Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 57 of 297
Found at i:20184808 original size:22 final size:22
Alignment explanation
Indices: 20184764--20184814 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20184754 TGCTGCGATG
* *
20184764 TTTACGACTATGTGATGTCCTA
1 TTTACGGCTATGTCATGTCCTA
* *
20184786 TTTACGGCTATGTCCTGTTCTA
1 TTTACGGCTATGTCATGTCCTA
*
20184808 TCTACGG
1 TTTACGG
20184815 TGTTGAGTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTACGGCTATGTCATGTCCTA
Found at i:20190699 original size:18 final size:18
Alignment explanation
Indices: 20190663--20190697 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20190653 GATAGGTCAA
20190663 AATGGGCTGTGTGGGCCC
1 AATGGGCTGTGTGGGCCC
20190681 AATGGGCT-TGTGGGCCC
1 AATGGGCTGTGTGGGCCC
20190698 CACACGGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (18 bp):
AATGGGCTGTGTGGGCCC
Found at i:20198254 original size:18 final size:18
Alignment explanation
Indices: 20198231--20198272 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
20198221 AATGAATTGT
20198231 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
20198249 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
20198267 ATTAAA
1 ATTAAA
20198273 AATGCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (18 bp):
ATTAAATTGCTTGATGTG
Found at i:20199464 original size:47 final size:47
Alignment explanation
Indices: 20199411--20199821 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
20199401 TTAGGATTCT
20199411 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199458 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199505 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199552 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199599 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199646 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
20199693 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
20199740 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
20199787 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
20199822 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:20199996 original size:37 final size:37
Alignment explanation
Indices: 20199940--20200018 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20199930 CCGAGCTCTA
* * *
20199940 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
20199977 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
20200014 AAGAC
1 AAGAC
20200019 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20226847 original size:23 final size:23
Alignment explanation
Indices: 20226821--20226870 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
20226811 ACCCCATGCA
20226821 ATGCAACATA-ATATCATACATGG-
1 ATGCAACATACATAT-A-ACATGGC
*
20226844 ATGCAATATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
20226867 ATGC
1 ATGC
20226871 TCAAATACAG
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:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:20227380 original size:24 final size:24
Alignment explanation
Indices: 20227345--20227390 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20227335 TCGACAACCC
*
20227345 ACTTTTCAGCTTTTTAGCCTTTCG
1 ACTTTTCAGCTTTCTAGCCTTTCG
*
20227369 ACTTTTCGGCTTTCTAGCCTTT
1 ACTTTTCAGCTTTCTAGCCTTT
20227391 GTAGTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.13, T:0.50
Consensus pattern (24 bp):
ACTTTTCAGCTTTCTAGCCTTTCG
Found at i:20228555 original size:10 final size:10
Alignment explanation
Indices: 20228540--20228565 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20228530 CGGCTAGCAA
20228540 CAAACTTATT
1 CAAACTTATT
20228550 CAAACTTATT
1 CAAACTTATT
20228560 CAAACT
1 CAAACT
20228566 CTTGGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAACTTATT
Found at i:20237931 original size:79 final size:81
Alignment explanation
Indices: 20237795--20237979 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 81
20237785 TCGAATGATG
*
20237795 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
20237859 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * **
20237874 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20237936 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
20237954 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20237980 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:20237993 original size:40 final size:40
Alignment explanation
Indices: 20237796--20237979 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
20237786 CGAATGATGT
* * * *
20237796 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20237836 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
20237876 CCGGGCTAAG-CCCGAAGGCATTTGTGCTAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20237914 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20237955 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20237980 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20238001 original size:79 final size:79
Alignment explanation
Indices: 20237848--20238012 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
20237838 GGACTAAGAT
* ** *
20237848 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCTAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20237913 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20237927 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20237990 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20238006 CCGAAGG
1 CCGAAGG
20238013 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:20238429 original size:47 final size:47
Alignment explanation
Indices: 20238360--20238449 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
20238350 TTATAGATTT
20238360 GGTTCTCCAGCTATCGGACTCGGGATCTTGAAGTCAAAGTCGCCCAC
1 GGTTCTCCAGCTATCGGACTCGGGATCTTGAAGTCAAAGTCGCCCAC
* * *
20238407 GGTTCTTCAGCTATCGGACTCGGGATTTTGAAGTCGAAGTCGC
1 GGTTCTCCAGCTATCGGACTCGGGATCTTGAAGTCAAAGTCGC
20238450 GCACACTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (47 bp):
GGTTCTCCAGCTATCGGACTCGGGATCTTGAAGTCAAAGTCGCCCAC
Found at i:20240399 original size:56 final size:56
Alignment explanation
Indices: 20240313--20240419 Score: 214
Period size: 56 Copynumber: 1.9 Consensus size: 56
20240303 TATGTAGTAT
20240313 ATATGTGAATTTGATTACTATGTTTAGTCTTGGTTTTACATGTCTTTGGTTGAAGC
1 ATATGTGAATTTGATTACTATGTTTAGTCTTGGTTTTACATGTCTTTGGTTGAAGC
20240369 ATATGTGAATTTGATTACTATGTTTAGTCTTGGTTTTACATGTCTTTGGTT
1 ATATGTGAATTTGATTACTATGTTTAGTCTTGGTTTTACATGTCTTTGGTT
20240420 AAAGAATTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (56 bp):
ATATGTGAATTTGATTACTATGTTTAGTCTTGGTTTTACATGTCTTTGGTTGAAGC
Found at i:20248160 original size:79 final size:81
Alignment explanation
Indices: 20248049--20248230 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 81
20248039 GCTACTCGTT
* *
20248049 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCCG
* *
20248113 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* * **
20248129 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
* *
20248192 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
20248209 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
20248231 AGACATCATT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 4 0.05
79 54 0.61
80 30 0.34
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:20248166 original size:39 final size:40
Alignment explanation
Indices: 20248049--20248230 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
20248039 GCTACTCGTT
* *
20248049 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
20248089 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
20248129 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
20248168 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
20248209 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
20248231 AGACATCATT
Statistics
Matches: 123, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 75 0.61
41 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:20251299 original size:49 final size:49
Alignment explanation
Indices: 20251227--20251324 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
20251217 CGGTTGCTAA
20251227 ACGGCAGGTGTTGCATGTGTTGCATGATCATTTTGGTCGGCTGTTTTAT
1 ACGGCAGGTGTTGCATGTGTTGCATGATCATTTTGGTCGGCTGTTTTAT
20251276 ACGGCAGGTGTTGCATGTGTTGCATGATCATTTTGGTCGGCTGTTTTAT
1 ACGGCAGGTGTTGCATGTGTTGCATGATCATTTTGGTCGGCTGTTTTAT
20251325 TATGTATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (49 bp):
ACGGCAGGTGTTGCATGTGTTGCATGATCATTTTGGTCGGCTGTTTTAT
Found at i:20258650 original size:21 final size:21
Alignment explanation
Indices: 20258605--20258651 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20258595 CTCCTATGCT
* * *
20258605 CGTGTGTGCAAGCCTCACGCT
1 CGTGTGTGCAAGCCCCACACC
*
20258626 CGTGTGTGCAAGCCCCATACC
1 CGTGTGTGCAAGCCCCACACC
20258647 CGTGT
1 CGTGT
20258652 TAATTTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (21 bp):
CGTGTGTGCAAGCCCCACACC
Found at i:20259228 original size:112 final size:112
Alignment explanation
Indices: 20259031--20259255 Score: 441
Period size: 112 Copynumber: 2.0 Consensus size: 112
20259021 CTTTAGTGAA
*
20259031 TGGTCATGGTGGTTTGAGGAGTTTATACTCATTCCTACTATCAATCTCGTCAAAATAAGGTTTTA
1 TGGTCATGGTGGTTTGAGGAGTTTATACTCATTCCTACTATCAATCTCATCAAAATAAGGTTTTA
20259096 ATCGGGTTTTGTTTACCTTAAAAGTGCCGAACTTGGGATGACTCACC
66 ATCGGGTTTTGTTTACCTTAAAAGTGCCGAACTTGGGATGACTCACC
20259143 TGGTCATGGTGGTTTGAGGAGTTTATACTCATTCCTACTATCAATCTCATCAAAATAAGGTTTTA
1 TGGTCATGGTGGTTTGAGGAGTTTATACTCATTCCTACTATCAATCTCATCAAAATAAGGTTTTA
20259208 ATCGGGTTTTGTTTACCTTAAAAGTGCCGAACTTGGGATGACTCACC
66 ATCGGGTTTTGTTTACCTTAAAAGTGCCGAACTTGGGATGACTCACC
20259255 T
1 T
20259256 CCACCATACC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (112 bp):
TGGTCATGGTGGTTTGAGGAGTTTATACTCATTCCTACTATCAATCTCATCAAAATAAGGTTTTA
ATCGGGTTTTGTTTACCTTAAAAGTGCCGAACTTGGGATGACTCACC
Found at i:20259547 original size:19 final size:22
Alignment explanation
Indices: 20259493--20259539 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
20259483 TGAACAGGTC
*
20259493 CTCTACTGGTGCTTGAGAACGA
1 CTCTACTAGTGCTTGAGAACGA
20259515 CTCTACTAGTGCTTGAGAACGA
1 CTCTACTAGTGCTTGAGAACGA
20259537 CTC
1 CTC
20259540 ATGTGCTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
CTCTACTAGTGCTTGAGAACGA
Found at i:20265529 original size:11 final size:11
Alignment explanation
Indices: 20265513--20265537 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20265503 CCAAGCCCCG
20265513 TTTTTTATGTT
1 TTTTTTATGTT
20265524 TTTTTTATGTT
1 TTTTTTATGTT
20265535 TTT
1 TTT
20265538 GGAGTCCTCG
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTATGTT
Found at i:20266358 original size:50 final size:50
Alignment explanation
Indices: 20266291--20266476 Score: 230
Period size: 50 Copynumber: 3.7 Consensus size: 50
20266281 TATTGAGGTT
* * * *
20266291 ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCGTTGG-CACTGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGC-ATGGACACCGAG
* *
20266341 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGACACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGACACCGAG
** * *
20266391 ATGAGAACTCCCATGTAAGACCATGTCTGGGATATGGCATGGACACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGACACCGAG
** * *
20266441 ATGAGAACTCCCATGTAAGACCATATCTGGGATATG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATG
20266477 ACATTGGCAG
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
49 3 0.02
50 121 0.98
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGACACCGAG
Found at i:20266761 original size:20 final size:20
Alignment explanation
Indices: 20266736--20266785 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20266726 TGAGTTATTT
20266736 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
20266756 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
*
20266776 AAGAAAGCAA
1 AAGTAAGCAA
20266786 AGACTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:20271122 original size:26 final size:27
Alignment explanation
Indices: 20271093--20271146 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
20271083 AGAAGTGCCG
*
20271093 AATATTCACTGACCATA-AAAG-TTTGA
1 AATATTCAATGACC-TAGAAAGATTTGA
*
20271119 AATATTTAATGACCTAGAAAGATTTGA
1 AATATTCAATGACCTAGAAAGATTTGA
20271146 A
1 A
20271147 CTTGAGGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 16 0.67
27 6 0.25
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (27 bp):
AATATTCAATGACCTAGAAAGATTTGA
Found at i:20286107 original size:9 final size:9
Alignment explanation
Indices: 20286093--20286139 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
20286083 TTTATAAATG
20286093 TTAATATTT
1 TTAATATTT
20286102 TTAATAATTT
1 TTAAT-ATTT
20286112 TTAATATTT
1 TTAATATTT
*
20286121 TT-CTATTT
1 TTAATATTT
*
20286129 TAAATATTT
1 TTAATATTT
20286138 TT
1 TT
20286140 TTATAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 9 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTAATATTT
Found at i:20286108 original size:19 final size:18
Alignment explanation
Indices: 20286081--20286122 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
20286071 TTTCTATATG
20286081 TTTTTATAAATGTTAATA
1 TTTTTATAAATGTTAATA
* *
20286099 TTTTTAATAATTTTTAATA
1 TTTTT-ATAAATGTTAATA
20286118 TTTTT
1 TTTTT
20286123 CTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAAATGTTAATA
Found at i:20286113 original size:10 final size:10
Alignment explanation
Indices: 20286093--20286181 Score: 62
Period size: 10 Copynumber: 9.1 Consensus size: 10
20286083 TTTATAAATG
20286093 TTAAT-ATTT
1 TTAATAATTT
20286102 TTAATAATTT
1 TTAATAATTT
20286112 TTAAT-ATTT
1 TTAATAATTT
*
20286121 TT-CT-ATTT
1 TTAATAATTT
* *
20286129 TAAATATTTT
1 TTAATAATTT
*
20286139 TTTATAATTT
1 TTAATAATTT
20286149 TTCCAAATAATTT
1 TT---AATAATTT
* *
20286162 TTTATAA-GT
1 TTAATAATTT
20286171 TTAATAATTT
1 TTAATAATTT
20286181 T
1 T
20286182 ATTGATATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
8 6 0.10
9 19 0.31
10 27 0.44
13 9 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTAATAATTT
Found at i:20286127 original size:27 final size:28
Alignment explanation
Indices: 20286097--20286151 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
20286087 TAAATGTTAA
*
20286097 TATTTTTAATAATTTTTAAT-ATTTTTC
1 TATTTTAAATAATTTTTAATAATTTTTC
* *
20286124 TATTTTAAATATTTTTTTATAATTTTTC
1 TATTTTAAATAATTTTTAATAATTTTTC
20286152 CAAATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
TATTTTAAATAATTTTTAATAATTTTTC
Found at i:20289962 original size:16 final size:16
Alignment explanation
Indices: 20289938--20289997 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
20289928 TATTTTGCAA
20289938 AAAAT-AAAAATAAAT
1 AAAATAAAAAATAAAT
20289953 AAAATAAAAAATAACACAAT
1 AAAATAAAAAAT---A-AAT
*
20289973 TAAATAAAAAAATAAA-
1 AAAAT-AAAAAATAAAT
20289989 AAAATAAAA
1 AAAATAAAA
20289998 TTAGAGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
15 9 0.24
16 10 0.27
17 2 0.05
18 1 0.03
19 1 0.03
20 7 0.19
21 7 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAATAAAT
Found at i:20289981 original size:25 final size:22
Alignment explanation
Indices: 20289936--20289996 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
20289926 ATTATTTTGC
20289936 AAAAAATAAAAATAAATAAAAT
1 AAAAAATAAAAATAAATAAAAT
20289958 AAAAAATAACACAATTAAATAAAA-
1 AAAAAATAA-A-AA-TAAATAAAAT
*
20289982 AAATAA-AAAAATAAA
1 AAAAAATAAAAATAAA
20289997 ATTAGAGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 4 0.11
21 2 0.06
22 10 0.29
23 3 0.09
24 7 0.20
25 9 0.26
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (22 bp):
AAAAAATAAAAATAAATAAAAT
Found at i:20289998 original size:21 final size:20
Alignment explanation
Indices: 20289936--20289998 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
20289926 ATTATTTTGC
20289936 AAAAAATAAAAATAAATAAAAT
1 AAAAAAT-AAAA-AAATAAAAT
* * *
20289958 AAAAAATAACACAATTAAAT
1 AAAAAATAAAAAAATAAAAT
20289978 AAAAAAATAAAAAAATAAAAT
1 -AAAAAATAAAAAAATAAAAT
20289999 TAGAGAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.21
21 20 0.59
22 7 0.21
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAAATAAAAAAATAAAAT
Found at i:20298067 original size:35 final size:35
Alignment explanation
Indices: 20297974--20298153 Score: 182
Period size: 35 Copynumber: 5.1 Consensus size: 35
20297964 CAAACCACTC
* * * * *
20297974 AAACACACCAGATGCTCGTAAGAGCCAATCCAACCA
1 AAACACGCC-GATGCTCATAAGAGCTAGTCCAACCG
* * *
20298010 AAACAAGTCGATGCTCACAAGAGCTAGTCCAACCG
1 AAACACGCCGATGCTCATAAGAGCTAGTCCAACCG
* * *
20298045 AAACACGCCGATGCTAATAAGAGTTATTCCAACCG
1 AAACACGCCGATGCTCATAAGAGCTAGTCCAACCG
** *
20298080 AAACACGCTAATGCTCATAAGAGCTAGTCCAACTG
1 AAACACGCCGATGCTCATAAGAGCTAGTCCAACCG
** * *
20298115 AAACACG-TTATGCTCAAAAGAGCTAGTTCAACCG
1 AAACACGCCGATGCTCATAAGAGCTAGTCCAACCG
20298149 AAACA
1 AAACA
20298154 TGCCAAACAG
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
34 28 0.23
35 86 0.72
36 6 0.05
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (35 bp):
AAACACGCCGATGCTCATAAGAGCTAGTCCAACCG
Found at i:20301795 original size:22 final size:22
Alignment explanation
Indices: 20301770--20301812 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20301760 TTGTCTGCAC
* *
20301770 GACTTATATTTTATGTAATTAA
1 GACTTATATCTTATCTAATTAA
*
20301792 GACTTGTATCTTATCTAATTA
1 GACTTATATCTTATCTAATTA
20301813 GGGCTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
GACTTATATCTTATCTAATTAA
Found at i:20311658 original size:19 final size:20
Alignment explanation
Indices: 20311634--20311679 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
20311624 ATTCTTGTCG
20311634 AAAAATAATTAAA-TAT-TAT
1 AAAAATAATTAAATTATGT-T
20311653 AAAAATAATTAAATTATGTT
1 AAAAATAATTAAATTATGTT
20311673 AAAAATA
1 AAAAATA
20311680 TGAACATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.52
20 11 0.44
21 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATAATTAAATTATGTT
Found at i:20314320 original size:49 final size:49
Alignment explanation
Indices: 20314198--20314324 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 49
20314188 TTATGAGAGG
* * *
20314198 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCA-CGACAAGAGAAC
* * * * *
20314248 TCCTATGTAATACCATATCTGGGATATGACATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACG-ACAAGAGAAC
*
20314296 ATCCCATGTAAGACCATGTTTGGGACATG
1 -TCCCATGTAAGACCATGTCTGGGACATG
20314325 GCTTTTGCAT
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
48 4 0.06
49 27 0.44
50 31 0.50
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACGACAAGAGAAC
Found at i:20317145 original size:36 final size:36
Alignment explanation
Indices: 20317105--20317176 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
20317095 GGGTAACCAA
20317105 CCAAAA-TCGAGGGACGCAAGGACTACAATCCAACTT
1 CCAAAACT-GAGGGACGCAAGGACTACAATCCAACTT
20317141 CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
1 CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
20317177 TTATAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14
Consensus pattern (36 bp):
CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
Found at i:20318993 original size:13 final size:14
Alignment explanation
Indices: 20318975--20319015 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
20318965 TTTTCAAAGA
20318975 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
20318988 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
20319002 TACGGTTTA-GACT
1 TATGGTTTAGGACT
20319015 T
1 T
20319016 TAGGGGTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:20321884 original size:47 final size:47
Alignment explanation
Indices: 20321809--20321902 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
20321799 GCTTCGATTC
**
20321809 CCCTTCCAAAAGATAATTTAGGGCTTGATTAATGCATATGGAGGTGG
1 CCCTTCCAAAAGATAATTTAGAACTTGATTAATGCATATGGAGGTGG
* * * *
20321856 CCCTTCTAAAATATAATTTAGAATTTGATTAATGCATGTGGAGGTGG
1 CCCTTCCAAAAGATAATTTAGAACTTGATTAATGCATATGGAGGTGG
20321903 TCTAGCGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (47 bp):
CCCTTCCAAAAGATAATTTAGAACTTGATTAATGCATATGGAGGTGG
Found at i:20322397 original size:9 final size:9
Alignment explanation
Indices: 20322383--20322683 Score: 116
Period size: 9 Copynumber: 32.6 Consensus size: 9
20322373 ATTAATATTA
*
20322383 TACATAAAT
1 TACATAACT
20322392 TACATAACT
1 TACATAACT
20322401 TA-ATTAA-T
1 TACA-TAACT
*
20322409 TA-AT-ATT
1 TACATAACT
20322416 ATACATAACT
1 -TACATAACT
20322426 TACATAACT
1 TACATAACT
20322435 TAC--AACT
1 TACATAACT
20322442 TACATAACT
1 TACATAACT
*
20322451 TACATTAATATT
1 TACA-T-A-ACT
*
20322463 ATACATAAAT
1 -TACATAACT
20322473 TACATAACT
1 TACATAACT
*
20322482 TACATTAATATT
1 TACA-T-A-ACT
*
20322494 ATACATAAAT
1 -TACATAACT
20322504 TACATAACT
1 TACATAACT
20322513 TA-ATTAA-T
1 TACA-TAACT
*
20322521 TA-AT-ATT
1 TACATAACT
20322528 ATACATAACT
1 -TACATAACT
20322538 TAC--AACT
1 TACATAACT
20322545 TACATAACT
1 TACATAACT
*
20322554 TACATTAATAT
1 TACA-TAA-CT
*
20322565 TACACATAAAT
1 T--ACATAACT
20322576 TACATAACT
1 TACATAACT
*
20322585 TACATTAATATT
1 TACA-T-A-ACT
*
20322597 ATACATAAAT
1 -TACATAACT
20322607 TACATAACT
1 TACATAACT
20322616 TA-ATTAA-T
1 TACA-TAACT
*
20322624 TA-AT-ATT
1 TACATAACT
20322631 ATACATAACT
1 -TACATAACT
20322641 TAC--AACT
1 TACATAACT
*
20322648 TACATTAATATT
1 TACA-T-A-ACT
*
20322660 ATACATAAAT
1 -TACATAACT
20322670 TACATAACT
1 TACATAACT
20322679 TACAT
1 TACAT
20322684 TAATACGACA
Statistics
Matches: 233, Mismatches: 18, Indels: 82
0.70 0.05 0.25
Matches are distributed among these distances:
6 3 0.01
7 27 0.12
8 21 0.09
9 115 0.49
10 20 0.09
11 13 0.06
12 15 0.06
13 19 0.08
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:20322443 original size:16 final size:16
Alignment explanation
Indices: 20322422--20322454 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20322412 TATTATACAT
20322422 AACTTACATAACTTAC
1 AACTTACATAACTTAC
20322438 AACTTACATAACTTAC
1 AACTTACATAACTTAC
20322454 A
1 A
20322455 TTAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:20322476 original size:31 final size:31
Alignment explanation
Indices: 20322471--20322688 Score: 269
Period size: 31 Copynumber: 6.7 Consensus size: 31
20322461 TTATACATAA
20322471 ATTACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTACATTAATATTATACATAA
*
20322502 ATTACATAACTTAATTAATTAATATTATACATAACTTACA
1 ATTACATAACTT-A--CATTAATATTATAC---A--TA-A
*
20322542 ACTTACATAACTTACATTAATATTACACATAA
1 A-TTACATAACTTACATTAATATTATACATAA
20322574 ATTACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTACATTAATATTATACATAA
*
20322605 ATTACATAACTTAATTAATTAATATTATACATAA
1 ATTACATAACTT-A--CATTAATATTATACATAA
*
20322639 CTTAC--AACTTACATTAATATTATACATAA
1 ATTACATAACTTACATTAATATTATACATAA
20322668 ATTACATAACTTACATTAATA
1 ATTACATAACTTACATTAATA
20322689 CGACATAACT
Statistics
Matches: 164, Mismatches: 8, Indels: 30
0.81 0.04 0.15
Matches are distributed among these distances:
29 21 0.13
31 68 0.41
32 9 0.05
33 2 0.01
34 34 0.21
35 1 0.01
37 1 0.01
38 12 0.07
39 2 0.01
40 3 0.02
41 11 0.07
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTACATAACTTACATTAATATTATACATAA
Found at i:20322572 original size:103 final size:103
Alignment explanation
Indices: 20322371--20322688 Score: 483
Period size: 103 Copynumber: 3.1 Consensus size: 103
20322361 CGTAGAAGCC
20322371 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATAACTT
1 ACATTAATATTATACATAAATTACATAACTTAATTAATT-A-A-TAT---T-A--TACATAACTT
20322436 ACAACTTACATAACTTACATTAATATTATACATAAATTACATAACTT
57 ACAACTTACATAACTTACATTAATATTATACATAAATTACATAACTT
20322483 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTAC
1 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTAC
*
20322548 ATAACTTACATTAATATTACACATAAATTACATAACTT
66 ATAACTTACATTAATATTATACATAAATTACATAACTT
20322586 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATAC---A--T--AACTTAC
1 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTAC
20322644 --AACTTACATTAATATTATACATAAATTACATAACTT
66 ATAACTTACATTAATATTATACATAAATTACATAACTT
20322680 ACATTAATA
1 ACATTAATA
20322689 CGACATAACT
Statistics
Matches: 204, Mismatches: 2, Indels: 18
0.91 0.01 0.08
Matches are distributed among these distances:
94 44 0.22
96 7 0.03
98 1 0.00
100 1 0.00
103 105 0.51
105 1 0.00
106 1 0.00
109 3 0.01
110 1 0.00
111 1 0.00
112 39 0.19
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (103 bp):
ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTAC
ATAACTTACATTAATATTATACATAAATTACATAACTT
Found at i:20322657 original size:29 final size:29
Alignment explanation
Indices: 20322607--20322688 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
20322597 ATACATAAAT
20322607 TACATAACTT--AA-TTA-ATTAATATTA
1 TACATAACTTACAACTTACATTAATATTA
20322632 TACATAACTTACAACTTACATTAATATTA
1 TACATAACTTACAACTTACATTAATATTA
*
20322661 TACATAAATTACATAACTTACATTAATA
1 TACATAACTTAC--AACTTACATTAATA
20322689 CGACATAACT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
25 10 0.20
27 2 0.04
28 3 0.06
29 21 0.42
31 14 0.28
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (29 bp):
TACATAACTTACAACTTACATTAATATTA
Found at i:20328431 original size:45 final size:44
Alignment explanation
Indices: 20328363--20328451 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 44
20328353 AGGAAGAAAG
20328363 ATGGAAACCCTATGACTCCTGAAGCTGCAGAAATTATGGTACGT
1 ATGGAAACCCTATGACTCCTGAAGCTGCAGAAATTATGGTACGT
*
20328407 NATGGAAACCCTATGACTCTTGAAGCTGCAGAAATTATGGTACGT
1 -ATGGAAACCCTATGACTCCTGAAGCTGCAGAAATTATGGTACGT
20328452 TTGCTTAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.26
Consensus pattern (44 bp):
ATGGAAACCCTATGACTCCTGAAGCTGCAGAAATTATGGTACGT
Found at i:20328975 original size:21 final size:21
Alignment explanation
Indices: 20328949--20328994 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20328939 CTACAACTTA
* * * *
20328949 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAC
20328970 AAGCAGAGGCAGCAACGAGAC
1 AAGCAGAGGCAGCAACGAGAC
20328991 AAGC
1 AAGC
20328995 TAAGGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.37, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAC
Found at i:20329085 original size:21 final size:21
Alignment explanation
Indices: 20329061--20329105 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20329051 CGAGAAAAGC
20329061 AGAGGCT-AAAGCGAGGGAAAT
1 AGAGGCTGAAA-CGAGGGAAAT
* *
20329082 AGAGGCTGCAACGAGGGAAGT
1 AGAGGCTGAAACGAGGGAAAT
20329103 AGA
1 AGA
20329106 ACAGCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.40, C:0.11, G:0.40, T:0.09
Consensus pattern (21 bp):
AGAGGCTGAAACGAGGGAAAT
Found at i:20329471 original size:43 final size:42
Alignment explanation
Indices: 20329410--20329704 Score: 371
Period size: 43 Copynumber: 7.0 Consensus size: 42
20329400 CAAAATTAGC
* *
20329410 GGCATTTTTTGCATAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCATTTTTTG-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
20329453 GGCATTTTTCGCCTAAGCGTCGCTAAAGACCATGGTCTATAGT
1 GGCATTTTTTG-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
20329496 GGCGTTTTTTGGTTAAGCGCCGCTAAAGACCATGGTCTGTAGT
1 GGCATTTTTT-GTTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
20329539 GGCGTTTTTTGGTTAAGCGCCGCTAAAGACCATTGTCTATAGT
1 GGCATTTTTT-GTTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
20329582 GGCATTTTTTGGTAAGCGCCGCTAAACA-CACGGTTTATAGT
1 GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
** *
20329623 GGCGGTTTTT-TTAAGCGCGGCTAAAGACCATGGTCTATAGT
1 GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
20329664 GGCATTTTTAT-TTAAGCGCCGCTACAGACCATGGTCTATAG
1 GGCATTTTT-TGTTAAGCGCCGCTAAAGACCATGGTCTATAG
20329705 CGGCGTTGTA
Statistics
Matches: 221, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
40 14 0.06
41 36 0.16
42 45 0.20
43 125 0.57
44 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:20334942 original size:13 final size:12
Alignment explanation
Indices: 20334924--20334965 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
20334914 TGTGAGCGAG
20334924 AAAAGAACATTGA
1 AAAAGAA-ATTGA
20334937 AAAAGAAATTG-
1 AAAAGAAATTGA
20334948 -AAAGAAA-TGA
1 AAAAGAAATTGA
20334958 AAAAGAAA
1 AAAAGAAA
20334966 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:20335025 original size:12 final size:12
Alignment explanation
Indices: 20335008--20335086 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
20334998 AGTGAAAAGC
20335008 AAAAAGAGATTG
1 AAAAAGAGATTG
*
20335020 AAAAAGAAATTG
1 AAAAAGAGATTG
* ***
20335032 AAAGAGAAGAAAA
1 AAAAAG-AGATTG
*
20335045 AAAAAGAG-TGG
1 AAAAAGAGATTG
* *
20335056 AAAAAGAAACTG
1 AAAAAGAGATTG
*
20335068 AAAAAGAGTTTG
1 AAAAAGAGATTG
*
20335080 CAAAAGA
1 AAAAAGA
20335087 AACGAGTGAA
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
11 7 0.15
12 34 0.71
13 7 0.15
ACGTcount: A:0.63, C:0.03, G:0.23, T:0.11
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:20346634 original size:27 final size:26
Alignment explanation
Indices: 20346593--20346654 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
20346583 AAAGGTTGTT
*
20346593 AAATGATCAAAATACCCTCAAAAGGTA
1 AAATGACCAAAATACCC-CAAAAGGTA
* * *
20346620 AAATGACCAACATACCCCTAGAGGTA
1 AAATGACCAAAATACCCCAAAAGGTA
*
20346646 AAATTACCA
1 AAATGACCA
20346655 TTTTACCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.48, C:0.23, G:0.11, T:0.18
Consensus pattern (26 bp):
AAATGACCAAAATACCCCAAAAGGTA
Found at i:20351058 original size:48 final size:46
Alignment explanation
Indices: 20351005--20351110 Score: 140
Period size: 48 Copynumber: 2.3 Consensus size: 46
20350995 ACAATAATGT
**
20351005 AGATAAACTGCCACATAATCAAAATTGTGGACAAGCCACCAAAATCGC
1 AGATAAACTGCCACATAATC-AAATCATGGACAAGCCACC-AAATCGC
* * *
20351053 AGATAAACTACCACATAATCAAATCATGGACAAGCCACCACATTGC
1 AGATAAACTGCCACATAATCAAATCATGGACAAGCCACCAAATCGC
*
20351099 AAATAAACTGCC
1 AGATAAACTGCC
20351111 CCATTCTGCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 15 0.29
47 17 0.33
48 19 0.37
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.17
Consensus pattern (46 bp):
AGATAAACTGCCACATAATCAAATCATGGACAAGCCACCAAATCGC
Found at i:20352735 original size:53 final size:53
Alignment explanation
Indices: 20352664--20352767 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
20352654 CAAGGAAAGA
20352664 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
1 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
* **
20352717 TGAAAATCATGAATTAGCTCGATTGTACTTTTACGCTCTAGTTGTCAAGCT
1 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCT
20352768 AAGTTCATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (53 bp):
TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
Found at i:20352879 original size:20 final size:19
Alignment explanation
Indices: 20352854--20352920 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
20352844 ACTGAATTAT
20352854 CCCCTGTTTGTACTTAGGTA
1 CCCCTGTTTGTACTTA-GTA
* * *
20352874 CCCCTGAATTGCACATACGTA
1 CCCCTG-TTTGTACTTA-GTA
* *
20352895 CCCTTATTTGTACTTTAGTA
1 CCCCTGTTTGTAC-TTAGTA
20352915 CCCCTG
1 CCCCTG
20352921 AATTACACAT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (19 bp):
CCCCTGTTTGTACTTAGTA
Found at i:20352897 original size:21 final size:21
Alignment explanation
Indices: 20352871--20352934 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
20352861 TTGTACTTAG
20352871 GTACCCCTGAATTGCACATAC
1 GTACCCCTGAATTGCACATAC
* * * *
20352892 GTA-CCCTTATTTGTACTTTA-
1 GTACCCCTGAATTGCAC-ATAC
*
20352912 GTACCCCTGAATTACACATAC
1 GTACCCCTGAATTGCACATAC
20352933 GT
1 GT
20352935 GCCCATGTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
GTACCCCTGAATTGCACATAC
Found at i:20352917 original size:41 final size:40
Alignment explanation
Indices: 20352860--20352960 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 40
20352850 TTATCCCCTG
* *
20352860 TTTGTACTTAGGTACCCCTGAATTGCACATACGTACCCTTA
1 TTTGTACTTA-GTACCCCTGAATTACACATACGTACCCATA
* *
20352901 TTTGTACTTTAGTACCCCTGAATTACACATACGTGCCCATG
1 TTTGTAC-TTAGTACCCCTGAATTACACATACGTACCCATA
*
20352942 TTTGTACATCAGTACCCCT
1 TTTGTAC-TTAGTACCCCT
20352961 CATATGTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 50 0.94
42 3 0.06
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.35
Consensus pattern (40 bp):
TTTGTACTTAGTACCCCTGAATTACACATACGTACCCATA
Found at i:20353018 original size:41 final size:40
Alignment explanation
Indices: 20352961--20353063 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 40
20352951 CAGTACCCCT
* *
20352961 CATATGTGTCCCTGTTTGTACTTC-AGTACCCCTAAATTGCA
1 CATATGTG-CCCTGTTTGCACTTCGA-TACCCCTAAATAGCA
* *
20353002 CATATGTGCCCCTGTTTGCACTTCGATACCCTTGAATAGCA
1 CATATGTG-CCCTGTTTGCACTTCGATACCCCTAAATAGCA
* *
20353043 CATACGTGCCCTGTTTACACT
1 CATATGTGCCCTGTTTGCACT
20353064 CCGGTAACTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 12 0.22
41 41 0.76
42 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (40 bp):
CATATGTGCCCTGTTTGCACTTCGATACCCCTAAATAGCA
Found at i:20359925 original size:41 final size:40
Alignment explanation
Indices: 20359787--20359950 Score: 168
Period size: 41 Copynumber: 4.0 Consensus size: 40
20359777 TGTAAACTGA
* * *
20359787 GGCATGTATATGCTATTCAAGGGTACCAAAGTACAAATAAA
1 GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAAT-AG
* * * *
20359828 GGCATGTATGTGCAATTTAAGGGTACCGAAGTACAAATAG
1 GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAATAG
* * *
20359868 GGCACGTATGTGCAATTCAATGGTACCAAAGTACAAACATG
1 GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAATA-G
* * * *
20359909 GGCACGTATATACAATTC-AGGCGTACCGAAGTGCAAACAG
1 GGCACGTATATGCAATTCAAGG-GTACCAAAGTACAAATAG
20359949 GG
1 GG
20359951 GATAATTCAA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
40 40 0.38
41 66 0.62
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (40 bp):
GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAATAG
Found at i:20359936 original size:81 final size:81
Alignment explanation
Indices: 20359787--20359950 Score: 195
Period size: 81 Copynumber: 2.0 Consensus size: 81
20359777 TGTAAACTGA
* * * * * *
20359787 GGCATGTATATGCTATTCAAGGGTACCAAAGTACAAATAAAGGCATGTATGTGCAATTTAAGGGT
1 GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAAAGGCACGTATATACAATTTAAGGGT
*
20359852 ACCGAAGTACAAATAG
66 ACCGAAGTACAAACAG
* * ** *
20359868 GGCACGTATGTGCAATTCAATGGTACCAAAGTACAAACATGGGCACGTATATACAA-TTCAGGCG
1 GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAAAGGCACGTATATACAATTTAAGG-G
*
20359932 TACCGAAGTGCAAACAG
65 TACCGAAGTACAAACAG
20359949 GG
1 GG
20359951 GATAATTCAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
80 5 0.07
81 64 0.93
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (81 bp):
GGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAAAGGCACGTATATACAATTTAAGGGT
ACCGAAGTACAAACAG
Found at i:20363487 original size:16 final size:16
Alignment explanation
Indices: 20363456--20363500 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
20363446 AAATATCTTA
20363456 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
20363470 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
20363486 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
20363501 CCAAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:20363498 original size:17 final size:16
Alignment explanation
Indices: 20363453--20363500 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
20363443 AATAAATATC
20363453 TTAAATTAATTT-T-AA
1 TTAAA-TAATTTCTCAA
*
20363468 TTAATTAATTTCTCAA
1 TTAAATAATTTCTCAA
20363484 TTAAATAATTTTCTCAA
1 TTAAATAA-TTTCTCAA
20363501 CCAAATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 9 0.32
17 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATAATTTCTCAA
Found at i:20366547 original size:56 final size:50
Alignment explanation
Indices: 20366237--20366583 Score: 417
Period size: 50 Copynumber: 6.8 Consensus size: 50
20366227 GATAATAACA
* * ** * * * *
20366237 TGCCAAAGCCATATCCCAGACATGGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * ** * *
20366286 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * ** *
20366336 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
20366386 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
20366436 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
20366486 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G
* *
20366541 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
20366584 TTACCCAAAT
Statistics
Matches: 265, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
49 40 0.15
50 178 0.67
53 5 0.02
54 1 0.00
55 1 0.00
56 40 0.15
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:20377162 original size:48 final size:48
Alignment explanation
Indices: 20377110--20377201 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
20377100 AAGTACCCTA
* * *
20377110 CTTGCCAGGTACCCAACTC-ACCATGTAGCCAGCTCATTGGATAGCCAG
1 CTTGCCAAGTACCCAAC-CGACCAGGTAGCCAGCTCACTGGATAGCCAG
* *
20377158 CTTGCCAAGTACCCAACCGACTAGGTAGCCAGCTCGCTGGATAG
1 CTTGCCAAGTACCCAACCGACCAGGTAGCCAGCTCACTGGATAG
20377202 AGGTTCTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 37 0.97
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (48 bp):
CTTGCCAAGTACCCAACCGACCAGGTAGCCAGCTCACTGGATAGCCAG
Found at i:20382492 original size:50 final size:50
Alignment explanation
Indices: 20382412--20382605 Score: 180
Period size: 50 Copynumber: 3.8 Consensus size: 50
20382402 CCAAACATAC
* * * **
20382412 TGCCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
20382462 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
20382512 TG-C---GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
20382564 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
20382606 TTCCCAAATG
Statistics
Matches: 117, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
46 34 0.29
49 3 0.03
50 42 0.36
52 3 0.03
53 1 0.01
56 34 0.29
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:20386830 original size:3 final size:3
Alignment explanation
Indices: 20386822--20386854 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20386812 AAATTAACAA
20386822 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20386855 CAAAACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20386985 original size:24 final size:26
Alignment explanation
Indices: 20386940--20387001 Score: 92
Period size: 24 Copynumber: 2.4 Consensus size: 26
20386930 AAAAAAAATA
*
20386940 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATA-TATAACTATTTTTATTT
20386967 ACCAAAATATAT-A-TATTTTTATTT
1 ACCAAAATATATAACTATTTTTATTT
20386991 ACCAAAATATA
1 ACCAAAATATA
20387002 CCAAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 21 0.62
25 1 0.03
26 3 0.09
27 9 0.26
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (26 bp):
ACCAAAATATATAACTATTTTTATTT
Found at i:20387160 original size:18 final size:18
Alignment explanation
Indices: 20387139--20387193 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
20387129 GGGAAAGAAA
20387139 GAAAGAAAGGAAGGAGAG
1 GAAAGAAAGGAAGGAGAG
**
20387157 GAAAGAAA-GAAAAAGAAG
1 GAAAGAAAGGAAGGAG-AG
20387175 GAAAGAAAAGGACAGGAGA
1 GAAAG-AAAGGA-AGGAGA
20387194 AGAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 3 0.10
20 3 0.10
21 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGGAAGGAGAG
Found at i:20387173 original size:10 final size:10
Alignment explanation
Indices: 20387158--20387286 Score: 52
Period size: 10 Copynumber: 12.6 Consensus size: 10
20387148 GAAGGAGAGG
20387158 AAAGAAAGAA
1 AAAGAAAGAA
*
20387168 AAAGAAGGAA
1 AAAGAAAGAA
*
20387178 AGAA-AAGGACA
1 A-AAGAAAGA-A
**
20387189 GGAGAAGAGAA
1 AAAGAA-AGAA
20387200 AAA-AAAGAA
1 AAAGAAAGAA
20387209 AGAAG-AAGAA
1 A-AAGAAAGAA
* * *
20387219 GAGGAAAGGA
1 AAAGAAAGAA
* *
20387229 GAAGAAAAAA
1 AAAGAAAGAA
20387239 GAAAGAAA-AA
1 -AAAGAAAGAA
*
20387249 GAAGGAAAGAA
1 -AAAGAAAGAA
20387260 AAAGAAAGGAGA
1 AAAGAAA-GA-A
*
20387272 AGAGAAA-AA
1 AAAGAAAGAA
20387281 AAAGAA
1 AAAGAA
20387287 GAAGACGAGG
Statistics
Matches: 91, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
9 13 0.14
10 52 0.57
11 17 0.19
12 9 0.10
ACGTcount: A:0.71, C:0.01, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:20387175 original size:27 final size:27
Alignment explanation
Indices: 20387121--20387177 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
20387111 GGTGGGGGGA
*
20387121 GAAGGAGAGGGAAAGAAAGAAAGAAAG
1 GAAGGAGAGGGAAAGAAAGAAAAAAAG
20387148 GAAGGAGA-GGAAAGAAAGAAAAAGAAG
1 GAAGGAGAGGGAAAGAAAGAAAAA-AAG
20387175 GAA
1 GAA
20387178 AGAAAAGGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (27 bp):
GAAGGAGAGGGAAAGAAAGAAAAAAAG
Found at i:20387247 original size:78 final size:73
Alignment explanation
Indices: 20387158--20387320 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 73
20387148 GAAGGAGAGG
* *
20387158 AAAGAAAGAAAAAGAAGGAAAGAAAAGGACAGGAGAAGAGAAAAAAAAGAAAGAAGAAGAAGAGG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAG-AAGAAGAAG-AG-GG
20387223 AAAGGAGAAGAAA
63 -AAGGA-AAGAAA
*
20387236 AAAGAAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAGAAGACGAGGGAAG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAGAAGAAGAGGGAAG
*
20387301 GAAGGAAA
66 GAAAGAAA
20387309 AAA-AAAGAAAAA
1 AAAGAAAGAAAAA
20387321 AATGTAATTT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
72 9 0.11
73 8 0.10
74 5 0.06
75 2 0.02
76 2 0.02
77 8 0.10
78 47 0.58
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.00
Consensus pattern (73 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAGAAGAAGAGGGAAG
GAAAGAAA
Found at i:20387265 original size:31 final size:32
Alignment explanation
Indices: 20387132--20387280 Score: 110
Period size: 32 Copynumber: 4.6 Consensus size: 32
20387122 AAGGAGAGGG
* *
20387132 AAAGAAAGAAAGAAAG-GAAGGAGAGGAAAGAA
1 AAAGAAA-AAAGAAAGAAAAAGAGAGGAAAGAA
* * *
20387164 AGAA-AAAGAAGGAAAGAAAAGGACAGGAGAAG-A
1 A-AAGAAA-AAAGAAAGAAAAAGAGAGGA-AAGAA
* * *
20387197 GAA-AAAAAAGAAAGAAGAAGAAGAGGAAAGGA
1 AAAGAAAAAAGAAAGAAAAAG-AGAGGAAAGAA
*
20387229 GAAGAAAAAAGAAAGAAAAAGA-AGGAAAGAA
1 AAAGAAAAAAGAAAGAAAAAGAGAGGAAAGAA
**
20387260 AAAGAAAGGAGAAGAGAAAAA
1 AAAGAAAAAAGAA-AGAAAAA
20387281 AAAGAAGAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
31 32 0.33
32 34 0.35
33 28 0.29
34 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (32 bp):
AAAGAAAAAAGAAAGAAAAAGAGAGGAAAGAA
Found at i:20387267 original size:4 final size:4
Alignment explanation
Indices: 20387131--20387260 Score: 53
Period size: 4 Copynumber: 32.0 Consensus size: 4
20387121 GAAGGAGAGG
* * *
20387131 GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
*
20387179 GAAAA GGACAG GAGAA GAGAA -AAA -AAA GAAA G-AA G-AA GAAGA GGAAA
1 G-AAA -GA-AA GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA
*
20387226 GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20387261 AAGAAAGGAG
Statistics
Matches: 102, Mismatches: 9, Indels: 30
0.72 0.06 0.21
Matches are distributed among these distances:
3 22 0.22
4 47 0.46
5 26 0.25
6 7 0.07
ACGTcount: A:0.68, C:0.01, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20387270 original size:41 final size:41
Alignment explanation
Indices: 20387130--20387291 Score: 181
Period size: 41 Copynumber: 4.0 Consensus size: 41
20387120 AGAAGGAGAG
* * *
20387130 GGAAAGAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAA
1 GGAAAG-AA-AAAGAAAGG-AGAAGAGAAAAAAAAGAAAAAGAA
* *
20387174 GGAAAGAAAAGGACAGGAGAAGAGAAAAAAAAG--AAAGAA
1 GGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAAAAGAA
* *
20387213 -G-AAGAAGAGGAAAGGAGAAGA-AAAAAGAAAGAAAAAGAA
1 GGAAAGAAAAAGAAAGGAGAAGAGAAAAA-AAAGAAAAAGAA
*
20387252 GGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAGAAGA
1 GGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAAAAGA
20387292 CGAGGGAAGG
Statistics
Matches: 102, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
36 5 0.05
37 22 0.22
38 1 0.01
39 12 0.12
40 1 0.01
41 41 0.40
42 12 0.12
43 2 0.02
44 6 0.06
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (41 bp):
GGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAGAAAAAGAA
Found at i:20388077 original size:27 final size:27
Alignment explanation
Indices: 20388047--20388102 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
20388037 AGAGAGGGTG
* * *
20388047 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGACGGAACCA
20388074 ATGGAGAGGAATAAAAAGACGGAACCA
1 ATGGAGAGGAATAAAAAGACGGAACCA
20388101 AT
1 AT
20388103 ATGTGGCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAGACGGAACCA
Found at i:20391672 original size:18 final size:18
Alignment explanation
Indices: 20391649--20391685 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20391639 ATCCCAATGA
20391649 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
20391667 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
20391685 T
1 T
20391686 TACCACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.46, G:0.08, T:0.35
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:20392194 original size:9 final size:9
Alignment explanation
Indices: 20392170--20392206 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20392160 TGAGTTTTCG
*
20392170 AATTCAAAT
1 AATTCGAAT
*
20392179 AACTCGAAT
1 AATTCGAAT
20392188 AATTCGAAT
1 AATTCGAAT
20392197 AATTCGAAT
1 AATTCGAAT
20392206 A
1 A
20392207 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20393798 original size:3 final size:3
Alignment explanation
Indices: 20393790--20393824 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20393780 TCTTAATACT
20393790 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
20393825 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20394654 original size:23 final size:23
Alignment explanation
Indices: 20394628--20394673 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20394618 GCGTAACTGC
20394628 TGTATAGTAATAGGGTGCCCGAA
1 TGTATAGTAATAGGGTGCCCGAA
* *
20394651 TGTATAGTTATAGGGTGCGCGAA
1 TGTATAGTAATAGGGTGCCCGAA
20394674 GCCCACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (23 bp):
TGTATAGTAATAGGGTGCCCGAA
Found at i:20394900 original size:26 final size:28
Alignment explanation
Indices: 20394868--20394931 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
20394858 GTTTTTTTGT
20394868 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
20394894 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
20394922 ATATTTTGGT
1 ATATTTTGGT
20394932 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:20395245 original size:21 final size:19
Alignment explanation
Indices: 20395214--20395259 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
20395204 AAAAAACCTT
**
20395214 AAAAATATTTAAAATTGCA
1 AAAAATATTTAAAATTAAA
20395233 AAAAATCATTTTAAAATTAAA
1 AAAAAT-A-TTTAAAATTAAA
20395254 AAAAAT
1 AAAAAT
20395260 TACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATTTAAAATTAAA
Found at i:20395726 original size:8 final size:8
Alignment explanation
Indices: 20395715--20395763 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
20395705 TTTTATTATT
20395715 TAATTTTA
1 TAATTTTA
20395723 TAATTTTA
1 TAATTTTA
20395731 TAATTTTAAA
1 TAATTTT--A
20395741 TAATTTTAA
1 TAATTTT-A
*
20395750 TGATTTT-
1 TAATTTTA
20395757 TAATTTT
1 TAATTTT
20395764 TTAAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.16
8 15 0.41
9 8 0.22
10 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
TAATTTTA
Found at i:20395775 original size:20 final size:21
Alignment explanation
Indices: 20395730--20395797 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
20395720 TTATAATTTT
* *
20395730 ATAATTTTAAATAATTTT--A
1 ATAATTTTTAATATTTTTAAA
*
20395749 ATGATTTTTAAT-TTTTTAAA
1 ATAATTTTTAATATTTTTAAA
**
20395769 ATAATTTTTTGTATTTTTAAA
1 ATAATTTTTAATATTTTTAAA
20395790 ATAATTTT
1 ATAATTTT
20395798 CCATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.10
19 10 0.25
20 10 0.25
21 16 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (21 bp):
ATAATTTTTAATATTTTTAAA
Found at i:20409505 original size:37 final size:36
Alignment explanation
Indices: 20409454--20409563 Score: 113
Period size: 37 Copynumber: 3.0 Consensus size: 36
20409444 ATTCAAAAAA
*
20409454 TAATATTATTTTAATAGTTTAATATTTAATTTAATT
1 TAATATTATCTTAATAGTTTAATATTTAATTTAATT
*
20409490 TAATACTTATCTTAATAGTATT-CTA-TTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTTAATTTAAT-T
20409527 TAAAGTAATTATCTTAATA--TTAA-ATTTAATTTAATT
1 T-AA-T-ATTATCTTAATAGTTTAATATTTAATTTAATT
20409563 T
1 T
20409564 TTATCTTGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
36 20 0.32
37 26 0.41
38 4 0.06
39 12 0.19
40 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTTAATTTAATT
Found at i:20409812 original size:25 final size:26
Alignment explanation
Indices: 20409762--20409812 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
20409752 AGTTGTAGAG
*
20409762 AGAAAATTCTCTCAAGAGATTATTTC
1 AGAAAATTCTCTAAAGAGATTATTTC
* *
20409788 AGAAAATT-TCTAAAGATATTTTTTC
1 AGAAAATTCTCTAAAGAGATTATTTC
20409813 TAATTTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTC
Found at i:20413686 original size:21 final size:21
Alignment explanation
Indices: 20413648--20413700 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20413638 ATGACAATAG
20413648 AAGCTCG-AA-AGCTGAACAA
1 AAGCTCGTAAGAGCTGAACAA
* *
20413667 AAGCTCGTAAGAGCTTAACAG
1 AAGCTCGTAAGAGCTGAACAA
*
20413688 AAGCTCATAAGAG
1 AAGCTCGTAAGAG
20413701 TTGATCTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 2 0.07
21 20 0.69
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (21 bp):
AAGCTCGTAAGAGCTGAACAA
Found at i:20415436 original size:29 final size:29
Alignment explanation
Indices: 20415401--20415458 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20415391 ATAATACATA
20415401 CATGATAATACATGTAAAAAGTTGAAATG
1 CATGATAATACATGTAAAAAGTTGAAATG
20415430 CATGATAATACATGTAAAAAGTTGAAATG
1 CATGATAATACATGTAAAAAGTTGAAATG
20415459 GGTGAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (29 bp):
CATGATAATACATGTAAAAAGTTGAAATG
Found at i:20415567 original size:11 final size:11
Alignment explanation
Indices: 20415546--20415611 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 11
20415536 GATTAATAAT
*
20415546 ATATCATAAATG
1 ATAT-ATAAATA
20415558 ATATATAAATA
1 ATATATAAATA
20415569 ATAT-TAAAT-
1 ATATATAAATA
* *
20415578 TTACATAAA-A
1 ATATATAAATA
20415588 ATATATAGAATA
1 ATATATA-AATA
*
20415600 ATACAT-AATA
1 ATATATAAATA
20415610 AT
1 AT
20415612 TTGAAGAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 2 0.05
10 20 0.45
11 12 0.27
12 10 0.23
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (11 bp):
ATATATAAATA
Found at i:20415659 original size:22 final size:23
Alignment explanation
Indices: 20415626--20415684 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
20415616 AGAATGATAC
*
20415626 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
20415647 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
20415671 GTGATAAATTTAAA
1 ATGATAAATTTAAA
20415685 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:20416579 original size:10 final size:10
Alignment explanation
Indices: 20416566--20416591 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20416556 AAATAAAAAT
20416566 AAAAATACAA
1 AAAAATACAA
20416576 AAAAATACAA
1 AAAAATACAA
20416586 AAAAAT
1 AAAAAT
20416592 CCTGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATACAA
Found at i:20417284 original size:50 final size:50
Alignment explanation
Indices: 20417216--20417847 Score: 427
Period size: 50 Copynumber: 12.6 Consensus size: 50
20417206 GTGATGTCGA
* * * * * *
20417216 GGAAGCAAGACTCGCTGTTGTAGCTTCAATCTGTTCCACTACACTGCCTG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * *
20417266 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATG-TTGG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCT-G
** * * ** *
20417316 GGAAGCAAGATTAACCGTTGT-GACTTTAATCTGTTTCACTGCACCGCCAG
1 GGAAGCAAGATTCGCTGTTGTAG-CTTTAATCTTTTTCACTGCAATGCCTG
** * * * *
20417366 GGAAATAAGATTCGTTGTTGTAGCTTTAATCTTTTTAACTACAATGTC-G
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * * * * ** *
20417415 GGAAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGCACCGCTTG
1 GG-AAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * * * *
20417466 AGAAGTAAGATTCGCTGTTGTATCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * * * *
20417516 GGAAGCAAGGTTCGCTATTGTGGCTTTAATCTATTCCACTGC-ATCCCCTAG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAAT-GCCT-G
* * * *
20417567 GG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * * * * ** *
20417616 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * **
20417666 GGAAGTAAGATTCGCTGTTCTAGCTTTAATCTTTTTAACTGCAATATC-G
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
* * * * * *
20417715 GGAAAGCAAGATTCACCGATGTGGCTTTAATCTGTTTCACTGC-ATCGCTTG
1 GG-AAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAAT-GCCTG
* * * * * *
20417766 GGGAGTAAGATTCGTTGTTGT-GACTTTAATCCTTTTAACTGCAATGTC-G
1 GGAAGCAAGATTCGCTGTTGTAG-CTTTAATCTTTTTCACTGCAATGCCTG
* * *
20417815 GGAAGGCAAGATTCACCGTTGTGGCTTTAATCT
1 GGAA-GCAAGATTCGCTGTTGTAGCTTTAATCT
20417848 GCTCCATTGC
Statistics
Matches: 429, Mismatches: 136, Indels: 34
0.72 0.23 0.06
Matches are distributed among these distances:
49 20 0.05
50 395 0.92
51 14 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (50 bp):
GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTTTTTCACTGCAATGCCTG
Found at i:20417323 original size:100 final size:100
Alignment explanation
Indices: 20417189--20417865 Score: 851
Period size: 100 Copynumber: 6.8 Consensus size: 100
20417179 TAACTCGTAA
* ** * * * * * *
20417189 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGACTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* *
20417254 CTACACTGCCTGGGAAGTAAGATTCACTGTTGTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
20417289 CTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTAACCGTTGTGACTTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * * *
20417354 CTGCACCGCCAGGGAAATAAGATTCGTTGTTGTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
20417389 CTTTAATCTTTTTAACTACAATGTCGGGAAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * * *
20417454 CTGCACCGCTTGAGAAGTAAGATTCGCTGTTGTAT
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * ** *
20417489 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCTATTGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
*
20417554 CTGCA-TCCCCTAGGG-AGTAAGATTCGCTGTTGTAG
66 CTGCACT-GCCT-GGGAAGTAAGATTCGCTGTTGTAG
*
20417589 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * *
20417654 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTCTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
20417689 CTTTAATCTTTTTAACTGCAATATCGGGAAAGCAAGATTCACCGATGTGGCTTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * *
20417754 CTGCA-TCGCTTGGGGAGTAAGATTCGTTGTTGT-G
66 CTGCACT-GCCTGGGAAGTAAGATTCGCTGTTGTAG
* *
20417788 ACTTTAATCCTTTTAACTGCAATGTC-GGGAAGGCAAGATTCACCGTTGTGGCTTTAATCTGCTC
1 -CTTTAATCTTTTTAACTGCAATGTCGGGGAA-GCAAGATTCACCGTTGTGGCTTTAATCTGTTC
*
20417852 CATTGCACTGCCTG
64 CACTGCACTGCCTG
20417866 AGAGGGTGAA
Statistics
Matches: 497, Mismatches: 72, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
99 8 0.02
100 486 0.98
101 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
Found at i:20419172 original size:13 final size:13
Alignment explanation
Indices: 20419156--20419185 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20419146 CATTTTTACT
*
20419156 TTTTCCTTTTTCA
1 TTTTCCATTTTCA
20419169 TTTTCCATTTTCA
1 TTTTCCATTTTCA
20419182 TTTT
1 TTTT
20419186 TCGCTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCCATTTTCA
Found at i:20424568 original size:22 final size:23
Alignment explanation
Indices: 20424535--20424593 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
20424525 AGAATGATAC
*
20424535 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
20424556 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
20424580 GTGATAAATTTAAA
1 ATGATAAATTTAAA
20424594 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:20425737 original size:24 final size:22
Alignment explanation
Indices: 20425681--20425739 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
20425671 AGAATGATAC
*
20425681 ATGA-AAACTTAAAATAATTAT
1 ATGATAAATTTAAAATAATTAT
*
20425702 ATGATAAGTTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT--TAT
*
20425726 GTGATAAATTTAAA
1 ATGATAAATTTAAA
20425740 CAACATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 4 0.13
22 12 0.39
24 15 0.48
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (22 bp):
ATGATAAATTTAAAATAATTAT
Found at i:20431732 original size:30 final size:31
Alignment explanation
Indices: 20431693--20431752 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20431683 GGAGGTGGGA
*
20431693 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
20431724 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
20431753 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:20431976 original size:9 final size:9
Alignment explanation
Indices: 20431962--20431998 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20431952 TATAGTTTGA
20431962 TATTCGAAT
1 TATTCGAAT
20431971 TATTCGAAT
1 TATTCGAAT
*
20431980 TATTCGAGT
1 TATTCGAAT
20431989 TATTCGAAT
1 TATTCGAAT
20431998 T
1 T
20431999 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20432423 original size:17 final size:18
Alignment explanation
Indices: 20432389--20432424 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20432379 TGAATTTTTA
20432389 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
20432407 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
20432424 T
1 T
20432425 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:20436711 original size:10 final size:9
Alignment explanation
Indices: 20436694--20436743 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
20436684 AAGTTAATTT
20436694 AATTTTTAA
1 AATTTTTAA
20436703 AATTTTTTAA
1 AA-TTTTTAA
*
20436713 AAATTTTACTA
1 AATTTTTA--A
*
20436724 TATTTTTAA
1 AATTTTTAA
20436733 AATTTTTAA
1 AATTTTTAA
20436742 AA
1 AA
20436744 AAATTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 18 0.53
10 9 0.26
11 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTTTAA
Found at i:20436751 original size:24 final size:24
Alignment explanation
Indices: 20436724--20436771 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20436714 AATTTTACTA
20436724 TATTTTTAAAATTTTTAAAA-AAAT
1 TATTTTT-AAATTTTTAAAATAAAT
* *
20436748 TATTTTTTATTTTTTAAAATAAAT
1 TATTTTTAAATTTTTAAAATAAAT
20436772 AATAATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTTTAAATTTTTAAAATAAAT
Found at i:20437092 original size:11 final size:11
Alignment explanation
Indices: 20437076--20437105 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20437066 ATTTTATTAA
20437076 TATAAATATTT
1 TATAAATATTT
20437087 TATAAATATTT
1 TATAAATATTT
*
20437098 TATTAATA
1 TATAAATA
20437106 AATAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATAAATATTT
Found at i:20446007 original size:17 final size:16
Alignment explanation
Indices: 20445987--20446019 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
20445977 TTTTAATAAA
20445987 TAAAATAATATTAATAT
1 TAAAATAATA-TAATAT
20446004 TAAAATAATATAATAT
1 TAAAATAATATAATAT
20446020 AAATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATAATATAATAT
Found at i:20446009 original size:22 final size:22
Alignment explanation
Indices: 20445984--20446026 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20445974 AAATTTTAAT
*
20445984 AAATAAAATAATATTAATATTA
1 AAATAAAATAATATAAATATTA
*
20446006 AAATAATATAATATAAATATT
1 AAATAAAATAATATAAATATT
20446027 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAAAATAATATAAATATTA
Found at i:20448053 original size:33 final size:33
Alignment explanation
Indices: 20447959--20448054 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
20447949 AACAGAGCCA
* * *
20447959 GTGTTTATTGTCCCGATGGACTTTA-TTTGTTTT
1 GTGTTTACTGTCCCAATGGAC-TTACTTTGTTTC
**
20447992 GTGTTTACTGTCCCAGCGGACTTACTTTGTTTC
1 GTGTTTACTGTCCCAATGGACTTACTTTGTTTC
*
20448025 GTGTTTACTGTCCCAATGGACTTGCTTTGT
1 GTGTTTACTGTCCCAATGGACTTACTTTGT
20448055 GGATGCCATG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 3 0.06
33 51 0.94
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
GTGTTTACTGTCCCAATGGACTTACTTTGTTTC
Found at i:20453119 original size:36 final size:36
Alignment explanation
Indices: 20453071--20453183 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
20453061 GTCGGTTATC
*
20453071 CGACTAGCGTTGGGTGCAATAATTTGTCGACTCGTT
1 CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
* * * * *
20453107 CGACTAGTGTT-GG-GCAA-AACTATTTTCG-GTTATC
1 CGACTAGCGTTGGGTGCAATAA-T-TTGTCGACTTGTT
* *
20453141 CGACTAGCGTTGAGTGCAATAATTTGTTGACTTGTT
1 CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
20453177 CGACTAG
1 CGACTAG
20453184 TGCTAGGCAT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
33 2 0.03
34 17 0.29
35 12 0.21
36 25 0.43
37 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (36 bp):
CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
Found at i:20453178 original size:70 final size:71
Alignment explanation
Indices: 20453057--20453217 Score: 229
Period size: 70 Copynumber: 2.3 Consensus size: 71
20453047 GATGAGTAAA
* * *
20453057 TATCG-TCGGTTATCCGACTAGCGTTGGGTGCAATAATTTGTCGACTCGTTCGACTAGTGTTGGG
1 TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
20453121 CAAAAC
66 CAAAAC
* * *
20453127 TAT-TTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTTGACTTGTTCGACTAGTGCTAGG
1 TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
*
20453191 CATAAC
66 CAAAAC
*
20453197 TATCGTT-GGTTATCTGACTAG
1 TATCGTTCGGTTATCCGACTAG
20453218 AGCTAGGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
70 78 0.98
71 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (71 bp):
TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
CAAAAC
Found at i:20470383 original size:36 final size:36
Alignment explanation
Indices: 20470343--20470414 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
20470333 ATGTAATTGC
* ** * *
20470343 TAATTCAATTGCATGGATTTTTATGGATGTATATGT
1 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
20470379 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
1 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
20470415 ATTTATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (36 bp):
TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
Found at i:20470531 original size:36 final size:35
Alignment explanation
Indices: 20470481--20470590 Score: 116
Period size: 34 Copynumber: 3.1 Consensus size: 35
20470471 AGTAACTATC
* *
20470481 GTCGATTATCTGACTAGCGCTGGGCGCAATAATTT
1 GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
* * * * *
20470516 GTCGTCTTGTTTGACTAGTGTTGGGCACAACT-A-TC
1 GTCG-ATTGTCTGACTAGCGCTGGGCACAA-TAATTT
*
20470551 GTCGATTGTCTGACTAGCACTGGGCACAATAATTT
1 GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
20470586 GTCGA
1 GTCGA
20470591 CTATTTTGGC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
33 1 0.02
34 21 0.36
35 15 0.26
36 20 0.34
37 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (35 bp):
GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
Found at i:20470587 original size:70 final size:70
Alignment explanation
Indices: 20470474--20470752 Score: 271
Period size: 70 Copynumber: 4.0 Consensus size: 70
20470464 ACGGATGAGT
*
20470474 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGTCTTGTTTGACTAGTGTTG
1 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTTGACTAGTGTTG
20470539 GGCAC
66 GGCAC
* * * * *
20470544 AACTATCGTCGATTGTCTGACTAGCACTGGGCACAATAATTTGTCGACTAT-TTTGGCTAATGTT
1 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACT-TGTTTGACTAGTGTT
*
20470608 GGGTAC
65 GGGCAC
* * * * * * * ***
20470614 AAATATCGTCGGTTATCCGGCTAGCGCTTGGCGCAATAATTTGTCGACTCGTTCGACTA--GCAA
1 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTTGACTAGTGTTG
20470677 GGCAC
66 GGCAC
* * * * * * **
20470682 AACTATCG-CCAGTTATCTGACTAGTGTTGGGCGTAATAATTTTTCGACTCGTTCAACTAGT-TC
1 AACTATCGTCGA-TTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTTGACTAGTGT-
20470745 TGGGCAC
64 TGGGCAC
20470752 A
1 A
20470753 CAAATGATCT
Statistics
Matches: 167, Mismatches: 36, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
67 1 0.01
68 51 0.31
70 114 0.68
71 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (70 bp):
AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTTGACTAGTGTTG
GGCAC
Found at i:20474129 original size:26 final size:28
Alignment explanation
Indices: 20474096--20474156 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 28
20474086 TAAGTTCATC
20474096 AAAATTAAAAT-TAATCTAAAC-TA-ATA
1 AAAATTAAAATATAATC-AAACATACATA
20474122 AAAATT-AAATATAATCAAACATATCATA
1 AAAATTAAAATATAATCAAACATA-CATA
20474150 AAAATTA
1 AAAATTA
20474157 TATAATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 8 0.27
26 13 0.43
28 9 0.30
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAATTAAAATATAATCAAACATACATA
Found at i:20477984 original size:40 final size:40
Alignment explanation
Indices: 20477923--20478109 Score: 250
Period size: 40 Copynumber: 4.6 Consensus size: 40
20477913 CATTTGAATG
* * *
20477923 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
*
20477963 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
20478003 ATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--AT
* * *
20478045 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
20478085 ATGTCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
20478110 AATGTGTTTG
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 93 0.70
41 3 0.02
42 36 0.27
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:20478082 original size:82 final size:80
Alignment explanation
Indices: 20477923--20478109 Score: 266
Period size: 82 Copynumber: 2.3 Consensus size: 80
20477913 CATTTGAATG
* * * *
20477923 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
* * *
20477988 TTTGTGCGAGTTGAT
66 ATTATGCAAGTTGAT
*
20478003 ATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGAT-TATATCCGGGCTAAGACCCGAAGG
20478068 CAATTATGCAAGTTGAT
64 CAATTATGCAAGTTGAT
* *
20478085 ATGTCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
20478110 AATGTGTTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 31 0.33
81 4 0.04
82 59 0.63
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
ATTATGCAAGTTGAT
Found at i:20499227 original size:40 final size:40
Alignment explanation
Indices: 20499183--20499301 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 40
20499173 AGCACTATGG
*
20499183 TGCTCCTAACAGTACTTTCGTACTTCTAATAGCACAACAA
1 TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACAA
* * **
20499223 TGCTCCTGACCGTACTTTCGTAC-TCTTAGTAGCACAACGG
1 TGCTCCTGACAGTACTTTCGTACTTC-TAATAGCACAACAA
* * *
20499263 TGCTCCTGACAGTACTTTCATACTCCTGATAGCACAACA
1 TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACA
20499302 GTAGATTCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.03
40 63 0.95
41 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (40 bp):
TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACAA
Found at i:20504319 original size:6 final size:6
Alignment explanation
Indices: 20504303--20504337 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20504293 TAGGTTTCTA
* *
20504303 AAAATG GAAATG AAAATG AAAATG AAAATG GAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
20504338 TTGCAATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:20504320 original size:12 final size:12
Alignment explanation
Indices: 20504303--20504337 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
20504293 TAGGTTTCTA
20504303 AAAATGGAAATG
1 AAAATGGAAATG
*
20504315 AAAATGAAAATG
1 AAAATGGAAATG
20504327 AAAATGGAAAT
1 AAAATGGAAAT
20504338 TTGCAATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:20504541 original size:5 final size:5
Alignment explanation
Indices: 20504531--20504556 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20504521 TGAGCATTCG
20504531 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
20504557 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:20505347 original size:30 final size:31
Alignment explanation
Indices: 20505308--20505367 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20505298 AGAGGTGAGA
*
20505308 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
20505339 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
20505368 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:20505595 original size:9 final size:9
Alignment explanation
Indices: 20505581--20505617 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20505571 TATAGTTTGA
20505581 TATTCGAAT
1 TATTCGAAT
20505590 TATTCGAAT
1 TATTCGAAT
*
20505599 TATTCGAGT
1 TATTCGAAT
20505608 TATTCGAAT
1 TATTCGAAT
20505617 T
1 T
20505618 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20508490 original size:19 final size:19
Alignment explanation
Indices: 20508466--20508506 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20508456 TCAATTTCAT
20508466 ACTTTTTCAATAATATCAA
1 ACTTTTTCAATAATATCAA
20508485 ACTTTTTCAATAATATCAA
1 ACTTTTTCAATAATATCAA
20508504 ACT
1 ACT
20508507 CAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (19 bp):
ACTTTTTCAATAATATCAA
Found at i:20518605 original size:17 final size:17
Alignment explanation
Indices: 20518583--20518615 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20518573 GTTTGGTGTA
20518583 TTTTTTATATACTTTAG
1 TTTTTTATATACTTTAG
*
20518600 TTTTTTATATATTTTA
1 TTTTTTATATACTTTA
20518616 TTATGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTTATATACTTTAG
Found at i:20531242 original size:13 final size:13
Alignment explanation
Indices: 20531224--20531248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20531214 TAATGGTATA
20531224 TTGAATCCATGAT
1 TTGAATCCATGAT
20531237 TTGAATCCATGA
1 TTGAATCCATGA
20531249 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:20540859 original size:24 final size:25
Alignment explanation
Indices: 20540829--20540878 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
20540819 TAAGGTTTTC
20540829 AAAAATTA-AAA-ATAAATAACATAA
1 AAAAATTACAAACATAAATAA-ATAA
*
20540853 AAAAATTACAAACATAACTAAATAA
1 AAAAATTACAAACATAAATAAATAA
20540878 A
1 A
20540879 TTAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (25 bp):
AAAAATTACAAACATAAATAAATAA
Found at i:20548844 original size:23 final size:22
Alignment explanation
Indices: 20548803--20548845 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20548793 AAAATTTATT
*
20548803 GGATTAAACTAAAATTTTTGTA
1 GGATTAAACTAAAACTTTTGTA
*
20548825 GGATTAAATTGAAAACTTTTG
1 GGATTAAACT-AAAACTTTTG
20548846 GAAGAGTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (22 bp):
GGATTAAACTAAAACTTTTGTA
Done.