Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 112 of 378
Found at i:31178056 original size:40 final size:39
Alignment explanation
Indices: 31178031--31178173 Score: 189
Period size: 40 Copynumber: 3.6 Consensus size: 39
31178021 GCTACTCGCT
* * *
31178031 CAAATGCCTTCGGAACTTAGCCCGGATATAGT-AGTTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTCA-CTAGCA
*
31178071 CAAATGCCTTCGGGACTTAGCCCAGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATTAGTCACTAGCA
*
31178111 CAAATGCCTTCGGGATTTAGCCCGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTCACTAGCA
*
31178151 CAAATGCCTTTGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
31178174 CGTTAGCATC
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
39 1 0.01
40 87 0.95
41 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTCACTAGCA
Found at i:31189843 original size:40 final size:40
Alignment explanation
Indices: 31189788--31189908 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
31189778 TACTGTAGTA
*
31189788 AATTAAAAGAAGCTCTGGGTACTCGATTTCATTTTAGCAC
1 AATTACAAGAAGCTCTGGGTACTCGATTTCATTTTAGCAC
31189828 AATTACAAGAAGCTCTGGGTACTCGATTTCATTTTAGCAC
1 AATTACAAGAAGCTCTGGGTACTCGATTTCATTTTAGCAC
*
31189868 AATTACAAGAAGCTCTGGGTACTCGATTGT-ATTTCAGCAC
1 AATTACAAGAAGCTCTGGGTACTCGATT-TCATTTTAGCAC
31189908 A
1 A
31189909 GCGTTTCATC
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 77 0.99
41 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (40 bp):
AATTACAAGAAGCTCTGGGTACTCGATTTCATTTTAGCAC
Found at i:31196162 original size:24 final size:24
Alignment explanation
Indices: 31196135--31196221 Score: 174
Period size: 24 Copynumber: 3.6 Consensus size: 24
31196125 CTTATTATGT
31196135 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
31196159 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
31196183 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
31196207 TCGCACACATAGTGC
1 TCGCACACATAGTGC
31196222 ATTTGAGATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:31199254 original size:23 final size:23
Alignment explanation
Indices: 31199221--31199275 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
31199211 TTTGACGTAT
*
31199221 TAAAACAAAAAATCTTACTGAAA
1 TAAAACAAAAAATCTTAATGAAA
*
31199244 TAAAACCAAAAATCTTAATGAAA
1 TAAAACAAAAAATCTTAATGAAA
31199267 TAAATACAA
1 TAAA-ACAA
31199276 CAATTCAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.22
Consensus pattern (23 bp):
TAAAACAAAAAATCTTAATGAAA
Found at i:31201945 original size:50 final size:50
Alignment explanation
Indices: 31201870--31201970 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
31201860 ACGATACCTG
*
31201870 ATGCTCTACTTTTACCTACAGACATATTTAATATTTAGCTAAAAATTTAA
1 ATGCTCTACTTTTACCTACAGACATATTTAACATTTAGCTAAAAATTTAA
31201920 ATGCTCTACTTTTACCTACAGACATATTTAACATTTAGCTAAAAATTTAA
1 ATGCTCTACTTTTACCTACAGACATATTTAACATTTAGCTAAAAATTTAA
31201970 A
1 A
31201971 AAATTCTCGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (50 bp):
ATGCTCTACTTTTACCTACAGACATATTTAACATTTAGCTAAAAATTTAA
Found at i:31204306 original size:17 final size:17
Alignment explanation
Indices: 31204271--31204309 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
31204261 TTTGTTGGGA
31204271 TTATGTTAGCATATAAGT
1 TTATGTTA-CATATAAGT
31204289 TTATGTTA-ATAGTAAGT
1 TTATGTTACATA-TAAGT
31204306 TTAT
1 TTAT
31204310 ATCCTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 9 0.45
18 8 0.40
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (17 bp):
TTATGTTACATATAAGT
Found at i:31205030 original size:17 final size:17
Alignment explanation
Indices: 31205008--31205043 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31204998 AGTAGAAATA
31205008 TTCATTTTATTACTATT
1 TTCATTTTATTACTATT
31205025 TTCATTTTATTACTATT
1 TTCATTTTATTACTATT
31205042 TT
1 TT
31205044 AATATCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCATTTTATTACTATT
Found at i:31206534 original size:26 final size:26
Alignment explanation
Indices: 31206501--31206555 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
31206491 ATGATTTCAA
*
31206501 GGTAAGTTTGTGATGGAATGAATTAT
1 GGTAAGTTTGTGATGGAAGGAATTAT
31206527 GGTAAGTTTGTGATGGAAGGAATTAT
1 GGTAAGTTTGTGATGGAAGGAATTAT
31206553 GGT
1 GGT
31206556 CATGAGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.36
Consensus pattern (26 bp):
GGTAAGTTTGTGATGGAAGGAATTAT
Found at i:31212587 original size:51 final size:50
Alignment explanation
Indices: 31212527--31212665 Score: 183
Period size: 49 Copynumber: 2.8 Consensus size: 50
31212517 GAAGCTATCT
* *
31212527 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT-TTC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGAGC-CAATTATTC
* *
31212577 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCG-GCCAATTATTC
1 -GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGAGCCAATTATTC
* * *
31212627 GGTACACGTAGTAGCCTGCACTTAGTACTATACACGTGA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
31212666 CCTCACAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
49 37 0.48
50 4 0.05
51 36 0.47
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (50 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGAGCCAATTATTC
Found at i:31214485 original size:24 final size:24
Alignment explanation
Indices: 31214453--31214502 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31214443 AGAGGTAGAG
31214453 TATGTGTACTGAAAAGATCAAAAC
1 TATGTGTACTGAAAAGATCAAAAC
31214477 TATGTGTACTGAAAAGATCAAAAC
1 TATGTGTACTGAAAAGATCAAAAC
31214501 TA
1 TA
31214503 GTACAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (24 bp):
TATGTGTACTGAAAAGATCAAAAC
Found at i:31224138 original size:14 final size:14
Alignment explanation
Indices: 31224119--31224146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31224109 ATAAATGCAA
31224119 TTAAAAGAAATTTT
1 TTAAAAGAAATTTT
31224133 TTAAAAGAAATTTT
1 TTAAAAGAAATTTT
31224147 AAAGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAAAAGAAATTTT
Found at i:31225839 original size:11 final size:11
Alignment explanation
Indices: 31225825--31225864 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
31225815 ACTTTCTCTT
31225825 TATTTTGCTAC
1 TATTTTGCTAC
* *
31225836 TATTTTACTAT
1 TATTTTGCTAC
*
31225847 TATGTTGCTAC
1 TATTTTGCTAC
31225858 TATTTTG
1 TATTTTG
31225865 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:31225950 original size:30 final size:31
Alignment explanation
Indices: 31225901--31225964 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
31225891 ACTTATTTTA
*
31225901 TTGTTAATTTTTTTTATTATTTTA-AAGACAT
1 TTGTTAATTTTTGTTATTATTTTAGAA-ACAT
31225932 TTGTTAA-TTTTGTTATTATTTTAGAAACAT
1 TTGTTAATTTTTGTTATTATTTTAGAAACAT
31225962 TTG
1 TTG
31225965 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAGAAACAT
Found at i:31228019 original size:25 final size:25
Alignment explanation
Indices: 31227981--31228048 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
31227971 CAGGCCCATT
*
31227981 TTCACAACTCGTGTGAGCATTCTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
* *
31228006 TTCACAGCTTGTGTGAGCATTTTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
*
31228031 TTCACAGCTCATGTGAGC
1 TTCACAGCTCGTGTGAGC
31228049 GTACATGTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTCTGA
Found at i:31254749 original size:40 final size:40
Alignment explanation
Indices: 31254705--31254960 Score: 279
Period size: 40 Copynumber: 6.5 Consensus size: 40
31254695 TATTCGAGCC
*
31254705 TAAAGACCCACAGGCTAT-ATGCTGGAATTATATCCGGGCT
1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT
* *
31254745 TAAAGACCCGCAGGCTAT-ATGCTGGAATTATATTCAGGCT
1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT
* * *
31254785 TAAAGATCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCT
1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT
*
31254825 TAAAGACCCGCAGGCTAT-ATGCTGGAATTGTATCCGGGCT
1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT
* * *
31254865 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACT
1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT
* ** * * * *
31254905 T-AAGATCAACAGGCTTCGTGCTGGTACTATATCCGGACT
1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT
**
31254944 T-AAGGTCCGCAGGCTTC
1 TAAAGACCCGCAGGCTTC
31254961 GTACTGGTGC
Statistics
Matches: 192, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 48 0.25
40 143 0.74
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT
Found at i:31254826 original size:80 final size:80
Alignment explanation
Indices: 31254705--31254907 Score: 318
Period size: 80 Copynumber: 2.5 Consensus size: 80
31254695 TATTCGAGCC
* * *
31254705 TAAAGACCCACAGGCTAT-ATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTATATGCTG
1 TAAAGACCCGCAGGCT-TCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTG
*
31254769 GAATTATATTCAGGCT
65 GAATTATATCCAGGCT
*
31254785 TAAAGATCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG
1 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG
* *
31254850 AATTGTATCCGGGCT
66 AATTATATCCAGGCT
*
31254865 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACTTAA
1 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAA
31254908 GATCAACAGG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 1 0.01
80 112 0.99
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG
AATTATATCCAGGCT
Found at i:31254938 original size:39 final size:39
Alignment explanation
Indices: 31254875--31254979 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 39
31254865 TAAAGACCCG
* * *
31254875 CAGGCTTCGTGCTGGAATTGTATCCGGACTTAAGATCAA
1 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA
* **
31254914 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGGTCCG
1 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA
* *
31254953 CAGGCTTCGTACTGGTGCTATATCCGG
1 CAGGCTTCGTGCTGGTACTATATCCGG
31254980 GGTTAACGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.29
Consensus pattern (39 bp):
CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA
Found at i:31255009 original size:40 final size:39
Alignment explanation
Indices: 31254872--31255009 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 39
31254862 GCTTAAAGAC
*** *
31254872 CCGCAGGCTTCGTGCTGGAATTGTATCCGGACTTAA-GAT
1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACG-T
** * *
31254911 CAACAGGCTTCGTGCTGGTACTATATCCGGACTTAAGGT
1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT
* **
31254950 CCGCAGGCTTCGTACTGGTGCTATATCCGGGGTTAACGT
1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT
* * *
31254989 CCCGTAGGCTTTGTGTTGGTG
1 -CCGCAGGCTTCGTGCTGGTG
31255010 ATTGAATTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 64 0.79
40 17 0.21
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (39 bp):
CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT
Found at i:31264913 original size:29 final size:29
Alignment explanation
Indices: 31264851--31264953 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
31264841 GTGACGAGAT
* * *
31264851 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
31264880 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
31264909 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
31264938 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31264954 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:31269643 original size:39 final size:39
Alignment explanation
Indices: 31269599--31269792 Score: 316
Period size: 39 Copynumber: 5.0 Consensus size: 39
31269589 ATTATATTAT
* *
31269599 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * * *
31269638 CAGCACAAAGCCTGCGGGACTTTGGCCCAGAGACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
31269677 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
31269716 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
31269755 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
31269793 TCAGTGTCTT
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 145 1.00
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:31275184 original size:50 final size:50
Alignment explanation
Indices: 31275104--31275302 Score: 220
Period size: 50 Copynumber: 4.0 Consensus size: 50
31275094 AAGCTCTCTG
* *
31275104 GTACGCATAGTAGCCTGCACTTAGTACTACAAATGTGACCTATCAATCTA
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTA
* * *
31275154 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACTTAACCATCTA
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTA
* * * * * ** * **
31275204 ATACACGTAGTACCCTGCAGTTAGTACTACACACGTGATCGAAGTTAA-CGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCTA
* *
31275255 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATC
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
31275303 ATCTCTTGTA
Statistics
Matches: 119, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 3 0.03
50 81 0.68
51 34 0.29
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTA
Found at i:31275186 original size:26 final size:26
Alignment explanation
Indices: 31275109--31275187 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
31275099 CTCTGGTACG
31275109 CATAGTAGCCTGCACTTAGTACTACA
1 CATAGTAGCCTGCACTTAGTACTACA
* * *
31275135 AAT-GT-GACCTATCAATCTAG---TACA
1 CATAGTAG-CCT-GCACT-TAGTACTACA
31275159 CATAGTAGCCTGCACTTAGTACTACA
1 CATAGTAGCCTGCACTTAGTACTACA
31275185 CAT
1 CAT
31275188 GTGACTTAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
23 3 0.08
24 10 0.26
25 10 0.26
26 13 0.33
27 3 0.08
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (26 bp):
CATAGTAGCCTGCACTTAGTACTACA
Found at i:31275661 original size:19 final size:20
Alignment explanation
Indices: 31275633--31275679 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
31275623 AAGAACATGT
31275633 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
31275654 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
31275673 TATATAT
1 TATATAT
31275680 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:31275957 original size:30 final size:30
Alignment explanation
Indices: 31275900--31275958 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
31275890 CAAAAATCAT
* *
31275900 ACTTTTACAAATTTGTATTTTGACCCCTAA
1 ACTTTCACAAATTTGTACTTTGACCCCTAA
* * *
31275930 ACTTTCACATATTTTTACTTTGTCCCCTA
1 ACTTTCACAAATTTGTACTTTGACCCCTA
31275959 GGCTCGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (30 bp):
ACTTTCACAAATTTGTACTTTGACCCCTAA
Found at i:31277594 original size:12 final size:12
Alignment explanation
Indices: 31277577--31277606 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31277567 TCAGGCAATT
31277577 ACACGGCCTAGC
1 ACACGGCCTAGC
*
31277589 ACACGGCCTGGC
1 ACACGGCCTAGC
31277601 ACACGG
1 ACACGG
31277607 GCATGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:31283398 original size:42 final size:40
Alignment explanation
Indices: 31283304--31283414 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 40
31283294 TTATGTTTGC
*
31283304 CACTTAGTGTGCGTATCGAGATAGCTTCGGCTATATAAAG
1 CACTTAGTGTGCGAATCGAGATAGCTTCGGCTATATAAAG
* **
31283344 CACTTAGTGTGCGAATCG-GAATAGCTTTGGCTATTTATATGG
1 CACTTAGTGTGCGAATCGAG-ATAGCTTCGGCTA--TATAAAG
*
31283386 CACTTAATGTGCGAGA-CTGAGATAGCTTC
1 CACTTAGTGTGCGA-ATC-GAGATAGCTTC
31283415 ATCTATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
39 1 0.02
40 29 0.49
42 19 0.32
43 9 0.15
44 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (40 bp):
CACTTAGTGTGCGAATCGAGATAGCTTCGGCTATATAAAG
Found at i:31284838 original size:231 final size:231
Alignment explanation
Indices: 31284435--31284897 Score: 863
Period size: 231 Copynumber: 2.0 Consensus size: 231
31284425 TCTGAACCGT
*
31284435 GTATGACACACGGTCATATTGTAAGGTCGTGTGTCCCCTAAGGTACCCTTTCGACTTAATGTAGT
1 GTATGACACACGGTCATATTGTAAGGCCGTGTGTCCCCTAAGGTACCCTTTCGACTTAATGTAGT
* *
31284500 ATACCCTACAAGTTTGACAGGGTCTAGACACACGGGTGTGTTTACTGGCCGTGTGTGACACACGG
66 ATACCCTACAAGTTTGACAGGGTCTAGACACACGGGTGTATTTACTGGCCGTGTGTGACACACAG
*
31284565 GCTAGCACATGGACGTGTGGCCGACCGTGTGACCCAAGTCAGTAACCCCTCTAGTTTTCCCAAGG
131 GCTAGCACATGGACGTGTGGCCGACCGTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCAAGG
31284630 CCATGGCACAAAGGCATGTCCTCGGCCGTGTAACAG
196 CCATGGCACAAAGGCATGTCCTCGGCCGTGTAACAG
31284666 GTATGACACACGGTCATATTGTAAGGCCGTGTGTCCCCTAAGGTACCCTTTCGACTTAATGTAGT
1 GTATGACACACGGTCATATTGTAAGGCCGTGTGTCCCCTAAGGTACCCTTTCGACTTAATGTAGT
31284731 ATACCCTACAAGTTTGACAGGGTCTAGACACACGGGTGTATTTACTGGCCGTGTGTGACACACAG
66 ATACCCTACAAGTTTGACAGGGTCTAGACACACGGGTGTATTTACTGGCCGTGTGTGACACACAG
*
31284796 GCTAGCACATGGACGTGTGGCCGACCGTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCACGG
131 GCTAGCACATGGACGTGTGGCCGACCGTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCAAGG
* *
31284861 CCATGGCATAAAGGCGTGTCCTCGGCCGTGTAACAG
196 CCATGGCACAAAGGCATGTCCTCGGCCGTGTAACAG
31284897 G
1 G
31284898 CCGATTTTGG
Statistics
Matches: 225, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
231 225 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.24
Consensus pattern (231 bp):
GTATGACACACGGTCATATTGTAAGGCCGTGTGTCCCCTAAGGTACCCTTTCGACTTAATGTAGT
ATACCCTACAAGTTTGACAGGGTCTAGACACACGGGTGTATTTACTGGCCGTGTGTGACACACAG
GCTAGCACATGGACGTGTGGCCGACCGTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCAAGG
CCATGGCACAAAGGCATGTCCTCGGCCGTGTAACAG
Found at i:31285403 original size:10 final size:9
Alignment explanation
Indices: 31285380--31285405 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31285370 TTTGATGTTG
31285380 GTTTTTGAT
1 GTTTTTGAT
31285389 GTTTTTGAT
1 GTTTTTGAT
31285398 GTTTTTGA
1 GTTTTTGA
31285406 GATCCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:31286355 original size:46 final size:45
Alignment explanation
Indices: 31286288--31286508 Score: 189
Period size: 46 Copynumber: 4.7 Consensus size: 45
31286278 TTATTTGTGT
31286288 GCCAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGATGTAA
1 GCCAGTGTAAGACATGTCTGGGACATGGCATC-GCCTCGAGATGT-A
* *
31286334 GCCAGTGTAAGACATGTCTGGGACAT-GCATCGACTACGAGAT-TT
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCGCCT-CGAGATGTA
** * * * *
31286378 GTTAGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCGCCTC-GAGATGT---A
* * *
31286428 GCTAGTGTAAGACAAATGTCTGGGACATGGCATCGACTTGATGGATG-A
1 GCCAGTGTAAGAC--ATGTCTGGGACATGGCATCGCCTCGA--GATGTA
*
31286476 GCCAGTGTAAGACCATGTTTGGGACATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATC
31286509 AGCATTATAC
Statistics
Matches: 145, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
44 10 0.07
45 19 0.13
46 47 0.32
47 19 0.13
48 12 0.08
49 2 0.01
50 13 0.09
51 20 0.14
52 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGGCATCGCCTCGAGATGTA
Found at i:31286493 original size:98 final size:92
Alignment explanation
Indices: 31286288--31286511 Score: 249
Period size: 98 Copynumber: 2.4 Consensus size: 92
31286278 TTATTTGTGT
31286288 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGTAAGCCAGTGTAAGACATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGTAAGCCAGTGTAAGACATGT
**
31286351 CTGGGACATGCATCGACTACGAGATTT
66 CTGGGACATGCATCGACTACGAGATGA
** ** * * *
31286378 GTTAGTGTAAGACCATGTCTGGGACATGGCATTGGCAC-GGATATGTGAGAGCTAGTGTAAGACA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTCGAGATGT-A-AGCCAGTGTAAGAC-
*
31286442 AATGTCTGGGACATGGCATCGACT-TGATGGATGA
62 -ATGTCTGGGACAT-GCATCGACTACGA--GATGA
*
31286476 GCCAGTGTAAGACCATGTTTGGGACATGGCATCAGC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC
31286512 ATTATACCCT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
90 10 0.09
91 14 0.13
92 12 0.11
93 2 0.02
94 13 0.12
96 15 0.14
97 9 0.08
98 34 0.31
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (92 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATGTAAGCCAGTGTAAGACATGT
CTGGGACATGCATCGACTACGAGATGA
Found at i:31290116 original size:16 final size:16
Alignment explanation
Indices: 31290095--31290125 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31290085 TTCACTATTA
31290095 TGTCTTTTTTATTTTT
1 TGTCTTTTTTATTTTT
31290111 TGTCTTTTTTATTTT
1 TGTCTTTTTTATTTT
31290126 GCATGCATAG
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:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (16 bp):
TGTCTTTTTTATTTTT
Found at i:31298203 original size:14 final size:14
Alignment explanation
Indices: 31298184--31298214 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31298174 TACTATACTC
*
31298184 AATTTATATACTTT
1 AATTTATATAATTT
31298198 AATTTATATAATTT
1 AATTTATATAATTT
31298212 AAT
1 AAT
31298215 CTTCTTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTATATAATTT
Found at i:31298690 original size:9 final size:9
Alignment explanation
Indices: 31298678--31298707 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
31298668 CTTGTACCTC
31298678 TTTTTCTTT
1 TTTTTCTTT
31298687 TTTTTCTTTT
1 TTTTTC-TTT
31298697 TTTTTCTTT
1 TTTTTCTTT
31298706 TT
1 TT
31298708 CTAGTCCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:31298697 original size:10 final size:10
Alignment explanation
Indices: 31298678--31298707 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31298668 CTTGTACCTC
31298678 TTTTTC-TTT
1 TTTTTCTTTT
31298687 TTTTTCTTTT
1 TTTTTCTTTT
31298697 TTTTTCTTTT
1 TTTTTCTTTT
31298707 T
1 T
31298708 CTAGTCCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:31299779 original size:14 final size:15
Alignment explanation
Indices: 31299754--31299782 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31299744 AAGAAAGGTC
31299754 AGAAACAGAAAAATA
1 AGAAACAGAAAAATA
31299769 AGAAA-AGAAAAATA
1 AGAAACAGAAAAATA
31299783 GAAGAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (15 bp):
AGAAACAGAAAAATA
Found at i:31299808 original size:32 final size:33
Alignment explanation
Indices: 31299764--31299827 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
31299754 AGAAACAGAA
*
31299764 AAATAAGAAAAGAAAA-ATAGAAGAAAATGAGGG
1 AAATAAGAAAAGAAAATA-AAAAGAAAATGAGGG
31299797 AAATAA-AAAAGAAAATAAAAAGAAAATGAGG
1 AAATAAGAAAAGAAAATAAAAAGAAAATGAGG
31299828 TATAATAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.09
Consensus pattern (33 bp):
AAATAAGAAAAGAAAATAAAAAGAAAATGAGGG
Found at i:31300196 original size:18 final size:19
Alignment explanation
Indices: 31300173--31300211 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31300163 AAATTAATTT
*
31300173 TTAAAAATATTAT-ATTAA
1 TTAAAAATAATATGATTAA
*
31300191 TTAAAATTAATATGATTAA
1 TTAAAAATAATATGATTAA
31300210 TT
1 TT
31300212 TAATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TTAAAAATAATATGATTAA
Found at i:31304044 original size:40 final size:40
Alignment explanation
Indices: 31303989--31304210 Score: 376
Period size: 40 Copynumber: 5.6 Consensus size: 40
31303979 TATTCGAATG
31303989 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
31304029 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
31304069 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
31304109 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
31304149 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
31304189 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
31304211 TACTTGGGTT
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.08
40 157 0.91
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:31310702 original size:76 final size:76
Alignment explanation
Indices: 31310570--31310725 Score: 199
Period size: 76 Copynumber: 2.1 Consensus size: 76
31310560 AAGATTAGTA
* * * * * *
31310570 TTAGCGGCGTTTTTAAAAAAACGCCGCAAAAGAATTTTGCAAAACATCGTCGTTTTGTATTGAGC
1 TTAGCGGCATTTTTAAAAAAACGACGCAAAAGAATTTTGCAAAACACCATCATTTTGTATTAAGC
31310635 TTTTAGTGGCT
66 TTTTAGTGGCT
** *
31310646 TTAGCGGCATTTTTTGAAAAAC-ACGACAAAAGAATTTTG-AGAAACACCATCATTTTGTCTTAA
1 TTAGCGGCATTTTTAAAAAAACGACG-CAAAAGAATTTTGCA-AAACACCATCATTTTGTATTAA
31310709 GCTTTTAGTGGCT
64 GCTTTTAGTGGCT
31310722 TTAG
1 TTAG
31310726 TGGTGCTTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 3 0.04
76 66 0.96
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (76 bp):
TTAGCGGCATTTTTAAAAAAACGACGCAAAAGAATTTTGCAAAACACCATCATTTTGTATTAAGC
TTTTAGTGGCT
Found at i:31310751 original size:76 final size:76
Alignment explanation
Indices: 31310586--31310752 Score: 201
Period size: 76 Copynumber: 2.2 Consensus size: 76
31310576 GCGTTTTTAA
* * * * *
31310586 AAAAACGCCGCAAAAGAATTTTGCAAAACATCGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGC
1 AAAAACGCCACAAAAGAATTTTGCAAAACACCATCATTTTGTATTAAGCTTTTAGTGGCTTTAGC
*
31310651 GGCATTTTTTG
66 GGCACTTTTTG
* * *
31310662 AAAAACACGACAAAAGAATTTTG-AGAAACACCATCATTTTGTCTTAAGCTTTTAGTGGCTTTAG
1 AAAAACGCCACAAAAGAATTTTGCA-AAACACCATCATTTTGTATTAAGCTTTTAGTGGCTTTAG
* **
31310726 TGGTGCTTTTTG
65 CGGCACTTTTTG
*
31310738 AAAAATGCCACAAAA
1 AAAAACGCCACAAAA
31310753 AATGAAAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
75 1 0.01
76 74 0.99
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (76 bp):
AAAAACGCCACAAAAGAATTTTGCAAAACACCATCATTTTGTATTAAGCTTTTAGTGGCTTTAGC
GGCACTTTTTG
Found at i:31311103 original size:7 final size:7
Alignment explanation
Indices: 31311022--31311127 Score: 54
Period size: 7 Copynumber: 14.9 Consensus size: 7
31311012 TGGGGTCTAA
31311022 GGTTTAG
1 GGTTTAG
*
31311029 GTGTTAAG
1 G-GTTTAG
*
31311037 GGTTAAG
1 GGTTTAG
31311044 GG-TTAG
1 GGTTTAG
31311050 TGG-TTAG
1 -GGTTTAG
* *
31311057 TGGTTCAT
1 -GGTTTAG
* *
31311065 GGTTCAA
1 GGTTTAG
*
31311072 GGTTTAT
1 GGTTTAG
* *
31311079 GTTTTCG
1 GGTTTAG
* *
31311086 GATTTAT
1 GGTTTAG
31311093 GGTTTAG
1 GGTTTAG
31311100 GGTTTAG
1 GGTTTAG
*
31311107 GGATTAG
1 GGTTTAG
31311114 GAGTTTAG
1 G-GTTTAG
31311122 GGTTTA
1 GGTTTA
31311128 AATTAATTAG
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
6 3 0.04
7 61 0.78
8 14 0.18
ACGTcount: A:0.19, C:0.03, G:0.36, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:31311242 original size:7 final size:7
Alignment explanation
Indices: 31311221--31311330 Score: 53
Period size: 7 Copynumber: 15.4 Consensus size: 7
31311211 TTAATTATCA
*
31311221 TTATAGT
1 TTATGGT
*
31311228 TTAGGGT
1 TTATGGT
31311235 TTATGGT
1 TTATGGT
*
31311242 TTAGGGT
1 TTATGGT
* *
31311249 ATATAGT
1 TTATGGT
*
31311256 TTAGGGT
1 TTATGGT
**
31311263 TTAAAGT
1 TTATGGT
*
31311270 GTATGAGT
1 TTATG-GT
31311278 TACTAT--T
1 T--TATGGT
*
31311285 TTAAGGT
1 TTATGGT
*
31311292 TTATGGA
1 TTATGGT
31311299 TTATGGGT
1 TTAT-GGT
* *
31311307 TTAGGGA
1 TTATGGT
31311314 TTATGGT
1 TTATGGT
31311321 TTATGGT
1 TTATGGT
31311328 TTA
1 TTA
31311331 AGGGTTGAGG
Statistics
Matches: 73, Mismatches: 24, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
5 2 0.03
7 61 0.84
8 7 0.10
10 3 0.04
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:31311243 original size:14 final size:14
Alignment explanation
Indices: 31311221--31311351 Score: 70
Period size: 14 Copynumber: 9.2 Consensus size: 14
31311211 TTAATTATCA
*
31311221 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
31311235 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
* *
31311249 ATATAGTTTAGGGT
1 TTATGGTTTAGGGT
** * *
31311263 TTAAAGTGTATGAGT
1 TTATGGTTTA-GGGT
*
31311278 TACTAT--TTTAAGGT
1 T--TATGGTTTAGGGT
*
31311292 TTATGGATTATGGGT
1 TTATGGTTTA-GGGT
* * *
31311307 TTAGGGATTATGGT
1 TTATGGTTTAGGGT
31311321 TTATGGTTTAAGGGT
1 TTATGGTTT-AGGGT
* *
31311336 TGA-GGTTTAAGGT
1 TTATGGTTTAGGGT
31311349 TTA
1 TTA
31311352 GGGGTCAAGG
Statistics
Matches: 89, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
12 3 0.03
13 6 0.07
14 53 0.60
15 25 0.28
17 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:31311309 original size:15 final size:15
Alignment explanation
Indices: 31311289--31311336 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
31311279 ACTATTTTAA
31311289 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
31311304 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* *
31311318 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
31311333 GGTT
1 GGTT
31311337 GAGGTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:31311309 original size:22 final size:21
Alignment explanation
Indices: 31311284--31311333 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
31311274 GAGTTACTAT
*
31311284 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
31311306 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
31311327 TTTAAGG
1 TTTAAGG
31311334 GTTGAGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:31311330 original size:21 final size:20
Alignment explanation
Indices: 31311232--31311354 Score: 72
Period size: 21 Copynumber: 5.8 Consensus size: 20
31311222 TATAGTTTAG
31311232 GGTTTATGGTTTAGGGTATAT
1 GGTTTATGGTTTAGGGT-TAT
* * **
31311253 AGTTTAGGGTTTAAAGTGTAT
1 GGTTTATGGTTTAGGGT-TAT
*
31311274 GAGTTACTAT--TTTAAGGTTTAT
1 G-GTT--TATGGTTT-AGGGTTAT
*
31311296 GGATTATGGGTTTAGGGATTAT
1 GGTTTAT-GGTTTAGGG-TTAT
31311318 GGTTTATGGTTTAAGGGTTGA-
1 GGTTTATGGTTT-AGGGTT-AT
*
31311339 GGTTTAAGGTTTAGGG
1 GGTTTATGGTTTAGGG
31311355 GTCAAGGGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
19 3 0.04
20 4 0.05
21 39 0.50
22 28 0.36
23 2 0.03
24 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.44
Consensus pattern (20 bp):
GGTTTATGGTTTAGGGTTAT
Found at i:31311423 original size:7 final size:7
Alignment explanation
Indices: 31311412--31311441 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
31311402 GATTTATGGT
31311412 TTAGGGG
1 TTAGGGG
*
31311419 GTAGGGG
1 TTAGGGG
31311426 TTAGGGG
1 TTAGGGG
31311433 TTAGGGG
1 TTAGGGG
31311440 TT
1 TT
31311442 TAAGGCTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.57, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:31312129 original size:8 final size:8
Alignment explanation
Indices: 31312118--31312179 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
31312108 TTTATATGTT
31312118 AATTTAAA
1 AATTTAAA
31312126 AATTATAAA
1 AATT-TAAA
31312135 AATATTCAAAAA
1 AAT-TT---AAA
31312147 AATTT-AA
1 AATTTAAA
31312154 AATTTAAA
1 AATTTAAA
31312162 AA-TTAAA
1 AATTTAAA
*
31312169 AATTAAAA
1 AATTTAAA
31312177 AAT
1 AAT
31312180 AAAAGATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
7 14 0.30
8 15 0.33
9 8 0.17
10 1 0.02
11 2 0.04
12 6 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
AATTTAAA
Found at i:31312157 original size:7 final size:7
Alignment explanation
Indices: 31312144--31312198 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
31312134 AAATATTCAA
31312144 AAAAATTT
1 AAAAA-TT
*
31312152 AAAATTT
1 AAAAATT
31312159 AAAAATT
1 AAAAATT
31312166 AAAAATT
1 AAAAATT
*
31312173 AAAAAAT
1 AAAAATT
*
31312180 AAAAGATA
1 AAAA-ATT
31312188 AAAAACTT
1 AAAAA-TT
31312196 AAA
1 AAA
31312199 TATTTAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 26 0.67
8 13 0.33
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:31312164 original size:15 final size:15
Alignment explanation
Indices: 31312143--31312198 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
31312133 AAAATATTCA
*
31312143 AAAAAATTTAAAATT
1 AAAAAATTAAAAATT
*
31312158 TAAAAATTAAAAATT
1 AAAAAATTAAAAATT
31312173 AAAAAA-TAAAAGA-T
1 AAAAAATTAAAA-ATT
31312187 AAAAAACTTAAA
1 AAAAAA-TTAAA
31312199 TATTTAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.34
15 19 0.54
16 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAAATTAAAAATT
Found at i:31319330 original size:26 final size:26
Alignment explanation
Indices: 31319300--31319356 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
31319290 ATGAATCATG
31319300 TTCAAAAATCTAAGAACTTCCAAAAT
1 TTCAAAAATCTAAGAACTTCCAAAAT
31319326 TTCAAAAATCTAAGAACTTCCAAAAT
1 TTCAAAAATCTAAGAACTTCCAAAAT
31319352 TTCAA
1 TTCAA
31319357 CTTAAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (26 bp):
TTCAAAAATCTAAGAACTTCCAAAAT
Found at i:31319771 original size:16 final size:16
Alignment explanation
Indices: 31319726--31319781 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
31319716 CAATTTAATT
*
31319726 TATTTTA-TAATCTAA
1 TATTTTATTAATATAA
*
31319741 TAATTTAATTTAATATAA
1 T-ATTTTA-TTAATATAA
31319759 TATTTTATTAATATAA
1 TATTTTATTAATATAA
*
31319775 TAATTTA
1 TATTTTA
31319782 ATATATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.03
16 20 0.59
17 5 0.15
18 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTTATTAATATAA
Found at i:31320287 original size:6 final size:6
Alignment explanation
Indices: 31320276--31320306 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
31320266 AAAGTCTAGG
31320276 AAAATA AAAAT- AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
31320307 TGGACTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:31320290 original size:11 final size:12
Alignment explanation
Indices: 31320276--31320306 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
31320266 AAAGTCTAGG
31320276 AAAATAAAAAT-
1 AAAATAAAAATA
31320287 AAAATAAAAATA
1 AAAATAAAAATA
31320299 AAAATAAA
1 AAAATAAA
31320307 TGGACTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:31321920 original size:16 final size:16
Alignment explanation
Indices: 31321899--31321988 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 16
31321889 AAATAACTGC
31321899 TAATAAATAATAATAA
1 TAATAAATAATAATAA
31321915 TAATAAATAAT-ATGGAA
1 TAATAAATAATAAT--AA
*
31321932 -AGA-AAATAAT-ATAG
1 TA-ATAAATAATAATAA
31321946 TAAT-AATAATATATAA
1 TAATAAATAATA-ATAA
* *
31321962 GAAATAAATAATTAATTA
1 -TAATAAATAA-TAATAA
31321980 -AATAAATAA
1 TAATAAATAA
31321989 CATAGAAGGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 33 0.55
17 6 0.10
18 8 0.13
19 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
TAATAAATAATAATAA
Found at i:31337750 original size:27 final size:27
Alignment explanation
Indices: 31337710--31337763 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
31337700 TTCTAGTTAT
*
31337710 AAACTAAATAAACCTGCCAGAAGCAAA
1 AAACTAAAGAAACCTGCCAGAAGCAAA
*
31337737 AAACTAAAGGAACCTGCCAGAAGCAAA
1 AAACTAAAGAAACCTGCCAGAAGCAAA
31337764 TAAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.54, C:0.22, G:0.15, T:0.09
Consensus pattern (27 bp):
AAACTAAAGAAACCTGCCAGAAGCAAA
Found at i:31340425 original size:18 final size:19
Alignment explanation
Indices: 31340391--31340426 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31340381 CTACATATAT
31340391 TTTTATAATTTATAATTTC
1 TTTTATAATTTATAATTTC
*
31340410 TTTTATATTTTA-AATTT
1 TTTTATAATTTATAATTT
31340427 TTTATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTATAATTTC
Found at i:31342958 original size:25 final size:26
Alignment explanation
Indices: 31342901--31342958 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 26
31342891 CATTAGCAAT
*
31342901 TAATTATTTTTTAAATTTTAAAAATA
1 TAATTAATTTTTAAATTTTAAAAATA
31342927 TAA--AATTTTTAAATTTTAAAAA-A
1 TAATTAATTTTTAAATTTTAAAAATA
31342950 TAATTAATT
1 TAATTAATT
31342959 GCTAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.14
24 18 0.62
25 4 0.14
26 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATTAATTTTTAAATTTTAAAAATA
Found at i:31344624 original size:4 final size:4
Alignment explanation
Indices: 31344615--31344642 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31344605 TTAATATACA
31344615 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
31344643 CTTTTCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:31351178 original size:33 final size:33
Alignment explanation
Indices: 31351134--31351286 Score: 157
Period size: 33 Copynumber: 4.7 Consensus size: 33
31351124 TACCTAAATG
* * *
31351134 GTAC-ACTTGAAAAGGTTATATACACTTTGTGT
1 GTACAACTTGAAAAGGCTATGTACACTTTGAGT
* *
31351166 GTACAATTTGAAAAGGCTATGTACACTTTGCGT
1 GTACAACTTGAAAAGGCTATGTACACTTTGAGT
* *
31351199 GTACAACTTGAAAAGACTACGTACACTTTGAGT
1 GTACAACTTGAAAAGGCTATGTACACTTTGAGT
* ** * *
31351232 GTACCACTTGAAAAGGGAATGTACACCTCGAGT
1 GTACAACTTGAAAAGGCTATGTACACTTTGAGT
* *
31351265 GTACGAC-TGAAAAAGGTTATGT
1 GTACAACTTG-AAAAGGCTATGT
31351287 CTATTGGAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
32 6 0.06
33 95 0.94
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (33 bp):
GTACAACTTGAAAAGGCTATGTACACTTTGAGT
Found at i:31354502 original size:18 final size:19
Alignment explanation
Indices: 31354470--31354507 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31354460 GCCATTTTTT
31354470 GTTAAAAAGGAAAAAAAAA
1 GTTAAAAAGGAAAAAAAAA
*
31354489 GTTAAAAATGAAAAAAAAA
1 GTTAAAAAGGAAAAAAAAA
31354508 CAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
GTTAAAAAGGAAAAAAAAA
Found at i:31354503 original size:20 final size:19
Alignment explanation
Indices: 31354470--31354507 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31354460 GCCATTTTTT
*
31354470 GTTAAAAAGGAAAAAAAAA
1 GTTAAAAAGAAAAAAAAAA
31354489 GTTAAAAATGAAAAAAAAA
1 GTTAAAAA-GAAAAAAAAA
31354508 CAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
GTTAAAAAGAAAAAAAAAA
Found at i:31354514 original size:19 final size:19
Alignment explanation
Indices: 31354473--31354515 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
31354463 ATTTTTTGTT
***
31354473 AAAAAGGAAAAAAAAAGTT
1 AAAAAGGAAAAAAAAACAA
*
31354492 AAAAATGAAAAAAAAACAA
1 AAAAAGGAAAAAAAAACAA
31354511 AAAAA
1 AAAAA
31354516 ATGGGATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAGGAAAAAAAAACAA
Found at i:31354564 original size:27 final size:28
Alignment explanation
Indices: 31354534--31354594 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
31354524 GTGTGGGTCC
31354534 CAGAGGCA-GCACCAATTGTGCCTCTGG
1 CAGAGGCAGGCACCAATTGTGCCTCTGG
*
31354561 CAGAGG-AGGCACCAGTTGTGCCTCTGG
1 CAGAGGCAGGCACCAATTGTGCCTCTGG
*
31354588 CATAGGC
1 CAGAGGC
31354595 GACACCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (28 bp):
CAGAGGCAGGCACCAATTGTGCCTCTGG
Found at i:31355091 original size:13 final size:13
Alignment explanation
Indices: 31355069--31355104 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
31355059 TTTTTAAACA
31355069 TATATTATTTTTT
1 TATATTATTTTTT
*
31355082 TATTTTA-TTTTT
1 TATATTATTTTTT
31355094 TATATTATTTT
1 TATATTATTTT
31355105 AGTACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATATTATTTTTT
Found at i:31355334 original size:292 final size:296
Alignment explanation
Indices: 31354908--31355587 Score: 988
Period size: 293 Copynumber: 2.3 Consensus size: 296
31354898 TTTTTGGATC
* *
31354908 TTATTTTTTAAAATATACTATTTTCATATTTTATTTTAT-TATTATTTTAATACATAATGTTTCA
1 TTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCA
* * *
31354972 AATGTATTATTTTA-ATTTTTTATATTAATTTAGTAAATAACCCTAAATTTGTCAATTTGTTTGC
66 AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCTAAATTTGGCAATTTCTTTGC
* **
31355036 ATTTTTAAAATTCCCGGATTTTA-TTTTTAAACATATATTATTTTTTTATTTTA-TTTTTTATAT
131 ATTTTTAAAATTCCCGGATTTTATTTTTTAAA-ATATACTATTTTAGTATTTTATTTTTTTATAT
*
31355099 TATTTTAGTACATAATATTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGA-AAATAA
195 TATTTTAGTACATAATATTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTA-ATAAATAA
* *
31355163 CCCTGATTTTGGCCTTTTGTTTGTATTTTTAA-A-ATT
259 CCCTGATTTTGACCCTTTGTTTGTATTTTTAATATATT
* * *
31355199 TTATTTTTAAAAATATACTATTTTCTTATTTTATTTTTTATATTATTTTAGTACATAATCTTTCA
1 TTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCA
* * ** *
31355264 AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAA-CCTGATTTTGGCCCTTTCTTTGT
66 AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCTAAATTTGGCAATTTCTTTGC
**
31355328 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTTATATT
131 ATTTTTAAAATTCCCGGATTTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTTATATT
*
31355393 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTAATAAATAACC
196 ATTTTAGTACATAATATTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTAATAAATAACC
31355458 CTGATTTTGACCCTTTGTTTGTATTTTTAATATTTTTGGATT
261 CTGATTTTGACCCTTTGTTTGTATTTTTAATA----T--ATT
*
31355500 TTATTTTTTAAAATATACTATTTTCGTA---T-TTTTTTATATTATTTTAGTACATAATGTTTCA
1 TTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCA
31355561 AATGTATTATTTTAGTGTTTTTTATAT
66 AATGTATTATTTTAGT-TTTTTTATAT
31355588 AAAAAAATGA
Statistics
Matches: 350, Mismatches: 25, Indels: 21
0.88 0.06 0.05
Matches are distributed among these distances:
291 36 0.10
292 93 0.27
293 133 0.38
294 1 0.00
297 47 0.13
298 11 0.03
301 29 0.08
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (296 bp):
TTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCA
AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCTAAATTTGGCAATTTCTTTGC
ATTTTTAAAATTCCCGGATTTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTTATATT
ATTTTAGTACATAATATTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTAATAAATAACC
CTGATTTTGACCCTTTGTTTGTATTTTTAATATATT
Found at i:31355441 original size:49 final size:49
Alignment explanation
Indices: 31355374--31355587 Score: 138
Period size: 49 Copynumber: 4.4 Consensus size: 49
31355364 ACTATTTTAG
31355374 TATTTTA-T-TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTAT
1 TATTTTAGTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTAT
* * * ** ***
31355421 TATTTTAGTATTTTTTATATTAATTTAATAAATAACCCTGATTTTGACCCT-T
1 TATTTTAGTATTTTTTATATTATTTTAGTACATAA---TG-TTTCAAATGTAT
* * * ** * * * * *
31355473 T-GTTT-GTA-TTTTTA-A-TATTTTTGGATTTTATTTTTTAAAATATAC
1 TATTTTAGTATTTTTTATATTATTTTAGTA-CATAATGTTTCAAATGTAT
*
31355518 TATTTTCGTATTTTTTTATATTATTTTAGTACATAATGTTTCAAATGTAT
1 TATTTTAGTA-TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTAT
*
31355568 TATTTTAGTGTTTTTTATAT
1 TATTTTAGTATTTTTTATAT
31355588 AAAAAAATGA
Statistics
Matches: 118, Mismatches: 35, Indels: 26
0.66 0.20 0.15
Matches are distributed among these distances:
44 5 0.04
45 2 0.02
46 3 0.03
47 16 0.14
48 4 0.03
49 44 0.37
50 24 0.20
51 11 0.09
52 4 0.03
53 5 0.04
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (49 bp):
TATTTTAGTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTAT
Found at i:31355510 original size:152 final size:150
Alignment explanation
Indices: 31354883--31355587 Score: 910
Period size: 143 Copynumber: 4.8 Consensus size: 150
31354873 ATAAAAAATT
* * * *
31354883 TTTGTATTTTTAAAATTTTTGGATCTTATTTTTTAAAATATACTATTTTCATATTTTA-TTTTAT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTT
* * *
31354947 -TATTATTTTAATACATAATGTTTCAAATGTATTATTTTA-ATTTTTTATATTAATTTAGTAAAT
66 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAAT
* * * ** *
31355010 AACCCTAAATTTGTCAATTTG
131 AA-CCTGATTTTGACCCTTTC
* ** * **
31355031 TTTGCATTTTTAAAATTCCCGGATTTTA-TTTTTAAACATATATTATTTTTTTATTTTA-TTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAA-ATATACTATTTTCGTATTTTATTTTTT
*
31355094 TATATTATTTTAGTACATAATATTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGA-A
65 TATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATATTAATTTA-ATA
* * *
31355158 AATAACCCTGATTTTGGCCTTTTG
128 AATAA-CCTGATTTTGACCCTTTC
* *
31355182 TTTGTATTTTT-AAA-------ATTTTATTTTTAAAAATATACTATTTTCTTATTTTA-TTTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTT
* *
31355238 ATATTATTTTAGTACATAATCTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAT
66 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAAT
*
31355303 AACCTGATTTTGGCCCTTTC
131 AACCTGATTTTGACCCTTTC
*
31355323 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTT
31355388 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTAATAAA
66 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATATTAATTTAATAAA
*
31355453 TAACCCTGATTTTGACCCTTTG
130 TAA-CCTGATTTTGACCCTTTC
* *
31355475 TTTGTATTTTTAATATTTTTGGATTTTATTTTTTAAAATATACTATTTTCG-----TATTTTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTT
31355535 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATAT
66 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATAT
31355588 AAAAAAATGA
Statistics
Matches: 502, Mismatches: 37, Indels: 37
0.87 0.06 0.06
Matches are distributed among these distances:
141 27 0.05
142 26 0.05
143 72 0.14
144 7 0.01
147 69 0.14
148 46 0.09
149 70 0.14
150 50 0.10
151 71 0.14
152 64 0.13
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (150 bp):
TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTT
ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAAT
AACCTGATTTTGACCCTTTC
Found at i:31355582 original size:147 final size:145
Alignment explanation
Indices: 31354883--31355587 Score: 838
Period size: 151 Copynumber: 4.8 Consensus size: 145
31354873 ATAAAAAATT
* * *
31354883 TTTGTATTTTTAAAATTTTTGGATCTTATTTTTTAAAATATACTATTTTCATATTTTATTTTATT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA-TTT-TTTTA-T
* * *
31354948 ATTATTTTAATACATAATGTTTCAAATGTATTATTTTA-ATTTTTTATATTAATTTAGTAAATAA
63 ATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAATAA
* * * ** *
31355012 CCCTAAATTTGTCAATTTG
128 -CCTGATTTTGACCCTTTC
* ** * **
31355031 TTTGCATTTTTAAAATTCCCGGATTTTA-TTTTTAAACATATATTATTTTTTTATTTTATTTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAA-ATATACTATTTTCGTA---T-TTTTTT
*
31355095 ATATTATTTTAGTACATAATATTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGA-AA
61 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATATTAATTTA-ATAA
* * *
31355159 ATAACCCTGATTTTGGCCTTTTG
124 ATAA-CCTGATTTTGACCCTTTC
* *
31355182 TTTGTATTTTT-AAA-------ATTTTATTTTTAAAAATATACTATTTTCTTATTTTATTTTTTA
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA---T-TTTTTTA
* *
31355239 TATTATTTTAGTACATAATCTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATA
62 TATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAATA
*
31355304 ACCTGATTTTGGCCCTTTC
127 ACCTGATTTTGACCCTTTC
*
31355323 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG-----TATTTTTTT
31355388 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTATATTAATTTAATAAA
61 ATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATATTAATTTAATAAA
*
31355453 TAACCCTGATTTTGACCCTTTG
125 TAA-CCTGATTTTGACCCTTTC
* *
31355475 TTTGTATTTTTAATATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTTTTATATT
1 TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTTTTATATT
31355540 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATAT
66 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATAT
31355588 AAAAAAATGA
Statistics
Matches: 497, Mismatches: 36, Indels: 49
0.85 0.06 0.08
Matches are distributed among these distances:
141 27 0.05
142 26 0.05
143 72 0.14
144 7 0.01
147 69 0.14
148 36 0.07
149 63 0.13
150 57 0.11
151 74 0.15
152 64 0.13
154 2 0.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (145 bp):
TTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTTTTATATT
ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAATAAATAACCT
GATTTTGACCCTTTC
Found at i:31355761 original size:27 final size:27
Alignment explanation
Indices: 31355716--31355786 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
31355706 AGTATAGCCA
*
31355716 AACCGGTGCCGCCTATGCTAGAGGCAC
1 AACCGGTGCCGCCTCTGCTAGAGGCAC
* *
31355743 AATCGGTGCCGCCTCTGCTAGAGGTAC
1 AACCGGTGCCGCCTCTGCTAGAGGCAC
* *
31355770 AACCGATGTCGCCTCTG
1 AACCGGTGCCGCCTCTG
31355787 GGACCCACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.20
Consensus pattern (27 bp):
AACCGGTGCCGCCTCTGCTAGAGGCAC
Found at i:31359655 original size:24 final size:24
Alignment explanation
Indices: 31359623--31359684 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
31359613 TAGGCTCTTC
* *
31359623 GTGAGCTTCCCAATATGATTCCTT
1 GTGAACTTCCCAATAAGATTCCTT
* * * *
31359647 GTGAACTTCTCGATAAGGTTCTTT
1 GTGAACTTCCCAATAAGATTCCTT
*
31359671 GTGAACTTTCCAAT
1 GTGAACTTCCCAAT
31359685 TATGGCTCTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (24 bp):
GTGAACTTCCCAATAAGATTCCTT
Found at i:31373223 original size:24 final size:24
Alignment explanation
Indices: 31373163--31373228 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
31373153 TTCCCTTTAC
* *
31373163 ATGGCTCTTTGTGAGCTTTCTAAT
1 ATGGCTCTTTGTGAGCTTCCCAAT
* *
31373187 A-GACTCTTCGTGAGCTTCCCAAT
1 ATGGCTCTTTGTGAGCTTCCCAAT
* *
31373210 ATGGTTCTTTGTGAACTTC
1 ATGGCTCTTTGTGAGCTTC
31373229 GTGATAAGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (24 bp):
ATGGCTCTTTGTGAGCTTCCCAAT
Found at i:31374141 original size:14 final size:14
Alignment explanation
Indices: 31374122--31374152 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31374112 ACTATACATA
31374122 TTAATGATGTTTCC
1 TTAATGATGTTTCC
31374136 TTAATGATGTTTCC
1 TTAATGATGTTTCC
31374150 TTA
1 TTA
31374153 GTTTCATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (14 bp):
TTAATGATGTTTCC
Found at i:31382874 original size:40 final size:40
Alignment explanation
Indices: 31382772--31382955 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
31382762 AAATTGAATG
* * * * *
31382772 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
31382812 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
31382852 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
31382892 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
31382932 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
31382956 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:31392410 original size:40 final size:40
Alignment explanation
Indices: 31392351--31392477 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
31392341 CAGAATACAA
* * *
31392351 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
31392391 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
31392431 CCGGAT-GTAGCCG-CTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATAG-A-ACGACTTGCACGAA-TGCCTTCGGGTCTTAGC
31392471 CCGGATA
1 CCGGATA
31392478 TAATTTCCAG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
39 3 0.04
40 72 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:31394460 original size:37 final size:37
Alignment explanation
Indices: 31394408--31394514 Score: 187
Period size: 37 Copynumber: 2.9 Consensus size: 37
31394398 ATGGCAAAGT
* *
31394408 ATGGAATGTAAGACCATAGCTAGGCTATGGCATCGTA
1 ATGGCATGTAAGACCATAGCTGGGCTATGGCATCGTA
31394445 ATGGCATGTAAGACCATAGCTGGGCTATGGCATCGTA
1 ATGGCATGTAAGACCATAGCTGGGCTATGGCATCGTA
*
31394482 ATGGCATGTAAGACCATAGTTGGGCTATGGCAT
1 ATGGCATGTAAGACCATAGCTGGGCTATGGCAT
31394515 TTTGATTTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (37 bp):
ATGGCATGTAAGACCATAGCTGGGCTATGGCATCGTA
Found at i:31394529 original size:37 final size:37
Alignment explanation
Indices: 31394380--31394552 Score: 186
Period size: 37 Copynumber: 4.7 Consensus size: 37
31394370 AATTGACGGA
* * * ** *
31394380 TAAGACCATGGTTGGACCATGGCAAAGT-ATGGAATG
1 TAAGACCATAGTTGGGCTATGGCATCGTAATGGCATG
* *
31394416 TAAGACCATAGCTAGGCTATGGCATCGTAATGGCATG
1 TAAGACCATAGTTGGGCTATGGCATCGTAATGGCATG
*
31394453 TAAGACCATAGCTGGGCTATGGCATCGTAATGGCATG
1 TAAGACCATAGTTGGGCTATGGCATCGTAATGGCATG
** * ****
31394490 TAAGACCATAGTTGGGCTATGGCATTTTGATTTTGTG
1 TAAGACCATAGTTGGGCTATGGCATCGTAATGGCATG
*
31394527 TAAGACCATAGTTGGACTATGGCATC
1 TAAGACCATAGTTGGGCTATGGCATC
31394553 AAGTAAACAA
Statistics
Matches: 117, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 21 0.18
37 96 0.82
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (37 bp):
TAAGACCATAGTTGGGCTATGGCATCGTAATGGCATG
Found at i:31398032 original size:48 final size:48
Alignment explanation
Indices: 31397967--31398139 Score: 189
Period size: 48 Copynumber: 3.6 Consensus size: 48
31397957 TATGTGTGCT
*
31397967 AGTGTAAGACCATGTCTGGGACATGGCATTGGCCACATTATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAAAGCC
* *
31398015 AGTGCAGGACCATGTCTGGGACATGGCATCGG---CATTGA-GACGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATGA--A-AGCC
*
31398063 AGTGTAAGACCATGTCTCGGACATGGCATCGGCCTCGACA-TATG--AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-C-C-ACATTATGAAAGCC
*
31398111 AGTGTAAGACCATGTCTGGGATATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
31398140 TGGCATTTTA
Statistics
Matches: 106, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
45 6 0.06
46 1 0.01
47 1 0.01
48 93 0.88
52 1 0.01
53 2 0.02
54 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAAAGCC
Found at i:31398090 original size:96 final size:96
Alignment explanation
Indices: 31397967--31398146 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 96
31397957 TATGTGTGCT
* * *
31397967 AGTGTAAGACCATGTCTGGGACATGGCATTGG-C-C-ACATTATGAAAGCCAGTGCAGGACCATG
1 AGTGTAAGACCATGTCTCGGACATGGCATCGGCCTCGACA-TATG--AGCCAGTGCAAGACCATG
31398029 TCTGGGACATGGCATCGGCATTGAGACGAGAGCC
63 TCTGGGACATGGCATCGGCATTGAGACGAGAGCC
*
31398063 AGTGTAAGACCATGTCTCGGACATGGCATCGGCCTCGACATATGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTCGGACATGGCATCGGCCTCGACATATGAGCCAGTGCAAGACCATGTCT
* *
31398128 GGGATATGGCATTGGCATT
66 GGGACATGGCATCGGCATT
31398147 TTACCCTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
96 66 0.88
97 1 0.01
98 5 0.07
99 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTCGGACATGGCATCGGCCTCGACATATGAGCCAGTGCAAGACCATGTCT
GGGACATGGCATCGGCATTGAGACGAGAGCC
Found at i:31402778 original size:55 final size:53
Alignment explanation
Indices: 31402651--31402839 Score: 263
Period size: 55 Copynumber: 3.5 Consensus size: 53
31402641 AACTTACCAT
* *
31402651 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* *
31402704 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
31402759 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
31402813 TGCCATGCCTTGACATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
31402840 ATATCCTTAT
Statistics
Matches: 121, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
52 2 0.02
53 36 0.30
54 36 0.30
55 45 0.37
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:31402943 original size:46 final size:47
Alignment explanation
Indices: 31402825--31402946 Score: 192
Period size: 47 Copynumber: 2.6 Consensus size: 47
31402815 CCATGCCTTG
* * *
31402825 ACATGGTCTTACATGATATCCTTATCTTACCAACTATCATGTTCCAA
1 ACATGGTCTTACATGGTATCCTTGTCTTACCAAATATCATGTTCCAA
* *
31402872 ACATGGTCTTACATGGTATTCTTGTCTTACCAAATGTCATGTTCCAA
1 ACATGGTCTTACATGGTATCCTTGTCTTACCAAATATCATGTTCCAA
31402919 ACA-GGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGGTATCCTTGTCTTA
31402947 GTGCCAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 24 0.35
47 45 0.65
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (47 bp):
ACATGGTCTTACATGGTATCCTTGTCTTACCAAATATCATGTTCCAA
Found at i:31409078 original size:16 final size:17
Alignment explanation
Indices: 31409051--31409083 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
31409041 ACTTACTTAA
31409051 TACTTGATAATCTCAAT
1 TACTTGATAATCTCAAT
31409068 TACTT-ATAATCTCAAT
1 TACTTGATAATCTCAAT
31409084 ATTAAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (17 bp):
TACTTGATAATCTCAAT
Found at i:31409271 original size:53 final size:53
Alignment explanation
Indices: 31409185--31409391 Score: 202
Period size: 53 Copynumber: 3.9 Consensus size: 53
31409175 TTTTCCTTTT
* * * * * * *
31409185 TGAACTTACCATTGCTATGTCTTGACATAGTCTTACGTGGTATCCTTGCCTTA
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTA
* ** *
31409238 TGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG--GGCCTTTTCCTTA
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTA
* * * *
31409290 TTGTAAGTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA
1 -TG-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTA
* * * *
31409345 TAAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
31409392 ATCTTACCAA
Statistics
Matches: 126, Mismatches: 23, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
51 2 0.02
52 7 0.06
53 74 0.59
54 34 0.27
55 7 0.06
56 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTA
Found at i:31413707 original size:2 final size:2
Alignment explanation
Indices: 31413700--31413732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31413690 ACTCAACTTC
31413700 AT AT AT 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 A
31413733 GCTGAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31420452 original size:27 final size:27
Alignment explanation
Indices: 31420404--31420677 Score: 221
Period size: 27 Copynumber: 9.8 Consensus size: 27
31420394 ATTACCAAAG
*
31420404 TACCC-CGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31420430 TACCCTCGATTTATAGAAGTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
31420457 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31420484 TACCCTTGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31420511 TACCC-CGATTTACATAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31420537 TACCC-CCATTTTACCCTCAACTTACAAAATTACCGTTT
1 TACCCTCGA-TTTA----C-A--GA----ATTACCGTTT
*
31420575 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** * **
31420602 TACTGTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
31420629 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
31420656 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
31420678 AGAAATACCC
Statistics
Matches: 206, Mismatches: 28, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
26 31 0.15
27 148 0.72
31 2 0.01
32 1 0.00
33 1 0.00
34 3 0.01
38 18 0.09
39 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:31420569 original size:38 final size:37
Alignment explanation
Indices: 31420505--31420579 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
31420495 TACAGAATTA
* * *
31420505 CCATTTTACCCCGATTTACATAATTACCATTTTACCC
1 CCATTTTACCCCAACTTACAAAATTACCATTTTACCC
*
31420542 CCATTTTACCCTCAACTTACAAAATTACCGTTTTACCC
1 CCATTTTACCC-CAACTTACAAAATTACCATTTTACCC
31420580 TCGATTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (37 bp):
CCATTTTACCCCAACTTACAAAATTACCATTTTACCC
Found at i:31420686 original size:27 final size:27
Alignment explanation
Indices: 31420656--31420879 Score: 129
Period size: 27 Copynumber: 8.2 Consensus size: 27
31420646 ATTACTATTT
*
31420656 TACCCTCGATTTACAAAATTACAGAAA
1 TACCCTCGATTTGCAAAATTACAGAAA
* *
31420683 TACCCTCAATTTGTAAAATTACCA-AAA
1 TACCCTCGATTTGCAAAATTA-CAGAAA
* *
31420710 TACCC-CTAGTTTGTAAAATTACCA-AAA
1 TACCCTCGA-TTTGCAAAATTA-CAGAAA
* * *
31420737 TACCACT-GGTTTGTAAAATTACCGAAA
1 TACC-CTCGATTTGCAAAATTACAGAAA
* * *
31420764 TACCCTCAATTTGTAAAATTGCCA-AAA
1 TACCCTCGATTTGCAAAATT-ACAGAAA
* * *
31420791 TACCC-CTAATTTACAAAGTTACAGAAA
1 TACCCTC-GATTTGCAAAATTACAGAAA
* *
31420818 TACCCTTGACTTT-CTAAAAATTATAGAAA
1 TACCCTCGA-TTTGC--AAAATTACAGAAA
* * * * *
31420847 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTGCAAAATTACAGAAA
31420874 TACCCT
1 TACCCT
31420880 TGGTTTGTAG
Statistics
Matches: 159, Mismatches: 24, Indels: 28
0.75 0.11 0.13
Matches are distributed among these distances:
26 8 0.05
27 122 0.77
28 10 0.06
29 19 0.12
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTGCAAAATTACAGAAA
Found at i:31420714 original size:81 final size:80
Alignment explanation
Indices: 31420629--31420821 Score: 194
Period size: 81 Copynumber: 2.4 Consensus size: 80
31420619 ATTACTATTT
* ***
31420629 TACCCTTGATTTACAGAATTACTATTTTACC-CTCGATTTACAAAATTACAGAAATACCCTCAAT
1 TACCCTTGATTTACA-AATTACCAAAATACCACT-GATTTACAAAATTACAGAAATACCCTCAAT
31420693 TTGTAAAATTACCAAAA
64 TTGTAAAATTACCAAAA
* * * ** *
31420710 TACCCCTAGTTTGTA-AAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAAT
1 TA-CCCTTGATT-TACAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAAT
*
31420774 TTGTAAAATTGCCAAAA
64 TTGTAAAATTACCAAAA
* *
31420791 TACCCCTAATTTACAAAGTTA-CAGAAATACC
1 TACCCTTGATTTACAAA-TTACCA-AAATACC
31420822 CTTGACTTTC
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
79 2 0.02
80 10 0.11
81 67 0.74
82 10 0.11
83 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (80 bp):
TACCCTTGATTTACAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAATTT
GTAAAATTACCAAAA
Found at i:31420818 original size:54 final size:54
Alignment explanation
Indices: 31420656--31420879 Score: 152
Period size: 54 Copynumber: 4.1 Consensus size: 54
31420646 ATTACTATTT
* ** **
31420656 TACCCTCGATTTACAAAATTA-CAGAAATACC-CTCAATTTGTAAAATTACCA-AAA
1 TACCCTCAATTTGTAAAATTACCA-AAATACCACT-AATTTACAAAATTA-CAGAAA
* ** ** *
31420710 TACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAA
* * *
31420764 TACCCTCAATTTGTAAAATTGCCAAAATACCCCTAATTTACAAAGTTACAGAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAA
* * * * * ** *
31420818 TACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAA
1 TACCC-TCAATTTGT-AAAATTACCA-AAATACCACTAATTTACAAAATTACAGAAA
31420874 TACCCT
1 TACCCT
31420880 TGGTTTGTAG
Statistics
Matches: 135, Mismatches: 27, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
53 2 0.01
54 85 0.63
55 13 0.10
56 35 0.26
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAA
Found at i:31420885 original size:27 final size:27
Alignment explanation
Indices: 31420629--31420881 Score: 127
Period size: 27 Copynumber: 9.3 Consensus size: 27
31420619 ATTACTATTT
* * **
31420629 TACCCTTGATTTACAGAATTA-CTATTT
1 TACCCTTGATTTACAAAATTACCGA-AA
* *
31420656 TACCCTCGATTTACAAAATTACAGAAA
1 TACCCTTGATTTACAAAATTACCGAAA
** ** *
31420683 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCGAAA
* ** *
31420710 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCGAAA
* **
31420737 TACCAC-TGGTTTGTAAAATTACCGAAA
1 TACC-CTTGATTTACAAAATTACCGAAA
** ** * *
31420764 TACCCTCAATTTGTAAAATTGCCAAAA
1 TACCCTTGATTTACAAAATTACCGAAA
* * * *
31420791 TACCCCTAATTTACAAAGTTACAGAAA
1 TACCCTTGATTTACAAAATTACCGAAA
**
31420818 TACCCTTGACTTT-CTAAAAATTATAGAAA
1 TACCCTTGA-TTTAC--AAAATTACCGAAA
* * *
31420847 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACCGAAA
31420874 TACCCTTG
1 TACCCTTG
31420882 GTTTGTAGAT
Statistics
Matches: 180, Mismatches: 37, Indels: 18
0.77 0.16 0.08
Matches are distributed among these distances:
26 2 0.01
27 151 0.84
28 8 0.04
29 19 0.11
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCGAAA
Found at i:31420978 original size:27 final size:27
Alignment explanation
Indices: 31420926--31421004 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
31420916 AAATGACTAA
* *
31420926 AATACCCCTATTAAGGTAAAATGACCGT
1 AATACCCCT-GTAGGGTAAAATGACCGT
31420954 AA-AGCCCCTGTAGGGTAAAATGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
*
31420981 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
31421005 GAATATACCC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 38 0.83
28 8 0.17
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:31421012 original size:27 final size:27
Alignment explanation
Indices: 31420902--31421014 Score: 95
Period size: 27 Copynumber: 4.1 Consensus size: 27
31420892 TTACCAAAAC
* * * **
31420902 ACCCTTGTAGGATGAAATGACTAAAAT
1 ACCCCTGTAGGGTAAAATGACCGAAAT
* *
31420929 ACCCCTATTAAGGTAAAATGACCGTAAA-
1 ACCCCT-GTAGGGTAAAATGACCG-AAAT
* *
31420957 GCCCCTGTAGGGTAAAATGACCGTAAT
1 ACCCCTGTAGGGTAAAATGACCGAAAT
*
31420984 ACCCCTGTATGGTAAAATGA-CGAATAT
1 ACCCCTGTAGGGTAAAATGACCGAA-AT
31421011 ACCC
1 ACCC
31421015 TTATGTTCCG
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
26 5 0.07
27 44 0.65
28 16 0.24
29 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
ACCCCTGTAGGGTAAAATGACCGAAAT
Found at i:31422271 original size:20 final size:20
Alignment explanation
Indices: 31422246--31422288 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
31422236 ATTTTGATAA
31422246 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
31422266 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
31422286 ACA
1 ACA
31422289 CGAGATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:31422296 original size:20 final size:20
Alignment explanation
Indices: 31422253--31422296 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
31422243 TAAACATGAT
* *
31422253 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACACGAG
31422273 ATGTATGATATGCACACGAG
1 ATGTATGATATGCACACGAG
31422293 ATGT
1 ATGT
31422297 TCATAAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACACGAG
Found at i:31422462 original size:23 final size:23
Alignment explanation
Indices: 31422343--31422460 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
31422333 AGGAAGTGCA
31422343 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
**
31422366 AAAGGGCTTATGCCATAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
31422389 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
31422412 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
31422435 AAAAGGGCTT-TGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
31422458 AAA
1 AAA
31422461 AGAGGCTTGG
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
22 3 0.03
23 78 0.87
24 9 0.10
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:31422710 original size:31 final size:31
Alignment explanation
Indices: 31422675--31422738 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
31422665 CGTTTACCAT
*
31422675 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* **
31422706 AAAGGCTTCGGCTCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
31422737 AA
1 AA
31422739 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:31426861 original size:584 final size:584
Alignment explanation
Indices: 31425753--31426962 Score: 2233
Period size: 584 Copynumber: 2.1 Consensus size: 584
31425743 CTTGAGGATT
31425753 TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTGGTGCGTCACATCAAACCATTTTT
1 TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTGGTGCGTCACATCAAACCATTTTT
31425818 CAAATTTGATCTTTCTGGTGAAAATCCATTACTGAATCTAAATTCCTTTATTATTGTTAAACTAA
66 CAAATTTGATCTTTCTGGTGAAAATCCATTACTGAATCTAAATTCCTTTATTATTGTTAAACTAA
31425883 AGTTCTCATCAAAACGTTTACCAATTTGTTTGCCTCTGGTATATTACCTCATTTAAAATCACGGA
131 AGTTCTCATCAAAACGTTTACCAATTTGTTTGCCTCTGGTATATTACCTCATTTAAAATCACGGA
*
31425948 AGCATTTTGAAAGCTTTGTTGTTGGAAGCTCGTGTTCCTTAGAAAAATCATGCCATTTTGAAATC
196 AGCATTTTGAAAACTTTGTTGTTGGAAGCTCGTGTTCCTTAGAAAAATCATGCCATTTTGAAATC
*
31426013 TCGAGTTTTCCTTGACTAGCAGTTTAGTATAAGAAATCACAATCCAAATTAAAACTTAAAACCCA
261 TCGAGTTTTCCTAGACTAGCAGTTTAGTATAAGAAATCACAATCCAAATTAAAACTTAAAACCCA
*
31426078 CCTACGGCCTTATTACATAATTTAAAAACACAAAACGAAATCTAATTGCAATTAAAAAAAACAGA
326 CCTACGGCCTTATTACATAATTTAAAAACACAAAACGAAATCTAATTACAATTAAAAAAAACAGA
* * *
31426143 AACAGTAGTGTGGCCATCTCCGAGTCCCTCGCAGCTCCAAACCATCTAAGCTTAGGGATTACCTG
391 AACAATAGTGTGGCCATCTCCAAGTCCCCCGCAGCTCCAAACCATCTAAGCTTAGGGATTACCTG
* *
31426208 TACAGTTAGAAACGGGGTGAGTTTACAAAAACTCAGTGTGTAATCCCAATAACAAACAAAGATTG
456 CACAGTTAGAAACGGGGTGAGTTTACAAAAACTCAGTGTGTAATCCCAATAACAAACAAACATTG
31426273 AATAACACGGTATCAGTACAATCTGGGCCAAAGCCCTATTCATTCTTGACATATACTAGGCCGA
521 AATAACACGGTATCAGTACAATCTGGGCCAAAGCCCTATTCATTCTTGACATATACTAGGCCGA
31426337 TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTGGTGCGTCACATCAAACCATTTTT
1 TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTGGTGCGTCACATCAAACCATTTTT
*
31426402 CAAATTTGATCTTT-TCGGTGAAAATCCATTATTGAATCTAAATTCCTTTATTATTGTTAAACTA
66 CAAATTTGATCTTTCT-GGTGAAAATCCATTACTGAATCTAAATTCCTTTATTATTGTTAAACTA
*
31426466 AAGTTCTCATCAAAACGTTTACCAATTTGTTTGCCTCTGGTATATTACCTCATTTAAAATCGCGG
130 AAGTTCTCATCAAAACGTTTACCAATTTGTTTGCCTCTGGTATATTACCTCATTTAAAATCACGG
31426531 AAGCATTTTGAAAACTTTGTTGTTGGAAGCTCGTGTTCCTTAGAAAAATCATGCCATTTTGAAAT
195 AAGCATTTTGAAAACTTTGTTGTTGGAAGCTCGTGTTCCTTAGAAAAATCATGCCATTTTGAAAT
31426596 CTCGAGTTTTCCTAGACTAGCAGTTTAGTATAAGAAATCACAATCCAAATTAAAACTTAAAACCC
260 CTCGAGTTTTCCTAGACTAGCAGTTTAGTATAAGAAATCACAATCCAAATTAAAACTTAAAACCC
* *
31426661 ACCTACGGCCTTATTACATAATTTAAAAACACAAAACGAAATCTAATTACAATTAAAAGAAATAG
325 ACCTACGGCCTTATTACATAATTTAAAAACACAAAACGAAATCTAATTACAATTAAAAAAAACAG
*
31426726 AGACAATAGTGTGGCCATCTCCAAGTCCCCCGCAGCTCCAAACCATCTAAGCTTAGGGATTACCT
390 AAACAATAGTGTGGCCATCTCCAAGTCCCCCGCAGCTCCAAACCATCTAAGCTTAGGGATTACCT
*
31426791 GCACAGTTAGAAACGGGGTGAGTTTACGAAAACTCAGTGTGTAATCCCAATAACAAACAAACATT
455 GCACAGTTAGAAACGGGGTGAGTTTACAAAAACTCAGTGTGTAATCCCAATAACAAACAAACATT
31426856 GAATAACACGGTATCAGTACAATCTGGGCCAAAGCCCTATTCATTCTTGACATATACTAGGCCGA
520 GAATAACACGGTATCAGTACAATCTGGGCCAAAGCCCTATTCATTCTTGACATATACTAGGCCGA
* * * * *
31426921 TGTAACACCCCAAACCCGACCCAGACATTATGGTCGAATCTG
1 TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTG
31426963 ACATGCCACA
Statistics
Matches: 606, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
583 1 0.00
584 605 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (584 bp):
TGTAACACCCCAAACCCGGCCTAGACGTTATGGCCAAATCTGGTGCGTCACATCAAACCATTTTT
CAAATTTGATCTTTCTGGTGAAAATCCATTACTGAATCTAAATTCCTTTATTATTGTTAAACTAA
AGTTCTCATCAAAACGTTTACCAATTTGTTTGCCTCTGGTATATTACCTCATTTAAAATCACGGA
AGCATTTTGAAAACTTTGTTGTTGGAAGCTCGTGTTCCTTAGAAAAATCATGCCATTTTGAAATC
TCGAGTTTTCCTAGACTAGCAGTTTAGTATAAGAAATCACAATCCAAATTAAAACTTAAAACCCA
CCTACGGCCTTATTACATAATTTAAAAACACAAAACGAAATCTAATTACAATTAAAAAAAACAGA
AACAATAGTGTGGCCATCTCCAAGTCCCCCGCAGCTCCAAACCATCTAAGCTTAGGGATTACCTG
CACAGTTAGAAACGGGGTGAGTTTACAAAAACTCAGTGTGTAATCCCAATAACAAACAAACATTG
AATAACACGGTATCAGTACAATCTGGGCCAAAGCCCTATTCATTCTTGACATATACTAGGCCGA
Found at i:31427250 original size:18 final size:18
Alignment explanation
Indices: 31427224--31427258 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31427214 TCGTAACGTT
*
31427224 GTGTTGTTTGGAAAACAA
1 GTGTCGTTTGGAAAACAA
*
31427242 GTGTCGTTTTGAAAACA
1 GTGTCGTTTGGAAAACA
31427259 CGTCCTAAGT
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:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (18 bp):
GTGTCGTTTGGAAAACAA
Found at i:31427728 original size:24 final size:24
Alignment explanation
Indices: 31427688--31427802 Score: 109
Period size: 24 Copynumber: 4.9 Consensus size: 24
31427678 CTAGAGGCCT
31427688 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTAATAAACTGGGGCAA
*
31427712 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTAATAAACTGGGGCAA
*
31427736 AGCCCTTTTCAATAAACT-AGG---
1 AGCCCTTTT-AATAAACTGGGGCAA
*
31427757 -G-CTTTTTCAATAAACTGGGGCATA
1 AGCCCTTTT-AATAAACTGGGGCA-A
31427781 AGCCCTTTTCAATAAACTGGGG
1 AGCCCTTTT-AATAAACTGGGG
31427803 TATAAGCCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
19 14 0.18
20 3 0.04
23 7 0.09
24 26 0.34
25 8 0.11
26 18 0.24
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAA
Found at i:31427765 original size:19 final size:19
Alignment explanation
Indices: 31427741--31427777 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31427731 GGCAAAGCCC
31427741 TTTTCAATAAACTAGGGCT
1 TTTTCAATAAACTAGGGCT
*
31427760 TTTTCAATAAACTGGGGC
1 TTTTCAATAAACTAGGGC
31427778 ATAAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (19 bp):
TTTTCAATAAACTAGGGCT
Found at i:31427795 original size:26 final size:26
Alignment explanation
Indices: 31427760--31427815 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
31427750 AACTAGGGCT
*
31427760 TTTTCAATAAACTGGGGCATAAGCCC
1 TTTTCAATAAACTGGGGCATAAGCCA
*
31427786 TTTTCAATAAACTGGGGTATAAGCCA
1 TTTTCAATAAACTGGGGCATAAGCCA
31427812 TTTT
1 TTTT
31427816 GCACTTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (26 bp):
TTTTCAATAAACTGGGGCATAAGCCA
Found at i:31427932 original size:20 final size:20
Alignment explanation
Indices: 31427866--31427922 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
31427856 TTATGAATAC
*
31427866 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
31427886 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31427906 GTCATGTGCATATCATA
1 ATCATGTGCATATCATA
31427923 TCAACCATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31435829 original size:25 final size:25
Alignment explanation
Indices: 31435761--31435869 Score: 152
Period size: 26 Copynumber: 4.4 Consensus size: 25
31435751 CTGGAGGCCT
31435761 AGCCTCTTTTAAT-AACTGGGGCA-A
1 AGCC-CTTTTAATAAACTGGGGCATA
*
31435785 AGCCCTTTTGATAAACTGGGGCA-A
1 AGCCCTTTTAATAAACTGGGGCATA
31435809 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTT-AATAAACTGGGGCATA
31435835 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTT-AATAAACTGGGGCATA
*
31435861 AGCCATTTT
1 AGCCCTTTT
31435870 GCACTTCCTC
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
23 7 0.09
24 24 0.30
25 13 0.16
26 35 0.44
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCATA
Found at i:31435984 original size:20 final size:20
Alignment explanation
Indices: 31435918--31435974 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
31435908 TTATGAATAC
*
31435918 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
31435938 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31435958 GTCATGTGCATATCATA
1 ATCATGTGCATATCATA
31435975 TCAACCATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31439451 original size:39 final size:40
Alignment explanation
Indices: 31439235--31439441 Score: 271
Period size: 40 Copynumber: 5.2 Consensus size: 40
31439225 TGGATGATAA
*
31439235 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCT-ACTATA-T
* *
31439275 TCGGGCTAAG-CCCGAAGGCATTAGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
31439314 CTGGGCTAAGTCCCTAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
31439354 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
31439394 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATAT
31439434 CC-GGCTAA
1 CCGGGCTAA
31439442 ATTCTGAAGG
Statistics
Matches: 149, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 39 0.26
40 110 0.74
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
Found at i:31441340 original size:25 final size:25
Alignment explanation
Indices: 31441312--31441381 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
31441302 CTCTTTTAAT
*
31441312 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
31441337 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
31441362 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
31441382 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:31441603 original size:27 final size:27
Alignment explanation
Indices: 31441573--31441631 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
31441563 TTAACACCCT
*
31441573 AAGGGCAAAATGGTAATTTTACCCCAC
1 AAGGGCAAAATGGTAATTCTACCCCAC
* *** *
31441600 AAGGGTATCTTGGTAATTCTACCCTAC
1 AAGGGCAAAATGGTAATTCTACCCCAC
31441627 AAGGG
1 AAGGG
31441632 TATTTCGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AAGGGCAAAATGGTAATTCTACCCCAC
Found at i:31441632 original size:27 final size:27
Alignment explanation
Indices: 31441584--31441798 Score: 274
Period size: 27 Copynumber: 8.0 Consensus size: 27
31441574 AGGGCAAAAT
* *
31441584 GGTAATTTTACCCCACAAGGGTATCTT-
1 GGTAATTCTACCCTACAAGGGTAT-TTC
31441611 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31441638 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
31441665 AGTAATTCTACACTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31441692 GGTAATTCTACCCTACAAGGTTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
31441719 AGTAATTCTACCCTAC-TGGGT-TTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
31441744 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
31441771 GATAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
31441798 G
1 G
31441799 ATATTTTACA
Statistics
Matches: 167, Mismatches: 18, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
25 19 0.11
26 9 0.05
27 139 0.83
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:31441847 original size:27 final size:27
Alignment explanation
Indices: 31441759--31441858 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
31441749 TTCTACCCTA
**
31441759 CAGGGGTATTTCGATAA-TTC-TATCCT
1 CAGGGGTATTTCGATAATTTCATA-AAT
* *
31441785 ACAGGGGTATTTCGAT-ATTTTACAAAT
1 -CAGGGGTATTTCGATAATTTCATAAAT
*
31441812 C-GAGAGTATTTCGATAATTTCATAAAT
1 CAG-GGGTATTTCGATAATTTCATAAAT
* *
31441839 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTCGATAATTT
31441859 TACAAGCTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.02
26 13 0.22
27 42 0.72
28 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTCGATAATTTCATAAAT
Found at i:31441870 original size:27 final size:27
Alignment explanation
Indices: 31441840--31441994 Score: 231
Period size: 27 Copynumber: 5.7 Consensus size: 27
31441830 TTCATAAATC
*
31441840 AGGGGTATTTTGGTAATTTTACAAGCT
1 AGGGGTATTTTGGTAATTTTACAAACT
31441867 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
31441894 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
31441921 AGGGGTATTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* **
31441948 AGAGGTATTTTGGTAATTTTACTGA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
*
31441974 CGAGGGTATTTTGGTAATTTT
1 AG-GGGTATTTTGGTAATTTT
31441995 GTAAACCAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 116 0.99
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:31441925 original size:81 final size:81
Alignment explanation
Indices: 31441801--31442021 Score: 239
Period size: 81 Copynumber: 2.7 Consensus size: 81
31441791 GTATTTCGAT
* * * * * * * *
31441801 ATTTTACAAATCGAGAGTATTTCGATAATTTCATAAA-TCAGGGGTATTTTGGTAATTTTACAAG
1 ATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTAGTAATTTTACAAA
* *
31441865 CTAGGGGTATTTTGGTA
65 CCAGAGGTATTTTGGTA
31441882 ATTTTACAAACTAG-GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAA
1 ATTTTACAAA-TAGAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAA
31441946 CCAGAGGTATTTTGGTA
65 CCAGAGGTATTTTGGTA
** * ** * ** *
31441963 ATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAATGGTATTTCAGTAATTTT
1 ATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTT
31442022 GTAAATCGAG
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.02
81 113 0.96
82 3 0.03
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (81 bp):
ATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAAC
CAGAGGTATTTTGGTA
Found at i:31442001 original size:54 final size:54
Alignment explanation
Indices: 31441801--31442021 Score: 223
Period size: 54 Copynumber: 4.1 Consensus size: 54
31441791 GTATTTCGAT
* * * * * * *
31441801 ATTTTACAAATCGA-GAGTATTTCGATAATTTCATAAATCAGGGGTATTTTGGTA
1 ATTTTAC-AATCGAGGGGTATTTTGGTAATTTTACAAACCAGAGGTATTTTGGTA
* * * *
31441855 ATTTTACAAGCTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTA
1 ATTTTACAATCGAGGGGTATTTTGGTAATTTTACAAACCAGAGGTATTTTGGTA
* * *
31441909 ATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAACCAGAGGTATTTTGGTA
1 ATTTTACAATCGAGGGGTATTTTGGTAATTTTACAAACCAGAGGTATTTTGGTA
* ** **
31441963 ATTTTACTGATCGA-GGGTATTTTGGTAATTTTGTAAACCA-ATGGTATTTCAGTA
1 ATTTTAC-AATCGAGGGGTATTTTGGTAATTTTACAAACCAGA-GGTATTTTGGTA
31442017 ATTTT
1 ATTTT
31442022 GTAAATCGAG
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.03
54 135 0.94
55 3 0.02
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (54 bp):
ATTTTACAATCGAGGGGTATTTTGGTAATTTTACAAACCAGAGGTATTTTGGTA
Found at i:31442008 original size:27 final size:27
Alignment explanation
Indices: 31441801--31442021 Score: 192
Period size: 27 Copynumber: 8.2 Consensus size: 27
31441791 GTATTTCGAT
* * * * *
31441801 ATTTTACAAATCGAGAGTATTTCGATA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* * * *
31441828 ATTTCATAAATCAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* * *
31441855 ATTTTACAAGCTAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* *
31441882 ATTTTACAAACTAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* * *
31441909 ATTTTACAAACTAGGGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
31441936 ATTTTACAAACC-AGAGGTATTTTGGTA
1 ATTTTACAAACCAAG-GGTATTTTGGTA
** * *
31441963 ATTTTACTGATCGAGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
** * **
31441990 ATTTTGTAAACCAATGGTATTTCAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
31442017 ATTTT
1 ATTTT
31442022 GTAAATCGAG
Statistics
Matches: 163, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 160 0.98
28 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTACAAACCAAGGGTATTTTGGTA
Found at i:31442035 original size:27 final size:27
Alignment explanation
Indices: 31441972--31442054 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 27
31441962 AATTTTACTG
**
31441972 ATCGAGGGTATTTTGGTAATTTTGTAA
1 ATCGAGGGTATTTCAGTAATTTTGTAA
* * *
31441999 ACCAATGGTATTTCAGTAATTTTGTAA
1 ATCGAGGGTATTTCAGTAATTTTGTAA
*** *
31442026 ATCGAGGGTAAAACAGTAATTCTGTAA
1 ATCGAGGGTATTTCAGTAATTTTGTAA
31442053 AT
1 AT
31442055 TAAGGGTAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.37
Consensus pattern (27 bp):
ATCGAGGGTATTTCAGTAATTTTGTAA
Found at i:31442061 original size:81 final size:81
Alignment explanation
Indices: 31441985--31442251 Score: 266
Period size: 81 Copynumber: 3.3 Consensus size: 81
31441975 GAGGGTATTT
* * ** * *
31441985 TGGTAATTTTGTAAACCAATGGT-ATTTCAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCT
1 TGGTAATTCTGTAAACCAAGGGTAAAAT-AGTAATTCTATAAATCGAGGGTAAAACAGTAATTCT
* *
31442049 GTAAATTAAGGGTAAAA
65 ATAAATCAAGGGTAAAA
** * * *
31442066 TGGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACAGTAATTCTA
1 TGGTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
31442131 TAAATCAAGGGTAAAA
66 TAAATCAAGGGTAAAA
* ** * * * ** *
31442147 CGGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTG
1 TGGTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
**
31442212 TAAATTGAGGGTAAAA
66 TAAATCAAGGGTAAAA
** * *
31442228 CAGTAATTCTGTAAATCGAGGGTA
1 TGGTAATTCTGTAAACCAAGGGTA
31442252 CTTTGGTAAT
Statistics
Matches: 164, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 162 0.99
82 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (81 bp):
TGGTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
TAAATCAAGGGTAAAA
Found at i:31442259 original size:81 final size:81
Alignment explanation
Indices: 31442014--31442278 Score: 377
Period size: 81 Copynumber: 3.3 Consensus size: 81
31442004 TGGTATTTCA
* * * *
31442014 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTGTA
1 GTAATTCTATAAATTGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAACGGTAATTCTGTA
31442079 AGTCGAGGGTAAAATG
66 AGTCGAGGGTAAAATG
* *
31442095 GTAATTCTATAAATTGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACGGTAATTCTGTA
1 GTAATTCTATAAATTGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAACGGTAATTCTGTA
31442160 AGTCGAGGGTAAAATG
66 AGTCGAGGGTAAAATG
** * *
31442176 GTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAACAGTAATTCTGTA
1 GTAATTCTATAAATTGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAACGGTAATTCTGTA
* ***
31442241 AATCGAGGGTACTTTG
66 AGTCGAGGGTAAAATG
* * *
31442257 GTAATTTTACAATTTGAGGGTA
1 GTAATTCTATAAATTGAGGGTA
31442279 TTTCAGTAAT
Statistics
Matches: 165, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 165 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (81 bp):
GTAATTCTATAAATTGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAACGGTAATTCTGTA
AGTCGAGGGTAAAATG
Found at i:31442262 original size:27 final size:27
Alignment explanation
Indices: 31442014--31442251 Score: 305
Period size: 27 Copynumber: 8.8 Consensus size: 27
31442004 TGGTATTTCA
* **
31442014 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
**
31442041 GTAATTCTGTAAATTAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
31442068 GTAATTCTGTAAGTCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * **
31442095 GTAATTCTATAAATTGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
31442122 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
31442149 GTAATTCTGTAAGTCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
31442176 GTAATTCTATAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* **
31442203 GTAATTCTGTAAATTGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
31442230 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
31442252 CTTTGGTAAT
Statistics
Matches: 184, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 184 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:31442274 original size:54 final size:53
Alignment explanation
Indices: 31442012--31442278 Score: 273
Period size: 54 Copynumber: 4.9 Consensus size: 53
31442002 AATGGTATTT
* * ** * *
31442012 CAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTAAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAT-AATTGAGGGTAAAA
** * *
31442066 TGGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAT-AATTGAGGGTAAAA
* * * *
31442120 CAGTAATTCTATAAATCAAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA-TTGAGGGTAAAA
** * *
31442174 TGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAT-AATTGAGGGTAAAA
* *** * *
31442228 CAGTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTACAATTTGAGGGTA
1 CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA-TTGAGGGTA
31442279 TTTCAGTAAT
Statistics
Matches: 178, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
53 4 0.02
54 172 0.97
55 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (53 bp):
CAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAATTGAGGGTAAAA
Found at i:31442784 original size:56 final size:56
Alignment explanation
Indices: 31442707--31442824 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
31442697 TATGTTAGCT
*
31442707 TCCCAATGTGGGATCCCTCCAACATCAGAGTTTAAATTCAACACCAACTCTTGTCG
1 TCCCAATGTGGGATCCCTCCAACATCAGAGTTTAAATTCAACACCAACTCTTGCCG
*
31442763 TCCCAATGTGGGATCCCTCCAACATCAGATTTTAAATTCAACACCAACTCTTGCCG
1 TCCCAATGTGGGATCCCTCCAACATCAGAGTTTAAATTCAACACCAACTCTTGCCG
31442819 TCCCAA
1 TCCCAA
31442825 CATAGCAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (56 bp):
TCCCAATGTGGGATCCCTCCAACATCAGAGTTTAAATTCAACACCAACTCTTGCCG
Found at i:31445231 original size:30 final size:30
Alignment explanation
Indices: 31445175--31445232 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
31445165 TAGGCACTTC
*
31445175 CACACAGGTGACGCACACGCCCGTGTGTGA
1 CACACAGGTGACGCACACGCCAGTGTGTGA
* *
31445205 CACACGGGTAGAC-CACATGCCAGTGTGT
1 CACACAGGT-GACGCACACGCCAGTGTGT
31445233 CATGGCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (30 bp):
CACACAGGTGACGCACACGCCAGTGTGTGA
Done.