Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 83 of 126
Found at i:25383800 original size:130 final size:130
Alignment explanation
Indices: 25383612--25383858 Score: 356
Period size: 130 Copynumber: 1.9 Consensus size: 130
25383602 GGTCATGGTC
* * * *
25383612 TTTAGCTGCGCTTTTCCCACAAACGCCGCTAAAGACCATCACCTTTAGCAGTGCTTTTCCCACAA
1 TTTAGCAGCACTTTTCCCACAAACACCGCTAAAGACCATCACCTTTAGCAGCGCTTTTCCCACAA
* *
25383677 ACGCAGCTAAAGACCATGACCTTTAGCGGCGCTCT-TCCCGAAAACGCCGCTATAGACCACAACC
66 ACGCAGCTAAAGACCACGACCTTTAGCGGCGCT-TATCCCAAAAACGCCGCTATAGACCACAACC
25383741 T
130 T
*
25383742 TTTAGCAGCACTTTTCCCACAAACACCGCTATAGACCA-CGACCTTTAGC-GACGCTTTTCCCAC
1 TTTAGCAGCACTTTTCCCACAAACACCGCTAAAGACCATC-ACCTTTAGCAG-CGCTTTTCCCAC
* * *
25383805 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTATCGCAAAAACGCCGCTA
64 AAACGCAGCTAAAGACCACGACCTTTAGCGGCGCTTATCCCAAAAACGCCGCTA
25383859 AAAAATAACC
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
129 3 0.03
130 101 0.97
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (130 bp):
TTTAGCAGCACTTTTCCCACAAACACCGCTAAAGACCATCACCTTTAGCAGCGCTTTTCCCACAA
ACGCAGCTAAAGACCACGACCTTTAGCGGCGCTTATCCCAAAAACGCCGCTATAGACCACAACCT
Found at i:25384054 original size:34 final size:35
Alignment explanation
Indices: 25384011--25384076 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
25384001 CTATGAAAAT
25384011 TTTAATTTTA-AAACTAAATATAA-AAATTAATGAA
1 TTTAATTTTAGAAACTAAA-ATAATAAATTAATGAA
**
25384045 TTTAATTTTAGAATTTAAAATAATAAATTAAT
1 TTTAATTTTAGAAACTAAAATAATAAATTAAT
25384077 AACACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (35 bp):
TTTAATTTTAGAAACTAAAATAATAAATTAATGAA
Found at i:25388015 original size:147 final size:146
Alignment explanation
Indices: 25387749--25388090 Score: 481
Period size: 147 Copynumber: 2.3 Consensus size: 146
25387739 TATTGCCGTA
* * * *
25387749 AAAAAATTATTTTATTTAGAATAAAACGATACTGTTTTGCTAT-ATAAAATGGTGCTATTTTTTA
1 AAAAAATTATTTTATTTGGAATAAAACGATACTGTTTTGCTATGCTAAAAGGGCGCTATTTTTTA
* *
25387813 AAATAAAATTATTTTTGTGATGTTTTTTAAAAAAACGCCGCTATTGCTTACCTTTTGCGGCGTTT
66 AAATAAAATTATTTTTGTGACGTTTTTTAAAAAAACGCCGCTATTGCTTACCTTTTGCGACGTTT
* * *
25387878 TCCATAAAAATGTCG-
131 TCCACAAAAACGCCGC
* * * *
25387893 TACAAATTATTTTATCTGGAATAAAACGATAGTGTTTTGCTATGCTAAAAGGGCGCTATTTTTTA
1 AAAAAATTATTTTATTTGGAATAAAACGATACTGTTTTGCTATGCTAAAAGGGCGCTATTTTTTA
* * *
25387958 AAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAATGCCGCTATTGCTTACCTTTTGCGACGT
66 AAA-TAAAATTA-TTTTTGTGACGTTTTTTAAAAAAACGCCGCTATTGCTTACCTTTTGCGACGT
*
25388023 TTTTCACAAAAACGCCGC
129 TTTCCACAAAAACGCCGC
* *
25388041 AAAAAATTATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAA
1 AAAAAATTATTTTATTTGGAATAAAACGATACTGTTTTGCTATGCTAAAA
25388091 ATCTTTTATT
Statistics
Matches: 171, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
144 38 0.22
145 21 0.12
146 8 0.05
147 60 0.35
148 44 0.26
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (146 bp):
AAAAAATTATTTTATTTGGAATAAAACGATACTGTTTTGCTATGCTAAAAGGGCGCTATTTTTTA
AAATAAAATTATTTTTGTGACGTTTTTTAAAAAAACGCCGCTATTGCTTACCTTTTGCGACGTTT
TCCACAAAAACGCCGC
Found at i:25389032 original size:82 final size:82
Alignment explanation
Indices: 25388937--25389091 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 82
25388927 TTAACCCCAA
* *
25388937 ACCCCTAACCCCTAAC-CCTTAAACCTTATTTAATATATAAATTAAAAAAAACTAATTAATCTAA
1 ACCCCGAACCCCTAACTCC-TAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATCTAA
25389001 ATCC-TAAACCCTAACCTG
65 A-CCATAAACCCTAACCTG
* * * *
25389019 ACCCCGAATCCCTAACTCCTAAACATTATTTAATATATAAATTAAAACACACTAATTACTCTAAA
1 ACCCCGAACCCCTAACTCCTAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATCTAAA
25389084 CCATAAAC
66 CCATAAAC
25389092 TGACACCGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 61 0.94
83 2 0.03
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (82 bp):
ACCCCGAACCCCTAACTCCTAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATCTAAA
CCATAAACCCTAACCTG
Found at i:25389084 original size:75 final size:79
Alignment explanation
Indices: 25388937--25389116 Score: 197
Period size: 82 Copynumber: 2.3 Consensus size: 79
25388927 TTAACCCCAA
* * * *
25388937 ACCCCTAACCCCTAACCCTTAAACCTTATTTAATATATAAATTAAAAAAAACTAATTAATCTAAA
1 ACCCCGAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATC---A
* *
25389002 TCCTAAACCCTAACCTG
63 TCCTAAACCATAAACTG
* * *
25389019 ACCCCGAATCCCTAACTCCTAAACATTATTTAATATATAAATTAAAACACACTAATT-A-C-T-C
1 ACCCCGAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATCATCC
25389080 TAAACCATAAACTG
66 TAAACCATAAACTG
* * *
25389094 ACACCGAATCCATAAACCCTAAA
1 ACCCCGAATCCCTAACCCCTAAA
25389117 TTCCTAACTA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
75 32 0.38
76 1 0.01
80 1 0.01
81 1 0.01
82 50 0.59
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.26
Consensus pattern (79 bp):
ACCCCGAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAAAACTAATTAATCATCC
TAAACCATAAACTG
Found at i:25389147 original size:13 final size:13
Alignment explanation
Indices: 25389131--25389169 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
25389121 TAACTAATCT
25389131 TAACCTCTAACCC
1 TAACCTCTAACCC
*
25389144 TAACCCCTAACCCC
1 TAACCTCTAA-CCC
*
25389158 TAACCTATAACC
1 TAACCTCTAACC
25389170 TTTAAATCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (13 bp):
TAACCTCTAACCC
Found at i:25389168 original size:14 final size:14
Alignment explanation
Indices: 25389131--25389169 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25389121 TAACTAATCT
25389131 TAACCTCTAA-CCC
1 TAACCTCTAACCCC
*
25389144 TAACCCCTAACCCC
1 TAACCTCTAACCCC
*
25389158 TAACCTATAACC
1 TAACCTCTAACC
25389170 TTTAAATCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (14 bp):
TAACCTCTAACCCC
Found at i:25390716 original size:41 final size:41
Alignment explanation
Indices: 25390452--25390719 Score: 392
Period size: 41 Copynumber: 6.5 Consensus size: 41
25390442 CAACGCTTTC
*** *
25390452 TCAAAAACGCCGCTAAAGAATCGAGCATTAGCGGCGCTTTT
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
* * *
25390493 TGAAAAACGCCACTAAAGGCCCGAGCATTAGCGGCGCTTTT
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
* * * *
25390534 TGAAAAACGCCGCTAAAGGCACGAGCATTAGCGGCACTTAT
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
*
25390575 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCT
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
*
25390616 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCT
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
* *
25390657 TCAAAAACGCCGCTAAAGGCCCGGGCATTAGCGGCGCTTCC
1 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
*
25390698 TCAAAAACGCCACTAAAGGCCC
1 TCAAAAACGCCGCTAAAGGCCC
25390720 CAAAAACTCA
Statistics
Matches: 209, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 209 1.00
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.18
Consensus pattern (41 bp):
TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCT
Found at i:25390821 original size:39 final size:39
Alignment explanation
Indices: 25390755--25390888 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 39
25390745 GGGCTTAGGC
* *
25390755 TTTTT-GCGGCGCATTTCA-AAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCG-TTTTCATAAAAGCGCCGCTAATGCTTA
* *
25390793 TTTTTAGCGGCGTTTTCCTAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCATAAAAGCGCCGCTAATGCT-TA
** * *
25390833 CCTTTAGCAGCGTTTTTATAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCATAAAAGCGCCGCTAATGCTT-A
*
25390873 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
25390889 TTGTCCAAGC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 9 0.12
39 23 0.29
40 46 0.59
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCATAAAAGCGCCGCTAATGCTTA
Found at i:25390906 original size:41 final size:40
Alignment explanation
Indices: 25390773--25390889 Score: 155
Period size: 40 Copynumber: 3.0 Consensus size: 40
25390763 GCGCATTTCA
* **
25390773 AAAAACGCCGCTAATGCTT-ATTTTTAGCGGCGTTTTCCT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTAT
* ** *
25390812 AAAAGCGCCGCTAATGCTCGACCTTTAGCAGCGTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTAT
*
25390852 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT
25390890 TGTCCAAGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 17 0.26
40 48 0.74
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTAT
Found at i:25391752 original size:26 final size:25
Alignment explanation
Indices: 25391723--25391779 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
25391713 ATAAAAATTA
*
25391723 TTTAGATTTATCAAAAATAAATAAAT
1 TTTA-ATTTATCAAAAATAAAGAAAT
* * *
25391749 TTTAACATAATTAAAAATAAAGAAAT
1 TTTAA-TTTATCAAAAATAAAGAAAT
25391775 TTTAA
1 TTTAA
25391780 ATTTTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
TTTAATTTATCAAAAATAAAGAAAT
Found at i:25394407 original size:26 final size:25
Alignment explanation
Indices: 25394378--25394469 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
25394368 TGTAATTGTG
25394378 ATATATGATAAAAAATAAAAATTATA
1 ATATAT-ATAAAAAATAAAAATTATA
* * * *
25394404 ATATATACAAATATTAAAATTTA-A
1 ATATATATAAAAAATAAAAATTATA
*
25394428 AAATATATAAAAAATTAAAAATTATTA
1 ATATATATAAAAAA-TAAAAATTA-TA
* *
25394455 AAAT-TTTAAAAAATA
1 ATATATATAAAAAATA
25394470 TATAAAAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
24 11 0.21
25 23 0.43
26 14 0.26
27 5 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (25 bp):
ATATATATAAAAAATAAAAATTATA
Found at i:25394435 original size:18 final size:18
Alignment explanation
Indices: 25394414--25394491 Score: 88
Period size: 18 Copynumber: 4.3 Consensus size: 18
25394404 ATATATACAA
25394414 ATATTAAAATTTAAAAAT
1 ATATTAAAATTTAAAAAT
* *
25394432 ATATAAAAAATTAAAAAT
1 ATATTAAAATTTAAAAAT
25394450 -TATTAAAATTTTAAAAAAT
1 ATATTAAAA-TTT-AAAAAT
* *
25394469 ATATAAAAATATAAAAAT
1 ATATTAAAATTTAAAAAT
25394487 A-ATTA
1 ATATTA
25394492 CCAACACAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.20
18 25 0.50
19 8 0.16
20 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATTAAAATTTAAAAAT
Found at i:25394440 original size:10 final size:10
Alignment explanation
Indices: 25394403--25394485 Score: 67
Period size: 10 Copynumber: 9.1 Consensus size: 10
25394393 TAAAAATTAT
*
25394403 AATATATACA
1 AATATATAAA
25394413 AATAT-T-AA
1 AATATATAAA
25394421 AAT-T-TAAA
1 AATATATAAA
25394429 AATATATAAA
1 AATATATAAA
25394439 AA-AT-TAAA
1 AATATATAAA
*
25394447 AAT-TATTAA
1 AATATATAAA
*
25394456 AAT-TTTAAAA
1 AATATAT-AAA
25394466 AATATATAAA
1 AATATATAAA
25394476 AATATA-AAA
1 AATATATAAA
25394485 A
1 A
25394486 TAATTACCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.03
8 16 0.26
9 16 0.26
10 25 0.41
11 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATATAAA
Found at i:25394476 original size:37 final size:35
Alignment explanation
Indices: 25394393--25394491 Score: 116
Period size: 37 Copynumber: 2.9 Consensus size: 35
25394383 TGATAAAAAA
* *
25394393 TAAAAAT-TAT-AATATATACAAA-TATTAAAATT
1 TAAAAATATATAAAAATATAAAAATTATTAAAATT
25394425 TAAAAATATATAAAAA-ATTAAAAATTATTAAAATTT
1 TAAAAATATATAAAAATA-TAAAAATTATTAAAA-TT
*
25394461 TAAAAAATATATAAAAATATAAAAATAATTA
1 T-AAAAATATATAAAAATATAAAAATTATTA
25394492 CCAACACAGC
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
32 7 0.12
33 4 0.07
34 8 0.14
35 8 0.14
36 3 0.05
37 26 0.46
38 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (35 bp):
TAAAAATATATAAAAATATAAAAATTATTAAAATT
Found at i:25394480 original size:8 final size:8
Alignment explanation
Indices: 25394385--25394487 Score: 57
Period size: 8 Copynumber: 12.1 Consensus size: 8
25394375 GTGATATATG
25394385 ATAAAAA-
1 ATAAAAAT
25394392 ATAAAAAT
1 ATAAAAAT
*
25394400 -TATAATAT
1 ATA-AAAAT
*
25394408 ATACAAAT
1 ATAAAAAT
*
25394416 ATTAAAAT
1 ATAAAAAT
*
25394424 TTAAAAAT
1 ATAAAAAT
*
25394432 ATATAAAAA
1 ATA-AAAAT
25394441 ATTAAAAATT
1 A-TAAAAA-T
*
25394451 ATTAAAATTTT
1 A-TAAAA--AT
*
25394462 AAAAAATAT
1 ATAAAA-AT
25394471 ATAAAAAT
1 ATAAAAAT
25394479 ATAAAAAT
1 ATAAAAAT
25394487 A
1 A
25394488 ATTACCAACA
Statistics
Matches: 74, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
7 9 0.12
8 32 0.43
9 18 0.24
10 13 0.18
11 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (8 bp):
ATAAAAAT
Found at i:25395031 original size:9 final size:9
Alignment explanation
Indices: 25394980--25395044 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
25394970 AAATTTTCTA
25394980 TATATTTTT
1 TATATTTTT
* *
25394989 ATAAATTTTA
1 -TATATTTTT
* *
25394999 TAAATTTTC
1 TATATTTTT
25395008 TATATTTTT
1 TATATTTTT
25395017 TATATTTTAT
1 TATATTTT-T
25395027 T-TA-TTTT
1 TATATTTTT
25395034 TATCATTTTT
1 TAT-ATTTTT
25395044 T
1 T
25395045 TCTATCTATC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 26 0.57
10 14 0.30
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (9 bp):
TATATTTTT
Found at i:25402262 original size:43 final size:43
Alignment explanation
Indices: 25402195--25402308 Score: 183
Period size: 43 Copynumber: 2.7 Consensus size: 43
25402185 TCGTCGCTAA
* *
25402195 CTTTTGCGGCGTTTTACCCACAAACGCCGCTAAAGAACATGAT
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAT
* *
25402238 CTTTATCGGCGCTTTACCCACAAACGCCGCTAAAGAACATTAT
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAT
*
25402281 CTTTAGCGACGCTTTACCCACAAACGCC
1 CTTTAGCGGCGCTTTACCCACAAACGCC
25402309 TTTAAAGGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAT
Found at i:25405798 original size:31 final size:31
Alignment explanation
Indices: 25405760--25405839 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
25405750 CATGGTTGAT
*
25405760 TTAGCAGCAAAAATCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
25405791 TTAGCAGCAAAAACCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
*
25405822 TTAGCTGCAAAAACCAAT
1 TTAGCAGCAAAAACCAAT
25405840 TAAAATTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (31 bp):
TTAGCAGCAAAAACCAATAGAAGGTACCATC
Found at i:25407347 original size:14 final size:14
Alignment explanation
Indices: 25407301--25407349 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
25407291 AAAAGTAATT
25407301 AAACCCTAAAATCCA
1 AAACCCT-AAATCCA
* * * *
25407316 TAACACTAAACCCT
1 AAACCCTAAATCCA
25407330 AAACCCTAAATCCA
1 AAACCCTAAATCCA
25407344 AAACCC
1 AAACCC
25407350 AAAACCATGC
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACCCTAAATCCA
Found at i:25407354 original size:28 final size:29
Alignment explanation
Indices: 25407300--25407355 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
25407290 CAAAAGTAAT
* *
25407300 TAAACCCTAAAATCCATAACACTAAACCC
1 TAAACCCTAAAATCCAAAACACAAAACCC
*
25407329 TAAACCCT-AAATCCAAAACCCAAAACC
1 TAAACCCTAAAATCCAAAACACAAAACC
25407356 ATGCATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (29 bp):
TAAACCCTAAAATCCAAAACACAAAACCC
Found at i:25409026 original size:51 final size:50
Alignment explanation
Indices: 25408890--25409276 Score: 339
Period size: 51 Copynumber: 7.6 Consensus size: 50
25408880 TATCATTCCA
* *
25408890 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTT-CGG
* * *
25408940 TTCACGTAGTAGCCTTCACATAGTACTATACATGTGACCAAAGCTTTTTGG
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACC-AAGCTTTTCGG
* * * * * *
25408991 TACACATAGCAGCCTTCACTTACTACTACACATGTGACC-ATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGC-TTT-TCGG
* * * * * *
25409042 TTCACGTAGTAGCCTTCACACAGTACTATACACGTGACAAAAGCTTCTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGAC-CAAGCTTTTCGG
* * * * * *
25409093 TACACATTGTAGCCTTCACTTAGAACTACACATGTGACC-ATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGC-TTT-TCGG
* * * * *
25409144 TTCACGTAGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTCTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACC-AAGCTTTTCGG
* * * *** * * *
25409195 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCTTTCGTTCCAG
1 TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTTCGG
*
25409245 TACACGTAGTAGCCTACACATAGTACTACACA
1 TACACGTAGTAGCCTTCACATAGTACTACACA
25409277 CGAGACCATC
Statistics
Matches: 260, Mismatches: 67, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
49 4 0.02
50 72 0.28
51 172 0.66
52 8 0.03
53 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAGCTTTTCGG
Found at i:25409070 original size:102 final size:102
Alignment explanation
Indices: 25408890--25409233 Score: 501
Period size: 102 Copynumber: 3.4 Consensus size: 102
25408880 TATCATTCCA
* * * * *** *
25408890 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* * * *
25408954 TTCACATAGTACTATACATGTGACCAAAGCTTTTTGG
66 TTCACACAGTACTATACACGTGACCAAAGCTTCTCGG
* *
25408991 TACACATAGCAGCCTTCACTTACTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
*
25409056 TTCACACAGTACTATACACGTGACAAAAGCTTCTCGG
66 TTCACACAGTACTATACACGTGACCAAAGCTTCTCGG
* *
25409093 TACACATTGTAGCCTTCACTTAGAACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
25409158 TTTACACAGTACTACACACGTGACCAAAGCTTCTCGG
66 TTCACACAGTACTATACACGTGACCAAAGCTTCTCGG
*
25409195 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACC
25409234 TTTCGTTCCA
Statistics
Matches: 219, Mismatches: 23, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
101 38 0.17
102 181 0.83
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTATACACGTGACCAAAGCTTCTCGG
Found at i:25414704 original size:50 final size:50
Alignment explanation
Indices: 25414642--25414975 Score: 325
Period size: 50 Copynumber: 6.6 Consensus size: 50
25414632 ATTCGATACG
* *
25414642 CGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACAGTTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACAGTTCA
* ** *
25414692 CGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTATGGTCCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACAGTTCA
* * * *
25414742 CGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTTTT-CGGTACA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACAGTTCA
* * * * ***
25414793 CATAATAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCA-TTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CAGTTCA
* * * *
25414843 CGTAGTAGCCTTCACACAGTATTACACACGTGACCAAAGCTTCT-CAGTACA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACAGTTCA
* * * * ***
25414894 CATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCA-TTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CAGTTCA
*
25414944 CGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGTAGTAGCCTTCACATAGTACTACACACGTG
25414976 TTCATCGATA
Statistics
Matches: 228, Mismatches: 47, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
49 5 0.02
50 144 0.63
51 73 0.32
52 6 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACAGTTCA
Found at i:25414845 original size:101 final size:101
Alignment explanation
Indices: 25414642--25414975 Score: 465
Period size: 101 Copynumber: 3.3 Consensus size: 101
25414632 ATTCGATACG
** * * *
25414642 CGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAG-TTTTACAGTTCACGTAGTAGCCTTC
1 CGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CAGTACACATAGTAGCCTTC
* * * *** ** *
25414705 ACATAGTACTACACACGTGATCAAGTTTTATGGTCCA
65 ACTTAGTACTACACATGTGACCATCATTTATCATTCA
* * *
25414742 CGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTTTTCGGTACACATAATAGCCTTCA
1 CGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCAGTACACATAGTAGCCTTCA
25414807 CTTAGTACTACACATGTGACCATCATTTATCATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCATTCA
* * *
25414843 CGTAGTAGCCTTCACACAGTATTACACACGTGACCAAAGCTTCTCAGTACACATTGTAGCCTTCA
1 CGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCAGTACACATAGTAGCCTTCA
25414908 CTTAGTACTACACATGTGACCATCATTTATCATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCATTCA
25414944 CGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGTAGTAGCCTTCACACAGTACTACACACGTG
25414976 TTCATCGATA
Statistics
Matches: 208, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
100 31 0.15
101 173 0.83
102 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (101 bp):
CGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCAGTACACATAGTAGCCTTCA
CTTAGTACTACACATGTGACCATCATTTATCATTCA
Found at i:25414953 original size:151 final size:149
Alignment explanation
Indices: 25414633--25414975 Score: 370
Period size: 151 Copynumber: 2.3 Consensus size: 149
25414623 ACTTTTATCA
* * **
25414633 TTCGATACGCGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACAGTTCACGTAGT
1 TTCGATACACGTAGTAGCCTTCACTTAGTACTACACACGTGACCAACATTTACAGTTCACGTAGT
* * * * *
25414698 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTATGGTCCACGTAGTAGCCTTCACACAATA
66 AGCCTTCACACAGTACTACACACGTGACCAAGTTTCA-GGTACACATAGTAGCCTTCACACAATA
25414763 CTACACACGTGACCAAAGCTT
130 CTACACACGTGACCAAA-CTT
* * * * *
25414784 TTCGGTACACATAATAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCA-TTCACGTAG
1 TTCGATACACGTAGTAGCCTTCACTTAGTACTACACACGTGACCAACATTTA-CAGTTCACGTAG
* * **
25414848 TAGCCTTCACACAGTATTACACACGTGACCAAAGCTTCTCA-GTACACATTGTAGCCTTCACTTA
65 TAGCCTTCACACAGTACTACACACGTGACC-AAG-TT-TCAGGTACACATAGTAGCCTTCACACA
* * *
25414912 GTACTACACATGTGACC-ATCATT
127 ATACTACACACGTGACCAAAC-TT
* **
25414935 TATC-ATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
1 T-TCGATACACGTAGTAGCCTTCACTTAGTACTACACACGTG
25414976 TTCATCGATA
Statistics
Matches: 158, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
150 1 0.01
151 113 0.72
152 40 0.25
153 2 0.01
154 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (149 bp):
TTCGATACACGTAGTAGCCTTCACTTAGTACTACACACGTGACCAACATTTACAGTTCACGTAGT
AGCCTTCACACAGTACTACACACGTGACCAAGTTTCAGGTACACATAGTAGCCTTCACACAATAC
TACACACGTGACCAAACTT
Found at i:25416674 original size:41 final size:41
Alignment explanation
Indices: 25416500--25416755 Score: 180
Period size: 41 Copynumber: 6.2 Consensus size: 41
25416490 AAAAGCCCCT
* ** *
25416500 GAGCATTAGCGGCACTTTCTAAAAAACACCGCTAAAGCCCA
1 GAGCATTAGCGGCGCTTTCTAAAAAATGCCGCTAAAGCCTA
* ** ** *** ** *
25416541 GAGAATTATTGGAACTTTCTAAAAACCACCTTTAAAGCCCA
1 GAGCATTAGCGGCGCTTTCTAAAAAATGCCGCTAAAGCCTA
* * *
25416582 GAGCAATAGTGGCGCTTTCTTCAAAAATGCCGCTAAAGCCTA
1 GAGCATTAGCGGCGCTTTC-TAAAAAATGCCGCTAAAGCCTA
* *
25416624 GAGAATTAGCGGCGTTTTCTAAAAAATGCCGCTAAAGCCTA
1 GAGCATTAGCGGCGCTTTCTAAAAAATGCCGCTAAAGCCTA
** **
25416665 GAGCATTAGCGTAGC-TTCTTCAAAATCGCCGCTAAAG-CTCA
1 GAGCATTAGCGGCGCTTTCTAAAAAAT-GCCGCTAAAGCCT-A
* *
25416706 GATCATTAGCGGCGCATCTTC-AAAAACA--CCGTTAAAGCCTA
1 GAGCATTAGCGGCGC-T-TTCTAAAAA-ATGCCGCTAAAGCCTA
*
25416747 GATCATTAG
1 GAGCATTAG
25416756 TGGCTCTTCT
Statistics
Matches: 171, Mismatches: 36, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
40 11 0.06
41 121 0.71
42 32 0.19
43 3 0.02
44 4 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTTCTAAAAAATGCCGCTAAAGCCTA
Found at i:25416767 original size:41 final size:41
Alignment explanation
Indices: 25416573--25416800 Score: 210
Period size: 41 Copynumber: 5.5 Consensus size: 41
25416563 AAACCACCTT
* * * *
25416573 TAAAGCCCAGAGCAATAGTGGCGCTTTCTTCAAAAATGCCGC
1 TAAAGCCTAGAGCATTAGCGGCGC-TTCTTCAAAAACGCCGC
* *
25416615 TAAAGCCTAGAGAATTAGCGGCG-TT-TTCTAAAAAATGCCGC
1 TAAAGCCTAGAGCATTAGCGGCGCTTCTTC--AAAAACGCCGC
** *
25416656 TAAAGCCTAGAGCATTAGCGTAGCTTCTTCAAAATCGCCGC
1 TAAAGCCTAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
* * * *
25416697 TAAAG-CTCAGATCATTAGCGGCGCATCTTCAAAAACACCGT
1 TAAAGCCT-AGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
* * * *
25416738 TAAAGCCTAGATCATTAGTGGCTCTTCTTCAAAAACGTCGC
1 TAAAGCCTAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
* ***
25416779 TAAATCCCCCAGCATTAGCGGC
1 TAAAGCCTAGAGCATTAGCGGC
25416801 ACTTTTTGAA
Statistics
Matches: 152, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
39 3 0.02
40 4 0.03
41 119 0.78
42 23 0.15
43 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (41 bp):
TAAAGCCTAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGC
Found at i:25416813 original size:82 final size:81
Alignment explanation
Indices: 25416521--25416813 Score: 244
Period size: 82 Copynumber: 3.6 Consensus size: 81
25416511 GCACTTTCTA
* * ** * * * * *
25416521 AAAAACACCGCTAAAGCCCAGAGAATTATTGGAACTTTCTAAAAACCACCTTTAAAGCCCAGAGC
1 AAAAACGCCGCTAAAGCCCAGAGCATTAGCGG-CCTTTTTAAAAAACACCGTTAAAGCCTAGAGC
*
25416586 AATAGTGGCGCTTTCTTC
65 ATTAGTGGCGC-TTCTTC
* * * * ** *
25416604 AAAAATGCCGCTAAAGCCTAGAGAATTAGCGGCGTTTTCTAAAAAATGCCGCTAAAGCCTAGAGC
1 AAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCCTTTT-TAAAAAACACCGTTAAAGCCTAGAGC
* **
25416669 ATTAGCGTAGCTTCTTC
65 ATTAGTGGCGCTTCTTC
* * * * * * *
25416686 AAAATCGCCGCTAAAGCTCAGATCATTAGCGGCGCATCTTCAAAAACACCGTTAAAGCCTAGATC
1 AAAAACGCCGCTAAAGCCCAGAGCATTAGCGGC-CTTTTTAAAAAACACCGTTAAAGCCTAGAGC
*
25416751 ATTAGTGGCTCTTCTTC
65 ATTAGTGGCGCTTCTTC
* * ** *
25416768 AAAAACGTCGCTAAATCCCCCAGCATTAGCGGCACTTTTTGAAAAA
1 AAAAACGCCGCTAAAGCCCAGAGCATTAGCGGC-CTTTTTAAAAAA
25416814 TATCGCTAAA
Statistics
Matches: 161, Mismatches: 47, Indels: 5
0.76 0.22 0.02
Matches are distributed among these distances:
82 105 0.65
83 56 0.35
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGCCCAGAGCATTAGCGGCCTTTTTAAAAAACACCGTTAAAGCCTAGAGCA
TTAGTGGCGCTTCTTC
Found at i:25416926 original size:40 final size:40
Alignment explanation
Indices: 25416882--25416983 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 40
25416872 TCCTTATAAA
25416882 CGCCGCTAATGCTCTATTTTTAGTGGCGTTTCTCAAAAAG
1 CGCCGCTAATGCTCTATTTTTAGTGGCGTTTCTCAAAAAG
* * * *
25416922 CGCCGCTAATGCTTTA-TTTTAGTGGCGTTTTTCTAAATG
1 CGCCGCTAATGCTCTATTTTTAGTGGCGTTTCTCAAAAAG
* *
25416961 CACCGCTAATGCTCGATTTTTAG
1 CGCCGCTAATGCTCTATTTTTAG
25416984 AGGCATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 33 0.61
40 21 0.39
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (40 bp):
CGCCGCTAATGCTCTATTTTTAGTGGCGTTTCTCAAAAAG
Found at i:25419286 original size:20 final size:21
Alignment explanation
Indices: 25419247--25419286 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25419237 ATTATCATCA
*
25419247 CATGTCAAATACTAGTTTCAC
1 CATGTCAAATACTAGATTCAC
*
25419268 CATGTCAAATATTA-ATTCA
1 CATGTCAAATACTAGATTCA
25419287 AAATCATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (21 bp):
CATGTCAAATACTAGATTCAC
Found at i:25420623 original size:15 final size:16
Alignment explanation
Indices: 25420596--25420628 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
25420586 TGTTGAAAAT
25420596 AATATTAATATATAAA
1 AATATTAATATATAAA
25420612 AATATT-ATATATAAA
1 AATATTAATATATAAA
25420627 AA
1 AA
25420629 GTTAATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATTAATATATAAA
Found at i:25429882 original size:12 final size:12
Alignment explanation
Indices: 25429857--25429894 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
25429847 GATTATTGTT
25429857 TTTATTTCGTTTA
1 TTTATTT-GTTTA
25429870 TTTATTTGTTTA
1 TTTATTTGTTTA
25429882 TATTATTT-TTTA
1 T-TTATTTGTTTA
25429894 T
1 T
25429895 GCCATTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTATTTGTTTA
Found at i:25440221 original size:59 final size:60
Alignment explanation
Indices: 25440148--25440305 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 60
25440138 CAAACTTTAG
*
25440148 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA-ATT-A-TATTTT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAA-TA-TTTAATATTAAGAATTTT
* * * ** * * *
25440207 A-TAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTT
1 ATTA-AATTATATATTTTTATTAAATTATATTTA-ATAATAATATTTAATATTAAGAATTTT
25440268 ATTAAATTATATATTTTTATTAAATTATATTTAATAAT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAAT
25440306 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 17, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
58 7 0.09
59 28 0.37
60 11 0.14
61 28 0.37
62 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (60 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATATTTAATATTAAGAATTTT
Found at i:25440540 original size:18 final size:17
Alignment explanation
Indices: 25440512--25440546 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25440502 ATTATTAAGA
*
25440512 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
25440529 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
25440547 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:25440800 original size:45 final size:44
Alignment explanation
Indices: 25440692--25440801 Score: 113
Period size: 45 Copynumber: 2.6 Consensus size: 44
25440682 TTTTCCATTA
25440692 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * * * ***
25440731 TACTATTACGCCTATATTCAATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
25440776 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
25440802 CCTCTATTCC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
39 15 0.28
44 16 0.30
45 23 0.43
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:25440801 original size:16 final size:16
Alignment explanation
Indices: 25440780--25440849 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
25440770 TTGATTTGCT
*
25440780 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
25440796 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
25440812 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
25440828 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
25440844 AATACA
1 ATTACA
25440850 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:25446666 original size:132 final size:132
Alignment explanation
Indices: 25445841--25446664 Score: 1423
Period size: 132 Copynumber: 6.2 Consensus size: 132
25445831 TGAATAAGAC
* * * *
25445841 AGCAGATTTAAGCCACCAAGCCTTGTCTCCTTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
25445906 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25445971 GA
131 GA
25445973 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
25446038 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25446103 GA
131 GA
25446105 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
25446170 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25446235 GA
131 GA
25446237 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
25446302 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25446367 GA
131 GA
25446369 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
* *
25446434 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATTTTTCCAAGATAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25446499 GA
131 GA
* * * * * * * *
25446501 AGTAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGTAGCGGAGAAGGTTGAAGATTATAGAT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
* * * * * * *
25446566 CTTATCTCCCTAAGCAGTAGCGGAGCAAATCAAAGTCGGCGAATCTTATCTTTCCAAGACAGTGG
66 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
25446631 GA
131 GA
* * * *
25446633 AGTAGATTTAAGCCACCAAATCTTATCTCCCT
1 AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCT
25446665 AAATTTGCAG
Statistics
Matches: 668, Mismatches: 24, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 668 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (132 bp):
AGCAGTTTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGTAGAT
CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGG
GA
Found at i:25448098 original size:13 final size:14
Alignment explanation
Indices: 25448075--25448111 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
25448065 ATAGTGCAAT
25448075 TATTATTTTTATTC
1 TATTATTTTTATTC
25448089 TATT-TTTTTATT-
1 TATTATTTTTATTC
25448101 TATATATTTTT
1 TAT-TATTTTT
25448112 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 9 0.43
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTATTTTTATTC
Found at i:25448158 original size:38 final size:35
Alignment explanation
Indices: 25448090--25448173 Score: 80
Period size: 38 Copynumber: 2.3 Consensus size: 35
25448080 TTTTTATTCT
* * *
25448090 ATTTTT-TTATTTATATATTTTTTTAAATTTTATATGTA
1 ATTTTTATT-TTTATATATGTATATAAATTTT-TA--TA
*
25448128 ATTTTTATTTTTATATATGTATATATATTTTTATA
1 ATTTTTATTTTTATATATGTATATAAATTTTTATA
*
25448163 ATTATTATTTT
1 ATTTTTATTTT
25448174 AAACTGATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
35 12 0.30
37 2 0.05
38 24 0.60
39 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (35 bp):
ATTTTTATTTTTATATATGTATATAAATTTTTATA
Found at i:25455483 original size:21 final size:21
Alignment explanation
Indices: 25455466--25455508 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
25455456 TAGAAGCCTC
25455466 GGTTCAGCAAGAACAAGCAGA
1 GGTTCAGCAAGAACAAGCAGA
*
25455487 GGTTCAGCAAGAACGAGCAGA
1 GGTTCAGCAAGAACAAGCAGA
25455508 G
1 G
25455509 AAGGAGGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.33, T:0.09
Consensus pattern (21 bp):
GGTTCAGCAAGAACAAGCAGA
Found at i:25456465 original size:23 final size:23
Alignment explanation
Indices: 25456439--25456504 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
25456429 TTCATTTAAC
*
25456439 TTAATCGAGCATGTTTACGAACA
1 TTAATCGAGCATGTTCACGAACA
* * *
25456462 TTAAACGAACATGTTCATGAACA
1 TTAATCGAGCATGTTCACGAACA
*
25456485 TATAATTGAGCATGTTCACG
1 T-TAATCGAGCATGTTCACG
25456505 GACAATGTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
TTAATCGAGCATGTTCACGAACA
Found at i:25457391 original size:26 final size:26
Alignment explanation
Indices: 25457362--25457440 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
25457352 TCCGTCTCAA
* *
25457362 TAAATTTATAATCAAATTTATAATTT
1 TAAATTTATAATAAAATATATAATTT
* *
25457388 TAAATTAATAATAAAAAATATATATTT
1 TAAATTTATAATAAAATATATA-ATTT
* *
25457415 AAAATTT-TAATTAAATATATAATTT
1 TAAATTTATAATAAAATATATAATTT
25457440 T
1 T
25457441 TATAAAAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
25 4 0.09
26 30 0.70
27 9 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATTTATAATAAAATATATAATTT
Found at i:25462640 original size:17 final size:20
Alignment explanation
Indices: 25462603--25462641 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25462593 AAACATTTTC
25462603 TTTCTTGTCTCTTTTCATTT
1 TTTCTTGTCTCTTTTCATTT
25462623 TTTCTT-TCT-TTTTC-TTT
1 TTTCTTGTCTCTTTTCATTT
25462640 TT
1 TT
25462642 AATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 3 0.16
20 6 0.32
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTCTTGTCTCTTTTCATTT
Found at i:25462641 original size:24 final size:24
Alignment explanation
Indices: 25462598--25462648 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
25462588 GAATTAAACA
*
25462598 TTTTCTTTCTTGTCTCTTTTCATT
1 TTTTCTTTCTTGTCTCTTTTAATT
*
25462622 TTTTCTTTCTT-TTTCTTTTTAATT
1 TTTTCTTTCTTGTCTC-TTTTAATT
25462646 TTT
1 TTT
25462649 ATTCTTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTCTTTCTTGTCTCTTTTAATT
Found at i:25473787 original size:17 final size:18
Alignment explanation
Indices: 25473762--25473797 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
25473752 AACAAATGAT
25473762 ATCACAAAAA-TATAAAA
1 ATCACAAAAATTATAAAA
*
25473779 ATCAGAAAAATTATAAAA
1 ATCACAAAAATTATAAAA
25473797 A
1 A
25473798 AATAAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (18 bp):
ATCACAAAAATTATAAAA
Found at i:25473834 original size:18 final size:19
Alignment explanation
Indices: 25473813--25473852 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
25473803 GATTTTTTAT
25473813 AAAAATATT-AAATATTAA
1 AAAAATATTAAAATATTAA
25473831 AAAAATATTAAAAATATTAA
1 AAAAATATT-AAAATATTAA
25473851 AA
1 AA
25473853 TTGATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATATTAAAATATTAA
Found at i:25473900 original size:19 final size:18
Alignment explanation
Indices: 25473840--25473928 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 18
25473830 AAAAAATATT
25473840 AAAAATATTAAAATTGATA
1 AAAAATATTAAAATTG-TA
** **
25473859 TAAACTTATTATAAATTAAA
1 -AAAAATATTA-AAATTGTA
*
25473879 AAAAATATTAGAATTGTTA
1 AAAAATATTAAAATTG-TA
*
25473898 AAAAA-ATAAAAAATTGTA
1 AAAAATAT-TAAAATTGTA
25473916 AAAAATATTAAAA
1 AAAAATATTAAAA
25473929 AATATTAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
18 17 0.32
19 22 0.42
20 9 0.17
21 5 0.09
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAATATTAAAATTGTA
Found at i:25473948 original size:11 final size:10
Alignment explanation
Indices: 25473822--25473948 Score: 72
Period size: 10 Copynumber: 13.0 Consensus size: 10
25473812 TAAAAATATT
25473822 AAATATTAAAA
1 AAATATT-AAA
25473833 AAATATT-AA
1 AAATATTAAA
25473842 AAATATT-AA
1 AAATATTAAA
*
25473851 AATTGA-TATAA
1 AAAT-ATTA-AA
** *
25473862 ACTTATTATA
1 AAATATTAAA
* *
25473872 AATTA-AAAA
1 AAATATTAAA
*
25473881 AAATATT-AG
1 AAATATTAAA
* *
25473890 AATTGTTAAA
1 AAATATTAAA
25473900 AAA-A-TAAA
1 AAATATTAAA
25473908 AAAT-TGTAAA
1 AAATAT-TAAA
25473918 AAATATTAAA
1 AAATATTAAA
25473928 AAATATTAAA
1 AAATATTAAA
25473938 AAATATGTAAA
1 AAATAT-TAAA
25473949 CTTATAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.08
9 27 0.30
10 38 0.42
11 19 0.21
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAATATTAAA
Found at i:25480921 original size:9 final size:9
Alignment explanation
Indices: 25480909--25481113 Score: 53
Period size: 10 Copynumber: 21.7 Consensus size: 9
25480899 TGAGAATTTT
25480909 TTTTTATAA
1 TTTTTATAA
25480918 TTTTTATAA
1 TTTTTATAA
*
25480927 GTTTATATCAA
1 -TTTTTAT-AA
*
25480938 TTTTAAT-A
1 TTTTTATAA
* *
25480946 CTTATAT-A
1 TTTTTATAA
*
25480954 TATTTATAA
1 TTTTTATAA
*
25480963 TTTTTATGA
1 TTTTTATAA
* *
25480972 TCTTTAAGATA
1 T-TTTTATA-A
*
25480983 TTTTTAGAA
1 TTTTTATAA
* *
25480992 TTTTAATACG
1 TTTTTATA-A
25481002 TTTTTATAAA
1 TTTTTAT-AA
*
25481012 ATTTTA-AA
1 TTTTTATAA
25481020 TATTTTA-AA
1 T-TTTTATAA
*
25481029 CCTGTTTCATTAA
1 --T-TTTTA-TAA
*
25481042 TTTTATAAAA
1 TTTT-TATAA
*
25481052 TTTTCATAA
1 TTTTTATAA
*
25481061 TTTATTAGAA
1 TTT-TTATAA
25481071 TTTTTAT--
1 TTTTTATAA
*
25481078 TTTTTACAA
1 TTTTTATAA
*
25481087 GTTTATATCAA
1 -TTTTTAT-AA
*
25481098 TTTTAATATA
1 TTTTTATA-A
25481108 TTTTTA
1 TTTTTA
25481114 ATATATATTA
Statistics
Matches: 140, Mismatches: 37, Indels: 37
0.65 0.17 0.17
Matches are distributed among these distances:
7 6 0.04
8 12 0.09
9 42 0.30
10 64 0.46
11 14 0.10
13 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (9 bp):
TTTTTATAA
Found at i:25481149 original size:11 final size:11
Alignment explanation
Indices: 25481135--25481204 Score: 54
Period size: 11 Copynumber: 6.3 Consensus size: 11
25481125 TTTTTGGTAA
25481135 TTTTTATGA-T
1 TTTTTATGATT
*
25481145 TTTTTATTAATT
1 TTTTTA-TGATT
25481157 TTTTTATGA-T
1 TTTTTATGATT
*
25481167 TTTTTATTAATT
1 TTTTTA-TGATT
*
25481179 TTATTAATGATT
1 TT-TTTATGATT
* *
25481191 TTTTAATCATT
1 TTTTTATGATT
25481202 TTT
1 TTT
25481205 ATGGAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 13 0.27
11 17 0.35
12 16 0.33
13 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTTATGATT
Found at i:25481161 original size:12 final size:12
Alignment explanation
Indices: 25481144--25481194 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
25481134 ATTTTTATGA
25481144 TTTTTTATTAAT
1 TTTTTTATTAAT
*
25481156 TTTTTTA-TGA-
1 TTTTTTATTAAT
25481166 TTTTTTATTAAT
1 TTTTTTATTAAT
* * *
25481178 TTTATTAATGAT
1 TTTTTTATTAAT
25481190 TTTTT
1 TTTTT
25481195 AATCATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 7 0.23
11 4 0.13
12 20 0.65
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTTTATTAAT
Found at i:25481170 original size:23 final size:22
Alignment explanation
Indices: 25481135--25481204 Score: 104
Period size: 22 Copynumber: 3.1 Consensus size: 22
25481125 TTTTTGGTAA
25481135 TTTTTATGATTTTTTATTAATT
1 TTTTTATGATTTTTTATTAATT
25481157 TTTTTATGATTTTTTATTAATT
1 TTTTTATGATTTTTTATTAATT
* * *
25481179 TTATTAATGATTTTTTAATCATT
1 TT-TTTATGATTTTTTATTAATT
25481202 TTT
1 TTT
25481205 ATGGAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 25 0.57
23 19 0.43
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTATGATTTTTTATTAATT
Found at i:25481793 original size:56 final size:56
Alignment explanation
Indices: 25481706--25481821 Score: 214
Period size: 56 Copynumber: 2.1 Consensus size: 56
25481696 CATCACCAAG
*
25481706 TTAGAGAGGATCATCCATTCATTTATTATTATTCTAAAGGCAAATGAGAGACATTC
1 TTAGAGAGGATCATCCATTCATTTATAATTATTCTAAAGGCAAATGAGAGACATTC
*
25481762 TTAGAGAGGATCATCCATTCATTTATAATTATTCTGAAGGCAAATGAGAGACATTC
1 TTAGAGAGGATCATCCATTCATTTATAATTATTCTAAAGGCAAATGAGAGACATTC
25481818 TTAG
1 TTAG
25481822 GTAGTATAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (56 bp):
TTAGAGAGGATCATCCATTCATTTATAATTATTCTAAAGGCAAATGAGAGACATTC
Found at i:25485797 original size:34 final size:31
Alignment explanation
Indices: 25485752--25485865 Score: 106
Period size: 34 Copynumber: 3.5 Consensus size: 31
25485742 TTAGTGTTTT
25485752 TTTTAAAAATTAATTAAATTAGGTTTTAGGGG
1 TTTTAAAAATTAATTAAATTAGGTTTTA-GGG
*
25485784 TTTTAAATTAATTAATTAAATTAAGGTTTCTA-GT
1 TTTTAAA--AATTAATTAAATT-AGGTTT-TAGGG
* **
25485818 TTTTAAGAAAATTAATTAAATTAGGGTTTAGTTT
1 TTTT-A-AAAATTAATTAAATTAGGTTTTAG-GG
25485852 TTTTAAAAA-TAATT
1 TTTTAAAAATTAATT
25485866 TTTTGTTTAG
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
31 5 0.07
32 13 0.18
33 6 0.08
34 36 0.51
35 7 0.10
36 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTTAAAAATTAATTAAATTAGGTTTTAGGG
Found at i:25486262 original size:124 final size:124
Alignment explanation
Indices: 25485937--25486309 Score: 477
Period size: 125 Copynumber: 3.0 Consensus size: 124
25485927 AGTAGTTTTA
* * * * * *
25485937 GAAAAATTAATTTTGAGGAGACGATTCTGAAAAGATAATGTCAAAAATGCTTCAAGTAAGATGCA
1 GAAAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGTAGGATGCA
* * *
25486002 CTATCAGCAAAATTACT-ACAAAAGTTCCCACGTGGACACTCTTTTTCTACAGTAGTTCCT
65 CTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC-CTCTTTTTCTACAGTAGTTCCT
* * * *
25486062 AAAAAAATAATTTTGAAAATACGGTTCTGAAAAAATAGT-TGCAAAAACGCTTCAAGCAGGATGC
1 -GAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGT-CAAAAACGCTTCAAGTAGGATGC
* * *
25486126 ACTGTTAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCT
64 ACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC-CTCTTTTTCTACAGTAGTTCCT
* *
25486188 GAAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAGTGTCAAAAACACTTCAAGTAGGATGCAT
1 GAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGTAGGATGCAC
* * *
25486252 TGTCAGCAAAATTACCG-AGAAAGCTCCCACGTGGA-CTTTTTTTCTACAGTAGTTCCT
66 TGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACCTCTTTTTCTACAGTAGTTCCT
25486309 G
1 G
25486310 TTTGACCTTA
Statistics
Matches: 215, Mismatches: 29, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
121 21 0.10
123 16 0.07
124 48 0.22
125 87 0.40
126 43 0.20
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (124 bp):
GAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGTAGGATGCAC
TGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACCTCTTTTTCTACAGTAGTTCCT
Found at i:25489546 original size:21 final size:21
Alignment explanation
Indices: 25489520--25489595 Score: 118
Period size: 21 Copynumber: 3.6 Consensus size: 21
25489510 GCTTCTGGCG
*
25489520 GGGGTTGTGGTTGCTCCGAC-
1 GGGGTTATGGTTGCTCCGACA
25489540 GAGGGTTATGGTTGCTCCGACA
1 G-GGGTTATGGTTGCTCCGACA
25489562 GGGGTTATGGTTGCTCCGACA
1 GGGGTTATGGTTGCTCCGACA
*
25489583 GGGGTTGTGGTTG
1 GGGGTTATGGTTG
25489596 TTCTGGTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.43, T:0.30
Consensus pattern (21 bp):
GGGGTTATGGTTGCTCCGACA
Found at i:25489872 original size:18 final size:18
Alignment explanation
Indices: 25489849--25489885 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25489839 GGAAAATGAA
*
25489849 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
25489867 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
25489885 A
1 A
25489886 TGCACCTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:25491094 original size:110 final size:107
Alignment explanation
Indices: 25490927--25491225 Score: 456
Period size: 109 Copynumber: 2.7 Consensus size: 107
25490917 ATTTGGTTAG
* *
25490927 ACGAGAAATCGAAACCCAGCACCTTAGAGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
* * *
25490992 TATTTTGAAATTTTTGAAAAGGATATTTAG-CTATTTTGTTGA
66 TATTTTGAAATTTTTGAAAAGGATATTAAGTC-ATTTGGTCGA
* * *
25491034 ACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTG
1 ACGAG--AAATCGAAACCCAGTACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAACATTG
25491099 CCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
63 CCTTATTTTG-AAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
*
25491145 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
25491210 TATTTTGAAATATTTT
66 TATTTTGAAAT-TTTT
25491226 CCTTTTTTGA
Statistics
Matches: 174, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
107 9 0.05
108 41 0.24
109 50 0.29
110 38 0.22
111 35 0.20
112 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (107 bp):
ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
TATTTTGAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
Found at i:25491222 original size:18 final size:17
Alignment explanation
Indices: 25491199--25491240 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
25491189 TCCAAACGCA
25491199 AAATATTGCCTTATTTTG
1 AAATATTGCCTT-TTTTG
*
25491217 AAATATTTTCCTTTTTTG
1 AAATA-TTGCCTTTTTTG
25491235 AAATAT
1 AAATAT
25491241 GAAGTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (17 bp):
AAATATTGCCTTTTTTG
Found at i:25491696 original size:3 final size:3
Alignment explanation
Indices: 25491675--25491708 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
25491665 TAATGAAAAT
* *
25491675 ATA ATG ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25491709 AGTTAACAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25493549 original size:95 final size:94
Alignment explanation
Indices: 25493378--25493557 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 94
25493368 AAGATCTGAA
* * * * * *
25493378 ATCTTCAATCTATTCCACTGCCAACCAGGGAATAGAATTATCGGCTTTAATATACTCTACTGTAG
1 ATCTCCAATCTATTCCACTGCCAACCAAGAAATAGAATTATCGGCTTCAATATACTCCACTGTAA
* * *
25493443 TCATAGTGAGGTACAATCTGCCATCTTCG
66 TCACAGGGAGGTAAAATCTGCCATCTTCG
* *
25493472 ATCTCCAATCTATTCCACTGCCTACCAAGAAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTCCAATCTATTCCACTGCCAACCAAGAA-ATAGAATTATCGGCTTCAATATACTCCACTGTA
25493537 ATCACAGGGAGGTAAAATCTG
65 ATCACAGGGAGGTAAAATCTG
25493558 AAATTCTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 27 0.36
95 47 0.64
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (94 bp):
ATCTCCAATCTATTCCACTGCCAACCAAGAAATAGAATTATCGGCTTCAATATACTCCACTGTAA
TCACAGGGAGGTAAAATCTGCCATCTTCG
Found at i:25493849 original size:88 final size:88
Alignment explanation
Indices: 25493745--25494126 Score: 631
Period size: 88 Copynumber: 4.3 Consensus size: 88
25493735 ATTCAATCTA
* *
25493745 CTCCGTCACAACCGAGAGAGGCAAGGTTTGTGTCTTTAACCTGCTTCGCTGTCACTGCAGGAAGG
1 CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
25493810 CAAGATCTTTTGTCTTCAACCAG
66 CAAGATCTTTTGTCTTCAACCAG
* * * * *
25493833 CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGCCAATGCAGAAAGA
1 CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
25493898 CAAGATCTTTTGTCTTCAACCAG
66 CAAGATCTTTTGTCTTCAACCAG
*
25493921 CTCCGTCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
1 CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
25493986 CAAGATCTTTTGTCTTCAACCAG
66 CAAGATCTTTTGTCTTCAACCAG
* * *
25494009 CTCCATCTCAACCGAGAGAGGCAAGGTTTGTGTCTTTGACATGCTTCACTGTCACTGCAGGAAGG
1 CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
* *
25494074 CAAGATCTGTTATCTTCAACCAG
66 CAAGATCTTTTGTCTTCAACCAG
25494097 CTCCA-CTACAACCGAGAGAGGCAAGGTTTG
1 CTCCATC-ACAACCGAGAGAGGCAAGGTTTG
25494127 CAACTTCATT
Statistics
Matches: 273, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
87 1 0.00
88 272 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (88 bp):
CTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCACTGCAGGAAGG
CAAGATCTTTTGTCTTCAACCAG
Found at i:25493855 original size:44 final size:44
Alignment explanation
Indices: 25493807--25494121 Score: 186
Period size: 44 Copynumber: 7.2 Consensus size: 44
25493797 CACTGCAGGA
25493807 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * *
25493851 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGC-TGC-CAA-TGCAGAA
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-CAT-CACAACCG-AGAG
* *
25493895 AGACAAGATCTTTTGTCTTCAACCAGCTCCGTCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * ** * * ** *
25493939 AGGCAAGGT-TTGTGTCTTTGACCTGCTTCGCTGTCACTGCAG-GA-
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACAACCGAGAG
*
25493983 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCTCAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * ** * ** *
25494027 AGGCAAGGT-TTGTGTCTTTGA-CATGCTTCACTGTC-ACTGCAG-G
1 AGGCAAGATCTTTTGTCTTCAACCA-GCTCCA-TCACAACCG-AGAG
* *
25494070 AAGGCAAGATCTGTTATCTTCAACCAGCTCCA-CTACAACCGAGAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAGAG
25494115 AGGCAAG
1 AGGCAAG
25494122 GTTTGCAACT
Statistics
Matches: 199, Mismatches: 49, Indels: 46
0.68 0.17 0.16
Matches are distributed among these distances:
42 7 0.04
43 51 0.26
44 83 0.42
45 49 0.25
46 9 0.05
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
Found at i:25495426 original size:23 final size:23
Alignment explanation
Indices: 25495400--25495497 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
25495390 ATAAGTGCCA
25495400 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
25495423 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
25495446 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
25495468 CACTGAAATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
25495491 CACTGAT
1 CACTGAT
25495498 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:25495465 original size:45 final size:45
Alignment explanation
Indices: 25495407--25495495 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
25495397 CCACACTGAT
* *
25495407 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
*
25495452 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGTTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
25495496 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:25503198 original size:23 final size:23
Alignment explanation
Indices: 25503172--25503246 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
25503162 ATAAGTGCCA
25503172 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
25503195 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
25503217 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
25503240 CACTGAT
1 CACTGAT
25503247 CAATAACACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.43
23 26 0.57
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:25505743 original size:21 final size:21
Alignment explanation
Indices: 25505704--25505741 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
25505694 TTTTTACTCT
25505704 TTCATTTTTTTCATTTTTTCA
1 TTCATTTTTTTCATTTTTTCA
25505725 TTCA-TTTTTT-ATTTTTT
1 TTCATTTTTTTCATTTTTT
25505742 TTGTTTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (21 bp):
TTCATTTTTTTCATTTTTTCA
Found at i:25506595 original size:13 final size:14
Alignment explanation
Indices: 25506577--25506606 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25506567 TGACCTCTCC
25506577 TTTTCTT-TTTCTT
1 TTTTCTTCTTTCTT
25506590 TTTTCTTCTTTCTT
1 TTTTCTTCTTTCTT
25506604 TTT
1 TTT
25506607 CTCCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTCTTTCTT
Found at i:25508979 original size:24 final size:27
Alignment explanation
Indices: 25508931--25508983 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 27
25508921 GCAATGCAGA
*
25508931 AAGATATAAAAATTTAAACTACAAAAC
1 AAGATATAAAAATATAAACTACAAAAC
25508958 AAGATA-AAAAATAT-AACT-CAAAAC
1 AAGATATAAAAATATAAACTACAAAAC
25508982 AA
1 AA
25508984 ATGAAATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 4 0.16
26 7 0.28
27 6 0.24
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (27 bp):
AAGATATAAAAATATAAACTACAAAAC
Found at i:25509648 original size:110 final size:107
Alignment explanation
Indices: 25509480--25509778 Score: 447
Period size: 109 Copynumber: 2.7 Consensus size: 107
25509470 ATTTGGCTAG
* *
25509480 ACGAGAAATCGAAACCCAGCACCTTAGAGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
* *
25509545 TATTTTGAAATTTTTGAAAAGGATATTTAG-CTATTTGGTTGA
66 TATTTTGAAATTTTTGAAAAGGATATTAAGTC-ATTTGGTCGA
* * *
25509587 ACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTG
1 ACGAG--AAATCGAAACCCAGTACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAACATTG
25509652 CCTTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
63 CCTTATTTTG-AAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
* * *
25509698 ACGAGAAATTGAAACCCAATACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
25509763 TATTTTGAAATATTTT
66 TATTTTGAAAT-TTTT
25509779 CCTTTTTTGA
Statistics
Matches: 173, Mismatches: 13, Indels: 11
0.88 0.07 0.06
Matches are distributed among these distances:
107 9 0.05
108 41 0.24
109 48 0.28
110 38 0.22
111 36 0.21
112 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
TATTTTGAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGA
Found at i:25509775 original size:18 final size:17
Alignment explanation
Indices: 25509752--25509793 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
25509742 TCCAAACGCA
25509752 AAATATTGCCTTATTTTG
1 AAATATTGCCTT-TTTTG
*
25509770 AAATATTTTCCTTTTTTG
1 AAATA-TTGCCTTTTTTG
25509788 AAATAT
1 AAATAT
25509794 GAAGTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (17 bp):
AAATATTGCCTTTTTTG
Found at i:25510248 original size:3 final size:3
Alignment explanation
Indices: 25510227--25510260 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
25510217 TAATGAAAAT
* *
25510227 ATA ATG ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25510261 AGTTAACAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25513769 original size:27 final size:27
Alignment explanation
Indices: 25513715--25513777 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
25513705 GTTAAGTCAG
*
25513715 TTAAATATA-TTTATATTTTCATTATT
1 TTAAATATATTTTATATTATCATTATT
25513741 TTAAATATATTTTATAATATAT-ATT-TT
1 TTAAATATATTTTAT-AT-TATCATTATT
25513768 TTAAATATAT
1 TTAAATATAT
25513778 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 9 0.27
27 17 0.52
28 5 0.15
29 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTAAATATATTTTATATTATCATTATT
Found at i:25513774 original size:15 final size:14
Alignment explanation
Indices: 25513745--25513787 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
25513735 ATTATTTTAA
25513745 ATATATTTTATAAT
1 ATATATTTTATAAT
*
25513759 ATATATTTTTTAAAT
1 ATATATTTTAT-AAT
25513774 ATATATTTTA-AAT
1 ATATATTTTATAAT
25513787 A
1 A
25513788 AATAGGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 10 0.38
15 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTTTATAAT
Found at i:25513777 original size:13 final size:13
Alignment explanation
Indices: 25513739--25513787 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
25513729 ATTTTCATTA
25513739 TTTTAAATATATT
1 TTTTAAATATATT
*
25513752 TTATAATATATATT
1 TTTTAA-ATATATT
*
25513766 TTTTAAATATATA
1 TTTTAAATATATT
25513779 TTTTAAATA
1 TTTTAAATA
25513788 AATAGGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:25531897 original size:316 final size:316
Alignment explanation
Indices: 25531324--25531955 Score: 1264
Period size: 316 Copynumber: 2.0 Consensus size: 316
25531314 TCTTCGACTT
25531324 CTAGTCGATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACCAATGAGACACTGGGTGTCAATT
1 CTAGTCGATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACCAATGAGACACTGGGTGTCAATT
25531389 TATATAGCACTGGGCGCGGTTAATACTTCGGATTTATTCGATGAGGCACTAGGTGTCAAACTGGT
66 TATATAGCACTGGGCGCGGTTAATACTTCGGATTTATTCGATGAGGCACTAGGTGTCAAACTGGT
25531454 GTGTTGGTTGGATCCATGTATCCGTCCGAGTCTGAGTCGTATTAATAGGGTTAATTAAATAAAAT
131 GTGTTGGTTGGATCCATGTATCCGTCCGAGTCTGAGTCGTATTAATAGGGTTAATTAAATAAAAT
25531519 GGTACTATGATTGATATTGGATGATATTGTATGTGAATTGAAAATGGGATAGTAATTTGAAACAT
196 GGTACTATGATTGATATTGGATGATATTGTATGTGAATTGAAAATGGGATAGTAATTTGAAACAT
25531584 GAAATGAGATACATGAGTTATGTACTCATGAATTGGATATGGAATGGATAATGTTA
261 GAAATGAGATACATGAGTTATGTACTCATGAATTGGATATGGAATGGATAATGTTA
25531640 CTAGTCGATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACCAATGAGACACTGGGTGTCAATT
1 CTAGTCGATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACCAATGAGACACTGGGTGTCAATT
25531705 TATATAGCACTGGGCGCGGTTAATACTTCGGATTTATTCGATGAGGCACTAGGTGTCAAACTGGT
66 TATATAGCACTGGGCGCGGTTAATACTTCGGATTTATTCGATGAGGCACTAGGTGTCAAACTGGT
25531770 GTGTTGGTTGGATCCATGTATCCGTCCGAGTCTGAGTCGTATTAATAGGGTTAATTAAATAAAAT
131 GTGTTGGTTGGATCCATGTATCCGTCCGAGTCTGAGTCGTATTAATAGGGTTAATTAAATAAAAT
25531835 GGTACTATGATTGATATTGGATGATATTGTATGTGAATTGAAAATGGGATAGTAATTTGAAACAT
196 GGTACTATGATTGATATTGGATGATATTGTATGTGAATTGAAAATGGGATAGTAATTTGAAACAT
25531900 GAAATGAGATACATGAGTTATGTACTCATGAATTGGATATGGAATGGATAATGTTA
261 GAAATGAGATACATGAGTTATGTACTCATGAATTGGATATGGAATGGATAATGTTA
25531956 TTATTTAAAT
Statistics
Matches: 316, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
316 316 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (316 bp):
CTAGTCGATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACCAATGAGACACTGGGTGTCAATT
TATATAGCACTGGGCGCGGTTAATACTTCGGATTTATTCGATGAGGCACTAGGTGTCAAACTGGT
GTGTTGGTTGGATCCATGTATCCGTCCGAGTCTGAGTCGTATTAATAGGGTTAATTAAATAAAAT
GGTACTATGATTGATATTGGATGATATTGTATGTGAATTGAAAATGGGATAGTAATTTGAAACAT
GAAATGAGATACATGAGTTATGTACTCATGAATTGGATATGGAATGGATAATGTTA
Found at i:25536390 original size:245 final size:244
Alignment explanation
Indices: 25535958--25536417 Score: 697
Period size: 245 Copynumber: 1.9 Consensus size: 244
25535948 ATACGAATAT
* * *
25535958 ATATGGAAACTATAAATTTTGAACACAAATACGTGTTTTAAAATAACATACAATAAATAATGAAA
1 ATATGGAAACCAAAAATTTAGAACACAAATA-GTGTTTTAAAATAACATACAATAAATAATGAAA
* *
25536023 CTTATAGTTTGAAACCAATTAATAATAACACATGAAATATGTACATTATTAAAATGAAGAAATTG
65 CTTATAGTTTGAAACCAATTAATAATAACACATGAAATATGTACATTATTAAAATGAAAAAATTA
* * * *
25536088 GATTAAATTGTTTATCACGGTGTTGTTATCAATCTTGAATCGGGGTCAAGCTAACTTGTGACACC
130 GATTAAATTGTTTATCAAGGTATTGTCATCAATCTTGAATCGAGGTCAAGCTAACTTGTGACACC
25536153 AACTCAATCAAATACATTATTAATATAGAAATACAATCACACATGTATGC
195 AACTCAATCAAATACATTATTAATATAGAAATACAATCACACATGTATGC
25536203 ATATGGAAACCAAAAATTTAGAACACAAAT-GTGTGTTTAAGAATAACATACAATAAATAATGAA
1 ATATGGAAACCAAAAATTTAGAACACAAATAGTGT-TTTAA-AATAACATACAATAAATAATGAA
* * * **
25536267 ACTTATGGTTTGAAACTAATTGATAATAACACATGAAATATGTATGTTATTAAAATGAAAAAATT
64 ACTTATAGTTTGAAACCAATTAATAATAACACATGAAATATGTACATTATTAAAATGAAAAAATT
* * * * * * *
25536332 AGATTAAATTGTTTGTCAATGTATTGTCATTAATCTTGAGTCGATGTCAAGTTAACTTGTGACGC
129 AGATTAAATTGTTTATCAAGGTATTGTCATCAATCTTGAATCGAGGTCAAGCTAACTTGTGACAC
25536397 CAACTCAATCAAATACATTAT
194 CAACTCAATCAAATACATTAT
25536418 AGAGTGGATC
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
243 4 0.02
244 5 0.03
245 183 0.95
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (244 bp):
ATATGGAAACCAAAAATTTAGAACACAAATAGTGTTTTAAAATAACATACAATAAATAATGAAAC
TTATAGTTTGAAACCAATTAATAATAACACATGAAATATGTACATTATTAAAATGAAAAAATTAG
ATTAAATTGTTTATCAAGGTATTGTCATCAATCTTGAATCGAGGTCAAGCTAACTTGTGACACCA
ACTCAATCAAATACATTATTAATATAGAAATACAATCACACATGTATGC
Found at i:25542196 original size:18 final size:18
Alignment explanation
Indices: 25542175--25542211 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25542165 CTTTTGATGA
25542175 AATTTTAAATTTTGGTCC
1 AATTTTAAATTTTGGTCC
25542193 AATTTTAAATTTTGGTCC
1 AATTTTAAATTTTGGTCC
25542211 A
1 A
25542212 CATAGCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
AATTTTAAATTTTGGTCC
Found at i:25543294 original size:24 final size:24
Alignment explanation
Indices: 25543266--25543317 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25543256 TTTGTAGGTC
* *
25543266 AAATAAATAATGCTAATAAATGCT
1 AAATAAATAATACTAATAAATACT
* *
25543290 AAATATATTATACTAATAAATACT
1 AAATAAATAATACTAATAAATACT
25543314 AAAT
1 AAAT
25543318 TTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATAATACTAATAAATACT
Found at i:25550255 original size:20 final size:21
Alignment explanation
Indices: 25550230--25550269 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25550220 AACCATTATA
25550230 ATAAA-TTACAACT-TCAACTT
1 ATAAATTTA-AACTATCAACTT
25550250 ATAAATTTAAACTATCAACT
1 ATAAATTTAAACTATCAACT
25550270 CAAAATAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATTTAAACTATCAACTT
Found at i:25558205 original size:26 final size:26
Alignment explanation
Indices: 25558176--25558237 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
25558166 CAAAGATCCT
*
25558176 TTGAGTTTGACTGGGTCTGAGGACT-C
1 TTGAGTTTGACTGGGTCGGAGG-CTCC
* * *
25558202 TTGAGTTTGAGTTGGTCGGAGGTTCC
1 TTGAGTTTGACTGGGTCGGAGGCTCC
25558228 TTGAGTTTGA
1 TTGAGTTTGA
25558238 ATGGATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.15, C:0.11, G:0.35, T:0.39
Consensus pattern (26 bp):
TTGAGTTTGACTGGGTCGGAGGCTCC
Found at i:25563188 original size:43 final size:43
Alignment explanation
Indices: 25563117--25563232 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
25563107 TATGTGTTAT
* * *
25563117 CATGTAAGACCACA-TCTGGTACGTTGGCATCGACT-TGCGTTTA
1 CATGTAAGACCA-AGTCTGGGACGTTGGCATCGA-TATGAGATTA
* **
25563160 CGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATATGAGATTA
1 CATGTAAGACCAAGTCTGGGAC-GTTGGCATCGATATGAGATTA
25563203 CATGTAAGACCAAGTCTGGGACGTTGGCAT
1 CATGTAAGACCAAGTCTGGGACGTTGGCAT
25563233 TGTACTAGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.03
43 57 0.95
44 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCAAGTCTGGGACGTTGGCATCGATATGAGATTA
Found at i:25564278 original size:47 final size:47
Alignment explanation
Indices: 25564225--25564315 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
25564215 GAATAGGTGG
*
25564225 TGCTTAAACGCTGCCCAATTTGATGCATATATGCTGTCCAATTTTGA
1 TGCTTAAACGCTGCCCAATTTGATGCATATATGCTGCCCAATTTTGA
* * * * * *
25564272 TGCTTAAATGTTGTCCAATTTGTTGTATATATGTTGCCCAATTT
1 TGCTTAAACGCTGCCCAATTTGATGCATATATGCTGCCCAATTT
25564316 GTTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (47 bp):
TGCTTAAACGCTGCCCAATTTGATGCATATATGCTGCCCAATTTTGA
Found at i:25564286 original size:24 final size:24
Alignment explanation
Indices: 25564225--25564292 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
25564215 GAATAGGTGG
* *
25564225 TGCTTAAACGCTGCCCAA-TTTGA
1 TGCTTAAATGCTGTCCAATTTTGA
* *
25564248 TGCATATATGCTGTCCAATTTTGA
1 TGCTTAAATGCTGTCCAATTTTGA
*
25564272 TGCTTAAATGTTGTCCAATTT
1 TGCTTAAATGCTGTCCAATTT
25564293 GTTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 14 0.38
24 23 0.62
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (24 bp):
TGCTTAAATGCTGTCCAATTTTGA
Found at i:25564325 original size:70 final size:69
Alignment explanation
Indices: 25564234--25564497 Score: 314
Period size: 70 Copynumber: 3.8 Consensus size: 69
25564224 GTGCTTAAAC
* * * * * *
25564234 GCTGCCCAATTTGATGCATATATGCTGTCCAATTTTGATGCTTAAATGTTGTCCAATTTGTTGTA
1 GCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGGTG-TAAAATGTTGTCCAAATTGTTGTA
25564299 TATAT
65 TATAT
* * *
25564304 GTTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGGTGTAAAAATGTTGTTCAAATTGTTGTA
1 GCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGGTGT-AAAATGTTGTCCAAATTGTTGTA
25564369 TATAT
65 TATAT
* * * * *
25564374 GCTGCCTAAATTGTTGAATTTATGCTGTCCAATTTTGGTATAACAATGCTG-CTCAAATTGTTGT
1 GCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGGTGTAA-AATGTTGTC-CAAATTGTTGT
25564438 ATATAT
64 ATATAT
* * *
25564444 GCTGCCCAAATTGTTGTATTTATGCTGCCCAAATTTTGGTGTGAAAATGCTGTC
1 GCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGGTGT-AAAATGTTGTC
25564498 TAATTTGGTA
Statistics
Matches: 169, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
69 3 0.02
70 146 0.86
71 17 0.10
72 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (69 bp):
GCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGGTGTAAAATGTTGTCCAAATTGTTGTAT
ATAT
Found at i:25564353 original size:47 final size:46
Alignment explanation
Indices: 25564283--25564377 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 46
25564273 GCTTAAATGT
* * * *
25564283 TGTCCAATTTGTTGTATATATGTTGCCCAATTTGTTGTATATATGC
1 TGTCCAATTTGGTGTAAAAATGTTGCCCAAATTGTTGTATATATGC
**
25564329 TGTCCAATTTTGGTGTAAAAATGTTGTTCAAATTGTTGTATATATGC
1 TGTCCAA-TTTGGTGTAAAAATGTTGCCCAAATTGTTGTATATATGC
25564376 TG
1 TG
25564378 CCTAAATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 7 0.17
47 35 0.83
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (46 bp):
TGTCCAATTTGGTGTAAAAATGTTGCCCAAATTGTTGTATATATGC
Found at i:25564368 original size:23 final size:23
Alignment explanation
Indices: 25564239--25564523 Score: 121
Period size: 23 Copynumber: 12.2 Consensus size: 23
25564229 TAAACGCTGC
* * * *
25564239 CCAATTTGATGCATATATGCTGT
1 CCAATTTGTTGTATAAATGTTGT
*
25564262 CCAATTTTGATGCT-TAAATGTTGT
1 CCAA-TTTGTTG-TATAAATGTTGT
* *
25564286 CCAATTTGTTGTATATATGTTGC
1 CCAATTTGTTGTATAAATGTTGT
* *
25564309 CCAATTTGTTGTATATATGCTGT
1 CCAATTTGTTGTATAAATGTTGT
* *
25564332 CCAATTTTGGTGTAAAAATGTTGT
1 CCAA-TTTGTTGTATAAATGTTGT
* * * *
25564356 TCAAATTGTTGTATATATGCTG-
1 CCAATTTGTTGTATAAATGTTGT
* * ** *
25564378 CCTAAATTGTTGAATTTATGCTGT
1 CC-AATTTGTTGTATAAATGTTGT
* *
25564402 CCAATTT-TGGTATAACAATGCTG-
1 CCAATTTGTTGTAT-A-AATGTTGT
* * * *
25564425 CTCAAATTGTTGTATATATGCTGC
1 C-CAATTTGTTGTATAAATGTTGT
* ** * *
25564449 CCAAATTGTTGTATTTATGCTGC
1 CCAATTTGTTGTATAAATGTTGT
* *
25564472 CCAAATTTTGGTGTGA-AAATGCTGT
1 CC-AA-TTTGTTGT-ATAAATGTTGT
* * *
25564497 CTAATTTGGTATATAAATGTTGT
1 CCAATTTGTTGTATAAATGTTGT
25564520 CCAA
1 CCAA
25564524 AAAGAGTAGA
Statistics
Matches: 208, Mismatches: 39, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
22 7 0.03
23 126 0.61
24 56 0.27
25 18 0.09
26 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (23 bp):
CCAATTTGTTGTATAAATGTTGT
Found at i:25564780 original size:9 final size:10
Alignment explanation
Indices: 25564760--25564784 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25564750 GAGTTAGTAT
25564760 AATTTAAAAA
1 AATTTAAAAA
25564770 AATTTAAAAA
1 AATTTAAAAA
25564780 AATTT
1 AATTT
25564785 CTAAGTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:25567553 original size:25 final size:25
Alignment explanation
Indices: 25567525--25567578 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
25567515 TTGTATGAGG
* * *
25567525 TTCCCGATATTTGGCTCGCAAGAGC
1 TTCCCGATATCTAGCTCACAAGAGC
* *
25567550 TTCCCGTTATCTAGCTCACATGAGC
1 TTCCCGATATCTAGCTCACAAGAGC
25567575 TTCC
1 TTCC
25567579 AGTTATATAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (25 bp):
TTCCCGATATCTAGCTCACAAGAGC
Found at i:25567599 original size:25 final size:24
Alignment explanation
Indices: 25567545--25567591 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
25567535 TTGGCTCGCA
* *
25567545 AGAGCTTCCCGTTATCTAGCTCAC
1 AGAGCTTCCAGTTATATAGCTCAC
25567569 ATGAGCTTCCAGTTATATAGCTC
1 A-GAGCTTCCAGTTATATAGCTC
25567592 GGGAGAGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (24 bp):
AGAGCTTCCAGTTATATAGCTCAC
Found at i:25576223 original size:28 final size:27
Alignment explanation
Indices: 25576174--25576238 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
25576164 ATTGGATTAA
*
25576174 AATTAAAATTAAAATTTATTATAAAATT
1 AATTAAAATTAAAATGTATTAT-AAATT
* *
25576202 AATTAAAATTCAACATGT-TTATAATTT
1 AATTAAAATT-AAAATGTATTATAAATT
*
25576229 AAGTAAAATT
1 AATTAAAATT
25576239 TAATTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 13 0.41
28 14 0.44
29 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (27 bp):
AATTAAAATTAAAATGTATTATAAATT
Found at i:25576278 original size:21 final size:19
Alignment explanation
Indices: 25576233--25576279 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
25576223 TAATTTAAGT
25576233 AAAATTTAATTATTTTATA
1 AAAATTTAATTATTTTATA
*
25576252 ATAATTATATATT-TTTTGATA
1 AAAATT-TA-ATTATTTT-ATA
25576273 AAAATTT
1 AAAATTT
25576280 TACCGAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AAAATTTAATTATTTTATA
Found at i:25578796 original size:23 final size:21
Alignment explanation
Indices: 25578745--25578797 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
25578735 TTATTTTTAG
25578745 AAATT-AAAAATATGTTTCAT
1 AAATTAAAAAATATGTTTCAT
* *
25578765 AAATAAAAAAATTTGTTTTCAAT
1 AAATTAAAAAATATG-TTTC-AT
25578788 AAATTAAAAA
1 AAATTAAAAA
25578798 TGAAAATACG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 8 0.30
22 4 0.15
23 11 0.41
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATTAAAAAATATGTTTCAT
Found at i:25583469 original size:24 final size:24
Alignment explanation
Indices: 25583442--25583503 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
25583432 TCTCTCTCCT
25583442 AAAAACGGCCTATTTCCCTAATTA
1 AAAAACGGCCTATTTCCCTAATTA
* ****
25583466 AAAAATGGCCTAAAGGCCTAATTA
1 AAAAACGGCCTATTTCCCTAATTA
25583490 AAAAACGGCC-ATTT
1 AAAAACGGCCTATTT
25583504 TTTATTAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (24 bp):
AAAAACGGCCTATTTCCCTAATTA
Found at i:25585350 original size:18 final size:18
Alignment explanation
Indices: 25585327--25585458 Score: 77
Period size: 18 Copynumber: 7.8 Consensus size: 18
25585317 TTATTATTAA
25585327 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
25585345 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
* *
25585362 ATGTGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * *
25585380 -TATAATAT-ATAATATT
1 ATATAATTTAATAAAAAT
* * *
25585396 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
25585415 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
*
25585427 ATATAATTTAACAAAAAT
1 ATATAATTTAATAAAAAT
25585445 ATATAATTTAATAA
1 ATATAATTTAATAA
25585459 TATTCTTAGT
Statistics
Matches: 84, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 3 0.04
16 8 0.10
17 20 0.24
18 40 0.48
19 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:25585398 original size:15 final size:15
Alignment explanation
Indices: 25585378--25585433 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
25585368 ATTTACTAAA
*
25585378 ATTATAATATATAAT
1 ATTATAAAATATAAT
25585393 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
25585406 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
25585419 ATTATTAAATATAAT
1 ATTATAAAATATAAT
25585434 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:25585428 original size:26 final size:25
Alignment explanation
Indices: 25585388--25585450 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
25585378 ATTATAATAT
25585388 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
25585413 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATAAAATATAATTTAA-A
*
25585440 AAAATA-TATAA
1 ATAATATTATAA
25585451 TTTAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.24
26 21 0.64
27 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:25585505 original size:120 final size:120
Alignment explanation
Indices: 25585365--25585603 Score: 451
Period size: 120 Copynumber: 2.0 Consensus size: 120
25585355 ATAAAATATG
* *
25585365 TGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTAAATA
1 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATA
*
25585430 TAATTTAACAAAAATATATAATTTAATAATATTCTTAGTATTAAATATTCTTATA
66 TAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTATA
25585485 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATA
1 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATA
25585550 TAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTAT
66 TAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTAT
25585604 GATTGTATCA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATA
TAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTATA
Found at i:25588930 original size:13 final size:13
Alignment explanation
Indices: 25588912--25588938 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25588902 GTATTAGATC
25588912 CGTAATAGATACA
1 CGTAATAGATACA
25588925 CGTAATAGATACA
1 CGTAATAGATACA
25588938 C
1 C
25588939 TGAACCAAAC
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:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (13 bp):
CGTAATAGATACA
Found at i:25595215 original size:3 final size:3
Alignment explanation
Indices: 25595207--25595238 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
25595197 ACATCAAATA
25595207 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25595239 GTGTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:25595865 original size:17 final size:18
Alignment explanation
Indices: 25595843--25595878 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
25595833 ATATATAAAT
*
25595843 TTAATAATAAAA-AATAG
1 TTAATAAAAAAACAATAG
25595860 TTAATAAAAAAACAATAG
1 TTAATAAAAAAACAATAG
25595878 T
1 T
25595879 GAGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
TTAATAAAAAAACAATAG
Found at i:25596077 original size:15 final size:17
Alignment explanation
Indices: 25596056--25596099 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
25596046 ATTTAAATTT
*
25596056 TAAAATTATT-TTTAAA
1 TAAAATTATTATTCAAA
25596072 -AAAATTATTATTCAAA
1 TAAAATTATTATTCAAA
25596088 TAAAATT-TTATT
1 TAAAATTATTATT
25596100 ATATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 10 0.40
17 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTATTATTCAAA
Found at i:25596192 original size:17 final size:18
Alignment explanation
Indices: 25596165--25596199 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
25596155 ATATTTCGTA
25596165 TTTTAATATTTTAAATTT
1 TTTTAATATTTTAAATTT
25596183 TTTTAA-ATTTTAAATTT
1 TTTTAATATTTTAAATTT
25596200 AAATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATATTTTAAATTT
Found at i:25596211 original size:23 final size:25
Alignment explanation
Indices: 25596164--25596211 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
25596154 AATATTTCGT
*
25596164 ATTTTAATATTTTAAATTTTTTTAA
1 ATTTTAATATTTTAAATTTTATTAA
25596189 ATTTTAA-A-TTTAAATTTTATTAA
1 ATTTTAATATTTTAAATTTTATTAA
25596212 TAATACAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
24 1 0.05
25 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTAATATTTTAAATTTTATTAA
Found at i:25606492 original size:32 final size:32
Alignment explanation
Indices: 25605580--25606469 Score: 1084
Period size: 32 Copynumber: 27.8 Consensus size: 32
25605570 ATATTTCATG
*
25605580 TATTGCTGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* ***
25605612 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25605644 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25605676 TATTGCCGAATTGAATTGTATAGGTATAC-AA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*** *
25605707 CTATTTTTGAATTGAATTGTATATGTATACTTG
1 -TATTGCCGAATTGAATTGTATATGTATACTTA
* * * ****
25605740 TATTGTCGAATTGAATTGCATAGGTATAAACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
25605772 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25605804 TATTGCCGAATTGAATTGTATACGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ***
25605836 TATTCCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ***
25605868 TATTGTCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25605900 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25605932 TATTGTCGAATTGAATTGTATATGTATAGTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ***
25605964 TATTTCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
25605996 TA-TGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25606027 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25606059 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * *
25606091 TATTACCAAATTGAGTTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* ***
25606123 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25606155 TATTGTCAAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
***
25606187 TATTTTTGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ****
25606219 TATTGCCAAATTGAATTGTATAGGTATAAACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
25606251 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25606283 TATTGCCGAATTGAATTGTATAGGTATAC-AA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
** *
25606314 CTATTTTCGAATTGAATTGTATATGTATACTTG
1 -TATTGCCGAATTGAATTGTATATGTATACTTA
* * ****
25606347 TATTGTCGAATTGAATTGTATAGGTATAAACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
25606379 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25606411 TATTGCCAAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * *
25606443 TGTTGTCGAATTGATTTGTATATGTAT
1 TATTGCCGAATTGAATTGTATATGTAT
25606470 TTATATATTG
Statistics
Matches: 734, Mismatches: 119, Indels: 10
0.85 0.14 0.01
Matches are distributed among these distances:
31 28 0.04
32 706 0.96
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATGTATACTTA
Found at i:25607560 original size:49 final size:49
Alignment explanation
Indices: 25607503--25607601 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
25607493 ACTTTTGAGT
25607503 TAGTTTGTGGACATGAAATGAGTGGTAAATGAATGGTTATAAAATAGTA
1 TAGTTTGTGGACATGAAATGAGTGGTAAATGAATGGTTATAAAATAGTA
25607552 TAGTTTGTGGACATGAAATGAGTGGTAAATGAATGGTTATAAAATAGTA
1 TAGTTTGTGGACATGAAATGAGTGGTAAATGAATGGTTATAAAATAGTA
25607601 T
1 T
25607602 GAAATGTGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (49 bp):
TAGTTTGTGGACATGAAATGAGTGGTAAATGAATGGTTATAAAATAGTA
Found at i:25613728 original size:32 final size:32
Alignment explanation
Indices: 25613683--25614221 Score: 654
Period size: 32 Copynumber: 16.8 Consensus size: 32
25613673 ATATTTTATG
*
25613683 TATTGCTGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
***
25613715 TATAT-CCGAATTGAATTGTATA-GATATACACC
1 TAT-TGCCGAATTGAATTGTATATG-TATACTTA
* *
25613747 TATTGTCGAATTGAATTGTATATGCATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25613779 TATTGCCGAATTGAATTTTATATTTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * * *
25613811 TATTGTCTAATTGAATTGTATAGGTATGCACCTA
1 TATTGCCGAATTGAATTGTATATGTAT--ACTTA
*
25613845 T-TT-CTGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25613875 TATTGTCGAATTAAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ***
25613907 TATTGCTGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25613939 TATTGTCGAATTGAATTGTATATGTATATTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25613971 TATTGCCGAATTGAATTGTATATGTGTACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * ****
25614003 TATTGTCGAATTGAATTGTATAGGTATAAACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
25614035 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
25614067 TATTGTCGAATTGAGTTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* ***
25614099 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25614131 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
25614163 TATTGCCAAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * *
25614195 TGTTGTCGAATTGATTTGTATATGTAT
1 TATTGCCGAATTGAATTGTATATGTAT
25614222 TTATATATTT
Statistics
Matches: 423, Mismatches: 76, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
30 5 0.01
31 4 0.01
32 405 0.96
33 4 0.01
34 5 0.01
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATGTATACTTA
Found at i:25613790 original size:96 final size:96
Alignment explanation
Indices: 25613683--25614221 Score: 839
Period size: 96 Copynumber: 5.6 Consensus size: 96
25613673 ATATTTTATG
* *
25613683 TATTGCTGAATTGAATTGTATATGTATACTTATATAT-CCGAATTGAATTGTATAGATATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTATAT-TGCCGAATTGAATTGTATAGGTATACACC
*
25613747 TATTGTCGAATTGAATTGTATATGCATACTTA
65 TATTGTCGAATTGAATTGTATATGTATACTTA
* * * * *
25613779 TATTGCCGAATTGAATTTTATATTTATACTTATATTGTCTAATTGAATTGTATAGGTATGCACCT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
25613844 ATT-TCTGAATTGAATTGTATATGTATACTTA
66 ATTGTC-GAATTGAATTGTATATGTATACTTA
* * *
25613875 TATTGTCGAATTAAATTGTATATGTATACTTATATTGCTGAATTGAATTGTATAGGTATACACCT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
*
25613940 ATTGTCGAATTGAATTGTATATGTATATTTA
66 ATTGTCGAATTGAATTGTATATGTATACTTA
* * *
25613971 TATTGCCGAATTGAATTGTATATGTGTACTTATATTGTCGAATTGAATTGTATAGGTATAAACCT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
*
25614036 ATTGCCGAATTGAATTGTATATGTATACTTA
66 ATTGTCGAATTGAATTGTATATGTATACTTA
* *
25614067 TATTGTCGAATTGAGTTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
25614132 ATTGTCGAATTGAATTGTATATGTATACTTA
66 ATTGTCGAATTGAATTGTATATGTATACTTA
* * * * *
25614163 TATTGCCAAATTGAATTGTATATGTATACTTATGTTGTCGAATTGATTTGTATATGTAT
1 TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTAT
25614222 TTATATATTT
Statistics
Matches: 402, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
95 3 0.01
96 397 0.99
97 2 0.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (96 bp):
TATTGCCGAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCT
ATTGTCGAATTGAATTGTATATGTATACTTA
Found at i:25614230 original size:64 final size:64
Alignment explanation
Indices: 25613690--25614221 Score: 721
Period size: 64 Copynumber: 8.3 Consensus size: 64
25613680 ATGTATTGCT
***
25613690 GAATTGAATTGTATATGTATACTTATATAT-CCGAATTGAATTGTATA-GATATACACCTATTGT
1 GAATTGAATTGTATATGTATACTTATAT-TGCCGAATTGAATTGTATATG-TATACTTATATTGT
25613753 C
64 C
* * *
25613754 GAATTGAATTGTATATGCATACTTATATTGCCGAATTGAATTTTATATTTATACTTATATTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
* * * *
25613818 TAATTGAATTGTATAGGTATGCACCTAT-TT-CTGAATTGAATTGTATATGTATACTTATATTGT
1 GAATTGAATTGTATATGTAT--ACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGT
25613881 C
64 C
* * * ***
25613882 GAATTAAATTGTATATGTATACTTATATTGCTGAATTGAATTGTATAGGTATACACCTATTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
* *
25613946 GAATTGAATTGTATATGTATATTTATATTGCCGAATTGAATTGTATATGTGTACTTATATTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
* ****
25614010 GAATTGAATTGTATAGGTATAAACCTATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
* * ***
25614074 GAATTGAGTTGTATATGTATACTTATATTGCCGAATTGAATTGTATAGGTATACACCTATTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
* *
25614138 GAATTGAATTGTATATGTATACTTATATTGCCAAATTGAATTGTATATGTATACTTATGTTGTC
1 GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
*
25614202 GAATTGATTTGTATATGTAT
1 GAATTGAATTGTATATGTAT
25614222 TTATATATTT
Statistics
Matches: 409, Mismatches: 53, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
62 5 0.01
63 3 0.01
64 394 0.96
65 2 0.00
66 5 0.01
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (64 bp):
GAATTGAATTGTATATGTATACTTATATTGCCGAATTGAATTGTATATGTATACTTATATTGTC
Found at i:25633014 original size:17 final size:18
Alignment explanation
Indices: 25632989--25633032 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
25632979 TTATAAAATA
* *
25632989 ATTTTATTTTT-ATTTTT
1 ATTTAATTTTTCATTCTT
25633006 ATTTAATTTTTCATTCTT
1 ATTTAATTTTTCATTCTT
25633024 -TTTAATTTT
1 ATTTAATTTT
25633033 GAAGTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTAATTTTTCATTCTT
Found at i:25633189 original size:10 final size:9
Alignment explanation
Indices: 25633170--25633205 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
25633160 TAAAATTATT
25633170 ATAATTTTA
1 ATAATTTTA
*
25633179 ATATCTTTTA
1 ATA-ATTTTA
25633189 ATAATTTTA
1 ATAATTTTA
25633198 ATAATTTT
1 ATAATTTT
25633206 TTAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
ATAATTTTA
Found at i:25633226 original size:20 final size:22
Alignment explanation
Indices: 25633193--25633233 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
25633183 CTTTTAATAA
*
25633193 TTTTAATAATTTTTTAAATTAT
1 TTTTAATAATTTTTAAAATTAT
25633215 TTTTAA-AA-TTTTAAAATTA
1 TTTTAATAATTTTTAAAATTA
25633234 ATTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAATAATTTTTAAAATTAT
Found at i:25634138 original size:14 final size:16
Alignment explanation
Indices: 25634119--25634150 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25634109 TCTGAGCCCA
25634119 TAAATA-TT-AAATAT
1 TAAATATTTAAAATAT
25634133 TAAATATTTAAAATAT
1 TAAATATTTAAAATAT
25634149 TA
1 TA
25634151 GTATTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATTTAAAATAT
Found at i:25635082 original size:22 final size:22
Alignment explanation
Indices: 25635057--25635104 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
25635047 AAGATTTGGT
*
25635057 AGTTTGTTGTTTTGACTAGGTA
1 AGTTTGTTATTTTGACTAGGTA
25635079 AGTTTGTTATTTTGACTAGGTA
1 AGTTTGTTATTTTGACTAGGTA
25635101 AGTT
1 AGTT
25635105 CATGTGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.50
Consensus pattern (22 bp):
AGTTTGTTATTTTGACTAGGTA
Found at i:25639715 original size:18 final size:18
Alignment explanation
Indices: 25639692--25639730 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25639682 GGTATTAAAA
*
25639692 AAACATAAAGAGGAACAT
1 AAACATAAAGAGAAACAT
25639710 AAACATAAAGAGAAACAT
1 AAACATAAAGAGAAACAT
25639728 AAA
1 AAA
25639731 ACCTAAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (18 bp):
AAACATAAAGAGAAACAT
Found at i:25640462 original size:25 final size:25
Alignment explanation
Indices: 25640434--25640481 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25640424 GGTCATGAGG
*
25640434 AGCTCGCAAAACACTGTTCATAATT
1 AGCTCACAAAACACTGTTCATAATT
* *
25640459 AGCTCACATATCACTGTTCATAA
1 AGCTCACAAAACACTGTTCATAA
25640482 AAACACATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (25 bp):
AGCTCACAAAACACTGTTCATAATT
Found at i:25641258 original size:23 final size:22
Alignment explanation
Indices: 25641200--25641258 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
25641190 AGGCCCACTA
25641200 GTGACCCCAACTTGTCAGACTG
1 GTGACCCCAACTTGTCAGACTG
*
25641222 GTGACCCCAACTTGTTAGACTG
1 GTGACCCCAACTTGTCAGACTG
*
25641244 GTGAACCCCAGCTTG
1 GTG-ACCCCAACTTG
25641259 CTATACCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (22 bp):
GTGACCCCAACTTGTCAGACTG
Found at i:25644366 original size:24 final size:24
Alignment explanation
Indices: 25644339--25644393 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
25644329 CCAAGCAGAA
25644339 TTTGTGCCAGTGTATTTATCAGGC
1 TTTGTGCCAGTGTATTTATCAGGC
* *
25644363 TTTGTG-CGGTGTGTTTATCAGGC
1 TTTGTGCCAGTGTATTTATCAGGC
25644386 TTTGTGCC
1 TTTGTGCC
25644394 TAGCAGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (24 bp):
TTTGTGCCAGTGTATTTATCAGGC
Found at i:25644629 original size:110 final size:109
Alignment explanation
Indices: 25644436--25644735 Score: 404
Period size: 110 Copynumber: 2.7 Consensus size: 109
25644426 TCTTGATTCG
*
25644436 GTGATACAGACCATAACGATGACTTAAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGTA
1 GTGATACAGACCATAACGATGACTTGAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGTA
*
25644501 AGTAGCATTATGAGCTGGGGATTAATTAGTAGGTACTATGCACTA
66 AGTAGCATCATGAGCTGGGGATTAATTAGTAGGTACTATGCAC-A
25644546 GTGATACAGACCATAACGATGACTTGAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGTG
1 GTGATACAGACCATAACGATGACTTGAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGT-
* * * *
25644611 AA-TATCATCATGTGCTGGGGATTAATTAGTAGGTACTATGTACC
65 AAGTAGCATCATGAGCTGGGGATTAATTAGTAGGTACTATGCACA
* ** * * * * ** *
25644655 GATGATACAAACTGTAACGATGGCTTGAGATCTTACATGTGTTGTGGATTCTCTACAGCTTGTGT
1 G-TGATACAGACCATAACGATGACTTGAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGT
* *
25644720 AAGCAGCATCGTGAGC
65 AAGTAGCATCATGAGC
25644736 CGGTCAAAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
109 3 0.02
110 162 0.97
111 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (109 bp):
GTGATACAGACCATAACGATGACTTGAGATCCTATATATGTTGCAGATTCTCTGCAGCTTGTGTA
AGTAGCATCATGAGCTGGGGATTAATTAGTAGGTACTATGCACA
Done.