Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 41 of 211
Found at i:12136530 original size:8 final size:8
Alignment explanation
Indices: 12136452--12136539 Score: 51
Period size: 9 Copynumber: 10.9 Consensus size: 8
12136442 ATAATATTAA
*
12136452 TATAAACT
1 TATAAAAT
12136460 TATAAATAT
1 TATAAA-AT
*
12136469 TATAAAAA
1 TATAAAAT
*
12136477 AATAAAAACT
1 TAT-AAAA-T
12136487 TATAAATAT
1 TATAAA-AT
12136496 TATACAAA-
1 TATA-AAAT
*
12136504 TATAAAAA
1 TATAAAAT
12136512 TAT-AAA-
1 TATAAAAT
12136518 -A-AAAAT
1 TATAAAAT
12136524 TATAAAAT
1 TATAAAAT
12136532 TAATAAAA
1 T-ATAAAA
12136540 CATATTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
5 4 0.06
7 7 0.11
8 22 0.34
9 26 0.41
10 5 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
TATAAAAT
Found at i:12136657 original size:9 final size:9
Alignment explanation
Indices: 12136459--12136659 Score: 86
Period size: 10 Copynumber: 21.0 Consensus size: 9
12136449 TAATATAAAC
*
12136459 TTATAAATA
1 TTATAAAAA
12136468 TTATAAAAA
1 TTATAAAAA
*
12136477 -AATAAAAA
1 TTATAAAAA
*
12136485 CTTATAAATA
1 -TTATAAAAA
*
12136495 TTATACAAA
1 TTATAAAAA
12136504 -TATAAAAA
1 TTATAAAAA
*
12136512 TATAAAAAAAA
1 T-T-ATAAAAA
12136523 TTAT-AAAA
1 TTATAAAAA
12136531 TTAATAAAACA
1 TT-ATAAAA-A
*
12136542 TATTTAAAATA
1 T-TATAAAA-A
* *
12136553 TTTTAAAATT
1 TTATAAAA-A
*
12136563 TTATAAAAT
1 TTATAAAAA
*
12136572 TTCTTAAAAA
1 TT-ATAAAAA
* *
12136582 CATAAAAAAA
1 -TTATAAAAA
*
12136592 TCATAAAAAA
1 TTAT-AAAAA
12136602 TTATAAGAATA
1 TTATAA-AA-A
**
12136613 TT-TGAAATT
1 TTAT-AAAAA
12136622 TTATAAAAA
1 TTATAAAAA
*
12136631 TTGATATAAA
1 TT-ATAAAAA
12136641 TGTATAAAAA
1 T-TATAAAAA
12136651 TTATAAAAA
1 TTATAAAAA
12136660 AATCATAAAA
Statistics
Matches: 146, Mismatches: 28, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
8 20 0.14
9 39 0.27
10 63 0.43
11 23 0.16
12 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:12136806 original size:17 final size:16
Alignment explanation
Indices: 12136784--12136826 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12136774 TTGAAGCAAT
*
12136784 TTTTTTATTTTTTAATG
1 TTTTTTATTTTTTAA-A
**
12136801 TTTTTTAAATTTTAAA
1 TTTTTTATTTTTTAAA
12136817 TTTTTTATTT
1 TTTTTTATTT
12136827 AATTGAACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTTATTTTTTAAA
Found at i:12136991 original size:12 final size:10
Alignment explanation
Indices: 12136953--12137070 Score: 86
Period size: 10 Copynumber: 12.2 Consensus size: 10
12136943 TAATAGTTGG
*
12136953 ATAATTTCTT
1 ATAATTTTTT
* *
12136963 AGATTTTTTT
1 ATAATTTTTT
12136973 ATAATTTTTT
1 ATAATTTTTT
*
12136983 ATAA-TATTT
1 ATAATTTTTT
12136992 ATAACTTTTTT
1 ATAA-TTTTTT
* *
12137003 ATAACTTGTT
1 ATAATTTTTT
12137013 ATAA-TTTTT
1 ATAATTTTTT
* *
12137022 ATAAGTTTAT
1 ATAATTTTTT
12137032 ATCAA--TTTT
1 AT-AATTTTTT
*
12137041 -TAATTTTTA
1 ATAATTTTTT
12137050 ATAA-TTTTT
1 ATAATTTTTT
*
12137059 ATATTTTTTT
1 ATAATTTTTT
12137069 AT
1 AT
12137071 GTTAGCTCGA
Statistics
Matches: 85, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
7 2 0.02
8 1 0.01
9 29 0.34
10 43 0.51
11 10 0.12
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:12136994 original size:19 final size:19
Alignment explanation
Indices: 12136969--12137041 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 19
12136959 TCTTAGATTT
12136969 TTTTATAATTTTTTATAA-
1 TTTTATAATTTTTTATAAC
12136987 TATTTATAACTTTTTTATAAC
1 T-TTTATAA-TTTTTTATAAC
*
12137008 TTGTTATAA-TTTTTATAAG
1 TT-TTATAATTTTTTATAAC
12137027 TTTATATCAATTTTT
1 TTT-TAT-AATTTTT
12137042 AATTTTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
18 2 0.04
19 21 0.45
20 13 0.28
21 11 0.23
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTATAAC
Found at i:12137067 original size:19 final size:17
Alignment explanation
Indices: 12136968--12137066 Score: 74
Period size: 19 Copynumber: 5.3 Consensus size: 17
12136958 TTCTTAGATT
12136968 TTTTTATAATTTTTTATAA
1 TTTTTATAA-TTTTTAT-A
*
12136987 TATTTATAACTTTTTTATAA
1 TTTTTATAA--TTTTTAT-A
*
12137007 CTTGTTATAATTTTTATAA
1 -TTTTTATAATTTTTAT-A
*
12137026 GTTTATATCAATTTTTA-A
1 -TTTTTAT-AATTTTTATA
12137044 TTTTTAATAATTTTTATA
1 TTTTT-ATAATTTTTATA
12137062 TTTTT
1 TTTTT
12137067 TTATGTTAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
17 12 0.18
18 9 0.13
19 22 0.32
20 18 0.26
21 7 0.10
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTATAATTTTTATA
Found at i:12138706 original size:30 final size:30
Alignment explanation
Indices: 12138670--12138727 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12138660 ACGAGCTTTG
*
12138670 GGGCAAAAGTGTAAATATGCAAAAGTTTAA
1 GGGCAAAAGTGTAAATATGAAAAAGTTTAA
* * *
12138700 GGGCAAAATTGTAATTTTGAAAAAGTTT
1 GGGCAAAAGTGTAAATATGAAAAAGTTT
12138728 GAGTCAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGCAAAAGTGTAAATATGAAAAAGTTTAA
Found at i:12139207 original size:23 final size:23
Alignment explanation
Indices: 12139179--12139273 Score: 136
Period size: 23 Copynumber: 4.1 Consensus size: 23
12139169 GTTATTGATT
*
12139179 AGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATC
* *
12139202 AATGGTAGCTACGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
* *
12139225 AGTGGTAGCTTTGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
*
12139248 AGTGGTAGCTTCAGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
12139271 AGT
1 AGT
12139274 ATGGCACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:12140240 original size:22 final size:22
Alignment explanation
Indices: 12140215--12140285 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
12140205 AATTAGTTAT
12140215 TATGAATTGAATTGTAAATTCA
1 TATGAATTGAATTGTAAATTCA
* ****
12140237 TATGGA-TGAAACCAAACAATT-A
1 TATGAATTG-AATTGTA-AATTCA
12140259 TTATGAATTGAATTGTAAATTCA
1 -TATGAATTGAATTGTAAATTCA
12140282 TATG
1 TATG
12140286 GATGAAACCA
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 13 0.38
24 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (22 bp):
TATGAATTGAATTGTAAATTCA
Found at i:12140264 original size:45 final size:45
Alignment explanation
Indices: 12140211--12140305 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
12140201 TTTCAATTAG
12140211 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
1 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
12140256 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
1 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
12140301 TTATT
1 TTATT
12140306 TGTTAGTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (45 bp):
TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
Found at i:12147116 original size:3 final size:3
Alignment explanation
Indices: 12147108--12147132 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12147098 AGCTCACAAA
12147108 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
12147133 GTTTGCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12147369 original size:20 final size:21
Alignment explanation
Indices: 12147344--12147386 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12147334 TTAAAAGAAA
* *
12147344 AAGAAGGAAA-AAGGAAAAAG
1 AAGAAGAAAATAAGAAAAAAG
12147364 AAGAAGAAAATAAGAAAAAAG
1 AAGAAGAAAATAAGAAAAAAG
12147385 AA
1 AA
12147387 AAATGAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (21 bp):
AAGAAGAAAATAAGAAAAAAG
Found at i:12148806 original size:89 final size:89
Alignment explanation
Indices: 12148655--12149321 Score: 960
Period size: 89 Copynumber: 7.5 Consensus size: 89
12148645 AAAACACCAG
* * * * * *
12148655 TCTTGCTTTCTTGTACTGACAGTGAAGCAGA-CTGAAGATATCAGATCTTGCCTTCCTGTACTGA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-CCTTGCCTTCCTGTACTGA
*
12148719 CAGCGGAGCAGACTGAAGATAGTAGA
64 CAGCGGAGCAGACTGAAGATAGCAGA
* * *
12148745 TCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCTTATACTGACA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
* * *
12148810 ACGGAGCAGACTAAAGATAGTAGA
66 GCGGAGCAGACTGAAGATAGCAGA
* * * * *
12148834 TCTTGCCTTCCTGTACTAACAACGAAGCAGATCGAAGACACCAGCTTTGCCTTCCTATACTAACA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
12148899 GCGGAGCAGACTGAAGATAGCAGA
66 GCGGAGCAGACTGAAGATAGCAGA
* * * *
12148923 TCTTACCTTCCTGTACTGACAGCGAAGTAGATCGAAGATACCAGCCTTGCCTTCCTGTACTGATA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
* *
12148988 GCAGAGCAGACTGAAGAGAGCAGA
66 GCGGAGCAGACTGAAGATAGCAGA
*
12149012 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCATTCCTGTACTGACA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
* * *
12149077 GCGGAGCAGACTAAAGGTAGCAAA
66 GCGGAGCAGACTGAAGATAGCAGA
* * * *
12149101 TCTTGTCTTCCTGTACTGACAGCGAAGCAGATCGAACACACCAGCGTTGCCTTCCTGTATTGACA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
*
12149166 GCGGAGCAGACTGAAGATAACAGA
66 GCGGAGCAGACTGAAGATAGCAGA
*
12149190 TCTTGCCTTCCTGTACTGACAGCGAAGCCA-ATCGAAGACACCAGCCTTGCCTTCCTGTTCTGAC
1 TCTTGCCTTCCTGTACTGACAGCGAAG-CAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGAC
* *
12149254 AGTGGAGCAGACTGAAGATAGTAGA
65 AGCGGAGCAGACTGAAGATAGCAGA
*
12149279 TCTTGCCTTCCTGTACTGACAGCGAAGTAGATCGAAGACACCA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
12149322 TAGTTTGAGC
Statistics
Matches: 515, Mismatches: 59, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
88 1 0.00
89 475 0.92
90 38 0.07
91 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACA
GCGGAGCAGACTGAAGATAGCAGA
Found at i:12149405 original size:44 final size:44
Alignment explanation
Indices: 12149334--12149567 Score: 272
Period size: 44 Copynumber: 5.2 Consensus size: 44
12149324 GTTTGAGCAA
* **
12149334 AGCAGATTAAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
12149379 AGCAGGTTGAAA-TTACAAGTCTTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATT-AAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGG
* * ** * *
12149423 AGCAGACTAAAGATAGCAAACCTTATCTCTCTGAATTTGCAGTGG
1 AGCAGATTAAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGG
* * *
12149468 AGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
12149512 AGCAGATTAAAGTTACTAGTCCTATCTCCCTGAAGTTTGCAGTGG
1 AGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAG-TTGCAGTGG
*
12149557 AGCGGATTAAA
1 AGCAGATTAAA
12149568 ATGATAGATC
Statistics
Matches: 159, Mismatches: 26, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
43 3 0.02
44 89 0.56
45 64 0.40
46 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
AGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:12149485 original size:89 final size:89
Alignment explanation
Indices: 12149334--12149594 Score: 343
Period size: 89 Copynumber: 2.9 Consensus size: 89
12149324 GTTTGAGCAA
*
12149334 AGCAGATTAAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAGT
1 AGCAGATTAAAGATAGCAAACCTTATCTCCCTGAATTTGCAGTGGAGCAGGTTGAAATTACAAGT
12149399 CTTATCTCCCTAAAGTTGCAGTGG
66 CTTATCTCCCTAAAGTTGCAGTGG
* *
12149423 AGCAGACTAAAGATAGCAAACCTTATCTCTCTGAATTTGCAGTGGAGCAGGTTGAAGA-TACAAG
1 AGCAGATTAAAGATAGCAAACCTTATCTCCCTGAATTTGCAGTGGAGCAGGTTGAA-ATTACAAG
*
12149487 TCTTATCTCCCTGAAGTTGCAGTGG
65 TCTTATCTCCCTAAAGTTGCAGTGG
* ** * * *
12149512 AGCAGATTAAAGTTA-CTAGTCC-TATCTCCCTGAAGTTTGCAGTGGAGC-GGATTAAAATGA-T
1 AGCAGATTAAAGATAGC-AAACCTTATCTCCCTGAA-TTTGCAGTGGAGCAGG-TTGAAATTACA
*
12149573 AGATCTTATCTCTCTAAAGTTG
63 AG-TCTTATCTCCCTAAAGTTG
12149595 TACTAGAGCA
Statistics
Matches: 152, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
88 17 0.11
89 134 0.88
90 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (89 bp):
AGCAGATTAAAGATAGCAAACCTTATCTCCCTGAATTTGCAGTGGAGCAGGTTGAAATTACAAGT
CTTATCTCCCTAAAGTTGCAGTGG
Found at i:12149604 original size:133 final size:131
Alignment explanation
Indices: 12149355--12149605 Score: 326
Period size: 133 Copynumber: 1.9 Consensus size: 131
12149345 GATAGCAAAC
* *
12149355 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAGTCTTATCTCCCTAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTCCTATCTCCCTAAAGTTGCAG
* * * *
12149420 TGGAGCAGACTAAAGATAGCAAACCTTATCTCTCTGAATTTGCAGTGGAGCAGGTTGAAGATACA
66 TGGAGCAGACTAAAGATAG--AACCTTATCTCTCTAAAGTTGCACTAGAGCAGGTTGAAGATACA
12149485 AGT
129 AGT
* *
12149488 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTTACTAGTCCTATCTCCCTGAAGTTTGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-TTACAAGTCCTATCTCCCTAAAG-TTGC
* * * *
12149552 AGTGGAGCGGATTAAAATGATAG-ATCTTATCTCTCTAAAGTTGTACTAGAGCAG
64 AGTGGAGCAGACT-AAA-GATAGAACCTTATCTCTCTAAAGTTGCACTAGAGCAG
12149606 ATCACACCAT
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
132 3 0.03
133 76 0.75
134 15 0.15
135 3 0.03
136 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (131 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTCCTATCTCCCTAAAGTTGCAG
TGGAGCAGACTAAAGATAGAACCTTATCTCTCTAAAGTTGCACTAGAGCAGGTTGAAGATACAAG
T
Found at i:12149759 original size:131 final size:132
Alignment explanation
Indices: 12149616--12149871 Score: 334
Period size: 131 Copynumber: 1.9 Consensus size: 132
12149606 ATCACACCAT
* **
12149616 AACCAGTCCTATCTCCCTAAGCAGTAATAGAGTAGGTTGAACATTGCAGATCCTGTCTCCCTAAG
1 AACCAATCCTATCTCCCTAAGCAACAATAGAGTAGGTTGAACATTGCAGATCCTGTCTCCCTAAG
* **** *
12149681 TAGTAGCAGAGCAGATTGTGGACGGCGAATCTTATCTTC-CAAGGTAGTAAAGAAGCAGATTTAG
66 CAGTAGCAGAGCAGATCAAAGACGGCAAATCTTATCTTCTCAAGGTAGTAAAGAAGCAGATTTAG
12149745 GC
131 GC
* * * * *
12149747 AACCAATCCTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAGATTGCAGATCCTGTTTCCCTAAG
1 AACCAATCCTATCTCCCTAAGCAACAATAGAGTAGGTTGAACATTGCAGATCCTGTCTCCCTAAG
** * **
12149812 CAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGA
66 CAGTAGCAGAGCAGATCAAAGACGGCAAATCTTATCTTCTCAAGGTAGTAAAGAAGCAGA
12149872 CTAAAACCAT
Statistics
Matches: 105, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
131 87 0.83
132 18 0.17
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
AACCAATCCTATCTCCCTAAGCAACAATAGAGTAGGTTGAACATTGCAGATCCTGTCTCCCTAAG
CAGTAGCAGAGCAGATCAAAGACGGCAAATCTTATCTTCTCAAGGTAGTAAAGAAGCAGATTTAG
GC
Found at i:12152474 original size:6 final size:6
Alignment explanation
Indices: 12152463--12152487 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12152453 GTGGCGACTC
12152463 TCGTTT TCGTTT TCGTTT TCGTTT T
1 TCGTTT TCGTTT TCGTTT TCGTTT T
12152488 TAAAATCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TCGTTT
Found at i:12152625 original size:11 final size:10
Alignment explanation
Indices: 12152606--12152782 Score: 59
Period size: 10 Copynumber: 18.8 Consensus size: 10
12152596 AAAAAAATTT
12152606 ATAAGTTTTTA
1 ATAA-TTTTTA
12152617 ATAATTTTTA
1 ATAATTTTTA
*
12152627 TACAATTTTATA
1 -ATAATTTT-TA
12152639 AT-ATTTTTA
1 ATAATTTTTA
12152648 AT-ATATTTTA
1 ATAAT-TTTTA
*
12152658 TTAATTTTATA
1 ATAATTTT-TA
*
12152669 A-AA--ATT-
1 ATAATTTTTA
12152675 ATAATTTTT-
1 ATAATTTTTA
12152684 AT-ATTTTT-
1 ATAATTTTTA
*
12152692 ATAATATTT-
1 ATAATTTTTA
12152701 ATAAGTTTTT-
1 ATAA-TTTTTA
*
12152711 AT--TTTTTT
1 ATAATTTTTA
*
12152719 ATAATATTT-
1 ATAATTTTTA
12152728 ATAAGTTTTT-
1 ATAA-TTTTTA
* *
12152738 AT-TTTTTTT
1 ATAATTTTTA
*
12152747 ATAA-ATTTA
1 ATAATTTTTA
*
12152756 TATCATTTTTA
1 -ATAATTTTTA
12152767 A-AATTTTTA
1 ATAATTTTTA
12152776 AT-ATTTT
1 ATAATTTT
12152783 CAATTTTCAA
Statistics
Matches: 130, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
6 1 0.01
7 8 0.06
8 16 0.12
9 41 0.32
10 42 0.32
11 20 0.15
12 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:12152637 original size:30 final size:30
Alignment explanation
Indices: 12152603--12152669 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
12152593 ATCAAAAAAA
*
12152603 TTTATAA-GTTTTTAATA-ATTTTTATACAAT
1 TTTATAATATTTTTAATATA-TTTTAT-CAAT
*
12152633 TTTATAATATTTTTAATATATTTTATTAAT
1 TTTATAATATTTTTAATATATTTTATCAAT
12152663 TTTATAA
1 TTTATAA
12152670 AAATTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 17 0.52
31 15 0.45
32 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTATAATATTTTTAATATATTTTATCAAT
Found at i:12152651 original size:9 final size:9
Alignment explanation
Indices: 12152611--12152782 Score: 50
Period size: 9 Copynumber: 18.4 Consensus size: 9
12152601 AATTTATAAG
12152611 TTTTTAATAA
1 TTTTTAAT-A
*
12152621 TTTTTATACAA
1 TTTTTA-A-TA
12152632 TTTTATAATA
1 TTTT-TAATA
12152642 TTTTTAATA
1 TTTTTAATA
*
12152651 TATTTTATTAA
1 T-TTTTAAT-A
*
12152662 TTTTATAAAA
1 TTTT-TAATA
* *
12152672 ATTAT-A-A
1 TTTTTAATA
12152679 TTTTT-ATA
1 TTTTTAATA
12152687 TTTTTATAATA
1 -TTTT-TAATA
* *
12152698 TTTATAA-G
1 TTTTTAATA
* *
12152706 TTTTTATTT
1 TTTTTAATA
12152715 TTTTATAATA
1 TTTT-TAATA
* *
12152725 TTTATAA-G
1 TTTTTAATA
*
12152733 TTTTT-ATT
1 TTTTTAATA
*
12152741 TTTTTTATA
1 TTTTTAATA
**
12152750 AATTTATATCA
1 TTTTTA-AT-A
*
12152761 TTTTTAAAA
1 TTTTTAATA
12152770 TTTTTAATA
1 TTTTTAATA
12152779 TTTT
1 TTTT
12152783 CAATTTTCAA
Statistics
Matches: 118, Mismatches: 28, Indels: 33
0.66 0.16 0.18
Matches are distributed among these distances:
7 6 0.05
8 16 0.14
9 39 0.33
10 36 0.31
11 19 0.16
12 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTAATA
Found at i:12152662 original size:22 final size:23
Alignment explanation
Indices: 12152614--12152662 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
12152604 TTATAAGTTT
12152614 TTAATAATTTTTATACAATTTTA
1 TTAATAATTTTTATACAATTTTA
*
12152637 -TAAT-ATTTTTAATA-TATTTTA
1 TTAATAATTTTT-ATACAATTTTA
12152658 TTAAT
1 TTAAT
12152663 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAATAATTTTTATACAATTTTA
Found at i:12152709 original size:27 final size:28
Alignment explanation
Indices: 12152632--12152757 Score: 152
Period size: 27 Copynumber: 4.6 Consensus size: 28
12152622 TTTTATACAA
* * *
12152632 TTTTATAATATTTTTAATATATTTTATTAA
1 TTTTATAATATTTATAA-GT-TTTTATTAT
* *
12152662 TTTTATAAAAATTATAA-TTTTTA-TAT
1 TTTTATAATATTTATAAGTTTTTATTAT
12152688 TTTTATAATATTTATAAGTTTTTATT-T
1 TTTTATAATATTTATAAGTTTTTATTAT
*
12152715 TTTTATAATATTTATAAGTTTTTATTTT
1 TTTTATAATATTTATAAGTTTTTATTAT
12152743 TTTTATAA-ATTTATA
1 TTTTATAATATTTATA
12152758 TCATTTTTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
26 17 0.20
27 45 0.52
28 11 0.13
30 14 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTATAATATTTATAAGTTTTTATTAT
Found at i:12152790 original size:7 final size:7
Alignment explanation
Indices: 12152778--12152852 Score: 150
Period size: 7 Copynumber: 10.7 Consensus size: 7
12152768 AATTTTTAAT
12152778 ATTTTCA
1 ATTTTCA
12152785 ATTTTCA
1 ATTTTCA
12152792 ATTTTCA
1 ATTTTCA
12152799 ATTTTCA
1 ATTTTCA
12152806 ATTTTCA
1 ATTTTCA
12152813 ATTTTCA
1 ATTTTCA
12152820 ATTTTCA
1 ATTTTCA
12152827 ATTTTCA
1 ATTTTCA
12152834 ATTTTCA
1 ATTTTCA
12152841 ATTTTCA
1 ATTTTCA
12152848 ATTTT
1 ATTTT
12152853 TATATAATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 68 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTCA
Found at i:12153440 original size:76 final size:76
Alignment explanation
Indices: 12153274--12153417 Score: 236
Period size: 76 Copynumber: 1.9 Consensus size: 76
12153264 ACTATTAAGG
*
12153274 ACATTAAATTAATAATTAAATATAAAAAACTTTTAAATTATTTTATTTTTAATGAAATTATTAAA
1 ACATTAAATTAATAATTAAATATAAAAAACTTTTAAATTATTTCATTTTTAATGAAATTATTAAA
12153339 AATATGTCAAA
66 AATATGTCAAA
* * *
12153350 ACATTAAACTAATAATTTAATATAACAAAAGTTTTAAATTATTTCATTTTT-ATGAAATTATTAA
1 ACATTAAATTAATAATTAAATATAA-AAAACTTTTAAATTATTTCATTTTTAATGAAATTATTAA
12153414 AAAT
65 AAAT
12153418 GTCCAATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
76 40 0.63
77 23 0.37
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (76 bp):
ACATTAAATTAATAATTAAATATAAAAAACTTTTAAATTATTTCATTTTTAATGAAATTATTAAA
AATATGTCAAA
Found at i:12172948 original size:18 final size:18
Alignment explanation
Indices: 12172915--12172962 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12172905 ATTCACCTAA
*
12172915 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
12172934 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
12172952 ACCCAACCCAA
1 ACCCAACCCAA
12172963 TCATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.42, C:0.46, G:0.02, T:0.10
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:12172955 original size:13 final size:13
Alignment explanation
Indices: 12172939--12172963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12172929 CAAGTATCCA
12172939 ACCCAACCCAATT
1 ACCCAACCCAATT
12172952 ACCCAACCCAAT
1 ACCCAACCCAAT
12172964 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:12173279 original size:9 final size:9
Alignment explanation
Indices: 12173262--12173299 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
12173252 GTAGTGATTC
12173262 AATTCGGTT
1 AATTCGGTT
*
12173271 AATTTGGTT
1 AATTCGGTT
12173280 AATTCAGG-T
1 AATTC-GGTT
12173289 AATTCGGTT
1 AATTCGGTT
12173298 AA
1 AA
12173300 ATGCGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:12188259 original size:42 final size:42
Alignment explanation
Indices: 12188174--12188258 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 42
12188164 AAAAAAAAAA
* *
12188174 TTCAAAAATTCCAAAAATATTTTCCATTTTTATTTTTAATTT
1 TTCAAAAATTCCAAAAATATTTTCCACTTTCATTTTTAATTT
* *
12188216 TTCAAAAA-TCCAAAAATATTTAT-TACTTTCATTTTTATTTT
1 TTCAAAAATTCCAAAAATATTT-TCCACTTTCATTTTTAATTT
12188257 TT
1 TT
12188259 TATTGCATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 29 0.76
42 9 0.24
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (42 bp):
TTCAAAAATTCCAAAAATATTTTCCACTTTCATTTTTAATTT
Found at i:12193110 original size:15 final size:15
Alignment explanation
Indices: 12193090--12193128 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
12193080 TCTCCAGGTA
12193090 TTGGCTGAGTTAAAT
1 TTGGCTGAGTTAAAT
12193105 TTGGCTGAGTTAAAT
1 TTGGCTGAGTTAAAT
*
12193120 TTGGATGAG
1 TTGGCTGAG
12193129 GTTGAATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.31, T:0.38
Consensus pattern (15 bp):
TTGGCTGAGTTAAAT
Found at i:12197739 original size:51 final size:53
Alignment explanation
Indices: 12197684--12197801 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 53
12197674 TATAAAACTT
** *
12197684 ATATATATATATAAAATACA-TAATGCATTTATGAAAACAAGGAAA-ATATAA
1 ATATATATATATAAAATACATTAATGCATTTACAAAAAAAAGGAAATATATAA
* * * *
12197735 ATATATACATATAAAATATATTCATGCATTTACAAAAAAAATGAAATATATAA
1 ATATATATATATAAAATACATTAATGCATTTACAAAAAAAAGGAAATATATAA
*
12197788 GTATA-ATATA-AAAA
1 ATATATATATATAAAA
12197802 CGTGGAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 22 0.39
52 24 0.43
53 10 0.18
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (53 bp):
ATATATATATATAAAATACATTAATGCATTTACAAAAAAAAGGAAATATATAA
Found at i:12198067 original size:3 final size:3
Alignment explanation
Indices: 12198059--12198102 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
12198049 TATATGTAGG
*
12198059 AAT AAT AAT AAT AAT ATAT AAT -AT AAT AAT AAA AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
12198103 CAAAGTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12198583 original size:21 final size:21
Alignment explanation
Indices: 12198557--12198637 Score: 130
Period size: 21 Copynumber: 4.0 Consensus size: 21
12198547 AGATTACATG
12198557 TCATATCTAAGATTGCATATA
1 TCATATCTAAGATTGCATATA
*
12198578 TCATATATAAGATTGCATATA
1 TCATATCTAAGATTGCATATA
12198599 TCATATCTAAGATTGC--ATA
1 TCATATCTAAGATTGCATATA
*
12198618 TCATATCTAAGATTTCATAT
1 TCATATCTAAGATTGCATAT
12198638 CCTCGAAGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 18 0.33
21 37 0.67
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
TCATATCTAAGATTGCATATA
Found at i:12198603 original size:42 final size:40
Alignment explanation
Indices: 12198557--12198637 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
12198547 AGATTACATG
12198557 TCATATCTAAGATTGCATATATCATATATAAGATTGCATATA
1 TCATATCTAAGATTGC--ATATCATATATAAGATTGCATATA
* *
12198599 TCATATCTAAGATTGCATATCATATCTAAGATTTCATAT
1 TCATATCTAAGATTGCATATCATATATAAGATTGCATAT
12198638 CCTCGAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 21 0.57
42 16 0.43
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (40 bp):
TCATATCTAAGATTGCATATCATATATAAGATTGCATATA
Found at i:12198636 original size:19 final size:19
Alignment explanation
Indices: 12198543--12198638 Score: 120
Period size: 21 Copynumber: 4.8 Consensus size: 19
12198533 AATCATATCT
* *
12198543 TCTAAGATTACATGTCATA
1 TCTAAGATTGCATATCATA
12198562 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
*
12198583 TATAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
12198604 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12198623 TCTAAGATTTCATATC
1 TCTAAGATTGCATATC
12198639 CTCGAAGATT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 33 0.47
21 37 0.53
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12199118 original size:44 final size:44
Alignment explanation
Indices: 12199066--12199173 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
12199056 GTTCTACTCT
* * * *
12199066 CTGCAACTTCAGAGAGATAAGATCTA-AGGTTTTAATCCGCTTCA
1 CTGCAACTTTAGGGAGATAAGAT-TATAGGCTTTAATCCGCTCCA
* * *
12199110 CTGCAACTTTAGGGAGATAGGATTATCGGCTTTAATCTGCTCCA
1 CTGCAACTTTAGGGAGATAAGATTATAGGCTTTAATCCGCTCCA
12199154 CTGCAACTTTAGGGAGATAA
1 CTGCAACTTTAGGGAGATAA
12199174 AATTTTCCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.04
44 53 0.96
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGCAACTTTAGGGAGATAAGATTATAGGCTTTAATCCGCTCCA
Found at i:12199553 original size:44 final size:44
Alignment explanation
Indices: 12199480--12199811 Score: 358
Period size: 44 Copynumber: 7.7 Consensus size: 44
12199470 GATATTTTCC
* * *
12199480 ACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* * * * * *
12199524 ACCTATTCAACTACTGACCAAGAAGATAGGA-CCTACAATATTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* *
12199568 ATCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * **
12199612 ACCTATTCCACTGTTGTCCAGATAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
12199650 ATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACC-AGGGAGATAGGATTCACAATCTTCA
*
12199694 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * * *
12199738 ACTTATTCCACTACTGTCAAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
12199782 ACCTATTCCACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
12199812 GCTGGGGTCA
Statistics
Matches: 238, Mismatches: 39, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
37 2 0.01
38 26 0.11
39 2 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 197 0.83
45 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:12199768 original size:170 final size:170
Alignment explanation
Indices: 12199486--12199794 Score: 444
Period size: 170 Copynumber: 1.8 Consensus size: 170
12199476 TTCCACCTAC
** *
12199486 TCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCAACTACTGACCAAGAAGAT
1 TCCACTGCTGCTCAGGGAGATAGAATTCACAATCTTCAACCTATTCAACTACTGACCAAGAAGAT
* *
12199551 AGGACCTACAATATTCAATCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCT
66 AGGACCTACAATATTCAATCTATTCCACTACTGACAAGGGAGATAGGATTCACAATCTTTAACCT
12199616 ATTCCACTGTTGTCCAGATAGATAGGATTCTTTAATCTAT
131 ATTCCACTGTTGTCCAGATAGATAGGATTCTTTAATCTAT
* * * * *
12199656 TCCACTGCTGC-CTAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGA
1 TCCACTGCTGCTC-AGGGAGATAGAATTCACAATCTTCAACCTATTCAACTACTGACCAAGAAGA
* * * *
12199720 TAGGA-TTCACAATCTTTAA-CTTATTCCACTACTGTCAAGGGAGATAGGATTCACAATCTTTAA
65 TAGGACCT-ACAATATTCAATC-TATTCCACTACTGACAAGGGAGATAGGATTCACAATCTTTAA
12199783 CCTATTCCACTG
128 CCTATTCCACTG
12199795 CTGACCAGGG
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
169 3 0.02
170 119 0.98
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (170 bp):
TCCACTGCTGCTCAGGGAGATAGAATTCACAATCTTCAACCTATTCAACTACTGACCAAGAAGAT
AGGACCTACAATATTCAATCTATTCCACTACTGACAAGGGAGATAGGATTCACAATCTTTAACCT
ATTCCACTGTTGTCCAGATAGATAGGATTCTTTAATCTAT
Found at i:12199870 original size:88 final size:87
Alignment explanation
Indices: 12199798--12200045 Score: 361
Period size: 88 Copynumber: 2.8 Consensus size: 87
12199788 TCCACTGCTG
* * * * *
12199798 ACCAGGGAGATAGGGCTGGGGTCATCGATCTGCTTCGCTGTCGGAGCAGGAAGGCAAGATCTGCT
1 ACCAGGGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT
* *
12199863 ATATTTAACCTGCTCTGCTGCA
66 ATTTTTAACCTGCTCCGCTGCA
* *
12199885 ACCTAGGGAGGTAAGGCTGGTGTCTTTGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
1 ACC-AGGGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
*
12199950 TATTTTTAGCCTGCTCCGCTGCA
65 TATTTTTAACCTGCTCCGCTGCA
* * *
12199973 ACCCAGGGAGGCAAGGCTAGTGTCTTCGATTTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
1 A-CCAGGGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
12200038 TATTTTTA
65 TATTTTTA
12200046 CCGATCTGCT
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
87 3 0.02
88 139 0.97
89 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (87 bp):
ACCAGGGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT
ATTTTTAACCTGCTCCGCTGCA
Found at i:12201280 original size:6 final size:6
Alignment explanation
Indices: 12201269--12201321 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
12201259 GGCCTCTTCA
12201269 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
12201317 TTTTT
1 TTTTT
12201322 ATCACTTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:12206469 original size:3 final size:3
Alignment explanation
Indices: 12206461--12206497 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
12206451 ATATGTAGGT
12206461 ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
12206498 CAAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12206507 original size:18 final size:21
Alignment explanation
Indices: 12206464--12206513 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
12206454 TGTAGGTATA
*
12206464 ATAATAATAATAATATATAAT
1 ATAATAATAATAACATATAAT
12206485 ATAATAATAATAACA-A-AAT
1 ATAATAATAATAACATATAAT
12206504 -TAATAA-AATA
1 ATAATAATAATA
12206514 GACTAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 3 0.11
20 1 0.04
21 14 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATAATAATAACATATAAT
Found at i:12206757 original size:19 final size:21
Alignment explanation
Indices: 12206719--12206757 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12206709 CCTTTTTTAA
*
12206719 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
12206740 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
12206758 AAAGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:12206955 original size:22 final size:21
Alignment explanation
Indices: 12206920--12206998 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 21
12206910 AAAGGGTATC
* * *
12206920 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
12206941 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
12206964 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
12206983 TGCATATATCATATCT
1 TACA-A-ATCATATCT
12206999 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 11 0.24
21 9 0.20
22 15 0.33
23 11 0.24
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:12206965 original size:23 final size:22
Alignment explanation
Indices: 12206920--12206977 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12206910 AAAGGGTATC
* * *
12206920 TACAAATTAAATC-TCTAATAT
1 TACAAATCATATCTTCTAAGAT
12206941 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
12206964 TACATATCATATCT
1 TACAAATCATATCT
12206978 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:12206980 original size:19 final size:19
Alignment explanation
Indices: 12206956--12207011 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
12206946 AATCATATCT
12206956 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
12206975 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
12206996 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
12207012 CGCAAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:12206993 original size:21 final size:21
Alignment explanation
Indices: 12206967--12207010 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12206957 CTAAGATTAC
12206967 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
12206988 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
12207009 AT
1 AT
12207011 CCGCAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:12211042 original size:43 final size:42
Alignment explanation
Indices: 12210964--12211128 Score: 111
Period size: 43 Copynumber: 3.9 Consensus size: 42
12210954 AACTCGTACA
* * * *
12210964 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTACCAGACAG-GGTCTTACACGAAATCAAAT-ACG
* * * *
12211007 ATGTCACTGTACCAGACAGGGTCTTACACGAAATCATATATG
1 ATGCCAATGTACCAGACAGGGTCTTACACGAAATCAAATACG
* * * *
12211049 ATGCCAATGTCCCGGACATGGTCTTACACGTAAATCTCGAAT-CG
1 ATGCCAATGTACCAGACAGGGTCTTACACG-AAA--TCAAATACG
* ** *
12211093 ATGCCAACGCCCCAGAC-GTGGTCTTACACGATATCA
1 ATGCCAATGTACCAGACAG-GGTCTTACACGAAATCA
12211129 CATATCAAAT
Statistics
Matches: 95, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 2 0.02
42 27 0.28
43 35 0.37
44 27 0.28
45 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTACCAGACAGGGTCTTACACGAAATCAAATACG
Found at i:12213046 original size:19 final size:19
Alignment explanation
Indices: 12213019--12213057 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12213009 ACTTCGCTTA
*
12213019 ATCAAACCAAACATATCAT
1 ATCAAACCAAACATAACAT
*
12213038 ATCATACCAAACATAACAT
1 ATCAAACCAAACATAACAT
12213057 A
1 A
12213058 ACATCAAGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (19 bp):
ATCAAACCAAACATAACAT
Found at i:12218358 original size:11 final size:11
Alignment explanation
Indices: 12218342--12218371 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12218332 TAGGCCGGGC
12218342 CGGGTCGGATT
1 CGGGTCGGATT
*
12218353 CGGGTCGAATT
1 CGGGTCGGATT
12218364 CGGGTCGG
1 CGGGTCGG
12218372 CCTCCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.10, C:0.20, G:0.47, T:0.23
Consensus pattern (11 bp):
CGGGTCGGATT
Found at i:12234782 original size:20 final size:21
Alignment explanation
Indices: 12234736--12234795 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
12234726 TTATTTTATT
*
12234736 TAATATTAATATA-TTTTTAA
1 TAATATTATTATATTTTTTAA
**
12234756 TTTTATTATTATATTTTTTAA
1 TAATATTATTATATTTTTTAA
*
12234777 -AATATT-TATGTATTTTTTA
1 TAATATTAT-TATATTTTTTA
12234796 TATATTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.75
21 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TAATATTATTATATTTTTTAA
Found at i:12235401 original size:18 final size:19
Alignment explanation
Indices: 12235360--12235401 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
12235350 TTCAAATATA
*
12235360 TATAATCTATAAAAAACAT
1 TATAATCTATAAAAAAAAT
*
12235379 AATAAT-TATAAAAAAAAT
1 TATAATCTATAAAAAAAAT
12235397 TATAA
1 TATAA
12235402 AAATAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAATCTATAAAAAAAAT
Found at i:12235675 original size:23 final size:22
Alignment explanation
Indices: 12235639--12235697 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
12235629 ATTATTTTTA
* *
12235639 ATTTTTAAAATTTAAAATCATAT
1 ATTTTTAAATTTTAAAA-CAAAT
*
12235662 A-TTTTAGAATTTTATAACAAAT
1 ATTTTTA-AATTTTAAAACAAAT
12235684 ATTTTTAAAATTTT
1 ATTTTT-AAATTTT
12235698 TAATCAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTTAAATTTTAAAACAAAT
Found at i:12235706 original size:22 final size:22
Alignment explanation
Indices: 12235639--12235707 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
12235629 ATTATTTTTA
**
12235639 ATTTTTAAAATTTAAAATC-AT
1 ATTTTTAAAATTTTTAATCAAT
*
12235660 ATATTTTAGAATTTTATAA-CAAAT
1 AT-TTTTAAAATTTT-TAATC-AAT
12235684 ATTTTTAAAATTTTTAATCAAT
1 ATTTTTAAAATTTTTAATCAAT
12235706 AT
1 AT
12235708 AATATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 2 0.05
22 19 0.49
23 14 0.36
24 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
ATTTTTAAAATTTTTAATCAAT
Found at i:12243251 original size:21 final size:21
Alignment explanation
Indices: 12243225--12243266 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12243215 ATCGAAGGTT
*
12243225 TCTGGTTCACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
12243246 TCTGGTACACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
12243267 CATTGCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTGGTACACATAAATCAAAA
Found at i:12250663 original size:54 final size:54
Alignment explanation
Indices: 12250594--12250720 Score: 159
Period size: 54 Copynumber: 2.4 Consensus size: 54
12250584 GTGTCCCAGC
* *
12250594 CCGTGTCTTAAACCGTGTAACTCACTGACTTAGAT-CACACGGTCATGTCGCAAA
1 CCGTGTCTCAGACCGTGTAACTCACTGACTT-GATACACACGGTCATGTCGCAAA
* ** **
12250648 CCGTGTGC-CAGACCGTGTGACTCACTGACTTGATACACACGGTTGTGTCGCAGG
1 CCGTGT-CTCAGACCGTGTAACTCACTGACTTGATACACACGGTCATGTCGCAAA
12250702 CCGTGTCTCAGACCGTGTA
1 CCGTGTCTCAGACCGTGTA
12250721 TGGCACACGG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
53 4 0.06
54 57 0.92
55 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (54 bp):
CCGTGTCTCAGACCGTGTAACTCACTGACTTGATACACACGGTCATGTCGCAAA
Found at i:12274223 original size:31 final size:31
Alignment explanation
Indices: 12274188--12274248 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12274178 ACAAAATAGT
*
12274188 CACTAAACAATTTAAAAGTTTTTATTTAAGC
1 CACTAAACAATATAAAAGTTTTTATTTAAGC
* * *
12274219 CACTAGACTATATGAAAGTTTTTATTTAAG
1 CACTAAACAATATAAAAGTTTTTATTTAAG
12274249 ATACTACGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
CACTAAACAATATAAAAGTTTTTATTTAAGC
Found at i:12275359 original size:16 final size:16
Alignment explanation
Indices: 12275304--12275359 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
12275294 AAAAAAAGCA
12275304 AGAAACATTAAAAATAT
1 AGAAA-ATTAAAAATAT
* *
12275321 -TAAAATAATAAAATAT
1 AGAAAATTA-AAAATAT
*
12275337 A-TAAATTAAAAATAT
1 AGAAAATTAAAAATAT
12275352 AGAAAATT
1 AGAAAATT
12275360 GTTTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AGAAAATTAAAAATAT
Found at i:12275379 original size:30 final size:29
Alignment explanation
Indices: 12275343--12275411 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
12275333 ATATATAAAT
**
12275343 TAAAAATATAGAAAATTGTTTAAAATA-TTA
1 TAAAAATATAGAAAA--GTACAAAATATTTA
* *
12275373 TAAAAATGTAGGAAAGTACAAAATATTTA
1 TAAAAATATAGAAAAGTACAAAATATTTA
12275402 TAAAAATATA
1 TAAAAATATA
12275412 AAATTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 8 0.24
29 12 0.36
30 13 0.39
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (29 bp):
TAAAAATATAGAAAAGTACAAAATATTTA
Found at i:12275426 original size:10 final size:10
Alignment explanation
Indices: 12275411--12275507 Score: 79
Period size: 10 Copynumber: 9.4 Consensus size: 10
12275401 ATAAAAATAT
12275411 AAAATTATAA
1 AAAATTATAA
12275421 AAAATTATAA
1 AAAATTATAA
**
12275431 AAAATTATTT
1 AAAATTATAA
*
12275441 CAAATTATTCAA
1 AAAATTA-T-AA
* *
12275453 AAAATAATAG
1 AAAATTATAA
12275463 AAAATTATAA
1 AAAATTATAA
* *
12275473 AAAGTTTCATAT
1 AAA-ATT-ATAA
12275485 AAAA-TATAA
1 AAAATTATAA
*
12275494 AAAATTTTAA
1 AAAATTATAA
12275504 AAAA
1 AAAA
12275508 CCTACAATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
9 7 0.10
10 45 0.67
11 4 0.06
12 11 0.16
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:12275457 original size:32 final size:30
Alignment explanation
Indices: 12275412--12275470 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
12275402 TAAAAATATA
*
12275412 AAATTATAAAAAATTATAAAAAATTATTTC
1 AAATTATAAAAAATAATAAAAAATTATTTC
*
12275442 AAATTATTCAAAAAATAATAGAAAATTAT
1 AAATTA-T-AAAAAATAATAAAAAATTAT
12275471 AAAAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 1 0.04
32 18 0.72
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATTATAAAAAATAATAAAAAATTATTTC
Found at i:12275683 original size:36 final size:38
Alignment explanation
Indices: 12275613--12275683 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
12275603 CCCCCTGATT
12275613 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
1 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
12275651 TTTATAG-TTTTATTTTTAATA-TTTTTTAGATTT
1 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTT
12275684 TTCTTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 12 0.36
37 14 0.42
38 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.68
Consensus pattern (38 bp):
TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
Found at i:12282398 original size:6 final size:6
Alignment explanation
Indices: 12282387--12282415 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12282377 ATGCCGAGAT
12282387 GCAGCG GCAGCG GCAGCG GCAGCG GCAGC
1 GCAGCG GCAGCG GCAGCG GCAGCG GCAGC
12282416 AACCGGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.48, T:0.00
Consensus pattern (6 bp):
GCAGCG
Found at i:12285441 original size:6 final size:6
Alignment explanation
Indices: 12285432--12285459 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12285422 ATCTGTATCC
12285432 ATATTT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
12285460 GAAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:12288913 original size:29 final size:29
Alignment explanation
Indices: 12288852--12288917 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
12288842 ATCTATGTTT
* **
12288852 AGATAATTATACATAGAATGTATAAGTTT
1 AGATTATTATACATAGAATGTATAAGTAA
*
12288881 AGATTATTATACATAGAATGTCCTAA-TAA
1 AGATTATTATACATAGAATGT-ATAAGTAA
12288910 AGA-TATTA
1 AGATTATTA
12288918 AGAATTTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.16
29 24 0.75
30 3 0.09
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (29 bp):
AGATTATTATACATAGAATGTATAAGTAA
Found at i:12290691 original size:19 final size:19
Alignment explanation
Indices: 12290640--12290694 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
12290630 AGTAAATTTT
*
12290640 TTAAAAGTCTAAAAAT-TA
1 TTAAAATTCTAAAAATATA
*
12290658 TTAAAATTCAGAAAAATATA
1 TTAAAATTC-TAAAAATATA
12290678 -TAAAATTCTCAAAAATA
1 TTAAAATTCT-AAAAATA
12290695 AAATACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.26
19 21 0.68
20 2 0.06
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAAAATTCTAAAAATATA
Found at i:12291201 original size:17 final size:17
Alignment explanation
Indices: 12291181--12291215 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12291171 ATATTAATAA
12291181 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
12291198 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
12291215 T
1 T
12291216 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:12291215 original size:119 final size:120
Alignment explanation
Indices: 12291065--12291353 Score: 535
Period size: 119 Copynumber: 2.4 Consensus size: 120
12291055 CAAACTTTAG
12291065 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
* *
12291130 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTT
66 TTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTT
12291185 ATTAAATTATAT-TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
12291249 TTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTT
* *
12291304 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAGTTATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
12291354 ATATGATTAA
Statistics
Matches: 164, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
119 117 0.71
120 47 0.29
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (120 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTT
Found at i:12291256 original size:43 final size:43
Alignment explanation
Indices: 12291175--12291342 Score: 119
Period size: 43 Copynumber: 4.1 Consensus size: 43
12291165 TATTTAATAT
* *
12291175 TAATAATTTTATTAAATTATATTTTTTATTAAATTATATTTAA
1 TAATAATTTTATTAAATTATATTTTATAGTAAATTATATTTAA
12291218 TAATAATTATT-TTAAATTATATTTTATAGT--ATTATA--T-A
1 TAATAATT-TTATTAAATTATATTTTATAGTAAATTATATTTAA
* * * * *
12291256 TTATGATTTTAATAAATTCATA---TA-AG-AATATT-TA-ATAT
1 TAATAATTTTATTAAATT-ATATTTTATAGTAA-ATTATATTTAA
* * *
12291294 TAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAA
1 TAATAATTTTATTAAATTATAT-TTTATAGTAAATTATATTTAA
12291338 TAATA
1 TAATA
12291343 GTTATGTTAA
Statistics
Matches: 94, Mismatches: 15, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
35 2 0.02
36 4 0.04
37 9 0.10
38 27 0.29
39 4 0.04
41 7 0.07
42 4 0.04
43 29 0.31
44 8 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (43 bp):
TAATAATTTTATTAAATTATATTTTATAGTAAATTATATTTAA
Found at i:12292310 original size:16 final size:16
Alignment explanation
Indices: 12292241--12292308 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
12292231 TTTGGTTCGC
12292241 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12292257 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12292273 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
12292289 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
12292305 TGTA
1 TGTA
12292309 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12292343 original size:45 final size:44
Alignment explanation
Indices: 12292289--12292383 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
12292279 GGATTAGAGG
* *
12292289 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
12292334 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
12292378 TGTAAT
1 TGTAAT
12292384 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:12292553 original size:25 final size:25
Alignment explanation
Indices: 12292521--12292575 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12292511 TAATTTAATC
*
12292521 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
12292545 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
12292570 ATATAT
1 ATATAT
12292576 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:12292757 original size:47 final size:46
Alignment explanation
Indices: 12292706--12292866 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
12292696 GATTTAATAA
12292706 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
12292753 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
12292794 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
12292841 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
12292867 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:12298027 original size:33 final size:33
Alignment explanation
Indices: 12297990--12298058 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
12297980 TTTTTATTTT
* *
12297990 TTTATACTTTTAATGATTTTT-ATTTTTTAAAAA
1 TTTATACTTATAAT-ATTTTTGAATTTTTAAAAA
* *
12298023 TTTATTCTTATAATTTTTTTGAATTTTTAAAAA
1 TTTATACTTATAATATTTTTGAATTTTTAAAAA
12298056 TTT
1 TTT
12298059 TAAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (33 bp):
TTTATACTTATAATATTTTTGAATTTTTAAAAA
Found at i:12298889 original size:14 final size:14
Alignment explanation
Indices: 12298872--12298899 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12298862 TTACCCGGGG
12298872 CCCAAAACCCAAAC
1 CCCAAAACCCAAAC
12298886 CCCAAAACCCAAAC
1 CCCAAAACCCAAAC
12298900 AGCCCAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCAAAACCCAAAC
Found at i:12300281 original size:34 final size:35
Alignment explanation
Indices: 12300237--12300303 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12300227 CAGTAAAATG
*
12300237 TTTTCCGTAAAATGAATT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
12300271 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
12300304 CTAGTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:12300282 original size:20 final size:20
Alignment explanation
Indices: 12300253--12300291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12300243 GTAAAATGAA
*
12300253 TTCTGGAAAATGTTTTACTT
1 TTCTGGAAAATGATTTACTT
*
12300273 TTCTGTAAAATGATTTACT
1 TTCTGGAAAATGATTTACT
12300292 GGAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTCTGGAAAATGATTTACTT
Found at i:12300415 original size:20 final size:20
Alignment explanation
Indices: 12300390--12300428 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12300380 GTTTTTACAT
12300390 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
12300410 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
12300429 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:12300488 original size:15 final size:15
Alignment explanation
Indices: 12300459--12300511 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
12300449 TATTGCAATG
*
12300459 ATTTATTTATAAATAA
1 ATTT-TTTATTAATAA
12300475 ATTTTTTATTAATAAA
1 ATTTTTTATTAAT-AA
12300491 AGTTTTTTATCTAATTAA
1 A-TTTTTTAT-TAA-TAA
12300509 ATT
1 ATT
12300512 CCAAATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 10 0.31
18 6 0.19
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:12303837 original size:14 final size:14
Alignment explanation
Indices: 12303815--12303871 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
12303805 GAATATGCTG
* *
12303815 AGAAGAGAAGATGA
1 AGAACAGAAGAAGA
12303829 AGAACAGAAGAAGA
1 AGAACAGAAGAAGA
12303843 A-AA-AG--GAATGA
1 AGAACAGAAGAA-GA
*
12303854 AGAACGGAAGAAGA
1 AGAACAGAAGAAGA
12303868 AGAA
1 AGAA
12303872 GGAGCCTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 4 0.11
13 3 0.09
14 19 0.54
15 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.32, T:0.04
Consensus pattern (14 bp):
AGAACAGAAGAAGA
Found at i:12303873 original size:25 final size:25
Alignment explanation
Indices: 12303825--12303874 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12303815 AGAAGAGAAG
12303825 ATGAAGAACAGAAGAAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
* *
12303850 ATGAAGAACGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
12303875 GCCTTACCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.32, T:0.04
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:12303957 original size:18 final size:18
Alignment explanation
Indices: 12303934--12303971 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12303924 TTTGCAATCC
12303934 AAGGGGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
*
12303952 AAGGGGAAGGGAAAGGGG
1 AAGGGGAAGGGAAAAGGG
12303970 AA
1 AA
12303972 AGGGTAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGAAAAGGG
Found at i:12303984 original size:24 final size:24
Alignment explanation
Indices: 12303934--12303985 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12303924 TTTGCAATCC
* **
12303934 AAGGGGAAGGGAAAAGGGAAGGGG
1 AAGGGAAAGGGAAAAGGGAAGAAG
* *
12303958 AAGGGAAAGGGGAAAGGGTAGAAG
1 AAGGGAAAGGGAAAAGGGAAGAAG
12303982 AAGG
1 AAGG
12303986 CATCATTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (24 bp):
AAGGGAAAGGGAAAAGGGAAGAAG
Found at i:12306844 original size:2 final size:2
Alignment explanation
Indices: 12306837--12306881 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12306827 GAATTTACAA
12306837 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12306879 AG A
1 AG A
12306882 ACAATGCCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12307271 original size:16 final size:16
Alignment explanation
Indices: 12307250--12307281 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12307240 AAAAGTATTT
*
12307250 TTAAAATATTTTAAAA
1 TTAAAAAATTTTAAAA
12307266 TTAAAAAATTTTAAAA
1 TTAAAAAATTTTAAAA
12307282 AATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:12307294 original size:18 final size:16
Alignment explanation
Indices: 12307251--12307294 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
12307241 AAAGTATTTT
*
12307251 TAAAATATTTTAAAAT
1 TAAAATATTTTAAAAA
*
12307267 TAAAAAATTTTAAAAAA
1 TAAAATATTTT-AAAAA
12307284 TAAATATATTT
1 TAAA-ATATTT
12307295 ATTATATCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 8 0.35
18 5 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATTTTAAAAA
Found at i:12307481 original size:25 final size:25
Alignment explanation
Indices: 12307447--12307497 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12307437 TGAGCACATC
12307447 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
12307472 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
12307497 T
1 T
12307498 CCATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.49
Consensus pattern (25 bp):
TATTTGATACCCATATCTTTGACTT
Found at i:12312108 original size:31 final size:30
Alignment explanation
Indices: 12312073--12312136 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
12312063 ATTTCTTATG
*
12312073 CCAATATCTCGGTACCCATATCTTTGACTTT
1 CCAATAT-TCGATACCCATATCTTTGACTTT
*
12312104 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTCGATACCCATATCTTTGACTTT
12312134 CCA
1 CCA
12312137 TAAATATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (30 bp):
CCAATATTCGATACCCATATCTTTGACTTT
Found at i:12312128 original size:15 final size:16
Alignment explanation
Indices: 12312085--12312131 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
12312075 AATATCTCGG
12312085 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
** *
12312101 TTTCCA-ATATTTGA-
1 TACCCATATCTTTGAC
12312115 TACCCATATCTTTGAC
1 TACCCATATCTTTGAC
12312131 T
1 T
12312132 TTCCATAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (16 bp):
TACCCATATCTTTGAC
Found at i:12313546 original size:10 final size:9
Alignment explanation
Indices: 12313517--12313557 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
12313507 AATATTACAA
12313517 TTTTAATAT
1 TTTTAATAT
12313526 TTTTAATAT
1 TTTTAATAT
*
12313535 TTTTAGTAAT
1 TTTTAAT-AT
*
12313545 TTTTTATAT
1 TTTTAATAT
12313554 TTTT
1 TTTT
12313558 TGCAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTAATAT
Found at i:12313602 original size:19 final size:17
Alignment explanation
Indices: 12313524--12313614 Score: 60
Period size: 19 Copynumber: 5.1 Consensus size: 17
12313514 CAATTTTAAT
*
12313524 ATTTTTAATATTTTTAGTA
1 ATTTTAAATATTTTT--TA
**
12313543 ATTTTTTATATTTTTTGCA
1 ATTTTAAATATTTTTT--A
* *
12313562 ATTTTATAA-GTTTTCT-
1 ATTTTA-AATATTTTTTA
12313578 ATTTTAAATAATTATTTTA
1 ATTTTAAAT-ATT-TTTTA
12313597 ATTTTAAATATTTTTTA
1 ATTTTAAATATTTTTTA
12313614 A
1 A
12313615 ATATTTTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
15 2 0.03
16 6 0.10
17 9 0.16
18 6 0.10
19 34 0.59
20 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAAATATTTTTTA
Found at i:12313614 original size:11 final size:11
Alignment explanation
Indices: 12313598--12313639 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
12313588 ATTATTTTAA
12313598 TTTTAAATATT
1 TTTTAAATATT
12313609 TTTTAAATA-T
1 TTTTAAATATT
12313619 TTTTATAAT-TT
1 TTTTA-AATATT
*
12313630 TTGTAAATAT
1 TTTTAAATAT
12313640 AAATTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:12313631 original size:21 final size:21
Alignment explanation
Indices: 12313598--12313639 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12313588 ATTATTTTAA
*
12313598 TTTTAAATATTTTTTAAATAT
1 TTTTAAATATTTTGTAAATAT
12313619 TTTTATAAT-TTTTGTAAATAT
1 TTTTA-AATATTTTGTAAATAT
12313640 AAATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTAAATATTTTGTAAATAT
Found at i:12313701 original size:21 final size:21
Alignment explanation
Indices: 12313658--12313703 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12313648 ATCTTTTCTA
* * *
12313658 TTTTTAAAATTTTTATTAGTT
1 TTTTTAAAATTTTAAATAATT
12313679 TTTTTAAAATTTTAAATAATT
1 TTTTTAAAATTTTAAATAATT
12313700 TTTT
1 TTTT
12313704 AATTTTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAAAATTTTAAATAATT
Found at i:12313711 original size:20 final size:19
Alignment explanation
Indices: 12313678--12313743 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
12313668 TTTTATTAGT
* *
12313678 TTTTTTAAAATTTTAAATAA
1 TTTTTT-AATTTTTAAATTA
* *
12313698 TTTTTTAATTTTTTGCAATTT
1 TTTTTTAA-TTTTT-AAATTA
12313719 TTTTTGTAATTTTTAAATTA
1 TTTTT-TAATTTTTAAATTA
12313739 TTTTT
1 TTTTT
12313744 GAAGGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 19 0.51
21 13 0.35
22 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTTTTAAATTA
Found at i:12313744 original size:20 final size:21
Alignment explanation
Indices: 12313688--12313744 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
12313678 TTTTTTAAAA
*
12313688 TTTTAAATAATTTTT-TAATT
1 TTTTAAATTATTTTTGTAATT
* *
12313708 TTTTGCAATTTTTTTTGTAA-T
1 TTTT-AAATTATTTTTGTAATT
12313729 TTTTAAATTATTTTTG
1 TTTTAAATTATTTTTG
12313745 AAGGTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 14 0.47
21 13 0.43
22 3 0.10
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTAAATTATTTTTGTAATT
Found at i:12317236 original size:57 final size:57
Alignment explanation
Indices: 12317167--12317285 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 57
12317157 GGCCACTCTA
12317167 CTGTTAAACTCCATTACCTCCCTAACAACAATCTTACGTGACAGTCCAATTAAGGGT
1 CTGTTAAACTCCATTACCTCCCTAACAACAATCTTACGTGACAGTCCAATTAAGGGT
*
12317224 CTGTTAAACTCCATTACCTCCTTAACAACAATCTTACGTGACAGTCCAATTAAGGGT
1 CTGTTAAACTCCATTACCTCCCTAACAACAATCTTACGTGACAGTCCAATTAAGGGT
12317281 CTGTT
1 CTGTT
12317286 TGATTGCAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (57 bp):
CTGTTAAACTCCATTACCTCCCTAACAACAATCTTACGTGACAGTCCAATTAAGGGT
Found at i:12318383 original size:13 final size:11
Alignment explanation
Indices: 12318355--12318388 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
12318345 ATTTTTTTCT
12318355 CATATATTGTA
1 CATATATTGTA
12318366 CATATATTGTA
1 CATATATTGTA
12318377 CATATATTGTA
1 CATATATTGTA
12318388 C
1 C
12318389 TAATTCCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (11 bp):
CATATATTGTA
Found at i:12319621 original size:20 final size:20
Alignment explanation
Indices: 12319596--12319635 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12319586 AATATTTTCC
* *
12319596 AGTAAATCATTTTACAGAAA
1 AGTAAAACACTTTACAGAAA
*
12319616 AGTAAAACACTTTCCAGAAA
1 AGTAAAACACTTTACAGAAA
12319636 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACACTTTACAGAAA
Found at i:12321849 original size:31 final size:32
Alignment explanation
Indices: 12321814--12321891 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 32
12321804 ATATGCTACA
12321814 AGTCCCTGTACTTTTCAAAAATT-AAGAATTT
1 AGTCCCTGTACTTTTCAAAAATTCAAGAATTT
* * *
12321845 AGTCCATGTACTTTT----ATTTCATGAATTT
1 AGTCCCTGTACTTTTCAAAAATTCAAGAATTT
*
12321873 AGTCCCTTTACTTTTCAAA
1 AGTCCCTGTACTTTTCAAA
12321892 TTTCAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
27 3 0.08
28 20 0.54
31 14 0.38
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (32 bp):
AGTCCCTGTACTTTTCAAAAATTCAAGAATTT
Found at i:12328368 original size:30 final size:30
Alignment explanation
Indices: 12328334--12328392 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
12328324 CTTAATAAGT
*
12328334 AAATGCCTCTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
12328364 AAATGCCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
12328393 TAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:12328994 original size:18 final size:18
Alignment explanation
Indices: 12328971--12329006 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12328961 ACTACAATAC
*
12328971 TGGAATAATTTAGAAACA
1 TGGAATAATTTAAAAACA
12328989 TGGAATAATTTAAAAACA
1 TGGAATAATTTAAAAACA
12329007 AACCAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.28
Consensus pattern (18 bp):
TGGAATAATTTAAAAACA
Found at i:12332440 original size:104 final size:105
Alignment explanation
Indices: 12332194--12332461 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
12332184 TTGTATATAA
** *
12332194 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
12332258 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
12332299 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
12332364 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
12332403 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
12332462 ATAACGGTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 85 0.55
105 68 0.44
106 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:12336552 original size:8 final size:8
Alignment explanation
Indices: 12336505--12336559 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
12336495 ACATAAAAAA
12336505 TTAATAAT
1 TTAATAAT
*
12336513 CTTAACAAT
1 -TTAATAAT
*
12336522 ATAATAA-
1 TTAATAAT
12336529 TTAACTAA-
1 TTAA-TAAT
12336537 TTAA-AAT
1 TTAATAAT
12336544 TTAATAAT
1 TTAATAAT
12336552 TTAATAAT
1 TTAATAAT
12336560 ATTTTCTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 2 0.05
7 7 0.18
8 23 0.59
9 7 0.18
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAATAAT
Found at i:12336559 original size:22 final size:22
Alignment explanation
Indices: 12336503--12336559 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
12336493 AAACATAAAA
12336503 AATTAATAATCTTAACAATATAAT
1 AATTAATAA--TTAACAATATAAT
*
12336527 AATTAACTAATTAA-AATTTAAT
1 AATTAA-TAATTAACAATATAAT
12336549 AATTTAATAAT
1 AA-TTAATAAT
12336560 ATTTTCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 13 0.43
23 8 0.27
24 6 0.20
25 3 0.10
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAATAATTAACAATATAAT
Found at i:12336734 original size:7 final size:7
Alignment explanation
Indices: 12336698--12336731 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12336688 AATTATTGAG
12336698 AGAATTA
1 AGAATTA
12336705 AGAATTA
1 AGAATTA
12336712 AGAATTA
1 AGAATTA
* *
12336719 AAAATTG
1 AGAATTA
12336726 AGAATT
1 AGAATT
12336732 GAGTTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (7 bp):
AGAATTA
Found at i:12348547 original size:39 final size:39
Alignment explanation
Indices: 12348503--12348580 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12348493 TTTAAGTCTC
*
12348503 TTTGTGTGGATTTCCTTAGATTGAATTGTATATGAGTGA
1 TTTGTGTGGATTTCCTTAAATTGAATTGTATATGAGTGA
12348542 TTTGTGTGGATTTCCTTAAATTGAATTGTATATGAGTGA
1 TTTGTGTGGATTTCCTTAAATTGAATTGTATATGAGTGA
12348581 ACACTGAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (39 bp):
TTTGTGTGGATTTCCTTAAATTGAATTGTATATGAGTGA
Found at i:12362528 original size:35 final size:35
Alignment explanation
Indices: 12362485--12362554 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
12362475 GAGAATGCTC
12362485 GCATTTATAAAGACAAAACAAAGTTGTTTCACAAT
1 GCATTTATAAAGACAAAACAAAGTTGTTTCACAAT
12362520 GCATTTATAAAGACAAAACAAAGTTGTTTCACAAT
1 GCATTTATAAAGACAAAACAAAGTTGTTTCACAAT
12362555 AAGAGAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (35 bp):
GCATTTATAAAGACAAAACAAAGTTGTTTCACAAT
Found at i:12362887 original size:5 final size:5
Alignment explanation
Indices: 12362879--12362939 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
12362869 AATTTTTATT
* *
12362879 TTTTA TTTTTA TTTTA TTTTTTA TTTTA -TTTA CTTTA TTTATTA CTTTA
1 TTTTA -TTTTA TTTTA --TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA
12362928 TTTTA TTTTA TT
1 TTTTA TTTTA TT
12362940 ATTTATTACT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 28 0.60
6 7 0.15
7 8 0.17
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:12362895 original size:18 final size:18
Alignment explanation
Indices: 12362872--12362943 Score: 85
Period size: 18 Copynumber: 3.8 Consensus size: 18
12362862 GACACCCAAT
12362872 TTTTATTTTTTATTTTTA
1 TTTTATTTTTTATTTTTA
12362890 TTTTATTTTTTA-TTTTA
1 TTTTATTTTTTATTTTTA
12362907 -TTTACTTTATTTATTACTTTA
1 TTTTA-TTT-TTTATT--TTTA
12362928 TTTTATTTTATTATTT
1 TTTTATTTT-TTATTT
12362944 ATTACTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.09
17 8 0.17
18 16 0.34
19 2 0.04
20 1 0.02
21 12 0.26
22 4 0.09
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTATTTTTA
Found at i:12362915 original size:9 final size:8
Alignment explanation
Indices: 12362873--12362946 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 8
12362863 ACACCCAATT
12362873 TTTATTT-
1 TTTATTTA
12362880 TTTA-TT-
1 TTTATTTA
12362886 TTTATTTTA
1 TTTA-TTTA
12362895 TTT-TTTA
1 TTTATTTA
12362902 TTTTATTTA
1 -TTTATTTA
12362911 CTTTATTTA
1 -TTTATTTA
12362920 -TTACTTTA
1 TTTA-TTTA
12362928 TTTTATTT-
1 -TTTATTTA
12362936 TATTATTTA
1 T-TTATTTA
12362945 TT
1 TT
12362947 ACTTATTTGG
Statistics
Matches: 56, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
6 6 0.11
7 12 0.21
8 16 0.29
9 19 0.34
10 3 0.05
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTTA
Found at i:12363088 original size:12 final size:12
Alignment explanation
Indices: 12363071--12363103 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12363061 CAAACAGCCT
12363071 CTATTCCAGATA
1 CTATTCCAGATA
*
12363083 CTATTCCAGATT
1 CTATTCCAGATA
12363095 CTATTCCAG
1 CTATTCCAG
12363104 CCCAGAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (12 bp):
CTATTCCAGATA
Found at i:12364288 original size:101 final size:101
Alignment explanation
Indices: 12364099--12364289 Score: 251
Period size: 101 Copynumber: 1.9 Consensus size: 101
12364089 AAGAACATGT
* * * * *
12364099 TGGGATGAGTAATCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTTGCGTCAAAAGGTTCGATGTG
1 TGGGATGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCGTCAAAAGGTTCGATATG
* *
12364164 TTCTTAAGAAAAAAATATAATAAATTAGGAGTCTGC
66 TCCTAAAGAAAAAAATATAATAAATTAGGAGTCTGC
* *
12364200 TGGGCTGAGTAACCAGGGTGGGGTGCTTGGCTATCATCTCTCTTCGCGTCAAAAGGTTCAGTATA
1 TGGGATGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCGTCAAAAGGTTC-G-ATA
* *
12364265 T-TCCTAAAGTATAAAATAT-ATAAAT
64 TGTCCTAAAGAAAAAAATATAATAAAT
12364290 AATAAATAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 59 0.77
102 15 0.19
103 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (101 bp):
TGGGATGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCGTCAAAAGGTTCGATATG
TCCTAAAGAAAAAAATATAATAAATTAGGAGTCTGC
Found at i:12364307 original size:6 final size:6
Alignment explanation
Indices: 12364275--12364387 Score: 63
Period size: 6 Copynumber: 19.0 Consensus size: 6
12364265 TTCCTAAAGT
* * *
12364275 ATAAAA TATATAA ATAATAA ATAAAA ATCAAA AT--AA ATAAAA AGAAAA
1 ATAAAA -ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * * * * *
12364323 AGAAAA AGAAAA AGAAAA A-AGAAA A-AAAA AGAAAA AGAAAA AGAAAA
1 ATAAAA ATAAAA ATAAAA ATA-AAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
12364370 AGAAAA AGAAAA AGAAAA
1 ATAAAA ATAAAA ATAAAA
12364388 TAATTTGGGG
Statistics
Matches: 97, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
4 4 0.04
5 5 0.05
6 77 0.79
7 11 0.11
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.09
Consensus pattern (6 bp):
ATAAAA
Found at i:12364317 original size:1 final size:1
Alignment explanation
Indices: 12364313--12364387 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
12364303 CAAAATAAAT
* * * * * * * * * *
12364313 AAAAAGAAAAAGAAAAAGAAAAAGAAAAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
12364378 AAAAAGAAAA
1 AAAAAAAAAA
12364388 TAATTTGGGG
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (1 bp):
A
Found at i:12364328 original size:12 final size:12
Alignment explanation
Indices: 12364313--12364387 Score: 127
Period size: 12 Copynumber: 6.3 Consensus size: 12
12364303 CAAAATAAAT
12364313 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12364325 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12364337 AAAAA-AGAAAA-
1 AAAAAGA-AAAAG
12364348 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12364360 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12364372 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12364384 AAAA
1 AAAA
12364388 TAATTTGGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.17
12 50 0.83
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:12364357 original size:35 final size:34
Alignment explanation
Indices: 12364304--12364387 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 34
12364294 AATAAAAATC
* *
12364304 AAAATAAATAAAAAGAAAAAGAAAAAGAAAAAGAA
1 AAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAAG-A
12364339 AAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAAGA
1 AAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAAGA
12364373 AAAAGAAAAAGAAAA
1 AAAAGAAAAA-AAAA
12364388 TAATTTGGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 11 0.24
35 35 0.76
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (34 bp):
AAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAAGA
Found at i:12364964 original size:15 final size:15
Alignment explanation
Indices: 12364939--12364973 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12364929 AACTCTATTT
*
12364939 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
12364953 TAATTAATATTAAGA
1 TAATTAATATTAAGA
12364968 TAATTA
1 TAATTA
12364974 TTAATGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:12366759 original size:30 final size:30
Alignment explanation
Indices: 12366725--12366782 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
12366715 GAGATATTCC
12366725 TCTTCATCCATACG-ATTAAGATTAGCCAAA
1 TCTTCATCCA-ACGTATTAAGATTAGCCAAA
*
12366755 TCTTCATCCAACGTATTAATATTAGCCA
1 TCTTCATCCAACGTATTAAGATTAGCCA
12366783 TGATGCACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (30 bp):
TCTTCATCCAACGTATTAAGATTAGCCAAA
Found at i:12372021 original size:12 final size:12
Alignment explanation
Indices: 12372006--12372084 Score: 78
Period size: 11 Copynumber: 6.8 Consensus size: 12
12371996 TTTTAATTTT
12372006 TTTGAAAAAAAA
1 TTTGAAAAAAAA
12372018 TTTGAAAAGAAAAAA
1 TTTG--AA-AAAAAA
*
12372033 TTTGAAAAACAA
1 TTTGAAAAAAAA
12372045 TTTG-AAAAAAA
1 TTTGAAAAAAAA
12372056 -TTG-AAAAAAA
1 TTTGAAAAAAAA
*
12372066 -TTGCAAAAAAA
1 TTTGAAAAAAAA
12372077 -TTGAAAAA
1 TTTGAAAAA
12372085 TAGAAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
10 13 0.22
11 20 0.33
12 13 0.22
13 2 0.03
14 2 0.03
15 10 0.17
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (12 bp):
TTTGAAAAAAAA
Done.