Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 11 of 18
Found at i:4563480 original size:16 final size:15
Alignment explanation
Indices: 4563447--4563485 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4563437 ATATATATAT
*
4563447 ATATATAT-AAAGAG
1 ATATATATGAAAGAC
4563461 ATATATATGAAAGATC
1 ATATATATGAAAGA-C
4563477 ATATATATG
1 ATATATATG
4563486 TTTACACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (15 bp):
ATATATATGAAAGAC
Found at i:4570425 original size:15 final size:15
Alignment explanation
Indices: 4570405--4570436 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4570395 CACTGTTATA
4570405 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
4570420 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
4570435 AT
1 AT
4570437 GATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:4570456 original size:48 final size:49
Alignment explanation
Indices: 4570404--4570535 Score: 146
Period size: 48 Copynumber: 2.7 Consensus size: 49
4570394 ACACTGTTAT
* *
4570404 AATTAAAATAAAAAATATTAAAATAAAATATATGAT-ATA-AGA-ATCAA-A
1 AATTAAAATAAAATATA-TAAAATAAAATATAT-ATAATATAGATA-AAACA
* *
4570452 AATTAAAATAAAATATAAAAAATTAAAATTTATATAATATAGATAAAACA
1 AATTAAAATAAAATATATAAAA-TAAAATATATATAATATAGATAAAACA
* *
4570502 AATTAAAATAAAATATATAATATAAAAAATATAT
1 AATTAAAATAAAATATATAAAATAAAATATATAT
4570536 TAAAAAAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
47 6 0.08
48 28 0.39
49 15 0.21
50 22 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (49 bp):
AATTAAAATAAAATATATAAAATAAAATATATATAATATAGATAAAACA
Found at i:4570528 original size:14 final size:14
Alignment explanation
Indices: 4570509--4570589 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
4570499 ACAAATTAAA
4570509 ATAAAATATATAAT
1 ATAAAATATATAAT
* *
4570523 ATAAAAAATATATT
1 ATAAAATATATAAT
* *
4570537 A-AAAAAATA-AAA
1 ATAAAATATATAAT
*
4570549 ATAAAATATATAAA
1 ATAAAATATATAAT
*
4570563 ATTATAATA-ATAA-
1 A-TAAAATATATAAT
4570576 ATAAAA-ATA-AAT
1 ATAAAATATATAAT
4570588 AT
1 AT
4570590 GTGACATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
11 3 0.05
12 9 0.16
13 16 0.29
14 21 0.38
15 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATATATAAT
Found at i:4570550 original size:6 final size:6
Alignment explanation
Indices: 4570539--4570586 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
4570529 AATATATTAA
* *
4570539 AAAAAT AAAAAT AAAATAT ATAAAAT TATAAT AATAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT AA-AAAT AAAAAT AAA
4570587 TATGTGACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 22 0.63
7 10 0.29
8 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:4570553 original size:83 final size:81
Alignment explanation
Indices: 4570400--4570582 Score: 200
Period size: 83 Copynumber: 2.2 Consensus size: 81
4570390 TTTCACACTG
* * *
4570400 TTATAATTA-AAATAAAAAATATTAAAATAAAATATATGATATAAGAATCAAAAATTAAAATAAA
1 TTATAATAATAAATAAAAAATATTAAAATAAAATATATAATATAAAAATCAAAAA-TAAAATAAA
4570464 ATATAAAAAAT-TAAAA
65 ATATAAAAAATATAAAA
4570480 TT-TATATAATATAGATAAAACAA-ATTAAAATAAAATATATAATATAAAAAAT-ATATTAAA-A
1 TTATA-ATAATA-A-ATAAAA-AATATTAAAATAAAATATATAATAT-AAAAATCA-A--AAATA
*
4570541 AAATAAAA-ATAAAATATATAAAA
58 AAATAAAATATAAAAAATATAAAA
4570564 TTATAATAATAAATAAAAA
1 TTATAATAATAAATAAAAA
4570583 TAAATATGTG
Statistics
Matches: 88, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
79 2 0.02
80 5 0.06
81 2 0.02
82 7 0.08
83 37 0.42
84 30 0.34
85 2 0.02
86 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (81 bp):
TTATAATAATAAATAAAAAATATTAAAATAAAATATATAATATAAAAATCAAAAATAAAATAAAA
TATAAAAAATATAAAA
Found at i:4570557 original size:33 final size:32
Alignment explanation
Indices: 4570506--4570586 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 32
4570496 AAAACAAATT
*
4570506 AAAATAAAATATATAATATAAAAAATATATTAA-A
1 AAAATAAAA-ATAAAATATAAAAAAT-TA-TAATA
*
4570540 AAAATAAAAATAAAATATATAAAATTATAATA
1 AAAATAAAAATAAAATATAAAAAATTATAATA
4570572 ATAAATAAAAATAAA
1 A-AAATAAAAATAAA
4570587 TATGTGACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 3 0.07
32 4 0.09
33 27 0.63
34 9 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATTATAATA
Found at i:4570568 original size:8 final size:9
Alignment explanation
Indices: 4570509--4570581 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
4570499 ACAAATTAAA
4570509 ATAAAATAT
1 ATAAAATAT
4570518 AT--AATAT
1 ATAAAATAT
*
4570525 AAAAAATAT
1 ATAAAATAT
*
4570534 ATTAAAA-AA
1 A-TAAAATAT
4570543 AT-AAA-A-
1 ATAAAATAT
4570549 ATAAAATAT
1 ATAAAATAT
4570558 ATAAAAT-T
1 ATAAAATAT
*
4570566 ATAATAATAA
1 ATAA-AATAT
4570576 ATAAAA
1 ATAAAA
4570582 ATAAATATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.04
7 13 0.25
8 7 0.13
9 22 0.42
10 8 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAAATAT
Found at i:4570827 original size:15 final size:15
Alignment explanation
Indices: 4570807--4570835 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4570797 TTATTTTTCC
4570807 TACAATCACATTACT
1 TACAATCACATTACT
4570822 TACAATCACATTAC
1 TACAATCACATTAC
4570836 CTGTAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (15 bp):
TACAATCACATTACT
Found at i:4585784 original size:11 final size:11
Alignment explanation
Indices: 4585768--4585793 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4585758 AAATATAAAT
4585768 AATTAAATTTA
1 AATTAAATTTA
4585779 AATTAAATTTA
1 AATTAAATTTA
4585790 AATT
1 AATT
4585794 CAGATATTTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:4599204 original size:127 final size:119
Alignment explanation
Indices: 4598931--4599222 Score: 340
Period size: 116 Copynumber: 2.4 Consensus size: 119
4598921 AAAATGTAAA
* * * *
4598931 AAATAAAAACAAATTAACATAAAAATCATATCAATATTTTAATAATATGTTATTAATTATTAATA
1 AAAT-AAAAGAAATTAA-A-AAAAATCATATTAATATTTTAATAATAAGCTATTAATTATTAATA
* *
4598996 TTTTAATAATATTTTTAATAAAAAATAAAAAAGAAAAACAGAAAAATAAAAATAGAG
63 ATTTAATAATATTTTTAAAAAAAAATAAAAAAGAAAAACAGAAAAATAAAAATAGAG
*
4599053 AAA-AAAAGAAATT--AAAAAATCATATTAATATTTTGATAATAAGCTATTGAATTATTAATAAT
1 AAATAAAAGAAATTAAAAAAAATCATATTAATATTTTAATAATAAGCTATT-AATTATTAATAAT
* * * *
4599115 TTAATAATATTTTTATAAAAAGAAATTTAAAAAGAGAAAA-AGACAGATGCAAAATAGAGG
65 TTAATAATATTTTTA-AAAAA-AAA-TAAAAAAGA-AAAACAGAAAAAT-AAAAATAGA-G
*
4599175 AAATAAAAGAAATTAAAAGAAAAATCATATTAATATTTTAAAAATAAG
1 AAATAAAAGAAATT-AAA-AAAAATCATATTAATATTTTAATAATAAG
4599223 ATAATAAAAT
Statistics
Matches: 145, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
116 30 0.21
117 28 0.19
118 4 0.03
119 3 0.02
120 23 0.16
121 12 0.08
122 7 0.05
123 10 0.07
126 1 0.01
127 27 0.19
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30
Consensus pattern (119 bp):
AAATAAAAGAAATTAAAAAAAATCATATTAATATTTTAATAATAAGCTATTAATTATTAATAATT
TAATAATATTTTTAAAAAAAAATAAAAAAGAAAAACAGAAAAATAAAAATAGAG
Found at i:4600208 original size:51 final size:51
Alignment explanation
Indices: 4600138--4600238 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
4600128 TATGCAAATA
4600138 ACCTCAAAGAGTACTAATTCACTATAAAATTATTATATTAATTATTTTTTC
1 ACCTCAAAGAGTACTAATTCACTATAAAATTATTATATTAATTATTTTTTC
* *
4600189 ACCTTAAAGAGTA-TGAATTCACTTTAAAATTATTATATTAATTATTTTTT
1 ACCTCAAAGAGTACT-AATTCACTATAAAATTATTATATTAATTATTTTTT
4600239 TTCAATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (51 bp):
ACCTCAAAGAGTACTAATTCACTATAAAATTATTATATTAATTATTTTTTC
Found at i:4604244 original size:32 final size:32
Alignment explanation
Indices: 4604159--4604251 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
4604149 TATATATATA
* ** *
4604159 TTCATTCTTTTTAATTTGGTCCCTCAAAACTT
1 TTCATTCTTTTCAATTAAGTCCCTCAACACTT
* *
4604191 TTCATTCTTTTGAATTTAGTCCCTCAACA-TT
1 TTCATTCTTTTCAATTAAGTCCCTCAACACTT
4604222 TT-ATTCCTCTTTCAATTAAGTCCCTTCAAC
1 TTCATT-CT-TTTCAATTAAGTCCC-TCAAC
4604252 CATCTTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 3 0.06
31 6 0.11
32 39 0.74
33 5 0.09
ACGTcount: A:0.23, C:0.25, G:0.05, T:0.47
Consensus pattern (32 bp):
TTCATTCTTTTCAATTAAGTCCCTCAACACTT
Found at i:4606798 original size:80 final size:79
Alignment explanation
Indices: 4606660--4606875 Score: 283
Period size: 80 Copynumber: 2.7 Consensus size: 79
4606650 ATATAATCAT
* * *
4606660 CATGCTTAGCCCATAGTGTATATGACTAT-CTCAACACATAGAT-TGCATGGCATGCATTTCATA
1 CATGCTTAGCCCATAGTGTATATGA-T-TGCTTAACACATATATCT-CATGGCATACATTTCATA
*
4606723 ACCTCATAAATCCCTCA
63 ACCTCATAAATCACTCA
* * *
4606740 CATGCTTAGCCTATAGTGTTTATGATTGCCTTAGCACATATATCTCATGGCATACATTTCATAAC
1 CATGCTTAGCCCATAGTGTATATGATTG-CTTAACACATATATCTCATGGCATACATTTCATAAC
* *
4606805 TTTATAAATCACTCA
65 CTCATAAATCACTCA
*
4606820 CATGCTTAGCCCATAGTGTATATGATATGCTTAACACATATATCTCATAGCATACA
1 CATGCTTAGCCCATAGTGTATATGAT-TGCTTAACACATATATCTCATGGCATACA
4606876 CGTTACAATC
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
78 1 0.01
79 1 0.01
80 114 0.96
81 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (79 bp):
CATGCTTAGCCCATAGTGTATATGATTGCTTAACACATATATCTCATGGCATACATTTCATAACC
TCATAAATCACTCA
Found at i:4607895 original size:21 final size:21
Alignment explanation
Indices: 4607871--4607929 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
4607861 TTGGAAAAAT
4607871 TGTATCAATACATTATGAATA
1 TGTATCAATACATTATGAATA
* **
4607892 TGTATCAATACATGA-CCATA
1 TGTATCAATACATTATGAATA
*
4607912 TGTATCTATACATT-TGAA
1 TGTATCAATACATTATGAA
4607930 ACAAAATGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
TGTATCAATACATTATGAATA
Found at i:4611917 original size:24 final size:25
Alignment explanation
Indices: 4611884--4611934 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
4611874 AGTTAAACAC
*
4611884 TTAAATATGGCGTGCAATAA-TTTT
1 TTAAACATGGCGTGCAATAACTTTT
*
4611908 TTAAACATGGCGTGTAATAACTTTT
1 TTAAACATGGCGTGCAATAACTTTT
4611933 TT
1 TT
4611935 TTAACATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (25 bp):
TTAAACATGGCGTGCAATAACTTTT
Found at i:4611940 original size:26 final size:24
Alignment explanation
Indices: 4611884--4611951 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 24
4611874 AGTTAAACAC
* *
4611884 TTAAATATGGCGTGCAATAATTTT
1 TTAAACATGGCGTGTAATAATTTT
4611908 TTAAACATGGCGTGTAATAACTTTTT
1 TTAAACATGGCGTGTAATAA--TTTT
* *
4611934 TTTAACATGACGTGTAAT
1 TTAAACATGGCGTGTAAT
4611952 TTGATATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 18 0.47
26 20 0.53
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (24 bp):
TTAAACATGGCGTGTAATAATTTT
Found at i:4615158 original size:792 final size:791
Alignment explanation
Indices: 4613623--4615204 Score: 2629
Period size: 792 Copynumber: 2.0 Consensus size: 791
4613613 CCGATTAATT
*
4613623 TTTTTCAATTTTGCTTCAAAGGTCATGATGACTTCATCTTGAATGAATATGTTTTTCAAGGGTCT
1 TTTTTCAATTTTGCTTCAAAGGTCATGATGACTTCATCTTGAATGAATATGTTCTTCAAGGGTCT
*
4613688 TGTGACTTGGATCTTGAATTAGCAATTTTGCTTCAAGGATTTATGGAAATTTGGAGAAGCTTTGA
66 TGTGACTTGGATCTTGAATTAGCAATTTTGCTTCAAGGATTTATGGAAATTTGGAGAAGATTTGA
*
4613753 TTCTTCAGATCTTGCTTCATGGATTTATTTGTAGAACTCTAAAAAGGCTTTGATCTTCGGATTTT
131 TTCTTCAGATCTTGCTTCATGGATTTACTTGTAGAACTCTAAAAAGGCTTTGATCTTCGGATTTT
4613818 TTTTCTTTGGGTATAACATTTTTCACATAGCATTCTAAAGTTAATTTTTTTCCACATAAAAGCTT
196 TTTTCTTTGGGTATAACATTTTTCACATAGCATTCTAAAGTTAATTTTTTTCCACATAAAAGCTT
* * * *
4613883 GTGTTAAATTTCTATTCTCGAAAGGGTAACAATTTTAAAGTTTTAGTTAGTTTTTTGTAAAACGA
261 GTGTTAAATTTCGATTCTCAAAAAGGTAACAATTTTAAAGTTTTAGTTAGTTTTTTGTAAAAAGA
*
4613948 CAATAAGAATTTTTTAAAATGTTTATATTTTTGGTTTGTTTAATTAAAAAAAATTCACTGATCCT
326 CAATAAGAATATTTTAAAATGTTTATATTTTTGGTTTGTTTAATTAAAAAAAATTCACTGATCCT
* *
4614013 CAAGAATCCTTATATTCTTTTTTACTGTGTCTCCTTCTTAGAGTATAATGCGCTAGATTTTCAAG
391 CAAGAATCCTTATATTCTTTCTTACTGTGTCTCCTTCTTAGAATATAATGCGCTAGATTTTCAAG
* * *
4614078 GTACGTCTATAAAAAATATGATTATGTATTTATAATAATTTCTTTTTTTGAAACTTATGTTATTG
456 GTACATCTATAAAAAATATGATTATGTATTTATAATAATTTCTTTTTTTGAAAATTATGTTATTA
* *
4614143 CTTCTATTACTTTTGAGGGAAATAATTTTTCCCTATTTTTGATACATCTTTTTTTCTAAATTTTA
521 CTTCTATTACTTTTGAGGGAAAGAATTTTTCCCTATTTTCGATACATCTTTTTTTCTAAATTTTA
* * * *
4614208 CACACATAAGTATACGTATTAAATAAGTAATATAGACAGTAAGCCAAAAATCATATCTCATAAAA
586 CACACATAAGTATACGTATTAAACAAATAATATAGACAGTAAGCCAAAAATCATATCCCACAAAA
4614273 TTTTGTTCTTAAATGTTCTCTAAGTATTAAATTATAACAAACTAATCTTATTTAAGTAACTTAAT
651 TTTTGTTCTTAAATGTTCTCTAAGTATTAAATTATAACAAACTAATCTTATTTAAGTAACTTAAT
*
4614338 TTTTTAAAAAATTAATTAAAACTAAATTAAAAAAAACTCTAAATTAATCAATAAAAACTAAAAAT
716 TTTTTAAAAAATTAATCAAAACTAAATTAAAAAAAA--CTAAATTAATCAATAAAAACTAAAAAT
4614403 TCACTTAAGAAAA
779 TCACTTAAGAAAA
* *
4614416 TTTTT-AATTTTGCTTCAAATGTCATGATGACTTCATCTTGAATGAATATGTTCTTCAAGGGTTT
1 TTTTTCAATTTTGCTTCAAAGGTCATGATGACTTCATCTTGAATGAATATGTTCTTCAAGGGTCT
*
4614480 TGTGACTT-GATCTTGAATTAGCAATTTTGCTTCAAGGATTTGTGGAAATTTGGAGAAGATTTGA
66 TGTGACTTGGATCTTGAATTAGCAATTTTGCTTCAAGGATTTATGGAAATTTGGAGAAGATTTGA
* *
4614544 TTCTTTAGATCTTGCTTCATGGATTTGCTTGTAGAACTCTAAAGAA-GCTTTGATCTTCGGATTT
131 TTCTTCAGATCTTGCTTCATGGATTTACTTGTAGAACTCTAAA-AAGGCTTTGATCTTCGGATTT
* *
4614608 TTTTTCTTTTGGTATAACTTTTTTTCACATAGCATTCTAAAGTTAA-TTTTTTCCACATAAAAGC
195 TTTTTCTTTGGGTATAAC-ATTTTTCACATAGCATTCTAAAGTTAATTTTTTTCCACATAAAAGC
* *
4614672 TTGTGTTAAATTTCGATTCTCAAAAAGGTAATAATTTTAAATTTTTAGTTAGTTTTTTGTAAAAA
259 TTGTGTTAAATTTCGATTCTCAAAAAGGTAACAATTTTAAAGTTTTAGTTAGTTTTTTGTAAAAA
4614737 GACAATAAGAATATTTTAAAATGTTTATATTTTTGGTTTGTTTAATTAAAAAAAAATTCACTGAT
324 GACAATAAGAATATTTTAAAATGTTTATATTTTTGGTTTGTTTAATT-AAAAAAAATTCACTGAT
* * * *
4614802 CCTCGAGAATCCTTATCTTCTTTCTTACTGTGTCTCTTTCTTAGAATATAATGCTCTAGATTTTC
388 CCTCAAGAATCCTTATATTCTTTCTTACTGTGTCTCCTTCTTAGAATATAATGCGCTAGATTTTC
*
4614867 AAGGTACATCTATAAAAAAATATTATTATGTATTTATAATAATTTCTTTTTTTGAAAATTATGTT
453 AAGGTACATCTAT-AAAAAATATGATTATGTATTTATAATAATTTCTTTTTTTGAAAATTATGTT
* * *
4614932 ATTACTTCTATTACTTTTGAGGGAAAGAATTTTTTCCTATTTTCGGTACATC-TTTTTTGTAAAT
517 ATTACTTCTATTACTTTTGAGGGAAAGAATTTTTCCCTATTTTCGATACATCTTTTTTTCTAAAT
*** * *
4614996 TTTGTGCACGTAAGTATACGTATTAAACAAATAATATAGACAGTAAGCCTAAAATCATATCCCAC
582 TTTACACACATAAGTATACGTATTAAACAAATAATATAGACAGTAAGCCAAAAATCATATCCCAC
4615061 AAAATTTTGTTCTTAAATGTTCAT-TAAGTATTAAAATTATAACAAACTAATCTTATTTAAGTAA
647 AAAATTTTGTTCTTAAATGTTC-TCTAAGTATT-AAATTATAACAAACTAATCTTATTTAAGTAA
* * * *
4615125 CTTAATTTTTTAGAAAA-TAATCAAAAGTAAATTAAAAAAAACTAAATTAATTAATAGAAACTAA
710 CTTAATTTTTTAAAAAATTAATCAAAACTAAATTAAAAAAAACTAAATTAATCAATAAAAACTAA
4615189 AAATTCACTTAAGAAA
775 AAATTCACTTAAGAAA
4615205 GACAATTAGA
Statistics
Matches: 737, Mismatches: 46, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
790 37 0.05
791 252 0.34
792 299 0.41
793 149 0.20
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (791 bp):
TTTTTCAATTTTGCTTCAAAGGTCATGATGACTTCATCTTGAATGAATATGTTCTTCAAGGGTCT
TGTGACTTGGATCTTGAATTAGCAATTTTGCTTCAAGGATTTATGGAAATTTGGAGAAGATTTGA
TTCTTCAGATCTTGCTTCATGGATTTACTTGTAGAACTCTAAAAAGGCTTTGATCTTCGGATTTT
TTTTCTTTGGGTATAACATTTTTCACATAGCATTCTAAAGTTAATTTTTTTCCACATAAAAGCTT
GTGTTAAATTTCGATTCTCAAAAAGGTAACAATTTTAAAGTTTTAGTTAGTTTTTTGTAAAAAGA
CAATAAGAATATTTTAAAATGTTTATATTTTTGGTTTGTTTAATTAAAAAAAATTCACTGATCCT
CAAGAATCCTTATATTCTTTCTTACTGTGTCTCCTTCTTAGAATATAATGCGCTAGATTTTCAAG
GTACATCTATAAAAAATATGATTATGTATTTATAATAATTTCTTTTTTTGAAAATTATGTTATTA
CTTCTATTACTTTTGAGGGAAAGAATTTTTCCCTATTTTCGATACATCTTTTTTTCTAAATTTTA
CACACATAAGTATACGTATTAAACAAATAATATAGACAGTAAGCCAAAAATCATATCCCACAAAA
TTTTGTTCTTAAATGTTCTCTAAGTATTAAATTATAACAAACTAATCTTATTTAAGTAACTTAAT
TTTTTAAAAAATTAATCAAAACTAAATTAAAAAAAACTAAATTAATCAATAAAAACTAAAAATTC
ACTTAAGAAAA
Found at i:4620631 original size:69 final size:67
Alignment explanation
Indices: 4620515--4620666 Score: 205
Period size: 69 Copynumber: 2.2 Consensus size: 67
4620505 AGGGTCATAA
* * *
4620515 TGACTTGATCTTCAATAAATATGTTCTTCCAGGGTCTTGTGACTTGATCTTGACTTCAAAGGCCT
1 TGACTTGATCTTGAATAAATATGTTCTTCAAGGGTCTGGTGACTTGATCTTGACTTC-AAGG-CT
4620580 CGTG
64 CGTG
* * * * * *
4620584 TGACTTGATCTAGAATGAATATGTTCTTCAAGGGTCTGGTGATTTGATCTTGACTTCATGGGTCT
1 TGACTTGATCTTGAATAAATATGTTCTTCAAGGGTCTGGTGACTTGATCTTGACTTCAAGGCTCG
4620649 TG
66 TG
4620651 TGACTTGATCTTGAAT
1 TGACTTGATCTTGAAT
4620667 TAGAGAATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 19 0.26
68 3 0.04
69 51 0.70
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (67 bp):
TGACTTGATCTTGAATAAATATGTTCTTCAAGGGTCTGGTGACTTGATCTTGACTTCAAGGCTCG
TG
Found at i:4620653 original size:28 final size:28
Alignment explanation
Indices: 4620609--4620664 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4620599 TGAATATGTT
*
4620609 CTTCAAGGGTCTGGTGATTTGATCTTGA
1 CTTCAAGGGTCTGGTGACTTGATCTTGA
* *
4620637 CTTCATGGGTCTTGTGACTTGATCTTGA
1 CTTCAAGGGTCTGGTGACTTGATCTTGA
4620665 ATTAGAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (28 bp):
CTTCAAGGGTCTGGTGACTTGATCTTGA
Found at i:4620769 original size:52 final size:52
Alignment explanation
Indices: 4620706--4620916 Score: 263
Period size: 52 Copynumber: 4.1 Consensus size: 52
4620696 TCTAGAGTAA
* * *
4620706 CTTTGATTCTTCATATCTTCTTTCTTGGATTTGTTTGTGGAACTATGGAGAGG
1 CTTTGATTCTTCATATCTT-TTTCTTGGATTTATTTGTGGAACTTTAGAGAGG
4620759 CTTTGA-TCTTCATATCTTTATTCTTGGATTTATTTGTGGAACTTTAGAGAGG
1 CTTTGATTCTTCATATCTTT-TTCTTGGATTTATTTGTGGAACTTTAGAGAGG
* * *
4620811 TTTTGA-TCTTCAGATCTGTTTTCTTGGATTCATTTGTGGAACTTTAGAGAGG
1 CTTTGATTCTTCATATCT-TTTTCTTGGATTTATTTGTGGAACTTTAGAGAGG
* * *
4620863 CTTTGATTTTTCATATCTTCCTTCTTGGATTT-GTT-T--AACTTTAGAGAGG
1 CTTTGATTCTTCATATCTT-TTTCTTGGATTTATTTGTGGAACTTTAGAGAGG
4620912 CTTTG
1 CTTTG
4620917 GATCTTCTGA
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
49 18 0.13
51 2 0.01
52 95 0.67
53 27 0.19
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.48
Consensus pattern (52 bp):
CTTTGATTCTTCATATCTTTTTCTTGGATTTATTTGTGGAACTTTAGAGAGG
Found at i:4623561 original size:26 final size:27
Alignment explanation
Indices: 4623530--4623586 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
4623520 TGCATAAAAA
* *
4623530 TGTTATATGTCATGGTT-AAAAAAAT-T
1 TGTTATAGGTCAT-ATTGAAAAAAATAT
4623556 TGTTATAGGTCATATTGAAAAAAATAT
1 TGTTATAGGTCATATTGAAAAAAATAT
4623583 TGTT
1 TGTT
4623587 GTTACACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 20 0.74
27 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.42
Consensus pattern (27 bp):
TGTTATAGGTCATATTGAAAAAAATAT
Found at i:4623628 original size:29 final size:29
Alignment explanation
Indices: 4623573--4623636 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
4623563 GGTCATATTG
* *
4623573 AAAAAAATATTGTTGTTACACATTATGTT
1 AAAAAAATATTATTGTTACACACTATGTT
**
4623602 AAAAAAATATTATTGTTACATGCTATGTT
1 AAAAAAATATTATTGTTACACACTATGTT
*
4623631 TAAAAA
1 AAAAAA
4623637 CTTTTTTTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (29 bp):
AAAAAAATATTATTGTTACACACTATGTT
Found at i:4630674 original size:21 final size:20
Alignment explanation
Indices: 4630640--4630681 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4630630 TAATTTAAAA
4630640 TAAAATAATATAAAATTTAAC
1 TAAAATAATAT-AAATTTAAC
4630661 TAAAATAACT-TAAA-TTAAC
1 TAAAATAA-TATAAATTTAAC
4630680 TA
1 TA
4630682 CTCAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 9 0.45
22 1 0.05
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAATATAAATTTAAC
Found at i:4639314 original size:16 final size:16
Alignment explanation
Indices: 4639295--4639328 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4639285 TGTTATGTGG
* *
4639295 TTTTTATTTTTAATGA
1 TTTTAATTTTTAAAGA
4639311 TTTTAATTTTTAAAGA
1 TTTTAATTTTTAAAGA
4639327 TT
1 TT
4639329 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTAATTTTTAAAGA
Found at i:4652617 original size:16 final size:17
Alignment explanation
Indices: 4652596--4652628 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4652586 TGACCCTCAA
4652596 AATAATT-TTTTTATTT
1 AATAATTATTTTTATTT
4652612 AATAATTATTTTTATTT
1 AATAATTATTTTTATTT
4652629 CTTAAACCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATAATTATTTTTATTT
Found at i:4663080 original size:2 final size:2
Alignment explanation
Indices: 4663073--4663098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4663063 GCTAAAGGAC
4663073 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4663099 GGCATCTTTA
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):
AT
Found at i:4666624 original size:130 final size:130
Alignment explanation
Indices: 4666316--4666704 Score: 532
Period size: 130 Copynumber: 3.0 Consensus size: 130
4666306 AACAAAAGTT
* * ** *
4666316 TGCATGTCCTTTTTTGCTTCTCATATTTTACTTGTCGAAAGCATTTACTTTGCACGTGTACTCTG
1 TGCATGTCCTTTTTTCCTTCTCATA-TTTACCTGAGGAAAGCATTTACTTTGCATGTGTACTCTG
* * * * *
4666381 CTTCTAAAAGATTATGACTTGGTGTGGTTTTAAAATTAATTGTACTTTAAGAAGCTGAATTTAGG
65 CTTCTAGAAGATTATGACATGGTGTTGTTTTAAAATTAATTGTACATTAAGAAGCTGAATTTAAG
4666446 C
130 C
* * *
4666447 TGCATGTCCTTTTCTCCTTCTCATATATTACCCGCGGAAAGCATTTACTTTGCATGTGTACTCTG
1 TGCATGTCCTTTTTTCCTTCTCATAT-TTACCTGAGGAAAGCATTTACTTTGCATGTGTACTCTG
* *
4666512 CTTCTAGAAGATTATGACATGGTGTTGTTTT-AAATTAATTGTAGATTATGAAGCTGAATTTAAG
65 CTTCTAGAAGATTATGACATGGTGTTGTTTTAAAATTAATTGTACATTAAGAAGCTGAATTTAAG
4666576 C
130 C
* *
4666577 TGCATGTCGTTTTTTCCTTCTCATATTTAACCTGAGGAAAACATTTACTTTGCATGTGTACTCTG
1 TGCATGTCCTTTTTTCCTTCTCATATTT-ACCTGAGGAAAGCATTTACTTTGCATGTGTACTCTG
* * *
4666642 CTTCT-GAAAGATTCTGACATGGT-TTGGTTTTAAAATAAATTATACATTAAGAAGCTGAATTTA
65 CTTCTAG-AAGATTATGACATGGTGTT-GTTTTAAAATTAATTGTACATTAAGAAGCTGAATTTA
4666705 GGTTCTGAGC
Statistics
Matches: 229, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
129 5 0.02
130 113 0.49
131 111 0.48
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (130 bp):
TGCATGTCCTTTTTTCCTTCTCATATTTACCTGAGGAAAGCATTTACTTTGCATGTGTACTCTGC
TTCTAGAAGATTATGACATGGTGTTGTTTTAAAATTAATTGTACATTAAGAAGCTGAATTTAAGC
Found at i:4676893 original size:45 final size:45
Alignment explanation
Indices: 4676840--4676939 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
4676830 GTATTGCTAT
* *
4676840 GGTGAGGGTTAAGGTTAGCGTTTCGATTAGGAATTGGGGA-TTTA
1 GGTGAGGGTTAAGATTAGCGTTTCAATTAGGAATTGGGGATTTTA
* *
4676884 GGATGAGGGTTAAGATTAGGGTTTCAATTAGGATTTGGGGATTTTA
1 GG-TGAGGGTTAAGATTAGCGTTTCAATTAGGAATTGGGGATTTTA
4676930 GGTGAGGGTT
1 GGTGAGGGTT
4676940 TACGGTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.04
45 42 0.84
46 6 0.12
ACGTcount: A:0.23, C:0.03, G:0.39, T:0.35
Consensus pattern (45 bp):
GGTGAGGGTTAAGATTAGCGTTTCAATTAGGAATTGGGGATTTTA
Found at i:4681142 original size:21 final size:21
Alignment explanation
Indices: 4681118--4681196 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
4681108 CCTTGTCTAA
*
4681118 GTCTTCATCAAAAGTTGTTGG
1 GTCTTCATCAAGAGTTGTTGG
* * *
4681139 GTCTTCATTAAGAGCTCTTGG
1 GTCTTCATCAAGAGTTGTTGG
4681160 GT-TTGCATCAAGAGTTGTTAGTGG
1 GTCTT-CATCAAGAGTTG-T--TGG
*
4681184 GTCTACATCAAGA
1 GTCTTCATCAAGA
4681197 ACATCAAGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.04
21 28 0.62
22 1 0.02
24 13 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
GTCTTCATCAAGAGTTGTTGG
Found at i:4687388 original size:29 final size:29
Alignment explanation
Indices: 4687355--4687423 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
4687345 CAATTAAGGG
4687355 CCAAACGTTTTAATTGTAACAATCAAAGA
1 CCAAACGTTTTAATTGTAACAATCAAAGA
*
4687384 CCAAACGTTTTAATTGTAACAATCAAGGA
1 CCAAACGTTTTAATTGTAACAATCAAAGA
4687413 CCAAACGTTTT
1 CCAAACGTTTT
4687424 CGATTTCTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (29 bp):
CCAAACGTTTTAATTGTAACAATCAAAGA
Found at i:4687528 original size:27 final size:27
Alignment explanation
Indices: 4687497--4687601 Score: 120
Period size: 27 Copynumber: 3.9 Consensus size: 27
4687487 AGTTGCATTG
* *
4687497 AAAATATAGTTGGTACACGCCATTTTA
1 AAAATATAGTTGTTACACGTCATTTTA
* * *
4687524 AAAATTTAATTGTTACACGTCATATTGA
1 AAAATATAGTTGTTACACGTCAT-TTTA
* *
4687552 AAAATATAGTTATTACACGTCATGTTA
1 AAAATATAGTTGTTACACGTCATTTTA
* *
4687579 AAAATTTAGTTATTACACGTCAT
1 AAAATATAGTTGTTACACGTCAT
4687602 AATAAAAAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
27 43 0.65
28 23 0.35
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (27 bp):
AAAATATAGTTGTTACACGTCATTTTA
Found at i:4687559 original size:55 final size:54
Alignment explanation
Indices: 4687493--4687602 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
4687483 AAAAAGTTGC
* * *
4687493 ATTGAAAATATAGTTGGTACACGCCATTTTAAAAATTTAATTGTTACACGTCAT
1 ATTGAAAATATAGTTAGTACACGCCATGTTAAAAATTTAATTATTACACGTCAT
* * *
4687547 ATTGAAAAATATAGTTATTACACGTCATGTTAAAAATTTAGTTATTACACGTCAT
1 ATTG-AAAATATAGTTAGTACACGCCATGTTAAAAATTTAATTATTACACGTCAT
4687602 A
1 A
4687603 ATAAAAAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 4 0.08
55 45 0.92
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (54 bp):
ATTGAAAATATAGTTAGTACACGCCATGTTAAAAATTTAATTATTACACGTCAT
Found at i:4687607 original size:27 final size:27
Alignment explanation
Indices: 4687510--4687609 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
4687500 ATATAGTTGG
* * * *
4687510 TACACGCCATTTTAAAAATTTAATTGT
1 TACACGTCATATTAAAAATTTAGTTAT
*
4687537 TACACGTCATATTGAAAAATATAGTTAT
1 TACACGTCATATT-AAAAATTTAGTTAT
*
4687565 TACACGTCATGTTAAAAATTTAGTTAT
1 TACACGTCATATTAAAAATTTAGTTAT
*
4687592 TACACGTCATAATAAAAA
1 TACACGTCATATTAAAAA
4687610 AGTTGTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 40 0.63
28 23 0.37
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (27 bp):
TACACGTCATATTAAAAATTTAGTTAT
Found at i:4721149 original size:4 final size:4
Alignment explanation
Indices: 4721140--4721164 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4721130 TAAAGAACAA
4721140 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
4721165 GAACAGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4723891 original size:6 final size:6
Alignment explanation
Indices: 4723880--4723910 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4723870 CAAAGTGACA
4723880 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC T
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC T
4723911 GCTAGCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCCTC
Found at i:4724038 original size:6 final size:6
Alignment explanation
Indices: 4724027--4724054 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4724017 AGCCTACTGA
4724027 CTTGAG CTTGAG CTTGAG CTTGAG CTTG
1 CTTGAG CTTGAG CTTGAG CTTGAG CTTG
4724055 TTCCCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (6 bp):
CTTGAG
Found at i:4729036 original size:21 final size:22
Alignment explanation
Indices: 4729001--4729041 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4728991 TTTTTAATGT
**
4729001 TGAATTTTTCTAAAA-ATTTCC
1 TGAATTTTTAGAAAACATTTCC
4729022 TGAATTTTTAGAAAACATTT
1 TGAATTTTTAGAAAACATTT
4729042 ATTTTTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (22 bp):
TGAATTTTTAGAAAACATTTCC
Found at i:4729735 original size:13 final size:14
Alignment explanation
Indices: 4729702--4729739 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4729692 CTGACCAGTT
*
4729702 TAAAGAGTAAAGTA
1 TAAATAGTAAAGTA
*
4729716 GAAATAGTAAAG-A
1 TAAATAGTAAAGTA
4729729 TAAATAGTAAA
1 TAAATAGTAAA
4729740 AAAAAGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (14 bp):
TAAATAGTAAAGTA
Found at i:4734290 original size:1 final size:1
Alignment explanation
Indices: 4734286--4734311 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4734276 GTTTTTGTTT
4734286 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
4734312 AGGTTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4735523 original size:17 final size:17
Alignment explanation
Indices: 4735503--4735535 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4735493 TCATTTATGT
4735503 GTTTTCATTTT-TGTTTA
1 GTTTTC-TTTTGTGTTTA
4735520 GTTTTCTTTTGTGTTT
1 GTTTTCTTTTGTGTTT
4735536 TTGTTCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.73
Consensus pattern (17 bp):
GTTTTCTTTTGTGTTTA
Found at i:4740643 original size:21 final size:20
Alignment explanation
Indices: 4740614--4740652 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
4740604 CAAAATAATA
4740614 TAAATTAAACTAAACTAACT
1 TAAATTAAACTAAACTAACT
4740634 TAAACTTAAACTAAACTAA
1 TAAA-TTAAACTAAACTAA
4740653 TCAACATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAATTAAACTAAACTAACT
Found at i:4744401 original size:17 final size:17
Alignment explanation
Indices: 4744372--4744404 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4744362 TTGTTTTTAG
4744372 TTTTACTTTAATTTCAA
1 TTTTACTTTAATTTCAA
4744389 TTTT-CTTTAAATTTCA
1 TTTTACTTT-AATTTCA
4744405 GTATCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTACTTTAATTTCAA
Found at i:4750919 original size:21 final size:22
Alignment explanation
Indices: 4750886--4750929 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4750876 AAATGACTAA
4750886 TTTAAGTTATTTT-TGTTAAAT
1 TTTAAGTTATTTTGTGTTAAAT
* * *
4750907 TTTATGTTGTTTTGTTTTAAAT
1 TTTAAGTTATTTTGTGTTAAAT
4750929 T
1 T
4750930 ACTTTAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (22 bp):
TTTAAGTTATTTTGTGTTAAAT
Found at i:4754661 original size:28 final size:28
Alignment explanation
Indices: 4754621--4754686 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
4754611 CGCGTATAGG
*
4754621 ACATGCACATAACGTGGACACATGTAGA
1 ACATGCACATAACATGGACACATGTAGA
* * *
4754649 ACATGCATATAACATGGACGCATGTAGG
1 ACATGCACATAACATGGACACATGTAGA
*
4754677 ACGTGCACAT
1 ACATGCACAT
4754687 GTAACAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (28 bp):
ACATGCACATAACATGGACACATGTAGA
Found at i:4754816 original size:55 final size:53
Alignment explanation
Indices: 4754749--4754866 Score: 128
Period size: 55 Copynumber: 2.2 Consensus size: 53
4754739 ATAATTACAT
* * * * *
4754749 TTTTCAATATAGCACACAACAAGTACCTTTTTCAACATGGCATGTGATAACTAAA
1 TTTTCAACATAGCACACAACAAGTACATTTTTCAACATGG--GGTAACAACTAAA
*** * *
4754804 TTTTCAACATAGCATGTAACAATTACATTTTTCAATATGGGGTAACAACTAAA
1 TTTTCAACATAGCACACAACAAGTACATTTTTCAACATGGGGTAACAACTAAA
4754857 TTTTCAACAT
1 TTTTCAACAT
4754867 GGCGTGTAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 20 0.38
55 33 0.62
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (53 bp):
TTTTCAACATAGCACACAACAAGTACATTTTTCAACATGGGGTAACAACTAAA
Found at i:4754833 original size:27 final size:26
Alignment explanation
Indices: 4754777--4755057 Score: 188
Period size: 27 Copynumber: 10.4 Consensus size: 26
4754767 ACAAGTACCT
* *
4754777 TTTTCAACATGGCATGTGATAACTAAA
1 TTTTCAACAT-GCATGTAACAACTAAA
* *
4754804 TTTTCAACATAGCATGTAACAATTACAT
1 TTTTCAACAT-GCATGTAACAACTA-AA
* **
4754832 TTTTCAATATG-GGGTAACAACTAAA
1 TTTTCAACATGCATGTAACAACTAAA
* *
4754857 TTTTCAACATGGCGTGTAACAATTAAA
1 TTTTCAACAT-GCATGTAACAACTAAA
* * *
4754884 TCTTCACCATGTCATGTAACAACTATAT
1 TTTTCAACATG-CATGTAACAACTA-AA
* * *
4754912 TTTTTAACATGACACGTAACAACAAAA
1 TTTTCAACATG-CATGTAACAACTAAA
*
4754939 GTTTCAACATAGCATGTAACAACTAAA
1 TTTTCAACAT-GCATGTAACAACTAAA
* * * *
4754966 TTTTCAAAATGACATGTAAAAATTACA
1 TTTTCAACATG-CATGTAACAACTAAA
* * * *
4754993 TTTTTAATATAACATGTAACAATTAAA
1 TTTTCAACAT-GCATGTAACAACTAAA
* * *
4755020 TTTTAGAACATGACGTGTAAC-ACTACAT
1 TTTT-CAACATG-CATGTAACAACTA-AA
4755048 TTTTCAACAT
1 TTTTCAACAT
4755058 AGCGTTAATA
Statistics
Matches: 197, Mismatches: 46, Indels: 22
0.74 0.17 0.08
Matches are distributed among these distances:
25 10 0.05
26 12 0.06
27 128 0.65
28 47 0.24
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (26 bp):
TTTTCAACATGCATGTAACAACTAAA
Found at i:4755030 original size:82 final size:80
Alignment explanation
Indices: 4754706--4755057 Score: 278
Period size: 82 Copynumber: 4.3 Consensus size: 80
4754696 TCATCATGAT
* * * * * **
4754706 ATGTAACAATTAAATTTTTTAACATGATATATAATAATTACATTTTTCAATATAGCACACAACAA
1 ATGTAACAACTAAA-TTTTCAACATGACATGTAACAATTACATTTTT-AATATA-CACGTAACAA
* **
4754771 GTACCTTTTTCAACATGGC
63 CTA-AATTTTCAACATGGC
* * ***
4754790 ATGTGATAACTAAATTTTCAACAT-AGCATGTAACAATTACATTTTTCAATAT-GGGGTAACAAC
1 ATGTAACAACTAAATTTTCAACATGA-CATGTAACAATTACATTTTT-AATATACACGTAACAAC
4754853 TAAATTTTCAACATGGC
64 TAAATTTTCAACATGGC
* * * * * * * *
4754870 GTGTAACAATTAAATCTTCACCATGTCATGTAACAACTATATTTTTTAACATGACACGTAACAAC
1 ATGTAACAACTAAATTTTCAACATGACATGTAACAATTACA-TTTTTAATAT-ACACGTAACAAC
* * *
4754935 AAAAGTTTCAACATAGC
64 TAAATTTTCAACATGGC
* * * *
4754952 ATGTAACAACTAAATTTTCAAAATGACATGTAAAAATTACATTTTTAATATAACATGTAACAATT
1 ATGTAACAACTAAATTTTCAACATGACATGTAACAATTACATTTTTAATAT-ACACGTAACAACT
* *
4755017 AAATTTTAGAACATGAC
65 AAATTTT-CAACATGGC
* *
4755034 GTGTAAC-ACTACATTTTTCAACAT
1 ATGTAACAACTA-AATTTTCAACAT
4755058 AGCGTTAATA
Statistics
Matches: 209, Mismatches: 52, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
80 48 0.23
81 41 0.20
82 77 0.37
83 32 0.15
84 11 0.05
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (80 bp):
ATGTAACAACTAAATTTTCAACATGACATGTAACAATTACATTTTTAATATACACGTAACAACTA
AATTTTCAACATGGC
Found at i:4755869 original size:31 final size:29
Alignment explanation
Indices: 4755827--4755897 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
4755817 TATCAACTTA
*
4755827 GCCCTTAATTGTAAGGAATTGAAAACGTTTG
1 GCCCTTAATTGTAA-CAATTG-AAACGTTTG
* *
4755858 GCCCTTGATTGTTACAATTGAAACGTTTG
1 GCCCTTAATTGTAACAATTGAAACGTTTG
4755887 GCCCTTAATTG
1 GCCCTTAATTG
4755898 CAAAAATGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
30 5 0.14
31 12 0.33
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (29 bp):
GCCCTTAATTGTAACAATTGAAACGTTTG
Found at i:4758212 original size:319 final size:320
Alignment explanation
Indices: 4757625--4758261 Score: 818
Period size: 319 Copynumber: 2.0 Consensus size: 320
4757615 ACTTCTACAT
* * ** ** *
4757625 TAACAATTGGTATCATAGCTTGGTCTCAAATTTTATAGGTCTAATTATTTTTGAGATATTCGTAG
1 TAACAATTGGTATCAAAGCTTCGTCTCAAATTTTATAGGTCTAACCACCTTTGAGATATTCATAG
* * * * * *
4757690 TAGAAGCTCACATCAATGAAAATAGAGGTAACGACAACAGTATTTGATGAAAGGCAATCGATCCA
66 TAGAAGCTCAAATCAACGAAAATAGAGGTAACAACAACAGTACTTAATGAAACGCAATCGATCCA
* * *
4757755 AACATCACCTCTCTTTTATAAATATTAACTATCCTTATTGGAAAAAGAGAATGAAAATATTTATT
131 AACACCACCTCTCTTTTATAAATACTAACTATCCTTATTGGAAAAAGAGAATGAAAACATTTATT
* * * *
4757820 CAATCTATGGATTTGGATATGTGGAATGTGATATTAGATGGCTTTAATGTCCCATGTAAATTAGC
196 CAATCTATGGATTTGGACATATGGAATGTGATAATAGATGGCTTTAATGTCCCATATAAATTAGC
* *
4757885 AAAAGGAAAATTAATGATTAAGGT-TAAAGATGAGTAGAGTGATACAGATAAGAAATTAGC
261 AAAAGGAAAATTAATGATTAA-GTCTAAAGATGAGTAGAGTGACAAAGATAAGAAATTAGC
* *
4757945 TAACAATTGGTATTAAAGCTTCGTCTCAAATTTTGTAGGTCTAACCACCTTTGAGATA-TCTATA
1 TAACAATTGGTATCAAAGCTTCGTCTCAAATTTTATAGGTCTAACCACCTTTGAGATATTC-ATA
* * * * *
4758009 GTAGAAGTTCAAATCGACGAAAA-AGTAGGTGACAACAATAGTACTTAATGAAACGCAATTGATC
65 GTAGAAGCTCAAATCAACGAAAATAG-AGGTAACAACAACAGTACTTAATGAAACGCAATCGATC
* ** ** * *
4758073 TAAAGGCCATTTCTC-TTTATAGATACTAACTATCCTTATT-GAAAAATGAGAATGAAAGCATTT
129 CAAACACCACCTCTCTTTTATAAATACTAACTATCCTTATTGGAAAAA-GAGAATGAAAACATTT
* *
4758136 ATTCAATCTATGGATTTGGACATAT-GACATGTGATAATAGATGGCTTTGATGTCTCATATAAAT
193 ATTCAATCTATGGATTTGGACATATGGA-ATGTGATAATAGATGGCTTTAATGTCCCATATAAAT
* * *
4758200 TAGTAGAAGGAAAATTAATGATTAAGTCTAGAGATGAGTAGAGTGACAAAGATAAGAAATTA
257 TAGCAAAAGGAAAATTAATGATTAAGTCTAAAGATGAGTAGAGTGACAAAGATAAGAAATTA
4758262 ATCCAAACAA
Statistics
Matches: 271, Mismatches: 41, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
318 10 0.04
319 150 0.55
320 111 0.41
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (320 bp):
TAACAATTGGTATCAAAGCTTCGTCTCAAATTTTATAGGTCTAACCACCTTTGAGATATTCATAG
TAGAAGCTCAAATCAACGAAAATAGAGGTAACAACAACAGTACTTAATGAAACGCAATCGATCCA
AACACCACCTCTCTTTTATAAATACTAACTATCCTTATTGGAAAAAGAGAATGAAAACATTTATT
CAATCTATGGATTTGGACATATGGAATGTGATAATAGATGGCTTTAATGTCCCATATAAATTAGC
AAAAGGAAAATTAATGATTAAGTCTAAAGATGAGTAGAGTGACAAAGATAAGAAATTAGC
Found at i:4769167 original size:14 final size:14
Alignment explanation
Indices: 4769148--4769211 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
4769138 GCATATACAC
4769148 ATGTATAAATATAT
1 ATGTATAAATATAT
* *
4769162 ATGTATACATATAC
1 ATGTATAAATATAT
**
4769176 ACATATAGACATATAT
1 ATGTATA-A-ATATAT
* *
4769192 ATGTATATATATGT
1 ATGTATAAATATAT
4769206 ATGTAT
1 ATGTAT
4769212 GCATAATGGG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 28 0.74
16 10 0.26
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (14 bp):
ATGTATAAATATAT
Found at i:4769168 original size:24 final size:25
Alignment explanation
Indices: 4769120--4769170 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
4769110 AAATTTTGCA
4769120 ACATTATAATATATATATGCATATAC
1 ACATTATAATATATATATG-ATATAC
4769146 ACATGTATAA-ATATATATG-TATAC
1 ACAT-TATAATATATATATGATATAC
4769170 A
1 A
4769171 TATACACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.25
26 13 0.54
27 5 0.21
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (25 bp):
ACATTATAATATATATATGATATAC
Found at i:4769173 original size:30 final size:30
Alignment explanation
Indices: 4769128--4769203 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
4769118 CAACATTATA
* * * *
4769128 ATATATATATGCATATACACATGTATAAAT
1 ATATATGTATACATATACACATATAGAAAT
*
4769158 ATATATGTATACATATACACATATAGACAT
1 ATATATGTATACATATACACATATAGAAAT
*
4769188 ATATATGTATATATAT
1 ATATATGTATACATAT
4769204 GTATGTATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
ATATATGTATACATATACACATATAGAAAT
Found at i:4771177 original size:52 final size:53
Alignment explanation
Indices: 4771119--4771225 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 53
4771109 GCATATGAAA
*
4771119 TAATATCTTGAAATTATGAGTCTTTC-TTTTTTGATTTATTTGGTAGATGTAT
1 TAATATCTTGAAATTATGAGTCTTTCTTTTTTTGATTTATTTGGTAAATGTAT
*
4771171 TAATATCTTGAAATTATGAGTCTTTCTTTTTTTGATTTATTTTGTAAATGTAT
1 TAATATCTTGAAATTATGAGTCTTTCTTTTTTTGATTTATTTGGTAAATGTAT
4771224 TA
1 TA
4771226 TTTGATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 26 0.50
53 26 0.50
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (53 bp):
TAATATCTTGAAATTATGAGTCTTTCTTTTTTTGATTTATTTGGTAAATGTAT
Found at i:4771357 original size:52 final size:52
Alignment explanation
Indices: 4771279--4771397 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
4771269 ATACTTACAC
4771279 TTAGTTTCA-ATGATTTGCTATGCAAGATTATATTTTATTTAATTCTAATATT
1 TTAGTTT-ATATGATTTGCTATGCAAGATTATATTTTATTTAATTCTAATATT
4771331 TTAGTTTATATGATTTGCTATGCAAGATTATATTTTATTTAATTCTAATATT
1 TTAGTTTATATGATTTGCTATGCAAGATTATATTTTATTTAATTCTAATATT
4771383 TTAGTTTATACTGAT
1 TTAGTTTATA-TGAT
4771398 AAGAAATGAG
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
51 1 0.02
52 60 0.92
53 4 0.06
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (52 bp):
TTAGTTTATATGATTTGCTATGCAAGATTATATTTTATTTAATTCTAATATT
Found at i:4771706 original size:38 final size:38
Alignment explanation
Indices: 4771662--4771754 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
4771652 TAAATTCATG
*
4771662 ATCAAGTCATAGACCCTTGAAGAAAATACTCATTCAAA
1 ATCAAGTTATAGACCCTTGAAGAAAATACTCATTCAAA
* * * *
4771700 ATCAAGTTATAGAACCTTGAGGAAAATATTCATTCAAG
1 ATCAAGTTATAGACCCTTGAAGAAAATACTCATTCAAA
*
4771738 ATCAAGTTGTAGACCCT
1 ATCAAGTTATAGACCCT
4771755 CCAGAATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (38 bp):
ATCAAGTTATAGACCCTTGAAGAAAATACTCATTCAAA
Found at i:4772229 original size:80 final size:80
Alignment explanation
Indices: 4772096--4772332 Score: 447
Period size: 80 Copynumber: 3.0 Consensus size: 80
4772086 ATTTTGATCG
4772096 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATGCTATTAA
1 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATGCTATTAA
4772161 ACGTTATTGGTATCC
66 ACGTTATTGGTATCC
*
4772176 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATTCTATTAA
1 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATGCTATTAA
4772241 ACGTTATTGGTATCC
66 ACGTTATTGGTATCC
* *
4772256 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTATCAAGTCTTTTTATATGGCAATGCTATTAA
1 TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATGCTATTAA
4772321 ACGTTATTGGTA
66 ACGTTATTGGTA
4772333 CCCCTCTTTT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 153 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (80 bp):
TAGAGTTAAAAGTTTCAGACCTCATGTAAGAATTGTCAAGCCTTTTTATATGGCAATGCTATTAA
ACGTTATTGGTATCC
Found at i:4775137 original size:3 final size:3
Alignment explanation
Indices: 4775129--4775155 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4775119 ACCTTTTCCG
4775129 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
4775156 CAATCGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:4795529 original size:12 final size:12
Alignment explanation
Indices: 4795512--4795551 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4795502 AAAAAGAGGA
4795512 AAGAAAGAAAGG
1 AAGAAAGAAAGG
4795524 AAGAAAGAAAGG
1 AAGAAAGAAAGG
*
4795536 AAG-GAGAAA-G
1 AAGAAAGAAAGG
4795546 AAGAAA
1 AAGAAA
4795552 AATATAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.16
11 6 0.24
12 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAAGG
Found at i:4804473 original size:66 final size:66
Alignment explanation
Indices: 4804353--4804481 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 66
4804343 TATTTCTTGC
* * *
4804353 AATCATGCTTATGCTTTAGTTGATCATAATATTCTTTTACGTGATTGCAATAAGTGAAAAATGTT
1 AATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATCGCAATAAGTGAAAAATGTT
4804418 T
66 T
* * *
4804419 AATCATGCTTATGCTTTCCTTGATCATAATATTCTTTTACATGATCGCATTAAGTGCAAAATG
1 AATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATCGCAATAAGTGAAAAATG
4804482 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (66 bp):
AATCATGCTTATGCTTTACTTGATCATAATATTCTTTTACATGATCGCAATAAGTGAAAAATGTT
T
Found at i:4805507 original size:15 final size:15
Alignment explanation
Indices: 4805469--4805510 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
4805459 AGTTTAGTTG
*
4805469 TTCTATGCTGAATGT
1 TTCTATGTTGAATGT
4805484 TT-T-TGTTGAATGT
1 TTCTATGTTGAATGT
4805497 TTCTATGTTGAATG
1 TTCTATGTTGAATG
4805511 GTGCTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TTCTATGTTGAATGT
Found at i:4810116 original size:11 final size:11
Alignment explanation
Indices: 4810095--4810125 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
4810085 ATAAATACGA
4810095 ATGGAATTATCG
1 ATGG-ATTATCG
4810107 ATGGATTATCG
1 ATGGATTATCG
4810118 ATGGATTA
1 ATGGATTA
4810126 CCAGTGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (11 bp):
ATGGATTATCG
Found at i:4811510 original size:17 final size:17
Alignment explanation
Indices: 4811490--4811522 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4811480 TTATTAATAA
4811490 AATAA-AACTCCTTATTG
1 AATAATAACT-CTTATTG
4811507 AATAATAACTCTTATT
1 AATAATAACTCTTATT
4811523 TTATTNNNNN
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:4811766 original size:31 final size:29
Alignment explanation
Indices: 4811664--4811769 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 29
4811654 TTAAGACAAC
*
4811664 TCTTGTCTGTAATTAAGACAAAAAATATTTT
1 TCTTGTCT-AAATTAAGA-AAAAAATATTTT
* ***
4811695 GTTTTGTCTAAATT--GAGGCAAATATGTTT
1 -TCTTGTCTAAATTAAGAAAAAAATAT-TTT
*
4811724 TCTTATCTAAATTAAGATAAAAAATATTTT
1 TCTTGTCTAAATTAAGA-AAAAAATATTTT
4811754 TCTTGTCTTAAATTAA
1 TCTTGTC-TAAATTAA
4811770 CACCAAACGT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
28 17 0.29
29 5 0.09
30 11 0.19
31 18 0.31
32 7 0.12
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGAAAAAAATATTTT
Found at i:4811794 original size:59 final size:59
Alignment explanation
Indices: 4811674--4811803 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 59
4811664 TCTTGTCTGT
* * ** * *
4811674 AATTAAGACAAAAAATATTTTGTTTTGTCTAAATTGAGGCAAATATGTTTTCTTATCTA
1 AATTAAGACAAAAAATATTTTGTCTTGTCTAAATTAAACCAAACATGTTTTCTTATATA
* * *
4811733 AATTAAGATAAAAAATATTTT-TCTTGTCTTAAATTAACACCAAACGTGTTTT-TTGTATA
1 AATTAAGACAAAAAATATTTTGTCTTGTC-TAAATTAA-ACCAAACATGTTTTCTTATATA
4811792 AATTAAGACAAA
1 AATTAAGACAAA
4811804 CATGTTACAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 6 0.10
59 43 0.73
60 10 0.17
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTTGTCTTGTCTAAATTAAACCAAACATGTTTTCTTATATA
Found at i:4814390 original size:15 final size:15
Alignment explanation
Indices: 4814370--4814398 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4814360 TGAATGAAAT
4814370 ATGAAAAAAATAAAA
1 ATGAAAAAAATAAAA
4814385 ATGAAAAAAATAAA
1 ATGAAAAAAATAAA
4814399 GTCATACAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
ATGAAAAAAATAAAA
Found at i:4819176 original size:16 final size:16
Alignment explanation
Indices: 4819155--4819186 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4819145 CTAAAATTTA
*
4819155 GATTTTGATTCTTTTG
1 GATTTTAATTCTTTTG
4819171 GATTTTAATTCTTTTG
1 GATTTTAATTCTTTTG
4819187 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.62
Consensus pattern (16 bp):
GATTTTAATTCTTTTG
Found at i:4819680 original size:19 final size:19
Alignment explanation
Indices: 4819638--4819683 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4819628 CTCTCAATTT
* **
4819638 ATTTTTGACTCTAATTTTC
1 ATTTTTGACTCAAAACTTC
4819657 ATTTTTGACTCAAAACTTC
1 ATTTTTGACTCAAAACTTC
*
4819676 TTTTTTGA
1 ATTTTTGA
4819684 TGATTAGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTTTTGACTCAAAACTTC
Found at i:4824840 original size:98 final size:98
Alignment explanation
Indices: 4824671--4824866 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
4824661 TTCTTGCATT
*
4824671 GCTTCTAGACTCCTATGAAGTATTTGTGAAATCTCTAATTTAAATGAAGGATACAATAACATTAA
1 GCTTCTAGACTCCTATGAAGTATTTGTGAAATCTCTAATTTAAATGAAAGATACAATAACATTAA
4824736 AACAAGCTTAAACTACGTTAATATGTCGTGAAG
66 AACAAGCTTAAACTACGTTAATATGTCGTGAAG
4824769 GCTTCTAGA-TCCCTATGAAGTATTTGTGAAATCTCTAATTTAAATGAAAGATACAATAACATTA
1 GCTTCTAGACT-CCTATGAAGTATTTGTGAAATCTCTAATTTAAATGAAAGATACAATAACATTA
* *
4824833 AAACAAGCTTAAACTATGTTAATATGTTGTGAAG
65 AAACAAGCTTAAACTACGTTAATATGTCGTGAAG
4824867 CATGAAAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 1 0.01
98 93 0.99
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (98 bp):
GCTTCTAGACTCCTATGAAGTATTTGTGAAATCTCTAATTTAAATGAAAGATACAATAACATTAA
AACAAGCTTAAACTACGTTAATATGTCGTGAAG
Found at i:4829257 original size:18 final size:18
Alignment explanation
Indices: 4829231--4829269 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4829221 TAGAAAAATT
4829231 CATGCTTTGATAAACAAA
1 CATGCTTTGATAAACAAA
*
4829249 CATGTTTTGATAAACAAA
1 CATGCTTTGATAAACAAA
4829267 CAT
1 CAT
4829270 TTGGCATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (18 bp):
CATGCTTTGATAAACAAA
Found at i:4832982 original size:39 final size:39
Alignment explanation
Indices: 4832935--4833014 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
4832925 TACTTTCTTG
*
4832935 CTTTGTTTTTGGCCT-TTCTTTTTCTAGAATAGTTGCTCT
1 CTTTGTTTTTGGCCTCTT-TGTTTCTAGAATAGTTGCTCT
*
4832974 CTTTGTTTTTGTCCTCTTTGTTTCTAGAATAGTTGCTCT
1 CTTTGTTTTTGGCCTCTTTGTTTCTAGAATAGTTGCTCT
4833013 CT
1 CT
4833015 ATCTCCTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.10, C:0.19, G:0.15, T:0.56
Consensus pattern (39 bp):
CTTTGTTTTTGGCCTCTTTGTTTCTAGAATAGTTGCTCT
Found at i:4840586 original size:49 final size:49
Alignment explanation
Indices: 4840527--4840626 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 49
4840517 AATGACAAAA
* * *
4840527 TTGATTGATCTATATCTAC-TTTGAGAATGAATGGAAAAT-TCTTTTAAAC
1 TTGATTGATCTAAATATACTTTTGA-AATGAATAGAAAATGT-TTTTAAAC
* *
4840576 TTGATTGATCTAAATATGCTTTTGAAATGATTAGAAAATGTTTTTAAAC
1 TTGATTGATCTAAATATACTTTTGAAATGAATAGAAAATGTTTTTAAAC
4840625 TT
1 TT
4840627 AAAGAAAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (49 bp):
TTGATTGATCTAAATATACTTTTGAAATGAATAGAAAATGTTTTTAAAC
Found at i:4841703 original size:57 final size:57
Alignment explanation
Indices: 4841615--4841732 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
4841605 TCTTGAGAAA
4841615 GCTCTCACCTTTTTATACTCAAATACCTATCAGCCTTGTTAGAGGTTTTAAGTTCAT
1 GCTCTCACCTTTTTATACTCAAATACCTATCAGCCTTGTTAGAGGTTTTAAGTTCAT
4841672 GCTCTCACCTTTTTATACTCAAATACCTATCAGCCTTGTTAGAGGTTTTAAGTTCAT
1 GCTCTCACCTTTTTATACTCAAATACCTATCAGCCTTGTTAGAGGTTTTAAGTTCAT
4841729 GCTC
1 GCTC
4841733 CTTCAGAATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.40
Consensus pattern (57 bp):
GCTCTCACCTTTTTATACTCAAATACCTATCAGCCTTGTTAGAGGTTTTAAGTTCAT
Found at i:4841872 original size:21 final size:21
Alignment explanation
Indices: 4841848--4841909 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
4841838 TTTTGGTTGT
4841848 AAAGGTTGTGCTTGATCTTAA
1 AAAGGTTGTGCTTGATCTTAA
* * *
4841869 AAAGGTAGTGACTTTA-GTT--
1 AAAGGTTGTG-CTTGATCTTAA
4841888 -AAGGTTGTGCTTGATCTTAA
1 AAAGGTTGTGCTTGATCTTAA
4841908 AA
1 AA
4841910 GGGCAGTGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 4 0.13
18 10 0.33
21 12 0.40
22 4 0.13
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (21 bp):
AAAGGTTGTGCTTGATCTTAA
Found at i:4841898 original size:39 final size:39
Alignment explanation
Indices: 4841849--4841951 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
4841839 TTTGGTTGTA
*
4841849 AAGGTTGTGCTTGATCTTAAAAAGGTAGTGACTTTAGTT
1 AAGGTTGTGCTTGATCTTAAAAAGGCAGTGACTTTAGTT
* *
4841888 AAGGTTGTGCTTGATCTTAAAAGGGCAGTGACTTTGGTT
1 AAGGTTGTGCTTGATCTTAAAAAGGCAGTGACTTTAGTT
* * * *
4841927 TAGGTAGTGTTTGATCCTTGAAAAG
1 AAGGTTGTGCTTGAT-CTTAAAAAG
4841952 TCATTTTGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 48 0.87
40 7 0.13
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (39 bp):
AAGGTTGTGCTTGATCTTAAAAAGGCAGTGACTTTAGTT
Found at i:4847228 original size:3 final size:3
Alignment explanation
Indices: 4847220--4847267 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
4847210 GGCTTACATA
4847220 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4847268 CTTCCACTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4853211 original size:28 final size:27
Alignment explanation
Indices: 4853171--4853304 Score: 133
Period size: 28 Copynumber: 4.8 Consensus size: 27
4853161 TGTTATAAAA
*
4853171 GTTATGCCTGATCCCTGAAAAGGCAATG
1 GTTATGCTTGATCCCTGAAAAGG-AATG
*
4853199 GTTATGCTTGATCCTTGAAAAGGGAATG
1 GTTATGCTTGATCCCTGAAAA-GGAATG
* * * *
4853227 ATTGTGCTTGATCCTTGAAAAGGTAGTG
1 GTTATGCTTGATCCCTGAAAAGG-AATG
* * **
4853255 GTTATGCTTGATCCCTAAAAAAGTGTGG
1 GTTATGCTTGATCCCTGAAAAGGAAT-G
*
4853283 GTTATGCTTGATCCATGAAAAG
1 GTTATGCTTGATCCCTGAAAAG
4853305 TAGGGCTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
27 4 0.04
28 83 0.93
29 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (27 bp):
GTTATGCTTGATCCCTGAAAAGGAATG
Found at i:4864612 original size:65 final size:65
Alignment explanation
Indices: 4864531--4864653 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
4864521 TACCTAGCAC
* * * *
4864531 TTTCACACAGTGTGAGGTAGCATTCCACACATGGTGATTGCATCTAGTATGATGGATGATAGTGT
1 TTTCACACAGTATGAGGTAACACTCCACACATGGTGATTACATCTAGTATGATGGATGATAGTGT
* *
4864596 TTTCACACAGTATGAGGTAACACTCCACACGTGGTGATTACGTCTAGTATGATGGATG
1 TTTCACACAGTATGAGGTAACACTCCACACATGGTGATTACATCTAGTATGATGGATG
4864654 GTAACATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (65 bp):
TTTCACACAGTATGAGGTAACACTCCACACATGGTGATTACATCTAGTATGATGGATGATAGTGT
Found at i:4864677 original size:65 final size:65
Alignment explanation
Indices: 4864534--4864696 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
4864524 CTAGCACTTT
* * * * * *** *
4864534 CACACAGTGTGAGGTAGCATTCCACACATGGTGATTGCATCTAGTATGATGGATGATAGTGTTTT
1 CACACAATATGAGGTAACATTCCACACGTGGTGATTACATCTAGTATGATGGATGATAACATTTC
* * * *
4864599 CACACAGTATGAGGTAACACTCCACACGTGGTGATTACGTCTAGTATGATGGATGGTAACATTTC
1 CACACAATATGAGGTAACATTCCACACGTGGTGATTACATCTAGTATGATGGATGATAACATTTC
* * *
4864664 CATACAATTTGAGGTAACATTCCAAACGTGGTG
1 CACACAATATGAGGTAACATTCCACACGTGGTG
4864697 CTAATGCACA
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 82 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (65 bp):
CACACAATATGAGGTAACATTCCACACGTGGTGATTACATCTAGTATGATGGATGATAACATTTC
Found at i:4872548 original size:36 final size:35
Alignment explanation
Indices: 4872449--4872550 Score: 89
Period size: 36 Copynumber: 2.8 Consensus size: 35
4872439 CTATCAATCT
* * *
4872449 TGCCTTTTCAATAGAGTCTGGCATAACCTTTACAACA
1 TGCCTTTT-AATAGA-TCAGGTATAACCTTCACAACA
* * * *
4872486 TCCCTTTTAACAAGATCA-ATCGTAACCTTCACAACA
1 TGCCTTTTAA-TAGATCAGGT-ATAACCTTCACAACA
4872522 TGCCTTTTAATAGGATCAGGTATAACCTT
1 TGCCTTTTAATA-GATCAGGTATAACCTT
4872551 TACCAAGACA
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
35 1 0.02
36 38 0.76
37 11 0.22
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (35 bp):
TGCCTTTTAATAGATCAGGTATAACCTTCACAACA
Found at i:4874841 original size:27 final size:27
Alignment explanation
Indices: 4874811--4874865 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4874801 TACTTGTAAG
*
4874811 TTTTATTTTCATAAAAATAATACATTA
1 TTTTATTGTCATAAAAATAATACATTA
* *
4874838 TTTTATTGTCATCAAAATAATATATTA
1 TTTTATTGTCATAAAAATAATACATTA
4874865 T
1 T
4874866 ATATATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTATTGTCATAAAAATAATACATTA
Found at i:4878465 original size:26 final size:27
Alignment explanation
Indices: 4878436--4878509 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 27
4878426 TTAAAAAATA
4878436 TTAATATTTATAATTAAAATATTAA-T
1 TTAATATTTATAATTAAAATATTAACT
4878462 TTAAT-TTT-TAAGTTTAAAATATTAACTT
1 TTAATATTTATAA--TTAAAATATTAAC-T
*
4878490 TTTATAATTTATAATTAAAA
1 TTAAT-ATTTATAATTAAAA
4878510 CTTAAACCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
24 3 0.08
25 3 0.08
26 17 0.43
28 5 0.12
29 6 0.15
30 3 0.08
31 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAATATTTATAATTAAAATATTAACT
Found at i:4878657 original size:24 final size:24
Alignment explanation
Indices: 4878630--4878677 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4878620 ATGAATAAAT
*
4878630 TGTTGTAAAATATAACTTTGAAAG
1 TGTTGTAAAATATAACTTTAAAAG
* *
4878654 TGTTGTGAAATATAATTTTAAAAG
1 TGTTGTAAAATATAACTTTAAAAG
4878678 AGAATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (24 bp):
TGTTGTAAAATATAACTTTAAAAG
Found at i:4889839 original size:60 final size:61
Alignment explanation
Indices: 4889672--4889841 Score: 218
Period size: 61 Copynumber: 2.8 Consensus size: 61
4889662 ATATTTGATT
*
4889672 GTAAAAGGGGGACTTGAAGCCCCCGATTTATATTGGGTGGCATGGGCAACTCCCAAGAGTAG
1 GTAAAAGGGGGACTTGAAG-CCCCGATTTATATTAGGTGGCATGGGCAACTCCCAAGAGTAG
* * * * * ** *
4889734 GAAAAAGGGGGACTTAAAGCCCCGATTCATATTAGGTGACGTGGGCAGTTCCCATGAGTAG
1 GTAAAAGGGGGACTTGAAGCCCCGATTTATATTAGGTGGCATGGGCAACTCCCAAGAGTAG
*
4889795 GTAAAA-GGGGACTTGAAGCCCCAATTTATA-TATGGTGGCATGGGCAA
1 GTAAAAGGGGGACTTGAAGCCCCGATTTATATTA-GGTGGCATGGGCAA
4889842 TTCTCACGAG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.02
60 32 0.35
61 40 0.44
62 17 0.19
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (61 bp):
GTAAAAGGGGGACTTGAAGCCCCGATTTATATTAGGTGGCATGGGCAACTCCCAAGAGTAG
Found at i:4889853 original size:60 final size:61
Alignment explanation
Indices: 4889672--4889853 Score: 224
Period size: 60 Copynumber: 3.0 Consensus size: 61
4889662 ATATTTGATT
* *
4889672 GTAAAAGGGGGACTTGAAGCCCCCGATTTATATTGGGTGGCATGGGCAACTCCCAAGAGTAG
1 GTAAAAGGGGGACTTGAAG-CCCCGATTTATATTAGGTGGCATGGGCAATTCCCAAGAGTAG
* * * * * * *
4889734 GAAAAAGGGGGACTTAAAGCCCCGATTCATATTAGGTGACGTGGGCAGTTCCCATGAGTAG
1 GTAAAAGGGGGACTTGAAGCCCCGATTTATATTAGGTGGCATGGGCAATTCCCAAGAGTAG
* * *
4889795 GTAAAA-GGGGACTTGAAGCCCCAATTTATA-TATGGTGGCATGGGCAATTCTCACGAGTA
1 GTAAAAGGGGGACTTGAAGCCCCGATTTATATTA-GGTGGCATGGGCAATTCCCAAGAGTA
4889854 AGTGATGGTG
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.02
60 42 0.42
61 40 0.40
62 17 0.17
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (61 bp):
GTAAAAGGGGGACTTGAAGCCCCGATTTATATTAGGTGGCATGGGCAATTCCCAAGAGTAG
Found at i:4903001 original size:42 final size:42
Alignment explanation
Indices: 4902954--4903067 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
4902944 AGGTAACCCC
*
4902954 TTTCAAAA-CTCTAG-GTACATTTTTCAAAACCTCCAAGAACAT
1 TTTCAAAACCT-TAGAGTACA-TCTTCAAAACCTCCAAGAACAT
* *
4902996 TTTCAAAACCTTCGAGTACATCTTCAAAACCTCCAAGTACAT
1 TTTCAAAACCTTAGAGTACATCTTCAAAACCTCCAAGAACAT
* * *
4903038 CTTCAAAATCTTCA-AGTACACTCTCCAAAA
1 TTTCAAAACCTT-AGAGTACA-TCTTCAAAA
4903068 TCTTCGAGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
42 46 0.75
43 15 0.25
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (42 bp):
TTTCAAAACCTTAGAGTACATCTTCAAAACCTCCAAGAACAT
Found at i:4903069 original size:22 final size:21
Alignment explanation
Indices: 4902976--4903072 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
4902966 AGGTACATTT
* * *
4902976 TTCAAAACCTCCAAGAACATT
1 TTCAAAACCTTCAAGTACATC
*
4902997 TTCAAAACCTTCGAGTACATC
1 TTCAAAACCTTCAAGTACATC
*
4903018 TTCAAAACCTCCAAGTACATC
1 TTCAAAACCTTCAAGTACATC
*
4903039 TTCAAAATCTTCAAGTACACTC
1 TTCAAAACCTTCAAGTACA-TC
* *
4903061 TCCAAAATCTTC
1 TTCAAAACCTTC
4903073 GAGTGCAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
21 53 0.80
22 13 0.20
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.28
Consensus pattern (21 bp):
TTCAAAACCTTCAAGTACATC
Found at i:4903450 original size:42 final size:42
Alignment explanation
Indices: 4903288--4903461 Score: 176
Period size: 42 Copynumber: 4.2 Consensus size: 42
4903278 AACATCATTC
* * * * *
4903288 AAAGTTGTGGAGCCTTTATGAAAAAAGCCATTTATTTTCTGT
1 AAAGTTGTCGAGCCTTTATGAGAAGAGCTATTTATTTTCTTT
*
4903330 AAAGTTG-CGAAGCCTTTATGAGAAGAGCCATTTATTTTCTTT
1 AAAGTTGTCG-AGCCTTTATGAGAAGAGCTATTTATTTTCTTT
* * * **
4903372 -AAGTTGTAGAGCCTTTATGAGAGGAGTTATAAATTTT-TGTT
1 AAAGTTGTCGAGCCTTTATGAGAAGAGCTATTTATTTTCT-TT
* *
4903413 AAAGTTGTTCG-GCCTTTATAAGATGAGCTATTTATTTTCTTT
1 AAAGTTG-TCGAGCCTTTATGAGAAGAGCTATTTATTTTCTTT
4903455 AAAGTTG
1 AAAGTTG
4903462 ATAAGCCTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
40 1 0.01
41 32 0.29
42 74 0.67
43 3 0.03
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (42 bp):
AAAGTTGTCGAGCCTTTATGAGAAGAGCTATTTATTTTCTTT
Found at i:4903470 original size:42 final size:41
Alignment explanation
Indices: 4903317--4903486 Score: 148
Period size: 42 Copynumber: 4.1 Consensus size: 41
4903307 GAAAAAAGCC
* * * * *
4903317 ATTTATTTTCTGTAAAGTTGCGAAGCCTTTATGAGAAGAGCC
1 ATTTATTTTCTTTAAAGTTG-TAAGCCTTTATAAGATGAGCT
* * *
4903359 ATTTATTTTCTTT-AAGTTGTAGAGCCTTTATGAGAGGAGTT
1 ATTTATTTTCTTTAAAGTTGTA-AGCCTTTATAAGATGAGCT
** **
4903400 ATAAATTTT-TGTTAAAGTTGTTCGGCCTTTATAAGATGAGCT
1 ATTTATTTTCT-TTAAAGTTG-TAAGCCTTTATAAGATGAGCT
* *
4903442 ATTTATTTTCTTTAAAGTTGATAAGCCTTTAAAATATGAG-T
1 ATTTATTTTCTTTAAAGTTG-TAAGCCTTTATAAGATGAGCT
4903483 ATTT
1 ATTT
4903487 TCAATTTGGT
Statistics
Matches: 104, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
40 2 0.02
41 36 0.35
42 64 0.62
43 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTTATTTTCTTTAAAGTTGTAAGCCTTTATAAGATGAGCT
Found at i:4906914 original size:16 final size:16
Alignment explanation
Indices: 4906890--4906920 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4906880 TTTTTATCAA
*
4906890 TTTATTTCTTTGTTTC
1 TTTAGTTCTTTGTTTC
4906906 TTTAGTTCTTTGTTT
1 TTTAGTTCTTTGTTT
4906921 AAAGATTTTA
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:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTAGTTCTTTGTTTC
Found at i:4907497 original size:18 final size:18
Alignment explanation
Indices: 4907466--4907506 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4907456 TAAACAAAAT
4907466 AAAAAATCATAAAATAAA
1 AAAAAATCATAAAATAAA
4907484 AGAAAAATCA-AAAATAAA
1 A-AAAAATCATAAAATAAA
4907502 AAAAA
1 AAAAA
4907507 TAAAAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAATCATAAAATAAA
Found at i:4908364 original size:13 final size:13
Alignment explanation
Indices: 4908346--4908370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4908336 GGGTTGAATT
4908346 TTATTTGCTTCAA
1 TTATTTGCTTCAA
4908359 TTATTTGCTTCA
1 TTATTTGCTTCA
4908371 TGGTTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATTTGCTTCAA
Found at i:4908902 original size:22 final size:23
Alignment explanation
Indices: 4908874--4908929 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
4908864 CTTAGAGTAG
4908874 AAATATAAAATACTCATGC-TTC
1 AAATATAAAATACTCATGCTTTC
* *
4908896 AAATAT--AATACTTATGCTTTT
1 AAATATAAAATACTCATGCTTTC
*
4908917 AAAAATAAAATAC
1 AAATATAAAATAC
4908930 AAAATGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.36
21 7 0.25
22 6 0.21
23 5 0.18
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (23 bp):
AAATATAAAATACTCATGCTTTC
Found at i:4909106 original size:20 final size:17
Alignment explanation
Indices: 4909081--4909125 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 17
4909071 CTTAAATCTC
4909081 AATATTTTTAATTCAAATAA
1 AATATTTTTAA-T-AAAT-A
4909101 AATATTTTTTAATAAATA
1 AATA-TTTTTAATAAATA
4909119 AATATTT
1 AATATTT
4909126 AGAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 4 0.17
20 5 0.21
21 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTTTAATAAATA
Found at i:4909123 original size:18 final size:21
Alignment explanation
Indices: 4909081--4909125 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
4909071 CTTAAATCTC
4909081 AATA-TTTTTAATTCAAATAA
1 AATATTTTTTAATTCAAATAA
4909101 AATATTTTTTAA-T-AAAT-A
1 AATATTTTTTAATTCAAATAA
4909119 AATATTT
1 AATATTT
4909126 AGAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 4 0.17
20 5 0.21
21 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTTTTAATTCAAATAA
Found at i:4912220 original size:38 final size:38
Alignment explanation
Indices: 4912111--4912208 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
4912101 TGTAATCTTA
* * * *
4912111 TGAGTGGTTATATCTTAGCCAATTGAAAAGGCAGTATT
1 TGAGTGGTTATACCTTAACCAATTGAAAAGGTAGTACT
* * *
4912149 TGAGTGGTTTTACTTTAACTAATTGAAAAGGTAGTACT
1 TGAGTGGTTATACCTTAACCAATTGAAAAGGTAGTACT
4912187 TGAGTGGTTATACCTTAACCAA
1 TGAGTGGTTATACCTTAACCAA
4912209 AGTAAAGGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (38 bp):
TGAGTGGTTATACCTTAACCAATTGAAAAGGTAGTACT
Found at i:4936785 original size:21 final size:21
Alignment explanation
Indices: 4936759--4936807 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4936749 GCATGGAGTG
4936759 AGGTGAATGTTGCACCAAATA
1 AGGTGAATGTTGCACCAAATA
4936780 AGGTGAATGTTGCACCAAATA
1 AGGTGAATGTTGCACCAAATA
4936801 AGGTGAA
1 AGGTGAA
4936808 CATTGAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (21 bp):
AGGTGAATGTTGCACCAAATA
Found at i:4936817 original size:21 final size:21
Alignment explanation
Indices: 4936772--4936817 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4936762 TGAATGTTGC
** *
4936772 ACCAAATAAGGTGAATGTTGC
1 ACCAAATAAGGTGAACATTGA
4936793 ACCAAATAAGGTGAACATTGA
1 ACCAAATAAGGTGAACATTGA
4936814 ACCA
1 ACCA
4936818 GATTAGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
ACCAAATAAGGTGAACATTGA
Found at i:4946127 original size:20 final size:17
Alignment explanation
Indices: 4946093--4946132 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4946083 TAAACCAATA
4946093 AATAAATAAATAAAAAT
1 AATAAATAAATAAAAAT
*
4946110 AATAATATAAATTAAAA-
1 AATAA-ATAAATAAAAAT
4946127 AATAAA
1 AATAAA
4946133 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAAATAAATAAAAAT
Found at i:4949963 original size:13 final size:13
Alignment explanation
Indices: 4949945--4949972 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4949935 TTTTTAATAC
4949945 TTTAATTTTTATT
1 TTTAATTTTTATT
4949958 TTTAATTTTTATT
1 TTTAATTTTTATT
4949971 TT
1 TT
4949973 CAAAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTAATTTTTATT
Found at i:4950230 original size:38 final size:39
Alignment explanation
Indices: 4950125--4950240 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 39
4950115 TGAGGCTACA
* * * * *
4950125 TAACTTTAAAGAAGGAACAAACTCTTCATCTAGAATGAGG
1 TAACTTTAAA-AATGAATAAACGCCTCATCTGGAATGAGG
* ** *
4950165 TAACTTTAAAAATGAATAAGCTTCTCATTTGGAATGAGG
1 TAACTTTAAAAATGAATAAACGCCTCATCTGGAATGAGG
* *
4950204 TCACTTTAAAAA-GAATAAACGCCTCATCTGAAATGAG
1 TAACTTTAAAAATGAATAAACGCCTCATCTGGAATGAG
4950241 ACTATATAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
38 20 0.32
39 33 0.52
40 10 0.16
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (39 bp):
TAACTTTAAAAATGAATAAACGCCTCATCTGGAATGAGG
Found at i:4950271 original size:41 final size:42
Alignment explanation
Indices: 4950206--4950297 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
4950196 GAATGAGGTC
*
4950206 ACTTTAAAAAGAATAAACGCCTCATCTGAAATGAGACTATATA
1 ACTTT-AAAAGAATAAACGCCTCATCTGAAATAAGACTATATA
** * * **
4950249 ACTTTAAAA-AATAAACTTCTCATTTGGAATAAGGTTATATA
1 ACTTTAAAAGAATAAACGCCTCATCTGAAATAAGACTATATA
4950290 ACTTTAAA
1 ACTTTAAA
4950298 GGAACTCCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 33 0.79
42 4 0.10
43 5 0.12
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.32
Consensus pattern (42 bp):
ACTTTAAAAGAATAAACGCCTCATCTGAAATAAGACTATATA
Found at i:4961178 original size:7 final size:7
Alignment explanation
Indices: 4961161--4961195 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
4961151 TCTTCTCTTT
4961161 TTTTTTCA
1 TTTTTT-A
4961169 TTTTTTA
1 TTTTTTA
4961176 TTTTTTA
1 TTTTTTA
*
4961183 TTTTATA
1 TTTTTTA
4961190 TTTTTT
1 TTTTTT
4961196 TCTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:4977247 original size:3 final size:3
Alignment explanation
Indices: 4977239--4977263 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4977229 TGGAGAGAGA
4977239 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
4977264 TATGTACATG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4985135 original size:2 final size:2
Alignment explanation
Indices: 4985092--4985125 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4985082 TTCCCTTTAG
4985092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4985126 AGTTTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4985480 original size:361 final size:353
Alignment explanation
Indices: 4984793--4985439 Score: 834
Period size: 346 Copynumber: 1.8 Consensus size: 353
4984783 ATCTCAAGCA
4984793 TAATTAATAATTTCATAAGTTACAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTTA
1 TAATTAATAATTTCATAAGTTACAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTTA
* *
4984858 TATTTAAAGTATATATATACTAAAAATATTTCAGTATATATATAATAGTAATTATATTTCTTATA
66 TATTTAAAATATATATATACTAAAAATATTTCAG-ATATATATAATAGTAA-TATATTCCTTATA
* * **
4984923 AATGAACCCAATGTATATAAAGTATATAGATTAAAAGACATTAATAGTCAATTAATAATCATTGC
129 AATGAAACC-A--TATAT-AAGTATATA-ATTAAAAGACATTAATAATCAATTAATAATCATAAC
* * *
4984988 TTTATTGATTGATTTAATTAACTATATGAATATGTCCTTAATTACATGAAATTCAAGAAAAAACT
189 TTTATTGATTAATTTAATTAACTATATGAATATGTCCTTAATTACATGAAATTAAAAAAAAAACT
* * * * *
4985053 AGGTTTCAAAACTATTCTAATCTCATAACTTCCCTTTAGATATATATATATATATATATATATAT
254 AGGTTTCAAAACTAATCTAATCTCACAACTTCCCTTTAGATATATATATATAAACAAATATATAT
4985118 ATATTATAAGTTTATATAAAAAAGGGTATCTATTG
319 ATATTATAAGTTTATATAAAAAAGGGTATCTATTG
* *
4985153 TAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAA-AAGAAAGTAAATATGTT
1 TAATTAATAATTTCATAAGTTACAA-TTTTGTAATGTTAACACAAAATAA-AAAGTAAATATGTT
* * *
4985217 TATA-TTAAAATACATATATATATTAAAAATATTTTA-ATATATGTAATAGT-A-ATATTCCTTA
64 TATATTTAAAAT--ATATATATACTAAAAATATTTCAGATATATATAATAGTAATATATTCCTTA
* * *
4985278 TAAAT-AAACC-TA-AT-A-TATAT-ATTAAAAGACATTACA-AATTAATTAATAATTATAATTT
127 TAAATGAAACCATATATAAGTATATAATTAAAAGACATTA-ATAATCAATTAATAATCATAACTT
* * *
4985336 TA-TGAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTATATGAAATTTAAAAAAAATAAC
191 TATTG-ATTAATTTAATTAACTATATGAATATGTCCTTAATTACATGAAA-TTAAAAAAAA-AAC
*
4985400 TAGGTTTCAAAACTAATCTAATCTCACAACTTCTCTTTAG
253 TAGGTTTCAAAACTAATCTAATCTCACAACTTCCCTTTAG
4985440 GTTTATATGT
Statistics
Matches: 256, Mismatches: 23, Indels: 28
0.83 0.07 0.09
Matches are distributed among these distances:
345 2 0.01
346 72 0.28
347 9 0.04
348 45 0.18
349 1 0.00
351 2 0.01
352 2 0.01
356 4 0.02
357 14 0.05
359 1 0.00
360 44 0.17
361 39 0.15
362 21 0.08
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (353 bp):
TAATTAATAATTTCATAAGTTACAATTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTTA
TATTTAAAATATATATATACTAAAAATATTTCAGATATATATAATAGTAATATATTCCTTATAAA
TGAAACCATATATAAGTATATAATTAAAAGACATTAATAATCAATTAATAATCATAACTTTATTG
ATTAATTTAATTAACTATATGAATATGTCCTTAATTACATGAAATTAAAAAAAAAACTAGGTTTC
AAAACTAATCTAATCTCACAACTTCCCTTTAGATATATATATATAAACAAATATATATATATTAT
AAGTTTATATAAAAAAGGGTATCTATTG
Found at i:4985607 original size:28 final size:28
Alignment explanation
Indices: 4985546--4985609 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
4985536 GTAAATATGT
4985546 TTATATTTAAAGTATATATATATACTAA
1 TTATATTTAAAGTATATATATATACTAA
** * *
4985574 AAATATTT-TAGTATATATATAATAGTAA
1 TTATATTTAAAGTATATATAT-ATACTAA
4985602 TTATATTT
1 TTATATTT
4985610 CTTATAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TTATATTTAAAGTATATATATATACTAA
Found at i:4985688 original size:345 final size:329
Alignment explanation
Indices: 4985115--4985812 Score: 893
Period size: 345 Copynumber: 2.1 Consensus size: 329
4985105 TATATATATA
* * * *
4985115 TATATATTATAAGTTTATATAAAAAAGGGTATCTATTGTAATTAATAATTTTATAAGTTATAATT
1 TATATATTATAAATTTATATAAAAAAGGATATATATTATAATTAATAATTTTATAAGTTATAATT
*
4985180 TTTGTAATGTTAACACAAAAAAGAAAGTAAATATGTTTATATTAAAATACATATATATATTAAAA
66 TTTGTAATGTTAACACAAAAAAGAAAGTAAATATGTTTATATTAAAATACATATATATACTAAAA
* *
4985245 ATATTTTAATATATGTAATAGTAATATTCCTTATAAATAAACCTAATATATATATTAAAAGACAT
131 ATATTTTAATATATATAATAGTAATATTCCTTATAAATAAACCTAATATAGATATTAAAAGACAT
* * *
4985310 TACAAATTAATTAATAATTATAATTTTATGAATTAATTTAATTAACTATAT-GAGTTTGTCCTTA
196 AACAAATTAATTAATAATCATAATTTCATGAATTAATTTAATTAACTATATGGA-TTTGTCCTTA
* * *
4985374 ATTAT-ATGAAATT-TAAAAAAAATAAC-TAGGTTTCAAAACTAATCTAATCTC-ACAACTTCTC
260 ATT-TCATGAAATTCAAAAAAAAAT-ACTTAGGTTCCAAAACTAATCTAATCTCAAAAAC-TCTC
4985435 TTTAGGTT
322 TTTAGGTT
*
4985443 TATATGTTATAAATTTATATAAACAAAGGTATATATATTATAATTAATAATTTTATAAGTTATAA
1 TATATATTATAAATTTATATAAA-AAAGG-ATATATATTATAATTAATAATTTTATAAGTTATAA
* * *
4985508 TTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTTTATATTTAAAGTATATATATATACTA
64 TTTTTGTAATGTTAACACAAAAAAGAAAGTAAATATGTTTATA-TTAAAATACATATATATACTA
* **
4985573 AAAATATTTTAGTATATATATAATAGTAATTATATTTCTTATAAATTAGCACAATATGTAAACTA
128 AAAATATTTTA--ATATATATAATAGT-A--ATATTCCTTATAAA-T-----AA-ACCT-AA-TA
* *
4985638 TAGATATTAAAAGACATAACAAGTTAATTAATAATCATAGTTTCATGAATTAATTTAATTAACTA
179 TAGATATTAAAAGACATAACAAATTAATTAATAATCATAATTTCATGAATTAATTTAATTAACTA
* * *
4985703 TATGGATTTGTCTTTAATTTCATGAAATTCAAAAAAAAATACTTAGGTTCCAAACCTATTCTAAT
244 TATGGATTTGTCCTTAATTTCATGAAATTCAAAAAAAAATACTTAGGTTCCAAAACTAATCTAAT
*
4985768 CTCAAAAACTCTCTTTAAGTGTG
309 CTCAAAAACTCTCTTT-AG-GTT
* *
4985791 TATATATATATATATATATATA
1 TATATAT-TATAAATTTATATA
4985813 TATATATATA
Statistics
Matches: 316, Mismatches: 29, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
328 21 0.07
329 5 0.02
330 74 0.23
331 29 0.09
333 13 0.04
334 1 0.00
336 13 0.04
337 1 0.00
342 2 0.01
343 2 0.01
344 3 0.01
345 86 0.27
346 40 0.13
347 6 0.02
348 8 0.03
349 12 0.04
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (329 bp):
TATATATTATAAATTTATATAAAAAAGGATATATATTATAATTAATAATTTTATAAGTTATAATT
TTTGTAATGTTAACACAAAAAAGAAAGTAAATATGTTTATATTAAAATACATATATATACTAAAA
ATATTTTAATATATATAATAGTAATATTCCTTATAAATAAACCTAATATAGATATTAAAAGACAT
AACAAATTAATTAATAATCATAATTTCATGAATTAATTTAATTAACTATATGGATTTGTCCTTAA
TTTCATGAAATTCAAAAAAAAATACTTAGGTTCCAAAACTAATCTAATCTCAAAAACTCTCTTTA
GGTT
Found at i:4985845 original size:2 final size:2
Alignment explanation
Indices: 4985791--4985835 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4985781 TTTAAGTGTG
4985791 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 TA
4985832 TA TA
1 TA TA
4985836 AGTTTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4985889 original size:15 final size:15
Alignment explanation
Indices: 4985823--4985890 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
4985813 TATATATATA
4985823 TATATATATTATAAGT
1 TATA-ATATTATAAGT
* *
4985839 T-T-ATATAAATAATGG
1 TATAATAT-TATAA-GT
4985854 TATATATATTATAA-T
1 TATA-ATATTATAAGT
4985869 TAATAATATTATAAGT
1 T-ATAATATTATAAGT
4985885 TATAAT
1 TATAAT
4985891 TTTTGTAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
13 4 0.10
14 4 0.10
15 18 0.44
16 7 0.17
17 4 0.10
18 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAATATTATAAGT
Found at i:4989001 original size:14 final size:15
Alignment explanation
Indices: 4988984--4989013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4988974 TTTCTTTAAG
4988984 ATTTT-TTTTTAAAA
1 ATTTTGTTTTTAAAA
4988998 ATTTTGTTTTTAAAA
1 ATTTTGTTTTTAAAA
4989013 A
1 A
4989014 AAACTACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTGTTTTTAAAA
Found at i:4991466 original size:36 final size:35
Alignment explanation
Indices: 4991408--4991489 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
4991398 ACACCGTTTG
* ** **
4991408 ATGATCTATTCTCTGTCAGTTGCTTTGAGGTTATGC
1 ATGATCTATTCGCTAACAGTTGCTTTGA-CATATGC
* *
4991444 ATGATCTATTCGCTAACCGTTGCTTTGACATGTGC
1 ATGATCTATTCGCTAACAGTTGCTTTGACATATGC
4991479 ATGATCTATTC
1 ATGATCTATTC
4991490 CTCTGCCACT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 15 0.38
36 24 0.62
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (35 bp):
ATGATCTATTCGCTAACAGTTGCTTTGACATATGC
Found at i:5001811 original size:23 final size:23
Alignment explanation
Indices: 5001782--5001829 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5001772 AATATGTTAG
*
5001782 TTTTTAAAATTTTTAACCTTTAT
1 TTTTTAAAATTTGTAACCTTTAT
5001805 TTTTTAAAATTTGTAACCTTTAT
1 TTTTTAAAATTTGTAACCTTTAT
5001828 TT
1 TT
5001830 CTCTATCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTAAAATTTGTAACCTTTAT
Found at i:5006997 original size:61 final size:61
Alignment explanation
Indices: 5006901--5007025 Score: 232
Period size: 61 Copynumber: 2.0 Consensus size: 61
5006891 TTATAAGATT
5006901 AGTAAACATGTATCTGATGGACATTCCACACACTAAATGCAACGAGTATAAGAGTTTAACG
1 AGTAAACATGTATCTGATGGACATTCCACACACTAAATGCAACGAGTATAAGAGTTTAACG
* *
5006962 AGTAAACATGTATCTGATGGACATTCCACATACTAAATGCAACGAGTATAAGAGTTTAATG
1 AGTAAACATGTATCTGATGGACATTCCACACACTAAATGCAACGAGTATAAGAGTTTAACG
5007023 AGT
1 AGT
5007026 GCGATTGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (61 bp):
AGTAAACATGTATCTGATGGACATTCCACACACTAAATGCAACGAGTATAAGAGTTTAACG
Found at i:5010719 original size:22 final size:23
Alignment explanation
Indices: 5010691--5010737 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5010681 ATTTTTATGT
5010691 ATTACTA-CAAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
5010713 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
5010736 AT
1 AT
5010738 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:5013858 original size:26 final size:27
Alignment explanation
Indices: 5013808--5013872 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
5013798 TTATTTTTTG
5013808 AATATTAATAATTTATAATTGATAATTT
1 AATATTAATAATTTAT-ATTGATAATTT
*
5013836 AAATATTAATACTTTAT-TT-ATAATTT
1 -AATATTAATAATTTATATTGATAATTT
5013862 AATCATTAATA
1 AAT-ATTAATA
5013873 GTATAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.09
26 14 0.41
27 2 0.06
29 15 0.44
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
AATATTAATAATTTATATTGATAATTT
Found at i:5013968 original size:27 final size:27
Alignment explanation
Indices: 5013938--5013991 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5013928 TTATTTTATT
*
5013938 TTTAAAATATTAATAATTTATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
*
5013965 TTTAAAATATTAATAATTGATACTTTA
1 TTTAAAATATTAATAATTGATAATTTA
5013992 AATATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:5014009 original size:42 final size:42
Alignment explanation
Indices: 5013961--5014052 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
5013951 TAATTTATAA
* *
5013961 TTTATTTAAAATATTAATAATTGATACTTT-AAATATTAATTT
1 TTTATTTAAAAT-TTAATAATTAATACTTTAAAATATTAATAT
* * **
5014003 TTTATTTATAATTTAATCATTAATGTTTTAAAATATTAATAT
1 TTTATTTAAAATTTAATAATTAATACTTTAAAATATTAATAT
5014045 TTT-TTTAA
1 TTTATTTAA
5014053 TGTAAATACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 17 0.40
42 25 0.60
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (42 bp):
TTTATTTAAAATTTAATAATTAATACTTTAAAATATTAATAT
Found at i:5014038 original size:155 final size:152
Alignment explanation
Indices: 5013822--5014105 Score: 444
Period size: 155 Copynumber: 1.8 Consensus size: 152
5013812 TTAATAATTT
5013822 ATAATTGATAATTTAAATATTAATACTTTATTTATAATTTAATCATTAATAGTATAAAATATTAA
1 ATAATTGATAATTTAAATATTAATACTTTATTTATAATTTAATCATTAATAGTATAAAATATTAA
* * **
5013887 TATTTTATTTATAATTTCAATGTTATTATGATTATTTATTTTTATTTTATTTTTAAAATATTAAT
66 TA-TTT-TTT-TAATGTAAATACTATTATGATTATTTATTTTTATTTTATTTTTAAAATATTAAT
5013952 AATTTATAATTTATTTAAAATATTA
128 AATTTATAATTTATTTAAAATATTA
* ** *
5013977 ATAATTGATACTTTAAATATTAATTTTTTATTTATAATTTAATCATTAAT-GTTTTAAAATATTA
1 ATAATTGATAATTTAAATATTAATACTTTATTTATAATTTAATCATTAATAG-TATAAAATATTA
*
5014041 ATATTTTTTTAATGTAAATACTATTATGATTATTTATTTTTATTTTATTTTTTAAATATTAATAA
65 ATATTTTTTTAATGTAAATACTATTATGATTATTTATTTTTATTTTATTTTTAAAATATTAATAA
5014106 AATATTAATA
Statistics
Matches: 119, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
152 51 0.43
153 3 0.03
154 4 0.03
155 61 0.51
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (152 bp):
ATAATTGATAATTTAAATATTAATACTTTATTTATAATTTAATCATTAATAGTATAAAATATTAA
TATTTTTTTAATGTAAATACTATTATGATTATTTATTTTTATTTTATTTTTAAAATATTAATAAT
TTATAATTTATTTAAAATATTA
Found at i:5014113 original size:136 final size:142
Alignment explanation
Indices: 5013787--5014161 Score: 319
Period size: 152 Copynumber: 2.6 Consensus size: 142
5013777 ATTATTTATT
*
5013787 TTTA-TTTTATTTTATTTTTTGAATATTAAT--AAT-TT-ATAATTGATAATTTAAATATTAATA
1 TTTATTTTTATTTTATTTTTTAAATATTAATAAAATATTAATAATTGATAATTTAAATATTAATA
* * * * *
5013847 CTTTATTTATAATTTAATCATTAATAGT-A-T-AAAATATTAATATTTTATTTATAATTTCAATG
66 TTTTATTTATAATTTAATCATTAATAATAAGTAAAAATATTAATATTTTATTTATAATGTAAATA
*
5013909 TTATTATGATTA
131 CTATTATGATTA
* * * *
5013921 TTTATTTTTATTTTATTTTTAAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTGAT
1 TTTATTTTTATTTTATTTTTTAAATATTAAT-A---A-AA--TA-TTAATA-ATTGATAATTTA-
* * * * * * *
5013986 ACT-TTAA-ATATTAATTTTTTATTT-ATAATTTAATCATTAATGTTTTAAAATATTAATA-TTT
56 AATATTAATAT-TTTATTTATAATTTAATCA-TTAAT-AATAA-G--TAAAAATATTAATATTTT
5014047 -TTT-TAATGTAAATACTATTATGATTA
115 ATTTATAATGTAAATACTATTATGATTA
*
5014073 TTTATTTTTATTTTATTTTTTAAATATTAATAAAATATTAATAATTGATAATTTACATATTAATA
1 TTTATTTTTATTTTATTTTTTAAATATTAATAAAATATTAATAATTGATAATTTAAATATTAATA
* *
5014138 TTTTCTTTAAAATTTAATCATTAA
66 TTTTATTTATAATTTAATCATTAA
5014162 CATCATAAAA
Statistics
Matches: 186, Mismatches: 28, Indels: 45
0.72 0.11 0.17
Matches are distributed among these distances:
134 4 0.02
135 24 0.13
142 3 0.02
143 27 0.15
144 11 0.06
145 2 0.01
146 2 0.01
147 8 0.04
148 31 0.17
149 4 0.02
150 1 0.01
151 1 0.01
152 49 0.26
153 3 0.02
154 4 0.02
155 12 0.06
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (142 bp):
TTTATTTTTATTTTATTTTTTAAATATTAATAAAATATTAATAATTGATAATTTAAATATTAATA
TTTTATTTATAATTTAATCATTAATAATAAGTAAAAATATTAATATTTTATTTATAATGTAAATA
CTATTATGATTA
Done.