Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 137 of 170
Found at i:41526632 original size:70 final size:71
Alignment explanation
Indices: 41526471--41526925 Score: 648
Period size: 70 Copynumber: 6.5 Consensus size: 71
41526461 TACCAAACTA
*
41526471 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526536 AAATTG
66 AAATTG
* * * * *
41526542 GGCAGAATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
* *
41526606 CATTTG
66 AAATTG
* *
41526612 GGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526677 AAATTG
66 AAATTG
* * * * *
41526683 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACTAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526747 AAATTG
66 AAATTG
* * * *
41526753 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
*
41526817 AATTTG
66 AAATTG
* * * *
41526823 GGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGCCTATATGCAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526888 AAATTG
66 AAATTG
* *
41526894 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
41526926 AAGCATCAAA
Statistics
Matches: 343, Mismatches: 39, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
70 200 0.58
71 143 0.42
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (71 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
AAATTG
Found at i:41526756 original size:211 final size:212
Alignment explanation
Indices: 41526471--41526925 Score: 770
Period size: 211 Copynumber: 2.2 Consensus size: 212
41526461 TACCAAACTA
*
41526471 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526536 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
66 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
* * *
41526601 ACAACCATTTGGGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGC
131 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
41526666 ATATATACAACAAATTG
196 ATATATACAACAAATTG
* * * * *
41526683 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACTAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
*
41526747 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
66 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
41526812 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
131 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
* *
41526877 CTATATGCAACAAATTG
196 ATATATACAACAAATTG
* *
41526894 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
41526926 AAGCATCAAA
Statistics
Matches: 226, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
210 8 0.04
211 183 0.81
212 35 0.15
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (212 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
ATATATACAACAAATTG
Found at i:41527680 original size:28 final size:28
Alignment explanation
Indices: 41527648--41527745 Score: 160
Period size: 28 Copynumber: 3.5 Consensus size: 28
41527638 TAATAAGTTT
41527648 GCACACTTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
41527676 GCACACTTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
* * * *
41527704 GCACACTTAGTGCTTTACAATTAAACTC
1 GCACACTTAGTGCTTAATAATCAATCTC
41527732 GCACACTTAGTGCT
1 GCACACTTAGTGCT
41527746 AATCTCATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTTAGTGCTTAATAATCAATCTC
Found at i:41553483 original size:34 final size:31
Alignment explanation
Indices: 41553445--41553567 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 31
41553435 GCTACCGAAT
*
41553445 TGATCTGTTATAAGCATGCTTATTGCTATCGTAA
1 TGATCTATTATAAGCATG-TTATTGCTA-C-TAA
* * *
41553479 TGATCTATTATAAGTATGATAATTTCTACTATA
1 TGATCTATTATAAGCATG-TTATTGCTACTA-A
* * *
41553512 TCGA-CTTGTTATAAGTATGTTATTGCTACCTTAT
1 T-GATC-TATTATAAGCATGTTATTGCTA-C-TAA
41553546 TGATCTATTATAAGCATGTTAT
1 TGATCTATTATAAGCATGTTAT
41553568 GTTACATTGC
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
32 2 0.03
33 28 0.39
34 40 0.56
35 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (31 bp):
TGATCTATTATAAGCATGTTATTGCTACTAA
Found at i:41553585 original size:17 final size:17
Alignment explanation
Indices: 41553563--41553595 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41553553 TTATAAGCAT
41553563 GTTATGTTACATTGCAC
1 GTTATGTTACATTGCAC
41553580 GTTATGTTACATTGCA
1 GTTATGTTACATTGCA
41553596 TGGGGTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (17 bp):
GTTATGTTACATTGCAC
Found at i:41556637 original size:28 final size:28
Alignment explanation
Indices: 41556605--41556736 Score: 176
Period size: 28 Copynumber: 4.7 Consensus size: 28
41556595 TGACTTTCGA
41556605 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
*
41556633 CACTAAGTGTGCGAGTTTAATTTGTAAAG
1 CACTAAGTGTGCGAATTTAA-TTGTAAAG
*
41556662 CACTAAGTGTGC-AAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAA-TTTAATTGTAAAG
* * * **
41556690 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
41556718 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAATTTA
41556737 TTAAATATTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 64 0.71
29 26 0.29
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTGTAAAG
Found at i:41556693 original size:57 final size:56
Alignment explanation
Indices: 41556605--41556736 Score: 196
Period size: 57 Copynumber: 2.3 Consensus size: 56
41556595 TGACTTTCGA
*
41556605 CACTAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATT-TGTAAAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTAT-T-AAG
* *
41556662 CACTAAGTGTGC-AAGTTTAATGGTAAAGCACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAA-TTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
41556718 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAATTTA
41556737 TTAAATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
56 20 0.29
57 48 0.70
58 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (56 bp):
CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
Found at i:41557496 original size:48 final size:48
Alignment explanation
Indices: 41557457--41557836 Score: 183
Period size: 46 Copynumber: 8.0 Consensus size: 48
41557447 TTTTATGCTT
*
41557457 AAATGCTGCCCAA-ATTGTCATATATATGCTGTCCAAATTTTTGATGTAA
1 AAATGCTGCCCAATATTGT-ATATACATGCTGT-CAAATTTTTGATGTAA
* * * *
41557506 AAATGCTGTCCAATTTTGTATATACATGCTGTTAAA-TTTTG-TGTAT
1 AAATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTTGATGTAA
* * * ** * * *
41557552 AAGTGCTGTCCAA-ATTGGTGTATGTATGCTGCCTAATTTTTGGTG-AA
1 AAATGCTGCCCAATATT-GTATATACATGCTGTCAAATTTTTGATGTAA
* * * * *
41557599 TCAATGCTGTCCAATTTTGTATATACATGCTGTTAAA-TTTTG-TGTAT
1 -AAATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTTGATGTAA
* * * ** * * *
41557646 AAGTGCTGTCCAA-ATTGGTGTATGTATGCTGCCTAATTTTTGGTG-AA
1 AAATGCTGCCCAATATT-GTATATACATGCTGTCAAATTTTTGATGTAA
* * * * * *
41557693 TCAATGCTGTCCAATTTTGTATACACATGCTGTTAAA-TTTTG-TGTAT
1 -AAATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTTGATGTAA
* * ** * * * *
41557740 AAGTGCTGTCCAA-ATTGGTATATGTATGCTGCCTAATTTTTGGTGAAAAA
1 AAATGCTGCCCAATATT-GTATATACATGCTGTCAAATTTTTGATG--TAA
* * * *
41557790 AAATGCTGTCCAATTTTATATATATATGCTGCTC-AATTTTTGATGTA
1 AAATGCTGCCCAATATTGTATATACATGCTG-TCAAATTTTTGATGTA
41557837 TAAGAGCTGT
Statistics
Matches: 248, Mismatches: 63, Indels: 41
0.70 0.18 0.12
Matches are distributed among these distances:
45 6 0.02
46 81 0.33
47 34 0.14
48 57 0.23
49 28 0.11
50 39 0.16
51 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.41
Consensus pattern (48 bp):
AAATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTTGATGTAA
Found at i:41557543 original size:23 final size:22
Alignment explanation
Indices: 41557471--41557755 Score: 137
Period size: 23 Copynumber: 12.0 Consensus size: 22
41557461 GCTGCCCAAA
41557471 TTGTCATATATATGCTGTCCAAATTT
1 TTGT-ATATA-ATGCTGT-CAAA-TT
* * *
41557497 TTGATGTAAAAATGCTGTCCAATT
1 TTG-TAT-ATAATGCTGTCAAATT
*
41557521 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
41557544 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
41557568 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
41557591 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
*
41557615 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
41557638 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
41557662 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
41557685 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
* *
41557709 TTGTATACACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
41557732 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
41557756 GGTATATGTA
Statistics
Matches: 195, Mismatches: 39, Indels: 52
0.68 0.14 0.18
Matches are distributed among these distances:
22 13 0.07
23 107 0.55
24 34 0.17
25 27 0.14
26 11 0.06
27 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (22 bp):
TTGTATATAATGCTGTCAAATT
Found at i:41557622 original size:94 final size:95
Alignment explanation
Indices: 41557481--41557851 Score: 568
Period size: 94 Copynumber: 3.9 Consensus size: 95
41557471 TTGTCATATA
* * *
41557481 TATGCTGTCCAAATTTTTGATGTAA-AAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
1 TATGCTG-CCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
41557545 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
65 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
*
41557576 TATGCTGCCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
41557640 GTGTATAAGTGCTGTCCAAATTGGTGTATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* *
41557670 TATGCTGCCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
*
41557734 GTGTATAAGTGCTGTCCAAATTGGTATATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* * * * *
41557764 TATGCTGCCTAATTTTTGGTGAAAAAAAATGCTGTCCAATTTTATATATATATGCTGCTCAATTT
1 TATGCTGCCTAATTTTTGGTG-AAATAAATGCTGTCCAATTTTGTATATACATGCTG-TTAAATT
*
41557829 TTGATGTATAAGAGCTGTCCAAA
64 TTG-TGTATAAGTGCTGTCCAAA
41557852 CAGGGTAGAT
Statistics
Matches: 258, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
93 2 0.01
94 194 0.75
95 7 0.03
96 29 0.11
97 8 0.03
98 18 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (95 bp):
TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
GTGTATAAGTGCTGTCCAAATTGGTGTATG
Found at i:41563415 original size:14 final size:15
Alignment explanation
Indices: 41563391--41563419 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41563381 GAAACTAGAG
41563391 AAAGAATAAAAGATA
1 AAAGAATAAAAGATA
41563406 AAAG-ATAAAAGATA
1 AAAGAATAAAAGATA
41563420 GGCTAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAGAATAAAAGATA
Found at i:41564190 original size:28 final size:28
Alignment explanation
Indices: 41564158--41564286 Score: 186
Period size: 28 Copynumber: 4.6 Consensus size: 28
41564148 CTTTCGACAT
*
41564158 TAAGTGTGCGAATTTAATTGTAAAGCAC
1 TAAGTGTGCGAGTTTAATTGTAAAGCAC
41564186 TAAGTGTGCGAGTTTAATTTGTAAAGCAC
1 TAAGTGTGCGAGTTTAA-TTGTAAAGCAC
*
41564215 TAAGTGTGCGAGTTTAATGGTAAAGCAC
1 TAAGTGTGCGAGTTTAATTGTAAAGCAC
* * **
41564243 TAAGTGTGCGAGTTTGATTATTGAGCAC
1 TAAGTGTGCGAGTTTAATTGTAAAGCAC
*
41564271 TAAGTGTGCGAATTTA
1 TAAGTGTGCGAGTTTA
41564287 TTAAATATTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 63 0.69
29 28 0.31
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTAATTGTAAAGCAC
Found at i:41564246 original size:57 final size:56
Alignment explanation
Indices: 41564158--41564286 Score: 197
Period size: 57 Copynumber: 2.3 Consensus size: 56
41564148 CTTTCGACAT
*
41564158 TAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATT-TGTAAAGCAC
1 TAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTAT-T-AAGCAC
* * *
41564215 TAAGTGTGCGAGTTTAATGGTAAAGCACTAAGTGTGCGAGTTTGATTATTGAGCAC
1 TAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAGCAC
41564271 TAAGTGTGCGAATTTA
1 TAAGTGTGCGAATTTA
41564287 TTAAATATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
56 20 0.30
57 45 0.68
58 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (56 bp):
TAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAGCAC
Found at i:41565088 original size:23 final size:23
Alignment explanation
Indices: 41565008--41565381 Score: 168
Period size: 23 Copynumber: 15.8 Consensus size: 23
41564998 TTTTTATGCT
* *
41565008 TAAATGCTGCCCAA-ATTGTCATA
1 TAAATGCTGTCCAATTTTGT-ATA
* *
41565031 TATATGCTGTCCAAATTTTTGATGTA
1 TAAATGCTGTCC-AA-TTTTG-TATA
*
41565057 AAAATGCTGTCCAATTTTGTATA
1 TAAATGCTGTCCAATTTTGTATA
** *
41565080 TAAATGCTGTTAAATTTTGTGTA
1 TAAATGCTGTCCAATTTTGTATA
* * * *
41565103 TAAGTGCTGTCCAAATTGGTGTA
1 TAAATGCTGTCCAATTTTGTATA
** *
41565126 TGTATGCT-ACCTAATTTTTGGTGA-A
1 TAAATGCTGTCC-AA-TTTT-GT-ATA
*
41565151 TCAATGCTGTCCAATTTTGTATA
1 TAAATGCTGTCCAATTTTGTATA
* ** *
41565174 TACATGCTGTTAAATTTTGTGTA
1 TAAATGCTGTCCAATTTTGTATA
* * * *
41565197 TAAGTGCTGTCCAAATTGGTGTA
1 TAAATGCTGTCCAATTTTGTATA
**
41565220 TGTATGCTG-CCTAATTTTTGGTGA-A
1 TAAATGCTGTCC-AA-TTTT-GT-ATA
*
41565245 TCAATGCTGTCCAATTTTGTATA
1 TAAATGCTGTCCAATTTTGTATA
* * ** *
41565268 CACATGCTGTTAAATTTTGTGTA
1 TAAATGCTGTCCAATTTTGTATA
* * *
41565291 TAAGTGCTGTCCAAATTGGTATA
1 TAAATGCTGTCCAATTTTGTATA
** *
41565314 TGTATGCTG-CCTAATTTTTGGTGAAAA
1 TAAATGCTGTCC-AA-TTTT-GT--ATA
* *
41565341 AAAATGCTGTCCAATTTTATATA
1 TAAATGCTGTCCAATTTTGTATA
*
41565364 TATATGCTG-CTCAATTTT
1 TAAATGCTGTC-CAATTTT
41565382 TGATGTATAA
Statistics
Matches: 256, Mismatches: 72, Indels: 46
0.68 0.19 0.12
Matches are distributed among these distances:
22 9 0.04
23 162 0.63
24 21 0.08
25 28 0.11
26 23 0.09
27 11 0.04
28 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (23 bp):
TAAATGCTGTCCAATTTTGTATA
Found at i:41565133 original size:46 final size:46
Alignment explanation
Indices: 41565012--41565403 Score: 286
Period size: 46 Copynumber: 8.2 Consensus size: 46
41565002 TATGCTTAAA
* * * *
41565012 TGCTGCCCAAATT-GTCATATATATGCTGTCCAAATTTTTGATGTAAAAA
1 TGCTGTCCAAATTGGT-ATATATATGCTGT-TAAA-TTTTG-TGTATAAG
* * *
41565061 TGCTGTCCAATTTTGTATATAAATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATATATGCTGTTAAATTTTGTGTATAAG
* * ** * *
41565107 TGCTGTCCAAATTGGTGTATGTATGCTACCTAATTTTTGGTGAATCAA-
1 TGCTGTCCAAATTGGTATATATATGCT-GTTAAATTTT-GTGTAT-AAG
* * *
41565155 TGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATATATGCTGTTAAATTTTGTGTATAAG
* * * * *
41565201 TGCTGTCCAAATTGGTGTATGTATGCTGCCTAATTTTTGGTGAATCAA-
1 TGCTGTCCAAATTGGTATATATATGCTG-TTAAATTTT-GTGTAT-AAG
* * * *
41565249 TGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATATATGCTGTTAAATTTTGTGTATAAG
* * * * * *
41565295 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTGAAAAAAAA
1 TGCTGTCCAAATTGGTATATATATGCTG-TTAAATTTT-GTG--TATAAG
* ** * *
41565345 TGCTGTCCAATTTTATATATATATGCTGCTCAATTTTTGATGTATAAG
1 TGCTGTCCAAATTGGTATATATATGCTG-TTAAATTTTG-TGTATAAG
*
41565393 AGCTGTCCAAA
1 TGCTGTCCAAA
41565404 CAGGGTAGAT
Statistics
Matches: 267, Mismatches: 62, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
45 4 0.01
46 84 0.31
47 40 0.15
48 72 0.27
49 28 0.10
50 39 0.15
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (46 bp):
TGCTGTCCAAATTGGTATATATATGCTGTTAAATTTTGTGTATAAG
Found at i:41565163 original size:94 final size:94
Alignment explanation
Indices: 41565033--41565403 Score: 555
Period size: 94 Copynumber: 3.9 Consensus size: 94
41565023 TTGTCATATA
* * * *
41565033 TATGCTGTCCAAATTTTTGATGTAA-AAATGCTGTCCAATTTTGTATATAAATGCTGTTAAATTT
1 TATGCTG-CCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
41565097 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
64 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
*
41565128 TATGCTACCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
41565193 TGTATAAGTGCTGTCCAAATTGGTGTATG
66 TGTATAAGTGCTGTCCAAATTGGTGTATG
*
41565222 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
*
41565287 TGTATAAGTGCTGTCCAAATTGGTATATG
66 TGTATAAGTGCTGTCCAAATTGGTGTATG
** * * * *
41565316 TATGCTGCCTAATTTTTGGTGAAAAAAAATGCTGTCCAATTTTATATATATATGCTGCTCAATTT
1 TATGCTGCCTAATTTTTGGTG--AATCAATGCTGTCCAATTTTGTATATACATGCTG-TTAAATT
*
41565381 TTGATGTATAAGAGCTGTCCAAA
63 TTG-TGTATAAGTGCTGTCCAAA
41565404 CAGGGTAGAT
Statistics
Matches: 255, Mismatches: 16, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
93 2 0.01
94 192 0.75
95 6 0.02
96 29 0.11
97 8 0.03
98 18 0.07
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (94 bp):
TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
TGTATAAGTGCTGTCCAAATTGGTGTATG
Found at i:41590564 original size:19 final size:19
Alignment explanation
Indices: 41590529--41590567 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41590519 CGACGCCAAT
41590529 TCTGTAAGTATTCTGAAAA
1 TCTGTAAGTATTCTGAAAA
*
41590548 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTATTCTGAAAA
41590567 T
1 T
41590568 ATGAGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (19 bp):
TCTGTAAGTATTCTGAAAA
Found at i:41596531 original size:9 final size:9
Alignment explanation
Indices: 41596517--41596552 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
41596507 GATAAAGTAA
41596517 AATTAAATT
1 AATTAAATT
41596526 AATTAAATT
1 AATTAAATT
*
41596535 AATCAAATT
1 AATTAAATT
41596544 AATTAAATT
1 AATTAAATT
41596553 TAATATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:41597030 original size:11 final size:11
Alignment explanation
Indices: 41597016--41597087 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 11
41597006 TTAATAAGAT
41597016 TTTATATTAAA
1 TTTATATTAAA
41597027 TTTA-ATCTAATA
1 TTTATAT-TAA-A
*
41597039 TTTATCTTGATAAA
1 TTTAT-AT--TAAA
41597053 TTTATATT-AA
1 TTTATATTAAA
41597063 TTTACTATTAAA
1 TTTA-TATTAAA
41597075 -TT-TATTAAA
1 TTTATATTAAA
41597084 TTTA
1 TTTA
41597088 ATCATAGTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
9 7 0.14
10 10 0.20
11 14 0.29
12 7 0.14
13 1 0.02
14 7 0.14
15 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:41599493 original size:16 final size:16
Alignment explanation
Indices: 41599472--41599530 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
41599462 TTAATCACTT
41599472 TAATATTAAATTAATA
1 TAATATTAAATTAATA
**
41599488 TAATATTTATCTTAATA
1 TAATA-TTAAATTAATA
* *
41599505 -AATATTATATTAATT
1 TAATATTAAATTAATA
41599520 TAATATTAAAT
1 TAATATTAAAT
41599531 CTTATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.25
16 18 0.50
17 9 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:41599508 original size:21 final size:20
Alignment explanation
Indices: 41599484--41599524 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
41599474 ATATTAAATT
*
41599484 AATATAATATTTATCTTAATA
1 AATATAATATTAAT-TTAATA
*
41599505 AATATTATATTAATTTAATA
1 AATATAATATTAATTTAATA
41599525 TTAAATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATAATATTAATTTAATA
Found at i:41599510 original size:32 final size:32
Alignment explanation
Indices: 41599473--41599586 Score: 98
Period size: 32 Copynumber: 3.7 Consensus size: 32
41599463 TAATCACTTT
41599473 AATATTAAATTAATATAATATTTATCTTAATA
1 AATATTAAATTAATATAATATTTATCTTAATA
* * *
41599505 AATATTATATTAATTTAATATTAAATCTT-AT-
1 AATATTAAATTAATATAATATT-TATCTTAATA
*
41599536 --TA--AAA-TAATAGAATATTTATCTTAGATA
1 AATATTAAATTAATATAATATTTATCTTA-ATA
* *
41599564 AACATTAAATTAAATTTAATATT
1 AATATTAAATT-AATATAATATT
41599587 AAACTATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
25 5 0.08
26 10 0.16
27 4 0.06
29 2 0.03
30 1 0.02
32 25 0.40
33 6 0.10
34 9 0.15
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (32 bp):
AATATTAAATTAATATAATATTTATCTTAATA
Found at i:41599522 original size:5 final size:6
Alignment explanation
Indices: 41599471--41599528 Score: 56
Period size: 5 Copynumber: 10.7 Consensus size: 6
41599461 CTTAATCACT
* *
41599471 TTAATA TTAA-A TTAATA -TAATA TTTATC TTAATA --AATA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
41599514 TTAAT- TTAATA TTAA
1 TTAATA TTAATA TTAA
41599529 ATCTTATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.10
5 20 0.48
6 18 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:41599537 original size:58 final size:58
Alignment explanation
Indices: 41599475--41599604 Score: 192
Period size: 58 Copynumber: 2.2 Consensus size: 58
41599465 ATCACTTTAA
* * *
41599475 TATTAAATTAATATAATATTTATCTTA-ATAAATATTATATT-AATTTAATATTAAATC
1 TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAA-C
*
41599532 TTATTAAAATAATAGAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
41599591 TATTAAAATAATAT
1 TATTAAAATAATAT
41599605 TATTTTTGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 38 0.58
59 13 0.20
60 14 0.22
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (58 bp):
TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
Found at i:41611608 original size:19 final size:19
Alignment explanation
Indices: 41611584--41611664 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 19
41611574 AAAAATTTTT
41611584 AAACACGAGAATTTTTTGA
1 AAACACGAGAATTTTTTGA
41611603 AAACACGA-AATTTTTTTTTGA
1 AAACACGAGAA---TTTTTTGA
* *
41611624 AAACAC-AAAAATTTTTGA
1 AAACACGAGAATTTTTTGA
41611642 AATAC-CG-GAA-TTTTTGA
1 AA-ACACGAGAATTTTTTGA
41611659 AAACAC
1 AAACAC
41611665 AAAGATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 14 0.26
19 10 0.19
20 1 0.02
21 16 0.30
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (19 bp):
AAACACGAGAATTTTTTGA
Found at i:41611618 original size:56 final size:58
Alignment explanation
Indices: 41611558--41611674 Score: 156
Period size: 56 Copynumber: 2.1 Consensus size: 58
41611548 ACAATAACTC
*
41611558 TTTTTTTTTTGAAAA-A-AAAAATTTTT-AAACA-CGAGAATTTTTTGAAAACACGAA-A
1 TTTTTTTTTTGAAAACACAAAAATTTTTGAAACACCG-GAA-TTTTTGAAAACACAAAGA
*
41611613 -TTTTTTTTTGAAAACACAAAAATTTTTGAAATACCGGAATTTTTGAAAACACAAAGA
1 TTTTTTTTTTGAAAACACAAAAATTTTTGAAACACCGGAATTTTTGAAAACACAAAGA
41611670 TTTTT
1 TTTTT
41611675 GAAACACGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
54 14 0.26
55 1 0.02
56 25 0.46
57 8 0.15
58 6 0.11
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (58 bp):
TTTTTTTTTTGAAAACACAAAAATTTTTGAAACACCGGAATTTTTGAAAACACAAAGA
Found at i:41611640 original size:18 final size:18
Alignment explanation
Indices: 41611563--41611678 Score: 82
Period size: 17 Copynumber: 6.5 Consensus size: 18
41611553 AACTCTTTTT
41611563 TTTTTGAAAA-A-AAAAA
1 TTTTTGAAAACACAAAAA
* *
41611579 TTTTT--AAACACGAGAAT
1 TTTTTGAAAACAC-AAAAA
**
41611596 TTTTTGAAAACACGAAATTTT
1 TTTTTGAAAACAC-AAA--AA
41611617 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACAAAAA
**
41611635 TTTTTGAAATAC-C-GGAA
1 TTTTTGAAA-ACACAAAAA
*
41611652 TTTTTGAAAACACAAAGA
1 TTTTTGAAAACACAAAAA
41611670 TTTTTGAAA
1 TTTTTGAAA
41611679 CACGAATTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 7 0.09
17 20 0.25
18 20 0.25
19 11 0.14
20 3 0.04
21 14 0.18
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (18 bp):
TTTTTGAAAACACAAAAA
Found at i:41611673 original size:17 final size:17
Alignment explanation
Indices: 41611563--41611678 Score: 78
Period size: 18 Copynumber: 6.5 Consensus size: 17
41611553 AACTCTTTTT
*
41611563 TTTTTGAAAA-AAAAAA
1 TTTTTGAAAACACAAAA
*
41611579 TTTTT--AAACACGAGAAT
1 TTTTTGAAAACAC-A-AAA
*
41611596 TTTTTGAAAACACGAAATTTT
1 TTTTTGAAAACAC-AAA---A
41611617 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACAC-AAAA
**
41611635 TTTTTGAAATAC-CGGAA
1 TTTTTGAAA-ACACAAAA
41611652 TTTTTGAAAACACAAAGA
1 TTTTTGAAAACACAAA-A
41611670 TTTTTGAAA
1 TTTTTGAAA
41611679 CACGAATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 8 0.10
17 20 0.25
18 22 0.27
19 10 0.12
21 17 0.21
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTTGAAAACACAAAA
Found at i:41611691 original size:17 final size:18
Alignment explanation
Indices: 41611584--41611690 Score: 89
Period size: 18 Copynumber: 5.9 Consensus size: 18
41611574 AAAAATTTTT
41611584 AAACACGAGAATTTTTTGA
1 AAACACGA-AATTTTTTGA
41611603 AAACACGAAATTTTTTTTTGA
1 AAACACGAAA---TTTTTTGA
* *
41611624 AAACACAAAAATTTTTGA
1 AAACACGAAATTTTTTGA
*
41611642 AATAC-CGGAA-TTTTTGA
1 AA-ACACGAAATTTTTTGA
*
41611659 AAACAC-AAAGATTTTTG-
1 AAACACGAAA-TTTTTTGA
41611676 AAACACG-AATTTTTT
1 AAACACGAAATTTTTT
41611691 TTAATTTTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
16 9 0.12
17 18 0.24
18 20 0.27
19 10 0.14
21 17 0.23
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
AAACACGAAATTTTTTGA
Found at i:41612219 original size:21 final size:22
Alignment explanation
Indices: 41612193--41612233 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41612183 CCCTCCCTTT
*
41612193 TTCCTTT-TTCTTTTTTTTTTC
1 TTCCTTTCTTCCTTTTTTTTTC
41612214 TTCCTTTCTTCCTTTTTTTT
1 TTCCTTTCTTCCTTTTTTTT
41612234 CTTTTTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTCCTTTCTTCCTTTTTTTTTC
Found at i:41612230 original size:29 final size:27
Alignment explanation
Indices: 41612188--41612241 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
41612178 CTTTCCCCTC
*
41612188 CCTTTTTCCTTTTTCTTTTTTTTTTCTT
1 CCTTTTTCCTTTTT-TTTCTTTTTTCTT
41612216 CCTTTCTTCCTTTTTTTTCTTTTTTC
1 CCTTT-TTCCTTTTTTTTCTTTTTTC
41612242 GGCTGGGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (27 bp):
CCTTTTTCCTTTTTTTTCTTTTTTCTT
Found at i:41612538 original size:16 final size:14
Alignment explanation
Indices: 41612519--41612572 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
41612509 AGATTTTTTA
*
41612519 TTTTTTCTCTTTCC
1 TTTTTTTTCTTTCC
41612533 TTTTTTTTCTTTCC
1 TTTTTTTTCTTTCC
*
41612547 -TTTTCTTCTTT-C
1 TTTTTTTTCTTTCC
*
41612559 TTCTTCTTTCTTTC
1 TT-TTTTTTCTTTC
41612573 TTTCTTATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 11 0.33
14 21 0.64
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCTTTCC
Found at i:41612545 original size:20 final size:19
Alignment explanation
Indices: 41612512--41612563 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
41612502 CTATTTTAGA
*
41612512 TTTTTTATTTTTTCTCTTTCC
1 TTTTTT-TTCTTTC-CTTTCC
*
41612533 TTTTTTTTCTTTCCTTTTC
1 TTTTTTTTCTTTCCTTTCC
*
41612552 TTCTTTCTTCTT
1 TT-TTTTTTCTT
41612564 CTTTCTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.26
20 14 0.52
21 6 0.22
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTTCTTTCCTTTCC
Found at i:41612557 original size:27 final size:26
Alignment explanation
Indices: 41612521--41612572 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
41612511 ATTTTTTATT
*
41612521 TTTTCTCTTTCCTT-TTTTTTCTTTCC
1 TTTTCTCTTT-CTTCTTCTTTCTTTCC
41612547 TTTTCTTCTTTCTTCTTCTTTCTTTC
1 TTTTC-TCTTTCTTCTTCTTTCTTTC
41612573 TTTCTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTCTCTTTCTTCTTCTTTCTTTCC
Found at i:41613301 original size:30 final size:30
Alignment explanation
Indices: 41613113--41613303 Score: 138
Period size: 30 Copynumber: 6.4 Consensus size: 30
41613103 TTTTTTGGGG
* * * * *
41613113 AAAATGTAATTTTAGGAAAATAT-GGGGAC
1 AAAATGTAATTTTAAGAAAGTTTAAGGGTC
* *
41613142 AAAATGTAATTTCT-AGAAAGTTTAGGGGCC
1 AAAATGTAATTT-TAAGAAAGTTTAAGGGTC
* * * * *
41613172 CAAATGAAAATTTAAGAAAGTTAAAAGGTC
1 AAAATGTAATTTTAAGAAAGTTTAAGGGTC
* * *
41613202 AAAATGTAAATGTAGGAAAGTTT-AGGGTCC
1 AAAATGTAATTTTAAGAAAGTTTAAGGGT-C
* * * *
41613232 AAAATGCAATTTTGA-AAAGTTAAAGGGTT
1 AAAATGTAATTTTAAGAAAGTTTAAGGGTC
** *
41613261 AAAAAATAATTTTAAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAAGAAAGTTTAAGGGTC
41613291 AAAATGTAATTTT
1 AAAATGTAATTTT
41613304 TTATTTAAAA
Statistics
Matches: 124, Mismatches: 32, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
29 40 0.32
30 84 0.68
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (30 bp):
AAAATGTAATTTTAAGAAAGTTTAAGGGTC
Found at i:41613673 original size:77 final size:76
Alignment explanation
Indices: 41613491--41614097 Score: 550
Period size: 77 Copynumber: 7.8 Consensus size: 76
41613481 GCGACCCAAA
* **
41613491 GCTCAACTCACCTCTCG-AATCATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAGAATACCT
1 GCTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTTAAAAGTAGAAATTG-AAA-AATACCT
* *
41613554 CAGCATGCGACCCGAG
63 C-G-ACGTGACCCGAG
* * *
41613570 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTAAAAGCAAAAATTGAAAAATACCTCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTAAAAGTAGAAATTGAAAAATACCTCG
*
41613635 ACGTGACTCGAG
65 ACGTGACCCGAG
* * * *
41613647 ACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTGAAAAGTAGTAATTGAAAATTACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTT-AAAAGTAGAAATTGAAAAATACCTC
41613712 GACGTGCGACCCGAG
64 GACGT--GACCCGAG
* * *
41613727 GCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGAAATTTAAAAGAAATA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT-TTT-AAAAGTAGAAA-TT-GAA-AAATA
* * *
41613792 CCTTGGCATGTGACTCGAG
60 CC-TCG-ACGTGACCCGAG
* * * * *
41613811 ACTCAACTCACCTCTCACAATATAAGTTGATTTTTTTGAAAAGTAGTAATTGAAAAATACCTCGA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAGTAGAAATTGAAAAATACCTCGA
* *
41613876 CGTGACTCAAG
66 CGTGACCCGAG
* * *
41613887 GCTCAACTTCACCTCTTGCAATATGAGTTGATTTTTTTT----GCAGAAATTTAAAAGAAATACC
1 GCTCAAC-TCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAGTAGAAA-TT-GAA-AAATACC
* *
41613948 TCGGCATGTAACCCGAG
62 TC-G-ACGTGACCCGAG
* * *
41613965 GCTCAACTCACATCTCGCGATATGAGTTGATTTTTTTGAAAAGTAGAAATTG-AAAATACCTC-A
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAGTAGAAATTGAAAAATACCTCGA
*
41614028 GCGTGACCTGAG
66 -CGTGACCCGAG
* * * * *
41614040 GCTCAACTCACTTTTCGCATTATGAGTTGA--TTTTTGAAAAATAGAAATTGCAAAAATA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAGTAGAAATTG-AAAAATA
41614098 TAATTCTTGA
Statistics
Matches: 442, Mismatches: 61, Indels: 54
0.79 0.11 0.10
Matches are distributed among these distances:
73 24 0.05
74 3 0.01
75 42 0.10
76 25 0.06
77 111 0.25
78 50 0.11
79 36 0.08
80 50 0.11
81 46 0.10
82 4 0.01
83 7 0.02
84 39 0.09
85 2 0.00
86 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (76 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAGTAGAAATTGAAAAATACCTCGA
CGTGACCCGAG
Found at i:41613922 original size:241 final size:234
Alignment explanation
Indices: 41613479--41614074 Score: 690
Period size: 240 Copynumber: 2.5 Consensus size: 234
41613469 ATAGCTTGGT
* * *
41613479 GTGCGACCCAAAGCTCAACTCACCTCTCG-AATCATGAGTTGA-TTTTTTGAAAAACAGAAATTG
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTGAAAAATAGAAATTG
* ** *
41613542 AAAAGAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
65 AAAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTTTT
* *
41613607 TTAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCGAGACTCAACTCACCTCTTGCAATATGA
130 TGAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAACTCACCTCTTGCAATATGA
**
41613672 GTTGATTTTTTTTTG-A-AAAGTAGTAATTGAAAATTACCTCGAC
195 GTTGA-TTTTTTTTGCAGAAA-T-GTAAAAG-AAA-TACCTCGAC
*
41613715 GTGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGAAAT
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT-TTTGAAAAATAGAAAT
* ** * *
41613780 TTAAAAGAAATACCTTGGCATGTGACTCGAGACTCAACTCACCTCTCACAATATAAGTTGA-TTT
63 TGAAAAG-AATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTT
* ** *
41613844 TTTTGAAAAGTAGTAATTGAAAAATACCTCGACGTGACTCAAGGCTCAACTTCACCTCTTGCAAT
127 TTTTGAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAAC-TCACCTCTTGCAAT
* *
41613909 ATGAGTTGATTTTTTTTGCAGAAATTTAAAAGAAATACCTCGGC
191 ATGAGTTGATTTTTTTTGCAGAAATGTAAAAGAAATACCTCGAC
* ** * * *
41613953 ATGTAACCCGAGGCTCAACTCACATCTCGCGATATGAGTTGATTTTTTTGAAAAGTAGAAATTG-
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGA
* * * * * * * *
41614017 -AA-AATACCTCAGC--GTGACCTGAGGCTCAACTCACTTTTCGCATTATGAGTTGATTTTT
66 AAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTT
41614075 GAAAAATAGA
Statistics
Matches: 309, Mismatches: 41, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
229 32 0.10
230 4 0.01
231 9 0.03
233 2 0.01
235 16 0.05
236 39 0.13
237 3 0.01
238 44 0.14
239 6 0.02
240 81 0.26
241 70 0.23
242 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (234 bp):
GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGA
AAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTTTTT
GAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAACTCACCTCTTGCAATATGAG
TTGATTTTTTTTGCAGAAATGTAAAAGAAATACCTCGAC
Found at i:41613975 original size:154 final size:154
Alignment explanation
Indices: 41613492--41614074 Score: 646
Period size: 154 Copynumber: 3.7 Consensus size: 154
41613482 CGACCCAAAG
**
41613492 CTCAACTCACCTCTCG-AATCATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAGAATACCTC
1 CTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTGAAAAGTAGAAATTG-AAA-AATACCTC
* * *
41613555 AGCATGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTTAAAAGCA-AAA
63 -G-ACGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTT----GCAGAAA
* * *
41613619 ATT-GAA-AAATACCTC-G-ACGTGACTCGAGA
122 TTTAAAAGAAATACCTCGGCATGTGACTCGAGA
* * *
41613648 CTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTGAAAAGTAGTAATTGAAAATTACCTCG
1 CTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAGTAGAAATTGAAAAATACCTCG
* *
41613713 ACGTGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGAA
64 ACGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-TTTG-----CAGAA
*
41613778 ATTTAAAAGAAATACCTTGGCATGTGACTCGAGA
121 ATTTAAAAGAAATACCTCGGCATGTGACTCGAGA
* * *
41613812 CTCAACTCACCTCTCACAATATAAGTTGATTTTTTTGAAAAGTAGTAATTGAAAAATACCTCGAC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGAC
* * *
41613877 GTGACTCAAGGCTCAACTTCACCTCTTGCAATATGAGTTGA-TTTTTTTTGCAGAAATTTAAAAG
66 GTGACCCGAGGCTCAAC-TCACCTCTCGCAATATGAGTTGATTTTTTTTTGCAGAAATTTAAAAG
* * *
41613941 AAATACCTCGGCATGTAACCCGAGG
130 AAATACCTCGGCATGTGACTCGAGA
* *
41613966 CTCAACTCACATCTCGCGATATGAGTTGATTTTTTTGAAAAGTAGAAATTG-AAAATACCTC-AG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGA-
* * * *
41614029 CGTGACCTGAGGCTCAACTCACTTTTCGCATTATGAGTTGATTTTT
65 CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
41614075 GAAAAATAGA
Statistics
Matches: 368, Mismatches: 39, Indels: 43
0.82 0.09 0.10
Matches are distributed among these distances:
152 20 0.05
153 29 0.08
154 81 0.22
155 2 0.01
156 25 0.07
157 52 0.14
158 6 0.02
159 23 0.06
160 23 0.06
161 23 0.06
162 45 0.12
163 1 0.00
164 38 0.10
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (154 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGAC
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGCAGAAATTTAAAAGA
AATACCTCGGCATGTGACTCGAGA
Found at i:41626024 original size:17 final size:17
Alignment explanation
Indices: 41625952--41626108 Score: 113
Period size: 17 Copynumber: 8.9 Consensus size: 17
41625942 AATAACTCTT
41625952 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
41625970 TTTGTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
41625987 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
*
41626004 TTTTTAAAACACGAGAAT
1 TTTTTAAAACACGA-AAA
* *
41626022 TTTTTGAAAAAACGAAATTTT
1 TTTTT-AAAACACGAAA---A
*
41626043 TTTTTAAAAACACGGAAA
1 TTTTT-AAAACACGAAAA
* * *
41626061 TTTTTGAAATACCAAAA
1 TTTTTAAAACACGAAAA
*
41626078 TTTTTGAAAACAC--AGA
1 TTTTT-AAAACACGAAAA
*
41626094 TTTTTGAAACACGAA
1 TTTTTAAAACACGAA
41626109 TTTTTTTTAT
Statistics
Matches: 111, Mismatches: 18, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.05
16 11 0.10
17 43 0.39
18 28 0.25
19 8 0.07
21 15 0.14
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:41626045 original size:21 final size:22
Alignment explanation
Indices: 41626021--41626065 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
41626011 AACACGAGAA
*
41626021 TTTTTTGAAAAA-AC-GAAATT
1 TTTTTTTAAAAACACGGAAATT
41626041 TTTTTTTAAAAACACGGAAATT
1 TTTTTTTAAAAACACGGAAATT
41626063 TTT
1 TTT
41626066 GAAATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 2 0.09
22 9 0.41
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTTTTTAAAAACACGGAAATT
Found at i:41626078 original size:74 final size:70
Alignment explanation
Indices: 41625975--41626116 Score: 180
Period size: 74 Copynumber: 2.0 Consensus size: 70
41625965 GAAAATTTGT
*
41625975 AAAACACGAGAATTTTAGAAACACGAAAATTTTT-AAAACACGAGAATTTTTTGAAAAAACGAAA
1 AAAACACGAGAATTTTAGAAACACCAAAATTTTTGAAAACAC-AG-A-TTTTTG-AAAAACG-AA
41626039 TTTTTTTTTA
61 TTTTTTTTTA
* * *
41626049 AAAACACG-GAAATTTTTGAAATACCAAAATTTTTGAAAACACAGATTTTTGAAACACGAATTTT
1 AAAACACGAG-AATTTTAGAAACACCAAAATTTTTGAAAACACAGATTTTTGAAAAACGAATTTT
41626113 TTTT
65 TTTT
41626117 ATTTTTCCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
70 10 0.16
71 6 0.10
72 6 0.10
73 2 0.03
74 31 0.50
75 7 0.11
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (70 bp):
AAAACACGAGAATTTTAGAAACACCAAAATTTTTGAAAACACAGATTTTTGAAAAACGAATTTTT
TTTTA
Found at i:41626079 original size:39 final size:39
Alignment explanation
Indices: 41626004--41626082 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
41625994 AACACGAAAA
* *
41626004 TTTTTAAAACACGAGAATTTTTTGAAAAAACGAAATTTT
1 TTTTTAAAACACGAGAAATTTTTGAAAAAACAAAATTTT
* *
41626043 TTTTTAAAAACACG-GAAATTTTTGAAATACCAAAATTTT
1 TTTTT-AAAACACGAGAAATTTTTGAAAAAACAAAATTTT
41626082 T
1 T
41626083 GAAAACACAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (39 bp):
TTTTTAAAACACGAGAAATTTTTGAAAAAACAAAATTTT
Found at i:41626111 original size:15 final size:15
Alignment explanation
Indices: 41626059--41626113 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
41626049 AAAACACGGA
*
41626059 AATTTTTGAAATACCAA
1 AATTTTTGAAA-A-CAC
41626076 AATTTTTGAAAACAC
1 AATTTTTGAAAACAC
41626091 AGATTTTTG-AAACAC
1 A-ATTTTTGAAAACAC
41626106 GAATTTTT
1 -AATTTTT
41626114 TTTATTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 15 0.43
16 9 0.26
17 11 0.31
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (15 bp):
AATTTTTGAAAACAC
Found at i:41626642 original size:22 final size:22
Alignment explanation
Indices: 41626617--41626659 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41626607 CTCCCTTTTT
* *
41626617 CTTTTTTCTTTTTTTTTTCTTC
1 CTTTCTTCCTTTTTTTTTCTTC
41626639 CTTTCTTCCTTTTTTTTTCTT
1 CTTTCTTCCTTTTTTTTTCTT
41626660 TTTTCGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
CTTTCTTCCTTTTTTTTTCTTC
Found at i:41626661 original size:29 final size:28
Alignment explanation
Indices: 41626603--41626664 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
41626593 ATTTTGGGCA
*
41626603 TTTTCTCCCTTTTTCTTTTTTCTTTTTT
1 TTTTCTCCCTTTTTCTTTTTTCTTTCTT
*
41626631 TTTTCTTCCTTTCTTCCTTTTTT-TTTCTT
1 TTTTCTCCCTTT-TT-CTTTTTTCTTTCTT
41626660 TTTTC
1 TTTTC
41626665 GGTTGGGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 12 0.40
30 7 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTCTCCCTTTTTCTTTTTTCTTTCTT
Found at i:41626963 original size:21 final size:20
Alignment explanation
Indices: 41626942--41626992 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
41626932 TTTTTTCTCT
41626942 TTCCTTTTTCTTCTTTCTTC
1 TTCCTTTTTCTTCTTTCTTC
* *
41626962 TT-CTTTCT-TTCTTTCTTA
1 TTCCTTTTTCTTCTTTCTTC
*
41626980 TTCCATTTTCTTC
1 TTCCTTTTTCTTC
41626993 CTTCCCCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.44
19 9 0.36
20 5 0.20
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCCTTTTTCTTCTTTCTTC
Found at i:41627167 original size:26 final size:26
Alignment explanation
Indices: 41627122--41627176 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
41627112 TGCTCTTTCG
41627122 TTTTTTCTCTTTTTTACTT-GTTGTT
1 TTTTTTCTCTTTTTTACTTGGTTGTT
*
41627147 TTTTTTC-CTTTTTGCTTCTTGGTTGTT
1 TTTTTTCTCTTTTT--TACTTGGTTGTT
41627174 TTT
1 TTT
41627177 GCTAGGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 7 0.27
26 4 0.15
27 9 0.35
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTTTCTCTTTTTTACTTGGTTGTT
Found at i:41627698 original size:30 final size:31
Alignment explanation
Indices: 41627652--41627709 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
41627642 TGCAATTTTG
41627652 AAAGGTTAAGGGGTCAAAAAATAATTTTAAA
1 AAAGGTTAAGGGGTCAAAAAATAATTTTAAA
* **
41627683 AAAGTTTAA-GGGTCAAAATGTAATTTT
1 AAAGGTTAAGGGGTCAAAAAATAATTTT
41627710 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (31 bp):
AAAGGTTAAGGGGTCAAAAAATAATTTTAAA
Found at i:41635683 original size:6 final size:6
Alignment explanation
Indices: 41635666--41635698 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
41635656 AAATTATATA
41635666 ATTAAC -TTAAC ATTAAC ATTAAC ATTAAC ATTA
1 ATTAAC ATTAAC ATTAAC ATTAAC ATTAAC ATTA
41635699 TTAAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTAAC
Found at i:41637938 original size:27 final size:26
Alignment explanation
Indices: 41637880--41637940 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
41637870 GACATTACGG
* * * *
41637880 TCATTTTACCCTATGGGGTTTTTTGG
1 TCATTTTACCCTAAGGGGTATTATGA
*
41637906 TAATTTTACCCTACAGGGGTATTATGA
1 TCATTTTACCCTA-AGGGGTATTATGA
41637933 TCATTTTA
1 TCATTTTA
41637941 AAAATATTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (26 bp):
TCATTTTACCCTAAGGGGTATTATGA
Found at i:41648924 original size:81 final size:81
Alignment explanation
Indices: 41648786--41648947 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 81
41648776 GATTCCCAAG
* * *
41648786 ATAAGGCATCTCCCTAATTAGATCTGATAAATAGCATATTAGTCTTCCAATCAGTTTGATCA-TT
1 ATAAGGCATCTCCCCAATTAGATATGATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
41648850 TCTGATTAGACTAAGGA
66 TC-GATTAGACTAAGGA
* * *
41648867 ATAAGGCATCTCCCCAATTGGATATGATAAATAGCATATTAGTCCTCCAATCGGTTTGATCGTTT
1 ATAAGGCATCTCCCCAATTAGATATGATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
41648932 TCGATTAGACTAAGGA
66 TCGATTAGACTAAGGA
41648948 CATATTTAGG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 70 0.95
82 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (81 bp):
ATAAGGCATCTCCCCAATTAGATATGATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
TCGATTAGACTAAGGA
Found at i:41651528 original size:17 final size:17
Alignment explanation
Indices: 41651506--41651544 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
41651496 GATGGTGAGA
*
41651506 ATCTTAAATTAGTTTCC
1 ATCTTAAATTAGTTACC
41651523 ATCTT-AATTAGTTACC
1 ATCTTAAATTAGTTACC
41651539 ATCTTA
1 ATCTTA
41651545 GTTGCACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (17 bp):
ATCTTAAATTAGTTACC
Found at i:41660781 original size:30 final size:30
Alignment explanation
Indices: 41660745--41660806 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
41660735 CTCCATCTAA
41660745 ACTCAATCCCATCGAATCCAAGAATTTACG
1 ACTCAATCCCATCGAATCCAAGAATTTACG
41660775 ACTCAATCCCATCGAATCCAAGAATTTACG
1 ACTCAATCCCATCGAATCCAAGAATTTACG
41660805 AC
1 AC
41660807 GCCGTTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (30 bp):
ACTCAATCCCATCGAATCCAAGAATTTACG
Found at i:41673381 original size:24 final size:24
Alignment explanation
Indices: 41673347--41673393 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41673337 GCTAAAGGAA
41673347 AAATGTAACAATAGGAAATACAAC
1 AAATGTAACAATAGGAAATACAAC
* *
41673371 AAATGTGACAATGGGAAATACAA
1 AAATGTAACAATAGGAAATACAA
41673394 TCATTGTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (24 bp):
AAATGTAACAATAGGAAATACAAC
Found at i:41677263 original size:13 final size:13
Alignment explanation
Indices: 41677245--41677270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41677235 TAATTTTTAA
41677245 AAAATTGATTTTT
1 AAAATTGATTTTT
41677258 AAAATTGATTTTT
1 AAAATTGATTTTT
41677271 CTTTCAGTAA
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:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AAAATTGATTTTT
Found at i:41682606 original size:24 final size:24
Alignment explanation
Indices: 41682560--41682606 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
41682550 ACACCAGATG
*
41682560 AAAATAATTACATAGTAAATTTAT
1 AAAATAATTAAATAGTAAATTTAT
*
41682584 AAAATAAATTAAATA-TAATTTTA
1 AAAAT-AATTAAATAGTAAATTTA
41682607 GTTAGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATAATTAAATAGTAAATTTAT
Found at i:41682879 original size:12 final size:12
Alignment explanation
Indices: 41682862--41682887 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41682852 AGGATATGCA
41682862 ATCTTAGATATG
1 ATCTTAGATATG
41682874 ATCTTAGATATG
1 ATCTTAGATATG
41682886 AT
1 AT
41682888 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:41682910 original size:19 final size:20
Alignment explanation
Indices: 41682874--41682921 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
41682864 CTTAGATATG
*
41682874 ATCTTAGATATGATATATGCA
1 ATCTTAGATACGA-ATATGCA
41682895 ATCTTAGATACG-ATATGCA
1 ATCTTAGATACGAATATGCA
41682914 ATCTTAGA
1 ATCTTAGA
41682922 AGATACGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
ATCTTAGATACGAATATGCA
Found at i:41682943 original size:23 final size:22
Alignment explanation
Indices: 41682888--41682945 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
41682878 TAGATATGAT
41682888 ATATGCAATCTT---AGATACG
1 ATATGCAATCTTAGAAGATACG
41682907 ATATGCAATCTTAGAAGATACG
1 ATATGCAATCTTAGAAGATACG
* *
41682929 ATTTTGTAATCTTAGAA
1 A-TATGCAATCTTAGAA
41682946 ATTTAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.36
22 8 0.24
23 13 0.39
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATACG
Found at i:41683268 original size:3 final size:3
Alignment explanation
Indices: 41683260--41683295 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
41683250 AGTTATTAAG
* *
41683260 TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41683296 CTATATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41683445 original size:17 final size:17
Alignment explanation
Indices: 41683414--41683457 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
41683404 CATAACTTTT
*
41683414 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
41683430 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
41683447 ATATACATTTT
1 ATATACATTTT
41683458 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:41683645 original size:30 final size:30
Alignment explanation
Indices: 41683611--41683667 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41683601 TATTTGTTTA
*
41683611 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTATATAAT-TTTTTTATAATC
41683641 TATATATATGTATATAATTTTTTTATA
1 TATATATATGTATATAATTTTTTTATA
41683668 TATGTACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (30 bp):
TATATATATGTATATAATTTTTTTATAATC
Found at i:41686725 original size:20 final size:19
Alignment explanation
Indices: 41686689--41686731 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
41686679 TCATATTTGT
*
41686689 ATTATTTTCTCAAAATTTTA
1 ATTATTTTCT-AAAAATTTA
41686709 ATTATTTT-TAAATAATTTA
1 ATTATTTTCTAAA-AATTTA
41686728 ATTA
1 ATTA
41686732 AAAGTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTTTCTAAAAATTTA
Found at i:41691460 original size:117 final size:117
Alignment explanation
Indices: 41691252--41691723 Score: 831
Period size: 117 Copynumber: 4.0 Consensus size: 117
41691242 GAAACGTTTA
41691252 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
41691317 AGCTAGACAGGTCATAACAATC-ACAACATGATACGTTTATACTCCTTAACCT
66 AGCTAGACAGGTCATAACAA-CGACAACATGATACATTTATACTCCTTAACCT
*
41691369 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTTGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
41691434 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACCCCTTAACCT
66 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
*
41691486 TAATAG-AGAAGAAAGGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
41691550 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
66 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
* * *
41691602 TAATAGAAGAAGAAAGGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
* * *
41691667 AGCTAGACAGATCATAACAACCACAACATGATACATTTATACTTCTTAACCT
66 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
41691719 TAATA
1 TAATA
41691724 AGATAAATCT
Statistics
Matches: 342, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
116 114 0.33
117 228 0.67
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (117 bp):
TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
Found at i:41691666 original size:233 final size:234
Alignment explanation
Indices: 41691252--41691723 Score: 831
Period size: 233 Copynumber: 2.0 Consensus size: 234
41691242 GAAACGTTTA
41691252 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
41691317 AGCTAGACAGGTCATAACAATCACAACATGATACGTTTATACTCCTTAACCTTAATAGAAGAAGA
66 AGCTAGACAGGTCATAACAATCACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
* * * *
41691382 AAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTTGACTCCACTAGCTAGACAGGTC
131 AAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGATC
*
41691447 ATAACAACGACAACATGATACATTTATACCCCTTAACCT
196 ATAACAACCACAACATGATACATTTATACCCCTTAACCT
*
41691486 TAATAG-AGAAGAAAGGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
41691550 AGCTAGACAGGTCATAACAA-CGACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAG
66 AGCTAGACAGGTCATAACAATC-ACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAG
*
41691614 AAAGGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGAT
130 AAAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGAT
**
41691679 CATAACAACCACAACATGATACATTTATACTTCTTAACCT
195 CATAACAACCACAACATGATACATTTATACCCCTTAACCT
41691719 TAATA
1 TAATA
41691724 AGATAAATCT
Statistics
Matches: 227, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
232 1 0.00
233 220 0.97
234 6 0.03
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (234 bp):
TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
AGCTAGACAGGTCATAACAATCACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
AAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGATC
ATAACAACCACAACATGATACATTTATACCCCTTAACCT
Found at i:41692027 original size:12 final size:12
Alignment explanation
Indices: 41691978--41692043 Score: 53
Period size: 13 Copynumber: 5.4 Consensus size: 12
41691968 ACAAATAAAT
*
41691978 AAAATTTTATTTA
1 AAAATATTA-TTA
* *
41691991 TAAATTTTATTA
1 AAAATATTATTA
*
41692003 AAAATACTAATTA
1 AAAATA-TTATTA
41692016 AAAATATTATT-
1 AAAATATTATTA
* *
41692027 AATATATTATTT
1 AAAATATTATTA
41692039 AAAAT
1 AAAAT
41692044 TTAAAAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
11 10 0.23
12 15 0.34
13 19 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
AAAATATTATTA
Found at i:41693486 original size:9 final size:9
Alignment explanation
Indices: 41693474--41693514 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
41693464 AATTTATTTT
41693474 AAAAAATTA
1 AAAAAATTA
41693483 AAAAAATTA
1 AAAAAATTA
41693492 AAAAAATTA
1 AAAAAATTA
*
41693501 AAAATATATA
1 AAAAAAT-TA
41693511 AAAA
1 AAAA
41693515 TTATTGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAAATTA
Found at i:41694428 original size:20 final size:19
Alignment explanation
Indices: 41694365--41694430 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
41694355 CACTACGGTG
*
41694365 CTCCTGATAGTACTTTTGTA
1 CTCCTGATAGCA-TTTTGTA
* ** *
41694385 CTCCTGTTAGCATTACAGTG
1 CTCCTGATAGCATT-TTGTA
41694405 CTCCTGATAGCATATTTGTA
1 CTCCTGATAGCAT-TTTGTA
41694425 CTCCTG
1 CTCCTG
41694431 TTTGCACTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (19 bp):
CTCCTGATAGCATTTTGTA
Found at i:41694451 original size:40 final size:40
Alignment explanation
Indices: 41694349--41694457 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
41694339 ATACGCATCA
*
41694349 TGTTAGCACTACGGTGCTCCTGATAGTACTTTTGTACTCC
1 TGTTAGCACTACGGTGCTCCTGATAGCACTTTTGTACTCC
* *
41694389 TGTTAGCATTACAGTGCTCCTGATAGCA-TATTTGTACTCC
1 TGTTAGCACTACGGTGCTCCTGATAGCACT-TTTGTACTCC
* * * *
41694429 TGTTTGCACTAGGGTGCCCCTGATTGCAC
1 TGTTAGCACTACGGTGCTCCTGATAGCAC
41694458 ATATGTGCCC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (40 bp):
TGTTAGCACTACGGTGCTCCTGATAGCACTTTTGTACTCC
Found at i:41713491 original size:16 final size:17
Alignment explanation
Indices: 41713460--41713492 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41713450 TAATATATAT
*
41713460 AAAAAATACAAGAAATA
1 AAAAAATACAAAAAATA
41713477 AAAAAATA-AAAAAATA
1 AAAAAATACAAAAAATA
41713493 TATAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAAATACAAAAAATA
Found at i:41713622 original size:11 final size:11
Alignment explanation
Indices: 41713593--41713637 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
41713583 TGGCCGAATT
* *
41713593 TCCCTTCCCCC
1 TCCCTTCTCTC
41713604 TCCCTTCTCTC
1 TCCCTTCTCTC
41713615 TCCCTTCTCTC
1 TCCCTTCTCTC
*
41713626 TTCCTTCTCTC
1 TCCCTTCTCTC
41713637 T
1 T
41713638 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (11 bp):
TCCCTTCTCTC
Found at i:41714125 original size:3 final size:3
Alignment explanation
Indices: 41714101--41714174 Score: 69
Period size: 3 Copynumber: 24.3 Consensus size: 3
41714091 AACATCCTTG
* * * *
41714101 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
41714148 TTA TGTA TTA GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA T-TA TTA TTA TTA T
41714175 GTACGTGTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:41714184 original size:23 final size:23
Alignment explanation
Indices: 41714119--41714177 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
41714109 ATATTATTAG
* * *
41714119 TATTATTAGTAT-TACTATTAT-
1 TATTATTATTATGTAGTAGTATA
*
41714140 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
41714163 TATTTTTATTATGTA
1 TATTATTATTATGTA
41714178 CGTGTATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 11 0.34
22 7 0.22
23 14 0.44
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:41714288 original size:3 final size:3
Alignment explanation
Indices: 41714275--41714321 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
41714265 TATTCCAATG
*
41714275 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41714322 GTTTATGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41717323 original size:266 final size:266
Alignment explanation
Indices: 41716849--41717380 Score: 1019
Period size: 266 Copynumber: 2.0 Consensus size: 266
41716839 CGTGATAAGA
41716849 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
*
41716914 AAGGATTATTTGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
*
41716979 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGACCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
* *
41717044 CGTGAGACTTATCTTAACGCTCGAATGAAGAAAATGATCGAATGTCTTCGCATATGAGGGCAAAG
196 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
41717109 CCGTAT
261 CCGTAT
41717115 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
*
41717180 AAGGATTATTCGAGAGCCGCTGAACTTTTTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
41717245 GAGCAACGAGTCACGACCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGACCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
41717310 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
196 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
41717375 CCGTAT
261 CCGTAT
41717381 ATGTATCCGC
Statistics
Matches: 261, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 261 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (266 bp):
GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
GAGCAACGAGTCACGACCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
CCGTAT
Found at i:41722537 original size:132 final size:132
Alignment explanation
Indices: 41722311--41723304 Score: 1740
Period size: 132 Copynumber: 7.5 Consensus size: 132
41722301 ATTGGCATGG
41722311 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
41722376 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41722441 GA
131 GA
41722443 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
*
41722508 CTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41722573 GA
131 GA
*
41722575 AGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
* * *
41722640 CTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGATAA
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41722705 GA
131 GA
* * *
41722707 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATGTAT--TGGCGAAGTAGATCGAAGAAAGTAGA
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATAT-TGGTGGCGAAGTAGATCGCAGAAAGCAGA
* * *
41722770 TCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTA
65 TCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATA
41722835 GGA
130 GGA
41722838 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
* * *
41722903 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41722968 GA
131 GA
41722970 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
* * *
41723035 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41723100 GA
131 GA
*
41723102 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATTGCAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
*
41723167 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGGTCCTATCTTCCTATATTGATAG
66 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
41723232 GA
131 GA
* * * * * *
41723234 AGTGGATCTAAGATACAGATCTTGTCTTCTCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGAT
1 AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
41723299 CTTGTC
66 CTTGTC
41723305 CCTGTATTTG
Statistics
Matches: 828, Mismatches: 31, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
130 1 0.00
131 120 0.14
132 706 0.85
133 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
AGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG
GA
Found at i:41723375 original size:46 final size:44
Alignment explanation
Indices: 41723293--41723388 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 44
41723283 ATCGAAGAAA
* * * *
41723293 GCAGATCTTGTCCCTGTATTTGGCAGTGGAATAGATTGAGGATT
1 GCAGATCTTGTCCCTGTATTTGGCAGTCGAACAGATTGACGATG
*
41723337 GCAGATCTTGCCTTCCTGTATTTGGCAG-CGAAGCAGATTGACGATG
1 GCAGATCTTG--TCCCTGTATTTGGCAGTCGAA-CAGATTGACGATG
41723383 GCAGAT
1 GCAGAT
41723389 TTTACCTCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 10 0.23
45 3 0.07
46 31 0.70
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (44 bp):
GCAGATCTTGTCCCTGTATTTGGCAGTCGAACAGATTGACGATG
Found at i:41724443 original size:16 final size:16
Alignment explanation
Indices: 41724410--41724444 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41724400 ATTAATATAT
* *
41724410 ATAAAAAATACAAGAA
1 ATAAAAAATAAAAAAA
41724426 ATAAAAAATAAAAAAA
1 ATAAAAAATAAAAAAA
41724442 ATA
1 ATA
41724445 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
ATAAAAAATAAAAAAA
Found at i:41724572 original size:11 final size:11
Alignment explanation
Indices: 41724556--41724589 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
41724546 CCCTTCCCCC
41724556 CTCCCTTCTCT
1 CTCCCTTCTCT
41724567 CTCCCTTCTCT
1 CTCCCTTCTCT
*
41724578 CTTCCTTCTCT
1 CTCCCTTCTCT
41724589 C
1 C
41724590 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:41725078 original size:3 final size:3
Alignment explanation
Indices: 41725054--41725128 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
41725044 AACATCCTTG
* * * *
41725054 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
41725101 TTA TGTA TTA GTA TATA TTT TTA TTA TT
1 TTA T-TA TTA TTA T-TA TTA TTA TTA TT
41725129 TACGTGTATG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.04
3 49 0.86
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:41725137 original size:29 final size:25
Alignment explanation
Indices: 41725063--41725128 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
41725053 GTTATTTTTA
*
41725063 TATTATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATTATGTATTAC
*
41725087 TATTATTATTATTATTATGTATTAG
1 TATTATTATTATTATTATGTATTAC
*
41725112 TATATATTTTTATTATT
1 TAT-TATTATTATTATT
41725129 TACGTGTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 16 0.43
25 9 0.24
26 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TATTATTATTATTATTATGTATTAC
Found at i:41725241 original size:3 final size:3
Alignment explanation
Indices: 41725228--41725275 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
41725218 TATTCCAATG
* *
41725228 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41725276 GTTTATGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41726100 original size:17 final size:18
Alignment explanation
Indices: 41726070--41726104 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41726060 TAAAAATGCT
*
41726070 TTTTGTATATTTCACATA
1 TTTTGTATAATTCACATA
41726088 TTTT-TATAATTCACATA
1 TTTTGTATAATTCACATA
41726105 CATATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTGTATAATTCACATA
Found at i:41732829 original size:13 final size:13
Alignment explanation
Indices: 41732808--41732842 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41732798 ATAGTAAATA
41732808 TTCAAAAATATTT
1 TTCAAAAATATTT
*
41732821 TTCATAAATATTT
1 TTCAAAAATATTT
41732834 TT-AAAAATA
1 TTCAAAAATA
41732843 AATCTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCAAAAATATTT
Found at i:41739068 original size:12 final size:13
Alignment explanation
Indices: 41739053--41739081 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41739043 AAAGAAAGAT
41739053 AAAT-AAAAAATA
1 AAATAAAAAAATA
41739065 AAATAAAAAAATA
1 AAATAAAAAAATA
41739078 AAAT
1 AAAT
41739082 GATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:41739224 original size:12 final size:12
Alignment explanation
Indices: 41739209--41739247 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41739199 AATTAGTAAA
41739209 ATAATAAATAAT
1 ATAATAAATAAT
*
41739221 ATAATAAAGAAT
1 ATAATAAATAAT
*
41739233 A-AATAAATAAA
1 ATAATAAATAAT
41739244 ATAA
1 ATAA
41739248 AAGAGGTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:41739235 original size:19 final size:20
Alignment explanation
Indices: 41739211--41739248 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41739201 TTAGTAAAAT
*
41739211 AATAAAT-AATATAATAAAG
1 AATAAATAAATAAAATAAAG
41739230 AATAAATAAATAAAATAAA
1 AATAAATAAATAAAATAAA
41739249 AGAGGTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (20 bp):
AATAAATAAATAAAATAAAG
Found at i:41739801 original size:178 final size:178
Alignment explanation
Indices: 41739499--41739859 Score: 544
Period size: 178 Copynumber: 2.0 Consensus size: 178
41739489 TGGCCTGGGC
* *
41739499 GCCGTGTCTTTCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAATTGAAA
1 GCCGTGTCTCTCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
*
41739564 AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCGTGTGTGTTTTCC
66 AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTCC
*
41739629 TTCACTTCTCCCACGCCCATGTGAGATCTCATACACTCGTGTGGCCAG
131 TTCACTTCTCCCACGCCCATGTGAGATCCCATACACTCGTGTGGCCAG
* * * *
41739677 GCCGTGTCTCTCACACGGCTGTGTGCCTTGCTCGTGTAACTCTCTGACTTGATTTAAAACTGAAA
1 GCCGTGTCTCTCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
* * * * *
41739742 AAAATTAGCTCCA-GGTTTCACACGGCCTAGGACACGCCCGTGTGTCTAGGCCATGTGTGTTTTC
66 AAAATTAGCT-CATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTC
* * * **
41739806 CTTCGCTTCTCTCACGCTCATGTGAGATCCCATATGCTCGTGTGGCCAG
130 CTTCACTTCTCCCACGCCCATGTGAGATCCCATACACTCGTGTGGCCAG
41739855 GCCGT
1 GCCGT
41739860 ATAGGTCACA
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
178 162 0.99
179 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (178 bp):
GCCGTGTCTCTCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTCC
TTCACTTCTCCCACGCCCATGTGAGATCCCATACACTCGTGTGGCCAG
Found at i:41739895 original size:178 final size:178
Alignment explanation
Indices: 41739533--41739896 Score: 489
Period size: 178 Copynumber: 2.0 Consensus size: 178
41739523 GCCTTGCCCG
*
41739533 TGTAACTCTCTGACGTGATTTAAAATTGAAAAAAATTAGCTCATGGTTTCACACGGCCTAAGACA
1 TGTAACTCTCTGACGTGATTTAAAACTGAAAAAAATTAGCTCATGGTTTCACACGGCCTAAGACA
* *
41739598 CACCCGTATGCCCAGGCCGTGTGTGTTTTCCTTCACTTCTCCCACGCCCATGTGAGATCTCATAC
66 CACCCGTATGCCCAGGCCATGTGTGTTTTCCTTCACTTCTCCCACGCCCATGTGAGATCCCATAC
* ** ** ** *
41739663 ACTCGTGTGGCCAGGCCGTGTCTCTCACACGGCTGTGTGCCTTGCTCG
131 ACTCGTGTGGCCAGGCCGTATAGCTCACACGGCCATGTGCCAAGCTCA
* *
41739711 TGTAACTCTCTGACTTGATTTAAAACTGAAAAAAATTAGCTCCA-GGTTTCACACGGCCTAGGAC
1 TGTAACTCTCTGACGTGATTTAAAACTGAAAAAAATTAGCT-CATGGTTTCACACGGCCTAAGAC
* * * * * * *
41739775 ACGCCCGTGTGTCTAGGCCATGTGTGTTTTCCTTCGCTTCTCTCACGCTCATGTGAGATCCCATA
65 ACACCCGTATGCCCAGGCCATGTGTGTTTTCCTTCACTTCTCCCACGCCCATGTGAGATCCCATA
** *
41739840 TGCTCGTGTGGCCAGGCCGTATAGGTCACACGGCCATGTCGCCAAG-TCA
130 CACTCGTGTGGCCAGGCCGTATAGCTCACACGGCCATGT-GCCAAGCTCA
41739889 TGTAACTC
1 TGTAACTC
41739897 ACTGTCAATT
Statistics
Matches: 161, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
178 155 0.96
179 6 0.04
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (178 bp):
TGTAACTCTCTGACGTGATTTAAAACTGAAAAAAATTAGCTCATGGTTTCACACGGCCTAAGACA
CACCCGTATGCCCAGGCCATGTGTGTTTTCCTTCACTTCTCCCACGCCCATGTGAGATCCCATAC
ACTCGTGTGGCCAGGCCGTATAGCTCACACGGCCATGTGCCAAGCTCA
Found at i:41745170 original size:17 final size:18
Alignment explanation
Indices: 41745142--41745191 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
41745132 TAATAAATAA
*
41745142 AATTATCCAACCCAACCC
1 AATTACCCAACCCAACCC
*
41745160 AATTA-CCAACCCAACCT
1 AATTACCCAACCCAACCC
41745177 AATTACCCAACCCAA
1 AATTACCCAACCCAA
41745192 TAAAACTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:41745237 original size:33 final size:33
Alignment explanation
Indices: 41745198--41745279 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 33
41745188 CCAATAAAAC
41745198 TAAAACTAAAA-TCTACCCAATTACCCAACCCAA
1 TAAAACTAAAAGTCTACCCAATTA-CCAACCCAA
41745231 TAAAACTAAAACTAAAGTCTACCCAATTACCAACCCAA
1 TAAAACT---A--AAAGTCTACCCAATTACCAACCCAA
*
41745269 TAAAAATAAAA
1 TAAAACTAAAA
41745280 CTAAAGTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
33 10 0.24
35 1 0.02
36 1 0.02
38 18 0.43
39 12 0.29
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (33 bp):
TAAAACTAAAAGTCTACCCAATTACCAACCCAA
Found at i:41745273 original size:38 final size:39
Alignment explanation
Indices: 41745177--41745289 Score: 201
Period size: 39 Copynumber: 2.9 Consensus size: 39
41745167 AACCCAACCT
*
41745177 AATTACCCAACCCAATAAAACTAAAACTAAAATCTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
41745216 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
*
41745255 AATTA-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTA
41745290 ACTCTTAAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 29 0.40
39 43 0.60
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.19
Consensus pattern (39 bp):
AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
Found at i:41745446 original size:37 final size:37
Alignment explanation
Indices: 41745419--41745493 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
41745409 TGTTAATTTC
* *
41745419 AAGAATTATGTAATGCTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
* * * *
41745456 AAGACTTATGTAATATTTTTAATTATATAGTGATTCA
1 AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
41745493 A
1 A
41745494 TTCGGGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (37 bp):
AAGAATTATGTAATACTTTTAATTATGTAGTAATTCA
Found at i:41746120 original size:26 final size:26
Alignment explanation
Indices: 41746091--41746143 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41746081 TAGGAGGAAG
41746091 CTGATTATTCTGATTATCACCCATCT
1 CTGATTATTCTGATTATCACCCATCT
41746117 CTGATTATTCTGATTATCACCCATCT
1 CTGATTATTCTGATTATCACCCATCT
41746143 C
1 C
41746144 CTTAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.42
Consensus pattern (26 bp):
CTGATTATTCTGATTATCACCCATCT
Found at i:41760285 original size:99 final size:99
Alignment explanation
Indices: 41760111--41760303 Score: 305
Period size: 99 Copynumber: 1.9 Consensus size: 99
41760101 CTCAGCATGT
* * *
41760111 CGTTTTAACTTCATCGCCAGAGGAGGAAACATTATTGCACATGCAATGGTGGCAGAGGGTTTGAA
1 CGTTTTAACTTCATCGCCAAAGGAGGAAACACTATTGCACATGCAATGGCGGCAGAGGGTTTGAA
**
41760176 AAACACAAAGGACTGGTTCTGGGTTGAAGTCGCG
66 AAACACAAAGGACCAGTTCTGGGTTGAAGTCGCG
**
41760210 CGTTTTAACTTCATCTTCAAAGGAGGAAACACTATTGCACATGCAATGGCGGCAGAGGGTTTGAA
1 CGTTTTAACTTCATCGCCAAAGGAGGAAACACTATTGCACATGCAATGGCGGCAGAGGGTTTGAA
* *
41760275 AAGCAGAAAGGACCAGTTCTGGGTTGAAG
66 AAACACAAAGGACCAGTTCTGGGTTGAAG
41760304 ATGCGCCTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (99 bp):
CGTTTTAACTTCATCGCCAAAGGAGGAAACACTATTGCACATGCAATGGCGGCAGAGGGTTTGAA
AAACACAAAGGACCAGTTCTGGGTTGAAGTCGCG
Found at i:41762590 original size:2 final size:2
Alignment explanation
Indices: 41762585--41762625 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41762575 AGGCACCTTT
41762585 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41762626 GTCCCTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41770019 original size:3 final size:3
Alignment explanation
Indices: 41770011--41770049 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
41770001 TATCTTAAGA
*
41770011 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41770050 GGAAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41772158 original size:22 final size:23
Alignment explanation
Indices: 41772115--41772158 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
41772105 TCTCTTCACC
*
41772115 TTTCTCTTTCTCTTTGTCTTTTT
1 TTTCTCTTTCTCTTTGTATTTTT
41772138 TTTCT-TTTC-CTTTGCTATTTT
1 TTTCTCTTTCTCTTTG-TATTTT
41772159 GAACCATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTCTCTTTCTCTTTGTATTTTT
Found at i:41773010 original size:54 final size:55
Alignment explanation
Indices: 41772885--41773011 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 55
41772875 TTGTTTATAG
* * * ** **
41772885 TTCGAAATAGTGTTACATGGCCGTGTCGTTAGACCGTGTGCCCGACTGTGTGCAA
1 TTCGAAATAGGGTCACATGGCCATGTCGACAGACCGTGTGCCAAACTGTGTGCAA
* * * **
41772940 TTCGAAACATGATCACATGGCCATGTC-ACAGACCGTGTGCCAAACTGTGTGTGA
1 TTCGAAATAGGGTCACATGGCCATGTCGACAGACCGTGTGCCAAACTGTGTGCAA
41772994 TTCGAAATAGGGTCACAT
1 TTCGAAATAGGGTCACAT
41773012 AGCCGTGTAA
Statistics
Matches: 57, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
54 36 0.63
55 21 0.37
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (55 bp):
TTCGAAATAGGGTCACATGGCCATGTCGACAGACCGTGTGCCAAACTGTGTGCAA
Found at i:41781279 original size:43 final size:43
Alignment explanation
Indices: 41781224--41781327 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
41781214 GGGTTACCAA
* * *
41781224 GATTACGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATGT
1 GATTACATGTAAGACCATGGT-TGGG-CTATTGGCATCGATACGG
*
41781267 GATTTCATGTAAGACCATGGTTGGGCTATTGGCATCGATACGG
1 GATTACATGTAAGACCATGGTTGGGCTATTGGCATCGATACGG
41781310 GATTACATGTAAGACCAT
1 GATTACATGTAAGACCAT
41781328 ATCTAGGATA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 51 0.94
44 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (43 bp):
GATTACATGTAAGACCATGGTTGGGCTATTGGCATCGATACGG
Found at i:41784064 original size:34 final size:32
Alignment explanation
Indices: 41784024--41784088 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
41784014 TAATGATAAT
*
41784024 ATTATTTTACATTAAAAAT-ATTATTATATTTTAA
1 ATTA-TTTAAATTAAAAATAATT-TT-TATTTTAA
*
41784058 ATTATTTAAATTAATAATAATTTTTATTTTA
1 ATTATTTAAATTAAAAATAATTTTTATTTTA
41784089 TTAATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.25
33 14 0.50
34 7 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTATTTAAATTAAAAATAATTTTTATTTTAA
Found at i:41791168 original size:18 final size:18
Alignment explanation
Indices: 41791145--41791181 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41791135 TATAGTTTGG
*
41791145 TATTTGATTTATTCGAAT
1 TATTTGAGTTATTCGAAT
41791163 TATTTGAGTTATTCGAAT
1 TATTTGAGTTATTCGAAT
41791181 T
1 T
41791182 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTTGAGTTATTCGAAT
Found at i:41795036 original size:34 final size:33
Alignment explanation
Indices: 41794992--41795055 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
41794982 TTTAATAACA
41794992 TTTTAACCTTTAAACATAT-AATATTATAACAACT
1 TTTTAACCTTTAAA-ATATAAATATTA-AACAACT
*
41795026 TTTTAGCCTTTAAAATATAAATATTAAACA
1 TTTTAACCTTTAAAATATAAATATTAAACA
41795056 CTTGCATGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (33 bp):
TTTTAACCTTTAAAATATAAATATTAAACAACT
Found at i:41799453 original size:19 final size:19
Alignment explanation
Indices: 41799410--41799453 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41799400 TTTAACGTAG
41799410 ATAATACAAAAATAATATT
1 ATAATACAAAAATAATATT
* *
41799429 -TAAATACCAAAATTATATT
1 AT-AATACAAAAATAATATT
41799448 ATAATA
1 ATAATA
41799454 TCAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAATACAAAAATAATATT
Found at i:41804373 original size:21 final size:20
Alignment explanation
Indices: 41804349--41804387 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41804339 GTTTTAATAC
41804349 TAAATAAATTAAAAATATTAT
1 TAAATAAA-TAAAAATATTAT
*
41804370 TAAATCAATAAAAATATT
1 TAAATAAATAAAAATATT
41804388 GTTATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAAATAAAAATATTAT
Found at i:41804398 original size:15 final size:15
Alignment explanation
Indices: 41804378--41804408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41804368 ATTAAATCAA
*
41804378 TAAAAATATTGTTAT
1 TAAAAATAATGTTAT
41804393 TAAAAATAATGTTAT
1 TAAAAATAATGTTAT
41804408 T
1 T
41804409 TGATGGGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
TAAAAATAATGTTAT
Found at i:41805589 original size:8 final size:8
Alignment explanation
Indices: 41805572--41805624 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
41805562 AATGATAAAA
41805572 TATATTAT
1 TATATTAT
*
41805580 TATTTTAT
1 TATATTAT
41805588 TATATTA-
1 TATATTAT
41805595 TA-A--AT
1 TATATTAT
*
41805600 TAAATTGAT
1 TATATT-AT
41805609 TATATTAT
1 TATATTAT
41805617 TATATTAT
1 TATATTAT
41805625 GAAATAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
4 1 0.03
5 2 0.05
6 2 0.05
7 2 0.05
8 23 0.62
9 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TATATTAT
Found at i:41805610 original size:29 final size:29
Alignment explanation
Indices: 41805569--41805634 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
41805559 TTTAATGATA
* *
41805569 AAATATATT-ATTATTTTATTATATTAT-
1 AAATAAATTGATTATATTATTATATTATG
41805596 AAATTAAATTGATTATATTATTATATTATG
1 AAA-TAAATTGATTATATTATTATATTATG
41805626 AAATAAATT
1 AAATAAATT
41805635 AAGAAAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 3 0.09
28 5 0.15
29 23 0.68
30 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
AAATAAATTGATTATATTATTATATTATG
Found at i:41806124 original size:26 final size:26
Alignment explanation
Indices: 41806089--41806151 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
41806079 AAGAAATGAA
* * * *
41806089 AGAAACAGAATAGAAACGAAACAGGG
1 AGAAAAAGAAAAGAAAAGAAAAAGGG
41806115 AGAAAAAGAAAAGAAAAGAAAAAGGG
1 AGAAAAAGAAAAGAAAAGAAAAAGGG
41806141 A-AAGAAAGAAA
1 AGAA-AAAGAAA
41806152 TGAGAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.02
Consensus pattern (26 bp):
AGAAAAAGAAAAGAAAAGAAAAAGGG
Found at i:41807092 original size:38 final size:38
Alignment explanation
Indices: 41807022--41807152 Score: 104
Period size: 38 Copynumber: 3.4 Consensus size: 38
41807012 ACCTCGAATC
* * * *
41807022 GATGAGACACTTGGTGTCACTATTTTACTTCGGATAGATCT
1 GATGAGACACTGGGTATCA--ACTTTACTTCGGATAG-GCT
* * *
41807063 GGTGAGATACTGGGTATC-ACTTTACTTCGGCTAGGCT
1 GATGAGACACTGGGTATCAACTTTACTTCGGATAGGCT
* * * *
41807100 GATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TCT
1 GATGAGACACTGGGTATCAACTTTACTTCGGA-TAGGCT
*
41807138 GATGAGGCACTGGGT
1 GATGAGACACTGGGT
41807153 GCCAATATGG
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 17 0.23
38 40 0.55
39 2 0.03
41 14 0.19
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (38 bp):
GATGAGACACTGGGTATCAACTTTACTTCGGATAGGCT
Found at i:41815146 original size:25 final size:25
Alignment explanation
Indices: 41815112--41815204 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
41815102 CAACTCTTAT
*
41815112 GAGCGTCCTGATATATGGCTTTCCG
1 GAGCTTCCTGATATATGGCTTTCCG
** **
41815137 GAGCTTCCTGATAT-TGGCTCGCTT
1 GAGCTTCCTGATATATGGCTTTCCG
*
41815161 GAACTT-CTCGATATATGGCTATT-CG
1 GAGCTTCCT-GATATATGGCT-TTCCG
*
41815186 GAGCTTCTTGA-ATATGGCT
1 GAGCTTCCTGATATATGGCT
41815205 CTTATGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
23 2 0.04
24 24 0.46
25 25 0.48
26 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (25 bp):
GAGCTTCCTGATATATGGCTTTCCG
Found at i:41816834 original size:41 final size:40
Alignment explanation
Indices: 41816789--41816950 Score: 184
Period size: 41 Copynumber: 4.0 Consensus size: 40
41816779 TTGTATAAAA
* * * *
41816789 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
*
41816829 CCACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
1 -CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACA-TT
*
41816871 CACCGGCACT-AAGGCTGCTAGACATAAAGTCTGAAGTA-ATT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATT
* * *
41816912 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
41816951 CTTATTTTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 94 0.90
42 4 0.04
43 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
Found at i:41817619 original size:16 final size:17
Alignment explanation
Indices: 41817598--41817632 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41817588 ATCTAATAAT
41817598 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
41817614 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
41817631 TT
1 TT
41817633 CAACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:41819790 original size:41 final size:40
Alignment explanation
Indices: 41819745--41819846 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 40
41819735 TGATTCAGTA
*
41819745 CACCGGCACTTAGCCTGCTAGACATATAGTTTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
41819786 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
41819827 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
41819847 AGCGCTAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 50 0.93
42 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:41819861 original size:41 final size:41
Alignment explanation
Indices: 41819745--41819861 Score: 103
Period size: 41 Copynumber: 2.9 Consensus size: 41
41819735 TGATTCAGTA
* * ** * *
41819745 CACCGGCACTTAGCCTGCTAGACA-TATAGTTTGAAATATTT
1 CACCGGCAATAAGCCTGCTAGACACTA-AGCCTGAAGTGTTT
* * * *
41819786 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
*
41819827 CACCGGCAATAAGCCTGCTA-AGCGCTAAGCCTGAA
1 CACCGGCAATAAGCCTGCTAGA-CACTAAGCCTGAA
41819862 AATCTCAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.02
41 61 0.97
42 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
Found at i:41821442 original size:13 final size:13
Alignment explanation
Indices: 41821424--41821448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41821414 CAATCAAATG
41821424 CACACAAAATAAA
1 CACACAAAATAAA
41821437 CACACAAAATAA
1 CACACAAAATAA
41821449 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:41821513 original size:17 final size:17
Alignment explanation
Indices: 41821491--41821525 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41821481 CCCGAAACCA
41821491 CTATGTCCGATTAGAGT
1 CTATGTCCGATTAGAGT
41821508 CTATGTCCGATTAGAGT
1 CTATGTCCGATTAGAGT
41821525 C
1 C
41821526 AAAACCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (17 bp):
CTATGTCCGATTAGAGT
Found at i:41825388 original size:50 final size:49
Alignment explanation
Indices: 41825260--41825454 Score: 214
Period size: 50 Copynumber: 3.9 Consensus size: 49
41825250 GGTAATAACA
* ** * * *
41825260 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CG
* * * **
41825309 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATC-G
* *
41825359 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATC-G
*
41825409 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
41825455 ATCTCAATGA
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.32
50 81 0.66
51 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:41825440 original size:100 final size:99
Alignment explanation
Indices: 41825267--41825454 Score: 243
Period size: 100 Copynumber: 1.9 Consensus size: 99
41825257 ACATGCCAAA
** * * * * * *
41825267 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCCAGATAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTACTGCCAACGCCATATCCCAGACAT
**
41825332 GGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
66 GGTCTTACATGGGACCTCTCATATCGGTGCCCAT
* *
41825366 GCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCT-ACTGCCAACGCCATATCCCAGAC
41825430 ATGGTCTTACATGGGACCTCTCATA
64 ATGGTCTTACATGGGACCTCTCATA
41825455 ATCTCAATGA
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
99 33 0.44
100 42 0.56
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTACTGCCAACGCCATATCCCAGACAT
GGTCTTACATGGGACCTCTCATATCGGTGCCCAT
Found at i:41825479 original size:56 final size:50
Alignment explanation
Indices: 41825262--41825506 Score: 188
Period size: 50 Copynumber: 4.8 Consensus size: 50
41825252 TAATAACATG
* ** * * * * *
41825262 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGT-ACTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTA
* * * * ** * * *
41825311 CCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTA
* * *
41825361 CCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCAGTG
1 CCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCAGTA
41825411 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G-TA
** * * *
41825467 CCAGTGTCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41825507 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
49 37 0.23
50 79 0.49
51 1 0.01
53 5 0.03
54 1 0.01
55 1 0.01
56 36 0.22
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTA
Done.