Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 97 of 202
Found at i:29469986 original size:25 final size:26
Alignment explanation
Indices: 29469947--29469996 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
29469937 TTGTCACATA
*
29469947 TACTATTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTCCTGCGT
29469973 TACTATT-CTGGCAGCTTTCCTGCG
1 TACTATTACTGGCAGCTTTCCTGCG
29469997 ATATTGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTCCTGCGT
Found at i:29470168 original size:28 final size:28
Alignment explanation
Indices: 29470107--29470185 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
29470097 ATTATTCTAT
* * ***
29470107 TTACTGTATTGGGCAAAGGCCCACATTG
1 TTACTGTAATGGGCTAAGGCCCACACCC
* *
29470135 TCACTGTACTGGGCTAAGGCCCACACCC
1 TTACTGTAATGGGCTAAGGCCCACACCC
*
29470163 TTACTGTAATGGGCTTAGGCCCA
1 TTACTGTAATGGGCTAAGGCCCA
29470186 TACTGTACCG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (28 bp):
TTACTGTAATGGGCTAAGGCCCACACCC
Found at i:29477201 original size:27 final size:27
Alignment explanation
Indices: 29477162--29477543 Score: 475
Period size: 27 Copynumber: 14.3 Consensus size: 27
29477152 GATTCGTGGG
*
29477162 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
29477189 GAATGACCAAAATACCCCCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29477216 AAATGACTGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** * *
29477243 AAACAACTGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29477270 AAATGACCAAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
**
29477297 AAATGACCGAAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29477324 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29477351 AAATGACAGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29477377 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
29477404 AAATGAGTGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
29477430 AAATGGCTGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
29477457 AAATGAGTGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29477483 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29477510 AATTGACCGAAATACCCTCGAAGGGTG
1 AAATGACCGAAATACCCTCGAAGGGTA
29477537 AAATGAC
1 AAATGAC
29477544 TGTTATACCC
Statistics
Matches: 306, Mismatches: 44, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
26 72 0.24
27 234 0.76
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:29477394 original size:53 final size:54
Alignment explanation
Indices: 29477162--29477543 Score: 475
Period size: 53 Copynumber: 7.1 Consensus size: 54
29477152 GATTCGTGGG
* * ** * *
29477162 AAATGATCGAAATACCCTCGAAGGGTAGAATGACCAAAATACCCCCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* * ** *
29477216 AAATGACTGAAATACCCCCGAAGGGTAAAACAACTGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* * **
29477270 AAATGACCAAAATACCC-CTGAAGGGTAAAATGACCGAAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* *
29477324 AAATGACCAAAATACCCTCGAAGGGTAAAATGACAGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* *
29477377 AAATGACCGAAATACCCTTGAAGGGTAAAATGAGTGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* * * *
29477430 AAATGGCTGAAATACCCTTGAAGGGTAAAATGAGTGAAATA-CCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
* * * * *
29477483 AAATGACTGAAATACCCTCGATGGGTAAATTGACCGAAATACCCTCGAAGGGTG
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
29477537 AAATGAC
1 AAATGAC
29477544 TGTTATACCC
Statistics
Matches: 292, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 146 0.50
54 145 0.50
55 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
Found at i:29477767 original size:25 final size:26
Alignment explanation
Indices: 29477706--29477771 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
29477696 TATGCTGTTG
* *
29477706 CTGGTAGCTTTGCTGCGTTACTGTTA
1 CTGGCAGCTTTGCTGCGTTACTATTA
* *
29477732 CTGGCAACTTTGCTGCGCTT-TTATT-
1 CTGGCAGCTTTGCTGCG-TTACTATTA
29477757 CTGGCAGCTTTGCTG
1 CTGGCAGCTTTGCTG
29477772 TGATATTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 14 0.41
26 18 0.53
27 2 0.06
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.41
Consensus pattern (26 bp):
CTGGCAGCTTTGCTGCGTTACTATTA
Found at i:29477926 original size:28 final size:28
Alignment explanation
Indices: 29477886--29477963 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
29477876 TATTCTATTT
*
29477886 ACTGTATTGGGCTAAGGCCCACATTGTC
1 ACTGTATTGGGCTAAGGCCCACACTGTC
*
29477914 ACTGTATTGGGCTAAGGCCCACACTGTT
1 ACTGTATTGGGCTAAGGCCCACACTGTC
*
29477942 ACTGTAATGGGCTAAGGCCCAC
1 ACTGTATTGGGCTAAGGCCCAC
29477964 TCAATACTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (28 bp):
ACTGTATTGGGCTAAGGCCCACACTGTC
Found at i:29477987 original size:33 final size:28
Alignment explanation
Indices: 29477885--29478009 Score: 110
Period size: 28 Copynumber: 4.3 Consensus size: 28
29477875 TTATTCTATT
* *
29477885 TACTGTATTGGGCTAAGGCCCACATTG-
1 TACTGTATAGGGCTAAGGCCCACACTGA
* *
29477912 TCACTGTATTGGGCTAAGGCCCACACTGT
1 T-ACTGTATAGGGCTAAGGCCCACACTGA
29477941 TACTGTA-ATGGGCTAAGGCCCACTCAATACTGA
1 TACTGTATA-GGGCTAAGGCCCA--C---ACTGA
* *
29477974 TACTGTATAGGGCTCAGGCCCAGACTGA
1 TACTGTATAGGGCTAAGGCCCACACTGA
*
29478002 TTCTGTAT
1 TACTGTAT
29478010 GTTGCATAGT
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.01
28 56 0.67
29 1 0.01
30 1 0.01
33 23 0.28
34 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (28 bp):
TACTGTATAGGGCTAAGGCCCACACTGA
Found at i:29486796 original size:26 final size:26
Alignment explanation
Indices: 29486757--29486837 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 26
29486747 TTTGCCACAT
* *
29486757 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTCGCTGCG
*
29486783 ATGCTGA-TACTGGCAGCTTCGCTGCG
1 ATACT-ATTACTGGCAGCTTCGCTGCG
29486809 ATACTATTACTGGCAGCTTCGCTGCG
1 ATACTATTACTGGCAGCTTCGCTGCG
29486835 ATA
1 ATA
29486838 TTGGTGTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.02
26 48 0.98
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.31
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTCGCTGCG
Found at i:29487007 original size:28 final size:27
Alignment explanation
Indices: 29486940--29487029 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
29486930 ATTGCACTGT
* **
29486940 ACTATTACTGTATTGGGCTAAGGAAAAAC
1 ACTATTATTGTATT-GGCTAAGG-ACCAC
*
29486969 ACTATTATTGTATTGGACTAAGGCCCAC
1 ACTATTATTGTATTGG-CTAAGGACCAC
*
29486997 ACTATTATTGTATTTGGCTAAGGTCCAC
1 ACTATTATTGTA-TTGGCTAAGGACCAC
29487025 ACTAT
1 ACTAT
29487030 ACTGTTACTG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 31 0.57
29 23 0.43
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (27 bp):
ACTATTATTGTATTGGCTAAGGACCAC
Found at i:29489299 original size:14 final size:14
Alignment explanation
Indices: 29489280--29489308 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29489270 GGCACCTTGG
29489280 GCATCTGATAGGCA
1 GCATCTGATAGGCA
29489294 GCATCTGATAGGCA
1 GCATCTGATAGGCA
29489308 G
1 G
29489309 AAGTCTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (14 bp):
GCATCTGATAGGCA
Found at i:29500282 original size:20 final size:20
Alignment explanation
Indices: 29500257--29500295 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29500247 AAATAAAAAT
29500257 CCCAATTTAAATTTTATAAA
1 CCCAATTTAAATTTTATAAA
29500277 CCCAATTTAAATTTTATAA
1 CCCAATTTAAATTTTATAA
29500296 CTTTATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
CCCAATTTAAATTTTATAAA
Found at i:29500889 original size:22 final size:22
Alignment explanation
Indices: 29500858--29500909 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
29500848 AATGGATAAG
* * *
29500858 AGCCGTAAACAGGATAGCTATA
1 AGCCATAAACAGAATAGCTACA
* *
29500880 AGCTATAAACAGAATTGCTACA
1 AGCCATAAACAGAATAGCTACA
29500902 AGCCATAA
1 AGCCATAA
29500910 GTACAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (22 bp):
AGCCATAAACAGAATAGCTACA
Found at i:29500952 original size:32 final size:32
Alignment explanation
Indices: 29500901--29501085 Score: 196
Period size: 32 Copynumber: 5.8 Consensus size: 32
29500891 GAATTGCTAC
* * * **
29500901 AAGCCATAAGT-ACAGTAATATTATTTGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
29500932 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
29500964 CAA-CCATCAGTAACAGTAGTATGATTGACACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
29500996 AAGCCATCAGTAGTAGTAATATGATCAGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
29501028 CAA-CCATCAGTAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
29501060 CAGCCATCAGTAATGGTAATATGATC
1 AAGCCATCAGTAATAGTAATATGATC
29501086 AATACAAAGC
Statistics
Matches: 128, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
31 13 0.10
32 111 0.87
33 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:29501013 original size:64 final size:64
Alignment explanation
Indices: 29500928--29501086 Score: 237
Period size: 64 Copynumber: 2.5 Consensus size: 64
29500918 ATATTATTTG
* * *
29500928 CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAGTAACAGTAGTATGATTGA
1 CACAAAGCCATCAGTAGTAGTAATATGATCAGCACACAACCATCAGTAACAGTAATATGATCGA
** *
29500992 CACAAAGCCATCAGTAGTAGTAATATGATCAGCACACAACCATCAGTAATGGTAATATGATCGG
1 CACAAAGCCATCAGTAGTAGTAATATGATCAGCACACAACCATCAGTAACAGTAATATGATCGA
* * *
29501056 CACACAGCCATCAGTAATGGTAATATGATCA
1 CACAAAGCCATCAGTAGTAGTAATATGATCA
29501087 ATACAAAGCC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 86 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (64 bp):
CACAAAGCCATCAGTAGTAGTAATATGATCAGCACACAACCATCAGTAACAGTAATATGATCGA
Found at i:29501083 original size:96 final size:95
Alignment explanation
Indices: 29500901--29501084 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 95
29500891 GAATTGCTAC
* ** *
29500901 AAGCCATAAGTACAGTAATATTATTTGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACA
1 AAGCCATAAGTACAGTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACA
*
29500966 ACCATCAGTAACAGTAGTATGATTGACACA
66 ACCATCAGTAACAGTAATATGATTGACACA
* * *
29500996 AAGCCATCAGTAGTAGTAATATGATCAGCACACAA-CCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATAAGTA-CAGTAATATGATCAGCACA-AAGCCATCAGTAATAGTAATATGATCGGCACA
* **
29501060 CAGCCATCAGTAATGGTAATATGAT
64 CAACCATCAGTAACAGTAATATGAT
29501085 CAATACAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
95 11 0.14
96 63 0.83
97 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (95 bp):
AAGCCATAAGTACAGTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACA
ACCATCAGTAACAGTAATATGATTGACACA
Found at i:29501135 original size:26 final size:26
Alignment explanation
Indices: 29501099--29501159 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
29501089 ACAAAGCCCT
* * *
29501099 CAATAGCATCGCAGCGAAGTTGCCAG
1 CAATAGTATCGCAGCAAAGCTGCCAG
29501125 CAATAGTATCGCAGCAAAGCTGCCAG
1 CAATAGTATCGCAGCAAAGCTGCCAG
* *
29501151 TAACAGTAT
1 CAATAGTAT
29501160 ATGTGGCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (26 bp):
CAATAGTATCGCAGCAAAGCTGCCAG
Found at i:29501301 original size:11 final size:11
Alignment explanation
Indices: 29501285--29501327 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
29501275 AATCAGTCAT
29501285 ACAAATCACAG
1 ACAAATCACAG
*
29501296 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
29501309 ACAAATCATAG
1 ACAAATCACAG
29501320 ACAAATCA
1 ACAAATCA
29501328 GTCATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.16
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:29501371 original size:24 final size:24
Alignment explanation
Indices: 29501275--29501408 Score: 133
Period size: 24 Copynumber: 5.6 Consensus size: 24
29501265 CCATGCACGG
**
29501275 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
** *
29501299 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATTTAAATCACAGACA
*
29501323 AATCAGTCATTTAAATCACAAACA
1 AATCAGTCATTTAAATCACAGACA
* ** *
29501347 AATCAGTCATTTAGATGTCGGACA
1 AATCAGTCATTTAAATCACAGACA
* * * *
29501371 AATCATTCATTTACATCATAGGCA
1 AATCAGTCATTTAAATCACAGACA
*
29501395 AATCAATCATTTAA
1 AATCAGTCATTTAA
29501409 CCCCGAGGGG
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:29501444 original size:27 final size:27
Alignment explanation
Indices: 29501426--29501531 Score: 185
Period size: 27 Copynumber: 3.9 Consensus size: 27
29501416 GGGCAAAATA
29501426 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
29501453 GTCATTTTACCCTACAGGGGCGTTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
29501480 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
29501507 GTCATTTTACCCTACAGGGGCATTA
1 GTCATTTTACCCTACAGGGGCATTA
29501532 TCCTACAGGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:29501472 original size:54 final size:54
Alignment explanation
Indices: 29501414--29501528 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
29501404 TTTAACCCCG
*
29501414 AGGGGCAAAATAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
1 AGGGGCAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
*** * * *
29501468 AGGGGCGTTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTAC
1 AGGGGCAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
29501522 AGGGGCA
1 AGGGGCA
29501529 TTATCCTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (54 bp):
AGGGGCAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
Found at i:29501562 original size:26 final size:27
Alignment explanation
Indices: 29501533--29501587 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
29501523 GGGGCATTAT
*
29501533 CCTACA-GGACCTTACGGTCATTTTAC
1 CCTACAGGGACATTACGGTCATTTTAC
*
29501559 CCTACAGGGGCATTACGGTCATTTTAC
1 CCTACAGGGACATTACGGTCATTTTAC
29501586 CC
1 CC
29501588 ATTGAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (27 bp):
CCTACAGGGACATTACGGTCATTTTAC
Found at i:29501637 original size:54 final size:53
Alignment explanation
Indices: 29501579--29501719 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 53
29501569 CATTACGGTC
* *
29501579 ATTTTACCCATTGAGGGTATTTCAGTCATTTTACCCTTTCG-GGGTATTTGGGTA
1 ATTTTACCC-TTGAGGGTATTTCAGTAATTTTACCCTTT-GAGGGTATTTGGATA
* * *
29501633 ATTTTACCCTTCGAAGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTTGATA
1 ATTTTACCCTT-GAGGGTATTTCAGTAATTTTACCCTTTGAGGGTATTTGGATA
* *
29501687 ATTTTACCCTCGAGGGTATTTCAATAATTTTAC
1 ATTTTACCCTTGAGGGTATTTCAGTAATTTTAC
29501720 AACCTTTCCG
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 22 0.29
54 54 0.71
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (53 bp):
ATTTTACCCTTGAGGGTATTTCAGTAATTTTACCCTTTGAGGGTATTTGGATA
Found at i:29501713 original size:26 final size:27
Alignment explanation
Indices: 29501547--29501719 Score: 165
Period size: 27 Copynumber: 6.4 Consensus size: 27
29501537 CAGGACCTTA
* * * *
29501547 CGGTCATTTTACCCTAC-AGGGGCATTA
1 CGGTAATTTTACCCTTCGA-GGGTATTT
*
29501574 CGGTCATTTTACCCATT-GAGGGTATTT
1 CGGTAATTTTACCC-TTCGAGGGTATTT
* *
29501601 CAGTCATTTTACCCTTTCG-GGGTATTT
1 CGGTAATTTTACCC-TTCGAGGGTATTT
* *
29501628 GGGTAATTTTACCCTTCGAAGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
*
29501655 CGGTAATTTTACCCTTTGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* *
29501682 TGATAATTTTACCC-TCGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
**
29501708 CAATAATTTTAC
1 CGGTAATTTTAC
29501720 AACCTTTCCG
Statistics
Matches: 125, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.20
27 97 0.78
28 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (27 bp):
CGGTAATTTTACCCTTCGAGGGTATTT
Found at i:29502479 original size:26 final size:26
Alignment explanation
Indices: 29502450--29502509 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
29502440 TATGACCAGT
*
29502450 TCAAACTTCCTTCGGTAGTATTTCAC
1 TCAAACTTCCTTCGGTAGTATTCCAC
29502476 TCAAACTTCCTTCGGTAGTATTCCAC
1 TCAAACTTCCTTCGGTAGTATTCCAC
29502502 TCAAACTT
1 TCAAACTT
29502510 TGCCTCTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.37
Consensus pattern (26 bp):
TCAAACTTCCTTCGGTAGTATTCCAC
Found at i:29512496 original size:17 final size:18
Alignment explanation
Indices: 29512466--29512499 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29512456 AACAACTCAT
29512466 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
29512484 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
29512500 ACTCAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:29513979 original size:5 final size:5
Alignment explanation
Indices: 29513965--29514018 Score: 56
Period size: 5 Copynumber: 11.0 Consensus size: 5
29513955 AAGTTTCCCC
* * * * *
29513965 TTTTA CTTTA TTTTA TTTT- TATTA TTTTA TTCTA TTTTA TTTTC TCTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
29514014 TTTTA
1 TTTTA
29514019 ATAATTTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
4 3 0.08
5 35 0.92
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:29514000 original size:24 final size:25
Alignment explanation
Indices: 29513965--29514018 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
29513955 AAGTTTCCCC
29513965 TTTTACTTTATTTTATTTT-TATTA
1 TTTTACTTTATTTTATTTTCTATTA
*
29513989 TTTTA-TTCTATTTTATTTTCTCTTA
1 TTTTACTT-TATTTTATTTTCTATTA
29514014 TTTTA
1 TTTTA
29514019 ATAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.07
24 16 0.59
25 9 0.33
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTACTTTATTTTATTTTCTATTA
Found at i:29514025 original size:24 final size:24
Alignment explanation
Indices: 29513974--29514026 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29513964 CTTTTACTTT
* *
29513974 ATTTTATTTTTATTATTTTATTCT
1 ATTTTATTTTTATTATTTTAATCA
*
29513998 ATTTTATTTTCTCTTATTTTAAT-A
1 ATTTTATTTT-TATTATTTTAATCA
29514022 ATTTT
1 ATTTT
29514027 TAGTTCTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTTATTTTTATTATTTTAATCA
Found at i:29519724 original size:21 final size:21
Alignment explanation
Indices: 29519698--29519773 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
29519688 AATCATATCT
29519698 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
29519719 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
*
29519740 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
29519759 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
29519774 CCTCGAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.36
21 32 0.64
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:29519733 original size:19 final size:19
Alignment explanation
Indices: 29519711--29519774 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
29519701 AAGATTGTAT
29519711 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
29519730 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
29519751 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
29519770 ATATC
1 ATATC
29519775 CTCGAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:29519928 original size:47 final size:47
Alignment explanation
Indices: 29519859--29519952 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
29519849 TCATAATAAA
29519859 ACGTGAAGTCTAGGTGGATTCTTTCTTGGATATTGTTTATCTCATTG
1 ACGTGAAGTCTAGGTGGATTCTTTCTTGGATATTGTTTATCTCATTG
29519906 ACGTGAAGTCTAGGTGGATTCTTTCTTGGATATTGTTTATCTCATTG
1 ACGTGAAGTCTAGGTGGATTCTTTCTTGGATATTGTTTATCTCATTG
29519953 GTTAATTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (47 bp):
ACGTGAAGTCTAGGTGGATTCTTTCTTGGATATTGTTTATCTCATTG
Found at i:29524242 original size:51 final size:51
Alignment explanation
Indices: 29524048--29524240 Score: 187
Period size: 51 Copynumber: 3.8 Consensus size: 51
29524038 AGTGAAAGTG
* * *
29524048 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATGA
1 ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAGATATTA
* * * * * *
29524098 AAGGTCGCATGTGTAGTACTATGT-ACAGGATACTATGCGTACCAGATAGCTT-
1 ATGGTCACGTGTGTAGTACTATGTGA-AGGCTACTACGTGTACCAGATA--TTA
* * * * * *
29524150 -CGATCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTATCATATATTA
1 ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAGATATTA
*
29524200 ATGGTCATGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
29524241 TCGAATGATA
Statistics
Matches: 113, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
49 2 0.02
50 37 0.33
51 73 0.65
53 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (51 bp):
ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCAGATATTA
Found at i:29528171 original size:9 final size:8
Alignment explanation
Indices: 29528159--29528229 Score: 67
Period size: 9 Copynumber: 8.5 Consensus size: 8
29528149 TAAGAAGAGG
29528159 AATAAGATA
1 AATAA-ATA
29528168 AATAAATA
1 AATAAATA
29528176 GAATAAATA
1 -AATAAATA
29528185 AATAGAATA
1 AATA-AATA
29528194 AA-ATAATA
1 AATA-AATA
29528202 AATTAAATA
1 AA-TAAATA
29528211 AAT-AA-A
1 AATAAATA
29528217 AATAAATTA
1 AATAAA-TA
29528226 AATA
1 AATA
29528230 GGGAAAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
6 4 0.07
7 4 0.07
8 15 0.28
9 30 0.56
10 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
AATAAATA
Found at i:29528174 original size:4 final size:4
Alignment explanation
Indices: 29528159--29528229 Score: 67
Period size: 4 Copynumber: 17.0 Consensus size: 4
29528149 TAAGAAGAGG
29528159 AATA AGATA AATA AATA GAATA AATA AATA GAATA AA-A TAATA AATTA
1 AATA A-ATA AATA AATA -AATA AATA AATA -AATA AATA -AATA AA-TA
29528207 AATA AAT- AA-A AATA AATTA AATA
1 AATA AATA AATA AATA AA-TA AATA
29528230 GGGAAAAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
3 5 0.09
4 32 0.55
5 21 0.36
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:29528181 original size:13 final size:13
Alignment explanation
Indices: 29528165--29528230 Score: 73
Period size: 13 Copynumber: 4.9 Consensus size: 13
29528155 GAGGAATAAG
29528165 ATAAATAAATAGA
1 ATAAATAAATAGA
29528178 ATAAATAAATAGA
1 ATAAATAAATAGA
29528191 ATAAA-ATAATA-A
1 ATAAATA-AATAGA
*
29528203 ATTAAATAAATAAAA
1 A-TAAATAAAT-AGA
29528218 ATAAATTAAATAG
1 ATAAA-TAAATAG
29528231 GGAAAAAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
12 3 0.07
13 29 0.63
14 7 0.15
15 7 0.15
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAGA
Found at i:29551692 original size:51 final size:50
Alignment explanation
Indices: 29551531--29551710 Score: 168
Period size: 51 Copynumber: 3.6 Consensus size: 50
29551521 AGTTGCTAGA
* * * *
29551531 TCACGTGTGTAGTACCATGTGCAAGCTACTACGTGTACTGGAATG-ATA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GG-ATGAAAATGG
* * * * * *** *
29551581 TCGCATGTGTAGTACTACGTGCAGGCTACTATGCGTACCAGAT-AGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGAAAAT-GG
*
29551632 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGAAAATGG
29551683 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
29551711 ATAAGTGAAC
Statistics
Matches: 101, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
49 2 0.02
50 31 0.31
51 66 0.65
52 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATGAAAATGG
Found at i:29555046 original size:18 final size:18
Alignment explanation
Indices: 29555023--29555058 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29555013 ACAGCAGAAA
29555023 CATGATCGTCACACTAAG
1 CATGATCGTCACACTAAG
29555041 CATGATCGTCACACTAAG
1 CATGATCGTCACACTAAG
29555059 TCGCTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (18 bp):
CATGATCGTCACACTAAG
Found at i:29555435 original size:32 final size:35
Alignment explanation
Indices: 29555375--29555441 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
29555365 ATTATTTTTT
*
29555375 AATATTATATTTTTAATTGCAATAATTAAA-ATAA
1 AATAATATATTTTTAATTGCAATAATTAAATATAA
* *
29555409 AATAATAT-TTTTTATTTG-AATTATTAAATATAA
1 AATAATATATTTTTAATTGCAATAATTAAATATAA
29555442 TTAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 9 0.31
33 13 0.45
34 7 0.24
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (35 bp):
AATAATATATTTTTAATTGCAATAATTAAATATAA
Found at i:29559638 original size:32 final size:32
Alignment explanation
Indices: 29559602--29559665 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
29559592 ACTATTATAA
29559602 TGTGGTTAGATAATATATATTTTATATATCAT
1 TGTGGTTAGATAATATATATTTTATATATCAT
29559634 TGTGGTTAGATAATATATATTTTATATATCAT
1 TGTGGTTAGATAATATATATTTTATATATCAT
29559666 ACCACAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (32 bp):
TGTGGTTAGATAATATATATTTTATATATCAT
Found at i:29562533 original size:50 final size:49
Alignment explanation
Indices: 29562297--29562533 Score: 307
Period size: 50 Copynumber: 4.8 Consensus size: 49
29562287 TCACATATCG
* *
29562297 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACTCATC-TC-
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGTCT
* * * * * * *
29562344 GAGCCGATGTCATGTCCCAAACATGGTCTTACACTGACTCTTCTCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTC-GTCT
*
29562394 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCCGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCT-CGTCT
* * * *
29562444 GTACTGATGCCATGTCCTAGACATGGTCTTACACCGGCACTCCTCGATCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCG-TCT
29562494 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
29562534 ACTTACTGCC
Statistics
Matches: 162, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
47 39 0.24
49 4 0.02
50 118 0.73
51 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (49 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGTCT
Found at i:29562607 original size:44 final size:44
Alignment explanation
Indices: 29562554--29562646 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
29562544 ATGGTCCAAC
* * *
29562554 CATGCTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGTCTTTTCAGTCAATTCTTCCTTAATTGCCATGTTATAAA
29562598 CATGGTCTTTTCAGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGTCTTTTCAGTCAATTCTTCCTTAATTGCCATGTTATAAA
*
29562642 AATGG
1 CATGG
29562647 ACCTTGAGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (44 bp):
CATGGTCTTTTCAGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:29564217 original size:45 final size:43
Alignment explanation
Indices: 29564131--29564217 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 43
29564121 ATTGTAAATT
* * *** *
29564131 AAAATATAATTATTTTTAAATGTGTAATTATTGCAACTTCTAA
1 AAAATATAATTATTTTAAAATGTATAATTATCAAAAATTCTAA
29564174 AAAATTATAATTATTTTCAAAATGTATAATTATCAAAAATTCTA
1 AAAA-TATAATTATTTT-AAAATGTATAATTATCAAAAATTCTA
29564218 TTTTACTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 4 0.11
44 12 0.33
45 20 0.56
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (43 bp):
AAAATATAATTATTTTAAAATGTATAATTATCAAAAATTCTAA
Found at i:29564663 original size:16 final size:16
Alignment explanation
Indices: 29564626--29564657 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29564616 TTTAATTTGG
29564626 GTTAAACTATTATGAT
1 GTTAAACTATTATGAT
29564642 GTTAAACTATTATGAT
1 GTTAAACTATTATGAT
29564658 AGTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
GTTAAACTATTATGAT
Found at i:29570026 original size:41 final size:40
Alignment explanation
Indices: 29569953--29570075 Score: 131
Period size: 42 Copynumber: 3.0 Consensus size: 40
29569943 GTAATCACAT
* * *
29569953 ATCGATGCCACTGTCCCAGATACGGTCTTACACGAAACAA
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAACAA
* *
29569993 ATACGATGCCAATGGT-TCAGACATGGTCATACACGTAACACAA
1 AT-CGATGCCAAT-GTCCCAGACATGGTCTTACACG-AA-ACAA
* *
29570036 GTCGATGCCAATGTCCCAGACGTGGTCTTACACGATAACA
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACGA-AACA
29570076 TATATCGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
40 2 0.03
41 30 0.44
42 31 0.46
43 5 0.07
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (40 bp):
ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAACAA
Found at i:29572446 original size:21 final size:19
Alignment explanation
Indices: 29572417--29572455 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
29572407 GTCCTAGTTT
29572417 AATTATGTTATAATTGTTGCA
1 AATTATGTTA-AATT-TTGCA
*
29572438 AATTGTGTTAAATTTTGC
1 AATTATGTTAAATTTTGC
29572456 TAAAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (19 bp):
AATTATGTTAAATTTTGCA
Found at i:29572819 original size:9 final size:9
Alignment explanation
Indices: 29572807--29572831 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29572797 TAAGAAACTG
29572807 AATCTTGGA
1 AATCTTGGA
29572816 AATCTTGGA
1 AATCTTGGA
29572825 AATCTTG
1 AATCTTG
29572832 CAGCTAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (9 bp):
AATCTTGGA
Found at i:29594485 original size:40 final size:41
Alignment explanation
Indices: 29594410--29594490 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
29594400 TGTTACTGAA
* *
29594410 TACTGCATGATTGCTACTGATACTGTGATGAGCTAAGGCCC
1 TACTGCATGATTGATACTGATACTGAGATGAGCTAAGGCCC
*
29594451 TACTGCAT-ATTTGATACTG-TACTGAGATGGGCTAAGGCCC
1 TACTGCATGA-TTGATACTGATACTGAGATGAGCTAAGGCCC
29594491 AAACTGCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 20 0.56
41 16 0.44
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TACTGCATGATTGATACTGATACTGAGATGAGCTAAGGCCC
Found at i:29605399 original size:25 final size:25
Alignment explanation
Indices: 29605365--29605428 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
29605355 CGTCATTTAC
* *
29605365 TTGTCACTTTATTAGTTGATAATGA
1 TTGTCACTTTATTAATTGATAACGA
*
29605390 TTGTCACTTTATTAATTGATAACGG
1 TTGTCACTTTATTAATTGATAACGA
29605415 TTGTCACTTTATTA
1 TTGTCACTTTATTA
29605429 CTTGTCACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (25 bp):
TTGTCACTTTATTAATTGATAACGA
Found at i:29605435 original size:15 final size:15
Alignment explanation
Indices: 29605415--29605447 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29605405 TTGATAACGG
29605415 TTGTCACTTTATTAC
1 TTGTCACTTTATTAC
29605430 TTGTCACTTTATTAC
1 TTGTCACTTTATTAC
29605445 TTG
1 TTG
29605448 ATAATGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (15 bp):
TTGTCACTTTATTAC
Found at i:29605449 original size:40 final size:40
Alignment explanation
Indices: 29605390--29605472 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
29605380 TTGATAATGA
29605390 TTGTCACTTTATTAATTGATAACGGTTGTCACTTTATTAC
1 TTGTCACTTTATTAATTGATAACGGTTGTCACTTTATTAC
* *
29605430 TTGTCACTTTATTACTTGATAATGGTTGTCACTTTATTAC
1 TTGTCACTTTATTAATTGATAACGGTTGTCACTTTATTAC
29605470 TTG
1 TTG
29605473 ATAACGGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.49
Consensus pattern (40 bp):
TTGTCACTTTATTAATTGATAACGGTTGTCACTTTATTAC
Found at i:29605458 original size:25 final size:25
Alignment explanation
Indices: 29605430--29605483 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
29605420 ACTTTATTAC
*
29605430 TTGTCACTTTATTACTTGATAATGG
1 TTGTCACTTTATTACTTGATAACGG
29605455 TTGTCACTTTATTACTTGATAACGG
1 TTGTCACTTTATTACTTGATAACGG
29605480 TTGT
1 TTGT
29605484 GTACACTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (25 bp):
TTGTCACTTTATTACTTGATAACGG
Found at i:29605465 original size:65 final size:65
Alignment explanation
Indices: 29605361--29605483 Score: 219
Period size: 65 Copynumber: 1.9 Consensus size: 65
29605351 AACTCGTCAT
*
29605361 TTACTTGTCACTTTATTAGTTGATAATGATTGTCACTTTATTAATTGATAACGGTTGTCACTTTA
1 TTACTTGTCACTTTATTACTTGATAATGATTGTCACTTTATTAATTGATAACGGTTGTCACTTTA
* *
29605426 TTACTTGTCACTTTATTACTTGATAATGGTTGTCACTTTATTACTTGATAACGGTTGT
1 TTACTTGTCACTTTATTACTTGATAATGATTGTCACTTTATTAATTGATAACGGTTGT
29605484 GTACACTTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (65 bp):
TTACTTGTCACTTTATTACTTGATAATGATTGTCACTTTATTAATTGATAACGGTTGTCACTTTA
Found at i:29609785 original size:51 final size:50
Alignment explanation
Indices: 29609705--29609902 Score: 222
Period size: 51 Copynumber: 3.9 Consensus size: 50
29609695 TACCTATAAA
*
29609705 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATA-GATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGA-AGGAT-ATGGT
* * * * * *
29609756 CACATGTGTAGTACTACGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAAGGATATGGT
* * *
29609807 CACGTGTGTAGTACTATGTGCAGGCTACTACGTG-ATCCGAA-AAGTTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAT-CGAAGGA-TATGGT
* *
29609857 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGGATA
29609903 ATAATTACAC
Statistics
Matches: 125, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
50 47 0.38
51 74 0.59
52 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGGATATGGT
Found at i:29619969 original size:50 final size:49
Alignment explanation
Indices: 29619904--29620092 Score: 209
Period size: 51 Copynumber: 3.8 Consensus size: 49
29619894 AAACTGAAAG
*
29619904 TGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
* * * *
29619953 TGATAGGCCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAG-A
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
* * * * * *
29620002 TAGCTTCGATCACGTGTGTAGTACTATGAGCAGGCTACTACGTGTATCGGATA
1 T-G-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A
*
29620055 GTGATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 -TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
29620093 TGTGAACCGG
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 6 0.05
50 39 0.35
51 64 0.57
52 1 0.01
53 2 0.02
54 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
Found at i:29620164 original size:33 final size:33
Alignment explanation
Indices: 29620122--29620357 Score: 162
Period size: 33 Copynumber: 6.8 Consensus size: 33
29620112 ATATAAAAGG
29620122 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
29620155 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG--GT
*
29620196 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
29620223 GGTTGCTAAGTGCTAATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
29620256 GGTTGCTAAGTGCTGATTCCACCG-TATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT
* * *
29620293 GAAAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
29620332 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
29620358 AACGGATAAC
Statistics
Matches: 161, Mismatches: 15, Indels: 53
0.70 0.07 0.23
Matches are distributed among these distances:
27 20 0.12
28 1 0.01
30 1 0.01
31 2 0.01
32 3 0.02
33 57 0.35
34 16 0.10
35 1 0.01
37 4 0.02
38 2 0.01
39 4 0.02
40 2 0.01
41 21 0.13
42 8 0.05
43 19 0.12
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:29626363 original size:18 final size:18
Alignment explanation
Indices: 29626342--29626391 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
29626332 CTTTTTGTCA
* *
29626342 GTTTCTTCTTTTTTTCTT
1 GTTTCCTCTATTTTTCTT
29626360 GTTTCCTCTATTTTTCTCT
1 GTTTCCTCTATTTTTCT-T
*
29626379 TTTTCCTTCTATT
1 GTTTCC-TCTATT
29626392 CTATTTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 6 0.22
20 6 0.22
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (18 bp):
GTTTCCTCTATTTTTCTT
Found at i:29626373 original size:20 final size:20
Alignment explanation
Indices: 29626346--29626391 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
29626336 TTGTCAGTTT
29626346 CTTCT-TTTTT-TCTTGTTTC
1 CTTCTATTTTTCTCTT-TTTC
29626365 C-TCTATTTTTCTCTTTTTC
1 CTTCTATTTTTCTCTTTTTC
29626384 CTTCTATT
1 CTTCTATT
29626392 CTATTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 10 0.42
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.70
Consensus pattern (20 bp):
CTTCTATTTTTCTCTTTTTC
Found at i:29642816 original size:14 final size:14
Alignment explanation
Indices: 29642797--29642826 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29642787 GTTCTTATAG
29642797 TGGAACTTGACACA
1 TGGAACTTGACACA
29642811 TGGAACTTGACACA
1 TGGAACTTGACACA
29642825 TG
1 TG
29642827 TAACAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (14 bp):
TGGAACTTGACACA
Found at i:29644296 original size:109 final size:109
Alignment explanation
Indices: 29644105--29644322 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 109
29644095 ACAAATAAGT
*
29644105 AATTAAACTAGTAAAGTGAAAACATACGAAGTGACATTAAAGTAATGAGTGAATATAATGAATGG
1 AATTAAACTAGTAAAGTGAAAACATACGAAGTGACATTAAAGTAATGAGTGAATATAACGAATGG
29644170 AAGTGAATATGAGTAAATTCCATGAATAAGTTATAAAGTGTACA
66 AAGTGAATATGAGTAAATTCCATGAATAAGTTATAAAGTGTACA
*
29644214 AATTAAACTAGTAAAGTGAAAACATACGAAGTGAGATTAAAGTAATGAGTGAATATAACGAATGG
1 AATTAAACTAGTAAAGTGAAAACATACGAAGTGACATTAAAGTAATGAGTGAATATAACGAATGG
29644279 AAGTGAATATGAGTAAATTCCATGAATAAGTTATAAAGTGTACA
66 AAGTGAATATGAGTAAATTCCATGAATAAGTTATAAAGTGTACA
29644323 CCCTCCTTTT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (109 bp):
AATTAAACTAGTAAAGTGAAAACATACGAAGTGACATTAAAGTAATGAGTGAATATAACGAATGG
AAGTGAATATGAGTAAATTCCATGAATAAGTTATAAAGTGTACA
Found at i:29644374 original size:16 final size:16
Alignment explanation
Indices: 29644353--29644394 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
29644343 TACTTTCTCC
29644353 CTTTTCTC-CTTCTCTT
1 CTTTTCTCTCTT-TCTT
29644369 CTTTTCTCTCTTTCTT
1 CTTTTCTCTCTTTCTT
29644385 CTTTTCTCTC
1 CTTTTCTCTC
29644395 CTTTTTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTTTCTCTCTTTCTT
Found at i:29644401 original size:19 final size:19
Alignment explanation
Indices: 29644365--29644419 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 19
29644355 TTTCTCCTTC
29644365 TCTTCTTTTCTCT-C--TT
1 TCTTCTTTTCTCTCCTTTT
29644381 TCTTCTTTTCTCTCCTTTT
1 TCTTCTTTTCTCTCCTTTT
* *
29644400 TCCTACCTTT-TCTCCTTTT
1 T-CTTCTTTTCTCTCCTTTT
29644419 T
1 T
29644420 TCTCCTCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 13 0.39
17 1 0.03
19 13 0.39
20 6 0.18
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTTCTTTTCTCTCCTTTT
Found at i:29648800 original size:28 final size:28
Alignment explanation
Indices: 29648760--29648814 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
29648750 AAATGGAAGT
* * * *
29648760 CTTTGTGGTGAAGTATGAAAAGAATAGC
1 CTTTATGGCGAAGTACGAAAAAAATAGC
29648788 CTTTATGGCGAAGTACGAAAAAAATAG
1 CTTTATGGCGAAGTACGAAAAAAATAG
29648815 ACTCTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (28 bp):
CTTTATGGCGAAGTACGAAAAAAATAGC
Found at i:29650235 original size:17 final size:17
Alignment explanation
Indices: 29650215--29650262 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
29650205 AAAATGACCC
29650215 CACAAAAAAATTGA-TCT
1 CACAAAAAAATTGACT-T
29650232 CACAAAAAAATTGACTT
1 CACAAAAAAATTGACTT
*
29650249 CATAAAAAAATTGA
1 CACAAAAAAATTGA
29650263 AAATGATCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (17 bp):
CACAAAAAAATTGACTT
Found at i:29652445 original size:56 final size:52
Alignment explanation
Indices: 29652217--29652458 Score: 156
Period size: 50 Copynumber: 4.7 Consensus size: 52
29652207 GATAATAACT
* * ** * **
29652217 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTC-T-TGTAT-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
* ** * * * ** * **
29652266 TGCAAATGCCAAATCCCAGATATGGTCTTACATGAGAGTTCTCATATC--GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
* * * *
29652316 TGCCCATGCCATGTCCCAGACAAGGTCTTACGGGGGACCTCTCATCTCAGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
* *
29652368 --CCAACGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A
* * *
29652422 TGCCAATGCCATGTCCCAAACATGGTATTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
29652459 TCTCATTCCC
Statistics
Matches: 146, Mismatches: 36, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
49 34 0.23
50 75 0.51
51 1 0.01
53 5 0.03
54 1 0.01
56 30 0.21
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
Found at i:29654935 original size:25 final size:26
Alignment explanation
Indices: 29654907--29655038 Score: 70
Period size: 27 Copynumber: 5.0 Consensus size: 26
29654897 CATTTCATCT
*
29654907 CCTA-GGGGTATAACAGTGATTTTAC
1 CCTACGGGGTATAACAGTCATTTTAC
** *
29654932 CCTACGGGGTATTTCGGTCATTTTAC
1 CCTACGGGGTATAACAGTCATTTTAC
* **
29654958 CCTATGGGGCTATTTC-GATCATTTTAC
1 CCTACGGGG-TATAACAG-TCATTTTAC
* ** * *
29654985 CCTATGGGGGTATTTCGGTCATTTTAT
1 CCTA-CGGGGTATAACAGTCATTTTAC
* ** *
29655012 CCTATAGGGGTATTTCGGTCATTTTAC
1 CCTA-CGGGGTATAACAGTCATTTTAC
29655039 ACTATAGGGG
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
25 4 0.04
26 26 0.28
27 58 0.62
28 5 0.05
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (26 bp):
CCTACGGGGTATAACAGTCATTTTAC
Found at i:29654979 original size:27 final size:26
Alignment explanation
Indices: 29654925--29655049 Score: 178
Period size: 27 Copynumber: 4.7 Consensus size: 26
29654915 TATAACAGTG
*
29654925 ATTTTACCCTACGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGTATTTCGGTC
*
29654951 ATTTTACCCTATGGGGCTATTTCGATC
1 ATTTTACCCTATGGGG-TATTTCGGTC
29654978 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
29655005 ATTTTATCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
29655032 ATTTTACACTATAGGGGT
1 ATTTTACCCTAT-GGGGT
29655050 CTCGTTATAG
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.17
27 71 0.79
28 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:29658470 original size:27 final size:27
Alignment explanation
Indices: 29658433--29658550 Score: 130
Period size: 27 Copynumber: 4.4 Consensus size: 27
29658423 ATAATAGTGA
* *
29658433 TTTACTCTATGGGGGTATTTCGGTTAT
1 TTTACTCTATGGGGGTATTTCGATCAT
* *
29658460 TTTACTCTATGGGGGTATTTCAATTAT
1 TTTACTCTATGGGGGTATTTCGATCAT
* *
29658487 TTTA-TCCTATGGGGATATTTCGGTCAT
1 TTTACT-CTATGGGGGTATTTCGATCAT
* **
29658514 TTTACCCTATAAGGGTATTTCGATCAT
1 TTTACTCTATGGGGGTATTTCGATCAT
*
29658541 TTTACCCTAT
1 TTTACTCTAT
29658551 TTTGGGGTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 77 0.99
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (27 bp):
TTTACTCTATGGGGGTATTTCGATCAT
Found at i:29658506 original size:54 final size:54
Alignment explanation
Indices: 29658433--29658550 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
29658423 ATAATAGTGA
* * * * ** *
29658433 TTTACTCTATGGGGGTATTTCGGTTATTTTACTCTATGGGGGTATTTCAATTAT
1 TTTACCCTATGGGGATATTTCGGTCATTTTACCCTATAAGGGTATTTCAATCAT
* *
29658487 TTTATCCTATGGGGATATTTCGGTCATTTTACCCTATAAGGGTATTTCGATCAT
1 TTTACCCTATGGGGATATTTCGGTCATTTTACCCTATAAGGGTATTTCAATCAT
29658541 TTTACCCTAT
1 TTTACCCTAT
29658551 TTTGGGGTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (54 bp):
TTTACCCTATGGGGATATTTCGGTCATTTTACCCTATAAGGGTATTTCAATCAT
Found at i:29661235 original size:4 final size:4
Alignment explanation
Indices: 29661228--29661252 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29661218 ATTGTGTCAT
29661228 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
29661253 CCTTTCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:29665721 original size:23 final size:23
Alignment explanation
Indices: 29665677--29665742 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
29665667 TGAGGAGTTA
*
29665677 AAAAGAATAAATT-GTAATTTTT
1 AAAAGAATAAATTAATAATTTTT
* *
29665699 ATAATAATAAATTAATAATTTTT
1 AAAAGAATAAATTAATAATTTTT
*
29665722 AAAAGATTAAATTAA-AATTTT
1 AAAAGAATAAATTAATAATTTT
29665743 ATCATTTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AAAAGAATAAATTAATAATTTTT
Found at i:29669068 original size:42 final size:43
Alignment explanation
Indices: 29669021--29669171 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 43
29669011 TTCCCTGAGG
* * *
29669021 GGTTGCTAAGTGTTGATTCC-CCGAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
* * *
29669063 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTAT-AAAGGT
* * * * * *
29669106 GGTTGTTATGTGATGATTCC-CCGTATCACTGAATAT-AAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
29669147 GGTTGCTAAGTGCTGATTCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
29669172 GTAACGGTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.04
41 17 0.19
42 34 0.38
43 29 0.33
44 5 0.06
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTATAAAGGT
Found at i:29682541 original size:23 final size:21
Alignment explanation
Indices: 29682509--29682559 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
29682499 TATATTTTAA
*
29682509 TAATTTATTAA-TAAAATTGAGTT
1 TAATTAATTAAGT-AAATTGA--T
29682532 TAATTAATTAAGTAAATTGAT
1 TAATTAATTAAGTAAATTGAT
29682553 TAATTAA
1 TAATTAA
29682560 AGTGGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
23 17 0.65
24 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (21 bp):
TAATTAATTAAGTAAATTGAT
Found at i:29706605 original size:16 final size:17
Alignment explanation
Indices: 29706579--29706611 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29706569 AAAGCAAACT
*
29706579 TACACATAGTTTCAATG
1 TACACATAGTTACAATG
29706596 TACA-ATAGTTACAATG
1 TACACATAGTTACAATG
29706612 GCGTTTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (17 bp):
TACACATAGTTACAATG
Found at i:29709219 original size:30 final size:30
Alignment explanation
Indices: 29709183--29709240 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29709173 CGTGTTGGCA
*
29709183 GTTATCTACTGGCCCTTCGGGGTGACACTG
1 GTTATCTACTAGCCCTTCGGGGTGACACTG
* *
29709213 GTTATCTACTAGTCCTTTGGGGTGACAC
1 GTTATCTACTAGCCCTTCGGGGTGACAC
29709241 CATGTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.33
Consensus pattern (30 bp):
GTTATCTACTAGCCCTTCGGGGTGACACTG
Found at i:29709351 original size:35 final size:36
Alignment explanation
Indices: 29709268--29709351 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 36
29709258 ACTAGTCTTT
* * *
29709268 CGGGGTGACACTGTGTAAATGGTATATAAAGGTCTTT
1 CGGGGTGACACCGTGTAAATGG-ATATAAAGGTCCTA
* ** *
29709305 TGGGGCAACACCGTGTAAATGG-TATACAGGTCCTA
1 CGGGGTGACACCGTGTAAATGGATATAAAGGTCCTA
29709340 CGGGGTGACACC
1 CGGGGTGACACC
29709352 TCGAAAAGGG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
35 19 0.51
37 18 0.49
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (36 bp):
CGGGGTGACACCGTGTAAATGGATATAAAGGTCCTA
Found at i:29715904 original size:16 final size:16
Alignment explanation
Indices: 29715883--29715915 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29715873 TTGAGTTGAG
29715883 AAAATT-ATTGAATTAA
1 AAAATTAATT-AATTAA
29715899 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
29715915 A
1 A
29715916 TAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:29732263 original size:20 final size:20
Alignment explanation
Indices: 29732198--29732263 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
29732188 AGAATAAATC
29732198 ATTTTATCTTTTAGTAGTTT
1 ATTTTATCTTTTAGTAGTTT
** * * *
29732218 ATTAGATATTCTAGGAATATTTT
1 ATTTTATCTTTTA-G--TAGTTT
29732241 ATTTTATCTTTTAGTAGTTT
1 ATTTTATCTTTTAGTAGTTT
29732261 ATT
1 ATT
29732264 AGAATAAGGG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
22 1 0.03
23 14 0.42
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.59
Consensus pattern (20 bp):
ATTTTATCTTTTAGTAGTTT
Found at i:29733524 original size:12 final size:12
Alignment explanation
Indices: 29733507--29733531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29733497 TAAATTATGA
29733507 ATGTCTCCTACG
1 ATGTCTCCTACG
29733519 ATGTCTCCTACG
1 ATGTCTCCTACG
29733531 A
1 A
29733532 GAACCAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTCTCCTACG
Found at i:29740758 original size:52 final size:52
Alignment explanation
Indices: 29740695--29740799 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 52
29740685 GGCCCATTTT
29740695 TATTTTAAAAATTTTAAAA-AATT-AAAAAAAGTATTTTAAAAATATTTTTAAAA
1 TATTTTAAAAA--TTAAAACAATTAAAAAAAAGTATTTTAAAAATA-TTTTAAAA
29740748 TATTTT-AAAATTAAAACAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAAATTAAAACAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
29740799 T
1 T
29740800 TAAAAAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
50 6 0.12
51 13 0.26
52 25 0.50
53 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (52 bp):
TATTTTAAAAATTAAAACAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:29740825 original size:39 final size:39
Alignment explanation
Indices: 29740695--29740887 Score: 235
Period size: 40 Copynumber: 4.8 Consensus size: 39
29740685 GGCCCATTTT
* **
29740695 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATATTT-TAAAATT-AAAAAA--ATTAAAAAAA
* *
29740737 TATTTTTAAAATATTTTAAAATTAAAACAATTAAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATT-AAAAAAA
29740777 GTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAA
1 -TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAA
* *
29740817 TATTTTAAAAATATTTTAAAATTTAAAAAATTTAAAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAA
* *
29740857 TATGTAAAAAATATTTTAAAATTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
29740888 AAATATATTT
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
39 33 0.24
40 47 0.35
41 35 0.26
42 17 0.13
43 3 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (39 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAA
Found at i:29740878 original size:10 final size:11
Alignment explanation
Indices: 29740695--29740877 Score: 89
Period size: 11 Copynumber: 17.9 Consensus size: 11
29740685 GGCCCATTTT
29740695 TATTTT-AAAA
1 TATTTTAAAAA
29740705 -ATTTTAAAAA
1 TATTTTAAAAA
**
29740715 -ATTAAAAAAA
1 TATTTTAAAAA
29740725 GTATTTTAAAAA
1 -TATTTTAAAAA
*
29740737 TATTTTTAAAA
1 TATTTTAAAAA
29740748 TATTTT--AAA
1 TATTTTAAAAA
29740757 -A--TTAAAACA
1 TATTTTAAAA-A
**
29740766 -ATTAAAAAAAA
1 TATT-TTAAAAA
29740777 GTATTTTAAAAA
1 -TATTTTAAAAA
29740789 TATTTT--AAA
1 TATTTTAAAAA
29740798 -A--TTAAAAA
1 TATTTTAAAAA
* **
29740806 AATTAAAAAAA
1 TATTTTAAAAA
29740817 TATTTTAAAAA
1 TATTTTAAAAA
29740828 TATTTT--AAA
1 TATTTTAAAAA
29740837 -A-TTTAAAAA
1 TATTTTAAAAA
*
29740846 -ATTTAAAAAA
1 TATTTTAAAAA
* *
29740856 GTATGTAAAAAA
1 -TATTTTAAAAA
29740868 TATTTTAAAA
1 TATTTTAAAA
29740878 TTAAAAAAAT
Statistics
Matches: 134, Mismatches: 18, Indels: 41
0.69 0.09 0.21
Matches are distributed among these distances:
6 4 0.03
7 3 0.02
8 8 0.06
9 21 0.16
10 19 0.14
11 50 0.37
12 26 0.19
13 3 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:29741508 original size:16 final size:16
Alignment explanation
Indices: 29741486--29741527 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29741476 TTTTTGTATT
29741486 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
29741502 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
29741518 ATATTAATAT
1 ATTTTAATAT
29741528 AACTTATTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:29746581 original size:46 final size:45
Alignment explanation
Indices: 29746474--29746751 Score: 292
Period size: 46 Copynumber: 6.6 Consensus size: 45
29746464 TACGTATGAT
29746474 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAGTGTAGCTAGGCTAC
* *
29746517 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGTTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
*
29746563 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
*
29746609 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TA----A-
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29746645 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TA-G----
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAGGCTAC
* *
29746681 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
* *
29746727 CACTTATCACTTTATCTCTTGATCA
1 CACTTATCACTTTCTCACTTGATCA
29746752 AAAGTACTCA
Statistics
Matches: 211, Mismatches: 9, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
36 64 0.30
37 1 0.00
38 3 0.01
40 1 0.00
41 2 0.01
42 3 0.01
43 13 0.06
44 4 0.02
45 19 0.09
46 101 0.48
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (45 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:29746647 original size:36 final size:36
Alignment explanation
Indices: 29746606--29746712 Score: 196
Period size: 36 Copynumber: 3.0 Consensus size: 36
29746596 TAGCTAAGGC
*
29746606 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
29746642 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
*
29746678 TAGCACTTATCACTTTTTCACTTGATCAGATAAGT
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGT
29746713 GTAGCTAAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (36 bp):
TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
Found at i:29772336 original size:40 final size:38
Alignment explanation
Indices: 29772281--29772375 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 38
29772271 TTATAAGTAT
* *
29772281 AATTACCATAATTATAATAATGTT-TGACCCAAAAAATTAC
1 AATTACAATAATTATAATAATATTCT-A-CC-AAAAATTAC
* * *
29772321 AATTACAATAATTATAATAATATTCTATCGAAAATTAT
1 AATTACAATAATTATAATAATATTCTACCAAAAATTAC
29772359 AATTACAATAATTATAA
1 AATTACAATAATTATAA
29772376 CAAGGATTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 24 0.49
39 1 0.02
40 23 0.47
41 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.36
Consensus pattern (38 bp):
AATTACAATAATTATAATAATATTCTACCAAAAATTAC
Found at i:29772364 original size:38 final size:40
Alignment explanation
Indices: 29772278--29772375 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
29772268 ATATTATAAG
* *
29772278 TATAATTACCATAATTATAATAATGTTTGACCCAAAAAAT
1 TATAATTACAATAATTATAATAATATTTGACCCAAAAAAT
* * *
29772318 TACAATTACAATAATTATAATAATATTCT-A-TC-GAAAAT
1 TATAATTACAATAATTATAATAATATT-TGACCCAAAAAAT
29772356 TATAATTACAATAATTATAA
1 TATAATTACAATAATTATAA
29772376 CAAGGATTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
38 24 0.47
39 1 0.02
40 25 0.49
41 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (40 bp):
TATAATTACAATAATTATAATAATATTTGACCCAAAAAAT
Found at i:29790191 original size:12 final size:12
Alignment explanation
Indices: 29790155--29790228 Score: 60
Period size: 12 Copynumber: 6.0 Consensus size: 12
29790145 GTTCATTTAA
**
29790155 TCATCAAGCCTT
1 TCATCAAGTTTT
29790167 TCATCAAATGTTTT
1 TCATC-AA-GTTTT
29790181 TCATCAAGTTTT
1 TCATCAAGTTTT
* *
29790193 TAAGCAAG-TTT
1 TCATCAAGTTTT
*
29790204 CCATCAAGTTTT
1 TCATCAAGTTTT
*
29790216 TAATCAAGATTTT
1 TCATCAAG-TTTT
29790229 ATCTTTTGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
11 8 0.16
12 25 0.51
13 8 0.16
14 8 0.16
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (12 bp):
TCATCAAGTTTT
Found at i:29797547 original size:22 final size:22
Alignment explanation
Indices: 29797521--29797565 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29797511 ATTAAATTAT
*
29797521 ATTTAATAATAATCTAATTAAA
1 ATTTAACAATAATCTAATTAAA
* *
29797543 ATTTAACAATCATCTACTTAAA
1 ATTTAACAATAATCTAATTAAA
29797565 A
1 A
29797566 AATTCTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAACAATAATCTAATTAAA
Found at i:29797720 original size:27 final size:27
Alignment explanation
Indices: 29797697--29797760 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
29797687 TTGATTACAA
29797697 CTCTATTTCATTACATCTCTATTATAG
1 CTCTATTTCATTACATCTCTATTATAG
*
29797724 CTCTA-TTCTATTACATCTCTAGTATAG
1 CTCTATTTC-ATTACATCTCTATTATAG
29797751 CTCTATTTCA
1 CTCTATTTCA
29797761 ATGAACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.09
27 28 0.82
28 3 0.09
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (27 bp):
CTCTATTTCATTACATCTCTATTATAG
Found at i:29804752 original size:11 final size:11
Alignment explanation
Indices: 29804719--29804746 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29804709 TAAGAGAAAT
29804719 TTGAGAGCAAA
1 TTGAGAGCAAA
29804730 TTGAGAGCAAA
1 TTGAGAGCAAA
29804741 TTGAGA
1 TTGAGA
29804747 TTAAATAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (11 bp):
TTGAGAGCAAA
Found at i:29804760 original size:51 final size:51
Alignment explanation
Indices: 29804698--29804797 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
29804688 AATAATTAAA
*
29804698 AAATAGGGATTTAAGAGAAATTT-GAGAGCAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGGAAAG-AAATTGAGAGCAAATTGAGATT
* *
29804749 AAATAGGGATTTGAGAGAAATTTGGAAAGAAATTGAGAGGAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTGGAAAGAAATTGAGAGCAAATTGAGA
29804798 GAATAATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTGGAAAGAAATTGAGAGCAAATTGAGATT
Found at i:29809547 original size:20 final size:20
Alignment explanation
Indices: 29809522--29809560 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29809512 CTCAATTTAG
29809522 GATAATTA-ATTATTTAATTA
1 GATAATTAGA-TATTTAATTA
29809542 GATAATTAGATATTTAATT
1 GATAATTAGATATTTAATT
29809561 GATCATAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
GATAATTAGATATTTAATTA
Found at i:29810305 original size:31 final size:32
Alignment explanation
Indices: 29810246--29810310 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
29810236 GGCAAATTAC
29810246 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
29810278 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
29810309 AA
1 AA
29810311 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:29813829 original size:106 final size:106
Alignment explanation
Indices: 29813424--29813842 Score: 603
Period size: 107 Copynumber: 4.0 Consensus size: 106
29813414 AGGAATGTTT
* *
29813424 TTCT-AAATAAGGCAATATTTTGCATTTGGAAAATCGAGGAAACGTACCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
29813488 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
* * * *
29813529 TT-TCAAAGTGAGGCAATATTT-GCGTTTGGAAAATTGAGAAAACGTGCCCTAACGTGTTGGGTT
1 TTCTCAAA-TAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTT
* *
29813592 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTCTTAAAC
65 TCGACTTCTCGTTCGACCAAATAGCCAAATATCCTT-TTAAAA
* *
29813635 TTTTAAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
*
29813700 CGACTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-AAAA
* * * * *
29813742 TTCTCAAATAAGGCAATGTTTCGCGTTTGGAAATTCGAGG-AACGTGCCCTAATGTGCTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
* ** *
29813806 CGATTTCTCGTTTAACTAAATAGCCAAATATCCTTTT
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
29813843 GAATTTCAAT
Statistics
Matches: 281, Mismatches: 27, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
104 1 0.00
105 78 0.28
106 87 0.31
107 115 0.41
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (106 bp):
TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
Found at i:29825543 original size:44 final size:44
Alignment explanation
Indices: 29825446--29825980 Score: 173
Period size: 44 Copynumber: 12.2 Consensus size: 44
29825436 AAGAATTTCA
* ***
29825446 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* * * * *
29825490 AATCCTATCTCCTTGAGATTACAGTGGAGCGGATTAAAAAAAAG-
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAAAAAGT
* * * *** **
29825534 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGCATCAG-
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAAAAAGT
* * *** * **
29825576 G-TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* * * *** *
29825619 CAGATCTTATCTCCTTGAGGTTACAGTGGAGCAGATTAAAGCCAGA
1 --GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
** * * *
29825665 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* * * *
29825709 -ATCCTATCTCCCT-AAAGTTACAGTGGAGCGGATTAAAATAAAG-
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAA-AAAGT
* * ** * *** **
29825752 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGA-TCGCATCAG-
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAAAAAGT
* * * ** * **
29825794 G-TCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* * * * * *** *
29825837 CAGATCTTATCTCCCTAAGGTTACAGTGGAACAGATTGAAGCCAGA
1 --GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* ** * * *
29825883 GATCTTATCTCCTTGAGATTACAGCGGAGCAGATCGAAGACACT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
* * *
29825927 -ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAG-
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAA-AAAGT
29825970 GATCTTATCTC
1 GATCTTATCTC
29825981 TCAAAAGTTA
Statistics
Matches: 356, Mismatches: 115, Indels: 40
0.70 0.23 0.08
Matches are distributed among these distances:
41 51 0.14
42 12 0.03
43 61 0.17
44 164 0.46
45 6 0.02
46 62 0.17
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAAAAGT
Found at i:29825687 original size:131 final size:129
Alignment explanation
Indices: 29825443--29826373 Score: 481
Period size: 131 Copynumber: 7.1 Consensus size: 129
29825433 CCGAAGAATT
* * * * *
29825443 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CT-AGTAATCCTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATCAG--ATCTTATCTCCTTGA
* * * * * ** *
29825506 GATTACAGTGGAGCGGATTAAA-AAAAAGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATC
64 GGTTACAGTGGAGCAGATTAAAGACAGA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATC
*
29825569 GCA
127 GAA
* *
29825572 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCTTGA
* *
29825637 GGTTACAGTGGAGCAGATTAAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGA
64 GGTTACAGTGGAGCAGATTAAAGACAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGA
29825702 A
129 A
* ** * * * * *
29825703 GACACTATCCTATCTCCCT-AAAGTTACAGTGGAGCGGAT-TAA-AATAAAGGATCTTATCT-CT
1 -TCA-GGTCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAAT-CA-GATCTTATCTCCT
* * * * *** * * *
29825764 CTAAAGTTACAGTAGAGTAGATCGCA-TCAG-G-TCTTATCTCTCTGAGGTTACAGTGGAGCAGA
61 -TGAGGTTACAGTGGAGCAGATTAAAGACAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGA
*
29825826 CCAAAGAA
125 TC---GAA
* * * * * * *
29825834 TTTCAGATCTTATCTCCCTAAGGTTACAGTGGAACAGATTGAAGCCA-GAGATCTTATCTCCTTG
1 --TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-AATCAGATCTTATCTCCTTG
* * ** ** * *
29825898 AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT
63 AGGTTACAGTGGAGCAGATTAAAGACAGAGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGA-T
**
29825961 AAAA
126 CGAA
* * * * * * * *
29825965 TAAAGGATCTTATCTCTC-AAAAGTTACAGTAGAGTAGATC--A-CATCAGGTCTTATCT-CTCT
1 T-CAGG-TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCT-T
* ** * * *
29826025 GAGGTTATAGTGGAGCAGACCAAAGA-ATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAACAG
62 GAGGTTACAGTGGAGCAGATTAAAGACA---GAGATCTTATCTCCCTGAGATTACAGTGGAGCAG
*
29826089 ATTGAA
124 ATCGAA
* * ** * * *
29826095 GCCAGAGATTTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAG-A-CACTATCCTATCTCCCT
1 -TCAG-G-TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATCA-GATCTTATCTCCTT
* * * * * * *
29826158 GAAGTTACAATGGAG-AGGATTAAA-ATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAG
62 GAGGTTACAGTGGAGCA-GATTAAAGACAGA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAG
*
29826220 ATCGCA
124 ATCGAA
* * * * * *
29826226 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGA
1 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAA--TCAGATCTTATCTCCTTGA
* * * * * * *
29826291 GGTTACAGTAGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTATAGTAGAACAGATCGC
64 GGTTACAGTGGAGCAGATTAAAGACAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGA
29826356 A
129 A
*
29826357 TCAAGTCTTATCTCCCT
1 TCAGGTCTTATCTCCCT
29826374 AAGTAGTAGT
Statistics
Matches: 609, Mismatches: 138, Indels: 108
0.71 0.16 0.13
Matches are distributed among these distances:
127 5 0.01
128 90 0.15
129 43 0.07
130 19 0.03
131 338 0.56
132 32 0.05
133 80 0.13
134 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATCAGATCTTATCTCCTTGAGG
TTACAGTGGAGCAGATTAAAGACAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAA
Found at i:29825756 original size:87 final size:88
Alignment explanation
Indices: 29825577--29826211 Score: 241
Period size: 87 Copynumber: 7.2 Consensus size: 88
29825567 TCGCATCAGG
* * * * * *
29825577 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAGAA--TCAGATCCTATCTCCCTAAAGTTA
**
29825642 CAGTGGAGCAGATTAAAGCCAGAGA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* *
29825667 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCTAAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAGAATCA-GATCCTATCTCCCTAAAGTTAC
* *
29825730 AGTGGAGCGGATTAAAATAAAG-GA
65 AGTGGAGCAGATT-AAAGAAAGAGA
* * ** * * * * * * * *
29825754 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATC---GCATCAGGTCTTATCTCTCTGAGGTTAC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGACCGAAGAATCAGATCCTATCTCCCTAAAGTTAC
** **
29825815 AGTGGAGCAGACCAAAGAATTTCAGA
65 AGTGGAGCAGATTAAAGAA--AGAGA
* * * * ** * * * **
29825841 TCTTATCTCCCTAAGGTTACAGTGGAACAGATTGAAGCCA-GAGATCTTATCT-CCTTGAGATTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAG-AATCAGATCCTATCTCCCTAAAG-TTA
* ** * **
29825904 CAGCGGAGCAGATCGAAGACA-CTA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* * * ** * * * *
29825928 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AATAAAGGATCTTATCTCTCAAAAGTT
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGACCGAAGAAT-CA-GATCCTATCTCCCTAAAGTT
* * * * **
29825990 ACAGTAGAGTAGATCACA-TCAG-G-
63 ACAGTGGAGCAGATTAAAGAAAGAGA
* * * * * * * *
29826013 TCTTATCTCTCTGAGGTTATAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAGAA--TCAGATCCTATCTCCCTAAAGTTA
* * **
29826078 CAGTGGAACAGATTGAAGCCAGAGA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* * * * *
29826103 TTTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAGAATCA-GATCCTATCTCCCTAAAGTTAC
* *
29826166 AATGGAG-AGGATTAAAATAAAG-GA
65 AGTGGAGCA-GATT-AAAGAAAGAGA
*
29826190 TCTTATCTCTCTGA-AGTTACAG
1 TCTTATCTCCCTGAGA-TTACAG
29826212 TAGAGTAGAT
Statistics
Matches: 407, Mismatches: 106, Indels: 67
0.70 0.18 0.12
Matches are distributed among these distances:
84 7 0.02
85 52 0.13
86 18 0.04
87 211 0.52
88 17 0.04
89 7 0.02
90 93 0.23
91 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGACCGAAGAATCAGATCCTATCTCCCTAAAGTTACA
GTGGAGCAGATTAAAGAAAGAGA
Found at i:29826242 original size:41 final size:42
Alignment explanation
Indices: 29825536--29826377 Score: 290
Period size: 44 Copynumber: 19.4 Consensus size: 42
29825526 AAAAAAAGGA
* * * *
29825536 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAGG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAGG
* * * *
29825577 TCTTATCTCCCTG-AGATTACAGTGGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAAG-TTACAGTAGAGCAGATC---GAA-TTCAGG
* * * ** **
29825623 TCTTATCTCCTTGAGGTTACAGTGGAGCAGATTAAAGCCAGAG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAG-G
** ** **
29825666 ATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACACTA
1 -TCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAATTCA-GG
* * * * ** **
29825710 TCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGA-TCGAATTCAGG
* * * *
29825753 ATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCA-TCAGG
1 -TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAGG
* * * * *
29825795 TCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATC---GAA-TTCAGG
* * * **
29825841 TCTTATCTCCCT-AAGGTTACAGTGGAACAGATTGAAGCCAGAG
1 TCTTATCTCCCTGAA-GTTACAGTAGAGCAGATCGAATTCAG-G
* ** ** **
29825884 ATCTTATCTCCTTG-AGATTACAGCGGAGCAGATCGAAGACACTA
1 -TCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAATTCA-GG
* * * ** **
29825928 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGA-TCGAATTCAGG
* ** *
29825971 ATCTTATCTCTCAAAAGTTACAGTAGAGTAGATC-ACA-TCAGG
1 -TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGA-ATTCAGG
* * * * * *
29826013 TCTTATCTCTCTGAGGTTATAGTGGAGCAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATC---GAA-TTCAGG
* * * * **
29826059 TCTTATCTCCCTGAGGTTACAGTGGAACAGATTGAAGCCAGAG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAG-G
* * ** **
29826102 ATTTTATCTCCCTG-AGATTACAGCAGAGCAGATCGAAGACACTA
1 -TCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAATTCA-GG
* * * ** **
29826146 TCCTATCTCCCTGAAGTTACAATGGAG-AGGATTAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCA-GA-TCGAATTCAGG
* * *
29826189 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAGG
1 -TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAGG
* * * * * *
29826231 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAAAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCG---AA-TTCAGG
* * **
29826277 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTGAAGCCAGAG
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAG-G
* * * *
29826320 ATCTTATCTCCCTG-AGATTATAGTAGAACAGATCGCA-TCAAG
1 -TCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAATTCAGG
29826362 TCTTATCTCCCT-AAGT
1 TCTTATCTCCCTGAAGT
29826378 AGTAGTGGAG
Statistics
Matches: 598, Mismatches: 150, Indels: 107
0.70 0.18 0.13
Matches are distributed among these distances:
40 3 0.01
41 125 0.21
42 24 0.04
43 91 0.15
44 226 0.38
45 3 0.01
46 125 0.21
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAATTCAGG
Found at i:29826354 original size:218 final size:218
Alignment explanation
Indices: 29825445--29826339 Score: 1490
Period size: 218 Copynumber: 4.1 Consensus size: 218
29825435 GAAGAATTTC
* * *
29825445 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTAATCCTATCTCCTTG-AGA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAC-ACT-ATCCTATCTCCCTGAAG-
* * *
29825508 TTACAGTGGAGCGGATTAAAAAAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
63 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCAT
* * * * *
29825573 CAGGTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAG
128 CAGGTCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
* *
29825638 GTTACAGTGGAGCAGATTAAAGCCAG
193 GTTACAGTGGAACAGATTGAAGCCAG
*
29825664 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTAAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
29825729 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
*
29825794 GTCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTAAGGTT
131 GTCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTT
29825859 ACAGTGGAACAGATTGAAGCCAG
196 ACAGTGGAACAGATTGAAGCCAG
*
29825882 AGATCTTATCTCCTTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* *
29825947 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCAAAAGTTACAGTAGAGTAGATCACATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
*
29826012 GTCTTATCTCTCTGAGGTTATAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTT
131 GTCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTT
29826077 ACAGTGGAACAGATTGAAGCCAG
196 ACAGTGGAACAGATTGAAGCCAG
* *
29826100 AGATTTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* * *
29826165 CAATGGAGAGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
*
29826230 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAA-AATTTCAGATCTTATCTCCCTGAGGT
131 GTCTTATCTCTCTGAGGTTACAGTGGAGCAGACC-AAAGAATTTCAGATCTTATCTCCCTGAGGT
* *
29826294 TACAGTAGAGCAGATTGAAGCCAG
195 TACAGTGGAACAGATTGAAGCCAG
29826318 AGATCTTATCTCCCTGAGATTA
1 AGATCTTATCTCCCTGAGATTA
29826340 TAGTAGAACA
Statistics
Matches: 639, Mismatches: 34, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
218 592 0.93
219 46 0.07
220 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (218 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCTCTGAGGTTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTT
ACAGTGGAACAGATTGAAGCCAG
Found at i:29826406 original size:44 final size:43
Alignment explanation
Indices: 29826354--29826524 Score: 138
Period size: 44 Copynumber: 4.0 Consensus size: 43
29826344 AGAACAGATC
*
29826354 GCATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACAGAA
1 GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAA
* * * ***
29826397 GAAATCAAGTCCTATCTTCCC-AAGCAGTAGTGGAGTAGGTTGAA
1 G-CATCAAGTCTTATC-TCCCTAAGCAGTAGTGGAGCAGACAGAA
* * * **
29826441 CCTTGC-AGATTTTATCTCCCTAAGCAGTAACGGAGCAGATC----
1 GCAT-CAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAA
*
29826482 GCATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACAGAA
1 GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAA
29826525 CCAATCCTAT
Statistics
Matches: 94, Mismatches: 23, Indels: 22
0.68 0.17 0.16
Matches are distributed among these distances:
39 1 0.01
40 27 0.29
41 4 0.04
43 8 0.09
44 50 0.53
45 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAA
Found at i:29829018 original size:106 final size:106
Alignment explanation
Indices: 29828607--29829025 Score: 576
Period size: 107 Copynumber: 4.0 Consensus size: 106
29828597 AGGAATGTTT
*
29828607 TTCT-AAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTACCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
29828671 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
** * * * *
29828712 TT-TCAAAGCGAGGCAATATTT-GCGTTTGGAAAATTGAGAAAACGTGCCTTAACGTGTTGGGTT
1 TTCTCAAA-TAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTT
* *
29828775 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
65 TCGACTTCTCGTTCGACCAAATAGCCAAATATCC-TTTTAAAA
* * *
29828818 TTTTAAAATATGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
* *
29828883 TGACTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAA
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-AAAA
* * * * *
29828925 TTCTCAAATAAGGCAATGTTTCGCGTTTGGAAATTCGAGG-AACGTGCCCTAATGTGCTGGGTTT
1 TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
* ** *
29828989 CGATTTCTCGTTTAACTAAATAGCCAAATATCCTTTT
66 CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
29829026 GAATTTCAAT
Statistics
Matches: 273, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
104 1 0.00
105 75 0.27
106 87 0.32
107 110 0.40
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (106 bp):
TTCTCAAATAAGGCAATATTTCGCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
CGACTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
Found at i:29834302 original size:31 final size:32
Alignment explanation
Indices: 29834243--29834307 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
29834233 GGTAAATTAC
29834243 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
29834275 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
29834306 AA
1 AA
29834308 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:29839605 original size:8 final size:8
Alignment explanation
Indices: 29839586--29839692 Score: 56
Period size: 8 Copynumber: 11.8 Consensus size: 8
29839576 AAAAGAAGTT
29839586 TTAATA-A
1 TTAATACA
29839593 TTAATACA
1 TTAATACA
29839601 TTAATATAACA
1 TT-A-AT-ACA
29839612 TGATATATAACA
1 T--TA-ATA-CA
29839624 TTAATACA
1 TTAATACA
29839632 TTAATATAACA
1 TT-A-AT-ACA
29839643 TTAATACA
1 TTAATACA
*
29839651 TTAATATAAA
1 TT-A-ATACA
29839661 GTTTTAATA-A
1 ---TTAATACA
29839671 TTAATACA
1 TTAATACA
29839679 TTAATACA
1 TTAATACA
29839687 TTAATA
1 TTAATA
29839693 TAACATTAAT
Statistics
Matches: 83, Mismatches: 1, Indels: 31
0.72 0.01 0.27
Matches are distributed among these distances:
7 12 0.14
8 27 0.33
9 8 0.10
10 12 0.14
11 13 0.16
12 8 0.10
13 3 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (8 bp):
TTAATACA
Found at i:29839640 original size:19 final size:19
Alignment explanation
Indices: 29839616--29839705 Score: 118
Period size: 19 Copynumber: 4.8 Consensus size: 19
29839606 ATAACATGAT
29839616 ATATAACATTAATACATTA
1 ATATAACATTAATACATTA
29839635 ATATAACATTAATACATTA
1 ATATAACATTAATACATTA
29839654 ATATAA-AGTTTTAATA-ATT-
1 ATATAACA---TTAATACATTA
29839673 A-AT-ACATTAATACATTA
1 ATATAACATTAATACATTA
29839690 ATATAACATTAATACA
1 ATATAACATTAATACA
29839706 AGCTTACAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.10
16 3 0.05
17 2 0.03
18 6 0.10
19 37 0.59
20 3 0.05
21 6 0.10
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (19 bp):
ATATAACATTAATACATTA
Found at i:29839686 original size:36 final size:36
Alignment explanation
Indices: 29839581--29839695 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
29839571 TAATTAAAAG
*
29839581 AAGTTTTAATAATTAATACATTAATATAACATGATATATA
1 AAGTTTTAATAATTAATACATT-A-AT-ACATTA-ATATA
29839621 ACA---TTAATACATTAATATAACATTAATACATTAATATA
1 A-AGTTTTAATA-ATT-A-AT-ACATTAATACATTAATATA
29839659 AAGTTTTAATAATTAATACATTAATACATTAATATA
1 AAGTTTTAATAATTAATACATTAATACATTAATATA
29839695 A
1 A
29839696 CATTAATACA
Statistics
Matches: 66, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
36 20 0.30
37 3 0.05
38 13 0.20
39 11 0.17
40 10 0.15
41 4 0.06
42 5 0.08
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (36 bp):
AAGTTTTAATAATTAATACATTAATACATTAATATA
Found at i:29844042 original size:57 final size:58
Alignment explanation
Indices: 29843981--29844137 Score: 205
Period size: 57 Copynumber: 2.8 Consensus size: 58
29843971 ACATTAACCC
* * * **
29843981 ATAAGATTATACCAATTACA-ATTAAATCATTTCAATGACATATCCCA-TTATCAATTT
1 ATAAGGTTATACCAATTACACA-TAATTCATTTCAATGACATATCCAAGTTATCAATCG
* * *
29844038 ATAAGGTTATACTATTTACACATAATTCATTTCAATTACATAT-CAAGTTATCAATCG
1 ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATCCAAGTTATCAATCG
29844095 ATAAGGTTATACCAATTACACATAATTCATTTCAATG-CATATC
1 ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATC
29844138 AAATTATTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 7 0.08
57 78 0.91
58 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (58 bp):
ATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATCCAAGTTATCAATCG
Found at i:29856922 original size:45 final size:45
Alignment explanation
Indices: 29856858--29856951 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
29856848 AACAGATATT
* *
29856858 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
29856903 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
29856948 CGGT
1 CGGT
29856952 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:29857131 original size:101 final size:101
Alignment explanation
Indices: 29856955--29857139 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 101
29856945 GTTCGGTTCA
* * * * * *
29856955 CATAGTAGCCTGCATATAGTACTACGCATGTGACTATTACCATCCAATACACGTAGTAGCCTGCG
1 CATAGTAGCCTGCACATAGTACTACACATGCGACTATTA-CATCCAATACACATACTAGCCTGCA
29857020 CATAGTACTACACACGTGATCGAAACTATCTGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTATG
**
29857057 CATAGTAGCCTGCACATAGTACTACACATGCGACCT-TT-CATTCCGGTACACATACTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGA-CTATTACA-TCCAATACACATACTAGCCTGC
29857120 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
29857140 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.03
101 37 0.51
102 32 0.44
103 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACTATTACATCCAATACACATACTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGGTATG
Found at i:29857162 original size:101 final size:101
Alignment explanation
Indices: 29856954--29857175 Score: 225
Period size: 101 Copynumber: 2.2 Consensus size: 101
29856944 TGTTCGGTTC
* * * * *
29856954 ACATAGTAGCCTGCATATAGTACTACGCATGTGACTATTACCATCCAATACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACTATTA-CATCCAATACACATACTAGCCTGC
* * **
29857019 GCATAGTACTACACACGTGATCGAAACTATCTGGTAT
65 ACATAGTACTACACACGTGATCCAAACTATCACGTAT
* **
29857056 GCATAGTAGCCTGCACATAGTACTACACATGCGACCT-TT-CATTCCGGTACACATACTAGCCTG
1 ACATAGTAGCCTGCACATAGTACTACACATGCGA-CTATTACA-TCCAATACACATACTAGCCTG
* * * *
29857119 CACATAGTACTACACACGTGA-CCATCACTTTCACTTTT
64 CACATAGTACTACACACGTGATCCA-AACTATCACGTAT
* *
29857157 ACATAGTGGCCTACACATA
1 ACATAGTAGCCTGCACATA
29857176 ATCCATGCCA
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
100 4 0.04
101 60 0.61
102 32 0.33
103 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (101 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACTATTACATCCAATACACATACTAGCCTGCA
CATAGTACTACACACGTGATCCAAACTATCACGTAT
Found at i:29858783 original size:18 final size:18
Alignment explanation
Indices: 29858762--29858798 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29858752 TAAATATCAA
29858762 ATGGAATAATAGTATCTG
1 ATGGAATAATAGTATCTG
29858780 ATGGAATAATAGTATCTG
1 ATGGAATAATAGTATCTG
29858798 A
1 A
29858799 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
ATGGAATAATAGTATCTG
Found at i:29859161 original size:25 final size:25
Alignment explanation
Indices: 29859118--29859169 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
29859108 TGTTTATAAA
29859118 AATATATAAATAATAATTA-ACATAG
1 AATATATAAATAATAATTAGA-ATAG
*
29859143 AATATAT-ACTAATATATTAGAATAG
1 AATATATAAATAATA-ATTAGAATAG
29859168 AA
1 AA
29859170 AAAGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 17 0.71
26 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
AATATATAAATAATAATTAGAATAG
Found at i:29860328 original size:8 final size:8
Alignment explanation
Indices: 29860315--29860340 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29860305 AGGCTAGGTG
29860315 TTGGGCCA
1 TTGGGCCA
29860323 TTGGGCCA
1 TTGGGCCA
29860331 TTGGGCCA
1 TTGGGCCA
29860339 TT
1 TT
29860341 AGGTTTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.31
Consensus pattern (8 bp):
TTGGGCCA
Found at i:29862938 original size:16 final size:15
Alignment explanation
Indices: 29862911--29862940 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29862901 AAATTCACAT
29862911 TTATACTATATATAA
1 TTATACTATATATAA
29862926 TTATACATATATATA
1 TTATAC-TATATATA
29862941 TATATATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATACTATATATAA
Found at i:29866152 original size:54 final size:55
Alignment explanation
Indices: 29866032--29866152 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 55
29866022 GAGTTGGGCA
* * *
29866032 ACACGGCCGTGTCGCAGGCCATGTACGAGACCGTGTAACTCTCTAACTTATGACAC
1 ACACGGTCGTGTCGCAGGCCATGTACGAGACCGTGTAACACACTAACTTA-GACAC
* * * * * *
29866088 ACA-GCT-GTGTCGCAGGTCGTGTGCTAGGCCGTGTAACACACTAACTTA-ACAC
1 ACACGGTCGTGTCGCAGGCCATGTACGAGACCGTGTAACACACTAACTTAGACAC
29866140 ACACGGTCGTGTC
1 ACACGGTCGTGTC
29866153 TCAAACCGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
52 7 0.13
53 2 0.04
54 40 0.75
55 1 0.02
56 3 0.06
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (55 bp):
ACACGGTCGTGTCGCAGGCCATGTACGAGACCGTGTAACACACTAACTTAGACAC
Found at i:29868009 original size:27 final size:26
Alignment explanation
Indices: 29867972--29868026 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
29867962 TAGGTTAATT
*
29867972 TTAAAATAAATAATATATAAAATAAC
1 TTAAAATAAATAACATATAAAATAAC
*
29867998 TTAAAATAAAATGACATATAAAATAAC
1 TTAAAAT-AAATAACATATAAAATAAC
29868025 TT
1 TT
29868027 GAAACAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAACATATAAAATAAC
Found at i:29876822 original size:463 final size:463
Alignment explanation
Indices: 29876191--29877118 Score: 1829
Period size: 463 Copynumber: 2.0 Consensus size: 463
29876181 GCCTAAAAAT
*
29876191 TTATAAAAATTATGAAATTACCCCACTGGTAATTTTTGTGAAATTTATTTTGATTCAAAGCGAGC
1 TTATAAAAATTATGAAATTACCCCACTAGTAATTTTTGTGAAATTTATTTTGATTCAAAGCGAGC
*
29876256 CCACACTCGGAAGATGTGAGCTTAAGGATTGCGGAGAAGACTACTCAGTTGAAGCGTTCATCTTA
66 CCACACTCAGAAGATGTGAGCTTAAGGATTGCGGAGAAGACTACTCAGTTGAAGCGTTCATCTTA
29876321 GACGAATCGAAAAGGTACAATTTTGATTAAATGTTTCTTACTTTAGATATCACAATCAAGTTCTT
131 GACGAATCGAAAAGGTACAATTTTGATTAAATGTTTCTTACTTTAGATATCACAATCAAGTTCTT
29876386 GTTTTAGAAAAAAATTAAAACTCTAGTTTTTCCCTAAATTTATTTTCTGCTGCCTTTTCCAAACC
196 GTTTTAGAAAAAAATTAAAACTCTAGTTTTTCCCTAAATTTATTTTCTGCTGCCTTTTCCAAACC
29876451 CGATTTTCCAACAAAAATTCTCTCAACAAAAACTTTCCATTTTGATAGACTCCCCTTCAAGAATA
261 CGATTTTCCAACAAAAATTCTCTCAACAAAAACTTTCCATTTTGATAGACTCCCCTTCAAGAATA
*
29876516 ACTTCCAACATCATCAAGCATCGTTTCTTTTCTTCCCCTTTTTGGTCAAAAAATGCCAAATTATT
326 ACTTCCAACATCATCAAGCATCGTTTCTTTTCTTCCCCTTTTTGGTCAAAAAATGCCAAACTATT
29876581 CTTCATCAAGCAAGGCATGAAGATAATGCATTCAAGCCTTCTATTTATCAACTAACTTCCTCACA
391 CTTCATCAAGCAAGGCATGAAGATAATGCATTCAAGCCTTCTATTTATCAACTAACTTCCTCACA
29876646 ACTTTGGC
456 ACTTTGGC
29876654 TTATAAAAATTATGAAATTACCCCACTAGTAATTTTTGTGAAATTTATTTTGATTCAAAGCGAGC
1 TTATAAAAATTATGAAATTACCCCACTAGTAATTTTTGTGAAATTTATTTTGATTCAAAGCGAGC
29876719 CCACACTCAGAAGATGTGAGCTTAAGGATTGCGGAGAAGACTACTCAGTTGAAGCGTTCATCTTA
66 CCACACTCAGAAGATGTGAGCTTAAGGATTGCGGAGAAGACTACTCAGTTGAAGCGTTCATCTTA
29876784 GACGAATCGAAAAGGTACAATTTTGATTAAATGTTTCTTACTTTAGATATCACAATCAAGTTCTT
131 GACGAATCGAAAAGGTACAATTTTGATTAAATGTTTCTTACTTTAGATATCACAATCAAGTTCTT
29876849 GTTTTAGAAAAAAATTAAAACTCTAGTTTTTCCCTAAATTTATTTTCTGCTGCCTTTTCCAAACC
196 GTTTTAGAAAAAAATTAAAACTCTAGTTTTTCCCTAAATTTATTTTCTGCTGCCTTTTCCAAACC
29876914 CGATTTTCCAACAAAAATTCTCTCAACAAAAACTTTCCATTTTGATAGACTCCCCTTCAAGAATA
261 CGATTTTCCAACAAAAATTCTCTCAACAAAAACTTTCCATTTTGATAGACTCCCCTTCAAGAATA
29876979 ACTTCCAACATCATCAAGCATCGTTTCTTTTCTTCCCCTTTTTGGTCAAAAAATGCCAAACTATT
326 ACTTCCAACATCATCAAGCATCGTTTCTTTTCTTCCCCTTTTTGGTCAAAAAATGCCAAACTATT
29877044 CTTCATCAAGCAAGGCATGAAGATAATGCATTCAAGCCTTCTATTTATCAACTAACTTCCTCACA
391 CTTCATCAAGCAAGGCATGAAGATAATGCATTCAAGCCTTCTATTTATCAACTAACTTCCTCACA
29877109 ACTTTGGC
456 ACTTTGGC
29877117 TT
1 TT
29877119 CAACTTGCAG
Statistics
Matches: 462, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
463 462 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (463 bp):
TTATAAAAATTATGAAATTACCCCACTAGTAATTTTTGTGAAATTTATTTTGATTCAAAGCGAGC
CCACACTCAGAAGATGTGAGCTTAAGGATTGCGGAGAAGACTACTCAGTTGAAGCGTTCATCTTA
GACGAATCGAAAAGGTACAATTTTGATTAAATGTTTCTTACTTTAGATATCACAATCAAGTTCTT
GTTTTAGAAAAAAATTAAAACTCTAGTTTTTCCCTAAATTTATTTTCTGCTGCCTTTTCCAAACC
CGATTTTCCAACAAAAATTCTCTCAACAAAAACTTTCCATTTTGATAGACTCCCCTTCAAGAATA
ACTTCCAACATCATCAAGCATCGTTTCTTTTCTTCCCCTTTTTGGTCAAAAAATGCCAAACTATT
CTTCATCAAGCAAGGCATGAAGATAATGCATTCAAGCCTTCTATTTATCAACTAACTTCCTCACA
ACTTTGGC
Found at i:29881221 original size:16 final size:17
Alignment explanation
Indices: 29881194--29881241 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
29881184 GTCTAAAATT
*
29881194 ATATGTATTAATTTATA
1 ATATATATTAATTTATA
29881211 ATATA-ATTAATTT-TA
1 ATATATATTAATTTATA
*
29881226 ATTTATATTCAATTTA
1 ATATATATT-AATTTA
29881242 ATTTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 11 0.42
17 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATATATATTAATTTATA
Found at i:29881310 original size:14 final size:14
Alignment explanation
Indices: 29881291--29881317 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29881281 GTGGTCTAGT
29881291 TGAACTGAACCGAG
1 TGAACTGAACCGAG
29881305 TGAACTGAACCGA
1 TGAACTGAACCGA
29881318 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:29885380 original size:9 final size:9
Alignment explanation
Indices: 29885359--29885407 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
29885349 TTAATAAATG
29885359 TTTTATATAT
1 TTTTATAT-T
29885369 TTTTATATT
1 TTTTATATT
*
29885378 TTTTGTATT
1 TTTTATATT
*
29885387 TTTTATA-A
1 TTTTATATT
*
29885395 TTTTATAAT
1 TTTTATATT
29885404 TTTT
1 TTTT
29885408 GCAAGTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.21
9 19 0.56
10 8 0.24
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTATATT
Found at i:29885393 original size:26 final size:26
Alignment explanation
Indices: 29885359--29885408 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29885349 TTAATAAATG
* *
29885359 TTTTATATATTTTTATATTTTTTGTA
1 TTTTATATAATTTTATAATTTTTGTA
*
29885385 TTTTTTATAATTTTATAATTTTTG
1 TTTTATATAATTTTATAATTTTTG
29885409 CAAGTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTATATAATTTTATAATTTTTGTA
Done.