Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 295 of 325
Found at i:90437455 original size:27 final size:27
Alignment explanation
Indices: 90437424--90437485 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
90437414 TAGTTTACCA
*
90437424 AATTACCAAAGTACCCCCGATTTACAG
1 AATTACCAAACTACCCCCGATTTACAG
*** * *
90437451 AATTACCGTTCTACCCTCGATTTATAG
1 AATTACCAAACTACCCCCGATTTACAG
90437478 AATTACCA
1 AATTACCA
90437486 TTTTACCTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (27 bp):
AATTACCAAACTACCCCCGATTTACAG
Found at i:90437492 original size:27 final size:27
Alignment explanation
Indices: 90437435--90437717 Score: 176
Period size: 27 Copynumber: 10.4 Consensus size: 27
90437425 ATTACCAAAG
* * * * *
90437435 TACCCCCGATTTACAGAATTACCGTTC
1 TACCCTCGATTTATAAAATTACCATTT
*
90437462 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCATTT
* * *
90437489 TACCTTCGATTTATAAAATTATCGTTT
1 TACCCTCGATTTATAAAATTACCATTT
* * ***
90437516 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCATTT
* * * ***
90437543 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTATAAAATTACCATTT
* * * **
90437570 TACCCCCTGATTTGTAAAATTACTGA-AA
1 TACCCTC-GATTTATAAAATTAC-CATTT
***
90437598 TACCCTCGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TATAAAATTACCATTT
* **
90437626 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACCATTT
**
90437653 TACCCTCGATTTATAAAATTATTATTT
1 TACCCTCGATTTATAAAATTACCATTT
* * *
90437680 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCATTT
90437707 TACCCTCGATT
1 TACCCTCGATT
90437718 GTGAAATTAT
Statistics
Matches: 209, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
26 3 0.01
27 160 0.77
28 44 0.21
29 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCATTT
Found at i:90437585 original size:28 final size:27
Alignment explanation
Indices: 90437516--90437648 Score: 131
Period size: 28 Copynumber: 4.9 Consensus size: 27
90437506 ATTATCGTTT
* **
90437516 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCCCGATTTGTAAAATTACTAAAA
* *
90437543 TACCCCTGGTTTGTAAAATTACTAAAA
1 TACCCCCGATTTGTAAAATTACTAAAA
*
90437570 TACCCCCTGATTTGTAAAATTACTGAAA
1 TACCCCC-GATTTGTAAAATTACTAAAA
* * * *
90437598 TACCCTCGACTTGTAAAAATTACCAAAG
1 TACCCCCGATTTGT-AAAATTACTAAAA
* * *
90437626 TACCCTCGATTTATAGAATTACT
1 TACCCCCGATTTGTAAAATTACT
90437649 GTTTTACCCT
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
27 41 0.47
28 46 0.53
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCCCGATTTGTAAAATTACTAAAA
Found at i:90437805 original size:27 final size:26
Alignment explanation
Indices: 90437749--90437842 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 26
90437739 TATAAGGTAG
* *
90437749 AATTACCAAAACACCCCAGTTTGTAA
1 AATTACCAAAATACCCTAGTTTGTAA
* *
90437775 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* *
90437802 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCT-AGTTTGTAA
90437829 AATTACCAAAATAC
1 AATTACCAAAATAC
90437843 TCTTGATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
26 16 0.28
27 41 0.72
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.27
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:90437851 original size:27 final size:27
Alignment explanation
Indices: 90437768--90437885 Score: 96
Period size: 27 Copynumber: 4.3 Consensus size: 27
90437758 AACACCCCAG
* *
90437768 TTTGTAAAATTACCAAAATAC-CACTGG
1 TTTGTAAAATTACCAAAATACTC-TTGA
* * * **
90437795 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACTCTTGA
90437822 TTTGTAAAATTACCAAAATACTCTTGA
1 TTTGTAAAATTACCAAAATACTCTTGA
** *
90437849 TTTACAAAGTTA-CAGAAATACTCTTGA
1 TTTGTAAAATTACCA-AAATACTCTTGA
*
90437876 CTTTCTAAAA
1 -TTTGTAAAA
90437886 ATTATGGAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
26 2 0.03
27 62 0.87
28 7 0.10
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACTCTTGA
Found at i:90437932 original size:27 final size:27
Alignment explanation
Indices: 90437827--90437934 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 27
90437817 CTCAATTTGT
** *
90437827 AAAATTACCAAAATACTCTTGATTTAC
1 AAAATTACTGAAATACTCTTGGTTTAC
* * *
90437854 AAAGTTACAGAAATACTCTTGACTTT-C
1 AAAATTACTGAAATACTCTTG-GTTTAC
**
90437881 TAAAAATTA-TGGAAATACTAATGGTTTAC
1 --AAAATTACT-GAAATACTCTTGGTTTAC
*
90437910 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACTCTTGGTTT
90437935 GTAGATTTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
27 39 0.62
28 7 0.11
29 17 0.27
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (27 bp):
AAAATTACTGAAATACTCTTGGTTTAC
Found at i:90438009 original size:27 final size:27
Alignment explanation
Indices: 90437979--90438074 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
90437969 GACTAAAATA
90437979 CCCCTGTAGGGTAAAGAGACCGTAAAG
1 CCCCTGTAGGGTAAAGAGACCGTAAAG
*
90438006 CCCCTGTAGGGTAAAGAGATCGTAAAG
1 CCCCTGTAGGGTAAAGAGACCGTAAAG
* * *
90438033 CCCCTGTAGGATAAAGTGACTGTAATA-
1 CCCCTGTAGGGTAAAGAGACCGTAA-AG
*
90438060 CCCCTGTATGGTAAA
1 CCCCTGTAGGGTAAA
90438075 ATAACGAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 60 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
CCCCTGTAGGGTAAAGAGACCGTAAAG
Found at i:90438826 original size:20 final size:20
Alignment explanation
Indices: 90438803--90438853 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
90438793 TTGATATGAT
90438803 ATGCACATGATATGTATAAA
1 ATGCACATGATATGTATAAA
*
90438823 ATGCACATGATATGTATGAA
1 ATGCACATGATATGTATAAA
*
90438843 ATACACATGAT
1 ATGCACATGAT
90438854 GTATTCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCACATGATATGTATAAA
Found at i:90438982 original size:25 final size:26
Alignment explanation
Indices: 90438903--90439024 Score: 178
Period size: 25 Copynumber: 4.8 Consensus size: 26
90438893 GAGGAAGTGC
**
90438903 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
90438929 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
90438955 AAAAGGGCTTATGACCC-GTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
90438980 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
90439005 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
90439025 ATTTAAAGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
24 5 0.06
25 42 0.48
26 40 0.46
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:90439007 original size:50 final size:52
Alignment explanation
Indices: 90438903--90439024 Score: 205
Period size: 50 Copynumber: 2.4 Consensus size: 52
90438893 GAGGAAGTGC
*
90438903 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGACCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
90438955 AAAAGGGCTTATGACCC-GTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGACCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
90439005 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGACCCAGTT
90439025 ATTTAAAGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
49 5 0.07
50 28 0.42
51 18 0.27
52 16 0.24
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGACCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:90439229 original size:42 final size:42
Alignment explanation
Indices: 90439170--90439261 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
90439160 TAGTCTCCCC
* ** *
90439170 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
90439212 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
90439254 AAATGGGC
1 AAATGGGC
90439262 CTATGGGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:90439323 original size:31 final size:31
Alignment explanation
Indices: 90439285--90439394 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
90439275 CGTTTACAGT
*
90439285 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
90439316 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
90439347 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
90439378 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
90439395 AACCGTTAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:90448055 original size:25 final size:23
Alignment explanation
Indices: 90448000--90448055 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
90447990 AATTATAAAG
90448000 ATTTTTTA-AAAAATTATTTTTA
1 ATTTTTTAGAAAAATTATTTTTA
*
90448022 ATTTATTAGAAAATATT-TATTTTA
1 ATTTTTTAGAAAA-ATTAT-TTTTA
90448046 ATGTTTTTAG
1 AT-TTTTTAG
90448056 TGTTTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.25
23 5 0.18
24 10 0.36
25 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
ATTTTTTAGAAAAATTATTTTTA
Found at i:90448944 original size:22 final size:22
Alignment explanation
Indices: 90448916--90448958 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
90448906 CTAATAAATA
* *
90448916 ATTAAAATTTTATTTTATTTAT
1 ATTAAAAATTTATTGTATTTAT
90448938 ATTAAAAATTTATTGTATTTA
1 ATTAAAAATTTATTGTATTTA
90448959 AATATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTAAAAATTTATTGTATTTAT
Found at i:90448951 original size:17 final size:17
Alignment explanation
Indices: 90448929--90448967 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
90448919 AAAATTTTAT
90448929 TTTATT-TATATTAAAAA
1 TTTATTGTAT-TTAAAAA
*
90448946 TTTATTGTATTTAAATA
1 TTTATTGTATTTAAAAA
90448963 TTTAT
1 TTTAT
90448968 AATTAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATTGTATTTAAAAA
Found at i:90451490 original size:21 final size:21
Alignment explanation
Indices: 90451451--90451491 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
90451441 TTCTTTTTAG
* **
90451451 TTAAAAAACTAAATTAAATTT
1 TTAAAAAAATAAAGGAAATTT
90451472 TTAAAAAAATAAAGGAAATT
1 TTAAAAAAATAAAGGAAATT
90451492 AAAAAGATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
TTAAAAAAATAAAGGAAATTT
Found at i:90451563 original size:21 final size:21
Alignment explanation
Indices: 90451539--90451579 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90451529 TTTTTTCCTG
90451539 TAAAAATTCAAGTTCTTCTCA
1 TAAAAATTCAAGTTCTTCTCA
* *
90451560 TAAAAGTTCAAGTTTTTCTC
1 TAAAAATTCAAGTTCTTCTC
90451580 TTGGGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TAAAAATTCAAGTTCTTCTCA
Found at i:90452489 original size:29 final size:29
Alignment explanation
Indices: 90452434--90452491 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
90452424 CATTCAATTA
*
90452434 ATTTTTAATTTTTACAAATTTTAAAAAAT
1 ATTTTTAATTATTACAAATTTTAAAAAAT
*
90452463 ATTTTTAATTATTA-AAATTATTTAAAAAT
1 ATTTTTAATTATTACAAATT-TTAAAAAAT
90452492 TATATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTTTAATTATTACAAATTTTAAAAAAT
Found at i:90452508 original size:29 final size:29
Alignment explanation
Indices: 90452449--90452513 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
90452439 TAATTTTTAC
* *
90452449 AAAT-TTTAAAAAATATTTTTAATTATTAA
1 AAATATTTAAAAAATATTATTAATTA-GAA
* *
90452478 AATTATTTAAAAATTA-TATTAATTAGAA
1 AAATATTTAAAAAATATTATTAATTAGAA
90452506 AAATATTT
1 AAATATTT
90452514 TTTAACATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 9 0.30
29 11 0.37
30 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
AAATATTTAAAAAATATTATTAATTAGAA
Found at i:90459195 original size:16 final size:16
Alignment explanation
Indices: 90459157--90459217 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
90459147 GAGTGATCTT
90459157 ATAATAATTTAA-ATTTA
1 ATAA-AATTTAAGA-TTA
*
90459174 AAAAAATTTAAGCA-TA
1 ATAAAATTTAAG-ATTA
*
90459190 ATAAAATTTGAGATTA
1 ATAAAATTTAAGATTA
*
90459206 ATTAAATTTAAG
1 ATAAAATTTAAG
90459218 TCCAACAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 31 0.86
17 3 0.08
18 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (16 bp):
ATAAAATTTAAGATTA
Found at i:90460083 original size:20 final size:21
Alignment explanation
Indices: 90460034--90460084 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
90460024 TCTCCTCTTG
* * *
90460034 AATTATGTTATTTAAGTTTTT
1 AATTATATTATTTAAGATTTA
90460055 AATTATATTATTTAA-ATTTA
1 AATTATATTATTTAAGATTTA
*
90460075 AATTTTATTA
1 AATTATATTA
90460085 ATTATGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTATATTATTTAAGATTTA
Found at i:90470306 original size:20 final size:20
Alignment explanation
Indices: 90470265--90470306 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
90470255 TTTTAAAAAA
* *
90470265 TTAAAAACTATAAAAGTTAT
1 TTAAAAACTATAAAAATAAT
*
90470285 TTAAAAATTATAAAAATAAT
1 TTAAAAACTATAAAAATAAT
90470305 TT
1 TT
90470307 TTAGTATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAAACTATAAAAATAAT
Found at i:90470908 original size:2 final size:2
Alignment explanation
Indices: 90470901--90470926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90470891 TTATTCCTTT
90470901 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
90470927 AAATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90474641 original size:122 final size:123
Alignment explanation
Indices: 90474514--90474749 Score: 330
Period size: 122 Copynumber: 1.9 Consensus size: 123
90474504 TGTAAAAAAA
*
90474514 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACCAT
1 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
* * * **
90474579 GTATAAA-TAGTGCTAAAGTTGCTATTATATTAATTTTAAAAGTTACCATGTCAACAT
66 ATATAAATTAATGCTAAAGTTACTATTATACCAATTTTAAAAGTTACCATGTCAACAT
* * * * *
90474636 TTAAATTACAAATGTGTAAATGTTGAATGTTAGATTTTTTTAAATCAAGAATAATTTAACACAAT
1 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
* *
90474701 ATATAAATGTTAATGTTAAAGTTACTATTATGCCAATTTTAAAAGTTAC
66 ATATAAA--TTAATGCTAAAGTTACTATTATACCAATTTTAAAAGTTAC
90474750 TATATTAGTC
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
122 65 0.66
125 33 0.34
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (123 bp):
TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
ATATAAATTAATGCTAAAGTTACTATTATACCAATTTTAAAAGTTACCATGTCAACAT
Found at i:90477502 original size:3 final size:3
Alignment explanation
Indices: 90477496--90477520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
90477486 AGAAAAACAA
90477496 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
90477521 CGACATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:90479050 original size:31 final size:33
Alignment explanation
Indices: 90478988--90479051 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
90478978 AATAATTGTA
*
90478988 TTATAAAGACAAAATTTTTGTACGTAAAGTTATC
1 TTATAAAGACAAAATTTTTATAC-TAAAGTTATC
*
90479022 TTATAAAGACATAA-TTTTATA-TAAAGTTAT
1 TTATAAAGACAAAATTTTTATACTAAAGTTAT
90479052 TTTGTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 9 0.32
33 6 0.21
34 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (33 bp):
TTATAAAGACAAAATTTTTATACTAAAGTTATC
Found at i:90482261 original size:44 final size:45
Alignment explanation
Indices: 90482208--90482306 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
90482198 TGTCTTTGAC
* * *
90482208 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
90482252 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
90482298 ATGGACTTA
1 ATGGACTTA
90482307 ATATATTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 33 0.70
46 14 0.30
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:90486480 original size:16 final size:17
Alignment explanation
Indices: 90486443--90486480 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
90486433 AGAATTTTTT
90486443 TATTTTTAAAAAATTAA
1 TATTTTTAAAAAATTAA
*
90486460 TATTTTTAAAAATTTAA
1 TATTTTTAAAAAATTAA
90486477 -ATTT
1 TATTT
90486481 AATTATTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTTAAAAAATTAA
Found at i:90486643 original size:22 final size:23
Alignment explanation
Indices: 90486615--90486663 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
90486605 TAATTAGATT
**
90486615 AAAAAATTAAATTTTA-AAAATA
1 AAAAAATTAAATTCCACAAAATA
*
90486637 AAAAAATTAGATTCCACAAAATA
1 AAAAAATTAAATTCCACAAAATA
90486660 AAAA
1 AAAA
90486664 TAAAAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAAAATTAAATTCCACAAAATA
Found at i:90488171 original size:18 final size:17
Alignment explanation
Indices: 90488139--90488174 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
90488129 TGGAGTTTGC
*
90488139 TGTTGTTTTTTTTTTAA
1 TGTTGTTTTTGTTTTAA
90488156 TGTTGTTTTTAGTTTTAA
1 TGTTGTTTTT-GTTTTAA
90488174 T
1 T
90488175 CTATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (17 bp):
TGTTGTTTTTGTTTTAA
Found at i:90494472 original size:47 final size:47
Alignment explanation
Indices: 90494403--90494498 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
90494393 CAAAACTTTG
90494403 AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
1 AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
90494450 AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
1 AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
90494497 AA
1 AA
90494499 TGACTTGATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (47 bp):
AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
Found at i:90494654 original size:16 final size:16
Alignment explanation
Indices: 90494633--90494663 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
90494623 TTTTAAATGT
90494633 TTTTAAAAATAATATA
1 TTTTAAAAATAATATA
*
90494649 TTTTAAAAATTATAT
1 TTTTAAAAATAATAT
90494664 TAATATTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATAATATA
Found at i:90497511 original size:18 final size:18
Alignment explanation
Indices: 90497477--90497513 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
90497467 GGAAACTGGG
* *
90497477 AATGAAGAGGGAGCTGAA
1 AATGAAGAGGAACCTGAA
90497495 AATGAAGAGGAACCTGAA
1 AATGAAGAGGAACCTGAA
90497513 A
1 A
90497514 CTGATGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.32, T:0.11
Consensus pattern (18 bp):
AATGAAGAGGAACCTGAA
Found at i:90504356 original size:20 final size:20
Alignment explanation
Indices: 90504333--90504371 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
90504323 AAATGGGTCA
*
90504333 TAGATATGTATGCTAGAAAT
1 TAGAAATGTATGCTAGAAAT
* *
90504353 TAGAAATTTATGTTAGAAA
1 TAGAAATGTATGCTAGAAA
90504372 ATGAAAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (20 bp):
TAGAAATGTATGCTAGAAAT
Found at i:90515947 original size:13 final size:13
Alignment explanation
Indices: 90515929--90515960 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
90515919 AAATATTTTT
90515929 CTATAAAAAATTA
1 CTATAAAAAATTA
90515942 CTAT--AAAATTA
1 CTATAAAAAATTA
90515953 CTATAAAA
1 CTATAAAA
90515961 TTTCTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (13 bp):
CTATAAAAAATTA
Found at i:90515951 original size:11 final size:11
Alignment explanation
Indices: 90515935--90515962 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
90515925 TTTTCTATAA
90515935 AAAATTACTAT
1 AAAATTACTAT
90515946 AAAATTACTAT
1 AAAATTACTAT
90515957 AAAATT
1 AAAATT
90515963 TCTTTATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACTAT
Found at i:90518317 original size:40 final size:40
Alignment explanation
Indices: 90518257--90518419 Score: 197
Period size: 40 Copynumber: 4.1 Consensus size: 40
90518247 GAGCGTTACA
* *
90518257 TACTGAAATGTATGCACTATTGAGCCATACCTACTAAATC
1 TACTAAAATGTATGCACTATTGAGCCATACCTACTGAATC
*
90518297 TACTAAAATGTATGCACTATTGAGCCATACCTACTGATTC
1 TACTAAAATGTATGCACTATTGAGCCATACCTACTGAATC
* ** * *
90518337 TACTGAAA-GTATGTTCTATCGAGCCATACCTA-TCGAATT
1 TACTAAAATGTATGCACTATTGAGCCATACCTACT-GAATC
* *
90518376 TACTAAAATGTATGCGCT-TTCGAGCCATACCTACTGATTC
1 TACTAAAATGTATGCACTATT-GAGCCATACCTACTGAATC
90518416 TACT
1 TACT
90518420 GAAAGTTGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 32 0.31
40 70 0.67
41 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (40 bp):
TACTAAAATGTATGCACTATTGAGCCATACCTACTGAATC
Found at i:90518366 original size:79 final size:79
Alignment explanation
Indices: 90518257--90518425 Score: 243
Period size: 79 Copynumber: 2.1 Consensus size: 79
90518247 GAGCGTTACA
*
90518257 TACTGAAATGTATGCACTATTGAGCCATACCTA-CTAAATCTACTAAAATGTATGCACTATT-GA
1 TACTGAAA-GTATGCACTATCGAGCCATACCTATC-AAATCTACTAAAATGTATGCACT-TTCGA
90518320 GCCATACCTACTGATTC
63 GCCATACCTACTGATTC
** * * *
90518337 TACTGAAAGTATGTTCTATCGAGCCATACCTATCGAATTTACTAAAATGTATGCGCTTTCGAGCC
1 TACTGAAAGTATGCACTATCGAGCCATACCTATCAAATCTACTAAAATGTATGCACTTTCGAGCC
90518402 ATACCTACTGATTC
66 ATACCTACTGATTC
90518416 TACTGAAAGT
1 TACTGAAAGT
90518426 TGCTCAAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 2 0.02
79 70 0.86
80 9 0.11
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (79 bp):
TACTGAAAGTATGCACTATCGAGCCATACCTATCAAATCTACTAAAATGTATGCACTTTCGAGCC
ATACCTACTGATTC
Found at i:90519906 original size:18 final size:18
Alignment explanation
Indices: 90519883--90519934 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
90519873 TCGCCCATTG
90519883 CAGTAACAGTAAATAGTA
1 CAGTAACAGTAAATAGTA
* *
90519901 CAGTAACAGT-AACAGTG
1 CAGTAACAGTAAATAGTA
*
90519918 CTGTAACAGTAAATAGT
1 CAGTAACAGTAAATAGT
90519935 GCAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (18 bp):
CAGTAACAGTAAATAGTA
Found at i:90520328 original size:27 final size:27
Alignment explanation
Indices: 90520275--90520381 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 27
90520265 AAACATACAT
* * * * *
90520275 CACATAGGGGTAAAACAGGCATCTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
90520302 CATAAAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
90520329 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
90520356 CCCATAAGGGAAAAATAGTCATTTTA
1 CACATAAGGGCAAAATAGTCATTTTA
90520382 TTAATTAGGG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:90520344 original size:54 final size:54
Alignment explanation
Indices: 90520275--90520381 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
90520265 AAACATACAT
* * * *
90520275 CACATAGGGGTAAAACAGGCATCTTACCATAAAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGGCATCTTACCACAAAAGGGAAAAATAGTCATTTTAC
* * * *
90520329 CACATAAGGGCAAAACAGTCATTTTACCCCATAAGGGAAAAATAGTCATTTTA
1 CACATAAGGGCAAAACAGGCATCTTACCACAAAAGGGAAAAATAGTCATTTTA
90520382 TTAATTAGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (54 bp):
CACATAAGGGCAAAACAGGCATCTTACCACAAAAGGGAAAAATAGTCATTTTAC
Found at i:90525996 original size:24 final size:25
Alignment explanation
Indices: 90525962--90526009 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
90525952 AGCTCCCCGA
90525962 TGGTCAGCAGTAGTT-AGCAGTAGT
1 TGGTCAGCAGTAGTTGAGCAGTAGT
* *
90525986 TGGTCATCAGTGGTTGAGCAGTAG
1 TGGTCAGCAGTAGTTGAGCAGTAG
90526010 AAGAGGCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.29
Consensus pattern (25 bp):
TGGTCAGCAGTAGTTGAGCAGTAGT
Found at i:90526097 original size:19 final size:19
Alignment explanation
Indices: 90526073--90526137 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
90526063 GTTTCAAAAA
*
90526073 TAATATTATTTTAATAGTT
1 TAATATTAATTTAATAGTT
90526092 TAATATTAATTTAA-A-TT
1 TAATATTAATTTAATAGTT
**
90526109 TAATACTTAGCTTAATAGTT
1 TAATA-TTAATTTAATAGTT
90526129 TAATATTAA
1 TAATATTAA
90526138 AATGATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 17 0.44
20 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATATTAATTTAATAGTT
Found at i:90526224 original size:12 final size:12
Alignment explanation
Indices: 90526207--90526231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90526197 TTTTAATAAG
90526207 ATTTAATATTAA
1 ATTTAATATTAA
90526219 ATTTAATATTAA
1 ATTTAATATTAA
90526231 A
1 A
90526232 GTGGTTAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:90528896 original size:10 final size:10
Alignment explanation
Indices: 90528881--90528968 Score: 51
Period size: 10 Copynumber: 9.2 Consensus size: 10
90528871 TAAACTTTTT
90528881 AAAATTATAA
1 AAAATTATAA
90528891 AAAATTATAA
1 AAAATTATAA
* *
90528901 AATACTAT-A
1 AAAATTATAA
**
90528910 ATTATTATAA
1 AAAATTATAA
90528920 AAATATT-T-A
1 AAA-ATTATAA
90528929 AAAA-T-TAA
1 AAAATTATAA
* *
90528937 TAAATTCTAA
1 AAAATTATAA
* *
90528947 TAATTTATAA
1 AAAATTATAA
*
90528957 AAAATTGTAA
1 AAAATTATAA
90528967 AA
1 AA
90528969 TTAATAAAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 12 0.20
10 39 0.64
11 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAATTATAA
Found at i:90528939 original size:20 final size:20
Alignment explanation
Indices: 90528916--90528988 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 20
90528906 TATAATTATT
90528916 ATAAAAATATTTAAAAATTA
1 ATAAAAATATTTAAAAATTA
* * *
90528936 AT--AAAT-TCTAATAATTT
1 ATAAAAATATTTAAAAATTA
90528953 ATAAAAA-ATTGT-AAAATTA
1 ATAAAAATATT-TAAAAATTA
*
90528972 ATAAAACTTATTTAAAA
1 ATAAAA-ATATTTAAAA
90528989 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 13
0.66 0.12 0.22
Matches are distributed among these distances:
17 10 0.26
18 4 0.10
19 15 0.38
20 4 0.10
21 6 0.15
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (20 bp):
ATAAAAATATTTAAAAATTA
Found at i:90528998 original size:37 final size:37
Alignment explanation
Indices: 90528956--90529036 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
90528946 ATAATTTATA
** * *
90528956 AAAAATTGTAAAATTAA-TAAAACTTATTTAAAATATT
1 AAAAATTAAAAAATGAATTAAAA-TTATTTAAAATAAT
* *
90528993 TAAAATTAAAAAATGAATTAAAATTCTTTAAAATAAT
1 AAAAATTAAAAAATGAATTAAAATTATTTAAAATAAT
90529030 AAAAATT
1 AAAAATT
90529037 TGAACCTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (37 bp):
AAAAATTAAAAAATGAATTAAAATTATTTAAAATAAT
Found at i:90529362 original size:8 final size:9
Alignment explanation
Indices: 90529340--90529436 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 9
90529330 CCAGTTCAAG
*
90529340 TTTTTATGAT
1 TTTTTAT-AA
90529350 TTTTTATAA
1 TTTTTATAA
90529359 TTTTTATAAA
1 TTTTTAT-AA
* *
90529369 TTTATATTAG
1 TTTTTA-TAA
* *
90529379 TTTTAATAC
1 TTTTTATAA
90529388 TTTTT-TGATA
1 TTTTTAT-A-A
*
90529398 TTTTTATGA
1 TTTTTATAA
90529407 TTTTTATAGAA
1 TTTTTAT--AA
*
90529418 TTTTAATACA
1 TTTTTATA-A
90529428 TTTTTATAA
1 TTTTTATAA
90529437 AATTTTAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
8 1 0.01
9 25 0.37
10 32 0.48
11 9 0.13
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:90529392 original size:39 final size:38
Alignment explanation
Indices: 90529349--90529436 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
90529339 GTTTTTATGA
90529349 TTTTTTATAATTTTTATAAATTTATATTAG-TTTTAATAC
1 TTTTTTATAATTTTTAT-AATTTATA-TAGATTTTAATAC
* *
90529388 TTTTTTGAT-ATTTTTATGATTTTTATAGAATTTTAATAC
1 TTTTTT-ATAATTTTTATAATTTATATAG-ATTTTAATAC
*
90529427 ATTTTTATAA
1 TTTTTTATAA
90529437 AATTTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 3 0.07
38 8 0.19
39 29 0.69
40 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (38 bp):
TTTTTTATAATTTTTATAATTTATATAGATTTTAATAC
Found at i:90529411 original size:29 final size:29
Alignment explanation
Indices: 90529340--90529434 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
90529330 CCAGTTCAAG
*
90529340 TTTTTATGATTTTTTATAATTTTTATAAA
1 TTTTTATGATTTTTAATAATTTTTATAAA
* * * * *
90529369 TTTATATTAGTTTTAATACTTTTT-TGATA
1 TTTTTATGATTTTTAATAATTTTTAT-AAA
* * *
90529398 TTTTTATGATTTTTATAGAATTTTAATACA
1 TTTTTATGATTTTTA-ATAATTTTTATAAA
90529428 TTTTTAT
1 TTTTTAT
90529435 AAAATTTTAA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.02
29 33 0.66
30 15 0.30
31 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTTATGATTTTTAATAATTTTTATAAA
Found at i:90529708 original size:28 final size:26
Alignment explanation
Indices: 90529674--90529748 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 26
90529664 ATTAAGAGAG
*
90529674 AAACTTACTTAATTATTTTAATTAACA
1 AAACTTAATTAATTATTTTAATTAA-A
*
90529701 AAGACTTAATTAATGTAAATTTAATTAAA
1 AA-ACTTAATTAAT-T-ATTTTAATTAAA
*
90529730 AAACTTAATTATTTATTTT
1 AAACTTAATTAATTATTTT
90529749 TATATTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 20 0.49
29 4 0.10
30 10 0.24
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (26 bp):
AAACTTAATTAATTATTTTAATTAAA
Found at i:90530214 original size:24 final size:24
Alignment explanation
Indices: 90530173--90530242 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
90530163 TGATTATTAA
90530173 TATTTAAATTTAGT-TTTAATTTTT
1 TATTT-AATTTAGTATTTAATTTTT
*
90530197 TATTTAATTTAGTATTTAA-GTTT
1 TATTTAATTTAGTATTTAATTTTT
*
90530220 AATTTTAATGTT-GTATTTAATTT
1 TA-TTTAAT-TTAGTATTTAATTT
90530243 ATCCTAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 12 0.31
24 24 0.62
25 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TATTTAATTTAGTATTTAATTTTT
Found at i:90530226 original size:36 final size:36
Alignment explanation
Indices: 90530173--90530243 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
90530163 TGATTATTAA
* * *
90530173 TATTTAAATTTAGTTTTAATTTTTTATTTAATTTAG
1 TATTTAAATTTAATTTTAATGTTGTATTTAATTTAG
*
90530209 TATTTAAGTTTAATTTTAATGTTGTATTTAATTTA
1 TATTTAAATTTAATTTTAATGTTGTATTTAATTTA
90530244 TCCTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (36 bp):
TATTTAAATTTAATTTTAATGTTGTATTTAATTTAG
Found at i:90533778 original size:13 final size:14
Alignment explanation
Indices: 90533750--90533782 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
90533740 GAATTTTTTT
*
90533750 ATTTATTTTTAGAA
1 ATTTAATTTTAGAA
90533764 ATTTAATTTTA-AA
1 ATTTAATTTTAGAA
90533777 ATTTAA
1 ATTTAA
90533783 AAGCAAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATTTAATTTTAGAA
Found at i:90536136 original size:15 final size:15
Alignment explanation
Indices: 90536116--90536145 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
90536106 ATGAAGCATT
90536116 ATCTTTATGCTCATC
1 ATCTTTATGCTCATC
90536131 ATCTTTATGCTCATC
1 ATCTTTATGCTCATC
90536146 GTTTGGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
ATCTTTATGCTCATC
Found at i:90544637 original size:20 final size:19
Alignment explanation
Indices: 90544609--90544686 Score: 50
Period size: 20 Copynumber: 3.9 Consensus size: 19
90544599 TGATTTTTAA
*
90544609 ATTAGAAATTATATAAAATT
1 ATTAAAAATTAT-TAAAATT
* *
90544629 ATTAAAAATAATTTAAAACT
1 ATTAAAAATTA-TTAAAATT
* * *
90544649 -CTAAAAAGTATTGAAATT
1 ATTAAAAATTATTAAAATT
*
90544667 ATATAAAAAAGTATTAAAAT
1 AT-T-AAAAATTATTAAAAT
90544687 GATAAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
18 6 0.14
19 7 0.16
20 16 0.36
21 15 0.34
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
ATTAAAAATTATTAAAATT
Found at i:90544677 original size:21 final size:20
Alignment explanation
Indices: 90544651--90544696 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
90544641 TTAAAACTCT
* *
90544651 AAAAAGTATTGAAATTATATA
1 AAAAAGTATTAAAATGATA-A
90544672 AAAAAGTATTAAAATGATAA
1 AAAAAGTATTAAAATGATAA
90544692 AAAAA
1 AAAAA
90544697 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAAAGTATTAAAATGATAA
Found at i:90544712 original size:21 final size:20
Alignment explanation
Indices: 90544651--90544712 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
90544641 TTAAAACTCT
* *
90544651 AAAAAGTATTGAAATTATATA
1 AAAAAATATTAAAATT-TATA
* *
90544672 AAAAAGTATTAAAA-TGATA
1 AAAAAATATTAAAATTTATA
*
90544691 AAAAAATTTATAAAATTTATA
1 AAAAAATAT-TAAAATTTATA
90544712 A
1 A
90544713 CATTTAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.29
20 6 0.18
21 18 0.53
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
AAAAAATATTAAAATTTATA
Found at i:90563879 original size:211 final size:210
Alignment explanation
Indices: 90563643--90564038 Score: 598
Period size: 211 Copynumber: 1.9 Consensus size: 210
90563633 TAAAACCTAC
* * * * * *
90563643 AATCTAAAAGTCCTAAAATCTAATTTCTAGAAATTTAATCGAAA-AATGCCTACTATTTAGATTC
1 AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAAGAAT-CATACTATTTAAATCC
* *
90563707 AAAATCCTAAAATGAACTAATTTAAAACCTAATATAAAAAAAAATTAAAGTATGAAATTCAAAAA
65 AAAATCCTAAAATGAACTAATTTAAAACCGAATAT-AAAAAAAATTAAAGGATGAAATTCAAAAA
* * * * *
90563772 TATGCTAA-CATACTATAAAGTACACAGTCCTACAGAGAAAACCTCAAATAATCCTAATACTTAA
129 GAAGCTAACCA-ACTATAAAATACACAATCCTAAAGAGAAAACCTCAAATAATCCTAATACTTAA
90563836 TTTATTTTTTTTAAAAAT
193 TTTATTTTTTTTAAAAAT
* *
90563854 AATCTAAAAGTATTAAAATCTAATTTCTAGAAATTTAACCAAAAGAATCATAGTATTTAAATCCA
1 AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAAGAATCATACTATTTAAATCCA
*
90563919 AGATCCTAAAATGAACTAATTTAAAACCGAATATAAAAAAAATTAAAGGATGAAATTCAAAAAGA
66 AAATCCTAAAATGAACTAATTTAAAACCGAATATAAAAAAAATTAAAGGATGAAATTCAAAAAGA
*
90563984 AGCTAACCAACTATAAAATACACAATCCTAAAGAGAAAACTTCAAATAATCCTAA
131 AGCTAACCAACTATAAAATACACAATCCTAAAGAGAAAACCTCAAATAATCCTAA
90564039 GACATAAAAA
Statistics
Matches: 166, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
210 76 0.46
211 87 0.52
212 3 0.02
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (210 bp):
AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAAGAATCATACTATTTAAATCCA
AAATCCTAAAATGAACTAATTTAAAACCGAATATAAAAAAAATTAAAGGATGAAATTCAAAAAGA
AGCTAACCAACTATAAAATACACAATCCTAAAGAGAAAACCTCAAATAATCCTAATACTTAATTT
ATTTTTTTTAAAAAT
Found at i:90564941 original size:68 final size:67
Alignment explanation
Indices: 90564848--90564983 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 67
90564838 AAACAACAAA
* * * *
90564848 TTCTAAAATAGTAAGTAGAAATAAAATATGAGAAATTACCATGGGATATAATACAAATCTAACAT
1 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATAC-AATCTAACAT
90564913 TAC
65 TAC
90564916 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
1 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
90564981 AC
66 AC
90564983 T
1 T
90564984 CAAACAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 14 0.22
68 50 0.78
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (67 bp):
TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
AC
Found at i:90565893 original size:284 final size:280
Alignment explanation
Indices: 90565153--90565965 Score: 1116
Period size: 279 Copynumber: 2.9 Consensus size: 280
90565143 CAATAATAAT
* *
90565153 AAAACAGAGAAATCTAAATCAATAGGATAAAATAAATCAAAATAAAAAATGAAATTAAAAAAGAA
1 AAAAAAGAGAAATCTAAATCAATAGGATAAAATAAATCAAAATAAAAAATGAAATTAAAAAAGGA
* * *
90565218 TTTAAAATCGAAAT-AAAAAACGTACGAAGCAAA-TGACCTATTTGGCACTTAATTTGCCTGAAA
66 TTTAAAATCGAAATAAAAAAATGTAAGAAGCAAAGT-ACCTATTTGGCAATTAATTTGCCTGAAA
* ** *
90565281 TTTCAAAATCTGGGAGAAACCAAAACCAAAGGGACAAGAACTACAATTAGTCCATGCGGCGATCC
130 TTTCAAAATCGGGGAGAATTCAAAAGCAAAGGGACAAGAACTACAATTAGTCCATGCGGCGATCC
** * * *
90565346 TTTTCTGCT-GATGGCAGGATGTAGAAGGAATTATGTAGAAAATATCCCTTTATATAACCCTATA
195 TTTT-TTATAAAAGGCAGGATGTAGAAGGAATTATGTAGAAAATATCCCTTTACATAACCCTATA
90565410 AATAACCCTAAAACACCAAAAA
259 AATAACCCTAAAACACCAAAAA
* * * * *
90565432 AAAAGAGAGAAATGTAAATCAATAGGATAAAATAAATTAAAATAAAAAATGAGATTAAAAAAAGA
1 AAAAAAGAGAAATCTAAATCAATAGGATAAAATAAATCAAAATAAAAAATGAAATTAAAAAAGGA
* ** *
90565497 TATAAAATC-AAA-ACAAAAAATGTAAGAAGCTGAGTACCTATGTGGCAATTAATTTGCCTGAAA
66 TTTAAAATCGAAATA-AAAAAATGTAAGAAGCAAAGTACCTATTTGGCAATTAATTTGCCTGAAA
* * * * *
90565560 TTTCAAAATTGAGGAGAATTTAAAAGCAAACGGACAAGAGCTACAATTAGTCCATGCGGCGATCC
130 TTTCAAAATCGGGGAGAATTCAAAAGCAAAGGGACAAGAACTACAATTAGTCCATGCGGCGATCC
* * *
90565625 TTTTTTATAAAAGGCAGGAGGTAGAAGGAATTATGTAGAAAATATCTCTTTACATAACCTTATAA
195 TTTTTTATAAAAGGCAGGATGTAGAAGGAATTATGTAGAAAATATCCCTTTACATAACCCTATAA
*
90565690 ATAACCTTAAAACACCAAAAAAAA
260 ATAACCCTAAAACACC---AAAAA
* *
90565714 AAAAAAGAGAAATCAAAATCAATAGGATAAAATAAATCAAAATAAAAAATGATATTAAAAAAGGA
1 AAAAAAGAGAAATCTAAATCAATAGGATAAAATAAATCAAAATAAAAAATGAAATTAAAAAAGGA
* *
90565779 TTTAAAATCGAAATAAAAAAAATGTAAGAAGAAAAGTACCTATTTGGCAATTAATTTGCATGAAA
66 TTTAAAATCGAAAT-AAAAAAATGTAAGAAGCAAAGTACCTATTTGGCAATTAATTTGCCTGAAA
* *
90565844 TTTCAAAATCGGGGAGAATTCAAAAGC-AGGGAGACAAGAACTGCAATTAGTCCATGCGGCGATC
130 TTTCAAAATCGGGGAGAATTCAAAAGCAAAGG-GACAAGAACTACAATTAGTCCATGCGGCGATC
* ** * **
90565908 CTTTTCTGCAAAAGGCGGGATGTAGAAATAATTATGTAGAAAATATCCCTTTACATAA
194 CTTTTTTATAAAAGGCAGGATGTAGAAGGAATTATGTAGAAAATATCCCTTTACATAA
90565966 TGTTATGGAA
Statistics
Matches: 465, Mismatches: 58, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
278 5 0.01
279 233 0.50
280 1 0.00
282 72 0.15
283 5 0.01
284 148 0.32
285 1 0.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (280 bp):
AAAAAAGAGAAATCTAAATCAATAGGATAAAATAAATCAAAATAAAAAATGAAATTAAAAAAGGA
TTTAAAATCGAAATAAAAAAATGTAAGAAGCAAAGTACCTATTTGGCAATTAATTTGCCTGAAAT
TTCAAAATCGGGGAGAATTCAAAAGCAAAGGGACAAGAACTACAATTAGTCCATGCGGCGATCCT
TTTTTATAAAAGGCAGGATGTAGAAGGAATTATGTAGAAAATATCCCTTTACATAACCCTATAAA
TAACCCTAAAACACCAAAAA
Found at i:90570406 original size:9 final size:9
Alignment explanation
Indices: 90570392--90570421 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
90570382 CGAGCTCTTG
90570392 TCAGATTCA
1 TCAGATTCA
90570401 TCAGATTCA
1 TCAGATTCA
90570410 TCAGATTCA
1 TCAGATTCA
90570419 TCA
1 TCA
90570422 CTGGATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (9 bp):
TCAGATTCA
Found at i:90573691 original size:433 final size:433
Alignment explanation
Indices: 90572885--90573749 Score: 1694
Period size: 433 Copynumber: 2.0 Consensus size: 433
90572875 ATACCAATGA
90572885 CGGGTGTGAGTTAATAGAAGAAACTAGAATCAAGAAGATGTAGCAGGTATGCTATGCCAACACTT
1 CGGGTGTGAGTTAATAGAAGAAACTAGAATCAAGAAGATGTAGCAGGTATGCTATGCCAACACTT
90572950 AAGCCCTTAATCCACACGGGCATTTCAACAGGCACTGCCTTTTAGCTACAAGGTCCTGACTCAAG
66 AAGCCCTTAATCCACACGGGCATTTCAACAGGCACTGCCTTTTAGCTACAAGGTCCTGACTCAAG
90573015 AATCTTATATTAATCACAACAAGATTGACATCATTCTGGAGTATTAATATTTCTGATGTGCAGGA
131 AATCTTATATTAATCACAACAAGATTGACATCATTCTGGAGTATTAATATTTCTGATGTGCAGGA
90573080 TCCATTAATAATGGCAAGCACAGAGCATACTCTATTAACGCTCTTTTGATAGCTCATCTAAAACA
196 TCCATTAATAATGGCAAGCACAGAGCATACTCTATTAACGCTCTTTTGATAGCTCATCTAAAACA
90573145 TTCTAAGAAGAAGAGGATTTAGAGAAAATAAGAGGAAACTTAGAAAGACATGTTGAGAAAACAAC
261 TTCTAAGAAGAAGAGGATTTAGAGAAAATAAGAGGAAACTTAGAAAGACATGTTGAGAAAACAAC
*
90573210 TAAGGATTTTTATTATTTTCTGCTTCTTATTTTACACGAGAGGACTCATCATCCTTTTATAGCCA
326 TAAGGATTTTTATTATTTTCTGCTTCTTATCTTACACGAGAGGACTCATCATCCTTTTATAGCCA
* * *
90573275 AAGGTGATGTAATACGACAAGATGATATTATAGTAGTTTTAGG
391 AAGGTGATGTAATACGACAAGATAATATTACAGTAGCTTTAGG
90573318 CGGGTGTGAGTTAATAGAAGAAACTAGAATCAAGAAGATGTAGCAGGTATGCTATGCCAACACTT
1 CGGGTGTGAGTTAATAGAAGAAACTAGAATCAAGAAGATGTAGCAGGTATGCTATGCCAACACTT
90573383 AAGCCCTTAATCCACACGGGCATTTCAACAGGCACTGCCTTTTAGCTACAAGGTCCTGACTCAAG
66 AAGCCCTTAATCCACACGGGCATTTCAACAGGCACTGCCTTTTAGCTACAAGGTCCTGACTCAAG
90573448 AATCTTATATTAATCACAACAAGATTGACATCATTCTGGAGTATTAATATTTCTGATGTGCAGGA
131 AATCTTATATTAATCACAACAAGATTGACATCATTCTGGAGTATTAATATTTCTGATGTGCAGGA
90573513 TCCATTAATAATGGCAAGCACAGAGCATACTCTATTAACGCTCTTTTGATAGCTCATCTAAAACA
196 TCCATTAATAATGGCAAGCACAGAGCATACTCTATTAACGCTCTTTTGATAGCTCATCTAAAACA
90573578 TTCTAAGAAGAAGAGGATTTAGAGAAAATAAGAGGAAACTTAGAAAGACATGTTGAGAAAACAAC
261 TTCTAAGAAGAAGAGGATTTAGAGAAAATAAGAGGAAACTTAGAAAGACATGTTGAGAAAACAAC
90573643 TAAGGATTTTTATTATTTTCTGCTTCTTATCTTACACGAGAGGACTCATCATCCTTTTATAGCCA
326 TAAGGATTTTTATTATTTTCTGCTTCTTATCTTACACGAGAGGACTCATCATCCTTTTATAGCCA
90573708 AAGGTGATGTAATACGACAAGATAATATTACAGTAGCTTTAG
391 AAGGTGATGTAATACGACAAGATAATATTACAGTAGCTTTAG
90573750 ATAAGCTTCA
Statistics
Matches: 428, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
433 428 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (433 bp):
CGGGTGTGAGTTAATAGAAGAAACTAGAATCAAGAAGATGTAGCAGGTATGCTATGCCAACACTT
AAGCCCTTAATCCACACGGGCATTTCAACAGGCACTGCCTTTTAGCTACAAGGTCCTGACTCAAG
AATCTTATATTAATCACAACAAGATTGACATCATTCTGGAGTATTAATATTTCTGATGTGCAGGA
TCCATTAATAATGGCAAGCACAGAGCATACTCTATTAACGCTCTTTTGATAGCTCATCTAAAACA
TTCTAAGAAGAAGAGGATTTAGAGAAAATAAGAGGAAACTTAGAAAGACATGTTGAGAAAACAAC
TAAGGATTTTTATTATTTTCTGCTTCTTATCTTACACGAGAGGACTCATCATCCTTTTATAGCCA
AAGGTGATGTAATACGACAAGATAATATTACAGTAGCTTTAGG
Found at i:90577876 original size:9 final size:9
Alignment explanation
Indices: 90577862--90577891 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
90577852 TCGAGCTTTG
90577862 TCAGATTCA
1 TCAGATTCA
90577871 TCAGATTCA
1 TCAGATTCA
90577880 TCAGATTCA
1 TCAGATTCA
90577889 TCA
1 TCA
90577892 CTGGATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (9 bp):
TCAGATTCA
Found at i:90587710 original size:43 final size:43
Alignment explanation
Indices: 90587631--90587720 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
90587621 CTTTGAAACA
* * * * *
90587631 AAAATACAATAGAAATGAAAATGGACTTCACAACTAAGTCACT
1 AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
* * *
90587674 AAAACACAATAGAAATGTAAACGAACCTCACGACTAAGCCTCT
1 AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
90587717 AAAA
1 AAAA
90587721 TGCAAGAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (43 bp):
AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
Found at i:90587929 original size:86 final size:86
Alignment explanation
Indices: 90587839--90588002 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 86
90587829 AATGCAACAA
* * * * *
90587839 AAACAT-AAATAGATCACACAATTAGGCCTCTAAAATGCAATAGAATGTAAGATGGACATCACAA
1 AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAA-ATGAACATCACAA
* *
90587903 CTAGGCCTCTAAAATATAATGG
65 CCAAGCCTCTAAAATATAATGG
* * * *
90587925 AAACATAAAATGGATCTCACAACTAAGCCTTTAAAATGAAATAAAATGTAAATGAACCTCACAAC
1 AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGAACATCACAAC
90587990 CAAGCCTCTAAAA
66 CAAGCCTCTAAAA
90588003 AGAAAATGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
86 29 0.44
87 37 0.56
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (86 bp):
AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGAACATCACAAC
CAAGCCTCTAAAATATAATGG
Found at i:90587949 original size:44 final size:44
Alignment explanation
Indices: 90587800--90587961 Score: 123
Period size: 43 Copynumber: 3.7 Consensus size: 44
90587790 AATGCAAATG
* ** * * * *
90587800 AAAATTGGACCTCACAACTAGGTTTTTAAAATGCAACAAAAACAT
1 AAAA-TGGATCTCACAACTAGGCCTCTAAAATACAATAGAAACAT
* * * * **
90587845 -AAATAGATCACACAATTAGGCCTCTAAAATGCAATAG-AATGT
1 AAAATGGATCTCACAACTAGGCCTCTAAAATACAATAGAAACAT
* * *
90587887 AAGATGGA-CATCACAACTAGGCCTCTAAAATATAATGGAAACAT
1 AAAATGGATC-TCACAACTAGGCCTCTAAAATACAATAGAAACAT
* *
90587931 AAAATGGATCTCACAACTAAGCCTTTAAAAT
1 AAAATGGATCTCACAACTAGGCCTCTAAAAT
90587962 GAAATAAAAT
Statistics
Matches: 90, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
42 4 0.04
43 53 0.59
44 32 0.36
45 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (44 bp):
AAAATGGATCTCACAACTAGGCCTCTAAAATACAATAGAAACAT
Found at i:90588177 original size:47 final size:46
Alignment explanation
Indices: 90588122--90588227 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 46
90588112 TGTTGGGAGC
* * **
90588122 AAAGATCCTAAGATAATCCCTA-AAGAGGTTGAGAAATATCTTCGAG
1 AAAGATCCTAAAATAATCCCGAGAA-AGGTCAAGAAATATCTTCGAG
* *
90588168 TAAAGATCCTAAAATAATCTCGAGAAAGGTCAAGAAATATCTTTGAG
1 -AAAGATCCTAAAATAATCCCGAGAAAGGTCAAGAAATATCTTCGAG
90588215 AAAGATCCTAAAA
1 AAAGATCCTAAAA
90588228 GAAGAGAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
46 13 0.25
47 37 0.71
48 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (46 bp):
AAAGATCCTAAAATAATCCCGAGAAAGGTCAAGAAATATCTTCGAG
Found at i:90588875 original size:16 final size:16
Alignment explanation
Indices: 90588854--90588891 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
90588844 CACTTTTTTA
90588854 TTTTTTTTC-CTCTCTC
1 TTTTTTTTCTCT-TCTC
*
90588870 TTTTTTTTCTCTTTTC
1 TTTTTTTTCTCTTCTC
90588886 TTTTTT
1 TTTTTT
90588892 CATTTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTTCTCTTCTC
Found at i:90589580 original size:26 final size:25
Alignment explanation
Indices: 90589551--90589600 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
90589541 ATTTCTCCTA
* *
90589551 TTTTTTCCTCTTTCTTTTTTTTTCTT
1 TTTTTTCCT-TTTCCTTTTATTTCTT
90589577 TTTTTTCCTTTTCCTTTTATTTCT
1 TTTTTTCCTTTTCCTTTTATTTCT
90589601 CTCTCCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTCCTTTTCCTTTTATTTCTT
Found at i:90591295 original size:21 final size:21
Alignment explanation
Indices: 90591265--90591305 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90591255 CGGGCCTAGA
* *
90591265 AATAAGTCCAAAAACAAAAAT
1 AATAAATCCAAAAAAAAAAAT
90591286 AATAAATCCAAAAAAAAAAA
1 AATAAATCCAAAAAAAAAAA
90591306 GTCCAAGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.12
Consensus pattern (21 bp):
AATAAATCCAAAAAAAAAAAT
Found at i:90591452 original size:36 final size:34
Alignment explanation
Indices: 90591422--90591492 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 34
90591412 AATCTTCAAC
90591422 GATATG-CAATCTTAGATATAATATGCAATCTTA
1 GATATGACAATCTTAGATATAATATGCAATCTTA
*
90591455 GATATGATACAATCTTAGATATGATATGCAATCTTA
1 GATATG--ACAATCTTAGATATAATATGCAATCTTA
90591491 GA
1 GA
90591493 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 6 0.18
36 28 0.82
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (34 bp):
GATATGACAATCTTAGATATAATATGCAATCTTA
Found at i:90591499 original size:17 final size:19
Alignment explanation
Indices: 90591422--90591492 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
90591412 AATCTTCAAC
90591422 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
90591441 AATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
90591460 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
90591477 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
90591493 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 17 0.35
19 31 0.65
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:90591518 original size:22 final size:22
Alignment explanation
Indices: 90591422--90591515 Score: 75
Period size: 19 Copynumber: 4.7 Consensus size: 22
90591412 AATCTTCAAC
90591422 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
90591441 AATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
90591460 GATA--CAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
90591477 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
90591499 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
90591516 GATTTAATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
17 17 0.26
19 28 0.43
22 8 0.12
23 12 0.18
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:90591803 original size:18 final size:19
Alignment explanation
Indices: 90591780--90591816 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
90591770 TGTTTCCCTG
*
90591780 ATTTTTTTATAT-ATTTTA
1 ATTTTTTTAAATAATTTTA
90591798 ATTTTTTTAAATAATTTTA
1 ATTTTTTTAAATAATTTTA
90591817 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAAATAATTTTA
Found at i:90601054 original size:220 final size:220
Alignment explanation
Indices: 90600672--90601262 Score: 898
Period size: 220 Copynumber: 2.7 Consensus size: 220
90600662 CAGGCTAAAG
* * * * * **
90600672 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCAGATCCAAGATAATTTAACATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* * *
90600737 TTGTCAGAGAACAAATCG-AGAAAACAGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGAA
66 CTGTCAGAGAACAAATTGAAG-AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAA
*
90600801 GACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGAATCCT
130 GACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGAGTTGGAATCCT
*
90600866 TGCGTTTACAAGGAGTAGATCGAAGA
195 TGCGTTTACAAGGAGCAGATCGAAGA
* * *
90600892 CATAGCAGATTTGGCTTTCACATGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATATTTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* ** *
90600957 CTGTCAGAGAACAAATTGAAGAAACATATTTGGCATCTCCATATTCGATAGAGAGCAGATCAAAG
66 CTGTCAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
90601022 ACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGAGTTGGTATCCTT
131 ACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGAGTTGGAATCCTT
90601087 GCGTTTACAAGGAGCAGATCGAAGA
196 GCGTTTACAAGGAGCAGATCGAAGA
* *
90601112 CATAGCAGATTTGGCTTTCACGTGTTTACGCTAAAGCATATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* *
90601177 CTGTTAAAGAACAAATCT-AAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAA
66 CTGTCAGAGAACAAAT-TGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAA
* * *
90601241 GACACAGTAGATCTGACCTTCA
130 GACATAGCAGATCTAACCTTCA
90601263 TTGAAGCAGA
Statistics
Matches: 333, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
220 330 0.99
221 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (220 bp):
CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
CTGTCAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
ACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGAGTTGGAATCCTT
GCGTTTACAAGGAGCAGATCGAAGA
Found at i:90601332 original size:78 final size:78
Alignment explanation
Indices: 90601203--90601491 Score: 445
Period size: 78 Copynumber: 3.7 Consensus size: 78
90601193 CTAAGAAACA
** * * *
90601203 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACACAGTAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
90601268 GCAGATCCAAGAT
66 GCAGATCCAAGAT
90601281 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
90601346 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * * **
90601359 GATTTGGCATATCTTTATTAGACGGGGAGAAGATCGAAGACATAATAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCT-GACCTTCATTGA
90601423 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* *
90601437 TATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGAC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGAC
90601492 TTTTATGTGT
Statistics
Matches: 192, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
77 1 0.01
78 190 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:90601646 original size:89 final size:90
Alignment explanation
Indices: 90601511--90601710 Score: 289
Period size: 89 Copynumber: 2.2 Consensus size: 90
90601501 TTTACATCAA
*
90601511 AGCAGATCCAAGAT-GACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATC-AGAGATAACA
1 AGCAGATCAAAGATAG-CAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGA-AGATAACA
* *
90601574 GATTTGGCATCTCTGTATTTGACGGGG
64 GATATGGCATCTCTGTATTAGACGGGG
** * *
90601601 AGCAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGA
1 AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGA
*
90601665 TATGGCGTCTCTGTATTAGACGGGG
66 TATGGCATCTCTGTATTAGACGGGG
90601690 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAGCAGAT
90601711 ATCGCCTTCC
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
89 78 0.80
90 20 0.20
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.23
Consensus pattern (90 bp):
AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGA
TATGGCATCTCTGTATTAGACGGGG
Found at i:90601712 original size:45 final size:45
Alignment explanation
Indices: 90601438--90601710 Score: 275
Period size: 45 Copynumber: 6.0 Consensus size: 45
90601428 ATCCAAGATT
*
90601438 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AA-AGATAGCAG
* * * * * * * ** *
90601485 ATCTGACTTTTATGTGTTTACATC--AAAGCAGATCCAAGAT-GACAG
1 ATTTGGCATCTCTGT-ATTAGA-CGGGGAGCAGATCAAAGATAG-CAG
* * *
90601530 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
* **
90601575 ATTTGGCATCTCTGTATTTGACGGGGAGCAGATTGAAGA-AGCAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
* * *
90601619 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
* *
90601664 ATATGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
90601709 AT
1 AT
90601711 ATCGCCTTCC
Statistics
Matches: 182, Mismatches: 37, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.01
44 45 0.25
45 112 0.62
46 1 0.01
47 18 0.10
48 4 0.02
49 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (45 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAG
Found at i:90602083 original size:19 final size:19
Alignment explanation
Indices: 90602059--90602129 Score: 121
Period size: 19 Copynumber: 3.9 Consensus size: 19
90602049 TAATCTTCAG
90602059 TGATATGCAATCTTAGATA
1 TGATATGCAATCTTAGATA
90602078 TGATATGCAATCTTAGATA
1 TGATATGCAATCTTAGATA
90602097 TGATA--CAATCTTAGATA
1 TGATATGCAATCTTAGATA
90602114 TGAT-TGCAATCTTAGA
1 TGATATGCAATCTTAGA
90602130 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.32
18 10 0.20
19 24 0.48
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
TGATATGCAATCTTAGATA
Found at i:90602152 original size:23 final size:21
Alignment explanation
Indices: 90602073--90602139 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 21
90602063 ATGCAATCTT
90602073 AGATATGATATGCAATCTT---
1 AGATATGAT-TGCAATCTTAGA
*
90602092 AGATATGA-TACAATCTTAG-
1 AGATATGATTGCAATCTTAGA
90602111 --ATATGATTGCAATCTTAGA
1 AGATATGATTGCAATCTTAGA
90602130 AGATATGATT
1 AGATATGATT
90602140 TTGTAATCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 14 0.35
18 10 0.25
19 8 0.20
21 8 0.20
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
AGATATGATTGCAATCTTAGA
Found at i:90602441 original size:18 final size:19
Alignment explanation
Indices: 90602418--90602453 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
90602408 GTTTCCCTAT
*
90602418 TTTTTTTATAT-ATTTTAA
1 TTTTTTTAAATAATTTTAA
90602436 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
90602454 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:90603654 original size:16 final size:18
Alignment explanation
Indices: 90603628--90603660 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
90603618 TAGAACTGGG
90603628 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
90603645 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
90603661 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:90604862 original size:29 final size:29
Alignment explanation
Indices: 90604822--90604879 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
90604812 GAATCTGGAG
90604822 TTTTGAACTGCAGTAAGTGAGAATTAGGT
1 TTTTGAACTGCAGTAAGTGAGAATTAGGT
90604851 TTTTGAACTGCAGTAAGTGAGAATTAGGT
1 TTTTGAACTGCAGTAAGTGAGAATTAGGT
90604880 GAGTCTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTGAACTGCAGTAAGTGAGAATTAGGT
Found at i:90605619 original size:27 final size:27
Alignment explanation
Indices: 90605581--90605632 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
90605571 CTTGTCAGCC
90605581 TTTGTGGCATACTCT-ATATAGATTATG
1 TTTGTGGCATACTCTAAT-TAGATTATG
*
90605608 TTTGTGTCATACTCTAATTAGATTA
1 TTTGTGGCATACTCTAATTAGATTA
90605633 CTTTAGAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (27 bp):
TTTGTGGCATACTCTAATTAGATTATG
Found at i:90606800 original size:2 final size:2
Alignment explanation
Indices: 90606793--90606817 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90606783 ATACATAATA
90606793 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
90606818 AATAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90606864 original size:32 final size:30
Alignment explanation
Indices: 90606805--90606861 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
90606795 ATATATATAT
*
90606805 ATATATATATATAAATAATAAAATAATAGA
1 ATATATATATATAAAGAATAAAATAATAGA
*
90606835 ATATATAT-TATAAAGAATAAAGTAATA
1 ATATATATATATAAAGAATAAAATAATA
90606862 ATATAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
ATATATATATATAAAGAATAAAATAATAGA
Found at i:90606970 original size:29 final size:30
Alignment explanation
Indices: 90606938--90607020 Score: 71
Period size: 34 Copynumber: 2.6 Consensus size: 30
90606928 TTTCAAAATT
*
90606938 ATATATAATAATATATAA-TAAAATATGAAA
1 ATATATAATAATATATAATTAAAACAT-AAA
*
90606968 TATCCTATTATATAATATATATATTAAAACATAAA
1 -AT-ATA-TA-ATAATATATA-ATTAAAACATAAA
90607003 ATAATATAAT-ATATATAA
1 AT-ATATAATAATATATAA
90607021 CATTTAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
30 1 0.02
31 9 0.21
32 4 0.09
33 4 0.09
34 14 0.33
35 4 0.09
36 7 0.16
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (30 bp):
ATATATAATAATATATAATTAAAACATAAA
Found at i:90607011 original size:5 final size:5
Alignment explanation
Indices: 90606940--90607086 Score: 70
Period size: 5 Copynumber: 29.0 Consensus size: 5
90606930 TCAAAATTAT
* * * *
90606940 ATATA ATA-A TATATA ATAAA ATATGAA ATATC CTATT ATATA ATAT-
1 ATATA ATATA -ATATA ATATA ATAT--A ATATA ATATA ATATA ATATA
* * * * * *
90606986 ATATA TTAAA ACATA AAATA ATATA ATAT- ATATAA CATTTA ATAAA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
* * * *
90607037 AAATA ATATA AAATA ATAT- ATGTTA ATATA ATATAA AAATA ATAT- ATATA
1 ATATA ATATA ATATA ATATA AT-ATA ATATA ATAT-A ATATA ATATA ATATA
90607087 CTTGGAAATG
Statistics
Matches: 104, Mismatches: 26, Indels: 24
0.68 0.17 0.16
Matches are distributed among these distances:
4 15 0.14
5 73 0.70
6 8 0.08
7 8 0.08
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:90607016 original size:36 final size:37
Alignment explanation
Indices: 90606938--90607086 Score: 141
Period size: 36 Copynumber: 4.1 Consensus size: 37
90606928 TTTCAAAATT
* *
90606938 ATATATAATAATATATAATAAAATATGAAAT-ATCCTA
1 ATATATAATAATATATAATAAAATATAAAATAAT-ATA
* * *
90606975 TTATATAAT-ATATATATTAAAACATAAAATAATATA
1 ATATATAATAATATATAATAAAATATAAAATAATATA
* *
90607011 ATATAT-ATAACATTTAATAAAATATAAAATAATATA
1 ATATATAATAATATATAATAAAATATAAAATAATATA
* *
90607047 A-A-ATAAT-ATATGTTAATATAATATAAAAATAATAT-
1 ATATATAATAATAT-ATAATAAAATAT-AAAATAATATA
90607082 ATATA
1 ATATA
90607087 CTTGGAAATG
Statistics
Matches: 93, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
34 5 0.05
35 17 0.18
36 60 0.65
37 11 0.12
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (37 bp):
ATATATAATAATATATAATAAAATATAAAATAATATA
Found at i:90607180 original size:25 final size:24
Alignment explanation
Indices: 90607150--90607205 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
90607140 TATATGATAT
*
90607150 TTAAAATAAATAAAATTAAAAATA
1 TTAAAAGAAATAAAATTAAAAATA
* *
90607174 TATAAAAGGATTAAAATTAAAAATGA
1 T-TAAAAGAAATAAAATTAAAAAT-A
90607200 TTAAAA
1 TTAAAA
90607206 CTTTGGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.89
26 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (24 bp):
TTAAAAGAAATAAAATTAAAAATA
Found at i:90613144 original size:23 final size:22
Alignment explanation
Indices: 90613075--90613149 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
90613065 CTGAGCTGAT
* *
90613075 GCTGAAAGGGTAAGCTCTATTGA
1 GCTGAAA-GGTAAGCTCCAATGA
* *
90613098 GCTGAATA-GTAAACT-CATACGA
1 GCTGAA-AGGTAAGCTCCA-ATGA
90613120 GCTGAAACGGTAAGCTCCAATGA
1 GCTGAAA-GGTAAGCTCCAATGA
90613143 GCTGAAA
1 GCTGAAA
90613150 ACAGTATATC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
21 2 0.05
22 14 0.34
23 22 0.54
24 3 0.07
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (22 bp):
GCTGAAAGGTAAGCTCCAATGA
Found at i:90615020 original size:131 final size:130
Alignment explanation
Indices: 90614872--90615375 Score: 338
Period size: 129 Copynumber: 3.9 Consensus size: 130
90614862 AATAAAGACC
* * * * *
90614872 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * *
90614937 C-CGAATTGTCAAACACC-GAGTATTGCCCTCGTTTTAAAGGATTTTTAGAAGAGC-CGAGTGAA
66 CACGAATTGCCAAACACCAGA-TATCGCCCTCGTTTT-AAGGA-TTTTAAAAGA-CACGAGTGAA
90614999 ATTT
127 ATTT
* * * * ** * * *
90615003 TGAAGGGATATTTGATTGTTTTAAACAATCGAGAAATTGCTACCCAACACGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * *
90615068 CACGAATTGCCAAATACCAGATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAGTGAAATTT
66 CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGTGAAATTT
* * * * ** * * *
90615133 TAAAGTGATATTCGATTATTTTGAGCAAA-TACGAAATTGCAACCCAACACGTTAGGGCACGATT
1 TAAAGGGATATTCGATTGTTTTGAACAAACGA-GAAATCACAACCCAACACGATAAGGCACGATC
* * * * ** *** * *
90615197 TCGCGAATTGCCAAACATCA-A-ATCTCATATCG-TTTAAGGGATTTTAAAAGATGTGAATGGAA
65 CCACGAATTGCCAAACACCAGATATCGC-CCTCGTTTTAA-GGATTTTAAAAGACACGAGTGAAA
90615259 TTT
128 TTT
** * * * * * * ** * * *
90615262 CGAAGGGAAATTCAATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * * * * * * *
90615327 CGCGAATTGCCGAACATCAAATTTCGTCTTCGTTTTGAAGAATTTTAAA
66 CACGAATTGCCAAACACCAGATATCGCCCTCGTTTT-AAGGATTTTAAA
90615376 TGAATACTTA
Statistics
Matches: 304, Mismatches: 58, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
128 8 0.03
129 102 0.34
130 93 0.31
131 70 0.23
132 29 0.10
133 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (130 bp):
TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGTGAAATTT
Found at i:90615169 original size:130 final size:128
Alignment explanation
Indices: 90614911--90615362 Score: 446
Period size: 129 Copynumber: 3.5 Consensus size: 128
90614901 CGAGAAATCA
* * * * * * *
90614911 CAACCCAGCACGATAAGGCATGATTCC-CGAATTGTCAAACACC-GAGTATTGCCCTCGTTTTAA
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAGA-TATCGCCTTCGTTTT-A
* * * * * *
90614974 AGGATTTTTAGAAGAGCCGAGTGAAATTTTGAAGGGATATTTGATTGTTTTAAAC-AATCGAGAA
64 GGGA-TTTTAAAAGA-CCGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATC--GAA
90615038 ATTG
125 ATTG
* * * *
90615042 CTACCCAACACGTTAGGGCACGATCCCACGAATTGCCAAATACCAGATATCGCCTTCGTTTTAGG
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAGATATCGCCTTCGTTTTAGG
* *
90615107 GATTTTAAAAGACACGAGTGAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATACGAAATTG
66 GATTTTAAAAGAC-CGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAAT-CGAAATTG
* * * * *
90615172 CAACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAACATCA-A-ATCTCATATCGTTTAAG
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAGATATCGCCT-TCGTTTTAG
** * * * * *
90615235 GGATTTTAAAAGATGTGAATGGAATTTCGAAGGGAAATTCAATTATTTTGAGCAAATGCGAAATT
65 GGATTTTAAAAGA-CCGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAAT-CGAAATT
90615300 G
128 G
* * * * *
90615301 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTTT
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAGATATCGCCTTCGTTTT
90615363 GAAGAATTTT
Statistics
Matches: 268, Mismatches: 44, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
128 5 0.02
129 108 0.40
130 94 0.35
131 31 0.12
132 28 0.10
133 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (128 bp):
CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAGATATCGCCTTCGTTTTAGG
GATTTTAAAAGACCGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATCGAAATTG
Found at i:90616408 original size:29 final size:23
Alignment explanation
Indices: 90616351--90616397 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
90616341 AATATAAACA
90616351 AGTATAAAAATAATTTAAACTTT
1 AGTATAAAAATAATTTAAACTTT
90616374 AGTATAAAAATAATTTAAACTTT
1 AGTATAAAAATAATTTAAACTTT
90616397 A
1 A
90616398 CGCAGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
AGTATAAAAATAATTTAAACTTT
Found at i:90616517 original size:2 final size:2
Alignment explanation
Indices: 90616510--90616538 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
90616500 GTATGTACAC
90616510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
90616539 AAAGAGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90618495 original size:43 final size:43
Alignment explanation
Indices: 90618442--90618631 Score: 132
Period size: 43 Copynumber: 4.3 Consensus size: 43
90618432 CAGCCTACTC
* * *
90618442 CACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTT
1 CACTGCAACTTCAGGGAGCTAGATTAGTGACTTAAATCTGCTT
* * * * ** *
90618485 CACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGATCTGCTC
1 CACTGCAACTTCAGGGAG-CTAGATTAGT-GACTTAAATCTGCTT
* * * ** * * * *
90618530 CACTACAACTTCAGGGAAACGAGATCTA-AAATTTCAACCTAC-T
1 CACTGCAACTTCAGGG-AGCTAGAT-TAGTGACTTAAATCTGCTT
* *
90618573 CTACTGCAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTT
1 C-ACTGCAACTTCAGGGAGCTAGATTAGTGACTTAAATCTGCTT
90618617 CACTGCAACTTCAGG
1 CACTGCAACTTCAGG
90618632 AAGCCAAGAT
Statistics
Matches: 105, Mismatches: 35, Indels: 14
0.68 0.23 0.09
Matches are distributed among these distances:
42 2 0.02
43 42 0.40
44 29 0.28
45 30 0.29
46 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGCTAGATTAGTGACTTAAATCTGCTT
Found at i:90618621 original size:132 final size:132
Alignment explanation
Indices: 90618302--90618952 Score: 824
Period size: 132 Copynumber: 4.9 Consensus size: 132
90618292 CAATCGTCAG
* * * * *
90618302 CCTACTCCATTACAACTTTAGGGAGCTAGGGCGATAGT--C-TAAATTTGCTTCACTACAACATC
1 CCTACTCCACTACAACTTTAGGGAGCTA--G-GTTAGTGACTTAAATCTGCTTCACTGCAACTTC
* ** * * * * * * *
90618364 AGGAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGGAA-TCCCAGGGAAACAAAATCTATAT
63 AGGAAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACT-TCAGGGAAACAAGATCTAAAA
*
90618428 TTCTCAG
127 TT-TCAA
90618435 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
* * *
90618500 AAGTCAAGATTCGTCGTCTTCGATCTGCTCCACTACAACTTCAGGGAAACGAGATCTAAAATTTC
66 AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTAAAATTTC
90618565 AA
131 AA
* *
90618567 CCTACTCTACTGCAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
* * *
90618632 AAGCCAAGATTCATCATCTTCGATCTGCTCCACTGTAACTTCAGGGAAACAAGATCTAAAATTTC
66 AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTAAAATTTC
90618697 AA
131 AA
* ** * * * *
90618699 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGTTTTAATCTACCTCACTGCAACTTCAAG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
* **
90618764 AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGTAACTTCAGATAAACAAGATCTAAAATTTC
66 AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTAAAATTTC
90618829 AA
131 AA
* * * * *
90618831 CCTACTCCATTACAACTTTAGGGAGCTAGGTTGGTGGCTTTAATCTGCCTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
* * * * * *
90618896 AAGCCTAGATTCGCCGTCTTTGATATGCTTCACTGCAACTTCAAGGAAACAAGATCT
66 AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCT
90618953 GTAGGATCAG
Statistics
Matches: 461, Mismatches: 53, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
130 5 0.01
131 1 0.00
132 356 0.77
133 98 0.21
134 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (132 bp):
CCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGG
AAGCCAAGATTCGTCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTAAAATTTC
AA
Found at i:90618722 original size:44 final size:43
Alignment explanation
Indices: 90618527--90618722 Score: 117
Period size: 44 Copynumber: 4.5 Consensus size: 43
90618517 CTTCGATCTG
* *
90618527 CTCCACTACAACTTCAGGGAAACGAGATCTAAAATTTCAACCTA
1 CTCCACTGCAACTTCAGGGAAACAAGAT-TAAAATTTCAACCTA
* * * * * ** * * * *
90618571 CTCTACTGCAACTTTAGGG-AGCTAGGTTAGTGACTTAAATCTG
1 CTCCACTGCAACTTCAGGGAAACAAGATTA-AAATTTCAACCTA
* * ** * * *
90618614 CTTCACTGCAACTTCA-GGAAGCCAAGATTCATCATCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAA-ACAAGATT-AAAAT-TTCAACCTA
*
90618659 CTCCACTGTAACTTCAGGGAAACAAGATCTAAAATTTCAACCTA
1 CTCCACTGCAACTTCAGGGAAACAAGAT-TAAAATTTCAACCTA
* *
90618703 CTCCACTACAACTTTAGGGA
1 CTCCACTGCAACTTCAGGGA
90618723 GCTAGGTTGG
Statistics
Matches: 112, Mismatches: 33, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
42 4 0.04
43 26 0.23
44 46 0.41
45 31 0.28
46 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAAACAAGATTAAAATTTCAACCTA
Found at i:90631055 original size:130 final size:130
Alignment explanation
Indices: 90630732--90631059 Score: 406
Period size: 130 Copynumber: 2.5 Consensus size: 130
90630722 AAACAATCGA
* * * * * *
90630732 GAAATTGCTACCCAACACGTTAGGGCACGATCCCACGAATTGCCAAATACCAGATATCG-CATTC
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTC-TTC
* * * * *
90630796 GTTTTAGGGATTTTAAAAGACACGAGCGAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATA
65 GTTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATA
90630861 C
130 C
* * ** * *
90630862 GAAATTGCAACCCAACACGATAGTGCACGATTTTGCGAATTGCCAAACATCAAATCTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
*** * * * *
90630927 TTTAAGGGATTTTAAAAGATGTGAATGGAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
66 TTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
* *
90630992 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
90631057 TTT
66 TTT
90631060 TGAAGAATTT
Statistics
Matches: 166, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 165 0.99
131 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (130 bp):
GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
TTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
Found at i:90634895 original size:16 final size:17
Alignment explanation
Indices: 90634874--90634932 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 17
90634864 ATATTCAGTC
90634874 ATATAATAAATTA-TTA
1 ATATAATAAATTATTTA
90634890 ATATAATAAATATAATTTA
1 ATATAATAAAT-T-ATTTA
90634909 TTATATTAATAAATTATTTA
1 --ATA-TAATAAATTATTTA
90634929 ATAT
1 ATAT
90634933 TTCAATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
18 4 0.11
19 3 0.08
20 5 0.14
21 4 0.11
22 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATAAATTATTTA
Found at i:90634904 original size:22 final size:22
Alignment explanation
Indices: 90634879--90634922 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
90634869 CAGTCATATA
90634879 ATAAATTATTA-ATATAATAAAT
1 ATAAATTATTATAT-TAATAAAT
*
90634901 ATAATTTATTATATTAATAAAT
1 ATAAATTATTATATTAATAAAT
90634923 TATTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTATATTAATAAAT
Found at i:90634958 original size:13 final size:14
Alignment explanation
Indices: 90634942--90634983 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
90634932 TTTCAATTTT
90634942 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
90634955 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
90634970 ATTTTAAATAATAT
1 ATTTT-AATAATAT
90634984 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:90634968 original size:16 final size:16
Alignment explanation
Indices: 90634946--90634982 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
90634936 AATTTTATTT
90634946 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
90634963 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
90634978 TAATA
1 TAATA
90634983 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:90635041 original size:17 final size:17
Alignment explanation
Indices: 90635009--90635064 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
90634999 GAAAATATTC
* *
90635009 AATATTAATATTTTAAT
1 AATATAAATATATTAAT
*
90635026 AATA-AATATTTATTAA-
1 AATATAA-ATATATTAAT
90635042 AATTATAAATATATTAAT
1 AA-TATAAATATATTAAT
90635060 AATAT
1 AATAT
90635065 TTTTTTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.10
17 24 0.77
18 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAAATATATTAAT
Found at i:90635470 original size:32 final size:34
Alignment explanation
Indices: 90635432--90635504 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
90635422 AACTTTTATG
*
90635432 AAATATTTTTA-AGA-AATCTACCAAACAACAGA
1 AAATATTTTTACACAGAATCTACCAAACAACAGA
* * *
90635464 AAATA-TTTTACACAGATTCTTCCAAACATCAGA
1 AAATATTTTTACACAGAATCTACCAAACAACAGA
90635497 AAATATTT
1 AAATATTT
90635505 GTTTTTCCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 20 0.59
34 2 0.06
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (34 bp):
AAATATTTTTACACAGAATCTACCAAACAACAGA
Found at i:90635543 original size:14 final size:14
Alignment explanation
Indices: 90635521--90635559 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
90635511 CCAGACAAGT
* *
90635521 AAATCATTTTCTAA
1 AAATTATTTTCCAA
90635535 AAATTATTTTCCAA
1 AAATTATTTTCCAA
*
90635549 AAGTTATTTTC
1 AAATTATTTTC
90635560 AATGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (14 bp):
AAATTATTTTCCAA
Found at i:90638104 original size:18 final size:18
Alignment explanation
Indices: 90638081--90638115 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
90638071 TACTCTAGGT
90638081 TTTACACAAAAAAAAATA
1 TTTACACAAAAAAAAATA
90638099 TTTACACAAAAAAAAAT
1 TTTACACAAAAAAAAAT
90638116 TTAGATTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (18 bp):
TTTACACAAAAAAAAATA
Found at i:90641169 original size:21 final size:21
Alignment explanation
Indices: 90641141--90641189 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
90641131 TTTACTCCTC
* *
90641141 TCTT-GTTCATTTTATAATTT
1 TCTTAGTTCATTTCACAATTT
90641161 TCTTAGTTCATTTCACAATTT
1 TCTTAGTTCATTTCACAATTT
*
90641182 TATTAGTT
1 TCTTAGTT
90641190 TATGAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (21 bp):
TCTTAGTTCATTTCACAATTT
Found at i:90655627 original size:9 final size:9
Alignment explanation
Indices: 90655615--90655665 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
90655605 TAAAAAATAT
90655615 TTTTTATAA
1 TTTTTATAA
90655624 TTTTTATACA
1 TTTTTATA-A
90655634 TTTTTAATAA
1 TTTTT-ATAA
* *
90655644 TTTTAATGA
1 TTTTTATAA
90655653 -TTTTA-AA
1 TTTTTATAA
90655660 TTTTTA
1 TTTTTA
90655666 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
7 1 0.03
8 9 0.26
9 11 0.31
10 11 0.31
11 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:90663026 original size:2 final size:2
Alignment explanation
Indices: 90663019--90663049 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
90663009 TACTACGGTG
90663019 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 T
90663050 CCTTAAGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90666595 original size:29 final size:32
Alignment explanation
Indices: 90666513--90666610 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 32
90666503 TAAGCCTGAC
* * *
90666513 TATATTATT-TTTTAATTTCTTTTAAAAA-TAT
1 TATA-TATTATTTTAATTTATATTAAAAATTTT
* *
90666544 T-TATATTATTTTAATTTAATATTTAATATTTT
1 TATATATTATTTTAATTT-ATATTAAAAATTTT
90666576 TATATATTATTTT-A-TT-TATTAAAAATTTT
1 TATATATTATTTTAATTTATATTAAAAATTTT
90666605 TATATA
1 TATATA
90666611 GTCATCTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
29 21 0.38
30 11 0.20
31 9 0.16
32 4 0.07
33 11 0.20
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TATATATTATTTTAATTTATATTAAAAATTTT
Found at i:90667091 original size:34 final size:34
Alignment explanation
Indices: 90667048--90667115 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
90667038 CCTAAATTAT
90667048 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
1 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
90667082 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
1 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
90667116 CTCTAGGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (34 bp):
GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
Found at i:90674382 original size:49 final size:49
Alignment explanation
Indices: 90674305--90674401 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
90674295 TACAATATTG
90674305 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
1 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
* *
90674354 TATCTACATTTGTTATTAATGAAGTCAGGTTAATTTCAAGTCACATGC
1 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGC
90674402 TTTCTATCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (49 bp):
TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
Found at i:90684671 original size:2 final size:2
Alignment explanation
Indices: 90684664--90684704 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
90684654 GGAGAACTTT
90684664 TA TA TA TA 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 TA TA TA TA T
90684705 GTATGTGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90687410 original size:21 final size:21
Alignment explanation
Indices: 90687358--90687412 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
90687348 CTTTCAATGG
* *
90687358 TATCGCGATATCCTTTTTGGA
1 TATCGTGATATCCTTTTAGGA
*
90687379 TATCGTAATATCCTCTTTAGG-
1 TATCGTGATATCCT-TTTAGGA
*
90687400 TATTGTGATATCC
1 TATCGTGATATCC
90687413 ACCCTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (21 bp):
TATCGTGATATCCTTTTAGGA
Found at i:90687469 original size:29 final size:30
Alignment explanation
Indices: 90687417--90687476 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
90687407 ATATCCACCC
*
90687417 TTCAAAGAGGACCTCAAGGTTCAACATTGA
1 TTCAAAGAGGACCTCAAGGCTCAACATTGA
90687447 TTCAAAGA-GACC-CTAAGGCTCAACATTGA
1 TTCAAAGAGGACCTC-AAGGCTCAACATTGA
90687476 T
1 T
90687477 CGAGGTATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.04
29 19 0.68
30 8 0.29
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (30 bp):
TTCAAAGAGGACCTCAAGGCTCAACATTGA
Found at i:90690430 original size:15 final size:16
Alignment explanation
Indices: 90690410--90690442 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
90690400 TCACAATTAT
90690410 TTTATA-AAGTAAATA
1 TTTATAGAAGTAAATA
*
90690425 TTTATAGAAGTTAATA
1 TTTATAGAAGTAAATA
90690441 TT
1 TT
90690443 CTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
TTTATAGAAGTAAATA
Found at i:90696569 original size:25 final size:26
Alignment explanation
Indices: 90696512--90696570 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
90696502 ATTAACAATG
90696512 TATATATGATAATAATAGTAATAATA
1 TATATATGATAATAATAGTAATAATA
* * *
90696538 CAAATATGA-AATAATAGTGAACATATA
1 TATATATGATAATAATAGT-AATA-ATA
90696565 TATATA
1 TATATA
90696571 AAACATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 9 0.35
26 10 0.38
27 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (26 bp):
TATATATGATAATAATAGTAATAATA
Found at i:90696800 original size:27 final size:25
Alignment explanation
Indices: 90696729--90696861 Score: 124
Period size: 25 Copynumber: 5.1 Consensus size: 25
90696719 AAGTATATAC
* *
90696729 ATAGTATTAGAAATATGTACATAAT
1 ATAGTATTAAAAATATATACATAAT
** *
90696754 ATAGCGTTAAAAATACATACATAAT
1 ATAGTATTAAAAATATATACATAAT
90696779 ATAGTTATTAAAAAATATATACATAAGAT
1 ATAG-TATT-AAAAATATATACAT-A-AT
** *
90696808 AATATGTAAGAAAAATATATAAATAAT
1 -ATA-GTATTAAAAATATATACATAAT
*
90696835 ATAGTATT-AAAATATTTACATAAT
1 ATAGTATTAAAAATATATACATAAT
90696859 ATA
1 ATA
90696862 TACATATTAG
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
24 17 0.20
25 27 0.31
26 5 0.06
27 15 0.17
28 2 0.02
29 15 0.17
30 5 0.06
31 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.34
Consensus pattern (25 bp):
ATAGTATTAAAAATATATACATAAT
Done.