Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold268
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: 336603
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:204534 original size:91 final size:91
Alignment explanation
Indices: 204379--204554 Score: 316
Period size: 91 Copynumber: 1.9 Consensus size: 91
204369 TTTTAACTAG
204379 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
204444 TGAAGAATGTATCGATACATTCATAC
66 TGAAGAATGTATCGATACATTCATAC
* * * *
204470 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAGAAGATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
204535 TGAAGAATGTATCGATACAT
66 TGAAGAATGTATCGATACAT
204555 CTAGGGTACT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
TGAAGAATGTATCGATACATTCATAC
Found at i:207078 original size:29 final size:30
Alignment explanation
Indices: 207019--207082 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
207009 TATACATTCT
*
207019 TTTTATTTATGTATTTATATTATATTCTTA
1 TTTTATTTATATATTTATATTATATTCTTA
* *
207049 TTTTATATTATAT-TTTA-ATTATTTTTTTA
1 TTTTAT-TTATATATTTATATTATATTCTTA
207078 TTTTA
1 TTTTA
207083 CGCTTAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.50
30 10 0.33
31 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTTATTTATATATTTATATTATATTCTTA
Found at i:207534 original size:62 final size:63
Alignment explanation
Indices: 207440--207562 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
207430 TAATATGATT
* **
207440 CCTTCTTTTAGTTTAACCAAAAGATT-TTAAAAAAATCTTTAAACTATTTCACCTTTTTTATG
1 CCTTCTTTTAGTTTAAACAAAAGATTAAAAAAAAAATCTTTAAACTATTTCACCTTTTTTATG
* *
207502 CCTTCTTTTAG-TTAAACAAAATATTAAAAAAAAAAATCTTTAAACTATTTCATCTTTTTTA
1 CCTTCTTTTAGTTTAAACAAAAGATT-AAAAAAAAAATCTTTAAACTATTTCACCTTTTTTA
207563 AGTTCTTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 12 0.22
62 11 0.20
63 31 0.57
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (63 bp):
CCTTCTTTTAGTTTAAACAAAAGATTAAAAAAAAAATCTTTAAACTATTTCACCTTTTTTATG
Found at i:209394 original size:5 final size:6
Alignment explanation
Indices: 209376--209400 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
209366 TTCACAGGGC
209376 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
209401 CAGGGTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:210474 original size:42 final size:39
Alignment explanation
Indices: 210337--210562 Score: 233
Period size: 42 Copynumber: 5.7 Consensus size: 39
210327 ACCTAGAAGA
* * *
210337 ATCCCTCTTCTGATCATCTTTCTCCCACCTAGAATATTC
1 ATCCCTCTTCCGATCATCTTTATCCCGCCTAGAATATTC
* * *
210376 GTCCCTCTTCCTATCATC-TCA-CTCCGCCTAGAATATTC
1 ATCCCTCTTCCGATCATCTTTATC-CCGCCTAGAATATTC
* * * *
210414 GTCCCTCTTCTGACCATCTTTATCCCGCCAAGAATATTCATC
1 ATCCCTCTTCCGATCATCTTTATCCCGCCTAGAATA-T--TC
210456 ATCCCTCTTCCGATCATCTTTA-CCCTGCCTAGAATATTCATC
1 ATCCCTCTTCCGATCATCTTTATCCC-GCCTAGAATA-T--TC
* *
210498 ATCCCTCTTCCAATCATCTTTATCCTGCCTAGAATATTC
1 ATCCCTCTTCCGATCATCTTTATCCCGCCTAGAATATTC
* *
210537 ATCCCTCTTCCGATAATCTTTCTCCC
1 ATCCCTCTTCCGATCATCTTTATCCC
210563 TAAAAGCTCT
Statistics
Matches: 158, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.01
38 30 0.19
39 52 0.33
40 2 0.01
41 4 0.03
42 67 0.42
43 2 0.01
ACGTcount: A:0.20, C:0.37, G:0.07, T:0.36
Consensus pattern (39 bp):
ATCCCTCTTCCGATCATCTTTATCCCGCCTAGAATATTC
Found at i:212932 original size:11 final size:11
Alignment explanation
Indices: 212903--212936 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
212893 TAAAAATATT
212903 TATAAATTAAA
1 TATAAATTAAA
212914 T-T-AATTAAA
1 TATAAATTAAA
212923 TATAAATTAAA
1 TATAAATTAAA
212934 TAT
1 TAT
212937 TATTTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.38
10 2 0.10
11 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAAATTAAA
Found at i:212955 original size:21 final size:20
Alignment explanation
Indices: 212929--212968 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
212919 TAAATATAAA
212929 TTAAATATT-ATTTATATTTAT
1 TTAAAT-TTAATTTA-ATTTAT
212950 TTAAATTTAATTTAATTTA
1 TTAAATTTAATTTAATTTA
212969 AAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAAATTTAATTTAATTTAT
Found at i:212964 original size:11 final size:11
Alignment explanation
Indices: 212909--212969 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
212899 TATTTATAAA
212909 TTAAA-TTAA-
1 TTAAATTTAAT
* *
212918 TTAAATATAAA
1 TTAAATTTAAT
212929 TTAAATATT-AT
1 TTAAAT-TTAAT
*
212940 TTATATTT-AT
1 TTAAATTTAAT
212950 TTAAATTTAAT
1 TTAAATTTAAT
212961 TT-AATTTAA
1 TTAAATTTAA
212970 AATATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 5 0.12
10 21 0.49
11 16 0.37
12 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:212990 original size:41 final size:40
Alignment explanation
Indices: 212909--213033 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 40
212899 TATTTATAAA
* *
212909 TTAAATTAATTA-A-ATATAAATTAAATATTATTTATATTTAT
1 TTAAATTAATTATACTTATAAA-TAAATA--ATTTAAATTTAT
*
212950 TTAAATTTAATT-TAATT-TAAAATATAA-AATTTAAATTTTAT
1 TTAAA-TTAATTATACTTAT-AAATA-AATAATTTAAA-TTTAT
212991 TTAAATTAATTATACTTATAAATAAATAATTTAAATTTAT
1 TTAAATTAATTATACTTATAAATAAATAATTTAAATTTAT
213031 TTA
1 TTA
213034 GGTAAAATCA
Statistics
Matches: 72, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
40 22 0.31
41 32 0.44
42 12 0.17
43 6 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
TTAAATTAATTATACTTATAAATAAATAATTTAAATTTAT
Found at i:212991 original size:51 final size:48
Alignment explanation
Indices: 212899--212993 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 48
212889 ATATTAAAAA
212899 TATTTATAAATTAAATTAATTAAATATAAATTAAATATTATTTATATT
1 TATTTATAAATTAAATTAATTAAATATAAATTAAATATTATTTATATT
* * *
212947 TATTTA-AATTTAATTTAATTTAAAATATAAAATTTAAATTTTATTTA
1 TATTTATAAATTAAATTAA-TT-AAATAT-AAA-TTAAATATTATTTA
212994 AATTAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 10 0.25
48 8 0.20
49 6 0.15
50 3 0.08
51 13 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (48 bp):
TATTTATAAATTAAATTAATTAAATATAAATTAAATATTATTTATATT
Found at i:213198 original size:20 final size:20
Alignment explanation
Indices: 213170--213222 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
213160 TAATATAATA
213170 TTATATTTTTATATGATATAT
1 TTAT-TTTTTATATGATATAT
*
213191 TTATTTTTTATATGATATGT
1 TTATTTTTTATATGATATAT
213211 TTA-TTTTTATAT
1 TTATTTTTTATAT
213223 AATAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (20 bp):
TTATTTTTTATATGATATAT
Found at i:213276 original size:28 final size:26
Alignment explanation
Indices: 213223--213282 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
213213 ATTTTTATAT
*
213223 AATAAAAATTATATAATATATATAAA
1 AATAAAAAATATATAATATATATAAA
* * *
213249 TATAAAAAATATGTATTATATAATTAAA
1 AATAAAAAATATATAATATAT-A-TAAA
213277 AATAAA
1 AATAAA
213283 TTAGATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 17 0.63
27 1 0.04
28 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AATAAAAAATATATAATATATATAAA
Found at i:221345 original size:59 final size:58
Alignment explanation
Indices: 221276--221515 Score: 234
Period size: 59 Copynumber: 4.1 Consensus size: 58
221266 TAAGCTAGAG
* *
221276 AAAATAGCTAAAGTGACCCTAAATTATGTAAAATAATCTAAATAGCTCTAAAATGCATA
1 AAAATTGCTAAAGTGACCCTAAATTATGTAAAATAACCTAAAT-GCTCTAAAATGCATA
*** * * * * *
221335 AAAATTGCTAAAAAAACCCCTAGATTATATAAAATAACCTAAATGGGTCTAAAATG-GTG
1 AAAATTGCTAAAGTGA-CCCTAAATTATGTAAAATAACCTAAAT-GCTCTAAAATGCATA
* * *
221394 AAATTTGCTAATA-TGACCTTAAATTATGTAAAATAACTTAAATCGC-CTTAAAATGCATA
1 AAAATTGCTAA-AGTGACCCTAAATTATGTAAAATAACCTAAAT-GCTC-TAAAATGCATA
* * * * *
221453 TAAATTACAAAAGTGACCCTAAATTATGTAAAATTACCTAAATGATCTAAAATGCATA
1 AAAATTGCTAAAGTGACCCTAAATTATGTAAAATAACCTAAATGCTCTAAAATGCATA
*
221511 GAAAT
1 AAAAT
221516 CATTAAAATG
Statistics
Matches: 144, Mismatches: 31, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
57 1 0.01
58 48 0.33
59 60 0.42
60 35 0.24
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.29
Consensus pattern (58 bp):
AAAATTGCTAAAGTGACCCTAAATTATGTAAAATAACCTAAATGCTCTAAAATGCATA
Found at i:221515 original size:118 final size:118
Alignment explanation
Indices: 221289--221515 Score: 275
Period size: 118 Copynumber: 1.9 Consensus size: 118
221279 ATAGCTAAAG
*
221289 TGACCCTAAATTATGTAAAATAATCTAAATAGCTCTAAAATGCATAAAAATTGCTAAAAAAACCC
1 TGACCCTAAATTATGTAAAATAATCTAAATAGCTCTAAAATGCATAAAAATTACTAAAAAAACCC
* * *
221354 CTAGATTATATAAAATAACCTAAATGGGTCTAAAATGGTGAAATTTGCTAATA
66 CTAAATTATATAAAATAACCTAAATGGATCTAAAATGATGAAATTTGCTAATA
* * * **
221407 TGACCTTAAATTATGTAAAATAA-CTTAAATCGC-CTTAAAATGCATATAAATTAC-AAAAGTGA
1 TGACCCTAAATTATGTAAAATAATC-TAAATAGCTC-TAAAATGCATAAAAATTACTAAAA-AAA
* *
221469 -CCCTAAATTATGTAAAATTACCTAAAT-GATCTAAAATGCATAGAAAT
63 CCCCTAAATTATATAAAATAACCTAAATGGATCTAAAATG-AT-GAAAT
221516 CATTAAAATG
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
116 10 0.11
117 31 0.33
118 52 0.56
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (118 bp):
TGACCCTAAATTATGTAAAATAATCTAAATAGCTCTAAAATGCATAAAAATTACTAAAAAAACCC
CTAAATTATATAAAATAACCTAAATGGATCTAAAATGATGAAATTTGCTAATA
Found at i:222934 original size:23 final size:23
Alignment explanation
Indices: 222901--222945 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
222891 TGATTTTCAT
222901 AAAAAAGTATAAATAAAAAAATAG
1 AAAAAAGTATAAA-AAAAAAATAG
*
222925 AAAAAA-TATAAAAAAATAATA
1 AAAAAAGTATAAAAAAAAAATA
222946 ATAATAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 6 0.30
24 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAAAAGTATAAAAAAAAAATAG
Found at i:222951 original size:19 final size:19
Alignment explanation
Indices: 222909--222951 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
222899 ATAAAAAAGT
222909 ATAA-ATAAAAAAATAGAA
1 ATAATATAAAAAAATAGAA
*
222927 AAAATATAAAAAAATA-ATA
1 ATAATATAAAAAAATAGA-A
222946 ATAATA
1 ATAATA
222952 AGTGTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
ATAATATAAAAAAATAGAA
Found at i:223547 original size:25 final size:25
Alignment explanation
Indices: 223513--223562 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
223503 ACAAGTTTGG
223513 AATGATTTTCCCAATTTAATGAAAC
1 AATGATTTTCCCAATTTAATGAAAC
223538 AATGATTTTCCCAATTTAATGAAAC
1 AATGATTTTCCCAATTTAATGAAAC
223563 CATTTACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (25 bp):
AATGATTTTCCCAATTTAATGAAAC
Found at i:230147 original size:30 final size:29
Alignment explanation
Indices: 230106--230188 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 29
230096 ATTGCACTTT
*
230106 TCTTTTAAAGTCCACAACTCTGTGGTACC
1 TCTTTTAAAGTCCACAACTCAGTGGTACC
* *
230135 TCTTTTCAAAGTCCATAACTCAGTGGTAAC
1 TCTTTT-AAAGTCCACAACTCAGTGGTACC
* * *
230165 -CTTCTAAAGCCCACAAGTCAGTGG
1 TCTTTTAAAGTCCACAACTCAGTGG
230189 CATCCCTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
28 16 0.35
29 10 0.22
30 20 0.43
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (29 bp):
TCTTTTAAAGTCCACAACTCAGTGGTACC
Found at i:230185 original size:28 final size:28
Alignment explanation
Indices: 230154--230294 Score: 183
Period size: 28 Copynumber: 5.0 Consensus size: 28
230144 AGTCCATAAC
* *
230154 TCAGTGGTAACCTTCTAAAGCCCACAAG
1 TCAGTGGCAACCTTCCAAAGCCCACAAG
* *
230182 TCAGTGGCATCCCTCCAAAGCCCACAAG
1 TCAGTGGCAACCTTCCAAAGCCCACAAG
* *
230210 TAAGTGGCAACCTTCCAAAGCCCATAAG
1 TCAGTGGCAACCTTCCAAAGCCCACAAG
* * *
230238 TCAGTAGCATCCTTCCAAAGCCTACAAG
1 TCAGTGGCAACCTTCCAAAGCCCACAAG
* *
230266 TCAGTGGCACCCTTTCAAAGCCCACAAG
1 TCAGTGGCAACCTTCCAAAGCCCACAAG
230294 T
1 T
230295 TGGTAGCACC
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 96 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (28 bp):
TCAGTGGCAACCTTCCAAAGCCCACAAG
Found at i:230285 original size:84 final size:84
Alignment explanation
Indices: 230141--230294 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 84
230131 TACCTCTTTT
* * * *
230141 CAAAGTCCATAACTCAGTGGTAACCTTCTAAAGCCCACAAGTCAGTGGCATCCCTCCAAAGCCCA
1 CAAAGCCCATAACTCAGTAGCAACCTTCCAAAGCCCACAAGTCAGTGGCATCCCTCCAAAGCCCA
230206 CAAGTAAGTGGCAACCTTC
66 CAAGTAAGTGGCAACCTTC
* * * *
230225 CAAAGCCCATAAGTCAGTAGCATCCTTCCAAAGCCTACAAGTCAGTGGCA-CCCTTTCAAAGCCC
1 CAAAGCCCATAACTCAGTAGCAACCTTCCAAAGCCCACAAGTCAGTGGCATCCC-TCCAAAGCCC
230289 ACAAGT
65 ACAAGT
230295 TGGTAGCACC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 3 0.05
84 58 0.95
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (84 bp):
CAAAGCCCATAACTCAGTAGCAACCTTCCAAAGCCCACAAGTCAGTGGCATCCCTCCAAAGCCCA
CAAGTAAGTGGCAACCTTC
Found at i:230303 original size:28 final size:28
Alignment explanation
Indices: 230170--230419 Score: 169
Period size: 28 Copynumber: 8.6 Consensus size: 28
230160 GTAACCTTCT
** *
230170 AAAGCCCACAAGTCAGTGGCATCCC-TCC
1 AAAGCCCACAAGTTGGTGGCA-CCCTTTC
** * *
230198 AAAGCCCACAAGTAAGTGGCAACCTTCC
1 AAAGCCCACAAGTTGGTGGCACCCTTTC
* ** * * *
230226 AAAGCCCATAAGTCAGTAGCATCCTTCC
1 AAAGCCCACAAGTTGGTGGCACCCTTTC
* **
230254 AAAGCCTACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTTGGTGGCACCCTTTC
* *
230282 AAAGCCCACAAGTTGGTAGCACCCTAGTC
1 AAAGCCCACAAGTTGGTGGCACCCT-TTC
* * *
230311 AAAGCCCGCAAGTTGGCGGCACCCTAGTC
1 AAAGCCCACAAGTTGGTGGCACCCT-TTC
* * *
230340 AAAGCTCGCACGAGTTGGTGTCACCCTAGTC
1 AAAGC-C-CACAAGTTGGTGGCACCCT-TTC
*
230371 AAAGCCCGCATGAGTTGGTGGCACCCTTGTC
1 AAAGCCCACA--AGTTGGTGGCACCCTT-TC
230402 AAAGCCTGCACAAGTTGG
1 AAAGCC--CACAAGTTGG
230420 CAGCACTTGA
Statistics
Matches: 185, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
27 2 0.01
28 91 0.49
29 35 0.19
30 2 0.01
31 52 0.28
33 3 0.02
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (28 bp):
AAAGCCCACAAGTTGGTGGCACCCTTTC
Found at i:230448 original size:93 final size:90
Alignment explanation
Indices: 230280--230487 Score: 240
Period size: 93 Copynumber: 2.3 Consensus size: 90
230270 TGGCACCCTT
* *
230280 TCAAAGCCCACA-AGTTGGTAGCACCCTAGTCAAAGCCCGCAAGTTGGCGGCACCCTAGTCAAAG
1 TCAAAGCCCACAGAGTTGGTAGCACCCTAGTCAAAGCCCACAAGTTGGCAGCACCCTAGTCAAAG
** * * *
230344 CTCGCACGAGTTGGTGTCACCCTAG
66 CTCGCACGAGTTGACGACACCCCAA
* * * * *
230369 TCAAAGCCCGCATGAGTTGGTGGCACCCTTGTCAAAGCCTGCACAAGTTGGCAGCA-CTTGAGTT
1 TCAAAGCCCACA-GAGTTGGTAGCACCCTAGTCAAAGCC--CACAAGTTGGCAGCACCCT-AGTC
*
230433 AAAGCTCGCATGAGTTGACGACACCCCAA
62 AAAGCTCGCACGAGTTGACGACACCCCAA
230462 TCAAAGCCCACACGAGTTGGTAGCAC
1 TCAAAGCCCACA-GAGTTGGTAGCAC
230488 TTGAGTCAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
89 11 0.11
91 23 0.23
92 2 0.02
93 62 0.63
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.19
Consensus pattern (90 bp):
TCAAAGCCCACAGAGTTGGTAGCACCCTAGTCAAAGCCCACAAGTTGGCAGCACCCTAGTCAAAG
CTCGCACGAGTTGACGACACCCCAA
Found at i:230497 original size:31 final size:31
Alignment explanation
Indices: 230272--230592 Score: 193
Period size: 31 Copynumber: 10.5 Consensus size: 31
230262 CAAGTCAGTG
* *
230272 GCACCCT-TTCAAAG-CC-CACAAGTTGGTA
1 GCACCCTAGTCAAAGCCCGCACGAGTTGGTA
**
230300 GCACCCTAGTCAAAGCCCGCA--AGTTGGCG
1 GCACCCTAGTCAAAGCCCGCACGAGTTGGTA
*
230329 GCACCCTAGTCAAAGCTCGCACGAGTTGGT-
1 GCACCCTAGTCAAAGCCCGCACGAGTTGGTA
* *
230359 GTCACCCTAGTCAAAGCCCGCATGAGTTGGTG
1 G-CACCCTAGTCAAAGCCCGCACGAGTTGGTA
* * * *
230391 GCACCCTTGTCAAAGCCTGCACAAGTTGGCA
1 GCACCCTAGTCAAAGCCCGCACGAGTTGGTA
* * * *
230422 GCA-CTTGAGTTAAAGCTCGCATGAGTT-G-A
1 GCACCCT-AGTCAAAGCCCGCACGAGTTGGTA
* * *
230451 CGACACCCCAATCAAAGCCCACACGAGTTGGTA
1 -G-CACCCTAGTCAAAGCCCGCACGAGTTGGTA
* * ** ** *
230484 GCA-CTTGAGTCAAAACCCAAAAAAGTTGGTG
1 GCACCCT-AGTCAAAGCCCGCACGAGTTGGTA
* * *
230515 GCACCCTTA-TCAAAGCCCGCATGAGTGGGCA
1 GCACCC-TAGTCAAAGCCCGCACGAGTTGGTA
* *
230546 GCACCC-AGTCAAAGCCCACTCGAGTTAGCG-A
1 GCACCCTAGTCAAAGCCCGCACGAGTT-G-GTA
*
230577 -TACCCTAGTCAAAGCC
1 GCACCCTAGTCAAAGCC
230593 TACACAAGAT
Statistics
Matches: 224, Mismatches: 49, Indels: 37
0.72 0.16 0.12
Matches are distributed among these distances:
28 7 0.03
29 34 0.15
30 26 0.12
31 148 0.66
32 7 0.03
33 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (31 bp):
GCACCCTAGTCAAAGCCCGCACGAGTTGGTA
Found at i:231486 original size:20 final size:20
Alignment explanation
Indices: 231461--231512 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
231451 TACAAGCCAA
**
231461 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
231481 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
231500 TGTATCGATACAA
1 TGTATCGATACAA
231513 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:232253 original size:21 final size:21
Alignment explanation
Indices: 232212--232255 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
232202 CTCCTCTTTA
* *
232212 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
232233 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
232254 TC
1 TC
232256 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:233522 original size:21 final size:20
Alignment explanation
Indices: 233493--233531 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
233483 AACTAGTGTG
*
233493 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
233514 GGGAGTGCCGGTCGCGAC
1 GGGACTGCCGGTCGCGAC
233532 TTGGTGGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.31, G:0.44, T:0.15
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:233985 original size:13 final size:13
Alignment explanation
Indices: 233967--234005 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
233957 ATAATCCCCC
*
233967 TGTATCGATACAG
1 TGTATCGATACAA
233980 TGTATCGATACAA
1 TGTATCGATACAA
233993 TGTATCGATACAA
1 TGTATCGATACAA
234006 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234242 original size:12 final size:12
Alignment explanation
Indices: 234225--234250 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
234215 ACAAAATTAC
234225 AAAATTTAATCA
1 AAAATTTAATCA
234237 AAAATTTAATCA
1 AAAATTTAATCA
234249 AA
1 AA
234251 TAAAACATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTTAATCA
Found at i:236121 original size:15 final size:15
Alignment explanation
Indices: 236101--236131 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
236091 ATTTCGTTTA
*
236101 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
236116 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
236131 G
1 G
236132 GACGTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:237964 original size:21 final size:21
Alignment explanation
Indices: 237935--237979 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
237925 AAGTTTTTAT
*
237935 TTTTCTTAG-CTAACTCATTA
1 TTTTCTTAGCCAAACTCATTA
*
237955 TTTTCATTAGCCAAATTCATTA
1 TTTTC-TTAGCCAAACTCATTA
237977 TTT
1 TTT
237980 CAACTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCTTAGCCAAACTCATTA
Found at i:240219 original size:20 final size:20
Alignment explanation
Indices: 240190--240241 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
240180 TACAAGCCAA
* **
240190 TGTATAGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
240210 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
240229 TGTATCGATACAA
1 TGTATCGATACAA
240242 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:240728 original size:32 final size:32
Alignment explanation
Indices: 240688--240982 Score: 181
Period size: 32 Copynumber: 9.1 Consensus size: 32
240678 TTTTTTTTTC
*
240688 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCTT
* * *
240720 TTTCAAAGCCCACATAAGTTGGTGGCATCCTTTT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC--TT
* * * *
240754 TTTCAAAGCCCACATAAGTTGGCGGCAACC-C
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCTT
* * * * *
240785 TCTCTAAAGTCCACACAAGTCGATGGCAACATC
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCTT
* *
240818 TTT-AAAGCCCACACAAGTAGGTGGC-ACTGTTTTT
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC----CTT
* * *
240852 TTTCAAAGCCCATATAAGTCGAG-AGCAA-CTCT
1 TTTCAAAGCCCACACAAGTCG-GTGGCAACCT-T
* * * * *
240884 TTTGAAAGTCTAAACAAGTCGGTGGCAACATT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCTT
* * **
240916 TTTC-AAGCCCACATAAGTCGATGGC-ATTTT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCTT
* *
240946 TTTTAAAGGCCCACACAAGTCGATGGCAACCATT
1 TTTCAAA-GCCCACACAAGTCGGTGGCAACC-TT
240980 TTT
1 TTT
240983 AAAACACTAT
Statistics
Matches: 201, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
30 8 0.04
31 42 0.21
32 90 0.45
33 5 0.02
34 38 0.19
35 16 0.08
36 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:240758 original size:66 final size:64
Alignment explanation
Indices: 240683--240981 Score: 232
Period size: 66 Copynumber: 4.6 Consensus size: 64
240673 ATTCCTTTTT
* *
240683 TTTTCTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTTGGTGGCAT
1 TTTT-TTT-AAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTCGATGGCA-
*
240748 CC
63 AC
* * * * * *
240750 TTTTTTTCAAAGCCCACATAAGTTGGCGGCAACCC-TCTCTAAAGTCCACACAAGTCGATGGCAA
1 TTTTTTT-AAAGCCCACACAAGTCGGTGGCAACCCTTTTC-AAAGCCCACATAAGTCGATGGCAA
240814 C
64 C
* * * ** *
240815 -ATCTTTAAAGCCCACACAAGTAGGTGGC-ACTGTTTTTTTTCAAAGCCCATATAAGTCGA-GAG
1 TTTTTTTAAAGCCCACACAAGTCGGTGGCAAC----CCTTTTCAAAGCCCACATAAGTCGATG-G
240877 CAAC
61 CAAC
* * * * * ** *
240881 TCTTTTGAAAGTCTAAACAAGTCGGTGGCAACATTTTTC-AAGCCCACATAAGTCGATGGC-AT
1 TTTTTTTAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTCGATGGCAAC
* *
240943 TTTTTTTAAAGGCCCACACAAGTCGATGGCAACCATTTT
1 TTTTTTTAAA-GCCCACACAAGTCGGTGGCAACCCTTTT
240982 TAAAACACTA
Statistics
Matches: 183, Mismatches: 38, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
62 11 0.06
63 59 0.32
64 11 0.06
65 5 0.03
66 67 0.37
67 28 0.15
68 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (64 bp):
TTTTTTTAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTCGATGGCAAC
Found at i:240762 original size:34 final size:34
Alignment explanation
Indices: 240683--240783 Score: 134
Period size: 34 Copynumber: 3.0 Consensus size: 34
240673 ATTCCTTTTT
* *
240683 TTTTCTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 TTTT-TTTCAAAGCCCACATAAGTTGGTGGCAACC
* *
240718 --CTTTTCAAAGCCCACATAAGTTGGTGGCATCC
1 TTTTTTTCAAAGCCCACATAAGTTGGTGGCAACC
*
240750 TTTTTTTCAAAGCCCACATAAGTTGGCGGCAACC
1 TTTTTTTCAAAGCCCACATAAGTTGGTGGCAACC
240784 CTCTCTAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
32 27 0.47
33 1 0.02
34 29 0.51
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (34 bp):
TTTTTTTCAAAGCCCACATAAGTTGGTGGCAACC
Found at i:240800 original size:98 final size:96
Alignment explanation
Indices: 240692--240976 Score: 280
Period size: 98 Copynumber: 2.9 Consensus size: 96
240682 TTTTTCTTTC
* * *
240692 AAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTTGGTGGCATCCTTTTTTT
1 AAAGTCCACACAAGTCGGTGGCAACCATTTTCAAAGCCCACATAAGTAGGTGGCAT--TTTTTTT
* *
240757 CAAAGCCCACATAAGTTG-GCGGCAACCCTCTCT-
64 CAAAGCCCACATAAGTCGAG-AGCAACCCT-TCTG
* *
240790 AAAGTCCACACAAGTCGATGGCAA-CATCTTT-AAAGCCCACACAAGTAGGTGGCACTGTTTTTT
1 AAAGTCCACACAAGTCGGTGGCAACCAT-TTTCAAAGCCCACATAAGTAGGTGGCA---TTTTTT
* * *
240853 TTCAAAGCCCATATAAGTCGAGAGCAACTCTTTTG
62 TTCAAAGCCCACATAAGTCGAGAGCAACCCTTCTG
* * * *
240888 AAAGTCTAAACAAGTCGGTGGCAA-CATTTTTC-AAGCCCACATAAGTCGATGGCATTTTTTTT-
1 AAAGTCCACACAAGTCGGTGGCAACCA-TTTTCAAAGCCCACATAAGTAGGTGGCATTTTTTTTC
*
240950 AAAGGCCCACACAAGTCGATG-GCAACC
65 AAA-GCCCACATAAGTCGA-GAGCAACC
240977 ATTTTTAAAA
Statistics
Matches: 158, Mismatches: 19, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
94 3 0.02
95 26 0.16
96 1 0.01
97 25 0.16
98 100 0.63
99 2 0.01
100 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (96 bp):
AAAGTCCACACAAGTCGGTGGCAACCATTTTCAAAGCCCACATAAGTAGGTGGCATTTTTTTTCA
AAGCCCACATAAGTCGAGAGCAACCCTTCTG
Found at i:241863 original size:10 final size:9
Alignment explanation
Indices: 241844--241877 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
241834 AAGTTATGAG
241844 AAAAATAAA
1 AAAAATAAA
*
241853 AAAAATCAA
1 AAAAATAAA
*
241862 AAAAATAAT
1 AAAAATAAA
241871 AAAAATA
1 AAAAATA
241878 TTGCAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:243003 original size:22 final size:23
Alignment explanation
Indices: 242971--243020 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
242961 AATTTCCACA
242971 AAAAAAATATAAATAAA-AA-AAT
1 AAAAAAATATAAA-AAATAATAAT
*
242993 AAAAAAGTATAAAAAATAATAAT
1 AAAAAAATATAAAAAATAATAAT
243016 AAAAA
1 AAAAA
243021 GTGTTTTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAAAATATAAAAAATAATAAT
Found at i:244915 original size:26 final size:26
Alignment explanation
Indices: 244886--244959 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
244876 TTTAAATCCC
244886 TTTTTTTTGTCTATTTTTTTACTCTT-
1 TTTTTTTT-TCTATTTTTTTACTCTTA
* *
244912 TTTTTTATTCCTATATTTTTTCCTCTTA
1 TTTTTT-TTTCTAT-TTTTTTACTCTTA
*
244940 TTTTTCTTTTATATTTTTTT
1 TTTTT-TTTTCTATTTTTTT
244960 CAAACCTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 10 0.25
27 19 0.47
28 10 0.25
29 1 0.03
ACGTcount: A:0.11, C:0.12, G:0.01, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTATTTTTTTACTCTTA
Found at i:246350 original size:22 final size:22
Alignment explanation
Indices: 246325--246367 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
246315 GACAAGTTTA
*
246325 AATGTTTTTCAAA-TAATAAATC
1 AATGTTATTCAAAGTAA-AAATC
246347 AATGTTATTCAAAGTAAAAAT
1 AATGTTATTCAAAGTAAAAAT
246368 ACTTATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (22 bp):
AATGTTATTCAAAGTAAAAATC
Found at i:246535 original size:20 final size:20
Alignment explanation
Indices: 246498--246547 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
246488 ATCGATACAT
* *
246498 TGTATCGATACAAAATAATA
1 TGTATTGATACAAAATAAAA
**
246518 TGTATTGATACACCATAAAA
1 TGTATTGATACAAAATAAAA
*
246538 TGTACTGATA
1 TGTATTGATA
246548 GATAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (20 bp):
TGTATTGATACAAAATAAAA
Found at i:250204 original size:20 final size:21
Alignment explanation
Indices: 250165--250206 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
250155 ACTTTTCAAC
*
250165 AAAATAGAATTATTGAAAGAA
1 AAAATAGAACTATTGAAAGAA
*
250186 AAAATAGAACT-TTGGAAGAA
1 AAAATAGAACTATTGAAAGAA
250206 A
1 A
250207 TGGCTAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATAGAACTATTGAAAGAA
Found at i:252909 original size:21 final size:20
Alignment explanation
Indices: 252862--252910 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
252852 AAATTTTCAA
*
252862 TCATCAAATTCATCCAATCC
1 TCATCAAATTCATCCAATAC
* * *
252882 ACTTCAAATTTCATCGAATAC
1 TCATCAAA-TTCATCCAATAC
252903 TCATCAAA
1 TCATCAAA
252911 ATCCATCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (20 bp):
TCATCAAATTCATCCAATAC
Found at i:255418 original size:13 final size:13
Alignment explanation
Indices: 255400--255424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
255390 AAGTTGCTAA
255400 GTATCGATACAAT
1 GTATCGATACAAT
255413 GTATCGATACAA
1 GTATCGATACAA
255425 ATTGCTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:255420 original size:33 final size:33
Alignment explanation
Indices: 255378--255443 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
255368 ACATACTAAG
*
255378 ATGTATCGATACAAGTTGCTAAGTATCGATACA
1 ATGTATCGATACAAATTGCTAAGTATCGATACA
**
255411 ATGTATCGATACAAATTGCTTTGTATCGATACA
1 ATGTATCGATACAAATTGCTAAGTATCGATACA
255444 CCATAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAAATTGCTAAGTATCGATACA
Found at i:256032 original size:35 final size:34
Alignment explanation
Indices: 255986--256053 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
255976 CAAGTGATTG
* *
255986 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGGGA
1 AGAGGTTCTATCGTAGCCTTCG-AAAAGATAGGGA
*
256021 AGAGGTTCTATCGTAGCCTTCGAAAATATAGGG
1 AGAGGTTCTATCGTAGCCTTCGAAAAGATAGGG
256054 TTGTCCAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (34 bp):
AGAGGTTCTATCGTAGCCTTCGAAAAGATAGGGA
Found at i:260401 original size:11 final size:11
Alignment explanation
Indices: 260387--260423 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
260377 AATTTTTTAT
260387 ATATTTATATC
1 ATATTTATATC
*
260398 ATATTTATATT
1 ATATTTATATC
260409 AT-TTTATATC
1 ATATTTATATC
260419 ATATT
1 ATATT
260424 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATTTATATC
Found at i:260406 original size:19 final size:21
Alignment explanation
Indices: 260382--260423 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
260372 TATATAATTT
260382 TTTATA-TA-TTTATATCATA
1 TTTATATTATTTTATATCATA
260401 TTTATATTATTTTATATCATA
1 TTTATATTATTTTATATCATA
260422 TT
1 TT
260424 AAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATTATTTTATATCATA
Found at i:271518 original size:59 final size:59
Alignment explanation
Indices: 271447--271569 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
271437 TTGCATTTTA
271447 TGGTTTGCGTTCATTCCCAATAAAATATCAGTTACTTTTATATTCATGTTCCAGTCATG
1 TGGTTTGCGTTCATTCCCAATAAAATATCAGTTACTTTTATATTCATGTTCCAGTCATG
271506 TGGTTTGCGTTCATTCCCAATAAAATATCAGTTACTTTTATATTCATGTTCCAGTCATG
1 TGGTTTGCGTTCATTCCCAATAAAATATCAGTTACTTTTATATTCATGTTCCAGTCATG
271565 TGGTT
1 TGGTT
271570 GGTCCACCCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (59 bp):
TGGTTTGCGTTCATTCCCAATAAAATATCAGTTACTTTTATATTCATGTTCCAGTCATG
Found at i:273029 original size:3 final size:3
Alignment explanation
Indices: 273021--273046 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
273011 CATCGACGTA
273021 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
273047 TCTCTTACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:278151 original size:21 final size:21
Alignment explanation
Indices: 278127--278199 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
278117 TTTGACGTGT
278127 TGTAGGTGCTATTTGGGGTAC
1 TGTAGGTGCTATTTGGGGTAC
* ** *
278148 TGTAGGTTCTATTTAAGGTGC
1 TGTAGGTGCTATTTGGGGTAC
* * *
278169 TGTAGGTTCTGTTTGGGGTAG
1 TGTAGGTGCTATTTGGGGTAC
278190 TGTAGGTGCT
1 TGTAGGTGCT
278200 GATATGGGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.14, C:0.08, G:0.37, T:0.41
Consensus pattern (21 bp):
TGTAGGTGCTATTTGGGGTAC
Found at i:279193 original size:129 final size:129
Alignment explanation
Indices: 278963--279221 Score: 484
Period size: 129 Copynumber: 2.0 Consensus size: 129
278953 GAACCTGTCA
*
278963 CATTAGCAGTAGTAGAGGGTACCCAAATATCAAAATGGACTAAATGGAAAGGAGCAGAACATTTT
1 CATTAGCAATAGTAGAGGGTACCCAAATATCAAAATGGACTAAATGGAAAGGAGCAGAACATTTT
279028 TTATTGCTAGTAGAAAAGGGTAATCTTTTATGTTTAGCAAACTCAG-ACACATCACAATGAAAGT
66 TTATTGCTAGTAGAAAAGGGTAATCTTTTATGTTTAGCAAACTC-GCACACATCACAATGAAAGT
*
279092 CATTAGCAATAGTAGAGGGTTCCCAAATATCAAAATGGACTAAATGGAAAGGAGCAGAACATTTT
1 CATTAGCAATAGTAGAGGGTACCCAAATATCAAAATGGACTAAATGGAAAGGAGCAGAACATTTT
279157 TTATTGCTAGTAGAAAAGGGTAATCTTTTATGTTTAGCAAACTCGCACACATCACAATGAAAGT
66 TTATTGCTAGTAGAAAAGGGTAATCTTTTATGTTTAGCAAACTCGCACACATCACAATGAAAGT
279221 C
1 C
279222 TTGTGTTTCT
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
128 1 0.01
129 126 0.99
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (129 bp):
CATTAGCAATAGTAGAGGGTACCCAAATATCAAAATGGACTAAATGGAAAGGAGCAGAACATTTT
TTATTGCTAGTAGAAAAGGGTAATCTTTTATGTTTAGCAAACTCGCACACATCACAATGAAAGT
Found at i:281734 original size:2 final size:2
Alignment explanation
Indices: 281727--281765 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
281717 TAAATAGCTT
*
281727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
281766 GTATGTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:281770 original size:4 final size:4
Alignment explanation
Indices: 281763--281797 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
281753 TATATATGTA
281763 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
281798 AATTTACTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:282366 original size:207 final size:204
Alignment explanation
Indices: 282007--282410 Score: 673
Period size: 207 Copynumber: 2.0 Consensus size: 204
281997 TTTTATCAGA
* *
282007 AATAATGAAAATTAAGTTCATCACCTTATTTTTGTTGCTTAAATTTATGGGTTAAATGCTAAGTC
1 AATAATGAAAATTAAGTTCACCACCTTATTTTCGTTGCTTAAATTTATGGGTTAAATGCTAAGTC
*
282072 CTGTAAAATGGTATTTATGTATGCATTATGGGTAAGGTTAGCATATGGCAAGGCAGTGGATCAAA
66 ATGTAAAATGGTATTTATGTATGCATTATGGGTAAGGTTAGCATATGGCAAGGCAGTGGATCAAA
* *
282137 CAAGCTACAACAGTGAAAGCTTTAGTTTCCTGGGAAGGGATGCTAGCATAGTGAAATGTGAGAGC
131 CAAGCTACAACAGTGAAAGCTTTAGTTTCCTGAGAAGGGATGCTAGCATAGTGAAATATGAGAGC
282202 ATATGGGTT
196 ATATGGGTT
*
282211 AATAGTGAAAATTAAGTTCACCACCTTATTTTCGTTGCTTAAATTTATGGGTTAAATGCTAAGTC
1 AATAATGAAAATTAAGTTCACCACCTTATTTTCGTTGCTTAAATTTATGGGTTAAATGCTAAGTC
* * *
282276 GGAATGTAAAATGGTATTTATGTATGCATTATGGGTAAGGTTAGCATATTGTAAGGTAGTGGATC
66 ---ATGTAAAATGGTATTTATGTATGCATTATGGGTAAGGTTAGCATATGGCAAGGCAGTGGATC
* * *
282341 AAACAAGCTACCACAGTGGAAGCTTTAGTTTCCTGAGAAGGGATGCTAGCGTAGTGAAATATGAG
128 AAACAAGCTACAACAGTGAAAGCTTTAGTTTCCTGAGAAGGGATGCTAGCATAGTGAAATATGAG
282406 AGCAT
193 AGCAT
282411 TAAACATCCA
Statistics
Matches: 185, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
204 62 0.34
207 123 0.66
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (204 bp):
AATAATGAAAATTAAGTTCACCACCTTATTTTCGTTGCTTAAATTTATGGGTTAAATGCTAAGTC
ATGTAAAATGGTATTTATGTATGCATTATGGGTAAGGTTAGCATATGGCAAGGCAGTGGATCAAA
CAAGCTACAACAGTGAAAGCTTTAGTTTCCTGAGAAGGGATGCTAGCATAGTGAAATATGAGAGC
ATATGGGTT
Found at i:283306 original size:18 final size:18
Alignment explanation
Indices: 283270--283307 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
283260 TCCTTCATCA
*
283270 TCTTTCTTTTTTTCTTTT
1 TCTTTCTTTTTTTCCTTT
283288 TCTTT-TTTTTTTACCTTT
1 TCTTTCTTTTTTT-CCTTT
283306 TC
1 TC
283308 CCTAATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTCTTTTTTTCCTTT
Found at i:284327 original size:2 final size:2
Alignment explanation
Indices: 284320--284351 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
284310 GTATCTGCGA
284320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
284352 GGCCAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284583 original size:59 final size:59
Alignment explanation
Indices: 284491--284607 Score: 234
Period size: 59 Copynumber: 2.0 Consensus size: 59
284481 AGTCAATAAG
284491 GAGCAGGGAGTCCATCTTTGTTTGAGATTCCCATCAAAGAGAATGGTATAAATTTAGTA
1 GAGCAGGGAGTCCATCTTTGTTTGAGATTCCCATCAAAGAGAATGGTATAAATTTAGTA
284550 GAGCAGGGAGTCCATCTTTGTTTGAGATTCCCATCAAAGAGAATGGTATAAATTTAGT
1 GAGCAGGGAGTCCATCTTTGTTTGAGATTCCCATCAAAGAGAATGGTATAAATTTAGT
284608 CCAATTTGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (59 bp):
GAGCAGGGAGTCCATCTTTGTTTGAGATTCCCATCAAAGAGAATGGTATAAATTTAGTA
Found at i:286332 original size:19 final size:19
Alignment explanation
Indices: 286308--286346 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
286298 AAAAAAAGAA
286308 AAGTTACATAGCTTAATTT
1 AAGTTACATAGCTTAATTT
*
286327 AAGTTACATGGCTTAATTT
1 AAGTTACATAGCTTAATTT
286346 A
1 A
286347 CATTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (19 bp):
AAGTTACATAGCTTAATTT
Found at i:290899 original size:28 final size:28
Alignment explanation
Indices: 290866--290926 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
290856 GCGATTAGAA
*
290866 TATCCCCTCGA-AAATAACGGGGTTGGAG
1 TATCCCC-CGAGAAATAACGAGGTTGGAG
290894 TAT-CCCCGATGAAATAACGAGGTTGGAG
1 TATCCCCCGA-GAAATAACGAGGTTGGAG
290922 TATCC
1 TATCC
290927 TCGATTGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 3 0.10
28 22 0.76
29 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (28 bp):
TATCCCCCGAGAAATAACGAGGTTGGAG
Found at i:290931 original size:28 final size:28
Alignment explanation
Indices: 290877--290931 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
290867 ATCCCCTCGA
*
290877 AAATAACGGGGTTGGAGTATCCCCGATG
1 AAATAACGAGGTTGGAGTATCCCCGATG
*
290905 AAATAACGAGGTTGGAGTATCCTCGAT
1 AAATAACGAGGTTGGAGTATCCCCGAT
290932 TGTGAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
AAATAACGAGGTTGGAGTATCCCCGATG
Found at i:290970 original size:51 final size:51
Alignment explanation
Indices: 290911--291079 Score: 184
Period size: 51 Copynumber: 3.3 Consensus size: 51
290901 GATGAAATAA
*
290911 CGAGGTTGGAGTATCCTCGATTGT-GAATAATTGGTGTTTTTA-AAATAAAAC
1 CGAGGTTGGAGTATCCTCGATTGTGGAA-AATTAGTG-TTTTAGAAATAAAAC
*
290962 CGGGGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
1 CGAGGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
* * * * * **
291013 CGAAGTTGGAGTATCCCCGATTAT-GAGAAATCAATAG-TTTAGAAATAAAGT
1 CGAGGTTGGAGTATCCTCGATTGTGGA-AAATTAGT-GTTTTAGAAATAAAAC
*
291064 CGAGGTTAGAGTATCC
1 CGAGGTTGGAGTATCC
291080 CCTCGGAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
50 7 0.07
51 91 0.89
52 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:291237 original size:212 final size:208
Alignment explanation
Indices: 290860--291324 Score: 617
Period size: 212 Copynumber: 2.2 Consensus size: 208
290850 AAAATTGCGA
* *
290860 TTAGAATATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT
1 TTAGAGTATCCCCTCGAAAA-AACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAC
* * * *** * * **
290925 CCTCGATTGTGAATAATTGGTGTTTTTAAAATAAAACCGGGGTTGGAGTATCCTCGATTGTGGAA
65 CCCCGATTATGAAAAATCAATATTTTTAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGGAA
290990 AATTAGTGTTTTAGAAATAAAACCGAAGTTGGAGTATCCCCGATTATGAGAAATCAATAGTTTAG
130 AATTAGTGTTTTAGAAATAAAACCGAAGTTGGAGTATCCCCGATTATGAGAAATCAATAGTTTAG
*
291055 AAATAAAGTC-GAGG
195 AAATAAAGCCGGA-G
* * * * * *
291069 TTAGAGTATCCCCTCGGAAAAACGGGGGTAGAGTATCCTCGATGAAATAGCGGGGTTGGAGTACC
1 TTAGAGTATCCCCTCGAAAAAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTACC
* * *
291134 CCCGATTATGAAAAAAATCAATATTTTTGGATATAAAGCCGGGGTTGGAGTATCCCCGATTAAAG
66 CCCGATTATG--AAAAATCAATATTTTT-AAAATAAAACCGGGGTTGGAGTATCCCCGATT-AAG
* ** *
291199 GAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATTCCCGATTATGAGAAATCAATAGTT
127 GAAAATTAGTGTTTTAGAAATAAAACCGAAGTTGGAGTATCCCCGATTATGAGAAATCAATAGTT
291264 TAGAAATAAAGCCGGAG
192 TAGAAATAAAGCCGGAG
*
291281 TTAGAGTATCTCCTCGAAAAAAACGGGGTTGGAGTATCCCCGAT
1 TTAGAGTATCCCCTCG-AAAAAACGGGGTTGGAGTATCCCCGAT
291325 TATGAGAAAT
Statistics
Matches: 219, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
208 47 0.21
209 18 0.08
210 11 0.05
211 28 0.13
212 90 0.41
213 25 0.11
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (208 bp):
TTAGAGTATCCCCTCGAAAAAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTACC
CCCGATTATGAAAAATCAATATTTTTAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGGAAA
ATTAGTGTTTTAGAAATAAAACCGAAGTTGGAGTATCCCCGATTATGAGAAATCAATAGTTTAGA
AATAAAGCCGGAG
Found at i:291359 original size:79 final size:80
Alignment explanation
Indices: 291214--291454 Score: 351
Period size: 83 Copynumber: 3.0 Consensus size: 80
291204 TTAGTGTTTT
* * **
291214 AGAAATAAAATCGGGGTTGGAGTATTCCCGATTATGAGAAATCAATAGTTTAGAAATAAAGCCGG
1 AGAAA-AAAA-CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGG
*
291279 AGTTAGAGTATCTCCTC
64 AGTTAGAATATCTCCTC
291296 -GAAAAAAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGGAG
1 AGAAAAAAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGGAG
291360 TTAGAATATCTCCTC
66 TTAGAATATCTCCTC
* *
291375 AGAAAAAAAAAACAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAATCG
1 AG---AAAAAAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCG
291440 GAG-TAGGAATATCTC
63 GAGTTA-GAATATCTC
291455 TGATTGTGAA
Statistics
Matches: 147, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
79 66 0.45
80 5 0.03
81 4 0.03
82 2 0.01
83 70 0.48
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (80 bp):
AGAAAAAAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGGAG
TTAGAATATCTCCTC
Found at i:291525 original size:28 final size:28
Alignment explanation
Indices: 291494--291561 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
291484 AAAATCAGGG
291494 TTGGAGTATCCCCTCGAAAATAACGGGA
1 TTGGAGTATCCCCTCGAAAATAACGGGA
*
291522 TTGGAGTATCCCCTCGGAAATAACGGGA
1 TTGGAGTATCCCCTCGAAAATAACGGGA
291550 TTGGAGTATCCC
1 TTGGAGTATCCC
291562 GATGAAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (28 bp):
TTGGAGTATCCCCTCGAAAATAACGGGA
Found at i:291754 original size:52 final size:52
Alignment explanation
Indices: 291575--291756 Score: 172
Period size: 52 Copynumber: 3.4 Consensus size: 52
291565 GAAATAGCAA
* ** * * * *
291575 GGTTGGAGTACCCCCGATTATGAAAAAAGATCAATATTTTTGAATATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAGGAAA-ATTAAT-GTTTTGAAAATAAAATC-G
* * * *
291630 GGTTTGAGTATCCCCAATTA-AAGGAAAATTAATGTTTT-AGAAATAAAACCG
1 GGTTGGAGTATCCCCGATTATGAGGAAAATTAATGTTTTGA-AAATAAAATCG
**
291681 AGGTTGGAGTATCCCCGATTATGA-GAAAATTGGTGTTTTGAAAATAAAATCG
1 -GGTTGGAGTATCCCCGATTATGAGGAAAATTAATGTTTTGAAAATAAAATCG
291733 GGATTGGAGTATCCCCGATTATGA
1 GG-TTGGAGTATCCCCGATTATGA
291757 ACAATTGAGA
Statistics
Matches: 105, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
51 4 0.04
52 73 0.70
53 7 0.07
54 4 0.04
55 17 0.16
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGAGGAAAATTAATGTTTTGAAAATAAAATCG
Found at i:294254 original size:55 final size:56
Alignment explanation
Indices: 294110--294404 Score: 280
Period size: 55 Copynumber: 5.2 Consensus size: 56
294100 AAGAAGTGTG
* * * *
294110 TCCTGTTCTTTGAGGACT-GAAAAGTGCCATCAACTCGTGTGGTCTTTGAAAAAAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTT---AAAAG---GCA
* *
294171 TCCTGCTTTTTGAGAACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
* * *
294226 TCTTGCTCTTTGAGGATTGGAAAA-TGCCACTAACTTGTGTGGGCTTTAAAAGG-A
1 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
* * * * * *
294280 GTCCTGCTCTTTGAAGACT--AAAAGGTGCTACCAACTTCTGTGGACTTTGAAAGGCG
1 -TCCTGCTCTTTGAGGACTGGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
* * * * * *
294336 TCCTGCTATTTGAGGACT-GAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
294391 TCCTGCTCTTTGAG
1 TCCTGCTCTTTGAG
294405 AACTAGAGGG
Statistics
Matches: 197, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
53 4 0.02
54 1 0.01
55 137 0.70
56 9 0.05
58 5 0.03
61 41 0.21
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
Found at i:294322 original size:110 final size:111
Alignment explanation
Indices: 294118--294408 Score: 313
Period size: 110 Copynumber: 2.6 Consensus size: 111
294108 TGTCCTGTTC
* * * * * *
294118 TTTGAGGACTGAAAAGTGCCATCAACTCGTGTGGTCTTTGAAAAAAGAAAGCATCCTGCTTTTTG
1 TTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGC-TT--CAAAAG--A-CGTCCTGCTCTTTG
* * * *
294183 -AGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGCTC
60 AAGAACTGAAAAGTGCCACCAACTTCTGTGGACTTTAAAAGGCATCCTGCTA
* * * * *
294234 TTTGAGGATTGGAAAATGCCACTAACTTGTGTGGGCTTTAAAAGGA-GTCCTGCTCTTTGAAG-A
1 TTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAA-GACGTCCTGCTCTTTGAAGAA
* * *
294297 CT-AAAAGGTGCTACCAACTTCTGTGGACTTTGAAAGGCGTCCTGCTA
65 CTGAAAA-GTGCCACCAACTTCTGTGGACTTTAAAAGGCATCCTGCTA
294344 TTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTG-AGAAC
1 TTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAAGAAC
294408 T
66 T
294409 AGAGGGCAAA
Statistics
Matches: 148, Mismatches: 22, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
109 8 0.05
110 101 0.68
111 2 0.01
112 1 0.01
113 4 0.03
114 1 0.01
115 2 0.01
116 29 0.20
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (111 bp):
TTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAAGAAC
TGAAAAGTGCCACCAACTTCTGTGGACTTTAAAAGGCATCCTGCTA
Found at i:294514 original size:55 final size:54
Alignment explanation
Indices: 294430--294594 Score: 240
Period size: 55 Copynumber: 3.0 Consensus size: 54
294420 GGAGAGAGCA
*
294430 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAG
* * *
294485 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAATGCG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAG
* * *
294540 TCCTACTCTTTGAAGACTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAGGAG
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAG
294595 AAGGCGTCTA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
54 3 0.03
55 92 0.94
56 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAG
Found at i:294551 original size:149 final size:149
Alignment explanation
Indices: 294281--294552 Score: 386
Period size: 149 Copynumber: 1.8 Consensus size: 149
294271 TTAAAAGGAG
* * *
294281 TCCTGCTCTTTGAAGACTAAAAGGTGCTACCAACTTCTGTGGACTTTGAAAGGCGTCCTGCTATT
1 TCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTCTGTGGACTTTAAAAGGAGTCCTGCTATT
*
294346 TGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAGAACTAG
66 TGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTACTCTTTGAGAACTAG
294411 AGGGCAAAAGGAGAGAGCA
131 AGGGCAAAAGGAGAGAGCA
* * * * *
294430 TCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTCT
1 TCCTGCTCTTTGAAGACTA-AAAGGTGCCACCAACTTCTGTGGACTTTAAAAGGAGTCCTGCTAT
** * * *
294494 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAATG-CGTCCTACTCTTTGA
65 TTGAGGACTGAAAAATGCCACCAACTCGTGTGGGC-TTCAAAAGACGTCCTACTCTTTGA
294553 AGACTGAAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
149 99 0.93
150 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (149 bp):
TCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTCTGTGGACTTTAAAAGGAGTCCTGCTATT
TGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTACTCTTTGAGAACTAG
AGGGCAAAAGGAGAGAGCA
Found at i:294582 original size:204 final size:204
Alignment explanation
Indices: 294223--294591 Score: 569
Period size: 204 Copynumber: 1.8 Consensus size: 204
294213 GCTTTAAAAG
* * *
294223 GCATCTTGCTCTTTGAGGATTGGAAAATGCCACTAACTTGTGTGGGCTTTAAAAGGAGTCCTGCT
1 GCATCCTGCTCTTTGAGGATAGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCT
* * *
294288 CTTTGAAGACTAAAAGGTGCTACCAACTTCTGTGGACTTTGAAAGGCGTCCTGCTATTTGAGGAC
66 CTTTGAAGACTAAAAGGTGCCACCAACTTCTGTGGACTTTGAAAGGCGTCCTACTATTTGAAGAC
*
294353 TGAAAAATGCCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAGAACTAGAGGGCAA
131 TGAAAAATACCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAGAACTAGAGGGCAA
294418 AAGGAGAGA
196 AAGGAGAGA
*
294427 GCATCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGC
1 GCATCCTGCTCTTTGAGGA-TAGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGC
* * * * * *
294491 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAATGCGTCCTACTCTTTGAAGA
65 TCTTTGAAGACTAAAAGGTGCCACCAACTTCTGTGGACTTTGAAAGGCGTCCTACTATTTGAAGA
* * *
294556 CTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAG
130 CTGAAAAATACCACCAACTCGTGTGGGCTTCAAAAG
294592 GAGAAGGCGT
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
204 144 0.98
205 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (204 bp):
GCATCCTGCTCTTTGAGGATAGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCT
CTTTGAAGACTAAAAGGTGCCACCAACTTCTGTGGACTTTGAAAGGCGTCCTACTATTTGAAGAC
TGAAAAATACCACCAACTCGTGTGGGCTTCAAAAGACGTCCTGCTCTTTGAGAACTAGAGGGCAA
AAGGAGAGA
Found at i:297674 original size:51 final size:51
Alignment explanation
Indices: 297603--297716 Score: 151
Period size: 51 Copynumber: 2.2 Consensus size: 51
297593 TTTCCGAAGA
* ** *
297603 GATACTCCAACCCCGGTTTTATTTCTAAAA-CA-CTAATTTTTCACAATCGGG
1 GATACTCCAACCCCGATTTTATTT-TAAAAGCATC-AATCCTTCACAATCGAG
*
297654 GATACTCCAATCCCGATTTTATTTTAAAAGCATCAATCCTTCACAATCGAG
1 GATACTCCAACCCCGATTTTATTTTAAAAGCATCAATCCTTCACAATCGAG
297705 GATACTCCAACC
1 GATACTCCAACC
297717 TCATTATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 5 0.09
51 49 0.89
52 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTTAAAAGCATCAATCCTTCACAATCGAG
Found at i:297741 original size:28 final size:28
Alignment explanation
Indices: 297699--297753 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
297689 ATCCTTCACA
*
297699 ATCGAGGATACTCCAACCTCATTATTTC
1 ATCGAGGATACTCCAACCCCATTATTTC
* *
297727 ATCGGGGATATTCCAACCCCATTATTT
1 ATCGAGGATACTCCAACCCCATTATTT
297754 TCGAGGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCATTATTTC
Found at i:297753 original size:158 final size:158
Alignment explanation
Indices: 297535--297826 Score: 361
Period size: 158 Copynumber: 1.8 Consensus size: 158
297525 ATTGATTTTT
* * * * * * * *
297535 TTCATAATCGGGGGTACTCCAACCCCGCTATTTCATCGGGGATACTCTAATCTCGTTATTTCCGA
1 TTCACAATCGAGGATACTCCAACCCCACTATTTCATCGGGGATACTCCAACCCCATTATTTCCGA
* *
297600 AGAGATACTCCAACCCCGGTTTTATTTCTAAAACA-CTAATTTTTCACAATCGGGGATACTCCAA
66 AGAGATACTCCAACCCCGATTTTATTTCTAAAACATC-AATTTTTCACAACCGGGGATACTCCAA
*
297664 TCCCGATTTTATTTTAAAAGCATCAATCC
130 CCCCGATTTTATTTTAAAAGCATCAATCC
* * * *
297693 TTCACAATCGAGGATACTCCAACCTCATTATTTCATCGGGGATATTCCAACCCCATTATTTTCGA
1 TTCACAATCGAGGATACTCCAACCCCACTATTTCATCGGGGATACTCCAACCCCATTATTTCCGA
* * * * * * * *
297758 GGGGATATTCTAATCCCGATTTTATTTCTCAATCATCGATTTTTCACAACCGGGGATACTCCAAC
66 AGAGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAACCGGGGATACTCCAAC
297823 CCCG
131 CCCG
297827 TTATTTTCAA
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
158 109 0.99
159 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (158 bp):
TTCACAATCGAGGATACTCCAACCCCACTATTTCATCGGGGATACTCCAACCCCATTATTTCCGA
AGAGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAACCGGGGATACTCCAAC
CCCGATTTTATTTTAAAAGCATCAATCC
Found at i:297761 original size:28 final size:27
Alignment explanation
Indices: 297704--297767 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
297694 TCACAATCGA
* *
297704 GGATACTCCAACCTCATTATTTCATCGG
1 GGATATTCCAACCCCATTATTTCA-CGG
297732 GGATATTCCAACCCCATTATTTTCGA-GG
1 GGATATTCCAACCCCATTA-TTTC-ACGG
297760 GGATATTC
1 GGATATTC
297768 TAATCCCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 27 0.84
29 4 0.12
30 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (27 bp):
GGATATTCCAACCCCATTATTTCACGG
Found at i:297804 original size:107 final size:107
Alignment explanation
Indices: 297651--297849 Score: 249
Period size: 107 Copynumber: 1.9 Consensus size: 107
297641 TTTCACAATC
*
297651 GGGGATACTCCAATCCCGATTTTATTTTAAAAGCATCAATCCTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAATCCCGATTTTATTTTAAAAGCATCAATCCTTCACAACCGAGGATACTCCAAC
* * *
297716 CTCATTA-TTTCATCGGGGATATTCCAACCCCATTATTTTCGA
66 CCCATTATTTTCA-AGGGGATACTCCAACCCCATTATTTTCGA
* * * * * ** *
297758 GGGGATATTCTAATCCCGATTTTATTTCT-CAATCATCGATTTTTCACAACCGGGGATACTCCAA
1 GGGGATACTCCAATCCCGATTTTATTT-TAAAAGCATCAATCCTTCACAACCGAGGATACTCCAA
*
297822 CCCCGTTATTTTCAAGGGGATACTCCAA
65 CCCCATTATTTTCAAGGGGATACTCCAA
297850 GCTGTCGCGA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 71 0.92
108 6 0.08
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (107 bp):
GGGGATACTCCAATCCCGATTTTATTTTAAAAGCATCAATCCTTCACAACCGAGGATACTCCAAC
CCCATTATTTTCAAGGGGATACTCCAACCCCATTATTTTCGA
Found at i:298165 original size:15 final size:14
Alignment explanation
Indices: 298141--298172 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
298131 AGGTTCGTGT
298141 TTGGGTATCCCCGG
1 TTGGGTATCCCCGG
298155 TTGGAGTATCCCCGG
1 TTGG-GTATCCCCGG
298170 TTG
1 TTG
298173 TGAAAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.09, C:0.25, G:0.34, T:0.31
Consensus pattern (14 bp):
TTGGGTATCCCCGG
Found at i:298240 original size:28 final size:28
Alignment explanation
Indices: 298209--298272 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
298199 ATCGGGATTA
** *
298209 GAATATCCCCTCGGAAATAACGGGGTTG
1 GAATATCCCCGAGGAAATAACGAGGTTG
*
298237 GAATATCCCCGATGAAATAACGAGGTTG
1 GAATATCCCCGAGGAAATAACGAGGTTG
*
298265 GAGTATCC
1 GAATATCC
298273 TCGATTGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (28 bp):
GAATATCCCCGAGGAAATAACGAGGTTG
Found at i:298277 original size:28 final size:28
Alignment explanation
Indices: 298222--298277 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
298212 TATCCCCTCG
*
298222 GAAATAACGGGGTTGGAATATCCCCGAT
1 GAAATAACGAGGTTGGAATATCCCCGAT
* *
298250 GAAATAACGAGGTTGGAGTATCCTCGAT
1 GAAATAACGAGGTTGGAATATCCCCGAT
298278 TGTGAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (28 bp):
GAAATAACGAGGTTGGAATATCCCCGAT
Found at i:298321 original size:51 final size:50
Alignment explanation
Indices: 298260--298426 Score: 162
Period size: 51 Copynumber: 3.3 Consensus size: 50
298250 GAAATAACGA
* * *
298260 GGTTGGAGTATCCTCGATTGT-GAAGGATTGGTGTTTTTA-AAATAAAACTGG
1 GGTTGGAGTATCC-CGATTGTGGAA-AATTAGTG-TTTTAGAAATAAAACCGG
*
298311 GGTTTGAGTATTCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTA-TCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
* * * *
298362 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATAG-TTTAGAAATAAAATCGG
1 GGTTGGAGTAT-CCCGATTGTGGA-AAATTAGT-GTTTTAGAAATAAAACCGG
*
298413 GGTTAGAGTATCCC
1 GGTTGGAGTATCCC
298427 TTCGAAAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
50 11 0.11
51 82 0.82
52 7 0.07
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (50 bp):
GGTTGGAGTATCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:298532 original size:55 final size:55
Alignment explanation
Indices: 298470--298654 Score: 250
Period size: 55 Copynumber: 3.4 Consensus size: 55
298460 AAATAGCAGA
298470 GTTGGAGTACCCCCGATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
1 GTTGGAGTACCCCCGATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
*
298525 GTTGGAGTACCCCCTATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
1 GTTGGAGTACCCCCGATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
* ** * * * * * *
298580 GTTGGAGTATCCCCGATTA--AAGGAAAATTAGT-GTTTTAGAAATAAAACCGGG
1 GTTGGAGTACCCCCGATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
*
298632 GTTGGAGTATCCCCGATTATGAA
1 GTTGGAGTACCCCCGATTATGAA
298655 CAATTGAGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
52 35 0.30
53 9 0.08
54 2 0.02
55 71 0.61
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (55 bp):
GTTGGAGTACCCCCGATTATGAAAAAAAATCAATATTTTTGGATATAAAGCCGGG
Found at i:299875 original size:35 final size:35
Alignment explanation
Indices: 299836--299970 Score: 216
Period size: 35 Copynumber: 3.9 Consensus size: 35
299826 TCATTTTTTT
* *
299836 ATGCCCATCATTCCATGCCTTCACTTTCATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
* *
299871 ATGCCCATCATTCCATACCTCCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
299906 ATGCCCATCATTTCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
299941 ATGCCCATCATTCCATGTCTTCATTTTTAT
1 ATGCCCATCATTCCATGCCTTCATTTTTAT
299971 TATTTTTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 91 1.00
ACGTcount: A:0.21, C:0.32, G:0.05, T:0.42
Consensus pattern (35 bp):
ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
Found at i:299887 original size:21 final size:21
Alignment explanation
Indices: 299840--299887 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
299830 TTTTTTATGC
*
299840 CCATCATTCCATGCCTTCACTT
1 CCAT-ATTCCATGCCATCACTT
*
299862 TCATATTCCATGCCCATCA-TT
1 CCATATTCCATG-CCATCACTT
299883 CCATA
1 CCATA
299888 CCTCCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.35
Consensus pattern (21 bp):
CCATATTCCATGCCATCACTT
Found at i:299993 original size:6 final size:6
Alignment explanation
Indices: 299977--300011 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
299967 TTATTATTTT
299977 TTTTGAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
300012 TTATTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:301614 original size:13 final size:13
Alignment explanation
Indices: 301596--301621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301586 CAATTTTTTG
301596 TGTATCGATACAT
1 TGTATCGATACAT
301609 TGTATCGATACAT
1 TGTATCGATACAT
301622 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301633 original size:32 final size:33
Alignment explanation
Indices: 301576--301639 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
301566 TACAAGCCAA
**
301576 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
301609 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
301640 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:305017 original size:16 final size:16
Alignment explanation
Indices: 304998--305049 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
304988 TAACTATCAA
304998 ATTTATAAATAATTAT
1 ATTTATAAATAATTAT
* * *
305014 ATTTA-ATATTCATTAA
1 ATTTATA-AATAATTAT
305030 ATTTATAAATAATT-T
1 ATTTATAAATAATTAT
305045 ATTTA
1 ATTTA
305050 ATATTTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 6 0.21
16 21 0.75
17 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTATAAATAATTAT
Found at i:305019 original size:32 final size:31
Alignment explanation
Indices: 304983--305098 Score: 119
Period size: 32 Copynumber: 3.7 Consensus size: 31
304973 ATTAAAATTT
304983 TTTAATAACTATCAAATTTATAAATAATTATA
1 TTTAAT-ACTATCAAATTTATAAATAATTATA
* *
305015 TTTAATATTCATTAAATTTATAAATAATT-TA
1 TTTAATACT-ATCAAATTTATAAATAATTATA
* * * * *
305046 TTTAATATTTATAAAATATACAAATAAATATA
1 TTTAATA-CTATCAAATTTATAAATAATTATA
*
305078 TTTAATTC-ATCAAATTTATAA
1 TTTAATACTATCAAATTTATAA
305099 TCAATATCGA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
30 10 0.14
31 26 0.37
32 34 0.49
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAATACTATCAAATTTATAAATAATTATA
Found at i:305050 original size:63 final size:60
Alignment explanation
Indices: 304978--305098 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 60
304968 ATAAGATTAA
* * * * *
304978 AATTTTTTAATAACTATCAAATTTATAAATAATTATATTTAATATTCATTAAATTTATAAAT
1 AATTTTTTAATAACTATAAAATATACAAATAAATATATTT-A-ATTCATCAAATTTATAAAT
**
305040 AATTTATTTAATATTTATAAAATATACAAATAAATATATTTAATTCATCAAATTTATAA
1 AATTT-TTTAATAACTATAAAATATACAAATAAATATATTTAATTCATCAAATTTATAA
305099 TCAATATCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 16 0.31
62 6 0.12
63 29 0.57
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (60 bp):
AATTTTTTAATAACTATAAAATATACAAATAAATATATTTAATTCATCAAATTTATAAAT
Found at i:305051 original size:31 final size:31
Alignment explanation
Indices: 304996--305098 Score: 120
Period size: 31 Copynumber: 3.3 Consensus size: 31
304986 AATAACTATC
*
304996 AAATTTATAAATAATTATATTTAATATTCATT
1 AAATTTATAAATAATT-TATTTAATATTCATA
*
305028 AAATTTATAAATAATTTATTTAATATTTATA
1 AAATTTATAAATAATTTATTTAATATTCATA
* * * *
305059 AAATATACAAATAAATATATTT-A-ATTCATC
1 AAATTTATAAAT-AATTTATTTAATATTCATA
305089 AAATTTATAA
1 AAATTTATAA
305099 TCAATATCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 13 0.21
31 24 0.39
32 24 0.39
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATTTATAAATAATTTATTTAATATTCATA
Found at i:306058 original size:18 final size:17
Alignment explanation
Indices: 306033--306072 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
306023 AATATGAATA
306033 TAAAATATAATAATTTT
1 TAAAATATAATAATTTT
*
306050 TAAATATATAATATTTTT
1 TAAA-ATATAATAATTTT
306068 TAAAA
1 TAAAA
306073 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATATAATAATTTT
Found at i:306279 original size:21 final size:21
Alignment explanation
Indices: 306255--306299 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
306245 AAAAATAGCA
* *
306255 ATAGTGATGAGATT-AATTATT
1 ATAGTAATAAGATTGAA-TATT
306276 ATAGTAATAAGATTGAATATT
1 ATAGTAATAAGATTGAATATT
306297 ATA
1 ATA
306300 ATATGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
ATAGTAATAAGATTGAATATT
Found at i:306542 original size:18 final size:19
Alignment explanation
Indices: 306521--306565 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
306511 ATAAATAATT
*
306521 TAAAAATT-TTAAATAAAA
1 TAAAAATTATAAAATAAAA
306539 T--AAATTACTAAAATAAAA
1 TAAAAATTA-TAAAATAAAA
306557 TAAAAATTA
1 TAAAAATTA
306566 GAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.23
18 11 0.50
20 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAATAAAA
Found at i:306595 original size:44 final size:45
Alignment explanation
Indices: 306505--306597 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 45
306495 TTATTGTATT
*
306505 AAAT-AAATAAATAATTTAAAAATTTTAAATAAAATAAATTACTA
1 AAATAAAATAAATAATTTAAAAATTTTAAATAAAATAAATAACTA
* * *
306549 AAATAAAATAAA-AA-TTAGAAA-TTTATATATAAATAAATAATTTA
1 AAATAAAATAAATAATTTAAAAATTTTAAATA-AAATAAATAA-CTA
306593 AAATA
1 AAATA
306598 TTTAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
42 7 0.17
43 15 0.36
44 13 0.31
45 7 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (45 bp):
AAATAAAATAAATAATTTAAAAATTTTAAATAAAATAAATAACTA
Found at i:306611 original size:29 final size:26
Alignment explanation
Indices: 306547--306625 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 26
306537 AATAAATTAC
*
306547 TAAAAT-AAAATAAAAATTAGAAATT
1 TAAAATAAAAATAAAAATTAAAAATT
* *
306572 T-ATATATAAATAAATAATTTAAAATATT
1 TAAAATAAAAATAAA-AA-TTAAAA-ATT
*
306600 TAAAATAAAAATAAAAATAAAAAATT
1 TAAAATAAAAATAAAAATTAAAAATT
306626 ATATAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 3 0.07
25 8 0.19
26 5 0.12
27 10 0.23
28 6 0.14
29 11 0.26
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (26 bp):
TAAAATAAAAATAAAAATTAAAAATT
Found at i:311188 original size:33 final size:32
Alignment explanation
Indices: 311142--311225 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
311132 ATTGCAGCAG
* * * *
311142 TTTCGACTGCATTCATTTACCTTTGAATTGCTA
1 TTTCGATTACATTCATTT-CCCTTGAACTGCTA
*
311175 TTTCGATTACATTCATTCTCCCTTGAACTGCTG
1 TTTCGATTACATTCATT-TCCCTTGAACTGCTA
*
311208 TTTCAATTACATTCATTT
1 TTTCGATTACATTCATTT
311226 GCAGTAGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 42 0.95
34 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (32 bp):
TTTCGATTACATTCATTTCCCTTGAACTGCTA
Found at i:311639 original size:14 final size:14
Alignment explanation
Indices: 311620--311752 Score: 84
Period size: 14 Copynumber: 9.7 Consensus size: 14
311610 GAAAGAAAAC
*
311620 ATGCATGAAATGTA
1 ATGCATGAAATGAA
*
311634 ATGCATGAAACGAA
1 ATGCATGAAATGAA
311648 ATGCATGAAATGAA
1 ATGCATGAAATGAA
* * *
311662 CATTACGTGAAATG-C
1 -A-TGCATGAAATGAA
*
311677 ATGCATGAAATGTA
1 ATGCATGAAATGAA
311691 AT--AT---ATGAA
1 ATGCATGAAATGAA
311700 ATGCATGAAATGAAA
1 ATGCATGAAATG-AA
* *
311715 ATG-ATGTGTAATG-C
1 ATGCA--TGAAATGAA
*
311729 ATGCATGAAATGTA
1 ATGCATGAAATGAA
311743 ATGCATGAAA
1 ATGCATGAAA
311753 CTAAAAGCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
9 6 0.07
11 2 0.02
12 2 0.02
13 15 0.16
14 45 0.49
15 7 0.08
16 15 0.16
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (14 bp):
ATGCATGAAATGAA
Found at i:311687 original size:29 final size:26
Alignment explanation
Indices: 311648--311740 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 26
311638 ATGAAACGAA
311648 ATGCATGAAATGAACATTACGTGAAATGC
1 ATGCATGAAATGAA-ATTA-GTG-AATGC
*
311677 ATGCATGAAATGTAATATA-TGAA---
1 ATGCATGAAATGAAAT-TAGTGAATGC
*
311700 ATGCATGAAATGAAAATGATGTGTAATGC
1 ATGCATGAAATG-AAATTA-GTG-AATGC
311729 ATGCATGAAATG
1 ATGCATGAAATG
311741 TAATGCATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
23 13 0.25
24 3 0.06
25 2 0.04
26 4 0.08
27 2 0.04
28 2 0.04
29 27 0.51
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.27
Consensus pattern (26 bp):
ATGCATGAAATGAAATTAGTGAATGC
Found at i:311751 original size:52 final size:52
Alignment explanation
Indices: 311619--311752 Score: 169
Period size: 52 Copynumber: 2.5 Consensus size: 52
311609 TGAAAGAAAA
* *
311619 CATGCATGAAATGTAATGCATGAAACGAAATGCATGAAATGAACATTACGTGAAATG
1 CATGCATGAAATGTAATGCAT-----GAAATGCATGAAATGAAAATGACGTGAAATG
** * *
311676 CATGCATGAAATGTAATATATGAAATGCATGAAATGAAAATGATGTGTAATG
1 CATGCATGAAATGTAATGCATGAAATGCATGAAATGAAAATGACGTGAAATG
311728 CATGCATGAAATGTAATGCATGAAA
1 CATGCATGAAATGTAATGCATGAAA
311753 CTAAAAGCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 50 0.72
57 19 0.28
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (52 bp):
CATGCATGAAATGTAATGCATGAAATGCATGAAATGAAAATGACGTGAAATG
Found at i:311996 original size:8 final size:8
Alignment explanation
Indices: 311948--312028 Score: 51
Period size: 8 Copynumber: 10.4 Consensus size: 8
311938 TTTAAAATTA
*
311948 ATTTTTTT
1 ATTTTATT
*
311956 ATTTTGTT
1 ATTTTATT
* *
311964 AATTAATT
1 ATTTTATT
*
311972 AATTTATT
1 ATTTTATT
*
311980 A--TTACT
1 ATTTTATT
311986 ATTTTATT
1 ATTTTATT
* *
311994 ATTATAAT
1 ATTTTATT
*
312002 ATTATTAAT
1 ATT-TTATT
312011 ATTTTATT
1 ATTTTATT
312019 -TTTTATT
1 ATTTTATT
312026 ATT
1 ATT
312029 CATGTTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
6 5 0.09
7 7 0.12
8 39 0.67
9 7 0.12
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (8 bp):
ATTTTATT
Found at i:312813 original size:127 final size:126
Alignment explanation
Indices: 312549--313098 Score: 518
Period size: 127 Copynumber: 4.3 Consensus size: 126
312539 AATGTGAAAA
* * ** * ** *
312549 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGATA
1 AGTCTCGAGGGTCAAAGCCGACAGGCAGACTAAAGATAAGAAAGTCTCCAGGGTCAAAGCCGATA
* * * * * * *
312614 TGCAGACTGAAAGCAGGAAAGTCTCCAAGGTTAAAGCCGACAGGCAGACTTTAGATGAGGC
66 GGCAGACTGAAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGC
* * * *
312675 AGTCTCTAGGGTCAAAACCGACAGGCAGACTGAAAG-TAAGAAAGTCTCCAGGGTCAAAGTCGAG
1 AGTCTCGAGGGTCAAAGCCGACAGGCAGACT-AAAGATAAGAAAGTCTCCAGGGTCAAAGCCGAT
* * * *
312739 AGGTAGACTGAAAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTTTAGATGAGGC
65 AGGCAGACTG-AAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGC
** ** * **
312802 AGTCTCGAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGTTGATA
1 AGTCTCGAGGGTCAAAGCCGACAGGCAGACTAAAGATAAGAAAGTCTCCAGGGTCAAAGCCGATA
* * * ** * **
312867 GGCAGACTGAGGGTAGGAAAGTCTTCCAGGGTCAAAGCCGACAAGCAGACTAAAGGGTAAGAA
66 GGCAGACTGAAGGTAAGAAAGTC-TCCAAGGTCAAAGCCGACAAGCAGACTTTA-GATAAGGC
* * ** ** * *
312930 AGTCTCCG-GGATCAAAGCCGACAGACAGACTTTAGATGGGGCAA-TCTCCAGGGTTAAAGCCGA
1 AGTCT-CGAGGGTCAAAGCCGACAGGCAGACTAAAGAT-AAGAAAGTCTCCAGGGTCAAAGCCGA
* * *
312993 CAGGCAGACTGAGGGT-AGAAAAGTCTCCAAGGTCAAAGCCGAC-AGACAAACTTTAGATAAGGC
64 TAGGCAGACTGAAGGTAAG-AAAGTCTCCAAGGTCAAAGCCGACAAG-CAGACTTTAGATAAGGC
* *
313056 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTGAAAG-TAAGAAA
1 AGTCTCGAGGGTCAAAGCCGACAGGCAGACT-AAAGATAAGAAA
313099 ATTCATATTG
Statistics
Matches: 346, Mismatches: 67, Indels: 23
0.79 0.15 0.05
Matches are distributed among these distances:
125 4 0.01
126 105 0.30
127 161 0.47
128 72 0.21
129 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (126 bp):
AGTCTCGAGGGTCAAAGCCGACAGGCAGACTAAAGATAAGAAAGTCTCCAGGGTCAAAGCCGATA
GGCAGACTGAAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGC
Found at i:312947 original size:43 final size:42
Alignment explanation
Indices: 312518--313098 Score: 384
Period size: 42 Copynumber: 13.8 Consensus size: 42
312508 TTCTCTCGGA
* * * *
312518 TCAAAGCCAACGGGCAGACAAAATGTGAA-AAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGT-AAGAAAGTCTCCAGGG
* ** * * ** *
312560 TCAAAGTCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
* * * * *
312602 TCAAAGCCGATATGCAGACTGAAA-GCAGGAAAGTCTCCAAGG
1 TCAAAGCCGACAGGCAGACT-AAAGGTAAGAAAGTCTCCAGGG
* ** * * ** *
312644 TTAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
*
312686 TCAAAACCGACAGGCAGACTGAAA-GTAAGAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-AAAGGTAAGAAAGTCTCCAGGG
* * *
312728 TCAAAGTCGAGAGGTAGACTGAAAGGTAAGAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-AAAGGTAAGAAAGTCTCCAGGG
* * ** * * ** *
312771 TCAAAGCCGACAAGTAGACTTTAGATGAGGCAGTCTCGAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
** * ** *
312813 TCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
** * * * *
312855 TCAAAGTTGATAGGCAGACTGAGGGTAGGAAAGTCTTCCAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTC-TCCAGGG
*
312898 TCAAAGCCGACAAGCAGACTAAAGGGTAAGAAAGTCTCC-GGG
1 TCAAAGCCGACAGGCAGACTAAA-GGTAAGAAAGTCTCCAGGG
* ** * ** *
312940 ATCAAAGCCGACAGACAGACTTTAGATGGGGCAA-TCTCCAGGG
1 -TCAAAGCCGACAGGCAGACTAAAGGT-AAGAAAGTCTCCAGGG
* * * *
312983 TTAAAGCCGACAGGCAGACTGAGGGT-AGAAAAGTCTCCAAGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAG-AAAGTCTCCAGGG
* * ** * ** *
313025 TCAAAGCCGACAGACAAACTTTAGATAAGGCAGTCTCTAGGG
1 TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
*
313067 TCAAAGCCGACAGGTAGACTGAAA-GTAAGAAA
1 TCAAAGCCGACAGGCAGACT-AAAGGTAAGAAA
313099 ATTCATATTG
Statistics
Matches: 405, Mismatches: 120, Indels: 28
0.73 0.22 0.05
Matches are distributed among these distances:
40 1 0.00
41 4 0.01
42 298 0.74
43 91 0.22
44 11 0.03
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (42 bp):
TCAAAGCCGACAGGCAGACTAAAGGTAAGAAAGTCTCCAGGG
Found at i:313020 original size:170 final size:169
Alignment explanation
Indices: 312547--313098 Score: 467
Period size: 169 Copynumber: 3.3 Consensus size: 169
312537 AAAATGTGAA
* * ** * * ** *
312547 AAAGTCTCCAGGGTCAAAGTCGACAGGCAGACT-TTAGATGAGGCAGTCTCTAGGGTCAAAGCCG
1 AAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAAGGTAAGAAAGTCTCCAGGGTCAAAGCCG
* * * * * * * * * *
312611 ATATGCAGAC-TGA-AAGCAGGAAAGTCTCCAAGGTTAAAGCCGACAGGCAGACTTTAGATGAGG
66 ACAAGCAGACTTTAGATG-AGGCAA-TCTCCAGGGTCAAAGCCGACAGGCAGACTTGAGATAAGA
* * * *** *
312674 CAGTCTCTAGGGTCAAAACCGACAGGCAGACTGAAAGTAAG
129 AAGTCTCCAAGGTCAAAGTTGATAGGCAGACTGAAAGTAAG
* * * *
312715 AAAGTCTCCAGGGTCAAAGTCGAGAGGTAGACTGAAAGGTAAGAAAGTCTCCAGGGTCAAAGCCG
1 AAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAAGGTAAGAAAGTCTCCAGGGTCAAAGCCG
* * * * **
312780 ACAAGTAGACTTTAGATGAGGCAGTCTCGAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCA
66 ACAAGCAGACTTTAGATGAGGCAATCTCCAGGGTCAAAGCCGACAGGCAGACTTGAGATAAGAAA
** *
312845 GTCTCCAAGGTCAAAGTTGATAGGCAGACTGAGGGTAGG
131 GTCTCCAAGGTCAAAGTTGATAGGCAGACTGAAAGTAAG
312884 AAAGTCTTCCAGGGTCAAAGCCGACAAGCAGACT-AAAGGGTAAGAAAGTCTCC-GGGATCAAAG
1 AAAGTC-TCCAGGGTCAAAGCCGACAAGCAGACTGAAA-GGTAAGAAAGTCTCCAGGG-TCAAAG
* * *
312947 CCGAC-AGACAGACTTTAGATGGGGCAATCTCCAGGGTTAAAGCCGACAGGCAGAC-TGAGGGT-
63 CCGACAAG-CAGACTTTAGATGAGGCAATCTCCAGGGTCAAAGCCGACAGGCAGACTTGA-GATA
** * * * **
313009 AGAAAAGTCTCCAAGGTCAAAGCCGACAGACAAACT-TTAGATAAG
126 AG-AAAGTCTCCAAGGTCAAAGTTGATAGGCAGACTGAAAG-TAAG
** * * *
313054 GCAGTCTCTAGGGTCAAAGCCGACAGGTAGACTGAAA-GTAAGAAA
1 AAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAAGGTAAGAAA
313099 ATTCATATTG
Statistics
Matches: 317, Mismatches: 56, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
168 39 0.12
169 141 0.44
170 135 0.43
171 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (169 bp):
AAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAAGGTAAGAAAGTCTCCAGGGTCAAAGCCG
ACAAGCAGACTTTAGATGAGGCAATCTCCAGGGTCAAAGCCGACAGGCAGACTTGAGATAAGAAA
GTCTCCAAGGTCAAAGTTGATAGGCAGACTGAAAGTAAG
Found at i:319519 original size:52 final size:51
Alignment explanation
Indices: 319434--319557 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
319424 ATATGAAAAG
* *
319434 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
319485 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
319537 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
319558 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:319570 original size:51 final size:51
Alignment explanation
Indices: 319434--319577 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
319424 ATATGAAAAG
*
319434 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
319486 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
319537 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
319578 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:319584 original size:13 final size:13
Alignment explanation
Indices: 319566--319590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319556 CAAAGATCAG
319566 TGTATCGATACAA
1 TGTATCGATACAA
319579 TGTATCGATACA
1 TGTATCGATACA
319591 TTTGCGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:319668 original size:33 final size:33
Alignment explanation
Indices: 319631--319697 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
319621 AGTAGCTTAA
319631 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
319664 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
319697 A
1 A
319698 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:319671 original size:13 final size:13
Alignment explanation
Indices: 319653--319677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319643 CAAAAAAATA
319653 TGTATCGATACAT
1 TGTATCGATACAT
319666 TGTATCGATACA
1 TGTATCGATACA
319678 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320579 original size:55 final size:52
Alignment explanation
Indices: 320478--320763 Score: 289
Period size: 49 Copynumber: 5.7 Consensus size: 52
320468 GAAAAGTGAT
* * * * * **
320478 AAAGATGCCAATATG-TCGATTCACGACCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGAACTTAAAGATG-G-A
* *
320532 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
*
320585 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
* * *
320628 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
*
320678 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
*
320726 AAAGGTGCCAATATGGTGATTCAAGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
320764 GGCTTAGAAG
Statistics
Matches: 206, Mismatches: 16, Indels: 25
0.83 0.06 0.10
Matches are distributed among these distances:
43 40 0.19
44 1 0.00
46 1 0.00
49 83 0.40
51 1 0.00
52 33 0.16
53 6 0.03
54 5 0.02
55 35 0.17
56 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
Found at i:320632 original size:22 final size:22
Alignment explanation
Indices: 320607--320675 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
320597 ATGCTGATTC
320607 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
320629 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
320650 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
320672 AAGG
1 AAGG
320676 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:320701 original size:49 final size:49
Alignment explanation
Indices: 320541--320769 Score: 326
Period size: 49 Copynumber: 4.7 Consensus size: 49
320531 AAAAGGATGT
* *
320541 CAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
320593 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
320636 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
320685 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
320734 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
320770 GAAGGGTTGC
Statistics
Matches: 162, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
43 41 0.25
48 1 0.01
49 87 0.54
52 33 0.20
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:320900 original size:30 final size:29
Alignment explanation
Indices: 320775--321006 Score: 256
Period size: 30 Copynumber: 7.9 Consensus size: 29
320765 GCTTAGAAGG
* *
320775 GTTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 GTTGCCACTGAC-T-TGTGGGCTTTTGAAAA
* * *
320806 GGGTGCCACTGATTTGTGGGC-TTTGAAGA
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
320835 -TTGCCACTGACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
320862 GTTGCCACTGACTTGTGGGCTTTTGAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
* *
320891 ATATGCCACTGACTTGTGGGCTTTTGAACAG
1 GT-TGCCACTGACTTGTGGGCTTTTGAA-AA
* * *
320922 GGTGCCACTAACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
320950 GTTGCCACTGACTTGTGGGCTTTTGAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTG-AAAA
** *
320980 AATGCCACTGACTTGTGGACTTTTGAA
1 GTTGCCACTGACTTGTGGGCTTTTGAA
321007 GGGTGATGAA
Statistics
Matches: 172, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
27 19 0.11
28 50 0.29
29 14 0.08
30 78 0.45
31 2 0.01
32 9 0.05
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (29 bp):
GTTGCCACTGACTTGTGGGCTTTTGAAAA
Found at i:320956 original size:58 final size:58
Alignment explanation
Indices: 320774--321008 Score: 278
Period size: 58 Copynumber: 4.0 Consensus size: 58
320764 GGCTTAGAAG
* * * *
320774 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
* *
320833 GATTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT-AAA
** * *
320890 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
*** * *
320949 GGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
321007 GG
1 GG
321009 GTGATGAATG
Statistics
Matches: 152, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
55 22 0.14
56 3 0.02
57 14 0.09
58 73 0.48
59 15 0.10
60 25 0.16
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32
Consensus pattern (58 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
Found at i:320959 original size:88 final size:87
Alignment explanation
Indices: 320774--321006 Score: 326
Period size: 88 Copynumber: 2.7 Consensus size: 87
320764 GGCTTAGAAG
* * *** * *
320774 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGATT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTTGAAAGAGT
*
320837 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
* *
320861 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTTGAA-AGAGTG
320926 CCACTAACTTGTGGGCTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
*
320949 GGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTTGAA
321007 GGGTGATGAA
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
85 32 0.24
86 5 0.04
87 13 0.10
88 82 0.62
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.33
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTTGAAAGAGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:322465 original size:11 final size:10
Alignment explanation
Indices: 322446--322504 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
322436 GGACCCCCTT
322446 TTTGTTTTTG
1 TTTGTTTTTG
322456 TTTGGTTTTT-
1 TTT-GTTTTTG
322466 TATTGTTTTTG
1 T-TTGTTTTTG
* *
322477 TTTTTTTTTC
1 TTTGTTTTTG
322487 TTT-TGTTTT-
1 TTTGT-TTTTG
322496 TTTGTTTTT
1 TTTGTTTTT
322505 TATCATCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 8 0.19
10 25 0.60
11 9 0.21
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.83
Consensus pattern (10 bp):
TTTGTTTTTG
Found at i:322472 original size:21 final size:20
Alignment explanation
Indices: 322447--322548 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 20
322437 GACCCCCTTT
322447 TTGTTTTTGTTTGGTTTTTTA
1 TTGTTTTTGTTT-GTTTTTTA
*
322468 TTGTTTTTGTTT-TTTTTTC
1 TTGTTTTTGTTTGTTTTTTA
*
322487 TT-TTGTTTTTTTGTTTTTTA
1 TTGTT-TTTGTTTGTTTTTTA
*
322507 TCATCATTTTT-TTTGTTTTTTCA
1 T--T-GTTTTTGTTTGTTTTTT-A
*
322530 TTTTTTTTTGTTT-TTTTTT
1 -TTGTTTTTGTTTGTTTTTT
322549 GGAGGACGCC
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.03
19 14 0.21
20 7 0.10
21 23 0.34
22 15 0.22
23 4 0.06
24 3 0.04
ACGTcount: A:0.05, C:0.04, G:0.10, T:0.81
Consensus pattern (20 bp):
TTGTTTTTGTTTGTTTTTTA
Found at i:322491 original size:42 final size:44
Alignment explanation
Indices: 322445--322548 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 44
322435 CGGACCCCCT
*
322445 TTTTGTTTTTGTTTGGTTTTTTAT-T-GTTTTTGTTT-TTTTTTC-
1 TTTTGTTTTTGTTT-GTTTTTTATATCATTTTT-TTTGTTTTTTCA
322487 TTTTG-TTTT-TTTGTTTTTTATCATCATTTTTTTTGTTTTTTCA
1 TTTTGTTTTTGTTTGTTTTTTAT-ATCATTTTTTTTGTTTTTTCA
322530 TTTT-TTTTTGTTT-TTTTTT
1 TTTTGTTTTTGTTTGTTTTTT
322549 GGAGGACGCC
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
39 9 0.17
40 3 0.06
41 8 0.15
42 17 0.31
43 14 0.26
44 3 0.06
ACGTcount: A:0.05, C:0.04, G:0.10, T:0.82
Consensus pattern (44 bp):
TTTTGTTTTTGTTTGTTTTTTATATCATTTTTTTTGTTTTTTCA
Found at i:322498 original size:15 final size:14
Alignment explanation
Indices: 322444--322549 Score: 70
Period size: 15 Copynumber: 7.0 Consensus size: 14
322434 CCGGACCCCC
322444 TTTTTGTTTTTGTTTGG
1 TTTTT-TTTTT-TTT-G
322461 TTTTTTATTGTTTTTG
1 TTTTTT-TT-TTTTTG
322477 TTTTTTTTTCTTTTG
1 TTTTTTTTT-TTTTG
*
322492 TTTTTTTGTTTTTTA
1 TTTTTTT-TTTTTTG
* **
322507 TCATCATTTTTTTTG
1 T-TTTTTTTTTTTTG
*
322522 TTTTTTCATTTTTT-
1 TTTTTT-TTTTTTTG
*
322536 TTTGTTTTTTTTTG
1 TTTTTTTTTTTTTG
322550 GAGGACGCCG
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
13 6 0.08
14 8 0.11
15 32 0.45
16 13 0.18
17 10 0.14
18 2 0.03
ACGTcount: A:0.05, C:0.04, G:0.10, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:322530 original size:17 final size:18
Alignment explanation
Indices: 322450--322545 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 18
322440 CCCCTTTTTG
*
322450 TTTTTGTTTGGTTTTTT-A
1 TTTTT-TTTTGTTTTTTCA
* *
322468 TTGTTTTTGTTTTTTTTTCTT
1 TT-TTTTT-TTGTTTTTTC-A
322489 TTGTTTTTTTGTTTTTTATCA
1 TT-TTTTTTTG-TTTTT-TCA
322510 TCATTTTTTTTGTTTTTTCA
1 T--TTTTTTTTGTTTTTTCA
322530 TTTTTTTTTGTTTTTT
1 TTTTTTTTTGTTTTTT
322546 TTTGGAGGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
18 19 0.29
19 10 0.15
20 6 0.09
21 19 0.29
22 10 0.15
23 1 0.02
ACGTcount: A:0.05, C:0.04, G:0.09, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTCA
Found at i:332253 original size:10 final size:10
Alignment explanation
Indices: 332238--332264 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
332228 ATGTATCAAG
332238 CAAAAACAAA
1 CAAAAACAAA
332248 CAAAAACAAA
1 CAAAAACAAA
332258 CAAAAAC
1 CAAAAAC
332265 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:336533 original size:51 final size:52
Alignment explanation
Indices: 336440--336540 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 52
336430 GTAGGATAAG
***
336440 TGGGCAAATTTGCCTGCATGTATCGATACATTTTCTAATGTATCGATACATC
1 TGGGCAAATTTGCCTGCATGTATCGATACAAGATCTAATGTATCGATACATC
*
336492 TGGGCAAA-TTGCCTGCATGTATCGATACAAAGATC-AGTGTATCGATACA
1 TGGGCAAATTTGCCTGCATGTATCGATAC-AAGATCTAATGTATCGATACA
336541 ATGTATCGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 33 0.75
52 11 0.25
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (52 bp):
TGGGCAAATTTGCCTGCATGTATCGATACAAGATCTAATGTATCGATACATC
Done.