Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 137 of 196
Found at i:40651290 original size:4 final size:4
Alignment explanation
Indices: 40651281--40651356 Score: 54
Period size: 4 Copynumber: 18.5 Consensus size: 4
40651271 CAACTCAATT
40651281 TTTA TTTA -TTA TTTA TTTA -TTA TTTTA TTT- TATTA TTTTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA -TTTA -TTTA
40651326 TTTA -TTA CTTTA TTTTA TTT- TATTA TTTA TT
1 TTTA TTTA -TTTA -TTTA TTTA T-TTA TTTA TT
40651357 ACTTATTTGG
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
3 11 0.18
4 30 0.50
5 18 0.30
6 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40651310 original size:5 final size:5
Alignment explanation
Indices: 40651300--40651349 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
40651290 TATTTATTTA
* *
40651300 TTATT TTATT TTA-- TTATT TTACT TTATTT ATTACT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT -TTATT TTATT TTATT TTATT
40651350 ATTTATTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.08
5 29 0.78
6 2 0.05
7 3 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:40651312 original size:13 final size:12
Alignment explanation
Indices: 40651280--40651353 Score: 75
Period size: 13 Copynumber: 6.2 Consensus size: 12
40651270 GCAACTCAAT
40651280 TTTTATTTATTA
1 TTTTATTTATTA
40651292 -TTTATTTATTA
1 TTTTATTTATTA
40651303 TTTTATTTTATTA
1 TTTTA-TTTATTA
40651316 TTTTACTTTATT-
1 TTTTA-TTTATTA
* *
40651328 TATTA-CT-TTA
1 TTTTATTTATTA
40651338 TTTTATTTTATTA
1 TTTTA-TTTATTA
40651351 TTT
1 TTT
40651354 ATTACTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 11 0.22
12 9 0.18
13 24 0.47
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:40652730 original size:24 final size:23
Alignment explanation
Indices: 40652681--40652736 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
40652671 TAAAAAATAT
* *
40652681 AAATAATAAATAAATCAAAATCA
1 AAATAATAAAAAAATCAAAAACA
* *
40652704 AAATAAGTAAAAAAATGAAAAAGA
1 AAATAA-TAAAAAAATCAAAAACA
*
40652728 AAAAAATAA
1 AAATAATAA
40652737 TTTGGGGGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (23 bp):
AAATAATAAAAAAATCAAAAACA
Found at i:40653335 original size:18 final size:17
Alignment explanation
Indices: 40653323--40653355 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40653313 ATAATTATTA
40653323 AGGA-TTATTTAATTTT
1 AGGATTTATTTAATTTT
40653339 AGGATTTTATTTAATTT
1 AGGA-TTTATTTAATTT
40653356 ATCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
AGGATTTATTTAATTTT
Found at i:40655137 original size:46 final size:46
Alignment explanation
Indices: 40655027--40655187 Score: 258
Period size: 46 Copynumber: 3.6 Consensus size: 46
40655017 TATGTATGAT
* *
40655027 CACTAATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
40655070 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
40655116 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
40655162 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40655188 AGTACTCAAA
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
43 9 0.08
44 5 0.05
45 29 0.27
46 66 0.61
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:40662791 original size:25 final size:25
Alignment explanation
Indices: 40662763--40662859 Score: 70
Period size: 25 Copynumber: 3.9 Consensus size: 25
40662753 AAGCTCTTCC
* * *
40662763 GAGCCATGTAACATGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATAT
* * *
40662788 GAGCTATATAACGGGAAGCTCTTAT
1 GAGCCATATAACAGGAAGCTCATAT
* * *
40662813 GAGCCA-ATTATCGGGAAGCTCATAC
1 GAGCCATA-TAACAGGAAGCTCATAT
* * *
40662838 CAGCCATATATCAGGAAACTCA
1 GAGCCATATAACAGGAAGCTCA
40662860 AGAGAGCTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 1 0.02
25 55 0.96
26 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAT
Found at i:40662949 original size:25 final size:25
Alignment explanation
Indices: 40662877--40662966 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
40662867 TATTAATTGG
* ** *
40662877 GAAGCTCATGAGAGCTAAATAAAGG
1 GAAGCTCATGAGAGCCAAATATCGA
* * *
40662902 GAATCTCGTGAGAGCCAAGTATCGA
1 GAAGCTCATGAGAGCCAAATATCGA
*
40662927 GAAGCTCATGAAAGCCAAATATCGA
1 GAAGCTCATGAGAGCCAAATATCGA
* *
40662952 GACGCTCATAAGAGC
1 GAAGCTCATGAGAGC
40662967 TGTGGTGTGT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAAATATCGA
Found at i:40665156 original size:32 final size:32
Alignment explanation
Indices: 40665115--40665179 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40665105 TACAAGTTAG
40665115 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
1 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
40665147 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
1 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
40665179 A
1 A
40665180 TTCAAGACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (32 bp):
AATTTTATTTTAAGACAAACTCAAAAAGGCGT
Found at i:40666183 original size:27 final size:27
Alignment explanation
Indices: 40666111--40666184 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
40666101 CTAACAGAAC
* *
40666111 ACGCCACAAAGGC-AACCATATAGAGT
1 ACGCCACAAAGGCTAATCTTATAGAGT
* * *
40666137 ACGCCACAAAGGTTATTCTTCTAGAGT
1 ACGCCACAAAGGCTAATCTTATAGAGT
*
40666164 TCGCCACAAAGGCTAATCTTA
1 ACGCCACAAAGGCTAATCTTA
40666185 GCTGTCGTGC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 12 0.32
27 26 0.68
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (27 bp):
ACGCCACAAAGGCTAATCTTATAGAGT
Found at i:40669630 original size:16 final size:16
Alignment explanation
Indices: 40669611--40669646 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40669601 TATTTGATTA
40669611 AATATATGATACTACT
1 AATATATGATACTACT
40669627 AATATATGATACTACT
1 AATATATGATACTACT
40669643 AATA
1 AATA
40669647 AAGAATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (16 bp):
AATATATGATACTACT
Found at i:40686340 original size:9 final size:9
Alignment explanation
Indices: 40686326--40686350 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40686316 TTATTTTTAG
40686326 AAATATTCA
1 AAATATTCA
40686335 AAATATTCA
1 AAATATTCA
40686344 AAATATT
1 AAATATT
40686351 AATATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATATTCA
Found at i:40692368 original size:25 final size:24
Alignment explanation
Indices: 40692340--40692389 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
40692330 TCATATTTTT
40692340 GAAACTTGATGCAAGATAGATTGTA
1 GAAACTTGATGCAAGATAGA-TGTA
* *
40692365 GAAAGTTGATGGAAGATAGATGTA
1 GAAACTTGATGCAAGATAGATGTA
40692389 G
1 G
40692390 TCTCACTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.40, C:0.04, G:0.30, T:0.26
Consensus pattern (24 bp):
GAAACTTGATGCAAGATAGATGTA
Found at i:40694637 original size:14 final size:15
Alignment explanation
Indices: 40694620--40694663 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
40694610 TTAAAGATTA
40694620 ATGATTAA-TTAATT
1 ATGATTAAGTTAATT
40694634 ATGATTAAGTTAATT
1 ATGATTAAGTTAATT
40694649 A--ATTAAGTTTAATT
1 ATGATTAAG-TTAATT
40694663 A
1 A
40694664 AAACTAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.21
14 15 0.54
15 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (15 bp):
ATGATTAAGTTAATT
Found at i:40694660 original size:19 final size:18
Alignment explanation
Indices: 40694623--40694664 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
40694613 AAGATTAATG
*
40694623 ATTAATTAATTATGATTA
1 ATTAATTAATTAAGATTA
*
40694641 AGTTAATTAATTAAGTTTA
1 A-TTAATTAATTAAGATTA
40694660 ATTAA
1 ATTAA
40694665 AACTAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
ATTAATTAATTAAGATTA
Found at i:40717856 original size:35 final size:36
Alignment explanation
Indices: 40717775--40717866 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
40717765 AATACATATG
* * *
40717775 CATATTATGTATATATTTTAT-TATTATTTTATTTT
1 CATAATATTTATATATTTTATATATCATTTTATTTT
* *
40717810 CATAGTTTTTATATATTTTATATA-CATTTATATTTT
1 CATAATATTTATATATTTTATATATCATTT-TATTTT
*
40717846 -ATAATATTTATAT-TTTCATAT
1 CATAATATTTATATATTTTATAT
40717867 TTTATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.15
35 33 0.69
36 8 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (36 bp):
CATAATATTTATATATTTTATATATCATTTTATTTT
Found at i:40717860 original size:52 final size:50
Alignment explanation
Indices: 40717786--40717882 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 50
40717776 ATATTATGTA
*
40717786 TATATTTTATTATTATTTTATTTTCATAGTTTTTATATATTT-TATATACATT
1 TATATTTTATTAATATTTTATTTTCATA--TTTTATA-ATTTATATATACATT
40717838 TATATTTTA-TAATATTTATATTTTCATATTTTATAATTTATATAT
1 TATATTTTATTAATATTT-TATTTTCATATTTTATAATTTATATAT
40717883 GTTTATACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
49 4 0.10
50 12 0.29
51 7 0.17
52 19 0.45
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (50 bp):
TATATTTTATTAATATTTTATTTTCATATTTTATAATTTATATATACATT
Found at i:40717868 original size:14 final size:16
Alignment explanation
Indices: 40717821--40717889 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
40717811 ATAGTTTTTA
*
40717821 TATATTTTATATACATT
1 TATATTTTATA-ATATT
40717838 TATATTTTATAATATT
1 TATATTTTATAATATT
40717854 TATATTTTCAT-AT-TT
1 TATATTTT-ATAATATT
* *
40717869 TATAATTTATATATGTT
1 TATATTTTATA-ATATT
40717886 TATA
1 TATA
40717890 CATTCTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.04
15 9 0.20
16 16 0.35
17 19 0.41
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TATATTTTATAATATT
Found at i:40717876 original size:22 final size:23
Alignment explanation
Indices: 40717787--40717880 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 23
40717777 TATTATGTAT
40717787 ATATTTTATTATTATTT-TATTTTC
1 ATATTTTA-TA-TATTTATATTTTC
40717811 ATAGTTTTTATATATTTTATATACATTT-
1 ATA--TTTTATATA-TTTATAT---TTTC
40717839 ATATTTTATAATATTTATATTTTC
1 ATATTTTAT-ATATTTATATTTTC
40717863 ATATTTTATA-ATTTATAT
1 ATATTTTATATATTTATAT
40717881 ATGTTTATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.13
23 4 0.07
24 14 0.23
25 5 0.08
26 21 0.34
27 3 0.05
28 3 0.05
29 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATATATTTATATTTTC
Found at i:40717889 original size:8 final size:7
Alignment explanation
Indices: 40717821--40717880 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
40717811 ATAGTTTTTA
40717821 TATATTT
1 TATATTT
40717828 TATATACATT
1 TATAT---TT
40717838 TATATTT
1 TATATTT
40717845 TATAATATT
1 TAT-AT-TT
40717854 TATATTT
1 TATATTT
40717861 TCATATTT
1 T-ATATTT
*
40717869 TATAATT
1 TATATTT
40717876 TATAT
1 TATAT
40717881 ATGTTTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 22 0.49
8 11 0.24
9 5 0.11
10 7 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTT
Found at i:40721671 original size:26 final size:26
Alignment explanation
Indices: 40721642--40721702 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
40721632 TACATCTTTG
**
40721642 CATTCATTTTTGAGCCAA-TATTTTTT
1 CATTC-TTTTTGAAACAATTATTTTTT
*
40721668 CATTCTTTTTGAAATAATTATTTTTT
1 CATTCTTTTTGAAACAATTATTTTTT
40721694 CATTCTTTT
1 CATTCTTTT
40721703 GGATTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (26 bp):
CATTCTTTTTGAAACAATTATTTTTT
Found at i:40722674 original size:21 final size:23
Alignment explanation
Indices: 40722650--40722693 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40722640 AATATAAAAA
40722650 AAAACAA-AAA-AAAATAGAGAG
1 AAAACAAGAAAGAAAATAGAGAG
* *
40722671 AAAAGAAGAAAGAAAATGGAGAG
1 AAAACAAGAAAGAAAATAGAGAG
40722694 GCCAAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (23 bp):
AAAACAAGAAAGAAAATAGAGAG
Found at i:40722829 original size:42 final size:42
Alignment explanation
Indices: 40722761--40722841 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
40722751 CCCGAAAAGG
*
40722761 GCAGCTCAAATATTGATTAGAATGGGGCATGA-GATGATCAGA
1 GCAGCTCAAATATTGATCAGAATGGGGCAT-ATGATGATCAGA
* * *
40722803 GCAGTTCAAATTTTGATCAGATTGGGGCATATGATGATC
1 GCAGCTCAAATATTGATCAGAATGGGGCATATGATGATC
40722842 TTGAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (42 bp):
GCAGCTCAAATATTGATCAGAATGGGGCATATGATGATCAGA
Found at i:40724944 original size:35 final size:36
Alignment explanation
Indices: 40724863--40724954 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
40724853 AATACATATG
* * *
40724863 CATATTATGTATATATTTTAT-TATTATTTTATTTT
1 CATAATATTTATATATTTTATATATCATTTTATTTT
* *
40724898 CATAGTTTTTATATATTTTATATA-CATTTATATTTT
1 CATAATATTTATATATTTTATATATCATTT-TATTTT
*
40724934 -ATAATATTTATAT-TTTCATAT
1 CATAATATTTATATATTTTATAT
40724955 TTTATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.15
35 33 0.69
36 8 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (36 bp):
CATAATATTTATATATTTTATATATCATTTTATTTT
Found at i:40724948 original size:52 final size:50
Alignment explanation
Indices: 40724874--40724970 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 50
40724864 ATATTATGTA
*
40724874 TATATTTTATTATTATTTTATTTTCATAGTTTTTATATATTT-TATATACATT
1 TATATTTTATTAATATTTTATTTTCATA--TTTTATA-ATTTATATATACATT
40724926 TATATTTTA-TAATATTTATATTTTCATATTTTATAATTTATATAT
1 TATATTTTATTAATATTT-TATTTTCATATTTTATAATTTATATAT
40724971 GTTTATACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
49 4 0.10
50 12 0.29
51 7 0.17
52 19 0.45
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (50 bp):
TATATTTTATTAATATTTTATTTTCATATTTTATAATTTATATATACATT
Found at i:40724956 original size:14 final size:16
Alignment explanation
Indices: 40724909--40724977 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
40724899 ATAGTTTTTA
*
40724909 TATATTTTATATACATT
1 TATATTTTATA-ATATT
40724926 TATATTTTATAATATT
1 TATATTTTATAATATT
40724942 TATATTTTCAT-AT-TT
1 TATATTTT-ATAATATT
* *
40724957 TATAATTTATATATGTT
1 TATATTTTATA-ATATT
40724974 TATA
1 TATA
40724978 CATTCTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.04
15 9 0.20
16 16 0.35
17 19 0.41
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TATATTTTATAATATT
Found at i:40724964 original size:22 final size:23
Alignment explanation
Indices: 40724875--40724968 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 23
40724865 TATTATGTAT
40724875 ATATTTTATTATTATTT-TATTTTC
1 ATATTTTA-TA-TATTTATATTTTC
40724899 ATAGTTTTTATATATTTTATATACATTT-
1 ATA--TTTTATATA-TTTATAT---TTTC
40724927 ATATTTTATAATATTTATATTTTC
1 ATATTTTAT-ATATTTATATTTTC
40724951 ATATTTTATA-ATTTATAT
1 ATATTTTATATATTTATAT
40724969 ATGTTTATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.13
23 4 0.07
24 14 0.23
25 5 0.08
26 21 0.34
27 3 0.05
28 3 0.05
29 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATATATTTATATTTTC
Found at i:40724977 original size:8 final size:7
Alignment explanation
Indices: 40724909--40724968 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
40724899 ATAGTTTTTA
40724909 TATATTT
1 TATATTT
40724916 TATATACATT
1 TATAT---TT
40724926 TATATTT
1 TATATTT
40724933 TATAATATT
1 TAT-AT-TT
40724942 TATATTT
1 TATATTT
40724949 TCATATTT
1 T-ATATTT
*
40724957 TATAATT
1 TATATTT
40724964 TATAT
1 TATAT
40724969 ATGTTTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 22 0.49
8 11 0.24
9 5 0.11
10 7 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTT
Found at i:40727281 original size:8 final size:8
Alignment explanation
Indices: 40727270--40727319 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
40727260 CCTGTTTTGG
40727270 GGTTTTAA
1 GGTTTTAA
40727278 GG-TTTAA
1 GGTTTTAA
40727285 GGTTTTAA
1 GGTTTTAA
**
40727293 -CCTTT-A
1 GGTTTTAA
*
40727299 GGGTTTAA
1 GGTTTTAA
40727307 GGTTTTAA
1 GGTTTTAA
40727315 GGTTT
1 GGTTT
40727320 AGGGTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
6 1 0.03
7 13 0.38
8 20 0.59
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.48
Consensus pattern (8 bp):
GGTTTTAA
Found at i:40727285 original size:7 final size:7
Alignment explanation
Indices: 40727273--40727332 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
40727263 GTTTTGGGGT
40727273 TTTAAGG
1 TTTAAGG
40727280 TTTAAGG
1 TTTAAGG
**
40727287 TTTTAACC
1 -TTTAAGG
*
40727295 TTTAGGG
1 TTTAAGG
40727302 TTTAAGG
1 TTTAAGG
40727309 TTTTAAGG
1 -TTTAAGG
*
40727317 TTTAGGG
1 TTTAAGG
*
40727324 TTTATGG
1 TTTAAGG
40727331 TT
1 TT
40727333 AAAAATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 31 0.72
8 12 0.28
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:40727290 original size:15 final size:15
Alignment explanation
Indices: 40727270--40727332 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
40727260 CCTGTTTTGG
40727270 GGTTTTAAGGTTTAA
1 GGTTTTAAGGTTTAA
**
40727285 GGTTTTAACCTTT-A
1 GGTTTTAAGGTTTAA
*
40727299 GGGTTTAAGGTTTTAA
1 GGTTTTAAGG-TTTAA
* *
40727315 GG-TTTAGGGTTTAT
1 GGTTTTAAGGTTTAA
40727329 GGTT
1 GGTT
40727333 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
14 14 0.37
15 21 0.55
16 3 0.08
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.48
Consensus pattern (15 bp):
GGTTTTAAGGTTTAA
Found at i:40727303 original size:22 final size:22
Alignment explanation
Indices: 40727273--40727332 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
40727263 GTTTTGGGGT
*
40727273 TTTAAGGTTTAAGGTTTTAACC
1 TTTAGGGTTTAAGGTTTTAACC
**
40727295 TTTAGGGTTTAAGGTTTTAAGG
1 TTTAGGGTTTAAGGTTTTAACC
*
40727317 TTTAGGGTTTATGGTT
1 TTTAGGGTTTAAGGTT
40727333 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (22 bp):
TTTAGGGTTTAAGGTTTTAACC
Found at i:40728155 original size:18 final size:18
Alignment explanation
Indices: 40728132--40728183 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
40728122 ATAAAAATTA
40728132 GATTAAGGTTAGGGTTAG
1 GATTAAGGTTAGGGTTAG
*
40728150 GATTAAGGTTAAGGTTAG
1 GATTAAGGTTAGGGTTAG
*
40728168 GGTTAAGGTTTAGGGT
1 GATTAAGG-TTAGGGT
40728184 GTTTTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (18 bp):
GATTAAGGTTAGGGTTAG
Found at i:40728171 original size:12 final size:13
Alignment explanation
Indices: 40728134--40728183 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 13
40728124 AAAAATTAGA
40728134 TTAAGG-TTAGGG
1 TTAAGGATTAGGG
*
40728146 TT-AGGATTAAGG
1 TTAAGGATTAGGG
40728158 TTAAGG-TTAGGG
1 TTAAGGATTAGGG
*
40728170 TTAAGGTTTAGGG
1 TTAAGGATTAGGG
40728183 T
1 T
40728184 GTTTTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 20 0.61
13 10 0.30
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (13 bp):
TTAAGGATTAGGG
Found at i:40730788 original size:18 final size:18
Alignment explanation
Indices: 40730762--40730804 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40730752 GACTCGGAAA
* *
40730762 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGTT
40730780 AGGATACATAAAAGGGTT
1 AGGATACATAAAAGGGTT
40730798 AGGATAC
1 AGGATAC
40730805 GCACTTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGTT
Found at i:40732602 original size:49 final size:51
Alignment explanation
Indices: 40732520--40732617 Score: 139
Period size: 49 Copynumber: 2.0 Consensus size: 51
40732510 AATAATTAAA
*
40732520 AAATAGGGATTTAAGAGAAATTTGAGAGGAAATT-A-AGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGAGAGCAAATTGAGAGCAAATTGAGATT
* *
40732569 AAATATGGATTTAAGAGAAATTTG-GAAGCAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTGAG-AGCAAATTGAGAGCAAATTGAGA
40732618 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 1 0.02
49 30 0.70
50 1 0.02
51 11 0.26
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTGAGAGCAAATTGAGAGCAAATTGAGATT
Found at i:40732609 original size:11 final size:11
Alignment explanation
Indices: 40732595--40732628 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40732585 GAAATTTGGA
40732595 AGCAAATTGAG
1 AGCAAATTGAG
*
40732606 AGCAATTTGAG
1 AGCAAATTGAG
*
40732617 AGGAAATTGAG
1 AGCAAATTGAG
40732628 A
1 A
40732629 TGTTGTTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.29, T:0.21
Consensus pattern (11 bp):
AGCAAATTGAG
Found at i:40732612 original size:22 final size:22
Alignment explanation
Indices: 40732582--40732628 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40732572 TATGGATTTA
40732582 AGAGAAATTTG-GAAGCAAATTG
1 AGAGAAATTTGAG-AGCAAATTG
* *
40732604 AGAGCAATTTGAGAGGAAATTG
1 AGAGAAATTTGAGAGCAAATTG
40732626 AGA
1 AGA
40732629 TGTTGTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.04, G:0.30, T:0.21
Consensus pattern (22 bp):
AGAGAAATTTGAGAGCAAATTG
Found at i:40733545 original size:10 final size:10
Alignment explanation
Indices: 40733532--40733612 Score: 71
Period size: 10 Copynumber: 8.5 Consensus size: 10
40733522 CTTTATAAAA
40733532 TTTTATAATT
1 TTTTATAATT
40733542 TTTTAT-A-T
1 TTTTATAATT
* *
40733550 TTCTATATTT
1 TTTTATAATT
40733560 TTTTATAATT
1 TTTTATAATT
**
40733570 TTTTACGA-T
1 TTTTATAATT
**
40733579 TTTTATAAAA
1 TTTTATAATT
*
40733589 TTTTACAATT
1 TTTTATAATT
40733599 TTTTAT-ATT
1 TTTTATAATT
40733608 TTTTA
1 TTTTA
40733613 ACGATTTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
8 6 0.11
9 16 0.29
10 33 0.60
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40733548 original size:20 final size:20
Alignment explanation
Indices: 40733523--40733605 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 20
40733513 TTCTTACGAC
*
40733523 TTTATAAAATTTTATAATTT
1 TTTATAAAATTTTACAATTT
* *
40733543 TTTAT---ATTTCTATATTTT
1 TTTATAAAATTT-TACAATTT
** *
40733561 TTTATAATTTTTTACGA-TT
1 TTTATAAAATTTTACAATTT
40733580 TTTATAAAATTTTACAATTT
1 TTTATAAAATTTTACAATTT
40733600 TTTATA
1 TTTATA
40733606 TTTTTTAACG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 4 0.08
18 12 0.24
19 16 0.32
20 15 0.30
21 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (20 bp):
TTTATAAAATTTTACAATTT
Found at i:40733561 original size:18 final size:17
Alignment explanation
Indices: 40733531--40733609 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 17
40733521 ACTTTATAAA
40733531 ATTTTATAATTTTTTAT
1 ATTTTATAATTTTTTAT
*
40733548 ATTTCTATATTTTTTTAT
1 ATTT-TATAATTTTTTAT
* *
40733566 AATTTTTTACGATTTTTATAAA
1 -ATTTTATA--ATTTTT-T-AT
*
40733588 ATTTTACAATTTTTTAT
1 ATTTTATAATTTTTTAT
40733605 ATTTT
1 ATTTT
40733610 TTAACGATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 10 0.20
18 16 0.33
19 10 0.20
20 5 0.10
21 7 0.14
22 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (17 bp):
ATTTTATAATTTTTTAT
Found at i:40733581 original size:19 final size:19
Alignment explanation
Indices: 40733559--40733652 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
40733549 TTTCTATATT
40733559 TTTTTATAATTTTTTACGA
1 TTTTTATAATTTTTTACGA
** *
40733578 TTTTTATAAAATTTTACAA
1 TTTTTATAATTTTTTACGA
40733597 TTTTT-TATATTTTTTAACGA
1 TTTTTATA-ATTTTTT-ACGA
40733617 TTTTTATATATTTTTCTA-G-
1 TTTTTATA-ATTTTT-TACGA
*
40733636 TTTTTAATAACTTTTTA
1 TTTTT-ATAATTTTTTA
40733653 ATATTTGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
18 4 0.06
19 36 0.57
20 12 0.19
21 10 0.16
22 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTTTTTACGA
Found at i:40733584 original size:57 final size:58
Alignment explanation
Indices: 40733486--40733608 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 58
40733476 ATTACGAAAA
* *
40733486 TTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATAATTTT
1 TTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTT
* * *
40733544 TTATATTTCTATA-TTTTTTTATAATTTT-TTACGATTTTTATAAAATTTTACAATTTT
1 TTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTACAATTTT
40733601 TTATATTT
1 TTATATTT
40733609 TTTAACGATT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
56 6 0.10
57 41 0.69
58 12 0.20
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (58 bp):
TTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTT
Found at i:40733629 original size:10 final size:10
Alignment explanation
Indices: 40733532--40733631 Score: 61
Period size: 10 Copynumber: 10.4 Consensus size: 10
40733522 CTTTATAAAA
40733532 TTTTATA-AT
1 TTTTATATAT
40733541 TTTT-TATAT
1 TTTTATATAT
* *
40733550 TTCTATATTT
1 TTTTATATAT
40733560 TTTTATA-AT
1 TTTTATATAT
*
40733569 TTTT-TACGAT
1 TTTTATA-TAT
* *
40733579 TTTTATAAAA
1 TTTTATATAT
*
40733589 TTTTACA-AT
1 TTTTATATAT
40733598 TTTT-TATAT
1 TTTTATATAT
*
40733607 TTTT-TAACGAT
1 TTTTAT-A-TAT
40733618 TTTTATATAT
1 TTTTATATAT
40733628 TTTT
1 TTTT
40733632 CTAGTTTTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
8 5 0.07
9 26 0.37
10 30 0.42
11 9 0.13
12 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:40733854 original size:89 final size:89
Alignment explanation
Indices: 40733749--40733922 Score: 251
Period size: 89 Copynumber: 2.0 Consensus size: 89
40733739 ATAAAAGCAT
* * *
40733749 GGGCTTAATTGCTTTTTTTGAAAAA-CTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTGAAGGA
1 GGGCCTAATTGCTTTTTTT-AAAAAGCTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGGA
* *
40733813 CCCAATTGAGTGCAAAAAAAACTAG
65 CCAAAATGAGTGCAAAAAAAACTAG
* * *
40733838 GGGCCTAATTGTTTTTTTTAAAAAGGTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGTAC
1 GGGCCTAATTGCTTTTTTTAAAAAGCTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGGAC
*
40733903 CAAAATGAGTGTAAAAAAAA
66 CAAAATGAGTGCAAAAAAAA
40733923 AGGGCTTATT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
88 5 0.07
89 70 0.93
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (89 bp):
GGGCCTAATTGCTTTTTTTAAAAAGCTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGGAC
CAAAATGAGTGCAAAAAAAACTAG
Found at i:40734050 original size:21 final size:23
Alignment explanation
Indices: 40734026--40734077 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
40734016 AGGTCTATAC
40734026 ATATATATT-T-TAATTTTTAAA
1 ATATATATTATATAATTTTTAAA
*
40734047 ATATATATTATATTATTTTTAAA
1 ATATATATTATATAATTTTTAAA
*
40734070 TTATATAT
1 ATATATAT
40734078 ATTCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.33
22 1 0.04
23 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATATTATATAATTTTTAAA
Found at i:40735742 original size:37 final size:38
Alignment explanation
Indices: 40735701--40735776 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
40735691 CCGAATATAA
40735701 TAAAATATTTTTTTA-TTTTTTAATTTTAAAATACTTT
1 TAAAATATTTTTTTATTTTTTTAATTTTAAAATACTTT
* *
40735738 TAAAATATTTTTTTATTTTTTTATTTTTAAAATATTTT
1 TAAAATATTTTTTTATTTTTTTAATTTTAAAATACTTT
40735776 T
1 T
40735777 TTAATGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 15 0.42
38 21 0.58
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (38 bp):
TAAAATATTTTTTTATTTTTTTAATTTTAAAATACTTT
Found at i:40735786 original size:26 final size:27
Alignment explanation
Indices: 40735735--40735788 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
40735725 TTTAAAATAC
* *
40735735 TTTTAAAATATTTTTTTATTTTTTTAT
1 TTTTAAAATATTTTTTTATATGTTTAT
40735762 TTTTAAAATATTTTTTTA-ATGTTTAT
1 TTTTAAAATATTTTTTTATATGTTTAT
40735788 T
1 T
40735789 AAAAATGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTTAAAATATTTTTTTATATGTTTAT
Found at i:40736566 original size:9 final size:9
Alignment explanation
Indices: 40736539--40736583 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
40736529 ATTTTATATT
40736539 TTATAAAAAA
1 TTAT-AAAAA
40736549 TTATAAAAA
1 TTATAAAAA
40736558 TTATAAAAAA
1 TTAT-AAAAA
40736568 TTA-AAAAA
1 TTATAAAAA
40736576 -TATAAAAA
1 TTATAAAAA
40736584 AAATTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 2 0.06
8 10 0.30
9 9 0.27
10 12 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TTATAAAAA
Found at i:40736585 original size:10 final size:9
Alignment explanation
Indices: 40736540--40736584 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
40736530 TTTTATATTT
40736540 TATAAAAAA
1 TATAAAAAA
*
40736549 TTATAAAAAT
1 -TATAAAAAA
40736559 TATAAAAAA
1 TATAAAAAA
40736568 T-TAAAAAA
1 TATAAAAAA
40736576 TATAAAAAA
1 TATAAAAAA
40736585 AATTGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 8 0.25
9 16 0.50
10 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TATAAAAAA
Found at i:40736593 original size:10 final size:9
Alignment explanation
Indices: 40736543--40736604 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
40736533 TATATTTTAT
40736543 AAAAAATTA
1 AAAAAATTA
*
40736552 TAAAAATTA
1 AAAAAATTA
40736561 TAAAAAATTA
1 -AAAAAATTA
*
40736571 AAAAATATAA
1 AAAAA-ATTA
*
40736581 AAAAAATTG
1 AAAAAATTA
**
40736590 AAAATTTTA
1 AAAAAATTA
40736599 AAAAAA
1 AAAAAA
40736605 ATTCTAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 25 0.61
10 16 0.39
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAAAATTA
Found at i:40736604 original size:19 final size:19
Alignment explanation
Indices: 40736543--40736607 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
40736533 TATATTTTAT
*
40736543 AAAAAATTATAAAAAT-TAT
1 AAAAAATTA-AAAAATATAA
40736562 AAAAAATTAAAAAATATAA
1 AAAAAATTAAAAAATATAA
* * *
40736581 AAAAAATTGAAAATTTTAA
1 AAAAAATTAAAAAATATAA
40736600 AAAAAATT
1 AAAAAATT
40736608 CTAAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.15
19 35 0.85
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAATTAAAAAATATAA
Found at i:40736807 original size:19 final size:19
Alignment explanation
Indices: 40736783--40736874 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
40736773 AATTTTTGAG
40736783 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40736802 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
40736821 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
40736840 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40736859 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40736875 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40738050 original size:98 final size:98
Alignment explanation
Indices: 40737927--40738121 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
40737917 AAAAATCATG
*
40737927 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
40737992 AAATCTTCGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTCGATAAGTGGATGTTCTTTTAAAGTA
*
40738025 AAGGAAATATTCCGAGTTT-AGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCT
1 AAGGAAATATTCCGAGTTTGA-GATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
* *
40738089 TAAATCTTGGATGAGTGGATGTTCTTTTAAAGT
65 TAAATCTTCGATAAGTGGATGTTCTTTTAAAGT
40738122 TTTATTGTAT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 1 0.01
98 91 0.99
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTCGATAAGTGGATGTTCTTTTAAAGTA
Found at i:40741666 original size:6 final size:6
Alignment explanation
Indices: 40741646--40741679 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
40741636 AGTTCAGATT
40741646 AAAA-A AAAACAA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAAC-A AAAACA AAAACA AAAACA AAAA
40741680 ATGAAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:40743169 original size:132 final size:132
Alignment explanation
Indices: 40742929--40743584 Score: 960
Period size: 132 Copynumber: 5.0 Consensus size: 132
40742919 TTTCTCGTTT
* *
40742929 GTAGTCGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
*
40742994 CAGTAATTCTACTTCCCTGGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
40743059 CA
131 CA
* *
40743061 GTAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGT
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* * * ** ** *
40743126 CAGTAATTCTACTTCTCTGGGCAGTAGTGGAATAGATTAAAGATAGCAGATCTTGCCTTCCT--G
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
40743189 CA
131 CA
* * * *
40743191 TTGACAGCGAAACAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGA
1 --G-TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGA
* *
40743256 AGCCAATAATTCTACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT
63 AGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT
40743321 AAGCA
128 AAGCA
*
40743326 GTAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* * *
40743391 CAGTAATTCTACTTCCTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCATAAG
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
40743456 CA
131 CA
* * * * *
40743458 GTAGTGGAGCAGATCGAATATGGTGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGT
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* * *
40743523 CAGTAATTCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
66 CAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
40743585 GCAGTTGCAG
Statistics
Matches: 466, Mismatches: 51, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
130 3 0.01
131 1 0.00
132 345 0.74
133 114 0.24
135 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (132 bp):
GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
CA
Found at i:40743422 original size:265 final size:263
Alignment explanation
Indices: 40742938--40743584 Score: 955
Period size: 265 Copynumber: 2.4 Consensus size: 263
40742928 TGTAGTCGAG
40742938 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
* *
40743003 TACTTCCCTGGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
40743068 AGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGTCAGTAAT
131 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** *
40743133 TCTACTTCTCTGGGCAGTAGTGGAATAGATTAAAGATAGCAGATCTTGCCTTCC-T-GCATTGAC
196 TCTACTTCTCTGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACC-TCCATAGCA--G-C
40743196 AGCGAAA
257 AGCGAAA
* *
40743203 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
40743268 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
40743333 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
131 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* ** * *
40743398 TCTACTTC-CTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCATAAGCAGTAG
196 TCTACTTCTC-TGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACCTCCAT-AGCAGCAG
* * *
40743462 TGGAG
259 CGAAA
* * * *
40743467 CAGATCGAATATGGTGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
* *
40743532 TA-TCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
66 TACT-TCCCTGGGT-AGCAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
40743585 GCAGTTGCAG
Statistics
Matches: 349, Mismatches: 26, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
263 4 0.01
264 108 0.31
265 234 0.67
267 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (263 bp):
CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCTCTGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACCTCCATAGCAGCAGCG
AAA
Found at i:40743837 original size:19 final size:19
Alignment explanation
Indices: 40743813--40743904 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
40743803 AATTTTTGAG
40743813 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40743832 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
40743851 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
40743870 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40743889 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40743905 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40744134 original size:20 final size:21
Alignment explanation
Indices: 40744097--40744135 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40744087 GGTGACTTAC
* *
40744097 TATTTTTTTTCTTCCGATTAT
1 TATTTTTTATCTTACGATTAT
40744118 TATTTTTTAT-TTACGATT
1 TATTTTTTATCTTACGATT
40744136 TTAAAAAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (21 bp):
TATTTTTTATCTTACGATTAT
Found at i:40745074 original size:98 final size:98
Alignment explanation
Indices: 40744952--40745143 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
40744942 AATCATGAAG
*
40744952 GAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
1 GAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
40745017 TCTTGGATAAGTGGATGTTCTTTTAAAGTAAAT
66 TCTTGGATAAGTGGATGTTCTTTTAAAGTAAAT
*
40745050 GAAATATTCCGAGTTT-AGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTTAA
1 GAAATATTCCGAGTTTGA-GATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAA
*
40745114 ATCTTGGATGAGTGGATGTTCTTTTAAAGT
65 ATCTTGGATAAGTGGATGTTCTTTTAAAGT
40745144 TTTATTGTAT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 1 0.01
98 89 0.99
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (98 bp):
GAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
TCTTGGATAAGTGGATGTTCTTTTAAAGTAAAT
Found at i:40756459 original size:22 final size:24
Alignment explanation
Indices: 40756415--40756460 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40756405 TTTTGAGCAC
* *
40756415 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAACTTTTTTCTTTTACGTTCT
40756439 TTTAACTTTTTT-TTTT-CGTTCT
1 TTTAACTTTTTTCTTTTACGTTCT
40756461 CTTCTGCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTAACTTTTTTCTTTTACGTTCT
Found at i:40784884 original size:20 final size:22
Alignment explanation
Indices: 40784859--40784919 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 22
40784849 TAAATCTATT
40784859 AATATATTAT-TTA-ATTATAA
1 AATATATTATATTATATTATAA
40784879 AATATATTATATTATATTAT--
1 AATATATTATATTATATTATAA
*
40784899 ATTATATTATATTATATTATA
1 AATATATTATATTATATTATA
40784920 TTATATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 29 0.78
21 3 0.08
22 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATATTATATTATATTATAA
Found at i:40784891 original size:5 final size:5
Alignment explanation
Indices: 40784881--40784928 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
40784871 AATTATAAAA
40784881 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
40784929 TATGTAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40785169 original size:16 final size:17
Alignment explanation
Indices: 40785148--40785179 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40785138 CAGGGGAGAA
40785148 AGAAAGAAA-GAAAAAG
1 AGAAAGAAAGGAAAAAG
40785164 AGAAAGAAAGGAAAAA
1 AGAAAGAAAGGAAAAA
40785180 CTAGGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAAAAAG
Found at i:40786236 original size:45 final size:45
Alignment explanation
Indices: 40786171--40786275 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
40786161 ATGTGCCGAC
* * * *
40786171 TACTGTTGCTGTTACTGATTC-GATACTTTATGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCAG-CACTTTATGTGTCGAATACTGT
* *
40786216 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTATGTGTCGAATACTGT
*
40786261 TCCTGTTACTGTTAC
1 TACTGTTACTGTTAC
40786276 TGTTGCTGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTATGTGTCGAATACTGT
Found at i:40786272 original size:6 final size:6
Alignment explanation
Indices: 40786255--40786302 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
40786245 GTGTGTTGAA
* * * *
40786255 TACTGT TCCTGT TACTGT TACTGT TGCTGC TACCGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
40786303 ATCAGGTACT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:40798347 original size:126 final size:126
Alignment explanation
Indices: 40798134--40798375 Score: 371
Period size: 126 Copynumber: 1.9 Consensus size: 126
40798124 GCTAATTGGT
* * * *
40798134 TTTGTCACTGATTTACCATTTCCTCCTTCAACCACATCCAAGTTAAAAGGGATGTGGACATTGTC
1 TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGGATGTGGACATTATC
40798199 CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
66 CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
* * * *
40798260 TTTGTCACTGATTCATCATTTCCACCTTCAAGCACGTCCAACTTAGAAGGGCTATG-GGA-ATTA
1 TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGG--ATGTGGACATTA
*
40798323 TCCTTCCCCAGCTTTCTATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATT
64 TCCTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATT
40798376 CTGCAGCTCA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 99 0.94
127 3 0.03
128 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (126 bp):
TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGGATGTGGACATTATC
CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
Found at i:40805577 original size:21 final size:23
Alignment explanation
Indices: 40805552--40805611 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
40805542 TTATTTCTCA
40805552 ATTTAATTTAATTTTTG-ATTT-
1 ATTTAATTTAATTTTTGTATTTG
*
40805573 ATTTAATTGTTTATTTTTGTTATTTG
1 ATTTAA-T-TTAATTTTTG-TATTTG
40805599 ATTT-ATTTAATTT
1 ATTTAATTTAATTT
40805612 CTAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 15 0.47
24 1 0.03
25 5 0.16
26 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTAATTTAATTTTTGTATTTG
Found at i:40807077 original size:41 final size:43
Alignment explanation
Indices: 40807003--40807082 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
40806993 AGCGCCACTG
* * *
40807003 TAGATCAAGACCTTTAGCGGCGCTTTTATC-AAAACGCCGCTT
1 TAGAACAAGACCTTTAGCGACGCTTTTAGCAAAAACGCCGCTT
40807045 TAGAACAA-ACCTTTAGCGACGCTTCTT-GCAAAAACGCC
1 TAGAACAAGACCTTTAGCGACGCTT-TTAGCAAAAACGCC
40807083 ACTAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 16 0.48
42 17 0.52
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
TAGAACAAGACCTTTAGCGACGCTTTTAGCAAAAACGCCGCTT
Found at i:40810509 original size:73 final size:72
Alignment explanation
Indices: 40810408--40810579 Score: 238
Period size: 73 Copynumber: 2.4 Consensus size: 72
40810398 CTGAGCATTA
* ** * *
40810408 GCGGCGCTTTCTTATTAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTAG
40810473 GTTTTTTT
66 G-TTTTTT
* * * *
40810481 GCGGTGCTTTC-CGAAAAACGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCCTTGGGCTTA
1 GCGGCGCTTTCTC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTA
40810545 GGTTTTTT
65 GGTTTTTT
40810553 GCGGCGCTTTCTCAAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
40810580 TGCTTATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 30 0.34
73 57 0.66
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTAG
GTTTTTT
Found at i:40810665 original size:12 final size:12
Alignment explanation
Indices: 40810648--40810673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40810638 TTTTTTATCC
40810648 AAACGCCGCTAA
1 AAACGCCGCTAA
40810660 AAACGCCGCTAA
1 AAACGCCGCTAA
40810672 AA
1 AA
40810674 GCCTATTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:40812491 original size:3 final size:3
Alignment explanation
Indices: 40812485--40812527 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
40812475 TTATTTAAGT
*
40812485 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40812528 ACTAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40825419 original size:41 final size:41
Alignment explanation
Indices: 40825374--40825652 Score: 524
Period size: 41 Copynumber: 6.8 Consensus size: 41
40825364 TGATTCAGTA
40825374 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40825415 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40825456 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40825497 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40825538 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40825579 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* *
40825620 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTG
40825653 TATTACATTC
Statistics
Matches: 235, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
40 2 0.01
41 233 0.99
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:40833121 original size:41 final size:41
Alignment explanation
Indices: 40833076--40833272 Score: 360
Period size: 41 Copynumber: 4.8 Consensus size: 41
40833066 TGATTCAGTA
40833076 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40833117 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40833158 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40833199 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* *
40833240 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTG
40833273 TATTACATTC
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
40 2 0.01
41 151 0.99
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:40846614 original size:16 final size:16
Alignment explanation
Indices: 40846550--40846617 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
40846540 GAAGTAATAT
* *
40846550 TATTTTAATAGTTTAA
1 TATTTTATTAATTTAA
*
40846566 TATTTAATTTAATTTAA
1 TATTTTA-TTAATTTAA
* *
40846583 TA-TTTATCTAA-ATAG
1 TATTTTAT-TAATTTAA
*
40846598 TATTTTATTAATTTAG
1 TATTTTATTAATTTAA
40846614 TATT
1 TATT
40846618 AAAGTGATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.20
16 24 0.59
17 9 0.22
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:40846650 original size:16 final size:16
Alignment explanation
Indices: 40846631--40846688 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
40846621 GTGATTATCT
40846631 TAATATTAAATTAATA
1 TAATATTAAATTAATA
* * *
40846647 TAATATT-TATCAAGA
1 TAATATTAAATTAATA
* *
40846662 TAAATATTATATTAATT
1 T-AATATTAAATTAATA
40846679 TAATATTAAA
1 TAATATTAAA
40846689 GTGATTAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 6 0.18
16 21 0.64
17 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:40846686 original size:68 final size:68
Alignment explanation
Indices: 40846562--40846695 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
40846552 TTTTAATAGT
* * * * *
40846562 TTAATATTTAATTTAATTTAATATTTATCTAAATAGTATTTTATTAATTTAGTATTAAAGTGATT
1 TTAATATTTAAATTAATATAATATTTATCTAAATAATATTATATTAATTTAATATTAAAGTGATT
40846627 ATC
66 ATC
40846630 TTAATA-TTAAATTAATATAATATTTATC-AAGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTAATATTTAAATTAATATAATATTTATCTAA-AT-AATATTATATTAATTTAATATTAAAGTGA
40846693 TTA
64 TTA
40846696 AGTTTAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 2 0.03
67 22 0.37
68 35 0.59
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (68 bp):
TTAATATTTAAATTAATATAATATTTATCTAAATAATATTATATTAATTTAATATTAAAGTGATT
ATC
Found at i:40850054 original size:33 final size:33
Alignment explanation
Indices: 40850017--40850079 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
40850007 ATCACTGCCC
*
40850017 CATCCACACCACAACC-CTAGGTGTCTCTCTCAA
1 CATCCACACCACAACCTC-AGGTGTCCCTCTCAA
40850050 CATCCACACCACAACCTCAGGTGTCCCTCT
1 CATCCACACCACAACCTCAGGTGTCCCTCT
40850080 GACTCTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (33 bp):
CATCCACACCACAACCTCAGGTGTCCCTCTCAA
Found at i:40851919 original size:15 final size:17
Alignment explanation
Indices: 40851881--40851921 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
40851871 TTACATAATA
40851881 AAAATAATATTGATATT
1 AAAATAATATTGATATT
*
40851898 AAAATAAT-TTTATATT
1 AAAATAATATTGATATT
40851914 -AAATAATA
1 AAAATAATA
40851922 ATTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATAATATTGATATT
Found at i:40851923 original size:18 final size:17
Alignment explanation
Indices: 40851879--40851930 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
40851869 TCTTACATAA
*
40851879 TAAAAATAATATTGATAT
1 TAAAAATAAT-TTTATAT
40851897 T-AAAATAATTTTATAT
1 TAAAAATAATTTTATAT
40851913 TAAATAATAATTTTATAT
1 TAAA-AATAATTTTATAT
40851931 ATTTATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 7 0.23
17 10 0.32
18 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAAAATAATTTTATAT
Found at i:40853755 original size:19 final size:20
Alignment explanation
Indices: 40853723--40853768 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
40853713 CGGAAAATAA
40853723 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40853743 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40853762 TTTCTGG
1 TTTCTGG
40853769 TGTTTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40864175 original size:35 final size:34
Alignment explanation
Indices: 40864136--40864202 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
40864126 TAAAATGCGC
*
40864136 ATATAAATACATACATGTAT-TAAAATATATAAAAA
1 ATATAAACACATACATGTATGT-AAATAT-TAAAAA
* *
40864171 ATATAAACATATATATGTATGTAAATATTAAA
1 ATATAAACACATACATGTATGTAAATATTAAA
40864203 TATGTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 23 0.82
36 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (34 bp):
ATATAAACACATACATGTATGTAAATATTAAAAA
Found at i:40877624 original size:24 final size:24
Alignment explanation
Indices: 40877597--40877644 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
40877587 TGTTCGATTG
40877597 AGCTCAACTTGAGTATCAAAACCT
1 AGCTCAACTTGAGTATCAAAACCT
40877621 AGCTCAACTTGAGTATCAAAACCT
1 AGCTCAACTTGAGTATCAAAACCT
40877645 TGAGTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (24 bp):
AGCTCAACTTGAGTATCAAAACCT
Found at i:40880502 original size:32 final size:31
Alignment explanation
Indices: 40880447--40880506 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
40880437 GTTTATAAAA
40880447 TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
1 TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
*
40880478 TTAA-GTTTAGGGTTTTATTTATTTTTAGG
1 TTAAGGTTTA-GGATTT-TTTATTTTTAGG
40880507 GTTTAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 9 0.35
32 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (31 bp):
TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
Found at i:40884234 original size:43 final size:43
Alignment explanation
Indices: 40884173--40884310 Score: 215
Period size: 43 Copynumber: 3.2 Consensus size: 43
40884163 TATAGACAAT
*
40884173 GCCGCTATAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
40884216 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
* * * *
40884259 GCTGCTAAAGGACATGACCTTTAGCGGCGCTTTTA-TCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGC-TTTACCCACAAAC
40884302 GCCGCTAAA
1 GCCGCTAAA
40884311 AGTACCGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 84 0.95
44 4 0.05
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
Found at i:40885416 original size:40 final size:41
Alignment explanation
Indices: 40885327--40885408 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 41
40885317 AAACACAAAA
**
40885327 AAATATTTTAAAAATAATAAAATAAAAATAAAAATATTTTT
1 AAATATTTTAAAAATAATAAAATAAAAATAAAAATACATTT
*
40885368 AAAGTATTTT-AAAAT--TAAAAAAAAAATAAAAAATACATTT
1 AAA-TATTTTAAAAATAATAAAATAAAAAT-AAAAATACATTT
40885408 A
1 A
40885409 TTATATTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 11 0.31
40 11 0.31
41 8 0.22
42 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (41 bp):
AAATATTTTAAAAATAATAAAATAAAAATAAAAATACATTT
Found at i:40887127 original size:108 final size:106
Alignment explanation
Indices: 40886873--40887176 Score: 413
Period size: 108 Copynumber: 2.9 Consensus size: 106
40886863 CGAGAAAAGT
*
40886873 AATTT-TTTTTTTGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTTAA-TTTTTTTTTACTTTT
1 AATTTATTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACC-TTTTAATTTTTTTTTTACTTTT
* *
40886936 TTCATGTCAGATAAGATATTAGTATACGAAAAAAGTAAAAAA
65 TTCATGTCAGATAAGCTATCAGTATACGAAAAAAGTAAAAAA
** *
40886978 AA---A-AATTTGGTGGTGGCCTAGCAATGGCCGGCACCACCTTTTAATTTTTTTTTTTTACTTT
1 AATTTATTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAA--TTTTTTTTTTACTTT
* **
40887039 TTTCTTGTCAGATAAGCTATCAGTATACGAAAAGGGTAAAAAA
64 TTTCATGTCAGATAAGCTATCAGTATACGAAAAAAGTAAAAAA
* * *
40887082 AATTTATTTTTTGGTGGTGGCCTGGTAATGGCCGACACCACCTTTTAAAATTTTTTTTTTACCTT
1 AATTTATTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTT--AATTTTTTTTTTACTTT
40887147 TTTCATGTCAGATAAGCTATCAGTATACGA
64 TTTCATGTCAGATAAGCTATCAGTATACGA
40887177 GCATGCGCAC
Statistics
Matches: 173, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
101 6 0.03
102 31 0.18
104 54 0.31
105 2 0.01
107 1 0.01
108 77 0.45
110 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (106 bp):
AATTTATTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAATTTTTTTTTTACTTTTT
TCATGTCAGATAAGCTATCAGTATACGAAAAAAGTAAAAAA
Found at i:40887204 original size:21 final size:21
Alignment explanation
Indices: 40887178--40887230 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
40887168 AGTATACGAG
*
40887178 CATGCGCACACGCAGTATGAA
1 CATGCGCACACGCAGCATGAA
*
40887199 CATGCGCACACGCTGCATGAA
1 CATGCGCACACGCAGCATGAA
40887220 CATGCGCACAC
1 CATGCGCACAC
40887231 AGATATCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.13
Consensus pattern (21 bp):
CATGCGCACACGCAGCATGAA
Found at i:40887889 original size:103 final size:104
Alignment explanation
Indices: 40887684--40888064 Score: 463
Period size: 107 Copynumber: 3.6 Consensus size: 104
40887674 TAAAGATTAC
* * * *
40887684 ATCTGACACGAAATAATTAAAATTTTTTTTT---AAAAGGTGGAGCGGGCCATTGCCAGGCCACC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACC
** * *
40887746 ACCAAAAAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTT
66 ACC-----AAT-TTTTTTTTTACTTTTTTCGTATATTGATATCTT
*
40887791 ATCTGACACGAAAAAAGTAAAATTTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCATGCCAC
1 ATCTGACACGAAAAAAGTAAAA-TTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCAGGCCAC
40887856 CACC-ATTTTTTTTTTACTTTTTT-GTATATTGATATCTT
65 CACCAATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
* *
40887894 ATCTGACACGAAAAAAGTAAAA-TTTTTTTT--AAAAAGGTGGTGTCGGCCATTGCTAGGCCACC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACC
*
40887956 ACCAATTTTTTTTTTACTTTTTTCGTCTATTGATATCTT
66 ACCAATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
** * * *
40887995 ATCTGACACGAAAAAAGTAAAACAATTTTTTTAAAAAAAAAGATGGTGCCGACCATTGTCAGGCC
1 ATCTGACACGAAAAAAGT--AA-AATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCAGGCC
40888060 ACCAC
63 ACCAC
40888065 AAAATATATA
Statistics
Matches: 242, Mismatches: 20, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
99 32 0.13
100 19 0.08
101 40 0.17
103 37 0.15
104 17 0.07
105 8 0.03
107 49 0.20
108 9 0.04
111 31 0.13
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (104 bp):
ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACC
ACCAATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
Found at i:40887994 original size:101 final size:100
Alignment explanation
Indices: 40887684--40888031 Score: 439
Period size: 103 Copynumber: 3.4 Consensus size: 100
40887674 TAAAGATTAC
* * * *
40887684 ATCTGACACGAAATAATTAAAATTTTTTTTTAAAAGGTGGAGCGGGCCATTGCCAGGCCACCACC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTGC-GGCCATTGCCAGGCCACCACC
** * *
40887749 AAAAAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTT
65 -----AAT-TTTTTTTTTACTTTTTTCGTATATTGATATCTT
*
40887791 ATCTGACACGAAAAAAGTAAAATTTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCATGCCAC
1 ATCTGACACGAAAAAAGTAAAA--TTTTTTTT--AAAAAGGTGGTG-CGGCCATTGCCAGGCCAC
40887856 CACC-ATTTTTTTTTTACTTTTTT-GTATATTGATATCTT
61 CACCAATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
*
40887894 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTGTCGGCCATTGCTAGGCCACCACC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTG-CGGCCATTGCCAGGCCACCACC
*
40887959 AATTTTTTTTTTACTTTTTTCGTCTATTGATATCTT
65 AATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
*
40887995 ATCTGACACGAAAAAAGTAAAACAATTTTTTTAAAAA
1 ATCTGACACGAAAAAAGT-AAA-ATTTTTTTTAAAAA
40888032 AAAAGATGGT
Statistics
Matches: 218, Mismatches: 14, Indels: 22
0.86 0.06 0.09
Matches are distributed among these distances:
99 32 0.15
100 19 0.09
101 40 0.18
102 3 0.01
103 48 0.22
104 15 0.07
105 2 0.01
107 20 0.09
109 8 0.04
111 30 0.14
112 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (100 bp):
ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTGCGGCCATTGCCAGGCCACCACCA
ATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
Found at i:40893837 original size:12 final size:11
Alignment explanation
Indices: 40893810--40893897 Score: 63
Period size: 12 Copynumber: 7.7 Consensus size: 11
40893800 AAGAATGTTA
*
40893810 AAAAAAACAAAC
1 AAAAAAA-AAAG
40893822 AAAAACAAAAAG
1 AAAAA-AAAAAG
*
40893834 AAAAGAAAAAG
1 AAAAAAAAAAG
40893845 AAAAAATAAAAG
1 AAAAAA-AAAAG
*
40893857 AAAGGAAAAAA-
1 AAA-AAAAAAAG
* *
40893868 TAAAAGAAAAG
1 AAAAAAAAAAG
*
40893879 -AAAAAAGAAG
1 AAAAAAAAAAG
40893889 AAAGAAAAA
1 AAA-AAAAA
40893898 GGAGAGGCCA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 13 0.22
11 15 0.25
12 28 0.47
13 4 0.07
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:40893842 original size:17 final size:16
Alignment explanation
Indices: 40893810--40893897 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 16
40893800 AAGAATGTTA
*
40893810 AAAAAAACAAACAAAA-
1 AAAAAAA-AAAGAAAAG
40893826 ACAAAAAGAAAAGAAAAAG
1 A-AAAAA-AAAAG-AAAAG
*
40893845 AAAAAATAAAAGAAAGG
1 AAAAAA-AAAAGAAAAG
40893862 AAAAAATAAAAGAAAAG
1 AAAAAA-AAAAGAAAAG
*
40893879 -AAAAAAGAAG-AAAG
1 AAAAAAAAAAGAAAAG
40893893 AAAAA
1 AAAAA
40893898 GGAGAGGCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
14 4 0.06
15 8 0.13
16 6 0.10
17 28 0.45
18 15 0.24
19 1 0.02
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:40894342 original size:103 final size:103
Alignment explanation
Indices: 40894222--40894524 Score: 428
Period size: 103 Copynumber: 2.9 Consensus size: 103
40894212 TTATTCTCAT
*
40894222 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTC
1 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
40894287 CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
66 CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
40894325 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
1 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
* * * * * *
40894390 TATCTTATCCATTGTCATAATACTTTTCATCTTATTCAG
66 CATATTGTCCATTGTGATAAT-CTTTTTATCTTATTCAA
* * *
40894429 TTCT-TGTCTTAGCAAAATTTGCTATCTTGATTAACTTATTCATTTTGAGCCTTATTCTCAATAA
1 TT-TGTATCTTAGCAAAATTTGCTATCTTGA-T---TTATTCATTTCGAGCCTTGTTCTCAATAA
* * *
40894493 AATTCCATTTTGTCCATTTTGATCATCTTTTT
61 AATTCCATATTGTCCATTGTGATAATCTTTTT
40894525 CAAGCATTTT
Statistics
Matches: 177, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
103 81 0.46
104 42 0.24
105 2 0.01
107 5 0.03
108 47 0.27
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (103 bp):
TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
Found at i:40895488 original size:46 final size:46
Alignment explanation
Indices: 40895418--40895809 Score: 613
Period size: 46 Copynumber: 8.5 Consensus size: 46
40895408 AGACTAAAAG
* * *
40895418 TAGCAGATCTTGTCTTCCTATATTTGGCAGTGGAGTAGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
* * * *
40895464 TAGCAGATCTTATCTTCCTGTATTTGGCATCGGAGTAGATCGAGGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
* * *
40895510 TAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGTGGATCAAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
40895556 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
* *
40895602 TAGCAGATCTTGCCTTTCTGTATTTGGCAGCGGAGTGGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
* * *
40895648 TAGCAGATATTGTCTTACTGTATTTGGCAGCAGAGTGGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
40895694 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
** *
40895740 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGAAGATTGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
40895786 TAGCAGATTCTTGTCTTCCTGTAT
1 TAGCAGA-TCTTGTCTTCCTGTAT
40895810 CCGACAGTGA
Statistics
Matches: 318, Mismatches: 27, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
46 302 0.95
47 16 0.05
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (46 bp):
TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
Found at i:40895988 original size:44 final size:44
Alignment explanation
Indices: 40895929--40896095 Score: 160
Period size: 44 Copynumber: 3.8 Consensus size: 44
40895919 TCAAATTTTG
* *
40895929 TCTCTCTGAAGTTGCAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAACCTTA
* * * **
40895973 TC-CCCATGAAGTTGCAATGGGGCAAGTTGAAGATACAAGTCTTA
1 TCTCCC-TGAAGTTGCAGTGGAGCAGGTTGAAGATACAAACCTTA
* * **
40896017 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC-TA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAC-AAACCTTA
* * *
40896061 TCTCCCTGAAGTTGCAGTGGGGCAAGTCGAAGATA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
40896096 ACAAGTCTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 2 0.02
44 89 0.90
45 8 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAACCTTA
Found at i:40896217 original size:44 final size:44
Alignment explanation
Indices: 40896116--40896205 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
40896106 TGGAAGCTAT
* ** *
40896116 AAATTACAAACCTTACCTCTCTGAAGTTGCAGTAGAGTAGGTTG
1 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
40896160 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
1 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
40896204 AA
1 AA
40896206 GTCACTAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
Found at i:40896231 original size:44 final size:44
Alignment explanation
Indices: 40896116--40896236 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 44
40896106 TGGAAGCTAT
* * * *
40896116 AAATTACAAACCTTA-CCTCTCTGAAGTTGCAGTAGAGTAGGTTG
1 AAATAACAAACCTTATCC-CCCTAAAGTTGCAGTAGAGCAGGTTG
* * * *
40896160 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
1 AAATAACAAACCTTATCCCCCTAAAGTTGCAGTAGAGCAGGTTG
* * * *
40896204 AAGTCACTAACCTTATCCCCCTAAAGTTACAGT
1 AAATAACAAACCTTATCCCCCTAAAGTTGCAGT
40896237 GGGGCAAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 63 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
AAATAACAAACCTTATCCCCCTAAAGTTGCAGTAGAGCAGGTTG
Found at i:40896275 original size:44 final size:44
Alignment explanation
Indices: 40896121--40896275 Score: 116
Period size: 44 Copynumber: 3.5 Consensus size: 44
40896111 GCTATAAATT
* * * * ** * *
40896121 ACAAACCTTACCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAATA
1 ACAAACCTTATCTCTCCGAAGTTACAGTAGAGCAAATTGAAGTC
* * * **
40896165 ACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTC
1 ACAAACCTTATCTCTCCGAAGTTACAGTAGAGCAAATTGAAGTC
* * * * *
40896209 ACTAACCTTATC-CCCCTAAAGTTACAGTGGGGCAAATTGAAG-C
1 ACAAACCTTATCTCTCC-GAAGTTACAGTAGAGCAAATTGAAGTC
40896252 TACAAACCTTATCTCTCCGAAGTT
1 -ACAAACCTTATCTCTCCGAAGTT
40896276 GTAGTGGAGT
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.03
44 84 0.93
45 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
ACAAACCTTATCTCTCCGAAGTTACAGTAGAGCAAATTGAAGTC
Found at i:40898459 original size:23 final size:25
Alignment explanation
Indices: 40898421--40898470 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
40898411 TTTGTATGTG
40898421 TATATACATAATTATAT-TTTTCTTA
1 TATATACATAATTATATATTTT-TTA
40898446 TATATACA-AA-TATATATTTTTTA
1 TATATACATAATTATATATTTTTTA
40898469 TA
1 TA
40898471 ACTTTGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.42
24 6 0.25
25 8 0.33
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATACATAATTATATATTTTTTA
Found at i:40901564 original size:21 final size:21
Alignment explanation
Indices: 40901540--40901629 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
40901530 ATTCCTAACT
*
40901540 CTTAACCCCTAACCCCTAAAC
1 CTTAATCCCTAACCCCTAAAC
*
40901561 CTTACATCCC-AACCCTTAAAC
1 CTTA-ATCCCTAACCCCTAAAC
* * * *
40901582 CATAATCCCTAATCCATAATC
1 CTTAATCCCTAACCCCTAAAC
* *
40901603 TCTAAATCCAT-ACTCCCTAAAC
1 -CTTAATCCCTAAC-CCCTAAAC
40901625 CTTAA
1 CTTAA
40901630 AATATGAACT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
20 5 0.10
21 30 0.58
22 17 0.33
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.26
Consensus pattern (21 bp):
CTTAATCCCTAACCCCTAAAC
Found at i:40901610 original size:15 final size:15
Alignment explanation
Indices: 40901577--40901623 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
40901567 TCCCAACCCT
40901577 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
40901591 T-AATCCATAATCTC
1 TAAATCCATAATCCC
*
40901605 TAAATCCATACTCCC
1 TAAATCCATAATCCC
40901620 TAAA
1 TAAA
40901624 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:40901905 original size:14 final size:15
Alignment explanation
Indices: 40901884--40901919 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
40901874 TCCCAACCCT
40901884 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
40901898 T-AATCCATAATCCC
1 TAAATCCATAATCCC
40901912 TAAATCCA
1 TAAATCCA
40901920 CTCCCTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 12 0.60
15 6 0.30
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:40902359 original size:41 final size:41
Alignment explanation
Indices: 40902277--40902379 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
40902267 TAAAATGTTT
* * * * * *
40902277 TTAGTAGCGCTTTTTCAAAATTGTCGCTACAGCCCCCAGCA
1 TTAGCAGCGCTTTTTCAAAAATGTCACTAAAACACCCAGCA
* *
40902318 TTAGCAGCGCTTTTTAAAAAATGTCACTAAAACACCGAGCA
1 TTAGCAGCGCTTTTTCAAAAATGTCACTAAAACACCCAGCA
*
40902359 TTAGCGGCGCTTTTTCAAAAA
1 TTAGCAGCGCTTTTTCAAAAA
40902380 CGCCGCGCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (41 bp):
TTAGCAGCGCTTTTTCAAAAATGTCACTAAAACACCCAGCA
Found at i:40902471 original size:41 final size:41
Alignment explanation
Indices: 40902307--40902476 Score: 164
Period size: 41 Copynumber: 4.1 Consensus size: 41
40902297 TTGTCGCTAC
* * * *
40902307 AGCCCCCAGCATTAGCAGCGCTTTTTAAAAAATGTCACTAA
1 AGCCCCGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAA
* * * * *
40902348 AACACCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCGCAA
1 AGCCCCGAGCATTAGCGGCGCTTTTTAAAAAACGCCAC-TAA
* * * * *
40902390 A-CCCCGAGCATTAGCGTCGCATTTTCAAAAACACCGCTAA
1 AGCCCCGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAA
* *
40902430 AGCCCCGAGCATTAGCGGCGCTTTCTT-GAAATCGCCACTAA
1 AGCCCCGAGCATTAGCGGCGCTTT-TTAAAAAACGCCACTAA
40902471 AGCCCC
1 AGCCCC
40902477 AAAAGGTAAG
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 3 0.03
41 98 0.92
42 5 0.05
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (41 bp):
AGCCCCGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAA
Found at i:40905070 original size:25 final size:24
Alignment explanation
Indices: 40905024--40905071 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40905014 AGTTGTAAAT
40905024 TAGAAAATATCTCTAGAAAATTTC
1 TAGAAAATATCTCTAGAAAATTTC
* * *
40905048 TAGAATAATCTCTTTAGAGAATTT
1 TAGAA-AATATCTCTAGAAAATTT
40905072 TCTCTCTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (24 bp):
TAGAAAATATCTCTAGAAAATTTC
Found at i:40905340 original size:37 final size:35
Alignment explanation
Indices: 40905283--40905353 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
40905273 TCACATCAGT
*
40905283 ATTAAATTAATAAAATACTATTAAGATAAGTATTAA
1 ATTAAATTAATAAAATACTATTAAAATAA-TATTAA
*
40905319 ATTAAATTTAATATTAA-ACTATTAAAATAATATTA
1 ATTAAA-TTAATA-AAATACTATTAAAATAATATTA
40905354 TTTTTAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.35
37 18 0.58
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATATTAA
Found at i:40909953 original size:20 final size:19
Alignment explanation
Indices: 40909928--40909966 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40909918 GTGTTAAAAC
*
40909928 ATATCACGCTTTATAAATAA
1 ATATCACGC-TAATAAATAA
*
40909948 ATATCATGCTAATAAATAA
1 ATATCACGCTAATAAATAA
40909967 TTTTTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATCACGCTAATAAATAA
Found at i:40912115 original size:18 final size:18
Alignment explanation
Indices: 40912089--40912125 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40912079 GCTGTGTGGA
*
40912089 GAATTCACATGCCCGTGT
1 GAATACACATGCCCGTGT
40912107 GAATACACATGCCCGTGT
1 GAATACACATGCCCGTGT
40912125 G
1 G
40912126 GTCAGGCCGT
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:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (18 bp):
GAATACACATGCCCGTGT
Found at i:40914186 original size:50 final size:50
Alignment explanation
Indices: 40914128--40914260 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 50
40914118 TATTAAGGTT
* *
40914128 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATAGCATGGGCACCGAG
* * * *
40914178 ATGAGAGGTCCCCCGTAAGAACCAAGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAG-ACCATGTCTGGGACATAGCATGGGCACCGAG
** * * *
40914229 ATGAGAACTCTCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGA
40914261 TATGACATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
50 29 0.42
51 40 0.58
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATAGCATGGGCACCGAG
Found at i:40914549 original size:20 final size:20
Alignment explanation
Indices: 40914524--40914572 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40914514 TGAGTTATTT
40914524 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
40914544 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
40914564 AAG-AAGCAA
1 AAGTAAGCAA
40914573 AGACAATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:40929432 original size:22 final size:20
Alignment explanation
Indices: 40929406--40929590 Score: 116
Period size: 22 Copynumber: 9.0 Consensus size: 20
40929396 TAGATTAGAA
*
40929406 TTTTGTATGAATATTTTAACTT
1 TTTTGTATGAATATTATAA--T
40929428 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTATAAT
*
40929448 TTTT-TATGAATATTGTAA-
1 TTTTGTATGAATATTATAAT
* *
40929466 TGTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
*
40929486 TATTT-TAT-AATTAAATT-TGTAT
1 T-TTTGTATGAA-T--ATTAT-AAT
* *
40929508 TTCTAGTTTTG-A-ATTAGTAATT
1 TT-TTG-TATGAATATTA-TAA-T
40929530 TTTTGTATGAATATTATAA-
1 TTTTGTATGAATATTATAAT
*
40929549 TTTTGTATGAATATTATATT
1 TTTTGTATGAATATTATAAT
*
40929569 CGTTTTGTATGAATATTGTAAT
1 --TTTTGTATGAATATTATAAT
40929591 ATTATAATTT
Statistics
Matches: 131, Mismatches: 13, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.02
19 47 0.36
20 16 0.12
21 11 0.08
22 51 0.39
24 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTTGTATGAATATTATAAT
Found at i:40929450 original size:41 final size:38
Alignment explanation
Indices: 40929399--40929590 Score: 104
Period size: 41 Copynumber: 4.7 Consensus size: 38
40929389 TATAGTTTAG
* * *
40929399 ATTAGAATTTTGTATGAATATTTTAACTTTTTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAA---TGTTGTATGAAT
*
40929440 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
* * * *
40929478 ATTGTAATTATTTTAT-AATTAAATTTGT-ATTTCTAGTTTTG-A-
1 ATTATAATT-TTGTATGAA-T--A-TTGTAATGT-T-G-TATGAAT
* *
40929520 ATTAGTAATTTTTTGTATGAATATTATAATTTTGTATGAAT
1 ATTA-TAA--TTTTGTATGAATATTGTAATGTTGTATGAAT
*
40929561 ATTATATTCGTTTTGTATGAATATTGTAAT
1 ATTATA---ATTTTGTATGAATATTGTAAT
40929591 ATTATAATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
38 21 0.17
39 10 0.08
40 4 0.03
41 54 0.45
42 13 0.11
43 5 0.04
44 9 0.08
45 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (38 bp):
ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
Found at i:40929455 original size:19 final size:19
Alignment explanation
Indices: 40929399--40929590 Score: 95
Period size: 19 Copynumber: 9.4 Consensus size: 19
40929389 TATAGTTTAG
* *
40929399 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
40929418 ATTTTAACTTTTTTGTATGAAT
1 ATTATAA--TTTTT-TATGAAT
40929440 ATTATAATTTTTTATGAAT
1 ATTATAATTTTTTATGAAT
* * *
40929459 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
40929478 ATTGTAATTATTTTAT-AATT
1 ATTATAATT-TTTTATGAA-T
* *
40929498 AAATT-TGTATTTCTAGTTTTG-A-
1 --ATTAT-AATTT-T--TTATGAAT
40929520 ATTAGTAATTTTTTGTATGAAT
1 ATTA-TAA-TTTTT-TATGAAT
*
40929542 ATTATAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
40929561 ATTATATTCGTTTTGTATGAAT
1 ATTATAAT--TTTT-TATGAAT
*
40929583 ATTGTAAT
1 ATTATAAT
40929591 ATTATAATTT
Statistics
Matches: 134, Mismatches: 18, Indels: 39
0.70 0.09 0.20
Matches are distributed among these distances:
19 53 0.40
20 21 0.16
21 15 0.11
22 41 0.31
24 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
ATTATAATTTTTTATGAAT
Found at i:40929483 original size:49 final size:49
Alignment explanation
Indices: 40929430--40929644 Score: 122
Period size: 49 Copynumber: 4.4 Consensus size: 49
40929420 TTTAACTTTT
* *
40929430 TTGTATGAATATTATAATTTTTTATGAATATTGTAATGTTGTATGAATA
1 TTGTATGAATATTATAATTTTGTATGAATATTATAATGTTGTATGAATA
* * *** * * * * * * *
40929479 TTGTAAT-TATTTTATAATTAAATTTGTAT-TTCTAGTTTTGAATTAGTAATTTT
1 TTGT-ATGAATATTATAATTTTGTATGAATATTATAATGTTGTA-T-G-AA--TA
*
40929532 TTGTATGAATATTATAATTTTGTATGAATATTATATTCGTTTTGTATGAATA
1 TTGTATGAATATTATAATTTTGTATGAATATTATAAT-G--TTGTATGAATA
* * *
40929584 TTG--T-AATATTATAATTTTGTATGAATATTTTAATATTG--T-AATT
1 TTGTATGAATATTATAATTTTGTATGAATATTATAATGTTGTATGAATA
*
40929627 TTGTATGAATATTGTAAT
1 TTGTATGAATATTATAAT
40929645 GTGGGGATAT
Statistics
Matches: 123, Mismatches: 29, Indels: 31
0.67 0.16 0.17
Matches are distributed among these distances:
43 6 0.05
44 1 0.01
45 1 0.01
46 13 0.11
48 9 0.07
49 48 0.39
50 4 0.03
51 2 0.02
52 6 0.05
53 20 0.16
54 7 0.06
55 1 0.01
56 1 0.01
57 4 0.03
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (49 bp):
TTGTATGAATATTATAATTTTGTATGAATATTATAATGTTGTATGAATA
Found at i:40929606 original size:27 final size:27
Alignment explanation
Indices: 40929571--40929644 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
40929561 ATTATATTCG
40929571 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
* *
40929598 TTTTGTATGAATATTTTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
40929625 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
40929645 GTGGGGATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAA
Found at i:40929627 original size:124 final size:123
Alignment explanation
Indices: 40929406--40929632 Score: 277
Period size: 124 Copynumber: 1.8 Consensus size: 123
40929396 TAGATTAGAA
* *
40929406 TTTTGTATGAATATTTTAACTTTTTTGTATGAATATTATAATTTTTTATGAATATTGTAATGTTG
1 TTTTGTATGAATATTATAA--TTTTTGTATGAATATTATAATTTTTTATGAATATTGTAATGATG
*
40929471 TATGAATATTGTAATTATTTTATAATTAAA-TTTGTATTTCTAGTTTTGAATTAGTAATT
64 TATGAATATTGTAAATATTTTATAATTAAATTTTGTATTTCTAGTTTTGAATTAGTAATT
*
40929530 TTTTGTATGAATATTATAA-TTTTGTATGAATATTATATTCGTTTTGTATGAATATTGTAAT-AT
1 TTTTGTATGAATATTATAATTTTTGTATGAATATTATAAT--TTTT-TATGAATATTGTAATGAT
* *
40929593 -TAT-AATTTTGTATGAATATTTTA-ATATTGTAATTTTGTAT
63 GTATGAATATTGTA--AATATTTTATA-ATT-AAATTTTGTAT
40929633 GAATATTGTA
Statistics
Matches: 89, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
121 27 0.30
122 4 0.04
123 16 0.18
124 35 0.39
125 7 0.08
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (123 bp):
TTTTGTATGAATATTATAATTTTTGTATGAATATTATAATTTTTTATGAATATTGTAATGATGTA
TGAATATTGTAAATATTTTATAATTAAATTTTGTATTTCTAGTTTTGAATTAGTAATT
Found at i:40929754 original size:60 final size:60
Alignment explanation
Indices: 40929686--40929807 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
40929676 TGTATGAATA
* * * * * *
40929686 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
40929746 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
40929806 TT
1 TT
40929808 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:40929886 original size:38 final size:38
Alignment explanation
Indices: 40929841--40929922 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
40929831 CATATAAAGT
40929841 TTATAAAAAAATTAAAAATCATTTAATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTAATTAAAAGTTTAA
*
40929879 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTAATTAAAAGTTTAA
40929917 TTATAA
1 TTATAA
40929923 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTAATTAAAAGTTTAA
Found at i:40931637 original size:6 final size:6
Alignment explanation
Indices: 40931626--40931671 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
40931616 GCATCATGCA
40931626 CCAGAG CCAGAG CCAG-G CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
40931672 ACTACATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.33, C:0.35, G:0.33, T:0.00
Consensus pattern (6 bp):
CCAGAG
Found at i:40934899 original size:18 final size:17
Alignment explanation
Indices: 40934867--40934911 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
40934857 ATTCAAAAGC
40934867 TAACAAAATTAATAACA
1 TAACAAAATTAATAACA
*
40934884 TGACAAAATCTAATAACA
1 TAACAAAAT-TAATAACA
40934902 TAACAAAATT
1 TAACAAAATT
40934912 TCCAAGTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24
Consensus pattern (17 bp):
TAACAAAATTAATAACA
Done.