Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008274.1 Hibiscus syriacus cultivar Beakdansim tig00110931_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1661830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:202005 original size:16 final size:16
Alignment explanation
Indices: 201984--202016 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
201974 TAATAAATAA
201984 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
202000 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
202016 A
1 A
202017 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:202103 original size:16 final size:16
Alignment explanation
Indices: 202082--202135 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
202072 CATTTAATAA
202082 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
202098 ATAAACAAATACGAAC
1 ATAAACGAACACGAAC
*
202114 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
202130 ATAAAC
1 ATAAAC
202136 AGACATAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:202394 original size:12 final size:11
Alignment explanation
Indices: 202368--202406 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
202358 GAGACTCGAA
202368 CTCGATTCAAG
1 CTCGATTCAAG
*
202379 CTCGATTCTGAG
1 CTCGATTC-AAG
202391 CTCGATTCAAG
1 CTCGATTCAAG
202402 CTCGA
1 CTCGA
202407 CATTGCCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:202398 original size:23 final size:24
Alignment explanation
Indices: 202341--202406 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
202331 AAAAAATTAA
* *
202341 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTCAAGCTCGAGACTC
* **
202365 GAACTCGATTCAAGCTCGATTCT-
1 GAGCTCGATTCAAGCTCGAGACTC
202388 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
202407 CATTGCCCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTCAAGCTCGAGACTC
Found at i:203264 original size:14 final size:14
Alignment explanation
Indices: 203245--203285 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
203235 AGATTGGTTA
*
203245 AACATAAATGAATG
1 AACATAAACGAATG
*
203259 AACATAAACGAACG
1 AACATAAACGAATG
203273 AACATAAACGAAT
1 AACATAAACGAAT
203286 ATAATCGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (14 bp):
AACATAAACGAATG
Found at i:203294 original size:24 final size:24
Alignment explanation
Indices: 203262--203308 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
203252 ATGAATGAAC
203262 ATAAACGAACGAACATAAACGAAT
1 ATAAACGAACGAACATAAACGAAT
* *
203286 ATAATCGAACGAACATAACCGAA
1 ATAAACGAACGAACATAAACGAA
203309 CGTTCACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
ATAAACGAACGAACATAAACGAAT
Found at i:203296 original size:14 final size:14
Alignment explanation
Indices: 203258--203310 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
203248 ATAAATGAAT
*
203258 GAACATAAACGAAC
1 GAACATAACCGAAC
203272 GAACAT-A---AAC
1 GAACATAACCGAAC
* *
203282 GAATATAATCGAAC
1 GAACATAACCGAAC
203296 GAACATAACCGAAC
1 GAACATAACCGAAC
203310 G
1 G
203311 TTCACGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
13 1 0.03
14 22 0.69
ACGTcount: A:0.53, C:0.21, G:0.15, T:0.11
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:205163 original size:46 final size:45
Alignment explanation
Indices: 205110--205202 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 45
205100 CGGATCCTCA
205110 AAGCTGAAAAGCAATTATAATTCCATTCCCAGTGATTCTATGCATG
1 AAGCTGAAAAGCAATTATAATTCCATTCCCAGTGATT-TATGCATG
205156 AAGCTGAAAAGCAATTATAATTCCATTCCCAGTGATTTATGCATG
1 AAGCTGAAAAGCAATTATAATTCCATTCCCAGTGATTTATGCATG
205201 AA
1 AA
205203 TGTGTGACTG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 10 0.21
46 37 0.79
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (45 bp):
AAGCTGAAAAGCAATTATAATTCCATTCCCAGTGATTTATGCATG
Found at i:208118 original size:19 final size:19
Alignment explanation
Indices: 208084--208142 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
208074 TATTTTCTTC
208084 TATTAATTAT-TTTATTTT
1 TATTAATTATATTTATTTT
208102 TATTAATTATATTTA-TTT
1 TATTAATTATATTTATTTT
* *
208120 TA-AAATTTTATTTATATTT
1 TATTAATTATATTTAT-TTT
208139 TATT
1 TATT
208143 CATATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.29
18 15 0.44
19 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTAATTATATTTATTTT
Found at i:212107 original size:21 final size:21
Alignment explanation
Indices: 212083--212142 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
212073 TGTCATTATC
* *
212083 CACCATAGACCGTCACGTTAG
1 CACCGTAGACCGTCACATTAG
* *
212104 CACCGTAGATCATCACATTAG
1 CACCGTAGACCGTCACATTAG
*
212125 CATCGTAGACCGTCACAT
1 CACCGTAGACCGTCACAT
212143 CAGTACCATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (21 bp):
CACCGTAGACCGTCACATTAG
Found at i:212318 original size:21 final size:21
Alignment explanation
Indices: 212268--212320 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
212258 ATCCACCATG
*
212268 GACCGTCACGTTAGCACCGTA
1 GACCGTCACATTAGCACCGTA
* * *
212289 GATCATCACATTAGCATCGTA
1 GACCGTCACATTAGCACCGTA
212310 GACCGTCACAT
1 GACCGTCACAT
212321 CAATACCATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
GACCGTCACATTAGCACCGTA
Found at i:212369 original size:178 final size:178
Alignment explanation
Indices: 212070--212428 Score: 691
Period size: 178 Copynumber: 2.0 Consensus size: 178
212060 AGCCTATAAA
212070 CCATGTCATTATCCACCATAGACCGTCACGTTAGCACCGTAGATCATCACATTAGCATCGTAGAC
1 CCATGTCATTATCCACCATAGACCGTCACGTTAGCACCGTAGATCATCACATTAGCATCGTAGAC
*
212135 CGTCACATCAGTACCATAAAATGTCATATCAACATCGTAATGATCAACGAAAAATCGTTGATTAA
66 CGTCACATCAATACCATAAAATGTCATATCAACATCGTAATGATCAACGAAAAATCGTTGATTAA
*
212200 AGGGCCACATTGTAACCCCCTAGACATGCCTGTGCGTTACGACCAGAT
131 AGGGCCACATTGTAACCCCCTAGACATGCCTATGCGTTACGACCAGAT
*
212248 CCATGTCATTATCCACCATGGACCGTCACGTTAGCACCGTAGATCATCACATTAGCATCGTAGAC
1 CCATGTCATTATCCACCATAGACCGTCACGTTAGCACCGTAGATCATCACATTAGCATCGTAGAC
212313 CGTCACATCAATACCATAAAATGTCATATCAACATCGTAATGATCAACGAAAAATCGTTGATTAA
66 CGTCACATCAATACCATAAAATGTCATATCAACATCGTAATGATCAACGAAAAATCGTTGATTAA
212378 AGGGCCACATTGTAACCCCCTAGACATGCCTATGCGTTACGACCAGAT
131 AGGGCCACATTGTAACCCCCTAGACATGCCTATGCGTTACGACCAGAT
212426 CCA
1 CCA
212429 CTGAGTTACA
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (178 bp):
CCATGTCATTATCCACCATAGACCGTCACGTTAGCACCGTAGATCATCACATTAGCATCGTAGAC
CGTCACATCAATACCATAAAATGTCATATCAACATCGTAATGATCAACGAAAAATCGTTGATTAA
AGGGCCACATTGTAACCCCCTAGACATGCCTATGCGTTACGACCAGAT
Found at i:216868 original size:2 final size:2
Alignment explanation
Indices: 216861--216889 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
216851 AATTAGCTTT
216861 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
216890 TATATTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:222332 original size:79 final size:79
Alignment explanation
Indices: 222201--222362 Score: 270
Period size: 79 Copynumber: 2.1 Consensus size: 79
222191 CCCTAAACTT
* * * *
222201 ATGGTTCTTTTAACTAATATCTAGTGGATGGAACGAGACCCACTATCTATATAGAGATAGGAACT
1 ATGGTTCTTTTAACTAATAACAAGTGGATAGAACGAGACCCACTATCTATATAGAGATAGGAACC
*
222266 AACGTTTTATAAAG
66 AACGTTATATAAAG
*
222280 ATGGTTCTTTTAACTAATAACAAGTGGATAGAACGTGACCCACTATCTATATAGAGATAGGAACC
1 ATGGTTCTTTTAACTAATAACAAGTGGATAGAACGAGACCCACTATCTATATAGAGATAGGAACC
222345 AACGTTATATAAAG
66 AACGTTATATAAAG
222359 ATGG
1 ATGG
222363 ATGAACGCCA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (79 bp):
ATGGTTCTTTTAACTAATAACAAGTGGATAGAACGAGACCCACTATCTATATAGAGATAGGAACC
AACGTTATATAAAG
Found at i:226999 original size:22 final size:22
Alignment explanation
Indices: 226969--227021 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
226959 AAAGTGAGAA
*
226969 AGAATGAAAGCTTAGAAAAGTG
1 AGAATGAAAGCTTAGAAAAGTC
*
226991 ATAATGAAAGCTTAGAAAAGTC
1 AGAATGAAAGCTTAGAAAAGTC
227013 AGAATGAAA
1 AGAATGAAA
227022 AATAGCTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.53, C:0.06, G:0.23, T:0.19
Consensus pattern (22 bp):
AGAATGAAAGCTTAGAAAAGTC
Found at i:232334 original size:2 final size:2
Alignment explanation
Indices: 232327--232353 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
232317 TTCAAACAAC
232327 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
232354 CTTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:243398 original size:2 final size:2
Alignment explanation
Indices: 243391--243425 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
243381 ATGATAATAC
243391 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
243426 AGGCTATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:245434 original size:18 final size:18
Alignment explanation
Indices: 245408--245452 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
245398 CTACAATAAT
** *
245408 ATCTTCATCTTCATCTAC
1 ATCTTCATCAACATCAAC
*
245426 ATCTACATCAACATCAAC
1 ATCTTCATCAACATCAAC
245444 ATCTTCATC
1 ATCTTCATC
245453 CAATTCCTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
ATCTTCATCAACATCAAC
Found at i:253149 original size:75 final size:75
Alignment explanation
Indices: 253057--253206 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
253047 ATAAATACCC
253057 ACATACATAATATGTGCATAACTGATACAAACTCATTATTTTATACTAATAACATATTTTGACCA
1 ACATACATAATATGTGCATAACTGATACAAACTCATTATTTTATACTAATAACATATTTTGACCA
253122 TCTGTGGGCT
66 TCTGTGGGCT
* *
253132 ACATATATAATATGTGCATTACTGATACAAACTCATTATTTTATACTAATAACATATTTTGACCA
1 ACATACATAATATGTGCATAACTGATACAAACTCATTATTTTATACTAATAACATATTTTGACCA
253197 TCTGTGGGCT
66 TCTGTGGGCT
253207 CAGATTTCAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (75 bp):
ACATACATAATATGTGCATAACTGATACAAACTCATTATTTTATACTAATAACATATTTTGACCA
TCTGTGGGCT
Found at i:254924 original size:21 final size:21
Alignment explanation
Indices: 254898--255009 Score: 79
Period size: 21 Copynumber: 5.3 Consensus size: 21
254888 ATTTTGGATT
254898 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
254919 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
254940 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
254961 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
* *
254982 ATCGCAATGAATTTGAAATAA
1 ATCGCAACGAATTTGGAATAA
255003 ATCGCAA
1 ATCGCAA
255010 TACGAACTTG
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
19 15 0.22
21 35 0.52
23 17 0.25
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:254956 original size:42 final size:42
Alignment explanation
Indices: 254897--255031 Score: 225
Period size: 42 Copynumber: 3.2 Consensus size: 42
254887 GATTTTGGAT
*
254897 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGAC
254939 TATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGAC
* ** *
254981 TATCGCAATGAATTTGAAATAAATCGCAATACGAACTTGGAC
1 TATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGAC
255023 TATCGCAAT
1 TATCGCAAT
255032 TCGAATACGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (42 bp):
TATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGAC
Found at i:255027 original size:21 final size:20
Alignment explanation
Indices: 254891--255036 Score: 73
Period size: 21 Copynumber: 7.0 Consensus size: 20
254881 CGTTGCGATT
* *
254891 TTGGATTATCGCAA-CGAAT
1 TTGGACTATCGCAATCGAAC
* *
254910 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-TCGAAC
* *
254933 TTCGACTATCGCAAT-GAAT
1 TTGGACTATCGCAATCGAAC
* *
254952 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-TCGAAC
* *
254975 TTCGACTATCGCAAT-GAAT
1 TTGGACTATCGCAATCGAAC
* *
254994 TTGAAATAAATCGCAATACGAAC
1 TTGGACT--ATCGCAAT-CGAAC
255017 TTGGACTATCGCAATTCGAA
1 TTGGACTATCGCAA-TCGAA
255037 TACGTAAATC
Statistics
Matches: 94, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
19 21 0.22
21 47 0.50
22 1 0.01
23 25 0.27
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
TTGGACTATCGCAATCGAAC
Found at i:255125 original size:21 final size:21
Alignment explanation
Indices: 255073--255126 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
255063 ATTGGAATAA
* * *
255073 ATCGCAACGCGAACTTGGATT
1 ATCGCAATGCGAACTTCGACT
255094 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
255115 ATCGCATTGCGA
1 ATCGCAATGCGA
255127 TTTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:255161 original size:21 final size:21
Alignment explanation
Indices: 255135--255200 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
255125 GATTTACATA
255135 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
255156 TTCGCATTGCGATAATCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
255177 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
255198 TTC
1 TTC
255201 ACGCTGCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:255208 original size:21 final size:21
Alignment explanation
Indices: 255135--255209 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
255125 GATTTACATA
*
255135 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
255156 TTCGCATTGCGATAATCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
255177 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
255198 TTCACGCTGCGA
1 TTCGCGTTGCGA
255210 ATCTGGAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:261774 original size:174 final size:176
Alignment explanation
Indices: 261484--261834 Score: 679
Period size: 174 Copynumber: 2.0 Consensus size: 176
261474 TCCTTCATTG
261484 GTTAAAGAAGGGCCATAGCAGAACAGCCGGAACTCACAATTCCAAAATGATCCCAATATTACACA
1 GTTAAAGAAGGGCCATAGCAGAACAGCCGGAACTCACAATTCCAAAATGATCCCAATATTACACA
261549 AAAACCTGATTCAGTTGCCAACTGATATCTATCATCCCTCGACTGTGATCTTAATTCCG-AACCT
66 AAAACCTGATTCAGTTGCCAACTGATATCTATCATCCCTCGACTGTGATCTTAATTCCGAAACCT
261613 TATCACATCAATAAAGCTTGGA-TATCAAGATCATGAGCCCAACGC
131 TATCACATCAATAAAGCTTGGATTATCAAGATCATGAGCCCAACGC
261658 GTTAAAGAAGGGCCATAGCAGAACAGCCGGAACTCACAATTCCAAAATGATCCCAATATTACACA
1 GTTAAAGAAGGGCCATAGCAGAACAGCCGGAACTCACAATTCCAAAATGATCCCAATATTACACA
261723 AAAACCTGATTCAGTTGCCAACTGATATCTATCATCCCTCGACTGTGATCTTAATTCCGATAACC
66 AAAACCTGATTCAGTTGCCAACTGATATCTATCATCCCTCGACTGTGATCTTAATTCCGA-AACC
261788 TTATCACATCAATAAAGCTTGGATTATCAAGATCATGAGCCCAACGC
130 TTATCACATCAATAAAGCTTGGATTATCAAGATCATGAGCCCAACGC
261835 AACAATGGCA
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 124 0.71
176 27 0.16
177 23 0.13
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (176 bp):
GTTAAAGAAGGGCCATAGCAGAACAGCCGGAACTCACAATTCCAAAATGATCCCAATATTACACA
AAAACCTGATTCAGTTGCCAACTGATATCTATCATCCCTCGACTGTGATCTTAATTCCGAAACCT
TATCACATCAATAAAGCTTGGATTATCAAGATCATGAGCCCAACGC
Found at i:266735 original size:13 final size:14
Alignment explanation
Indices: 266695--266736 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
266685 ATGTGAATGT
*
266695 ATTTATATTCTTTTG
1 ATTTGTATTC-TTTG
266710 ATTTGTATTCTTTG
1 ATTTGTATTCTTTG
266724 ATTTGT-TTCTTTG
1 ATTTGTATTCTTTG
266737 GCTTCCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 7 0.27
14 10 0.38
15 9 0.35
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (14 bp):
ATTTGTATTCTTTG
Found at i:279114 original size:21 final size:21
Alignment explanation
Indices: 279050--279121 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
279040 TTAATTAGGG
*
279050 TTTAGGGTTTAAGGTTTTAGAA
1 TTTAAGGTTT-AGGTTTTAGAA
*
279072 TGTAAGGTTTAGG-TTTAGAA
1 TTTAAGGTTTAGGTTTTAGAA
*
279092 TTTAAGGTTTGGGTTTTAGAA
1 TTTAAGGTTTAGGTTTTAGAA
*
279113 TTTAGGGTT
1 TTTAAGGTT
279122 CAAATAGGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 18 0.41
21 18 0.41
22 8 0.18
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTAGGTTTTAGAA
Found at i:291473 original size:32 final size:31
Alignment explanation
Indices: 291432--291525 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
291422 AAAAAAAGCC
** *
291432 ATATCAATTTGGATTAAAAAAATTAAATTTAA
1 ATATCAATTTCAATT-AAAAAATTAAACTTAA
*
291464 ATATTAATTTCAATTAAAAAATTAAACTTAA
1 ATATCAATTTCAATTAAAAAATTAAACTTAA
* * * * * *
291495 ACATCAATATAAATTAACAAATCAAATTTAA
1 ATATCAATTTCAATTAAAAAATTAAACTTAA
291526 GTATATCATT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 39 0.76
32 12 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.35
Consensus pattern (31 bp):
ATATCAATTTCAATTAAAAAATTAAACTTAA
Found at i:291486 original size:31 final size:31
Alignment explanation
Indices: 291448--291525 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
291438 ATTTGGATTA
* * * *
291448 AAAAAATTAAATTTAAATATTAATTTCAATT
1 AAAAAATTAAATTTAAACATCAATATAAATT
*
291479 AAAAAATTAAACTTAAACATCAATATAAATT
1 AAAAAATTAAATTTAAACATCAATATAAATT
* *
291510 AACAAATCAAATTTAA
1 AAAAAATTAAATTTAA
291526 GTATATCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAAATTAAATTTAAACATCAATATAAATT
Found at i:292109 original size:60 final size:60
Alignment explanation
Indices: 291955--292110 Score: 149
Period size: 61 Copynumber: 2.6 Consensus size: 60
291945 GGAATGTTCA
** * *
291955 AAAAGTTATAG-GACCAATTTAGAATGCAG-GTCATAGTTTGGAGATGGAATTGAAAACGTTC
1 AAAAGTT-TAGAGA-CAATTTAGAATG-AGAGTCATAGTTTACAGATGAAATTGAAAACATTC
* * * *
292016 AAAAGTTT-GAGGAAAAGTTTAGAATGATAGTCATAGTTTACAGATGAAATTG-GAACATTT
1 AAAAGTTTAGA-GACAA-TTTAGAATGAGAGTCATAGTTTACAGATGAAATTGAAAACATTC
*
292076 AAAAGTTTAGAGATCAATTTAAAATGAGAGTCATA
1 AAAAGTTTAGAGA-CAATTTAGAATGAGAGTCATA
292111 CTGTGAGGAC
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
59 1 0.01
60 35 0.45
61 42 0.54
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (60 bp):
AAAAGTTTAGAGACAATTTAGAATGAGAGTCATAGTTTACAGATGAAATTGAAAACATTC
Found at i:296822 original size:21 final size:20
Alignment explanation
Indices: 296789--296827 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
296779 GAATGTGTCT
*
296789 GCAGAGGACAAAACCACCGG
1 GCAGAAGACAAAACCACCGG
*
296809 GCAGAAGAGCAAAATCACC
1 GCAGAAGA-CAAAACCACC
296828 ATTACAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.28, G:0.26, T:0.03
Consensus pattern (20 bp):
GCAGAAGACAAAACCACCGG
Found at i:297829 original size:22 final size:20
Alignment explanation
Indices: 297795--297837 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
297785 ATATTTATTT
* *
297795 AAAATATTTTTTATCAAATAA
1 AAAATATGTTTTA-AAAATAA
297816 AAAATTATGTTTTAAAAATAA
1 AAAA-TATGTTTTAAAAATAA
297837 A
1 A
297838 TATTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAATATGTTTTAAAAATAA
Found at i:308013 original size:7 final size:7
Alignment explanation
Indices: 308001--308026 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
307991 TAACAATGTA
308001 TTAAATT
1 TTAAATT
308008 TTAAATT
1 TTAAATT
308015 TTAAATT
1 TTAAATT
308022 TTAAA
1 TTAAA
308027 AAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:311266 original size:23 final size:22
Alignment explanation
Indices: 311236--311283 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
311226 GGATGGATTT
311236 ATAAAATTTTAA-AAGAAATGAAA
1 ATAAAATTTTAATAA-AAAT-AAA
311259 ATAAAATTTTAATAAAAATAAA
1 ATAAAATTTTAATAAAAATAAA
311281 ATA
1 ATA
311284 TATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 6 0.25
23 16 0.67
24 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAAAATTTTAATAAAAATAAA
Found at i:311944 original size:2 final size:2
Alignment explanation
Indices: 311939--311963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
311929 ATACAAAAAA
311939 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
311964 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:312350 original size:66 final size:66
Alignment explanation
Indices: 312244--312377 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
312234 AAAATAAAAA
312244 AAATGAAAATAGTATTATATTATTAAAGAATTTGATATAATTCATGCATAAAGTAGTATTTAATC
1 AAATGAAAATAGTATTATATTATTAAAGAATTTGATATAATTCATGCATAAAGTAGTATTTAATC
312309 T
66 T
312310 AAATGAAAATAGTATTATATTATTAAAGAATTTGATATAATTCATGCATAAAGTAGTATTTAATC
1 AAATGAAAATAGTATTATATTATTAAAGAATTTGATATAATTCATGCATAAAGTAGTATTTAATC
312375 T
66 T
312376 AA
1 AA
312378 CTAAAAATCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.39
Consensus pattern (66 bp):
AAATGAAAATAGTATTATATTATTAAAGAATTTGATATAATTCATGCATAAAGTAGTATTTAATC
T
Found at i:324702 original size:23 final size:21
Alignment explanation
Indices: 324676--324717 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
324666 TCAAATTTTG
324676 ATTTGAATTAATTATATAAAATA
1 ATTT-AATT-ATTATATAAAATA
*
324699 ATTTAATTCTTATATAAAA
1 ATTTAATTATTATATAAAA
324718 CCCACAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTAATTATTATATAAAATA
Found at i:328033 original size:46 final size:46
Alignment explanation
Indices: 327955--328061 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
327945 TCGTGGGAGT
* *
327955 AGTAGTCTTAACAGTCGACGGGGATTCGGATTTTGCAGGGCCGAAC
1 AGTAGTCTTAACAGTCGACGGGGATCCAGATTTTGCAGGGCCGAAC
* * * * ** *
328001 AGTATTCTTAACAGTCGTCGGTGCTCCAGATTTTGCAGGGGGGAGC
1 AGTAGTCTTAACAGTCGACGGGGATCCAGATTTTGCAGGGCCGAAC
328047 AGTAGTCTTAACAGT
1 AGTAGTCTTAACAGT
328062 TGCAGGAGCG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (46 bp):
AGTAGTCTTAACAGTCGACGGGGATCCAGATTTTGCAGGGCCGAAC
Found at i:337759 original size:17 final size:16
Alignment explanation
Indices: 337730--337764 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
337720 TTCAAATTAG
*
337730 TATTTTTGTTTTTTTA
1 TATTTTTATTTTTTTA
337746 TATTTTTATATTTTTTA
1 TATTTTTAT-TTTTTTA
337763 TA
1 TA
337765 GAAAGACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TATTTTTATTTTTTTA
Found at i:339288 original size:31 final size:28
Alignment explanation
Indices: 339212--339302 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 28
339202 TTTGGATGAA
339212 TTTGGGGATGAAATTAGAAATTTCAAAG
1 TTTGGGGATGAAATTAGAAATTTCAAAG
* * * *
339240 TTTGAGAACT-AATTTAGAAATAGGTTCATAG
1 TTTGGGGA-TGAAATTAGAAAT---TTCAAAG
*
339271 TTTGGGGATGAAATTAGAATGTTTCAAAG
1 TTTGGGGATGAAATTAGAA-ATTTCAAAG
339300 TTT
1 TTT
339303 AAAGACTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
28 16 0.33
29 10 0.21
30 1 0.02
31 20 0.42
32 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (28 bp):
TTTGGGGATGAAATTAGAAATTTCAAAG
Found at i:339391 original size:60 final size:59
Alignment explanation
Indices: 339210--339399 Score: 204
Period size: 60 Copynumber: 3.2 Consensus size: 59
339200 TATTTGGATG
* * *
339210 AATTTGGGGATGAAATTAGAA-ATTTCAAAGTTTGAGAACTAATTTAGAAATAG-GTTCAT
1 AATTTGGGGATGAAATTAGAATATTTCAAAGTTTAAGGACTAATTTA-AAATGGAGTT-AT
* * * * **
339269 AGTTTGGGGATGAAATTAGAATGTTTCAAAGTTTAAAGACTAATTTAGAATGAGAGACAT
1 AATTTGGGGATGAAATTAGAATATTTCAAAGTTTAAGGACTAATTTAAAATG-GAGTTAT
* * * *
339329 AATTTGAGGATGAAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAATTGGAGTTAT
1 AATTTGGGGATGAAATTAGAATATTTCAAAGTTTAAGGACTAATTTAAAA-TGGAGTTAT
*
339389 AATTTAGGGAT
1 AATTTGGGGAT
339400 ATATGATGCA
Statistics
Matches: 106, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
59 23 0.22
60 80 0.75
61 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (59 bp):
AATTTGGGGATGAAATTAGAATATTTCAAAGTTTAAGGACTAATTTAAAATGGAGTTAT
Found at i:341738 original size:31 final size:33
Alignment explanation
Indices: 341681--341747 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
341671 CAAAAATAAT
341681 AAAATAATAAATGAATATTAAATAAATC-AAAGA
1 AAAATAATAAATGAATA-TAAATAAATCAAAAGA
341714 AAAATAATCAAAT-AATA-AAATAAATCAAAAGA
1 AAAATAAT-AAATGAATATAAATAAATCAAAAGA
341746 AA
1 AA
341748 GAACGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 9 0.28
32 7 0.22
33 12 0.38
34 4 0.12
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (33 bp):
AAAATAATAAATGAATATAAATAAATCAAAAGA
Found at i:341901 original size:12 final size:10
Alignment explanation
Indices: 341849--341895 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
341839 AGAAAGAAAA
341849 AAAAAATAA-
1 AAAAAATAAG
*
341858 AATAAATAAG
1 AAAAAATAAG
*
341868 AATATAATAAG
1 AA-AAAATAAG
341879 AAAAAATAAG
1 AAAAAATAAG
341889 AAAAAAT
1 AAAAAAT
341896 CAAAGACAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAAAATAAG
Found at i:343256 original size:84 final size:84
Alignment explanation
Indices: 343106--344137 Score: 1096
Period size: 84 Copynumber: 12.4 Consensus size: 84
343096 AATTTATTGA
* * * * * * * * *
343106 CAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATCTGATTTGCCTCT-GAGCTAAGTGTAATC
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGCGTAGTC
* *
343170 GAACTCGAAGGTATTTGGTCGG
63 GAACTCGAAGGTCTTTGGTTGG
* * * *
343192 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTAAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
343257 CTCGAAGGTCTTTTGTTGA
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * * ** *
343276 CAGATAACCCTTTTAG-CCTGAGTTATGTTGAAAATGATGTGCCCTCGACGCTGAGTTTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA-GCTGAGCGTAGTCGA
*
343340 ACTCG-AGGGC--T--TTGG
65 ACTCGAAGGTCTTTGGTTGG
* *
343355 CAGATAA-CCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
343419 CTCGAAGGTCTTTGGTTGA
66 CTCGAAGGTCTTTGGTTGG
* *
343438 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
343503 CTCGAAGGTCTTT-TTTGA
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * * *
343521 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATTATGTGCCCTCGAAGCTGAGTGTAATTGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
343586 ACTCG-AGAGTC--T--TTGG
65 ACTCGAAG-GTCTTTGGTTGG
* * * *
343602 CAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
343667 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* *
343686 CAGATAACCCTTCTCGACTTAAGTTATGCTGC-AATAATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* **
343750 CTCGAAAGTCTTTAGG-TCA
66 CTCGAAGGTCTTT-GGTTGG
* * * * * * ** *
343769 CAGATAACCCTTCTAGACTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
*
343834 ACTCGAGGGTC--T--TTGG
65 ACTCGAAGGTCTTTGGTTGG
* *
343850 CAGATAGCCCTTCTCGATTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
343915 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* *
343934 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
343999 CTCAAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * *
344018 AAGATAGCTCTTCTCGATTTAAGTTATGTTGTAAATGATGTGCCTTTGAGCTGACCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
344083 CTCGAAAGTCTTTTGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * *
344102 CAGATAACCCTTATAGCCTTGAGTTATGCTGCAAAT
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
344138 AGTTTCTTTA
Statistics
Matches: 786, Mismatches: 136, Indels: 50
0.81 0.14 0.05
Matches are distributed among these distances:
78 23 0.03
79 39 0.05
80 53 0.07
81 79 0.10
82 3 0.00
83 153 0.19
84 382 0.49
85 26 0.03
86 28 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGG
Found at i:344084 original size:248 final size:249
Alignment explanation
Indices: 343168--344087 Score: 1361
Period size: 248 Copynumber: 3.7 Consensus size: 249
343158 CTAAGTGTAA
* * * * *
343168 TCGAACTCGAAGGTATTTGGTCGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * * * *
343233 ACCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTTTAG-CCTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGACTTGA
* * * *
343297 GTTATGTTGAAAATGATGTGCCCTCGACGCTGAGTTTAATCGAACTCGAGGG-CTTTGGCAGATA
131 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
* * *
343361 -ACCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
196 GCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
343414 TCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * *
343479 GCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT-TTGACAGATAACCCTTCTAGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGACTTGA
* * * *
343543 GTTATGCTGCAAATTATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGAGAGTCTTTGGCAGATA
131 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
*
343608 GCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAG
196 GCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
343662 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC-AATAATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * *
343726 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAA-GTCTTTAGGTCACAGATAACCCTTCTAGACTTG
66 GCCTTGGAGCTGAGCGTAGTCGAACTC-AAAGGTCTTTTGTTGACAGATAACCCTTCTAGACTTG
* *
343790 AGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGGCAGAT
130 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
*
343855 AGCCCTTCTCGATTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
195 AGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
343910 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * * * * *
343975 GCCTTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTTGGA-AGATAGCTCTTCTCGATTTA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTT-GACAGATAACCCTTCTAGACTTG
* * * ** *
344039 AGTTATGTTGTAAATGATGTGCCTTTG-AGCTGACCGTAGTCGAACTCGA
130 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
344088 AAGTCTTTTG
Statistics
Matches: 610, Mismatches: 56, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
245 19 0.03
246 143 0.23
247 51 0.08
248 317 0.52
249 79 0.13
250 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (249 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGACTTGA
GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
GCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:345354 original size:81 final size:88
Alignment explanation
Indices: 345252--345472 Score: 212
Period size: 81 Copynumber: 2.5 Consensus size: 88
345242 GGCTAGCTGG
* *
345252 ATCCATAAAG-CTGGGGCGTTTAACCAATTTCTCTAGAGGGACAACTTAAT-T-TA-TA-AA-TA
1 ATCCATAAAGTC-GGAGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATGTATAGTATAATTA
*
345311 CATTTATCAGGTTAGCT-AA-ATT
65 CATTTATCAGGCTAGCTGAATATT
* *
345333 ATCCATAAAGTCGGAGCGTTTAACC-ATTGC-CTTTGAGGGACAGCTCAAACTTTATTGTATAGT
1 ATCCATAAAGTCGGAGCGTTTAACCAATTGCTC-TAGAGGG--A---C-AAC-TTAATGTATAGT
*
345396 ATAATTACCTTTATCAGGCTAGCTGAATATT
58 ATAATTACATTTATCAGGCTAGCTGAATATT
*
345427 ATCCATAAA-TCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACT
1 ATCCATAAAGTCGGA-GCGTTTAACCAATTGCTCTAGAGGGACAACT
345473 CAAGCTTTAT
Statistics
Matches: 113, Mismatches: 8, Indels: 31
0.74 0.05 0.20
Matches are distributed among these distances:
79 1 0.01
80 10 0.09
81 22 0.19
82 2 0.02
85 1 0.01
86 3 0.03
87 4 0.04
88 2 0.02
89 5 0.04
90 3 0.03
91 2 0.02
92 17 0.15
93 7 0.06
94 22 0.19
95 11 0.10
96 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (88 bp):
ATCCATAAAGTCGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATGTATAGTATAATTAC
ATTTATCAGGCTAGCTGAATATT
Found at i:345495 original size:94 final size:92
Alignment explanation
Indices: 345303--345495 Score: 257
Period size: 94 Copynumber: 2.1 Consensus size: 92
345293 CAACTTAATT
* * * *
345303 TATAAATACATTTATCAGGTTAGCTAAATTATCCATAAAGTCGGAGCGTTTAACCATTGCCTTTG
1 TATAATTACATTTATCAGGCTAGCTAAATTATCCATAAAGTCCGAGCGTTTAACCATTGCCTTAG
*
345368 AGGGACAGCTCAAACTTTATTGTATAG
66 AGGGACAACTCAAACTTTATTGTATAG
*
345395 TATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAA-TCCGAGGCGTTTAACCAATTG-C
1 TATAATTACATTTATCAGGCTAGCT-AA-ATTATCCATAAAGTCCGA-GCGTTTAACC-ATTGCC
*
345458 TCTAGAGGGACAACTCAAGCTTTATTGTATA-
62 T-TAGAGGGACAACTCAAACTTTATTGTATAG
345489 TATAATT
1 TATAATT
345496 TTAATCTGGG
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
92 22 0.25
93 6 0.07
94 31 0.35
95 30 0.34
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (92 bp):
TATAATTACATTTATCAGGCTAGCTAAATTATCCATAAAGTCCGAGCGTTTAACCATTGCCTTAG
AGGGACAACTCAAACTTTATTGTATAG
Found at i:349153 original size:140 final size:140
Alignment explanation
Indices: 348832--349112 Score: 449
Period size: 140 Copynumber: 2.0 Consensus size: 140
348822 ATAATTAAAG
****
348832 GTAAATAATCGAATAAATAAATTAAAA-TAAATTTTA-CATTTTCGCATAAAAAGACAACCAAAA
1 GTAAATAATCGAATAAATAAATTAAAATTAAAACCGACCATTTTCGCATAAAAAGACAACCAAAA
348895 ATTCCTGACTCATTACTGTCCCCAGCGGAGTCGCCAAGCTGTCGAAACGTCTTTCGGTTGGGCCC
66 ATTCCTGACTCATTACTGTCCCCAGCGGAGTCGCCAAGCTGTCGAAACGTCTTTCGGTTGGGCCC
348960 GGAATTGGGC
131 GGAATTGGGC
*** *
348970 GTAAATAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTCGCATAAAAAGACAACCAAAA
1 GTAAATAATCGAATAAATAAATTAAAATTAAAACCGACCATTTTCGCATAAAAAGACAACCAAAA
349035 ATTCCTGACTCATTTACATGTCCCCAGCGGAGTCGCCAAGCTGTCGAAACCGTCTTTCGGTTGGG
66 ATTCCTGACTCA-TTAC-TGTCCCCAGCGGAGTCGCCAAGCTGTCGAAA-CGTCTTTCGGTTGGG
349100 CCCGGAATTGGGC
128 CCCGGAATTGGGC
349113 TTCGACGTGA
Statistics
Matches: 136, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
138 27 0.20
139 8 0.06
140 38 0.28
141 4 0.03
142 31 0.23
143 28 0.21
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (140 bp):
GTAAATAATCGAATAAATAAATTAAAATTAAAACCGACCATTTTCGCATAAAAAGACAACCAAAA
ATTCCTGACTCATTACTGTCCCCAGCGGAGTCGCCAAGCTGTCGAAACGTCTTTCGGTTGGGCCC
GGAATTGGGC
Found at i:349460 original size:9 final size:9
Alignment explanation
Indices: 349402--349479 Score: 56
Period size: 9 Copynumber: 8.3 Consensus size: 9
349392 AAAATGTTAG
349402 AAATAATAAT
1 AAATAA-AAT
349412 -AATAATAAT
1 AAATAA-AAT
349421 AAATATTAAAT
1 AAATA--AAAT
349432 AAATCAAAGA-
1 AAAT-AAA-AT
*
349442 AAAAAAAAT
1 AAATAAAAT
349451 AAATAAAAT
1 AAATAAAAT
349460 --ATAAAAT
1 AAATAAAAT
349467 AAATCAAAAT
1 AAAT-AAAAT
349477 AAA
1 AAA
349480 GAATGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
7 7 0.12
8 1 0.02
9 22 0.39
10 17 0.30
11 8 0.14
12 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:349467 original size:16 final size:17
Alignment explanation
Indices: 349421--349477 Score: 62
Period size: 16 Copynumber: 3.3 Consensus size: 17
349411 TAATAATAAT
*
349421 AAATATTAAATAAATCAA
1 AAATATAAAATAAATC-A
* *
349439 AGAAAAAAAAATAAAT-A
1 A-AATATAAAATAAATCA
349456 AAATATAAAATAAATCA
1 AAATATAAAATAAATCA
349473 AAATA
1 AAATA
349478 AAGAATGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 12 0.38
17 8 0.25
18 1 0.03
19 11 0.34
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATATAAAATAAATCA
Found at i:349549 original size:60 final size:58
Alignment explanation
Indices: 349433--349549 Score: 130
Period size: 60 Copynumber: 2.0 Consensus size: 58
349423 ATATTAAATA
* * **
349433 AATCAAAGAAAAAAAAATAAATAAAATATAAAATAAATCAAAATAAAGAATGAAAAAC
1 AATCAAAGAAAAAAAAATAAACAAAATAAAAAATAAATCAAAATAAAGAAAAAAAAAC
* *
349491 AATCAAAGAAAAGAAAGATTAAACAAAA-AAAATAATAAATTGAAAAT-AAGAAAAAAAAA
1 AATCAAAGAAAA-AAA-AATAAACAAAATAAAA-AATAAA-TCAAAATAAAGAAAAAAAAA
349550 TAAAAGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
58 12 0.24
59 6 0.12
60 25 0.51
61 6 0.12
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (58 bp):
AATCAAAGAAAAAAAAATAAACAAAATAAAAAATAAATCAAAATAAAGAAAAAAAAAC
Found at i:349595 original size:21 final size:21
Alignment explanation
Indices: 349571--349623 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
349561 TAATCAAAGA
349571 AAGAAAAAAAT-AAAAATATAT
1 AAGAAAAAAATAAAAAATA-AT
* *
349592 AAGAATAGAATAAAAAATAAT
1 AAGAAAAAAATAAAAAATAAT
349613 AAGAAAAAAAT
1 AAGAAAAAAAT
349624 CGAAGACAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (21 bp):
AAGAAAAAAATAAAAAATAAT
Found at i:350356 original size:33 final size:35
Alignment explanation
Indices: 350314--350380 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
350304 CTAGTATGAA
350314 CTCCCGTTGTA-TTTCCTTG-AAACTCTATATTTT
1 CTCCCGTTGTATTTTCCTTGAAAACTCTATATTTT
350347 CTCCCGTTGTATTTTCCTTGAAAACTCTATATTT
1 CTCCCGTTGTATTTTCCTTGAAAACTCTATATTT
350381 CCGTCCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 11 0.34
34 8 0.25
35 13 0.41
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.48
Consensus pattern (35 bp):
CTCCCGTTGTATTTTCCTTGAAAACTCTATATTTT
Found at i:358688 original size:16 final size:18
Alignment explanation
Indices: 358648--358692 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
358638 TGTTTATGAG
*
358648 GGAATTGAAATATGTGAA
1 GGAATTGGAATATGTGAA
358666 GGAATTGGAATATGT-AA
1 GGAATTGGAATATGTGAA
358683 -GAATTGGAAT
1 GGAATTGGAAT
358693 CCAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.38
17 2 0.08
18 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATATGTGAA
Found at i:358744 original size:33 final size:33
Alignment explanation
Indices: 358701--358781 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
358691 ATCCAATTTA
* *
358701 ATATTCTGTTTGGTTGACAGGAAATGGAATTGG
1 ATATTCTGTTTGGTTGACAAGAAATGAAATTGG
* *
358734 ATATTATGTTTGGTTGGCAAGAAATGAAATTGG
1 ATATTCTGTTTGGTTGACAAGAAATGAAATTGG
358767 ATATTCTGTTTGGTT
1 ATATTCTGTTTGGTT
358782 CGCAGACATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (33 bp):
ATATTCTGTTTGGTTGACAAGAAATGAAATTGG
Found at i:359634 original size:215 final size:218
Alignment explanation
Indices: 359222--359752 Score: 713
Period size: 215 Copynumber: 2.4 Consensus size: 218
359212 TAAAAGGTAA
*
359222 AATTATATATATTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCTGACCCG
1 AATTATATATATTTTT-GGGTCGGTCCGGTTTTTTT-ACCCTAAACCCGAACCCGACCCGACCCG
* * * *
359287 AATATCACACTT----AACACGACCCGACCTGAACAAAATAAAGTTTCATCCTACCCGACTCGAA
64 AATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAA
* *
359348 TATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAA
129 AATATGAATTAGAAAT-C-A-CCGACCCGACACGAAATAATAAAAAAATATTTTTATTTAATAAA
*
359413 AACAGTGACTTAAT-CTGACCCGACCCG
191 AACAGTGACTTAATCCCGACCCGACCCG
* *
359440 AA-T-TATATA-TTTTGGGTCGGTCCGGTTTTTTTACCCTAAACCCGAACTCGACCCGACCCAAA
1 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTACCCTAAACCCGAACCCGACCCGACCCGAA
359502 TATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCC
66 TATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGA---
* **
359567 AAATATGAATTAGAAAT-A-CGATCCGACACGAAATAATAAAAATTTATTTTTATTTAATAAAAA
128 AAATATGAATTAGAAATCACCGACCCGACACGAAATAATAAAAAAATATTTTTATTTAATAAAAA
359630 CAGTGACTTAATCCGACCCGACCCGACCCG
193 CAGTGACTTAAT----CCCGACCCGACCCG
* * * * *
359660 AATTATATATATTTTTGGGTCGGTCTGGTTTTTTCACCCTAAACCTGAACCCGACCCAACCTGAA
1 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTACCCTAAACCCGAACCCGACCCGACCCGAA
359725 TATCACACTTAAAAAAACCCGACCCGAC
66 TATCACACTT-AAAAAACCCGACCCGAC
359753 TCGACCCGAA
Statistics
Matches: 277, Mismatches: 20, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
213 37 0.13
214 19 0.07
215 57 0.21
216 6 0.02
217 46 0.17
218 2 0.01
220 30 0.11
221 1 0.00
222 6 0.02
223 56 0.20
224 17 0.06
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (218 bp):
AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTACCCTAAACCCGAACCCGACCCGACCCGAA
TATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAAAA
TATGAATTAGAAATCACCGACCCGACACGAAATAATAAAAAAATATTTTTATTTAATAAAAACAG
TGACTTAATCCCGACCCGACCCG
Found at i:359786 original size:37 final size:38
Alignment explanation
Indices: 359708--359788 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
359698 CTAAACCTGA
*
359708 ACCCGACCCAACCTGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAAACCCG
* *
359746 ACCCGACTCGACCCGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAAACCCG
359783 ACCCGA
1 ACCCGA
359789 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 16 0.40
38 24 0.60
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (38 bp):
ACCCGACCCAACCCGAATATCACACTTAAAAAAACCCG
Found at i:359937 original size:241 final size:243
Alignment explanation
Indices: 359477--359989 Score: 664
Period size: 241 Copynumber: 2.1 Consensus size: 243
359467 TTTTTACCCT
*
359477 AAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAA
1 AAACCCG-ACCCGACCCGACCCAAATATCACACTTAAAAAA--C-ACCCGACCCGAACAAAATAA
* *
359542 AGTTTCATCCGACCCGACCCGACCCAAATATGAATTAGAAATACGATCCGACACGAAATAATAAA
62 AGTTTCAT----CCCGACCCG---CAAATATGAATTAGAAATACAACCCGACACGAAATAATAAA
*
359607 AATTTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGACCCGAATTATATATAT
120 AAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGA--C-AATTATATATAT
* * *
359672 TTTTGGGTCGGTCTGGTTTTTTCACCCTAAACCTGAACCCGACCCAACCTGAATATCACAC-TTA
182 TTTCGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGA--C--CC-GAATATCAC-CTTTA
359736 AAA
241 AAA
* *
359739 AAACCCGACCCGACTCGACCCGAATATCACACTT-AAAAA-ACCCGACCCGAACAAAATAAAGTT
1 AAACCCGACCCGACCCGACCCAAATATCACACTTAAAAAACACCCGACCCGAACAAAATAAAGTT
* * *
359802 TCAT-CCGACCCG-ATATATGAATTAGAAATCCAACCCGACCCGAAATAATAAAAAATTA-TTTT
66 TCATCCCGACCCGCAAATATGAATTAGAAATACAACCCGACACGAAATAATAAAAAATTATTTTT
*
359864 ATTTAATAAAAACAGTGACTTAATCCGACCCGA-CCTA-AATTATATATATTTTCGGGTCGGTCC
131 ATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGACAATTATATATATTTTCGGGTCGGTCC
*
359927 GGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCACCTTTATAA
196 GGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCACCTTTAAAA
359975 AAACCCGACCCGACC
1 AAACCCGACCCGACC
359990 AAAATAAAGT
Statistics
Matches: 235, Mismatches: 15, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
235 1 0.00
236 28 0.12
237 2 0.01
239 1 0.00
241 51 0.22
245 3 0.01
246 37 0.16
247 40 0.17
251 8 0.03
256 28 0.12
260 5 0.02
261 24 0.10
262 7 0.03
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (243 bp):
AAACCCGACCCGACCCGACCCAAATATCACACTTAAAAAACACCCGACCCGAACAAAATAAAGTT
TCATCCCGACCCGCAAATATGAATTAGAAATACAACCCGACACGAAATAATAAAAAATTATTTTT
ATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGACAATTATATATATTTTCGGGTCGGTCC
GGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCACCTTTAAAA
Found at i:374305 original size:29 final size:29
Alignment explanation
Indices: 374243--374317 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
374233 TCCACAAATT
* *
374243 AACACCTATGTACTTT-AAGAAATGATTG
1 AACACCTATGTGCTTTAAAAAAATGATTG
*
374271 AACACCTCTGTGCTTTAAAAAAATGATTG
1 AACACCTATGTGCTTTAAAAAAATGATTG
* *
374300 AGCACCTATGTGTTTTAA
1 AACACCTATGTGCTTTAA
374318 TCTACAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 14 0.35
29 26 0.65
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (29 bp):
AACACCTATGTGCTTTAAAAAAATGATTG
Found at i:375489 original size:21 final size:21
Alignment explanation
Indices: 375463--375507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
375453 GATTTCTGGG
* *
375463 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
375484 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
375505 CAA
1 CAA
375508 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:377167 original size:13 final size:13
Alignment explanation
Indices: 377149--377189 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
377139 TCTACGGGCA
377149 CTACGGTGCAATT
1 CTACGGTGCAATT
377162 CTACGG-GC-A--
1 CTACGGTGCAATT
377171 CTACGGTGCAATT
1 CTACGGTGCAATT
377184 CTACGG
1 CTACGG
377190 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:377210 original size:22 final size:22
Alignment explanation
Indices: 377137--377202 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
377127 TATGGACATC
377137 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
377159 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
377181 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
377203 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:380325 original size:21 final size:21
Alignment explanation
Indices: 380299--380343 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
380289 GATTTCTGGG
* *
380299 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
380320 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
380341 CAA
1 CAA
380344 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:382013 original size:13 final size:13
Alignment explanation
Indices: 381995--382035 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
381985 TCTACGGGCA
381995 CTACGGTGCAATT
1 CTACGGTGCAATT
382008 CTACGG-GC-A--
1 CTACGGTGCAATT
382017 CTACGGTGCAATT
1 CTACGGTGCAATT
382030 CTACGG
1 CTACGG
382036 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:382056 original size:22 final size:22
Alignment explanation
Indices: 381983--382048 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
381973 TATGGACATC
381983 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
382005 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
382027 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
382049 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:396764 original size:30 final size:30
Alignment explanation
Indices: 396728--396789 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
396718 AAAAATTATC
*
396728 AAGAATGAAAATACTTTTTTTATTAAGAAG
1 AAGAATGAAAATAATTTTTTTATTAAGAAG
396758 AAGAATGAAAATAATTTTTTTATTAAGAAG
1 AAGAATGAAAATAATTTTTTTATTAAGAAG
396788 AA
1 AA
396790 AAAAATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (30 bp):
AAGAATGAAAATAATTTTTTTATTAAGAAG
Found at i:405596 original size:20 final size:19
Alignment explanation
Indices: 405554--405596 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
405544 TTTTATTAAT
**
405554 TTTTTAATTTAAAATATTT
1 TTTTTAATTTAAAATATAA
*
405573 TTTTTAATTATAATATATAA
1 TTTTTAATT-TAAAATATAA
405593 TTTT
1 TTTT
405597 GAAGAGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAATTTAAAATATAA
Found at i:406907 original size:5 final size:5
Alignment explanation
Indices: 406891--406920 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
406881 CAGATTTTCA
406891 AACCG AAACCG AACCG AACCG AACCG AACC
1 AACCG -AACCG AACCG AACCG AACCG AACC
406921 AATCGAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.43, C:0.40, G:0.17, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:406976 original size:16 final size:17
Alignment explanation
Indices: 406955--406987 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
406945 ACATACTAAA
*
406955 TCGG-TTTCGGTTTTTT
1 TCGGTTTTCAGTTTTTT
406971 TCGGTTTTCAGTTTTTT
1 TCGGTTTTCAGTTTTTT
406988 GGATCGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.12, G:0.21, T:0.64
Consensus pattern (17 bp):
TCGGTTTTCAGTTTTTT
Found at i:408567 original size:26 final size:26
Alignment explanation
Indices: 408537--408587 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
408527 TCGGTTATTA
*
408537 AAGATTATCTAAAAGATTAATATTTG
1 AAGATTATCTAAAAGATTAAAATTTG
* *
408563 AAGATTATCTTAAAGGTTAAAATTT
1 AAGATTATCTAAAAGATTAAAATTT
408588 TCTAAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (26 bp):
AAGATTATCTAAAAGATTAAAATTTG
Found at i:411110 original size:31 final size:33
Alignment explanation
Indices: 411074--411138 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
411064 GTAATCACAT
411074 TGAATCG-AAATTTAG-AAATTTTGCTAGATAA
1 TGAATCGAAAATTTAGAAAATTTTGCTAGATAA
411105 TGAATCGAAAATTTAGAAAATTTTGCTAGATAA
1 TGAATCGAAAATTTAGAAAATTTTGCTAGATAA
411138 T
1 T
411139 AGAGCAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 7 0.22
32 8 0.25
33 17 0.53
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (33 bp):
TGAATCGAAAATTTAGAAAATTTTGCTAGATAA
Found at i:414948 original size:47 final size:48
Alignment explanation
Indices: 414879--414974 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
414869 CCAAGGAGGA
414879 ACCACTGTACGAACATGAGGCATCATGCGAT-AACCTCGTGTGCAACG
1 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
414926 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
1 ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
414974 A
1 A
414975 GTTTCACTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 31 0.65
48 17 0.35
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (48 bp):
ACCACTGTACGAACATGAGGCATCATGCGATAAACCTCGTGTGCAACG
Found at i:417321 original size:662 final size:663
Alignment explanation
Indices: 416462--417769 Score: 2429
Period size: 663 Copynumber: 2.0 Consensus size: 663
416452 GAATACAGGT
416462 TATATTATAATCCAATGGGATCTCTCATGTATGCCTTATCCAGACTTATCATATATAATCAGAAC
1 TATATTATAATCCAATGGGATCTCTCATGTATGCCTTATCCAGACTTATCATATATAATCAGAAC
416527 GGTAAGTATCATATAAAGAACACTAAAAGGTAATTCGGTGGATCTTGAGATACTTACAAGGTACT
66 GGTAAGTATCATATAAAGAACACTAAAA-G-AATTCGGTGGATCTTGAGATACTTACAAGGTACT
416592 ATTATGTTTGTTTACACTTTGGAATAATTTAAGATGGATTCATGGGTTCGTTAATTTTAATTTGC
129 ATTATGTTTGTTTACACTTTGGAATAATTTAAGATGGATTCATGGGTTCGTTAATTTTAATTTGC
416657 ATGAAATCTTGAT-AAGATCTATCACGGGGAACTTCTTTAATATTGGAGGCTACATTATTAGTTG
194 ATGAAATCTTGATAAAGATCTATCACGGGGAACTTCTTTAATATTGGAGGCTAC---ATTAGTTG
*
416721 CAAAGTCA-TTAGCAGACTACAATTA-TTTATCAATTACTTAAACTAAGTACAAGACAATTACCG
256 CAAAGTCACTTAGCAGACTACAATTATTTTATCAATTACTTAAACCAAGTACAAGACAATTACCG
416784 AGGCTTGTAAAGAATCAATTTGATTTAATAGACTTTTTGGTGAACTCAACGAAGAGCTTTAGATC
321 AGGCTTGTAAAGAATCAATTTGATTTAATAGACTTTTTGGTGAACTCAACGAAGAGCTTTAGATC
416849 AATAC-TTA-TTTTTTTTATAGTTAGAGTGTCGTTTTACTTACAAATAATCAAATGTTTCATGAA
386 AATACATTATTTTTTTTTATAGTTAGAGTGTCG-TTTACTTACAAATAATCAAATGTTTCATGAA
416912 AGGACGGGATACATTAATGTTTGATAACATTTTGTATACGATATTATTTCTCTTGAT-ACATTAT
450 AGGACGGGATACATTAATGTTTGATAACATTTTGTATACGATATTATTTCTCTTGATAACATTAT
416976 TGTGATCAAATTAGCATTCATGTCAACCCTACAGATATATTGATTAAGTCACTTTCTATAGTTAA
515 TGTGATCAAATTAGCATTCATGTCAACCCTACAGATATATTGATTAAGTCACTTTCTATAGTTAA
417041 GTTTG-ATACCGTTTGAATTTGGTCGATGTTAATTATTG-AAAATATCTTTTTAAGTGA-TTTAT
580 GTTTGAATACCGTTTG-ATTTGGTCGATGTTAATTATTGAAAAATATC-TTTTAAGTGATTTTAT
417103 AGGAATACATATCACAGGTTA
643 AGGAATACATATCACAGGTTA
417124 TATATTATAATCCAATGGGATCTCTCATGTATGCCTTAGTCCAGACTTATCATATATAATCAGAA
1 TATATTATAATCCAATGGGATCTCTCATGTATGCCTTA-TCCAGACTTATCATATATAATCAGAA
417189 CGGTAAGTATCATATAAAGAACACTAAAA-AATTCGGTGGATCTTGAGATACTTACAAGGTACTA
65 CGGTAAGTATCATATAAAGAACACTAAAAGAATTCGGTGGATCTTGAGATACTTACAAGGTACTA
417253 TTTATGTTTGTTTACACTTTGGAATAATTTAAGATGGATTCATTGGGTTCGTTAATTTTAATTTG
130 -TTATGTTTGTTTACACTTTGGAATAATTTAAGATGGATTCA-TGGGTTCGTTAATTTTAATTTG
417318 CATGAAATCTTGATAAAGATCTATCACGGGGAACTTCTTTAATATTGGAGGCTACATTAGTTGCA
193 CATGAAATCTTGATAAAGATCTATCACGGGGAACTTCTTTAATATTGGAGGCTACATTAGTTGCA
417383 AAGTCACTTAGCAGACTACAATTATTTTATCAATTACTTAAACCAAGTACAAGACAATTACCGAG
258 AAGTCACTTAGCAGACTACAATTATTTTATCAATTACTTAAACCAAGTACAAGACAATTACCGAG
417448 GCTTGTAAAGAATCAATTTGATTTAATAGACTTTTTGGTGAACTCAACGAAGAGCTTTAGATCAA
323 GCTTGTAAAGAATCAATTTGATTTAATAGACTTTTTGGTGAACTCAACGAAGAGCTTTAGATCAA
417513 TACATTATTTTTTTTTATAGTTAGAGTGTCGTTTACTTACAAATAATCAAATGTTTCATGAAAGG
388 TACATTATTTTTTTTTATAGTTAGAGTGTCGTTTACTTACAAATAATCAAATGTTTCATGAAAGG
417578 ACGGGATACATTAATGTTTGATAACATTTTGTATACGATATTATTTCTCTTGATAACATTATTGT
453 ACGGGATACATTAATGTTTGATAACATTTTGTATACGATATTATTTCTCTTGATAACATTATTGT
*
417643 GATCAAATTAGCATTCATGTCAACCCTATAGATATATTGATTAAGTCACTTTCTATAGTTAAGTT
518 GATCAAATTAGCATTCATGTCAACCCTACAGATATATTGATTAAGTCACTTTCTATAGTTAAGTT
417708 TGAATACCGTTTGATTTGGTCGATGTTAATTATTGAAAAATATCTTTTAAGTGATTTTATAG
583 TGAATACCGTTTGATTTGGTCGATGTTAATTATTGAAAAATATCTTTTAAGTGATTTTATAG
417770 AAGAGGTAGA
Statistics
Matches: 632, Mismatches: 2, Indels: 21
0.96 0.00 0.03
Matches are distributed among these distances:
660 51 0.08
661 58 0.09
662 181 0.29
663 186 0.29
664 131 0.21
665 25 0.04
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (663 bp):
TATATTATAATCCAATGGGATCTCTCATGTATGCCTTATCCAGACTTATCATATATAATCAGAAC
GGTAAGTATCATATAAAGAACACTAAAAGAATTCGGTGGATCTTGAGATACTTACAAGGTACTAT
TATGTTTGTTTACACTTTGGAATAATTTAAGATGGATTCATGGGTTCGTTAATTTTAATTTGCAT
GAAATCTTGATAAAGATCTATCACGGGGAACTTCTTTAATATTGGAGGCTACATTAGTTGCAAAG
TCACTTAGCAGACTACAATTATTTTATCAATTACTTAAACCAAGTACAAGACAATTACCGAGGCT
TGTAAAGAATCAATTTGATTTAATAGACTTTTTGGTGAACTCAACGAAGAGCTTTAGATCAATAC
ATTATTTTTTTTTATAGTTAGAGTGTCGTTTACTTACAAATAATCAAATGTTTCATGAAAGGACG
GGATACATTAATGTTTGATAACATTTTGTATACGATATTATTTCTCTTGATAACATTATTGTGAT
CAAATTAGCATTCATGTCAACCCTACAGATATATTGATTAAGTCACTTTCTATAGTTAAGTTTGA
ATACCGTTTGATTTGGTCGATGTTAATTATTGAAAAATATCTTTTAAGTGATTTTATAGGAATAC
ATATCACAGGTTA
Found at i:419568 original size:48 final size:49
Alignment explanation
Indices: 419513--419614 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 49
419503 ACCACCCAGG
419513 TTTGTCCTTAGTTCTTAATTTTGCACTCATGGACTAC-TGTTCACTCAT
1 TTTGTCCTTAGTTCTTAATTTTGCACTCATGGACTACTTGTTCACTCAT
419561 TTTGTCCTTAGTTCTTAATTTTGCACTCATGGACTACTTGTTCACTCAT
1 TTTGTCCTTAGTTCTTAATTTTGCACTCATGGACTACTTGTTCACTCAT
419610 TTTGT
1 TTTGT
419615 TAAGCTTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 37 0.70
49 16 0.30
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.48
Consensus pattern (49 bp):
TTTGTCCTTAGTTCTTAATTTTGCACTCATGGACTACTTGTTCACTCAT
Found at i:426971 original size:17 final size:17
Alignment explanation
Indices: 426952--426989 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
426942 TTTTTAATAA
*
426952 AAAATACATAA-AATTT
1 AAAATAAATAATAATTT
426968 AAAATAAATAATAATTT
1 AAAATAAATAATAATTT
*
426985 TAAAT
1 AAAAT
426990 TTCAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAATAATAATTT
Found at i:429494 original size:21 final size:21
Alignment explanation
Indices: 429425--429499 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
429415 AATGTCTAAC
*
429425 AATAATAAAAT-GATTAAAAAA
1 AATAATAAAATCGA-TAAAAAT
*
429446 AATAATAAAATCGATAGCATCTCTAAT
1 AATAATAAAATCGATA--A----AAAT
429473 AATAATAAAATCGATAAAAAT
1 AATAATAAAATCGATAAAAAT
429494 AATAAT
1 AATAAT
429500 GTTTTTGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
21 22 0.50
22 2 0.05
23 1 0.02
25 1 0.02
27 18 0.41
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (21 bp):
AATAATAAAATCGATAAAAAT
Found at i:429906 original size:60 final size:59
Alignment explanation
Indices: 429793--429912 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 59
429783 TGAAATAAAC
429793 TAGAAGACAATAACCCCCAACACTATATAGTTTCATCCCTAAACAGACTCTATTAAAAAT
1 TAGAAGACAATAACCCCCAACACTATATAGTTTCATCCCTAAACAGAC-CTATTAAAAAT
* * *
429853 TAGAAGACAATAACCTCCAACGCTATACATAGTTTCTTCCCTAAACAGA-CTATTAAAAAT
1 TAGAAGACAATAACCCCCAACACTAT--ATAGTTTCATCCCTAAACAGACCTATTAAAAAT
429913 AGATTTTACG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
60 35 0.64
62 20 0.36
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.26
Consensus pattern (59 bp):
TAGAAGACAATAACCCCCAACACTATATAGTTTCATCCCTAAACAGACCTATTAAAAAT
Found at i:438662 original size:29 final size:30
Alignment explanation
Indices: 438621--438690 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
438611 TTAAATTTTA
*
438621 AAAT-TATCTTTATTTTTGTTTTAACTTATT
1 AAATATAT-TTTATTTTTGTCTTAACTTATT
*
438651 AAATAT-TTTTATTTTTGTCTTAATTTATT
1 AAATATATTTTATTTTTGTCTTAACTTATT
438680 AAATATATTTT
1 AAATATATTTT
438691 GTTTGTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 26 0.72
30 9 0.25
31 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (30 bp):
AAATATATTTTATTTTTGTCTTAACTTATT
Found at i:438794 original size:26 final size:26
Alignment explanation
Indices: 438765--438815 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
438755 ATATCTTAAC
* *
438765 TTAAAATATATTTAAATATTTTACTA
1 TTAAAATATATATAAATATATTACTA
* *
438791 TTAATATATATATATATATATTACT
1 TTAAAATATATATAAATATATTACT
438816 CTTATTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAAATATATATAAATATATTACTA
Found at i:453462 original size:20 final size:20
Alignment explanation
Indices: 453437--453534 Score: 169
Period size: 20 Copynumber: 4.9 Consensus size: 20
453427 AATCCTATTC
*
453437 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
453457 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
453477 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
453497 CTGGTAATCTTATATTCCCA
1 CTGGTAATCTTACATTCCCA
*
453517 TTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
453535 GTGAACCAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:455704 original size:234 final size:235
Alignment explanation
Indices: 455295--455763 Score: 931
Period size: 234 Copynumber: 2.0 Consensus size: 235
455285 CATAAAGAAG
455295 TGGTGACCACTTATAGCAGCGTGTGTGGCTCACGTGCTGGGAATCTGTCAATCAAATTTTGTAAT
1 TGGTGACCACTTATAGCAGCGTGTGTGGCTCACGTGCTGGGAATCTGTCAATCAAATTTTGTAAT
455360 CTGGTCGAACGACTCACGATGGACCTCCCTGTGCTGGTGGTGTCAAACGTGGAGCCTCCAAAACT
66 CTGGTCGAACGACTCACGATGGACCTCCCTGTGCTGGTGGTGTCAAACGTGGAGCCTCCAAAACT
455425 GCCCTTTTGAATTTCAACAATACCCTACACCCCAATCATCCCAGGGGG-AAATAGTGATGAACAA
131 GCCCTTTTGAATTTCAACAATACCCTACACCCCAATCATCCCAGGGGGAAAATAGTGATGAACAA
455489 GGAAAAAATTTCTTAAAATTTAGTTTAGGGCATTTGATAC
196 GGAAAAAATTTCTTAAAATTTAGTTTAGGGCATTTGATAC
455529 TGGTGACCACTTATAGCAGCGTGTGTGGCTCACGTGCTGGGAATCTGTCAATCAAATTTTGTAAT
1 TGGTGACCACTTATAGCAGCGTGTGTGGCTCACGTGCTGGGAATCTGTCAATCAAATTTTGTAAT
455594 CTGGTCGAACGACTCACGATGGACCTCCCTGTGCTGGTGGTGTCAAACGTGGAGCCTCCAAAACT
66 CTGGTCGAACGACTCACGATGGACCTCCCTGTGCTGGTGGTGTCAAACGTGGAGCCTCCAAAACT
455659 GCCCTTTTGAATTTCAACAATACCCTACACCCCAATCATCCCAGGGGGAAAATAGTGATGAACAA
131 GCCCTTTTGAATTTCAACAATACCCTACACCCCAATCATCCCAGGGGGAAAATAGTGATGAACAA
455724 GGAAAAAATTTCTTAAAATTTAGTTTAGGGCATTTGATAC
196 GGAAAAAATTTCTTAAAATTTAGTTTAGGGCATTTGATAC
455764 CATGTAAATT
Statistics
Matches: 234, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
234 178 0.76
235 56 0.24
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (235 bp):
TGGTGACCACTTATAGCAGCGTGTGTGGCTCACGTGCTGGGAATCTGTCAATCAAATTTTGTAAT
CTGGTCGAACGACTCACGATGGACCTCCCTGTGCTGGTGGTGTCAAACGTGGAGCCTCCAAAACT
GCCCTTTTGAATTTCAACAATACCCTACACCCCAATCATCCCAGGGGGAAAATAGTGATGAACAA
GGAAAAAATTTCTTAAAATTTAGTTTAGGGCATTTGATAC
Found at i:462973 original size:14 final size:14
Alignment explanation
Indices: 462954--462980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
462944 GAATTAGATG
462954 CCCATTTGCCATTC
1 CCCATTTGCCATTC
462968 CCCATTTGCCATT
1 CCCATTTGCCATT
462981 TCTGACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (14 bp):
CCCATTTGCCATTC
Found at i:464620 original size:20 final size:20
Alignment explanation
Indices: 464597--464684 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
464587 AATATGTAAA
464597 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
** *
464617 TCGCAATGC-GATAATCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
464637 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * * *
464657 TCACAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
464678 TCGCAAC
1 TCGCAAC
464685 TGAATTTCAA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.04
20 37 0.71
21 13 0.25
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:464641 original size:40 final size:41
Alignment explanation
Indices: 464580--464684 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 41
464570 CCCAGTTTCG
* * *
464580 CAACGC-GAATATGTAAA-TCGCAACACAGAAGTCAAATTCG
1 CAACGCGGAATAT-CAAATTCGCAACACAAAAGTCAAATTCA
*
464620 CAATGC-G-ATAATCAAATTCGCAACACAAAAGTCAAATTCA
1 CAACGCGGAAT-ATCAAATTCGCAACACAAAAGTCAAATTCA
*
464660 CAACGCGGAATTTCAAATTCGCAAC
1 CAACGCGGAATATCAAATTCGCAAC
464685 TGAATTTCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
39 5 0.09
40 34 0.62
41 14 0.25
42 2 0.04
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (41 bp):
CAACGCGGAATATCAAATTCGCAACACAAAAGTCAAATTCA
Found at i:464677 original size:21 final size:19
Alignment explanation
Indices: 464651--464717 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
464641 AACACAAAAG
464651 TCAAATTCACAACGCGGAATT
1 TCAAATTCACAA--CGGAATT
* *
464672 TCAAATTCGCAACTGAATT
1 TCAAATTCACAACGGAATT
***
464691 TCAAATTCACAATTAAATT
1 TCAAATTCACAACGGAATT
464710 TCAAATTC
1 TCAAATTC
464718 GTAACTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 30 0.73
21 11 0.27
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (19 bp):
TCAAATTCACAACGGAATT
Found at i:464691 original size:19 final size:19
Alignment explanation
Indices: 464667--464760 Score: 84
Period size: 19 Copynumber: 4.9 Consensus size: 19
464657 TCACAACGCG
464667 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* *
464686 GAATTTCAAATTCACAATT
1 GAATTTCAAATTCGCAACT
* *
464705 AAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGCAACT
* *
464724 -ATATTTTCGAATTCGCAACAC
1 GA-A-TTTCAAATTCGCAAC-T
*
464745 GAATTT-AATTTCGCAA
1 GAATTTCAAATTCGCAA
464761 TAGGTTTTAG
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.02
19 41 0.68
20 16 0.27
21 1 0.02
22 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:465343 original size:24 final size:24
Alignment explanation
Indices: 465311--465362 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
465301 AGAAGAAAAG
*
465311 GCCATGGGAGTATAACTGGAATAT
1 GCCACGGGAGTATAACTGGAATAT
465335 GCCACGGGAGTATAACTGGAATAT
1 GCCACGGGAGTATAACTGGAATAT
465359 GCCA
1 GCCA
465363 GAATTACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (24 bp):
GCCACGGGAGTATAACTGGAATAT
Found at i:467734 original size:20 final size:20
Alignment explanation
Indices: 467711--467756 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
467701 AATAAGCGTT
*
467711 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
467731 GCGAAAATCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
*
467751 GTGAAA
1 GCGAAA
467757 TCGCAAACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:468272 original size:18 final size:18
Alignment explanation
Indices: 468251--468287 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
468241 GTAATTGGAG
468251 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
468269 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
468287 T
1 T
468288 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:468294 original size:24 final size:24
Alignment explanation
Indices: 468243--468295 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
468233 TTTCATATGT
* * *
468243 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
468267 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
468291 AATTT
1 AATTT
468296 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:469888 original size:22 final size:22
Alignment explanation
Indices: 469861--469911 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
469851 GATGGAGATA
469861 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
469883 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
469905 GACGGAT
1 GACGGAT
469912 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:470073 original size:20 final size:20
Alignment explanation
Indices: 470025--470114 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
470015 ATTGTGTTTC
* *
470025 GCGTTGCGAATTTGAAATTAT
1 GCGTTGCGAATTTG-ACTTTT
470046 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
* * *
470066 GTGTTGCGAATTTGACTATG
1 GCGTTGCGAATTTGACTTTT
* * *
470086 GCGTTGTGAATTTAACTTCT
1 GCGTTGCGAATTTGACTTTT
470106 GCGTTGCGA
1 GCGTTGCGA
470115 TTTACATATT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTT
Found at i:470112 original size:40 final size:40
Alignment explanation
Indices: 470025--470114 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
470015 ATTGTGTTTC
* * *
470025 GCGTTGCGAATTTGAAATTATGCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTG-AACTATGCGTTGCGAATTTAACTTCT
* *
470066 GTGTTGCGAATTTG-ACTATGGCGTTGTGAATTTAACTTCT
1 GCGTTGCGAATTTGAACTAT-GCGTTGCGAATTTAACTTCT
470106 GCGTTGCGA
1 GCGTTGCGA
470115 TTTACATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.10
40 25 0.60
41 13 0.31
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (40 bp):
GCGTTGCGAATTTGAACTATGCGTTGCGAATTTAACTTCT
Found at i:470130 original size:40 final size:40
Alignment explanation
Indices: 470025--470138 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 40
470015 ATTGTGTTTC
* * *
470025 GCGTTGCGAATTTGAAATTAT-GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTG--ACTATCGCGTTGCGAATTTAACTTCT
* * *
470066 GTGTTGCGAATTTGACTATGGCGTTGTGAATTTAACTTCT
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCT
*
470106 GCGTTGCG-ATTT-ACATATTCGCGTTGCAAATTT
1 GCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTT
470139 GGAAAATCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.03
39 10 0.16
40 36 0.59
41 13 0.21
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (40 bp):
GCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCT
Found at i:470132 original size:60 final size:61
Alignment explanation
Indices: 470025--470139 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 61
470015 ATTGTGTTTC
* * *
470025 GCGTTGCGAATTTGAAATTATGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATG
1 GCGTTGCGAATTTGAAATTATGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTATG
* * *
470086 GCGTTGTGAATTT-AACTTCTGCGTTGCG-ATTT-ACATATTCGCGTTGCAAATTTG
1 GCGTTGCGAATTTGAAATTATGCGTTGCGAATTTGAC-T-TTCGCGTTGCAAATTTG
470140 GAAAATCACA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
58 2 0.04
59 5 0.11
60 27 0.59
61 12 0.26
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (61 bp):
GCGTTGCGAATTTGAAATTATGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTATG
Found at i:470158 original size:21 final size:21
Alignment explanation
Indices: 470134--470176 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
470124 TCGCGTTGCA
470134 AATTTGGAAAATCACAACGCG
1 AATTTGGAAAATCACAACGCG
* *
470155 AATTTGGAAAATCGCAATGCG
1 AATTTGGAAAATCACAACGCG
470176 A
1 A
470177 TTTACATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
AATTTGGAAAATCACAACGCG
Found at i:470233 original size:20 final size:19
Alignment explanation
Indices: 470184--470237 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
470174 CGATTTACAT
470184 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
470203 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
470223 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
470238 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:470769 original size:2 final size:2
Alignment explanation
Indices: 470764--470797 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
470754 TCTATCGATC
470764 AT 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 AT
470798 TTGTAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:471926 original size:2 final size:2
Alignment explanation
Indices: 471919--471955 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
471909 CGTCTATAAG
471919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
471956 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:475068 original size:22 final size:22
Alignment explanation
Indices: 475005--475069 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
474995 TAGCCTGATC
*
475005 AAATGTAATAGATCCTTAAATG
1 AAATGTAATAGATCCTTGAATG
* *
475027 AAA--TAATA-A-CC--GGATC
1 AAATGTAATAGATCCTTGAATG
475043 AAATGTAATAGATCCTTGAATG
1 AAATGTAATAGATCCTTGAATG
475065 AAATG
1 AAATG
475070 ATATTACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
16 5 0.16
18 7 0.22
19 2 0.06
20 7 0.22
22 11 0.34
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (22 bp):
AAATGTAATAGATCCTTGAATG
Found at i:476664 original size:37 final size:37
Alignment explanation
Indices: 476499--476832 Score: 268
Period size: 39 Copynumber: 9.2 Consensus size: 37
476489 TTATATATAC
*
476499 ATATATATATATATATAG-TTTAAAAACATTTTTAAAAA
1 ATATATATAT-TATATAGTTTTTAAAACATTTTT-AAAA
* * * *
476537 CATACATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 -ATATATATATTATATAGTTTTTAAAACAT-TTTTAAAA
* * *
476576 CATTTATATATTATATAGTTTTTAAAATA-TTTTGAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
* *
476613 ATAAATATAATATATAGTTTTTAAAACATTTTTAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
* *
476650 ATATATATATTATATAATTTTTAAAACATTTTT-GAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
* *
476686 A-ATATATATTATATAATTTTT-AAACA-TTTT---G
1 ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
*
476717 A-A-A-ATA-TATATAGTTTTTAAAAAATATTTTGAAAAA
1 ATATATATATTATATAGTTTTTAAAACAT-TTTT--AAAA
* * *
476753 CATATATATATTATATAGTTTTGAAATCATTTTGAAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
* * *
476791 CT-TACA-A-TATATAGTTTTAAAAACATTTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTT-AAAA
*
476826 CTATATA
1 ATATATA
476833 ATTTTGAAAA
Statistics
Matches: 243, Mismatches: 34, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
28 11 0.05
29 7 0.03
30 1 0.00
31 6 0.02
33 4 0.02
34 25 0.10
35 27 0.11
36 33 0.14
37 45 0.19
38 12 0.05
39 47 0.19
40 9 0.04
41 16 0.07
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTAAAA
Found at i:476809 original size:102 final size:105
Alignment explanation
Indices: 476508--476924 Score: 317
Period size: 104 Copynumber: 4.1 Consensus size: 105
476498 CATATATATA
* * * * *
476508 TATATATAG-TTTAAAAACATTTTT-AAAAACATACATATAATATATAGTTTTGAAAACATGTTT
1 TATATATAGTTTTTAAAACATTTTTGAAAAA-ATATATATATTATATAATTTTGAAAACATTTTT
* ** * *
476571 GAAAACATTTATATATTATATAGTTTTTAAA-ATATTTTGAAAATAAATA
65 GAAAATATACA-ATA-TATA-AGTTTTAAAACAT-TTTTG---A-AAA-C
*
476620 TAATATATAGTTTTTAAAACATTTTT--AAAAATATATATATTATATAATTTTTAAAACATTTTT
1 T-ATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATATAATTTTGAAAACATTTTT
* * *
476683 GAAAATATATATTATATAA-TTTTTAAACA-TTTTGAAAA-
65 GAAAATATACAATATATAAGTTTTAAAACATTTTTGAAAAC
* * *
476721 TATATATAGTTTTTAAAAAATATTTTGAAAAACATATATATATTATATAGTTTTGAAATCA-TTT
1 TATATATAGTTTTTAAAACAT-TTTTGAAAAA-ATATATATATTATATAATTTTGAAAACATTTT
476785 TGAAAACT-TACAATATAT-AGTTTTAAAAACATTTTTGAAAAC
64 TGAAAA-TATACAATATATAAGTTTT-AAAACATTTTTGAAAAC
* *
476827 TATATA-A-TTTTGAAAACATTTTTG-------A-A-A-ATTATATAATTTTGAAAACATTTTTT
1 TATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATATAATTTTGAAAACATTTTTG
* * * *
476880 AAAATAAATAATATATAA-TTTTAAAATACTTTTGAAAA-
66 AAAATATACAATATATAAGTTTTAAAACATTTTTGAAAAC
476918 TATATAT
1 TATATAT
476925 TATATAGTTT
Statistics
Matches: 264, Mismatches: 25, Indels: 52
0.77 0.07 0.15
Matches are distributed among these distances:
91 6 0.02
92 33 0.12
93 21 0.08
94 2 0.01
95 1 0.00
100 19 0.07
101 5 0.02
102 1 0.00
103 33 0.12
104 42 0.16
105 10 0.04
106 6 0.02
107 5 0.02
108 8 0.03
109 2 0.01
110 4 0.02
111 2 0.01
112 38 0.14
113 12 0.05
114 14 0.05
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (105 bp):
TATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATATAATTTTGAAAACATTTTTG
AAAATATACAATATATAAGTTTTAAAACATTTTTGAAAAC
Found at i:476831 original size:29 final size:29
Alignment explanation
Indices: 476798--476891 Score: 136
Period size: 29 Copynumber: 3.3 Consensus size: 29
476788 AAACTTACAA
* *
476798 TATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATTTTGAAAACATTTTTGAAAAC
*
476827 TATATAATTTTGAAAACATTTTTGAAAAT
1 TATATAATTTTGAAAACATTTTTGAAAAC
*
476856 TATATAATTTTGAAAACATTTTTTAAAA-
1 TATATAATTTTGAAAACATTTTTGAAAAC
*
476884 TAAATAAT
1 TATATAAT
476892 ATATAATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
28 7 0.12
29 53 0.88
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (29 bp):
TATATAATTTTGAAAACATTTTTGAAAAC
Found at i:476839 original size:17 final size:17
Alignment explanation
Indices: 476817--476872 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
476807 TTAAAAACAT
476817 TTTTGAAAACTATATAA
1 TTTTGAAAACTATATAA
476834 TTTTGAAAAC---AT--
1 TTTTGAAAACTATATAA
*
476846 TTTTGAAAATTATATAA
1 TTTTGAAAACTATATAA
476863 TTTTGAAAAC
1 TTTTGAAAAC
476873 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 9 0.28
14 2 0.06
15 2 0.06
17 19 0.59
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (17 bp):
TTTTGAAAACTATATAA
Found at i:476956 original size:25 final size:24
Alignment explanation
Indices: 476909--476953 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
476899 TTTAAAATAC
476909 TTTTGAAAATATATATTATATAGT
1 TTTTGAAAATATATATTATATAGT
476933 TTTTGGAAAATAT-T-TTATATA
1 TTTT-GAAAATATATATTATATA
476954 TAGCAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTTGAAAATATATATTATATAGT
Found at i:478207 original size:4 final size:4
Alignment explanation
Indices: 478198--478296 Score: 57
Period size: 4 Copynumber: 25.8 Consensus size: 4
478188 TCTTCCCTTT
* * * *
478198 TTTA TTTA TTTA TTTA TTTA -TTA TTT- TCTC TTAA TTTA -TCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
478243 TTTA TTTT TATTC CTTA -TTC CTTA TTTA TTTA TTTA TTTA TTGT- TTT-
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
478290 TTTA TTT
1 TTTA TTT
478297 TTTTTACTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
3 13 0.18
4 58 0.78
5 3 0.04
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:478224 original size:26 final size:26
Alignment explanation
Indices: 478195--478251 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
478185 AATTCTTCCC
* *
478195 TTTTTTATTTATTTATTTATTTA-TTA
1 TTTTTTATTAATTTA-TCATTTATTTA
* *
478221 TTTTCTCTTAATTTATCATTTATTTA
1 TTTTTTATTAATTTATCATTTATTTA
478247 TTTTT
1 TTTTT
478252 ATTCCTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTTATTAATTTATCATTTATTTA
Found at i:480568 original size:11 final size:11
Alignment explanation
Indices: 480552--480593 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
480542 AGTAACTAAC
480552 ATAACAAACTA
1 ATAACAAACTA
480563 ATAACAAACTA
1 ATAACAAACTA
*
480574 ATAACAAGCTA
1 ATAACAAACTA
480585 ATAACAAAC
1 ATAACAAAC
480594 CATAACACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:482558 original size:11 final size:11
Alignment explanation
Indices: 482542--482590 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
482532 AGTAACCAAC
482542 ATAACAAACTA
1 ATAACAAACTA
*
482553 ATAACAAGCTA
1 ATAACAAACTA
*
482564 ATAACAAA-TT
1 ATAACAAACTA
482574 ATAACAAACTA
1 ATAACAAACTA
482585 ATAACA
1 ATAACA
482591 CTCTTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.20
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:482579 original size:21 final size:22
Alignment explanation
Indices: 482542--482590 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
482532 AGTAACCAAC
*
482542 ATAACAAACTAATAACAAGCTA
1 ATAACAAACTAATAACAAACTA
*
482564 ATAACAAA-TTATAACAAACTA
1 ATAACAAACTAATAACAAACTA
482585 ATAACA
1 ATAACA
482591 CTCTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.20
Consensus pattern (22 bp):
ATAACAAACTAATAACAAACTA
Found at i:490403 original size:34 final size:33
Alignment explanation
Indices: 490343--490407 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
490333 TTTCTTGAGA
*
490343 ATTGTTTTCTCCTTTTTATCAAGAGAGAATTGTC
1 ATTGTTTTCTCCTTTTGATC-AGAGAGAATTGTC
490377 ATTGTTTTCTCCTTGTTAGATC-GAGAGAATT
1 ATTGTTTTCTCCTT-TT-GATCAGAGAGAATT
490408 TGTAATTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 23 0.82
35 2 0.07
36 3 0.11
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (33 bp):
ATTGTTTTCTCCTTTTGATCAGAGAGAATTGTC
Found at i:491253 original size:60 final size:59
Alignment explanation
Indices: 491103--491258 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 59
491093 TTTTGTCCCT
* * * * * * *
491103 AAACTTTTAAATATTCAAATTTCATCATCAAACTATGACTATCATTCTCACTTAGTCCTT
1 AAACTTTTGAACATTCCAATTTCATC-CCAAACTATGACTATCATTCTAAATTAGTCCTC
* * *
491163 AAACTTTTGAACATTTCAGTTCCATCCCCAAACTATGACCT-TCATTCTAAATTAGTCCTC
1 AAACTTTTGAACATTCCAATTTCAT-CCCAAACTATGA-CTATCATTCTAAATTAGTCCTC
491223 AAACTTTTTGAACGA-TCCAATTTCATCCCAAACTAT
1 AAAC-TTTTGAAC-ATTCCAATTTCATCCCAAACTAT
491259 ACATATATAC
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
60 59 0.75
61 19 0.24
62 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (59 bp):
AAACTTTTGAACATTCCAATTTCATCCCAAACTATGACTATCATTCTAAATTAGTCCTC
Found at i:491491 original size:60 final size:60
Alignment explanation
Indices: 491376--491535 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
491366 GGATGAATTT
* ** * * *
491376 GTGATGAAATTTGAATGTTCAAAAAGTTTGGGGAATAATTTAGAAAGAGGGTCATAGTTTA
1 GTGATGAAATTAGAATGTTC-AAAAGTTTAAGGATTAATTCAGAAAGAGAGTCATAGTTTA
* * * *
491437 GTGATGAAATTAAAATGTTCAAAAGTTTAAGGATTAATTCAGAATGATAGTCATAGTTTG
1 GTGATGAAATTAGAATGTTCAAAAGTTTAAGGATTAATTCAGAAAGAGAGTCATAGTTTA
* * * *
491497 GGGATGAAATTAGAATATTCAAAAGTTTAATGATCAATT
1 GTGATGAAATTAGAATGTTCAAAAGTTTAAGGATTAATT
491536 TAAAATAAGA
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 66 0.79
61 18 0.21
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (60 bp):
GTGATGAAATTAGAATGTTCAAAAGTTTAAGGATTAATTCAGAAAGAGAGTCATAGTTTA
Found at i:491553 original size:60 final size:60
Alignment explanation
Indices: 491427--491560 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
491417 AGAAAGAGGG
* * * * * * * *
491427 TCATAGTTTAGTGATGAAATTAAAATGTTCAAAAGTTTAAGGATTAATTCAGAATGATAG
1 TCATAGTTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTCAAAATAAGAA
* * *
491487 TCATAGTTTGGGGATGAAATTAGAATATTCAAAAGTTTAATGATCAATTTAAAATAAGAA
1 TCATAGTTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTCAAAATAAGAA
* *
491547 TTATAGTATGGGGA
1 TCATAGTTTGGGGA
491561 CATATGATGC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (60 bp):
TCATAGTTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTCAAAATAAGAA
Found at i:494992 original size:21 final size:20
Alignment explanation
Indices: 494967--495005 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
494957 GGACTTCAGG
*
494967 GTTTTGTGATTTATGTTTTAT
1 GTTTTATGATTT-TGTTTTAT
*
494988 GTTTTATGCTTTTGTTTT
1 GTTTTATGATTTTGTTTT
495006 TTCTTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (20 bp):
GTTTTATGATTTTGTTTTAT
Found at i:497633 original size:18 final size:21
Alignment explanation
Indices: 497607--497656 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
497597 GATTATATTG
*
497607 TTATCATATAT-ATATAT-A-
1 TTATAATATATAATATATGAT
497625 TTATAATAT-TAATATATGAT
1 TTATAATATATAATATATGAT
497645 TTATTAATATAT
1 TTA-TAATATAT
497657 TGATTACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
19 1 0.04
20 3 0.12
21 6 0.23
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATAATATATAATATATGAT
Found at i:497641 original size:20 final size:21
Alignment explanation
Indices: 497616--497654 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
497606 GTTATCATAT
497616 ATATAT-ATATTA-TAATATTA
1 ATATATGAT-TTATTAATATTA
497636 ATATATGATTTATTAATAT
1 ATATATGATTTATTAATAT
497655 ATTGATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
ATATATGATTTATTAATATTA
Found at i:497651 original size:15 final size:16
Alignment explanation
Indices: 497631--497661 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
497621 TATATTATAA
497631 TATTAATATA-TGATT
1 TATTAATATATTGATT
497646 TATTAATATATTGATT
1 TATTAATATATTGATT
497662 ACAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TATTAATATATTGATT
Found at i:502612 original size:66 final size:66
Alignment explanation
Indices: 502506--502635 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
502496 TATATGAAGA
*
502506 CTCTGGCAAGTTCAGTCAATGCTGGTAATTCCTTGTATAGGTTCTA-CACCGACTGGTAATTCCT
1 CTCTGGCAAGTTCAGTCAATGCTAGTAATTCCTTGTATAGGTTC-AGCACCGACTGGTAATTCCT
502570 AT
65 AT
* * ** * *
502572 CTCTGGCAGGTTTAGTCTCTGCTAGTAATTCCTTTTATAGGTTCAGCACTGACTGGTAATTCCT
1 CTCTGGCAAGTTCAGTCAATGCTAGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCCT
502636 TATGGACCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 55 0.98
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (66 bp):
CTCTGGCAAGTTCAGTCAATGCTAGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCCTA
T
Done.