Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 92 of 153
Found at i:29021741 original size:40 final size:40
Alignment explanation
Indices: 29021697--29021778 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
29021687 TTATAATGTT
* *
29021697 TATGAAAAATAATATAGGTAATGGTTATATAAATCGGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
* * *
29021737 TATGAAAAATAATATATGAAATTGTTATATGAATCAGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
29021777 TA
1 TA
29021779 CGGAAAGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (40 bp):
TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
Found at i:29021792 original size:27 final size:27
Alignment explanation
Indices: 29021762--29021828 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
29021752 ATGAAATTGT
29021762 TATATGAATCAG-TTATACGGAAAGAGA
1 TATATGAAT-AGATTATACGGAAAGAGA
* * *
29021789 TATATGAATTGATTATATGGAAATAGA
1 TATATGAATAGATTATACGGAAAGAGA
29021816 TATATGAAATAGA
1 TATATG-AATAGA
29021829 ACATCAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.03
27 28 0.82
28 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.31
Consensus pattern (27 bp):
TATATGAATAGATTATACGGAAAGAGA
Found at i:29021824 original size:13 final size:13
Alignment explanation
Indices: 29021743--29021828 Score: 61
Period size: 13 Copynumber: 6.5 Consensus size: 13
29021733 GTTATATGAA
29021743 AAATA-ATATATG
1 AAATAGATATATG
* *
29021755 AAATTGTTATATG
1 AAATAGATATATG
* *
29021768 -AATCAGTTATACGG
1 AAAT-AGATATA-TG
*
29021782 AAAGAGATATATG
1 AAATAGATATATG
*
29021795 -AATTGATTATATGG
1 AAATAGA-TATAT-G
29021809 AAATAGATATATG
1 AAATAGATATATG
29021822 AAATAGA
1 AAATAGA
29021829 ACATCAGATA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
12 11 0.19
13 26 0.46
14 13 0.23
15 7 0.12
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (13 bp):
AAATAGATATATG
Found at i:29038489 original size:51 final size:51
Alignment explanation
Indices: 29038413--29038516 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
29038403 CTGAATATTG
*
29038413 TAGAGTTATACTCACAGTTTAAAAAAAATTACATCTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
29038464 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
29038515 TA
1 TA
29038517 TAACGAGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (51 bp):
TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
Found at i:29039656 original size:23 final size:24
Alignment explanation
Indices: 29039612--29039667 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
29039602 CATATTTTTT
* *
29039612 AAAAAAGAATCGAAAAGGAAAA-G
1 AAAAAAGAATCCAAAAGAAAAAGG
**
29039635 AAAAAAGAATCCAATCGAAAAAGG
1 AAAAAAGAATCCAAAAGAAAAAGG
29039659 AAAAAAGAA
1 AAAAAAGAA
29039668 AACCTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAAAAGAATCCAAAAGAAAAAGG
Found at i:29040523 original size:15 final size:16
Alignment explanation
Indices: 29040505--29040537 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29040495 TGGTAAGCAA
29040505 TGAAATG-AATTAAGT
1 TGAAATGTAATTAAGT
29040520 TGAAATGTTAATTAAGT
1 TGAAATG-TAATTAAGT
29040537 T
1 T
29040538 AAGGGTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (16 bp):
TGAAATGTAATTAAGT
Found at i:29040948 original size:40 final size:40
Alignment explanation
Indices: 29040893--29040996 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
29040883 GATAAATATG
* *
29040893 TATATGAAAAATGATATAGGTAGTCGTTATATGAATCAGT
1 TATATGAAAAATGATATAGGAAATCGTTATATGAATCAGT
* *
29040933 TATATGAAAAATGATATATGAAATGGTTATATGAATCAGT
1 TATATGAAAAATGATATAGGAAATCGTTATATGAATCAGT
* * *
29040973 TTTATG-GAAATAGATATATGAAAT
1 TATATGAAAAAT-GATATAGGAAAT
29040997 AAAACATTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.07
40 53 0.93
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (40 bp):
TATATGAAAAATGATATAGGAAATCGTTATATGAATCAGT
Found at i:29040995 original size:13 final size:13
Alignment explanation
Indices: 29040918--29040997 Score: 65
Period size: 13 Copynumber: 6.0 Consensus size: 13
29040908 ATAGGTAGTC
29040918 GTTATATG-AATCA
1 GTTATATGAAAT-A
*
29040931 GTTATATGAAAAA
1 GTTATATGAAATA
* *
29040944 TGATATATGAAATG
1 -GTTATATGAAATA
29040958 GTTATATG-AATCA
1 GTTATATGAAAT-A
*
29040971 GTTTTATGGAAATA
1 GTTATAT-GAAATA
*
29040985 GATATATGAAATA
1 GTTATATGAAATA
29040998 AAACATTAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
12 3 0.06
13 28 0.53
14 19 0.36
15 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (13 bp):
GTTATATGAAATA
Found at i:29041172 original size:40 final size:40
Alignment explanation
Indices: 29041092--29041173 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
29041082 TTGTAATGTT
* *
29041092 TATGAAAAATAATATAGGTAATGGTTAAATAAATCGGTTA
1 TATGAAAAATAATATAGGAAATGGTTAAATAAATCAGTTA
* * * *
29041132 TATGAAAAATAATATATGAAATTGTTATATGAATCAGTTA
1 TATGAAAAATAATATAGGAAATGGTTAAATAAATCAGTTA
29041172 TA
1 TA
29041174 CGGAAAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (40 bp):
TATGAAAAATAATATAGGAAATGGTTAAATAAATCAGTTA
Found at i:29042490 original size:50 final size:50
Alignment explanation
Indices: 29041436--29042491 Score: 308
Period size: 50 Copynumber: 21.1 Consensus size: 50
29041426 TCGGGGAAGC
* * * * *
29041436 AAGAATCACCGATGTGGTTTTAATCTGTTCCACCGCACCGCCAAGGAAAT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041486 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * ** * *
29041536 AAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCACCGA-TGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041586 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * ** * *
29041636 AAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCACCGA-TGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041686 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * ** * *
29041736 AAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCACCGA-TGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041786 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * ** * *
29041836 AAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCACCGA-TGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041886 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * ** * *
29041936 AAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCACCGA-TGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29041986 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * * * * *
29042036 AAGATTCGCCGTTGTAGCGTTAATCTGTCCCACTGTACCGCCAGGGAAGT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
*** * * * ** * * **
29042086 AAGATTCGTTG-TGGTAGCTTTAATCTTTT-TATCTGTAATGTCGGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCA-CTGCACCGCCAGGGAAAT
* * * *
29042136 AATATTCACCGATGTGGCTTTAATCTGTTCCATTGCACCACCAGGGAAAT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
** * * ** ** * * **
29042186 AAGATTTGCTG-TGGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * *
29042236 AAGAATCACCGATGTGGTTTTAATCTGTTCCACCGCACCGCCAAGGAAAT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
* * * * ** ** * **
29042286 AAGATTCGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
*
29042336 AAGATTCACCGATGTGGCTTTAATCTATTCCACTGCACCGCCAGGGAAAT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
** * * * ** ** * **
29042386 AAGATTTGCTG-TGGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCACCGAT-GTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
*
29042436 AAGATTCACCGATGTGGCTTTAATCTATTCCACTGCACCGCCAGGGAAAT
1 AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
29042486 AAGATT
1 AAGATT
29042492 TGCTATTCTC
Statistics
Matches: 692, Mismatches: 282, Indels: 64
0.67 0.27 0.06
Matches are distributed among these distances:
49 11 0.02
50 670 0.97
51 11 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (50 bp):
AAGATTCACCGATGTGGCTTTAATCTTTTCCACTGCACCGCCAGGGAAAT
Found at i:29042495 original size:100 final size:100
Alignment explanation
Indices: 29041222--29042491 Score: 1724
Period size: 100 Copynumber: 12.7 Consensus size: 100
29041212 CTTGACTGTG
* * * * ** *
29041222 ATGTCGGGGAAGTAAGATTCACCGTTGTGGC-TTCCATCTGTTCCACTATAGCGCCTGGGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTT-AATCTGTTCCACTGCACCGCCTGGGAAGTA
* *
29041286 AGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * * * ** * * * *
29041322 TTGTCGGGGAAGCAAGATTCACCGTTGTGGCATTAAAATAGTTTCACTGCACTGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCT-GTTCCACTGCACCGCCTGGGAAGTA
*
29041387 AGATTCGCTGTGGTAGCTTTAATCTTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * ** * ** *
29041423 ATGTCGGGGAAGCAAGAATCACCGATGTGGTTTTAATCTGTTCCACCGCACCGCCAAGGAAATAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
29041488 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
66 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * *
29041523 ATGTCAGGGAAGCAAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGA-TGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTA
29041587 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * *
29041623 ATGTCAGGGAAGCAAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGA-TGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTA
29041687 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * *
29041723 ATGTCAGGGAAGCAAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGA-TGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTA
29041787 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * *
29041823 ATGTCAGGGAAGCAAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGA-TGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTA
29041887 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * *
29041923 ATGTCAGGGAAGCAAGATTCGCC-ATTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTA
1 ATGTCAGGGAAGCAAGATTCACCGA-TGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTA
29041987 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
65 AGATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * * * * *
29042023 ATGTCAGGGAAGCAAGATTCGCCGTTGTAGCGTTAATCTGTCCCACTGTACCGCCAGGGAAGTAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
* * * *
29042088 GATTCGTTGTGGTAGCTTTAATCTTTTTATCTGTA
66 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * * * * * *
29042123 ATGTCGGGGAAGCAATATTCACCGATGTGGCTTTAATCTGTTCCATTGCACCACCAGGGAAATAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
* *
29042188 GATTTGCTGTGGTAGCTTTAATCTTTTTAACTGCA
66 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * ** * ** *
29042223 ATGTCGGGGAAGCAAGAATCACCGATGTGGTTTTAATCTGTTCCACCGCACCGCCAAGGAAATAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
29042288 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
66 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * * *
29042323 ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGCACCGCCAGGGAAATAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
*
29042388 GATTTGCTGTGGTAGCTTTAATATTTTTAACTGCA
66 GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
* * * *
29042423 ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGCACCGCCAGGGAAATAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
29042488 GATT
66 GATT
29042492 TGCTATTCTC
Statistics
Matches: 1084, Mismatches: 82, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
99 1 0.00
100 996 0.92
101 87 0.08
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (100 bp):
ATGTCAGGGAAGCAAGATTCACCGATGTGGCGTTAATCTGTTCCACTGCACCGCCTGGGAAGTAA
GATTCGCTGTGGTAGCTTTAATATTTTTAACTGCA
Found at i:29044033 original size:6 final size:6
Alignment explanation
Indices: 29044031--29044092 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
29044021 ACTTTTTCAT
* * * *
29044031 TTTTCA TTTTGA CTTTAA TTTTGA TTTTGA TTTT-- TTCTT-T TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT-TTGA TTTTGA
29044077 TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTT
29044093 TTTTAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 2 0.04
5 4 0.09
6 41 0.87
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:29044797 original size:7 final size:7
Alignment explanation
Indices: 29044778--29044817 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
29044768 TTGTCCTCTC
29044778 CATTTTT
1 CATTTTT
29044785 -ACTTTTT
1 CA-TTTTT
29044792 CATTTTT
1 CATTTTT
29044799 CATTTTT
1 CATTTTT
29044806 CATTTTT
1 CATTTTT
29044813 CATTT
1 CATTT
29044818 CCATTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 1 0.03
7 29 0.94
8 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:29044797 original size:14 final size:14
Alignment explanation
Indices: 29044778--29044850 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
29044768 TTGTCCTCTC
29044778 CATTTTTACTTTTT
1 CATTTTTACTTTTT
29044792 CATTTTT-CATTTTT
1 CATTTTTAC-TTTTT
* *
29044806 CATTTTT-CATTTC
1 CATTTTTACTTTTT
*
29044819 CATTTTGAC--TTT
1 CATTTTTACTTTTT
* *
29044831 GATTTTTATTTTTT
1 CATTTTTACTTTTT
29044845 C-TTTTT
1 CATTTTT
29044851 TTGATTTTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
12 8 0.17
13 15 0.32
14 24 0.51
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.70
Consensus pattern (14 bp):
CATTTTTACTTTTT
Found at i:29044871 original size:22 final size:22
Alignment explanation
Indices: 29044828--29044873 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29044818 CCATTTTGAC
* *
29044828 TTTGATTTTTATTTTTTCTTTT
1 TTTGATTTTGATTTTATCTTTT
29044850 TTTGATTTTGATTTTGAT-TTTT
1 TTTGATTTTGATTTT-ATCTTTT
29044872 TT
1 TT
29044874 AAAAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTGATTTTGATTTTATCTTTT
Found at i:29049985 original size:12 final size:12
Alignment explanation
Indices: 29049921--29049987 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
29049911 AAGTATAATC
29049921 AAAT-ATAATAA
1 AAATAATAATAA
* * *
29049932 TAATAACAATAT
1 AAATAATAATAA
* *
29049944 AAATAGTGATGAA
1 AAATAATAAT-AA
*
29049957 AAATAATAATAG
1 AAATAATAATAA
*
29049969 CAATAATAATAA
1 AAATAATAATAA
29049981 AAATAAT
1 AAATAAT
29049988 TAAATGATTA
Statistics
Matches: 40, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
11 3 0.08
12 28 0.70
13 9 0.22
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:29051885 original size:40 final size:40
Alignment explanation
Indices: 29051841--29051922 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
29051831 TTATAATGTT
* *
29051841 TATGAAAAATAATATAGGTAATGGTTATATAAATCGGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
* * *
29051881 TATGAAAAATAATATATGAAATTGTTATATGAATCAGTTA
1 TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
29051921 TA
1 TA
29051923 CGGAAAGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (40 bp):
TATGAAAAATAATATAGGAAATGGTTATATAAATCAGTTA
Found at i:29051936 original size:27 final size:27
Alignment explanation
Indices: 29051906--29051972 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
29051896 ATGAAATTGT
29051906 TATATGAATCAG-TTATACGGAAAGAGA
1 TATATGAAT-AGATTATACGGAAAGAGA
* * *
29051933 TATATGAATTGATTATATGGAAATAGA
1 TATATGAATAGATTATACGGAAAGAGA
29051960 TATATGAAATAGA
1 TATATG-AATAGA
29051973 ACATCAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.03
27 28 0.82
28 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.31
Consensus pattern (27 bp):
TATATGAATAGATTATACGGAAAGAGA
Found at i:29051968 original size:13 final size:13
Alignment explanation
Indices: 29051887--29051972 Score: 61
Period size: 13 Copynumber: 6.5 Consensus size: 13
29051877 GTTATATGAA
29051887 AAATA-ATATATG
1 AAATAGATATATG
* *
29051899 AAATTGTTATATG
1 AAATAGATATATG
* *
29051912 -AATCAGTTATACGG
1 AAAT-AGATATA-TG
*
29051926 AAAGAGATATATG
1 AAATAGATATATG
*
29051939 -AATTGATTATATGG
1 AAATAGA-TATAT-G
29051953 AAATAGATATATG
1 AAATAGATATATG
29051966 AAATAGA
1 AAATAGA
29051973 ACATCAGATA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
12 11 0.19
13 26 0.46
14 13 0.23
15 7 0.12
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (13 bp):
AAATAGATATATG
Found at i:29068633 original size:51 final size:51
Alignment explanation
Indices: 29068557--29068660 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
29068547 CTGAATATTG
*
29068557 TAGAGTTATACTCACAGTTTAAAAAAAATTACATCTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
29068608 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
29068659 TA
1 TA
29068661 TAACGAGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (51 bp):
TAGAGTTATACTCACAGTTTAAAAAAAATTACAACTTTAGGTGCATCCAAC
Found at i:29073250 original size:26 final size:26
Alignment explanation
Indices: 29073176--29073255 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 26
29073166 TTGTCAAAAA
* *
29073176 TATAACAA-ATATATATGTATATATAAAT
1 TATAA-AATATATATAAGTATATGT--AT
*
29073204 TATAAAATATATGTACA-TATATGTAT
1 TATAAAATATATATA-AGTATATGTAT
29073230 TATAAAATATATATAAGTATATGTAT
1 TATAAAATATATATAAGTATATGTAT
29073256 ATTTTAAGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 25 0.56
27 2 0.04
28 17 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (26 bp):
TATAAAATATATATAAGTATATGTAT
Found at i:29073258 original size:28 final size:28
Alignment explanation
Indices: 29073176--29073273 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
29073166 TTGTCAAAAA
* * *
29073176 TATAACAA-ATATATATGTATATATAAAT
1 TATAA-AATATATATAAGTATATGTATAT
*
29073204 TATAAAATATATGTACA-TATATG--TAT
1 TATAAAATATATATA-AGTATATGTATAT
29073230 TATAAAATATATATAAGTATATGTATAT
1 TATAAAATATATATAAGTATATGTATAT
* *
29073258 TTTAAGATAATATATA
1 TATAAAAT-ATATATA
29073274 CAAAAAAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
25 1 0.02
26 22 0.39
27 2 0.04
28 25 0.44
29 7 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (28 bp):
TATAAAATATATATAAGTATATGTATAT
Found at i:29073356 original size:58 final size:56
Alignment explanation
Indices: 29073279--29073387 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
29073269 ATATACAAAA
* * *
29073279 AAGAATATATGTATGTATATATATATAGGAGTTATAAAATGTAAAACACATATATTAT
1 AAGAATATATGTATATATATAT-TATA-AAGTTATAAAATATAAAACACATATATTAT
* *
29073337 AAGAAT-TCATGTATATATATATTTTAAAGTTATAGAATATAAAACACATAT
1 AAGAATAT-ATGTATATATATATTATAAAGTTATAAAATATAAAACACATAT
29073388 GTATGTATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 22 0.49
57 4 0.09
58 19 0.42
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (56 bp):
AAGAATATATGTATATATATATTATAAAGTTATAAAATATAAAACACATATATTAT
Found at i:29075132 original size:44 final size:44
Alignment explanation
Indices: 29075084--29075391 Score: 158
Period size: 44 Copynumber: 7.2 Consensus size: 44
29075074 GTTTTAATCC
* * *
29075084 GCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTTTGTTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
* * * *
29075128 GCTCCACTACTACTT-AGGGAGATAAGACTT-G-ATC---CGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTCTTTTG-TCT
* ** * * ** *
29075168 GCTCTACTGCAACTTCAAAGAGATAAGATTTGTGGT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGT-TTCTTTTGTCT
*
29075212 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
* ** * * * **
29075256 GCTCCACTACTGCTT-ACGGAGATAACACTT-G--AC--GCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTCTTTTG-TCT
* * * * * ** *
29075296 GCTCTACTGCAACTTAAGAGAGATAAGATTTGTGGT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGT-TTCTTTTGTCT
* *
29075340 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
29075384 GCTCCACT
1 GCTCCACT
29075392 ACTGCTTAGG
Statistics
Matches: 189, Mismatches: 55, Indels: 40
0.67 0.19 0.14
Matches are distributed among these distances:
39 2 0.01
40 32 0.17
41 22 0.12
42 2 0.01
43 25 0.13
44 106 0.56
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
Found at i:29075277 original size:128 final size:128
Alignment explanation
Indices: 29075074--29075501 Score: 698
Period size: 128 Copynumber: 3.3 Consensus size: 128
29075064 ATGATTCATC
*
29075074 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
* *
29075139 ACTTAGGGAGATAAGACTTGATCCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
66 GCTTAGGGAGATAACACTTGATCCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
*
29075202 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
*
29075267 GCTTACGGAGATAACACTTGA-CGCGATCTGCTCTACTGCAACTT-AAGAGAGATAAGATTTGTG
66 GCTTAGGGAGATAACACTTGATC-CGATCTGCTCTACTGCAACTTCAA-AGAGATAAGATTTGTG
29075330 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
* * * * *
29075395 GCTTAGGGATATAATACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTG
66 GCTTAGGGAGATAACACTTGATCCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
* * * *
29075458 GTTTTAATCTGCTCCACTACAACTTTAGAGAGATAGGATTGGTT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
29075502 CTTCCGCTCT
Statistics
Matches: 280, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
127 3 0.01
128 276 0.99
129 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (128 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
GCTTAGGGAGATAACACTTGATCCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
Found at i:29075488 original size:44 final size:44
Alignment explanation
Indices: 29075164--29075497 Score: 172
Period size: 44 Copynumber: 7.8 Consensus size: 44
29075154 ACTTGATCCG
* *
29075164 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTA
* * * * * *
29075208 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGT-TTCTTTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGT-TTTA
* * ** * * ** **
29075252 GTCTGCTCCACTACTGCTT-ACG-GAGATAACACTTGACG---CG
1 ATCTGCTCCACTGCAACTTCA-GAGAGATAAGATTTGTGGTTTTA
* *
29075292 ATCTGCTCTACTGCAACTTAAGAGAGATAAGATTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTA
* * * * * *
29075336 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGT-TTCTTTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGT-TTTA
* * * ** * * * *
29075380 GTTTGCTCCACTACTGCTT-AGGGATATAATACTTGATGCG-----
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG-TG-GTTTTA
* *
29075420 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTA
* * *
29075464 ATCTGCTCCACTACAACTTTAGAGAGATAGGATT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
29075498 GGTTCTTCCG
Statistics
Matches: 204, Mismatches: 68, Indels: 36
0.66 0.22 0.12
Matches are distributed among these distances:
39 1 0.00
40 29 0.14
41 25 0.12
43 23 0.11
44 126 0.62
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTA
Found at i:29075578 original size:45 final size:45
Alignment explanation
Indices: 29075513--29075694 Score: 265
Period size: 45 Copynumber: 4.0 Consensus size: 45
29075503 TTCCGCTCTG
* * * * * *
29075513 CTTCCCTGCCACTACAGGAAGGCAAAATTTACTATCTTCGACCTA
1 CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
*
29075558 CTTCGCTGCCAATACCGGAAGACAAGATCTACAATCTTCGACCTA
1 CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
* * *
29075603 CTTCGTTGCAAATACAGGAAGACAAGATCTACAATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
*
29075648 CTTCGCTGCCAATATAGGAAGACAAGATCTACAATCTTCGACCTA
1 CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
29075693 CT
1 CT
29075695 CCACTGATGT
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (45 bp):
CTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCGACCTA
Found at i:29076729 original size:16 final size:16
Alignment explanation
Indices: 29076708--29076741 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29076698 TTTTTCGTTC
29076708 TTCTTTTCT-TTTCTTT
1 TTCTTTT-TGTTTCTTT
29076724 TTCTTTTTGTTTCTTT
1 TTCTTTTTGTTTCTTT
29076740 TT
1 TT
29076742 TCAAGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTTGTTTCTTT
Found at i:29077199 original size:17 final size:17
Alignment explanation
Indices: 29077177--29077209 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29077167 CCGGTAGAGG
29077177 TTTTTTTATGTTTTTTA
1 TTTTTTTATGTTTTTTA
*
29077194 TTTTTTTTTGTTTTTT
1 TTTTTTTATGTTTTTT
29077210 TTTGCCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (17 bp):
TTTTTTTATGTTTTTTA
Found at i:29081297 original size:26 final size:26
Alignment explanation
Indices: 29081264--29081327 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
29081254 AAAAATATAA
** *
29081264 AAAATATATATGTATTTATAAATTAT
1 AAAATATATATACATATATAAATTAT
* **
29081290 AAAATATATGTACATATATGTATTAT
1 AAAATATATATACATATATAAATTAT
29081316 AAAATATATATA
1 AAAATATATATA
29081328 TATAAGTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAATATATATACATATATAAATTAT
Found at i:29081330 original size:24 final size:25
Alignment explanation
Indices: 29081285--29081336 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
29081275 GTATTTATAA
*
29081285 ATTATAAAATATATGTACATATATGT
1 ATTATAAAATATA-GTACATATAAGT
*
29081311 ATTATAAAATATA-TATATATAAGT
1 ATTATAAAATATAGTACATATAAGT
29081335 AT
1 AT
29081337 ACGTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
ATTATAAAATATAGTACATATAAGT
Found at i:29089111 original size:11 final size:11
Alignment explanation
Indices: 29089095--29089119 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29089085 TACATTTCAT
29089095 AAATTATAATA
1 AAATTATAATA
29089106 AAATTATAATA
1 AAATTATAATA
29089117 AAA
1 AAA
29089120 GCGTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATAATA
Found at i:29092277 original size:20 final size:20
Alignment explanation
Indices: 29092252--29092305 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29092242 AAATCAAATG
29092252 AAAATGATTTTAACCAA-TT
1 AAAATGATTTTAACCAAGTT
* *
29092271 CAAAATGATTTCAATCAAGTT
1 -AAAATGATTTTAACCAAGTT
*
29092292 AAAATTATTTTAAC
1 AAAATGATTTTAAC
29092306 ACATCAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGTT
Found at i:29092302 original size:40 final size:40
Alignment explanation
Indices: 29092243--29092337 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
29092233 ATAATTTTAA
* * *
29092243 AATCAAATGAAAATGATTTTAAC-CAATTCAAAATGA-TTTC
1 AATCAAGTTAAAATTATTTTAACAC-A-TCAAAATGATTTTC
*
29092283 AATCAAGTTAAAATTATTTTAACACATCAAAATTATTTTC
1 AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
* *
29092323 AAACAAGTTAGAATT
1 AATCAAGTTAAAATT
29092338 GCTCCAGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.17
40 38 0.81
41 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (40 bp):
AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
Found at i:29092337 original size:21 final size:21
Alignment explanation
Indices: 29092279--29092337 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
29092269 TTCAAAATGA
*
29092279 TTTCAATCAAGTTAAAATTAT
1 TTTCAAACAAGTTAAAATTAT
*
29092300 TTT--AACACA-TCAAAATTAT
1 TTTCAAACA-AGTTAAAATTAT
*
29092319 TTTCAAACAAGTTAGAATT
1 TTTCAAACAAGTTAAAATT
29092338 GCTCCAGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
19 15 0.50
20 2 0.07
21 13 0.43
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (21 bp):
TTTCAAACAAGTTAAAATTAT
Found at i:29098877 original size:16 final size:16
Alignment explanation
Indices: 29098856--29098907 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
29098846 TTTGGTTCGC
29098856 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29098872 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
29098888 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
29098904 TGTA
1 TGTA
29098908 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29098954 original size:45 final size:44
Alignment explanation
Indices: 29098888--29098982 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
29098878 GGATTAGAGG
* * *
29098888 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
29098933 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
29098977 TGTAAT
1 TGTAAT
29098983 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:29099165 original size:18 final size:17
Alignment explanation
Indices: 29099144--29099178 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29099134 TTATTATTTA
*
29099144 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29099162 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29099179 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29099172 original size:28 final size:27
Alignment explanation
Indices: 29099102--29099174 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
29099092 TTTATTATCA
*
29099102 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
29099130 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
29099157 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
29099175 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:29099312 original size:18 final size:17
Alignment explanation
Indices: 29099291--29099325 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29099281 TTATTATTAA
*
29099291 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29099309 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29099326 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29099337 original size:147 final size:149
Alignment explanation
Indices: 29099063--29099337 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
29099053 ATGATTATTG
*
29099063 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
29099128 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
29099193 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
29099212 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
29099275 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
29099338 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:29108038 original size:30 final size:31
Alignment explanation
Indices: 29108004--29108063 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29107994 AAACCTTTTA
*
29108004 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
29108034 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
29108064 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:29108489 original size:5 final size:5
Alignment explanation
Indices: 29108479--29108504 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29108469 GAACAAATAT
29108479 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
29108505 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:29109919 original size:17 final size:18
Alignment explanation
Indices: 29109897--29109938 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
29109887 GTTCAAGGTG
29109897 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
29109914 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
29109932 TAATTAA
1 TAATTAA
29109939 AAACATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:29109934 original size:14 final size:14
Alignment explanation
Indices: 29109897--29109939 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
29109887 GTTCAAGGTG
29109897 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
29109914 TAATTAATTAAATT
1 TAATTAATTAAATT
*
29109928 TATTTAATTAAA
1 TAATTAATTAAA
29109940 AACATATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:29110135 original size:31 final size:29
Alignment explanation
Indices: 29110071--29110139 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
29110061 ATAATAACGT
** *
29110071 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATGGCAAACAA
*
29110100 AAGTGACTAAAATGTAATATGAGGCAAACAA
1 AAGTGACTAAAACGTAATAT--GGCAAACAA
29110131 AAGTGACTA
1 AAGTGACTA
29110140 TTTTTATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATGGCAAACAA
Found at i:29121411 original size:40 final size:40
Alignment explanation
Indices: 29121356--29121432 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
29121346 ATAATATTTA
29121356 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
1 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
* *
29121396 TAGACTCGATTTATAAAAATGAGGTGTCAGCTTTTTT
1 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTT
29121433 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (40 bp):
TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
Found at i:29124969 original size:24 final size:24
Alignment explanation
Indices: 29124937--29124985 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29124927 GACAATGACA
29124937 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
29124961 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
29124985 T
1 T
29124986 GGTTCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (24 bp):
TAGTTACAGCATGAAAGGGTAGTT
Found at i:29127697 original size:12 final size:11
Alignment explanation
Indices: 29127665--29127691 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29127655 TAAAGAGATG
29127665 AAAAAAGAAAA
1 AAAAAAGAAAA
29127676 AAAAAAGAAAA
1 AAAAAAGAAAA
29127687 AAAAA
1 AAAAA
29127692 GGGAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:29129836 original size:24 final size:22
Alignment explanation
Indices: 29129759--29129833 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
29129749 CAAGTAAAAA
*
29129759 TAATTAACAAATACTATATAATT
1 TAATTAATAAATACTATATAA-T
* * *
29129782 TAATTGAAATTAGTA-TAAATAAT
1 TAATT--AATAAATACTATATAAT
*
29129805 TTA-TAATAAATACTATATAAT
1 TAATTAATAAATACTATATAAT
29129826 GTAATTAA
1 -TAATTAA
29129834 ATATTTAGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 3 0.08
23 11 0.29
24 6 0.16
25 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATTAATAAATACTATATAAT
Found at i:29134750 original size:110 final size:110
Alignment explanation
Indices: 29134621--29134877 Score: 272
Period size: 113 Copynumber: 2.3 Consensus size: 110
29134611 CAAGGCACCT
* *
29134621 TTTTTTTTTACTTTGGGACACTGATGACCGGCACCAATGT-ATT-TAAAAAATTTTGGGTGCTGG
1 TTTTTTTTTACTTTGGGACACTGATGACCGGCACCAATGTCATTAAAAAAAATTTGGGGTGCTGG
* * * *
29134684 CCAGTAGATGGCTAACACCAAGTACAATTTTTA-GTTC-CTAATGCATA
66 CAAGTAGATGACCAACACCAAGTAC-ATTTTTAGGCTCTC-AATG--TA
* * * * *
29134731 TTTTTTTTTATTTTGGGACACTAAT-AGCCAGCACCAGTGTCATTAAAAAAAAATTTGGGGTGTT
1 TTTTTTTTTACTTTGGGACACTGATGA-CCGGCACCAATGTCATT-AAAAAAAATTTGGGGTGCT
** *
29134795 GGCAAGTAGATGACCGGCACCAAGTACATTTTTCGGCTCTCAATGTA
64 GGCAAGTAGATGACCAACACCAAGTACATTTTTAGGCTCTCAATGTA
* * *
29134842 TTTTTTTTTACTTTGGGATACTGATGGCCGACACCA
1 TTTTTTTTTACTTTGGGACACTGATGACCGGCACCA
29134878 CCTTTTTCGG
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
109 1 0.01
110 34 0.28
111 34 0.28
112 6 0.05
113 44 0.37
114 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (110 bp):
TTTTTTTTTACTTTGGGACACTGATGACCGGCACCAATGTCATTAAAAAAAATTTGGGGTGCTGG
CAAGTAGATGACCAACACCAAGTACATTTTTAGGCTCTCAATGTA
Found at i:29134817 original size:113 final size:110
Alignment explanation
Indices: 29134586--29134827 Score: 258
Period size: 110 Copynumber: 2.2 Consensus size: 110
29134576 AAAAAAATTT
* * * *
29134586 AGCACCAGGTACAATTTTCAGTTTCCAAGGCACCTTTTTTTTTTACTTTGGGACACTGATGACCG
1 AGCACCAAGTACAATTTTTAGTTTCCAAGGCA-CTTTTTTTTTTACTTTGGGACACTAATGACCA
* * * * *
29134651 GCACCAATGTATTTAAAAAATTTTGGGTGCTGGCCAGTAGATGGCT
65 GCACCAATGTATTAAAAAAATTTGGGGTGCTGGCAAGTAGATGACC
* * *
29134697 AACACCAAGTACAATTTTTAG-TTCCTAATGCA-TATTTTTTTTTATTTTGGGACACTAAT-AGC
1 AGCACCAAGTACAATTTTTAGTTTCC-AAGGCACT-TTTTTTTTTACTTTGGGACACTAATGA-C
* *
29134759 CAGCACCAGTGTCATTAAAAAAAAATTTGGGGTGTTGGCAAGTAGATGACC
63 CAGCACCAATGT-ATT--AAAAAAATTTGGGGTGCTGGCAAGTAGATGACC
*
29134810 GGCACCAAGTAC-ATTTTT
1 AGCACCAAGTACAATTTTT
29134828 CGGCTCTCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
109 2 0.02
110 38 0.35
111 26 0.24
112 6 0.06
113 37 0.34
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (110 bp):
AGCACCAAGTACAATTTTTAGTTTCCAAGGCACTTTTTTTTTTACTTTGGGACACTAATGACCAG
CACCAATGTATTAAAAAAATTTGGGGTGCTGGCAAGTAGATGACC
Found at i:29138123 original size:22 final size:22
Alignment explanation
Indices: 29138098--29138166 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
29138088 AATACCATAT
29138098 ACATGCATATTTAATTTAAAGC
1 ACATGCATATTTAATTTAAAGC
* * ** *
29138120 ACAT-TAAATTATAATACAATA-T
1 ACATGCATATT-TAATTTAA-AGC
29138142 ACATGCATATTTAATTTAAAGC
1 ACATGCATATTTAATTTAAAGC
29138164 ACA
1 ACA
29138167 ATAAATTATA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
21 5 0.15
22 23 0.70
23 5 0.15
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (22 bp):
ACATGCATATTTAATTTAAAGC
Found at i:29138127 original size:44 final size:44
Alignment explanation
Indices: 29138065--29138322 Score: 399
Period size: 44 Copynumber: 5.9 Consensus size: 44
29138055 TTCTTATTCC
* * * *
29138065 TAATTTAAAACACGTTAAATTATAATACCATATACATGCATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
*
29138109 TAATTTAAAGCACATTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
* *
29138153 TAATTTAAAGCACAATAAATTATAATACAATATACATATATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
* *
29138197 TATTTTAAAGCACATTAAATTATAATACAATATACATAAATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
*
29138241 TAATTTAAAGCACGTTAAATTATAATACAATATACATACATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
* * *
29138285 TATTTTAAAACTCATTAAATTATAATACAATATACATA
1 TAATTTAAAGCACATTAAATTATAATACAATATACATA
29138323 ACATGTCGAA
Statistics
Matches: 198, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 198 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (44 bp):
TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
Found at i:29139127 original size:16 final size:16
Alignment explanation
Indices: 29139106--29139141 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29139096 AATAGGCTAA
29139106 AAATAATAAACAAAAC
1 AAATAATAAACAAAAC
**
29139122 AAATAATAAGGAAAAC
1 AAATAATAAACAAAAC
29139138 AAAT
1 AAAT
29139142 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAATAAACAAAAC
Found at i:29139219 original size:3 final size:3
Alignment explanation
Indices: 29139211--29139245 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29139201 ACAATCTAAG
* *
29139211 AAT AAT AAT AAT GAT AAT GAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29139246 ATCTAAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29139469 original size:27 final size:27
Alignment explanation
Indices: 29139426--29139499 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
29139416 GGAAAGTGGC
* * * *
29139426 TGGCGGCACCAAAGGTGCCAATGTGAT
1 TGGCGGCACCGATGGTGCCAAAGAGAT
29139453 TGGCGGCACCGATGGTGCCAAAGAGAT
1 TGGCGGCACCGATGGTGCCAAAGAGAT
* *
29139480 TGGTGGCACAGATGGTGCCA
1 TGGCGGCACCGATGGTGCCA
29139500 TACTAAGTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.18
Consensus pattern (27 bp):
TGGCGGCACCGATGGTGCCAAAGAGAT
Found at i:29139784 original size:22 final size:22
Alignment explanation
Indices: 29139756--29139797 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29139746 GGGTTTTTTT
29139756 ACCAAAATATTACAAAAAAAAA
1 ACCAAAATATTACAAAAAAAAA
*
29139778 ACCAAAATATTATAAAAAAA
1 ACCAAAATATTACAAAAAAA
29139798 GTTTATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (22 bp):
ACCAAAATATTACAAAAAAAAA
Found at i:29139933 original size:27 final size:26
Alignment explanation
Indices: 29139873--29139985 Score: 75
Period size: 28 Copynumber: 4.0 Consensus size: 26
29139863 ATATTTTGGT
29139873 ATTTTTTTGTAATATTTTAGTAAAAA
1 ATTTTTTTGTAATATTTTAGTAAAAA
* *
29139899 ACCCTTTTTTGTATTATTTT-GTTAAATAA
1 A--TTTTTTTGTAATATTTTAG-TAAA-AA
* * **
29139928 ATTTTTTTTATAATATTTTGGTATATTATT
1 A-TTTTTTTGTAATATTTTAGTA-A--AAA
*
29139958 ATTATTTTTGTAATATTTTGGTAAAAA
1 ATT-TTTTTGTAATATTTTAGTAAAAA
29139985 A
1 A
29139986 CCCGTTTAGT
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 35 0.52
29 8 0.12
30 19 0.28
31 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.57
Consensus pattern (26 bp):
ATTTTTTTGTAATATTTTAGTAAAAA
Found at i:29140875 original size:15 final size:18
Alignment explanation
Indices: 29140847--29140891 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29140837 TTGATATGGT
* *
29140847 TGGTGGTGAAGAAGAAAG
1 TGGTGGCGAAGAAGAAGG
29140865 TGGTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
29140883 TGGTGGCGA
1 TGGTGGCGA
29140892 TCATTGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.49, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:29143249 original size:14 final size:14
Alignment explanation
Indices: 29143230--29143272 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
29143220 TAACTAAAAC
29143230 TAGAATAATTAAAT
1 TAGAATAATTAAAT
29143244 TAGAATAATTAAAT
1 TAGAATAATTAAAT
*
29143258 TGGAATAATTAAAT
1 TAGAATAATTAAAT
29143272 T
1 T
29143273 TATACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:29143702 original size:12 final size:12
Alignment explanation
Indices: 29143666--29143718 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
29143656 TTGTTCCGAA
29143666 TCTGGCTGGGGC
1 TCTGGCTGGGGC
* *
29143678 ACTGGCTGTGGC
1 TCTGGCTGGGGC
*
29143690 TCTGGTTGGGGC
1 TCTGGCTGGGGC
*
29143702 TCCT-GCTCGGGC
1 T-CTGGCTGGGGC
29143714 TCTGG
1 TCTGG
29143719 TGGTTCCGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.02, C:0.26, G:0.43, T:0.28
Consensus pattern (12 bp):
TCTGGCTGGGGC
Found at i:29145379 original size:308 final size:308
Alignment explanation
Indices: 29144821--29145438 Score: 1227
Period size: 308 Copynumber: 2.0 Consensus size: 308
29144811 AAATTTTAAA
29144821 CTCGAAAAATATGACTCACCGTCCTCTGGCGAGTCTCCTAGGAGCTGATAACAAAGTGCAACCGG
1 CTCGAAAAATATGACTCACCGTCCTCTGGCGAGTCTCCTAGGAGCTGATAACAAAGTGCAACCGG
29144886 ATCGCTAAATGAAGATACTCCCGTTACGGGACTCTCGTCAATTGGGAGCCCAAGCTGCCATGCAA
66 ATCGCTAAATGAAGATACTCCCGTTACGGGACTCTCGTCAATTGGGAGCCCAAGCTGCCATGCAA
29144951 CATCCTCCAAGGTCACCGTGCACTCCCCGCACGGAAAATGAAAAGTGTAGGTCTCCGGGCGCCAC
131 CATCCTCCAAGGTCACCGTGCACTCCCCGCACGGAAAATGAAAAGTGTAGGTCTCCGGGCGCCAC
29145016 CGCTTCACTAGCGCAGATAATAAATCAAAGCGCAAGTCGGAGGACCGGATCAATGCTACTGACCC
196 CGCTTCACTAGCGCAGATAATAAATCAAAGCGCAAGTCGGAGGACCGGATCAATGCTACTGACCC
29145081 AAATCCGGCTTGCTCCAAGTACGACATCAATCGTGCATCCGGAGCTTT
261 AAATCCGGCTTGCTCCAAGTACGACATCAATCGTGCATCCGGAGCTTT
29145129 CTCGAAAAATATGACTCACCGTCCTCTGGCGAGTCTCCTAGGAGCTGATAACAAAGTGCAACCGG
1 CTCGAAAAATATGACTCACCGTCCTCTGGCGAGTCTCCTAGGAGCTGATAACAAAGTGCAACCGG
29145194 ATCGCTAAATGAAGATACTCCCGTTACGGGACTCTCGTCAATTGGGAGCCCAAGCTGCCATGCAA
66 ATCGCTAAATGAAGATACTCCCGTTACGGGACTCTCGTCAATTGGGAGCCCAAGCTGCCATGCAA
29145259 CATCCTCCAAGGTCACCGTGCACTCCCCGCACGGAAAATGAAAAGTGTAGGTCTCCGGGCGCCAC
131 CATCCTCCAAGGTCACCGTGCACTCCCCGCACGGAAAATGAAAAGTGTAGGTCTCCGGGCGCCAC
29145324 CGCTTCACTAGCGCAGATAATAAATCAAAGCGCAAGTCGGAGGACCGGATCAATGCTACTGACCC
196 CGCTTCACTAGCGCAGATAATAAATCAAAGCGCAAGTCGGAGGACCGGATCAATGCTACTGACCC
*
29145389 AAATCCGGCTTGCTCCAAGTACGACATCAATCGTGCATCCGGAGTTTT
261 AAATCCGGCTTGCTCCAAGTACGACATCAATCGTGCATCCGGAGCTTT
29145437 CT
1 CT
29145439 TTAAAACACT
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 309 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (308 bp):
CTCGAAAAATATGACTCACCGTCCTCTGGCGAGTCTCCTAGGAGCTGATAACAAAGTGCAACCGG
ATCGCTAAATGAAGATACTCCCGTTACGGGACTCTCGTCAATTGGGAGCCCAAGCTGCCATGCAA
CATCCTCCAAGGTCACCGTGCACTCCCCGCACGGAAAATGAAAAGTGTAGGTCTCCGGGCGCCAC
CGCTTCACTAGCGCAGATAATAAATCAAAGCGCAAGTCGGAGGACCGGATCAATGCTACTGACCC
AAATCCGGCTTGCTCCAAGTACGACATCAATCGTGCATCCGGAGCTTT
Found at i:29146978 original size:4 final size:4
Alignment explanation
Indices: 29146971--29147127 Score: 101
Period size: 4 Copynumber: 36.8 Consensus size: 4
29146961 CCTCTTCTTC
*
29146971 TTCT TTCT TT-T TTTT TCTCT TCTCAT TTCCTT TTCT TTCCT CTT-T TTCT
1 TTCT TTCT TTCT TTCT T-TCT T-TC-T TT-C-T TTCT TT-CT -TTCT TTCT
*
29147020 TTC- TT-T TTCT TCTCCT TTCCT TTCT TTCA TTC- TT-T TTCT TTCT TTCT
1 TTCT TTCT TTCT T-T-CT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
29147067 TTCCT CTCCT TTCATT TTCT TTCTT TTCCT TTCT TTCT TTCT TTCT TTCT
1 TT-CT -TTCT TTC--T TTCT TTC-T TT-CT TTCT TTCT TTCT TTCT TTCT
29147117 TTCT TTCT TTC
1 TTCT TTCT TTC
29147128 CCTCTCCTTC
Statistics
Matches: 129, Mismatches: 5, Indels: 38
0.75 0.03 0.22
Matches are distributed among these distances:
3 13 0.10
4 72 0.56
5 27 0.21
6 17 0.13
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:29146999 original size:22 final size:21
Alignment explanation
Indices: 29146966--29147046 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 21
29146956 CCTTCCCTCT
*
29146966 TCTTCTTCTTTCTTTTTTTTTC
1 TCTTC-TCTTTCTTTTTTTTCC
*
29146988 TCTTCTCATTTCCTTTTCTTTCC
1 TCTTCTC-TTT-CTTTTTTTTCC
*
29147011 TCTTTTTCTTTCTTTTTCTTCTCC
1 TC-TTCTCTTTCTTTTT-TT-TCC
29147035 T-TTC-CTTTCTTT
1 TCTTCTCTTTCTTT
29147047 CATTCTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
21 10 0.20
22 15 0.31
23 16 0.33
24 8 0.16
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTTCTCTTTCTTTTTTTTCC
Found at i:29147031 original size:39 final size:40
Alignment explanation
Indices: 29146940--29147106 Score: 141
Period size: 39 Copynumber: 4.2 Consensus size: 40
29146930 TTACCTTTTT
** *
29146940 TTTCTTTTT-TT-TCC-TTCCTTCCCTCTTCTTCTTCTTTC
1 TTTCTTTTTCTTCTCCTTTCCTTTTCT-TTCCTCTTCTTTC
* *
29146978 TTTTTTTTTCTCTTCTCATTTCCTTTTCTTTCCTCTT-TTTC
1 -TTTCTTTT-TCTTCTCCTTTCCTTTTCTTTCCTCTTCTTTC
*
29147019 TTTCTTTTTCTTCTCCTTTCC-TTTCTTTCATTCTT-TTTC
1 TTTCTTTTTCTTCTCCTTTCCTTTTCTTTC-CTCTTCTTTC
* * *
29147058 TTTCTTTCTTTCCTCTCCTTTCATTTTCTTT-CTTTTCCTTTC
1 TTTC-TT-TTTCTTCTCCTTTCCTTTTCTTTCCTCTT-CTTTC
29147100 TTTCTTT
1 TTTCTTT
29147107 CTTTCTTTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
38 8 0.08
39 31 0.29
40 14 0.13
41 21 0.20
42 24 0.23
43 8 0.08
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (40 bp):
TTTCTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTCTTTC
Found at i:29147100 original size:38 final size:35
Alignment explanation
Indices: 29146934--29147126 Score: 144
Period size: 38 Copynumber: 5.2 Consensus size: 35
29146924 TAAAAATTAC
* *
29146934 CTTT-TTTTTCTTTTTTTTCCTTCCTTCCCTCTTCTTCTT
1 CTTTCTTTTTC-TTTCTTTCTTTCCTT-CCT-TTC-T-TT
* *
29146973 CTTTCTTTTT-TTT-TCTCTTCTCATTTCCTTTTCTTT
1 CTTTCTTTTTCTTTCTTTCTT-TC-CTTCC-TTTCTTT
*
29147009 C-CTCTTTTTCTTTCTTTTTCTTCTCCTTTCCTTTCTTT
1 CTTTCTTTTTCTTTC--TTTCTT-TCC-TTCCTTTCTTT
*
29147047 CATTCTTTTTCTTTCTTTCTTTCCTCTCCTTTCATTTT
1 CTTTCTTTTTCTTTCTTTCTTTCCT-TCCTTTC--TTT
* *
29147085 CTTTCTTTTCCTTTCTTTCTTT-CTTTCTTTCTTT
1 CTTTCTTTTTCTTTCTTTCTTTCCTTCCTTTCTTT
29147119 CTTTCTTT
1 CTTTCTTT
29147127 CCCTCTCCTT
Statistics
Matches: 131, Mismatches: 10, Indels: 31
0.76 0.06 0.18
Matches are distributed among these distances:
34 11 0.08
35 8 0.06
36 22 0.17
37 13 0.10
38 41 0.31
39 31 0.24
40 5 0.04
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (35 bp):
CTTTCTTTTTCTTTCTTTCTTTCCTTCCTTTCTTT
Found at i:29147100 original size:42 final size:39
Alignment explanation
Indices: 29146965--29147127 Score: 149
Period size: 41 Copynumber: 4.1 Consensus size: 39
29146955 TCCTTCCCTC
*
29146965 TTCTTCTTCTTTCTTT-TTTTTTCTCTTCTCATTTCCTTTTCT
1 TTCTTCTT-TTTCTTTCTTTTTTC-C-TCTCCTTT-CTTTTCT
* * *
29147007 TTCCTCTTTTTCTTTC-TTTTTCTTCTCCTTTCCTTTCT
1 TTCTTCTTTTTCTTTCTTTTTTCCTCTCCTTTCTTTTCT
29147045 TTCATTCTTTTTCTTTCTTTCTTTCCTCTCCTTTCATTTTCT
1 TTC-TTCTTTTTCTTTCTTT-TTTCCTCTCCTTTC-TTTTCT
*
29147087 TTCTT-TTCCTTTCTTTCTTTCTTT-CT-TTCTTTC-TTTCT
1 TTCTTCTT--TTTCTTTCTTT-TTTCCTCTCCTTTCTTTTCT
29147125 TTC
1 TTC
29147128 CCTCTCCTTC
Statistics
Matches: 106, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
38 17 0.16
39 19 0.18
40 10 0.09
41 30 0.28
42 30 0.28
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (39 bp):
TTCTTCTTTTTCTTTCTTTTTTCCTCTCCTTTCTTTTCT
Found at i:29149058 original size:39 final size:40
Alignment explanation
Indices: 29148964--29149058 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 40
29148954 GTTTGGAACA
* * *
29148964 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTAGCC
1 AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
* * * * * *
29149004 AAAGCGCCGCTAAAAATAG-GAATTAGTGGCGTTTTATAT
1 AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
29149043 AAAGCGCCACAAAAAA
1 AAAGCGCCACAAAAAA
29149059 CCTAAGACCA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
39 28 0.64
40 16 0.36
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
Found at i:29149157 original size:41 final size:41
Alignment explanation
Indices: 29149096--29149358 Score: 287
Period size: 41 Copynumber: 6.4 Consensus size: 41
29149086 ATTTTTTAAA
* *
29149096 CCTTTAGCGGCGTTTGTATCTAAGCGCCGCTAATTCTCTGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
** *
29149137 CCTTTAGCGGCGTTTTTATCTAAGCGCCTATAATGCTCGGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * *
29149178 TCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * *
29149219 CCTTTGGCGGCATTTTTATATAAGCGCCGCTAATGCTC-GG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * * * * * *
29149259 ATCTTTAGCGGCGTTTTTAACTGAGCGCCACAAATTCTCTTG
1 -CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * * **
29149301 TCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TTA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCTGG
29149342 CCTTTAGCGGCGTTTTT
1 CCTTTAGCGGCGTTTTT
29149359 GCCGAAACGC
Statistics
Matches: 183, Mismatches: 36, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.01
41 179 0.98
42 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
Found at i:29149235 original size:82 final size:82
Alignment explanation
Indices: 29149097--29149358 Score: 337
Period size: 82 Copynumber: 3.2 Consensus size: 82
29149087 TTTTTTAAAC
* *
29149097 CTTTAGCGGCGTTTGTATCTAAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
* *
29149162 GCCTATAATGCTCGGGT
66 GCCGATAATGCTCGGAT
* * *
29149179 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTGGCGGCATTTTTATATAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
*
29149244 GCCGCTAATGCTCGGAT
66 GCCGATAATGCTCGGAT
* * * * * * *
29149261 CTTTAGCGGCGTTTTTAACTGAGCGCCACAAATTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
* ** *
29149326 GCCGCTAATGCAT-TTAC
66 GCCGATAATGC-TCGGAT
29149343 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
29149359 GCCGAAACGC
Statistics
Matches: 158, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
82 157 0.99
83 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
GCCGATAATGCTCGGAT
Found at i:29149346 original size:123 final size:123
Alignment explanation
Indices: 29149095--29149358 Score: 318
Period size: 123 Copynumber: 2.1 Consensus size: 123
29149085 GATTTTTTAA
* * * *
29149095 ACCTTTAGCGGCGTTTGTATCTAAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAA
1 ACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTAACTAA
* * * * *
29149160 GCGCCTATAATGCTCGGGTCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTG
66 GCGCCTAAAATGCTCGGGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCTCTG
* * * * *
29149218 GCCTTTGGCGGCATTTTTATATAAGCGCCGCTAATGCTC-GGATCTTTAGCGGCGTTTTTAACTG
1 ACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAATGCTCTGG-CCTTTAGCGGCGTTTTTAACTA
* ** *
29149282 AGCGCC-ACAAATTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TT
65 AGCGCCTA-AAATGCTCGGGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGC-TCTG
29149341 ACCTTTAGCGGCGTTTTT
1 ACCTTTAGCGGCGTTTTT
29149359 GCCGAAACGC
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
122 3 0.03
123 113 0.97
124 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (123 bp):
ACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTAACTAA
GCGCCTAAAATGCTCGGGTCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCTCTG
Found at i:29150333 original size:7 final size:7
Alignment explanation
Indices: 29150323--29150401 Score: 50
Period size: 7 Copynumber: 10.4 Consensus size: 7
29150313 AATTTAATGT
29150323 TTAGGGG
1 TTAGGGG
29150330 TTAGGGGG
1 TTA-GGGG
29150338 ATGTAGGGG
1 -T-TAGGGG
*
29150347 TTAAGGG
1 TTAGGGG
* **
29150354 TTATGCT
1 TTAGGGG
29150361 TTAGGGG
1 TTAGGGG
29150368 TTAGGGG
1 TTAGGGG
*
29150375 ATTTAAGGG
1 --TTAGGGG
*
29150384 TAAGGGG
1 TTAGGGG
29150391 TTAAGGGG
1 TT-AGGGG
29150399 TTA
1 TTA
29150402 TGGATTTGGG
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
7 30 0.55
8 12 0.22
9 11 0.20
10 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.47, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:29153125 original size:17 final size:18
Alignment explanation
Indices: 29153074--29153166 Score: 55
Period size: 21 Copynumber: 4.8 Consensus size: 18
29153064 ATTGCTTACA
29153074 TTACTTACTAAAATATAT
1 TTACTTACTAAAATATAT
* *
29153092 TACATAATTACTTAAATAT-T
1 T---TACTTACTAAAATATAT
*
29153112 TTACTTACTAAAATTTATAAC
1 TTACTTACTAAAA--TAT-AT
*
29153133 TTACATTACTTAAATATA-
1 TTAC-TTACTAAAATATAT
29153151 TTACATTACTTAAAAT
1 TTAC-TTAC-TAAAAT
29153167 TTATATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
19 9 0.15
20 5 0.08
21 17 0.29
22 8 0.14
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
TTACTTACTAAAATATAT
Found at i:29153193 original size:45 final size:39
Alignment explanation
Indices: 29153073--29153171 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 39
29153063 CATTGCTTAC
* *
29153073 ATTACTTACTAAAATATATTACA-TA-ATTACTTAAATAT
1 ATTACTTACTAAAATTTA-TAAATTACATTACTTAAATAT
* *
29153111 TTTACTTACTAAAATTTATAACTTACATTACTTAAATAT
1 ATTACTTACTAAAATTTATAAATTACATTACTTAAATAT
29153150 ATTACATTACTTAAAATTTATA
1 ATTAC-TTAC-TAAAATTTATA
29153172 TATATATTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.04
38 18 0.35
39 17 0.33
40 4 0.08
41 11 0.21
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (39 bp):
ATTACTTACTAAAATTTATAAATTACATTACTTAAATAT
Found at i:29153765 original size:34 final size:34
Alignment explanation
Indices: 29153722--29153786 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
29153712 CATAACTTAA
29153722 TTAATTAATTAATATTATACATAAATTACATCAC
1 TTAATTAATTAATATTATACATAAATTACATCAC
*
29153756 TTAATTAATTAATATTATACATAACTTACAT
1 TTAATTAATTAATATTATACATAAATTACAT
29153787 TAATATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAATTAATTAATATTATACATAAATTACATCAC
Found at i:29153791 original size:22 final size:22
Alignment explanation
Indices: 29153758--29153808 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
29153748 TACATCACTT
29153758 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
29153779 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
29153801 AATTACAT
1 AATTACAT
29153809 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:29153797 original size:56 final size:56
Alignment explanation
Indices: 29153729--29153842 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
29153719 TAATTAATTA
*
29153729 ATTAATATTATACATAAATTACATCACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
29153785 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
29153841 AT
1 AT
29153843 AACTTACAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (56 bp):
ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Found at i:29153809 original size:9 final size:9
Alignment explanation
Indices: 29153795--29154046 Score: 102
Period size: 9 Copynumber: 30.2 Consensus size: 9
29153785 ATTAATATTA
*
29153795 TACATAAAT
1 TACATAACT
29153804 TACATAACT
1 TACATAACT
29153813 TA-ATTAA-T
1 TACA-TAACT
*
29153821 TA-AT-ATT
1 TACATAACT
29153828 ATACATAACT
1 -TACATAACT
29153838 TACATAACT
1 TACATAACT
29153847 TAC--AACT
1 TACATAACT
29153854 TACATAACT
1 TACATAACT
***
29153863 TACATTTTTT
1 TACA-TAACT
*
29153873 TA-ATTA-T
1 TACATAACT
*
29153880 T-CATAAAT
1 TACATAACT
29153888 TACATAACT
1 TACATAACT
* *
29153897 TACTTAATT
1 TACATAACT
*
29153906 TTCATAA--
1 TACATAACT
*
29153913 TAAATAACT
1 TACATAACT
*
29153922 TACACAACT
1 TACATAACT
29153931 TACATAA--
1 TACATAACT
*
29153938 TACTTAACT
1 TACATAACT
* *
29153947 TATATGACT
1 TACATAACT
29153956 TACATAACT
1 TACATAACT
29153965 T--AT-A--
1 TACATAACT
*
29153969 TAGCATAATT
1 TA-CATAACT
*
29153979 TTCATAA--
1 TACATAACT
*
29153986 TACACAACT
1 TACATAACT
*
29153995 TACATAATT
1 TACATAACT
*
29154004 TTCATAA--
1 TACATAACT
*
29154011 TAAATAACT
1 TACATAACT
29154020 TACATAA--
1 TACATAACT
29154027 TACATAACT
1 TACATAACT
*
29154036 TACATAGCT
1 TACATAACT
29154045 TA
1 TA
29154047 ATTATACTTA
Statistics
Matches: 183, Mismatches: 33, Indels: 54
0.68 0.12 0.20
Matches are distributed among these distances:
4 1 0.01
6 2 0.01
7 46 0.25
8 12 0.07
9 115 0.63
10 7 0.04
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:29153855 original size:16 final size:16
Alignment explanation
Indices: 29153834--29153866 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29153824 TATTATACAT
29153834 AACTTACATAACTTAC
1 AACTTACATAACTTAC
29153850 AACTTACATAACTTAC
1 AACTTACATAACTTAC
29153866 A
1 A
29153867 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:29153922 original size:25 final size:25
Alignment explanation
Indices: 29153888--29154027 Score: 117
Period size: 25 Copynumber: 5.7 Consensus size: 25
29153878 ATTCATAAAT
*
29153888 TACATAACTTACTTAATTTTCATAA
1 TACATAACTTACATAATTTTCATAA
* * * *
29153913 TAAATAACTTACACAACTTACATAA
1 TACATAACTTACATAATTTTCATAA
* * * * *
29153938 TACTTAACTTATATGACTTACAT-A
1 TACATAACTTACATAATTTTCATAA
*
29153962 -AC-TTA-TATAGCATAATTTTCATAA
1 TACATAACT-TA-CATAATTTTCATAA
*
29153986 TACACAACTTACATAATTTTCATAA
1 TACATAACTTACATAATTTTCATAA
*
29154011 TAAATAACTTACATAAT
1 TACATAACTTACATAAT
29154028 ACATAACTTA
Statistics
Matches: 90, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
21 1 0.01
22 4 0.04
23 10 0.11
24 2 0.02
25 69 0.77
26 3 0.03
27 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.38
Consensus pattern (25 bp):
TACATAACTTACATAATTTTCATAA
Found at i:29153925 original size:34 final size:34
Alignment explanation
Indices: 29153850--29153938 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
29153840 CATAACTTAC
* * **
29153850 AACTTACATAACTTACATT-TTTTTAATTATTCAT
1 AACTTACATAACTTAC-TTAATTTTAATAATAAAT
* *
29153884 AAATTACATAACTTACTTAATTTTCATAATAAAT
1 AACTTACATAACTTACTTAATTTTAATAATAAAT
* *
29153918 AACTTACACAACTTACATAAT
1 AACTTACATAACTTACTTAAT
29153939 ACTTAACTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 2 0.04
34 43 0.96
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.42
Consensus pattern (34 bp):
AACTTACATAACTTACTTAATTTTAATAATAAAT
Found at i:29153946 original size:84 final size:84
Alignment explanation
Indices: 29153791--29153948 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
29153781 TTACATTAAT
* * * *
29153791 ATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATAACTTACAACTTA
1 ATTATACATAAATTACATAACTTAATTAATTAATATAATAAATAACTTACACAACTTACAACATA
29153856 CATAACTTACATTTTTTTA
66 CATAACTTACATTTTTTTA
* * *
29153875 ATTATTCATAAATTACATAACTTACTTAATT-TTCATAATAAATAACTTACACAACTTACATA-A
1 ATTATACATAAATTACATAACTTAATTAATTAAT-ATAATAAATAACTTACACAACTTACA-ACA
*
29153938 TACTTAACTTA
64 TACATAACTTA
29153949 TATGACTTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.02
84 62 0.97
85 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (84 bp):
ATTATACATAAATTACATAACTTAATTAATTAATATAATAAATAACTTACACAACTTACAACATA
CATAACTTACATTTTTTTA
Found at i:29154017 original size:16 final size:16
Alignment explanation
Indices: 29154006--29154041 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
29153996 ACATAATTTT
29154006 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
29154022 CATAATACATAACTTA
1 CATAATAAATAACTTA
29154038 CATA
1 CATA
29154042 GCTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:29156596 original size:23 final size:23
Alignment explanation
Indices: 29156566--29156611 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
29156556 TTGTATATTG
29156566 TGTTTAGGTTCCTATCCAAATTA
1 TGTTTAGGTTCCTATCCAAATTA
*
29156589 TGTTTAGGTTTCTATCCAAATTA
1 TGTTTAGGTTCCTATCCAAATTA
29156612 AAGTCTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (23 bp):
TGTTTAGGTTCCTATCCAAATTA
Found at i:29159558 original size:21 final size:21
Alignment explanation
Indices: 29159532--29159602 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
29159522 CTACAACTTA
* *
29159532 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
29159553 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
29159574 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
29159595 AAGCAGAG
1 AAGCAGAG
29159603 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:29160001 original size:42 final size:42
Alignment explanation
Indices: 29159955--29160047 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
29159945 ATCAAATAGT
* *
29159955 GGCGTTTTTGACC-AAGCGCCGCTATAGAAAATTA-CTTTTAGC
1 GGCGTTTTT-ACCTAAGCGCCGCTAAAGAAAATGATC-TTTAGC
* * *
29159997 GGCGTTTTTTCCTAAGCGCTGCTAAAGAACATGATCTTTAGC
1 GGCGTTTTTACCTAAGCGCCGCTAAAGAAAATGATCTTTAGC
29160039 GGCGTTTTT
1 GGCGTTTTT
29160048 TTCTGTAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 41 0.93
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
GGCGTTTTTACCTAAGCGCCGCTAAAGAAAATGATCTTTAGC
Found at i:29161152 original size:15 final size:16
Alignment explanation
Indices: 29161124--29161157 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29161114 ATACATATTT
29161124 AAATGAAATGAGAAAA
1 AAATGAAATGAGAAAA
*
29161140 AAAT-AAATTAGAAAA
1 AAATGAAATGAGAAAA
29161155 AAA
1 AAA
29161158 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATGAAATGAGAAAA
Found at i:29161184 original size:5 final size:5
Alignment explanation
Indices: 29161166--29161238 Score: 92
Period size: 5 Copynumber: 13.6 Consensus size: 5
29161156 AAGATAATTT
*
29161166 AAATG AAATGG AAATG AAATG AGATGG AAATAG AAATG AAATG AAATGG
1 AAATG AAAT-G AAATG AAATG AAAT-G AAAT-G AAATG AAATG AAAT-G
29161215 AAATAG AAATG AAATG AAATG AAA
1 AAAT-G AAATG AAATG AAATG AAA
29161239 AAAAAAAGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
5 37 0.61
6 24 0.39
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:29161196 original size:27 final size:27
Alignment explanation
Indices: 29161167--29161238 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 27
29161157 AGATAATTTA
* *
29161167 AATGAAATGGAAATGAAAT-GAGATGGA
1 AATGAAAT-GAAATGAAATGGAAATAGA
29161194 AATAGAAATGAAATGAAATGGAAATAGA
1 AAT-GAAATGAAATGAAATGGAAATAGA
29161222 AATGAAATGAAATGAAA
1 AATGAAATGAAATGAAA
29161239 AAAAAAAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 27 0.66
28 14 0.34
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (27 bp):
AATGAAATGAAATGAAATGGAAATAGA
Found at i:29161201 original size:22 final size:22
Alignment explanation
Indices: 29161166--29161235 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
29161156 AAGATAATTT
*
29161166 AAAT-GAAATGGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
*
29161187 AGATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
29161209 AAATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
29161231 AAATG
1 AAATG
29161236 AAAAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 3 0.07
22 42 0.93
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (22 bp):
AAATGGAAATAGAAATGAAATG
Found at i:29161775 original size:25 final size:26
Alignment explanation
Indices: 29161725--29161778 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
29161715 AGGAAATGAG
*
29161725 AAAATTTTGAAATTTAAATGAAATTT
1 AAAATTTTGAAATTGAAATGAAATTT
* *
29161751 AAAATTTTGAAA-TGGAATGATATTT
1 AAAATTTTGAAATTGAAATGAAATTT
29161776 AAA
1 AAA
29161779 TTGAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (26 bp):
AAAATTTTGAAATTGAAATGAAATTT
Found at i:29161976 original size:21 final size:21
Alignment explanation
Indices: 29161946--29161997 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29161936 TTGTATATTA
29161946 GGAAA-AAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
29161966 GGAAATAAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
*
29161987 GGAAATGAAAT
1 GGAAATAAAAT
29161998 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (21 bp):
GGAAATAAAATAAATTTAAAT
Found at i:29168208 original size:19 final size:20
Alignment explanation
Indices: 29168182--29168230 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
29168172 AGGTAGGTAA
29168182 CTTTTTTTTTGCGGTTTTTG
1 CTTTTTTTTTGCGGTTTTTG
29168202 CTTTTTTTTTGCGGTTTTTG
1 CTTTTTTTTTGCGGTTTTTG
29168222 CTTTTTTTT
1 CTTTTTTTT
29168231 AAAGAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.73
Consensus pattern (20 bp):
CTTTTTTTTTGCGGTTTTTG
Found at i:29168784 original size:31 final size:31
Alignment explanation
Indices: 29168746--29168807 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29168736 AGGCAAATTA
29168746 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
29168777 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
29168808 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:29170174 original size:90 final size:89
Alignment explanation
Indices: 29170030--29170358 Score: 416
Period size: 90 Copynumber: 3.7 Consensus size: 89
29170020 ATTCTACAAT
* * * * * * *
29170030 ATTAATACAC-AAAATTATAAAATTCAAATAAAAATATTACG-TACTAAGTTAAATTTAAGCACC
1 ATTAATACACGAAAATT-TTAAATTCAAATACATATAATACGAGACTAAATTAAATTTAAACACC
*
29170093 CAACAAACTACAAACATATAGGTAAA
65 CAACAAACTACAAACAGAT-GGTAAA
*
29170119 ATTAATATACGAAAATTTTAAATTCAAACTACATATAATACGA-ACTAAATTAAATTTAAACACC
1 ATTAATACACGAAAATTTTAAATTCAAA-TACATATAATACGAGACTAAATTAAATTTAAACACC
29170183 CAACAAACTACAAACAGATGGATAAA
65 CAACAAACTACAAACAGATGG-TAAA
* * * * * *
29170209 ATTAGTGCATGAAATTTTTAAATTCAAATGATATATAACAC-AGACTAAATTAAATTTAAACACC
1 ATTAATACACGAAAATTTTAAATTCAAAT-ACATATAATACGAGACTAAATTAAATTTAAACACC
29170273 CAACAAACTACAAACAGATGGGTAAA
65 CAACAAACTACAAACAGAT-GGTAAA
*
29170299 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATA-TAGACTAAATTAAATTTAAA
1 ATTAATACACGAAAATTTTAAATTCAAA-TACATATAATACGAGACTAAATTAAATTTAAA
29170359 GATACAAAAA
Statistics
Matches: 210, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
89 23 0.11
90 184 0.88
91 3 0.01
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.27
Consensus pattern (89 bp):
ATTAATACACGAAAATTTTAAATTCAAATACATATAATACGAGACTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGTAAA
Found at i:29171279 original size:112 final size:111
Alignment explanation
Indices: 29171014--29171343 Score: 380
Period size: 112 Copynumber: 2.9 Consensus size: 111
29171004 GAAAAAGGTA
* **
29171014 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAAAATTG-CATTGGGAGAC-AAAAATGTATTTGG
1 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAG--AATTGTC-TTGGGACACGAAAAATGTACCTGG
* ** *
29171077 TGCCGGCCATCTACTGGCCAGCACTCCAAAAAAATATTTTT-AATAGACACTG
63 TGCCGACCATCTACTGGCCAGCAC-CC---AATTTTTTTTTAAATAGACACTG
* * * *
29171129 ATG-CTGGCTATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACTCGAAAAATGTACCTGGTG
1 ATGTC-GGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTG
* * *
29171193 TCGACCATCTATTGGCCAGCACCCAATTTTTTTTTTAAATTGACACTG
65 CCGACCATCTACTGGCCAGCACCCAA-TTTTTTTTTAAATAGACACTG
* * *
29171241 GTGTCGACCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACCCGAAAAATGTACCTGGTGC
1 ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTGC
* *
29171306 CGACCACCTACTGGCTAGCACCCAATTTTTTTTTAAAT
66 CGACCATCTACTGGCCAGCACCCAATTTTTTTTTAAAT
29171344 GTCTCTGGTG
Statistics
Matches: 185, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
110 2 0.01
111 19 0.10
112 88 0.48
113 14 0.08
114 35 0.19
115 27 0.15
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (111 bp):
ATGTCGGCCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACACGAAAAATGTACCTGGTGC
CGACCATCTACTGGCCAGCACCCAATTTTTTTTTAAATAGACACTG
Found at i:29172376 original size:9 final size:9
Alignment explanation
Indices: 29172364--29172406 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
29172354 TAAAAATTAA
29172364 TAAAAAAAT
1 TAAAAAAAT
29172373 TAAATAAAAT
1 TAAA-AAAAT
* *
29172383 TCAAAAAGT
1 TAAAAAAAT
29172392 TAAAAAAA-
1 TAAAAAAAT
29172400 TAAAAAA
1 TAAAAAA
29172407 TGAATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:29172406 original size:18 final size:18
Alignment explanation
Indices: 29172362--29172406 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
29172352 TTTAAAAATT
29172362 AATAAAAAAATTAAATAA
1 AATAAAAAAATTAAATAA
* *
29172380 AATTCAAAAAGTTAAA-AA
1 AA-TAAAAAAATTAAATAA
29172398 AATAAAAAA
1 AATAAAAAA
29172407 TGAATCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAAAAATTAAATAA
Found at i:29173642 original size:20 final size:20
Alignment explanation
Indices: 29173619--29173658 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29173609 AAAAATCTAA
29173619 ATAAACAAA-TTAAAAAATAT
1 ATAAA-AAATTTAAAAAATAT
*
29173639 ATAAAAAATTTAAATAATAT
1 ATAAAAAATTTAAAAAATAT
29173659 GTACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAAATTTAAAAAATAT
Found at i:29177828 original size:26 final size:26
Alignment explanation
Indices: 29177799--29177855 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
29177789 CCATTTTTTT
* * *
29177799 AATAAACACCAAAAAGTTATTTTAAA
1 AATAAAAACAAAAAAATTATTTTAAA
*
29177825 AATAAAAAATAAAAAAATTATTTTAAA
1 AAT-AAAAACAAAAAAATTATTTTAAA
29177852 AATA
1 AATA
29177856 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (26 bp):
AATAAAAACAAAAAAATTATTTTAAA
Found at i:29183417 original size:29 final size:32
Alignment explanation
Indices: 29183366--29183425 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
29183356 AATTTTGTGC
*
29183366 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAAA
*
29183398 AGGAA-ACAA-TT-GGGCCAAATTGAAGAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAA
29183426 GAAGCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 2 0.08
31 4 0.15
32 5 0.19
ACGTcount: A:0.50, C:0.08, G:0.25, T:0.17
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCCAAATAGAAGAAAA
Found at i:29190571 original size:21 final size:22
Alignment explanation
Indices: 29190521--29190572 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29190511 AAAAAAAACC
* * *
29190521 CCTTACACCCATCACATCCTAA
1 CCTTTCACCCATCAAATCCAAA
29190543 CCTTTCACCCATCAAAT-CAAA
1 CCTTTCACCCATCAAATCCAAA
*
29190564 CTTTTCACC
1 CCTTTCACC
29190573 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (22 bp):
CCTTTCACCCATCAAATCCAAA
Found at i:29202280 original size:21 final size:23
Alignment explanation
Indices: 29202254--29202295 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
29202244 TTCACTGGAT
*
29202254 ACGACGGTG-CCTA-TGGTTGCA
1 ACGACGGCGTCCTAGTGGTTGCA
29202275 ACGACGGCGTCCTAGTGGTTG
1 ACGACGGCGTCCTAGTGGTTG
29202296 GTGGCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (23 bp):
ACGACGGCGTCCTAGTGGTTGCA
Found at i:29205946 original size:42 final size:42
Alignment explanation
Indices: 29205900--29206037 Score: 204
Period size: 42 Copynumber: 3.3 Consensus size: 42
29205890 ATAGTCAGCT
*
29205900 ATGGTCTTACACGAATCTCATATCGATGCCATTGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
*
29205942 ATGGTCTTACATGAATCTCATATCGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
* * * * *
29205984 ATGGTCTTACATGAATCACATAACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
*
29206026 ATGGTTTTACAC
1 ATGGTCTTACAC
29206038 ATAATCACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
Found at i:29205988 original size:84 final size:84
Alignment explanation
Indices: 29205858--29206036 Score: 213
Period size: 84 Copynumber: 2.1 Consensus size: 84
29205848 GATCCCATAT
* * * *
29205858 ATGGTCTTACATGCTATCATATATCGATGCCAATAGTCAGCTATGGTCTTACACGAATCTCATAT
1 ATGGTCTTACATGCAATCATATATCGATGCCAATAGTCAACTATGGTCTTACACGAATCACATAA
* *
29205923 CGATGCCATTGTCCCAAAC
66 CAATGCCAATGTCCCAAAC
*
29205942 ATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GTCCCAAAC-ATGGTCTTACATGAATCAC
1 ATGGTCTTACATGCAATCAT-ATATCGATGCCAATAGT--C-AACTATGGTCTTACACGAATCAC
*
29206003 ATAACAATGCCAATGTCCCAGAC
62 ATAACAATGCCAATGTCCCAAAC
*
29206026 ATGGTTTTACA
1 ATGGTCTTACA
29206037 CATAATCACA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
82 3 0.04
83 17 0.21
84 60 0.73
85 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (84 bp):
ATGGTCTTACATGCAATCATATATCGATGCCAATAGTCAACTATGGTCTTACACGAATCACATAA
CAATGCCAATGTCCCAAAC
Found at i:29214516 original size:30 final size:30
Alignment explanation
Indices: 29214446--29214523 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
29214436 AAAGAATAAG
* * * *
29214446 AAATGAAATGGAAA-AAGAAAATTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
29214475 AAATGAAGTG-AAAGAAAAAAAGTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
29214504 AAGA-GAAAGTGAAAAGAAAA
1 AA-ATG-AAGTGAAAAGAAAA
29214524 CAAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.07
29 25 0.60
30 6 0.14
31 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (30 bp):
AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
Found at i:29219047 original size:29 final size:30
Alignment explanation
Indices: 29219012--29219079 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
29219002 TGAAAACTTC
29219012 ATGTATAAAATTACACA-AAATCAAAGTTT
1 ATGTATAAAATTACACATAAATCAAAGTTT
* *
29219041 ATTTATAACATTACACATTAAATCAAAGTTT
1 ATGTATAAAATTACACA-TAAATCAAAGTTT
29219072 ATGTATAA
1 ATGTATAA
29219080 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
ATGTATAAAATTACACATAAATCAAAGTTT
Found at i:29224678 original size:26 final size:23
Alignment explanation
Indices: 29224627--29224680 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
29224617 TGTTTATGCT
**
29224627 AATTACTTTAAATAGTAAAAGTA
1 AATTACTTTAAATAGTAAAACAA
29224650 AATTACTATTAAATAGAATAAAACAA
1 AATTACT-TTAAATAG--TAAAACAA
29224676 AATTA
1 AATTA
29224681 TTAGTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
26 11 0.42
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
AATTACTTTAAATAGTAAAACAA
Found at i:29226351 original size:2 final size:2
Alignment explanation
Indices: 29226344--29226400 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
29226334 TTTATAACAT
29226344 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29226386 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
29226401 CTAACTTATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29227790 original size:21 final size:21
Alignment explanation
Indices: 29227748--29227790 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29227738 AGGGAAAATG
*
29227748 AAATAAGGAAAAGAAGACAAA
1 AAATAAGGAAAAGAAGAAAAA
*
29227769 AAATAATGTAAAAGAA-AAAAA
1 AAATAA-GGAAAAGAAGAAAAA
29227790 A
1 A
29227791 TATGTTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.09
Consensus pattern (21 bp):
AAATAAGGAAAAGAAGAAAAA
Found at i:29237081 original size:18 final size:18
Alignment explanation
Indices: 29237060--29237098 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29237050 AAAGGAAGAT
29237060 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
29237078 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
29237096 AGA
1 AGA
29237099 GCCAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:29238913 original size:33 final size:34
Alignment explanation
Indices: 29238869--29238943 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
29238859 GAGTTAGTTT
*
29238869 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
* * *
29238902 ATTCATTTTAGTTCAGCTTAAATAATTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
29238936 ATTAATTT
1 ATTAATTT
29238944 GTTTAAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:29254818 original size:16 final size:16
Alignment explanation
Indices: 29254797--29254827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29254787 TATGTTAAAG
29254797 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
29254813 CATATATATTTGAAA
1 CATATAAATTTGAAA
29254828 ACTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:29255030 original size:18 final size:19
Alignment explanation
Indices: 29255009--29255045 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29254999 TTAAAAAATA
29255009 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
29255027 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
29255046 AAAAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:29255044 original size:19 final size:20
Alignment explanation
Indices: 29255014--29255082 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
29255004 AAATATATAA
29255014 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
*
29255034 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
*
29255053 AGTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAATT
29255073 ATTTTGAATT
1 ATTTTGAATT
29255083 ATTTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 23 0.53
21 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:29263140 original size:17 final size:18
Alignment explanation
Indices: 29263120--29263159 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
29263110 TAATTACAAT
29263120 AAATA-TTAATTAATGAA
1 AAATATTTAATTAATGAA
*
29263137 AAATATTTTAATTAATGCA
1 AAATA-TTTAATTAATGAA
29263156 AAAT
1 AAAT
29263160 TGTGGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
19 15 0.75
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATATTTAATTAATGAA
Found at i:29263277 original size:131 final size:130
Alignment explanation
Indices: 29263027--29263297 Score: 353
Period size: 131 Copynumber: 2.1 Consensus size: 130
29263017 CTTTTAATTC
* * * * * * *
29263027 AATTGTGGCGCATCAATAAATTGTATGGACAATGATAATAAAATGATAATAGTAATTGTGATGCA
1 AATTGTGGTGCATCAATAAATTGCATGGACAATGACAATAAAATCATAACAGTAATTATGATGAA
* *
29263092 TCAATTAAATCAAATGAGTAATTACAATAAATATTAATTAATGAAAAATATTTTAATTAATGCAA
66 TCAATTAAATCAAATGAGTAATTAAAATAAAAATTAATTAATGAAAAATATTTTAATTAATGCAA
** * *
29263157 AATTGTGGTGCATCAATTAAATTGCATGGGTAATTACAATAAAATCATAACAGTAATTATGGTGA
1 AATTGTGGTGCATCAA-TAAATTGCATGGACAATGACAATAAAATCATAACAGTAATTATGATGA
* *** * * *
29263222 ATTAATTAAATTGCATGAGTAATTAAAATAAAAATTAATTAATGGAAAATCTTTTAATTGATGCA
65 ATCAATTAAATCAAATGAGTAATTAAAATAAAAATTAATTAATGAAAAATATTTTAATTAATGCA
29263287 A
130 A
29263288 AATTGTGGTG
1 AATTGTGGTG
29263298 TAAAATCTTG
Statistics
Matches: 120, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
130 15 0.12
131 105 0.88
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.34
Consensus pattern (130 bp):
AATTGTGGTGCATCAATAAATTGCATGGACAATGACAATAAAATCATAACAGTAATTATGATGAA
TCAATTAAATCAAATGAGTAATTAAAATAAAAATTAATTAATGAAAAATATTTTAATTAATGCAA
Found at i:29270769 original size:10 final size:10
Alignment explanation
Indices: 29270734--29270771 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
29270724 CCTCGACAAA
29270734 TATTAAAAAT
1 TATTAAAAAT
* *
29270744 TCTTTAAAAT
1 TATTAAAAAT
29270754 TA-TAAAAAT
1 TATTAAAAAT
29270763 TATTAAAAA
1 TATTAAAAA
29270772 GGTGGTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TATTAAAAAT
Found at i:29272275 original size:43 final size:41
Alignment explanation
Indices: 29272216--29272371 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 41
29272206 ATGTATTTTC
* *
29272216 GTGTAACACCACGTCTGGGACGTTGGCATTGAATTGTGTATAT
1 GTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTG-ATAT
* * * *
29272259 GTGTAAGACCATGTCTGGGGCATTGGCATCGTATT-TGATTT
1 GTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTGATAT
*
29272300 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TGTGA-TAT
* *
29272343 ATGTAAGACCACGTCTGGGATGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
29272372 TTTACGAGCC
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
40 2 0.02
41 30 0.33
42 6 0.07
43 53 0.58
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATTGTGATAT
Done.