Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 17 of 136
Found at i:5316674 original size:21 final size:21
Alignment explanation
Indices: 5316640--5316701 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
5316630 AATTGGGTAA
5316640 TTAGGG-TTATGAGTTTGGGA-
1 TTAGGGTTTA-GAGTTTGGGAT
* *
5316660 TTAGAGGTTTAGAGTTAGAGAT
1 TTAG-GGTTTAGAGTTTGGGAT
5316682 TTAGGGTTTAGAGATTTGGG
1 TTAGGGTTTAGAG-TTTGGG
5316702 GTCGAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 19 0.56
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTGGGAT
Found at i:5317304 original size:29 final size:30
Alignment explanation
Indices: 5317233--5317304 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
5317223 GCCAATGTCC
* *
5317233 AATTTAAGGTTTAGGGGTTAGGGGTTTAAG
1 AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
* * *
5317263 AATTAAATG-TTAGGGGTTAAGAG-TTAGG
1 AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
5317291 AATTTAAGGTTTAG
1 AATTTAAGGTTTAG
5317305 AGATTTAGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 11 0.32
29 16 0.47
30 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (30 bp):
AATTTAAGGTTTAGGGGTTAAGAGTTTAAG
Found at i:5322219 original size:43 final size:42
Alignment explanation
Indices: 5322129--5322456 Score: 327
Period size: 43 Copynumber: 7.6 Consensus size: 42
5322119 TGTTTTTAGT
* * * * *
5322129 GGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTATAGC
1 GGCGTTTGTGGAA-AAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
5322171 GGCGTTTGTGGTAAAAGCACCGCTAAAGGTCTTCAGCTATAGC
1 GGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
5322214 GGCGTTTGTGGAAAAAGCGTCGCTAAAGATCTTAATCTATAGC
1 GGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * *
5322257 GGCATTTGTAAGAAAAGCGCCGCTAAAGATCCTGATCTATAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
5322300 GGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
1 GGCGTTTG-TGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * * *
5322343 GGCGTTTGTAGCAAAAGCGCCGTTAAAAGTCATGGTCTTTAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * *
5322386 GGCGTTTGTAGG-AAAGCGCCGCTAAAGCTCATGGTCTTTAGC
1 GGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
*
5322428 GGCGTTTGTTGCGGAAAGCGCCGCTAAAG
1 GGCGTTTG-TG-GAAAAGCGCCGCTAAAG
5322457 TTAGCGATGC
Statistics
Matches: 247, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
42 60 0.24
43 170 0.69
44 17 0.07
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (42 bp):
GGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
Found at i:5322394 original size:129 final size:128
Alignment explanation
Indices: 5322163--5322456 Score: 367
Period size: 129 Copynumber: 2.3 Consensus size: 128
5322153 AAAGGTTTGT
* * *
5322163 TCTATAGCGGCGTTTG-TGGTAAAAGCACCGCTAAAGGTCTTCAGCTATAGCGGCGTTTGTGGAA
1 TCTATAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAA
* * *
5322227 AAAGCGTCGCTAAAGATCTTAATCTATAGCGGCATTTGTAAGAAAAGCGCCGCTAAAGATCCTGA
65 AAAGCGCCGCTAAAGATCATAATCTATAGCGGCATTTGT-AGAAAAGCGCCGCTAAAGATCATGA
* * *
5322292 TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTAGCAA
1 TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAAA
* ** * * * * *
5322357 AAGCGCCGTTAAA-AGTCATGGTCTTTAGCGGCGTTTGTAGGAAAGCGCCGCTAAAGCTCATGG
66 AAGCGCCGCTAAAGA-TCATAATCTATAGCGGCATTTGTAGAAAAGCGCCGCTAAAGATCATGA
* *
5322420 TCTTTAGCGGCGTTTGTTGCGGAAAGCGCCGCTAAAG
1 TCTATAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAG
5322457 TTAGCGATGC
Statistics
Matches: 143, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
128 40 0.28
129 100 0.70
130 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (128 bp):
TCTATAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATCAGCTATAGCGGCGTTTGTAGAAA
AAGCGCCGCTAAAGATCATAATCTATAGCGGCATTTGTAGAAAAGCGCCGCTAAAGATCATGA
Found at i:5323117 original size:15 final size:16
Alignment explanation
Indices: 5323097--5323130 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5323087 GAAAGATGAG
*
5323097 AAAAAAAT-AACAATA
1 AAAAAAATGAAAAATA
5323112 AAAAAAATGAAAAATA
1 AAAAAAATGAAAAATA
5323128 AAA
1 AAA
5323131 GAAACTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAATGAAAAATA
Found at i:5323625 original size:41 final size:41
Alignment explanation
Indices: 5323545--5323634 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
5323535 TACATATTCC
*
5323545 CGGCGTTTGGACAAAAAATTGCCACTATTGCTCAACTTTTTG
1 CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAAC-TTTTG
* *
5323587 CGGCGTTTGGACCAAAAA-CGCCACTATTGCTCACCTTTTG
1 CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAACTTTTG
*
5323627 CAGCGTTT
1 CGGCGTTT
5323635 TTCTTGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 12 0.27
41 15 0.34
42 17 0.39
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (41 bp):
CGGCGTTTGGACAAAAAATCGCCACTATTGCTCAACTTTTG
Found at i:5335041 original size:16 final size:16
Alignment explanation
Indices: 5335020--5335060 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5335010 CATAGATAAA
*
5335020 TTTTAAGGTCCAAACT
1 TTTTAAGGACCAAACT
5335036 TTTTAAGGACCAAACT
1 TTTTAAGGACCAAACT
5335052 TTTTAAGGA
1 TTTTAAGGA
5335061 GGGAATGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (16 bp):
TTTTAAGGACCAAACT
Found at i:5337065 original size:21 final size:22
Alignment explanation
Indices: 5337025--5337066 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5337015 GAGCATTTGA
5337025 GATTTTTTTTACTTTCTTATTC
1 GATTTTTTTTACTTTCTTATTC
5337047 GATTCTTTTTTA-TTT-TTATT
1 GATT-TTTTTTACTTTCTTATT
5337067 TTATTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (22 bp):
GATTTTTTTTACTTTCTTATTC
Found at i:5340439 original size:3 final size:3
Alignment explanation
Indices: 5340431--5340464 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5340421 ATTAGTTTAC
5340431 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5340465 TCCAAACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5345419 original size:14 final size:14
Alignment explanation
Indices: 5345401--5345435 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5345391 GTGATGTGAA
*
5345401 AAAAATGAAAAGAT
1 AAAAATGAAAAAAT
*
5345415 GAAAATGAAAAAAT
1 AAAAATGAAAAAAT
5345429 AAAAATG
1 AAAAATG
5345436 GAGAGGCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAAAAT
Found at i:5347327 original size:44 final size:44
Alignment explanation
Indices: 5346745--5347391 Score: 689
Period size: 44 Copynumber: 14.7 Consensus size: 44
5346735 AGATATTATA
** * * * *
5346745 TTCATGTATTAACATGAAGTAGATCAGAGAAAACATATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* *
5346789 TTCATGTATTGACATGAAGTAGATCAAAGATAATG--GATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGA-AA-GCAGATCTTGTC
* * * * *
5346833 TTCATGTATTGACATGAAGTAGATTAGAGTTAATG--GATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAG--AAAGCAGATCTTGTC
* * * * *
5346877 TTCATGTATTGACATGAAGTGGATCAGAGAAAACAGATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
** *
5346921 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGTGGATCTTATC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* **
5346965 TTCATGTATTGGCGTGAAGTAGATCCAAGAAAGTGGATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* * * *
5347009 TTCATGTATTGACATGAAGTAGATCAGAGATAA-CAGATCTTATC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTC
* * *
5347053 TTCATGTATTGGCGTGAAGTAGATCGAAGAAATCAAATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* * *
5347097 TTCATGTATTAGCGTGAAGTAGATCAAAGAAAGTATATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* * * *
5347141 TTCATGTATTGGCGTGAAGTAGATCGAAGAAAGGAGGTCTTATC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* *
5347185 TTCATGTATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
* * * *
5347229 TTCATGTGTTGGCATGAAGTAGATCGAAGATAGCAGATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
5347273 TTCATGTATTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGTC
1 TTCATGTATTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTC
*** * * * *
5347317 TTCCCATATTGGGGGCGAAGTAGATCGAAGAAAGTAGATCTTGTC
1 TTCATGTATT-GGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
*
5347362 TTCCCATGTATTGGC--GAAATAGATCAAAGA
1 TT--CATGTATTGGCGTGAAGTAGATCAAAGA
5347392 TACAAGTCTT
Statistics
Matches: 522, Mismatches: 68, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
42 2 0.00
43 2 0.00
44 475 0.91
45 35 0.07
46 3 0.01
47 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (44 bp):
TTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTC
Found at i:5348888 original size:3 final size:3
Alignment explanation
Indices: 5348880--5348913 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5348870 ATTAGTTTAC
5348880 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5348914 TCCATACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5377706 original size:45 final size:45
Alignment explanation
Indices: 5377642--5377728 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
5377632 AACAAATACT
*
5377642 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
5377687 CGGTGGAATT-AGCACATAGCAACCACCTTACTAATCAATGAT
1 CGGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGAT
5377729 ATTCAGTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:5377837 original size:51 final size:49
Alignment explanation
Indices: 5377737--5377924 Score: 160
Period size: 51 Copynumber: 3.7 Consensus size: 49
5377727 ATATTCAGTT
* * * * *
5377737 CACATAGTAGCCTGCACATAGTACTACTCATGTGACCATTACCACCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CA-AAACATCCGATA
*
5377788 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CAAAAC-ATCCGATA
** * * * * ** * * *
5377839 TGCATAATAACCTGCACATGGTACTACACACGCGACCCATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACA-TCCGATA
**
5377889 CATTTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
5377925 CATCACTTTC
Statistics
Matches: 108, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.01
50 38 0.35
51 69 0.64
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACATCCGATA
Found at i:5382840 original size:14 final size:16
Alignment explanation
Indices: 5382821--5382852 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5382811 CTAAAAAGAC
5382821 ATTTAG-AATGA-ACA
1 ATTTAGCAATGATACA
5382835 ATTTAGCAATGATACA
1 ATTTAGCAATGATACA
5382851 AT
1 AT
5382853 AAATATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (16 bp):
ATTTAGCAATGATACA
Found at i:5389082 original size:48 final size:48
Alignment explanation
Indices: 5389011--5389107 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
5389001 AAATTCGTGA
*
5389011 AGCAATAGCACTCACCTTATTAGTGTGGCTTTTGTTTATTTATTTTTC
1 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
5389059 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
1 AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
5389107 A
1 A
5389108 TGACATATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (48 bp):
AGCAATAGCACTCACCTCATTAGTGTGGCTTTTGTTTATTTATTTTTC
Found at i:5395963 original size:40 final size:37
Alignment explanation
Indices: 5395904--5395990 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 37
5395894 AATTTAATCT
* *
5395904 AATACTATTAGATTAAATTTAAAATTAAATCTCTATTAA
1 AATAATATTAAATTAAATTTAAAATTAAA--TCTATTAA
* * *
5395943 GATAAATATTAAATTTAATTTAATATTAAATCTATTAA
1 AAT-AATATTAAATTAAATTTAAAATTAAATCTATTAA
5395981 AATAATATTA
1 AATAATATTA
5395991 TTTTTGGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 7 0.17
38 10 0.24
39 2 0.05
40 22 0.54
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (37 bp):
AATAATATTAAATTAAATTTAAAATTAAATCTATTAA
Found at i:5399973 original size:22 final size:21
Alignment explanation
Indices: 5399939--5399982 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5399929 TTCCCATACA
5399939 TCTCTCTCTCTTTCACTTACTT
1 TCTCTCTCTCTTTCACTT-CTT
*
5399961 TCTCTCT-TCCTTTCCCTTCTT
1 TCTCTCTCT-CTTTCACTTCTT
5399982 T
1 T
5399983 GTTTTCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.57
Consensus pattern (21 bp):
TCTCTCTCTCTTTCACTTCTT
Found at i:5403674 original size:27 final size:29
Alignment explanation
Indices: 5403635--5403700 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
5403625 TACTCATGGA
* *
5403635 TTATATATATAATT-TTTAGAATTTA-TT
1 TTATAAATTTAATTATTTAGAATTTATTT
**
5403662 TTATAAATTTAATTATTTTTAATTTATTT
1 TTATAAATTTAATTATTTAGAATTTATTT
5403691 TTATAGAATT
1 TTATA-AATT
5403701 ATTGTTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 12 0.38
28 9 0.28
29 7 0.22
30 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
TTATAAATTTAATTATTTAGAATTTATTT
Found at i:5404912 original size:3 final size:3
Alignment explanation
Indices: 5404904--5404938 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5404894 ATAGTTTACC
5404904 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5404939 AACTACTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5405091 original size:25 final size:25
Alignment explanation
Indices: 5405057--5405109 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5405047 GAGTGCCTTA
5405057 TCAATCAGTCTGGGAAAGGTTTGAT
1 TCAATCAGTCTGGGAAAGGTTTGAT
5405082 TCAATCAGTCTGGGAAAGGTTTGAT
1 TCAATCAGTCTGGGAAAGGTTTGAT
5405107 TCA
1 TCA
5405110 GAAGATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (25 bp):
TCAATCAGTCTGGGAAAGGTTTGAT
Found at i:5405345 original size:2 final size:2
Alignment explanation
Indices: 5405338--5405363 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5405328 CCTTCTTTAT
5405338 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5405364 AAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5405565 original size:2 final size:2
Alignment explanation
Indices: 5405558--5405583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5405548 CCTTCTTTAT
5405558 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5405584 AAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5405579 original size:220 final size:220
Alignment explanation
Indices: 5405197--5405640 Score: 879
Period size: 220 Copynumber: 2.0 Consensus size: 220
5405187 GTTGGATAGT
5405197 AAAAACTTGTCCAAAAAAGCAATCTAACCTTTTAATTATTGATTTTCCTACTACTTTTTATGTTA
1 AAAAACTTGTCCAAAAAAGCAATCTAACCTTTTAATTATTGATTTTCCTACTACTTTTTATGTTA
5405262 GAAAACTTTTGTTAGAAACTAAATTGGATAATTCTTTTGTAAAGAATAAATGAAGGCACTTAATT
66 GAAAACTTTTGTTAGAAACTAAATTGGATAATTCTTTTGTAAAGAATAAATGAAGGCACTTAATT
5405327 ACCTTCTTTATTATATATATATATATATATATATATAAAACATATAAAAACACTAGTGCAACAAA
131 ACCTTCTTTATTATATATATATATATATATATATATAAAACATATAAAAACACTAGTGCAACAAA
5405392 GCAACTATAGAGAACAAAATCTTTA
196 GCAACTATAGAGAACAAAATCTTTA
5405417 AAAAACTTGTCCAAAAAAGCAATCTAACCTTTTAATTATTGATTTTCCTACTACTTTTTATGTTA
1 AAAAACTTGTCCAAAAAAGCAATCTAACCTTTTAATTATTGATTTTCCTACTACTTTTTATGTTA
5405482 GAAAACTTTTGTTAGAAACTAAATTGGATAATTCTTTTGTAAAGAATAAATGAAGGCACTTAATT
66 GAAAACTTTTGTTAGAAACTAAATTGGATAATTCTTTTGTAAAGAATAAATGAAGGCACTTAATT
5405547 ACCTTCTTTATTATATATATATATATATATATATATAAAACATATAAAAACACTAGTGCAACAAA
131 ACCTTCTTTATTATATATATATATATATATATATATAAAACATATAAAAACACTAGTGCAACAAA
*
5405612 GCAACTATAGTGAACAAAATCTTTA
196 GCAACTATAGAGAACAAAATCTTTA
5405637 AAAA
1 AAAA
5405641 TTCTTCAACA
Statistics
Matches: 223, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 223 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (220 bp):
AAAAACTTGTCCAAAAAAGCAATCTAACCTTTTAATTATTGATTTTCCTACTACTTTTTATGTTA
GAAAACTTTTGTTAGAAACTAAATTGGATAATTCTTTTGTAAAGAATAAATGAAGGCACTTAATT
ACCTTCTTTATTATATATATATATATATATATATATAAAACATATAAAAACACTAGTGCAACAAA
GCAACTATAGAGAACAAAATCTTTA
Found at i:5407443 original size:12 final size:12
Alignment explanation
Indices: 5407426--5407450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5407416 ACTTCAGCAA
5407426 TTGGATATAAAG
1 TTGGATATAAAG
5407438 TTGGATATAAAG
1 TTGGATATAAAG
5407450 T
1 T
5407451 CACAAAAAAA
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TTGGATATAAAG
Found at i:5408160 original size:321 final size:321
Alignment explanation
Indices: 5407578--5408220 Score: 1286
Period size: 321 Copynumber: 2.0 Consensus size: 321
5407568 TCTCCCAGAA
5407578 TATATGAAGATATGTTTCCTTGCTCTTTACAACTCCATAAACGAAATAGCATTTGATAATCTCAA
1 TATATGAAGATATGTTTCCTTGCTCTTTACAACTCCATAAACGAAATAGCATTTGATAATCTCAA
5407643 GGAACATGGATTTCATACCATTCCTTTCTTGAAGAAAGCGGTACTAAGTTCTCATCTTAGTTTTG
66 GGAACATGGATTTCATACCATTCCTTTCTTGAAGAAAGCGGTACTAAGTTCTCATCTTAGTTTTG
5407708 ATTCGTAACCATTTTCCTTCAATTTTTACATATTAAAAAAGAGTTATTATGTGTTCAGTGGGCAG
131 ATTCGTAACCATTTTCCTTCAATTTTTACATATTAAAAAAGAGTTATTATGTGTTCAGTGGGCAG
5407773 AGTTATGCAAATCTTATTTAGTGGAGGCAAAGTGGTATTACAGCGGATACATTCCAACATTTAAA
196 AGTTATGCAAATCTTATTTAGTGGAGGCAAAGTGGTATTACAGCGGATACATTCCAACATTTAAA
5407838 GAGTATATCGATAATGCATGGATTTCTATTTCGGCTCCCGTTATACTATCACATGTTTTTT
261 GAGTATATCGATAATGCATGGATTTCTATTTCGGCTCCCGTTATACTATCACATGTTTTTT
5407899 TATATGAAGATATGTTTCCTTGCTCTTTACAACTCCATAAACGAAATAGCATTTGATAATCTCAA
1 TATATGAAGATATGTTTCCTTGCTCTTTACAACTCCATAAACGAAATAGCATTTGATAATCTCAA
5407964 GGAACATGGATTTCATACCATTCCTTTCTTGAAGAAAGCGGTACTAAGTTCTCATCTTAGTTTTG
66 GGAACATGGATTTCATACCATTCCTTTCTTGAAGAAAGCGGTACTAAGTTCTCATCTTAGTTTTG
5408029 ATTCGTAACCATTTTCCTTCAATTTTTACATATTAAAAAAGAGTTATTATGTGTTCAGTGGGCAG
131 ATTCGTAACCATTTTCCTTCAATTTTTACATATTAAAAAAGAGTTATTATGTGTTCAGTGGGCAG
5408094 AGTTATGCAAATCTTATTTAGTGGAGGCAAAGTGGTATTACAGCGGATACATTCCAACATTTAAA
196 AGTTATGCAAATCTTATTTAGTGGAGGCAAAGTGGTATTACAGCGGATACATTCCAACATTTAAA
5408159 GAGTATATCGATAATGCATGGATTTCTATTTCGGCTCCCGTTATACTATCACATGTTTTTT
261 GAGTATATCGATAATGCATGGATTTCTATTTCGGCTCCCGTTATACTATCACATGTTTTTT
5408220 T
1 T
5408221 CTCATCAAAT
Statistics
Matches: 322, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
321 322 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (321 bp):
TATATGAAGATATGTTTCCTTGCTCTTTACAACTCCATAAACGAAATAGCATTTGATAATCTCAA
GGAACATGGATTTCATACCATTCCTTTCTTGAAGAAAGCGGTACTAAGTTCTCATCTTAGTTTTG
ATTCGTAACCATTTTCCTTCAATTTTTACATATTAAAAAAGAGTTATTATGTGTTCAGTGGGCAG
AGTTATGCAAATCTTATTTAGTGGAGGCAAAGTGGTATTACAGCGGATACATTCCAACATTTAAA
GAGTATATCGATAATGCATGGATTTCTATTTCGGCTCCCGTTATACTATCACATGTTTTTT
Found at i:5434563 original size:215 final size:217
Alignment explanation
Indices: 5434174--5434611 Score: 610
Period size: 215 Copynumber: 2.0 Consensus size: 217
5434164 ACGGTCAAAC
* * *
5434174 CTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTATCCTGGATACTCAGTTCAAACAGTCTT
1 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
* * *
5434239 CTTTCTTTTTTTCTTTTTTTTTTTGGAGGCTCGGTTAGCGGAATGTTTGTAAGTTTTCAATTTGT
66 CTTTC-----TTC--TTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGT
* * * *
5434304 CACTTGAACCTTTTTACGCGAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCA
124 CACTCGAACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCA
5434369 GTCACATTTTCGAAACTTTCACTCATAAA
189 GTCACATTTTCGAAACTTTCACTCATAAA
*
5434398 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGTTACTCAATTCAAACAGTCTT
1 CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
* *
5434463 CTTTC-TC-TTTTTTTTGGAGGCCCGGTTGGCGAAATGTTTGTAAGTTCTCAATTTTTCACTCGA
66 CTTTCTTCTTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGTCACTCGA
* * * * * **
5434526 ACCGTTTTACATAAGATGAAATGACAACCCAAGCACTTCACTCTGGTTACTAAGTTCGGTCATGT
131 ACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCAGTCACAT
*
5434591 TTTTGAAACTTTCACTCATAA
196 TTTCGAAACTTTCACTCATAA
5434612 CTTGAGCCTT
Statistics
Matches: 193, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
215 125 0.65
218 2 0.01
224 66 0.34
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (217 bp):
CTTTTTACGCGAACTAGGATGACAACCAAAGCACCCTATCCTAGATACTCAATTCAAACAGTCTT
CTTTCTTCTTTTTTTTTGGAGGCCCGGTTAGCGAAATGTTTGTAAGTTCTCAATTTGTCACTCGA
ACCGTTTTACACAAGATGAAATGACAACCCAAGCACTTCACCCCGGTTACTAAATTCAGTCACAT
TTTCGAAACTTTCACTCATAAA
Found at i:5434924 original size:22 final size:22
Alignment explanation
Indices: 5434892--5434933 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5434882 GCAGCAAAAA
5434892 TCATGCATATTTACCATTTTTC
1 TCATGCATATTTACCATTTTTC
*
5434914 TCATGCTTATTTACCATTTT
1 TCATGCATATTTACCATTTT
5434934 ACTTACCATT
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:0.21, C:0.21, G:0.05, T:0.52
Consensus pattern (22 bp):
TCATGCATATTTACCATTTTTC
Found at i:5442628 original size:12 final size:12
Alignment explanation
Indices: 5442613--5442637 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5442603 AATAATTAAA
5442613 TAAATTTGAATT
1 TAAATTTGAATT
5442625 TAAATTTGAATT
1 TAAATTTGAATT
5442637 T
1 T
5442638 TGTAATCAAA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAAATTTGAATT
Found at i:5443099 original size:20 final size:20
Alignment explanation
Indices: 5443039--5443104 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
5443029 TCCAGCTCCT
* *
5443039 TTAGCTCGTTTCAGCTCCAA
1 TTAGCTCGTTTAAGCTCAAA
* * ** * *
5443059 TCAGTTCACTTGAGCTTAAA
1 TTAGCTCGTTTAAGCTCAAA
5443079 TTAGCTCGTTTAAGCTCAAA
1 TTAGCTCGTTTAAGCTCAAA
5443099 TTAGCT
1 TTAGCT
5443105 GACTTTCAGC
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
TTAGCTCGTTTAAGCTCAAA
Found at i:5443802 original size:23 final size:21
Alignment explanation
Indices: 5443776--5443827 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5443766 TAATGATTTT
5443776 TGTGTGAACATGTTAAATAAC
1 TGTGTGAACATGTTAAATAAC
5443797 TGTGTGAACATGTTAAATAAC
1 TGTGTGAACATGTTAAATAAC
*
5443818 TATGTGAACA
1 TGTGTGAACA
5443828 AAATTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGTGAACATGTTAAATAAC
Found at i:5445754 original size:15 final size:15
Alignment explanation
Indices: 5445734--5445780 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5445724 GTTTAATGGC
5445734 TTAATAATGGCCATG
1 TTAATAATGGCCATG
5445749 TTAATAAT-GCCAAT-
1 TTAATAATGGCC-ATG
* *
5445763 ATGATAATGGCCATG
1 TTAATAATGGCCATG
5445778 TTA
1 TTA
5445781 CGAATAGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (15 bp):
TTAATAATGGCCATG
Found at i:5452196 original size:25 final size:25
Alignment explanation
Indices: 5452147--5452460 Score: 152
Period size: 25 Copynumber: 12.6 Consensus size: 25
5452137 GAATTAATTA
* *
5452147 GAAAGCCTTTGTGTCGTAAT-ATATG
1 GAAAGCCTTTGTGGC-TAATCTTATG
*
5452172 GAAAGCCTTTGTGGTTAATCTTAT-
1 GAAAGCCTTTGTGGCTAATCTTATG
** * * *
5452196 GAAATGTTTTTGTGG-TGTAT-TGTCTA
1 GAAA-GCCTTTGTGGCT-AATCT-TATG
*
5452222 GAAAACCTTTGTGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* * * * * *
5452247 AAAAACATTTATGGCTATTATT-TG
1 GAAAGCCTTTGTGGCTAATCTTATG
*
5452271 GAAAGCCTTTATGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* * *
5452296 AAAAACCTTTGTGGCGT-AT-TATCTG
1 GAAAGCCTTTGTGGC-TAATCT-TATG
* * *
5452321 GAAATCCTTTGTGGATAATTTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
* **
5452346 AAAAAACTTTGTGGCATAGTATC-TA--
1 GAAAGCCTTTGTGGC-TA--ATCTTATG
* *
5452371 GAAAGCCTTTGTGGCTAATATTA-A
1 GAAAGCCTTTGTGGCTAATCTTATG
* *
5452395 GAGAAGCTTTTGTGGCGT-AT-TGTCTG
1 GA-AAGCCTTTGTGGC-TAATCT-TATG
5452421 GAAAGCCTTTGTGGCTAATCTTATG
1 GAAAGCCTTTGTGGCTAATCTTATG
5452446 GAAAG-CTATTGTGGC
1 GAAAGCCT-TTGTGGC
5452461 GTATTGTATG
Statistics
Matches: 220, Mismatches: 45, Indels: 48
0.70 0.14 0.15
Matches are distributed among these distances:
22 2 0.01
23 2 0.01
24 39 0.18
25 159 0.72
26 14 0.06
27 2 0.01
28 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (25 bp):
GAAAGCCTTTGTGGCTAATCTTATG
Found at i:5452231 original size:50 final size:50
Alignment explanation
Indices: 5452154--5452475 Score: 333
Period size: 50 Copynumber: 6.5 Consensus size: 50
5452144 TTAGAAAGCC
* * * * ***
5452154 TTTGTGTCGTAATATATGGAAAGCCTTTGTGGTTAATCTTATGAAATGTT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * * * *
5452204 TTTGTGGTGTATTGTCTAGAAAACCTTTGTGGCTAATCTTATGAAAAACA
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * * *
5452254 TTTATGGC-TATTATTTGGAAAGCCTTTATGGCTAATCTTATGAAAAACC
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
5452303 TTTGTGGCGTATTATCTGGAAATCCTTTGTGGATAATTTTATGAAAAAAC-
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATG-AAAAACT
* * * * * * *
5452353 TTTGTGGCATAGTATCTAGAAAGCCTTTGTGGCTAATATTAAGAGAAGCT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
5452403 TTTGTGGCGTATTGTCTGGAAAGCCTTTGTGGCTAATCTTATGGAAAGCT
1 TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
* * *
5452453 ATTGTGGCGTATTGTATGGAAAG
1 TTTGTGGCGTATTATCTGGAAAG
5452476 ATTGTTGAAG
Statistics
Matches: 224, Mismatches: 45, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
49 46 0.21
50 172 0.77
51 6 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (50 bp):
TTTGTGGCGTATTATCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAACT
Found at i:5452408 original size:100 final size:98
Alignment explanation
Indices: 5452172--5452445 Score: 334
Period size: 99 Copynumber: 2.8 Consensus size: 98
5452162 GTAATATATG
* * * *
5452172 GAAAGCCTTTGTGGTTAATCTTATGAAATGTTTTTGTGGTGTATTGTCTAGAAAACCTTTGTGGC
1 GAAAGCCTTTGTGGCTAATCTTATGAAA-GCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
* * *
5452237 TAATCTTATGAAAAACATTTATGGCTATTATTTG
65 TAATCTTATGAAAAACATTTATGGCTAGTATCTA
* * * * * *
5452271 GAAAGCCTTTATGGCTAATCTTATGAAAAACCTTTGTGGCGTATTATCTGGAAATCCTTTGTGGA
1 GAAAGCCTTTGTGGCTAATCTTATG-AAAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
* *
5452336 TAATTTTATGAAAAA-ACTTTGTGGCATAGTATCTA
65 TAATCTTATGAAAAACA-TTTATGGC-TAGTATCTA
* * *
5452371 GAAAGCCTTTGTGGCTAATATTAAGAGAAGCTTTTGTGGCGTATTGTCTGGAAAGCCTTTGTGGC
1 GAAAGCCTTTGTGGCTAATCTTATGA-AAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGC
5452436 TAATCTTATG
65 TAATCTTATG
5452446 GAAAGCTATT
Statistics
Matches: 147, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
98 1 0.01
99 73 0.50
100 73 0.50
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (98 bp):
GAAAGCCTTTGTGGCTAATCTTATGAAAGCTTTTGTGGCGTATTGTCTGGAAAACCTTTGTGGCT
AATCTTATGAAAAACATTTATGGCTAGTATCTA
Found at i:5452470 original size:25 final size:24
Alignment explanation
Indices: 5452398--5452475 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 24
5452388 ATATTAAGAG
*
5452398 AAGCTTTTGTGGCGTATTGTCTGGA
1 AAGC-TTTGTGGCGTATTGTATGGA
5452423 AAGCCTTTGTGGC-TAATCT-TATGGA
1 AAG-CTTTGTGGCGT-AT-TGTATGGA
5452448 AAGCTATTGTGGCGTATTGTATGGA
1 AAGCT-TTGTGGCGTATTGTATGGA
5452473 AAG
1 AAG
5452476 ATTGTTGAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
24 4 0.09
25 39 0.85
26 3 0.07
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (24 bp):
AAGCTTTGTGGCGTATTGTATGGA
Found at i:5461593 original size:31 final size:31
Alignment explanation
Indices: 5461557--5461635 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
5461547 TGATAGTACA
*
5461557 GTATAAATATGCAAATCTGATAGATTACAAG
1 GTATAAATATGCAAATCTGATAGATCACAAG
* *
5461588 GTATAAATATGCAAATATGATAGATCACATG
1 GTATAAATATGCAAATCTGATAGATCACAAG
*
5461619 GTAT-GATATGCAAATCT
1 GTATAAATATGCAAATCT
5461636 AAATGATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (31 bp):
GTATAAATATGCAAATCTGATAGATCACAAG
Found at i:5463316 original size:20 final size:20
Alignment explanation
Indices: 5463278--5463316 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5463268 GTAAATTAGT
* *
5463278 CGATAACCTTCTCTTTTCCC
1 CGATAACCTTCACTATTCCC
*
5463298 CGATCACCTTCACTATTCC
1 CGATAACCTTCACTATTCC
5463317 TTCTTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.05, T:0.36
Consensus pattern (20 bp):
CGATAACCTTCACTATTCCC
Found at i:5473817 original size:33 final size:33
Alignment explanation
Indices: 5473774--5473839 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5473764 GGCAACATAA
*
5473774 GATTGTGTAGATCCTATTTCTATCAATGCAGTG
1 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
5473807 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
1 GATTGCGTAGATCCTATTTCTATCAATGCAGTG
5473840 TAAGGCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (33 bp):
GATTGCGTAGATCCTATTTCTATCAATGCAGTG
Found at i:5475278 original size:26 final size:26
Alignment explanation
Indices: 5475248--5475309 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
5475238 TACCTACAGT
5475248 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* * * * *
5475274 AGTTTTAGATTATCATAGCATGTTTC
1 AGTTTCAGAATATCATAACATATATC
5475300 AGTTTCAGAA
1 AGTTTCAGAA
5475310 CACTTACAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:5476063 original size:34 final size:33
Alignment explanation
Indices: 5476019--5476085 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
5476009 GCACAGTTGA
*
5476019 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCC-ATTCAGTAT-AGTG
*
5476054 ACAGT-TTGGGCCTTAGCCCATTCAGTATAGTG
1 ACAGTCTTGGGCCTAAGCCCATTCAGTATAGTG
5476086 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.13
33 8 0.27
34 13 0.43
35 5 0.17
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (33 bp):
ACAGTCTTGGGCCTAAGCCCATTCAGTATAGTG
Found at i:5478816 original size:17 final size:16
Alignment explanation
Indices: 5478794--5478875 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 16
5478784 AAATAAGTTT
5478794 AAGAAAATAAATAATAA
1 AAGAAAATAAA-AATAA
5478811 AAGAAAATAAAGCAACTAA
1 AAGAAAATAAA--AA-TAA
* *
5478830 AACAAAATTAAAAA-GA
1 AAGAAAA-TAAAAATAA
5478846 AAGATAAATAAAAATAA
1 AAGA-AAATAAAAATAA
*
5478863 AAGAAAACAAAAA
1 AAGAAAATAAAAA
5478876 AAATAAATTC
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
16 18 0.33
17 19 0.35
18 4 0.07
19 9 0.17
20 4 0.07
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (16 bp):
AAGAAAATAAAAATAA
Found at i:5478821 original size:10 final size:10
Alignment explanation
Indices: 5478806--5478882 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
5478796 GAAAATAAAT
5478806 AATAAAAGAA
1 AATAAAAGAA
*
5478816 AAT-AAAGCA
1 AATAAAAGAA
* *
5478825 ACTAAAACAA
1 AATAAAAGAA
5478835 AATTAAAAAGAA
1 AA-T-AAAAGAA
5478847 AGATAAATA-AA
1 A-ATAAA-AGAA
5478858 AATAAAAGAA
1 AATAAAAGAA
*
5478868 AACAAAA-AA
1 AATAAAAGAA
5478877 AATAAA
1 AATAAA
5478883 TTCAATGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 15 0.28
10 21 0.40
11 7 0.13
12 9 0.17
13 1 0.02
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.12
Consensus pattern (10 bp):
AATAAAAGAA
Found at i:5478954 original size:26 final size:26
Alignment explanation
Indices: 5478915--5478965 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5478905 AAGGTAATTG
*
5478915 TAATAATAACAGTA-AAAAATTAAAAA
1 TAATAAAAACAGTAGAAAAA-TAAAAA
*
5478941 TAATAAAAATAGTAGAAAAATAAAA
1 TAATAAAAACAGTAGAAAAATAAAA
5478966 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.22
Consensus pattern (26 bp):
TAATAAAAACAGTAGAAAAATAAAAA
Found at i:5479054 original size:23 final size:22
Alignment explanation
Indices: 5479020--5479063 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
5479010 AAAATTAGGA
*
5479020 AAATAAAAATAAATAATATAAC
1 AAATAAAAATAAATAAAATAAC
5479042 AAATAATAAATAAATAAAATAA
1 AAATAA-AAATAAATAAAATAA
5479064 AAGGGGTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAAAATAAATAAAATAAC
Found at i:5479063 original size:16 final size:15
Alignment explanation
Indices: 5478989--5479055 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
5478979 TAAGTATAAG
5478989 AATAAAAAATAAATA
1 AATAAAAAATAAATA
*
5479004 GAATAAAAAATTAGGA-A
1 -AATAAAAAA-TA-AATA
5479021 AAT-AAAAATAAATA
1 AATAAAAAATAAATA
*
5479035 ATATAACAAAT-AATA
1 A-ATAAAAAATAAATA
5479050 AATAAA
1 AATAAA
5479056 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 1 0.02
14 8 0.19
15 12 0.29
16 17 0.40
17 3 0.07
18 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (15 bp):
AATAAAAAATAAATA
Found at i:5486416 original size:11 final size:11
Alignment explanation
Indices: 5486400--5486429 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5486390 AATTTTACGT
5486400 ATTACCAATGC
1 ATTACCAATGC
5486411 ATTACCAATGC
1 ATTACCAATGC
5486422 ATTACCAA
1 ATTACCAA
5486430 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (11 bp):
ATTACCAATGC
Found at i:5494626 original size:30 final size:30
Alignment explanation
Indices: 5494592--5494648 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5494582 CGAGCTTTGA
5494592 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
1 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
* * * *
5494622 GGCAAAATTGTAATTTTGCCAAAGTTT
1 GGCAAAAGTGTAAATATGCAAAAGTTT
5494649 GAGTTAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (30 bp):
GGCAAAAGTGTAAATATGCAAAAGTTTAGG
Found at i:5495021 original size:26 final size:26
Alignment explanation
Indices: 5494984--5495034 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5494974 ATTGGATAAA
5494984 AAGGGGTCGCTAAGTGCAGATTCCCC
1 AAGGGGTCGCTAAGTGCAGATTCCCC
* *
5495010 AAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGTCGCTAAGTGCAGATTCCC
5495035 AAATTATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (26 bp):
AAGGGGTCGCTAAGTGCAGATTCCCC
Found at i:5495102 original size:43 final size:42
Alignment explanation
Indices: 5495010--5495375 Score: 331
Period size: 43 Copynumber: 8.7 Consensus size: 42
5495000 CAGATTCCCC
** *
5495010 AAGGGGTTGCTAAGTGCTGATT-C-CCAAAT-TATTGATTCTA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATAT-TTGATTGTA
5495050 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
** * * * *
5495094 AAGGGGTTGCTCTGTGCTGATTCC-CCATATCA-CTGAATATA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTA
*
5495135 AAGGTGGTTGCTAAGTGCTGATTACACCGTATATTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * *
5495179 AAGGGGTTGCTATGTGTTGATTCCACCATATATTTGATTGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * * *
5495222 AAGGGGTTGCTATGTGCTGATTCC-CCGTATCA-CTGAATATA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTA
* *
5495263 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGT-A
* * *
5495307 AAGGGGTTGCTATGTGCTGATTCC-CTGTATCA-CTGAATT-T-
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTG-ATTGTA
*
5495347 AAGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGG-GGTTGCTAAGTGCTGATTCCACCG
5495376 AGTAACGGAT
Statistics
Matches: 268, Mismatches: 39, Indels: 36
0.78 0.11 0.10
Matches are distributed among these distances:
40 8 0.03
41 46 0.17
42 67 0.25
43 131 0.49
44 16 0.06
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTA
Found at i:5495240 original size:128 final size:126
Alignment explanation
Indices: 5495010--5495330 Score: 486
Period size: 128 Copynumber: 2.5 Consensus size: 126
5495000 CAGATTCCCC
** * *
5495010 AAGG-GGTTGCTAAGTGCTGATTC-CCAAATTATTGATTCT-AAAGGTGGTTGCTAAGTGCTGAT
1 AAGGTGGTTGCTAAGTGCTGATTCACCGTATT-TTGATTGTGAAAGG-GGTTGCTATGTGCTGAT
* *
5495072 TCCACCGTATATTTGATTGTGAAAGGGGTTGCTCTGTGCTGATTCCCCATATCACTGAATATA
64 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
*
5495135 AAGGTGGTTGCTAAGTGCTGATTACACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGAT
1 AAGGTGGTTGCTAAGTGCTGATT-CACCGTAT-TTTGATTGTGAAAGGGGTTGCTATGTGCTGAT
*
5495200 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATA
64 TCCACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
*
5495263 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGAAAGGGGTTGCTATGTGCTGAT
1 AAGGTGGTTGCTAAGTGCTGATT-CACCGTAT-TTTGATTGTGAAAGGGGTTGCTATGTGCTGAT
5495328 TCC
64 TCC
5495331 CTGTATCACT
Statistics
Matches: 179, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
125 4 0.02
126 18 0.10
127 1 0.01
128 150 0.84
129 6 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (126 bp):
AAGGTGGTTGCTAAGTGCTGATTCACCGTATTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTC
CACCATATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTGAATATA
Found at i:5495331 original size:85 final size:86
Alignment explanation
Indices: 5495010--5495374 Score: 344
Period size: 85 Copynumber: 4.3 Consensus size: 86
5495000 CAGATTCCCC
* * *
5495010 AAGGGGTTGCTAAGTGCTGATT-C-CCAAAT-TATTGATTCT-AAAGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATCT-TTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* *
5495071 TTCCACCGTATATTTGATTGTGA
65 TTCC-CCGTATATCTGAATGTGA
** * * *
5495094 AAGGGGTTGCTCTGTGCTGATTCC-CCATATCACTGAA-TAT-AAAGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATC-TTTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* * *
5495156 TTACACCGTATATTTGATTGTGA
65 TT-CCCCGTATATCTGAATGTGA
* * * * *
5495179 AAGGGGTTGCTATGTGTTGATTCCACCATATATTTGATTGTGAAAGG-GGTTGCTATGTGCTGAT
1 AAGGGGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGAT
*
5495243 TCCCCGTATCA-CTGAATAT-A
66 TCCCCGTAT-ATCTGAATGTGA
* *
5495263 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTGTGAAAGG-GGTTGCTATGTGCTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGA
* *
5495327 TTCCCTGTATCA-CTGAAT-T-T
65 TTCCCCGTAT-ATCTGAATGTGA
*
5495347 AAGGTGGTTGCTAAGTGCTGAATCCACC
1 AAGG-GGTTGCTAAGTGCTGATTCCACC
5495375 GAGTAACGGA
Statistics
Matches: 244, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
84 53 0.22
85 157 0.64
86 29 0.12
87 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (86 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCATATCTTTAATTGTGAAAGGTGGTTGCTAAGTGCTGAT
TCCCCGTATATCTGAATGTGA
Found at i:5503524 original size:3 final size:3
Alignment explanation
Indices: 5503516--5503582 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
5503506 TACTTTACAA
* *
5503516 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5503564 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
5503583 TGGTTGTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5518919 original size:25 final size:25
Alignment explanation
Indices: 5518882--5518968 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
5518872 AACTCACCAC
5518882 AGCTCGTATGAGCTTACCGATTTAT
1 AGCTCGTATGAGCTTACCGATTTAT
* * * *
5518907 AGCTCGTAGGAGCTTATCTATATT-C
1 AGCTCGTATGAGCTTACCGAT-TTAT
* *
5518932 AGCTCGGAAGAGCTTACCG-TTTAT
1 AGCTCGTATGAGCTTACCGATTTAT
*
5518956 CGCTCGTATGAGC
1 AGCTCGTATGAGC
5518969 CTACATGTAC
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 33 0.69
26 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTTAT
Found at i:5520277 original size:28 final size:29
Alignment explanation
Indices: 5520245--5520302 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
5520235 GTCGTGTGTC
5520245 CCCATTCCGAATG-CCACACGGCCTGAGA
1 CCCATTCCGAATGCCCACACGGCCTGAGA
*
5520273 CCCATTTCGAATGCCCACACGGCCTGAGA
1 CCCATTCCGAATGCCCACACGGCCTGAGA
5520302 C
1 C
5520303 ACGGGCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.24, C:0.40, G:0.21, T:0.16
Consensus pattern (29 bp):
CCCATTCCGAATGCCCACACGGCCTGAGA
Found at i:5520929 original size:12 final size:12
Alignment explanation
Indices: 5520894--5520936 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5520884 TTTAAATACA
* *
5520894 TTAAAAGTTAAA
1 TTAAAATTTAAT
*
5520906 TAAAAATTTAAT
1 TTAAAATTTAAT
5520918 TTAAAATTTAAT
1 TTAAAATTTAAT
5520930 TTAAAAT
1 TTAAAAT
5520937 AATCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAAATTTAAT
Found at i:5521099 original size:107 final size:107
Alignment explanation
Indices: 5520977--5521205 Score: 404
Period size: 107 Copynumber: 2.1 Consensus size: 107
5520967 ATAAGTTGAT
* * *
5520977 TATTAACCGAAACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAACCAAACTAA
1 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
5521042 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
66 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
*
5521084 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAATCAAACTAA
1 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
* *
5521149 AACATATACTACTTTGTACTCGTTTAAGATTGAAATGATATA
66 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
5521191 TATTAACCGATACAA
1 TATTAACCGATACAA
5521206 CCCATACCTA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 116 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (107 bp):
TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
Found at i:5527004 original size:15 final size:14
Alignment explanation
Indices: 5526980--5527011 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5526970 TGGTCTCTCA
5526980 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
5526994 TTTTCTCTTTTTCTT
1 TTTT-TCTTTTTCTT
5527009 TTT
1 TTT
5527012 GAAACATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:5530529 original size:44 final size:44
Alignment explanation
Indices: 5530479--5530678 Score: 207
Period size: 44 Copynumber: 4.5 Consensus size: 44
5530469 TTTGAGTACT
5530479 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
5530523 TCTGATCAGTGACAAGTGACAAGTGATGAGTGGTAGCTTTATCTACACTTA
1 TCTG---A-T--CAA-TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
5530574 TCTGATCAGTGACAAGTG---A----TAGCTTTAACTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
5530611 TCTGATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
5530655 TCTGATTAAGGACAAGTGACAAGT
1 TCTGATCAATGACAAGTGATAAGT
5530679 AATAAATGTG
Statistics
Matches: 132, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
37 35 0.27
40 1 0.01
41 1 0.01
44 49 0.37
45 2 0.02
47 2 0.02
48 2 0.02
50 3 0.02
51 37 0.28
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5530569 original size:51 final size:51
Alignment explanation
Indices: 5530488--5530592 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
5530478 TTCTGATCAA
5530488 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
5530539 TGACAAGTGATGAGTGGTAGCTTTATCTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
5530590 TGA
1 TGA
5530593 TAGCTTTAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
Found at i:5530597 original size:37 final size:37
Alignment explanation
Indices: 5530551--5530630 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
5530541 ACAAGTGATG
* *
5530551 AGTGGTAGCTTTATCTACACTTATCTGATCAGTGACA
1 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
5530588 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
1 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
5530625 AGTGAT
1 AGTGAT
5530631 GAGTGGTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (37 bp):
AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
Found at i:5533341 original size:24 final size:25
Alignment explanation
Indices: 5533314--5533366 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
5533304 GGTCTTTTCG
*
5533314 TGAAATTTAATGCAAATG-ATGCAA
1 TGAAATGTAATGCAAATGAATGCAA
* *
5533338 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATGCAAATGAATGCAA
5533363 TGAA
1 TGAA
5533367 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGCAA
Found at i:5535419 original size:3 final size:3
Alignment explanation
Indices: 5535398--5535501 Score: 68
Period size: 3 Copynumber: 33.7 Consensus size: 3
5535388 CACGAAAAAT
* * ** *
5535398 ATA ATA CTA ATA GTA ATA ATA ACG ATA ATA ATA ATA GTA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
5535444 ATG TTA ATA TTA ATAA ATA ATA A-A CATA ATA ATA A-A GTTA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
5535490 ATA ATGA ATA AT
1 ATA AT-A ATA AT
5535502 CGAAATTTGA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
2 2 0.03
3 63 0.83
4 11 0.14
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5535566 original size:18 final size:19
Alignment explanation
Indices: 5535537--5535580 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
5535527 AATATAAATA
5535537 TGTAAAT-A-AATAAATAA-
1 TGTAAATGACAAT-AATAAG
5535554 TG-AAATGACAATAATAAG
1 TGTAAATGACAATAATAAG
5535572 TGTAAATGA
1 TGTAAATGA
5535581 TAAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 5 0.22
19 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (19 bp):
TGTAAATGACAATAATAAG
Found at i:5535759 original size:3 final size:3
Alignment explanation
Indices: 5535744--5535887 Score: 54
Period size: 3 Copynumber: 47.0 Consensus size: 3
5535734 TAAAACAAAT
* * * * * * *
5535744 TAA TAA CAA TAA TAA TAA TAA TAA TAG TAA AAA TAA AAA TAT TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * * * *
5535792 TTG TAA TAA TGGAA GTAA TAG TAA CAG TAA TAA TAA CAA TAA TAG TAC
1 TAA TAA TAA T--AA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
5535840 TAC TAC TAC TAC TAC TAC TAC TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5535888 AAGGACAAAA
Statistics
Matches: 110, Mismatches: 28, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
3 105 0.95
4 2 0.02
5 2 0.02
6 1 0.01
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5544062 original size:12 final size:12
Alignment explanation
Indices: 5544047--5544080 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5544037 TTATTTTTCT
5544047 TTACTTTATTTA
1 TTACTTTATTTA
5544059 TTACTTTATTTTA
1 TTACTTTA-TTTA
5544072 TTA-TTTATT
1 TTACTTTATT
5544081 ACTTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:5544071 original size:17 final size:15
Alignment explanation
Indices: 5544030--5544073 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
5544020 CAACCCAATT
5544030 TTTATTATTATTTTTC
1 TTTATT-TTATTTTTC
*
5544046 TTTACTTTATTTATTAC
1 TTTATTTTATTT-TT-C
5544063 TTTATTTTATT
1 TTTATTTTATT
5544074 ATTTATTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTATTTTTC
Found at i:5546985 original size:13 final size:12
Alignment explanation
Indices: 5546967--5546996 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
5546957 AAGAGTTAAA
5546967 TAAAAATTTAATT
1 TAAAAA-TTAATT
5546980 TAAAAATTAATT
1 TAAAAATTAATT
5546992 TAAAA
1 TAAAA
5546997 TATCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:5547257 original size:107 final size:107
Alignment explanation
Indices: 5547047--5547264 Score: 409
Period size: 107 Copynumber: 2.0 Consensus size: 107
5547037 ATTAACTAAA
5547047 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
1 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
* *
5547112 CTTTGTACTCATTTAAGATTGAAATGATATATATTAACCTAT
66 CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
5547154 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
1 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
*
5547219 CTTTGTACCCGTTTAAGATTGAAATGATATATATTAACCGAT
66 CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
5547261 ACAA
1 ACAA
5547265 CCCATACCTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (107 bp):
ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
Found at i:5568104 original size:29 final size:29
Alignment explanation
Indices: 5568065--5568204 Score: 158
Period size: 29 Copynumber: 4.8 Consensus size: 29
5568055 ACAAAAAATA
5568065 AAAATTTACATTTTGACCCCAAACTTTGCT-
1 AAAA-TTACATTTTGACCCCAAACTTT-CTC
*
5568095 AAAATTACATTTTGGCCCCAAACTTTCTC
1 AAAATTACATTTTGACCCCAAACTTTCTC
* * *
5568124 AAAATTACACTTTGACCCCTAAACTTTTTG
1 AAAATTACATTTTGACCCC-AAACTTTCTC
* * *
5568154 AAAATTACATTTTGGCCCCATATTTTC-C
1 AAAATTACATTTTGACCCCAAACTTTCTC
*
5568182 TAAAATTACATTTTTACCCCAAA
1 -AAAATTACATTTTGACCCCAAA
5568205 TATTTTGTGT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.02
29 62 0.67
30 29 0.31
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAACTTTCTC
Found at i:5568158 original size:59 final size:58
Alignment explanation
Indices: 5568065--5568204 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 58
5568055 ACAAAAAATA
5568065 AAAATTTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTT-CT
1 AAAA-TTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTTCCT
* * * *
5568123 CAAAATTACACTTTGACCCCTAAACTTT-TTGAAAATTACATTTTGGCCCCATATTTTCCT
1 -AAAATTACATTTTGACCCC-AAACTTTGCT-AAAATTACATTTTGGCCCCAAACTTTCCT
*
5568183 AAAATTACATTTTTACCCCAAA
1 AAAATTACATTTTGACCCCAAA
5568205 TATTTTGTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
58 18 0.25
59 52 0.72
60 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAATTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTTCCT
Found at i:5568298 original size:24 final size:24
Alignment explanation
Indices: 5568267--5568314 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5568257 TCAACAGCCG
5568267 AGCGTGCTTCCCCTCACCCCCAGC
1 AGCGTGCTTCCCCTCACCCCCAGC
*
5568291 AGCGTGCTTCCCCTCACCTCCAGC
1 AGCGTGCTTCCCCTCACCCCCAGC
5568315 TACTTCAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.52, G:0.17, T:0.19
Consensus pattern (24 bp):
AGCGTGCTTCCCCTCACCCCCAGC
Found at i:5568402 original size:25 final size:24
Alignment explanation
Indices: 5568372--5568418 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
5568362 AGACAAGAAG
5568372 AAAAAGGACAAAAAAT-GAAGAGATT
1 AAAAA-GA-AAAAAATGGAAGAGATT
*
5568397 AAAAAGAAGAAAATGGAAGAGA
1 AAAAAGAAAAAAATGGAAGAGA
5568419 AGAAAGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (24 bp):
AAAAAGAAAAAAATGGAAGAGATT
Found at i:5568747 original size:13 final size:12
Alignment explanation
Indices: 5568729--5568805 Score: 82
Period size: 13 Copynumber: 6.0 Consensus size: 12
5568719 GGTGCTGCCC
5568729 GAAGAAGAAGAAA
1 GAAGAAGAA-AAA
5568742 GAAGAAAGATAAAA
1 GAAG-AAGA-AAAA
5568756 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
5568768 GGGAGAAGAAAAA
1 -GAAGAAGAAAAA
*
5568781 GAAAAAGAAAAA
1 GAAGAAGAAAAA
*
5568793 GAAAAAAGAAAAA
1 G-AAGAAGAAAAA
5568806 AAATTAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
12 15 0.26
13 30 0.53
14 11 0.19
15 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5568806 original size:7 final size:6
Alignment explanation
Indices: 5568733--5568805 Score: 74
Period size: 6 Copynumber: 11.3 Consensus size: 6
5568723 CTGCCCGAAG
* * *
5568733 AAGAAGA AAGAAGA AAGATAA AAGAAG AAGAAA AAGGGAG AAGAAA AAGAAA
1 AAGAA-A AAGAA-A AAGA-AA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA
5568785 AAGAAA AAGAAAA AAGAAA AA
1 AAGAAA AAG-AAA AAGAAA AA
5568806 AAATTAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
6 30 0.53
7 26 0.46
8 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:5569084 original size:23 final size:23
Alignment explanation
Indices: 5569038--5569081 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5569028 TCCAGTCCAG
5569038 GCCCAACAGCACCTAGCAGGCCA
1 GCCCAACAGCACCTAGCAGGCCA
* *
5569061 GCCCAGCAGCAGC-AGCAGGCC
1 GCCCAACAGCACCTAGCAGGCC
5569082 CAGTACCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.43, G:0.27, T:0.02
Consensus pattern (23 bp):
GCCCAACAGCACCTAGCAGGCCA
Found at i:5569211 original size:21 final size:20
Alignment explanation
Indices: 5569186--5569224 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5569176 GCAGGCCCAA
5569186 AAAAAAAAAAAAAAAGGAAG
1 AAAAAAAAAAAAAAAGGAAG
*
5569206 AAAAAAAAGAAAAAAGGAA
1 AAAAAAAAAAAAAAAGGAA
5569225 AAGGGCCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGGAAG
Found at i:5575512 original size:7 final size:7
Alignment explanation
Indices: 5575496--5575528 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5575486 TGGCCTCTCA
5575496 TTTTTC-
1 TTTTTCT
5575502 TTTTTCT
1 TTTTTCT
5575509 TTTTTCT
1 TTTTTCT
5575516 TTTTTCT
1 TTTTTCT
5575523 CTTTTT
1 -TTTTT
5575529 TTGAAACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 14 0.56
8 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:5575519 original size:14 final size:14
Alignment explanation
Indices: 5575491--5575528 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
5575481 CACCTTGGCC
5575491 TCTCATTTTTCTTTT
1 TCTC-TTTTTCTTTT
5575506 TCT-TTTTTCTTTTT
1 TCTCTTTTTC-TTTT
5575520 TCTCTTTTT
1 TCTCTTTTT
5575529 TTGAAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTCTTTTTCTTTT
Found at i:5579138 original size:51 final size:51
Alignment explanation
Indices: 5579057--5579264 Score: 286
Period size: 51 Copynumber: 4.2 Consensus size: 51
5579047 ACTTCTTAAA
* *
5579057 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* * *
5579108 TGACAAGTGATGAGTGGAAGCTTTATCTACACTTATCTAATCAGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
5579159 TG---A--GA--AGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
5579203 TGACAAGTGATGAGTAGTAGCTTTAGCTACACTTATCTGATCAGGGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
5579254 TGACAAGTGAT
1 TGACAAGTGAT
5579265 AAATGTGATC
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
44 37 0.27
46 2 0.01
47 1 0.01
48 1 0.01
49 2 0.01
51 94 0.69
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
Found at i:5579154 original size:44 final size:43
Alignment explanation
Indices: 5579106--5579256 Score: 151
Period size: 44 Copynumber: 3.3 Consensus size: 43
5579096 ATCGGTGACA
*
5579106 AGTGACAAGTGATGAGTGGAAGCTTTATCTACACTTATCTAATC
1 AGTGACAAGTGATGAGT-GAAGCTTTAACTACACTTATCTAATC
5579150 AGTGACAAGTGA-GAAGTGATAGCTTTAACTACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATG-AGTGA-AGCTTTAACTACACTTATCT-A--A-T--C
* * *
5579200 AAGTGACAAGTGATGAGTAGTAGCTTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATGAGT-GAAGCTTTAACTACACTTATCTAATC
*
5579245 AGGGACAAGTGA
1 AGTGACAAGTGA
5579257 CAAGTGATAA
Statistics
Matches: 91, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
43 3 0.03
44 45 0.49
45 2 0.02
47 2 0.02
48 2 0.02
50 1 0.01
51 34 0.37
52 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (43 bp):
AGTGACAAGTGATGAGTGAAGCTTTAACTACACTTATCTAATC
Found at i:5579225 original size:95 final size:95
Alignment explanation
Indices: 5579057--5579265 Score: 328
Period size: 95 Copynumber: 2.2 Consensus size: 95
5579047 ACTTCTTAAA
* * * *
5579057 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAGTGACAAGTGATGAG
1 TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
* *
5579122 TGGAAGCTTTATCTACACTTATCTAATCAG
66 TAGAAGCTTTAGCTACACTTATCTAATCAG
*
5579152 TGACAAGTGAGAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
1 TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
* *
5579217 TAGTAGCTTTAGCTACACTTATCTGATCAG
66 TAGAAGCTTTAGCTACACTTATCTAATCAG
*
5579247 GGACAAGTGACAAGTGATA
1 TGACAAGTGACAAGTGATA
5579266 AATGTGATCT
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 104 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (95 bp):
TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
TAGAAGCTTTAGCTACACTTATCTAATCAG
Found at i:5584001 original size:3 final size:3
Alignment explanation
Indices: 5583980--5584083 Score: 59
Period size: 3 Copynumber: 33.7 Consensus size: 3
5583970 CACGAAAAAT
* * ** *
5583980 ATA ATA CTA ATA GTA ATA ATA ACG ATA ATA ATA ATA GTA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * *
5584026 ATG TTA ATA TTA ATAA ATA A-A AAA CATA ATA ATA A-A GTTA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
5584072 ATA ATGA ATA AT
1 ATA AT-A ATA AT
5584084 CGAAATTTGA
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
2 3 0.04
3 60 0.80
4 12 0.16
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5584148 original size:18 final size:19
Alignment explanation
Indices: 5584119--5584162 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
5584109 AATATAAATA
5584119 TGTAAAT-A-AATAAATAA-
1 TGTAAATGACAAT-AATAAG
5584136 TG-AAATGACAATAATAAG
1 TGTAAATGACAATAATAAG
5584154 TGTAAATGA
1 TGTAAATGA
5584163 TAAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 5 0.22
19 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (19 bp):
TGTAAATGACAATAATAAG
Found at i:5584402 original size:12 final size:12
Alignment explanation
Indices: 5584387--5584420 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5584377 TAATAATGGA
5584387 AGTAATAGTAAC
1 AGTAATAGTAAC
*
5584399 AGTAATAATAAC
1 AGTAATAGTAAC
*
5584411 AATAATAGTA
1 AGTAATAGTA
5584421 GTACCTACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (12 bp):
AGTAATAGTAAC
Found at i:5587871 original size:3 final size:3
Alignment explanation
Indices: 5587865--5588031 Score: 109
Period size: 3 Copynumber: 54.7 Consensus size: 3
5587855 CAACAACAAC
*
5587865 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * ** * *
5587913 AGT AAA AAT AAA AAT ATT AGT ATT TGT AAT AAT GGAAGT AAT AGT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT --AA-T AAT AAT AAT
* * * * * * * * * * *
5587961 AGT AAT AAT AAC AAT AAT AGT AGT AGT ACT ACT ACT ACT ACT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5588009 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
5588032 AAGGACAAAA
Statistics
Matches: 135, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
3 130 0.96
4 2 0.01
5 2 0.01
6 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5595266 original size:28 final size:27
Alignment explanation
Indices: 5595214--5595266 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
5595204 TTTGAATACC
*
5595214 CACATGGCCTGAGACACGGGCGTGTCT
1 CACATGGCCTGAGACACAGGCGTGTCT
5595241 CACATGGCCTG-GCCACACAGGCGTGT
1 CACATGGCCTGAG--ACACAGGCGTGT
5595267 GTCCTCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 11 0.48
28 11 0.48
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (27 bp):
CACATGGCCTGAGACACAGGCGTGTCT
Found at i:5600900 original size:13 final size:12
Alignment explanation
Indices: 5600882--5600911 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
5600872 AAGAGTTAAA
5600882 TAAAAATTTAATT
1 TAAAAA-TTAATT
5600895 TAAAAATTAATT
1 TAAAAATTAATT
5600907 TAAAA
1 TAAAA
5600912 TATCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:5605067 original size:375 final size:378
Alignment explanation
Indices: 5604369--5605122 Score: 1444
Period size: 375 Copynumber: 2.0 Consensus size: 378
5604359 AATTTGAATG
5604369 ATGAAAAATTAGAACAAAATTAAAATGCAATTGACTCAAAATATTGGTGTATAATGAATACAAAA
1 ATGAAAAATTAGAACAAAATTAAAATGCAATTGACTCAAAATATTGGTGTATAATGAATACAAAA
5604434 ATTAACAAAAAAAAGTAATAATTTATTACATTTTGAACTATAATAATAAATTTAAACACTATTAA
66 ATTAACAAAAAAAAGTAATAATTTATTACATTTTGAACTATAATAATAAATTTAAACACTATTAA
5604499 AAATAAATATCACAAATAATATTAAATATTACAATATACGAAAGTAGGATTTAATTAATTAAAAA
131 AAATAAATATCACAAATAATATTAAATATTACAATATACGAAAGTAGGATTTAATTAATTAAAAA
5604564 TATTTTGGAATTTAAAAAAAGAAAACTGAATTTGTATTAAATCGAAATCAGTTTCAACATTGACG
196 TATTTTGGAATTTAAAAAAAGAAAACTGAATTTGTATTAAATCGAAATCAGTTTCAACATTGACG
5604629 AACTAAACTAGCAATTAAACGCAAGCATTAAAATAATTACAATCAACCACATAAAACGATACCGT
261 AACTAAACTAGCAATTAAACGCAAGCATTAAAATAATTACAATCAACCACATAAAACGATACCGT
5604694 TTCAAGTTGGACCTCAATGAAAACAAGTTACATGCACCATACAAATTACAAAA
326 TTCAAGTTGGACCTCAATGAAAACAAGTTACATGCACCATACAAATTACAAAA
*
5604747 ATGATAAATTAGAACAAAATTAAAATGCAATTGACTCAAAATATTGGTGTATAATGAATA-AAAA
1 ATGAAAAATTAGAACAAAATTAAAATGCAATTGACTCAAAATATTGGTGTATAATGAATACAAAA
* *
5604811 A-TAA-ACAAAAAAGTAATAATTTATTACATTTTGAACTATTATAATAAATTTAAACACTATTAA
66 ATTAACAAAAAAAAGTAATAATTTATTACATTTTGAACTATAATAATAAATTTAAACACTATTAA
5604874 AAATAAATATCACAAA-AATATTAAATTATTACAATATACGAAAGTAGGATTTAATTAATTAAAA
131 AAATAAATATCACAAATAATATTAAA-TATTACAATATACGAAAGTAGGATTTAATTAATTAAAA
5604938 ATATTTTGGAATTTAAAAAAAGAAAACTGAATTTGTATTAAATCGAAATCAGTTTCAACATTGAC
195 ATATTTTGGAATTTAAAAAAAGAAAACTGAATTTGTATTAAATCGAAATCAGTTTCAACATTGAC
5605003 GAACTAAACTAGCAATTAAACGCAAGCATTAAAATAATTACAATCAACCACATAAAACGATACCG
260 GAACTAAACTAGCAATTAAACGCAAGCATTAAAATAATTACAATCAACCACATAAAACGATACCG
5605068 TTTCAAGTTGGACCTCAATGAAAACAAGTTACATGCACCATACAAATTACAAAA
325 TTTCAAGTTGGACCTCAATGAAAACAAGTTACATGCACCATACAAATTACAAAA
5605122 A
1 A
5605123 ATTAAAGAAA
Statistics
Matches: 372, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
374 9 0.02
375 296 0.80
376 3 0.01
377 5 0.01
378 59 0.16
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.29
Consensus pattern (378 bp):
ATGAAAAATTAGAACAAAATTAAAATGCAATTGACTCAAAATATTGGTGTATAATGAATACAAAA
ATTAACAAAAAAAAGTAATAATTTATTACATTTTGAACTATAATAATAAATTTAAACACTATTAA
AAATAAATATCACAAATAATATTAAATATTACAATATACGAAAGTAGGATTTAATTAATTAAAAA
TATTTTGGAATTTAAAAAAAGAAAACTGAATTTGTATTAAATCGAAATCAGTTTCAACATTGACG
AACTAAACTAGCAATTAAACGCAAGCATTAAAATAATTACAATCAACCACATAAAACGATACCGT
TTCAAGTTGGACCTCAATGAAAACAAGTTACATGCACCATACAAATTACAAAA
Found at i:5606043 original size:18 final size:21
Alignment explanation
Indices: 5606017--5606054 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5606007 ACTGATATTA
5606017 TTGGACTTT-TA-ATTTTTAT
1 TTGGACTTTATATATTTTTAT
5606036 TTGG-CTTTATATATTTTTA
1 TTGGACTTTATATATTTTTA
5606055 AATGTTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (21 bp):
TTGGACTTTATATATTTTTAT
Found at i:5606655 original size:44 final size:43
Alignment explanation
Indices: 5606557--5607047 Score: 260
Period size: 44 Copynumber: 11.5 Consensus size: 43
5606547 ATTTTAATTC
* * * *
5606557 GCTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
*
5606601 AG-TCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCT
1 -GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
* * **
5606645 GCTCTACTGTAACCTCA-GGAGATAAGA-TT-T--TTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
** *
5606683 ATTCCACTGTAATCTCAGGGAGATAAGA--T-T-CTTCAGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
** * * * * *
5606722 ATTCCATTGTAATCTCAGGGAGATAAGA-CT-TGATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
* * * ** * *
5606763 ACTCTACTGTAAT-TCTAGAGAGATAAGATCCTT-TATTTTAATCC
1 GCTCCACTGTAATCTC-AGGGAGATAAGAT--TTCTGCTTCAATCT
* * *
5606807 GCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
* * * **
5606851 GCTCCACTGTAACCTCAGGGAGATAAGATTTGAAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTT---CTGCTTCAATCT
** * * ** * *
5606897 ATTCCACTGTAATATCAGGGAGATAAGA--CCTAATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
* * * * * ** *
5606938 ACTCTACTGTGATTTCAGAGAGATAAGATCCTT-TATTTTAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT--TTCTGCTTCAATCT
* * *
5606982 GCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
*
5607026 GCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAATCTCAGGGAG
5607048 GTAAAATCCG
Statistics
Matches: 343, Mismatches: 82, Indels: 43
0.73 0.18 0.09
Matches are distributed among these distances:
38 21 0.06
39 44 0.13
40 4 0.01
41 57 0.17
42 4 0.01
43 13 0.04
44 165 0.48
45 3 0.01
46 31 0.09
47 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
Found at i:5606701 original size:38 final size:39
Alignment explanation
Indices: 5606592--5606749 Score: 165
Period size: 39 Copynumber: 3.9 Consensus size: 39
5606582 GGATTACTGG
* * *
5606592 CTTCAATCTAGTCCGCTGTAATCTCAGGGAGATAAGATTTCT
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGA--T-T
* ** * *
5606634 GGCTTCAATCTGCTCTACTGTAACCTCA-GGAGATAAGATT
1 --CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
* *
5606674 TTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
*
5606713 CTTCAGTCTATTCCATTGTAATCTCAGGGAGATAAGA
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGA
5606750 CTTGATGCGA
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 19 0.19
39 46 0.47
40 1 0.01
41 1 0.01
43 10 0.10
44 21 0.21
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (39 bp):
CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
Found at i:5606969 original size:175 final size:175
Alignment explanation
Indices: 5606710--5607047 Score: 579
Period size: 175 Copynumber: 1.9 Consensus size: 175
5606700 GGGAGATAAG
* * * *
5606710 ATTCTTCAGTCTATTCCATTGTAATCTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAA
1 ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
5606775 TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
66 TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
5606840 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
131 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
* *
5606885 ATTCTTCGGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTGA
1 ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
*
5606950 TT-TCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAAATAGGATTAC
66 TTCT-AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* *
5607014 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
130 TGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
5607048 GTAAAATCCG
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
174 1 0.01
175 152 0.99
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (175 bp):
ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
Found at i:5610489 original size:551 final size:551
Alignment explanation
Indices: 5609448--5610549 Score: 2204
Period size: 551 Copynumber: 2.0 Consensus size: 551
5609438 CCCTCATGGA
5609448 CTTCTTCCAGGATCTTTCTAGCCTTCACGGTATCTATACATCTTAACAGCACTTGATCTTTCCCT
1 CTTCTTCCAGGATCTTTCTAGCCTTCACGGTATCTATACATCTTAACAGCACTTGATCTTTCCCT
5609513 CTCTTGTACAACACTTCCCCATCTAAGACATATTCAATGGCTATTCTTCTCAATGTTCTTTTGTC
66 CTCTTGTACAACACTTCCCCATCTAAGACATATTCAATGGCTATTCTTCTCAATGTTCTTTTGTC
5609578 GTTCTCTGTCGCTTGATCAGGGTATTTTCGATTCTTCACATATTGTAGTATGCTCTGATGCCAAG
131 GTTCTCTGTCGCTTGATCAGGGTATTTTCGATTCTTCACATATTGTAGTATGCTCTGATGCCAAG
5609643 GATGATCATCTTTTCCCTCCTCTTCAATATTGTAGCAATGAGCCGAAACCTCATATATGCTCATC
196 GATGATCATCTTTTCCCTCCTCTTCAATATTGTAGCAATGAGCCGAAACCTCATATATGCTCATC
5609708 TGAATAGGCTTCATGATTTCCAACTTGTTCACCCTAATCATCGAGGCTAAAGTAGCCAATGCGTC
261 TGAATAGGCTTCATGATTTCCAACTTGTTCACCCTAATCATCGAGGCTAAAGTAGCCAATGCGTC
5609773 AACCATCTGGTTTTCATATCGTGGGAGGTAACAGAAGGTGATGTCATCAAACTCATCAATCAATT
326 AACCATCTGGTTTTCATATCGTGGGAGGTAACAGAAGGTGATGTCATCAAACTCATCAATCAATT
5609838 CAAGAACCAGATCTTTATAATTGATCAACTTAGGGTCCCTAGTTTCCCATTCTCCATTGAGTTGG
391 CAAGAACCAGATCTTTATAATTGATCAACTTAGGGTCCCTAGTTTCCCATTCTCCATTGAGTTGG
5609903 TATATCACCAATGCAGAATCTCCATACACTTTTAGCACTTTAATTTTTCGTTCAATGGTTGCACG
456 TATATCACCAATGCAGAATCTCCATACACTTTTAGCACTTTAATTTTTCGTTCAATGGTTGCACG
5609968 AATACCCATAATACATGCTTCATATTCTGCC
521 AATACCCATAATACATGCTTCATATTCTGCC
5609999 CTTCTTCCAGGATCTTTCTAGCCTTCACGGTATCTATACATCTTAACAGCACTTGATCTTTCCCT
1 CTTCTTCCAGGATCTTTCTAGCCTTCACGGTATCTATACATCTTAACAGCACTTGATCTTTCCCT
5610064 CTCTTGTACAACACTTCCCCATCTAAGACATATTCAATGGCTATTCTTCTCAATGTTCTTTTGTC
66 CTCTTGTACAACACTTCCCCATCTAAGACATATTCAATGGCTATTCTTCTCAATGTTCTTTTGTC
5610129 GTTCTCTGTCGCTTGATCAGGGTATTTTCGATTCTTCACATATTGTAGTATGCTCTGATGCCAAG
131 GTTCTCTGTCGCTTGATCAGGGTATTTTCGATTCTTCACATATTGTAGTATGCTCTGATGCCAAG
5610194 GATGATCATCTTTTCCCTCCTCTTCAATATTGTAGCAATGAGCCGAAACCTCATATATGCTCATC
196 GATGATCATCTTTTCCCTCCTCTTCAATATTGTAGCAATGAGCCGAAACCTCATATATGCTCATC
5610259 TGAATAGGCTTCATGATTTCCAACTTGTTCACCCTAATCATCGAGGCTAAAGTAGCCAATGCGTC
261 TGAATAGGCTTCATGATTTCCAACTTGTTCACCCTAATCATCGAGGCTAAAGTAGCCAATGCGTC
5610324 AACCATCTGGTTTTCATATCGTGGGAGGTAACAGAAGGTGATGTCATCAAACTCATCAATCAATT
326 AACCATCTGGTTTTCATATCGTGGGAGGTAACAGAAGGTGATGTCATCAAACTCATCAATCAATT
5610389 CAAGAACCAGATCTTTATAATTGATCAACTTAGGGTCCCTAGTTTCCCATTCTCCATTGAGTTGG
391 CAAGAACCAGATCTTTATAATTGATCAACTTAGGGTCCCTAGTTTCCCATTCTCCATTGAGTTGG
5610454 TATATCACCAATGCAGAATCTCCATACACTTTTAGCACTTTAATTTTTCGTTCAATGGTTGCACG
456 TATATCACCAATGCAGAATCTCCATACACTTTTAGCACTTTAATTTTTCGTTCAATGGTTGCACG
5610519 AATACCCATAATACATGCTTCATATTCTGCC
521 AATACCCATAATACATGCTTCATATTCTGCC
5610550 ATATTATTTG
Statistics
Matches: 551, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
551 551 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (551 bp):
CTTCTTCCAGGATCTTTCTAGCCTTCACGGTATCTATACATCTTAACAGCACTTGATCTTTCCCT
CTCTTGTACAACACTTCCCCATCTAAGACATATTCAATGGCTATTCTTCTCAATGTTCTTTTGTC
GTTCTCTGTCGCTTGATCAGGGTATTTTCGATTCTTCACATATTGTAGTATGCTCTGATGCCAAG
GATGATCATCTTTTCCCTCCTCTTCAATATTGTAGCAATGAGCCGAAACCTCATATATGCTCATC
TGAATAGGCTTCATGATTTCCAACTTGTTCACCCTAATCATCGAGGCTAAAGTAGCCAATGCGTC
AACCATCTGGTTTTCATATCGTGGGAGGTAACAGAAGGTGATGTCATCAAACTCATCAATCAATT
CAAGAACCAGATCTTTATAATTGATCAACTTAGGGTCCCTAGTTTCCCATTCTCCATTGAGTTGG
TATATCACCAATGCAGAATCTCCATACACTTTTAGCACTTTAATTTTTCGTTCAATGGTTGCACG
AATACCCATAATACATGCTTCATATTCTGCC
Found at i:5625291 original size:24 final size:24
Alignment explanation
Indices: 5625244--5625291 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5625234 ATGGAATAAT
*
5625244 ATTTTATTTAAATAAATATTAATA
1 ATTTTATTTAAATAAATATAAATA
*
5625268 ATTTTGTTTAAATATAAT-TAAATA
1 ATTTTATTTAAATA-AATATAAATA
5625292 TTAAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTATTTAAATAAATATAAATA
Found at i:5626873 original size:18 final size:19
Alignment explanation
Indices: 5626852--5626903 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
5626842 TTCCTTTACA
5626852 TTATTTCTCTCTT-TATTT
1 TTATTTCTCTCTTCTATTT
* *
5626870 TTATTTTTGCTTCTTCTTTTT
1 TTATTTCT-C-TCTTCTATTT
5626891 TTATTTCT-TCTTC
1 TTATTTCTCTCTTC
5626904 CTTTATAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.43
19 1 0.04
20 4 0.14
21 11 0.39
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTTCTCTCTTCTATTT
Found at i:5626903 original size:21 final size:20
Alignment explanation
Indices: 5626852--5626909 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
5626842 TTCCTTTACA
5626852 TTATTTC-TC-TCTTTATTT
1 TTATTTCTTCTTCTTTATTT
*
5626870 TTATTT-TTGCTTCTTCTTTTT
1 TTATTTCTT-CTTCTT-TATTT
5626891 TTATTTCTTCTTCCTTTAT
1 TTATTTCTTCTT-CTTTAT
5626910 AATGTCAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.22
19 1 0.03
20 4 0.12
21 15 0.47
22 5 0.16
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (20 bp):
TTATTTCTTCTTCTTTATTT
Found at i:5633252 original size:6 final size:7
Alignment explanation
Indices: 5633236--5633265 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5633226 TCTCTCTTTG
5633236 TTTTT-A
1 TTTTTCA
5633242 TTTTTCA
1 TTTTTCA
5633249 TTTTTCA
1 TTTTTCA
5633256 TTTTTCA
1 TTTTTCA
5633263 TTT
1 TTT
5633266 CTTCTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:5639131 original size:13 final size:15
Alignment explanation
Indices: 5639094--5639132 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
5639084 ATAAAATGAA
5639094 ACAGAAAAAATATAT
1 ACAGAAAAAATATAT
5639109 ACAGAAAAAATATAT
1 ACAGAAAAAATATAT
*
5639124 AAAGAAAAA
1 ACAGAAAAA
5639133 TAATAATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (15 bp):
ACAGAAAAAATATAT
Found at i:5644282 original size:20 final size:21
Alignment explanation
Indices: 5644250--5644291 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
5644240 GTCCCATACC
5644250 ACAGTTTGAAATAA-AATAAT
1 ACAGTTTGAAATAATAATAAT
5644270 ACAGTCTTG-AATAATAATAAT
1 ACAGT-TTGAAATAATAATAAT
5644291 A
1 A
5644292 AAATAGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (21 bp):
ACAGTTTGAAATAATAATAAT
Found at i:5658244 original size:18 final size:17
Alignment explanation
Indices: 5658217--5658250 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5658207 TATCAAAAGG
*
5658217 TTTATATTTTTTTTTCT
1 TTTATATTTTATTTTCT
5658234 TTTATTATTTTATTTTC
1 TTTA-TATTTTATTTTC
5658251 CCAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATATTTTATTTTCT
Found at i:5658896 original size:17 final size:17
Alignment explanation
Indices: 5658870--5658912 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
5658860 TCGTGTGGTA
5658870 GACCGTGTGTGACACAT
1 GACCGTGTGTGACACAT
*
5658887 GACTGTGTGTGACACAT
1 GACCGTGTGTGACACAT
5658904 GACCGTGTG
1 GACCGTGTG
5658913 ACAGGCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (17 bp):
GACCGTGTGTGACACAT
Found at i:5659944 original size:11 final size:11
Alignment explanation
Indices: 5659930--5660021 Score: 65
Period size: 11 Copynumber: 8.9 Consensus size: 11
5659920 ATTTTTTTTA
5659930 TTTTAAAATAT
1 TTTTAAAATAT
5659941 TTTTAAAATACT
1 TTTTAAAATA-T
**
5659953 TTTTTTAAT-T
1 TTTTAAAATAT
*
5659963 TTTT----TAA
1 TTTTAAAATAT
5659970 TTTTAAAATAT
1 TTTTAAAATAT
5659981 TTTTAAAATACT
1 TTTTAAAATA-T
**
5659993 TTTTTTAAT-T
1 TTTTAAAATAT
5660003 TTTTAAAA-A-
1 TTTTAAAATAT
5660012 TTTTAAAATA
1 TTTTAAAATA
5660022 AAAATGGGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.06
9 8 0.12
10 13 0.20
11 22 0.34
12 16 0.25
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5659957 original size:40 final size:40
Alignment explanation
Indices: 5659881--5660021 Score: 212
Period size: 40 Copynumber: 3.5 Consensus size: 40
5659871 AAATATATTT
* * *
5659881 ATTTTTTAAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
5659920 ATTTTTTTTATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
5659960 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
5660000 ATTTTTTAAAAATTTTAAAATA
1 ATTTTTT--TAATTTTAAAATA
5660022 AAAATGGGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 28 0.30
40 53 0.57
42 12 0.13
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:5659999 original size:31 final size:30
Alignment explanation
Indices: 5659961--5660021 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
5659951 CTTTTTTTAA
5659961 TTTTTTTAA-TTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTTAAAA-A-TTTTAAAATAC
5659992 TTTTTTTAATTTTTTAAAAATTTTAAAATA
1 TTTTTTTAA-TTTTTAAAAATTTTAAAATA
5660022 AAAATGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 19 0.68
32 1 0.04
33 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTTTAATTTTTAAAAATTTTAAAATAC
Found at i:5665060 original size:30 final size:30
Alignment explanation
Indices: 5665024--5665101 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
5665014 TCTTCTTTTT
5665024 TTTTTAAAATTTTCATTAAACCT-CTAAAAA
1 TTTTTAAAATTTTCATTAAACCTAC-AAAAA
* * * *
5665054 TTTTTAAAGTTTTAATTAGACCTACCAAAA
1 TTTTTAAAATTTTCATTAAACCTACAAAAA
5665084 TTTTTATAAATTTTCATT
1 TTTTTA-AAATTTTCATT
5665102 TATAAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 30 0.75
31 10 0.25
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTTAAAATTTTCATTAAACCTACAAAAA
Found at i:5665105 original size:14 final size:14
Alignment explanation
Indices: 5665086--5665113 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5665076 TACCAAAATT
5665086 TTTATAAATTTTCA
1 TTTATAAATTTTCA
5665100 TTTATAAATTTTCA
1 TTTATAAATTTTCA
5665114 CAGAAACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAAATTTTCA
Found at i:5671596 original size:12 final size:12
Alignment explanation
Indices: 5671579--5671613 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5671569 ATATTATTAG
5671579 GTTAAGTAAACT
1 GTTAAGTAAACT
5671591 GTTAAGTAAACT
1 GTTAAGTAAACT
* *
5671603 ATTAAATAAAC
1 GTTAAGTAAAC
5671614 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (12 bp):
GTTAAGTAAACT
Found at i:5678214 original size:17 final size:17
Alignment explanation
Indices: 5678192--5678235 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
5678182 TGCTCATATG
5678192 GGCCCACACGCCCGTGT
1 GGCCCACACGCCCGTGT
5678209 GGCCCACACGCCCGTGT
1 GGCCCACACGCCCGTGT
5678226 GGCCCACACG
1 GGCCCACACG
5678236 GCCCAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.14, C:0.48, G:0.30, T:0.09
Consensus pattern (17 bp):
GGCCCACACGCCCGTGT
Found at i:5686676 original size:22 final size:22
Alignment explanation
Indices: 5686642--5686924 Score: 352
Period size: 22 Copynumber: 12.9 Consensus size: 22
5686632 GCTCAAAAAC
* * * *
5686642 GGACAGCAATTAACCAACATTC
1 GGACAACATTTAATCAACATTT
*
5686664 GGACAACATTTAATCAACAATT
1 GGACAACATTTAATCAACATTT
** *
5686686 ATACAACATTCAATCAACATTT
1 GGACAACATTTAATCAACATTT
5686708 GGACAACATTTAATCAACATTT
1 GGACAACATTTAATCAACATTT
*
5686730 GGACAACATTTAATCAACAATT
1 GGACAACATTTAATCAACATTT
* *
5686752 GGACAACATTCAATCAACAATT
1 GGACAACATTTAATCAACATTT
*
5686774 GGACAACATTCAATCAACATTT
1 GGACAACATTTAATCAACATTT
*
5686796 GAACATA-ATTTAATCAACATTT
1 GGACA-ACATTTAATCAACATTT
* * *
5686818 GGACAGCTTTTAATCAACAATT
1 GGACAACATTTAATCAACATTT
* * *
5686840 GGACAACATTCAATGAACAATT
1 GGACAACATTTAATCAACATTT
*
5686862 GGACAACATTCAATCAACATTT
1 GGACAACATTTAATCAACATTT
* *
5686884 AGACAAAATTTAATCAACATTT
1 GGACAACATTTAATCAACATTT
5686906 GGACAACATTTAATCAACA
1 GGACAACATTTAATCAACA
5686925 ATATTTACTT
Statistics
Matches: 227, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
22 226 1.00
23 1 0.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (22 bp):
GGACAACATTTAATCAACATTT
Found at i:5686758 original size:88 final size:87
Alignment explanation
Indices: 5686642--5686926 Score: 428
Period size: 88 Copynumber: 3.2 Consensus size: 87
5686632 GCTCAAAAAC
* * * * **
5686642 GGACAGCAATTAACCAAC-ATTCGGACAACATTTAATCAACAATTATACAACATTCAATCAACAT
1 GGACAACATTTAATCAACAATT-GGACAACATTCAATCAACAATTGGACAACATTCAATCAACAT
5686706 TTGGACAACATTTAATCAACATTT
65 TTGGACAA-ATTTAATCAACATTT
5686730 GGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATTGGACAACATTCAATCAACATT
1 GGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATTGGACAACATTCAATCAACATT
*
5686795 TGAACATAATTTAATCAACATTT
66 TGGACA-AATTTAATCAACATTT
* * *
5686818 GGACAGCTTTTAATCAACAATTGGACAACATTCAATGAACAATTGGACAACATTCAATCAACATT
1 GGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATTGGACAACATTCAATCAACATT
*
5686883 TAGACAAAATTTAATCAACATTT
66 TGGAC-AAATTTAATCAACATTT
5686906 GGACAACATTTAATCAACAAT
1 GGACAACATTTAATCAACAAT
5686927 ATTTACTTCA
Statistics
Matches: 180, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
88 175 0.97
89 5 0.03
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (87 bp):
GGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATTGGACAACATTCAATCAACATT
TGGACAAATTTAATCAACATTT
Found at i:5689896 original size:23 final size:23
Alignment explanation
Indices: 5689870--5689919 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
5689860 GAAAAATCGT
5689870 AAAAAAAAGCAAACAGCGCAAAA
1 AAAAAAAAGCAAACAGCGCAAAA
5689893 AAAAAAAAGCAAACAGCGCAAAA
1 AAAAAAAAGCAAACAGCGCAAAA
5689916 AAAA
1 AAAA
5689920 GTTGTCTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAAAGCAAACAGCGCAAAA
Found at i:5698597 original size:66 final size:66
Alignment explanation
Indices: 5698493--5698662 Score: 216
Period size: 66 Copynumber: 2.6 Consensus size: 66
5698483 AATATCGGAT
* * * ** *
5698493 CTTCCCAAGCTCTTGAACAAGATAACAAGTCTTTTCAATCTTAAGCTCCTAAACGCA-ATATCGA
1 CTTCCCAAGCTCTTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTAAACG-AGATATCGA
5698557 GC
65 GC
** * * *
5698559 CTTCCCAAGCTCTTGAATGAGATATCAGGTCGTCTCAATCCCAAGATCTTGAACGAGATATCGAG
1 CTTCCCAAGCTCTTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTAAACGAGATATCGAG
*
5698624 T
66 C
5698625 CTTCCCAAGCTCTTGAACAAGATATCAGGTCTTCTCAA
1 CTTCCCAAGCTCTTGAACAAGATATCAGGTCTTCTCAA
5698663 GCTTCTGAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 1 0.01
66 87 0.99
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (66 bp):
CTTCCCAAGCTCTTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTAAACGAGATATCGAG
C
Found at i:5698657 original size:30 final size:31
Alignment explanation
Indices: 5698550--5698673 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 31
5698540 CCTAAACGCA
* **
5698550 ATATC-GAGCCTTCCCAAGCTCTTGAATGAG
1 ATATCAGAGTCTTCCCAAGCTCTTGAACAAG
* * *
5698580 ATATCAGGTCGTCTCAATCCCAAGATCTTGAACGAG
1 ATATCA-G-AGTCT---TCCCAAGCTCTTGAACAAG
5698616 ATATC-GAGTCTTCCCAAGCTCTTGAACAAG
1 ATATCAGAGTCTTCCCAAGCTCTTGAACAAG
*
5698646 ATATCAG-GTCTTCTCAAGCT-TCTGAACA
1 ATATCAGAGTCTTCCCAAGCTCT-TGAACA
5698674 TCCTCGTAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
29 1 0.01
30 45 0.58
31 1 0.01
32 1 0.01
33 7 0.09
34 1 0.01
36 22 0.28
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (31 bp):
ATATCAGAGTCTTCCCAAGCTCTTGAACAAG
Found at i:5714301 original size:29 final size:29
Alignment explanation
Indices: 5714255--5714315 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
5714245 AGAAGTACTT
* *
5714255 ACAAGATCGACGCTGAAACTCGGTATACC
1 ACAAGATCGACACCGAAACTCGGTATACC
5714284 ACAAGATCGACACCGAAACTCGGTATACC
1 ACAAGATCGACACCGAAACTCGGTATACC
5714313 ACA
1 ACA
5714316 TACTTACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.15
Consensus pattern (29 bp):
ACAAGATCGACACCGAAACTCGGTATACC
Found at i:5719515 original size:40 final size:38
Alignment explanation
Indices: 5719455--5719532 Score: 86
Period size: 40 Copynumber: 2.0 Consensus size: 38
5719445 CGTCATCATT
5719455 TAATAAAATTTTAAAAA-TTTTAAAAGTTCAAAAAATTA
1 TAATAAAATTTTAAAAATTTTTAAAA-TTCAAAAAATTA
* * * *
5719493 TAATAAAATATTTTTAATATTTTTTAAATTTAAAAAATTA
1 TAAT-AAA-ATTTTAAAAATTTTTAAAATTCAAAAAATTA
5719533 ATTAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
38 4 0.12
39 3 0.09
40 19 0.58
41 7 0.21
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (38 bp):
TAATAAAATTTTAAAAATTTTTAAAATTCAAAAAATTA
Found at i:5720518 original size:7 final size:7
Alignment explanation
Indices: 5720506--5720542 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
5720496 TAATTACTAT
5720506 AATTTAA
1 AATTTAA
5720513 AATTTAA
1 AATTTAA
5720520 AATTTAA
1 AATTTAA
* *
5720527 ATTTTTA
1 AATTTAA
5720534 AATTTAA
1 AATTTAA
5720541 AA
1 AA
5720543 AATTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:5724151 original size:1 final size:1
Alignment explanation
Indices: 5724145--5724193 Score: 89
Period size: 1 Copynumber: 49.0 Consensus size: 1
5724135 AAGTTCCGGA
*
5724145 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5724194 GGGGGGGGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:5736796 original size:21 final size:22
Alignment explanation
Indices: 5736771--5736839 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
5736761 AGTCTAGGCT
5736771 GTGTGAAAG-GTCTACACGGCC
1 GTGTGAAAGAGTCTACACGGCC
* *
5736792 GTGTGAAAGAGGC-ACACGCCC
1 GTGTGAAAGAGTCTACACGGCC
* * *
5736813 GTTTGAAAGAGT-TACATGGTC
1 GTGTGAAAGAGTCTACACGGCC
5736834 GTGTGA
1 GTGTGA
5736840 GTAGCCCGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (22 bp):
GTGTGAAAGAGTCTACACGGCC
Found at i:5741019 original size:24 final size:24
Alignment explanation
Indices: 5740974--5741019 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5740964 AATAATCTAG
* * **
5740974 AATAATCAGAGTTTGATTGAAACA
1 AATAAACAGAGTTTAACGGAAACA
5740998 AATAAACAGAGTTTAACGGAAA
1 AATAAACAGAGTTTAACGGAAA
5741020 GATTATTTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (24 bp):
AATAAACAGAGTTTAACGGAAACA
Done.