Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_pilon, whole genome shotgun sequence
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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1257127 original size:37 final size:37
Alignment explanation
Indices: 1257038--1257138 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
1257028 ATTTTCGTCA
* * *
1257038 TACTAGGATTCAGACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
1257075 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** * *
1257112 TACTATTATTTAAACTCCTAAAGATAG
1 TACTAGGATTCAAACTCCTAAAAATAG
1257139 AATCCACAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:1257697 original size:284 final size:283
Alignment explanation
Indices: 1257183--1257743 Score: 1059
Period size: 284 Copynumber: 2.0 Consensus size: 283
1257173 CTATTGTAAC
1257183 ACAACAAGGGGATATACGAAATACCAAGCAAAAAAATTACAAGCAACTCGTAGCCATTTTTCGAA
1 ACAACAAGGGGATATACGAAATACCAAGCAAAAAAATTACAAGCAACTCGTAGCCATTTTTCGAA
1257248 GCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGCTATTTTTCCTTACCCTTGATGTGT
66 GCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGCTATTTTTCCTTACCCTTGATGTGT
1257313 TTTGATTCAAAAGAAAACTGAGAGAAGTGTTTTTGGCCGATGAACGAGGGCGTTTTCGAGATCTA
131 TTTGATTCAAAAGAAAACTGAGAGAAGTGTTTTTGGCCGATGAACGAGGGCGTTTTCGAGATCTA
1257378 TTTTTGTAGATCTAGTCCCCGAGGCTTGTGTTTTTGAAAAACTATTCGGATTTTTATAAACGGGT
196 TTTTTGTAGATCTAGTCCCCGAGGCTTGTGTTTTTGAAAAACTATTCGGATTTTTATAAACGGGT
1257443 CGTGTGGATCCGCGTGTAACACA
261 CGTGTGGATCCGCGTGTAACACA
1257466 ACAAGCAAGGGGATATACGAAATACCAAGCAAAAAAATTACAAGCAACTCGTAGCCATTTTTCGA
1 ACAA-CAAGGGGATATACGAAATACCAAGCAAAAAAATTACAAGCAACTCGTAGCCATTTTTCGA
* *
1257531 AGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTTCCTTACCCTTGCTGTG
65 AGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGCTATTTTTCCTTACCCTTGATGTG
* * *
1257596 TTTTGATTCGAAAGAAAACTGAGAGAAGTGTTTTTGGCCGATGAACGGGGGTGTTTTCGAGATCT
130 TTTTGATTCAAAAGAAAACTGAGAGAAGTGTTTTTGGCCGATGAACGAGGGCGTTTTCGAGATCT
*
1257661 ATTTTTGTAGATCTAGTCCCCGATGCTTGTGTTTTTGAAAAACTATTCGGATTTTTATAAACGGG
195 ATTTTTGTAGATCTAGTCCCCGAGGCTTGTGTTTTTGAAAAACTATTCGGATTTTTATAAACGGG
1257726 TCGTGTGGATCCGCGTGT
260 TCGTGTGGATCCGCGTGT
1257744 TTTGTCGTTT
Statistics
Matches: 271, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
283 4 0.01
284 267 0.99
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (283 bp):
ACAACAAGGGGATATACGAAATACCAAGCAAAAAAATTACAAGCAACTCGTAGCCATTTTTCGAA
GCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGCTATTTTTCCTTACCCTTGATGTGT
TTTGATTCAAAAGAAAACTGAGAGAAGTGTTTTTGGCCGATGAACGAGGGCGTTTTCGAGATCTA
TTTTTGTAGATCTAGTCCCCGAGGCTTGTGTTTTTGAAAAACTATTCGGATTTTTATAAACGGGT
CGTGTGGATCCGCGTGTAACACA
Found at i:1257862 original size:18 final size:18
Alignment explanation
Indices: 1257816--1257869 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1257806 TTAACCCTTA
*
1257816 TTATTTA-TATATATATAT
1 TTATTTATTATAT-TTTAT
*
1257834 ATATTTAATTATATTTTAT
1 TTATTT-ATTATATTTTAT
1257853 TTATTTATTATAATTTT
1 TTATTTATTAT-ATTTT
1257870 TTTCATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.33
19 15 0.50
20 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTATTATATTTTAT
Found at i:1258156 original size:17 final size:16
Alignment explanation
Indices: 1258129--1258166 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
1258119 TTATACATAC
1258129 ATTTTTATATTTTTATAT
1 ATTTTTATA-TTTTAT-T
1258147 ATTTTT-TATTTTATT
1 ATTTTTATATTTTATT
1258162 ATTTT
1 ATTTT
1258167 ATTTATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 2 0.10
18 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTATATTTTATT
Found at i:1258168 original size:13 final size:14
Alignment explanation
Indices: 1258144--1258185 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
1258134 TATATTTTTA
1258144 TATATT-TTTTATT
1 TATATTATTTTATT
1258157 T-TATTATTTTATT
1 TATATTATTTTATT
*
1258170 TATACTA-TTTATT
1 TATATTATTTTATT
1258183 TAT
1 TAT
1258186 TTTCATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATATTATTTTATT
Found at i:1268625 original size:14 final size:14
Alignment explanation
Indices: 1268606--1268635 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1268596 TGAAAACCCA
1268606 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
*
1268620 AAAAAAAGAAATAG
1 AAAAAAAGAAAAAG
1268634 AA
1 AA
1268636 GTTATAAATA
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:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:1269219 original size:20 final size:20
Alignment explanation
Indices: 1269194--1269236 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1269184 TCTAAAAGCT
*
1269194 CATTTAGGACCATTTAGATG
1 CATTTAGAACCATTTAGATG
* *
1269214 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATTTAGATG
1269234 CAT
1 CAT
1269237 GTGGTGGATT
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:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (20 bp):
CATTTAGAACCATTTAGATG
Found at i:1271706 original size:18 final size:19
Alignment explanation
Indices: 1271671--1271706 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1271661 ACCTTACTAA
*
1271671 CTCTTTTCATTTTTTTTCT
1 CTCTTTTCATTTTATTTCT
1271690 CTCTTTT-ATTTTATTTC
1 CTCTTTTCATTTTATTTC
1271707 CATCATCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.72
Consensus pattern (19 bp):
CTCTTTTCATTTTATTTCT
Found at i:1275045 original size:8 final size:8
Alignment explanation
Indices: 1275034--1275111 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
1275024 CAAAAAAGGG
1275034 AAAAAAGA
1 AAAAAAGA
1275042 AAAAAAGA
1 AAAAAAGA
1275050 AAAAAAGA
1 AAAAAAGA
*
1275058 AAAAAAGG
1 AAAAAAGA
*
1275066 AAAAAACA
1 AAAAAAGA
1275074 AAAGAACA-A
1 AAA-AA-AGA
1275083 AAAGAAAGA
1 AAA-AAAGA
*
1275092 ACAAAAA-T
1 A-AAAAAGA
*
1275100 CAAAAAGA
1 AAAAAAGA
1275108 AAAA
1 AAAA
1275112 GGGACAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
7 5 0.09
8 36 0.62
9 14 0.24
10 3 0.05
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1275047 original size:17 final size:16
Alignment explanation
Indices: 1275025--1275076 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1275015 CAATCAGAAC
*
1275025 AAAAAAGGGAAAAAAG
1 AAAAAAAGGAAAAAAG
*
1275041 AAAAAAAGAAAAAAAG
1 AAAAAAAGGAAAAAAG
*
1275057 AAAAAAAGGAAAAAAC
1 AAAAAAAGGAAAAAAG
1275073 AAAA
1 AAAA
1275077 GAACAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGGAAAAAAG
Found at i:1275060 original size:13 final size:13
Alignment explanation
Indices: 1275036--1275098 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
1275026 AAAAAGGGAA
1275036 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
*
1275049 AAAA-AAAGAAA-
1 AAAAGAAAAAAAG
* *
1275060 AAAAGGAAAAAAC
1 AAAAGAAAAAAAG
1275073 AAAAGAACAAAAAG
1 AAAAGAA-AAAAAG
1275087 -AAAGAACAAAAA
1 AAAAGAA-AAAAA
1275099 TCAAAAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
11 4 0.10
12 11 0.26
13 22 0.52
14 5 0.12
ACGTcount: A:0.83, C:0.05, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:1275105 original size:20 final size:21
Alignment explanation
Indices: 1275052--1275111 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1275042 AAAAAAGAAA
1275052 AAAAGAA-AAAAAGGAAAAAAC
1 AAAAGAACAAAAA-GAAAAAAC
*
1275073 AAAAGAACAAAAAGAAAGAAC
1 AAAAGAACAAAAAGAAAAAAC
*
1275094 AAAA-ATCAAAAAGAAAAA
1 AAAAGAACAAAAAGAAAAA
1275112 GGGACAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.34
21 18 0.51
22 5 0.14
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAGAACAAAAAGAAAAAAC
Found at i:1275105 original size:29 final size:30
Alignment explanation
Indices: 1275043--1275111 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
1275033 GAAAAAAGAA
*
1275043 AAAAAGAAAAAAAGAAAAAAAGGAAAAAAC
1 AAAAAGAAAAAAAGAAAAAAAGCAAAAAAC
* *
1275073 -AAAAGAACAAAAAG-AAAGAA-CAAAAATC
1 AAAAAGAA-AAAAAGAAAAAAAGCAAAAAAC
1275101 AAAAAGAAAAA
1 AAAAAGAAAAA
1275112 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 9 0.26
29 19 0.56
30 6 0.18
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (30 bp):
AAAAAGAAAAAAAGAAAAAAAGCAAAAAAC
Found at i:1276949 original size:106 final size:106
Alignment explanation
Indices: 1276573--1277939 Score: 2014
Period size: 106 Copynumber: 13.0 Consensus size: 106
1276563 ATATCGTGCC
* * * * * * *
1276573 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1276637 AATTTCGGAGACAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1276678 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
**
1276743 AATTTCAGAGCCAATTTCAAC-TCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1276783 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1276848 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1276889 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1276954 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1276995 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1277060 AATTCCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1277101 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1277166 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA-T--
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1277204 --T---GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1277264 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1277305 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1277370 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1277411 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1277476 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1277517 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1277582 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *** * * *
1277623 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGTGGCTGATTATCAA-CAA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* *
1277683 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
1277723 AATCGAGACAGCACAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* *
1277788 CAATTTCAAAGCCAATTTCAACTTCATAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1277830 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * * *
1277895 GGTTCCAGAGCCAATTTCAACTTTAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1277936 ACTC
1 ACTC
1277940 GGAACAATGC
Statistics
Matches: 1154, Mismatches: 88, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
98 93 0.08
99 1 0.00
100 56 0.05
101 22 0.02
102 3 0.00
103 5 0.00
104 4 0.00
105 156 0.14
106 754 0.65
107 60 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1277429 original size:416 final size:416
Alignment explanation
Indices: 1276573--1277939 Score: 2005
Period size: 416 Copynumber: 3.3 Consensus size: 416
1276563 ATATCGTGCC
* * * *
1276573 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * * *
1276637 AATTTCGGAGACAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
1276702 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAAC-TC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
**
1276766 ACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATA-T----T-C-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
1276831 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
254 TCAATAAACAA-TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
1276896 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
318 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
1276961 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
383 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
1276995 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1277060 AATTCCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCTAGACAACGCAAGTTCAACT
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
1277125 TCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1277190 ACAGCGAAGGATATT-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
196 ACAGCGAAGGATATTCGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
* *
1277254 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCCAGACAATGC
261 ACAA-TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
*
1277319 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
325 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
* *
1277384 TTTCAACTTCACAACGAAAGATATTGG
390 TTTCAACTTCACAGCGAAGGATATTGG
* *
1277411 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1277476 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
1277541 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * * * *** * *
1277606 TCAGCGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAGGGGTGGCTGATTA
196 ACAGCGAAGGATATT-----C--GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * * * * *
1277671 TCAA-CAA-AATT-TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAATCGAGA
254 TCAATAAACAATTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * *
1277731 CAGCACAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCA
319 CAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* *
1277796 AAGCCAATTTCAACTTCATAGCGAAGGATATTGG
383 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1277830 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * *
1277895 GGTTCCAGAGCCAATTTCAACTTTAC-GACGGAGGATATTGGACTC
66 AATTCCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1277940 GGAACAATGC
Statistics
Matches: 865, Mismatches: 68, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
416 397 0.46
418 59 0.07
419 172 0.20
420 1 0.00
421 2 0.00
422 49 0.06
423 133 0.15
424 52 0.06
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (416 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTCGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
ACAATTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
TTCAACTTCACAGCGAAGGATATTGG
Found at i:1278762 original size:37 final size:36
Alignment explanation
Indices: 1278672--1278773 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
1278662 CATTTTCGTC
*
1278672 CTACTAGGATTCAGACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATA-GATAGAATT
* * *
1278709 TTGCTAGGATTCAAACTCCTAAAAATAGAATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAG-ATAGAATT
** * *
1278746 CTACTATTATTTAAACTCCTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAAAATAG
1278774 GATCCACAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 1 0.02
37 53 0.98
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAAATAGATAGAATT
Found at i:1279270 original size:24 final size:25
Alignment explanation
Indices: 1279243--1279289 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1279233 TTCTTTGCGT
*
1279243 TATATTATATTATT-TTTATTATTA
1 TATATCATATTATTATTTATTATTA
*
1279267 TATATCATATTATTATTTTTTAT
1 TATATCATATTATTATTTATTAT
1279290 CTATGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TATATCATATTATTATTTATTATTA
Found at i:1279342 original size:2 final size:2
Alignment explanation
Indices: 1279335--1279359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1279325 TTCCTAACGT
1279335 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1279360 CTTATCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1279491 original size:4 final size:4
Alignment explanation
Indices: 1279482--1279518 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
1279472 TATATACATT
1279482 TTTA TTTA TTTA TTTA TTTA TTTTA TTTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTT
1279519 TCATTATGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 23 0.72
5 9 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1279525 original size:18 final size:18
Alignment explanation
Indices: 1279482--1279518 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1279472 TATATACATT
1279482 TTTAT-TTA-TTTATTTA
1 TTTATATTATTTTATTTA
*
1279498 TTTATTTTATTTTATTTA
1 TTTATATTATTTTATTTA
1279516 TTT
1 TTT
1279519 TCATTATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATATTATTTTATTTA
Found at i:1279631 original size:18 final size:19
Alignment explanation
Indices: 1279609--1279652 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1279599 TATATATATA
*
1279609 TTTTTCTTC-ATTT-ATTT
1 TTTTTATTCAATTTCATTT
1279626 TATTTTATTCAATTTCATTT
1 T-TTTTATTCAATTTCATTT
1279646 TTTTTAT
1 TTTTTAT
1279653 ATATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.30
19 10 0.43
20 5 0.22
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTCAATTTCATTT
Found at i:1281125 original size:6 final size:6
Alignment explanation
Indices: 1281108--1281140 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
1281098 TGAAAAATTC
1281108 AAGAGCA AAGAGA AAGAGA AAGAGA AAGAGA AA
1 AAGAG-A AAGAGA AAGAGA AAGAGA AAGAGA AA
1281141 TAACCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:1286944 original size:34 final size:32
Alignment explanation
Indices: 1286891--1286960 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1286881 ACCTTACAAC
*
1286891 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
1286923 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1286957 TCCC
1 TCCC
1286961 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1287270 original size:21 final size:21
Alignment explanation
Indices: 1287244--1287285 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1287234 CCAGAATGGG
*
1287244 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1287265 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1287286 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1287413 original size:21 final size:21
Alignment explanation
Indices: 1287387--1287467 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1287377 GCTTTAGACA
*
1287387 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCT-G
*
1287409 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
1287426 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
1287445 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
1287466 GG
1 GG
1287468 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 20 0.40
22 12 0.24
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:1287431 original size:15 final size:15
Alignment explanation
Indices: 1287411--1287440 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1287401 CCCCCTGGGG
1287411 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1287426 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1287441 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1287456 original size:36 final size:37
Alignment explanation
Indices: 1287389--1287461 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
1287379 TTTAGACAGG
*
1287389 GGGGAATCGGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
* *
1287426 GGGGTATCTGTACCCCCT-GGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
1287462 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (37 bp):
GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
Found at i:1287798 original size:21 final size:21
Alignment explanation
Indices: 1287773--1287818 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1287763 TAAGCTCCCC
1287773 TTTTTCATTAAGAAATTGAAT
1 TTTTTCATTAAGAAATTGAAT
*
1287794 TTTTTTATTAAGAAATTGAAT
1 TTTTTCATTAAGAAATTGAAT
1287815 TTTT
1 TTTT
1287819 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (21 bp):
TTTTTCATTAAGAAATTGAAT
Found at i:1288935 original size:19 final size:20
Alignment explanation
Indices: 1288892--1288939 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1288882 TCTAAATCCT
*
1288892 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1288912 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1288931 TTTTCAAAA
1 TTTTCAAAA
1288940 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1289852 original size:34 final size:32
Alignment explanation
Indices: 1289799--1289868 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1289789 ACCTTACAAC
*
1289799 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
1289831 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1289865 TCCC
1 TCCC
1289869 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1290178 original size:21 final size:21
Alignment explanation
Indices: 1290152--1290193 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1290142 CCAGAATGGG
*
1290152 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1290173 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1290194 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1290254 original size:20 final size:20
Alignment explanation
Indices: 1290229--1290269 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1290219 CTGTTGAACA
1290229 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
1290249 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
1290269 G
1 G
1290270 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.41, T:0.15
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:1290321 original size:21 final size:21
Alignment explanation
Indices: 1290295--1290375 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1290285 GCTTTAGACA
*
1290295 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCT-G
*
1290317 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
1290334 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
1290353 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
1290374 GG
1 GG
1290376 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 20 0.40
22 12 0.24
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:1290339 original size:15 final size:15
Alignment explanation
Indices: 1290319--1290348 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1290309 CCCCCTGGGG
1290319 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1290334 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1290349 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1290364 original size:36 final size:37
Alignment explanation
Indices: 1290297--1290369 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
1290287 TTTAGACAGG
*
1290297 GGGGAATCGGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
* *
1290334 GGGGTATCTGTACCCCCT-GGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
1290370 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (37 bp):
GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
Found at i:1303866 original size:27 final size:27
Alignment explanation
Indices: 1303810--1303876 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
1303800 ATTTTTTATA
* * *
1303810 TAATTTCTTTATATATAATTATTAAAT
1 TAATTTTTTTAAATATAATTAATAAAT
**
1303837 TAATTTTTTTAAATATAATTAATATTT
1 TAATTTTTTTAAATATAATTAATAAAT
1303864 TAATTTTATTTAA
1 TAATTTT-TTTAA
1303877 TGATTGTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATTTTTTTAAATATAATTAATAAAT
Found at i:1305609 original size:37 final size:36
Alignment explanation
Indices: 1305551--1305667 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
1305541 CCATTACAAA
* *
1305551 TTTTC-AACAAACATCTACCAAACTTTGAAAAACCAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
*
1305587 TTTTCAAAGAAACGTTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
*
1305622 TTTTCAAAGAAACATTTACCAAACTTTGAAAATCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-T
1305659 TTTTCAAAG
1 TTTTCAAAG
1305668 TTGGTTGCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.45
36 12 0.16
37 28 0.38
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:1310198 original size:37 final size:36
Alignment explanation
Indices: 1310140--1310258 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
1310130 TCCCATTACA
* *
1310140 ATTTTTC-AACAAACATATACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1310176 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
* *
1310212 A-TTTTCAAATAAACATTTACCAAACTTTGAAAATC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1310247 ATTTTTTCAAAG
1 A-TTTTTCAAAG
1310259 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.44
36 14 0.19
37 28 0.37
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:1310214 original size:21 final size:20
Alignment explanation
Indices: 1310187--1310250 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1310177 TTTTTCAAAG
1310187 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
1310207 AAACCATTT-TCAAA---T--
1 AAA-CATTTACCAAACTTTGA
1310222 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
1310242 AAATCATTT
1 AAA-CATTT
1310251 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
17 1 0.03
18 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:1326128 original size:19 final size:18
Alignment explanation
Indices: 1326087--1326122 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1326077 TTAATTATTA
*
1326087 ATAAAATAAATATTTTTT
1 ATAAAATAAATATATTTT
1326105 ATAAAAT-AATATATTTT
1 ATAAAATAAATATATTTT
1326122 A
1 A
1326123 GGTAAACCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAAATAAATATATTTT
Found at i:1332283 original size:22 final size:22
Alignment explanation
Indices: 1332201--1332283 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 22
1332191 TTCTCTTTCC
* *
1332201 CAGTGCTATGGTACTTTAGTAT
1 CAGTGCTAAGGCACTTTAGTAT
* * * *
1332223 CAGTGCGAATGCACTTTTGTAC
1 CAGTGCTAAGGCACTTTAGTAT
* * *
1332245 CAGTGCTACGACGCTTTAGTAT
1 CAGTGCTAAGGCACTTTAGTAT
*
1332267 TAGTGCTAAGGCACTTT
1 CAGTGCTAAGGCACTTT
1332284 CGTTATACAA
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (22 bp):
CAGTGCTAAGGCACTTTAGTAT
Found at i:1338901 original size:22 final size:20
Alignment explanation
Indices: 1338867--1338908 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1338857 AAATTGATGC
1338867 AATTAAATGAATTCGAAGATAA
1 AATTAAATGAATT--AAGATAA
1338889 AATTAATAT-AATTAAGATAA
1 AATTAA-ATGAATTAAGATAA
1338909 GAACAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (20 bp):
AATTAAATGAATTAAGATAA
Found at i:1349883 original size:13 final size:14
Alignment explanation
Indices: 1349865--1349912 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
1349855 AGAAAATCAA
*
1349865 ATGCACTAGT-GAC
1 ATGCACTAATCGAC
*
1349878 ATGCACTAATCGCC
1 ATGCACTAATCGAC
*
1349892 ATGCACTAATCGCC
1 ATGCACTAATCGAC
1349906 ATGCACT
1 ATGCACT
1349913 TGTGTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (14 bp):
ATGCACTAATCGAC
Found at i:1349896 original size:14 final size:14
Alignment explanation
Indices: 1349877--1349912 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1349867 GCACTAGTGA
1349877 CATGCACTAATCGC
1 CATGCACTAATCGC
1349891 CATGCACTAATCGC
1 CATGCACTAATCGC
1349905 CATGCACT
1 CATGCACT
1349913 TGTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.22
Consensus pattern (14 bp):
CATGCACTAATCGC
Found at i:1359332 original size:25 final size:24
Alignment explanation
Indices: 1359304--1359354 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
1359294 AATTTAACAC
* *
1359304 TAAATTTTAAAAAAAATTAAAAGTT
1 TAAATATTAAAAAAAATCAAAA-TT
*
1359329 TAAATATTAAAATAAATCAAAATT
1 TAAATATTAAAAAAAATCAAAATT
1359353 TA
1 TA
1359355 CGATTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAATATTAAAAAAAATCAAAATT
Found at i:1365341 original size:36 final size:37
Alignment explanation
Indices: 1365290--1365361 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1365280 TTTTGTTCGG
*
1365290 GTCGGGTCGG-GTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGATTTTTTAAGTGTGATATTCGGGTCGA
*
1365326 GTCGGGTCGGATTTTTTACGTGTGATATTCGGGTCG
1 GTCGGGTCGGATTTTTTAAGTGTGATATTCGGGTCG
1365362 GGTTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (37 bp):
GTCGGGTCGGATTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1365367 original size:27 final size:27
Alignment explanation
Indices: 1365327--1365386 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1365317 TCGGGTCGAG
*
1365327 TCGGGTCGGATTTTTTACGTGTGATAT
1 TCGGGTCGGATTTTTTAAGTGTGATAT
*
1365354 TCGGGTCGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGATTTTTTAAGTGTGATAT
1365381 TCGGGT
1 TCGGGT
1365387 TGGTTCGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.13, C:0.10, G:0.33, T:0.43
Consensus pattern (27 bp):
TCGGGTCGGATTTTTTAAGTGTGATAT
Found at i:1367821 original size:84 final size:76
Alignment explanation
Indices: 1367714--1367923 Score: 235
Period size: 84 Copynumber: 2.7 Consensus size: 76
1367704 TATCAAGACC
* * * *
1367714 CAAACTTACTCGACAAATATTTTCATAAAGTTGGAGAAATTACATAGGGTCCATTAAGAAAAAGA
1 CAAACTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACAGAGGGTCCATCAAG---AAGA
1367779 AGAAGAAGTTTTATGAAGATT
63 AGAAG-A-----A-GAAGATT
** *
1367800 C-AACTTACCCAA-AAATATTTTCATAAAGTTGGAGAAATTACAGAGACTCCATCATGAAGAAGA
1 CAAACTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACAGAGGGTCCATCAAGAAGAAGA
1367863 AGAAGAAGATT
66 AGAAGAAGATT
* *
1367874 CAAACTTACCCAACAAATATTTTCAGAAAGTTGAAGAAATTACAGAGGGT
1 CAAACTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACAGAGGGT
1367924 TTGTGATGAT
Statistics
Matches: 111, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
74 8 0.07
75 12 0.11
76 32 0.29
80 1 0.01
81 9 0.08
84 39 0.35
85 9 0.08
86 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (76 bp):
CAAACTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACAGAGGGTCCATCAAGAAGAAGA
AGAAGAAGATT
Found at i:1369698 original size:18 final size:18
Alignment explanation
Indices: 1369660--1369700 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1369650 AACATTCCCA
* *
1369660 GTAATCTTATTCATGCCG
1 GTAATCTTATTCATACAG
*
1369678 GTAATCTTATTCGTACAG
1 GTAATCTTATTCATACAG
1369696 GTAAT
1 GTAAT
1369701 ATTACATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
GTAATCTTATTCATACAG
Found at i:1380182 original size:18 final size:18
Alignment explanation
Indices: 1380135--1380187 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 18
1380125 ACTCTACCCA
*
1380135 CAGTACCGATACTTCTCTT
1 CAGTACCGATAC-CCTCTT
1380154 CTATGGTACCGATACCCTCTT
1 C-A--GTACCGATACCCTCTT
1380175 CAGTACCGATACC
1 CAGTACCGATACC
1380188 ATTTTAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 2 0.07
21 6 0.20
22 10 0.33
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (18 bp):
CAGTACCGATACCCTCTT
Found at i:1385832 original size:64 final size:64
Alignment explanation
Indices: 1385719--1385928 Score: 205
Period size: 64 Copynumber: 3.2 Consensus size: 64
1385709 TGCACTAAGA
* * *
1385719 GTGCATCGATGCATGAATTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
1385781 TT
63 TT
* * * **
1385783 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGTATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * *
1385847 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAACTT-ATTCATTGA-TGCATCGATGCATGGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAAATCA--GAGTGCATCGATGCATGG-
1385910 ATT
62 ATT
*
1385913 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
1385929 CCTTTGAAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
64 83 0.67
65 16 0.13
66 8 0.07
67 16 0.13
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1385849 original size:19 final size:19
Alignment explanation
Indices: 1385825--1385876 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1385815 TAATTAAATC
1385825 AGAGTGCATCGATGTATGG
1 AGAGTGCATCGATGTATGG
* *
1385844 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGTATGG
1385863 A-A-TGCATTCGATGT
1 AGAGTGCA-TCGATGT
1385877 TTCAACTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.25, C:0.13, G:0.35, T:0.27
Consensus pattern (19 bp):
AGAGTGCATCGATGTATGG
Found at i:1385913 original size:21 final size:21
Alignment explanation
Indices: 1385889--1385928 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1385879 CAACTTATTC
1385889 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1385910 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1385929 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1388512 original size:24 final size:23
Alignment explanation
Indices: 1388441--1388520 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
1388431 CATGATCTTG
*
1388441 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
1388464 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
1388485 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
1388509 TGCATCGATGCA
1 TGCATCGATGCA
1388521 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1388533 original size:44 final size:42
Alignment explanation
Indices: 1388419--1388540 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
1388409 AAACCCGACC
*
1388419 GATGCATCGATGCA-TGATCTTGTGCATCGATGCACATTCAAGG
1 GATGCATCGATGCATTG-T-TAGTGCATCGATGCACATTCAAGG
* * **
1388462 CATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAGG
*
1388507 GATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GATGCATCGATGCATTGTT-AGTGCATCGATGCA
1388541 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
43 15 0.24
44 28 0.44
45 18 0.29
46 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (42 bp):
GATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAGG
Found at i:1394412 original size:64 final size:62
Alignment explanation
Indices: 1394338--1394500 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 62
1394328 GTGCACTCTA
*
1394338 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTGGTGCATCGATGCATG
1 AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG---AGTGCATCGATGCATG
*
1394401 T
62 G
** * *
1394402 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCAGAGTGCATCGATGCATGG
*
1394466 AGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1394501 CAACTTATTC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
64 76 0.90
65 2 0.02
66 4 0.05
67 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAGAGTGCATCGATGCATGG
Found at i:1394471 original size:19 final size:19
Alignment explanation
Indices: 1394447--1394497 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1394437 TAATTAAATC
1394447 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1394466 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1394485 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1394498 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1394535 original size:21 final size:21
Alignment explanation
Indices: 1394511--1394550 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1394501 CAACTTATTC
1394511 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1394532 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1394551 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1396634 original size:40 final size:40
Alignment explanation
Indices: 1396579--1396658 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1396569 ATTCCAATCG
1396579 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1396619 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1 ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
1396659 TTATACATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
ATGGAAGTGGAACCATTGGAACATATTTAATATTATCCTC
Found at i:1397643 original size:30 final size:30
Alignment explanation
Indices: 1397609--1397670 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1397599 AATACCACTT
*
1397609 GCTCCAACAATACCTTGGTTACCTTGGCTA
1 GCTCCAACAATACCTGGGTTACCTTGGCTA
1397639 GCTCCAACAATACCTGGGTTACCTTGGCTA
1 GCTCCAACAATACCTGGGTTACCTTGGCTA
1397669 GC
1 GC
1397671 CCCATCTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (30 bp):
GCTCCAACAATACCTGGGTTACCTTGGCTA
Found at i:1404037 original size:27 final size:27
Alignment explanation
Indices: 1404007--1404062 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1403997 CATCACTTCC
*
1404007 TCCAATCTTTTAAAATCTATAATTTAG
1 TCCAATCTTTTAAAATCTAAAATTTAG
*
1404034 TCCAATCTTTTAAAATTTAAAATTTAG
1 TCCAATCTTTTAAAATCTAAAATTTAG
1404061 TC
1 TC
1404063 TTTAGTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (27 bp):
TCCAATCTTTTAAAATCTAAAATTTAG
Found at i:1404227 original size:2 final size:2
Alignment explanation
Indices: 1404220--1404248 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1404210 TTGGTTAAAC
1404220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1404249 CAATTTCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1405841 original size:60 final size:59
Alignment explanation
Indices: 1405727--1405886 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 59
1405717 TTTAATTTGA
* ** * * *
1405727 CCTCAATACTTTTAAATTTTTTAATTTTATTTTTAAAATCTGACTATCAATCTAAATCAAT
1 CCTCAA-ACTTTTAAATATTTTAA-TTTATCCTCAAACTATGACTATCAATCTAAATCAAT
* * *
1405788 CCTCAAACTTTTAAATATTTTAATTTCATCCTCAAACTATGACCT-TCATTCTAAATTAGT
1 CCTCAAACTTTTAAATATTTTAATTT-ATCCTCAAACTATGA-CTATCAATCTAAATCAAT
* * *
1405848 CCCCAAACTTGTTAAACATTCTAATTTATCC-CAAACTAT
1 CCTCAAACTT-TTAAATATTTTAATTTATCCTCAAACTAT
1405887 ACATATATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
59 11 0.13
60 51 0.61
61 22 0.26
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (59 bp):
CCTCAAACTTTTAAATATTTTAATTTATCCTCAAACTATGACTATCAATCTAAATCAAT
Found at i:1418466 original size:29 final size:30
Alignment explanation
Indices: 1418432--1418494 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
1418422 ATTTACCAAG
*
1418432 AGGGGTTGAAGTGGATTTATG-AAATAATT
1 AGGGGTTGAAGTGGATTTATGAAAAAAATT
1418461 AGGGGTTGAAGTGGATTTATGAAAAAAATT
1 AGGGGTTGAAGTGGATTTATGAAAAAAATT
1418491 AGGG
1 AGGG
1418495 ATTAAGGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (30 bp):
AGGGGTTGAAGTGGATTTATGAAAAAAATT
Found at i:1420963 original size:153 final size:156
Alignment explanation
Indices: 1420746--1421084 Score: 481
Period size: 157 Copynumber: 2.2 Consensus size: 156
1420736 AAAATCGAAT
** * *
1420746 TTAAAATAAATGACAAATTGAAGGAATATGGAGATTATGAAAATTGAAAGACTAAATTGAAA-AA
1 TTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAATTGAAAGACTAAATTGAAATAA
* * * *
1420810 ACAATTGTTATCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTG
66 AAAATTATTATCAAAAAGAGAAATTGAAAGTACACATATATTCTACTATGGTTTAGAAGCATGTG
*
1420875 ACTCAAATTTGGTAAAAA-ACAT-AC
131 ACTCAAATTTGGTAAAAACAAATGAC
1420899 TTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATT-AAAGGACTAAATTGAAAA
1 TTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATG-AAAATTGAAA-GACTAAATTG--AA
*
1420963 ATAAAAAATTATTATCAAAAAGAGGAATTGAAAGTACACATATATTCTACTATGGTTTAGAAGCA
62 ATAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATATATTCTACTATGGTTTAGAAGCA
*
1421028 TGTGATTCAAATTTGGTAAAAACAAATGGAC
127 TGTGACTCAAATTTGGTAAAAACAAAT-GAC
* *
1421059 TT-AAATAAAGGATGAATTGAAAAAAT
1 TTAAAATAAATGATGAATTGAAGAAAT
1421085 TGAAAGTTTA
Statistics
Matches: 165, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
153 38 0.23
154 16 0.10
156 3 0.02
157 79 0.48
158 3 0.02
159 22 0.13
160 4 0.02
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (156 bp):
TTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAATTGAAAGACTAAATTGAAATAA
AAAATTATTATCAAAAAGAGAAATTGAAAGTACACATATATTCTACTATGGTTTAGAAGCATGTG
ACTCAAATTTGGTAAAAACAAATGAC
Found at i:1437954 original size:15 final size:15
Alignment explanation
Indices: 1437934--1437964 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1437924 CAACAAATCG
1437934 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1437949 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1437964 A
1 A
1437965 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1444008 original size:16 final size:16
Alignment explanation
Indices: 1443987--1444017 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1443977 TATGTTGTGA
1443987 GTTCTAGAATAGTTTT
1 GTTCTAGAATAGTTTT
1444003 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
1444018 GTTAGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
GTTCTAGAATAGTTTT
Found at i:1444080 original size:19 final size:19
Alignment explanation
Indices: 1444039--1444080 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1444029 GTAGTTAAGT
* * *
1444039 TGTTGAGCTGTTAGTCGTT
1 TGTTGAGCTGTTAATCATA
1444058 TGTTGAGCTGTTAATCATA
1 TGTTGAGCTGTTAATCATA
1444077 TGTT
1 TGTT
1444081 TTCCTGACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (19 bp):
TGTTGAGCTGTTAATCATA
Found at i:1450575 original size:30 final size:29
Alignment explanation
Indices: 1450522--1450591 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
1450512 AGGTCCTATC
1450522 TGCTCTCCATCAATGCGTAATGCTCCCATG
1 TGCTCTCCATCAATGCGTAATGCT-CCATG
* * * *
1450552 TGCTCTTCATCCATTCGTGATGCTCCATG
1 TGCTCTCCATCAATGCGTAATGCTCCATG
*
1450581 TGATGCTCCAT
1 TGCT-CTCCAT
1450592 TGGATTCGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (29 bp):
TGCTCTCCATCAATGCGTAATGCTCCATG
Found at i:1452981 original size:2 final size:2
Alignment explanation
Indices: 1452974--1453003 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1452964 CGCTATAAGG
1452974 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1453004 ACTCTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1453423 original size:2 final size:2
Alignment explanation
Indices: 1453416--1453466 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1453406 CTATACATGC
* * * *
1453416 TA TA TA TA TA CA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1453458 TA TA TA TA T
1 TA TA TA TA T
1453467 GTATGTATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1460326 original size:2 final size:2
Alignment explanation
Indices: 1460313--1460347 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1460303 AGATTCTTTA
*
1460313 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1460348 CTGCTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1461604 original size:30 final size:30
Alignment explanation
Indices: 1461538--1461633 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 30
1461528 AAATTCTAGT
* * * *
1461538 GTTAAATTGATATTTTATCTCAAGTTTAATG
1 GTTAAAATGATATTATATCTAAAGTTCAA-G
**
1461569 GTTAAAATGATATTGCATCTAAAGTTCAAG
1 GTTAAAATGATATTATATCTAAAGTTCAAG
*
1461599 GTTAAAATAATATTATATCTAAAGTTCAAAG
1 GTTAAAATGATATTATATCTAAAGTTC-AAG
1461630 GTTA
1 GTTA
1461634 CATTAAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.45
31 31 0.55
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (30 bp):
GTTAAAATGATATTATATCTAAAGTTCAAG
Found at i:1462499 original size:37 final size:36
Alignment explanation
Indices: 1462439--1462508 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
1462429 GTTAAATGAC
* * **
1462439 TAAAAAAAATCTAATATATTAAGTTCAATAAAAAAA
1 TAAAAAAAATCAAATATAATAAGTGAAATAAAAAAA
1462475 TAAAAAAAATCAAAGTATAATAAGTGAAATAAAA
1 TAAAAAAAATCAAA-TATAATAAGTGAAATAAAA
1462509 GAGATAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 13 0.45
37 16 0.55
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (36 bp):
TAAAAAAAATCAAATATAATAAGTGAAATAAAAAAA
Found at i:1465750 original size:111 final size:112
Alignment explanation
Indices: 1465522--1465736 Score: 247
Period size: 111 Copynumber: 1.9 Consensus size: 112
1465512 TTTTTTATCA
* * * * * * * * *
1465522 TTTACATTGATAACATTTTAATGGTCATATTAATAAAAATGTAAATATAGATGATTAAAAAGTTA
1 TTTAAATTAATAACATTTTAATGATCAAATTAATAAAAATATAAACATAGAGGACTAAAAAATTA
* * * *
1465587 TTTTAATTTCTTTTATAACTTCTATATCAATAATTAATAGACTCTAG
66 TTTTAATCTCTTTTATAACTTCTAGATCAACAATTAATAGACTCAAG
* * * *
1465634 ATTAAATTAATAAC-TTTTAGTGATCAAATTGATAAAATTATAAACATAGAGGACTAAAAAATTA
1 TTTAAATTAATAACATTTTAATGATCAAATTAATAAAAATATAAACATAGAGGACTAAAAAATTA
*
1465698 TTTT-ATCT-TTTTATAACTTCTAGGTCAACAATTAATAGA
66 TTTTAATCTCTTTTATAACTTCTAGATCAACAATTAATAGA
1465737 GATTCAATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
109 28 0.33
110 3 0.03
111 44 0.51
112 11 0.13
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (112 bp):
TTTAAATTAATAACATTTTAATGATCAAATTAATAAAAATATAAACATAGAGGACTAAAAAATTA
TTTTAATCTCTTTTATAACTTCTAGATCAACAATTAATAGACTCAAG
Found at i:1467841 original size:18 final size:18
Alignment explanation
Indices: 1467820--1467857 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1467810 TCAGAAGTTT
1467820 AGGAACCAATTTAAAATC
1 AGGAACCAATTTAAAATC
1467838 AGGAACCAATTTAAAATC
1 AGGAACCAATTTAAAATC
1467856 AG
1 AG
1467858 AGTAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (18 bp):
AGGAACCAATTTAAAATC
Found at i:1468605 original size:15 final size:16
Alignment explanation
Indices: 1468587--1468620 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1468577 TAAAAAGGGA
1468587 AAATAATAA-AATAAT
1 AAATAATAATAATAAT
*
1468602 AAATAATAATAGTAAT
1 AAATAATAATAATAAT
1468618 AAA
1 AAA
1468621 GATAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:1469323 original size:20 final size:20
Alignment explanation
Indices: 1469298--1469337 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1469288 TAAAGATAAT
*
1469298 TCCTAAA-ATAACATCTTAAA
1 TCCTAAATAAAACA-CTTAAA
1469318 TCCTAAATAAAACACTTAAA
1 TCCTAAATAAAACACTTAAA
1469338 ACTATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.28
Consensus pattern (20 bp):
TCCTAAATAAAACACTTAAA
Found at i:1471376 original size:30 final size:30
Alignment explanation
Indices: 1471342--1471402 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1471332 TTTTTCACTG
* *
1471342 TTCGAACCAAAATTGTAATGTTGTTTTTTT
1 TTCGAACCAAAACTGTAATGTTATTTTTTT
*
1471372 TTCGAACCAAAACTGTACTGTTATTTTTTT
1 TTCGAACCAAAACTGTAATGTTATTTTTTT
1471402 T
1 T
1471403 ACATTGCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (30 bp):
TTCGAACCAAAACTGTAATGTTATTTTTTT
Found at i:1471581 original size:27 final size:28
Alignment explanation
Indices: 1471540--1471607 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
1471530 TTCTTCTAAC
* * *
1471540 TTTTCTGCACAGTTCGAACCAAGTC-TT
1 TTTTCTGCACTGTTCGAACCAAATCAGT
*
1471567 TTTTCTGCTCTGTTCGAACCAAATCAGT
1 TTTTCTGCACTGTTCGAACCAAATCAGT
1471595 TTTTCTGCACTGT
1 TTTTCTGCACTGT
1471608 CCTAACAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 22 0.63
28 13 0.37
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (28 bp):
TTTTCTGCACTGTTCGAACCAAATCAGT
Found at i:1473316 original size:21 final size:20
Alignment explanation
Indices: 1473290--1473342 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1473280 GCTTTAGAAT
* *
1473290 TTTTCCTGGGATGCAACTAGC
1 TTTTCCTGGGACG-AACCAGC
*
1473311 TTTTCCTTGGACGAACCAGC
1 TTTTCCTGGGACGAACCAGC
1473331 TTTT-CTGGGACG
1 TTTTCCTGGGACG
1473343 TAGTCAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 11 0.39
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (20 bp):
TTTTCCTGGGACGAACCAGC
Found at i:1474843 original size:15 final size:16
Alignment explanation
Indices: 1474823--1474856 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1474813 TTAATAAGAA
1474823 AAATAATAA-AATAAT
1 AAATAATAACAATAAT
*
1474838 AAATAATAACAGTAAT
1 AAATAATAACAATAAT
1474854 AAA
1 AAA
1474857 GATAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATAATAACAATAAT
Found at i:1475632 original size:20 final size:19
Alignment explanation
Indices: 1475588--1475660 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1475578 TTTTTCGACT
* *
1475588 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATTATG-AC
*
1475608 ATCGCAATACGATTATGAC
1 ATCGCAATGCGATTATGAC
* *
1475627 TGTCGCAACGCGATTATGAC
1 -ATCGCAATGCGATTATGAC
1475647 ATCGCAATGCGATT
1 ATCGCAATGCGATT
1475661 TTCAAAGCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
ATCGCAATGCGATTATGAC
Found at i:1476011 original size:18 final size:18
Alignment explanation
Indices: 1475975--1476012 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1475965 TATTTTACAA
*
1475975 AAATAAATCAAAACGAAT
1 AAATAAATCAAAACAAAT
1475993 AAATAAATCACAAA-AAAT
1 AAATAAATCA-AAACAAAT
1476011 AA
1 AA
1476013 TGATTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.16
Consensus pattern (18 bp):
AAATAAATCAAAACAAAT
Found at i:1482562 original size:33 final size:34
Alignment explanation
Indices: 1482520--1482590 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 34
1482510 GCCCTGATTA
1482520 TATATATATAATATTATATAT-TTTTATATTAAT
1 TATATATATAATATTATATATATTTTATATTAAT
*
1482553 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTATATATATTTTATATTAAT
1482587 TATA
1 TATA
1482591 AACCCTAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTATATATATTTTATATTAAT
Found at i:1482992 original size:19 final size:19
Alignment explanation
Indices: 1482957--1482994 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1482947 TTTCTCGAAA
*
1482957 TCGGGTCGGGTTTGGGTTC
1 TCGGGTCGGGTTCGGGTTC
1482976 TCGGGATCGGG-TCGGGTTC
1 TCGGG-TCGGGTTCGGGTTC
1482995 AGGGACGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.03, C:0.18, G:0.47, T:0.32
Consensus pattern (19 bp):
TCGGGTCGGGTTCGGGTTC
Found at i:1485070 original size:2 final size:2
Alignment explanation
Indices: 1485063--1485095 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1485053 ATTATACTTT
*
1485063 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1485096 GTGTGTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1498551 original size:33 final size:33
Alignment explanation
Indices: 1498514--1498576 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1498504 TCGAACAATA
1498514 ATGCTTCTCCTGAGCATGTTGAATCACACGTGG
1 ATGCTTCTCCTGAGCATGTTGAATCACACGTGG
1498547 ATGCTTCTCCTGAGCATGTTGAATCACACG
1 ATGCTTCTCCTGAGCATGTTGAATCACACG
1498577 CAGATGTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.30
Consensus pattern (33 bp):
ATGCTTCTCCTGAGCATGTTGAATCACACGTGG
Found at i:1502946 original size:12 final size:12
Alignment explanation
Indices: 1502929--1502962 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1502919 AATACTGGAT
1502929 GAATTAGGGAAA
1 GAATTAGGGAAA
1502941 GAATTAGGGAAA
1 GAATTAGGGAAA
*
1502953 AAATTAGGGA
1 GAATTAGGGA
1502963 TTTAAGCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (12 bp):
GAATTAGGGAAA
Found at i:1503954 original size:24 final size:24
Alignment explanation
Indices: 1503926--1503977 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1503916 ATGAGTTTTG
*
1503926 AGGAGTAGTATCGATACATCTTGA
1 AGGAGTAGTATCGATACACCTTGA
*
1503950 A-G-G-AGTATCGATACCCCTTGA
1 AGGAGTAGTATCGATACACCTTGA
1503971 AGGAGTA
1 AGGAGTA
1503978 TCGATACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 2 0.09
24 2 0.09
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (24 bp):
AGGAGTAGTATCGATACACCTTGA
Found at i:1503958 original size:21 final size:21
Alignment explanation
Indices: 1503932--1503984 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1503922 TTTGAGGAGT
*
1503932 AGTATCGATACATCTTGAAGG
1 AGTATCGATACACCTTGAAGG
*
1503953 AGTATCGATACCCCTTGAAGG
1 AGTATCGATACACCTTGAAGG
1503974 AGTATCGATAC
1 AGTATCGATAC
1503985 TGAGGGTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (21 bp):
AGTATCGATACACCTTGAAGG
Found at i:1504020 original size:21 final size:21
Alignment explanation
Indices: 1503994--1504035 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1503984 CTGAGGGTCT
*
1503994 GGTATCGAGACCAAGGGGCTC
1 GGTATCCAGACCAAGGGGCTC
1504015 GGTATCCAGACCAAGGGGCTC
1 GGTATCCAGACCAAGGGGCTC
1504036 TAGAATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (21 bp):
GGTATCCAGACCAAGGGGCTC
Found at i:1510239 original size:17 final size:17
Alignment explanation
Indices: 1510217--1510250 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1510207 GGGAAGGCCC
1510217 TTGTCCGAGGACTAAGG
1 TTGTCCGAGGACTAAGG
1510234 TTGTCCGAGGACTAAGG
1 TTGTCCGAGGACTAAGG
1510251 GAAGCGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (17 bp):
TTGTCCGAGGACTAAGG
Found at i:1514179 original size:6 final size:6
Alignment explanation
Indices: 1514165--1514199 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1514155 GTAATAGAGG
*
1514165 GAAGAA GAAGGA GAAGGA GAAGGA GAAGGA GAAGG
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGG
1514200 GGGAGTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:1515313 original size:34 final size:34
Alignment explanation
Indices: 1515269--1515351 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
1515259 TATCAATTGT
*
1515269 TATATATATATATATATAAGTGAATCTTAATTCA
1 TATATTTATATATATATAAGTGAATCTTAATTCA
1515303 TATATTTATATATATATAAGTGAATCTTAATTCA
1 TATATTTATATATATATAAGTGAATCTTAATTCA
1515337 TATATTTATATATAT
1 TATATTTATATATAT
1515352 TGTTGCATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (34 bp):
TATATTTATATATATATAAGTGAATCTTAATTCA
Found at i:1518356 original size:24 final size:23
Alignment explanation
Indices: 1518324--1518400 Score: 99
Period size: 19 Copynumber: 3.5 Consensus size: 23
1518314 TTTGCCCACC
*
1518324 GTCGAATTACACCGAATCGAATTG
1 GTCGAATTAAACCGAATCG-ATTG
1518348 GTCGAATTAAACCGAATC----G
1 GTCGAATTAAACCGAATCGATTG
*
1518367 GTTGAATTAAACCGAATCGATTG
1 GTCGAATTAAACCGAATCGATTG
1518390 GTCGAATTAAA
1 GTCGAATTAAA
1518401 ATTTTAAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 18 0.39
23 11 0.24
24 17 0.37
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (23 bp):
GTCGAATTAAACCGAATCGATTG
Found at i:1518643 original size:19 final size:19
Alignment explanation
Indices: 1518619--1518659 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1518609 TGATCAAATC
1518619 GTTGAATCAGAAATTAAGG
1 GTTGAATCAGAAATTAAGG
*
1518638 GTTGAATCAGAAATTGAGG
1 GTTGAATCAGAAATTAAGG
1518657 GTT
1 GTT
1518660 TTATTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (19 bp):
GTTGAATCAGAAATTAAGG
Found at i:1519205 original size:2 final size:2
Alignment explanation
Indices: 1519198--1519222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1519188 TTACCCTATT
1519198 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1519223 GTATCCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1520614 original size:44 final size:44
Alignment explanation
Indices: 1520565--1521098 Score: 377
Period size: 44 Copynumber: 12.2 Consensus size: 44
1520555 CTCTCTATGC
* *
1520565 GATGGAAACGAGCGAAATGTTGATTTTGACCCAACTCCTTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * * * * *
1520609 TATGGAATCAAGCGAGATGTTGAGGTTGACCCAATTCCCTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * * * *
1520653 TATGGAATCGAGCAAAATGTTGATGTGGACTCGACTTCC-TCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAAC-TCCTTCTGT
* * * * *
1520697 TATGGAATCGAGCGTAATGTTTATGTTGACCCAACTCCCTCTAT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * * * * *
1520741 TATGGAATCAAGCAAAATGTTTATGTTGATCCAACTTATTTCTTTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAAC-----TCCTTCTGT
* **** *
1520790 GATGGAATCGAGCGAAATATTGATAAACACTCAACTCCTTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * ** *** *
1520834 GATAGAATAGAGCGAAATGTTGATG-AAATTTAACTCATTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * * *
1520877 GATGGAATCGAACGAAATGTTGATTTTAACCCAACTCATTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * *
1520921 TATGGAATCGAGCGAAATGTT--TGTTGACCCGAGTCCTTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
* * * **
1520963 GATAGAATCAAGAGAAATGTTGATGTTG-TTCAACTCCTTCTGT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
** * *
1521006 GATGGAATCGAATGAAAATGCTT-A--TTGACCCAACTTCTTTTGT
1 GATGGAATCGAGCG-AAATG-TTGATGTTGACCCAACTCCTTCTGT
* * ** * * *
1521049 GATGGAATTGAACGAAATACT--TGTTGACTCGACTCCTTCTAT
1 GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
1521091 GATGGAAT
1 GATGGAAT
1521099 GTGATAGAAT
Statistics
Matches: 385, Mismatches: 90, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.00
42 62 0.16
43 82 0.21
44 205 0.53
45 5 0.01
49 30 0.08
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (44 bp):
GATGGAATCGAGCGAAATGTTGATGTTGACCCAACTCCTTCTGT
Found at i:1521066 original size:86 final size:86
Alignment explanation
Indices: 1520865--1521066 Score: 201
Period size: 86 Copynumber: 2.3 Consensus size: 86
1520855 GATGAAATTT
* * * *
1520865 AACTCATTCTGTGATGGAATCGAACGAAATGTTGATTTTAACCCAACTCATTCTGTTATGGAATC
1 AACTCCTTCTGTGATGGAATTGAACGAAATGTTGATGTTAACCCAACTCATTCTGTGATGGAATC
* * *
1520930 GAGCGAAATGTTTGTTGACCC
66 GAACGAAATGCTTATTGACCC
* * * * * *** *
1520951 GAGTCCTTCTGTGATAGAA-TCAAGAGAAATGTTGATGTT-GTTCAACTCCTTCTGTGATGGAAT
1 AACTCCTTCTGTGATGGAATTGAA-CGAAATGTTGATGTTAACCCAACTCATTCTGTGATGGAAT
*
1521014 CGAATGAAAATGCTTATTGACCC
65 CGAACG-AAATGCTTATTGACCC
* *
1521037 AACTTCTTTTGTGATGGAATTGAACGAAAT
1 AACTCCTTCTGTGATGGAATTGAACGAAAT
1521067 ACTTGTTGAC
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
85 25 0.28
86 61 0.69
87 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (86 bp):
AACTCCTTCTGTGATGGAATTGAACGAAATGTTGATGTTAACCCAACTCATTCTGTGATGGAATC
GAACGAAATGCTTATTGACCC
Found at i:1521095 original size:42 final size:43
Alignment explanation
Indices: 1520865--1521098 Score: 133
Period size: 42 Copynumber: 5.5 Consensus size: 43
1520855 GATGAAATTT
* * *
1520865 AACTCATTCTGTGATGGAATCGAACG-AAAT-GTTGATTTTAACCC
1 AACTCCTTCTGTGATGGAATCGAACGAAAATACTT-A--TTGACCC
* * * ** *
1520909 AACTCATTCTGTTATGGAATCGAGCG-AAATGTTTGTTGACCC
1 AACTCCTTCTGTGATGGAATCGAACGAAAATACTTATTGACCC
* * * * **
1520951 GAGTCCTTCTGTGATAGAATC-AA-GAGAAAT-GTTGATGTTG-TTC
1 AACTCCTTCTGTGATGGAATCGAACGA-AAATACTT-A--TTGACCC
* *
1520994 AACTCCTTCTGTGATGGAATCGAATGAAAATGCTTATTGACCC
1 AACTCCTTCTGTGATGGAATCGAACGAAAATACTTATTGACCC
* * * * *
1521037 AACTTCTTTTGTGATGGAATTGAACG-AAATACTTGTTGACTC
1 AACTCCTTCTGTGATGGAATCGAACGAAAATACTTATTGACCC
* *
1521079 GACTCCTTCTATGATGGAAT
1 AACTCCTTCTGTGATGGAAT
1521099 GTGATAGAAT
Statistics
Matches: 148, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 58 0.39
43 42 0.28
44 38 0.26
45 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (43 bp):
AACTCCTTCTGTGATGGAATCGAACGAAAATACTTATTGACCC
Found at i:1521749 original size:42 final size:42
Alignment explanation
Indices: 1521667--1521752 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1521657 CCTGAAGTAC
* * ** *
1521667 TTAATCACCATGCTCGAAAGACTTACTAGTGATTCGAAGGAT
1 TTAATCACCATGCTCGAAAAACTTACTAATGACCCAAAGGAT
*
1521709 TTAATCATCATGCTCGAAAAACTTACTAATGACCCAAAGGAT
1 TTAATCACCATGCTCGAAAAACTTACTAATGACCCAAAGGAT
1521751 TT
1 TT
1521753 TCTTATTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (42 bp):
TTAATCACCATGCTCGAAAAACTTACTAATGACCCAAAGGAT
Found at i:1524111 original size:2 final size:2
Alignment explanation
Indices: 1524104--1524144 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1524094 TTTTATTGTG
1524104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1524145 ATTGCCTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1527004 original size:43 final size:44
Alignment explanation
Indices: 1526957--1527379 Score: 261
Period size: 43 Copynumber: 9.9 Consensus size: 44
1526947 TGCAAATTTA
* * *
1526957 ATTCCATCACAGAAGGAGTTGATCAAACATCAATA-ATCGCTCA
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
* **** * * *
1527000 ATTCCATCATAGAAGTG-GTTGATTTTTCAGCAACATTTCGGTTG
1 ATTCCATCACAGAAG-GAGTTGATCAAACATCAACATTTCGCTCG
* * * * *
1527044 ATTCCATCACAGAAGGACTTGAACAAA-AACAACATTTTGATCG
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
* * * * *
1527087 ATTCCATCACTGAAGGAGTTGGTCAAACATCAATATTTCCCTCA
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
* * * * *
1527131 ATTCTATCACTGAAGGAGTTAAATCAGA-A--AACATTTCGTTCG
1 ATTCCATCACAGAAGGAGTT-GATCAAACATCAACATTTCGCTCG
* * *
1527173 ATTTCATCACAGAAGTAGTTGA-AAAACATCAACATTTCGCTCG
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
* * * * * *
1527216 TTTCCATCACAGAAGGAGTCAGGTC-AACA--AGCATTTCGTTAG
1 ATTCCATCACAGAAGGAGT-TGATCAAACATCAACATTTCGCTCG
* * *
1527258 ATTCCATCAC---AGGAGTTGAAC-AACATCAATATTTCTCTCG
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
* * * * * *
1527298 ATTCCATCAAAGAAAGAGTAGGGTC-AACA--AACATTTTGCTCA
1 ATTCCATCACAGAAGGAGT-TGATCAAACATCAACATTTCGCTCG
* *
1527340 ATTCCATAACAGAAGGAGTTGGGTCAAA-ATCAACATTTCG
1 ATTCCATCACAGAAGGAGTT-GATCAAACATCAACATTTCG
1527380 TTCAACTTAA
Statistics
Matches: 280, Mismatches: 80, Indels: 39
0.70 0.20 0.10
Matches are distributed among these distances:
38 6 0.02
39 6 0.02
40 19 0.07
41 2 0.01
42 74 0.26
43 97 0.35
44 72 0.26
45 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (44 bp):
ATTCCATCACAGAAGGAGTTGATCAAACATCAACATTTCGCTCG
Found at i:1527209 original size:129 final size:129
Alignment explanation
Indices: 1526957--1527234 Score: 316
Period size: 129 Copynumber: 2.1 Consensus size: 129
1526947 TGCAAATTTA
*
1526957 ATTCCATCACAGAAGGAGTTGATCAAACATCAATAATCGCTCAATTCCATCATAGAAGTGGTTGA
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAATAATCCCTCAATTCCATCATAGAAGTGGTTGA
** * *
1527022 TTTTTCAGCAACATTTCGGTTGATTCCATCACAGAAGGACTTGAACAAAAACAACATTTTGATCG
66 -TAATCAGAAACATTTCGGTTGATTCCATCACAGAAGGACTTGAACAAAAACAACATTTCGATCG
* * * *
1527087 ATTCCATCACTGAAGGAGTTGGTCAAACATCAATATTTCCCTCAATTCTATCACT-GAAG-GAGT
1 ATTCCATCACAGAAGGAGTTGATCAAACATCAATA-ATCCCTCAATTCCATCA-TAGAAGTG-GT
* * * *
1527150 T-A-AATCAGAAAACATTTC-GTTCGATTTCATCACAGAAGTAGTTGAA-AAACATCAACATTTC
63 TGATAATCAG-AAACATTTCGGTT-GATTCCATCACAGAAGGACTTGAACAAA-AACAACATTTC
*
1527211 GCTCG
125 GATCG
*
1527216 TTTCCATCACAGAAGGAGT
1 ATTCCATCACAGAAGGAGT
1527235 CAGGTCAACA
Statistics
Matches: 126, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
128 10 0.08
129 59 0.47
130 35 0.28
131 21 0.17
132 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (129 bp):
ATTCCATCACAGAAGGAGTTGATCAAACATCAATAATCCCTCAATTCCATCATAGAAGTGGTTGA
TAATCAGAAACATTTCGGTTGATTCCATCACAGAAGGACTTGAACAAAAACAACATTTCGATCG
Found at i:1527231 original size:85 final size:83
Alignment explanation
Indices: 1527030--1527360 Score: 247
Period size: 85 Copynumber: 3.9 Consensus size: 83
1527020 GATTTTTCAG
* * * * * *
1527030 CAACATTTCGGTTGATTCCATCACAGAAGGACTTGAACA-AAAACAACATTTTGATCGATTCCAT
1 CAACATTTCGCTCGATTCCATCACAGAAGGAGTT-AA-ATCAAA-AACATTTCGTTCGATTCCAT
* **
1527094 CACTGAAGGAGTTGGTCAAACAT
63 CACAGAA-GAGTT-GAAAAACAT
* * * * * *
1527117 CAATATTTCCCTCAATTCTATCACTGAAGGAGTTAAATCAGAAAACATTTCGTTCGATTTCATCA
1 CAACATTTCGCTCGATTCCATCACAGAAGGAGTTAAATCA-AAAACATTTCGTTCGATTCCATCA
1527182 CAGAAGTAGTTGAAAAACAT
65 CAGAAG-AGTTGAAAAACAT
* * ** * *
1527202 CAACATTTCGCTCGTTTCCATCACAGAAGGAGTCAGGTCAACAAGCATTTCGTTAGATTCCATCA
1 CAACATTTCGCTCGATTCCATCACAGAAGGAGTTAAATCAA-AAACATTTCGTTCGATTCCATCA
*
1527267 CAG--GAGTTGAACAACAT
65 CAGAAGAGTTGAAAAACAT
* * * * ** * * * *
1527284 CAATATTTCTCTCGATTCCATCAAAGAAAGAG-TAGGGTCAACAAACATTTTGCTCAATTCCATA
1 CAACATTTCGCTCGATTCCATCACAGAAGGAGTTA-AATCAA-AAACATTTCGTTCGATTCCATC
1527348 ACAGAAGGAGTTG
64 ACAGAA-GAGTTG
1527361 GGTCAAAATC
Statistics
Matches: 196, Mismatches: 40, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
81 1 0.01
82 66 0.34
83 1 0.01
84 1 0.01
85 69 0.35
86 30 0.15
87 28 0.14
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (83 bp):
CAACATTTCGCTCGATTCCATCACAGAAGGAGTTAAATCAAAAACATTTCGTTCGATTCCATCAC
AGAAGAGTTGAAAAACAT
Found at i:1527323 original size:82 final size:84
Alignment explanation
Indices: 1527159--1527333 Score: 230
Period size: 82 Copynumber: 2.1 Consensus size: 84
1527149 TTAAATCAGA
* * *
1527159 AAACATTTCGTTCGATTTCATCACAGAAGTAGTTGAAAAACATCAACATTTCGCTCGTTTCCATC
1 AAACATTTCGTTAGATTCCATCACAG-AGTAGTTGAAAAACATCAACATTTCGCTCGATTCCATC
* *
1527224 ACAGAAGGAGTCAGGTCAAC
65 AAAGAAAGAGTCAGGTCAAC
* * * *
1527244 AAGCATTTCGTTAGATTCCATCACAG-G-AGTTGAACAACATCAATATTTCTCTCGATTCCATCA
1 AAACATTTCGTTAGATTCCATCACAGAGTAGTTGAAAAACATCAACATTTCGCTCGATTCCATCA
1527307 AAGAAAGAGT-AGGGTCAAC
66 AAGAAAGAGTCA-GGTCAAC
1527326 AAACATTT
1 AAACATTT
1527334 TGCTCAATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 54 0.68
83 1 0.01
85 23 0.29
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (84 bp):
AAACATTTCGTTAGATTCCATCACAGAGTAGTTGAAAAACATCAACATTTCGCTCGATTCCATCA
AAGAAAGAGTCAGGTCAAC
Found at i:1527344 original size:82 final size:82
Alignment explanation
Indices: 1527189--1527351 Score: 204
Period size: 82 Copynumber: 2.0 Consensus size: 82
1527179 TCACAGAAGT
* * * *
1527189 AGTTGAAAAACATCAACATTTCGCTCGTTTCCATCACAGAAGGAGTCAGGTCAACAAGCATTTCG
1 AGTTGAAAAACATCAACATTTCGCTCGATTCCATCAAAGAAAGAGTCAGGTCAACAAACATTTCG
* *
1527254 TTAGATTCCATCACAGG
66 TCAGATTCCATAACAGG
* * * *
1527271 AGTTGAACAACATCAATATTTCTCTCGATTCCATCAAAGAAAGAGT-AGGGTCAACAAACATTTT
1 AGTTGAAAAACATCAACATTTCGCTCGATTCCATCAAAGAAAGAGTCA-GGTCAACAAACATTTC
1527335 GCTCA-ATTCCATAACAG
65 G-TCAGATTCCATAACAG
1527352 AAGGAGTTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
82 66 0.96
83 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (82 bp):
AGTTGAAAAACATCAACATTTCGCTCGATTCCATCAAAGAAAGAGTCAGGTCAACAAACATTTCG
TCAGATTCCATAACAGG
Found at i:1535657 original size:20 final size:20
Alignment explanation
Indices: 1535632--1535834 Score: 135
Period size: 20 Copynumber: 10.1 Consensus size: 20
1535622 GATTTTCCAT
* *
1535632 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* * **
1535652 AATCGCAACGTGAACATATA
1 AATCGCAACGCGAATACGTA
*
1535672 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * * *
1535691 CTATCGCAATGAGTATCCGTA
1 -AATCGCAACGCGAATACGTA
1535712 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
1535733 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
1535753 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
1535773 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
1535793 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
1535813 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
1535833 AA
1 AA
1535835 AGATGATTTG
Statistics
Matches: 140, Mismatches: 34, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 114 0.81
21 21 0.15
22 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:1535756 original size:101 final size:101
Alignment explanation
Indices: 1535632--1535820 Score: 220
Period size: 101 Copynumber: 1.9 Consensus size: 101
1535622 GATTTTCCAT
* * * *
1535632 AATCGCAACGCGAATATGAAAATCGCAACGTGAACATATAAATCGCAACGCG-ATTCTG-ACTAT
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTA-TCTGTA-AAT
* * *
1535695 CGCAATGAGTATCCGTAAATCGCAACGACAATACGTAA
64 CGCAACGAGAATACGTAAATCGCAACGACAATACGTAA
* * * * * * *
1535733 AATCGCAACGCGTATCCGTAAATCGTAACGAGAATACGTAAATCGCAATGCGTATCTGTAAATCG
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCG
1535798 CAACGAGAATACGTAAATCGCAA
66 CAACGAGAATACGTAAATCGCAA
1535821 TGCGTATCCG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
101 70 0.97
102 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (101 bp):
AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCG
CAACGAGAATACGTAAATCGCAACGACAATACGTAA
Found at i:1535787 original size:40 final size:40
Alignment explanation
Indices: 1535693--1535834 Score: 230
Period size: 40 Copynumber: 3.5 Consensus size: 40
1535683 GATTCTGACT
* *
1535693 ATCGCAATGAGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGT-AA
* *
1535734 ATCGCAACGCGTATCCGTAAATCGTAACGAGAATACGTAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
*
1535774 ATCGCAATGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
1535814 ATCGCAATGCGTATCCGTAAA
1 ATCGCAATGCGTATCCGTAAA
1535835 AGATGATTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 59 0.63
41 34 0.37
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:1535849 original size:14 final size:14
Alignment explanation
Indices: 1535830--1535859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1535820 ATGCGTATCC
1535830 GTAAAAGATGATTT
1 GTAAAAGATGATTT
*
1535844 GTAAAAGTTGATTT
1 GTAAAAGATGATTT
1535858 GT
1 GT
1535860 TTAATTGATG
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:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
GTAAAAGATGATTT
Found at i:1536017 original size:33 final size:33
Alignment explanation
Indices: 1535975--1536164 Score: 238
Period size: 33 Copynumber: 5.6 Consensus size: 33
1535965 TATCACAATA
1535975 CGAAATGAAAATCGCAACGAGAGAATCGCAACG
1 CGAAATGAAAATCGCAACGAGAGAATCGCAACG
* *
1536008 CGAAATGAAAATCGCAACGACAAAATCGCAACG
1 CGAAATGAAAATCGCAACGAGAGAATCGCAACG
* *
1536041 CGAAACT-AAAATCGCAACGTGAAAATGACTATCGCAATG
1 CGAAA-TGAAAATCGCAAC--G-AGA-GA--ATCGCAACG
*
1536080 CGAAATGAAAATCGCAACGAGAGAATCGCAATG
1 CGAAATGAAAATCGCAACGAGAGAATCGCAACG
* * *
1536113 CGAAATGAAAATCGCAATGAGGGAATCGCAAAG
1 CGAAATGAAAATCGCAACGAGAGAATCGCAACG
1536146 CGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCAACG
1536165 CGAATTTAGT
Statistics
Matches: 139, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
33 104 0.75
34 1 0.01
35 3 0.02
36 4 0.03
37 2 0.01
38 1 0.01
39 24 0.17
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
CGAAATGAAAATCGCAACGAGAGAATCGCAACG
Found at i:1536083 original size:72 final size:66
Alignment explanation
Indices: 1535975--1536164 Score: 222
Period size: 72 Copynumber: 2.8 Consensus size: 66
1535965 TATCACAATA
* *
1535975 CGAAATGAAAATCGCAACG-AGAGAATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAA
1 CGAAATGAAAATCGCAATGAAG-GAATCGCAAAGCGAAATGAAAATCGCAACGACAAAATCGCAA
1536039 CG
65 CG
* * * *
1536041 CGAAACT-AAAATCGCAACGTGAAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 CGAAA-TGAAAATCGCAA--TG--AAGGA--ATCGCAAAGCGAAATGAAAATCGCAACGACAAAA
*
1536105 TCGCAATG
59 TCGCAACG
*
1536113 CGAAATGAAAATCGCAATGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCAATGAAGGAATCGCAAAGCGAAATGAAAATCGCAACG
1536165 CGAATTTAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
66 42 0.40
67 1 0.01
68 4 0.04
70 4 0.04
71 2 0.02
72 53 0.50
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (66 bp):
CGAAATGAAAATCGCAATGAAGGAATCGCAAAGCGAAATGAAAATCGCAACGACAAAATCGCAAC
G
Found at i:1536140 original size:105 final size:105
Alignment explanation
Indices: 1535957--1536164 Score: 328
Period size: 105 Copynumber: 2.0 Consensus size: 105
1535947 GTTGAAGGCA
1535957 AAAATGACTATCACAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCG
1 AAAATGACTATCACAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCG
*
1536022 CAACGACAAAATCGCAACGCGAAACT-AAAATCGCAACGTG
66 CAACGACAAAATCGCAAAGCGAAA-TGAAAATCGCAACGTG
* * *
1536062 AAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCG
1 AAAATGACTATCACAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCG
* ***
1536127 CAATGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
66 CAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACG
1536165 CGAATTTAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 1 0.01
105 93 0.99
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.13
Consensus pattern (105 bp):
AAAATGACTATCACAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCG
CAACGACAAAATCGCAAAGCGAAATGAAAATCGCAACGTG
Found at i:1536206 original size:19 final size:19
Alignment explanation
Indices: 1536164--1536209 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1536154 AAATCGCAAC
*
1536164 GCGAATTTAGTTCTGCGTT
1 GCGATTTTAGTTCTGCGTT
1536183 GCGATTTTAGTT-TCGCGTT
1 GCGATTTTAGTTCT-GCGTT
1536202 GCGATTTT
1 GCGATTTT
1536210 CATTTCGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTCTGCGTT
Found at i:1536215 original size:19 final size:19
Alignment explanation
Indices: 1536178--1536258 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
1536168 ATTTAGTTCT
1536178 GCGTTGCGATTTT-AGTTTC
1 GCGTTGCGATTTTCA-TTTC
1536197 GCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
** *
1536216 GTATTACGA--TTC---TC
1 GCGTTGCGATTTTCATTTC
*
1536230 TCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
*
1536249 GCATTGCGAT
1 GCGTTGCGAT
1536259 AGTAATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
14 7 0.15
16 3 0.06
17 3 0.06
19 33 0.70
20 1 0.02
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
GCGTTGCGATTTTCATTTC
Found at i:1536384 original size:14 final size:14
Alignment explanation
Indices: 1536365--1536401 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1536355 CATCAATTAA
1536365 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1536379 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1536393 ACAAATCAA
1 ACAAATCAA
1536402 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1539000 original size:46 final size:49
Alignment explanation
Indices: 1538948--1539039 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1538938 GAAATTGTCT
1538948 CTATTATTAGAA-ATTAAAAAT-TCAAAAATATAT-TTAATTTATAATC
1 CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATAATC
** * * *
1538994 CTATTATTTTAAGATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATA
1539040 TATATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 10 0.26
47 7 0.18
48 11 0.29
49 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (49 bp):
CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATAATC
Found at i:1539162 original size:20 final size:19
Alignment explanation
Indices: 1539123--1539174 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1539113 TTTCTTTGAT
1539123 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1539142 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1539162 ATTTATAAAATAA
1 A-TTAAAAAATAA
1539175 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Done.