Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 122 of 131
Found at i:40241233 original size:114 final size:113
Alignment explanation
Indices: 40241052--40241312 Score: 292
Period size: 114 Copynumber: 2.3 Consensus size: 113
40241042 TAATTTTTTA
*
40241052 AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGTTCAATTTTCCAAAACATCG
1 AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCAAAACATCG
* *
40241117 AAGCTCAAATTGGTATCGATACCAGGTCATGGGTATCAATACTTTGAAG
66 AAGCTCAAATTGGTATCAATACCAAG-CATGGGTATCAATACTTTGAAG
* * * * * *
40241166 AAGGTATTGATACTTT-TATAAGGGTATTGATACTTTTGATTTTTGCTCTATTTT-TATGATCTT
1 AAGGTATCGATACTTTGT-TAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCA-AAACAT
** ** * ***
40241229 CGAAGCTCATTTTGGTATCAATACCAAGCATGGGTATGGATACTTGGTTC
64 CGAAGCTCAAATTGGTATCAATACCAAGCATGGGTATCAATACTTTGAAG
* * * *
40241279 AAGGTATCGATACCTTATTGAGGGTATCGATACT
1 AAGGTATCGATACTTTGTTAAGGGTATTGATACT
40241313 ATGGTCCTTA
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
113 46 0.37
114 77 0.63
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (113 bp):
AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCAAAACATCG
AAGCTCAAATTGGTATCAATACCAAGCATGGGTATCAATACTTTGAAG
Found at i:40247921 original size:42 final size:42
Alignment explanation
Indices: 40247808--40247924 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
40247798 CTCATTGGAT
* * * *
40247808 AATTCGAAGTAATAATTTGACACCCAGTGTCTCATCG-GTTA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
* * **
40247849 AA-CCG--A-AGTAAATTGGCACCCAGTACCTCATCGAATTA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
*
40247887 AATTCGAAATAGTAAATTGACACCCAATGTCTCATCGA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGA
40247925 CTCGAAGTCG
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
37 22 0.38
38 5 0.09
39 2 0.03
40 2 0.03
41 3 0.05
42 24 0.41
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (42 bp):
AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
Found at i:40248066 original size:13 final size:13
Alignment explanation
Indices: 40248048--40248073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40248038 TTCATTTCAT
40248048 TTCAATATATATA
1 TTCAATATATATA
40248061 TTCAATATATATA
1 TTCAATATATATA
40248074 CCAATTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCAATATATATA
Found at i:40248080 original size:17 final size:14
Alignment explanation
Indices: 40248048--40248100 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
40248038 TTCATTTCAT
*
40248048 TTCAAT-ATATATA
1 TTCAATAATATAAA
40248061 TTCAATATATATACCAA
1 TTCAATA-ATATA--AA
40248078 TTCAATCAATATAAA
1 TTCAAT-AATATAAA
40248093 TTCAATAA
1 TTCAATAA
40248101 ATTCATCACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 13 0.38
17 12 0.35
18 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
TTCAATAATATAAA
Found at i:40248096 original size:15 final size:16
Alignment explanation
Indices: 40248049--40248098 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
40248039 TCATTTCATT
*
40248049 TCAATATATATATTCAA
1 TCAATATACA-ATTCAA
40248066 T-ATATATACCAATTCAA
1 TCA-ATATA-CAATTCAA
40248083 TCAATATA-AATTCAA
1 TCAATATACAATTCAA
40248098 T
1 T
40248099 AAATTCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 18 0.62
18 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (16 bp):
TCAATATACAATTCAA
Found at i:40251470 original size:41 final size:41
Alignment explanation
Indices: 40251360--40251474 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
40251350 TGGACCTTCT
* *
40251360 AGGGCTTTAGAGGCATTTTTAAAAAAGCGTCGCTAATGCTC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
* * ** *
40251401 AGAGCTTTAGCGGTATTTTCCAAGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
* * *
40251442 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGC
40251475 AAAAACATTT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (41 bp):
AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
Found at i:40251687 original size:7 final size:7
Alignment explanation
Indices: 40251675--40251707 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
40251665 TAATTTTAAG
40251675 GGATTAT
1 GGATTAT
40251682 GGATTAT
1 GGATTAT
40251689 GGATTAT
1 GGATTAT
*
40251696 GGATTAG
1 GGATTAT
40251703 GGATT
1 GGATT
40251708 CTGGTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (7 bp):
GGATTAT
Found at i:40252794 original size:11 final size:11
Alignment explanation
Indices: 40252778--40252802 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40252768 AGTTCTTCGA
40252778 TCCTTTCCGTC
1 TCCTTTCCGTC
40252789 TCCTTTCCGTC
1 TCCTTTCCGTC
40252800 TCC
1 TCC
40252803 AAAGCTCTCC
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:0.00, C:0.48, G:0.08, T:0.44
Consensus pattern (11 bp):
TCCTTTCCGTC
Found at i:40256458 original size:24 final size:22
Alignment explanation
Indices: 40256430--40256473 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
40256420 AATTTAAAAA
40256430 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
40256454 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
40256474 ATTAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:40256557 original size:43 final size:43
Alignment explanation
Indices: 40256504--40256724 Score: 217
Period size: 43 Copynumber: 5.1 Consensus size: 43
40256494 AGGTTATATT
* * *
40256504 TTTAGCAGCGTTTTTTGCAAAAACGTCGCTAAAGGTCATGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * *
40256547 TTTAACAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * * *
40256590 TTTAGCGGCGTTTGTGGGAGAAATGCCGCCAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * * * *
40256633 TTTAGCGGCGTTTGTGGGAGAAGCGCCACCAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * *
40256676 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
40256719 TTTAGC
1 TTTAGC
40256725 GGCATTTTTT
Statistics
Matches: 160, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
Found at i:40256725 original size:43 final size:43
Alignment explanation
Indices: 40256530--40256727 Score: 315
Period size: 43 Copynumber: 4.6 Consensus size: 43
40256520 GCAAAAACGT
* * * *
40256530 CGCTAAAGGTCATGGTCTTTAACAGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
**
40256573 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAATGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
*
40256616 CGCCAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
* *
40256659 CACCAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
40256702 CGCTAAAGGTCTTGGTCTTTAGCGGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGC
40256728 ATTTTTTTCG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 143 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
Found at i:40259247 original size:45 final size:45
Alignment explanation
Indices: 40259183--40259308 Score: 225
Period size: 45 Copynumber: 2.8 Consensus size: 45
40259173 TGGTGGTGGC
*
40259183 GGAGGAGCTCCATATGAAGGATAGCCAGAAAAAGATTGGGGCGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
*
40259228 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGTGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
*
40259273 GGAGGAGCTCCATACGAAGGATAGCCAGAAAGAGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGAT
40259309 GGTGATGGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.37, C:0.14, G:0.35, T:0.14
Consensus pattern (45 bp):
GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
Found at i:40265771 original size:16 final size:16
Alignment explanation
Indices: 40265750--40265788 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40265740 TGAATTATAA
*
40265750 AAAAATAAAATAAGAT
1 AAAAATAAAATAAAAT
*
40265766 AAAAATAACATAAAAT
1 AAAAATAAAATAAAAT
40265782 AAAAATA
1 AAAAATA
40265789 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:40265976 original size:3 final size:3
Alignment explanation
Indices: 40265968--40266088 Score: 115
Period size: 3 Copynumber: 40.3 Consensus size: 3
40265958 AAGCTATTAT
* *
40265968 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATG ATA AGTA ATA ATG AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* *
40266012 ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA GATG ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * *
40266059 AT- ATA TTA AAA ATA ATGA AGA A-A ATA ATA A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
40266089 AAATGCTAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 16
0.79 0.09 0.13
Matches are distributed among these distances:
2 8 0.08
3 83 0.84
4 8 0.08
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:40266778 original size:15 final size:14
Alignment explanation
Indices: 40266760--40266798 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
40266750 TCGAAAATAT
*
40266760 GAAAAGAAAAAATG
1 GAAAAGAAAAAACG
40266774 AGAAAA-AAAAAACG
1 -GAAAAGAAAAAACG
40266788 GAAAAGAAAAA
1 GAAAAGAAAAA
40266799 GAACAACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 12 0.55
15 5 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (14 bp):
GAAAAGAAAAAACG
Found at i:40270941 original size:41 final size:41
Alignment explanation
Indices: 40270880--40270959 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
40270870 TGATCGAATG
*
40270880 TAATACAGACTTTACATCTAGCAGGTTTGATGCCGGTGAAA
1 TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGAAA
*
40270921 TAATACAGACTTTACGTCTAGCAGGTTTAATGCCGGTGA
1 TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGA
40270960 TACATTTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (41 bp):
TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGAAA
Found at i:40270981 original size:41 final size:41
Alignment explanation
Indices: 40270881--40270986 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
40270871 GATCGAATGT
* * * *
40270881 AATACAGACTTTACATCTAGCAGGTTTGATGCCGGTGAAAT
1 AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
* *
40270922 AATACAGACTTTACGTCTAGCAGGTTTAATGCCGGTGATAC
1 AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
* * * *
40270963 ATTTCGGACTATAGGTCTAGCAGG
1 AATACAGACTATACGTCTAGCAGG
40270987 CTAAAGGCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
Found at i:40277721 original size:9 final size:9
Alignment explanation
Indices: 40277702--40277738 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40277692 TGAGTTTTTG
*
40277702 AATTTGAAT
1 AATTCGAAT
*
40277711 AACTCGAAT
1 AATTCGAAT
40277720 AATTCGAAT
1 AATTCGAAT
40277729 AATTCGAAT
1 AATTCGAAT
40277738 A
1 A
40277739 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40279828 original size:43 final size:43
Alignment explanation
Indices: 40279763--40279907 Score: 150
Period size: 43 Copynumber: 3.4 Consensus size: 43
40279753 CCTAGATATA
* * * **
40279763 GTCTTACATGTAATCTCGTATCGATGCCAATAGCCCAGCCATG
1 GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
* *
40279806 GTCTTACACGAAATCACATATCGATGCCAAT-GTCCCAGAAACG
1 GTCTTACACGAAATCTCATATCGATGCCAATAG-CCCAGAAATG
* * * **
40279849 GTGTTACACGAAGTCTCATATCGATGCC-ATATCCCAGATGTG
1 GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
*
40279891 GTCTTACACGTAATCTC
1 GTCTTACACGAAATCTC
40279908 GATAACCCTA
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
42 24 0.29
43 59 0.71
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
Found at i:40286995 original size:21 final size:22
Alignment explanation
Indices: 40286964--40287008 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
40286954 ACCCTAAAAA
40286964 TAATATTATTAAAAGAAATAAT
1 TAATATTATTAAAAGAAATAAT
*
40286986 TAAT-TTATTAAAAGAAATCAT
1 TAATATTATTAAAAGAAATAAT
40287007 TA
1 TA
40287009 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
TAATATTATTAAAAGAAATAAT
Found at i:40295576 original size:174 final size:174
Alignment explanation
Indices: 40295244--40295577 Score: 399
Period size: 174 Copynumber: 1.9 Consensus size: 174
40295234 TTGTGACTCA
* * * *
40295244 TGAGGTGGAAAAGGTAGAGAGAGGGCAATGCAGGAGCAAGGAAAGGAGTGAAAATGTTTATTCAG
1 TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTCAG
* * * * * * *
40295309 GTAGAGTAACTAGATCACGAAGTTCAATCCATCCTTCCATGTCTGAGAGTGGGCCTTCAGGTACA
66 GTAGAGTAACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAAAATGGGCCTTCAGGTACA
*
40295374 GGCAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
131 GGAAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
40295418 TGAGGTGGAAAAAGG-AGAAAGAGTGG-AATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTC
1 TGAGGTGG-AAAAGGTAGAAAGAG-GGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTC
* * * * * *
40295481 TGGTCGAGTCACAAGATCAAGAGGTTC-AGCTCAACCTTCAAAGTCT-ATAAATGGGCTTTCAGG
64 AGGTAGAGTAACAAGATCAAGAAGTTCAATC-CAACCTTCAAAGTCTGA-AAATGGGCCTTCAGG
* * *
40295544 TGCAGGAAAC-ACTTCTTCTGTTGCTAAGCAGGAT
127 TACAGGAAACGACTCCTT-TGTTGCAAAGCAGGAT
40295578 GGTGTGGTAC
Statistics
Matches: 134, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
173 9 0.07
174 117 0.87
175 8 0.06
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (174 bp):
TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTCAG
GTAGAGTAACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAAAATGGGCCTTCAGGTACA
GGAAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
Found at i:40305638 original size:119 final size:120
Alignment explanation
Indices: 40305418--40305664 Score: 399
Period size: 119 Copynumber: 2.0 Consensus size: 120
40305408 TTTCTGTTGC
* *
40305418 TTGAATACTTACAATGTATATACTTCCATTTGTAGCAATCCCTTCTGGTAAGTTTATTGATCTAG
1 TTGAATACTTACAATGTATATACTT-C-TTTGTAGCAATCCCTTCTGGTAAGTTTATTCATCCAG
**
40305483 AAAGGTTGATCAAGCTAGAAAACATGGGAACAATGAATCAGAATCCAGTGACAAAAAA
64 AAAGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAAT-CAGTGACAAAAAA
* *
40305541 TTGAGTACTTACAATGTATATAC-T-TTTGTTGCAATCCCTTCTGGTAAGTTTATTCATCCAGAA
1 TTGAATACTTACAATGTATATACTTCTTTGTAGCAATCCCTTCTGGTAAGTTTATTCATCCAGAA
40305604 AGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
66 AGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
40305659 TTGAAT
1 TTGAAT
40305665 CAGCATTTTA
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
118 18 0.15
119 76 0.65
122 1 0.01
123 22 0.19
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (120 bp):
TTGAATACTTACAATGTATATACTTCTTTGTAGCAATCCCTTCTGGTAAGTTTATTCATCCAGAA
AGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
Found at i:40306763 original size:21 final size:21
Alignment explanation
Indices: 40306737--40306778 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40306727 AGAAGGACAT
40306737 CCAAGTTGCTACTCAACTTGG
1 CCAAGTTGCTACTCAACTTGG
40306758 CCAAGTTGCTACTCAACTTGG
1 CCAAGTTGCTACTCAACTTGG
40306779 GGAGGCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (21 bp):
CCAAGTTGCTACTCAACTTGG
Found at i:40310391 original size:21 final size:21
Alignment explanation
Indices: 40310366--40310443 Score: 95
Period size: 21 Copynumber: 3.6 Consensus size: 21
40310356 ATCTTCGAGG
40310366 ATATGTAATCTTAAATATGAT
1 ATATGTAATCTTAAATATGAT
* *
40310387 ATATGCAATCTTAGATATGAT
1 ATATGTAATCTTAAATATGAT
40310408 ATATGTAATCTTAGAAGATATGAT
1 ATATGTAATCTT--AA-ATATGAT
*
40310432 -TTTGTAATCTTA
1 ATATGTAATCTTA
40310444 GAGATTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 31 0.63
23 11 0.22
24 7 0.14
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATGTAATCTTAAATATGAT
Found at i:40310455 original size:22 final size:23
Alignment explanation
Indices: 40310411--40310455 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40310401 ATATGATATA
*
40310411 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
40310434 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
40310456 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:40311117 original size:104 final size:104
Alignment explanation
Indices: 40311007--40311739 Score: 1339
Period size: 104 Copynumber: 7.0 Consensus size: 104
40310997 TTTTTAAGTT
* * * * *
40311007 TATATATGTAATTATTATTTTTATGATTTATATATTTATT-ACCT-TATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACG--TAT
40311070 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
64 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311111 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
40311176 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311215 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
40311280 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311319 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
40311384 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311423 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
40311488 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311527 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
40311592 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATTATACTTTCTATACATATTTTATAATTTCTATATA
40311631 TATATATATAATCATTATCTTTATGATCTATATATTTATTAAC-T-TATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
* *
40311694 ATGTATTATACTTTCTATCCATATTTTATAATTTCTATATG
66 A--TATTATACTTTCTATACATATTTTATAATTTCTATATA
40311735 TATAT
1 TATAT
40311740 TTTTCTTTAT
Statistics
Matches: 618, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
102 20 0.03
103 1 0.00
104 580 0.94
105 3 0.00
106 14 0.02
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.52
Consensus pattern (104 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
ATATTATACTTTCTATACATATTTTATAATTTCTATATA
Found at i:40315467 original size:22 final size:22
Alignment explanation
Indices: 40315459--40315502 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
40315449 AAGTGATAAA
40315459 AAAAGAAAAAGAAAAAGAAAAAG
1 AAAAG-AAAAGAAAAAGAAAAAG
40315482 AAAAGAAAAG-AAAAGAAAAAG
1 AAAAGAAAAGAAAAAGAAAAAG
40315503 GAGAGGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 5 0.24
23 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAGAAAAAGAAAAAG
Found at i:40315469 original size:6 final size:6
Alignment explanation
Indices: 40315458--40315502 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
40315448 AAAGTGATAA
40315458 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
40315503 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.39
6 23 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:40315473 original size:5 final size:5
Alignment explanation
Indices: 40315459--40315500 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
40315449 AAGTGATAAA
40315459 AAAAG AAAAAG AAAAAG AAAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
40315501 AGGAGAGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.53
6 17 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40316801 original size:44 final size:45
Alignment explanation
Indices: 40316753--40317400 Score: 566
Period size: 44 Copynumber: 14.7 Consensus size: 45
40316743 GTATTGGCGT
* * * *
40316753 GAAGTAGATCAAAGATAGCAGGTCCTATTTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * *
40316797 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * * * * *
40316841 GAAGTAGACCGAAAAAAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * *
40316885 GAAGTAGATCAAAGATAGCAGGTCCTATTTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * *
40316929 GAAGTGGATCGAAGAT-GTAGAGCTTATCTTCCCATATTGGTAGC
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * * * * * *
40316973 CAAGTATATCGAAGAAAGCAGATCTTGTCCTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
*
40317017 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* ** * *
40317061 GAAGTGGATCGAAGAT-GCAGATCTTGGCTTCCGATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * *
40317105 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* *
40317149 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTA-T
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * *
40317193 GAAGTGGATCGAAGAT-GCAGATCTTATCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * * *
40317237 GAAATAGATCGAAGAAAGCAGATCTTGTCTTCATATACTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * * *
40317282 AAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * * *
40317326 GAAGTAGATCGAATATAGCAGATCATGTCTTCTTATATTGGTAGT
1 GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
* * * *
40317371 AAAGTGGA-CAGAAGATGGCAAATCTTATCT
1 GAAGTAGATC-GAAGATAGCAGATCTTATCT
40317401 CCCTGAAGTT
Statistics
Matches: 483, Mismatches: 108, Indels: 25
0.78 0.18 0.04
Matches are distributed among these distances:
43 89 0.18
44 252 0.52
45 142 0.29
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (45 bp):
GAAGTAGATCGAAGATAGCAGATCTTATCTTCCTATATTGGTAGC
Found at i:40316959 original size:132 final size:132
Alignment explanation
Indices: 40316730--40317367 Score: 884
Period size: 132 Copynumber: 4.8 Consensus size: 132
40316720 GAAAAAATAA
* *
40316730 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTATTTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTGGT
* * *
40316795 AGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGACCGAAAAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
40316860 AG
131 AG
* *
40316862 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTATTTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTGGT
* * * * *
40316927 AGGAAGTGGATCGAAGATGTAGAGCTTATCTTCCCATATTGGTAGCCAAGTATATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
40316992 AG
131 AG
* * * *
40316994 ATCTTGTCCTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTGGT
** *
40317059 AGGAAGTGGATCGAAGATGCAGATCTTGGCTTCCGATATTGGTGGCGAAGTAGATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
40317124 AG
131 AG
* *
40317126 ATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTGGT
* *
40317191 ATGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
40317256 AG
131 AG
* * * * * * * *
40317258 ATCTTGTCTTCATATACTGGTG-GCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTG
1 ATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTG
* * * * * **
40317322 G-CGTGAAGTAGATCGAATATAGCAGATCATGTCTTCTTATATTGGT
64 GTAG-GAAGTGGATCGAAGAT-GCAGATCTTATCTTCCCATATTGGT
40317368 AGTAAAGTGG
Statistics
Matches: 455, Mismatches: 47, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 383 0.84
133 50 0.11
134 21 0.05
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (132 bp):
ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATATTGGT
AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
AG
Found at i:40317295 original size:177 final size:176
Alignment explanation
Indices: 40316974--40317400 Score: 561
Period size: 177 Copynumber: 2.4 Consensus size: 176
40316964 ATTGGTAGCC
* * * * * ** *
40316974 AAGTATATCGAAGAAAGCAGATCTTGTCCTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGA
1 AAGTAGATCGAAGATAGCAGATCATGTCTTCATATATTGGTATGAAGTGGATCGAAGATAGCAGA
* * * * * * *
40317039 TCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGGCTTCCGATATTGGTGG
66 TCTTATCTTCCCATATTGGTAGGAAATAGATCGAAGAAGCAGATCTTGGCTTCAGATACTGGTGG
*
40317104 CGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
131 CAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
* * *
40317150 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTATGAAGTGGATCGAAGAT-GCAGA
1 AAGTAGATCGAAGATAGCAGATCATGTCTTCATATATTGGTATGAAGTGGATCGAAGATAGCAGA
* * *
40317214 TCTTATCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATATACTGGT
66 TCTTATCTTCCCATATTGGTAG-GAAATAGATCGAAG-AAGCAGATCTTGGCTTCAGATACTGGT
40317279 GGCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
129 GGCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
* * * *
40317327 AAGTAGATCGAATATAGCAGATCATGTCTTCTTATATTGGTAGTAAAGTGGA-CAGAAGATGGCA
1 AAGTAGATCGAAGATAGCAGATCATGTCTTCATATATTGGTA-TGAAGTGGATC-GAAGATAGCA
*
40317391 AATCTTATCT
64 GATCTTATCT
40317401 CCCTGAAGTT
Statistics
Matches: 219, Mismatches: 27, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
175 24 0.11
176 61 0.28
177 108 0.49
178 14 0.06
179 12 0.05
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (176 bp):
AAGTAGATCGAAGATAGCAGATCATGTCTTCATATATTGGTATGAAGTGGATCGAAGATAGCAGA
TCTTATCTTCCCATATTGGTAGGAAATAGATCGAAGAAGCAGATCTTGGCTTCAGATACTGGTGG
CAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
Found at i:40317758 original size:17 final size:18
Alignment explanation
Indices: 40317736--40317828 Score: 73
Period size: 19 Copynumber: 5.0 Consensus size: 18
40317726 TATGGAAACA
*
40317736 TAATCTTCG-AGGATATG
1 TAATCTTAGAAGGATATG
*
40317753 TAATCTTAGATATGATATG
1 TAATCTTAGA-AGGATATG
*
40317772 TAATCTTAGATATGATATATG
1 TAATCTTAGA-A-G-GATATG
* * *
40317793 CAATCTTAGATATGATACG
1 TAATCTTAGA-AGGATATG
40317812 TAATCTTAGAA-GATATG
1 TAATCTTAGAAGGATATG
40317829 ATTTTGTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
17 13 0.21
18 1 0.02
19 32 0.52
21 16 0.26
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (18 bp):
TAATCTTAGAAGGATATG
Found at i:40317771 original size:19 final size:19
Alignment explanation
Indices: 40317747--40317821 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
40317737 AATCTTCGAG
40317747 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
40317766 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
40317785 GATATATGCAATCTTAGATAT
1 G--ATATGTAATCTTAGATAT
*
40317806 GATACGTAATCTTAGA
1 GATATGTAATCTTAGA
40317822 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:40317854 original size:22 final size:23
Alignment explanation
Indices: 40317811--40317854 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
40317801 GATATGATAC
* *
40317811 GTAATCTTAGAAGATATGATTTT
1 GTAATCTCAGAAGATATAATTTT
*
40317834 GTAATCTCAG-AGATTTAATTT
1 GTAATCTCAGAAGATATAATTT
40317855 GTAGATACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (23 bp):
GTAATCTCAGAAGATATAATTTT
Found at i:40328375 original size:9 final size:8
Alignment explanation
Indices: 40328332--40328388 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
40328322 TTTTTATTAA
*
40328332 AAAATTAT
1 AAAATTTT
*
40328340 AAAATATT
1 AAAATTTT
40328348 AAAATTATAT
1 AAAATT-T-T
40328358 AAAATTTT
1 AAAATTTT
40328366 AAAGATTTT
1 AAA-ATTTT
40328375 ATAAATTTAT
1 A-AAATTT-T
40328385 AAAA
1 AAAA
40328389 AAATAGCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 15 0.37
9 15 0.37
10 11 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
AAAATTTT
Found at i:40328380 original size:18 final size:18
Alignment explanation
Indices: 40328336--40328388 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40328326 TATTAAAAAA
*
40328336 TTATAAAATATTAAAATT
1 TTATAAAATTTTAAAATT
*
40328354 ATATAAAATTTTAAAGATT
1 TTATAAAATTTTAAA-ATT
40328373 TTAT-AAATTTATAAAA
1 TTATAAAATTT-TAAAA
40328389 AAATAGCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 20 0.67
19 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATAAAATTTTAAAATT
Found at i:40328636 original size:9 final size:9
Alignment explanation
Indices: 40328614--40328831 Score: 112
Period size: 9 Copynumber: 23.9 Consensus size: 9
40328604 ATTTTCTCAT
40328614 AAAATTATCAA
1 AAAATTAT--A
40328625 AAAATTATA
1 AAAATTATA
40328634 AAAA--ATA
1 AAAATTATA
*
40328641 ATAAGTTATA
1 A-AAATTATA
*
40328651 AATATTATA
1 AAAATTATA
*
40328660 AAAAATATA
1 AAAATTATA
*
40328669 CAAATTA-A
1 AAAATTATA
* *
40328677 AAGATCATA
1 AAAATTATA
40328686 AAAATTATA
1 AAAATTATA
*
40328695 AATAATAATA
1 AA-AATTATA
*
40328705 AACATTAT-
1 AAAATTATA
*
40328713 TAAA-TATTA
1 AAAATTA-TA
40328722 AAAA-TATTA
1 AAAATTA-TA
40328731 AAAATTGATA
1 AAAATT-ATA
*
40328741 TAAATTTATA
1 -AAAATTATA
40328751 AAAATTATA
1 AAAATTATA
*
40328760 AAATCTTATA
1 AAA-ATTATA
40328770 AATAA-TATA
1 AA-AATTATA
40328779 AAAATCTA-A
1 AAAAT-TATA
*
40328788 CAAATTAT-
1 AAAATTATA
* *
40328796 AAAATCATT
1 AAAATTATA
* *
40328805 AAAATTGTT
1 AAAATTATA
*
40328814 AAAAGTATA
1 AAAATTATA
40328823 TAAAATTAT
1 -AAAATTAT
40328832 TTTTTTTTAA
Statistics
Matches: 159, Mismatches: 31, Indels: 35
0.71 0.14 0.16
Matches are distributed among these distances:
7 6 0.04
8 20 0.13
9 84 0.53
10 34 0.21
11 15 0.09
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:40328663 original size:35 final size:35
Alignment explanation
Indices: 40328610--40328706 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
40328600 TTATATTTTC
40328610 TCAT-AAAATTATCAAAAAATTATAAAAAATAATAAG-
1 TCATAAAAATTAT--AAAAATTATAAAAAATAA-AAGA
* * * * *
40328646 TTATAAATATTATAAAAAATATACAAATTAAAAGA
1 TCATAAAAATTATAAAAATTATAAAAAATAAAAGA
*
40328681 TCATAAAAATTATAAATAATAATAAA
1 TCATAAAAATTATAAA-AATTATAAA
40328707 CATTATTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
34 3 0.06
35 29 0.60
36 9 0.19
37 7 0.15
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (35 bp):
TCATAAAAATTATAAAAATTATAAAAAATAAAAGA
Found at i:40328686 original size:26 final size:27
Alignment explanation
Indices: 40328631--40328694 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
40328621 TCAAAAAATT
* * * *
40328631 ATAAAAAATA-ATAAGTTATAAATATT
1 ATAAAAAATATACAAATTATAAAGATC
40328657 ATAAAAAATATACAAATTA-AAAGATC
1 ATAAAAAATATACAAATTATAAAGATC
*
40328683 ATAAAAATTATA
1 ATAAAAAATATA
40328695 AATAATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAAAAAATATACAAATTATAAAGATC
Found at i:40328705 original size:19 final size:19
Alignment explanation
Indices: 40328614--40328783 Score: 96
Period size: 19 Copynumber: 9.3 Consensus size: 19
40328604 ATTTTCTCAT
*
40328614 AAAATTATCAAAAAATTATA
1 AAAATTAT-AAATAATTATA
40328634 AAAA--AT-AATAAGTTATA
1 AAAATTATAAATAA-TTATA
* *
40328651 AATATTATAAA-AAATATA
1 AAAATTATAAATAATTATA
* * *
40328669 CAAATTA-AAA-GATCATA
1 AAAATTATAAATAATTATA
*
40328686 AAAATTATAAATAATAATA
1 AAAATTATAAATAATTATA
*
40328705 AACATTATTAAAT-A-T-TA
1 AAAATTA-TAAATAATTATA
40328722 AAAA-TATTAAA-AATTGATA
1 AAAATTA-TAAATAATT-ATA
*
40328741 TAAATTTATAAA-AATTATA
1 -AAAATTATAAATAATTATA
*
40328760 AAATCTTATAAATAA-TATA
1 AAA-ATTATAAATAATTATA
40328779 AAAAT
1 AAAAT
40328784 CTAACAAATT
Statistics
Matches: 118, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
16 12 0.10
17 27 0.23
18 18 0.15
19 35 0.30
20 24 0.20
21 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATAATTATA
Found at i:40328752 original size:29 final size:27
Alignment explanation
Indices: 40328690--40328762 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
40328680 ATCATAAAAA
*
40328690 TTATAAATAATAATAAACATTATTAAAT
1 TTATAAA-AATAATAAAAATTATTAAAT
* *
40328718 AT-TAAAAATATTAAAAATTGATATAAAT
1 TTATAAAAATAATAAAAATT-AT-TAAAT
*
40328746 TTATAAAAATTATAAAA
1 TTATAAAAATAATAAAA
40328763 TCTTATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 7 0.19
29 12 0.33
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TTATAAAAATAATAAAAATTATTAAAT
Found at i:40328801 original size:17 final size:17
Alignment explanation
Indices: 40328752--40328801 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
40328742 AAATTTATAA
* *
40328752 AAATTATAAAATCTTAT
1 AAATTATAAAATCTAAC
40328769 AAATAATATAAAAATCTAAC
1 AAAT--TAT-AAAATCTAAC
40328789 AAATTATAAAATC
1 AAATTATAAAATC
40328802 ATTAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 10 0.36
18 3 0.11
19 3 0.11
20 12 0.43
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATAAAATCTAAC
Found at i:40329883 original size:29 final size:28
Alignment explanation
Indices: 40329852--40329973 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 28
40329842 AAGTTTATGT
40329852 TTTTTATAAGTTTTTATAATTTATTAT-A
1 TTTTTATAAGTTTTTATAATTT-TTATAA
* * *
40329880 TTTTT-T-TGTTTTTTTATATTTTTGTAA
1 TTTTTATAAGTTTTTATA-ATTTTTATAA
* *
40329907 TGTTTATAAGTTTTTATATTTTTTTATAA
1 TTTTTATAAGTTTTTATA-ATTTTTATAA
* *
40329936 TTTTTATAAGTTTATTTATAAATTTTAATGA
1 TTTTTATAAG-TT-TTTAT-AATTTTTATAA
40329967 TTTTTAT
1 TTTTTAT
40329974 GAGAAAATGT
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
26 11 0.15
27 10 0.13
28 6 0.08
29 26 0.35
30 2 0.03
31 19 0.25
32 1 0.01
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (28 bp):
TTTTTATAAGTTTTTATAATTTTTATAA
Found at i:40329890 original size:37 final size:40
Alignment explanation
Indices: 40329852--40329948 Score: 50
Period size: 38 Copynumber: 2.6 Consensus size: 40
40329842 AAGTTTATGT
* *
40329852 TTTTTATAAGTTT-TTATAA-TTTATTATAT-TTTTTTGT-T
1 TTTTTATAA-TTTATTATAAGTTT-TTATATGTTTTTTATAA
* * * *
40329890 TTTTTAT-ATTT-TTGTAA-TGTTTATAAG-TTTTTATATT
1 TTTTTATAATTTATTATAAGTTTTTATATGTTTTTTATA-A
40329927 TTTTTATAATTT-TTATAAGTTT
1 TTTTTATAATTTATTATAAGTTT
40329949 ATTTATAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
35 11 0.23
36 10 0.21
37 9 0.19
38 16 0.33
39 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (40 bp):
TTTTTATAATTTATTATAAGTTTTTATATGTTTTTTATAA
Found at i:40329901 original size:9 final size:9
Alignment explanation
Indices: 40329845--40329943 Score: 60
Period size: 9 Copynumber: 10.7 Consensus size: 9
40329835 TTTAAAAAAG
*
40329845 TTTATGTTT
1 TTTATATTT
*
40329854 TTTATAAGTT
1 TTTAT-ATTT
40329864 TTTATAATTT
1 TTTAT-ATTT
*
40329874 ATTATATTT
1 TTTATATTT
*
40329883 TTT-TGTTTT
1 TTTAT-ATTT
40329892 TTTATATTT
1 TTTATATTT
*
40329901 TTGTA-A-TG
1 TT-TATATTT
*
40329909 TTTATAAGTT
1 TTTAT-ATTT
40329919 TTTATATTTT
1 TTTATA-TTT
*
40329929 TTTATAATT
1 TTTATATTT
40329938 TTTATA
1 TTTATA
40329944 AGTTTATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 33 0.46
10 32 0.45
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (9 bp):
TTTATATTT
Found at i:40329975 original size:9 final size:9
Alignment explanation
Indices: 40329852--40329973 Score: 77
Period size: 10 Copynumber: 12.8 Consensus size: 9
40329842 AAGTTTATGT
40329852 TTTTTATAA
1 TTTTTATAA
40329861 GTTTTTATAA
1 -TTTTTATAA
40329871 TTTATTAT-A
1 TTT-TTATAA
**
40329880 TTTTT-TTG
1 TTTTTATAA
*
40329888 TTTTTTTATA
1 TTTTTATA-A
*
40329898 TTTTTGTAA
1 TTTTTATAA
*
40329907 TGTTTATAA
1 TTTTTATAA
*
40329916 GTTTTTATATT
1 -TTTTTATA-A
40329927 TTTTTATAA
1 TTTTTATAA
40329936 TTTTTATAA
1 TTTTTATAA
40329945 GTTTATTTATAAA
1 --TT-TTTAT-AA
* *
40329958 TTTTAATGA
1 TTTTTATAA
40329967 TTTTTAT
1 TTTTTAT
40329974 GAGAAAATGT
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
7 1 0.01
8 7 0.08
9 32 0.36
10 39 0.43
11 4 0.04
12 5 0.06
13 2 0.02
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40330258 original size:17 final size:17
Alignment explanation
Indices: 40330236--40330304 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 17
40330226 ATAAAAATCC
40330236 ATAAAAACTTATAAATA
1 ATAAAAACTTATAAATA
40330253 ATAAAAA-TATAATAAAT-
1 ATAAAAACT-T-ATAAATA
*
40330270 ATAATAAATTTATAAA-A
1 ATAA-AAACTTATAAATA
40330287 ACTATTAAAACTTATAAA
1 A-TA--AAAACTTATAAA
40330305 AAATCATCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
16 1 0.02
17 18 0.42
18 12 0.28
19 11 0.26
20 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAACTTATAAATA
Found at i:40330284 original size:11 final size:9
Alignment explanation
Indices: 40330246--40330278 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
40330236 ATAAAAACTT
40330246 ATAAATAATA
1 ATAAAT-ATA
40330256 A-AAATATA
1 ATAAATATA
40330264 ATAAATATA
1 ATAAATATA
40330273 ATAAAT
1 ATAAAT
40330279 TTATAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 17 0.77
10 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAAATATA
Found at i:40330303 original size:27 final size:26
Alignment explanation
Indices: 40330224--40330304 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
40330214 CGTATAAAAC
40330224 TAATAAAAATCCATA-AAAACTTATAAA
1 TAATAAAAAT--ATATAAAACTTATAAA
*
40330251 TAATAAAAATATAATAAATA-TAATAAA
1 TAATAAAAATAT-ATAAA-ACTTATAAA
*
40330278 TTTATAAAAACTAT-TAAAACTTATAAA
1 -TAATAAAAA-TATATAAAACTTATAAA
40330305 AAATCATCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 29 0.64
28 9 0.20
29 3 0.07
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
TAATAAAAATATATAAAACTTATAAA
Found at i:40330714 original size:24 final size:24
Alignment explanation
Indices: 40330687--40330737 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
40330677 TTTCGAGCCA
*
40330687 TTTGA-TTTTTTTCTTTTATGTTCT
1 TTTGACTTTCTTTCTTTT-TGTTCT
*
40330711 TTTGACTTTCTTTCTTTTTTTTCT
1 TTTGACTTTCTTTCTTTTTGTTCT
40330735 TTT
1 TTT
40330738 TTTTTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTGACTTTCTTTCTTTTTGTTCT
Found at i:40331732 original size:89 final size:89
Alignment explanation
Indices: 40331632--40331977 Score: 470
Period size: 89 Copynumber: 3.9 Consensus size: 89
40331622 AACAATGAGG
* *
40331632 GTTTGTAATTTGTGGGGTGAGAATATGCGGATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
1 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
40331697 CTTTTTTCATAAACATAAATTTTT
66 CTTTTTTCATAAACATAAATTTTT
40331721 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
1 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
*
40331786 CTTTTTTCATAAGCAT---TTTTT
66 CTTTTTTCATAAACATAAATTTTT
* * *
40331807 -TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTGGTTTTAGCTTTTGCCTTCT
1 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTT-T
*****
40331871 T-TTTTTTCATAAACATAAAAAAAA
65 TCTTTTTTCATAAACATAAATTTTT
** * * * * * *
40331895 AATTGTAATTTGTGGGGTGAGAATATGAGAATCAATTTTTATTTTGGTTTTAGCTTTTGCCTTTT
1 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
40331960 C-TTTTTCATAAACATAAA
66 CTTTTTTCATAAACATAAA
40331978 AAAAAATTTA
Statistics
Matches: 235, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
85 73 0.31
86 7 0.03
88 19 0.08
89 136 0.58
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (89 bp):
GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
CTTTTTTCATAAACATAAATTTTT
Found at i:40331929 original size:174 final size:173
Alignment explanation
Indices: 40331633--40331970 Score: 489
Period size: 174 Copynumber: 1.9 Consensus size: 173
40331623 ACAATGAGGG
* *
40331633 TTTGTAATTTGTGGGGTGAGAATATGCGGATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
******* *
40331698 TTTTTTCATAAACATAAATTTTTGTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTAT
66 TTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTAT
40331763 TTTAGTTTCAGCTTTCGCCTTTTCTTTTTTCATAAGCATTTTTT
131 TTTAGTTTCAGCTTTCGCCTTTTC-TTTTTCATAAGCATTTTTT
* * *
40331807 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTGGTTTTAGCTTTTGCCTTCTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTT-TT
* *
40331872 -TTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTGGGGTGAGAATATGAGAATCAATTTTTA
65 CTTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTA
* * *
40331936 TTTTGGTTTTAGCTTTTGCCTTTTCTTTTTCATAA
130 TTTTAGTTTCAGCTTTCGCCTTTTCTTTTTCATAA
40331971 ACATAAAAAA
Statistics
Matches: 145, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
173 10 0.07
174 133 0.92
175 2 0.01
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (173 bp):
TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
TTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTAT
TTTAGTTTCAGCTTTCGCCTTTTCTTTTTCATAAGCATTTTTT
Found at i:40332624 original size:10 final size:10
Alignment explanation
Indices: 40332583--40332718 Score: 54
Period size: 10 Copynumber: 13.8 Consensus size: 10
40332573 CCAAAAAATG
40332583 AATTTTTATA
1 AATTTTTATA
*
40332593 TA-TTTTAT-
1 AATTTTTATA
*
40332601 AATTATTA-A
1 AATTTTTATA
40332610 TAATTTTTATA
1 -AATTTTTATA
*
40332621 AATTGTT-TA
1 AATTTTTATA
*
40332630 GATTTTT-TA
1 AATTTTTATA
*
40332639 CAATTTTTTTA
1 -AATTTTTATA
40332650 TAATTTTTAT-
1 -AATTTTTATA
** *
40332660 GTTTTTTTTCA
1 AATTTTTAT-A
40332671 TAATTTTTATA
1 -AATTTTTATA
* *
40332682 AGTTTATATA
1 AATTTTTATA
*
40332692 AACTTTTA-A
1 AATTTTTATA
*
40332701 TATTTTT-TA
1 AATTTTTATA
40332710 TAATTTTTA
1 -AATTTTTA
40332719 ATTTTTTAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 23
0.66 0.18 0.17
Matches are distributed among these distances:
8 1 0.01
9 32 0.36
10 39 0.43
11 12 0.13
12 6 0.07
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (10 bp):
AATTTTTATA
Found at i:40332678 original size:30 final size:30
Alignment explanation
Indices: 40332609--40332736 Score: 85
Period size: 30 Copynumber: 4.4 Consensus size: 30
40332599 ATAATTATTA
40332609 ATAATTTTTATAAATTGTTTAGATTTTTTAC
1 ATAATTTTTAT-AATTGTTTAGATTTTTTAC
* * *
40332640 A-ATTTTTTTATAATT-TTTATGTTTTTTTTC
1 ATA-ATTTTTATAATTGTTTA-GATTTTTTAC
**
40332670 ATAATTTTTATAAGTT-TATATA-AACTTTTA-
1 ATAATTTTTATAA-TTGT-T-TAGATTTTTTAC
*
40332700 ATATTTTTTATAATT-TTTA-ATTTTTTA-
1 ATAATTTTTATAATTGTTTAGATTTTTTAC
40332727 AT-ATTTTTAT
1 ATAATTTTTAT
40332737 GAGAAAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
26 7 0.09
27 10 0.13
28 1 0.01
29 7 0.09
30 35 0.44
31 16 0.20
32 1 0.01
33 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (30 bp):
ATAATTTTTATAATTGTTTAGATTTTTTAC
Found at i:40332732 original size:10 final size:9
Alignment explanation
Indices: 40332585--40332734 Score: 50
Period size: 10 Copynumber: 15.4 Consensus size: 9
40332575 AAAAAATGAA
40332585 TTTTTATAT
1 TTTTTATAT
*
40332594 ATTTTATAAT
1 TTTTTAT-AT
* *
40332604 TATTAATAAT
1 TTTTTAT-AT
*
40332614 TTTTATAAAT
1 TTTT-TATAT
* *
40332624 TGTTTAGAT
1 TTTTTATAT
*
40332633 TTTTTACAATT
1 TTTTTA-TA-T
40332644 TTTTTATAAT
1 TTTTTAT-AT
* *
40332654 TTTTATGTTT
1 TTTT-TATAT
*
40332664 TTTTTCATAA
1 TTTTT-ATAT
40332674 TTTTTATAAGT
1 TTTTTAT-A-T
* * *
40332685 TTATATAAAC
1 TT-TTTATAT
*
40332695 TTTTAATAT
1 TTTTTATAT
*
40332704 TTTTTATAA
1 TTTTTATAT
40332713 TTTTTA-AT
1 TTTTTATAT
40332721 TTTTTAATAT
1 TTTTT-ATAT
40332731 TTTT
1 TTTT
40332735 ATGAGAAAAA
Statistics
Matches: 101, Mismatches: 28, Indels: 23
0.66 0.18 0.15
Matches are distributed among these distances:
8 6 0.06
9 35 0.35
10 43 0.43
11 14 0.14
12 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTATAT
Found at i:40332735 original size:9 final size:9
Alignment explanation
Indices: 40332695--40332735 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
40332685 TTATATAAAC
40332695 TTTTAATAT
1 TTTTAATAT
*
40332704 TTTTTATAAT
1 TTTTAAT-AT
40332714 TTTTAAT-T
1 TTTTAATAT
40332722 TTTTAATAT
1 TTTTAATAT
40332731 TTTTA
1 TTTTA
40332736 TGAGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.29
9 12 0.43
10 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTAATAT
Found at i:40334195 original size:2 final size:2
Alignment explanation
Indices: 40334190--40334222 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40334180 AGCAACTGAG
*
40334190 AT AT AT TT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40334223 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:40343424 original size:24 final size:24
Alignment explanation
Indices: 40343404--40343496 Score: 91
Period size: 24 Copynumber: 3.9 Consensus size: 24
40343394 AAGATTTAGT
* *
40343404 ATTTATGAGTATAATATATTTAAC
1 ATTTATTAATATAATATATTTAAC
* * **
40343428 ATTTATTAATATGGA-AGATTTAGT
1 ATTTATTAATAT-AATATATTTAAC
40343452 ATTTA-TAAGTATAATATATTTAAC
1 ATTTATTAA-TATAATATATTTAAC
*
40343476 ATTTATTAATGTAATATATTT
1 ATTTATTAATATAATATATTT
40343497 GACTTTGATT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.07
24 46 0.85
25 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
ATTTATTAATATAATATATTTAAC
Found at i:40343464 original size:48 final size:48
Alignment explanation
Indices: 40343393--40343485 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
40343383 ATTCTTTCTT
*
40343393 GAAGATTTAGTATTTATGAGTATAATATATTTAACATTTATTAATATG
1 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAATATG
40343441 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAAT
1 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAAT
40343486 GTAATATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (48 bp):
GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAATATG
Found at i:40345331 original size:17 final size:16
Alignment explanation
Indices: 40345296--40345333 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
40345286 AAATAACCTC
40345296 ATATAAAATGTAAAGT
1 ATATAAAATGTAAAGT
40345312 ATATAAATATGTACAA-T
1 ATATAAA-ATGTA-AAGT
40345329 ATATA
1 ATATA
40345334 TATACCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (16 bp):
ATATAAAATGTAAAGT
Found at i:40354431 original size:21 final size:21
Alignment explanation
Indices: 40354405--40354445 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40354395 GAATAGGGCA
* *
40354405 GATGATGATATGGCTGATGAG
1 GATGATGACATGGCGGATGAG
40354426 GATGATGACATGGCGGATGA
1 GATGATGACATGGCGGATGA
40354446 TGGGGAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.39, T:0.24
Consensus pattern (21 bp):
GATGATGACATGGCGGATGAG
Found at i:40354455 original size:12 final size:12
Alignment explanation
Indices: 40354440--40354487 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
40354430 ATGACATGGC
*
40354440 GGATGATGGGGA
1 GGATGATGAGGA
40354452 GGATGATGAGGA
1 GGATGATGAGGA
* *
40354464 TGATGATGAGGG
1 GGATGATGAGGA
*
40354476 GGAGGATGAGGA
1 GGATGATGAGGA
40354488 TGAGGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.54, T:0.17
Consensus pattern (12 bp):
GGATGATGAGGA
Found at i:40354468 original size:24 final size:24
Alignment explanation
Indices: 40354441--40354490 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40354431 TGACATGGCG
*
40354441 GATGATG-GGGAGGATGATGAGGAT
1 GATGATGAGGG-GGAGGATGAGGAT
40354465 GATGATGAGGGGGAGGATGAGGAT
1 GATGATGAGGGGGAGGATGAGGAT
40354489 GA
1 GA
40354491 GGATATAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.52, T:0.18
Consensus pattern (24 bp):
GATGATGAGGGGGAGGATGAGGAT
Found at i:40354486 original size:6 final size:6
Alignment explanation
Indices: 40354456--40354494 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
40354446 TGGGGAGGAT
* **
40354456 GATGAG GATGAT GATGAG GGGGAG GATGAG GATGAG GAT
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GAT
40354495 ATAGCTGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18
Consensus pattern (6 bp):
GATGAG
Found at i:40361719 original size:3 final size:3
Alignment explanation
Indices: 40361713--40361739 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40361703 GAAAGAAAAA
40361713 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
40361740 CTGCCAAGAA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40362085 original size:30 final size:35
Alignment explanation
Indices: 40362049--40362116 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 35
40362039 TATAACTTTT
40362049 AAAAATTAAA-T-TAAAATT-TTATTA-T-ATTTA
1 AAAAATTAAAGTATAAAATTATTATTATTAATTTA
*
40362079 AAAAATTAAAGTATAAAATTATTTTTATTAATTTA
1 AAAAATTAAAGTATAAAATTATTATTATTAATTTA
40362114 AAA
1 AAA
40362117 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
32 7 0.22
33 5 0.16
34 1 0.03
35 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (35 bp):
AAAAATTAAAGTATAAAATTATTATTATTAATTTA
Found at i:40369979 original size:41 final size:42
Alignment explanation
Indices: 40369863--40369979 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 42
40369853 TTGCATAAAA
* *
40369863 CACCAGCATAAAGCCTGCTAGGCACAAAGCCTG-ATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAATACATTT
* * *
40369904 CACCGGCATAAAGCCTGCTAGACATCAAGTCTGAATTA-A-TT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAA-TACATTT
* * *
40369945 CACCGGCATCAAGCCTGCTAGGCATTAGGCCTGAA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAA
40369980 AATCTCAGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 60 0.94
42 2 0.03
43 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (42 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAATACATTT
Found at i:40387835 original size:2 final size:2
Alignment explanation
Indices: 40387828--40387859 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40387818 NNNNNNNNNN
40387828 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40387860 TCTTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40396007 original size:126 final size:125
Alignment explanation
Indices: 40395726--40396000 Score: 408
Period size: 126 Copynumber: 2.2 Consensus size: 125
40395716 GGCCAAATAG
* * * *
40395726 GAACTACTGTAGCAAAAGAGTGTCCACATGGGAGATTCTTTCAGTACTTTAGCTGACATTACATC
1 GAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGATTCTTTCAGTACTTTAGCTGACAATACATC
*
40395791 CTGCTTGAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
66 CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
* * *
40395851 GAAACTACTGTAGCAAAAGAACGTCCACGTGAGA-ACTTCTTTCAGTACTTTTGCTGACAATGCA
1 G-AACTACTGTAGCAAAAGAGCGTCCACGTGAGAGA-TTCTTTCAGTACTTTAGCTGACAATACA
* * * *
40395915 TTCTGCTTAAAGCGTTTTTGACATTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCA
64 TCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
40395977 TGAACTACTGTAGCAAAAGAGCGT
1 -GAACTACTGTAGCAAAAGAGCGT
40396001 TTACGTGGGA
Statistics
Matches: 134, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
125 2 0.01
126 131 0.98
127 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (125 bp):
GAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGATTCTTTCAGTACTTTAGCTGACAATACATC
CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
Found at i:40396221 original size:89 final size:91
Alignment explanation
Indices: 40396094--40396439 Score: 448
Period size: 97 Copynumber: 3.7 Consensus size: 91
40396084 AAAACCTTAA
* * *
40396094 ACACTAAACCCTAATCTATTTTTTTTAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAA
1 ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAA
40396159 TTTATTTGATTTTTTTCTT-AAAA-C
66 TTTATTTGATTTTTTTCTTAAAAACC
*
40396183 -C-CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACCCTAAACCCT
1 ACACTAAACCCTAATCTAA-TTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACCCT
40396246 AATTTATTTGATTTTTTTCCTTAAAAACCC
64 AATTTATTTGATTTTTTT-CTTAAAAA-CC
* *
40396276 TAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAATCCTAGACC
1 ---ACACTAAACCCTAATCTAATTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACC
*
40396341 CTAATTTATTTGATTTTTTCCTTAAAAACC
62 CTAATTTATTTGATTTTTTTCTTAAAAACC
* * * * *
40396371 ATAAACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTTAATTAAGAAACCTTAAACC
1 ----ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACC
40396436 CTAA
62 CTAA
40396440 ACCCTTATTT
Statistics
Matches: 230, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
87 15 0.07
88 7 0.03
89 53 0.23
90 3 0.01
91 4 0.02
93 1 0.00
95 36 0.16
96 35 0.15
97 60 0.26
98 16 0.07
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (91 bp):
ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAA
TTTATTTGATTTTTTTCTTAAAAACC
Found at i:40396330 original size:186 final size:184
Alignment explanation
Indices: 40396052--40396439 Score: 514
Period size: 186 Copynumber: 2.1 Consensus size: 184
40396042 GTAACCTTGG
* *
40396052 ACCCCAAACCCTAATTTATTTAAATTTTCCTTAAAACCTTAAACACTAAACCCTAATCTATTTTT
1 ACCCTAAACCCTAATTTATTTAAATTTTCCTTAAAACCCTAAACACTAAACCCTAATCTATTTTT
** *
40396117 TTTAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTTCTT-AAA
66 TAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAA
* * *
40396181 A-C-C-CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTA
131 ACCACACTAAACCCTAATCTAA-TTTCTT-AAATTTATAATTAATTCAATCAAGAA
**
40396234 ACCCTAAACCCTAATTTATTTGATTTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
1 ACCCTAAACCCTAATTTATTT-A-AATTTTCCTT-AAAACCCTAAACACTAAACCCTAATCT-AT
* * *
40396299 TTTTTAAAATTTATAATTAATTTACTCAAGTAATCCTAGACCCTAATTTATTTGATTTTTTCCTT
62 TTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTT
* *
40396364 AAAAACCATAAACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTTAATTAAGAA
127 AAAAACC----ACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTCAATCAAGAA
*
40396426 ACCTTAAACCCTAA
1 ACCCTAAACCCTAA
40396440 ACCCTTATTT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
182 20 0.11
183 1 0.01
184 8 0.04
185 26 0.15
186 61 0.34
187 4 0.02
188 1 0.01
192 35 0.20
193 6 0.03
194 16 0.09
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (184 bp):
ACCCTAAACCCTAATTTATTTAAATTTTCCTTAAAACCCTAAACACTAAACCCTAATCTATTTTT
TAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAA
ACCACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTCAATCAAGAA
Found at i:40402203 original size:2 final size:2
Alignment explanation
Indices: 40402198--40402250 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
40402188 AAACTCTCAT
* *
40402198 TC TC TC GC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40402240 TC TC TC TC TC T
1 TC TC TC TC TC T
40402251 TTCTTCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40408568 original size:29 final size:29
Alignment explanation
Indices: 40408510--40408568 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 29
40408500 ACTCAACTTT
* *
40408510 TAAAAAATAACAAAACAGTCACTAATATTA
1 TAAAAAATAACAAAACAATCACT-AGATTA
*
40408540 TAAAAAAGTGACAAAACAATCACT-GATTA
1 TAAAAAA-TAACAAAACAATCACTAGATTA
40408569 ACTGTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 4 0.16
30 7 0.28
31 14 0.56
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.22
Consensus pattern (29 bp):
TAAAAAATAACAAAACAATCACTAGATTA
Found at i:40410585 original size:18 final size:17
Alignment explanation
Indices: 40410562--40410605 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
40410552 TAAAAAAATA
*
40410562 TATAAATTGTTGAATTTT
1 TATAAATT-TGGAATTTT
40410580 TATAAATATTGGAATTTT
1 TATAAAT-TTGGAATTTT
40410598 TATAAATT
1 TATAAATT
40410606 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAATTTGGAATTTT
Found at i:40410712 original size:130 final size:131
Alignment explanation
Indices: 40410569--40410830 Score: 517
Period size: 130 Copynumber: 2.0 Consensus size: 131
40410559 ATATATAAAT
40410569 TGTTGAATTTTTATAAATATTGGAATTTTTATAAATTACTTTGATTTTTTTGAAAATTTTTAAAT
1 TGTTGAATTTTTATAAATATTGGAATTTTTATAAATTACTTTGATTTTTTTGAAAATTTTTAAAT
40410634 TTTTGTTGACAGAGACCAATTTGTTCATTTTCAAAATTGGCAGGACCAAAGGGATACTTACACCA
66 TTTTGTTGACAGAGACCAATTTGTTCATTTTCAAAATTGGCAGGACCAAAGGGATACTTACACCA
40410699 A
131 A
40410700 TGTTGAA-TTTTATAAATATTGGAATTTTTATAAATTACTTTGATTTTTTTGAAAATTTTTAAAT
1 TGTTGAATTTTTATAAATATTGGAATTTTTATAAATTACTTTGATTTTTTTGAAAATTTTTAAAT
40410764 TTTTGTTGACAGAGACCAATTTGTTCATTTTCAAAATTGGCAGGACCAAAGGGATACTTACACCA
66 TTTTGTTGACAGAGACCAATTTGTTCATTTTCAAAATTGGCAGGACCAAAGGGATACTTACACCA
40410829 A
131 A
40410830 T
1 T
40410831 CTGCCATTTG
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
130 124 0.95
131 7 0.05
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.43
Consensus pattern (131 bp):
TGTTGAATTTTTATAAATATTGGAATTTTTATAAATTACTTTGATTTTTTTGAAAATTTTTAAAT
TTTTGTTGACAGAGACCAATTTGTTCATTTTCAAAATTGGCAGGACCAAAGGGATACTTACACCA
A
Found at i:40411891 original size:2 final size:2
Alignment explanation
Indices: 40411886--40411912 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40411876 AGAGATTCTC
40411886 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40411913 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40414634 original size:20 final size:21
Alignment explanation
Indices: 40414609--40414659 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
40414599 AAGTTTTATA
* *
40414609 ATATATATTCATTA-TAACAT
1 ATATATATACAATAGTAACAT
*
40414629 ATATATGTACAATAGTTAACAT
1 ATATATATACAATAG-TAACAT
40414651 ATATATATA
1 ATATATATA
40414660 TATATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
22 14 0.56
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (21 bp):
ATATATATACAATAGTAACAT
Found at i:40421964 original size:47 final size:47
Alignment explanation
Indices: 40421905--40421995 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 47
40421895 CTTTTCCTAA
*
40421905 TTTTTTTATTTATTTGTCCTTT-TTTGTTTTTTATTTACTTTTTCAGT
1 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTT-CTTTTTCAGT
40421952 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTC
1 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTC
40421996 TTTATTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (47 bp):
TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTCAGT
Found at i:40421998 original size:25 final size:26
Alignment explanation
Indices: 40421906--40422009 Score: 103
Period size: 25 Copynumber: 4.2 Consensus size: 26
40421896 TTTTCCTAAT
*
40421906 TTTTTTATTTATTTGTCCTTT-TTTG
1 TTTTTTATTTATTTCTCCTTTATTTG
* * *
40421931 TTTTTTATTTACTT-T--TTCAGTT-
1 TTTTTTATTTATTTCTCCTTTATTTG
40421953 TTTTTTATTTATTTCTCCTTTATTTG
1 TTTTTTATTTATTTCTCCTTTATTTG
* * *
40421979 TTTTTTATTTCTTT-TTCTTTATTTC
1 TTTTTTATTTATTTCTCCTTTATTTG
40422004 TTTTTT
1 TTTTTT
40422010 TCTGCTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 15 0.23
23 3 0.05
24 1 0.02
25 33 0.51
26 13 0.20
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTTTATTTATTTCTCCTTTATTTG
Found at i:40422001 original size:14 final size:14
Alignment explanation
Indices: 40421982--40422008 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40421972 TTATTTGTTT
40421982 TTTATTTCTTTTTC
1 TTTATTTCTTTTTC
40421996 TTTATTTCTTTTT
1 TTTATTTCTTTTT
40422009 TTCTGCTTTT
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:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTCTTTTTC
Found at i:40422017 original size:25 final size:25
Alignment explanation
Indices: 40421970--40422019 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
40421960 TTTATTTCTC
* *
40421970 CTTTATTTGTTTTTTATTTCTTTTT
1 CTTTATTTCTTTTTTATTGCTTTTT
40421995 CTTTATTTCTTTTTT-TCTGCTTTTT
1 CTTTATTTCTTTTTTAT-TGCTTTTT
40422020 TATTTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (25 bp):
CTTTATTTCTTTTTTATTGCTTTTT
Found at i:40430468 original size:51 final size:51
Alignment explanation
Indices: 40430391--40430518 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 51
40430381 GAGCAGATCG
* ** *
40430391 AAGGCAGCGAATCATATCTCTTTGGCGTTACAGTGGAACAGATTAAAGCTA
1 AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
* * * * ** *
40430442 AAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGTAGATTAAAGCTG
1 AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
*
40430493 AAGGCAGCTAATCTTATCTCCCTGGC
1 AAGGCAGCGAATCTTATCTCCCTGGC
40430519 CTTAAAGCTA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (51 bp):
AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
Found at i:40430918 original size:44 final size:44
Alignment explanation
Indices: 40430865--40431006 Score: 187
Period size: 44 Copynumber: 3.2 Consensus size: 44
40430855 TTCCTGAGCG
40430865 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
*
40430909 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCATGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
* * * ** * *
40430953 GCAATGGAGCAGATTGAAGCTATTAA-TCCTATCACCTTGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACT-TTATCTCCTTGAAGTT
*
40430997 GAAGTGGAGC
1 GCAGTGGAGC
40431007 GGATTAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 1 0.01
44 85 0.99
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
Found at i:40430919 original size:132 final size:132
Alignment explanation
Indices: 40430535--40430885 Score: 598
Period size: 132 Copynumber: 2.7 Consensus size: 132
40430525 GCTAAAGATA
*
40430535 GTGAATCTTAT-TTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCTTATCTCCCTGAG
1 GTGAATCTTATCTTT-CCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAG
40430599 CAACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAG
65 CAACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAG
40430664 ACG
130 ACG
40430667 GTGAATCTTATC-TTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAG
1 GTGAATCTTATCTTTC-CAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAG
*
40430731 CAACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAAATCAAAG
65 CAACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAG
40430796 ACG
130 ACG
* *
40430799 GTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTTCCTGAGC
1 GTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAGC
** * *
40430864 GGCAGTGGAGCAGGTTGAAGAT
66 AACAGCGGAGTAGGTTGAAGAT
40430886 ACCAACTTTA
Statistics
Matches: 208, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
131 1 0.00
132 204 0.98
133 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
GTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAGC
AACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGA
CG
Found at i:40432242 original size:3 final size:3
Alignment explanation
Indices: 40432224--40432309 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
40432214 CAAATTTTGG
* * * * * *
40432224 ATT ATC ATT GTT ATT ATT ATT GTT ATT GTT GTT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40432272 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT AGTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT
40432310 TATTTTCCTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 67 0.92
4 6 0.08
ACGTcount: A:0.27, C:0.01, G:0.07, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:40435614 original size:13 final size:12
Alignment explanation
Indices: 40435574--40435647 Score: 50
Period size: 13 Copynumber: 6.4 Consensus size: 12
40435564 AATAATTTAA
40435574 AAAAATTATATT
1 AAAAATTATATT
* * *
40435586 TAATATT-T-TA
1 AAAAATTATATT
40435596 AAAAATTATATTT
1 AAAAATTATA-TT
40435609 AAAAATT-TA--
1 AAAAATTATATT
40435618 AAAAATTATATTT
1 AAAAATTATA-TT
* *
40435631 TAAAATTTTATT
1 AAAAATTATATT
40435643 AAAAA
1 AAAAA
40435648 AAATAATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
9 7 0.15
10 8 0.17
11 2 0.04
12 13 0.28
13 16 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAAAATTATATT
Found at i:40435640 original size:23 final size:22
Alignment explanation
Indices: 40435567--40435640 Score: 112
Period size: 22 Copynumber: 3.3 Consensus size: 22
40435557 CTTTAAAAAT
*
40435567 AATTTAAAAAAATTATATTTAA
1 AATTTTAAAAAATTATATTTAA
*
40435589 TATTTTAAAAAATTATATTTAA
1 AATTTTAAAAAATTATATTTAA
*
40435611 AAATTTAAAAAATTATATTTTAA
1 AATTTTAAAAAATTATA-TTTAA
40435634 AATTTTA
1 AATTTTA
40435641 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 35 0.76
23 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAAAAAATTATATTTAA
Found at i:40435690 original size:15 final size:14
Alignment explanation
Indices: 40435670--40435725 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
40435660 AATAAAAGAG
*
40435670 AAATAAAGGATAAAT
1 AAATAAA-GAAAAAT
*
40435685 AAATAATTGAAAAAGT
1 AAATAA-AGAAAAA-T
*
40435701 AAATAAAGAAAAAC
1 AAATAAAGAAAAAT
40435715 AAATAAA-AAAA
1 AAATAAAGAAAA
40435726 CGAAAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 4 0.11
14 7 0.20
15 17 0.49
16 7 0.20
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (14 bp):
AAATAAAGAAAAAT
Found at i:40436832 original size:29 final size:29
Alignment explanation
Indices: 40436799--40436858 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
40436789 TCCTCTAACT
40436799 TTACAAAAAAAAAATATTTTAACTTTTCA
1 TTACAAAAAAAAAATATTTTAACTTTTCA
**
40436828 TTACAAAAAAAATTTATTTTAACTTTTCA
1 TTACAAAAAAAAAATATTTTAACTTTTCA
40436857 TT
1 TT
40436859 TAGTTTTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (29 bp):
TTACAAAAAAAAAATATTTTAACTTTTCA
Found at i:40437724 original size:15 final size:16
Alignment explanation
Indices: 40437704--40437735 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40437694 AGATGTTGTA
40437704 TGTAATTCATCT-ATT
1 TGTAATTCATCTGATT
40437719 TGTAATTCATCTGATT
1 TGTAATTCATCTGATT
40437735 T
1 T
40437736 AGTAGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TGTAATTCATCTGATT
Found at i:40438450 original size:23 final size:22
Alignment explanation
Indices: 40438423--40438485 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
40438413 AGAAAAAGAC
40438423 AGATGAACAATGAAGATTCTCT
1 AGATGAACAATGAAGATTCTCT
* * *
40438445 ACGATGAATAGT-AAAATTCTCT
1 A-GATGAACAATGAAGATTCTCT
40438467 AGCATGAACAATGAAGATT
1 AG-ATGAACAATGAAGATT
40438486 TTCCGTAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.56
23 13 0.41
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (22 bp):
AGATGAACAATGAAGATTCTCT
Found at i:40438616 original size:19 final size:19
Alignment explanation
Indices: 40438579--40438617 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40438569 AATATTTTTA
*
40438579 TTTAAAATTTTTATGATTT
1 TTTAAAATTTTTATAATTT
40438598 TTTAATAATTTTT-TAATTT
1 TTTAA-AATTTTTATAATTT
40438617 T
1 T
40438618 AAAAGGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTAAAATTTTTATAATTT
Found at i:40446044 original size:15 final size:15
Alignment explanation
Indices: 40446024--40446055 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40446014 TATTTCACTA
*
40446024 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
40446039 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
40446054 TT
1 TT
40446056 TGCATGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:40447022 original size:22 final size:21
Alignment explanation
Indices: 40446996--40447266 Score: 256
Period size: 22 Copynumber: 12.2 Consensus size: 21
40446986 AGAAATTATC
*
40446996 CAACATTCAGACAACATTTAAT
1 CAACATT-GGACAACATTTAAT
*
40447018 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
40447040 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
*
40447062 CAATATTATTTGGACAACATTTAAT
1 C-A-A-CA-TTGGACAACATTTAAT
*
40447087 CAACAATTGGACAACATTAAAT
1 CAAC-ATTGGACAACATTTAAT
40447109 CAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
* * * * *
40447131 AAAAAATTGGATAGCATTCAAT
1 -CAACATTGGACAACATTTAAT
*
40447153 CAATATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
40447175 CAACAATTGGACAACATTAAAT
1 CAAC-ATTGGACAACATTTAAT
**
40447197 CAACATTTGGACAGTATTTAAT
1 CAACA-TTGGACAACATTTAAT
40447219 CAACAATTGGACAACA-TTAAT
1 CAAC-ATTGGACAACATTTAAT
* *
40447240 CAATATTTGGACAGCATTTAAT
1 CAACA-TTGGACAACATTTAAT
40447262 CAACA
1 CAACA
40447267 ATTTTTACTT
Statistics
Matches: 205, Mismatches: 29, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.00
21 22 0.11
22 152 0.74
23 11 0.05
24 3 0.01
25 16 0.08
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (21 bp):
CAACATTGGACAACATTTAAT
Found at i:40447053 original size:44 final size:44
Alignment explanation
Indices: 40447005--40447269 Score: 370
Period size: 44 Copynumber: 6.0 Consensus size: 44
40446995 CCAACATTCA
* *
40447005 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* *
40447049 GACAACATTCAATCAATATTATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATC-A-A-CATTTGGACAACATTTAATCAACAATTG
* *
40447096 GACAACATTAAATCAACATTTGGACAACATTTAATAAAAAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * * *
40447140 GATAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
**
40447184 GACAACATTAAATCAACATTTGGACAGTATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* *
40447228 GACAACATT-AATCAATATTTGGACAGCATTTAATCAACAATT
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATT
40447270 TTTACTTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
43 31 0.16
44 122 0.62
45 2 0.01
46 2 0.01
47 40 0.20
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
Found at i:40448164 original size:42 final size:42
Alignment explanation
Indices: 40448058--40448213 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 42
40448048 TCATACAATA
* * * * * *
40448058 CCAACGTCCCAGACATGGTCTTTCATGTAATCAAACAACGATG
1 CCAATGTCCCAGACATGGTCTTACACGTAATCATA-AACTACG
* *
40448101 CCACTGTCCCAGACA-GAGTCTTACACGTAATCATATACTACG
1 CCAATGTCCCAGACATG-GTCTTACACGTAATCATAAACTACG
* * *
40448143 CCAATGTCCCAGATATGGTCTTACACGTAAATC-TCAAATTGAGG
1 CCAATGTCCCAGACATGGTCTTACACGT-AATCAT-AAACT-ACG
*
40448187 CCAATGTCCCAGACGTGGTCTTACACG
1 CCAATGTCCCAGACATGGTCTTACACG
40448214 ATGTCACATT
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.32
43 36 0.39
44 27 0.29
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
CCAATGTCCCAGACATGGTCTTACACGTAATCATAAACTACG
Found at i:40452406 original size:2 final size:2
Alignment explanation
Indices: 40452399--40452425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40452389 NNNNNNNNTG
40452399 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
40452426 TCAATTTACC
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:40453396 original size:42 final size:43
Alignment explanation
Indices: 40453295--40453407 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
40453285 AGCTCGTATA
* **
40453295 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATAAAATCAAATATCG
* *
40453338 ATGCCATTGTCCCAGACAGGGTCTTACATAAAATCATATAT-G
1 ATGCCAATGTCCCAGACAGGGTCTTACATAAAATCAAATATCG
* *
40453380 ATGCCAATATCCCAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACAGGGTCTTACA
40453408 CGTAAATCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 26 0.43
43 34 0.56
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATAAAATCAAATATCG
Found at i:40456250 original size:28 final size:28
Alignment explanation
Indices: 40456218--40456290 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
40456208 ATAAGATTTA
*
40456218 ATATTAAATTTAATCTAATATTAAATTG
1 ATATTAAATTTAATATAATATTAAATTG
* * *
40456246 ATATTAGATTAAATTTAATATTAAATTG
1 ATATTAAATTTAATATAATATTAAATTG
40456274 --ATTAAATTTAATATAAT
1 ATATTAAATTTAATATAAT
40456291 TGAACTCTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 14 0.36
28 25 0.64
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATTAAATTTAATATAATATTAAATTG
Found at i:40460870 original size:23 final size:23
Alignment explanation
Indices: 40460837--40460905 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
40460827 CCGAGTTGAT
*
40460837 AAACGGTAAGCTCTATCA-AGCTG
1 AAACGGTAAGCTCCAT-AGAGCTG
*
40460860 AAACGGAAAGCTCCATAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
40460883 AAACGGTAAGCT-CATATGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
40460906 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:40469153 original size:24 final size:25
Alignment explanation
Indices: 40469116--40469168 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
40469106 TCTTTTTGCA
*
40469116 TTCATTCCATTCATCTGCATTACAT
1 TTCATTCCATTCATCTGCATTAAAT
* * *
40469141 TTCATTGCA-TCATTTGTATTAAAT
1 TTCATTCCATTCATCTGCATTAAAT
40469165 TTCA
1 TTCA
40469169 CGAAAGAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (25 bp):
TTCATTCCATTCATCTGCATTAAAT
Found at i:40472312 original size:9 final size:9
Alignment explanation
Indices: 40472298--40472353 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
40472288 ACAAAAATAA
40472298 AAGAAAAAG
1 AAGAAAAAG
*
40472307 AAGAAAAAA
1 AAGAAAAAG
*
40472316 AAGAAAAAAAT
1 AAG--AAAAAG
40472327 AAGAAAAAG
1 AAGAAAAAG
40472336 AAG-AAAA-
1 AAGAAAAAG
40472343 AAGAAAAAG
1 AAGAAAAAG
40472352 AA
1 AA
40472354 ATAAAAGGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 3 0.08
8 8 0.20
9 21 0.52
11 8 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:40472324 original size:20 final size:20
Alignment explanation
Indices: 40472301--40472344 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
40472291 AAAATAAAAG
40472301 AAAAAGAAGAAAAAAAAGAA
1 AAAAAGAAGAAAAAAAAGAA
* *
40472321 AAAAATAAGAAAAAGAAGAA
1 AAAAAGAAGAAAAAAAAGAA
40472341 AAAA
1 AAAA
40472345 GAAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAGAA
Found at i:40472332 original size:29 final size:29
Alignment explanation
Indices: 40472290--40472357 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
40472280 AATATTCTAC
*
40472290 AAAAATAA-AAGAAAAAGAAGAAAAAA-A
1 AAAAAAAATAAGAAAAAGAAGAAAAAAGA
40472317 AGAAAAAAATAAGAAAAAGAAGAAAAAAGA
1 A-AAAAAAATAAGAAAAAGAAGAAAAAAGA
*
40472347 AAAAGAAATAA
1 AAAAAAAATAA
40472358 AAGGAGAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 6 0.17
29 27 0.75
30 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (29 bp):
AAAAAAAATAAGAAAAAGAAGAAAAAAGA
Found at i:40472333 original size:16 final size:16
Alignment explanation
Indices: 40472296--40472359 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
40472286 CTACAAAAAT
*
40472296 AAAAGAAAAAGAAGAAAA
1 AAAAGAAAAA-AA-AAGA
40472314 AAAAGAAAAAAATAAGA
1 AAAAGAAAAAAA-AAGA
*
40472331 AAAAGAAGAAAAAAGA
1 AAAAGAAAAAAAAAGA
40472347 AAAAGAAATAAAA
1 AAAAGAAA-AAAA
40472360 GGAGAGGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
16 11 0.27
17 20 0.49
18 10 0.24
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAAAAGA
Found at i:40472359 original size:9 final size:8
Alignment explanation
Indices: 40472296--40472360 Score: 60
Period size: 9 Copynumber: 7.6 Consensus size: 8
40472286 CTACAAAAAT
40472296 AAAAGAAA
1 AAAAGAAA
40472304 AAGAAGAAAA
1 AA-AAG-AAA
40472314 AAAAGAAA
1 AAAAGAAA
*
40472322 AAAATAAGA
1 AAAAGAA-A
40472331 AAAAGAAGA
1 AAAAGAA-A
*
40472340 AAAA-AGA
1 AAAAGAAA
40472347 AAAAGAAA
1 AAAAGAAA
40472355 TAAAAG
1 -AAAAG
40472361 GAGAGGCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
7 5 0.10
8 14 0.29
9 24 0.50
10 5 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:40473300 original size:50 final size:50
Alignment explanation
Indices: 40473244--40474246 Score: 607
Period size: 50 Copynumber: 20.2 Consensus size: 50
40473234 GCAGTTAAAA
* * *
40473244 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *** * * * ** * * ** *
40473294 AAATTGAAGCTACAATTATGAATCTTGCTCCCCCGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *
40473344 AGATTGAAGCTACAACAGTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAA-C
* * * * * * ** *
40473394 AGATTGAAACTACAACGGCGAATCTTGCTTCGCC-GAC-TTGGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTC-CCTGGCAGT-GCAGTGGAAC
* * * *
40473444 AGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGC-GATACAGTGGAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAG-TGCAGTGGAAC
* * * * * * * ** *
40473494 AGTTTAAAGCTACAACGGCT-AATCTTACTTCCCCGACATTACAATTAAAA
1 AGATTGAAGCTACAACGG-TGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
40473544 AGATTGAAGCTACAACAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** * * * * * ** *
40473594 AGATTGAAGCTATAACAATGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * ** *
40473644 AGATTGAAGCCACAACGATGAATCTTACTTCTCTGGTGGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
** * * ** *
40473694 AGATTGAAGCTACAACGGAT-AATCTTGTTTTCCC-GACATTGCAGTTAAAA
1 AGATTGAAGCTACAACGG-TGAATCTT-ACTTCCCTGGCAGTGCAGTGGAAC
* * * * *
40473744 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTACAGTGGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * ** *
40473794 AGATTGAAGCTACAACGGTGAATATTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *
40473844 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * *
40473894 AGATTGAAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * *
40473944 AGATTGAAACTACAACGGCGAATCTTGCTTCCC---C-G-ACA-TTG--T
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *
40473986 A-ATTAAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *** ** * * * * ** *
40474035 AGATTAAAGCTACAACAACGAATCTTGTTTCCCCGACATTACAGTTAAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *** * * *
40474085 AGATTAAAGCTACTACGACAAATCTTACTTCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** * * * ** *
40474135 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
*** * *
40474185 AGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *
40474235 ATATTAAAGCTA
1 AGATTGAAGCTA
40474247 TAAATTACTG
Statistics
Matches: 703, Mismatches: 228, Indels: 44
0.72 0.23 0.05
Matches are distributed among these distances:
41 26 0.04
42 2 0.00
44 3 0.00
45 3 0.00
46 3 0.00
47 3 0.00
49 12 0.02
50 640 0.91
51 11 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
Found at i:40473969 original size:100 final size:100
Alignment explanation
Indices: 40473232--40473924 Score: 859
Period size: 100 Copynumber: 6.9 Consensus size: 100
40473222 ACCCCTAAGG
* * * *
40473232 TTGCAGTTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
**** * * *
40473297 TTGAAGCTACAATTATGAATCTTGCTCCCCCGATA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* *
40473332 TTGCAATTAAAAAGATTGAAGCTACAACAGTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGCAG
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAA-CAG
* * *
40473396 ATTGAAACTACAACGGCGAATCTTGCTTCGCCGAC-
65 ATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * *
40473431 TTGGCAATTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGCGATACAGTGGAGCAG
1 TT-GCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAG
* * *
40473496 TTTAAAGCTACAACGGCTAATCTTACTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * *
40473532 TTACAATTAAAAAGATTGAAGCTACAACAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *** *
40473597 TTGAAGCTATAACAATGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * *
40473632 TTGCAATTAAAAAGATTGAAGCCACAACGATGAATCTTACTTCTCTGGTGGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
** ** *
40473697 TTGAAGCTACAACGGATAATCTTGTTTTCCCGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * *
40473732 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTACAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * *
40473797 TTGAAGCTACAACGGTGAATATTACTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * *
40473832 TTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
*
40473897 TTGAAGCCACAACGGCGAATCTTACTTC
66 TTGAAGCTACAACGGCGAATCTTACTTC
40473925 TCAGGCGGTG
Statistics
Matches: 505, Mismatches: 84, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
99 5 0.01
100 496 0.98
101 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
Found at i:40474057 original size:91 final size:91
Alignment explanation
Indices: 40473900--40474074 Score: 262
Period size: 91 Copynumber: 1.9 Consensus size: 91
40473890 GAGCAGATTG
* * * **
40473900 AAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACAACGGCGA
1 AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAACTACAACAACGA
40473965 ATCTTGCTTCCCCGACATTGTAATTA
66 ATCTTGCTTCCCCGACATTGTAATTA
* *
40473991 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATT-AAAGCTACAACAACG
1 AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAA-CTACAACAACG
*
40474055 AATCTTGTTTCCCCGACATT
65 AATCTTGCTTCCCCGACATT
40474075 ACAGTTAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
90 3 0.04
91 72 0.96
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (91 bp):
AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAACTACAACAACGA
ATCTTGCTTCCCCGACATTGTAATTA
Found at i:40474109 original size:141 final size:141
Alignment explanation
Indices: 40473850--40474117 Score: 349
Period size: 141 Copynumber: 1.9 Consensus size: 141
40473840 AAAAAGATTG
* * **
40473850 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTGAAGCCACAACGGCGA
1 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
* * * * * * * *
40473915 ATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACAACGGCGAATCTTGCTTCCCCGA
66 ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAACTACAACGACAAATCTTACTTCCCCGA
40473980 CATTGTAATTA
131 CATTGTAATTA
*
40473991 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAACGA
1 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
** * * * *
40474056 ATCTTGTTTCCCCGACATTACAGTTAAATAGATT-AAAGCTACTACGACAAATCTTACTTCCC
66 ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAA-CTACAACGACAAATCTTACTTCCC
40474118 TGGCGGTGTA
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
140 3 0.03
141 104 0.97
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (141 bp):
AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAACTACAACGACAAATCTTACTTCCCCGA
CATTGTAATTA
Found at i:40474188 original size:241 final size:241
Alignment explanation
Indices: 40473763--40474217 Score: 550
Period size: 241 Copynumber: 1.9 Consensus size: 241
40473753 CTACAACAGC
* * * *** *
40473763 GAATCTTACTTCCCTGGCGGTACAGTGGAATAGATTGAAGCTACAACGGTGAATATTACTTCCCT
1 GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
* * *** *
40473828 GACATTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAG
66 GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
* * * *
40473893 CAGATTGAAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACA
131 CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
** *
40473958 ACGGCGAATCTTGCTTCCCCGACATTGTAATTAAAGCCACAACGGT
196 ACAACGAATCTTACTTCCCCGACATTGTAATTAAAGCCACAACGGT
* * **
40474004 GAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAACGAATCTTGTTTCCCC
1 GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
* * * * * *
40474069 GACATTACAGTTAAATAGATTAAAGCTACTACGACAAATCTTACTTCCCTGGCGGTGTAGTGGAA
66 GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
* * * * ** * * * *
40474134 TAGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACA
131 CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
40474199 ACAACGAATCTTACTTCCC
196 ACAACGAATCTTACTTCCC
40474218 TGGCGGTACA
Statistics
Matches: 174, Mismatches: 40, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
241 174 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (241 bp):
GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
ACAACGAATCTTACTTCCCCGACATTGTAATTAAAGCCACAACGGT
Found at i:40474402 original size:45 final size:44
Alignment explanation
Indices: 40474345--40474462 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 44
40474335 ATTTGAAATA
*
40474345 ACAAACCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
* * * * *
40474389 ACCCAATCTTATCTC-CTTGAAGTTGCTGTGAAGCAGATTGAAGCT
1 A-CAAATCTTATCTCTC-TGAAGTTGCAGTGAAGCAGGTTAAAGAT
* * *
40474434 ACTAATCATATCTCCCTGAAGTTGCAGTG
1 ACAAATCTTATCTCTCTGAAGTTGCAGTG
40474463 GAGCGGATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
44 25 0.40
45 37 0.60
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
Found at i:40482982 original size:25 final size:25
Alignment explanation
Indices: 40482943--40482997 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
40482933 AATCCATGTG
** * *
40482943 AATCATGTATCTCATGTAACTTTTA
1 AATCATGTAAATCATATAACATTTA
40482968 AATCATGTAAATCATATAACATTTA
1 AATCATGTAAATCATATAACATTTA
*
40482993 TATCA
1 AATCA
40482998 ATTCTTTCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (25 bp):
AATCATGTAAATCATATAACATTTA
Found at i:40483094 original size:20 final size:20
Alignment explanation
Indices: 40483046--40483095 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
40483036 TAACAAAAAT
*
40483046 TTATCCGTATCAACCGTAAA
1 TTATCCATATCAACCGTAAA
* *
40483066 TTATACATATCAACGGT-AA
1 TTATCCATATCAACCGTAAA
40483085 TTCATCCATAT
1 TT-ATCCATAT
40483096 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (20 bp):
TTATCCATATCAACCGTAAA
Found at i:40483300 original size:23 final size:23
Alignment explanation
Indices: 40483267--40483335 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
40483257 CCGAGTTGAT
*
40483267 AAACGGTAAGCTCTATCA-AGCTG
1 AAACGGTAAGCTCCAT-AGAGCTG
*
40483290 AAACGGAAAGCTCCATAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
40483313 AAACGGTAAGCT-CATATGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
40483336 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:40485641 original size:15 final size:15
Alignment explanation
Indices: 40485621--40485649 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40485611 TGCTTTCATA
40485621 CACAACCATCAATTC
1 CACAACCATCAATTC
40485636 CACAACCATCAATT
1 CACAACCATCAATT
40485650 ATAATATTCC
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:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
CACAACCATCAATTC
Found at i:40490638 original size:22 final size:22
Alignment explanation
Indices: 40490613--40490662 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
40490603 CCTAATCAAC
* *
40490613 TTAAATAATTGGGTTAGTACT-
1 TTAAATAATTGGATCAGTACTG
*
40490634 TTTAATAATTGGATCAGTACTG
1 TTAAATAATTGGATCAGTACTG
40490656 TTAAATA
1 TTAAATA
40490663 GAAAAGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
TTAAATAATTGGATCAGTACTG
Found at i:40492192 original size:24 final size:24
Alignment explanation
Indices: 40492156--40492204 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
40492146 AATTTTTCAA
*
40492156 ATTTAATCTTTAAATTATT-ATTT
1 ATTTAATATTTAAATTATTAATTT
40492179 ATTTAGATATTTAAATTATTAATTT
1 ATTTA-ATATTTAAATTATTAATTT
40492204 A
1 A
40492205 GTCTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTAATATTTAAATTATTAATTT
Found at i:40498034 original size:9 final size:9
Alignment explanation
Indices: 40498020--40498060 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
40498010 TTTCGAATTT
40498020 GAATAACTC
1 GAATAACTC
* *
40498029 GAATAATTT
1 GAATAACTC
40498038 GAATAACTC
1 GAATAACTC
*
40498047 GAATAATTC
1 GAATAACTC
40498056 GAATA
1 GAATA
40498061 TCAAACTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (9 bp):
GAATAACTC
Done.