Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 50
Found at i:5327068 original size:108 final size:108
Alignment explanation
Indices: 5326879--5327115 Score: 438
Period size: 108 Copynumber: 2.2 Consensus size: 108
5326869 TTTAAAAATA
* * * *
5326879 TTTTTATCTTAAAATAAAAAAATGGCAAAATACATAACCCTAAAGAGCTTACCTTTTCCTTAGTC
1 TTTTTACCCTAAAATAAAATAATGGCAAAATACATAACCCTAAAGAGCTTACATTTTCCTTAGTC
5326944 GCTCTCTCCTTTGTCTTCCTTTCCCCCTTTTTCTTATTTGAGC
66 GCTCTCTCCTTTGTCTTCCTTTCCCCCTTTTTCTTATTTGAGC
5326987 TTTTTACCCTAAAATAAAATAATGGCAAAATACATAACCCTAAAGAGCTTACATTTTCCTTAGTC
1 TTTTTACCCTAAAATAAAATAATGGCAAAATACATAACCCTAAAGAGCTTACATTTTCCTTAGTC
5327052 GCTCTCTCCTTTGTCTTCCTTTCCCCCTTTTTCTTATTTGAGC
66 GCTCTCTCCTTTGTCTTCCTTTCCCCCTTTTTCTTATTTGAGC
5327095 TTTTTACCCTAAAATAAAATA
1 TTTTTACCCTAAAATAAAATA
5327116 TTGAAGATCT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 125 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (108 bp):
TTTTTACCCTAAAATAAAATAATGGCAAAATACATAACCCTAAAGAGCTTACATTTTCCTTAGTC
GCTCTCTCCTTTGTCTTCCTTTCCCCCTTTTTCTTATTTGAGC
Found at i:5327453 original size:23 final size:23
Alignment explanation
Indices: 5327427--5327507 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
5327417 ATTATGCCCA
5327427 TGTTGCACGTTTATCTATG-CTT
1 TGTTGCACGTTTATCTATGCCTT
* *
5327449 GTGTTGCACGTTTATATATGTCTT
1 -TGTTGCACGTTTATCTATGCCTT
*
5327473 TG-TGACACGTTTATCTTTGCCTT
1 TGTTG-CACGTTTATCTATGCCTT
*
5327496 TGTGGCACGTTT
1 TGTTGCACGTTT
5327508 TTCAATTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.04
23 44 0.88
24 4 0.08
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (23 bp):
TGTTGCACGTTTATCTATGCCTT
Found at i:5328348 original size:35 final size:35
Alignment explanation
Indices: 5328302--5328425 Score: 185
Period size: 35 Copynumber: 3.5 Consensus size: 35
5328292 TCTGTCATCG
5328302 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
*
5328337 AGAATCGAAAGTGATATGCCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
* *
5328372 AGAATCGAAAGTGCTATACCTCTTTTCGTTCTACT
1 AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
** * *
5328407 CTAATCAAAAGTGTGATGC
1 AGAATCGAAAGTGTTATGC
5328426 TTTCTTCTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 80 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (35 bp):
AGAATCGAAAGTGTTATGCCTCTTTTCGTTCTACT
Found at i:5328488 original size:42 final size:42
Alignment explanation
Indices: 5328409--5328503 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
5328399 GTTCTACTCT
* * * *
5328409 AATCAAAAGTGTGATGCTTTCTTCTGTTATACATTAGACGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
* * *
5328451 AATCGAAAGTGTGATCCTTCCTTCCGTTCTACTTTAGATGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
*
5328493 AATTGAAAGTG
1 AATCGAAAGTG
5328504 CTATGCCTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (42 bp):
AATCGAAAGTGTGATCCTTCCTTCCGTTATACATTAGACGAG
Found at i:5328515 original size:42 final size:42
Alignment explanation
Indices: 5328409--5328526 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
5328399 GTTCTACTCT
* * * * *
5328409 AATCAAAAGTGTGATGCTTTCTTCTGTT-ATACATTAGACGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTCA-ACTTTAGACGAG
* *
5328451 AATCGAAAGTGTGATCCTTCCTTCCGTTCTACTTTAGATGAG
1 AATCGAAAGTGTGATCCTTCCTTCCGTTCAACTTTAGACGAG
* *
5328493 AATTGAAAGTGCT-ATGCC-TCCTTTCGTTCAACTT
1 AATCGAAAGTG-TGAT-CCTTCCTTCCGTTCAACTT
5328527 GAATCGAAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (42 bp):
AATCGAAAGTGTGATCCTTCCTTCCGTTCAACTTTAGACGAG
Found at i:5335907 original size:35 final size:35
Alignment explanation
Indices: 5335850--5336044 Score: 219
Period size: 35 Copynumber: 5.5 Consensus size: 35
5335840 TAGTAAACCA
* * * * *
5335850 TCCGTTCTAGTTGAATCAAAAGTGCGGTGCCTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
** *
5335885 TTTGTTCGACTTGAATCGAAAGTGCGATGTTTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
*
5335920 TCCGTTCGACTTGAATCGAAAGTGTGATGCTTCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
* * *
5335955 TCCGTTTGACTTGAATCAAAAGTGCCAATGCTTCCT
1 TCCGTTCGACTTGAATCGAAAGTG-CGATGCTTCCT
* * **
5335991 TCCGTTCAACTTGAATCGAAAGTGCGATTCCCCCT
1 TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
* *
5336026 TCCGTTTGACTTAAATCGA
1 TCCGTTCGACTTGAATCGA
5336045 TGAAAACTTT
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 103 0.77
36 30 0.23
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (35 bp):
TCCGTTCGACTTGAATCGAAAGTGCGATGCTTCCT
Found at i:5336013 original size:71 final size:70
Alignment explanation
Indices: 5335850--5336042 Score: 233
Period size: 71 Copynumber: 2.7 Consensus size: 70
5335840 TAGTAAACCA
* * * * ** * * * *
5335850 TCCGTTCTAGTTGAATCAAAAGTGCGGTGCCTCCTTTTGTTCGACTTGAATCGAAAGTGCGATGT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTGCAATGC
5335915 TTCCT
66 TTCCT
* * *
5335920 TCCGTTCGACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTTGACTTGAATCAAAAGTGCCAATG
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTG-CAATG
5335985 CTTCCT
65 CTTCCT
* * *
5335991 TCCGTTCAACTTGAATCGAAAGTGCGATTCCCCCTTCCGTTTGACTTAAATC
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATC
5336043 GATGAAAACT
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
70 49 0.47
71 55 0.53
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (70 bp):
TCCGTTCAACTTGAATCGAAAGTGCGATGCCTCCTTCCGTTTGACTTGAATCAAAAGTGCAATGC
TTCCT
Found at i:5337624 original size:26 final size:25
Alignment explanation
Indices: 5337595--5337649 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
5337585 TATCATTTTC
* * *
5337595 ATTATTATTATTTTATTATTAATAA
1 ATTAGTATTATATTATCATTAATAA
5337620 TATTAGTATTATATTATCATTAATAA
1 -ATTAGTATTATATTATCATTAATAA
5337646 ATTA
1 ATTA
5337650 CAAATACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTAGTATTATATTATCATTAATAA
Found at i:5337643 original size:23 final size:23
Alignment explanation
Indices: 5337597--5337644 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5337587 TCATTTTCAT
* * *
5337597 TATTATTATTTTATTATTAATAA
1 TATTAGTATTATATTATCAATAA
*
5337620 TATTAGTATTATATTATCATTAA
1 TATTAGTATTATATTATCAATAA
5337643 TA
1 TA
5337645 AATTACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTAGTATTATATTATCAATAA
Found at i:5338420 original size:12 final size:12
Alignment explanation
Indices: 5338403--5338427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5338393 AGGCCTATTT
5338403 ATACCCTCATCA
1 ATACCCTCATCA
5338415 ATACCCTCATCA
1 ATACCCTCATCA
5338427 A
1 A
5338428 AACTAAGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (12 bp):
ATACCCTCATCA
Found at i:5338993 original size:15 final size:16
Alignment explanation
Indices: 5338973--5339009 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5338963 TAAAATACTA
*
5338973 TATTTAATTTAT-TTT
1 TATTTAAATTATATTT
5338988 TATTTAAATTATATTT
1 TATTTAAATTATATTT
5339004 T-TTTAA
1 TATTTAA
5339010 GAAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTAAATTATATTT
Found at i:5341418 original size:20 final size:19
Alignment explanation
Indices: 5341364--5341443 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
5341354 AACTCCTTCG
* *
5341364 TTGCATTTTCATTTTCATT
1 TTGCATTTGCATTTTTATT
* *
5341383 TTGCATTCT-TACTTTTATGT
1 TTGCATT-TGCATTTTTAT-T
5341403 TTGCATTTGCATTTTTATAT
1 TTGCATTTGCATTTTTAT-T
*
5341423 TTTCATTTGCATTTTTATT
1 TTGCATTTGCATTTTTATT
5341442 TT
1 TT
5341444 ATATTTTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 17 0.33
20 34 0.67
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.64
Consensus pattern (19 bp):
TTGCATTTGCATTTTTATT
Found at i:5341431 original size:26 final size:26
Alignment explanation
Indices: 5341368--5341450 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
5341358 CCTTCGTTGC
* *
5341368 ATTTTCATTTTCATTTTGCATTCTTACT
1 ATTTTCATTTGCA-TTTGCATTTTTA-T
*
5341396 -TTTAT-GTTTGCATTTGCATTTTTAT
1 ATTT-TCATTTGCATTTGCATTTTTAT
**
5341421 ATTTTCATTTGCATTTTTA-TTTTAT
1 ATTTTCATTTGCATTTGCATTTTTAT
5341446 ATTTT
1 ATTTT
5341451 TCTTCATTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
25 13 0.28
26 24 0.52
27 8 0.17
28 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (26 bp):
ATTTTCATTTGCATTTGCATTTTTAT
Found at i:5343488 original size:3 final size:3
Alignment explanation
Indices: 5343475--5343569 Score: 167
Period size: 3 Copynumber: 32.0 Consensus size: 3
5343465 GGGCATGCTC
5343475 GAA GTAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5343521 GAA GAA -AA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5343567 GAA
1 GAA
5343570 AAAGGAAAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.04
3 83 0.92
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:5345747 original size:54 final size:54
Alignment explanation
Indices: 5345658--5345760 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
5345648 TATCGAGAAT
* *
5345658 TCTGGGCAGAAGCCACAAGAAATGATGAATGTGTTGTAAAATGTTTTACGAACA
1 TCTGGGCAGAAACCACAAGAAATGATGAATATGTTGTAAAATGTTTTACGAACA
* *
5345712 TCTGTGCAGAAACCACAAGAAATGATGAATATGTTGTCAAATGTTTTAC
1 TCTGGGCAGAAACCACAAGAAATGATGAATATGTTGTAAAATGTTTTAC
5345761 AAACCAGTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (54 bp):
TCTGGGCAGAAACCACAAGAAATGATGAATATGTTGTAAAATGTTTTACGAACA
Found at i:5347139 original size:20 final size:20
Alignment explanation
Indices: 5347114--5347185 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
5347104 TCTTGATTTG
5347114 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGGGCCATCTA
* * * * *
5347134 TAAGTCTTTCGAGCATGATGTT
1 TAAGTCCTTCGGGC--CATCTA
* *
5347156 TAAATCCTTCGGGTCATCTA
1 TAAGTCCTTCGGGCCATCTA
*
5347176 TAAGACCTTC
1 TAAGTCCTTC
5347186 AGTGCTTGAT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
20 23 0.64
22 13 0.36
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCTA
Found at i:5347310 original size:223 final size:218
Alignment explanation
Indices: 5346732--5347384 Score: 786
Period size: 216 Copynumber: 3.0 Consensus size: 218
5346722 GTAAGACCTC
* * *
5346732 CGGGCCATCGATAAGACCTTCGGACATGATGTTTTTAAATGAGATTTTGGAAATTAAGC-A-TTT
1 CGGGCCATCTATAAGACCTTCGG-CATGATGTTTTCAAATGAGATTTTGGAAACTAAGCTATTTT
* *
5346795 CAGGGGTTTCTTAATTATCTCAAAGAGTTGTGAAATGAAGCTAAGCCTTTTAAGGGGTTCCTTGA
65 TAGGGGTTTCTTAATTATCTCAAAGAGTTGTGAAATGAAACTAAGCCTTTTAAGGGGTTCCTTGA
* * * * *
5346860 CAACCAAAAAACTAAGAT-TTCGAGGGTTTATTGATGTT-TAAATCCTCCGGGTCATCTGTAAGT
130 CAACCAAGAAACTAAG-TCTTCGAGGGTTTCTTGAT-TTGTAAGTCCTTCGGGCCATCTGTAAGT
* * *
5346923 C-CTCTGAGCAAGATG-ATAAGA-CCTC
193 CTTTC-GAGCATGATGTATAA-ATCCTT
* * * *
5346948 CGGGCCATCCATAAGACCTCTGGGCAGGATGTTTTCAAATGAGATTTTGGAAACTAAGC--CTTT
1 CGGGCCATCTATAAGACCT-TCGGCATGATGTTTTCAAATGAGATTTTGGAAACTAAGCTATTTT
* **
5347011 CATTGGTTTCTTAATTATCTCAAAGAGTTGTGAAATGAAGA-TAAGCCTTTTAAGGGGTTCCTTG
65 TAGGGGTTTCTTAATTATCTCAAAGAGTTGTGAAATGAA-ACTAAGCCTTTTAAGGGGTTCCTTG
*
5347075 ACAACCAAGAAACTAAGTCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCTATAAGTC
129 ACAACCAAGAAACTAAGTCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCTGTAAGTC
*
5347140 TTTCGAGCATGATGTTTAAATCCTT
194 TTTCGAGCATGATGTATAAATCCTT
* * **
5347165 CGGGTCATCTATAAGACCTTCAGTGCTTGATGTTTTCAAATGAGATTTTAAAAACTAAGCATAAT
1 CGGGCCATCTATAAGACCTTC-G-GCATGATGTTTTCAAATGAGATTTTGGAAACTAAGC-T-AT
* * * *
5347230 TTTTAGGGGTTTCTTAATTATCTCAAAAGAGTTCTTAAAGGAAACTAAGCCTTTTAAGGGGTTTC
62 TTTTAGGGGTTTCTTAATTATCTC-AAAGAGTTGTGAAATGAAACTAAGCCTTTTAAGGGGTTCC
* * * * * *
5347295 GTGACAGCTAAGAAACTATGTCTTTGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCTGTAA
126 TTGACAACCAAGAAACTAAGTCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCTGTAA
* *
5347360 GTCTTTCGAGAATGATGTGTAAATC
191 GTCTTTCGAGCATGATGTATAAATC
5347385 TTTCAGGTCA
Statistics
Matches: 379, Mismatches: 42, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
215 3 0.01
216 178 0.47
217 29 0.08
218 32 0.08
222 22 0.06
223 115 0.30
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (218 bp):
CGGGCCATCTATAAGACCTTCGGCATGATGTTTTCAAATGAGATTTTGGAAACTAAGCTATTTTT
AGGGGTTTCTTAATTATCTCAAAGAGTTGTGAAATGAAACTAAGCCTTTTAAGGGGTTCCTTGAC
AACCAAGAAACTAAGTCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCTGTAAGTCTT
TCGAGCATGATGTATAAATCCTT
Found at i:5347397 original size:42 final size:42
Alignment explanation
Indices: 5347341--5347439 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
5347331 GATTTGTAAG
* * *
5347341 TCCTTCGGGCCATCTGTAAGTCTTTCGAGAATGATG-TGTAAA
1 TCCTTCAGGTCATCTGTAAGTCTTTCAAGAATGATGCT-TAAA
* * * *
5347383 TCTTTCAGGTCATCTGTAGGTTTTTCAAGCATGATGCTTAAA
1 TCCTTCAGGTCATCTGTAAGTCTTTCAAGAATGATGCTTAAA
*
5347425 TCCTTCGGGTCATCT
1 TCCTTCAGGTCATCT
5347440 CTAGCCTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
TCCTTCAGGTCATCTGTAAGTCTTTCAAGAATGATGCTTAAA
Found at i:5348040 original size:26 final size:27
Alignment explanation
Indices: 5348011--5348061 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
5348001 TCATTTTAAT
* *
5348011 TATTATTATTTTATTATTAA-AAATAA
1 TATTATTATATTATCATTAATAAATAA
5348037 TATTATTATATTATCATTAATAAAT
1 TATTATTATATTATCATTAATAAAT
5348062 TACAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTATTATATTATCATTAATAAATAA
Found at i:5348885 original size:30 final size:28
Alignment explanation
Indices: 5348832--5348896 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
5348822 ATGAGGGAGT
*
5348832 TTAGAGATAAGTGAGAGCTTCTCTCTCC
1 TTAGAGAGAAGTGAGAGCTTCTCTCTCC
5348860 TTAGAGAGAAGTGAGAGCTTCTCTCTCC
1 TTAGAGAGAAGTGAGAGCTTCTCTCTCC
*
5348888 ATAGAGAGA
1 TTAGAGAGA
5348897 GAAGCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (28 bp):
TTAGAGAGAAGTGAGAGCTTCTCTCTCC
Found at i:5349544 original size:2 final size:2
Alignment explanation
Indices: 5349537--5349569 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5349527 AAACCCTAAG
5349537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5349570 TTACTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5351050 original size:18 final size:20
Alignment explanation
Indices: 5351020--5351070 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
5351010 TCTTGGGACA
* *
5351020 AAAATTAAA-GAAAGAAA-G
1 AAAATAAAAGGAAAAAAAGG
5351038 AAAA-AAAAGGAAAAAAAGG
1 AAAATAAAAGGAAAAAAAGG
5351057 AAAATAAAA-GAAAA
1 AAAATAAAAGGAAAA
5351071 TAAAACAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 10 0.36
20 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (20 bp):
AAAATAAAAGGAAAAAAAGG
Found at i:5351052 original size:10 final size:11
Alignment explanation
Indices: 5351037--5351075 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
5351027 AAGAAAGAAA
5351037 GAAAA-AAAAG
1 GAAAATAAAAG
5351047 G-AAA-AAAAG
1 GAAAATAAAAG
5351056 GAAAATAAAA-
1 GAAAATAAAAG
5351066 GAAAATAAAA
1 GAAAATAAAA
5351076 CAGGTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 14 0.52
11 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
GAAAATAAAAG
Found at i:5352209 original size:36 final size:35
Alignment explanation
Indices: 5352169--5352358 Score: 164
Period size: 36 Copynumber: 5.5 Consensus size: 35
5352159 TAAAAAAACC
5352169 ATTTTTAAAAATTTTTTTAAAAACTATATAATATAT
1 ATTTTTAAAAA-TTTTTTAAAAACTATATAATATAT
**
5352205 A-TTTTAAAAA-CATTTAAAAACTATATATATATAT
1 ATTTTTAAAAATTTTTTAAAAACTATATA-ATATAT
* * *
5352239 AAGTTTTCAAAA--TTTCAAAAACTATATAATATAT
1 -ATTTTTAAAAATTTTTTAAAAACTATATAATATAT
* *
5352273 ATATTTTCAAAATGTTTTAAAAACTATATAATATAT
1 AT-TTTTAAAAATTTTTTAAAAACTATATAATATAT
** *
5352309 A-----AAATTTTTTTTTAAAACTATATAATATAT
1 ATTTTTAAAAATTTTTTAAAAACTATATAATATAT
5352339 AATTTTTCAAAAATGTTTTT
1 -ATTTTT-AAAAAT-TTTTT
5352359 CAACCATATA
Statistics
Matches: 126, Mismatches: 14, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
30 24 0.19
31 1 0.01
33 16 0.13
34 21 0.17
35 24 0.19
36 31 0.25
37 4 0.03
38 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (35 bp):
ATTTTTAAAAATTTTTTAAAAACTATATAATATAT
Found at i:5352271 original size:34 final size:33
Alignment explanation
Indices: 5352183--5352350 Score: 177
Period size: 36 Copynumber: 5.0 Consensus size: 33
5352173 TTAAAAATTT
*
5352183 TTTTAAAAACTATATAATATAT-ATTTTAAAAA
1 TTTTAAAAACTATATAATATATAATTTTCAAAA
*
5352215 CATTTAAAAACTATATATATATATAAGTTTTCAAAA
1 -TTTTAAAAACTATATA-ATATATAA-TTTTCAAAA
*
5352251 TTTCAAAAACTATATAATATATATATTTTCAAAA
1 TTTTAAAAACTATATAATATATA-ATTTTCAAAA
5352285 TGTTTTAAAAACTATATAATATATAAAATTTT-----
1 --TTTTAAAAACTATATAATATAT--AATTTTCAAAA
*
5352317 TTTTTAAAACTATATAATATATAATTTTTCAAAA
1 TTTTAAAAACTATATAATATATAA-TTTTCAAAA
5352351 ATGTTTTTCA
Statistics
Matches: 115, Mismatches: 6, Indels: 27
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.02
29 4 0.03
30 21 0.18
33 15 0.13
34 22 0.19
35 16 0.14
36 29 0.25
37 5 0.04
38 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (33 bp):
TTTTAAAAACTATATAATATATAATTTTCAAAA
Found at i:5352375 original size:2 final size:2
Alignment explanation
Indices: 5352364--5352472 Score: 106
Period size: 2 Copynumber: 57.5 Consensus size: 2
5352354 TTTTTCAACC
* *
5352364 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5352404 AT GT -T TT CAA AA AT -T AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5352444 A- AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5352473 AACAAAATAA
Statistics
Matches: 93, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
1 7 0.08
2 86 0.92
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5352391 original size:52 final size:47
Alignment explanation
Indices: 5352327--5352444 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 47
5352317 TTTTTAAAAC
*
5352327 TATATA-ATATATAAT-TTTTCAAAAATGTTTTTCAACCATATATTATATATA
1 TATATATATATATAATATATT-AAAAATGTTT-TCAA--A-A-ATTATATATA
5352378 TATATATATATATATATATATTAAAAATGTTTTCAAAAATTATATATA
1 TATATATATATATA-ATATATTAAAAATGTTTTCAAAAATTATATATA
5352426 TATATATATATATAATATA
1 TATATATATATATAATATA
5352445 ATATATATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
47 5 0.08
48 24 0.38
49 1 0.02
50 1 0.02
51 6 0.10
52 11 0.17
53 12 0.19
54 3 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (47 bp):
TATATATATATATAATATATTAAAAATGTTTTCAAAAATTATATATA
Found at i:5353230 original size:36 final size:36
Alignment explanation
Indices: 5353143--5353590 Score: 346
Period size: 36 Copynumber: 12.8 Consensus size: 36
5353133 TTGTTTTGTG
* * *
5353143 TGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * *
5353180 TATTTCAAGGGAAACTGTCTTAAGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
5353216 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * * * *
5353253 AGTTCCAAAAGAAACTGTCTCAAGGGAGAATAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
5353289 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGAAAAAATT
* * * *
5353318 TCTTTCAAGGGAAACTTTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
5353354 TGTTTCTAG-GTAAACTGTCTCAAGAGAG--AAAATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGAAAAAATT
*
5353388 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATT
* * * * * **
5353425 AGTTCCAAAAGAAATTGTCTCAAGGGAGATGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
5353461 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGAAAAAATT
* * *
5353490 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
* *
5353526 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
*
5353562 TGTTTAAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
5353591 TAACTTTGTT
Statistics
Matches: 329, Mismatches: 52, Indels: 61
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.01
29 31 0.09
30 5 0.02
31 2 0.01
32 4 0.01
33 4 0.01
34 31 0.09
35 7 0.02
36 152 0.46
37 89 0.27
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
Found at i:5353415 original size:17 final size:17
Alignment explanation
Indices: 5353365--5353416 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5353355 GTTTCTAGGT
5353365 AAACTGTCTCAAGAGAG
1 AAACTGTCTCAAGAGAG
* *
5353382 AAAATTTGTTTC-A-AGAG
1 -AAA-CTGTCTCAAGAGAG
5353399 AAACTGTCTCAAGAGAG
1 AAACTGTCTCAAGAGAG
5353416 A
1 A
5353417 CAAAACTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 9 0.33
18 4 0.15
19 5 0.19
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (17 bp):
AAACTGTCTCAAGAGAG
Found at i:5353449 original size:172 final size:173
Alignment explanation
Indices: 5353153--5353590 Score: 720
Period size: 172 Copynumber: 2.5 Consensus size: 173
5353143 TGTTTTAAGA
* * *
5353153 GAAATTGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACTGTCTTAAGAGAGAAAAAATTTG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG-AAAAATTTG
5353218 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAA
64 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG-A
*
5353283 T-AAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTCTTTCAAGG
128 TGAAATTTGTTT-AATGGAAAACATATTCAAAGATTTTATTTCAAGG
* * *
5353328 GAAACTTTCTCAAGAGAGACAAAATTTGTTTCTAGGTAAACTGTCTCAAGAGAG-AAAATTTGTT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTT
*
5353392 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGATGA
66 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGA
*
5353457 AATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGG
131 AATTTGTTTAATGGAAAACATATTCAAAGATTTTATTTCAAGG
5353500 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAATTTGT
*
5353565 TTAAAGAGAAACTGTCTCAAGAGAGA
65 TTCAAGAGAAACTGTCTCAAGAGAGA
5353591 TAACTTTGTT
Statistics
Matches: 246, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
171 4 0.02
172 160 0.65
174 60 0.24
175 22 0.09
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (173 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTT
TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGA
AATTTGTTTAATGGAAAACATATTCAAAGATTTTATTTCAAGG
Found at i:5353518 original size:138 final size:134
Alignment explanation
Indices: 5353356--5353601 Score: 359
Period size: 138 Copynumber: 1.8 Consensus size: 134
5353346 ACAAAATTTG
* * *
5353356 TTTCTAGGTAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 TTTCAAGGGAAACTGTCTCAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
* *
5353421 ACTTAGTTCCAAA-AGAAATTGTCTCAAGGGAGATGAAATTTGTTTAATGTAAAACATATTCAAA
66 A-TTAGTT-CAAAGAGAAACTGTCTCAAGAGAGAT-AAATTTGTTTAATGTAAAACATATTCAAA
5353485 GATTTTA
128 GATTTTA
*
5353492 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTC-A-AGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* * *
5353557 AAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGATAACTTTGTTT
64 AAATTAGTTCAAAGAGAAACTGTCTCAAGAGAGATAAATTTGTTT
5353602 TGAGTAAATT
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
136 29 0.30
137 25 0.26
138 44 0.45
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (134 bp):
TTTCAAGGGAAACTGTCTCAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
ATTAGTTCAAAGAGAAACTGTCTCAAGAGAGATAAATTTGTTTAATGTAAAACATATTCAAAGAT
TTTA
Found at i:5357977 original size:20 final size:20
Alignment explanation
Indices: 5357936--5357977 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5357926 ACAAACAAAC
* *
5357936 AATAAATAAGCAAATAAGTA
1 AATAAATAAGCAAAAAAATA
5357956 AATAAATAAG-AATAAAAATA
1 AATAAATAAGCAA-AAAAATA
5357976 AA
1 AA
5357978 ACAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (20 bp):
AATAAATAAGCAAAAAAATA
Found at i:5357992 original size:21 final size:21
Alignment explanation
Indices: 5357959--5358017 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
5357949 ATAAGTAAAT
*
5357959 AAATAAGAATAAAAATAAAACA
1 AAATAA-AATAAAAAGAAAACA
**
5357981 AAATAAAATAAAAAGGGAACA
1 AAATAAAATAAAAAGAAAACA
5358002 ATAATAAAATGAAAAA
1 A-AATAAAAT-AAAAA
5358018 AAGTATTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (21 bp):
AAATAAAATAAAAAGAAAACA
Found at i:5359203 original size:3 final size:3
Alignment explanation
Indices: 5359193--5359231 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5359183 AAAAATAAAT
*
5359193 TAA T-A TAA TAAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5359232 ATATTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5359308 original size:12 final size:12
Alignment explanation
Indices: 5359265--5359307 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
5359255 TATATAATAT
5359265 ATATTTTAAAAA
1 ATATTTTAAAAA
5359277 ATA-TTTAAAAA
1 ATATTTTAAAAA
* *
5359288 ACCATTTTTAAAA
1 A-TATTTTAAAAA
5359301 ATATTTT
1 ATATTTT
5359308 TTAAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.35
12 9 0.35
13 8 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATTTTAAAAA
Found at i:5359365 original size:39 final size:38
Alignment explanation
Indices: 5359307--5359547 Score: 233
Period size: 39 Copynumber: 6.4 Consensus size: 38
5359297 AAAAATATTT
* *
5359307 TTTAAAAACAATAT-A-ATATATATATTTT-AAAAACA
1 TTTAAAAACTATATAATATATATATATTTTCAAAAATA
*
5359342 TTTAAAAACTATATATTATATATA-AGTTTTCAAAAAT-
1 TTTAAAAACTATATAATATATATATA-TTTTCAAAAATA
* * * *
5359379 TTCAAAAACTATATAATATATATCTATTTTCAAAATGTT
1 TTTAAAAACTATATAATATATATATATTTTCAAAA-ATA
* * *
5359418 TTTAAAAACTATAGAATATATAAATGTTTTCAAAAATA
1 TTTAAAAACTATATAATATATATATATTTTCAAAAATA
* * * *
5359456 TTTTAAAAACTATATAATAAATAAATGTTTTCAAAAATG
1 -TTTAAAAACTATATAATATATATATATTTTCAAAAATA
** * *
5359495 TTTTCAAACCATATATTATATATATATTTT-AAAAATA
1 TTTAAAAACTATATAATATATATATATTTTCAAAAATA
5359532 TTTTCAAAAACTATAT
1 -TTT-AAAAACTATAT
5359548 TACTACATAC
Statistics
Matches: 168, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
35 13 0.08
36 1 0.01
37 47 0.28
38 34 0.20
39 73 0.43
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (38 bp):
TTTAAAAACTATATAATATATATATATTTTCAAAAATA
Found at i:5359377 original size:63 final size:61
Alignment explanation
Indices: 5359256--5359377 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
5359246 GAAAAAATTT
* * * *
5359256 ATATAATATATATTTTAAAAAATATTTAAAAAACCATTTTTAAAAATATTTTTTAAAAACA
1 ATATAATATATATTTTAAAAAACATTTAAAAAACCATTATTAAAAATAGTTTTCAAAAACA
* * * *
5359317 ATATAATATATATATTTTAAAAACATTT-AAAAACTATATATTATATATAAGTTTTCAAAAA
1 ATATAATATATAT-TTTAAAAAACATTTAAAAAACCAT-TATTAAAAAT-AGTTTTCAAAAA
5359378 TTTCAAAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 21 0.42
62 19 0.38
63 10 0.20
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (61 bp):
ATATAATATATATTTTAAAAAACATTTAAAAAACCATTATTAAAAATAGTTTTCAAAAACA
Found at i:5359560 original size:4 final size:4
Alignment explanation
Indices: 5359551--5360458 Score: 1624
Period size: 4 Copynumber: 229.5 Consensus size: 4
5359541 ACTATATTAC
5359551 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
5359599 TACA CACA TACA TACA TACA T--A TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359645 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359691 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359738 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359784 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359830 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
5359878 TACA TACA TACA CACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5359926 TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA-CA
5359973 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
5360021 TACA TACA TACA TACA TACA TACA TACA TACTA CACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TAC-A TACA TACA TACA TACA
5360070 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360118 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360166 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360214 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360262 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360309 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
5360357 TACA TACA TACA TACG TACA TACA TACG TACG TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
5360405 TACA TACA TACA TACA TACA TACG TACG TACG TACG TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5360453 TACA TA
1 TACA TA
5360459 AACTCCGGGC
Statistics
Matches: 878, Mismatches: 12, Indels: 28
0.96 0.01 0.03
Matches are distributed among these distances:
2 10 0.01
3 6 0.01
4 855 0.97
5 7 0.01
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:5361750 original size:43 final size:42
Alignment explanation
Indices: 5361689--5361770 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
5361679 TTTAGTGTAA
* * *
5361689 AAACACCGTGATAGACTCATCTTTTGTGATGCTTTTTTAGTC
1 AAACACCGTAATAGACTCATATTTAGTGATGCTTTTTTAGTC
* *
5361731 AAACGCCGTAATAGGACTCATATTTAGTGATGTTTTTTTA
1 AAACACCGTAATA-GACTCATATTTAGTGATGCTTTTTTA
5361771 TTTAAAACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 11 0.32
43 23 0.68
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (42 bp):
AAACACCGTAATAGACTCATATTTAGTGATGCTTTTTTAGTC
Found at i:5361783 original size:43 final size:42
Alignment explanation
Indices: 5361688--5361785 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 42
5361678 GTTTAGTGTA
* * *
5361688 AAAACACCGTGATAGACTCATCTTTTGTGATGCTTTTTTAGT
1 AAAACACCGTAATAGACTCATATTTAGTGATGCTTTTTTAGT
* * * *
5361730 CAAACGCCGTAATAGGACTCATATTTAGTGATGTTTTTTTATTT
1 AAAACACCGTAATA-GACTCATATTTAGTGATGCTTTTTTA-GT
5361774 AAAAC-CCGTAAT
1 AAAACACCGTAAT
5361786 TTTAAGTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 11 0.24
43 30 0.65
44 5 0.11
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (42 bp):
AAAACACCGTAATAGACTCATATTTAGTGATGCTTTTTTAGT
Found at i:5364680 original size:13 final size:13
Alignment explanation
Indices: 5364650--5364674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5364640 TCTATGACAC
5364650 GCATTTATGACGT
1 GCATTTATGACGT
5364663 GCATTTATGACG
1 GCATTTATGACG
5364675 CTCATTGCGC
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:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (13 bp):
GCATTTATGACGT
Found at i:5374102 original size:3 final size:3
Alignment explanation
Indices: 5374080--5374130 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
5374070 GGTATGTAAA
*
5374080 AAT AA- AAT AAA AATT AAT AAT AAT AAT AGA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
5374125 AGAT AA
1 A-AT AA
5374131 CCAGACGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 3 0.07
3 32 0.78
4 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:5374115 original size:18 final size:19
Alignment explanation
Indices: 5374080--5374127 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
5374070 GGTATGTAAA
*
5374080 AATAA-AATAAAAATTAAT
1 AATAATAATAGAAATTAAT
5374098 AATAATAATAGAAA-TAAT
1 AATAATAATAGAAATTAAT
5374116 AATAATAATAGA
1 AATAATAATAGA
5374128 TAACCAGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AATAATAATAGAAATTAAT
Found at i:5374553 original size:134 final size:134
Alignment explanation
Indices: 5374246--5374933 Score: 709
Period size: 134 Copynumber: 5.1 Consensus size: 134
5374236 ATGTTGTTCT
* * *
5374246 TTAGGGAAGATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAG
1 TTAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAAG
* * * * *
5374311 AGAGGGTTATGTTAT-GCTTCTTCTTGAGGGAAAAT-ATATATGAGGATGTTGATTTATTCCACT
66 AGAGGGATATGTT-TCACTTTTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCATTCCACT
*
5374374 GTC-C
130 ATCAC
* ** *
5374378 TTTAGGGAAGATTGAATCGAGGCAGACTCATTCCACTGTTACTTAGAGAATATCAAATCTTGAAA
1 -TTAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAA
* * * * * * * * *
5374443 GAGAGGGATCTGTTCCACTTTTTCTTGACGGAAAATCATATTTGGGGACGTTGGTTTATTTCATT
65 GAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCATTCCACT
5374508 ATCAC
130 ATCAC
* *
5374513 TAAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCA-AGGAATATCAAATATTGAAA
1 TTAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGA-GAATATCAAATCTTGAAA
* * * * *
5374577 GAGAGAGATATG-TTCAGCTTCTTT-TTTAGGGAAAATCATATCTAGGGATGTTGCTTCATTCCA
65 GAGAGGGATATGTTTCA-CTT-TTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCATTCCA
5374640 CTATCAC
128 CTATCAC
* * * * *
5374647 TCAGAGAAGGTTGAATCGAGGCATA-TATGTTCTACTGTTACTCATGA-AATATCAAATCTTGAA
1 TTAGGGAAGATTGAATCGAGGCAAACT-TGTTCCACTGTTACTCA-GAGAATATCAAATCTTGAA
** * * * * **
5374710 AGAGAGGGACCTGTTTCACTTTTTCATGAGGGCAAATCAGATTTGGGGGCGTTGATTCATTCCAC
64 AGAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCATTCCAC
5374775 TATC-C
129 TATCAC
* * * * * * *
5374780 TTTAGGGATGGTTGAATCAAGG-AAGAATTGTTCCACAGTTACTCAGGGAATATTAAATCTTGAA
1 -TTAGGGAAGATTGAATCGAGGCAA-ACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAA
* * *
5374844 AGAGAGGGATTTGTTTCACTTATTT-TTGAGAGAAAATCA-ATATGGGGATGTTAATTCACTT-C
64 AGAGAGGGATATGTTTCACTT-TTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCA-TTCC
*
5374906 ACTGTCAC
127 ACTATCAC
5374914 TTAGGGAAGATTGAATCGAG
1 TTAGGGAAGATTGAATCGAG
5374934 TTCGATTAGC
Statistics
Matches: 461, Mismatches: 76, Indels: 36
0.80 0.13 0.06
Matches are distributed among these distances:
133 137 0.30
134 311 0.67
135 12 0.03
136 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (134 bp):
TTAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAAG
AGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATCATATATGGGGATGTTGATTCATTCCACTA
TCAC
Found at i:5374756 original size:268 final size:267
Alignment explanation
Indices: 5374248--5374933 Score: 836
Period size: 268 Copynumber: 2.6 Consensus size: 267
5374238 GTTGTTCTTT
*
5374248 AGGGAAGATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
1 AGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
* * *
5374313 AGGGTTATGTT-ATGCTTCTTCTTGAGGGAAAAT-ATATATGAGGATGTTGATTTATTCCACTGT
66 AGGGATATGTTCA-GCTTCTTTTTGAGGGAAAATCATATATG-GGATGTTGATTCATTCCACTGT
*
5374376 C-CTTTAGGGAAGATTGAATCGAGGCAGACTCATTCCACTGTTACTTAGAGAATATCAAATCTTG
129 CAC-TTAGGGAAGATTGAATCGAGGCAGACTCATTCCACTGTTACTCAGAGAATATCAAATCTTG
* * * * * *
5374440 AAAGAGAGGGATCTGTTCCACTTTTTCTTGACGGAAAATCATATTTGGGGACGTTGGTTTATTTC
193 AAAGAGAGGGACCTGTTCCACTTTTTCATGACGGAAAATCAGATTTGGGGACGTTGATTCATTCC
*
5374505 ATTATCAC-TA
258 ACTATC-CTTA
* * *
5374515 AGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAAGGAATATCAAATATTGAAAGAG
1 AGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
* * * * *
5374580 AGAGATATGTTCAGCTTCTTTTTTAGGGAAAATCATATCTAGGGATGTTGCTTCATTCCACTATC
66 AGGGATATGTTCAGCTTCTTTTTGAGGGAAAATCATATAT-GGGATGTTGATTCATTCCACTGTC
* * * * *
5374645 ACTCAGAGAAGGTTGAATCGAGGCATA-T-ATGTTCTACTGTTACTCATGA-AATATCAAATCTT
130 ACTTAGGGAAGATTGAATCGAGGCAGACTCA--TTCCACTGTTACTCA-GAGAATATCAAATCTT
* * * *
5374707 GAAAGAGAGGGACCTGTTTCACTTTTTCATGAGGGCAAATCAGATTTGGGGGCGTTGATTCATTC
192 GAAAGAGAGGGACCTGTTCCACTTTTTCATGACGGAAAATCAGATTTGGGGACGTTGATTCATTC
*
5374772 CACTATCCTTT
257 CACTATCCTTA
* * * * *
5374783 AGGGATGGTTGAATCAAGG-AAGAATTGTTCCACAGTTACTCAGGGAATATTAAATCTTGAAAGA
1 AGGGAAGATTGAATCAAGGCAA-ACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGA
* * * *
5374847 GAGGGATTTGTTTCA-CTTATTTTTGAGAGAAAATCA-ATATGGGGATGTTAATTCACTT-CACT
65 GAGGGATATG-TTCAGCTTCTTTTTGAGGGAAAATCATATAT-GGGATGTTGATTCA-TTCCACT
5374909 GTCACTTAGGGAAGATTGAATCGAG
127 GTCACTTAGGGAAGATTGAATCGAG
5374934 TTCGATTAGC
Statistics
Matches: 357, Mismatches: 51, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
266 1 0.00
267 132 0.37
268 216 0.61
269 8 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (267 bp):
AGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
AGGGATATGTTCAGCTTCTTTTTGAGGGAAAATCATATATGGGATGTTGATTCATTCCACTGTCA
CTTAGGGAAGATTGAATCGAGGCAGACTCATTCCACTGTTACTCAGAGAATATCAAATCTTGAAA
GAGAGGGACCTGTTCCACTTTTTCATGACGGAAAATCAGATTTGGGGACGTTGATTCATTCCACT
ATCCTTA
Found at i:5376034 original size:29 final size:29
Alignment explanation
Indices: 5375984--5376070 Score: 124
Period size: 29 Copynumber: 3.0 Consensus size: 29
5375974 CTTATTTGAG
5375984 GTAGAATAAGCCTCAAT-AGCTTCTAAGAT
1 GTAGAATAAGCCT-AATCAGCTTCTAAGAT
* *
5376013 GTAGAATAAGCCTTATCGGCTTCTAAGAT
1 GTAGAATAAGCCTAATCAGCTTCTAAGAT
5376042 GTAGAATAAGCCTCAA-CAGCTTCTAAGAT
1 GTAGAATAAGCCT-AATCAGCTTCTAAGAT
5376071 CTTCATTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.04
29 49 0.94
30 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (29 bp):
GTAGAATAAGCCTAATCAGCTTCTAAGAT
Found at i:5376911 original size:65 final size:65
Alignment explanation
Indices: 5376767--5376915 Score: 158
Period size: 65 Copynumber: 2.3 Consensus size: 65
5376757 TTTCGAATAC
* ** ***
5376767 AATTTATGCACCGATGCAC-AGCCATGAATCGATGCACTCTGGATTTTATTAAAACATCGAATTG
1 AATTTATGCACCGATGCACAAGCCATGAATCGATGCACCCCAGATTTTATTAAAACATCGAAGCA
* * * * * *
5376831 ATTTTGTGCACCGATGCACAAGTCATGCATCGATGCACCCCAGCTATTT-TTGAAACATCGAAGC
1 AATTTATGCACCGATGCACAAGCCATGAATCGATGCACCCCAGAT-TTTATTAAAACATCGAAGC
5376895 A
65 A
*
5376896 AATTTATGCATCGATGCACA
1 AATTTATGCACCGATGCACA
5376916 CCCTAGTGTA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
64 17 0.25
65 48 0.71
66 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
AATTTATGCACCGATGCACAAGCCATGAATCGATGCACCCCAGATTTTATTAAAACATCGAAGCA
Found at i:5381148 original size:26 final size:26
Alignment explanation
Indices: 5381117--5381179 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
5381107 AGTGATATTC
5381117 TTGGATCATTTCCATTCTAGGGGTAT
1 TTGGATCATTTCCATTCTAGGGGTAT
*
5381143 TTGGATCATTTCCTTTCTAGGGGTAT
1 TTGGATCATTTCCATTCTAGGGGTAT
*
5381169 TTTGATCATTT
1 TTGGATCATTT
5381180 TACAGATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (26 bp):
TTGGATCATTTCCATTCTAGGGGTAT
Found at i:5384185 original size:21 final size:22
Alignment explanation
Indices: 5384159--5384202 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5384149 TTTAAAAAAT
*
5384159 TAATTTTATTAATTT-AATTTA
1 TAATTTTATAAATTTGAATTTA
5384180 TAATTTTATAAATTTGAATTTA
1 TAATTTTATAAATTTGAATTTA
5384202 T
1 T
5384203 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TAATTTTATAAATTTGAATTTA
Found at i:5391272 original size:65 final size:64
Alignment explanation
Indices: 5391201--5391353 Score: 182
Period size: 64 Copynumber: 2.4 Consensus size: 64
5391191 TACACTAGGG
* * * * **
5391201 GTGCATCGGTGCACTAATTACATTCAATGTTTGAAAAGAGCCTGGAGTGCATCGATGCATGGTC-
1 GTGCATCGGTACACAAAATACATTCAATG-TTCAAAAGAGCCAAGAGTGCATCGATGCATGG-CA
5391265 T
64 T
* * **
5391266 GTGCATCGGTACACAAAATGCATTCAATGTTCAAAATATTCAAGAGTGCATCGATGCATGGCAT
1 GTGCATCGGTACACAAAATACATTCAATGTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCAT
*
5391330 GTGCATCGGTACACAAAATCCATT
1 GTGCATCGGTACACAAAATACATT
5391354 TGAAATGGGT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
63 1 0.01
64 50 0.66
65 25 0.33
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTCAATGTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCAT
Found at i:5392012 original size:2 final size:2
Alignment explanation
Indices: 5392005--5392036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5391995 ACTAAACCAA
5392005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5392037 TAAGTTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5393982 original size:21 final size:21
Alignment explanation
Indices: 5393898--5393982 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
5393888 AAAACCCGAT
*
5393898 GAGTGTATCGATGCACA-GCA
1 GAGTGTATCGATGCACATTCA
* *
5393918 GAGTGCATCGATGTACATTCAA
1 GAGTGTATCGATGCACATTC-A
* * * *
5393940 GAAATGTATCGGTGTACCTTCA
1 G-AGTGTATCGATGCACATTCA
5393962 TG-GTGTATCGATGCACATTCA
1 -GAGTGTATCGATGCACATTCA
5393983 AGGGATGCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 15 0.30
21 16 0.32
22 3 0.06
23 16 0.32
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (21 bp):
GAGTGTATCGATGCACATTCA
Found at i:5403578 original size:20 final size:21
Alignment explanation
Indices: 5403542--5403589 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5403532 GGCAATGACT
5403542 AAAATATTAAACTTTTTAAGA
1 AAAATATTAAACTTTTTAAGA
5403563 AAAATATTAAACTTTTTAAGA
1 AAAATATTAAACTTTTTAAGA
5403584 AAAATA
1 AAAATA
5403590 CAATGACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAATATTAAACTTTTTAAGA
Found at i:5404634 original size:277 final size:277
Alignment explanation
Indices: 5404140--5404663 Score: 850
Period size: 277 Copynumber: 1.9 Consensus size: 277
5404130 TTTACCCTTT
* *
5404140 AATGTTCATTTGTGTAAATATTTTTGATTAATTTTATCATTATGTCATTTAATAATTGATTAAAG
1 AATGTTCATTTGTGTAAATATTTGTGACTAATTTTATCATTATGTCATTTAATAATTGATTAAAG
* * * *
5404205 TAACATAATCAACCAGATCAAAGAGATTAATTAGAAATTTAAAATCACATTAGTTTCATCGATTT
66 CAACACAATCAACCAGATCAAAGAGATTAACTAGAAATTTAAAATCACATTAGTTTCATCGACTT
* * * *
5404270 TATTAATTAAAAAGTAAATAATTTATATTTTATAAATATATTTAAATCTCAATAAGAGTGTAAAT
131 TAATAATAAAAAAATAAATAATTTATATTTTATAAATATATTTAAAGCTCAATAAGAGTGTAAAT
* *
5404335 GAATAGAGTGTTAGATGAATTGTTTGTGAACTGTTTATATAACATTTGTTTAAATATCATGTTAG
196 GAATAGAGTGTTAGATGAATTGTTTGTGAACCGTTTACATAACATTTGTTTAAATATCATGTTAG
5404400 ATGAAAAATGTTAATTA
261 ATGAAAAATGTTAATTA
*
5404417 AATGTTCATTTGTGTAAATATTTGTGACTAATTTTATCGTTATGTCATTTAATAATTGATTAAAG
1 AATGTTCATTTGTGTAAATATTTGTGACTAATTTTATCATTATGTCATTTAATAATTGATTAAAG
* ** *
5404482 CAACACAATCAACCATATCAAATTGATTAACTAGAAATTTATAATCACATTAGTTTCATCGACTT
66 CAACACAATCAACCAGATCAAAGAGATTAACTAGAAATTTAAAATCACATTAGTTTCATCGACTT
* * * *
5404547 TAATAATAAAAAAATAAATATTTTATATTTTATATATATATTTAAAGCTTAGTAAGAGTGTAAAT
131 TAATAATAAAAAAATAAATAATTTATATTTTATAAATATATTTAAAGCTCAATAAGAGTGTAAAT
*
5404612 GAATAGAGTGTTCGATGAATTGTTTGTGAACCGTTTACATAACATTTGTTTA
196 GAATAGAGTGTTAGATGAATTGTTTGTGAACCGTTTACATAACATTTGTTTA
5404664 TGTTCATTTA
Statistics
Matches: 225, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
277 225 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (277 bp):
AATGTTCATTTGTGTAAATATTTGTGACTAATTTTATCATTATGTCATTTAATAATTGATTAAAG
CAACACAATCAACCAGATCAAAGAGATTAACTAGAAATTTAAAATCACATTAGTTTCATCGACTT
TAATAATAAAAAAATAAATAATTTATATTTTATAAATATATTTAAAGCTCAATAAGAGTGTAAAT
GAATAGAGTGTTAGATGAATTGTTTGTGAACCGTTTACATAACATTTGTTTAAATATCATGTTAG
ATGAAAAATGTTAATTA
Found at i:5409892 original size:32 final size:32
Alignment explanation
Indices: 5409846--5409934 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
5409836 TTGGGCGTAG
* * * *
5409846 GAGCCAACCTAAGGGAGTACCTTAGGGCCTGA
1 GAGCCTACCCAAGGGAATACCTTAGGGCCTCA
* * *
5409878 GAGCCTACCCAAGGGAACATCTCAGGGCCTCA
1 GAGCCTACCCAAGGGAATACCTTAGGGCCTCA
*
5409910 GAGCCTACCCAAGGG-TTACCTTAGG
1 GAGCCTACCCAAGGGAATACCTTAGG
5409935 TCCGTAAGGA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 6 0.13
32 40 0.87
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.16
Consensus pattern (32 bp):
GAGCCTACCCAAGGGAATACCTTAGGGCCTCA
Found at i:5415639 original size:82 final size:82
Alignment explanation
Indices: 5415524--5415688 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
5415514 AGAATAGACT
*
5415524 TTAATCTCAAACTCAACTTCTTCTATCCGGCGGTAATCCAGGCAACTCCTCAGAAAAAACATCGG
1 TTAATCTCAAACTCAACTTCTTCTATCCAGCGGTAATCCAGGCAACTCCTCAGAAAAAACATCGG
5415589 GAAATTCCTTGACAATC
66 GAAATTCCTTGACAATC
5415606 TTAATCTCAAACTCAACTTCTTCTATCCAGCGGTAATCCAGGCAACTCCTCAGAAAAAACATCGG
1 TTAATCTCAAACTCAACTTCTTCTATCCAGCGGTAATCCAGGCAACTCCTCAGAAAAAACATCGG
5415671 GAAATTCCTTGACAATC
66 GAAATTCCTTGACAATC
5415688 T
1 T
5415689 GAATGCCTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (82 bp):
TTAATCTCAAACTCAACTTCTTCTATCCAGCGGTAATCCAGGCAACTCCTCAGAAAAAACATCGG
GAAATTCCTTGACAATC
Found at i:5421535 original size:3 final size:3
Alignment explanation
Indices: 5421529--5421558 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5421519 AATATTAATA
5421529 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5421559 ATATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5422038 original size:46 final size:44
Alignment explanation
Indices: 5421983--5422126 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 44
5421973 TGGGTTTCAT
5421983 TACTACTCTTTCGTGAAGTTCTCATACTTTGTTGAAAAATCCTTTC
1 TACTACTCTTTCGTGAAG-TCTCATACTTTGTTGAAAAAT-CTTTC
* * **
5422029 TACTACTCTTTCGTGGAGT-TCAGA-TTTGCTT---TTA-C-TTC
1 TACTACTCTTTCGTGAAGTCTCATACTTTG-TTGAAAAATCTTTC
*
5422067 -ACTACTCTTTCGTGAAGATCTCATACTTTGCTGAAAAATCTATTC
1 TACTACTCTTTCGTGAAG-TCTCATACTTTGTTGAAAAATCT-TTC
*
5422112 TACTACTCTTCCGTG
1 TACTACTCTTTCGTG
5422127 GTGTTCAGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
37 16 0.21
38 4 0.05
39 6 0.08
40 4 0.05
41 1 0.01
42 1 0.01
43 5 0.06
44 6 0.08
45 4 0.05
46 30 0.39
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (44 bp):
TACTACTCTTTCGTGAAGTCTCATACTTTGTTGAAAAATCTTTC
Found at i:5422089 original size:83 final size:83
Alignment explanation
Indices: 5421984--5422141 Score: 264
Period size: 83 Copynumber: 1.9 Consensus size: 83
5421974 GGGTTTCATT
* * *
5421984 ACTACTCTTTCGTGAAGTTCTCATACTTTGTTGAAAAATCCT-TTCTACTACTCTTTCGTGGAGT
1 ACTACTCTTTCGTGAAGATCTCATACTTTGCTGAAAAAT-CTATTCTACTACTCTTCCGTGGAGT
5422048 TCAGATTTGCTTTTACTTC
65 TCAGATTTGCTTTTACTTC
*
5422067 ACTACTCTTTCGTGAAGATCTCATACTTTGCTGAAAAATCTATTCTACTACTCTTCCGTGGTGTT
1 ACTACTCTTTCGTGAAGATCTCATACTTTGCTGAAAAATCTATTCTACTACTCTTCCGTGGAGTT
5422132 CAGATTTGCT
66 CAGATTTGCT
5422142 CTAGCTTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 2 0.03
83 68 0.97
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (83 bp):
ACTACTCTTTCGTGAAGATCTCATACTTTGCTGAAAAATCTATTCTACTACTCTTCCGTGGAGTT
CAGATTTGCTTTTACTTC
Found at i:5422477 original size:140 final size:140
Alignment explanation
Indices: 5422278--5422566 Score: 463
Period size: 140 Copynumber: 2.1 Consensus size: 140
5422268 GTGGAAGTTG
* * * *
5422278 TCCGTGGAGACTGATCTAAAATGACTTGAACATAATTTGTTTCACTACTCTTCCGTGAAGTTCAT
1 TCCGTGGAGACTGATCTAAAATGACTTGAACAGAATCTGTTTCACTACTCTTCCATGAAGTTCAG
*
5422343 ACTCAAAGTTTAATTTGCTTCCACTACTCTTCCATGGAGTTGTATACTTTACTGAAAAATTCT-T
66 ACTCAAAGTTTAATTTGCTTCCACTACTCTTCCATGGAGTTGTATAATTTACTGAAAAA-TCTGT
5422407 TCCACTACTCT
130 TCCACTACTCT
* *
5422418 TCCGTGGAGACTGATCTGAAATGACTTGAACAGAATCTGTTTCACTATTCTTCCATGAAGTTCAG
1 TCCGTGGAGACTGATCTAAAATGACTTGAACAGAATCTGTTTCACTACTCTTCCATGAAGTTCAG
* * * *
5422483 ACTCAAAGTTTAATTTGCTTCCACTATTCTTTCGTGGAGTTGTATAATTTGCTGAAAAATCTGTT
66 ACTCAAAGTTTAATTTGCTTCCACTACTCTTCCATGGAGTTGTATAATTTACTGAAAAATCTGTT
5422548 CCACTACTCT
131 CCACTACTCT
5422558 TCCGTGGAG
1 TCCGTGGAG
5422567 TTTAGATTTG
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
139 3 0.02
140 134 0.98
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (140 bp):
TCCGTGGAGACTGATCTAAAATGACTTGAACAGAATCTGTTTCACTACTCTTCCATGAAGTTCAG
ACTCAAAGTTTAATTTGCTTCCACTACTCTTCCATGGAGTTGTATAATTTACTGAAAAATCTGTT
CCACTACTCT
Found at i:5422565 original size:45 final size:44
Alignment explanation
Indices: 5422501--5422649 Score: 116
Period size: 45 Copynumber: 3.5 Consensus size: 44
5422491 TTTAATTTGC
* *
5422501 TTCCACTATTCTTTCGTGGAGTTGTATAATTTGCTGAAAAATCTG
1 TTCCACTACTCTTCCGTGGAGTT-TATAATTTGCTGAAAAATCTG
* ***
5422546 TTCCACTACTCTTCCGTGGAGTTTA-GATTTGCT--CTTA-C--
1 TTCCACTACTCTTCCGTGGAGTTTATAATTTGCTGAAAAATCTG
* ** *
5422584 TT-CATTACTCTTCCGTAAAGATCTCATAATTTGCTGAAAAAT-TCG
1 TTCCACTACTCTTCCGTGGAG-T-TTATAATTTGCTGAAAAATCT-G
5422629 TTCCACTACTCTTCCGTGGAG
1 TTCCACTACTCTTCCGTGGAG
5422650 ACTGATTTAA
Statistics
Matches: 77, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
37 15 0.19
38 3 0.04
39 2 0.03
40 8 0.10
41 1 0.01
42 1 0.01
43 7 0.09
44 2 0.03
45 23 0.30
46 15 0.19
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (44 bp):
TTCCACTACTCTTCCGTGGAGTTTATAATTTGCTGAAAAATCTG
Found at i:5423382 original size:22 final size:24
Alignment explanation
Indices: 5423357--5423412 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
5423347 AAAGCTTTGG
*
5423357 TCTTTAAAATGG-GAATTTATCA-
1 TCTTTAAAATGGAGAATCTATCAT
*
5423379 TCTTTGAAA-GGAGAATCTATCAT
1 TCTTTAAAATGGAGAATCTATCAT
5423402 TCTTGTAAAAT
1 TCTT-TAAAAT
5423413 ATAGACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 4 0.15
24 4 0.15
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (24 bp):
TCTTTAAAATGGAGAATCTATCAT
Found at i:5434919 original size:22 final size:22
Alignment explanation
Indices: 5434891--5434934 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5434881 CACGTGTCAC
5434891 CATCCAGTTAAATAAAAATCAA
1 CATCCAGTTAAATAAAAATCAA
5434913 CATCCAGTTAAATAAAAATCAA
1 CATCCAGTTAAATAAAAATCAA
5434935 TTAGAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.05, T:0.23
Consensus pattern (22 bp):
CATCCAGTTAAATAAAAATCAA
Found at i:5435853 original size:13 final size:13
Alignment explanation
Indices: 5435835--5435860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5435825 ACATGTGTCA
5435835 CCATTTAATTAGT
1 CCATTTAATTAGT
5435848 CCATTTAATTAGT
1 CCATTTAATTAGT
5435861 AGATTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CCATTTAATTAGT
Found at i:5437691 original size:16 final size:16
Alignment explanation
Indices: 5437670--5437735 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 16
5437660 AGATAAAATG
5437670 AAATATATAAAATAAT
1 AAATATATAAAATAAT
*
5437686 AAATATATAACAT-AT
1 AAATATATAAAATAAT
*
5437701 AATTATAGTAATAA-AA-
1 AAATATA-TAA-AATAAT
5437717 AAATATATATAAATAAT
1 AAATATATA-AAATAAT
5437734 AA
1 AA
5437736 TGATATACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.30
16 24 0.60
17 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
AAATATATAAAATAAT
Found at i:5439421 original size:110 final size:110
Alignment explanation
Indices: 5439277--5439480 Score: 282
Period size: 110 Copynumber: 1.9 Consensus size: 110
5439267 CTGGAAATTG
* * * * * *
5439277 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGCCTCGAGTTCAATATCC
1 TTTGTTGACAATCAATCACCCCTTCACTGTGAAGTTAAGCTTGTGTTGCCTCGAGTCCAATATCC
*
5439342 TTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTA
66 CTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTA
* * * *
5439387 TTTGTTGACAATCAATCACCCCTTTATTGTGAAGTTAAGCTTGTGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAATCAATCACCCCTTCACTGTGAAGTTAAGCTTGTGTTGCCTCGAGTCCAATATCC
* * *
5439452 CTCGCTGTTAAGTTGAAATTGGCTCTGAA
66 CTCGCTGTGAAGTTAAAATTGACTCTGAA
5439481 ACTGGAAAGC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
110 80 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAATCAATCACCCCTTCACTGTGAAGTTAAGCTTGTGTTGCCTCGAGTCCAATATCC
CTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTA
Found at i:5451110 original size:18 final size:17
Alignment explanation
Indices: 5451089--5451136 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
5451079 AAAAATATAT
5451089 ATAAATAAAATACATAA-A
1 ATAAA-AAAATA-ATAACA
*
5451107 ATAAAGAAGATAATAACA
1 ATAAA-AAAATAATAACA
5451125 ATAAAAAAATAA
1 ATAAAAAAATAA
5451137 AAATAGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (17 bp):
ATAAAAAAATAATAACA
Found at i:5452697 original size:42 final size:43
Alignment explanation
Indices: 5452638--5452740 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
5452628 TTTTACAGGA
5452638 AAATTTGAAAA-AATAAAAA-ATCTTAAAAA-TAAAAA-TAGTTTT
1 AAATTT-AAAATAATAAAAATAT-TTAAAAACTAAAAATTA-TTTT
5452680 AAATTTAAAATAATAAAAATATTTAAAAATCTAAAAATTATTTT
1 AAATTTAAAATAATAAAAATATTTAAAAA-CTAAAAATTATTTT
5452724 AATATTAATAAAATAAT
1 AA-ATT--TAAAATAAT
5452741 GAAATTTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
41 4 0.08
42 21 0.40
43 2 0.04
44 12 0.23
45 5 0.09
47 9 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (43 bp):
AAATTTAAAATAATAAAAATATTTAAAAACTAAAAATTATTTT
Found at i:5452709 original size:26 final size:26
Alignment explanation
Indices: 5452653--5452716 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
5452643 TGAAAAAATA
5452653 AAAAATCTT-AAAAATAAAAATAGTTT
1 AAAAAT-TTAAAAAATAAAAATAGTTT
*
5452679 -TAAATTTAAAATAATAAAAATA-TTT
1 AAAAATTTAAAA-AATAAAAATAGTTT
*
5452704 AAAAATCTAAAAA
1 AAAAATTTAAAAA
5452717 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 11 0.34
26 19 0.59
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAATTTAAAAAATAAAAATAGTTT
Found at i:5452774 original size:29 final size:29
Alignment explanation
Indices: 5452695--5452775 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
5452685 TAAAATAATA
* *
5452695 AAAATATTTAAAAAT-CTAAAAATTATTT
1 AAAATATTTAAAAATATTAAATATTATTT
* * * *
5452723 -TAATATTAATAAAATAATGAAATTTTATTT
1 AAAATATTTA-AAAAT-ATTAAATATTATTT
5452753 AAAATATTTAAAAATATTAAATA
1 AAAATATTTAAAAATATTAAATA
5452776 CAATGATGTC
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
27 7 0.18
28 5 0.13
29 6 0.15
30 14 0.36
31 7 0.18
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATATTTAAAAATATTAAATATTATTT
Found at i:5453453 original size:15 final size:14
Alignment explanation
Indices: 5453435--5453480 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
5453425 TGTTCTTATT
5453435 TTTTATTTATTTTAC
1 TTTTA-TTATTTTAC
5453450 TTTTATT-TTTTA-
1 TTTTATTATTTTAC
*
5453462 TTTTATTATTTTTC
1 TTTTATTATTTTAC
5453476 TTTTA
1 TTTTA
5453481 AATTTAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.25
13 9 0.32
14 7 0.25
15 5 0.18
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTATTTTAC
Found at i:5453491 original size:26 final size:27
Alignment explanation
Indices: 5453435--5453491 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
5453425 TGTTCTTATT
**
5453435 TTTTATTTATTTTACTTTTATTTTTTA
1 TTTTATTTATTTTACTTTTATAATTTA
*
5453462 TTTTA-TTATTTTTCTTTTA-AATTTA
1 TTTTATTTATTTTACTTTTATAATTTA
5453487 GTTTT
1 -TTTT
5453492 TAGTGATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTATTTATTTTACTTTTATAATTTA
Found at i:5453799 original size:13 final size:13
Alignment explanation
Indices: 5453777--5453824 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
5453767 ATTTGGATCA
*
5453777 AATTTTACTTTTT
1 AATTTAACTTTTT
**
5453790 AATTTAAC-TTGC
1 AATTTAACTTTTT
*
5453802 AATTTTACTTTTT
1 AATTTAACTTTTT
5453815 AATTTAACTT
1 AATTTAACTT
5453825 GCAATTTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.58
Consensus pattern (13 bp):
AATTTAACTTTTT
Found at i:5453807 original size:25 final size:25
Alignment explanation
Indices: 5453777--5453832 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
5453767 ATTTGGATCA
5453777 AATTTTACTTTTTAATTTAACTTGC
1 AATTTTACTTTTTAATTTAACTTGC
5453802 AATTTTACTTTTTAATTTAACTTGC
1 AATTTTACTTTTTAATTTAACTTGC
5453827 AATTTT
1 AATTTT
5453833 CTCAATTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.57
Consensus pattern (25 bp):
AATTTTACTTTTTAATTTAACTTGC
Found at i:5454800 original size:29 final size:29
Alignment explanation
Indices: 5454731--5454800 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
5454721 TATATCGTTC
* *
5454731 CTCATTGAACTTTACTCTTTCCTATTTTA
1 CTCATTGAACTTTAATCTTTCCTAATTTA
* * * *
5454760 CTCATCGTACTTTCAAT-TTTTCTAATTTG
1 CTCATTGAACTTT-AATCTTTCCTAATTTA
5454789 CTCATTGAACTT
1 CTCATTGAACTT
5454801 GACAGATTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (29 bp):
CTCATTGAACTTTAATCTTTCCTAATTTA
Found at i:5455296 original size:3 final size:3
Alignment explanation
Indices: 5455288--5455347 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5455278 AACCTATTAC
5455288 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5455336 ATA ATA ATA ATA
1 ATA ATA ATA ATA
5455348 TTATTATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5455352 original size:3 final size:3
Alignment explanation
Indices: 5455346--5455388 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5455336 ATAATAATAA
*
5455346 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5455389 TTAAATAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5456257 original size:27 final size:26
Alignment explanation
Indices: 5456204--5456263 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5456194 CATATAATAA
* **
5456204 ATATATAATATAAATATATGTTCAAT
1 ATATATAATATAAACATAAATTCAAT
*
5456230 ACTATATAATATAAACATAAATTTAAT
1 A-TATATAATATAAACATAAATTCAAT
5456257 ATATATA
1 ATATATA
5456264 TAACGGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATATAATATAAACATAAATTCAAT
Found at i:5457095 original size:85 final size:85
Alignment explanation
Indices: 5456947--5457438 Score: 658
Period size: 85 Copynumber: 5.9 Consensus size: 85
5456937 CGCTGTCATC
* * * * * *
5456947 GAGCTGAATGGAATCAAACTCTAAGGTTTTTGTTGACAGATAACCCTTATTGCCTTGACCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
5457012 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* *
5457032 GAGCTGAATGGAATCGAACTCGAAGGTTTTTCTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
5457097 TGTAAATTTGATATGCTCTT
66 TGTAAATTTGATATGCCCTT
* * * * *
5457117 GAGTTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
5457182 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCCTT
* * * *
5457202 GAGATGAATGTAATCGAACTCGAAGG-TTTT-TTG--AGATATCCCTTCTCTCCTT--G-TATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
5457260 TGTAAATTCT-ATATGCCCTT
66 TGTAAATT-TGATATGCCCTT
* * *
5457280 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGATAGATAACCCTTCTCGCTTTGAACTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
5457345 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * * * *
5457365 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATAGCCCTTCTCACATTGAACTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
5457430 TTTAAATTT
66 TGTAAATTT
5457439 TGCTGGGAGA
Statistics
Matches: 361, Mismatches: 37, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
78 45 0.12
79 6 0.02
80 3 0.01
81 17 0.05
82 16 0.04
83 3 0.01
84 5 0.01
85 266 0.74
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:5457351 original size:163 final size:166
Alignment explanation
Indices: 5456947--5457438 Score: 668
Period size: 163 Copynumber: 2.9 Consensus size: 166
5456937 CGCTGTCATC
* * * *
5456947 GAGCTGAATGGAATCAAACTCTAAGGTTTTTGTTGACAGATAACCCTTATTGCCTTGACCTATGT
1 GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAACTATGT
*
5457012 TGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTCTTGACAGATAGCC
66 TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTT-TTGA-AGATAGCC
*
5457077 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCTCTT
128 CTTCTCGCCTT-AGCTATGCTGTAAATTTGATATGCCCTT
* * * *
5457117 GAGTTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGT
1 GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAACTATGT
* * *
5457182 TGTAAATTTGATATGCCTTTGAGATGAATGTAATCGAACTCGAAGGTTTTTTG-AGATATCCCTT
66 TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGAAGATAGCCCTT
*
5457246 CTCTCCTT-G-TATGCTGTAAATTCT-ATATGCCCTT
131 CTCGCCTTAGCTATGCTGTAAATT-TGATATGCCCTT
* * * *
5457280 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGATAGATAACCCTTCTCGCTTTGAACTATGC
1 GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAACTATGT
*
5457345 TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTAACAGATAGCC
66 TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTT-TTGA-AGATAGCC
* * * *
5457410 CTTCTCACATTGAACTATGCTTTAAATTT
128 CTTCTCGCCTT-AGCTATGCTGTAAATTT
5457439 TGCTGGGAGA
Statistics
Matches: 285, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
163 123 0.43
164 6 0.02
165 2 0.01
166 17 0.06
167 16 0.06
168 3 0.01
169 5 0.02
170 113 0.40
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (166 bp):
GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAACTATGT
TGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGAAGATAGCCCTT
CTCGCCTTAGCTATGCTGTAAATTTGATATGCCCTT
Found at i:5463322 original size:14 final size:14
Alignment explanation
Indices: 5463292--5463328 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5463282 AAAACTAATT
*
5463292 TAAAAG-AAAATAA
1 TAAAAGTAAAAAAA
5463305 -AAAAGTAAAAAAA
1 TAAAAGTAAAAAAA
5463318 TAAAAGTAAAA
1 TAAAAGTAAAA
5463329 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 6 0.29
14 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (14 bp):
TAAAAGTAAAAAAA
Found at i:5463397 original size:20 final size:21
Alignment explanation
Indices: 5463337--5463395 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
5463327 AATATTTTAA
5463337 AAAAATAGAACAAAAAACTGAATT
1 AAAAA-AGAA-AAAAAA-TGAATT
5463361 AAAAAAGAAAAAAAATGAA-T
1 AAAAAAGAAAAAAAATGAATT
5463381 AAAAAGAGAAAAAAA
1 AAAAA-AGAAAAAAA
5463396 TGGAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.18
21 13 0.38
22 6 0.18
23 4 0.12
24 5 0.15
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAAAGAAAAAAAATGAATT
Found at i:5463402 original size:28 final size:26
Alignment explanation
Indices: 5463371--5463448 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 26
5463361 AAAAAAGAAA
5463371 AAAAATGAATAAAAAGAGAAAAAAATGG
1 AAAAATGAA-AAAAA-AGAAAAAAATGG
* *
5463399 AAAAATTAAAAAAAAGAAATAAAT-G
1 AAAAATGAAAAAAAAGAAAAAAATGG
* * *
5463424 AAATAAT-ATAAAAAACACAAAAATG
1 AAA-AATGAAAAAAAAGAAAAAAATG
5463449 TTAGCTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 17 0.40
26 12 0.29
27 5 0.12
28 8 0.19
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAATGAAAAAAAAGAAAAAAATGG
Found at i:5463410 original size:26 final size:27
Alignment explanation
Indices: 5463381--5463438 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
5463371 AAAAATGAAT
*
5463381 AAAAAGAGAAAAAAATGGAAA-AAT-TA
1 AAAAAAAGAAAAAAAT-GAAATAATATA
*
5463407 AAAAAAAGAAATAAATGAAATAATATA
1 AAAAAAAGAAAAAAATGAAATAATATA
5463434 AAAAA
1 AAAAA
5463439 CACAAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 17 0.61
27 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (27 bp):
AAAAAAAGAAAAAAATGAAATAATATA
Found at i:5463480 original size:10 final size:10
Alignment explanation
Indices: 5463465--5463508 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
5463455 AAATAATAGG
5463465 AAAAAAAATA
1 AAAAAAAATA
*
5463475 AAAAAAAGTAA
1 AAAAAAAAT-A
5463486 AAAATAAAATA
1 AAAA-AAAATA
*
5463497 AAATAAAATA
1 AAAAAAAATA
5463507 AA
1 AA
5463509 CAATTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 16 0.55
11 9 0.31
12 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:5463489 original size:17 final size:17
Alignment explanation
Indices: 5463467--5463504 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
5463457 ATAATAGGAA
5463467 AAAAAATAAAA-AAAAGT
1 AAAAAATAAAATAAAA-T
5463484 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
5463501 AAAA
1 AAAA
5463505 TAAACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:5463496 original size:22 final size:22
Alignment explanation
Indices: 5463465--5463517 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
5463455 AAATAATAGG
5463465 AAAA-AAAATAAAA-AAAAGTAA
1 AAAATAAAATAAAATAAAA-TAA
5463486 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
* *
5463508 ACAATTAAAT
1 AAAATAAAAT
5463518 TAAACATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAA
Found at i:5469212 original size:18 final size:18
Alignment explanation
Indices: 5469175--5469219 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5469165 AAAAAGATAT
**
5469175 TTAAAT-AATAAAAGTGA
1 TTAAATAAATAAAAGCAA
5469192 TTAAATAAATAAAAGCAA
1 TTAAATAAATAAAAGCAA
5469210 TTAAAGTAAA
1 TTAAA-TAAA
5469220 AATAAGAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (18 bp):
TTAAATAAATAAAAGCAA
Found at i:5469815 original size:22 final size:23
Alignment explanation
Indices: 5469790--5469836 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5469780 TTAGCATATT
5469790 AAAAACAAAACTTGAAAA-TAAA
1 AAAAACAAAACTTGAAAACTAAA
**
5469812 AAAAATGAAACTTGAAAACTAAA
1 AAAAACAAAACTTGAAAACTAAA
5469835 AA
1 AA
5469837 GAGAAAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAACAAAACTTGAAAACTAAA
Found at i:5472173 original size:16 final size:16
Alignment explanation
Indices: 5472152--5472192 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5472142 ACGATCTATT
5472152 TGCCGAAATGGATTTG
1 TGCCGAAATGGATTTG
5472168 TGCCGAAATGGATTTG
1 TGCCGAAATGGATTTG
*
5472184 TGACGAAAT
1 TGCCGAAAT
5472193 CGAACAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
TGCCGAAATGGATTTG
Found at i:5473847 original size:19 final size:19
Alignment explanation
Indices: 5473825--5473892 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
5473815 TTTATGGGTA
5473825 ATTATTATATTTTTTTATT
1 ATTATTATATTTTTTTATT
* *** *
5473844 ATTATTTTATTTCCCTACT
1 ATTATTATATTTTTTTATT
5473863 ATTATTATAATTTTTTCTATT
1 ATTATTAT-ATTTTTT-TATT
*
5473884 -TAATTATAT
1 ATTATTATAT
5473893 GTATCTATAC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 23 0.64
20 10 0.28
21 3 0.08
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATTATATTTTTTTATT
Found at i:5474076 original size:16 final size:16
Alignment explanation
Indices: 5474045--5474088 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
5474035 ATATATATAA
*
5474045 TTATTTTATATTATTAT
1 TTATTTTCT-TTATTAT
5474062 TTATTTTCTTTATTAT
1 TTATTTTCTTTATTAT
5474078 TT-TTTCTCTTT
1 TTATTT-TCTTT
5474089 CTTTCTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.56
17 8 0.32
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTTCTTTATTAT
Found at i:5474077 original size:19 final size:20
Alignment explanation
Indices: 5474053--5474092 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5474043 AATTATTTTA
5474053 TATTATTATTTAT-TTTCTT
1 TATTATTATTTATCTTTCTT
* *
5474072 TATTATTTTTTCTCTTTCTT
1 TATTATTATTTATCTTTCTT
5474092 T
1 T
5474093 CTGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTATTATTTATCTTTCTT
Found at i:5474159 original size:29 final size:26
Alignment explanation
Indices: 5474101--5474161 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 26
5474091 TTCTGTTTTC
5474101 ATTTATTTATTATTATACTTTTTAGT
1 ATTTATTTATTATTATACTTTTTAGT
5474127 ATTTATTCTATTATATATACATTTTTTA-T
1 ATTTATT-TATTAT-TATAC--TTTTTAGT
5474156 ATTTAT
1 ATTTAT
5474162 AAATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.23
27 6 0.19
28 5 0.16
29 7 0.23
30 6 0.19
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTTATTTATTATTATACTTTTTAGT
Found at i:5474275 original size:16 final size:16
Alignment explanation
Indices: 5474256--5474312 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
5474246 ACACTTTACT
5474256 TTTTATTATCTTTTTA
1 TTTTATTATCTTTTTA
* *
5474272 TTTTTTTCTCTTTTATA
1 TTTTATTATCTTTT-TA
*
5474289 TATT-TTATCTTCATTTA
1 TTTTATTATCTT--TTTA
5474306 TTTTATT
1 TTTTATT
5474313 TTATTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 18 0.56
17 10 0.31
18 4 0.12
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTATCTTTTTA
Found at i:5474275 original size:17 final size:17
Alignment explanation
Indices: 5474250--5474296 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
5474240 TTTTTAACAC
5474250 TTTACTTTTTATTATCTT
1 TTTA-TTTTTATTATCTT
*
5474268 TTTATTTTT-TTCTCTT
1 TTTATTTTTATTATCTT
5474284 TTATATATTTTAT
1 TT-TAT-TTTTAT
5474297 CTTCATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 8 0.32
19 1 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTATTATCTT
Found at i:5474309 original size:15 final size:14
Alignment explanation
Indices: 5474289--5474323 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5474279 CTCTTTTATA
5474289 TATTTTATCTTCATT
1 TATTTTAT-TTCATT
*
5474304 TATTTTATTTTATT
1 TATTTTATTTCATT
5474318 TATTTT
1 TATTTT
5474324 CACTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTATTTCATT
Found at i:5474336 original size:24 final size:24
Alignment explanation
Indices: 5474267--5474337 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
5474257 TTTATTATCT
*
5474267 TTTTATTT-TTTTCTC-TTTTATA
1 TTTTATTTATTTTCACTTTTTATA
* * *
5474289 -TAT-TTTATCTTCA-TTTATTTTA
1 TTTTATTTATTTTCACTTT-TTATA
5474311 TTTTATTTATTTTCACTTTTTATA
1 TTTTATTTATTTTCACTTTTTATA
5474335 TTT
1 TTT
5474338 ATAAATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
20 3 0.08
21 8 0.22
22 4 0.11
23 2 0.06
24 16 0.44
25 3 0.08
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTATTTATTTTCACTTTTTATA
Found at i:5481480 original size:74 final size:75
Alignment explanation
Indices: 5481351--5481489 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
5481341 TTCGCTTAGG
*
5481351 ATGAAAACCCGATAGGGTGTCCTAAGTCGAAGAAGAAAAAGAAAAAAAGAAAAG-AAAGAACAAA
1 ATGAAAACCCGAAAGGGTGTCCTAAGTCGAAGAAGAAAAAGAAAAAAAGAAAAGAAAAGAA-AAA
5481415 AAAGAGAAAAC
65 AAAGAGAAAAC
* * *
5481426 ATGAAAACCCGAAAGGGT-TCCTAATTTGAA-AA-AAAAAGAGAAAAAGAATGAAGAAAAGAAAA
1 ATGAAAACCCGAAAGGGTGTCCTAAGTCGAAGAAGAAAAAGAAAAAAAGAA--AAGAAAAGAAAA
5481488 AA
64 AA
5481490 GAAAAAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
72 15 0.26
73 2 0.04
74 17 0.30
75 23 0.40
ACGTcount: A:0.60, C:0.09, G:0.20, T:0.10
Consensus pattern (75 bp):
ATGAAAACCCGAAAGGGTGTCCTAAGTCGAAGAAGAAAAAGAAAAAAAGAAAAGAAAAGAAAAAA
AAGAGAAAAC
Found at i:5481498 original size:19 final size:20
Alignment explanation
Indices: 5481454--5481501 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5481444 TCCTAATTTG
5481454 AAAAA-AAAAGAGAAAAAGA
1 AAAAAGAAAAGAGAAAAAGA
**
5481473 ATGAAGAAAAGA-AAAAAGA
1 AAAAAGAAAAGAGAAAAAGA
5481492 AAAAAGAAAA
1 AAAAAGAAAA
5481502 TAAGGTGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAGAGAAAAAGA
Found at i:5482528 original size:124 final size:124
Alignment explanation
Indices: 5482308--5482745 Score: 597
Period size: 124 Copynumber: 3.6 Consensus size: 124
5482298 GACTCGAAGA
* * *
5482308 AACATTCATCTTTAGATTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAGGCTCCACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* * * * *
5482373 ACAACCAATGGGTCGTCCACGATTTTAACTTCACGAAGAATGATATTGTGCCCACCAGC
66 ACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAAGATATTGTGCCCACCAGC
* *
5482432 AACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTT
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* * *
5482497 ACAACGAAGGGGCCATCTACGATTTCAACTTCACGAAGAAAGAAATTGTGCCCACCAGC
66 ACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAAGATATTGTGCCCACCAGC
* * * * *
5482556 GACATTCATCTTTGGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGTTTAACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* * *
5482621 ACAATGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAGGATATTGTGCCCA-TA-C
66 ACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAAGATATTGTGCCCACCAGC
*
5482678 -A-A--C-TC--TAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* *
5482736 ATAGCGAAGG
66 ACAACGAAGG
5482746 AACTTTCCAG
Statistics
Matches: 282, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
115 55 0.20
117 2 0.01
118 1 0.00
120 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 220 0.78
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (124 bp):
AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
ACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAAGATATTGTGCCCACCAGC
Found at i:5484541 original size:2 final size:2
Alignment explanation
Indices: 5484534--5484563 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5484524 TTTTAGTATT
5484534 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5484564 TAATTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5484558 original size:11 final size:11
Alignment explanation
Indices: 5484530--5484584 Score: 59
Period size: 10 Copynumber: 5.5 Consensus size: 11
5484520 TACATTTTAG
5484530 TATT-TATATA
1 TATTATATATA
5484540 TA-TATATATA
1 TATTATATATA
5484550 TATTATATATA
1 TATTATATATA
5484561 TATTA-AT-TA
1 TATTATATATA
*
5484570 T-TTATTTAT-
1 TATTATATATA
5484579 TATTAT
1 TATTAT
5484585 TATTCTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 3 0.08
9 6 0.15
10 17 0.44
11 13 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATATATA
Found at i:5484558 original size:15 final size:14
Alignment explanation
Indices: 5484533--5484596 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 14
5484523 ATTTTAGTAT
5484533 TTATATATATATATA
1 TTAT-TATATATATA
5484548 TATATTATATATATA
1 T-TATTATATATATA
* *
5484563 TTAATTATTTATTTA
1 TT-ATTATATATATA
*
5484578 TTATTAT-TAT-TC
1 TTATTATATATATA
5484590 TTATTAT
1 TTATTAT
5484597 TTTTCTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.18
13 3 0.07
14 6 0.14
15 24 0.55
16 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATATATATA
Found at i:5484588 original size:17 final size:17
Alignment explanation
Indices: 5484530--5484588 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
5484520 TACATTTTAG
5484530 TATTTATATA-TATATAT
1 TATTTATATATTAT-TAT
5484547 ATATATTATATATATATTAAT
1 -TAT-TTATATAT-TATT-AT
*
5484568 TATTTATTTATTATTAT
1 TATTTATATATTATTAT
5484585 TATT
1 TATT
5484589 CTTATTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 6 0.17
18 7 0.19
19 14 0.39
20 4 0.11
21 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATATATTATTAT
Found at i:5493741 original size:4 final size:4
Alignment explanation
Indices: 5493727--5493758 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
5493717 TGCGAACATG
5493727 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
5493759 AGGTTAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5494025 original size:127 final size:128
Alignment explanation
Indices: 5493813--5494064 Score: 373
Period size: 127 Copynumber: 2.0 Consensus size: 128
5493803 AAAAAATAGC
* *
5493813 AGTTAGCAGAGTCCGAATCATAATAATGCAGATCATACCCTGGATCGGGTCACCACAAGGTCGAA
1 AGTTAGCAAAGTCCGAATCATAATAATGCAGATCATACCATGGATCGGGTCACCACAAGGTCGAA
* * *
5493878 TCAAATATTAGAAA-TAATAAATAAATAAACAAAGGTTAGAGTGCAATAAAATAAAATTCAGT
66 TCAAATAATAGAAACAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAATTCAGT
* * *
5493940 AGTTAGCAAAGTCTGAATCATAATAATATC-GATCATACCATGGATCTGGTCACCACAAGGTCGA
1 AGTTAGCAAAGTCCGAATCATAATAAT-GCAGATCATACCATGGATCGGGTCACCACAAGGTCGA
*
5494004 ATCGAATAATAGAAACAATAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAA
65 ATCAAATAATAGAAAC---AAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAA
5494065 GTTAGTGGTT
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
127 70 0.63
128 1 0.01
131 40 0.36
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (128 bp):
AGTTAGCAAAGTCCGAATCATAATAATGCAGATCATACCATGGATCGGGTCACCACAAGGTCGAA
TCAAATAATAGAAACAAATAAATAAATAAACAAAGGTTAAAGTGCAATAAAATAAAATTCAGT
Found at i:5494678 original size:2 final size:2
Alignment explanation
Indices: 5494671--5494700 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5494661 AACGAGGCTA
5494671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5494701 GAAAGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5495663 original size:132 final size:130
Alignment explanation
Indices: 5495375--5495734 Score: 324
Period size: 132 Copynumber: 2.7 Consensus size: 130
5495365 GTTCTGGTCG
* * * * * *** ** *
5495375 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGATCGATGACACTATTCCTACGT
1 TCTAAGGGTGACGCGACTCCTACGTGATCAGAAGATCTAGTCGGGGGAT-ACACGGTTCCTACAT
* ** * * * * *
5495440 GATGAGGACATCTTGGCCATCTTTAGGCATGATGATAACACGATTCCTGCGCGATGAGGATGGCT
65 GATGAGGATA-GATGACCATCTTTAGG---GATGATAACACGATTCCTACGCGATAAGGACGACT
*
5495505 GGTTA
126 AGTTA
* * * * *
5495510 TCTAGGGGTGACGCGGCTCCTACGTTATCAGAAGATCTAGTCGGGGGGATGACATGGTTCCTACG
1 TCTAAGGGTGACGCGACTCCTACGTGATCAGAAGATCTAGTC-GGGGGAT-ACACGGTTCCTACA
* * *
5495575 TGATGAGGATGGATGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATAAGGACGACTAGT
64 TGATGAGGATAGATGACCATCTTTAGGGATGATAACACGATTCCTACGCGATAAGGACGACTAGT
5495640 TA
129 TA
* * * * * * *
5495642 TTTAAGGGTGATGCGACTCCTACGTGATGAGGAGATCTGGTCGGTGGATATACGGTTCCTACATG
1 TCTAAGGGTGACGCGACTCCTACGTGATCAGAAGATCTAGTCGGGGGATACACGGTTCCTACATG
* *
5495707 ATGAGGATAGTTGGCCATCTTTAGGGAT
66 ATGAGGATAGATGACCATCTTTAGGGAT
5495735 AAATGTTTCA
Statistics
Matches: 185, Mismatches: 39, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
130 38 0.21
131 6 0.03
132 67 0.36
135 49 0.26
136 25 0.14
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (130 bp):
TCTAAGGGTGACGCGACTCCTACGTGATCAGAAGATCTAGTCGGGGGATACACGGTTCCTACATG
ATGAGGATAGATGACCATCTTTAGGGATGATAACACGATTCCTACGCGATAAGGACGACTAGTTA
Found at i:5495869 original size:21 final size:21
Alignment explanation
Indices: 5495818--5495876 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 21
5495808 TCAAGAGAAA
5495818 TTGTCTCAAGGGAGACAAAAC
1 TTGTCTCAAGGGAGACAAAAC
*
5495839 -TGTCTCAAGGGAGGCAAAAC
1 TTGTCTCAAGGGAGACAAAAC
* *
5495859 TTGTTTCAAGGGAAACAA
1 TTGTCTCAAGGGAGACAA
5495877 TCTCAAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (21 bp):
TTGTCTCAAGGGAGACAAAAC
Found at i:5495894 original size:86 final size:86
Alignment explanation
Indices: 5495749--5495937 Score: 245
Period size: 86 Copynumber: 2.2 Consensus size: 86
5495739 GTTTCAAGAG
*
5495749 AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATGGGTGTTTCAAGA
1 AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAGA
*
5495814 GAAATTGTCTCAAGGGAGACA
66 GAAACTGTCTCAAGGGAGACA
* * * * * * *
5495835 AAACTGTCTCAAGGGAGGCAAAACTT-GTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATG
1 AAACTGTCTCAAGAGAGACAAAA-TTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAG
*
5495899 AGAAACTGTCTCAAGGGAGATA
65 AGAAACTGTCTCAAGGGAGACA
* *
5495921 AAATTTGTTTCAAGAGA
1 AAA-CTGTCTCAAGAGA
5495938 AATAATTGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
86 76 0.86
87 12 0.14
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (86 bp):
AAACTGTCTCAAGAGAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCAAGA
GAAACTGTCTCAAGGGAGACA
Found at i:5496117 original size:36 final size:37
Alignment explanation
Indices: 5496072--5496163 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 37
5496062 AGGAAAAATA
* *
5496072 TCTCAAGCGAGACGAAATTTGTTTTGAGAG-AAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAACTG
*
5496108 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACTG
1 TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAACTG
*
5496145 TCTCAAGCTAGACAAAATT
1 TCTCAAGCGAGACAAAATT
5496164 CATTCAAGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (37 bp):
TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAACTG
Found at i:5496170 original size:138 final size:137
Alignment explanation
Indices: 5495966--5496287 Score: 339
Period size: 138 Copynumber: 2.3 Consensus size: 137
5495956 CTTAAGGAAG
* * ** **
5495966 ATTGTCTCAAGTGAGACAAAGTTTGTTTTGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTC
1 ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAACAATCTCAAGTGAGATCAAAATTCATTC
*
5496031 AAGTTAAACAAAC-TCGAAATTTGTA-TCTCAAAGGAAAAATATCTCAAGCGAGACGAAATTTGT
66 AAGTAAAAC-AACTTCGAAATTTGTATTCT-AAAGG-AAAATATCTCAAGCGAGACGAAATTTGT
5496094 TTTG-AGAGAA
128 TTTGAAGA-AA
* **
5496104 ATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACTGTCTCAAGCT-AGA-CAAAATTCAT
1 ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGA-AAAACAATCTCAAG-TGAGATCAAAATTCAT
* * * * * * *
5496167 TCAAGTAAAACAACTTTGAAATTTGTGTTCTGATGGAAAATTTCTCAAGTGAGATGAAATTTGTT
64 TCAAGTAAAACAACTTCGAAATTTGTATTCTAAAGGAAAATATCTCAAGCGAGACGAAATTTGTT
*
5496232 TTTAAGAAA
129 TTGAAGAAA
* * * * *
5496241 ATTGTCTCTAGCGAGACGACACTTTGTTTCGAGAGAAACAATCTCAA
1 ATTGTCTCAAGCGAGAC-AAAATTTGTTTTGAGAAAAACAATCTCAA
5496288 AGGCAACAAA
Statistics
Matches: 152, Mismatches: 26, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
137 59 0.39
138 74 0.49
139 18 0.12
140 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (137 bp):
ATTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAACAATCTCAAGTGAGATCAAAATTCATTC
AAGTAAAACAACTTCGAAATTTGTATTCTAAAGGAAAATATCTCAAGCGAGACGAAATTTGTTTT
GAAGAAA
Found at i:5497333 original size:16 final size:16
Alignment explanation
Indices: 5497312--5497344 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5497302 GCGTCCTTTT
*
5497312 TGATCTTTTGGTGAAC
1 TGATCTTCTGGTGAAC
5497328 TGATCTTCTGGTGAAC
1 TGATCTTCTGGTGAAC
5497344 T
1 T
5497345 AATTCTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (16 bp):
TGATCTTCTGGTGAAC
Found at i:5497472 original size:30 final size:29
Alignment explanation
Indices: 5497432--5497495 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
5497422 TGTGCTTCTA
*
5497432 TCTTTTTTTTCTTTGATTTTTCCATTTTTC
1 TCTTTGTTTTCTTTGATTTTT-CATTTTTC
* *
5497462 TCTTTGTTTTCTTTTATTTTTGATTTTTC
1 TCTTTGTTTTCTTTGATTTTTCATTTTTC
5497491 T-TTTG
1 TCTTTG
5497496 GATTTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.13
29 8 0.26
30 19 0.61
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.75
Consensus pattern (29 bp):
TCTTTGTTTTCTTTGATTTTTCATTTTTC
Found at i:5498810 original size:114 final size:114
Alignment explanation
Indices: 5498610--5498844 Score: 346
Period size: 114 Copynumber: 2.1 Consensus size: 114
5498600 TCGTAGTTTA
**
5498610 CCATTATGATCCTGACGTTGCACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
1 CCATTATGATCCTGACGTCACACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
* *
5498675 GCTAATGACATGGTAGATGGGCTAAAATTAAGCAAAAAGGCACCTCATG
66 GCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
* * * * *
5498724 CCATTATGATCTTGACGTCACACTTCAC-GATGTTGATGTGACAGTCCACGATTGTTGGTGATAT
1 CCATTATGATCCTGACGTCACACTTCACAG-TGCTCATGTGAAAGTCCACGATTGTTGATGATAT
* *
5498788 GTCTAATGACATGGTAGATGGGCTAAAAATAGGCAAAAAGGCACCTCAAG
65 GGCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
*
5498838 CCCTTAT
1 CCATTAT
5498845 ACTTTCCAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
113 1 0.01
114 107 0.99
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (114 bp):
CCATTATGATCCTGACGTCACACTTCACAGTGCTCATGTGAAAGTCCACGATTGTTGATGATATG
GCTAATGACATGGTAGATGGGCTAAAAATAAGCAAAAAGGCACCTCAAG
Found at i:5501714 original size:33 final size:34
Alignment explanation
Indices: 5501677--5501745 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
5501667 AAAGATAAAT
*
5501677 TTATAATTTGAATCTTAAATT-TTTTTCTTA-TGA
1 TTATAATTTGAATATTAAATTATTTTT-TTAGTGA
5501710 TTATAATTTGAATATTAAATTATTTTTTTAGTGA
1 TTATAATTTGAATATTAAATTATTTTTTTAGTGA
5501744 TT
1 TT
5501746 TCACATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (34 bp):
TTATAATTTGAATATTAAATTATTTTTTTAGTGA
Found at i:5502206 original size:22 final size:22
Alignment explanation
Indices: 5502159--5502237 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 22
5502149 CATTTCAGCT
** *
5502159 TGGTTTCGAAATTCCTT-TGCC
1 TGGTTTCGAAACCCCTTGTACC
5502180 TGGTTTCGAAACCCCTTGTACC
1 TGGTTTCGAAACCCCTTGTACC
* *
5502202 TGGTTTCGAATCCCCCTG-A-C
1 TGGTTTCGAAACCCCTTGTACC
*
5502222 TGGTTTCTAAAGCCCC
1 TGGTTTCGAAA-CCCC
5502238 CCGTCTGGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 10 0.20
21 20 0.41
22 19 0.39
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.34
Consensus pattern (22 bp):
TGGTTTCGAAACCCCTTGTACC
Found at i:5502226 original size:20 final size:22
Alignment explanation
Indices: 5502178--5502238 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5502168 AATTCCTTTG
*
5502178 CCTGGTTTCGAAACCCCTTGTA
1 CCTGGTTTCGAAACCCCCTGTA
*
5502200 CCTGGTTTCGAATCCCCCTG-A
1 CCTGGTTTCGAAACCCCCTGTA
*
5502221 -CTGGTTTCTAAAGCCCCC
1 CCTGGTTTCGAAA-CCCCC
5502239 CGTCTGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 6 0.18
22 18 0.53
ACGTcount: A:0.16, C:0.36, G:0.18, T:0.30
Consensus pattern (22 bp):
CCTGGTTTCGAAACCCCCTGTA
Found at i:5505061 original size:29 final size:29
Alignment explanation
Indices: 5505019--5505077 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
5505009 AGATTCTCAA
*
5505019 ATAAAAAAATAATATAAAAACTCAA-TTTT
1 ATAAAAAAACAATATAAAAACT-AAGTTTT
*
5505048 ATAAAAATACAATATAAAAACTAAGTTTT
1 ATAAAAAAACAATATAAAAACTAAGTTTT
5505077 A
1 A
5505078 AATTCTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAAAAAAACAATATAAAAACTAAGTTTT
Done.