Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 35
Found at i:367303 original size:36 final size:36
Alignment explanation
Indices: 367263--367561 Score: 221
Period size: 37 Copynumber: 8.4 Consensus size: 36
367253 ATATTTTGAA
*
367263 AATATATATTTTTTAAAACATTTTTGAAAACTATAT
1 AATATATAGTTTTTAAAACATTTTTGAAAACTATAT
** *
367299 AATATATAGTTTTTAAAACATTTAAGAAAATATATAT
1 AATATATAGTTTTTAAAACATTTTTGAAAA-CTATAT
* ***
367336 AATATATAGTTTTGAAATTTTTTTTTGAAAACTTATAT
1 AATATATAGTTTTTAAA-ACATTTTTGAAAAC-TATAT
* *
367374 AATATATGGTTTTGAAAACA--TTT----A-TATAT
1 AATATATAGTTTTTAAAACATTTTTGAAAACTATAT
*
367403 --TATATAGTTTTTGAAAACA-TTTTGAATATATATATAT
1 AATATATAGTTTTT-AAAACATTTTTGAA-A-A-CTATAT
*
367440 ATATAATATAGTTTTTTAAAATAATTTTT-AAAA-TATAT
1 A-AT-ATATAG-TTTTTAAAA-CATTTTTGAAAACTATAT
*
367478 -ATATATAGTTTTTAAATCATTTTTGAAAACATATAT
1 AATATATAGTTTTTAAAACATTTTTGAAAAC-TATAT
* * * **
367514 ATTATATAGTTTTCAAAACATTTTAGAAATTTATAT
1 AATATATAGTTTTTAAAACATTTTTGAAAACTATAT
*
367550 ATTATAT-GTTTT
1 AATATATAGTTTT
367562 GGAAAATATT
Statistics
Matches: 213, Mismatches: 26, Indels: 49
0.74 0.09 0.17
Matches are distributed among these distances:
27 10 0.05
28 6 0.03
29 8 0.04
31 1 0.00
33 6 0.03
34 12 0.06
35 15 0.07
36 46 0.22
37 50 0.23
38 34 0.16
40 2 0.01
41 11 0.05
42 8 0.04
43 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (36 bp):
AATATATAGTTTTTAAAACATTTTTGAAAACTATAT
Found at i:367360 original size:138 final size:140
Alignment explanation
Indices: 367188--367536 Score: 305
Period size: 140 Copynumber: 2.5 Consensus size: 140
367178 ATATATATAT
* *
367188 ATATATATATATATTATAGTTTGCAAA-TGGTTTTTGAAAATACGTATATGAT-TATAGTTTTTA
1 ATATATATATATATTATAGTTTGCAAATTGGTTTTTG-AAA-ACGTATATAATATATAGTTTTGA
* *
367251 AAATATTT-TGAAAATATATA-TTTTTTAAAACATTTTTGAAAACTATATA-ATATATAGTTTTT
64 AAACATTTAT-AAAATATATAGTTTTTGAAAACA-TTTTGAAAA-TATATATATATATAGTTTTT
367313 AAAACATTTAAGAAA
126 AAAACATTTAAGAAA
** * *
367328 ATATATATA-ATA-TATAGTTTTG-AAATTTTTTTTTGAAAACTTATATAATATATGGTTTTGAA
1 ATATATATATATATTATAG-TTTGCAAATTGGTTTTTGAAAACGTATATAATATATAGTTTTGAA
* *
367390 AACATTTATATATTATATAGTTTTTGAAAACATTTTGAATATATATATATATATAATATAGTTTT
65 AACATTTATAAAATATATAGTTTTTGAAAACATTTTG-A-A-A-ATATATATAT-ATATAG-TTT
* **
367455 TTAAAATAATTT-TTAAA
124 TTAAAA-CATTTAAGAAA
* ** * * *
367472 ATATATATATATAGT-T--TTT--AAA-TCATTTTTGAAAACATATATATTATATAGTTTTCAAA
1 ATATATATATATATTATAGTTTGCAAATTGGTTTTTGAAAACGTATATAATATATAGTTTTGAAA
367531 ACATTT
66 ACATTT
367537 TAGAAATTTA
Statistics
Matches: 175, Mismatches: 19, Indels: 30
0.78 0.08 0.13
Matches are distributed among these distances:
137 9 0.05
138 40 0.23
139 27 0.15
140 47 0.27
141 10 0.06
142 6 0.03
143 6 0.03
144 21 0.12
145 8 0.05
146 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (140 bp):
ATATATATATATATTATAGTTTGCAAATTGGTTTTTGAAAACGTATATAATATATAGTTTTGAAA
ACATTTATAAAATATATAGTTTTTGAAAACATTTTGAAAATATATATATATATAGTTTTTAAAAC
ATTTAAGAAA
Found at i:367386 original size:27 final size:27
Alignment explanation
Indices: 367357--367423 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
367347 TTGAAATTTT
367357 TTTTTGAAAAC-TTATATAATATAT-G
1 TTTTTGAAAACATTATATAATATATAG
* *
367382 GTTTTGAAAACATTTATATATTATATAG
1 TTTTTGAAAACA-TTATATAATATATAG
367410 TTTTTGAAAACATT
1 TTTTTGAAAACATT
367424 TTGAATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 10 0.28
27 14 0.39
28 12 0.33
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (27 bp):
TTTTTGAAAACATTATATAATATATAG
Found at i:367434 original size:28 final size:27
Alignment explanation
Indices: 367358--367438 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 27
367348 TGAAATTTTT
367358 TTTTGAAAAC--TTATATA-ATATATGG
1 TTTTGAAAACATTTATATATATATA-GG
*
367383 TTTTGAAAACATTTATATATTATATAGT
1 TTTTGAAAACATTTATATA-TATATAGG
367411 TTTTGAAAACATTTTGAATATATATATA
1 TTTTGAAAACA-TTT--ATATATATATA
367439 TATATAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
25 10 0.21
27 7 0.15
28 12 0.25
29 8 0.17
30 6 0.12
31 5 0.10
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTTGAAAACATTTATATATATATAGG
Found at i:367476 original size:42 final size:41
Alignment explanation
Indices: 367383--367484 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
367373 TAATATATGG
* * *
367383 TTTTGAAAACAT-T-TATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATAATATAGTTTTTGAAAAAA
* *
367422 TTTTGAATATATATATATATATAATATAGTTTTTTAAAATAA
1 TTTTGAAAATATATATATATATAATATAGTTTTTGAAAA-AA
*
367464 TTTTTAAAATATATATATATA
1 TTTTGAAAATATATATATATA
367485 GTTTTTAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.19
40 1 0.02
41 22 0.42
42 20 0.38
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (41 bp):
TTTTGAAAATATATATATATATAATATAGTTTTTGAAAAAA
Found at i:367476 original size:102 final size:100
Alignment explanation
Indices: 367294--367484 Score: 224
Period size: 102 Copynumber: 1.8 Consensus size: 100
367284 TTTTGAAAAC
* **
367294 TATATAATATATAGTTTTTAAAACATTTAAGAAAATATATATAATATATAGTTTTGAAATTTTTT
1 TATATAATATATAGTTTTTAAAACATTTAAGAAAATATATATAATATATAGTTTTGAAAATAATT
*
367359 TTTGAAAACT-TATATAATATATGGTTTTGAAAACATT
66 TTT-AAAA-TATATAT-ATATATAGTTTTGAAAACATT
* * *
367396 TATATATTATATAGTTTTTGAAAACATTT-TGAATATATATATATATATAATATAGTTTTTTAAA
1 TATATAATATATAGTTTTT-AAAACATTTAAGAA-A-ATATATATA-AT-ATATAG-TTTTGAAA
367460 ATAATTTTTAAAATATATATATATA
60 ATAATTTTTAAAATATATATATATA
367485 GTTTTTAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
102 21 0.28
103 10 0.13
104 9 0.12
105 8 0.11
106 15 0.20
107 13 0.17
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (100 bp):
TATATAATATATAGTTTTTAAAACATTTAAGAAAATATATATAATATATAGTTTTGAAAATAATT
TTTAAAATATATATATATATAGTTTTGAAAACATT
Found at i:367515 original size:32 final size:35
Alignment explanation
Indices: 367440--367515 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 35
367430 ATATATATAT
*
367440 ATATAATATAGTTTTTTAAAATAATTTTTAAAATAT
1 ATAT-ATATAGTTTTTTAAAATAATTTTTAAAATAC
* *
367476 ATATATATAG-TTTTT-AAATCATTTTTGAAA-AC
1 ATATATATAGTTTTTTAAAATAATTTTTAAAATAC
367508 ATATATAT
1 ATATATAT
367516 TATATAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 9 0.24
33 13 0.35
34 5 0.14
35 6 0.16
36 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (35 bp):
ATATATATAGTTTTTTAAAATAATTTTTAAAATAC
Found at i:367549 original size:72 final size:78
Alignment explanation
Indices: 367393--367573 Score: 195
Period size: 72 Copynumber: 2.4 Consensus size: 78
367383 TTTTGAAAAC
* *
367393 ATTTATATATTATATAGTTTTTGAAAACATTTTGAATATATATATATATATAATATAGTTTTTTA
1 ATTTATATA-TATATAGTTTTTGAAAACATTTTGAATATACATATATATATAATATAGTTTTTCA
367458 AAATAATTTTTAAA
65 AAATAATTTTTAAA
*
367472 A--TATATATATATAGTTTTT-AAATCATTTTTGAA-A-ACATATATAT-T-ATATAG-TTTTCA
1 ATTTATATATATATAGTTTTTGAAAACA-TTTTGAATATACATATATATATAATATAGTTTTTCA
*
367529 AAA-CA-TTTTAGAA
65 AAATAATTTTTA-AA
* *
367542 ATTTATATAT-TATATGTTTTGGAAAATATTTT
1 ATTTATATATATATA-GTTTTTGAAAACATTTT
367574 TATATATATA
Statistics
Matches: 89, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
69 5 0.06
70 4 0.04
71 12 0.13
72 22 0.25
73 5 0.06
74 9 0.10
75 6 0.07
76 19 0.21
77 6 0.07
79 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (78 bp):
ATTTATATATATATAGTTTTTGAAAACATTTTGAATATACATATATATATAATATAGTTTTTCAA
AATAATTTTTAAA
Found at i:367573 original size:36 final size:36
Alignment explanation
Indices: 367393--367573 Score: 133
Period size: 36 Copynumber: 4.9 Consensus size: 36
367383 TTTTGAAAAC
*
367393 ATTTATATATTATATAGTTTTTGAAAACATTTT-GAA
1 ATTTATATATTATATAG-TTTTGAAAATATTTTAGAA
*
367429 TATATATATATATATAATATAGTTTTTTAAAATAATTTTTA-AA
1 -AT-T-TATATAT-T-ATATAG-TTTTGAAAAT-A-TTTTAGAA
* *
367472 A--TATATA-TATATAGTTTT-TAAATCATTTTTGAAA
1 ATTTATATATTATATAGTTTTGAAAAT-ATTTTAG-AA
** * *
367506 ACATATATATTATATAGTTTTCAAAACATTTTAGAA
1 ATTTATATATTATATAGTTTTGAAAATATTTTAGAA
367542 ATTTATATATTATAT-GTTTTGGAAAATATTTT
1 ATTTATATATTATATAGTTTT-GAAAATATTTT
367574 TATATATATA
Statistics
Matches: 118, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
32 4 0.03
33 5 0.04
34 7 0.06
35 11 0.09
36 31 0.26
37 19 0.16
38 10 0.08
39 7 0.06
40 1 0.01
41 15 0.13
42 2 0.02
43 6 0.05
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (36 bp):
ATTTATATATTATATAGTTTTGAAAATATTTTAGAA
Found at i:369363 original size:55 final size:55
Alignment explanation
Indices: 369274--369809 Score: 741
Period size: 55 Copynumber: 9.8 Consensus size: 55
369264 CACTACCAAG
* * * * * *
369274 ACGGAAATTCATAAACTTATTATGAATTTTTTAGTTTCGTACACATATTTCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
* * *
369329 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTACACACATAGTGCTCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
* *
369384 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACATAGTGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
** *
369439 ACAAAAATTCATAAACTTATTATGAATTTCTTAGTCTTGCACACACAGTGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
** * * * * *
369494 ATAGAAATTCATAGACTTATTATGAATTTATTAGTCTTACACACAAAGTGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
* * * *
369549 AAGGAAATTAATAAACTTATTATGAATTTCTTAGTCTTGCACACACAATGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
*
369604 ACGGAAATTCATAAACTTGTTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
* * * *
369659 ACGGAAATTTATAAACTTATTATGAATTACTTAGTTTTGAACACAAAGTGCCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
** * * *
369714 ACATAAATTTATAAACTTATTATGAATTACTTAGTTTTGCACACACAGTACCCAT
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
*
369769 ACGAAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCAC
1 ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCAC
369810 GTATAGTGCC
Statistics
Matches: 435, Mismatches: 46, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 7 0.02
55 428 0.98
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (55 bp):
ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCAT
Found at i:370296 original size:19 final size:22
Alignment explanation
Indices: 370258--370304 Score: 73
Period size: 19 Copynumber: 2.3 Consensus size: 22
370248 CGCTTAGTAC
370258 CGATACTTCTACACTATGGTAT
1 CGATACTTCTACACTATGGTAT
370280 CGATAC-TCT-CA-TATGGTAT
1 CGATACTTCTACACTATGGTAT
370299 CGATAC
1 CGATAC
370305 CATTTATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.56
20 2 0.08
21 3 0.12
22 6 0.24
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (22 bp):
CGATACTTCTACACTATGGTAT
Found at i:376539 original size:53 final size:53
Alignment explanation
Indices: 376459--376582 Score: 187
Period size: 53 Copynumber: 2.4 Consensus size: 53
376449 GTAAATGAGT
* *
376459 TGCACCCA-AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATAGA
1 TGCACACATAGTGCCGAAATGGTAATTCACAAACTCATTATGAATACCATAGA
* * * *
376511 TGCACACATAGTGCCGAAATGGTCATTCATAAACTCATTATGAATACCATGGG
1 TGCACACATAGTGCCGAAATGGTAATTCACAAACTCATTATGAATACCATAGA
376564 TGCACACATAGTGCCGAAA
1 TGCACACATAGTGCCGAAA
376583 GTACATATAG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
52 7 0.11
53 58 0.89
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (53 bp):
TGCACACATAGTGCCGAAATGGTAATTCACAAACTCATTATGAATACCATAGA
Found at i:376646 original size:24 final size:24
Alignment explanation
Indices: 376618--376688 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
376608 GAAACATATG
376618 CATTAAACAAAATCGATCGATAAC
1 CATTAAACAAAATCGATCGATAAC
* * * * **
376642 CATTATACGAAAATCCAAC-TTATG
1 CATTAAAC-AAAATCGATCGATAAC
*
376666 CATTAAACAAAATTGATCGATAA
1 CATTAAACAAAATCGATCGATAA
376689 ATATCATACA
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
23 7 0.21
24 18 0.55
25 8 0.24
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (24 bp):
CATTAAACAAAATCGATCGATAAC
Found at i:383232 original size:102 final size:104
Alignment explanation
Indices: 383065--383252 Score: 256
Period size: 103 Copynumber: 1.8 Consensus size: 104
383055 GTTGGTATCG
* * * * *
383065 ATACTAAGGCATTTTTAAAAACATCGAAGCCAAATTTGGTATAGATACTCATGGGAGTATCGATA
1 ATACCAAGGCATTTTTAAAAACATCAAAGCCAAATTTGATATAGATAATCATGAGAGTATCGATA
383130 CCCAA-GGTAAAGTATCGATACTCCTCATAGGAGTTTTA
66 CCCAACGGTAAAGTATCGATACTCCTCATAGGAGTTTTA
* * *
383168 ATACCAAGGTATTTTTAAAAACATTAAAG-CAAATTTGATATCA-ATAATCATGAGAGTATTGAT
1 ATACCAAGGCATTTTTAAAAACATCAAAGCCAAATTTGATAT-AGATAATCATGAGAGTATCGAT
**
383231 ACCCAACGGTTCAGTATCGATA
65 ACCCAACGGTAAAGTATCGATA
383253 TTGTTGGCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
102 34 0.47
103 39 0.53
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (104 bp):
ATACCAAGGCATTTTTAAAAACATCAAAGCCAAATTTGATATAGATAATCATGAGAGTATCGATA
CCCAACGGTAAAGTATCGATACTCCTCATAGGAGTTTTA
Found at i:391218 original size:159 final size:160
Alignment explanation
Indices: 391003--391322 Score: 579
Period size: 160 Copynumber: 2.0 Consensus size: 160
390993 ATTTCCACTT
391003 TGATTCAAGCATGAATTCAAGCTCCTAAGTTCAATTTCAAGCTATTCCAATCATTCTAACATCAA
1 TGATTCAAGCATGAATTCAAGCTCCTAAGTTCAATTTCAAGCTATTCCAATCATTCTAACATCAA
*
391068 ATTCAATAAAAA-AATAATTCCTCTAAAACCCTAAATTACTCGAAACTTATATAAGGCTTTATAC
66 ATTCAATAAAAATAATAATTCCTCTAAAACCCTAAAGTACTCGAAACTTATATAAGGCTTTATAC
*
391132 ATGTCTTTAATCATTACACATGCTTAGAAA
131 ATGTCTTTAATCATTACAAATGCTTAGAAA
* *
391162 TGATTTAAGCATGAATTCAAGCTCCTAAGTTCAATTTCAAGCTATTCCAATCATTCTCACATCAA
1 TGATTCAAGCATGAATTCAAGCTCCTAAGTTCAATTTCAAGCTATTCCAATCATTCTAACATCAA
* *
391227 ATTCAATAAAAATAATAATTCCTCTAAAACCCTAAAGTGCTTGAAACTTATATAAGGCTTTATAC
66 ATTCAATAAAAATAATAATTCCTCTAAAACCCTAAAGTACTCGAAACTTATATAAGGCTTTATAC
391292 ATGTCTTTAATCATTACAAATGCTTAGAAA
131 ATGTCTTTAATCATTACAAATGCTTAGAAA
391322 T
1 T
391323 TAATCTACAA
Statistics
Matches: 154, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
159 75 0.49
160 79 0.51
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (160 bp):
TGATTCAAGCATGAATTCAAGCTCCTAAGTTCAATTTCAAGCTATTCCAATCATTCTAACATCAA
ATTCAATAAAAATAATAATTCCTCTAAAACCCTAAAGTACTCGAAACTTATATAAGGCTTTATAC
ATGTCTTTAATCATTACAAATGCTTAGAAA
Found at i:394585 original size:44 final size:44
Alignment explanation
Indices: 394535--394786 Score: 202
Period size: 44 Copynumber: 5.7 Consensus size: 44
394525 TGAGGAGTCG
* * *
394535 GATCAGCATCACTCTTTTACTTGATTCCATCACATAAAAAGTTA
1 GATCAGCATCACCCTTTTGCTAGATTCCATCACATAAAAAGTTA
* *
394579 GATCAGCATCACCCTTTTGCTAGATTCTAT-ATCATAAAGAGTTA
1 GATCAGCATCACCCTTTTGCTAGATTCCATCA-CATAAAAAGTTA
* * * * *
394623 AATCAACATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTG
1 GATCAGCATCACCCTTTTGCTAGATTCCATCACATAAAAAGTTA
* * * * ** *
394667 GATTAGCATCACCCTTTTGCTAAATTCTATCTCATAAGGAGTTG
1 GATCAGCATCACCCTTTTGCTAGATTCCATCACATAAAAAGTTA
* ** * ** * ** * *
394711 GATCAGGATTTCCCTTTTGCTCGATTTAATCCCATAAGGAGATG
1 GATCAGCATCACCCTTTTGCTAGATTCCATCACATAAAAAGTTA
* *
394755 GATCAACATCGA-CCTTTTGCTAGATTCAATCA
1 GATCAGCATC-ACCCTTTTGCTAGATTCCATCA
394787 TAGAAGGAGG
Statistics
Matches: 166, Mismatches: 39, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
43 1 0.01
44 164 0.99
45 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (44 bp):
GATCAGCATCACCCTTTTGCTAGATTCCATCACATAAAAAGTTA
Found at i:394665 original size:88 final size:88
Alignment explanation
Indices: 394536--394806 Score: 287
Period size: 88 Copynumber: 3.1 Consensus size: 88
394526 GAGGAGTCGG
* * * * *
394536 ATCAGCATCACTCTTTTACTTGATTCCATCACATAAAAAGTTAGATCAGCATCACCCTTTTGCTA
1 ATCAGCATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTGGATCAGCATCACCCTTTTGCTA
394601 GATTCTATATCATAAAGAGTTAA
66 GATTCTATATCATAAAGAGTTAA
* *
394624 ATCAACATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTGGATTAGCATCACCCTTTTGCTA
1 ATCAGCATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTGGATCAGCATCACCCTTTTGCTA
* * * **
394689 AATTCTATCTCATAAGGAGTTGG
66 GATTCTATATCATAAAGAGTTAA
* ** * * ** * *
394712 ATCAGGATTTCCCTTTTGCTCGATTTAATCCCATAAGGAGATGGATCAACATCGA-CCTTTTGCT
1 ATCAGCATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTGGATCAGCATC-ACCCTTTTGCT
* *
394776 AGATTC-A-ATCATAGAAGGAGGTGA
65 AGATTCTATATCATA-AA-GAGTTAA
394800 ATCAGCA
1 ATCAGCA
394807 CAATCAAATG
Statistics
Matches: 151, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
86 5 0.03
87 2 0.01
88 143 0.95
89 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (88 bp):
ATCAGCATCACCCTTTTGCTCGATTTCATCACATAAAAAGTTGGATCAGCATCACCCTTTTGCTA
GATTCTATATCATAAAGAGTTAA
Found at i:395016 original size:17 final size:17
Alignment explanation
Indices: 394960--395016 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
394950 AAAAAAAAAG
* *
394960 AAAAATGGAAAAGAATT
1 AAAAAAGGAAAAGAAAT
* *
394977 AAAAAAGGAAAATAGAT
1 AAAAAAGGAAAAGAAAT
*
394994 GAAAAAGGAAAA-AAAT
1 AAAAAAGGAAAAGAAAT
395010 AAGAAAA
1 AA-AAAA
395017 AACGAAACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.11
Consensus pattern (17 bp):
AAAAAAGGAAAAGAAAT
Found at i:409931 original size:65 final size:65
Alignment explanation
Indices: 409856--409996 Score: 169
Period size: 65 Copynumber: 2.2 Consensus size: 65
409846 GAATACATTT
* ** * * *
409856 TACCGATGCACA-AGCCATGCATCGATGCACTCTTGAAT-ATTTTGAAACATCGAATGCATTTTG
1 TACCGATGCACAGA-CCATGCATCGATACACTCCAGAATCA-TTTGAAACATCGAATACAATTAG
409919 TG
64 TG
** *
409921 TACCGATGCACAGACCATGCATCGATACACTCCAGGCTCATTTGAAACATCGAATATAATTAGTG
1 TACCGATGCACAGACCATGCATCGATACACTCCAGAATCATTTGAAACATCGAATACAATTAGTG
409986 TACCGATGCAC
1 TACCGATGCAC
409997 CTAGTGTACC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 63 0.97
66 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
TACCGATGCACAGACCATGCATCGATACACTCCAGAATCATTTGAAACATCGAATACAATTAGTG
Found at i:410003 original size:17 final size:17
Alignment explanation
Indices: 409981--410013 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
409971 CGAATATAAT
409981 TAGTGTACCGATGCACC
1 TAGTGTACCGATGCACC
409998 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
410014 TAAGTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (17 bp):
TAGTGTACCGATGCACC
Found at i:415812 original size:21 final size:23
Alignment explanation
Indices: 415787--415870 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 23
415777 GATGCATCTC
*
415787 TTGAATGTGCATCGATATA-TCA
1 TTGAATGTGCATCGATACACTCA
* *
415809 -TGAA-GATGCACCGATGCACTCA
1 TTGAATG-TGCATCGATACACTCA
*
415831 TTGAATGTGCATCGATGCACTC-
1 TTGAATGTGCATCGATACACTCA
*
415853 -TG-CTGTGCATCGATACAC
1 TTGAATGTGCATCGATACAC
415871 CATCGGGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 15 0.29
21 15 0.29
22 3 0.06
23 18 0.35
24 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (23 bp):
TTGAATGTGCATCGATACACTCA
Found at i:415835 original size:44 final size:43
Alignment explanation
Indices: 415749--415846 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 43
415739 TTTTATGCTT
*
415749 TGTGCATCGATACACAAGACAGTGTACCGATGCATCTCTTGAA
1 TGTGCATCGATACACAAGACAGTGCACCGATGCATCTCTTGAA
* *
415792 TGTGCATCGATATATCATGA-AGATGCACCGATGCA-CTCATTGAA
1 TGTGCATCGATACA-CAAGACAG-TGCACCGATGCATCTC-TTGAA
415836 TGTGCATCGAT
1 TGTGCATCGAT
415847 GCACTCTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 18 0.37
44 31 0.63
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (43 bp):
TGTGCATCGATACACAAGACAGTGCACCGATGCATCTCTTGAA
Found at i:415841 original size:23 final size:23
Alignment explanation
Indices: 415774--415852 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
415764 AAGACAGTGT
415774 ACCGATGCATCTC-TTGAATGTGC
1 ACCGATGCA-CTCATTGAATGTGC
* **
415797 ATCGATATA-TCA-TGAA-GATGC
1 ACCGATGCACTCATTGAATG-TGC
415818 ACCGATGCACTCATTGAATGTGC
1 ACCGATGCACTCATTGAATGTGC
*
415841 ATCGATGCACTC
1 ACCGATGCACTC
415853 TGCTGTGCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
22 3 0.07
23 24 0.55
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (23 bp):
ACCGATGCACTCATTGAATGTGC
Found at i:417832 original size:22 final size:22
Alignment explanation
Indices: 417792--417834 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
417782 GTTATATTTG
* *
417792 AATTGGATGATTTATATGTTTA
1 AATTGAATGATTTAGATGTTTA
*
417814 AATTGAATGATTTGGATGTTT
1 AATTGAATGATTTAGATGTTT
417835 GAATGTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (22 bp):
AATTGAATGATTTAGATGTTTA
Found at i:418669 original size:65 final size:64
Alignment explanation
Indices: 418544--418679 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 64
418534 CACACCCAAT
*
418544 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTC-TCAATATTTTGAAACA
*
418609 TCGATTGCATTTTGTGTACCGATGCAC-AGACCATGCATCGATGCACTC-CAAGCTCA-TTTGAA
1 TCGAATGCATTTTGTGTACCGATGCACAAG-CCATGCATCGATGCACTCTCAA--T-ATTTTGAA
418671 ACA
62 ACA
418674 TCGAAT
1 TCGAAT
418680 ATAATTAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
63 2 0.03
64 2 0.03
65 59 0.92
66 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (64 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCTCAATATTTTGAAACA
Found at i:418691 original size:65 final size:64
Alignment explanation
Indices: 418557--418699 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 64
418547 AATGCATTTT
* * * * *
418557 GTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCGATTGCATTTT
1 GTGTACCGATGCACAAGCCATGCATCGATGCACTC-TCAATATTTTGAAACATCGAATACAATTA
*
418622 GTGTACCGATGCAC-AGACCATGCATCGATGCACTC-CAAGCTCA-TTTGAAACATCGAATATAA
1 GTGTACCGATGCACAAG-CCATGCATCGATGCACTCTCAA--T-ATTTTGAAACATCGAATACAA
418684 TTA
62 TTA
*
418687 GTGTATCGATGCA
1 GTGTACCGATGCA
418700 TCCCAAGTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 2 0.03
64 2 0.03
65 62 0.93
66 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (64 bp):
GTGTACCGATGCACAAGCCATGCATCGATGCACTCTCAATATTTTGAAACATCGAATACAATTA
Found at i:419726 original size:75 final size:75
Alignment explanation
Indices: 419639--420018 Score: 471
Period size: 75 Copynumber: 5.1 Consensus size: 75
419629 CTTAACCGGT
* * * * * * *
419639 TAAAATAAAATAGGCGTTACCTATTATGTTAAATTACTTATTGTTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAATA
* *
419704 ACGTAAATGG
66 ATGTAAACGG
* * *
419714 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAATA
*
419779 ATGTAAACAG
66 ATGTAAACGG
* *
419789 TAAAATAAAATAGGCACTA--TATTACGTCAAACTACCTA-TGTGTTTGTTTAAAGGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTG-GTTTGTTTAAAGGTTACTAAT
*
419851 AATGTAAACAG
65 AATGTAAACGG
* * * * *
419862 TAAAATAAAATAGACGCTATCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAATA
*
419927 ATGTAAATGG
66 ATGTAAACGG
* * * * *
419937 TAAAATAAAATAGGCGTTACCTATTATGTTAAACTATCTACAT-GTTTGTTTAAAGATTAATAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTAC-TGGTTTGTTTAAAGGTTACTAAT
420001 AATGTAAACGG
65 AATGTAAACGG
420012 TAAAATA
1 TAAAATA
420019 TATACAACTT
Statistics
Matches: 267, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
72 1 0.00
73 65 0.24
75 200 0.75
76 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:419928 original size:148 final size:149
Alignment explanation
Indices: 419639--420018 Score: 467
Period size: 148 Copynumber: 2.5 Consensus size: 149
419629 CTTAACCGGT
** * * * * * *
419639 TAAAATAAAATAGGCGTTACCTATTATGTTAAATTACTTA-TTGTTTTGTTTGAAGGTTACTAAT
1 TAAAATAAAATAGGCACTA-CTATTACGTCAAACTACCTACATG-TTTGTTTAAAGGTTACTAAT
* * * *
419703 AACGTAAATGGTAAAATAAAATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAA
64 AATGTAAACGGTAAAATAAAATAGACGCTACCTATTACGTTAAAATAACTACCGGTTTGTTTAAA
* *
419768 TGTTACTAATAATGTAAACAG
129 GGTTAATAATAATGTAAACAG
**
419789 TAAAATAAAATAGGCACTA-TATTACGTCAAACTACCTATGTGTTTGTTTAAAGGTTACTAATAA
1 TAAAATAAAATAGGCACTACTATTACGTCAAACTACCTACATGTTTGTTTAAAGGTTACTAATAA
* * *
419853 TGTAAACAGTAAAATAAAATAGACGCTATCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGG
66 TGTAAACGGTAAAATAAAATAGACGCTACCTATTACGTTAAAATAACTACCGGTTTGTTTAAAGG
**
419918 TTAATAATAATGTAAATGG
131 TTAATAATAATGTAAACAG
** * * * * *
419937 TAAAATAAAATAGGCGTTACCTATTATGTTAAACTATCTACATGTTTGTTTAAAGATTAATAATA
1 TAAAATAAAATAGGCACTA-CTATTACGTCAAACTACCTACATGTTTGTTTAAAGGTTACTAATA
420002 ATGTAAACGGTAAAATA
65 ATGTAAACGGTAAAATA
420019 TATACAACTT
Statistics
Matches: 198, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
148 126 0.64
149 2 0.01
150 70 0.35
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (149 bp):
TAAAATAAAATAGGCACTACTATTACGTCAAACTACCTACATGTTTGTTTAAAGGTTACTAATAA
TGTAAACGGTAAAATAAAATAGACGCTACCTATTACGTTAAAATAACTACCGGTTTGTTTAAAGG
TTAATAATAATGTAAACAG
Found at i:420756 original size:108 final size:108
Alignment explanation
Indices: 420479--420972 Score: 404
Period size: 108 Copynumber: 4.5 Consensus size: 108
420469 TGTTAATATT
* * * * * * * *
420479 TATTTATAACAAAATAAG-ATATTAACCTATTTTGTTGTTGTGGGATTTCGAATGCACCATCAGC
1 TATTGATAACAAATTAAGTA-ATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAGC
* * * *
420543 TTAAATTTTGGTAACATTTTACGCGCTACCTAATATTTTGATAA
65 TTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
* * * * * * *
420587 TATTAATAATAAAATAAGTAATTAACATTTTTTGTTATCGTCGGATTTTTAAAGC-CTCATCAGC
1 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTC-CATCAGC
* * *
420651 TTAAACTTTGATAATATTTTAGGCTCTACCTAATAAGTTGATAA
65 TTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
* *
420695 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAACT
1 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAGC-
* * * * * * *
420760 TTAAAAAGTCGTTACTTATTACATTAAATAAGCGCTACTTATTATGTT-ATTA
65 TT--AAA--C-TT--TGATAACATT--TTAGGCGCTACCTAATATGTTGATAA
* * * * ** * * *
420812 TGGTTGGTAA-TATTTCTTGTAATTAACCTATCTTGTTATAGCCGGATTTCTAAGGCTCCATC-G
1 T-ATTGATAACAAATT-AAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
* * ***
420875 ACTTAAAATTTGGTAACATTTTAGGTATTACCTAATATGTTGATAA
64 -CTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
*
420921 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTTGGATTTCTAA
1 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAA
420973 AACCCTATCA
Statistics
Matches: 299, Mismatches: 69, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
107 1 0.00
108 191 0.64
109 11 0.04
110 7 0.02
111 3 0.01
112 2 0.01
113 1 0.00
114 2 0.01
115 3 0.01
116 7 0.02
117 9 0.03
118 62 0.21
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (108 bp):
TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAGCT
TAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
Found at i:420898 original size:226 final size:226
Alignment explanation
Indices: 420650--421061 Score: 596
Period size: 226 Copynumber: 1.8 Consensus size: 226
420640 GCCTCATCAG
* *
420650 CTTAAACTTTGATAATATTTTAGGCT-CTACCTAATAAGTTGATAATATTGATAACAAATTAAGT
1 CTTAAAATTTGATAACATTTTAGG-TACTACCTAATAAGTTGATAATATTGATAACAAATTAAGT
** * *
420714 AATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCC-ATCA-ACTTTAAAAAGTCGTTACTT
65 AATTAACCTATTTTGTTATCGTCAGATTTCTAAAAC-CCTATCAGACTTTAAAAAGT-GATACCT
* * *
420777 ATTACATTAAATAAGCGCTACTTATTATGTTATTATGGTTGGTAATATTTCTTGTAATTAACCTA
128 ATTACATTAAATAAGCGCTAATTATTATGTTATTATGGTTGATAATATTTCTAGTAATTAACCTA
420842 TCTTGTTATAGCCGGATTTCTAAGGCTCCATCGA
193 TCTTGTTATAGCCGGATTTCTAAGGCTCCATCGA
* * *
420876 CTTAAAATTTGGTAACATTTTAGGTATTACCTAATATGTTGATAATATTGATAACAAATTAAGTA
1 CTTAAAATTTGATAACATTTTAGGTACTACCTAATAAGTTGATAATATTGATAACAAATTAAGTA
** ** *
420941 ATTAACCTATTTTGTTATCGTTGGATTTCTAAAACCCTATCAGTTTTTAAAAGGTGATACCTATT
66 ATTAACCTATTTTGTTATCGTCAGATTTCTAAAACCCTATCAGACTTTAAAAAGTGATACCTATT
* **
421006 ACGTTACTTAAGCGCTAATTATTATGTTATTATGGTTGATAATATTTCTAGTAATT
131 ACATTAAATAAGCGCTAATTATTATGTTATTATGGTTGATAATATTTCTAGTAATT
421062 CACCGATTAT
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
225 3 0.02
226 151 0.93
227 9 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (226 bp):
CTTAAAATTTGATAACATTTTAGGTACTACCTAATAAGTTGATAATATTGATAACAAATTAAGTA
ATTAACCTATTTTGTTATCGTCAGATTTCTAAAACCCTATCAGACTTTAAAAAGTGATACCTATT
ACATTAAATAAGCGCTAATTATTATGTTATTATGGTTGATAATATTTCTAGTAATTAACCTATCT
TGTTATAGCCGGATTTCTAAGGCTCCATCGA
Found at i:421438 original size:26 final size:28
Alignment explanation
Indices: 421389--421440 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
421379 AAAGATGTTA
**
421389 TTGAAAATATTATTATTTTTAATATTTT
1 TTGAAAATATTATTATTTAAAATATTTT
421417 TTGAAAA-A-TATTATTTAAAATATT
1 TTGAAAATATTATTATTTAAAATATT
421441 ATTATTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 1 0.05
28 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTGAAAATATTATTATTTAAAATATTTT
Found at i:421445 original size:15 final size:15
Alignment explanation
Indices: 421386--421447 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
421376 AAGAAAGATG
*
421386 TTATTGAAAATATTA
1 TTATTTAAAATATTA
**
421401 TTATTTTTAATATT-
1 TTATTTAAAATATTA
*
421415 TT-TTGAAAA-A-TA
1 TTATTTAAAATATTA
421427 TTATTTAAAATATTA
1 TTATTTAAAATATTA
421442 TTATTT
1 TTATTT
421448 CTACCAGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 10 0.28
14 3 0.08
15 19 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTATTTAAAATATTA
Found at i:422155 original size:6 final size:6
Alignment explanation
Indices: 422135--422240 Score: 149
Period size: 6 Copynumber: 17.7 Consensus size: 6
422125 TTAAGGTTGC
* * * *
422135 ATTTGG TTTTGG ATTTTG ATTTGG ATTTGG ATTTAG ATTTAG ATTTGG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG
* *
422183 ATTTAG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGA ATTTGG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG
*
422231 ATTTGA ATTT
1 ATTTGG ATTT
422241 ATATTTTAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (6 bp):
ATTTGG
Found at i:425604 original size:15 final size:15
Alignment explanation
Indices: 425578--425626 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
425568 ATTTAGTTGG
*
425578 GCGGGCGGATGCGGT
1 GCGGGTGGATGCGGT
*
425593 GTGGGTGGATGCGGT
1 GCGGGTGGATGCGGT
425608 GCGGGTGGATGCGGT
1 GCGGGTGGATGCGGT
425623 GCGG
1 GCGG
425627 ATGCGGGGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.06, C:0.14, G:0.61, T:0.18
Consensus pattern (15 bp):
GCGGGTGGATGCGGT
Found at i:427026 original size:50 final size:51
Alignment explanation
Indices: 426953--427064 Score: 140
Period size: 50 Copynumber: 2.2 Consensus size: 51
426943 TACTAAATTA
* * *
426953 AAAAGAATAATAAACTAAAGATAATG-TTGTGA-TTTATTCCTAATTCCTATT
1 AAAATAATAA-AAACTAAAGATAATGTTTGTAACTTTATT-CTAATTCCTAAT
* *
427004 AAAATAATAAAAACTAAAGATAATGTTTTTAACTTTATTTTAATTCCTAAT
1 AAAATAATAAAAACTAAAGATAATGTTTGTAACTTTATTCTAATTCCTAAT
427055 -AAATAATAAA
1 AAAATAATAAA
427065 TCTAATCCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 25 0.46
51 23 0.43
52 6 0.11
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (51 bp):
AAAATAATAAAAACTAAAGATAATGTTTGTAACTTTATTCTAATTCCTAAT
Found at i:431316 original size:45 final size:44
Alignment explanation
Indices: 431266--431479 Score: 252
Period size: 45 Copynumber: 4.8 Consensus size: 44
431256 ATCCAATATT
* * *
431266 TTACCA-TTATTTCTATAAGCTCGTAAGCTTATTTTACCAAAATAA
1 TTACCATTTA-TTCCATAAGCTCGTAAGCTTATTTTACC-ATATAC
* * *
431311 TTACCATTTGTCCCATAAGCTTGTAAGCTTATTTTTACCCATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTTA-CCATATAC
* * *
431357 TTACCATTTAATCATATAAGCTCATAAGCTTATTTTACCATATAC
1 TTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCATATAC
*
431402 TTACCATTTAATCACATAAGCTCGTAAGCTTATTTTACCATATAC
1 TTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCATATAC
* *
431447 TTGCCA-TTATTCCATAAGCTCGCAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
431480 GCATGCTTAC
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
43 20 0.14
44 5 0.03
45 80 0.54
46 26 0.18
47 17 0.11
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (44 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCATATAC
Found at i:431385 original size:92 final size:88
Alignment explanation
Indices: 431266--431479 Score: 268
Period size: 92 Copynumber: 2.4 Consensus size: 88
431256 ATCCAATATT
* * *
431266 TTACCATTATTTCTATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTT-GTCCCATAAG
1 TTACCATTA-ATCTATAAGCTCGTAAGCTTATTTTACC-AAATAATTACCATTTAATCACATAAG
*
431330 CTTGTAAGCTTATTTTTACCCATATAC
64 CTCGTAAGCTTA-TTTTA-CCATATAC
* * *
431357 TTACCATTTAATCATATAAGCTCATAAGCTTATTTTACCATATACTTACCATTTAATCACATAAG
1 TTACCA-TTAATC-TATAAGCTCGTAAGCTTATTTTACCAAATAATTACCATTTAATCACATAAG
431422 CTCGTAAGCTTATTTTACCATATAC
64 CTCGTAAGCTTATTTTACCATATAC
* * * *
431447 TTGCCATTATTCCATAAGCTCGCAAGCTTATTT
1 TTACCATTAATCTATAAGCTCGTAAGCTTATTT
431480 GCATGCTTAC
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
88 18 0.17
89 5 0.05
90 13 0.12
91 26 0.24
92 46 0.43
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (88 bp):
TTACCATTAATCTATAAGCTCGTAAGCTTATTTTACCAAATAATTACCATTTAATCACATAAGCT
CGTAAGCTTATTTTACCATATAC
Found at i:431640 original size:40 final size:40
Alignment explanation
Indices: 431561--431641 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
431551 ATATGAGTCA
* * * *
431561 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
431601 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
431641 A
1 A
431642 GTACACCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Found at i:433491 original size:30 final size:31
Alignment explanation
Indices: 433457--433514 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
433447 TTGGTCCCTG
*
433457 AACTTT-CCAAAGTTTATACTTTGATCACCA
1 AACTTTACCAAAGTTTATAATTTGATCACCA
*
433487 AACTTTACCAAATTTTATAATTTGATCA
1 AACTTTACCAAAGTTTATAATTTGATCA
433515 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (31 bp):
AACTTTACCAAAGTTTATAATTTGATCACCA
Found at i:434269 original size:51 final size:50
Alignment explanation
Indices: 434194--434320 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 50
434184 TACTAAATAA
* ** *
434194 AAAAGAATAATAAACTAAATATAATGTTGTGATTCTTTCCTAATTCTCAAT
1 AAAA-AATAATAAACTAAAGATAATGTTACGATTCTATCCTAATTCTCAAT
*
434245 AAAATAATAATAAACTAAAGATAATGTTACGATTGTATCCTAATTCTCAAT
1 AAAA-AATAATAAACTAAAGATAATGTTACGATTCTATCCTAATTCTCAAT
*
434296 --AAAATAATAAACTAAAGATGATGTT
1 AAAAAATAATAAACTAAAGATAATGTT
434321 TTTAACTCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 22 0.32
49 2 0.03
51 45 0.65
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (50 bp):
AAAAAATAATAAACTAAAGATAATGTTACGATTCTATCCTAATTCTCAAT
Found at i:436342 original size:61 final size:60
Alignment explanation
Indices: 436198--436344 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
436188 GAAGGTGTAT
* * * ** * *
436198 CGATGC-CAGGTAGTTCATCGATGCACTCTTTTAAATAAAAACATTGAATGCAAGTGCAT
1 CGATGCACAAGTAGTGCATCGATGCATTCCATTAAATAAAAACATCGAATGCAAGTGCAC
* * **
436257 CGATGCATAAGGCA-TGCATCGATGCATTCCATT-AATAATAAACATCGAATGCATTTTGCAC
1 CGATGCACAA-GTAGTGCATCGATGCATTCCATTAAATAA-AAACATCGAATGCA-AGTGCAC
436318 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGTAGTGCATCGATGCAT
436345 ACCTTCATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
59 11 0.16
60 31 0.44
61 28 0.40
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CGATGCACAAGTAGTGCATCGATGCATTCCATTAAATAAAAACATCGAATGCAAGTGCAC
Found at i:436877 original size:15 final size:15
Alignment explanation
Indices: 436859--436892 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
436849 GAGGGTATAA
436859 TAGTCCTTCAGGACG
1 TAGTCCTTCAGGACG
* *
436874 TAGTCCTTCGGGATG
1 TAGTCCTTCAGGACG
436889 TAGT
1 TAGT
436893 GGTCCTACGG
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:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCAGGACG
Found at i:437174 original size:41 final size:41
Alignment explanation
Indices: 437117--437199 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
437107 TGTAATAGAT
437117 ACATGCATATTGAAATGTCATGAAGGAAATGGTAAGAATGC
1 ACATGCATATTGAAATGTCATGAAGGAAATGGTAAGAATGC
437158 ACATGCATATTGAAATGTCATGAAGGAAATGGTAAGAATGC
1 ACATGCATATTGAAATGTCATGAAGGAAATGGTAAGAATGC
437199 A
1 A
437200 TACTCATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (41 bp):
ACATGCATATTGAAATGTCATGAAGGAAATGGTAAGAATGC
Found at i:438479 original size:40 final size:40
Alignment explanation
Indices: 438424--438506 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
438414 CTGGCAAAAC
438424 TTTGGGAGAAAATTAGAGAGAAAAGATGAATGCCTAGCTT
1 TTTGGGAGAAAATTAGAGAGAAAAGATGAATGCCTAGCTT
438464 TTTGGGAGAAAATTAGAGAGAAAAGATGAATGCCTAGCTT
1 TTTGGGAGAAAATTAGAGAGAAAAGATGAATGCCTAGCTT
438504 TTT
1 TTT
438507 ACCCTTCCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.28
Consensus pattern (40 bp):
TTTGGGAGAAAATTAGAGAGAAAAGATGAATGCCTAGCTT
Found at i:439394 original size:32 final size:31
Alignment explanation
Indices: 439296--439404 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 31
439286 ACCTGAACCA
* * *
439296 AAAGCAATCCGAACCGAAATTAACCCAA-CCT
1 AAAGCAACCCGAACCGAATTTAA-CCAATCCG
* * **
439327 AAAGCAACCCAAACC-AATTTTAACCCGATTTG
1 AAAGCAACCCGAACCGAA-TTTAA-CCAATCCG
439359 AAAGCAACCCGAACCGAATTTAACCATATCCG
1 AAAGCAACCCGAACCGAATTTAACCA-ATCCG
439391 AAAGCAACCCGAAC
1 AAAGCAACCCGAAC
439405 AAATTGAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
30 2 0.03
31 23 0.37
32 36 0.57
33 2 0.03
ACGTcount: A:0.43, C:0.31, G:0.11, T:0.15
Consensus pattern (31 bp):
AAAGCAACCCGAACCGAATTTAACCAATCCG
Found at i:439515 original size:19 final size:19
Alignment explanation
Indices: 439461--439515 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
439451 TAATAAATTA
439461 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TGATAG
439479 ATTTAT--TAAAAT-ATTAG
1 ATTTATAATAAAATGA-TAG
439496 ATTTATAATAAAATGATAG
1 ATTTATAATAAAATGATAG
439515 A
1 A
439516 AAGTTTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 11 0.35
18 5 0.16
19 10 0.32
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTTATAATAAAATGATAG
Found at i:441324 original size:7 final size:7
Alignment explanation
Indices: 441304--441340 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
441294 GTCAAAGAAA
441304 GTCAACG
1 GTCAACG
441311 GTC-ACG
1 GTCAACG
441317 GTCAACG
1 GTCAACG
441324 GTCAACG
1 GTCAACG
441331 GTCAACG
1 GTCAACG
441338 GTC
1 GTC
441341 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:441352 original size:17 final size:17
Alignment explanation
Indices: 441330--441386 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
441320 AACGGTCAAC
*
441330 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
441347 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
441364 GGTCAACAGTCGGGTTG
1 GGTCAACAGTCGGGTCG
441381 GGTCAA
1 GGTCAA
441387 ACCGGTTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:441402 original size:10 final size:10
Alignment explanation
Indices: 441383--441451 Score: 81
Period size: 9 Copynumber: 7.1 Consensus size: 10
441373 TCGGGTTGGG
441383 TCAAACCGGT
1 TCAAACCGGT
*
441393 TCAGACCGG-
1 TCAAACCGGT
441402 TCAAACCGGT
1 TCAAACCGGT
*
441412 TCGAACCGG-
1 TCAAACCGGT
441421 TCAAACCGGT
1 TCAAACCGGT
*
441431 TCAAAACTGG-
1 TC-AAACCGGT
441441 TCAAACCGGT
1 TCAAACCGGT
441451 T
1 T
441452 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 22 0.45
10 21 0.43
11 6 0.12
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:441405 original size:19 final size:19
Alignment explanation
Indices: 441381--441451 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
441371 AGTCGGGTTG
441381 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
441400 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
441419 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
441439 GGTCAAACCGGTT
1 GGTCAAACCGGTT
441452 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.02
19 31 0.66
20 15 0.32
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:444497 original size:109 final size:109
Alignment explanation
Indices: 444306--444523 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
444296 AATTGATCCA
*
444306 ATATGGTCGGAACACCCGATTCATCAAATCCATGAAAGCTGCAGGAGCGTTCGTCAAACCAAAAG
1 ATATGGTCGGAACACCCGATTCATCAAATCCATGAAAGCTACAGGAGCGTTCGTCAAACCAAAAG
444371 GCATCACTAAGAATTCATAATGACCATATCTAGTGCGAATAGCC
66 GCATCACTAAGAATTCATAATGACCATATCTAGTGCGAATAGCC
444415 ATATGGTCGGAACACCCGATTCATCAAATCCATGAAAGCTACAGGAGCGTTCGTCAAACCAAAAG
1 ATATGGTCGGAACACCCGATTCATCAAATCCATGAAAGCTACAGGAGCGTTCGTCAAACCAAAAG
444480 GCATCACTAAGAATTCATAATGACCATATCTAGTGCGAATAGCC
66 GCATCACTAAGAATTCATAATGACCATATCTAGTGCGAATAGCC
444524 GTTTTGCAAT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (109 bp):
ATATGGTCGGAACACCCGATTCATCAAATCCATGAAAGCTACAGGAGCGTTCGTCAAACCAAAAG
GCATCACTAAGAATTCATAATGACCATATCTAGTGCGAATAGCC
Found at i:448434 original size:7 final size:7
Alignment explanation
Indices: 448422--448465 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
448412 GTCAAAGAAA
448422 GTCAACG
1 GTCAACG
448429 GTCAACG
1 GTCAACG
448436 GTC-ACG
1 GTCAACG
448442 GTCAACG
1 GTCAACG
448449 GTCAACG
1 GTCAACG
448456 GTCAACG
1 GTCAACG
448463 GTC
1 GTC
448466 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:448447 original size:20 final size:21
Alignment explanation
Indices: 448422--448465 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
448412 GTCAAAGAAA
448422 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
448442 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
448463 GTC
1 GTC
448466 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:448477 original size:17 final size:17
Alignment explanation
Indices: 448455--448512 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
448445 AACGGTCAAC
*
448455 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
448472 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
448489 GGTCAACAGTCGTGTCG
1 GGTCAACAGTCGGGTCG
448506 GGTCAAC
1 GGTCAAC
448513 CCGGTTTAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.40, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:448530 original size:19 final size:19
Alignment explanation
Indices: 448506--448570 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
448496 AGTCGTGTCG
* *
448506 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTCAGACC
448525 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
448544 GGTCAAACCGGTTCAAACC
1 GGTCAAACCGGTTCAGACC
448563 GGTTCAAA
1 GG-TCAAA
448571 ACTGGTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 37 0.88
20 5 0.12
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:448544 original size:10 final size:10
Alignment explanation
Indices: 448508--448586 Score: 83
Period size: 10 Copynumber: 8.1 Consensus size: 10
448498 TCGTGTCGGG
*
448508 TCAACCCGGT
1 TCAAACCGGT
* *
448518 TTAGACCGG-
1 TCAAACCGGT
448527 TCAAACCGGT
1 TCAAACCGGT
*
448537 TCAGACCGG-
1 TCAAACCGGT
448546 TCAAACCGGT
1 TCAAACCGGT
448556 TCAAACCGGT
1 TCAAACCGGT
*
448566 TCAAAACTGG-
1 TC-AAACCGGT
448576 TCAAACCGGT
1 TCAAACCGGT
448586 T
1 T
448587 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 21 0.38
10 29 0.52
11 6 0.11
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:449666 original size:32 final size:32
Alignment explanation
Indices: 449630--449718 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
449620 CTAACATATC
*
449630 TGGTATTAACCT-GACCCAAAAATCAATCGATA
1 TGGTATT-ACCTCGACCAAAAAATCAATCGATA
** *
449662 TGGTATTGTCTCGATCAAAAAATCAATCGATA
1 TGGTATTACCTCGACCAAAAAATCAATCGATA
** *
449694 TGGTATTGTCTCGATCAAAAAATCA
1 TGGTATTACCTCGACCAAAAAATCA
449719 TCCGATCCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 2 0.04
32 50 0.96
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (32 bp):
TGGTATTACCTCGACCAAAAAATCAATCGATA
Found at i:449733 original size:32 final size:32
Alignment explanation
Indices: 449647--449733 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
449637 AACCTGACCC
* *
449647 AAAAATCAATCGATATGGTATTGTCTCGATCA
1 AAAAATCAATCGATACGATATTGTCTCGATCA
* *
449679 AAAAATCAATCGATATGGTATTGTCTCGATCA
1 AAAAATCAATCGATACGATATTGTCTCGATCA
*
449711 AAAAATC-ATCCGATCCGATATTG
1 AAAAATCAAT-CGATACGATATTG
449734 ATCCGAACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
31 2 0.04
32 49 0.96
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (32 bp):
AAAAATCAATCGATACGATATTGTCTCGATCA
Found at i:451127 original size:60 final size:60
Alignment explanation
Indices: 451043--451220 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 60
451033 TATATGTCCC
** * ** * * *
451043 CAAACTATGAT-CTTCATTTTAAATTGGTCCCTCTACTTTTGAATATTCTAATTTCATTAT
1 CAAACTATGATAC-TCATTAGAAATTAGTCCCTAAACTTTTGAACATTATAATTTCATCAT
*
451103 CAAACTATGATACT-ATTTAGAAATTAGTCCTTAAACTTTTGAACATTATAATTTCATCAT
1 CAAACTATGATACTCA-TTAGAAATTAGTCCCTAAACTTTTGAACATTATAATTTCATCAT
* * * * *
451163 CAAACTATGATACTCATTATAAATTAGTCCCTAAACTTCTAAACCTTCTAATTTCATC
1 CAAACTATGATACTCATTAGAAATTAGTCCCTAAACTTTTGAACATTATAATTTCATC
451221 CTTAAATTCA
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 97 0.97
61 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (60 bp):
CAAACTATGATACTCATTAGAAATTAGTCCCTAAACTTTTGAACATTATAATTTCATCAT
Found at i:453953 original size:25 final size:26
Alignment explanation
Indices: 453891--453954 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 26
453881 TTGTTCATTT
* *
453891 AATTTTTTTTAAAA-ATATTTGTTGA
1 AATTTTTATTAAAATATATTTGTTCA
453916 AAGTTTTTA--AAAATATATTT-TTCA
1 AA-TTTTTATTAAAATATATTTGTTCA
*
453940 TATTTTTATTAAAAT
1 AATTTTTATTAAAAT
453955 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 6 0.19
24 8 0.25
25 13 0.41
26 5 0.16
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (26 bp):
AATTTTTATTAAAATATATTTGTTCA
Found at i:456791 original size:145 final size:145
Alignment explanation
Indices: 456556--456849 Score: 552
Period size: 145 Copynumber: 2.0 Consensus size: 145
456546 CAGAGTGTTT
456556 TTACTAAACCCTATTACATGCCAACTAAAATATAACAAAAAGTAGACAGGTGTGTCATACGGTTA
1 TTACTAAACCCTATTACATGCCAACTAAAATATAACAAAAAGTAGACAGGTGTGTCATACGGTTA
*
456621 CCGATGAGGCGACTCTGACTGGATGTCCAAAAGATCTCCTTACTTAGCTATATTTAACCTACACG
66 CCGATGAGGCAACTCTGACTGGATGTCCAAAAGATCTCCTTACTTAGCTATATTTAACCTACACG
*
456686 TGAAATGATCACACG
131 TGAAATGAGCACACG
*
456701 TTACTAAACCCTATTACATGCCAACTAAATTATAACAAAAAGTAGACAGGTGTGTCATACGGTTA
1 TTACTAAACCCTATTACATGCCAACTAAAATATAACAAAAAGTAGACAGGTGTGTCATACGGTTA
*
456766 CCGATGAGGCAACTCTGACTGGATGTCCAAAAGATCTCCTTACTTAGCTGTATTTAACCTACACG
66 CCGATGAGGCAACTCTGACTGGATGTCCAAAAGATCTCCTTACTTAGCTATATTTAACCTACACG
456831 TGAAATGAGCACACG
131 TGAAATGAGCACACG
456846 TTAC
1 TTAC
456850 GTATTACATA
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (145 bp):
TTACTAAACCCTATTACATGCCAACTAAAATATAACAAAAAGTAGACAGGTGTGTCATACGGTTA
CCGATGAGGCAACTCTGACTGGATGTCCAAAAGATCTCCTTACTTAGCTATATTTAACCTACACG
TGAAATGAGCACACG
Found at i:457119 original size:59 final size:59
Alignment explanation
Indices: 457039--457426 Score: 579
Period size: 59 Copynumber: 6.6 Consensus size: 59
457029 ATACAAACAA
* * * *
457039 TATGAATTCCTTATCAATTTAGCACACAGAGTGCCCTATCTGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* * *
457098 TATGATTTCCTTACTC-TTTTAGCACACAAAATGCCCTATCTGGAAATTCTTACACATAG
1 TATGATTTCCTTAC-CATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* * * *
457157 TATGATTTCCTTGCCATTTTAGCACACAAAGTGTCCTATCTGGAAATTCATACCCTTTG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* *
457216 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGAAATTCATACAC--AT
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* *
457273 TATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTA-CTGGAAATTCATACACATAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
*
457331 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACA-TATAT
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACT-TAG
457390 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
457427 TTGGTAATTT
Statistics
Matches: 297, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
56 15 0.05
57 37 0.12
58 39 0.13
59 205 0.69
60 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
Found at i:457362 original size:174 final size:176
Alignment explanation
Indices: 457020--457426 Score: 599
Period size: 174 Copynumber: 2.3 Consensus size: 176
457010 TAAATTCAAT
* * * * * * * * *
457020 TGGAATTTCATACAAACAATATGAATTCCTTATCAATTTAGCACACAGAGTGCCCTATCTGGAAA
1 TGGAAATTCATACATATATTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGAAA
*
457085 TTCATACACTTAGTATGATTTCCTTACTCTTTTAGCACACAAAATGCCCTATCTGGAAATTCTTA
66 TTCATACAC-TAGTATGATTTCCTTACTCTTTTAGCACACAAAATGCCCTATCTGGAAATTCATA
* *
457150 CACATAGTATGATTTCCTTGCCATTTTAGCACACAAAGTGTCCTATC
130 CACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
457197 TGGAAATTCATACCCT-T-TGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGA
1 TGGAAATTCATA-CATATAT-TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGA
* * *
457260 AATTCATACAC-ATTATGATTTCCTTAC-CATTTTAGCACACGAAGTGCCCTA-CTGGAAATTCA
64 AATTCATACACTAGTATGATTTCCTTACTC-TTTTAGCACACAAAATGCCCTATCTGGAAATTCA
457322 TACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
128 TACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
457371 TGGAAATTCATACATATATTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACATATATTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
457427 TTGGTAATTT
Statistics
Matches: 208, Mismatches: 17, Indels: 13
0.87 0.07 0.05
Matches are distributed among these distances:
173 2 0.01
174 108 0.52
175 36 0.17
177 61 0.29
178 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (176 bp):
TGGAAATTCATACATATATTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATATGGAAA
TTCATACACTAGTATGATTTCCTTACTCTTTTAGCACACAAAATGCCCTATCTGGAAATTCATAC
ACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:457793 original size:22 final size:23
Alignment explanation
Indices: 457747--457799 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
457737 TGGCCTTTAC
*
457747 GTATCGATAC--CCCTACTTATG
1 GTATCGATACTACCCTACTTAGG
*
457768 GTATTGATACTACCCTA-TTAGG
1 GTATCGATACTACCCTACTTAGG
457790 GTATCGATAC
1 GTATCGATAC
457800 CCCGTTCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.33
22 13 0.48
23 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (23 bp):
GTATCGATACTACCCTACTTAGG
Found at i:457867 original size:20 final size:20
Alignment explanation
Indices: 457842--457916 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 20
457832 GAAGTAAACT
457842 TGGTATCGATACCCTCATCA
1 TGGTATCGATACCCTCATCA
* *
457862 TGGTATCGATACCCCTAAGCTA
1 TGGTATCGATA-CCCTCATC-A
* *
457884 TGGTACCGATACCC-CCTC-
1 TGGTATCGATACCCTCATCA
457902 TAGGTATCGATACCC
1 T-GGTATCGATACCC
457917 AAATTAGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 12 0.27
20 12 0.27
21 9 0.20
22 11 0.24
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (20 bp):
TGGTATCGATACCCTCATCA
Found at i:465399 original size:24 final size:24
Alignment explanation
Indices: 465367--465412 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
465357 TCATATAAAT
465367 TGCACCGAAGTACCACGTAGAATA
1 TGCACCGAAGTACCACGTAGAATA
* *
465391 TGCATCGAAGTGCCACGTAGAA
1 TGCACCGAAGTACCACGTAGAA
465413 ATGTCCTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
TGCACCGAAGTACCACGTAGAATA
Found at i:465504 original size:23 final size:23
Alignment explanation
Indices: 465403--465496 Score: 152
Period size: 23 Copynumber: 4.1 Consensus size: 23
465393 CATCGAAGTG
* *
465403 CCACGTAGAAATGTCCTGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
465426 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
*
465449 CCACATAAAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
*
465472 CCGCATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
465495 CC
1 CC
465497 GCGTAGAACC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:465600 original size:14 final size:14
Alignment explanation
Indices: 465581--465644 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
465571 TTATACCATT
465581 TCACATAGCTTATA
1 TCACATAGCTTATA
**
465595 TCACATAGACAAATAA
1 TCACATAG-CTTAT-A
** * *
465611 TCACATATATCATG
1 TCACATAGCTTATA
465625 TCACATAGCTTATA
1 TCACATAGCTTATA
465639 TCACAT
1 TCACAT
465645 TTTCAAATAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
14 24 0.65
15 5 0.14
16 8 0.22
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (14 bp):
TCACATAGCTTATA
Found at i:465634 original size:44 final size:44
Alignment explanation
Indices: 465572--465677 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
465562 CTTTATCATT
* *
465572 TATACCATTTCACATAGCTTATATCACATAGACAAATAATCACA
1 TATATCATATCACATAGCTTATATCACATAGACAAATAATCACA
* ***
465616 TATATCATGTCACATAGCTTATATCACATTTTCAAATAATCACA
1 TATATCATATCACATAGCTTATATCACATAGACAAATAATCACA
465660 T-TGATCATATCACATAGC
1 TAT-ATCATATCACATAGC
465678 ATGAAATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 54 0.98
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.33
Consensus pattern (44 bp):
TATATCATATCACATAGCTTATATCACATAGACAAATAATCACA
Found at i:465705 original size:18 final size:18
Alignment explanation
Indices: 465684--465719 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
465674 TAGCATGAAA
465684 TATAAACAATGCATGTTC
1 TATAAACAATGCATGTTC
465702 TATAAACAATGCATGTTC
1 TATAAACAATGCATGTTC
465720 AATTAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
TATAAACAATGCATGTTC
Found at i:472455 original size:23 final size:23
Alignment explanation
Indices: 472429--472522 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
472419 CACCGAAGTG
472429 CCACGTAGAAATGTCCTGAAGGA
1 CCACGTAGAAATGTCCTGAAGGA
* *
472452 CCACATAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCTGAAGGA
** *
472475 CTGCGTAGAAATATCCTGAAGGA
1 CCACGTAGAAATGTCCTGAAGGA
* *
472498 CTACGTAGAATTGTCCTGAAGGA
1 CCACGTAGAAATGTCCTGAAGGA
472521 CC
1 CC
472523 GCGTTGAACT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
CCACGTAGAAATGTCCTGAAGGA
Found at i:476433 original size:45 final size:46
Alignment explanation
Indices: 476345--476435 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
476335 TTGAAATAGC
* *
476345 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
476391 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
476436 TTTGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:488372 original size:16 final size:17
Alignment explanation
Indices: 488347--488378 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
488337 TTGTTGTTTT
488347 TTTTTCTTCTTTCTCTG
1 TTTTTCTTCTTTCTCTG
488364 TTTTT-TTCTTTCTCT
1 TTTTTCTTCTTTCTCT
488379 CCGGTTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTCTTCTTTCTCTG
Found at i:488854 original size:3 final size:3
Alignment explanation
Indices: 488846--488931 Score: 129
Period size: 3 Copynumber: 28.0 Consensus size: 3
488836 GTATTTATAT
488846 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
488892 GTA TATAA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA -AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
488932 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.03
3 68 0.88
4 6 0.08
5 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:489275 original size:116 final size:116
Alignment explanation
Indices: 489090--489813 Score: 1025
Period size: 116 Copynumber: 6.3 Consensus size: 116
489080 TTCTTTAGAT
** * *
489090 GAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCAA-ATGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATGATCCATCAATATGATGAATTCAAGTAA
*
489154 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
65 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
* * * * *
489206 CGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCA
1 -GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAGTA
*
489269 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
64 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
* * *
489322 CGAGTTCTTCTCATTATGAAC--TCTCTGGAAAAGATAATCCATCAATTTGATGAATTC-AGAAA
1 -GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAG-TA
*
489384 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG-
64 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
* * * *
489436 G-GTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAATTTGATGACTTCAGGTAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAGTAAA
489500 AGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTC--A-GA
66 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
* * *
489545 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAGTAAA
489610 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
66 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
* * *
489661 CGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTCAGGTAA
1 -GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAGTAA
*
489725 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--
65 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
*
489775 GAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCTGATC
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATC
489814 TTTCAAATGA
Statistics
Matches: 564, Mismatches: 27, Indels: 37
0.90 0.04 0.06
Matches are distributed among these distances:
108 1 0.00
109 2 0.00
110 88 0.16
111 14 0.02
112 37 0.07
113 36 0.06
114 82 0.15
115 63 0.11
116 174 0.31
117 65 0.12
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (116 bp):
GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAATATGATGAATTCAAGTAAA
AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
Found at i:489801 original size:339 final size:341
Alignment explanation
Indices: 489071--489824 Score: 1092
Period size: 339 Copynumber: 2.2 Consensus size: 341
489061 ATTGAATAAA
* * ** * *
489071 TTCTTC-TCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGCTGATCCATC
489135 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAA--TCTTCTTCCTTCTTC
* * * *
489200 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCA
128 A-ATGACGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGATAATCCATCAAATGATGAATTCA
489265 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCT
192 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCT
*
489330 TCTCATTATGAACTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGAAAAAAGGTTGAAC
257 TCTCATTATGAACTCTCTGGAAAAGATAATCCATCAATATGATGAATTCAGAAAAAAGGTTGAAC
*
489395 AAATTCTTCTCATTATGAAC
322 AAATTATTCTCATTATGAAC
*
489415 TTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
* * * * *
489480 ATTTGATGACTTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAA-CTTCTTCCTTCTTC-A
66 A-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAATCTTCTTCCTTCTTCAA
* * *
489543 -GA-GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAG
130 TGACGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAGATAATCCATCAA-ATGATGAATTCAA
* *
489605 GTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
193 GCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
* * * **
489670 CTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTCAGGTAAAAGGTTGAA
258 CTCATTATGAAC--TCTCTGGAAAAGATAATCCATCAATATGATGAATTCAGAAAAAAGGTTGAA
*
489734 CAAGTTATTCTCATTATGAAC
321 CAAATTATTCTCATTATGAAC
**
489755 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCTGATCTTTCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
489819 AATGAT
66 AATGAT
489825 AGATTTGAAT
Statistics
Matches: 371, Mismatches: 33, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
337 2 0.01
338 42 0.11
339 111 0.30
340 81 0.22
341 22 0.06
342 14 0.04
344 23 0.06
345 76 0.20
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (341 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAATCTTCTTCCTTCTTCAAT
GACGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGATAATCCATCAAATGATGAATTCAAGCA
AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
ATTATGAACTCTCTGGAAAAGATAATCCATCAATATGATGAATTCAGAAAAAAGGTTGAACAAAT
TATTCTCATTATGAAC
Found at i:490859 original size:84 final size:82
Alignment explanation
Indices: 490562--490852 Score: 512
Period size: 84 Copynumber: 3.5 Consensus size: 82
490552 CCTACTGAAT
490562 CAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
490626 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
490643 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
490708 TGATTGGTTCTGTCCAAC
66 TGATT-GTTCTGTCCAAC
* * * *
490726 CAGATCAGATAACTCAAAGAACACTTTCAGAAGGTGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
490791 ATGATTAGTTCTGTCCAAC
65 ATGATT-GTTCTGTCCAAC
490810 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
490853 GCACATTATA
Statistics
Matches: 200, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
81 15 0.08
82 54 0.27
83 53 0.26
84 78 0.39
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAC
Found at i:491668 original size:16 final size:16
Alignment explanation
Indices: 491647--491686 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
491637 GAATTTCCAA
*
491647 AAATAAATTG-ACTCTT
1 AAATAAATTGAACT-TG
491663 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
491679 AAATAAAT
1 AAATAAAT
491687 AGAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:492016 original size:9 final size:9
Alignment explanation
Indices: 492004--492091 Score: 66
Period size: 9 Copynumber: 10.3 Consensus size: 9
491994 GATCCCCTTT
492004 TTCTTTTTC
1 TTCTTTTTC
*
492013 TTCTTTTTT
1 TTCTTTTTC
*
492022 TTCATTTTC
1 TTCTTTTTC
*
492031 -TATTTTT-
1 TTCTTTTTC
492038 TTC-TTTTC
1 TTCTTTTTC
492046 TT-TCTTTT-
1 TTCT-TTTTC
492054 TTCTATTTTC
1 TTCT-TTTTC
492064 TTC-TTTTC
1 TTCTTTTTC
492072 TT-TCTTTT-
1 TTCT-TTTTC
492080 TTCTTTTTC
1 TTCTTTTTC
492089 TTC
1 TTC
492092 AAGCATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
7 4 0.06
8 23 0.37
9 32 0.52
10 3 0.05
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:492045 original size:33 final size:34
Alignment explanation
Indices: 492001--492092 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 34
491991 CTTGATCCCC
492001 TTTTTCTTTTTCTTCTTTTTTTTCATTTTC-TATT
1 TTTTTC-TTTTCTTCTTTTTTTTCATTTTCTTATT
* *
492035 TTTTTCTTTTCTT-TCTTTTTTCTATTTTCTTCTT
1 TTTTTCTTTTCTTCTTTTTTTTC-ATTTTCTTATT
*
492069 TTCTTTCTTTT-TTCTTTTTCTTCA
1 TT-TTTCTTTTCTTCTTTTTTTTCA
492093 AGCATAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
32 8 0.16
33 13 0.26
34 14 0.28
35 15 0.30
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTTCTTTTCTTCTTTTTTTTCATTTTCTTATT
Found at i:492055 original size:26 final size:25
Alignment explanation
Indices: 492001--492091 Score: 130
Period size: 26 Copynumber: 3.6 Consensus size: 25
491991 CTTGATCCCC
*
492001 TTTTTCTTTTTCTTCTTTTTTTTC-
1 TTTTTCTTTTTCTTCTTTTCTTTCT
* *
492025 ATTTTCTATTTTTTTCTTTTCTTTCT
1 TTTTTCT-TTTTCTTCTTTTCTTTCT
492051 TTTTTCTATTTTCTTCTTTTCTTTCT
1 TTTTTCT-TTTTCTTCTTTTCTTTCT
492077 TTTTTCTTTTTCTTC
1 TTTTTCTTTTTCTTC
492092 AAGCATAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
24 6 0.10
25 23 0.38
26 31 0.52
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTCTTTTTCTTCTTTTCTTTCT
Found at i:498516 original size:82 final size:83
Alignment explanation
Indices: 498379--498670 Score: 523
Period size: 84 Copynumber: 3.5 Consensus size: 83
498369 CCTACTGAAT
498379 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
498444 TGATT-GTTCTGTCCAAC
66 TGATTAGTTCTGTCCAAC
498461 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
*
498526 TGATTGGTTCTGTCCAAC
66 TGATTAGTTCTGTCCAAC
* * * *
498544 CAGATCAGATAACTCAAAGAACACTTTCAGAAGGTGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
498609 ATGATTAGTTCTGTCCAAC
65 ATGATTAGTTCTGTCCAAC
498628 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
498671 GCACATTATA
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 70 0.35
83 53 0.26
84 78 0.39
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTAGTTCTGTCCAAC
Found at i:499485 original size:16 final size:16
Alignment explanation
Indices: 499464--499503 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
499454 GAATTTCCAA
*
499464 AAATAAATTG-ACTCTT
1 AAATAAATTGAACT-TG
499480 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
499496 AAATAAAT
1 AAATAAAT
499504 AGAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:499833 original size:9 final size:8
Alignment explanation
Indices: 499818--499909 Score: 71
Period size: 9 Copynumber: 10.5 Consensus size: 8
499808 CTTGATCCCC
499818 TTTTTCTT
1 TTTTTCTT
499826 TTTCTTCTT
1 TTT-TTCTT
499835 TTTTT-TT
1 TTTTTCTT
499842 TCATTTTCTATTT
1 T--TTTTC---TT
499855 TTTTTCTT
1 TTTTTCTT
499863 TTCTTTCTT
1 TT-TTTCTT
*
499872 TTTTCTATT
1 TTTT-TCTT
499881 TTCTTTCTT
1 TT-TTTCTT
499890 TTCTTTC-T
1 TT-TTTCTT
499898 TTTTTCTT
1 TTTTTCTT
499906 TTTT
1 TTTT
499910 CTTCAAGCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
7 7 0.10
8 19 0.27
9 35 0.49
10 2 0.03
11 5 0.07
13 3 0.04
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:499855 original size:16 final size:17
Alignment explanation
Indices: 499830--499884 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
499820 TTTCTTTTTC
*
499830 TTCTTTTTTTTTTCATT
1 TTCTATTTTTTTTCATT
499847 TTCTATTTTTTTTC-TT
1 TTCTATTTTTTTTCATT
499863 TTCT-TTCTTTTTTCTATT
1 TTCTATT-TTTTTTC-ATT
499881 TTCT
1 TTCT
499885 TTCTTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.06
16 13 0.38
17 13 0.38
18 6 0.18
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTATTTTTTTTCATT
Found at i:499891 original size:16 final size:15
Alignment explanation
Indices: 499817--499907 Score: 66
Period size: 16 Copynumber: 6.0 Consensus size: 15
499807 CCTTGATCCC
499817 CTTTTTCTTT-TTCTT
1 CTTTTTCTTTCTT-TT
*
499832 CTTTTTTTTTTCATTTT
1 C-TTTTTCTTTC-TTTT
*
499849 CTATTTTTTTTCTTTT
1 CT-TTTTCTTTCTTTT
499865 C--TTTC-TT-TTTT
1 CTTTTTCTTTCTTTT
499876 CTATTTTCTTTCTTTT
1 CT-TTTTCTTTCTTTT
*
499892 CTTTCTTTTTTCTTTT
1 CTTT-TTCTTTCTTTT
499908 TTCTTCAAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 3 0.05
14 4 0.06
15 5 0.08
16 30 0.48
17 12 0.19
18 2 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTTCTTTT
Found at i:499910 original size:27 final size:27
Alignment explanation
Indices: 499818--499912 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
499808 CTTGATCCCC
499818 TTTTTCTTTTTCTTCTTT-TTTT-TTTC-
1 TTTTTC-TTTT-TTCTTTCTTTTCTTTCT
*
499844 ATTTTCTATTTTT-TTTCTTTTCTTTCT
1 TTTTTCT-TTTTTCTTTCTTTTCTTTCT
*
499871 TTTTTCTATTTTCTTTCTTTTCTTTCT
1 TTTTTCTTTTTTCTTTCTTTTCTTTCT
499898 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
499913 CAAGCATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
24 3 0.05
25 7 0.12
26 16 0.27
27 34 0.57
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTCTTTTTTCTTTCTTTTCTTTCT
Found at i:499910 original size:34 final size:32
Alignment explanation
Indices: 499824--499911 Score: 108
Period size: 34 Copynumber: 2.7 Consensus size: 32
499814 CCCCTTTTTC
499824 TTTTTCTTCTTTT-TTTTTTC-ATTTTCTATTT
1 TTTTTCTT-TTTTCTTTTTTCTATTTTCTATTT
*
499855 TTTTTCTTTTCTTTCTTTTTTCTATTTTCTTTCTT
1 TTTTTC-TTT-TTTCTTTTTTCTATTTTCTAT-TT
499890 TTCTTTCTTTTTTCTTTTTTCT
1 TT-TTTCTTTTTTCTTTTTTCT
499912 TCAAGCATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
31 7 0.14
32 5 0.10
33 7 0.14
34 20 0.40
35 7 0.14
36 4 0.08
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTTCTTTTTTCTTTTTTCTATTTTCTATTT
Found at i:503443 original size:18 final size:19
Alignment explanation
Indices: 503417--503453 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
503407 ATTTATGAAA
*
503417 TAAATAAATGTAAA-AATG
1 TAAAAAAATGTAAAGAATG
503435 TAAAAAAATGTAAAGAATG
1 TAAAAAAATGTAAAGAATG
503454 ATTGCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAAAAAATGTAAAGAATG
Found at i:507218 original size:21 final size:20
Alignment explanation
Indices: 507190--507228 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
507180 TAGTGAAAAT
507190 TATGAAATGAATG-ATGAATG
1 TATGAAATG-ATGTATGAATG
507210 TATGCAAATGATGTATGAA
1 TATG-AAATGATGTATGAA
507229 AAAAACATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (20 bp):
TATGAAATGATGTATGAATG
Found at i:510450 original size:27 final size:27
Alignment explanation
Indices: 510378--510450 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 27
510368 CTTTGACAGA
*
510378 AAATAAATAATGATAAAATACTTGCAAAT
1 AAATAAAT-AT-ATAAAATACTTGAAAAT
* *
510407 AAATAAA-ACATATAAATATTATGAAAAT
1 AAATAAATATATA-AAATACT-TGAAAAT
510435 -AATAAATATATAAAAT
1 AAATAAATATATAAAAT
510451 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.08
27 17 0.46
28 10 0.27
29 7 0.19
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (27 bp):
AAATAAATATATAAAATACTTGAAAAT
Found at i:512067 original size:16 final size:17
Alignment explanation
Indices: 512042--512073 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
512032 TTGTTGTTTT
512042 TTTTTCTTCTTTCTCTG
1 TTTTTCTTCTTTCTCTG
512059 TTTTT-TTCTTTCTCT
1 TTTTTCTTCTTTCTCT
512074 CCGGTTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTCTTCTTTCTCTG
Found at i:512567 original size:3 final size:3
Alignment explanation
Indices: 512559--512647 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
512549 TTAATATATT
* * *
512559 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
512607 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
512648 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:527025 original size:2 final size:2
Alignment explanation
Indices: 527018--527099 Score: 112
Period size: 2 Copynumber: 41.5 Consensus size: 2
527008 ATAACTAAAT
527018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
527059 TA TA TA TA TA TA CA CA CA CA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
527100 TCTTCAATCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:528773 original size:40 final size:40
Alignment explanation
Indices: 528729--528806 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
528719 ACCAATATCT
528729 AAGGCATATGGAATCTTATTCATTCAATCTCTTTCATGCC
1 AAGGCATATGGAATCTTATTCATTCAATCTCTTTCATGCC
528769 AAGGCATATGGAATCTTATTCATTCAATCTCTTTCATG
1 AAGGCATATGGAATCTTATTCATTCAATCTCTTTCATG
528807 TGGAGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (40 bp):
AAGGCATATGGAATCTTATTCATTCAATCTCTTTCATGCC
Found at i:531893 original size:44 final size:44
Alignment explanation
Indices: 531844--531950 Score: 178
Period size: 44 Copynumber: 2.4 Consensus size: 44
531834 CTACTCTAAA
* *
531844 ATAAATGAAAATGCATAACGGTGCATTATTAGCATAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAGGTGCC
*
531888 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAGGTGCC
*
531932 ATAAATGAGAATGCATAAC
1 ATAAATGAAAATGCATAAC
531951 AGTACTAGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAGGTGCC
Found at i:531911 original size:25 final size:25
Alignment explanation
Indices: 531844--531911 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 25
531834 CTACTCTAAA
531844 ATAAATGAAAATGCATAACGGTG-C
1 ATAAATGAAAATGCATAACGGTGCC
** **
531868 AT---T-ATTA-GCATAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCC
531888 ATAAATGAAAATGCATAACGGTGC
1 ATAAATGAAAATGCATAACGGTGC
531912 ATTATTGGCA
Statistics
Matches: 30, Mismatches: 8, Indels: 11
0.61 0.16 0.22
Matches are distributed among these distances:
19 9 0.30
20 5 0.17
21 1 0.03
23 1 0.03
24 4 0.13
25 10 0.33
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (25 bp):
ATAAATGAAAATGCATAACGGTGCC
Found at i:531966 original size:39 final size:40
Alignment explanation
Indices: 531844--531989 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 40
531834 CTACTCTAAA
* * *
531844 ATAAATGAAAATGCATAACGGTGCATTATTAGCATAAATGTGCC
1 ATAAATGAAAATGCATAACAGT-C---ACTAGCATAAAGGTGCC
* * *
531888 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACAGT-CACTA---GCATAAAGGTGCC
* *
531932 ATAAATGAGAATGCATAACAGT-ACTAGCATAAAGGTGTC
1 ATAAATGAAAATGCATAACAGTCACTAGCATAAAGGTGCC
* *
531971 ATAAATAAAAATGTATAAC
1 ATAAATGAAAATGCATAAC
531990 GGTGCTATAA
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
39 27 0.30
41 4 0.04
42 3 0.03
44 55 0.62
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (40 bp):
ATAAATGAAAATGCATAACAGTCACTAGCATAAAGGTGCC
Found at i:531988 original size:25 final size:25
Alignment explanation
Indices: 531958--532019 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
531948 AACAGTACTA
*
531958 GCATAAAGGTG-TCATAAATAAAAAT
1 GCATAACGGTGCT-ATAAATAAAAAT
*
531983 GTATAACGGTGCTATAAATAAAAAT
1 GCATAACGGTGCTATAAATAAAAAT
532008 GCATAACGGTGC
1 GCATAACGGTGC
532020 ATTATTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.24
Consensus pattern (25 bp):
GCATAACGGTGCTATAAATAAAAAT
Found at i:532296 original size:173 final size:172
Alignment explanation
Indices: 531991--532363 Score: 509
Period size: 173 Copynumber: 2.1 Consensus size: 172
531981 ATGTATAACG
* * * * *
531991 GTGCTATAAATAAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATAAATGAAATGCATA
1 GTGCCATAAATGAAAATGCATAACGGTCCATTATT-G-AAAAAGGTGCCATAAATAAAATGCATA
**
532056 ACGGTGCATTATTGGCAGAAAGGTGCCATAAAATGAAATGCATAACGGTGCATTATTGGTAGAAA
64 ACGGTGCATTATTGGCAGAAAGGTGCCATAAAATGAAATGCATAACGGTGCATTATTGACAGAAA
*
532121 GGTACCATAAATAAAAATGAATAACAG-TGCATAATTGGGAGAAAA
129 GGTACCATAAATAAAAATGAATAA-AGTTGCATAATTGGCA-AAAA
*
532166 GTGCCATAAATGAGAATGCATAACGGTCCATTATT-AAAAAGGTGCCATAAATAAAAATGCATAA
1 GTGCCATAAATGAAAATGCATAACGGTCCATTATTGAAAAAGGTGCCATAAAT-AAAATGCATAA
* *
532230 CGGTGCATTATTGGCAGAAAGGTGCCA-CAAATGAAAATGTATAACGGTGCATTATTGACAGAAA
65 CGGTGCATTATTGGCAGAAAGGTGCCATAAAATG-AAATGCATAACGGTGCATTATTGACAGAAA
* * * * *
532294 GGTGCCATAAATAAAAATGCATAATGTTGCATTATTGGCATAAA
129 GGTACCATAAATAAAAATGAATAAAGTTGCATAATTGGCAAAAA
*
532338 GATGCCATAAATGAAAATACATAACG
1 G-TGCCATAAATGAAAATGCATAACG
532364 ATATATTATT
Statistics
Matches: 176, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
172 26 0.15
173 119 0.68
175 31 0.18
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (172 bp):
GTGCCATAAATGAAAATGCATAACGGTCCATTATTGAAAAAGGTGCCATAAATAAAATGCATAAC
GGTGCATTATTGGCAGAAAGGTGCCATAAAATGAAATGCATAACGGTGCATTATTGACAGAAAGG
TACCATAAATAAAAATGAATAAAGTTGCATAATTGGCAAAAA
Found at i:532388 original size:44 final size:44
Alignment explanation
Indices: 531990--532381 Score: 506
Period size: 44 Copynumber: 9.0 Consensus size: 44
531980 AATGTATAAC
* *
531990 GGTGCTATAAATAAAAATGCATAACGGTGCATTATTGGCAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
532034 GGTGCCATAAATG-AAATGCATAACGGTGCATTATTGGCAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
*
532077 GGTGCCATAAAATG-AAATGCATAACGGTGCATTATTGGTAGAAA
1 GGTGCCAT-AAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
* * * * * *
532121 GGTACCATAAATAAAAATGAATAACAGTGCATAATTGGGAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
* * * *
532165 AGTGCCATAAATGAGAATGCATAACGGTCCATTATT---AAAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
*
532206 GGTGCCATAAATAAAAATGCATAACGGTGCATTATTGGCAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
* * *
532250 GGTGCCACAAATGAAAATGTATAACGGTGCATTATTGACAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
* * * *
532294 GGTGCCATAAATAAAAATGCATAATGTTGCATTATTGGCATAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
* * * **
532338 GATGCCATAAATGAAAATACATAACGATATATTATTGGCAGAAA
1 GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
532382 TATGCCACTC
Statistics
Matches: 301, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 36 0.12
43 42 0.14
44 223 0.74
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (44 bp):
GGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
Found at i:533772 original size:74 final size:74
Alignment explanation
Indices: 533685--533838 Score: 290
Period size: 74 Copynumber: 2.1 Consensus size: 74
533675 TCGTTCACTC
* *
533685 ATTTTGCTTTGAAATATAGATTTAGAGGTTTTGTACCTCTCTTGATGTGCTTTTCCCTTATATAA
1 ATTTTGCATTGAAATATAGATTTAGAGGTTTTGTACCTCTCTTGATATGCTTTTCCCTTATATAA
533750 TTCCTTGAT
66 TTCCTTGAT
533759 ATTTTGCATTGAAATATAGATTTAGAGGTTTTGTACCTCTCTTGATATGCTTTTCCCTTATATAA
1 ATTTTGCATTGAAATATAGATTTAGAGGTTTTGTACCTCTCTTGATATGCTTTTCCCTTATATAA
533824 TTCCTTGAT
66 TTCCTTGAT
533833 ATTTTG
1 ATTTTG
533839 AATCATATCA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (74 bp):
ATTTTGCATTGAAATATAGATTTAGAGGTTTTGTACCTCTCTTGATATGCTTTTCCCTTATATAA
TTCCTTGAT
Found at i:537968 original size:179 final size:179
Alignment explanation
Indices: 537669--538022 Score: 692
Period size: 179 Copynumber: 2.0 Consensus size: 179
537659 CCAGGAAAAA
537669 TCTAGATTCGTACTAGAGCCACTTACAAGAGATAAACAAGCAAATGAGTTAACTTGCTCAAACCG
1 TCTAGATTCGTACTAGAGCCACTTACAAGAGATAAACAAGCAAATGAGTTAACTTGCTCAAACCG
537734 TAGGCTGCTTGGAATCACAAGGTAAACTTCCATCCCAAACTGAGGTAAACACAAGGGAGAATGTC
66 TAGGCTGCTTGGAATCACAAGGTAAACTTCCATCCCAAACTGAGGTAAACACAAGGGAGAATGTC
537799 AGCGTCATCACTATTCAGAGTGGTAAAGTAGTGG-GCCAGCTGTTAAAT
131 AGCGTCATCACTATTCAGAGTGGTAAAGTAGTGGTGCCAGCTGTTAAAT
537847 TCTAGATTCGTACTAGAGCCCACTTACAAGAGATAAACAAGCAAATGAGTTAACTTGCTCAAACC
1 TCTAGATTCGTACTAGAG-CCACTTACAAGAGATAAACAAGCAAATGAGTTAACTTGCTCAAACC
537912 GTAGGCTGCTTGGAATCACAAGGTAAACTTCCATCCCAAACTGAGGTAAACACAAGGGAGAATGT
65 GTAGGCTGCTTGGAATCACAAGGTAAACTTCCATCCCAAACTGAGGTAAACACAAGGGAGAATGT
537977 CAGCGTCATCACTATTCAGAGTGGTAAAGTAGTGGTGCCAGCTGTT
130 CAGCGTCATCACTATTCAGAGTGGTAAAGTAGTGGTGCCAGCTGTT
538023 CCATCAGATG
Statistics
Matches: 174, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
178 18 0.10
179 146 0.84
180 10 0.06
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (179 bp):
TCTAGATTCGTACTAGAGCCACTTACAAGAGATAAACAAGCAAATGAGTTAACTTGCTCAAACCG
TAGGCTGCTTGGAATCACAAGGTAAACTTCCATCCCAAACTGAGGTAAACACAAGGGAGAATGTC
AGCGTCATCACTATTCAGAGTGGTAAAGTAGTGGTGCCAGCTGTTAAAT
Found at i:539809 original size:78 final size:78
Alignment explanation
Indices: 539678--539831 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
539668 ATTGAGAAAG
*
539678 GTATTGAAGTCTTCATGGATGACTTCACTGTTTACGGTAATTCATTCAGTGAGTGTCTATTAAAC
1 GTATTGAAGTCTTCATGGATGACTTCACTGTTTACGGTAATTCATTCAATGAGTGTCTATTAAAC
539743 TTGACAAATGTGT
66 TTGACAAATGTGT
539756 GTATTGAAGTCTTCATGGATGACTTCACTGTTTACGGTAATTCATTCAATGAGTGTCTATTAAAC
1 GTATTGAAGTCTTCATGGATGACTTCACTGTTTACGGTAATTCATTCAATGAGTGTCTATTAAAC
539821 TTGACAAATGT
66 TTGACAAATGT
539832 TTTGCGTCGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (78 bp):
GTATTGAAGTCTTCATGGATGACTTCACTGTTTACGGTAATTCATTCAATGAGTGTCTATTAAAC
TTGACAAATGTGT
Found at i:545056 original size:19 final size:20
Alignment explanation
Indices: 545032--545080 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
545022 AAAGACATGC
545032 ACAAAAAAATG-GAAAACA-A
1 ACAAAAAAATGTGAAAA-ATA
545051 ACAAAAAAAATGTGAAAAATA
1 AC-AAAAAAATGTGAAAAATA
545072 A-AAAAAAAT
1 ACAAAAAAAT
545081 CAATACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (20 bp):
ACAAAAAAATGTGAAAAATA
Found at i:545059 original size:20 final size:19
Alignment explanation
Indices: 545034--545080 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
545024 AGACATGCAC
545034 AAAAAAATG-GAAAACAAACA
1 AAAAAAATGTGAAAA-AAA-A
*
545054 AAAAAAATGTGAAAAATAA
1 AAAAAAATGTGAAAAAAAA
545073 AAAAAAAT
1 AAAAAAAT
545081 CAATACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 11 0.44
21 5 0.20
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAAATGTGAAAAAAAA
Found at i:545077 original size:21 final size:20
Alignment explanation
Indices: 545034--545079 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
545024 AGACATGCAC
*
545034 AAAAAAATGGAAAACAAACA
1 AAAAAAATGGAAAACAAAAA
545054 AAAAAAATGTGAAAA-ATAAAA
1 AAAAAAATG-GAAAACA-AAAA
545075 AAAAA
1 AAAAA
545080 TCAATACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (20 bp):
AAAAAAATGGAAAACAAAAA
Found at i:547325 original size:15 final size:14
Alignment explanation
Indices: 547297--547354 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 14
547287 ACAAGTTTTA
547297 ATTATTAT-TA-TT
1 ATTATTATCTATTT
547309 ATTATTATCATATTT
1 ATTATTATC-TATTT
547324 ATTATTAT-TA-TT
1 ATTATTATCTATTT
547336 ATTATTA-C-ATTT
1 ATTATTATCTATTT
547348 ATTATTA
1 ATTATTA
547355 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.02
12 26 0.63
13 2 0.05
14 2 0.05
15 10 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATCTATTT
Found at i:547330 original size:24 final size:24
Alignment explanation
Indices: 547298--547354 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
547288 CAAGTTTTAA
*
547298 TTATTATTATTATTATTATCATAT
1 TTATTATTATTATTATTATCACAT
*
547322 TTATTATTATTATTATTATTACAT
1 TTATTATTATTATTATTATCACAT
547346 TTATTATTA
1 TTATTATTA
547355 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATTATTATTATTATCACAT
Found at i:547354 original size:3 final size:3
Alignment explanation
Indices: 547297--547342 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
547287 ACAAGTTTTA
*
547297 ATT ATT ATT ATT ATT ATT ATC A-T ATTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
547342 A
1 A
547343 CATTTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 36 0.92
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:547851 original size:23 final size:22
Alignment explanation
Indices: 547824--547871 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
547814 ACACTGACAG
547824 AAAATTACACCAAATCAGTCAAA
1 AAAATTA-ACCAAATCAGTCAAA
** *
547847 AAAATTAAGTAAATCAGTCTAA
1 AAAATTAACCAAATCAGTCAAA
547869 AAA
1 AAA
547872 TCCCATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAATTAACCAAATCAGTCAAA
Found at i:551071 original size:49 final size:50
Alignment explanation
Indices: 551015--551115 Score: 195
Period size: 49 Copynumber: 2.0 Consensus size: 50
551005 TACAGAGCGC
551015 TTGAAGGGAACATTTTCTAGGATGAATATATGA-GTTAAGAACCTACCCA
1 TTGAAGGGAACATTTTCTAGGATGAATATATGAGGTTAAGAACCTACCCA
551064 TTGAAGGGAACATTTTCTAGGATGAATATATGAGGTTAAGAACCTACCCA
1 TTGAAGGGAACATTTTCTAGGATGAATATATGAGGTTAAGAACCTACCCA
551114 TT
1 TT
551116 TCAGACTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 33 0.65
50 18 0.35
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (50 bp):
TTGAAGGGAACATTTTCTAGGATGAATATATGAGGTTAAGAACCTACCCA
Found at i:551304 original size:19 final size:20
Alignment explanation
Indices: 551280--551318 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
551270 AAACATTTTC
*
551280 ACAT-GGATCATTCATGAAA
1 ACATGGGATAATTCATGAAA
551299 ACATGGGGATAATTCATGAA
1 ACAT-GGGATAATTCATGAA
551319 GAATTCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
ACATGGGATAATTCATGAAA
Found at i:554411 original size:90 final size:90
Alignment explanation
Indices: 554294--554473 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
554284 TTCTCTTTTC
554294 AAACCATCTGGCAGGGATGATGATGGTATCATAAGGGAAGCTCTATTGTATTTCTACACAAGTTT
1 AAACCATCTGGCAGGGATGATGATGGTATCATAAGGGAAGCTCTATTGTATTTCTACACAAGTTT
554359 AGATAAGGGAAACCAATTTATCAGG
66 AGATAAGGGAAACCAATTTATCAGG
554384 AAACCATCTGGCAGGGATGATGATGGTATCATAAGGGAAGCTCTATTGTATTTCTACACAAGTTT
1 AAACCATCTGGCAGGGATGATGATGGTATCATAAGGGAAGCTCTATTGTATTTCTACACAAGTTT
554449 AGATAAGGGAAACCAATTTATCAGG
66 AGATAAGGGAAACCAATTTATCAGG
554474 GGCAAAATTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (90 bp):
AAACCATCTGGCAGGGATGATGATGGTATCATAAGGGAAGCTCTATTGTATTTCTACACAAGTTT
AGATAAGGGAAACCAATTTATCAGG
Found at i:555523 original size:100 final size:102
Alignment explanation
Indices: 555159--555615 Score: 392
Period size: 99 Copynumber: 4.5 Consensus size: 102
555149 CATGTCGCCT
* ** ** * * *
555159 TTGAGATTGTTTCTCTCGAAACAAAATTTCATCTCGCTTGAGAC-AGTTTTTCCCTCAAAATATA
1 TTGAGATTGTTTTTCTTAAAAC-AAATTTTGTCTCACTTGAGACAAG--TTTCCCTCAAAACACA
* * * **
555223 AATTTTGAAATTTATTTCACTTGAAACAAAATTAATCTCAC
63 AATTTT-AAAATTGTTTCACTTGAAACAAAATTGATAACAC
* * * * * * *
555264 TTGACATTGTTTTTCCTATAAACGAATTTTGTCTCGCTTGAGA-TAGTTTTCCCTCAAAATACAT
1 TTGAGATTGTTTTTCTTA-AAACAAATTTTGTCTCACTTGAGACAAG-TTTCCCTCAAAACACAA
* **
555328 ATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
64 ATTTTAAAATTGTTTCACTTGAAACAAAATTGATAACAC
* * * * ** * *
555367 TTTAGATTG---TTCTCAAAACAAATTTTGTCTCATTTCAGACATTTTTTCTTCAAAACACAAAT
1 TTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCACTTGAGACAAGTTTCCCTCAAAACACAAAT
* *
555429 TCTAAAATTGTTTCACTTGAAACTAAATTGATAACA-
66 TTTAAAATTGTTTCACTTGAAACAAAATTGATAACAC
* *
555465 TTGAGATTGTTTTTCTTAAAAC-AATTTCGTCTCATTTGAGACAAGTTTCCCTCAAAACACAAAT
1 TTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCACTTGAGACAAGTTTCCCTCAAAACACAAAT
** * **
555529 TTTGGAATTTTTTCACTTGAAACAAAATACATAA-ACC
66 TTTAAAATTGTTTCACTTGAAACAAAATTGATAACA-C
* * *
555566 ATTGAGATTGTTTATCTTGAAACAAATTTTGTCTCGCTTGAGAC-AGTTTC
1 -TTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCACTTGAGACAAGTTTC
555616 TCTTGAAACA
Statistics
Matches: 288, Mismatches: 54, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
98 8 0.03
99 67 0.23
100 67 0.23
101 9 0.03
102 26 0.09
103 54 0.19
104 21 0.07
105 32 0.11
106 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (102 bp):
TTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCACTTGAGACAAGTTTCCCTCAAAACACAAAT
TTTAAAATTGTTTCACTTGAAACAAAATTGATAACAC
Found at i:555627 original size:66 final size:66
Alignment explanation
Indices: 555557--555757 Score: 323
Period size: 66 Copynumber: 3.0 Consensus size: 66
555547 GAAACAAAAT
* * *
555557 ACATAAACCATTGAGATTGTTTATCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGA
1 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTCAGACAGTTTCTCTTGA
555622 A
66 A
* *
555623 ACATAAACCTTTGAGATTGTTTCTCTTGAAAAAAAAATTTGTCTCGCTTCAGACAGTTT-TCTTG
1 ACATAAACCTTTGAGATTGTTTCTCTTG-AAACAAATTTTGTCTCGCTTCAGACAGTTTCTCTTG
555687 AA
65 AA
* *
555689 ACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTCAGACAGTTTCTCTTGA
1 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTCAGACAGTTTCTCTTGA
555754 A
66 A
555755 ACA
1 ACA
555758 AATATCCCTA
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
65 27 0.22
66 70 0.56
67 27 0.22
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (66 bp):
ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTCAGACAGTTTCTCTTGA
A
Found at i:555645 original size:30 final size:30
Alignment explanation
Indices: 555611--555721 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 30
555601 GCTTGAGACA
555611 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
* * * * **
555641 GTTTCTCTTGAAAAAAAAATTTGTCTCGCTTCAGACA
1 GTTTCTCTTGAAACATAAA-----C-C-TTTGAGATT
555678 GTTT-TCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
*
555707 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
555722 AATTTTGTCT
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
29 9 0.15
30 27 0.45
31 1 0.02
35 1 0.02
36 13 0.22
37 9 0.15
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACCTTTGAGATT
Found at i:556114 original size:137 final size:138
Alignment explanation
Indices: 555756--556124 Score: 458
Period size: 138 Copynumber: 2.7 Consensus size: 138
555746 TCTCTTGAAA
* * *
555756 CAAATATCCCTAAAGATGGCTAGACATCCTCATCACG-AGGAACAATGTCATCCACTGACTAGAT
1 CAAATATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGAT
* * *
555820 CTCCTCAATGCGCAAGAGCAGCGTCATCCTCAGGCAATCCGACTTCCTCATCACGTACGAACCAT
66 CTCCTCAACGCGTAAGAGCAGCGTCATCCTCAGGCAATCAGACTTCCTCATCACGTACGAACCAT
555885 GTTGTCTC
131 GTTGTCTC
* * * *
555893 CAAAGTATTCCTAAAGATGACTAGACGTCCTCATCACGTA-GAACAATATCGTCCACCAACTAGA
1 CAAA-TATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGA
* * * * * * * **
555957 TCTCCTCAACGCATAAGAGCAGTGTCATTCTCATGTAATCAGACTTCTTCATCACGTAGGAA-TG
65 TCTCCTCAACGCGTAAGAGCAGCGTCATCCTCAGGCAATCAGACTTCCTCATCACGTACGAACCA
556021 TGTTGTCTC
130 TGTTGTCTC
* * *
556030 CAAATTATCCCTAAAGATGGCTAGACGTCCTTAGCACGTAGGAACAATGTCGTCCACCGACCA-A
1 CAAA-TATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGA
* * * *
556094 TCTCCTCAACACGTAGGAGCAACATCATCCT
65 TCTCCTCAACGCGTAAGAGCAGCGTCATCCT
556125 AAGATAACTA
Statistics
Matches: 195, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
137 73 0.37
138 121 0.62
139 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (138 bp):
CAAATATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGAT
CTCCTCAACGCGTAAGAGCAGCGTCATCCTCAGGCAATCAGACTTCCTCATCACGTACGAACCAT
GTTGTCTC
Found at i:556146 original size:137 final size:137
Alignment explanation
Indices: 555756--556167 Score: 447
Period size: 138 Copynumber: 3.0 Consensus size: 137
555746 TCTCTTGAAA
* * *
555756 CAAATATCCCTAAAGATGGCTAGACATCCTCATCACG-AGGAACAATGTCATCCACTGACTAGAT
1 CAAATATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGAT
* * * * *
555820 CTCCTCAATGCGCAAGAGCAGCGTCATCCTCAGGCAATCCGACTTCCTCATCACGTACGAACCAT
66 CTCCTCAACGCGTAAGAGCAGCGTCATCCT-AAGTAATCAGACTTCCTCATCACGTACGAACCAT
555885 GTTGTCTC
130 GTTGTCTC
* * * *
555893 CAAAGTATTCCTAAAGATGACTAGACGTCCTCATCACGTA-GAACAATATCGTCCACCAACTAGA
1 CAAA-TATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGA
* * * * * * **
555957 TCTCCTCAACGCATAAGAGCAGTGTCATTCTCATGTAATCAGACTTCTTCATCACGTAGGAA-TG
65 TCTCCTCAACGCGTAAGAGCAGCGTCATCCT-AAGTAATCAGACTTCCTCATCACGTACGAACCA
556021 TGTTGTCTC
129 TGTTGTCTC
* * *
556030 CAAATTATCCCTAAAGATGGCTAGACGTCCTTAGCACGTAGGAACAATGTCGTCCACCGACCA-A
1 CAAA-TATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGA
* * * * * ** *
556094 TCTCCTCAACACGTAGGAGCAACATCATCCTAAGATAA-CTAGGCTTCCTCATCATATAGGAACC
65 TCTCCTCAACGCGTAAGAGCAGCGTCATCCTAAG-TAATC-AGACTTCCTCATCACGTACGAACC
*
556158 ATGTTATCTC
128 ATGTTGTCTC
556168 TAAAATCATC
Statistics
Matches: 227, Mismatches: 42, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
136 3 0.01
137 94 0.41
138 129 0.57
139 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (137 bp):
CAAATATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCACCGACTAGAT
CTCCTCAACGCGTAAGAGCAGCGTCATCCTAAGTAATCAGACTTCCTCATCACGTACGAACCATG
TTGTCTC
Found at i:557898 original size:16 final size:16
Alignment explanation
Indices: 557863--557892 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
557853 GTTCTTCATT
557863 ATTT-ATCCTTTTATG
1 ATTTAATCCTTTTATG
557878 ATTTAATCCTTTTAT
1 ATTTAATCCTTTTAT
557893 CGTTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTTAATCCTTTTATG
Done.