Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 85 of 325
Found at i:28767330 original size:26 final size:26
Alignment explanation
Indices: 28767301--28767352 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28767291 AAATGTATTT
*
28767301 TTGAGGCTCTATTTTTATAAATTAGA
1 TTGAGGCTCCATTTTTATAAATTAGA
*
28767327 TTGAGGCTCCGTTTTTATAAATTAGA
1 TTGAGGCTCCATTTTTATAAATTAGA
28767353 CTCGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (26 bp):
TTGAGGCTCCATTTTTATAAATTAGA
Found at i:28767618 original size:37 final size:37
Alignment explanation
Indices: 28767552--28767638 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
28767542 AGGCCCCATA
* * *
28767552 ATATATTATTATAAAATTTAAAGTAAATATATATATTAT
1 ATATATTA-TATAAAATTAAAACTAAATATATA-AGTAT
* * *
28767591 A-ATATTATATAATATTAAAACTTAATATTTAAGTAT
1 ATATATTATATAAAATTAAAACTAAATATATAAGTAT
28767627 ATATATTATATA
1 ATATATTATATA
28767639 TTATATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 5 0.12
37 29 0.71
38 6 0.15
39 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATATTATATAAAATTAAAACTAAATATATAAGTAT
Found at i:28767666 original size:15 final size:14
Alignment explanation
Indices: 28767648--28767709 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
28767638 ATTATATTAT
*
28767648 AATATAAAACAAAGA
1 AATA-AAAAAAAAGA
28767663 AATAAAAGAAAAAGA
1 AATAAAA-AAAAAGA
*
28767678 AATAGAAAAGAAAGA
1 AATA-AAAAAAAAGA
*
28767693 AAGAAAACAAAACAGA
1 AATAAAA-AAAA-AGA
28767709 A
1 A
28767710 GGGAAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 6 0.15
15 26 0.67
16 7 0.18
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.06
Consensus pattern (14 bp):
AATAAAAAAAAAGA
Found at i:28767694 original size:30 final size:31
Alignment explanation
Indices: 28767648--28767709 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
28767638 ATTATATTAT
* * *
28767648 AATATAAAACAAAGAAATAAAAGAAAA-AGA
1 AATAGAAAACAAAGAAAGAAAACAAAACAGA
*
28767678 AATAGAAAAGAAAGAAAGAAAACAAAACAGA
1 AATAGAAAACAAAGAAAGAAAACAAAACAGA
28767709 A
1 A
28767710 GGGAAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.06
Consensus pattern (31 bp):
AATAGAAAACAAAGAAAGAAAACAAAACAGA
Found at i:28771515 original size:20 final size:20
Alignment explanation
Indices: 28771490--28771532 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28771480 TCATCAAGGT
28771490 TGTAAAGCTTTTTTAGCCTA
1 TGTAAAGCTTTTTTAGCCTA
28771510 TGTAAAGCTTTTTTAGCCTA
1 TGTAAAGCTTTTTTAGCCTA
28771530 TGT
1 TGT
28771533 TATCAATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (20 bp):
TGTAAAGCTTTTTTAGCCTA
Found at i:28776218 original size:32 final size:32
Alignment explanation
Indices: 28776181--28776245 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
28776171 AATGCTTACC
*
28776181 ATGCCCATCATCCATTAATTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
28776213 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
28776245 A
1 A
28776246 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:28777735 original size:30 final size:31
Alignment explanation
Indices: 28777694--28777766 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
28777684 GTTATAATAT
* * *
28777694 AAAATAAAGAAATAAAA-CAAAAAGAA-GTA
1 AAAAGAAAGAAAGAAAATCAAAAAGAACGGA
* *
28777723 GAAAAGAAAGAAAGAAAATGAAACAGAACGGA
1 -AAAAGAAAGAAAGAAAATCAAAAAGAACGGA
28777755 AAAAGAAAGAAA
1 AAAAGAAAGAAA
28777767 AAGGAAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 15 0.42
31 19 0.53
32 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (31 bp):
AAAAGAAAGAAAGAAAATCAAAAAGAACGGA
Found at i:28779038 original size:27 final size:27
Alignment explanation
Indices: 28779003--28779114 Score: 131
Period size: 27 Copynumber: 4.1 Consensus size: 27
28778993 AGCATGGCAG
* *
28779003 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
28779029 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
28779057 CCAG-GACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
28779084 CCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
28779111 CCAG
1 CCAG
28779115 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
26 6 0.08
27 53 0.72
28 15 0.20
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:28779066 original size:54 final size:54
Alignment explanation
Indices: 28779003--28779117 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
28778993 AGCATGGCAG
* *
28779003 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGGACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
* * * *
28779057 CCAGGACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGGACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
28779111 CCAGGAC
1 CCAGGAC
28779118 GCTTCCTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGGACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:28785672 original size:26 final size:24
Alignment explanation
Indices: 28785634--28785700 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 24
28785624 AATAAAATGT
*
28785634 TTTAAAAATATAATAAATCAAATACA
1 TTTAAAAACATAA-AAA-CAAATACA
28785660 TTTAAAAACATAAAAACAAAT--A
1 TTTAAAAACATAAAAACAAATACA
28785682 -TT-AAAACA-AAAAACAAATA
1 TTTAAAAACATAAAAACAAATA
28785701 AAAAATGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
21 2 0.05
22 1 0.03
24 5 0.13
25 3 0.08
26 12 0.31
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATACA
Found at i:28797211 original size:20 final size:20
Alignment explanation
Indices: 28797163--28797207 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
28797153 CTTATCATGT
* *
28797163 TAAAAATAAATTATTATTTA
1 TAAAAATAAATCATTATATA
28797183 TAAAAATAAA-CATTATATA
1 TAAAAATAAATCATTATATA
28797202 TAAAAA
1 TAAAAA
28797208 ATAATGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAATCATTATATA
Found at i:28797509 original size:189 final size:185
Alignment explanation
Indices: 28797125--28797554 Score: 718
Period size: 189 Copynumber: 2.3 Consensus size: 185
28797115 AAATATTAGG
28797125 TTTCAACTTGTGTTGATCAAAATTTTAACTTATCATGTTAAAAATAAATTATTATTTATAAAAAT
1 TTTCAACTTGTGTTGATCAAAATTTTAACTTATCATGTTAAAAATAAATTATTATTTATAAAAAT
*
28797190 AAACATTATATATAAAAAATAATGCCAAAACAACTCTAATGTTTGAAATTTTATAAAAATAACGT
66 AAACATTATATATAAAAAATAATGCCAAAACAACTCTAATGTTTGAAATTTTATAAAAATAACAT
* * *
28797255 TAATTTAAATATTAGATTGTTTACTTAACGAAAATATTAGTGTTTAAGAAATTCA
131 TAATATAAATATTACATTGTTTACTTAACGAAAATATTAGTGTTTAAGAAACTCA
* * *
28797310 TTTCAACTTGTGTTGGTCGAAATTTTAACTTATCATATTAAAAATAAATTATTATTTATAATAAA
1 TTTCAACTTGTGTTGATCAAAATTTTAACTTATCATGTTAAAAATAAATTATTATTTATAA-AAA
28797375 TAAACATTATATATAACAAAAATAATGCCAAAACAACTCTAA-GTTTTGAAATTTTATAAAAATA
65 TAAACATTATATAT-A-AAAAATAATGCCAAAACAACTCTAATG-TTTGAAATTTTATAAAAATA
*
28797439 ACATTAATATAAAGTATTACATTGTTTACTTAATGAAAATATTAGTGTTTAAGAAACTCA
127 ACATTAATATAAA-TATTACATTGTTTACTTAACGAAAATATTAGTGTTTAAGAAACTCA
* *
28797499 TTTCAACTTGTGTTGATCAAAATTTTAACTTATCGTGTTAAAAATAAATTACTATT
1 TTTCAACTTGTGTTGATCAAAATTTTAACTTATCATGTTAAAAATAAATTATTATT
28797555 GATGTAAGAC
Statistics
Matches: 227, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
185 58 0.26
186 17 0.07
187 2 0.01
188 56 0.25
189 94 0.41
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (185 bp):
TTTCAACTTGTGTTGATCAAAATTTTAACTTATCATGTTAAAAATAAATTATTATTTATAAAAAT
AAACATTATATATAAAAAATAATGCCAAAACAACTCTAATGTTTGAAATTTTATAAAAATAACAT
TAATATAAATATTACATTGTTTACTTAACGAAAATATTAGTGTTTAAGAAACTCA
Found at i:28798003 original size:36 final size:36
Alignment explanation
Indices: 28797956--28798032 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
28797946 ACATTATTCA
28797956 TGAAATGATGCGTAAAGGCTTTATACCTGATACTAG
1 TGAAATGATGCGTAAAGGCTTTATACCTGATACTAG
*
28797992 TGAAATGATGCGTAAAGGCTTTATCCCTGATACTAG
1 TGAAATGATGCGTAAAGGCTTTATACCTGATACTAG
28798028 T-AAAT
1 TGAAAT
28798033 ACTCCAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (36 bp):
TGAAATGATGCGTAAAGGCTTTATACCTGATACTAG
Found at i:28799313 original size:40 final size:40
Alignment explanation
Indices: 28799269--28799419 Score: 196
Period size: 40 Copynumber: 3.7 Consensus size: 40
28799259 TTGACGACAA
28799269 TTCGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
* *
28799309 TTCGGCTATGTATGGCATTTAGTGTGCAATTCGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
* * * *
28799349 TTCGACTATGTATGACACTTAGTGTGCGAGATT-AAAATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGC--GATTCGAGATAGC
* *
28799390 TTCAGTTATGTATTGGCACTTAGTGTGCGA
1 TTCGGCTATGTA-TGGCACTTAGTGTGCGA
28799420 GAATTCGAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 64 0.67
41 15 0.16
42 17 0.18
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (40 bp):
TTCGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
Found at i:28808227 original size:16 final size:15
Alignment explanation
Indices: 28808201--28808235 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28808191 TGATGTGAAT
28808201 AATATAAAATATTAA
1 AATATAAAATATTAA
*
28808216 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
28808232 AATA
1 AATA
28808236 ATAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:28808418 original size:20 final size:21
Alignment explanation
Indices: 28808376--28808418 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
28808366 CCTTTTTTAG
* *
28808376 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
28808397 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
28808417 AA
1 AA
28808419 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:28808635 original size:11 final size:11
Alignment explanation
Indices: 28808619--28808648 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28808609 TAACATTAAG
28808619 AATATATATAT
1 AATATATATAT
*
28808630 AATATAAATAT
1 AATATATATAT
28808641 AATATATA
1 AATATATA
28808649 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:28809478 original size:26 final size:26
Alignment explanation
Indices: 28809428--28809506 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 26
28809418 GGTTTCTTGG
28809428 TTTTTTTTTTTGGAGGTTAGG-TTTTTC
1 TTTTTTTTTTT-G-GGTTAGGTTTTTTC
28809455 TTTTTTTTTTTGGGTTAGGTTTTTTC
1 TTTTTTTTTTTGGGTTAGGTTTTTTC
*
28809481 TTTTTTTTTTTTGGTTAGGTCTTTTT
1 TTTTTTTTTTTGGGTTAGGT-TTTTT
28809507 TTTGGAGGGC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
25 7 0.14
26 26 0.53
27 16 0.33
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (26 bp):
TTTTTTTTTTTGGGTTAGGTTTTTTC
Found at i:28809896 original size:40 final size:40
Alignment explanation
Indices: 28809823--28809920 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
28809813 ACGGTACCAT
* * *
28809823 TTGGTGTGTAGGGTTGGATGGGTTGATGTTATCCCCATAC
1 TTGGTGTGTAGGGCTGGATGAGTCGATGTTATCCCCATAC
*
28809863 TTGGTGTGTAGGGCTGGGTGAGTCGAT-TCTATCCCC--AC
1 TTGGTGTGTAGGGCTGGATGAGTCGATGT-TATCCCCATAC
* * *
28809901 ATGGTGTGTTGGGTTGGATG
1 TTGGTGTGTAGGGCTGGATG
28809921 GAGATGGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 18 0.37
39 1 0.02
40 30 0.61
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.36
Consensus pattern (40 bp):
TTGGTGTGTAGGGCTGGATGAGTCGATGTTATCCCCATAC
Found at i:28809927 original size:23 final size:23
Alignment explanation
Indices: 28809901--28809944 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28809891 CTATCCCCAC
**
28809901 ATGGTGTGTTGGGTTGGATGGAG
1 ATGGTGTGCAGGGTTGGATGGAG
28809924 ATGGTGTGCAGGGTTGGATGG
1 ATGGTGTGCAGGGTTGGATGG
28809945 GATAGCATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.52, T:0.32
Consensus pattern (23 bp):
ATGGTGTGCAGGGTTGGATGGAG
Found at i:28810057 original size:27 final size:27
Alignment explanation
Indices: 28809990--28810057 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
28809980 TGTTACTGAG
* * *
28809990 ATGGGC-TAGGCCCAATTGATTCTGTT
1 ATGGGCTTTGGCCCAAATGATTCTGTA
* *
28810016 ATGGGCTGTGACCCAAATGATAT-TGTA
1 ATGGGCTTTGGCCCAAATGAT-TCTGTA
28810043 ATGGGCTTTGGCCCA
1 ATGGGCTTTGGCCCA
28810058 CGTATGCTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 6 0.18
27 26 0.79
28 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (27 bp):
ATGGGCTTTGGCCCAAATGATTCTGTA
Found at i:28811633 original size:10 final size:11
Alignment explanation
Indices: 28811601--28811630 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28811591 ATGATACAAC
28811601 CTTTTATTTTA
1 CTTTTATTTTA
28811612 -TTTTATTTTA
1 CTTTTATTTTA
28811622 CTTTTATTT
1 CTTTTATTT
28811631 ACTAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTATTTTA
Found at i:28812081 original size:18 final size:18
Alignment explanation
Indices: 28812055--28812089 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28812045 AAATTAACTT
*
28812055 TTTTTAAAAATAATATTA
1 TTTTAAAAAATAATATTA
*
28812073 TTTTAAAAAATTATATT
1 TTTTAAAAAATAATATT
28812090 TAATTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAAATAATATTA
Found at i:28813538 original size:30 final size:30
Alignment explanation
Indices: 28813504--28813568 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
28813494 ACTTAACAAG
28813504 CAAATACCTCAAAAATAATAACAAAATTAA
1 CAAATACCTCAAAAATAATAACAAAATTAA
* **
28813534 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCAAAAATAATAACAAAATTAA
28813564 -AAATA
1 CAAATA
28813569 AAATAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.23
Consensus pattern (30 bp):
CAAATACCTCAAAAATAATAACAAAATTAA
Found at i:28825983 original size:20 final size:20
Alignment explanation
Indices: 28825947--28825985 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28825937 TAAAAAAAAA
28825947 TCAATATTTTCGTTTTTTTC
1 TCAATATTTTCGTTTTTTTC
*
28825967 TCAATTATTTTTGTTTTTT
1 TCAA-TATTTTCGTTTTTT
28825986 ATATAAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (20 bp):
TCAATATTTTCGTTTTTTTC
Found at i:28827266 original size:27 final size:27
Alignment explanation
Indices: 28827236--28827298 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28827226 ATACATACAG
* *
28827236 GTTGTGCCTACCTGACAAGCTCAACTA
1 GTTGAGCCTACCTGACAAGCACAACTA
* * * *
28827263 GTTGAACCTATCTGACAGGCACAACTT
1 GTTGAGCCTACCTGACAAGCACAACTA
28827290 GTTGAGCCT
1 GTTGAGCCT
28827299 TCTTGGTAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (27 bp):
GTTGAGCCTACCTGACAAGCACAACTA
Found at i:28833142 original size:14 final size:16
Alignment explanation
Indices: 28833104--28833135 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28833094 AATAATAATA
28833104 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
28833119 ATATAAAAATTACATT
1 ATATAAAAATTACATT
28833135 A
1 A
28833136 AAAAAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:28833526 original size:106 final size:105
Alignment explanation
Indices: 28833124--28833527 Score: 438
Period size: 113 Copynumber: 3.8 Consensus size: 105
28833114 ACATTATATA
* * *
28833124 AAAATTACATTA--AAAAAATCACAAAACACTAAACTA-GAAACACTAACAA--TT-T-A--TAA
1 AAAATTACATTACTAAAAAATCACAATACACTAAACCACTAAACACTAACAATTTTGTAACCTAA
28833180 TCATAAATTACTAACACAAAATAACTA-AAAATTATTATTTTT
66 TCATAAATTACT-A-ACAAAATAACTATAAAATTATT-TTTTT
* * *
28833222 TAAA-TACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAGCAATTTATGTAACCTA
1 AAAATTACATTACTAAAAAATCACAATACACTAAACCACTAAACACTAACAATTT-TGTAACCTA
* *
28833286 ATCATAAATTACTAATAAAATAGCTATAAAATTA-TTTTTT
65 ATCATAAATTACTAACAAAATAACTATAAAATTATTTTTTT
** * *
28833326 AAAAACATATTACTAAAAAATCACAATACACTAATATACTAAACCACAAAACACTAACAATTTTT
1 AAAATTACATTACTAAAAAATCACAAT--AC------ACTAAACCACTAAACACTAACAA-TTTT
*
28833391 ATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTTTTTT
57 GTAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTTTTTT
* *
28833440 AAAATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAA-TTTGTAACTTAA
1 AAAATTACATTACTAAAAAATCACAATACACTAAACCACTAAACACTAACAATTTTGTAACCTAA
*
28833504 TCCCATAAATTATTAACAAAATAA
66 T--CATAAATTACTAACAAAATAA
28833528 ATAACTATAA
Statistics
Matches: 257, Mismatches: 25, Indels: 40
0.80 0.08 0.12
Matches are distributed among these distances:
97 7 0.03
98 3 0.01
99 21 0.08
100 11 0.04
102 1 0.00
103 1 0.00
104 20 0.08
105 31 0.12
106 49 0.19
107 17 0.07
112 2 0.01
113 61 0.24
114 33 0.13
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (105 bp):
AAAATTACATTACTAAAAAATCACAATACACTAAACCACTAAACACTAACAATTTTGTAACCTAA
TCATAAATTACTAACAAAATAACTATAAAATTATTTTTTT
Found at i:28833725 original size:160 final size:165
Alignment explanation
Indices: 28833371--28833769 Score: 650
Period size: 160 Copynumber: 2.4 Consensus size: 165
28833361 ATACTAAACC
28833371 ACAAAACACTAACAATTTTTATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
1 ACAAAA-ACTAACAA--TTTATAACCTAATCATAAATTACTAACAAAATAACTAT-AAA-T-TTT
28833436 TTTTAAAATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAATTTGTAACT
60 TTTT-AAATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAA-TTGTAACT
28833501 TAATCCCATAAATTATTAACAAAATAAATAACTATAACAAAAT
123 TAATCCCATAAATTATTAACAAAATAAATAACTATAACAAAAT
28833544 ACAAAAACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTAT-AATTTTTTTTAA
1 ACAAAAACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAAATTTTTTTTAA
28833608 ATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAA-T-TAAC-TAA-CCCA
66 ATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAATTGTAACTTAATCCCA
28833669 TAAATTATTAACAAAATAAATAACTATAACAAAAT
131 TAAATTATTAACAAAATAAATAACTATAACAAAAT
*
28833704 ACAAAAACTAACAATTTATAACCTAATCAT--ACTACTAACAAAATAACTATACAATTATTTTTT
1 ACAAAAACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATA-AATT-TTTTTT
28833767 AAA
64 AAA
28833770 AAAAATTTAC
Statistics
Matches: 222, Mismatches: 1, Indels: 18
0.92 0.00 0.07
Matches are distributed among these distances:
158 19 0.09
160 73 0.33
161 12 0.05
162 4 0.02
163 1 0.00
165 51 0.23
166 7 0.03
167 1 0.00
168 2 0.01
170 38 0.17
172 8 0.04
173 6 0.03
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.30
Consensus pattern (165 bp):
ACAAAAACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTATAAATTTTTTTTAA
ATTACATTACTAAAAAATCACAATACCCTAAACCACTAAACACTAACAATTGTAACTTAATCCCA
TAAATTATTAACAAAATAAATAACTATAACAAAAT
Found at i:28834623 original size:21 final size:20
Alignment explanation
Indices: 28834599--28834638 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
28834589 TATATATTTC
28834599 TATAATTTTAAAAAATAATAA
1 TATAATTTTAAAAAA-AATAA
*
28834620 TATAGTTTTAAAAAAAATA
1 TATAATTTTAAAAAAAATA
28834639 TAAATTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TATAATTTTAAAAAAAATAA
Found at i:28836239 original size:24 final size:24
Alignment explanation
Indices: 28836206--28836279 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
28836196 AAATCTGTCT
*
28836206 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28836230 GGAGAGGATTTAGGAGCTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28836254 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
28836278 GG
1 GG
28836280 TGAACTGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.31, C:0.05, G:0.42, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:28837796 original size:28 final size:26
Alignment explanation
Indices: 28837709--28837818 Score: 87
Period size: 27 Copynumber: 4.1 Consensus size: 26
28837699 ATGAAGCGTC
* *
28837709 CTGGTGGCTATGCCACAATTATCTGATT
1 CTGGTGACTCTGCCAC-ATTATCTG-TT
* * * *
28837737 -TGGTGGCACTGGCATATATATCTGTT
1 CTGGTGACTCTGCCACAT-TATCTGTT
**
28837763 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGACTCTGCCAC-ATTATCTGT-T
*
28837791 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGACTCTGCCACATTATCTGTT
28837817 CT
1 CT
28837819 AGCAGCCATG
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
26 7 0.10
27 44 0.66
28 16 0.24
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (26 bp):
CTGGTGACTCTGCCACATTATCTGTT
Found at i:28837813 original size:54 final size:54
Alignment explanation
Indices: 28837709--28837818 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
28837699 ATGAAGCGTC
* * *
28837709 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCACTGGCATATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGGCACATATATCTGTT
* * * * *
28837763 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACACTGGCACATATATCTGTT
28837817 CT
1 CT
28837819 AGCAGCCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 32 0.68
55 15 0.32
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGGCACATATATCTGTT
Found at i:28844100 original size:24 final size:24
Alignment explanation
Indices: 28844028--28844092 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
28844018 AGTCTGTCTA
*
28844028 GAGAAGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
* *
28844052 GAGAGGATTTAGGTGCTGATCAGG
1 GAGAGGATTTAGGAGCTGATAAGG
28844076 GAGAGGATTTAGGAGCT
1 GAGAGGATTTAGGAGCT
28844093 AATTAGGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.40, T:0.23
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:28845579 original size:27 final size:26
Alignment explanation
Indices: 28845530--28845641 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
28845520 ATGAAGCGTC
* *
28845530 CTGGTGGCTATGCTACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28845557 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28845584 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
28845612 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
28845638 CTGG
1 CTGG
28845642 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28847099 original size:38 final size:38
Alignment explanation
Indices: 28847048--28847122 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
28847038 CATCGTCAAG
* *
28847048 AAAAGCTCATAAGAGCTGGTCCTCCCGAAT-ACGCCAAC
1 AAAAGCTCATAAGAGCTGATCCACCC-AATCACGCCAAC
*
28847086 AAAAGCTCGTAAGAGCTGATCCACCCAATCACGCCAA
1 AAAAGCTCATAAGAGCTGATCCACCCAATCACGCCAA
28847123 ACAGGAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 30 0.91
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (38 bp):
AAAAGCTCATAAGAGCTGATCCACCCAATCACGCCAAC
Found at i:28854627 original size:218 final size:216
Alignment explanation
Indices: 28854336--28854754 Score: 703
Period size: 218 Copynumber: 1.9 Consensus size: 216
28854326 GGAAAAATAC
* *
28854336 GACATTTTGTAGATTGAAAGAAAGTATAGTGGGAATAAGACTTACAAGGATCCTCCTAGTTTTCT
1 GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
* * * *
28854401 CCTTTCTTTGTATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAATAGGTGT
66 CATTTCTTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
*
28854466 TAATTTTTTATCGAATAGCTCCTGGGCAACTATGTAAGACTTCCTGGTGGATATTGACTGGATTT
131 TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAG--TTCCTGGTGGATATTGACTGGATTT
28854531 ATTATTTTTTGATAAGAAAGTAG
194 ATTATTTTTTGATAAGAAAGTAG
* * *
28854554 GACATTTCGTAGGTTGAAAGGAAGTATAGTGGGAACAAGACTTACAATGATCCTCCTAGTTTTCT
1 GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
28854619 CATTTCTTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
66 CATTTCTTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
* **
28854684 TAATTTTTTATCAAATAGCTCTTGGGCAACTATGTAAGTTTTTGGTGGATATTGACTGGATTTAT
131 TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAGTTCCTGGTGGATATTGACTGGATTTAT
28854749 TATTTT
196 TATTTT
28854755 CTGACAAAAA
Statistics
Matches: 188, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
216 31 0.16
218 157 0.84
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (216 bp):
GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
CATTTCTTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAGTTCCTGGTGGATATTGACTGGATTTAT
TATTTTTTGATAAGAAAGTAG
Found at i:28860892 original size:136 final size:136
Alignment explanation
Indices: 28860648--28860924 Score: 554
Period size: 136 Copynumber: 2.0 Consensus size: 136
28860638 TGGAATATAG
28860648 TTTACACATAAGGACAACTAATACATTCAACAGTTCAAGTATGAATACATGCAACACGCATACAA
1 TTTACACATAAGGACAACTAATACATTCAACAGTTCAAGTATGAATACATGCAACACGCATACAA
28860713 TACACTTCACTCATATAGACAGTTCGCCTTCACCCTCTGCGAACATATGTGTTATGGAAAGTCTA
66 TACACTTCACTCATATAGACAGTTCGCCTTCACCCTCTGCGAACATATGTGTTATGGAAAGTCTA
28860778 GGTGGA
131 GGTGGA
28860784 TTTACACATAAGGACAACTAATACATTCAACAGTTCAAGTATGAATACATGCAACACGCATACAA
1 TTTACACATAAGGACAACTAATACATTCAACAGTTCAAGTATGAATACATGCAACACGCATACAA
28860849 TACACTTCACTCATATAGACAGTTCGCCTTCACCCTCTGCGAACATATGTGTTATGGAAAGTCTA
66 TACACTTCACTCATATAGACAGTTCGCCTTCACCCTCTGCGAACATATGTGTTATGGAAAGTCTA
28860914 GGTGGA
131 GGTGGA
28860920 TTTAC
1 TTTAC
28860925 CCCTCTAGGT
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 141 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (136 bp):
TTTACACATAAGGACAACTAATACATTCAACAGTTCAAGTATGAATACATGCAACACGCATACAA
TACACTTCACTCATATAGACAGTTCGCCTTCACCCTCTGCGAACATATGTGTTATGGAAAGTCTA
GGTGGA
Found at i:28860933 original size:18 final size:18
Alignment explanation
Indices: 28860910--28860946 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28860900 TTATGGAAAG
28860910 TCTAGGTGGATTTACCCC
1 TCTAGGTGGATTTACCCC
28860928 TCTAGGTGGATTTACCCC
1 TCTAGGTGGATTTACCCC
28860946 T
1 T
28860947 GTAGACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (18 bp):
TCTAGGTGGATTTACCCC
Found at i:28861442 original size:79 final size:78
Alignment explanation
Indices: 28861312--28861468 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 78
28861302 TTAATTGATA
28861312 ATATTAGTGAATAAATAATAAGTTGACAAATGTAGGATCATGAGATGATACATGTGTAATAATAT
1 ATATTAGTGAATAAATAATAAGTTGACAAATGTAGGATCATGAGATGATACATGTGTAATAATAT
28861377 GTATAATACAATT
66 GTATAATACAATT
28861390 ATATTAGTGAATAAATTAATAAGTTGACAAATGTAGGATCATGAGATGATACATGTGTAATAATA
1 ATATTAGTGAATAAA-TAATAAGTTGACAAATGTAGGATCATGAGATGATACATGTGTAATAATA
28861455 TGTATAATACAATT
65 TGTATAATACAATT
28861469 GTAATAAAAG
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 15 0.19
79 63 0.81
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.34
Consensus pattern (78 bp):
ATATTAGTGAATAAATAATAAGTTGACAAATGTAGGATCATGAGATGATACATGTGTAATAATAT
GTATAATACAATT
Found at i:28862697 original size:40 final size:40
Alignment explanation
Indices: 28862652--28862734 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
28862642 AATTATGGAA
* * *
28862652 TACTGAATATTGTTTTG-ATTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTATGTA-TACTGAATTGAACTGTGAAAT
*
28862692 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTATACTGAATTGAACTGTGAAAT
28862732 TAC
1 TAC
28862735 AGAAGTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (40 bp):
TACTGAATATTGTTATGTATACTGAATTGAACTGTGAAAT
Found at i:28862998 original size:51 final size:50
Alignment explanation
Indices: 28862929--28863061 Score: 161
Period size: 45 Copynumber: 2.7 Consensus size: 50
28862919 CAGGCACTTA
28862929 TGTGTCGACA-ACTGTTACTGTTATCGTTACTGTTACCGATTCAGCACTTTG
1 TGTGTCGA-ATACTGTTACTGTTA-CGTTACTGTTACCGATTCAGCACTTTG
* *
28862980 TGTGTCGAATACTATTACTGTTAC----C-GTTACTGATTCAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACGTTACTGTTACCGATTCAGCACTTTG
* *
28863025 TGTGTTGAATACTGTTACTGTTACTGTTACTGCTACC
1 TGTGTCGAATACTGTTACTGTTAC-GTTACTGTTACC
28863062 CTTACTGATT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
45 41 0.59
46 1 0.01
50 3 0.04
51 24 0.35
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (50 bp):
TGTGTCGAATACTGTTACTGTTACGTTACTGTTACCGATTCAGCACTTTG
Found at i:28863055 original size:45 final size:45
Alignment explanation
Indices: 28862944--28863056 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
28862934 CGACAACTGT
*
28862944 TACTGTTA-TCGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
1 TACTGTTACT-GTTACTGTTACTGATTCAGCACTTTGTGTGTCGAA
* * *
28862989 TACTATTACTGTTACCGTTACTGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACTGATTCAGCACTTTGTGTGTCGAA
28863034 TACTGTTACTGTTACTGTTACTG
1 TACTGTTACTGTTACTGTTACTG
28863057 CTACCCTTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 60 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACTGATTCAGCACTTTGTGTGTCGAA
Found at i:28865585 original size:34 final size:34
Alignment explanation
Indices: 28865513--28865585 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
28865503 GACAGTCTAG
* *
28865513 TATCAGTGTGGGCCTTAGCCCATTACAAAAATAG
1 TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
**
28865547 TATCAGTGTGGGCCTTAGCCCATTACAGTAACAA
1 TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
28865581 TATCA
1 TATCA
28865586 TAAATGCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (34 bp):
TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
Found at i:28869861 original size:60 final size:60
Alignment explanation
Indices: 28869783--28869919 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
28869773 CAGTGTTAAC
* *
28869783 TGGGCCTTAGCCCATATCAATATTAATCTGGGTCATAGCCC-ATTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
28869844 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
28869904 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
28869920 TAACATAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 52 0.76
61 14 0.21
62 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:28869883 original size:28 final size:27
Alignment explanation
Indices: 28869782--28869883 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
28869772 TCAGTGTTAA
* *
28869782 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
28869810 CTGGGTCATAGCCCAT-TACAGTATCAGAGTAT
1 CTGGG-CCTAGCCCATAT-CAGTATC--A--AT
*
28869842 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
28869870 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
28869884 TATTACAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
27 7 0.12
28 26 0.44
29 1 0.02
30 2 0.03
32 18 0.31
33 5 0.08
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:28871383 original size:14 final size:12
Alignment explanation
Indices: 28871358--28871422 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 12
28871348 GCTATAGGGG
28871358 AGAAAAGAAAAACA
1 AGAAAAG-AAAA-A
28871372 AGAAGAAGAAAAA
1 AGAA-AAGAAAAA
28871385 TAGAAGAAGAAAAA
1 -AGAA-AAGAAAAA
28871399 ATGAAAA-AAAAA
1 A-GAAAAGAAAAA
28871411 AGAAAAGAAAAA
1 AGAAAAGAAAAA
28871423 TATAAATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.11
12 11 0.23
13 4 0.09
14 24 0.51
15 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:28872598 original size:3 final size:3
Alignment explanation
Indices: 28872590--28872622 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28872580 AAACATACTA
*
28872590 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28872623 TAAAACATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28874213 original size:25 final size:25
Alignment explanation
Indices: 28874173--28874222 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28874163 CTAACATAAT
*
28874173 ATTAACTCCCTCAAACTTATACCTA
1 ATTAACTACCTCAAACTTATACCTA
* *
28874198 ATTAACTACCTTAAACTTATGCCTA
1 ATTAACTACCTCAAACTTATACCTA
28874223 CACCTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTAACTACCTCAAACTTATACCTA
Found at i:28876446 original size:47 final size:46
Alignment explanation
Indices: 28876395--28876571 Score: 184
Period size: 47 Copynumber: 3.8 Consensus size: 46
28876385 TGGTTGAACA
* *
28876395 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-CAACG
* *
28876442 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACCAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTCAA-C--G
* *
28876487 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGAT-TCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTC-AACG
* *
28876535 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28876572 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
44 5 0.05
45 1 0.01
46 35 0.32
47 56 0.51
48 3 0.03
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTCAACG
Found at i:28877501 original size:61 final size:61
Alignment explanation
Indices: 28877426--28877547 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
28877416 CCCCCTGTTC
28877426 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
1 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
28877487 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
1 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
28877548 GGAATCCTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (61 bp):
CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
Found at i:28880350 original size:24 final size:24
Alignment explanation
Indices: 28880323--28880374 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28880313 TTAGTAAGTC
*
28880323 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
28880347 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28880371 AAAT
1 AAAT
28880375 CTTATAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28882320 original size:24 final size:24
Alignment explanation
Indices: 28882293--28882344 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28882283 TTAGTAAGTC
*
28882293 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
28882317 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28882341 AAAT
1 AAAT
28882345 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28884290 original size:24 final size:24
Alignment explanation
Indices: 28884263--28884314 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28884253 TTAGTAAGTC
*
28884263 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
28884287 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28884311 AAAT
1 AAAT
28884315 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28897314 original size:23 final size:24
Alignment explanation
Indices: 28897271--28897316 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
28897261 TATTATTTTA
*
28897271 TGTTAATAATTATTATTTAATTAG
1 TGTTAATAATTATTATCTAATTAG
28897295 TGTT-ATAATTA-TATGCTAATTA
1 TGTTAATAATTATTAT-CTAATTA
28897317 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (24 bp):
TGTTAATAATTATTATCTAATTAG
Found at i:28899497 original size:6 final size:6
Alignment explanation
Indices: 28899462--28899493 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28899452 ATTTAAACAT
*
28899462 TAAATA TAAATA TAAATA TAAATA TATATA TA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TA
28899494 TATAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:28906912 original size:17 final size:17
Alignment explanation
Indices: 28906881--28906922 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28906871 ATTTAAGTTT
*
28906881 TAATTTTTATAAAAAT-
1 TAATTTTAATAAAAATC
*
28906897 TAAATTTTAATTAAAATC
1 T-AATTTTAATAAAAATC
28906915 TAATTTTA
1 TAATTTTA
28906923 TTTATAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTTTAATAAAAATC
Found at i:28909506 original size:29 final size:31
Alignment explanation
Indices: 28909469--28909537 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
28909459 AAATTTACTT
* *
28909469 AAAACTACATTTATC-TC-ATATTTAAAATA
1 AAAATTACATATATCATCTATATTTAAAATA
*
28909498 AAAATTACATATATCTATCTATTTTTAAAATA
1 AAAATTACATATATC-ATCTATATTTAAAATA
28909530 AAATATTA
1 AAA-ATTA
28909538 AGTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.39
31 2 0.06
32 14 0.42
33 4 0.12
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATTACATATATCATCTATATTTAAAATA
Found at i:28912892 original size:33 final size:33
Alignment explanation
Indices: 28912839--28912901 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
28912829 TTAGGAGTCA
*
28912839 GGGATCTCAGACCGGATGTTGGAATCACTTCTT
1 GGGAGCTCAGACCGGATGTTGGAATCACTTCTT
* *
28912872 GGGAGCTCAGACTGGGTGTTGGAATCACTT
1 GGGAGCTCAGACCGGATGTTGGAATCACTT
28912902 GTTTGGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29
Consensus pattern (33 bp):
GGGAGCTCAGACCGGATGTTGGAATCACTTCTT
Found at i:28913968 original size:22 final size:23
Alignment explanation
Indices: 28913943--28913988 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28913933 CAACCAAATC
28913943 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
28913965 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
28913988 A
1 A
28913989 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:28913994 original size:23 final size:23
Alignment explanation
Indices: 28913950--28913994 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28913940 ATCAATTCAA
*
28913950 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
28913973 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
28913995 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:28917364 original size:42 final size:42
Alignment explanation
Indices: 28917305--28917392 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
28917295 GTATTGTATG
28917305 ATTGATAATTAGTGAACAAGTTAAAATTGAACATATATAAAT
1 ATTGATAATTAGTGAACAAGTTAAAATTGAACATATATAAAT
28917347 ATTGATAATTAGTGAACAAGTTAAAATTGAACATATATAAAT
1 ATTGATAATTAGTGAACAAGTTAAAATTGAACATATATAAAT
28917389 ATTG
1 ATTG
28917393 TTAAATAGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (42 bp):
ATTGATAATTAGTGAACAAGTTAAAATTGAACATATATAAAT
Found at i:28917447 original size:2 final size:2
Alignment explanation
Indices: 28917442--28917474 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28917432 ATATATATAT
*
28917442 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28917475 TAATGAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28917810 original size:47 final size:47
Alignment explanation
Indices: 28917756--28917851 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
28917746 GTGACAGCCC
*
28917756 TAATTTGACCCTATTCGGGAAGTGGTTTCGGGACCACAAAACCAAGT
1 TAATTTGACCCTATTCGGGAAGTGGTTTCAGGACCACAAAACCAAGT
* *
28917803 TAATTTGACCCTATTCGGGAAGTGGTTTCAGGACTACAAAACCGAGT
1 TAATTTGACCCTATTCGGGAAGTGGTTTCAGGACCACAAAACCAAGT
28917850 TA
1 TA
28917852 TAAAAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (47 bp):
TAATTTGACCCTATTCGGGAAGTGGTTTCAGGACCACAAAACCAAGT
Found at i:28920422 original size:39 final size:39
Alignment explanation
Indices: 28920365--28920488 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
28920355 ATTTGATGTG
* *
28920365 TATCCGGACTTAGAGTCCGCAGGCTATGTGTTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
28920404 TATCCGGACTTAGGGTCCGCATGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
28920443 TATCTGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
28920482 TGTCCGG
1 TATCCGG
28920489 GCTAAAGTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:28922410 original size:28 final size:28
Alignment explanation
Indices: 28922370--28922430 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
28922360 CTAGTCAGCT
28922370 TAAATAAACGATTGACTACTATTAAAAA
1 TAAATAAACGATTGACTACTATTAAAAA
28922398 TAAATAAACGATTGACTACTATTAAAAA
1 TAAATAAACGATTGACTACTATTAAAAA
28922426 TAAAT
1 TAAAT
28922431 GTAAACTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAATAAACGATTGACTACTATTAAAAA
Found at i:28929564 original size:23 final size:22
Alignment explanation
Indices: 28929525--28929569 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28929515 TATTAAAATA
* * *
28929525 ATAAAATTATATTTTTATTATC
1 ATAAAAATATATATTTAATATC
28929547 ATAAAAATATATAATTTAATATC
1 ATAAAAATATAT-ATTTAATATC
28929570 GTCTTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAAATATATATTTAATATC
Found at i:28929794 original size:21 final size:21
Alignment explanation
Indices: 28929754--28929794 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28929744 AAATTTCTTC
*
28929754 AAACTTTTTTTATTAAAATAG
1 AAACTTTGTTTATTAAAATAG
* *
28929775 AAACTTTGTTTCTTACAATA
1 AAACTTTGTTTATTAAAATA
28929795 CTTTAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (21 bp):
AAACTTTGTTTATTAAAATAG
Found at i:28929993 original size:2 final size:2
Alignment explanation
Indices: 28929986--28930019 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28929976 GCTATCTATC
28929986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28930020 AATAAAGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28948162 original size:28 final size:28
Alignment explanation
Indices: 28948109--28948163 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
28948099 ATTAAGTTTA
* *
28948109 CTTAAAATATTTGAAAATTCTGATTAAT
1 CTTAAAATATTTCAAAATTCTAATTAAT
*
28948137 CTTAAAA-ATTTCAAATATTTTAATTAA
1 CTTAAAATATTTCAAA-ATTCTAATTAA
28948164 ACCCCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
CTTAAAATATTTCAAAATTCTAATTAAT
Found at i:28948908 original size:2 final size:2
Alignment explanation
Indices: 28948901--28948930 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28948891 AATGTCTTTT
28948901 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28948931 GCTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28954206 original size:21 final size:21
Alignment explanation
Indices: 28954182--28954221 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28954172 TATGCCTTTA
*
28954182 AAAAT-TTTAATTATATTTAGT
1 AAAATATTTAAATAT-TTTAGT
28954203 AAAATATTTAAATATTTTA
1 AAAATATTTAAATATTTTA
28954222 ATTATATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAATATTTAAATATTTTAGT
Found at i:28954865 original size:25 final size:25
Alignment explanation
Indices: 28954810--28954865 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
28954800 AGTATACATA
28954810 TTTTTA-AAAAAATTTATTTTCAAT
1 TTTTTAGAAAAAATTTATTTTCAAT
* *
28954834 TTGTTAGAAAACATTTATTTT-AAT
1 TTTTTAGAAAAAATTTATTTTCAAT
28954858 GTTTTTAG
1 -TTTTTAG
28954866 TATTTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
TTTTTAGAAAAAATTTATTTTCAAT
Found at i:28956263 original size:11 final size:11
Alignment explanation
Indices: 28956247--28956280 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28956237 CGTATCTAGT
28956247 TTTGTTCTTGA
1 TTTGTTCTTGA
*
28956258 TTTGTTCTTAA
1 TTTGTTCTTGA
*
28956269 TTTATTCTTGA
1 TTTGTTCTTGA
28956280 T
1 T
28956281 GATTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTGTTCTTGA
Found at i:28964537 original size:24 final size:24
Alignment explanation
Indices: 28964505--28964551 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28964495 CTGTCAGGAG
**
28964505 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
28964529 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
28964552 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:28966029 original size:27 final size:26
Alignment explanation
Indices: 28965971--28966083 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
28965961 AGGAAGCGTC
* *
28965971 CTGGTGGCTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCAC--ATTATCTGTT
28965999 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
28966026 CTGGTGGTTCTGCCACGATTATCTCTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
28966054 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
28966080 CTGG
1 CTGG
28966084 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.09
27 36 0.49
28 31 0.42
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:28966056 original size:55 final size:54
Alignment explanation
Indices: 28965971--28966083 Score: 147
Period size: 55 Copynumber: 2.1 Consensus size: 54
28965961 AGGAAGCGTC
*
28965971 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * * * *
28966026 CTGGTGGTTCTGCCAC-GATTATCTCTATCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAAATTATCT-GATCTGGTGACTCTGCCACATTATCTGTT
28966080 CTGG
1 CTGG
28966084 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 19 0.37
55 32 0.63
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:28969249 original size:8 final size:8
Alignment explanation
Indices: 28969236--28969266 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28969226 AACAAAGTAC
28969236 TCGACTAA
1 TCGACTAA
28969244 TCGACTAA
1 TCGACTAA
28969252 TCGACTAA
1 TCGACTAA
*
28969260 TCAACTA
1 TCGACTA
28969267 GTTTCGTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (8 bp):
TCGACTAA
Found at i:28969531 original size:40 final size:40
Alignment explanation
Indices: 28969404--28969553 Score: 169
Period size: 40 Copynumber: 3.7 Consensus size: 40
28969394 ATTATGTTTG
* * * *
28969404 GCACTTAGTGTGCGTATTGAGATAACTTCGGCTATATAAA
1 GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
* * * *
28969444 GCACTTAATGTACGTATCGAGATAGCTGCAGCTATATAAA
1 GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
**
28969484 GCACTTAGTGTGCGAATCG-GAATAGCTTCAGCTATATATG
1 GCACTTAGTGTGCGAATCGAG-ATAGCTTCAGCTATATAAA
28969524 GCACTTAGTGTGCGAGA-CTGAGATAGCTTC
1 GCACTTAGTGTGCGA-ATC-GAGATAGCTTC
28969554 GACTGTGAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 82 0.87
41 10 0.11
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (40 bp):
GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
Found at i:28971338 original size:19 final size:20
Alignment explanation
Indices: 28971285--28971338 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
28971275 TTTGTAACCA
28971285 ATTAGTTTAGGAAAAACCTTC
1 ATTA-TTTAGGAAAAACCTTC
*
28971306 ATTATTTATG-AAAACCTT-
1 ATTATTTAGGAAAAACCTTC
28971324 AGTT-TTTAGGAAAAA
1 A-TTATTTAGGAAAAA
28971339 ATTGATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 14 0.48
20 5 0.17
21 4 0.14
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
ATTATTTAGGAAAAACCTTC
Found at i:28990024 original size:46 final size:46
Alignment explanation
Indices: 28989937--28990108 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
28989927 GGGGTAGGAT
* * *
28989937 GCCGATGCCATGTCCTAGACATGGTCTTAAACTGGC-TCATCTCGTA-
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTTCATCTCG-AG
* *
28989983 GCCGATG-CATGTCCAAGACACGTCTTACACTAGCTTACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTT-CATCTCGAG
* * * * * *
28990029 GCCAATG-CATGTCCCAGATATGCCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCT-TCATCTCGAG
*
28990075 GCTGATGCCATGTCCCAGACATGTCTTACACTAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAG
28990109 GTCACAATAA
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 11 0.10
45 14 0.13
46 55 0.52
47 25 0.24
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATCTCGAG
Found at i:28994230 original size:19 final size:19
Alignment explanation
Indices: 28994206--28994243 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28994196 CATTTCTTTA
28994206 TTATCAGCCTAAGAAAATG
1 TTATCAGCCTAAGAAAATG
*
28994225 TTATCAGCCTTAGAAAATG
1 TTATCAGCCTAAGAAAATG
28994244 ATTTCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TTATCAGCCTAAGAAAATG
Found at i:29003019 original size:24 final size:26
Alignment explanation
Indices: 29002963--29003028 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 26
29002953 TATTTTTTAA
* *
29002963 TTCTTTATTTTCTTTTACATTATTTTC
1 TTCTTTATTTT-TCTTACATTATTTCC
29002990 TCTCTTTATTTTTCTTAC-TT-TTTCC
1 T-TCTTTATTTTTCTTACATTATTTCC
*
29003015 TTC-TTCTTTTTCTT
1 TTCTTTATTTTTCTT
29003029 GTTTTCTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 10 0.29
24 2 0.06
25 5 0.14
26 2 0.06
27 6 0.17
28 10 0.29
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (26 bp):
TTCTTTATTTTTCTTACATTATTTCC
Found at i:29008364 original size:9 final size:10
Alignment explanation
Indices: 29008342--29008366 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29008332 AATAAGGCCG
29008342 TTTTAATTAT
1 TTTTAATTAT
29008352 TTTTAATTAT
1 TTTTAATTAT
29008362 TTTTA
1 TTTTA
29008367 GTATGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:29018161 original size:25 final size:24
Alignment explanation
Indices: 29018127--29018192 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
29018117 AGAATAAACT
* * *
29018127 ATATACATAATAGATTTGAAAGGAA
1 ATATATATAATAAATTT-AAAAGAA
29018152 ATATATATAAATAAATTTAAAAGAA
1 ATATATAT-AATAAATTTAAAAGAA
* *
29018177 ATTTTATATAAAAAAT
1 A-TATATATAATAAAT
29018193 AACAACGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (24 bp):
ATATATATAATAAATTTAAAAGAA
Found at i:29018174 original size:26 final size:26
Alignment explanation
Indices: 29018126--29018192 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
29018116 AAGAATAAAC
* * *
29018126 TATATACATAATAGATTTGAAAGGAAA-
1 TATATATA-AATAAATTT-AAAAGAAAT
29018153 TATATATAAATAAATTTAAAAGAAAT
1 TATATATAAATAAATTTAAAAGAAAT
*
29018179 TTTATATAAA-AAAT
1 TATATATAAATAAAT
29018193 AACAACGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 17 0.49
27 7 0.20
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (26 bp):
TATATATAAATAAATTTAAAAGAAAT
Found at i:29023498 original size:19 final size:20
Alignment explanation
Indices: 29023474--29023513 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
29023464 AATCTTCGAG
29023474 GATATGCAATCTTAG-ATAT
1 GATATGCAATCTTAGAATAT
*
29023493 GATATGTAATCTTAGAATAT
1 GATATGCAATCTTAGAATAT
29023513 G
1 G
29023514 GGATTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (20 bp):
GATATGCAATCTTAGAATAT
Found at i:29031721 original size:20 final size:21
Alignment explanation
Indices: 29031678--29031721 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29031668 ATTACAATTG
* **
29031678 TATTTTATTATTATAAAACTT
1 TATTTTATAATTATAAAAAAT
29031699 TATTTTATAATT-TAAAAAAT
1 TATTTTATAATTATAAAAAAT
29031719 TAT
1 TAT
29031722 ATAGATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTATAATTATAAAAAAT
Found at i:29034022 original size:12 final size:13
Alignment explanation
Indices: 29033995--29034023 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29033985 TATGTGACAT
29033995 AATTTAAAATAAA
1 AATTTAAAATAAA
29034008 AATTTAAAA-AAA
1 AATTTAAAATAAA
29034020 AATT
1 AATT
29034024 GAATGCTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:29035911 original size:31 final size:32
Alignment explanation
Indices: 29035876--29035943 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
29035866 CCAACTTAAG
* *
29035876 AAAAAGTGTCAAGTTTAGGTATCAAATTAGA-
1 AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
*
29035907 AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
1 AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
29035939 AAAAA
1 AAAAA
29035944 AAAATTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
Found at i:29042708 original size:3 final size:3
Alignment explanation
Indices: 29042700--29042732 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29042690 TATTTACACA
29042700 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29042733 CATCATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29042737 original size:3 final size:3
Alignment explanation
Indices: 29042731--29042774 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
29042721 TATTATTATT
29042731 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
29042775 TATTGACCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:29051870 original size:47 final size:47
Alignment explanation
Indices: 29051792--29052302 Score: 713
Period size: 47 Copynumber: 10.6 Consensus size: 47
29051782 CCCTTCGGGA
* * * * *
29051792 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
29051839 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
29051886 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
29051933 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
29051979 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
29052026 CTTATCACATATATATACACTTTCACATCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATAT--A---T---A-CACTTTCACATTCATCACATTGGCCATTAGGC
29052086 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
29052132 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
29052178 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
29052225 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
29052274 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
29052303 TATTCAAATA
Statistics
Matches: 426, Mismatches: 21, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
46 134 0.31
47 174 0.41
48 1 0.00
49 66 0.15
51 5 0.01
53 1 0.00
54 1 0.00
56 5 0.01
59 1 0.00
60 38 0.09
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:29052110 original size:38 final size:41
Alignment explanation
Indices: 29052074--29052288 Score: 196
Period size: 46 Copynumber: 4.7 Consensus size: 41
29052064 TTCATCACAT
29052074 TGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
1 TGGCCATTCGGCCTTATCACATATATACACTTT-ACA-TCAT---A
*
29052120 TGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
1 TGGCCATTCGGCCTTATCACATATATACACTTT-ACA-TCAT---A
29052166 TGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
1 TGGCCATTCGGCCTTATCACATATATACACTTT-ACA-TCAT---A
29052212 TCGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 T-GGCCATTCGGCCTTATCAC--ATATATACACTTT-ACA-TCAT---A
*
29052261 TTGGCCATTAGGCCTTATCACATATATA
1 -TGGCCATTCGGCCTTATCACATATATA
29052289 TACACTTTCA
Statistics
Matches: 162, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
46 91 0.56
47 26 0.16
49 44 0.27
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (41 bp):
TGGCCATTCGGCCTTATCACATATATACACTTTACATCATA
Found at i:29052195 original size:199 final size:200
Alignment explanation
Indices: 29051854--29052252 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 200
29051844 CACATATATA
29051854 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
*
29051919 ATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTAT
66 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTAT
29051984 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT
131 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT
29052049 CACAT
196 CACAT
* *
29052054 CACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
*
29052119 AT-GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATGGCCATTCGGCCTTAT
66 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTAT
*
29052183 CACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATACACTTT
131 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT
29052248 CACAT
196 CACAT
29052253 TCATCACATT
Statistics
Matches: 194, Mismatches: 5, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
199 129 0.66
200 65 0.34
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (200 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTAT
CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT
CACAT
Found at i:29052252 original size:40 final size:42
Alignment explanation
Indices: 29052207--29052301 Score: 104
Period size: 49 Copynumber: 2.1 Consensus size: 42
29052197 TTCACATTCA
*
29052207 TCACAT-C-GGCCATTCGGCCTTATCACATATATATACACTT
1 TCACATACTGGCCATTAGGCCTTATCACATATATATACACTT
29052247 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTT
1 T--CA--CAT-AC--TGGCCATTAGGCCTTATCACATATATATACACTT
29052296 TCACAT
1 TCACAT
29052302 TTATTCAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
40 1 0.02
42 2 0.04
44 3 0.07
45 3 0.07
46 1 0.02
47 2 0.04
49 33 0.73
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (42 bp):
TCACATACTGGCCATTAGGCCTTATCACATATATATACACTT
Found at i:29055770 original size:40 final size:40
Alignment explanation
Indices: 29055738--29056045 Score: 438
Period size: 40 Copynumber: 7.7 Consensus size: 40
29055728 CCAGCATGAT
* * * * *
29055738 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *** * *
29055778 TGTTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
29055818 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
29055858 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
29055898 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
29055938 TGCTCTTCGAAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* * *
29055978 TGCTCTTCGGAACTTAGCTCGGATACATCACTATCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
29056018 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGAACTTAGCCCGGATACATC
29056046 GTCGAGACCT
Statistics
Matches: 244, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
39 4 0.02
40 240 0.98
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:29055943 original size:120 final size:120
Alignment explanation
Indices: 29055725--29056045 Score: 482
Period size: 120 Copynumber: 2.7 Consensus size: 120
29055715 CGAATACACG
* * * * * * * *
29055725 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGTTCTTCGGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
* * * *
29055790 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
*
29055845 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
29055910 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
* * * *
29055965 TCACTAGCATGAATGCTCTTCGGAACTTAGCTCGGATACATCACTATCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
29056030 CTTAGCCCGGAT-CATC
66 CTTAGCCCGGATACATC
29056046 GTCGAGACCT
Statistics
Matches: 183, Mismatches: 18, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
119 4 0.02
120 179 0.98
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
Found at i:29056168 original size:38 final size:38
Alignment explanation
Indices: 29056099--29056173 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
29056089 GAATTTTAAT
*
29056099 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* * *
29056137 CCGGACATAATCTCTTTATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTA
29056174 AACTCGGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:29058480 original size:49 final size:49
Alignment explanation
Indices: 29058306--29058773 Score: 731
Period size: 49 Copynumber: 9.8 Consensus size: 49
29058296 CCCTTCGGGA
* * *
29058306 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
29058353 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29058400 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
29058447 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29058496 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29058545 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
29058592 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
29058641 CTTATCACATATATATACACTTTCACATCCATCACGTTGGCCTTTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29058690 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
29058737 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATATACACTTTCACATTCATCACAT
29058774 ATATATACAC
Statistics
Matches: 391, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 178 0.46
49 212 0.54
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:29058503 original size:96 final size:96
Alignment explanation
Indices: 29058306--29058773 Score: 728
Period size: 96 Copynumber: 4.9 Consensus size: 96
29058296 CCCTTCGGGA
* * * * * *
29058306 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
*
29058369 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTCGGC
* *
29058400 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
*
29058465 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTCGGC
*
29058496 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
29058559 ACACTTTCACATTCATCACATCGGCCATTCGGC
64 ACACTTTCACATTCATCACATCGGCCATTCGGC
29058592 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
* * * *
29058657 ACACTTTCACATCCATCACGTTGGCCTTTCGGC
64 ACACTTTCACATTCATCACATCGGCCATTCGGC
*
29058690 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
29058755 ACTTTCACATTCATCACAT
66 ACTTTCACATTCATCACAT
29058774 ATATATACAC
Statistics
Matches: 348, Mismatches: 20, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
94 47 0.14
96 212 0.61
98 89 0.26
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:29058578 original size:145 final size:145
Alignment explanation
Indices: 29058306--29058773 Score: 809
Period size: 145 Copynumber: 3.3 Consensus size: 145
29058296 CCCTTCGGGA
* * * * *
29058306 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
*
29058367 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
29058432 CATCGGCCATTAGGC
131 CATCGGCCATTCGGC
29058447 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
29058512 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
29058577 CATCGGCCATTCGGC
131 CATCGGCCATTCGGC
29058592 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
* * * *
29058657 ACACTTTCACATCCATCACGTTGGCCTTTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
29058722 CATCGGCCATTCGGC
131 CATCGGCCATTCGGC
29058737 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATATACACTTTCACATTCATCACAT
29058774 ATATATACAC
Statistics
Matches: 312, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
141 10 0.03
142 1 0.00
143 39 0.12
145 262 0.84
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (145 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
CATCGGCCATTCGGC
Found at i:29058778 original size:27 final size:27
Alignment explanation
Indices: 29058740--29058800 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
29058730 ATTCGGCCTT
29058740 ATCACATATATATACACTTTCACATTC
1 ATCACATATATATACACTTTCACATTC
29058767 ATCACATATATATACACTTTCACATTC
1 ATCACATATATATACACTTTCACATTC
29058794 ATCACAT
1 ATCACAT
29058801 TGGCCATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (27 bp):
ATCACATATATATACACTTTCACATTC
Found at i:29058784 original size:76 final size:76
Alignment explanation
Indices: 29058698--29058841 Score: 270
Period size: 76 Copynumber: 1.9 Consensus size: 76
29058688 GCCTTATCAC
*
29058698 ATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
29058763 ATTCATCACAT
66 ATTCATCACAT
*
29058774 ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
29058839 ATT
66 ATT
29058842 TATTCAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (76 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
ATTCATCACAT
Found at i:29064608 original size:94 final size:94
Alignment explanation
Indices: 29064496--29064724 Score: 314
Period size: 94 Copynumber: 2.4 Consensus size: 94
29064486 GTTATAATGG
* * *
29064496 CAAATCTTATCTCCCTAAAGTTGTAGTAGAGCATATTGAAGTTATCATGGCGAATCTTATCTCCC
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
29064561 TGAAGTTGCATTGGAGCATATTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
* * * * * **
29064590 CTAATCTCATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGTTATCATGGTGAATCTTATCTCTT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
29064655 TGAAGTTGCAGTGGAGTAGGTTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
* *
29064684 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAG
29064725 CCACAAATCT
Statistics
Matches: 116, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 116 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (94 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATTAAAGCCA
Found at i:29064611 original size:44 final size:44
Alignment explanation
Indices: 29064548--29065145 Score: 269
Period size: 44 Copynumber: 13.1 Consensus size: 44
29064538 TATCATGGCG
* * *
29064548 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * **
29064592 AATCTCATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGTTATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CA
** * *
29064637 TGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTTAAAGCCACA
1 -----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * *
29064686 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* ** * * * *
29064730 AATCTTATCTCCCTAAAGTTATAATAGAGCTGATTGAAGTTATCACAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA---AGC-CA-CA
* *
29064780 AATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTGAAA-CCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * * * * *
29064824 AAACTTATCTCCC-AAAGTTGTAGTGGGATGGATTGAAATTATTAAG--GCG
1 AATCTTATCTCCCTGAAGTTGCAGT-GGA-GCA--G--ATTA--AAGCCACA
** * *
29064873 AATCTTATCTCTTTGAAGTTGCAGTGGAACAGATTGAAA-CCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * *
29064917 AATCTTATCTCCCTGAAGTTGCAGTGG-G-ATGGATTAAAATCATTAAAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA--GATT-AAAGC----CA-CA
* * * * * ** * *
29064967 AATCTTATATCCCTGAAATAGTAGTAGAATAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * ** *
29065011 AA-CTTTATCTTCTTGAAGATGCAGTGGAGCAGGA-TAAAGTTACT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAGCCACA
* * * * * *
29065055 AATCTTATCTCCTTGAAGATACAGTGGAGCAAATTAAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * *
29065099 AATCTTATCTACTTGAAGTTGCAGTAGAGCAGGTTAAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
29065143 AAT
1 AAT
29065146 TATATACCTT
Statistics
Matches: 413, Mismatches: 102, Indels: 78
0.70 0.17 0.13
Matches are distributed among these distances:
42 1 0.00
43 12 0.03
44 250 0.61
45 12 0.03
46 2 0.00
47 2 0.00
48 4 0.01
49 26 0.06
50 103 0.25
52 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
Found at i:29064667 original size:50 final size:50
Alignment explanation
Indices: 29064479--29064910 Score: 216
Period size: 50 Copynumber: 9.1 Consensus size: 50
29064469 TAGTGGGACG
* * * *
29064479 GATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGTAGTAGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * *
29064529 TATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCATTGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * * * *
29064579 TATTAAAG---CCA---CTAATCTCATCTCCCTAAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* ** * *
29064623 GATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * * * *
29064673 GGTTAAAG---CCA---CAAATCTTATCTCCCTGAAGTTGCAATGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * ** * * *
29064717 AATTGAAG---CCA---CAAATCTTATCTCCCTAAAGTTATAATAGAGCT
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
** * * **
29064761 GATTGAAGTTATCACAGCAAATCTTATCTCCTTGGAGTTGCAGTGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * *
29064811 GATTGAA---ACCA---CAAAACTTATCTCCC-AAAGTTGTAGTGG-G-A
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * ** * *
29064852 TGGATTGAAATTATTAAGGCGAATCTTATCTCTTTGAAGTTGCAGTGGAACA
1 --GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
29064904 GATTGAA
1 GATTGAA
29064911 ACCATAAATC
Statistics
Matches: 294, Mismatches: 65, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 17 0.06
44 117 0.40
46 2 0.01
47 11 0.04
49 11 0.04
50 133 0.45
52 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (50 bp):
GATTGAAGTTATCATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCA
Found at i:29064734 original size:138 final size:138
Alignment explanation
Indices: 29064548--29064836 Score: 384
Period size: 138 Copynumber: 2.1 Consensus size: 138
29064538 TATCATGGCG
* * * *
29064548 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACTAATCTCATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
* * ** ** * * *
29064613 CAGTGGAG-TAGATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTT
66 CAATAGAGCT-GATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATT
29064677 -AAAGCCACA
130 GAAA-CCACA
* *
29064686 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCCCTAAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
* *
29064751 TAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTG
66 CAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
29064816 AAACCACA
131 AAACCACA
*
29064824 AAACTTATCTCCC
1 AATCTTATCTCCC
29064837 AAAGTTGTAG
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
138 127 0.97
139 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (138 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
CAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
AAACCACA
Found at i:29064782 original size:94 final size:94
Alignment explanation
Indices: 29064684--29064936 Score: 314
Period size: 93 Copynumber: 2.7 Consensus size: 94
29064674 GTTAAAGCCA
* * * *
29064684 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCCCTAAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
* *
29064749 TATAATAGAGCT-GATTGAAGTTATCACA-G
66 TATAAT-GAGATGGATTGAAATTATCA-AGG
* *
29064778 CAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTGAAACCACAAAACTTATCTCCC-AAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
* * * *
29064842 TGTAGTGGGATGGATTGAAATTATTAAGG
66 TATAATGAGATGGATTGAAATTATCAAGG
* * * * *
29064871 CGAATCTTATCTCTTTGAAGTTGCAGTGGAACAGATTGAAACCATAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
29064936 T
66 T
29064937 GCAGTGGGAT
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
92 4 0.03
93 75 0.55
94 58 0.42
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (94 bp):
CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
TATAATGAGATGGATTGAAATTATCAAGG
Found at i:29064896 original size:93 final size:93
Alignment explanation
Indices: 29064686--29064983 Score: 348
Period size: 94 Copynumber: 3.2 Consensus size: 93
29064676 TAAAGCCACA
* * * * *
29064686 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCCCTAAAGTTA
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGTTG
* * * * * *
29064751 TAATAGAGCT-GATTGAAGTTATCACAGCA
66 TAGT-GGGATGGATTGAAATTATTA-AGCG
* *
29064780 AATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTGAAACCACAAAACTTATCTCCC-AAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGTTG
29064844 TAGTGGGATGGATTGAAATTATTAAGGCG
66 TAGTGGGATGGATTGAAATTATTAA-GCG
* * * *
29064873 AATCTTATCTCTTTGAAGTTGCAGTGGAACAGATTGAAACCATAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGTTG
* * *
29064938 CAGTGGGATGGATTAAAATCATTAAAGCG
66 TAGTGGGATGGATTGAAATTATT-AAGCG
* *
29064967 AATCTTATATCCCTGAA
1 AATCTTATCTCCTTGAA
29064984 ATAGTAGTAG
Statistics
Matches: 175, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
92 4 0.02
93 75 0.43
94 94 0.54
95 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (93 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGTTG
TAGTGGGATGGATTGAAATTATTAAGCG
Found at i:29065001 original size:94 final size:93
Alignment explanation
Indices: 29064800--29065037 Score: 246
Period size: 94 Copynumber: 2.5 Consensus size: 93
29064790 CCTTGGAGTT
* * * * * * *
29064800 GCAGTGGAGCAGATTGAAACCACAAAACTTATCTCCC-AAAGTTGTAGTGGGATGGATTGAAATT
1 GCAGTAGAACAGATTGAAACCA-TAAACTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATC
* * ** * *
29064864 ATTAAGGCGAATCTTATCTCTTTGAAGTT
65 ATTAAAGCGAATCTTATATCCCTGAAATA
*
29064893 GCAGTGGAACAGATTGAAACCATAAATCTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATC
1 GCAGTAGAACAGATTGAAACCATAAA-CTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATC
29064958 ATTAAAGCGAATCTTATATCCCTGAAATA
65 ATTAAAGCGAATCTTATATCCCTGAAATA
* * * * * *
29064987 GTAGTAGAATAGATT-AAAGCTATAAACTTTATCTTCTTGAAGATGCAGTGG
1 GCAGTAGAACAGATTGAAA-CCATAAAC-TTATCTCCCTGAAGTTGCAGTGG
29065038 AGCAGGATAA
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
92 3 0.02
93 35 0.29
94 84 0.69
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (93 bp):
GCAGTAGAACAGATTGAAACCATAAACTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCA
TTAAAGCGAATCTTATATCCCTGAAATA
Found at i:29077307 original size:43 final size:43
Alignment explanation
Indices: 29077232--29077463 Score: 369
Period size: 43 Copynumber: 5.4 Consensus size: 43
29077222 AATAAATCCC
* * *
29077232 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
29077273 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
29077316 GCAGGCTTAGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
29077359 GCAGGCTTCGTACCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
29077402 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
29077445 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
29077464 AATGATATGT
Statistics
Matches: 178, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
41 15 0.08
42 2 0.01
43 161 0.90
ACGTcount: A:0.13, C:0.24, G:0.34, T:0.29
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:29081233 original size:39 final size:39
Alignment explanation
Indices: 29081174--29081262 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
29081164 AAAATTAGTA
*
29081174 ATTTTTCTCAACTGATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTC-AAACTGATACAAAGAAATCCAACATTTTGCTC
*
29081214 ATTTTTCAAACTTATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTCAAACTGATACAAAGAAATCCAACATTTTGCTC
29081253 ATTTTTCAAA
1 ATTTTTCAAA
29081263 TTTACATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 40 0.85
40 7 0.15
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (39 bp):
ATTTTTCAAACTGATACAAAGAAATCCAACATTTTGCTC
Found at i:29085068 original size:11 final size:11
Alignment explanation
Indices: 29085046--29085074 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29085036 AGTTTTAACT
29085046 ATTTTA-ATAA
1 ATTTTATATAA
29085056 ATTTTATATAA
1 ATTTTATATAA
29085067 ATTTTATA
1 ATTTTATA
29085075 AATTTCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTATATAA
Found at i:29091370 original size:13 final size:14
Alignment explanation
Indices: 29091352--29091380 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29091342 CGTCTCCTTC
29091352 TTTTC-TTCTTTCT
1 TTTTCTTTCTTTCT
29091365 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
29091379 TT
1 TT
29091381 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:29091458 original size:25 final size:26
Alignment explanation
Indices: 29091424--29091477 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
29091414 TACCTATTTG
* *
29091424 TTTTATTAAT-ATT-ATATAATATAT
1 TTTTATTAATAATTAAGATAACATAT
29091448 TTTTACTTAATAATTAAGATAACATAT
1 TTTTA-TTAATAATTAAGATAACATAT
29091475 TTT
1 TTT
29091478 ATCTGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 3 0.12
27 12 0.48
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTATTAATAATTAAGATAACATAT
Found at i:29092559 original size:3 final size:3
Alignment explanation
Indices: 29092544--29092584 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
29092534 CCATTTTTTC
*
29092544 TCT TCT ACT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
29092585 CTGTTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:29094343 original size:3 final size:3
Alignment explanation
Indices: 29094335--29094424 Score: 71
Period size: 3 Copynumber: 31.0 Consensus size: 3
29094325 TACTTTTACC
** *
29094335 ATT ATT ATT ATT -TT -TT ATT ATT A-T ATTT ACC ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
* * * **
29094378 ATT ATT ATT ATT ATT AGT A-T ATT TTT ACT ATT ATT AGA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29094425 TTTAGTTTCA
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 8 0.12
3 58 0.85
4 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:29094364 original size:31 final size:30
Alignment explanation
Indices: 29094316--29094392 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
29094306 TTTAACTTAG
29094316 TTTTTA-TATTACTTTTACCATTATTATTAT
1 TTTTTATTATTA-TTTTACCATTATTATTAT
*
29094346 TTTTTATTATTATATTTACCATTATTGTTAT
1 TTTTTATTATTAT-TTTACCATTATTATTAT
29094377 TATTATTATTATTATT
1 T-TT-TTATTATTATT
29094393 AGTATATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
30 7 0.17
31 22 0.52
32 3 0.07
33 10 0.24
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.65
Consensus pattern (30 bp):
TTTTTATTATTATTTTACCATTATTATTAT
Found at i:29094660 original size:20 final size:20
Alignment explanation
Indices: 29094621--29094660 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29094611 ATAAATATTA
*
29094621 GTATATATTTTATTACATAT
1 GTATATATTTTAATACATAT
*
29094641 GTATATATTTTAATATATAT
1 GTATATATTTTAATACATAT
29094661 TTATGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
GTATATATTTTAATACATAT
Done.