Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 171 of 295
Found at i:58403976 original size:21 final size:21
Alignment explanation
Indices: 58403946--58403999 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
58403936 ACTGCCCTTA
* *
58403946 ATGTCGCGACATGATCCTCCT
1 ATGTTGCGACATGATCCCCCT
*
58403967 ATGTTTCGACATGATCCCCCT
1 ATGTTGCGACATGATCCCCCT
58403988 ATGTTGCGACAT
1 ATGTTGCGACAT
58404000 ACCCCTTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (21 bp):
ATGTTGCGACATGATCCCCCT
Found at i:58405418 original size:44 final size:43
Alignment explanation
Indices: 58405331--58405427 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 43
58405321 CATAGGATTT
* * ** *
58405331 TCGATATGTGATTTCGTGTAAGACCACTTCTAGGATGTTGGCA
1 TCGATTTGAGATTTCGTGTAAGACCACTTCTAGGACATCGGCA
*
58405374 TCGATTTGAGATTTACGTGTAAGACCA-TGTCTGGGACATCGGCA
1 TCGATTTGAGATTT-CGTGTAAGACCACT-TCTAGGACATCGGCA
58405418 TCGTATTTGA
1 TCG-ATTTGA
58405428 TTTTGTTGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 13 0.29
44 26 0.58
45 6 0.13
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
TCGATTTGAGATTTCGTGTAAGACCACTTCTAGGACATCGGCA
Found at i:58405483 original size:43 final size:40
Alignment explanation
Indices: 58405391--58405497 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 40
58405381 GAGATTTACG
58405391 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTT
1 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTT
* *
58405431 TGTTGAAGACCCTGTTTGGGACAGT-GGCATCGATATTTGATTAT
1 TG-T-AAGACCATGTCTGGGACA-TCGGCATCG-TATTTGATT-T
* *
58405475 ATGTAAGACCACGTCTAGGACAT
1 -TGTAAGACCATGTCTGGGACAT
58405498 TGTACGAGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
40 2 0.04
41 1 0.02
42 24 0.44
43 24 0.44
44 2 0.04
45 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTT
Found at i:58406997 original size:30 final size:30
Alignment explanation
Indices: 58406961--58407022 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
58406951 ACGGGTTAGG
58406961 AGTGTTAAAATCTATCCTAGTCAAATTCTA
1 AGTGTTAAAATCTATCCTAGTCAAATTCTA
*
58406991 AGTGTTAAAATCTGTCCTAGTCAAATTCTA
1 AGTGTTAAAATCTATCCTAGTCAAATTCTA
58407021 AG
1 AG
58407023 GACTTAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (30 bp):
AGTGTTAAAATCTATCCTAGTCAAATTCTA
Found at i:58409615 original size:21 final size:20
Alignment explanation
Indices: 58409586--58409624 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58409576 AATATACCAT
*
58409586 ATTACAATCAATTCCAAAAGA
1 ATTACAATC-ATGCCAAAAGA
*
58409607 ATTATAATCATGCCAAAA
1 ATTACAATCATGCCAAAA
58409625 CATCATTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (20 bp):
ATTACAATCATGCCAAAAGA
Found at i:58415084 original size:46 final size:45
Alignment explanation
Indices: 58415034--58415209 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
58415024 TGTTTGGGCA
58415034 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
58415080 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
58415127 TCCGAGCTCGTTGAGTTGAGTCTGGGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
58415173 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58415210 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 62 0.59
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:58415189 original size:93 final size:93
Alignment explanation
Indices: 58415030--58415201 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
58415020 AGGATGTTTG
* *
58415030 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
58415095 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
58415123 GGCATCCGAGCTCGTTGAGTTGAGTCTGGGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGA
58415187 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
58415202 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:58418150 original size:15 final size:15
Alignment explanation
Indices: 58418130--58418198 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
58418120 ATATCTTGGG
58418130 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
58418145 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
58418160 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
58418175 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
58418190 TTTCTTTAT
1 TTTCTTTAT
58418199 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:58418199 original size:30 final size:30
Alignment explanation
Indices: 58418121--58418208 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
58418111 CATAGTATCA
* * * *
58418121 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
58418151 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
58418181 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
58418209 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:58420735 original size:46 final size:45
Alignment explanation
Indices: 58420580--58420753 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 45
58420570 GTTTGGGCAT
* *
58420580 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
*** * * * *
58420625 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCAACGC
* *
58420670 ATCCGAGCTCGTTGAGTTGAGTCCGGGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
* *
58420718 CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58420754 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
45 31 0.30
46 44 0.42
47 27 0.26
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:58425581 original size:33 final size:33
Alignment explanation
Indices: 58425544--58425621 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
58425534 ATAACCTGGT
* * *
58425544 TATGGTCATT-TTAGTCGATTGCCATAGTCCAGC
1 TATGGTC-TTATTAGTCGATTACCATAGCCCAAC
*
58425577 TATGGTCTTATTATTCGATTACCATAGCCCAAC
1 TATGGTCTTATTAGTCGATTACCATAGCCCAAC
58425610 TATGGTCTTATT
1 TATGGTCTTATT
58425622 CGGCAACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.05
33 38 0.95
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (33 bp):
TATGGTCTTATTAGTCGATTACCATAGCCCAAC
Found at i:58426119 original size:43 final size:43
Alignment explanation
Indices: 58426047--58426224 Score: 182
Period size: 43 Copynumber: 4.2 Consensus size: 43
58426037 TCACATAAAG
* * * * *
58426047 CTCATA-CAATGCC-ATATCTCAGATATGGTCTTACATGTTAT
1 CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* *
58426088 CTCATATCAATGCTAATGTCCCAGACATGGTCTTACACGAAAT
1 CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* * * *
58426131 CACATAACAATGCCAATGTCCTAGACATTGTCTTACACGTAAT
1 CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* * * * *
58426174 CACCGTA-CATTACCAATGTCCCAGACATGGTCTTACATGTAAT
1 C-TCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
58426217 CTCATATC
1 CTCATATC
58426225 GGTAATCCTA
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
41 6 0.05
42 9 0.08
43 93 0.84
44 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (43 bp):
CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
Found at i:58429437 original size:22 final size:21
Alignment explanation
Indices: 58429397--58429438 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
58429387 ATCTTTATTT
*
58429397 TAGTTAAGTTTCTTAACATTG
1 TAGTTAAGTTTATTAACATTG
*
58429418 TAGTTAAGGTTTATTTACATT
1 TAGTTAA-GTTTATTAACATT
58429439 TCAAGCCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (21 bp):
TAGTTAAGTTTATTAACATTG
Found at i:58430204 original size:32 final size:32
Alignment explanation
Indices: 58430163--58430227 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
58430153 TATTAGTAAC
58430163 CACTTAGACTCTATTGTGTACGCTAGTTATAG
1 CACTTAGACTCTATTGTGTACGCTAGTTATAG
58430195 CACTTAGACTCTATTGTGTACGCTAGTTATAG
1 CACTTAGACTCTATTGTGTACGCTAGTTATAG
58430227 C
1 C
58430228 TCAATCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (32 bp):
CACTTAGACTCTATTGTGTACGCTAGTTATAG
Found at i:58437240 original size:45 final size:45
Alignment explanation
Indices: 58437176--58437393 Score: 368
Period size: 45 Copynumber: 4.9 Consensus size: 45
58437166 TGTACAGTAC
*
58437176 TATTCGGGCCTTTGAGCCTAGCAGACTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
*
58437221 TATTCGGGCCTTTGAGCCTAGCAGGCTTTAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* * *
58437266 TATTCGGGCCTTTGAGCCTAGCAGGTTATAATGCAGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
58437311 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
*
58437356 TATTCGGGCC-TTGAGCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
58437394 ATGAATTCGG
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
43 11 0.07
44 16 0.10
45 136 0.83
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
Found at i:58445634 original size:43 final size:43
Alignment explanation
Indices: 58445512--58445634 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
58445502 AAAGCTAGTA
* * * *
58445512 CAATGCCAATGTCCCAGACGTGATCTTACATGT-AATCAAATAT
1 CAATGCC-ATGTCCCAAACATGGTCTTACACGTAAATCAAATAT
* *
58445555 CGATGCCACTGTCCCAAACAGGGTCTTACACG-AAATCAAATAT
1 CAATGCCA-TGTCCCAAACATGGTCTTACACGTAAATCAAATAT
58445598 -AATGCCGATGTCCCAAACATGGTCTTACACGTAAATC
1 CAATGCC-ATGTCCCAAACATGGTCTTACACGTAAATC
58445635 TCAAATCGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
42 28 0.41
43 40 0.59
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (43 bp):
CAATGCCATGTCCCAAACATGGTCTTACACGTAAATCAAATAT
Found at i:58446165 original size:17 final size:16
Alignment explanation
Indices: 58446123--58446165 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
58446113 TCACACATGC
*
58446123 CTAGTCAAATTTTCCT
1 CTAGCCAAATTTTCCT
58446139 CTAGCCAAATTTTCCT
1 CTAGCCAAATTTTCCT
*
58446155 TTAGCCCAAAT
1 CTAG-CCAAAT
58446166 AAATCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (16 bp):
CTAGCCAAATTTTCCT
Found at i:58453563 original size:44 final size:45
Alignment explanation
Indices: 58453426--58453589 Score: 183
Period size: 45 Copynumber: 3.7 Consensus size: 45
58453416 TGGGATTTTG
* *
58453426 ATATGTG-TTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGCT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * * *
58453470 ATATGTCTTTTCGTGTAAGACCATGTCTGAGACGTTGGTATTGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* *
58453515 ATATGTGTTTTCGTGTAAGACC-CGTTTGGGACGTTGACATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * *
58453559 ATATG-G-TTACGAGTAAGACCATGTATGGGAC
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGAC
58453590 ATCGACATCG
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 12 0.12
43 9 0.09
44 27 0.27
45 52 0.52
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:58456480 original size:20 final size:19
Alignment explanation
Indices: 58456457--58456513 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
58456447 CATTACAAAT
58456457 ATATCTTATCATATACATAA
1 ATATCTTATCATATACAT-A
* * *
58456477 ATATCATATCA-AAACATT
1 ATATCTTATCATATACATA
58456495 ATATACTTATACATATACA
1 ATAT-CTTAT-CATATACA
58456514 AATGCCGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 12 0.41
21 4 0.14
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATCTTATCATATACATA
Found at i:58459529 original size:12 final size:12
Alignment explanation
Indices: 58459512--58459540 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
58459502 TGTATACACG
58459512 TTTTATTTTATT
1 TTTTATTTTATT
58459524 TTTTATTTTATT
1 TTTTATTTTATT
58459536 TTTTA
1 TTTTA
58459541 AAGAACAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:58462201 original size:122 final size:120
Alignment explanation
Indices: 58461977--58462201 Score: 344
Period size: 122 Copynumber: 1.9 Consensus size: 120
58461967 CCAAAATCAC
* * * *
58461977 CATGAGAATGATAATAATAATGTCATGGGTATGAGGTTTTCCTAATCTCTATTTAACACGGAATG
1 CATGAGAATGAGAATAATAATGTCATGGGTATGAGGTTTTCCTAATCTCGATTTAACAAGAAATG
*
58462042 TATGATAACTAACCTAAGAATGCAAATTAAATTATAGACATTGGCATGGTAATAG
66 TATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGTAATAG
* *
58462097 CATGAGAATGAGCATAGTAATGTCATGGGTATGAGGTTTTCCTAATAACTCGATTTAA-AAGAAA
1 CATGAGAATGAGAATAATAATGTCATGGGTATGAGGTTTTCCTAAT--CTCGATTTAACAAG-AA
*
58462161 ATTTATGATAACTAACCTAAGAATGCAAATTAAATGATAGA
63 ATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAGA
58462202 ATAATGAGCA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
120 43 0.46
121 2 0.02
122 49 0.52
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (120 bp):
CATGAGAATGAGAATAATAATGTCATGGGTATGAGGTTTTCCTAATCTCGATTTAACAAGAAATG
TATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGTAATAG
Found at i:58465897 original size:29 final size:28
Alignment explanation
Indices: 58465861--58465938 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
58465851 TCATGAGATT
58465861 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
58465891 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
58465918 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
58465939 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:58466212 original size:173 final size:174
Alignment explanation
Indices: 58465891--58466217 Score: 566
Period size: 173 Copynumber: 1.9 Consensus size: 174
58465881 AAATTGTACA
* *
58465891 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
58465956 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
58466021 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
58466065 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
58466130 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
58466194 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
58466218 ACCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 80 0.56
174 64 0.44
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:58474060 original size:29 final size:28
Alignment explanation
Indices: 58474024--58474101 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
58474014 TCATGAGATT
58474024 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
58474054 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
58474081 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
58474102 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:58474376 original size:173 final size:174
Alignment explanation
Indices: 58474054--58474380 Score: 575
Period size: 173 Copynumber: 1.9 Consensus size: 174
58474044 AAATTGTACA
* *
58474054 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
58474119 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
58474184 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * *
58474228 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
58474293 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
58474357 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
58474381 ACCTTGAGTT
Statistics
Matches: 145, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
173 80 0.55
174 65 0.45
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:58478705 original size:11 final size:11
Alignment explanation
Indices: 58478689--58478714 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58478679 CGAAGCCTAC
58478689 ATCACAATAAT
1 ATCACAATAAT
58478700 ATCACAATAAT
1 ATCACAATAAT
58478711 ATCA
1 ATCA
58478715 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:58479230 original size:27 final size:27
Alignment explanation
Indices: 58479200--58479342 Score: 80
Period size: 27 Copynumber: 5.3 Consensus size: 27
58479190 TTCGTCAATC
* *
58479200 ATTTTACACAACAATG-GTATTTTGGTA
1 ATTTTACACAACAA-GAGTATTTCGATA
* *
58479227 ATTTTAAACTACAAGAGTATTTCGATA
1 ATTTTACACAACAAGAGTATTTCGATA
** * *
58479254 ATTTTACA-AATCGGGGGTGTTTC-AGTA
1 ATTTTACACAA-CAAGAGTATTTCGA-TA
* * *
58479281 ATTTTACA-AATCGAGGGTATTTCGGTA
1 ATTTTACACAA-CAAGAGTATTTCGATA
* * *
58479308 ATTTTACA-AATCGAGGGTGTTTCGATA
1 ATTTTACACAA-CAAGAGTATTTCGATA
58479335 ATTTTACA
1 ATTTTACA
58479343 AATTGAGGGT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.03
27 94 0.97
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACACAACAAGAGTATTTCGATA
Found at i:58479308 original size:81 final size:80
Alignment explanation
Indices: 58479215--58479580 Score: 366
Period size: 81 Copynumber: 4.5 Consensus size: 80
58479205 ACACAACAAT
* * * * *
58479215 GGTATTTTGGTAATTTTA-AACTACAAGAGTATTTCGATAATTTTACAAATCGGGGGTGTTTCAG
1 GGTATTTCGGTAATTTTACAAAT-CAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAG
58479279 TAATTTTACAAATCGAG
65 TAATTTTACAAAT-GAG
* * *
58479296 GGTATTTCGGTAATTTTACAAATCGAGGGTGTTTCGATAATTTTACAAATTGAGGGTATTTCAGT
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGT
* * *
58479361 AATTCTATAATTGAG
66 AATTTTACAAATGAG
* * * * *
58479376 GGTATTTCAGTAATTTTATAAATCAAGGGTATTT-TAGTAATTTTTCAAATCGAGGTTATTTC-G
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGA-TAATTTTACAAATCGAGGGTATTTCAG
*
58479439 ATAATTTTACAAAATGGG
65 -TAATTTTAC-AAATGAG
* * * * * *
58479457 GGTATTTCGGTAATTTTACAAA-CTAGGGGTACTTCGGTAATTTTAGAAACTGGA-GGTATTTCG
1 GGTATTTCGGTAATTTTACAAATC-AAGGGTATTTCGATAATTTTACAAA-TCGAGGGTATTTCA
* *
58479520 GTAGTTTTACAAATTAGG
64 GTAATTTTACAAATGA-G
* *
58479538 GGTATTTCGGTAATTTTACGAATCGAGGGTATTTC-AGTAATTT
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGA-TAATTT
58479581 ATCTTTATTA
Statistics
Matches: 233, Mismatches: 41, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
79 2 0.01
80 67 0.29
81 156 0.67
82 8 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (80 bp):
GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGT
AATTTTACAAATGAG
Found at i:58479343 original size:27 final size:27
Alignment explanation
Indices: 58479243--58479580 Score: 300
Period size: 27 Copynumber: 12.6 Consensus size: 27
58479233 AACTACAAGA
*
58479243 GTATTTCGATAATTTTACAAATCGGGG
1 GTATTTCGATAATTTTACAAATCGAGG
*
58479270 GTGTTTC-AGTAATTTTACAAATCGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
*
58479297 GTATTTCGGTAATTTTACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
58479324 GTGTTTCGATAATTTTACAAATTGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * *
58479351 GTATTTC-AGTAATTCTA-TAATTGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
* *
58479377 GTATTTC-AGTAATTTTATAAATCAAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
* *
58479404 GTATTT-TAGTAATTTTTCAAATCGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
* *
58479431 TTATTTCGATAATTTTACAAAAT-GGGG
1 GTATTTCGATAATTTTAC-AAATCGAGG
* *
58479458 GTATTTCGGTAATTTTACAAA-CTAGGG
1 GTATTTCGATAATTTTACAAATCGA-GG
* * * *
58479485 GTACTTCGGTAATTTTAGAAACTGGA-G
1 GTATTTCGATAATTTTACAAA-TCGAGG
* * *
58479512 GTATTTCGGTAGTTTTACAAAT-TAGGG
1 GTATTTCGATAATTTTACAAATCGA-GG
* *
58479539 GTATTTCGGTAATTTTACGAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
58479566 GTATTTC-AGTAATTT
1 GTATTTCGA-TAATTT
58479581 ATCTTTATTA
Statistics
Matches: 259, Mismatches: 37, Indels: 30
0.79 0.11 0.09
Matches are distributed among these distances:
25 1 0.00
26 30 0.12
27 221 0.85
28 6 0.02
29 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GTATTTCGATAATTTTACAAATCGAGG
Found at i:58483777 original size:46 final size:46
Alignment explanation
Indices: 58483710--58483876 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
58483700 TATAACCCGC
*
58483710 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
58483756 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * * *
58483806 -C-TCA-CGAACTCGGACTCAACTCAAAGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
58483849 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGCGAACTCGGACTCAACTCAAC
58483877 AAGTTCGGAT
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 52 0.54
47 25 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:58483846 original size:93 final size:93
Alignment explanation
Indices: 58483717--58483889 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
58483707 CGCCCATAAG
* * * *
58483717 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
**
58483782 ATGAGCTCGGATGCCTAGTTACATCTCA
66 ACAAGCTCGGATGCCTAGTTACATCTCA
* *
58483810 CGAACTCGGACTCAACTCAAAGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
58483875 ACAAGTTCGGATGCC
66 ACAAGCTCGGATGCC
58483890 CAAATATCCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGCTCGGATGCCTAGTTACATCTCA
Found at i:58486526 original size:42 final size:41
Alignment explanation
Indices: 58486436--58486582 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 41
58486426 GTCCCAATCG
* * * *
58486436 TGGTCTTACATGTATTCAAATATCGATGTCACTGTCTCAGATA
1 TGGTCTTACACGAAATCAAATA-CGATGTCAC-GTCTCAGACA
* *
58486479 GGGTCTTACACGAAATCAAATACGATGTCGACGTCCCAGACA
1 TGGTCTTACACGAAATCAAATACGATGTC-ACGTCTCAGACA
* *
58486521 TGGTCTTACACGTAAAACTCAAAT-C-AGTGCCAACGTCTAAGACA
1 TGGTCTTACACG--AAA-TCAAATACGA-TGTC-ACGTCTCAGACA
58486565 TGGTCTTACACGAAATCA
1 TGGTCTTACACGAAATCA
58486583 CATATCAGAA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
41 3 0.03
42 29 0.33
43 21 0.24
44 29 0.33
45 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
TGGTCTTACACGAAATCAAATACGATGTCACGTCTCAGACA
Found at i:58490093 original size:30 final size:30
Alignment explanation
Indices: 58490059--58490119 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
58490049 TTCTTAACTC
*
58490059 AAACTTTTGCAAAATTACAATTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * * *
58490089 AAACTTTTTCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
58490119 A
1 A
58490120 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.43
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:58495995 original size:41 final size:41
Alignment explanation
Indices: 58495950--58496030 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
58495940 AGAATATTGT
* *
58495950 TGAATTGCACATACATGCCTCTGTTTGTACTTCAGTACCCC
1 TGAATTACACATACATGCCCCTGTTTGTACTTCAGTACCCC
*
58495991 TGAATTACACATACGTGCCCCTGTTTGTACTTCAGTACCC
1 TGAATTACACATACATGCCCCTGTTTGTACTTCAGTACCC
58496031 TTAAATGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (41 bp):
TGAATTACACATACATGCCCCTGTTTGTACTTCAGTACCCC
Found at i:58499470 original size:48 final size:48
Alignment explanation
Indices: 58499410--58499721 Score: 382
Period size: 48 Copynumber: 6.5 Consensus size: 48
58499400 TATGTGTGCT
*
58499410 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCC
*
58499458 AGTGT-AGAACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAG-ACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCC
* * * * * *
58499506 AGTGTAAGACCATGTTTGGAACTTGGCATCGATCATGCTATGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCC
* * *
58499554 AGTGTAAGACAATGTTTGGGGCATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCC
* * * *
58499602 AGTGTAAGACCATGTTTGGAACATGGAATC-AGCCACGATATAAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGA-CCACGATATGAGAGCC
* ** *
58499650 AGTGTAAGACCATCTTTGAAACATGGCATCAGA--ATG-TAATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GACCACGAT-ATGAGAGCC
58499697 AGTGTAAGACCATGTTTGGGACATG
1 AGTGTAAGACCATGTTTGGGACATG
58499722 TAACAACCCG
Statistics
Matches: 224, Mismatches: 34, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
46 1 0.00
47 33 0.15
48 187 0.83
49 2 0.01
50 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCC
Found at i:58499677 original size:144 final size:143
Alignment explanation
Indices: 58499407--58499721 Score: 456
Period size: 144 Copynumber: 2.2 Consensus size: 143
58499397 TGATATGTGT
*
58499407 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACGATATGAGAGCCAGTGTAGAACCATG
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCCAGTGTAGAACCATG
* * * * * * *
58499472 TTTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTAAGACCATGTTTGGAACTTGGCATC-
66 TTTGGAACATGGAATCAGCCACGATATAAGAGCCAGTGTAAGACCATCTTTGAAACATGGCATCA
58499536 GATCATGCT-ATGAGA
131 GA--ATG-TAATGAGA
* * *
58499551 GCTAGTGTAAGACAATGTTTGGGGCATGGCATCGGCCACGATATGAGAGCCAGTGTA-AGACCAT
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCCAGTGTAGA-ACCAT
*
58499615 GTTTGGAACATGGAATCAGCCACGATATAAGAGCTAGTGTAAGACCATCTTTGAAACATGGCATC
65 GTTTGGAACATGGAATCAGCCACGATATAAGAGCCAGTGTAAGACCATCTTTGAAACATGGCATC
58499680 AGAATGTAATGAGA
130 AGAATGTAATGAGA
*
58499694 GCCAGTGTAAGACCATGTTTGGGACATG
1 GCTAGTGTAAGACCATGTTTGGGACATG
58499722 TAACAACCCG
Statistics
Matches: 153, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
142 1 0.01
143 35 0.23
144 115 0.75
145 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (143 bp):
GCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACGATATGAGAGCCAGTGTAGAACCATG
TTTGGAACATGGAATCAGCCACGATATAAGAGCCAGTGTAAGACCATCTTTGAAACATGGCATCA
GAATGTAATGAGA
Found at i:58503055 original size:48 final size:48
Alignment explanation
Indices: 58502925--58503080 Score: 159
Period size: 48 Copynumber: 3.2 Consensus size: 48
58502915 GGGTGTTACA
* * * * *
58502925 GGACATGGCATCGACATTGATATGTGCGCTAGTGTAAGACCATGTCTG
1 GGACATGGCATTGGCATCGACATGTGAGCTAGTGTAAGACCATGTCTG
* * * * * * * *
58502973 GGATATGCCATCGGTATTGAGAGGAGAGCTAGTGTAAGACCATGTCTG
1 GGACATGGCATTGGCATCGACATGTGAGCTAGTGTAAGACCATGTCTG
* * *
58503021 GGACATGGCATTGGCCTCGACATGTGAGCCAGTGTAAGACCATGTTTG
1 GGACATGGCATTGGCATCGACATGTGAGCTAGTGTAAGACCATGTCTG
*
58503069 GAACATGGCATT
1 GGACATGGCATT
58503081 AGCGATTCAC
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (48 bp):
GGACATGGCATTGGCATCGACATGTGAGCTAGTGTAAGACCATGTCTG
Found at i:58510327 original size:48 final size:48
Alignment explanation
Indices: 58510268--58510634 Score: 497
Period size: 48 Copynumber: 7.6 Consensus size: 48
58510258 TATGTGTGCT
*
58510268 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
*
58510316 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* * *
58510364 AATGAAAGACCATGTTTGGAACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* * *
58510412 AGTGTAATACCATGTTTGGGACGTGGCGTCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* ** *
58510460 AGTGTAAGACTATGTTTGAAACATGCCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
* ** *
58510508 AGTGTAAGACCATGTTTGGAACATGGCATCGGTAATG-TAGTGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATA-TGAGAGCC
* * * *
58510556 AGTATAAGACCATGTTT-GGAGCATGGCATTGGCAATG-TAATGAGAGCC
1 AGTGTAAGACCATGTTTGGGA-CATGGCATCGGCCACGAT-ATGAGAGCC
*
58510604 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
58510635 ACATTAATAT
Statistics
Matches: 283, Mismatches: 32, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
47 4 0.01
48 275 0.97
49 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCC
Found at i:58512038 original size:49 final size:48
Alignment explanation
Indices: 58511975--58512149 Score: 224
Period size: 49 Copynumber: 3.5 Consensus size: 48
58511965 CTGGTATGCA
*
58511975 TAGTAGTCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAAT-ATCTGGTACACG
* * * * * * *
58512024 TAGTAGCCTACACTTAGTACTACACACGTGATCACAATTTTTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATATCT-GGTACACG
*
58512075 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAA-TATCTGGTACACG
58512124 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
58512150 CGTGACCTCA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
49 62 0.58
50 6 0.06
51 38 0.36
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATATCTGGTACACG
Found at i:58512145 original size:100 final size:101
Alignment explanation
Indices: 58511967--58512163 Score: 333
Period size: 100 Copynumber: 2.0 Consensus size: 101
58511957 GAAGCTATCT
* * *
58511967 GGTATGCATAGTAGTCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
58512032 TACACTTAGTACTACACACGTGA-TCACAATTTTTG
66 TACACTTAGTACTACACACGTGACTCACAATTTTTG
*
58512067 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
*
58512132 TGCACTTAGTACTACACACGTGACCTCACAAT
66 TACACTTAGTACTACACACGTGA-CTCACAAT
58512164 AGTTCATTTG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 83 0.92
102 7 0.08
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (101 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCC
TACACTTAGTACTACACACGTGACTCACAATTTTTG
Found at i:58528131 original size:49 final size:49
Alignment explanation
Indices: 58528072--58528296 Score: 288
Period size: 49 Copynumber: 4.5 Consensus size: 49
58528062 CTGGTATGCA
* * * *
58528072 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
58528121 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* ** * *
58528170 TAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * * *
58528220 TAGTAGCTTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
58528271 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
58528297 TGCGACCTCA
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
49 77 0.50
50 41 0.27
51 34 0.22
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:58528244 original size:99 final size:100
Alignment explanation
Indices: 58528070--58528296 Score: 296
Period size: 99 Copynumber: 2.3 Consensus size: 100
58528060 ATCTGGTATG
* ** ** * *
58528070 CATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACATGTAGTAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACACGACCAACCATCCGATACACGTAGTAGCCTGCACT
58528135 TAGTACTACACACGTGA-C-CAATTATCCGGTACA
66 TAGTACTACACACGTGATCACAATTATCCGGTACA
* * * *
58528168 CGTAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCTTGCAC
1 CATAGTAGCCTGCACTTAGTACTACACACACGACC-AACCATCCGATACACGTAGTAGCCTGCAC
* * * *
58528233 TTAGTACTACACACGTGATCACAGTTTTCGGGTACG
65 TTAGTACTACACACGTGATCACAATTATCCGGTACA
58528269 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
58528297 TGCGACCTCA
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
98 30 0.27
99 41 0.37
100 1 0.01
101 38 0.35
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (100 bp):
CATAGTAGCCTGCACTTAGTACTACACACACGACCAACCATCCGATACACGTAGTAGCCTGCACT
TAGTACTACACACGTGATCACAATTATCCGGTACA
Found at i:58542212 original size:30 final size:28
Alignment explanation
Indices: 58542172--58542231 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
58542162 CAAGAGAAAG
*
58542172 AAAAAATAAATT-AATTAGTAATAATAATA
1 AAAAAATAAATTAAATT-GTAA-AAAAATA
58542201 AAAAAATTAAATTAAATTGTAAAAAAATA
1 AAAAAA-TAAATTAAATTGTAAAAAAATA
58542230 AA
1 AA
58542232 TAGCTAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 10 0.36
31 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAAATAAATTAAATTGTAAAAAAATA
Found at i:58546327 original size:24 final size:24
Alignment explanation
Indices: 58546300--58546397 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
58546290 AAGGCTGTCA
58546300 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
58546324 GGAGAGGATTTAGGTGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
58546348 GGAGAGGATTTAGGATCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
58546372 GGAGAAGATTTAGGAGCTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
58546397 G
1 G
58546398 AGCAGAGTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
24 62 0.95
25 3 0.05
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:58552728 original size:24 final size:24
Alignment explanation
Indices: 58552628--58552721 Score: 143
Period size: 24 Copynumber: 3.9 Consensus size: 24
58552618 AAAGGCTGTC
58552628 AGGAGAAGATTTAGGAGCTGATAA
1 AGGAGAAGATTTAGGAGCTGATAA
* *
58552652 AGGAGAGGACTTAGGAGCTGATAA
1 AGGAGAAGATTTAGGAGCTGATAA
* *
58552676 GGGAGAGGATTTAGGAGCTGATAA
1 AGGAGAAGATTTAGGAGCTGATAA
*
58552700 AGGAGAAGATTTAGGATCTGAT
1 AGGAGAAGATTTAGGAGCTGAT
58552722 CGAGGAGCAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.37, C:0.05, G:0.36, T:0.21
Consensus pattern (24 bp):
AGGAGAAGATTTAGGAGCTGATAA
Found at i:58555204 original size:46 final size:45
Alignment explanation
Indices: 58555048--58555211 Score: 124
Period size: 46 Copynumber: 3.6 Consensus size: 45
58555038 TAGGGATCCG
*
58555048 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG-TCC
1 AACTAGTTGAGTTGAGTCTGAGTTCACTTAT-GATGCAAATGCTCC
* * * *
58555093 GAACTCA-TTGAGTTGAGT-TCGAGTTC-GTGA-GATGTAACTAGGCATCC
1 -AACT-AGTTGAGTTGAGTCT-GAGTTCACTTATGATGCAA--ATGC-TCC
* *
58555140 AAACTCGTTGATTTGAGTCTGAGTTCACTTATGAATGCAAATGCT-C
1 -AACTAGTTGAGTTGAGTCTGAGTTCACTTATG-ATGCAAATGCTCC
*
58555186 AAGCTAGTTGAGTTGAGTCCGAGTTC
1 AA-CTAGTTGAGTTGAGTCTGAGTTC
58555212 GATTATGGGT
Statistics
Matches: 91, Mismatches: 15, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
43 6 0.07
45 7 0.08
46 42 0.46
47 24 0.26
48 6 0.07
49 1 0.01
50 5 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (45 bp):
AACTAGTTGAGTTGAGTCTGAGTTCACTTATGATGCAAATGCTCC
Found at i:58555209 original size:93 final size:93
Alignment explanation
Indices: 58555038--58555212 Score: 257
Period size: 93 Copynumber: 1.9 Consensus size: 93
58555028 TTCAGATATT
* * *
58555038 TAGGGATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCATTG
1 TAGGCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAATGTCCGAACTCATTG
*
58555103 AGTTGAGTTCGAGTTCGTGAGATGTAAC
66 AGTTGAGTCCGAGTTCGTGAGATGTAAC
*
58555131 TAGGCATCCAAACTCGTTGATTTGAGTCTGAGTTCACTTATGAATGCAAATG-CTC-AAGCT-AG
1 TAGGCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAATGTC-CGAA-CTCA-
58555193 TTGAGTTGAGTCCGAGTTCG
63 TTGAGTTGAGTCCGAGTTCG
58555213 ATTATGGGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 4 0.05
93 70 0.95
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (93 bp):
TAGGCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCAAATGTCCGAACTCATTG
AGTTGAGTCCGAGTTCGTGAGATGTAAC
Found at i:58556956 original size:15 final size:15
Alignment explanation
Indices: 58556936--58556966 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58556926 ACTGGTCTAG
58556936 ACCCACATTTCAAAC
1 ACCCACATTTCAAAC
*
58556951 ACCCACATTTTAAAC
1 ACCCACATTTCAAAC
58556966 A
1 A
58556967 TTCTGGTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (15 bp):
ACCCACATTTCAAAC
Found at i:58561287 original size:9 final size:10
Alignment explanation
Indices: 58561262--58561288 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
58561252 TATTGAGCTC
58561262 GATTTTTGAT
1 GATTTTTGAT
58561272 GATTTTTGAT
1 GATTTTTGAT
58561282 GATTTTT
1 GATTTTT
58561289 ACGTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (10 bp):
GATTTTTGAT
Found at i:58567061 original size:43 final size:43
Alignment explanation
Indices: 58566941--58567098 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
58566931 AGCTCGTACA
* * *
58566941 ATGCCAATGTCCCAGACGTGGTCTTACATAT-AATCAAATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATAT-G
* * * * *
58566984 ACGCCACTATCCCAGACAGGGTCTTACAC-GAAATCAAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATATG
* * *
58567026 ATGCCGATGTCCCAAACATGGTCTTACACATAAATCATAAGT-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCA-AA-TATG
**
58567070 ATGGAAATGTCCCAGACATGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
58567099 GAAAACACAT
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
42 23 0.25
43 39 0.43
44 28 0.31
45 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAATATG
Found at i:58569831 original size:29 final size:29
Alignment explanation
Indices: 58569776--58569865 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
58569766 GTTAGCATGA
* * * *
58569776 ATATGAATGTGA-CTGGGCCGAACGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
58569804 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
58569833 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
58569862 ATAT
1 ATAT
58569866 GAATACGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 11 0.20
29 44 0.80
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:58569861 original size:58 final size:57
Alignment explanation
Indices: 58569789--58569899 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
58569779 TGAATGTGAC
** * *
58569789 TGGGCCGAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCGAACGGGCCATATAAATACGA-TTAGGCCTAATGGGCCAGATACAGGTGATT
* * * *
58569847 TGGGCCTAATGGGCCATATGAATACGATTAGGCTTAATGGGCCAGATACAGGT
1 TGGGCCGAACGGGCCATATAAATACGATTAGGCCTAATGGGCCAGATACAGGT
58569900 ATGTGAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 23 0.51
58 22 0.49
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (57 bp):
TGGGCCGAACGGGCCATATAAATACGATTAGGCCTAATGGGCCAGATACAGGTGATT
Found at i:58578968 original size:15 final size:14
Alignment explanation
Indices: 58578929--58578968 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
58578919 GGGATATCAA
58578929 AACAAG-AATTAAG
1 AACAAGTAATTAAG
*
58578942 AACACGTAATTAAG
1 AACAAGTAATTAAG
58578956 AACAAGTTAATTA
1 AACAAG-TAATTA
58578969 TTTACCATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (14 bp):
AACAAGTAATTAAG
Found at i:58579462 original size:20 final size:21
Alignment explanation
Indices: 58579437--58579481 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
58579427 GAGTTCGTAC
58579437 TTTGGCCCATTT-TC-TTCGCT
1 TTTGGCCCATTTCTCGTTC-CT
*
58579457 TTTGGCTCATTTCTCGTTCCT
1 TTTGGCCCATTTCTCGTTCCT
58579478 TTTG
1 TTTG
58579482 CTCTCATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 8 0.36
22 3 0.14
ACGTcount: A:0.04, C:0.27, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGGCCCATTTCTCGTTCCT
Found at i:58586181 original size:19 final size:19
Alignment explanation
Indices: 58586157--58586195 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
58586147 TGCATGGAAC
58586157 AGGATTTCGATTAACCGCA
1 AGGATTTCGATTAACCGCA
58586176 AGGATTTCGATTAACCGCA
1 AGGATTTCGATTAACCGCA
58586195 A
1 A
58586196 TTGCAGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
AGGATTTCGATTAACCGCA
Found at i:58599339 original size:20 final size:20
Alignment explanation
Indices: 58599314--58599356 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
58599304 GGCCTGGCCC
58599314 CACGGGCATGTCCCAAGCCA
1 CACGGGCATGTCCCAAGCCA
*
58599334 CACGGGCATGTCCCAGGCCA
1 CACGGGCATGTCCCAAGCCA
58599354 CAC
1 CAC
58599357 AGGCGTGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.09
Consensus pattern (20 bp):
CACGGGCATGTCCCAAGCCA
Found at i:58601300 original size:8 final size:8
Alignment explanation
Indices: 58601287--58601343 Score: 114
Period size: 8 Copynumber: 7.1 Consensus size: 8
58601277 AAATTAGCCC
58601287 TCACATTT
1 TCACATTT
58601295 TCACATTT
1 TCACATTT
58601303 TCACATTT
1 TCACATTT
58601311 TCACATTT
1 TCACATTT
58601319 TCACATTT
1 TCACATTT
58601327 TCACATTT
1 TCACATTT
58601335 TCACATTT
1 TCACATTT
58601343 T
1 T
58601344 AGTCCCTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 49 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (8 bp):
TCACATTT
Found at i:58612552 original size:38 final size:38
Alignment explanation
Indices: 58612501--58612577 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
58612491 AAAAAGATAG
*
58612501 ATACATCTTTACATGCCTTCATTTGGATATCAAATGAC
1 ATACATCTTTACATGCCTTCATTTGGAAATCAAATGAC
58612539 ATACATCTTTACATGCCTTCATTTGGAAATCAAATGAC
1 ATACATCTTTACATGCCTTCATTTGGAAATCAAATGAC
58612577 A
1 A
58612578 CATAACAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (38 bp):
ATACATCTTTACATGCCTTCATTTGGAAATCAAATGAC
Found at i:58627138 original size:34 final size:33
Alignment explanation
Indices: 58627100--58627194 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 33
58627090 GCGAATACAT
58627100 TCTGGGCTTAAGCCCATATT-AGTAACAGTAGCAG
1 TCTGGGCTT-AGCCCAT-TTCAGTAACAGTAGCAG
*
58627134 TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCGG
1 TCTGGG-CTTAGCCCATTTCAGTAACAGTAGCAG
*
58627168 TCTGGGCTTTAGCCCATTTCAATAACA
1 TCTGGGC-TTAGCCCATTTCAGTAACA
58627195 TTAATCAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.05
34 50 0.89
35 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (33 bp):
TCTGGGCTTAGCCCATTTCAGTAACAGTAGCAG
Found at i:58627217 original size:18 final size:18
Alignment explanation
Indices: 58627190--58627227 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
58627180 CCCATTTCAA
*
58627190 TAACATTAATCAATGCAG
1 TAACAGTAATCAATGCAG
*
58627208 TAACAGTAATCAGTGCAG
1 TAACAGTAATCAATGCAG
58627226 TA
1 TA
58627228 TGCAAGCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (18 bp):
TAACAGTAATCAATGCAG
Found at i:58627631 original size:27 final size:27
Alignment explanation
Indices: 58627597--58627716 Score: 145
Period size: 27 Copynumber: 4.5 Consensus size: 27
58627587 TATTACAATT
*
58627597 ATTTTACCCTACAGGGGTATTTAGGTC
1 ATTTTACCCTATAGGGGTATTTAGGTC
* * * *
58627624 ATTCTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATAGGGGTATTTAGGTC
* *
58627651 ATTTTACCATATAGGGGTATTTTGGTC
1 ATTTTACCCTATAGGGGTATTTAGGTC
*
58627678 ATTTTACCCTATAAGGGTATTTCA-GTC
1 ATTTTACCCTATAGGGGTATTT-AGGTC
58627705 A-TTTACCCTATA
1 ATTTTACCCTATA
58627717 AGGGCAAAAC
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.14
27 68 0.86
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATAGGGGTATTTAGGTC
Found at i:58627667 original size:54 final size:53
Alignment explanation
Indices: 58627582--58627716 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 53
58627572 GTTACTTTAA
* * *
58627582 AGGGGTATTACAATTATTTTACCCTACAGGGGTATTTAGGTCATTCTACCCTAT
1 AGGGGTATTTC-ATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
* * * *
58627636 GGGGGTATTTCGATCATTTTACCATATAGGGGTATTTTGGTCATTTTACCCTAT
1 AGGGGTATTTC-ATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
*
58627690 AAGGGTATTTCAGTCA-TTTACCCTATA
1 AGGGGTATTTCA-TCATTTTACCCTATA
58627717 AGGGCAAAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
53 11 0.16
54 58 0.84
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (53 bp):
AGGGGTATTTCATCATTTTACCCTATAGGGGTATTTAGGTCATTCTACCCTAT
Found at i:58627720 original size:26 final size:27
Alignment explanation
Indices: 58627582--58627716 Score: 141
Period size: 27 Copynumber: 5.0 Consensus size: 27
58627572 GTTACTTTAA
* * * *
58627582 AGGGGTATTACAATTATTTTACCCTAC
1 AGGGGTATTTCAGTCATTTTACCCTAT
*
58627609 AGGGGTATTT-AGGTCATTCTACCCTAT
1 AGGGGTATTTCA-GTCATTTTACCCTAT
* *
58627636 GGGGGTATTTC-GATCATTTTACCATAT
1 AGGGGTATTTCAG-TCATTTTACCCTAT
**
58627663 AGGGGTATTTTGGTCATTTTACCCTAT
1 AGGGGTATTTCAGTCATTTTACCCTAT
*
58627690 AAGGGTATTTCAGTCA-TTTACCCTAT
1 AGGGGTATTTCAGTCATTTTACCCTAT
58627716 A
1 A
58627717 AGGGCAAAAC
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
26 13 0.14
27 76 0.84
28 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTCAGTCATTTTACCCTAT
Found at i:58627729 original size:26 final size:26
Alignment explanation
Indices: 58627675--58627734 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
58627665 GGGTATTTTG
* ***
58627675 GTCATTTTACCCTATAAGGGTATTTCA
1 GTCA-TTTACCCTATAAGGGCAAAACA
58627702 GTCATTTACCCTATAAGGGCAAAACA
1 GTCATTTACCCTATAAGGGCAAAACA
58627728 GTCATTT
1 GTCATTT
58627735 CAACACATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (26 bp):
GTCATTTACCCTATAAGGGCAAAACA
Found at i:58628829 original size:19 final size:20
Alignment explanation
Indices: 58628805--58628842 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
58628795 GGTACCACCA
58628805 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
58628824 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
58628843 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:58629230 original size:93 final size:92
Alignment explanation
Indices: 58629072--58629241 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 92
58629062 GCCCCTAAGT
*
58629072 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
58629137 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* * *
58629164 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAATGAACTCGGACTCAACTCAA
58629229 CGAGTTCGGATGC
65 CGAGTTCGGATGC
58629242 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 27 0.37
93 46 0.63
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:58629231 original size:46 final size:46
Alignment explanation
Indices: 58629067--58629238 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 46
58629057 AACCCGCCCC
* * *
58629067 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
58629112 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
58629160 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
58629205 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
58629239 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 33 0.31
46 29 0.27
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:58672700 original size:44 final size:42
Alignment explanation
Indices: 58672569--58672715 Score: 136
Period size: 42 Copynumber: 3.5 Consensus size: 42
58672559 AGTGCCAACA
* * *
58672569 TCCCAGACGTGGTCTTACACGT-AATCAAATTTGATGCCACTG
1 TCCCAGACATGGTCTTACACGTAAATCAAA-TCGATGCCAATG
* * * * **
58672611 TCCCAAAGAGGGTCTTACAC-TAAATCAAATACAATGCTGATG
1 TCCCAGACATGGTCTTACACGTAAATCAAAT-CGATGCCAATG
*
58672653 TCCCAGACATGGTCTTGCACGTAAATCATAAGTCGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAAATCA-AA-TCGATGCCAATG
* *
58672697 TCCCATACGTGGTCTTACA
1 TCCCAGACATGGTCTTACA
58672716 AGAAAACACA
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 2 0.02
42 45 0.56
43 7 0.09
44 26 0.32
45 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGTAAATCAAATCGATGCCAATG
Found at i:58673095 original size:8 final size:8
Alignment explanation
Indices: 58673082--58673106 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58673072 AAATTAGCCC
58673082 TCACATTT
1 TCACATTT
58673090 TCACATTT
1 TCACATTT
58673098 TCACATTT
1 TCACATTT
58673106 T
1 T
58673107 AGTCCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:58685878 original size:27 final size:27
Alignment explanation
Indices: 58685848--58686025 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
58685838 ATATTGAGTC
* * * *
58685848 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
58685875 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58685902 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
58685930 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
58685957 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
58685984 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58686011 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58686026 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:58685987 original size:82 final size:81
Alignment explanation
Indices: 58685869--58686024 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
58685859 TGCTATATAA
* *
58685869 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
58685934 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
58685951 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
58686015 CACTTAGTGC
65 CACTTAGTGC
58686025 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:58702428 original size:34 final size:34
Alignment explanation
Indices: 58702372--58702466 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 34
58702362 GCGAATACAT
* *
58702372 TCTGGGCCTAAGCCCATATCAGTAACAATAGCAG
1 TCTGGGCCTTAGCCCATTTCAGTAACAATAGCAG
* * *
58702406 TCTGAGCCTTAGCCCATTTCAGTAACAGTAGCGG
1 TCTGGGCCTTAGCCCATTTCAGTAACAATAGCAG
* *
58702440 TCTGGGCTTTAGCCCATTTCAATAACA
1 TCTGGGCCTTAGCCCATTTCAGTAACA
58702467 TTAATTAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (34 bp):
TCTGGGCCTTAGCCCATTTCAGTAACAATAGCAG
Found at i:58702883 original size:27 final size:27
Alignment explanation
Indices: 58702841--58702990 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
58702831 GAACAAATCT
* * * *
58702841 ATCATTTTACCTTACAGGGGTATTACA
1 ATCATTTTACCCTATAGGGGTATTTCG
* *
58702868 ATCATTTTACCCTACAGGGGTATTTAG
1 ATCATTTTACCCTATAGGGGTATTTCG
* * *
58702895 GTCATTCTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATAGGGGTATTTCG
*
58702922 ATCATTTTACCCTATAGGGGTATTTTG
1 ATCATTTTACCCTATAGGGGTATTTCG
* *
58702949 GTCATTTTACCCTATAAGGGTATTTC-
1 ATCATTTTACCCTATAGGGGTATTTCG
58702975 AGTCA-TTTACCCTATA
1 A-TCATTTTACCCTATA
58702991 AGGGCAAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
26 11 0.10
27 94 0.90
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (27 bp):
ATCATTTTACCCTATAGGGGTATTTCG
Found at i:58702980 original size:81 final size:80
Alignment explanation
Indices: 58702841--58702989 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 80
58702831 GAACAAATCT
* *
58702841 ATCATTTTACCTTACAGGGGTATTACAATCATTTTACCCTACAGGGGTATTTAGGTCATTCTACC
1 ATCATTTTACCCTACAGGGGTATTACAATCATTTTACCCTACAAGGGTATTTAGGTCATT-TACC
58702906 CTATGGGGGTATTTCG
65 CTATGGGGGTATTTCG
* **** *
58702922 ATCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTCA-GTCATTTACC
1 ATCATTTTACCCTACAGGGGTATTACAATCATTTTACCCTACAAGGGTATTT-AGGTCATTTACC
58702986 CTAT
65 CTAT
58702990 AAGGGCAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
80 8 0.14
81 50 0.85
82 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (80 bp):
ATCATTTTACCCTACAGGGGTATTACAATCATTTTACCCTACAAGGGTATTTAGGTCATTTACCC
TATGGGGGTATTTCG
Found at i:58703004 original size:26 final size:26
Alignment explanation
Indices: 58702949--58703008 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
58702939 GGGTATTTTG
* **
58702949 GTCATTTTACCCTATAAGGGTATTTCA
1 GTCA-TTTACCCTATAAGGGAAAATCA
58702976 GTCATTTACCCTATAAGGGCAAAAT-A
1 GTCATTTACCCTATAAGGG-AAAATCA
58703002 GTCATTT
1 GTCATTT
58703009 CAACACATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (26 bp):
GTCATTTACCCTATAAGGGAAAATCA
Found at i:58705586 original size:293 final size:291
Alignment explanation
Indices: 58705061--58705647 Score: 1093
Period size: 293 Copynumber: 2.0 Consensus size: 291
58705051 GTTATGCAAA
*
58705061 TTAATTTTAAGTTGGGTTATCTTATATATATAATATATAATCTATGGGGTAATGTTAAGTGGATC
1 TTAATTTTAAGTTGGGTTATCTTATATATATAATATATAATCTATGGGGTAATGTTAACTGGATC
58705126 AATTGATCGATTAAATAGTTGTTTTACTTTAATTAAAGCTCAAGACCCAAAGAACCGAGATTTGG
66 AATTGATCGATTAAATAGTTGTTTTACTTTAATTAAAGCTCAAGACCCAAAGAACCGAGATTTGG
* *
58705191 ATCGGGAAAGGCGAAGTTAGTCGAGTAGTCGACACTATTGTACAAAGTTGTCGATGTAACATCCT
131 ATCGGGAAAGGCGAAGTTAGCCAAGTAGTCGACACTATTGTACAAAGTTGTCGATGTAACATCCT
58705256 GATTTTCGGGTTTTTCCGCGATTCTCGATATTTTGGTAAAGTTTTTAAAATTTGGTATTTGGTTG
196 GATTTTCGGGTTTTTCCGCGATTCTCGATATTTTGGTAAAGTTTTTAAAATTTGGTATTTGGTTG
58705321 TGAAATTCATAATTTGAGTATGTAAATAGGC
261 TGAAATTCATAATTTGAGTATGTAAATAGGC
58705352 TTAATTTTAAGTTGGGTTATCTTATATATATATAATATATAATCTATGGGGTAATGTTAACTGGA
1 TTAATTTTAAGTTGGGTTATC-T-TATATATATAATATATAATCTATGGGGTAATGTTAACTGGA
*
58705417 TCAATTGATCGATTAAATAGTTGTTTTACTTTAATTCAAGCTCAAGACCCAAAGAACCGAGATTT
64 TCAATTGATCGATTAAATAGTTGTTTTACTTTAATTAAAGCTCAAGACCCAAAGAACCGAGATTT
* *
58705482 GGATCGGGAAAGGCGAAGTTAGCCAAGTAGTCGACACTATTGTACGAAGTTGTCGATGTAATATC
129 GGATCGGGAAAGGCGAAGTTAGCCAAGTAGTCGACACTATTGTACAAAGTTGTCGATGTAACATC
*
58705547 CTGATTTTCGGGTTTTTCTGCGATTCTCGATATTTTGGTAAAGTTTTTAAAATTTGGTATTTGGT
194 CTGATTTTCGGGTTTTTCCGCGATTCTCGATATTTTGGTAAAGTTTTTAAAATTTGGTATTTGGT
58705612 TGTGAAATTCATAATTTGAGTATGTAAATAGGC
259 TGTGAAATTCATAATTTGAGTATGTAAATAGGC
58705645 TTA
1 TTA
58705648 TGGAAGGCCC
Statistics
Matches: 287, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
291 21 0.07
292 1 0.00
293 265 0.92
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (291 bp):
TTAATTTTAAGTTGGGTTATCTTATATATATAATATATAATCTATGGGGTAATGTTAACTGGATC
AATTGATCGATTAAATAGTTGTTTTACTTTAATTAAAGCTCAAGACCCAAAGAACCGAGATTTGG
ATCGGGAAAGGCGAAGTTAGCCAAGTAGTCGACACTATTGTACAAAGTTGTCGATGTAACATCCT
GATTTTCGGGTTTTTCCGCGATTCTCGATATTTTGGTAAAGTTTTTAAAATTTGGTATTTGGTTG
TGAAATTCATAATTTGAGTATGTAAATAGGC
Found at i:58706133 original size:10 final size:10
Alignment explanation
Indices: 58706118--58706152 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
58706108 GTAGGAGTAG
58706118 TCTTCTTTTT
1 TCTTCTTTTT
58706128 TCTTCTTTTT
1 TCTTCTTTTT
*
58706138 TCTTCTTTCT
1 TCTTCTTTTT
58706148 TCTTC
1 TCTTC
58706153 CCTAGCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:58707373 original size:20 final size:20
Alignment explanation
Indices: 58707348--58707394 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
58707338 GTTTTGATAT
58707348 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
58707368 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
58707388 ACATGAT
1 ACATGAT
58707395 GTATTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:58707533 original size:24 final size:24
Alignment explanation
Indices: 58707442--58707549 Score: 130
Period size: 25 Copynumber: 4.4 Consensus size: 24
58707432 AGGAAGTGCA
*
58707442 AAAAGGG-TTATGCCCCAGTTTACC
1 AAAAGGGCTT-TGCCCCAGTTTATC
*
58707466 GAAAAGGGCTTTTGCCCCAGTTTATT
1 -AAAAGGGC-TTTGCCCCAGTTTATC
58707492 AAAAGGGCTTTTGCCCCAGTTTATC
1 AAAAGGGC-TTTGCCCCAGTTTATC
*
58707517 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
58707540 AAAAGAGGCT
1 AAAAG-GGCT
58707550 AGGCCTCCAG
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
23 9 0.12
24 14 0.18
25 39 0.51
26 12 0.16
27 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:58707560 original size:49 final size:51
Alignment explanation
Indices: 58707442--58707561 Score: 151
Period size: 49 Copynumber: 2.4 Consensus size: 51
58707432 AGGAAGTGCA
*
58707442 AAAAGGG-TTATGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTAGGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
** *
58707492 AAAAGGGCTTTTGCCCCAGTTTATC-AAAAGGGC-TTTGCCCCAG-TTATT
1 AAAAGGGCTTAGGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
58707540 AAAAGAGGC-TAGGCCTCCAGTT
1 AAAAG-GGCTTAGGCC-CCAGTT
58707562 ATATGATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
48 14 0.22
49 19 0.30
50 15 0.24
51 15 0.24
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTAGGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
Found at i:58707793 original size:31 final size:31
Alignment explanation
Indices: 58707758--58707821 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
58707748 CGTTTACAGT
58707758 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
58707789 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
58707820 AA
1 AA
58707822 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:58715518 original size:20 final size:20
Alignment explanation
Indices: 58715485--58715551 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
58715475 GTTTTGATAT
58715485 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
*
58715505 ACATTATATGTATGATATGC
1 ACATGATATGTATGATATGC
58715525 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
58715545 ACATGAT
1 ACATGAT
58715552 GTATTCATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:58715530 original size:11 final size:11
Alignment explanation
Indices: 58715496--58715551 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
58715486 CATGATTGAT
58715496 ATGATATGCAC
1 ATGATATGCAC
* *
58715507 ATTATATG--T
1 ATGATATGCAC
58715516 ATGATATGCAC
1 ATGATATGCAC
*
58715527 ATGATATG--T
1 ATGATATGCAC
58715536 ATGATATGCAC
1 ATGATATGCAC
58715547 ATGAT
1 ATGAT
58715552 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:58715565 original size:40 final size:40
Alignment explanation
Indices: 58715485--58715565 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
58715475 GTTTTGATAT
* *
58715485 ACATGATTGATATGATATGCACATTATATGTATGATATGC
1 ACATGATTGATATGATATGCACATTAGATGTATCATATGC
58715525 ACATGATATG-TATGATATGCACA-T-GATGTATTCATAATGC
1 ACATGAT-TGATATGATATGCACATTAGATGTA-TCAT-ATGC
58715565 A
1 A
58715566 TTGGCTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 5 0.14
39 4 0.11
40 25 0.69
41 2 0.06
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (40 bp):
ACATGATTGATATGATATGCACATTAGATGTATCATATGC
Found at i:58715652 original size:25 final size:25
Alignment explanation
Indices: 58715624--58715706 Score: 143
Period size: 25 Copynumber: 3.4 Consensus size: 25
58715614 TAGTTTACCG
58715624 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
58715649 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
58715674 AAAAGGGC-TTTGCCCCAG-TTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
58715697 AAAAGAGGCT
1 AAAAG-GGCT
58715707 AGGCCTCCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.18
24 13 0.23
25 33 0.59
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTATT
Found at i:58715690 original size:24 final size:24
Alignment explanation
Indices: 58715599--58715706 Score: 137
Period size: 25 Copynumber: 4.4 Consensus size: 24
58715589 AGGAAGTGCA
* * **
58715599 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TT
58715624 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGC-TTTGCCCCAGTTTATT
58715649 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGC-TTTGCCCCAGTTTATT
58715674 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATT
58715697 AAAAGAGGCT
1 AAAAG-GGCT
58715707 AGGCCTCCAG
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
23 10 0.13
24 14 0.18
25 41 0.53
26 12 0.16
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATT
Found at i:58715717 original size:49 final size:50
Alignment explanation
Indices: 58715624--58715718 Score: 133
Period size: 49 Copynumber: 1.9 Consensus size: 50
58715614 TAGTTTACCG
**
58715624 AAAAGGGCTTTTGCCCCAGTTTATTAAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATTAAAAGGGCTTAGGCCCCAGTTTATT
58715674 AAAAGGGC-TTTGCCCCAG-TTATTAAAAGAGGC-TAGGCCTCCAGTT
1 AAAAGGGCTTTTGCCCCAGTTTATTAAAAG-GGCTTAGGCC-CCAGTT
58715719 ATATGATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
48 14 0.34
49 19 0.46
50 8 0.20
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
AAAAGGGCTTTTGCCCCAGTTTATTAAAAGGGCTTAGGCCCCAGTTTATT
Found at i:58715958 original size:31 final size:31
Alignment explanation
Indices: 58715915--58715978 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
58715905 CGTTTACAGT
*
58715915 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGCCTTCGGCCCAGTAATATGAAATATGA
**
58715946 AAAGCCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGCCTTCGGCCCAGTAATATGAAATATGA
58715977 AA
1 AA
58715979 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGCCTTCGGCCCAGTAATATGAAATATGA
Found at i:58726951 original size:40 final size:40
Alignment explanation
Indices: 58726860--58727009 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
58726850 CTCGAATTCA
* * * **
58726860 CGCACACAAAGTGCCACTACATAGCCAAAGCTA-CTTTAATAT
1 CGCACACTAAGTGCCA-TACATAGTCGAAGCTATC-TCGA-AT
*
58726902 CGCACACTAAGTGCCATACATAATCGAAGCTATCTCGAAT
1 CGCACACTAAGTGCCATACATAGTCGAAGCTATCTCGAAT
* * *
58726942 CGCACACTAAGTGTCATACATAGCCAAAGCTATCTCGAAT
1 CGCACACTAAGTGCCATACATAGTCGAAGCTATCTCGAAT
58726982 CGCACACTAAGTGCCATACATAGTCGAA
1 CGCACACTAAGTGCCATACATAGTCGAA
58727010 TTGTAGTCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
40 63 0.67
41 15 0.16
42 16 0.17
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (40 bp):
CGCACACTAAGTGCCATACATAGTCGAAGCTATCTCGAAT
Found at i:58726996 original size:80 final size:82
Alignment explanation
Indices: 58726860--58727009 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 82
58726850 CTCGAATTCA
*
58726860 CGCACACAAAGTGCCACTACATAGCCAAAGCTACTTTAATATCGCACACTAAGTGCCATACATAA
1 CGCACACAAAGTGCCACTACATAGCCAAAGCTACTTCAATATCGCACACTAAGTGCCATACATAA
58726925 TCGAAGCTATCTCGAAT
66 TCGAAGCTATCTCGAAT
* * *
58726942 CGCACACTAAGTGTCA-TACATAGCCAAAGCTA-TCTCGA-ATCGCACACTAAGTGCCATACATA
1 CGCACACAAAGTGCCACTACATAGCCAAAGCTACT-TCAATATCGCACACTAAGTGCCATACATA
*
58727004 GTCGAA
65 ATCGAA
58727010 TTGTAGTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
80 30 0.48
81 18 0.29
82 14 0.23
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (82 bp):
CGCACACAAAGTGCCACTACATAGCCAAAGCTACTTCAATATCGCACACTAAGTGCCATACATAA
TCGAAGCTATCTCGAAT
Found at i:58736247 original size:21 final size:21
Alignment explanation
Indices: 58736223--58736274 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
58736213 CAAGACACAT
*
58736223 GCCCATGTGGAAGGGCAACAC
1 GCCCGTGTGGAAGGGCAACAC
*
58736244 GCCCGTGTGGAAGGGTAACAC
1 GCCCGTGTGGAAGGGCAACAC
58736265 GCCCGTGTGG
1 GCCCGTGTGG
58736275 CCATTAGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.27, G:0.38, T:0.13
Consensus pattern (21 bp):
GCCCGTGTGGAAGGGCAACAC
Found at i:58739790 original size:68 final size:68
Alignment explanation
Indices: 58739641--58739798 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 68
58739631 CTAGCCGATT
* * * *
58739641 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
*
58739706 TTTA
65 TATA
* *
58739710 TATCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
58739772 CTATATA
63 C-ATATA
58739779 GTATCTCGTAGC-CTTCTTGT
1 -TATCTCGTAGCTC-TCTTGT
58739799 ACACATGATG
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.43
69 9 0.12
70 7 0.09
71 26 0.34
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAT
ATA
Found at i:58740239 original size:34 final size:34
Alignment explanation
Indices: 58740197--58740262 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
58740187 AACTTTTACA
58740197 AAATTATGATTTTGCCCCAAGGCTCGGAAATTGT
1 AAATTATGATTTTGCCCCAAGGCTCGGAAATTGT
58740231 AAATTATGATTTTGCCCCAAGGCTCGGAAATT
1 AAATTATGATTTTGCCCCAAGGCTCGGAAATT
58740263 TAATTTCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (34 bp):
AAATTATGATTTTGCCCCAAGGCTCGGAAATTGT
Found at i:58762586 original size:25 final size:25
Alignment explanation
Indices: 58762535--58762587 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
58762525 TGACCCACAA
* * *
58762535 CTCGTGAGAGCAAGCCTATTTATAG
1 CTCGTGAGAGCAAGCCGATCTACAG
58762560 CTCGTGAGAGCATA-CCGATCTACAG
1 CTCGTGAGAGCA-AGCCGATCTACAG
58762585 CTC
1 CTC
58762588 AAATGAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (25 bp):
CTCGTGAGAGCAAGCCGATCTACAG
Found at i:58768597 original size:30 final size:29
Alignment explanation
Indices: 58768563--58768619 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
58768553 ATATTTTTAT
58768563 TTTTCCCCCAAAACTTTTACTCCTCCTCAC
1 TTTTCCCCCAAAACTTTTACTCC-CCTCAC
58768593 TTTTCCCCCAAAACTTTTACTCCCCTC
1 TTTTCCCCCAAAACTTTTACTCCCCTC
58768620 CTATCCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTTCCCCCAAAACTTTTACTCCCCTCAC
Found at i:58776863 original size:46 final size:46
Alignment explanation
Indices: 58776811--58776947 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
58776801 TATATATACA
* * * *
58776811 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCGCATGTC
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCGCATATC
** *
58776857 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCGCATATC
** *
58776903 CATCTCATATGTATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCGCATAT
58776948 ATACACTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (46 bp):
CATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCGCATATC
Found at i:58776992 original size:47 final size:47
Alignment explanation
Indices: 58776921--58777159 Score: 336
Period size: 47 Copynumber: 5.1 Consensus size: 47
58776911 ATGTATTTCG
* * * * *
58776921 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTCCACATTCATCA
* * *
58776968 CATTGGCCATTCTGCCTTGTCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
58777015 CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
* * *
58777062 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
* * *
58777109 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
58777156 CATT
1 CATT
58777160 TATCACACAT
Statistics
Matches: 177, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.01
47 176 0.99
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTCCACATTCATCA
Found at i:58777132 original size:22 final size:22
Alignment explanation
Indices: 58777011--58777085 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
58777001 GTTCACATTC
58777011 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* ** *
58777033 ATCACATATATG-CATGTCCACATT
1 ATCACAT-T-GGCCAT-TCGGCCTT
58777057 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
58777080 ATCACA
1 ATCACA
58777086 CATACGCATG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 13 0.32
23 10 0.25
24 10 0.25
25 7 0.17
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:58777165 original size:34 final size:34
Alignment explanation
Indices: 58777125--58777193 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
58777115 CCATTCGGCC
58777125 TTATCACACATACGCATGTTCACATTCATCACAT
1 TTATCACACATACGCATGTTCACATTCATCACAT
*
58777159 TTATCACACATATGCATGTTCACATTCATCACAT
1 TTATCACACATACGCATGTTCACATTCATCACAT
58777193 T
1 T
58777194 GGCCATTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (34 bp):
TTATCACACATACGCATGTTCACATTCATCACAT
Found at i:58777176 original size:81 final size:81
Alignment explanation
Indices: 58777078--58777240 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
58777068 CCATTCGGCC
58777078 TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
1 TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
58777143 TTCACATTCATCACAT
66 TTCACATTCATCACAT
* * * *
58777159 TTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCGTTATCACATATATGCATG
1 TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
58777224 TTCACATTCATCACAT
66 TTCACATTCATCACAT
58777240 T
1 T
58777241 GGCCATTCGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (81 bp):
TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
TTCACATTCATCACAT
Found at i:58777197 original size:128 final size:128
Alignment explanation
Indices: 58777031--58777287 Score: 442
Period size: 128 Copynumber: 2.0 Consensus size: 128
58777021 CCATTCGGCC
*
58777031 TTATCACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
1 TTATCACACATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
58777096 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
66 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
* * * *
58777159 TTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCGTTATCACATATATGCATG
1 TTATCACACATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
* * *
58777224 TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACAT
66 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
58777287 T
1 T
58777288 GAATCCTAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 121 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.33
Consensus pattern (128 bp):
TTATCACACATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
Found at i:58777219 original size:47 final size:47
Alignment explanation
Indices: 58777159--58777288 Score: 233
Period size: 47 Copynumber: 2.8 Consensus size: 47
58777149 TTCATCACAT
* *
58777159 TTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCG
1 TTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
58777206 TTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
1 TTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
*
58777253 TTATCTCATATATGCATGTTCACATTCATCACATTG
1 TTATCACATATATGCATGTTCACATTCATCACATTG
58777289 AATCCTAAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 80 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (47 bp):
TTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
Found at i:58782156 original size:35 final size:35
Alignment explanation
Indices: 58782110--58782181 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
58782100 ATTAATATGT
58782110 TAGATTGATTGGAATAGTATTCATAGTTACTCCGG
1 TAGATTGATTGGAATAGTATTCATAGTTACTCCGG
*
58782145 TAGATTGATTGGAATTGTATTCATAGTTACTCCGG
1 TAGATTGATTGGAATAGTATTCATAGTTACTCCGG
58782180 TA
1 TA
58782182 ATGAATGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (35 bp):
TAGATTGATTGGAATAGTATTCATAGTTACTCCGG
Found at i:58782593 original size:20 final size:20
Alignment explanation
Indices: 58782565--58782604 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
58782555 AATTTTTTTA
58782565 TTTTTTTCAAAT-AATATAT
1 TTTTTTTCAAATAAATATAT
*
58782584 TTTTTCTTCAATTAAATATAT
1 TTTTT-TTCAAATAAATATAT
58782605 CTTATTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTTTCAAATAAATATAT
Found at i:58786266 original size:25 final size:26
Alignment explanation
Indices: 58786236--58786287 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
58786226 TTTAAAAATA
58786236 TTTAAA-AATATTAAA-ATATTATATT
1 TTTAAATAATATTAAACATA-TATATT
*
58786261 TTTAAATATTATTAAACATATATATT
1 TTTAAATAATATTAAACATATATATT
58786287 T
1 T
58786288 AATTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 15 0.62
27 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAAATAATATTAAACATATATATT
Found at i:58786288 original size:24 final size:24
Alignment explanation
Indices: 58786233--58786294 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
58786223 ATTTTTAAAA
*
58786233 ATATTTAAA-AATATTAAAATATT
1 ATATTTAAATATTATTAAAATATT
58786256 ATATTTTTAAATATTATTAAACATA-T
1 ATA--TTTAAATATTATTAAA-ATATT
*
58786282 ATATTTAATTATT
1 ATATTTAAATATT
58786295 TATATTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 3 0.09
24 9 0.27
25 6 0.18
26 12 0.36
27 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTTAAATATTATTAAAATATT
Found at i:58786329 original size:16 final size:14
Alignment explanation
Indices: 58786308--58786351 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
58786298 ATTTAGTGAC
58786308 ATAATAAATTATTAAT
1 ATAATAAA-TA-TAAT
58786324 ATAATAAATATAAT
1 ATAATAAATATAAT
*
58786338 ATATTAAA-ATAAT
1 ATAATAAATATAAT
58786351 A
1 A
58786352 AATTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 6 0.22
14 11 0.41
15 2 0.07
16 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATAAATATAAT
Found at i:58786342 original size:22 final size:20
Alignment explanation
Indices: 58786310--58786354 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
58786300 TTAGTGACAT
*
58786310 AATAAATTATTAATATAATA
1 AATAAATTATTAAAATAATA
58786330 AATATAATATATTAAAATAATA
1 AATA-AAT-TATTAAAATAATA
58786352 AAT
1 AAT
58786355 TATTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTATTAAAATAATA
Found at i:58786358 original size:16 final size:19
Alignment explanation
Indices: 58786308--58786364 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
58786298 ATTTAGTGAC
58786308 ATAATAAATTATTAATATA
1 ATAATAAATTATTAATATA
58786327 ATAAATATAATATATT-A-A-A
1 AT-AATA-AAT-TATTAATATA
58786346 ATAATAAATTATTTAATAT
1 ATAATAAATTA-TTAATAT
58786365 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
16 2 0.06
17 5 0.16
18 5 0.16
19 6 0.19
20 5 0.16
21 4 0.13
22 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATAAATTATTAATATA
Found at i:58786464 original size:15 final size:15
Alignment explanation
Indices: 58786446--58786501 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
58786436 ATTCAATATT
58786446 AATATTTTAATAATA
1 AATATTTTAATAATA
*
58786461 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
58786480 AATATATTAATAATA
1 AATATTTTAATAATA
58786495 AAT-TTTT
1 AATATTTT
58786502 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 13 0.39
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:58789874 original size:21 final size:22
Alignment explanation
Indices: 58789848--58789888 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58789838 TACTAGATAC
58789848 AGGGGC-ACACGCCCGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
*
58789869 AGGGGCAACACGCCCTTGTG
1 AGGGGCAACACGCCCGTGTG
58789889 ACAAATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.29, G:0.41, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:58798293 original size:7 final size:7
Alignment explanation
Indices: 58798281--58798311 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
58798271 CTTTTTCAAC
58798281 CATCCCT
1 CATCCCT
58798288 CATCCCT
1 CATCCCT
58798295 CATCCCT
1 CATCCCT
*
58798302 TATCCCT
1 CATCCCT
58798309 CAT
1 CAT
58798312 TCATCCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (7 bp):
CATCCCT
Found at i:58809314 original size:40 final size:40
Alignment explanation
Indices: 58809210--58809465 Score: 376
Period size: 40 Copynumber: 6.5 Consensus size: 40
58809200 GGATGATAAT
* *
58809210 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
58809250 CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * *
58809289 TGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
58809329 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
58809369 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
58809409 CGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
58809449 C-GGCTAAATTCCGAAGG
1 CGGGCTAAGTCCCGAAGG
58809466 TACTTGGTTT
Statistics
Matches: 199, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
39 50 0.25
40 149 0.75
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:58809446 original size:120 final size:119
Alignment explanation
Indices: 58809205--58809465 Score: 384
Period size: 119 Copynumber: 2.2 Consensus size: 119
58809195 TATTCGGATG
* *
58809205 ATAATCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
* * * *
58809270 TTGTGCGAGTTACTATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
66 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
*
58809324 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAG-CCCGAAGGC
58809388 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
64 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CT
* * *
58809444 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
58809466 TACTTGGTTT
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
118 2 0.02
119 64 0.50
120 63 0.49
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
Found at i:58815225 original size:7 final size:7
Alignment explanation
Indices: 58815213--58815241 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
58815203 ACTTTTTCAA
58815213 TCATCCC
1 TCATCCC
58815220 TCATCCC
1 TCATCCC
58815227 TCATCCC
1 TCATCCC
58815234 TCATCCC
1 TCATCCC
58815241 T
1 T
58815242 TATTCATCCC
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:0.55, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:58817653 original size:46 final size:46
Alignment explanation
Indices: 58817507--58817728 Score: 168
Period size: 46 Copynumber: 4.7 Consensus size: 46
58817497 TGCAGGTGTT
* * *
58817507 GATGCCATGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATGCC
1 GATGCCATGTCCCAGACAT-GTCTTACACTAGCT-TA-CATCTCGA-GCC
* * *
58817557 AATGCCATGTCCCAGACAAGGTCTTACACTAAC--ACATCTCGTAGCC
1 GATGCCATGTCCCAGAC-ATGTCTTACACTAGCTTACATCTCG-AGCC
* *
58817603 GATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCC
1 GATGCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGA-GCC
* * * * *
58817649 GATG-CATGTCCCAAACACGTCTTACACTAGC--ACTTGTCTCAATGCT
1 GATGCCATGTCCCAGACATGTCTTACACTAGCTTAC--ATCTCGA-GCC
* *
58817695 GATGCCATATCCCAGACATGGTCTTACATTAGCT
1 GATGCCATGTCCCAGACAT-GTCTTACACTAGCT
58817729 CTCATAATGT
Statistics
Matches: 141, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
44 14 0.10
45 13 0.09
46 61 0.43
47 13 0.09
48 12 0.09
50 27 0.19
51 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGCC
Found at i:58826644 original size:42 final size:42
Alignment explanation
Indices: 58826583--58826669 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
58826573 TTCCATACGA
*
58826583 CCTAAGACGCGGGCATGTCTACTAGCCGTGTAAGGCACACGG
1 CCTAAGACACGGGCATGTCTACTAGCCGTGTAAGGCACACGG
* * * *
58826625 CCTAAGACACTGGCGTGTCTACTAGCTGTGTGAGGCACACGG
1 CCTAAGACACGGGCATGTCTACTAGCCGTGTAAGGCACACGG
58826667 CCT
1 CCT
58826670 GTTCACATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.20
Consensus pattern (42 bp):
CCTAAGACACGGGCATGTCTACTAGCCGTGTAAGGCACACGG
Found at i:58834402 original size:43 final size:44
Alignment explanation
Indices: 58834289--58834403 Score: 110
Period size: 43 Copynumber: 2.6 Consensus size: 44
58834279 TGCATCCATT
* *
58834289 ATGAACTC-GAACCAACTCAACGAGCTCGGATGCCACATACATATC
1 ATGAACTCAG-ACCAACTCAAAGAGTTCGGATGCCACATA-ATATC
** * * *
58834334 ACAAACCCAGAACAATTCAAAGAGTTCGGATTG-CACAT-ATATC
1 ATGAACTCAGACCAACTCAAAGAGTTCGGA-TGCCACATAATATC
*
58834377 ATGAACTCAGACCAACTCAATGAGTTC
1 ATGAACTCAGACCAACTCAAAGAGTTC
58834404 AGATCTTATA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
43 26 0.47
45 26 0.47
46 3 0.05
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (44 bp):
ATGAACTCAGACCAACTCAAAGAGTTCGGATGCCACATAATATC
Found at i:58837154 original size:21 final size:21
Alignment explanation
Indices: 58837128--58837169 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
58837118 ATATGAGTAA
58837128 GTGTATATCATGTACGTATTT
1 GTGTATATCATGTACGTATTT
58837149 GTGTATATCATGTACGTATTT
1 GTGTATATCATGTACGTATTT
58837170 ATGTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.48
Consensus pattern (21 bp):
GTGTATATCATGTACGTATTT
Found at i:58838365 original size:45 final size:45
Alignment explanation
Indices: 58838301--58838416 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
58838291 GTTGTACAGT
* **
58838301 ATTATTCGGGCCTTGGAGCCTAGCAGGCTATAATGCTGGTGAGAC
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* * * *
58838346 ATTATTCGGGCCTTTGAGCCGAGCAAGCTATAATGCCAGTGAGAT
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
58838391 ATTTTTTGGGCC-TCGAGCCTAGCAGG
1 ATTATTCGGGCCTTCGAGCCTAGCAGG
58838417 AAAAATGCCG
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
44 11 0.18
45 49 0.82
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
Done.