Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold50
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: 2541760
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Warning! 26494 characters in sequence are not A, C, G, or T
File 14 of 16
Found at i:2171237 original size:13 final size:13
Alignment explanation
Indices: 2171219--2171244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2171209 CAATTTTTTG
2171219 TGTATCGATACAT
1 TGTATCGATACAT
2171232 TGTATCGATACAT
1 TGTATCGATACAT
2171245 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2171241 original size:33 final size:33
Alignment explanation
Indices: 2171199--2171263 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2171189 TACAAGCCAA
* *
2171199 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
2171232 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
2171264 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:2171341 original size:20 final size:21
Alignment explanation
Indices: 2171293--2171347 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2171283 AATCCCAATG
* *
2171293 ACATGTATCGATACATATTTT
1 ACATGTATCGATACATATGTA
**
2171314 TGATGTATCGATACAT-TGTA
1 ACATGTATCGATACATATGTA
2171334 ACATGTATCGATAC
1 ACATGTATCGATAC
2171348 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
ACATGTATCGATACATATGTA
Found at i:2173844 original size:13 final size:13
Alignment explanation
Indices: 2173815--2173853 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2173805 ATAATCCCCC
* *
2173815 TGTATCGATATAG
1 TGTATCGATACAA
2173828 TGTATCGATACAA
1 TGTATCGATACAA
*
2173841 TGTATCCATACAA
1 TGTATCGATACAA
2173854 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2175115 original size:28 final size:28
Alignment explanation
Indices: 2175075--2175146 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2175065 GGAATAAAGC
** *
2175075 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2175103 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2175131 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2175147 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2175204 original size:52 final size:52
Alignment explanation
Indices: 2175135--2175471 Score: 169
Period size: 52 Copynumber: 6.4 Consensus size: 52
2175125 AAATAACGAG
*
2175135 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
2175187 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACTAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAA-TCGGA
* * * *
2175240 -TTGGAGTATCCCCGATCGTGGAAAAATTAGTGTTTTAGCG--ATAAAA-CTGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATC-GGA
* **** * * *
2175291 GTTGGAGTATCCCC--TCG-GAAATAACGAGGTTGG-AGTATCCCCGACGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTG-AA-AA--A--TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
2175346 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * * *
2175400 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
2175451 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
2175472 GAGAATTGAT
Statistics
Matches: 212, Mismatches: 46, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 5 0.02
51 36 0.17
52 76 0.36
53 34 0.16
54 28 0.13
55 18 0.08
56 3 0.01
57 8 0.04
58 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2175331 original size:28 final size:27
Alignment explanation
Indices: 2175291--2175361 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2175281 TAAAACTGGA
*
2175291 GTTGGAGTATCCCC-TCGGAAATAACGAG
1 GTTGGAGTATCCCCGAC-G-AATAACGAG
* *
2175319 GTTGGAGTATCCCCGACGATTAACGGG
1 GTTGGAGTATCCCCGACGAATAACGAG
2175346 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
2175362 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.59
28 15 0.38
29 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.23
Consensus pattern (27 bp):
GTTGGAGTATCCCCGACGAATAACGAG
Found at i:2175380 original size:107 final size:105
Alignment explanation
Indices: 2175021--2175413 Score: 275
Period size: 107 Copynumber: 3.7 Consensus size: 105
2175011 CTTTCGAAAA
* * * * * * * *
2175021 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTT-GGAATAAAACTGGAGTTGGAG
* * * *
2175086 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAAG-AT
* * *
2175128 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAA-TCGGAGTTGG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTA-TTTTGG-AATAAAACT-GGAGTTGG
* * ** * ** *
2175192 AGTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
63 AGTATCCCCTCGGAAAT-AACG-AGGTTGGAGTATCCCCGAAGAT
* * * * *
2175230 AAAACTAGGATTGGAGTATCCCCGATCGTGGAAAAATTAGTGTTTTAGCG-ATAAAACTGGAGTT
1 -TAAC-GGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTT-G-GAATAAAACTGGAGTT
*
2175294 GGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGACGAT
61 GGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAAGAT
* *
2175339 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAA-TCGGAGTT
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT--AGTATTTTGG-AATAAAACT-GGAGTT
*
2175403 AGAGTATCCCC
61 GGAGTATCCCC
2175414 GATTATAGAA
Statistics
Matches: 216, Mismatches: 46, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
102 1 0.00
103 5 0.02
104 43 0.20
105 20 0.09
106 19 0.09
107 67 0.31
108 29 0.13
109 32 0.15
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAATAAAACTGGAGTTGGAGT
ATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAAGAT
Found at i:2175446 original size:51 final size:53
Alignment explanation
Indices: 2175350--2175468 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 53
2175340 AACGGGGTTG
* * * *
2175350 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGAAGTTA
*
2175404 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGAAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGAAGTTA
* *
2175455 GAATATCCTCGATT
1 GAGTATCCCCGATT
2175469 GTGGAGAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
51 32 0.56
52 2 0.04
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGAAGTTA
Found at i:2177849 original size:13 final size:13
Alignment explanation
Indices: 2177831--2177856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2177821 ACAAAGATCC
2177831 ATGTATCGATACA
1 ATGTATCGATACA
2177844 ATGTATCGATACA
1 ATGTATCGATACA
2177857 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2177852 original size:33 final size:33
Alignment explanation
Indices: 2177810--2177876 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2177800 AAAATTTCCA
***
2177810 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2177843 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2177876 A
1 A
2177877 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2177920 original size:19 final size:18
Alignment explanation
Indices: 2177896--2177995 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
2177886 CAGTAGCTAA
2177896 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2177915 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2177930 TTA--TATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2177947 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2177962 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2177979 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2177996 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 20 0.29
14 1 0.01
15 3 0.04
16 4 0.06
17 3 0.04
18 4 0.06
19 34 0.49
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2177942 original size:32 final size:32
Alignment explanation
Indices: 2177901--2177993 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
2177891 GCTAATTATG
*
2177901 TATCGATACAATACTTATGTATCGATACATTA
1 TATCGATACAAAACTTATGTATCGATACATTA
*
2177933 TATCGATACAAAACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTA
2177965 TATCGATACAAAACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
2177994 AATTGTTGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTA
Found at i:2178113 original size:12 final size:12
Alignment explanation
Indices: 2178096--2178136 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
2178086 TTGGATAATT
2178096 TTTTTTTTATTA
1 TTTTTTTTATTA
2178108 TTTTTTTTATTA
1 TTTTTTTTATTA
*
2178120 -TTTATTTATT-
1 TTTTTTTTATTA
2178130 TTTTTTT
1 TTTTTTT
2178137 CAAACACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTATTA
Found at i:2178874 original size:28 final size:28
Alignment explanation
Indices: 2178843--2178929 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
2178833 TGAGGAGTAA
2178843 AAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAGTGCCACCAACTCGTGTGGGCTTTG
** ** *
2178871 AAAG-GCGTCCTGCTC-TTTGAGGAC--TG
1 AAAGTGCCACCAACTCGTGTG-GG-CTTTG
*
2178897 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAA-GTGCCACCAACTCGTGTGGGCTTTG
2178926 AAAG
1 AAAG
2178930 GTGTCCTGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
26 8 0.20
27 11 0.27
28 14 0.34
29 8 0.20
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (28 bp):
AAAGTGCCACCAACTCGTGTGGGCTTTG
Found at i:2178918 original size:55 final size:55
Alignment explanation
Indices: 2178823--2179775 Score: 1449
Period size: 55 Copynumber: 17.3 Consensus size: 55
2178813 ATAAAGTGTA
* * * * * * *
2178823 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2178878 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2178933 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
2178988 TCTTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
2179043 TCCTGCTCTTTGGGGAATGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
2179098 TCCTGCTCTTTAAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2179153 TCCTGCTCTTTGAGGACTGGAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179208 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179263 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* **
2179318 TCCTGTTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2179373 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179428 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2179483 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2179538 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179593 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179648 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2179703 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2179758 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2179776 AAAAAGCGGA
Statistics
Matches: 831, Mismatches: 52, Indels: 30
0.91 0.06 0.03
Matches are distributed among these distances:
54 23 0.03
55 786 0.95
56 22 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2178953 original size:26 final size:26
Alignment explanation
Indices: 2178869--2178958 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
2178859 GTGTGGGCTT
* *
2178869 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
2178895 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
2178922 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
2178950 TGAAAGGTG
1 TGAAAGGTG
2178959 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 20 0.41
27 6 0.12
28 5 0.10
29 12 0.24
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:2178987 original size:29 final size:28
Alignment explanation
Indices: 2178897--2178987 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
2178887 TTGAGGACTG
2178897 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2178925 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
2178952 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
2178980 AAGAGGTG
1 AA-AGGTG
2178988 TCTTGCTCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 10 0.21
27 7 0.15
28 9 0.19
29 15 0.32
30 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:2180794 original size:23 final size:23
Alignment explanation
Indices: 2180768--2180811 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2180758 TTTTTCTTTG
2180768 TTTTGTTTTTTTG-TTTTTTTTCC
1 TTTT-TTTTTTTGCTTTTTTTTCC
2180791 TTTTTTTTTTTGCTTTTTTTT
1 TTTTTTTTTTTGCTTTTTTTT
2180812 TTGAAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTTTGCTTTTTTTTCC
Found at i:2180811 original size:14 final size:14
Alignment explanation
Indices: 2180775--2180813 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2180765 TTGTTTTGTT
*
2180775 TTTTTGTTTTTTTTC
1 TTTTT-TTTTTTTGC
*
2180790 CTTTTTTTTTTTGC
1 TTTTTTTTTTTTGC
2180804 TTTTTTTTTT
1 TTTTTTTTTT
2180814 GAAGAGAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTTGC
Found at i:2180814 original size:12 final size:13
Alignment explanation
Indices: 2180781--2180813 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2180771 TGTTTTTTTG
*
2180781 TTTTTTTTCCTTT
1 TTTTTTTTGCTTT
2180794 TTTTTTTTGCTTT
1 TTTTTTTTGCTTT
2180807 TTTTTTT
1 TTTTTTT
2180814 GAAGAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTGCTTT
Found at i:2193414 original size:28 final size:28
Alignment explanation
Indices: 2193374--2193445 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2193364 GGAATAAAGC
** *
2193374 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2193402 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2193430 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2193446 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2193503 original size:52 final size:52
Alignment explanation
Indices: 2193434--2193770 Score: 194
Period size: 52 Copynumber: 6.4 Consensus size: 52
2193424 AAATAACGAG
*
2193434 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
2193486 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
2193539 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
2193590 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
2193645 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
2193699 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
2193750 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
2193771 GAGAATTGAT
Statistics
Matches: 215, Mismatches: 43, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.17
52 79 0.37
53 33 0.15
54 28 0.13
55 18 0.08
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2193630 original size:28 final size:27
Alignment explanation
Indices: 2193590--2193660 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
2193580 TAAAACCGGA
**
2193590 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
2193618 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
2193645 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
2193661 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:2193673 original size:107 final size:106
Alignment explanation
Indices: 2193320--2193712 Score: 343
Period size: 107 Copynumber: 3.7 Consensus size: 106
2193310 CCTTCGAAAA
* * * * * * * *
2193320 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
2193385 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
2193427 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
2193492 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
2193529 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
2193593 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
2193638 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
2193703 GAGTATCCCC
63 GAGTATCCCC
2193713 GATTATAGAA
Statistics
Matches: 220, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 46 0.21
105 20 0.09
106 18 0.08
107 72 0.33
108 32 0.15
109 27 0.12
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (106 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:2193726 original size:212 final size:212
Alignment explanation
Indices: 2193367--2193772 Score: 638
Period size: 212 Copynumber: 1.9 Consensus size: 212
2193357 TATTTTGGGA
* * *
2193367 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2193432 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* *
2193497 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
2193561 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
2193579 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2193643 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
2193708 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
2193772 A
194 A
2193773 GAATTGATAA
Statistics
Matches: 177, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 32 0.18
212 106 0.60
213 39 0.22
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:2193745 original size:51 final size:53
Alignment explanation
Indices: 2193649--2193767 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
2193639 AACGGGGTTG
* * *
2193649 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
2193703 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
2193754 GAATATCCTCGATT
1 GAGTATCCCCGATT
2193768 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:2196150 original size:13 final size:13
Alignment explanation
Indices: 2196132--2196157 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2196122 ACAAAGATCC
2196132 ATGTATCGATACA
1 ATGTATCGATACA
2196145 ATGTATCGATACA
1 ATGTATCGATACA
2196158 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2196153 original size:33 final size:33
Alignment explanation
Indices: 2196111--2196177 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2196101 AAAATTTCCA
***
2196111 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2196144 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2196177 A
1 A
2196178 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2196221 original size:19 final size:18
Alignment explanation
Indices: 2196197--2196264 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2196187 CAGTAGCTAA
2196197 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2196216 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2196231 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2196248 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2196265 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2196237 original size:13 final size:13
Alignment explanation
Indices: 2196219--2196243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2196209 ACAATACTTA
2196219 TGTATCGATACAT
1 TGTATCGATACAT
2196232 TGTATCGATACA
1 TGTATCGATACA
2196244 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2196241 original size:32 final size:32
Alignment explanation
Indices: 2196200--2196262 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2196190 TAGCTAATTA
*
2196200 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2196232 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2196263 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2196344 original size:21 final size:21
Alignment explanation
Indices: 2196320--2196376 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2196310 CATTTGTAGG
2196320 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2196341 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
*
2196362 ATGTATCTATACATT
1 ATGTATCGATACATT
2196377 TGATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2197140 original size:28 final size:28
Alignment explanation
Indices: 2197109--2197195 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
2197099 TGAGGAGTAA
2197109 AAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAGTGCCACCAACTCGTGTGGGCTTTG
** ** *
2197137 AAAG-GCGTCCTGCTC-TTTGAGGAC--TG
1 AAAGTGCCACCAACTCGTGTG-GG-CTTTG
*
2197163 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAA-GTGCCACCAACTCGTGTGGGCTTTG
2197192 AAAG
1 AAAG
2197196 GTGTCCTGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
26 8 0.20
27 11 0.27
28 14 0.34
29 8 0.20
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (28 bp):
AAAGTGCCACCAACTCGTGTGGGCTTTG
Found at i:2197184 original size:55 final size:55
Alignment explanation
Indices: 2197089--2198044 Score: 1437
Period size: 55 Copynumber: 17.3 Consensus size: 55
2197079 ATAAAGTGTA
* * * * * * *
2197089 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2197144 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2197199 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
2197254 TCTTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
2197309 TCCTGCTCTTTGGGGAATGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2197364 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
2197419 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2197474 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2197529 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* **
2197584 TCCTGTTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2197639 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2197694 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2197749 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2197804 TCCTGCTCTTTGGGGACTGAAAGGTGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA---GGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2197862 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2197917 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2197972 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2198027 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2198045 AAAAAACGGA
Statistics
Matches: 835, Mismatches: 48, Indels: 36
0.91 0.05 0.04
Matches are distributed among these distances:
54 21 0.03
55 746 0.89
56 18 0.02
57 2 0.00
58 44 0.05
59 4 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2197219 original size:26 final size:26
Alignment explanation
Indices: 2197135--2197224 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
2197125 GTGTGGGCTT
* *
2197135 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
2197161 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
2197188 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
2197216 TGAAAGGTG
1 TGAAAGGTG
2197225 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 20 0.41
27 6 0.12
28 5 0.10
29 12 0.24
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:2197253 original size:29 final size:28
Alignment explanation
Indices: 2197163--2197253 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
2197153 TTGAGGACTG
2197163 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
2197191 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
2197218 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
2197246 AAGAGGTG
1 AA-AGGTG
2197254 TCTTGCTCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 10 0.21
27 7 0.15
28 9 0.19
29 15 0.32
30 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:2197941 original size:26 final size:26
Alignment explanation
Indices: 2197912--2197997 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
2197902 GGGCTTTAAG
2197912 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
2197938 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
*
2197966 GAGGTGTCCTGCTCTTTGAGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
2197993 AGGTG
1 AGGTG
2197998 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.18
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:2199040 original size:9 final size:8
Alignment explanation
Indices: 2199011--2199082 Score: 53
Period size: 8 Copynumber: 9.4 Consensus size: 8
2199001 CTTAAGTAGG
2199011 TTTTTTC-
1 TTTTTTCT
*
2199018 TTTTCTCT
1 TTTTTTCT
*
2199026 CTTTTTCT
1 TTTTTTCT
*
2199034 TTGTTTTGT
1 TT-TTTTCT
*
2199043 TTTTTTAT
1 TTTTTTCT
2199051 TTTTTTC-
1 TTTTTTCT
*
2199058 CTTTTT-T
1 TTTTTTCT
*
2199065 TTTTTGCT
1 TTTTTTCT
2199073 TTTTTT-T
1 TTTTTTCT
2199080 TTT
1 TTT
2199083 GAAGAGAAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 19 0.38
8 24 0.48
9 7 0.14
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:2199062 original size:22 final size:22
Alignment explanation
Indices: 2199037--2199078 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2199027 TTTTTCTTTG
2199037 TTTTGTTTTTTT-ATTTTTTTCC
1 TTTT-TTTTTTTGATTTTTTTCC
*
2199059 TTTTTTTTTTTGCTTTTTTT
1 TTTTTTTTTTTGATTTTTTT
2199079 TTTTGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTGATTTTTTTCC
Found at i:2199083 original size:13 final size:13
Alignment explanation
Indices: 2199045--2199083 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2199035 TGTTTTGTTT
*
2199045 TTTTATTTTTTTCC
1 TTTT-TTTTTTTGC
2199059 TTTTTTTTTTTGC
1 TTTTTTTTTTTGC
2199072 TTTTTTTTTTTG
1 TTTTTTTTTTTG
2199084 AAGAGAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTGC
Found at i:2204561 original size:22 final size:20
Alignment explanation
Indices: 2204512--2204563 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2204502 ATCATGCAAG
2204512 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
2204533 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
2204555 TTTTTATTT
1 TTTTTATTT
2204564 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:2206198 original size:13 final size:13
Alignment explanation
Indices: 2206180--2206205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2206170 CAATTTTTTG
2206180 TGTATCGATACAT
1 TGTATCGATACAT
2206193 TGTATCGATACAT
1 TGTATCGATACAT
2206206 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2206202 original size:33 final size:33
Alignment explanation
Indices: 2206160--2206224 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2206150 TACAAGCCAA
* *
2206160 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
2206193 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
2206225 AGTTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:2208394 original size:34 final size:35
Alignment explanation
Indices: 2208356--2208422 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2208346 CCTTACAACA
2208356 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2208390 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2208423 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2208911 original size:13 final size:13
Alignment explanation
Indices: 2208892--2208930 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2208882 ACTATTTATG
2208892 ATGTATCGATACA
1 ATGTATCGATACA
*
2208905 CTGTATCGATACA
1 ATGTATCGATACA
2208918 ATGTATCGATACA
1 ATGTATCGATACA
2208931 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2208998 original size:41 final size:42
Alignment explanation
Indices: 2208926--2209009 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
2208916 CAATGTATCG
*
2208926 ATACATGAATAGTGATGAACAGTGATTTTTAACGTTACATGA
1 ATACATGAACAGTGATGAACAGTGATTTTTAACGTTACATGA
* *
2208968 ATACGTGAACAGTG-TGAACAGTGATTTTTAACTTTACATGA
1 ATACATGAACAGTGATGAACAGTGATTTTTAACGTTACATGA
2209009 A
1 A
2209010 AGTGATGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 27 0.69
42 12 0.31
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (42 bp):
ATACATGAACAGTGATGAACAGTGATTTTTAACGTTACATGA
Found at i:2209045 original size:10 final size:10
Alignment explanation
Indices: 2209026--2209056 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2209016 GTATCGATAT
2209026 ATGAACAGTG
1 ATGAACAGTG
*
2209036 ATGAATAGTG
1 ATGAACAGTG
2209046 ATGAACAGTG
1 ATGAACAGTG
2209056 A
1 A
2209057 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2209199 original size:21 final size:20
Alignment explanation
Indices: 2209151--2209205 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
2209141 TACATATTTG
**
2209151 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATAAAA
* *
2209171 TCTGTATCGATACATTTAAAA
1 TGTGTATCGATAC-TATAAAA
2209192 TGTGTATCGATACT
1 TGTGTATCGATACT
2209206 TTTTAGGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (20 bp):
TGTGTATCGATACTATAAAA
Found at i:2215371 original size:105 final size:105
Alignment explanation
Indices: 2215185--2215392 Score: 344
Period size: 105 Copynumber: 2.0 Consensus size: 105
2215175 ACCTTGATTA
* * *
2215185 AAGAAATATGATGAAAATTTGATCAAAGTATTTGTATTACATGACATTCATCACCTATACTAAAT
1 AAGAAATATGATGAAAATTTGATCAAAGTATTTGCACTACATGACATTCATCACATATACTAAAT
*
2215250 AGCGCTACATGATATGGTTTATGACATTGCATTACATTTG
66 AGCACTACATGATATGGTTTATGACATTGCATTACATTTG
* *
2215290 AAGAAATATGATGAAAATTTGATCGAAGTATTTGCACTACATGACATTCATTACATATACTAAAT
1 AAGAAATATGATGAAAATTTGATCAAAGTATTTGCACTACATGACATTCATCACATATACTAAAT
* *
2215355 AGCACTACATGGTATGGTTTATGGCATTGCATTACATT
66 AGCACTACATGATATGGTTTATGACATTGCATTACATT
2215393 CGCAATATGC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (105 bp):
AAGAAATATGATGAAAATTTGATCAAAGTATTTGCACTACATGACATTCATCACATATACTAAAT
AGCACTACATGATATGGTTTATGACATTGCATTACATTTG
Found at i:2216044 original size:14 final size:15
Alignment explanation
Indices: 2216027--2216056 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2216017 AAGAAGGTTA
2216027 AAAAGAA-AAAAAAT
1 AAAAGAAGAAAAAAT
2216041 AAAAGAAGAAAAAAT
1 AAAAGAAGAAAAAAT
2216056 A
1 A
2216057 CAAGCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAGAAGAAAAAAT
Found at i:2222408 original size:20 final size:19
Alignment explanation
Indices: 2222381--2222472 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 19
2222371 TAGCTACTAC
*
2222381 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
** *
2222401 TGTGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
2222420 CATGTATCGATACAAAGTATA
1 CATGTATCGATACAATG-A-A
* *
2222441 -ATGTATCGATACATCTGGA
1 CATGTATCGATACA-ATGAA
*
2222460 CGTGTATCGATAC
1 CATGTATCGATAC
2222473 TTTCTAGGGT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
19 17 0.30
20 37 0.66
21 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2234336 original size:20 final size:20
Alignment explanation
Indices: 2234308--2234375 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
2234298 TACCCAGATA
*
2234308 TATCGATACATTTTTTAATG
1 TATCGATACATTTTTAAATG
* * * *
2234328 TATCAATACATGTATGAATG
1 TATCGATACATTTTTAAATG
*
2234348 TATCGATACATTCTTAAATG
1 TATCGATACATTTTTAAATG
2234368 TATCGATA
1 TATCGATA
2234376 TATTCTATCC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
TATCGATACATTTTTAAATG
Found at i:2236264 original size:13 final size:13
Alignment explanation
Indices: 2236246--2236271 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2236236 CAATTTTTTG
2236246 TGTATCGATACAT
1 TGTATCGATACAT
2236259 TGTATCGATACAT
1 TGTATCGATACAT
2236272 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2237390 original size:13 final size:13
Alignment explanation
Indices: 2237372--2237397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2237362 TACAGCAAGT
2237372 ATGTATCGATACA
1 ATGTATCGATACA
2237385 ATGTATCGATACA
1 ATGTATCGATACA
2237398 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2239650 original size:21 final size:21
Alignment explanation
Indices: 2239617--2239661 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2239607 TTGCAAGTTG
*
2239617 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2239639 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2239659 AAA
1 AAA
2239662 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2241485 original size:15 final size:15
Alignment explanation
Indices: 2241465--2241495 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2241455 TAAAAATGTC
*
2241465 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2241480 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2241495 C
1 C
2241496 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2243362 original size:8 final size:8
Alignment explanation
Indices: 2243349--2243380 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
2243339 ATTTGATTAA
2243349 ATTTTGTG
1 ATTTTGTG
2243357 ATTTTGTG
1 ATTTTGTG
2243365 ATTTTGTG
1 ATTTTGTG
2243373 ATTTTGTG
1 ATTTTGTG
2243381 TTGAATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:2243599 original size:13 final size:13
Alignment explanation
Indices: 2243581--2243606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2243571 ACATTTTTCT
2243581 TTGTATCGATACA
1 TTGTATCGATACA
2243594 TTGTATCGATACA
1 TTGTATCGATACA
2243607 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2245457 original size:59 final size:59
Alignment explanation
Indices: 2245381--2245502 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
2245371 GGGGAGAGAA
2245381 AATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATTAAGGGGGAGAATTATT
1 AATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATTAAGGGGGAGAATTATT
2245440 AATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATTAAGGGGGAGAATTATT
1 AATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATTAAGGGGGAGAATTATT
2245499 AATA
1 AATA
2245503 AACGGGGGAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (59 bp):
AATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATTAAGGGGGAGAATTATT
Found at i:2246238 original size:13 final size:13
Alignment explanation
Indices: 2246220--2246245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2246210 TACAGCAAGT
2246220 ATGTATCGATACA
1 ATGTATCGATACA
2246233 ATGTATCGATACA
1 ATGTATCGATACA
2246246 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2248845 original size:13 final size:13
Alignment explanation
Indices: 2248827--2248863 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2248817 AATCACCCTA
2248827 TATCGATACAATG
1 TATCGATACAATG
2248840 TATCGATACAATG
1 TATCGATACAATG
2248853 TATCGATACAA
1 TATCGATACAA
2248864 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:2250961 original size:15 final size:15
Alignment explanation
Indices: 2250941--2250971 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2250931 ATTTCGTTTG
*
2250941 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2250956 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2250971 G
1 G
2250972 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2252802 original size:21 final size:21
Alignment explanation
Indices: 2252773--2252817 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2252763 AAGTTTTTAT
*
2252773 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2252793 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2252815 TTT
1 TTT
2252818 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2257320 original size:21 final size:22
Alignment explanation
Indices: 2257289--2257331 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2257279 GTTATGATTT
2257289 CAATAAAAAATAAAC-TTAATTA
1 CAATAAAAAAT-AACTTTAATTA
2257311 CAAT-AAAAATAACTTTAATTA
1 CAATAAAAAATAACTTTAATTA
2257332 TTACTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 13 0.65
22 4 0.20
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
CAATAAAAAATAACTTTAATTA
Found at i:2258061 original size:25 final size:24
Alignment explanation
Indices: 2258007--2258061 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2257997 CTAAAAATTC
*
2258007 AATT-ATAAAAATAAAAAATTATT
1 AATTAATAAAAATAAAAAATTATG
* *
2258030 ATTTTAATAAAAATCAAACAATTATG
1 A-ATTAATAAAAAT-AAAAAATTATG
2258056 AATTAA
1 AATTAA
2258062 ATCCATCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 2 0.08
25 12 0.48
26 10 0.40
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTAATAAAAATAAAAAATTATG
Found at i:2259382 original size:2 final size:2
Alignment explanation
Indices: 2259375--2259410 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2259365 TTTTGTATTC
2259375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2259411 TCGTTTCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2260445 original size:7 final size:7
Alignment explanation
Indices: 2260433--2260509 Score: 63
Period size: 7 Copynumber: 11.1 Consensus size: 7
2260423 ATAATATAAT
2260433 TATATTA
1 TATATTA
2260440 TATATTA
1 TATATTA
2260447 TATATTTA
1 TATA-TTA
2260455 TATAAATTA
1 TAT--ATTA
*
2260464 TAAATTA
1 TATATTA
2260471 TATATT-
1 TATATTA
2260477 TATA-TA
1 TATATTA
* *
2260483 AATTTTA
1 TATATTA
*
2260490 -ATTTTA
1 TATATTA
2260496 TATATT-
1 TATATTA
2260502 TATATTA
1 TATATTA
2260509 T
1 T
2260510 TTAATATTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
5 1 0.02
6 18 0.31
7 27 0.47
8 6 0.10
9 5 0.09
10 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:2260463 original size:17 final size:17
Alignment explanation
Indices: 2260436--2260525 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 17
2260426 ATATAATTAT
2260436 ATTATATA-TTATAT-A
1 ATTATATATTTATATAA
* **
2260451 TTTATATAAAT-TATAA
1 ATTATATATTTATATAA
2260467 ATTATATATTTATATAA
1 ATTATATATTTATATAA
* *
2260484 ATTTTA-ATTT-TATAT
1 ATTATATATTTATATAA
*
2260499 ATT-TATA-TTATTTAA
1 ATTATATATTTATATAA
2260514 TATTATAT-TTTA
1 -ATTATATATTTA
2260526 ATTATTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.07
15 21 0.36
16 17 0.29
17 16 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATATTTATATAA
Found at i:2260463 original size:24 final size:24
Alignment explanation
Indices: 2260436--2260525 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
2260426 ATATAATTAT
2260436 ATTATATATTATATATTTATATAA
1 ATTATATATTATATATTTATATAA
*
2260460 ATTATAAATTATATATTTATATAA
1 ATTATATATTATATATTTATATAA
* * *
2260484 ATTTTAATTTTATATATTTATATTA
1 ATTAT-ATATTATATATTTATATAA
*
2260509 TTTA-ATATTATAT-TTTA
1 ATTATATATTATATATTTA
2260526 ATTATTTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
22 4 0.07
23 8 0.14
24 27 0.47
25 18 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTATATATTATATATTTATATAA
Found at i:2260497 original size:23 final size:23
Alignment explanation
Indices: 2260447--2260523 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
2260437 TTATATATTA
* *
2260447 TATATTTATATAAATTATAAATTA
1 TATATTTATATAAATT-TTAATTT
2260471 TATATTTATATAAATTTTAATTT
1 TATATTTATATAAATTTTAATTT
* *
2260494 TATATATT-TAT-ATTATTTAATAT
1 TATAT-TTATATAAAT-TTTAATTT
2260517 TATATTT
1 TATATTT
2260524 TAATTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.09
23 25 0.53
24 18 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTTATATAAATTTTAATTT
Found at i:2260518 original size:10 final size:9
Alignment explanation
Indices: 2260403--2260519 Score: 50
Period size: 9 Copynumber: 13.1 Consensus size: 9
2260393 ATCTTTATGT
*
2260403 TTTATAGTA
1 TTTATATTA
*
2260412 TGTATATT-
1 TTTATATTA
2260420 TTTATAATATA
1 TTTAT-AT-TA
*
2260431 ATTATATTA
1 TTTATATTA
*
2260440 TATATTATATA
1 TTTA-TAT-TA
*
2260451 TTTATATAA
1 TTTATATTA
*
2260460 ATTATA--A
1 TTTATATTA
*
2260467 ATTATA-TA
1 TTTATATTA
*
2260475 TTTATATAAA
1 TTTATAT-TA
*
2260485 TTT-TAAT-
1 TTTATATTA
2260492 TTTATA-TA
1 TTTATATTA
2260500 TTTATATTA
1 TTTATATTA
2260509 TTTAATATTA
1 TTT-ATATTA
2260519 T
1 T
2260520 ATTTTAATTA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
7 11 0.13
8 18 0.22
9 25 0.30
10 20 0.24
11 9 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTATATTA
Found at i:2263224 original size:236 final size:236
Alignment explanation
Indices: 2262810--2263512 Score: 1183
Period size: 236 Copynumber: 3.0 Consensus size: 236
2262800 ATTACCTTGC
* * * * *
2262810 ATGAGAGAAACACAAAGAGAAATAGAAATGACGTGGTCCAATGAAATTAGTCGAAATGACACGGT
1 ATGAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGGACGAAATGACATGGT
*
2262875 GCACCTCGGACAATGCATGAATGATATGTATTCATGATCAATTGCCTAAAAAGAGACAACCAACT
66 GCACCTCGTACAATGCATGAATGATATGTATTCATGATCAATTGCCTAAAAAGAGACAACCAACT
* * * * *
2262940 TGTCTAATATGACACTGCACCAACTTATCTGTTTATTTTGACTAAAGTTAAGCTCCTAAGCCTAA
131 TGTCTAAGATGACACTGCACCAACTTGTTTGTTTATTTTAATTAAAGTTAAGCTCCTAAGCCTAA
2263005 ATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGTATATA
196 ATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGTATATA
*
2263046 ATGAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGGCCGAAATGACATGGT
1 ATGAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGGACGAAATGACATGGT
*
2263111 GCACCTCGTACAATGCATGAATGATATGTATTCACGATCAATTGCCTAAAAAGAGACAACCAACT
66 GCACCTCGTACAATGCATGAATGATATGTATTCATGATCAATTGCCTAAAAAGAGACAACCAACT
*
2263176 TGTCTAAGATGACACTGCACCAACTTGTTTGTTTATTTTAATTAAAGTTAAGCTACTAAGCCTAA
131 TGTCTAAGATGACACTGCACCAACTTGTTTGTTTATTTTAATTAAAGTTAAGCTCCTAAGCCTAA
*
2263241 ATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGTATATG
196 ATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGTATATA
* *
2263282 ATAAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGAACGAAATGACATGGT
1 ATGAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGGACGAAATGACATGGT
*
2263347 GCACCTCGTACAATGCATGAATGATATGTATTCATGATCAATTGCTTAAAAAGAGACAACCAACT
66 GCACCTCGTACAATGCATGAATGATATGTATTCATGATCAATTGCCTAAAAAGAGACAACCAACT
* *
2263412 TGTCTAAGATGACACAGCATCAACTTGTTTGTTTATTTTAATT-AAGCTTAAGCTCCTAAGCCTA
131 TGTCTAAGATGACACTGCACCAACTTGTTTGTTTATTTTAATTAAAG-TTAAGCTCCTAAGCCTA
* * *
2263476 AATGTTTTCTGTATCCAGTGAGATTTTAAATTAAGGT
195 AATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGT
2263513 TTGTGTAGGT
Statistics
Matches: 441, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
235 3 0.01
236 438 0.99
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (236 bp):
ATGAGAGAAACACAGAGAGAAATAGGAATGACGTGGTCCAATGAAATTGGACGAAATGACATGGT
GCACCTCGTACAATGCATGAATGATATGTATTCATGATCAATTGCCTAAAAAGAGACAACCAACT
TGTCTAAGATGACACTGCACCAACTTGTTTGTTTATTTTAATTAAAGTTAAGCTCCTAAGCCTAA
ATGTCTACTGTATCCAGTGAGATTTTAAACTAAGGTATATA
Found at i:2267961 original size:13 final size:13
Alignment explanation
Indices: 2267943--2267969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2267933 ACTGTTCATA
2267943 TATCGATACAGTG
1 TATCGATACAGTG
2267956 TATCGATACAGTG
1 TATCGATACAGTG
2267969 T
1 T
2267970 GAATAGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:2273778 original size:2 final size:2
Alignment explanation
Indices: 2273771--2273812 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2273761 TTGGACGTGC
2273771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2273813 TAATAATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2274634 original size:3 final size:3
Alignment explanation
Indices: 2274626--2274651 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2274616 CATGGCTGTA
2274626 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2274652 AAATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2276734 original size:2 final size:2
Alignment explanation
Indices: 2276727--2276778 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
2276717 GCATTGTATT
* *
2276727 TA TA TA TA TA TA TA TA TA TA TG TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2276769 TA TA TA TA TA
1 TA TA TA TA TA
2276779 GAGAGAGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2278224 original size:2 final size:2
Alignment explanation
Indices: 2278217--2278250 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2278207 GAAATGGCTC
2278217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2278251 TCTTGGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2280037 original size:25 final size:24
Alignment explanation
Indices: 2279998--2280090 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 24
2279988 AATATATTTT
*
2279998 TATTATTATAATTATATTAAATAAAA
1 TATTA-TATATTTATATTAAAT-AAA
2280024 TATTATATATTTATAAAAATTTAAATAAA
1 TATTATATATTTAT----A-TTAAATAAA
*
2280053 TA--ATA-ATTTATATTATATAAA
1 TATTATATATTTATATTAAATAAA
*
2280074 TTTTAATATATTTATAT
1 TATT-ATATATTTATAT
2280091 GTTTATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
21 9 0.16
22 1 0.02
24 3 0.05
25 16 0.29
26 11 0.20
27 3 0.05
29 6 0.11
30 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTATATATTTATATTAAATAAA
Found at i:2280069 original size:31 final size:34
Alignment explanation
Indices: 2280015--2280081 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 34
2280005 ATAATTATAT
2280015 TAAATAAAATATTATATATTTATAAAAATTTAAA
1 TAAATAAAATATTATATATTTATAAAAATTTAAA
* * *
2280049 TAAATAATA-ATT-TATA-TTATATAAATTTTAA
1 TAAATAAAATATTATATATTTATAAAAATTTAAA
2280080 TA
1 TA
2280082 TATTTATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.50
32 4 0.13
33 3 0.10
34 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
TAAATAAAATATTATATATTTATAAAAATTTAAA
Found at i:2280115 original size:14 final size:14
Alignment explanation
Indices: 2280058--2280120 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
2280048 ATAAATAATA
**
2280058 ATTTATATTATATAA
1 ATTT-TATTATATTT
*
2280073 ATTTTAATATATTT
1 ATTTTATTATATTT
*
2280087 ATATGT-TTATA-TT
1 AT-TTTATTATATTT
2280100 ATTTTATTATATTT
1 ATTTTATTATATTT
2280114 ATTTTAT
1 ATTTTAT
2280121 ATTTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
12 2 0.05
13 9 0.23
14 22 0.56
15 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
ATTTTATTATATTT
Found at i:2281018 original size:21 final size:20
Alignment explanation
Indices: 2280976--2281018 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2280966 ATCTTTAAAA
* *
2280976 TTTTTAAAATAATTTTTTAT
1 TTTTTAAAATAATTATTAAT
*
2280996 TTTTTAAAAATAGTTATTAAT
1 TTTTT-AAAATAATTATTAAT
2281017 TT
1 TT
2281019 ATAGTGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAAAATAATTATTAAT
Found at i:2281156 original size:2 final size:2
Alignment explanation
Indices: 2281149--2281212 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
2281139 GCATACATAC
* *
2281149 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2281191 AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2281213 GAAGGGGGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2281168 original size:14 final size:14
Alignment explanation
Indices: 2281141--2281212 Score: 108
Period size: 14 Copynumber: 5.1 Consensus size: 14
2281131 CCATGCATGC
*
2281141 ATACATACATATAT
1 ATACATATATATAT
*
2281155 ATATATATATATAT
1 ATACATATATATAT
2281169 ATACATATATATAT
1 ATACATATATATAT
2281183 ATACATATATATAT
1 ATACATATATATAT
* *
2281197 ATATATATAAATAT
1 ATACATATATATAT
2281211 AT
1 AT
2281213 GAAGGGGGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 53 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:2281531 original size:3 final size:3
Alignment explanation
Indices: 2281525--2281557 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2281515 CTTCTTCCCA
2281525 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2281558 CTATACAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2282007 original size:27 final size:27
Alignment explanation
Indices: 2281977--2282031 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2281967 GTTTGTATAT
*
2281977 TTATACTATA-TTTATATTATTTTTTTA
1 TTATACTATATTTTA-ATTATTATTTTA
**
2282004 TTATGTTATATTTTAATTATTATTTTA
1 TTATACTATATTTTAATTATTATTTTA
2282031 T
1 T
2282032 GTTATCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTATACTATATTTTAATTATTATTTTA
Found at i:2282068 original size:11 final size:11
Alignment explanation
Indices: 2281972--2282071 Score: 55
Period size: 11 Copynumber: 9.3 Consensus size: 11
2281962 AATATGTTTG
*
2281972 TATATTTATAC
1 TATATTTATAT
2281983 TATATTTATAT
1 TATATTTATAT
* *
2281994 TATTTTTTTAT
1 TATATTTATAT
*
2282005 TAT-GTTATAT
1 TATATTTATAT
* *
2282015 TTTA-AT-TAT
1 TATATTTATAT
*
2282024 TAT-TTTATGT
1 TATATTTATAT
* *
2282034 TATCTTTGTAT
1 TATATTTATAT
* *
2282045 CATACAATTATAT
1 --TATATTTATAT
2282058 TATATTTATAT
1 TATATTTATAT
2282069 TAT
1 TAT
2282072 CAAATTAAAT
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
9 6 0.09
10 13 0.20
11 39 0.60
13 7 0.11
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2282792 original size:24 final size:24
Alignment explanation
Indices: 2282758--2282806 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2282748 TTTATAATTT
*
2282758 TATTTATTATA-TTATATTAAATAA
1 TATTTAATATATTTAT-TTAAATAA
2282782 TATTTAATATATTTATTTAAATAA
1 TATTTAATATATTTATTTAAATAA
2282806 T
1 T
2282807 TAAAAATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTAATATATTTATTTAAATAA
Found at i:2283857 original size:17 final size:16
Alignment explanation
Indices: 2283833--2283872 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2283823 ATTTAAAATA
2283833 TTTTTAAAGATTATAT
1 TTTTTAAAGATTATAT
*
2283849 TTATTTAAAATATTATAT
1 TT-TTT-AAAGATTATAT
2283867 TTTTTA
1 TTTTTA
2283873 TAATCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 6 0.29
18 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTAAAGATTATAT
Found at i:2284228 original size:12 final size:13
Alignment explanation
Indices: 2284207--2284249 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
2284197 TTTCTTTAGT
2284207 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
2284220 AAAAA-AAAAAAG
1 AAAAAGAAAAAAG
**
2284232 AAAAAGTGAAAAG
1 AAAAAGAAAAAAG
2284245 AAAAA
1 AAAAA
2284250 TATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:2284243 original size:19 final size:20
Alignment explanation
Indices: 2284207--2284249 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2284197 TTTCTTTAGT
2284207 AAAAAGAAAAAAGAAAAA-A
1 AAAAAGAAAAAAGAAAAAGA
*
2284226 AAAAAG-AAAAAGTGAAAAGA
1 AAAAAGAAAAAAG-AAAAAGA
2284246 AAAA
1 AAAA
2284250 TATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAGA
Found at i:2286693 original size:20 final size:20
Alignment explanation
Indices: 2286670--2286742 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2286660 ACAATTCAAA
2286670 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2286690 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2286711 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2286731 GTATCGATACAT
1 GTATCGATACAT
2286743 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2286721 original size:41 final size:42
Alignment explanation
Indices: 2286670--2286764 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2286660 ACAATTCAAA
*
2286670 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2286711 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2286753 GTATCGATACAT
1 GTATCGATACAT
2286765 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:2286821 original size:13 final size:13
Alignment explanation
Indices: 2286803--2286828 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2286793 TACAGCAAGT
2286803 ATGTATCGATACA
1 ATGTATCGATACA
2286816 ATGTATCGATACA
1 ATGTATCGATACA
2286829 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2288540 original size:97 final size:97
Alignment explanation
Indices: 2288353--2288540 Score: 236
Period size: 97 Copynumber: 1.9 Consensus size: 97
2288343 AAAACGAGGC
* * * * *
2288353 TGGAGTATCTCTTCGGAGGAATGGGGTTGGAGTATCCCCGATGATGACAATTTATGTAAAAATAA
1 TGGAGTATCTCTTAGAAGGAATAGGGTTAGAGTATCCCCGATGATGACAATTTAAGTAAAAATAA
* ** *
2288418 GATTTAAATCTTGGGAAGTTTAAAAATAGAGT
66 AATTTAAATCTTACGAAGTTAAAAAATAGAGT
*
2288450 TGGAGTATCTTCTTAGAAGG-ATAGGGTTAGAGTATCCCCGATGTTGACAATTTAAGTAAAAATA
1 TGGAGTATC-TCTTAGAAGGAATAGGGTTAGAGTATCCCCGATGATGACAATTTAAGTAAAAATA
* *
2288514 AAATTTAAGTTTTAACG-AGTTAAAAAA
65 AAATTTAAATCTT-ACGAAGTTAAAAAA
2288541 AAAACAAGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
97 68 0.88
98 9 0.12
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (97 bp):
TGGAGTATCTCTTAGAAGGAATAGGGTTAGAGTATCCCCGATGATGACAATTTAAGTAAAAATAA
AATTTAAATCTTACGAAGTTAAAAAATAGAGT
Found at i:2288958 original size:20 final size:20
Alignment explanation
Indices: 2288933--2288987 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2288923 ACAAATAGTA
2288933 AATGTATCGATATATAAGTG
1 AATGTATCGATATATAAGTG
* *
2288953 AATGTATCAATACATAAGTG
1 AATGTATCGATATATAAGTG
2288973 AATGTATCGATATAT
1 AATGTATCGATATAT
2288988 GCCTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (20 bp):
AATGTATCGATATATAAGTG
Found at i:2289058 original size:20 final size:20
Alignment explanation
Indices: 2289033--2289084 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2289023 TTAGAAAGGA
2289033 AATGTATCGATACATAAGTG
1 AATGTATCGATACATAAGTG
2289053 AATGTATCGATACATAAGTG
1 AATGTATCGATACATAAGTG
2289073 AATGTATCGATA
1 AATGTATCGATA
2289085 TATGCCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATAAGTG
Found at i:2289067 original size:100 final size:100
Alignment explanation
Indices: 2288932--2289167 Score: 445
Period size: 100 Copynumber: 2.4 Consensus size: 100
2288922 TACAAATAGT
*
2288932 AAATGTATCGATATATAAGTGAATGTATCAATACATAAGTGAATGTATCGATATATGCCTAAAAT
1 AAATGTATCGATACATAAGTGAATGTATCAATACATAAGTGAATGTATCGATATATGCCTAAAAT
2288997 ATATCAATACAAAACCACTCTGCATTTTAGAAAGG
66 ATATCAATACAAAACCACTCTGCATTTTAGAAAGG
*
2289032 AAATGTATCGATACATAAGTGAATGTATCGATACATAAGTGAATGTATCGATATATGCCTAAAAT
1 AAATGTATCGATACATAAGTGAATGTATCAATACATAAGTGAATGTATCGATATATGCCTAAAAT
2289097 ATATCAATACAAAACCACTCTGCATTTTAGAAAGG
66 ATATCAATACAAAACCACTCTGCATTTTAGAAAGG
*
2289132 AAATGTATCGATACATAAGTAAATGTATCAATACAT
1 AAATGTATCGATACATAAGTGAATGTATCAATACAT
2289168 GCTCATAATT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 132 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (100 bp):
AAATGTATCGATACATAAGTGAATGTATCAATACATAAGTGAATGTATCGATATATGCCTAAAAT
ATATCAATACAAAACCACTCTGCATTTTAGAAAGG
Found at i:2292040 original size:13 final size:13
Alignment explanation
Indices: 2292022--2292047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2292012 CAATTTTTGG
2292022 TGTATCGATACAT
1 TGTATCGATACAT
2292035 TGTATCGATACAT
1 TGTATCGATACAT
2292048 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2292059 original size:32 final size:33
Alignment explanation
Indices: 2292002--2292065 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2291992 TACAAGCCAA
** *
2292002 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCAATACAT
2292035 TGTATCGATAC-ATACTTGGTGTATCAATACA
1 TGTATCGATACAATACTTGGTGTATCAATACA
2292066 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCAATACAT
Found at i:2294630 original size:13 final size:13
Alignment explanation
Indices: 2294612--2294637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2294602 ATAATCACCC
2294612 TGTATCGATACAA
1 TGTATCGATACAA
2294625 TGTATCGATACAA
1 TGTATCGATACAA
2294638 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2294648 original size:20 final size:20
Alignment explanation
Indices: 2294623--2294676 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2294613 GTATCGATAC
2294623 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
2294643 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
2294663 AATGTATCGATACA
1 AATGTATCGATACA
2294677 TTGAATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2296759 original size:15 final size:15
Alignment explanation
Indices: 2296739--2296769 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2296729 ATTTCTTGTG
*
2296739 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2296754 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2296769 G
1 G
2296770 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2298601 original size:21 final size:21
Alignment explanation
Indices: 2298572--2298616 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2298562 AAGTTTTTAT
*
2298572 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2298592 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2298614 TTT
1 TTT
2298617 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2300850 original size:13 final size:13
Alignment explanation
Indices: 2300832--2300857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2300822 CAATTTTTGG
2300832 TGTATCGATACAT
1 TGTATCGATACAT
2300845 TGTATCGATACAT
1 TGTATCGATACAT
2300858 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2300869 original size:32 final size:33
Alignment explanation
Indices: 2300812--2300875 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2300802 TACAAGCCAA
**
2300812 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2300845 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2300876 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2300882 original size:19 final size:18
Alignment explanation
Indices: 2300812--2300882 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
2300802 TACAAGCCAA
2300812 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
2300832 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
2300845 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
2300864 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
2300883 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:2300969 original size:15 final size:15
Alignment explanation
Indices: 2300949--2300977 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2300939 CATTGCAACA
2300949 TGTATCGATACTTTG
1 TGTATCGATACTTTG
2300964 TGTATCGATACTTT
1 TGTATCGATACTTT
2300978 TAAGGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
TGTATCGATACTTTG
Found at i:2303163 original size:13 final size:13
Alignment explanation
Indices: 2303145--2303171 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2303135 ACATGCTGCT
2303145 TTGTATCGATACA
1 TTGTATCGATACA
2303158 TTGTATCGATACA
1 TTGTATCGATACA
2303171 T
1 T
2303172 GGACAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2308462 original size:34 final size:34
Alignment explanation
Indices: 2308424--2308507 Score: 168
Period size: 34 Copynumber: 2.5 Consensus size: 34
2308414 CTTTGTTAAG
2308424 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308458 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308492 TGTATTTGGTGAGAAT
1 TGTATTTGGTGAGAAT
2308508 AGGAAACATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:2308630 original size:180 final size:180
Alignment explanation
Indices: 2308328--2308687 Score: 711
Period size: 180 Copynumber: 2.0 Consensus size: 180
2308318 TATGATTTCA
2308328 AGGAAACATATCAAGGAGGAAATTAATGATGAGGGGGAGTGTTAAAAATCATCATTAATTTGGGT
1 AGGAAACATATCAAGGAGGAAATTAATGATGAGGGGGAGTGTTAAAAATCATCATTAATTTGGGT
2308393 GCTAGATCTACATATTAATTTCTTTGTTAAGTGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
66 GCTAGATCTACATATTAATTTCTTTGTTAAGTGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308458 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAAT
131 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAAT
2308508 AGGAAACATATCAAGGAGGAAATTAATGATGAGGGGGAGTGTTAAAAATCATCATTAATTTGGGT
1 AGGAAACATATCAAGGAGGAAATTAATGATGAGGGGGAGTGTTAAAAATCATCATTAATTTGGGT
*
2308573 GCTAGATCTACATATTAATTTCTTTGTTAAGTGTATTTGGTGAGAATGTTTGGTGTGTTAGGTGA
66 GCTAGATCTACATATTAATTTCTTTGTTAAGTGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308638 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAAT
131 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAAT
2308688 GTTAGGTGTG
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 179 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (180 bp):
AGGAAACATATCAAGGAGGAAATTAATGATGAGGGGGAGTGTTAAAAATCATCATTAATTTGGGT
GCTAGATCTACATATTAATTTCTTTGTTAAGTGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAAT
Found at i:2308642 original size:34 final size:34
Alignment explanation
Indices: 2308604--2308739 Score: 245
Period size: 34 Copynumber: 4.0 Consensus size: 34
2308594 CTTTGTTAAG
*
2308604 TGTATTTGGTGAGAATGTTTGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308638 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308672 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* *
2308706 TGTGTTTGGTGACAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2308740 GAATGTTAGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 99 1.00
ACGTcount: A:0.19, C:0.01, G:0.38, T:0.42
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:2308729 original size:13 final size:12
Alignment explanation
Indices: 2308645--2308781 Score: 55
Period size: 9 Copynumber: 12.0 Consensus size: 12
2308635 TGATGTATTT
2308645 GGTGAGAATGTTA
1 GGTGA-AATGTTA
2308658 GGTG---TGTTA
1 GGTGAAATGTTA
** * *
2308667 GGTGATGTATTT
1 GGTGAAATGTTA
2308679 GGTGAGAATGTTA
1 GGTGA-AATGTTA
2308692 GGTG---TGTTA
1 GGTGAAATGTTA
** *
2308701 GGTGATGTGTTT
1 GGTGAAATGTTA
2308713 GGTGACAATGTTA
1 GGTGA-AATGTTA
2308726 GGTG---TGTTA
1 GGTGAAATGTTA
2308735 GGTGAGAATGTTA
1 GGTGA-AATGTTA
2308748 GGTG---TGTTA
1 GGTGAAATGTTA
* * *
2308757 GGTGATATATTT
1 GGTGAAATGTTA
2308769 GGTGAGAATGTTA
1 GGTGA-AATGTTA
2308782 AGTGTGTTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
9 36 0.39
12 25 0.27
13 32 0.34
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.39
Consensus pattern (12 bp):
GGTGAAATGTTA
Found at i:2308738 original size:22 final size:22
Alignment explanation
Indices: 2308706--2308761 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
2308696 TGTTAGGTGA
*
2308706 TGTGTTTGGTGACAATGTTAGG
1 TGTGTTAGGTGACAATGTTAGG
*
2308728 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGACAATGTTAGG
2308750 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2308762 TATATTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGACAATGTTAGG
Found at i:2308770 original size:56 final size:56
Alignment explanation
Indices: 2308679--2308790 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
2308669 TGATGTATTT
* * *
2308679 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGACAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTGACAATGTTAAGTGTGTTA
*
2308735 GGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTGAGAATGTTAAGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTGACAATGTTAAGTGTGTTA
2308791 ACATGTATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATATATTTGGTGACAATGTTAAGTGTGTTA
Found at i:2308800 original size:34 final size:34
Alignment explanation
Indices: 2308735--2308801 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
2308725 AGGTGTGTTA
* **
2308735 GGTGAGAATGTTAGGTGTGTTAGGTGATATATTT
1 GGTGAGAATGTTAAGTGTGTTACATGATATATTT
2308769 GGTGAGAATGTTAAGTGTGTTAACATGTATATA
1 GGTGAGAATGTTAAGTGTGTT-ACATG-ATATA
2308802 AAGGGCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 20 0.71
35 3 0.11
36 5 0.18
ACGTcount: A:0.28, C:0.01, G:0.31, T:0.39
Consensus pattern (34 bp):
GGTGAGAATGTTAAGTGTGTTACATGATATATTT
Found at i:2314390 original size:19 final size:19
Alignment explanation
Indices: 2314358--2314398 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2314348 TTGATGTTTG
2314358 TTATGTTGTATAAT-TGAA
1 TTATGTTGTATAATATGAA
*
2314376 TTATGTTTGTTTAATATGAA
1 TTATG-TTGTATAATATGAA
2314396 TTA
1 TTA
2314399 GGGTCTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TTATGTTGTATAATATGAA
Found at i:2314681 original size:21 final size:21
Alignment explanation
Indices: 2314657--2314697 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2314647 CAAAATTTCC
2314657 ACAAAT-TTTCTATTTTTCACT
1 ACAAATATTTC-ATTTTTCACT
2314678 ACAAATACTTTCATTTTTCA
1 ACAAATA-TTTCATTTTTCA
2314698 TCAAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.49
Consensus pattern (21 bp):
ACAAATATTTCATTTTTCACT
Found at i:2317011 original size:21 final size:19
Alignment explanation
Indices: 2316964--2317021 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
2316954 TTATATCGAT
*
2316964 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2316983 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2317002 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
2317022 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2320129 original size:62 final size:62
Alignment explanation
Indices: 2320055--2320176 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
2320045 AGCTTTATTT
2320055 TGGATGGCAGAGTTTGGTATAAGAAAAGTTGAGATGTACTACATAGGTGCGTAGATGCCTCC
1 TGGATGGCAGAGTTTGGTATAAGAAAAGTTGAGATGTACTACATAGGTGCGTAGATGCCTCC
2320117 TGGATGGCAGAGTTTGGTATAAGAAAAGTTGAGATGTACTACATAGGTGCGTAGATGCCT
1 TGGATGGCAGAGTTTGGTATAAGAAAAGTTGAGATGTACTACATAGGTGCGTAGATGCCT
2320177 TCGAAGCTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (62 bp):
TGGATGGCAGAGTTTGGTATAAGAAAAGTTGAGATGTACTACATAGGTGCGTAGATGCCTCC
Done.