Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008802.1 Hibiscus syriacus cultivar Beakdansim tig00111952_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: 1147353
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:285588 original size:32 final size:32
Alignment explanation
Indices: 285529--285616 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
285519 AGATACTAGC
*
285529 AGTGTTGCATTCAGATAATGTATAATAAAATT
1 AGTGTTGCATTCAGATAATGTACAATAAAATT
* * *
285561 AGTGCTGCATTCATATACTGTACAATAAAATT
1 AGTGTTGCATTCAGATAATGTACAATAAAATT
*
285593 AGTGTTGCATTCA-ATAATGCACAA
1 AGTGTTGCATTCAGATAATGTACAA
285617 GAGTGTCAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 9 0.18
32 40 0.82
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (32 bp):
AGTGTTGCATTCAGATAATGTACAATAAAATT
Found at i:288179 original size:15 final size:15
Alignment explanation
Indices: 288147--288199 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
288137 TAAGATCGAA
* *
288147 ATTCAGATATATGAT
1 ATTCAAATATATGTT
*
288162 ATTCAAATAAATGTT
1 ATTCAAATATATGTT
** *
288177 ATTCGGATATGTGTT
1 ATTCAAATATATGTT
288192 ATTCAAAT
1 ATTCAAAT
288200 CAGATATCAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (15 bp):
ATTCAAATATATGTT
Found at i:291217 original size:55 final size:55
Alignment explanation
Indices: 291064--291444 Score: 570
Period size: 55 Copynumber: 6.9 Consensus size: 55
291054 TAATTTGTTT
*
291064 ATGAATTTCC--ATGGGCATTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
291117 ATGAATTTTTCGTATGGACACTTTATGTGCAAACTTAAGAAATTCATACTAAGTGG
1 ATGAA-TTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
291173 ATGAATTTCCATATGGGCACTTTATGTGTAAACTTAAGAGATTCATACTAGGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
291228 ATGAATTTTCGTATGGGCACTTTATGTGTAACCTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
291283 ATGAATTTCCGTATGGGCACTTTATGTGTAAAGTTAAGAAATTCATTCTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
291338 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACCAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
291393 ATGCATTTCCGTATGGGCACTTTGTATGCAAAAC-TAAGAAATTCATAATAAG
1 ATGAATTTCCGTATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTAAG
291445 GGTTTGTTTG
Statistics
Matches: 296, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.02
54 4 0.01
55 238 0.80
56 49 0.17
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:291496 original size:15 final size:14
Alignment explanation
Indices: 291472--291530 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
291462 GTAATTGGTT
*
291472 TTCTGGAAATTGAA
1 TTCTGAAAATTGAA
291486 TTCTAGAAAA-TGAA
1 TTCT-GAAAATTGAA
* *
291500 TTACTGGAATTTGAA
1 TT-CTGAAAATTGAA
291515 TTCTGGAAAATT-AA
1 TTCT-GAAAATTGAA
291529 TT
1 TT
291531 ACATTTCTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 19 0.53
15 17 0.47
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (14 bp):
TTCTGAAAATTGAA
Found at i:291516 original size:29 final size:29
Alignment explanation
Indices: 291474--291532 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
291464 AATTGGTTTT
291474 CTGGAAATTGAATTCTAGAAAATGAATTA
1 CTGGAAATTGAATTCTAGAAAATGAATTA
* * *
291503 CTGGAATTTGAATTCTGGAAAATTAATTA
1 CTGGAAATTGAATTCTAGAAAATGAATTA
291532 C
1 C
291533 ATTTCTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (29 bp):
CTGGAAATTGAATTCTAGAAAATGAATTA
Found at i:291530 original size:14 final size:14
Alignment explanation
Indices: 291472--291523 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
291462 GTAATTGGTT
291472 TTCTGGAAATTGAA
1 TTCTGGAAATTGAA
* *
291486 TTCTAGAAAATGAA
1 TTCTGGAAATTGAA
*
291500 TTACTGGAATTTGAA
1 TT-CTGGAAATTGAA
291515 TTCTGGAAA
1 TTCTGGAAA
291524 ATTAATTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:291920 original size:23 final size:22
Alignment explanation
Indices: 291872--291939 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
291862 GTGTTATATT
**
291872 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
291894 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
* *
291917 ATATTATTATATTATTATATTAA
1 ATATT-TTAAAATATTA-ATTAA
291940 TATTAAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.29
23 16 0.46
24 9 0.26
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:291977 original size:28 final size:30
Alignment explanation
Indices: 291928--292032 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 30
291918 TATTATTATA
*
291928 TTATTATATTAATATTAAATATATAAATAA-
1 TTATTATA-TATTATTAAATATATAAATAAT
291958 TT-TTAT-TCATTATTAAATATATAAATAAT
1 TTATTATAT-ATTATTAAATATATAAATAAT
*
291987 TTATTATATATTATTAAA-ATAAAAATATAAT
1 TTATTATATATTATTAAATAT-ATAA-ATAAT
*
292018 ATATTATATTATTAT
1 TTATTATA-TATTAT
292033 AATATAATTG
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.02
28 19 0.29
29 8 0.12
30 18 0.28
31 13 0.20
32 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
TTATTATATATTATTAAATATATAAATAAT
Found at i:292040 original size:23 final size:23
Alignment explanation
Indices: 292010--292060 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
292000 TTAAAATAAA
292010 AATATAATAT-ATTATATTATTAT
1 AATATAAT-TGATTATATTATTAT
* *
292033 AATATAATTGATTCTTTTATTAT
1 AATATAATTGATTATATTATTAT
292056 AATAT
1 AATAT
292061 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATATAATTGATTATATTATTAT
Found at i:292126 original size:30 final size:31
Alignment explanation
Indices: 292050--292126 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
292040 TTGATTCTTT
*
292050 TATTATAAT-ATTAA-AAATATAATTTTATA
1 TATTTTAATAATTAATAAATATAATTTTATA
* *
292079 T-TATTAGAAATATTAATAAATAT-ATTTTATA
1 TATTTTA-ATA-ATTAATAAATATAATTTTATA
292110 TATTTTAATAATTAATA
1 TATTTTAATAATTAATA
292127 TTTTGATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
28 3 0.08
29 2 0.05
30 7 0.18
31 16 0.42
32 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
TATTTTAATAATTAATAAATATAATTTTATA
Found at i:292356 original size:42 final size:42
Alignment explanation
Indices: 292300--292391 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
292290 TTCCTCCAAC
*
292300 CAAACATTGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACATGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
292342 CAAACATGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACATGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
292384 CAAACATG
1 CAAACATG
292392 AGATTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (42 bp):
CAAACATGGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
Found at i:292409 original size:51 final size:51
Alignment explanation
Indices: 292352--292458 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
292342 CAAACATGGG
* *
292352 AAAACATTTTCCGGAAAACGAATTACGTGAAACAAACATGAGATTTCGGGA
1 AAAACATTTTCCAGAAAACGAATTACGTGAAACAAACACGAGATTTCGGGA
* * * * *
292403 AAAACATTTTTCAGAAAATGAATTACGTGAAACAACCACGGGATTTCGGGG
1 AAAACATTTTCCAGAAAACGAATTACGTGAAACAAACACGAGATTTCGGGA
292454 AAAAC
1 AAAAC
292459 CAATTCCGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (51 bp):
AAAACATTTTCCAGAAAACGAATTACGTGAAACAAACACGAGATTTCGGGA
Found at i:299847 original size:22 final size:22
Alignment explanation
Indices: 299822--299869 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
299812 ACTTGGGCGT
*
299822 AAGCCCTCAACAAACCACTTGC
1 AAGCCCTCAACAAACCACTCGC
299844 AAGCCCTCAACAAACCACTCGC
1 AAGCCCTCAACAAACCACTCGC
299866 AAGC
1 AAGC
299870 ATCTTTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.42, G:0.10, T:0.10
Consensus pattern (22 bp):
AAGCCCTCAACAAACCACTCGC
Found at i:306685 original size:16 final size:16
Alignment explanation
Indices: 306664--306695 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
306654 GGAGGGCACC
*
306664 AAGGACGGTCGAGTGG
1 AAGGACGCTCGAGTGG
306680 AAGGACGCTCGAGTGG
1 AAGGACGCTCGAGTGG
306696 GAGAACGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.47, T:0.12
Consensus pattern (16 bp):
AAGGACGCTCGAGTGG
Found at i:309888 original size:13 final size:13
Alignment explanation
Indices: 309858--309890 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
309848 AAAAGAAAAG
309858 GAAAG-AAAGGTT
1 GAAAGAAAAGGTT
309870 -AAAGAAAAGGTT
1 GAAAGAAAAGGTT
309882 GAAAGAAAA
1 GAAAGAAAA
309891 ACAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 7 0.37
13 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (13 bp):
GAAAGAAAAGGTT
Found at i:314528 original size:12 final size:12
Alignment explanation
Indices: 314511--314535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
314501 ATCACACACT
314511 TCAAGGAATGCA
1 TCAAGGAATGCA
314523 TCAAGGAATGCA
1 TCAAGGAATGCA
314535 T
1 T
314536 GGACAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (12 bp):
TCAAGGAATGCA
Found at i:321218 original size:40 final size:40
Alignment explanation
Indices: 321162--321503 Score: 320
Period size: 40 Copynumber: 8.6 Consensus size: 40
321152 TAGGAAATAT
* * * * *
321162 ATTTTTAGGTTACAACCTAATTTATCTTATATAAACTTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * * *
321202 ATTTTTAGGTTGCAACCTCATTTATC-TTTATAAACCTAA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* *
321241 ATTTTTAGGTTGCAACCTGACTTATCATATAGAAACCTAA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * * *
321281 ATTTTTAGGTTACAACCTAATTTATCTTTTAGAAACCT-A
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
**
321320 ATTTTTTATATTGCAACCTGATTTATCATATAGAAACCTGA
1 A-TTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
** * * * *
321361 ATTTTTATATTGCAACTTAATTTATCATATAAAAACCTAA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* *
321401 ATTTTTAGGCTGCAACCTGATTTATCATATAGAAACTTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * *
321441 TTTCTTTTTA-GTTGCAACCTGATTTTTGCATATA-TAA-CT-A
1 ---ATTTTTAGGTTGCAACCTGATTTAT-CATATAGAAACCTGA
*
321481 GA-TTTTAGGTTGCAACCTTATTT
1 -ATTTTTAGGTTGCAACCTGATTT
321504 TTTATGAAAA
Statistics
Matches: 254, Mismatches: 40, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
37 5 0.02
38 14 0.06
39 36 0.14
40 167 0.66
41 3 0.01
42 17 0.07
43 12 0.05
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (40 bp):
ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
Found at i:321257 original size:20 final size:20
Alignment explanation
Indices: 321234--321300 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
321224 TATCTTTATA
321234 AACCTAAATTTTTAGGTTGC
1 AACCTAAATTTTTAGGTTGC
* * * * ** * *
321254 AACCTGACTTATCATATAGA
1 AACCTAAATTTTTAGGTTGC
*
321274 AACCTAAATTTTTAGGTTAC
1 AACCTAAATTTTTAGGTTGC
321294 AACCTAA
1 AACCTAA
321301 TTTATCTTTT
Statistics
Matches: 30, Mismatches: 17, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (20 bp):
AACCTAAATTTTTAGGTTGC
Found at i:321351 original size:80 final size:79
Alignment explanation
Indices: 321162--321436 Score: 361
Period size: 80 Copynumber: 3.5 Consensus size: 79
321152 TAGGAAATAT
* * * * * *
321162 ATTTTTAGGTTACAACCTAATTTATCTTATATAAACTTGAATTTTTAGGTTGCAACCTCATTTAT
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTTTAGGTTGCAACCTAATTTAT
*
321227 CTTTATAAACCTAA
66 CTTTAAAAACCTAA
* * *
321241 ATTTTTAGGTTGCAACCTGACTTATCATATAGAAACCTAAATTTTTAGGTTACAACCTAATTTAT
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTTTAGGTTGCAACCTAATTTAT
*
321306 CTTTTAGAAACCTAA
66 C-TTTAAAAACCTAA
* ** ** *
321321 TTTTTTATATTGCAACCTGATTTATCATATAGAAACCTGAATTTTTATATTGCAACTTAATTTAT
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTTTAGGTTGCAACCTAATTTAT
*
321386 CATATAAAAACCTAA
66 C-TTTAAAAACCTAA
*
321401 ATTTTTAGGCTGCAACCTGATTTATCATATAGAAAC
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAAC
321437 TTGATTTCTT
Statistics
Matches: 169, Mismatches: 26, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 57 0.34
80 112 0.66
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (79 bp):
ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTTTAGGTTGCAACCTAATTTAT
CTTTAAAAACCTAA
Found at i:321403 original size:21 final size:21
Alignment explanation
Indices: 321262--321404 Score: 77
Period size: 20 Copynumber: 7.1 Consensus size: 21
321252 GCAACCTGAC
321262 TTATCATATAGAAACCTAAAT
1 TTATCATATAGAAACCTAAAT
* *
321283 TT-TTAGGT-TA-CAACCT-AAT
1 TTATCA--TATAGAAACCTAAAT
* *
321302 TTATCTTTTAGAAACCT-AAT
1 TTATCATATAGAAACCTAAAT
* * * * *
321322 TTTTTATATTGCAACCT-GAT
1 TTATCATATAGAAACCTAAAT
*
321342 TTATCATATAGAAACCTGAAT
1 TTATCATATAGAAACCTAAAT
* * * *
321363 TT-TTATATTGCAA-CTTAAT
1 TTATCATATAGAAACCTAAAT
*
321382 TTATCATATAAAAACCTAAAT
1 TTATCATATAGAAACCTAAAT
321403 TT
1 TT
321405 TTAGGCTGCA
Statistics
Matches: 88, Mismatches: 26, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
18 1 0.01
19 14 0.16
20 57 0.65
21 15 0.17
22 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (21 bp):
TTATCATATAGAAACCTAAAT
Found at i:321417 original size:120 final size:120
Alignment explanation
Indices: 321162--321498 Score: 378
Period size: 120 Copynumber: 2.8 Consensus size: 120
321152 TAGGAAATAT
* ** *
321162 ATTTTTAGGTTACAACCTAATTTATCTTATATAAACTTGAA-TTTTTAGGTTGCAACCTCATTTA
1 ATTTTTAGGTTACAACCTAATTTATCTTATAGAAACTT-AATTTTTTATATTGCAACCTGATTTA
* * * * *
321226 TC-TTTATAAACCTAAATTTTTAGGTTGCAACCTGACTTATCATATAGAAACCTAA
65 TCATATAGAAACCTAAATTTTTAGATTGCAACCTAACTTATCATATAAAAACCTAA
* *
321281 ATTTTTAGGTTACAACCTAATTTATCTTTTAGAAACCTAATTTTTTATATTGCAACCTGATTTAT
1 ATTTTTAGGTTACAACCTAATTTATCTTATAGAAACTTAATTTTTTATATTGCAACCTGATTTAT
* * * *
321346 CATATAGAAACCTGAATTTTTATATTGCAACTTAATTTATCATATAAAAACCTAA
66 CATATAGAAACCTAAATTTTTAGATTGCAACCTAACTTATCATATAAAAACCTAA
* * * * * *
321401 ATTTTTAGGCTGCAACCTGATTTATCATATAGAAACTTGATTTCTTTTTAGTTGCAACCTGATTT
1 ATTTTTAGGTTACAACCTAATTTATCTTATAGAAACTTAATTT-TTTATA-TTGCAACCTGATTT
* * * *
321466 TTGCATATA-TAA-CTAGA-TTTTAGGTTGCAACCT
64 AT-CATATAGAAACCTAAATTTTTAGATTGCAACCT
321499 TATTTTTTAT
Statistics
Matches: 183, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
118 2 0.01
119 57 0.31
120 93 0.51
121 8 0.04
122 17 0.09
123 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (120 bp):
ATTTTTAGGTTACAACCTAATTTATCTTATAGAAACTTAATTTTTTATATTGCAACCTGATTTAT
CATATAGAAACCTAAATTTTTAGATTGCAACCTAACTTATCATATAAAAACCTAA
Found at i:321579 original size:39 final size:36
Alignment explanation
Indices: 321497--321582 Score: 93
Period size: 39 Copynumber: 2.3 Consensus size: 36
321487 AGGTTGCAAC
*
321497 CTTATTTTTTATGAAAACCAAATTTTAGGTTAAAAA
1 CTTATTTTTTATGAAAACCAAATTCTAGGTTAAAAA
* *
321533 CCTTATTTTTTGCATGAAAACCAAAGTTCTAGTTTAATAA
1 -CTTATTTTTT--ATGAAAACCAAA-TTCTAGGTTAAAAA
321573 -TATATTTTTT
1 CT-TATTTTTT
321583 TGATAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 10 0.24
38 1 0.02
39 20 0.48
40 11 0.26
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (36 bp):
CTTATTTTTTATGAAAACCAAATTCTAGGTTAAAAA
Found at i:321891 original size:40 final size:40
Alignment explanation
Indices: 321828--322130 Score: 391
Period size: 40 Copynumber: 7.6 Consensus size: 40
321818 AAGGAAATAG
*
321828 ATTTTTAGGTTGCAACCTGATTTATCTTATAGAAACCTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * *
321868 ATGTTTAGGTTGCAACCTCATTTATCATATAGAAACCTAA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
*
321908 ATTTTTAGGTTCCAACCTGATTTATCATATAGAAACCTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * **
321948 ATTTTTATGTTGCAACCTGATATATCATATCTAAACCTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
*
321988 ATTTTTAGGTTGCAACTTGATTTATCATATAGAAACCTGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
*
322028 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCCGA
1 ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * *
322068 TTTCATTTTA-GTTGCAACCTAATTTTTGCATATAG-AA-CT-A
1 -AT--TTTTAGGTTGCAACCTGATTTAT-CATATAGAAACCTGA
*
322108 GA-TTTTAGGTTGCAACGTGATTT
1 -ATTTTTAGGTTGCAACCTGATTT
322131 TTTTAGATTG
Statistics
Matches: 230, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
37 5 0.02
38 13 0.06
40 181 0.79
41 2 0.01
42 17 0.07
43 12 0.05
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (40 bp):
ATTTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
Found at i:321944 original size:20 final size:20
Alignment explanation
Indices: 321921--322070 Score: 81
Period size: 20 Copynumber: 7.5 Consensus size: 20
321911 TTTAGGTTCC
321921 AACCTGATTTATCATATAGA
1 AACCTGATTTATCATATAGA
* * * *
321941 AACCTGAATTT-TTATGTTGC
1 AACCTG-ATTTATCATATAGA
* **
321961 AACCTGATATATCATATCTA
1 AACCTGATTTATCATATAGA
* ** * *
321981 AACCTGAATTT-TTAGGTTGC
1 AACCTG-ATTTATCATATAGA
*
322001 AACTTGATTTATCATATAGA
1 AACCTGATTTATCATATAGA
* ** * *
322021 AACCTGAATTT-TTAGGTTGC
1 AACCTG-ATTTATCATATAGA
322041 AACCTGATTTATCATATAGA
1 AACCTGATTTATCATATAGA
*
322061 AACCCGATTT
1 AACCTGATTT
322071 CATTTTAGTT
Statistics
Matches: 89, Mismatches: 35, Indels: 12
0.65 0.26 0.09
Matches are distributed among these distances:
19 11 0.12
20 67 0.75
21 11 0.12
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
AACCTGATTTATCATATAGA
Found at i:322477 original size:40 final size:40
Alignment explanation
Indices: 322426--322575 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 40
322416 TTCAATTTAG
* * *
322426 GAAACA-G-ATTTTTGGGTAGCAACCTAATTTATCTTATA
1 GAAACATGAATTTTTAGGTTGCAACCTGATTTATCTTATA
*
322464 GAAATC-TGAATTTTTAGGTTGCAACATGATTTATCTTATA
1 GAAA-CATGAATTTTTAGGTTGCAACCTGATTTATCTTATA
* * * *
322504 GAAACATGAATGTTTAGGTTGTAACCTGATTTGTCATATA
1 GAAACATGAATTTTTAGGTTGCAACCTGATTTATCTTATA
* ** * *
322544 GAAACCTGGTTTTTTATGTTGTAACCTGATTT
1 GAAACATGAATTTTTAGGTTGCAACCTGATTT
322576 TTAGTTGCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
38 4 0.04
39 3 0.03
40 87 0.93
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (40 bp):
GAAACATGAATTTTTAGGTTGCAACCTGATTTATCTTATA
Found at i:322582 original size:18 final size:19
Alignment explanation
Indices: 322554--322593 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
322544 GAAACCTGGT
* *
322554 TTTTTATGTTGTAACCTGA
1 TTTTTATGTTGCAACCTAA
322573 TTTTTA-GTTGCAACCTAA
1 TTTTTATGTTGCAACCTAA
322591 TTT
1 TTT
322594 ATCATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (19 bp):
TTTTTATGTTGCAACCTAA
Found at i:322631 original size:41 final size:42
Alignment explanation
Indices: 322573--322676 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 42
322563 TGTAACCTGA
322573 TTTTTAGTTGCAACCTAATTTATCATATAGAAACTTGATTT-
1 TTTTTAGTTGCAACCTAATTTATCATATAGAAACTTGATTTC
* *
322614 TTTTTAGTTGCATCCTAATTTATCATATAGAAACTTGGTTTC
1 TTTTTAGTTGCAACCTAATTTATCATATAGAAACTTGATTTC
* *
322656 TTTCTAGTTGCAACCTGATTT
1 TTTTTAGTTGCAACCTAATTT
322677 TTGTATATAG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 39 0.68
42 18 0.32
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (42 bp):
TTTTTAGTTGCAACCTAATTTATCATATAGAAACTTGATTTC
Found at i:322653 original size:99 final size:101
Alignment explanation
Indices: 322473--322678 Score: 249
Period size: 99 Copynumber: 2.1 Consensus size: 101
322463 AGAAATCTGA
* * * * *
322473 ATTTTTAGGTTGCAACATGATTTATCTTATAGAAACATGAATGTTTAGGTTGTAACCTGATTTGT
1 ATTTTTAGGTTGCAACATAATTTATCATATAGAAACATGAATGTTTAGGTTGCAACCTAATTTAT
*
322538 CATATAGAAACCTGGTTT-TTTAT-GTTGTAACCTG
66 CATATAGAAACCTGGTTTCTTTATAGTTGCAACCTG
* * * * *
322572 ATTTTTA-GTTGCAACCTAATTTATCATATAGAAACTTGATTTTTTTTA-GTTGCATCCTAATTT
1 ATTTTTAGGTTGCAACATAATTTATCATATAGAAACATGA--ATGTTTAGGTTGCAACCTAATTT
* *
322635 ATCATATAGAAACTTGGTTTCTTTCTAGTTGCAACCTG
64 ATCATATAGAAACCTGGTTTCTTTATAGTTGCAACCTG
322673 ATTTTT
1 ATTTTT
322679 GTATATAGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
98 28 0.31
99 37 0.41
100 9 0.10
101 16 0.18
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (101 bp):
ATTTTTAGGTTGCAACATAATTTATCATATAGAAACATGAATGTTTAGGTTGCAACCTAATTTAT
CATATAGAAACCTGGTTTCTTTATAGTTGCAACCTG
Found at i:322713 original size:38 final size:37
Alignment explanation
Indices: 322662--322754 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 37
322652 TTTCTTTCTA
*
322662 GTTGCAACCTGATTTTTGTATATAGA-ACCAGATTTTAG
1 GTTGCAACCTGATTTTT-T-TATAGACACAAGATTTTAG
** *
322700 GTTGCAATTTGATTTTTTTATGGACACAAGATTTTAG
1 GTTGCAACCTGATTTTTTTATAGACACAAGATTTTAG
* *
322737 GTTGGAAACCTCATTTTT
1 GTT-GCAACCTGATTTTT
322755 GGTATAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 5 0.11
37 15 0.33
38 25 0.56
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (37 bp):
GTTGCAACCTGATTTTTTTATAGACACAAGATTTTAG
Found at i:326824 original size:32 final size:32
Alignment explanation
Indices: 326778--326859 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
326768 ATACTAGCAT
* * *
326778 TGTTGCATTCAGATAATGCGCAACAAAGTTAG
1 TGTTGTATTCAGATAATGCACAACAAAGTCAG
*
326810 TGTTGTATTTAGATAATGCACAACAAAGTCAG
1 TGTTGTATTCAGATAATGCACAACAAAGTCAG
326842 TGTT-TCATTCAGATAATG
1 TGTTGT-ATTCAGATAATG
326860 TATAGAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTTGTATTCAGATAATGCACAACAAAGTCAG
Found at i:328939 original size:2 final size:2
Alignment explanation
Indices: 328927--328982 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
328917 AACATTAATT
328927 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
328970 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
328983 GCACACATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:332616 original size:23 final size:23
Alignment explanation
Indices: 332588--332664 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
332578 TGATAATCCA
* * *
332588 AATACATAAGTAAAGTTCCTATG
1 AATACACAAGTAAAGGTCATATG
332611 AATACACAAGTAAAGGTCATATG
1 AATACACAAGTAAAGGTCATATG
332634 AATACACAAGTAAAGGTCATATG
1 AATACACAAGTAAAGGTCATATG
332657 AATACACA
1 AATACACA
332665 TGTCCACTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (23 bp):
AATACACAAGTAAAGGTCATATG
Found at i:334376 original size:31 final size:31
Alignment explanation
Indices: 334340--334429 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
334330 CAAATGACCT
*
334340 ATCCATATGTTCTGAAGAACATAGGTAAACT
1 ATCCATATGTTCTGAAGAACATAGGTAAACA
* * *
334371 GTCCATATGTCCCGAATG-ACATAGGTAAACA
1 ATCCATATGTTCTGAA-GAACATAGGTAAACA
334402 ATCCATATG-TCTCGAA-AGACATAGGTAA
1 ATCCATATGTTCT-GAAGA-ACATAGGTAA
334430 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
30 1 0.02
31 46 0.96
32 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (31 bp):
ATCCATATGTTCTGAAGAACATAGGTAAACA
Found at i:339141 original size:22 final size:22
Alignment explanation
Indices: 339108--339164 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
339098 GGCATGTAAA
* *
339108 ATATATCCCGAAGGACCTATGC
1 ATATGTCCCGAAGGACCTATCC
* *
339130 ATGTGTCCCGAATGACCTATCC
1 ATATGTCCCGAAGGACCTATCC
*
339152 ATATGTTCCGAAG
1 ATATGTCCCGAAG
339165 AACATAGGTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATCC
Found at i:339187 original size:31 final size:31
Alignment explanation
Indices: 339146--339237 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
339136 CCCGAATGAC
339146 CTATCCATATGTTCCGAAGAACATAGGTAAA
1 CTATCCATATGTTCCGAAGAACATAGGTAAA
* * *
339177 TTGTCCATATGTCCCGAATG-ACATAGGTAAA
1 CTATCCATATGTTCCGAA-GAACATAGGTAAA
339208 CTATCCATATG-TCTCGAA-AGACATAGGTAA
1 CTATCCATATGTTC-CGAAGA-ACATAGGTAA
339238 CCCTCGAGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 1 0.02
31 49 0.96
32 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
CTATCCATATGTTCCGAAGAACATAGGTAAA
Found at i:339684 original size:16 final size:16
Alignment explanation
Indices: 339663--339703 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
339653 TTTCATATGA
339663 ACACATATACTCAAGC
1 ACACATATACTCAAGC
339679 ACACATATACTCAAGC
1 ACACATATACTCAAGC
*
339695 GCACATATA
1 ACACATATA
339704 AATCATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (16 bp):
ACACATATACTCAAGC
Found at i:352417 original size:42 final size:42
Alignment explanation
Indices: 352367--352456 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
352357 TGGGAATGTA
* *
352367 ACCC-TGCGGAGAT-GACATATGAACTGGTGGGCTTGG-CATAT
1 ACCCTTGCGGAGATGGA-ATATGAACTGGCGAG-TTGGCCATAT
*
352408 ACCCTTGCGGAGATGGAATCTGAACTGGCGAGTTGGCCATAT
1 ACCCTTGCGGAGATGGAATATGAACTGGCGAGTTGGCCATAT
352450 ACCCTTG
1 ACCCTTG
352457 TGGCATCATC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 8 0.19
42 33 0.77
43 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (42 bp):
ACCCTTGCGGAGATGGAATATGAACTGGCGAGTTGGCCATAT
Found at i:355254 original size:17 final size:17
Alignment explanation
Indices: 355232--355267 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
355222 GCTTGATATA
355232 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
355249 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
355266 AT
1 AT
355268 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:379120 original size:21 final size:22
Alignment explanation
Indices: 379094--379135 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
379084 ATTTTAATTT
379094 TTATTTT-TTAATTTTCTTTTA
1 TTATTTTATTAATTTTCTTTTA
*
379115 TTATTTTATTATTTTTCTTTT
1 TTATTTTATTAATTTTCTTTT
379136 TTCTCAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (22 bp):
TTATTTTATTAATTTTCTTTTA
Found at i:381510 original size:198 final size:199
Alignment explanation
Indices: 381172--381568 Score: 787
Period size: 198 Copynumber: 2.0 Consensus size: 199
381162 TTTTGAATCG
381172 GTGAGTATCGAGTCTCGCAATCGGTAAAATTCTTACTCAAGTAATAAATGACTCTTTCTTTTCTT
1 GTGAGTATCGAGTCTCGCAATCGGTAAAATTCTTACTCAAGTAATAAATGACTCTTTCTTTTCTT
381237 CCTGATTCATCATGTTGCCCTAGTACACAACCCATTGAATTCTCAAAAACTGTTAAGTAGAGAAT
66 CCTGATTCATCATGTTGCCCTAGTACACAACCCATTGAATTCTCAAAAACTGTTAAGTAGAGAAT
381302 TAATGGTCTGCCAGGTACTGGTGATACTAATATGGGGGCATT-AATAGGTACCTTTTGATAACTT
131 TAATGGTCTGCCAGGTACTGGTGATACTAATATGGGGGCATTAAATAGGTACCTTTTGATAACTT
381366 CCAA
196 CCAA
381370 GTGAGTATCGAGTCTCGCAATCGGTAAAATTCTTACTCAAGTAATAAATGACTCTTTCTTTTCTT
1 GTGAGTATCGAGTCTCGCAATCGGTAAAATTCTTACTCAAGTAATAAATGACTCTTTCTTTTCTT
381435 CCTGATTCATCATGTTGCCCTAGTACACAACCCATTGAATTCTCAAAAACTGTTAAGTAGAGAAT
66 CCTGATTCATCATGTTGCCCTAGTACACAACCCATTGAATTCTCAAAAACTGTTAAGTAGAGAAT
381500 TAATGGTCTGCCAGGTACTGGTGATACTAATATGGGGGCATTAAATAGGTACCTTTTGATAACTT
131 TAATGGTCTGCCAGGTACTGGTGATACTAATATGGGGGCATTAAATAGGTACCTTTTGATAACTT
381565 CCAA
196 CCAA
381569 AGCCTGATGG
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
198 172 0.87
199 26 0.13
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (199 bp):
GTGAGTATCGAGTCTCGCAATCGGTAAAATTCTTACTCAAGTAATAAATGACTCTTTCTTTTCTT
CCTGATTCATCATGTTGCCCTAGTACACAACCCATTGAATTCTCAAAAACTGTTAAGTAGAGAAT
TAATGGTCTGCCAGGTACTGGTGATACTAATATGGGGGCATTAAATAGGTACCTTTTGATAACTT
CCAA
Found at i:390889 original size:20 final size:18
Alignment explanation
Indices: 390864--390910 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
390854 ATAAGAAAAT
390864 TAAATAAAATTATAAAATTA
1 TAAATAAAA--ATAAAATTA
390884 TAAATAGATAAATAAAATTA
1 TAAATA-A-AAATAAAATTA
390904 -AAATAAA
1 TAAATAAA
390911 TAAGGATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 5 0.20
20 15 0.60
21 1 0.04
22 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAATAAAAATAAAATTA
Found at i:390999 original size:50 final size:50
Alignment explanation
Indices: 390942--391053 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
390932 ATTGAAATAC
*
390942 AAGGACTAAATTGCAAGAAAATAAAAGAAAGTAACTTAATAAAAAATAAT
1 AAGGACTAAATTGCAAGAAAATAAAAGAAAGTAACTAAATAAAAAATAAT
* * *** * * * *
390992 AAGGACTAAAATGCAAGAAATTAAAATTCAGTAGCTAAATCAAAACTATT
1 AAGGACTAAATTGCAAGAAAATAAAAGAAAGTAACTAAATAAAAAATAAT
391042 AAGGACTAAATT
1 AAGGACTAAATT
391054 AAAAAAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.22
Consensus pattern (50 bp):
AAGGACTAAATTGCAAGAAAATAAAAGAAAGTAACTAAATAAAAAATAAT
Found at i:392851 original size:19 final size:18
Alignment explanation
Indices: 392827--392864 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
392817 TAATATAAAA
392827 TATTAACTT-TAAAATCATT
1 TATTAA-TTCTAAAA-CATT
392846 TATTAATTCTAAAACATT
1 TATTAATTCTAAAACATT
392864 T
1 T
392865 CGGTAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATTCTAAAACATT
Found at i:392975 original size:19 final size:19
Alignment explanation
Indices: 392915--392977 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
392905 TAAAATTTTT
* *
392915 TATTAACTCGAATATCAAA
1 TATTAACCCTAATATCAAA
* *
392934 TATAAATCCTAATATCAAA
1 TATTAACCCTAATATCAAA
*
392953 TATTAACCCTAATCTCAAA
1 TATTAACCCTAATATCAAA
392972 TATTAA
1 TATTAA
392978 TTTCAAAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (19 bp):
TATTAACCCTAATATCAAA
Found at i:393525 original size:25 final size:21
Alignment explanation
Indices: 393479--393541 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
393469 GTCGAGATAA
*
393479 TTATTATTA-TTATTTTAATT
1 TTATTATTATTTATATTAATT
393499 TTAAATTATTATTTATATTAGATT
1 TT--ATTATTATTTATATTA-ATT
*
393523 TTTTTA-TATTTATATTAAT
1 TTATTATTATTTATATTAAT
393542 AATTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 4 0.11
21 11 0.30
22 10 0.27
23 7 0.19
24 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTATTATTTATATTAATT
Found at i:394767 original size:8 final size:8
Alignment explanation
Indices: 394754--394782 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
394744 TTTAAACTTT
394754 GAAAAAAA
1 GAAAAAAA
394762 GAAAAAAA
1 GAAAAAAA
394770 GAAAAAAA
1 GAAAAAAA
394778 -AAAAA
1 GAAAAA
394783 TGGGATCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:395278 original size:31 final size:31
Alignment explanation
Indices: 395243--395319 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
395233 TAAAAAAACA
* * *
395243 TAAGATTTTGTCACTTTT-GTTTCATTTTAAT
1 TAAGATTTGGTCA-TTTTCATTACATTTTAAT
*
395274 TAAGATTTGGTCATTTTCATTACGTTTTAAT
1 TAAGATTTGGTCATTTTCATTACATTTTAAT
*
395305 TAAGATGTGGTCATT
1 TAAGATTTGGTCATT
395320 GAAGGTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (31 bp):
TAAGATTTGGTCATTTTCATTACATTTTAAT
Found at i:395733 original size:42 final size:41
Alignment explanation
Indices: 395620--395733 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 41
395610 GGTTTAGGAT
* * * *
395620 TGATCCCTTTACAAAAAGGATCGATCCCTCGAGGAAAATGAA
1 TGATCCCTTCAC-CAAAGGATCAATCCCTTGAGGAAAATGAA
* * *
395662 TGATCCCTTCACCAAATGGGTCAACCCCTTGATGAAAA-GAA
1 TGATCCCTTCACCAAA-GGATCAATCCCTTGAGGAAAATGAA
395703 TTGATCCCTTC-CCTTAAAGGATCAATCCCTT
1 -TGATCCCTTCACC--AAAGGATCAATCCCTT
395734 TCTTGCAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
41 8 0.14
42 48 0.81
43 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (41 bp):
TGATCCCTTCACCAAAGGATCAATCCCTTGAGGAAAATGAA
Found at i:396231 original size:15 final size:15
Alignment explanation
Indices: 396194--396231 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
396184 AATCCTTAGT
*
396194 GTGGATGCTAAGAGA
1 GTGGATGTTAAGAGA
396209 GTGGATGTTAAGAGA
1 GTGGATGTTAAGAGA
396224 GTGGATGT
1 GTGGATGT
396232 AGACTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.03, G:0.42, T:0.26
Consensus pattern (15 bp):
GTGGATGTTAAGAGA
Found at i:397219 original size:19 final size:20
Alignment explanation
Indices: 397182--397220 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
397172 TACACTTTTC
*
397182 ATTCTATATCAATTTGTTTA
1 ATTCTATATCAATTAGTTTA
*
397202 ATTC-ATATCCATTAGTTTA
1 ATTCTATATCAATTAGTTTA
397221 TTTAGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTCTATATCAATTAGTTTA
Found at i:403035 original size:23 final size:23
Alignment explanation
Indices: 403009--403054 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
402999 TTCAATGGAA
*
403009 AATGGATGATGGTGTTGAAGTTG
1 AATGGATGATGGTGATGAAGTTG
403032 AATGGATGATGGTGATGAAGTTG
1 AATGGATGATGGTGATGAAGTTG
403055 TATCTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (23 bp):
AATGGATGATGGTGATGAAGTTG
Found at i:423900 original size:606 final size:594
Alignment explanation
Indices: 422874--424076 Score: 2189
Period size: 606 Copynumber: 2.0 Consensus size: 594
422864 TAAATCCTTA
422874 AACTCAATAACACTTATCATAACCAACTTATAACACTTAAATCCCTTTATCATCCAAAATTCTCT
1 AACTCAATAACACTTATCATAACCAACTTATAACACTTAAATCCCTTTATCATCCAAAATTCTCT
422939 ATAGAACACTTGAATCTAAAAATCTACCAATCTTCAAACATGTTCTTAATCCTTCTAACACTTCT
66 ATAGAACACTTGAATCTAAAAATCTACCAATCTTCAAACATGTTCTTAATCCTTCTAACACTTCT
423004 AACATCTTATCTAAACCCTTGACAGTGAAATATACCTTTAGAAATCCAAATACAATCAATTTTAA
131 AACATCTTATCTAAACCCTTGACAGTGAAATATACCTTTAGAAATCCAAATACAATCAATTTTAA
423069 TAGATTCTCTTAAAACCAATTTTAAATTTACCAATAACTTATTAATTCCATGGTTTTTAGTTATC
196 TAGATTCTCTTAAAACCAATTTTAAATTTACCAATAACTTATTAATTCCATGGTTTTTAGTTATC
423134 TTTAAGCTTCCTTAAGCTTTATCACCCAATGAATAAAAAACCAATTCAAAAACGAAAGAAACAAC
261 TTTAAGCTTCCTTAAGCTTTATCACCCAATGAATAAAAAACCAATTCAAAAACGAAAGAAACAAC
423199 ATCTTTAACTCACTTATCTTAGCCATGGTGTTCACGATGGGAAGAACAGAAAAAGTTTCCAGACT
326 ATCTTTAACTCACTTATCTTAGCCATGGTGTTCACGATGGGAAGAACAGAAAAAGTTTCCAGACT
423264 TTCTTTCCCTTTCTCTAAACCTCGTGTTTCAAATAAACTTAAAAGAATGAATTTTAAATTCATTC
391 TTCTTTCCCTTTCTCTAAACCTCGTGTTTCAAATAAACTTAAAAGAATGAATTTTAAATTCATTC
423329 ATGCTAAAAGACCTCTTTACCCTTCCATTCTTTCATCTTTGATAATAAGTCCTAGACACAAATTC
456 ATGCTAAAAGACCTCTTTACCCTTCCA-T-TTTCATC-TTGATAATAAGT-CTAGACACAAATTC
423394 TAGAATCAGTCCTTGAACTTTTTAATTTATTTAAATT-AACCACCAAACTTTAAATCCTT-ACTT
517 TAGAATCAGTCCTTGAACTTTTTAATTTATTTAAATTAAACCACCAAACTTTAAATCCTTAACTT
423457 TAGTCACTGACTC
582 TAGTCACTGACTC
423470 AACTCAATAACACTTATCATAACCAACTTATAACACTTAAATCCCCTTTATCATCCAAAATTCTC
1 AACTCAATAACACTTATCATAACCAACTTATAACACTTAAAT-CCCTTTATCATCCAAAATTCTC
423535 TATAGAACACTTGAATCTAAAAATCATACCAATCTTCAAACATGTTCTTAATCCTTTCTAACACT
65 TATAGAACACTTGAATCTAAAAATC-TACCAATCTTCAAACATGTTCTTAATCC-TTCTAACACT
423600 TCTAACATCTTATCTAAACCCTTGACAAGTGAAATATACCTTTAGAAATCCAAATACAATCAATT
128 TCTAACATCTTATCTAAACCCTTGAC-AGTGAAATATACCTTTAGAAATCCAAATACAATCAATT
423665 TTAATAGATTCTCTTAAAACCAATTTTACTAATTTACCAATAACTTATTAATTCCATGGTTTTTA
192 TTAATAGATTCTCTTAAAACCAATTTTA--AATTTACCAATAACTTATTAATTCCATGGTTTTTA
423730 GTTATCTTTAAGCTTCCTTAAGCTTTTATATCACCCAATGAAT-AAAAACCAATTCAAAAACGAA
255 GTTATCTTTAAGCTTCCTTAAGC--TT-TATCACCCAATGAATAAAAAACCAATTCAAAAACGAA
423794 AGAAACAATCATCTTTAAACTCACTTATCTTAGCCATGGTGTTCACGATGGGAAGAACAG-AAAA
317 AGAAACAA-CATCTTT-AACTCACTTATCTTAGCCATGGTGTTCACGATGGGAAGAACAGAAAAA
* *
423858 GTTTCCAGACTTTTCTTTCCCTTTCTCTAAACCTCTTGTTTCAAATAACCTTAAAAGAATGAATT
380 GTTTCCAGAC-TTTCTTTCCCTTTCTCTAAACCTCGTGTTTCAAATAAACTTAAAAGAATGAATT
* *
423923 TTAAATTCATTCATGCTAAAAGACCTCTTTGCCCTTCCATTTTCATCTTGATAATAAGTCTATAC
444 TTAAATTCATTCATGCTAAAAGACCTCTTTACCCTTCCATTTTCATCTTGATAATAAGTCTAGAC
423988 ACAAATTCTAGAATCAGTCCTTGAACTTTTTAATTTATTTAAATTAAACCACCAAACTTTAAATC
509 ACAAATTCTAGAATCAGTCCTTGAACTTTTTAATTTATTTAAATTAAACCACCAAACTTTAAATC
424053 CTTACACTTTAGTCACTGACTC
574 CTTA-ACTTTAGTCACTGACTC
424075 AA
1 AA
424077 TTTTTGGGAT
Statistics
Matches: 588, Mismatches: 4, Indels: 21
0.96 0.01 0.03
Matches are distributed among these distances:
596 42 0.07
597 47 0.08
598 28 0.05
599 36 0.06
600 66 0.11
602 108 0.18
603 34 0.06
604 38 0.06
605 56 0.10
606 133 0.23
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (594 bp):
AACTCAATAACACTTATCATAACCAACTTATAACACTTAAATCCCTTTATCATCCAAAATTCTCT
ATAGAACACTTGAATCTAAAAATCTACCAATCTTCAAACATGTTCTTAATCCTTCTAACACTTCT
AACATCTTATCTAAACCCTTGACAGTGAAATATACCTTTAGAAATCCAAATACAATCAATTTTAA
TAGATTCTCTTAAAACCAATTTTAAATTTACCAATAACTTATTAATTCCATGGTTTTTAGTTATC
TTTAAGCTTCCTTAAGCTTTATCACCCAATGAATAAAAAACCAATTCAAAAACGAAAGAAACAAC
ATCTTTAACTCACTTATCTTAGCCATGGTGTTCACGATGGGAAGAACAGAAAAAGTTTCCAGACT
TTCTTTCCCTTTCTCTAAACCTCGTGTTTCAAATAAACTTAAAAGAATGAATTTTAAATTCATTC
ATGCTAAAAGACCTCTTTACCCTTCCATTTTCATCTTGATAATAAGTCTAGACACAAATTCTAGA
ATCAGTCCTTGAACTTTTTAATTTATTTAAATTAAACCACCAAACTTTAAATCCTTAACTTTAGT
CACTGACTC
Found at i:426161 original size:46 final size:46
Alignment explanation
Indices: 426121--426231 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
426111 ATTTTAAATT
*
426121 ATTAGTTTGATAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
1 ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
*
426167 ATTAGTTTGTTAGTTTAGGGTTTAAGGTAAAACAAAATTTTAGTTA
1 ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
426213 ATTAGTTTGTTAGTTTAAG
1 ATTAGTTTGTTAGTTTAAG
426232 TTATATTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (46 bp):
ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
Found at i:426391 original size:44 final size:46
Alignment explanation
Indices: 426296--426392 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 46
426286 AGTTTGTTTG
* * **
426296 ATAGTTATATATTAAAAAAATAATTAATTAGTTTGTTTGTTAGTCG
1 ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
* *
426342 TTAGTTATA-AAT-AAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAG-TAA
426386 ATAGTTA
1 ATAGTTA
426393 AGTTATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 6 0.14
44 27 0.63
45 2 0.05
46 8 0.19
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.45
Consensus pattern (46 bp):
ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
Found at i:427599 original size:13 final size:14
Alignment explanation
Indices: 427583--427611 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
427573 ATTCTCTATT
427583 TTAA-TATAAAATA
1 TTAATTATAAAATA
427596 TTAATTATAAAATA
1 TTAATTATAAAATA
427610 TT
1 TT
427612 TATTTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATTATAAAATA
Found at i:429773 original size:28 final size:30
Alignment explanation
Indices: 429733--429795 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
429723 ATTTTTTATA
429733 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
429763 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
429791 TAATA
1 TAATA
429796 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:429802 original size:28 final size:28
Alignment explanation
Indices: 429737--429802 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
429727 TTTATATAAT
429737 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
429765 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
429793 ATAATTTATA
1 ATAATATATA
429803 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:429805 original size:21 final size:21
Alignment explanation
Indices: 429772--429820 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
429762 CTAATATAAT
429772 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
429793 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
429814 ATTAACT
1 A-TAACT
429821 AAAATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:435425 original size:18 final size:20
Alignment explanation
Indices: 435402--435442 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
435392 CACTTGTCAA
435402 ATTATTAGTTTT-AAA-AAT
1 ATTATTAGTTTTGAAAGAAT
*
435420 ATTATTTGTTTTGAAAGAAT
1 ATTATTAGTTTTGAAAGAAT
435440 ATT
1 ATT
435443 CACCCTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 3 0.15
20 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTATTAGTTTTGAAAGAAT
Found at i:443291 original size:59 final size:59
Alignment explanation
Indices: 443158--443330 Score: 163
Period size: 59 Copynumber: 2.9 Consensus size: 59
443148 TCAAACTATA
* * * * * **
443158 ACTCTCATTCTAACTTAGCCCCTAAACATTTGAACATTTCAATGTCA-TCCCTAATTATG
1 ACTCTCATTCCAAATTAGTCCC-AAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
** ** ** *
443217 ACTCTCATTTTAAATTAGTCTTTACGCTTTTGAACATTTTAATTTCATTCCAAAATTATG
1 ACTCTCATTCCAAATTAGTC-CCAAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
*
443277 AC-CTCATTCCAAATTGGTCCCAAACTTTTGAACATTTCAATTTC-TTCACAAAAT
1 ACTCTCATTCCAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATTC-CAAAAT
443331 ATAGGTATAT
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
57 3 0.03
58 26 0.29
59 50 0.55
60 12 0.13
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.39
Consensus pattern (59 bp):
ACTCTCATTCCAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
Found at i:445057 original size:5 final size:6
Alignment explanation
Indices: 445029--445079 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
445019 ATTTTGGTCC
* *
445029 TTTTTCA TTTTCA TTTTTA TTTTTA TTTTTA TTTTATTA TTTTTC TTTTTA
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA -TTT-TTA TTTTTA TTTTTA
445080 CTAACTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 25 0.66
7 10 0.26
8 3 0.08
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:445100 original size:22 final size:22
Alignment explanation
Indices: 445043--445116 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
445033 TCATTTTCAT
*
445043 TTTTATTT-TTATTTTTAT-T-
1 TTTTATTTATCATTTTTATCTA
*
445062 TTATTATTTTTC-TTTTTA-CTAA
1 TT-TTATTTATCATTTTTATCT-A
445084 CTTTTATTTATCATTTTTATCTA
1 -TTTTATTTATCATTTTTATCTA
445107 TTTTATTTAT
1 TTTTATTTAT
445117 TTTATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 1 0.02
22 18 0.40
23 9 0.20
24 2 0.04
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTTATCATTTTTATCTA
Found at i:449031 original size:91 final size:90
Alignment explanation
Indices: 448867--449048 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 90
448857 CAGTTAAAAC
**
448867 TTTCAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTGAGACAACGCAAGTTCAACTTCA
1 TTTCAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
448932 TGATGAAGGGACCGATGGTTGTCAA
66 CGACGAAGGGACCGATGGTTGTCAA
448957 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCA-AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
449022 ACGACGAAGGGACCGCTGGTTGTCAA
65 ACGACGAAGGGACCGATGGTTGTCAA
449048 T
1 T
449049 AACCAACTTC
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
90 5 0.06
91 81 0.94
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (90 bp):
TTTCAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGATGGTTGTCAA
Found at i:449137 original size:43 final size:43
Alignment explanation
Indices: 449076--449231 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
449066 CAGAGCCAAT
449076 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
449119 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTC-CAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA----CGCAAG
*
449170 TTCAACTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
449213 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
449232 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
42 1 0.01
43 36 0.44
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 18 0.22
52 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:449138 original size:106 final size:106
Alignment explanation
Indices: 448953--449978 Score: 1768
Period size: 106 Copynumber: 10.0 Consensus size: 106
448943 CCGATGGTTG
448953 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
449018 CTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449059 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449124 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA----
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
*
449161 T---TTT-----CCAATTTCAACTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449218 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449259 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449323 CTTCACGACGAAGGGACCGCTGGTTGTCAAT-AA-AACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449362 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
449427 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449467 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449532 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA----
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
* *
449569 T---TTT-----CCAATTTCAATTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449626 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449667 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
449732 CTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449773 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
449838 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
449878 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
449943 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
66 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
449979 TTTCCCAGTT
Statistics
Matches: 876, Mismatches: 15, Indels: 58
0.92 0.02 0.06
Matches are distributed among these distances:
94 177 0.20
98 2 0.00
99 6 0.01
101 6 0.01
102 2 0.00
103 45 0.05
104 57 0.07
105 264 0.30
106 317 0.36
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
Found at i:449348 original size:105 final size:106
Alignment explanation
Indices: 449165--449978 Score: 1437
Period size: 105 Copynumber: 7.8 Consensus size: 106
449155 AAACAATTTT
*
449165 CCAATTTCAACTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449230 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449271 CCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449335 GGGACCGCTGGTTGTCAAT-AA-AACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449374 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
449439 GGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449479 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449544 GGGACCGCTGGTTGTCAATAAACAA----T---TTT-----
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
* *
449573 CCAATTTCAATTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449638 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449679 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
449744 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449785 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
449850 GGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
449890 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449955 GGGACCGCTGGTTGTCAATAAACA
66 GGGACCGCTGGTTGTCAATAAACA
449979 TTTCCCAGTT
Statistics
Matches: 678, Mismatches: 13, Indels: 34
0.94 0.02 0.05
Matches are distributed among these distances:
94 88 0.13
98 1 0.00
99 3 0.00
101 3 0.00
102 1 0.00
103 45 0.07
104 57 0.08
105 264 0.39
106 216 0.32
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
Found at i:449545 original size:43 final size:43
Alignment explanation
Indices: 449484--449639 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 43
449474 CAGAGCCAAT
449484 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
449527 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTC-CAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA----CGCAAG
* *
449578 TTCAATTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
449621 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
449640 GACCGCTGGT
Statistics
Matches: 80, Mismatches: 23, Indels: 20
0.65 0.19 0.16
Matches are distributed among these distances:
42 1 0.01
43 35 0.44
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 17 0.21
52 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:449653 original size:408 final size:409
Alignment explanation
Indices: 448867--449978 Score: 2011
Period size: 408 Copynumber: 2.7 Consensus size: 409
448857 CAGTTAAAAC
**
448867 TTTCA-AGCCAATTTCAACTTCACAACGAAGGATATTGGACTTGAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * *
448931 ATGATGAAGGGACCGATGGTTG-------------TCAATTTCAGAGCCAATTTCAACTTCACAA
66 ACGACGAAGGGACCGCTGGTTGTCAATAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
448983 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
449048 TAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
196 CAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
449113 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAACTT
260 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAACTT
449178 CTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
325 CTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
449243 GTCAATAAACAACTTCTCAA
390 GTCAATAAACAACTTCTCAA
449263 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
449327 ACGACGAAGGGACCGCTGGTTGTCAATAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 ACGACGAAGGGACCGCTGGTTGTCAATAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
449392 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
449457 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
196 CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
*
449522 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAATTTC
261 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAACTTC
449587 TCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
326 TCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
449652 TCAATAAACAACTTCTCAA
391 TCAATAAACAACTTCTCAA
449671 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
449736 ACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
66 ACGACGAAGGGACCGCTGGTTGTCAATAA--AACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
449801 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
129 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
449866 AACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
194 AACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
449931 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
259 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
449979 TTTCCCAGTT
Statistics
Matches: 690, Mismatches: 9, Indels: 19
0.96 0.01 0.03
Matches are distributed among these distances:
396 51 0.07
397 29 0.04
408 242 0.35
409 156 0.23
411 212 0.31
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (409 bp):
TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAATAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAACTTC
TCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAATAAACAACTTCTCAA
Found at i:449952 original size:211 final size:212
Alignment explanation
Indices: 449573--449975 Score: 763
Period size: 211 Copynumber: 1.9 Consensus size: 212
449563 AAACAATTTT
* *
449573 CCAATTTCAATTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
449638 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
449703 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
449768 ACTTCTCAATTTCAGAG
196 ACTTCTCAATTTCAGAG
449785 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
449850 GGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
449914 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
449976 ACATTTCCCA
Statistics
Matches: 187, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
211 102 0.55
212 85 0.45
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (212 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
ACTTCTCAATTTCAGAG
Found at i:450028 original size:105 final size:105
Alignment explanation
Indices: 449573--450029 Score: 752
Period size: 106 Copynumber: 4.3 Consensus size: 105
449563 AAACAATTTT
* *
449573 CCAATTTCAATTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
449638 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAAC-ACTTCTCAATTTCAGAG
449679 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
449744 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAAC-ACTTCTCAATTTCAGAG
449785 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
449850 GGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACACTTCTCAATTTCAGAG
449890 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * * *
449955 GGGACCGCTGGTTGTCAATAAACATTTCCCAGTTCCAGAA
66 GGGACCGCTGGTTGTCAATAAACACTTCTCAATTTCAGAG
* * *** *
449995 CCAATTTCGACTCCACGGTGGAGGATATTGGACTC
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTC
450030 GAAACAATAC
Statistics
Matches: 334, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 145 0.43
106 189 0.57
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACACTTCTCAATTTCAGAG
Found at i:450561 original size:13 final size:13
Alignment explanation
Indices: 450551--450577 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
450541 TAATTATTTG
450551 TTATTATTATTAA
1 TTATTATTATTAA
450564 TTATTATTATTAA
1 TTATTATTATTAA
450577 T
1 T
450578 ATTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:452119 original size:5 final size:6
Alignment explanation
Indices: 452091--452141 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
452081 ATTTTGGTCC
* *
452091 TTTTTCA TTTTCA TTTTTA TTTTTA TTTTTA TTTTATTA TTTTTC TTTTTA
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA -TTT-TTA TTTTTA TTTTTA
452142 CTAACTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 25 0.66
7 10 0.26
8 3 0.08
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:452162 original size:22 final size:22
Alignment explanation
Indices: 452105--452178 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
452095 TCATTTTCAT
*
452105 TTTTATTT-TTATTTTTAT-T-
1 TTTTATTTATCATTTTTATCTA
*
452124 TTATTATTTTTC-TTTTTA-CTAA
1 TT-TTATTTATCATTTTTATCT-A
452146 CTTTTATTTATCATTTTTATCTA
1 -TTTTATTTATCATTTTTATCTA
452169 TTTTATTTAT
1 TTTTATTTAT
452179 TTTATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 1 0.02
22 18 0.40
23 9 0.20
24 2 0.04
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTTATCATTTTTATCTA
Found at i:453669 original size:21 final size:20
Alignment explanation
Indices: 453645--453684 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
453635 TAATTACTTA
453645 ATTAAATACTATAAATTTTTT
1 ATTAAA-ACTATAAATTTTTT
* *
453666 ATTAAAATTATATATTTTT
1 ATTAAAACTATAAATTTTT
453685 ATCCCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAAAACTATAAATTTTTT
Found at i:455577 original size:36 final size:33
Alignment explanation
Indices: 455532--455611 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 33
455522 ATGTAAGCTC
*
455532 AACTCGACTCGAAAACTCGCAAGCCTAAAATTTTCA
1 AACTCGACTCGAAAACTCGAAAG---AAAATTTTCA
* *
455568 AACTCGACTCG--AACTCGAAAGATAATTTTGA
1 AACTCGACTCGAAAACTCGAAAGAAAATTTTCA
455599 AACTCGACTCGAA
1 AACTCGACTCGAA
455612 CTCGAACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 19 0.49
34 9 0.23
36 11 0.28
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.23
Consensus pattern (33 bp):
AACTCGACTCGAAAACTCGAAAGAAAATTTTCA
Found at i:455709 original size:23 final size:23
Alignment explanation
Indices: 455669--455712 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
455659 CTCGAGACTC
* * *
455669 GAGCTCTATTGAAGCTCGATTTT
1 GAGCTCGATTCAAACTCGATTTT
455692 GAGCTCGATTCAAACTCGATT
1 GAGCTCGATTCAAACTCGATT
455713 CAAGCTCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
GAGCTCGATTCAAACTCGATTTT
Found at i:455730 original size:17 final size:17
Alignment explanation
Indices: 455704--455744 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
455694 GCTCGATTCA
*
455704 AACTCGATTCAAGCTCG
1 AACTCAATTCAAGCTCG
455721 AACTCAATTCAAGCTCG
1 AACTCAATTCAAGCTCG
455738 AACTCAA
1 AACTCAA
455745 ACTCGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (17 bp):
AACTCAATTCAAGCTCG
Found at i:458404 original size:6 final size:6
Alignment explanation
Indices: 458393--458427 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
458383 TATGGTTTAT
458393 GGTTAG GGTTAG GGTTAG GGTTAG GGTTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GG-TTAG GGTT
458428 TACGATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (6 bp):
GGTTAG
Found at i:458425 original size:7 final size:7
Alignment explanation
Indices: 458367--458429 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
458357 AGGGTTAGAA
*
458367 TTTATGG
1 TTTAGGG
* *
458374 TTTATGT
1 TTTAGGG
*
458381 TTTATGG
1 TTTAGGG
*
458388 TTTATGG
1 TTTAGGG
458395 -TTAGGG
1 TTTAGGG
458401 -TTAGGG
1 TTTAGGG
458407 -TTAGGG
1 TTTAGGG
458413 -TTAGGG
1 TTTAGGG
458419 TTTAGGG
1 TTTAGGG
458426 TTTA
1 TTTA
458430 CGATTCATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
6 23 0.44
7 29 0.56
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:459953 original size:2 final size:2
Alignment explanation
Indices: 459946--459973 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
459936 TATCAAACCT
459946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
459974 GTTGTACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:461641 original size:22 final size:22
Alignment explanation
Indices: 461604--461668 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
461594 AGGCGATGAC
* **
461604 GTCAGCACCTTCTAGAAGTTCCA
1 GTCAGCA-TTTCTAGAAGCACCA
461627 GTCAGCATTTCTAGAAGCACCA
1 GTCAGCATTTCTAGAAGCACCA
*
461649 GTCAGCGTTTCTAGAAGCAC
1 GTCAGCATTTCTAGAAGCAC
461669 GAATGGATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 31 0.82
23 7 0.18
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (22 bp):
GTCAGCATTTCTAGAAGCACCA
Found at i:461836 original size:75 final size:74
Alignment explanation
Indices: 461739--461962 Score: 317
Period size: 75 Copynumber: 3.0 Consensus size: 74
461729 ATTTTAAACA
*
461739 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
461804 -GATATTATTT
66 TGATA-T-TTT
*
461814 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
461879 TGATATTTT
66 TGATATTTT
* * * * *
461888 TTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTTAATTAGGATT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGT-ATTTTAATTAAGATT
* *
461952 TAAGATGTTTT
64 TATGATATTTT
461963 AGCTTGTTTT
Statistics
Matches: 138, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
73 5 0.04
74 42 0.30
75 87 0.63
76 4 0.03
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.59
Consensus pattern (74 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
TGATATTTT
Found at i:461873 original size:19 final size:19
Alignment explanation
Indices: 461770--461878 Score: 57
Period size: 19 Copynumber: 5.8 Consensus size: 19
461760 GGTATTTTAG
*
461770 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
461789 TTTAATTAAGTTTTAGATAT
1 TTTAATTAGGTTTTAG-TAT
* ** *
461809 TATT-TTTATATTTTA-TCT
1 T-TTAATTAGGTTTTAGTAT
* *
461827 TTGT-TTTAGGTATTT--TAG
1 TT-TAATTAGGT-TTTAGTAT
*
461845 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
461864 TTTAATTAGGATTTA
1 TTTAATTAGGTTTTA
461879 TGATATTTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
17 5 0.07
18 17 0.25
19 32 0.47
20 12 0.18
21 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:461887 original size:65 final size:66
Alignment explanation
Indices: 461816--461981 Score: 158
Period size: 74 Copynumber: 2.4 Consensus size: 66
461806 TATTATTTTT
461816 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGT-ATTTTAATTAGGATTTA
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGATTTTAATTAGGATTTA
*
461879 TG
65 AG
* *
461881 ATATTTTTTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTTAATT
1 ATA-----T---T-TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGATTTTAATT
461946 AGGATTTAAG
57 AGGATTTAAG
* * *
461956 ATGTTTTAGC-TTGTTTTTAGGAATTT
1 ATATTTTATCTTTG-TTTTAGGTATTT
461982 GAAGGCTATA
Statistics
Matches: 82, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
65 6 0.07
66 14 0.17
67 1 0.01
70 2 0.02
73 6 0.07
74 34 0.41
75 19 0.23
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (66 bp):
ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGATTTTAATTAGGATTTAA
G
Found at i:470344 original size:73 final size:75
Alignment explanation
Indices: 470220--470432 Score: 263
Period size: 73 Copynumber: 2.9 Consensus size: 75
470210 ATTTTAAACA
470220 TTATATTTTATCTTTGTTTTA-ATTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAG-TTT
1 TTATATTTTATCTTTGTTTTAGA-TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTT
470283 AGGATATT-TT
65 AGGATATTATT
* * * *
470293 TTATGTTTTATCTTTATTTTAGATATTTCAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
470358 TGATATTATT
66 GGATATTATT
* * * ** * * *
470368 TTAAATATTATTTTTGTTTTAGGCATTTTAGTTTAAATA-GTTTAAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTT-TAGTATTTTAATTAAGATTT
470432 A
65 A
470433 AGATGTTTTA
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
73 54 0.45
74 15 0.12
75 52 0.43
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GGATATTATT
Found at i:470421 original size:75 final size:74
Alignment explanation
Indices: 470227--470441 Score: 238
Period size: 75 Copynumber: 2.9 Consensus size: 74
470217 ACATTATATT
* * *
470227 TTATCTTTGTTTTA-ATTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAG-TTTAGGATAT
1 TTATCTTTATTTTAGA-CATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATAT
** *
470290 TTTTTATGTT
65 TTTTTAAATA
* * *
470300 TTATCTTTATTTTAGATATTTCAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATGATATT
1 TTATCTTTATTTTAGACATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATT
470365 ATTTTAAATA
66 -TTTTAAATA
* * * * * * *
470375 TTATTTTTGTTTTAGGCATTTTAGTTTAAATA-GTTTAAAGTGTTTTAATTAGGATTTAAGATGT
1 TTATCTTTATTTTAGACATTTTAGTTTAAATAGGTTT-TAGTATTTTAATTAGGATTTAGGATAT
470439 TTT
65 TTT
470442 AGCTTGTTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
73 48 0.39
74 17 0.14
75 57 0.47
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (74 bp):
TTATCTTTATTTTAGACATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATT
TTTTAAATA
Found at i:471020 original size:4 final size:4
Alignment explanation
Indices: 471011--471047 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
471001 CTTTATCCCA
*
471011 ATTT ATTT ATTT ATTT ATTT ATTT GTTT ATTT CATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT
471048 TTATCTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:471233 original size:22 final size:21
Alignment explanation
Indices: 471193--471233 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
471183 AAATTATATT
* *
471193 TTTTCCTAAATCAAGAAACAA
1 TTTTACTAAATCAAAAAACAA
471214 TTTTACTAAATCACAAAAAC
1 TTTTACTAAATCA-AAAAAC
471234 CATAGTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (21 bp):
TTTTACTAAATCAAAAAACAA
Found at i:478371 original size:141 final size:141
Alignment explanation
Indices: 478117--478377 Score: 506
Period size: 141 Copynumber: 1.9 Consensus size: 141
478107 GTTAAAGGGA
478117 GATCATCCTGATTCCATGATTTTTTTGCGTTCCCTTTGGGATGATGGCATGGAATTTCACACTAA
1 GATCATCCTGATTCCATGATTTTTTTGCGTTCCCTTTGGGATGATGGCATGGAATTTCACACTAA
478182 TTTGCAGGAGCTTCGATGCAAAGTTAAAATTTGGAATGAGGAAGTATTCAAGCATCATTATATTG
66 TTTGCAGGAGCTTCGATGCAAAGTTAAAATTTGGAATGAGGAAGTATTCAAGCATCATTATATTG
478247 TTGCGTGGAAT
131 TTGCGTGGAAT
478258 GATCATCCTGAGTTCCATGA-TTTTTTGCGTTCCCTTTGGGATGATGGCATGGAATTTCACACTA
1 GATCATCCTGA-TTCCATGATTTTTTTGCGTTCCCTTTGGGATGATGGCATGGAATTTCACACTA
478322 ATTTGCAGGAGCTTCGATGCAAAGTTAAAATTTGGAATGAGGAAGTATTCAAGCAT
65 ATTTGCAGGAGCTTCGATGCAAAGTTAAAATTTGGAATGAGGAAGTATTCAAGCAT
478378 TTCTTCCAAT
Statistics
Matches: 119, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
141 111 0.93
142 8 0.07
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (141 bp):
GATCATCCTGATTCCATGATTTTTTTGCGTTCCCTTTGGGATGATGGCATGGAATTTCACACTAA
TTTGCAGGAGCTTCGATGCAAAGTTAAAATTTGGAATGAGGAAGTATTCAAGCATCATTATATTG
TTGCGTGGAAT
Found at i:478792 original size:21 final size:21
Alignment explanation
Indices: 478759--478800 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
478749 TTAGTTAATT
*
478759 ATATTTATCGTTAAATATATA
1 ATATTGATCGTTAAATATATA
*
478780 ATATTGATTGTTAAATATATA
1 ATATTGATCGTTAAATATATA
478801 GTTATATGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
ATATTGATCGTTAAATATATA
Found at i:478866 original size:6 final size:6
Alignment explanation
Indices: 478857--478919 Score: 80
Period size: 6 Copynumber: 11.2 Consensus size: 6
478847 ATATTGATAT
* *
478857 TAAATA TAAATG T--ATA TAAGTA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
478903 T-AATA T-AATA TAAATA T
1 TAAATA TAAATA TAAATA T
478920 GTAGGATGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.06
5 10 0.20
6 37 0.74
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:478889 original size:28 final size:27
Alignment explanation
Indices: 478857--478919 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
478847 ATATTGATAT
*
478857 TAAATATAAATGT-ATATAAGTATAAATA
1 TAAATATAAATATAATATAA-TAT-AATA
478885 TAAATATAAATATAAATATAATATAATA
1 TAAATATAAATAT-AATATAATATAATA
478913 TAAATAT
1 TAAATAT
478920 GTAGGATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 23 0.72
29 3 0.09
30 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
TAAATATAAATATAATATAATATAATA
Found at i:478893 original size:18 final size:16
Alignment explanation
Indices: 478859--478919 Score: 79
Period size: 16 Copynumber: 3.7 Consensus size: 16
478849 ATTGATATTA
*
478859 AATATAAATGT-ATAT
1 AATATAAATATAATAT
478874 AAGTATAAATATAAATAT
1 AA-TATAAATAT-AATAT
478892 AAATATAAATATAATAT
1 -AATATAAATATAATAT
478909 AATATAAATAT
1 AATATAAATAT
478920 GTAGGATGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
15 2 0.05
16 19 0.46
17 5 0.12
18 13 0.32
19 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:480234 original size:90 final size:88
Alignment explanation
Indices: 480120--480289 Score: 304
Period size: 90 Copynumber: 1.9 Consensus size: 88
480110 TCCCGAATAT
*
480120 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
480185 GGTAACTTGGATATAAGAGGATTA
65 GGTAACTTGGATATAAGAGGATTA
480209 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
480274 GGTAACTTGGCTATAA
65 GGTAACTTGGATATAA
480290 AAGAGTGTGT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 37 0.47
90 41 0.53
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAGAGGATTA
Found at i:487082 original size:90 final size:89
Alignment explanation
Indices: 486971--487143 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
486961 TAATCCCAAA
*
486971 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCATAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCATAATATGAT
487036 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
* * *
487061 TATTAAATTTTAATTAATTAAATATAGATTTAATTACTTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
*
487126 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
487144 AAGAGTGTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 29 0.37
90 49 0.63
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:489009 original size:2 final size:2
Alignment explanation
Indices: 489002--489026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
488992 TTTGCATTCT
489002 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
489027 TTACATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492282 original size:108 final size:107
Alignment explanation
Indices: 492098--492546 Score: 571
Period size: 108 Copynumber: 4.2 Consensus size: 107
492088 ATGTATCGAT
* * **
492098 ACTAAGTGTGCAACCCACATATTTCATAATAAGTTTATGAACAACTATATCGACACTAAGTGTGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAAC-ACCGTATCGACACTAAGTGTGC
* *
492163 AACCCACAGAATTTATAATAAGTTTATGAATGACCGTATCGGC
65 AACCCATAGAATTCATAATAAGTTTATGAATGACCGTATCGGC
* * *
492206 GCTACGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCTTATCGACACTAAGTGTGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAAC-ACCGTATCGACACTAAGTGTGC
* *
492271 AACCCATAGAATTCATAATAAGTTTATGAAAGACTGTATCGGC
65 AACCCATAGAATTCATAATAAGTTTATGAATGACCGTATCGGC
* * **
492314 ACTAAGTGTGCAATCCACAAAATGT-ATACCAAGTTTATGAACGACCGTATCGACACTAAGTGTG
1 ACTAAGTGTGCAACCCACAGAAT-TCATAATAAGTTTATGAAC-ACCGTATCGACACTAAGTGTG
* ** ** *
492378 CAACCCATAGAATTCATAATAAGTTTATGAACGGTCGTATTTGT
64 CAACCCATAGAATTCATAATAAGTTTATGAATGACCGTATCGGC
* *
492422 ACTAAGTGTGTAACCCAC-GTAATTCATAATAAGTTTATAAACAGCCGTATC-ATCACTAAGTGT
1 ACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACA-CCGTATCGA-CACTAAGTGT
* **
492485 GCAACCCATGGAATTCATAATAAGTTTATGAATGATTGTATCGGC
63 GCAACCCATAGAATTCATAATAAGTTTATGAATGACCGTATCGGC
*
492530 ACTAAGTGTGCACCCCA
1 ACTAAGTGTGCAACCCA
492547 TGAAACTTAT
Statistics
Matches: 296, Mismatches: 40, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
107 3 0.01
108 292 0.99
109 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (107 bp):
ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACACCGTATCGACACTAAGTGTGCA
ACCCATAGAATTCATAATAAGTTTATGAATGACCGTATCGGC
Found at i:492548 original size:54 final size:54
Alignment explanation
Indices: 492089--492547 Score: 500
Period size: 54 Copynumber: 8.5 Consensus size: 54
492079 TGCATTTTTA
* * * * *
492089 TGTATCGATACTAAGTGTGCAACCCACATATTTCATAATAAGTTTATGAACAAC
1 TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
* * * *
492143 TATATCGACACTAAGTGTGCAACCCACAGAATTTATAATAAGTTTATGAATGAC
1 TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
* * * * *
492197 CGTATCGGCGCTACGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
1 TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGA-C
*
492252 T-TATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAAAGAC
1 TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
* * * * **
492305 TGTATCGGCACTAAGTGTGCAATCCACAAAATGT-ATACCAAGTTTATGAACGAC
1 TGTATCGACACTAAGTGTGCAACCCATAGAAT-TCATAATAAGTTTATGAACGAC
* *
492359 CGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACG-G
1 TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
* * * * *
492412 TCGTATTTG-TACTAAGTGTGTAACCCA-CGTAATTCATAATAAGTTTATAAAC-AGC
1 T-GTA-TCGACACTAAGTGTGCAACCCATAG-AATTCATAATAAGTTTATGAACGA-C
* * * *
492467 CGTATC-ATCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGAT
1 TGTATCGA-CACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
* *
492521 TGTATCGGCACTAAGTGTGCACCCCAT
1 TGTATCGACACTAAGTGTGCAACCCAT
492548 GAAACTTATA
Statistics
Matches: 338, Mismatches: 53, Indels: 28
0.81 0.13 0.07
Matches are distributed among these distances:
53 5 0.01
54 327 0.97
55 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (54 bp):
TGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGAC
Found at i:499136 original size:54 final size:54
Alignment explanation
Indices: 499057--499561 Score: 539
Period size: 54 Copynumber: 9.3 Consensus size: 54
499047 TATGTATCAA
* *
499057 CACTAAGTGTGTAACCCAC-GAAATTCATAATAAGTTTATGAACAACTGTATCGG
1 CACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACTGTATCGG
* * * *
499111 TACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGA-TCGTATTGG
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACT-GTATCGG
** * * *
499165 CACTAAGTGTGCAACTTACAAAATTCATAATAAGTTTATGAACGACCGTATCGA
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
* * * *
499219 CACTAAATGTGCAACCCACATAATTCATTATAAGTTTATGAACGACTGTATCAG
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
* * ** *** * *
499273 TACCAAGTGTGCAACCCATGGAATTCATAACCGGTTTATGAACAACCGTATCGG
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
* * ** *
499327 CACTAAGTGTGCAACCCACACAATTCATAATAAGTTTATGAATGACCATATCAG
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
* * * *
499381 CACTAAGTGTGCAACCCA-TGAAATTCATAATAAATTTATGAATGACTTTATCGG
1 CACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACTGTATCGG
* ** * * *
499435 CACTAAGTGTGCAATCCATGGAATTCATAATAAGTTTATCAACGACCGTATCGA
1 CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
* * * * *
499489 CACTAAGTATGCAACACAAAGAATTCATAATAAAGTTTATGAATGATTGTATCGG
1 CACTAAGTGTGCAACCCACAGAATTCATAAT-AAGTTTATGAACGACTGTATCGG
* *
499544 CACTACGTGTGCACCCCA
1 CACTAAGTGTGCAACCCA
499562 TGAAACTTAT
Statistics
Matches: 370, Mismatches: 75, Indels: 11
0.81 0.16 0.02
Matches are distributed among these distances:
53 1 0.00
54 336 0.91
55 33 0.09
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGG
Found at i:499331 original size:162 final size:158
Alignment explanation
Indices: 499050--499531 Score: 595
Period size: 162 Copynumber: 3.0 Consensus size: 158
499040 GCATTTCTAT
* *
499050 GTATCAACACTAAGTGTGTAACCCACGAAATTCATAATAAGTTTATGAACAACTGTATCGGTACT
1 GTATC-ACACTAAGTGTGCAACCCAC-AAATTCATAATAAGTTTATGAACGACTGTATCGGTACT
*** * * *
499115 AAGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGATCGTATTGGCACTAAGTGTGCAAC
64 AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAAC
499180 TTACAAAATTCATAATAAGTTTATGAACGACC
129 --ACAAAATTCATAATAAGTTTATGAACGACC
* * * *
499212 GTATCGACACTAAATGTGCAACCCACATAATTCATTATAAGTTTATGAACGACTGTATCAGTACC
1 GTATC-ACACTAAGTGTGCAACCCACA-AATTCATAATAAGTTTATGAACGACTGTATCGGTACT
*** *
499277 AAGTGTGCAACCCATGGAATTCATAACCGGTTTATGAACAACCGTATCGGCACTAAGTGTGCAAC
64 AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAA-
* *
499342 CCACACAATTCATAATAAGTTTATGAATGACC
128 -CACAAAATTCATAATAAGTTTATGAACGACC
* * * * * *
499374 ATATCAGCACTAAGTGTGCAACCCATGAAATTCATAATAAATTTATGAATGACTTTATCGGCACT
1 GTATCA-CACTAAGTGTGCAACCCA-CAAATTCATAATAAGTTTATGAACGACTGTATCGGTACT
* * * *
499439 AAGTGTGCAATCCATGGAATTCATAATAAGTTTATCAACGACCGTATCGACACTAAGTATGCAAC
64 AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAAC
499504 ACAAAGAATTCATAATAAAGTTTATGAA
129 AC-AA-AATTCATAAT-AAGTTTATGAA
499532 TGATTGTATC
Statistics
Matches: 274, Mismatches: 38, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
160 3 0.01
161 3 0.01
162 255 0.93
163 12 0.04
164 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (158 bp):
GTATCACACTAAGTGTGCAACCCACAAATTCATAATAAGTTTATGAACGACTGTATCGGTACTAA
GTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACAC
AAAATTCATAATAAGTTTATGAACGACC
Found at i:500433 original size:64 final size:63
Alignment explanation
Indices: 500358--500507 Score: 214
Period size: 64 Copynumber: 2.4 Consensus size: 63
500348 TAAGAGTGAT
* * * *
500358 TCGATGTATAAAATGCATTCTATGTTTT-A-AACAAGCTTGAGTGCATCGATGCATGGTCTGTGC
1 TCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAGTGCATCGATGCATGGT-AGTGC
500421 A
63 A
500422 TCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGTAGTGCA
1 TCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGTAGTGCA
*
500485 TTGATGCATAAAATGCATTCGAT
1 TCGATGCATAAAATGCATTCGAT
500508 ATGGTGAGTG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
63 27 0.34
64 47 0.59
65 3 0.04
66 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (63 bp):
TCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGTAGTGCA
Found at i:503221 original size:23 final size:22
Alignment explanation
Indices: 503191--503277 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
503181 GCATGGACTT
503191 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
503213 CGTGCATCGGTGCATC-TTC-ATG
1 -GTGCATCGATGCA-CATTCAAGG
* *
503235 ATGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
* *
503258 GATTCATCGATGCACTTTCA
1 G-TGCATCGATGCACATTCA
503278 TAGTGTATCG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 2 0.04
23 18 0.37
24 15 0.31
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:503250 original size:44 final size:45
Alignment explanation
Indices: 503195--503292 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
503185 GGACTTGTGC
*
503195 ATCGATGCACATTC-AAGGCG-TGCATCGGTGCA-TCTTCAT-GATGT
1 ATCGATGCACATTCAAAGG-GATGCATCGATGCACT-TTCATAG-TGT
*
503239 ATCGATGCACATTCAAAGGGATTCATCGATGCACTTTCATAGTGT
1 ATCGATGCACATTCAAAGGGATGCATCGATGCACTTTCATAGTGT
503284 ATCGATGCA
1 ATCGATGCA
503293 TGCACAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
44 15 0.31
45 31 0.65
46 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (45 bp):
ATCGATGCACATTCAAAGGGATGCATCGATGCACTTTCATAGTGT
Found at i:503253 original size:21 final size:21
Alignment explanation
Indices: 503229--503292 Score: 51
Period size: 24 Copynumber: 2.9 Consensus size: 21
503219 TCGGTGCATC
503229 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* *
503250 TTCAAAGGGAT-TCATCGATGCACT
1 TTC--A-TGATGT-ATCGATGCACA
503274 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
503293 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 2 0.06
23 2 0.06
24 16 0.47
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:509122 original size:64 final size:63
Alignment explanation
Indices: 509070--509225 Score: 208
Period size: 64 Copynumber: 2.5 Consensus size: 63
509060 GTGCACTAAG
* *
509070 AGTGCACCAATGCATAAAATGCATTCAATGCTTT-A-AACAAGCATGAGTGCATCGATGCATAGT
1 AGTGCATCGATGCATAAAATGCATTCAATGCTTTCATAA-AA-CATGAGTGCATCGATGCATAGT
* * * * *
509133 CTGTGCATCGATACATAAAATGCATTCAATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 -AGTGCATCGATGCATAAAATGCATTCAATGCTTTCATAAAACATGAGTGCATCGATGCATAGT
509197 AGTGCATCGATGCATAAAATGCATTCAAT
1 AGTGCATCGATGCATAAAATGCATTCAAT
509226 ATAGTGAGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
63 27 0.33
64 49 0.60
65 3 0.04
66 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCAATGCTTTCATAAAACATGAGTGCATCGATGCATAGT
Found at i:510904 original size:58 final size:57
Alignment explanation
Indices: 510835--511272 Score: 302
Period size: 58 Copynumber: 7.8 Consensus size: 57
510825 TTTCCCATAT
* * *
510835 GGAAATTCATACATTTAGTATGAATCTCTTAACTATTTGCACACAAAATGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAACT-TTTGCACACGAAGTGCCCAATAC
* *
510893 GGATATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAAAAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAATAC
*
510950 -GAAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAATAC
* * * *** * * * ** *
511006 GAAAATTCATACA-TT--TA--ACT-TTTTCACAC-GAAGTAC-CCAA-TACGAAAATTC
1 GGAAATTCATACACTTAGTATGAATCTCTT-A-ACTTTTGCACACGAAGTGC-CCAATAC
** * * * * * *
511057 ATACACTT-AGTATGAATT--TTTTAA---C---ATTTTTGCACACGAAGTGCCCAATAC
1 GGA-AATTCA-TA-CACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAATAC
* * * * ** *
511108 AGAAATTAATACACTTAGTATAAATTTCTTAACATTTTTTACACGAAGTGCCTAATAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAAC-TTTTGCACACGAAGTGCCCAATAC
* * *
511166 AGAAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCATTAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAATAC
* * *
511223 GAAAATTCATATACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGT
1 GGAAATTCATACACTTAGTATGAATCTCTTAAC--TTTTGCACACGAAGT
511273 ACCATTTGGT
Statistics
Matches: 299, Mismatches: 56, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
49 4 0.01
50 10 0.03
51 26 0.09
52 13 0.04
53 3 0.01
54 6 0.02
56 56 0.19
57 82 0.27
58 84 0.28
59 15 0.05
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (57 bp):
GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAATAC
Found at i:511025 original size:43 final size:43
Alignment explanation
Indices: 510977--511061 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
510967 TATGAATTTC
*
510977 TTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACAT
1 TTAACTTTTGCACACGAAGTACCCAATACGAAAATTCATACAT
*
511020 TTAACTTTTTCACACGAAGTACCCAATACGAAAATTCATACA
1 TTAACTTTTGCACACGAAGTACCCAATACGAAAATTCATACA
511062 CTTAGTATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (43 bp):
TTAACTTTTGCACACGAAGTACCCAATACGAAAATTCATACAT
Found at i:511104 original size:59 final size:59
Alignment explanation
Indices: 511020--511272 Score: 367
Period size: 59 Copynumber: 4.4 Consensus size: 59
511010 ATTCATACAT
* *
511020 TTAAC-TTTTT-CACACGAAGTACCCAATAC-GAAAATTCATACACTTAGTATGAATTTT
1 TTAACATTTTTGCACACGAAGTGCCCAATACAG-AAATTCATACACTTAGTATGAATTTC
* *
511077 TTAACATTTTTGCACACGAAGTGCCCAATACAGAAATTAATACACTTAGTATAAATTTC
1 TTAACATTTTTGCACACGAAGTGCCCAATACAGAAATTCATACACTTAGTATGAATTTC
* *
511136 TTAACATTTTT-TACACGAAGTGCCTAATACAGAAATTCATACACTTAGTATGAATTTC
1 TTAACATTTTTGCACACGAAGTGCCCAATACAGAAATTCATACACTTAGTATGAATTTC
* *
511194 TTAAC--TTTTGCACACGAAGTGCCCATTAC-GAAAATTCATATACTTAGTATGAATTTC
1 TTAACATTTTTGCACACGAAGTGCCCAATACAG-AAATTCATACACTTAGTATGAATTTC
511251 TTAACATTTTTGCACACGAAGT
1 TTAACATTTTTGCACACGAAGT
511273 ACCATTTGGT
Statistics
Matches: 177, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
56 5 0.03
57 51 0.29
58 53 0.30
59 67 0.38
60 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (59 bp):
TTAACATTTTTGCACACGAAGTGCCCAATACAGAAATTCATACACTTAGTATGAATTTC
Found at i:511120 original size:102 final size:99
Alignment explanation
Indices: 510921--511120 Score: 312
Period size: 102 Copynumber: 2.0 Consensus size: 99
510911 TATGAATCTC
*
510921 TTAACTTTTGCACACGAAGTGCCCAAAACGAAATTCATACACTTAGTATGAATTTCTTAACTTTT
1 TTAACTTTTGCACACGAAGTACCCAAAACGAAATTCATACACTTAGTATGAATTTCTTAACTTTT
*
510986 GCACACGAAGTGCCCAATACGAAAATTCATACAT
66 GCACACGAAGTGCCCAATACGAAAATTAATACAT
* * *
511020 TTAACTTTTTCACACGAAGTACCCAATACGAAAATTCATACACTTAGTATGAATTTTTTAACATT
1 TTAACTTTTGCACACGAAGTACCCAAAACG-AAATTCATACACTTAGTATGAATTTCTTAAC--T
511085 TTTGCACACGAAGTGCCCAATAC-AGAAATTAATACA
63 TTTGCACACGAAGTGCCCAATACGA-AAATTAATACA
511121 CTTAGTATAA
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
99 27 0.29
100 30 0.33
101 1 0.01
102 34 0.37
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (99 bp):
TTAACTTTTGCACACGAAGTACCCAAAACGAAATTCATACACTTAGTATGAATTTCTTAACTTTT
GCACACGAAGTGCCCAATACGAAAATTAATACAT
Found at i:511209 original size:217 final size:214
Alignment explanation
Indices: 510837--511233 Score: 623
Period size: 217 Copynumber: 1.8 Consensus size: 214
510827 TCCCATATGG
* * * *
510837 AAATTCATACATTTAGTATGAATCTCTTAACTATTTGCACACAAAATGCCCAATACGGATATTCA
1 AAATTCATACACTTAGTATGAATCTCTTAACTATTTGCACACAAAATGCCCAATACAGAAATTAA
*
510902 TACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCCCAAAACGAAATTCATACACTTAG
66 TACACTTAGTATAAATCTCTTAACTTTTGCACACGAAGTGCCCAAAACGAAATTCATACACTTAG
510967 TATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACATTTAACTTTTTCA
131 TATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACATTTAACTTTTTCA
511032 CACGAAGTACCCAATACGA
196 CACGAAGTACCCAATACGA
* * * * *
511051 AAATTCATACACTTAGTATGAATTTTTTAACATTTTTGCACACGAAGTGCCCAATACAGAAATTA
1 AAATTCATACACTTAGTATGAATCTCTTAAC-TATTTGCACACAAAATGCCCAATACAGAAATTA
* ** * *
511116 ATACACTTAGTATAAATTTCTTAACATTTTTTACACGAAGTGCCTAATACAGAAATTCATACACT
65 ATACACTTAGTATAAATCTCTTAAC-TTTTGCACACGAAGTGCCCAAAAC-GAAATTCATACACT
*
511181 TAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCATTACGAAAATTCATA
128 TAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATA
511234 TACTTAGTAT
Statistics
Matches: 164, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
214 28 0.17
215 50 0.30
216 20 0.12
217 66 0.40
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (214 bp):
AAATTCATACACTTAGTATGAATCTCTTAACTATTTGCACACAAAATGCCCAATACAGAAATTAA
TACACTTAGTATAAATCTCTTAACTTTTGCACACGAAGTGCCCAAAACGAAATTCATACACTTAG
TATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACATTTAACTTTTTCA
CACGAAGTACCCAATACGA
Found at i:511627 original size:20 final size:21
Alignment explanation
Indices: 511598--511649 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
511588 TGGCTCTTAA
*
511598 GTATCAATAC-CCCTACCATG
1 GTATCGATACACCCTACCATG
*
511618 GTATCGATACTACCCTACTATG
1 GTATCGATAC-ACCCTACCATG
*
511640 GTATTGATAC
1 GTATCGATAC
511650 TCCTTTCGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
22 18 0.67
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (21 bp):
GTATCGATACACCCTACCATG
Found at i:511640 original size:22 final size:22
Alignment explanation
Indices: 511608--511650 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
511598 GTATCAATAC
511608 CCCTACCATGGTATCGATACTA
1 CCCTACCATGGTATCGATACTA
* *
511630 CCCTACTATGGTATTGATACT
1 CCCTACCATGGTATCGATACT
511651 CCTTTCGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (22 bp):
CCCTACCATGGTATCGATACTA
Found at i:511715 original size:20 final size:20
Alignment explanation
Indices: 511690--511745 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
511680 CGATGTGGCC
*
511690 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCATACCA
*
511710 TGGTATCGATACTACCATACTA
1 TGGTATCGATAC--CCATACCA
*
511732 TGGTACCGATACCC
1 TGGTATCGATACCC
511746 CTTTCCAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
TGGTATCGATACCCATACCA
Found at i:511804 original size:95 final size:94
Alignment explanation
Indices: 511599--511820 Score: 318
Period size: 95 Copynumber: 2.4 Consensus size: 94
511589 GGCTCTTAAG
* * * ** * **
511599 TATCAATACCCCTACCATGGTATCGATACTACCCTACTATGGTATTGATACTCCTTTCGGTATCG
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTCAATATCG
* *
511664 ATACCAATTTTAGATTCGATGTGGCCTGG
66 ATACCAATTTTAGATTCAATGTGGCCTGA
511693 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTCCAATATC
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTT-CAATATC
* * *
511758 GATGCCAATTTTAGATTTAATGTTGCCTGA
65 GATACCAATTTTAGATTCAATGTGGCCTGA
511788 TATCGATACCCTTACCATGGTATCGATACTACC
1 TATCGATACCCTTACCATGGTATCGATACTACC
511821 TCGTCGGTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 51 0.45
95 63 0.55
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (94 bp):
TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTTCAATATCG
ATACCAATTTTAGATTCAATGTGGCCTGA
Found at i:517447 original size:103 final size:103
Alignment explanation
Indices: 517222--517439 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
517212 GTCGAGGGTC
517222 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
517287 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
517325 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
517390 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
517428 TATGTGGTCCTT
1 TATGTGGTCCTT
517440 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:517489 original size:23 final size:23
Alignment explanation
Indices: 517456--517518 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
517446 ATTATTATAT
*
517456 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
517479 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
517502 GGCACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
517519 ATATGAGCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:522039 original size:64 final size:64
Alignment explanation
Indices: 521970--522126 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
521960 TTGAAGGTGT
*** *
521970 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATGCATATTA-T
522032 GC
63 GC
* * * * *
522034 ATCGATTCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCATATTATGC
*
522098 ACCGATGCACAGGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
522127 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
63 6 0.08
64 61 0.81
65 8 0.11
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCATATTATGC
Found at i:523079 original size:103 final size:103
Alignment explanation
Indices: 522854--523071 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
522844 GTCGAGGGTC
522854 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
522919 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
522957 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
523022 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
523060 TATGTGGTCCTT
1 TATGTGGTCCTT
523072 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:523122 original size:23 final size:23
Alignment explanation
Indices: 523087--523150 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
523077 CATTATTATA
523087 TGGCACTAC-GGTGCAATTCTACG
1 TGGCACT-CTGGTGCAATTCTACG
*
523110 TGGCACTCTGGTGTAATTCTACG
1 TGGCACTCTGGTGCAATTCTACG
523133 TGGCACT-TCGGTGCAATT
1 TGGCACTCT-GGTGCAATT
523151 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTCTACG
Found at i:530078 original size:33 final size:33
Alignment explanation
Indices: 530036--530106 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
530026 ATCAGAGTAC
* * *
530036 ATTTTTGTAAGCGCTAGAAGCTATTTTACAATG
1 ATTTCTGTAAGCACTAGAAACTATTTTACAATG
530069 ATTTCTGTAAGCACTAGAAACTATTTTACAATG
1 ATTTCTGTAAGCACTAGAAACTATTTTACAATG
530102 ATTTC
1 ATTTC
530107 AGGCTTCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (33 bp):
ATTTCTGTAAGCACTAGAAACTATTTTACAATG
Done.