Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold337
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: 2178121
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 137747 characters in sequence are not A, C, G, or T
File 6 of 7
Found at i:1442020 original size:43 final size:43
Alignment explanation
Indices: 1441959--1442045 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
1441949 TCCCTCAAGG
1441959 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
*
1442002 TGTTCCACCAGAGTGTAAACGCCCAGGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
1442045 T
1 T
1442046 CTCCTCTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
Found at i:1443909 original size:26 final size:27
Alignment explanation
Indices: 1443860--1443910 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1443850 AATAACTAAA
* *
1443860 TAAATAATTAAAAATTCATAAAATTTT
1 TAAAGAATAAAAAATTCATAAAATTTT
*
1443887 TAAAGAATAAAAAATT-ATTAAATT
1 TAAAGAATAAAAAATTCATAAAATT
1443911 GGTTCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TAAAGAATAAAAAATTCATAAAATTTT
Found at i:1446255 original size:3 final size:3
Alignment explanation
Indices: 1446247--1446283 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1446237 ATTTTTGCAA
1446247 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1446284 TGCCAACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1450772 original size:49 final size:46
Alignment explanation
Indices: 1450700--1450808 Score: 137
Period size: 49 Copynumber: 2.3 Consensus size: 46
1450690 CCGAATAAAT
** * **
1450700 AAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTA
1 AAAGGCAAAACTATATCATTTTGATAAATATTTA-CTAAT-T-AAGTTA
*
1450749 AAAGGCAAAACTATATCGTTTTGATAAATATTTACTAATTAAGTTA
1 AAAGGCAAAACTATATCATTTTGATAAATATTTACTAATTAAGTTA
1450795 AAAGGCAAAACTAT
1 AAAGGCAAAACTAT
1450809 TATATTTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
46 20 0.37
47 1 0.02
48 3 0.06
49 30 0.56
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (46 bp):
AAAGGCAAAACTATATCATTTTGATAAATATTTACTAATTAAGTTA
Found at i:1455021 original size:2 final size:2
Alignment explanation
Indices: 1455014--1455056 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1455004 TAAATTTCAT
1455014 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1455056 T
1 T
1455057 TATCATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1458133 original size:24 final size:23
Alignment explanation
Indices: 1458090--1458135 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1458080 AGTGTTGTTA
*
1458090 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
1458113 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
1458136 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:1460038 original size:20 final size:21
Alignment explanation
Indices: 1460000--1460040 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1459990 TATTATATAA
*
1460000 ATATTTTTTATTTAACACATTC
1 ATATTTTATATTT-ACACATTC
1460022 ATATTTTATATTT-CACATT
1 ATATTTTATATTTACACATT
1460041 TCGACTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATATTTACACATTC
Found at i:1463458 original size:31 final size:31
Alignment explanation
Indices: 1463420--1463478 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1463410 GTCACTGAAC
*
1463420 TATTCGAAAGTTT-TCATTTAAGTAACTAAAT
1 TATTCGAAA-TTTATAATTTAAGTAACTAAAT
*
1463451 TATTCGAAATTTATAATTTAAGTCACTA
1 TATTCGAAATTTATAATTTAAGTAACTA
1463479 GGCCGTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (31 bp):
TATTCGAAATTTATAATTTAAGTAACTAAAT
Found at i:1465135 original size:24 final size:23
Alignment explanation
Indices: 1465092--1465137 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1465082 AGTGTTGTTA
*
1465092 ATATATTTTGAAAACGAATTTAG
1 ATATATTCTGAAAACGAATTTAG
1465115 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CGAATTTA
1465138 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACGAATTTAG
Found at i:1467962 original size:46 final size:46
Alignment explanation
Indices: 1467857--1468014 Score: 277
Period size: 46 Copynumber: 3.5 Consensus size: 46
1467847 CTTACGTATG
1467857 ACCACTTATCA-TTTGTC-CTTGATCAGATAAGTGTAGCT-AGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1467900 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
* *
1467946 ACCACTTATCACTTTGTCACTTGATCATATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1467992 ACCACTTATCACTTTGTCACTTG
1 ACCACTTATCACTTTGTCACTTG
1468015 TCACTGATCA
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
43 11 0.10
44 6 0.05
45 21 0.19
46 72 0.65
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
Found at i:1470609 original size:33 final size:35
Alignment explanation
Indices: 1470560--1470641 Score: 114
Period size: 33 Copynumber: 2.4 Consensus size: 35
1470550 TTATATTTAT
* * *
1470560 TTATTATTATATTGTTTATATTGTTTATTA-ATAA
1 TTATTACTATATTGTTTATATTATTCATTAGATAA
1470594 TTATTA-TATATTGTTTATATTATTCATTAGTATAA
1 TTATTACTATATTGTTTATATTATTCATTAG-ATAA
1470629 TTATTACTATATT
1 TTATTACTATATT
1470642 ATTATTATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 21 0.49
34 6 0.14
35 10 0.23
36 6 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (35 bp):
TTATTACTATATTGTTTATATTATTCATTAGATAA
Found at i:1470804 original size:18 final size:17
Alignment explanation
Indices: 1470765--1470807 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1470755 ATAGTTTATA
1470765 TATATTTTATATACATT
1 TATATTTTATATACATT
* * *
1470782 CATATTTTTTATGATATT
1 TATATTTTATAT-ACATT
1470800 TATATTTT
1 TATATTTT
1470808 CATGTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTTTATATACATT
Found at i:1471009 original size:87 final size:88
Alignment explanation
Indices: 1470910--1471085 Score: 336
Period size: 87 Copynumber: 2.0 Consensus size: 88
1470900 TTTATATTTA
1470910 CTAATACATTATACTTATACATTTTTTAAAAAAGTATTAATATATTTTATATGTATTTTATCATT
1 CTAATACATTATACTTATACATTTTTTAAAAAAGTATTAATATATTTTATATGTATTTTATCATT
1470975 GTTTTATTTTTA-ACTTACGTTT
66 GTTTTATTTTTAGACTTACGTTT
1470997 CTAATACATTATACTTATACATTTTTTAAAAAAGTATTAATATATTTTATATGTATTTTATCATT
1 CTAATACATTATACTTATACATTTTTTAAAAAAGTATTAATATATTTTATATGTATTTTATCATT
1471062 GTTTTATTTTTATGACTTACGTTT
66 GTTTTATTTTTA-GACTTACGTTT
1471086 TTTCTCTCAT
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 77 0.89
89 10 0.11
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (88 bp):
CTAATACATTATACTTATACATTTTTTAAAAAAGTATTAATATATTTTATATGTATTTTATCATT
GTTTTATTTTTAGACTTACGTTT
Found at i:1475059 original size:64 final size:61
Alignment explanation
Indices: 1474950--1475071 Score: 145
Period size: 64 Copynumber: 2.0 Consensus size: 61
1474940 TAGTATTTGT
*
1474950 ATTTTGAAAATATCTAATGTGACACCTGAACTACTAATATATTTTTTTATTATGGTACCTGCA
1 ATTTTGAAAATATCTAATGTGACACCTGAACTACTAATACA--TTTTTATTATGGTACCTGCA
* * ** * * *
1475013 ATTTTGTAAAATATTTAATGTGATATTTGAACTATTAATGCGTTTTTATTATGGTACCT
1 ATTTTG-AAAATATCTAATGTGACACCTGAACTACTAATACATTTTTATTATGGTACCT
1475072 AGTGTTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 17 0.34
63 6 0.12
64 27 0.54
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (61 bp):
ATTTTGAAAATATCTAATGTGACACCTGAACTACTAATACATTTTTATTATGGTACCTGCA
Found at i:1475559 original size:24 final size:24
Alignment explanation
Indices: 1475532--1475583 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1475522 TTCGTAGGTA
** *
1475532 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTACACTAATAAATACT
* *
1475556 AAATATATTACACTAATAAGTACT
1 AAATAAATTACACTAATAAATACT
1475580 AAAT
1 AAAT
1475584 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAATTACACTAATAAATACT
Found at i:1478924 original size:21 final size:21
Alignment explanation
Indices: 1478895--1478943 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1478885 AGTTTTGAAT
1478895 TAATATTTTGCATGAATATTG
1 TAATATTTTGCATGAATATTG
* *
1478916 TAATTTTTTGTATGAATATTG
1 TAATATTTTGCATGAATATTG
1478937 TAATATT
1 TAATATT
1478944 ATAATTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (21 bp):
TAATATTTTGCATGAATATTG
Found at i:1478946 original size:61 final size:61
Alignment explanation
Indices: 1478838--1478962 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 61
1478828 GAATATTGTA
* * *
1478838 ATTTTGCATGAATATTATAATTATTTTATAATTAAATTTGTATTTATAGTTTTGAATTAAT
1 ATTTTGCATGAATATTATAATTATTTTATAATGAAATTTGTATTTATAATTTTGAATGAAT
* * *
1478899 ATTTTGCATGAATATTGTAATT-TTTTGT-ATG-AATATTGTAATATTATAATTTTGTATGAAT
1 ATTTTGCATGAATATTATAATTATTTTATAATGAAAT-TTGT-AT-TTATAATTTTGAATGAAT
1478960 ATT
1 ATT
1478963 GAATGTCGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 3 0.05
59 6 0.11
60 7 0.13
61 39 0.71
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (61 bp):
ATTTTGCATGAATATTATAATTATTTTATAATGAAATTTGTATTTATAATTTTGAATGAAT
Found at i:1479084 original size:19 final size:19
Alignment explanation
Indices: 1479062--1479099 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1479052 TATAAATTTA
*
1479062 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
1479081 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
1479100 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:1479142 original size:27 final size:26
Alignment explanation
Indices: 1479106--1479159 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
1479096 TAATAAATTA
*
1479106 AATTTTTATGAATTTTGTAATTTTGT
1 AATTTTTATGAATATTGTAATTTTGT
1479132 AATTTTATATGAATATTGTAATTTTGT
1 AATTTT-TATGAATATTGTAATTTTGT
1479159 A
1 A
1479160 TGAATATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (26 bp):
AATTTTTATGAATATTGTAATTTTGT
Found at i:1479152 original size:19 final size:19
Alignment explanation
Indices: 1479128--1479196 Score: 93
Period size: 19 Copynumber: 3.4 Consensus size: 19
1479118 TTTTGTAATT
*
1479128 TTGTAATTTTATATGAATA
1 TTGTAATTTTGTATGAATA
1479147 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
1479166 TTGTAATATTGTTTGTATGAATA
1 TTGT-A-A-T-TTTGTATGAATA
1479189 TTGTAATT
1 TTGTAATT
1479197 ATTTTATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
19 23 0.51
20 2 0.04
21 2 0.04
22 2 0.04
23 16 0.36
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (19 bp):
TTGTAATTTTGTATGAATA
Found at i:1479256 original size:60 final size:60
Alignment explanation
Indices: 1479189--1479310 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
1479179 TGTATGAATA
* * * * *
1479189 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
1479249 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1479309 TT
1 TT
1479311 AGTTTAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:1481467 original size:27 final size:27
Alignment explanation
Indices: 1481428--1481526 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
1481418 TTGGCGCCTA
*
1481428 TCTGGGAGGCGCCAATGGTGGTG-C-T
1 TCTGAGAGGCGCCAATGGTGGTGCCAT
*
1481453 TACCTGGGAGGCGCCAATGGTGGTGCCAT
1 T--CTGAGAGGCGCCAATGGTGGTGCCAT
*
1481482 TCTGAGAGGCGCCAATGGTGGTGTCAT
1 TCTGAGAGGCGCCAATGGTGGTGCCAT
1481509 TCTGAGAGGCGCCAATGG
1 TCTGAGAGGCGCCAATGG
1481527 GCCGGGCCGG
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
25 1 0.01
27 64 0.94
28 1 0.01
29 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.39, T:0.22
Consensus pattern (27 bp):
TCTGAGAGGCGCCAATGGTGGTGCCAT
Found at i:1481935 original size:49 final size:49
Alignment explanation
Indices: 1481815--1482128 Score: 519
Period size: 49 Copynumber: 6.4 Consensus size: 49
1481805 AATTAATTAT
* * *
1481815 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-ATAC
1 AAAAAAATTGCAATATTCATAC--AAAATTATAATATTACAATATTCATAC
** * *
1481864 --CGACATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1481911 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1481960 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1482009 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1482058 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1482107 AAAAAAATTGCAATATTCATAC
1 AAAAAAATTGCAATATTCATAC
1482129 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
45 19 0.08
46 1 0.00
47 20 0.08
49 212 0.84
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (49 bp):
AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
Found at i:1482123 original size:30 final size:27
Alignment explanation
Indices: 1481868--1482110 Score: 265
Period size: 27 Copynumber: 9.7 Consensus size: 27
1481858 ATATACCGAC
*
1481868 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1481895 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
1481917 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1481944 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
1481966 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1481993 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
1482015 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1482042 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
1482064 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1482091 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
1482111 AAATTGCAAT
Statistics
Matches: 188, Mismatches: 8, Indels: 40
0.80 0.03 0.17
Matches are distributed among these distances:
22 60 0.32
23 20 0.11
24 4 0.02
25 4 0.02
26 20 0.11
27 80 0.43
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:1482574 original size:5 final size:5
Alignment explanation
Indices: 1482564--1482588 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1482554 GATAGGCGCC
1482564 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
1482589 TTGACCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1482631 original size:12 final size:12
Alignment explanation
Indices: 1482616--1482647 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1482606 CGTATTTTTT
1482616 TTAAAAAAATTA
1 TTAAAAAAATTA
1482628 TTAAAAAAA-TA
1 TTAAAAAAATTA
1482639 -TAAAAAAAT
1 TTAAAAAAAT
1482648 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:1485662 original size:13 final size:13
Alignment explanation
Indices: 1485622--1485669 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1485612 TCGAAAGCAT
* *
1485622 TTTTTAAAAGTAC
1 TTTTCAAAAATAC
* * *
1485635 TTTTCCACAACAC
1 TTTTCAAAAATAC
1485648 TTTTCAAAAATAC
1 TTTTCAAAAATAC
1485661 TTTTCAAAA
1 TTTTCAAAA
1485670 GCAATGAAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATAC
Found at i:1486095 original size:31 final size:31
Alignment explanation
Indices: 1486060--1486220 Score: 164
Period size: 31 Copynumber: 5.3 Consensus size: 31
1486050 TTCATTTGAA
* * *
1486060 TTGATTTGTTTATGGTTATATATTGCCGAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
*
1486091 TTGATTTGTATATGGATATACATTGCTGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * * * * *
1486121 TTAATTTATATATTGTTATACATTACCAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * *
1486152 TTGATTTGTATATAGATATACATTGACAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * *
1486183 TTGATTCGTATATGGATATATATCGCCGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
1486213 TTGATTTG
1 TTGATTTG
1486221 AGCTTTGGAT
Statistics
Matches: 105, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
30 30 0.29
31 75 0.71
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (31 bp):
TTGATTTGTATATGGATATACATTGCCGAAT
Found at i:1486217 original size:61 final size:61
Alignment explanation
Indices: 1486058--1486220 Score: 186
Period size: 61 Copynumber: 2.7 Consensus size: 61
1486048 TCTTCATTTG
* * *
1486058 AATTGATTTGTTTATGGTTATATATTGCCGAATTTGATTTGTATATGGATATACATTGCTG
1 AATTGATTTGTATATGGTTATATATTGCCGAATTTGATTTGTATATAGATATACATTGCTA
* * * * * *
1486119 AATTAATTTATATATTGTTATACATTACCAAATTTGATTTGTATATAGATATACATTGAC-A
1 AATTGATTTGTATATGGTTATATATTGCCGAATTTGATTTGTATATAGATATACATTG-CTA
* * *
1486180 AATTTGATTCGTATATGGATATATATCGCCGAA-TTGATTTG
1 AA-TTGATTTGTATATGGTTATATATTGCCGAATTTGATTTG
1486221 AGCTTTGGAT
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
61 60 0.73
62 22 0.27
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (61 bp):
AATTGATTTGTATATGGTTATATATTGCCGAATTTGATTTGTATATAGATATACATTGCTA
Found at i:1515626 original size:3 final size:3
Alignment explanation
Indices: 1515618--1515643 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1515608 TTAACTGTTG
1515618 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1515644 TCAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1517505 original size:10 final size:10
Alignment explanation
Indices: 1517483--1517514 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
1517473 TTACTAATTT
1517483 AAAATTT-TA
1 AAAATTTCTA
1517492 AAAATTTCTA
1 AAAATTTCTA
1517502 AAAA-TTCTA
1 AAAATTTCTA
1517511 AAAA
1 AAAA
1517515 ATAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTTCTA
Found at i:1526973 original size:23 final size:24
Alignment explanation
Indices: 1526919--1526973 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
1526909 AATCTATATT
1526919 TTTAAATTTTAAAAAAATAAAAAA
1 TTTAAATTTTAAAAAAATAAAAAA
* * *
1526943 -TCATATTTT-TAAAAATAAAAAA
1 TTTAAATTTTAAAAAAATAAAAAA
1526965 TTTAAATTT
1 TTTAAATTT
1526974 AAACTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTAAATTTTAAAAAAATAAAAAA
Found at i:1531694 original size:123 final size:124
Alignment explanation
Indices: 1531474--1531747 Score: 496
Period size: 123 Copynumber: 2.2 Consensus size: 124
1531464 GCTATAATTT
*
1531474 TATTCCTACTTCATTTGCTAATTTGAGCAATTTGGTCCGCAGGGACAACAGGCTTTTTGGTTCCA
1 TATTCCTACTTCATTTGCTAATTTGAGCAATTTGGTCCGCAGGGACAACAGGCTTTTTGGTCCCA
*
1531539 TTCCTGAAGAAGTAGGAAGCTTGAAATTATTGATTTTTCTAGAGCTGACTCAATGGTTG
66 TTCCTGAAGAAGTAAGAAGCTTGAAATTATTGATTTTTCTAGAGCTGACTCAATGGTTG
*
1531598 TATTCCTACTTCATTTGCTAATTTGAGCAATTTGGTCCTCA-GGACAACAGGCTTTTTGGTCCCA
1 TATTCCTACTTCATTTGCTAATTTGAGCAATTTGGTCCGCAGGGACAACAGGCTTTTTGGTCCCA
* *
1531662 TTCCTGAAGAATTAAGAAGCTTGAAATTATTGATTTTTCTAGAGTTGACTCAATGGTTG
66 TTCCTGAAGAAGTAAGAAGCTTGAAATTATTGATTTTTCTAGAGCTGACTCAATGGTTG
1531721 TATTCCTACTTCATTTGCTAATTTGAG
1 TATTCCTACTTCATTTGCTAATTTGAG
1531748 TCCCGTCCCA
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
123 105 0.72
124 40 0.28
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (124 bp):
TATTCCTACTTCATTTGCTAATTTGAGCAATTTGGTCCGCAGGGACAACAGGCTTTTTGGTCCCA
TTCCTGAAGAAGTAAGAAGCTTGAAATTATTGATTTTTCTAGAGCTGACTCAATGGTTG
Found at i:1533083 original size:20 final size:19
Alignment explanation
Indices: 1533054--1533102 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1533044 GCCACTAGCC
*
1533054 TTATTGATATTGTAATTAT
1 TTATTTATATTGTAATTAT
* *
1533073 GTTATTTATATTTTATTTAT
1 -TTATTTATATTGTAATTAT
*
1533093 CTATTTATAT
1 TTATTTATAT
1533103 ATATATGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (19 bp):
TTATTTATATTGTAATTAT
Found at i:1533202 original size:23 final size:22
Alignment explanation
Indices: 1533176--1533290 Score: 63
Period size: 23 Copynumber: 4.9 Consensus size: 22
1533166 TATATTAGCA
*
1533176 TTAAATTTCATTATGTATTATTT
1 TTAAATTT-ATTATGTATTATTC
* *
1533199 TTAAATTACAATATAT-TATTAACATC
1 TTAAATT--TAT-TATGTATT-A-TTC
* *
1533225 ATAAACTT-TTATGTATTATTAGC
1 TTAAATTTATTATGTATTATT--C
* * *
1533248 TTAGATTTATTATATATTTATTT
1 TTAAATTTATTATGTA-TTATTC
1533271 TTAAATTTATTATGTATTAT
1 TTAAATTTATTATGTATTAT
1533291 CATTTCAGAT
Statistics
Matches: 68, Mismatches: 14, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
21 1 0.01
22 8 0.12
23 32 0.47
24 12 0.18
25 9 0.13
26 6 0.09
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (22 bp):
TTAAATTTATTATGTATTATTC
Found at i:1533569 original size:2 final size:2
Alignment explanation
Indices: 1533564--1533590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1533554 TGTGTGTTTG
1533564 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 T
1533591 GTATGTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1534031 original size:483 final size:483
Alignment explanation
Indices: 1533098--1534045 Score: 1650
Period size: 484 Copynumber: 2.0 Consensus size: 483
1533088 TTTATCTATT
1533098 TATATATATATGTACATATTACTTTACGTACTACACTTGAATTTTTTTTCATATATATTACAATC
1 TATATATATATGTACATATTACTTTACGTACTACACTTGAATTTTTTTTCATATATATTACAATC
* *
1533163 ATATATATTAGCATTAAATTTCATTATGTATTATTTTTAAATTACAATATATTATTAACATCATA
66 ATATATATTAGCATTAAATTTCATTATGTATTATTTTTAAATTAAAATATACTATTAACATCATA
* *
1533228 AACTTTTATGTATTATTAGCTTAGATTTATTATATATTTATTTTTAAATTTATTATGTATTATCA
131 AACTTTTATGTATTATTAGCTTAAATTTATTATATATTTATTTTTAAATTCATTATGTATTATCA
*
1533293 TTTCAGATTTATTAGGCATTATTTTAAAAGAAAAATATTATGTATTGGTATATATATATTTTGTT
196 TTTCAGATTTATTAGGCATTATTTTAAAAGAAAAATATTATGTATTGGTATATATATATATTGTT
* *
1533358 TATTTCAAGACTTTGGCATGTATAATTTATTGATTGTGATTTCTCTTGTTGCCACTGTTATCTTA
261 CATTTCAAGACTTTGGCATATATAATTTATTGATTGTGATTTCTCTTGTTGCCACTGTTATCTTA
** * *
1533423 GTATATGTTTTAAAATTGATTATTAATTCGTTTGAAGTTTAATTGGTAATATTGATGTTTGCATA
326 GTATACATTTTAAAATCGATTATTAATTCATTTGAAGTTTAATTGGTAATATTGATGTTTGCATA
*
1533488 ATAGGATTAAAATTATTGTTGCTATTCTTGTTAACATTTATCTATTGCTTGGTTATTA-TTTTTT
391 ATAGGATTAAAATTATTGTTGCTATTCTTGTTAACATTTATCTATTGCTTGGTCATTATTTTTTT
1533552 AGTGTGTGTTTGTATATATATATATATA
456 AGTGTGTGTTTGTATATATATATATATA
** *
1533580 TATATATATATGTATGTATTACTTTACGTACTACACTTTAATTTTTTTTTTCATATATATTACAA
1 TATATATATATGTACATATTACTTTACGTACTACACTTGAA--TTTTTTTTCATATATATTACAA
*
1533645 TCATATATATTAGCATTAAATTTCATTATGTATTATTTTTAAATTAAAATATACTATTAGCATCA
64 TCATATATATTAGCATTAAATTTCATTATGTATTATTTTTAAATTAAAATATACTATTAACATCA
*
1533710 TAAATTTTTATGTATTATTAGCTTAAATTTATTATATATTTATTTTTAAATTCATTATGTATTAT
129 TAAACTTTTATGTATTATTAGCTTAAATTTATTATATATTTATTTTTAAATTCATTATGTATTAT
* *
1533775 TATTTTAGATTTATTAGGCATTATTTTAAAAGAAAAATATTATGTATT-GTATATATATATATTG
194 CATTTCAGATTTATTAGGCATTATTTTAAAAGAAAAATATTATGTATTGGTATATATATATATTG
* *
1533839 TTCATTTTAAGACTTTGGCATATATAATTTATTGATTGTGATTTC-CTTTGTTGCCACTGTTTTC
259 TTCATTTCAAGACTTTGGCATATATAATTTATTGATTGTGATTTCTC-TTGTTGCCACTGTTATC
*
1533903 TTAGTATACATTTTAAAATCGATTATTAATTCATTTGATGTTTAATTGGTAATATTGATGTTTGC
323 TTAGTATACATTTTAAAATCGATTATTAATTCATTTGAAGTTTAATTGGTAATATTGATGTTTGC
1533968 ATAATAGGATTAAAATTATTGTTGCTATTCTTGTTAACATTTATCTATTGCTTGGTCATTATTTT
388 ATAATAGGATTAAAATTATTGTTGCTATTCTTGTTAACATTTATCTATTGCTTGGTCATTATTTT
1534033 TTTAGTGTGTGTT
453 TTTAGTGTGTGTT
1534046 CGGATTGCCA
Statistics
Matches: 440, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
482 39 0.09
483 193 0.44
484 208 0.47
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.51
Consensus pattern (483 bp):
TATATATATATGTACATATTACTTTACGTACTACACTTGAATTTTTTTTCATATATATTACAATC
ATATATATTAGCATTAAATTTCATTATGTATTATTTTTAAATTAAAATATACTATTAACATCATA
AACTTTTATGTATTATTAGCTTAAATTTATTATATATTTATTTTTAAATTCATTATGTATTATCA
TTTCAGATTTATTAGGCATTATTTTAAAAGAAAAATATTATGTATTGGTATATATATATATTGTT
CATTTCAAGACTTTGGCATATATAATTTATTGATTGTGATTTCTCTTGTTGCCACTGTTATCTTA
GTATACATTTTAAAATCGATTATTAATTCATTTGAAGTTTAATTGGTAATATTGATGTTTGCATA
ATAGGATTAAAATTATTGTTGCTATTCTTGTTAACATTTATCTATTGCTTGGTCATTATTTTTTT
AGTGTGTGTTTGTATATATATATATATA
Found at i:1541418 original size:17 final size:16
Alignment explanation
Indices: 1541396--1541450 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
1541386 CTAAATCTTA
1541396 AAAATATTTAATAATAT
1 AAAATA-TTAATAATAT
1541413 AAAATATTAA-AATATT
1 AAAATATTAATAATA-T
*
1541429 AAAATTAAATAATAATAT
1 AAAA-T-ATTAATAATAT
1541447 AAAA
1 AAAA
1541451 ATGAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 7 0.21
18 9 0.27
19 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATTAATAATAT
Found at i:1541425 original size:8 final size:8
Alignment explanation
Indices: 1541396--1541433 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1541386 CTAAATCTTA
1541396 AAAATATTT
1 AAAATA-TT
1541405 AATAATA-T
1 AA-AATATT
1541413 AAAATATT
1 AAAATATT
1541421 AAAATATT
1 AAAATATT
1541429 AAAAT
1 AAAAT
1541434 TAAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 4 0.15
8 17 0.63
9 2 0.07
10 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATATT
Found at i:1541432 original size:34 final size:33
Alignment explanation
Indices: 1541388--1541458 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
1541378 TATATGAACT
* ** *
1541388 AAATCTTAAAAATATTTAATAATATAAAATATTA
1 AAATATTAAAAATAAATAATAATATAAAA-ATGA
*
1541422 AAATATTAAAATTAAATAATAATATAAAAATGA
1 AAATATTAAAAATAAATAATAATATAAAAATGA
1541455 AAAT
1 AAAT
1541459 TTTTCTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (33 bp):
AAATATTAAAAATAAATAATAATATAAAAATGA
Found at i:1542076 original size:16 final size:15
Alignment explanation
Indices: 1542031--1542073 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1542021 CATTTTTAAT
*
1542031 AAATATAAAACATAAA
1 AAATATTAAA-ATAAA
1542047 AAATATTAAAATAAA
1 AAATATTAAAATAAA
1542062 ATAATAATTAAA
1 A-AAT-ATTAAA
1542074 TAATGATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATTAAAATAAA
Found at i:1547754 original size:28 final size:28
Alignment explanation
Indices: 1547714--1547780 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
1547704 GCCTATTTCC
*
1547714 AACATTATTTACGGAATGGGCCACTTAA
1 AACATTATTTACGGAATAGGCCACTTAA
1547742 AACATTATTTACGGAATAGGCCACTTAA
1 AACATTATTTACGGAATAGGCCACTTAA
1547770 AACATTATTTA
1 AACATTATTTA
1547781 TAGAAATAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (28 bp):
AACATTATTTACGGAATAGGCCACTTAA
Found at i:1547815 original size:28 final size:29
Alignment explanation
Indices: 1547714--1547815 Score: 104
Period size: 28 Copynumber: 3.6 Consensus size: 29
1547704 GCCTATTTCC
* * *
1547714 AACATTATTTAC-GGAATGGGCCACTTAA
1 AACATTATTTACTGAAATAGACCACTTAA
* *
1547742 AACATTATTTAC-GGAATAGGCCACTTAA
1 AACATTATTTACTGAAATAGACCACTTAA
*
1547770 AACATTATTTA-TAGAAATAGATCACTTAA
1 AACATTATTTACT-GAAATAGACCACTTAA
*
1547799 AA-AATATTTACTGAAAT
1 AACATTATTTACTGAAAT
1547816 GGTCCAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
28 50 0.76
29 16 0.24
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (29 bp):
AACATTATTTACTGAAATAGACCACTTAA
Found at i:1549042 original size:95 final size:95
Alignment explanation
Indices: 1548922--1549105 Score: 323
Period size: 95 Copynumber: 1.9 Consensus size: 95
1548912 AATAATTCAT
*
1548922 CCATTAAGACTAATAGCTTCATCATCACCCTCTGCTGTGATATGACTCTGGCTTGAATTTAAAGA
1 CCATTAAGACTAATAGCTTCATCATCACCCTCTGCTGTGATATGACTCTGGCTTGAATATAAAGA
1548987 AGCAAATATGAAGAACTCATCATGGTCGAG
66 AGCAAATATGAAGAACTCATCATGGTCGAG
* * *
1549017 CCATTAAGACTGATAGCTTCATCATCATCCTTTGCTGTGATATGACTCTGGCTTGAATATAAAGA
1 CCATTAAGACTAATAGCTTCATCATCACCCTCTGCTGTGATATGACTCTGGCTTGAATATAAAGA
*
1549082 AGCAAATATGAAGTACTCATCATG
66 AGCAAATATGAAGAACTCATCATG
1549106 CGAGAGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (95 bp):
CCATTAAGACTAATAGCTTCATCATCACCCTCTGCTGTGATATGACTCTGGCTTGAATATAAAGA
AGCAAATATGAAGAACTCATCATGGTCGAG
Found at i:1550310 original size:19 final size:19
Alignment explanation
Indices: 1550273--1550310 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1550263 CTACCTTTCT
*
1550273 TCTTTCTCTTCTCATCCTC
1 TCTTTCTCATCTCATCCTC
1550292 TCTTTCTCAATCTCA-CCTC
1 TCTTTCTC-ATCTCATCCTC
1550311 CCCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTTCTCATCTCATCCTC
Found at i:1550817 original size:154 final size:155
Alignment explanation
Indices: 1550565--1550849 Score: 545
Period size: 154 Copynumber: 1.8 Consensus size: 155
1550555 AATATTATAA
1550565 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTTCTCCAAATTTCTCAT
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTTCTCCAAATTTCTCAT
*
1550630 CCAAATATAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAAT
66 CCAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAAT
1550695 TATATATTGTATCATCAAAATTTTC
131 TATATATTGTATCATCAAAATTTTC
*
1550720 AACATGAAAATATTAAAATTAAATAATAATATAGAAATGGAA-TTTTTTTCTCCAAATTTCTCAT
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTTCTCCAAATTTCTCAT
1550784 CCAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAAT
66 CCAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAAT
1550849 T
131 T
1550850 TCTCATCAAA
Statistics
Matches: 128, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
154 87 0.68
155 41 0.32
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.34
Consensus pattern (155 bp):
AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTTCTCCAAATTTCTCAT
CCAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAAT
TATATATTGTATCATCAAAATTTTC
Found at i:1554031 original size:906 final size:905
Alignment explanation
Indices: 1552280--1554088 Score: 3566
Period size: 906 Copynumber: 2.0 Consensus size: 905
1552270 GCATGTATAG
1552280 TTATATGCAACCCTTGGATAAATTTCTTCAAAAGTTATATGATTATTGCTCTGGAATGACCTGGC
1 TTATATGCAACCCTTGGATAAATTTCTTCAAAAGTTATATGATTATTGCTCTGGAATGACCTGGC
1552345 CCGACTTAATCCAATTATGATTTTATGTTTGTTCATGTAAAAAGGAAGAAAGAAAGATAACGAAT
66 CCGACTTAATCCAATTATGATTTTATGTTTGTTCATGTAAAAAGGAAGAAAGAAAGATAACGAAT
1552410 TTAAATAATTGAAGAGAATAAAAATTAATTATGTAAATCACCGATAAAAAGAATCTAATTTTGGA
131 TTAAATAATTGAAGAGAATAAAAATTAATTATGTAAATCACCGATAAAAAGAATCTAATTTTGGA
1552475 CTTAAAAAACTATATGGTGGTTGCATTTCAATTGGTTGGACAAACTTTGAAAGTGTAAAGGATTG
196 CTTAAAAAACTATATGGTGGTTGCATTTCAATTGGTTGGACAAACTTTGAAAGTGTAAAGGATTG
1552540 AAAAGTAGCATATTATAAAAGACATTTCAACTAAGCTCTGATCATCATTTTCAATCAACCCAAAA
261 AAAAGTAGCATATTAT-AAAGACATTTCAACTAAGCTCTGATCATCATTTTCAATCAACCCAAAA
1552605 TATAAATTTTGGAATTTTTATGAATATTTTAAAAGTTTTGTTGAGAGATAATTTTTTTAAGTTTC
325 TATAAATTTTGGAATTTTTATGAATATTTTAAAAGTTTTGTTGAGAGATAATTTTTTTAAGTTTC
1552670 AAAATTTATAGGGATCAAATGAGTATGTATACTAATCTGTTGTATGAATTATTCAAATTATTTGA
390 AAAATTTATAGGGATCAAATGAGTATGTATACTAATCTGTTGTATGAATTATTCAAATTATTTGA
1552735 GTTATTCAAATTTTAAAATTTAACTCGAAACTTGACTTATAAATATTTTTATGTTTTATATTTAA
455 GTTATTCAAATTTTAAAATTTAACTCGAAACTTGACTTATAAATATTTTTATGTTTTATATTTAA
1552800 TAATATAAAACATAAAAAATTATTTAAATTAAAAAATAATGTAAAAATGAAAGTCTTTCTCCAAA
520 TAATATAAAACATAAAAAATTATTTAAATTAAAAAATAATGTAAAAATGAAAGTCTTTCTCCAAA
1552865 CTTCACCCAAAAACACTTTAAGAAAATTTCACTCCTTGTGTCCATCAATCCATCTCAACCAACTA
585 CTTCACCCAAAAACACTTTAAGAAAATTTCACTCCTTGTGTCCATCAATCCATCTCAACCAACTA
1552930 ACAAATTTACTATAATTTTGTCTTTATAATGTGACTTCACTTGTGCACAATGGTTGAACGTTTGT
650 ACAAATTTACTATAATTTTGTCTTTATAATGTGACTTCACTTGTGCACAATGGTTGAACGTTTGT
1552995 TTTTGTGCAATCAAAATTTGGACGTTTGTATGCAACGCCAAAGACTTATGATATTTCATACTATC
715 TTTTGTGCAATCAAAATTTGGACGTTTGTATGCAACGCCAAAGACTTATGATATTTCATACTATC
1553060 ATTTTTTTCGATCCAAAATTAAAGATATTAAAAATTTCAAATTAGAACATTATTTATAATTTGAG
780 ATTTTTTTCGATCCAAAATTAAAGATATTAAAAATTTCAAATTAGAACATTATTTATAATTTGAG
1553125 CACTTAATTAGAACATTATGAAATCTAGAAAATTTAAAAAATTTTATAATTTTTAAAACTA
845 CACTTAATTAGAACATTATGAAATCTAGAAAATTTAAAAAATTTTATAATTTTTAAAACTA
1553186 TTATATGCAACCCTTGGATAAATTTCTTCAAAAGTTATATGATTATTGCTCTGGAATGACCTGGC
1 TTATATGCAACCCTTGGATAAATTTCTTCAAAAGTTATATGATTATTGCTCTGGAATGACCTGGC
1553251 CCGACTTAATCCAATTATGATTTTATGTTTGTTCATGTAAAAAGGAAGAAAGAAAGATAACGAAT
66 CCGACTTAATCCAATTATGATTTTATGTTTGTTCATGTAAAAAGGAAGAAAGAAAGATAACGAAT
1553316 TTAAATAATTGAAGAGAATAAAAATTAATTATGTAAATCACCGATAAAAAGAATCTAATTTTGGA
131 TTAAATAATTGAAGAGAATAAAAATTAATTATGTAAATCACCGATAAAAAGAATCTAATTTTGGA
1553381 CTTAAAAAACTATATGGTGGTTGCATTTCAATTGGTTGGACAAACTTTGAAAGTGTAAAGGATTG
196 CTTAAAAAACTATATGGTGGTTGCATTTCAATTGGTTGGACAAACTTTGAAAGTGTAAAGGATTG
1553446 AAAAGTAGCTAATATTAT-AAGACATTTCAACTAAGCTCTGATCATCATTTTCAATCAACCCAAA
261 AAAAGTAGC--ATATTATAAAGACATTTCAACTAAGCTCTGATCATCATTTTCAATCAACCCAAA
1553510 ATATAAATTTTGGAATTTTTATGAATATTTTAAAAGTTTTGTTGAGAGATAATTTTTTTAAGTTT
324 ATATAAATTTTGGAATTTTTATGAATATTTTAAAAGTTTTGTTGAGAGATAATTTTTTTAAGTTT
1553575 CAAAATTTATAGGGATCAAATGAGTATGTATACTAATCTGTTGTATGAATTATTCAAATTATTTG
389 CAAAATTTATAGGGATCAAATGAGTATGTATACTAATCTGTTGTATGAATTATTCAAATTATTTG
1553640 AGTTATTCAAATTTTAAAATTTAACTCGAAACTTGACTTATAAATATTTTTATGTTTTATATTTA
454 AGTTATTCAAATTTTAAAATTTAACTCGAAACTTGACTTATAAATATTTTTATGTTTTATATTTA
1553705 ATAATATAAAACATAAAAAATTATTTAAATTAAAAAATAATGTAAAAATGAAAGTCTTTCTCCAA
519 ATAATATAAAACATAAAAAATTATTTAAATTAAAAAATAATGTAAAAATGAAAGTCTTTCTCCAA
1553770 ACTTCACCCAAAAACACTTTAAGAAAATTTCACTCCTTGTGTCCATCAATCCATCTCAACCAACT
584 ACTTCACCCAAAAACACTTTAAGAAAATTTCACTCCTTGTGTCCATCAATCCATCTCAACCAACT
1553835 AACAAATTTACTATAATTTTGTCTTTATAATGTGACTTCACTTGTGCACAATGGTTGAACGTTTG
649 AACAAATTTACTATAATTTTGTCTTTATAATGTGACTTCACTTGTGCACAATGGTTGAACGTTTG
1553900 TTTTTGTGCAATCAAAATTTGGACGTTTGTATGCAACGCCAAAGACTTATGATATTTCATACTAT
714 TTTTTGTGCAATCAAAATTTGGACGTTTGTATGCAACGCCAAAGACTTATGATATTTCATACTAT
1553965 CATTTTTTTCGATCCAAAATTAAAGATATTAAAAATTTCAAATTAGAACATTATTTATAATTTGA
779 CATTTTTTTCGATCCAAAATTAAAGATATTAAAAATTTCAAATTAGAACATTATTTATAATTTGA
* *
1554030 GCACTTAATTAGAACATTATGAAATCTAGATACTTTAAAAAATTTTATAATTTTTAAAA
844 GCACTTAATTAGAACATTATGAAATCTAGAAAATTTAAAAAATTTTATAATTTTTAAAA
1554089 ATAGATTTTT
Statistics
Matches: 899, Mismatches: 2, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
906 892 0.99
908 7 0.01
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (905 bp):
TTATATGCAACCCTTGGATAAATTTCTTCAAAAGTTATATGATTATTGCTCTGGAATGACCTGGC
CCGACTTAATCCAATTATGATTTTATGTTTGTTCATGTAAAAAGGAAGAAAGAAAGATAACGAAT
TTAAATAATTGAAGAGAATAAAAATTAATTATGTAAATCACCGATAAAAAGAATCTAATTTTGGA
CTTAAAAAACTATATGGTGGTTGCATTTCAATTGGTTGGACAAACTTTGAAAGTGTAAAGGATTG
AAAAGTAGCATATTATAAAGACATTTCAACTAAGCTCTGATCATCATTTTCAATCAACCCAAAAT
ATAAATTTTGGAATTTTTATGAATATTTTAAAAGTTTTGTTGAGAGATAATTTTTTTAAGTTTCA
AAATTTATAGGGATCAAATGAGTATGTATACTAATCTGTTGTATGAATTATTCAAATTATTTGAG
TTATTCAAATTTTAAAATTTAACTCGAAACTTGACTTATAAATATTTTTATGTTTTATATTTAAT
AATATAAAACATAAAAAATTATTTAAATTAAAAAATAATGTAAAAATGAAAGTCTTTCTCCAAAC
TTCACCCAAAAACACTTTAAGAAAATTTCACTCCTTGTGTCCATCAATCCATCTCAACCAACTAA
CAAATTTACTATAATTTTGTCTTTATAATGTGACTTCACTTGTGCACAATGGTTGAACGTTTGTT
TTTGTGCAATCAAAATTTGGACGTTTGTATGCAACGCCAAAGACTTATGATATTTCATACTATCA
TTTTTTTCGATCCAAAATTAAAGATATTAAAAATTTCAAATTAGAACATTATTTATAATTTGAGC
ACTTAATTAGAACATTATGAAATCTAGAAAATTTAAAAAATTTTATAATTTTTAAAACTA
Found at i:1554106 original size:23 final size:22
Alignment explanation
Indices: 1554071--1554112 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1554061 ACTTTAAAAA
1554071 ATTTTATAATTTTTAAAAATAG
1 ATTTTATAATTTTTAAAAATAG
*
1554093 ATTTTTTAATTTTTAAAAAT
1 ATTTTATAATTTTTAAAAAT
1554113 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTATAATTTTTAAAAATAG
Found at i:1557395 original size:44 final size:44
Alignment explanation
Indices: 1557332--1557419 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
1557322 AAAAAAAAAT
*
1557332 CAATTCTCTTATTGTAAAACATTTATAAGAATTTATTCAAGGGA
1 CAATTCTCTTATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
*
1557376 CAATTCTCTTATTGTAAAACATTTAAAAGAATTTATTTAAGGGA
1 CAATTCTCTTATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
1557420 AAGGATGGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (44 bp):
CAATTCTCTTATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
Found at i:1563878 original size:39 final size:40
Alignment explanation
Indices: 1563792--1563879 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
1563782 AATTCTTTAC
* *
1563792 TTCAGTAATTTCACAATTCAATGCATTATGCATAACAATA
1 TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
*
1563832 TTCAGTATTTTCACAATTCACT-CAGTAAT-CA-AGACAATA
1 TTCAGTATTTTCACAATTCAATGCA-TAATGCATA-ACAATA
1563871 TTCAGTATT
1 TTCAGTATT
1563880 CCATAATTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.44
40 23 0.53
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (40 bp):
TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
Found at i:1564614 original size:11 final size:11
Alignment explanation
Indices: 1564600--1564625 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1564590 CTTTTTCTTC
1564600 TTTCTCCCCTG
1 TTTCTCCCCTG
1564611 TTTCTCCCCTG
1 TTTCTCCCCTG
1564622 TTTC
1 TTTC
1564626 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:1567288 original size:245 final size:246
Alignment explanation
Indices: 1566858--1567348 Score: 975
Period size: 245 Copynumber: 2.0 Consensus size: 246
1566848 TTAAAAATTC
1566858 AATTCTCTACTAATAAATCAAATAATTGTTTGTTTTTAGTGTTATTTTTGAGCTTTTATGAATTT
1 AATTCTCTACTAATAAATCAAATAATTGTTTGTTTTTAGTGTTATTTTTGAGCTTTTATGAATTT
1566923 GTATTTTACCTGTGTTTATACTGGTGACAGGTCAAAATTATAGACTATATAAAAAACATTATGGT
66 GTATTTTACCTGTGTTTATACTGGTGACAGGTCAAAATTATAGACTATATAAAAAACATTATGGT
1566988 GTGAAATTGTTTGATTTAAATTAAAAAATTAAACATGTTAAATTAAAATATTATTAAAATATAAT
131 GTGAAATTGTTTGATTTAAATTAAAAAATTAAACATGTTAAATTAAAATATTATTAAAATATAAT
1567053 TAATATTTGAAATCATAAATATTTGAAAACTGTTTCAAAG-AAAATAATAA
196 TAATATTTGAAATCATAAATATTTGAAAACTGTTTCAAAGCAAAATAATAA
1567103 AATTCTCTACTAATAAATCAAATAATTGTTTGTTTTTAGTGTTATTTTTGAGCTTTTATGAATTT
1 AATTCTCTACTAATAAATCAAATAATTGTTTGTTTTTAGTGTTATTTTTGAGCTTTTATGAATTT
1567168 GTATTTTACCTGTGTTTATACTGGTGACAGGTCAAAATTATAGACTATATAAAAAACATTATGGT
66 GTATTTTACCTGTGTTTATACTGGTGACAGGTCAAAATTATAGACTATATAAAAAACATTATGGT
1567233 GTGAAATTGTTTGATTTAAATTAAAAAATTAAACATGTTAAATTAAAATATTATTAAAATATAAT
131 GTGAAATTGTTTGATTTAAATTAAAAAATTAAACATGTTAAATTAAAATATTATTAAAATATAAT
1567298 TAATATTTGAAATCATAAATATTTGAAAACTGTTTCAAAGCAAAATAATAA
196 TAATATTTGAAATCATAAATATTTGAAAACTGTTTCAAAGCAAAATAATAA
1567349 TAAAAATTAT
Statistics
Matches: 245, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
245 235 0.96
246 10 0.04
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (246 bp):
AATTCTCTACTAATAAATCAAATAATTGTTTGTTTTTAGTGTTATTTTTGAGCTTTTATGAATTT
GTATTTTACCTGTGTTTATACTGGTGACAGGTCAAAATTATAGACTATATAAAAAACATTATGGT
GTGAAATTGTTTGATTTAAATTAAAAAATTAAACATGTTAAATTAAAATATTATTAAAATATAAT
TAATATTTGAAATCATAAATATTTGAAAACTGTTTCAAAGCAAAATAATAA
Found at i:1585465 original size:127 final size:128
Alignment explanation
Indices: 1585226--1585482 Score: 471
Period size: 127 Copynumber: 2.0 Consensus size: 128
1585216 AATGCTTTAC
1585226 AGAGTTTGTTGCTTTCTTATACAAATTTCAGTGGAAAACTACCTCAATCAATTGGTAATCTGAAG
1 AGAGTTTGTTGC-TTCTTATACAAATTTCAGTGGAAAACTACCTCAATCAATTGGTAATCTGAAG
1585291 TTCTTGACAGATTTAGATCTTTATTATTGCAATTTTTTTGGACCCATTCCATCGTCAATTGCAA
65 TTCTTGACAGATTTAGATCTTTATTATTGCAATTTTTTTGGACCCATTCCATCGTCAATTGCAA
1585355 AGAGTTTGTTG-TTCTTATACAAATTTCAGTGGAAAACTACCTCAATCAATTGGTAATCTGAAGT
1 AGAGTTTGTTGCTTCTTATACAAATTTCAGTGGAAAACTACCTCAATCAATTGGTAATCTGAAGT
***
1585419 TCTTGACAGATTTAGATCTTTATTATTTTGATTTTTTTGGACCCATTCCATCGTCAATTGCAA
66 TCTTGACAGATTTAGATCTTTATTATTGCAATTTTTTTGGACCCATTCCATCGTCAATTGCAA
1585482 A
1 A
1585483 TCTTAGTCAC
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
127 114 0.91
129 11 0.09
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (128 bp):
AGAGTTTGTTGCTTCTTATACAAATTTCAGTGGAAAACTACCTCAATCAATTGGTAATCTGAAGT
TCTTGACAGATTTAGATCTTTATTATTGCAATTTTTTTGGACCCATTCCATCGTCAATTGCAA
Found at i:1590149 original size:25 final size:27
Alignment explanation
Indices: 1590121--1590175 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1590111 TTTATGTTTT
*
1590121 ATATTT-AA-TAATATAAAACA-AAAAA
1 ATATTTCAATTAA-ATAAAAAATAAAAA
1590146 ATATTTCAATTAAATAAAAAATAAAAA
1 ATATTTCAATTAAATAAAAAATAAAAA
1590173 ATA
1 ATA
1590176 ATGTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.23
26 9 0.35
27 11 0.42
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
ATATTTCAATTAAATAAAAAATAAAAA
Found at i:1590537 original size:18 final size:18
Alignment explanation
Indices: 1590514--1590574 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
1590504 AAATTATACT
1590514 ATTTTTTTATATTTTTTA
1 ATTTTTTTATATTTTTTA
*
1590532 ATTTTTTTATAATTTATTA
1 ATTTTTTTAT-ATTTTTTA
* *
1590551 CTTTTTTTA-ATAATTTTA
1 ATTTTTTTATAT-TTTTTA
1590569 ATTTTT
1 ATTTTT
1590575 AAAAATAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 2 0.06
18 19 0.53
19 15 0.42
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTTTATATTTTTTA
Found at i:1590539 original size:9 final size:9
Alignment explanation
Indices: 1590514--1590574 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
1590504 AAATTATACT
1590514 ATTTTTTT-
1 ATTTTTTTA
1590522 ATATTTTTTA
1 AT-TTTTTTA
1590532 ATTTTTTTA
1 ATTTTTTTA
* *
1590541 TAATTTATTA
1 -ATTTTTTTA
*
1590551 CTTTTTTTA
1 ATTTTTTTA
**
1590560 ATAATTTTA
1 ATTTTTTTA
1590569 ATTTTT
1 ATTTTT
1590575 AAAAATAGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
8 2 0.05
9 29 0.73
10 9 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:1590556 original size:20 final size:20
Alignment explanation
Indices: 1590510--1590566 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1590500 AAAAAAATTA
*
1590510 TACTATTTTTTTAT-ATTTTT
1 TACT-TTTTTTTATAATTTAT
*
1590530 TA-ATTTTTTTATAATTTAT
1 TACTTTTTTTTATAATTTAT
*
1590549 TACTTTTTTTAATAATTT
1 TACTTTTTTTTATAATTT
1590567 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 15 0.48
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TACTTTTTTTTATAATTTAT
Found at i:1593052 original size:29 final size:30
Alignment explanation
Indices: 1592993--1593052 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1592983 CATATTTCAG
* * *
1592993 GAGCCACATAGGTTGGACACATGACCGTGT
1 GAGCCACACAGGCTGGACACATGACCATGT
1593023 GAGCCACACAGGCTGGCACACA-G-CCATGT
1 GAGCCACACAGGCTGG-ACACATGACCATGT
1593052 G
1 G
1593053 CCAGACCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 6 0.23
30 15 0.58
31 5 0.19
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (30 bp):
GAGCCACACAGGCTGGACACATGACCATGT
Found at i:1593313 original size:18 final size:18
Alignment explanation
Indices: 1593290--1593325 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1593280 GTTTCTTTAT
1593290 CTAATCTTATAGTTATAC
1 CTAATCTTATAGTTATAC
1593308 CTAATCTTATAGTTATAC
1 CTAATCTTATAGTTATAC
1593326 TGACTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (18 bp):
CTAATCTTATAGTTATAC
Found at i:1595936 original size:298 final size:299
Alignment explanation
Indices: 1595600--1596196 Score: 1187
Period size: 298 Copynumber: 2.0 Consensus size: 299
1595590 TATATAAATA
1595600 TAAAAAAAATTTAAAAAAGTTTACTATCAATACATCTCACAAAAATATATATAATTTTTATTTTA
1 TAAAAAAAATTTAAAAAAGTTTACTATCAATACATCTCACAAAAATATATATAATTTTTATTTTA
1595665 TTTTAAAAATTATAAGTTAATTAGAATAAAAATAAATGATAAATTTACCCAAAGTCATTAAACTA
66 TTTTAAAAATTATAAGTTAATTAGAATAAAAATAAATGATAAATTTACCCAAAGTCATTAAACTA
1595730 TTAATAAATTTACGTTTTAGTCACTTAACTTCAAAAAGTTATAAATGATCACTTTTTATACGATC
131 TTAATAAATTTACGTTTTAGTCACTTAACTTCAAAAAGTTATAAATGATCACTTTTTATACGATC
1595795 TGTACTAATAAAAAACTTTATTTCCTTTTTCTTCTATAGTTTAGTTTTTTCTATGAAACTTCTTC
196 TGTACTAATAAAAAACTTTATTTCCTTTTTCTTCTATAGTTTAGTTTTTTCTATGAAACTTCTTC
1595860 AATTTCAGATACTAATTGTTAAATTAACTTGGATCCAAT
261 AATTTCAGATACTAATTGTTAAATTAACTTGGATCCAAT
1595899 TAAAAAAAA-TTAAAAAAGTTTACTATCAATACATCTCACAAAAATATATATAATTTTTATTTTA
1 TAAAAAAAATTTAAAAAAGTTTACTATCAATACATCTCACAAAAATATATATAATTTTTATTTTA
1595963 TTTTAAAAATTATAAGTTAATTAGAATAAAAATAAATGATAAATTTACCCAAAGTCATTAAACTA
66 TTTTAAAAATTATAAGTTAATTAGAATAAAAATAAATGATAAATTTACCCAAAGTCATTAAACTA
1596028 TTAATAAATTTACGTTTTAGTCACTTAACTTCAAAAAGTTATAAATGATCACTTTTTATACGATC
131 TTAATAAATTTACGTTTTAGTCACTTAACTTCAAAAAGTTATAAATGATCACTTTTTATACGATC
1596093 TGTACTAATAAAAAACTTTATTTCCTTTTTCTTCTATAGTTTAGTTTTTTCTATGAAACTTCTTC
196 TGTACTAATAAAAAACTTTATTTCCTTTTTCTTCTATAGTTTAGTTTTTTCTATGAAACTTCTTC
1596158 AATTTCAGATACTAATTGTTAAATTAACTTGGATCCAAT
261 AATTTCAGATACTAATTGTTAAATTAACTTGGATCCAAT
1596197 GTATGTTTTT
Statistics
Matches: 298, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
298 289 0.97
299 9 0.03
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (299 bp):
TAAAAAAAATTTAAAAAAGTTTACTATCAATACATCTCACAAAAATATATATAATTTTTATTTTA
TTTTAAAAATTATAAGTTAATTAGAATAAAAATAAATGATAAATTTACCCAAAGTCATTAAACTA
TTAATAAATTTACGTTTTAGTCACTTAACTTCAAAAAGTTATAAATGATCACTTTTTATACGATC
TGTACTAATAAAAAACTTTATTTCCTTTTTCTTCTATAGTTTAGTTTTTTCTATGAAACTTCTTC
AATTTCAGATACTAATTGTTAAATTAACTTGGATCCAAT
Found at i:1600934 original size:200 final size:201
Alignment explanation
Indices: 1600580--1600980 Score: 795
Period size: 200 Copynumber: 2.0 Consensus size: 201
1600570 ATATTAAAAT
1600580 TATAATTTTTATATTAGAGTTTAAATTTTTAATAAATATTAATTTGTTTATTCAAATATATAATT
1 TATAATTTTTATATTAGAGTTTAAATTTTTAATAAATATTAATTTGTTTATTCAAATATATAATT
1600645 ATATTGAATCTAAACTAGTTTACTTGATAAATGCATTTTATTTTCACAATTTATATAGCATAATA
66 ATATTGAATCTAAACTAGTTTACTTGATAAATGCATTTTATTTTCACAATTTATATAGCATAATA
1600710 TTAAAAAAATTATGCAATAATTTACAATTGTTTTGTCGATGCAATTAAATAATAATTCAAATTAA
131 TTAAAAAAATTATGCAATAATTTACAATTGTTTTGTCGATGCAATTAAATAATAATTCAAATTAA
1600775 AACCGA
196 AACCGA
1600781 TATAATTTTT-TATTAGAGTTTAAATTTTTAATAAATATTAATTTGTTTATTCAAATATATAATT
1 TATAATTTTTATATTAGAGTTTAAATTTTTAATAAATATTAATTTGTTTATTCAAATATATAATT
1600845 ATATTGAATCTAAACTAGTTTACTTGATAAATGCATTTTATTTTCACAATTTATATAGCATAATA
66 ATATTGAATCTAAACTAGTTTACTTGATAAATGCATTTTATTTTCACAATTTATATAGCATAATA
1600910 TTAAAAAAATTATGCAATAATTTACAATTGTTTTGTCGATGCAATTAAATAATAATTCAAATTAA
131 TTAAAAAAATTATGCAATAATTTACAATTGTTTTGTCGATGCAATTAAATAATAATTCAAATTAA
1600975 AACCGA
196 AACCGA
1600981 ACAAACTACA
Statistics
Matches: 200, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
200 190 0.95
201 10 0.05
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (201 bp):
TATAATTTTTATATTAGAGTTTAAATTTTTAATAAATATTAATTTGTTTATTCAAATATATAATT
ATATTGAATCTAAACTAGTTTACTTGATAAATGCATTTTATTTTCACAATTTATATAGCATAATA
TTAAAAAAATTATGCAATAATTTACAATTGTTTTGTCGATGCAATTAAATAATAATTCAAATTAA
AACCGA
Found at i:1608281 original size:2 final size:2
Alignment explanation
Indices: 1608270--1608305 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1608260 AATTGACAAG
1608270 AT AT -T AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1608306 TTAATGGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1609596 original size:27 final size:27
Alignment explanation
Indices: 1609562--1609617 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1609552 TATAAATGAA
* *
1609562 TTTTTTTTTT-ATAA-TATTTTTTAAT
1 TTTTTTTTTTGAAAATTATTTTGTAAT
1609587 TTTTTATTTTTGAAAATTATTTTGTAAT
1 TTTTT-TTTTTGAAAATTATTTTGTAAT
1609615 TTT
1 TTT
1609618 CGCTGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 5 0.19
27 3 0.12
28 13 0.50
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (27 bp):
TTTTTTTTTTGAAAATTATTTTGTAAT
Found at i:1610303 original size:26 final size:26
Alignment explanation
Indices: 1610257--1610306 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1610247 TTAATTATAA
*
1610257 TAATTAAAAATATATTATATAAAAAC
1 TAATTAAAAATATAATATATAAAAAC
*
1610283 TAATTAAAAAT-TAAATGTATAAAA
1 TAATTAAAAATAT-AATATATAAAA
1610307 TCACATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAATTAAAAATATAATATATAAAAAC
Found at i:1625591 original size:13 final size:13
Alignment explanation
Indices: 1625573--1625605 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1625563 ACGAGATGAC
1625573 AATAAAATAA-AAA
1 AATAAAA-AATAAA
1625586 AATAAAAAATAAA
1 AATAAAAAATAAA
1625599 AATAAAA
1 AATAAAA
1625606 CAACAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:1625695 original size:16 final size:16
Alignment explanation
Indices: 1625676--1625715 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1625666 TTAATAATTT
1625676 ATTTATATAAATTAAA
1 ATTTATATAAATTAAA
* *
1625692 ATTTAAAAAAATTAAA
1 ATTTATATAAATTAAA
1625708 ATTT-TATA
1 ATTTATATA
1625716 TTAATATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATATAAATTAAA
Found at i:1626736 original size:3 final size:3
Alignment explanation
Indices: 1626723--1626752 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1626713 GGTAATGATT
1626723 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TT
1626753 TTTGTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1632290 original size:4 final size:4
Alignment explanation
Indices: 1632281--1632310 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1632271 GCTCAAAGTA
1632281 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1632311 TTTGAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1635618 original size:28 final size:28
Alignment explanation
Indices: 1635547--1635621 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
1635537 AATTTATAAA
* *
1635547 ATGAATGTTT-AGATTTTAATAATTTTT
1 ATGAATGTTTAAAATTTTTATAATTTTT
** ** *
1635574 ATTTATGTTTATTATTTTTTTAATTTTT
1 ATGAATGTTTAAAATTTTTATAATTTTT
1635602 ATGAATGTTTAAAATTTTTA
1 ATGAATGTTTAAAATTTTTA
1635622 ATGAGTTCTC
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (28 bp):
ATGAATGTTTAAAATTTTTATAATTTTT
Found at i:1635800 original size:14 final size:13
Alignment explanation
Indices: 1635776--1635819 Score: 79
Period size: 13 Copynumber: 3.3 Consensus size: 13
1635766 AATGATTTTA
1635776 AATTTTTAAAAAT
1 AATTTTTAAAAAT
1635789 AATTTTTAAAAAT
1 AATTTTTAAAAAT
1635802 AATTTTTAAAAAAT
1 AATTTTT-AAAAAT
1635816 AATT
1 AATT
1635820 AAATACTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:1636768 original size:3 final size:3
Alignment explanation
Indices: 1636762--1636836 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
1636752 TATTGGGTGG
1636762 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1636809 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1636837 GATACTACAA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1637351 original size:21 final size:21
Alignment explanation
Indices: 1637322--1637393 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
1637312 TTGATATGTT
*
1637322 AAAAGAAATGGAGAAGGTAGG
1 AAAATAAATGGAGAAGGTAGG
1637343 AAAATAAATGGAGAAGGTAGG
1 AAAATAAATGGAGAAGGTAGG
*
1637364 AAAATAAAAGGAGAA-GTA-G
1 AAAATAAATGGAGAAGGTAGG
1637383 AAAAT-AATGGA
1 AAAATAAATGGA
1637394 AAATAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.10
19 6 0.12
20 3 0.06
21 34 0.71
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.12
Consensus pattern (21 bp):
AAAATAAATGGAGAAGGTAGG
Found at i:1638206 original size:29 final size:31
Alignment explanation
Indices: 1638165--1638226 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
1638155 TAAACCTCTT
1638165 CACTTTCCTCCCAAAACTTTTACTC-CCTCC
1 CACTTTCCTCCCAAAACTTTTACTCTCCTCC
*
1638195 CACTTTCC-CCCATAACTTTTACTCTCCTCC
1 CACTTTCCTCCCAAAACTTTTACTCTCCTCC
1638225 CA
1 CA
1638227 TCCCACCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (31 bp):
CACTTTCCTCCCAAAACTTTTACTCTCCTCC
Found at i:1641556 original size:53 final size:53
Alignment explanation
Indices: 1641494--1641600 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1641484 GTCCTTAATG
1641494 AAGAGTATCTATTCTTCTTTATCTTTGATGCAGGGGCTGTTGAAAGAAGAATT
1 AAGAGTATCTATTCTTCTTTATCTTTGATGCAGGGGCTGTTGAAAGAAGAATT
1641547 AAGAGTATCTATTCTTCTTTATCTTTGATGCAGGGGCTGTTGAAAGAAGAATT
1 AAGAGTATCTATTCTTCTTTATCTTTGATGCAGGGGCTGTTGAAAGAAGAATT
1641600 A
1 A
1641601 TACTTGTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (53 bp):
AAGAGTATCTATTCTTCTTTATCTTTGATGCAGGGGCTGTTGAAAGAAGAATT
Found at i:1653838 original size:30 final size:30
Alignment explanation
Indices: 1653802--1653863 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1653792 GAATTAGTCT
1653802 AATTATATATTT-TTATCATTTAAGTTATAA
1 AATTATATATTTATTATCATTTAA-TTATAA
* *
1653832 AATTATATTTTTATTATTATTTAATTATAA
1 AATTATATATTTATTATCATTTAATTATAA
1653862 AA
1 AA
1653864 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
AATTATATATTTATTATCATTTAATTATAA
Found at i:1669643 original size:12 final size:12
Alignment explanation
Indices: 1669626--1669650 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1669616 CGAACTAGAG
1669626 TACCCTTATGTT
1 TACCCTTATGTT
1669638 TACCCTTATGTT
1 TACCCTTATGTT
1669650 T
1 T
1669651 TACTTGAATA
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:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TACCCTTATGTT
Found at i:1676449 original size:14 final size:14
Alignment explanation
Indices: 1676430--1676456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1676420 GAATAGTGTT
1676430 TATTTATTTATTTA
1 TATTTATTTATTTA
1676444 TATTTATTTATTT
1 TATTTATTTATTT
1676457 TAAATTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTATTTATTTA
Found at i:1676555 original size:33 final size:34
Alignment explanation
Indices: 1676492--1676555 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
1676482 GAATATTCTA
* **
1676492 TATTTATGTATTTAAAATTATATGTGTTTGTATT
1 TATTTATGTATTTAAAATTAAATGAATTTGTATT
*
1676526 TATTTATTTATTT-AAATTAAATGAATTTGT
1 TATTTATGTATTTAAAATTAAATGAATTTGT
1676556 TTATAAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (34 bp):
TATTTATGTATTTAAAATTAAATGAATTTGTATT
Found at i:1676649 original size:21 final size:20
Alignment explanation
Indices: 1676623--1676682 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
1676613 AGTGATCTAT
1676623 TAAATGAGTCTTGAATAAATA
1 TAAATGAGT-TTGAATAAATA
* *
1676644 TAAATGAATTTGTTTATAAATA
1 TAAATGAGTTTG--AATAAATA
1676666 TAAATG-GTTTGAATAAA
1 TAAATGAGTTTGAATAAA
1676683 ATTTGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 12 0.36
22 13 0.39
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (20 bp):
TAAATGAGTTTGAATAAATA
Found at i:1678884 original size:15 final size:15
Alignment explanation
Indices: 1678866--1678895 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1678856 ACCTTACTTG
1678866 AAAAAAAAAAGTAAA
1 AAAAAAAAAAGTAAA
*
1678881 AAAAAAAAAATTAAA
1 AAAAAAAAAAGTAAA
1678896 GAGGTGAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAAGTAAA
Found at i:1682042 original size:20 final size:20
Alignment explanation
Indices: 1682017--1682057 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1682007 AATTTCGTTG
1682017 GGTTAAATTCGATTAATTGT
1 GGTTAAATTCGATTAATTGT
1682037 GGTTAAATTCGATTAATTGT
1 GGTTAAATTCGATTAATTGT
1682057 G
1 G
1682058 TTATACTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (20 bp):
GGTTAAATTCGATTAATTGT
Found at i:1689939 original size:4 final size:5
Alignment explanation
Indices: 1689917--1689964 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 5
1689907 CTTTCCCCTA
1689917 ATTTCT ATTTT ATTTT A-TTT ATTTT ATTTT CATTTT CATTTT CATTTT
1 ATTT-T ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT -ATTTT -ATTTT
1689965 CCCCTTCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.10
5 15 0.38
6 21 0.52
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (5 bp):
ATTTT
Found at i:1689941 original size:14 final size:15
Alignment explanation
Indices: 1689922--1689965 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 15
1689912 CCCTAATTTC
1689922 TATTTTATTTT-ATT
1 TATTTTATTTTCATT
1689936 TATTTTATTTTCATTT
1 TATTTTATTTTCA-TT
1689952 TCATTTTCATTTTC
1 T-ATTTT-ATTTTC
1689966 CCCTTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 3 0.12
17 5 0.19
18 6 0.23
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTATTTTCATT
Found at i:1700190 original size:12 final size:13
Alignment explanation
Indices: 1700173--1700201 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1700163 ACAGATAATA
1700173 TTATTTTTAT-TT
1 TTATTTTTATGTT
1700185 TTATTTTTATGTT
1 TTATTTTTATGTT
1700198 TTAT
1 TTAT
1700202 CCTAACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTATTTTTATGTT
Found at i:1701144 original size:17 final size:17
Alignment explanation
Indices: 1701112--1701160 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1701102 TATAATACAT
1701112 ATTTTATATTT-A-TTAA
1 ATTTTA-ATTTAATTTAA
*
1701128 TATTTT-ATTTAGTTTAA
1 -ATTTTAATTTAATTTAA
1701145 ATTTTAATTTAATTTA
1 ATTTTAATTTAATTTA
1701161 GTTGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTAATTTAATTTAA
Found at i:1701170 original size:22 final size:22
Alignment explanation
Indices: 1701129--1701170 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1701119 ATTTATTAAT
* *
1701129 ATTTTATTTAGTTTAAATTTTA
1 ATTTAATTTAGTTGAAATTTTA
*
1701151 ATTTAATTTAGTTGATATTT
1 ATTTAATTTAGTTGAAATTT
1701171 ATAAATAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTAATTTAGTTGAAATTTTA
Found at i:1708952 original size:16 final size:16
Alignment explanation
Indices: 1708931--1708999 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1708921 TTTGGTTCGC
1708931 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1708947 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1708963 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
1708980 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1708996 TGTA
1 TGTA
1709000 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1708977 original size:33 final size:32
Alignment explanation
Indices: 1708931--1708999 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1708921 TTTGGTTCGC
1708931 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1708963 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
1708996 TGTA
1 TGTA
1709000 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:1709064 original size:44 final size:45
Alignment explanation
Indices: 1708980--1709070 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1708970 GGATTAGAGG
* * *
1708980 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
1709025 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
1709069 TG
1 TG
1709071 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:1725238 original size:12 final size:12
Alignment explanation
Indices: 1725221--1725272 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
1725211 GGAAATGACG
1725221 AAAAAAGGGAAA
1 AAAAAAGGGAAA
1725233 AAAAAAGGGAAA
1 AAAAAAGGGAAA
*
1725245 AAAAAGGAGGAAA
1 AAAAAAG-GGAAA
*
1725258 AAGAAA--GAAA
1 AAAAAAGGGAAA
1725268 AAAAA
1 AAAAA
1725273 TACAAGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 8 0.23
12 18 0.51
13 9 0.26
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAAGGGAAA
Found at i:1726910 original size:45 final size:45
Alignment explanation
Indices: 1726860--1726956 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
1726850 CTTCCTCTGT
* * *
1726860 GATGCTTGCCATCAAAAGATCTTGACCTTGACCTCTTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
**
1726905 GATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
1726950 GATGCTT
1 GATGCTT
1726957 AGATTTCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (45 bp):
GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
Found at i:1727715 original size:42 final size:42
Alignment explanation
Indices: 1727669--1727757 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
1727659 ATAAGAGCGA
* * *
1727669 GACCTCCTCCTTCGCCTATAACTGATAGGTGATCTTGACTTT
1 GACCTCCACCTTCGCCTATAAATGATAGGTGATCTTGACTTG
** * *
1727711 GACCTTGACTTTCGCCTATAAATGATCGGTGATCTTGACTTG
1 GACCTCCACCTTCGCCTATAAATGATAGGTGATCTTGACTTG
1727753 GACCT
1 GACCT
1727758 TGATCTTCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (42 bp):
GACCTCCACCTTCGCCTATAAATGATAGGTGATCTTGACTTG
Found at i:1727758 original size:42 final size:42
Alignment explanation
Indices: 1727678--1727844 Score: 156
Period size: 42 Copynumber: 4.0 Consensus size: 42
1727668 AGACCTCCTC
*
1727678 CTTCGCCTATAACTGATAGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCTATAACTGATAGGTGATCTTGACTTGGACCTTGAT
* *
1727719 CTTTCGCCTATAAATGATCGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCTATAACTGATAGGTGATCTTGACTTGGACCTTGAT
* * * * * * *
1727762 CTTCGCCGATAACTAATTGGTGATCTAGTCTTTGATCTTGAT
1 CTTCGCCTATAACTGATAGGTGATCTTGACTTGGACCTTGAT
* * * ** * * *
1727804 CTTCTCCGATAACTAAGGGGTGATTTTGATTTGGATCTTGA
1 CTTCGCCTATAACTGATAGGTGATCTTGACTTGGACCTTGA
1727845 CCTTGCACGA
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
41 1 0.01
42 103 0.98
43 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (42 bp):
CTTCGCCTATAACTGATAGGTGATCTTGACTTGGACCTTGAT
Found at i:1742639 original size:72 final size:72
Alignment explanation
Indices: 1742545--1742735 Score: 269
Period size: 72 Copynumber: 2.7 Consensus size: 72
1742535 TTTAGAAGAA
* * * * *
1742545 TTCGACGCATCTTCTAACAATTTGAGTGGCCCAATTCCAAATTGGTTATG-TAATATGAGTCAAC
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT-GGACAATATGAGTCAAC
1742609 TT-TACAGT
65 TTGT-CAGT
* *
1742617 TTCGATGCATCTTATAATAATTTGAGTGGCTCAATTCCAAATTGCTTGGACAATATGAGTCAACT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACT
1742682 TGTCAGT
66 TGTCAGT
* *
1742689 TTCGATGTATCTTATAACAATTTGAGTGGCCCAATTCCCAATTGCTT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT
1742736 CGGCAAAATG
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.01
72 104 0.98
73 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (72 bp):
TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAACT
TGTCAGT
Found at i:1748665 original size:16 final size:15
Alignment explanation
Indices: 1748620--1748662 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1748610 CATTTTTAAT
*
1748620 AAATATAAAACATAAA
1 AAATATTAAA-ATAAA
1748636 AAATATTAAAATAAA
1 AAATATTAAAATAAA
1748651 ATAATAATTAAA
1 A-AAT-ATTAAA
1748663 TAATGATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATTAAAATAAA
Found at i:1758522 original size:14 final size:11
Alignment explanation
Indices: 1758490--1758514 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1758480 AAAATATTAA
1758490 AATTAAATAAT
1 AATTAAATAAT
1758501 AATTAAATAAT
1 AATTAAATAAT
1758512 AAT
1 AAT
1758515 ATAGAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAAATAAT
Found at i:1768329 original size:12 final size:12
Alignment explanation
Indices: 1768299--1768331 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1768289 ATGCAATAGG
1768299 AAACCAGCA-GC
1 AAACCAGCATGC
1768310 AAACCAGCATGC
1 AAACCAGCATGC
*
1768322 AGACCAGCAT
1 AAACCAGCAT
1768332 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:1770319 original size:12 final size:11
Alignment explanation
Indices: 1770281--1770325 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
1770271 AAAAGATTAT
1770281 TTATTATTTATA
1 TTATTATTT-TA
*
1770293 TTATCATTTTCA
1 TTATTATTTT-A
1770305 TTATTATTATTA
1 TTATTATT-TTA
1770317 TTATTATTT
1 TTATTATTT
1770326 GTTTATGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:1776718 original size:18 final size:19
Alignment explanation
Indices: 1776681--1776719 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1776671 GATCGAATAC
1776681 ATCGAAATAAAAAAATGAA
1 ATCGAAATAAAAAAATGAA
*
1776700 ATCGAAATACAAAAA-GAA
1 ATCGAAATAAAAAAATGAA
1776718 AT
1 AT
1776720 ATTAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (19 bp):
ATCGAAATAAAAAAATGAA
Found at i:1776791 original size:11 final size:11
Alignment explanation
Indices: 1776775--1776799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1776765 CATTTTATTG
1776775 TTTATTATTAT
1 TTTATTATTAT
1776786 TTTATTATTAT
1 TTTATTATTAT
1776797 TTT
1 TTT
1776800 TCTCTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:1783929 original size:24 final size:24
Alignment explanation
Indices: 1783899--1784212 Score: 123
Period size: 24 Copynumber: 13.6 Consensus size: 24
1783889 GTGTATTGTA
*
1783899 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* * * *
1783923 TTTTATTGTTTGT-GATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
1783946 TATTATTATTTTAAATTTAT--TG
1 TATTATTATTTTAAATTTATCATG
**
1783968 TTAACATTATTTTAAATTTATCATG
1 -TATTATTATTTTAAATTTATCATG
*
1783993 TA-TATCTATTTCAAATTTATCAT-
1 TATTAT-TATTTTAAATTTATCATG
* * *
1784016 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* ** *
1784038 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
1784062 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
*
1784085 CA--A-T-TTTTAAA-TTAT--TG
1 TATTATTATTTTAAATTTATCATG
** *
1784102 TATGCTATTATTTTGGATTTATCACG
1 TAT--TATTATTTTAAATTTATCATG
* *
1784128 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
1784151 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
* * *
1784173 TATTATTATTTCAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
1784197 TATTATTTATTGTAAA
1 TATTA-TTATTTTAAA
1784213 CTATCCAATT
Statistics
Matches: 213, Mismatches: 47, Indels: 59
0.67 0.15 0.18
Matches are distributed among these distances:
16 1 0.00
17 1 0.00
18 6 0.03
19 4 0.02
20 3 0.01
21 21 0.10
22 14 0.07
23 52 0.24
24 94 0.44
25 13 0.06
26 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:1783988 original size:11 final size:11
Alignment explanation
Indices: 1783951--1783988 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1783941 ATCAATATTA
1783951 TTATTTTAAAT
1 TTATTTTAAAT
1783962 TTATTGTTAACA-
1 TTATT-TTAA-AT
1783974 TTATTTTAAAT
1 TTATTTTAAAT
1783985 TTAT
1 TTAT
1783989 CATGTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 9 0.38
13 1 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:1784118 original size:66 final size:67
Alignment explanation
Indices: 1784009--1784179 Score: 267
Period size: 66 Copynumber: 2.6 Consensus size: 67
1783999 TATTTCAAAT
* *
1784009 TTATCATTAATATTTTTAAATTTATTATATACTATTATTTTGGATTTATCACGTATGATTATTCT
1 TTATCATCAA-ATTTTTAAA-TTATTATATGCTATTATTTTGGATTTATCACGTATGATTATTCT
1784074 AGAA
64 AGAA
*
1784078 TTATCATC-AATTTTTAAATTATTGTATGCTATTATTTTGGATTTATCACGTATGATTATTCTAG
1 TTATCATCAAATTTTTAAATTATTATATGCTATTATTTTGGATTTATCACGTATGATTATTCTAG
1784142 AA
66 AA
1784144 TTATCATCAAAATTTTTAAATT-TTATATG-TATTATT
1 TTATCATC-AAATTTTTAAATTATTATATGCTATTATT
1784180 ATTTCAAATT
Statistics
Matches: 96, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
66 61 0.64
67 15 0.16
68 13 0.14
69 7 0.07
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (67 bp):
TTATCATCAAATTTTTAAATTATTATATGCTATTATTTTGGATTTATCACGTATGATTATTCTAG
AA
Found at i:1787533 original size:12 final size:12
Alignment explanation
Indices: 1787516--1787542 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1787506 CCTGAGGAAG
1787516 CTGTTCTTAAGA
1 CTGTTCTTAAGA
1787528 CTGTTCTTAAGA
1 CTGTTCTTAAGA
1787540 CTG
1 CTG
1787543 AGGAAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (12 bp):
CTGTTCTTAAGA
Found at i:1791549 original size:44 final size:44
Alignment explanation
Indices: 1791354--1791550 Score: 128
Period size: 44 Copynumber: 4.5 Consensus size: 44
1791344 CATTGGAAAT
* * *
1791354 AGCAAATCTTGTCTCCCTAAACAGTAGTGGAGCAGATCGAGGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* * * * * *
1791398 AGCAAATCTTATATTCCTAAGATAGTAATGAAGCAGATTC-AAGCC
1 AGCAAATCTTATCTCCCTAAG-CAGTAGTGGAGCAGA-TCGAAGAC
*** * * * * * * *
1791443 A-CCGGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAATAT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* * * * *
1791486 TGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* *
1791530 GGCAAATCTTATCTTCCTAAG
1 AGCAAATCTTATCTCCCTAAG
1791551 ATAGTAGAGA
Statistics
Matches: 107, Mismatches: 42, Indels: 8
0.68 0.27 0.05
Matches are distributed among these distances:
42 1 0.01
43 11 0.10
44 77 0.72
45 16 0.15
46 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
Found at i:1791600 original size:132 final size:132
Alignment explanation
Indices: 1791363--1792050 Score: 822
Period size: 132 Copynumber: 5.3 Consensus size: 132
1791353 TAGCAAATCT
* * * *
1791363 TGTCTCCCTAAACAGTAGTGGAGCAGATCGAGGACAGCAAATCTTATATTCCTAAGATAGTA-AT
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGA-
* * * *
1791427 GAAGCAGATTCAAGCCACCGGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAATATTGTAGA
65 GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGA
1791492 TCC
130 TCC
1791495 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* * * *
1791560 AAGTAGATTTAAGCCACCGGTCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTATAGA-
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1791624 CTC
131 C-C
* * ** * * *
1791627 TGTCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGACGGTGAATCTTATCTTCTTAAGATAGCAGTG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* * *
1791692 AAGCAAATTTAAGCCACCAATCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
*
1791757 TC
131 CC
* * * ** * * * *
1791759 TGTCTCCCTAAGCAGTAGCGGAACAGGTCGAAGACGGTGAATTTTATCTTCCCAAGGTGGTAG-G
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* *
1791823 AAAGC-GAATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAGAATGTAG
66 -AAGCAG-ATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
*
1791887 ATAC
129 ATCC
* * * * *
1791891 TGTTTCCCTAAGCAGTAGTGGAGCAGATC----A-TG--AATCTTATCTTCCCAAGGTAGTAGGG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
** * * * *
1791949 AAGCAGATTTAAATCACTAGTCCTATCTCCCTGAGTAGCGGTGGAGTAGGTTGAAGATTGCAGAT
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
*
1792014 CA
131 CC
* *
1792016 TGTCTCCCTGAGCAGTAGTGGAGCAGATCTAAGAC
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1792051 AGAGAATTTT
Statistics
Matches: 487, Mismatches: 57, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
125 104 0.21
126 2 0.00
127 1 0.00
128 1 0.00
129 1 0.00
131 2 0.00
132 375 0.77
133 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
CC
Found at i:1792577 original size:19 final size:19
Alignment explanation
Indices: 1792553--1792606 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1792543 CTTGAAAAAG
* *
1792553 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAA
1792572 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
1792591 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
1792607 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:1792628 original size:23 final size:22
Alignment explanation
Indices: 1792566--1792629 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 22
1792556 ATGCAGTCTT
*
1792566 AGATATGATATGCAATCTT---
1 AGATAAGATATGCAATCTTAGA
1792585 AGATAAGATATGCAATCTTAGA
1 AGATAAGATATGCAATCTTAGA
* *
1792607 AGATAAGATTTTGTAATCTTAGA
1 AGATAAGA-TATGCAATCTTAGA
1792630 TATTTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.47
22 8 0.21
23 12 0.32
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (22 bp):
AGATAAGATATGCAATCTTAGA
Found at i:1793098 original size:33 final size:33
Alignment explanation
Indices: 1793036--1793101 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1793026 TCTTATTTAC
1793036 ATATTGTTCATTCATTTAACCATTCTTATCATT
1 ATATTGTTCATTCATTTAACCATTCTTATCATT
1793069 ATATTGTTCATTCATTTAACCATTCTTATCATT
1 ATATTGTTCATTCATTTAACCATTCTTATCATT
1793102 CTTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (33 bp):
ATATTGTTCATTCATTTAACCATTCTTATCATT
Found at i:1807377 original size:21 final size:21
Alignment explanation
Indices: 1807351--1807394 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1807341 CCCAAAATTG
1807351 GTACCAAATCGATTGTTTAAT
1 GTACCAAATCGATTGTTTAAT
1807372 GTACCAAATCGATTGTTTAAT
1 GTACCAAATCGATTGTTTAAT
1807393 GT
1 GT
1807395 CTTAGTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (21 bp):
GTACCAAATCGATTGTTTAAT
Found at i:1809630 original size:19 final size:19
Alignment explanation
Indices: 1809597--1809635 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1809587 AATAAAAGAA
*
1809597 AAAAAGAAAGCAAAGAATCG
1 AAAAAGAAAGAAAAG-ATCG
1809617 AAAAAGAAA-AAAAGATCG
1 AAAAAGAAAGAAAAGATCG
1809635 A
1 A
1809636 GAGCCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.69, C:0.08, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAGAAAAGATCG
Found at i:1813828 original size:17 final size:18
Alignment explanation
Indices: 1813785--1813830 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
1813775 TAAATATTTT
1813785 TAATAATATAAAACATAAA
1 TAATAAT-TAAAACATAAA
* *
1813804 AAAT-ATTAAAA-TTAAA
1 TAATAATTAAAACATAAA
1813820 TAATAATTAAA
1 TAATAATTAAA
1813831 TAATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 2 0.09
19 3 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAATTAAAACATAAA
Found at i:1813829 original size:11 final size:11
Alignment explanation
Indices: 1813813--1813837 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1813803 AAAATATTAA
1813813 AATTAAATAAT
1 AATTAAATAAT
1813824 AATTAAATAAT
1 AATTAAATAAT
1813835 AAT
1 AAT
1813838 ATATTTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAAATAAT
Found at i:1819824 original size:15 final size:15
Alignment explanation
Indices: 1819781--1819830 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1819771 CATTTTTTCG
*
1819781 AATTGAGTCGAGTGA
1 AATTGAATCGAGTGA
*
1819796 AA-TGAAATTCGAGTCA
1 AATTG-AA-TCGAGTGA
1819812 AATTGAATCGAGTGA
1 AATTGAATCGAGTGA
1819827 AATT
1 AATT
1819831 ATTCAAGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 11 0.38
17 2 0.07
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (15 bp):
AATTGAATCGAGTGA
Found at i:1820020 original size:18 final size:19
Alignment explanation
Indices: 1819999--1820035 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1819989 AATTTAAAAT
*
1819999 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
1820017 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
1820036 ATATTAGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:1820116 original size:80 final size:80
Alignment explanation
Indices: 1820017--1820187 Score: 317
Period size: 80 Copynumber: 2.1 Consensus size: 80
1820007 ATATTTTGAA
1820017 TTTTAAAAATTATTTTGAAATATTAGCAGGTAAGCATTAGTCTAATTAAGCATTAGTCTTTCTAA
1 TTTTAAAAA-TATTTTGAAATATTAGCAGGTAAGCATTAGTCTAATTAAGCATTAGTCTTTCTAA
1820082 TTTGAAAAGATAGTTG
65 TTTGAAAAGATAGTTG
1820098 TTTTAAAAATATTTTGAAATATTAGCAGGTAAGCATTAGTCTAATTAAGCATTAGTCTTTCTAAT
1 TTTTAAAAATATTTTGAAATATTAGCAGGTAAGCATTAGTCTAATTAAGCATTAGTCTTTCTAAT
1820163 TTGAAAAGATAGTTG
66 TTGAAAAGATAGTTG
*
1820178 -TTGAAAAATA
1 TTTTAAAAATA
1820188 AATTTCTCTA
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
79 9 0.10
80 71 0.80
81 9 0.10
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.40
Consensus pattern (80 bp):
TTTTAAAAATATTTTGAAATATTAGCAGGTAAGCATTAGTCTAATTAAGCATTAGTCTTTCTAAT
TTGAAAAGATAGTTG
Found at i:1820675 original size:139 final size:139
Alignment explanation
Indices: 1820425--1820708 Score: 518
Period size: 139 Copynumber: 2.0 Consensus size: 139
1820415 GCTTGACACT
1820425 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
1 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
1820490 TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
66 TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
1820555 AATCTAGTA
131 AATCTAGTA
* *
1820564 TGTTTTTATATTAGTCTATTTATCCTTTCAATGATAGTCTTATTACGTTAAAAATTA-CTGTTCA
1 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATC-GTTCA
1820628 ATTACA-CTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTT
65 ATTA-AGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTT
1820692 ACAATCTAGTA
129 ACAATCTAGTA
1820703 TGTTTT
1 TGTTTT
1820709 CCAATGTTAG
Statistics
Matches: 141, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
138 1 0.01
139 139 0.99
140 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (139 bp):
TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
AATCTAGTA
Found at i:1829003 original size:18 final size:18
Alignment explanation
Indices: 1828980--1829017 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1828970 AATACTAACA
1828980 ATAAGTAATTTATGCATC
1 ATAAGTAATTTATGCATC
1828998 ATAAGTAATTTATGCATC
1 ATAAGTAATTTATGCATC
1829016 AT
1 AT
1829018 GACTAACAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
ATAAGTAATTTATGCATC
Found at i:1829411 original size:9 final size:9
Alignment explanation
Indices: 1829398--1829446 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
1829388 TTTATTCAAG
1829398 TTATTATAA
1 TTATTATAA
*
1829407 ATATTAT-A
1 TTATTATAA
1829415 TCTA-TATAA
1 T-TATTATAA
1829424 TTATTATAA
1 TTATTATAA
1829433 TTATTATAA
1 TTATTATAA
1829442 TTATT
1 TTATT
1829447 TATTCAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 6 0.17
9 29 0.83
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TTATTATAA
Found at i:1829653 original size:19 final size:19
Alignment explanation
Indices: 1829637--1829683 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1829627 AAAGTAAATA
1829637 AAAGAAAATAAAATAAAAG
1 AAAGAAAATAAAATAAAAG
* *
1829656 AAAGCAAATGAAATAAAAAG
1 AAAGAAAATAAAAT-AAAAG
*
1829676 AAACAAAA
1 AAAGAAAA
1829684 GAAGAACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.77, C:0.04, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAGAAAATAAAATAAAAG
Done.