Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 99 of 356
Found at i:31310986 original size:5 final size:5
Alignment explanation
Indices: 31310976--31311020 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
31310966 TTAATACTTA
31310976 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
31311021 TTTTAACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:31311118 original size:5 final size:5
Alignment explanation
Indices: 31311108--31311151 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
31311098 TTAATACTTA
31311108 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
31311152 ACAAAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:31311123 original size:132 final size:132
Alignment explanation
Indices: 31310886--31311151 Score: 532
Period size: 132 Copynumber: 2.0 Consensus size: 132
31310876 AATTTTAACC
31310886 TATTTTTAACAATTGTATAGAGTTGGTGGTTACATGTGTAAAAATTATATACATATATATAAAAT
1 TATTTTTAACAATTGTATAGAGTTGGTGGTTACATGTGTAAAAATTATATACATATATATAAAAT
31310951 AATAAATTATACTACTTAATACTTAATTATATTATATTATATTATATTATATTATATTATATTAT
66 AATAAATTATACTACTTAATACTTAATTATATTATATTATATTATATTATATTATATTATATTAT
31311016 AT
131 AT
31311018 TATTTTTAACAATTGTATAGAGTTGGTGGTTACATGTGTAAAAATTATATACATATATATAAAAT
1 TATTTTTAACAATTGTATAGAGTTGGTGGTTACATGTGTAAAAATTATATACATATATATAAAAT
31311083 AATAAATTATACTACTTAATACTTAATTATATTATATTATATTATATTATATTATATTATATTAT
66 AATAAATTATACTACTTAATACTTAATTATATTATATTATATTATATTATATTATATTATATTAT
31311148 AT
131 AT
31311150 TA
1 TA
31311152 ACAAAACAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (132 bp):
TATTTTTAACAATTGTATAGAGTTGGTGGTTACATGTGTAAAAATTATATACATATATATAAAAT
AATAAATTATACTACTTAATACTTAATTATATTATATTATATTATATTATATTATATTATATTAT
AT
Found at i:31311242 original size:26 final size:26
Alignment explanation
Indices: 31311200--31311251 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
31311190 AAGTTCAAAC
31311200 AAAATAGAGAAGAAAAAGAATGAAAAG
1 AAAATAGAGAAGAAAAAGAA-GAAAAG
*
31311227 AAAA-AGAGAA-AGAAAAGGAGAAAAG
1 AAAATAGAGAAGA-AAAAGAAGAAAAG
31311252 TTAGGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAATAGAGAAGAAAAAGAAGAAAAG
Found at i:31317413 original size:17 final size:16
Alignment explanation
Indices: 31317380--31317413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31317370 ATATATAATC
*
31317380 TGAAGTTTAATTTATT
1 TGAAGTTTAAATTATT
31317396 TGAAGTTTATAATTATT
1 TGAAGTTTA-AATTATT
31317413 T
1 T
31317414 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TGAAGTTTAAATTATT
Found at i:31317819 original size:16 final size:16
Alignment explanation
Indices: 31317794--31317838 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
31317784 ACCATCATTG
*
31317794 ATATACTTAATAATTA
1 ATATAATTAATAATTA
31317810 ATATAATTAATAA-T-
1 ATATAATTAATAATTA
31317824 ATATAATT-ATAATTA
1 ATATAATTAATAATTA
31317839 TAGCACAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 1 0.04
16 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAATTAATAATTA
Found at i:31319413 original size:14 final size:14
Alignment explanation
Indices: 31319378--31319415 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
31319368 TGTTTCACTA
*
31319378 AAAATGACTTTCGG
1 AAAATGATTTTCGG
*
31319392 AAAATGATTTTTGG
1 AAAATGATTTTCGG
31319406 AAAATGATTT
1 AAAATGATTT
31319416 AATTTTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTTCGG
Found at i:31325785 original size:39 final size:41
Alignment explanation
Indices: 31325731--31325816 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
31325721 TGTTGATGAT
*
31325731 AATTCAATATGGTTATG-TTTT-TTTTTATTTTTAGAGTTC
1 AATTCTATATGGTTATGTTTTTATTTTTATTTTTAGAGTTC
31325770 AATTCTATATGGTTATGTTTTTATTTTTATTTTTAGAGTTC
1 AATTCTATATGGTTATGTTTTTATTTTTATTTTTAGAGTTC
31325811 AATTCT
1 AATTCT
31325817 TACTCACTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 16 0.36
40 4 0.09
41 24 0.55
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59
Consensus pattern (41 bp):
AATTCTATATGGTTATGTTTTTATTTTTATTTTTAGAGTTC
Found at i:31325963 original size:66 final size:65
Alignment explanation
Indices: 31325893--31326091 Score: 201
Period size: 66 Copynumber: 3.2 Consensus size: 65
31325883 AAATATATTT
31325893 AATATTAATTATTTCAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
31325958 G
65 G
* *
31325959 AATATTAATTA-TTAAGA--A--TTTTAT--TA-AAT-TA-TAT-ATTTTAATTAAGA-T-ATAT
1 AATATTAATTATTTAA-ATTATCTTTTATAGTATAATATATTATGA-TTTGAGTAA-ATTCATAT
**
31326011 -TT
63 AAG
* *
31326013 AATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
31326078 G
65 G
31326079 AATATTAATTATT
1 AATATTAATTATT
31326092 AAGAATTTAT
Statistics
Matches: 104, Mismatches: 11, Indels: 37
0.68 0.07 0.24
Matches are distributed among these distances:
54 10 0.10
55 6 0.06
56 15 0.14
57 4 0.04
58 3 0.03
59 8 0.08
61 8 0.08
62 2 0.02
63 4 0.04
64 13 0.12
65 9 0.09
66 22 0.21
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (65 bp):
AATATTAATTATTTAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAG
Found at i:31326134 original size:15 final size:15
Alignment explanation
Indices: 31326099--31326150 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31326089 ATTAAGAATT
*
31326099 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31326113 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31326127 TATTTAATAATAAT-
1 TATTTAATTATAATA
31326141 TATGTTAATT
1 TAT-TTAATT
31326151 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31326166 original size:119 final size:120
Alignment explanation
Indices: 31325855--31326263 Score: 714
Period size: 120 Copynumber: 3.4 Consensus size: 120
31325845 AATTATTTTA
* *
31325855 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
*
31325919 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
31325975 AATTTTATTAAATTATATATTTTAATTAAGATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
31326040 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
31326095 AA-TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
* *
31326159 ATAGTATCATATATTATTATTTGAGTAAATTCATATCAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
31326214 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
31326264 ATTTAAATAT
Statistics
Matches: 276, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 113 0.41
120 161 0.58
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:31326243 original size:18 final size:18
Alignment explanation
Indices: 31326215--31326265 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
31326205 ATTATTAAGA
31326215 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
31326232 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
31326248 A-TTTAATAATAATTATAT
1 ATTTTAATTA-AATTATAT
31326266 TTAAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
17 5 0.17
18 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:31326494 original size:45 final size:44
Alignment explanation
Indices: 31326395--31326504 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 44
31326385 TTTTCCATTA
31326395 TGCTATTACACCTCTATT-C----CATTCAACCAAACATAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACATAAGAT
* *
31326434 TACTATTACACCTCTATTCCATTACATTCAACCAAACAGT-TGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACA-TAAGA-T
31326479 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
31326505 CCTCTAATCC
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
44 16 0.26
45 27 0.44
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACATAAGAT
Found at i:31326532 original size:16 final size:16
Alignment explanation
Indices: 31326485--31326534 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
31326475 GATTTGCTAT
* *
31326485 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
31326501 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31326517 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
31326533 TA
1 TA
31326535 TAGCGAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31327398 original size:31 final size:31
Alignment explanation
Indices: 31327363--31327422 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
31327353 TAACAACCAA
*
31327363 GTGACTTAAATAAAAATTTTCA-AATAGTTTT
1 GTGACTTAAATAAAAACTTT-AGAATAGTTTT
*
31327394 GTGACTTAAATGAAAACTTTAGAATAGTT
1 GTGACTTAAATAAAAACTTTAGAATAGTT
31327423 AGAAATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (31 bp):
GTGACTTAAATAAAAACTTTAGAATAGTTTT
Found at i:31330363 original size:13 final size:12
Alignment explanation
Indices: 31330327--31330363 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
31330317 CCTTTCCCCC
31330327 TCCCTTCTCTC-
1 TCCCTTCTCTCT
31330338 TCCCTTCTCTCT
1 TCCCTTCTCTCT
31330350 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
31330363 T
1 T
31330364 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 5 0.21
13 8 0.33
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:31330869 original size:3 final size:3
Alignment explanation
Indices: 31330828--31330901 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
31330818 AATATCCTTG
* * * * * *
31330828 TTA TTT TTA -TA TTA TTA GTA CTA TTA GTA TCA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
31330875 TTA TGTA TTA GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA T-TA TTA TTA TTA T
31330902 GTACGTGTAT
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:31330911 original size:23 final size:23
Alignment explanation
Indices: 31330867--31330912 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
31330857 TCACTATTAT
*
31330867 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
31330890 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
31330913 CATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:31330978 original size:25 final size:24
Alignment explanation
Indices: 31330931--31330978 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31330921 TATATTTTCA
*
31330931 TATTTAATATTTTTATTTCATTTT
1 TATTTAATATTTTTATTTAATTTT
31330955 TATTCTAATA-TTTTATTATAATTT
1 TATT-TAATATTTTTATT-TAATTT
31330979 ATATATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTAATATTTTTATTTAATTTT
Found at i:31333458 original size:19 final size:20
Alignment explanation
Indices: 31333418--31333461 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
31333408 GTCTCTTTAG
* *
31333418 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
31333437 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
31333456 GCATTA
1 GCATTA
31333462 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:31337671 original size:86 final size:86
Alignment explanation
Indices: 31337542--31337805 Score: 402
Period size: 86 Copynumber: 3.1 Consensus size: 86
31337532 AGTAAAAATT
* * * * *
31337542 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGTAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
*
31337607 GCATTGACAGTGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * *
31337628 GAAGACAAACCTTACCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAACAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGTAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
*
31337693 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
31337714 GAAGACAAACCTTGCCTCTCTCGTTTGTAGTAGAGCTGGTTGAAGATATCAGATCTTGCTTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGTAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
* *
31337779 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
31337801 GAAGA
1 GAAGA
31337806 TGGCAGATTT
Statistics
Matches: 160, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
86 139 0.87
87 21 0.13
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCTCTCTCGTTTGTAGTAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:31338037 original size:44 final size:43
Alignment explanation
Indices: 31337988--31338124 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 43
31337978 GATATCAGAT
31337988 CTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAG
1 CTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAG
* * * * * * * * *
31338031 CTTTGCCTTCATTG-GTT-ACAGTGGAGCT-GGTTGAAGATAGCAGAT
1 C-TTGCCTTC-CTGCATTAACAGCGAAG-TAGATCGAA-A-AACAAAG
31338076 CTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAG
1 CTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAG
31338119 CCTTGC
1 -CTTGC
31338125 TCCATCGGTT
Statistics
Matches: 67, Mismatches: 18, Indels: 17
0.66 0.18 0.17
Matches are distributed among these distances:
43 19 0.28
44 29 0.43
45 19 0.28
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAG
Found at i:31338186 original size:175 final size:173
Alignment explanation
Indices: 31337887--31338212 Score: 501
Period size: 175 Copynumber: 1.9 Consensus size: 173
31337877 GTGGAATAGA
* * * *
31337887 TTGAAGATTGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAGCTTTGCCTT
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTC
* * * *
31337952 CATTGGTTACAGTGGAGCTGGTTGAAGATATCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAG
66 CATCGGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAG
*
31338017 ATCGAAAAACAAAGCTTTGCCTTCATTGGTTACAGTGGAGCTGG
131 ATCG-AAAACAAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGG
* *
31338061 TTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCCTTG-C
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCG-AAAAC-AAGCCTTGCC
* *
31338125 TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGC
64 TCCATCGGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGC
31338190 AGATCGAAAACAAAGCCTTGCCT
129 AGATCGAAAACAAAGCCTTGCCT
31338213 CTCTCGGGTG
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
174 60 0.44
175 70 0.51
176 7 0.05
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (173 bp):
TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTC
CATCGGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAG
ATCGAAAACAAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGG
Found at i:31338187 original size:87 final size:87
Alignment explanation
Indices: 31337887--31338212 Score: 503
Period size: 88 Copynumber: 3.7 Consensus size: 87
31337877 GTGGAATAGA
* * *
31337887 TTGAAGATTGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAAC-AAGCTTTGCCT
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
31337951 TCATTGGTTACAGTGGAGCTGG
66 TCATTGGTTACAGTGGAGCTGG
* * * *
31337973 TTGAAGATATCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCTTTGCC
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCG-AAAACAAAGCCTTGCC
31338038 TTCATTGGTTACAGTGGAGCTGG
65 TTCATTGGTTACAGTGGAGCTGG
* *
31338061 TTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCCTTG-C
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCG-AAAACAAAGCCTTGCC
* * *
31338125 TCCATCGGTTGCAGTGGAGCTGG
65 TTCATTGGTTACAGTGGAGCTGG
*
31338148 TTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
1 TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
31338213 CTCTCGGGTG
Statistics
Matches: 224, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
86 57 0.25
87 73 0.33
88 94 0.42
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TTGAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
TCATTGGTTACAGTGGAGCTGG
Found at i:31338259 original size:87 final size:88
Alignment explanation
Indices: 31337887--31338315 Score: 489
Period size: 87 Copynumber: 5.0 Consensus size: 88
31337877 GTGGAATAGA
* * *
31337887 TTGAAGATTGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAAC-AAGCTTTGCCT
1 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
* *
31337951 -TCATTGGTTACAGTGGAGCTGG
66 CTCATCGGTTGCAGTGGAGCTGG
* * * *
31337973 TTGAAGATATCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCTTTGCC
1 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG-AAAACAAAGCCTTGCC
* *
31338038 T-TCATTGGTTACAGTGGAGCTGG
65 TCTCATCGGTTGCAGTGGAGCTGG
* *
31338061 TTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCCTTG-C
1 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG-AAAACAAAGCCTTGCC
31338125 TC-CATCGGTTGCAGTGGAGCTGG
65 TCTCATCGGTTGCAGTGGAGCTGG
*
31338148 TTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
1 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
* * ** *
31338213 CTC-TCGGGTGTAGAAGAGTTGG
66 CTCATCGGTTGCAGTGGAGCTGG
* * * * ** * * * * * *
31338235 TTGAAGACAACTGATTTTATCTTCCTGCGTTGACAGTGAAGCAGGTTGAAGAC-AA-CCTTACCT
1 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
*
31338298 CTC-TCGGTTGTAGTGGAG
66 CTCATCGGTTGCAGTGGAG
31338316 TTAGTGAAGA
Statistics
Matches: 305, Mismatches: 33, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
85 22 0.07
86 59 0.19
87 129 0.42
88 95 0.31
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
CTCATCGGTTGCAGTGGAGCTGG
Found at i:31338738 original size:46 final size:46
Alignment explanation
Indices: 31338666--31338981 Score: 139
Period size: 46 Copynumber: 6.8 Consensus size: 46
31338656 GTAGATCGTA
* *
31338666 TCAGGTCTTATCACCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
* ** * *
31338712 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCATAG
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AAT-T
* * * ** * *
31338760 T-A-ATCTTATCTCCCTGAGATTACAGCGGAGTAAATTGAAG-CTAG
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAT-T
* * * ** **
31338804 T-A-ATCCTATCTCTCTGAAGTTACAGTGGAGCGGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
** * * *
31338845 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCAC-ATCAG-ATT
1 TCA-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGA-C-CGA--AGAATT
* * ** *
31338894 GAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATT
1 ----TC--AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
* *
31338946 TCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGA
31338982 TTGAAGATAG
Statistics
Matches: 207, Mismatches: 42, Indels: 42
0.71 0.14 0.14
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 57 0.28
46 103 0.50
47 3 0.01
48 4 0.02
49 1 0.00
51 1 0.00
52 4 0.02
53 2 0.01
54 27 0.13
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
Found at i:31338811 original size:221 final size:226
Alignment explanation
Indices: 31338574--31339015 Score: 630
Period size: 221 Copynumber: 2.0 Consensus size: 226
31338564 GTAGAGTATA
31338574 TGAAGCTAGTAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCT
1 TGAAGCTAGTAATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCT
* *
31338638 CTCTGAAGTTACAGCAGAGTAG-ATC-G-T-A-TCAG-G-TCTTATCACCCTGAGGTTACAGTGG
65 CTCTGAAGTTACAGCAGAGTAGAATCAGATAAGCCAGAGATCTTATCACCCTGAGATTACAGTGG
** * * *
31338696 AGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCATAGT
130 AACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG--ATAGT
*
31338761 AATCTTATCTCCCTGAGATTACAGCGGAGTAAAT
193 AATCCTATCTCCCTGAGATTACAGCGGAGTAAAT
*
31338795 TGAAGCTAGTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
1 TGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
* *
31338860 TCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTAC
66 TCTGAAGTTACAGCAGAGTAG---A-ATCAGA-T-AAGCCAGAGATCTTATCACCCTGAGATTAC
*
31338925 AGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGAT
125 AGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT
*
31338990 AGTAATCCTATCTGCCTGAGATTACA
190 AGTAATCCTATCTCCCTGAGATTACA
31339016 ATGGAGTGGA
Statistics
Matches: 194, Mismatches: 13, Indels: 17
0.87 0.06 0.08
Matches are distributed among these distances:
221 81 0.42
222 2 0.01
226 3 0.02
227 1 0.01
229 1 0.01
231 1 0.01
232 29 0.15
233 1 0.01
234 75 0.39
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (226 bp):
TGAAGCTAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
TCTGAAGTTACAGCAGAGTAGAATCAGATAAGCCAGAGATCTTATCACCCTGAGATTACAGTGGA
ACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAAT
CCTATCTCCCTGAGATTACAGCGGAGTAAAT
Found at i:31338827 original size:44 final size:46
Alignment explanation
Indices: 31338720--31338834 Score: 146
Period size: 46 Copynumber: 2.5 Consensus size: 46
31338710 TTTCAGATCT
* * *
31338720 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCATAGTAATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAAATTGAAGCCATAGTAATCC
* *
31338766 TATCTCCCTG-AGATTACAGCGGAGTAAATTGAAG-C-TAGTAATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAAATTGAAGCCATAGTAATCC
*
31338810 TATCTCTCTGAAGTTACAGTGGAGC
1 TATCTCCCTGAAGTTACAGTGGAGC
31338835 GGATTAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
44 27 0.46
45 4 0.07
46 28 0.47
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (46 bp):
TATCTCCCTGAAGTTACAGTGGAGCAAATTGAAGCCATAGTAATCC
Found at i:31338987 original size:188 final size:187
Alignment explanation
Indices: 31338713--31339103 Score: 556
Period size: 188 Copynumber: 2.1 Consensus size: 187
31338703 CGAAGAATTT
* * ** **
31338713 CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCATAGTAATCTTATCTCCCTGAG
1 CAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATAGTAATCTTATCTCCCTGAG
* *
31338778 ATTACAGCGGAGTAAATTGAAGCTAGTAATCCTATCT-CTCTGA-AGTTACAGTGGAGCGGATTA
66 ATTACAGCGGAGTAAATTGAAGATAGTAATCCTATCTGC-CTGAGA-TTACAATGGAGCGGATTA
* ** *
31338841 AAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCA
129 AAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAGCAGA-CAAAACCA
* *
31338901 GAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAA-AAAT-TTCAGATCTTATCTCCCTG
1 CAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATAGT-A-ATCTTATCTCCCTG
* *
31338964 AGATTACAGCGGAGTAGATTGAAGATAGTAATCCTATCTGCCTGAGATTACAATGGAGTGGATTA
64 AGATTACAGCGGAGTAAATTGAAGATAGTAATCCTATCTGCCTGAGATTACAATGGAGCGGATTA
*
31339029 AAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAGCAGACAAAACCA
129 AAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAGCAGACAAAACCA
31339088 CAGATCTTATCTCCCT
1 CAGATCTTATCTCCCT
31339104 AAGCAGTTAG
Statistics
Matches: 181, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
186 1 0.01
187 23 0.13
188 155 0.86
189 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (187 bp):
CAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATAGTAATCTTATCTCCCTGAG
ATTACAGCGGAGTAAATTGAAGATAGTAATCCTATCTGCCTGAGATTACAATGGAGCGGATTAAA
ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAGCAGACAAAACCA
Found at i:31339046 original size:44 final size:44
Alignment explanation
Indices: 31338949--31339052 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
31338939 AAAAATTTCA
* * *
31338949 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGT
1 GATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAAATAAT
* * * * *
31338993 AATCCTATCTGCCTGAGATTACAATGGAGTGGATT-AAAATAAAT
1 GATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAAAT-AAT
*
31339037 GATCTTATCTCTCTGA
1 GATCTTATCTCCCTGA
31339053 AGTTACAGTA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 4 0.09
44 43 0.91
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAAATAAT
Found at i:31340198 original size:13 final size:12
Alignment explanation
Indices: 31340162--31340198 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
31340152 CCTTTCCCCC
31340162 TCCCTTCTCTC-
1 TCCCTTCTCTCT
31340173 TCCCTTCTCTCT
1 TCCCTTCTCTCT
31340185 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
31340198 T
1 T
31340199 TTTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 5 0.21
13 8 0.33
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:31340702 original size:3 final size:3
Alignment explanation
Indices: 31340661--31340734 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
31340651 AATATCCTTG
* * * * * *
31340661 TTA TTT TTA -TA TTA TTA GTA CTA TTA GTA TCA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
31340708 TTA TGTA TTA GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA T-TA TTA TTA TTA T
31340735 GTACGTGTAT
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:31340744 original size:23 final size:23
Alignment explanation
Indices: 31340700--31340745 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
31340690 TCACTATTAT
*
31340700 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
31340723 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
31340746 CATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:31340811 original size:25 final size:24
Alignment explanation
Indices: 31340764--31340811 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31340754 TATATTTTCA
*
31340764 TATTTAATATTTTTATTTCATTTT
1 TATTTAATATTTTTATTTAATTTT
31340788 TATTCTAATA-TTTTATTATAATTT
1 TATT-TAATATTTTTATT-TAATTT
31340812 ATATATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTAATATTTTTATTTAATTTT
Found at i:31346396 original size:37 final size:37
Alignment explanation
Indices: 31346337--31346445 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
31346327 AGCTCAGACG
* *
31346337 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
31346374 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
31346411 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
31346446 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:31346676 original size:47 final size:47
Alignment explanation
Indices: 31346607--31346790 Score: 282
Period size: 47 Copynumber: 4.0 Consensus size: 47
31346597 TTTCACACTA
* * * *
31346607 GCCATTCGGCTTTA-C-CACATATGCATGTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
*
31346652 GGCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
*
31346699 GCCATTCGGCCTTATCACATATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* *
31346746 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
31346791 AAAATCCTAA
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 12 0.09
46 1 0.01
47 116 0.90
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
Found at i:31346717 original size:22 final size:22
Alignment explanation
Indices: 31346690--31346765 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
31346680 GCTCACATTC
31346690 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
31346712 ATCACATATATG-CATGCTC-ACATT
1 ATCACAT-T-GGCCAT--TCGGCCTT
31346736 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
31346759 ATCACAT
1 ATCACAT
31346766 ATATGCATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 16 0.39
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:31351695 original size:20 final size:20
Alignment explanation
Indices: 31351647--31351696 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
31351637 TATGGAATAC
*
31351647 GCCATAAAGGTTAACAGAGT
1 GCCATAAAGGTTAACAGAAT
* *
31351667 ACCATAAAGGTTAATAGAAT
1 GCCATAAAGGTTAACAGAAT
*
31351687 GCCACAAAGG
1 GCCATAAAGG
31351697 CCAAACCAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (20 bp):
GCCATAAAGGTTAACAGAAT
Found at i:31353442 original size:17 final size:16
Alignment explanation
Indices: 31353411--31353475 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
31353401 TATTTTAGAT
31353411 TATTATTCATTTTTTA
1 TATTATTCATTTTTTA
31353427 TATTATTCATTGTTTTA
1 TATTATTCATT-TTTTA
31353444 -A--ATT-A--TTTTA
1 TATTATTCATTTTTTA
*
31353454 TGTTATTCATTTTTTA
1 TATTATTCATTTTTTA
31353470 T-TTATT
1 TATTATT
31353476 TTCGTTTGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
10 5 0.12
13 4 0.10
14 4 0.10
15 5 0.12
16 18 0.44
17 5 0.12
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTATTCATTTTTTA
Found at i:31353459 original size:27 final size:25
Alignment explanation
Indices: 31353422--31353477 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
31353412 ATTATTCATT
31353422 TTTTATATTATTCATTGTTTTAAATTA
1 TTTTATATTATTCATT-TTTT-AATTA
* *
31353449 TTTTATGTTATTCATTTTTTATTTA
1 TTTTATATTATTCATTTTTTAATTA
31353474 TTTT
1 TTTT
31353478 CGTTTGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 8 0.30
26 4 0.15
27 15 0.56
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTATATTATTCATTTTTTAATTA
Found at i:31358337 original size:79 final size:79
Alignment explanation
Indices: 31358193--31358410 Score: 239
Period size: 79 Copynumber: 2.7 Consensus size: 79
31358183 AAATCACGTA
* * * * *
31358193 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAG
31358257 TAACTCGCACAAATG
65 TAACTCGCACAAATG
*
31358272 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATA
*
31358335 GTATCTCGCACAAATG
64 GTAACTCGCACAAATG
* * * *
31358351 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
31358411 CATCATTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 68 0.57
80 48 0.40
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCACAAATG
Found at i:31358410 original size:40 final size:40
Alignment explanation
Indices: 31358207--31358410 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
31358197 CGGAATTTAA
** *
31358207 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31358247 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31358287 CCGGATTTAGTAACTCGTACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31358326 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
31358366 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31358406 CCGGA
1 CCGGA
31358411 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31364780 original size:20 final size:21
Alignment explanation
Indices: 31364755--31364794 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31364745 CACTTAGAAC
31364755 AGGGC-ACACGCCCGTGTAGA
1 AGGGCAACACGCCCGTGTAGA
31364775 AGGGCAACACGCCCGTGTAG
1 AGGGCAACACGCCCGTGTAG
31364795 CCCTATTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTAGA
Found at i:31366116 original size:49 final size:49
Alignment explanation
Indices: 31366061--31366184 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 49
31366051 GTCGATACAG
*
31366061 TGTCCCAGACAGGTCTTACACTGACTTTCATATATCGA-GACCAATGCCA
1 TGTCCCAGACAGGTCTTACACTGACTCTCATATATCGATG-CCAATGCCA
* * * ***
31366110 TGTCCCAGACCAGGTCTTAAACTGGCTCTCATTTATCGATGTTGATGCCA
1 TGTCCCAGA-CAGGTCTTACACTGACTCTCATATATCGATGCCAATGCCA
* *
31366160 TGTCCCAAATAGGTCTTACACTGAC
1 TGTCCCAGACAGGTCTTACACTGAC
31366185 ACACAACAAG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 22 0.35
50 39 0.63
51 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTGACTCTCATATATCGATGCCAATGCCA
Found at i:31366346 original size:46 final size:45
Alignment explanation
Indices: 31366247--31366365 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
31366237 CCCGAGGCCA
*
31366247 ATGCATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTA-TCTCAATGCCG
*
31366293 ATGCATGTCCCAGACATGTCTTACATTAGCT-T-TCAT-AATGTGTCCG
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTATC-TCAA--TG-CCG
* *
31366339 ATTCATGTCCTAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
31366366 GACTCACATA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
43 4 0.06
44 1 0.02
45 3 0.05
46 56 0.88
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCTATCTCAATGCCG
Found at i:31368947 original size:11 final size:11
Alignment explanation
Indices: 31368931--31368955 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31368921 AAAAAAGTAG
31368931 CACTTAAATCC
1 CACTTAAATCC
31368942 CACTTAAATCC
1 CACTTAAATCC
31368953 CAC
1 CAC
31368956 AAAACCCAAA
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:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (11 bp):
CACTTAAATCC
Found at i:31371509 original size:26 final size:26
Alignment explanation
Indices: 31371480--31371537 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
31371470 AGGAAAAGTA
* **
31371480 AATAATAGTATATATATGTTAAGTGT
1 AATAATAGTATAGATATAATAAGTGT
* * *
31371506 AATAAAATTTTAGATATAATAAGTGT
1 AATAATAGTATAGATATAATAAGTGT
31371532 AATAAT
1 AATAAT
31371538 TAATGGTTAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (26 bp):
AATAATAGTATAGATATAATAAGTGT
Found at i:31375968 original size:27 final size:27
Alignment explanation
Indices: 31375937--31375997 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
31375927 CTATTATGGT
31375937 CCATAGAAACACAAAAAAAATTTTTCG
1 CCATAGAAACACAAAAAAAATTTTTCG
*
31375964 CCATAGAAACACAAAAATAATTTTTCG
1 CCATAGAAACACAAAAAAAATTTTTCG
31375991 CCA-AGAA
1 CCATAGAA
31375998 CATAAAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.51, C:0.20, G:0.08, T:0.21
Consensus pattern (27 bp):
CCATAGAAACACAAAAAAAATTTTTCG
Found at i:31377863 original size:32 final size:31
Alignment explanation
Indices: 31377790--31377864 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
31377780 CTATTTTCTT
* * *
31377790 ATTTTAGTCACTTTTATTAAATAAATTGTTA
1 ATTTTAGTCACTCTTATTAAATAAATTATCA
* *
31377821 ATTTTAGTCACTCTTATTAATTAATTTATCA
1 ATTTTAGTCACTCTTATTAAATAAATTATCA
*
31377852 GCTTTTAGTCACT
1 -ATTTTAGTCACT
31377865 TTACAGTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (31 bp):
ATTTTAGTCACTCTTATTAAATAAATTATCA
Found at i:31399520 original size:43 final size:43
Alignment explanation
Indices: 31399446--31399529 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
31399436 CATCAGTGTC
* * * *
31399446 ATATTTGATTTCGTGTAAGACCCTGTTTGGGATAGTGGCATCG
1 ATATTTGATTACATGTAAGACCCTGTATGGGACAGTGGCATCG
*
31399489 ATATTTGATTACATGTAAGACCAC-GTATGGGACATTGGCAT
1 ATATTTGATTACATGTAAGACC-CTGTATGGGACAGTGGCAT
31399530 TGTATGAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 34 0.97
44 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (43 bp):
ATATTTGATTACATGTAAGACCCTGTATGGGACAGTGGCATCG
Found at i:31403626 original size:46 final size:45
Alignment explanation
Indices: 31403576--31403751 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
31403566 TGGTTGAGCA
31403576 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
31403622 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
31403669 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
31403715 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31403752 GCGGGTTATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31403732 original size:93 final size:93
Alignment explanation
Indices: 31403573--31403743 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
31403563 GGATGGTTGA
* *
31403573 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31403638 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
31403666 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31403731 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31403744 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:31426275 original size:475 final size:475
Alignment explanation
Indices: 31425385--31426328 Score: 1602
Period size: 475 Copynumber: 2.0 Consensus size: 475
31425375 AAACAACAAA
**
31425385 ATCAACTGGGAATATAAATTTGTCAATTTTAACGAGTACGTCTTCAATGATACCCCTAGGAAATC
1 ATCAACTAAGAATATAAATTTGTCAATTTTAACGAGTACGTCTTCAATGATACCCCTAGGAAATC
31425450 TGACAGTTTTATCTGCTAATTGAATACTCATCCTAGTTTGTTTGGGTTTCCCTAGACCTAGTTGC
66 TGACAGTTTTATCTGCTAATTGAATACTCATCCTAGTTTGTTTGGGTTTCCCTAGACCTAGTTGC
* *
31425515 TTAAACAATTTGTAAGGCATAACATTGATACTAGTCTCTAGATCAGCCAACGCATTATTAACATC
131 TTAAACAATTTGTAAGGCATAACATTGATACTAGCCCCTAGATCAGCCAACGCATTATTAACATC
*
31425580 TAAACTACCAATTAAACAAGGAATCATAAAACTCCCTAGATCTTTTAGTTTGTTGGTTAGCTTAT
196 TAAACTACCAATTAAACAAGGAATCATAAAACTCCCTAGATCTTTTAGTTTGTTGGGTAGCTTAT
* *
31425645 TCAGAAGAATGGCTGAGCAAACCGCGTTCAGCTCCATATGCGACCTTTCATCTAACTTTCATTTA
261 TCAGAAGAATGGCTGAGCAAACCGCGTTCAGCTCCACATGCAACCTTTCATCTAACTTTCATTTA
* * *
31425710 TTTGCTAAGAGTTCCTTTAAAAATTTGACTGCATTGGGAATTTGCGAAAGTGCTTCAATAAACGG
326 TTTGCTAAGAGCTCCTTTAAAAATTTGACTGCATTGCGAATCTGCGAAAGTGCTTCAATAAACGG
31425775 TAGGTTAATATGTAGTTTCTTTAAAAGTTTAAAGAATTTACCAAATTGTTCGTCTGAGCGGTCTT
391 TAGGTTAATATGTAGTTTCTTTAAAAGTTTAAAGAATTTACCAAATTGTTCGTCTGAGCGGTCTT
31425840 TCCTTGTCGCATTGAGCTTT
456 TCCTTGTCGCATTGAGCTTT
* *
31425860 ATCAACTAAGAATATAAATTTGTGAATTTTAACGAGTATGTCTTCAATGATACCCCTAGGAAATC
1 ATCAACTAAGAATATAAATTTGTCAATTTTAACGAGTACGTCTTCAATGATACCCCTAGGAAATC
* * *
31425925 TGACAGTTTTATCTGCTAATTGAATGCTTATCCTAGTTTGTTTTGGTTTCCCTAGACCTAGTTGC
66 TGACAGTTTTATCTGCTAATTGAATACTCATCCTAGTTTGTTTGGGTTTCCCTAGACCTAGTTGC
* *
31425990 TTAAACAATTTGTAAGGCATAACATTGATACTAGCCCCTAGATCAGCCAACTCATTATTAAGATC
131 TTAAACAATTTGTAAGGCATAACATTGATACTAGCCCCTAGATCAGCCAACGCATTATTAACATC
*
31426055 TAAACTACCAATTAAACAAGGAATCATAAAACTCCCTGGATCTTTTAGTTTGTTGGGTAGCTTAT
196 TAAACTACCAATTAAACAAGGAATCATAAAACTCCCTAGATCTTTTAGTTTGTTGGGTAGCTTAT
* * **
31426120 TCTGAAGAATGGCTGAGCAAACCGCGTTCAGTTCCACATGCAACCTTTCATCTAACTTTTGTTTA
261 TCAGAAGAATGGCTGAGCAAACCGCGTTCAGCTCCACATGCAACCTTTCATCTAACTTTCATTTA
* * * *
31426185 TTTGCTAGGGGCTCCTTTAAAAATTTGACTGCATT-CTACATCTGTGAAAGTGCTTCAATAAACG
326 TTTGCTAAGAGCTCCTTTAAAAATTTGACTGCATTGCGA-ATCTGCGAAAGTGCTTCAATAAACG
* * *
31426249 GTGGGTTAATATGTAGTTTCTTTAAAAGTTTAAGGAATTTACCAAATTGTTCGTCTGAGCGGTTT
390 GTAGGTTAATATGTAGTTTCTTTAAAAGTTTAAAGAATTTACCAAATTGTTCGTCTGAGCGGTCT
*
31426314 TTCCTTGTCGTATTG
455 TTCCTTGTCGCATTG
31426329 GGGTATGGCA
Statistics
Matches: 438, Mismatches: 30, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
474 1 0.00
475 437 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (475 bp):
ATCAACTAAGAATATAAATTTGTCAATTTTAACGAGTACGTCTTCAATGATACCCCTAGGAAATC
TGACAGTTTTATCTGCTAATTGAATACTCATCCTAGTTTGTTTGGGTTTCCCTAGACCTAGTTGC
TTAAACAATTTGTAAGGCATAACATTGATACTAGCCCCTAGATCAGCCAACGCATTATTAACATC
TAAACTACCAATTAAACAAGGAATCATAAAACTCCCTAGATCTTTTAGTTTGTTGGGTAGCTTAT
TCAGAAGAATGGCTGAGCAAACCGCGTTCAGCTCCACATGCAACCTTTCATCTAACTTTCATTTA
TTTGCTAAGAGCTCCTTTAAAAATTTGACTGCATTGCGAATCTGCGAAAGTGCTTCAATAAACGG
TAGGTTAATATGTAGTTTCTTTAAAAGTTTAAAGAATTTACCAAATTGTTCGTCTGAGCGGTCTT
TCCTTGTCGCATTGAGCTTT
Found at i:31433892 original size:40 final size:40
Alignment explanation
Indices: 31433796--31434056 Score: 312
Period size: 40 Copynumber: 6.5 Consensus size: 40
31433786 CTCGTTCAAG
* * * * *
31433796 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* *
31433835 TGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
31433875 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
*
31433915 TGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* *
31433955 TGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* ** * * * *
31433995 GGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AA
1 TGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAA
* *
31434035 AGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
31434057 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 154 0.78
41 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
Found at i:31434065 original size:41 final size:41
Alignment explanation
Indices: 31433988--31434065 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31433978 TTAATATCTC
* * *
31433988 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31434029 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31434066 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31451825 original size:178 final size:178
Alignment explanation
Indices: 31451511--31452573 Score: 1339
Period size: 178 Copynumber: 6.0 Consensus size: 178
31451501 TCGATGAATT
* * * ** *
31451511 TAGATTTTGTCTTCC-TGAAATAGCAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCAAG
1 TAGATTTTGTC-TCCTTGAGATAGCAGTGGGGCAGATCAAAGACGGTGAATCTTATCTTCCCGAG
* ** *
31451575 GTATCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTTTGAGGTAGCAAAGGAGCAGGCTGAA
65 GTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAA
*
31451640 GATTGTAGTCTTATCTTCCCGAGGTAGCAAGGGAGCAGACTGAAGATTG
130 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATTG
* * * * * * *
31451689 TAGATCTTGTCTCCCTGAAATAACAGTGGAGCAAATCAAAGACGATGAATCTTATCTTCCCGAGG
1 TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATCAAAGACGGTGAATCTTATCTTCCCGAGG
* * *
31451754 TAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGGGAGCATGCTGAAA
66 TAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAG
*
31451819 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAACAGACTGAAGATTG
131 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATTG
*
31451867 TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATCAAA-AGCTGTGAATCTTATCTTCCCGAG
1 TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATCAAAGA-CGGTGAATCTTATCTTCCCGAG
* * * * * * * *
31451931 GTAGCAAGGGAGCAAATTTTAGCCACCATCCTTATCTCTCTAAGGCAGCAAGGGAGTAGGCTGAA
65 GTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAA
* *
31451996 GATTGTAGTCTTATCTTCTTGAGGTAGCAAGGGAGAAGACTGAAGATTG
130 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATTG
* * * * *
31452045 TAGATCTTGTCTCCTTGAGATAGCAGTGGGGCAGATAAAAAATGGTGAATCTTATCTTCTCGAGG
1 TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATCAAAGACGGTGAATCTTATCTTCCCGAGG
* * *
31452110 TAGTAGGGGAGTAGATTTTAGCCACTGGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAG
66 TAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAG
** * * *
31452175 ATTGTAGTCTTATCTTTTTGAGGTAGCAAGGGAGCAAACTGATGACT-
131 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATTG
* * * * * * *
31452222 CAGATTTTGTCT-CTTCGAGATAGCAGTAGGGCAGATTAAAAATGGTGAATCTTTTCTTCCTGAG
1 TAGATTTTGTCTCCTT-GAGATAGCAGTGGGGCAGATCAAAGACGGTGAATCTTATCTTCCCGAG
* * *
31452286 GTAGCAGAGGAGCAGATTTTAGCCACTAGCCTTATCCCCCTAAGGTAGCAAGGGAGCAGGCTGAA
65 GTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAA
* * * * * *
31452351 GATTGTAGTATTATCTTCTTGAGGTAACAAGGGAGAAGACTGATGACTCG
130 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGA-TTG
* * *** **
31452401 --GATTTTGTCTCCTTGGGATAGAAGTGGGGCAGATCGAAAG-CGACAAATCTTATCTTCCTAAG
1 TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATC-AAAGACGGTGAATCTTATCTTCCCGAG
* * * * ** *
31452463 GTAGTAGGGGAGCAGATTTCAGCAACCAATCTTATCTCCCTGGGGTAGCAAGGGAGCAGGCTGAA
65 GTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAA
*
31452528 GATTGTAGTCTCATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGA
130 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGA
31452574 CTGGAGATCT
Statistics
Matches: 774, Mismatches: 103, Indels: 17
0.87 0.12 0.02
Matches are distributed among these distances:
176 3 0.00
177 295 0.38
178 475 0.61
179 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (178 bp):
TAGATTTTGTCTCCTTGAGATAGCAGTGGGGCAGATCAAAGACGGTGAATCTTATCTTCCCGAGG
TAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAG
ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGATTG
Found at i:31452187 original size:44 final size:44
Alignment explanation
Indices: 31451605--31452595 Score: 297
Period size: 44 Copynumber: 22.3 Consensus size: 44
31451595 AGCCACTAGC
** * *
31451605 CTTATCTCTTTGAGGTAGCAAAGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
31451649 CTTATCTTCCC-GAGGTAGCAAGGGAGCAGACTGAAGATTGTAGAT
1 CTTATC-TCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* ** * * * * *
31451694 CTTGTCTCCCTGAAATAAC-AGTGGAGCA-AATCAAAGA-CGATGAAT
1 CTTATCTCCCTGAGGTAGCAAG-GGAGCAGACT-GAAGATTG-T-AGT
* * ** **** *
31451739 CTTATCTTCCC-GAGGTAGCAGGGGAGCAGATTTTAGCCACTAGC
1 CTTATC-TCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* *
31451783 CTTATCTCTCTGAGGTAGCAAGGGAGCATG-CTGAAAATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCA-GACTGAAGATTGTAGT
* *
31451827 CTTATCTTCCTGAGGTAGCAAGGGAACAGACTGAAGATTGTAGAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * * * * * * * *
31451872 TTTGTCTCCTTGAGATAGC-AGTGGGGCAGA-TCAAAAGCTGTGAAT
1 CTTATCTCCCTGAGGTAGCAAG-GGAGCAGACTGAAGA-TTGT-AGT
* * ** *****
31451917 CTTATCTTCCC-GAGGTAGCAAGGGAGCAAATTTTAGCCACCA-T
1 CTTATC-TCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * * * *
31451960 CCTTATCTCTCTAAGGCAGCAAGGGAGTAGGCTGAAGATTGTAGT
1 -CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * *
31452005 CTTATCTTCTTGAGGTAGCAAGGGAGAAGACTGAAGATTGTAGAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * * * * * * *
31452050 CTTGTCTCCTTGAGATAGC-AGTGGGGCAGA-TAAAAAATGGTGAAT
1 CTTATCTCCCTGAGGTAGCAAG-GGAGCAGACT-GAAGATTGT-AGT
* * * * * ** * *
31452095 CTTATCT-TCTCGAGGTAGTAGGGGAGTAGATTTTAGCCACTG--GC
1 CTTATCTCCCT-GAGGTAGCAAGGGAGCAGACTGAAG--ATTGTAGT
*
31452139 CTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
*** * * * *
31452183 CTTATCTTTTTGAGGTAGCAAGGGAGCAAACTGATGACT-CAGAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * * * * * * * *
31452227 TTTGTCT-CTTCGAGATAGC-AGTAGG-GCAGATTAAAAATGGTGAAT
1 CTTATCTCCCT-GAGGTAGCAAG--GGAGCAGACTGAAGATTGT-AGT
* * * ** **** *
31452272 CTTTTCTTCCTGAGGTAGC-AGAGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAG-GGAGCAGACTGAAGATTGTAGT
* * *
31452316 CTTATCCCCCTAAGGTAGCAAGGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * * * * * * *
31452360 ATTATCTTCTTGAGGTAACAAGGGAGAAGACTGATGACTCGGA-T
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGA-TTGTAGT
* * * * ** * *
31452404 TTTGTCTCCTTG-GGATAG-AAGTGGGGCAGA-TCGAA-AGCGACAAAT
1 CTTATCTCCCTGAGG-TAGCAAG-GGAGCAGACT-GAAGATTG--TAGT
* * * * * ** *** *
31452449 CTTATCTTCCTAAGGTAGTAGGGGAGCAGATTTCAGCA-ACCAAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAG-ATTGTAGT
* *
31452493 CTTATCTCCCTGGGGTAGCAAGGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * * *
31452537 CTCATCTTCCTGAGGTAGCAAGGGAGCAGACTGAAGACTGGAGAT
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
*
31452582 CTTATATCCCTGAG
1 CTTATCTCCCTGAG
31452596 TAATAGGGAG
Statistics
Matches: 668, Mismatches: 220, Indels: 117
0.66 0.22 0.12
Matches are distributed among these distances:
42 5 0.01
43 22 0.03
44 409 0.61
45 202 0.30
46 27 0.04
47 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
Found at i:31454291 original size:12 final size:11
Alignment explanation
Indices: 31454264--31454302 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
31454254 TATTTAATCT
*
31454264 TTTTTTATTTCA
1 TTTTTTATAT-A
31454276 TTTTTTATA-A
1 TTTTTTATATA
31454286 TTTTTTATATA
1 TTTTTTATATA
31454297 TTTTTT
1 TTTTTT
31454303 CTTTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 10 0.40
11 7 0.28
12 8 0.32
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTATATA
Found at i:31454368 original size:3 final size:3
Alignment explanation
Indices: 31454360--31454399 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
31454350 TTTTTCATTC
* * *
31454360 TAT TAT TAT TAC TAC TAT TAT TCT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31454400 TTAAAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:31455561 original size:11 final size:10
Alignment explanation
Indices: 31455537--31455572 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
31455527 AAACATATAC
31455537 TTTGGTATGA
1 TTTGGTATGA
*
31455547 TTTGGTTTAGA
1 TTTGGTAT-GA
31455558 TTTGGTATGA
1 TTTGGTATGA
31455568 TTTGG
1 TTTGG
31455573 CTGGTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.53
Consensus pattern (10 bp):
TTTGGTATGA
Found at i:31462133 original size:39 final size:39
Alignment explanation
Indices: 31462072--31462286 Score: 342
Period size: 39 Copynumber: 5.5 Consensus size: 39
31462062 ACAAAGCATG
31462072 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGAC-TT-AGCCCGGATATAATACCAGCACGAATGCCTT
* **
31462113 CGGGACTTAGCCTGGATATAACGCCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
**
31462152 CGGGACTTAGCCCGGATATAGCACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
*
31462191 CGGGACTTAGCCTGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
*
31462230 CAGGACTTAGCCCGGATATAATACCAGCA-GAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
31462268 CGGGACTTAGCCCGGATAT
1 CGGGACTTAGCCCGGATAT
31462287 TTTTCTAGCA
Statistics
Matches: 162, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
38 27 0.17
39 127 0.78
40 2 0.01
41 6 0.04
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
Found at i:31462324 original size:39 final size:39
Alignment explanation
Indices: 31462300--31462410 Score: 195
Period size: 39 Copynumber: 2.8 Consensus size: 39
31462290 TCTAGCACTT
*
31462300 AGCCTGCGGACTTTAAGTCCGGATATATTTCCAGCATAA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
31462339 AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
* *
31462378 AGCCTGTGGACTTCAAGTCCGGATATTTTTCCA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCA
31462411 ATACCATGCA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (39 bp):
AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
Found at i:31465069 original size:22 final size:22
Alignment explanation
Indices: 31465038--31465083 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
31465028 CTATCTATTC
*
31465038 ATGTTTTCATGATTAGTCTCCA
1 ATGTTGTCATGATTAGTCTCCA
31465060 ATGTTGTCATGATTAGTCTCCA
1 ATGTTGTCATGATTAGTCTCCA
31465082 AT
1 AT
31465084 TATAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (22 bp):
ATGTTGTCATGATTAGTCTCCA
Found at i:31467543 original size:39 final size:40
Alignment explanation
Indices: 31467426--31467648 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
31467416 GCTCCTCGTT
* *
31467426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
31467466 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31467506 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
31467545 CAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
31467584 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
31467625 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31467649 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 63 0.38
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:31467544 original size:79 final size:80
Alignment explanation
Indices: 31467426--31467648 Score: 255
Period size: 79 Copynumber: 2.8 Consensus size: 80
31467416 GCTCCTCGTT
* * *
31467426 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCC
*
31467489 GGATTTAGTAACTCGCA
64 GGAATTAGTAACTCGCA
*
31467506 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCTGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31467569 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
* * * *
31467584 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTAATC-TCGCACAAATGCCTTCGGGACTTAGCC
31467645 CGGA
63 CGGA
31467649 CATCATTCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 45 0.36
79 57 0.45
80 24 0.19
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:31471008 original size:21 final size:21
Alignment explanation
Indices: 31470982--31471022 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31470972 ACAAGAGACA
31470982 AGGTTTATTCATATTAAAAAT
1 AGGTTTATTCATATTAAAAAT
*
31471003 AGGTTTCTTCATATTAAAAA
1 AGGTTTATTCATATTAAAAA
31471023 CAAAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (21 bp):
AGGTTTATTCATATTAAAAAT
Found at i:31476298 original size:22 final size:22
Alignment explanation
Indices: 31476249--31476291 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31476239 TAACATATGT
31476249 CACATATA-TCATGAGCTCAGAC
1 CACATA-ACTCATGAGCTCAGAC
31476271 CACATAACTCATGAGCTCAGA
1 CACATAACTCATGAGCTCAGA
31476292 TTGCATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (22 bp):
CACATAACTCATGAGCTCAGAC
Found at i:31478372 original size:27 final size:27
Alignment explanation
Indices: 31478330--31478383 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31478320 GTGTCATGTG
* *
31478330 AAATTGAATGGCAAATTATTGTTACAT
1 AAATTGAATGGCAAATTACTATTACAT
**
31478357 AAATTGAATGTTAAATTACTATTACAT
1 AAATTGAATGGCAAATTACTATTACAT
31478384 GGGTTGTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (27 bp):
AAATTGAATGGCAAATTACTATTACAT
Found at i:31478808 original size:50 final size:48
Alignment explanation
Indices: 31478630--31478852 Score: 261
Period size: 50 Copynumber: 4.6 Consensus size: 48
31478620 CTATTGTGAG
* *
31478630 GTCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATT
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
31478678 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTT
1 -GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA--TT
* * *
31478729 GATTACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTT
1 G-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
31478778 ACGTCACGTGTGTAGTACTAAGCGCAGGCTACTATGTGTACCAGATAATT
1 --GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
31478828 GGCA--TGTGTAGTACTAAGTGCAGGC
1 GTCACGTGTGTAGTACTAAGTGCAGGC
31478853 AACTGAGTAT
Statistics
Matches: 148, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
46 20 0.14
48 3 0.02
49 42 0.28
50 43 0.29
51 40 0.27
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (48 bp):
GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:31486146 original size:24 final size:24
Alignment explanation
Indices: 31486112--31486204 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
31486102 TACCAATATA
*
31486112 TCAGCTCGTAAGAGCTTACTTTTT
1 TCAGCTCGTAAGAGCTTACTGTTT
*
31486136 TTAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCGTAAGAGCTTACTGTTT
* *
31486160 TCAGCTCGTCAGAGCTTACCG-TT
1 TCAGCTCGTAAGAGCTTACTGTTT
*
31486183 TCAGCTC-AATAGAGCTTACTGT
1 TCAGCTCGTA-AGAGCTTACTGT
31486205 CCATCAGCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 19 0.32
24 40 0.68
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (24 bp):
TCAGCTCGTAAGAGCTTACTGTTT
Found at i:31488029 original size:56 final size:56
Alignment explanation
Indices: 31487962--31488074 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
31487952 CTAATTTCAT
31487962 ATTTGAAGATGTAAATTTAAAACCATATATGTTTGAAAACTCTTTCGAAGAAAAAA
1 ATTTGAAGATGTAAATTTAAAACCATATATGTTTGAAAACTCTTTCGAAGAAAAAA
31488018 ATTTGAAGATGTAAATTTAAAACCATATATGTTTGAAAACTCTTTCGAAGAAAAAA
1 ATTTGAAGATGTAAATTTAAAACCATATATGTTTGAAAACTCTTTCGAAGAAAAAA
31488074 A
1 A
31488075 ATACTTTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (56 bp):
ATTTGAAGATGTAAATTTAAAACCATATATGTTTGAAAACTCTTTCGAAGAAAAAA
Found at i:31488137 original size:22 final size:21
Alignment explanation
Indices: 31488112--31488176 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
31488102 TCCTAAAAAT
31488112 TATTATTTTAATTTTGTTTATA
1 TATTATTTTAATTTT-TTTATA
31488134 TATTA-TTTAGATTTTTTTA-A
1 TATTATTTTA-ATTTTTTTATA
31488154 -A-TATTTATAATTTTATTTATA
1 TATTATTT-TAATTTT-TTTATA
31488175 TA
1 TA
31488177 CTTTAGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.05
19 8 0.22
20 7 0.19
21 9 0.24
22 11 0.30
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TATTATTTTAATTTTTTTATA
Found at i:31488186 original size:21 final size:20
Alignment explanation
Indices: 31488128--31488193 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 20
31488118 TTTAATTTTG
*
31488128 TTTATATAT-TATTTAG-AT
1 TTTATTTATATATTTAGAAT
* *
31488146 TTT-TTTAAATATTTATAAT
1 TTTATTTATATATTTAGAAT
31488165 TTTATTTATATACTTTAGAATT
1 TTTATTTATATA-TTTAGAA-T
31488187 TTTATTT
1 TTTATTT
31488194 TTTTAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.08
18 9 0.24
19 5 0.13
20 7 0.18
21 6 0.16
22 8 0.21
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTATTTATATATTTAGAAT
Found at i:31503301 original size:96 final size:95
Alignment explanation
Indices: 31503130--31503449 Score: 363
Period size: 96 Copynumber: 3.3 Consensus size: 95
31503120 TGATATGTGT
* * * * * *
31503130 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCACTATATGAGAGCTAGTGTAAGGCGATG
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATC-AGCAATATATGAGAGCTAGTGTAAGACCATG
* * * **
31503195 TTTGGAACATGGCATCGGCGATGTTGTGAGA
65 TCTGGGACATGGCATCGGCCATGTCATGAGA
* ** * *
31503226 GCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGTTAATATGTGCGCTAGTGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCAAT-ATATGAGAGCTAGTGTAAGACCATG
**
31503291 TCTGGGACATGGCATCGGCCACATCATGAGA
65 TCTGGGACATGGCATCGGCCATGTCATGAGA
* * * *
31503322 GCCAGTGTAAGACTATGTCTAGGACATGGCATCGGCAATGAGACGAGAGCTAGTGTAAGACCATG
1 GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCAAT-ATATGAGAGCTAGTGTAAGACCATG
* * *
31503387 TCTGGGACATGGCATCGGCCTTGACATGTGA
65 TCTGGGACATGGCATCGGCCATGTCATGAGA
*
31503418 GCCAGTGTAAGACCATGTTTA-GAGCATGGCAT
1 GCCAGTGTAAGACCATGTCTAGGA-CATGGCAT
31503450 AGGCAATTCA
Statistics
Matches: 188, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
95 5 0.03
96 183 0.97
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCAATATATGAGAGCTAGTGTAAGACCATGT
CTGGGACATGGCATCGGCCATGTCATGAGA
Found at i:31503449 original size:48 final size:48
Alignment explanation
Indices: 31503120--31503435 Score: 321
Period size: 48 Copynumber: 6.6 Consensus size: 48
31503110 GACATTTGGG
* * * *
31503120 TGATATGTGTGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* * * * * *
31503168 CT-ATATGAGAGCTAGTGTAAGGCGATGTTTGGAACATGGCATCGGCGA
1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* * * ** **
31503216 TGTTGTGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCGT
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* * * *
31503264 TAATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* * * *
31503312 -CATCATGAGAGCCAGTGTAAGACTATGTCTAGGACATGGCATCGGCAA
1 TGAT-ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* * * *
31503360 TGAGACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
* *
31503408 TGACATGTGAGCCAGTGTAAGACCATGT
1 TGATATGAGAGCCAGTGTAAGACCATGT
31503436 TTAGAGCATG
Statistics
Matches: 215, Mismatches: 49, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
47 3 0.01
48 210 0.98
49 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA
Found at i:31503449 original size:144 final size:144
Alignment explanation
Indices: 31503124--31503437 Score: 409
Period size: 144 Copynumber: 2.2 Consensus size: 144
31503114 TTTGGGTGAT
* *
31503124 ATGTGTGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCACTATATGAGAGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCACTATATGAGAGCCAGTGTAAG
* * * * *
31503189 GCGATGTTTGGAACATGGCATCGGCGATGTTGTGAGAGCCAGTGTAAGACCATGTCTAGGACATG
66 ACGATGTTAGGAACATGGCATCGGCAATGTAGCGAGAGCCAGTGTAAGACCATGTCTAGGACATG
* * *
31503254 GCATTAGCGTTAAT
131 GCATCAGCCTTAAC
* * * *
31503268 ATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATCATGAGAGCCAGTGTAA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCACTAT-ATGAGAGCCAGTGTAA
* * *
31503332 GACTATGTCTAGG-ACATGGCATCGGCAATG-AGACGAGAGCTAGTGTAAGACCATGTCTGGGAC
65 GACGATGT-TAGGAACATGGCATCGGCAATGTAG-CGAGAGCCAGTGTAAGACCATGTCTAGGAC
* *
31503395 ATGGCATCGGCCTTGAC
128 ATGGCATCAGCCTTAAC
31503412 ATGTGAGCCAGTGTAAGACCATGTTT
1 ATGTGAGCCAGTGTAAGACCATGTTT
31503438 AGAGCATGGC
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
143 3 0.02
144 140 0.96
145 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (144 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACCACTATATGAGAGCCAGTGTAAG
ACGATGTTAGGAACATGGCATCGGCAATGTAGCGAGAGCCAGTGTAAGACCATGTCTAGGACATG
GCATCAGCCTTAAC
Found at i:31504319 original size:55 final size:55
Alignment explanation
Indices: 31504230--31504334 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
31504220 ACACACGGGT
*
31504230 GTGTGTCTAGGCCGTCTGTGACACACGGTCTGCCCCACTAGCATGTAGTCCGCCC
1 GTGTGTCTAGGCCGTCTGTGACACACGGTCTGCCCCACGAGCATGTAGTCCGCCC
* * *
31504285 GTGTGTCTTGGCCGTCTGTGACACACGGTTTGCCCCACGAGCGTGTAGTC
1 GTGTGTCTAGGCCGTCTGTGACACACGGTCTGCCCCACGAGCATGTAGTC
31504335 TGATCGTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.13, C:0.31, G:0.30, T:0.26
Consensus pattern (55 bp):
GTGTGTCTAGGCCGTCTGTGACACACGGTCTGCCCCACGAGCATGTAGTCCGCCC
Found at i:31508272 original size:19 final size:19
Alignment explanation
Indices: 31508248--31508287 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31508238 TGTGTCATCA
*
31508248 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
31508267 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
31508286 TA
1 TA
31508288 CACATTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:31511232 original size:12 final size:12
Alignment explanation
Indices: 31511212--31511242 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31511202 ATCATACTGT
*
31511212 CCCTTGAATGGA
1 CCCTCGAATGGA
31511224 CCCTCGAATGGA
1 CCCTCGAATGGA
31511236 CCCTCGA
1 CCCTCGA
31511243 GGTCCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (12 bp):
CCCTCGAATGGA
Found at i:31512171 original size:43 final size:43
Alignment explanation
Indices: 31512110--31512193 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
31512100 TAAGTTTACT
31512110 ATTTATACCAAAGCAAGTTGTAGGATAGTGTGAAGATGCTCTG
1 ATTTATACCAAAGCAAGTTGTAGGATAGTGTGAAGATGCTCTG
31512153 ATTTATACCAAAGCAAGTTGTAGGATAGTGTGAAGATGCTC
1 ATTTATACCAAAGCAAGTTGTAGGATAGTGTGAAGATGCTC
31512194 CGACCGATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (43 bp):
ATTTATACCAAAGCAAGTTGTAGGATAGTGTGAAGATGCTCTG
Found at i:31520177 original size:40 final size:40
Alignment explanation
Indices: 31520094--31520356 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
31520084 TTGAATGCTG
* * * * * *
31520094 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
31520134 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
31520174 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
31520214 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
31520254 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
31520294 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
31520333 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31520357 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:31520376 original size:79 final size:80
Alignment explanation
Indices: 31520133--31520391 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
31520123 AAGTGAATAT
* * * * * *
31520133 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
31520197 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
31520213 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
31520278 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
31520293 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
31520357 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
31520372 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
31520392 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:31526052 original size:40 final size:40
Alignment explanation
Indices: 31526021--31526151 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 40
31526011 GGACTAAGAT
* **
31526021 CCGAAGGCATTTGTGCGACTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGACATACAAATTCCGGGTTAAGTC
* *
31526061 CCGAAGGCCTTTGTGCGAGATACAAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGACATACAAATTCCGGGTTAAGTC
* ** ** *
31526101 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGACATACAAATTCCGGGTTAAGTC
31526141 CCGAAGGCATT
1 CCGAAGGCATT
31526152 GTATGAGTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGACATACAAATTCCGGGTTAAGTC
Found at i:31526181 original size:39 final size:40
Alignment explanation
Indices: 31525968--31526188 Score: 130
Period size: 40 Copynumber: 5.5 Consensus size: 40
31525958 TTGAATGCTG
* * * * *
31525968 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTAC-GAGT-TCTAAAA
* * * * * * *
31526008 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGACTTATTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTACGAGTTCTAAAA
* * * * * *
31526048 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATAC-AAAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTACGAG-TTCTAAAA
* * *
31526088 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTACGAGTTCTAAAA
* * *
31526128 TCCGGGTTAAGTCCCGAAGGCATT-GTATGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTACGAGTT-CTAAAA
*
31526168 T-CGGGCTATGTCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCA
31526189 CTTGAACGAG
Statistics
Matches: 149, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
39 28 0.19
40 112 0.75
41 9 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTACGAGTTCTAAAA
Found at i:31529569 original size:15 final size:15
Alignment explanation
Indices: 31529545--31529607 Score: 83
Period size: 15 Copynumber: 4.2 Consensus size: 15
31529535 AGGAAACCGA
31529545 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
31529560 ATAGAGAAATCCAAA
1 ATAAAGAAATCCAAG
31529575 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
*
31529589 AATAAAGAAACCCAAG
1 -ATAAAGAAATCCAAG
31529605 ATA
1 ATA
31529608 CGATACTATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.02
15 38 0.93
16 2 0.05
ACGTcount: A:0.60, C:0.14, G:0.13, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31532644 original size:93 final size:93
Alignment explanation
Indices: 31532537--31532706 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
31532527 CCCATAAGTG
* * *
31532537 AACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTAGCATCCATAAGTGAACTCGAACTCAACTCAAC
31532602 GAGCTCGGATGCCTAGTTACATCTCTCA
66 GAGCTCGGATGCCTAGTTACATCTCTCA
*
31532630 AACTCGGACTCAACTCAACGAGTTCGGACATTAGCATCCATAAGTGAACTCGAACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTAGCATCCATAAGTGAACTCGAACTCAACTCAAC
*
31532695 GAGTTCGGATGC
66 GAGCTCGGATGC
31532707 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTAGCATCCATAAGTGAACTCGAACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTCA
Found at i:31532703 original size:46 final size:46
Alignment explanation
Indices: 31532528--31532703 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
31532518 TGTAACCCGC
* *
31532528 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTAGCAT
31532574 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTAGCAT
* *
31532624 CTC-TCA---AACTCGGACTCAACTCAACGAGTTCGGACATTAGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTAGCAT
* *
31532667 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
31532704 TGCTCAACCA
Statistics
Matches: 113, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
42 4 0.04
43 7 0.06
44 1 0.01
46 63 0.56
47 27 0.24
49 1 0.01
50 7 0.06
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTAGCAT
Found at i:31544884 original size:58 final size:57
Alignment explanation
Indices: 31544806--31544914 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
31544796 CATTACAGAA
*
31544806 AGGATTTAGCCTGGACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTATAGAT
1 AGGATTTAGCCTGGACTGGTAATCCTGAT-TAAGCCCTCTTGAGCATATGTTATAGAT
* * *
31544864 AGGATTTAG-CTCGGATTGGTAATCCTGATTAAGCTCTTTTGAGCATATGTT
1 AGGATTTAGCCT-GGACTGGTAATCCTGATTAAGCCCTCTTGAGCATATGTT
31544915 GGAAACAGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
57 21 0.46
58 25 0.54
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (57 bp):
AGGATTTAGCCTGGACTGGTAATCCTGATTAAGCCCTCTTGAGCATATGTTATAGAT
Found at i:31544930 original size:57 final size:59
Alignment explanation
Indices: 31544806--31544931 Score: 159
Period size: 57 Copynumber: 2.2 Consensus size: 59
31544796 CATTACAGAA
* * * *
31544806 AGGATTTAGC-CTGGACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTATAGAT
1 AGGATTTAGCTCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTAGAAAC
* * * *
31544864 AGGATTTAGCTC-GGATTGGTAATCCTGAT-TAAGCTCTTTTGAGCATATGTTGGAAAC
1 AGGATTTAGCTCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTAGAAAC
31544921 AGGATTTAGCT
1 AGGATTTAGCT
31544932 TAGACAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
57 32 0.54
58 26 0.44
59 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (59 bp):
AGGATTTAGCTCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTAGAAAC
Found at i:31551922 original size:42 final size:42
Alignment explanation
Indices: 31551874--31551992 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
31551864 CCGAAATTCT
* *
31551874 ATATAAGACCATATCTGGGATATGGCATCGGTATG-TGATTTC
1 ATATAAGACCATATCAGGGATATGGCATCGATATGAT-ATTTC
* * * **
31551916 GTATAAGACCATTTCAAGGCCATGGCATCGATATGATATTTC
1 ATATAAGACCATATCAGGGATATGGCATCGATATGATATTTC
* * *
31551958 ATGTAAGACCATATCCGGGATATGGCATTGATATG
1 ATATAAGACCATATCAGGGATATGGCATCGATATG
31551993 GTACTGTGGG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 60 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
ATATAAGACCATATCAGGGATATGGCATCGATATGATATTTC
Found at i:31558543 original size:44 final size:43
Alignment explanation
Indices: 31558461--31558573 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
31558451 GATACCACTA
* * * * *
31558461 TCCCAGACAGGGTCTTACACATAATCGATTAACGATGCCCAATG
1 TCCCAGACATGGTCTTACACGTAATCCAATAACAATG-CCAATG
31558505 TCCCAGACATGGTCTTACACGTAATCACAAT-ACAATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATC-CAATAACAATGCCAATG
* * *
31558548 TCCTAGACATAGTCTTACATGTAATC
1 TCCCAGACATGGTCTTACACGTAATC
31558574 TCATCTCAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 29 0.48
44 29 0.48
45 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCCAATAACAATGCCAATG
Found at i:31563058 original size:2 final size:2
Alignment explanation
Indices: 31563051--31563102 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
31563041 TTAATTGCCC
31563051 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31563093 CT CT CT CT CT
1 CT CT CT CT CT
31563103 TTTTATGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31566027 original size:20 final size:20
Alignment explanation
Indices: 31566002--31566058 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
31565992 ACACGTCAAC
31566002 ATTTAATTAATTTTTTAAA-A
1 ATTTAATTAA-TTTTTAAACA
*
31566022 ATTTAAATAATTTTTAAACA
1 ATTTAATTAATTTTTAAACA
*
31566042 ATATTAA-TCATTTTTAA
1 AT-TTAATTAATTTTTAA
31566059 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.24
20 21 0.64
21 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAATTAATTTTTAAACA
Found at i:31572482 original size:2 final size:2
Alignment explanation
Indices: 31572475--31572525 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
31572465 ACAAGTACTG
* * *
31572475 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CG CA CA TA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
31572517 CA AA CA CA C
1 CA CA CA CA C
31572526 TAACTTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.47, G:0.04, T:0.02
Consensus pattern (2 bp):
CA
Found at i:31573730 original size:21 final size:21
Alignment explanation
Indices: 31573704--31573743 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31573694 TAATGGGATT
31573704 GCTGATGTGGCAAGTTAACCA
1 GCTGATGTGGCAAGTTAACCA
31573725 GCTGATGTGGCAAGTTAAC
1 GCTGATGTGGCAAGTTAAC
31573744 TTACCACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACCA
Found at i:31574230 original size:6 final size:6
Alignment explanation
Indices: 31574191--31574242 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
31574181 TTCTAATTCA
* * * * * *
31574191 ATTTTA ATTTCG ATTCTG ATTCTG ATTTTG ATTTTG ATTTCG ATTTTA
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
31574239 ATTT
1 ATTT
31574243 CAATTTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.60
Consensus pattern (6 bp):
ATTTTG
Found at i:31574272 original size:6 final size:6
Alignment explanation
Indices: 31574261--31574326 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
31574251 AAACACTCAC
* ** * * *
31574261 TGATTT TGATTT TGATTT TGATTC CAATTT TGATCT CGATTT AGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* *
31574309 AGAATT TGATTT TGATTT
1 TGATTT TGATTT TGATTT
31574327 CGATCTGGAT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (6 bp):
TGATTT
Found at i:31574482 original size:47 final size:47
Alignment explanation
Indices: 31574399--31574595 Score: 331
Period size: 47 Copynumber: 4.2 Consensus size: 47
31574389 ATTATTTGTT
*
31574399 TCTGCCATTGTATGAATGCCATTATCAAATTGATGTGTATTGTGTATA
1 TCTGCCATTGTATGAATG-CATTATCAAACTGATGTGTATTGTGTATA
*
31574447 TCTGTCATTGTATGAATGCATTATCAAACTGATGTGTATTGTGTATA
1 TCTGCCATTGTATGAATGCATTATCAAACTGATGTGTATTGTGTATA
*
31574494 TCTGCCATTGTATGAATGCATTATCAAACTGATGTGTATTATGTATA
1 TCTGCCATTGTATGAATGCATTATCAAACTGATGTGTATTGTGTATA
* * *
31574541 TCTACCATTGTATGAATGCATTATCGAACTGATGTTTATTGTGTATA
1 TCTGCCATTGTATGAATGCATTATCAAACTGATGTGTATTGTGTATA
31574588 TCTGCCAT
1 TCTGCCAT
31574596 GATGTTTATT
Statistics
Matches: 140, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 123 0.88
48 17 0.12
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (47 bp):
TCTGCCATTGTATGAATGCATTATCAAACTGATGTGTATTGTGTATA
Found at i:31574920 original size:15 final size:15
Alignment explanation
Indices: 31574900--31574928 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31574890 AAAGAAAACA
31574900 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
31574915 TGTCTGGTAGTGAT
1 TGTCTGGTAGTGAT
31574929 AGTGATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.38, T:0.41
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:31576562 original size:41 final size:42
Alignment explanation
Indices: 31576510--31576642 Score: 148
Period size: 41 Copynumber: 3.2 Consensus size: 42
31576500 TTGCTGATCA
*
31576510 CATGCACTGATTGTTAGAAAGCTATTGACT-TTTTTAATATG
1 CATGCAATGATTGTTAGAAAGCTATTGACTATTTTTAATATG
* * * *
31576551 TATGCAATGATTTTTGGAAAGCTGTTGACTATTTTTAATATG
1 CATGCAATGATTGTTAGAAAGCTATTGACTATTTTTAATATG
** * *
31576593 CATGCAATGATTGTT-G-GTG-TGTTGCCTATTTTTTAATATG
1 CATGCAATGATTGTTAGAAAGCTATTGACTA-TTTTTAATATG
31576633 CATGCAATGA
1 CATGCAATGA
31576643 GTTTTTTTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.10
40 22 0.28
41 26 0.32
42 24 0.30
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (42 bp):
CATGCAATGATTGTTAGAAAGCTATTGACTATTTTTAATATG
Found at i:31576599 original size:42 final size:42
Alignment explanation
Indices: 31576510--31576642 Score: 166
Period size: 42 Copynumber: 3.2 Consensus size: 42
31576500 TTGCTGATCA
* * *
31576510 CATGCACTGATTGTTAGAAAGCTATTGACT-TTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTAATATG
* *
31576551 TATGCAATGATTTTTGGAAAGCTGTTGACTATTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTAATATG
* *
31576593 CATGCAATGATTGTTGG--TG-TGTTGCCTATTTTTTAATATG
1 CATGCAATGATTGTTGGAAAGCTGTTGACTA-TTTTTAATATG
31576633 CATGCAATGA
1 CATGCAATGA
31576643 GTTTTTTTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
39 8 0.10
40 22 0.27
41 25 0.31
42 26 0.32
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (42 bp):
CATGCAATGATTGTTGGAAAGCTGTTGACTATTTTTAATATG
Found at i:31577877 original size:59 final size:59
Alignment explanation
Indices: 31577785--31577923 Score: 224
Period size: 59 Copynumber: 2.4 Consensus size: 59
31577775 TATTTGTTAT
*
31577785 CCAACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACTAGCAGCCATGTATA
1 CCAACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
* * * *
31577844 CCAACTGTTAAGCAATTTGTATATCAATTGTTATCTTTTCTAGCCAGCAGGCATGTATA
1 CCAACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
*
31577903 CCAAGTGTTAAGCAATTTGTA
1 CCAACTGTTAAGCAATTTGTA
31577924 AACAACAACA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
59 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (59 bp):
CCAACTGTTAAGCAATTTGTATACCAACTGTTATCTTTTCTAACCAGCAGCCATGTATA
Found at i:31583554 original size:85 final size:85
Alignment explanation
Indices: 31583411--31583583 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 85
31583401 GTTGCTTGCG
31583411 GGTCTCTTCGGTGAGTTCTCATGATGCCACGTGTCCTCATCAAGGTAGAGGTATAACAATAGTCC
1 GGTCTCTTCGGTGAGTTCTCATGATGCCACGTGTCCTCATCAAGGTAGAGGTATAACAATAGTCC
*
31583476 CCTCACTTAGTCAATAGGTA
66 CATCACTTAGTCAATAGGTA
31583496 GGTCTCTTCGGTGAGTTCTCATGATGCCACGTGTCCTCATCAAGGTAGAGGTATAACAATAGTCC
1 GGTCTCTTCGGTGAGTTCTCATGATGCCACGTGTCCTCATCAAGGTAGAGGTATAACAATAGTCC
31583561 CATCACTTAGTCAATAGGTA
66 CATCACTTAGTCAATAGGTA
31583581 GGT
1 GGT
31583584 TATAAAGTGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (85 bp):
GGTCTCTTCGGTGAGTTCTCATGATGCCACGTGTCCTCATCAAGGTAGAGGTATAACAATAGTCC
CATCACTTAGTCAATAGGTA
Found at i:31584168 original size:22 final size:23
Alignment explanation
Indices: 31584143--31584187 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31584133 AAATAGGGAG
*
31584143 AAAACAAC-AAGAAAATAACATT
1 AAAACAACAAAAAAAATAACATT
31584165 AAAACAACAAAAAAAATAACATT
1 AAAACAACAAAAAAAATAACATT
31584188 TTTTCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.71, C:0.13, G:0.02, T:0.13
Consensus pattern (23 bp):
AAAACAACAAAAAAAATAACATT
Found at i:31587548 original size:71 final size:71
Alignment explanation
Indices: 31587432--31587585 Score: 256
Period size: 71 Copynumber: 2.2 Consensus size: 71
31587422 CTAGCCAGTA
*
31587432 GATGGCCGGCACTAAGTACATTTTTCAGCTCTCAATGCACTTTTTATTTTTTATTTTTACTTTGG
1 GATGGCCGGCACTAAGTACATTTTTCAGCTCTCAATGCACTTTTTATTTTCTATTTTTACTTTGG
31587497 GACACT
66 GACACT
* *
31587503 GATGGTCGGTACTAAGTACATTTTTC-GTCTCTCAATGCACTTTTTATTTTCTATTTTTACTTTG
1 GATGGCCGGCACTAAGTACATTTTTCAG-CTCTCAATGCACTTTTTATTTTCTATTTTTACTTTG
31587567 GGACACT
65 GGACACT
*
31587574 GATGGCCAGCAC
1 GATGGCCGGCAC
31587586 CATCTTTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
70 1 0.01
71 75 0.99
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (71 bp):
GATGGCCGGCACTAAGTACATTTTTCAGCTCTCAATGCACTTTTTATTTTCTATTTTTACTTTGG
GACACT
Found at i:31588383 original size:89 final size:90
Alignment explanation
Indices: 31588313--31588637 Score: 474
Period size: 90 Copynumber: 3.6 Consensus size: 90
31588303 TGTATCTGTT
31588313 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCAAT
1 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCAAT
*
31588378 CTGTTTATAGTTTGTTGGGTGTTTA
66 CTGTTTGTAGTTTGTTGGGTGTTTA
* * * * * *
31588403 AATTTAATTTAGTCTGTATTATATATAGTTTGAATTTAAAAATTTCGTGCACTAATTTTTTCC-A
1 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAA-TTTTACCAA
31588467 TCTGTTTGTAGTTTGTTGGGTGTTTA
65 TCTGTTTGTAGTTTGTTGGGTGTTTA
* *
31588493 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTTGTGTATTAATTTTACCTAT
1 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCAAT
*
31588558 CTGATTGTAGTTTGTTGGGTGTTTA
66 CTGTTTGTAGTTTGTTGGGTGTTTA
* * * * * * *
31588583 AATTTAATTTAGTGCATATTAT-TTTTGTTTGAATTTTATATTTTTGTGTATTAAT
1 AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
31588638 ATTCTAGAAT
Statistics
Matches: 212, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
89 35 0.17
90 171 0.81
91 6 0.03
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (90 bp):
AATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCAAT
CTGTTTGTAGTTTGTTGGGTGTTTA
Found at i:31595042 original size:177 final size:176
Alignment explanation
Indices: 31594713--31595502 Score: 899
Period size: 177 Copynumber: 4.5 Consensus size: 176
31594703 GAAATATGAC
* * ** * *
31594713 TGGCTTAAATCTGCTCCATTGCCAATATC-TAGAGATAAGATTCGCCATCTTCGATCTGTTCCAC
1 TGGCTTAAATCTGCTCCATTGCCGATA-CATGGAGATAAGATTTACCATCTTCGATCTGCTCCGC
** * * * * * * * * * * *
31594777 CACTACTTGA-GGAAATAAAATCTTTAATCTTTAGTCCGCTGCCTTGCTACCTCAGAAATATAAG
65 TGCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAA
* * *
31594841 ACTCATTCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGG
130 AC-CATTCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAG
*
31594889 TGGCTTAAATTTGCTCCATTGCCGATACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGCT
1 TGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGCT
* *
31594954 GCAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTACTACCTCAGAAAGATAAAA
66 GCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAAA
* * *
31595019 CTCATTCTTCAACCTGCTCTCTTGCTACTTTAGAGAGATAAGGCTAG
131 C-CATTCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAG
* ** ** *
31595066 TGGCTT-AATCTGTTCCATTTTCGATACATGGAGATAAGATTCGCCATCTTCGATCTACTCCGCT
1 TGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGCT
* * * * * * *
31595130 GCAACTTTAGGGAGATAAGATTTTCAGTCTTCATTCTGCTTCCTTGCTACTTCAGGAAGATAATA
66 GCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAA-A
* * *
31595195 CCACCA-TCTTCAACATGCTCTCCTACTACCTCAGAGAGATAAGGTTAG
130 --ACCATTCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAG
* * * * * *
31595243 TGACTTAAATCTGCTCCATTGCCGGTACATGGAGATAAGATTTATCGTCTTTGATCTGCTCCACT
1 TGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGCT
* * * * * * *
31595308 ACTACTT-AGAGAGATAAGATCTTTAATCTTCAGTCTGCTTCCTTACTACTTCAGGAAGATAAGA
66 GCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAAA
*
31595372 CCACTATCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGTTAG
131 CCA-T-TCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAG
* * * *
31595420 TGACTTAAATCTGCTCCATTGCC-AGTACATGGAGATAAGATTTATCATCTTTGATATGCTCCGC
1 TGGCTTAAATCTGCTCCATTGCCGA-TACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGC
31595484 TGCAACTTCAGGGAGATAA
65 TGCAACTTCAGGGAGATAA
31595503 AATTTGACTT
Statistics
Matches: 527, Mismatches: 76, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
174 4 0.01
175 1 0.00
176 166 0.31
177 291 0.55
178 63 0.12
179 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (176 bp):
TGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTTACCATCTTCGATCTGCTCCGCT
GCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAAA
CCATTCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAG
Found at i:31596760 original size:54 final size:54
Alignment explanation
Indices: 31596647--31596801 Score: 170
Period size: 54 Copynumber: 2.8 Consensus size: 54
31596637 TTATTTTTTC
* * * ***
31596647 ATTTTTATTTAGTCTCAAAGCGCTCTTTGGGGGTTTTCACTTTGG-CTCTTTTTT
1 ATTTTTA-TTAGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCCCCCTTT
*
31596701 ATTTTTATTAGGTCTCAAAGCGCCCATTGCGGGTTTTCACTTTGGCCCCCCCTTT
1 ATTTTTATTA-GTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCCCCCTTT
** *
31596756 -TTTTTAAGAAAGTCTCAAAGTGCCCTTTGCGGGTTTTCACTTTGGC
1 ATTTTT-A-TTAGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGC
31596802 TTCTTCCCCT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
53 3 0.03
54 43 0.50
55 39 0.45
56 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (54 bp):
ATTTTTATTAGTCTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCCCCCTTT
Found at i:31604998 original size:42 final size:42
Alignment explanation
Indices: 31604935--31605061 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
31604925 CTTCGTTTTC
** *
31604935 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
* *
31604978 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
31605019 TCGATGCCATAGCCCAACTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
31605060 TC
1 TC
31605062 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:31605121 original size:47 final size:46
Alignment explanation
Indices: 31605020--31605143 Score: 160
Period size: 47 Copynumber: 2.7 Consensus size: 46
31605010 ATTCATATAT
* * * *
31605020 CGATGCCATAGCCCA-ACTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGA-TATGGTCTTATACGAAGCACATATCACAC
* * *
31605066 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
31605113 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
31605144 GAAATCACTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 26 0.38
47 42 0.62
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:31605160 original size:7 final size:7
Alignment explanation
Indices: 31605148--31605176 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
31605138 TATACGGAAA
31605148 TCACTTG
1 TCACTTG
31605155 TCACTTG
1 TCACTTG
31605162 TCACTTG
1 TCACTTG
31605169 TCACTTG
1 TCACTTG
31605176 T
1 T
31605177 AGCCGAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:31605210 original size:31 final size:31
Alignment explanation
Indices: 31605175--31605323 Score: 210
Period size: 31 Copynumber: 4.8 Consensus size: 31
31605165 CTTGTCACTT
*
31605175 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
31605206 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
31605237 ATAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
31605268 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
**
31605299 GTAGATGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
31605324 TGTCATTTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
30 3 0.03
31 100 0.95
32 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:31605398 original size:50 final size:51
Alignment explanation
Indices: 31605305--31605427 Score: 194
Period size: 50 Copynumber: 2.4 Consensus size: 51
31605295 TCAGGTAGAT
* * *
31605305 GAAGCTACCACTTTTCACTTGTCATTTGTCGTTGATCAAATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAAATAAGTGTAGCC
* *
31605356 GAAGCTATCACTTATCACTT-TCATTTTTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAAATAAGTGTAGCC
31605406 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
31605428 TGCCATGGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 47 0.71
51 19 0.29
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAAATAAGTGTAGCC
Found at i:31612838 original size:27 final size:26
Alignment explanation
Indices: 31612808--31612889 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
31612798 TTATTTCATT
31612808 TCCATTTCATTTAAATCATCTTTTTTC
1 TCCATTTCATTTAAAT-ATCTTTTTTC
* *
31612835 TCCATTTAAATTT--A-ATC-TTTTCC
1 TCCATTT-CATTTAAATATCTTTTTTC
*
31612858 T-CATTTCATTTAAATTATCTTTCTT-
1 TCCATTTCATTTAAA-TATCTTTTTTC
31612883 TCCATTT
1 TCCATTT
31612890 TAATTTACGT
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
21 4 0.09
22 5 0.12
23 7 0.16
24 3 0.07
25 4 0.09
26 9 0.21
27 7 0.16
28 4 0.09
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (26 bp):
TCCATTTCATTTAAATATCTTTTTTC
Found at i:31612888 original size:21 final size:21
Alignment explanation
Indices: 31612815--31612894 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 21
31612805 ATTTCCATTT
* *
31612815 CATTTAAATCATCTTTTTTCTC
1 CATTTAAATTATCTTTCTT-TC
*
31612837 CATTTAAATTTAATCTTTTCCTCATTT
1 CATTTAAA-TT-ATC-TTT-CT--TTC
31612864 CATTTAAATTATCTTTCTTTC
1 CATTTAAATTATCTTTCTTTC
*
31612885 CATTTTAATT
1 CATTTAAATT
31612895 TACGTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
21 11 0.23
22 8 0.17
23 3 0.06
24 6 0.13
25 6 0.13
26 3 0.06
27 9 0.19
28 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (21 bp):
CATTTAAATTATCTTTCTTTC
Found at i:31612980 original size:22 final size:22
Alignment explanation
Indices: 31612955--31613068 Score: 74
Period size: 22 Copynumber: 5.2 Consensus size: 22
31612945 TGTGTTTCAA
31612955 ATTAAATATGTATGTATATTGT
1 ATTAAATATGTATGTATATTGT
** * * **
31612977 ATTATAAT-TCAATGCATTTTAA
1 ATTA-AATATGTATGTATATTGT
31612999 ATTAAATATGTATGTATATTGT
1 ATTAAATATGTATGTATATTGT
* * **
31613021 ATTATAAT-TCAATACGT-T-TTAA
1 ATTA-AATAT--GTATGTATATTGT
31613043 ATTAAATATGTATGTATATTGT
1 ATTAAATATGTATGTATATTGT
31613065 ATTA
1 ATTA
31613069 TAATTTAATG
Statistics
Matches: 64, Mismatches: 20, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
20 4 0.06
21 7 0.11
22 42 0.66
23 7 0.11
24 4 0.06
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTAAATATGTATGTATATTGT
Found at i:31613002 original size:44 final size:44
Alignment explanation
Indices: 31612943--31613134 Score: 276
Period size: 44 Copynumber: 4.4 Consensus size: 44
31612933 TATTTCATTT
* *
31612943 AATGTGTTTCAAATTAAATATGTATGTATATTGTATTATAATTC
1 AATGCGTTTTAAATTAAATATGTATGTATATTGTATTATAATTC
*
31612987 AATGCATTTTAAATTAAATATGTATGTATATTGTATTATAATTC
1 AATGCGTTTTAAATTAAATATGTATGTATATTGTATTATAATTC
* *
31613031 AATACGTTTTAAATTAAATATGTATGTATATTGTATTATAATTT
1 AATGCGTTTTAAATTAAATATGTATGTATATTGTATTATAATTC
* * * * *
31613075 AATGTGCTTTAAATTAAATATGCATGTATATTATATTATAATTT
1 AATGCGTTTTAAATTAAATATGTATGTATATTGTATTATAATTC
* *
31613119 AACGTGTTTTAAATTA
1 AATGCGTTTTAAATTA
31613135 GGAATAAGAA
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 135 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (44 bp):
AATGCGTTTTAAATTAAATATGTATGTATATTGTATTATAATTC
Found at i:31613090 original size:22 final size:22
Alignment explanation
Indices: 31613065--31613134 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
31613055 TGTATATTGT
*
31613065 ATTATAATTTAATGTGCTTTAA
1 ATTATAATTTAATGTGATTTAA
** *
31613087 ATTA-AATATGCATGT-ATATTAT
1 ATTATAAT-TTAATGTGAT-TTAA
* *
31613109 ATTATAATTTAACGTGTTTTAA
1 ATTATAATTTAATGTGATTTAA
31613131 ATTA
1 ATTA
31613135 GGAATAAGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
21 4 0.11
22 27 0.77
23 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTATAATTTAATGTGATTTAA
Found at i:31613222 original size:18 final size:19
Alignment explanation
Indices: 31613201--31613238 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31613191 AAAGTATATC
*
31613201 ATTTGTATAA-GTTTTTAT
1 ATTTGTACAATGTTTTTAT
*
31613219 ATTTTTACAATGTTTTTAT
1 ATTTGTACAATGTTTTTAT
31613238 A
1 A
31613239 AGAACATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
ATTTGTACAATGTTTTTAT
Found at i:31615765 original size:52 final size:51
Alignment explanation
Indices: 31615699--31615800 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
31615689 TCTGATAAAA
* *
31615699 TTGGTGCCGGCCATC-TGATTCCCAAAATTAA-GAAAACTAATTTTTTTAATAC
1 TTGGTGCCGACCATCATG-TT-CCAAAA-TAAGGAAAAATAATTTTTTTAATAC
31615751 TTGGTGCCGACCATCAGTGTTCCAAAATAAGGAAAAATAATTTTTTTAAT
1 TTGGTGCCGACCATCA-TGTTCCAAAATAAGGAAAAATAATTTTTTTAAT
31615801 GTGATATGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
51 3 0.07
52 38 0.84
53 2 0.04
54 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (51 bp):
TTGGTGCCGACCATCATGTTCCAAAATAAGGAAAAATAATTTTTTTAATAC
Done.