Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold354
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: 1591162
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 188200 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:876 original size:41 final size:41
Alignment explanation
Indices: 831--920 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
821 AATTCGGCCA
*
831 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
*
872 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
913 AACATGTA
1 AACATGTA
921 TGAAAATAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (41 bp):
AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
Found at i:1932 original size:3 final size:3
Alignment explanation
Indices: 1850--1917 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
1840 ACAACAACGG
1850 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1897 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1918 CACAAACAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4321 original size:19 final size:17
Alignment explanation
Indices: 4297--4335 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
4287 GATTTTATTA
4297 AATTAATTAATCTTAAGCT
1 AATTAATTAAT-TTAA-CT
*
4316 AATTAATTTATTTAACT
1 AATTAATTAATTTAACT
4333 AAT
1 AAT
4336 CAACAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTAATTAATTTAACT
Found at i:6772 original size:22 final size:22
Alignment explanation
Indices: 6742--6810 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
6732 TATGCACTAT
* *
6742 TAAATAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAATGTGC
*
6764 TATACAGAGAGCAC-AGATGTGC
1 TAAACAGAGAGCACTA-ATGTGC
*
6786 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAATGTGC
6808 TAA
1 TAA
6811 TAATCGGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATGTGC
Found at i:12877 original size:26 final size:26
Alignment explanation
Indices: 12842--12918 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
12832 GTAGCTCTTA
*
12842 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-ATGGCTCTTCG
* *
12868 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAATGGCTCTTCG
*
12894 TGAGCTTCCTGATTAATGGCTCTTC
1 TGAGCTTCCCGATTAATGGCTCTTC
12919 AGAGTTACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 41 0.93
27 3 0.07
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCCGATTAATGGCTCTTCG
Found at i:12997 original size:25 final size:25
Alignment explanation
Indices: 12969--13034 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
12959 GGCTCTCATG
* **
12969 AGCTTCCCGTTATATGTCCCGGATA
1 AGCTTCCCGTTATATGACCCACATA
* * * *
12994 AGCTTCCTGTTACATGACTCACATG
1 AGCTTCCCGTTATATGACCCACATA
13019 AGCTTCCCGTTATATG
1 AGCTTCCCGTTATATG
13035 GCTCGAGAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (25 bp):
AGCTTCCCGTTATATGACCCACATA
Found at i:14574 original size:9 final size:9
Alignment explanation
Indices: 14560--14593 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
14550 ACAAGTTAGA
14560 TAAAATAAT
1 TAAAATAAT
*
14569 TAAAATAAA
1 TAAAATAAT
*
14578 TAAGATAAT
1 TAAAATAAT
14587 TAAAATA
1 TAAAATA
14594 GAATAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (9 bp):
TAAAATAAT
Found at i:14585 original size:18 final size:19
Alignment explanation
Indices: 14559--14599 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
14549 TACAAGTTAG
14559 ATAAAATAATTAAAATA-A
1 ATAAAATAATTAAAATAGA
*
14577 ATAAGATAATTAAAATAGA
1 ATAAAATAATTAAAATAGA
14596 ATAA
1 ATAA
14600 TAAATCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAAAATAATTAAAATAGA
Found at i:17439 original size:21 final size:21
Alignment explanation
Indices: 17409--17448 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17399 TTACTATTAC
*
17409 TATTAATATAAATTTTAAATT
1 TATTAATATAAATATTAAATT
* *
17430 TATTATTATATATATTAAA
1 TATTAATATAAATATTAAA
17449 AATATTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAATATAAATATTAAATT
Found at i:18298 original size:8 final size:8
Alignment explanation
Indices: 18285--18312 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
18275 TAAAAATTAT
18285 ATAAAATG
1 ATAAAATG
18293 ATAAAATG
1 ATAAAATG
18301 ATAAAATG
1 ATAAAATG
18309 ATAA
1 ATAA
18313 TCATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (8 bp):
ATAAAATG
Found at i:18938 original size:21 final size:21
Alignment explanation
Indices: 18908--18947 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18898 TTACTATTAC
*
18908 TATTAATATAAATTTTAAATT
1 TATTAATATAAATATTAAATT
* *
18929 TATTATTATATATATTAAA
1 TATTAATATAAATATTAAA
18948 AATATTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAATATAAATATTAAATT
Found at i:19797 original size:8 final size:8
Alignment explanation
Indices: 19784--19811 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
19774 TAAAAATTAT
19784 ATAAAATG
1 ATAAAATG
19792 ATAAAATG
1 ATAAAATG
19800 ATAAAATG
1 ATAAAATG
19808 ATAA
1 ATAA
19812 TCATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (8 bp):
ATAAAATG
Found at i:19902 original size:10 final size:10
Alignment explanation
Indices: 19879--19912 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
19869 ATTTTAAAAT
19879 TTTATTATATA
1 TTTATTA-ATA
19890 TTTATTAATA
1 TTTATTAATA
19900 TTTATTAATA
1 TTTATTAATA
19910 TTT
1 TTT
19913 TACTATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTATTAATA
Found at i:19902 original size:22 final size:20
Alignment explanation
Indices: 19872--19912 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
19862 TAAAATAATT
19872 TTAAAATTTTATTATATATTTA
1 TTAAAA-TTTATTA-ATATTTA
*
19894 TTAATATTTATTAATATTT
1 TTAAAATTTATTAATATTT
19913 TACTATACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAAATTTATTAATATTTA
Found at i:24154 original size:51 final size:51
Alignment explanation
Indices: 24054--24161 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
24044 TAAAATATTC
* *
24054 ATAATAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGCTTCACCAAT
1 ATAA-AAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGATACACCAAT
* * * * *
24106 ATAAAAAAATTATTTTTTATGGGTGGAGGGAGAGAGTTG-GATGACACCAGT
1 ATAAAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGAT-ACACCAAT
24157 ATAAA
1 ATAAA
24162 TTTTTTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 2 0.04
51 42 0.88
52 4 0.08
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (51 bp):
ATAAAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGATACACCAAT
Found at i:42511 original size:46 final size:46
Alignment explanation
Indices: 42460--42558 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
42450 TTAAAAATTT
*
42460 AAATTAAGTCAAGCATTTGTTATAGTTTAATAAATTAATACAAACA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
* *
42506 AAATTAAGTCAAGCATTTTTTATAATTTAATAAATTAATTCAAACA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
42552 AAATTAA
1 AAATTAA
42559 CACAATCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (46 bp):
AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
Found at i:50217 original size:54 final size:54
Alignment explanation
Indices: 50131--50248 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
50121 TTAAGTAAAT
* * * *
50131 GAGTTACACGGCCTAGCACACGGCTTGTGACACGGCCATGTG-CCACAAGTTAGA
1 GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACC-CAACTTAGA
* * * * *
50185 GAGTTACACGGTCTGGCACATGACTTGCGACACGACCGTGTGACCCAACTTAGT
1 GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACCCAACTTAGA
50239 G-GTTACACGG
1 GAGTTACACGG
50249 GTGGAGGCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
53 9 0.17
54 43 0.80
55 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (54 bp):
GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACCCAACTTAGA
Found at i:51760 original size:16 final size:16
Alignment explanation
Indices: 51721--51761 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
51711 AATGAGCCAT
* *
51721 ATCCATGAATCCAGCC
1 ATCCATGTACCCAGCC
51737 ATCCATGTACCCAGCC
1 ATCCATGTACCCAGCC
*
51753 ATTCATGTA
1 ATCCATGTA
51762 TGCTCCCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.24
Consensus pattern (16 bp):
ATCCATGTACCCAGCC
Found at i:52903 original size:28 final size:28
Alignment explanation
Indices: 52842--52904 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
52832 AGATGAACTG
* *
52842 CACAATT--AATAACATAGATGTAATAA
1 CACAATTAAAATAAAATAGAGGTAATAA
** *
52868 CATGATTAAAATAAAATAGAGGTAGTAA
1 CACAATTAAAATAAAATAGAGGTAATAA
52896 CACAATTAA
1 CACAATTAA
52905 TAACATGTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (28 bp):
CACAATTAAAATAAAATAGAGGTAATAA
Found at i:54589 original size:10 final size:9
Alignment explanation
Indices: 54563--54587 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54553 CTAGTTAATT
54563 AAAAAAACA
1 AAAAAAACA
54572 AAAAAAACA
1 AAAAAAACA
54581 AAAAAAA
1 AAAAAAA
54588 ACTAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:56192 original size:256 final size:257
Alignment explanation
Indices: 55737--56249 Score: 1019
Period size: 256 Copynumber: 2.0 Consensus size: 257
55727 CAATTTTTAA
55737 CCAATTTTTAACAATAGAAATGAATAAAATTTTAAATAGAAAGTACCGATTTGCTTTTTGATCTA
1 CCAATTTTTAACAATAGAAATGAATAAAATTTTAAATAGAAAGTACCGATTTGCTTTTTGATCTA
55802 ACGTACAGGGACTATTTACTTATTTGTTAATAAATAGGACAAAATGCAATTTAGCTCCTAATATA
66 ACGTACAGGGACTATTTACTTATTTGTTAATAAATAGGACAAAATGCAATTTAGCTCCTAATATA
55867 GGAGCCTTCATGATACTTTTACCTAAAAACAACTTATTACATTAAAGAGCATCCTTCAATACCAA
131 GGAGCCTTCATGATACTTTTACCTAAAAACAACTTATTACATTAAAGAGCATCCTTCAATACCAA
55932 CAAATATTTAAATCAATTGTTTCATAACTTGTGAAATTTTTATTAATTA-TTAAAAATATTT
196 CAAATATTTAAATCAATTGTTTCATAACTTGTGAAATTTTTATTAATTATTTAAAAATATTT
55993 CCAATTTTTAACAATAGAAATGAATAAAATTTTAAATAGAAAGTACCGATTTGCTTTTTGATCTA
1 CCAATTTTTAACAATAGAAATGAATAAAATTTTAAATAGAAAGTACCGATTTGCTTTTTGATCTA
56058 ACGTACAGGGACTATTTACTTATTTGTTAATAAATAGGACAAAATGCAATTTAGCTCCTAATATA
66 ACGTACAGGGACTATTTACTTATTTGTTAATAAATAGGACAAAATGCAATTTAGCTCCTAATATA
56123 GGAGCCTTCATGATACTTTTACCTAAAAACAACTTATTACATTAAAGAGCATCCTTCAATACCAA
131 GGAGCCTTCATGATACTTTTACCTAAAAACAACTTATTACATTAAAGAGCATCCTTCAATACCAA
56188 CAAATATTTAAATCAATTGTTTCATAACTTGTGAAATTTTTATTAATTATTTAAAAATATTT
196 CAAATATTTAAATCAATTGTTTCATAACTTGTGAAATTTTTATTAATTATTTAAAAATATTT
56250 AAAATTAATA
Statistics
Matches: 256, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
256 244 0.95
257 12 0.05
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (257 bp):
CCAATTTTTAACAATAGAAATGAATAAAATTTTAAATAGAAAGTACCGATTTGCTTTTTGATCTA
ACGTACAGGGACTATTTACTTATTTGTTAATAAATAGGACAAAATGCAATTTAGCTCCTAATATA
GGAGCCTTCATGATACTTTTACCTAAAAACAACTTATTACATTAAAGAGCATCCTTCAATACCAA
CAAATATTTAAATCAATTGTTTCATAACTTGTGAAATTTTTATTAATTATTTAAAAATATTT
Found at i:56952 original size:28 final size:29
Alignment explanation
Indices: 56912--56971 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
56902 ATTTAATTTT
*
56912 AATTTTAATTAAATAAATAA-AAATAATTA
1 AATTCTAATTAAA-AAATAACAAATAATTA
*
56941 AATTCTAA-TAAAAAATAACATATAATTA
1 AATTCTAATTAAAAAATAACAAATAATTA
56969 AAT
1 AAT
56972 GAAGGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATTCTAATTAAAAAATAACAAATAATTA
Found at i:60870 original size:148 final size:147
Alignment explanation
Indices: 60616--60885 Score: 351
Period size: 148 Copynumber: 1.8 Consensus size: 147
60606 AGTCTATTCT
* * * *
60616 ACTGCAACCTCAGTGAGATAAGACTTGTAGCTTCAATAAAGTCTGATGCGATCTGCTCTACTGCA
1 ACTGCAACCTCAGGGAGATAAGACTCGTAACTTCAATAAAGTCTGATGCGATCCGCTCTACTGCA
* * * * * *
60681 ACTTCGGAGAGATAAGATCCATCCTTTTAATCTACTTCACTGCAACTTTAGGAAGATTGGACTAG
66 ACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGATTGGACTAG
60746 TAACTTCAATCTGCTCC
131 TAACTTCAATCTGCTCC
* * * * *
60763 ACTGCAACTTCAGGGAGATAAGGCTCGTAATTTCCAATAAAGTCTGATGTGATCCGTTCTACTGC
1 ACTGCAACCTCAGGGAGATAAGACTCGTAACTT-CAATAAAGTCTGATGCGATCCGCTCTACTGC
* * * * *
60828 AACTTCAGAGAGATAAGGTCTATCATTTTGACCCGCTCCACTGCAACTTCAGGGAGAT
65 AACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGAT
60886 AAGACTTATA
Statistics
Matches: 102, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
147 27 0.26
148 75 0.74
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (147 bp):
ACTGCAACCTCAGGGAGATAAGACTCGTAACTTCAATAAAGTCTGATGCGATCCGCTCTACTGCA
ACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGATTGGACTAG
TAACTTCAATCTGCTCC
Found at i:61413 original size:46 final size:46
Alignment explanation
Indices: 61346--61609 Score: 384
Period size: 46 Copynumber: 5.7 Consensus size: 46
61336 AACCTAGTCT
* *
61346 GCTGCCAAATACAGGAAGACAAGATCTACTATCCACGATCTACTCC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * * * *
61392 GCTGCCAAATATAGGAAGACAAAATCTGCTATCTTCAATCTACTTC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * * *
61438 GCTGCCAAATATAGGAAGACAATATCTGCTATCTTCGATCTACTCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * *
61484 GCTACCAAATACAGGAAGACAAGATATGCTATCTACGATCTACTCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
61530 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* *
61576 TCTGCCAAATACAGGAAGATAAGATCTGCTATCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCT
61610 TTAATCTGTT
Statistics
Matches: 197, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 197 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (46 bp):
GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
Found at i:62102 original size:24 final size:24
Alignment explanation
Indices: 62064--62121 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
62054 CGGATTGCTC
*
62064 CCACTGTAATCTTC-AGAGTTCAAT
1 CCACTGTAATATTCAAG-GTTCAAT
* *
62088 CCATTGTAATATTCAAGGTTCAGT
1 CCACTGTAATATTCAAGGTTCAAT
62112 CCACTGTAAT
1 CCACTGTAAT
62122 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (24 bp):
CCACTGTAATATTCAAGGTTCAAT
Found at i:62759 original size:108 final size:106
Alignment explanation
Indices: 62586--62894 Score: 388
Period size: 108 Copynumber: 2.9 Consensus size: 106
62576 GGAAAATGCT
* * * * * * *
62586 TGAAAAAGATTATCACAACGGGAAAGGTGAAATCTTATTGAGAGCAGAGCTCTGAACAAAGAAAT
1 TGAAAAGGATTATCACAA-TGGAAAGATGAAATTTTATTGAGAGCAAAGCTC-GAATAAATAAAT
* *
62651 TAATCAGGATAGCAAATTTTGCTAAGATTCAAAATGAATAAGA
64 TAATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGA
* *
62694 TGAAAAGGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGAGATGAATAAAT
1 TGAAAAGGATTATCACAATGGA-AAGATGAAATTTTATTGAGAGCAAAGCTCGA-ATAAATAAAT
* * * *
62759 TAACCAAGATAGCAACTTTTGCTAAGATACGAACTGAATAAGA
64 TAATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGA
** *
62802 TGAAAAGGATTATCACAATGGATAAGATGGGATTTTATTGAGAGCAATGCTCGAAATAAATAAA-
1 TGAAAAGGATTATCACAATGGA-AAGATGAAATTTTATTGAGAGCAAAGCTCG-AATAAATAAAT
62866 TAATCAAGATAGCAAA-TTTGCTAAGATAC
64 TAATCAAGATAGCAAATTTTGCTAAGATAC
62895 GATGAGAATA
Statistics
Matches: 175, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
106 13 0.07
107 19 0.11
108 142 0.81
109 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (106 bp):
TGAAAAGGATTATCACAATGGAAAGATGAAATTTTATTGAGAGCAAAGCTCGAATAAATAAATTA
ATCAAGATAGCAAATTTTGCTAAGATACAAAATGAATAAGA
Found at i:63239 original size:5 final size:5
Alignment explanation
Indices: 63220--63270 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
63210 GGCCTCTCCT
*
63220 TTTTC TTTT- TCTTC TTTTC TTTTC -TTT- TTTTC TTTTC TTTTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC --TTTTC TTTTC
63269 TT
1 TT
63271 CTTTTTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 9 0.23
5 25 0.64
7 5 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:63239 original size:8 final size:7
Alignment explanation
Indices: 63219--63277 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
63209 AGGCCTCTCC
63219 TTTTTC-
1 TTTTTCT
63225 TTTTTCT
1 TTTTTCT
63232 TCTTTTC-
1 T-TTTTCT
63239 -TTTTCT
1 TTTTTCT
63245 TTTTT-T
1 TTTTTCT
*
63251 CTTTTCT
1 TTTTTCT
63258 TTTTTCT
1 TTTTTCT
63265 TTTCTTCT
1 TTT-TTCT
63273 TTTTT
1 TTTTT
63278 TGTTTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
5 5 0.11
6 11 0.24
7 17 0.38
8 12 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:63244 original size:13 final size:13
Alignment explanation
Indices: 63220--63275 Score: 87
Period size: 13 Copynumber: 4.3 Consensus size: 13
63210 GGCCTCTCCT
63220 TTTTCTTTTTCTTC
1 TTTTC-TTTTCTTC
*
63234 TTTTCTTTTCTTT
1 TTTTCTTTTCTTC
63247 TTTTCTTTTCTT-
1 TTTTCTTTTCTTC
63259 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
63272 TTTT
1 TTTT
63276 TTTGTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
12 12 0.30
13 23 0.57
14 5 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:65611 original size:12 final size:12
Alignment explanation
Indices: 65580--65613 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65570 CTTTTCTAGT
65580 TGTTCTTGCATC
1 TGTTCTTGCATC
**
65592 TGGGCTTGCATC
1 TGTTCTTGCATC
65604 TGTTCTTGCA
1 TGTTCTTGCA
65614 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:65769 original size:19 final size:20
Alignment explanation
Indices: 65745--65791 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
65735 TGTGAAAATC
*
65745 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
65764 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
65784 -AATGCAAA
1 TAATGCAAA
65792 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:67835 original size:17 final size:17
Alignment explanation
Indices: 67802--67835 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
67792 TTGTGTTTTG
*
67802 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
67819 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
67836 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:68079 original size:21 final size:21
Alignment explanation
Indices: 68053--68115 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
68043 AGAATATATA
68053 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTGAATTT
68074 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTGAATTT
*
68095 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTGAATTT
68116 GATTTTATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTGAATTT
Found at i:68718 original size:41 final size:41
Alignment explanation
Indices: 68673--68775 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
68663 GGCTATGTGC
* * *
68673 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
68714 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
68755 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
68776 TACTGAATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:78596 original size:8 final size:8
Alignment explanation
Indices: 78578--78609 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
78568 TGGAACTCAG
78578 AGATT-AA
1 AGATTCAA
78585 AGATTCAA
1 AGATTCAA
78593 AGATTCAA
1 AGATTCAA
78601 AGATTCAA
1 AGATTCAA
78609 A
1 A
78610 CACCAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (8 bp):
AGATTCAA
Found at i:83611 original size:50 final size:50
Alignment explanation
Indices: 83552--83788 Score: 219
Period size: 50 Copynumber: 4.7 Consensus size: 50
83542 AAAGTGATGG
* *
83552 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ACGAAAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATGA
* * ** **
83602 TCACATGTGTAGTACTATGTGCAAGCTACTATGCATACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAAT-GA
** *** * *
83653 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTTGGATATTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATGA
* * * **
83704 T--CATGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGTTTGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATGA
* * *
83752 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA
83789 TCAAATAATA
Statistics
Matches: 145, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
48 3 0.02
49 33 0.23
50 68 0.47
51 40 0.28
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATGA
Found at i:83778 original size:99 final size:100
Alignment explanation
Indices: 83552--83788 Score: 266
Period size: 99 Copynumber: 2.4 Consensus size: 100
83542 AAAGTGATGG
* *
83552 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAACGAAAGATCACATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGAACGAAAGAT-ACATGTGTAGTAC
* *
83617 TATGTGCAAGCTACTATGCATACCGGATAGCTTCGA
65 TATGTGCAAGCTACTATGCATACCAGAAAGCTTCGA
* * *** ** * *
83653 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTTGGATATTAATGGT-CATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGA-ACGAAAGATACATGTGTAGTAC
* *
83717 TATGTGCAGGCTACTACGTG-A-ACCAGAAAG-TTTGA
65 TATGTGCAAGCTACTA--TGCATACCAGAAAGCTTCGA
*
83752 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
83789 TCAAATAATA
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
99 37 0.32
100 34 0.30
101 37 0.32
102 7 0.06
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGAACGAAAGATACATGTGTAGTACT
ATGTGCAAGCTACTATGCATACCAGAAAGCTTCGA
Found at i:110599 original size:20 final size:20
Alignment explanation
Indices: 110569--110619 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
110559 AATTTAACTT
110569 AGTCTAGCTCACTCGAGCTCA
1 AGTC-AGCTCACTCGAGCTCA
* *
110590 AGTCAGCTCATTTGAGCTCA
1 AGTCAGCTCACTCGAGCTCA
*
110610 ATTCAGCTCA
1 AGTCAGCTCA
110620 ATCTTAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTCAGCTCACTCGAGCTCA
Found at i:113190 original size:21 final size:19
Alignment explanation
Indices: 113118--113191 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
113108 GGGAAACGAA
113118 AAAAAGAAATGAAAGAAAAAG
1 AAAAAGAAATG--AGAAAAAG
*
113139 AACAAGAAAT-AG-AAAAG
1 AAAAAGAAATGAGAAAAAG
* *
113156 AAAATGAGAGTGAGAAAAAG
1 AAAAAGA-AATGAGAAAAAG
113176 AAAAAAGAAATTGAGA
1 -AAAAAGAAA-TGAGA
113192 TTGAAAAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 2 0.05
20 6 0.14
21 20 0.48
ACGTcount: A:0.69, C:0.01, G:0.22, T:0.08
Consensus pattern (19 bp):
AAAAAGAAATGAGAAAAAG
Found at i:117279 original size:34 final size:34
Alignment explanation
Indices: 117236--117303 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
117226 AAATCTTGTG
*
117236 TTAGCTTGAAATGATGAAAACTGTTAATCGTGAC
1 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
117270 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
1 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
117304 CCAATATCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (34 bp):
TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
Found at i:119112 original size:20 final size:20
Alignment explanation
Indices: 119087--119128 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
119077 AATATAATTG
*
119087 TTATTTGCTTCT-ATAACATT
1 TTATTTACTTCTCA-AACATT
119107 TTATTTACTTCTCAAACATT
1 TTATTTACTTCTCAAACATT
119127 TT
1 TT
119129 CATTCCCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTTACTTCTCAAACATT
Found at i:123535 original size:14 final size:16
Alignment explanation
Indices: 123516--123548 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
123506 GGCAACCCAT
123516 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
123530 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
123546 ATT
1 ATT
123549 AAGTTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:126779 original size:18 final size:18
Alignment explanation
Indices: 126735--126779 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
126725 AAATTGCTAG
126735 TAGTT-AAATTAATTAAT
1 TAGTTAAAATTAATTAAT
*
126752 TAGTTTAAATTAATTAATT
1 TAGTTAAAATTAATTAA-T
126771 TA-TTAAAAT
1 TAGTTAAAAT
126780 CTGGACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 17 0.68
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAGTTAAAATTAATTAAT
Found at i:142114 original size:20 final size:20
Alignment explanation
Indices: 142089--142139 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
142079 CATTTTTGGT
*
142089 TCATTCGAGCTCAAGTTAGC
1 TCATTCGAGCTCAAGTCAGC
142109 TCATTCGAGCTCAAGTCAGC
1 TCATTCGAGCTCAAGTCAGC
*
142129 ACATT-GAGCTC
1 TCATTCGAGCTC
142140 GTTATTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCATTCGAGCTCAAGTCAGC
Found at i:144707 original size:11 final size:11
Alignment explanation
Indices: 144691--144719 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
144681 CGAGATTGTA
144691 AAAAAAATTCG
1 AAAAAAATTCG
144702 AAAAAAATTCG
1 AAAAAAATTCG
144713 AAAAAAA
1 AAAAAAA
144720 AGTTTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:161387 original size:20 final size:22
Alignment explanation
Indices: 161362--161411 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
161352 GAACATGGAC
*
161362 TAAACAGCAT-GT-AGACAAAT
1 TAAACAACATGGTAAGACAAAT
*
161382 TAAACAATATGGTAAGACAAAT
1 TAAACAACATGGTAAGACAAAT
161404 TAAA-AACA
1 TAAACAACA
161412 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (22 bp):
TAAACAACATGGTAAGACAAAT
Found at i:163172 original size:14 final size:14
Alignment explanation
Indices: 163153--163188 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
163143 TCAAGTTGTG
163153 AAAAAAAATTTGAA
1 AAAAAAAATTTGAA
*
163167 AAAAAAATTTTGAA
1 AAAAAAAATTTGAA
163181 AAAAAAAA
1 AAAAAAAA
163189 GAGAGCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:172829 original size:17 final size:17
Alignment explanation
Indices: 172807--172839 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
172797 AAAGAAAGAA
172807 AAAAATTGAAAAAAAAT
1 AAAAATTGAAAAAAAAT
172824 AAAAATTGAAAAAAAA
1 AAAAATTGAAAAAAAA
172840 GAGGATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAATTGAAAAAAAAT
Found at i:173864 original size:20 final size:22
Alignment explanation
Indices: 173834--173877 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
173824 AATCTTGAAT
*
173834 GAAATTGAGAGAAGAA-AAAAA
1 GAAATTGAGAGAAAAATAAAAA
173855 GAAA-TGAGAGAAAAATAAAAA
1 GAAATTGAGAGAAAAATAAAAA
173876 GA
1 GA
173878 TGAAAATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (22 bp):
GAAATTGAGAGAAAAATAAAAA
Found at i:173933 original size:12 final size:12
Alignment explanation
Indices: 173916--173989 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
173906 AGTGAAAAGC
173916 AAAAAGAGATTG
1 AAAAAGAGATTG
*
173928 AAAAAGAAATTG
1 AAAAAGAGATTG
173940 AAAAAGA-A--G
1 AAAAAGAGATTG
*
173949 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
173964 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
173976 AAAGAGAGCTTG
1 AAAAAGAGATTG
173988 AA
1 AA
173990 CAGAAATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:180501 original size:18 final size:18
Alignment explanation
Indices: 180461--180501 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
180451 GCTGCTAGTT
* *
180461 AAATTAATCAATTAGTTT
1 AAATTAATCAATTAATTA
*
180479 TAATTAATCAATTAATTA
1 AAATTAATCAATTAATTA
180497 AAATT
1 AAATT
180502 TGGACATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
AAATTAATCAATTAATTA
Found at i:198429 original size:22 final size:23
Alignment explanation
Indices: 198401--198449 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
198391 GCAGTTTTGG
198401 TAATATTCTTGTCAAAAAA-ATA
1 TAATATTCTTGTCAAAAAATATA
198423 TAATATTCTTGTCAAAAAATATA
1 TAATATTCTTGTCAAAAAATATA
198446 TAAT
1 TAAT
198450 TATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATATTCTTGTCAAAAAATATA
Found at i:211493 original size:20 final size:20
Alignment explanation
Indices: 211468--211514 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
211458 AGCTCATTTC
*
211468 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
211488 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
211508 CAGCTCA
1 CAGCTCA
211515 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:211517 original size:10 final size:10
Alignment explanation
Indices: 211458--211517 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
211448 AGCTCTGTTT
*
211458 AGCTCATTTCC
1 AGCTCAATT-C
* *
211469 AGCTCACTTG
1 AGCTCAATTC
*
211479 AGCTCAAGTC
1 AGCTCAATTC
211489 AGCTC-ATTC
1 AGCTCAATTC
*
211498 GAGATCAATTC
1 -AGCTCAATTC
211509 AGCTCAATT
1 AGCTCAATT
211518 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:212725 original size:13 final size:14
Alignment explanation
Indices: 212709--212738 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
212699 AAAAAAAATC
212709 AAAATTC-AAAAAA
1 AAAATTCGAAAAAA
212722 AAAATTCGAAAAAA
1 AAAATTCGAAAAAA
212736 AAA
1 AAA
212739 GAAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAATTCGAAAAAA
Found at i:212759 original size:40 final size:40
Alignment explanation
Indices: 212715--212790 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
212705 AATCAAAATT
*
212715 CAAAAAAAAAATTCGAAAAAAAAAG-A-AAAAAAGAAGTGAG
1 CAAAAAAAAAA-GC-AAAAAAAAAGAAGAAAAAAGAAGTGAG
*
212755 CAAAAAAAAGAGCAAAAAAAAAGAAGAAAAAAGAAG
1 CAAAAAAAAAAGCAAAAAAAAAGAAGAAAAAAGAAG
212791 AAGTGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 10 0.31
39 2 0.06
40 20 0.62
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (40 bp):
CAAAAAAAAAAGCAAAAAAAAAGAAGAAAAAAGAAGTGAG
Found at i:212793 original size:13 final size:12
Alignment explanation
Indices: 212729--212791 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
212719 AAAAAAATTC
212729 GAAAAAAAAAGA
1 GAAAAAAAAAGA
*
212741 -AAAAAAGAAGTGA
1 GAAAAAA-AA-AGA
*
212754 GCAAAAAAAAGA
1 GAAAAAAAAAGA
212766 GCAAAAAAAAAGAA
1 G-AAAAAAAAAG-A
*
212780 GAAAAAAGAAGA
1 GAAAAAAAAAGA
212792 AGTGAAAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 6 0.15
12 6 0.15
13 22 0.54
14 7 0.17
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:223887 original size:20 final size:19
Alignment explanation
Indices: 223851--223911 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
223841 TATAAACGCA
*
223851 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
223871 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
223892 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
223911 A
1 A
223912 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:231003 original size:20 final size:20
Alignment explanation
Indices: 230952--231003 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
230942 GAGCTTAAAA
*
230952 TGAGCTGATTGACCTAAGAG
1 TGAGCTGAATGACCTAAGAG
*
230972 TGAGCTCG-ATGAGCTAA-AG
1 TGAGCT-GAATGACCTAAGAG
230991 TTGAGCTGAATGA
1 -TGAGCTGAATGA
231004 ACTTGAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (20 bp):
TGAGCTGAATGACCTAAGAG
Found at i:234524 original size:17 final size:17
Alignment explanation
Indices: 234504--234553 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
234494 AAAAGAGTCC
*
234504 GCCAAACCCTAGAGTTT
1 GCCAAACCTTAGAGTTT
234521 GCCAAACCTTAGAGTTT
1 GCCAAACCTTAGAGTTT
*
234538 TCCAAACCTTAGAGTT
1 GCCAAACCTTAGAGTT
234554 CTCCAGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (17 bp):
GCCAAACCTTAGAGTTT
Found at i:242353 original size:17 final size:17
Alignment explanation
Indices: 242318--242365 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
242308 ATTGTAGCTT
* *
242318 AGAAAAAAAATTGGAAAA
1 AGAAAAAAAAAT-CAAAA
*
242336 AAAATAAAAAAATCAAAA
1 AGAA-AAAAAAATCAAAA
242354 AGAAAAAAAAAT
1 AGAAAAAAAAAT
242366 TGGATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.10
Consensus pattern (17 bp):
AGAAAAAAAAATCAAAA
Found at i:242493 original size:17 final size:17
Alignment explanation
Indices: 242473--242527 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
242463 AAAAGAGTCC
242473 GCCAAAGCC-TAGAGTTT
1 GCCAAA-CCTTAGAGTTT
242490 GCCAAACCTTAGAGTTT
1 GCCAAACCTTAGAGTTT
* *
242507 TCCAAACCTTAGAGTTC
1 GCCAAACCTTAGAGTTT
242524 GCCA
1 GCCA
242528 GATCATCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 2 0.06
17 32 0.94
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (17 bp):
GCCAAACCTTAGAGTTT
Found at i:261088 original size:17 final size:16
Alignment explanation
Indices: 261074--261111 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
261064 TCGAAAAAGT
261074 GAAAAAATAGAAAAATA
1 GAAAAAA-AGAAAAATA
261091 CGAAAAAAAGAAAAATA
1 -GAAAAAAAGAAAAATA
261108 -AAAA
1 GAAAA
261112 TATTATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (16 bp):
GAAAAAAAGAAAAATA
Found at i:263529 original size:18 final size:19
Alignment explanation
Indices: 263500--263535 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
263490 TGATATGGCC
*
263500 AAAATCACTTTTTCACTTA
1 AAAATCACTTTTACACTTA
263519 AAAATCA-TTTTACACTT
1 AAAATCACTTTTACACTT
263536 TGGCATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATCACTTTTACACTTA
Found at i:279203 original size:21 final size:19
Alignment explanation
Indices: 279160--279204 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
279150 GAGCTCAAAT
* *
279160 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
279179 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
279200 GAGCT
1 GAGCT
279205 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:308186 original size:21 final size:22
Alignment explanation
Indices: 308161--308203 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
308151 AGCCAAACAA
*
308161 ATGGCCA-TTTAACCAAAATAC
1 ATGGCCACATTAACCAAAATAC
*
308182 ATGGCCACATTAGCCAAAATAC
1 ATGGCCACATTAACCAAAATAC
308204 CTATGCATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (22 bp):
ATGGCCACATTAACCAAAATAC
Found at i:308706 original size:25 final size:25
Alignment explanation
Indices: 308637--308723 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
308627 TTCTATATGA
* * *
308637 ATGCTCACACGAGCTATAAATTGGT
1 ATGCTCTCACGAGTTATAAATCGGT
* *
308662 ATGCTCTCACAAGTAATAAATCGGT
1 ATGCTCTCACGAGTTATAAATCGGT
* * *
308687 TTGCTCTCACGAGTTGTAAA-CAGT
1 ATGCTCTCACGAGTTATAAATCGGT
308711 ATGCTCTCACGAG
1 ATGCTCTCACGAG
308724 CTGTGGGTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 15 0.29
25 36 0.71
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
ATGCTCTCACGAGTTATAAATCGGT
Found at i:312854 original size:30 final size:30
Alignment explanation
Indices: 312802--312858 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
312792 CCCTCTGTGC
* **
312802 CGCATTTTCTAGTGCAGTAAACCCTAGCAT
1 CGCATTTTCTAATGCAAAAAACCCTAGCAT
*
312832 CGCATTTTCTAATGTAAAAAACCCTAG
1 CGCATTTTCTAATGCAAAAAACCCTAG
312859 TGCCGTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (30 bp):
CGCATTTTCTAATGCAAAAAACCCTAGCAT
Found at i:316572 original size:16 final size:16
Alignment explanation
Indices: 316517--316575 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
316507 GCTTTTACTT
316517 GATTTCTTTCTTCACTC
1 GATTTCTTTC-TCACTC
316534 G-TTTCTTT-TGCAGACTC
1 GATTTCTTTCT-C--ACTC
**
316551 TTTTTCTTTCTCACTC
1 GATTTCTTTCTCACTC
316567 GATTTCTTT
1 GATTTCTTT
316576 TCAAACTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 18 0.53
17 5 0.15
18 8 0.24
19 1 0.03
ACGTcount: A:0.10, C:0.25, G:0.08, T:0.56
Consensus pattern (16 bp):
GATTTCTTTCTCACTC
Found at i:316584 original size:33 final size:34
Alignment explanation
Indices: 316519--316592 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
316509 TTTTACTTGA
* *
316519 TTTCTTTCTTCACTCGTTTCTTTTGCAGACTCTT
1 TTTCTTTCTTCACTCGTTTCTTTTGCAAACTCTC
316553 TTTCTTTC-TCACTCGATTTCTTTT-CAAACTCTC
1 TTTCTTTCTTCACTCG-TTTCTTTTGCAAACTCTC
316586 TTTCTTT
1 TTTCTTT
316593 TTCTTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTCTTTCTTCACTCGTTTCTTTTGCAAACTCTC
Found at i:316601 original size:12 final size:12
Alignment explanation
Indices: 316586--316634 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
316576 TCAAACTCTC
*
316586 TTTCTTTTTCTT
1 TTTCATTTTCTT
316598 TTTC-TTTTC--
1 TTTCATTTTCTT
*
316607 TTTCAATTTCTT
1 TTTCATTTTCTT
*
316619 TTTCATTTTCAT
1 TTTCATTTTCTT
316631 TTTC
1 TTTC
316635 TCGCTCGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 4 0.13
10 4 0.13
11 5 0.16
12 18 0.58
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:316611 original size:33 final size:34
Alignment explanation
Indices: 316569--316635 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
316559 TCTCACTCGA
* *
316569 TTTCTTTTCAAACTCTCTTTCTTTTTCTTTTTCT
1 TTTCTTTTCAAACTCTCTTTCATTTTCATTTTCT
** *
316603 TTTC-TTTCAATTTCTTTTTCATTTTCATTTTCT
1 TTTCTTTTCAAACTCTCTTTCATTTTCATTTTCT
316636 CGCTCGCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (34 bp):
TTTCTTTTCAAACTCTCTTTCATTTTCATTTTCT
Found at i:320649 original size:27 final size:27
Alignment explanation
Indices: 320611--320678 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
320601 CATAGACCAT
*
320611 ATAGTCAATTTATAACATAGGGGAATA
1 ATAGTCATTTTATAACATAGGGGAATA
* * * *
320638 ATAGTCATTTTATCACGTGGGGGCATA
1 ATAGTCATTTTATAACATAGGGGAATA
*
320665 ACAGTCATTTTATA
1 ATAGTCATTTTATA
320679 TCAGTTTTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (27 bp):
ATAGTCATTTTATAACATAGGGGAATA
Found at i:338764 original size:26 final size:26
Alignment explanation
Indices: 338742--338792 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
338732 TCAATTTATA
338742 ACATAGGGGCATAACAATCATTTTAC
1 ACATAGGGGCATAACAATCATTTTAC
* * *
338768 ACGTGGGGGCATAACAGTCATTTTA
1 ACATAGGGGCATAACAATCATTTTA
338793 TATCAGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (26 bp):
ACATAGGGGCATAACAATCATTTTAC
Found at i:340643 original size:16 final size:17
Alignment explanation
Indices: 340624--340656 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
340614 ATAGTTAAAC
340624 AAATT-GGAAATAAATT
1 AAATTGGGAAATAAATT
340640 AAATTGGGAAATAAATT
1 AAATTGGGAAATAAATT
340657 TGGATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (17 bp):
AAATTGGGAAATAAATT
Found at i:342238 original size:4 final size:4
Alignment explanation
Indices: 342229--342277 Score: 71
Period size: 4 Copynumber: 12.0 Consensus size: 4
342219 AACTAGAGCT
* *
342229 TTTA TTTA TTTA TTTA TTCA TTCA TTTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
342278 CAAGCAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 39 0.93
5 3 0.07
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:342257 original size:21 final size:21
Alignment explanation
Indices: 342233--342276 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
342223 AGAGCTTTTA
342233 TTTATTTATTTATTCATTCAT
1 TTTATTTATTTATTCATTCAT
* *
342254 TTTATTTATTTATTTATTTAT
1 TTTATTTATTTATTCATTCAT
342275 TT
1 TT
342277 ACAAGCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATTTATTTATTCATTCAT
Found at i:342852 original size:16 final size:17
Alignment explanation
Indices: 342832--342892 Score: 83
Period size: 16 Copynumber: 3.8 Consensus size: 17
342822 GTTTTGTTCA
342832 CTGTAATGGAATATGA-
1 CTGTAATGGAATATGAG
*
342848 CTGTAATTGAATA-GAG
1 CTGTAATGGAATATGAG
342864 CTGTAATGGAATAT-AG
1 CTGTAATGGAATATGAG
*
342880 TTGTAATGGAATA
1 CTGTAATGGAATA
342893 AAGTTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 2 0.05
16 38 0.95
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (17 bp):
CTGTAATGGAATATGAG
Found at i:342885 original size:32 final size:32
Alignment explanation
Indices: 342832--342902 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
342822 GTTTTGTTCA
* *
342832 CTGTAATGGAATATGACTGTAATTGAATAGAG
1 CTGTAATGGAATATGACTGTAATGGAATAAAG
*
342864 CTGTAATGGAATAT-AGTTGTAATGGAATAAAG
1 CTGTAATGGAATATGA-CTGTAATGGAATAAAG
*
342896 TTGTAAT
1 CTGTAAT
342903 CAGTAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (32 bp):
CTGTAATGGAATATGACTGTAATGGAATAAAG
Found at i:342897 original size:16 final size:16
Alignment explanation
Indices: 342849--342902 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
342839 GGAATATGAC
* * *
342849 TGTAATTGAATAGAGC
1 TGTAATGGAATAAAGT
*
342865 TGTAATGGAATATAGT
1 TGTAATGGAATAAAGT
342881 TGTAATGGAATAAAGT
1 TGTAATGGAATAAAGT
342897 TGTAAT
1 TGTAAT
342903 CAGTAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (16 bp):
TGTAATGGAATAAAGT
Found at i:345925 original size:13 final size:13
Alignment explanation
Indices: 345902--345970 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
345892 GACGAGCGAG
345902 CTGCGAGCTCAGT
1 CTGCGAGCTCAGT
* *
345915 CCGCGATCTCA-T
1 CTGCGAGCTCAGT
345927 CATGCGAGCTCAGT
1 C-TGCGAGCTCAGT
* *
345941 CTGCGATCTC-TT
1 CTGCGAGCTCAGT
345953 CATGCGAGCTCAGT
1 C-TGCGAGCTCAGT
345967 CTGC
1 CTGC
345971 AACCTCGTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.26
Consensus pattern (13 bp):
CTGCGAGCTCAGT
Found at i:345968 original size:26 final size:26
Alignment explanation
Indices: 345903--345970 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
345893 ACGAGCGAGC
*
345903 TGCGAGCTCAGTCCGCGATCTCATCA
1 TGCGAGCTCAGTCTGCGATCTCATCA
*
345929 TGCGAGCTCAGTCTGCGATCTCTTCA
1 TGCGAGCTCAGTCTGCGATCTCATCA
345955 TGCGAGCTCAGTCTGC
1 TGCGAGCTCAGTCTGC
345971 AACCTCGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.16, C:0.32, G:0.25, T:0.26
Consensus pattern (26 bp):
TGCGAGCTCAGTCTGCGATCTCATCA
Found at i:346006 original size:48 final size:48
Alignment explanation
Indices: 345944--346039 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
345934 GCTCAGTCTG
* *
345944 CGATCTCTTCATGCGAGCTCAGTCTGCAACCTCGTGTGTTTGGGCCAA
1 CGATCTCTTCATGCGAGCTCAGTCTGCAACCACGTGGGTTTGGGCCAA
* * **
345992 CGATCT-TATCATGCGAGTTCAGTTTGCGGCCACGTGGGTTTGGGCCAA
1 CGATCTCT-TCATGCGAGCTCAGTCTGCAACCACGTGGGTTTGGGCCAA
346040 TGTCGGCCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (48 bp):
CGATCTCTTCATGCGAGCTCAGTCTGCAACCACGTGGGTTTGGGCCAA
Found at i:350928 original size:12 final size:12
Alignment explanation
Indices: 350889--350932 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
350879 CTTAACTCTC
*
350889 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
350901 ATTTTAAAAATA
1 TTTTTTAAAATA
350913 TTTTTTAAAAT-
1 TTTTTTAAAATA
350924 TTTTTTAAA
1 TTTTTTAAA
350933 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:352046 original size:7 final size:7
Alignment explanation
Indices: 352034--352058 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
352024 AGTTGATTGA
352034 TATTTAG
1 TATTTAG
352041 TATTTAG
1 TATTTAG
352048 TATTTAG
1 TATTTAG
352055 TATT
1 TATT
352059 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:353583 original size:18 final size:19
Alignment explanation
Indices: 353552--353588 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
353542 AAATATAAAT
353552 TTTTGAAATTTTTG-AATA
1 TTTTGAAATTTTTGTAATA
353570 TTTTG-AATATTTTGTAATA
1 TTTTGAAAT-TTTTGTAATA
353589 CCCTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTGAAATTTTTGTAATA
Found at i:357740 original size:123 final size:123
Alignment explanation
Indices: 357446--357814 Score: 612
Period size: 123 Copynumber: 3.0 Consensus size: 123
357436 CCCAAACATG
* * * * *
357446 CTACTGTAGCAAAAGCGCCTCCACGAGGGCGTGATTTTCATAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTG
357511 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-TTATTTCTTCCATGAC
357571 CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
357636 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATGATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
357694 CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *
357759 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAACTCAAAATTATTTCTTCCA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCCA
357815 GGATCTAAAA
Statistics
Matches: 230, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
123 114 0.50
124 71 0.31
125 45 0.20
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACTAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
Found at i:359134 original size:22 final size:22
Alignment explanation
Indices: 359109--359151 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
359099 TGTGACAGAT
359109 AGAAGTAATATAATGGTGGTAG
1 AGAAGTAATATAATGGTGGTAG
359131 AGAAGTAATATAATGGTGGTA
1 AGAAGTAATATAATGGTGGTA
359152 AAATGATGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (22 bp):
AGAAGTAATATAATGGTGGTAG
Found at i:380825 original size:24 final size:24
Alignment explanation
Indices: 380777--380828 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
380767 ACATGTAACA
* *
380777 CCCACTCAACCTGCTACCGAGGAG
1 CCCACTCAAACTGCTACCGAAGAG
* *
380801 CCCACTCAAACTGCTGCTGAAGAG
1 CCCACTCAAACTGCTACCGAAGAG
380825 CCCA
1 CCCA
380829 AAATGATGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.40, G:0.19, T:0.13
Consensus pattern (24 bp):
CCCACTCAAACTGCTACCGAAGAG
Found at i:385976 original size:20 final size:19
Alignment explanation
Indices: 385951--386001 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
385941 TATGAACCAC
*
385951 TCCATTTACTTCCTTATCAT
1 TCCATTTACTTACTTA-CAT
*
385971 TCCATTTATTTACTTACAT
1 TCCATTTACTTACTTACAT
* *
385990 TTCATATACTTA
1 TCCATTTACTTA
386002 GCACAAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (19 bp):
TCCATTTACTTACTTACAT
Found at i:388030 original size:49 final size:50
Alignment explanation
Indices: 387971--388093 Score: 194
Period size: 49 Copynumber: 2.5 Consensus size: 50
387961 TCATTCGATA
*
387971 CACGTAGTAGCCTTCACATAGTACAACACACGAGATC-AGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACAACACACGAGATCAAGTTTTACAGCT
* * *
388020 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACAACACACGAGATCAAGTTTTACAGCT
*
388070 GACGTAGTAGCCTTCACATAGTAC
1 CACGTAGTAGCCTTCACATAGTAC
388094 TACATACGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 35 0.51
50 33 0.49
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACAACACACGAGATCAAGTTTTACAGCT
Found at i:388133 original size:51 final size:51
Alignment explanation
Indices: 387969--388307 Score: 282
Period size: 51 Copynumber: 6.7 Consensus size: 51
387959 TATCATTCGA
* * * * *
387969 TACACGTAGTAGCCTTCACATAGTACAACACACGAGATC--AGTTTTACAG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCCGG
* * *
388018 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCCGG
* *
388068 CT-GACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGTTTTCCGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCCGG
* * * * * * * * *
388119 TATC-CATAGTAGCCTTCACTTAGTACCATACATGTAACCATAGTTTACCGA
1 TA-CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCCGG
* * **
388170 TACACGTAGTAGCTTTCACACAGTACTACACACGTG-CTCAAA-ACTTCTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGTTTTC-CGG
* * * * *
388221 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT-CGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCCGG
* * *
388272 TAAACGTAGTAGCCTTCACACAGTACTACATACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
388308 TTCATCGATA
Statistics
Matches: 232, Mismatches: 47, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
49 36 0.16
50 48 0.21
51 144 0.62
52 3 0.01
53 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (51 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCCGG
Found at i:388199 original size:102 final size:102
Alignment explanation
Indices: 388071--388307 Score: 320
Period size: 102 Copynumber: 2.3 Consensus size: 102
388061 TTTACGGCTG
* * *
388071 ACGTAGTAGCCTTCACATAGTACTACATACGTGAC-C-AAAGTTTTCCGGTATC-CATAGTAGCC
1 ACGTAGTAGCCTTCACACAGTACTACATACGTG-CTCAAAACTTCT-CGGTA-CACATAGTAGCC
* *
388133 TTCACTTAGTACCATACATGTAACCA-TAGTTTACCGATAC
63 TTCACTTAGTACCACACATGTAACCATTA-TTTACCGATAA
* *
388173 ACGTAGTAGCTTTCACACAGTACTACACACGTGCTCAAAACTTCTCGGTACACATAGTAGCCTTC
1 ACGTAGTAGCCTTCACACAGTACTACATACGTGCTCAAAACTTCTCGGTACACATAGTAGCCTTC
* * *
388238 ACTTAGTACTACACATGTGACCATTATTTATCGATAA
66 ACTTAGTACCACACATGTAACCATTATTTACCGATAA
388275 ACGTAGTAGCCTTCACACAGTACTACATACGTG
1 ACGTAGTAGCCTTCACACAGTACTACATACGTG
388308 TTCATCGATA
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
101 2 0.02
102 109 0.92
103 8 0.07
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
ACGTAGTAGCCTTCACACAGTACTACATACGTGCTCAAAACTTCTCGGTACACATAGTAGCCTTC
ACTTAGTACCACACATGTAACCATTATTTACCGATAA
Found at i:388297 original size:153 final size:152
Alignment explanation
Indices: 388020--388297 Score: 330
Period size: 153 Copynumber: 1.8 Consensus size: 152
388010 TTTTACAGTT
* * * * *
388020 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCTGACGTAGTAGCCTTC
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGATCAACTTCTACGGCTCACATAGTAGCCTTC
* * ** **
388085 ACATAGTACTACATACGTGACCAAAGTTTTCCGGTATCCATAGTAGCCTTCACTTAGTACCATAC
66 ACATAGTACTACACACGTGACCAAAGTTTTCCGATAAACATAGTAGCCTTCACACAGTACCATAC
388150 ATGTAACCATAGTTTACCGATA
131 ATGTAACCATAGTTTACCGATA
* *
388172 CACGTAGTAGCTTTCACACAGTACTACACACGTGCTCAAAACTTCT-CGG-TACACATAGTAGCC
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGATC--AACTTCTACGGCT-CACATAGTAGCC
* * * *
388235 TTCACTTAGTACTACACATGTGACCATTA-TTTAT-CGATAAACGTAGTAGCCTTCACACAGTAC
63 TTCACATAGTACTACACACGTGACCA-AAGTTT-TCCGATAAACATAGTAGCCTTCACACAGTAC
388298 TACATACGTG
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
152 35 0.34
153 62 0.60
154 7 0.07
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (152 bp):
CACGTAGTAGCCTTCACACAGTACTACACACGTGATCAACTTCTACGGCTCACATAGTAGCCTTC
ACATAGTACTACACACGTGACCAAAGTTTTCCGATAAACATAGTAGCCTTCACACAGTACCATAC
ATGTAACCATAGTTTACCGATA
Found at i:389675 original size:16 final size:17
Alignment explanation
Indices: 389652--389696 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
389642 ATTATACTAG
389652 AATAAAATAAAAATGA-
1 AATAAAATAAAAATGAT
* *
389668 AATGAAATGAAAATGAT
1 AATAAAATAAAAATGAT
389685 AATAAAATAAAA
1 AATAAAATAAAA
389697 GAAACAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (17 bp):
AATAAAATAAAAATGAT
Found at i:390145 original size:36 final size:34
Alignment explanation
Indices: 390105--390200 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 34
390095 GGTTTACCCG
*
390105 ACTAGCGCTGGGCGCAACTCATTGTTGGTACATCCA
1 ACTAGCGCTGGGCGCAA-TCATTGTCGGT-CATCCA
* * * * * *
390141 ACTAGTGCAGTGCACAATTATTGTCGGTTATCCA
1 ACTAGCGCTGGGCGCAATCATTGTCGGTCATCCA
* *
390175 ACTAGCGCTGGGTGCAATCTTTGTCG
1 ACTAGCGCTGGGCGCAATCATTGTCG
390201 ATTTATTCGA
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
34 24 0.52
35 9 0.20
36 13 0.28
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (34 bp):
ACTAGCGCTGGGCGCAATCATTGTCGGTCATCCA
Found at i:390199 original size:34 final size:34
Alignment explanation
Indices: 390090--390200 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
390080 AGAATTTAAA
* * *
390090 TTGTCGGTTTACCCGACTAGCGCTGGGCGCAACTCA
1 TTGTCGG-TTATCCAACTAGCGCTGGGCGCAA-TCT
* * * * * *
390126 TTGTTGGTACATCCAACTAGTGCAGTGCACAAT-T
1 TTGTCGGT-TATCCAACTAGCGCTGGGCGCAATCT
*
390160 ATTGTCGGTTATCCAACTAGCGCTGGGTGCAATCT
1 -TTGTCGGTTATCCAACTAGCGCTGGGCGCAATCT
390195 TTGTCG
1 TTGTCG
390201 ATTTATTCGA
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
34 24 0.43
35 10 0.18
36 22 0.39
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (34 bp):
TTGTCGGTTATCCAACTAGCGCTGGGCGCAATCT
Found at i:390262 original size:75 final size:73
Alignment explanation
Indices: 390175--390374 Score: 220
Period size: 75 Copynumber: 2.7 Consensus size: 73
390165 CGGTTATCCA
390175 ACTAGCGCTGGGTGCAATCTTTGTCGATTTATTCGACTAGTGCTGGGCACACCATAATATTTATC
1 ACTAGCGCTGGGTGCAA-CTTTGTC-ATTTATTCGACTAGTGCTGGGCACACCATAATATTTATC
**
390240 GGTTTATTAG
64 GGTTTACCAG
* * * * *
390250 ACTAGCGCTGGGTGTAACCTTTGTCAGTTTATTTGACTAGTGTTGGGCACACCATTATATTTGTC
1 ACTAGCGCTGGGTGCAA-CTTTGTCA-TTTATTCGACTAGTGCTGGGCACACCATAATATTTATC
390315 GGTTTACCAG
64 GGTTTACCAG
* * * * * **
390325 GCTAGTGCTAGGCGCAACTTTTATCAATTCGTTCGACTAGTGCTGGGCAC
1 ACTAGCGCTGGGTGCAAC-TTTGTC-ATTTATTCGACTAGTGCTGGGCAC
390375 GTCTATCGTC
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
74 2 0.02
75 101 0.97
76 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (73 bp):
ACTAGCGCTGGGTGCAACTTTGTCATTTATTCGACTAGTGCTGGGCACACCATAATATTTATCGG
TTTACCAG
Found at i:391050 original size:8 final size:8
Alignment explanation
Indices: 391039--391063 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
391029 TATATATATA
391039 TATTTGGT
1 TATTTGGT
391047 TATTTGGT
1 TATTTGGT
391055 TATTTGGT
1 TATTTGGT
391063 T
1 T
391064 GATGTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (8 bp):
TATTTGGT
Found at i:393438 original size:17 final size:18
Alignment explanation
Indices: 393413--393446 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
393403 TTTAATTTCT
393413 ATTTCTTATTTATTTATG
1 ATTTCTTATTTATTTATG
*
393431 ATTT-TTATTTTTTTAT
1 ATTTCTTATTTATTTAT
393447 TCTCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTCTTATTTATTTATG
Found at i:393478 original size:22 final size:22
Alignment explanation
Indices: 393438--393526 Score: 72
Period size: 23 Copynumber: 4.0 Consensus size: 22
393428 ATGATTTTTA
* *
393438 TTTTTTTATTCTCAAATTTCTTC
1 TTTTATTATTTTC-AATTTCTTC
*
393461 TTTTATTATTTTCGATTTCTT-
1 TTTTATTATTTTCAATTTCTTC
* ** **
393482 TATTACAAATTTTTTTATTTCTTC
1 TTTTA-TTA-TTTTCAATTTCTTC
393506 TTTTATTATTTTCAATTTCTT
1 TTTTATTATTTTCAATTTCTT
393527 TATTACAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
21 4 0.08
22 19 0.38
23 23 0.46
24 4 0.08
ACGTcount: A:0.19, C:0.12, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTTCAATTTCTTC
Found at i:393504 original size:45 final size:45
Alignment explanation
Indices: 393453--393554 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
393443 TTATTCTCAA
*
393453 ATTTCTTCTTTTATTATTTTCGATTTCTTTATTACAAATTTTTTT
1 ATTTCTTCTTTTATTATTTTCAATTTCTTTATTACAAATTTTTTT
393498 ATTTCTTCTTTTATTATTTTCAATTTCTTTATTACAAATTTTTTT
1 ATTTCTTCTTTTATTATTTTCAATTTCTTTATTACAAATTTTTTT
*
393543 ATTTCTTTTTTT
1 ATTTCTTCTTTT
393555 TCAGATCATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.20, C:0.11, G:0.01, T:0.69
Consensus pattern (45 bp):
ATTTCTTCTTTTATTATTTTCAATTTCTTTATTACAAATTTTTTT
Found at i:417592 original size:7 final size:7
Alignment explanation
Indices: 417582--417613 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
417572 TTATATACAT
417582 AATACTA
1 AATACTA
417589 AATACTA
1 AATACTA
417596 AATACTA
1 AATACTA
417603 AATACTA
1 AATACTA
417610 AATA
1 AATA
417614 TCAATCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:418831 original size:12 final size:11
Alignment explanation
Indices: 418797--418831 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
418787 GAATTTTGGA
418797 AGGAAATTGAG
1 AGGAAATTGAG
418808 AGG-AATTGAG
1 AGGAAATTGAG
418818 AGGAAATATGAG
1 AGGAAAT-TGAG
418830 AG
1 AG
418832 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:421583 original size:12 final size:12
Alignment explanation
Indices: 421566--421607 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
421556 TTTTTTAAAG
421566 TTAAATAAATAT
1 TTAAATAAATAT
*
421578 TTAAATATAATTT
1 TTAAATA-AATAT
421591 TTCAAA-AAATAT
1 TT-AAATAAATAT
421603 TTAAA
1 TTAAA
421608 CATAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 7 0.27
14 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAATAAATAT
Found at i:422181 original size:16 final size:16
Alignment explanation
Indices: 422160--422190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
422150 AGGAAAAATA
*
422160 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
422176 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
422191 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:422482 original size:9 final size:9
Alignment explanation
Indices: 422468--422495 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
422458 TATAGTTTGA
422468 TATTCGAAT
1 TATTCGAAT
422477 TATTCGAAT
1 TATTCGAAT
422486 TATTCGAAT
1 TATTCGAAT
422495 T
1 T
422496 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:433673 original size:15 final size:17
Alignment explanation
Indices: 433655--433700 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
433645 TGTGTCCTAT
433655 TTTAAAG-T-GTTCTCG
1 TTTAAAGATAGTTCTCG
*
433670 TTTATAGATAGTTCTCG
1 TTTAAAGATAGTTCTCG
* *
433687 TTTAGAGATTGTTC
1 TTTAAAGATAGTTC
433701 CGGTCCAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 6 0.23
16 1 0.04
17 19 0.73
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (17 bp):
TTTAAAGATAGTTCTCG
Found at i:433685 original size:17 final size:17
Alignment explanation
Indices: 433663--433700 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
433653 ATTTTAAAGT
*
433663 GTTCTCGTTTATAGATA
1 GTTCTCGTTTAGAGATA
*
433680 GTTCTCGTTTAGAGATT
1 GTTCTCGTTTAGAGATA
433697 GTTC
1 GTTC
433701 CGGTCCAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (17 bp):
GTTCTCGTTTAGAGATA
Found at i:433917 original size:10 final size:10
Alignment explanation
Indices: 433895--433931 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
433885 TTCTTTAGAT
433895 AAATTAGTAAA
1 AAATTA-TAAA
433906 AAATTATAAA
1 AAATTATAAA
*
433916 AAAATATAAA
1 AAATTATAAA
433926 AAATTA
1 AAATTA
433932 GTTGAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAATTATAAA
Found at i:435755 original size:42 final size:42
Alignment explanation
Indices: 435691--435799 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
435681 ACGGCCAAGC
*
435691 CACACGCCCGTGTGCTAGGCCGTGTAACACTCGAAATAGCCT
1 CACATGCCCGTGTGCTAGGCCGTGTAACACTCGAAATAGCCT
435733 CACATGCCCGTGTGCTAGGCCGTGTAACACTCGAAATAGCCT
1 CACATGCCCGTGTGCTAGGCCGTGTAACACTCGAAATAGCCT
* *
435775 CACATGCCCGTGTGCCAGGCTGTGT
1 CACATGCCCGTGTGCTAGGCCGTGT
435800 GTTAGGCCCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (42 bp):
CACATGCCCGTGTGCTAGGCCGTGTAACACTCGAAATAGCCT
Found at i:436743 original size:35 final size:35
Alignment explanation
Indices: 436700--436768 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
436690 ACACACCAAA
* *
436700 TGCTCATAAGAG-TTGATCCAACTGAAACACGCCAG
1 TGCTCATAAGAGCTAG-TCCAACCGAAACACGCCAG
*
436735 TGCTCATAAGAGCTAGTCTAACCGAAACACGCCA
1 TGCTCATAAGAGCTAGTCCAACCGAAACACGCCA
436769 AACATAGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (35 bp):
TGCTCATAAGAGCTAGTCCAACCGAAACACGCCAG
Found at i:439053 original size:110 final size:110
Alignment explanation
Indices: 438860--439105 Score: 474
Period size: 110 Copynumber: 2.2 Consensus size: 110
438850 AAAATTGCAG
438860 GGGTCACACGGCCAAGAGACACGCCCATGTCTTAGGCTGTGTGGGCATTCGAAGTAGGGACACAC
1 GGGTCACACGGCCAAGAGACACGCCCATGTCTTAGGCTGTGTGGGCATTCGAAGTAGGGACACAC
438925 AACTGTGTCCCAGCCCGTGTCCATACCAGTGTAACTCACTGACTT
66 AACTGTGTCCCAGCCCGTGTCCATACCAGTGTAACTCACTGACTT
438970 GGGTCACACGGCCAAGAGACACGCCCATGTCTTAGGCTGTGTGGGCATTCGAAGTAGGGACACAC
1 GGGTCACACGGCCAAGAGACACGCCCATGTCTTAGGCTGTGTGGGCATTCGAAGTAGGGACACAC
439035 AACTGTGTCCCAGCCCGTGTCCATACCAGTGTAACTCACTGACTT
66 AACTGTGTCCCAGCCCGTGTCCATACCAGTGTAACTCACTGACTT
**
439080 GGGTCACACGGCCAAGCCACACGCCC
1 GGGTCACACGGCCAAGAGACACGCCC
439106 GTGTGCCAGG
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 134 1.00
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (110 bp):
GGGTCACACGGCCAAGAGACACGCCCATGTCTTAGGCTGTGTGGGCATTCGAAGTAGGGACACAC
AACTGTGTCCCAGCCCGTGTCCATACCAGTGTAACTCACTGACTT
Found at i:442848 original size:50 final size:50
Alignment explanation
Indices: 442781--442972 Score: 204
Period size: 50 Copynumber: 3.7 Consensus size: 50
442771 TTTTTGTACT
* * * **
442781 GCCAATGCCATATCCCAGATATGGTCGTACATGGGAGTTCTCATATCGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGA
* ** * *
442831 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGA
* *
442881 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GGA
* *
442936 TGCCAATGCCATATCCCATACATGGTCTTACATGGGA
1 -GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
442973 TCTCATCCTC
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 80 0.69
53 2 0.02
55 1 0.01
56 33 0.28
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGA
Found at i:450411 original size:50 final size:51
Alignment explanation
Indices: 450344--450585 Score: 256
Period size: 50 Copynumber: 4.7 Consensus size: 51
450334 TTTCTGTACT
* * **
450344 GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT-ATCGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCGGA
* ** ** *
450394 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCGT-GGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCGGA
* * *
450444 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCGGA
* * * * *
450494 GCTAATGCCACGTCCCAGACATGGTCGTACATGAGACCTCTCATAATCTCATTGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAA--TC--GGA
450549 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
450586 TCTCATCTTC
Statistics
Matches: 158, Mismatches: 26, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 121 0.77
51 1 0.01
53 2 0.01
55 1 0.01
56 32 0.20
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (51 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCGGA
Found at i:450486 original size:100 final size:103
Alignment explanation
Indices: 450343--450585 Score: 294
Period size: 100 Copynumber: 2.4 Consensus size: 103
450333 TTTTCTGTAC
* * ** * *
450343 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGAGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGAGCCAATGCCACGTC
* * * *
450408 CCAGACATGGTCTTACGGGGGACCTCTC-A-TC-GTGG
66 CCAGACATGGTCGTACAGGAGACCTCTCAACTCAGTGA
* * * *
450443 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCTAATGCCACGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGAGCCAATGCCACGTC
* *
450508 CCAGACATGGTCGTACATGAGACCTCTCATAATCTCATTGA
66 CCAGACATGGTCGTACAGGAGACCTCTC--AA-CTCAGTGA
450549 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
450586 TCTCATCTTC
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 79 0.66
103 1 0.01
105 2 0.02
106 38 0.32
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (103 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGAGCCAATGCCACGTC
CCAGACATGGTCGTACAGGAGACCTCTCAACTCAGTGA
Found at i:456360 original size:18 final size:19
Alignment explanation
Indices: 456319--456360 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
456309 CTGCGTTCTA
*
456319 CTCAATTTGAACTTTCTTT
1 CTCAATTTGAACTATCTTT
*
456338 C-CAATTT-ATCTATCTTT
1 CTCAATTTGAACTATCTTT
456355 CTCAAT
1 CTCAAT
456361 AATCATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (19 bp):
CTCAATTTGAACTATCTTT
Found at i:457437 original size:23 final size:23
Alignment explanation
Indices: 457411--457463 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
457401 ATAAGTGCCA
457411 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
457434 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
457457 CACTGAT
1 CACTGAT
457464 CAATAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:457701 original size:18 final size:17
Alignment explanation
Indices: 457675--457713 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
457665 ATTTTCCTTC
457675 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
457692 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
457710 CACA
1 CACA
457714 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:457933 original size:30 final size:30
Alignment explanation
Indices: 457898--457955 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
457888 TCATTGACTC
457898 AAACTTTGGCAAAATTACAATTTTGCCCTT
1 AAACTTTGGCAAAATTACAATTTTGCCCTT
* * * *
457928 AAACTTTTGCATATTTACATTTTTGCCC
1 AAACTTTGGCAAAATTACAATTTTGCCC
457956 AAAGCTCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCTT
Done.