Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 131 of 295
Found at i:40149691 original size:80 final size:80
Alignment explanation
Indices: 40149558--40149794 Score: 366
Period size: 80 Copynumber: 3.0 Consensus size: 80
40149548 CTTTTAGTGA
* *
40149558 TATATCCGGGTTAAGTCCCGAAGAGCATACGTGTTGGTGTTATATCTGGGCTAAGTCTCGAAGAG
1 TATATCAGGGTTAAGTCCCGAAGAGCATACGTGTTGGTGTTATATCCGGGCTAAGTCTCGAAGAG
40149623 CATTCGTGCTGGAGT
66 CATTCGTGCTGGAGT
* *
40149638 TATATCAGGGCTAAGTCCCGAAGAGCATACGTGTTGGTGTCATATCCGGGCTAAGTCTCGAAGAG
1 TATATCAGGGTTAAGTCCCGAAGAGCATACGTGTTGGTGTTATATCCGGGCTAAGTCTCGAAGAG
40149703 CATTCGTGCTGGAGT
66 CATTCGTGCTGGAGT
* * ** * * *
40149718 TATATTAGGGTTAAGTCCCGAAGAGCATTCGTACTAGTGTTATATCCGGGCTAAGTCCCAAAGAG
1 TATATCAGGGTTAAGTCCCGAAGAGCATACGTGTTGGTGTTATATCCGGGCTAAGTCTCGAAGAG
*
40149783 CATTCATGCTGG
66 CATTCGTGCTGG
40149795 TGATGTGTAT
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 143 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (80 bp):
TATATCAGGGTTAAGTCCCGAAGAGCATACGTGTTGGTGTTATATCCGGGCTAAGTCTCGAAGAG
CATTCGTGCTGGAGT
Found at i:40150010 original size:25 final size:25
Alignment explanation
Indices: 40149960--40150012 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
40149950 TGTGTAACAA
* *
40149960 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
40149985 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
40150010 CAA
1 CAA
40150013 GTTCTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:40152482 original size:18 final size:19
Alignment explanation
Indices: 40152459--40152495 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40152449 GACAAAGTGA
40152459 AAGTATATGTGG-TATTTG
1 AAGTATATGTGGATATTTG
*
40152477 AAGTATATTTGGATATTTG
1 AAGTATATGTGGATATTTG
40152496 TGATGTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (19 bp):
AAGTATATGTGGATATTTG
Found at i:40152882 original size:22 final size:22
Alignment explanation
Indices: 40152811--40152882 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
40152801 TGATAAGGCC
*
40152811 GAATGGCCAATGTGATGAATAT
1 GAATGGCCAATGTGATGAATGT
*** *
40152833 GAACATGTATATATGTGAT-AAGGTT
1 G-A-ATGGCCA-ATGTGATGAATG-T
40152858 GAATGGCCAATGTGATGAATGT
1 GAATGGCCAATGTGATGAATGT
40152880 GAA
1 GAA
40152883 CATGTATATG
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
22 12 0.33
23 8 0.22
24 7 0.19
25 9 0.25
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (22 bp):
GAATGGCCAATGTGATGAATGT
Found at i:40153037 original size:47 final size:47
Alignment explanation
Indices: 40152569--40153017 Score: 718
Period size: 47 Copynumber: 9.6 Consensus size: 47
40152559 ATACATGAGC
* * *
40152569 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
40152616 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
40152663 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
*
40152710 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
*
40152757 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
* *
40152804 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGTATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
**
40152851 TAAGGTTGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
* * * *
40152898 TAAGGCCGAATGGCCAATGTGAAGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
* * * * **
40152945 TAAGGCCGAATGGCCAACGTGATAAATATGAACATGCATACATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
*
40152992 TAAGGCAGAATGGCCAATGTGATGAA
1 TAAGGCCGAATGGCCAATGTGATGAA
40153018 CGTGGATGTG
Statistics
Matches: 378, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 378 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
Found at i:40153050 original size:47 final size:47
Alignment explanation
Indices: 40152538--40153051 Score: 704
Period size: 47 Copynumber: 10.9 Consensus size: 47
40152528 TTAGGATTTT
* ** * * * *
40152538 ATGTGATGGATGTGAATGTGTATACATGAGCTAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
40152585 ATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
40152632 ATGTGATGAATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
40152679 ATGTGATGAATGTGAACATGTATATGTGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
40152726 ATGTGATGAATGTGAACATGTATATGTGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
40152773 ATGTGATGAATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* **
40152820 ATGTGATGAATATGAACATGTATATATGTGATAAGGTTGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
40152867 ATGTGATGAATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
40152914 ATGTGAAGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * * * * *
40152961 ACGTGATAAATATGAACATGCATACATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * ** ** *
40153008 ATGTGATGAACGTGGATGTGTATATATGTGGGAAAGCCGAATGG
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGG
40153052 TTAATGCGAA
Statistics
Matches: 423, Mismatches: 44, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 423 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:40153084 original size:46 final size:46
Alignment explanation
Indices: 40153031--40153121 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
40153021 GGATGTGTAT
* * *
40153031 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* *
40153077 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
40153122 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.35, C:0.07, G:0.31, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:40154917 original size:23 final size:23
Alignment explanation
Indices: 40154890--40154938 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
40154880 GATTAAATGA
40154890 AACGCATTCAACCCACTTAAACT
1 AACGCATTCAACCCACTTAAACT
40154913 AACGCATTCAACCCACTTAAACT
1 AACGCATTCAACCCACTTAAACT
40154936 AAC
1 AAC
40154939 TTGATTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.35, G:0.04, T:0.20
Consensus pattern (23 bp):
AACGCATTCAACCCACTTAAACT
Found at i:40158454 original size:2 final size:2
Alignment explanation
Indices: 40158447--40158471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40158437 TCATTTGTAA
40158447 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
40158472 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40163264 original size:34 final size:34
Alignment explanation
Indices: 40163198--40163265 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
40163188 GCTCAAGCAG
*** **
40163198 AACAATACAGTAGCATTTAATATGCTTTTAACAA
1 AACAATACAGTAGCAAACAATATGCTCATAACAA
40163232 AACAATACAGTAGCAAACAATATGCTCATAACAA
1 AACAATACAGTAGCAAACAATATGCTCATAACAA
40163266 TTCGATTCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.25
Consensus pattern (34 bp):
AACAATACAGTAGCAAACAATATGCTCATAACAA
Found at i:40170818 original size:16 final size:16
Alignment explanation
Indices: 40170797--40170829 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40170787 TTGTAACGAC
40170797 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
40170813 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
40170829 C
1 C
40170830 TTGAATTTTT
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:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:40172331 original size:29 final size:28
Alignment explanation
Indices: 40172263--40172379 Score: 87
Period size: 29 Copynumber: 4.1 Consensus size: 28
40172253 TGAGCATGAG
* *
40172263 TATAATATGATTTGGGCCTAATGGGCCA
1 TATAATATGAATTGGGCCTAGTGGGCCA
**
40172291 TATGAAGGTGAATTGGGCCTAGTGGGCCA
1 TAT-AATATGAATTGGGCCTAGTGGGCCA
* *
40172320 TAATAATATGAACTAGGCC-AGATGGGCCA
1 T-ATAATATGAATTGGGCCTAG-TGGGCCA
* * *
40172349 TTTGAATCA-G-ACTGGGCCTAGTGGGCTA
1 TAT-AAT-ATGAATTGGGCCTAGTGGGCCA
40172377 TAT
1 TAT
40172380 GCATGTATGT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
28 21 0.30
29 47 0.66
30 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (28 bp):
TATAATATGAATTGGGCCTAGTGGGCCA
Found at i:40176593 original size:14 final size:14
Alignment explanation
Indices: 40176574--40176603 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40176564 TATCTTATAA
40176574 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
40176588 ATATGCGTTAATCT
1 ATATGCGTGAATCT
40176602 AT
1 AT
40176604 CTTGAAAATA
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:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:40179632 original size:2 final size:2
Alignment explanation
Indices: 40179625--40179649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40179615 GAGAAAAGAA
40179625 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40179650 AAAGGAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40184819 original size:24 final size:24
Alignment explanation
Indices: 40184759--40184832 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 24
40184749 GTACGCATAA
40184759 ACTTTGCATAGATAGTTCACACAC
1 ACTTTGCATAGATAGTTCACACAC
* *
40184783 AGAACTTTACATA-ATCAGTTCGCACAC
1 ---ACTTTGCATAGAT-AGTTCACACAC
40184810 ACTTTGCATAGATAGTTCACACA
1 ACTTTGCATAGATAGTTCACACA
40184833 TAAAACTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 18 0.44
25 2 0.05
26 2 0.05
27 19 0.46
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.28
Consensus pattern (24 bp):
ACTTTGCATAGATAGTTCACACAC
Found at i:40184916 original size:24 final size:24
Alignment explanation
Indices: 40184888--40184967 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
40184878 CACACATAGA
40184888 ACTTTACATAATCAGTATACATAT
1 ACTTTACATAATCAGTATACATAT
* * *
40184912 ACTTTGCATAGAT-AGTTCACACATAGA
1 ACTTTACATA-ATCAG-T-ATACATA-T
* **
40184939 ACTTTACATAATCAATATGTATAT
1 ACTTTACATAATCAGTATACATAT
40184963 ACTTT
1 ACTTT
40184968 GCATTGATAG
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
24 16 0.38
25 7 0.17
26 9 0.21
27 10 0.24
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (24 bp):
ACTTTACATAATCAGTATACATAT
Found at i:40184977 original size:51 final size:51
Alignment explanation
Indices: 40184633--40184979 Score: 363
Period size: 51 Copynumber: 6.8 Consensus size: 51
40184623 TGCATATAAT
* * * * * *
40184633 ACTTTACATAATTAATATGCACATACTTTGCATAGACAGATCACATATAGA
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
* * * ** * *
40184684 AATATATATAATCAGTACACACACATTTTGCATAGACAGTTCACACATAGA
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
** * * * *
40184735 ACTTTATGTAATCAGTACGCATAAACTTTGCATAGATAGTTCACACACAGA
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
*
40184786 ACTTTACATAATCAGT-TCGCACACACTTTGCATAGATAGTTCACACATAAA
1 ACTTTACATAATCAGTAT-GCACACACTTTGCATAGATAGTTCACACATAGA
* ** * * * *
40184837 ACTTTACATAATCAGAACACGCACACTTTGCATGGACAATTCACACATAGA
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
* * *
40184888 ACTTTACATAATCAGTATACATATACTTTGCATAGATAGTTCACACATAGA
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
* * * * *
40184939 ACTTTACATAATCAATATGTATATACTTTGCATTGATAGTT
1 ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTT
40184980 ATGTTGGATC
Statistics
Matches: 247, Mismatches: 47, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
51 247 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (51 bp):
ACTTTACATAATCAGTATGCACACACTTTGCATAGATAGTTCACACATAGA
Found at i:40184977 original size:153 final size:153
Alignment explanation
Indices: 40184633--40184979 Score: 464
Period size: 153 Copynumber: 2.3 Consensus size: 153
40184623 TGCATATAAT
* * * * *
40184633 ACTTTACATAATTAATATGCACATACTTTGCATAGACAGATCACATATAGAAATATATATAATCA
1 ACTTTACATAATCAATATGCACATACTTTGCATAGATAGTTCACACATAGAAATATACATAATCA
* * * ** *
40184698 GTACACACACATTTTGCATAGACAGTTCACACATAGAACTTTATGTAATCAGTACGCATAAACTT
66 GAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACATAAACTT
40184763 TGCATAGATAGTTCACACACAGA
131 TGCATAGATAGTTCACACACAGA
* * *
40184786 ACTTTACATAATCAGT-TCGCACACACTTTGCATAGATAGTTCACACATA-AAACTTTACATAAT
1 ACTTTACATAATCAATAT-GCACATACTTTGCATAGATAGTTCACACATAGAAA-TATACATAAT
* * * *
40184849 CAGAACACGCACACTTTGCATGGACAATTCACACATAGAACTTTACATAATCAGTATACATATAC
64 CAGAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACATAAAC
*
40184914 TTTGCATAGATAGTTCACACATAGA
129 TTTGCATAGATAGTTCACACACAGA
* * *
40184939 ACTTTACATAATCAATATGTATATACTTTGCATTGATAGTT
1 ACTTTACATAATCAATATGCACATACTTTGCATAGATAGTT
40184980 ATGTTGGATC
Statistics
Matches: 167, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
152 4 0.02
153 162 0.97
154 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (153 bp):
ACTTTACATAATCAATATGCACATACTTTGCATAGATAGTTCACACATAGAAATATACATAATCA
GAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACATAAACTT
TGCATAGATAGTTCACACACAGA
Found at i:40188566 original size:21 final size:21
Alignment explanation
Indices: 40188537--40188581 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40188527 TTATTCATGA
*
40188537 ATTATATTAATACTTTGTATT
1 ATTACATTAATACTTTGTATT
40188558 ATTACATTAATACTTTGTATT
1 ATTACATTAATACTTTGTATT
40188579 ATT
1 ATT
40188582 GTTCTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTACATTAATACTTTGTATT
Found at i:40193028 original size:21 final size:23
Alignment explanation
Indices: 40193003--40193044 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
40192993 GAAATAGAAA
*
40193003 AAATCATAA-TAAA-CTTCAAAG
1 AAATCAAAAGTAAATCTTCAAAG
40193024 AAATCAAAAGTAAATCTTCAA
1 AAATCAAAAGTAAATCTTCAA
40193045 TCTTGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (23 bp):
AAATCAAAAGTAAATCTTCAAAG
Found at i:40195250 original size:18 final size:18
Alignment explanation
Indices: 40195223--40195258 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40195213 GAACATAATT
*
40195223 AAATTGAAAAAAAAGAAA
1 AAATTAAAAAAAAAGAAA
40195241 AAATTAAAAAAAAAGAAA
1 AAATTAAAAAAAAAGAAA
40195259 TATCTTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (18 bp):
AAATTAAAAAAAAAGAAA
Found at i:40198664 original size:14 final size:14
Alignment explanation
Indices: 40198645--40198671 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40198635 TTATTGTGCA
40198645 AAAGAAATTATTTT
1 AAAGAAATTATTTT
40198659 AAAGAAATTATTT
1 AAAGAAATTATTT
40198672 AATCATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAGAAATTATTTT
Found at i:40208448 original size:42 final size:42
Alignment explanation
Indices: 40208387--40208500 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 42
40208377 TTTGACATTA
40208387 CTTGTAAGACCATATCTGGGATATGGCATCGATATGAGGAT-T
1 CTTGTAAGACCATATCTGGGATATGGCATCGATATGA-GATCT
* * * * *
40208429 TTTGTAAGACCATAGCTGGGCTATTAGCATCGATGTGAGATCT
1 CTTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATCT
*
40208472 CATGTAAGACCATATCTGGGATATGGCAT
1 CTTGTAAGACCATATCTGGGATATGGCAT
40208501 TGTTATGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 28 0.47
43 32 0.53
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
CTTGTAAGACCATATCTGGGATATGGCATCGATATGAGATCT
Found at i:40209774 original size:10 final size:10
Alignment explanation
Indices: 40209747--40209806 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
40209737 TTAAATTCTA
40209747 AAAGATAAAT
1 AAAGATAAAT
40209757 ACAA-ATAAAT
1 A-AAGATAAAT
*
40209767 AAAGATAATT
1 AAAGATAAAT
*
40209777 AAGGAT-AAT
1 AAAGATAAAT
40209786 GAAAGATAAAT
1 -AAAGATAAAT
*
40209797 AAAAATAAAT
1 AAAGATAAAT
40209807 CCTAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 4 0.10
10 32 0.78
11 5 0.12
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40209839 original size:13 final size:13
Alignment explanation
Indices: 40209823--40209847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40209813 TTTAAATCTA
40209823 AATAATTATCCTT
1 AATAATTATCCTT
40209836 AATAATTATCCT
1 AATAATTATCCT
40209848 AGTATAATAA
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTATCCTT
Found at i:40210426 original size:7 final size:7
Alignment explanation
Indices: 40210414--40210454 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
40210404 ATATCCTCCC
40210414 TTTTTTA
1 TTTTTTA
40210421 TTTTTTA
1 TTTTTTA
40210428 TTTTTTA
1 TTTTTTA
*
40210435 TTTTTAA
1 TTTTTTA
40210442 TTTATTTA
1 TTT-TTTA
40210450 TTTTT
1 TTTTT
40210455 ACTTAGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:40210611 original size:96 final size:97
Alignment explanation
Indices: 40210446--40210629 Score: 289
Period size: 96 Copynumber: 1.9 Consensus size: 97
40210436 TTTTAATTTA
* * * * *
40210446 TTTATTTTTACTTAGGAATATATTGAGCCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAAAGATGACAGCCAAGCACCCCA
40210511 CCCCGATTACTCAGCCCAACACACTCCTAATT
66 CCCCGATTACTCAGCCCAACACACTCCTAATT
* *
40210543 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCAAAGAAAGATGACAGCCGAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAAAGATGACAGCCAAGCACCCCA
*
40210607 CCCCGGTTACTCAGCCCAACACA
66 CCCCGATTACTCAGCCCAACACA
40210630 TTTTTAAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 70 0.89
97 9 0.11
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAAAGATGACAGCCAAGCACCCCA
CCCCGATTACTCAGCCCAACACACTCCTAATT
Found at i:40214782 original size:29 final size:29
Alignment explanation
Indices: 40214746--40214804 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40214736 TCATTAATTA
40214746 TAAATTCAATTTTATCTTCATAAATTGAC
1 TAAATTCAATTTTATCTTCATAAATTGAC
*
40214775 TAAATTCAGTTTTATCTTCATAAATTGAC
1 TAAATTCAATTTTATCTTCATAAATTGAC
40214804 T
1 T
40214805 CAAAAGTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (29 bp):
TAAATTCAATTTTATCTTCATAAATTGAC
Found at i:40218120 original size:10 final size:10
Alignment explanation
Indices: 40218105--40218154 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
40218095 TTAAATTCTA
40218105 AAAAATAAAT
1 AAAAATAAAT
*
40218115 ACAAATAAAT
1 AAAAATAAAT
*
40218125 AAAAATAATT
1 AAAAATAAAT
*
40218135 AAAGATAAAT
1 AAAAATAAAT
40218145 AAAAATAAAT
1 AAAAATAAAT
40218155 CCTAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:40222102 original size:3 final size:3
Alignment explanation
Indices: 40222094--40222140 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40222084 AAATAAACTC
40222094 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40222141 ATATCAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40226201 original size:39 final size:39
Alignment explanation
Indices: 40226155--40226233 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
40226145 ATAATTTCGA
40226155 GATCAAACTGGCACTGATACAAATGATCCAAAATAATCT
1 GATCAAACTGGCACTGATACAAATGATCCAAAATAATCT
40226194 GATCAAACTGGCACTGATACAAATGATCCAAAATAATCT
1 GATCAAACTGGCACTGATACAAATGATCCAAAATAATCT
40226233 G
1 G
40226234 TAGTTTAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (39 bp):
GATCAAACTGGCACTGATACAAATGATCCAAAATAATCT
Found at i:40230435 original size:17 final size:17
Alignment explanation
Indices: 40230402--40230435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40230392 TTGTATTTTG
*
40230402 TGCAAAAAGGACTAAAT
1 TGCAAAAAGGACAAAAT
*
40230419 TGCAAAAAGTACAAAAT
1 TGCAAAAAGGACAAAAT
40230436 GTTAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGACAAAAT
Found at i:40231251 original size:41 final size:41
Alignment explanation
Indices: 40231193--40231464 Score: 465
Period size: 41 Copynumber: 6.6 Consensus size: 41
40231183 ATACAAACTT
* *
40231193 TAAGTCTAGCAGACTTAATGCCGGTGATACATTTCAGACTT
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
40231234 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
* *
40231275 TATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTT
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
40231316 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
*
40231357 TATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
*
40231398 TATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
*
40231439 TATGTCTAGCAGGC-TAAGTGCCGGTG
1 TAAGTCTAGCAGGCTTAA-TGCCGGTG
40231465 TACTGAATCA
Statistics
Matches: 223, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 3 0.01
41 220 0.99
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
Found at i:40231333 original size:82 final size:82
Alignment explanation
Indices: 40231196--40231506 Score: 502
Period size: 82 Copynumber: 3.8 Consensus size: 82
40231186 CAAACTTTAA
*
40231196 GTCTAGCAGACTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
40231261 TACATTTCAGACTATAT
66 TACATTTCAGACTATAT
40231278 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
40231343 TACATTTCAGACTATAT
66 TACATTTCAGACTATAT
* *
40231360 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
40231425 TACATTTCAGACTATAT
66 TACATTTCAGACTATAT
* * * **
40231442 GTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGG
1 GTCTAGCAGGCTTAA-TGCCGGTGATACAT--TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
40231504 TGA
63 TGA
40231507 ATCTGTTTAA
Statistics
Matches: 216, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
80 1 0.00
81 6 0.03
82 209 0.97
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (82 bp):
GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
TACATTTCAGACTATAT
Found at i:40231489 original size:123 final size:123
Alignment explanation
Indices: 40231193--40231506 Score: 481
Period size: 123 Copynumber: 2.6 Consensus size: 123
40231183 ATACAAACTT
* *
40231193 TAAGTCTAGCAGACTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
*
40231258 TGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTT
66 TGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
* * *
40231316 TAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGG
1 TAAGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
40231381 TGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
66 TGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
* * * **
40231439 TATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGCAAAATGC
1 TAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--ATCAGACTTTAAGTCTAGCAGGCTTAATGC
40231501 CGGTGA
63 CGGTGA
40231507 ATCTGTTTAA
Statistics
Matches: 176, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
121 1 0.01
122 6 0.03
123 169 0.96
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (123 bp):
TAAGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
TGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTA
Found at i:40238702 original size:29 final size:29
Alignment explanation
Indices: 40238667--40238726 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
40238657 CTATAATGAC
40238667 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
1 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
40238696 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
1 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
40238725 TT
1 TT
40238727 TCAGAACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (29 bp):
TTAGTTTCCAGTGGTGTCAAAAAATGCAA
Found at i:40242409 original size:17 final size:17
Alignment explanation
Indices: 40242387--40242433 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
40242377 CTAAATCAAA
40242387 TATAAATAAAATATAAG
1 TATAAATAAAATATAAG
*
40242404 TATAAAT--AATATAAT
1 TATAAATAAAATATAAG
40242419 TAATAAATATAAATA
1 T-ATAAATA-AAATA
40242434 ATGTAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 7 0.28
19 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TATAAATAAAATATAAG
Found at i:40242424 original size:22 final size:22
Alignment explanation
Indices: 40242399--40242441 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40242389 TAAATAAAAT
*
40242399 ATAAGTATAAATAATATAATTA
1 ATAAATATAAATAATATAATTA
*
40242421 ATAAATATAAATAATGTAATT
1 ATAAATATAAATAATATAATT
40242442 CAAAAAGGAA
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:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAAATATAAATAATATAATTA
Found at i:40253688 original size:40 final size:40
Alignment explanation
Indices: 40253635--40253777 Score: 209
Period size: 40 Copynumber: 3.6 Consensus size: 40
40253625 ACTACTTGCT
40253635 CAAATGCCTTCGGGACTTAGCCCGGGTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGGTATAGTAACTCGCA
*
40253675 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGGTATAGTAACTCGCA
* * * *
40253715 CAAATGCCTTC-AGAGCTTAGCCC-GGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGGTA-TAGTAACTCGCA
40253755 CAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
40253778 AGTTATCATC
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
39 4 0.04
40 87 0.94
41 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGGTATAGTAACTCGCA
Found at i:40259036 original size:16 final size:16
Alignment explanation
Indices: 40258965--40259036 Score: 92
Period size: 16 Copynumber: 4.6 Consensus size: 16
40258955 ACAACTGAAT
* *
40258965 TATT-CATTAAAGGTC
1 TATTCCATTACAGCTC
*
40258980 TATTCTATTACAGCTC
1 TATTCCATTACAGCTC
40258996 TATTCCATTACAGCTC
1 TATTCCATTACAGCTC
* *
40259012 TATTACATTACAACTC
1 TATTCCATTACAGCTC
40259028 TATTCCATT
1 TATTCCATT
40259037 CCCCCAATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 4 0.08
16 45 0.92
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:40260642 original size:40 final size:40
Alignment explanation
Indices: 40260551--40260773 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
40260541 TCCTCGTTCA
* * * * *
40260551 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40260590 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
40260630 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40260670 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
40260710 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40260750 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40260774 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 36 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40260782 original size:41 final size:41
Alignment explanation
Indices: 40260705--40260782 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40260695 TTAGTATCTC
* * *
40260705 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40260746 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40260783 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:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40268545 original size:40 final size:40
Alignment explanation
Indices: 40268454--40268676 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
40268444 TCCTCGTTCA
* * * * *
40268454 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40268493 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
40268533 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40268573 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
40268613 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40268653 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40268677 CAGCATTTAA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 36 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40280191 original size:68 final size:64
Alignment explanation
Indices: 40280074--40280224 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 64
40280064 ATACAGATGG
* * * * *
40280074 TATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTATGAGACAT
1 TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTGTACAAGAGAGCTACG-G-CA-
40280139 TA
63 TA
* * *
40280141 TAATGTAGCTAGGTCGCATGGGTGATGCT-ATGTGTACACCATGTAG-ACAAGAGAGCTACGGGA
1 T-ATGTAGCTAGGTCGCATGGATGATGCTGA-GTGCACACCATGT-GTACAAGAGAGCTACGGCA
40280204 TA
63 TA
40280206 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
40280225 CGTGGTTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 18 0.25
65 3 0.04
66 1 0.01
67 3 0.04
68 47 0.64
69 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTGTACAAGAGAGCTACGGCATA
Found at i:40286371 original size:21 final size:22
Alignment explanation
Indices: 40286345--40286386 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40286335 GCACTTTTTA
40286345 AAAATTTA-AAAA-ATTATAAAC
1 AAAATTTATAAAACATT-TAAAC
40286366 AAAATTTATAAAACATTTAAA
1 AAAATTTATAAAACATTTAAA
40286387 ATTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTTATAAAACATTTAAAC
Found at i:40296129 original size:32 final size:32
Alignment explanation
Indices: 40296088--40296149 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
40296078 CATCTATTTT
40296088 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
40296120 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
40296150 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:40297931 original size:5 final size:5
Alignment explanation
Indices: 40297921--40297949 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40297911 GGGAGAGTTC
40297921 TTTCT TTTCT TTTCT TTTCT TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
40297950 AAATGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:40299977 original size:30 final size:31
Alignment explanation
Indices: 40299933--40299995 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
40299923 ATGATATTAA
40299933 CAATTTATGAAAATTAAATCAAA-AAAAAATT
1 CAATTTATGAAAATTAAA-CAAATAAAAAATT
* **
40299964 CAATTT-TTAAAATTGTACAAATAAAAAATT
1 CAATTTATGAAAATTAAACAAATAAAAAATT
40299994 CA
1 CA
40299996 TAACATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 18 0.64
31 6 0.21
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (31 bp):
CAATTTATGAAAATTAAACAAATAAAAAATT
Found at i:40304907 original size:12 final size:12
Alignment explanation
Indices: 40304890--40304919 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40304880 AAAACATAAT
40304890 TTGAAATATTTA
1 TTGAAATATTTA
40304902 TTGAAATATTTA
1 TTGAAATATTTA
40304914 TTGAAA
1 TTGAAA
40304920 GAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (12 bp):
TTGAAATATTTA
Found at i:40305079 original size:20 final size:19
Alignment explanation
Indices: 40305054--40305097 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40305044 TGGAGAATGA
40305054 TTTCTGAAAAATGATTTACT
1 TTTCTG-AAAATGATTTACT
*
40305074 TTTCTGGAAATGATTTACT
1 TTTCTGAAAATGATTTACT
40305093 TTTCT
1 TTTCT
40305098 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTGAAAATGATTTACT
Found at i:40306255 original size:23 final size:24
Alignment explanation
Indices: 40306229--40306278 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
40306219 AATATTGTGA
40306229 TTTAACTCTTAAT-TTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
40306252 TTTAACTCTTAATATTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
40306276 TTT
1 TTT
40306279 CTTTCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAACTCTTAATATTTATAAAAT
Found at i:40310114 original size:14 final size:14
Alignment explanation
Indices: 40310095--40310121 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40310085 AGAAAAGCCT
40310095 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
40310109 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
40310122 AGGTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:40312387 original size:20 final size:19
Alignment explanation
Indices: 40312346--40312388 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40312336 AAAAAAATAA
** *
40312346 TTAAAAATCATAAATTTTT
1 TTAAAAATCATAAAAATCT
40312365 TTAAAAATTCATAAAAATCT
1 TTAAAAA-TCATAAAAATCT
40312385 TTAA
1 TTAA
40312389 GGGTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAAATCATAAAAATCT
Found at i:40315539 original size:34 final size:34
Alignment explanation
Indices: 40315496--40315563 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
40315486 TCAATTGAAA
* * *
40315496 AAGTTGGAAATATCAAATGTCATGGCCTTGACTT
1 AAGTTGGAAATATCAAATGCCATGACATTGACTT
40315530 AAGTTGGAAATATCAAATGCCATGACATTGACTT
1 AAGTTGGAAATATCAAATGCCATGACATTGACTT
40315564 GCAATCTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGTTGGAAATATCAAATGCCATGACATTGACTT
Found at i:40315887 original size:22 final size:23
Alignment explanation
Indices: 40315862--40315904 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40315852 GGTCGATGAG
*
40315862 AAAAAATAAATAT-AAATTATAA
1 AAAAAATAAACATAAAATTATAA
*
40315884 AAAAAGTAAACATAAAATTAT
1 AAAAAATAAACATAAAATTAT
40315905 TTTAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAAATAAACATAAAATTATAA
Found at i:40315901 original size:23 final size:21
Alignment explanation
Indices: 40315862--40315904 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
40315852 GGTCGATGAG
*
40315862 AAAAAATAAATATAAATTATA
1 AAAAAATAAACATAAATTATA
40315883 AAAAAAGTAAACATAAAATTAT
1 AAAAAA-TAAACAT-AAATTAT
40315905 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAATAAACATAAATTATA
Found at i:40315935 original size:20 final size:20
Alignment explanation
Indices: 40315898--40315945 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
40315888 AGTAAACATA
40315898 AAATTATTTTAAATATTTTT
1 AAATTATTTTAAATATTTTT
*
40315918 AAATATATTTTATA-ATTTTT
1 AAAT-TATTTTAAATATTTTT
40315938 AGAATTAT
1 A-AATTAT
40315946 AATTAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTATTTTAAATATTTTT
Found at i:40319420 original size:56 final size:56
Alignment explanation
Indices: 40319359--40319469 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
40319349 TTTTAAAATT
* * * *
40319359 TTATAACTTTTATTACTCAG-GGTTTGTTTAGGGTTACACACAAAATTAATGAAAAA
1 TTATAACCTCTATTACT-AGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
* * *
40319415 TTATAACCTCTGTTGCTTGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
1 TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
40319470 TAATTATAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (56 bp):
TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
Found at i:40322177 original size:49 final size:50
Alignment explanation
Indices: 40322124--40322264 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 50
40322114 CAAAATATTT
40322124 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA-TTATCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGTTATCC
* * * * *
40322173 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAAGTTATCC
*
40322224 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
40322265 TAGCTACATA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
49 36 0.45
50 4 0.05
51 40 0.50
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (50 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGTTATCC
Found at i:40323466 original size:52 final size:52
Alignment explanation
Indices: 40323388--40323494 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
40323378 GCCCTAGCTT
40323388 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAA
1 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAA
40323440 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAA
1 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAA
40323492 AAA
1 AAA
40323495 ACTTGAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (52 bp):
AAATTATTGCTAGAATAAGCTTAATCAAATTACCGGGATTCCAAAAACGTAA
Found at i:40325882 original size:13 final size:13
Alignment explanation
Indices: 40325850--40325887 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40325840 CAGTTAATTA
40325850 AATTAT-TTAATTT
1 AATTATATT-ATTT
40325863 AATTTATATTATTT
1 AA-TTATATTATTT
40325877 AATTATATTAT
1 AATTATATTAT
40325888 ACATTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 10 0.43
15 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:40327859 original size:18 final size:18
Alignment explanation
Indices: 40327836--40327875 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40327826 AATAAAAAAG
40327836 TAAAAAAATAAGAAATAT
1 TAAAAAAATAAGAAATAT
* *
40327854 TAAAAAGATAATAAATAT
1 TAAAAAAATAAGAAATAT
40327872 TAAA
1 TAAA
40327876 CATTTATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
TAAAAAAATAAGAAATAT
Found at i:40330870 original size:27 final size:27
Alignment explanation
Indices: 40330839--40331016 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
40330829 TAAATTGTAC
40330839 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40330866 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40330892 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40330920 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
40330948 AGCACTAAGTGTACGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
40330975 AGCACTAAGTGTGTGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40331002 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40331017 GACTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 103 0.82
28 22 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40331007 original size:82 final size:81
Alignment explanation
Indices: 40330836--40331016 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
40330826 GATTAAATTG
* * *
40330836 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAA
40330901 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40330917 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTACGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTACGAAATGAATACGAT-GCACT
* * **
40330981 AAGTGTGTGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40330999 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40331017 GACTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40333015 original size:42 final size:42
Alignment explanation
Indices: 40332953--40333081 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
40332943 CTAAGTCCGG
* *
40332953 ATATAGTACCAGCACTAAGCCTGCGGGATTTAACCTGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCTGGATAT
* * *
40332995 ATATATTACCAGCACGAAGCCTGCAGGATTTAGCCCGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCTGGATAT
40333037 ATAT-TTACCAGCACGAAGCCTGCGGGATTTAACCTGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCTGGATAT
40333078 ATAT
1 ATAT
40333082 TATATCGAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 38 0.48
42 41 0.52
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTAACCTGGATAT
Found at i:40333057 original size:41 final size:41
Alignment explanation
Indices: 40332959--40333082 Score: 203
Period size: 41 Copynumber: 3.0 Consensus size: 41
40332949 CCGGATATAG
*
40332959 TACCAGCACTAAGCCTGCGGGATTTAACCTGGATATATATAT
1 TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATATAT-T
* * *
40333001 TACCAGCACGAAGCCTGCAGGATTTAGCCCGGATATATATT
1 TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATATATT
40333042 TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATATATT
1 TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATATATT
40333083 ATATCGAGAG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 39 0.52
42 36 0.48
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (41 bp):
TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATATATT
Found at i:40346265 original size:14 final size:14
Alignment explanation
Indices: 40346227--40346269 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
40346217 CAAAATTTAC
40346227 AATATAATTAAA-T
1 AATATAATTAAATT
40346240 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
40346255 AA-ATAATTTAATT
1 AATATAATTAAATT
40346268 AA
1 AA
40346270 CTGTTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:40357059 original size:21 final size:21
Alignment explanation
Indices: 40357035--40357077 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40357025 CTCCTCTTTT
40357035 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
40357056 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
40357077 T
1 T
40357078 TTCTTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.14, G:0.19, T:0.63
Consensus pattern (21 bp):
TGTCTATTTTCTTTGTGTTGC
Found at i:40360562 original size:6 final size:6
Alignment explanation
Indices: 40360546--40360583 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
40360536 TGAGTATTGG
*
40360546 TTTTAT TTTTTT ATTTTAT TTTTAT TTTTA- TTTTAT TT
1 TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TT
40360584 GGTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:40371717 original size:27 final size:27
Alignment explanation
Indices: 40371687--40371858 Score: 245
Period size: 27 Copynumber: 6.4 Consensus size: 27
40371677 ATACTAGACC
* *
40371687 CCCTTATGTGATAAAATAACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* * *
40371714 CCCTTATATAGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* *
40371741 CCCTCATGTGGTAAAATGACTATTTTA
1 CCCTTATGTGGTAAAATGACTATTTTG
* *
40371768 CCCTTATATGGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
40371795 CCCTCATGTGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
40371822 CCCTTATGTGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
40371849 CCCCTATGTG
1 CCCTTATGTG
40371859 ATATATGTTT
Statistics
Matches: 126, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (27 bp):
CCCTTATGTGGTAAAATGACTATTTTG
Found at i:40374659 original size:22 final size:22
Alignment explanation
Indices: 40374634--40374677 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40374624 TAGTCATATA
40374634 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
40374656 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
40374678 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:40374713 original size:13 final size:14
Alignment explanation
Indices: 40374697--40374738 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40374687 TTTCAATTTT
40374697 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
40374710 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
40374725 ATTTTAAATAATAT
1 ATTTT-AATAATAT
40374739 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:40374723 original size:16 final size:16
Alignment explanation
Indices: 40374701--40374737 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40374691 AATTTTATTT
40374701 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
40374718 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
40374733 TAATA
1 TAATA
40374738 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:40377141 original size:20 final size:19
Alignment explanation
Indices: 40377107--40377146 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
40377097 CATTTCAATT
*
40377107 TCATTTATCATTTCACATG
1 TCATTTATCAATTCACATG
*
40377126 TCATTTAATCAATTCATATG
1 TCATTT-ATCAATTCACATG
40377146 T
1 T
40377147 TTATAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (19 bp):
TCATTTATCAATTCACATG
Found at i:40378531 original size:63 final size:63
Alignment explanation
Indices: 40378422--40378540 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
40378412 CAAGTTGTGA
* * *
40378422 AACTCACTGTTTGTGATTTAGGGTCACATGAGGTAGGGACATGGGCGTGTGTCCAGACTGTTT
1 AACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTTT
* *
40378485 AACTCACTATTTGTGATTTAGTGTCACATG-GGTCATAGACACGGGCGTGTGTCCAG
1 AACTCACTATTTGTGATTTAGGGTCACATGAGGT-AGAGACACGGGCGTGTGTCCAG
40378541 GTTGTGTGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
62 3 0.06
63 47 0.94
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (63 bp):
AACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTTT
Found at i:40379694 original size:22 final size:21
Alignment explanation
Indices: 40379646--40379696 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
40379636 ATAAACTATT
40379646 ACTATTTTAGGGAAAAATAAC
1 ACTATTTTAGGGAAAAATAAC
* * * *
40379667 AATATTTTAGAGTAACAATATC
1 ACTATTTTAG-GGAAAAATAAC
40379689 ACTATTTT
1 ACTATTTT
40379697 CGCCTGGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
ACTATTTTAGGGAAAAATAAC
Found at i:40380568 original size:14 final size:14
Alignment explanation
Indices: 40380551--40380578 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40380541 ACTAATTTGT
40380551 TTGAAAAAATTACA
1 TTGAAAAAATTACA
40380565 TTGAAAAAATTACA
1 TTGAAAAAATTACA
40380579 AGTGTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TTGAAAAAATTACA
Found at i:40382226 original size:23 final size:23
Alignment explanation
Indices: 40382199--40382243 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40382189 TTGTATTAAT
40382199 TTACTAAATTAAACTTAAAAATG
1 TTACTAAATTAAACTTAAAAATG
* *
40382222 TTACTAAATTTATCTTAAAAAT
1 TTACTAAATTAAACTTAAAAAT
40382244 TATAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
TTACTAAATTAAACTTAAAAATG
Found at i:40387110 original size:25 final size:25
Alignment explanation
Indices: 40387061--40387208 Score: 101
Period size: 25 Copynumber: 6.0 Consensus size: 25
40387051 TGTCATTAGA
*
40387061 TTACCGAT-TCTCAGCTCG-AGAGAGC
1 TTACCGATAT-TCAGCTCGTA-TGAGC
40387086 TTACCGATATTCAGCTCGTATGAGC
1 TTACCGATATTCAGCTCGTATGAGC
* * * * *
40387111 TTATCGTTATTCAACTTGTATGAGT
1 TTACCGATATTCAGCTCGTATGAGC
* *
40387136 TTA-CTATTACTCAGCTCGTATGAGC
1 TTACCGA-TATTCAGCTCGTATGAGC
*
40387161 TTACC-A-ATTACAGCTCGTAAGAGC
1 TTACCGATATT-CAGCTCGTATGAGC
* * *
40387185 ATACCAAT-TTAGAGCTCGTATGAG
1 TTACCGATATT-CAGCTCGTATGAG
40387209 TATACATGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.02
24 18 0.18
25 76 0.77
26 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGTATGAGC
Found at i:40387213 original size:25 final size:24
Alignment explanation
Indices: 40387147--40387213 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
40387137 TACTATTACT
40387147 CAGCTCGTATGAGCT-TACCAATTA
1 CAGCTCGTATGAG-TATACCAATTA
* *
40387171 CAGCTCGTAAGAGCATACCAATTTA
1 CAGCTCGTATGAGTATACCAA-TTA
*
40387196 GAGCTCGTATGAGTATAC
1 CAGCTCGTATGAGTATAC
40387214 ATGTACAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (24 bp):
CAGCTCGTATGAGTATACCAATTA
Found at i:40387920 original size:10 final size:10
Alignment explanation
Indices: 40387905--40387943 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
40387895 ATTTGGAAGA
40387905 GTTTAAAATT
1 GTTTAAAATT
40387915 GTTTAAAATT
1 GTTTAAAATT
40387925 GTTTAAAATT
1 GTTTAAAATT
40387935 GTTTAAAAT
1 GTTTAAAAT
40387944 CCTACTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (10 bp):
GTTTAAAATT
Found at i:40391214 original size:52 final size:52
Alignment explanation
Indices: 40391156--40391356 Score: 159
Period size: 52 Copynumber: 4.0 Consensus size: 52
40391146 GATGGAAAAT
* *
40391156 ATGTGATATGTGCTTCCGTAAAAGACCATAGCTAGGCTATGGCATCGGTACA
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * * ***
40391208 ATGTGAT-TCGAG-TTCCCGTATAAGACCATGGCTGGGCAATAGCATCGGTGTG
1 ATGTGATAT-GTGCTT-CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
40391260 ATGTGATAATATGAC-TCCGTATAAGACCATATCTGGGATATGGCATCGGT---
1 ATGTGAT-ATGTG-CTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * *
40391310 ATGT--TATGTG-ATCCGTATAAGACCATGGCAGGGCTATGGCTTCGGTA
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
40391357 TGTGATGTGT
Statistics
Matches: 119, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
46 30 0.25
47 4 0.03
48 1 0.01
50 4 0.03
51 3 0.03
52 45 0.38
53 30 0.25
54 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (52 bp):
ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:40391348 original size:46 final size:46
Alignment explanation
Indices: 40391275--40391365 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
40391265 ATAATATGAC
* * *
40391275 TCCGTATAAGACCATATCTGGGATATGGCATCGGTATGTTATGTGA
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
* * *
40391321 TCCGTATAAGACCATGGCAGGGCTATGGCTTCGGTATGTGATGTG
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTG
40391366 TGACAATGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
Found at i:40391406 original size:28 final size:28
Alignment explanation
Indices: 40391366--40391428 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
40391356 ATGTGATGTG
40391366 TGACAATGTGAAAGTCCATAGTTTACTA
1 TGACAATGTGAAAGTCCATAGTTTACTA
40391394 TGACAATGTGAAAGTCCATAGTTTACTA
1 TGACAATGTGAAAGTCCATAGTTTACTA
*
40391422 TGGCAAT
1 TGACAAT
40391429 ATGATAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (28 bp):
TGACAATGTGAAAGTCCATAGTTTACTA
Found at i:40394754 original size:24 final size:23
Alignment explanation
Indices: 40394722--40394772 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
40394712 TTAGTACTTA
*
40394722 TTTTTTTCTTCTTTTTTTTCTTCT
1 TTTTTTTCTTCTTTTTTTTATT-T
40394746 TTTTTTTCTTCTTTTTTTTATTT
1 TTTTTTTCTTCTTTTTTTTATTT
40394769 TTTT
1 TTTT
40394773 AAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTTCTTCTTTTTTTTATTT
Found at i:40394772 original size:12 final size:12
Alignment explanation
Indices: 40394722--40394764 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
40394712 TTAGTACTTA
40394722 TTTTTTTCTTCT
1 TTTTTTTCTTCT
40394734 TTTTTTTCTTCT
1 TTTTTTTCTTCT
40394746 TTTTTTTCTTCT
1 TTTTTTTCTTCT
40394758 TTTTTTT
1 TTTTTTT
40394765 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:40395128 original size:118 final size:118
Alignment explanation
Indices: 40394810--40395115 Score: 365
Period size: 118 Copynumber: 2.6 Consensus size: 118
40394800 GAATATATTA
* *
40394810 AACCTTTTGACGCGAAG-AGAGATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAA-CAT
1 AACCTTTTGACGCGAAGTAGA-ATGACAACCCAAGCACCCTACCCCGGTTACTCAG-TCAATCA-
* * * * ** *
40394873 C-CTCCTAA--AATTATTTAT-TTCT-GGTTAGCGGAGTTTTACCCAACACGTCACAC
63 CAAT-CTAAGCCA-TACTCATAACCTCGGCTAGCGGAGTTTTACCCAACACGTCACAC
*
40394926 AACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAGTCAGTCACAA
1 AACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAGTCAATCACAA
* * ****
40394991 TTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGTCACGTCACAC
66 TCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACCCAACACGTCACAC
*
40395044 AACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAGTCAATCACGA
1 AACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAGTCAATCACAA
40395109 TCTAAGC
66 TCTAAGC
40395116 TGTGCTCATA
Statistics
Matches: 163, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
115 5 0.03
116 58 0.36
117 6 0.04
118 94 0.58
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (118 bp):
AACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAGTCAATCACAA
TCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACCCAACACGTCACAC
Found at i:40395927 original size:42 final size:42
Alignment explanation
Indices: 40395881--40395971 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
40395871 TGAAAAGGGG
* **
40395881 TGTTTGGCTGCAGGTTTATGACATTCTGGGCTGGAATAGAAC
1 TGTTTGGCAGCAGGGATATGACATTCTGGGCTGGAATAGAAC
* *
40395923 TGTTTGGCAGCAGGGATATGGCATTTTGGGCTGGAATAGAAC
1 TGTTTGGCAGCAGGGATATGACATTCTGGGCTGGAATAGAAC
40395965 TGTTTGG
1 TGTTTGG
40395972 TACCATGGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (42 bp):
TGTTTGGCAGCAGGGATATGACATTCTGGGCTGGAATAGAAC
Found at i:40395982 original size:42 final size:42
Alignment explanation
Indices: 40395897--40395982 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
40395887 GCTGCAGGTT
*
40395897 TATGACATTCTGGGCTGGAATAGAACTGTTTGGCAGCAGGGA
1 TATGACATTCTGGGCTGGAATAGAACTGTTTGGCACCAGGGA
* * * *
40395939 TATGGCATTTTGGGCTGGAATAGAACTGTTTGGTACCATGGA
1 TATGACATTCTGGGCTGGAATAGAACTGTTTGGCACCAGGGA
40395981 TA
1 TA
40395983 GGGTTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (42 bp):
TATGACATTCTGGGCTGGAATAGAACTGTTTGGCACCAGGGA
Found at i:40396101 original size:7 final size:7
Alignment explanation
Indices: 40396089--40396150 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
40396079 AAATAAAATA
40396089 AAATAAT
1 AAATAAT
40396096 AAATAAT
1 AAATAAT
40396103 AAATAAT
1 AAATAAT
40396110 AAA-AGA-
1 AAATA-AT
*
40396116 AAATAAAGGA
1 AAAT-AA--T
40396126 AAATAAT
1 AAATAAT
40396133 AAATAA-
1 AAATAAT
40396139 AAATAA-
1 AAATAAT
40396145 AAATAA
1 AAATAA
40396151 AGATTGGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
6 16 0.33
7 25 0.52
8 1 0.02
9 2 0.04
10 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (7 bp):
AAATAAT
Found at i:40396110 original size:27 final size:29
Alignment explanation
Indices: 40396080--40396153 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 29
40396070 ATTTAACTAA
*
40396080 AATAAAATAAAAT-AA-TAAATAATAAAT
1 AATAAAATAAAATAAAGAAAATAATAAAT
*
40396107 AATAAAAGAAAATAAAGGAAAATAATAAAT
1 AATAAAATAAAATAAA-GAAAATAATAAAT
40396137 -A-AAAATAAAAATAAAGA
1 AATAAAAT-AAAATAAAGA
40396154 TTGGGTTGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 12 0.30
28 8 0.20
29 9 0.22
30 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (29 bp):
AATAAAATAAAATAAAGAAAATAATAAAT
Found at i:40396132 original size:30 final size:29
Alignment explanation
Indices: 40396096--40396152 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
40396086 ATAAAATAAT
40396096 AAATAATAAATAATAAA-AGAAAATAAAGGA
1 AAATAATAAATAA-AAATA-AAAATAAAGGA
40396126 AAATAATAAATAAAAATAAAAATAAAG
1 AAATAATAAATAAAAATAAAAATAAAG
40396153 ATTGGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (29 bp):
AAATAATAAATAAAAATAAAAATAAAGGA
Found at i:40398803 original size:22 final size:22
Alignment explanation
Indices: 40398778--40398829 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
40398768 TTTTGTTTCC
40398778 TTTCGATTAGCTTTCGCAGTCT
1 TTTCGATTAGCTTTCGCAGTCT
40398800 TTTCGATTAGCTTTCGCAGTCT
1 TTTCGATTAGCTTTCGCAGTCT
40398822 TTTCGATT
1 TTTCGATT
40398830 TCTGAGTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.48
Consensus pattern (22 bp):
TTTCGATTAGCTTTCGCAGTCT
Found at i:40401057 original size:25 final size:25
Alignment explanation
Indices: 40401024--40401256 Score: 76
Period size: 25 Copynumber: 9.4 Consensus size: 25
40401014 ACAATACTTT
* *
40401024 ACAAGGGTTTCTCACAAGATTAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* * *
40401049 ACAAAGGTTTTTCATAGGAATAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* *
40401074 ACAAAGGTTT-TC-CATATAATATACC
1 ACAAAGGTTTCTCACA-AGAATA-GCC
* *
40401099 ATAAAGGCTTTC-CA-AAAAATA-CC
1 ACAAAGG-TTTCTCACAAGAATAGCC
* * *
40401122 ACAAAAACG-TT-TCATAAGATTAGCC
1 AC--AAAGGTTTCTCACAAGAATAGCC
* * *
40401147 ACAAAGGCTTTCT-A-GATAATACACC
1 ACAAAGG-TTTCTCACAAGAATA-GCC
* * * *
40401172 ACAAATGCTTCTCATAAGATTAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* *
40401197 ATAAAGGCTTTC-CA-AATAATATGCC
1 ACAAAGG-TTTCTCACAAGAATA-GCC
* * *
40401222 AAAAAGGCTTT-TCATAAGATTAGCC
1 ACAAAGG-TTTCTCACAAGAATAGCC
40401247 ACAAAGGTTT
1 ACAAAGGTTT
40401257 TCTAGATAAT
Statistics
Matches: 153, Mismatches: 35, Indels: 41
0.67 0.15 0.18
Matches are distributed among these distances:
23 12 0.08
24 27 0.18
25 96 0.63
26 18 0.12
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (25 bp):
ACAAAGGTTTCTCACAAGAATAGCC
Found at i:40401189 original size:50 final size:50
Alignment explanation
Indices: 40401133--40401266 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
40401123 CAAAAACGTT
* *
40401133 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCACAAATGCTTC
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
* * * ** *
40401183 TCATAAGATTAGCCATAAAGGCTTTCCAAATAATATGCCAAAAAGGCTTT
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
*
40401233 TCATAAGATTAGCCACAAAGGTTTTCTAGATAAT
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAAT
40401267 CCATTTTTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (50 bp):
TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
Found at i:40403637 original size:29 final size:29
Alignment explanation
Indices: 40403605--40403672 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
40403595 ATACTATTAT
*
40403605 TATTTATATAATTTTTAT-TTATCTATTTA
1 TATTTATATAATTATTATATT-TCTATTTA
* *
40403634 TATTTCTACT-ATTATTATATTTCTATTTC
1 TATTTATA-TAATTATTATATTTCTATTTA
40403663 TATTTATATA
1 TATTTATATA
40403673 CTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 28 0.88
30 3 0.09
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTATATAATTATTATATTTCTATTTA
Found at i:40403646 original size:23 final size:23
Alignment explanation
Indices: 40403596--40403664 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
40403586 GTTATTCCAA
*
40403596 TACTATTATTAT-TTATATAATTTT
1 TACTATTATTATATT-TAT-ATTTC
*
40403620 TA-T-TTA-TCTATTTATATTTC
1 TACTATTATTATATTTATATTTC
*
40403640 TACTATTATTATATTTCTATTTC
1 TACTATTATTATATTTATATTTC
40403663 TA
1 TA
40403665 TTTATATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.16
21 6 0.16
22 8 0.22
23 15 0.41
24 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (23 bp):
TACTATTATTATATTTATATTTC
Found at i:40403821 original size:3 final size:3
Alignment explanation
Indices: 40403806--40403916 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
40403796 TTTAAAACTT
* * * * *
40403806 TTA TTA CTA TTA TTA TTA TTA -TA TTTA TGTA TCA ATA TCA TT- TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA
* * * * * *
40403851 TTA TATA TTA TTA TCA TTA TTA TTA TTG CTA TTA GTA CTA TTA TTC
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
40403897 TTT TCTA TTA TTA TTT TTA T
1 TTA T-TA TTA TTA TTA TTA T
40403917 ATTTATTTAT
Statistics
Matches: 79, Mismatches: 23, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
2 4 0.05
3 65 0.82
4 10 0.13
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:40406080 original size:19 final size:19
Alignment explanation
Indices: 40406056--40406100 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
40406046 CGTCTCTTTT
*
40406056 TGCATT-CATTTCATGCATC
1 TGCATTGCATTTCAT-CATA
40406075 TGCATTGCATTTCATCATA
1 TGCATTGCATTTCATCATA
40406094 TGCATTG
1 TGCATTG
40406101 AATGTCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCATTGCATTTCATCATA
Found at i:40409560 original size:11 final size:11
Alignment explanation
Indices: 40409544--40409571 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40409534 TAATAATAAT
40409544 AAAAAAATCAA
1 AAAAAAATCAA
40409555 AAAAAAATCAA
1 AAAAAAATCAA
40409566 AAAAAA
1 AAAAAA
40409572 GATAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:40411267 original size:46 final size:44
Alignment explanation
Indices: 40411208--40411322 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
40411198 ACAGGACAGA
* *
40411208 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
40411254 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
40411298 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
40411323 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:40411303 original size:44 final size:45
Alignment explanation
Indices: 40411208--40411341 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
40411198 ACAGGACAGA
* *
40411208 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
40411254 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
40411298 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
40411342 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:40413518 original size:44 final size:44
Alignment explanation
Indices: 40413470--40413809 Score: 183
Period size: 44 Copynumber: 7.7 Consensus size: 44
40413460 AGCCACCAGC
* *
40413470 CTTAT-TTCCCTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
** * *
40413514 CTTATCTTTTTGAGGTAGCAAGGGAGCAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
* ** * * * *
40413559 CTTATC-TCTCTGAGATAGCAGTGGAGTA-GATCGAATA-TGACAAAT
1 CTTATCTTC-CTGAGGTAGCAAAGGAGCAGGCT-GAAGATTG--AAGT
* * ** ** ***** *
40413604 CTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGC
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * * *
40413648 CTTAT-TTCCCTGAGGTAGCAAGGGAGTAGGCTAAAGATTGCAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * *
40413692 CTTATCTTTCTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
* * * * *
40413737 CTTGTATTCCTGA-GCAGCAATA-GAGCAGGCTGAGGATTGTAGAT
1 CTTATCTTCCTGAGGTAGCAA-AGGAGCAGGCTGAAGATTGAAG-T
*
40413781 CTTATCTTCATGAGGTAGCAATA-GAGCAG
1 CTTATCTTCCTGAGGTAGCAA-AGGAGCAG
40413810 ATCGAAGATG
Statistics
Matches: 219, Mismatches: 63, Indels: 27
0.71 0.20 0.09
Matches are distributed among these distances:
43 2 0.01
44 134 0.61
45 78 0.36
46 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
Found at i:40413829 original size:222 final size:222
Alignment explanation
Indices: 40413479--40413882 Score: 519
Period size: 222 Copynumber: 1.8 Consensus size: 222
40413469 CCTTATTTCC
** * * * ** * *
40413479 CTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGTCTTATCTTTTTGAGGTAGCAAGGGAGCAGA
1 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGTCTTATATTCCTGAGGCAGCAAGAGAGCAGA
* * * *
40413544 CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAGTGGAGTAGATCGAATATGACAAATCTTAT
66 CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTTAT
* * *
40413609 CTTCC-CGAGGTAGCAGA-GGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAGCAAGGG
131 C-TCCACAAGGTAGCA-ATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTAGCAAGGG
40413672 AGTAGGCTAAAGATTGCAGTCTTATCTTT
194 AGTAGGCTAAAGATTGCAGTCTTATCTTT
* *
40413701 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGATCTTGTATTCCTGA-GCAGCAATAGAGCAG
1 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAG-TCTTATATTCCTGAGGCAGCAAGAGAGCAG
* * * * * *
40413765 GCTGAGGATTGTAGATCTTATCT-TCATGAGGTAGCAATAGAGCAGATCGAAGATGGCGAATCTT
65 ACTGAAGATTGAAGATCTTATCTCTC-TGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTT
*
40413829 ATCTCCATAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGA
129 ATCTCCACAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGA
40413883 AGTTGCAGTG
Statistics
Matches: 153, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
221 6 0.04
222 137 0.90
223 10 0.07
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (222 bp):
CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGTCTTATATTCCTGAGGCAGCAAGAGAGCAGA
CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTTAT
CTCCACAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTAGCAAGGGAG
TAGGCTAAAGATTGCAGTCTTATCTTT
Found at i:40413994 original size:45 final size:45
Alignment explanation
Indices: 40413869--40414331 Score: 228
Period size: 44 Copynumber: 10.4 Consensus size: 45
40413859 AAGCCACCAG
* *
40413869 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTCGAA-ATTACAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
* * *
40413913 CCTTATCTCCCTGAAGTTGCATTGGAGTAGACTGAAGA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* * * * *
40413958 TCTTATTTCCCTGAAGATGCAGTGGAACAGATTGAAGCTATAAATAAACAGA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT---T--ACAAA
* * * *
40414010 TCTTATCTCTCTGAA-TTGCAGTAGAGCAGA-T---CA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* * * **
40414050 CTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG-TAACAGG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
* * * * * * ** * *
40414094 TCTTATCTCCTTGAGGTAGCAG-GGAAGAAGATTTAAG-CCACCAG
1 CCTTATCTCCCTGAAGTTGCAGTGG-AGCAGATTGAAGATTACAAA
* * *
40414138 CCTTATCTCCCTGAA-TTACAGTGGAGCA-AGTTG-ACATTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATTA-CAAA
* * * * * *
40414182 CCTTATCTCCCTAAAGTTGTAGTGGAGCA-A--GAAAATAAACGAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-TACAAA
* * * *
40414225 TCTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTGAAG-TCACGAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATTACAAA
* * *
40414269 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAA-ATTATCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* *
40414314 TCTTATCTCCTTGAAGTT
1 CCTTATCTCCCTGAAGTT
40414332 TCAGCAGAGT
Statistics
Matches: 316, Mismatches: 72, Indels: 61
0.70 0.16 0.14
Matches are distributed among these distances:
39 1 0.00
40 15 0.05
41 14 0.04
42 4 0.01
43 45 0.14
44 134 0.42
45 68 0.22
46 3 0.01
47 1 0.00
50 1 0.00
51 13 0.04
52 16 0.05
53 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (45 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
Found at i:40414232 original size:87 final size:87
Alignment explanation
Indices: 40414139--40414297 Score: 241
Period size: 87 Copynumber: 1.8 Consensus size: 87
40414129 AGCCACCAGC
*
40414139 CTTATCTCCCTGAA-TTACAGTGGAGCAAGTTGACA-TTACCAATCCTTATCTCCCTAAAGTTGT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA-AGTCACCAA-CCTTATCTCCCTAAAGTTGT
40414202 AGTGGAGCAAGAAAATAAACGAGT
64 AGTGGAGCAAGAAAATAAACGAGT
** * *
40414226 CTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTCACGAACCTTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAAGTCACCAACCTTATCTCCCTAAAGTTGTAG
40414291 TGGAGCA
66 TGGAGCA
40414298 GGTTGAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
87 43 0.66
88 22 0.34
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (87 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAAGTCACCAACCTTATCTCCCTAAAGTTGTAG
TGGAGCAAGAAAATAAACGAGT
Found at i:40414775 original size:19 final size:19
Alignment explanation
Indices: 40414751--40414806 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
40414741 AGGAAGATAA
* * *
40414751 TTATTTGTTTTTGTTTTAT
1 TTATTTATTTTTATTTCAT
40414770 TTATTTATTTTTATTTCAT
1 TTATTTATTTTTATTTCAT
*
40414789 TTCATTTTATTTTAATTT
1 TT-A-TTTATTTTTATTT
40414807 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 18 0.58
20 1 0.03
21 12 0.39
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (19 bp):
TTATTTATTTTTATTTCAT
Found at i:40415379 original size:15 final size:14
Alignment explanation
Indices: 40415353--40415439 Score: 70
Period size: 15 Copynumber: 6.0 Consensus size: 14
40415343 TATTCTAATA
*
40415353 CTATTATTATTTAT
1 CTATTTTTATTTAT
40415367 CTAATTTTTATTTAT
1 CT-ATTTTTATTTAT
* *
40415382 CTATTTATATTTCT
1 CTATTTTTATTTAT
*
40415396 ACTATTATTATATT-T
1 -CTATTTTTAT-TTAT
40415411 CTATTTATTATATT-T
1 CTATTT-TTAT-TTAT
*
40415426 CTATTTGTATTTAT
1 CTATTTTTATTTAT
40415440 ATACTAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.03
14 21 0.34
15 36 0.59
16 2 0.03
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.64
Consensus pattern (14 bp):
CTATTTTTATTTAT
Found at i:40415392 original size:29 final size:28
Alignment explanation
Indices: 40415325--40415461 Score: 93
Period size: 29 Copynumber: 4.6 Consensus size: 28
40415315 ATTGCTATTA
*
40415325 TTATTATGTTTCTATTGTTATTCTAATACTA-
1 TTATTAT-TTTCTATTTTTATT-T-AT-CTAT
40415356 TTATTATTTATCTAATTTTTATTTATCTAT
1 TTATTATTT-TCT-ATTTTTATTTATCTAT
*
40415386 TTA-TATTTCTACTATTATTATATT-TCTAT
1 TTATTATTT-T-CTATTTTTAT-TTATCTAT
* *
40415415 TTATTATATTTCTATTTGTATTTATATACT
1 TTATTAT-TTTCTATTTTTATTTATCTA-T
*
40415445 AATATTATTTTC-ATTTT
1 -TTATTATTTTCTATTTT
40415462 AGTTTTCTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
28 2 0.02
29 39 0.44
30 20 0.23
31 19 0.22
32 8 0.09
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (28 bp):
TTATTATTTTCTATTTTTATTTATCTAT
Found at i:40415408 original size:17 final size:15
Alignment explanation
Indices: 40415386--40415431 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
40415376 ATTTATCTAT
40415386 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
40415403 TTATATTTCTATTTA
1 TTATATTTCTATTTA
40415418 TTATATTTCTATTT
1 TTATATTTCTATTT
40415432 GTATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 11 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:40415429 original size:44 final size:44
Alignment explanation
Indices: 40415325--40415454 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
40415315 ATTGCTATTA
40415325 TTATTATGTTTCTATTGTTATTCTAATACTATTATTATTTATCTAAT
1 TTATTAT-TTTCTATT-TTATT-TAATACTATTATTATTTATCTAAT
*
40415372 TT-TTATTTATCTATTTATATTT-CTACTATTATTATATT-TCT-AT
1 TTATTATTT-TCTATTT-TATTTAATACTATTATTAT-TTATCTAAT
*
40415415 TTATTATATTTCTATTTGTATTTATATACTAATATTATTT
1 TTATTAT-TTTCTATTT-TATTTA-ATACTATTATTATTT
40415455 TCATTTTAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
43 4 0.06
44 31 0.43
45 10 0.14
46 25 0.35
47 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (44 bp):
TTATTATTTTCTATTTTATTTAATACTATTATTATTTATCTAAT
Found at i:40415580 original size:3 final size:3
Alignment explanation
Indices: 40415565--40415728 Score: 176
Period size: 3 Copynumber: 55.0 Consensus size: 3
40415555 ATTTTAAAAC
*
40415565 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
40415613 TAT TAT TAT ATAT ATAT GTAT CAA TAT CAT TAT T-T TAT T-T TAT T-T
1 TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
40415658 TAT TAT ATAT TAT TAT TAT CAT TAT TAT TAT TAC TAT TAG TAC TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
40415704 TAT TAT T-T T-T TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
40415729 ATTTATTTAT
Statistics
Matches: 137, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
2 10 0.07
3 114 0.83
4 13 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40417418 original size:25 final size:25
Alignment explanation
Indices: 40417336--40417409 Score: 132
Period size: 26 Copynumber: 3.0 Consensus size: 25
40417326 CCCTCCCAAA
40417336 AAAAAACCTAACCCCCAAAAAAAAG
1 AAAAAACCTAACCCCCAAAAAAAAG
40417361 AAAAAACCTAACCCCCCAAAAAAAAG
1 AAAAAACCTAA-CCCCCAAAAAAAAG
40417387 AAAAAACCTAA-CCCCAAAAAAAA
1 AAAAAACCTAACCCCCAAAAAAAA
40417410 CCAAGAAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
24 12 0.25
25 11 0.23
26 25 0.52
ACGTcount: A:0.65, C:0.28, G:0.03, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCCCAAAAAAAAG
Found at i:40418252 original size:21 final size:23
Alignment explanation
Indices: 40418226--40418268 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40418216 ATACTTCTTG
*
40418226 TATATT-TCT-ATGTATATACTT
1 TATATTGTCTCATGTACATACTT
40418247 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
40418269 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:40418606 original size:16 final size:15
Alignment explanation
Indices: 40418582--40418616 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40418572 TAATTATTAT
40418582 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
40418598 TATTTTAATATTTTA
1 TATTCTAATATTTTA
40418613 TATT
1 TATT
40418617 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:40430521 original size:74 final size:74
Alignment explanation
Indices: 40430431--40431065 Score: 896
Period size: 72 Copynumber: 8.7 Consensus size: 74
40430421 TGATGTTTTT
* *
40430431 ATTTCTG-TTTCAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGA
1 ATTTCTGTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40430495 GGTAATTTCA
65 GGTAATTTCA
* * *
40430505 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
40430570 GTAATTTCA
66 GTAATTTCA
*
40430579 ATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
40430642 GTAATTTCA
66 GTAATTTCA
* ** * *
40430651 ATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
* *
40430714 GTATTTTTA
66 GTAATTTCA
* * *
40430723 ATTTTTGTCTTT-AAAAAAATCAACTCATACTGCGAGAGTTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40430787 GGTAATTTCA
65 GGTAATTTCA
**
40430797 ATTTCTGTTGTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
40430861 GGTAATTTCA
65 GGTAATTTCA
* ** * *
40430871 ATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
40430934 GTATTTTCA
66 GTAATTTCA
* * *
40430943 ATTTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTG
1 A-TTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
40431008 AGGTAATTTCA
64 AGGTAATTTCA
*
40431019 ATTTCTGTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGC
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40431066 TTCAAATCAC
Statistics
Matches: 508, Mismatches: 43, Indels: 22
0.89 0.08 0.04
Matches are distributed among these distances:
72 221 0.44
73 11 0.02
74 215 0.42
75 8 0.02
76 53 0.10
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (74 bp):
ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTTCA
Found at i:40430601 original size:146 final size:146
Alignment explanation
Indices: 40430445--40431065 Score: 913
Period size: 146 Copynumber: 4.2 Consensus size: 146
40430435 CTGTTTCAAA
* *
40430445 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
** * *
40430510 TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAGGTAAT
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
40430575 TTCAATTTCTGTTTTC
131 TTCAATTTCTGTTTTC
*
40430591 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * * * *
40430656 TGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATT
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
* * *
40430719 TTTAATTTTTGTCTTTAA
131 TTCAATTTCTGT-TTT-C
* *
40430737 AAAAATCAACTCATACTGCGAGAGTTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
40430802 TGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
40430867 TTCAATTTCTGTTTTC
131 TTCAATTTCTGTTTTC
* ** * * *
40430883 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-TTT
* * ** * *
40430948 TTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAGGTA
65 CTG-TTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA
40431013 ATTTCAATTTCTGTTTTC
129 ATTTCAATTTCTGTTTTC
*
40431031 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40431066 TTCAAATCAC
Statistics
Matches: 424, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
144 58 0.14
145 3 0.01
146 189 0.45
147 8 0.02
148 166 0.39
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (146 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
TTCAATTTCTGTTTTC
Found at i:40431953 original size:26 final size:25
Alignment explanation
Indices: 40431925--40431998 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
40431915 CCCTCCCAAA
40431925 AAAAAACCTAACCCCCAAAAAAAAG
1 AAAAAACCTAACCCCCAAAAAAAAG
40431950 AAAAAACCTAACCCCCCAAAAAAAAG
1 AAAAAACCTAA-CCCCCAAAAAAAAG
*
40431976 -AAAAACCTAACCCCAAAAAAAAA
1 AAAAAACCTAACCCCCAAAAAAAA
40431999 CCAAGAAACT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 12 0.26
25 21 0.45
26 14 0.30
ACGTcount: A:0.65, C:0.28, G:0.03, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCCCAAAAAAAAG
Found at i:40432244 original size:15 final size:14
Alignment explanation
Indices: 40432215--40432260 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
40432205 CCTAAAGGTG
*
40432215 ATTTTATCTTCTTT
1 ATTTTATCTTTTTT
40432229 ATTTTACTCTTTTTT
1 ATTTTA-TCTTTTTT
40432244 ATTTTA--TTTTTT
1 ATTTTATCTTTTTT
40432256 ATTTT
1 ATTTT
40432261 TTTCCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.37
14 6 0.20
15 13 0.43
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTATCTTTTTT
Found at i:40432269 original size:27 final size:29
Alignment explanation
Indices: 40432215--40432270 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
40432205 CCTAAAGGTG
*
40432215 ATTTTATCTTCTTTATTTTACTCTTTTTT
1 ATTTTATCTTCTTTATTTTACTCCTTTTT
**
40432244 ATTTTAT-TT-TTTATTTTTTTCCTTTTT
1 ATTTTATCTTCTTTATTTTACTCCTTTTT
40432271 TGGATCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.62
28 2 0.08
29 7 0.29
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (29 bp):
ATTTTATCTTCTTTATTTTACTCCTTTTT
Done.