAA
1 AAACCTTAAACCCTAAA
17154 AAACC-TAAACCCTAAA
1 AAACCTTAAACCCTAAA
17170 CCATAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (17 bp):
AAACCTTAAACCCTAAA
Found at i:17210 original size:7 final size:7
Alignment explanation
Indices: 17200--17231 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
17190 CTTAAAACCC
17200 CTAAACA
1 CTAAACA
17207 CTAAACA
1 CTAAACA
17214 CTAAACA
1 CTAAACA
17221 CTAAAC-
1 CTAAACA
17227 CTAAA
1 CTAAA
17232 AACCATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACA
Found at i:17234 original size:22 final size:22
Alignment explanation
Indices: 17222--17277 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
17212 CACTAAACAC
17222 TAAACCTAAAAACCATAAACCA
1 TAAACCTAAAAACCATAAACCA
* ** *
17244 TAAACCTTAAATATTAAAAACCA
1 TAAACC-TAAAAACCATAAACCA
17267 TAAACCCTAAA
1 TAAA-CCTAAA
17278 CCTAAAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.21
23 20 0.71
24 2 0.07
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAACCTAAAAACCATAAACCA
Found at i:17286 original size:22 final size:22
Alignment explanation
Indices: 17086--17291 Score: 99
Period size: 22 Copynumber: 9.5 Consensus size: 22
17076 CCATTAACTT
* *
17086 AAAACCTTAAACCCTAAA-ATA
1 AAAACCATAAACCCTAAACCTA
** *
17107 TAAAACTC-TAAACTTTAAACTTA
1 -AAAAC-CATAAACCCTAAACCTA
* *
17130 AAAACCACAAACCTTAAACCTAA
1 AAAACCATAAACCCTAAACCT-A
17153 AAAACC-TAAACCCTAAACC-A
1 AAAACCATAAACCCTAAACCTA
* * * *
17173 TAAATCAT-AACTC-ATAACTTA
1 AAAACCATAAACCCTA-AACCTA
* * *
17194 AAACCCCTAAACACTAAACACTA
1 AAAACCATAAACCCTAAAC-CTA
*
17217 AACA-C-TAAA-CCTAAAAACC-A
1 AAAACCATAAACCCT--AAACCTA
* * **
17237 TAAACCATAAACCTTAAATATTA
1 AAAACCATAAACCCTAAA-CCTA
17260 AAAACCATAAACCCTAAACCTA
1 AAAACCATAAACCCTAAACCTA
17282 AAAACCATAA
1 AAAACCATAA
17292 CCGTTGACTT
Statistics
Matches: 137, Mismatches: 30, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
19 1 0.01
20 17 0.12
21 16 0.12
22 69 0.50
23 34 0.25
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAACCATAAACCCTAAACCTA
Found at i:17306 original size:21 final size:22
Alignment explanation
Indices: 17238--17291 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
17228 TAAAAACCAT
* *
17238 AAACCATAAACCTTAAATATTAA
1 AAACCATAAACCCTAAA-CTTAA
*
17261 AAACCATAAACCCTAAACCTAA
1 AAACCATAAACCCTAAACTTAA
17283 AAACCATAA
1 AAACCATAA
17292 CCGTTGACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (22 bp):
AAACCATAAACCCTAAACTTAA
Found at i:17391 original size:43 final size:43
Alignment explanation
Indices: 17343--17569 Score: 142
Period size: 43 Copynumber: 5.1 Consensus size: 43
17333 TTAAAAACAC
* *
17343 TAAACCTTAAACTCTAAACTCTAAACCTTAAAACCATAAATCT
1 TAAACCTTAAACTCTAAACTCTAAACCTTAAAACCCTAAACCT
* * * * *
17386 TAAACCCTAAA-TCTTAAACTATTAAACTTTAAAATCCTAAACCC
1 TAAACCTTAAACTC-TAAACT-CTAAACCTTAAAACCCTAAACCT
*
17430 TAAACCTAAAAATATAACTACTAAACCCTAAACCTT-AAACCCT-AA-CT
1 TAAACCT-----TA-AACT-CTAAACTCTAAACCTTAAAACCCTAAACCT
* * *
17477 TAAAAACCATAAACTCTAAACTCCAAATAC-T-AAACCCTAAACCT
1 T--AAACCTTAAACTCTAAACTCTAAA-CCTTAAAACCCTAAACCT
* * * * *
17521 AAAAACCTTAAACTTTAAACACTAAACATTAAAAACCCTAAACCA
1 -TAAACCTTAAACTCTAAACTCTAAACCTT-AAAACCCTAAACCT
17566 TAAA
1 TAAA
17570 ATTAAAAACC
Statistics
Matches: 139, Mismatches: 26, Indels: 37
0.69 0.13 0.18
Matches are distributed among these distances:
42 20 0.14
43 44 0.32
44 30 0.22
45 12 0.09
47 2 0.01
48 2 0.01
49 13 0.09
50 9 0.06
51 6 0.04
52 1 0.01
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (43 bp):
TAAACCTTAAACTCTAAACTCTAAACCTTAAAACCCTAAACCT
Found at i:17470 original size:14 final size:14
Alignment explanation
Indices: 17451--17569 Score: 59
Period size: 14 Copynumber: 8.3 Consensus size: 14
17441 ATATAACTAC
17451 TAAACCCTAAACCT
1 TAAACCCTAAACCT
17465 TAAACCCT-AA-CT
1 TAAACCCTAAACCT
*
17477 TAAAAACCATAAA-CT
1 T--AAACCCTAAACCT
*
17492 CTAAACTCC-AAATAC-
1 -TAAAC-CCTAAA-CCT
17507 TAAACCCTAAACCT
1 TAAACCCTAAACCT
* * *
17521 AAAAACCTTAAACTT
1 -TAAACCCTAAACCT
* *
17536 TAAACACTAAACAT
1 TAAACCCTAAACCT
*
17550 TAAAAACCCTAAACCA
1 T--AAACCCTAAACCT
17566 TAAA
1 TAAA
17570 ATTAAAAACC
Statistics
Matches: 80, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
12 3 0.04
13 5 0.06
14 43 0.54
15 16 0.20
16 13 0.16
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:17474 original size:21 final size:21
Alignment explanation
Indices: 17342--17569 Score: 61
Period size: 21 Copynumber: 10.2 Consensus size: 21
17332 CTTAAAAACA
* *
17342 CTAAACCTTAAACTCTAAACT
1 CTAAACCTTAAACCCTAAACC
* *
17363 CTAAACCTTAAAACCATAAATC
1 CTAAACCTT-AAACCCTAAACC
* * * * *
17385 TTAAACCCTAAATCTTAAACTA
1 CTAAACCTTAAACCCTAAAC-C
* * *
17407 TTAAACTTTAAAATCCTAAACC
1 CTAAACCTT-AAACCCTAAACC
*
17429 CTAAACCTAAAAATATAACTACTAAACC
1 CTAAACCT-----TA-AAC-CCTAAACC
17457 CTAAACCTTAAACCCT-AA-C
1 CTAAACCTTAAACCCTAAACC
* * *
17476 TTAAAAACCATAAACTCTAAACTC
1 CT--AAACCTTAAACCCTAAAC-C
*
17500 C-AAATAC-TAAACCCTAAA-C
1 CTAAA-CCTTAAACCCTAAACC
** *
17519 CTAAAAACCTTAAACTTTAAACA
1 CT--AAACCTTAAACCCTAAACC
*
17542 CTAAACATTAAAAACCCTAAACC
1 CTAAACCTT--AAACCCTAAACC
*
17565 ATAAA
1 CTAAA
17570 ATTAAAAACC
Statistics
Matches: 150, Mismatches: 34, Indels: 44
0.66 0.15 0.19
Matches are distributed among these distances:
19 4 0.03
20 2 0.01
21 51 0.34
22 46 0.31
23 27 0.18
24 1 0.01
26 1 0.01
27 3 0.02
28 15 0.10
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAAACCTTAAACCCTAAACC
Found at i:17592 original size:22 final size:22
Alignment explanation
Indices: 17508--17592 Score: 77
Period size: 22 Copynumber: 3.8 Consensus size: 22
17498 TCCAAATACT
17508 AAACCCTAAACCTAAAAACCTT--
1 AAACCCTAAACCTAAAAA--TTAA
** *
17530 AAACTTTAAACACTAAACATTAA
1 AAACCCTAAAC-CTAAAAATTAA
17553 AAACCCTAAACC-ATAAAATTAA
1 AAACCCTAAACCTA-AAAATTAA
*
17575 AAACCTTAAACCTAAAAA
1 AAACCCTAAACCTAAAAA
17593 CTATAACCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.06
22 32 0.63
23 16 0.31
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACCCTAAACCTAAAAATTAA
Found at i:17603 original size:22 final size:22
Alignment explanation
Indices: 17508--17605 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
17498 TCCAAATACT
*
17508 AAACCC-TAAACCTAAAAACCTT
1 AAACCCTTAAACCTAAAAA-CTA
* * *
17530 AAA-CTTTAAACACTAAACATTAA
1 AAACCCTTAAAC-CTAAAAACT-A
*
17553 AAACCC-TAAACC-ATAAAATTA
1 AAACCCTTAAACCTA-AAAACTA
*
17574 AAAACCTTAAACCTAAAAACTA
1 AAACCCTTAAACCTAAAAACTA
*
17596 TAACCCTTAA
1 AAACCCTTAA
17606 CTTAAAACCA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
21 8 0.14
22 35 0.59
23 15 0.25
24 1 0.02
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.21
Consensus pattern (22 bp):
AAACCCTTAAACCTAAAAACTA
Found at i:17633 original size:32 final size:32
Alignment explanation
Indices: 17596--17690 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 32
17586 CTAAAAACTA
17596 TAACCCTTAACTTAAAACCATAATCTTAATCC
1 TAACCCTTAACTTAAAACCATAATCTTAATCC
* * * *
17628 TAACCCTTAACTTAAAATCTATAACCATAATCT
1 TAACCCTTAACTTAAAA-CCATAATCTTAATCC
* *
17661 TAA-CCTTAAACTTTAAACCCTAAATCTTAA
1 TAACCCTT-AACTTAAAACCAT-AATCTTAA
17691 ACATTTGAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
32 23 0.45
33 28 0.55
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (32 bp):
TAACCCTTAACTTAAAACCATAATCTTAATCC
Found at i:17843 original size:33 final size:33
Alignment explanation
Indices: 17805--17895 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 33
17795 ACCATACCCC
*
17805 TTAACTTAAAAAATCTAATCC-TAATCCTAACCA
1 TTAACTTAAAAAACCTAA-CCTTAATCCTAACCA
* *
17838 TTAACTTAAAAACCCTAACCTTAATCCTAACCC
1 TTAACTTAAAAAACCTAACCTTAATCCTAACCA
17871 TTAACTT-AAAAACCTTAAACCTTAA
1 TTAACTTAAAAAACC-T-AACCTTAA
17896 ACTCTAAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 8 0.16
33 35 0.69
34 8 0.16
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (33 bp):
TTAACTTAAAAAACCTAACCTTAATCCTAACCA
Found at i:17878 original size:18 final size:18
Alignment explanation
Indices: 17826--17879 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
17816 AATCTAATCC
*
17826 TAATCCTAACCATTAACT
1 TAATCCTAACCCTTAACT
*
17844 TAA---AAACCC-TAACCT
1 TAATCCTAACCCTTAA-CT
17859 TAATCCTAACCCTTAACT
1 TAATCCTAACCCTTAACT
17877 TAA
1 TAA
17880 AAACCTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
18 13 0.46
19 3 0.11
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATCCTAACCCTTAACT
Found at i:17897 original size:14 final size:14
Alignment explanation
Indices: 17880--18041 Score: 88
Period size: 14 Copynumber: 11.6 Consensus size: 14
17870 CTTAACTTAA
*
17880 AAACCTTAAACCTT
1 AAACCTTAAACCCT
*
17894 AAA-CTCTAAACACT
1 AAACCT-TAAACCCT
* *
17908 AAACTCTAAAACACT
1 AAAC-CTTAAACCCT
* *
17923 AAGCATTAAACCCT
1 AAACCTTAAACCCT
*
17937 AAATCC-TAAACCTTT
1 AAA-CCTTAAACC-CT
*
17952 AAACTTTAAACCCCT
1 AAACCTTAAA-CCCT
* *
17967 AAACCCTAAA-CTT
1 AAACCTTAAACCCT
17980 AAA----AAACCCT
1 AAACCTTAAACCCT
17990 AAACAC-TAAACCCT
1 AAAC-CTTAAACCCT
* *
18004 AAGCCTTAAGCCCT
1 AAACCTTAAACCCT
*
18018 AAACATTAAACCCCT
1 AAACCTTAAA-CCCT
18033 AAACCTTAA
1 AAACCTTAA
18042 CTTAAAACCA
Statistics
Matches: 112, Mismatches: 22, Indels: 27
0.70 0.14 0.17
Matches are distributed among these distances:
9 3 0.03
10 5 0.04
13 8 0.07
14 52 0.46
15 40 0.36
16 4 0.04
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:17932 original size:15 final size:15
Alignment explanation
Indices: 17893--17924 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17883 CCTTAAACCT
17893 TAAACTCT-AAACAC
1 TAAACTCTAAAACAC
17907 TAAACTCTAAAACAC
1 TAAACTCTAAAACAC
17922 TAA
1 TAA
17925 GCATTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACTCTAAAACAC
Found at i:18106 original size:21 final size:20
Alignment explanation
Indices: 18082--18125 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
18072 ATTAACTTAA
*
18082 AAACCCTAAAATTTAAACCCT
1 AAACCCTAAAATCTAAA-CCT
*
18103 AAACCCTAAACTCTAAACCT
1 AAACCCTAAAATCTAAACCT
18123 AAA
1 AAA
18126 AACTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (20 bp):
AAACCCTAAAATCTAAACCT
Found at i:18156 original size:15 final size:15
Alignment explanation
Indices: 18103--18157 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
18093 TTTAAACCCT
*
18103 AAACCCTAAACTCT-
1 AAACCCTAAACTTTA
18117 AAA-CCTAAAAACTTTA
1 AAACCCT--AAACTTTA
**
18133 AAATACTAAACTTTA
1 AAACCCTAAACTTTA
18148 AAACCCTAAA
1 AAACCCTAAA
18158 ACCCTAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 22 0.67
16 3 0.09
17 2 0.06
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (15 bp):
AAACCCTAAACTTTA
Found at i:18189 original size:22 final size:22
Alignment explanation
Indices: 18155--18222 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
18145 TTAAAACCCT
* * *
18155 AAAACCCTAAACCTTAAAATTA
1 AAAACCATTAACCTTAAACTTA
* *
18177 AAAACCATTAACCCTAAACCTA
1 AAAACCATTAACCTTAAACTTA
* *
18199 AAAACTA-TAACCTTTAACTTA
1 AAAACCATTAACCTTAAACTTA
18220 AAA
1 AAA
18223 CCCCAAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAACCATTAACCTTAAACTTA
Found at i:18264 original size:28 final size:27
Alignment explanation
Indices: 18228--18346 Score: 69
Period size: 35 Copynumber: 3.9 Consensus size: 27
18218 TAAAACCCCA
*
18228 AACTCTAAACCTAAAAACCTTAAACCATTT
1 AACT-TAAACCT-AAAACCCTAAACC-TTT
*
18258 -ACTTAAAACCTCAAACCCTAAACCTTT
1 AACTT-AAACCTAAAACCCTAAACCTTT
18285 AACTTAAAAACCCTAACCCTATACCCTAAACCTTT
1 AACTT--AAA-CCTAA----A-ACCCTAAACCTTT
*
18320 AATTTTAAAACCTAAAAACCCTAAACC
1 AA-CTT-AAACCT-AAAACCCTAAACC
18347 ATAAAACCTA
Statistics
Matches: 74, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
27 3 0.04
28 16 0.22
29 13 0.18
30 14 0.19
31 1 0.01
34 4 0.05
35 21 0.28
36 2 0.03
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (27 bp):
AACTTAAACCTAAAACCCTAAACCTTT
Found at i:18296 original size:43 final size:43
Alignment explanation
Indices: 18155--18282 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
18145 TTAAAACCCT
* * * *
18155 AAAACCCTAAACCTTAAAATTAAAA-ACCATTAACCCTAAACCTA
1 AAAACCTTAAACCTTTAACTTAAAACCCCA--AACCCTAAACCTA
*
18199 AAAA-C-TATAACCTTTAACTTAAAACCCCAAACTCTAAACCTA
1 AAAACCTTA-AACCTTTAACTTAAAACCCCAAACCCTAAACCTA
*
18241 AAAACCTTAAACCATTT-ACTTAAAACCTCAAACCCTAAACCT
1 AAAACCTTAAACC-TTTAACTTAAAACCCCAAACCCTAAACCT
18283 TTAACTTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 18 0.25
43 43 0.59
44 12 0.16
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (43 bp):
AAAACCTTAAACCTTTAACTTAAAACCCCAAACCCTAAACCTA
Found at i:18314 original size:22 final size:22
Alignment explanation
Indices: 18270--18358 Score: 56
Period size: 22 Copynumber: 4.0 Consensus size: 22
18260 TTAAAACCTC
* *
18270 AAACCCTAAACCTTTAACTTAA
1 AAACCCTAAACCTATAACCTAA
* *
18292 AAACCCTAACCCTATACCCT--
1 AAACCCTAAACCTATAACCTAA
* *** *
18312 AAACCTTTAATTTTAAAACCTAA
1 AAACC-CTAAACCTATAACCTAA
*
18335 AAACCCTAAACCATAAAACCTAA
1 AAACCCTAAACC-TATAACCTAA
18358 A
1 A
18359 TTAACCATTA
Statistics
Matches: 49, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
20 5 0.10
21 9 0.18
22 19 0.39
23 16 0.33
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCTATAACCTAA
Found at i:22144 original size:125 final size:125
Alignment explanation
Indices: 21462--22147 Score: 923
Period size: 125 Copynumber: 5.5 Consensus size: 125
21452 CATGCTACTA
* * *
21462 TAGCAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* * * *
21527 CG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTAATTCTACCAGGACCAACTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATT-ATTTTTCCAGGACCAACTG
* * * *
21587 TAGCAAAAGCGCGTCCACGAGGGCGTGATTTCAGAAATTCTTCTCA-AATAGCATCCTACTTAAA
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTGAA
** * * *
21651 GCGTTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATAATTTTTTTCAGGACCTACTG
65 GCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTA-TTTTTCCAGGACCAACTG
* * * * *
21713 TAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCTTGGTAGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* *
21778 CG-ATTTTATACTATTTGCTCAGAAATGTCAACTCAAAATTATTTCTTCCAGGA-CAACTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAGGACCAACTG
* * *
21837 TAGCAAAAGCGCGTCCAGGAGGGCGCGATTTCACAAATTCTTCGCATATAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
*
21902 CGTTTTTTATACTATTTGCTCAGAAATGTCAACTCAAAATTATTTCTTCCAGGA-CAACTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAGGACCAACTG
* * *
21962 TAGCAAAAGCGCGTCCAGGAGGGCGCGATTTCACAAATTCTTCGCATATAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* *
22027 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCGACTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
* * * * * * * * *
22087 TAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATCCTTCTGATAAATCGTCCTGCTT
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
22148 TGATTTTATC
Statistics
Matches: 500, Mismatches: 54, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
124 76 0.15
125 318 0.64
126 104 0.21
127 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
Found at i:22258 original size:21 final size:21
Alignment explanation
Indices: 22209--22258 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
22199 AATTTTAATT
22209 AATTTAATTACGAAACCCTAA
1 AATTTAATTACGAAACCCTAA
* * * *
22230 TATCTAATTCCTAAACCCTAA
1 AATTTAATTACGAAACCCTAA
22251 AATTTAAT
1 AATTTAAT
22259 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (21 bp):
AATTTAATTACGAAACCCTAA
Found at i:23023 original size:29 final size:30
Alignment explanation
Indices: 22989--23050 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
22979 GTTTCACGTG
*
22989 TATAATTTTAC-CAAATTAAAATTCATGTA
1 TATAATTGTACACAAATTAAAATTCATGTA
*
23018 TATAATTGTACATTAAATTAAAATTCATGTA
1 TATAATTGTACA-CAAATTAAAATTCATGTA
23049 TA
1 TA
23051 ATTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.34
31 19 0.66
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
TATAATTGTACACAAATTAAAATTCATGTA
Found at i:23410 original size:18 final size:16
Alignment explanation
Indices: 23377--23414 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
23367 TCCGTCCGTA
23377 TTAATTTTTTTAATTT
1 TTAATTTTTTTAATTT
23393 TTAATTTTTGTATAATTT
1 TTAATTTTT-T-TAATTT
23411 TTAA
1 TTAA
23415 ATATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTAATTTTTTTAATTT
Found at i:23581 original size:18 final size:18
Alignment explanation
Indices: 23560--23611 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
23550 TAATAACAAA
*
23560 ATTAACAATAAAATAAGT
1 ATTAACAATAAAATAAAT
**
23578 ATTATACAAT-ATCTAAAT
1 ATTA-ACAATAAAATAAAT
*
23596 ATTAACAACAAAATAA
1 ATTAACAATAAAATAA
23612 TAGCAGTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (18 bp):
ATTAACAATAAAATAAAT
Found at i:23990 original size:27 final size:28
Alignment explanation
Indices: 23943--23999 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
23933 AAATAACTTT
* *
23943 AATGAAATATTAATACCAAAAA-TATTA
1 AATGAAATATTAAAAACAAAAATTATTA
*
23970 AATGAAATATTAAAAATAAAAATTATTA
1 AATGAAATATTAAAAACAAAAATTATTA
23998 AA
1 AA
24000 ATCCAGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
AATGAAATATTAAAAACAAAAATTATTA
Found at i:25160 original size:14 final size:14
Alignment explanation
Indices: 25141--25169 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25131 AGTTATACAA
25141 TAACAACATAATAG
1 TAACAACATAATAG
25155 TAACAACATAATAG
1 TAACAACATAATAG
25169 T
1 T
25170 GAAATGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (14 bp):
TAACAACATAATAG
Found at i:29042 original size:34 final size:34
Alignment explanation
Indices: 28999--29067 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28989 TTAGTCTTGA
28999 ACTAAATTTCCATTCTTACCAAAAGAAAAATTGT
1 ACTAAATTTCCATTCTTACCAAAAGAAAAATTGT
29033 ACTAAATTTCCATTCTTACCAAAAGAAAAATTGT
1 ACTAAATTTCCATTCTTACCAAAAGAAAAATTGT
29067 A
1 A
29068 TTAGATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (34 bp):
ACTAAATTTCCATTCTTACCAAAAGAAAAATTGT
Found at i:37629 original size:42 final size:42
Alignment explanation
Indices: 37525--37679 Score: 123
Period size: 42 Copynumber: 3.7 Consensus size: 42
37515 CCGAAGGCTG
* * * * * *
37525 AACAGGAGCTCATGAGAGCTAAATAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGGGTTA
* *
37567 AACGGAAGCTCGTAAGAGCTGAACAAAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGGGTTA
* * ** * * *
37609 AATAGAAGTTCAATAA-AGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTC-ATAAGAGCTGAACAAAAACCCATAAGGGTTA
* * * *
37651 AACAGAAGCTCGTGAGAGCTAAACGAAAA
1 AACAGAAGCTCATAAGAGCTGAACAAAAA
37680 GTAAACACGA
Statistics
Matches: 88, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
41 2 0.02
42 83 0.94
43 3 0.03
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGGGTTA
Found at i:54031 original size:4 final size:4
Alignment explanation
Indices: 54022--54090 Score: 57
Period size: 4 Copynumber: 15.8 Consensus size: 4
54012 TTTGTTCTGT
* * *
54022 TTTA TTTA TTTA TTTA TTTA TCCTTACA TTTC TTTA TTTC TTTA TTTT
1 TTTA TTTA TTTA TTTA TTTA T--TT--A TTTA TTTA TTTA TTTA TTTA
54070 TTTACA TTTA TTTA TTTA TTT
1 TTT--A TTTA TTTA TTTA TTT
54091 TTCTTGTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 44 0.83
6 7 0.13
8 2 0.04
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:59646 original size:17 final size:17
Alignment explanation
Indices: 59624--59661 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
59614 ATCACTCGAG
59624 ATTTAGTACGACGACTA
1 ATTTAGTACGACGACTA
* *
59641 ATTTAGTATGACGACTG
1 ATTTAGTACGACGACTA
59658 ATTT
1 ATTT
59662 CCTGAACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (17 bp):
ATTTAGTACGACGACTA
Found at i:62717 original size:59 final size:59
Alignment explanation
Indices: 62604--62718 Score: 133
Period size: 59 Copynumber: 1.9 Consensus size: 59
62594 TGTTTTTAGA
* * * ** **
62604 TGGTGTAGTACTAGTAATGCACTTGGACAATATTATTATGTGGTGAACTATTAATTATG
1 TGGTGTAGTACTAATAATGCACTTGAACAATACTATTAAATAATGAACTATTAATTATG
* *
62663 TGGTGTAGTACTAA-ATATGCACTTGAACAATACTATTAAATAATGTACTGTTAATT
1 TGGTGTAGTACTAATA-ATGCACTTGAACAATACTATTAAATAATGAACTATTAATT
62719 TATTATTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (59 bp):
TGGTGTAGTACTAATAATGCACTTGAACAATACTATTAAATAATGAACTATTAATTATG
Found at i:74230 original size:22 final size:22
Alignment explanation
Indices: 74181--74235 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
74171 NNNNNNNNNA
* ** *
74181 ATTAAAATTAAAATTTTTTTTT
1 ATTAAAATTAAAACTAATTGTT
*
74203 AATAAAATTAAAACTAATTGTT
1 ATTAAAATTAAAACTAATTGTT
74225 ATTAAAATTAA
1 ATTAAAATTAA
74236 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAAATTAAAACTAATTGTT
Found at i:74248 original size:16 final size:16
Alignment explanation
Indices: 74211--74250 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
74201 TTAATAAAAT
* *
74211 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
74227 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
74243 TAAAATTA
1 TAAAATTA
74251 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:74283 original size:59 final size:67
Alignment explanation
Indices: 74239--74372 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 67
74229 AAATTAATTG
74239 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
74303 GA
66 GA
* *
74305 TTAGT-AAATT-T---ATCA--AATT-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
74362 GA
66 GA
74364 TTAGTAAAA
1 TTAGTAAAA
74373 CAAACTTGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
59 47 0.73
60 3 0.05
61 3 0.05
64 1 0.02
65 5 0.08
66 5 0.08
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:74309 original size:66 final size:59
Alignment explanation
Indices: 74253--74372 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
74243 TAAAATTATC
* * *
74253 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
74311 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
74370 AAA
1 AAA
74373 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:76578 original size:43 final size:44
Alignment explanation
Indices: 76493--76607 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
76483 TAACTTCTAT
* *
76493 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAAC
1 CTGCGCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAAC
* *
76537 TTGCGCCACTG-AACTTCATGGG-GATAAGTTTTTCTAT-TTCAAC
1 CTGCGCCACTGCAACTTCA-GGGAGATAAG-ATTTCTATCTTCAAC
* * *
76580 CTGCTCTACTGCAACTTCAGAGAGATAA
1 CTGCGCCACTGCAACTTCAGGGAGATAA
76608 AAAATTTGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
43 29 0.49
44 30 0.51
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
CTGCGCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAAC
Found at i:76607 original size:44 final size:43
Alignment explanation
Indices: 76493--76607 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 43
76483 TAACTTCTAT
*
76493 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAAC
1 CTGCTCCACTGCAACTTCA-GGAGATAAGATTTCTATCTTCAAC
* * * *
76537 TTGCGCCACTG-AACTTCATGGGGATAAGTTTTTCTAT-TTCAAC
1 CTGCTCCACTGCAACTTCA-GGAGATAAG-ATTTCTATCTTCAAC
*
76580 CTGCTCTACTGCAACTTCAGAGAGATAA
1 CTGCTCCACTGCAACTTCAG-GAGATAA
76608 AAAATTTGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 30 0.52
44 28 0.48
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
CTGCTCCACTGCAACTTCAGGAGATAAGATTTCTATCTTCAAC
Found at i:78062 original size:20 final size:20
Alignment explanation
Indices: 78019--78064 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
78009 TTGATATACC
**
78019 AAAAGTAAAAAAATTTGAGA
1 AAAAGTAAAAAAAAATGAGA
78039 AAAAGTAAAAAAAAAATGAGA
1 AAAAGT-AAAAAAAAATGAGA
78060 AAAAG
1 AAAAG
78065 GGGTGCTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAAGTAAAAAAAAATGAGA
Found at i:78617 original size:16 final size:15
Alignment explanation
Indices: 78577--78619 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
78567 AACTTTATCA
*
78577 TTTTACATAATTTAT
1 TTTTAAATAATTTAT
*
78592 TTAATAAATATATTTAT
1 TT-TTAAATA-ATTTAT
78609 TTTTAAATAAT
1 TTTTAAATAAT
78620 ATAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTAAATAATTTAT
Found at i:78619 original size:23 final size:23
Alignment explanation
Indices: 78593--78648 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
78583 ATAATTTATT
78593 TAATAAATATATTTATTT-TTAAA-
1 TAATAAAT-TA-TTATTTATTAAAG
78616 TAATATAATTATTATTTATTAAAG
1 TAATA-AATTATTATTTATTAAAG
*
78640 TACTAAATT
1 TAATAAATT
78649 TTGACATGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 16 0.55
24 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATAAATTATTATTTATTAAAG
Found at i:80365 original size:23 final size:23
Alignment explanation
Indices: 80320--80374 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
80310 GCATTTCAAA
*
80320 ATTTAGTACTTTAATAAATAATA-
1 ATTTATTA-TTTAATAAATAATAT
80343 ATTATATTATTTAA-AAATAAATAT
1 ATT-TATTATTTAATAAAT-AATAT
80367 ATTTATTA
1 ATTTATTA
80375 AAGAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 17 0.61
24 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTATTATTTAATAAATAATAT
Found at i:80375 original size:19 final size:20
Alignment explanation
Indices: 80329--80376 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
80319 AATTTAGTAC
* *
80329 TTTAATAAATAATAATTATA
1 TTTATTAAATAATAAATATA
80349 -TTATTTAAA-AATAAATATA
1 TTTA-TTAAATAATAAATATA
80368 TTTATTAAA
1 TTTATTAAA
80377 GAAATTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATTAAATAATAAATATA
Found at i:81744 original size:16 final size:16
Alignment explanation
Indices: 81707--81746 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
81697 TTAATAAAAT
* *
81707 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
81723 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
81739 TAAAATTA
1 TAAAATTA
81747 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:81816 original size:66 final size:59
Alignment explanation
Indices: 81749--81868 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
81739 TAAAATTATC
* * *
81749 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
81807 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
81866 AAA
1 AAA
81869 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:91376 original size:20 final size:21
Alignment explanation
Indices: 91343--91395 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
91333 TCTAATTGTG
*
91343 TATTAT-ATTGATTTGATTATA
1 TATTATAATT-ATTTGAATATA
91364 T-TTATAATTATTTGAATATA
1 TATTATAATTATTTGAATATA
*
91384 TATTATGATTAT
1 TATTATAATTAT
91396 ATTTGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TATTATAATTATTTGAATATA
Found at i:99774 original size:17 final size:15
Alignment explanation
Indices: 99752--99798 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
99742 ATTACTTATA
99752 AAAAATAATATTTCAAT
1 AAAAATAA-ATTT-AAT
99769 AAAAATAAATTTAAT
1 AAAAATAAATTTAAT
*
99784 AATTAAT-AATTTAAT
1 AA-AAATAAATTTAAT
99799 CTAAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 13 0.46
16 7 0.25
17 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATAAATTTAAT
Found at i:100663 original size:13 final size:14
Alignment explanation
Indices: 100645--100674 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
100635 TACATACGGC
100645 AAAAAAGAAAA-AG
1 AAAAAAGAAAAGAG
100658 AAAAAAGAAAAGAG
1 AAAAAAGAAAAGAG
100672 AAA
1 AAA
100675 GTCAATTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAGAG
Found at i:101087 original size:29 final size:28
Alignment explanation
Indices: 101054--101124 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
101044 TGATTTAACC
101054 TAAATTTAATTTAAATAAAAAATATTTTT
1 TAAATTTAATTTAAATAAAAAA-ATTTTT
* *
101083 TAAATTTAATTT--ATTATAAAATTTTT
1 TAAATTTAATTTAAATAAAAAAATTTTT
*
101109 TAAATATTAATATAAA
1 TAAAT-TTAATTTAAA
101125 ATATTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.31
27 12 0.33
29 13 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAATTTAATTTAAATAAAAAAATTTTT
Found at i:101089 original size:24 final size:24
Alignment explanation
Indices: 101061--101139 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
101051 ACCTAAATTT
101061 AATTTAAATAAAAAATATTTTTTA
1 AATTTAAATAAAAAATATTTTTTA
* *
101085 AATTTAATTTATTATAAA-ATTTTTTA
1 AATTTAA---ATAAAAAATATTTTTTA
* *
101111 AATATT-AATATAAAATATTTTATA
1 AAT-TTAAATAAAAAATATTTTTTA
101135 AATTT
1 AATTT
101140 GCCAACAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 7 0.16
24 17 0.39
26 12 0.27
27 8 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTTAAATAAAAAATATTTTTTA
Found at i:102347 original size:98 final size:98
Alignment explanation
Indices: 102178--102372 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
102168 ATACAATAAA
*
102178 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
102243 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
102276 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
102341 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
102373 CATGATTTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:105436 original size:6 final size:6
Alignment explanation
Indices: 105427--105462 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
105417 TCACTTTCAT
105427 TTTTTG TTTTTG TTTTTG TTTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG
105463 AATCTGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:105442 original size:12 final size:12
Alignment explanation
Indices: 105427--105462 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
105417 TCACTTTCAT
105427 TTTTTGTTTTTG
1 TTTTTGTTTTTG
105439 TTTTTGTTTTTTG
1 TTTTTG-TTTTTG
105452 TTTTT-TTTTTG
1 TTTTTGTTTTTG
105463 AATCTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTGTTTTTG
Found at i:105450 original size:19 final size:18
Alignment explanation
Indices: 105426--105462 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
105416 TTCACTTTCA
105426 TTTTTTGTTTTTGTTTTTG
1 TTTTTTGTTTTT-TTTTTG
105445 TTTTTTGTTTTTTTTTTG
1 TTTTTTGTTTTTTTTTTG
105463 AATCTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTTTG
Found at i:110097 original size:33 final size:33
Alignment explanation
Indices: 110055--110141 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
110045 GCTATTACAA
110055 TATTT-ATTCCATTCAACCAAACACAAGAATAC
1 TATTTCATTCCATTCAACCAAACACAAGAATAC
* * *
110087 TATTTCATTCCAATT-AACCTAACGCAAGAATAT
1 TATTTCATTCC-ATTCAACCAAACACAAGAATAC
* *
110120 TATTCCATTTCATTCAACCAAA
1 TATTTCATTCCATTCAACCAAA
110142 TAATTGAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
32 8 0.17
33 35 0.76
34 3 0.07
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.32
Consensus pattern (33 bp):
TATTTCATTCCATTCAACCAAACACAAGAATAC
Found at i:112127 original size:18 final size:18
Alignment explanation
Indices: 112104--112138 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
112094 TCATATCTTA
112104 AATTAATACCACATCATT
1 AATTAATACCACATCATT
* *
112122 AATTAATTCCACCTCAT
1 AATTAATACCACATCAT
112139 AAAACTAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTAATACCACATCATT
Found at i:114845 original size:22 final size:20
Alignment explanation
Indices: 114820--114880 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
114810 AAACCAATTT
*
114820 TAAATAAAAAAGAAATAGTAA
1 TAAATAAAAAA-AAATAATAA
114841 GTAAATAAATAAAAAATAATAA
1 -TAAATAAA-AAAAAATAATAA
* *
114863 TACATAAAAACAAATAAT
1 TAAATAAAAAAAAATAAT
114881 CATGGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.26
21 7 0.20
22 16 0.46
23 3 0.09
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAATAAAAAAAAATAATAA
Found at i:125665 original size:13 final size:14
Alignment explanation
Indices: 125629--125672 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 14
125619 TTACTTATAA
125629 AAAAAATAATATTT
1 AAAAAATAATATTT
125643 CAATAAAAATAA-ATTT
1 --A-AAAAATAATATTT
125659 AAAAAATAATATTT
1 AAAAAATAATATTT
125673 TAATCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAAATAATATTT
Found at i:125669 original size:16 final size:16
Alignment explanation
Indices: 125626--125672 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
125616 TTTTTACTTA
125626 TAAAAAAAATAATATT
1 TAAAAAAAATAATATT
*
125642 TCAATAAAAATAA-ATT
1 T-AAAAAAAATAATATT
125658 T--AAAAAATAATATT
1 TAAAAAAAATAATATT
125672 T
1 T
125673 TAATCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
16 5 0.19
17 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAAAATAATATT
Done.