Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 399999
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:3364 original size:51 final size:48
Alignment explanation
Indices: 3284--3470 Score: 189
Period size: 51 Copynumber: 3.7 Consensus size: 48
3274 TGCCTATAAA
* *
3284 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAA-AG-T-TTGGT
* * *
3335 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGC-AGGTTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAC---CAAAG-TTTGGT
* * *
3386 CACGTGTGTAATACTAGGTGCAGGCTACTACGTGAACCGGAAAGTTTGAG-
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC--AAAGTTTG-GT
*
3436 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGT
3471 GTCGAATGAT
Statistics
Matches: 113, Mismatches: 16, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
48 1 0.01
50 35 0.31
51 73 0.65
52 2 0.02
53 1 0.01
54 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (48 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAGTTTGGT
Found at i:8245 original size:20 final size:20
Alignment explanation
Indices: 8220--8260 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
8210 ATGTTACATG
8220 TTAATTTTTACTCAATTTGT
1 TTAATTTTTACTCAATTTGT
8240 TTAATTTTTACTCAATTTGT
1 TTAATTTTTACTCAATTTGT
8260 T
1 T
8261 GCAGTTGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAATTTTTACTCAATTTGT
Found at i:9939 original size:14 final size:13
Alignment explanation
Indices: 9915--9975 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
9905 TTATTTCTTG
*
9915 TATTTTGTTTATT
1 TATTTTTTTTATT
9928 TATTTTTATTTAATT
1 TATTTTT-TTT-ATT
* *
9943 AATTTTTTATTCTT
1 TATTTTTT-TTATT
*
9957 TATTTTTTTGATT
1 TATTTTTTTTATT
9970 TATTTT
1 TATTTT
9976 CAGGTGTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 15 0.38
14 13 0.33
15 11 0.28
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (13 bp):
TATTTTTTTTATT
Found at i:14366 original size:20 final size:20
Alignment explanation
Indices: 14319--14358 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
14309 CTTGTATGAG
*
14319 ATTTTCACTTTGATGCCTCT
1 ATTTGCACTTTGATGCCTCT
*
14339 ATTTGCACTTTGGTGCCTCT
1 ATTTGCACTTTGATGCCTCT
14359 GATTGCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.47
Consensus pattern (20 bp):
ATTTGCACTTTGATGCCTCT
Found at i:16663 original size:17 final size:18
Alignment explanation
Indices: 16632--16665 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16622 TGCTACCTAC
16632 CCTGTTTGCCACCACAAT
1 CCTGTTTGCCACCACAAT
*
16650 CCTG-TTGCCGCCACAA
1 CCTGTTTGCCACCACAA
16666 CTTCATCGCC
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:0.41, G:0.15, T:0.24
Consensus pattern (18 bp):
CCTGTTTGCCACCACAAT
Found at i:26207 original size:63 final size:63
Alignment explanation
Indices: 26061--26210 Score: 169
Period size: 63 Copynumber: 2.4 Consensus size: 63
26051 GATGGCAAGA
* * * * * *
26061 AATGATTGCATGTGCTG-GGATGCTTGTGTGTAATAAACTTGTGATGAATGTGTCGGTGTAGGG
1 AATGATTGCACGTGATGTGG-TGCTTGTGTGAAATAAACTGGTGATAAATGTGTCGGTATAGGG
* * * * *
26124 AAAGATTGCCCAT-ATAGTGGTGCTTGTGTGAAATAAAGTGGTGATAAATGTGTTGGTATAGGG
1 AATGATTGCACGTGAT-GTGGTGCTTGTGTGAAATAAACTGGTGATAAATGTGTCGGTATAGGG
26187 AATGATTGCACGTGATGTGGTGCT
1 AATGATTGCACGTGATGTGGTGCT
26211 CATGTAAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
62 1 0.01
63 65 0.93
64 4 0.06
ACGTcount: A:0.25, C:0.08, G:0.33, T:0.33
Consensus pattern (63 bp):
AATGATTGCACGTGATGTGGTGCTTGTGTGAAATAAACTGGTGATAAATGTGTCGGTATAGGG
Found at i:27926 original size:53 final size:53
Alignment explanation
Indices: 27810--27915 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
27800 TATTAATTTG
* * * ** *
27810 AACAACATAATAATTAACTATTTAAATTTAAATAATTTGATAAATTTTTTCTT
1 AACATCATAATAATTAACTAATTAAAATTAAATAATTAAATAAATATTTTCTT
27863 AACATCATAATAATTAA-TAGATTAAAATTAAATAATTAAAT-AATATTTTCTT
1 AACATCATAATAATTAACTA-ATTAAAATTAAATAATTAAATAAATATTTTCTT
27915 A
1 A
27916 CAATTTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 13 0.28
53 33 0.72
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (53 bp):
AACATCATAATAATTAACTAATTAAAATTAAATAATTAAATAAATATTTTCTT
Found at i:28070 original size:14 final size:14
Alignment explanation
Indices: 28053--28090 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28043 TTAGAATAAA
28053 AAATTGAGAACAAT
1 AAATTGAGAACAAT
*
28067 AAATCGAGAACAAT
1 AAATTGAGAACAAT
*
28081 AAGTTGAGAA
1 AAATTGAGAA
28091 TTGAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (14 bp):
AAATTGAGAACAAT
Found at i:34330 original size:3 final size:3
Alignment explanation
Indices: 34322--34351 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34312 ATTTAAACAC
34322 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34352 CATTTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35140 original size:9 final size:9
Alignment explanation
Indices: 35128--35180 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
35118 AAAAAGATAA
35128 AAAAATATT
1 AAAAATATT
*
35137 AAAAATTTATA
1 AAAAA--TATT
*
35148 AAAAATATA
1 AAAAATATT
35157 AAAAATATT
1 AAAAATATT
*
35166 TAAAATATT
1 AAAAATATT
*
35175 TAAAAT
1 AAAAAT
35181 TATAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
9 31 0.79
11 8 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATATT
Found at i:35141 original size:19 final size:19
Alignment explanation
Indices: 35117--35164 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
35107 TGAAGATTAC
35117 TAAAAAGATA-AAAAAATA
1 TAAAAAGATATAAAAAATA
**
35135 TTAAAAATTTATAAAAAATA
1 -TAAAAAGATATAAAAAATA
35155 TAAAAA-ATAT
1 TAAAAAGATAT
35165 TTAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAAGATATAAAAAATA
Found at i:35150 original size:20 final size:20
Alignment explanation
Indices: 35127--35187 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
35117 TAAAAAGATA
35127 AAAAAATATTAAAAATTTAT
1 AAAAAATATTAAAAATTTAT
*
35147 AAAAAATATAAAAAATATT-T
1 AAAAAATATTAAAAAT-TTAT
*
35167 --AAAATATTTAAAA-TTAT
1 AAAAAATATTAAAAATTTAT
35184 AAAA
1 AAAA
35188 TTTATAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 11 0.32
19 2 0.06
20 16 0.47
21 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATTAAAAATTTAT
Found at i:35179 original size:29 final size:29
Alignment explanation
Indices: 35117--35176 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
35107 TGAAGATTAC
35117 TAAAAAGATA-AAAAAATATTAAAAATTTA
1 TAAAAA-ATATAAAAAATATTAAAAATTTA
35146 TAAAAAATATAAAAAATATTTAAAATATTTA
1 TAAAAAATATAAAAAATA-TTAAAA-ATTTA
35177 AAATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 14 0.50
30 6 0.21
31 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
TAAAAAATATAAAAAATATTAAAAATTTA
Found at i:36947 original size:19 final size:20
Alignment explanation
Indices: 36918--36955 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
36908 GAATAATATA
*
36918 AATAGTAAATAAACAAAATT
1 AATAGTAAATAAAAAAAATT
36938 AATA-TAAATAAAAAAAAT
1 AATAGTAAATAAAAAAAAT
36956 AAACAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AATAGTAAATAAAAAAAATT
Found at i:37400 original size:31 final size:31
Alignment explanation
Indices: 37356--37415 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
37346 TGTGCACGTG
** *
37356 TATATATGGATTATGAAAA-TAATAATAATTA
1 TATATATAAATTAT-AAAATTAAAAATAATTA
37387 TATATATAAATTATAAAATTAAAAATAAT
1 TATATATAAATTATAAAATTAAAAATAAT
37416 AATTACATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (31 bp):
TATATATAAATTATAAAATTAAAAATAATTA
Found at i:38040 original size:11 final size:11
Alignment explanation
Indices: 38026--38050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38016 AAATCAACGA
38026 AAAAACCCTAG
1 AAAAACCCTAG
38037 AAAAACCCTAG
1 AAAAACCCTAG
38048 AAA
1 AAA
38051 CCTTTCGGCT
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:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAACCCTAG
Found at i:39168 original size:45 final size:44
Alignment explanation
Indices: 39107--39227 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
39097 TTGGCCTAAA
* *
39107 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGACTTG-CATATTCAG
* * * **
39152 TCTGCCCCACTACAACTTCAAGGG-GATAAGACTTGTTTATTCAG
1 TCTGCTCCACTGCAACTT-TAGGGAGATAAGACTTGCATATTCAG
** *
39196 TCTGCTCTGCTGCAACCTTAGGGAGATAAGAC
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGAC
39228 CTGATATCTT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
43 4 0.07
44 27 0.44
45 26 0.43
46 4 0.07
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCATATTCAG
Found at i:39372 original size:50 final size:50
Alignment explanation
Indices: 39318--39592 Score: 167
Period size: 50 Copynumber: 5.5 Consensus size: 50
39308 CCAAGGAAGT
* *
39318 AAGATTCACCGTTGTGGATTCAATCTTTTTAATTGCAATGTTGGGGAAAC
1 AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* ** ** * * ** ***** **
39368 AAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCCAATGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* * **
39418 AAGATTCGCCTTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
1 AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
** ** * * ****** *
39468 AAGATTCACCGTTGTAGCTTCAATCTACTCCACTAC-ACCACCAGGAAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAA-C
** **
39518 AAGATTCGGCGTTGCGGCTTCAATC-TTTTAATTGCAATGTTGGGGAAAC
1 AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
*
39567 AAGATTCACCGTCGTAGCTTCAATCT
1 AAGATTCACCGTTGTAGCTTCAATCT
39593 GTTCCATTAC
Statistics
Matches: 145, Mismatches: 77, Indels: 6
0.64 0.34 0.03
Matches are distributed among these distances:
49 30 0.21
50 115 0.79
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
AAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
Found at i:39409 original size:100 final size:100
Alignment explanation
Indices: 39277--39642 Score: 538
Period size: 100 Copynumber: 3.7 Consensus size: 100
39267 TAAGATTTGT
* * * * * *
39277 CGTCGTAGCTTCGATCTGTTTCACTAAACCGCCAAGGAAGTAAGATTCACCGTTGTGGATTCAAT
1 CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGGAAGTAAGATTCACCGTTGCGGCTTCAAT
39342 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
66 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
* * *
39377 CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAATGAAGTAAGATTCGCCTTTGCGGCTTCAAT
1 CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGGAAGTAAGATTCACCGTTGCGGCTTCAAT
39442 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
66 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
* * * **
39477 CGTTGTAGCTTCAATCTACTCCACTACACCACC-AGGAAAGTAAGATTCGGCGTTGCGGCTTCAA
1 CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGG-AAGTAAGATTCACCGTTGCGGCTTCAA
39541 TC-TTTTAATTGCAATGTTGGGGAAACAAGATTCAC
65 TCTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
* * * * *
39576 CGTCGTAGCTTCAATCTGTTCCATTACACCGCCAGGGGAGTAAGATTCACCGTTGCAGCTTCAAT
1 CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGGAAGTAAGATTCACCGTTGCGGCTTCAAT
39641 CT
66 CT
39643 GCTCCACTGT
Statistics
Matches: 238, Mismatches: 25, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
99 88 0.37
100 150 0.63
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (100 bp):
CGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGGAAGTAAGATTCACCGTTGCGGCTTCAAT
CTTTTTAATTGCAATGTTGGGGAAACAAGATTCAC
Found at i:47916 original size:19 final size:19
Alignment explanation
Indices: 47887--47923 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
47877 AAATAGTATA
47887 AATAGTAAATAAATAAAATT
1 AATAGTAAATAAA-AAAATT
47907 AATA-TAAATAAAAAAAT
1 AATAGTAAATAAAAAAAT
47924 AAACAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAGTAAATAAAAAAATT
Found at i:48364 original size:31 final size:31
Alignment explanation
Indices: 48306--48365 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
48296 TGTGCACGTG
* *
48306 TATATATAGATTATAAAAATAATAATAATTA
1 TATATATAAATTATAAAAATAAAAATAATTA
48337 TATATATAAATTATAAAAGA-AAAAATAAT
1 TATATATAAATTATAAAA-ATAAAAATAAT
48366 AATTACATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TATATATAAATTATAAAAATAAAAATAATTA
Found at i:49017 original size:10 final size:11
Alignment explanation
Indices: 49002--49027 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48992 CAAAATCAAC
49002 GAAAAACCCTA
1 GAAAAACCCTA
49013 GAAAAACCCTA
1 GAAAAACCCTA
49024 GAAA
1 GAAA
49028 GCTTTTGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.08
Consensus pattern (11 bp):
GAAAAACCCTA
Found at i:50300 original size:24 final size:24
Alignment explanation
Indices: 50273--50321 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
50263 TCGTTAGAAA
*
50273 AAAAAAATATACATATACATATAT
1 AAAAAAATAGACATATACATATAT
*
50297 AAAAAAATAGATATATACATATAT
1 AAAAAAATAGACATATACATATAT
50321 A
1 A
50322 TATAGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAAATAGACATATACATATAT
Found at i:51598 original size:33 final size:32
Alignment explanation
Indices: 51537--51599 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
51527 AACAAAAATC
* * *
51537 GGGTCTGGGTTTGGGCCTATTTTGTTGTAATT
1 GGGTCTGGGTTTAGGCCCATTTTATTGTAATT
*
51569 GGGTTTGGGTTTTAGGCCCATTTTATTGTAA
1 GGGTCTGGG-TTTAGGCCCATTTTATTGTAA
51600 AAGGACTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.13, C:0.10, G:0.32, T:0.46
Consensus pattern (32 bp):
GGGTCTGGGTTTAGGCCCATTTTATTGTAATT
Found at i:52037 original size:45 final size:45
Alignment explanation
Indices: 51975--52191 Score: 260
Period size: 45 Copynumber: 4.8 Consensus size: 45
51965 GATTTGTTTA
*
51975 TTCAGTCTGCCCCACTGCAATTTCAAGGGGATAAGACTTGCTTTC
1 TTCAGTCTGCCCCACTGCAACTTCAAGGGGATAAGACTTGCTTTC
* * * **
52020 TTGAGTTTGCTCCACTGCAACTTC-AGGGAGATAAGACTTGCCATC
1 TTCAGTCTGCCCCACTGCAACTTCAAGGG-GATAAGACTTGCTTTC
* *
52065 TTCAGTCTGCCCCACTGCAACTTC-AGGAGGATAAGACTTACTTAC
1 TTCAGTCTGCCCCACTGCAACTTCAAGG-GGATAAGACTTGCTTTC
* * *
52110 -TCAGTCTGCTCCACTGCAACTTGAAGGAGATAAGACTTGCTTTC
1 TTCAGTCTGCCCCACTGCAACTTCAAGGGGATAAGACTTGCTTTC
* ** *
52154 TTGAGTCTGCCCCACTGCAACCCCAGGGGGATAAGACT
1 TTCAGTCTGCCCCACTGCAACTTCAAGGGGATAAGACT
52192 AGATGCGATC
Statistics
Matches: 143, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
44 39 0.27
45 103 0.72
46 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (45 bp):
TTCAGTCTGCCCCACTGCAACTTCAAGGGGATAAGACTTGCTTTC
Found at i:52149 original size:89 final size:89
Alignment explanation
Indices: 51975--52364 Score: 311
Period size: 89 Copynumber: 4.4 Consensus size: 89
51965 GATTTGTTTA
* * * * *
51975 TTCAGTCTGCCCCACTGCAATTTCAAGGGGATAAGACTTGCTTTCTTGAGTTTGCTCCACTGCAA
1 TTCAGTCTGCCCCACTGCAACTTC-AGGGGATAAGACTTACTTACTTCAGTCTGCTCCACTGCAA
*
52040 CTTCAGGGAGATAAGACTTGCCATC
65 CTTCAAGGAGATAAGACTTGCCATC
52065 TTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTACTTAC-TCAGTCTGCTCCACTGCAA
1 TTCAGTCTGCCCCACTGCAACTTCAGG-GGATAAGACTTACTTACTTCAGTCTGCTCCACTGCAA
* **
52129 CTTGAAGGAGATAAGACTTGCTTTC
65 CTTCAAGGAGATAAGACTTGCCATC
* ** * * *
52154 TTGAGTCTGCCCCACTGCAACCCCAGGGGGATAAGAC-TA--GA-TGC-GATCTGCT-CTCTGCA
1 TTCAGTCTGCCCCACTGCAACTTCA-GGGGATAAGACTTACTTACTTCAG-TCTGCTCCACTGCA
52213 ACTTC-AGAGAGATAAGATCTAT--CA-C
64 ACTTCAAG-GAGATAAGA-CT-TGCCATC
* * * * * * * * * * *
52238 TTTAATCCGCTCCACTTCAACTTCAGGGAGATAGGA-TTA-TTGGCTTTAATCTGATCCACTACA
1 TTCAGTCTGCCCCACTGCAACTTCAGGG-GATAAGACTTACTT-ACTTCAGTCTGCTCCACTGCA
* *
52301 ACTTCAGGGAGATAAGATTTGCCATC
64 ACTTCAAGGAGATAAGACTTGCCATC
* * * *
52327 GTCATTCTGCCCCACTACAATTTCAGGAGGATAAGACT
1 TTCAGTCTGCCCCACTGCAACTTCAGG-GGATAAGACT
52365 GGATGCGATA
Statistics
Matches: 236, Mismatches: 44, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
83 3 0.01
84 29 0.12
85 20 0.08
86 11 0.05
87 8 0.03
88 23 0.10
89 100 0.42
90 42 0.18
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (89 bp):
TTCAGTCTGCCCCACTGCAACTTCAGGGGATAAGACTTACTTACTTCAGTCTGCTCCACTGCAAC
TTCAAGGAGATAAGACTTGCCATC
Found at i:52261 original size:44 final size:44
Alignment explanation
Indices: 52211--52319 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
52201 CTGCTCTCTG
* * *
52211 CAACTTCAGAGAGATAAGATCTA-TCACTTTAATCCGCTCCACTT
1 CAACTTCAGGGAGATAAGAT-TATTCACTTTAATCCGATCCACTA
* ** *
52255 CAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGATCCACTA
1 CAACTTCAGGGAGATAAGATTATTCACTTTAATCCGATCCACTA
52299 CAACTTCAGGGAGATAAGATT
1 CAACTTCAGGGAGATAAGATT
52320 TGCCATCGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.04
44 54 0.96
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTATTCACTTTAATCCGATCCACTA
Found at i:52340 original size:173 final size:174
Alignment explanation
Indices: 52114--52449 Score: 467
Period size: 173 Copynumber: 1.9 Consensus size: 174
52104 ACTTACTCAG
* * * ** * * *
52114 TCTGCTCCACTGCAACTTGAAGGAGATAAGACTTGCTTTCTTGAGTCTGCCCCACTGCAACCCCA
1 TCTGATCCACTACAACTTCAAGGAGATAAGACTTGCCATCGTCAGTCTGCCCCACTACAACCCCA
* * *
52179 GGGGGATAAGACTAGATGCGATCTGCTC-TCTGCAACTTCAGAGAGATAAGATCTATCACTTTAA
66 GGAGGATAAGACTAGATGCGATATGCTCTTCTGCAACTTCAGAGAGATAAGATCCATCACTTTAA
*
52243 TCCGCTCCACTTCAACTTCAGGGAGATAGGATTATTGGCTTTAA
131 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
* * * ***
52287 TCTGATCCACTACAACTTCAGGGAGATAAGATTTGCCATCGTCATTCTGCCCCACTACAATTTCA
1 TCTGATCCACTACAACTTCAAGGAGATAAGACTTGCCATCGTCAGTCTGCCCCACTACAACCCCA
* * *
52352 GGAGGATAAGACTGGATGCGATATGCTCTTTTGCAACTTCAGAGAGATAAGATCCATCAGTTTAA
66 GGAGGATAAGACTAGATGCGATATGCTCTTCTGCAACTTCAGAGAGATAAGATCCATCACTTTAA
*
52417 TCCGCTCCACTGCAACTTTAGGGAGATAGGATT
131 TCCGCTCCACTGCAACTTCAGGGAGATAGGATT
52450 GGTTCTTCTA
Statistics
Matches: 140, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
173 76 0.54
174 64 0.46
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (174 bp):
TCTGATCCACTACAACTTCAAGGAGATAAGACTTGCCATCGTCAGTCTGCCCCACTACAACCCCA
GGAGGATAAGACTAGATGCGATATGCTCTTCTGCAACTTCAGAGAGATAAGATCCATCACTTTAA
TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
Found at i:52434 original size:44 final size:43
Alignment explanation
Indices: 52208--52444 Score: 119
Period size: 44 Copynumber: 5.4 Consensus size: 43
52198 GATCTGCTCT
* * *
52208 CTGCAACTTCAGAGAGATAAGATCTATCACTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCCATC-GTTTAATCCGCTCCA
* * * * * *
52252 CTTCAACTTCAGGGAGATAGGAT-TATTGGCTTTAATCTGATCCA
1 CTGCAACTTCAGGGAGATAAGATCCA-TCG-TTTAATCCGCTCCA
* * * * *
52296 CTACAACTTCAGGGAGATAAGATTTGCCATCG-TCATTCTGCCCCA
1 CTGCAACTTCAGGGAGATAAGA--T-CCATCGTTTAATCCGCTCCA
* * ** * **
52341 CTACAATTTCA-GGAGGATAAGACTGGATGCG-AT-AT--GCTCTT
1 CTGCAACTTCAGGGA-GATAAGA-TCCAT-CGTTTAATCCGCTCCA
* *
52382 TTGCAACTTCAGAGAGATAAGATCCATCAGTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCCATC-GTTTAATCCGCTCCA
*
52426 CTGCAACTTTAGGGAGATA
1 CTGCAACTTCAGGGAGATA
52445 GGATTGGTTC
Statistics
Matches: 142, Mismatches: 37, Indels: 28
0.69 0.18 0.14
Matches are distributed among these distances:
39 1 0.01
40 4 0.03
41 19 0.13
42 4 0.03
43 5 0.04
44 79 0.56
45 26 0.18
46 1 0.01
47 2 0.01
48 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
CTGCAACTTCAGGGAGATAAGATCCATCGTTTAATCCGCTCCA
Found at i:52688 original size:49 final size:48
Alignment explanation
Indices: 52536--52690 Score: 130
Period size: 49 Copynumber: 3.1 Consensus size: 48
52526 ATGAAGTAAT
*
52536 ATTCACCGTTGTGGCCTCAATCTTTTTAATTGCAATGTTGGGAAACAAG
1 ATTCACCG-TGTGGCCTCAATCTTTTTAATTGCAATGTCGGGAAACAAG
** * * * ** * **** * **
52585 ATTCGTCGTCGTAGCTTCAATCTGTTCCACTGCACCACCAAGGAAGTAAG
1 ATTCACCGT-GTGGCCTCAATCTTTTTAATTGCAATGTC-GGGAAACAAG
52635 ATTCACCGCTGTGGCCTCAATCTTTTTAATTGCAATGTCGGGAAACAAG
1 ATTCACCG-TGTGGCCTCAATCTTTTTAATTGCAATGTCGGGAAACAAG
52684 ATTCACC
1 ATTCACC
52691 ATCGTAGCTT
Statistics
Matches: 72, Mismatches: 31, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.53
50 32 0.44
51 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (48 bp):
ATTCACCGTGTGGCCTCAATCTTTTTAATTGCAATGTCGGGAAACAAG
Found at i:52704 original size:49 final size:48
Alignment explanation
Indices: 52552--52706 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 48
52542 CGTTGTGGCC
* * *
52552 TCAATCTTTTTAATTGCAATGTTGGGAAACAAGATTCGTCGTCGTAGCT
1 TCAATCTTTTTAATTGCAATGTCGGGAAACAAGATTC-ACCTCGTAGCT
* ** * **** * ** * * *
52601 TCAATCTGTTCCACTGCACCACCAAGGAAGTAAGATTCACCGCTGTGGCC
1 TCAATCTTTTTAATTGCAATGTC-GGGAAACAAGATTCACCTC-GTAGCT
52651 TCAATCTTTTTAATTGCAATGTCGGGAAACAAGATTCACCATCGTAGCT
1 TCAATCTTTTTAATTGCAATGTCGGGAAACAAGATTCACC-TCGTAGCT
52700 TCAATCT
1 TCAATCT
52707 GTTCCACTAC
Statistics
Matches: 72, Mismatches: 31, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
49 41 0.57
50 31 0.43
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (48 bp):
TCAATCTTTTTAATTGCAATGTCGGGAAACAAGATTCACCTCGTAGCT
Found at i:52751 original size:50 final size:50
Alignment explanation
Indices: 52483--52862 Score: 167
Period size: 50 Copynumber: 7.7 Consensus size: 50
52473 TCGGGAAGAC
* * * * **
52483 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGC-ACTGCCAATGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAAC-GCCAGGGAAGT
* * * * ** * * * ** **
52533 AATATTCACCGTTGTGGCCTCAATCTTTTTAATTGCAATG-TTGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
* * * * * * * *
52582 AAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTGCACCACCAAGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
* * * * ** * * * * **
52632 AAGATTCACCGCTGTGGCCTCAATCTTTTTAATTGCAATGTC-GGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
* * * * * * *
52681 AAGATTCACCATCGTAGCTTCAATCTGTTCCACTACAGCGCCAGAGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
* * * * **
52731 AAGATTCGCCGTTGTGGCTTCAATCTATT-AATTACAATGTC-GGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
* * * ** * * *
52779 AACATTCACCGTAGCAGCTTCAATCTGTTCCACTACATCGCTAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
*
52829 AAGATTCGCGGTTGTGGCTTCAATCTATTCCACT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACT
52863 GTAATGCCAA
Statistics
Matches: 224, Mismatches: 101, Indels: 10
0.67 0.30 0.03
Matches are distributed among these distances:
48 27 0.12
49 76 0.34
50 120 0.54
51 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (50 bp):
AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTACAACGCCAGGGAAGT
Found at i:52857 original size:98 final size:98
Alignment explanation
Indices: 52469--52854 Score: 488
Period size: 99 Copynumber: 3.9 Consensus size: 98
52459 ATTTAACTGT
* * *
52469 AATGTCGGGAAGACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAATGAAGTA
1 AATGTCGGGAA-ACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACAC-GCCAAGGAAGTA
* *
52534 ATATTCACCGTTGTGGCCTCAATCTTTTTAATTGC
64 AGATTCACCGTTGTGGCCTCAATCTTATTAATTGC
* ** * *
52569 AATGTTGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTGCACCACCAAGGAAGTAA
1 AATGTCGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACA-CGCCAAGGAAGTAA
* *
52634 GATTCACCGCTGTGGCCTCAATCTTTTTAATTGC
65 GATTCACCGTTGTGGCCTCAATCTTATTAATTGC
*
52668 AATGTCGGGAAACAAGATTCACCATCGTAGCTTCAATCTGTTCCACTACAGCGCC-AGAGAAGTA
1 AATGTCGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACA-CGCCAAG-GAAGTA
* * *
52732 AGATTCGCCGTTGTGGCTTCAATC-TATTAATTAC
64 AGATTCACCGTTGTGGCCTCAATCTTATTAATTGC
* * * * *
52766 AATGTCGGGAAACAACATTCACCGTAGCAGCTTCAATCTGTTCCACTACATCGCTAGGGAAGTAA
1 AATGTCGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACA-CGCCAAGGAAGTAA
* * *
52831 GATTCGCGGTTGTGGCTTCAATCT
65 GATTCACCGTTGTGGCCTCAATCT
52855 ATTCCACTGT
Statistics
Matches: 256, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
98 88 0.34
99 157 0.61
100 11 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (98 bp):
AATGTCGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACGCCAAGGAAGTAAG
ATTCACCGTTGTGGCCTCAATCTTATTAATTGC
Found at i:53220 original size:44 final size:45
Alignment explanation
Indices: 53079--53300 Score: 140
Period size: 44 Copynumber: 5.0 Consensus size: 45
53069 TTGCTGCTAG
* *
53079 TACAGGAAGGCAAGATCTG-TCATTTTCAACCTACTCTACTGCTGC
1 TACAGGAAGACAAGATCTGCT-ATTTTCAACCTACTCCACTGCTGC
* * * * * * ***
53124 T-CAGGGAGACAAG-GCTGGTATCTT-AGATCC-ACTTCGCTGCCAA
1 TACAGGAAGACAAGATCTGCTATTTTCA-A-CCTACTCCACTGCTGC
53167 TACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
1 TACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
* * * * * * *
53212 TGA-A-GAAGACAAGGA--TGGTATCTTCGATCTACTTCGCTGCTGA
1 T-ACAGGAAGACAA-GATCTGCTATTTTCAACCTACTCCACTGCTGC
* *
53255 TACAGGAAGACAAGATCTGCTAGTTTT-AACCTACTCTATTGCTGC
1 TACAGGAAGACAAGATCTGCTA-TTTTCAACCTACTCCACTGCTGC
53300 T
1 T
53301 CAGAGAGATA
Statistics
Matches: 128, Mismatches: 35, Indels: 28
0.67 0.18 0.15
Matches are distributed among these distances:
42 2 0.02
43 41 0.32
44 42 0.33
45 38 0.30
46 5 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
TACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
Found at i:53222 original size:88 final size:88
Alignment explanation
Indices: 53061--53302 Score: 335
Period size: 88 Copynumber: 2.8 Consensus size: 88
53051 GGGTGTCTCC
* * *
53061 GATCTACTTTGCTGCTAGTACAGGAAGGCAAGATCTG-TCATTTTCAACCTACTCTACTGCTGCT
1 GATCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCT-ATTTTCAACCTACTCTACTGCTGCT
* * *
53125 CAGGGAGACAAGGCTGGTATCTTA
65 CAAGAAGACAAGGATGGTATCTTA
* * * *
53149 GATCCACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTG
1 GATCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCTACTGCTGCTC
*
53214 AAGAAGACAAGGATGGTATCTTC
66 AAGAAGACAAGGATGGTATCTTA
* *
53237 GATCTACTTCGCTGCTGATACAGGAAGACAAGATCTGCTAGTTTT-AACCTACTCTATTGCTGCT
1 GATCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTA-TTTTCAACCTACTCTACTGCTGCT
53301 CA
65 CA
53303 GAGAGATAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
88 130 0.96
89 5 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (88 bp):
GATCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCTACTGCTGCTC
AAGAAGACAAGGATGGTATCTTA
Found at i:54533 original size:21 final size:21
Alignment explanation
Indices: 54509--54557 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
54499 TTAGCCTTTC
*
54509 CATTTTTACTTTTTCATTT-TT
1 CATTTTT-CATTTTCATTTCTT
54530 CATTTTTCATTTTCATTTCTT
1 CATTTTTCATTTTCATTTCTT
54551 CATTTTT
1 CATTTTT
54558 TCACATCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATTTCTT
Found at i:54560 original size:8 final size:7
Alignment explanation
Indices: 54509--54557 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
54499 TTAGCCTTTC
54509 CATTTTT
1 CATTTTT
54516 -ACTTTTT
1 CA-TTTTT
54523 CATTTTT
1 CATTTTT
54530 CATTTTT
1 CATTTTT
54537 CA-TTTT
1 CATTTTT
54543 CATTTCTT
1 CATTT-TT
54551 CATTTTT
1 CATTTTT
54558 TCACATCACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 23 0.61
8 8 0.21
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:61328 original size:33 final size:33
Alignment explanation
Indices: 61280--61352 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
61270 TTCGTTAGAA
*
61280 AAAAAATATAAATAT-ATATACATATACATATAT
1 AAAAAATAGAAATATAATATACATATACAT-TAT
* * *
61313 AAAAAATAGATATATACATATATATATAGATTAT
1 AAAAAATAGAAATATA-ATATACATATACATTAT
61347 AAAAAA
1 AAAAAA
61353 ATAATTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 13 0.38
34 9 0.26
35 12 0.35
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (33 bp):
AAAAAATAGAAATATAATATACATATACATTAT
Found at i:61336 original size:31 final size:31
Alignment explanation
Indices: 61281--61382 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
61271 TCGTTAGAAA
* * * *
61281 AAAAATATAAATATATATACATATACATATAT
1 AAAAA-ATAGATATATACATATATAAATATAT
* *
61313 AAAAAATAGATATATACATATATATATAGATT
1 AAAAAATAGATATATACATATATAAATATA-T
61345 ATAAAAA-A-ATA-ATTACATATATAAAT-TAT
1 A-AAAAATAGATATA-TACATATATAAATATAT
61374 -AAAAATAGA
1 AAAAAATAGA
61383 AACAATAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.09
28 1 0.02
29 2 0.03
30 2 0.03
31 35 0.60
32 8 0.14
33 5 0.09
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAAATAGATATATACATATATAAATATAT
Found at i:61353 original size:35 final size:34
Alignment explanation
Indices: 61278--61355 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 34
61268 TATTCGTTAG
* *
61278 AAAAAAA-ATATAAATATATATACATATACATAT
1 AAAAAAATAGATAAATACATATACATATACATAT
* * *
61311 ATAAAAAATAGATATATACATATATATATAGATTAT
1 A-AAAAAATAGATAAATACATATACATATACA-TAT
61347 AAAAAAATA
1 AAAAAAATA
61356 ATTACATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.03
34 6 0.16
35 26 0.70
36 4 0.11
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (34 bp):
AAAAAAATAGATAAATACATATACATATACATAT
Found at i:79899 original size:64 final size:64
Alignment explanation
Indices: 79798--79930 Score: 196
Period size: 64 Copynumber: 2.1 Consensus size: 64
79788 TTTGCAAGCC
* *
79798 ATTTGTGTTTTATATTATTTGGATGGCATATTTTGACTGAAACTATTAGAGTTTTTAAATACAT
1 ATTTGTATTTTATATTATTTGGATGGCATATTTTGACTAAAACTATTAGAGTTTTTAAATACAT
* * * *
79862 ATTTGTATTTTATCTTATTT-GATTGGCATATTTTGACTAAAACTATTGGATTTTTTAAATGCAT
1 ATTTGTATTTTATATTATTTGGA-TGGCATATTTTGACTAAAACTATTAGAGTTTTTAAATACAT
79926 ATTTG
1 ATTTG
79931 AGGGCTTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
63 2 0.03
64 60 0.97
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (64 bp):
ATTTGTATTTTATATTATTTGGATGGCATATTTTGACTAAAACTATTAGAGTTTTTAAATACAT
Found at i:81162 original size:63 final size:63
Alignment explanation
Indices: 81063--81182 Score: 240
Period size: 63 Copynumber: 1.9 Consensus size: 63
81053 ATCAGAAATT
81063 AGCAAACTAATTGAAAGTCTACTATGTCATTTATCAAGTCCAATTGGTAGATGATTTTGCTCA
1 AGCAAACTAATTGAAAGTCTACTATGTCATTTATCAAGTCCAATTGGTAGATGATTTTGCTCA
81126 AGCAAACTAATTGAAAGTCTACTATGTCATTTATCAAGTCCAATTGGTAGATGATTT
1 AGCAAACTAATTGAAAGTCTACTATGTCATTTATCAAGTCCAATTGGTAGATGATTT
81183 GTCTTGAGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (63 bp):
AGCAAACTAATTGAAAGTCTACTATGTCATTTATCAAGTCCAATTGGTAGATGATTTTGCTCA
Found at i:81171 original size:33 final size:33
Alignment explanation
Indices: 81071--81171 Score: 77
Period size: 33 Copynumber: 3.2 Consensus size: 33
81061 TTAGCAAACT
81071 AATTGAAAGTCTACTATGTCATTTATCAAGTCC
1 AATTGAAAGTCTACTATGTCATTTATCAAGTCC
** * * * * * *
81104 AATTGGTAGAT-GATTTTGCTCA---AGCAA-ACT
1 AATTGAAAG-TCTACTATG-TCATTTATCAAGTCC
81134 AATTGAAAGTCTACTATGTCATTTATCAAGTCC
1 AATTGAAAGTCTACTATGTCATTTATCAAGTCC
81167 AATTG
1 AATTG
81172 GTAGATGATT
Statistics
Matches: 45, Mismatches: 16, Indels: 14
0.60 0.21 0.19
Matches are distributed among these distances:
29 4 0.09
30 12 0.27
31 4 0.09
32 4 0.09
33 17 0.38
34 4 0.09
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (33 bp):
AATTGAAAGTCTACTATGTCATTTATCAAGTCC
Found at i:82196 original size:16 final size:16
Alignment explanation
Indices: 82175--82210 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
82165 AATTTGGTTG
*
82175 AGAAAATTATTTAAGT
1 AGAAAATTAATTAAGT
*
82191 AGAAAATTAATTAATT
1 AGAAAATTAATTAAGT
82207 AGAA
1 AGAA
82211 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (16 bp):
AGAAAATTAATTAAGT
Found at i:84726 original size:44 final size:45
Alignment explanation
Indices: 84671--84777 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 45
84661 TATGTTTTGC
84671 TGTACATCCATAGCCAAAGACAGATTCCATCTGCGGGTACTTGTTG
1 TGTA-ATCCATAGCCAAAGACAGATTCCATCTGCGGGTACTTGTTG
** * * * * *
84717 TGT-ATCCATAATCAGAGATAGATTCCATCTGTGGTTAGTTGTTG
1 TGTAATCCATAGCCAAAGACAGATTCCATCTGCGGGTACTTGTTG
84761 TGTAATCCATAGCCAAA
1 TGTAATCCATAGCCAAA
84778 AGTAGGTTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 37 0.74
45 10 0.20
46 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (45 bp):
TGTAATCCATAGCCAAAGACAGATTCCATCTGCGGGTACTTGTTG
Found at i:97146 original size:14 final size:15
Alignment explanation
Indices: 97109--97151 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
97099 CTTCATCTTC
97109 TATTTATTTTCTCTCT
1 TATTT-TTTTCTCTCT
*
97125 T-TTCTTTTC-CTCT
1 TATTTTTTTCTCTCT
97138 TATTTTTTTCTCTC
1 TATTTTTTTCTCTC
97152 GTACTTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 5 0.22
16 1 0.04
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTTTCTCTCT
Found at i:97830 original size:38 final size:38
Alignment explanation
Indices: 97699--97879 Score: 179
Period size: 38 Copynumber: 4.8 Consensus size: 38
97689 ACACTACGAT
* * *
97699 TGTTG-ACTTGAAAGCATGTGAAGCATGCCTACTGCGAC
1 TGTTGAAC-TGAAAACATGTTAAGCATGTCTACTGCGAC
* * * * * *
97737 TGTTGACCTGAAAGCATGTGAAACATGCCTACTACGAC
1 TGTTGAACTGAAAACATGTTAAGCATGTCTACTGCGAC
* *
97775 TGTTGACCTGAAAACATGTTAAGCATGTCTACTGCAAC
1 TGTTGAACTGAAAACATGTTAAGCATGTCTACTGCGAC
* *
97813 TGTTGAACT-AAATACATGTTAAGCATGTCTAATGCTA-
1 TGTTGAACTGAAA-ACATGTTAAGCATGTCTACTGCGAC
**
97850 TCGTTGAACTGATTACATGTTAAGCATGTC
1 T-GTTGAACTGAAAACATGTTAAGCATGTC
97880 CATTGTTTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
37 4 0.03
38 119 0.95
39 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (38 bp):
TGTTGAACTGAAAACATGTTAAGCATGTCTACTGCGAC
Found at i:98509 original size:18 final size:19
Alignment explanation
Indices: 98486--98521 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
98476 ATTATAATTT
98486 ATGTTTT-GTTGAACTGTA
1 ATGTTTTAGTTGAACTGTA
*
98504 ATGTTTTATTTGAACTGT
1 ATGTTTTAGTTGAACTGT
98522 GGCATGAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (19 bp):
ATGTTTTAGTTGAACTGTA
Found at i:104438 original size:38 final size:37
Alignment explanation
Indices: 104387--104483 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 37
104377 GAACTGAAAG
* * *
104387 CATGTGAAGCATGTTTACTGTGATTGTTTAATTGAA-TA
1 CATGTTAAGCATGTTTACTGT-ACTGTTGAATT-AATTA
*
104425 CATGTTAAGCATGTTTATTGCTACTGTTGAATTAATTA
1 CATGTTAAGCATGTTTACTG-TACTGTTGAATTAATTA
*
104463 CATGTTAAGCATGTCTACTGT
1 CATGTTAAGCATGTTTACTGT
104484 TTCTGTATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.06
38 47 0.92
39 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (37 bp):
CATGTTAAGCATGTTTACTGTACTGTTGAATTAATTA
Found at i:104607 original size:16 final size:16
Alignment explanation
Indices: 104583--104636 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
104573 TTTGGTTCGA
* *
104583 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
104599 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
104615 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
104631 TGTAAT
1 TGTAAT
104637 AACAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:104887 original size:16 final size:16
Alignment explanation
Indices: 104850--104917 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
104840 TTAATCATAT
*
104850 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
104866 TT-AAATATATTATAA
1 TTAAAATATATTATAA
*
104881 TTAAAATATATAATTTAA
1 TTAAAATATAT--TATAA
104899 -TAAAAT-TATTAATAA
1 TTAAAATATATT-ATAA
104914 TTAA
1 TTAA
104918 TATTCTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 13 0.30
16 16 0.37
17 6 0.14
18 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:104891 original size:18 final size:18
Alignment explanation
Indices: 104870--104917 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
104860 TTATTATTAA
104870 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
104888 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
104905 -TAT-TAATAATTAA
1 ATATATTATAATTAA
104918 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:104898 original size:14 final size:15
Alignment explanation
Indices: 104859--104900 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
104849 TTTAAACATA
*
104859 ATTATTATTAAATAT
1 ATTATAATTAAATAT
104874 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
104888 A-TATAATTTAATA
1 ATTATAATTAAATA
104901 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:105237 original size:91 final size:91
Alignment explanation
Indices: 105041--105296 Score: 473
Period size: 91 Copynumber: 2.8 Consensus size: 91
105031 TAATTATACC
* *
105041 TAATAAATTTTCTTATATGAATTTATATATTTTAAAATAATTATTATTAAATATAATTTAAT-A-
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
105104 -ATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
105129 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
105194 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
105220 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
105285 GATATATAATTT
66 GATATATAATTT
105297 GTACATTTAA
Statistics
Matches: 163, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
88 60 0.37
89 1 0.01
91 102 0.63
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:105291 original size:44 final size:43
Alignment explanation
Indices: 105064--105296 Score: 179
Period size: 44 Copynumber: 5.2 Consensus size: 43
105054 TATATGAATT
* *
105064 TATATATTTTAAAATAATTATTATTAAATATAATTTAATAATA
1 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATA
* ** * * * *
105107 TATA-ATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATT
1 TATATAATT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATA
105152 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
1 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-A
** * * * *
105196 TATATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATT
1 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATA
105243 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
1 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-A
105287 TATATAATTT
1 TATATAATTT
105297 GTACATTTAA
Statistics
Matches: 146, Mismatches: 26, Indels: 35
0.71 0.13 0.17
Matches are distributed among these distances:
42 5 0.03
43 14 0.10
44 70 0.48
45 18 0.12
46 11 0.08
47 25 0.17
48 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (43 bp):
TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATA
Found at i:106314 original size:17 final size:17
Alignment explanation
Indices: 106292--106327 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
106282 GCACTTAATA
106292 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
106309 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
106326 TA
1 TA
106328 CAGCAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TAACTCATATTTCAAAT
Found at i:107896 original size:30 final size:30
Alignment explanation
Indices: 107862--107922 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
107852 CCACTGCTGT
* *
107862 TGATGTTGTTGTTGTT-ACAGATGATGATGA
1 TGATGTTGCTGTTGTTGA-AAATGATGATGA
107892 TGATGTTGCTGTTGTTGAAAATGATGATGA
1 TGATGTTGCTGTTGTTGAAAATGATGATGA
107922 T
1 T
107923 TCTGCACCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.43
Consensus pattern (30 bp):
TGATGTTGCTGTTGTTGAAAATGATGATGA
Found at i:109749 original size:32 final size:32
Alignment explanation
Indices: 109708--109778 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
109698 ATTTTAGAGG
* ** *
109708 TTGATTAATACAAATCCTTGAAGAAATTAATA
1 TTGATTAATACAAACCCTCAAAGAAATTAAGA
*
109740 TTGATTAATACAAACCCTCAAAGAAATTAGGA
1 TTGATTAATACAAACCCTCAAAGAAATTAAGA
109772 TTGATTA
1 TTGATTA
109779 GAAATTTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (32 bp):
TTGATTAATACAAACCCTCAAAGAAATTAAGA
Found at i:111502 original size:10 final size:10
Alignment explanation
Indices: 111452--111495 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
111442 TGGCCTCTCA
*
111452 TTTTTCTGTTC
1 TTTTTCT-TTT
111463 TTTTTCTTTT
1 TTTTTCTTTT
111473 TTTTTCTTTT
1 TTTTTCTTTT
111483 TTTTTCTTTT
1 TTTTTCTTTT
111493 TTT
1 TTT
111496 CTTTTTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:115712 original size:6 final size:6
Alignment explanation
Indices: 115652--115710 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
115642 AGAACAAAAA
* *
115652 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TACTAA
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
*
115700 TAATAA TAATA
1 TAATAC TAATA
115711 ATGAAAAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
TAATAC
Found at i:115923 original size:23 final size:22
Alignment explanation
Indices: 115883--115926 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
115873 AAATTATAAA
*
115883 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
115905 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
115927 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:116655 original size:23 final size:22
Alignment explanation
Indices: 116612--116669 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
116602 AATGGGTATC
* *
116612 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
116633 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
116656 TGCATATCATATCT
1 TACAAATCATATCT
116670 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:116685 original size:21 final size:21
Alignment explanation
Indices: 116648--116702 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
116638 AATCATATCT
116648 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
116667 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
116688 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
116703 CCTTGAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.32
21 23 0.68
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:117779 original size:16 final size:16
Alignment explanation
Indices: 117752--117786 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
117742 ATTACCATAT
117752 TTAAATTAATTTACTTA
1 TTAAATTAATTTA-TTA
117769 TTAAA-TAATTTATTA
1 TTAAATTAATTTATTA
117784 TTA
1 TTA
117787 GATTCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 7 0.39
17 5 0.28
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAATTAATTTATTA
Found at i:122671 original size:42 final size:43
Alignment explanation
Indices: 122593--122718 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 43
122583 TCTAGGACGT
* * * *
122593 TGGCATCAATT-TAAGATTTACGTGTAAGACCATGTCTGGGGCAT
1 TGGCATC-ATTATATGA-TTACGTGTAAGACCCTGTCTGGGACAG
*
122637 TGGCGTCA-TATATGATTACGTGTAAGACCCTGTCTGGGACAG
1 TGGCATCATTATATGATTACGTGTAAGACCCTGTCTGGGACAG
* *
122679 TGGCATCATTATTTGATTACATGTAAGACCAC-GTCTGGGA
1 TGGCATCATTATATGATTACGTGTAAGACC-CTGTCTGGGA
122719 TGTTGGCATT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
42 32 0.45
43 32 0.45
44 7 0.10
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
TGGCATCATTATATGATTACGTGTAAGACCCTGTCTGGGACAG
Found at i:122726 original size:43 final size:42
Alignment explanation
Indices: 122569--122727 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 42
122559 AATGTGTTAT
* *
122569 CGTGTAAGACCACATCTAGGACGTTGGCATCA-ATTTAAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCATATTT--GA-TTA
* * * * *
122613 CGTGTAAGACCATGTCTGGGGCATTGGCGTCATATATGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTA
122655 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCATTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCA-TATTTGATTA
* *
122698 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
122728 TGTACGAGCC
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
42 30 0.32
43 35 0.37
44 27 0.28
45 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTA
Found at i:126367 original size:18 final size:20
Alignment explanation
Indices: 126344--126390 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
126334 TAGCAAATGG
*
126344 TGTGAAATGGAA-GTGAAA-
1 TGTGAAATGGAATATGAAAT
126362 TGTGAAATGGAATATGAAAT
1 TGTGAAATGGAATATGAAAT
126382 TGTGAAATG
1 TGTGAAATG
126391 AGTTGGGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
19 5 0.19
20 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (20 bp):
TGTGAAATGGAATATGAAAT
Found at i:136701 original size:19 final size:19
Alignment explanation
Indices: 136677--136721 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
136667 CCTATTTTTT
*
136677 TGCATT-CATCTCATTCATC
1 TGCATTACATCTCA-TCATA
*
136696 TGCATTACATGTCATCATA
1 TGCATTACATCTCATCATA
136715 TGCATTA
1 TGCATTA
136722 AGTTTCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (19 bp):
TGCATTACATCTCATCATA
Found at i:144200 original size:45 final size:45
Alignment explanation
Indices: 144136--144225 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
144126 TCCATTTCAT
*
144136 TCATTTTGTATTTTGGCAAAATGTGCTATCTTGATTAATTTATTC
1 TCATTTTGTATTTTAGCAAAATGTGCTATCTTGATTAATTTATTC
* *
144181 TCATTTTGTATTTTAGCAAAATTTTCTATCTTGATTAATTTATTC
1 TCATTTTGTATTTTAGCAAAATGTGCTATCTTGATTAATTTATTC
144226 ATTTCAAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (45 bp):
TCATTTTGTATTTTAGCAAAATGTGCTATCTTGATTAATTTATTC
Found at i:153700 original size:25 final size:25
Alignment explanation
Indices: 153672--153726 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
153662 CTCGCATGAA
*
153672 CTTCCCGATATATATCTTGATTAAG
1 CTTCCCGATATATAGCTTGATTAAG
* *
153697 CTTCTCGATATATAGCTTGATTGAG
1 CTTCCCGATATATAGCTTGATTAAG
153722 CTTCC
1 CTTCC
153727 TGTTATATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (25 bp):
CTTCCCGATATATAGCTTGATTAAG
Found at i:158236 original size:40 final size:41
Alignment explanation
Indices: 158133--158238 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 41
158123 TAACTCATTC
*
158133 AATGCCTTC-GGACTTAACCCGG-ATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAATTTTAAAACTCACACG
158172 AATGCCTTCGGGACTTAACCCGGAATTTT-AAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGAATTTTAAAACTCACACG
158212 AATGCCTTCGGGACTTAACCCGGAATT
1 AATGCCTTCGGGACTTAACCCGGAATT
158239 AGTATCTCGC
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
39 9 0.14
40 50 0.78
41 5 0.08
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (41 bp):
AATGCCTTCGGGACTTAACCCGGAATTTTAAAACTCACACG
Found at i:158259 original size:40 final size:41
Alignment explanation
Indices: 158133--158314 Score: 166
Period size: 40 Copynumber: 4.6 Consensus size: 41
158123 TAACTCATTC
* *
158133 AATGCCTTC-GGACTTAACCCGG-ATT-TTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAATTAGT-AAACTCGCACA
* * *
158172 AATGCCTTCGGGACTTAACCCGGAATT-TTAAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAAACTCGCACA
*
158212 AATGCCTTCGGGACTTAACCCGGAATTAGT-ATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAAACTCGCACA
* ** * *
158252 AAGGCCTTC-GGACTTAGTCCGG-ATATAGT-CACTTAGCACA
1 AATGCCTTCGGGACTTAACCCGGAAT-TAGTAAAC-TCGCACA
*
158292 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
158315 CAACATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 85 0.69
41 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (41 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAAACTCGCACA
Found at i:166100 original size:40 final size:40
Alignment explanation
Indices: 166024--166114 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
166014 TAACTCATTC
* *
166024 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
* *
166064 AATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACA
*
166104 AAGGCCTTCGG
1 AATGCCTTCGG
166115 ATCTTAGTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
Found at i:168104 original size:43 final size:41
Alignment explanation
Indices: 168034--168188 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 41
168024 TGAGTTGTTG
* * *
168034 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATTT--GATTACA
* * *
168077 TGTAAGACCATGTCTAGGACATAGGCATCGTATTTGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCG-ATTTGATTACA
* *
168119 TGTAAGACCTTGTCTGGGACATTGGTATCGATATTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGAT-TTGATTACA
* **
168161 TGTAAGACCAGGTCTGGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
168189 TGTACGTGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.02
42 62 0.66
43 26 0.28
44 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATTTGATTACA
Found at i:168493 original size:25 final size:25
Alignment explanation
Indices: 168458--168509 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
168448 CATGAGCTAA
*
168458 TTGAATTAATTTGATTATAAATGTT
1 TTGAATGAATTTGATTATAAATGTT
*
168483 TTGAATGAATTTGATTTTAAATGTT
1 TTGAATGAATTTGATTATAAATGTT
168508 TT
1 TT
168510 ATGTGATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (25 bp):
TTGAATGAATTTGATTATAAATGTT
Found at i:170836 original size:43 final size:47
Alignment explanation
Indices: 170728--170849 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 47
170718 TAACTTCAGT
* * * *
170728 TATATACATATATTGGCACTTAGTGTGCGTGATTGAGATAGCTCCTGC
1 TATATATA-ATATTGGCACTTAGTGTGCGAGATTGAGATAGATCCGGC
* *
170776 TATATATACATATTGGCACTTAGTGTGCGAGATTGATATAGATTCGGC
1 TATATATA-ATATTGGCACTTAGTGTGCGAGATTGAGATAGATCCGGC
*
170824 TAT-T-T-AT-TTGGCACTAAGTGTGCGAG
1 TATATATAATATTGGCACTTAGTGTGCGAG
170850 TTTCTGGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
43 18 0.27
44 2 0.03
46 1 0.02
47 1 0.02
48 44 0.67
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (47 bp):
TATATATAATATTGGCACTTAGTGTGCGAGATTGAGATAGATCCGGC
Found at i:176143 original size:48 final size:47
Alignment explanation
Indices: 176091--176264 Score: 179
Period size: 48 Copynumber: 3.6 Consensus size: 47
176081 GTGATATGTG
176091 TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATCCA
1 TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATAT-CA
* * * * *** *
176139 TGCTAGTGTAAGACAATGTTTGGAACATGGTATCGGC-CACATTATGA
1 TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGA-TATCA
* * * **
176186 GAGATAGTGTAAGACCATGTCTGGGACATGGCATCAGCGTTGATATGTG
1 -TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATAT-CA
*
176235 TGCTAGTGTAAGTCCATGTCTGGGACATGG
1 TGCTAGTGTAAGACCATGTCTGGGACATGG
176265 TGTAACACCC
Statistics
Matches: 99, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
47 2 0.02
48 96 0.97
49 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (47 bp):
TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATCA
Found at i:177163 original size:18 final size:20
Alignment explanation
Indices: 177121--177157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
177111 ATATTTTATG
*
177121 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
177140 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
177158 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:179371 original size:46 final size:46
Alignment explanation
Indices: 179319--179637 Score: 419
Period size: 46 Copynumber: 7.0 Consensus size: 46
179309 AGTGTGCTCT
179319 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
179365 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
179411 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCGTGGC-AC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
179456 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** *
179502 ATGACGA-GAAATAAATAAGACCATGGTTGAAAGATACCATGGCATC
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
179548 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
179594 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
179638 TCATGTCAAA
Statistics
Matches: 248, Mismatches: 21, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
45 45 0.18
46 202 0.81
47 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:179567 original size:137 final size:137
Alignment explanation
Indices: 179319--179660 Score: 438
Period size: 137 Copynumber: 2.5 Consensus size: 137
179309 AGTGTGCTCT
* * ***
179319 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAATAAATAAG
* **
179384 ACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAACGTGTAAGACCATGGTTGAAAGATACC
65 ACCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACC
*
179449 GTGGC-AC
130 ATGGCAAC
*
179456 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATAAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATAAATAAG
* * *
179521 ACCATGGTTGAAAGATACCATGGCATCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACC
65 ACCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACC
179586 ATGGCAAC
130 ATGGCAAC
* * * * * * * *
179594 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAATAA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAA-ATAAATAA
179657 GACC
64 GACC
179661 GTGGATGGGA
Statistics
Matches: 179, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
136 2 0.01
137 134 0.75
138 43 0.24
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (137 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATAAATAAGA
CCATGGTTGAAAGATACCATGGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGATACCA
TGGCAAC
Found at i:181472 original size:52 final size:50
Alignment explanation
Indices: 181365--181541 Score: 214
Period size: 52 Copynumber: 3.5 Consensus size: 50
181355 AGATACCCGA
* ** * *
181365 TGGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACAAAG
1 TGGCCTTCACATAGTACCATACTTGTGA-CCAAA-CTATCTTCTTCACAAAG
181416 TGGCCTTCACATAGTACCATACTTGTGACCTAAACTATCTTTCTTCACAAAG
1 TGGCCTTCACATAGTACCATACTTGTGACC-AAACTATC-TTCTTCACAAAG
* * *
181468 TGGCCTTCACATAGTACCATACTTGTGACCAAGCTATC-TCTTCTCAATG
1 TGGCCTTCACATAGTACCATACTTGTGACCAAACTATCTTCTTCACAAAG
* *
181517 TGGCTTTCACATAGTACCACACTTG
1 TGGCCTTCACATAGTACCATACTTG
181542 AGTCACTAGT
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
49 32 0.28
51 35 0.31
52 46 0.41
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (50 bp):
TGGCCTTCACATAGTACCATACTTGTGACCAAACTATCTTCTTCACAAAG
Found at i:182411 original size:9 final size:9
Alignment explanation
Indices: 182397--182422 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
182387 TAAAAATATT
182397 CTATTTCAC
1 CTATTTCAC
182406 CTATTTCAC
1 CTATTTCAC
182415 CTATTTCA
1 CTATTTCA
182423 TGTCCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (9 bp):
CTATTTCAC
Found at i:182802 original size:48 final size:47
Alignment explanation
Indices: 182721--182971 Score: 243
Period size: 48 Copynumber: 5.2 Consensus size: 47
182711 GGGCTGTTAC
*** *
182721 ACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGG
1 ACATGGCATCGGCTTGA-TATGAGAGCTAGTGTAAGACCATGTCTGGG
* * * * * *
182769 ACATGGCACCGACGTTGATATGTGTGCTAGTGTAAGACCATGTTTGGA
1 ACATGGCATCGGC-TTGATATGAGAGCTAGTGTAAGACCATGTCTGGG
* *** *
182817 ACATGCCATCGGCCACATTATGAGAGCTAGTGTAAAACCATGTCTGGG
1 ACATGGCATCGGCTTGA-TATGAGAGCTAGTGTAAGACCATGTCTGGG
*
182865 ACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACCATGTCTGGG
1 ACATGGCATCGGC-TTGATATGAGAGCTAGTGTAAGACCATGTCTGGG
* * * * * *
182913 ACATGGCATCGGCCTCGACATGTA-AGCCAATGTAAAACCATGTTTGGG
1 ACATGGCATCGG-CTTGATATG-AGAGCTAGTGTAAGACCATGTCTGGG
182961 ACATGGCATCG
1 ACATGGCATCG
182972 AAAATTTACC
Statistics
Matches: 165, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
47 1 0.01
48 160 0.97
49 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (47 bp):
ACATGGCATCGGCTTGATATGAGAGCTAGTGTAAGACCATGTCTGGG
Found at i:182894 original size:96 final size:96
Alignment explanation
Indices: 182721--182972 Score: 337
Period size: 96 Copynumber: 2.6 Consensus size: 96
182711 GGGCTGTTAC
* * *
182721 ACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCACCGACGTTG
1 ACATGGCATCGGCCACATTATGAGAGCCAGTGTAAAACCATGTCTGGGACATGGCATCGACATTG
* * * *
182786 ATATGTGTGCTAGTGTAAGACCATGTTTGGA
66 AGATGAGAGCTAGTGTAAGACCATGTCTGGA
* * *
182817 ACATGCCATCGGCCACATTATGAGAGCTAGTGTAAAACCATGTCTGGGACATGGCATCGGCATTG
1 ACATGGCATCGGCCACATTATGAGAGCCAGTGTAAAACCATGTCTGGGACATGGCATCGACATTG
*
182882 AGATGAGAGCTAGTGTAAGACCATGTCTGGG
66 AGATGAGAGCTAGTGTAAGACCATGTCTGGA
* * * *
182913 ACATGGCATCGGCCTCGA-CATGTA-AGCCAATGTAAAACCATGTTTGGGACATGGCATCGA
1 ACATGGCATCGGCCAC-ATTATG-AGAGCCAGTGTAAAACCATGTCTGGGACATGGCATCGA
182973 AAATTTACCC
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 134 0.99
97 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (96 bp):
ACATGGCATCGGCCACATTATGAGAGCCAGTGTAAAACCATGTCTGGGACATGGCATCGACATTG
AGATGAGAGCTAGTGTAAGACCATGTCTGGA
Found at i:183477 original size:14 final size:16
Alignment explanation
Indices: 183458--183507 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
183448 CAAAGATAAC
183458 AAGAAAAT-C-GAATA
1 AAGAAAATCCAGAATA
183472 AAG-AAATCCAGAATA
1 AAGAAAATCCAGAATA
* *
183487 AAG-AGATCCAGGATA
1 AAGAAAATCCAGAATA
183502 AAGAAA
1 AAGAAA
183508 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 21 0.70
16 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.18, T:0.12
Consensus pattern (16 bp):
AAGAAAATCCAGAATA
Found at i:183487 original size:15 final size:15
Alignment explanation
Indices: 183467--183507 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
183457 CAAGAAAATC
183467 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
183482 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
*
183497 GGATAAAGAAA
1 GAATAAAGAAA
183508 CCCAAGATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:183516 original size:15 final size:15
Alignment explanation
Indices: 183469--183516 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
183459 AGAAAATCGA
183469 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
183483 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
183499 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
183514 ATA
1 ATA
183517 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:186522 original size:46 final size:46
Alignment explanation
Indices: 186447--186575 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
186437 TGTAACCCGC
* * * *
186447 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
186493 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
186539 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
186576 TGCCAACCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:188969 original size:14 final size:16
Alignment explanation
Indices: 188950--188999 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
188940 CAAAGATAAC
188950 AAGAAAAT-CA-AATA
1 AAGAAAATCCAGAATA
188964 AAG-AAATCCAGAATA
1 AAGAAAATCCAGAATA
* *
188979 AAG-AGATCCAGGATA
1 AAGAAAATCCAGAATA
188994 AAGAAA
1 AAGAAA
189000 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 5 0.17
15 20 0.67
16 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.16, T:0.12
Consensus pattern (16 bp):
AAGAAAATCCAGAATA
Found at i:188980 original size:15 final size:15
Alignment explanation
Indices: 188960--188999 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
188950 AAGAAAATCA
188960 AATAAAGAAATCCAG
1 AATAAAGAAATCCAG
*
188975 AATAAAGAGATCCAG
1 AATAAAGAAATCCAG
*
188990 GATAAAGAAA
1 AATAAAGAAA
189000 CCCAAGATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12
Consensus pattern (15 bp):
AATAAAGAAATCCAG
Found at i:189008 original size:15 final size:15
Alignment explanation
Indices: 188961--189008 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
188951 AGAAAATCAA
188961 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
188975 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
188991 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
189006 ATA
1 ATA
189009 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:192044 original size:47 final size:49
Alignment explanation
Indices: 191922--192099 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 49
191912 TGTAACCCGC
* *
191922 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACAT
* *
191968 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
192018 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
192060 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
192100 TCAACCATCC
Statistics
Matches: 110, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
42 6 0.05
43 2 0.02
44 2 0.02
45 26 0.24
46 37 0.34
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
Found at i:192087 original size:92 final size:93
Alignment explanation
Indices: 191929--192099 Score: 290
Period size: 92 Copynumber: 1.8 Consensus size: 93
191919 CGCCCATAAG
* * *
191929 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
191994 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
192022 CGAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
192086 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
192100 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 47 0.64
93 26 0.36
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:198201 original size:54 final size:54
Alignment explanation
Indices: 198098--198202 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
198088 TGTGTTCGCC
* * * *
198098 AGTCTGTTTGGCGAGCTGGTGTTCACTAGGTAAGTTGCGAGCTGTGGGTTCGTT
1 AGTCTGTTTGGCGAGCTAGTGTTCACCAAGTAAGTTGCGAACTGTGGGTTCGTT
* * *
198152 AGTCTGTTTGGTGAGCTAGTGTTCACCAATTAAGTTGTGAACTAG-GGGTTC
1 AGTCTGTTTGGCGAGCTAGTGTTCACCAAGTAAGTTGCGAACT-GTGGGTTC
198203 ACCAGTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.35
Consensus pattern (54 bp):
AGTCTGTTTGGCGAGCTAGTGTTCACCAAGTAAGTTGCGAACTGTGGGTTCGTT
Found at i:201064 original size:18 final size:18
Alignment explanation
Indices: 201041--201079 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
201031 TTAAATTATG
*
201041 AAATAA-AAAAATTAACTA
1 AAATAAGAAAAAATAA-TA
201059 AAATAAGAAAAAATAATA
1 AAATAAGAAAAAATAATA
201077 AAA
1 AAA
201080 AGAAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAGAAAAAATAATA
Found at i:202695 original size:45 final size:45
Alignment explanation
Indices: 202631--202763 Score: 223
Period size: 45 Copynumber: 3.0 Consensus size: 45
202621 ATACGTACGG
*
202631 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
202676 TACTACTT-GGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGA
1 TACTA-TTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
202721 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
202764 AATGATATCG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
44 2 0.02
45 78 0.95
46 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:202789 original size:26 final size:26
Alignment explanation
Indices: 202750--202801 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
202740 CCTAGCAGGC
**
202750 TATAATGCCGGTGAAATGATATCGGG
1 TATAATGCAAGTGAAATGATATCGGG
202776 TATAATGCAAGTGAAATGATATCGGG
1 TATAATGCAAGTGAAATGATATCGGG
202802 CTTCGAGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.27
Consensus pattern (26 bp):
TATAATGCAAGTGAAATGATATCGGG
Found at i:203783 original size:21 final size:21
Alignment explanation
Indices: 203745--203784 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
203735 CCTACAGTTC
* *
203745 AAAATTTTCAACTCTTTTCCT
1 AAAATTTCCAAATCTTTTCCT
*
203766 AAAATTTCCAAATGTTTTC
1 AAAATTTCCAAATCTTTTC
203785 AATTTAGTCC
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:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (21 bp):
AAAATTTCCAAATCTTTTCCT
Found at i:223949 original size:42 final size:42
Alignment explanation
Indices: 223902--224049 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
223892 GATTACGTGG
*
223902 AAGACCATATCTGGGATATGGCATCAATATAAGACTTCATGT
1 AAGACCATATCTGGGATATGGCATCGATATAAGACTTCATGT
* ** *
223944 AAGACCATATCTGGGATATGACATCGATATGAAG-CTTTGTAT
1 AAGACCATATCTGGGATATGGCATCGATAT-AAGACTTCATGT
* * * ** *
223986 AAAACCATAGCTGGGCTATTGGCATCGATACGAGA-TCCCATGT
1 AAGACCATATCTGGGATA-TGGCATCGATATAAGACT-TCATGT
224029 AAGACCATATCTAGGGTATAT
1 AAGACCATATCT-GGG-ATAT
224050 CATTGGCATG
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
42 51 0.62
43 25 0.30
44 4 0.05
45 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (42 bp):
AAGACCATATCTGGGATATGGCATCGATATAAGACTTCATGT
Found at i:225865 original size:27 final size:27
Alignment explanation
Indices: 225459--225864 Score: 598
Period size: 27 Copynumber: 15.0 Consensus size: 27
225449 GGAAAGTTAT
225459 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
**
225486 CGAAATACCTTTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
225513 CGAAATACCCTTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
225540 CGAAATACCCTTGTAGGGTGGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
225567 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
225594 CGAAATACCCTTTTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
225621 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
225648 CGAAATACCCCTGTAGGGTAGAATTAT
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
225675 CGAAATACCCCTGTAAGGTAGAATTGC
1 CGAAATACCCCTGTAGGGTAGAATTAC
** *
225702 TAAAATACCCCTGTATGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
225729 CGAAATACCCTTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
225756 CGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
225783 TGAAATACCCCTGTAGGGTAGAACTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
225810 TGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * *
225837 C-AAGATACCCTTGTGGGGTAAAATTAC
1 CGAA-ATACCCCTGTAGGGTAGAATTAC
225864 C
1 C
225865 ATTTTGCCCC
Statistics
Matches: 344, Mismatches: 34, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
26 2 0.01
27 342 0.99
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:226130 original size:28 final size:28
Alignment explanation
Indices: 226089--226177 Score: 137
Period size: 28 Copynumber: 3.2 Consensus size: 28
226079 GGAGGAAGCG
226089 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
226117 TTCTGGTGGTTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
226144 TTCTGGTGGCTCTGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
226171 ATCTGGT
1 TTCTGGT
226178 AACTCTGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 8 0.14
27 22 0.39
28 26 0.46
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:226159 original size:27 final size:26
Alignment explanation
Indices: 226088--226198 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 26
226078 TGGAGGAAGC
226088 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
226115 GTTTCTGGTGGTTATGCCACAAATATCT
1 G-TTCTGGTGGCTATGCCAC-AATATCT
*
226143 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
** * *
226169 GTATCTGGTAACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
226196 GTT
1 GTT
226199 GACTGATCGA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 10 0.13
27 40 0.53
28 26 0.34
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:226728 original size:31 final size:31
Alignment explanation
Indices: 226693--226765 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
226683 TTGCATTCAC
* * * *
226693 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTAATTATGTCACCTGATACTG
*
226724 ATTCTGATTCTAATTATGTCACCTGATTCTG
1 ATTCTGATTCTAATTATGTCACCTGATACTG
226755 ATTCTGATTCT
1 ATTCTGATTCT
226766 CATTTTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTAATTATGTCACCTGATACTG
Found at i:226732 original size:6 final size:6
Alignment explanation
Indices: 226693--226786 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
226683 TTGCATTCAC
* * * *
226693 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTATG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
226742 -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCTA ATTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT
226787 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
5 3 0.05
6 56 0.85
7 5 0.08
8 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:226795 original size:18 final size:17
Alignment explanation
Indices: 226774--226807 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
226764 CTCATTTTGA
226774 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
226792 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
226808 GGCTAAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:229357 original size:27 final size:27
Alignment explanation
Indices: 228818--229357 Score: 740
Period size: 27 Copynumber: 20.0 Consensus size: 27
228808 AAAGTTATCG
* *
228818 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
*
228845 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
*
228872 AAATACCCTTGTAGGGTAGAATTATCA
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
228899 AAAAACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
*
228926 AAATACCCTTGTAGGGTCGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
**
228953 AAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACCA
*
228980 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
* * *
229007 AAATACCCCTATAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
229034 AAATACCCCTATAGGGTAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
*
229061 AAATACCCTTGTAGGGTAGAATTACGA
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
229088 AAATACCCTTGTAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACCA
* * *
229115 AAATACCCCTGTAAGATAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
229142 AAATATCCC-TGTAGGATAGAATTATCA
1 AAATA-CCCTTGTAGGGTAGAATTACCA
* *
229169 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAATTACCA
* * *
229196 AAATACCCCTGTATGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCA
229223 AAATACCCTTGTAGGGTAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
229250 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAATTACCA
* *
229277 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAATTACCA
*
229304 AAATACCCCTGTAGGGTAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
* * *
229331 AGATACCCTTGTGGGGTAAAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCA
229358 TTTTGCCCGT
Statistics
Matches: 466, Mismatches: 45, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
26 3 0.01
27 460 0.99
28 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AAATACCCTTGTAGGGTAGAATTACCA
Found at i:229622 original size:28 final size:28
Alignment explanation
Indices: 229581--229690 Score: 145
Period size: 27 Copynumber: 4.0 Consensus size: 28
229571 GGAGGAAGCG
229581 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
229609 TTCTGGTGGTTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
229636 TTCTGGTGGCTCTGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
* * * *
229663 ATCTGGTGACTCTGTCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
229690 T
1 T
229691 GACTGATCGA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.11
27 40 0.54
28 26 0.35
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:230220 original size:31 final size:31
Alignment explanation
Indices: 230185--230257 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
230175 TTGCATTCAC
* * * *
230185 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTAATTATGTCACCTGATACTG
*
230216 ATTCTGATTCTAATTATGTCACCTGATTCTG
1 ATTCTGATTCTAATTATGTCACCTGATACTG
230247 ATTCTGATTCT
1 ATTCTGATTCT
230258 CATTTTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTAATTATGTCACCTGATACTG
Found at i:230224 original size:6 final size:6
Alignment explanation
Indices: 230185--230278 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
230175 TTGCATTCAC
* * * *
230185 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTATG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
230234 -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCTA ATTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT
230279 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
5 3 0.05
6 56 0.85
7 5 0.08
8 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:230287 original size:18 final size:17
Alignment explanation
Indices: 230266--230299 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
230256 CTCATTTTGA
230266 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
230284 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
230300 GGCTAAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:235359 original size:24 final size:25
Alignment explanation
Indices: 235306--235370 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
235296 GAGGAAGTGC
235306 AAAAGGGCTTTTGCCCTAGTTTACCGA
1 AAAAGGGC-TTTGCCCTAGTTTACC-A
*
235333 AAAA-GGCTTTGCCC-AGTTTATCA
1 AAAAGGGCTTTGCCCTAGTTTACCA
235356 AAAAGGGCTTTGCCC
1 AAAAGGGCTTTGCCC
235371 CAGTCATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 5 0.14
24 17 0.47
25 7 0.19
26 3 0.08
27 4 0.11
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGTTTACCA
Found at i:235633 original size:30 final size:32
Alignment explanation
Indices: 235597--235672 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 32
235587 CATTTACAGT
*
235597 AAAGGCTTCGGCCCAA-TGATATG-ATAATGA
1 AAAGGCTTCGGCCCAAGTGACATGAATAATGA
*
235627 AAAGGCTTCGG-CCAAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAAGTGACATGAATAATGA
235658 AAAGGCTTCGGCCCA
1 AAAGGCTTCGGCCCA
235673 GTATATGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 17 0.41
31 17 0.41
32 3 0.07
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAAGTGACATGAATAATGA
Found at i:235662 original size:31 final size:29
Alignment explanation
Indices: 235597--235670 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 29
235587 CATTTACAGT
*
235597 AAAGGCTTCGGCCCAATGATATGATAATGA
1 AAAGGCTTCGG-CCAATGACATGATAATGA
*
235627 AAAGGCTTCGGCCAAGTGACATGAATAATGC
1 AAAGGCTTCGGCCAA-TGACATG-ATAATGA
235658 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
235671 CAGTATATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.10
30 17 0.43
31 19 0.47
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (29 bp):
AAAGGCTTCGGCCAATGACATGATAATGA
Found at i:241288 original size:55 final size:55
Alignment explanation
Indices: 241195--241316 Score: 140
Period size: 55 Copynumber: 2.2 Consensus size: 55
241185 AGCCCCGCGT
** * *
241195 CCGTGTTAATTTAACAGGTTTGACCACGGGTGTTCCACACGGGCGTGTCGA-ACGC
1 CCGTGTTGTTTTAACAGGTTTGACCACGGGTCTTCCACACGGCCGTGTC-ATACGC
* * *
241250 CCGTTTTGTTTTAACAGGTTCT-CCCACGGTTCTTCCACACGGCCGTGTCATACGC
1 CCGTGTTGTTTTAACAGGTT-TGACCACGGGTCTTCCACACGGCCGTGTCATACGC
*
241305 TCGTGTTGTTTT
1 CCGTGTTGTTTT
241317 GGCAGGCTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 1 0.02
55 54 0.96
56 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.33
Consensus pattern (55 bp):
CCGTGTTGTTTTAACAGGTTTGACCACGGGTCTTCCACACGGCCGTGTCATACGC
Found at i:241332 original size:55 final size:55
Alignment explanation
Indices: 241195--241333 Score: 136
Period size: 55 Copynumber: 2.5 Consensus size: 55
241185 AGCCCCGCGT
** * * * *
241195 CCGTGTTAATTTAACAGGTTTGACCACGGGTGTTCCACACGGGCGTGTCGAACGC
1 CCGTGTTGTTTTAACAGGCTCGACCACGGGTCTTCCACACGGCCGTGTCGAACGC
* * ** *
241250 CCGTTTTGTTTTAACAGGTTCTCCCACGGTTCTTCCACACGGCCGTGTC-ATACGC
1 CCGTGTTGTTTTAACAGGCTCGACCACGGGTCTTCCACACGGCCGTGTCGA-ACGC
* **
241305 TCGTGTTGTTTTGGCAGGCTCGACCACGG
1 CCGTGTTGTTTTAACAGGCTCGACCACGG
241334 CCCTATCGCA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
54 1 0.01
55 66 0.99
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (55 bp):
CCGTGTTGTTTTAACAGGCTCGACCACGGGTCTTCCACACGGCCGTGTCGAACGC
Found at i:244071 original size:27 final size:27
Alignment explanation
Indices: 244033--244089 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
244023 TAAATAATTC
244033 ACTTAACTTATTTAATAATGAACGTAT
1 ACTTAACTTATTTAATAATGAACGTAT
*
244060 ACTTAACTTATTTAATAATGAATGTAT
1 ACTTAACTTATTTAATAATGAACGTAT
244087 ACT
1 ACT
244090 CCTGCTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (27 bp):
ACTTAACTTATTTAATAATGAACGTAT
Found at i:251708 original size:23 final size:22
Alignment explanation
Indices: 251656--251708 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
251646 TCCACGTCTT
*
251656 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
251678 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
251701 TTTCTTTT
1 TTTCTTTT
251709 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:258917 original size:23 final size:23
Alignment explanation
Indices: 258887--258934 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
258877 CCAATAATCG
258887 CAGAACCCCACAGACTTAACACC
1 CAGAACCCCACAGACTTAACACC
258910 CAGAACCCCACAGACTTAACACC
1 CAGAACCCCACAGACTTAACACC
258933 CA
1 CA
258935 CGTACTGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.44, G:0.08, T:0.08
Consensus pattern (23 bp):
CAGAACCCCACAGACTTAACACC
Found at i:265962 original size:34 final size:33
Alignment explanation
Indices: 265919--266006 Score: 131
Period size: 34 Copynumber: 2.6 Consensus size: 33
265909 TCAGGGCCTT
* *
265919 AGCCCATTTCGGTAACAGTAGCAGTCTAGGCATG
1 AGCCCATTTCAGTAACAGTAG-AGTCTAGCCATG
*
265953 AGCCCATTTCAGTAACAGTAAGAGTCTAGCCCTG
1 AGCCCATTTCAGTAACAGT-AGAGTCTAGCCATG
265987 AGCCCATTTCAGTAACAGTA
1 AGCCCATTTCAGTAACAGTA
266007 TCAATTGGGC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 1 0.02
34 47 0.94
35 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (33 bp):
AGCCCATTTCAGTAACAGTAGAGTCTAGCCATG
Found at i:267555 original size:46 final size:45
Alignment explanation
Indices: 267502--267676 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
267492 TATTTGGGCA
*
267502 TCCGAACTCGTCGAGTTGAGTCCCAGTTCACTTATGGATGCGAAT
1 TCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAAT
** *** * *
267547 GTCCGAACTCGTTGAGTTGAGTCAGAGTTCGAGAGATGTAACTG-GCA-
1 -TCCGAACTCGTTGAGTTGAGTCCCAGTTC-ACTTATG-GA-TGCGAAT
*
267594 TCCGAGCTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAACT
1 TCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAA-T
* * * *
267640 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGG
267677 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 4 0.04
46 86 0.83
47 4 0.04
48 3 0.03
49 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAAT
Done.