Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 50 of 343
Found at i:16603009 original size:21 final size:20
Alignment explanation
Indices: 16602947--16603011 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
16602937 TAGAAATAGT
*
16602947 ATACGACACATAAAGTGCCTA
1 ATACGACACAT-AAGTGCCTG
* *
16602968 AAACGACACACAAGGTGCCTG
1 ATACGACACATAA-GTGCCTG
16602989 ATACGACACATATAGTGCCTG
1 ATACGACACATA-AGTGCCTG
16603010 AT
1 AT
16603012 CGGCAAAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 34 0.92
22 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:16603410 original size:75 final size:72
Alignment explanation
Indices: 16603331--16603499 Score: 171
Period size: 79 Copynumber: 2.3 Consensus size: 72
16603321 ATTCATTTTA
* * * *
16603331 CAATTAAATTCAAATCACTAATTACTTTTCAATCAATATACATTTCAAATAGTCACATATTTTCT
1 CAATTAAATTCAAATCACT-ATTACTTTCCAATCAATAAAC-TTTCAAATAGTCACATA-ATTCA
*
16603396 TCATTCAATT
63 TAATTCAATT
* * *
16603406 CAATTTTATTCAATTCAAATCACTTTTAGTTTCCAATCAATAAACTTTCAAATATTCACATAATT
1 CAA--TTA---AATTCAAATCACTATTACTTTCCAATCAATAAACTTTCAAATAGTCACATAATT
16603471 CATAATTCAATT
61 CATAATTCAATT
*
16603483 -ACTT-AATTCAAATCACT
1 CAATTAAATTCAAATCACT
16603500 TTTAATTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
70 13 0.16
74 2 0.03
75 3 0.04
76 1 0.01
77 15 0.19
78 16 0.20
79 17 0.21
80 13 0.16
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (72 bp):
CAATTAAATTCAAATCACTATTACTTTCCAATCAATAAACTTTCAAATAGTCACATAATTCATAA
TTCAATT
Found at i:16603423 original size:20 final size:19
Alignment explanation
Indices: 16603389--16603433 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
16603379 ATAGTCACAT
* *
16603389 ATTTTCTTCATTCAATTCA
1 ATTTTATTCATTCAAATCA
16603408 ATTTTATTCAATTCAAATCA
1 ATTTTATTC-ATTCAAATCA
*
16603428 CTTTTA
1 ATTTTA
16603434 GTTTCCAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTATTCATTCAAATCA
Found at i:16604808 original size:5 final size:5
Alignment explanation
Indices: 16604800--16604839 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
16604790 TATTTATTTC
*
16604800 ATAAT ATAAT ATAAT ATAATT ATAAT ATAAT -TATT ATAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
16604840 TTAACATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
ATAAT
Found at i:16604825 original size:11 final size:11
Alignment explanation
Indices: 16604800--16604833 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
16604790 TATTTATTTC
16604800 ATAATATAA-T
1 ATAATATAATT
16604810 ATAATATAATT
1 ATAATATAATT
16604821 ATAATATAATT
1 ATAATATAATT
16604832 AT
1 AT
16604834 TATAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATAATT
Found at i:16627390 original size:54 final size:54
Alignment explanation
Indices: 16627308--16627414 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
16627298 CTACAATTTA
*
16627308 AAGTTAGTCTCGAGCACGGCCTAGACACACGGGCGTGTCTGGTGGCTGTGTGCC
1 AAGTTAGTCTCGAGCACGGCCTAGACACACAGGCGTGTCTGGTGGCTGTGTGCC
16627362 AAGTTAGTCTCGAGCACGGCCTAGACACACAGGCGTGTCTGGTGGCTGTGTGC
1 AAGTTAGTCTCGAGCACGGCCTAGACACACAGGCGTGTCTGGTGGCTGTGTGC
16627415 GGCACAAACC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (54 bp):
AAGTTAGTCTCGAGCACGGCCTAGACACACAGGCGTGTCTGGTGGCTGTGTGCC
Found at i:16633925 original size:42 final size:42
Alignment explanation
Indices: 16633825--16633993 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 42
16633815 TTCCGATATG
* * * * * *
16633825 TGATTTTGTGTAAAACCACGTTTGGGACGTCAGCATCG-ATT
1 TGATTTCGTGTAAGACCACGTCTGGGACATCGGCATTGTATT
*
16633866 TGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATTGTATT
1 T--GATTT-CGTGTAAGACCACGTCTGGGACATCGGCATTGTATT
*
16633911 TGATTTCGTGTAAGACC-CTGTCTGGGACAAT-GGCATTAATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGGAC-ATCGGCATT-GTATT
* * * *
16633954 TGATTACATGTAAGACCACGTCTGGGACGTTGGCATTGTA
1 TGATTTCGTGTAAGACCACGTCTGGGACATCGGCATTGTA
16633994 CGAGATTTCT
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 29 0.27
43 46 0.43
44 26 0.25
45 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCACGTCTGGGACATCGGCATTGTATT
Found at i:16635790 original size:112 final size:112
Alignment explanation
Indices: 16635593--16635816 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
16635583 AATCCCATCC
* *
16635593 CAAGTACTCATTGGATGGTAGGTTTCTTAAGAGAAAAGGGAAAGTGATGATCAGTCACAACACAA
1 CAAGTACTCATTGGATGGCAAGTTTCTTAAGAGAAAAGGGAAAGTGATGATCAGTCACAACACAA
*
16635658 ACCTCATGAAGGCAATTTTTTAGTTGTTCCACAATGAGGCCATTGGT
66 ACCTCATGAAGGCAATTTTTTAGCTGTTCCACAATGAGGCCATTGGT
16635705 CAAGTACTCATTGGATGGCAAGTTTCTTAAGAGAAAAGGGAAAGTGATGATCAGTCACAACACAA
1 CAAGTACTCATTGGATGGCAAGTTTCTTAAGAGAAAAGGGAAAGTGATGATCAGTCACAACACAA
16635770 ACCTCATGAAGGCAATTTTTTAGCTGTTCCACAATGAGGCCATTGGT
66 ACCTCATGAAGGCAATTTTTTAGCTGTTCCACAATGAGGCCATTGGT
16635817 GGCCACTCAG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (112 bp):
CAAGTACTCATTGGATGGCAAGTTTCTTAAGAGAAAAGGGAAAGTGATGATCAGTCACAACACAA
ACCTCATGAAGGCAATTTTTTAGCTGTTCCACAATGAGGCCATTGGT
Found at i:16637548 original size:13 final size:13
Alignment explanation
Indices: 16637503--16637548 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
16637493 TATTTTATGC
16637503 ATATATTATTGTT
1 ATATATTATTGTT
*
16637516 ATAGTATTTTTCGCTT
1 ATA-TATTATT-G-TT
16637532 ATATATTATTGTT
1 ATATATTATTGTT
16637545 ATAT
1 ATAT
16637549 GTAAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 9 0.32
14 7 0.25
15 7 0.25
16 5 0.18
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (13 bp):
ATATATTATTGTT
Found at i:16638870 original size:12 final size:12
Alignment explanation
Indices: 16638840--16638872 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
16638830 TATATATTTT
16638840 AAAATT-ATATA
1 AAAATTAATATA
16638851 AAAA-TAATATA
1 AAAATTAATATA
16638862 AAAATTAATAT
1 AAAATTAATAT
16638873 GAGCGGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:16639519 original size:176 final size:173
Alignment explanation
Indices: 16639110--16639520 Score: 394
Period size: 175 Copynumber: 2.3 Consensus size: 173
16639100 ATCCACAATC
* * * *
16639110 GTTGATCATTTGGGCTTCGTTGAGCTACT-TTTATGGGCTAAACACCGACAACCCATTTTCTAAA
1 GTTGATCATTTAGGCTTCGTTGAGCT-CTGTTTATGGACTAAACA-CGA-AACCCATTCTCCAAA
** ** ** * * *
16639174 TGTGACAGAACCGACCATCAAGTGAGTCTTTATGCCGCCAAGAAGAAAGCCGGTGAGGAATCGCT
63 CATGACAGAACCGACCATCAAGCAAGTCTTTACACCACCAAGAAGAAAGCCAGTGAGGAACCGCT
* * * * * *
16639239 CGTACTTATAATGATATCTACGATCTTTCTTTCAATGGACTCAACT
128 CATACTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAACT
* * * ** * *
16639285 GTCGATCGTTTAGGCTTCATTGAGCTCTGTTTATAAACTTAACACTGAAAACCCATTCTCCGAAC
1 GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACAC-G-AAACCCATTCTCCAAAC
** * * *
16639350 ATGACAGAACCGACCATCCGGCAAGTCTTTACATCACCATGAAGAAAGTCAGTGAGGAAACCGCT
64 ATGACAGAACCGACCATCAAGCAAGTCTTTACACCACCAAGAAGAAAGCCAGTGAGG-AACCGCT
* * * * *
16639415 TATGCTTATAATCATATTTACAACCTTTCCTTCACTAGACTCAGCAT
128 CATACTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAAC-T
*
16639462 -TTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTCAACATCGAAAGCCCATTCTC
1 GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACA-CGAAA-CCCATTCTC
16639521 TGCATGTAAT
Statistics
Matches: 187, Mismatches: 42, Indels: 13
0.77 0.17 0.05
Matches are distributed among these distances:
174 3 0.02
175 94 0.50
176 88 0.47
177 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (173 bp):
GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACACGAAACCCATTCTCCAAACAT
GACAGAACCGACCATCAAGCAAGTCTTTACACCACCAAGAAGAAAGCCAGTGAGGAACCGCTCAT
ACTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAACT
Found at i:16639572 original size:176 final size:172
Alignment explanation
Indices: 16639110--16639620 Score: 427
Period size: 176 Copynumber: 2.9 Consensus size: 172
16639100 ATCCACAATC
* * * **
16639110 GTTGATCATTTGGGCTTCGTTGAGCTACT-TTTATGGGCTAAACACCGACAACCCATTTTCTAAA
1 GTTGATCATTTAGGCTTCGTTGAGCT-CTGTTTATGGACTAAACA-CGA-AACCCATTCTCTGCA
* * * * *
16639174 TGTGACAGAACCGACCA-TCAAGTGAGTCTTTATGCCGCCAAGAAGAAAGCCGGTGAGGAATCGC
63 TGT-ACAGAACCGACCATTC-GGTGAGTCTTTACGCCGCCAAGAAGAAAGTCAGTGAGGAACCGC
* * * * * *
16639238 TCGTACTTATAATGATATCTACGATCTTTCTTTCAATGGACTCAACT
126 TCATACTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAACT
* * * ** * *
16639285 GTCGATCGTTTAGGCTTCATTGAGCTCTGTTTATAAACTTAACACTGAAAACCCATTCTCCGAAC
1 GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACAC-G-AAACCCATTCTCTG--C
* ** ** * *
16639350 ATG-ACAGAACCGACCATCCGGCAAGTCTTTACATCACCATGAAGAAAGTCAGTGAGGAAACCGC
62 ATGTACAGAACCGACCATTCGGTGAGTCTTTACGCCGCCAAGAAGAAAGTCAGTGAGG-AACCGC
* * * * *
16639414 TTATGCTTATAATCATATTTACAACCTTTCCTTCACTAGACTCAGCAT
126 TCATACTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAAC-T
*
16639462 -TTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTCAACATCGAAAGCCCATTCTCTGCAT
1 GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACA-CGAAA-CCCATTCTCTGCAT
* ** * ** * **
16639526 GTAATAGAACCGATTATTCGGTGAGTCTTTACGCCGCCACGAAGAAAGTTGGTAAGGAAATTGCT
64 GT-ACAGAACCGACCATTCGGTGAGTCTTTACGCCGCCAAGAAGAAAGTCAGTGAGG-AACCGCT
* **
16639591 CATACTTATAACCATATCTATGACCTTTCC
127 CATACTTATAATCATATCTACAACCTTTCC
16639621 CTCACCAAAC
Statistics
Matches: 261, Mismatches: 63, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
174 7 0.03
175 88 0.34
176 161 0.62
177 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (172 bp):
GTTGATCATTTAGGCTTCGTTGAGCTCTGTTTATGGACTAAACACGAAACCCATTCTCTGCATGT
ACAGAACCGACCATTCGGTGAGTCTTTACGCCGCCAAGAAGAAAGTCAGTGAGGAACCGCTCATA
CTTATAATCATATCTACAACCTTTCCTTCAATAGACTCAACT
Found at i:16641698 original size:17 final size:18
Alignment explanation
Indices: 16641666--16641699 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16641656 TAAGTTAGTG
*
16641666 AAAATAAAATTCAATATT
1 AAAATAAAATTAAATATT
16641684 AAAAT-AAATTAAATAT
1 AAAATAAAATTAAATAT
16641700 CGACCAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAATTAAATATT
Found at i:16643326 original size:21 final size:21
Alignment explanation
Indices: 16643302--16643357 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
16643292 CACCATTGTT
16643302 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
16643323 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
16643344 ACTAATCTCACCGC
1 TCTAATCTCACCGC
16643358 CACCGCTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.27
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:16644888 original size:11 final size:11
Alignment explanation
Indices: 16644862--16644920 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
16644852 GCCTGGGGCG
*
16644862 TAAAAATTTGT
1 TAAAAATATGT
*
16644873 GAAAAATATGT
1 TAAAAATATGT
16644884 T-AAAATAATGT
1 TAAAAAT-ATGT
* **
16644895 T-AAATTAAAT
1 TAAAAATATGT
16644905 TAAAAATATGT
1 TAAAAATATGT
16644916 TAAAA
1 TAAAA
16644921 CAATAATAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAAAAATATGT
Found at i:16646483 original size:21 final size:22
Alignment explanation
Indices: 16646459--16646505 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
16646449 TAATTTTAAT
16646459 ATTTTATGATAT-AAA-AATAAA
1 ATTTTAT-ATATAAAATAATAAA
*
16646480 ATTTTATATTTAAAATAATAAA
1 ATTTTATATATAAAATAATAAA
16646502 ATTT
1 ATTT
16646506 ATTTAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTTATATATAAAATAATAAA
Found at i:16646567 original size:22 final size:22
Alignment explanation
Indices: 16646527--16646576 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
16646517 CTTAAAAATT
16646527 TAAAAATTTATAATATTTATAA
1 TAAAAATTTATAATATTTATAA
* *
16646549 TAAAAACTTTA-AATTTTTATCA
1 TAAAAA-TTTATAATATTTATAA
16646571 -AAAAAT
1 TAAAAAT
16646577 ATTCAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
22 15 0.60
23 4 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATTTATAATATTTATAA
Found at i:16657450 original size:19 final size:19
Alignment explanation
Indices: 16657426--16657470 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
16657416 CGAAGCCTTG
16657426 TTAATAGCTACATATCTTA
1 TTAATAGCTACATATCTTA
16657445 TTAATAGCTACATATCTTA
1 TTAATAGCTACATATCTTA
16657464 TTAATAG
1 TTAATAG
16657471 AATGCCCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (19 bp):
TTAATAGCTACATATCTTA
Found at i:16659832 original size:19 final size:19
Alignment explanation
Indices: 16659786--16659833 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16659776 GTATATATTT
16659786 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
16659804 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
16659823 TAAATTTTATT
1 TAAATTTTATT
16659834 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:16659888 original size:42 final size:43
Alignment explanation
Indices: 16659842--16659937 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
16659832 TTCATATTCT
** *
16659842 AGGAA-TATTTTTATTTTATCTTTTAGTTGTTTATTAGAATAA
1 AGGAACTATTTTTACCTTATCTTTTAGTAGTTTATTAGAATAA
* * *
16659884 AGGAACTA-TTTTCCCTTATGTTTTAGTAGTTTGTTAGAATAA
1 AGGAACTATTTTTACCTTATCTTTTAGTAGTTTATTAGAATAA
*
16659926 GGGAACTATTTT
1 AGGAACTATTTT
16659938 CCAATTAGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 40 0.89
43 5 0.11
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (43 bp):
AGGAACTATTTTTACCTTATCTTTTAGTAGTTTATTAGAATAA
Found at i:16659938 original size:42 final size:42
Alignment explanation
Indices: 16659857--16659939 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
16659847 TATTTTTATT
*
16659857 TTATCTTTTAGTTGTTTATTAGAATAAAGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAAGGAACTATTTTCCC
* * *
16659899 TTATGTTTTAGTAGTTTGTTAGAATAAGGGAACTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAAGGAACTATTTTCC
16659940 AATTAGGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.47
Consensus pattern (42 bp):
TTATCTTTTAGTAGTTTATTAGAATAAAGGAACTATTTTCCC
Found at i:16670138 original size:24 final size:26
Alignment explanation
Indices: 16670080--16670131 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
16670070 TGGTATAATG
*
16670080 ATAAATTTAATCCTTGATTTTTTTAC
1 ATAAATTTAATCCTTGATATTTTTAC
16670106 ATAAATTTAATCCTT-A-ATTTTTAC
1 ATAAATTTAATCCTTGATATTTTTAC
16670130 AT
1 AT
16670132 CATTTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 15 0.60
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.52
Consensus pattern (26 bp):
ATAAATTTAATCCTTGATATTTTTAC
Found at i:16670385 original size:18 final size:18
Alignment explanation
Indices: 16670362--16670396 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16670352 TTGAATTTTG
*
16670362 AATTTTAAATTTTTTATA
1 AATTTTAAATTATTTATA
16670380 AATTTTAAATTATTTAT
1 AATTTTAAATTATTTAT
16670397 TGACGTGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTAAATTATTTATA
Found at i:16670390 original size:7 final size:7
Alignment explanation
Indices: 16670336--16670374 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
16670326 ACTAATTCTT
16670336 TTTTGAA
1 TTTTGAA
16670343 TTTTGAA
1 TTTTGAA
16670350 TTTTGAA
1 TTTTGAA
16670357 TTTTGAA
1 TTTTGAA
*
16670364 TTTTAAA
1 TTTTGAA
16670371 TTTT
1 TTTT
16670375 TTATAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (7 bp):
TTTTGAA
Found at i:16670756 original size:31 final size:30
Alignment explanation
Indices: 16670654--16670757 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 30
16670644 TACACCGCAA
**
16670654 GTCACCCAACTATGGACCATTTTCTTTTTTG
1 GTCACCCAACTATGGA-TTTTTTCTTTTTTG
* * * ***
16670685 GTAACCCAACTATGAATTTATT-TAAATTG
1 GTCACCCAACTATGGATTTTTTCTTTTTTG
16670714 GTCA-CCAACTATGGATTTGTTTCTTTTTTG
1 GTCACCCAACTATGGATTT-TTTCTTTTTTG
16670744 GTCACCCAACTATG
1 GTCACCCAACTATG
16670758 AACTTTTTAA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
28 13 0.23
29 9 0.16
30 11 0.20
31 23 0.41
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (30 bp):
GTCACCCAACTATGGATTTTTTCTTTTTTG
Found at i:16670778 original size:29 final size:27
Alignment explanation
Indices: 16670690--16670783 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 27
16670680 TTTTGGTAAC
16670690 CCAACTATGAATTTATTTAAATTGGTCA
1 CCAACTATGAATTT-TTTAAATTGGTCA
* ***
16670718 CCAACTATGGATTTGTTTCTTTTTTGGTCA
1 CCAACTAT-GAATT-TTT-TAAATTGGTCA
*
16670748 CCCAACTATGAACTTTTTAAAATTGGTCA
1 -CCAACTATGAA-TTTTTTAAATTGGTCA
16670777 CCAACTA
1 CCAACTA
16670784 ATTGAGATTG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 15 0.29
29 13 0.25
30 14 0.27
31 10 0.19
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (27 bp):
CCAACTATGAATTTTTTAAATTGGTCA
Found at i:16671071 original size:19 final size:19
Alignment explanation
Indices: 16671037--16671093 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 19
16671027 CTAGAAATAA
*
16671037 TATATAAAAA--TAAAAAT
1 TATATAAAAATTTTAAAAT
*
16671054 TATATAAAAATTTTAAAAA
1 TATATAAAAATTTTAAAAT
* *
16671073 TATAATGATAATTTTAAAAT
1 TAT-ATAAAAATTTTAAAAT
16671093 T
1 T
16671094 TAAAATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 10 0.31
19 8 0.25
20 14 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TATATAAAAATTTTAAAAT
Found at i:16671072 original size:20 final size:20
Alignment explanation
Indices: 16671047--16671091 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16671037 TATATAAAAA
16671047 TAAAAAT-TATATAAAAATTT
1 TAAAAATATA-ATAAAAATTT
* *
16671067 TAAAAATATAATGATAATTT
1 TAAAAATATAATAAAAATTT
16671087 TAAAA
1 TAAAA
16671092 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAAATATAATAAAAATTT
Found at i:16671117 original size:6 final size:6
Alignment explanation
Indices: 16671106--16671171 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
16671096 AAATTTAAAA
16671106 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
16671154 T-A-AT T-ATAT TAATAT TAA
1 TAATAT TAATAT TAATAT TAA
16671172 ATAGGGTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 50 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:16671879 original size:12 final size:12
Alignment explanation
Indices: 16671853--16671899 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
16671843 TTTGGTTTCA
* *
16671853 ATTTTAATTTCG
1 ATTTTGATTTTG
16671865 ATTTTGATTTTG
1 ATTTTGATTTTG
16671877 ATTTTGATTTCT-
1 ATTTTGATTT-TG
*
16671889 ATTTCGATTTT
1 ATTTTGATTTT
16671900 TATTACAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (12 bp):
ATTTTGATTTTG
Found at i:16671903 original size:12 final size:12
Alignment explanation
Indices: 16671865--16671903 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16671855 TTTAATTTCG
*
16671865 ATTTTGATTTTG
1 ATTTTGATTTTT
*
16671877 ATTTTGATTTCT
1 ATTTTGATTTTT
*
16671889 ATTTCGATTTTT
1 ATTTTGATTTTT
16671901 ATT
1 ATT
16671904 ACAATTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (12 bp):
ATTTTGATTTTT
Found at i:16671952 original size:6 final size:6
Alignment explanation
Indices: 16671923--16672012 Score: 54
Period size: 6 Copynumber: 15.0 Consensus size: 6
16671913 AAACACTCAC
* * ** * * * *
16671923 TGATTC TGATTT AGATTT TGATTT TGATTT CAATTT CGATCT CGATCT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* * * * * *
16671971 CGATTT AGAATT AGAATT TGATTT TGATTT CGATTT TGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
16672013 CAATTTAGGG
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTT
Found at i:16672008 original size:18 final size:18
Alignment explanation
Indices: 16671930--16672012 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
16671920 CACTGATTCT
* *
16671930 GATTTAGATTTTGATTTT
1 GATTTCGATTTTGATTTC
* * *
16671948 GATTTCAATTTCGATCTC
1 GATTTCGATTTTGATTTC
* * * *
16671966 GATCTCGATTTAGAATTA
1 GATTTCGATTTTGATTTC
16671984 GAATTT-GATTTTGATTTC
1 G-ATTTCGATTTTGATTTC
*
16672002 GATTTTGATTT
1 GATTTCGATTT
16672013 CAATTTAGGG
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
17 4 0.08
18 41 0.85
19 3 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (18 bp):
GATTTCGATTTTGATTTC
Found at i:16672013 original size:12 final size:12
Alignment explanation
Indices: 16671930--16672018 Score: 63
Period size: 12 Copynumber: 7.4 Consensus size: 12
16671920 CACTGATTCT
* *
16671930 GATTTAGATTTT
1 GATTTTGATTTC
16671942 GATTTTGATTTC
1 GATTTTGATTTC
* * *
16671954 AATTTCGATCTC
1 GATTTTGATTTC
* * *
16671966 GATCTCGATTTA
1 GATTTTGATTTC
* *
16671978 GAATTAGAATTT-
1 GATTTTG-ATTTC
16671990 GATTTTGATTTC
1 GATTTTGATTTC
16672002 GATTTTGATTTC
1 GATTTTGATTTC
*
16672014 AATTT
1 GATTT
16672019 AGGGTTATTT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 4 0.07
12 52 0.87
13 4 0.07
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.52
Consensus pattern (12 bp):
GATTTTGATTTC
Found at i:16672019 original size:42 final size:42
Alignment explanation
Indices: 16671931--16672020 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
16671921 ACTGATTCTG
* * * *
16671931 ATTTAGATTTTGATTTTGATTTCAATTTCGATCTCGATCTCG
1 ATTTAGAATTAGAATTTGATTTCAATTTCGATCTCGATCTCA
** * * *
16671973 ATTTAGAATTAGAATTTGATTTTGATTTCGATTTTGATTTCA
1 ATTTAGAATTAGAATTTGATTTCAATTTCGATCTCGATCTCA
16672015 ATTTAG
1 ATTTAG
16672021 GGTTATTTCA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (42 bp):
ATTTAGAATTAGAATTTGATTTCAATTTCGATCTCGATCTCA
Found at i:16672240 original size:64 final size:64
Alignment explanation
Indices: 16672131--16672270 Score: 226
Period size: 64 Copynumber: 2.2 Consensus size: 64
16672121 CATGATGTTT
** *
16672131 ATTGTTTGTATCTGCCATTGTACGAATGCCATTATCAGACAGATGTTTATTGTGTATATCTGCC
1 ATTGTTTGTATCTGCCATTGTACGAATAACATTATCAAACAGATGTTTATTGTGTATATCTGCC
* * *
16672195 ATTGTTTGTATCTGCCATTGTATGAATAACATTATCAAACTGATGTTTGTTGTGTATATCTGCC
1 ATTGTTTGTATCTGCCATTGTACGAATAACATTATCAAACAGATGTTTATTGTGTATATCTGCC
16672259 ATTGTTTGTATC
1 ATTGTTTGTATC
16672271 CAAGCTTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (64 bp):
ATTGTTTGTATCTGCCATTGTACGAATAACATTATCAAACAGATGTTTATTGTGTATATCTGCC
Found at i:16672606 original size:21 final size:21
Alignment explanation
Indices: 16672580--16672624 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
16672570 AGAAAACATG
16672580 TCTGGTAGTGATAGTGATGCA
1 TCTGGTAGTGATAGTGATGCA
16672601 TCTGGTAGTGATAGTGATGCA
1 TCTGGTAGTGATAGTGATGCA
16672622 TCT
1 TCT
16672625 AAAAGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (21 bp):
TCTGGTAGTGATAGTGATGCA
Found at i:16674322 original size:40 final size:40
Alignment explanation
Indices: 16674227--16674332 Score: 142
Period size: 39 Copynumber: 2.7 Consensus size: 40
16674217 TTAGTGAATG
* * * *
16674227 TTTTTTAATATGCACGCACTGATTGTTGGTGTGTTTACTA
1 TTTTTTAATATGCATGCAGTGATTATTGGTGTGTTGACTA
*
16674267 -TTTTTAATATGCATGCAGTGATTATTGGTGTGTTGCCTA
1 TTTTTTAATATGCATGCAGTGATTATTGGTGTGTTGACTA
* *
16674306 TTTTTTAAAATGCATGCAGTGAGTATT
1 TTTTTTAATATGCATGCAGTGATTATT
16674333 TTTTTTATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.59
40 24 0.41
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (40 bp):
TTTTTTAATATGCATGCAGTGATTATTGGTGTGTTGACTA
Found at i:16674413 original size:38 final size:38
Alignment explanation
Indices: 16674351--16674477 Score: 211
Period size: 38 Copynumber: 3.4 Consensus size: 38
16674341 AATATGTATA
*
16674351 TTGGTGGGGCT-TTTTTTTAGGGGTGTGTGTATCATTT
1 TTGGTGGGGCTATTTTTTTAGGGGTGTGTGTATCATTG
*
16674388 TTGGTGGGGTTATTTTTTTAGGGGTGTGTGTATCATTG
1 TTGGTGGGGCTATTTTTTTAGGGGTGTGTGTATCATTG
* *
16674426 TCGGTGGGGCTGTTTTTTTAGGGGTGTGTGTATCATTG
1 TTGGTGGGGCTATTTTTTTAGGGGTGTGTGTATCATTG
16674464 TTGGTGGGGCTATT
1 TTGGTGGGGCTATT
16674478 CACAATGTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 10 0.12
38 72 0.88
ACGTcount: A:0.09, C:0.06, G:0.38, T:0.48
Consensus pattern (38 bp):
TTGGTGGGGCTATTTTTTTAGGGGTGTGTGTATCATTG
Found at i:16675129 original size:21 final size:21
Alignment explanation
Indices: 16675099--16675166 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
16675089 AAGTTGGTGT
* *
16675099 CCCAACTCAGCAACAGGCTAC
1 CCCAAATCAGCAAGAGGCTAC
*
16675120 CCCAAATCAGCAAGAGGCTGC
1 CCCAAATCAGCAAGAGGCTAC
*
16675141 CCCAAATCAGCAAGAGGGTAC
1 CCCAAATCAGCAAGAGGCTAC
16675162 CCCAA
1 CCCAA
16675167 CTCAATAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (21 bp):
CCCAAATCAGCAAGAGGCTAC
Found at i:16676082 original size:38 final size:36
Alignment explanation
Indices: 16676031--16676114 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
16676021 CTTAGCCATG
* ***
16676031 TATACCAGCAGCCATATATCACATATGTTAAGCAACAA
1 TATACCAACAGCCATATAT-AC-TAACATAAGCAACAA
*
16676069 TATACCAACAGCCATGTATACTAACATAAGCAACAA
1 TATACCAACAGCCATATATACTAACATAAGCAACAA
*
16676105 TTTACCAACA
1 TATACCAACA
16676115 ACAAAATTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 21 0.52
37 2 0.05
38 17 0.43
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (36 bp):
TATACCAACAGCCATATATACTAACATAAGCAACAA
Found at i:16676491 original size:20 final size:20
Alignment explanation
Indices: 16676466--16676509 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
16676456 TTTTCATATT
16676466 TTCTCTT-CTCCTTCTTCTTC
1 TTCTCTTCCT-CTTCTTCTTC
*
16676486 TTCTCTTCCTCTTCTTTTTC
1 TTCTCTTCCTCTTCTTCTTC
16676506 TTCT
1 TTCT
16676510 ACTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTCTTCCTCTTCTTCTTC
Found at i:16677676 original size:32 final size:32
Alignment explanation
Indices: 16677620--16677680 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
16677610 TAAAATTTAA
* *
16677620 ATTTATTATTATATTTTTTGAAAATGTTTATGT
1 ATTTATTATTATATTTCTTAAAAAT-TTTATGT
*
16677653 ATTTTTTA-TATATTTCTTAAAAATTTTA
1 ATTTATTATTATATTTCTTAAAAATTTTA
16677681 GAATTAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 14 0.56
33 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (32 bp):
ATTTATTATTATATTTCTTAAAAATTTTATGT
Found at i:16682368 original size:25 final size:25
Alignment explanation
Indices: 16682340--16682394 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
16682330 AATTTAAGCT
* *
16682340 AATTTTAAATAAAAACTCTTATGAA
1 AATTTTAAATAAAAACTCTAAAGAA
*
16682365 AATTTTAAATAAAAATTCTAAAGAA
1 AATTTTAAATAAAAACTCTAAAGAA
16682390 AATTT
1 AATTT
16682395 GAAACTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTTTAAATAAAAACTCTAAAGAA
Found at i:16683656 original size:21 final size:20
Alignment explanation
Indices: 16683632--16683672 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
16683622 TTTTTTTTGC
16683632 AAAATCAAAATTTTCTTTAAA
1 AAAATCAAAATTTT-TTTAAA
**
16683653 AAAATCACTATTTTTTTAAA
1 AAAATCAAAATTTTTTTAAA
16683673 TTAAAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATCAAAATTTTTTTAAA
Found at i:16687847 original size:28 final size:28
Alignment explanation
Indices: 16687792--16687848 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
16687782 TACTCAATTA
* *
16687792 ATATAAAAAATAATTAATTATGAGAAAT
1 ATATAAAAAATAATTAATTATCAAAAAT
*
16687820 ATATGAAAAATATATTAATTA-CAAAAAT
1 ATATAAAAAATA-ATTAATTATCAAAAAT
16687848 A
1 A
16687849 AATATTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
ATATAAAAAATAATTAATTATCAAAAAT
Found at i:16688459 original size:17 final size:16
Alignment explanation
Indices: 16688430--16688468 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
16688420 TTAAAATTAG
*
16688430 CTTTTT-ATAAAAATA
1 CTTTTTGATAAAAAAA
16688445 CTTTTTGATAGAAAAAA
1 CTTTTTGATA-AAAAAA
16688462 CTTTTTG
1 CTTTTTG
16688469 GACTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 3 0.14
17 12 0.57
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (16 bp):
CTTTTTGATAAAAAAA
Found at i:16688902 original size:21 final size:21
Alignment explanation
Indices: 16688857--16688905 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
16688847 AAAAAATCAC
*
16688857 ATTTTTTAAAAAACAATAGTT
1 ATTTTTTAAAAAACAATAATT
*
16688878 -TTTTTTAAAAAA-ATTTAATT
1 ATTTTTTAAAAAACA-ATAATT
16688898 ATTTTTTA
1 ATTTTTTA
16688906 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTTAAAAAACAATAATT
Found at i:16688939 original size:23 final size:22
Alignment explanation
Indices: 16688913--16688961 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16688903 TTATTATTTT
*
16688913 AAATTAAATATTTTATAAAATAA
1 AAATTAAATA-TATATAAAATAA
* *
16688936 AAATTAATTATATATTAAATAA
1 AAATTAAATATATATAAAATAA
16688958 AAAT
1 AAAT
16688962 AGAATTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAAATATATATAAAATAA
Found at i:16689271 original size:12 final size:13
Alignment explanation
Indices: 16689247--16689275 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16689237 GCTCGTGCTC
16689247 CAACGGTCAATTT
1 CAACGGTCAATTT
16689260 CAACGG-CAATTT
1 CAACGGTCAATTT
16689272 CAAC
1 CAAC
16689276 TAGCCGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (13 bp):
CAACGGTCAATTT
Found at i:16692217 original size:26 final size:26
Alignment explanation
Indices: 16692188--16692304 Score: 82
Period size: 27 Copynumber: 4.6 Consensus size: 26
16692178 ATTATGAGCG
16692188 TCCCGATATATGGCTCTTCATGAACT
1 TCCCGATATATGGCTCTTCATGAACT
* **
16692214 TCCCGAT-TAAAGGCTCTTTCATGAGTT
1 TCCCGATAT-ATGGCTC-TTCATGAACT
* * *
16692241 TCCTGAT-TAATGGCTCTTC-GGAGCT
1 TCCCGATAT-ATGGCTCTTCATGAACT
** *
16692266 TCCCGATAT-TGGCT-AGCTTGAACT
1 TCCCGATATATGGCTCTTCATGAACT
*
16692290 ACCCGATATATGGCT
1 TCCCGATATATGGCT
16692305 ATCCGAAGCT
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
23 1 0.01
24 17 0.23
25 16 0.22
26 17 0.23
27 22 0.30
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (26 bp):
TCCCGATATATGGCTCTTCATGAACT
Found at i:16692363 original size:24 final size:24
Alignment explanation
Indices: 16692336--16692396 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
16692326 GGCTCTTTGA
*
16692336 AGCTACCCGTTATTGGCTCGCATG
1 AGCTTCCCGTTATTGGCTCGCATG
* **
16692360 AGCTTCCTGATTA-TGGCTCTTATG
1 AGCTTCCCG-TTATTGGCTCGCATG
16692384 AGCTTCCCGTTAT
1 AGCTTCCCGTTAT
16692397 ACAGCCCGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.10
24 24 0.80
25 3 0.10
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.36
Consensus pattern (24 bp):
AGCTTCCCGTTATTGGCTCGCATG
Found at i:16692415 original size:49 final size:50
Alignment explanation
Indices: 16692310--16692447 Score: 133
Period size: 49 Copynumber: 2.8 Consensus size: 50
16692300 TGGCTATCCG
* * ** *
16692310 AAGCTTTCTGATTAATGGCTCTT-TGAAGCTACCCGTTAT-TGGCTCGCAT
1 AAGCTTCCTGATTAATGGCTCTTATG-AGCTTCCCGTTATACAGCCCGCAT
* *
16692359 GAGCTTCCTGATT-ATGGCTCTTATGAGCTTCCCGTTATACAGCCCGGAT
1 AAGCTTCCTGATTAATGGCTCTTATGAGCTTCCCGTTATACAGCCCGCAT
* *
16692408 AAGCTTCCTG-TTACACGGCT-TACATGAGCTTCCCGTTATA
1 AAGCTTCCTGATTA-ATGGCTCT-TATGAGCTTCCCGTTATA
16692448 TGGCTTGAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
48 23 0.31
49 29 0.39
50 22 0.30
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (50 bp):
AAGCTTCCTGATTAATGGCTCTTATGAGCTTCCCGTTATACAGCCCGCAT
Found at i:16692706 original size:26 final size:26
Alignment explanation
Indices: 16692677--16692730 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
16692667 TGATATGTGC
* *
16692677 ATGTTCATGTACACTTGAAGTGATAA
1 ATGTTCATGGAAACTTGAAGTGATAA
16692703 ATGTTCATGGAAACTTGAAGTGATAA
1 ATGTTCATGGAAACTTGAAGTGATAA
16692729 AT
1 AT
16692731 ACATGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (26 bp):
ATGTTCATGGAAACTTGAAGTGATAA
Found at i:16694798 original size:24 final size:24
Alignment explanation
Indices: 16694771--16694819 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16694761 TGGCAATGAG
16694771 TATGTTGTGCTTATGTTTATTTAT
1 TATGTTGTGCTTATGTTTATTTAT
16694795 TATGTTGTGCTTATGTTTATTTAT
1 TATGTTGTGCTTATGTTTATTTAT
16694819 T
1 T
16694820 GTATTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.63
Consensus pattern (24 bp):
TATGTTGTGCTTATGTTTATTTAT
Found at i:16697140 original size:9 final size:9
Alignment explanation
Indices: 16697126--16697162 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16697116 TATAGTTTGA
16697126 TATTCGAAT
1 TATTCGAAT
16697135 TATTCGAAT
1 TATTCGAAT
*
16697144 TATTCGAGT
1 TATTCGAAT
16697153 TATTCGAAT
1 TATTCGAAT
16697162 T
1 T
16697163 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16697228 original size:9 final size:9
Alignment explanation
Indices: 16697214--16697255 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
16697204 ATTCAAGTTG
16697214 ACTCGAATA
1 ACTCGAATA
*
16697223 ACTCGATTA
1 ACTCGAATA
16697232 ACTCGAATA
1 ACTCGAATA
16697241 ACTCGAATA
1 ACTCGAATA
16697250 ACTCGA
1 ACTCGA
16697256 TTCATTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:16700887 original size:43 final size:43
Alignment explanation
Indices: 16700822--16700909 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
16700812 GCATGAGCGC
* *
16700822 ATAGAAAATAAAGTGTATCAAATATCCCACAATCGCAAGTCCT
1 ATAGAAAATAAAGTGCACCAAATATCCCACAATCGCAAGTCCT
* *
16700865 ATAGAAAATAAAGTGCACCAAATATCCCACAATTGCAAGTTCT
1 ATAGAAAATAAAGTGCACCAAATATCCCACAATCGCAAGTCCT
16700908 AT
1 AT
16700910 TTCTTAAGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.24
Consensus pattern (43 bp):
ATAGAAAATAAAGTGCACCAAATATCCCACAATCGCAAGTCCT
Found at i:16708691 original size:10 final size:10
Alignment explanation
Indices: 16708666--16708713 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
16708656 AAATTCTAAG
16708666 AGATAAATACA
1 AGATAAATA-A
16708677 A-ATAAATAA
1 AGATAAATAA
*
16708686 AGATAATTAA
1 AGATAAATAA
16708696 AGA-AAATTAA
1 AGATAAA-TAA
16708706 AGATAAAT
1 AGATAAAT
16708714 GCTAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 4 0.12
10 24 0.75
11 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AGATAAATAA
Found at i:16709364 original size:19 final size:20
Alignment explanation
Indices: 16709340--16709377 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16709330 AATACATCAC
16709340 CTTTTTT-TTTCTTTTTATA
1 CTTTTTTCTTTCTTTTTATA
16709359 CTTTTTTCTTTCTTTTTAT
1 CTTTTTTCTTTCTTTTTAT
16709378 CATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTTTTCTTTCTTTTTATA
Found at i:16710719 original size:7 final size:7
Alignment explanation
Indices: 16710700--16710740 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
16710690 ATCCAAACAA
16710700 AATAAAGT
1 AATAAA-T
16710708 AATAAAT
1 AATAAAT
16710715 AAT-AA-
1 AATAAAT
16710720 AATAAAAT
1 AAT-AAAT
16710728 AATAAAT
1 AATAAAT
16710735 AATAAA
1 AATAAA
16710741 CATAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 3 0.10
6 2 0.07
7 16 0.53
8 9 0.30
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:16710723 original size:20 final size:20
Alignment explanation
Indices: 16710698--16710751 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
16710688 ATATCCAAAC
*
16710698 AAAATAAAGTAATAAATAAT
1 AAAATAAAATAATAAATAAT
16710718 AAAATAAAATAATAAATAAT
1 AAAATAAAATAATAAATAAT
16710738 AAACATAAACATAA
1 AAA-ATAAA-ATAA
16710752 AACTAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 22 0.71
21 5 0.16
22 4 0.13
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAAATAATAAATAAT
Found at i:16710751 original size:15 final size:15
Alignment explanation
Indices: 16710700--16710745 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
16710690 ATCCAAACAA
16710700 AATAAAGTAAT-AAAT
1 AATAAA-TAATAAAAT
16710715 AAT-AA-AATAAAAT
1 AATAAATAATAAAAT
16710728 AATAAATAATAAACAT
1 AATAAATAATAAA-AT
16710744 AA
1 AA
16710746 ACATAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 7 0.26
14 4 0.15
15 9 0.33
16 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (15 bp):
AATAAATAATAAAAT
Found at i:16711977 original size:36 final size:36
Alignment explanation
Indices: 16711937--16712008 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
16711927 CTCATGCTTT
*
16711937 TCTTGGTCGGAATCTTGGCTAAGATTTCTAACAGGA
1 TCTTGGTCGGAATCTTGGCCAAGATTTCTAACAGGA
* *
16711973 TCTTGGTTGGAATCTTGGCCAAGATTTCTATCAGGA
1 TCTTGGTCGGAATCTTGGCCAAGATTTCTAACAGGA
16712009 ATTGGTTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (36 bp):
TCTTGGTCGGAATCTTGGCCAAGATTTCTAACAGGA
Found at i:16714570 original size:20 final size:20
Alignment explanation
Indices: 16714547--16714594 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16714537 AAATTCTAAG
16714547 AGATAAATACAAAT-AATTAA
1 AGATAAATA-AAATAAATTAA
* *
16714567 AGATAATTAAATTAAATTAA
1 AGATAAATAAAATAAATTAA
*
16714587 ATATAAAT
1 AGATAAAT
16714595 GCTAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
AGATAAATAAAATAAATTAA
Found at i:16719246 original size:24 final size:24
Alignment explanation
Indices: 16719196--16719254 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
16719186 AATTTATGTA
* *
16719196 TACATCTGGAGGTGCAATCAGAGG
1 TACATCTGGAGGTGCAACCAGAAG
16719220 TACATCTGGAGGTGCAACC-GAAAG
1 TACATCTGGAGGTGCAACCAG-AAG
*
16719244 TACATTTGGAG
1 TACATCTGGAG
16719255 ACTCAATCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (24 bp):
TACATCTGGAGGTGCAACCAGAAG
Found at i:16722242 original size:68 final size:68
Alignment explanation
Indices: 16722133--16722265 Score: 230
Period size: 68 Copynumber: 2.0 Consensus size: 68
16722123 GCACATTGAA
* * * *
16722133 ACAATTAAAATATATTTTGATTGAAGAGGGGTGTAAACTACTTTGTACTAGTTTAAGATTGAAAT
1 ACAATCAAAATATAATTTGATTGAAGAGGGATATAAACTACTTTGTACTAGTTTAAGATTGAAAT
16722198 TCT
66 TCT
16722201 ACAATCAAAATATAATTTGATTGAAGAGGGATATAAACTACTTTGTACTAGTTTAAGATTGAAAT
1 ACAATCAAAATATAATTTGATTGAAGAGGGATATAAACTACTTTGTACTAGTTTAAGATTGAAAT
16722266 GGTATGTATC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (68 bp):
ACAATCAAAATATAATTTGATTGAAGAGGGATATAAACTACTTTGTACTAGTTTAAGATTGAAAT
TCT
Found at i:16729458 original size:23 final size:23
Alignment explanation
Indices: 16729411--16729458 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
16729401 AGCTCTGTTC
*
16729411 TTTCTCGTAAGATTTTGCTAGAA
1 TTTCTCGTAAGATTTTGCTAAAA
16729434 TTTC-CGTAAGACTCTTTG-TAAAA
1 TTTCTCGTAAGA-T-TTTGCTAAAA
16729457 TT
1 TT
16729459 GGAGTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 7 0.32
23 11 0.50
24 4 0.18
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (23 bp):
TTTCTCGTAAGATTTTGCTAAAA
Found at i:16732704 original size:41 final size:41
Alignment explanation
Indices: 16732647--16732730 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
16732637 CTAAAGTTCA
16732647 AACAAACTTCAATTTAAAACTGAAGAATCATATTAAACATT
1 AACAAACTTCAATTTAAAACTGAAGAATCATATTAAACATT
16732688 AACAAACTTCAATTTAAAACTGAAGAATCATATTAAACATT
1 AACAAACTTCAATTTAAAACTGAAGAATCATATTAAACATT
16732729 AA
1 AA
16732731 TAATTAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (41 bp):
AACAAACTTCAATTTAAAACTGAAGAATCATATTAAACATT
Found at i:16738207 original size:46 final size:46
Alignment explanation
Indices: 16738155--16738415 Score: 416
Period size: 46 Copynumber: 5.7 Consensus size: 46
16738145 GTGTGCTCTT
16738155 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
16738201 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCT
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
16738247 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
16738293 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*** *
16738339 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * *
16738385 TGACA-GAAAATGAGTAAGACCATAGTTGAAA
1 TGATATG-AAATGTGTAAGACCATGGTTGAAA
16738416 AACATTATGG
Statistics
Matches: 201, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 200 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:16741771 original size:24 final size:23
Alignment explanation
Indices: 16741681--16741771 Score: 64
Period size: 24 Copynumber: 3.8 Consensus size: 23
16741671 TGTAATTATT
16741681 TATAT-ATTATAAATATATAAAA
1 TATATAATTATAAATATATAAAA
* *
16741703 -ATAATATTTATTAAAATCTATAAAA
1 TAT-ATAATTA-T-AAATATATAAAA
*
16741728 TCTA-AATT-TAATGATAATATAAAA
1 TATATAATTATAA--AT-ATATAAAA
16741752 TATATAATTATAGAATATAT
1 TATATAATTATA-AATATAT
16741772 TAATTTAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
21 4 0.08
22 3 0.06
23 5 0.10
24 18 0.35
25 18 0.35
26 3 0.06
27 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TATATAATTATAAATATATAAAA
Found at i:16741837 original size:16 final size:16
Alignment explanation
Indices: 16741816--16741851 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16741806 TCTTAAATGA
16741816 TTAAACAATATTTATT
1 TTAAACAATATTTATT
* *
16741832 TTAAACCATATTTCTT
1 TTAAACAATATTTATT
16741848 TTAA
1 TTAA
16741852 TAAAATGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAACAATATTTATT
Found at i:16742115 original size:37 final size:37
Alignment explanation
Indices: 16742061--16742139 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
16742051 GCAACATTCA
16742061 AATTTCAACCTACATTATTATCTCTATATTAAGTTTT
1 AATTTCAACCTACATTATTATCTCTATATTAAGTTTT
*
16742098 AATTTCAACCTATATTATTATCTCTATATTAAGTTTT
1 AATTTCAACCTACATTATTATCTCTATATTAAGTTTT
16742135 AATTT
1 AATTT
16742140 AGTCGAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.51
Consensus pattern (37 bp):
AATTTCAACCTACATTATTATCTCTATATTAAGTTTT
Found at i:16742235 original size:19 final size:20
Alignment explanation
Indices: 16742194--16742237 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
16742184 TCCAAATATT
** *
16742194 ATTATAATATTTTTTTTACA
1 ATTATAATATTTTTCATAAA
16742214 ATTATAAT-TTTTTCATAAA
1 ATTATAATATTTTTCATAAA
16742233 ATTAT
1 ATTAT
16742238 TTATAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTATAATATTTTTCATAAA
Found at i:16742616 original size:44 final size:42
Alignment explanation
Indices: 16742536--16742631 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 42
16742526 AAATAAAAAA
*
16742536 TAAAAACTAAAAAATTATAAATTTTTCAAAAAATAAAAA-ATT
1 TAAAAAATAAAAAATTATAAA-TTTTCAAAAAATAAAAAGATT
* *
16742578 ATGAAAAATAAAAACATTTTAAA-TTTCAAAAACTATAAAAAGATT
1 -TAAAAAATAAAAA-ATTATAAATTTTCAAAAA--ATAAAAAGATT
16742623 TAAAAAATA
1 TAAAAAATA
16742632 TAGCAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
42 9 0.20
43 11 0.24
44 22 0.49
45 3 0.07
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (42 bp):
TAAAAAATAAAAAATTATAAATTTTCAAAAAATAAAAAGATT
Found at i:16743162 original size:16 final size:17
Alignment explanation
Indices: 16743141--16743178 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16743131 TCAAAATTCA
16743141 AAAATATAA-TTATTTT
1 AAAATATAATTTATTTT
*
16743157 AAAATATAATTTTTTTT
1 AAAATATAATTTATTTT
16743174 AAAAT
1 AAAAT
16743179 TCAATGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATATAATTTATTTT
Found at i:16743594 original size:27 final size:24
Alignment explanation
Indices: 16743564--16743619 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
16743554 ATAACATTGA
*
16743564 ATTTTAGAATTTTTAAAAATTATTTTT
1 ATTTTAG-ACTTTTAAAAA--ATTTTT
* *
16743591 ATTTTTGACTTTTAAAGAATTTTT
1 ATTTTAGACTTTTAAAAAATTTTT
16743615 ATTTT
1 ATTTT
16743620 CTTCATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 11 0.42
26 9 0.35
27 6 0.23
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (24 bp):
ATTTTAGACTTTTAAAAAATTTTT
Found at i:16748748 original size:16 final size:16
Alignment explanation
Indices: 16748717--16748753 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
16748707 ATGTGAATAA
16748717 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
16748733 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
16748749 TATTA
1 TATTA
16748754 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:16748776 original size:17 final size:18
Alignment explanation
Indices: 16748739--16748773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16748729 TTATTATTTT
* *
16748739 TAAAATTTATTATTAAAA
1 TAAAATTGAATATTAAAA
16748757 TAAAATTGAATATTAAA
1 TAAAATTGAATATTAAA
16748774 TAATTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAATTGAATATTAAAA
Found at i:16750948 original size:22 final size:22
Alignment explanation
Indices: 16750920--16750966 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16750910 CGATCCAAAT
16750920 ATATATTGTTTAGGTGAAAACC
1 ATATATTGTTTAGGTGAAAACC
16750942 ATATATTGTTTAGGTGAAAACC
1 ATATATTGTTTAGGTGAAAACC
16750964 ATA
1 ATA
16750967 CTAAGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
ATATATTGTTTAGGTGAAAACC
Found at i:16750974 original size:22 final size:22
Alignment explanation
Indices: 16750920--16750976 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
16750910 CGATCCAAAT
*
16750920 ATATATTGTTTAGGTGAAAACC
1 ATATATAGTTTAGGTGAAAACC
*
16750942 ATATATTGTTTAGGTGAAAACC
1 ATATATAGTTTAGGTGAAAACC
16750964 ATACTA-AGTTTAG
1 ATA-TATAGTTTAG
16750977 TTTTATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
ATATATAGTTTAGGTGAAAACC
Found at i:16758060 original size:51 final size:51
Alignment explanation
Indices: 16757984--16758087 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
16757974 TTTAGAAGGT
*
16757984 AAGATTTTGGTGTTTCGTTGATAGAATGTTATCTAAAAAGACATTTTCTTA
1 AAGATTTTGGTGTTTCGTTGATAGAATGTTATCTAAAAAGACATTTTCATA
* *
16758035 AAGATTTTGGTGTTTGGTTGATAGAATGTTATCTAAAAGGACATTTTCATA
1 AAGATTTTGGTGTTTCGTTGATAGAATGTTATCTAAAAAGACATTTTCATA
16758086 AA
1 AA
16758088 TTTTCTTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (51 bp):
AAGATTTTGGTGTTTCGTTGATAGAATGTTATCTAAAAAGACATTTTCATA
Found at i:16761249 original size:19 final size:19
Alignment explanation
Indices: 16761216--16761255 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16761206 AAAATAAGAT
*
16761216 ATTAATTTTAATTGATTTG
1 ATTAATTTTAATTGACTTG
16761235 ATTAA-TTTAATTTGACTTG
1 ATTAATTTTAA-TTGACTTG
16761254 AT
1 AT
16761256 CAAAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (19 bp):
ATTAATTTTAATTGACTTG
Found at i:16774882 original size:18 final size:18
Alignment explanation
Indices: 16774851--16774889 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16774841 AAATAAAATG
16774851 AATAAAATTGAAAAGATA
1 AATAAAATTGAAAAGATA
*
16774869 AATATAAATT-AAAATATA
1 AATA-AAATTGAAAAGATA
16774887 AAT
1 AAT
16774890 GAGAAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AATAAAATTGAAAAGATA
Found at i:16775585 original size:19 final size:19
Alignment explanation
Indices: 16775558--16775594 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16775548 AATATAAAAT
16775558 AAAAATTATTAAATTTTAG
1 AAAAATTATTAAATTTTAG
*
16775577 AAAATTTATTAAATTTTA
1 AAAAATTATTAAATTTTA
16775595 ATAACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAAAATTATTAAATTTTAG
Found at i:16775662 original size:16 final size:16
Alignment explanation
Indices: 16775641--16775671 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16775631 AGAATTTTTT
16775641 ATAAAAATTGTAAAAA
1 ATAAAAATTGTAAAAA
16775657 ATAAAAATTGTAAAA
1 ATAAAAATTGTAAAA
16775672 TTTTATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
ATAAAAATTGTAAAAA
Found at i:16775903 original size:10 final size:10
Alignment explanation
Indices: 16775863--16775949 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 10
16775853 CTTTATAAAA
*
16775863 TTTTATATTT
1 TTTTATAATT
16775873 TTTTAT-A-T
1 TTTTATAATT
* *
16775881 TTCTAT-ATA
1 TTTTATAATT
16775890 TTTTATAATT
1 TTTTATAATT
*
16775900 TTTTACAA-T
1 TTTTATAATT
* **
16775909 CTTTATAAAA
1 TTTTATAATT
*
16775919 TTTTACAATT
1 TTTTATAATT
16775929 TTTTAT-A-T
1 TTTTATAATT
16775937 TTTTAT-ATT
1 TTTTATAATT
16775946 TTTT
1 TTTT
16775950 TCTAGTTTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
8 15 0.25
9 18 0.31
10 26 0.44
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:16775913 original size:56 final size:56
Alignment explanation
Indices: 16775839--16775949 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
16775829 ACATTTTGTT
* * *
16775839 TAATTTTCTTACGACTTTATAAAATTTTATATTTTTTTATATTTCTATATATTTTA
1 TAATTTTCTTACAACTTTATAAAATTTTACAATTTTTTATATTTCTATATATTTTA
* *
16775895 TAATTTT-TTACAATCTTTATAAAATTTTACAATTTTTTATATTTTTATATTTTTT
1 TAATTTTCTTACAA-CTTTATAAAATTTTACAATTTTTTATATTTCTATATATTTT
16775950 TCTAGTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
55 5 0.10
56 44 0.90
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (56 bp):
TAATTTTCTTACAACTTTATAAAATTTTACAATTTTTTATATTTCTATATATTTTA
Found at i:16775915 original size:19 final size:18
Alignment explanation
Indices: 16775889--16775940 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
16775879 ATTTCTATAT
16775889 ATTTTATAATTTTTTACA
1 ATTTTATAATTTTTTACA
**
16775907 ATCTTTATAAAATTTTACA
1 AT-TTTATAATTTTTTACA
*
16775926 ATTTTTTATATTTTT
1 ATTTTATA-ATTTTT
16775941 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTTTTACA
Found at i:16775950 original size:10 final size:9
Alignment explanation
Indices: 16775863--16775949 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
16775853 CTTTATAAAA
16775863 TTTTATATT
1 TTTTATATT
16775872 TTTT-TATAT
1 TTTTATAT-T
* *
16775881 TTCTATATA
1 TTTTATATT
16775890 TTTTATAATT
1 TTTTAT-ATT
* *
16775900 TTTTACAAT
1 TTTTATATT
* **
16775909 CTTTATAAAA
1 TTTTAT-ATT
*
16775919 TTTTACAATT
1 TTTTA-TATT
16775929 TTTTATA-T
1 TTTTATATT
16775937 TTTTATATT
1 TTTTATATT
16775946 TTTT
1 TTTT
16775950 TCTAGTTTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
8 11 0.19
9 25 0.43
10 22 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATATT
Found at i:16777538 original size:16 final size:16
Alignment explanation
Indices: 16777517--16777547 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16777507 AAAGTTTTTG
16777517 CTCATTGCTCATTGTT
1 CTCATTGCTCATTGTT
16777533 CTCATTGCTCATTGT
1 CTCATTGCTCATTGT
16777548 ACTTGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (16 bp):
CTCATTGCTCATTGTT
Found at i:16785635 original size:19 final size:20
Alignment explanation
Indices: 16785580--16785628 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16785570 TTTTTCCTTA
* *
16785580 TTATTATT-TTTTATATTTAT
1 TTATTATTATTCT-TATTGAT
16785600 TTATTATTATTCTTATTGAT
1 TTATTATTATTCTTATTGAT
16785620 TT-TTATTAT
1 TTATTATTAT
16785629 ATTTATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 16 0.62
21 3 0.12
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTATTATTCTTATTGAT
Found at i:16785721 original size:25 final size:25
Alignment explanation
Indices: 16785577--16785724 Score: 88
Period size: 25 Copynumber: 5.9 Consensus size: 25
16785567 ACCTTTTTCC
* * *
16785577 TTATTATTATTTTT-TATATTTAT-
1 TTATTATTATTTTTATTTTTTTTTA
* **
16785600 TTATTATTATTCTTATTGATTTTTA
1 TTATTATTATTTTTATTTTTTTTTA
* ** * *
16785625 TTA-TATT-TATTATGCTTTGTTTTC
1 TTATTATTAT-TTTTATTTTTTTTTA
* *
16785649 TTATTATTCTTTTTATTTGTTTTTA
1 TTATTATTATTTTTATTTTTTTTTA
* *
16785674 TTATTATTATGTTTATTACTTTTATTTT
1 TTATTATTATTTTTATT--TTTT-TTTA
*
16785702 TTATTTTTATTTTTATTTTTTTT
1 TTATTATTATTTTTATTTTTTTT
16785725 GTTTCGCTAT
Statistics
Matches: 93, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
23 14 0.15
24 20 0.22
25 33 0.35
26 5 0.05
27 3 0.03
28 18 0.19
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (25 bp):
TTATTATTATTTTTATTTTTTTTTA
Found at i:16785722 original size:7 final size:6
Alignment explanation
Indices: 16785577--16785721 Score: 53
Period size: 6 Copynumber: 22.3 Consensus size: 6
16785567 ACCTTTTTCC
* * * * *
16785577 TTATTA TTATTTT TTATAT TTATTT ATTATTA TTCTTAT TGATTT TTA-TT
1 TTATTT TTA-TTT TTATTT TTATTT -TTATTT TTATT-T TTATTT TTATTT
* * *
16785627 ATATTT ATTATGCTT TGT-TTT CTTATTA TTCTTT TTATTT GTT-TTT
1 TTATTT -TTAT--TT T-TATTT -TTATTT TTATTT TTATTT -TTATTT
* *
16785673 ATTATTAT TATGTTT ATTACTT TTATTTT TTATTT TTATTT TTATTT TT
1 -TTATT-T T-TATTT -TTATTT TTA-TTT TTATTT TTATTT TTATTT TT
16785722 TTTGTTTCGC
Statistics
Matches: 103, Mismatches: 20, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
5 4 0.04
6 56 0.54
7 33 0.32
8 7 0.07
9 3 0.03
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:16787439 original size:18 final size:18
Alignment explanation
Indices: 16787412--16787477 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
16787402 ATTGAGTTTA
16787412 TTTA-TTTTCTTTTTAGT
1 TTTATTTTTCTTTTTAGT
16787429 TTTATTTTTCTTTTTA-T
1 TTTATTTTTCTTTTTAGT
*
16787446 GTTTATTTTT-TTCGTT-GT
1 -TTTATTTTTCTT-TTTAGT
*
16787464 TTTATTTTTATTTT
1 TTTATTTTTCTTTT
16787478 CTTAAACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
17 17 0.40
18 25 0.60
ACGTcount: A:0.11, C:0.05, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTATTTTTCTTTTTAGT
Found at i:16807719 original size:38 final size:38
Alignment explanation
Indices: 16807670--16807786 Score: 153
Period size: 38 Copynumber: 3.0 Consensus size: 38
16807660 AAACCCAAAC
* *
16807670 ATAACACCAGCACAAAGCCTGCGGGATTTAACCTGGAT
1 ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
*
16807708 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
* * * *
16807746 ATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGAT
1 ATAATACCAGCACAAAGCCTGCGGG-ATTTAA-CCCGGAT
16807786 A
1 A
16807787 CACATCAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 56 0.81
39 5 0.07
40 8 0.12
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (38 bp):
ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
Found at i:16814744 original size:44 final size:44
Alignment explanation
Indices: 16814647--16814758 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
16814637 CTGGCATTTC
* * * *
16814647 GCCTGCTAGGCTTGAAGCCCGAT-ATCATTTCACCGGCATTATA
1 GCCTGCTAGGCTCGAAGCCCAATAATCATTTCACCAGCATTAAA
16814690 GCCTGCTAGGCTCGAAGCCCAATAAT-ATTATTCACCAGC-TTAAA
1 GCCTGCTAGGCTCGAAGCCCAATAATCA-T-TTCACCAGCATTAAA
* *
16814734 GCTTGCTAGGCTCAAAGCCCGAATA
1 GCCTGCTAGGCTCGAAGCCC-AATA
16814759 TCACAATTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
43 22 0.37
44 25 0.42
45 12 0.20
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (44 bp):
GCCTGCTAGGCTCGAAGCCCAATAATCATTTCACCAGCATTAAA
Found at i:16814911 original size:28 final size:28
Alignment explanation
Indices: 16814880--16814942 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
16814870 TTGATATTTT
16814880 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
* *
16814908 GCACACTAATTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
16814936 GTACACT
1 GCACACT
16814943 GAGTACCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:16825297 original size:72 final size:72
Alignment explanation
Indices: 16825207--16825361 Score: 274
Period size: 72 Copynumber: 2.2 Consensus size: 72
16825197 AATGCTTGAT
16825207 CTTTAGCGGCGTTCAAAAAACGCCGCAAAAAAATTAACACAACGCCGTCGTTTTGTATTGAGCCT
1 CTTTAGCGGCGTTCAAAAAACGCCGCAAAAAAATTAACACAACGCCGTCGTTTTGTATTGAGCCT
16825272 TTAGTGC
66 TTAGTGC
* * *
16825279 CTTTAGTGGTGTTCAAAAAACGCCGCAAAAAAATTAACACAATGCCGTCGTTTTGTATTGAGCCT
1 CTTTAGCGGCGTTCAAAAAACGCCGCAAAAAAATTAACACAACGCCGTCGTTTTGTATTGAGCCT
16825344 TTAGTGC
66 TTAGTGC
*
16825351 CTTTAACGGCG
1 CTTTAGCGGCG
16825362 CTTTTTAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (72 bp):
CTTTAGCGGCGTTCAAAAAACGCCGCAAAAAAATTAACACAACGCCGTCGTTTTGTATTGAGCCT
TTAGTGC
Found at i:16825865 original size:22 final size:22
Alignment explanation
Indices: 16825840--16825882 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16825830 GTTATTATTT
* *
16825840 TAAGGTTTATGGATTATGGGTC
1 TAAGGATTATGGATTAAGGGTC
*
16825862 TAAGGATTATGGTTTAAGGGT
1 TAAGGATTATGGATTAAGGGT
16825883 GGTTTATGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.40
Consensus pattern (22 bp):
TAAGGATTATGGATTAAGGGTC
Found at i:16826586 original size:43 final size:45
Alignment explanation
Indices: 16826505--16826592 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
16826495 GTCATGCCCG
16826505 ACACTTAGCCATTTCCCCCAAAATCCCAAAAACAGA-TTTCCCAA
1 ACACTTAGCCATTTCCCCCAAAATCCCAAAAACAGATTTTCCCAA
** * *
16826549 ACACTTAGCCA-TTCCCAGTAAAA-CCCTAAAATAGATTTTCCCAA
1 ACACTTAGCCATTTCCC-CCAAAATCCCAAAAACAGATTTTCCCAA
16826593 TTCTCTACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 15 0.39
44 23 0.61
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.23
Consensus pattern (45 bp):
ACACTTAGCCATTTCCCCCAAAATCCCAAAAACAGATTTTCCCAA
Found at i:16828927 original size:16 final size:16
Alignment explanation
Indices: 16828902--16828936 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
16828892 AATTTCATTT
*
16828902 TATGTGTGAATGCCTA
1 TATGTATGAATGCCTA
16828918 TATGTATGAATGCCTA
1 TATGTATGAATGCCTA
16828934 TAT
1 TAT
16828937 CTATCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (16 bp):
TATGTATGAATGCCTA
Found at i:16842119 original size:49 final size:50
Alignment explanation
Indices: 16842023--16842170 Score: 153
Period size: 49 Copynumber: 3.0 Consensus size: 50
16842013 TCATTAGGGA
* *
16842023 TTACCGATTT--TAACTCGTGAGAGCTTACCAATTCTCAGCTCGA-ATGAGC
1 TTACCGATTTACT-ACTCGTGAGAGCTTACCGATTCTTAGCTC-ATATGAGC
* * * *
16842072 TTGCCGATTT-C-ATCTTGTGAGAGTTTACCGATTCTTAGCTTATATGAGC
1 TTACCGATTTACTA-CTCGTGAGAGCTTACCGATTCTTAGCTCATATGAGC
* * *
16842121 TTATCGATTTACTACTCGTGAGAGCATACCGATTCATAGCTCATATGAGC
1 TTACCGATTTACTACTCGTGAGAGCTTACCGATTCTTAGCTCATATGAGC
16842171 ATACATGTAC
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
48 2 0.02
49 46 0.57
50 32 0.40
51 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (50 bp):
TTACCGATTTACTACTCGTGAGAGCTTACCGATTCTTAGCTCATATGAGC
Found at i:16842170 original size:25 final size:25
Alignment explanation
Indices: 16842097--16842174 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
16842087 TGTGAGAGTT
* * *
16842097 TACCGATTCTTAGCTTATATGAGCT
1 TACCGATTCATAGCTCATATGAGCA
* * *
16842122 TATCGATTTACTA-CTCGTGA-GAGCA
1 TACCGATTCA-TAGCTCAT-ATGAGCA
16842147 TACCGATTCATAGCTCATATGAGCA
1 TACCGATTCATAGCTCATATGAGCA
16842172 TAC
1 TAC
16842175 ATGTACAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.08
25 34 0.85
26 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (25 bp):
TACCGATTCATAGCTCATATGAGCA
Found at i:16855350 original size:9 final size:9
Alignment explanation
Indices: 16855336--16855360 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16855326 AATTAAAAGA
16855336 TTTTAAATC
1 TTTTAAATC
16855345 TTTTAAATC
1 TTTTAAATC
16855354 TTTTAAA
1 TTTTAAA
16855361 CTCATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTAAATC
Found at i:16865106 original size:41 final size:41
Alignment explanation
Indices: 16865009--16865195 Score: 254
Period size: 40 Copynumber: 4.6 Consensus size: 41
16864999 ACTTGATACC
* * *
16865009 TCGCACACAAAGTGCCGT-TCATAGCCGAAGCTATCTC-AAA
1 TCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATCTCGATA
* *
16865049 TCGCACACTAAGTGCCAAATATAGCCGAAGCTATCTCGATC
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGATA
*
16865090 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGA-A
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGATA
* * * *
16865130 TCACAAACTAAGTGCCATATATAGCCGAAGCTATCTCAATC
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGATA
16865171 TCGCACACTAAGTGCCATATATAGC
1 TCGCACACTAAGTGCCATATATAGC
16865196 TGATTAGTCT
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 67 0.52
41 62 0.48
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGATA
Found at i:16865210 original size:81 final size:81
Alignment explanation
Indices: 16865008--16865195 Score: 288
Period size: 81 Copynumber: 2.3 Consensus size: 81
16864998 TACTTGATAC
* * * * * *
16865008 CTCGCACACAAAGTGCCGT-TCATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCAAATATA
1 CTCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATGTCGAATCACAAACTAAGTGCCAAATATA
*
16865072 GCCGAAGCTATCTCGAT
65 GCCGAAGCTATCTCAAT
*
16865089 CTCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCACAAACTAAGTGCCATATATAG
1 CTCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCACAAACTAAGTGCCAAATATAG
16865154 CCGAAGCTATCTCAAT
66 CCGAAGCTATCTCAAT
16865170 CTCGCACACTAAGTGCCATATATAGC
1 CTCGCACACTAAGTGCCATATATAGC
16865196 TGATTAGTCT
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 97 0.99
82 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (81 bp):
CTCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCACAAACTAAGTGCCAAATATAG
CCGAAGCTATCTCAAT
Found at i:16865862 original size:13 final size:13
Alignment explanation
Indices: 16865844--16865868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16865834 GACTAAAAAT
16865844 GGGCTGTTACAAC
1 GGGCTGTTACAAC
16865857 GGGCTGTTACAA
1 GGGCTGTTACAA
16865869 TCTTAAATGT
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:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (13 bp):
GGGCTGTTACAAC
Found at i:16867244 original size:28 final size:28
Alignment explanation
Indices: 16867198--16867251 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
16867188 TAGATTAAAC
* *
16867198 TAAAACGAACTCAACAATATAAAATTGT
1 TAAAACAAACTCAAAAATATAAAATTGT
*
16867226 TAAAACAAACTTAAAAATATAAAATT
1 TAAAACAAACTCAAAAATATAAAATT
16867252 TACTAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (28 bp):
TAAAACAAACTCAAAAATATAAAATTGT
Found at i:16872359 original size:32 final size:32
Alignment explanation
Indices: 16872316--16872380 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
16872306 TTTAAAGATC
*
16872316 AACTTTAATGAAAGTATGTAGATAACT-GTCTA
1 AACTTTAATGAAAATATGTAGATAA-TAGTCTA
* *
16872348 AACTTTTATGAAAATATTTAGATAATAGTCTA
1 AACTTTAATGAAAATATGTAGATAATAGTCTA
16872380 A
1 A
16872381 TTAGTTATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (32 bp):
AACTTTAATGAAAATATGTAGATAATAGTCTA
Found at i:16873316 original size:19 final size:21
Alignment explanation
Indices: 16873284--16873327 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
16873274 TTTATGTCAC
*
16873284 TTCAATATTCTTATCC-GAAT
1 TTCAAGATTCTTATCCTGAAT
16873304 TTCAAGATT-TTATCCTGAAT
1 TTCAAGATTCTTATCCTGAAT
16873324 TTCA
1 TTCA
16873328 GTATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (21 bp):
TTCAAGATTCTTATCCTGAAT
Found at i:16873333 original size:20 final size:19
Alignment explanation
Indices: 16873284--16873335 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
16873274 TTTATGTCAC
*
16873284 TTCAATATTCTTATCCGAAT
1 TTCAGTATT-TTATCCGAAT
16873304 TTCAAG-ATTTTATCCTGAAT
1 TTC-AGTATTTTATCC-GAAT
16873324 TTCAGTATTTTA
1 TTCAGTATTTTA
16873336 ATTTGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 19 0.68
21 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (19 bp):
TTCAGTATTTTATCCGAAT
Found at i:16875836 original size:22 final size:22
Alignment explanation
Indices: 16875808--16875852 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
16875798 TAGTGTGTGC
16875808 CTTGATCCACAAACAAAAATCA
1 CTTGATCCACAAACAAAAATCA
16875830 CTTGATCCACAAACAAAAATCA
1 CTTGATCCACAAACAAAAATCA
16875852 C
1 C
16875853 ATCAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.29, G:0.04, T:0.18
Consensus pattern (22 bp):
CTTGATCCACAAACAAAAATCA
Found at i:16888745 original size:16 final size:17
Alignment explanation
Indices: 16888718--16888749 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16888708 ATATAAATTG
16888718 AATTCAATCATGAATAT
1 AATTCAATCATGAATAT
16888735 AATTC-ATCATGAATA
1 AATTCAATCATGAATA
16888750 AAGATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (17 bp):
AATTCAATCATGAATAT
Found at i:16893058 original size:37 final size:36
Alignment explanation
Indices: 16893017--16893109 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 36
16893007 ACTTTGAAGT
*
16893017 GTTGAAGGAAGGCAGAAGAACGTACGGAGCTTGGACG
1 GTTGAAGGAA-GCAGAAGAACGTACGGAGCTTGAACG
* * * * *
16893054 GTTGAAGAAAACTGAAGAACGTAGGGAGCTTGAAGG
1 GTTGAAGGAAGCAGAAGAACGTACGGAGCTTGAACG
16893090 GTTGAAGGAAGCGAGAAGAA
1 GTTGAAGGAAGC-AGAAGAA
16893110 AATATGGAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
36 31 0.67
37 15 0.33
ACGTcount: A:0.38, C:0.10, G:0.39, T:0.14
Consensus pattern (36 bp):
GTTGAAGGAAGCAGAAGAACGTACGGAGCTTGAACG
Found at i:16895684 original size:93 final size:93
Alignment explanation
Indices: 16895571--16895742 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
16895561 CGCCCATAAG
* *
16895571 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16895636 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
16895664 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16895729 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
16895743 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16895739 original size:46 final size:46
Alignment explanation
Indices: 16895564--16895739 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
16895554 TGTAACCCGC
* * *
16895564 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
16895610 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
16895660 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
16895703 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16895740 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:16896195 original size:30 final size:30
Alignment explanation
Indices: 16896161--16896220 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16896151 ATTTAATACG
16896161 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
16896191 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
16896221 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:16903246 original size:93 final size:93
Alignment explanation
Indices: 16903133--16903304 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
16903123 CGCCCATAAG
* *
16903133 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16903198 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
16903226 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16903291 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
16903305 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16903301 original size:46 final size:46
Alignment explanation
Indices: 16903126--16903301 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
16903116 TGTAACCCGC
* * *
16903126 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
16903172 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
16903222 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
16903265 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16903302 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.