Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 73 of 135
Found at i:28667318 original size:44 final size:44
Alignment explanation
Indices: 28667270--28667367 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
28667260 TAGAAAAATA
28667270 CCACAAAGGCCAAATCAAAATACGCCACAAATGCTAACAGAATG
1 CCACAAAGGCCAAATCAAAATACGCCACAAATGCTAACAGAATG
* * *
28667314 CCACAAAGGCCAAATCAGAATACGCCATAAATGCTAGCAGAATG
1 CCACAAAGGCCAAATCAAAATACGCCACAAATGCTAACAGAATG
28667358 CCACAAAGGC
1 CCACAAAGGC
28667368 TAGCAGAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.45, C:0.28, G:0.16, T:0.11
Consensus pattern (44 bp):
CCACAAAGGCCAAATCAAAATACGCCACAAATGCTAACAGAATG
Found at i:28667387 original size:20 final size:20
Alignment explanation
Indices: 28667293--28667377 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
28667283 ATCAAAATAC
* *
28667293 GCCACAAATGCTAACAGAAT
1 GCCACAAAGGCTAGCAGAAT
* *
28667313 GCCACAAAGGCCAAATCAGAAT
1 GCCACAAAGG-C-TAGCAGAAT
* *
28667335 ACGCCATAAATGCTAGCAGAAT
1 --GCCACAAAGGCTAGCAGAAT
28667357 GCCACAAAGGCTAGCAGAAT
1 GCCACAAAGGCTAGCAGAAT
28667377 G
1 G
28667378 TCACTCAGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 28 0.54
21 1 0.02
22 14 0.27
23 1 0.02
24 8 0.15
ACGTcount: A:0.42, C:0.25, G:0.20, T:0.13
Consensus pattern (20 bp):
GCCACAAAGGCTAGCAGAAT
Found at i:28672616 original size:52 final size:50
Alignment explanation
Indices: 28672551--28672729 Score: 186
Period size: 51 Copynumber: 3.5 Consensus size: 50
28672541 AAAGGTCGCA
* * *
28672551 TGTGTGGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGAATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTAACGGATAG-TT-GAATCACG
*
28672603 TGTGTAGTACTATGTGTAGGCTACTATGTGTAACGGATA-TT-AATGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTAACGGATAGTTGAA---TCACG
* * * *
28672654 TGTGTAGTACGATGTGCAGGCTACTACGTG-AACCAGAAAGTTTG-ATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTAA-CGGATAG-TTGAATCACG
*
28672704 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
28672730 CGTATATCGA
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
48 2 0.02
50 33 0.30
51 36 0.33
52 35 0.32
53 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTAACGGATAGTTGAATCACG
Found at i:28672719 original size:50 final size:50
Alignment explanation
Indices: 28672496--28672732 Score: 190
Period size: 50 Copynumber: 4.7 Consensus size: 50
28672486 AAAGTGATGG
* * * * * *** *
28672496 TCACGTGTGTAGTACTATGTGTAGACTACTACATGTACCGGAATGAAAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGTTTGA
* * * * * * * * *
28672546 TCGCATGTGTGGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGAA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAG-TTTG-A
* * * *
28672598 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTAA-CGGATA-TTAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTG-AACCGGAAAGTT--TGA
* *
28672649 TCACGTGTGTAGTACGATGTGCAGGCTACTACGTGAACCAGAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGTTTGA
*
28672699 TCACGTGTGTAGTACTATGTGAAGGCTACTACGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGT
28672733 ATATCGAATG
Statistics
Matches: 149, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
50 72 0.48
51 37 0.25
52 39 0.26
53 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGTTTGA
Found at i:28672770 original size:101 final size:103
Alignment explanation
Indices: 28672496--28672772 Score: 294
Period size: 101 Copynumber: 2.7 Consensus size: 103
28672486 AAAGTGATGG
* * * *
28672496 TCACGTGTGTAGTACTATGTGTAGACTACTACATGTACCGGAATGA-AA-GGTCGCATGTGTGGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTAAC-GAATGATAATGGTCACATGTGTGGT
* * * * *
28672559 ACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGAA
65 ACTATGTGCAGGCTACTACGCGAACCAGAAAGCTTCGAA
* * * *
28672598 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTAACGGAT-ATTAATGGTCACGTGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTAACGAATGA-TAATGGTCACATGTGTGGT
* * *
28672662 ACGATGTGCAGGCTACTACGTGAACCAGAAAG-TTTG-A
65 ACTATGTGCAGGCTACTACGCGAACCAGAAAGCTTCGAA
* * * * * * *
28672699 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTATATCGAATGATAATAGTTAAATGAGTGGTA
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTAACGAATGATAATGGTCACATGTGTGGTA
28672764 CTATGTGCA
66 CTATGTGCA
28672773 AGCCACTGAA
Statistics
Matches: 143, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
100 1 0.01
101 64 0.45
102 41 0.29
103 37 0.26
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (103 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTAACGAATGATAATGGTCACATGTGTGGTA
CTATGTGCAGGCTACTACGCGAACCAGAAAGCTTCGAA
Found at i:28676519 original size:23 final size:23
Alignment explanation
Indices: 28676481--28676553 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
28676471 ATCTACATTG
*
28676481 TTTGGACAACTCTTATACATC-AA
1 TTTGGACAGCT-TTATACATCAAA
*
28676504 TTTGGACAGCATTTATATATCAAAA
1 TTTGGACAGC-TTTATACATC-AAA
*
28676529 TTTGGACAGCTTATATACAGCAAA
1 TTTGGACAGCTT-TATACATCAAA
28676553 T
1 T
28676554 AGACAGCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 17 0.40
24 7 0.17
25 18 0.43
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (23 bp):
TTTGGACAGCTTTATACATCAAA
Found at i:28676616 original size:24 final size:23
Alignment explanation
Indices: 28676534--28676616 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 23
28676524 CAAAATTTGG
* *
28676534 ACAGCTTATATACAGCAAA--TA
1 ACAGCATATATACACCAAATTTA
* *
28676555 GACAGCATATACATACCAAATTTA
1 -ACAGCATATATACACCAAATTTA
* *
28676579 ACAACACT-TTTACACCAAAATTTA
1 ACAGCA-TATATACACC-AAATTTA
28676603 ACAGCATATATACA
1 ACAGCATATATACA
28676617 ATACATCATA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
22 15 0.33
23 11 0.24
24 20 0.43
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (23 bp):
ACAGCATATATACACCAAATTTA
Found at i:28677222 original size:41 final size:41
Alignment explanation
Indices: 28677174--28677345 Score: 211
Period size: 41 Copynumber: 4.2 Consensus size: 41
28677164 ATTTATAGAA
** *
28677174 CATAAAGCCTTG-TATAAAACACCGGCATAAAGCCTGCTAGG
1 CATAAAGCC-TGATATAATTCACCGGCACAAAGCCTGCTAGG
* * * * * *
28677215 CACAAAGCCCGATACATTTCACCGGCACAAAGCATGCTAGA
1 CATAAAGCCTGATATAATTCACCGGCACAAAGCCTGCTAGG
* * *
28677256 CATAAAGTCTGATATAATTCACCGGCACAGAGTCTGCTAGG
1 CATAAAGCCTGATATAATTCACCGGCACAAAGCCTGCTAGG
*
28677297 CATAAAGCCTGATATAATTCACCGGCATAAAGCCTGCTAGG
1 CATAAAGCCTGATATAATTCACCGGCACAAAGCCTGCTAGG
28677338 CATAAAGC
1 CATAAAGC
28677346 TTGAACTTAC
Statistics
Matches: 108, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 107 0.99
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (41 bp):
CATAAAGCCTGATATAATTCACCGGCACAAAGCCTGCTAGG
Found at i:28678202 original size:3 final size:3
Alignment explanation
Indices: 28678194--28678242 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
28678184 TTGTCTTCTC
28678194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28678242 T
1 T
28678243 AACTTTATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28680890 original size:19 final size:18
Alignment explanation
Indices: 28680858--28680893 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28680848 AAAAGTATTC
28680858 CAAAGTTTTCATTTAAGT
1 CAAAGTTTTCATTTAAGT
*
28680876 CAAAGGTTTTTATTTAAG
1 CAAA-GTTTTCATTTAAG
28680894 ATAGTAGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (18 bp):
CAAAGTTTTCATTTAAGT
Found at i:28681277 original size:11 final size:11
Alignment explanation
Indices: 28681261--28681290 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28681251 CTTTTTGAAG
28681261 TTATTAATAAT
1 TTATTAATAAT
28681272 TTATTAATAAT
1 TTATTAATAAT
*
28681283 TTAATAAT
1 TTATTAAT
28681291 CTTAGATGAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTAATAAT
Found at i:28682647 original size:50 final size:51
Alignment explanation
Indices: 28682572--28682671 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
28682562 TATTTTTTTT
* * *
28682572 TTTATAATTTGGAGGTTTGACTGTGTAAGTGAATATTCTAGAA-TAAAAAA
1 TTTATAATTGGGAAGTTTGACTGTGTAAGTGAAGATTCTAGAACTAAAAAA
*
28682622 TTTATAATTGGGAAGTTTGATTGTGTAAGTGAAGATTCTAGAACTAAAAA
1 TTTATAATTGGGAAGTTTGACTGTGTAAGTGAAGATTCTAGAACTAAAAA
28682672 TTTGAATCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 39 0.87
51 6 0.13
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (51 bp):
TTTATAATTGGGAAGTTTGACTGTGTAAGTGAAGATTCTAGAACTAAAAAA
Found at i:28687661 original size:88 final size:88
Alignment explanation
Indices: 28687569--28687825 Score: 238
Period size: 88 Copynumber: 3.1 Consensus size: 88
28687559 TTACATTTTG
28687569 TATTATAAAAATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGAT
1 TATTATAAAAATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGAT
28687634 ATTTAAAATAATTTTATAGTTAC
66 ATTTAAAATAATTTTATAGTTAC
** * ** * * * *
28687657 TA-T-TAATCATTAT-C-A-AGAATTTATGAATT--AAT--TATTAATTAT-TA-TAT--TATAA
1 TATTATAAAAATTATGCTACATAATGAAT-AATTCCTATGCTATCAATAATGTACTATGATATGA
*** * * **
28687709 AGCTTAAAGTATAA--TTACATTTTG
65 TATTTAAA--ATAATTTTATAGTTAC
28687733 TATTATAAAAATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGAT
1 TATTATAAAAATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGAT
28687798 ATTTAAAATAATTTTATAGTTAC
66 ATTTAAAATAATTTTATAGTTAC
28687821 TATTA
1 TATTA
28687826 ATCATTATCA
Statistics
Matches: 119, Mismatches: 32, Indels: 36
0.64 0.17 0.19
Matches are distributed among these distances:
76 17 0.14
77 1 0.01
78 15 0.13
79 3 0.03
80 13 0.11
81 6 0.05
82 4 0.03
83 6 0.05
84 13 0.11
85 3 0.03
86 15 0.13
87 1 0.01
88 22 0.18
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (88 bp):
TATTATAAAAATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGAT
ATTTAAAATAATTTTATAGTTAC
Found at i:28687705 original size:164 final size:165
Alignment explanation
Indices: 28687514--28687844 Score: 655
Period size: 164 Copynumber: 2.0 Consensus size: 165
28687504 ATGTCACTCG
28687514 ATGAATTAATCTATTAATTATTATATTATAAAGCTTAAAGTATAATTACATTTTGTATTATAAAA
1 ATGAATTAATCTATTAATTATTATATTATAAAGCTTAAAGTATAATTACATTTTGTATTATAAAA
28687579 ATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGATATTTAAAATA
66 ATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGATATTTAAAATA
28687644 ATTTTATAGTTACTATTAATCATTATCAAGAATTT
131 ATTTTATAGTTACTATTAATCATTATCAAGAATTT
28687679 ATGAATTAAT-TATTAATTATTATATTATAAAGCTTAAAGTATAATTACATTTTGTATTATAAAA
1 ATGAATTAATCTATTAATTATTATATTATAAAGCTTAAAGTATAATTACATTTTGTATTATAAAA
28687743 ATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGATATTTAAAATA
66 ATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGATATTTAAAATA
28687808 ATTTTATAGTTACTATTAATCATTATCAAGAATTT
131 ATTTTATAGTTACTATTAATCATTATCAAGAATTT
28687843 AT
1 AT
28687845 TTTATTATGT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 156 0.94
165 10 0.06
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (165 bp):
ATGAATTAATCTATTAATTATTATATTATAAAGCTTAAAGTATAATTACATTTTGTATTATAAAA
ATTATGCTACATAATGAATAATTCCTATGCTATCAATAATGTACTATGATATGATATTTAAAATA
ATTTTATAGTTACTATTAATCATTATCAAGAATTT
Found at i:28690138 original size:89 final size:89
Alignment explanation
Indices: 28689987--28690167 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
28689977 CATATATGTA
* **
28689987 ATTTAAAGTATAATATCAATAAAAATAAATATATATTTTTAATTTGTTTTTTTTGTACATTTACA
1 ATTTAAAGTATAATATCAATAAAAATAAATATATATTTTTAATTTGCTTTTTACGTACATTTACA
*
28690052 TGTGAATTTTTAAAATATACTTTT
66 TGTGAATTTTTAAAATACACTTTT
28690076 ATTTAAAGTATAATATCAATAAAAATAAATATATATTTTTAATTTGCTTTTTACGTACATTTACA
1 ATTTAAAGTATAATATCAATAAAAATAAATATATATTTTTAATTTGCTTTTTACGTACATTTACA
28690141 TGTGAATTTTTAAAATACACTTTT
66 TGTGAATTTTTAAAATACACTTTT
28690165 ATT
1 ATT
28690168 AGTTAAAGTG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (89 bp):
ATTTAAAGTATAATATCAATAAAAATAAATATATATTTTTAATTTGCTTTTTACGTACATTTACA
TGTGAATTTTTAAAATACACTTTT
Found at i:28692252 original size:4 final size:4
Alignment explanation
Indices: 28692243--28692307 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
28692233 TTTTCTTTTC
*
28692243 TTTA TTTA TTTCA TTTA CTTA TTTA TTTTA TTATA TTTA CTTT- TTTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TT-TA TTTA -TTTA TTTA
*
28692290 TTTTA TTATA TATA TTTA
1 -TTTA TT-TA TTTA TTTA
28692308 CTTAAATGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
3 3 0.06
4 25 0.50
5 22 0.44
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:28692272 original size:22 final size:22
Alignment explanation
Indices: 28692243--28692300 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
28692233 TTTTCTTTTC
28692243 TTTA-TTTATT-TCATTTACTTA
1 TTTATTTTATTAT-ATTTACTTA
*
28692264 TTTATTTTATTATATTTACTTT
1 TTTATTTTATTATATTTACTTA
28692286 TTTATTTTATTATAT
1 TTTATTTTATTATAT
28692301 ATATTTACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 4 0.12
22 29 0.85
23 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATTTTATTATATTTACTTA
Found at i:28692272 original size:26 final size:24
Alignment explanation
Indices: 28692243--28692311 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 24
28692233 TTTTCTTTTC
28692243 TTTATTTATTTCATTTACTTATTTAT
1 TTTATTTA-TT-ATTTACTTATTTAT
*
28692269 TTTA-TTA-TATTTACTTTTTTAT
1 TTTATTTATTATTTACTTATTTAT
28692291 TTTATTATATATATTTACTTA
1 TTTATT-TAT-TATTTACTTA
28692312 AATGTTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 17 0.46
23 2 0.05
24 2 0.05
25 3 0.08
26 13 0.35
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTATTATTTACTTATTTAT
Found at i:28714946 original size:10 final size:10
Alignment explanation
Indices: 28714931--28714956 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28714921 AACATAGTAT
28714931 TACAATTTCA
1 TACAATTTCA
28714941 TACAATTTCA
1 TACAATTTCA
28714951 TACAAT
1 TACAAT
28714957 CCCTTCTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (10 bp):
TACAATTTCA
Found at i:28732828 original size:44 final size:43
Alignment explanation
Indices: 28732755--28732840 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
28732745 NNNNNNNNNN
* *
28732755 AATTATAATTATTTTAAATGTATTCTTATCAG-AACTTCTATTA
1 AATTATAATTATTTTAAATATATTATTATC-GCAACTTCTATTA
*
28732798 AATTGTAATTATTTTTAAATATATTATTATCGCAACTTCTATT
1 AATTATAATTA-TTTTAAATATATTATTATCGCAACTTCTATT
28732841 TTACTACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 11 0.29
44 27 0.71
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (43 bp):
AATTATAATTATTTTAAATATATTATTATCGCAACTTCTATTA
Found at i:28735089 original size:27 final size:28
Alignment explanation
Indices: 28735053--28735107 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
28735043 TTGTGAAGGA
*
28735053 AAAAATAAAGAAAGAG-AAAGAGAGAAAT
1 AAAAATAAAGAAAAAGAAAAGAG-GAAAT
28735081 AAAAA-AAAGAAAAAGAAAAGAGGAAAT
1 AAAAATAAAGAAAAAGAAAAGAGGAAAT
28735108 GGAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (28 bp):
AAAAATAAAGAAAAAGAAAAGAGGAAAT
Found at i:28735655 original size:7 final size:7
Alignment explanation
Indices: 28735642--28735675 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
28735632 TTTTTAATAC
28735642 CAAAATT
1 CAAAATT
*
28735649 TAAAATT
1 CAAAATT
28735656 CAAAATT
1 CAAAATT
*
28735663 CAAAATC
1 CAAAATT
28735670 CAAAAT
1 CAAAAT
28735676 GAAATTTGTT
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:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
CAAAATT
Found at i:28756320 original size:41 final size:41
Alignment explanation
Indices: 28756267--28756358 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
28756257 AAAAATTATA
* * *
28756267 TTTAATACAATAAAACATTTACTATATTTATGGTATTATTT
1 TTTAATATAATAAAACATTTACTATATTTATGGAAGTATTT
* * * *
28756308 TTTAATATAATAAAATATTTATTATATTTGTGGAAGTGTTT
1 TTTAATATAATAAAACATTTACTATATTTATGGAAGTATTT
28756349 TTTAATATAA
1 TTTAATATAA
28756359 ATACTTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (41 bp):
TTTAATATAATAAAACATTTACTATATTTATGGAAGTATTT
Found at i:28757376 original size:28 final size:26
Alignment explanation
Indices: 28757345--28757407 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
28757335 GTCCATATTA
*
28757345 TTTAT-TATTTTTAATTTAATTATAATAT
1 TTTATATATTTTTAATCT-ATTA-AA-AT
*
28757373 TTTATATGTTTTTAATCTATTAAAAT
1 TTTATATATTTTTAATCTATTAAAAT
28757399 TTTATATAT
1 TTTATATAT
28757408 AATTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.32
27 2 0.06
28 9 0.29
29 10 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATATATTTTTAATCTATTAAAAT
Found at i:28757405 original size:26 final size:29
Alignment explanation
Indices: 28757352--28757405 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
28757342 TTATTTATTA
*
28757352 TTTTTAATTTAATTATAATATTTTATATG
1 TTTTTAATCTAATTATAATATTTTATATG
28757381 TTTTTAATCT-ATTA-AA-ATTTTATAT
1 TTTTTAATCTAATTATAATATTTTATAT
28757406 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 4 0.17
29 9 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAATCTAATTATAATATTTTATATG
Found at i:28760876 original size:7 final size:7
Alignment explanation
Indices: 28760866--28760890 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28760856 TACATATTTT
28760866 TTATTAA
1 TTATTAA
28760873 TTATTAA
1 TTATTAA
28760880 TTATTAA
1 TTATTAA
28760887 TTAT
1 TTAT
28760891 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTAA
Found at i:28767689 original size:27 final size:26
Alignment explanation
Indices: 28767643--28767713 Score: 106
Period size: 27 Copynumber: 2.7 Consensus size: 26
28767633 AAATTAAAAA
*
28767643 TTACCAAAATGTTATAAATTTTTTTAT
1 TTACCAAAAT-ATATAAATTTTTTTAT
*
28767670 TTATCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATA-AATTTTTTTAT
28767697 TTACCAAAATATATAAA
1 TTACCAAAATATATAAA
28767714 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (26 bp):
TTACCAAAATATATAAATTTTTTTAT
Found at i:28767807 original size:27 final size:27
Alignment explanation
Indices: 28767777--28767896 Score: 204
Period size: 27 Copynumber: 4.4 Consensus size: 27
28767767 GGGAACACTA
* **
28767777 TTGGCGGCACCAAACAAGAGAACCCTG
1 TTGGCGGCACCAAACAAGGGTTCCCTG
28767804 TTGGCGGCACCAAACAAGGGTTCCCTG
1 TTGGCGGCACCAAACAAGGGTTCCCTG
28767831 TTGGCGGCACCAAACAAGGGTTCCCTG
1 TTGGCGGCACCAAACAAGGGTTCCCTG
28767858 TTGGCGGCACCAAACAAGGGTTCCCTG
1 TTGGCGGCACCAAACAAGGGTTCCCTG
*
28767885 TTGGCGACACCA
1 TTGGCGGCACCA
28767897 CTCGTGTTAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (27 bp):
TTGGCGGCACCAAACAAGGGTTCCCTG
Found at i:28768191 original size:3 final size:3
Alignment explanation
Indices: 28768183--28768232 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
28768173 AATTTTATAG
28768183 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28768231 TA
1 TA
28768233 AGATGTTAGN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28771747 original size:27 final size:27
Alignment explanation
Indices: 28771674--28771753 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
28771664 ATAACATGAG
**
28771674 TGGTGCCGCCAACAGGGAGCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
28771701 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
* *
28771728 TGGTGCCGCCAACAGTGTTCCATTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
28771754 CTCAGAGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:28771873 original size:27 final size:27
Alignment explanation
Indices: 28771810--28771883 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
28771800 GTTTTTTTTG
28771810 TTTTTTTATATATTTTGGTAAATAAAA
1 TTTTTTTATATATTTTGGTAAATAAAA
*** *
28771837 AAATTATATATATTTTGGTAAATAAAA
1 TTTTTTTATATATTTTGGTAAATAAAA
*
28771864 TTTTTTTATAACATTTTGGT
1 TTTTTTTAT-ATATTTTGGT
28771884 CATTTTTAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 28 0.76
28 9 0.24
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (27 bp):
TTTTTTTATATATTTTGGTAAATAAAA
Found at i:28782649 original size:2 final size:2
Alignment explanation
Indices: 28782642--28782672 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28782632 CAATGAAGAC
28782642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28782673 TATGAGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28783925 original size:18 final size:19
Alignment explanation
Indices: 28783888--28783924 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28783878 TTTTAAAAGA
28783888 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
28783906 TATAAATATTTGGAATTTT
1 TATAAATATTTGGAATTTT
28783925 AAAATTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:28787241 original size:3 final size:3
Alignment explanation
Indices: 28787233--28787260 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28787223 ATCAAGAGAA
28787233 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28787261 TACCTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28787885 original size:20 final size:20
Alignment explanation
Indices: 28787862--28787902 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28787852 TATACACTAT
28787862 ATAATAATTAAACCTTCCTA
1 ATAATAATTAAACCTTCCTA
28787882 ATAATAATTAAACCTTCCTA
1 ATAATAATTAAACCTTCCTA
28787902 A
1 A
28787903 AAACAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAATAATTAAACCTTCCTA
Found at i:28790252 original size:33 final size:33
Alignment explanation
Indices: 28790210--28790285 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
28790200 AATCAGTAAT
* *
28790210 GGTAACAGTATTCGACACACAAATTGCCGAATC
1 GGTAACAGTATTCGACACACAAAGTGCCAAATC
28790243 GGTAACAGTATTCGACACACAAAGTGCCAAATC
1 GGTAACAGTATTCGACACACAAAGTGCCAAATC
*
28790276 GGAAACAGTA
1 GGTAACAGTA
28790286 ACAGTAACAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (33 bp):
GGTAACAGTATTCGACACACAAAGTGCCAAATC
Found at i:28790293 original size:45 final size:45
Alignment explanation
Indices: 28790244--28790336 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
28790234 TGCCGAATCG
28790244 GTAACAGTATTCGACACACAAAGTGCCAAATCGGAAACAGTAACA
1 GTAACAGTATTCGACACACAAAGTGCCAAATCGGAAACAGTAACA
* * * *
28790289 GTAACAGTATTCGACACACAAAGTGCCGAATTGGTAACAGTAATA
1 GTAACAGTATTCGACACACAAAGTGCCAAATCGGAAACAGTAACA
28790334 GTA
1 GTA
28790337 GTCGGCACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (45 bp):
GTAACAGTATTCGACACACAAAGTGCCAAATCGGAAACAGTAACA
Found at i:28791390 original size:9 final size:9
Alignment explanation
Indices: 28791376--28791426 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
28791366 GCTTCTGCTG
*
28791376 TTCTTTTGT
1 TTCTTTTCT
28791385 TTCTTTTAC-
1 TTCTTTT-CT
28791394 TTC-TTTCT
1 TTCTTTTCT
28791402 TTCTTTTCT
1 TTCTTTTCT
**
28791411 TTCTTTAGT
1 TTCTTTTCT
28791420 TTCTTTT
1 TTCTTTT
28791427 ATTTACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 1 0.03
8 6 0.17
9 28 0.80
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:28791396 original size:26 final size:26
Alignment explanation
Indices: 28791367--28791416 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28791357 GTTCGAATGG
*
28791367 CTTC-TGCTGTTCTTTTGTTTCTTTTA
1 CTTCTTGCT-TTCTTTTCTTTCTTTTA
*
28791393 CTTCTTTCTTTCTTTTCTTTCTTT
1 CTTCTTGCTTTCTTTTCTTTCTTT
28791417 AGTTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.02, C:0.22, G:0.06, T:0.70
Consensus pattern (26 bp):
CTTCTTGCTTTCTTTTCTTTCTTTTA
Found at i:28798880 original size:19 final size:19
Alignment explanation
Indices: 28798856--28798894 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28798846 GTAGAAGGAA
28798856 GGAACAGAAGAGGCAAAGG
1 GGAACAGAAGAGGCAAAGG
*
28798875 GGAACAGAAGAGGCAGAGG
1 GGAACAGAAGAGGCAAAGG
28798894 G
1 G
28798895 TAAAGTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.46, T:0.00
Consensus pattern (19 bp):
GGAACAGAAGAGGCAAAGG
Found at i:28799373 original size:21 final size:21
Alignment explanation
Indices: 28799333--28799374 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28799323 AAATATTTAT
*
28799333 TTCAATTTATTTAATTTTGAA
1 TTCAATTTATTTAATGTTGAA
28799354 TTCAATTTAGTTT-ATGTTGAA
1 TTCAATTTA-TTTAATGTTGAA
28799375 AATAAAAAAA
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:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (21 bp):
TTCAATTTATTTAATGTTGAA
Found at i:28800821 original size:381 final size:382
Alignment explanation
Indices: 28800107--28800869 Score: 1519
Period size: 381 Copynumber: 2.0 Consensus size: 382
28800097 TGTTTTTAGT
28800107 TTATTTTATATTTGTTTTTATATTATTATCCTTATCAACTAAAACCCCACCTTTTTATTTATTTT
1 TTATTTTATATTTGTTTTTATATTATTATCCTTATCAACTAAAACCCCACCTTTTTATTTATTTT
28800172 TCAAAAATTTGATTACAAAAACAGGAAAATTAGAAATCCTAATTCCTTTGGGATCGACCTACTAC
66 TCAAAAATTTGATTACAAAAACAGGAAAATTAGAAATCCTAATTCCTTTGGGATCGACCTACTAC
28800237 TTTATACTACTATTTAATTAAGTTAGAACGTAGAAATTTATATTTGGTGGTCTCGACCCCATTAA
131 TTTATACTACTATTTAATTAAGTTAGAACGTAGAAATTTATATTTGGTGGTCTCGACCCCATTAA
28800302 AAGTTTATCCAACAAAGAATTGGAACAGTTGTGCTGTTGCTGATGGTGTCCAATGCCTTCTTCAG
196 AAGTTTATCCAACAAAGAATTGGAACAGTTGTGCTGTTGCTGATGGTGTCCAATGCCTTCTTCAG
28800367 TTGTGGAAGAAATCTGAAGGTATTGAAGGAGGGCAATACTTCTTTGCAACACATTTATACTGTGC
261 TTGTGGAAGAAATCTGAAGGTATTGAAGGAGGGCAATACTTCTTTGCAACACATTTATACTGTGC
28800432 CAAAAACAAAAAAAACAAAATTAAGACATTTCAGCTATGCAAAGCAGCAGCAAATAA
326 CAAAAACAAAAAAAACAAAATTAAGACATTTCAGCTATGCAAAGCAGCAGCAAATAA
28800489 TTATTTTATA-TTGTTTTTATATTATTATCCTTATCAACTAAAACCCCACCTTTTTATTTATTTT
1 TTATTTTATATTTGTTTTTATATTATTATCCTTATCAACTAAAACCCCACCTTTTTATTTATTTT
28800553 TCAAAAATTTGATTACAAAAACAGGAAAATTAGAAATCCTAATTCCTTTGGGATCGACCTACTAC
66 TCAAAAATTTGATTACAAAAACAGGAAAATTAGAAATCCTAATTCCTTTGGGATCGACCTACTAC
28800618 TTTATACTACTATTTAATTAAGTTAGAACGTAGAAATTTATATTTGGTGGTCTCGACCCCATTAA
131 TTTATACTACTATTTAATTAAGTTAGAACGTAGAAATTTATATTTGGTGGTCTCGACCCCATTAA
28800683 AAGTTTATCCAACAAAGAATTGGAACAGTTGTGCTGTTGCTGATGGTGTCCAATGCCTTCTTCAG
196 AAGTTTATCCAACAAAGAATTGGAACAGTTGTGCTGTTGCTGATGGTGTCCAATGCCTTCTTCAG
28800748 TTGTGGAAGAAATCTGAAGGTATTGAAGGAGGGCAATACTTCTTTGCAACACATTTATACTGTGC
261 TTGTGGAAGAAATCTGAAGGTATTGAAGGAGGGCAATACTTCTTTGCAACACATTTATACTGTGC
28800813 CAAAAACAAAAAAAACAAAATTAAGACATTTCAGCTATGCAAAGCAGCAGCAAATAA
326 CAAAAACAAAAAAAACAAAATTAAGACATTTCAGCTATGCAAAGCAGCAGCAAATAA
28800870 CATTTTACAG
Statistics
Matches: 381, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
381 371 0.97
382 10 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (382 bp):
TTATTTTATATTTGTTTTTATATTATTATCCTTATCAACTAAAACCCCACCTTTTTATTTATTTT
TCAAAAATTTGATTACAAAAACAGGAAAATTAGAAATCCTAATTCCTTTGGGATCGACCTACTAC
TTTATACTACTATTTAATTAAGTTAGAACGTAGAAATTTATATTTGGTGGTCTCGACCCCATTAA
AAGTTTATCCAACAAAGAATTGGAACAGTTGTGCTGTTGCTGATGGTGTCCAATGCCTTCTTCAG
TTGTGGAAGAAATCTGAAGGTATTGAAGGAGGGCAATACTTCTTTGCAACACATTTATACTGTGC
CAAAAACAAAAAAAACAAAATTAAGACATTTCAGCTATGCAAAGCAGCAGCAAATAA
Found at i:28806734 original size:165 final size:165
Alignment explanation
Indices: 28806550--28806869 Score: 577
Period size: 165 Copynumber: 1.9 Consensus size: 165
28806540 ATCATTTTTA
*
28806550 TTTCTTGTTACACTTTAATCACATATTTTATATTAATATATTGTTTCACATATCAATTTCTATAT
1 TTTCTTGTTACACTTTAATCACATATTTTATATTAATATATTGTTTCACATATCAATTTCTATAA
* * *
28806615 ATTTCACTTATATTATTTTATCCACATATTTTCTCAAGTTTGACAATTTAGTCCTTGTCATCATA
66 ATTTCACTTATACTATTTAATCCACATATTTTCTCAAGTTTAACAATTTAGTCCTTGTCATCATA
28806680 AAAAATCCATATTTTTCTACAATTTCACAGTTTCC
131 AAAAATCCATATTTTTCTACAATTTCACAGTTTCC
*
28806715 TTTCTTGTTACACTTTAATCACATATTTTATATTAATATATTGTTTCACGTATCAATTTCTATAA
1 TTTCTTGTTACACTTTAATCACATATTTTATATTAATATATTGTTTCACATATCAATTTCTATAA
*
28806780 ATTTCACTTCTACTATTTAATCCACATATTTTCTCAAGTTTAACAATTTAGTCCTTGTCATCATA
66 ATTTCACTTATACTATTTAATCCACATATTTTCTCAAGTTTAACAATTTAGTCCTTGTCATCATA
*
28806845 AAAATTCCATATTTTTCTACAATTT
131 AAAAATCCATATTTTTCTACAATTT
28806870 AACATTTTTA
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 148 1.00
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (165 bp):
TTTCTTGTTACACTTTAATCACATATTTTATATTAATATATTGTTTCACATATCAATTTCTATAA
ATTTCACTTATACTATTTAATCCACATATTTTCTCAAGTTTAACAATTTAGTCCTTGTCATCATA
AAAAATCCATATTTTTCTACAATTTCACAGTTTCC
Found at i:28809515 original size:19 final size:19
Alignment explanation
Indices: 28809493--28809535 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28809483 GCATAAGAAC
28809493 AAAATAATAATAAC-TACAT
1 AAAATAATAA-AACATACAT
* *
28809512 AAAAAAATAAAACATAGAT
1 AAAATAATAAAACATACAT
28809531 AAAAT
1 AAAAT
28809536 TTGAAATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAATAAAACATACAT
Found at i:28809822 original size:19 final size:18
Alignment explanation
Indices: 28809795--28809830 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28809785 TTAACAGAGG
28809795 TAAAGAAATAATAAATAAA
1 TAAAGAAATAA-AAATAAA
*
28809814 TAAATAAATAAAAATAA
1 TAAAGAAATAAAAATAA
28809831 TTCATAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
TAAAGAAATAAAAATAAA
Found at i:28811358 original size:21 final size:21
Alignment explanation
Indices: 28811319--28811360 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28811309 TTTGCCTAAG
*
28811319 ATGTGAATTTGATGGAATTGA
1 ATGTGAATTTGATGAAATTGA
* *
28811340 ATGTGAATTTTATTAAATTGA
1 ATGTGAATTTGATGAAATTGA
28811361 GTTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (21 bp):
ATGTGAATTTGATGAAATTGA
Found at i:28811577 original size:25 final size:26
Alignment explanation
Indices: 28811512--28811577 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
28811502 AGCTCGAAAT
*
28811512 AGCATCCTG-TTAT-TAGCTCTCATG
1 AGCATCCCGATTATATAGCTCTCATG
* *
28811536 AGCATCCCGA-TAAATAGCTCTCTTG
1 AGCATCCCGATTATATAGCTCTCATG
*
28811561 AGCTTCCC-ATTATATAG
1 AGCATCCCGATTATATAG
28811578 TTCCTACGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 11 0.32
25 23 0.68
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (26 bp):
AGCATCCCGATTATATAGCTCTCATG
Found at i:28818430 original size:6 final size:7
Alignment explanation
Indices: 28818413--28818439 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28818403 AATTGAGCCT
28818413 TTTTTTA
1 TTTTTTA
28818420 TTTTTTA
1 TTTTTTA
28818427 TTTTTTA
1 TTTTTTA
28818434 TTTTTT
1 TTTTTT
28818440 CTTCGAGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:28821726 original size:17 final size:18
Alignment explanation
Indices: 28821704--28821739 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28821694 TTGTTTATGA
28821704 CAAATCAAA-AAAAATCC
1 CAAATCAAAGAAAAATCC
*
28821721 CAAATCAAAGGAAAATCC
1 CAAATCAAAGAAAAATCC
28821739 C
1 C
28821740 TCCTCTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.25, G:0.06, T:0.11
Consensus pattern (18 bp):
CAAATCAAAGAAAAATCC
Found at i:28825292 original size:7 final size:7
Alignment explanation
Indices: 28825280--28825312 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28825270 TTATCTGATC
28825280 AGTGACA
1 AGTGACA
28825287 AGTGACA
1 AGTGACA
28825294 AGTGACA
1 AGTGACA
28825301 AGTGACA
1 AGTGACA
28825308 AGTGA
1 AGTGA
28825313 TAAGCGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.30, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:28825324 original size:14 final size:14
Alignment explanation
Indices: 28825280--28825325 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28825270 TTATCTGATC
*
28825280 AGTGACAAGTGACA
1 AGTGACAAGCGACA
*
28825294 AGTGACAAGTGACA
1 AGTGACAAGCGACA
* *
28825308 AGTGATAAGCGATA
1 AGTGACAAGCGACA
28825322 AGTG
1 AGTG
28825326 GTAGCTTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.17
Consensus pattern (14 bp):
AGTGACAAGCGACA
Found at i:28825324 original size:21 final size:21
Alignment explanation
Indices: 28825280--28825325 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
28825270 TTATCTGATC
*
28825280 AGTGACAAGTGACAAGTGACA
1 AGTGACAAGTGACAAGCGACA
* *
28825301 AGTGACAAGTGATAAGCGATA
1 AGTGACAAGTGACAAGCGACA
28825322 AGTG
1 AGTG
28825326 GTAGCTTAGC
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:0.41, C:0.11, G:0.30, T:0.17
Consensus pattern (21 bp):
AGTGACAAGTGACAAGCGACA
Found at i:28825350 original size:71 final size:72
Alignment explanation
Indices: 28825236--28825368 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 72
28825226 ACTTCTGATC
* * *
28825236 AGTGACAAGTGATAAGTGGTGGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTGACA
1 AGTGACAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGACA
28825301 AGTGACA
66 AGTGACA
* * *
28825308 AGTGATAAGCGATAAGTGGTAGC-TTAGCTACACTTATTTGATCAGTGACAAGTGATAAGTG
1 AGTGACAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
28825369 GTAGCTTAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
71 35 0.64
72 20 0.36
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (72 bp):
AGTGACAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGACA
AGTGACA
Found at i:28825369 original size:43 final size:43
Alignment explanation
Indices: 28825308--28825408 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
28825298 ACAAGTGACA
* * *
28825308 AGTGATAAGCGATAAGTGGTAGCTTAGCTACACTTATTTGATC
1 AGTGACAAGAGATAAGTGGTAGCTTAGCTACACTTATCTGATC
*
28825351 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGAGATAAGTGGTAGCTTAGCTACACTTATCTGATC
28825394 AGTGACAAGAGATAA
1 AGTGACAAGAGATAA
28825409 ATGATAAGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTGACAAGAGATAAGTGGTAGCTTAGCTACACTTATCTGATC
Found at i:28825474 original size:8 final size:8
Alignment explanation
Indices: 28825455--28825491 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
28825445 ATGGCATCGG
28825455 TATGTG-T
1 TATGTGAT
28825462 TATGTGAT
1 TATGTGAT
28825470 TATGTGAT
1 TATGTGAT
28825478 TATGTGAT
1 TATGTGAT
28825486 TATGTG
1 TATGTG
28825492 TAAGACCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (8 bp):
TATGTGAT
Found at i:28826058 original size:22 final size:23
Alignment explanation
Indices: 28826024--28826067 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
28826014 CAACCAATCA
28826024 ATTTCAACATATTT-TCAAGATAG
1 ATTTCAACATATTTAT-AAGATAG
*
28826047 ATTT-AACGTATTTATAAGATA
1 ATTTCAACATATTTATAAGATA
28826068 ACATCATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTTCAACATATTTATAAGATAG
Found at i:28830633 original size:11 final size:11
Alignment explanation
Indices: 28830619--28830655 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
28830609 TTTCGCAAAG
28830619 TTTTTATTTTA
1 TTTTTATTTTA
28830630 TTTTTTATTTTA
1 -TTTTTATTTTA
*
28830642 TTTTGATTTTA
1 TTTTTATTTTA
28830653 TTT
1 TTT
28830656 CCTTAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:28830634 original size:12 final size:12
Alignment explanation
Indices: 28830619--28830655 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
28830609 TTTCGCAAAG
28830619 TTTTTATTTTAT
1 TTTTTATTTTAT
28830631 TTTTTATTTTA-
1 TTTTTATTTTAT
*
28830642 TTTTGATTTTAT
1 TTTTTATTTTAT
28830654 TT
1 TT
28830656 CCTTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:28831359 original size:3 final size:3
Alignment explanation
Indices: 28831351--28831385 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28831341 CTTGGCAATT
28831351 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28831386 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28838052 original size:15 final size:15
Alignment explanation
Indices: 28838034--28838093 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
28838024 TAAAAAATAC
28838034 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
*
28838049 AAAAAAAGAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
28838064 AGAAGAAGAAGAAGAG
1 AAAAAAAAAAGAA-AG
* *
28838080 AAAATAAAAGGAAA
1 AAAAAAAAAAGAAA
28838094 AAAGGAGAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 26 0.70
16 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:28838275 original size:43 final size:43
Alignment explanation
Indices: 28838173--28838275 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
28838163 AAAAAGGGCG
* *
28838173 GCTCAAATTTTGGAACAAAATGGGGCACGAAGTGATCAGAGCG
1 GCTCAAATTTTGGATCAAAATGGGGCACGAAGTGATCAGAGCA
* * * ** *
28838216 GCTTAAATTTTGGATCAAATTGGGGCATGGTGGTGATTAGAGCA
1 GCTCAAATTTTGGATCAAAATGGGGCA-CGAAGTGATCAGAGCA
28838260 GCTCAAATTTT-GATCA
1 GCTCAAATTTTGGATCA
28838276 GATCGAGGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 29 0.58
44 21 0.42
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (43 bp):
GCTCAAATTTTGGATCAAAATGGGGCACGAAGTGATCAGAGCA
Found at i:28839432 original size:50 final size:48
Alignment explanation
Indices: 28839378--28840286 Score: 659
Period size: 50 Copynumber: 19.1 Consensus size: 48
28839368 GCAATTAGAA
* * * *
28839378 AGATTGAAGCTACAACAGTGAATCTTACTTTCTTATTGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTC-TA-CGTTGCAGTGAAAC
* * * * *
28839428 AGATTGAAGCTACAACAGCGGATCTTGC-TTC--CCTTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
*
28839473 AGATTAAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * * * * *
28839523 AGATTGAAGCTACAGCAGCGGATCTTGC-TTC--CCTGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* * * * * * *
28839568 AGATTGAAGCTACAACAACGAATCTTATTTTCCTAGCATTACACTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * ** * *
28839618 AGATTGAAGCTACAGCAGCGGATCTTGC-TTCCCCG--GCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* * * * * * *
28839663 AGATTGAAGCTACAACAACGAATCTTATTTTCCTAGCATTACACTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * ** * *
28839713 AGATTGAAGCTACAGCAGCGGATCTTGC-TTCCCCG--GCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* * *
28839758 AGATTGAAGCTACAACAGGCAGATCTT-GTTCCCTAGCGTTGCAGTGAAAC
1 AGATTGAAGCTACAACA-GCGGATCTTACTT-TCTA-CGTTGCAGTGAAAC
* * * * * * *
28839808 ATATTGAAGCTACAGCAGCGGATCTTGC-TTC--CCTGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* *
28839853 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * * ** * * *
28839903 AGATTGAAGCTATAGCAGCGGATCTTGC-TTCCCCG--GAAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
28839948 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * * * * *
28839998 AGATTGAAGCTACAGCAGCGGATCTTGC-TTC--CCTAGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* *
28840043 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
* * * ** * *
28840093 AGATTGAAGCTACAGCAGCGAATCTTGC-TTCCCCG--GCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
* * * *
28840138 AGATTGAAGCTACAACAGCGGATTTTACTTTTCTAGTGTTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTTCTA-CGTTGCAGTGAAAC
* * * * *
28840188 AGATTGAAGCTACAACAACGGATCTTGCTTCCT-CG--GCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
28840233 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTA-CGTTGCAGTGAAAC
28840283 AGAT
1 AGAT
28840287 GTGATGCTTG
Statistics
Matches: 649, Mismatches: 163, Indels: 94
0.72 0.18 0.10
Matches are distributed among these distances:
45 283 0.44
46 23 0.04
47 15 0.02
48 15 0.02
49 28 0.04
50 285 0.44
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (48 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCTACGTTGCAGTGAAAC
Found at i:28839483 original size:95 final size:95
Alignment explanation
Indices: 28839376--28840286 Score: 1385
Period size: 95 Copynumber: 9.6 Consensus size: 95
28839366 TTGCAATTAG
* * * **
28839376 AAAGATTGAAGCTACAACAGTGAATCTTACTTTCTTATTGTTGCAGTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
* * *
28839441 AACAGCGGATCTTGCTTCCCTTGCAATTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* *
28839471 AAAGATTAAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
28839536 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* * * * * *
28839566 AAAGATTGAAGCTACAACAACGAATCTTATTTTCCTAGCATTACACTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
*
28839631 AGCAGCGGATCTTGCTTCCCCGGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* * * * * *
28839661 AAAGATTGAAGCTACAACAACGAATCTTATTTTCCTAGCATTACACTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
*
28839726 AGCAGCGGATCTTGCTTCCCCGGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* * * * *
28839756 AAAGATTGAAGCTACAACAGGCAGATCTT-GTTCCCTAGCGTTGCAGTGAAACATATTGAAGCTA
1 AAAGATTGAAGCTACAACA-GCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTA
28839820 CAGCAGCGGATCTTGCTTCCCTGGCAGTTAA
65 CAGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* *
28839851 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTAT
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
* *
28839916 AGCAGCGGATCTTGCTTCCCCGGAAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
*
28839946 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
*
28840011 AGCAGCGGATCTTGCTTCCCTAGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
*
28840041 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
* *
28840106 AGCAGCGAATCTTGCTTCCCCGGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
* * * *
28840136 AAAGATTGAAGCTACAACAGCGGATTTTACTTTTCTAGTGTTGTAGTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
* *
28840201 AACAACGGATCTTGCTT-CCTCGGCAGTTAA
66 AGCAGCGGATCTTGCTTCCCT-GGCAGTTAA
*
28840231 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGAAACAGAT
1 AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
28840287 GTGATGCTTG
Statistics
Matches: 749, Mismatches: 64, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
94 10 0.01
95 733 0.98
96 6 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (95 bp):
AAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTAC
AGCAGCGGATCTTGCTTCCCTGGCAGTTAA
Found at i:28840623 original size:27 final size:27
Alignment explanation
Indices: 28840587--28840655 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
28840577 AAATAAAAAA
* *
28840587 TTACCAAAATGTTATA-ATTTTTTTTAT
1 TTACCAAAAT-ATATACAATTTTTTTAT
28840614 TTACCAAAATATATACAATTTTTTTAT
1 TTACCAAAATATATACAATTTTTTTAT
28840641 TTACCAAAATATATA
1 TTACCAAAATATATA
28840656 AAAAAAACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 4 0.10
27 35 0.90
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATACAATTTTTTTAT
Found at i:28840742 original size:27 final size:27
Alignment explanation
Indices: 28840712--28840806 Score: 163
Period size: 27 Copynumber: 3.5 Consensus size: 27
28840702 ATGCCAATGG
28840712 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
*
28840739 CATTGGCGACACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* *
28840766 CATTGGCGGCACCAATGGTGCCAATAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
28840793 CATTGGCGGCACCA
1 CATTGGCGGCACCA
28840807 GTTGATAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.14
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:28840858 original size:4 final size:4
Alignment explanation
Indices: 28840849--28840931 Score: 68
Period size: 4 Copynumber: 21.0 Consensus size: 4
28840839 AAAGGAGAGG
* *
28840849 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
*
28840897 G-AA G-AA GAAGA GAAA -AGAA GAAA GAAG GAAA GAAA
1 GAAA GAAA GAA-A GAAA GA-AA GAAA GAAA GAAA GAAA
28840932 AGGAAATGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
3 11 0.17
4 44 0.68
5 9 0.14
6 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:28840924 original size:31 final size:29
Alignment explanation
Indices: 28840850--28840963 Score: 73
Period size: 28 Copynumber: 4.0 Consensus size: 29
28840840 AAGGAGAGGG
* *
28840850 AAAGAAAGAAAGAAAGAAAGGAGAGGA-AAG
1 AAAGAAAG-AAGAAAG-AAGGAAAGAAGAAG
* *
28840880 AAAGAAA-AAGAAGGAAAG-AAGAAGAAG
1 AAAGAAAGAAGAAAGAAGGAAAGAAGAAG
*
28840907 AGA-AAAGAAGAAAGAAGGAAAGAA-AAGG
1 AAAGAAAGAAGAAAGAAGGAAAGAAGAA-G
*
28840935 AAATGAGAAG-AGAAA-AA-AAAAGAAGAAG
1 AAA-GA-AAGAAGAAAGAAGGAAAGAAGAAG
28840963 A
1 A
28840964 GGAAAGGAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
26 6 0.09
27 19 0.28
28 22 0.33
29 4 0.06
30 13 0.19
31 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (29 bp):
AAAGAAAGAAGAAAGAAGGAAAGAAGAAG
Found at i:28840944 original size:41 final size:40
Alignment explanation
Indices: 28840875--28840991 Score: 111
Period size: 41 Copynumber: 3.0 Consensus size: 40
28840865 GAAAGGAGAG
* * *
28840875 GAAAGAAAGAAAAAGAAGGAAAGAAGAAGAAGAGAAAAGAA
1 GAAAGAAGGAAAAAGAAGGAAAGAAGAAG-AGAAAAAAAAA
28840916 GAAAGAAGGAAAGAA-AAGGAAATG-AGAAGAGAAAAAAAAA
1 GAAAGAAGGAAA-AAGAAGGAAA-GAAGAAGAGAAAAAAAAA
* *
28840956 G-AAGAAGAGGAAAGGAAGGAAA-AA-AA-AGAAAAAAAA
1 GAAAGAAG-GAAAAAGAAGGAAAGAAGAAGAGAAAAAAAA
28840992 GGTAATTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
37 10 0.15
38 2 0.03
39 8 0.12
40 20 0.30
41 23 0.35
42 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (40 bp):
GAAAGAAGGAAAAAGAAGGAAAGAAGAAGAGAAAAAAAAA
Found at i:28840948 original size:18 final size:19
Alignment explanation
Indices: 28840898--28840972 Score: 75
Period size: 18 Copynumber: 4.0 Consensus size: 19
28840888 AGAAGGAAAG
*
28840898 AAGAAGAAGAGAAAAGAAGA
1 AAGAAGAAGAGAAAAGGA-A
28840918 AAGAAGGAA-AGAAAAGGAA
1 AAGAA-GAAGAGAAAAGGAA
* *
28840937 ATG-AGAAGAGAAAA-AAA
1 AAGAAGAAGAGAAAAGGAA
*
28840954 AAGAAGAAGAGGAAAGGAA
1 AAGAAGAAGAGAAAAGGAA
28840973 GGAAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.16
18 17 0.38
19 5 0.11
20 13 0.29
21 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (19 bp):
AAGAAGAAGAGAAAAGGAA
Found at i:28840957 original size:59 final size:59
Alignment explanation
Indices: 28840850--28840993 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 59
28840840 AAGGAGAGGG
* *
28840850 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAGAAGAAGAGA
1 AAAGAAAGAAAGAAAGAAAGAAAAGGAAAGAAAGAAAAAGAA-GAAAGAAGAAGAAGAGA
*
28840910 AAAG-AAGAAAGAAGGAAAGAAAAGGAAATGAGAAGAGAAAA-AA-AAAGAAGAAG-AG-GA
1 AAAGAAAGAAAGAAAGAAAGAAAAGGAAA-GA-AAGA-AAAAGAAGAAAGAAGAAGAAGAGA
* * * *
28840967 AAGGAAGGAAAAAAAAGAAAAAAAAGG
1 AAAGAAAG-AAAGAAAGAAAGAAAAGG
28840994 TAATTTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
57 5 0.07
58 4 0.06
59 46 0.65
60 6 0.08
61 6 0.08
62 4 0.06
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (59 bp):
AAAGAAAGAAAGAAAGAAAGAAAAGGAAAGAAAGAAAAAGAAGAAAGAAGAAGAAGAGA
Found at i:28840967 original size:31 final size:28
Alignment explanation
Indices: 28840926--28840990 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 28
28840916 GAAAGAAGGA
28840926 AAGAAAAGGAAATGAGAAGAGAAAAAAAAAG
1 AAGAAAAGGAAA-G-GAAG-GAAAAAAAAAG
*
28840957 AAGAAGAGGAAAGGAAGG-AAAAAAAAG
1 AAGAAAAGGAAAGGAAGGAAAAAAAAAG
*
28840984 AAAAAAA
1 AAGAAAA
28840991 AGGTAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 14 0.45
28 1 0.03
29 4 0.13
30 1 0.03
31 11 0.35
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (28 bp):
AAGAAAAGGAAAGGAAGGAAAAAAAAAG
Found at i:28841016 original size:17 final size:18
Alignment explanation
Indices: 28840994--28841029 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
28840984 AAAAAAAAGG
28840994 TAATTTTTTTGTAA-ATT
1 TAATTTTTTTGTAATATT
28841011 TAATTTTTTTGTAATATT
1 TAATTTTTTTGTAATATT
28841029 T
1 T
28841030 GTGTGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TAATTTTTTTGTAATATT
Found at i:28848642 original size:3 final size:3
Alignment explanation
Indices: 28848634--28848665 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28848624 TCTTAATACT
28848634 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
28848666 TAATACTAAC
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:28848960 original size:27 final size:27
Alignment explanation
Indices: 28848888--28848962 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
28848878 AATACGAATA
28848888 GTGCCGCCAAT--CAGTATGGCACCATTG
1 GTGCCGCCAATGCCA-T-TGGCACCATTG
*** *
28848915 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGCCATTGGCACCATTG
*
28848942 GTGCCGCTAATGCCATTGGCA
1 GTGCCGCCAATGCCATTGGCA
28848963 TGACCAAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAATGCCATTGGCACCATTG
Found at i:28849079 original size:28 final size:27
Alignment explanation
Indices: 28849019--28849079 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
28849009 TTTTGTTTTT
**
28849019 TTATATATTTTGGTAAATAAAAAAATT
1 TTATATATTTTGGTAAATAAAAAAAAG
28849046 TATATATATTTTGGTAAATAAAAAAAAAG
1 T-TATATATTTTGGTAAAT-AAAAAAAAG
28849075 TTATA
1 TTATA
28849080 ACAATTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 21 0.70
29 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (27 bp):
TTATATATTTTGGTAAATAAAAAAAAG
Found at i:28849087 original size:29 final size:28
Alignment explanation
Indices: 28849027--28849091 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
28849017 TTTTATATAT
* * *
28849027 TTTGGTAAATAAAAAAATTTATATATAT
1 TTTGGTAAATAAAAAAAGTTATATACAA
28849055 TTTGGTAAATAAAAAAAAAGTTATA-ACAA
1 TTTGGTAAAT--AAAAAAAGTTATATACAA
28849084 TTTGGTAA
1 TTTGGTAA
28849092 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.31
29 10 0.31
30 12 0.38
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (28 bp):
TTTGGTAAATAAAAAAAGTTATATACAA
Found at i:28849323 original size:3 final size:3
Alignment explanation
Indices: 28849315--28849343 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28849305 AAATAGATAT
28849315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28849344 TCAGATTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28850799 original size:57 final size:57
Alignment explanation
Indices: 28850738--28850910 Score: 160
Period size: 57 Copynumber: 3.1 Consensus size: 57
28850728 ATTGATTAAG
28850738 ATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGACC
1 ATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGACC
** * ** * * * * * **
28850795 ATAAAATAAAGA-ACCTATAAAAATTATTAATAATAT--TAT-TTAA-AA-TTTGATTA
1 ATAAAGCAAACATAAATAT-AACATTATAAAAAAAATCAAATATTAACAATTTTGA-CC
*
28850848 AGAAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGACC
1 A-TAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGACC
28850906 ATAAA
1 ATAAA
28850911 ATAAAGAACC
Statistics
Matches: 81, Mismatches: 26, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
52 5 0.06
53 3 0.04
54 24 0.30
55 6 0.07
56 6 0.07
57 29 0.36
58 3 0.04
59 5 0.06
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (57 bp):
ATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGACC
Found at i:28850855 original size:111 final size:112
Alignment explanation
Indices: 28850729--28850930 Score: 397
Period size: 111 Copynumber: 1.8 Consensus size: 112
28850719 ATTACATTAA
28850729 TTGATTAAGATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGAC
1 TTGATTAAGATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGAC
28850794 CATAAAATAAAGAACCTATAAAAATTATTAATAATATTATTTAAAAT
66 CATAAAATAAAGAACCTATAAAAATTATTAATAATATTATTTAAAAT
28850841 TTGATTAAGA-AAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGAC
1 TTGATTAAGATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGAC
28850905 CATAAAATAAAGAACCTATAAAAATT
66 CATAAAATAAAGAACCTATAAAAATT
28850931 TTTTTCCTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 80 0.89
112 10 0.11
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (112 bp):
TTGATTAAGATAAAGCAAACATAAATATAACATTATAAAAAAAATCAAATATTAACAATTTTGAC
CATAAAATAAAGAACCTATAAAAATTATTAATAATATTATTTAAAAT
Found at i:28851109 original size:3 final size:3
Alignment explanation
Indices: 28851101--28851129 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28851091 AAATAGATAT
28851101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28851130 TCAGATTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28860602 original size:17 final size:17
Alignment explanation
Indices: 28860580--28860620 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
28860570 TCAGGAAAAC
28860580 TCGAATCAAATAATTTA
1 TCGAATCAAATAATTTA
28860597 TCGAATCAAATAATTTA
1 TCGAATCAAATAATTTA
28860614 TCGAATC
1 TCGAATC
28860621 TTTGGCGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (17 bp):
TCGAATCAAATAATTTA
Found at i:28864412 original size:20 final size:20
Alignment explanation
Indices: 28864387--28864426 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28864377 CGTAAAATGA
*
28864387 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28864407 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28864427 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28864416 original size:34 final size:35
Alignment explanation
Indices: 28864372--28864438 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28864362 CAGTAAAATA
*
28864372 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
28864406 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
28864439 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:28864442 original size:14 final size:15
Alignment explanation
Indices: 28864366--28864442 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28864356 GATTGCCAGT
* *
28864366 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
28864380 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
28864394 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
28864414 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
28864429 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
28864443 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:28869941 original size:18 final size:18
Alignment explanation
Indices: 28869920--28869962 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
28869910 AAATAGGTTT
28869920 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
28869938 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
28869956 TTAATTA
1 TTAATTA
28869963 CACCTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:28886075 original size:2 final size:2
Alignment explanation
Indices: 28886068--28886101 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28886058 TTAGCTGAGT
28886068 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28886102 AAGAACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28897979 original size:47 final size:47
Alignment explanation
Indices: 28897910--28898003 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
28897900 AGGAGGATAG
28897910 AATGGTGGACCCAAATTCTCGTACTTTTATCTAGAATATTGCTTTGT
1 AATGGTGGACCCAAATTCTCGTACTTTTATCTAGAATATTGCTTTGT
28897957 AATGGTGGACCCAAATTCTCGTACTTTTATCTAGAATATTGCTTTGT
1 AATGGTGGACCCAAATTCTCGTACTTTTATCTAGAATATTGCTTTGT
28898004 TATTAACTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (47 bp):
AATGGTGGACCCAAATTCTCGTACTTTTATCTAGAATATTGCTTTGT
Found at i:28909147 original size:30 final size:30
Alignment explanation
Indices: 28909111--28909201 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
28909101 TCAAGGAGAT
*
28909111 CGGTATAAATCTGTCTTTAAAACCCAGAAA
1 CGGTATAAATCTATCTTTAAAACCCAGAAA
28909141 CGGTATAAATCTATCTTTAAAACCCAGAAA
1 CGGTATAAATCTATCTTTAAAACCCAGAAA
*
28909171 TGGTATAAATCTATCTTTAAAACCCAGAAA
1 CGGTATAAATCTATCTTTAAAACCCAGAAA
28909201 C
1 C
28909202 TACTCGTGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (30 bp):
CGGTATAAATCTATCTTTAAAACCCAGAAA
Found at i:28909519 original size:13 final size:13
Alignment explanation
Indices: 28909490--28909518 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28909480 AGCTTTTCCC
28909490 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
28909503 TTTTCTTTTTT-T
1 TTTTCTTTTTTCT
28909515 TTTT
1 TTTT
28909519 TGGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:28910198 original size:129 final size:128
Alignment explanation
Indices: 28909901--28910198 Score: 395
Period size: 128 Copynumber: 2.3 Consensus size: 128
28909891 AAAAGAGTGT
* * *
28909901 TTATTTTAT-TTTATATATTGC--ATATGAATAGTTATGTTTATTATATTTGAATTTTAATTTTG
1 TTATTTTATGTTTATATATTGCATATATAAATAATTATATTTATTATATTTGAATTTTAATTTTG
** * * * **
28909963 TATAATTTTATATACGAAATTTTGATTTGATTCAATTTTAAAAATACAATTATTTATATATTA
66 TATAATTTTATATAAAAAATTTTAATTTGAATCAATTTTAAAAATACAATTATTGATATAGCA
* * * * *
28910026 TTATTTTAGGTTTATATATTGTATATAAAAATAATTTTATTTATTATATTTGAATTTTGATTTTG
1 TTATTTTATGTTTATATATTGCATATATAAATAATTATATTTATTATATTTGAATTTTAATTTTG
* *
28910091 TGTAATTTTATATAAAAAATTTTAATTTGAATCAATTTTTATAAATACAATTATTGATATAGCA
66 TATAATTTTATATAAAAAATTTTAATTTGAATCAA-TTTTAAAAATACAATTATTGATATAGCA
* *
28910155 TTGTTTTATGTTTATATATTACATATATAAATAATTATATTTAT
1 TTATTTTATGTTTATATATTGCATATATAAATAATTATATTTAT
28910199 CAAATATAGA
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
125 8 0.05
126 11 0.08
128 65 0.45
129 62 0.42
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (128 bp):
TTATTTTATGTTTATATATTGCATATATAAATAATTATATTTATTATATTTGAATTTTAATTTTG
TATAATTTTATATAAAAAATTTTAATTTGAATCAATTTTAAAAATACAATTATTGATATAGCA
Found at i:28910215 original size:129 final size:128
Alignment explanation
Indices: 28909901--28910216 Score: 325
Period size: 129 Copynumber: 2.5 Consensus size: 128
28909891 AAAAGAGTGT
* * * * * * * * * *
28909901 TTATTTTA-TTTTATATATTGCATAT--GAATAGTTATGTTTATTATATTTGAATTTTAATTTTG
1 TTATTTTAGGTTTATATATTACATATAAAAATAATTATATTTATCAAATTAGAATATTGATTTTG
** * * * **
28909963 TATAATTTTATATACGAAATTTTGATTTGATTCAATTTTAAAAATACAATTATTTATATATTA
66 TATAATTTTATATAAAAAATTTTAATTTGAATCAATTTTAAAAATACAATTATTGATATAGCA
** * * * * *
28910026 TTATTTTAGGTTTATATATTGTATATAAAAATAATTTTATTTATTATATTTGAATTTTGATTTTG
1 TTATTTTAGGTTTATATATTACATATAAAAATAATTATATTTATCAAATTAGAATATTGATTTTG
* *
28910091 TGTAATTTTATATAAAAAATTTTAATTTGAATCAATTTTTATAAATACAATTATTGATATAGCA
66 TATAATTTTATATAAAAAATTTTAATTTGAATCAA-TTTTAAAAATACAATTATTGATATAGCA
* * *
28910155 TTGTTTTATGTTTATATATTACATATATAAATAATTATATTTATCAAATATAGAA-ATTGATT
1 TTATTTTAGGTTTATATATTACATATAAAAATAATTATATTTATCAAAT-TAGAATATTGATT
28910217 AATGTATTTA
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
125 8 0.05
126 15 0.09
128 62 0.39
129 71 0.44
130 4 0.03
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (128 bp):
TTATTTTAGGTTTATATATTACATATAAAAATAATTATATTTATCAAATTAGAATATTGATTTTG
TATAATTTTATATAAAAAATTTTAATTTGAATCAATTTTAAAAATACAATTATTGATATAGCA
Found at i:28914168 original size:11 final size:11
Alignment explanation
Indices: 28914126--28914179 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
28914116 GGCCCATTTT
28914126 TATTTTAAAAA
1 TATTTTAAAAA
*
28914137 T-TTTAAAAAA
1 TATTTTAAAAA
* **
28914147 AATTAAAAAAA
1 TATTTTAAAAA
28914158 GTATTTTAAAAA
1 -TATTTTAAAAA
28914170 TATTTTAAAA
1 TATTTTAAAA
28914180 TTAAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 8 0.23
11 19 0.54
12 8 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:28914197 original size:41 final size:42
Alignment explanation
Indices: 28914126--28914222 Score: 142
Period size: 41 Copynumber: 2.3 Consensus size: 42
28914116 GGCCCATTTT
* * *
28914126 TATTTTAAAAATTTTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAAAATTAAAAAAAGTATGTAAAAAA
28914170 TATTTTAAAATTAAAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATGTAAAAAA
28914211 TATTTTAAAATT
1 TATTTTAAAATT
28914223 TTAAAGTGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
41 28 0.56
42 12 0.24
43 4 0.08
44 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATGTAAAAAA
Found at i:28932903 original size:5 final size:5
Alignment explanation
Indices: 28932893--28932919 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28932883 GAAATCTCGA
28932893 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
28932920 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:28941848 original size:7 final size:7
Alignment explanation
Indices: 28941836--28941865 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
28941826 TGATCAACTG
28941836 CATAGAC
1 CATAGAC
28941843 CATAGAC
1 CATAGAC
28941850 CATAGAC
1 CATAGAC
28941857 CATAGAC
1 CATAGAC
28941864 CA
1 CA
28941866 GCTGGTCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.13
Consensus pattern (7 bp):
CATAGAC
Found at i:28946799 original size:15 final size:16
Alignment explanation
Indices: 28946775--28946812 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28946765 CGTATCTAGC
* *
28946775 TGGACATATTTTT-TT
1 TGGACGTATTTTTAAT
28946790 TGGACGTATTTTTAAT
1 TGGACGTATTTTTAAT
28946806 TGGACGT
1 TGGACGT
28946813 GCTTTCCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (16 bp):
TGGACGTATTTTTAAT
Found at i:28953517 original size:33 final size:31
Alignment explanation
Indices: 28953452--28953518 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
28953442 CTCTCTCAAC
* * *
28953452 AAAAATTACAAAAAAAATTCAAAATATTTAT
1 AAAAATTACAAAAAAAAATCAAAAGATATAT
*
28953483 AAAAATTTCCAAAAAAAAATCTAAAAGATATAT
1 AAAAA-TTACAAAAAAAAATC-AAAAGATATAT
28953516 AAA
1 AAA
28953519 GAAAGTTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 13 0.43
33 12 0.40
ACGTcount: A:0.66, C:0.07, G:0.01, T:0.25
Consensus pattern (31 bp):
AAAAATTACAAAAAAAAATCAAAAGATATAT
Found at i:28954150 original size:23 final size:23
Alignment explanation
Indices: 28954124--28954168 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
28954114 GGAGATCCAA
*
28954124 TGCTTAATGTAGGAATCAATTTG
1 TGCTTAACGTAGGAATCAATTTG
28954147 TGCTTAACGTAGGAATCAATTT
1 TGCTTAACGTAGGAATCAATTT
28954169 AATTACACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (23 bp):
TGCTTAACGTAGGAATCAATTTG
Found at i:28956299 original size:31 final size:29
Alignment explanation
Indices: 28956247--28956318 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 29
28956237 GATTTGGTGT
*
28956247 AATTATACCTATGAAATTTTGATTGTAATTC
1 AATTATA-C-ATGAAACTTTGATTGTAATTC
* *
28956278 AAATATATACATGAAACTTTGATTTTGATTC
1 -AAT-TATACATGAAACTTTGATTGTAATTC
28956309 AATTATACAT
1 AATTATACAT
28956319 ATGTAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 7 0.19
30 3 0.08
31 18 0.50
32 4 0.11
33 4 0.11
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (29 bp):
AATTATACATGAAACTTTGATTGTAATTC
Found at i:28965327 original size:21 final size:21
Alignment explanation
Indices: 28965211--28965326 Score: 178
Period size: 21 Copynumber: 5.5 Consensus size: 21
28965201 TGAAAATGCC
*
28965211 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTG
* * *
28965232 AATAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
28965253 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
28965274 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
28965295 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
28965316 AACAGAAGCTC
1 AACAGAAGCTC
28965327 GAAAGGGATA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28965341 original size:42 final size:42
Alignment explanation
Indices: 28965211--28965343 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 42
28965201 TGAAAATGCC
* * * *
28965211 AACAGAAGCTCATAAGAGCTTAATAGAAACTC-ATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGA-AAGAGATG
* *
28965253 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGAAAGAGATG
* * *
28965295 AACAGAAGCTCGTAAGAGCTGAACAGAAGCTCGAAAGGGATA
1 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGAAAGAGATG
28965337 AACAGAA
1 AACAGAA
28965344 AGTAAAACAC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGAAAGAGATG
Found at i:28965341 original size:63 final size:63
Alignment explanation
Indices: 28965211--28965343 Score: 169
Period size: 63 Copynumber: 2.1 Consensus size: 63
28965201 TGAAAATGCC
* * * * *
28965211 AACAGAAGCTCATAAGAGCTTAATAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAGCTCATAAGAGATA
* * * *
28965274 AACAGAAGCTCGTAAGAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAGCTCGA-AAGGGATA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAGCTC-ATAAGAGATA
28965337 AACAGAA
1 AACAGAA
28965344 AGTAAAACAC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
63 59 0.98
64 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (63 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAGCTCATAAGAGATA
Found at i:28967341 original size:17 final size:17
Alignment explanation
Indices: 28967316--28967355 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
28967306 CTAATAAATT
28967316 AACCTCGAGAATACAATC
1 AACC-CGAGAATACAATC
28967334 AACCCGAGAATACAATC
1 AACCCGAGAATACAATC
28967351 AACCC
1 AACCC
28967356 AATTACATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.45, C:0.33, G:0.10, T:0.12
Consensus pattern (17 bp):
AACCCGAGAATACAATC
Found at i:28974573 original size:30 final size:31
Alignment explanation
Indices: 28974537--28974600 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
28974527 TGATTTCAAT
28974537 TCAGTTATTTAAC-TT-TCGAAAAA-TAAGAAA
1 TCAGTTA-TTAACGTTATC-AAAAAGTAAGAAA
*
28974567 TCAGTTATTAACGTTATCAAAAAGTAATAAA
1 TCAGTTATTAACGTTATCAAAAAGTAAGAAA
28974598 TCA
1 TCA
28974601 ATCACTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 14 0.47
31 11 0.37
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (31 bp):
TCAGTTATTAACGTTATCAAAAAGTAAGAAA
Found at i:28975163 original size:33 final size:34
Alignment explanation
Indices: 28975117--28975182 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
28975107 TAACAATTAG
* * *
28975117 TTGAGGTTCAAAAAGAGG-TTCATCTTCAAAATT
1 TTGAGGTTAAAAAAAAGGCTTCACCTTCAAAATT
28975150 TTGAGGTTAAAAAAAAGGTCTTCACCTTCAAAA
1 TTGAGGTTAAAAAAAAGG-CTTCACCTTCAAAA
28975183 ATTTCAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 16 0.57
35 12 0.43
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (34 bp):
TTGAGGTTAAAAAAAAGGCTTCACCTTCAAAATT
Found at i:28978851 original size:7 final size:7
Alignment explanation
Indices: 28978839--28978869 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
28978829 CAAGAACATC
28978839 TTTGATT
1 TTTGATT
28978846 TTTGATT
1 TTTGATT
28978853 TTTGATT
1 TTTGATT
28978860 TTTGATT
1 TTTGATT
28978867 TTT
1 TTT
28978870 TATTACATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (7 bp):
TTTGATT
Found at i:28981682 original size:5 final size:5
Alignment explanation
Indices: 28981672--28981697 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28981662 TGAGCATTCG
28981672 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
28981698 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:28984812 original size:29 final size:29
Alignment explanation
Indices: 28984744--28984816 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
28984734 TAAAAATGAT
*
28984744 TCAAAATATTATTTTCTAATTTTAAGGGGC
1 TCAAAAT-TTTTTTTCTAATTTTAAGGGGC
* ** *
28984774 CCAATTTTTTTTTTTTAACTTTTAA-GGGC
1 TCAAAATTTTTTTTCTAA-TTTTAAGGGGC
28984803 TCAAAATTTTTTTT
1 TCAAAATTTTTTTT
28984817 ATCAAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (29 bp):
TCAAAATTTTTTTTCTAATTTTAAGGGGC
Found at i:28984813 original size:30 final size:30
Alignment explanation
Indices: 28984744--28984828 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
28984734 TAAAAATGAT
* *
28984744 TCAAAATATTATTTTCTAATTTTAAGGGGC
1 TCAAAATTTTTTTTTCTAATTTTAAGGGGC
* * *
28984774 -CCAATTTTTTTTTTTTAACTTTTAA-GGGC
1 TCAAAATTTTTTTTTCTAA-TTTTAAGGGGC
*
28984803 TCAAAATTTTTTTTATCAAATTTTAA
1 TCAAAATTTTTTTT-TCTAATTTTAA
28984829 TGAATCTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 17 0.40
30 23 0.53
31 3 0.07
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (30 bp):
TCAAAATTTTTTTTTCTAATTTTAAGGGGC
Found at i:28985150 original size:24 final size:24
Alignment explanation
Indices: 28985107--28985152 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28985097 TATTTATTGA
*
28985107 TTTAAAAATAATATATTAAAACAT
1 TTTAAAAATAAAATATTAAAACAT
28985131 TTTAAAAATAAAA-ATATAAAAC
1 TTTAAAAATAAAATAT-TAAAAC
28985153 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTAAAAATAAAATATTAAAACAT
Found at i:28997695 original size:99 final size:98
Alignment explanation
Indices: 28997513--28997701 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 98
28997503 ACAAAAATTT
* *
28997513 AAATTTCAACTTGTTTCTTTAATGCACAAACAGCATACTTTAAAGACAACAAAGAATTGCAATAA
1 AAATTTCAACTTGTTTCTTTAATGCACAAACAGCATACTATAAAGACAACAAAGAAATGCAATAA
*
28997578 TCACCAGATGTTACATCAACAAACTCACACTTC
66 TCACCAGAGGTTACATCAACAAACTCACACTTC
* * * *
28997611 AAATTTTAACTTTGTTTGTTTAATGCACAAACAGCATACTATCAAGAGAA-AAAGGAAATGCAAT
1 AAATTTCAAC-TTGTTTCTTTAATGCACAAACAGCATACTATAAAGACAACAAA-GAAATGCAAT
*
28997675 AATCACACA-AGGTTATATCAACAAACT
64 AATCAC-CAGAGGTTACATCAACAAACT
28997702 GACTCAAAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 12 0.15
99 66 0.82
100 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (98 bp):
AAATTTCAACTTGTTTCTTTAATGCACAAACAGCATACTATAAAGACAACAAAGAAATGCAATAA
TCACCAGAGGTTACATCAACAAACTCACACTTC
Found at i:29003747 original size:15 final size:15
Alignment explanation
Indices: 29003723--29003756 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29003713 TATTGAAAAC
*
29003723 TCAACTCTTAATTAT
1 TCAACACTTAATTAT
*
29003738 TCAACACTTAATTTT
1 TCAACACTTAATTAT
29003753 TCAA
1 TCAA
29003757 GTTATCGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (15 bp):
TCAACACTTAATTAT
Found at i:29005545 original size:18 final size:18
Alignment explanation
Indices: 29005510--29005546 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29005500 CATATTAAAA
* *
29005510 TGATATAATATTATATTT
1 TGATATAATATGACATTT
29005528 TGATATAATATGACATTT
1 TGATATAATATGACATTT
29005546 T
1 T
29005547 AAATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
TGATATAATATGACATTT
Found at i:29006514 original size:8 final size:8
Alignment explanation
Indices: 29006501--29006526 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29006491 TTATTTTAGA
29006501 AAAATTTT
1 AAAATTTT
29006509 AAAATTTT
1 AAAATTTT
29006517 AAAATTTT
1 AAAATTTT
29006525 AA
1 AA
29006527 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAAATTTT
Found at i:29009850 original size:19 final size:20
Alignment explanation
Indices: 29009826--29009870 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
29009816 ATTTTGGATG
29009826 ATTTACA-TAACAAATCTTA
1 ATTTACAGTAACAAATCTTA
***
29009845 ATTTACAGTTTTAAATCTTA
1 ATTTACAGTAACAAATCTTA
29009865 ATTTAC
1 ATTTAC
29009871 TATGCTCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTACAGTAACAAATCTTA
Found at i:29012335 original size:15 final size:16
Alignment explanation
Indices: 29012307--29012336 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29012297 AACTTCTTAA
29012307 TTATTTCTTCAAAAAC
1 TTATTTCTTCAAAAAC
29012323 TTATTTC-TCAAAAA
1 TTATTTCTTCAAAAA
29012337 TAATTTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (16 bp):
TTATTTCTTCAAAAAC
Found at i:29014843 original size:18 final size:18
Alignment explanation
Indices: 29014820--29014856 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29014810 TATAGTCTGA
*
29014820 TATTCGATTTATTTGAAT
1 TATTCGAGTTATTTGAAT
29014838 TATTCGAGTTATTTGAAT
1 TATTCGAGTTATTTGAAT
29014856 T
1 T
29014857 TGAAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTCGAGTTATTTGAAT
Found at i:29015066 original size:58 final size:58
Alignment explanation
Indices: 29014993--29015103 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
29014983 TTGAATTCGG
* * *
29014993 TAAATTTTTTTATATT-AGAGTATGAAATTTTTTT-TTCAAAGTTAGATTTTGAACTTGA
1 TAAATATTTTCATATTGAGA-TATCAAATTTTTTTATTC-AAGTTAGATTTTGAACTTGA
* * *
29015051 TAAATATTTTCATATTGAGATTTCAATTTTTTTTATTCAAGTTAGTTTTTGAA
1 TAAATATTTTCATATTGAGATATCAAATTTTTTTATTCAAGTTAGATTTTGAA
29015104 AATCCTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 39 0.87
59 6 0.13
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (58 bp):
TAAATATTTTCATATTGAGATATCAAATTTTTTTATTCAAGTTAGATTTTGAACTTGA
Found at i:29017237 original size:22 final size:21
Alignment explanation
Indices: 29017212--29017253 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29017202 AACTTCCCAA
29017212 TAATTTGATCAAAGAAATTATT
1 TAATTT-ATCAAAGAAATTATT
* *
29017234 TAATTTTTTAAAGAAATTAT
1 TAATTTATCAAAGAAATTAT
29017254 AATTATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
TAATTTATCAAAGAAATTATT
Found at i:29017949 original size:23 final size:24
Alignment explanation
Indices: 29017897--29017949 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
29017887 GCCAAACAAT
29017897 TAATATTTAATTAACTTACTAAGAAA
1 TAATATTTAATTAA--TACTAAGAAA
29017923 -AATATTTAAATTAA-ACTAA-AAA
1 TAATATTT-AATTAATACTAAGAAA
29017945 TAATA
1 TAATA
29017950 AATTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
22 3 0.12
23 9 0.36
25 7 0.28
26 6 0.24
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATATTTAATTAATACTAAGAAA
Done.