Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 60 of 172
Found at i:19552745 original size:18 final size:18
Alignment explanation
Indices: 19552722--19552777 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
19552712 TAGCCCATTT
19552722 CAGTAACAGTAATTAGTG
1 CAGTAACAGTAATTAGTG
* * * *
19552740 CAGTAACCA-TGATCAATA
1 CAGTAA-CAGTAATTAGTG
*
19552758 CAGTAACAGTAATTGGTG
1 CAGTAACAGTAATTAGTG
19552776 CA
1 CA
19552778 ATATGCAACC
Statistics
Matches: 27, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (18 bp):
CAGTAACAGTAATTAGTG
Found at i:19553088 original size:23 final size:23
Alignment explanation
Indices: 19553039--19553088 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
19553029 ACCCTATGCA
*
19553039 ATGCAACGTAATATCATACATGG
1 ATGCAACATAATATCATACATGG
19553062 ATGCAACATACATAT-A-ACATGG
1 ATGCAACATA-ATATCATACATGG
19553084 CATGC
1 -ATGC
19553089 TCAAATGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (23 bp):
ATGCAACATAATATCATACATGG
Found at i:19553165 original size:27 final size:27
Alignment explanation
Indices: 19553123--19553188 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
19553113 GAACAAATCT
* *
19553123 GTCATTTTAACTTACAAGGGTATTATA
1 GTCATTTTACCCTACAAGGGTATTATA
* *
19553150 GTCATTTTACCCTACAGGGGTATTTTA
1 GTCATTTTACCCTACAAGGGTATTATA
*
19553177 GTCATTCTACCC
1 GTCATTTTACCC
19553189 CATGGGGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGTATTATA
Found at i:19553196 original size:27 final size:27
Alignment explanation
Indices: 19553140--19553215 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
19553130 TAACTTACAA
* *
19553140 GGGTATTATAGTCATTTTACCCTACAG
1 GGGTATTTTAGTCATTTTACCCCACAG
* **
19553167 GGGTATTTTAGTCATTCTACCCCATGG
1 GGGTATTTTAGTCATTTTACCCCACAG
**
19553194 GGGTATTTCGGTCATTTTACCC
1 GGGTATTTTAGTCATTTTACCC
19553216 TATGAGGGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTTAGTCATTTTACCCCACAG
Found at i:19553228 original size:27 final size:27
Alignment explanation
Indices: 19553150--19553237 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
19553140 GGGTATTATA
* **
19553150 GTCATTTTACCCTA-CAGGGGTATTTTA
1 GTCATTTTACCCTATGA-GGGTATTTCG
* * *
19553177 GTCATTCTACCCCATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
19553204 GTCATTTTACCCTATGAGGGAATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
19553231 ATCATTT
1 GTCATTT
19553238 GATCATATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:19553315 original size:27 final size:27
Alignment explanation
Indices: 19553232--19553489 Score: 317
Period size: 27 Copynumber: 9.7 Consensus size: 27
19553222 GGAATTTCGA
* *
19553232 TCATTTGATCATATAA-GGCAAAATCG
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553258 TCATTTTATCACATAA-GGTAAAATTG
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553284 TCATTTTATCATATAAGGGCAAAATCT
1 TCATTTTATCACATAAGGGCAAAATCG
*
19553311 TCATTTTATCACATAAGGGAAAAATCG
1 TCATTTTATCACATAAGGGCAAAATCG
* * *
19553338 TCATTTTATCATATGAGGGCAAAATTG
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553365 TCATTTTATCACATGAGGGTAAAATCG
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553392 TCATTTTATCAC--AAGGACAAAATCA
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553417 TCATTTTATCACATAAGGGCGAAACCG
1 TCATTTTATCACATAAGGGCAAAATCG
* *
19553444 TTATTTTATCACATAAGGGCAAAACCG
1 TCATTTTATCACATAAGGGCAAAATCG
*
19553471 TCATTTTATCACATGAGGG
1 TCATTTTATCACATAAGGG
19553490 TTCAGGTACG
Statistics
Matches: 199, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
25 21 0.11
26 37 0.19
27 141 0.71
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (27 bp):
TCATTTTATCACATAAGGGCAAAATCG
Found at i:19553413 original size:106 final size:106
Alignment explanation
Indices: 19553232--19553490 Score: 351
Period size: 106 Copynumber: 2.4 Consensus size: 106
19553222 GGAATTTCGA
* * * *
19553232 TCATTTGATCATATAAGGCAAAATCGTCATTTTATCACAT-AAGGTAAAATTGTCATTTTATCAT
1 TCATTTTATCATATAGGGCAAAATCGTCATTTTATCACATGAGGGTAAAATCGTCATTTTATCA-
* * * *
19553296 ATAAGGGCAAAATCTTCATTTTATCACATAAGGGAAAAATCG
65 ACAAGGACAAAATCATCATTTTATCACATAAGGGAAAAACCG
*
19553338 TCATTTTATCATATGAGGGCAAAATTGTCATTTTATCACATGAGGGTAAAATCGTCATTTTATC-
1 TCATTTTATCATAT-AGGGCAAAATCGTCATTTTATCACATGAGGGTAAAATCGTCATTTTATCA
**
19553402 ACAAGGACAAAATCATCATTTTATCACATAAGGGCGAAACCG
65 ACAAGGACAAAATCATCATTTTATCACATAAGGGAAAAACCG
* * *
19553444 TTATTTTATCACATAAGGGCAAAACCGTCATTTTATCACATGAGGGT
1 TCATTTTATCATAT-AGGGCAAAATCGTCATTTTATCACATGAGGGT
19553491 TCAGGTACGC
Statistics
Matches: 135, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
106 91 0.67
107 24 0.18
108 20 0.15
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (106 bp):
TCATTTTATCATATAGGGCAAAATCGTCATTTTATCACATGAGGGTAAAATCGTCATTTTATCAA
CAAGGACAAAATCATCATTTTATCACATAAGGGAAAAACCG
Found at i:19556931 original size:43 final size:43
Alignment explanation
Indices: 19556787--19556934 Score: 124
Period size: 43 Copynumber: 3.4 Consensus size: 43
19556777 GTGATTTCAT
* * * *
19556787 GTCTGGGATGTTGGCATCGAT-TTGAGATTTACGTGTAAGACCAT
1 GTCTGGGACGTTGGCATTGATATT-TGA-TTACGTGTAAGACCAC
* * * ** *
19556831 GTCTGGGACATGGGCA-TCATATTTGATTTTGTGTAAAACC-C
1 GTCTGGGACGTTGGCATTGATATTTGATTACGTGTAAGACCAC
* *
19556872 TGTCTGGGA-TTGTGGCATTGATATTTGATTACATGTAAGACCAC
1 -GTCTGGGACGT-TGGCATTGATATTTGATTACGTGTAAGACCAC
19556916 GTCTGGGACGTTGGCATTG
1 GTCTGGGACGTTGGCATTG
19556935 TACGAGCTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 23 0.29
43 39 0.49
44 17 0.21
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.34
Consensus pattern (43 bp):
GTCTGGGACGTTGGCATTGATATTTGATTACGTGTAAGACCAC
Found at i:19565220 original size:8 final size:8
Alignment explanation
Indices: 19565203--19565232 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19565193 GAGGAACAGC
19565203 AAAAGCTG
1 AAAAGCTG
*
19565211 AAAAGTTG
1 AAAAGCTG
19565219 AAAAGCTG
1 AAAAGCTG
19565227 AAAAGC
1 AAAAGC
19565233 CAAAAGCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (8 bp):
AAAAGCTG
Found at i:19574433 original size:189 final size:189
Alignment explanation
Indices: 19574202--19574579 Score: 729
Period size: 189 Copynumber: 2.0 Consensus size: 189
19574192 CTCATTATCG
*
19574202 GAAATTTCTTTGCTTACACGGTTTCTTTTATAAGAAACTAGACTCATTAAGATTTAATTTCATGT
1 GAAATTCCTTTGCTTACACGGTTTCTTTTATAAGAAACTAGACTCATTAAGATTTAATTTCATGT
*
19574267 CTCATTCAGTCTCTAATTCAAATCCATAAATTTATGGTTATTTTCTAAAGTCACGTTACTGCTGC
66 CTCATTCAGCCTCTAATTCAAATCCATAAATTTATGGTTATTTTCTAAAGTCACGTTACTGCTGC
*
19574332 TGTCCTAAGCAGACTATTTCGAATTACCCTTGAATTCCCAAGCTCAAACACTTAAGAAC
131 TGTCCTAAGCAGACTATTTCAAATTACCCTTGAATTCCCAAGCTCAAACACTTAAGAAC
19574391 GAAATTCCTTTGCTTACACGGTTTCTTTTATAAGAAACTAGACTCATTAAGATTTAATTTCATGT
1 GAAATTCCTTTGCTTACACGGTTTCTTTTATAAGAAACTAGACTCATTAAGATTTAATTTCATGT
19574456 CTCATTCAGCCTCTAATTCAAATCCATAAATTTATGGTTATTTTCTAAAGTCACGTTACTGCTGC
66 CTCATTCAGCCTCTAATTCAAATCCATAAATTTATGGTTATTTTCTAAAGTCACGTTACTGCTGC
19574521 TGTCCTAAGCAGACTATTTCAAATTACCCTTGAATTCCCAAGCTCAAACACTTAAGAAC
131 TGTCCTAAGCAGACTATTTCAAATTACCCTTGAATTCCCAAGCTCAAACACTTAAGAAC
19574580 TTACCATTTG
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 186 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (189 bp):
GAAATTCCTTTGCTTACACGGTTTCTTTTATAAGAAACTAGACTCATTAAGATTTAATTTCATGT
CTCATTCAGCCTCTAATTCAAATCCATAAATTTATGGTTATTTTCTAAAGTCACGTTACTGCTGC
TGTCCTAAGCAGACTATTTCAAATTACCCTTGAATTCCCAAGCTCAAACACTTAAGAAC
Found at i:19577655 original size:17 final size:17
Alignment explanation
Indices: 19577615--19577657 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
19577605 CAGAATTATG
*
19577615 GGCCCATATGCCCATGT
1 GGCCCACATGCCCATGT
**
19577632 GGCCCCACATGCCTGTGT
1 GG-CCCACATGCCCATGT
19577650 GGCCCACA
1 GGCCCACA
19577658 CGCTCAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (17 bp):
GGCCCACATGCCCATGT
Found at i:19592841 original size:32 final size:32
Alignment explanation
Indices: 19592805--19592893 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 32
19592795 ATGCGGCTCT
* *
19592805 AAGCCTTCAGTAGCGGTATTATAATTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* * **
19592837 AAGCCATCGGTAACTGTATTATGTTTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* * ** *
19592869 TAGCCATTAGCGACGGTAATATAAT
1 AAGCCATCAGTAACGGTATTATAAT
19592894 CGATACACAG
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTATTATAATTGGCACA
Found at i:19593144 original size:50 final size:50
Alignment explanation
Indices: 19593067--19593240 Score: 258
Period size: 50 Copynumber: 3.5 Consensus size: 50
19593057 GTCCATCGGC
* * *
19593067 CCACAGTCGTCTCGTGCGACCCATGTGACCTTAACAGATAAATACTAGAT
1 CCACAGTCGTCTCGTACGACCCGTGTGACCTTAACAGATAAATACTGGAT
* *
19593117 CCACAGCCGTCTCATACGACCCGTGTGACCTTAACAGATAAATACTGGAT
1 CCACAGTCGTCTCGTACGACCCGTGTGACCTTAACAGATAAATACTGGAT
* *
19593167 CCACAGTCGTCTTGTACGACCCGTGTGACCTTAATAGATAAATACTGGAT
1 CCACAGTCGTCTCGTACGACCCGTGTGACCTTAACAGATAAATACTGGAT
* * *
19593217 CCACAATCGTCTCGTGCGGCCCGT
1 CCACAGTCGTCTCGTACGACCCGT
19593241 ACAATCCTAT
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (50 bp):
CCACAGTCGTCTCGTACGACCCGTGTGACCTTAACAGATAAATACTGGAT
Found at i:19593517 original size:26 final size:27
Alignment explanation
Indices: 19593488--19593548 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
19593478 CAAAACAGTC
*
19593488 ATTTTACCCTACAAGGGTA-TTCGATA
1 ATTTTACACTACAAGGGTATTTCGATA
19593514 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGATA
19593541 ATTTTACA
1 ATTTTACA
19593549 AATTGGGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGATA
Found at i:19593560 original size:27 final size:27
Alignment explanation
Indices: 19593527--19593685 Score: 157
Period size: 27 Copynumber: 5.9 Consensus size: 27
19593517 TTACACTACA
19593527 AGGGTATTTC-GATAATTTTACAAATTG
1 AGGGTATTTCAG-TAATTTTACAAATTG
* * *
19593554 -GGAGTATTTTAGTAATTTTACAAGTAG
1 AGG-GTATTTCAGTAATTTTACAAATTG
* *
19593581 -GGGTATTTCAGTAATTTCAAAAATTG
1 AGGGTATTTCAGTAATTTTACAAATTG
* *
19593607 AGGGTATTTCAATAATTTCACAAA-TG
1 AGGGTATTTCAGTAATTTTACAAATTG
* * *
19593633 AGGGGTATTTC-GATAATTTTGCAACTCG
1 A-GGGTATTTCAG-TAATTTTACAAATTG
19593661 AGGGTATTTCAGTAATTTTACAAAT
1 AGGGTATTTCAGTAATTTTACAAAT
19593686 CAGGGGTCTT
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
26 24 0.22
27 80 0.74
28 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATTG
Found at i:19593664 original size:54 final size:53
Alignment explanation
Indices: 19593528--19593692 Score: 199
Period size: 54 Copynumber: 3.1 Consensus size: 53
19593518 TACACTACAA
* *
19593528 GGGTATTTCGATAATTTTACAAATTG-GGAGTATTTTAGTAATTTTACAAGTAG
1 GGGTATTTCGATAATTTTACAAATTGAGG-GTATTTCAGTAATTTTACAAATAG
* * * *
19593581 GGGTATTTC-AGTAATTTCAAAAATTGAGGGTATTTCAATAATTTCACAAATGAG
1 GGGTATTTCGA-TAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAAT-AG
* * *
19593635 GGGTATTTCGATAATTTTGCAACTCGAGGGTATTTCAGTAATTTTACAAATCAG
1 GGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAAT-AG
19593689 GGGT
1 GGGT
19593693 CTTCAACTGA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
53 40 0.43
54 52 0.55
55 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (53 bp):
GGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAATAG
Found at i:19602605 original size:40 final size:39
Alignment explanation
Indices: 19602561--19602637 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
19602551 AGTGACCATA
* *
19602561 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCAAAGGCATTTGTGCGAGATACTAAT
* *
19602601 TCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTA
1 TCCGGACTAAGCCCAAAGGCATTTGTGCGAGATACTA
19602638 TAACCGGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 23 0.70
40 10 0.30
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCAAAGGCATTTGTGCGAGATACTAAT
Found at i:19602672 original size:40 final size:39
Alignment explanation
Indices: 19602522--19602665 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 39
19602512 TGAATGATGT
* * *
19602522 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 CCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAATA
* * * *
19602561 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATT
1 -CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAATA
*
19602602 CCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT-A
*
19602641 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAG-CCCGAAGGCATTTG
19602666 AACGAGTAGC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.36
40 43 0.51
41 9 0.11
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:19602684 original size:79 final size:80
Alignment explanation
Indices: 19602521--19602671 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
19602511 TTGAATGATG
* *
19602521 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
19602586 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
19602601 TCCGGGCTAAG-CCCAAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
19602663 TTGAACGAG
64 TTGAACGAG
19602672 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:19610653 original size:40 final size:39
Alignment explanation
Indices: 19610609--19610685 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
19610599 AGTGACCATA
* *
19610609 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCAAAGGCATTTGTGCGAGATACTAAT
* *
19610649 TCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTA
1 TCCGGACTAAGCCCAAAGGCATTTGTGCGAGATACTA
19610686 TAACCGGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 23 0.70
40 10 0.30
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCAAAGGCATTTGTGCGAGATACTAAT
Found at i:19610720 original size:40 final size:39
Alignment explanation
Indices: 19610570--19610713 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 39
19610560 TGAATGATGT
* * *
19610570 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 CCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAATA
* * * *
19610609 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATT
1 -CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAATA
*
19610650 CCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT-A
*
19610689 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAG-CCCGAAGGCATTTG
19610714 AACGAGTAGC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.36
40 43 0.51
41 9 0.11
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:19610732 original size:79 final size:80
Alignment explanation
Indices: 19610569--19610719 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
19610559 TTGAATGATG
* *
19610569 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
19610634 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
19610649 TCCGGGCTAAG-CCCAAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
19610711 TTGAACGAG
64 TTGAACGAG
19610720 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:19613252 original size:56 final size:56
Alignment explanation
Indices: 19613187--19613312 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 56
19613177 TCCTAGACAG
* * *
19613187 GGTCTTACTCGTAAACACATATCGGAATCACCTATCGATACCAACGCATTAAACGT
1 GGTCTTACTCATAAACACATATCAGAATCACATATCGATACCAACGCATTAAACGT
* * **
19613243 GGTCTTACTCATACACACATATCAGAATCACATATCGATGCCAACTTATTAAACGT
1 GGTCTTACTCATAAACACATATCAGAATCACATATCGATACCAACGCATTAAACGT
*
19613299 GGTTTTACTCATAA
1 GGTCTTACTCATAA
19613313 TAACATGTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCATAAACACATATCAGAATCACATATCGATACCAACGCATTAAACGT
Found at i:19613342 original size:43 final size:43
Alignment explanation
Indices: 19613268--19613537 Score: 310
Period size: 43 Copynumber: 6.3 Consensus size: 43
19613258 CACATATCAG
* *** * * *
19613268 AATCACATATCGATGCCAACTTATTAAACGTGGTTTTACTCAT
1 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
* * * *
19613311 AATAACATGTCGATGCCAACGTCCCAGACGTGCTCTTACACGT
1 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
* * * *
19613354 AATCAAATATCGATGTCAACGTCCTAGACGTGGTCTTACACGT
1 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
*
19613397 ACTCACATA-CTGATGCCAACGTCCCAGACGTGGTCTTACACAT
1 AATCACATATC-GATGCCAACGTCCCAGACGTGGTCTTACACAT
* * *
19613440 AATCACATATC-ATGCCAACGTCCCAAATGTGGTCTTACACGT
1 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
* * * *
19613482 CATCACATATCGATGCCAACATCCCAAATGTGGTCTTACACAT
1 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
19613525 AATCACATATCGA
1 AATCACATATCGA
19613538 AAATCCTATG
Statistics
Matches: 194, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 39 0.20
43 154 0.79
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (43 bp):
AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACAT
Found at i:19613515 original size:128 final size:129
Alignment explanation
Indices: 19613295--19613533 Score: 327
Period size: 128 Copynumber: 1.9 Consensus size: 129
19613285 AACTTATTAA
* * * *
19613295 ACGTGGTTTTACTCATAATAACATGTCGATGCCAACGTCCCAGACGTGCTCTTACACGTAATCAA
1 ACGTGGTCTTACACATAATAACATATCGATGCCAACGTCCCAAACGTGCTCTTACACGTAATCAA
* * * * * *
19613360 ATATCGATGTCAACGTCCTAGACGTGGTCTTACACGTACTCACATACTGATGCCAACGTCCCAG
66 ATATCGATGCCAACATCCCAAACGTGGTCTTACACATAATCACATACTGATGCCAACGTCCCAG
* * * * *
19613424 ACGTGGTCTTACACATAATCACATATC-ATGCCAACGTCCCAAATGTGGTCTTACACGTCATCAC
1 ACGTGGTCTTACACATAATAACATATCGATGCCAACGTCCCAAACGTGCTCTTACACGTAATCAA
*
19613488 ATATCGATGCCAACATCCCAAATGTGGTCTTACACATAATCACATA
66 ATATCGATGCCAACATCCCAAACGTGGTCTTACACATAATCACATA
19613534 TCGAAAATCC
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
128 71 0.76
129 23 0.24
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (129 bp):
ACGTGGTCTTACACATAATAACATATCGATGCCAACGTCCCAAACGTGCTCTTACACGTAATCAA
ATATCGATGCCAACATCCCAAACGTGGTCTTACACATAATCACATACTGATGCCAACGTCCCAG
Found at i:19621483 original size:16 final size:16
Alignment explanation
Indices: 19621462--19621531 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
19621452 TTTGGTTTGC
* *
19621462 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* * *
19621478 TGTATTGGATTAGGGG
1 TGTAATGGAATAGAGG
19621494 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
19621510 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
19621526 TGTAAT
1 TGTAAT
19621532 AGCAAATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:19637917 original size:46 final size:46
Alignment explanation
Indices: 19637850--19638121 Score: 374
Period size: 46 Copynumber: 5.9 Consensus size: 46
19637840 NNNNTTTGAA
*
19637850 GAATGTCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGC
1 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
19637896 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
19637942 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
19637988 GAATGTCCGAACTCGTTGAGTTGAGTCCGATTTC-GTGA--GATG-
1 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* *
19638030 TAACTAGGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAA-T--G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * * *
19638081 GAACG-CCCAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19638122 GCGGGTTACA
Statistics
Matches: 203, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
45 36 0.18
46 124 0.61
47 27 0.13
48 3 0.01
50 4 0.02
51 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:19649433 original size:27 final size:26
Alignment explanation
Indices: 19649398--19649506 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 26
19649388 AGCATGGCTG
* *
19649398 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
19649424 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
19649452 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
19649479 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
19649507 TCAGGACGCT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.08
27 38 0.53
28 28 0.39
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:19650957 original size:24 final size:24
Alignment explanation
Indices: 19650930--19650976 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
19650920 CTAGATTTCC
** *
19650930 TCCCTTATCTGCTCCTGAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
19650954 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
19650977 CTCCTGACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:19657259 original size:27 final size:26
Alignment explanation
Indices: 19657224--19657318 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 26
19657214 AGCATGGCTG
*
19657224 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
19657250 CCAGATACAGATAATCGT-AGCAGAACCA
1 CCAGA-ACAGATAAT-GTGA-CAGAGCCA
*
19657278 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
*
19657305 CCAGATCAGATAAT
1 CCAGAACAGATAAT
19657319 TTGTGGCATA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
26 7 0.12
27 37 0.63
28 15 0.25
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:19657332 original size:28 final size:28
Alignment explanation
Indices: 19657224--19657332 Score: 100
Period size: 27 Copynumber: 4.0 Consensus size: 28
19657214 AGCATGGCTG
* * *
19657224 CCAGAACAGATAA--TGTGACAGAGTCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
* * *
19657250 CCAGATACAGATAA-TCGTAGCAGAACCA
1 CCAGAT-CAGATAATTTGTGGCAGAGCCA
* *
19657278 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
*
19657305 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
19657333 TCAGGACGCT
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
26 6 0.09
27 32 0.49
28 27 0.42
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (28 bp):
CCAGATCAGATAATTTGTGGCAGAGCCA
Found at i:19658783 original size:24 final size:24
Alignment explanation
Indices: 19658756--19658826 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
19658746 CTAGATTTCC
**
19658756 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
19658780 TCCCTTATCAACTCCTTAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
19658804 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
19658827 CTCCTGACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.24, C:0.38, G:0.01, T:0.37
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:19661944 original size:43 final size:43
Alignment explanation
Indices: 19661883--19662095 Score: 216
Period size: 43 Copynumber: 5.0 Consensus size: 43
19661873 GTACAGGTTA
* * *
19661883 TACTTTGGTATATTCGATGATGCATTGTGTGTGCCAGTATAGT
1 TACTTCGGGATATTCGATGATGCACTGTGTGTGCCAGTATAGT
* * *
19661926 TACTTCAGAATATTCGATGATGCATTGTGTGTGCCAGTATAGT
1 TACTTCGGGATATTCGATGATGCACTGTGTGTGCCAGTATAGT
* * * *
19661969 TACTTTGGGATA-TCTGATGATGCACTATTTGTGCCAGTATAAT
1 TACTTCGGGATATTC-GATGATGCACTGTGTGTGCCAGTATAGT
** * * *
19662012 TGTTTCGGGATATTTGATGATGCACTGTGTGTACCTGTATAGT
1 TACTTCGGGATATTCGATGATGCACTGTGTGTGCCAGTATAGT
* * *
19662055 TGCTT--TGATATATCTAATGATGCACTGTGTGTGCCAGTATA
1 TACTTCGGGATAT-TC-GATGATGCACTGTGTGTGCCAGTATA
19662096 TGTGATTCGG
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.04
42 3 0.02
43 132 0.94
44 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (43 bp):
TACTTCGGGATATTCGATGATGCACTGTGTGTGCCAGTATAGT
Found at i:19662031 original size:86 final size:86
Alignment explanation
Indices: 19661883--19662095 Score: 266
Period size: 86 Copynumber: 2.5 Consensus size: 86
19661873 GTACAGGTTA
* *
19661883 TACTTTGGTATAT-TCGATGATGCATTGTGTGTGCCAGTATAGTTACTTCAGAATATTCGATGAT
1 TACTTTGGTATATCT-GATGATGCACTGTGTGTGCCAGTATAATTACTTCAGAATATTCGATGAT
* *
19661947 GCATTGTGTGTGCCAGTATAGT
65 GCACTGTGTGTACCAGTATAGT
* * * ** * * *
19661969 TACTTTGGGATATCTGATGATGCACTATTTGTGCCAGTATAATTGTTTCGGGATATTTGATGATG
1 TACTTTGGTATATCTGATGATGCACTGTGTGTGCCAGTATAATTACTTCAGAATATTCGATGATG
*
19662034 CACTGTGTGTACCTGTATAGT
66 CACTGTGTGTACCAGTATAGT
* * *
19662055 TGCTTTGATATATCTAATGATGCACTGTGTGTGCCAGTATA
1 TACTTTGGTATATCTGATGATGCACTGTGTGTGCCAGTATA
19662096 TGTGATTCGG
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
86 106 0.99
87 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (86 bp):
TACTTTGGTATATCTGATGATGCACTGTGTGTGCCAGTATAATTACTTCAGAATATTCGATGATG
CACTGTGTGTACCAGTATAGT
Found at i:19662105 original size:86 final size:86
Alignment explanation
Indices: 19661899--19662124 Score: 249
Period size: 86 Copynumber: 2.6 Consensus size: 86
19661889 GGTATATTCG
* * * * *
19661899 ATGATGCATTGTGTGTGCCAGTATA-GTTACTTCAGAATATTCGATGATGCATTGTGTGTGCCAG
1 ATGATGCACTGTGTGTGCCAGTATATGTGA-TTCGGAATATTCGATGATGCACTGTGTGTACCAG
* *
19661963 TATAGTTACTTTGGGATATCTG
65 TATAGTTACTTTGAGATATCTA
* * * * * *
19661985 ATGATGCACTATTTGTGCCAGTATAAT-TGTTTCGGGATATTTGATGATGCACTGTGTGTACCTG
1 ATGATGCACTGTGTGTGCCAGTAT-ATGTGATTCGGAATATTCGATGATGCACTGTGTGTACCAG
* *
19662049 TATAGTTGCTTTGATATATCTA
65 TATAGTTACTTTGAGATATCTA
** *
19662071 ATGATGCACTGTGTGTGCCAGTATATGTGATTCGGTTTCATCCGATGATGCACT
1 ATGATGCACTGTGTGTGCCAGTATATGTGATTCGGAAT-ATTCGATGATGCACT
19662125 TACGTGCCAG
Statistics
Matches: 114, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
85 2 0.02
86 97 0.85
87 15 0.13
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (86 bp):
ATGATGCACTGTGTGTGCCAGTATATGTGATTCGGAATATTCGATGATGCACTGTGTGTACCAGT
ATAGTTACTTTGAGATATCTA
Found at i:19662132 original size:129 final size:129
Alignment explanation
Indices: 19661892--19662136 Score: 291
Period size: 129 Copynumber: 1.9 Consensus size: 129
19661882 ATACTTTGGT
* * * *
19661892 ATATTCGATGATGCATTGTGTGTGCCAGTATAGTTACTTCAGAATATTCGATGATGCATTGTGTG
1 ATATTCGATGATGCACTGTGTGTACCAGTATAGTTACTTCAGAATATTCAATGATGCACTGTGTG
* * * **
19661957 TGCCAGTATAGTTACTTTGGGATATCTGATGATGCACTATTTGTGCCAGTATAATTGTTTCGGG
66 TGCCAGTATAGTGACTTCGGGATATCCGATGATGCACTATACGTGCCAGTATAATTGTTTCGGG
* * * *
19662021 ATATTTGATGATGCACTGTGTGTACCTGTATAGTTGCTT-TG-ATATATCTAATGATGCACTGTG
1 ATATTCGATGATGCACTGTGTGTACCAGTATAGTTACTTCAGAATAT-TC-AATGATGCACTGTG
**
19662084 TGTGCCAGTATATGTGA-TTCGGTTTCATCCGATGATGCACT-TACGTGCCAGTA
64 TGTGCCAGTATA-GTGACTTCGGGAT-ATCCGATGATGCACTATACGTGCCAGTA
19662137 CATGTGTGTC
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
127 4 0.04
128 3 0.03
129 73 0.75
130 17 0.18
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (129 bp):
ATATTCGATGATGCACTGTGTGTACCAGTATAGTTACTTCAGAATATTCAATGATGCACTGTGTG
TGCCAGTATAGTGACTTCGGGATATCCGATGATGCACTATACGTGCCAGTATAATTGTTTCGGG
Found at i:19664563 original size:34 final size:34
Alignment explanation
Indices: 19664502--19664592 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
19664492 ACACTCGTAG
* *
19664502 TGCCATAACCCAG-TTTTGGTCTTATCATTAGGA
1 TGCCATAGCCCAGCTTATGGTCTTATCATTAGGA
*
19664535 TGCCATAGCCCAGCTTATAGTCTTATCATTAGGA
1 TGCCATAGCCCAGCTTATGGTCTTATCATTAGGA
*
19664569 TGTCATAGCCCAGC-TATGGTCTTA
1 TGCCATAGCCCAGCTTATGGTCTTA
19664593 CAAGTATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 21 0.40
34 31 0.60
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (34 bp):
TGCCATAGCCCAGCTTATGGTCTTATCATTAGGA
Found at i:19664657 original size:33 final size:33
Alignment explanation
Indices: 19664620--19664695 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
19664610 TGGTCCAACC
* *
19664620 ATGGTCTTACGTTCAC-AGTGCCATAACCCAGTT
1 ATGGTCTTAC-TTCACAAATGCCATAACCCAGCT
19664653 ATGGTCTT--TTCACTAAAATGCCATAACCCAGCT
1 ATGGTCTTACTTCAC--AAATGCCATAACCCAGCT
19664686 ATGGTCTTAC
1 ATGGTCTTAC
19664696 ATTTAAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 5 0.14
33 31 0.86
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACTTCACAAATGCCATAACCCAGCT
Found at i:19668729 original size:40 final size:40
Alignment explanation
Indices: 19668631--19668893 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
19668621 TCCTCGTTCA
* * * ** *
19668631 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
19668670 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
19668710 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
19668750 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
19668790 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
19668830 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
19668870 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
19668894 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:19675773 original size:39 final size:40
Alignment explanation
Indices: 19675728--19675952 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
19675718 GCTCCTCGTT
* * * *
19675728 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
19675768 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
19675807 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
19675847 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
19675887 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
19675928 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
19675953 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 39 0.25
40 105 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:19675961 original size:41 final size:41
Alignment explanation
Indices: 19675884--19675961 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
19675874 TTTGTATCTC
* * *
19675884 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
19675925 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
19675962 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19678715 original size:17 final size:17
Alignment explanation
Indices: 19678695--19678730 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19678685 TTTATCATTT
19678695 TTACGTTTTTCCAATTG
1 TTACGTTTTTCCAATTG
*
19678712 TTACGTTTTTCTAATTG
1 TTACGTTTTTCCAATTG
19678729 TT
1 TT
19678731 GTTTAGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (17 bp):
TTACGTTTTTCCAATTG
Found at i:19688365 original size:47 final size:47
Alignment explanation
Indices: 19688289--19688422 Score: 193
Period size: 47 Copynumber: 2.9 Consensus size: 47
19688279 GTCATTTGTG
19688289 TGTGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTATGAAA
1 TGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TGAAA
* * *
19688335 TGAT-AGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGA
1 TG-TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAAA
*
19688382 TGTGAGCCAGTGTAAGACCGTGTCTGGGACATGGCATCGGC
1 TGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
19688423 ACCTTACCCA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
46 15 0.19
47 55 0.71
48 8 0.10
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (47 bp):
TGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAAA
Found at i:19689482 original size:17 final size:17
Alignment explanation
Indices: 19689460--19689493 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19689450 GTGAATTACA
19689460 AATTAATTCTACATGGG
1 AATTAATTCTACATGGG
19689477 AATTAATTCTACATGGG
1 AATTAATTCTACATGGG
19689494 TGTGGGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
AATTAATTCTACATGGG
Found at i:19705327 original size:112 final size:113
Alignment explanation
Indices: 19705125--19705355 Score: 403
Period size: 112 Copynumber: 2.1 Consensus size: 113
19705115 CCCATACCTG
* *
19705125 TATCCTACAGCGTGACGGAATATAAGGCGTTACCTCACTTAAACTCGTGCTTACAACCATTTTCG
1 TATCCTACACCGTGACGGAATACAAGGCGTTACCTCACTTAAACTCGTGCTTACAACCATTTTCG
19705190 AGTCCCCATGACTTGGACAAATTTAAAACTTTCTCAAACATACCAACA
66 AGTCCCCATGACTTGGACAAATTTAAAACTTTCTCAAACATACCAACA
* *
19705238 TATCCTACACCGTGACGG-ATACGAGGCGTTACTTCACTTAAACTCGTGCTTACAACCATTTTCG
1 TATCCTACACCGTGACGGAATACAAGGCGTTACCTCACTTAAACTCGTGCTTACAACCATTTTCG
19705302 AGTCCCCATGACTTGGA-AAATTTTAAAACTTTCTCAAACATACCAACA
66 AGTCCCCATGACTTGGACAAA-TTTAAAACTTTCTCAAACATACCAACA
19705350 TATCCT
1 TATCCT
19705356 TAATATAGGC
Statistics
Matches: 113, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
111 3 0.03
112 93 0.82
113 17 0.15
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.29
Consensus pattern (113 bp):
TATCCTACACCGTGACGGAATACAAGGCGTTACCTCACTTAAACTCGTGCTTACAACCATTTTCG
AGTCCCCATGACTTGGACAAATTTAAAACTTTCTCAAACATACCAACA
Found at i:19705476 original size:21 final size:21
Alignment explanation
Indices: 19705450--19705489 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19705440 CACTTGACAT
19705450 AGGGGCACACGCCCGTGTGAA
1 AGGGGCACACGCCCGTGTGAA
19705471 AGGGGCACACGCCCGTGTG
1 AGGGGCACACGCCCGTGTG
19705490 GCCAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.30, G:0.40, T:0.10
Consensus pattern (21 bp):
AGGGGCACACGCCCGTGTGAA
Found at i:19707464 original size:13 final size:13
Alignment explanation
Indices: 19707446--19707523 Score: 105
Period size: 13 Copynumber: 6.5 Consensus size: 13
19707436 AGATTTTTCT
19707446 TAAATATTATCAC
1 TAAATATTATCAC
19707459 TAAATA--ATC-C
1 TAAATATTATCAC
19707469 TAAATATTATCAC
1 TAAATATTATCAC
19707482 TAAATATTATCAC
1 TAAATATTATCAC
*
19707495 TAAATA--AT-TC
1 TAAATATTATCAC
19707505 TAAATATTATCAC
1 TAAATATTATCAC
19707518 TAAATA
1 TAAATA
19707524 ATTCAAATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
10 14 0.25
11 5 0.09
12 5 0.09
13 33 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:19707493 original size:36 final size:36
Alignment explanation
Indices: 19707446--19707523 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
19707436 AGATTTTTCT
19707446 TAAATATTATCACTAAATAATCCTAAATATTATCAC
1 TAAATATTATCACTAAATAATCCTAAATATTATCAC
*
19707482 TAAATATTATCACTAAATAATTCTAAATATTATCAC
1 TAAATATTATCACTAAATAATCCTAAATATTATCAC
19707518 TAAATA
1 TAAATA
19707524 ATTCAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (36 bp):
TAAATATTATCACTAAATAATCCTAAATATTATCAC
Found at i:19707507 original size:23 final size:23
Alignment explanation
Indices: 19707481--19707531 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
19707471 AATATTATCA
19707481 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
19707504 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
19707527 C-AAAT
1 CTAAAT
19707532 TTAAACTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:19708048 original size:7 final size:7
Alignment explanation
Indices: 19708036--19708074 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
19708026 GATTAATGTT
19708036 AAAATTA
1 AAAATTA
19708043 AAAATTA
1 AAAATTA
19708050 AAAATT-
1 AAAATTA
19708056 AAAA-TA
1 AAAATTA
19708062 AAATATTA
1 AAA-ATTA
19708070 AAAAT
1 AAAAT
19708075 AATTTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 7 0.24
7 16 0.55
8 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:19708059 original size:20 final size:20
Alignment explanation
Indices: 19708034--19708074 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
19708024 AAGATTAATG
19708034 TTAAAATTAAAA-ATTAAAAA
1 TTAAAA-TAAAATATTAAAAA
19708054 TTAAAATAAAATATTAAAAA
1 TTAAAATAAAATATTAAAAA
19708074 T
1 T
19708075 AATTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAATAAAATATTAAAAA
Found at i:19709761 original size:17 final size:17
Alignment explanation
Indices: 19709739--19709781 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19709729 CTTCATGTTT
*
19709739 TTTTTTAATTTTATGAA
1 TTTTTTAATTTTATAAA
* *
19709756 TTTTTTTATTTTTTAAA
1 TTTTTTAATTTTATAAA
19709773 TATTTTTAA
1 T-TTTTTAA
19709782 AGTAAACCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTTTAATTTTATAAA
Found at i:19710172 original size:18 final size:17
Alignment explanation
Indices: 19710136--19710174 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19710126 TAATGCATGA
19710136 TATTTAAAATTGTTTAT
1 TATTTAAAATTGTTTAT
* *
19710153 TATTTAGAATTTTATTAT
1 TATTTAAAATTGT-TTAT
19710171 TATT
1 TATT
19710175 AATGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTTAAAATTGTTTAT
Found at i:19713279 original size:54 final size:54
Alignment explanation
Indices: 19713220--19713328 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
19713210 CAGTGACGGG
*
19713220 GGTGCGGGTGGGGGAAGGGGAGAGGGAGAGGAACAGGGTGGGGGAGTTTTTTTT
1 GGTGCGGGGGGGGGAAGGGGAGAGGGAGAGGAACAGGGTGGGGGAGTTTTTTTT
19713274 GGTGCGGGGGGGGGAAGGGGAGAGGGAGAGGAACAGGGTGGGGGAGTTTTTTTT
1 GGTGCGGGGGGGGGAAGGGGAGAGGGAGAGGAACAGGGTGGGGGAGTTTTTTTT
19713328 G
1 G
19713329 TAACAACCCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.18, C:0.04, G:0.59, T:0.19
Consensus pattern (54 bp):
GGTGCGGGGGGGGGAAGGGGAGAGGGAGAGGAACAGGGTGGGGGAGTTTTTTTT
Found at i:19713686 original size:28 final size:27
Alignment explanation
Indices: 19713650--19713705 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
19713640 GTTAATAATG
19713650 AAGGTTAAATAAGTAATTTAGTAGAATA
1 AAGGTTAAATAAGTAATTTAGTA-AATA
19713678 AAGGTTAAATAAGTAATTTAGTAAATA
1 AAGGTTAAATAAGTAATTTAGTAAATA
19713705 A
1 A
19713706 GTATAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (27 bp):
AAGGTTAAATAAGTAATTTAGTAAATA
Found at i:19715713 original size:29 final size:29
Alignment explanation
Indices: 19715680--19715749 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
19715670 ATAAAGGGAT
*
19715680 TAAATTTTTAAAAATATAACTACAATGAC
1 TAAATTTTTAAAAATATAACTACAATAAC
* *
19715709 TAAATTCTTT-AAAATATAATTACATTAAC
1 TAAATT-TTTAAAAATATAACTACAATAAC
19715738 TAAATTTTTAAA
1 TAAATTTTTAAA
19715750 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 30 0.83
30 3 0.08
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (29 bp):
TAAATTTTTAAAAATATAACTACAATAAC
Found at i:19716401 original size:18 final size:19
Alignment explanation
Indices: 19716375--19716418 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
19716365 TAATCATATG
19716375 TTTAGTTATTTTT-TTTAA
1 TTTAGTTATTTTTGTTTAA
* *
19716393 TTTATTTATTTTTGTTTTA
1 TTTAGTTATTTTTGTTTAA
19716412 TTTAGTT
1 TTTAGTT
19716419 TTTCACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTAGTTATTTTTGTTTAA
Found at i:19716411 original size:15 final size:15
Alignment explanation
Indices: 19716380--19716421 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19716370 ATATGTTTAG
19716380 TTATTT-TTTTTAAT
1 TTATTTATTTTTAAT
**
19716394 TTATTTATTTTTGTT
1 TTATTTATTTTTAAT
19716409 TTATTTAGTTTTT
1 TTATTTA-TTTTT
19716422 CACATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.25
15 13 0.54
16 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
TTATTTATTTTTAAT
Found at i:19716656 original size:31 final size:31
Alignment explanation
Indices: 19716596--19716656 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
19716586 TAGATATCAC
* **
19716596 ATTAGACATTTTATGAAGGTACATGTACCAT
1 ATTAGACATTTTATGAAAGTACAAATACCAT
*
19716627 ATTAGACATTTTATGAAAGTATAAATACCA
1 ATTAGACATTTTATGAAAGTACAAATACCA
19716657 AATATGGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (31 bp):
ATTAGACATTTTATGAAAGTACAAATACCAT
Found at i:19722206 original size:8 final size:7
Alignment explanation
Indices: 19722172--19722216 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
19722162 CCATGTTAGT
19722172 AAAAATA
1 AAAAATA
19722179 AAATAATTA
1 AAA-AA-TA
*
19722188 AAAAATC
1 AAAAATA
19722195 AAAAATA
1 AAAAATA
19722202 AAAAATA
1 AAAAATA
19722209 AAAAATA
1 AAAAATA
19722216 A
1 A
19722217 TTTGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 25 0.74
8 4 0.12
9 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:19722320 original size:23 final size:23
Alignment explanation
Indices: 19722270--19722320 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
19722260 TCCAAGTTCA
19722270 TTAAAAAATTAATTTTTTAAATT
1 TTAAAAAATTAATTTTTTAAATT
*
19722293 ATAAAAAA-T-ATTTTTATGAAATT
1 TTAAAAAATTAATTTTT-T-AAATT
19722316 TTAAA
1 TTAAA
19722321 TTTTTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAAAATTAATTTTTTAAATT
Found at i:19722575 original size:31 final size:30
Alignment explanation
Indices: 19722509--19722572 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
19722499 CTTCGGCCAC
* * *
19722509 TTTAGTCCTAATGTCATCAAATGTTTTCAT
1 TTTAGTCCTAATATCATCAAATATTCTCAT
*
19722539 TTTAGTCCCTAATATTATCAAATATTCTCGAT
1 TTTAGT-CCTAATATCATCAAATATTCTC-AT
19722571 TT
1 TT
19722573 AGTGCTTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTAGTCCTAATATCATCAAATATTCTCAT
Found at i:19722657 original size:11 final size:11
Alignment explanation
Indices: 19722641--19722665 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19722631 TGTCATACAA
19722641 TGATGTCATAG
1 TGATGTCATAG
19722652 TGATGTCATAG
1 TGATGTCATAG
19722663 TGA
1 TGA
19722666 CATCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (11 bp):
TGATGTCATAG
Found at i:19722728 original size:19 final size:18
Alignment explanation
Indices: 19722706--19722759 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
19722696 TAAAAATGAA
*
19722706 AAAAAGTACAAAAATATTT
1 AAAAAGTA-AAAAATAATT
*
19722725 AAAAATTAAAAAATAATT
1 AAAAAGTAAAAAATAATT
19722743 AAGGAAA-TAAAAAATAA
1 AA--AAAGTAAAAAATAA
19722760 AAAATTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 11 0.35
19 17 0.55
20 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAAAGTAAAAAATAATT
Found at i:19722736 original size:18 final size:17
Alignment explanation
Indices: 19722715--19722782 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
19722705 AAAAAAGTAC
19722715 AAAAATATTTAAAAATTA
1 AAAAATA-TTAAAAATTA
19722733 AAAAATAATTAAGGAAA-TA
1 AAAAAT-ATTAA--AAATTA
19722752 AAAAATA--AAAAATTA
1 AAAAATATTAAAAATTA
19722767 CAAAAA-ATTAAAAATT
1 -AAAAATATTAAAAATT
19722783 TACTAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 7 0.16
17 7 0.16
18 11 0.26
19 9 0.21
20 3 0.07
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAATATTAAAAATTA
Found at i:19722780 original size:19 final size:19
Alignment explanation
Indices: 19722697--19722780 Score: 54
Period size: 19 Copynumber: 4.6 Consensus size: 19
19722687 AAAAATCTTT
* *
19722697 AAAAATGAAAAAAAGTACA
1 AAAAATTAAAAAAATTACA
* *
19722716 AAAATATT-TAAAAATTAAA
1 AAAA-ATTAAAAAAATTACA
**
19722735 AAATAATTAAGGAAA-T--A
1 AAA-AATTAAAAAAATTACA
19722752 AAAAA-T-AAAAAATTACA
1 AAAAATTAAAAAAATTACA
19722769 AAAAATTAAAAA
1 AAAAATTAAAAA
19722781 TTTACTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
14 4 0.08
15 2 0.04
16 2 0.04
17 10 0.21
18 1 0.02
19 23 0.48
20 6 0.12
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (19 bp):
AAAAATTAAAAAAATTACA
Found at i:19722785 original size:18 final size:18
Alignment explanation
Indices: 19722750--19722790 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19722740 ATTAAGGAAA
19722750 TAAAAAATAAAAAATTAC
1 TAAAAAATAAAAAATTAC
*
19722768 -AAAAAATTAAAAATTTAC
1 TAAAAAA-TAAAAAATTAC
19722786 TAAAA
1 TAAAA
19722791 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAATAAAAAATTAC
Found at i:19724866 original size:50 final size:49
Alignment explanation
Indices: 19724754--19724940 Score: 189
Period size: 50 Copynumber: 3.8 Consensus size: 49
19724744 TGAGGTCGCA
* * * * *
19724754 TGTGTAGTATTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT-GATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGACTGTAGGTCACG
* **
19724805 TGTGTGGTACTAAGTGCAGGCTACTACGTGTATTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-AGGTCACG
* * *
19724855 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGGTCACG
* * *
19724904 TGTGTAGTGCTAAGTGCAGGCTACTATGCGTACCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
19724941 TAGTTTCGGC
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 39 0.34
50 42 0.37
51 29 0.25
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGGTCACG
Found at i:19726555 original size:129 final size:130
Alignment explanation
Indices: 19726324--19726578 Score: 415
Period size: 129 Copynumber: 2.0 Consensus size: 130
19726314 ATTTAGAAAA
19726324 CATGAGTGAAATTCTAAAGGAACATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAACATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCACG
* * *
19726389 ATAGGGCACGATTCCCCGAATTCCCAAACATCGAACGTTGCCTTCGTTTTAAAGAGTTTTTGAAG
66 ATAGGACACGATTCCCCGAATTCCCAAACATCGAACGTTGCCTTCATTTTAAAGAATTTTTGAAG
*
19726454 CATGAGTGAAATT-TCAAAGGAATATTCGATTATTTTGAACAAAC-GGAAATTGCAACCCAGCAC
1 CATGAGTGAAATTCT-AAAGGAACATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCAC
* * **
19726517 GATTGGACATGATTCTTCGAATTCCCAAACATCGAACGTTGCCTTCATTTTAAAGAATTTTT
65 GATAGGACACGATTCCCCGAATTCCCAAACATCGAACGTTGCCTTCATTTTAAAGAATTTTT
19726579 AAATGAATAA
Statistics
Matches: 116, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
129 75 0.65
130 41 0.35
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (130 bp):
CATGAGTGAAATTCTAAAGGAACATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCACG
ATAGGACACGATTCCCCGAATTCCCAAACATCGAACGTTGCCTTCATTTTAAAGAATTTTTGAAG
Found at i:19729235 original size:14 final size:14
Alignment explanation
Indices: 19729218--19729247 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19729208 TAACTTCAGT
*
19729218 CTGCTCTACTGCAA
1 CTGCTCCACTGCAA
19729232 CTGCTCCACTGCAA
1 CTGCTCCACTGCAA
19729246 CT
1 CT
19729248 TTAGGGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.13, T:0.27
Consensus pattern (14 bp):
CTGCTCCACTGCAA
Found at i:19729338 original size:44 final size:44
Alignment explanation
Indices: 19729232--19729349 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 44
19729222 TCTACTGCAA
* * *
19729232 CTGCTCCACTGCAACTTTAGGGAGATATGGTTCGTGTATTTTAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTCGTGTATTTGAT
* *
19729276 CTTGCTCTAC-GACAACTTCAGAGAGATAAGGATT-GTG-ATTTCGAT
1 C-TGCTCCACTG-CAACTTCAGGGAGATAAGG-TTCGTGTATTT-GAT
19729321 CTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAG
19729350 ATCTGCTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
44 30 0.48
45 30 0.48
46 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGGTTCGTGTATTTGAT
Found at i:19729462 original size:88 final size:88
Alignment explanation
Indices: 19729339--19729707 Score: 418
Period size: 88 Copynumber: 4.2 Consensus size: 88
19729329 CTGCAACTTC
* * ** *
19729339 AGGGAGATAAGATCTGCTAATCTTTGGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAATGT
1 AGGGAGACAAGATCTAC-AATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGT
*
19729404 CTTTGCTTTGCTCCACTACTGCTT
65 CTTTGATTTGCTCCACTACTGCTT
* * *
19729428 AAGGAGACAAGATCTACAATCTTCGGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGTG
1 AGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGTC
* * *
19729493 TTTGATCTGTTCCACT-GTAGCTT
66 TTTGATTTGCTCCACTACT-GCTT
* * * **
19729516 CAGGGAGACAAGATATATAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGACTTGCT-T
1 -AGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGT
* *
19729580 CTTTGATTTGCTCTACTACTGTTT
65 CTTTGATTTGCTCCACTACTGCTT
* * * * ** *
19729604 AGGGAGACAAGATCTGCAATTTTTAGCCTGTTACCCTATTACTTAGGGGGTTAAGGCTTGCCGTC
1 AGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGTC
* * **
19729669 TTTGATCTGTTCCACTACAACTT
66 TTTGATTTGCTCCACTACTGCTT
19729692 CAGGGAGACAAGATCT
1 -AGGGAGACAAGATCT
19729708 GTGAATTCAC
Statistics
Matches: 238, Mismatches: 37, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
87 55 0.23
88 98 0.41
89 85 0.36
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (88 bp):
AGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGTC
TTTGATTTGCTCCACTACTGCTT
Found at i:19729638 original size:176 final size:178
Alignment explanation
Indices: 19729309--19729705 Score: 528
Period size: 176 Copynumber: 2.2 Consensus size: 178
19729299 AGATAAGGAT
* * * * **
19729309 TGTGATTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAATCTTTGGCCTGTTAC
1 TGTG-TTT-GATCTGTTCCACTGCAACTTCAGGGAGACAAGATATGATAATCTTCAGCCTGTTAC
* *
19729374 CCTACTACTTAGGGGGTTAAGGCTCAATGTCTTTGCTTTGCTCCACTACTGCTTAAGGAGACAAG
64 CCTACTACTTAGGGGGTTAAGACTCAATGTCTTTGATTTGCTCCACTACTGCTTAAGGAGACAAG
*
19729439 ATCTACAATCTTCGGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAC
129 ATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAC
* *
19729489 TGTGTTTGATCTGTTCCACTGTAGCTTCAGGGAGACAAGATAT-ATAATCTTCAGCCTGTTACCC
1 TGTGTTTGATCTGTTCCACTGCAACTTCAGGGAGACAAGATATGATAATCTTCAGCCTGTTACCC
*** * * *
19729553 TACTACTTAGGGGGTTAAGACTTGCT-TCTTTGATTTGCTCTACTACTGTTTAGGGAGACAAGAT
66 TACTACTTAGGGGGTTAAGACTCAATGTCTTTGATTTGCTCCACTACTGCTTAAGGAGACAAGAT
* * * * **
19729617 CTGCAATTTTTAGCCTGTTACCCTATTACTTAGGGGGTTAAGGCTTGC
131 CTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAC
* * *
19729665 CGTCTTTGATCTGTTCCACTACAACTTCAGGGAGACAAGAT
1 TGTGTTTGATCTGTTCCACTGCAACTTCAGGGAGACAAGAT
19729706 CTGTGAATTC
Statistics
Matches: 189, Mismatches: 28, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
176 111 0.59
177 40 0.21
178 31 0.16
179 3 0.02
180 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (178 bp):
TGTGTTTGATCTGTTCCACTGCAACTTCAGGGAGACAAGATATGATAATCTTCAGCCTGTTACCC
TACTACTTAGGGGGTTAAGACTCAATGTCTTTGATTTGCTCCACTACTGCTTAAGGAGACAAGAT
CTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCAC
Found at i:19733008 original size:16 final size:17
Alignment explanation
Indices: 19732978--19733010 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19732968 GTGGTGGAGA
19732978 TGACTCTTGTATGGATT
1 TGACTCTTGTATGGATT
*
19732995 TGACT-TTGTCTGGATT
1 TGACTCTTGTATGGATT
19733011 GATCTCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.15, C:0.12, G:0.24, T:0.48
Consensus pattern (17 bp):
TGACTCTTGTATGGATT
Found at i:19737647 original size:21 final size:21
Alignment explanation
Indices: 19737618--19737657 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19737608 TGGGACAACT
19737618 GATTCATCATCT-CTCTTTGG
1 GATTCATCATCTGCTCTTTGG
*
19737638 GATTCCATCATTTGCTCTTT
1 GATT-CATCATCTGCTCTTT
19737658 CATCTCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (21 bp):
GATTCATCATCTGCTCTTTGG
Found at i:19741387 original size:26 final size:26
Alignment explanation
Indices: 19741351--19741402 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
19741341 CGTTGCCTTT
19741351 GTTTTAAAGAGTTTTTGAAGCATGAG
1 GTTTTAAAGAGTTTTTGAAGCATGAG
19741377 GTTTTAAAGAGTTTTTGAAGCATGAG
1 GTTTTAAAGAGTTTTTGAAGCATGAG
19741403 TGAAATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (26 bp):
GTTTTAAAGAGTTTTTGAAGCATGAG
Found at i:19743020 original size:78 final size:78
Alignment explanation
Indices: 19742891--19743047 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
19742881 GCAATGTGCG
* * *
19742891 ATTAAATGTTTATGCAAATGAGGGGGACTTAACGCGCAATTACCCCTCTCCGTAGAAACGCGCGG
1 ATTAAATGCTTATGCAAATGAGGGGGACTTAACGCACAATTACCCCTCTCCGCAGAAACGCGCGG
19742956 ATCCCAGGGGTAA
66 ATCCCAGGGGTAA
*
19742969 ATTAAATGCTTATGGAAATGAGGGGGACTTAACGCACAATTACCCCTCTCCGCAGAAACGCGCGG
1 ATTAAATGCTTATGCAAATGAGGGGGACTTAACGCACAATTACCCCTCTCCGCAGAAACGCGCGG
19743034 ATCCCAGGGGTAA
66 ATCCCAGGGGTAA
19743047 A
1 A
19743048 GAACCGGATC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (78 bp):
ATTAAATGCTTATGCAAATGAGGGGGACTTAACGCACAATTACCCCTCTCCGCAGAAACGCGCGG
ATCCCAGGGGTAA
Found at i:19747590 original size:5 final size:5
Alignment explanation
Indices: 19747580--19747604 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19747570 CCTGTTATTG
19747580 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
19747605 TGCCAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:19750070 original size:55 final size:54
Alignment explanation
Indices: 19749975--19750124 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
19749965 CTACTTTGTT
* ** * *
19749975 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
19750029 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
19750084 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
19750125 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:19750087 original size:27 final size:27
Alignment explanation
Indices: 19749947--19750124 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
19749937 TAAATTGTAC
19749947 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
19749974 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
19750000 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
19750028 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
19750056 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
19750083 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
19750110 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19750125 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:19750088 original size:82 final size:81
Alignment explanation
Indices: 19749948--19750103 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
19749938 AAATTGTACA
* * * *
19749948 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
19750013 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
19750029 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
19750092 TGTGCGAGTTGA
63 TGTGCGAATTGA
19750104 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:19758168 original size:27 final size:27
Alignment explanation
Indices: 19758137--19758314 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19758127 TAAATTGTAC
19758137 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19758164 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19758190 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19758218 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
19758246 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19758273 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19758300 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19758315 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19758251 original size:82 final size:81
Alignment explanation
Indices: 19758138--19758293 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19758128 AAATTGTACA
* *
19758138 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
19758202 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
19758219 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
19758284 TGCGAGTTGA
65 TGCGAATTGA
19758294 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19758305 original size:82 final size:81
Alignment explanation
Indices: 19758134--19758314 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
19758124 GATTAAATTG
* *
19758134 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
19758199 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
19758215 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
19758279 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19758297 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19758315 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19761352 original size:38 final size:38
Alignment explanation
Indices: 19761296--19761372 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
19761286 TTCCTTATCT
*
19761296 ATTTATGGACTACACATTGAGGACAATGTGTCAACTAA
1 ATTTATGGACTACACATTGAAGACAATGTGTCAACTAA
* *
19761334 ATTTATGGGCTACGCATTGAAGACAATGTGTCAACTAA
1 ATTTATGGACTACACATTGAAGACAATGTGTCAACTAA
19761372 A
1 A
19761373 GTGTGGGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (38 bp):
ATTTATGGACTACACATTGAAGACAATGTGTCAACTAA
Found at i:19762802 original size:21 final size:20
Alignment explanation
Indices: 19762754--19762802 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
19762744 ATCTAAAATT
* *
19762754 AATTAAACAATAATCCAGAA
1 AATTAAAAAATAATCCAAAA
*
19762774 AATCTAAAAAATATTTCCAAAA
1 AAT-TAAAAAATA-ATCCAAAA
19762796 AATTAAA
1 AATTAAA
19762803 TTTAAAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 9 0.38
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.24
Consensus pattern (20 bp):
AATTAAAAAATAATCCAAAA
Found at i:19765201 original size:130 final size:130
Alignment explanation
Indices: 19764968--19765360 Score: 786
Period size: 130 Copynumber: 3.0 Consensus size: 130
19764958 ATTGCTATAC
19764968 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
1 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
19765033 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
66 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
19765098 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
1 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
19765163 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
66 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
19765228 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
1 TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
19765293 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
66 CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
19765358 TAA
1 TAA
19765361 GTATTTTCGG
Statistics
Matches: 263, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 263 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (130 bp):
TAACTTACTAAGCTTTATAGCTTACTTTGTTAATTTTCCATGTTTTATAGTGAAACTAAAGCTAG
CTCAGATTCGGGGACCGTCGGAGACTTCATCACACTATCCAACTATCACTTGGTAACTTTGAACT
Found at i:19772308 original size:38 final size:38
Alignment explanation
Indices: 19772253--19772329 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
19772243 TTAGATTAGG
19772253 GAAAGAACAAAGATTCAGATTAATCGACTTAATTCACC
1 GAAAGAACAAAGATTCAGATTAATCGACTTAATTCACC
*
19772291 GAAAGAACAAAGTTTCAGATTAATCGACTTAATTCACC
1 GAAAGAACAAAGATTCAGATTAATCGACTTAATTCACC
19772329 G
1 G
19772330 TTTTTGCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (38 bp):
GAAAGAACAAAGATTCAGATTAATCGACTTAATTCACC
Found at i:19782809 original size:23 final size:24
Alignment explanation
Indices: 19782765--19782811 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
19782755 TCCTGTTATT
* *
19782765 TGGCTCTTTGTGAGCTTCCTGATA
1 TGGCTCTCTGTGAACTTCCTGATA
19782789 TGGCTCTCT-TGAACTTCCTGATA
1 TGGCTCTCTGTGAACTTCCTGATA
19782812 GATGGCTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (24 bp):
TGGCTCTCTGTGAACTTCCTGATA
Found at i:19786030 original size:47 final size:47
Alignment explanation
Indices: 19785979--19786185 Score: 324
Period size: 47 Copynumber: 4.4 Consensus size: 47
19785969 TTGTGATGTG
** *
19785979 AGTGTATATATGTGATAAGGCATAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
19786026 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
19786073 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
* * * * * *
19786120 AGTGTATATATGTGACAGGGCCGACTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
*
19786167 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
19786186 TCCCGAAGGG
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
47 148 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAA
Found at i:19786360 original size:37 final size:37
Alignment explanation
Indices: 19786304--19786382 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
19786294 CCGAGCTCTA
* *
19786304 AAGACCCGATGACTACGTGTGGGGATT-TCGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTAT-GTCCGGGT
*
19786341 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
19786378 AAGAC
1 AAGAC
19786383 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:19787881 original size:25 final size:25
Alignment explanation
Indices: 19787853--19787900 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19787843 CATATTTCGT
19787853 TAAGTGATTT-TTGGTAAAAATGTCA
1 TAAG-GATTTATTGGTAAAAATGTCA
* *
19787878 TAAGGATTTATTTGTGAAAATGT
1 TAAGGATTTATTGGTAAAAATGT
19787901 GAAAATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (25 bp):
TAAGGATTTATTGGTAAAAATGTCA
Found at i:19788464 original size:43 final size:43
Alignment explanation
Indices: 19788408--19788564 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 43
19788398 TTAACAAGAC
** *
19788408 GTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCATATT
1 GTGATTACATGTAAGACCATATCTGGGACATTGGCATCATATT
* * *
19788451 GCGATTACATGTAAGACCATATTTGGGACATTGGCATCGT-TAT
1 GTGATTACATGTAAGACCATATCTGGGACATTGGCATCATAT-T
* * * *
19788494 GTGATTTCATGTAAGACCATGTCTAGAACATTGGCATCGATA-T
1 GTGATTACATGTAAGACCATATCTGGGACATTGGCATC-ATATT
*
19788537 GTGATAACATGTAAGACCATATCTGGGA
1 GTGATTACATGTAAGACCATATCTGGGA
19788565 TATGACATTG
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
42 1 0.01
43 91 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (43 bp):
GTGATTACATGTAAGACCATATCTGGGACATTGGCATCATATT
Found at i:19796531 original size:18 final size:18
Alignment explanation
Indices: 19796510--19796560 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
19796500 AGGCCAATTT
*
19796510 GGGCGTGTGGGCCCACAC
1 GGGCATGTGGGCCCACAC
19796528 GGGCATGTGGGCCCACAC
1 GGGCATGTGGGCCCACAC
19796546 GGGCATGTGGGCCCA
1 GGGCATGTGGGCCCA
19796561 AATTTCTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.12
Consensus pattern (18 bp):
GGGCATGTGGGCCCACAC
Found at i:19799387 original size:35 final size:34
Alignment explanation
Indices: 19799336--19799404 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 34
19799326 TCATATACAT
*
19799336 CAAGTAAGAATGGATGAGCTCATCACGCAACACTC
1 CAAGTAAGAATAGATGAGCTCATCACGCAA-ACTC
*
19799371 CAAGTAAGAATAGATGAGCTCATCATGCAAACTC
1 CAAGTAAGAATAGATGAGCTCATCACGCAAACTC
19799405 TTTCAAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.12
35 28 0.88
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (34 bp):
CAAGTAAGAATAGATGAGCTCATCACGCAAACTC
Found at i:19802850 original size:100 final size:100
Alignment explanation
Indices: 19802432--19802831 Score: 791
Period size: 100 Copynumber: 4.0 Consensus size: 100
19802422 GAGAAAGAGG
*
19802432 AAGAAGTTTTTTTCTTGTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
1 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
19802497 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
66 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
19802532 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
1 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
19802597 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
66 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
19802632 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
1 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
19802697 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
66 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
19802732 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
1 AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
19802797 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
66 TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
19802832 TCCCACCCCC
Statistics
Matches: 299, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 299 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (100 bp):
AAGAAGTTTTTTTCTTTTTTCCTTTGAAAAACAATGAGGTTAAAATGAAAGAATGAATAGTTTTT
TTTTCATTTATAGGTGCCAAAAAGGGATAATTTAT
Found at i:19803193 original size:21 final size:19
Alignment explanation
Indices: 19803169--19803228 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
19803159 ACTTGTATAA
19803169 TTTTTATTTATTCTTATTTC
1 TTTTTATTTATT-TTATTTC
*
19803189 GTTTTTATTTATTTTTATGTC
1 -TTTTTATTTA-TTTTATTTC
19803210 TATTTATATTTATTTTATT
1 T-TTT-TATTTATTTTATT
19803229 ATTATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTTATTTATTTTATTTC
Found at i:19803198 original size:11 final size:10
Alignment explanation
Indices: 19803168--19803238 Score: 63
Period size: 10 Copynumber: 6.7 Consensus size: 10
19803158 CACTTGTATA
19803168 ATTTTTATTT
1 ATTTTTATTT
*
19803178 ATTCTTATTT
1 ATTTTTATTT
*
19803188 CGTTTTTATTT
1 -ATTTTTATTT
19803199 ATTTTTATGTCT
1 ATTTTTAT-T-T
*
19803211 ATTTATATTT
1 ATTTTTATTT
19803221 A-TTTTATTATT
1 ATTTTTA-T-TT
19803232 ATTTTTA
1 ATTTTTA
19803239 CACATTCCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
9 4 0.08
10 19 0.39
11 13 0.27
12 13 0.27
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:19811504 original size:14 final size:14
Alignment explanation
Indices: 19811485--19811535 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
19811475 TCATTCCGAA
19811485 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
** *
19811499 AAAAAGGGAAAACG
1 AAAAAGAAAAAAAG
*
19811513 AATAAGAAACAAAA-
1 AAAAAGAAA-AAAAG
19811527 AAAAAGAAA
1 AAAAAGAAA
19811536 GGAAATAGGA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:19812528 original size:28 final size:28
Alignment explanation
Indices: 19812487--19812543 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
19812477 GTAATCAAGA
19812487 AAATGCATGCATTTCATTTTACGAGCCT
1 AAATGCATGCATTTCATTTTACGAGCCT
*
19812515 AAATGCATGTATTTCATTTTACGAGCCT
1 AAATGCATGCATTTCATTTTACGAGCCT
19812543 A
1 A
19812544 GGGACTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (28 bp):
AAATGCATGCATTTCATTTTACGAGCCT
Found at i:19822791 original size:43 final size:43
Alignment explanation
Indices: 19822694--19822816 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
19822684 AACTAAGAAG
* * * * *
19822694 TCCGAACTCATTGAGTGGTCCGAGTTCGTGA-GGTATG-TAGCA
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGG-ATGCAAGCA
*
19822736 TCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAAGCA
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCAAGCA
* ** *
19822779 TTCGAGCTCGTTGAGTTGTCTGAGTTCATGATGGATGC
1 TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGC
19822817 GATTCATGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 29 0.43
43 39 0.57
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (43 bp):
TCCGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGCAAGCA
Found at i:19824284 original size:13 final size:13
Alignment explanation
Indices: 19824266--19824290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19824256 GATTTGTTTA
19824266 TTAAACTAATTAT
1 TTAAACTAATTAT
19824279 TTAAACTAATTA
1 TTAAACTAATTA
19824291 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:19826881 original size:37 final size:37
Alignment explanation
Indices: 19826818--19826888 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
19826808 AAGATGGAAG
* * * * *
19826818 GAGGTGAAACTCGCTGTTATATGGATGTGGAGCTAAA
1 GAGGTGAAACTCCCTATTAGAAGGATGCGGAGCTAAA
19826855 GAGGTGAAACTCCCTATTAGAAGGATGCGGAGCT
1 GAGGTGAAACTCCCTATTAGAAGGATGCGGAGCT
19826889 TGATTCTGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (37 bp):
GAGGTGAAACTCCCTATTAGAAGGATGCGGAGCTAAA
Found at i:19827200 original size:17 final size:17
Alignment explanation
Indices: 19827180--19827222 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
19827170 AAATTGAAAT
19827180 GAAAATAAAAATCAA-AA
1 GAAAATAAAAAT-AAGAA
19827197 G-AAATAAAAATAAGAA
1 GAAAATAAAAATAAGAA
*
19827213 TAAAATAAAA
1 GAAAATAAAA
19827223 GGAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (17 bp):
GAAAATAAAAATAAGAA
Found at i:19827207 original size:6 final size:6
Alignment explanation
Indices: 19827176--19827260 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
19827166 AAGAAAATTG
* * * *
19827176 AAATGA AAATAA AAAT-C AAA-AG AAATAA AAATAA GAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
** * *
19827221 AAGGAA ATAATAA TAATAA ATAATAA GAATAA AAATAA AA
1 AAATAA A-AATAA AAATAA A-AATAA AAATAA AAATAA AA
19827261 TTGGAGGATT
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
5 10 0.17
6 42 0.70
7 8 0.13
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:19827241 original size:13 final size:13
Alignment explanation
Indices: 19827199--19827258 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
19827189 AATCAAAAGA
19827199 AATAAA-AATAAG
1 AATAAATAATAAG
19827211 AAT-AA-AATAA-
1 AATAAATAATAAG
* *
19827221 AAGGAAATAATAAT
1 AA-TAAATAATAAG
19827235 AATAAATAATAAG
1 AATAAATAATAAG
19827248 AATAAA-AATAA
1 AATAAATAATAA
19827259 AATTGGAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.05
11 7 0.17
12 10 0.24
13 20 0.49
14 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAATAAG
Found at i:19830460 original size:39 final size:39
Alignment explanation
Indices: 19830401--19830478 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
19830391 TATGAAAGTC
*
19830401 TCAGAATATGAAAGAGAGTTTGTTCGATTGAGTAAGTAT
1 TCAGAATATGAAAGAGAGTTTGTTCGATTAAGTAAGTAT
*
19830440 TCAGTATATGAAAGAGAGTTTGTTCGATTAAGTAAGTAT
1 TCAGAATATGAAAGAGAGTTTGTTCGATTAAGTAAGTAT
19830479 GCCAGGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (39 bp):
TCAGAATATGAAAGAGAGTTTGTTCGATTAAGTAAGTAT
Found at i:19834652 original size:68 final size:68
Alignment explanation
Indices: 19834574--19834705 Score: 228
Period size: 68 Copynumber: 1.9 Consensus size: 68
19834564 AATTAGGGCC
* * *
19834574 TAATCGGAATAGTGGTTTCGTGACCATAAATCCGAGATAGAAATAATTATTTTATAATTATTTTT
1 TAATCGGAATAGTGGTTTCGTGACCACAAATCCGAGATACAAATAATAATTTTATAATTATTTTT
19834639 AGG
66 AGG
*
19834642 TAATCGGAATAGTGGTTTTGTGACCACAAATCCGAGATACAAATAATAATTTTATAATTATTTT
1 TAATCGGAATAGTGGTTTCGTGACCACAAATCCGAGATACAAATAATAATTTTATAATTATTTT
19834706 GATGATTATG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (68 bp):
TAATCGGAATAGTGGTTTCGTGACCACAAATCCGAGATACAAATAATAATTTTATAATTATTTTT
AGG
Found at i:19835223 original size:78 final size:78
Alignment explanation
Indices: 19835093--19835247 Score: 251
Period size: 78 Copynumber: 2.0 Consensus size: 78
19835083 TAAGTGATTC
19835093 CAAGCCCCGTTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAGCTCGATTAAGCTTATGCTAA
1 CAAGCCCCGTTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAGCTCGATTAAGCTTATGCTAA
19835158 CAATAATTCAACT
66 CAATAATTCAACT
* *
19835171 CAAGCCCCGTTTTTAATG-TTCTTTACGTTTTTG-GAATCCCGGTAGCTTGATTAAGCTTATGTT
1 CAAGCCCCGTTTTTAATGATT-TTTACGTTTTTGAG-ATCCCGGTAGCTCGATTAAGCTTATGCT
*
19835234 AGCAATAATTCAAC
64 AACAATAATTCAAC
19835248 CTAGGGTTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
77 3 0.04
78 69 0.96
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (78 bp):
CAAGCCCCGTTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAGCTCGATTAAGCTTATGCTAA
CAATAATTCAACT
Found at i:19843965 original size:40 final size:40
Alignment explanation
Indices: 19843920--19844111 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
19843910 ATAACCACAA
* * *
19843920 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
19843960 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * * *
19844000 GCACAAATGCCTTCGGTTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
19844040 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * *
19844080 GCATAAATGCCTTCAGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
19844112 CATTCAAATG
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 134 0.96
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:19848696 original size:13 final size:13
Alignment explanation
Indices: 19848678--19848702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19848668 GATTTGTTTA
19848678 TTAAACTAATTAT
1 TTAAACTAATTAT
19848691 TTAAACTAATTA
1 TTAAACTAATTA
19848703 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:19851195 original size:45 final size:45
Alignment explanation
Indices: 19851105--19851195 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
19851095 GAACCATGTG
* * * *
19851105 ATCTGAACTCATTAAGTTGTGGTTTGAGTTCATGATATATGTGAC
1 ATCTGAACTCACTAAGTTGTAGTCTGAGTTCATGATATATATGAC
* *
19851150 ATCTGATCTCACTGAGTTGTAGTCTGAGTTCATGATGA-ATATGAC
1 ATCTGAACTCACTAAGTTGTAGTCTGAGTTCATGAT-ATATATGAC
19851195 A
1 A
19851196 CATGTTTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCACTAAGTTGTAGTCTGAGTTCATGATATATATGAC
Found at i:19856600 original size:79 final size:82
Alignment explanation
Indices: 19856489--19856673 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
19856479 GCTCCTCGTT
* *
19856489 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
19856552 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* ** *
19856569 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
19856632 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
19856649 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19856674 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:19856606 original size:39 final size:40
Alignment explanation
Indices: 19856489--19856673 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
19856479 GCTCCTCGTT
*
19856489 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
19856529 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
19856569 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
19856608 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
19856649 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19856674 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:19861258 original size:21 final size:23
Alignment explanation
Indices: 19861232--19861275 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
19861222 TTGGATTATT
19861232 AATTAGA-G-GTCCTTAAATAGC
1 AATTAGATGAGTCCTTAAATAGC
19861253 AATTAGATGAAGTCCTTAAATAG
1 AATTAGATG-AGTCCTTAAATAG
19861276 GAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
24 12 0.60
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (23 bp):
AATTAGATGAGTCCTTAAATAGC
Found at i:19862300 original size:45 final size:45
Alignment explanation
Indices: 19862243--19862333 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
19862233 GAACCATGTG
* *
19862243 ATCTGAACTCATTGAGTTGTGGTCTAAGTTCATGATATATGTGAC
1 ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
* * *
19862288 ATCTGAGCTCATTCAGTTGTGGTCTGAGTTCATGATGTATATGAC
1 ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
19862333 A
1 A
19862334 CATGTTTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCATTCAGTTGTGGTCTAAGTTCATGATATATATGAC
Found at i:19862973 original size:148 final size:151
Alignment explanation
Indices: 19862668--19862983 Score: 387
Period size: 148 Copynumber: 2.1 Consensus size: 151
19862658 AAAAGTTTCA
* * * *
19862668 ATTTTTTTAAAAAAAATAGAAAGTTTAGATTTTAATAAATAAAAATCTGTTTTTTTTAGTCATTT
1 ATTTTTTTAAAAAAAAGAGAAAATTTAGATTTTAATAAATAAAAA-CTATTTTTTTAAGTCATTT
*
19862733 TAAATGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
65 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
*
19862798 TTAATATTTAAGAAAATAGTGG
130 TTAATATTTAAGAAAATAATGG
**
19862820 A--TTTTTAAAAAATGGAGAAAATTTAGATTTTGAA-AAATAAAAA-TATTTTTTTAAGTCATTT
1 ATTTTTTTAAAAAAAAGAGAAAATTTAGATTTT-AATAAATAAAAACTATTTTTTTAAGTCATTT
* ** * *
19862881 TAAAGGAAAGTTT-AAATTTTTAAACAAAGTTTTTGATTTTTTT-AACTATTTTGAAAT-AAGGT
65 TAAAGGAAAGTTTAAAATTTTAAAACAAAG-TTTTGATTTTTTTCAACTATTTCAAAATAAAAGC
* *
19862943 TTTTATTTTTAAGAAAAGTAAT-G
129 TTTAATATTTAAGAAAA-TAATGG
19862966 ATTTTTTTCAAAATAAAA
1 ATTTTTTT-AAAA-AAAA
19862984 CTTTGGTTTT
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
146 20 0.14
147 30 0.21
148 46 0.33
149 4 0.03
150 37 0.26
151 2 0.01
152 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (151 bp):
ATTTTTTTAAAAAAAAGAGAAAATTTAGATTTTAATAAATAAAAACTATTTTTTTAAGTCATTTT
AAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTT
TAATATTTAAGAAAATAATGG
Found at i:19863585 original size:10 final size:10
Alignment explanation
Indices: 19863551--19863608 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
19863541 CTTGTATAAT
19863551 TTTTTATTTA
1 TTTTTATTTA
* *
19863561 TTCTTATTTTG
1 TTTTTA-TTTA
19863572 TTTTTATTTA
1 TTTTTATTTA
*
19863582 TTTTCATGTATA
1 TTTTTAT-T-TA
*
19863594 TTTATATTTA
1 TTTTTATTTA
19863604 TTTTT
1 TTTTT
19863609 TTTTTTACAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
10 20 0.54
11 10 0.27
12 7 0.19
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:19868043 original size:27 final size:27
Alignment explanation
Indices: 19868002--19868071 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
19867992 AAACATACAT
*
19868002 CACATAGGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * * *
19868029 CATATAAGGGCAAAATATTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
19868056 CACATAAGGGCAAAAC
1 CACATAAGGGCAAAAC
19868072 GATTATTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATCTTAC
Found at i:19868079 original size:27 final size:26
Alignment explanation
Indices: 19868002--19868081 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
19867992 AAACATACAT
* * *
19868002 CACATAGGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACA-TTATTTTAC
* *
19868029 CATATAAGGGCAAAATATTCATTTTAC
1 CACATAAGGGCAAAACATT-ATTTTAC
19868056 CACATAAGGGCAAAACGATTATTTTA
1 CACATAAGGGCAAAAC-ATTATTTTA
19868082 TCAATTTGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.02
27 40 0.91
28 3 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (26 bp):
CACATAAGGGCAAAACATTATTTTAC
Done.