Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 164 of 208
Found at i:53033241 original size:27 final size:27
Alignment explanation
Indices: 53033211--53033262 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53033201 TTCTTCAATT
53033211 TCTTTTTCACTCTCAATCTCTTTTTGC
1 TCTTTTTCACTCTCAATCTCTTTTTGC
* **
53033238 TCTTTTTCATTCTCTTTCTCTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTT
53033263 CCTCACTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.02, T:0.63
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTGC
Found at i:53067944 original size:61 final size:61
Alignment explanation
Indices: 53067849--53067971 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
53067839 TCTAACCATG
53067849 ACCCATAGCCTCTATTAATGGTATCTAAGGGATAGTATAATAATACTTTGAGCCAGTTTTA
1 ACCCATAGCCTCTATTAATGGTATCTAAGGGATAGTATAATAATACTTTGAGCCAGTTTTA
*
53067910 ACCCATAGCCTCTATTAATGGTATCTAAGGGATAGTGTAATAATACTTTGAGCCAGTTTTA
1 ACCCATAGCCTCTATTAATGGTATCTAAGGGATAGTATAATAATACTTTGAGCCAGTTTTA
53067971 A
1 A
53067972 TCTGGCTGCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (61 bp):
ACCCATAGCCTCTATTAATGGTATCTAAGGGATAGTATAATAATACTTTGAGCCAGTTTTA
Found at i:53076953 original size:3 final size:3
Alignment explanation
Indices: 53076945--53076996 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
53076935 TTTTCAAAGC
53076945 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53076993 ATA A
1 ATA A
53076997 GATACTTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53077161 original size:18 final size:19
Alignment explanation
Indices: 53077140--53077180 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53077130 ATTTTATAAT
*
53077140 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
53077158 TTTTAAAAATTGTTTTGAA
1 TTTTAAAAATTATTTTGAA
53077177 TTTT
1 TTTT
53077181 TTTTTGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:53077161 original size:19 final size:18
Alignment explanation
Indices: 53077125--53077181 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
53077115 TTTTAAAAAA
53077125 TATAAATTTTAT-AATTTT
1 TATAAATTTT-TGAATTTT
53077143 TATAAATATTTTGAA-TTT
1 TATAAAT-TTTTGAATTTT
*
53077161 TAAAAATTGTTTTGAATTTT
1 TATAAA-T-TTTTGAATTTT
53077181 T
1 T
53077182 TTTTGTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 16 0.48
19 13 0.39
20 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TATAAATTTTTGAATTTT
Found at i:53082130 original size:13 final size:13
Alignment explanation
Indices: 53082112--53082141 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53082102 TCTCCACTAG
53082112 AATTATACTATTT
1 AATTATACTATTT
*
53082125 AATTATATTATTT
1 AATTATACTATTT
53082138 AATT
1 AATT
53082142 TTTTATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATACTATTT
Found at i:53084367 original size:15 final size:16
Alignment explanation
Indices: 53084337--53084371 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
53084327 TTCTATAGGG
*
53084337 ATTTTACTTTTATTTT
1 ATTTTACTTGTATTTT
53084353 ATTTTAC-TGTATTTT
1 ATTTTACTTGTATTTT
53084368 ATTT
1 ATTT
53084372 AAATAAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTTTACTTGTATTTT
Found at i:53088341 original size:3 final size:3
Alignment explanation
Indices: 53088333--53088392 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
53088323 ATGAAGAGCT
* * * *
53088333 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TGA TGA -AA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
53088378 TACA TAA TAA TAA TA
1 TA-A TAA TAA TAA TA
53088393 CAAAAAGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 1 0.02
3 45 0.87
4 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53090570 original size:44 final size:44
Alignment explanation
Indices: 53090266--53090570 Score: 152
Period size: 44 Copynumber: 7.1 Consensus size: 44
53090256 TCTTTAGGAG
* * * * *
53090266 GATAAGATCTGCTTA-CTCAGTCTGCTTCGCTGCAACCTCGGGGA
1 GATAAGATCTG-TTATTTCAATCTGCTCCACTGCAACCTCAGGGA
* ** *
53090310 GATAAGA--T-TTATTTTAATCCACTCCACTGCAACTTCAGGGA
1 GATAAGATCTGTTATTTCAATCTGCTCCACTGCAACCTCAGGGA
* * * * *
53090351 GATAGGACTACTG--ACTTCAATCTGCTCCACTACTA-CTTAGGGA
1 GATAAGA-T-CTGTTATTTCAATCTGCTCCACTGCAACCTCAGGGA
** * ** *
53090394 GATAAGATCTGCCATCTTCGATCTGCTCCACT--ATTGCTTAGGGA
1 GATAAGATCTGTTAT-TTCAATCTGCTCCACTGCA-ACCTCAGGGA
* * * *
53090438 GATAAGATTTGTT-TCTT-ATGTCTGCTCCGCTGCAACCTCAGAGA
1 GATAAGATCTGTTAT-TTCA-ATCTGCTCCACTGCAACCTCAGGGA
* * * * * * *
53090482 GATAAGACCTG--A-TGCGATCTACTCTACTGCAACTTCAGAGA
1 GATAAGATCTGTTATTTCAATCTGCTCCACTGCAACCTCAGGGA
* *
53090523 GATAAGATCTGTTATTTTAATCCGCTCCACTGCAACCTCAGGGA
1 GATAAGATCTGTTATTTCAATCTGCTCCACTGCAACCTCAGGGA
53090567 GATA
1 GATA
53090571 GGATTAGTGG
Statistics
Matches: 191, Mismatches: 51, Indels: 38
0.68 0.18 0.14
Matches are distributed among these distances:
40 3 0.02
41 60 0.31
42 2 0.01
43 28 0.15
44 96 0.50
45 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
GATAAGATCTGTTATTTCAATCTGCTCCACTGCAACCTCAGGGA
Found at i:53090679 original size:216 final size:216
Alignment explanation
Indices: 53090318--53090756 Score: 614
Period size: 216 Copynumber: 2.0 Consensus size: 216
53090308 GAGATAAGAT
* *
53090318 TTATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGACTACTGACTTCAATCTGCTCCACTA
1 TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAGGACTACTGACTTCAATCTACTCCACTA
* * ** * **
53090383 CTACTTAGGGAGATAAGATCTGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATTT
66 CAACTTAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCC
* *
53090448 GTTTCTTATGTCTGCTCCGCTGCAACCTC-AGAGAGATAAGACCTGATGCGATCTACTCTACTGC
131 CTTTCTTAGGTCTGCTCCGCTGCAACCTCAAG-GAGATAAGACCTGATGCGATCTACTCTACTGC
53090512 AACTTCAGAGAGATAAGATCTG
195 AACTTCAGAGAGATAAGATCTG
* * * *
53090534 TTATTTTAATCCGCTCCACTGCAACCTCAGGGAGATAGGATTAGTGGCTTCAATCTACTCCACTG
1 TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAGGACTACTGACTTCAATCTACTCCAC--
* *
53090599 TA-AACTTAGGGAGGTAAAATCCACCATCTTCGATCTGCTCGACTACTGCTTAGGGAGATAAGA-
64 TACAACTTAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
* * * *
53090662 CCCTTTCTTCGGTCTGCTCTGCTGTAACCTTAAGGAGATAAGACCTGATGCGATCTACTCTACTG
129 CCCTTTCTTAGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTG
* *
53090727 TAACTTCAGATAGATAAGATCTG
194 CAACTTCAGAGAGATAAGATCTG
*
53090750 TAATTTT
1 TTATTTT
53090757 TTTTTCAACC
Statistics
Matches: 196, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
216 138 0.70
217 56 0.29
218 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (216 bp):
TTATTTTAATCCACTCCACTGCAACCTCAGGGAGATAGGACTACTGACTTCAATCTACTCCACTA
CAACTTAGGGAGATAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCC
CTTTCTTAGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGCA
ACTTCAGAGAGATAAGATCTG
Found at i:53090908 original size:44 final size:44
Alignment explanation
Indices: 53090848--53091056 Score: 253
Period size: 44 Copynumber: 4.8 Consensus size: 44
53090838 TTTGTAATTT
* *
53090848 TTCAATCTATTCCACTACTGACCAGGGAGATAGAATCAACAATC
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGAATCTACAATC
* *
53090892 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACCTACAATC
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGAATCTACAATC
* **
53090936 TTCAATCTATTCCACTACTGTTCAGGGAGATAGAATTCT-CAATC
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGAA-TCTACAATC
* * *
53090980 TTCAACCTATTCCACTGCTGACCAGAGAGATAGGA-CTTACAATCC
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGAATC-TACAAT-C
* **
53091025 TT-AACCTATTCCATTACTTTCCAGGGAGATAG
1 TTCAACCTATTCCACTACTGACCAGGGAGATAG
53091057 GACTAGTATC
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 134 0.95
45 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTACTGACCAGGGAGATAGAATCTACAATC
Found at i:53090945 original size:88 final size:89
Alignment explanation
Indices: 53090848--53091056 Score: 307
Period size: 88 Copynumber: 2.4 Consensus size: 89
53090838 TTTGTAATTT
*
53090848 TTCAATCTATTCCACTACTGACCAGGGAGATAGAA-TCAACAATCTTCAACCTATTCCACTACTG
1 TTCAATCTATTCCACTACTGTCCAGGGAGATAGAATTC-ACAATCTTCAACCTATTCCACTACTG
*
53090912 ACCAGGGAGATAGGACCTACAAT-C
65 ACCAGAGAGATAGGACCTACAATCC
* * *
53090936 TTCAATCTATTCCACTACTGTTCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGA
1 TTCAATCTATTCCACTACTGTCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTACTGA
*
53091001 CCAGAGAGATAGGACTTACAATCC
66 CCAGAGAGATAGGACCTACAATCC
* * *
53091025 TT-AACCTATTCCATTACTTTCCAGGGAGATAG
1 TTCAATCTATTCCACTACTGTCCAGGGAGATAG
53091057 GACTAGTATC
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
88 104 0.95
89 5 0.05
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (89 bp):
TTCAATCTATTCCACTACTGTCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTACTGA
CCAGAGAGATAGGACCTACAATCC
Found at i:53093460 original size:22 final size:22
Alignment explanation
Indices: 53093435--53093484 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
53093425 ATGATTGATA
*
53093435 TTTTTTAATTTTGAATT-TTCTT
1 TTTTTTAATTTTG-ATTCTTATT
*
53093457 TTTTTTATTTTTGATTCTTATT
1 TTTTTTAATTTTGATTCTTATT
53093479 TTTTTT
1 TTTTTT
53093485 GTGAATTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTTTAATTTTGATTCTTATT
Found at i:53094577 original size:25 final size:25
Alignment explanation
Indices: 53094527--53094592 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
53094517 AAGAAAATCC
*
53094527 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
*
53094552 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
53094577 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
53094593 TGTATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 3 0.08
25 23 0.64
26 5 0.14
27 5 0.14
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:53099962 original size:17 final size:16
Alignment explanation
Indices: 53099940--53099982 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
53099930 TACTGGACTA
53099940 TTATTTTACATTTTATT
1 TTATTTTA-ATTTTATT
*
53099957 TTATTTTATTTTTA-T
1 TTATTTTAATTTTATT
53099972 TTAGTTTTAAT
1 TTA-TTTTAAT
53099983 AAGCCGGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTTAATTTTATT
Found at i:53101868 original size:44 final size:44
Alignment explanation
Indices: 53101818--53101934 Score: 110
Period size: 44 Copynumber: 2.7 Consensus size: 44
53101808 TTTTAATCCA
* * **
53101818 CTCCACTGCAACTTCAAGGAGATAGGA-CTACTGTCTTCAATCTG
1 CTCCACTACAACTT-AAGGAGATAAGATCTACCATCTTCAATCTG
** * *
53101862 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTG
1 CTCCACTACAACTTAAGGAGATAAGATCTACCATCTTCAATCTG
*** *
53101906 CTCCACTATTGCTTAGGGAGATAAGATCT
1 CTCCACTACAACTTAAGGAGATAAGATCT
53101935 GTTTCTTCGT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 10 0.16
44 53 0.84
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCCACTACAACTTAAGGAGATAAGATCTACCATCTTCAATCTG
Found at i:53102181 original size:217 final size:215
Alignment explanation
Indices: 53101805--53102238 Score: 620
Period size: 217 Copynumber: 2.0 Consensus size: 215
53101795 GAGATAAGAT
* * * *
53101805 TTATTTTAATCCACTCCACTGCAACTTCAAGGAGATAGGACTACTGTCTTCAATCTGCTCCACTA
1 TTATTTTAATCCACTCCACTACAACCTCAAGGAGATAGGACTACTGGCTTCAATCTACTCCACTA
* * * * * *
53101870 CTGCTTAGGGAGATAAGATCTACCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCT
66 C-GCTAAGGGAGATAAAATCCACAATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCC
* *
53101935 GTTTCTTCGTTCTGCTCCGCTGCAACCTCACGGAGATAAGACCTGATGCGATCTACTCTACTGCA
130 GTTTCTTCGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGCA
53102000 ACTTCAGAGAGATAAGATCTG
195 ACTTCAGAGAGATAAGATCTG
* * * *
53102021 TTATTTTAATCCGCTCCACTACAACCTC-AGAGAGATAGGATTAGTGGCTTCAATCTACTCTACT
1 TTATTTTAATCCACTCCACTACAACCTCAAG-GAGATAGGACTACTGGCTTCAATCTACTCCAC-
53102085 GTAAC-CTAAGGGAGATAAAATCCACAATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
64 -T-ACGCTAAGGGAGATAAAATCCACAATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
* *
53102149 TCCGTTTCTTCGGTCTGCTCCGTTGTAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACT
127 TCCGTTTCTTCGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACT
* * *
53102214 TCAACTTTAGAGATATAAGATCTG
192 GCAACTTCAGAGAGATAAGATCTG
53102238 T
1 T
53102239 AATATTTTTT
Statistics
Matches: 193, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
215 2 0.01
216 52 0.27
217 136 0.70
218 1 0.01
219 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (215 bp):
TTATTTTAATCCACTCCACTACAACCTCAAGGAGATAGGACTACTGGCTTCAATCTACTCCACTA
CGCTAAGGGAGATAAAATCCACAATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCG
TTTCTTCGGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGCAA
CTTCAGAGAGATAAGATCTG
Found at i:53102398 original size:132 final size:131
Alignment explanation
Indices: 53102248--53102549 Score: 333
Period size: 132 Copynumber: 2.3 Consensus size: 131
53102238 TAATATTTTT
* **** * *
53102248 TTCAACCTACTCCACTGCTG-CTCAGGGAGACAAGG-CTGGGGTCTTCGATCTACTCCACTACTG
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGA-AAGGACTACAATCTTCAATCTACTCCACTACTA
** * * * * *
53102311 CTTAGGGAGATAAGATTTGT-AATTTTTCAATCTATTCCACTGTTGACCAGGGAGATA-GAATTC
64 CCCAGGGAGAT-AGAATTCTCAA-TCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAATT-
53102374 ACAATC
126 ACAATC
* *
53102380 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTACTAC
1 TTCAACCTATTCCACTGCTGACCAGGGAGAAAGGA-CTACAATCTTCAATCTACTCCACTACTAC
*
53102445 CCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAA
65 CCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAATTACAA
53102510 TC
130 TC
* ** *
53102512 CTCAACCTATTCCACTGCTTTCCAGGGAGATAGGACTA
1 TTCAACCTATTCCACTGCTGACCAGGGAGAAAGGACTA
53102550 GTATCTTCGA
Statistics
Matches: 145, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
131 6 0.04
132 102 0.70
133 37 0.26
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (131 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGAAAGGACTACAATCTTCAATCTACTCCACTACTACC
CAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAATTACAAT
C
Found at i:53102428 original size:88 final size:87
Alignment explanation
Indices: 53102336--53102544 Score: 328
Period size: 88 Copynumber: 2.4 Consensus size: 87
53102326 TTTGTAATTT
53102336 TTCAATCTATTCCACTGTTGACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGA
1 TTCAATCTATTCCACTGTT-ACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGA
53102401 CCAGGGAGATAGGACCTACAATC
65 CCAGGGAGATAGGACCTACAATC
** *
53102424 TTCAATCTATTCCACTACTACCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGA
1 TTCAATCTATTCCACTGTTA-CCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGA
*
53102489 CCAGGGAGATAGGACTTACAATC
65 CCAGGGAGATAGGACCTACAATC
* * *
53102512 CTCAACCTATTCCACTGCTTTCCAGGGAGATAG
1 TTCAATCTATTCCACTG-TTACCAGGGAGATAG
53102545 GACTAGTATC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
87 1 0.01
88 108 0.98
89 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (87 bp):
TTCAATCTATTCCACTGTTACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGAC
CAGGGAGATAGGACCTACAATC
Found at i:53102545 original size:44 final size:45
Alignment explanation
Indices: 53102336--53102548 Score: 283
Period size: 44 Copynumber: 4.8 Consensus size: 45
53102326 TTTGTAATTT
* * *
53102336 TTCAATCTATTCCACTGTTGACCAGGGAGATA-GAATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTCACAATC
*
53102380 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACCT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTCACAATC
* * * *
53102424 TTCAATCTATTCCACTACT-ACCCAGGGAGATA-GAATTCTCAATC
1 TTCAACCTATTCCACTGCTGA-CCAGGGAGATAGGACTTCACAATC
53102468 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTCACAATC
* **
53102512 CTCAACCTATTCCACTGCTTTCCAGGGAGATAGGACT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT
53102549 AGTATCTTCG
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
43 4 0.03
44 136 0.92
45 8 0.05
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (45 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTCACAATC
Found at i:53104008 original size:45 final size:46
Alignment explanation
Indices: 53103958--53104045 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
53103948 TATTTTTTTA
* *
53103958 TTTTTT-GGACTCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTGTT
1 TTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTGTT
* *
53104003 TTTTTTAGGAATCAAGGCGCCCTTTGTGGGTTTTCACCTTGGT
1 TTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGT
53104046 CACTTCTCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 6 0.16
46 32 0.84
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.43
Consensus pattern (46 bp):
TTTTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTGTT
Found at i:53109088 original size:3 final size:3
Alignment explanation
Indices: 53109080--53109134 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
53109070 ATGAAGAGCT
*
53109080 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TATA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA
53109127 TAA TAA TA
1 TAA TAA TA
53109135 CAAAAAGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53123229 original size:17 final size:15
Alignment explanation
Indices: 53123171--53123229 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
53123161 AGGGAGAAGC
*
53123171 AAAAGAGAAAGGAAA
1 AAAAGAGAAAAGAAA
*
53123186 AAAAAAGAAAAGAAA
1 AAAAGAGAAAAGAAA
53123201 AAAA-AGTTAAAAGAACA
1 AAAAGAG--AAAAGAA-A
53123218 TAAAAGAGAAAA
1 -AAAAGAGAAAA
53123230 AATAAATTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 17 0.46
16 7 0.19
17 5 0.14
18 4 0.11
19 2 0.05
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAGAGAAAAGAAA
Found at i:53124584 original size:15 final size:15
Alignment explanation
Indices: 53124538--53124585 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
53124528 GGAACGTAAC
53124538 GAAAAATTAAGTGTT
1 GAAAAATTAAGTGTT
* *
53124553 CTAAAAA-TAAGTATT
1 -GAAAAATTAAGTGTT
*
53124568 GAAAAATTAAATGTT
1 GAAAAATTAAGTGTT
53124583 GAA
1 GAA
53124586 TTTAATTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (15 bp):
GAAAAATTAAGTGTT
Found at i:53126673 original size:13 final size:13
Alignment explanation
Indices: 53126655--53126680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53126645 GACAATTAGC
53126655 ATATATATATATA
1 ATATATATATATA
53126668 ATATATATATATA
1 ATATATATATATA
53126681 TTCCAATTAG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:53127369 original size:15 final size:15
Alignment explanation
Indices: 53127349--53127382 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
53127339 TAAAAATTTT
53127349 AAATAAATATTGTAA
1 AAATAAATATTGTAA
*
53127364 AAATAAATATTTTAA
1 AAATAAATATTGTAA
53127379 AAAT
1 AAAT
53127383 CTTAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AAATAAATATTGTAA
Found at i:53131888 original size:26 final size:26
Alignment explanation
Indices: 53131853--53131916 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
53131843 TCATACTATC
* *
53131853 CATTTTATATATTCAACATCATAGCT
1 CATTTCATATACTCAACATCATAGCT
*
53131879 CATTTCATATACTCAACATTATAGCT
1 CATTTCATATACTCAACATCATAGCT
*
53131905 TATTTCATATAC
1 CATTTCATATAC
53131917 GTACCTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (26 bp):
CATTTCATATACTCAACATCATAGCT
Found at i:53134026 original size:25 final size:26
Alignment explanation
Indices: 53133970--53134027 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
53133960 CCTTATCAGA
*
53133970 AAGCTCACAAAGATCCAATTAACGGG
1 AAGCTCACAAAGAGCCAATTAACGGG
53133996 AAGCTCACAAAGAGCC-A-TAATCGGG
1 AAGCTCACAAAGAGCCAATTAA-CGGG
53134021 AAGCTCA
1 AAGCTCA
53134028 TAAGATCTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 3 0.10
25 12 0.40
26 15 0.50
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (26 bp):
AAGCTCACAAAGAGCCAATTAACGGG
Found at i:53136478 original size:106 final size:107
Alignment explanation
Indices: 53136232--53136486 Score: 350
Period size: 107 Copynumber: 2.4 Consensus size: 107
53136222 ACGAGATTGT
* * * * ** *
53136232 TCACACAAGCTGACGAGAATCCGCAACATATGCAAGATCTCAGCCATTTGAATGGACTATAACAT
1 TCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAACCATCGGAACGGACTATAACAT
* *
53136297 CATAATAGAGTAGCCATTCTATTCACCAGTTCACGATGCTAC
66 CATAATAGAGTAGCCATTCAATTCACCAATTCACGATGCTAC
* * **
53136339 TCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTTAACCATCGGAACGGTCTATGTCAT
1 TCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAACCATCGGAACGGACTATAACAT
*
53136404 CATAATAGAGTAGCCATTCAATTCACCAATTCA-GATGCTGC
66 CATAATAGAGTAGCCATTCAATTCACCAATTCACGATGCTAC
* * *
53136445 TCATACAAGCTGTCGAGATTCCGCAACATATGTAGAATCTCA
1 TCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCA
53136487 GACATCGCGA
Statistics
Matches: 130, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 45 0.35
107 85 0.65
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (107 bp):
TCACACAAGCTGTCGAGAATCCGCAACATATGTAGGATCTCAACCATCGGAACGGACTATAACAT
CATAATAGAGTAGCCATTCAATTCACCAATTCACGATGCTAC
Found at i:53140904 original size:14 final size:15
Alignment explanation
Indices: 53140870--53140914 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
53140860 ATTAATCTTC
53140870 AATTATAATAAATAT
1 AATTATAATAAATAT
53140885 AA-TATAATAAATA-
1 AATTATAATAAATAT
*
53140898 AATTATAGTAAAATAT
1 AATTATAAT-AAATAT
53140914 A
1 A
53140915 CCTGATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 16 0.62
15 7 0.27
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:53143978 original size:16 final size:18
Alignment explanation
Indices: 53143957--53143990 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
53143947 TACTATAGGG
53143957 ATTTTACT-TT-TATTTT
1 ATTTTACTGTTGTATTTT
53143973 ATTTTACTGTTGTATTTT
1 ATTTTACTGTTGTATTTT
53143991 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTACTGTTGTATTTT
Found at i:53147090 original size:26 final size:26
Alignment explanation
Indices: 53147054--53147108 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
53147044 AACACACCAA
*
53147054 TATCGCAGCAAAGCTACTAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
* *
53147080 TATCGTAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
53147106 TAT
1 TAT
53147109 ACTTCCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAACAG
Found at i:53147277 original size:27 final size:27
Alignment explanation
Indices: 53147255--53147508 Score: 364
Period size: 27 Copynumber: 9.4 Consensus size: 27
53147245 GAGTATAACA
* *
53147255 GTCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
53147282 GTCATTTTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
53147309 GTCATTTTAGCCTATGGGGGTATTTGG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
53147336 GTCATTTTACCTTACGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
**
53147363 GTCATTTTACCCTACAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
53147390 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
53147417 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
53147444 ATCATTTTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
53147471 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
53147498 GTCATTTTACC
1 GTCATTTTACC
53147509 TGTTAGAGTA
Statistics
Matches: 208, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 208 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:53147364 original size:81 final size:81
Alignment explanation
Indices: 53147255--53147509 Score: 411
Period size: 81 Copynumber: 3.1 Consensus size: 81
53147245 GAGTATAACA
*
53147255 GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTAGC
1 GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
*
53147320 CTATGGGGGTATTTGG
66 CTATGGGGGTATTTCG
* * *
53147336 GTCATTTTACCTTACGGGGGTATTTTGGTCATTTTACCCTACAGGGGTATTTCGATCATTTTACC
1 GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
*
53147401 CTATAGGGGTATTTCG
66 CTATGGGGGTATTTCG
* * * * *
53147417 ATCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
53147482 CTATGGGGGTATTTCG
66 CTATGGGGGTATTTCG
53147498 GTCATTTTACCT
1 GTCATTTTACCT
53147510 GTTAGAGTAT
Statistics
Matches: 157, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 157 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (81 bp):
GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
CTATGGGGGTATTTCG
Found at i:53149040 original size:27 final size:27
Alignment explanation
Indices: 53149006--53149078 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
53148996 CATTCCAACA
53149006 TTACCCTATGAGGGTATTTTGGTCATT
1 TTACCCTATGAGGGTATTTTGGTCATT
*
53149033 TTACCCTA-CAGGGGTATTTTGGTCATT
1 TTACCCTATGA-GGGTATTTTGGTCATT
*
53149060 TTATCCTATGAGGGTATTT
1 TTACCCTATGAGGGTATTT
53149079 CAATCATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (27 bp):
TTACCCTATGAGGGTATTTTGGTCATT
Found at i:53151377 original size:27 final size:26
Alignment explanation
Indices: 53151343--53151555 Score: 219
Period size: 27 Copynumber: 7.9 Consensus size: 26
53151333 CCCTCCTGAT
* * *
53151343 CGAAATACCCTCGAAGGGGAAATTGA
1 CGAAATACCCTCAAAGGGTAAAATGA
*
53151369 TCGAAATACCCTCAAAGGATAAAATGA
1 -CGAAATACCCTCAAAGGGTAAAATGA
*
53151396 CTGAAATACCCTCAAAGAGTAAAATGA
1 C-GAAATACCCTCAAAGGGTAAAATGA
* * *
53151423 CCAAAATACCCCCGAAGGGTAAAATGA
1 -CGAAATACCCTCAAAGGGTAAAATGA
*
53151450 CTGAAATACCCTCAAAGGGTAAGATGA
1 C-GAAATACCCTCAAAGGGTAAAATGA
* *
53151477 CCAAAATACCCTTAAAGGGTAAAATGA
1 -CGAAATACCCTCAAAGGGTAAAATGA
*
53151504 CTGAAATACCCTTAAAGGGTAAAATGA
1 C-GAAATACCCTCAAAGGGTAAAATGA
* * * *
53151531 TCAAAATACCCCCATAGGTTAAAAT
1 -CGAAATACCCTCAAAGGGTAAAAT
53151556 AACTGTTTTA
Statistics
Matches: 157, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.02
27 151 0.96
28 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (26 bp):
CGAAATACCCTCAAAGGGTAAAATGA
Found at i:53151484 original size:81 final size:81
Alignment explanation
Indices: 53151345--53151555 Score: 253
Period size: 81 Copynumber: 2.6 Consensus size: 81
53151335 CTCCTGATCG
* * **
53151345 AAATACCCTCGAAGGGGAAATTGATCGAAATACCCTCAAAGGATAAAATGACTGAAATACCCTCA
1 AAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGATAAAATGACCAAAATACCCTCA
53151410 AAGAGTAAAATGACCA
66 AAGAGTAAAATGACCA
* * * *
53151426 AAATACCCCCGAAGGGTAAAATGA-CTGAAATACCCTCAAAGGGTAAGATGACCAAAATACCCTT
1 AAATACCCTCGAAGGGTAAAATGATC-GAAATACCCTCAAAGGATAAAATGACCAAAATACCCTC
* **
53151490 AAAGGGTAAAATGACTG
65 AAAGAGTAAAATGACCA
** * * * *
53151507 AAATACCCTTAAAGGGTAAAATGATCAAAATACCCCCATAGGTTAAAAT
1 AAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGATAAAAT
53151556 AACTGTTTTA
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 107 0.98
82 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.18
Consensus pattern (81 bp):
AAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGATAAAATGACCAAAATACCCTCA
AAGAGTAAAATGACCA
Found at i:53151568 original size:54 final size:54
Alignment explanation
Indices: 53151344--53151560 Score: 281
Period size: 54 Copynumber: 4.0 Consensus size: 54
53151334 CCTCCTGATC
* * * * * * *
53151344 GAAATACCCTCGAAGGGGAAATTGATCGAAATACCCTCAAAGGATAAAATGACT
1 GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGACT
* *
53151398 GAAATACCCTCAAAGAGTAAAATGACCAAAATACCCCCGAAGGGTAAAATGACT
1 GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGACT
* **
53151452 GAAATACCCTCAAAGGGTAAGATGACCAAAATACCCTTAAAGGGTAAAATGACT
1 GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGACT
* * * * *
53151506 GAAATACCCTTAAAGGGTAAAATGATCAAAATACCCCCATAGGTTAAAATAACT
1 GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGACT
53151560 G
1 G
53151561 TTTTACCCCT
Statistics
Matches: 141, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 141 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (54 bp):
GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGGTAAAATGACT
Found at i:53151804 original size:26 final size:26
Alignment explanation
Indices: 53151738--53151809 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
53151728 ACGTATACTG
** *
53151738 TTACTGGCAGCTTTAATGCGTTACTA
1 TTACTGGCAGCTTTGCTGCGTCACTA
* *
53151764 TTTCTGGCAGTTTTGCTGCGTCACTA
1 TTACTGGCAGCTTTGCTGCGTCACTA
53151790 TTACTGGCAGCTTTGCTGCG
1 TTACTGGCAGCTTTGCTGCG
53151810 ATATTGGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTCACTA
Found at i:53151958 original size:28 final size:28
Alignment explanation
Indices: 53151926--53152016 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
53151916 CTGATTATTG
53151926 TATTGGGCTAAGGCCCACACTGTTACTA
1 TATTGGGCTAAGGCCCACACTGTTACTA
* * *
53151954 TATTGGGTTAAGGCCCACACATTGTTATTG
1 TATTGGGCTAAGGCCCACAC--TGTTACTA
*
53151984 TAATGGGCTAAGGCCCACACTG-TACTGA
1 TATTGGGCTAAGGCCCACACTGTTACT-A
53152012 TATTG
1 TATTG
53152017 TATAGGGCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 3 0.06
28 25 0.48
30 24 0.46
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACACTGTTACTA
Found at i:53151996 original size:30 final size:28
Alignment explanation
Indices: 53151915--53152006 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
53151905 ACTGTATTTT
53151915 ACTGATTATTGTATTGGGCTAAGGCCCAC
1 ACTG-TTATTGTATTGGGCTAAGGCCCAC
* * *
53151944 ACTGTTACTATATTGGGTTAAGGCCCAC
1 ACTGTTATTGTATTGGGCTAAGGCCCAC
*
53151972 ACATTGTTATTGTAATGGGCTAAGGCCCAC
1 AC--TGTTATTGTATTGGGCTAAGGCCCAC
53152002 ACTGT
1 ACTGT
53152007 ACTGATATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 26 0.48
29 4 0.07
30 24 0.44
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
ACTGTTATTGTATTGGGCTAAGGCCCAC
Found at i:53152025 original size:33 final size:33
Alignment explanation
Indices: 53151914--53152031 Score: 94
Period size: 33 Copynumber: 3.8 Consensus size: 33
53151904 TACTGTATTT
*
53151914 TACTGATTATTGTATTGGGCTAAGGCCCACACTG
1 TACTGA-TATTGTATAGGGCTAAGGCCCACACTG
*
53151948 TTACT-ATA---T-T-GGGTTAAGGCCCACAC--
1 -TACTGATATTGTATAGGGCTAAGGCCCACACTG
* *
53151974 -ATTGTTATTGTA-ATGGGCTAAGGCCCACACTG
1 TACTGATATTGTATA-GGGCTAAGGCCCACACTG
*
53152006 TACTGATATTGTATAGGGCTCAGGCC
1 TACTGATATTGTATAGGGCTAAGGCC
53152032 TAGACTGATT
Statistics
Matches: 65, Mismatches: 7, Indels: 24
0.68 0.07 0.25
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
28 16 0.25
29 1 0.02
30 16 0.25
33 22 0.34
34 2 0.03
35 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (33 bp):
TACTGATATTGTATAGGGCTAAGGCCCACACTG
Found at i:53156731 original size:41 final size:41
Alignment explanation
Indices: 53156674--53156756 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
53156664 CTGGGATGGT
53156674 GAATGTTTCAATTGTGGCAAGAAGGGCCA-TTTTGCTCGTGA
1 GAATGTTTCAATTGTGGCAAGAAGGGCCAGTTTT-CTCGTGA
*
53156715 GAATGTTTCAATTGTGGCAAGAAGGGCTAGTTTTCTCGTGA
1 GAATGTTTCAATTGTGGCAAGAAGGGCCAGTTTTCTCGTGA
53156756 G
1 G
53156757 TGTAGATTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (41 bp):
GAATGTTTCAATTGTGGCAAGAAGGGCCAGTTTTCTCGTGA
Found at i:53163767 original size:27 final size:27
Alignment explanation
Indices: 53163737--53163788 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53163727 ATCTTATAGA
53163737 GGTATCATAGTAATTTTACCCTATGAT
1 GGTATCATAGTAATTTTACCCTATGAT
** * *
53163764 GGTATTTTGGTCATTTTACCCTATG
1 GGTATCATAGTAATTTTACCCTATG
53163789 GGGGTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (27 bp):
GGTATCATAGTAATTTTACCCTATGAT
Found at i:53163794 original size:27 final size:27
Alignment explanation
Indices: 53163749--53163984 Score: 314
Period size: 27 Copynumber: 8.8 Consensus size: 27
53163739 TATCATAGTA
**
53163749 ATTTTACCCTATGATGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
53163776 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
* *
53163803 GTTTTACCCTATGGGGGTATTTTGTTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
* * * *
53163830 GTTTTACCGTATAGGGGTATTTTGGTT
1 ATTTTACCCTATGGGGGTATTTTGGTC
* * *
53163857 ATTTTATCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
* ***
53163884 ATTTTACCCTATGAGGGTATTTCAATC
1 ATTTTACCCTATGGGGGTATTTTGGTC
*
53163911 ATTTTATCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
53163937 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTTGGTC
53163964 ATTTTACCCTAT-GGGGTATTT
1 ATTTTACCCTATGGGGGTATTT
53163985 CGGTTATTCT
Statistics
Matches: 184, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
26 30 0.16
27 154 0.84
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTTGGTC
Found at i:53171638 original size:64 final size:65
Alignment explanation
Indices: 53171563--53171692 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 65
53171553 GGATATTCTC
* *
53171563 TAGAAGGCTAGATATTATACATGAACATTCTAGTTATTAGAT-TTTTTTAAATTAATGGTAAGGA
1 TAGAAGACTAGATATTATACATGAACATTCTAGTTATTAGATATTTTTGAAATTAATGGTAAGGA
53171627 TAGAAGACTAGATATTATACATGAACATTCTAGTTATTAGATATTTTTGAAATTAATGGTAAGGA
1 TAGAAGACTAGATATTATACATGAACATTCTAGTTATTAGATATTTTTGAAATTAATGGTAAGGA
53171692 T
1 T
53171693 GTTGACATGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 41 0.65
65 22 0.35
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (65 bp):
TAGAAGACTAGATATTATACATGAACATTCTAGTTATTAGATATTTTTGAAATTAATGGTAAGGA
Found at i:53178697 original size:9 final size:9
Alignment explanation
Indices: 53178664--53178730 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
53178654 TAAAATGATA
53178664 AATGATAAAT
1 AATGAT-AAT
53178674 AAT-ATAAT
1 AATGATAAT
53178682 ACTATGATAAT
1 A--ATGATAAT
*
53178693 AATGAT-GT
1 AATGATAAT
*
53178701 AATTATAAT
1 AATGATAAT
*
53178710 AATGATAAC
1 AATGATAAT
53178719 AAT-ATTAAT
1 AATGA-TAAT
53178728 AAT
1 AAT
53178731 CAGATCGCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 11 0.24
9 24 0.52
10 5 0.11
11 6 0.13
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (9 bp):
AATGATAAT
Found at i:53181112 original size:11 final size:11
Alignment explanation
Indices: 53181076--53181145 Score: 99
Period size: 11 Copynumber: 6.4 Consensus size: 11
53181066 TAAATCCTTT
*
53181076 CTCTC-AATTT
1 CTCTCAAATTC
53181086 CTCTCCAATATT-
1 CTCT-CAA-ATTC
53181098 CTCTCAAATTC
1 CTCTCAAATTC
53181109 CTCTCAAATTC
1 CTCTCAAATTC
53181120 CTCTCAAATTC
1 CTCTCAAATTC
53181131 CTCTCAAATTC
1 CTCTCAAATTC
53181142 CTCT
1 CTCT
53181146 TAAAAAAGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.12
11 41 0.73
12 5 0.09
13 3 0.05
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:53184712 original size:125 final size:125
Alignment explanation
Indices: 53184463--53184753 Score: 492
Period size: 126 Copynumber: 2.3 Consensus size: 125
53184453 TTAAGCCAAA
* **
53184463 CAGGAGCTACTGTAGCAAAAGCACGTCCACGTAAGAGCTTCTTTCAGTACTTTGCTGACAAAGCA
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTGCTGACAAAGCA
*
53184528 TCCTGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
66 TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
53184588 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTAC-TTTGCTGACAAAGC
* * *
53184653 ATCCTGCTTAAAGCGTTTTTGACACTATTTGGTTAGAAACGTCTTCTCGAAATTATTTTTT
65 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* *
53184714 CAGGAGCTACTGTAGCAAAAGAGCGTCCACATGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
53184754 TTTTAAATTA
Statistics
Matches: 156, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 47 0.30
126 109 0.70
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (125 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTGCTGACAAAGCA
TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:53184992 original size:29 final size:27
Alignment explanation
Indices: 53184947--53185000 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
53184937 TTTTCTTTAA
*
53184947 AACCCTAAATCTAAAAACCATAAAACCCT
1 AACCCTAAACCTAAAAA-CA-AAAACCCT
53184976 AACCCTAAACCCT-AAAACAAAAACC
1 AACCCTAAA-CCTAAAAACAAAAACC
53185001 TAAAACCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 6 0.26
28 2 0.09
29 13 0.57
30 2 0.09
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (27 bp):
AACCCTAAACCTAAAAACAAAAACCCT
Found at i:53187758 original size:88 final size:84
Alignment explanation
Indices: 53187579--53187755 Score: 205
Period size: 88 Copynumber: 2.0 Consensus size: 84
53187569 TTAAGGGTAT
* **
53187579 AAAAA-GCCCTCAAATTTTTTCAAAAAAAAGCAATTAAGCCATTTTTTTTGCATTCAATTGGGTA
1 AAAAAGGCCCTCAAAATTTTTCAAAAAAAAAAAATTAAGCCATTTTTTTTGCA-TCAATTGGGTA
**
53187643 CTTGAAATTTCAAAATACAC
65 CTTGAAATGCCAAAATACAC
*
53187663 AAAAAGGCCCTCAAAATTTTTCAAAAAAAGAAAACATTAAGCCCTTTTTTTTTTTGC-TCAATTG
1 AAAAAGGCCCTCAAAATTTTTCAAAAAAA-AAAA-ATTAAG-CC--ATTTTTTTTGCATCAATTG
* *
53187727 GGTATTTGAACTGCCAAAATACATC
61 GGTACTTGAAATGCCAAAATACA-C
53187752 AAAA
1 AAAA
53187756 GGCATCAGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
84 5 0.06
85 22 0.28
86 2 0.03
87 6 0.08
88 28 0.36
89 5 0.06
90 10 0.13
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (84 bp):
AAAAAGGCCCTCAAAATTTTTCAAAAAAAAAAAATTAAGCCATTTTTTTTGCATCAATTGGGTAC
TTGAAATGCCAAAATACAC
Found at i:53187887 original size:21 final size:21
Alignment explanation
Indices: 53187840--53187888 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
53187830 ATAAAAGTTC
*
53187840 TAAAAAAATATTAAATTTTAG
1 TAAAAAAATATTAAAATTTAG
*
53187861 TAAAAAAATATTAAAAATTTAT
1 TAAAAAAATATT-AAAATTTAG
53187883 TAAAAA
1 TAAAAA
53187889 TGATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAAAAATATTAAAATTTAG
Found at i:53188213 original size:19 final size:18
Alignment explanation
Indices: 53188191--53188303 Score: 59
Period size: 19 Copynumber: 6.0 Consensus size: 18
53188181 TATGCATTTA
53188191 ATAATCTTTTATGATTTTT
1 ATAAT-TTTTATGATTTTT
* *
53188210 ATAAAATTTTATAATTTTT
1 AT-AATTTTTATGATTTTT
* *
53188229 TTATATTTTTAATGATATTT
1 ATA-ATTTTT-ATGATTTTT
* * * *
53188249 ATATTTTTTATTAAAATTTA
1 ATAATTTTTA-T-GATTTTT
*
53188269 ATAAATTTTATTGATTTTT
1 ATAATTTTTA-TGATTTTT
*
53188288 AT--TTTTTATAATTTTT
1 ATAATTTTTATGATTTTT
53188304 CCTGCATGTC
Statistics
Matches: 70, Mismatches: 19, Indels: 13
0.69 0.19 0.13
Matches are distributed among these distances:
16 7 0.10
17 5 0.07
18 2 0.03
19 32 0.46
20 24 0.34
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (18 bp):
ATAATTTTTATGATTTTT
Found at i:53188302 original size:9 final size:9
Alignment explanation
Indices: 53188191--53188303 Score: 59
Period size: 9 Copynumber: 12.0 Consensus size: 9
53188181 TATGCATTTA
53188191 ATAATCTTTT
1 ATAAT-TTTT
*
53188201 ATGATTTTT
1 ATAATTTTT
*
53188210 ATAAAATTTT
1 AT-AATTTTT
53188220 ATAATTTTT
1 ATAATTTTT
*
53188229 TTATATTTTT
1 ATA-ATTTTT
* *
53188239 AATGATATTT
1 -ATAATTTTT
*
53188249 ATATTTTTT
1 ATAATTTTT
* *
53188258 ATTAAAATTTA
1 A-T-AATTTTT
*
53188269 ATAAATTTT
1 ATAATTTTT
*
53188278 ATTGATTTTT
1 A-TAATTTTT
53188288 AT--TTTTT
1 ATAATTTTT
53188295 ATAATTTTT
1 ATAATTTTT
53188304 CCTGCATGTC
Statistics
Matches: 78, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
7 7 0.09
9 34 0.44
10 31 0.40
11 6 0.08
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:53192970 original size:32 final size:32
Alignment explanation
Indices: 53192934--53192996 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
53192924 CAGTTAATCA
* *
53192934 ATGAGTTATCAAATTAAATTTATTAATTTATC
1 ATGAGTTATCAAATTAAAGTAATTAATTTATC
* *
53192966 ATGAGTTATTAAATTTAAGTAATTAATTTAT
1 ATGAGTTATCAAATTAAAGTAATTAATTTAT
53192997 AAGTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATTAATTTATC
Found at i:53199956 original size:16 final size:15
Alignment explanation
Indices: 53199937--53199994 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
53199927 TAATAAATAA
53199937 TAAATAAACTAAAAAT
1 TAAA-AAACTAAAAAT
* *
53199953 TAAAATACTCAAAAT
1 TAAAAAACTAAAAAT
*
53199968 T--AAAACTAAAAAA
1 TAAAAAACTAAAAAT
53199981 TAAAAATACTAAAA
1 TAAAAA-ACTAAAA
53199995 TTATTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 10 0.29
15 13 0.38
16 11 0.32
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAAAAACTAAAAAT
Found at i:53199968 original size:15 final size:14
Alignment explanation
Indices: 53199948--53199997 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
53199938 AAATAAACTA
53199948 AAAATTAAAATACT
1 AAAATTAAAATACT
*
53199962 CAAAATTAAAACTA-A
1 -AAAATTAAAA-TACT
*
53199977 AAAATAAAAATACT
1 AAAATTAAAATACT
53199991 AAAATTA
1 AAAATTA
53199998 TTATATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.07
14 15 0.52
15 10 0.34
16 2 0.07
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATTAAAATACT
Found at i:53199974 original size:28 final size:28
Alignment explanation
Indices: 53199942--53199997 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
53199932 AATAATAAAT
*
53199942 AAACT-AAAAATTAAAATACTCAAAATTA
1 AAACTAAAAAATAAAAATACT-AAAATTA
53199970 AAACTAAAAAATAAAAATACTAAAATTA
1 AAACTAAAAAATAAAAATACTAAAATTA
53199998 TTATATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (28 bp):
AAACTAAAAAATAAAAATACTAAAATTA
Found at i:53200014 original size:29 final size:29
Alignment explanation
Indices: 53199982--53200037 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53199972 ACTAAAAAAT
* * *
53199982 AAAAATAC-TAAAATTATTATATTAATGA
1 AAAAATACTTAAAAGTAATACATTAATGA
53200010 AAAAATACTTAAAAGTAATACATTAATG
1 AAAAATACTTAAAAGTAATACATTAATG
53200038 GCAAAACACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAAATACTTAAAAGTAATACATTAATGA
Found at i:53200737 original size:11 final size:11
Alignment explanation
Indices: 53200721--53200745 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53200711 TGATTTCCAT
53200721 TTATGAATAAA
1 TTATGAATAAA
53200732 TTATGAATAAA
1 TTATGAATAAA
53200743 TTA
1 TTA
53200746 AGATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
TTATGAATAAA
Found at i:53217038 original size:14 final size:14
Alignment explanation
Indices: 53217021--53217059 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
53217011 ACATATGTTT
*
53217021 TAATTTTTTATTTA
1 TAATTTTTAATTTA
*
53217035 TAATTTATAATTTA
1 TAATTTTTAATTTA
53217049 TATATTTTTAA
1 TA-ATTTTTAA
53217060 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTTAATTTA
Found at i:53224371 original size:2 final size:2
Alignment explanation
Indices: 53224366--53224486 Score: 228
Period size: 2 Copynumber: 61.5 Consensus size: 2
53224356 ACTTAAAGCA
53224366 AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
53224407 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
53224448 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
53224487 TATATATGTC
Statistics
Matches: 117, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
1 2 0.02
2 115 0.98
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:53226842 original size:2 final size:2
Alignment explanation
Indices: 53226835--53226859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53226825 TTGTGGTGGC
53226835 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
53226860 TGGTGGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53231357 original size:38 final size:38
Alignment explanation
Indices: 53231315--53231393 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
53231305 CTAACCCGGG
53231315 TCTGATTTTCACGAACACAGTACCCTAACTTTTCAAAA
1 TCTGATTTTCACGAACACAGTACCCTAACTTTTCAAAA
53231353 TCTGATTTTCACGAACACAGTACCCTAACTTTTCAAAA
1 TCTGATTTTCACGAACACAGTACCCTAACTTTTCAAAA
53231391 TCT
1 TCT
53231394 AAATCCAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.33
Consensus pattern (38 bp):
TCTGATTTTCACGAACACAGTACCCTAACTTTTCAAAA
Found at i:53234444 original size:46 final size:46
Alignment explanation
Indices: 53234377--53234532 Score: 264
Period size: 46 Copynumber: 3.5 Consensus size: 46
53234367 TGATTAGTGA
*
53234377 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
53234423 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
53234469 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
53234514 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
53234533 ATCATACGTA
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 19 0.18
46 71 0.66
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:53239994 original size:36 final size:36
Alignment explanation
Indices: 53239954--53240027 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
53239944 AGTTAGCTTT
53239954 TACTTTAGTATGAGTCATTGTACTATGATTTATCTG
1 TACTTTAGTATGAGTCATTGTACTATGATTTATCTG
53239990 TACTTTAGTATGAGTCATTGTACTATGATTTATCTG
1 TACTTTAGTATGAGTCATTGTACTATGATTTATCTG
53240026 TA
1 TA
53240028 TGTCCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (36 bp):
TACTTTAGTATGAGTCATTGTACTATGATTTATCTG
Found at i:53240013 original size:20 final size:20
Alignment explanation
Indices: 53239954--53240013 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
53239944 AGTTAGCTTT
53239954 TACTTTAGTATGAGTCATTG
1 TACTTTAGTATGAGTCATTG
* *
53239974 TAC-----TATGATTTATCTG
1 TACTTTAGTATGAGTCAT-TG
53239990 TACTTTAGTATGAGTCATTG
1 TACTTTAGTATGAGTCATTG
53240010 TACT
1 TACT
53240014 ATGATTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
20 9 0.30
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.47
Consensus pattern (20 bp):
TACTTTAGTATGAGTCATTG
Found at i:53243441 original size:49 final size:49
Alignment explanation
Indices: 53243369--53243468 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
53243359 GGGTTTAGAT
53243369 ATCACCCATGCAAGATTTAAATATGTCCACACTACTGTTGAAACAAGAC
1 ATCACCCATGCAAGATTTAAATATGTCCACACTACTGTTGAAACAAGAC
*
53243418 ATCACCCATGCAAGGTTTAAATATGTCCACACTACTGTTGAAACAAGAC
1 ATCACCCATGCAAGATTTAAATATGTCCACACTACTGTTGAAACAAGAC
53243467 AT
1 AT
53243469 TCTCGAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (49 bp):
ATCACCCATGCAAGATTTAAATATGTCCACACTACTGTTGAAACAAGAC
Found at i:53244040 original size:17 final size:17
Alignment explanation
Indices: 53244020--53244056 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
53244010 GAACGTGATG
53244020 GGCTCAAATTACCACAA
1 GGCTCAAATTACCACAA
53244037 GGCTCAAATTACCACAA
1 GGCTCAAATTACCACAA
53244054 GGC
1 GGC
53244057 CCAATAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.30, G:0.16, T:0.16
Consensus pattern (17 bp):
GGCTCAAATTACCACAA
Found at i:53244865 original size:22 final size:22
Alignment explanation
Indices: 53244835--53244909 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
53244825 GTGTTTCTAC
*
53244835 ATTGGAGGGTAGATTGGAGCTG
1 ATTGAAGGGTAGATTGGAGCTG
** *
53244857 ATTGAAGGG-AG-TTGTGAAATC
1 ATTGAAGGGTAGATTG-GAGCTG
* **
53244878 TTTCTTAGGGTAGATTGGAGCTG
1 ATT-GAAGGGTAGATTGGAGCTG
53244901 ATTGAAGGG
1 ATTGAAGGG
53244910 AGTTGTGAAA
Statistics
Matches: 36, Mismatches: 13, Indels: 8
0.63 0.23 0.14
Matches are distributed among these distances:
20 3 0.08
21 7 0.19
22 16 0.44
23 7 0.19
24 3 0.08
ACGTcount: A:0.25, C:0.05, G:0.39, T:0.31
Consensus pattern (22 bp):
ATTGAAGGGTAGATTGGAGCTG
Found at i:53244903 original size:44 final size:44
Alignment explanation
Indices: 53244840--53244927 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
53244830 TCTACATTGG
53244840 AGGGTAGATTGGAGCTGATTGAAGGGAGTTGTGAAATCTTTCTT
1 AGGGTAGATTGGAGCTGATTGAAGGGAGTTGTGAAATCTTTCTT
53244884 AGGGTAGATTGGAGCTGATTGAAGGGAGTTGTGAAATCTTTCTT
1 AGGGTAGATTGGAGCTGATTGAAGGGAGTTGTGAAATCTTTCTT
53244928 GATTTCAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (44 bp):
AGGGTAGATTGGAGCTGATTGAAGGGAGTTGTGAAATCTTTCTT
Found at i:53252738 original size:66 final size:66
Alignment explanation
Indices: 53252632--53252763 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
53252622 CAAACACAAA
*
53252632 TATTTTAATACAAGACCAAATGGTAAGTTGTAGCCTTACCACTGAACTAGCAAACCCATTCTTGT
1 TATTTTAATACAAGACCAAATGGTAAGTTGCAGCCTTACCACTGAACTAGCAAACCCATTCTTGT
53252697 C
66 C
*
53252698 TATTTTAATACAAGACCAAATGGTAAGTTGCAGCCTTACCACTGAACTAGCAAACCCGTTCTTGT
1 TATTTTAATACAAGACCAAATGGTAAGTTGCAGCCTTACCACTGAACTAGCAAACCCATTCTTGT
53252763 C
66 C
53252764 AACACAATTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (66 bp):
TATTTTAATACAAGACCAAATGGTAAGTTGCAGCCTTACCACTGAACTAGCAAACCCATTCTTGT
C
Found at i:53256842 original size:22 final size:23
Alignment explanation
Indices: 53256801--53256858 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
53256791 TAAAATAAAT
53256801 AAATAAAACTTTAAAACAAAAC-A
1 AAATAAAAC-TTAAAACAAAACTA
*
53256824 AAATAAAACTTAAACCAAAACTA
1 AAATAAAACTTAAAACAAAACTA
*
53256847 GAATAAAA-TTAA
1 AAATAAAACTTAA
53256859 TTCCACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.19
Consensus pattern (23 bp):
AAATAAAACTTAAAACAAAACTA
Found at i:53263447 original size:36 final size:36
Alignment explanation
Indices: 53263400--53263468 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
53263390 GAGTGTACGA
*
53263400 GGAAACTGCACAACTAGAATGAACTAAGGCAAACGG
1 GGAAACTGCACAACGAGAATGAACTAAGGCAAACGG
53263436 GGAAACTGCACAACGAGAATGAACTAAGGCAAA
1 GGAAACTGCACAACGAGAATGAACTAAGGCAAA
53263469 AAGCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (36 bp):
GGAAACTGCACAACGAGAATGAACTAAGGCAAACGG
Found at i:53265130 original size:27 final size:27
Alignment explanation
Indices: 53265046--53265133 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
53265036 AGAGGTCAAT
53265046 AAATGACCAAATTACCCCTACAAGGTA
1 AAATGACCAAATTACCCCTACAAGGTA
* * * *
53265073 AAAAGATCAAATTACCCCTATAGGGTA
1 AAATGACCAAATTACCCCTACAAGGTA
* * *
53265100 AAATGACCGAATTACCCCCACAAGATA
1 AAATGACCAAATTACCCCTACAAGGTA
53265127 AAATGAC
1 AAATGAC
53265134 TGAAATACCC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (27 bp):
AAATGACCAAATTACCCCTACAAGGTA
Found at i:53265143 original size:54 final size:54
Alignment explanation
Indices: 53265046--53265157 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
53265036 AGAGGTCAAT
* *
53265046 AAATGACCAAATTACCCCTACAAGGTAAAAAGATCAAATTACCC-CTATAGGGTA
1 AAATGACCAAATTACCCCCACAAGATAAAAAGATCAAATTACCCTC-ATAGGGTA
* * * *
53265100 AAATGACCGAATTACCCCCACAAGATAAAATGACTGAAA-TACCCTCCTAGGGTA
1 AAATGACCAAATTACCCCCACAAGATAAAAAGA-TCAAATTACCCTCATAGGGTA
53265154 AAAT
1 AAAT
53265158 AACTGTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 45 0.90
55 5 0.10
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (54 bp):
AAATGACCAAATTACCCCCACAAGATAAAAAGATCAAATTACCCTCATAGGGTA
Found at i:53265155 original size:27 final size:27
Alignment explanation
Indices: 53265085--53265171 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
53265075 AAGATCAAAT
* * *
53265085 TACCCCTATAGGGTAAAATGACCGAAT
1 TACCCCCATAGGGTAAAATGACTGAAA
* * *
53265112 TACCCCCACAAGATAAAATGACTGAAA
1 TACCCCCATAGGGTAAAATGACTGAAA
* **
53265139 TACCCTCC-TAGGGTAAAATAACTGTTA
1 TACCC-CCATAGGGTAAAATGACTGAAA
53265166 TACCCC
1 TACCCC
53265172 TAGGAGATGA
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
26 1 0.02
27 44 0.94
28 2 0.04
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (27 bp):
TACCCCCATAGGGTAAAATGACTGAAA
Found at i:53265589 original size:27 final size:28
Alignment explanation
Indices: 53265527--53265628 Score: 179
Period size: 28 Copynumber: 3.7 Consensus size: 28
53265517 ACTGTACCGA
53265527 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
53265555 TACTGTATTGGGCTAAGGCCCAC-TTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
53265582 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
53265610 TACTCTTTTGGGCTAAGGC
1 TACTGTATTGGGCTAAGGC
53265629 TAACACTGTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
27 27 0.38
28 44 0.62
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:53266528 original size:23 final size:22
Alignment explanation
Indices: 53266487--53266529 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53266477 TTTTTTAGTT
* *
53266487 AAATTTGACCTCAATCTTTTTC
1 AAATTTGACATCAACCTTTTTC
53266509 AAATTTGACAATCAACCTTTT
1 AAATTTGAC-ATCAACCTTTT
53266530 GAAAAAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTTGACATCAACCTTTTTC
Found at i:53267171 original size:7 final size:7
Alignment explanation
Indices: 53267150--53267359 Score: 138
Period size: 7 Copynumber: 30.1 Consensus size: 7
53267140 TTAAAATTAG
53267150 ACCCTAA
1 ACCCTAA
*
53267157 ACACTAA
1 ACCCTAA
*
53267164 ACCATAA
1 ACCCTAA
53267171 ACCCTAA
1 ACCCTAA
*
53267178 GCCCATAA
1 ACCC-TAA
53267186 ACCCTAA
1 ACCCTAA
*
53267193 ACCATAA
1 ACCCTAA
**
53267200 ACTTTAA
1 ACCCTAA
* *
53267207 ATCTTAA
1 ACCCTAA
53267214 ACCCTAA
1 ACCCTAA
*
53267221 GCCCCTAA
1 -ACCCTAA
*
53267229 GCCCTAA
1 ACCCTAA
*
53267236 ACCATAA
1 ACCCTAA
*
53267243 A-CCTAC
1 ACCCTAA
53267249 ACCCTAA
1 ACCCTAA
* *
53267256 GCCATAA
1 ACCCTAA
*
53267263 A-CCTAC
1 ACCCTAA
53267269 ACCCTAA
1 ACCCTAA
*
53267276 ACCGTAA
1 ACCCTAA
*
53267283 ACACTAA
1 ACCCTAA
* *
53267290 ACTCTTA
1 ACCCTAA
**
53267297 ACATTAA
1 ACCCTAA
* *
53267304 ATCATAA
1 ACCCTAA
*
53267311 ACCTTAA
1 ACCCTAA
*
53267318 ACCTTAA
1 ACCCTAA
53267325 ACCCTAA
1 ACCCTAA
*
53267332 ACCATAA
1 ACCCTAA
*
53267339 A-CCTAT
1 ACCCTAA
53267345 ACCCTAA
1 ACCCTAA
53267352 ACCCTAA
1 ACCCTAA
53267359 A
1 A
53267360 TATATATTAC
Statistics
Matches: 154, Mismatches: 44, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
6 12 0.08
7 130 0.84
8 12 0.08
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:53267253 original size:20 final size:20
Alignment explanation
Indices: 53267230--53267359 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
53267220 AGCCCCTAAG
53267230 CCCTAAACCATAAACCTACA
1 CCCTAAACCATAAACCTACA
*
53267250 CCCTAAGCCATAAACCTACA
1 CCCTAAACCATAAACCTACA
* *
53267270 CCCTAAACCGTAAACACTAAA
1 CCCTAAACCATAAAC-CTACA
* *
53267291 CTCTTAA-CATTAAA--T-CA
1 CCCTAAACCA-TAAACCTACA
* *
53267308 ---TAAACCTTAAACCTTAAA
1 CCCTAAACCATAAACC-TACA
*
53267326 CCCTAAACCATAAACCTATA
1 CCCTAAACCATAAACCTACA
*
53267346 CCCTAAACCCTAAA
1 CCCTAAACCATAAA
53267360 TATATATTAC
Statistics
Matches: 86, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
14 7 0.08
15 1 0.01
17 2 0.02
18 2 0.02
20 49 0.57
21 25 0.29
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (20 bp):
CCCTAAACCATAAACCTACA
Found at i:53267802 original size:41 final size:41
Alignment explanation
Indices: 53267757--53267861 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 41
53267747 TTTTGCGGTA
*
53267757 TTTTCTAAAAAGCGCTGCTAATGCTCGATCTA-TATTGGCAT
1 TTTTCTAAAAAGCGCTGCTAATGCTCGACCTACTA-TGGCAT
* * * **
53267798 TTTTC-AAATAGGGCCGCTAATGCTCGACCTACTATGGTGT
1 TTTTCTAAAAAGCGCTGCTAATGCTCGACCTACTATGGCAT
*
53267838 TTTTTTAAAAAGCG-TCGCTAATGC
1 TTTTCTAAAAAGCGCT-GCTAATGC
53267862 CACTAAAGCT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
40 30 0.59
41 21 0.41
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
TTTTCTAAAAAGCGCTGCTAATGCTCGACCTACTATGGCAT
Found at i:53267860 original size:156 final size:153
Alignment explanation
Indices: 53267541--53267974 Score: 394
Period size: 156 Copynumber: 2.9 Consensus size: 153
53267531 ATCACAAACA
* *
53267541 CCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTT-CTTAACTTTTTTACGGCATTTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGA-GTCGTTTTGCTCAACTTTTTTGCGGCATTTT
* * * * ** * * *
53267605 GC-AAAAAGTGCCACTAACGCTCGATCTATAGCGGCGTTTTTCGACAAAGCATCACTAATTCTTG
65 -CTAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTC-A-AAAGCGCCGCTAATGCTCG
* * *
53267669 ATCTATTGCGGCATTTTTTAAAATGTT
127 ACCTATTGCGGCATTTTTTAAAAAGGT
* * *
53267696 CCGTTAATGCCACTAAATCTCAACAACAAACGATGTCGTTTTGCTCAACTTTTTTGCGGTATTTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGA-GTCGTTTTGCTCAACTTTTTTGCGGCATTTT
* * * *
53267761 CTAAAAAGCGCTGCTAATGCTCGATCTATATTGGCATTTTTCAAATAGGGCCGCTAATGCTCGAC
65 CTAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAAA-AGCGCCGCTAATGCTCGAC
*
53267826 CTACTATG-GTG-TTTTTTTAAAAAGCGT
129 CTA-T-TGCG-GCATTTTTTAAAAAG-GT
* * *
53267853 -CGCTAATGCCACTAAAGCT---C-A-AAA--A---GTTTTGCTCAACTTTTTTGTGGCGTTTTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGAGTCGTTTTGCTCAACTTTTTTGCGGCATTTTC
* * * * *
53267907 TGAAAAGCACCGCTAATGCTTGATCTATAGTGGCGTTTTTTAAAAAGTGCCGCTAATGCTCGACC
66 TAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCG-TTTTTCAAAAGCGCCGCTAATGCTCGACC
53267972 TAT
130 TAT
53267975 AGCGAAGTTT
Statistics
Matches: 234, Mismatches: 37, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
144 1 0.00
145 75 0.32
146 8 0.03
149 1 0.00
151 3 0.01
152 1 0.00
153 1 0.00
154 2 0.01
155 56 0.24
156 82 0.35
157 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (153 bp):
CCGCTAATGCCACTAAAGCTCAACAACAAACGAGTCGTTTTGCTCAACTTTTTTGCGGCATTTTC
TAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAAAAGCGCCGCTAATGCTCGACCT
ATTGCGGCATTTTTTAAAAAGGT
Found at i:53267940 original size:40 final size:40
Alignment explanation
Indices: 53267896--53267976 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
53267886 CAACTTTTTT
* * *
53267896 GTGGCGTTTTTTGAAAAGCACCGCTAATGCTTGATCTATA
1 GTGGCGTTTTTTAAAAAGCACCGCTAATGCTCGACCTATA
**
53267936 GTGGCGTTTTTTAAAAAGTGCCGCTAATGCTCGACCTATA
1 GTGGCGTTTTTTAAAAAGCACCGCTAATGCTCGACCTATA
53267976 G
1 G
53267977 CGAAGTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
GTGGCGTTTTTTAAAAAGCACCGCTAATGCTCGACCTATA
Found at i:53268002 original size:145 final size:145
Alignment explanation
Indices: 53267733--53268006 Score: 356
Period size: 145 Copynumber: 1.9 Consensus size: 145
53267723 AAACGATGTC
* * * *
53267733 GTTTTGCTCAACTTTTTTGCGGTATTTTCTAAAAAGCGCTGCTAATGCTCGATCTATATTGGCAT
1 GTTTTGCTCAACTTTTTTGCGGCATTTTCTAAAAAGCACCGCTAATGCTCGATCTATAGTGGCAT
* * *
53267798 TTTTCAAATAGGGCCGCTAATGCTCGACCTACTATGGTGTTTTTTTAAAAAGCGTCGCTAATGCC
66 TTTTCAAAAAGGGCCGCTAATGCTCGACCTACTATGGAGTTTTTTTAAAAAGCGCCGCTAATGCC
53267863 ACTAAAGCTCAAAAA
131 ACTAAAGCTCAAAAA
* * * * * *
53267878 GTTTTGCTCAACTTTTTTGTGGCGTTTTTTGAAAAGCACCGCTAATGCTTGATCTATAGTGGCGT
1 GTTTTGCTCAACTTTTTTGCGGCATTTTCTAAAAAGCACCGCTAATGCTCGATCTATAGTGGCAT
* * *
53267943 TTTTTAAAAAGTGCCGCTAATGCTCGACCTA-TA-GCGAAGTTTGTTTTAGAAA-CGCCGCTAAT
66 TTTTCAAAAAGGGCCGCTAATGCTCGACCTACTATG-G-AGTTT-TTTTAAAAAGCGCCGCTAAT
53268005 GC
128 GC
53268007 TTGACCTTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
143 1 0.01
144 3 0.03
145 98 0.89
146 8 0.07
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (145 bp):
GTTTTGCTCAACTTTTTTGCGGCATTTTCTAAAAAGCACCGCTAATGCTCGATCTATAGTGGCAT
TTTTCAAAAAGGGCCGCTAATGCTCGACCTACTATGGAGTTTTTTTAAAAAGCGCCGCTAATGCC
ACTAAAGCTCAAAAA
Found at i:53283647 original size:19 final size:21
Alignment explanation
Indices: 53283608--53283653 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
53283598 ATCTCTTCAT
53283608 ATAA-ATATCATATATCATAC
1 ATAATATATCATATATCATAC
*
53283628 ATTATATATC-TATATC-TAC
1 ATAATATATCATATATCATAC
53283647 ATAATAT
1 ATAATAT
53283654 GTATTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATATCATATATCATAC
Found at i:53284288 original size:16 final size:18
Alignment explanation
Indices: 53284267--53284304 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
53284257 TTTAAATTGC
53284267 ATATTTAA-AAGAATA-A
1 ATATTTAACAAGAATAGA
*
53284283 ATATTTAACAATAATAGA
1 ATATTTAACAAGAATAGA
53284301 ATAT
1 ATAT
53284305 AAAAAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
ATATTTAACAAGAATAGA
Found at i:53291482 original size:18 final size:19
Alignment explanation
Indices: 53291437--53291482 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
53291427 TCTTATGCTT
*
53291437 AATTCCAATACGTGTCTTCA
1 AATTCCAA-ACGTGTATTCA
53291457 AATT-CAAACGTG-ATTCA
1 AATTCCAAACGTGTATTCA
*
53291474 TATTCCAAA
1 AATTCCAAA
53291483 GTTATTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 3 0.13
20 4 0.17
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.33
Consensus pattern (19 bp):
AATTCCAAACGTGTATTCA
Found at i:53292489 original size:17 final size:18
Alignment explanation
Indices: 53292454--53292490 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53292444 GCCCACATTG
*
53292454 CATGCCCGTGTGCGCCCA
1 CATGCCCATGTGCGCCCA
53292472 CATGCCCATGTG-GCCCA
1 CATGCCCATGTGCGCCCA
53292489 CA
1 CA
53292491 CGACCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.16
Consensus pattern (18 bp):
CATGCCCATGTGCGCCCA
Found at i:53296166 original size:21 final size:22
Alignment explanation
Indices: 53296108--53296192 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 22
53296098 CCTGATCAGT
*
53296108 ATACGAAACAT-AAGTGCCTA-
1 ATACGACACATAAAGTGCCTAG
* * ** *
53296128 AAACGAGACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTAG
53296149 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT-AG
53296172 ATACGACACATAAAGTGCCTA
1 ATACGACACATAAAGTGCCTA
53296193 ATCGGCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 8 0.15
21 22 0.42
22 1 0.02
23 21 0.40
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.16
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAG
Found at i:53296178 original size:23 final size:23
Alignment explanation
Indices: 53296148--53296191 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
53296138 CGAGGTGCCT
53296148 GATACGACACATAAAGTGCCTGA
1 GATACGACACATAAAGTGCCTGA
53296171 GATACGACACATAAAGTGCCT
1 GATACGACACATAAAGTGCCT
53296192 AATCGGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (23 bp):
GATACGACACATAAAGTGCCTGA
Found at i:53297237 original size:18 final size:19
Alignment explanation
Indices: 53297214--53297257 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
53297204 TTTCGTCTCT
*
53297214 TTCTTTTTTTC-TTTTCTA
1 TTCTTTTTCTCTTTTTCTA
53297232 TTCTTTTTCTCTTTTTCTA
1 TTCTTTTTCTCTTTTTCTA
53297251 TTCTTTT
1 TTCTTTT
53297258 ATTTTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTTCTCTTTTTCTA
Found at i:53297246 original size:24 final size:24
Alignment explanation
Indices: 53297213--53297263 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
53297203 TTTTCGTCTC
* * *
53297213 TTTCTTTTTTTCTTTTCTATTCTT
1 TTTCTCTTTTTCTATTCTATTATT
*
53297237 TTTCTCTTTTTCTATTCTTTTATT
1 TTTCTCTTTTTCTATTCTATTATT
53297261 TTT
1 TTT
53297264 TGTTATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCTCTTTTTCTATTCTATTATT
Found at i:53299951 original size:18 final size:17
Alignment explanation
Indices: 53299925--53299990 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
53299915 AATAAAAATA
*
53299925 AACGTTTTGAAATTGAAT
1 AACGATTTGAAA-TGAAT
53299943 AACGATTTGTAAATGAAT
1 AACGATTTG-AAATGAAT
* *
53299961 AATGTTTTGAAAATGAAT
1 AACGATTTG-AAATGAAT
53299979 GACACGATTTGA
1 -A-ACGATTTGA
53299991 GGTTATGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 28 0.72
19 5 0.13
20 6 0.15
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
AACGATTTGAAATGAAT
Found at i:53311303 original size:43 final size:41
Alignment explanation
Indices: 53311209--53311357 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
53311199 AGATGCCCCG
** *
53311209 AGGGGTTGCTAAGTGCTGATTCCCC-TAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGT-ATCCTTGATTATAA
* * *
53311250 ATGTGATTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAA
1 A-GGGGTTGCTAAGTGCTGATTCC-CCGTATCCTTGATTAT-AA
* *
53311294 AGGGGTTGCTATGTGCTGATTCCCCGTATCAC-TGAATAT-A
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATC-CTTGATTATAA
53311334 AGGTGGTTGCTAAGTGCTGATTCC
1 AGG-GGTTGCTAAGTGCTGATTCC
53311358 ACCGAGTAAC
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
40 4 0.04
41 20 0.22
42 32 0.35
43 31 0.34
44 4 0.04
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCCTTGATTATAA
Found at i:53314774 original size:25 final size:25
Alignment explanation
Indices: 53314746--53314800 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
53314736 CACCGATTTT
*
53314746 AGCTCATATGAGCTTACCAATACTC
1 AGCTCACATGAGCTTACCAATACTC
* * *
53314771 AGCTCGCATGAGCTTACCATTATTC
1 AGCTCACATGAGCTTACCAATACTC
53314796 AGCTC
1 AGCTC
53314801 GGAGGAGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (25 bp):
AGCTCACATGAGCTTACCAATACTC
Found at i:53314801 original size:25 final size:25
Alignment explanation
Indices: 53314753--53314810 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
53314743 TTTAGCTCAT
53314753 ATGAGCTTACCAATACTCAGCTCGC
1 ATGAGCTTACCAATACTCAGCTCGC
* * *
53314778 ATGAGCTTACCATTATTCAGCTCGG
1 ATGAGCTTACCAATACTCAGCTCGC
*
53314803 AGGAGCTT
1 ATGAGCTT
53314811 TCCGTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
ATGAGCTTACCAATACTCAGCTCGC
Found at i:53317242 original size:44 final size:43
Alignment explanation
Indices: 53317164--53317247 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
53317154 ACCTCTAACT
* * *
53317164 TGGACAAATGTAGAAGAAAATATCAATGGATCCCCTACTCCTAA
1 TGGAAAAATGTAAAAGAAAATATCAAAGGATCCCC-ACTCCTAA
* * *
53317208 TGGAAAAATGTAAAAGCAAATATGAAAGGGTCCCCACTCC
1 TGGAAAAATGTAAAAGAAAATATCAAAGGATCCCCACTCC
53317248 CAACGCCACT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.15
44 29 0.85
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (43 bp):
TGGAAAAATGTAAAAGAAAATATCAAAGGATCCCCACTCCTAA
Found at i:53321709 original size:636 final size:637
Alignment explanation
Indices: 53320127--53321803 Score: 1983
Period size: 645 Copynumber: 2.6 Consensus size: 637
53320117 GGGCATTACA
* * * *
53320127 GATAACAATGACTCTAATTAGACGC-CCAACTTGGACAAATGTAGAAGCAAATATCTATGGATCC
1 GATAACAATGACTCTGATTTGAC-CTCCAACTTAGACAAATGTAGAAGCAAATATCAATGGATCC
* * * * * * *
53320191 CTTACTCCTAATGGACAAATATGAAAGCATATATGAAAGGTTCCCCACTCCCAATGCTACCTAAT
65 CCTACTCCTAATGGACAAATGTAAAAGCAAATATAAAAGG-TCCCCACTCCCAACGCTGCCTAAT
*
53320256 ATATTCAAATTTGACTACTCACATATTATTATTATTATTCACAATTATCAATATTTTTTTGTCAA
129 ATATTCAAATTTGACTACT--C--A-TAGTATTATTATTCACAATTATCAATATTTTTTTGTCAA
* * * * * *
53320321 AATCACGTTGTTCATTGTCGGTAGCAATGACTAATCTCTTCGTCTTGGGTGCTCTTAAAAAAAGT
189 AATCA-GGTGTTCATTGTCGATAGCAATGACTAATCCCTTAGTC-TGGGTACTCTTCAAAAAAGT
* * * ** **
53320386 AAACAGTGGCCATGAAATGTGCTCCATTCCCATGGGCTAGGATCCAACTCCTTACCTCATAATTA
252 AAACGGTGACCATGAAATGTGCTCCATTCCCATGAGCGGGGATCCAACTCCAAACCTCATAATTA
* *
53320451 AAGGATTAGGTGAGCAACGACCACACCATTATTAATAACACAGTTAAAATG-TCATCATTGTG-T
317 AA-GATTAGGTGAGTAACGACCACACCATTATTAATAACACAGTTAAAATGCT-ATCATTATGTT
* * * * *
53320514 TGTTTTCTAAATAAAGAAAAAAACACGAAAACTATTTTGTTTTATAATAGAAATGGGAAATTTGG
380 TTTTTTCTAAACAAAGAAAAAAACACGAAAAATATTTTGTTTTATAATAGAAAAGAGAAATTTGG
* * *
53320579 AATTTAAGGAGTAGTTAGATGAAAATGGCTAAACGATATTGTAATTATCATAATAGAATGTTATA
445 AATTTAAGGAGTAGTTAGATGAAAATGGCTAAACGATATGGGAATTATCATAATAGAAGGTTATA
* * * *
53320644 AAAGCAATTATGAAAGGTCCCCTCACAACCGTCTCTGCTAAACTCATATTCAAATTTGATTACCC
510 AAAGCAATTATGAAA-GT---CTCAC-ACCGACGCTGCCAAACTCATAGTCAAATTTGATTACCC
* * *
53320709 ATAGTATTATTATTATTATTTACAATTATCAACCATTTTTTTTTGTTGAAATCAAGGTGTCCAAT
570 AGAGTATTACTATTATTATTTACAATTATCAACCATTTTTTTTTGTTAAAATCAAGGTGTCCAAT
*
53320774 GTT
635 GCT
* * * * *
53320777 GATAACAATGATTCTTATTTGACCTCCAACTTAGACAAAGGTAGAAACAAATATCAGTGGATCCC
1 GATAACAATGACTCTGATTTGACCTCCAACTTAGACAAATGTAGAAGCAAATATCAATGGATCCC
* * * *
53320842 CCACTCCTAATGGACAAATGTAAAAGAAAATGTTAAATGGTCCCCACTCCCAACGCTGCCTAATA
66 CTACTCCTAATGGACAAATGTAAAAGCAAAT-ATAAAAGGTCCCCACTCCCAACGCTGCCTAATA
* * *
53320907 TATGCAAAATAT-ACTACTCATAGTATTATTATTCATAATTATCAATATTTTTTTGTCAAAATCA
130 TATTC-AAATTTGACTACTCATAGTATTATTATTCACAATTATCAATATTTTTTTGTCAAAATCA
* * *
53320971 TGGTGTTCATTGTCGATAGCAATGACTAATCCCTTCATTGTGGGTGA-TGTTCAAAAAAGTAAAC
194 -GGTGTTCATTGTCGATAGCAATGACTAATCCCTT-AGTCTGGGT-ACTCTTCAAAAAAGTAAAC
* **
53321035 GGT-AGCCATGAAATGTGATCCATTTTCAT-AGGCGGGGATCCAACTCCAAACCTCATAATTAAG
256 GGTGA-CCATGAAATGTGCTCCATTCCCATGA-GCGGGGATCCAACTCCAAACCTCATAATTAA-
* *
53321098 AGATTAGGTGAGTAATGACCACACCATTATTAATAACACAGTTAAGATGCTATCATTATGTTTTT
318 AGATTAGGTGAGTAACGACCACACCATTATTAATAACACAGTTAAAATGCTATCATTATGTTTTT
*
53321163 TTTCTAAACAAAGAAAAAAACACGAAAAATATTTT-TTTTATAATAGAAAAGAGAAATTTGGGAT
383 TTTCTAAACAAAGAAAAAAACACGAAAAATATTTTGTTTTATAATAGAAAAGAGAAATTTGGAAT
* * * *
53321227 TTAATGAGTAGTTAGATGAAAATGGCTAAACGATCTGGGAATTTTCATAATAGAAGGTTGTAAAA
448 TTAAGGAGTAGTTAGATGAAAATGGCTAAACGATATGGGAATTATCATAATAGAAGGTTATAAAA
* * *
53321292 GTAA-TATGAAA-T-T-TC-CCGACGCTGCCAAACTCATAGTCAAATTTGATTACTCACGA-TAT
513 GCAATTATGAAAGTCTCACACCGACGCTGCCAAACTCATAGTCAAATTTGATTACCCA-GAGTAT
* * *
53321351 TACTATTTTTATTTACAATTATCGACCA-TTTTTTTTGTTAAAAT-AAGGATGTCCACTGCT
577 TACTATTATTATTTACAATTATCAACCATTTTTTTTTGTTAAAATCAAGG-TGTCCAATGCT
* * * * *
53321411 GATAGCAATGACTCTGATTTGACCTCCCAGTT-GAACAAATGTAGAAGCAAATATCAAAGGGTCC
1 GATAACAATGACTCTGATTTGACCTCCAACTTAG-ACAAATGTAGAAGCAAATATCAATGGATCC
* *
53321475 CCTACTCGTAATGGACAAATGTAAAAGCAAATATCAAAAGGTCCCCCCACTCCCAACGTTGCCTA
65 CCTACTCCTAATGGACAAATGTAAAAGCAAATAT-AAAAGGT--CCCCACTCCCAACGCTGCCTA
* * *
53321540 ATATATTCAAATTTGATTAGTCATAGCATTATTATTCACAATTATCAATATTTTTTTGTCAAAAT
127 ATATATTCAAATTTGACTACTCATAGTATTATTATTCACAATTATCAATATTTTTTTGTCAAAAT
** *
53321605 CAGGATGTTCATTGTCGATAGTGATGACTAATCCCTTAGTCTCGGGTACTCTCCAAAAAAGTAAA
192 CAGG-TGTTCATTGTCGATAGCAATGACTAATCCCTTAGTCT-GGGTACTCTTCAAAAAAGTAAA
* * * * *
53321670 TGGTGACCATGAAATGTGCTGCATTCCCATGAACGGGGATACAACTCCCAA-C-C--------A-
255 CGGTGACCATGAAATGTGCTCCATTCCCATGAGCGGGGATCCAACTCCAAACCTCATAATTAAAG
* * *
53321724 ATTAGGTGAGTAACGACCACACCATTATTAATAACACAATTAAAATGCCATAATTA--TTTTTTT
320 ATTAGGTGAGTAACGACCACACCATTATTAATAACACAGTTAAAATGCTATCATTATGTTTTTTT
* *
53321787 TATAAACCAAGAAAAAA
385 TCTAAACAAAGAAAAAA
53321804 GGGAAATTTG
Statistics
Matches: 888, Mismatches: 117, Indels: 72
0.82 0.11 0.07
Matches are distributed among these distances:
622 22 0.02
624 51 0.06
625 1 0.00
633 6 0.01
634 112 0.13
635 73 0.08
636 163 0.18
637 3 0.00
638 1 0.00
642 1 0.00
644 7 0.01
645 283 0.32
646 40 0.05
648 1 0.00
649 1 0.00
650 113 0.13
651 10 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (637 bp):
GATAACAATGACTCTGATTTGACCTCCAACTTAGACAAATGTAGAAGCAAATATCAATGGATCCC
CTACTCCTAATGGACAAATGTAAAAGCAAATATAAAAGGTCCCCACTCCCAACGCTGCCTAATAT
ATTCAAATTTGACTACTCATAGTATTATTATTCACAATTATCAATATTTTTTTGTCAAAATCAGG
TGTTCATTGTCGATAGCAATGACTAATCCCTTAGTCTGGGTACTCTTCAAAAAAGTAAACGGTGA
CCATGAAATGTGCTCCATTCCCATGAGCGGGGATCCAACTCCAAACCTCATAATTAAAGATTAGG
TGAGTAACGACCACACCATTATTAATAACACAGTTAAAATGCTATCATTATGTTTTTTTTCTAAA
CAAAGAAAAAAACACGAAAAATATTTTGTTTTATAATAGAAAAGAGAAATTTGGAATTTAAGGAG
TAGTTAGATGAAAATGGCTAAACGATATGGGAATTATCATAATAGAAGGTTATAAAAGCAATTAT
GAAAGTCTCACACCGACGCTGCCAAACTCATAGTCAAATTTGATTACCCAGAGTATTACTATTAT
TATTTACAATTATCAACCATTTTTTTTTGTTAAAATCAAGGTGTCCAATGCT
Found at i:53322249 original size:16 final size:14
Alignment explanation
Indices: 53322224--53322267 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
53322214 AATTTACTAC
53322224 AAATATTTATTCTT
1 AAATATTTATTCTT
* *
53322238 ATATTCATTTATTGTT
1 A-AAT-ATTTATTCTT
53322254 AAATATTTATTCTT
1 AAATATTTATTCTT
53322268 TTAAATATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (14 bp):
AAATATTTATTCTT
Found at i:53325477 original size:13 final size:13
Alignment explanation
Indices: 53325461--53325492 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53325451 ATATTTGTCC
*
53325461 ACCCAATTTTTTT
1 ACCCAATTTTTGT
53325474 ACCCAATTTTTGT
1 ACCCAATTTTTGT
53325487 ACCCAA
1 ACCCAA
53325493 AAAATAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (13 bp):
ACCCAATTTTTGT
Found at i:53332277 original size:21 final size:22
Alignment explanation
Indices: 53332235--53332287 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
53332225 ACCCCACTTT
*
53332235 ACCAGATTTT-TAACCATCAAA
1 ACCATATTTTATAACCATCAAA
*
53332256 ACACTTATTTTATAACC-T-AAA
1 AC-CATATTTTATAACCATCAAA
53332277 ACCATATTTTA
1 ACCATATTTTA
53332288 CCTTTAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 8 0.30
21 7 0.26
22 7 0.26
23 5 0.19
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.36
Consensus pattern (22 bp):
ACCATATTTTATAACCATCAAA
Found at i:53336656 original size:46 final size:46
Alignment explanation
Indices: 53336582--53336724 Score: 189
Period size: 46 Copynumber: 3.1 Consensus size: 46
53336572 TGGACAACAT
53336582 TTATACATCAAATTGGAAAGCATCAATATGCTCAAAATGGAAAGCA
1 TTATACATCAAATTGGAAAGCATCAATATGCTCAAAATGGAAAGCA
* * * * * *
53336628 TTATACATCAAAATGGATAGCTTTAATATGCTCAAATTGGATAGCA
1 TTATACATCAAATTGGAAAGCATCAATATGCTCAAAATGGAAAGCA
* * *
53336674 TTAGACATCAAATTGGACAGCATCAATATACTCAAAATGGACAA-CA
1 TTATACATCAAATTGGAAAGCATCAATATGCTCAAAATGGA-AAGCA
53336720 TTATA
1 TTATA
53336725 ACATATAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
46 80 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (46 bp):
TTATACATCAAATTGGAAAGCATCAATATGCTCAAAATGGAAAGCA
Found at i:53336716 original size:24 final size:24
Alignment explanation
Indices: 53336583--53336714 Score: 98
Period size: 24 Copynumber: 5.7 Consensus size: 24
53336573 GGACAACATT
*
53336583 TATACATCAAATTGGAAAGCATCAA
1 TATACATCAAAATGGAAAGCAT-AA
*
53336608 TATGC-TCAAAATGGAAAGCAT--
1 TATACATCAAAATGGAAAGCATAA
* *
53336629 TATACATCAAAATGGATAGCTTTAA
1 TATACATCAAAATGGAAAGC-ATAA
* * *
53336654 TATGC-TCAAATTGGATAGCAT--
1 TATACATCAAAATGGAAAGCATAA
* * *
53336675 TAGACATCAAATTGGACAGCATCAA
1 TATACATCAAAATGGAAAGCAT-AA
53336700 TATAC-TCAAAATGGA
1 TATACATCAAAATGGA
53336715 CAACATTATA
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
21 7 0.08
22 28 0.33
23 2 0.02
24 37 0.43
25 12 0.14
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (24 bp):
TATACATCAAAATGGAAAGCATAA
Found at i:53344517 original size:42 final size:44
Alignment explanation
Indices: 53344452--53344536 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
53344442 GCAGGCCACC
53344452 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* *
53344495 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA
53344537 ACATAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 12 0.32
43 22 0.58
44 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT
Found at i:53345184 original size:10 final size:10
Alignment explanation
Indices: 53345132--53345183 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
53345122 GTTTTAGTGA
53345132 TTTTATATAT
1 TTTTATATAT
**
53345142 TTAAATATAT
1 TTTTATATAT
53345152 TTTTATAT-T
1 TTTTATATAT
*
53345161 TTTTATAAAT
1 TTTTATATAT
53345171 TTTTATAT-T
1 TTTTATATAT
53345180 TTTT
1 TTTT
53345184 TTCAAAATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
9 13 0.37
10 22 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:53345254 original size:25 final size:26
Alignment explanation
Indices: 53345200--53345256 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
53345190 ATACTATAAG
* *
53345200 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTATAATTGTATAC
*
53345226 ATTTTTATA-ATTTTATAATT-TATAT
1 ATTTTTATATA-TTTATAATTGTATAC
53345251 ATTTTT
1 ATTTTT
53345257 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTTATATATTTATAATTGTATAC
Found at i:53345761 original size:16 final size:18
Alignment explanation
Indices: 53345725--53345762 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53345715 ACTATATTGA
*
53345725 ATAAAATATAAAATATGT
1 ATAAAATATAAAATATAT
*
53345743 ATAAAATAAAAAATATAT
1 ATAAAATATAAAATATAT
53345761 AT
1 AT
53345763 TTATTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAATATAAAATATAT
Found at i:53346177 original size:31 final size:31
Alignment explanation
Indices: 53346118--53346207 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 31
53346108 TATGTGATAG
* * *
53346118 TACAGGGTTTGAATATG-AAATATTAATGA-
1 TACATGGTATGAATATGAAAATATGAATGAT
53346147 TA-ATAGGATATGAATATGAAAATATGAATGAT
1 TACAT-GG-TATGAATATGAAAATATGAATGAT
53346179 TACATGGTATGAATATGAAAATATGAATG
1 TACATGGTATGAATATGAAAATATGAATG
53346208 GTTGATACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 9 0.17
31 33 0.62
32 4 0.08
33 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (31 bp):
TACATGGTATGAATATGAAAATATGAATGAT
Found at i:53347593 original size:13 final size:13
Alignment explanation
Indices: 53347575--53347599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53347565 AGGTGCAGGG
53347575 GTCACACGCCCAA
1 GTCACACGCCCAA
53347588 GTCACACGCCCA
1 GTCACACGCCCA
53347600 TGTGCTAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.48, G:0.16, T:0.08
Consensus pattern (13 bp):
GTCACACGCCCAA
Found at i:53348814 original size:26 final size:26
Alignment explanation
Indices: 53348773--53348830 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
53348763 ATAAGAGCAA
* *
53348773 TAATCAGGAAATTCACAAAGAACTTT
1 TAATCAGGAAACTCACAAAGAACCTT
* * *
53348799 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAACTCACAAAGAACCTT
53348825 TAATCA
1 TAATCA
53348831 AGAGCTCCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (26 bp):
TAATCAGGAAACTCACAAAGAACCTT
Found at i:53348846 original size:24 final size:26
Alignment explanation
Indices: 53348797--53348846 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
53348787 ACAAAGAACT
*
53348797 TTTAATCAGGAAGCTCACGAAGAGCC
1 TTTAATCAAGAAGCTCACGAAGAGCC
*
53348823 TTTAATCAAG-AGCTC-CGAATAGCC
1 TTTAATCAAGAAGCTCACGAAGAGCC
53348847 ATATATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 5 0.23
26 9 0.41
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (26 bp):
TTTAATCAAGAAGCTCACGAAGAGCC
Found at i:53350176 original size:26 final size:26
Alignment explanation
Indices: 53350118--53350182 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
53350108 ATAAGAGCAA
* * *
53350118 TAATCAAGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
53350144 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
53350170 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
53350183 CGGATAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:53351082 original size:14 final size:15
Alignment explanation
Indices: 53351063--53351093 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
53351053 GATTTATAGC
53351063 TTTTATTTTT-TTTT
1 TTTTATTTTTATTTT
53351077 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
53351092 TT
1 TT
53351094 ACAAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTATTTTTATTTT
Found at i:53351718 original size:25 final size:25
Alignment explanation
Indices: 53351687--53351740 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
53351677 TAGAAAATTG
53351687 TTATTTATTATCATTATTATTATTA
1 TTATTTATTATCATTATTATTATTA
* * *
53351712 TTATTTATTATCTTTATTTTTATTT
1 TTATTTATTATCATTATTATTATTA
53351737 TTAT
1 TTAT
53351741 ATTCATGCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTTATTATCATTATTATTATTA
Found at i:53352179 original size:23 final size:23
Alignment explanation
Indices: 53352153--53352196 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
53352143 CGATTTTGTT
53352153 TATT-CATT-TATTCATATTATTTC
1 TATTCCATTGTATT-AT-TTATTTC
53352176 TATTCCATTGTATTATTTATT
1 TATTCCATTGTATTATTTATT
53352197 ATTGCATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 6 0.32
25 4 0.21
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTCCATTGTATTATTTATTTC
Found at i:53352204 original size:20 final size:20
Alignment explanation
Indices: 53352167--53352213 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53352157 CATTTATTCA
53352167 TATTATTT-CTATTCCATTG
1 TATTATTTACTATTCCATTG
* *
53352186 TATTATTTATTATTGCATTG
1 TATTATTTACTATTCCATTG
53352206 TA-TATTTA
1 TATTATTTA
53352214 ATGTAGCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (20 bp):
TATTATTTACTATTCCATTG
Found at i:53352222 original size:19 final size:20
Alignment explanation
Indices: 53352181--53352222 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53352171 ATTTCTATTC
* *
53352181 CATTGTATTATTTATTATTG
1 CATTGTATTATTTAATATAG
*
53352201 CATTGTA-TATTTAATGTAG
1 CATTGTATTATTTAATATAG
53352220 CAT
1 CAT
53352223 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (20 bp):
CATTGTATTATTTAATATAG
Found at i:53354883 original size:44 final size:44
Alignment explanation
Indices: 53354805--53354889 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
53354795 ACCTCCAACT
* * * *
53354805 TGGACAAAGGTAGAAGAAAATATTAGTGGATCCCCTACTCCTAA
1 TGGACAAAGGTAAAAGAAAATATAAATGGATCCCCCACTCCTAA
*
53354849 TGGACAAATGTAAAAGAAAATATCAAATGG-TCCCCCACTCC
1 TGGACAAAGGTAAAAGAAAATAT-AAATGGATCCCCCACTCC
53354890 CAACGTTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 31 0.89
45 4 0.11
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (44 bp):
TGGACAAAGGTAAAAGAAAATATAAATGGATCCCCCACTCCTAA
Found at i:53357011 original size:43 final size:43
Alignment explanation
Indices: 53356964--53357048 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
53356954 GCAGGCCACC
53356964 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACT-TCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* * *
53357007 TAAAATATAGTTCTAGATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTTCTAAAGAAGTAATTTTATTAATTTATTTAA
53357049 ACATAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 11 0.30
43 22 0.59
44 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (43 bp):
TAAAATATACTTCTAAAGAAGTAATTTTATTAATTTATTTAAT
Done.