Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold22
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: 1926927
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.27
Warning! 314813 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:281234 original size:118 final size:120
Alignment explanation
Indices: 280956--281333 Score: 500
Period size: 118 Copynumber: 3.2 Consensus size: 120
280946 GAAGATGCAC
* * *
280956 TTTTCTTTTT-AAAGCCCACACAAGCTAGTGGCACCCGTTTTATACATTTTTA-TCCTCAAAGAG
1 TTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCC---TT-TACCTTTTTAGTCCTCAAAGAG
* * *
281019 CATGACACTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCACC--TTT-TT
62 CATGACGCTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTTCTT
* * * * *
281075 TTTTCTTTTTCAAAACCTATACAAGTTGGTAGCACCCTTTACCTTTTTAGTCCTCAAAGAGCAAG
1 TTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
* *
281140 AGGCTTTTCCTTTTTC-TTTTCAAAG-CCATACAAGCTGGTGGCACCTTTTTCTT
66 ACGCTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTTCTT
* *
281193 TTTTGTTTTTCAAAGCCCACAGAAGTTGGTGGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
1 TTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
* * * *
281258 ACGTTTTTCTTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTTCCT
66 ACGCTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTTCTT
281313 TTTTCTTTTTCAAAGCCCACA
1 TTTTCTTTTTCAAAGCCCACA
281334 AAAATTGGAG
Statistics
Matches: 225, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
115 18 0.08
116 18 0.08
117 32 0.14
118 73 0.32
119 19 0.08
120 65 0.29
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (120 bp):
TTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
ACGCTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTTCTT
Found at i:281324 original size:44 final size:44
Alignment explanation
Indices: 281144--281333 Score: 156
Period size: 44 Copynumber: 4.6 Consensus size: 44
281134 AGCAAGAGGC
* *
281144 TTTTCCTTTTTC-TTTTCAAAG-CCATACAAGCTGGTGGCACCT
1 TTTTCCTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * *
281186 TTTTCTTTTTTGTTTTTCAAAGCCCACAGAAGTTGGTGGCACCC
1 TTTTCCTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* ** ** * *
281230 TTTACCTTTTTAGTCCTCAAAG---A-GC-A-----T-G-ACGT
1 TTTTCCTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
*
281262 TTTTCTTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
1 TTTTCCTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
281306 TTTTCCTTTTTCTTTTTCAAAGCCCACA
1 TTTTCCTTTTTCTTTTTCAAAGCCCACA
281334 AAAATTGGAG
Statistics
Matches: 109, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
32 18 0.17
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
37 1 0.01
39 1 0.01
41 1 0.01
42 11 0.10
43 10 0.09
44 63 0.58
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (44 bp):
TTTTCCTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCT
Found at i:281360 original size:45 final size:44
Alignment explanation
Indices: 281268--281360 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
281258 ACGTTTTTCT
* * * *
281268 TTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTTCC
1 TTTTTCTTTTTCAAAGCCCACAAAAATTGGAGGCACCTTTTCCC
*
281312 TTTTTCTTTTTCAAAGCCCACAAAAATTGGAGTCA-CTTAATTCCC
1 TTTTTCTTTTTCAAAGCCCACAAAAATTGGAGGCACCTT--TTCCC
281357 TTTT
1 TTTT
281361 GTCCTTAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.07
44 31 0.74
45 8 0.19
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (44 bp):
TTTTTCTTTTTCAAAGCCCACAAAAATTGGAGGCACCTTTTCCC
Found at i:288718 original size:38 final size:39
Alignment explanation
Indices: 288666--288744 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 39
288656 ATGAGGATGA
288666 TAAAAGGGAGGTTAAAATAGGAACCACAATTAATCAATC
1 TAAAAGGGAGGTTAAAATAGGAACCACAATTAATCAATC
* *
288705 TAAAA-GGAGGTTAAAATAGGAACCATAATTAATTAATC
1 TAAAAGGGAGGTTAAAATAGGAACCACAATTAATCAATC
288743 TA
1 TA
288745 CTTGACAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 33 0.87
39 5 0.13
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (39 bp):
TAAAAGGGAGGTTAAAATAGGAACCACAATTAATCAATC
Found at i:293592 original size:42 final size:42
Alignment explanation
Indices: 293470--293862 Score: 269
Period size: 42 Copynumber: 9.3 Consensus size: 42
293460 TGATTTGACG
* * *
293470 TGTCGGCTTTGACCTTGGAAACTACCTCACCTCAAGTCTACC
1 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
** * * * *
293512 TGTTAGCTTTGACCCTAGAGACTTTCGT-ACCTTC-AGTCTGCC
1 TGTCGGCTTTGACCTTGGAGA-TTACCTCACC-TCAAGTCTGCC
**
293554 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGTT
1 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
* ** *
293596 TGTCGGCTTTAACCTTGGAGACTT-TTTTACCCTC-AGTCTGCC
1 TGTCGGCTTTGACCTTGGAGA-TTACCTCA-CCTCAAGTCTGCC
* * * * * *
293638 TATCGACTTTGACCTTGGAGACTGCCTCATCTCAAGTCTACC
1 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
* * * * *
293680 TGTCAGCTTTGACCCTGGAGACTTTCCT-ACCTTC-ACTATGCC
1 TGTCGGCTTTGACCTTGGAGA-TTACCTCACC-TCAAGTCTGCC
* * * * *
293722 TGTCGACTTTGACCTTGGAGACTGCCTCATCTTAAGTCTGCC
1 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
* * * * * * * *
293764 TGTCGACTTTGACCCTAGAGACTATCTCATCTCAAATCTGCT
1 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
* * * *
293806 TGTCGGCTTTGACCCTAGAGACTT-CCTTACCCTAAAGTCTGCC
1 TGTCGGCTTTGACCTTGGAGA-TTACCTCA-CCTCAAGTCTGCC
*
293849 TATCGGCTTTGACC
1 TGTCGGCTTTGACC
293863 CTAGAGACTT
Statistics
Matches: 270, Mismatches: 67, Indels: 27
0.74 0.18 0.07
Matches are distributed among these distances:
41 15 0.06
42 215 0.80
43 40 0.15
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.33
Consensus pattern (42 bp):
TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGCC
Found at i:293617 original size:84 final size:84
Alignment explanation
Indices: 293470--293873 Score: 391
Period size: 84 Copynumber: 4.8 Consensus size: 84
293460 TGATTTGACG
* * * *
293470 TGTCGGCTTTGACCTTGGAAACTACCTCACCTCAAGTCTACCTGTTAGCTTTGACCCTAGAGACT
1 TGTCGACTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGACT
*
293535 TTCGTACCTTCAGTCTGCC
66 TTCCTACCTTCAGTCTGCC
* * *** * * *
293554 TGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGTTTGTCGGCTTTAACCTTGGAGACT
1 TGTCGACTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGACT
** *
293619 TTTTTACCCTCAGTCTGCC
66 TTCCTACCTTCAGTCTGCC
* * *
293638 TATCGACTTTGACCTTGGAGACTGCCTCATCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGACT
1 TGTCGACTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGACT
* *
293703 TTCCTACCTTCACTATGCC
66 TTCCTACCTTCAGTCTGCC
* * * * *
293722 TGTCGACTTTGACCTTGGAGACTGCCTCATCTTAAGTCTGCCTGTC-GACTTTGACCCTAGAGAC
1 TGTCGACTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTCAG-CTTTGACCCTGGAGAC
* * * *
293786 TAT-CT-CATCTCAAATCTGCT
65 TTTCCTACCT-TC-AGTCTGCC
* * * * * * * * * *
293806 TGTCGGCTTTGACCCTAGAGACTTCCTTACCCTAAAGTCTGCCTATCGGCTTTGACCCTAGAGAC
1 TGTCGACTTTGACCTTGGAGACTACCTCA-CCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGAC
293871 TTT
65 TTT
293874 TTCACCTTTT
Statistics
Matches: 268, Mismatches: 47, Indels: 9
0.83 0.15 0.03
Matches are distributed among these distances:
82 2 0.01
83 5 0.02
84 228 0.85
85 32 0.12
86 1 0.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (84 bp):
TGTCGACTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTCAGCTTTGACCCTGGAGACT
TTCCTACCTTCAGTCTGCC
Found at i:293699 original size:126 final size:125
Alignment explanation
Indices: 293546--293879 Score: 348
Period size: 126 Copynumber: 2.6 Consensus size: 125
293536 TCGTACCTTC
* ** *
293546 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCACCTCAAGTCTGTTTGTCGGCTTTAACC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTT-CCT-ACCTCAAGTCTGCCTGTCGGCTTTGACC
* * * * *
293610 TTGGAGACTTTTTTACCCTCAGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCATCTCA
64 TTGGAGACTTTTTCACCCTAAGTCTGCCTATCGACTTTGACCCTAGAGACTACCTCATCTCA
* * * * *
293672 AGTCTACCTGTCAGCTTTGACCCTGGAGACTTTCCTACCTTC-ACTATGCCTGTCGACTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTACC-TCAAGTCTGCCTGTCGGCTTTGACC
*** * * * *
293736 TTGGAGACTGCCTCATCTTAAGTCTGCCTGTCGACTTTGACCCTAGAGACTATCTCATCTCA
64 TTGGAGACTTTTTCACCCTAAGTCTGCCTATCGACTTTGACCCTAGAGACTACCTCATCTCA
* * * * *
293798 AATCTGCTTGTCGGCTTTGACCCTAGAGACTTCCTTACCCTAAAGTCTGCCTATCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCC-TA-CCTCAAGTCTGCCTGTCGGCTTTGACC
* *
293863 CTAGAGACTTTTTCACC
64 TTGGAGACTTTTTCACC
293880 TTTTATCTGC
Statistics
Matches: 165, Mismatches: 37, Indels: 11
0.77 0.17 0.05
Matches are distributed among these distances:
125 4 0.02
126 123 0.75
127 36 0.22
128 2 0.01
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (125 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTACCTCAAGTCTGCCTGTCGGCTTTGACCTT
GGAGACTTTTTCACCCTAAGTCTGCCTATCGACTTTGACCCTAGAGACTACCTCATCTCA
Found at i:293911 original size:85 final size:85
Alignment explanation
Indices: 293755--293911 Score: 188
Period size: 85 Copynumber: 1.8 Consensus size: 85
293745 GCCTCATCTT
* * ** *
293755 AAGTCTGCCTGTCGACTTTGACCCTAGAGACTATCTCATCTCAAATCTGCTTGTCGGCTTTGACC
1 AAGTCTGCCTATCGACTTTGACCCTAGAGACTATCTCACCTCAAATCTGCCCGTCAGCTTTGACC
*
293820 CTAGAGACTTCCTTACCCTA
66 CGAGAGACTTCCTTACCCTA
* * * *** * *
293840 AAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTTTCACCTTTTATCTGCCCGTTAGCTTTGACT
1 AAGTCTGCCTATCGACTTTGACCCTAGAGACTATCTCACCTCAAATCTGCCCGTCAGCTTTGACC
293905 CGAGAGA
66 CGAGAGA
293912 ATCTTTTCTT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
85 58 1.00
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (85 bp):
AAGTCTGCCTATCGACTTTGACCCTAGAGACTATCTCACCTCAAATCTGCCCGTCAGCTTTGACC
CGAGAGACTTCCTTACCCTA
Found at i:294589 original size:62 final size:61
Alignment explanation
Indices: 294492--294667 Score: 288
Period size: 57 Copynumber: 2.9 Consensus size: 61
294482 CCGAATTTGG
294492 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCACTGCATTGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCA-TGCATTGCATTGCAT
* *
294554 TGGATTTCGTGTTTAATTTGTTGCCACCTAAGCTTTCTAGGTGTCA--C--TGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATGCATTGCATTGCAT
294611 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCA-TGCATTGCAT
294668 GCTTTCATTT
Statistics
Matches: 105, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
57 54 0.51
59 1 0.01
60 1 0.01
62 49 0.47
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (61 bp):
TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATGCATTGCATTGCAT
Found at i:295650 original size:22 final size:22
Alignment explanation
Indices: 295617--295668 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
295607 CACCTGCAAG
* *
295617 CAAGCAAACACCAGCAAAACAG
1 CAAGCAAGCACCAGCAAAACAA
*
295639 TAAGCAAGCACCAGCAAAACAA
1 CAAGCAAGCACCAGCAAAACAA
295661 CAAGCAAG
1 CAAGCAAG
295669 GAAGACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.29, G:0.15, T:0.02
Consensus pattern (22 bp):
CAAGCAAGCACCAGCAAAACAA
Found at i:297103 original size:20 final size:20
Alignment explanation
Indices: 297078--297129 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
297068 ACCCTAGAAA
297078 GTATCGATACATA-TCTAGA-T
1 GTATCGATACATACTC-A-ATT
297098 GTATCGATACATACTCAATT
1 GTATCGATACATACTCAATT
297118 GTATCGATACAT
1 GTATCGATACAT
297130 GGGACATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (20 bp):
GTATCGATACATACTCAATT
Found at i:297154 original size:13 final size:13
Alignment explanation
Indices: 297136--297160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297126 ACATGGGACA
297136 TTGTATCAATACG
1 TTGTATCAATACG
297149 TTGTATCAATAC
1 TTGTATCAATAC
297161 ACGATACAAA
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:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCAATACG
Found at i:301913 original size:16 final size:16
Alignment explanation
Indices: 301889--301919 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301879 AAAGGCATTC
*
301889 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
301905 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
301920 GGAAATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:305937 original size:19 final size:19
Alignment explanation
Indices: 305910--305965 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
305900 TGTATTGATA
*
305910 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
305929 CATTTTATCGATACATACT
1 CATTGTATCGATACATGCT
305948 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
305966 AAACTAGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:306032 original size:13 final size:13
Alignment explanation
Indices: 306014--306038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
306004 CATGGGACAT
306014 TGTATCGATACAC
1 TGTATCGATACAC
306027 TGTATCGATACA
1 TGTATCGATACA
306039 TTGTGCCCAA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:309282 original size:20 final size:21
Alignment explanation
Indices: 309252--309308 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
309242 CAATATTTTG
309252 TAAATATTTATTATTTAAA-AA
1 TAAA-ATTTATTATTTAAATAA
309273 TAAAATTTATTATTTAAATAA
1 TAAAATTTATTATTTAAATAA
309294 TAAAATTTATTATTT
1 TAAAATTTATTATTT
309309 TTGTTAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATTTATTATTTAAATAA
Found at i:309363 original size:46 final size:45
Alignment explanation
Indices: 309253--309365 Score: 108
Period size: 47 Copynumber: 2.5 Consensus size: 45
309243 AATATTTTGT
*
309253 AAATATTTATTATTTAA-AA-A-TAAAATTTATTATTTAAATAATA
1 AAATATTTA-TATTTAATAATATTAAAATTTATTATTAAAATAATA
* * **
309296 AAATTTATTATTTTTGTTAATATTAATAATTTATTATTAAAAT-ATAA
1 AAATAT-TTATATTTAATAATATTAA-AATTTATTATTAAAATAAT-A
*
309343 AAATATTTATGTTTAATAATATT
1 AAATATTTATATTTAATAATATT
309366 CAAGAAGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
43 9 0.16
44 5 0.09
45 1 0.02
46 19 0.35
47 21 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (45 bp):
AAATATTTATATTTAATAATATTAAAATTTATTATTAAAATAATA
Found at i:309440 original size:16 final size:15
Alignment explanation
Indices: 309392--309436 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
309382 TTAAAATATC
309392 AAATACTTTTCATTT
1 AAATACTTTTCATTT
309407 AAATACTTTTCATTT
1 AAATACTTTTCATTT
*
309422 AAATACTTTTTATTT
1 AAATACTTTTCATTT
309437 TAAAAGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATACTTTTCATTT
Found at i:310916 original size:18 final size:19
Alignment explanation
Indices: 310895--310934 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
310885 CAATATTTTG
310895 AAAATATTTATTATTTAAA
1 AAAATATTTATTATTTAAA
310914 AAATATAATTTATTATTTAAA
1 AAA-AT-ATTTATTATTTAAA
310935 TAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 2 0.11
21 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTATTATTTAAA
Found at i:310926 original size:21 final size:21
Alignment explanation
Indices: 310900--310952 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
310890 TTTTGAAAAT
*
310900 ATTTATTATTTAAAAAATATA
1 ATTTATTATTTAAAAAATAAA
*
310921 ATTTATTATTTAAATAATAAA
1 ATTTATTATTTAAAAAATAAA
*
310942 ATATATTATTT
1 ATTTATTATTT
310953 TTGTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATTATTTAAAAAATAAA
Found at i:311861 original size:21 final size:21
Alignment explanation
Indices: 311837--311876 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
311827 ATATATTCAC
311837 ATAAAATATTGATACATTTAT
1 ATAAAATATTGATACATTTAT
**
311858 ATAATGTATTGATACATTT
1 ATAAAATATTGATACATTT
311877 TCACTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAAAATATTGATACATTTAT
Found at i:313743 original size:21 final size:21
Alignment explanation
Indices: 313712--313768 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
313702 ATATTTTTGA
313712 AAATATTTATTATTTAAAAAAT
1 AAAT-TTTATTATTTAAAAAAT
*
313734 AAATTTTATTATTTAAATAAT
1 AAATTTTATTATTTAAAAAAT
* *
313755 AAAATATATTATTT
1 AAATTTTATTATTT
313769 TTATTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTTATTATTTAAAAAAT
Found at i:313775 original size:26 final size:26
Alignment explanation
Indices: 313729--313794 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
313719 TATTATTTAA
*
313729 AAAATAAATT-TTATTATTTAAATAAT
1 AAAATATATTATTATTATTT-AATAAT
* *
313755 AAAATATATTATTTTTA-TTAATATT
1 AAAATATATTATTATTATTTAATAAT
*
313780 AATAATTTATTATTA
1 AA-AATATATTATTA
313795 AAATATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 7 0.21
26 21 0.64
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AAAATATATTATTATTATTTAATAAT
Found at i:313885 original size:16 final size:15
Alignment explanation
Indices: 313850--313881 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
313840 AATTAAAATA
313850 TTAAATACTTTTCAT
1 TTAAATACTTTTCAT
*
313865 TTAAATACTTTTTAT
1 TTAAATACTTTTCAT
313880 TT
1 TT
313882 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAATACTTTTCAT
Found at i:317197 original size:62 final size:62
Alignment explanation
Indices: 317090--317378 Score: 203
Period size: 61 Copynumber: 4.5 Consensus size: 62
317080 AAAGAAGCGT
* * * * * *
317090 CCTGCTTTTTAAGGACTAGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGAAAAAAGGT-G
1 CCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAAGGTCC
* * * * *
317151 TCTCGCTCTTTGAGGAGTAAAAAGTGTCACCAACTTATGTGCGCTTTGAAAAG--AAAAGGTCC
1 CCT-GCTCTTTAAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTT-AAAAGAAAAAAGGTCC
* *
317213 CCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTATATGGGCTTTAAGATAGAAAAGAAGAGAA
1 CCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAA-A-AGAAAA-AAG-G--
* *
317278 ACAT
60 TC-C
* * * *
317282 CCTGCTATTTGAA-GACT-AGAAGATGCCACCAGCTTGTGTGGGCTTTAAAAGAAAAAAGGAAGT
1 CCTGCTCTTT-AAGGACTAAAAAG-TGCCACCAACTTATGTGGGCTTTAAAAGAAAAAA-G--GT
317345 CTC
61 C-C
* * *
317348 CC-GTTCTTTGAGGACTAAAAGGTGCCACCAA
1 CCTGCTCTTTAAGGACTAAAAAGTGCCACCAA
317379 GAAAAGGCAT
Statistics
Matches: 175, Mismatches: 35, Indels: 32
0.72 0.14 0.13
Matches are distributed among these distances:
60 2 0.01
61 47 0.27
62 38 0.22
63 5 0.03
64 3 0.02
65 20 0.11
66 9 0.05
67 7 0.04
68 7 0.04
69 35 0.20
70 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (62 bp):
CCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAAGGTCC
Found at i:317472 original size:58 final size:58
Alignment explanation
Indices: 317388--317565 Score: 198
Period size: 58 Copynumber: 2.9 Consensus size: 58
317378 AGAAAAGGCA
* * *
317388 TCTTGCTCTTAAGGACTAAAACGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-TG
1 TCTTGCTCTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTG
* *
317445 TCTTGCTCTATGAGGACTAGAAGGTGCCACTAACTTGTATGGGCTTTAAAAGAAAAAAGAAAAGT
1 TCTTGCTCT-TGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG------G-AAAGT
317510 G
58 G
* *
317511 TCTTGCTCTTTGAGGACT-GAAGGTGCCACCTACTTGTGTAGGCTTTAAAAGGAAA
1 TCTTGCTC-TTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
317566 AGGCGTCCTA
Statistics
Matches: 102, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
57 9 0.09
58 40 0.39
59 1 0.01
64 1 0.01
65 32 0.31
66 18 0.18
67 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (58 bp):
TCTTGCTCTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTG
Found at i:317546 original size:65 final size:65
Alignment explanation
Indices: 317434--317566 Score: 189
Period size: 65 Copynumber: 2.0 Consensus size: 65
317424 TGTGGGCTTT
* *
317434 AAAAGGAAATGTCTTGCTCTATGAGGACTAGAAGGTGCCACTAACTTGTATGGGCTTTAAAAGAA
1 AAAAGAAAATGTCTTGCTCTATGAGGACTAGAAGGTGCCACTAACTTGTATAGGCTTTAAAAGAA
* *
317499 AAAAGAAAAGTGTCTTGCTCTTTGAGGACT-GAAGGTGCCACCT-ACTTGTGTAGGCTTTAAAAG
1 AAAAGAAAA-TGTCTTGCTCTATGAGGACTAGAAGGTGCCA-CTAACTTGTATAGGCTTTAAAAG
*
317562 GA
64 AA
317564 AAA
1 AAA
317567 GGCGTCCTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
65 40 0.66
66 21 0.34
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (65 bp):
AAAAGAAAATGTCTTGCTCTATGAGGACTAGAAGGTGCCACTAACTTGTATAGGCTTTAAAAGAA
Found at i:326271 original size:20 final size:19
Alignment explanation
Indices: 326221--326276 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
326211 ATATTATGCT
**
326221 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGAACA
*
326240 TTATATCGATACATGAACAA
1 TTGTATCGATACATGAAC-A
*
326260 TTGTATCAATACATGAA
1 TTGTATCGATACATGAA
326277 ACTGGCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGAACA
Found at i:327955 original size:3 final size:3
Alignment explanation
Indices: 327941--327974 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
327931 CATCAAAAAC
*
327941 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
327975 TTGACTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:334612 original size:71 final size:71
Alignment explanation
Indices: 334491--334628 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
334481 AATGAGGGGT
* * * *
334491 TGATGAAAACCAAGGAAGGTCCATTGAATACAATGACCTGAATGCATTGGAAGGGTTTCAAGGAC
1 TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCATTGGAAGGATTTCAAGGAC
334556 CACTGA
66 CACTGA
*
334562 TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTGGAAGGATTTCAAGGAC
1 TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCATTGGAAGGATTTCAAGGAC
334627 CA
66 CA
334629 ATAACGAGGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (71 bp):
TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCATTGGAAGGATTTCAAGGAC
CACTGA
Found at i:337371 original size:475 final size:474
Alignment explanation
Indices: 336224--338230 Score: 2407
Period size: 475 Copynumber: 4.2 Consensus size: 474
336214 AATAGGCGCT
* * *
336224 ATATTGACGCTTTGGTTTCGCAAGGAAGGCTTTCTTC-CAACCAATTTTTGGAAAGTGTAAGTTC
1 ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCAC-ACCAATTTTTGTAAAGTCTAAGTTC
* * * * *
336288 GTGCCTCAAATGAGACAAACATTGATTCTAGTAATTATCTTCGTTAATTATGTGATTAGGCACTA
65 GTGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTA
* * *
336353 TAAACACATTCTCTTTCTTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCATTTCT
130 TAAACACATTCTCCTTATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCT
* * * * * *
336418 TTGTCATATTTTCCTTAAAATCAAAGTTCATCCCTTTAATCTGACAAGCATCGATTCTCGCAACA
195 TTGCCCTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACAAGCATCGATTCTTG--ACA
*
336483 ATC-CCGATTCTTTTCAAGATCT-GGAACCAAG-A-ACA------C---A--ATACATGACATTG
258 ATCTCCGATTCTTTTCAAGAT-TGGGAGCCAAGAACACATTTCTTCATTAGGATACATGACATTG
* * *
336533 ATGCTTTAGTGTCGCAA-CAAATGCTTTTCTTTCCACTGTTTTTGATAAAATCAAAGTTTGTCTC
322 ATGCTTTGGTGTCGCAAGAAAATG-TTTTCTTTCCACTGTTTTTGATAGAATCAAAGTTTGTCTC
* *
336597 TTAAATAAGACAAATATGAATAGTCA-A-AATAGTCCCTATTCTTTTCGAGAGATTAGGCACCAT
386 TTAAATAAGACAAACATGAATAGTCATACAA-A-TCCCCATTCTTTTC-A-AGATTAGGCACCAT
** * * *** *
336660 ATGCAAAGTCTACTCAAAAGGATGTGCC
447 AAACATAGTCTACTCATAAGGATACACG
* *
336688 ATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCG
1 ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
** * * * * * * * *
336753 TGCCTCAAACAAGAAAAACAAGGATTCTTGTAATGATTTTCATTTATTTTGT-ATTAAGAACTAA
66 TGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTAT
* *
336817 AAACACATTCT-CTTCATTAGGATAAATGATATTGATGATTTTCTTTTGAATGGAAATCTTTTCT
131 AAACACATTCTCCTT-ATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCT
* *
336881 TTGCCTTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACGAGCATCGATTCTTGACATA
195 TTGCCCTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACAAGCATCGATTCTTGACA-A
* * * *
336946 GTCTGC-ATTGTTTTCATGATTGGGAGCCAAGAACACATTCTCTTCATTAGGATACTTGACATTG
259 -TCTCCGATTCTTTTCAAGATTGGGAGCCAAGAACACATT-TCTTCATTAGGATACATGACATTG
337010 ATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACTGTTTTTGATAGAATCAAAGTTTGTCTCT
322 ATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACTGTTTTTGATAGAATCAAAGTTTGTCTCT
* * *
337075 TAAATAAGGCAAACATGAATAGTGATACAAATCCCCATTCTTTTCAGGATTAGGCACCATAAACA
387 TAAATAAGACAAACATGAATAGTCATACAAATCCCCATTCTTTTCAAGATTAGGCACCATAAACA
* *
337140 TAGTATTCTCATAAGGATACACG
452 TAGTCTACTCATAAGGATACACG
* * * * *
337163 ATATTGATGCTTTAGTTTCGTAAGGAAGGCTTTATTCACACAAATTTTTGTAAAGTCTAAGTTCA
1 ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
** * * * *
337228 TTTCTCAAATGAGATAAACATGGATTCCAGTAGTGATCTTCATTCATTTTGTGAGTAGGCACTAT
66 TGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTAT
* * * *
337293 GAACACATTTTCCTTATTAGGATAAATGATATTGATGATTTT-TTTTGTATGGAAATCTTTTCTT
131 AAACACATTCTCCTTATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTT
* * * *
337357 TGCCCTAATTTCCTTAAAATCAATATTCATCCCCTAAATATGACAAGCATCTATTCTTGACATAG
196 TGCCCTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACAAGCATCGATTCTTGACA-A-
* * * *
337422 TCTCC-ATTCTTTTCAAGATTGGGAGCTAAGAACACAATCTCTTCATTAGGATACCTAACATTGA
259 TCTCCGATTCTTTTCAAGATTGGGAGCCAAGAACAC-ATTTCTTCATTAGGATACATGACATTGA
*
337486 TGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCT-TTTTTGATAGCATCAAAGTTTGTCTCT
323 TGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCA-CTGTTTTTGATAGAATCAAAGTTTGTCTCT
* * * * *
337550 TAAATAAGGCAAACATGAATAGTGACACTAATCACCATTCTTTTCAAGATTAGGCACCATAAACA
387 TAAATAAGACAAACATGAATAGTCATACAAATCCCCATTCTTTTCAAGATTAGGCACCATAAACA
* * *
337615 TAGTCTTCTCATTAGGATACATG
452 TAGTCTACTCATAAGGATACACG
* * * * *
337638 ATGTTGATGCTCTAGTTTTGTAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
1 ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
* *
337703 TGCCTCAAATGAGACAAACACGGATTCTAGTAATGATCTTCATTCATTTTATGATTAGGCACTAT
66 TGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTAT
* * * * *
337768 GAATATATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTAGCATGAAAATCTTTTCTT
131 AAACACATTCTCCTTATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTT
* * * ** * * *
337833 TACCCTATTTTCCTTAAATTTAAGGTTCATCCCTTAAATATGGCAAGCATCAATTCTCATAACAA
196 TGCCCTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACAAGCATCGATTCT--TGACAA
* * * *
337898 TCT-CTATTCTTTTCTAGATTGGGAGCCAAGAACA-ATTTGCCTTCATTAGGATACAAGACATTA
259 TCTCCGATTCTTTTCAAGATTGGGAGCCAAGAACACATTT--CTTCATTAGGATACATGACATTG
* * * *
337961 ATGCTTTGGGGTCGCAAGAAAAGGTTTTCTTTCAACCGTTTTTCG-TAGAATCAAAGTTTGTCTC
322 ATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACTGTTTTT-GATAGAATCAAAGTTTGTCTC
* * * * *
338025 TTAAATAACACAAA-ATGAATAGTCATACTAATCCCTATTCTTTTCAAGATTAGGCGCCATATAC
386 TTAAATAAGACAAACATGAATAGTCATACAAATCCCCATTCTTTTCAAGATTAGGCACCATAAAC
* *
338089 ATAGTCTACTCACAAGGATACACA
451 ATAGTCTACTCATAAGGATACACG
* * * * ** * *
338113 ATACTGATGCTTTGGTTTCACAATGAAGGCTTTCTTCCCACCAATTTTTGTAAAGAGTATGTTCT
1 ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
* * *
338178 TACATCAAATGAGACAAACATGGATTCTAGAAATGATCTTCATTCATTTTGTG
66 TGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTG
338231 GTTTTCTTTA
Statistics
Matches: 1335, Mismatches: 173, Indels: 59
0.85 0.11 0.04
Matches are distributed among these distances:
461 3 0.00
462 4 0.00
463 140 0.10
464 102 0.08
465 4 0.00
472 1 0.00
474 3 0.00
475 725 0.54
476 232 0.17
477 108 0.08
478 11 0.01
479 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (474 bp):
ATATTGATGCTTTGGTTTCGCAAGGAAGGCTTTCTTCACACCAATTTTTGTAAAGTCTAAGTTCG
TGCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTAT
AAACACATTCTCCTTATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTT
TGCCCTATTTTCCTTAAAATCAAAATTCATCCCTTAAATATGACAAGCATCGATTCTTGACAATC
TCCGATTCTTTTCAAGATTGGGAGCCAAGAACACATTTCTTCATTAGGATACATGACATTGATGC
TTTGGTGTCGCAAGAAAATGTTTTCTTTCCACTGTTTTTGATAGAATCAAAGTTTGTCTCTTAAA
TAAGACAAACATGAATAGTCATACAAATCCCCATTCTTTTCAAGATTAGGCACCATAAACATAGT
CTACTCATAAGGATACACG
Found at i:337645 original size:159 final size:161
Alignment explanation
Indices: 336520--338128 Score: 425
Period size: 159 Copynumber: 10.1 Consensus size: 161
336510 CAAGAACACA
* * * * *
336520 ATACATGACATTGATGCTTTAGTGTCGCAA-CAAATGCTTTTCTTTCCA-CTGTTTTTGATAAAA
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATG-TTTTCTTTCCACCTATTTTTGATAGAA
** * * * * *
336583 TCAAAGTTTGTCTCTTAAATAAGACAAATAT-GAATAGTCAAAATAGTC-CCTATTCTTTTCGAG
65 TCAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCC-ATTCTTTTC-A-
** * * **
336646 AGATTAGGCACCATATGCAAAGTCTACTCAAAAGG
127 AGATTAGGCACCATAAACACAGTCTTCTCATTAGG
* * * * * *
336681 AT--GTGCCATATTGATGCTTTGGTTTCGCAAG-AAAGGCTTTCTTCCCACCAATTTTTG-TA-A
1 ATACATG--ATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGA
* * * * * ** * ** * * *
336741 AGTCTAAGTTCGTGC-CTCAAACAAGAAAAACAAGGATTCTTGTA-A-TGATTTTCATT-TATTT
64 A-TCAAAGTTCAT-CTCTTAAATAAGACAAACATCGAATAGTG-ACACTAATCTCCATTCT-TTT
* * * * * *
336802 --TGTATTAAGAACTAAAAACACATTC-TCTTCATTAGG
125 CAAG-ATTAGGCACCATAAACACAGTCTTC-TCATTAGG
* * ** * * * * * * *** *
336838 ATAAATGATATTGATGATTTTCTTTTG-AATGGAAATCTTTTCTTTGC-CTTATTTTCCTTAAAA
1 ATACATGATATTGATGCTTTGGTGTCGCAA-GAAAATGTTTTCTTTCCACCTATTTTTGATAGAA
* * * * * * ** * * * *
336901 TCAAAATTCATCCCTTAAATATGACGAGCATCGATTCTTGACA-TAGTCTGCATTGTTTTCATGA
65 TCAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCCATTCTTTTCAAGA
* *
336965 TT-GGGAGCCA-AGAACACATTC-TCTTCATTAGG
130 TTAGGCA-CCATA-AACACAGTCTTC-TCATTAGG
* * *
336997 ATACTTGACATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCA-CTGTTTTTGATAGAAT
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGAAT
** * * * * *
337061 CAAAGTTTGTCTCTTAAATAAGGCAAACAT-GAATAGTGATACAAATCCCCATTCTTTTCAGGAT
66 CAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCCATTCTTTTCAAGAT
* * *
337125 TAGGCACCATAAACATAGTATTCTCATAAGG
131 TAGGCACCATAAACACAGTCTTCTCATTAGG
* * * * * * * * **
337156 ATACACGATATTGATGCTTTAGTTTCGTAAG-GAAGGCTTT-ATTCACACAAATTTTTG-TA-AA
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTC-CACCTATTTTTGATAGAA
* * * * * * * * * *
337217 GTCTAAGTTCATTTCTCAAATGAGATAAACATGGATTCCAGT---AGTGATCTTCATTCATTTT-
65 -TCAAAGTTCATCTCTTAAATAAGACAAACATCGAAT--AGTGACACTAATCTCCATTC-TTTTC
** * * * * *
337278 GTGAGTAGGCACTATGAACACA-TTTTCCTTATTAGG
126 AAGATTAGGCACCATAAACACAGTCTT-CTCATTAGG
* * * * * * * * * * * *** *
337314 ATAAATGATATTGATGATTT-TTTTTGTATGGAAATCTTTTCTTTGC-CCTAATTTCCTTAAAAT
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGAAT
* * * * * * ** *
337377 CAATA-TTCATCCCCTAAATATGACAAGCATCTATTCTTGACA-TAGTCTCCATTCTTTTCAAGA
66 CAA-AGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCCATTCTTTTCAAGA
* * *
337440 TT-GGGAGC-TAAGAACACAATC-TCTTCATTAGG
130 TTAGGCACCAT-A-AACACAGTCTTC-TCATTAGG
* * * *
337472 ATACCTAACATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCT-TTTTTGATAGCAT
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGAAT
** * *
337536 CAAAGTTTGTCTCTTAAATAAGGCAAACAT-GAATAGTGACACTAATCACCATTCTTTTCAAGAT
66 CAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCCATTCTTTTCAAGAT
*
337600 TAGGCACCATAAACATAGTCTTCTCATTAGG
131 TAGGCACCATAAACACAGTCTTCTCATTAGG
* * * * * * * * * *
337631 ATACATGATGTTGATGCTCTAGTTTTGTAAG-GAAGGCTTTC-TTCACACCAATTTTTG-TA-AA
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTC-CACCTATTTTTGATAGAA
* * * * * * *
337692 GTCTAAGTTCGTGC-CTCAAATGAGACAAACA-CGGATTCTAGT-A-A-TGATCTTCATTCATTT
65 -TCAAAGTTCAT-CTCTTAAATAAGACAAACATC-GA--ATAGTGACACTAATCTCCATTC-TTT
* * * * * * *
337752 T-ATGATTAGGCACTATGAATATATTCTCCTCATTAGG
124 TCAAGATTAGGCACCATAAACACAGTCTTCTCATTAGG
* * ** * * * * * ***
337789 ATAAATGATATTGATGATTTTCTTTAGCATGAAAATCTTTTCTTTAC-CCTATTTTCCTTA-AAT
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGAA-
* * * * * * ** * * * *
337852 TTAAGGTTCATCCCTTAAATATGGCAAGCATC-AATTCTCATAAC-AATCTCTATTCTTTTCTAG
65 TCAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGA-CACTAATCTCCATTCTTTTCAAG
*
337915 ATT-GGGAGCCA-AGAACA-A-T-TTGCCTTCATTAGG
129 ATTAGGCA-CCATA-AACACAGTCTT--C-TCATTAGG
* * * * * * *
337948 ATACAAGACATTAATGCTTTGGGGTCGCAAGAAAAGGTTTTCTTTCAACCGT-TTTTCG-TAGAA
1 ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACC-TATTTTTGATAGAA
** * * *
338011 TCAAAGTTTGTCTCTTAAATAACACAAA-AT-GAATAGTCATACTAATC-CCTATTCTTTTCAAG
65 TCAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCC-ATTCTTTTCAAG
* * * * **
338073 ATTAGGCGCCATATACATAGTCTACTCACAAGG
129 ATTAGGCACCATAAACACAGTCTTCTCATTAGG
** *
338106 ATACACAATACTGATGCTTTGGT
1 ATACATGATATTGATGCTTTGGT
338129 TTCACAATGA
Statistics
Matches: 1021, Mismatches: 333, Indels: 191
0.66 0.22 0.12
Matches are distributed among these distances:
156 9 0.01
157 84 0.08
158 392 0.38
159 410 0.40
160 75 0.07
161 50 0.05
162 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (161 bp):
ATACATGATATTGATGCTTTGGTGTCGCAAGAAAATGTTTTCTTTCCACCTATTTTTGATAGAAT
CAAAGTTCATCTCTTAAATAAGACAAACATCGAATAGTGACACTAATCTCCATTCTTTTCAAGAT
TAGGCACCATAAACACAGTCTTCTCATTAGG
Found at i:343314 original size:20 final size:20
Alignment explanation
Indices: 343289--343341 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
343279 TCCTGTAGCC
343289 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
343309 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
343329 ATGTATCGATACA
1 ATGTATCGATACA
343342 TTGATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:343423 original size:20 final size:20
Alignment explanation
Indices: 343381--343434 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
343371 GTTAGAAGCA
*
343381 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
343401 ATGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCACC
* *
343421 ATGCATCTATACAA
1 ATGTATCGATACAA
343435 ACAATGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:343494 original size:21 final size:19
Alignment explanation
Indices: 343462--343536 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
343452 ACTGCGAGTT
343462 TCATGTATCGATACAACT-A
1 TCATGTATCGATACAA-TGA
343481 TCCATGTAATCGATACAATGA
1 T-CATGT-ATCGATACAATGA
*
343502 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
343522 TAATGTATCGATACA
1 TCATGTATCGATACA
343537 TCTGGGTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.24
20 26 0.52
21 12 0.24
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:344103 original size:36 final size:36
Alignment explanation
Indices: 344059--344132 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
344049 AAGGTTCTCG
344059 TTGAAAAAATTT-TCCTTAAAAA-AA-ATTTCCTCCCC
1 TTGAAAAAATTTAT-CTTAAAAACAATATTT-CTCCCC
*
344094 TTGATAAAAATTTATTTTAAAAACAATATTTCTCCCC
1 TTGA-AAAAATTTATCTTAAAAACAATATTTCTCCCC
344131 TT
1 TT
344133 TTTTGTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
35 4 0.12
36 15 0.44
37 11 0.32
38 4 0.12
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (36 bp):
TTGAAAAAATTTATCTTAAAAACAATATTTCTCCCC
Found at i:348354 original size:15 final size:15
Alignment explanation
Indices: 348334--348369 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
348324 ATTATTTAAA
348334 ACAAAACATTTACAT
1 ACAAAACATTTACAT
348349 ACAAAACATTTACAT
1 ACAAAACATTTACAT
*
348364 CCAAAA
1 ACAAAA
348370 GGATGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (15 bp):
ACAAAACATTTACAT
Found at i:352135 original size:13 final size:13
Alignment explanation
Indices: 352116--352148 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
352106 TCGTTAGAAG
352116 CAATGTATCGATA
1 CAATGTATCGATA
*
352129 CACTGTATCGATA
1 CAATGTATCGATA
352142 CAATGTA
1 CAATGTA
352149 CCATGTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:352237 original size:19 final size:19
Alignment explanation
Indices: 352192--352245 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
352182 ACTGTTAGTT
*
352192 TCATGTATCAATACAATTG
1 TCATGTATCGATACAATTG
352211 TCCATGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
352230 ATCATGTATCGATACA
1 -TCATGTATCGATACA
352246 TCTGGGTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:358480 original size:20 final size:21
Alignment explanation
Indices: 358433--358487 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
358423 GCCAATGACC
**
358433 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
358454 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
358474 TGTATCGATACATT
1 TGTATCGATACATT
358488 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:359537 original size:20 final size:20
Alignment explanation
Indices: 359510--359562 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
359500 TAGAAAAACA
359510 AAATGTATCGATACATTCAT
1 AAATGTATCGATACATTCAT
* * *
359530 ACATGTATCCATACATTGAT
1 AAATGTATCGATACATTCAT
*
359550 AAATGTGTCGATA
1 AAATGTATCGATA
359563 TATCTAGGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTCAT
Found at i:359554 original size:71 final size:70
Alignment explanation
Indices: 359461--359595 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 70
359451 TTTTAACTAG
* * *
359461 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAGAAAAACAAAATG-TATCGATACA
1 ATGTATCCATACATTGAAAAATGTATCGATACATCTAGG--CAAAAACAAAAGGTTATCGATACA
359525 TTCATAC
64 TTCATAC
* * * *
359532 ATGTATCCATACATTGATAAATGTGTCGATATATCTAGGCAAAAACAAAAGGTTTTCGATACAT
1 ATGTATCCATACATTGAAAAATGTATCGATACATCTAGGCAAAAACAAAAGGTTATCGATACAT
359596 GTACTGTTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
69 11 0.20
70 10 0.18
71 35 0.62
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (70 bp):
ATGTATCCATACATTGAAAAATGTATCGATACATCTAGGCAAAAACAAAAGGTTATCGATACATT
CATAC
Found at i:361389 original size:476 final size:475
Alignment explanation
Indices: 359815--362859 Score: 3696
Period size: 476 Copynumber: 6.4 Consensus size: 475
359805 TAAAGTCTCC
* ** * * *
359815 TCAATATTAGGCACCATAAATGTAGTCTCCTCATAAGGGTACACGATATTGACGCTTTGCTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* * * ** *
359880 CAAGAAAGGCTTTATTCCCACCAATTTTTATAAAGTCCAAGTTCATGCCTCCGATGAGGCAAACA
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAACA
*
359945 AGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
131 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
**
360010 GATAAA-AGATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGAATGATTTTCCTTAAAA
196 GATAAATA-ATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCT-ATTTTCCTTAAAA
* * * *
360074 TCAAGGTTCATCCCTTAAAAAAGGCAAGCATTGATTCTCATAACAATATCCACTCTTTTCAAGAT
259 TCAAAGTTCATCCCTTAAAAAAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAGAT
* * * * * * * *
360139 TTGGAACCAAGAACATATTCCATTCATTAGGATACATGAGATTAATGCTTTGGTATCGTAGGAAA
324 TGGGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAA
**** *
360204 AGGTTTTCTTTCCAAAAATTTTGATAGAATCAAAGTTTGC-GTCTTAAATAAGACAAACATGAAT
389 AGGTTTTCTTTCCACCGTTTTTGATAGAATCAAAGTTT-CTCTCTTAAATAAGACAAACATGAAT
* *
360268 AGTCATACTAATCCCAATTCTTT
453 AGTCACACTAATCCCCATTCTTT
* *
360291 TCAGGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACAATATTGACGCTTTGGTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* ** *
360356 CAAGAAAGGCGTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTTGTGCCTCAGAA-GAGGCAAAC
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCA-AATGAGACAAAC
* *
360420 ATAGATTCTAGCAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTA
130 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTA
* * * * *
360485 GGATAAATGATATTGATAATTTTTTTTGGCATGAAAATCTTTTCTTTGCCTGATTTTCCTAAAAA
195 GGATAAATAATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCT-ATTTTCCT-TAAA
** * * * * *
360550 AAAAAAGTTCATCCCTTAAAAAAGGCAAGTATTGATTCTCGTAACAATCTCCACTTTTTTCAAGA
258 ATCAAAGTTCATCCCTTAAAAAAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAGA
* * * *
360615 TTTGGAACCATGAACACATTCCCTTCAATAGG----AT-ACA-TG--GCTTTGGTGTTGCAAGAA
323 TTGGGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAA
* ** **
360672 AAGGTTTTCTTTCCACCGCTTTTGATTAGAATCAAAGTTTGC-CTCCAAAATAAGGGAAACATGA
388 AAGGTTTTCTTTCCACCGTTTTTGA-TAGAATCAAAGTTT-CTCTCTTAAATAAGACAAACATGA
* *
360736 ATAGTTACAATAATCCCCATTCTTT
451 ATAGTCACACTAATCCCCATTCTTT
* * *
360761 TCAAGATTAGGCACCATAAATC-TAGTCTCCTCATAAGGATACACGATATTGACACTTTGGTTTT
1 TCAAGATTAGGCACCATAAA-CATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTC
* * ** *
360825 GCAAGAAAGGTTTTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCCGATGAGGCAAAC
65 GCAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAAC
* * *** * * * *
360890 ACGGATTTTTCCAATGGTCTTCATTCATTTTGTGATTAGGCACAATAAACATATTCTTCTAATTA
130 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTA
360955 GGATAAATAATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCTAATTTTCCTTAAAA
195 GGATAAATAATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCT-ATTTTCCTTAAAA
* * * * *
361020 TCAAAGTTCATGCCTTAAAAAAGGCAAGCATTGATTCTCGTAATAGTCTCCACTTTTTTCAAGAT
259 TCAAAGTTCATCCCTTAAAAAAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAGAT
* * * * *
361085 TTGGAACCAAGAACACATTCCTTTCATTAGGATACATGACATTGAAGCTCTGGTGTCGCAACAAA
324 TGGGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAA
* * * *
361150 AGGTTTTTTTTCCACCGTTTTTGGTAGAATCAAAGTTTACT-TCCTAAATAAGAGAAACATGAAT
389 AGGTTTTCTTTCCACCGTTTTTGATAGAATCAAAGTTT-CTCTCTTAAATAAGACAAACATGAAT
*
361214 AGTCACACTAATCCCCATTCTTC
453 AGTCACACTAATCCCCATTCTTT
** * * *
361237 TCAAGATTAGGCACCATAAATGTAGTCTCCTCAAAAGGATACACGATATTGATGCTTTGGTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* * ** * * * * *
361302 CAAGGAAGGCTTTCTTCCCACCAATTTTTGTAAAATCCGAGGTCAAGCCTCAAATAAGACTAATA
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAACA
** * * * * *
361367 TGGATTCTAGTAAAAATCTTCATTCATTTTGTGATTAGACACTGT-ACCACATTTTCCTCATTAG
131 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
* * *
361431 GATAAATAATATTGATGATTTTTTTTAGCATGG-AA----TTC-TT---T-TCTT--TT--AATC
196 GATAAATAATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCTATTTTCCTTAAAATC
* ** * * **
361482 AAAGTTCATCTCTTAAAAAAGATAAGCATCAATTCTCACAACAGTCTCTGCTCTTTTCAAGATTG
261 AAAGTTCATCCCTTAAAAAAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAGATTG
* * *
361547 GGAACCTAGAACACATTCCCTTCGTTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAG
326 GGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAG
* *
361612 GTTATCTTTCCACCGATTTTT-ATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAG
391 GTTTTCTTTCCACCG-TTTTTGATAGAATCAAAGTTTCTCTCTTAAATAAGACAAACATGAATAG
* *
361676 TCATACTAATCCCAATTCTTT
455 TCACACTAATCCCCATTCTTT
* * * * *
361697 TTAAGATTAGGGACCATAAACATAGTCTTCTCAAAATGATACACAATATTGACGCTTTGGTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* * * *
361762 CAAGAAAGGCATTCTTCCCCCCAATTTTTGTAATGTCTAATAAGTTCTTGCCTCAAATGAGACAA
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTC---TAAGTTCATGCCTCAAATGAGACAA
* * * * * *
361827 ACCTAGATTCTTGTAATGATCTTAATTCATTTTGTGATTAGGCACTATAAACATATTCTCCTCAT
128 ACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAAT
* * * * *
361892 TAGGATAAATGATATTGATGATTTTCATTTGG-ATGGAAATCTATTCGTTGCCTAATTTTTCGTA
193 TAGGATAAATAATATTGATGATTTTC-TTTGGCATGGAAATCTTTTCTTTGCCT-ATTTTCCTTA
* * * * *
361956 AAATCAAAATTCATCCCTTAAATACAA--CAAGCATCAATTCTCCTAACATTCTTCACTCTTTTC
256 AAATCAAAGTTCATCCCTTAAA-A-AAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTC
* * * *
362019 AAGATTGGGAACTAAGAACACATTCCCTTCATTAGGATACATGACGTTGATGCGTTGGTCTCGCA
319 AAGATTGGGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCA
* * * *
362084 AGAAAAGGTTTTCTTTCCAACGTTTCTAATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACAT
384 AGAAAAGGTTTTCTTTCCACCGTTTTTGATAGAATCAAAGTTTCTCTCTTAAATAAGACAAACAT
*
362149 GAATAGTCATACTAATCCCCATTCTTT
449 GAATAGTCACACTAATCCCCATTCTTT
* * * * *
362176 TTAGGATTTGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGATGGTTTGGTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* * *
362241 CAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAGTCTAAGTTCTTGGCTCAAATGAGACAAACA
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAACA
*
362306 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATTAG
131 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
* * * *
362371 GATAAATGATAGTAATGATTTTTCTTT-GCATGAAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
196 GATAAATAATATTGATGA-TTTTCTTTGGCATGGAAATCTTTTCTTTG-CCTATTTTCCTTAAAA
* * * * * * * * *
362435 TTAAAATTCACCCCCTAAATATAA--TAAGTATCGATTCTCATCATAGTCTCCATTCTTTTCAAG
259 TCAAAGTTCATCCCTTAAA-A-AAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAG
* *
362498 ATTGGGAACCAAGAACATATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGA
322 ATTGGGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGA
* * *
362563 AAAGGTTTTCTTTCCACCGTTTTTTATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATAAA
387 AAAGGTTTTCTTTCCACCGTTTTTGATAGAATCAAAGTTTCTCTCTTAAATAAGACAAACATGAA
* *
362628 TTGTCACACTAATCCCCATTCTTC
452 TAGTCACACTAATCCCCATTCTTT
* * *
362652 TCAGGATTAGGCACCATAAACATAGTCTTCTCATAAGGGTACACGATATTGATGCTTTGGTTTCG
1 TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
* * ** *
362717 CAAGAAAGGCTTTCTTCCCTCCAATTTTTGTAAAATCTAAGTTTGTGCCTCAAATTAGACAAACA
66 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAACA
*** * * ** *
362782 CAAATTCTAGTAATGATCTTCATTTATTTTGTAATTAGGCACTATAAACACATTCTCCTCGTTAA
131 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
*
362847 GATAAATGATATT
196 GATAAATAATATT
362860 TGTAAGCTCA
Statistics
Matches: 2227, Mismatches: 298, Indels: 88
0.85 0.11 0.03
Matches are distributed among these distances:
459 1 0.00
460 271 0.12
461 5 0.00
462 2 0.00
463 57 0.03
464 44 0.02
465 6 0.00
466 1 0.00
469 132 0.06
470 283 0.13
471 2 0.00
472 2 0.00
473 5 0.00
474 5 0.00
475 51 0.02
476 938 0.42
477 136 0.06
478 4 0.00
479 279 0.13
480 1 0.00
481 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (475 bp):
TCAAGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGACGCTTTGGTTTCG
CAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGAGACAAACA
TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTAATTAG
GATAAATAATATTGATGATTTTCTTTGGCATGGAAATCTTTTCTTTGCCTATTTTCCTTAAAATC
AAAGTTCATCCCTTAAAAAAGGCAAGCATCGATTCTCATAACAGTCTCCACTCTTTTCAAGATTG
GGAACCAAGAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAG
GTTTTCTTTCCACCGTTTTTGATAGAATCAAAGTTTCTCTCTTAAATAAGACAAACATGAATAGT
CACACTAATCCCCATTCTTT
Found at i:362347 original size:158 final size:156
Alignment explanation
Indices: 361573--362841 Score: 474
Period size: 159 Copynumber: 8.0 Consensus size: 156
361563 TCCCTTCGTT
* * * * * * *
361573 AGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGG-TTATCTTTCCACCGATTTTTATAG
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAG-AAAGGCTT-TCTTCCCACCAATTTTTATAA
* * * ** * *
361637 AATCAAAG-TTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATC-CCAATTCTTTT-T
64 AATCTAAGTTTTGCCTC-TAAAT-AGACAAACATAAATTCTCATAATGATCTCC-ATTCTTTTGT
* * *
361699 AAGATTAGGGACCATAAACATAGTCTTCTCAAA
126 --GATTAGGCACCATAAACATAGTCTCCTCATA
* * * * * * **
361732 ATGATACACAATATTGACGCTTTGGTTTCGCAAGAAAGGCATTCTTCCCCCCAATTTTTGTAATG
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAA
* * ** **
361797 TCTAATAAGTTCTTGCCTC-AAATGAGACAAACCTAGATTCTTGTAATGATCTTAATTCATTTTG
66 TC---TAAGTT-TTGCCTCTAAAT-AGACAAACATAAATTCTCATAATGATCTCCATTC-TTTTG
* * *
361861 TGATTAGGCACTATAAACATATTCTCCTCATT
125 TGATTAGGCACCATAAACATAGTCTCCTCATA
* * * ** * * * * * *
361893 AGGATAAATGATATTGATGATTTTCATTT-GGATGGAAA-TCTATTCGTT-GC-CTAATTTTTCG
1 AGGATACACGATATTGATG-CTTTGGTTTCGCA-AGAAAGGCT-TTC-TTCCCACCAATTTTT-A
* * * * * * * * * * *
361954 TAAAATCAAAATTCATCCCT-TAAATACAACAAGCATCAATTCTCCTAA-CATTCTTCACTCTTT
61 TAAAATCTAAGTT-TTGCCTCTAAATA-GACAAACATAAATTCTCATAATGA-TCTCCATTCTTT
** * * * * * *
362017 TCAAGATTGGGAACTA-AGAACACATTC-CCTTCATT
123 T-GTGATTAGGCACCATA-AACATAGTCTCC-TCATA
* ** * * * * * * * *
362052 AGGATACATGACGTTGATGCGTTGGTCTCGCAAGAAAAGGTTTTCTTTCCAAC-GTTTCTAATAG
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAG-AAAGGCTTTCTTCCCACCAATTT-TTATAA
* * * ** * * *
362116 AATCAAAG-TTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCCATTCTTTT-TA
64 AATCTAAGTTTTGCCTC-TAAAT-AGACAAACATAAATTCTCATAATGATCTCCATTCTTTTGT-
* *
362179 GGATTTGGCACCATAAACATAGTCTTCTCATA
126 -GATTAGGCACCATAAACATAGTCTCCTCATA
* *
362211 AGGATACACGATATTGATGGTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAG
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAA
* ** *
362276 TCTAAGTTCTTGGCTC-AAATGAGACAAACATGGATTCT-AGTAATGATCTTCATTCATTTTGTG
66 TCTAAGTT-TTGCCTCTAAAT-AGACAAACATAAATTCTCA-TAATGATCTCCATTC-TTTTGTG
* * * *
362339 ATTAGGCACTATAAACACATTCTCCTCATT
127 ATTAGGCACCATAAACATAGTCTCCTCATA
* * * * * * * * ** ** *
362369 AGGATAAATGATAGTAATGATTT-TTCTTTGCATGAAAATCTTTTCTTTGC-CCTATTTTCCT-T
1 AGGATACACGATATTGATGCTTTGGT-TTCGCAAGAAAGGC-TTTCTTCCCACCAATTTT--TAT
* *** * * * ** *
362431 AAAAT-TAAAATTCACCCCCTAAATATA-ATAAGTATCGATTCTCATCAT-AGTCTCCATTCTTT
62 AAAATCT-AAGTTTTGCCTCTAAATAGACA-AA-CATAAATTCTCATAATGA-TCTCCATTCTTT
** * * * *
362493 TCAAGATTGGGAACCA-AGAACATATTC-CCTTCATT
123 T-GTGATTAGGCACCATA-AACATAGTCTCC-TCATA
* * * * * * ** *
362528 AGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTTATAGA
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAG-AAAGGCTTTCTTCCCACCAATTTTTATAAA
* * * * * * * *
362593 ATCAAAG-TTTGTCTCTTAAATAAGACAAACATAAATTGTCACACTAATCCCCATTCTTCTCAG-
65 ATCTAAGTTTTGCCTC-TAAAT-AGACAAACATAAATTCTCATAATGATCTCCATTCTT-T-TGT
*
362656 GATTAGGCACCATAAACATAGTCTTCTCATA
126 GATTAGGCACCATAAACATAGTCTCCTCATA
* * *
362687 AGGGTACACGATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCTCCAATTTTTGTAAAA
1 AGGATACACGATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAA
* * * *
362752 TCTAAGTTTGTGCCTC-AAATTAGACAAACACAAATTCT-AGTAATGATCTTCATTTATTTTGTA
66 TCTAAGTTT-TGCCTCTAAA-TAGACAAACATAAATTCTCA-TAATGATCTCCA-TTCTTTTGTG
* * *
362815 ATTAGGCACTATAAACACATTCTCCTC
127 ATTAGGCACCATAAACATAGTCTCCTC
362842 GTTAAGATAA
Statistics
Matches: 798, Mismatches: 240, Indels: 145
0.67 0.20 0.12
Matches are distributed among these distances:
157 8 0.01
158 251 0.31
159 387 0.48
160 38 0.05
161 80 0.10
162 25 0.03
163 9 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (156 bp):
AGGATACACGATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTCTTCCCACCAATTTTTATAAAA
TCTAAGTTTTGCCTCTAAATAGACAAACATAAATTCTCATAATGATCTCCATTCTTTTGTGATTA
GGCACCATAAACATAGTCTCCTCATA
Found at i:363737 original size:13 final size:13
Alignment explanation
Indices: 363719--363805 Score: 58
Period size: 13 Copynumber: 7.6 Consensus size: 13
363709 TAAGAACACA
363719 TATCGATATAATG
1 TATCGATATAATG
363732 TATCGATACTAA-G
1 TATCGATA-TAATG
363745 ---C-A-AT-ATG
1 TATCGATATAATG
363752 TATCGATATAATG
1 TATCGATATAATG
363765 TATCGATACTAA-G
1 TATCGATA-TAATG
363778 --T--A-AT-ATG
1 TATCGATATAATG
363785 TATCGATATAATG
1 TATCGATATAATG
363798 TATCGATA
1 TATCGATA
363806 CTAAGTAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 32
0.64 0.00 0.36
Matches are distributed among these distances:
6 2 0.03
7 4 0.07
8 2 0.03
9 3 0.05
10 2 0.03
11 3 0.05
12 4 0.07
13 32 0.55
14 6 0.10
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (13 bp):
TATCGATATAATG
Found at i:363754 original size:20 final size:19
Alignment explanation
Indices: 363729--363826 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 19
363719 TATCGATATA
363729 ATGTATCGATACTAAGCAAT
1 ATGTATCGATACTAAG-AAT
363749 ATGTATCGATA-T----A-
1 ATGTATCGATACTAAGAAT
363762 ATGTATCGATACTAAGTAAT
1 ATGTATCGATACTAAG-AAT
363782 ATGTATCGATA-T----A-
1 ATGTATCGATACTAAGAAT
363795 ATGTATCGATACTAAGTAAT
1 ATGTATCGATACTAAG-AAT
363815 ATGTATCGATAC
1 ATGTATCGATAC
363827 ATCTGGCTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.34
14 4 0.06
19 4 0.06
20 34 0.53
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACTAAGAAT
Found at i:363761 original size:33 final size:33
Alignment explanation
Indices: 363697--363825 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
363687 ATAATTCAAT
* * **
363697 ATGTATCGAAACTAAG-AACACATATCGATATA
1 ATGTATCGATACTAAGTAATATGTATCGATATA
*
363729 ATGTATCGATACTAAGCAATATGTATCGATATA
1 ATGTATCGATACTAAGTAATATGTATCGATATA
363762 ATGTATCGATACTAAGTAATATGTATCGATATA
1 ATGTATCGATACTAAGTAATATGTATCGATATA
363795 ATGTATCGATACTAAGTAATATGTATCGATA
1 ATGTATCGATACTAAGTAATATGTATCGATA
363826 CATCTGGCTG
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 15 0.16
33 76 0.84
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACTAAGTAATATGTATCGATATA
Found at i:364486 original size:25 final size:25
Alignment explanation
Indices: 364458--364505 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
364448 GCAAATTTCA
*
364458 ATTTAGTACTCCCCCTTAACAAAAC
1 ATTTAATACTCCCCCTTAACAAAAC
*
364483 ATTTAATACTCTCCCTTAACAAA
1 ATTTAATACTCCCCCTTAACAAA
364506 TTTTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTTAATACTCCCCCTTAACAAAAC
Found at i:364779 original size:35 final size:36
Alignment explanation
Indices: 364714--364797 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 36
364704 ATCTCCCCCA
* *
364714 TGCATTCATAAAAATAATATCAAGGCAAACATTAAT
1 TGCATTCATGAAAATAATAGCAAGGCAAACATTAAT
* * *
364750 TGCATTCATGAAAA-GATAGCAAGGTAAACATTCAT
1 TGCATTCATGAAAATAATAGCAAGGCAAACATTAAT
* *
364785 TACAATCATGAAA
1 TGCATTCATGAAA
364798 GTAAACATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 28 0.68
36 13 0.32
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (36 bp):
TGCATTCATGAAAATAATAGCAAGGCAAACATTAAT
Found at i:373235 original size:20 final size:20
Alignment explanation
Indices: 373210--373265 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
373200 ACATGTTCAT
373210 TGTATCGATACATGAACAAA
1 TGTATCGATACATGAACAAA
373230 TGTATCGATACATGAACAAA
1 TGTATCGATACATGAACAAA
373250 TGTATCGATACATGAA
1 TGTATCGATACATGAA
373266 ATTAGTAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATGAACAAA
Found at i:387104 original size:26 final size:26
Alignment explanation
Indices: 387075--387137 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
387065 TATTAGACTT
387075 TATATCATGCAACCATGATAACATTC
1 TATATCATGCAACCATGATAACATTC
387101 TATATCATGCAACCATGATAACATTC
1 TATATCATGCAACCATGATAACATTC
*
387127 AATATCATGCA
1 TATATCATGCA
387138 TTCATAATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (26 bp):
TATATCATGCAACCATGATAACATTC
Found at i:387453 original size:28 final size:28
Alignment explanation
Indices: 387416--388607 Score: 750
Period size: 28 Copynumber: 41.8 Consensus size: 28
387406 AATACAACCT
* **
387416 CTTTTCAAAGCCCACAAGTTAGTGAAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
387444 CTTCTCAAAGCCCACAAGCCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
387473 CCTTTCAAAGCCCATAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
387501 CTTTTCAAAGCCCATAAATCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
387529 CTTCTT-AAAGCCCACAAGTTAGTGGCAT
1 CTT-TTCAAAGCCCACAAGTCAGTGGCAC
**
387557 CTTTTCAAAATCCACAAGTCAGTGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
387584 CTGTTTCAAAGCCCATAAGTTAGTTGCACC
1 CT-TTTCAAAGCCCACAAGTCAGTGGCA-C
* *
387614 CTTTTCAAAGCCCACGAGTTAGT-G-AC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
387640 CCTTTCTAAGCCCACGAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
387668 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
387696 CCTTTCTAAGCCCATAAGTCAATGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
387725 CTTTT-AAAGCCCAGACGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
387753 CTTTT-AAAGCCCAGACGTCAGTGGCGTC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
387781 C-TTTCAAAGCCCACGAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
387809 C-TTTCGAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAC
*** * **
387837 CAAGTAAAAGCCCACACAAGTTGGTGGCACC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCA-C
** ** * * *
387868 CTAGTCAAAGCCTGCATGAC-TTGGCAGC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* ** *
387896 ATTTGAGTCAAAGCCCACACAAGTTGGCGGCA-
1 CTTT---TCAAAG-CC-CACAAGTCAGTGGCAC
*
387928 CTTGATTCAAAGCCCACACAAGGT-GGTGGCAC
1 CTT--TTCAAAG-CC-CACAA-GTCAGTGGCAC
* ** *
387960 CTTAGTT-AAAGGCCGCACGAGTTGGCGGCACC
1 CTT--TTCAAA-GCC-CACAAGTCAGTGGCA-C
** *
387992 CCATTCAAAGCCTGCACGAGTC-GATGGCAACC
1 CTTTTCAAAGCC--CACAAGTCAG-TGGC-A-C
* *
388024 CTTCTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-A-C
* *
388056 CTTTT-GAAGCCCACACAAG-CTGGTGGCAACC
1 CTTTTCAAAG-CC-CACAAGTC-AGTGGC-A-C
* *
388087 CTTTT-GATGCCCACACAAGTCAGTGGCAAC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
* * * *
388117 CCTTTCTAAGCCCACAAGTTAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
388145 CTTTTGAAAGCCCACGAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
388173 CTTTTTAAAGCCCACAAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
388201 CATTTCAAAGCCC-CTGAGTTAGTGTCAC
1 CTTTTCAAAGCCCAC-AAGTCAGTGGCAC
* *
388229 TCTTTT-AAAGGCCATAAGTCAGTGGCACC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCA-C
388258 CTTTT-AAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
388285 CCTTTCAAAGCCCATAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
388313 CTTTTCAAAGCCCACGAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
388341 CTTTTTAAAGCCCACAAGTTAGTAGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
388370 CTTTT-AAAGCCCACGAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
388397 CCTTTCAAAGCTCACGAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
388425 CCTTTCTAAGCCCTCAAGTCAGTCGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
388453 CTTTTCTAAGCCCACGAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
388481 CTTTTCAAAGCCTATAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
388510 CTTTT-TAAGCCCATAAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
388537 CTTTTTAAAGCCCAC--G--A---G-AC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
388557 CCTTTCTAAGCCCACAAGTTAATGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
388585 CTTTTCAAAAGCCCACAAGTCAG
1 CTTTTC-AAAGCCCACAAGTCAG
388608 CGACATCCAG
Statistics
Matches: 944, Mismatches: 163, Indels: 113
0.77 0.13 0.09
Matches are distributed among these distances:
20 14 0.01
21 1 0.00
22 1 0.00
24 2 0.00
26 22 0.02
27 27 0.03
28 557 0.59
29 118 0.12
30 33 0.03
31 114 0.12
32 44 0.05
33 6 0.01
34 5 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:387923 original size:31 final size:31
Alignment explanation
Indices: 387843--387949 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
387833 GCATCAAGTA
** *
387843 AAAGCCCACACAAGTTGGTGGCACCCT-AGTC
1 AAAGCCCACACAAGTTGGCAGCA-CTTGAGTC
** ** * *
387874 AAAGCCTGCATGACTTGGCAGCATTTGAGTC
1 AAAGCCCACACAAGTTGGCAGCACTTGAGTC
* *
387905 AAAGCCCACACAAGTTGGCGGCACTTGATTC
1 AAAGCCCACACAAGTTGGCAGCACTTGAGTC
387936 AAAGCCCACACAAG
1 AAAGCCCACACAAG
387950 GTGGTGGCAC
Statistics
Matches: 58, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 1 0.02
31 57 0.98
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (31 bp):
AAAGCCCACACAAGTTGGCAGCACTTGAGTC
Found at i:387959 original size:31 final size:31
Alignment explanation
Indices: 387889--387990 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
387879 CTGCATGACT
* * *
387889 TGGCAGCATTTGAGTCAAAGCCCACACAAGT
1 TGGCGGCACTTGAGTCAAAGCCCACACAAGG
*
387920 TGGCGGCACTTGATTCAAAGCCCACACAAGG
1 TGGCGGCACTTGAGTCAAAGCCCACACAAGG
* * * * * *
387951 TGGTGGCACCTT-AGTTAAAGGCCGCACGAGT
1 TGGCGGCA-CTTGAGTCAAAGCCCACACAAGG
387982 TGGCGGCAC
1 TGGCGGCAC
387991 CCCATTCAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
30 1 0.02
31 54 0.93
32 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (31 bp):
TGGCGGCACTTGAGTCAAAGCCCACACAAGG
Found at i:388035 original size:32 final size:32
Alignment explanation
Indices: 387996--388132 Score: 122
Period size: 31 Copynumber: 4.4 Consensus size: 32
387986 GGCACCCCAT
** *
387996 TCAAAGCCTGCACGAGTCGATGGCAACCCTTC
1 TCAAAGCCCACACAAGTCGATGGCAACCCTTC
*
388028 TCAAAGCCCACACAAGTCGGTGGCAACCCTT-
1 TCAAAGCCCACACAAGTCGATGGCAACCCTTC
** *
388059 TTGAAGCCCACACAAG-CTGGTGGCAACCCTT-
1 TCAAAGCCCACACAAGTC-GATGGCAACCCTTC
** *
388090 TTGATGCCCACACAAGTC-AGTGGCAACCCTT-
1 TCAAAGCCCACACAAGTCGA-TGGCAACCCTTC
*
388121 TCTAAGCCCACA
1 TCAAAGCCCACA
388133 AGTTAGTAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
30 1 0.01
31 62 0.68
32 28 0.31
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (32 bp):
TCAAAGCCCACACAAGTCGATGGCAACCCTTC
Found at i:388069 original size:31 final size:31
Alignment explanation
Indices: 388010--388132 Score: 160
Period size: 31 Copynumber: 3.9 Consensus size: 31
388000 AGCCTGCACG
* **
388010 AGTCGATGGCAACCCTTCTCAAAGCCCACACA
1 AGTCGGTGGCAACCCTT-TTGAAGCCCACACA
388042 AGTCGGTGGCAACCCTTTTGAAGCCCACACA
1 AGTCGGTGGCAACCCTTTTGAAGCCCACACA
*
388073 AG-CTGGTGGCAACCCTTTTGATGCCCACACA
1 AGTC-GGTGGCAACCCTTTTGAAGCCCACACA
*
388104 AGTCAGTGGCAACCCTTTCT-AAGCCCACA
1 AGTCGGTGGCAACCCTTT-TGAAGCCCACA
388133 AGTTAGTAGC
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
30 1 0.01
31 63 0.77
32 18 0.22
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.20
Consensus pattern (31 bp):
AGTCGGTGGCAACCCTTTTGAAGCCCACACA
Found at i:388581 original size:48 final size:49
Alignment explanation
Indices: 388507--388600 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
388497 AGTCAGTGGC
* * *
388507 ACCCTTTTTAAGCCCATAAGTCAATGGCACCTTTT-TAAAGCCCACGAG
1 ACCCTTTCTAAGCCCACAAGTCAATGGCACCTTTTCAAAAGCCCACGAG
* *
388555 ACCCTTTCTAAGCCCACAAGTTAATGGCATCTTTTCAAAAGCCCAC
1 ACCCTTTCTAAGCCCACAAGTCAATGGCACCTTTTCAAAAGCCCAC
388601 AAGTCAGCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 31 0.77
49 9 0.22
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.27
Consensus pattern (49 bp):
ACCCTTTCTAAGCCCACAAGTCAATGGCACCTTTTCAAAAGCCCACGAG
Found at i:388707 original size:31 final size:32
Alignment explanation
Indices: 388647--388717 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
388637 GTTGCATTTG
*
388647 AGTC-AAAGCCCACACAAGTTAGCGACACCTA
1 AGTCAAAAGCCCACACAAGCTAGCGACACCTA
* * * *
388678 AGT-AAAAGCCCACATAAGCTAGTGGCACCTT
1 AGTCAAAAGCCCACACAAGCTAGCGACACCTA
388709 AGTCAAAAG
1 AGTCAAAAG
388718 TCGCATGAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.15
Consensus pattern (32 bp):
AGTCAAAAGCCCACACAAGCTAGCGACACCTA
Found at i:388792 original size:32 final size:32
Alignment explanation
Indices: 388756--389218 Score: 409
Period size: 32 Copynumber: 14.6 Consensus size: 32
388746 AGCTTGCACG
* *
388756 AGTCGATAGCAACCCTTCTCAAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
*
388788 AGTCGATGGCAACCCTT-TTGAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * *
388819 AGTCGGTGACAACCCTT-TTGAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * *
388850 AGTTGGTGGCAACCCTT-TTGAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * * * * * *
388881 AGTCAATAGCAAACCTTTTCTAAAGTCGATACA
1 AGTCGATGGCAACCCTTCT-TAAAGCCCACACA
*
388914 AGTC-AGTGGTAACCCTT-TTCAAAGCCCACACA
1 AGTCGA-TGGCAACCCTTCTT-AAAGCCCACACA
*
388946 AGTCGATGGCAACCTTTCTTAAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * * * *
388978 AGTCGGTGGTAACCTTTCTCAAAGCCCACATA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * *
389010 AGTCAATGACAACCCTTC-TAAAGCCCACATA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * * * * *
389041 AATTGGTGGTAACCATTTTTAAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
*
389073 AGTCGATGGCAACCTTTCTTAAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * * * *
389105 AGTCGGTGGTAACCTTTCTCAAAGCCCACATA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * *
389137 AGTCAATGACAACCCTTC-TAAAGCCCACATA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* * * * * *
389168 AATTGGTGGTAACCATTTTTAAAGCCCACACA
1 AGTCGATGGCAACCCTTCTTAAAGCCCACACA
* *
389200 AGTCGGTAGCAACCCTTCT
1 AGTCGATGGCAACCCTTCT
389219 AATCCCAATG
Statistics
Matches: 349, Mismatches: 74, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
31 127 0.36
32 198 0.57
33 24 0.07
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (32 bp):
AGTCGATGGCAACCCTTCTTAAAGCCCACACA
Found at i:389029 original size:127 final size:127
Alignment explanation
Indices: 388765--389218 Score: 576
Period size: 127 Copynumber: 3.6 Consensus size: 127
388755 GAGTCGATAG
* * * * * * *
388765 CAACCCTTCTCAAAGCCCACACAAGTCGATGGCAACC-CTTTTGAAGCCCACACAAGTCGGTGAC
1 CAACCCTTCT-AAAGCCCACACAAATCGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGC
* * * * *
388829 AACCCTT-TTGAAGCCCACACAAGTTGGTGGCAACCCTTT-T-GAAGCCCACACAAGTCAAT-A
65 AACCCTTCTTAAAGCCCACACAAGTCGGTGGTAA-CCTTTCTCAAAGCCCACATAAGTCAATGA
* * * * * * * *
388889 GCAAACCTTTTCTAAAGTCGATACAAGTCAGTGGTAACCCTTTTCAAAGCCCACACAAGTCGATG
1 -C-AACC-CTTCTAAAGCCCACACAAATCGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATG
*
388954 GCAACCTTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAAGTCAATGA
63 GCAACCCTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAAGTCAATGA
* *
389019 CAACCCTTCTAAAGCCCACATAAATTGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGCA
1 CAACCCTTCTAAAGCCCACACAAATCGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGCA
*
389084 ACCTTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAAGTCAATGA
66 ACCCTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAAGTCAATGA
* * * *
389146 CAACCCTTCTAAAGCCCACATAAATTGGTGGTAACCATTTTTAAAGCCCACACAAGTCGGTAGCA
1 CAACCCTTCTAAAGCCCACACAAATCGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGCA
389211 ACCCTTCT
66 ACCCTTCT
389219 AATCCCAATG
Statistics
Matches: 291, Mismatches: 31, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
125 1 0.00
126 24 0.08
127 219 0.75
128 28 0.10
129 18 0.06
130 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (127 bp):
CAACCCTTCTAAAGCCCACACAAATCGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGCA
ACCCTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAAGTCAATGA
Found at i:389159 original size:95 final size:93
Alignment explanation
Indices: 388756--389216 Score: 431
Period size: 95 Copynumber: 4.8 Consensus size: 93
388746 AGCTTGCACG
* * *
388756 AGTCGATAGCAACCCTTCTCAAAGCCCACACAAGTCGATGGCAACCCTTTTGAAGCCCACACAAG
1 AGTCGATGGCAACCCTTCT-AAAGCCCACACAAGTCGATGGCAACCTTTTTAAAGCCCACACAAG
*
388821 TCGGTGACAACCCTTTTGAAGCCCACACA
65 TCGGTGACAACCCTTTTAAAGCCCACACA
* * * * * * * * *
388850 AGTTGGTGGCAACCCTTTTGAAGCCCACACAAGTCAATAGCAAACCTTTTCTAAAGTCGATACAA
1 AGTCGATGGCAACCCTTCTAAAGCCCACACAAGTCGATGGC-AACCTTTT-TAAAGCCCACACAA
* **
388915 GTCAGTGGTAACCCTTTTCAAAGCCCACACA
64 GTCGGTGACAACCCTTTT-AAAGCCCACACA
* * * * *
388946 AGTCGATGGCAACCTTTCTTAAAGCCCACACAAGTCGGTGGTAACCTTTCTCAAAGCCCACATAA
1 AGTCGATGGCAACCCTTC-TAAAGCCCACACAAGTCGATGGCAACCTTT-TTAAAGCCCACACAA
** * *
389011 GTCAATGACAACCCTTCTAAAGCCCACATA
64 GTCGGTGACAACCCTTTTAAAGCCCACACA
* * * * * *
389041 AATTGGTGGTAACCATTTTTAAAGCCCACACAAGTCGATGGCAACCTTTCTTAAAGCCCACACAA
1 AGTCGATGGCAACC-CTTCTAAAGCCCACACAAGTCGATGGCAACCTTT-TTAAAGCCCACACAA
** *
389106 GTCGGTGGTAA-CCTTTCTCAAAGCCCACATA
64 GTCGGTGACAACCCTTT-T-AAAGCCCACACA
* * * * * * *
389137 AGTCAATGACAACCCTTCTAAAGCCCACATAAATTGGTGGTAACCATTTTTAAAGCCCACACAAG
1 AGTCGATGGCAACCCTTCTAAAGCCCACACAAGTCGATGGCAACC-TTTTTAAAGCCCACACAAG
389202 TCGGT-AGCAACCCTT
65 TCGGTGA-CAACCCTT
389217 CTAATCCCAA
Statistics
Matches: 292, Mismatches: 64, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
93 19 0.07
94 26 0.09
95 143 0.49
96 85 0.29
97 19 0.07
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (93 bp):
AGTCGATGGCAACCCTTCTAAAGCCCACACAAGTCGATGGCAACCTTTTTAAAGCCCACACAAGT
CGGTGACAACCCTTTTAAAGCCCACACA
Found at i:389333 original size:52 final size:52
Alignment explanation
Indices: 389276--389378 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
389266 TTTTCTTTAT
*
389276 TTTAAGCCCAATAT-TGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATC
1 TTTAAGCCCAATATCT-CTAGCCTTGAATCAGCATATTGACACCTTTATCATC
* * *
389328 TTTAAGTCCAATATCTTTAGCCTTGAATCAGCATATTGACACTTTTATCAT
1 TTTAAGCCCAATATCTCTAGCCTTGAATCAGCATATTGACACCTTTATCAT
389379 TTTTCTTGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 45 0.98
53 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (52 bp):
TTTAAGCCCAATATCTCTAGCCTTGAATCAGCATATTGACACCTTTATCATC
Found at i:390347 original size:8 final size:9
Alignment explanation
Indices: 390324--390381 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
390314 ATAAATTCAA
390324 AAAATTAAT-
1 AAAA-TAATC
*
390333 AAAAAAATC
1 AAAATAATC
*
390342 AAAAAAAGTC
1 AAAATAA-TC
390352 AAAATTAAT-
1 AAAA-TAATC
390361 AAAATAAT-
1 AAAATAATC
390369 AAAATAATC
1 AAAATAATC
390378 AAAA
1 AAAA
390382 AAATGATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 15 0.35
9 19 0.44
10 7 0.16
11 2 0.05
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAATAATC
Found at i:390383 original size:28 final size:30
Alignment explanation
Indices: 390320--390383 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 30
390310 CGATATAAAT
390320 TCAAAAAATTAATAAAAAAATCAAAAAAAG
1 TCAAAAAATTAATAAAAAAATCAAAAAAAG
* *
390350 TC--AAAATTAATAAAATAAT-AAAATAA-
1 TCAAAAAATTAATAAAAAAATCAAAAAAAG
390376 TCAAAAAA
1 TCAAAAAA
390384 ATGATGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 2 0.07
27 6 0.20
28 20 0.67
30 2 0.07
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (30 bp):
TCAAAAAATTAATAAAAAAATCAAAAAAAG
Found at i:391340 original size:20 final size:21
Alignment explanation
Indices: 391294--391340 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
391284 ATGCTGCAAC
*
391294 GTGAAAGGTAGCAACCAACAA
1 GTGAAAGGTAGAAACCAACAA
** *
391315 CAGAAAGGT-GAAACCATCAA
1 GTGAAAGGTAGAAACCAACAA
391335 GTGAAA
1 GTGAAA
391341 ACAAGCAACA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (21 bp):
GTGAAAGGTAGAAACCAACAA
Found at i:391575 original size:9 final size:9
Alignment explanation
Indices: 391563--391600 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
391553 AAAAAGATGG
391563 AAAAAG-AA
1 AAAAAGAAA
391571 AAAAAGAAA
1 AAAAAGAAA
391580 AAAAAGAAA
1 AAAAAGAAA
391589 AAAAGAGAAA
1 AAAA-AGAAA
391599 AA
1 AA
391601 GAAAAACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:391576 original size:8 final size:8
Alignment explanation
Indices: 391563--391606 Score: 70
Period size: 8 Copynumber: 5.4 Consensus size: 8
391553 AAAAAGATGG
391563 AAAAAGAA
1 AAAAAGAA
391571 AAAAAGAAA
1 AAAAAG-AA
391580 AAAAAGAA
1 AAAAAGAA
*
391588 AAAAAGAG
1 AAAAAGAA
391596 AAAAAGAA
1 AAAAAGAA
391604 AAA
1 AAA
391607 CAAGGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 25 0.76
9 8 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:391591 original size:25 final size:25
Alignment explanation
Indices: 391563--391615 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
391553 AAAAAGATGG
391563 AAAAAGAAAAAAAGAAAAAAAAGAA
1 AAAAAGAAAAAAAGAAAAAAAAGAA
* * *
391588 AAAAAGAGAAAAAGAAAAACAAGGA
1 AAAAAGAAAAAAAGAAAAAAAAGAA
391613 AAA
1 AAA
391616 TCTTTACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAAAAAAAAGAA
Found at i:391615 original size:15 final size:16
Alignment explanation
Indices: 391552--391615 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 16
391542 GAGTTCAGCT
391552 AAAAAAGATGGAAAAAGA
1 AAAAAAGA--GAAAAAGA
*
391570 AAAAAAGAAAAAAAAGA
1 AAAAAAG-AGAAAAAGA
391587 AAAAAAGAGAAAAAGA
1 AAAAAAGAGAAAAAGA
391603 AAAACAAG-GAAAA
1 AAAA-AAGAGAAAA
391616 TCTTTACATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 17 0.40
17 17 0.40
18 7 0.17
19 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAAGAGAAAAAGA
Found at i:395130 original size:157 final size:156
Alignment explanation
Indices: 394648--395274 Score: 643
Period size: 157 Copynumber: 4.0 Consensus size: 156
394638 TAGAACCCTT
* * * * * * * * **
394648 AAAGGATTATAAAAGGGGTGAACCTATCCTAAATACCTATCTTCAACATAAAAACAGACCCGGTG
1 AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGACCAGAAG
* *
394713 ATAA-TCTAGGACTCGATTTTAAAAAAATTATGAAAATACCCCTAGGGGATTCCTTCGACGTGAA
66 ATAACT-TAGGACTCGATTCT-AAAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAA
** ** **
394777 AGTATCCTAGT-ACATTTAAAGGACCAAA
129 AGTATCCCGGTAAC-CCTAAAGGACTTAA
* * *
394805 AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCTACCTTCGACATAAAA-CAGACCCGAGG
1 AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGACCAGAAG
* * * * * * *
394869 ATAACTTAGGACTTTG-TTTTAGAAAATTATCAAAATATCCCTAGGGGATACCTTTGATGTGAAA
66 ATAACTTAGGAC-TCGATTCTAAAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAA
*
394933 GTATCCCGGTACCCCTAAAGGACTTAA
130 GTATCCCGGTAACCCTAAAGGACTTAA
* * * * * * * *
394960 AAATGACTATAAAAGGAATAAACCTATCTTTAATACCCACCTTCGACATAAAAGCGGACTAGAAG
1 AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGACCAGAAG
* * *** *
395025 ATAACTTAGGACTTGATTCTAAAAAATTATGAAAATGCCCCTATGACTACACCTTCGACGTGAAA
66 ATAACTTAGGACTCGATTCTAAAAAATTATGAAAATACCCCTA-GGGGATACCTTCGACGTGAAA
** *
395090 GTATCTTGGTAACCCTAAAGAACTTAA
130 GTATCCCGGTAACCCTAAAGGACTTAA
* * * * *
395117 AAAGGATTTTAAAAGGGATGAACCTATCCTAAATACCCACATTCGGCATGAAAGCAGACCCAG-T
1 AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGA-CCAGAA
* * * * *
395181 GATAACTTAGCACTCGATTCTAGAAAATTACGAAAATACTCCTAAGGGATACCTTCGACGTGAAA
65 GATAACTTAGGACTCGATTCTAAAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAA
* *
395246 GTATCTCGGTAACTCTAAAGGACTTAA
130 GTATCCCGGTAACCCTAAAGGACTTAA
395273 AA
1 AA
395275 CAACTAGAGA
Statistics
Matches: 389, Mismatches: 74, Indels: 15
0.81 0.15 0.03
Matches are distributed among these distances:
155 105 0.27
156 107 0.28
157 174 0.45
158 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (156 bp):
AAAGGATTTTAAAAGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGACCAGAAG
ATAACTTAGGACTCGATTCTAAAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAAG
TATCCCGGTAACCCTAAAGGACTTAA
Found at i:397451 original size:10 final size:10
Alignment explanation
Indices: 397437--397472 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
397427 TTGCTTTCTT
*
397437 TTTTTTTTCT
1 TTTTTTTTCA
397447 TTTTTTTTCA
1 TTTTTTTTCA
*
397457 TTTTTTATCA
1 TTTTTTTTCA
397467 TTTTTT
1 TTTTTT
397473 GATTGGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:397460 original size:11 final size:11
Alignment explanation
Indices: 397431--397472 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
397421 CCATGTTTGC
*
397431 TTTCTTTTTTT
1 TTTCATTTTTT
397442 TTTC-TTTTTT
1 TTTCATTTTTT
397452 TTTCA-TTTTT
1 TTTCATTTTTT
*
397462 TATCATTTTTT
1 TTTCATTTTTT
397473 GATTGGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCATTTTTT
Found at i:400110 original size:78 final size:79
Alignment explanation
Indices: 400007--400197 Score: 235
Period size: 78 Copynumber: 2.4 Consensus size: 79
399997 TTGGGGTGTT
* * * * * *
400007 CCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGATTAGAA-AAAAAATC
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTAGAAGAAAAAAGC
400071 -GGGATTAGAGTATC
65 AGGGATTAGAGTATC
* ** *
400085 CCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCA
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTAGAAGAAAAAAGCA
* *
400150 GGGGTTGGAGTATC
66 GGGATTAGAGTATC
400164 CCCTC-AGAAATAACGGGGTTGGAGTATCCCCGAT
1 CCCTCGA-AAATAACGGGGTTGGAGTATCCCCGAT
400198 GATTAACGGG
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
77 5 0.05
78 49 0.51
79 43 0.44
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (79 bp):
CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTAGAAGAAAAAAGCA
GGGATTAGAGTATC
Found at i:400212 original size:27 final size:28
Alignment explanation
Indices: 400150--400224 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 28
400140 GAATAAAGCA
*
400150 GGGGTTGGAGTATCCCCTCA-GAAATAAC
1 GGGGTTGGAGTATCCCC-GATGAAATAAC
*
400178 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
400205 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
400225 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.59
28 18 0.41
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:400295 original size:54 final size:51
Alignment explanation
Indices: 400208--400330 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
400198 GATTAACGGG
* *
400208 GTTGGAGTATCCCCGATTGTGAAAAATTTGTGTTTTTTAAAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTT-AAAAATAAAATCGGA
*
400262 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTAAAAATAAAATCGGA
* * *
400313 GATGGAATATCCCTGATT
1 GTTGGAGTATCCCCGATT
400331 GCGGAGAGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 29 0.47
52 4 0.06
53 1 0.02
54 28 0.45
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAATCGGA
Found at i:402708 original size:13 final size:13
Alignment explanation
Indices: 402690--402715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
402680 ACAAAGATCC
402690 ATGTATCGATACA
1 ATGTATCGATACA
402703 ATGTATCGATACA
1 ATGTATCGATACA
402716 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:402711 original size:33 final size:33
Alignment explanation
Indices: 402669--402735 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
402659 AAAATTTCCA
***
402669 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
402702 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
402735 A
1 A
402736 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:402779 original size:19 final size:18
Alignment explanation
Indices: 402755--402820 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
402745 CAGTAGCTAA
402755 TTATGTATCGATACAATAC
1 TTATGTATCGATAC-ATAC
402774 TTATGTATCGATAC--A-
1 TTATGTATCGATACATAC
402789 -T-TGTATCGATACATAAC
1 TTATGTATCGATACAT-AC
402806 TTATGTATCGATACA
1 TTATGTATCGATACA
402821 AATTGTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACATAC
Found at i:402795 original size:13 final size:13
Alignment explanation
Indices: 402777--402802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
402767 ACAATACTTA
402777 TGTATCGATACAT
1 TGTATCGATACAT
402790 TGTATCGATACAT
1 TGTATCGATACAT
402803 AACTTATGTA
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:402799 original size:32 final size:32
Alignment explanation
Indices: 402758--402820 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
402748 TAGCTAATTA
402758 TGTATCGATACA-ATACTTATGTATCGATACAT
1 TGTATCGATACATA-ACTTATGTATCGATACAT
402790 TGTATCGATACATAACTTATGTATCGATACA
1 TGTATCGATACATAACTTATGTATCGATACA
402821 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAACTTATGTATCGATACAT
Found at i:403510 original size:33 final size:32
Alignment explanation
Indices: 403451--403518 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
403441 GTAGCTAAAT
* * *
403451 TTGTATCGATACACACAATATATATCGATGCA
1 TTGTATCAATACACACAAAATATATCGATACA
*
403483 TTGTATCAATACATCACAAAATGTATCGATACA
1 TTGTATCAATACA-CACAAAATATATCGATACA
403516 TTG
1 TTG
403519 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
TTGTATCAATACACACAAAATATATCGATACA
Found at i:406785 original size:51 final size:51
Alignment explanation
Indices: 406716--406831 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
406706 AAAAATAACA
*
406716 GGGTTGGAGTATCCCCGATGGTGAGAAA-TCAATATTTTGAAAATAAAAAT-T
1 GGGTTGGAGTATCCCCGATGGTGA-AAAGTCAATATTTTGAAAA-AAAAATCG
* * *
406767 GGGTTGGAGTATCTCCGATGGTGAAAAGTCAATATTTTGGAAACAAAATCG
1 GGGTTGGAGTATCCCCGATGGTGAAAAGTCAATATTTTGAAAAAAAAATCG
406818 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
406832 TCTTAGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 8 0.14
51 50 0.86
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATGGTGAAAAGTCAATATTTTGAAAAAAAAATCG
Found at i:406807 original size:130 final size:129
Alignment explanation
Indices: 406667--406908 Score: 332
Period size: 130 Copynumber: 1.9 Consensus size: 129
406657 TTAAAAATTT
*
406667 AATATTTTGGAGATA-AAAAT-GGGGTTGGAGTATCC-CTTCAAAAATAAC-AGGGTTGGAGTAT
1 AATATTTTGGA-A-ACAAAATCGGGGTTGGAGTATCCTCTT-AAAAATAACGA-GGTTAGAGTAT
* *
406728 CCCCGATGGTGAGAAATCAATATTTTGAAAATAAAAATTG-GGTTGGAGTATCTCCGATGGTGAA
62 CCCCGATGGTG-GAAATCAATATTTTAAAAAT-AAAATTGAGATTGGAGTATCTCCGATGGTGAA
406792 AAGTC
125 AAGTC
* *
406797 AATATTTTGGAAACAAAATCGGGGTTGGAGTATCCTCTTAGAAATAACGAGGTTAGAGTATCCCT
1 AATATTTTGGAAACAAAATCGGGGTTGGAGTATCCTCTTAAAAATAACGAGGTTAGAGTATCCCC
* *
406862 GATGGTGGAAATCGATGTTTTAAAAATAAAATTGAGATTGGAGTATC
66 GATGGTGGAAATCAATATTTTAAAAATAAAATTGAGATTGGAGTATC
406909 CCCTCAAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
128 8 0.08
129 34 0.34
130 54 0.54
131 4 0.04
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (129 bp):
AATATTTTGGAAACAAAATCGGGGTTGGAGTATCCTCTTAAAAATAACGAGGTTAGAGTATCCCC
GATGGTGGAAATCAATATTTTAAAAATAAAATTGAGATTGGAGTATCTCCGATGGTGAAAAGTC
Found at i:406856 original size:79 final size:78
Alignment explanation
Indices: 406768--407444 Score: 583
Period size: 79 Copynumber: 8.6 Consensus size: 78
406758 ATAAAAATTG
* * * * *
406768 GGTTGGAGTATCTCCGATGGT-GAAAAGTCAATATTTTGGAAACAAAATCGGGGTTGGAGTATCC
1 GGTTAGAGTATC-CCGATGGTGGAAAA-TCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
*
406832 TCTTAGAAATAACGA
64 CCTTAGAAATAACGA
* * * *
406847 GGTTAGAGTATCCCTGATGGTGG-AAATCGATGTTTTAAAAATAAAATTGAGATTGGAGTATCCC
1 GGTTAGAGTATCCC-GATGGTGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
* *
406911 CTCAAAAATAACG-
65 CTTAGAAATAACGA
* * * * * * *
406924 GGATAAGAGTATCCCTGATGGTGGAAAATTGATATTTTAGAAAGAAAA-CTAGGGTTGGAGTTTT
1 GG-TTAGAGTATCCC-GATGGTGGAAAATCGATGTTTTAGAAATAAAATC-GGGGTTGGAGTATC
* *
406988 CCCTAAAAAATAGA-GA
63 CCCTTAGAAATA-ACGA
* *
407004 GGTTAGAGTATCCCCGATAGTGGAAAATCGATGTTTTAGAAATAAAATCGGGATTGGAGTATCCC
1 GGTTAGAGTAT-CCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
407069 CTT-GAAAATAAC-A
65 CTTAG-AAATAACGA
* * *
407082 GGGTTGGAGTATCCCTGATGGTGGAAAAT-TAGTGTTTTAGAAATAAAATCGGGGTTAGAGTATC
1 -GGTTAGAGTATCCC-GATGGTGGAAAATCGA-TGTTTTAGAAATAAAATCGGGGTTGGAGTATC
* * **
407146 CTC-TCGAAA-AAATA
63 CCCTTAGAAATAACGA
* * * * *
407160 GGGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAGAAATAAAATCAGGATTGGAGTATCC
1 -GGTTAGAGTAT-CCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
* *
407225 CC-TCGAAAATAATG-
64 CCTTAG-AAATAACGA
*
407239 GGATTAGAGTATCTCCGATGGTGGAAAATC-AGTGTTTTAGAAATAAAATCAGGGTTGGAGTATC
1 GG-TTAGAGTATC-CCGATGGTGGAAAATCGA-TGTTTTAGAAATAAAATCGGGGTTGGAGTATC
*
407303 CCCTTAGAAAAAACGA
63 CCCTTAGAAATAACGA
* * * ** * *
407319 GGTTGGAGTATCCTCGATGGTGGAAAA-CTAGTGTTTTAAAAATAAAA-CTAAGGTAGAAGTATC
1 GGTTAGAGTATCC-CGATGGTGGAAAATCGA-TGTTTTAGAAATAAAATC-GGGGTTGGAGTATC
* ** *
407382 TCCTCGGAAATAACGG
63 CCCTTAGAAATAACGA
* *
407398 GGTTGGAGTATCCTCGATGGTGGAAAATCGATATTTTAGAAATAAAA
1 GGTTAGAGTATCC-CGATGGTGGAAAATCGATGTTTTAGAAATAAAA
407445 ACATCAATGA
Statistics
Matches: 497, Mismatches: 72, Indels: 58
0.79 0.11 0.09
Matches are distributed among these distances:
77 4 0.01
78 136 0.27
79 341 0.69
80 16 0.03
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (78 bp):
GGTTAGAGTATCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
TTAGAAATAACGA
Found at i:407171 original size:236 final size:232
Alignment explanation
Indices: 406766--407444 Score: 738
Period size: 236 Copynumber: 2.9 Consensus size: 232
406756 AAATAAAAAT
* * * *
406766 TGGGTTGGAGTATCTCCGATGGT-GAAAAGTCAATATTTTGGAAACAAAATCGGGGTTGGAGTAT
1 TGGGTTAGAGTATCTCCGATGGTGGAAAA-TC-ATGTTTTAGAAATAAAATC-GGGTTGGAGTAT
* * *
406830 CCTCTT-AGAAATAACGAGGTTAGAGTATCCCTGATGGTGG-AAATCGATGTTTTAAAAATAAAA
63 CCCCTTGA-AAATAACGAGGTTGGAGTATCCCTGATGGTGGAAAATAG-TGTTTTAAAAATAAAA
* * * * *
406893 TTGAGATTGGAGTATCCCCTC--AAAAATAACGGGATAAGAGTATCCCTGATGGTGGAAAATTGA
126 TCGAGGTTAGAGTATCCTCTCGAAAAAAT-A-GGG-TTAGAGTATCCCTGATGGTGGAAAATTGA
* * * *
406956 TATTTTAGAAAGAAAA-CTAGGGTTGGAGTTTTCCCTAAAAAATAGA
188 TATTTTAGAAATAAAATC-AGGATTGGAGTATCCCCTAAAAAATA-A
* *
407002 -GAGGTTAGAGTATCCCCGATAGTGGAAAATCGATGTTTTAGAAATAAAATCGGGATTGGAGTAT
1 TG-GGTTAGAGTATCTCCGATGGTGGAAAATC-ATGTTTTAGAAATAAAATCGGG-TTGGAGTAT
*
407066 CCCCTTGAAAATAAC-AGGGTTGGAGTATCCCTGATGGTGGAAAATTAGTGTTTTAGAAATAAAA
63 CCCCTTGAAAATAACGA-GGTTGGAGTATCCCTGATGGTGGAAAA-TAGTGTTTTAAAAATAAAA
* * * * *
407130 TCGGGGTTAGAGTATCCTCTCGAAAAAATAGGGTTAGAGTATCCCCGATGGTGAAAAATTGGTGT
126 TCGAGGTTAGAGTATCCTCTCGAAAAAATAGGGTTAGAGTATCCCTGATGGTGGAAAATTGATAT
**
407195 TTTAGAAATAAAATCAGGATTGGAGTATCCCCTCGAAAATAA
191 TTTAGAAATAAAATCAGGATTGGAGTATCCCCTAAAAAATAA
407237 TGGGATTAGAGTATCTCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATCAGGGTTGGAGTAT
1 TGGG-TTAGAGTATCTCCGATGGTGGAAAATCA-TGTTTTAGAAATAAAATC-GGGTTGGAGTAT
407302 CCCCTTAGAAAA-AACGAGGTTGGAGTAT-CCTCGATGGTGGAAAACTAGTGTTTTAAAAATAAA
63 CCCCTT-GAAAATAACGAGGTTGGAGTATCCCT-GATGGTGGAAAA-TAGTGTTTTAAAAATAAA
* * ** *
407365 A-CTAAGG-TAGAAGTAT-CTCCTCGGAAATAACGGGGTTGGAGTAT-CCTCGATGGTGGAAAAT
125 ATC-GAGGTTAG-AGTATCCT-CTC-GAAAAAATAGGGTTAGAGTATCCCT-GATGGTGGAAAAT
*
407426 CGATATTTTAGAAATAAAA
185 TGATATTTTAGAAATAAAA
407445 ACATCAATGA
Statistics
Matches: 379, Mismatches: 42, Indels: 43
0.82 0.09 0.09
Matches are distributed among these distances:
235 18 0.05
236 254 0.67
237 98 0.26
238 3 0.01
239 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (232 bp):
TGGGTTAGAGTATCTCCGATGGTGGAAAATCATGTTTTAGAAATAAAATCGGGTTGGAGTATCCC
CTTGAAAATAACGAGGTTGGAGTATCCCTGATGGTGGAAAATAGTGTTTTAAAAATAAAATCGAG
GTTAGAGTATCCTCTCGAAAAAATAGGGTTAGAGTATCCCTGATGGTGGAAAATTGATATTTTAG
AAATAAAATCAGGATTGGAGTATCCCCTAAAAAATAA
Found at i:407266 original size:315 final size:315
Alignment explanation
Indices: 406767--407444 Score: 790
Period size: 315 Copynumber: 2.2 Consensus size: 315
406757 AATAAAAATT
* * * * *
406767 GGGTTGGAGTATCTCC-GATGGT-GAAAAGTCAATATTTTGGAAACAAAATCGGGGTTGGAGTAT
1 GGGTTGGAGTATC-CCTGATGGTGGAAAA-TTAGTATTTTAGAAATAAAATCGGGGTTAGAGTAT
* * * * *
406830 CCTCTTAGAAATAACGAGGTTAGAGTATCCCTGATGGTGGAAATCGATGTTTTAAAAATAAAATT
64 CCTCTTAGAAAAAAAGAGGTTAGAGTATCCCCGATGGTGAAAATCGATGTTTTAAAAATAAAATA
*
406895 GAGATTGGAGTATCCCCTCAAAAATAACGGGATAAGAGTATCCCTGATGGTGGAAAAT-TGATAT
129 GAGATTGGAGTATCCCCTCAAAAATAACGGGATAAGAGTATCCCTGATGGTGGAAAATCAG-TAT
* *
406959 TTTAGAAAGAAAA-CTAGGGTTGGAGTTTTCCC-TA-AAAAATAGAGAGGTTAGAGTATCCCCGA
193 TTTAGAAAGAAAATC-AGGGTTGGAGTATCCCCTTAGAAAAA-A-AGAGGTTAGAGTATCCCCGA
* ** * * *
407021 TAGTGGAAAATCGA-TGTTTTAGAAATAAAA-TCGGGATTGGAGTATCCCCTTGAAAATAACA
255 TAGTGGAAAA-CGAGTGTTTTAAAAATAAAACTAAGG-TAGAAGTATCCCCTCGAAAATAACA
*
407082 GGGTTGGAGTATCCCTGATGGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTAGAGTATCC
1 GGGTTGGAGTATCCCTGATGGTGGAAAATTAGTATTTTAGAAATAAAATCGGGGTTAGAGTATCC
* * * *
407147 TC-TCGAAAAAATAG-GGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAGAAATAAAATC
66 TCTTAGAAAAAA-AGAGGTTAGAGTATCCCCGATGGTG-AAAATCGATGTTTTAAAAATAAAAT-
* * * *
407210 AG-GATTGGAGTATCCCCTCGAAAATAATGGGATTAGAGTATCTCC-GATGGTGGAAAATCAGTG
128 AGAGATTGGAGTATCCCCTCAAAAATAACGGGATAAGAGTATC-CCTGATGGTGGAAAATCAGTA
* * * * *
407273 TTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTTAGAAAAAACGAGGTTGGAGTATCCTCGATG
192 TTTTAGAAAGAAAATCAGGGTTGGAGTATCCCCTTAGAAAAAAAGAGGTTAGAGTATCCCCGATA
* * * *
407338 GTGGAAAACTAGTGTTTTAAAAATAAAACTAAGGTAGAAGTATCTCCTCGGAAATAACG
257 GTGGAAAACGAGTGTTTTAAAAATAAAACTAAGGTAGAAGTATCCCCTCGAAAATAACA
*
407397 GGGTTGGAGTAT-CCTCGATGGTGGAAAA-TCGATATTTTAGAAATAAAA
1 GGGTTGGAGTATCCCT-GATGGTGGAAAATTAG-TATTTTAGAAATAAAA
407445 ACATCAATGA
Statistics
Matches: 310, Mismatches: 39, Indels: 28
0.82 0.10 0.07
Matches are distributed among these distances:
314 37 0.12
315 252 0.81
316 16 0.05
317 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (315 bp):
GGGTTGGAGTATCCCTGATGGTGGAAAATTAGTATTTTAGAAATAAAATCGGGGTTAGAGTATCC
TCTTAGAAAAAAAGAGGTTAGAGTATCCCCGATGGTGAAAATCGATGTTTTAAAAATAAAATAGA
GATTGGAGTATCCCCTCAAAAATAACGGGATAAGAGTATCCCTGATGGTGGAAAATCAGTATTTT
AGAAAGAAAATCAGGGTTGGAGTATCCCCTTAGAAAAAAAGAGGTTAGAGTATCCCCGATAGTGG
AAAACGAGTGTTTTAAAAATAAAACTAAGGTAGAAGTATCCCCTCGAAAATAACA
Found at i:411421 original size:20 final size:20
Alignment explanation
Indices: 411396--411449 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
411386 GTTACAAGCA
*
411396 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
411416 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
411436 ATGTATCGATACAA
1 ATGTATCGATACAA
411450 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:411522 original size:19 final size:19
Alignment explanation
Indices: 411478--411533 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
411468 CTGCCAGTTT
**
411478 CATGTATCGATACAACTGTC
1 CATGTATCGATACAA-TGAA
411498 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
411517 CATGTATCGATACAATG
1 CATGTATCGATACAATG
411534 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:411536 original size:13 final size:13
Alignment explanation
Indices: 411518--411544 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
411508 TACAATGAAC
411518 ATGTATCGATACA
1 ATGTATCGATACA
411531 ATGTATCGATACA
1 ATGTATCGATACA
411544 A
1 A
411545 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:411540 original size:32 final size:33
Alignment explanation
Indices: 411499--411562 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
411489 ACAACTGTCC
*
411499 ATGTATCGATACAATG-A-ACATGTATCGATACA
1 ATGTATCGATACAAAGCATA-ATGTATCGATACA
411531 ATGTATCGATACAAAGCATAATGTATCGATAC
1 ATGTATCGATACAAAGCATAATGTATCGATAC
411563 TTCTGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:416743 original size:20 final size:20
Alignment explanation
Indices: 416697--416751 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
416687 ATATTGATAC
***
416697 ATTGTATCGATACATGTTTA
1 ATTGTATCGATACATGGACA
416717 A-TGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
416736 ATTGTATCGATACATG
1 ATTGTATCGATACATG
416752 AAACTAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:421088 original size:13 final size:13
Alignment explanation
Indices: 421070--421095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
421060 AGGGTAGCTT
421070 TTGTATCGATACA
1 TTGTATCGATACA
421083 TTGTATCGATACA
1 TTGTATCGATACA
421096 ACACTTATGT
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):
TTGTATCGATACA
Found at i:422019 original size:39 final size:39
Alignment explanation
Indices: 421956--422093 Score: 130
Period size: 39 Copynumber: 3.7 Consensus size: 39
421946 AAAGATGAAG
* *
421956 GTGCTAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* *
421995 GTGCCAAGGTGCTGATTCAAGGCCAGC-A-A---AG---
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* * *
422026 GTGCCAATATGCTAATTCAAGGCCAGCAATATTGGGCTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* * *
422065 ATACCAATGTGCTGATTCAAGGTCAGCGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCGA
422094 CGTTGGTCTT
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
31 24 0.31
32 1 0.01
33 1 0.01
34 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 47 0.61
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (39 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
Found at i:422044 original size:31 final size:31
Alignment explanation
Indices: 421995--422054 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
421985 TATTGGGCTT
* *
421995 GTGCCAAGGTGCTGATTCAAGGCCAGCAAAG
1 GTGCCAAGATGCTAATTCAAGGCCAGCAAAG
*
422026 GTGCCAATATGCTAATTCAAGGCCAGCAA
1 GTGCCAAGATGCTAATTCAAGGCCAGCAA
422055 TATTGGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (31 bp):
GTGCCAAGATGCTAATTCAAGGCCAGCAAAG
Found at i:422077 original size:70 final size:70
Alignment explanation
Indices: 421953--422091 Score: 215
Period size: 70 Copynumber: 2.0 Consensus size: 70
421943 CTTAAAGATG
* * * * *
421953 AAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTGCCAAGGTGCTGATTCAAGGC
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
422018 CAGCA
66 CAGCA
* *
422023 AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGGCTTATACCAATGTGCTGATTCAAGGT
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
422088 CAGC
66 CAGC
422092 GACGTTGGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (70 bp):
AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
CAGCA
Found at i:422173 original size:43 final size:43
Alignment explanation
Indices: 422111--422196 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
422101 CTTAAAGGTG
* *
422111 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTA
1 AAGGTGCAAATATGCTGATTCAAGGCCAGCAACATTGGACTTA
* * *
422154 AAGGTGCAAATATGTTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCAAATATGCTGATTCAAGGCCAGCAACATTGGACTTA
422197 GAAGAAGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (43 bp):
AAGGTGCAAATATGCTGATTCAAGGCCAGCAACATTGGACTTA
Found at i:422274 original size:27 final size:27
Alignment explanation
Indices: 422218--422482 Score: 212
Period size: 27 Copynumber: 9.5 Consensus size: 27
422208 CACCAACTTG
*
422218 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGC-TTTG-AA-GGTTGCCACTAACT
**
422247 TGTATGCTTTTGAAGGTTGCCACT-ACTT
1 TGTGGGC-TTTGAAGGTTGCCACTAAC-T
422275 TGTGGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTAACT
* * * * *
422302 TGTGGGTTTTTGAAAAGATGCCCCTGACT
1 TGTGGG-CTTTG-AAGGTTGCCACTAACT
* * *
422331 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTAACT
422360 TGTGGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTAACT
* * *
422387 TATGGGCTTTGAAGGTTGCGACT-GCTT
1 TGTGGGCTTTGAAGGTTGCCACTAAC-T
*
422414 TGTTGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTAACT
* ** * * *
422441 TATAGGTTTTTGAAAAGATGCCACTGACT
1 TGT-GGGCTTTG-AAGGTTGCCACTAACT
422470 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
422483 AAGTGAGGAA
Statistics
Matches: 194, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.01
27 90 0.46
28 33 0.17
29 70 0.36
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (27 bp):
TGTGGGCTTTGAAGGTTGCCACTAACT
Found at i:423911 original size:16 final size:16
Alignment explanation
Indices: 423891--423943 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 16
423881 ATCCGGACCC
423891 TTTTTGTTGTTTG-TT
1 TTTTTGTTGTTTGTTT
*
423906 TGTTT-TTGTTT-TTT
1 TTTTTGTTGTTTGTTT
423920 TTTTTGTT-TGTTGTTT
1 TTTTTGTTGT-TTGTTT
423936 TTTTTGTT
1 TTTTTGTT
423944 TTTTTGGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 13 0.41
15 8 0.25
16 11 0.34
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTTTGTTGTTTGTTT
Found at i:423927 original size:26 final size:24
Alignment explanation
Indices: 423891--423949 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 24
423881 ATCCGGACCC
*
423891 TTTTTGTTGTTTGTTTGTTTTTGTTT
1 TTTTTTTTGTTTG-TTGTTTTT-TTT
423917 TTTTTTTTGTTTGTTGTTTTTTTT
1 TTTTTTTTGTTTGTTGTTTTTTTT
*
423941 GTTTTTTTG
1 TTTTTTTTG
423950 GCGAAGGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 11 0.35
25 8 0.26
26 12 0.39
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (24 bp):
TTTTTTTTGTTTGTTGTTTTTTTT
Found at i:423933 original size:29 final size:28
Alignment explanation
Indices: 423891--423948 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 28
423881 ATCCGGACCC
423891 TTTTTGTTGTTTGTTTGTTTTTGTTTTTT
1 TTTTTGTTGTTTGTTT-TTTTTGTTTTTT
423920 TTTTTGTT-TGTTGTTTTTTTTGTTTTTT
1 TTTTTGTTGT-TTGTTTTTTTTGTTTTTT
423948 T
1 T
423949 GGCGAAGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (28 bp):
TTTTTGTTGTTTGTTTTTTTTGTTTTTT
Found at i:423944 original size:16 final size:16
Alignment explanation
Indices: 423893--423944 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
423883 CCGGACCCTT
423893 TTTGTTGTTTGTTTGTT-
1 TTTGTTGTTT-TTT-TTG
*
423910 TTTGTTTTTTTTTTTG
1 TTTGTTGTTTTTTTTG
423926 TTTGTTGTTTTTTTTG
1 TTTGTTGTTTTTTTTG
423942 TTT
1 TTT
423945 TTTTGGCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 2 0.06
16 21 0.66
17 9 0.28
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTGTTGTTTTTTTTG
Found at i:423945 original size:22 final size:22
Alignment explanation
Indices: 423891--423946 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
423881 ATCCGGACCC
423891 TTTTTGTTGTTTGTTTGTTTTTG
1 TTTTTGTT-TTTGTTTGTTTTTG
*
423914 TTTTTTTTTTTGTTTGTTGTTT-
1 TTTTTGTTTTTGTTTGTT-TTTG
423936 TTTTTGTTTTT
1 TTTTTGTTTTT
423947 TTGGCGAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (22 bp):
TTTTTGTTTTTGTTTGTTTTTG
Found at i:439544 original size:21 final size:20
Alignment explanation
Indices: 439511--439549 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
439501 ATTTTAAATT
439511 TATTTTAATATTAATATTTTA
1 TATTTTAATATTAA-ATTTTA
439532 TATTTT-ATAATTAAATTT
1 TATTTTAAT-ATTAAATTT
439550 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTAATATTAAATTTTA
Found at i:440302 original size:30 final size:30
Alignment explanation
Indices: 440256--440335 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
440246 ATTTGTTTTT
*
440256 ATTTTAAGATTTTTTATTTT-TCTTTAAAA
1 ATTTTAAAATTTTTTATTTTATCTTTAAAA
*
440285 ATTTTAAAATTTATTTATTTTATTTTTAAAA
1 ATTTTAAAATTT-TTTATTTTATCTTTAAAA
*
440316 ATTTTTAGAA-TTTTTATTTT
1 A-TTTTAAAATTTTTTATTTT
440336 CTATTTGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.24
30 16 0.36
31 11 0.24
32 7 0.16
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (30 bp):
ATTTTAAAATTTTTTATTTTATCTTTAAAA
Found at i:440341 original size:32 final size:31
Alignment explanation
Indices: 440256--440320 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
440246 ATTTGTTTTT
* *
440256 ATTTTAAGATTT-TTTATTTT-TCTTTAAAA
1 ATTTTAAAATTTATTTATTTTATTTTTAAAA
440285 ATTTTAAAATTTATTTATTTTATTTTTAAAA
1 ATTTTAAAATTTATTTATTTTATTTTTAAAA
440316 ATTTT
1 ATTTT
440321 TAGAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.34
30 8 0.25
31 13 0.41
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
ATTTTAAAATTTATTTATTTTATTTTTAAAA
Found at i:441385 original size:11 final size:11
Alignment explanation
Indices: 441369--441445 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
441359 ATTAATTAAC
*
441369 ATAATATGAAT
1 ATAATATAAAT
*
441380 ATAATATAAAAA
1 ATAATAT-AAAT
*
441392 ATAATATGAAT
1 ATAATATAAAT
*
441403 ATGATAT-AA-
1 ATAATATAAAT
441412 AT-ATATAAAT
1 ATAATATAAAT
*
441422 ATATTA-AAAT
1 ATAATATAAAT
*
441432 AT-ATATAAAA
1 ATAATATAAAT
441442 ATAA
1 ATAA
441446 ATTATTATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 4 0.08
9 6 0.12
10 15 0.29
11 18 0.35
12 9 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:441399 original size:23 final size:23
Alignment explanation
Indices: 441369--441412 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
441359 ATTAATTAAC
441369 ATAATATGAATATAATATAAAAA
1 ATAATATGAATATAATATAAAAA
*
441392 ATAATATGAATATGATATAAA
1 ATAATATGAATATAATATAAA
441413 TATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
ATAATATGAATATAATATAAAAA
Found at i:441414 original size:29 final size:28
Alignment explanation
Indices: 441371--441446 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
441361 TAATTAACAT
*
441371 AATATGA-ATATAATATAAAAAATAATATG
1 AATATGATATA-AATATAAAAAATAATA-A
* *
441400 AATATGATATAAATATATAAATATATTAA
1 AATATGATATAAATATA-AAAAATAATAA
*
441429 AATAT-ATATAAAAATAAA
1 AATATGATATAAATATAAA
441447 TTATTATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 10 0.24
29 18 0.44
30 11 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
AATATGATATAAATATAAAAAATAATAA
Found at i:441863 original size:38 final size:40
Alignment explanation
Indices: 441813--441914 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 40
441803 CATGTAATCT
* * * *
441813 ATTA-AAAATTAAAAAATTTACTAAATATAT-TAATTTTA
1 ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
*
441851 ATT-TAAATTTAAAAAATTTAATTAATAAATATAAATTTA
1 ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
*
441890 ATTAT-AATTTATAAAAAATTAATAA
1 ATTATAAATTTA-AAAAATTTAATAA
441915 TTTAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
38 25 0.47
39 16 0.30
40 12 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
ATTATAAATTTAAAAAATTTAATAAATAAATATAAATTTA
Found at i:441870 original size:15 final size:15
Alignment explanation
Indices: 441850--441890 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
441840 TATTAATTTT
441850 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
*
441865 AATTT-AA-TTAATA
1 AATTTAAATTTAAAA
*
441878 AATATAAATTTAA
1 AATTTAAATTTAA
441891 TTATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTAAATTTAAAA
Found at i:441902 original size:19 final size:19
Alignment explanation
Indices: 441868--441929 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
441858 TTTAAAAAAT
*
441868 TTAATTAATAA-ATATAAA
1 TTAATTAATAATTTATAAA
441886 TTTAATT-ATAATTTATAAA
1 -TTAATTAATAATTTATAAA
*
441905 -AAATTAATAATTTA-AAA
1 TTAATTAATAATTTATAAA
441922 TTAATTAA
1 TTAATTAA
441930 CTTACACCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.19
18 18 0.49
19 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATTAATAATTTATAAA
Found at i:442229 original size:2 final size:2
Alignment explanation
Indices: 442222--442255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
442212 TGTCACACTT
442222 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
442256 CGCCCTCTAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:450127 original size:2 final size:2
Alignment explanation
Indices: 450110--450152 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
450100 TAAATCTGAA
* *
450110 AT AT AC AT AC 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 AT AT AT AT
450152 A
1 A
450153 AATTATGTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:457824 original size:19 final size:19
Alignment explanation
Indices: 457802--457862 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
457792 AATAAATTCA
457802 AGATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
*
457821 AGATTTG-TGT--GAA-AAG
1 AGATTTGCT-TAAAAATAAG
*
457837 ATATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
457856 AGATTTG
1 AGATTTG
457863 TGTGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 10 0.30
17 3 0.09
18 3 0.09
19 17 0.52
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (19 bp):
AGATTTGCTTAAAAATAAG
Found at i:457845 original size:35 final size:35
Alignment explanation
Indices: 457804--457873 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
457794 TAAATTCAAG
457804 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
457839 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
457874 TTTAGAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
Found at i:457870 original size:19 final size:19
Alignment explanation
Indices: 457813--457870 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
457803 GATTTGCTTA
457813 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
* *
457832 --AA-AAGATATTTGCT-TA
1 AAAATAAGAGATTTG-TGTG
457848 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
457867 AAAA
1 AAAA
457871 GATTTTAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 3 0.10
19 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (19 bp):
AAAATAAGAGATTTGTGTG
Found at i:458719 original size:70 final size:70
Alignment explanation
Indices: 458606--458748 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 70
458596 TGAATAAGTA
* * *
458606 TAAATGATATTAGTACTCTACTTAGGCCAATCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
458671 TATTT
66 TATTT
* *
458676 TAAATGATATTAATGCTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATTTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
458741 TATTT
66 TATTT
458746 TAA
1 TAA
458749 CTTAGTAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (70 bp):
TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
TATTT
Found at i:463656 original size:188 final size:187
Alignment explanation
Indices: 463339--463714 Score: 707
Period size: 188 Copynumber: 2.0 Consensus size: 187
463329 TCGTTGTTGA
463339 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
*
463404 TACATGCATTTGAAATTTATAGCCGTTAGGAGAATGTATCGATACTTTTCATTATGTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
* *
463469 AATGTACTACGTATCGATACCAACAATGGTAGGGTAGCTACTTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTAC-TGCCAGTTTCATGTAT
463527 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
463592 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
*
463657 AATGTACTACGTATCGATACAAATAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
463714 C
1 C
463715 GATACAATTG
Statistics
Matches: 184, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
187 17 0.09
188 167 0.91
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (187 bp):
CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
Found at i:463731 original size:16 final size:14
Alignment explanation
Indices: 463709--463750 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 14
463699 GCCAGTTTCA
463709 TGTATCGATACAAT
1 TGTATCGATACAAT
463723 TGAGTATCGATAC-AT
1 T--GTATCGATACAAT
463738 TGTATCGATACAA
1 TGTATCGATACAA
463751 AGCATAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 3 0.12
16 10 0.40
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (14 bp):
TGTATCGATACAAT
Found at i:468665 original size:55 final size:55
Alignment explanation
Indices: 468562--468677 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 55
468552 ACCCAAAATG
* * * ** *
468562 GGCATCTATAATAAAAAGAAATAAAAAACAAAAAAAATGGATGAAAACCTGAGAAA
1 GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCT-AAAAA
* *
468618 GGCATCCAAAATAAAAGGAAACAAAAAACAAAAAAATTAAATG-AAACCTAAAAA
1 GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCTAAAAA
468672 GGCATC
1 GGCATC
468678 TAATCCAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 10 0.19
55 6 0.12
56 36 0.69
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.13
Consensus pattern (55 bp):
GGCATCCAAAATAAAAAGAAACAAAAAACAAAAAAAATAAATGAAAACCTAAAAA
Done.