Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 12 of 144
Found at i:2863738 original size:52 final size:52
Alignment explanation
Indices: 2863662--2863835 Score: 249
Period size: 52 Copynumber: 3.3 Consensus size: 52
2863652 TAGCTAAAGC
* * *
2863662 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
2863715 TTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* ** *
2863767 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
2863819 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
2863836 ATCAGAAGTA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
52 91 0.84
53 17 0.16
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:2863807 original size:98 final size:98
Alignment explanation
Indices: 2863618--2863841 Score: 235
Period size: 98 Copynumber: 2.3 Consensus size: 98
2863608 ATAAGTGTAG
* * * * *
2863618 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAACCAAAGCTATCACTTATCACTTTGCCAC
* *
2863683 TTGATCAGATAAGTATAGCCGAAGCTATCA-CTTT
66 TTGATCAGATAAGTATAGCCGAAGCTA-AAGC-TA
* * *
2863717 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACTTATCACTTT-CCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAACCAAAGCTATCACTTATCACTTTGCCAC
* * *
2863780 TTG-TCACTTGATCAG-ATAAG-TGTAGCTAAAGCTA
66 TTGATCA---GATAAGTAT-AGCCGAAGCTAAAGCTA
2863814 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
2863842 AGTACTCAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
96 3 0.03
97 16 0.15
98 69 0.66
99 16 0.15
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAACCAAAGCTATCACTTATCACTTTGCCAC
TTGATCAGATAAGTATAGCCGAAGCTAAAGCTA
Found at i:2870286 original size:49 final size:49
Alignment explanation
Indices: 2870141--2870305 Score: 145
Period size: 49 Copynumber: 3.2 Consensus size: 49
2870131 GAGATCGCAT
** *
2870141 GTAAGACCATGTCTGGGACATGAAATTGGCATCATTGAGATTATGAGAGGTCCCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCA-C--T-A-A-TATGAGAGGTCCCA
* *
2870196 TGTAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGGTCTCCCA
1 -GTAAGACCATGTCTGGGACATGGCATGGGCACTAATATGAGAGG--TCCCA
* * **
2870248 -TAAGACCATGTC-GGGACATGGCATGGGTACTGATATGAGAACTCCCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCACTAATATGAGAGGTCCCA
2870295 TGTAAGACCAT
1 -GTAAGACCAT
2870306 ATCTTGTAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
47 5 0.05
49 33 0.34
50 20 0.21
51 1 0.01
52 6 0.06
53 1 0.01
55 1 0.01
56 29 0.30
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACTAATATGAGAGGTCCCA
Found at i:2871610 original size:44 final size:45
Alignment explanation
Indices: 2871515--2871648 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
2871505 ACAGGACAGA
* *
2871515 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2871561 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
2871605 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2871649 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2877976 original size:44 final size:45
Alignment explanation
Indices: 2877881--2878014 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
2877871 ACAGGACAGA
* *
2877881 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2877927 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
2877971 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2878015 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2895542 original size:15 final size:15
Alignment explanation
Indices: 2895519--2895548 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2895509 TATAGGGAGA
2895519 AGGTAAACATTCCAT
1 AGGTAAACATTCCAT
*
2895534 AGGTGAACATTCCAT
1 AGGTAAACATTCCAT
2895549 CTGATAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (15 bp):
AGGTAAACATTCCAT
Found at i:2907348 original size:12 final size:12
Alignment explanation
Indices: 2907331--2907355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2907321 TTCAAGGGGG
2907331 AATGTATTAGAA
1 AATGTATTAGAA
2907343 AATGTATTAGAA
1 AATGTATTAGAA
2907355 A
1 A
2907356 CAATGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AATGTATTAGAA
Found at i:2908203 original size:25 final size:25
Alignment explanation
Indices: 2908173--2908220 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2908163 TAGACAAATG
2908173 AAAAAAT-ATATACAATATAATACTA
1 AAAAAATAATAT-CAATATAATACTA
*
2908198 AAAAAATAATATGAATATAATAC
1 AAAAAATAATATCAATATAATAC
2908221 GAATAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAATAATATCAATATAATACTA
Found at i:2908233 original size:25 final size:25
Alignment explanation
Indices: 2908186--2908234 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2908176 AAATATATAC
* *
2908186 AATATAATACTAAAAAAATAATATG
1 AATATAATACGAAAAAAACAATATG
* *
2908211 AATATAATACGAATAAACCAATAT
1 AATATAATACGAAAAAAACAATAT
2908235 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (25 bp):
AATATAATACGAAAAAAACAATATG
Found at i:2910318 original size:6 final size:6
Alignment explanation
Indices: 2910307--2910340 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2910297 ACTTTTAAAA
2910307 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
2910341 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:2911792 original size:6 final size:6
Alignment explanation
Indices: 2911783--2911819 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2911773 AAATTTATAT
*
2911783 TAATAG TAATAC TAATAC TAATAC TAATAC TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC T
2911820 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (6 bp):
TAATAC
Found at i:2914817 original size:6 final size:6
Alignment explanation
Indices: 2914801--2914830 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2914791 TGACCACAAA
*
2914801 TTTTAT CTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
2914831 AAAATGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:2920295 original size:2 final size:2
Alignment explanation
Indices: 2920290--2920314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2920280 GTGTGTGTGT
2920290 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2920315 GAAGTGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2926423 original size:49 final size:49
Alignment explanation
Indices: 2926344--2926440 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
2926334 AACCCCTCTA
*
2926344 TTTTTTTACACTCAATCGAGCACTTGAACTTTCAAAATGCATCAAAAAC
1 TTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAAC
* * *
2926393 TTTTTTTTCACTCAATTGAGTACTTAAACTTTCAAAATGCATCAAAAA
1 TTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
2926441 TACCCTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (49 bp):
TTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAAC
Found at i:2926860 original size:37 final size:36
Alignment explanation
Indices: 2926811--2926892 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
2926801 ATTTCTTACG
* *
2926811 AATTTATAAAATTTTATAA-TTTTTTACGATTTTTTTA
1 AATTT-TAAAATTTT-TAATTTTTTTACAATTTTTCTA
2926848 AATTTTACAAATTTTTAATTTTTTTACAATTTTTCTA
1 AATTTTA-AAATTTTTAATTTTTTTACAATTTTTCTA
*
2926885 ATTTTTAA
1 AATTTTAA
2926893 TAAATTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 6 0.15
37 34 0.85
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (36 bp):
AATTTTAAAATTTTTAATTTTTTTACAATTTTTCTA
Found at i:2926862 original size:28 final size:28
Alignment explanation
Indices: 2926793--2926891 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
2926783 TCTTTACATT
* * * *
2926793 TTTTATAAATTTCTTACGAATTTATAAAA
1 TTTTACAAATTT-TTACGATTTTTTTAAA
* *
2926822 TTTTATAATTTTTTACGATTTTTTTAAA
1 TTTTACAAATTTTTACGATTTTTTTAAA
2926850 TTTTACAAATTTTTA--ATTTTTTTACAA
1 TTTTACAAATTTTTACGATTTTTTTA-AA
* *
2926877 TTTTTCTAATTTTTA
1 TTTTACAAATTTTTA
2926892 ATAAATTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.15
27 15 0.25
28 26 0.43
29 11 0.18
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTACAAATTTTTACGATTTTTTTAAA
Found at i:2926871 original size:18 final size:18
Alignment explanation
Indices: 2926819--2926910 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
2926809 CGAATTTATA
2926819 AAATTTTATAATTTTTTAC
1 AAATTTT-TAATTTTTTAC
** *
2926838 GATTTTTTTAA-ATTTTAC
1 -AAATTTTTAATTTTTTAC
2926856 AAATTTTTAATTTTTTTAC
1 AAATTTTTAA-TTTTTTAC
* * *
2926875 AATTTTTCTAATTTTTAAT
1 AAATTTT-TAATTTTTTAC
* *
2926894 AAATTATTAATATTTTA
1 AAATTTTTAATTTTTTA
2926911 ATATTTTATT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
17 8 0.14
18 14 0.25
19 26 0.46
20 8 0.14
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (18 bp):
AAATTTTTAATTTTTTAC
Found at i:2926909 original size:19 final size:19
Alignment explanation
Indices: 2926883--2926932 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2926873 ACAATTTTTC
2926883 TAAT-TTTTAATAAATTAT
1 TAATATTTTAATAAATTAT
**
2926901 TAATATTTTAATATTTTAT
1 TAATATTTTAATAAATTAT
*
2926920 TAA-AATTTAATAA
1 TAATATTTTAATAA
2926933 TATTTATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTTTAATAAATTAT
Found at i:2927158 original size:91 final size:91
Alignment explanation
Indices: 2926995--2927164 Score: 227
Period size: 91 Copynumber: 1.9 Consensus size: 91
2926985 AAAAGCATGG
* *
2926995 GCTTAATTGCATTTTTTGAAAAAGTTTGAGCATCTTTTTGATCTATTTTGAAAGTTCAAGTACCT
1 GCTTAATTGCATTTTTTGAAAAAGTTTGAGCACCTTTTTGATCTATTTTAAAAGTTCAAGTACCT
* *
2927060 AATTGAGTGTAAAAGATAAAGTAGGA
66 AAATGAGTGAAAAAGATAAAGTAGGA
* * * * *
2927086 GCTTAATTG-ATTTCTTTGAAAAGGTTTGAGGACCTTTTTGATGTATTTTAAAATTTTAAGTA-C
1 GCTTAATTGCATTT-TTTGAAAAAGTTTGAGCACCTTTTTGATCTATTTTAAAAGTTCAAGTACC
2927149 TCAAATGAGTGAAAAA
65 T-AAATGAGTGAAAAA
2927165 AAAATTAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 6 0.09
91 62 0.91
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (91 bp):
GCTTAATTGCATTTTTTGAAAAAGTTTGAGCACCTTTTTGATCTATTTTAAAAGTTCAAGTACCT
AAATGAGTGAAAAAGATAAAGTAGGA
Found at i:2927202 original size:21 final size:21
Alignment explanation
Indices: 2927161--2927203 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2927151 AAATGAGTGA
*
2927161 AAAAAAAATTAAATACTTTTT
1 AAAAAAAATTAAACACTTTTT
*
2927182 AAAAAAAATTAGAGCACTTTTT
1 AAAAAAAATTA-AACACTTTTT
2927204 GCACCCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAAAAATTAAACACTTTTT
Found at i:2929679 original size:14 final size:13
Alignment explanation
Indices: 2929645--2929682 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
2929635 CGGTTCAAAT
2929645 AATATAA-TTTTA
1 AATATAATTTTTA
2929657 AAT-TAATTTTTA
1 AATATAATTTTTA
2929669 AATTATAATTTTTA
1 AA-TATAATTTTTA
2929683 TTTTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 10 0.43
13 1 0.04
14 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATAATTTTTA
Found at i:2932804 original size:26 final size:26
Alignment explanation
Indices: 2932736--2932804 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
2932726 ATCAGGAAGC
*
2932736 TCCCGA-TATATGGCTCATTGTGAGCT
1 TCCCGATTA-ATGGCTCTTTGTGAGCT
*
2932762 TCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCCGATTAATGGCTCTTTGTGAGCT
*
2932788 TCCTGATTAATGGCTCT
1 TCCCGATTAATGGCTCT
2932805 CCGAAGCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 36 0.95
27 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
TCCCGATTAATGGCTCTTTGTGAGCT
Found at i:2934224 original size:30 final size:29
Alignment explanation
Indices: 2934158--2934241 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
2934148 AAGCAAAAAA
* *
2934158 TAAAGATT-ACATTTTAACCCCTATACTTTT
1 TAAA-ATTCACATTTTAACCCC-AAACTTAT
* *
2934188 TGAAATTTC-TATTTTAACCCCAAACCTTAT
1 T-AAAATTCACATTTTAACCCCAAA-CTTAT
2934218 TAAAATTCACATTTTAACCCCAAA
1 TAAAATTCACATTTTAACCCCAAA
2934242 AATTTCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
29 8 0.18
30 33 0.75
31 3 0.07
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
TAAAATTCACATTTTAACCCCAAACTTAT
Found at i:2934252 original size:30 final size:29
Alignment explanation
Indices: 2934198--2934260 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
2934188 TGAAATTTCT
** *
2934198 ATTTTAACCCCAAACCTTATTAAAATTCAC
1 ATTTTAACCCCAAAAATTATTAAAAAT-AC
2934228 ATTTTAACCCCAAAAATT-TCTAAAAATAC
1 ATTTTAACCCCAAAAATTAT-TAAAAATAC
2934257 ATTT
1 ATTT
2934261 CGACCCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTTAACCCCAAAAATTATTAAAAATAC
Found at i:2934855 original size:6 final size:6
Alignment explanation
Indices: 2934848--2934906 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
2934838 CGGCCCGAAG
* * *
2934848 AAGAAG AAGAAA AAGAAA AAGAAA GAAGGAAA AAGAGAG AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA -AA-GAAA AAGA-AA AAGAAA AAGAAA
2934899 AAGAAA AA
1 AAGAAA AA
2934907 AAGAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 32 0.71
7 9 0.20
8 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2934981 original size:10 final size:10
Alignment explanation
Indices: 2934963--2935000 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2934953 GACCCGAGAG
2934963 GAAAAAAGAA
1 GAAAAAAGAA
*
2934973 GATAAAAGAA
1 GAAAAAAGAA
2934983 GAAAAAAGAA
1 GAAAAAAGAA
*
2934993 AAAAAAAG
1 GAAAAAAG
2935001 GGTTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:2935170 original size:5 final size:5
Alignment explanation
Indices: 2935160--2935200 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
2935150 TATTTATATT
*
2935160 TTTAA TTTAA TTTAA TTTAA TTTAA TTTTAA TTTAT TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA
2935201 ATAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:2935178 original size:15 final size:16
Alignment explanation
Indices: 2935160--2935200 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2935150 TATTTATATT
2935160 TTTAATTTAA-TTTAA
1 TTTAATTTAATTTTAA
2935175 TTTAATTTAATTTTAA
1 TTTAATTTAATTTTAA
*
2935191 TTTATTTTAA
1 TTTAATTTAA
2935201 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATTTAATTTTAA
Found at i:2935205 original size:20 final size:21
Alignment explanation
Indices: 2935165--2935211 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2935155 ATATTTTTAA
*
2935165 TTTAATTTAATTTAATTTAAT
1 TTTAATTTAATTTAATATAAT
*
2935186 TTTAATTTATTTTAA-ATAAT
1 TTTAATTTAATTTAATATAAT
2935206 TTTAAT
1 TTTAAT
2935212 AAATAAGGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATTTAATTTAATATAAT
Found at i:2935576 original size:53 final size:53
Alignment explanation
Indices: 2935492--2935628 Score: 136
Period size: 53 Copynumber: 2.6 Consensus size: 53
2935482 TCAAAAATTG
* * * * *
2935492 TCGTGTTTTAAAATTTTTCATGTTTCTAAAATGTTTGT-ATTTCAAAAAATCC
1 TCGTGTTTTAAAAATTCTCATGTCTCAAAAATCTTTGTGATTTCAAAAAATCC
* *
2935544 TCGTGTTTTTAAAAATTCTCATGTCTCAAAAATCTTTGTGTTTTC--AAAATTC
1 TCGTG-TTTTAAAAATTCTCATGTCTCAAAAATCTTTGTGATTTCAAAAAATCC
* * * *
2935596 TAGTGTTTCAAAAATTTTCATGTTTTCAAAAAT
1 TCGTGTTTTAAAAATTCTCATG-TCTCAAAAAT
2935629 TTCCCATGTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
51 15 0.21
52 24 0.34
53 28 0.39
54 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (53 bp):
TCGTGTTTTAAAAATTCTCATGTCTCAAAAATCTTTGTGATTTCAAAAAATCC
Found at i:2935590 original size:18 final size:18
Alignment explanation
Indices: 2935569--2935628 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
2935559 TTCTCATGTC
2935569 TCAAAAATCTTTGTGTTT
1 TCAAAAATCTTTGTGTTT
* *
2935587 TCAAAATTC-TAGTG-TT
1 TCAAAAATCTTTGTGTTT
*
2935603 TCAAAAAT-TTTCATGTTT
1 TCAAAAATCTTT-GTGTTT
2935621 TCAAAAAT
1 TCAAAAAT
2935629 TTCCCATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 10 0.29
17 6 0.18
18 18 0.53
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (18 bp):
TCAAAAATCTTTGTGTTT
Found at i:2935636 original size:19 final size:18
Alignment explanation
Indices: 2935601--2935648 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
2935591 AATTCTAGTG
*
2935601 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTTCCATGT
2935619 TTTCAAAAATTTCCCATGT
1 TTTCAAAAATTT-CCATGT
2935638 TTTCAAAAATT
1 TTTCAAAAATT
2935649 CTTGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTCAAAAATTTCCATGT
Found at i:2935682 original size:19 final size:18
Alignment explanation
Indices: 2935480--2935681 Score: 111
Period size: 17 Copynumber: 11.5 Consensus size: 18
2935470 AAAAATCAGG
* *
2935480 TTTCAAAAATTGTCGTGT
1 TTTCAAAAATTTTCATGT
*
2935498 TTT-AAAATTTTTCATG-
1 TTTCAAAAATTTTCATGT
* *
2935514 TTTCTAAAATGTT--TGT
1 TTTCAAAAATTTTCATGT
** *
2935530 ATTTCAAAAAATCCTCGTGT
1 -TTTC-AAAAATTTTCATGT
* *
2935550 TTTTAAAAATTCTCATG-
1 TTTCAAAAATTTTCATGT
* *
2935567 TCTCAAAAATCTTT-GTGT
1 TTTCAAAAAT-TTTCATGT
*
2935585 TTTC-AAAATTCT-A-GT
1 TTTCAAAAATTTTCATGT
2935600 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAATTTTCATGT
*
2935619 TTTCAAAAATTTCCCATGT
1 TTTCAAAAATTT-TCATGT
*
2935638 TTTCAAAAA--TTCTTGT
1 TTTCAAAAATTTTCATGT
** *
2935654 ATTTTGAAAATTTTCTTGT
1 -TTTCAAAAATTTTCATGT
2935673 TTTCAAAAA
1 TTTCAAAAA
2935682 AAAAACTTTC
Statistics
Matches: 141, Mismatches: 27, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
15 4 0.03
16 13 0.09
17 50 0.35
18 45 0.32
19 26 0.18
20 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTTCATGT
Found at i:2935812 original size:22 final size:22
Alignment explanation
Indices: 2935769--2935810 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2935759 ATAATTTATC
*
2935769 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
2935791 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
2935811 ATTCTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:2935827 original size:17 final size:18
Alignment explanation
Indices: 2935800--2935849 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2935790 TAAAATTTTG
*
2935800 TGTTTTAAAAAATTCTCA
1 TGTTTTCAAAAATTCTCA
* * *
2935818 TG-TTTCAAAAACTGTCG
1 TGTTTTCAAAAATTCTCA
2935835 TGTTTTCAAAAATTC
1 TGTTTTCAAAAATTC
2935850 CCGTGTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (18 bp):
TGTTTTCAAAAATTCTCA
Found at i:2935906 original size:43 final size:43
Alignment explanation
Indices: 2935832--2935919 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 43
2935822 TCAAAAACTG
2935832 TCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATTTT-ATGTTT
1 TCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATTTTCATGTTT
* ** *
2935874 TCGTGTTTTCAAAAAAATT-TCGTGTTTCAAAAATTTTCGTGTTT
1 TCGTGTTTTC--AAAAATTCCCGTGTTAAAAAAATTTTCATGTTT
2935918 TC
1 TC
2935920 AAAAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 10 0.26
43 15 0.38
44 14 0.36
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (43 bp):
TCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATTTTCATGTTT
Found at i:2935906 original size:44 final size:42
Alignment explanation
Indices: 2935832--2935919 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 42
2935822 TCAAAAACTG
2935832 TCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATTTT-ATGTTT
1 TCGTGTTTTCAAAAATTCCCGTGTT-AAAAAATTTTCATGTTT
* * *
2935874 TCGTGTTTTCAAAAAAATT-TCGTGTTTCAAAAATTTTCGTGTTT
1 TCGTGTTTTC--AAAAATTCCCGTG-TTAAAAAATTTTCATGTTT
2935918 TC
1 TC
2935920 AAAAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
42 10 0.26
43 13 0.33
44 16 0.41
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (42 bp):
TCGTGTTTTCAAAAATTCCCGTGTTAAAAAATTTTCATGTTT
Found at i:2935911 original size:17 final size:18
Alignment explanation
Indices: 2935791--2935926 Score: 89
Period size: 18 Copynumber: 7.3 Consensus size: 18
2935781 TTTTCAAAAT
*
2935791 AAAATTTT-GTGTTTTAA
1 AAAATTTTCGTGTTTTCA
* *
2935808 AAAATTCTCATG-TTTCA
1 AAAATTTTCGTGTTTTCA
* *
2935825 AAAACTGTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
** ***
2935843 AAAATTCCCGTGTTAAAA
1 AAAATTTTCGTGTTTTCA
2935861 AAATTTTATGTTTTCGTGTTTTCAA
1 AAA----A--TTTTCGTGTTTTC-A
*
2935886 AAAAATTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
2935903 AAAATTTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
2935921 AAAATT
1 AAAATT
2935927 ATTATTTTGT
Statistics
Matches: 90, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
17 32 0.36
18 37 0.41
19 7 0.08
21 1 0.01
22 1 0.01
24 8 0.09
25 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:2946737 original size:29 final size:29
Alignment explanation
Indices: 2946695--2946752 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2946685 CCATGACAAA
2946695 AAGGAGCGGCCAAGAGAATTTCCCGAAGG
1 AAGGAGCGGCCAAGAGAATTTCCCGAAGG
* *
2946724 AAGGTGCGGCCAAGAGAATTTCGCGAAGG
1 AAGGAGCGGCCAAGAGAATTTCCCGAAGG
2946753 GGAGCTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.12
Consensus pattern (29 bp):
AAGGAGCGGCCAAGAGAATTTCCCGAAGG
Found at i:2946957 original size:1 final size:1
Alignment explanation
Indices: 2946953--2947019 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
2946943 AAAAGTAGAC
* * * * * * * *
2946953 AAAAAACAAAAAAAAACAAAAAAAACAAAAAAAGAAAAAAGAAAAAAGAAAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2947018 AA
1 AA
2947020 TCAAGATGAA
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2946963 original size:7 final size:7
Alignment explanation
Indices: 2946953--2947019 Score: 70
Period size: 7 Copynumber: 9.7 Consensus size: 7
2946943 AAAAGTAGAC
*
2946953 AAAAAAC
1 AAAAAAG
2946960 AAAAAA-
1 AAAAAAG
2946966 AAACAAA-
1 AAA-AAAG
2946973 AAAAACA-
1 AAAAA-AG
2946980 AAAAAAG
1 AAAAAAG
2946987 AAAAAAG
1 AAAAAAG
2946994 AAAAAAG
1 AAAAAAG
2947001 AAAAAA-
1 AAAAAAG
2947007 AGAAAAAG
1 A-AAAAAG
2947015 AAAAA
1 AAAAA
2947020 TCAAGATGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.13
7 47 0.85
8 1 0.02
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2946965 original size:19 final size:19
Alignment explanation
Indices: 2946953--2947013 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
2946943 AAAAGTAGAC
2946953 AAAAAACAAAAAAAAACAA
1 AAAAAACAAAAAAAAACAA
2946972 AAAAAACAAAAAAAGAA-AA
1 AAAAAACAAAAAAA-AACAA
*
2946991 AAGAAAA-AAGAAAAAAAGAA
1 AA-AAAACAA-AAAAAAACAA
2947011 AAA
1 AAA
2947014 GAAAAATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAAACAA
Found at i:2946977 original size:14 final size:14
Alignment explanation
Indices: 2946953--2947019 Score: 82
Period size: 14 Copynumber: 4.9 Consensus size: 14
2946943 AAAAGTAGAC
*
2946953 AAAAAACAAAAAAA
1 AAAAAAGAAAAAAA
* *
2946967 AACAAA-AAAAACA
1 AAAAAAGAAAAAAA
*
2946980 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAA
2946994 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
*
2947008 GAAAAAGAAAAA
1 AAAAAAGAAAAA
2947020 TCAAGATGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 11 0.24
14 34 0.76
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:2947804 original size:83 final size:84
Alignment explanation
Indices: 2947609--2947947 Score: 435
Period size: 82 Copynumber: 4.1 Consensus size: 84
2947599 CTGAGAGAAA
2947609 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA
**
2947674 TTTTC--TTT-TAAATCTCT
65 TTTTCAATTTATATTTCTCT
* *
2947691 GTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGT-CACGCTGAGGTAT
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCCACGCTGAGGTAT
* *
2947755 CTTCAATTTATGTTTCTCT
66 TTTCAATTTATATTTCTCT
* * * *
2947774 GTTTTTCAAAAAAATCAACTTATATTGCGAGAAGTGAGTTGGGCCTCAGGTCGCACGCTGAGTTA
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA
** *
2947839 -TTTCTTTTTA-ATTTCTGT
65 TTTTCAATTTATATTTCTCT
* *
2947857 -TTTTTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTAT
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCCACGCTGAGGTAT
* *
2947919 TTTCAATTTATGTTTTTCT
66 TTTCAATTTATATTTCTCT
*
2947938 ATTTTTCAAA
1 GTTTTTCAAA
2947948 GTGCATTGCA
Statistics
Matches: 220, Mismatches: 28, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
79 11 0.05
80 24 0.11
81 43 0.20
82 64 0.29
83 60 0.27
84 7 0.03
85 11 0.05
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (84 bp):
GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCCACGCTGAGGTAT
TTTCAATTTATATTTCTCT
Found at i:2947913 original size:164 final size:165
Alignment explanation
Indices: 2947609--2947947 Score: 556
Period size: 164 Copynumber: 2.1 Consensus size: 165
2947599 CTGAGAGAAA
*
2947609 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTA
* *
2947674 TTTTCTTTTAAATCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG
66 TTTTCTTTTAAATCTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
2947739 GGTCACGCTGAGGTATCTTCAATTTATGTTTCTCT
131 GGTCACGCTGAGGTATCTTCAATTTATGTTTCTCT
* * *
2947774 GTTTTTCAAAAAAATCAACTTATATTGCGAGAAGTGAGTTGGGCCTCAGGTCGCACGCTGAGTTA
1 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTA
* *
2947839 -TTTCTTTTTAATTTCTGTTTTTTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC
66 TTTTCTTTTAAATCTCTG-TTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC
* *
2947902 GGGTCACGCTGAGGTATTTTCAATTTATGTTTTTCT
130 GGGTCACGCTGAGGTATCTTCAATTTATGTTTCTCT
*
2947938 ATTTTTCAAA
1 GTTTTTCAAA
2947948 GTGCATTGCA
Statistics
Matches: 162, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
164 95 0.59
165 67 0.41
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (165 bp):
GTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTA
TTTTCTTTTAAATCTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGGTATCTTCAATTTATGTTTCTCT
Found at i:2948433 original size:76 final size:76
Alignment explanation
Indices: 2948159--2948977 Score: 1144
Period size: 76 Copynumber: 10.6 Consensus size: 76
2948149 AATCTCTGCT
* *
2948159 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCA
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT-TTC-
* **
2948224 ATTTATGTTTCTCTG
64 TTTTAAATTTC-C-G
* * * * * * *
2948239 TTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGGGCATCGGGTCGCATGCTGGGGTAT
1 TTTTTC--AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CATGCCGAGGTAT
* *
2948304 TTCTTTTTAATTTCTG
61 TTCTTTTAAATTTCCG
2948320 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTC
1 -TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTC
2948385 TTTTAAATTTCCG
64 TTTTAAATTTCCG
*
2948398 TTTTTCAAAAATCAATTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
2948463 TTAAATTTCCG
66 TTAAATTTCCG
2948474 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
2948539 TTAAATTTCCG
66 TTAAATTTCCG
*
2948550 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCCGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
*
2948615 TTAAATTTTCG
66 TTAAATTTCCG
*
2948626 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCCGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
**
2948691 TTAAATTTTTG
66 TTAAATTTCCG
2948702 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
2948767 TTAAATTTCCG
66 TTAAATTTCCG
**
2948778 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
**
2948843 TTAAATTTATG
66 TTAAATTTCCG
* * * * *
2948854 TTTTTTGAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTA--
1 -TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GGG-TCATGCCGAGGTATT
* **
2948917 T-TTTT-GATTT-TT
62 TCTTTTAAATTTCCG
* * *
2948929 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
2948978 GCACGCCGAG
Statistics
Matches: 682, Mismatches: 47, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
72 1 0.00
73 3 0.00
74 39 0.06
75 1 0.00
76 442 0.65
77 32 0.05
78 44 0.06
79 2 0.00
80 36 0.05
81 19 0.03
82 23 0.03
83 26 0.04
84 3 0.00
85 11 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (76 bp):
TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
TTAAATTTCCG
Found at i:2949391 original size:30 final size:30
Alignment explanation
Indices: 2949353--2949423 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
2949343 ACCTCAAACC
2949353 TTTT-TAAAATTTACATCTT-AACCCCAAAA
1 TTTTCTAAAATTTACAT-TTCAACCCCAAAA
* **
2949382 TTTTCTAAAA-TTACATTTCGACCCTTAAA
1 TTTTCTAAAATTTACATTTCAACCCCAAAA
2949411 TTTTCTTAAAATT
1 TTTTC-TAAAATT
2949424 GCACTTTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 2 0.06
29 22 0.63
30 10 0.29
31 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTTCTAAAATTTACATTTCAACCCCAAAA
Found at i:2949395 original size:29 final size:29
Alignment explanation
Indices: 2949353--2949436 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
2949343 ACCTCAAACC
2949353 TTTT-TAAAATTTACATCTTAACCCCAAAA
1 TTTTCTAAAA-TTACATCTTAACCCCAAAA
* **
2949382 TTTTCTAAAATTACAT-TTCGACCCTTAAA
1 TTTTCTAAAATTACATCTT-AACCCCAAAA
*
2949411 TTTTCTTAAAATTGCA-CTTTAACCCC
1 TTTTC-TAAAATTACATC-TTAACCCC
2949437 TAAACTCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.05
29 22 0.50
30 18 0.41
31 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTTCTAAAATTACATCTTAACCCCAAAA
Found at i:2949993 original size:6 final size:6
Alignment explanation
Indices: 2949986--2950044 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
2949976 CGGCCCGAAG
* * *
2949986 AAGAAG AAGAAA AAGAAA AAGAAA GAAGGAAA AAGAGAG AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA -AA-GAAA AAGA-AA AAGAAA AAGAAA
2950037 AAGAAA AA
1 AAGAAA AA
2950045 AAGAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 32 0.71
7 9 0.20
8 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2950245 original size:34 final size:33
Alignment explanation
Indices: 2950207--2950271 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
2950197 AGCCCAAATG
*
2950207 CAGGCCCAGCGCAGCAGCAGGCCCAGCAGGCCCC
1 CAGGCCCAGCGCAGCAGCA-GCCCAACAGGCCCC
*
2950241 CAGGCCCAGTGCAGCAGCAGCCCAACAGGCC
1 CAGGCCCAGCGCAGCAGCAGCCCAACAGGCC
2950272 AGCCCAGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.23, C:0.45, G:0.31, T:0.02
Consensus pattern (33 bp):
CAGGCCCAGCGCAGCAGCAGCCCAACAGGCCCC
Found at i:2950297 original size:10 final size:10
Alignment explanation
Indices: 2950284--2950339 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
2950274 CCCAGTCCAG
2950284 AAAAAAAAG-
1 AAAAAAAAGA
2950293 AAAAAAAAGA
1 AAAAAAAAGA
**
2950303 GGAAAAAAGA
1 AAAAAAAAGA
* *
2950313 AGATAAAAGA
1 AAAAAAAAGA
*
2950323 AGAAAAAAGA
1 AAAAAAAAGA
2950333 AAAAAAA
1 AAAAAAA
2950340 TGGTTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 9 0.22
10 31 0.77
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2950310 original size:20 final size:19
Alignment explanation
Indices: 2950282--2950339 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
2950272 AGCCCAGTCC
2950282 AGAA-AAAAAAGAAAAAAA
1 AGAAGAAAAAAGAAAAAAA
* *
2950300 AGAGGAAAAAAGAAGATAAA
1 AGAAGAAAAAAGAA-AAAAA
2950320 AGAAGAAAAAAGAAAAAAA
1 AGAAGAAAAAAGAAAAAAA
2950339 A
1 A
2950340 TGGTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.09
19 14 0.41
20 17 0.50
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AGAAGAAAAAAGAAAAAAA
Found at i:2950606 original size:19 final size:19
Alignment explanation
Indices: 2950578--2950624 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
2950568 AAATTTCTCG
*
2950578 TGTTTCAAAAAAATTGTCA
1 TGTTTTAAAAAAATTGTCA
*
2950597 TGTTTT--AAAAATTTTCA
1 TGTTTTAAAAAAATTGTCA
2950614 TGTTTCTAAAA
1 TGTTT-TAAAA
2950625 TGTTTGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 15 0.65
18 1 0.04
19 5 0.22
20 2 0.09
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (19 bp):
TGTTTTAAAAAAATTGTCA
Found at i:2950623 original size:18 final size:17
Alignment explanation
Indices: 2950586--2950783 Score: 107
Period size: 17 Copynumber: 11.3 Consensus size: 17
2950576 CGTGTTTCAA
*
2950586 AAAAATTGTCATGTTTT
1 AAAAATTTTCATGTTTT
2950603 AAAAATTTTCATGTTTCT
1 AAAAATTTTCATGTTT-T
*
2950621 -AAAATGTT--TGTATTT
1 AAAAATTTTCATGT-TTT
** *
2950636 CAAAAAATCCTCGTGTTTT
1 --AAAAATTTTCATGTTTT
* *
2950655 CAAAAATTCTCATGTTTA
1 -AAAAATTTTCATGTTTT
* *
2950673 AAAAATCTTCGTGTTTT
1 AAAAATTTTCATGTTTT
* * *
2950690 CAAAATTCT-AGTGTTTC
1 AAAAATTTTCA-TGTTTT
2950707 AAAAATTTTCATGTTTT
1 AAAAATTTTCATGTTTT
* *
2950724 CAAAAATTTCCCCTGTTTT
1 -AAAAATTT-TCATGTTTT
* * *
2950743 CAAAAATTCTCGTATTTT
1 -AAAAATTTTCATGTTTT
* *
2950761 GAAAATTTTCTTGTTTT
1 AAAAATTTTCATGTTTT
2950778 CAAAAA
1 -AAAAA
2950784 AAAACTTTCG
Statistics
Matches: 138, Mismatches: 31, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
15 4 0.03
16 2 0.01
17 71 0.51
18 40 0.29
19 18 0.13
20 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCATGTTTT
Found at i:2950668 original size:70 final size:69
Alignment explanation
Indices: 2950586--2950750 Score: 172
Period size: 70 Copynumber: 2.3 Consensus size: 69
2950576 CGTGTTTCAA
* * *
2950586 AAAAATTGTCATGTTTTAAAAATTTTCATG-TTTCTAAAATGT-TTGTATTTCAAAAAATCCTCG
1 AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTC-AAAAT-TCTAGTATTTC-AAAAATCCTCA
2950649 TGTTTTC
63 TGTTTTC
* * * * **
2950656 AAAAATTCTCATGTTTAAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATGT
1 AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
2950721 TTTC
66 TTTC
* *
2950725 AAAAATTTCCCCTGTTTTCAAAAATT
1 AAAAA-TTCTCATGTTTT-AAAAATT
2950751 CTCGTATTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
69 21 0.27
70 47 0.60
71 10 0.13
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (69 bp):
AAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
TTTC
Found at i:2950695 original size:34 final size:34
Alignment explanation
Indices: 2950637--2950728 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
2950627 TTTGTATTTC
*
2950637 AAAAAATCCTCGTGTTTTCAAAAATTCTCA-TGTTT
1 AAAAAATCTTCGTGTTTTC-AAAATTCT-AGTGTTT
2950672 AAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTT
1 AAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTT
* * *
2950706 CAAAAATTTTCATGTTTTCAAAA
1 AAAAAATCTTCGTGTTTTCAAAA
2950729 ATTTCCCCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.02
34 33 0.63
35 18 0.35
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (34 bp):
AAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTT
Found at i:2950837 original size:18 final size:17
Alignment explanation
Indices: 2950814--2950858 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2950804 ATCTCCGTGT
2950814 TTTCAAAAAATTCTCGTC
1 TTTCAAAAAATTC-CGTC
* *
2950832 TTTCAAAAATTTCCGTG
1 TTTCAAAAAATTCCGTC
2950849 TTTCAAAAAA
1 TTTCAAAAAA
2950859 AAATCCTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (17 bp):
TTTCAAAAAATTCCGTC
Found at i:2950853 original size:35 final size:36
Alignment explanation
Indices: 2950633--2950858 Score: 136
Period size: 35 Copynumber: 6.3 Consensus size: 36
2950623 AATGTTTGTA
* *
2950633 TTTCAAAAAATCCTCGTGTTTTCAAAAA-TTCTCATG-
1 TTTCAAAAAATTCTCGT-TTTTCAAAAATTTC-CGTGT
*
2950669 TTT-AAAAAA-TCTTCGTGTTTTC-AAAA-TTCTAGTG-
1 TTTCAAAAAATTC-TCGT-TTTTCAAAAATTTC-CGTGT
* * *
2950703 TTTC-AAAAATTTTCATGTTTTCAAAAATTTCCCCTGT
1 TTTCAAAAAATTCTCGT-TTTTCAAAAATTT-CCGTGT
* * *
2950740 TTTC-AAAAATTCTCGTATTTT-GAAAATTTTCTTGT
1 TTTCAAAAAATTCTCGT-TTTTCAAAAATTTCCGTGT
* *
2950775 TTTCAAAAAAAAACTT-TCGTGTTTT-ATAAATCTCCGTGT
1 TTTC---AAAAAA-TTCTCGT-TTTTCAAAAATTTCCGTGT
*
2950814 TTTCAAAAAATTCTCGTCTTTCAAAAATTTCCGTG-
1 TTTCAAAAAATTCTCGTTTTTCAAAAATTTCCGTGT
2950849 TTTCAAAAAA
1 TTTCAAAAAA
2950859 AAATCCTCGT
Statistics
Matches: 154, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
34 28 0.18
35 44 0.29
36 35 0.23
37 19 0.12
39 26 0.17
40 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTCAAAAAATTCTCGTTTTTCAAAAATTTCCGTGT
Found at i:2950859 original size:36 final size:36
Alignment explanation
Indices: 2950719--2950859 Score: 112
Period size: 36 Copynumber: 3.9 Consensus size: 36
2950709 AAATTTTCAT
*
2950719 GTTTTCAAAAATTTCCCCTGTTTTC--AAAAATTCTC
1 GTTTTCAAAAATTT-CCGTGTTTTCAAAAAAATTCTC
** * *
2950754 GTATTTTGAAAATTTTCTTGTTTTCAAAAAAAAACTT-TC
1 GT-TTTCAAAAATTTCCGTGTTTTC--AAAAAAA-TTCTC
* * *
2950793 GTGTTTTATAAATCTCCGTGTTTTC-AAAAAATTCTC
1 GT-TTTCAAAAATTTCCGTGTTTTCAAAAAAATTCTC
2950829 GTCTTTCAAAAATTTCCGTG-TTTCAAAAAAA
1 GT-TTTCAAAAATTTCCGTGTTTTCAAAAAAA
2950860 AATCCTCGTG
Statistics
Matches: 84, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
35 16 0.19
36 40 0.48
39 26 0.31
40 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (36 bp):
GTTTTCAAAAATTTCCGTGTTTTCAAAAAAATTCTC
Found at i:2950869 original size:74 final size:74
Alignment explanation
Indices: 2950737--2950877 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
2950727 AAATTTCCCC
** * * * *
2950737 TGTTTTCAAAAATTCTCGTATTTTGAAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAT
1 TGTTTTCAAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACTCTCGTGTTTCAT
2950802 AAATCTCCG
66 AAATCTCCG
*
2950811 TGTTTTCAAAAAATTCTCGTCTTTCAAAAATTTCCGTG-TTTCAAAAAAAAA-TCCTCGTGTTTC
1 TGTTTTC-AAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACT-CTCGTGTTTC
2950874 ATAA
64 ATAA
2950878 TTTATCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
73 1 0.02
74 32 0.55
75 25 0.43
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (74 bp):
TGTTTTCAAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACTCTCGTGTTTCAT
AAATCTCCG
Found at i:2950927 original size:22 final size:22
Alignment explanation
Indices: 2950884--2950925 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2950874 ATAATTTATC
*
2950884 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
2950906 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
2950926 ATTCTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:2950959 original size:121 final size:120
Alignment explanation
Indices: 2950762--2950979 Score: 268
Period size: 121 Copynumber: 1.8 Consensus size: 120
2950752 TCGTATTTTG
* *
2950762 AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTATAAATCTCCGTGTTTTCAAAAAATTC
1 AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAAAAATCTCCATGTTTTCAAAAAATTC
* *
2950827 TCGTCTTTCAAAAATTTCCGTGTTTCAAAAAAAAATCCTCGTGTTTCATAATTTATC
66 TCGTCTTTCAAAAATTCCCATG-TT-AAAAAAAAATCCTCGTGTTTCATAATTTATC
* * *
2950884 AAAATTTT-TGTGTTTTCAAAATAAAA-TTTTGTGTTTTAAAAAAT-TCTCATG-TTTCAAAAAC
1 AAAATTTTCT-TGTTTTCAAAAAAAAACTTTCGTGTTTT-AAAAATCTC-CATGTTTTCAAAAAA
2950945 TGTCGT-GT-TTTCAAAAATTCCCATGTTAAAAAAAA
63 T-TC-TCGTCTTTCAAAAATTCCCATGTTAAAAAAAA
2950980 TTTATGTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
119 8 0.10
120 2 0.02
121 38 0.45
122 35 0.42
123 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (120 bp):
AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAAAAATCTCCATGTTTTCAAAAAATTC
TCGTCTTTCAAAAATTCCCATGTTAAAAAAAAATCCTCGTGTTTCATAATTTATC
Found at i:2950971 original size:18 final size:18
Alignment explanation
Indices: 2950915--2950971 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2950905 TAAAATTTTG
*
2950915 TGTTTTAAAAAATTCTCA
1 TGTTTTCAAAAATTCTCA
* * *
2950933 TG-TTTCAAAAACTGTCG
1 TGTTTTCAAAAATTCTCA
*
2950950 TGTTTTCAAAAATTCCCA
1 TGTTTTCAAAAATTCTCA
2950968 TGTT
1 TGTT
2950972 AAAAAAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (18 bp):
TGTTTTCAAAAATTCTCA
Found at i:2951040 original size:18 final size:17
Alignment explanation
Indices: 2950987--2951041 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 17
2950977 AAATTTATGT
2950987 TTTCGTGTTTTCAAAAAAA
1 TTTCGTGTTTTC--AAAAA
2951006 TTTCGTG-TTTCAAAAA
1 TTTCGTGTTTTCAAAAA
2951022 TCTTCGTGTTTTCAAAAA
1 T-TTCGTGTTTTCAAAAA
2951040 TT
1 TT
2951042 ATTATTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 14 0.41
19 7 0.21
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
TTTCGTGTTTTCAAAAA
Found at i:2952517 original size:14 final size:15
Alignment explanation
Indices: 2952498--2952530 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2952488 AATTAATAAC
*
2952498 AAAAATAAAGT-ATA
1 AAAAATAAACTGATA
2952512 AAAAATAAACTGATA
1 AAAAATAAACTGATA
2952527 AAAA
1 AAAA
2952531 TAATATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAATAAACTGATA
Found at i:2964441 original size:33 final size:33
Alignment explanation
Indices: 2964395--2964478 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
2964385 CCCAGATTCT
**
2964395 CCTCCACCACCACCACCTTTGCCACCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* * * * * *
2964428 CCTCCGCCCCCACCTCCATCATCTCCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* *
2964461 CCTCCTCCTCCACCACCT
1 CCTCCACCACCACCACCT
2964479 CTACCAACAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.61, G:0.02, T:0.20
Consensus pattern (33 bp):
CCTCCACCACCACCACCTTCACCACCTTCACCA
Found at i:2964474 original size:15 final size:15
Alignment explanation
Indices: 2964450--2964479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2964440 CCTCCATCAT
*
2964450 CTCCTTCACCACCTC
1 CTCCTCCACCACCTC
2964465 CTCCTCCACCACCTC
1 CTCCTCCACCACCTC
2964480 TACCAACACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.63, G:0.00, T:0.23
Consensus pattern (15 bp):
CTCCTCCACCACCTC
Found at i:2968722 original size:15 final size:15
Alignment explanation
Indices: 2968702--2968734 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2968692 ATATAGAAAC
2968702 TCTAATGAATAAATA
1 TCTAATGAATAAATA
2968717 TCTAATGAATAAATA
1 TCTAATGAATAAATA
2968732 TCT
1 TCT
2968735 CTCAGTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (15 bp):
TCTAATGAATAAATA
Found at i:2978348 original size:20 final size:21
Alignment explanation
Indices: 2978297--2978350 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
2978287 TCTATTGATT
*
2978297 TTTTTAATATTATTAAATAATA
1 TTTTTAATA-TATCAAATAATA
2978319 TTTATTAATATATCAAATAA-A
1 TTT-TTAATATATCAAATAATA
2978340 TTTTTAATATA
1 TTTTTAATATA
2978351 ACTTTATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 8 0.27
21 4 0.13
22 12 0.40
23 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAATATATCAAATAATA
Found at i:2986485 original size:31 final size:32
Alignment explanation
Indices: 2986450--2986509 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2986440 TAATTAAATT
2986450 ATATTTAATT-AATTCAACTCAAAATTTACAA
1 ATATTTAATTAAATTCAACTCAAAATTTACAA
* * *
2986481 ATATTTACTTAAATTCGATTCAAAATTTA
1 ATATTTAATTAAATTCAACTCAAAATTTA
2986510 ATGAAGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (32 bp):
ATATTTAATTAAATTCAACTCAAAATTTACAA
Found at i:3006740 original size:18 final size:18
Alignment explanation
Indices: 3006713--3006805 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
3006703 TACGACCGTT
3006713 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3006731 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3006749 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3006767 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3006785 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
3006803 TAC
1 TAC
3006806 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:3011766 original size:10 final size:9
Alignment explanation
Indices: 3011750--3011823 Score: 76
Period size: 9 Copynumber: 7.7 Consensus size: 9
3011740 AATTATACAA
3011750 ATAAAAATT
1 ATAAAAATT
3011759 ACTAAAAATT
1 A-TAAAAATT
3011769 ATAAAAATT
1 ATAAAAATT
**
3011778 ATTAAATTTT
1 A-TAAAAATT
3011788 AATAAAAATT
1 -ATAAAAATT
3011798 ATAAAAATCGT
1 ATAAAAAT--T
*
3011809 AAAAAAATT
1 ATAAAAATT
3011818 ATAAAA
1 ATAAAA
3011824 CATAATATAG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
9 24 0.44
10 21 0.39
11 9 0.17
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3011814 original size:20 final size:18
Alignment explanation
Indices: 3011736--3011823 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 18
3011726 GACATGTAGT
*
3011736 AAAAAATTATACAAA-T-
1 AAAAAATTATAAAAATTA
3011752 -AAAAATTACTAAAAATTA
1 AAAAAATTA-TAAAAATTA
* **
3011770 TAAAAATTATTAAATTTTA
1 AAAAAATTA-TAAAAATTA
3011789 ATAAAAATTATAAAAATCGTA
1 A-AAAAATTATAAAAAT--TA
3011810 AAAAAATTATAAAA
1 AAAAAATTATAAAA
3011824 CATAATATAG
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
15 8 0.14
16 5 0.09
17 1 0.02
19 20 0.34
20 21 0.36
21 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAAAATTATAAAAATTA
Found at i:3011821 original size:29 final size:28
Alignment explanation
Indices: 3011752--3011823 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
3011742 TTATACAAAT
*
3011752 AAAAATTACTAAAAATTATAAAAATTATT
1 AAAAATTA-TAAAAATTATAAAAATTATA
**
3011781 AAATTTTAATAAAAATTATAAAAATCGTA-A
1 AAAAATT-ATAAAAATTATAAAAAT--TATA
3011811 AAAAATTATAAAA
1 AAAAATTATAAAA
3011824 CATAATATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 27 0.77
30 6 0.17
31 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATTATAAAAATTATAAAAATTATA
Found at i:3014775 original size:18 final size:17
Alignment explanation
Indices: 3014749--3014782 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3014739 TTTTTTTCTC
3014749 TCTTTTCCTTGTCCTTG
1 TCTTTTCCTTGTCCTTG
3014766 TCTTTGTCCTTGTCCTT
1 TCTTT-TCCTTGTCCTT
3014783 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.59
Consensus pattern (17 bp):
TCTTTTCCTTGTCCTTG
Found at i:3016944 original size:95 final size:94
Alignment explanation
Indices: 3016758--3017085 Score: 446
Period size: 95 Copynumber: 3.4 Consensus size: 94
3016748 ACGGGCAACC
* * *
3016758 ACTTGGGAAACCTACTG-TTTCCTTATGCCAAGCTACTTCAACAATGCCCCAAATAGAAAGATAA
1 ACTTGGGAAACCTACTGCTTT-CTTATGCCAAG---C-T-AACAATTCCCCGAATAGGAAGAT-A
3016822 TTTCAAGAAATGCTCTTTTGATCAATAATTCTAGCTCAGAA
59 ----AAGAAA-GCTCTTTTGATCAATAATTCTAGCTCAGAA
3016863 ACTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAC
1 ACTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAA-
3016928 GCTCTTTTGATCAATAATTCTAGCTCAGAA
65 GCTCTTTTGATCAATAATTCTAGCTCAGAA
*
3016958 ACTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAACG-AAG
1 ACTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAG
*
3017022 CTCTTTTGATCAATAATTCTCGCTCAGAA
66 CTCTTTTGATCAATAATTCTAGCTCAGAA
* *
3017051 ACTTAGGG-AACCTACTGTTTTCTTATTCCAAGCTA
1 ACTT-GGGAAACCTACTGCTTTCTTATGCCAAGCTA
3017086 CTTCAACAAT
Statistics
Matches: 213, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
93 58 0.27
94 5 0.02
95 96 0.45
99 1 0.00
100 20 0.09
101 1 0.00
102 1 0.00
105 28 0.13
106 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (94 bp):
ACTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAG
CTCTTTTGATCAATAATTCTAGCTCAGAA
Found at i:3021543 original size:824 final size:824
Alignment explanation
Indices: 3019956--3021604 Score: 3271
Period size: 824 Copynumber: 2.0 Consensus size: 824
3019946 ATGATGATGA
3019956 ATCATCTTCTCCCATGCATTCCAACATATGAAGAGAAAAGAAAGAAAGAAACTTTTTTTATTTAC
1 ATCATCTTCTCCCATGCATTCCAACATATGAAGAGAAAAGAAAGAAAGAAACTTTTTTTATTTAC
3020021 AATTTGGTCCTCTCACTAAAAATTTTTACTTAGAAATCAAAGAAATTTCCATAGCCACTAAGAGA
66 AATTTGGTCCTCTCACTAAAAATTTTTACTTAGAAATCAAAGAAATTTCCATAGCCACTAAGAGA
3020086 TAAAATTGATAAGGAGACCATGGGGAGCTAGAATATCAAGTTAGATTCAAGAAACAGAGGCTGGA
131 TAAAATTGATAAGGAGACCATGGGGAGCTAGAATATCAAGTTAGATTCAAGAAACAGAGGCTGGA
3020151 GGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAGGGTAAGAACATCAAGATTTCAAT
196 GGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAGGGTAAGAACATCAAGATTTCAAT
3020216 ATATTTTTTAGTTTGATATTATTGAAAAAGTATGAAATTGATGTTAATGTAGGGTTTTATTATAT
261 ATATTTTTTAGTTTGATATTATTGAAAAAGTATGAAATTGATGTTAATGTAGGGTTTTATTATAT
3020281 AAGGTTCTATGTTCTTGATATGTTAGTGAAGGGAAATAAGAGGAATTGATAGCAAATGTTGTAGA
326 AAGGTTCTATGTTCTTGATATGTTAGTGAAGGGAAATAAGAGGAATTGATAGCAAATGTTGTAGA
3020346 GAAAGGAAAGGAGGGTGTTATAAATTTGATTATCAACATCTTGCACAAAAACAGTTTAGGACAGC
391 GAAAGGAAAGGAGGGTGTTATAAATTTGATTATCAACATCTTGCACAAAAACAGTTTAGGACAGC
3020411 ATCAGTAGGTTAAATTTGAAAAATCACCATAAATCGTGGAAATTTAATTAAAAGATGAAAAAATA
456 ATCAGTAGGTTAAATTTGAAAAATCACCATAAATCGTGGAAATTTAATTAAAAGATGAAAAAATA
3020476 TGGAATTAAATCTTATTGAGTCTAATTTCTCATAGAAGAAACGGTGTAAGCAATGGAATGGTAAA
521 TGGAATTAAATCTTATTGAGTCTAATTTCTCATAGAAGAAACGGTGTAAGCAATGGAATGGTAAA
*
3020541 TGATGAGTTAGAATAAATTTTGTGAGATAAGGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTT
586 TCATGAGTTAGAATAAATTTTGTGAGATAAGGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTT
3020606 TGGAAAATCATAAAAAAATGGATAAAAATTAATAGGGGCTTAAATTTATATGTTTAAAATTATGA
651 TGGAAAATCATAAAAAAATGGATAAAAATTAATAGGGGCTTAAATTTATATGTTTAAAATTATGA
3020671 ATGAGTCTATTTTCAATAGAAACAAACAATAACATCATCCAACTTCTATACAAAGAGATAATTAT
716 ATGAGTCTATTTTCAATAGAAACAAACAATAACATCATCCAACTTCTATACAAAGAGATAATTAT
3020736 TTTTTAGTGAAGAGGGGTCAGAACTGTCAAACAGTGAAACAGAT
781 TTTTTAGTGAAGAGGGGTCAGAACTGTCAAACAGTGAAACAGAT
3020780 ATCATCTTCTCCCATGCATTCCAACATATGAAGAGAAAAGAAAGAAAGAAACTTTTTTTATTTAC
1 ATCATCTTCTCCCATGCATTCCAACATATGAAGAGAAAAGAAAGAAAGAAACTTTTTTTATTTAC
3020845 AATTTGGTCCTCTCACTAAAAATTTTTACTTAGAAATCAAAGAAATTTCCATAGCCACTAAGAGA
66 AATTTGGTCCTCTCACTAAAAATTTTTACTTAGAAATCAAAGAAATTTCCATAGCCACTAAGAGA
3020910 TAAAATTGATAAGGAGACCATGGGGAGCTAGAATATCAAGTTAGATTCAAGAAACAGAGGCTGGA
131 TAAAATTGATAAGGAGACCATGGGGAGCTAGAATATCAAGTTAGATTCAAGAAACAGAGGCTGGA
3020975 GGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAGGGTAAGAACATCAAGATTTCAAT
196 GGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAGGGTAAGAACATCAAGATTTCAAT
3021040 ATATTTTTTAGTTTGATATTATTGAAAAAGTATGAAATTGATGTTAATGTAGGGTTTTATTATAT
261 ATATTTTTTAGTTTGATATTATTGAAAAAGTATGAAATTGATGTTAATGTAGGGTTTTATTATAT
3021105 AAGGTTCTATGTTCTTGATATGTTAGTGAAGGGAAATAAGAGGAATTGATAGCAAATGTTGTAGA
326 AAGGTTCTATGTTCTTGATATGTTAGTGAAGGGAAATAAGAGGAATTGATAGCAAATGTTGTAGA
3021170 GAAAGGAAAGGAGGGTGTTATAAATTTGATTATCAACATCTTGCACAAAAACAGTTTAGGACAGC
391 GAAAGGAAAGGAGGGTGTTATAAATTTGATTATCAACATCTTGCACAAAAACAGTTTAGGACAGC
3021235 ATCAGTAGGTTAAATTTGAAAAATCACCATAAATCGTGGAAATTTAATTAAAAGATGAAAAAATA
456 ATCAGTAGGTTAAATTTGAAAAATCACCATAAATCGTGGAAATTTAATTAAAAGATGAAAAAATA
*
3021300 TGGAATTAAATCTTATTGAGTCTAATTTCTCATAGAAGAAACGGTGTAAGCAATGGAATTGTAAA
521 TGGAATTAAATCTTATTGAGTCTAATTTCTCATAGAAGAAACGGTGTAAGCAATGGAATGGTAAA
*
3021365 TCATGAGTTATAATAAATTTTGTGAGATAAGGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTT
586 TCATGAGTTAGAATAAATTTTGTGAGATAAGGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTT
3021430 TGGAAAATCATAAAAAAATGGATAAAAATTAATAGGGGCTTAAATTTATATGTTTAAAATTATGA
651 TGGAAAATCATAAAAAAATGGATAAAAATTAATAGGGGCTTAAATTTATATGTTTAAAATTATGA
3021495 ATGAGTCTATTTTCAATAGAAACAAACAATAACATCATCCAACTTCTATACAAAGAGATAATTAT
716 ATGAGTCTATTTTCAATAGAAACAAACAATAACATCATCCAACTTCTATACAAAGAGATAATTAT
3021560 TTTTTAGTGAAGAGGGGTCAGAACTGTCAAACAGTGAAACAGAT
781 TTTTTAGTGAAGAGGGGTCAGAACTGTCAAACAGTGAAACAGAT
3021604 A
1 A
3021605 AACTTTAAAG
Statistics
Matches: 822, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
824 822 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (824 bp):
ATCATCTTCTCCCATGCATTCCAACATATGAAGAGAAAAGAAAGAAAGAAACTTTTTTTATTTAC
AATTTGGTCCTCTCACTAAAAATTTTTACTTAGAAATCAAAGAAATTTCCATAGCCACTAAGAGA
TAAAATTGATAAGGAGACCATGGGGAGCTAGAATATCAAGTTAGATTCAAGAAACAGAGGCTGGA
GGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGAGCAGGGTAAGAACATCAAGATTTCAAT
ATATTTTTTAGTTTGATATTATTGAAAAAGTATGAAATTGATGTTAATGTAGGGTTTTATTATAT
AAGGTTCTATGTTCTTGATATGTTAGTGAAGGGAAATAAGAGGAATTGATAGCAAATGTTGTAGA
GAAAGGAAAGGAGGGTGTTATAAATTTGATTATCAACATCTTGCACAAAAACAGTTTAGGACAGC
ATCAGTAGGTTAAATTTGAAAAATCACCATAAATCGTGGAAATTTAATTAAAAGATGAAAAAATA
TGGAATTAAATCTTATTGAGTCTAATTTCTCATAGAAGAAACGGTGTAAGCAATGGAATGGTAAA
TCATGAGTTAGAATAAATTTTGTGAGATAAGGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTT
TGGAAAATCATAAAAAAATGGATAAAAATTAATAGGGGCTTAAATTTATATGTTTAAAATTATGA
ATGAGTCTATTTTCAATAGAAACAAACAATAACATCATCCAACTTCTATACAAAGAGATAATTAT
TTTTTAGTGAAGAGGGGTCAGAACTGTCAAACAGTGAAACAGAT
Found at i:3022486 original size:54 final size:54
Alignment explanation
Indices: 3022404--3022533 Score: 260
Period size: 54 Copynumber: 2.4 Consensus size: 54
3022394 GAGGGTCTGA
3022404 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTATTGGGG
1 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTATTGGGG
3022458 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTATTGGGG
1 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTATTGGGG
3022512 ATTTAGCCTGGACTGGTAATCC
1 ATTTAGCCTGGACTGGTAATCC
3022534 TGCTGCAATG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (54 bp):
ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTATTGGGG
Found at i:3023595 original size:13 final size:13
Alignment explanation
Indices: 3023579--3023629 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
3023569 AATAAATACC
3023579 AAAAATTTATTTT
1 AAAAATTTATTTT
*
3023592 AAAAATTTA---A
1 AAAAATTTATTTT
3023602 AAAAATTTATTTT
1 AAAAATTTATTTT
3023615 AAAAA--TATTTT
1 AAAAATTTATTTT
3023626 AAAA
1 AAAA
3023630 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 9 0.27
11 10 0.30
13 14 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAATTTATTTT
Found at i:3023656 original size:13 final size:13
Alignment explanation
Indices: 3023640--3023671 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
3023630 TTAAAATTTT
3023640 TTTTAAAAAAGTA
1 TTTTAAAAAAGTA
3023653 TTTT--AAAAGTA
1 TTTTAAAAAAGTA
3023664 TTTTAAAA
1 TTTTAAAA
3023672 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTAAAAAAGTA
Found at i:3023658 original size:31 final size:29
Alignment explanation
Indices: 3023580--3023660 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 29
3023570 ATAAATACCA
3023580 AAAATTTATTTT-AAAA-A-TTT-AAA--
1 AAAATTTATTTTAAAAATATTTTAAAATT
3023603 AAAATTTATTTTAAAAATATTTTAAAATT
1 AAAATTTATTTTAAAAATATTTTAAAATT
*
3023632 AAAATTTTTTTTAAAAAAGTATTTTAAAA
1 AAAATTTATTTT-AAAAA-TATTTTAAAA
3023661 GTATTTTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
23 12 0.24
24 4 0.08
25 1 0.02
26 3 0.06
27 3 0.06
29 11 0.22
30 5 0.10
31 10 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
AAAATTTATTTTAAAAATATTTTAAAATT
Found at i:3023662 original size:11 final size:11
Alignment explanation
Indices: 3023646--3023671 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3023636 TTTTTTTTAA
3023646 AAAAGTATTTT
1 AAAAGTATTTT
3023657 AAAAGTATTTT
1 AAAAGTATTTT
3023668 AAAA
1 AAAA
3023672 TTTTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3031359 original size:39 final size:39
Alignment explanation
Indices: 3031305--3031384 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
3031295 ATCAAAGACA
*
3031305 TCCACCTCACGCGTTTCGTAATGATTGTTAAATGATAAG
1 TCCACCTCACACGTTTCGTAATGATTGTTAAATGATAAG
* *
3031344 TCCACCTCATACGTTTCGTAATGATTGTTAGATGATAAG
1 TCCACCTCACACGTTTCGTAATGATTGTTAAATGATAAG
3031383 TC
1 TC
3031385 TAACACGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (39 bp):
TCCACCTCACACGTTTCGTAATGATTGTTAAATGATAAG
Found at i:3031967 original size:18 final size:19
Alignment explanation
Indices: 3031946--3031994 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
3031936 TTTTTCATAT
* *
3031946 AATTATTATTTCAAAAA-A
1 AATTATAATTTAAAAAATA
3031964 AATTATAATTCTAAAAAATA
1 AATTATAATT-TAAAAAATA
*
3031984 AATTATGATTT
1 AATTATAATTT
3031995 TATTTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.35
19 7 0.27
20 10 0.38
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTATAATTTAAAAAATA
Found at i:3045795 original size:18 final size:19
Alignment explanation
Indices: 3045774--3045813 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3045764 TTATTAAAAA
*
3045774 TTAGAAATA-TAATAAATT
1 TTAGAAAAATTAATAAATT
*
3045792 TTAGAAAAATTATTAAATT
1 TTAGAAAAATTAATAAATT
3045811 TTA
1 TTA
3045814 ATAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAGAAAAATTAATAAATT
Found at i:3045810 original size:19 final size:19
Alignment explanation
Indices: 3045764--3045813 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
3045754 GCCTCTGCTC
** *
3045764 TTATTAAAAATTAGAAATA
1 TTATTAAATTTTAGAAAAA
*
3045783 -TAATAAATTTTAGAAAAA
1 TTATTAAATTTTAGAAAAA
3045801 TTATTAAATTTTA
1 TTATTAAATTTTA
3045814 ATAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TTATTAAATTTTAGAAAAA
Found at i:3045828 original size:19 final size:19
Alignment explanation
Indices: 3045778--3045829 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3045768 TAAAAATTAG
3045778 AAATATAATAAATTTTAGAA
1 AAATATAA-AAATTTTAGAA
*
3045798 AAAT-TATTAAATTTTA-ATA
1 AAATATA-AAAATTTTAGA-A
3045817 AAATATAAAAATT
1 AAATATAAAAATT
3045830 AAAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 20 0.74
20 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATATAAAAATTTTAGAA
Found at i:3045845 original size:19 final size:19
Alignment explanation
Indices: 3045820--3045866 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3045810 TTTAATAAAA
3045820 TATAAAAATTAAAATTTAT
1 TATAAAAATTAAAATTTAT
* *
3045839 TA-AAAAA-TAGAATTTTT
1 TATAAAAATTAAAATTTAT
3045856 TAATAAAAATT
1 T-ATAAAAATT
3045867 GTAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 7 0.30
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAAATTAAAATTTAT
Found at i:3045991 original size:6 final size:6
Alignment explanation
Indices: 3045980--3046009 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3045970 GGAAAATTAT
3045980 AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
3046010 TAAAAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:3046123 original size:29 final size:27
Alignment explanation
Indices: 3046090--3046183 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 27
3046080 TTACATTTTG
*
3046090 TATAATTTTCTTACGACTTTATAAAGTTT
1 TATAATTTT-TTACGATTTTATAAA-TTT
* *
3046119 TATAATTTTTTTA-TATTTCTATATATTT
1 TATAA-TTTTTTACGATTT-TATAAATTT
3046147 TATAATTTTTTACGAATTTTATAAAATTT
1 TATAATTTTTTACG-ATTTTAT-AAATTT
*
3046176 TACAATTT
1 TATAATTT
3046184 ATATATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.13
28 14 0.26
29 29 0.54
30 4 0.07
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (27 bp):
TATAATTTTTTACGATTTTATAAATTT
Found at i:3046165 original size:19 final size:18
Alignment explanation
Indices: 3046143--3046188 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
3046133 ATTTCTATAT
**
3046143 ATTTTATAATTTTTTACGA
1 ATTTTATAAAATTTTAC-A
3046162 ATTTTATAAAATTTTACA
1 ATTTTATAAAATTTTACA
3046180 ATTTATATA
1 ATTT-TATA
3046189 TATATTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTATAAAATTTTACA
Found at i:3046170 original size:57 final size:61
Alignment explanation
Indices: 3046068--3046198 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 61
3046058 TTTTCATGGA
* * *
3046068 ATTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAGTTTTATAATTT-T
1 ATTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTAT
* *
3046128 -TTTATATTTCTATATA-TTT-TATAATTTT-TTACGAATTTTATAAAATTTTACAATTTAT
1 ATTTATATTTCTATACATTTTGTATAATTTTCTTACG-ACTTTATAAAATTTTACAATTTAT
*
3046186 ATATATATTTCTA
1 ATTTATATTTCTA
3046199 ATTTCTAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
56 5 0.08
57 28 0.45
58 4 0.06
59 25 0.40
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (61 bp):
ATTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTAT
Found at i:3051733 original size:18 final size:19
Alignment explanation
Indices: 3051700--3051736 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3051690 GTTCTTTTTT
*
3051700 GTGTTTGGGTGATGGGAAA
1 GTGTCTGGGTGATGGGAAA
3051719 GTGTCTGGG-GATGGGAAA
1 GTGTCTGGGTGATGGGAAA
3051737 ATGATGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.27
Consensus pattern (19 bp):
GTGTCTGGGTGATGGGAAA
Found at i:3057273 original size:17 final size:17
Alignment explanation
Indices: 3057245--3057292 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3057235 TATATTATCT
3057245 TAATTTTT-AATTTTTA
1 TAATTTTTCAATTTTTA
*
3057261 TAATTTTTCAATTTTTG
1 TAATTTTTCAATTTTTA
*
3057278 TGATTTTTCGAATTT
1 TAATTTTTC-AATTT
3057293 CTCTTTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.29
17 15 0.54
18 5 0.18
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (17 bp):
TAATTTTTCAATTTTTA
Found at i:3061303 original size:17 final size:20
Alignment explanation
Indices: 3061267--3061305 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
3061257 GTCTAAAGAC
3061267 TTTTCTTTTAATTATATTTG
1 TTTTCTTTTAATTATATTTG
3061287 TTTT-TTTTAA-TAT-TTTG
1 TTTTCTTTTAATTATATTTG
3061304 TT
1 TT
3061306 ATATTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 6 0.32
20 4 0.21
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTAATTATATTTG
Found at i:3065594 original size:31 final size:30
Alignment explanation
Indices: 3065515--3065604 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
3065505 AACCCCTCAA
*
3065515 TTTAAAAAATTTAATTAAATCCCTCAAAAGT
1 TTTAAAAAATTTAATT-AAGCCCTCAAAAGT
* * * *
3065546 TTT-GATAATTCTTATTAAGCCTTCCAAAAGT
1 TTTAAAAAATT-TAATTAAGCCCT-CAAAAGT
* *
3065577 TTTAAAAAATTTAATTAAACCCTAAAAA
1 TTTAAAAAATTTAATTAAGCCCTCAAAA
3065605 ATTGAAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
30 14 0.31
31 26 0.58
32 5 0.11
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTAAAAAATTTAATTAAGCCCTCAAAAGT
Found at i:3067082 original size:16 final size:17
Alignment explanation
Indices: 3067051--3067086 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3067041 ATTTTTTCAG
3067051 ATTAATTTTTATTTAAA
1 ATTAATTTTTATTTAAA
*
3067068 ATTAATTTTTATTAAAA
1 ATTAATTTTTATTTAAA
3067085 AT
1 AT
3067087 ATATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATTTTTATTTAAA
Found at i:3067212 original size:38 final size:39
Alignment explanation
Indices: 3067152--3067238 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 39
3067142 TTAAAAATAT
* * *
3067152 TTATATTAAAAAACTACCATAAATATTATAAATGTTTTA
1 TTATATTAAAAAACTACAATAAATATAATAAATATTTTA
3067191 TTATATT-AAAAA-TACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACTAC-AATAAATATAATAAATATTTTA
*
3067229 TTTTATTAAA
1 TTATATTAAA
3067239 TGAACTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 3 0.07
38 30 0.71
39 9 0.21
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (39 bp):
TTATATTAAAAAACTACAATAAATATAATAAATATTTTA
Found at i:3067403 original size:29 final size:28
Alignment explanation
Indices: 3067340--3067404 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
3067330 AGTGATTTAA
3067340 TATAA-ATATAAATATATAATTATTATT
1 TATAACATATAAATATATAATTATTATT
*
3067367 TA-ACACATATAATTAATATAA-TATTATTT
1 TATA-ACATATAAAT-ATATAATTATTA-TT
3067396 TATAACATA
1 TATAACATA
3067405 ATATTTAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 3 0.09
28 12 0.38
29 15 0.47
30 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAACATATAAATATATAATTATTATT
Found at i:3067804 original size:14 final size:14
Alignment explanation
Indices: 3067785--3067813 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3067775 TTAACAATAA
3067785 AACAACAAAATAGT
1 AACAACAAAATAGT
3067799 AACAACAAAATAGT
1 AACAACAAAATAGT
3067813 A
1 A
3067814 GTAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AACAACAAAATAGT
Found at i:3067871 original size:22 final size:22
Alignment explanation
Indices: 3067846--3067890 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3067836 ACAAAATAAC
*
3067846 AACATAACAACAACATAACAAT
1 AACAAAACAACAACATAACAAT
3067868 AACAAAACAACAACATAACAAT
1 AACAAAACAACAACATAACAAT
3067890 A
1 A
3067891 GTAAACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (22 bp):
AACAAAACAACAACATAACAAT
Found at i:3074729 original size:25 final size:24
Alignment explanation
Indices: 3074693--3074741 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3074683 TTAAAAATAA
3074693 AAATGAACATGT-GAATTAAGTGTT
1 AAATGAACATGTAG-ATTAAGTGTT
*
3074717 AAATGATATATGTAGATTAAGTGTT
1 AAATGA-ACATGTAGATTAAGTGTT
3074742 TATGTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (24 bp):
AAATGAACATGTAGATTAAGTGTT
Found at i:3080080 original size:18 final size:18
Alignment explanation
Indices: 3080057--3080149 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
3080047 CCCAACTACT
*
3080057 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
3080075 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
3080093 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
3080111 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3080129 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
3080147 GTA
1 GTA
3080150 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3080109 original size:36 final size:36
Alignment explanation
Indices: 3080057--3080149 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
3080047 CCCAACTACT
*
3080057 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
3080093 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
3080129 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
3080150 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:3082707 original size:15 final size:15
Alignment explanation
Indices: 3082679--3082720 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3082669 ATATATGCAT
* *
3082679 ACATACACATATATA
1 ACATACATACATATA
*
3082694 ATATACATACATATA
1 ACATACATACATATA
3082709 ACATACATACAT
1 ACATACATACAT
3082721 TTTGTATGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
ACATACATACATATA
Found at i:3090312 original size:24 final size:22
Alignment explanation
Indices: 3090275--3090330 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
3090265 TTTACAATAA
3090275 TTTTTATTTTATTTTAATTCTTG
1 TTTTTATTTTATTTTAATT-TTG
*
3090298 TTTTTTTTTTCATTTTAATTTTG
1 TTTTTATTTT-ATTTTAATTTTG
*
3090321 TTTCTATTTT
1 TTTTTATTTT
3090331 TAATATTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTATTTTAATTTTG
Found at i:3090331 original size:24 final size:23
Alignment explanation
Indices: 3090276--3090332 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
3090266 TTACAATAAT
3090276 TTTTA-TTTTATTTTAATTCTTG
1 TTTTATTTTTATTTTAATTCTTG
*
3090298 TTTTTTTTTTCATTTTAATT-TTG
1 TTTTATTTTT-ATTTTAATTCTTG
3090321 TTTCTATTTTTA
1 TTT-TATTTTTA
3090333 ATATTTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.13
23 11 0.37
24 15 0.50
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATTTTAATTCTTG
Found at i:3091073 original size:32 final size:32
Alignment explanation
Indices: 3091037--3091100 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3091027 GAGAAAGTTA
*
3091037 ATTGGATACATATAAAATTACTTGCTAAATTT
1 ATTGGATACATATAAAATTACTTCCTAAATTT
* *
3091069 ATTGGTTACGTATAAAATTACTTCCTAAATTT
1 ATTGGATACATATAAAATTACTTCCTAAATTT
3091101 TACTGAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (32 bp):
ATTGGATACATATAAAATTACTTCCTAAATTT
Found at i:3097855 original size:18 final size:18
Alignment explanation
Indices: 3097832--3097924 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
3097822 CCCAACTACT
*
3097832 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
3097850 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
3097868 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
3097886 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3097904 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
3097922 GTA
1 GTA
3097925 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3097884 original size:36 final size:36
Alignment explanation
Indices: 3097832--3097924 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
3097822 CCCAACTACT
*
3097832 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
3097868 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
3097904 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
3097925 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:3106420 original size:19 final size:18
Alignment explanation
Indices: 3106373--3106421 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3106363 TTTATGTGGG
*
3106373 TTTTTTTTCTAGTTCTTC
1 TTTTTTTTCTAGTTCTTA
**
3106391 TTTTGGCTTCTAGTTTCTTA
1 TTTT-TTTTCTAG-TTCTTA
3106411 TTTTTTTTCTA
1 TTTTTTTTCTA
3106422 TTTTTATAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.08, C:0.14, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTTTTTCTAGTTCTTA
Found at i:3111795 original size:33 final size:33
Alignment explanation
Indices: 3111734--3111825 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
3111724 ATAGACCTCG
* *
3111734 AACTTGAATCCTGAACCTTGAACTCTAAACCCAA
1 AACTTGAATCTTGAACC-TGAACCCTAAACCCAA
*
3111768 AACTTAAATCTTGAACCTGAACCCTAAACCCAA
1 AACTTGAATCTTGAACCTGAACCCTAAACCCAA
* *
3111801 ACCTTGAA-CTTGAACCCCGAACCCT
1 AACTTGAATCTTGAA-CCTGAACCCT
3111826 GAATCTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 6 0.12
33 30 0.59
34 15 0.29
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.22
Consensus pattern (33 bp):
AACTTGAATCTTGAACCTGAACCCTAAACCCAA
Found at i:3111796 original size:26 final size:26
Alignment explanation
Indices: 3111747--3111817 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
3111737 TTGAATCCTG
* **
3111747 AACCTTGAACTCTAAACCCAAAACTTA
1 AACCTTGAAC-CTGAACCCAAAACCCA
* *
3111774 AATCTTGAACCTGAACCCTAAACCCA
1 AACCTTGAACCTGAACCCAAAACCCA
*
3111800 AACCTTGAACTTGAACCC
1 AACCTTGAACCTGAACCC
3111818 CGAACCCTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 28 0.76
27 9 0.24
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.21
Consensus pattern (26 bp):
AACCTTGAACCTGAACCCAAAACCCA
Found at i:3113029 original size:29 final size:28
Alignment explanation
Indices: 3112996--3113059 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
3112986 TAGAGATTGG
*
3112996 ATCAAATTAATCCCTCTATTATTAAATAA
1 ATCAAATTAATCACTCTATTATTAAA-AA
* * *
3113025 ATCAATTTAATCATTGTATTATTAAAAA
1 ATCAAATTAATCACTCTATTATTAAAAA
3113053 ATCAAAT
1 ATCAAAT
3113060 AAGTTGAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (28 bp):
ATCAAATTAATCACTCTATTATTAAAAA
Found at i:3115581 original size:16 final size:16
Alignment explanation
Indices: 3115556--3115595 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3115546 TTAATAAAAC
* *
3115556 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3115572 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3115588 TAAAATTA
1 TAAAATTA
3115596 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3115657 original size:66 final size:67
Alignment explanation
Indices: 3115584--3115727 Score: 263
Period size: 68 Copynumber: 2.1 Consensus size: 67
3115574 AAATTAATTG
3115584 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
3115648 GA
66 GA
*
3115650 TTAGTAAATTTATCAAATTATTAATTGCATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3115715 TGA
65 TGA
3115718 TTAGTAAAAT
1 TTAGTAAAAT
3115728 AAACTTGATG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 26 0.35
68 48 0.65
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:3115826 original size:16 final size:18
Alignment explanation
Indices: 3115796--3115829 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3115786 AAATTTAAAA
3115796 TAAAAAACTATTATATTT
1 TAAAAAACTATTATATTT
3115814 TAAAAAA-TA-TATATTT
1 TAAAAAACTATTATATTT
3115830 AATATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAAACTATTATATTT
Found at i:3116829 original size:29 final size:29
Alignment explanation
Indices: 3116789--3116850 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
3116779 AAAAATCAAT
*
3116789 TAATTGAGTGACCAAAATAAGAAA-AATGA
1 TAATTGAGTGACCAAAATAA-AAATAATAA
*
3116818 TAATT-AGATGACCGAAATAAAAATAATAA
1 TAATTGAG-TGACCAAAATAAAAATAATAA
3116847 TAAT
1 TAAT
3116851 AATAATTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24
Consensus pattern (29 bp):
TAATTGAGTGACCAAAATAAAAATAATAA
Found at i:3125949 original size:7 final size:7
Alignment explanation
Indices: 3125937--3125961 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3125927 ACCGAGAGAG
3125937 GAAGGGA
1 GAAGGGA
3125944 GAAGGGA
1 GAAGGGA
3125951 GAAGGGA
1 GAAGGGA
3125958 GAAG
1 GAAG
3125962 CAGATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAAGGGA
Found at i:3127567 original size:16 final size:16
Alignment explanation
Indices: 3127543--3127594 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3127533 TGGTTCATTA
*
3127543 TAATGGAATATAACTG
1 TAATGGAATAAAACTG
* * *
3127559 TAATTGAATAGAGCTG
1 TAATGGAATAAAACTG
*
3127575 TAATGGAATAAAATTG
1 TAATGGAATAAAACTG
3127591 TAAT
1 TAAT
3127595 CAGTAATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (16 bp):
TAATGGAATAAAACTG
Done.