Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold430
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: 426104
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
File 1 of 4
Found at i:987 original size:20 final size:19
Alignment explanation
Indices: 962--1019 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
952 AAGTACCCAA
*
962 AATGTATCGATACATTCTTC
1 AATGTATCGATACATT-ATC
* *
982 AATGTATTGATACATGTATG
1 AATGTATCGATACAT-TATC
1002 AATGTATCGATACATTAT
1 AATGTATCGATACATTAT
1020 GTGTTTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 29 0.88
21 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
AATGTATCGATACATTATC
Found at i:4970 original size:13 final size:14
Alignment explanation
Indices: 4944--4992 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
4934 ACATGGTAAA
*
4944 AATAATAATATTTT
1 AATAATATTATTTT
*
4958 AATAA-CTTATTTT
1 AATAATATTATTTT
4971 AAAATAATATTATTTT
1 --AATAATATTATTTT
4987 AATAAT
1 AATAAT
4993 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 5 0.17
16 7 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:5018 original size:30 final size:29
Alignment explanation
Indices: 4940--5019 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
4930 TTTTACATGG
*
4940 TAAAAATAATAATATTTTAATAACTTATT
1 TAAAAATAATATTATTTTAATAACTTATT
*
4969 TTAAAATAATATTATTTTAATAA-TTAATT
1 TAAAAATAATATTATTTTAATAACTT-ATT
* *
4998 TCAAAAATAACATTAATTTAAT
1 T-AAAAATAATATTATTTTAAT
5020 CAATGAGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 2 0.05
29 25 0.57
30 17 0.39
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAAATAATATTATTTTAATAACTTATT
Found at i:5868 original size:11 final size:11
Alignment explanation
Indices: 5852--5876 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5842 TTATATAGAT
5852 TTTTAATTGGG
1 TTTTAATTGGG
5863 TTTTAATTGGG
1 TTTTAATTGGG
5874 TTT
1 TTT
5877 AGGTTTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTTAATTGGG
Found at i:5882 original size:45 final size:45
Alignment explanation
Indices: 5830--5934 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
5820 ATTTTATGAG
*
5830 TTAGGTTTAAGTTTATATAGATTTTTAATTGGGTTTTAATTGGGT
1 TTAGGTTTAAGTTTATATAGATTTTTAATTGGGCTTTAATTGGGT
* *
5875 TTAGGTTTAAGCTTATATAGATTTTTAGTTGGGCTTTAATTGGGT
1 TTAGGTTTAAGTTTATATAGATTTTTAATTGGGCTTTAATTGGGT
*
5920 TTGGGTTTAAGTTTA
1 TTAGGTTTAAGTTTA
5935 AATTTATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.51
Consensus pattern (45 bp):
TTAGGTTTAAGTTTATATAGATTTTTAATTGGGCTTTAATTGGGT
Found at i:6262 original size:17 final size:17
Alignment explanation
Indices: 6240--6278 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6230 GTTTTAATAA
6240 TTTAATA-TTAATTATTT
1 TTTAATATTTAA-TATTT
6257 TTTAATATTTTAATATTT
1 TTTAATA-TTTAATATTT
6275 TTTA
1 TTTA
6279 TTTATATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAATATTTAATATTT
Found at i:7118 original size:17 final size:17
Alignment explanation
Indices: 7074--7121 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
7064 AATAAAATTT
*
7074 ACAAATATAAAAAATTAG
1 ACAAAT-TAAAAAATAAG
*
7092 ACAAAATAAAAAATAAG
1 ACAAATTAAAAAATAAG
7109 TA-AAATTAAAAAA
1 -ACAAATTAAAAAA
7122 AGGGTTGCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (17 bp):
ACAAATTAAAAAATAAG
Found at i:8829 original size:195 final size:192
Alignment explanation
Indices: 8464--8839 Score: 601
Period size: 195 Copynumber: 1.9 Consensus size: 192
8454 TTTTTAATAT
**
8464 TTTAAATATACAAAAAAAACATAAATATGGCATTAAAAATTAATTAAAACACAATAAAAAATAAA
1 TTTAAATATACAAAAAAAACATAAATATAACATTAAAAATTAATTAAAACACAATAAAAAATAAA
* * *
8529 TATGACATGAATATATAAATATAAAAAATATTTATAACTATTATATAAATTTATAATATTTTAAA
66 TATGACATGAACAGATAAATATAAAAAATATTTATAAATATTATATAAATTTATAATATTTTAAA
* *
8594 TAATAAAAAAACAAATAAAAAATATAAACACCTAAAATTTTCTCTCTTCTTTCTTTTTTTTAC
131 TAATAAAAAAACAAATAAAAAACATAAACACCTAAAATTTT-TCTCTCCTTTCTTTTTTTTAC
* * *
8657 TTTAAATATATAAAAAATAACGTAAATATAACATTAAAAATTAATTAAAATACAATAAAAAAATA
1 TTTAAATATACAAAAAA-AACATAAATATAACATTAAAAATTAATTAAAACACAAT-AAAAAATA
8722 AATATGACATGAACAGATAAATATAAAAAATATTTATAAATATTATATAAATTTATAATATTTTA
64 AATATGACATGAACAGATAAATATAAAAAATATTTATAAATATTATATAAATTTATAATATTTTA
* *
8787 AATAATAAAAAATACAAATAAAAAACATAAATATCT-AAATTTTTCTCTCCTTT
129 AATAATAAAAAA-ACAAATAAAAAACATAAACACCTAAAATTTTTCTCTCCTTT
8840 TCTCTCTTTT
Statistics
Matches: 168, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
193 16 0.10
194 43 0.26
195 89 0.53
196 20 0.12
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (192 bp):
TTTAAATATACAAAAAAAACATAAATATAACATTAAAAATTAATTAAAACACAATAAAAAATAAA
TATGACATGAACAGATAAATATAAAAAATATTTATAAATATTATATAAATTTATAATATTTTAAA
TAATAAAAAAACAAATAAAAAACATAAACACCTAAAATTTTTCTCTCCTTTCTTTTTTTTAC
Found at i:8859 original size:10 final size:10
Alignment explanation
Indices: 8846--8875 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
8836 CTTTTCTCTC
8846 TTTTTCTTTT
1 TTTTTCTTTT
8856 TTTTTCTTTT
1 TTTTTCTTTT
8866 TTTCTTCTTT
1 TTT-TTCTTT
8876 CTCTCTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:8981 original size:3 final size:3
Alignment explanation
Indices: 8973--9013 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
8963 TTTAAGATAG
8973 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9014 CATCATCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9574 original size:23 final size:23
Alignment explanation
Indices: 9514--9574 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 23
9504 TATTTGAGCT
* *
9514 AATTAAATT-AAATTATTATTTA
1 AATTTAATTAAAAATATTATTTA
*
9536 AA--TAA-TAAAAAAATTATTTA
1 AATTTAATTAAAAATATTATTTA
9556 AATTTAATTAAAAATATTA
1 AATTTAATTAAAAATATTA
9575 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 1 0.03
20 15 0.48
22 5 0.16
23 10 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATTAAAAATATTATTTA
Found at i:9610 original size:33 final size:31
Alignment explanation
Indices: 9535--9613 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 31
9525 ATTATTATTT
9535 AAATAATAAAAAAATTATTTAAATTTAATTAAA
1 AAATAAT-AAAAAATTATTT-AATTTAATTAAA
*
9568 AATATTAATAAAAAATTATTT-TTTTACATTATCAA
1 AA-A-TAATAAAAAATTATTTAATTTA-ATTA--AA
9603 AAATAATAAAA
1 AAATAATAAAA
9614 TAAAATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
32 4 0.10
33 14 0.35
34 14 0.35
35 8 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATAATAAAAAATTATTTAATTTAATTAAA
Found at i:10155 original size:20 final size:21
Alignment explanation
Indices: 10118--10167 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
10108 ACTATACAAG
10118 TCTTTGGATAGTTTGGAGAAT
1 TCTTTGGATAGTTTGGAGAAT
10139 TCTTTGGATAG-TTGGAGAAT
1 TCTTTGGATAGTTTGGAGAAT
*
10159 TCTATGGAT
1 TCTTTGGAT
10168 TTGCCACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42
Consensus pattern (21 bp):
TCTTTGGATAGTTTGGAGAAT
Found at i:10855 original size:19 final size:21
Alignment explanation
Indices: 10809--10862 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
10799 TTTCAACAAT
10809 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
10830 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
10849 TTGTATCGATACAA
1 TTGTATCGATACAA
10863 TGTATCGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:11816 original size:20 final size:20
Alignment explanation
Indices: 11791--11840 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
11781 TAAACCTTGA
11791 TCATGCATTTTTACTATGCT
1 TCATGCATTTTTACTATGCT
11811 TCATGCATTTTTACTATGCT
1 TCATGCATTTTTACTATGCT
11831 TCATGCATTT
1 TCATGCATTT
11841 ATAGCATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (20 bp):
TCATGCATTTTTACTATGCT
Found at i:16453 original size:2 final size:2
Alignment explanation
Indices: 16446--16473 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16436 CTTCTCTTCA
16446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16474 TACTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17385 original size:16 final size:17
Alignment explanation
Indices: 17354--17412 Score: 67
Period size: 13 Copynumber: 3.8 Consensus size: 17
17344 AACTCATTGA
17354 TTAAAATAATATTATTT
1 TTAAAATAATATTATTT
*
17371 TTAAAAT--TA--ATTA
1 TTAAAATAATATTATTT
17384 TTAAAATAATATTA-TT
1 TTAAAATAATATTATTT
17400 TTAAAATAA-ATTA
1 TTAAAATAATATTA
17413 ACAAGATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 10 0.28
15 8 0.22
16 10 0.28
17 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATAATATTATTT
Found at i:17411 original size:29 final size:30
Alignment explanation
Indices: 17353--17412 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
17343 AAACTCATTG
*
17353 ATTAAAATAATATTATTTTTAAAATTAATT
1 ATTAAAATAATATTATTTTTAAAATAAATT
17383 ATTAAAATAATATTA-TTTTAAAATAAATT
1 ATTAAAATAATATTATTTTTAAAATAAATT
17412 A
1 A
17413 ACAAGATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTAAAATAATATTATTTTTAAAATAAATT
Found at i:17712 original size:20 final size:19
Alignment explanation
Indices: 17687--17724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
17677 ATTATTTTGA
*
17687 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
17707 TATATTTATATATAAAAT
1 TATATTTATATATAAAAT
17725 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:19012 original size:30 final size:29
Alignment explanation
Indices: 18970--19027 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
18960 TGAAAACTTC
*
18970 TTTATGTCTGTGTATGTATATATATATAAA
1 TTTATGTCTGTGTATATATATA-ATATAAA
19000 TTTATG-CTTGTGTATATATATAATATAA
1 TTTATGTC-TGTGTATATATATAATATAA
19028 TATAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTATGTCTGTGTATATATATAATATAAA
Found at i:19032 original size:10 final size:11
Alignment explanation
Indices: 19012--19044 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
19002 TATGCTTGTG
19012 TATATATATAA
1 TATATATATAA
19023 TATA-ATATAA
1 TATATATATAA
19033 TATATATTATAA
1 TATATA-TATAA
19045 AGTTATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATATATATAA
Found at i:20758 original size:19 final size:19
Alignment explanation
Indices: 20734--20802 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
20724 ACTATGTGAC
20734 AAAATGATTTCAAGTATCA
1 AAAATGATTTCAAGTATCA
*
20753 AAAATGATTTACTATGTGAT--
1 AAAATGATTT-C-AAGT-ATCA
20773 AAAATGATTTCAAGTATCA
1 AAAATGATTTCAAGTATCA
20792 AAAATG-TTTCA
1 AAAATGATTTCA
20803 GAGACAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 8 0.19
19 17 0.40
20 11 0.26
21 3 0.07
22 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.35
Consensus pattern (19 bp):
AAAATGATTTCAAGTATCA
Found at i:20778 original size:20 final size:20
Alignment explanation
Indices: 20724--20782 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
20714 TTTCTTTAAA
*
20724 ACTATGTGACAAAATGATTT
1 ACTATGTGATAAAATGATTT
*
20744 -C-AAGT-ATCAAAAATGATTT
1 ACTATGTGAT--AAAATGATTT
20763 ACTATGTGATAAAATGATTT
1 ACTATGTGATAAAATGATTT
20783 CAAGTATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
17 1 0.03
18 3 0.10
19 11 0.35
20 11 0.35
21 3 0.10
22 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (20 bp):
ACTATGTGATAAAATGATTT
Found at i:20993 original size:13 final size:13
Alignment explanation
Indices: 20975--20999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20965 CAAGTTGCAA
20975 TGTATCGATACAT
1 TGTATCGATACAT
20988 TGTATCGATACA
1 TGTATCGATACA
21000 AGTTGCAGTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21128 original size:19 final size:21
Alignment explanation
Indices: 21087--21145 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
21077 ACATGCATAG
21087 GAATGCATCGATACAATTCCA
1 GAATGCATCGATACAATTCCA
*
21108 GAATGCATTGATAC-A-TCCA
1 GAATGCATCGATACAATTCCA
*
21127 GAATTGTATCGATACAATT
1 GAA-TGCATCGATACAATT
21146 AGCCTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.22
20 10 0.31
21 14 0.44
22 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (21 bp):
GAATGCATCGATACAATTCCA
Found at i:27230 original size:20 final size:20
Alignment explanation
Indices: 27183--27257 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
27173 AAAAAGACAT
*
27183 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
27202 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
27223 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
27243 AATGTATCGATACAT
1 AATGTATCGATACAT
27258 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:27251 original size:40 final size:39
Alignment explanation
Indices: 27180--27257 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
27170 GGTAAAAAGA
* *
27180 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
27219 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
27258 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:27972 original size:28 final size:28
Alignment explanation
Indices: 27830--29602 Score: 1770
Period size: 28 Copynumber: 61.2 Consensus size: 28
27820 CCACTAGCTT
* *
27830 TTGTAGGCTTTGAAAAAAGTTGCCACTGACAC
1 TTGTGGGCTTTG-AAAGAG-TGCCACTG--AC
* **
27862 ATGTGGGCTTTGAAAAGAGTGTTACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
27891 TTGCGTGGGCTTTAAAAGGGTGCCACTGAC
1 TT--GTGGGCTTTGAAAGAGTGCCACTGAC
*
27921 TTGCGTGGGCTTTTGAAAGGGTGCCACTGAC
1 TT--GTGGGC-TTTGAAAGAGTGCCACTGAC
* *
27952 TCGTGGGTTTTGAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
27980 TTGTGGGCTTTGAAAG-GTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
28007 TCGTGGGCTTTGAAA-AGGTACCACTGAC
1 TTGTGGGCTTTGAAAGA-GTGCCACTGAC
* *
28035 TCGTGGGC-TTGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
28062 TTGTGAGCTTTGAAAGAGTGCCACTAAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28090 TCGTGGGCTTT-AAAAAGGTGCCACTAAC
1 TTGTGGGCTTTGAAAGA-GTGCCACTGAC
*
28118 TTGCGTGGGCTTTGAAAAGAGTGCCACTTAC
1 TT--GTGGGCTTTG-AAAGAGTGCCACTGAC
* *
28149 TTGTGTGGGCTTTGAAAGGGTGCCACTAAC
1 -T-TGTGGGCTTTGAAAGAGTGCCACTGAC
*
28179 TCGTGGGCTTTGAAAG-GATGCCACTGAC
1 TTGTGGGCTTTGAAAGAG-TGCCACTGAC
28207 TTGTGGGCTTTGAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28235 TCGTGGGCTTTGAAA-AGGTACCACTAAC
1 TTGTGGGCTTTGAAAGA-GTGCCACTGAC
* *
28263 TTGCTTGAGCTTTGAAAGGAGTGCCATTGAC
1 TTG--TGGGCTTTGAAA-GAGTGCCACTGAC
* *
28294 TTGTGTGGGCTTTAAAAGGGTGCCACTGAC
1 -T-TGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28324 TTGTGGGCTTTGAGAGAGAGCCACTGAA
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
28352 TTGTGGGCTTCGCAATG-GTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
28380 TTGTGGGCTTCGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28408 TTGTGGGCTCTGAAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
28436 TTGTGGGCTTTGAAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
28464 TTGTGGGCTTTGAAAAGAGTGCCACTGAT
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
28493 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
*
28522 TTGTGGACTTTGAAAGGAGTGCCACTGAC
1 TTGTGGGCTTTGAAA-GAGTGCCACTGAC
28551 TTGTGGGCTTTGAAAGGAGTGCCACTGAC
1 TTGTGGGCTTTGAAA-GAGTGCCACTGAC
* *
28580 TTGTGTGGGCTTTAAAAGGGTGCCACTGAC
1 -T-TGTGGGCTTTGAAAGAGTGCCACTGAC
*
28610 TTGTGGGCTTTGAAAGAGTGCCACTGAA
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
28638 TTGTGGGCTTCGCAATG-GTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
28666 TTGTGGGCTTCGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
28694 TTGCGTGGGCTTTGAAAAGGGTGCCACTGAC
1 TT--GTGGGCTTTG-AAAGAGTGCCACTGAC
*
28725 TTGTGGGCTTTGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28753 TTATGGGCTTTGAAAAGAGTGCCAATAAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* * *
28782 TTGTGGGCTTTAAAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
28810 TTGCGTGGGCTTTGAAAGGGGTGCCACTGAC
1 TT--GTGGGCTTTGAAA-GAGTGCCACTGAC
* *
28841 TTGTGGGCTTTGAAAGGGTGCCACCGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
28869 TTGTGTGGGCTTTGAAAG-GATGCCACTGAC
1 -T-TGTGGGCTTTGAAAGAG-TGCCACTGAC
28899 TTGTGGGCTTTGAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
28927 TCGTGGGATTTGAAA-AGGTACCACTGAC
1 TTGTGGGCTTTGAAAGA-GTGCCACTGAC
* *
28955 TTGCGTGAGCTTTAAAAGGAGTGCCACTGAC
1 TT--GTGGGCTTTGAAA-GAGTGCCACTGAC
* *
28986 TTGTGTGGGCTTTAAAAGGGTGCCACTGAC
1 -T-TGTGGGCTTTGAAAGAGTGCCACTGAC
* *
29016 TTGTGGGCTTTAAAAGAGTGCCACTGAA
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
29044 TTGTGGGCTTCGCAATG-GTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
29072 TTGTGGGCTTCGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * *
29100 TTGTGGGCTCTGAAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
29128 TTGTGGGCTTTGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
29156 TTGTGGGCTTTGAAAAGAGTGCCACTGAT
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
*
29185 TTGTGGGTTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
29214 TTGTGGGCTTTGAAAGGAGTGCCACTGAC
1 TTGTGGGCTTTGAAA-GAGTGCCACTGAC
* *
29243 TTGTGTGGGCTTTAAAAGGGTGCCACTGAC
1 -T-TGTGGGCTTTGAAAGAGTGCCACTGAC
* *
29273 TTGTGAGCTTTGAAAGAGTGCCACTGAA
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
29301 TTGTGGGCTTCGCAATG-GTGCCACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
29329 TTGTGGGCTTCGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
29357 TTGCGTGGGCTTTGAAAAGGGTGCCACTGAC
1 TT--GTGGGCTTTG-AAAGAGTGCCACTGAC
* *
29388 TTGTGGGCTTTGAAAAGTGTTGCCACCGAC
1 TTGTGGGCTTTG-AAAGAG-TGCCACTGAC
* *
29418 TTGTGTGGGCTTTGAAATGGGTTGCCACCGAC
1 -T-TGTGGGCTTTGAAA-GAG-TGCCACTGAC
* *
29450 TTGTGTGGGCTTTGAAATGGGTTGCCACCGAC
1 -T-TGTGGGCTTTGAAA-GAG-TGCCACTGAC
* * *
29482 TTGTGTGGGCTTTGAAATGGGTGCCACAGAG
1 -T-TGTGGGCTTTGAAA-GAGTGCCACTGAC
** * * * *
29513 TTGTGGATTTTAAAAGAGTACCACGGAG
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
** * * * *
29541 TTGTGGATTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
** * * * *
29569 TTGTGGATTTTAAAAGGGTGCCACAGAG
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
29597 TTGTGG
1 TTGTGG
29603 ACTCAAAAGA
Statistics
Matches: 1534, Mismatches: 143, Indels: 132
0.85 0.08 0.07
Matches are distributed among these distances:
27 66 0.04
28 739 0.48
29 260 0.17
30 180 0.12
31 183 0.12
32 102 0.07
33 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (28 bp):
TTGTGGGCTTTGAAAGAGTGCCACTGAC
Found at i:28219 original size:145 final size:141
Alignment explanation
Indices: 27830--30184 Score: 1888
Period size: 145 Copynumber: 16.5 Consensus size: 141
27820 CCACTAGCTT
* * * * * **
27830 TTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAGTGTTACTGACTTGC
1 TTGTGGGCTTTG-AAAAGGGTGCCACTG--ACTTGTGGGCTTTG-AAAGGGTGCCACTGACTT--
* * * * *
27895 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTTGAAAGGGTGCCACTGACTCGTGGGT
60 GTGGGCTTTGAAAGGATGCCACTGACTT--GTGGGC-TTTGAAAGAGTGCCACTGACTTGTGGGC
*
27960 TTTGAAAGAGTGCCACTGAC
122 TTTGAAAGGGTGCCACTGAC
* * * *
27980 TTGTGGGCTTTG-AAA-GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGC
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * * *
28043 -TTGAAAGGGTGCCACTGACTTGTGAGCTTTGAAAGAGTGCCACTAACTCGTGGGCTTTAAAAAG
66 TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
*
28107 GTGCCACTAAC
131 GTGCCACTGAC
* * * *
28118 TTGCGTGGGCTTTGAAAAGAGTGCCACTTACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGT
1 TT--GTGGGCTTTGAAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGT
*
28183 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGA
62 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGA
* * *
28248 AAAGGTACCACTAAC
127 AAGGGTGCCACTGAC
* * *
28263 TTGCTTGAGCTTTG-AAAGGAGTGCCATTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTG
1 TTG--TGGGCTTTGAAAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
28327 TGGGCTTTGAGAGAGA-GCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTT
61 TGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTT
*
28390 CGAAAGGGTGCCACTGAC
124 TGAAAGGGTGCCACTGAC
* * *
28408 TTGTGGGCTCTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
28472 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGACTTTGAAA
66 TTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA
28537 GGAGTGCCACTGAC
129 GG-GTGCCACTGAC
*
28551 TTGTGGGCTTTG-AAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
1 TTGTGGGCTTTGAAAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
* * * *
28615 GGCTTTGAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCG
63 GGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTG
28678 AAAGGGTGCCACTGAC
126 AAAGGGTGCCACTGAC
*
28694 TTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGG
1 TT--GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
* * * * * *
28759 GCTTTGAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTG
64 GCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTTTG
28824 AAAGGGGTGCCACTGAC
126 AAA-GGGTGCCACTGAC
* *
28841 TTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGG
1 TTGTGGGCTTTGAAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
* * * *
28905 GCTTTGAAA-GAGTGCCACTGACTCGTGGGATTTGAAA-AGGTACCACTGACTTGCGTGAGCTTT
64 GCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTT
*
28968 AAAAGGAGTGCCACTGAC
125 GAAAGG-GTGCCACTGAC
* * *
28986 TTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGAGTGCCACTGAATTGTGG
1 -T-TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
* * * * *
29050 GCTTCGCAATGG-TGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAA
64 GCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAA
*
29114 AGGGTGCCACTAAC
128 AGGGTGCCACTGAC
* *
29128 TTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGG
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGG
* * *
29192 TTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTA
65 CTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTG
29257 AAAGGGTGCCACTGAC
126 AAAGGGTGCCACTGAC
* * * * * *
29273 TTGTGAGCTTTG-AAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGC
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
29337 TTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAA
66 TTTGAAAGGATGCCACTGACTT--GTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTG-A
* *
29402 AAGTGTTGCCACCGAC
127 AAG-GGTGCCACTGAC
* * *
29418 TTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACT
1 -T-TGTGGGCTTTGAAAAGGG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACTGAC-
* * * ** * * * * *
29483 TGTGTGGGCTTTGAAATGGGTGCCACAGAGTTGTGGATTTTAAAAGAGTACCACGGAGTTGTGGA
58 T-TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGG
* * * *
29548 TTTTAAAAGGGTGCCACGGAG
121 CTTTGAAAGGGTGCCACTGAC
* * * * * ** * * * * *
29569 TTGT-GGATTTTAAAAGGGTGCCACAGAGTTGTGGAC-TCAAAAGAGATGCCACGGAGTTATGGA
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG-GGTGCCACTGACTTGTGGG
* * * * * * * * * *
29632 C-TTAAAAGGGTGCCA-TGGAGTTGTGGTC-TTAAAAG-GATACCACGGAGTTGTGGAC-TTAAA
65 CTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAA
* * *
29692 AAGGTGCCACGGAG
128 AGGGTGCCACTGAC
* * * * * * * *
29706 TTGTGGAC-TT-AAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGAC
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * * ** * * * * *
29768 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
66 TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
29831 GTGCCACAGAG
131 GTGCCACTGAC
* * * * * * * * * *
29842 TTGTGGAC-TT-AAAAGAGATGCCACGGAGTTATGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
1 TTGTGGGCTTTGAAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* * * * * * * * * * *
29904 C-TTAAAAGGGTGCCACGGAGTTGTGGTC-TTAAAAGGGATGCCACGGAGTTGTGGAC-TTAAAA
65 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAA
* *
29966 GGGTGCCACGGAG
129 GGGTGCCACTGAC
* * * * * * *
29979 TTGTGGAC-TT-AAAAGGGTTCCAC-GAAGTTGTGGAC-TTAAAAGGATGCCAC-GAAGTTGTGG
1 TTGTGGGCTTTGAAAAGGGTGCCACTG-ACTTGTGGGCTTTGAAAGGGTGCCACTG-ACTTGTGG
* * * * * * * * * *
30039 ACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGGTGCCA-TGGAGTTGTGGAC-TTAA
64 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACT-GACTTGTGGGCTTTGA
* *
30101 AAGGGTGCCACGGAG
127 AAGGGTGCCACTGAC
* * * * * * * *
30116 TTGTAGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGGC
1 TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
30178 TTT-AAAG
66 TTTGAAAG
30185 AGGTCACACT
Statistics
Matches: 1919, Mismatches: 210, Indels: 166
0.84 0.09 0.07
Matches are distributed among these distances:
135 66 0.03
136 107 0.06
137 258 0.13
138 91 0.05
139 24 0.01
140 94 0.05
141 77 0.04
142 86 0.04
143 152 0.08
144 170 0.09
145 482 0.25
146 111 0.06
147 68 0.04
148 18 0.01
149 11 0.01
150 13 0.01
151 21 0.01
152 6 0.00
153 30 0.02
154 8 0.00
155 13 0.01
156 13 0.01
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (141 bp):
TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
GTGCCACTGAC
Found at i:29160 original size:692 final size:691
Alignment explanation
Indices: 27863--29466 Score: 2523
Period size: 692 Copynumber: 2.3 Consensus size: 691
27853 CACTGACACA
* ** *
27863 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTG
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTT--GTG
* * *
27928 GGCTTTTGAAAGGGTGCCACTGACTCGTGGGTTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGA
64 GGC-TTTGAAA-GGTGCCACTGACTTGTGGGCTTCGAAAG-GTGCCACTGACTTGTGGGCTTTGA
* *
27993 AA-GGTGCCACTGAC-TCGTGGGCTTTGAAAA-GGTACCACTGACTCGTGGGC-TTGAAAGGGTG
126 AAGGGTGCCACTGACTTCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
* *
28054 CCACTGACTTGTGAGCTTTG-AAAGAGTGCCACTAACTCGTGGGCTTTAAAAAGGTGCCACTAAC
191 CCACTGACTTGTGGGCTTTGAAAAGAGTGCCAATAACTCGTGGGCTTTAAAAAGGTGCCACTAAC
* *
28118 TTGCGTGGGCTTTGAAAAGAGTGCCACTTACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGT
256 TTGCGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACCAACTCGT
*
28183 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGA
321 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGATTTGA
* * *
28248 AAAGGTACCACTAACTTGCTTGAGCTTTGAAAGGAGTGCCATTGACTTGTGTGGGCTTTAAAAGG
386 AAAGGTACCACTAACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGG
* *
28313 GTGCCACTGACTTGTGGGCTTTGAGAGAGAGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTG
451 GTGCCACTGACTTGTGGGCTTTAAAAGAGAGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTG
28378 ACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGG
516 ACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGG
28443 CTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAA
581 CTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAA
28508 AGAGTGCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGAC-T-
646 AGAGTGCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTG
28552 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
* * *
28617 CTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAG
66 CTTTGAAAG-GTGCCACTGACTTGTGGGCTTCG-AAAGGTGCCACTGACTTGTGGGCTTTGAAAG
28682 GGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
129 GGTGCCACTGACTT-CGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
* * *
28747 ACTGACTTATGGGCTTTGAAAAGAGTGCCAATAACTTGTGGGCTTTAAAAGGGTGCCACTAACTT
193 ACTGACTTGTGGGCTTTGAAAAGAGTGCCAATAACTCGTGGGCTTTAAAAAGGTGCCACTAACTT
* * * *
28812 GCGTGGGCTTTGAAAGGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGT
258 GCGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACCAAC-T-CGT
28875 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGATTTGA
321 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGATTTGA
*
28940 AAAGGTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGG
386 AAAGGTACCACTAACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGG
*
29005 GTGCCACTGACTTGTGGGCTTTAAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTG
451 GTGCCACTGACTTGTGGGCTTTAAAAGAGAGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTG
29070 ACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGG
516 ACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGG
* *
29135 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGTTTTGAAA
581 CTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAA
*
29200 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
646 AGAGTGCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTG
* * * * *
29246 TGTGGGCTTTAAAAGG-GTGCCACTGAC-T-TGTGAGCTTTGAAAGAGTGCCACTGAATTGTGGG
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
* *
29308 CTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAA
66 CTTTG-AAAGGTGCCACTGACTTGTGGGCTTCGAAA-GGTGCCACTGACTT--GTGGGCTTTG-A
* *
29373 AAGGGTGCCACTGACTT-GTGGGCTTTGAAAAGTGTTGCCACCGACTTGTGTGGGCTTTGAAATG
126 AAGGGTGCCACTGACTTCGTGGGCTTTGAAAAG-GGTGCCACTGAC-T-TGTGGGCTTTGAAA-G
*
29437 GGTTGCCACCGACTTGTGTGGGCTTTGAAA
187 GG-TGCCACTGAC-T-TGTGGGCTTTGAAA
29467 TGGGTTGCCA
Statistics
Matches: 843, Mismatches: 48, Indels: 38
0.91 0.05 0.04
Matches are distributed among these distances:
685 1 0.00
686 51 0.06
687 21 0.02
688 1 0.00
689 71 0.08
690 45 0.05
691 101 0.12
692 447 0.53
693 31 0.04
694 34 0.04
695 14 0.02
696 3 0.00
697 9 0.01
698 1 0.00
699 13 0.02
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.28
Consensus pattern (691 bp):
TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
CTTTGAAAGGTGCCACTGACTTGTGGGCTTCGAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGG
TGCCACTGACTTCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
GACTTGTGGGCTTTGAAAAGAGTGCCAATAACTCGTGGGCTTTAAAAAGGTGCCACTAACTTGCG
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACCAACTCGTGGGCT
TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGATTTGAAAAGG
TACCACTAACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCC
ACTGACTTGTGGGCTTTAAAAGAGAGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTG
TGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGT
GCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTG
Found at i:29653 original size:27 final size:27
Alignment explanation
Indices: 28368--30184 Score: 1028
Period size: 28 Copynumber: 64.0 Consensus size: 27
28358 GCTTCGCAAT
* * * *
28368 GGTGCCACTGACTTGTGGGCTTCGAAAG
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * * *
28396 GGTGCCACTGACTTGTGGGCTCTGAAAG
1 GGTGCCACGGAGTTGTGGACT-TAAAAG
** * * *
28424 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
** * *
28452 GGTGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
* * * *
28481 AGTGCCACTGATTTGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
* * * *
28510 AGTGCCACTGACTTGTGGACTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
28538 GAGTGCCACTGACTTGTGGGCTTTGAAAG
1 G-GTGCCACGGAGTTGTGGAC-TTAAAAG
* * *
28567 GAGTGCCACTGACTTGTGTGGGCTTTAAAAG
1 G-GTGCCACGGA-GT-TGTGGAC-TTAAAAG
* * * *
28598 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * * ** *
28626 AGTGCCACTGAATTGTGGGCTTCGCAAT
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * * *
28654 GGTGCCACTGACTTGTGGGCTTCGAAAG
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * *
28682 GGTGCCACTGACTTGCGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTT--GTGGAC-TT-AAAAG
* * * *
28713 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
28741 GGTGCCACTGACTTATGGGCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
* *** * *
28770 AGTGCCAATAACTTGTGGGCTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
** * * *
28798 GGTGCCACTAACTTGCGTGGGCTTTGAAAGG
1 GGTGCCACGGAGTT--GTGGAC-TT-AAAAG
* * * *
28829 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
28857 GGTGCCACCGACTTGTGTGGGCTTTGAAAG
1 GGTGCCACGGA-GT-TGTGGAC-TTAAAAG
* * * * *
28887 GATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * * *
28915 AGTGCCACTGACTCGTGGGATTTGAAAA-
1 GGTGCCACGGAGTTGT-GGACTT-AAAAG
* * * *
28943 GGTACCACTGACTTGCGTGAGCTTTAAAAG
1 GGTGCCACGGAGTTGTG-GA-C-TTAAAAG
* * *
28973 GAGTGCCACTGACTTGTGTGGGCTTTAAAAG
1 G-GTGCCACGGA-GT-TGTGGAC-TTAAAAG
* * *
29004 GGTGCCACTGACTTGTGGGCTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * * ** *
29032 AGTGCCACTGAATTGTGGGCTTCGCAAT
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * * *
29060 GGTGCCACTGACTTGTGGGCTTCGAAAG
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * * *
29088 GGTGCCACTGACTTGTGGGCTCTGAAAG
1 GGTGCCACGGAGTTGTGGACT-TAAAAG
** * * *
29116 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * *
29144 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
* * * **
29173 AGTGCCACTGATTTGTGGGTTTTGAAAAG
1 GGTGCCACGGAGTTGT-GGACTT-AAAAG
* * * * *
29202 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
* * *
29230 GAGTGCCACTGACTTGTGTGGGCTTTAAAAG
1 G-GTGCCACGGA-GT-TGTGGAC-TTAAAAG
* * *
29261 GGTGCCACTGACTTGT-GAGCTTTGAAAG
1 GGTGCCACGGAGTTGTGGA-C-TTAAAAG
* * * * ** *
29289 AGTGCCACTGAATTGTGGGCTTCGCAAT
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * * *
29317 GGTGCCACTGACTTGTGGGCTTCGAAAG
1 GGTGCCACGGAGTTGTGGACTT-AAAAG
* * *
29345 GGTGCCACTGACTTGCGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTT--GTGGAC-TT-AAAAG
* * *
29376 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG
* * * * *
29405 TGTTGCCACCGACTTGTGTGGGCTTTGAAATG
1 -GGTGCCACGGA-GT-TGTGGAC-TT-AAAAG
* * * *
29437 GGTTGCCACCGACTTGTGTGGGCTTTGAAATG
1 GG-TGCCACGGA-GT-TGTGGAC-TT-AAAAG
* * * *
29469 GGTTGCCACCGACTTGTGTGGGCTTTGAAATG
1 GG-TGCCACGGA-GT-TGTGGAC-TT-AAAAG
* *
29501 GGTGCCACAGAGTTGTGGATTTTAAAAG
1 GGTGCCACGGAGTTGTGGA-CTTAAAAG
* * *
29529 AGTACCACGGAGTTGTGGATTTTAAAAG
1 GGTGCCACGGAGTTGTGGA-CTTAAAAG
*
29557 GGTGCCACGGAGTTGTGGATTTTAAAAG
1 GGTGCCACGGAGTTGTGGA-CTTAAAAG
* *
29585 GGTGCCACAGAGTTGTGGACTCAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
29612 AGATGCCACGGAGTTATGGACTTAAAAG
1 -GGTGCCACGGAGTTGTGGACTTAAAAG
* *
29640 GGTGCCATGGAGTTGTGGTCTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* * *
29667 GATACCACGGAGTTGTGGACTTAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAG
29694 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
29721 GGTGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
29748 GGTGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
29775 GGTGCCACGGAGTTGTGGACTAAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
29802 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
29830 GGTGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
29857 AGATGCCACGGAGTTATGGACTTAAAAG
1 -GGTGCCACGGAGTTGTGGACTTAAAAG
29885 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
29912 GGTGCCACGGAGTTGTGGTCTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
29939 GGATGCCACGGAGTTGTGGACTTAAAAG
1 GG-TGCCACGGAGTTGTGGACTTAAAAG
29967 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
29994 GGTTCCACGAAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
30021 GATGCCACGAAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAG
*
30049 GATGCCACGGAGTTGTGGACTTAAAAGG
1 GGTGCCACGGAGTTGTGGACTTAAAA-G
*
30077 GGTGCCATGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
*
30104 GGTGCCACGGAGTTGTAGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
30131 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
* *
30158 GGTGCCACGGAGTTGTGGGCTTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
30185 AGGTCACACT
Statistics
Matches: 1585, Mismatches: 153, Indels: 103
0.86 0.08 0.06
Matches are distributed among these distances:
27 392 0.25
28 678 0.43
29 224 0.14
30 92 0.06
31 116 0.07
32 80 0.05
33 3 0.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:29916 original size:137 final size:135
Alignment explanation
Indices: 28368--30184 Score: 1028
Period size: 137 Copynumber: 12.8 Consensus size: 135
28358 GCTTCGCAAT
* * * * * * * * *
28368 GGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACT
1 GGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACG
* * * * ** * * * * *
28433 AACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTG
64 GAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTG
*
28498 GGCTTTGAAAAG
126 GAC-TT-AAAAG
* * * * * * * *
28510 AGTGCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGG-GTGCCACGGAGTTGTGGAC-TTAAAAGG-GTGCCA
* * * * * * * * * *
28575 CTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAATT
62 CGGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTT
* ** *
28640 GTGGGCTTCGCAAT
123 GTGGACTT-AAAAG
* * * * * * *
28654 GGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCC
1 GGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTT--GTGGAC-TT-AAAAGGGTGCC
* * * * * * * * * *** *
28719 ACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGAGTGCCAATAACTT
61 ACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTT
*
28784 GTGGGCTTTAAAAG
123 GTGGAC-TTAAAAG
** * * * * * * *
28798 GGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
1 GGTGCCACGGAGTT--GTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCC
* * * * * * * * * * * *
28863 ACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
61 ACGGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGT
* *
28928 CGTGGGATTTGAAAA-
122 TGT-GGACTT-AAAAG
* * * * * * *
28943 GGTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTG
1 GGTGCCACGGAGTTGTG-GA-C-TTAAAAGG-GTGCCACGGA-GT-TGTGGAC-TTAAAAGGGTG
* * * * * * * ** * * *
29008 CCACTGACTTGTGGGCTTTAAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACT
59 CCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGT
* *
29073 TGTGGGCTTCGAAAG
122 TGTGGACTT-AAAAG
* * * * ** * * * *
29088 GGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACT
1 GGTGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
* * * * * ** * * *
29153 GACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGTTTTGAAAAGAGTGCCACTGACTTGT
64 GAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGT-GGACTT-AAAAGGGTGCCACGGAGTTGT
* *
29218 GGGCTTTGAAAG
125 GGAC-TTAAAAG
* * * * * * *
29230 GAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGT-GAGCTTTGAAAGAGTGC
1 G-GTGCCACGGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA-C-TTAAAAGGGTGC
* * * ** * * * * * * *
29294 CACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTT
60 CACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTT
*
29359 GCGTGGGCTTTGAAAAG
123 --GTGGAC-TT-AAAAG
* * * * * * * *
29376 GGTGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTT
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG-GGTGCCACGGA-GT-TGTGGAC-TT-AAAAGGG-T
* * * * * * * *
29441 GCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTGC
58 GCCACGGA-GT-TGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGAC-TT-AAAAGGGTGC
* *
29506 CACAGAGTTGTGGATTTTAAAAG
114 CACGGAGTTGTGGA-CTTAAAAG
* * * * *
29529 AGTACCACGGAGTTGTGGATTTTAAAAGGGTGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACG
* * * * *
29594 GAGTTGTGGACTCAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCATGGAGTTGTGGT
64 GAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
29659 CTTAAAAG
128 CTTAAAAG
* * * *
29667 GATACCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
* *
29732 GTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTA
66 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
29797 AAAAG
131 AAAAG
* *
29802 GGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACG
* *
29867 GAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTC
64 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
29932 TTAAAAG
129 TTAAAAG
* *
29939 GGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTTCCACGA
1 GG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* * *
30004 AGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC
65 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
30069 TTAAAAGG
129 TTAAAA-G
* *
30077 GGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGGA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
* *
30142 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAG
66 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
30185 AGGTCACACT
Statistics
Matches: 1430, Mismatches: 184, Indels: 128
0.82 0.11 0.07
Matches are distributed among these distances:
135 66 0.05
136 112 0.08
137 258 0.18
138 45 0.03
139 20 0.01
140 39 0.03
141 26 0.02
142 66 0.05
143 143 0.10
144 133 0.09
145 251 0.18
146 99 0.07
147 58 0.04
148 11 0.01
149 15 0.01
150 2 0.00
151 16 0.01
152 10 0.01
153 29 0.02
154 7 0.00
155 7 0.00
156 17 0.01
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (135 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGA
GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
AAAAG
Found at i:33453 original size:21 final size:22
Alignment explanation
Indices: 33408--33461 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
33398 TGGACATGTT
33408 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
33430 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
33451 AAAAATGCATG
1 AAAAATGCATG
33462 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:34404 original size:20 final size:19
Alignment explanation
Indices: 34375--34446 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
34365 AAAAAGACAT
34375 AATGTATCGATATATTGTA
1 AATGTATCGATATATTGTA
* * *
34394 GAATATATCGATACATTCATA
1 -AATGTATCGATATATT-GTA
* *
34415 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-TA
34435 AATGTATCGATA
1 AATGTATCGATA
34447 CATCAAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
AATGTATCGATATATTGTA
Found at i:34431 original size:40 final size:39
Alignment explanation
Indices: 34372--34449 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
34362 GGTAAAAAGA
* *
34372 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
34411 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
34450 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:34872 original size:20 final size:20
Alignment explanation
Indices: 34847--34888 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34837 CTCGGCTCCT
34847 AGAACTCCTCAACAAAATGG
1 AGAACTCCTCAACAAAATGG
34867 AGAACTCCTCAACAAAATGG
1 AGAACTCCTCAACAAAATGG
34887 AG
1 AG
34889 TTGTTAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
AGAACTCCTCAACAAAATGG
Found at i:37451 original size:48 final size:49
Alignment explanation
Indices: 37348--37452 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 49
37338 TTTGCTCAAA
* *
37348 GTATCGATACTTCTGGAATTTTTTAGAATGTGTCGATAAAAGGCAAAAT
1 GTATCGATACTTCTGGAATTTTCTAGAATGTATCGATAAAAGGCAAAAT
* * **
37397 GTATCGATA-TATCTGG-GTTTTCTAGATTGTATCGATACAAA-GCAATTT
1 GTATCGATACT-TCTGGAATTTTCTAGAATGTATCGATA-AAAGGCAAAAT
37445 GTATCGAT
1 GTATCGAT
37453 TCAATTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
48 31 0.65
49 17 0.35
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (49 bp):
GTATCGATACTTCTGGAATTTTCTAGAATGTATCGATAAAAGGCAAAAT
Found at i:39927 original size:20 final size:20
Alignment explanation
Indices: 39904--39956 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
39894 ATACATGTAG
*
39904 ATGTATTAATACAAGTTGCA
1 ATGTATCAATACAAGTTGCA
* *
39924 ATGTATCGATACAAGTTGTA
1 ATGTATCAATACAAGTTGCA
*
39944 ATGTATCGATACA
1 ATGTATCAATACA
39957 CTATAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGTATCAATACAAGTTGCA
Found at i:40050 original size:21 final size:21
Alignment explanation
Indices: 40024--40082 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
40014 ACATACATAG
40024 GAATGTATCGATACAATTCCA
1 GAATGTATCGATACAATTCCA
40045 GAATGTATCGATAC-A-TCCA
1 GAATGTATCGATACAATTCCA
40064 GAATTGTATCGATACAATT
1 GAA-TGTATCGATACAATT
40083 AGCCTAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.20
20 12 0.34
21 15 0.43
22 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (21 bp):
GAATGTATCGATACAATTCCA
Found at i:40050 original size:43 final size:41
Alignment explanation
Indices: 40003--40082 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
39993 CTACCTTTCA
*
40003 AATGTATCAATACATACATAGGAA-TGTATCGATACAATTCCAG
1 AATGTATCAATACAT-C-CA-GAATTGTATCGATACAATTCCAG
*
40046 AATGTATCGATACATCCAGAATTGTATCGATACAATT
1 AATGTATCAATACATCCAGAATTGTATCGATACAATT
40083 AGCCTAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.09
41 16 0.47
42 1 0.03
43 14 0.41
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (41 bp):
AATGTATCAATACATCCAGAATTGTATCGATACAATTCCAG
Found at i:41391 original size:20 final size:17
Alignment explanation
Indices: 41371--41404 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41361 ATTTTTATAA
41371 TTTAA-TATATA-TATC
1 TTTAATTATATATTATC
41386 TTTAATTATATATTATC
1 TTTAATTATATATTATC
41403 TT
1 TT
41405 ATGTTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAATTATATATTATC
Found at i:43507 original size:13 final size:13
Alignment explanation
Indices: 43489--43513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43479 CATAAAGTGT
43489 TGTATCGATACAA
1 TGTATCGATACAA
43502 TGTATCGATACA
1 TGTATCGATACA
43514 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:43511 original size:33 final size:33
Alignment explanation
Indices: 43469--43535 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
43459 TTCAACGATT
43469 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
43502 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
43535 T
1 T
43536 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:43594 original size:13 final size:13
Alignment explanation
Indices: 43576--43600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43566 ATCACTTAAA
43576 TGTATCGATACAT
1 TGTATCGATACAT
43589 TGTATCGATACA
1 TGTATCGATACA
43601 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43665 original size:52 final size:52
Alignment explanation
Indices: 43609--43737 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
43599 CACTGATCTT
* *
43609 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
43661 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
43713 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
43738 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:46887 original size:17 final size:17
Alignment explanation
Indices: 46865--46912 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
46855 CGATATAAAT
46865 ATATAAAAAATTTACAA
1 ATATAAAAAATTTACAA
* *
46882 ATATAAGAAATTAGACAA
1 ATATAAAAAATT-TACAA
46900 A-ATAAAAAATTTA
1 ATATAAAAAATTTA
46913 AGTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 1 0.04
17 20 0.77
18 5 0.19
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (17 bp):
ATATAAAAAATTTACAA
Found at i:47025 original size:3 final size:3
Alignment explanation
Indices: 47019--47062 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
47009 CATCATCATC
*
47019 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47063 ATAAATTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:47592 original size:24 final size:24
Alignment explanation
Indices: 47539--47593 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
47529 CTTATTATTT
* *
47539 AAATAA-TAAAAAAATTTATTTAA
1 AAATAATTAAAAAAATTAATATAA
** *
47562 ATTTAATTAAAAATATTAATATAA
1 AAATAATTAAAAAAATTAATATAA
47586 AAATAATT
1 AAATAATT
47594 TTTTATATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATTAAAAAAATTAATATAA
Found at i:48352 original size:315 final size:315
Alignment explanation
Indices: 47777--48411 Score: 1261
Period size: 315 Copynumber: 2.0 Consensus size: 315
47767 GAGCAAAGTC
47777 ATCAAAAGCCATTGTTATTACACATCACAGCTCAAGTTCATATAGCACATATACCAAACATACAA
1 ATCAAAAGCCATTGTTATTACACATCACAGCTCAAGTTCATATAGCACATATACCAAACATACAA
47842 TACACGCAATCCTTCTAAGAGTAATTCGATCAAAGGTACAAAAACGTATTCTTGATCCCTTAACC
66 TACACGCAATCCTTCTAAGAGTAATTCGATCAAAGGTACAAAAACGTATTCTTGATCCCTTAACC
47907 TAAAAAACTCAAGTTTTTAAGTTAGGGTTCAAAAATATGTTTTTTTGGGTCCCGTTTGAGAGCCC
131 TAAAAAACTCAAGTTTTTAAGTTAGGGTTCAAAAATATGTTTTTTTGGGTCCCGTTTGAGAGCCC
*
47972 TATCGCAGGCAACCAAACCGCTCCGAGAGTGTCGTTTTATGACTTGGACTCATAAAACGACACTC
196 TATCGCAGGCAACCAAACCGCTCCGAGAGTGTCGTTTTATGACTTGGACTCATAAAACAACACTC
48037 TCGATGCGACGGGGTGCCTACAATCGGATTCCCAGACGAATCCTTAACCTATGAT
261 TCGATGCGACGGGGTGCCTACAATCGGATTCCCAGACGAATCCTTAACCTATGAT
48092 ATCAAAAGCCATTGTTATTACACATCACAGCTCAAGTTCATATAGCACATATACCAAACATACAA
1 ATCAAAAGCCATTGTTATTACACATCACAGCTCAAGTTCATATAGCACATATACCAAACATACAA
48157 TACACGCAATCCTTCTAAGAGTAATTCGATCAAAGGTACAAAAACGTATTCTTGATCCCTTAACC
66 TACACGCAATCCTTCTAAGAGTAATTCGATCAAAGGTACAAAAACGTATTCTTGATCCCTTAACC
48222 TAAAAAACTCAAGTTTTTAAGTTAGGGTTCAAAAATATGTTTTTTTGGGTCCCGTTTGAGAGCCC
131 TAAAAAACTCAAGTTTTTAAGTTAGGGTTCAAAAATATGTTTTTTTGGGTCCCGTTTGAGAGCCC
48287 TATCGCAGGCAACCAAACCGCTCCGAGAGTGTCGTTTTATGACTTGGACTCATAAAACAACACTC
196 TATCGCAGGCAACCAAACCGCTCCGAGAGTGTCGTTTTATGACTTGGACTCATAAAACAACACTC
48352 TCGATGCGACGGGGTGCCTACAATCGGATTCCCAGACGAATCCTTAACCTATGAT
261 TCGATGCGACGGGGTGCCTACAATCGGATTCCCAGACGAATCCTTAACCTATGAT
48407 ATCAA
1 ATCAA
48412 CGACAGTATG
Statistics
Matches: 319, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
315 319 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (315 bp):
ATCAAAAGCCATTGTTATTACACATCACAGCTCAAGTTCATATAGCACATATACCAAACATACAA
TACACGCAATCCTTCTAAGAGTAATTCGATCAAAGGTACAAAAACGTATTCTTGATCCCTTAACC
TAAAAAACTCAAGTTTTTAAGTTAGGGTTCAAAAATATGTTTTTTTGGGTCCCGTTTGAGAGCCC
TATCGCAGGCAACCAAACCGCTCCGAGAGTGTCGTTTTATGACTTGGACTCATAAAACAACACTC
TCGATGCGACGGGGTGCCTACAATCGGATTCCCAGACGAATCCTTAACCTATGAT
Found at i:48495 original size:20 final size:21
Alignment explanation
Indices: 48458--48507 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
48448 ACTATACAAG
48458 TCTTTGGATAGTTTGGAGAAT
1 TCTTTGGATAGTTTGGAGAAT
48479 TCTTTGGATAG-TTGGAGAAT
1 TCTTTGGATAGTTTGGAGAAT
*
48499 TCTATGGAT
1 TCTTTGGAT
48508 TTGCCACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42
Consensus pattern (21 bp):
TCTTTGGATAGTTTGGAGAAT
Found at i:51551 original size:20 final size:18
Alignment explanation
Indices: 51523--51561 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
51513 TATTTAAATT
51523 ATAAATTAAATCTAATCAAA
1 ATAAATTAAAT-T-ATCAAA
*
51543 ATAATTTAAATTATCAAA
1 ATAAATTAAATTATCAAA
51561 A
1 A
51562 CTTTTATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAATTAAATTATCAAA
Found at i:52009 original size:22 final size:22
Alignment explanation
Indices: 51968--52009 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
51958 TTTAAATATT
* *
51968 AAATATATTAAATTATTAATAA
1 AAATATACTAAATTAGTAATAA
*
51990 AAATATACTAATTTAGTAAT
1 AAATATACTAAATTAGTAAT
52010 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATACTAAATTAGTAATAA
Found at i:52281 original size:2 final size:2
Alignment explanation
Indices: 52274--52299 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52264 AGTATAGATT
52274 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
52300 AAGTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52645 original size:2 final size:2
Alignment explanation
Indices: 52638--52672 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52628 CTTCTCTTCA
52638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52673 CTTTTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53583 original size:30 final size:27
Alignment explanation
Indices: 53549--53606 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 27
53539 GAACTCATTG
*
53549 ATTAAAATAATATTATTTTTAAAATTAATT
1 ATTAAAAT-A-ATT-TTTTTAAAATAAATT
53579 ATTAAAATAATTTTTTTAAAATAAATT
1 ATTAAAATAATTTTTTTAAAATAAATT
53606 A
1 A
53607 ACAAGATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 15 0.56
28 3 0.11
29 1 0.04
30 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAAAATAATTTTTTTAAAATAAATT
Found at i:53694 original size:16 final size:16
Alignment explanation
Indices: 53655--53694 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
53645 TTCAAGCTTA
*
53655 TTCGGGTTTTAGGCTTT
1 TTCGGG-TTTAGGCATT
53672 TTC-GGTTTAGGCATT
1 TTCGGGTTTAGGCATT
53687 TTCGGGTT
1 TTCGGGTT
53695 CGGACCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 12 0.57
16 6 0.29
17 3 0.14
ACGTcount: A:0.07, C:0.12, G:0.30, T:0.50
Consensus pattern (16 bp):
TTCGGGTTTAGGCATT
Found at i:53908 original size:20 final size:19
Alignment explanation
Indices: 53883--53920 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53873 TTATTTTTGA
*
53883 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
53903 TATATTTATATATAAAAT
1 TATATTTATATATAAAAT
53921 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:54021 original size:24 final size:27
Alignment explanation
Indices: 53994--54047 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
53984 TGTATATTCA
53994 TATCATA-TTT-ATT-TTTTTGTGTTT
1 TATCATATTTTAATTATTTTTGTGTTT
*
54018 TATCATATTTTAATTATTTTTTTGTTT
1 TATCATATTTTAATTATTTTTGTGTTT
54045 TAT
1 TAT
54048 TTGCTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.27
25 3 0.12
26 3 0.12
27 13 0.50
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (27 bp):
TATCATATTTTAATTATTTTTGTGTTT
Found at i:55185 original size:2 final size:2
Alignment explanation
Indices: 55180--55246 Score: 54
Period size: 2 Copynumber: 35.5 Consensus size: 2
55170 TATGTGTGTG
* * * *
55180 TA TA TA TA TA TA TA TA TA TA AA TA TA TGC T- TG TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
55222 TA -A TA TA -A TA TA -A TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55247 TATCAAGTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
1 5 0.09
2 49 0.89
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:55214 original size:34 final size:33
Alignment explanation
Indices: 55168--55238 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 33
55158 AAAACTTCTT
55168 TATATGTGTGTGTATATATAT-ATATATATATAAA
1 TATATGTGTGTGTATATATATAATATA-ATAT-AA
55202 TATATGCT-TGTGTATATATATAATATAATATAA
1 TATATG-TGTGTGTATATATATAATATAATATAA
55235 TATA
1 TATA
55239 ATATATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.17
34 23 0.66
35 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.46
Consensus pattern (33 bp):
TATATGTGTGTGTATATATATAATATAATATAA
Found at i:55229 original size:5 final size:5
Alignment explanation
Indices: 55214--55243 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
55204 TATGCTTGTG
55214 TATATA TATAA TATAA TATAA TATAA TATA
1 TATA-A TATAA TATAA TATAA TATAA TATA
55244 TATTATCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:56691 original size:13 final size:13
Alignment explanation
Indices: 56673--56698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56663 CATTACGAAA
56673 TGTATCGATACAT
1 TGTATCGATACAT
56686 TGTATCGATACAT
1 TGTATCGATACAT
56699 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:60550 original size:19 final size:19
Alignment explanation
Indices: 60526--60589 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
60516 ACTATGTGAC
*
60526 AAAATGATTTCAAGTATCA
1 AAAATGATTTCAAGTATAA
*
60545 AAAATGATTT-AA-TATGTGAC
1 AAAATGATTTCAAGTA--T-AA
60565 AAAATGATTTCAAGTATAA
1 AAAATGATTTCAAGTATAA
60584 AAAATG
1 AAAATG
60590 TTTTAGAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 18 0.49
20 11 0.30
21 2 0.05
22 2 0.05
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (19 bp):
AAAATGATTTCAAGTATAA
Found at i:60561 original size:39 final size:39
Alignment explanation
Indices: 60518--60594 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
60508 TCTTTAAAAC
*
60518 TATGTGACAAAATGATTTCAAGTATCAAAAATGATTTAA
1 TATGTGACAAAATGATTTCAAGTATAAAAAATGATTTAA
*
60557 TATGTGACAAAATGATTTCAAGTATAAAAAATGTTTTA
1 TATGTGACAAAATGATTTCAAGTATAAAAAATGATTTA
60595 GAGACAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (39 bp):
TATGTGACAAAATGATTTCAAGTATAAAAAATGATTTAA
Found at i:60570 original size:20 final size:20
Alignment explanation
Indices: 60518--60574 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
60508 TCTTTAAAAC
*
60518 TATGTGACAAAATGATTTCA
1 TATGTGACAAAATGATTTAA
60538 -A-GT-ATCAAAAATGATTTAA
1 TATGTGA-C-AAAATGATTTAA
60557 TATGTGACAAAATGATTT
1 TATGTGACAAAATGATTT
60575 CAAGTATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 3 0.10
19 12 0.39
20 11 0.35
21 3 0.10
22 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (20 bp):
TATGTGACAAAATGATTTAA
Found at i:60897 original size:21 final size:21
Alignment explanation
Indices: 60871--60929 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
60861 GCATGCATAG
60871 GAATGTATCGATACAATTCCA
1 GAATGTATCGATACAATTCCA
*
60892 GAATGTATCGATAC-A-TCTA
1 GAATGTATCGATACAATTCCA
60911 GAATTGTATCGATACAATT
1 GAA-TGTATCGATACAATT
60930 AGCCTAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.18
20 12 0.35
21 15 0.44
22 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (21 bp):
GAATGTATCGATACAATTCCA
Found at i:64337 original size:20 final size:20
Alignment explanation
Indices: 64312--64350 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
64302 CGGCTCCTAG
64312 AACTCCTCAACAAAATGGAA
1 AACTCCTCAACAAAATGGAA
*
64332 AACTCCTCAATAAAATGGA
1 AACTCCTCAACAAAATGGA
64351 GTTGTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (20 bp):
AACTCCTCAACAAAATGGAA
Found at i:68879 original size:21 final size:20
Alignment explanation
Indices: 68845--68883 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
68835 CACATTTTTG
*
68845 TCTAAATGTATCGATACATT
1 TCTAAATCTATCGATACATT
68865 TCTAGAATCTATCGATACA
1 TCTA-AATCTATCGATACA
68884 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATCTATCGATACATT
Found at i:74469 original size:52 final size:52
Alignment explanation
Indices: 74380--74528 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 52
74370 CGAAATATGA
**
74380 AAATTTGCCTGCATGTATCGATACACTGATCTTTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACACTGATCAATGTATCGATACATCTGGGC
* *
74432 AAATTTGCCTGCATGTATCGATACATTTTAT-AATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-CTGATCAATGTATCGATACATCTGGGC
** *
74484 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACACTGATCAATGTATCGATACA
74529 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.94
53 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACACTGATCAATGTATCGATACATCTGGGC
Found at i:74535 original size:13 final size:13
Alignment explanation
Indices: 74517--74541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74507 CAAAGATCAG
74517 TGTATCGATACAA
1 TGTATCGATACAA
74530 TGTATCGATACA
1 TGTATCGATACA
74542 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:74621 original size:13 final size:13
Alignment explanation
Indices: 74603--74627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74593 ACAAAACTTA
74603 TGTATCGATACAT
1 TGTATCGATACAT
74616 TGTATCGATACA
1 TGTATCGATACA
74628 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74623 original size:32 final size:33
Alignment explanation
Indices: 74582--74647 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
74572 AGTAGCTTAA
74582 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
74614 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
74647 A
1 A
74648 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:75548 original size:55 final size:52
Alignment explanation
Indices: 75444--75735 Score: 196
Period size: 43 Copynumber: 6.0 Consensus size: 52
75434 GAAAAGTGAT
* * * * **
75444 AAAGATGCCAATATGTTGATTCACA-GCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGATGCCAATATGCTGATTCA-AGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
75498 AAATGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAA-GATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
75551 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-TT-----T---
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * * *
75594 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
75644 AATG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
75690 ---G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
75736 AAGATGAGAA
Statistics
Matches: 200, Mismatches: 24, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
43 73 0.37
44 4 0.02
45 1 0.00
46 2 0.01
47 1 0.00
48 2 0.01
49 34 0.17
50 3 0.01
51 2 0.01
52 32 0.16
53 4 0.02
54 5 0.03
55 37 0.19
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:75612 original size:43 final size:43
Alignment explanation
Indices: 75551--76276 Score: 433
Period size: 43 Copynumber: 16.1 Consensus size: 43
75541 TAAAGATGGA
* *
75551 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
75594 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
75637 AAAGAAGAATGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-AAG---GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
75686 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * * * **
75729 AAAGATG--AAGATG-AGAAAAGTGATAAAGATGCCA-ATATGTT-GA-TT
1 AAAGGTGCCAATATGCTG---A-T--TCAAG--GCCAGCTACATTGGACTT
* * * * * * * * **
75774 -CACG-GCC-A-ACGAT-ATT--GGGCTTA--AAGA-TGAGA-AA
1 AAAGGTGCCAATATGCTGATTCAAGGC-CAGCTACATTG-GACTT
* * ** * *
75808 AAGGATGTTAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
*
75857 AGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
75903 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
75946 AAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 --A-AAG--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
75995 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* *
76044 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
** * *
76087 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
76130 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
** *
76179 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* * * *
76228 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
76271 AGAAGG
1 A-AAGG
76277 GTTGCCATCG
Statistics
Matches: 531, Mismatches: 87, Indels: 129
0.71 0.12 0.17
Matches are distributed among these distances:
32 1 0.00
33 3 0.01
34 3 0.01
35 1 0.00
36 1 0.00
37 2 0.00
38 2 0.00
39 4 0.01
40 3 0.01
41 7 0.01
42 3 0.01
43 237 0.45
44 10 0.02
45 4 0.01
46 19 0.04
47 6 0.01
48 7 0.01
49 183 0.34
51 1 0.00
52 34 0.06
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:75681 original size:49 final size:48
Alignment explanation
Indices: 75507--75738 Score: 250
Period size: 43 Copynumber: 4.9 Consensus size: 48
75497 AAAATGATGT
* * *
75507 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAA-GTGC
* *
75559 CAATATGCTGATTCAAGGCCAGCTATATTGGA-TT-TA-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
* *
75602 TAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAATGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAA-GTGC
* *
75651 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
* *
75694 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG
75739 ATGAGAAAAG
Statistics
Matches: 152, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
43 69 0.45
44 2 0.01
45 2 0.01
46 9 0.06
47 1 0.01
48 1 0.01
49 36 0.24
50 1 0.01
51 2 0.01
52 29 0.19
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTGC
Found at i:75688 original size:92 final size:93
Alignment explanation
Indices: 75507--75733 Score: 375
Period size: 92 Copynumber: 2.4 Consensus size: 93
75497 AAAATGATGT
*
75507 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--GAAAAGGTGCCAATATGCTGATT
* *
75572 CAAGGCCAGCTATATTGGATTTAAAGGTGC
64 CAAGGCCAGCGATATTGGACTTAAAGGTGC
* * *
75602 TAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAATGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAAGGTGCCAATATGCTGATTCA
75666 AGGCCAGCGATATTGGACTTAAAGGTGC
66 AGGCCAGCGATATTGGACTTAAAGGTGC
75694 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
75734 TGAAGATGAG
Statistics
Matches: 125, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 87 0.70
95 38 0.30
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (93 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGTGC
Found at i:75907 original size:22 final size:22
Alignment explanation
Indices: 75882--75949 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
75872 ATGCTGATTC
75882 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
75904 AAGGTGCCA-ATGTGTT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
75925 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
75947 AAG
1 AAG
75950 AAGAAGATGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 9 0.28
23 5 0.16
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:75935 original size:309 final size:309
Alignment explanation
Indices: 75376--76043 Score: 1230
Period size: 309 Copynumber: 2.2 Consensus size: 309
75366 GACTTAAAGA
* *
75376 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATTAAGATGAGAAAAGT
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGT
*
75441 GATAAAGATGCCAATATGTTGATTCACAGCCAACGATATTGGGCTTAAAGATGAGAAAAATGATG
66 GATAAAGATGCCAATATGTTGATTCACAGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
*
75506 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
131 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGCTGAT
* *
75571 TCAAGGCCAGCTATATTGGATTTAAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACT
196 TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
75636 TAAAGAAGAATG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
261 TAAAGAAGAA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
75685 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGT
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGT
*
75750 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
66 GATAAAGATGCCAATATGTTGATTCACAGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
*
75815 TTAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGCTGAT
131 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGCTGAT
*
75880 TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACT
196 TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
*
75945 TAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
261 TAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
75994 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
76044 AAAGGTGCCA
Statistics
Matches: 348, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
308 1 0.00
309 347 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (309 bp):
TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGT
GATAAAGATGCCAATATGTTGATTCACAGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGCTGAT
TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
TAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
Found at i:75993 original size:92 final size:93
Alignment explanation
Indices: 75817--76276 Score: 748
Period size: 92 Copynumber: 5.0 Consensus size: 93
75807 AAAGGATGTT
*
75817 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAG--AAGGTGCCAATATGCTGATTC
75882 AAGGCCAGCTATATTGGACTTAAAGGTGCC
64 AAGGCCAGCTATATTGGACTTAAAGGTGCC
* *
75912 AATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGATGCCAATATGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAGAAGGTGCCAATATGCTGATTCAA
75976 GGCCAGCTATATTGGACTTAAAGGTGCC
66 GGCCAGCTATATTGGACTTAAAGGTGCC
76004 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAGAAGGTGCCAATATGCTGATTCAA
* **
76068 GGCCAGCGATATTGGACTTGGAGGTGCC
66 GGCCAGCTATATTGGACTTAAAGGTGCC
*
76096 AATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGA-AGAAGGTGCCAATATGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAGAAGGTGCCAATATGCTGATTCAA
* **
76160 GGCCAGCGATATTGGACTTGGAGGTGCC
66 GGCCAGCTATATTGGACTTAAAGGTGCC
* *
76188 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGTCAATGTGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAGAAGGTGCCAATATGCTGATTCAA
*
76252 GGCCAGCTATATTGGGCTTAGAAGG
66 GGCCAGCTATATTGGACTTA-AAGG
76277 GTTGCCATCG
Statistics
Matches: 345, Mismatches: 16, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
91 1 0.00
92 300 0.87
93 5 0.01
94 2 0.01
95 37 0.11
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (93 bp):
AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGCC
Found at i:76315 original size:33 final size:33
Alignment explanation
Indices: 76271--76473 Score: 308
Period size: 33 Copynumber: 6.2 Consensus size: 33
76261 TATTGGGCTT
*
76271 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
76304 AGAAGGTTTGCCACCGACTTATGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
76337 AGAAGGGTTTTCCACCGACTTGTGTGGGCTTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGC-TTTAG
*
76372 AG-AGGGTTGCCATCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
76403 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
76434 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
76467 A-AAGGGT
1 AGAAGGGT
76474 GAAAGATGCA
Statistics
Matches: 156, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
31 34 0.22
32 36 0.23
33 56 0.36
34 23 0.15
35 7 0.04
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:76368 original size:67 final size:66
Alignment explanation
Indices: 76271--76473 Score: 308
Period size: 67 Copynumber: 3.1 Consensus size: 66
76261 TATTGGGCTT
* * *
76271 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGTTTGCCACCGACTTATGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
76336 G
66 G
* *
76337 AGAAGGGTTTTCCACCGACTTGTGTGGGCTTTTAGAG-AGGGTTGCCATCGACTTGTGTGGGCTT
1 AGAAGGG-TTGCCACCGACTTGTGTGGGC-TTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTT
76401 T-G
64 TAG
76403 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
76466 G
66 G
76467 A-AAGGGT
1 AGAAGGGT
76474 GAAAGATGCA
Statistics
Matches: 126, Mismatches: 7, Indels: 11
0.88 0.05 0.08
Matches are distributed among these distances:
62 2 0.02
63 33 0.26
64 5 0.04
65 20 0.16
66 15 0.12
67 44 0.35
68 7 0.06
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (66 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
G
Found at i:76530 original size:69 final size:69
Alignment explanation
Indices: 76455--76974 Score: 525
Period size: 67 Copynumber: 7.7 Consensus size: 69
76445 CACCGACTTG
** * * * *
76455 TGTGGGCTTTAGAAAGGGTGAAAGATGCAACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCAC
1 TGTGGGCTTTA-AAAGGGAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
*
76519 GGAGG
65 GGAGT
*
76524 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
*
76586 GAAGT
65 GGAGT
* * *
76591 CGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
*
76656 GAAGT
65 GGAGT
* *
76661 TGTGGGCTTTAAAA-AGAAAAATG-TGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCA
1 TGTGGGCTTTAAAAGGGAAAAA-GATGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAAGGTGCCA
76724 CGGAGT
64 CGGAGT
* ** * * * *
76730 TGTGGAC-TTAAAAAAGAAAATGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACA
1 TGTGGGCTTTAAAAGGGAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACG
76794 GAGT
66 GAGT
* * * * *
76798 TGTGGGCTTTGAAAA--G---AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTGCCAC
1 TGTGGGCTTT-AAAAGGGAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
76857 GGAGT
65 GGAGT
* *
76862 TGTGGACTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTTAAAAAG---AAGGTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
*
76924 AGAGT
65 GGAGT
** * * *
76929 CATGGACTTTAAGAA-GGAAAAAGAGTGCCACGGAGGTGTGGACTTT
1 TGTGGGCTTTAA-AAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTT
76975 GATGCCACTG
Statistics
Matches: 391, Mismatches: 41, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.01
64 31 0.08
65 20 0.05
67 115 0.29
68 71 0.18
69 104 0.27
70 46 0.12
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (69 bp):
TGTGGGCTTTAAAAGGGAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACG
GAGT
Found at i:76536 original size:34 final size:34
Alignment explanation
Indices: 76488--76974 Score: 519
Period size: 34 Copynumber: 14.4 Consensus size: 34
76478 GATGCAACGA
* *
76488 AGTTGTGGAC-TTAAAAAGAACAAGGTGCCACGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* *
76521 AGGTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGG
* *
76557 AGTTGTGGGCTTTGAAAAG---AAGGTGCCACGA
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * *
76588 AGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGG
* *
76624 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGA
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* *
76658 AGTTGTGGGCTTTAAAAAGAAAAATGTGCCATGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
76692 AGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACGG
1 AGTTGTGGGCTTTAAAAAG-AAAAAGGTGCCACGG
* * *
76727 AGTTGTGGACTTAAAAAAGAAAATGGTGCCACGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* *
76761 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
*
76795 AGTTGTGGGCTTTGAAAAG---AAGGTGCCACGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * * *
76826 AGTCGTGGAC-TTAAAAGGAACAAGGTGCCACGG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * *
76859 AGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGG
1 AGTTGTGGGCTTTAAAA-AGAAAAA-GGTGCCACGG
*
76895 AGTTGTGGGCTTTAAAAAG---AAGGTGCCACAG
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
** * *
76926 AGTCATGGACTTTAAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGGCTTTAA-AAAGAAAAAG-GTGCCACGG
* *
76962 AGGTGTGGACTTT
1 AGTTGTGGGCTTT
76975 GATGCCACTG
Statistics
Matches: 382, Mismatches: 52, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
30 6 0.02
31 61 0.16
32 9 0.02
33 29 0.08
34 131 0.34
35 57 0.15
36 89 0.23
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (34 bp):
AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
Found at i:76603 original size:67 final size:66
Alignment explanation
Indices: 76509--77127 Score: 549
Period size: 67 Copynumber: 9.5 Consensus size: 66
76499 TAAAAAGAAC
* *
76509 AAGGTGCCACGGAGGT-GTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGTGCCAC-GAAGTCGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
76573 AAG
64 AAG
76576 AAGGTGCCACGAAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAGGTGCCACGAAGTCGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
76641 AG
65 AG
* * * * * *
76643 AAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAA-TGTGCCATGGAGTTGTGGGCTTTAA
1 ---AAGGTGCCACGAAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
76707 AAAG
63 AAAG
* * * * *
76711 AAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAAGAAAATG-GTGCCACGGAGTTGTGGGCTTTG
1 ----AAGGTGCCACGAAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG
76775 AAAAG
62 AAAAG
* * * * *
76780 AAAAAGGTGCCAC-AGAGTTGTGGGCTTTGAAAA-G---AAG-GTGCCACGGAGTCGTGGACTTA
1 ---AAGGTGCCACGA-AGTCGTGGACTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
76839 AAAGGAAC
61 GAA--AAG
* * * *
76847 AAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAGGTGCCACGAAGTCGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
76912 AG
65 AG
* * *
76914 AAGGTGCCAC-AGAGTCATGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGGTGTGGACTTT---
1 AAGGTGCCACGA-AGTCGTGGACTTTAA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
76975 --G
64 AAG
*
76976 -A--TGCCACTG-AGTCGTGGAC-TTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTT----
1 AAGGTGCCAC-GAAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
77032 -G
65 AG
*
77033 -A--TGCCACTAAGTCGTGGAC-TTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAGGTGCCACGAAGTCGTGGACTTTAAAAGGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
77094 AG
65 AG
* *
77096 AAGGTGCCATGGAGTCGTGGACTTTAAGAAGG
1 AAGGTGCCACGAAGTCGTGGACTTTAA-AAGG
77128 TATTTGACGA
Statistics
Matches: 476, Mismatches: 43, Indels: 65
0.82 0.07 0.11
Matches are distributed among these distances:
57 60 0.13
58 30 0.06
59 15 0.03
61 1 0.00
62 1 0.00
63 5 0.01
64 23 0.05
65 24 0.05
66 19 0.04
67 119 0.25
68 59 0.12
69 93 0.20
70 27 0.06
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (66 bp):
AAGGTGCCACGAAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
G
Found at i:76722 original size:103 final size:102
Alignment explanation
Indices: 76488--76974 Score: 539
Period size: 103 Copynumber: 4.8 Consensus size: 102
76478 GATGCAACGA
* * * *
76488 AGTTGTGGAC-TTAAAAAGAACAAGGTGCCACGGAGGTGTGGGCTTTAAAAGGGAAAAAGAGTGC
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-GGAAAAAG-GTGC
* *
76552 CACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGA
64 CACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * * *
76588 AGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAAAAGGTG
1 AGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGACTTT-AAAAGGAAAAAGGTG
* * *
76652 CCACGAAGTTGTGGGCTTTAAAAAGAAAAATGTGCCATGG
63 CCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * *
76692 AGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAAGAAAATGGTGCC
1 AGTTGTGGGCTTTAAAAAG-AAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCC
* *
76757 ACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAG
65 ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
* * *
76795 AGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTGCCA
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCA
* * *
76856 CGGAGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGG
66 CGGAGTTGTGGGCTTTAAAA-AGAAAAA-GGTGCCACGG
* **
76895 AGTTGTGGGCTTTAAAAAG---AAGGTGCCACAGAGTCATGGACTTTAAGAAGGAAAAAGAGTGC
1 AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAA-AAGGAAAAAG-GTGC
* *
76957 CACGGAGGTGTGGACTTT
64 CACGGAGTTGTGGGCTTT
76975 GATGCCACTG
Statistics
Matches: 337, Mismatches: 36, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
98 34 0.10
99 27 0.08
100 55 0.16
101 36 0.11
102 26 0.08
103 125 0.37
104 34 0.10
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (102 bp):
AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCA
CGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
Found at i:77016 original size:57 final size:57
Alignment explanation
Indices: 76918--77091 Score: 276
Period size: 57 Copynumber: 3.0 Consensus size: 57
76908 AAAAAGAAGG
* * *
76918 TGCCACAGAGTCATGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGGTGTGGACTTTGA
1 TGCCACTGAGTCGTGGAC-TTAA-AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGA
76977 TGCCACTGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGA
1 TGCCACTGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGA
* *
77034 TGCCACTAAGTCGTGGACTTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 TGCCACTGAGTCGTGGACTTAAAAGGAA-AAAGAGTGCCACGGAGTTGTGGACTTTGA
77092 AAAGAAGGTG
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
57 61 0.56
58 32 0.29
59 16 0.15
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (57 bp):
TGCCACTGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGA
Found at i:78091 original size:18 final size:17
Alignment explanation
Indices: 78064--78107 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
78054 GGTTTTTCCC
78064 TTTTTTTTTTATTTGTG
1 TTTTTTTTTTATTTGTG
78081 TTTTGTTTTTT-TTT-TG
1 TTTT-TTTTTTATTTGTG
78097 TTTCTTTTTTT
1 TTT-TTTTTTT
78108 GGAAAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.44
17 8 0.32
18 6 0.24
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTATTTGTG
Found at i:78105 original size:16 final size:18
Alignment explanation
Indices: 78066--78107 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
78056 TTTTTCCCTT
78066 TTTTTTTTATTTGTGTT-
1 TTTTTTTTATTTGTGTTC
*
78083 TTGTTTTTTTTTTGT-TTC
1 TT-TTTTTTATTTGTGTTC
78101 TTTTTTT
1 TTTTTTT
78108 GGAAAAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (18 bp):
TTTTTTTTATTTGTGTTC
Found at i:78106 original size:12 final size:11
Alignment explanation
Indices: 78064--78108 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
78054 GGTTTTTCCC
*
78064 TTTTTTTTTTA
1 TTTTTTTTTTG
* *
78075 TTTGTGTTTTG
1 TTTTTTTTTTG
78086 TTTTTTTTTTG
1 TTTTTTTTTTG
78097 TTTCTTTTTTTG
1 TTT-TTTTTTTG
78109 GAAAAGAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:78367 original size:18 final size:16
Alignment explanation
Indices: 78346--78385 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
78336 ACTTTGCACC
* *
78346 TTTTTTTCTGTGTTTT
1 TTTTTTTTTTTGTTTT
*
78362 TTTTTTGTTTTGTTTT
1 TTTTTTTTTTTGTTTT
78378 TTTTTTTT
1 TTTTTTTT
78386 GTGTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTGTTTT
Found at i:78386 original size:13 final size:14
Alignment explanation
Indices: 78346--78387 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
78336 ACTTTGCACC
*
78346 TTTTTTTCTGTGTT-
1 TTTTTTT-TGTTTTG
78360 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
78374 TTTTTTTT-TTTTG
1 TTTTTTTTGTTTTG
78387 T
1 T
78388 GTTTACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:78397 original size:20 final size:18
Alignment explanation
Indices: 78358--78397 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
78348 TTTTTCTGTG
*
78358 TTTTTTTTTTGTTTTGTT
1 TTTTTTTTTTGTTTTCTT
78376 TTTTTTTTTTGTGTTTACTT
1 TTTTTTTTTTGT-TTT-CTT
78396 TT
1 TT
78398 GACTTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 3 0.16
20 4 0.21
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTGTTTTCTT
Found at i:85337 original size:52 final size:52
Alignment explanation
Indices: 85259--85387 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
85249 CGAAATATGA
* *
85259 AAATTTGCCTGCATGTATTGATACATTTAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
* *
85311 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
85363 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
85388 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
Found at i:85400 original size:52 final size:51
Alignment explanation
Indices: 85259--85407 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
85249 CGAAATATGA
* *
85259 AAATTTGCCTGCATGTATTGATACATTTAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
85311 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
85363 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
85408 ATGTATTGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:85500 original size:13 final size:13
Alignment explanation
Indices: 85482--85506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85472 ACAAAACTTA
85482 TGTATCGATACAT
1 TGTATCGATACAT
85495 TGTATCGATACA
1 TGTATCGATACA
85507 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:85502 original size:32 final size:33
Alignment explanation
Indices: 85461--85526 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
85451 AGTAGCTTAA
85461 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
85493 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
85526 A
1 A
85527 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:87331 original size:21 final size:22
Alignment explanation
Indices: 87292--87350 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
87282 TTCAAGTATC
*
87292 AAAAATG-TTTTAAAGAC-AAG
1 AAAAATGTTTTTCAAGACAAAG
87312 AACAAATGTTTTTCAA-ACAAAG
1 AA-AAATGTTTTTCAAGACAAAG
87334 AAATAATGTTTTTCAAG
1 AAA-AATGTTTTTCAAG
87351 TAAATACACT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 23 0.70
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAAATGTTTTTCAAGACAAAG
Found at i:87465 original size:20 final size:20
Alignment explanation
Indices: 87436--87488 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
87426 AACCCTTATT
87436 TGTATCGATACACA-TGCAGA
1 TGTATCGATACACATTGCA-A
* *
87456 TGTATTGATACAAATTGCAA
1 TGTATCGATACACATTGCAA
87476 TGTATCGATACAC
1 TGTATCGATACAC
87489 TATAAGAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACACATTGCAA
Found at i:87584 original size:21 final size:21
Alignment explanation
Indices: 87555--87695 Score: 195
Period size: 21 Copynumber: 6.9 Consensus size: 21
87545 ATATACATAG
*
87555 GAATATATCGATACAATTCCA
1 GAATGTATCGATACAATTCCA
87576 GAATGTATCGATAC-A-TCCA
1 GAATGTATCGATACAATTCCA
87595 GAATTGTATCGATACAATTCCA
1 GAA-TGTATCGATACAATTCCA
87617 GAATGTATCGATAC-A-TCCA
1 GAATGTATCGATACAATTCCA
*
87636 AAATTGTATCGATACAATTCCA
1 GAA-TGTATCGATACAATTCCA
87658 GAATGTATCGATAC-A-TCCA
1 GAATGTATCGATACAATTCCA
87677 GAATTGTATCGATACAATT
1 GAA-TGTATCGATACAATT
87696 AGCCTAACAG
Statistics
Matches: 108, Mismatches: 3, Indels: 17
0.84 0.02 0.13
Matches are distributed among these distances:
19 20 0.19
20 36 0.33
21 38 0.35
22 14 0.13
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (21 bp):
GAATGTATCGATACAATTCCA
Found at i:87604 original size:20 final size:20
Alignment explanation
Indices: 87555--87692 Score: 183
Period size: 20 Copynumber: 6.8 Consensus size: 20
87545 ATATACATAG
*
87555 GAATATATCGATACAATTCCA
1 GAATGTATCGATAC-ATTCCA
87576 GAATGTATCGATACA-TCCA
1 GAATGTATCGATACATTCCA
87595 GAATTGTATCGATACAATTCCA
1 GAA-TGTATCGATAC-ATTCCA
87617 GAATGTATCGATACA-TCCA
1 GAATGTATCGATACATTCCA
*
87636 AAATTGTATCGATACAATTCCA
1 GAA-TGTATCGATAC-ATTCCA
87658 GAATGTATCGATACA-TCCA
1 GAATGTATCGATACATTCCA
87677 GAATTGTATCGATACA
1 GAA-TGTATCGATACA
87693 ATTAGCCTAA
Statistics
Matches: 107, Mismatches: 3, Indels: 15
0.86 0.02 0.12
Matches are distributed among these distances:
19 20 0.19
20 37 0.35
21 37 0.35
22 13 0.12
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
GAATGTATCGATACATTCCA
Found at i:87611 original size:41 final size:41
Alignment explanation
Indices: 87560--87695 Score: 263
Period size: 41 Copynumber: 3.3 Consensus size: 41
87550 CATAGGAATA
87560 TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
1 TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
*
87601 TATCGATACAATTCCAGAATGTATCGATACATCCAAAATTG
1 TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
87642 TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
1 TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
87683 TATCGATACAATT
1 TATCGATACAATT
87696 AGCCTAACAG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (41 bp):
TATCGATACAATTCCAGAATGTATCGATACATCCAGAATTG
Found at i:89005 original size:16 final size:16
Alignment explanation
Indices: 88981--89014 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
88971 ATTTTTATGA
88981 TTTAATATATA-TATC
1 TTTAATATATATTATC
88996 TTTAATTATATATTATC
1 TTTAA-TATATATTATC
89013 TT
1 TT
89015 ATGTTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAATATATATTATC
Found at i:94803 original size:16 final size:16
Alignment explanation
Indices: 94778--94924 Score: 64
Period size: 16 Copynumber: 8.9 Consensus size: 16
94768 AATTTATTAG
94778 ATTT-AATTATTTTAA
1 ATTTAAATTATTTTAA
94793 ATTTAAATTATTTCGAGTTAA
1 ATTTAAATTA-TT----TTAA
* **
94814 TTTTTAAATTATTTTGT
1 -ATTTAAATTATTTTAA
*** *
94831 ATTTTGGTTATTTTAC
1 ATTTAAATTATTTTAA
* *
94847 TTTTAAGTTATTTT-A
1 ATTTAAATTATTTTAA
*
94862 ATTTCAAATTATTTTGA
1 ATTT-AAATTATTTTAA
* *
94879 ATTTAAAATATTTTAG
1 ATTTAAATTATTTTAA
* * *
94895 ATTTAAGTAATTTCAA
1 ATTTAAATTATTTTAA
* *
94911 GTTCAAATTATTTT
1 ATTTAAATTATTTT
94925 TGAATTTGAG
Statistics
Matches: 95, Mismatches: 28, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
15 7 0.07
16 64 0.67
17 9 0.09
21 6 0.06
22 9 0.09
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:94873 original size:48 final size:48
Alignment explanation
Indices: 94839--94931 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
94829 GTATTTTGGT
* *
94839 TATTTTACTTTTAAGTTATTTTAATTTCAAATTATTTTGAATTTAAAA
1 TATTTTACATTTAAGTAATTTTAATTTCAAATTATTTTGAATTTAAAA
* * *
94887 TATTTTAGATTTAAGTAATTTCAAGTTCAAATTATTTTTGAATTT
1 TATTTTACATTTAAGTAATTTTAATTTCAAATTA-TTTTGAATTT
94932 GAGTTGATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 29 0.74
49 10 0.26
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (48 bp):
TATTTTACATTTAAGTAATTTTAATTTCAAATTATTTTGAATTTAAAA
Found at i:94887 original size:17 final size:16
Alignment explanation
Indices: 94838--94900 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
94828 TGTATTTTGG
* * *
94838 TTATTTTACTTTTAAG
1 TTATTTTAATTTAAAA
*
94854 TTATTTTAATTTCAAA
1 TTATTTTAATTTAAAA
94870 TTATTTTGAATTTAAAA
1 TTATTTT-AATTTAAAA
94887 -TATTTTAGATTTAA
1 TTATTTTA-ATTTAA
94901 GTAATTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 1 0.02
16 32 0.78
17 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (16 bp):
TTATTTTAATTTAAAA
Found at i:96604 original size:38 final size:36
Alignment explanation
Indices: 96530--96606 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 36
96520 TAAAAAAGTT
*
96530 TTATTAAGTAGTTTTTTAAGATATGATTTATTTTTAA
1 TTATTAAGTAGTTTTTT-AGATATGATTTATATTTAA
96567 TTATTAAAGTA-TTTTTT-GATATGATTATATGAATTTAA
1 TTATT-AAGTAGTTTTTTAGATATGATT-TAT--ATTTAA
96605 TT
1 TT
96607 TAGCTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
35 9 0.26
36 3 0.09
37 11 0.31
38 12 0.34
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (36 bp):
TTATTAAGTAGTTTTTTAGATATGATTTATATTTAA
Found at i:96741 original size:16 final size:15
Alignment explanation
Indices: 96722--96751 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96712 TAAATAATAT
96722 TTTTTAAAATAAAAA
1 TTTTTAAAATAAAAA
*
96737 TTTTTAAATTAAAAA
1 TTTTTAAAATAAAAA
96752 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTTAAAATAAAAA
Found at i:97169 original size:71 final size:71
Alignment explanation
Indices: 97084--97277 Score: 225
Period size: 73 Copynumber: 2.7 Consensus size: 71
97074 AGAGTTATTT
* *
97084 ATTTATTTCTATTTGAAGAAGTTTAAATTTATTTTTTATTTGATTATATGGGTTTAAATTTTTAA
1 ATTTATTT-TATTTGAAGAAATTTAAATTTATTTTTTATTTGATTATATGAGTTTAAATTTTTAA
97149 -GGTGTA
65 TGGTGTA
* * * *
97155 ATTTATTTTGATTTGTAGAAATTT-AATTATGTTTTTTATTAAGTATGATATGAGTTTAAATTTT
1 ATTTATTTT-ATTTGAAGAAATTTAAATT-TATTTTTTATT-TG-ATTATATGAGTTTAAATTTT
97219 TAATGGTGTA
62 TAATGGTGTA
97229 ATTTAATTTTATTT-ATA-AAATTTAAGATTTATTTTTTAATTTGATTATA
1 ATTT-ATTTTATTTGA-AGAAATTTAA-ATTTATTTTTT-ATTTGATTATA
97278 AAACTTAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
70 5 0.05
71 30 0.29
72 1 0.01
73 32 0.31
74 24 0.23
75 11 0.11
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.56
Consensus pattern (71 bp):
ATTTATTTTATTTGAAGAAATTTAAATTTATTTTTTATTTGATTATATGAGTTTAAATTTTTAAT
GGTGTA
Found at i:104202 original size:87 final size:88
Alignment explanation
Indices: 104000--104233 Score: 294
Period size: 88 Copynumber: 2.7 Consensus size: 88
103990 AATAGAAATT
* * * * **
104000 TGATTCTTAAATATAATTCATGCATTAATCTAATTCTTGCAGCCTAACATTTACAATCAATTAAC
1 TGATTCTTAAATATAATTCATGCATTACTCTAATTCTTTCAGTCTAATATTTACAATCAACCAAC
104065 TTTTTTTTCCACAAAAAAGAATC
66 TTTTTTTTCCACAAAAAAGAATC
* * ** *
104088 CGATTCTCAAATACCATTCATGCATTACTCTAATTCTTTCAGTTTAATATTTACAATCAACCAA-
1 TGATTCTTAAATATAATTCATGCATTACTCTAATTCTTTCAGTCTAATATTTACAATCAACCAAC
* *
104152 -TTTTTTTCTTACTAAAAAGAATC
66 TTTTTTTTC-CACAAAAAAGAATC
** *
104175 TGATTCTTAGGTATAATTCATGCATTACTCTAA-TCTTTTAGTCTAATATTTACAATCAA
1 TGATTCTTAAATATAATTCATGCATTACTCTAATTCTTTCAGTCTAATATTTACAATCAA
104234 TGCATTACTC
Statistics
Matches: 124, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
86 32 0.26
87 39 0.31
88 53 0.43
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (88 bp):
TGATTCTTAAATATAATTCATGCATTACTCTAATTCTTTCAGTCTAATATTTACAATCAACCAAC
TTTTTTTTCCACAAAAAAGAATC
Found at i:106533 original size:15 final size:15
Alignment explanation
Indices: 106513--106548 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
106503 GGAAGCACTA
106513 AGCGCTACTTGCAAT
1 AGCGCTACTTGCAAT
*
106528 AGCGCTACTTGTAAT
1 AGCGCTACTTGCAAT
106543 AGCGCT
1 AGCGCT
106549 TTCACATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (15 bp):
AGCGCTACTTGCAAT
Found at i:106617 original size:16 final size:16
Alignment explanation
Indices: 106598--106632 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
106588 ATTTAAATTT
*
106598 TAATTAATTTTATTAA
1 TAATTAATTATATTAA
106614 TAATTAATTATATTAA
1 TAATTAATTATATTAA
106630 TAA
1 TAA
106633 ATATTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTAATTATATTAA
Found at i:106644 original size:27 final size:26
Alignment explanation
Indices: 106614--106674 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
106604 ATTTTATTAA
* * *
106614 TAATTAATTATATTAATAAATATTTAG
1 TAATTAACTATA-AAATAAATATTGAG
*
106641 TAATTATACTATAAAATAAATATTGAT
1 TAATTA-ACTATAAAATAAATATTGAG
106668 TAATTAA
1 TAATTAA
106675 AAAGATGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 23 0.79
28 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (26 bp):
TAATTAACTATAAAATAAATATTGAG
Found at i:106913 original size:14 final size:15
Alignment explanation
Indices: 106879--106914 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
106869 TAAAGTTATA
106879 ATTTA-TAATTTTTT
1 ATTTATTAATTTTTT
106893 ATTTATTAA-TTTTT
1 ATTTATTAATTTTTT
106907 ATTTATTA
1 ATTTATTA
106915 TATATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTATTAATTTTTT
Found at i:112737 original size:2 final size:2
Alignment explanation
Indices: 112730--112762 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112720 AGATGAGATA
112730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112763 GTTATTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113731 original size:21 final size:21
Alignment explanation
Indices: 113680--113745 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
113670 TTTGGTTATT
*
113680 AAAAGTTGCATTCTTTCATCC
1 AAAAATTGCATTCTTTCATCC
*
113701 AAAAAATGCATTCTTTCATCC
1 AAAAATTGCATTCTTTCATCC
**
113722 AACCATTGCA-TCATTTCAT-C
1 AAAAATTGCATTC-TTTCATCC
113742 AAAA
1 AAAA
113746 TACACTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 5 0.14
21 32 0.86
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAAATTGCATTCTTTCATCC
Found at i:117496 original size:20 final size:20
Alignment explanation
Indices: 117451--117503 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
117441 TTTTACCCAG
* *
117451 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* *
117471 AAGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
*
117491 ATGTATCAATACA
1 ATGTATCGATACA
117504 CTCTTCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:117617 original size:20 final size:20
Alignment explanation
Indices: 117542--117618 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
117532 TTTTACCCAG
*
117542 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *** *
117562 GTGTATCGATACATGAATGA
1 ATGTATCGATACATTCTTCA
117582 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
117602 TTGTATCGATACATTCT
1 ATGTATCGATACATTCT
117619 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:117658 original size:91 final size:91
Alignment explanation
Indices: 117440--117647 Score: 328
Period size: 91 Copynumber: 2.3 Consensus size: 91
117430 AAAAGTCACA
* *
117440 TTTTTACCCAGATGTATCGATACATTTTTCAAAGTATCGATACATGTATGAATGTATCAATACAC
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGAATGAATGTATCAATACAC
*
117505 TCTTCAATTTGTCGATAAATTCTATC
66 TCTTCAATTTATCGATAAATTCTATC
* * *
117531 TTTTTACCCAGATGTATCGATACATTTTTCAGTGTATCGATACATGAATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGAATGAATGTATCAATACAC
* *
117596 TCTTC-ATTGTATCGATACATTCTGTC
66 TCTTCAATT-TATCGATAAATTCTATC
117622 TTTTTACCCAGATGTATCGATACATT
1 TTTTTACCCAGATGTATCGATACATT
117648 GAATAATGTA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
90 3 0.03
91 105 0.97
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (91 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGAATGAATGTATCAATACAC
TCTTCAATTTATCGATAAATTCTATC
Found at i:126792 original size:21 final size:21
Alignment explanation
Indices: 126743--126812 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
126733 AAAATGACAA
* *
126743 AAAAAAAGGTCAAAAGCAAAAGT
1 AAAAAAATG-CAAAAG-AAAAAT
*
126766 ACAAAATATG-AAAAGAAAAAT
1 A-AAAAAATGCAAAAGAAAAAT
*
126787 AAAAAAATGCAAAAGCAAAAT
1 AAAAAAATGCAAAAGAAAAAT
126808 AAAAA
1 AAAAA
126813 GGGAACAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.17
21 21 0.52
22 5 0.12
23 1 0.03
24 6 0.15
ACGTcount: A:0.71, C:0.07, G:0.11, T:0.10
Consensus pattern (21 bp):
AAAAAAATGCAAAAGAAAAAT
Found at i:128157 original size:32 final size:32
Alignment explanation
Indices: 128108--128638 Score: 443
Period size: 32 Copynumber: 17.4 Consensus size: 32
128098 TAGCATTTCT
*
128108 TTTCAAAGGCCCACATAAGTCGGTGGCAACTCA
1 TTTCAAA-GCCCACACAAGTCGGTGGCAACTCA
* * ** *
128141 TTTGAAAGCCCACATAAGTTAGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
*
128173 TTTCAAAGCCCACACAAGTCGGTGGAAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * * *
128205 TTTGAAAGCACACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* *
128237 TTTCAAAGTCCACACAAGTCGGTGACAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
128269 TTTGAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
*
128301 TTTCAAAGCCCACACAAGTCAGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* **
128333 TTTCAAAG-CC-TACAAGTTAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
*
128361 TTTCAAAGCCCACACTAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* *
128393 TTTGAAAGCCCACACAAGTTGGTGGCAAC-CAA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTC-A
* *
128425 TTTTAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * * *
128457 TTTCAAAG--CTCACAAGTCAGTGG-TA-TCC
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* *
128485 TTTCAAAG-CC-CACAAGTCCGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
128513 TTTTAAAG-CC-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * ** *
128541 TTTTAAA-ACC-CACAAGTTAGTGGC-AC-CT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
128569 TTTCAAAG-CC-TACAAGTCAGTGGCATAC-CT
1 TTTCAAAGCCCACACAAGTCGGTGGCA-ACTCA
* *
128599 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
128627 TTTCAAAGCCCA
1 TTTCAAAGCCCA
128639 TAAGTTAGTG
Statistics
Matches: 427, Mismatches: 56, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
28 118 0.28
29 7 0.02
30 62 0.15
31 4 0.01
32 229 0.54
33 7 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
Done.