Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 90 of 345
Found at i:29772396 original size:15 final size:15
Alignment explanation
Indices: 29772378--29772434 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
29772368 TATCTGTTTT
29772378 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
29772393 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
29772408 ATTGAATTTATATTG
1 ATTGAATTTATATTG
29772423 ATTGAA-TTATAT
1 ATTGAATTTATAT
29772435 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:29772413 original size:30 final size:28
Alignment explanation
Indices: 29772374--29772432 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
29772364 TGAATATCTG
29772374 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
29772403 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
29772432 T
1 T
29772433 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:29772865 original size:21 final size:22
Alignment explanation
Indices: 29772806--29772871 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 22
29772796 GCTTTACCGA
29772806 TTAGGCACTTTATGTGTCGTAT
1 TTAGGCACTTTATGTGTCGTAT
* **
29772828 TTCAGGCACCTCGTGTGTCGT-T
1 TT-AGGCACTTTATGTGTCGTAT
29772850 TTAGGCACTTTATGTGTCGTAT
1 TTAGGCACTTTATGTGTCGTAT
29772872 ACTGATCAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 15 0.42
22 6 0.17
23 15 0.42
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.42
Consensus pattern (22 bp):
TTAGGCACTTTATGTGTCGTAT
Found at i:29773054 original size:18 final size:19
Alignment explanation
Indices: 29773033--29773073 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29773023 AATGAAATGA
29773033 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
29773051 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
29773070 GAAA
1 GAAA
29773074 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:29785324 original size:18 final size:17
Alignment explanation
Indices: 29785296--29785330 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29785286 ATTTTTAAGA
*
29785296 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29785313 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29785331 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29785584 original size:16 final size:16
Alignment explanation
Indices: 29785563--29785601 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29785553 TTGATTTGCT
*
29785563 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
*
29785579 ATTACACATCTATTCC
1 ATTACACAGCTATTCC
29785595 ATTACAC
1 ATTACAC
29785602 CTCTAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:29785623 original size:16 final size:16
Alignment explanation
Indices: 29785576--29785632 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
29785566 ACACAGCTTT
* * *
29785576 TCCATTACACATCTAT
1 TCCAATACACCTCTAA
*
29785592 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
29785608 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
*
29785624 TCTAATACA
1 TCCAATACA
29785633 GCGAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:29786333 original size:26 final size:26
Alignment explanation
Indices: 29786304--29786355 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29786294 TTAAATAGAT
29786304 GTTGTTCATAAAACTCTATTAACAAA
1 GTTGTTCATAAAACTCTATTAACAAA
29786330 GTTGTTCATAAAACTCTATTAACAAA
1 GTTGTTCATAAAACTCTATTAACAAA
29786356 ATAAATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (26 bp):
GTTGTTCATAAAACTCTATTAACAAA
Found at i:29790022 original size:6 final size:6
Alignment explanation
Indices: 29790011--29790055 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
29790001 TGACATAGAG
29790011 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGT
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGT
29790056 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (6 bp):
TGTGTA
Found at i:29796088 original size:6 final size:6
Alignment explanation
Indices: 29796081--29796126 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
29796071 ACTTGTTCAC
* *
29796081 CCTCAC CCTCAA CCTCAA CCTCAA CCTCAA CCTCAC CCTCAA CCTC
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTC
29796127 TTTCCTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.26, C:0.57, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCAA
Found at i:29798301 original size:95 final size:95
Alignment explanation
Indices: 29798131--29798309 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 95
29798121 CATGGCGTTA
* * * *
29798131 TTTATAGTAGTGTAATTCATAGCCCAGTAAAAGATAAATGATATCCTCTCATGGGTATTACATGG
1 TTTATAGTAGTGAAATTCATAACCCAGTAAAAGATAAATGATATCCTCTCATGAGCATTACATGG
*
29798196 TTGTTAGAAAAGTAACATGACATGACTTCC
66 TTGATAGAAAAGTAACATGACATGACTTCC
* *
29798226 TTTATAGTAGTGAAATTCATAACTC-GATAAAAGGTAAATGATATCCTCTCATGAGCATTACATG
1 TTTATAGTAGTGAAATTCATAACCCAG-TAAAAGATAAATGATATCCTCTCATGAGCATTACATG
*
29798290 GTTGATGGAAAAGTAACATG
65 GTTGATAGAAAAGTAACATG
29798310 GTCATGGGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (95 bp):
TTTATAGTAGTGAAATTCATAACCCAGTAAAAGATAAATGATATCCTCTCATGAGCATTACATGG
TTGATAGAAAAGTAACATGACATGACTTCC
Found at i:29805222 original size:25 final size:25
Alignment explanation
Indices: 29805162--29805223 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
29805152 CATTTCACAA
* * *
29805162 CTTGTGTGAGCATTTATAGATACGG
1 CTTGTGTGAGCAATTACAGATACAG
* * *
29805187 CTCGTGAGAGCAATTACAGTTACAG
1 CTTGTGTGAGCAATTACAGATACAG
29805212 CTTGTGTGAGCA
1 CTTGTGTGAGCA
29805224 TCTTTCCCGC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (25 bp):
CTTGTGTGAGCAATTACAGATACAG
Found at i:29813601 original size:19 final size:20
Alignment explanation
Indices: 29813577--29813615 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
29813567 GTCCCATTAT
29813577 TTATTTATTTTT-TGTTTTA
1 TTATTTATTTTTATGTTTTA
29813596 TTATTTATTTTTATGTTTTA
1 TTATTTATTTTTATGTTTTA
29813616 AATGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTATTTATTTTTATGTTTTA
Found at i:29813607 original size:20 final size:19
Alignment explanation
Indices: 29813577--29813615 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
29813567 GTCCCATTAT
*
29813577 TTATTTATTTTTTGTTTTA
1 TTATTTATTTTATGTTTTA
29813596 TTATTTATTTTTATGTTTTA
1 TTATTTA-TTTTATGTTTTA
29813616 AATGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTATTTATTTTATGTTTTA
Found at i:29813623 original size:19 final size:19
Alignment explanation
Indices: 29813582--29813624 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29813572 ATTATTTATT
* *
29813582 TATTTTTTGTTTTATTATT
1 TATTTTTTGTTTTATAATG
29813601 TATTTTTATGTTTTA-AATG
1 TATTTTT-TGTTTTATAATG
29813620 TATTT
1 TATTT
29813625 GATTTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TATTTTTTGTTTTATAATG
Found at i:29817787 original size:27 final size:27
Alignment explanation
Indices: 29817749--29817802 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29817739 TCCAACATTG
29817749 GATGATTCTGCAATATCGTGCTTGCAA
1 GATGATTCTGCAATATCGTGCTTGCAA
29817776 GATGATTCTGCAATATCGTGCTTGCAA
1 GATGATTCTGCAATATCGTGCTTGCAA
29817803 CGCATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (27 bp):
GATGATTCTGCAATATCGTGCTTGCAA
Found at i:29819046 original size:17 final size:17
Alignment explanation
Indices: 29819026--29819060 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29819016 ATTTATTTAA
*
29819026 TCAATTAATTTAATTTC
1 TCAATTAAATTAATTTC
*
29819043 TCAATTAAATTATTTTC
1 TCAATTAAATTAATTTC
29819060 T
1 T
29819061 TAATCCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
TCAATTAAATTAATTTC
Found at i:29822487 original size:60 final size:60
Alignment explanation
Indices: 29822394--29822515 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
29822384 TGATAGTTAT
* **
29822394 ATTGTGGATGAATTGTAAATGAGGTTATAAGTGTAATGTTGGTTTGGTATATATATAAAC
1 ATTGTGGATGAATTGTAAATGAGGTTATAAGTGTAATGTTAGTTTAATATATATATAAAC
*
29822454 ATTGTGGATGGATTGTAAATGAGGTTATAAGTGTAATGTTAGTTTAATATATATATAAAC
1 ATTGTGGATGAATTGTAAATGAGGTTATAAGTGTAATGTTAGTTTAATATATATATAAAC
29822514 AT
1 AT
29822516 GTGTTTGTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (60 bp):
ATTGTGGATGAATTGTAAATGAGGTTATAAGTGTAATGTTAGTTTAATATATATATAAAC
Found at i:29824978 original size:27 final size:27
Alignment explanation
Indices: 29824930--29825088 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
29824920 GCGAGGCTGC
* *
29824930 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
* *
29824957 CAGATATTGTGCCAGAGCCACCA-AAA
1 CAGATATTGTGGCAGAGCCACCAGATA
29824983 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
29825010 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
29825037 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
29825064 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
29825089 GACACTTGGC
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
26 11 0.10
27 97 0.85
28 6 0.05
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:29825088 original size:54 final size:54
Alignment explanation
Indices: 29824948--29825088 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
29824938 GTGACGAAGT
* * *
29824948 CACCAGATACAGAT-ATTGTGCCAGAGCCACCAAAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
29825002 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
29825056 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
29825089 GACACTTGGC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:29826769 original size:26 final size:26
Alignment explanation
Indices: 29826663--29826770 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
29826653 TGAAATGCCC
*
29826663 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29826689 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
29826715 ATCATAGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29826741 ATCATGGAACATTTACCTACCCCAGT
1 ATCATGGAACATTTACCTAACCCATT
29826767 ATCA
1 ATCA
29826771 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29827882 original size:25 final size:25
Alignment explanation
Indices: 29827854--29827904 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29827844 AGTTTCCACC
*
29827854 AACAATTTCTTACAAATTTATTCAT
1 AACAATTTCTAACAAATTTATTCAT
* *
29827879 AACAGTTTCTAATAAATTTATTCAT
1 AACAATTTCTAACAAATTTATTCAT
29827904 A
1 A
29827905 TAACTCGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (25 bp):
AACAATTTCTAACAAATTTATTCAT
Found at i:29828697 original size:17 final size:19
Alignment explanation
Indices: 29828677--29828714 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29828667 CCAACTACCC
*
29828677 ACCCAA-TAC-AACCCAAA
1 ACCCAATTACTAAACCAAA
29828694 ACCCAATTACTAAACCAAA
1 ACCCAATTACTAAACCAAA
29828713 AC
1 AC
29828715 AGCCCAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.11
Consensus pattern (19 bp):
ACCCAATTACTAAACCAAA
Found at i:29830196 original size:46 final size:46
Alignment explanation
Indices: 29830137--29830307 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
29830127 GCCCATAAGC
* *
29830137 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAAT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
* * * * ** *
29830183 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TTACATCTGAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATG-CTCGCATCCAT-AAAT
* * *
29830230 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
*
29830276 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGC
29830308 CCAAATATCC
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 67 0.66
47 35 0.34
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCATCCATAAAT
Found at i:29830295 original size:93 final size:93
Alignment explanation
Indices: 29830136--29830308 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
29830126 CGCCCATAAG
** *
29830136 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAATGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCAGACTCAACTCA
29830201 ACGAGCTCGGATGCCTAGTTACATCTGA
66 ACGAGCTCGGATGCCTAGTTACATCTGA
* * *
29830229 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCAGACTCAACTCA
*
29830294 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
29830309 CAAATATCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTGA
Found at i:29832544 original size:3 final size:3
Alignment explanation
Indices: 29832536--29832662 Score: 71
Period size: 3 Copynumber: 42.7 Consensus size: 3
29832526 TGTCTAACAC
** * * *
29832536 TAT TAT TAT TAT TAT TAT CCT TAT TAT TAC TAT TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** ** * * *
29832584 TGC TAT TGC TAT TAT TA- TAT TGT TAT T-T T-T TAT TTT CTAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * *
29832627 CAA TAT CAT TAT TAT TAC TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
29832663 GTGAATACTT
Statistics
Matches: 89, Mismatches: 31, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
2 6 0.07
3 78 0.88
4 5 0.06
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:29832786 original size:140 final size:137
Alignment explanation
Indices: 29832627--29833037 Score: 395
Period size: 132 Copynumber: 2.9 Consensus size: 137
29832617 TTTCTATTAC
* * *
29832627 CAATATCATTATTATTACTATTATTATTATATATTAGTGAATACTTTTTATTATATATGTATAGG
1 CAATATTAATATTATTACTATTATTATTATATATTAGTGTATA-TTTTTATTATATATGTATA-G
*
29832692 TATATATATTTATATATAGTATTATTTTTTATTTACTTTATTTTAATATTTTTATTATATTATAT
64 TATATATATTTATATATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATAT
***
29832757 TTGTTTTTTT
129 TT-TGGGTTT
** * * *
29832767 GTATTTTAATATTATTACTATTATCATTATTATTATTAATATTTGTGTGTATTTTTATTATATAT
1 CAATATTAATATTATTAC-----T-ATTATTATTA-T-ATATTAGTGTATATTTTTATTATATAT
* * *
29832832 GGGTAT-GTATATGTATATATTTATATATAGCATTATTCTTT-GTTACTTTATTTTAATATTTTT
58 --GTATAG--TA--TATATATTTATATATAGTATTATTTTTTAATTACTTTATTTTAATATTTTT
* *
29832895 ATTATATTTTCTTTTGGGTTT
117 ATTATATTATATTTTGGGTTT
* * * *
29832916 CAATATTATTATTATTATTATTATTATTAT-TATTAGTGTATATTTTTATTATATTTGCATA-TA
1 CAATATTAATATTATTACTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATAGTA
* * * *
29832979 TATGTA-TT-TATATAGTAGTA-TTTTTAATTACCTTATTTTAATATTATTATTATATTATA
66 TATATATTTATATATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATA
29833038 CACTCTCCTT
Statistics
Matches: 221, Mismatches: 34, Indels: 40
0.75 0.12 0.14
Matches are distributed among these distances:
131 4 0.02
132 38 0.17
133 2 0.01
134 5 0.02
136 2 0.01
138 3 0.01
140 36 0.16
142 1 0.00
143 10 0.05
144 1 0.00
145 1 0.00
146 10 0.05
147 16 0.07
148 10 0.05
149 23 0.10
150 33 0.15
151 26 0.12
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (137 bp):
CAATATTAATATTATTACTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATAGTA
TATATATTTATATATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTT
TGGGTTT
Found at i:29832910 original size:143 final size:142
Alignment explanation
Indices: 29832627--29833037 Score: 416
Period size: 140 Copynumber: 2.9 Consensus size: 142
29832617 TTTCTATTAC
* * * *
29832627 CAATATCATTATTATTACTATTATTATTATATATTAGTGAATACTTTTTATTATATATGTATAGG
1 CAATATTATTATTATTATTATTATTATTA-ATATTAGTGTATA-TTTTTATTATATATGTATAGA
* * *
29832692 TATATATATTTATATATAGTATTATTTTTTATTTACTTTATTTTAATATTTTTATTATATTATAT
64 TATATATATTTATATATAGCATTATTCTTTAGTTACTTTATTTTAATA--TTTATTATATTATAT
* *
29832757 TTGTTTTTTTGTATTT
127 TTGTTCTTTTGGATTT
* * * *
29832773 TAATATTATTACTATTATCATTATTATTATTAATATTTGTGTGTATTTTTATTATATATGGGTAT
1 CAATATTA-T--TATTATTATTATTATTATTAATATTAGTGTATATTTTTATTATATAT--GTAT
29832838 -GTATATGTATATATTTATATATAGCATTATTCTTT-GTTACTTTATTTTAATA-TT-TT-TATT
61 AG-ATA--TATATATTTATATATAGCATTATTCTTTAGTTACTTTATTTTAATATTTATTATATT
*
29832898 ATA-TT-TTCTTTTGGGTTT
123 ATATTTGTTCTTTTGGATTT
* * *
29832916 CAATATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTATATTTGCAT--ATA
1 CAATATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATAGATA
* * *
29832979 TATGTATTTATATAGTAG---TATT-TTTAATTACCTTATTTTAATATTATTATTATATTATA
66 TATATATTTATATA-TAGCATTATTCTTTAGTTACTTTATTTTAATA-T-TTATTATATTATA
29833038 CACTCTCCTT
Statistics
Matches: 226, Mismatches: 24, Indels: 39
0.78 0.08 0.13
Matches are distributed among these distances:
131 3 0.01
132 19 0.08
134 13 0.06
135 5 0.02
136 5 0.02
137 7 0.03
138 3 0.01
140 42 0.19
142 1 0.00
143 17 0.08
144 2 0.01
145 7 0.03
146 8 0.04
147 17 0.08
148 11 0.05
149 24 0.11
150 16 0.07
151 26 0.12
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (142 bp):
CAATATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATAGATA
TATATATTTATATATAGCATTATTCTTTAGTTACTTTATTTTAATATTTATTATATTATATTTGT
TCTTTTGGATTT
Found at i:29832967 original size:3 final size:3
Alignment explanation
Indices: 29832919--29832950 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29832909 TGGGTTTCAA
29832919 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29832951 GTGTATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29833286 original size:15 final size:15
Alignment explanation
Indices: 29833268--29833306 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
29833258 TATTGTTATA
*
29833268 TTTATTATTATTACT
1 TTTATTATAATTACT
29833283 TTTATTATAATTACT
1 TTTATTATAATTACT
*
29833298 ATTATTATA
1 TTTATTATA
29833307 GCTTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATAATTACT
Found at i:29833290 original size:24 final size:24
Alignment explanation
Indices: 29833247--29833304 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29833237 ATTTTTTATC
* * *
29833247 ACTAATATTACTATTGTTATATTT
1 ACTATTATTACTATTATTATAATT
* *
29833271 ATTATTATTACTTTTATTATAATT
1 ACTATTATTACTATTATTATAATT
29833295 ACTATTATTA
1 ACTATTATTA
29833305 TAGCTTTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (24 bp):
ACTATTATTACTATTATTATAATT
Found at i:29845861 original size:39 final size:39
Alignment explanation
Indices: 29845803--29845889 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
29845793 TTCAGTGATG
* *
29845803 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
29845842 TATATTCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
*
29845881 TATGTCCGG
1 TATATCCGG
29845890 GCTAAAGTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:29845903 original size:39 final size:39
Alignment explanation
Indices: 29845803--29845905 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 39
29845793 TTCAGTGATG
** * *
29845803 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* *
29845842 TATATTCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* *
29845881 TATGTCCGGGC-TAAAGTCCCGCAGG
1 TATATCCGGACTTAAAGT-CCGCAGG
29845906 TTTCGAGCTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 5 0.09
39 50 0.91
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.25
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
Found at i:29847798 original size:76 final size:76
Alignment explanation
Indices: 29847593--29847913 Score: 414
Period size: 77 Copynumber: 4.2 Consensus size: 76
29847583 GGTATCCTGA
* * *
29847593 TATTTTT-ATTTCTGTTTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGCC
1 TATTTTTAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
29847657 ACATGCCGA-G
66 ACACGCCGAGG
*
29847667 -ATTTTTCAATTTCTATTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TATTTTT-AATTTCTA--TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
29847731 GTCACACGCTGAGG
63 GTCACACGCCGAGG
** * * * *
29847745 TACCTTTAGTTCCTATTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGAC
1 TATTTTTAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
29847810 ACAAGCCGATG
66 ACACGCCGAGG
* * *
29847821 TATTTTTAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGT
1 TATTTTTAATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
29847886 CACACGCTGAGG
65 CACACGCCGAGG
*
29847898 TATTTTTAGTTTCTAT
1 TATTTTTAATTTCTAT
29847914 CAACTCATAT
Statistics
Matches: 209, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
73 6 0.03
75 6 0.03
76 70 0.33
77 116 0.56
78 7 0.03
79 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (76 bp):
TATTTTTAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACACGCCGAGG
Found at i:29847805 original size:153 final size:153
Alignment explanation
Indices: 29847607--29847913 Score: 485
Period size: 153 Copynumber: 2.0 Consensus size: 153
29847597 TTTATTTCTG
* * *
29847607 TTTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGCCACATGCCGA-G-ATT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACAAGCCGATGTATT
* *
29847670 TTTCAATTTCTAT-TTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
66 TTT-AATTT-T-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTC
29847734 ACACGCTGAGGTACCTTTAGTTCCTA
128 ACACGCTGAGGTACCTTTAGTTCCTA
*
29847760 TTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACAAGCCGATGTATT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACAAGCCGATGTATT
29847825 TTTAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCACA
66 TTTAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCACA
** *
29847890 CGCTGAGGTATTTTTAGTTTCTA
131 CGCTGAGGTACCTTTAGTTCCTA
29847913 T
1 T
29847914 CAACTCATAT
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
152 1 0.01
153 129 0.91
154 6 0.04
155 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (153 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACAAGCCGATGTATT
TTTAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCACA
CGCTGAGGTACCTTTAGTTCCTA
Found at i:29847922 original size:64 final size:64
Alignment explanation
Indices: 29847848--29847967 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
29847838 TTTCAAAAAA
* * *
29847848 ATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCACACGCTGAGGTATTTTTAGTTTCT
1 ATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGGTCACACACTGAGGTATTTTTAGTTTCT
*
29847912 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTTT
1 ATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGGTCACACACTGAGGTATTTT
29847968 CAATTTTTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
ATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGGTCACACACTGAGGTATTTTTAGTTTCT
Found at i:29848227 original size:28 final size:28
Alignment explanation
Indices: 29848195--29848249 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
29848185 AGTTGCATGA
*
29848195 AGTGGATCGAAA-CAACAAGATGCAGTGG
1 AGTGGATC-AAAGCAACAAGACGCAGTGG
*
29848223 AGTGGATCAAAGTAACAAGACGCAGTG
1 AGTGGATCAAAGCAACAAGACGCAGTG
29848250 CACTAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.40, C:0.15, G:0.31, T:0.15
Consensus pattern (28 bp):
AGTGGATCAAAGCAACAAGACGCAGTGG
Found at i:29848441 original size:17 final size:19
Alignment explanation
Indices: 29848421--29848458 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29848411 CCAACTACCC
*
29848421 ACCCAA-TAC-AACCCAAA
1 ACCCAATTACTAAACCAAA
29848438 ACCCAATTACTAAACCAAA
1 ACCCAATTACTAAACCAAA
29848457 AC
1 AC
29848459 AGCCTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.11
Consensus pattern (19 bp):
ACCCAATTACTAAACCAAA
Found at i:29849476 original size:3 final size:3
Alignment explanation
Indices: 29849446--29849657 Score: 117
Period size: 3 Copynumber: 70.3 Consensus size: 3
29849436 GTCTAACATG
* * *
29849446 ATT ATT TTT ATT -TT TTT A-T ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
29849492 ATT ATT ATT ATT ATT CATAT GTGT ATT ATT ATT A-C ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT -AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT
** * * * * * **
29849539 ATT GCT ATT ATC CTT ATT ATT ACT ATT ATT TTT ATT TTT ATT GCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * * ** * *
29849587 GCT ATT ATT A-T ATC GTT ATT TTT ATT TTCT ATT ACC AAT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
*
29849632 ATT ATT ACT ATT ATT ATT ATAT ATT A
1 ATT ATT ATT ATT ATT ATT AT-T ATT A
29849658 GTGAATACTT
Statistics
Matches: 150, Mismatches: 51, Indels: 16
0.69 0.24 0.07
Matches are distributed among these distances:
2 7 0.05
3 132 0.88
4 10 0.07
5 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:29849794 original size:145 final size:146
Alignment explanation
Indices: 29849623--29849897 Score: 344
Period size: 145 Copynumber: 1.9 Consensus size: 146
29849613 TTCTATTACC
*
29849623 AATATCATTATTATTACTATTATTATTATATATTAGTGAATACTTTTTATTATATA-TGTA-TAG
1 AATATCATTACTATTACTATTATTATTA-ATATTAGTGAATA-TTTTTATTATATAGTGTAGTAG
* * * *
29849686 GTATA-TA-TATTTATGTATAGTATTATTTTTTATTTACTTTATTTTAACATTTTTATTATATTA
64 GTATAGTATTATTTATATATAGCATTATTCTTT-GTTACTTTATTTTAACATTTTTATTATATTA
29849749 TATTTGTTTTTTGTATTTT
128 TATTTGTTTTTTGTATTTT
* * **
29849768 AATATTATTACTATTA-TCATTATTATTAATATTTGTGTGTATTTTTATTATATATGTGTATGTA
1 AATATCATTACTATTACT-ATTATTATTAATATTAGTGAATATTTTTATTATATA-GTGTA-GTA
* *
29849832 TGTATATGTATTTATTTATATATAGCATTATTCTTTGTTACTTTATTTTAATATTTTTATTATAT
63 GGTATA-GTA-TTATTTATATATAGCATTATTCTTTGTTACTTTATTTTAACATTTTTATTATAT
29849897 T
126 T
29849898 TGCTTTTGGG
Statistics
Matches: 110, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
143 13 0.12
144 11 0.10
145 28 0.25
147 7 0.06
149 2 0.02
150 28 0.25
151 21 0.19
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (146 bp):
AATATCATTACTATTACTATTATTATTAATATTAGTGAATATTTTTATTATATAGTGTAGTAGGT
ATAGTATTATTTATATATAGCATTATTCTTTGTTACTTTATTTTAACATTTTTATTATATTATAT
TTGTTTTTTGTATTTT
Found at i:29849831 original size:23 final size:22
Alignment explanation
Indices: 29849790--29849832 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29849780 ATTATCATTA
* *
29849790 TTATTAATATTTGTGTGTATTT
1 TTATTAATATGTGTATGTATTT
29849812 TTATTATATATGTGTATGTAT
1 TTATTA-ATATGTGTATGTAT
29849833 GTATATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (22 bp):
TTATTAATATGTGTATGTATTT
Found at i:29850207 original size:21 final size:21
Alignment explanation
Indices: 29850172--29850221 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29850162 ATTATTATTA
* *
29850172 CTATTATTCTTTATTGTCATGG
1 CTATTA-TGTTTATTGTCATAG
* *
29850194 TTATTATGTTTATTTTCATAG
1 CTATTATGTTTATTGTCATAG
29850215 CTATTAT
1 CTATTAT
29850222 TTTTTATCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.58
Consensus pattern (21 bp):
CTATTATGTTTATTGTCATAG
Found at i:29850269 original size:15 final size:15
Alignment explanation
Indices: 29850251--29850291 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
29850241 TATTGTTATA
29850251 TTTATTATTATTACT
1 TTTATTATTATTACT
*
29850266 TTTATTATAATTACT
1 TTTATTATTATTACT
*
29850281 ATTATTATTAT
1 TTTATTATTAT
29850292 AGCTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATTATTACT
Found at i:29850273 original size:24 final size:24
Alignment explanation
Indices: 29850230--29850287 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29850220 ATTTTTTATC
* * *
29850230 ACTAATATTACTATTGTTATATTT
1 ACTATTATTACTATTATTATAATT
* *
29850254 ATTATTATTACTTTTATTATAATT
1 ACTATTATTACTATTATTATAATT
29850278 ACTATTATTA
1 ACTATTATTA
29850288 TTATAGCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (24 bp):
ACTATTATTACTATTATTATAATT
Found at i:29852886 original size:21 final size:20
Alignment explanation
Indices: 29852820--29852887 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
29852810 ATAAAATTTA
* *
29852820 ATTAGAATATATAAATTATTT
1 ATTA-AATATTTAAATTATAT
* *
29852841 TTTAAATATTTAAA-TATAACC
1 ATTAAATATTTAAATTAT-A-T
29852862 ATTAAATATTTATAATTATAT
1 ATTAAATATTTA-AATTATAT
29852883 ATTAA
1 ATTAA
29852888 CACATTTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 19 0.51
22 3 0.08
23 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (20 bp):
ATTAAATATTTAAATTATAT
Found at i:29854098 original size:56 final size:56
Alignment explanation
Indices: 29854038--29854153 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
29854028 TCCATTTCAC
29854038 TAAAAATTCTTATTTTAAAGTTGAATCATTTAAATGTTTTATATTCTTTTTGGAAA
1 TAAAAATTCTTATTTTAAAGTTGAATCATTTAAATGTTTTATATTCTTTTTGGAAA
29854094 TAAAAATTCTTATTTTAAAGTTGAATCATTTAAATGTTTTATATTCTTTTTGGAAA
1 TAAAAATTCTTATTTTAAAGTTGAATCATTTAAATGTTTTATATTCTTTTTGGAAA
29854150 TAAA
1 TAAA
29854154 TTATATTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (56 bp):
TAAAAATTCTTATTTTAAAGTTGAATCATTTAAATGTTTTATATTCTTTTTGGAAA
Found at i:29855732 original size:44 final size:45
Alignment explanation
Indices: 29855652--29855737 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 45
29855642 GAGTGAAAAT
*
29855652 TAAAAGTTTAGGGGGAAAATAAAAAGATTTTAGGG-TTGTGGGAG
1 TAAAAGTTTAGGGGGAAAATAAAAAGATTTGAGGGTTTGTGGGAG
* * * * *
29855696 TAAAATTTTGGGGGGAAAGTAAAAAGCTTTGGGGGTTTGTGG
1 TAAAAGTTTAGGGGGAAAATAAAAAGATTTGAGGGTTTGTGG
29855738 TAAAAATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 29 0.83
45 6 0.17
ACGTcount: A:0.34, C:0.01, G:0.36, T:0.29
Consensus pattern (45 bp):
TAAAAGTTTAGGGGGAAAATAAAAAGATTTGAGGGTTTGTGGGAG
Found at i:29856512 original size:25 final size:28
Alignment explanation
Indices: 29856483--29856569 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 28
29856473 AAAAATACAT
29856483 TTTTATATAATATTTTGATTT-TTT-AA
1 TTTTATATAATATTTTGATTTATTTAAA
29856509 -TTTATATAAT-TTTAT-ATTTTTATTTAAA
1 TTTTATATAATATTT-TGA--TTTATTTAAA
* *
29856537 TTTTTATATAATATTTTGATTTATATACA
1 -TTTTATATAATATTTTGATTTATTTAAA
29856566 TTTT
1 TTTT
29856570 TATTTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
24 4 0.08
25 11 0.22
26 3 0.06
27 3 0.06
28 6 0.12
29 8 0.16
30 11 0.22
31 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATATAATATTTTGATTTATTTAAA
Found at i:29856562 original size:12 final size:12
Alignment explanation
Indices: 29856519--29856562 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
29856509 TTTATATAAT
29856519 TTTATATTTTTA
1 TTTATATTTTTA
*
29856531 TTTAAATTTTTA
1 TTTATATTTTTA
* *
29856543 TATAATATTTTGA
1 T-TTATATTTTTA
29856556 TTTATAT
1 TTTATAT
29856563 ACATTTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTATATTTTTA
Found at i:29856562 original size:47 final size:46
Alignment explanation
Indices: 29856503--29856594 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
29856493 TATTTTGATT
29856503 TTTTAATTTATATA-ATTTTATATTTTTATTTAAATTTTTATATAATA
1 TTTTAATTTATATACATTTT-TATTTTT-TTTAAATTTTTATATAATA
* * *
29856550 TTTTGATTTATATACATTTTTATTTTTTTTCAGTTTTTATATAAT
1 TTTTAATTTATATACATTTTTATTTTTTTTAAATTTTTATATAAT
29856595 TTGAAAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
46 16 0.39
47 20 0.49
48 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (46 bp):
TTTTAATTTATATACATTTTTATTTTTTTTAAATTTTTATATAATA
Found at i:29863980 original size:199 final size:199
Alignment explanation
Indices: 29863640--29864035 Score: 738
Period size: 199 Copynumber: 2.0 Consensus size: 199
29863630 TTCTGAGTTA
* *
29863640 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTTCCTATGAGAACCAATACAAGTAGTCATCTT
1 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
*
29863705 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCTTAAATTCAGTGAAATC
66 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
* * *
29863770 TCTTCAGGGAAATTCAATTATATTCTCCTACAAGTTGCTAACACATACAGCTATCCATACGTTTA
131 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
29863835 TCAT
196 TCAT
29863839 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
1 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
29863904 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
66 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
29863969 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
131 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
29864034 TC
196 TC
29864036 GTGACAACCT
Statistics
Matches: 191, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 191 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (199 bp):
GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
TCAT
Found at i:29871785 original size:44 final size:44
Alignment explanation
Indices: 29871737--29872622 Score: 292
Period size: 44 Copynumber: 20.1 Consensus size: 44
29871727 GAAGTATAGA
* *
29871737 ATTTGTCGCTTCAATCTACTCCATTGCAACTTTAGGGAGATAAA
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* * * * * *
29871781 ATTTGTAGCTCCAATATGCTCCACTGCAACTTCT-GCGAAATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTT-TAGGGAGATAAG
** * * *
29871825 ATTCACTAC-TTTCAATCTACTCCACTGCAACTTCAGGGAAATAAG
1 ATT-TGT-CGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
** ** * *
29871870 ATTT-TCTATTTTTGATCTACTCCACTGCAACTTCAAGGAGATAAG
1 ATTTGTC--GCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
** * *
29871915 ATTTGTAACTTCAATCTGCTCCATTGCAACTTTAGGGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* ** * * ** * * * *
29871959 ATTTGTAATTCGTAGCTTTAATCTGTTTCATTGCCTCTTCAGAGAAATAAA
1 ATTTG----TC---GCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* * * * **
29872010 ATTTGTAGCTTCAATCTGCTCCACTACGACTTCGGGGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* ** * * * * *
29872054 ATTCGTAACTTTAA-CTTGCCCCACTACAACTTCAGGGAGAT-AG
1 ATTTGTCGCTTCAATC-TACTCCACTGCAACTTTAGGGAGATAAG
* * * * ***
29872097 CTTTAAT--C-T--GT-TA-T--ACTGCAACTTCAAATAGATAAG
1 ATTT-GTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
** * * * * *
29872133 ATTTGCTATCTTCAGTCTGCTCCACTACAACTTTAAGGAGATAAA
1 ATTTG-TCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* ** * * * *
29872178 ACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATATG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* * * * * * **
29872222 GTTTATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
** ** * *
29872266 ATTCACTATCTTCAGTCTACTCCACTGTAACTTTAGGGAGATAAG
1 ATT-TGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* ** * * * * *
29872311 ACTTGTAACTTCAATTTGCTCCACTGAAACTTCAGAGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* * * * ** * * *
29872355 GTTTATAGCTTTAATCGGCTCTACTGCAACTTCAGAGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* *** ** * *
29872399 ATTCGCTATATTCTGTCTGCTCCACTGCAACTTCA-GGAGATAAG
1 ATTTG-TCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* ** * *
29872443 ACTTGTAACTTCAA-CTTGCTCCACTGCAACTTCAGGGAGATAAG
1 ATTTGTCGCTTCAATC-TACTCCACTGCAACTTTAGGGAGATAAG
* * * * * ** *
29872487 GTTTATAGCTTTAATCTGCTCCACTATAACTTTAGAGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
** * * * **
29872531 ATTTGCTATCTTCAGTATACTCCACTGCAACTTCAGGGAGATCCG
1 ATTTG-TCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
* * * * *
29872576 ATTTGTGGCTTTAGTATACTCCACTACAACTTTAGGGAGATAAG
1 ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
29872620 ATT
1 ATT
29872623 CGCCACGATG
Statistics
Matches: 635, Mismatches: 172, Indels: 70
0.72 0.20 0.08
Matches are distributed among these distances:
35 15 0.02
36 6 0.01
38 2 0.00
39 1 0.00
41 3 0.00
42 4 0.01
43 30 0.05
44 359 0.57
45 180 0.28
46 1 0.00
47 1 0.00
48 1 0.00
51 32 0.05
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
ATTTGTCGCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAG
Found at i:29871851 original size:45 final size:45
Alignment explanation
Indices: 29871799--29871961 Score: 152
Period size: 45 Copynumber: 3.6 Consensus size: 45
29871789 CTCCAATATG
*
29871799 CTCCACTGCAACTTCTGCGAAATAAGATTCACTACTTTCAATCTA
1 CTCCACTGCAACTTCAGCGAAATAAGATTCACTACTTTCAATCTA
* ** * **
29871844 CTCCACTGCAACTTCAGGGAAATAAGATTTTCTATTTTTGATCTA
1 CTCCACTGCAACTTCAGCGAAATAAGATTCACTACTTTCAATCTA
* ** *
29871889 CTCCACTGCAACTTCAAG-GAGATAAGATT-TGTAAC-TTCAATCTG
1 CTCCACTGCAACTTC-AGCGAAATAAGATTCACT-ACTTTCAATCTA
* * * *
29871933 CTCCATTGCAACTTTAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGCGAAATAAGATT
29871962 TGTAATTCGT
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
43 2 0.02
44 32 0.32
45 64 0.64
46 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGCGAAATAAGATTCACTACTTTCAATCTA
Found at i:29871854 original size:89 final size:88
Alignment explanation
Indices: 29871745--29871965 Score: 230
Period size: 89 Copynumber: 2.5 Consensus size: 88
29871735 GAATTTGTCG
*
29871745 CTTCAATCTACTCCATTGCAACTTTAGGGAGATAAAATTTGTAGCTCCAATATGCTCCACTGCAA
1 CTTCAATCTACTCCATTGCAACTTTAGGGAGATAAAATTTGTAGCTCCAATATACTCCACTGCAA
*
29871810 CTTC-TGCGAAATAAGATTCACT-A
66 CTTCAAG-GAAATAAGATT-ACTAA
* * * * * ** *** *
29871833 CTTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTTCTATTTTTGATCTACTCCACTGC
1 C-TTCAATCTACTCCATTGCAACTTTAGGGAGATAA-AATTTGTAGCTCCAATATACTCCACTGC
* **
29871898 AACTTCAAGGAGATAAGATTTGTAA
64 AACTTCAAGGAAATAAGATTACTAA
* *
29871923 CTTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATTTGTA
1 CTTCAATCTACTCCATTGCAACTTTAGGGAGATAAAATTTGTA
29871966 ATTCGTAGCT
Statistics
Matches: 106, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
88 6 0.06
89 62 0.58
90 37 0.35
91 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (88 bp):
CTTCAATCTACTCCATTGCAACTTTAGGGAGATAAAATTTGTAGCTCCAATATACTCCACTGCAA
CTTCAAGGAAATAAGATTACTAA
Found at i:29872331 original size:133 final size:133
Alignment explanation
Indices: 29872093--29872572 Score: 651
Period size: 133 Copynumber: 3.6 Consensus size: 133
29872083 CTTCAGGGAG
* * * *
29872093 ATAGCTTTAATCTGTTATACTGCAACTTCA-AATAGATAAGATTTGCTATCTTCAGTCTGCTCCA
1 ATAGCTTTAATCTGCTCTACTGCAACTTCAGAA-AGATAAGATTCGCTATCTTCAGTCTACTCCA
* * * * * * *
29872157 CTACAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATATG
65 CTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTACAACTTCAGGGAGATAAG
29872222 GTTT
130 GTTT
* *
29872226 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATCTTCAGTCTACTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTCAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
* * * *
29872291 TGTAACTTTAGGGAGATAAGACTTGTAACTTCAATTTGCTCCACTGA-AACTTCAGAGAGATAAG
66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACT-ACAACTTCAGGGAGATAAG
29872355 GTTT
130 GTTT
* * * * *
29872359 ATAGCTTTAATCGGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATATTCTGTCTGCTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTCAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
*
29872424 TGCAACTTCA-GGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGG
66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTACAACTTCAGGGAGATAAGG
29872488 TTT
131 TTT
* ** * * * *
29872491 ATAGCTTTAATCTGCTCCACTATAACTTTAGAGAGATAAGATTTGCTATCTTCAGTATACTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTCAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
29872556 TGCAACTTCAGGGAGAT
66 TGCAACTTCAGGGAGAT
29872573 CCGATTTGTG
Statistics
Matches: 306, Mismatches: 37, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
132 118 0.39
133 185 0.60
134 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (133 bp):
ATAGCTTTAATCTGCTCTACTGCAACTTCAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTACAACTTCAGGGAGATAAGG
TTT
Found at i:29872600 original size:265 final size:266
Alignment explanation
Indices: 29872093--29872619 Score: 716
Period size: 265 Copynumber: 2.0 Consensus size: 266
29872083 CTTCAGGGAG
* * * * *
29872093 ATAGCTTTAATCTGTTATACTGCAACTTCAAATAGATAAGATTTGCTATCTTCAGTCTGCTCCAC
1 ATAGCTTTAATCGGCTATACTGCAACTTCAAAGAGATAAGATTCGCTATATTCAGTCTGCTCCAC
* *
29872158 TACAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACTACAACTTTAGGGAGATATGG
66 TACAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGG
* * *
29872223 TTTATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATCTTCAGTCTACTC
131 TTTATAGCTTTAATCTGCTCCACTACAACTTTAGAAAGATAAGATTCACTATCTTCAGTATACTC
* * * *
29872288 CACTGTAACTTTAGGGAGATAAGACTTGTAACTTCAATTTGCTCCACTGA-AACTTCAGAGAGAT
196 CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATATACTCCACT-ACAACTTCAGAGAGAT
29872352 AAGGTTT
260 AAGGTTT
* * *
29872359 ATAGCTTTAATCGGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATATTCTGTCTGCTCCAC
1 ATAGCTTTAATCGGCTATACTGCAACTTCAAAGAGATAAGATTCGCTATATTCAGTCTGCTCCAC
* * * * *
29872424 TGCAAC-TTCAGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGG
66 TACAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGG
* * **
29872488 TTTATAGCTTTAATCTGCTCCACTATAACTTTAGAGAGATAAGATTTGCTATCTTCAGTATACTC
131 TTTATAGCTTTAATCTGCTCCACTACAACTTTAGAAAGATAAGATTCACTATCTTCAGTATACTC
** * ** * * * *
29872553 CACTGCAACTTCAGGGAGATCCGATTTGTGGCTTTAGTATACTCCACTACAACTTTAGGGAGATA
196 CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATATACTCCACTACAACTTCAGAGAGATA
29872618 AG
261 AG
29872620 ATTCGCCACG
Statistics
Matches: 225, Mismatches: 35, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
264 1 0.00
265 162 0.72
266 62 0.28
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (266 bp):
ATAGCTTTAATCGGCTATACTGCAACTTCAAAGAGATAAGATTCGCTATATTCAGTCTGCTCCAC
TACAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGG
TTTATAGCTTTAATCTGCTCCACTACAACTTTAGAAAGATAAGATTCACTATCTTCAGTATACTC
CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATATACTCCACTACAACTTCAGAGAGATA
AGGTTT
Found at i:29888945 original size:21 final size:21
Alignment explanation
Indices: 29888921--29888985 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
29888911 AAGTCTAGCT
29888921 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*
29888942 GAAGC-C-TGAAG-GCT-AACT
1 GAAGCACAT-AAGTGCTAAACG
29888960 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
29888981 GAAGC
1 GAAGC
29888986 TAACTGAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 8 0.22
21 13 0.35
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:29888962 original size:39 final size:38
Alignment explanation
Indices: 29888903--29889034 Score: 161
Period size: 39 Copynumber: 3.6 Consensus size: 38
29888893 ATCGTGATCT
* *
29888903 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAAC
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
*
29888941 GGAAGCCTGAAGGCTAACTGAAGCACATAAGTGCTAAAC
1 -GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
*
29888980 ---G---GAA-GCTAACTGAAGCACATAAGTGTTAAAC
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
29889011 AGAAGCCCGAAGGCTAACTGAAGC
1 -GAAGCCCGAAGGCTAACTGAAGC
29889035 TTATCAAAGC
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
31 26 0.32
32 3 0.04
35 2 0.02
38 3 0.04
39 47 0.58
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (38 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
Found at i:29888991 original size:31 final size:31
Alignment explanation
Indices: 29888953--29889016 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
29888943 AAGCCTGAAG
*
29888953 GCTAACTGAAGCACATAAGTGCTAAACGGAA
1 GCTAACTGAAGCACATAAGTGCTAAACAGAA
*
29888984 GCTAACTGAAGCACATAAGTGTTAAACAGAA
1 GCTAACTGAAGCACATAAGTGCTAAACAGAA
29889015 GC
1 GC
29889017 CCGAAGGCTA
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:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (31 bp):
GCTAACTGAAGCACATAAGTGCTAAACAGAA
Found at i:29895869 original size:21 final size:22
Alignment explanation
Indices: 29895838--29895888 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
29895828 GTAAATGGAC
*
29895838 TTTGATGTTTTGGACTTATTTA
1 TTTGATTTTTTGGACTTATTTA
**
29895860 TTT-ATTTTTTGGTTTTATTTA
1 TTTGATTTTTTGGACTTATTTA
29895881 TTTGATTT
1 TTTGATTT
29895889 AGTGGGCCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTGATTTTTTGGACTTATTTA
Found at i:29898856 original size:31 final size:31
Alignment explanation
Indices: 29898818--29898879 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29898808 ACAAGAAAGA
29898818 TTGAATAGAGGAGTGGCTAATCCGGAATGGT
1 TTGAATAGAGGAGTGGCTAATCCGGAATGGT
29898849 TTGAATAGAGGAGTGGCTAATCCGGAATGGT
1 TTGAATAGAGGAGTGGCTAATCCGGAATGGT
29898880 GGGATTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.26
Consensus pattern (31 bp):
TTGAATAGAGGAGTGGCTAATCCGGAATGGT
Found at i:29907716 original size:17 final size:17
Alignment explanation
Indices: 29907686--29907733 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
29907676 TGTAATGTGG
* *
29907686 TTTCACTTATATTATCA
1 TTTCATTTAAATTATCA
**
29907703 TTTCATTTAAATTATTT
1 TTTCATTTAAATTATCA
29907720 TTTCGATTTAAATT
1 TTTC-ATTTAAATT
29907734 TAATTATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTCATTTAAATTATCA
Found at i:29907754 original size:21 final size:21
Alignment explanation
Indices: 29907700--29907764 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
29907690 ACTTATATTA
*
29907700 TCATTTC-ATTTAAATTATTTTT
1 TCATTTCAATTT-AATTA-TTTC
*
29907722 TCGATTTAAATTTAATTATTTC
1 TC-ATTTCAATTTAATTATTTC
**
29907744 TCATTTCAATTTTTTTATTTC
1 TCATTTCAATTTAATTATTTC
29907765 AATTTATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.44
22 7 0.19
23 9 0.25
24 4 0.11
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (21 bp):
TCATTTCAATTTAATTATTTC
Found at i:29907824 original size:5 final size:5
Alignment explanation
Indices: 29907814--29907865 Score: 68
Period size: 5 Copynumber: 9.6 Consensus size: 5
29907804 CATAATCATA
29907814 ATTTC ATTTC ATGTTC ATTTAAC ATTTC ATTTC ATTTC ATTTC ATATTC
1 ATTTC ATTTC AT-TTC ATTT--C ATTTC ATTTC ATTTC ATTTC AT-TTC
29907863 ATT
1 ATT
29907866 ACAAATTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 28 0.65
6 10 0.23
7 5 0.12
ACGTcount: A:0.25, C:0.17, G:0.02, T:0.56
Consensus pattern (5 bp):
ATTTC
Found at i:29910952 original size:29 final size:30
Alignment explanation
Indices: 29910912--29910985 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 30
29910902 AACATATTAA
*
29910912 TAATTAATTAATA-TAAT-TAACTCTAAAAT-
1 TAATTAAATAATATTAATAT-ACT-TAAAATC
29910941 TAATTAAATAATAATTAATATACTTAAAATC
1 TAATTAAATAAT-ATTAATATACTTAAAATC
29910972 TAATTTAAATAATA
1 TAA-TTAAATAATA
29910986 ATTCTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 11 0.28
30 7 0.18
31 11 0.28
32 10 0.26
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATTAAATAATATTAATATACTTAAAATC
Found at i:29921470 original size:57 final size:59
Alignment explanation
Indices: 29921393--29921524 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 59
29921383 CAGGTCTTTT
** * * * *
29921393 TCATTTTT-CATTTTGTTTTTCATTTAG-GAGAAAACCACATTTATTTCCAAATGATTC
1 TCATTTTTCCATTTTCATTTTCATTTAGAAAAAAAACCACAATCATTTCCAAATGATTC
* * * *
29921450 T-ATTTTTCCATTTTCATTTTCATTTTGAAAAAAAACCATAATCATTTTCAAATGTTTC
1 TCATTTTTCCATTTTCATTTTCATTTAGAAAAAAAACCACAATCATTTCCAAATGATTC
*
29921508 TCATTTCTCCATTTTCA
1 TCATTTTTCCATTTTCA
29921525 CCATTTCTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
56 6 0.10
57 17 0.28
58 24 0.39
59 14 0.23
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (59 bp):
TCATTTTTCCATTTTCATTTTCATTTAGAAAAAAAACCACAATCATTTCCAAATGATTC
Found at i:29926983 original size:54 final size:54
Alignment explanation
Indices: 29926916--29927023 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
29926906 TTGATTTGAT
*
29926916 TACATATGTTGTCATTATTAGGCTACTAACACTAGCTTCGGATTAGGGTTGCTA
1 TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTGCTA
*
29926970 TACATATGTTGTCATTATCGGGCTACTAACACTAGCTTCGGATTAGGGTTGCTA
1 TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTGCTA
29927024 ACACTAGCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (54 bp):
TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTGCTA
Found at i:29927024 original size:26 final size:26
Alignment explanation
Indices: 29926941--29927059 Score: 95
Period size: 26 Copynumber: 4.5 Consensus size: 26
29926931 TATTAGGCTA
29926941 CTAACACTAGCTTCGGATTAGGGTTG
1 CTAACACTAGCTTCGGATTAGGGTTG
* * *
29926967 CTATACA-TATG-TT-GTCATTATCGGGCTA
1 CTA-ACACTA-GCTTCG-GATTA--GGGTTG
29926995 CTAACACTAGCTTCGGATTAGGGTTG
1 CTAACACTAGCTTCGGATTAGGGTTG
* **
29927021 CTAACACTAGCTT-GG-TTCGATTCTG
1 CTAACACTAGCTTCGGATTAGGGT-TG
29927046 CTAACACTAGCTTC
1 CTAACACTAGCTTC
29927060 AAAGGATCTA
Statistics
Matches: 74, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
24 4 0.05
25 18 0.24
26 28 0.38
27 8 0.11
28 15 0.20
29 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (26 bp):
CTAACACTAGCTTCGGATTAGGGTTG
Found at i:29927173 original size:25 final size:26
Alignment explanation
Indices: 29927145--29927193 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29927135 GCTGACATAT
29927145 TCAGG-CTACTAACACTAGCTTCAAA
1 TCAGGACTACTAACACTAGCTTCAAA
* *
29927170 TCAGGATTGCTAACACTAGCTTCA
1 TCAGGACTACTAACACTAGCTTCA
29927194 GAAAATCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (26 bp):
TCAGGACTACTAACACTAGCTTCAAA
Found at i:29935124 original size:28 final size:28
Alignment explanation
Indices: 29935084--29935162 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
29935074 GTAATCAAAT
* * *
29935084 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
29935112 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
29935140 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
29935163 CAAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:29935375 original size:43 final size:42
Alignment explanation
Indices: 29935322--29935402 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
29935312 TGAATAATAT
** *
29935322 TATCGGGCTTCGGGCCTAGCAGGCTATAATACCGGTGAAATGA
1 TATCGGGCTTCAAGCCTAGCAGGCGA-AATACCGGTGAAATGA
*
29935365 TATCGGGCTTCAAGCCTAGCAGGCGAAATGCCGGTGAA
1 TATCGGGCTTCAAGCCTAGCAGGCGAAATACCGGTGAA
29935403 TGAGTTCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 11 0.32
43 23 0.68
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (42 bp):
TATCGGGCTTCAAGCCTAGCAGGCGAAATACCGGTGAAATGA
Found at i:29935478 original size:40 final size:40
Alignment explanation
Indices: 29935379--29935483 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 40
29935369 GGGCTTCAAG
* * *
29935379 CCTAGCAGGCGAAATGCCGGTGAATGAGTTCAGACTTAAAG
1 CCTAGCAGGCTAAATGCCGGTG-ATGAATTCAGACTTAAAA
* *** * * **
29935420 TCTAGCAGGCTTCGTGCCGATGATGAATTCGGGTTTAAAA
1 CCTAGCAGGCTAAATGCCGGTGATGAATTCAGACTTAAAA
29935460 CCTAGCAGGCTAAATGCCGGTGAT
1 CCTAGCAGGCTAAATGCCGGTGAT
29935484 TTGATAAAAG
Statistics
Matches: 48, Mismatches: 16, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
40 32 0.67
41 16 0.33
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (40 bp):
CCTAGCAGGCTAAATGCCGGTGATGAATTCAGACTTAAAA
Found at i:29958722 original size:14 final size:14
Alignment explanation
Indices: 29958703--29958757 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
29958693 TTGCTTACAC
*
29958703 TTAAGGTTAAGTAA
1 TTAAGGTTAATTAA
29958717 TTAAGGTTAATTAA
1 TTAAGGTTAATTAA
**
29958731 GTTAATCTTAATTAA
1 -TTAAGGTTAATTAA
29958746 TTAA--TTAATTAA
1 TTAAGGTTAATTAA
29958758 CTAGTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 8 0.22
14 17 0.46
15 12 0.32
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (14 bp):
TTAAGGTTAATTAA
Found at i:29958729 original size:10 final size:9
Alignment explanation
Indices: 29958709--29958757 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 9
29958699 ACACTTAAGG
29958709 TTAAG-TAA
1 TTAAGTTAA
29958717 TTAAGGTTAA
1 TTAA-GTTAA
29958727 TTAAGTTAA
1 TTAAGTTAA
29958736 TCTTAA-TTAA
1 --TTAAGTTAA
29958746 TTAA-TTAA
1 TTAAGTTAA
29958754 TTAA
1 TTAA
29958758 CTAGTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 16 0.43
9 6 0.16
10 11 0.30
11 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (9 bp):
TTAAGTTAA
Found at i:29967383 original size:22 final size:21
Alignment explanation
Indices: 29967349--29967389 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
29967339 GTAGTAAATT
29967349 TTGAATTGATAATTATAGTTAA
1 TTGAATTGATAATTA-AGTTAA
29967371 TTGAA-TGATTAATTAAGTT
1 TTGAATTGA-TAATTAAGTT
29967390 CAAATGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (21 bp):
TTGAATTGATAATTAAGTTAA
Found at i:29971739 original size:23 final size:23
Alignment explanation
Indices: 29971713--29971757 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29971703 ATGATATACA
29971713 AAAATGATA-TCAATGAAAAGGTC
1 AAAATGATAGT-AATGAAAAGGTC
*
29971736 AAAATGATAGTACTGAAAAGGT
1 AAAATGATAGTAATGAAAAGGT
29971758 TGGCATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (23 bp):
AAAATGATAGTAATGAAAAGGTC
Found at i:29973635 original size:93 final size:93
Alignment explanation
Indices: 29973476--29973647 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
29973466 AGGATATTTG
* * * *
29973476 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
29973541 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
29973569 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
*
29973634 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
29973648 ACTTATGGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29973652 original size:46 final size:46
Alignment explanation
Indices: 29973481--29973655 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
29973471 ATTTGGGCAT
* * *
29973481 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*** * * * *
29973527 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC
*
29973572 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
29973620 CCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29973656 GTGGGTTACA
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 2 0.02
46 68 0.65
47 32 0.30
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:29976377 original size:35 final size:35
Alignment explanation
Indices: 29976299--29976377 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
29976289 TAAATTACTT
*
29976299 ATTAT-TTAAGTAAATAGATATTTATTATTTATCA
1 ATTATATTAAGTAAATAGATATTTATTATTAATCA
*
29976333 TTTATTATTAAGTAAA-AGATATTTATTAATTAAAT-A
1 ATTA-TATTAAGTAAATAGATATTTATT-ATT-AATCA
29976369 ATTATATTA
1 ATTATATTA
29976378 TAAGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 3 0.08
35 17 0.45
36 16 0.42
37 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (35 bp):
ATTATATTAAGTAAATAGATATTTATTATTAATCA
Found at i:29976655 original size:14 final size:14
Alignment explanation
Indices: 29976636--29976668 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
29976626 TTTGGAAGCT
29976636 TTAAGCTTTAATTG
1 TTAAGCTTTAATTG
29976650 TTAAGCTTTAATTG
1 TTAAGCTTTAATTG
29976664 TTAAG
1 TTAAG
29976669 TTAATTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (14 bp):
TTAAGCTTTAATTG
Found at i:29977457 original size:44 final size:44
Alignment explanation
Indices: 29977408--29977499 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
29977398 TGTTCAGAGA
29977408 TACTTCAACCTT-GAGTCGATGAGGCA-CTATAAGTGTCATACTGT
1 TACTTCAA-CTTCGAGTCGATGAGGCACCT-TAAGTGTCATACTGT
* * *
29977452 TACTTCGACTTCGAGTCGATGAGGCACCTTATGTGTCGTACTGT
1 TACTTCAACTTCGAGTCGATGAGGCACCTTAAGTGTCATACTGT
29977496 TACT
1 TACT
29977500 GTTACTTCGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.07
44 38 0.88
45 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (44 bp):
TACTTCAACTTCGAGTCGATGAGGCACCTTAAGTGTCATACTGT
Found at i:29977587 original size:47 final size:47
Alignment explanation
Indices: 29977468--29977588 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 47
29977458 GACTTCGAGT
* ** *
29977468 CGATGAGGCACCTTATGTGTCGTACTGTTACTGTTACTTCGGTTTAATC
1 CGATGAGGCA-C-TAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
* * **
29977517 CGTTGAGGTACTAAGTACCGTACTGTTACTGTTTACTTCGG-CAAAGC
1 CGATGAGGCACTAAGTGTCGTACTGTTACTG-TTACTTCGGTCAAAGC
*
29977564 CGATGAGGCACTAAGTGTTGTACTG
1 CGATGAGGCACTAAGTGTCGTACTG
29977589 GTGTGTTGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
47 40 0.69
48 10 0.17
49 8 0.14
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (47 bp):
CGATGAGGCACTAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
Found at i:29977743 original size:39 final size:39
Alignment explanation
Indices: 29977657--29977791 Score: 128
Period size: 39 Copynumber: 3.5 Consensus size: 39
29977647 TACTGTACTG
* ** * *
29977657 AATAATTGAT-TTTACTGAATAACTAAATTACTGTATTG
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* *
29977695 AATAATTGATAGTTATTGAATAACTAAACTACTACACTA
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* * * ** *
29977734 AATATTTGATAGTTACTAAATGACTAAATTACTGTACTG
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* *
29977773 AATAACTGATTGTTACTGA
1 AATAATTGATAGTTACTGA
29977792 TTAAATATGA
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
38 10 0.13
39 67 0.87
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (39 bp):
AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
Found at i:29977764 original size:78 final size:77
Alignment explanation
Indices: 29977642--29977787 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 77
29977632 TTAATAGGGG
** * * * * *
29977642 TAAACTACTGTACTGAATAATTGATTTTACTGAATAACTAAATTACTGTATTGAATAATTGATAG
1 TAAACTACTACACTAAATAATTGATGTTACTAAATAACTAAATTACTGTACTGAATAACTGATAG
29977707 TTATTGAATAAC
66 TTATTGAATAAC
* * *
29977719 TAAACTACTACACTAAATATTTGATAGTTACTAAATGACTAAATTACTGTACTGAATAACTGATT
1 TAAACTACTACACTAAATAATTGAT-GTTACTAAATAACTAAATTACTGTACTGAATAACTGATA
29977784 GTTA
65 GTTA
29977788 CTGATTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
77 21 0.36
78 37 0.64
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (77 bp):
TAAACTACTACACTAAATAATTGATGTTACTAAATAACTAAATTACTGTACTGAATAACTGATAG
TTATTGAATAAC
Found at i:29979282 original size:13 final size:13
Alignment explanation
Indices: 29979264--29979290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29979254 TCACTCTACC
29979264 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
29979277 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
29979290 T
1 T
29979291 CACCCAACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTTAT
Found at i:29983406 original size:12 final size:12
Alignment explanation
Indices: 29983389--29983416 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29983379 CACTATTAAC
29983389 CGATTTTTGAAT
1 CGATTTTTGAAT
29983401 CGATTTTTGAAT
1 CGATTTTTGAAT
29983413 CGAT
1 CGAT
29983417 CTTTAACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (12 bp):
CGATTTTTGAAT
Found at i:29991383 original size:219 final size:224
Alignment explanation
Indices: 29990976--29991415 Score: 746
Period size: 219 Copynumber: 2.0 Consensus size: 224
29990966 TTTGCTTTCA
29990976 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTTTGGTGCTATGAATCA
1 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCA---T--T-CTATGAATCA
29991041 AATGCTGTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTAC
60 AATGCTGTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTAC
*
29991106 ATTTTGTCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAGTGGTTTTGATAAAAAA
125 ATTTTGTCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAA
29991171 AAAAATTGTATCAAACAAGCTCTCTGGAGCTTTGG
190 AAAAATTGTATCAAACAAGCTCTCTGGAGCTTTGG
29991206 GACTTGGGTGGCGGGC-T-AATGGTTATGCTGTAATGCTTAATCTCA-T-T-TGAATCAAATGCT
1 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTCTATGAATCAAATGCT
* *
29991266 GTTATGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTATATTTTG
66 GTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTACATTTTG
* *
29991331 TCATTGCATTGAAGCACCTAGCTGGTGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAGAAAAT
131 TCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAAAAAAT
29991396 TGTATCAAACAAGCTCTCTG
196 TGTATCAAACAAGCTCTCTG
29991416 TTGCAACTTA
Statistics
Matches: 205, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
219 158 0.77
220 1 0.00
222 1 0.00
228 28 0.14
229 1 0.00
230 16 0.08
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (224 bp):
GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTCTATGAATCAAATGCT
GTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTACATTTTG
TCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAAAAAAT
TGTATCAAACAAGCTCTCTGGAGCTTTGG
Found at i:29993681 original size:111 final size:110
Alignment explanation
Indices: 29993441--29993739 Score: 494
Period size: 111 Copynumber: 2.7 Consensus size: 110
29993431 TAATTGTAAA
* *
29993441 ACATTTGAGGCTCTTGTTGTTATGTGTATAGTTTGGAGTGGCAGAG-TAAAATT-TTCCCATTAA
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAG-GTTAAAATTCTTCCCATTAA
* *
29993504 TCATATCATCCTGAAGTTCTCATAATTGTGGAGATTTTAAGTTTCC
65 TCATACCATCCTGAAGTTCTCATAATTCTGGAGATTTTAAGTTTCC
*
29993550 ACATTTGAGGCTCTTTTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
29993615 CATACCATCCTGAAGTTCTCATAAATTCTGGAGATTTTAAGTTTCC
66 CATACCATCCTGAAGTTCTCAT-AATTCTGGAGATTTTAAGTTTCC
*
29993661 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGATTAAAATTCTTCCCATTAAT
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
*
29993726 AAATACCATCCTGA
66 -CATACCATCCTGA
29993740 TTAAAGTTTC
Statistics
Matches: 178, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
108 1 0.01
109 48 0.27
110 32 0.18
111 85 0.48
112 12 0.07
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (110 bp):
ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
CATACCATCCTGAAGTTCTCATAATTCTGGAGATTTTAAGTTTCC
Found at i:29994991 original size:37 final size:37
Alignment explanation
Indices: 29994941--29995015 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
29994931 GATGCTTGAC
29994941 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
29994978 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
29995015 T
1 T
29995016 CAGTGTGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (37 bp):
TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
Found at i:29995665 original size:27 final size:27
Alignment explanation
Indices: 29995635--29995686 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
29995625 ATAGAATAGC
*
29995635 TGGTAATGAATTTGTGTTATCTGGTCT
1 TGGTAATGAAATTGTGTTATCTGGTCT
*
29995662 TGGTAATGAAATTGTGTTGTCTGGT
1 TGGTAATGAAATTGTGTTATCTGGT
29995687 TTTGATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.46
Consensus pattern (27 bp):
TGGTAATGAAATTGTGTTATCTGGTCT
Found at i:29996204 original size:13 final size:13
Alignment explanation
Indices: 29996186--29996211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29996176 ATGTTAGTAA
29996186 CAGTCGATGCCTT
1 CAGTCGATGCCTT
29996199 CAGTCGATGCCTT
1 CAGTCGATGCCTT
29996212 AGGTTTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
CAGTCGATGCCTT
Found at i:30002205 original size:8 final size:9
Alignment explanation
Indices: 30002189--30002213 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30002179 TTTTATATTC
30002189 AATTTTTTT
1 AATTTTTTT
30002198 AATTTTTTT
1 AATTTTTTT
30002207 AATTTTT
1 AATTTTT
30002214 ATTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
AATTTTTTT
Found at i:30003510 original size:35 final size:35
Alignment explanation
Indices: 30003464--30003534 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
30003454 CCTCATCTTC
* *
30003464 CTCTATTTGAGCATTTGAGGGTAAAGCCGAATTAT
1 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
30003499 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
1 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
30003534 C
1 C
30003535 ATTGGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (35 bp):
CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
Found at i:30012052 original size:41 final size:41
Alignment explanation
Indices: 30012007--30012089 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
30011997 TTGTCAAAAT
* *
30012007 GAGATTTTTAAATTAATTTGGCCATTAATTTTAAAATTTGA
1 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
30012048 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
1 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
30012089 G
1 G
30012090 GCGAAACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (41 bp):
GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
Found at i:30013064 original size:11 final size:11
Alignment explanation
Indices: 30013050--30013079 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30013040 TTAGCCTATC
30013050 ATTAATTAGAA
1 ATTAATTAGAA
*
30013061 ATTAATTAGGA
1 ATTAATTAGAA
30013072 ATTAATTA
1 ATTAATTA
30013080 CTAGATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (11 bp):
ATTAATTAGAA
Found at i:30013470 original size:19 final size:22
Alignment explanation
Indices: 30013430--30013470 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
30013420 AAACCGAGTA
30013430 CTCAGAAAATTTTTCGCAAAAT
1 CTCAGAAAATTTTTCGCAAAAT
30013452 CTCA-AAAA-TTTTC-CAAAAT
1 CTCAGAAAATTTTTCGCAAAAT
30013471 GCAAGGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 4 0.21
22 4 0.21
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (22 bp):
CTCAGAAAATTTTTCGCAAAAT
Found at i:30015736 original size:20 final size:20
Alignment explanation
Indices: 30015711--30015748 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30015701 CTAGGAACTA
30015711 TGTGTTCTGAGCTCATGAGT
1 TGTGTTCTGAGCTCATGAGT
*
30015731 TGTGTTCTGAGTTCATGA
1 TGTGTTCTGAGCTCATGA
30015749 TGTATGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (20 bp):
TGTGTTCTGAGCTCATGAGT
Found at i:30017951 original size:24 final size:25
Alignment explanation
Indices: 30017910--30017964 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
30017900 GCTTATTCGG
30017910 GCTTAATAGCAGAAAGCTCATAAGA
1 GCTTAATAGCAGAAAGCTCATAAGA
* **
30017935 GCTTAA-ATCAGAAAGCTCATGCGA
1 GCTTAATAGCAGAAAGCTCATAAGA
30017959 GCTTAA
1 GCTTAA
30017965 CAGGTAACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
GCTTAATAGCAGAAAGCTCATAAGA
Found at i:30019920 original size:23 final size:24
Alignment explanation
Indices: 30019894--30019938 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30019884 GGAGTTCAAG
*
30019894 AGAGCC-ATGTCAGGAAGCTCATA
1 AGAGCCTATATCAGGAAGCTCATA
*
30019917 AGAGCCTATATCAGGATGCTCA
1 AGAGCCTATATCAGGAAGCTCA
30019939 CGTAGAGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
AGAGCCTATATCAGGAAGCTCATA
Found at i:30023110 original size:39 final size:39
Alignment explanation
Indices: 30022906--30023128 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
30022896 TTGAATGCTG
* * * * *
30022906 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
30022946 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
30022985 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
30023026 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
30023066 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * * *
30023105 ACCGGGCTATGTCTCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
30023129 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:30026341 original size:52 final size:49
Alignment explanation
Indices: 30026278--30026439 Score: 170
Period size: 52 Copynumber: 3.3 Consensus size: 49
30026268 CGACGGAAAA
* *
30026278 GATGTGATATGTGCACCCGTTTAAGACCATAGTTGGGCTATGGCATCGGT
1 GATGTGATATGTG-ACCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
* * *
30026328 GCAATGTGATATGTGTTCCCGTATAAGACCAAAGCTGGGATATGGCATCGGT
1 G--ATGTGATATGTG-ACCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
* * * *
30026380 G-TGTG--ATGTGATCCGTGTAAGACCATAGCAGGGCTATGGCTTCGGT
1 GATGTGATATGTGACCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
*
30026426 G-TGTGATGTGTGAC
1 GATGTGATATGTGAC
30026440 AATGTGAAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
46 34 0.37
47 5 0.05
48 5 0.05
49 4 0.04
50 1 0.01
52 44 0.47
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (49 bp):
GATGTGATATGTGACCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
Found at i:30026402 original size:46 final size:47
Alignment explanation
Indices: 30026293--30026435 Score: 162
Period size: 46 Copynumber: 3.0 Consensus size: 47
30026283 GATATGTGCA
* * *
30026293 CCCGTTTAAGACCATAGTTGGGCTATGGCATCGGTGCAATGTGATATGTGTT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG---TGTG--ATGTGAT
* *
30026345 CCCGTATAAGACCAAAGCTGGGATATGGCATCGGTGTGTGATGTGAT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTGAT
* * *
30026392 -CCGTGTAAGACCATAGCAGGGCTATGGCTTCGGTGTGTGATGTG
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTG
30026436 TGACAATGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
46 39 0.48
47 6 0.07
49 4 0.05
52 32 0.40
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (47 bp):
CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTGAT
Found at i:30029323 original size:46 final size:46
Alignment explanation
Indices: 30029223--30029346 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 46
30029213 GGTTGAGCAT
***
30029223 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGAGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACAC
* ** *
30029268 CTGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCGAACAC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACAC
*
30029314 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
30029347 AGGGCGGGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 27 0.40
46 40 0.60
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACAC
Found at i:30034989 original size:95 final size:95
Alignment explanation
Indices: 30034814--30035003 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
30034804 GCACTTGTAA
30034814 AAGTGTTGTGGAAAAAGCATGGGGTAGAAGAGACTACATGGGAACCTGAAGAAACTATGAGAAAC
1 AAGTGTTGTGGAAAAAGCATGGGGTAGAAGAGACTACATGGGAACCTGAAGAAACTATGAGAAAC
30034879 CAATATCCACACTGTTTACCGGTAAGATTT
66 CAATATCCACACTGTTTACCGGTAAGATTT
30034909 AAGTGTTGTGGAAAAAGCATGGGGTAGAAGAGACTACATGGGAACCTGAAGAAACTATGAG-AAC
1 AAGTGTTGTGGAAAAAGCATGGGGTAGAAGAGACTACATGGGAACCTGAAGAAACTATGAGAAAC
30034973 CAATATCCACACCTGTTTACCGGTAAGATTT
66 CAATATCCACA-CTGTTTACCGGTAAGATTT
30035004 TCGAGGACGA
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 14 0.15
95 80 0.85
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (95 bp):
AAGTGTTGTGGAAAAAGCATGGGGTAGAAGAGACTACATGGGAACCTGAAGAAACTATGAGAAAC
CAATATCCACACTGTTTACCGGTAAGATTT
Found at i:30036487 original size:93 final size:93
Alignment explanation
Indices: 30036328--30036499 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
30036318 GGATGGTTGA
***
30036328 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACACCCGAACTCGTTGAGT
30036393 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
** * * *
30036421 GCATCCGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACACCCGAACTCGTTGAGT
30036486 TGAGTCCGAGTTCA
66 TGAGTCCGAGTTCA
30036500 CTTAAGGGCG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:30036501 original size:46 final size:45
Alignment explanation
Indices: 30036332--30036503 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
30036322 GGTTGAGCAT
* ***
30036332 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACAC
* *
30036378 CCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC-A--C
**
30036423 ATCCGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCGAACAC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACAC
*
30036471 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
30036504 AGGGCGGGTT
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 1 0.01
46 59 0.57
47 27 0.26
48 3 0.03
50 5 0.05
51 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACAC
Found at i:30045856 original size:50 final size:50
Alignment explanation
Indices: 30045781--30045878 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
30045771 TTCTAGGTAC
*
30045781 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTGT
1 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTTGT
* *
30045831 TGAAGTTAAATTAATCTCAGAACAGACCAGATTAAGAATGATACCTTT
1 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTT
30045879 TTTTGTATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (50 bp):
TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTTGT
Found at i:30058579 original size:75 final size:75
Alignment explanation
Indices: 30058482--30058620 Score: 217
Period size: 75 Copynumber: 1.9 Consensus size: 75
30058472 ATTTGATTAT
* * * *
30058482 AAAATTAATAAATTGTTTATAATTTAAAATTTATGCCACCTATATTTAAAAAATT-ACTTCATTT
1 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAAC-TCATTT
30058546 TTTCAAAAAAA
65 TTTCAAAAAAA
*
30058557 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAACAATTAACTCATTT
1 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAACTCATTT
30058621 CTATATTCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 56 0.97
76 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (75 bp):
AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAACTCATTTT
TTCAAAAAAA
Found at i:30059122 original size:87 final size:86
Alignment explanation
Indices: 30058952--30059130 Score: 295
Period size: 86 Copynumber: 2.1 Consensus size: 86
30058942 AATCTTTCTT
* * * * *
30058952 CATCAATGGCCTTTGCTACGTGGGCATCCCTCATACTAAAAAAGGAGAGGATTCTAACCTGAAAG
1 CATCAATGGCCTTTGCTACATGGGCATCCCTCATACTAAAAAAAGAGAAGATTCTAACATGAAAA
30059017 TATCGAGTGAGTGAAGCTTAA
66 TATCGAGTGAGTGAAGCTTAA
*
30059038 CATCAATGGCCTTTGTTACATGGGCATCCCTCATACTAAAAAAAGAGAAGATTTCTAACATGAAA
1 CATCAATGGCCTTTGCTACATGGGCATCCCTCATACTAAAAAAAGAGAAGA-TTCTAACATGAAA
30059103 ATATCGAGTGAGTGAAGCTTAA
65 ATATCGAGTGAGTGAAGCTTAA
30059125 CATCAA
1 CATCAA
30059131 AGGTTAAAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
86 47 0.55
87 39 0.45
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (86 bp):
CATCAATGGCCTTTGCTACATGGGCATCCCTCATACTAAAAAAAGAGAAGATTCTAACATGAAAA
TATCGAGTGAGTGAAGCTTAA
Found at i:30061411 original size:11 final size:11
Alignment explanation
Indices: 30061395--30061438 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
30061385 TAGAAGAATG
30061395 GAATTGAAATT
1 GAATTGAAATT
*
30061406 GAATTGAAGAATG
1 GAATTG-A-AATT
30061419 GAATTGAAATT
1 GAATTGAAATT
30061430 GAATTGAAA
1 GAATTGAAA
30061439 AATGAAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 18 0.62
12 2 0.07
13 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (11 bp):
GAATTGAAATT
Found at i:30061415 original size:24 final size:24
Alignment explanation
Indices: 30061387--30061442 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
30061377 GAGGGTTGTA
30061387 GAAGAATGGAATTGAAATTGAATT
1 GAAGAATGGAATTGAAATTGAATT
30061411 GAAGAATGGAATTGAAATTGAATT
1 GAAGAATGGAATTGAAATTGAATT
*
30061435 GAAAAATG
1 GAAGAATG
30061443 AAGCTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (24 bp):
GAAGAATGGAATTGAAATTGAATT
Found at i:30061424 original size:13 final size:13
Alignment explanation
Indices: 30061387--30061426 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
30061377 GAGGGTTGTA
30061387 GAAGAATGGAATT
1 GAAGAATGGAATT
*
30061400 G-A-AATTGAATT
1 GAAGAATGGAATT
30061411 GAAGAATGGAATT
1 GAAGAATGGAATT
30061424 GAA
1 GAA
30061427 ATTGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
13 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (13 bp):
GAAGAATGGAATT
Found at i:30061441 original size:13 final size:13
Alignment explanation
Indices: 30061401--30061441 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
30061391 AATGGAATTG
30061401 AAATTGAATTGAA
1 AAATTGAATTGAA
* *
30061414 GAATGGAATTG--
1 AAATTGAATTGAA
30061425 AAATTGAATTGAA
1 AAATTGAATTGAA
30061438 AAAT
1 AAAT
30061442 GAAGCTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (13 bp):
AAATTGAATTGAA
Found at i:30061569 original size:26 final size:26
Alignment explanation
Indices: 30061540--30061622 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
30061530 AATAAAATTG
30061540 ATATATTGTGGTAATAAGCTATTAAA
1 ATATATTGTGGTAATAAGCTATTAAA
** * *
30061566 ATATATT-CAG-AAT-TG--ATAAAA
1 ATATATTGTGGTAATAAGCTATTAAA
30061587 TTGATATATTGTGGTAATAAGCTATTAAA
1 ---ATATATTGTGGTAATAAGCTATTAAA
30061616 ATATATT
1 ATATATT
30061623 CAGAATTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
21 5 0.12
23 1 0.02
24 10 0.24
25 2 0.05
26 17 0.41
27 1 0.02
29 5 0.12
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (26 bp):
ATATATTGTGGTAATAAGCTATTAAA
Found at i:30061606 original size:50 final size:50
Alignment explanation
Indices: 30061531--30061639 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
30061521 GTAAAATGGA
30061531 ATAAAATTGATATATTGTGGTAATAAGCTATTAAAATATATTCAGAATTG
1 ATAAAATTGATATATTGTGGTAATAAGCTATTAAAATATATTCAGAATTG
30061581 ATAAAATTGATATATTGTGGTAATAAGCTATTAAAATATATTCAGAATTG
1 ATAAAATTGATATATTGTGGTAATAAGCTATTAAAATATATTCAGAATTG
30061631 AT-AAATTGA
1 ATAAAATTGA
30061640 AATGAATTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 7 0.12
50 52 0.88
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.38
Consensus pattern (50 bp):
ATAAAATTGATATATTGTGGTAATAAGCTATTAAAATATATTCAGAATTG
Found at i:30066230 original size:47 final size:45
Alignment explanation
Indices: 30066159--30066303 Score: 137
Period size: 47 Copynumber: 3.1 Consensus size: 45
30066149 CATGGAAACA
* * *
30066159 TGTGATATGTGATTTCCGTATAAGACCATAGTAGGGCTATGGCATCGG
1 TGTGATATGTGA--TCCATGTAAGACTATAGT-GGGCTATGGCATCGG
* * * * **
30066207 TGTGATATGTGCTTCTATGTAAGACTATATCTGGGATATGGCATTAG
1 TGTGATATGTG-ATCCATGTAAGACTATA-GTGGGCTATGGCATCGG
* *
30066254 TGTGATATGTGATCCATGTAAGACTATGGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATCCATGTAAGACTATAG-TGGGCTATGGCATCGG
30066300 TGTG
1 TGTG
30066304 TGATATATGA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
46 30 0.39
47 35 0.45
48 12 0.16
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (45 bp):
TGTGATATGTGATCCATGTAAGACTATAGTGGGCTATGGCATCGG
Found at i:30071224 original size:18 final size:18
Alignment explanation
Indices: 30071201--30071235 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30071191 TCAAGTTGTG
30071201 TTTTTAAGTTATCTTTTT
1 TTTTTAAGTTATCTTTTT
*
30071219 TTTTTAAGTTATGTTTT
1 TTTTTAAGTTATCTTTT
30071236 ATGCATGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTAAGTTATCTTTTT
Found at i:30074646 original size:16 final size:16
Alignment explanation
Indices: 30074627--30074657 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30074617 CTTCTTCACT
30074627 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
30074643 TACTTACTTACTTAA
1 TACTCACTTACTTAA
30074658 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:30074663 original size:20 final size:20
Alignment explanation
Indices: 30074624--30074663 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30074614 AAACTTCTTC
* *
30074624 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
30074644 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
30074664 TTATTAATAC
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:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:30074984 original size:53 final size:54
Alignment explanation
Indices: 30074849--30075103 Score: 229
Period size: 55 Copynumber: 4.8 Consensus size: 54
30074839 ACACGGGTAC
* * * * *
30074849 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGGAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
30074898 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * * * *
30074951 CTCACCAATGCCATGCCTTGGCATCGTCCTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * * *
30075006 CTTATCAATGCCATGTCTTGACATGGTCTTGCATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
30075059 CCTTACCAATTTCCATGCCTTGGCATGCTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
30075104 AAACCCTAAT
Statistics
Matches: 166, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
49 38 0.23
50 1 0.01
52 2 0.01
53 47 0.28
54 10 0.06
55 66 0.40
56 2 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Done.