Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 14 of 16
Found at i:2259357 original size:69 final size:68
Alignment explanation
Indices: 2259196--2259562 Score: 508
Period size: 69 Copynumber: 5.4 Consensus size: 68
2259186 TAGGTGAAAT
2259196 ATGCCACGGAGTTGTGGACTTAAAA-GAAGCAAGGGTGCCACAGAGTTGTGGACTT-AAAAGGAA
1 ATGCCACGGAGTTGTGGACTTAAAAGGAA-CAA-GGTGCCACAGAGTTGTGGACTTAAAAAGGAA
*
2259259 CAAGG
64 AAAGG
* * *
2259264 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTAGACTTAAAAAGGAAC
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG-TGCCACAGAGTTGTGGACTTAAAAAGGAAA
2259329 AAGG
65 AAGG
* * * *
2259333 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGATGCCACTGAGGTGTGGGCTTAAAAGGGAAA
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG-TGCCACAGAGTTGTGGACTTAAAAAGGAAA
2259398 AAGG
65 AAGG
* * *
2259402 GTGCCACGGAGTCGTGGACTTAAAAGGAA-AAGGTGCCACAGAGTTGTGGACTTTAAAAGGAAAA
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAAGGAAAA
2259466 A-G
66 AGG
* * * * *
2259468 ATGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGGTGTGGGCTTAAAAGGGAAAA
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAAGGAAAA
2259533 AGG
66 AGG
* *
2259536 GTGCCACGGAGTCGTGGACTTAAAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGG
2259563 GTGCCACGAA
Statistics
Matches: 268, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
66 27 0.10
67 60 0.22
68 75 0.28
69 106 0.40
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.17
Consensus pattern (68 bp):
ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAAGGAAAA
AGG
Found at i:2259560 original size:27 final size:27
Alignment explanation
Indices: 2259530--2259638 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 27
2259520 TTAAAAGGGA
2259530 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* * *
2259557 AAAAGGGTGCCACGAAGTCATAGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
2259584 AAAAGGGTGCCACAGAGTCGTGGGCTTT
1 AAAAGGGTGCCACGGAGTCGTGGAC-TT
* * *
2259612 AAAAAGAGTGCCATGGAGTTGTGGACT
1 -AAAAGGGTGCCACGGAGTCGTGGACT
2259639 ATGAAGAAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
27 44 0.66
28 3 0.04
29 20 0.30
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:2259563 original size:35 final size:34
Alignment explanation
Indices: 2259196--2259562 Score: 501
Period size: 34 Copynumber: 10.8 Consensus size: 34
2259186 TAGGTGAAAT
2259196 ATGCCACGGAGTTGTGGACTTAAAA-GAAGCAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAA-CAAGG
* *
2259230 GTGCCACAGAGTTGTGGACTTAAAAGGAACAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
2259264 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
*
2259298 ATGCCACGGAGTTGTAGACTTAAAAAGGAACAAGG
1 ATGCCACGGAGTTGTGGACTT-AAAAGGAACAAGG
2259333 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
* * * *
2259367 ATGCCACTGAGGTGTGGGCTTAAAAGGGAAAAAGG
1 ATGCCACGGAGTTGTGGACTTAAAA-GGAACAAGG
* *
2259402 GTGCCACGGAGTCGTGGACTTAAAAGGAA-AAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
* *
2259435 -TGCCACAGAGTTGTGGACTTTAAAAGGAA-AAAG
1 ATGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGG
*
2259468 ATGCCACAGAGTTGTGGACTTAAAAGGAACAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
* * *
2259502 -TGCCACGGAGGTGTGGGCTTAAAAGGGAAAAAGG
1 ATGCCACGGAGTTGTGGACTTAAAA-GGAACAAGG
* *
2259536 GTGCCACGGAGTCGTGGACTTAAAAGG
1 ATGCCACGGAGTTGTGGACTTAAAAGG
2259563 GTGCCACGAA
Statistics
Matches: 299, Mismatches: 26, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
32 16 0.05
33 48 0.16
34 150 0.50
35 85 0.28
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.17
Consensus pattern (34 bp):
ATGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
Found at i:2259662 original size:60 final size:61
Alignment explanation
Indices: 2259591--2259735 Score: 195
Period size: 62 Copynumber: 2.4 Consensus size: 61
2259581 CTTAAAAGGG
* * * *
2259591 TGCCACAGAGTCGTGGGCTTTAAAA-AGAGTGCCA-TGGAGTTGTGGACTATGAAGAAAAAA
1 TGCCACTGAGTCATGGACTTTAAAAGAGAGTGCCACT-AAGTTGTGGACTATGAAGAAAAAA
* * *
2259651 TGCCACTGAGTCATGGACTTTGAAAAGAGATTGCCACTAAGTTGTGGACTTTGGAGAAAAAA
1 TGCCACTGAGTCATGGACTTT-AAAAGAGAGTGCCACTAAGTTGTGGACTATGAAGAAAAAA
2259713 TGCCACTGAGTCATGGACTTTAA
1 TGCCACTGAGTCATGGACTTTAA
2259736 GAAGGTATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 18 0.24
61 6 0.08
62 50 0.67
63 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (61 bp):
TGCCACTGAGTCATGGACTTTAAAAGAGAGTGCCACTAAGTTGTGGACTATGAAGAAAAAA
Found at i:2259668 original size:31 final size:31
Alignment explanation
Indices: 2259633--2259738 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 31
2259623 CATGGAGTTG
*
2259633 TGGACTATGAAGAAAAAATGCCACTGAGTCA
1 TGGACTTTGAAGAAAAAATGCCACTGAGTCA
* * * **
2259664 TGGACTTTGAA-AAGAGATTGCCACTAAGTTG
1 TGGACTTTGAAGAA-AAAATGCCACTGAGTCA
*
2259695 TGGACTTTGGAGAAAAAATGCCACTGAGTCA
1 TGGACTTTGAAGAAAAAATGCCACTGAGTCA
2259726 TGGACTTT-AAGAA
1 TGGACTTTGAAGAA
2259739 GGTATTTGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
30 6 0.10
31 52 0.87
32 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
TGGACTTTGAAGAAAAAATGCCACTGAGTCA
Found at i:2259810 original size:142 final size:142
Alignment explanation
Indices: 2259640--2259919 Score: 497
Period size: 142 Copynumber: 2.0 Consensus size: 142
2259630 TTGTGGACTA
*
2259640 TGAAGAAAAAATGCCACTGAGTCATGGACTTTGAAAAGAGATTGCCACTAAGTTGTGGACTTTGG
1 TGAAGAAAAAATGCCACTGAGTCATGGACTTTGAAAAGAGACTGCCACTAAGTTGTGGACTTTGG
* *
2259705 AGAAAAAATGCCACTGAGTCATGGACTTTAAGAAGGTATTTGAAGAATTGAGACATGCTCAACCA
66 AGAAAAAATGCCACTGAGTCATGGACATTAAAAAGGTATTTGAAGAATTGAGACATGCTCAACCA
2259770 GGGATTGAACTT
131 GGGATTGAACTT
* * *
2259782 TGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAAAGAGACTGCCACTGAGTTGTGGACTTTGG
1 TGAAGAAAAAATGCCACTGAGTCATGGACTTTGAAAAGAGACTGCCACTAAGTTGTGGACTTTGG
*
2259847 AGAAAAAATGCCATTGAGTCATGGACATTAAAAAGGTATTTGAAGAATTGAGACATGCTCAACCA
66 AGAAAAAATGCCACTGAGTCATGGACATTAAAAAGGTATTTGAAGAATTGAGACATGCTCAACCA
2259912 GGGATTGA
131 GGGATTGA
2259920 TGGGAGCAAG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 131 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.25
Consensus pattern (142 bp):
TGAAGAAAAAATGCCACTGAGTCATGGACTTTGAAAAGAGACTGCCACTAAGTTGTGGACTTTGG
AGAAAAAATGCCACTGAGTCATGGACATTAAAAAGGTATTTGAAGAATTGAGACATGCTCAACCA
GGGATTGAACTT
Found at i:2259816 original size:31 final size:31
Alignment explanation
Indices: 2259778--2259872 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
2259768 CAGGGATTGA
2259778 ACTTTGAAGAAAAGATGCCACTGAGTCGTGG
1 ACTTTGAAGAAAAGATGCCACTGAGTCGTGG
* *
2259809 ACTTTGAA-AAGAGACTGCCACTGAGTTGTGG
1 ACTTTGAAGAAAAGA-TGCCACTGAGTCGTGG
* * * *
2259840 ACTTTGGAGAAAAAATGCCATTGAGTCATGG
1 ACTTTGAAGAAAAGATGCCACTGAGTCGTGG
2259871 AC
1 AC
2259873 ATTAAAAAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.09
31 45 0.83
32 4 0.07
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (31 bp):
ACTTTGAAGAAAAGATGCCACTGAGTCGTGG
Found at i:2261170 original size:13 final size:12
Alignment explanation
Indices: 2261151--2261197 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2261141 TTGTGTTTTG
2261151 TTTTTTTTTATT
1 TTTTTTTTTATT
*
2261163 TTTGTTTTTT-TG
1 TTT-TTTTTTATT
*
2261175 TTTTTTTTCATT
1 TTTTTTTTTATT
*
2261187 ATTTTTTTTAT
1 TTTTTTTTTAT
2261198 CATTTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 5 0.18
12 17 0.61
13 6 0.21
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:2261180 original size:16 final size:16
Alignment explanation
Indices: 2261137--2261181 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2261127 TGTTGTTCCC
*
2261137 TTTTTTG-TGTTTTGT
1 TTTTTTGTTTTTTTGT
2261152 TTTTTT-TTATTTTTGT
1 TTTTTTGTT-TTTTTGT
2261168 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
2261182 TCATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (16 bp):
TTTTTTGTTTTTTTGT
Found at i:2261194 original size:24 final size:24
Alignment explanation
Indices: 2261138--2261195 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2261128 GTTGTTCCCT
* *
2261138 TTTTTG-TGTTTTGTTTTTTTTTA
1 TTTTTGTTTTTTTGTTTTTTTTCA
2261161 TTTTTGTTTTTTTGTTTTTTTTCA
1 TTTTTGTTTTTTTGTTTTTTTTCA
*
2261185 TTATT-TTTTTT
1 TTTTTGTTTTTT
2261196 ATCATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (24 bp):
TTTTTGTTTTTTTGTTTTTTTTCA
Found at i:2268137 original size:13 final size:13
Alignment explanation
Indices: 2268119--2268145 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2268109 ACAAAGATCA
2268119 AATGTATCGATAC
1 AATGTATCGATAC
2268132 AATGTATCGATAC
1 AATGTATCGATAC
2268145 A
1 A
2268146 TTGAGTAGTA
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2268219 original size:19 final size:18
Alignment explanation
Indices: 2268195--2268255 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
2268185 GCGATAGCAT
2268195 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
2268214 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2268227 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
*
2268246 TATCCATACA
1 TATCGATACA
2268256 TTGTATCGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:2268230 original size:13 final size:13
Alignment explanation
Indices: 2268212--2268268 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2268202 ACAAAACTTA
2268212 TGTATCGATACAT
1 TGTATCGATACAT
2268225 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
2268243 ATGTATCCATACAT
1 -TGTATCGATACAT
2268257 TGTATCGATACA
1 TGTATCGATACA
2268269 AATTGTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2268231 original size:32 final size:32
Alignment explanation
Indices: 2268195--2268270 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
2268185 GCGATAGCAT
*
2268195 TATCGATACAAAACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCCATACATTG
*
2268227 TATCGATACAACACTTATGTATCCATACATTG
1 TATCGATACAAAACTTATGTATCCATACATTG
2268259 TATCGATACAAA
1 TATCGATACAAA
2268271 TTGTTGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCCATACATTG
Found at i:2268648 original size:52 final size:52
Alignment explanation
Indices: 2268564--2268779 Score: 274
Period size: 52 Copynumber: 4.1 Consensus size: 52
2268554 ATTGGCACCT
* * * *
2268564 TCATCTTTAAG-CCTAATGTTACTGGCCTTGAATCAGCACATTGGCACCTTTT
1 TCATCTTTAAGTCC-AATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* *
2268616 TC-TTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG
1 TCATCT-TTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * * *
2268668 TCATCTTTAAGTCCGATATCACTGGCATTGAATTAGCATATTGGTACCTTTG
1 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * *
2268720 TCATCTTTAAGCCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTTA
1 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
2268772 TCACTCTT
1 TCA-TCTT
2268780 CTCATCTTCA
Statistics
Matches: 141, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
51 2 0.01
52 131 0.93
53 8 0.06
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
Found at i:2269557 original size:20 final size:19
Alignment explanation
Indices: 2269532--2269611 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 19
2269522 ACTACCAAGG
2269532 AAATGTATCGATACATTATT
1 AAATGTATCGATACATT-TT
* *
2269552 AAATGTATCAATACATGCTT
1 AAATGTATCGATACAT-TTT
*
2269572 ACAATTGTATTGATACATTTCT
1 A-AA-TGTATCGATACATTT-T
* *
2269594 CATTGTATCGATACATTT
1 AAATGTATCGATACATTT
2269612 CGAGTTTTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 32 0.67
21 4 0.08
22 12 0.25
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (19 bp):
AAATGTATCGATACATTTT
Found at i:2272173 original size:26 final size:24
Alignment explanation
Indices: 2272131--2272178 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
2272121 GTGAATTATT
2272131 TCATACAACATTATTTCACTTGTTG
1 TCATACAACATTATTTC-CTTGTTG
2272156 TCATACTAACA-TATTTTCCTTGT
1 TCATAC-AACATTA-TTTCCTTGT
2272179 GTTGATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (24 bp):
TCATACAACATTATTTCCTTGTTG
Found at i:2280205 original size:1 final size:1
Alignment explanation
Indices: 2280199--2280297 Score: 72
Period size: 1 Copynumber: 99.0 Consensus size: 1
2280189 CTTTGTATAT
* * * * * * ** ** *
2280199 AAAAAAACAAACAAATAAAACAAAAAAATAAAAAAAAACAAAAAACCAAAAAAACCAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
2280264 AAAAAAAACAAAAAAACAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2280298 TGGTCTAGAT
Statistics
Matches: 74, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:2280231 original size:8 final size:8
Alignment explanation
Indices: 2280199--2280295 Score: 90
Period size: 8 Copynumber: 11.9 Consensus size: 8
2280189 CTTTGTATAT
2280199 AAAAAAAC
1 AAAAAAAC
* *
2280207 AAACAAAT
1 AAAAAAAC
2280215 AAAACAAA-
1 AAAA-AAAC
*
2280223 AAAATAA-
1 AAAAAAAC
2280230 AAAAAAAC
1 AAAAAAAC
*
2280238 AAAAAACC
1 AAAAAAAC
2280246 AAAAAAACC
1 AAAAAAA-C
*
2280255 AAAAAAATAA
1 -AAAAAA-AC
2280265 AAAAAAAC
1 AAAAAAAC
2280273 AAAAAAAC
1 AAAAAAAC
*
2280281 AAAAAAAT
1 AAAAAAAC
2280289 AAAAAAA
1 AAAAAAA
2280296 AATGGTCTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
7 8 0.11
8 49 0.66
9 10 0.14
10 6 0.08
11 1 0.01
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2280236 original size:18 final size:18
Alignment explanation
Indices: 2280215--2280298 Score: 109
Period size: 18 Copynumber: 4.7 Consensus size: 18
2280205 ACAAACAAAT
2280215 AAAACAAAAAAATAAAAA
1 AAAACAAAAAAATAAAAA
**
2280233 AAAAC-AAAAAACCAAAA
1 AAAACAAAAAAATAAAAA
*
2280250 AAACCAAAAAAATAAAAA
1 AAAACAAAAAAATAAAAA
*
2280268 AAAACAAAAAAACAAAAA
1 AAAACAAAAAAATAAAAA
2280286 AATAA-AAAAAAAT
1 AA-AACAAAAAAAT
2280299 GGTCTAGATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.25
18 40 0.71
19 2 0.04
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAACAAAAAAATAAAAA
Found at i:2280248 original size:26 final size:27
Alignment explanation
Indices: 2280199--2280297 Score: 123
Period size: 26 Copynumber: 3.7 Consensus size: 27
2280189 CTTTGTATAT
* *
2280199 AAAAAAACAAACAAATAAAACAAAAAAAT
1 AAAAAAA-TAACAAA-AAAACAAAAAAAC
*
2280228 AAAAAAA-AACAAAAAACCAAAAAAACC
1 AAAAAAATAACAAAAAAACAAAAAAA-C
2280255 AAAAAAATAA-AAAAAAACAAAAAAAC
1 AAAAAAATAACAAAAAAACAAAAAAAC
2280281 AAAAAAATAA-AAAAAAA
1 AAAAAAATAACAAAAAAA
2280298 TGGTCTAGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
26 29 0.45
27 27 0.42
28 2 0.03
29 7 0.11
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (27 bp):
AAAAAAATAACAAAAAAACAAAAAAAC
Found at i:2280296 original size:35 final size:34
Alignment explanation
Indices: 2280202--2280295 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 34
2280192 TGTATATAAA
2280202 AAAACAAACAAATAAAACAAAAAAATAAAAAAAAAC
1 AAAA-AAACAAA-AAAACAAAAAAATAAAAAAAAAC
*
2280238 AAAAAACCAAAAAAACCAAAAAAATAAAAAAAAAC
1 AAAAAAACAAAAAAA-CAAAAAAATAAAAAAAAAC
*
2280273 AAAAAAACAAAAAAATAAAAAAA
1 AAAAAAACAAAAAAACAAAAAAA
2280296 AATGGTCTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
34 11 0.20
35 39 0.72
36 4 0.07
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.04
Consensus pattern (34 bp):
AAAAAAACAAAAAAACAAAAAAATAAAAAAAAAC
Found at i:2281235 original size:28 final size:27
Alignment explanation
Indices: 2281203--2281270 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
2281193 AATCTTCAAT
*
2281203 GGAATCAAGAAAAGTGCTAATCCCCAGG
1 GGAATCAAGAAAAGTGC-AATCCCCAAG
* * *
2281231 GGAATCATGACAAATTGCAATCCCCAAT
1 GGAATCAAGA-AAAGTGCAATCCCCAAG
*
2281259 AGAATCAAGAAA
1 GGAATCAAGAAA
2281271 CTTGCAATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.06
28 25 0.76
29 6 0.18
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (27 bp):
GGAATCAAGAAAAGTGCAATCCCCAAG
Found at i:2281933 original size:34 final size:32
Alignment explanation
Indices: 2281895--2282034 Score: 97
Period size: 34 Copynumber: 4.2 Consensus size: 32
2281885 ACAAGCTCTA
*
2281895 TGGCACTTCATCCTATTAAGCCTACACAAGTTGG
1 TGGCACTTCATCCT-TTAAGCC-ACACAAGTCGG
* * * *
2281929 TGGCACCTT-TTTCTTTAAAGCC-CACAACTCCG
1 TGGCA-CTTCATCCTTT-AAGCCACACAAGTCGG
*
2281961 TGGCACTTCATCCTTTTAAGCCCACACAAGTCGA
1 TGGCACTTCATCC-TTTAAG-CCACACAAGTCGG
* * *
2281995 TGGCACCTT-TTTCTTCAAAGCCCACACAAGTCGG
1 TGGCA-CTTCATCCTT-TAAG-CCACACAAGTCGG
2282029 TGGCAC
1 TGGCAC
2282035 CTTTTTCTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
31 3 0.04
32 17 0.20
33 10 0.12
34 48 0.57
35 6 0.07
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (32 bp):
TGGCACTTCATCCTTTAAGCCACACAAGTCGG
Found at i:2281965 original size:66 final size:66
Alignment explanation
Indices: 2281895--2282020 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
2281885 ACAAGCTCTA
* * * *
2281895 TGGCACTTCATCCTATTAAGCCTACACAAGTTGGTGGCACCTTTTTCTTTAAAGCCCACAACTCC
1 TGGCACTTCATCCTATTAAGCCCACACAAGTCGATGGCACCTTTTTCTTCAAAGCCCACAACTCC
2281960 G
66 G
*
2281961 TGGCACTTCATCCTTTTAAGCCCACACAAGTCGATGGCACCTTTTTCTTCAAAGCCCACA
1 TGGCACTTCATCCTATTAAGCCCACACAAGTCGATGGCACCTTTTTCTTCAAAGCCCACA
2282021 CAAGTCGGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (66 bp):
TGGCACTTCATCCTATTAAGCCCACACAAGTCGATGGCACCTTTTTCTTCAAAGCCCACAACTCC
G
Found at i:2282035 original size:34 final size:34
Alignment explanation
Indices: 2281912--2282104 Score: 193
Period size: 34 Copynumber: 5.8 Consensus size: 34
2281902 TCATCCTATT
* * *
2281912 AAGCCTACACAAGTTGGTGGCACCTTTTTCTTTA
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCA
* * * * **
2281946 AAG-CC-CACAACTCCGTGGCA-CTTCATCCTTTT
1 AAGCCCACACAAGTCGGTGGCACCTT-TTTCTTCA
*
2281978 AAGCCCACACAAGTCGATGGCACCTTTTTCTTCA
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCA
2282012 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCA
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCA
*
2282046 AAGCCCACACAAG-CTGGTGGCAACC---TTCCTCA
1 AAGCCCACACAAGTC-GGTGGC-ACCTTTTTCTTCA
*
2282078 AAGCCCACACAAGTTGGTGGCAACCTT
1 AAGCCCACACAAGTCGGTGGC-ACCTT
2282105 CTAAAAAGTC
Statistics
Matches: 133, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
31 3 0.02
32 49 0.37
33 4 0.03
34 71 0.53
35 6 0.05
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (34 bp):
AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCA
Found at i:2282084 original size:32 final size:32
Alignment explanation
Indices: 2281978--2282131 Score: 143
Period size: 32 Copynumber: 4.7 Consensus size: 32
2281968 TCATCCTTTT
* * *
2281978 AAGCCCACACAAGTCGATGGC-ACCTTTTTCTTCA
1 AAGCCCACACAAGTTGGTGGCAACC---TTCCTCA
* *
2282012 AAGCCCACACAAGTCGGTGGC-ACCTTTTTCTTCA
1 AAGCCCACACAAGTTGGTGGCAACC---TTCCTCA
*
2282046 AAGCCCACACAAGCTGGTGGCAACCTTCCTCA
1 AAGCCCACACAAGTTGGTGGCAACCTTCCTCA
*
2282078 AAGCCCACACAAGTTGGTGGCAACCTT-CTAAA
1 AAGCCCACACAAGTTGGTGGCAACCTTCCT-CA
* *
2282110 AAGTCCACACAGGTTGGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
2282132 TCCCTTTCCA
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
31 2 0.02
32 53 0.48
34 52 0.47
35 3 0.03
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.21
Consensus pattern (32 bp):
AAGCCCACACAAGTTGGTGGCAACCTTCCTCA
Found at i:2282099 original size:100 final size:100
Alignment explanation
Indices: 2281912--2282104 Score: 232
Period size: 100 Copynumber: 1.9 Consensus size: 100
2281902 TCATCCTATT
* * * *
2281912 AAGCCTACACAAGTTGGTGGCACCTTTTTCTTTAAAGCCCACAACTCCGTGGCACTTCATCCTTT
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCAAAGCCCACAACTCCGTGGCAC-TCATCCTTC
*
2281977 TAAGCCCACACAAGTCGATGGC-ACCTTTTTCTTCA
65 AAAGCCCACACAAGTCGATGGCAACCTTTTTCTTCA
* *
2282012 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCAAAGCCCACACAAGCT-GGTGGCAAC-CTTCC
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCAAAG-CC-CACAA-CTCCGTGGC-ACTCATCC
* *
2282075 -TCAAAGCCCACACAAGTTGGTGGCAACCTT
62 TTCAAAGCCCACACAAGTCGATGGCAACCTT
2282105 CTAAAAAGTC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
100 54 0.68
101 11 0.14
102 10 0.13
103 4 0.05
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (100 bp):
AAGCCCACACAAGTCGGTGGCACCTTTTTCTTCAAAGCCCACAACTCCGTGGCACTCATCCTTCA
AAGCCCACACAAGTCGATGGCAACCTTTTTCTTCA
Found at i:2282297 original size:59 final size:58
Alignment explanation
Indices: 2282155--2282298 Score: 148
Period size: 59 Copynumber: 2.5 Consensus size: 58
2282145 CCAATGTTGT
* * *
2282155 TGGCCTTGAATCAACATATTAGCATTTGTCAGACCTTCGTTCTCAAGCCTAATATCGT
1 TGGCCTTGAATCAACATATTAGCACTTGTCAAACCTTCGTTCTCAAGCCTAATATCGC
* * * * * * *
2282213 TAGCCTTGAA-CTAGCACATTGGCACTTGTCAAATCTTTC-TTTTCAAAGTCTAATATCGC
1 TGGCCTTGAATC-AACATATTAGCACTTGTCAAA-CCTTCGTTCTC-AAGCCTAATATCGC
*
2282272 TGGCCCTGAATCAACATATTAGCACTT
1 TGGCCTTGAATCAACATATTAGCACTT
2282299 TCTTCATCTT
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
57 1 0.01
58 29 0.43
59 36 0.54
60 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (58 bp):
TGGCCTTGAATCAACATATTAGCACTTGTCAAACCTTCGTTCTCAAGCCTAATATCGC
Found at i:2282417 original size:52 final size:52
Alignment explanation
Indices: 2282361--2282517 Score: 169
Period size: 52 Copynumber: 3.0 Consensus size: 52
2282351 TCACGATCTC
* * *
2282361 TAAGTC-CAATATCGCTGGCTTTGAATCAGCATATTGGCAT-TTTTTTCATTTT
1 TAAGTCTC-ATATCGCTGGCATTGAATCAGCATATTGGCATCTTTATT-ATTCT
* * *
2282413 TAAGTCTCATATCGCTAGCCTTGAATCAGCATATTAGCATCTTTATTATTCT
1 TAAGTCTCATATCGCTGGCATTGAATCAGCATATTGGCATCTTTATTATTCT
* * *
2282465 GAAG-CTCGATATCACTGGCCATT-AATCAGCATATTGGCACCTTTATTATTCT
1 TAAGTCTC-ATATCGCTGG-CATTGAATCAGCATATTGGCATCTTTATTATTCT
2282517 T
1 T
2282518 TGCATCTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
51 3 0.03
52 77 0.87
53 9 0.10
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (52 bp):
TAAGTCTCATATCGCTGGCATTGAATCAGCATATTGGCATCTTTATTATTCT
Found at i:2282622 original size:61 final size:61
Alignment explanation
Indices: 2282488--2282640 Score: 148
Period size: 61 Copynumber: 2.5 Consensus size: 61
2282478 ACTGGCCATT
* * * *
2282488 AATCAGCATATTGGCACCTTTATTATTCTTT-GCATCTTTAAGTCTAATGTCATTGACCTTG
1 AATCAGCACATTGGCACCTTTATCA-TCTTTAGCATCTTTAAGTCCAATGTCATAGACCTTG
* ** * * * *
2282549 AATTAGTGCATTGGCACCCTTCTCATCTTTATCATCTTTAAGTCCAATGTCACTAG-CTTTG
1 AATCAGCACATTGGCACCTTTATCATCTTTAGCATCTTTAAGTCCAATGTCA-TAGACCTTG
* * *
2282610 AATCAGCACATTGACGCCTTTGTCATCTTTA
1 AATCAGCACATTGGCACCTTTATCATCTTTA
2282641 AGCCTGATAT
Statistics
Matches: 72, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
60 5 0.07
61 65 0.90
62 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (61 bp):
AATCAGCACATTGGCACCTTTATCATCTTTAGCATCTTTAAGTCCAATGTCATAGACCTTG
Found at i:2282821 original size:52 final size:52
Alignment explanation
Indices: 2282581--2282823 Score: 124
Period size: 52 Copynumber: 4.7 Consensus size: 52
2282571 TCATCTTTAT
* * *
2282581 CATCTTTAAGTCC-AATGTCACTAGCTTTGAATCAGCACATTGACGCCTT-TGT--
1 CATCTTTAAG-CCTAATATCACTAGCCTTGAATCAGCACATTG--GCATTCT-TCA
* * * * * * *
2282633 CATCTTTAAGCCTGATATCACTAGGTCTTGAATCAGTATATCGGTA-TCTTTAA
1 CATCTTTAAGCCTAATATCACTA-GCCTTGAATCAGCACATTGGCATTC-TTCA
* ** ** * *** *
2282686 CAT-TCCTAAG-CTCAATATTGCTAATCTTGAATAAGCACATTGGTGCTCTTCT
1 CATCT-TTAAGCCT-AATATCACTAGCCTTGAATCAGCACATTGGCATTCTTCA
* * * * *
2282738 CATCTTCAAGTCTAATGTCGA-TGGCCGTGAATCAGCACATTGGCATTCTTCA
1 CATCTTTAAGCCTAATATC-ACTAGCCTTGAATCAGCACATTGGCATTCTTCA
2282790 CATCTTTAAGCCTAATATCACTAGCCTTGAATCA
1 CATCTTTAAGCCTAATATCACTAGCCTTGAATCA
2282824 ATATATTGGC
Statistics
Matches: 138, Mismatches: 40, Indels: 26
0.68 0.20 0.13
Matches are distributed among these distances:
50 1 0.01
51 5 0.04
52 99 0.72
53 33 0.24
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CATCTTTAAGCCTAATATCACTAGCCTTGAATCAGCACATTGGCATTCTTCA
Found at i:2282908 original size:62 final size:61
Alignment explanation
Indices: 2282781--2282917 Score: 175
Period size: 62 Copynumber: 2.2 Consensus size: 61
2282771 AGCACATTGG
* * * *
2282781 CATTCTTCACATCTTTAAGCCTAATATCACTAGCCTTGAATCAATATATTGGCACCTTTAT
1 CATTCTTCTCATCTTTAAGCCCAATATCACTAGCCGTGAATCAATATATTGGCACCTTTAC
* * * * *
2282842 CATTCTTCTCATCTTTAAGCCCGATATCGCTAGGTCGTGAATTAGTATATTGGCACCTTTAC
1 CATTCTTCTCATCTTTAAGCCCAATATCACTA-GCCGTGAATCAATATATTGGCACCTTTAC
*
2282904 CATTCCTCTCATCT
1 CATTCTTCTCATCT
2282918 CCAATATCGT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
61 28 0.43
62 37 0.57
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (61 bp):
CATTCTTCTCATCTTTAAGCCCAATATCACTAGCCGTGAATCAATATATTGGCACCTTTAC
Found at i:2284830 original size:97 final size:96
Alignment explanation
Indices: 2284667--2284913 Score: 293
Period size: 95 Copynumber: 2.6 Consensus size: 96
2284657 AAAATTTCCT
*
2284667 TCATTGGGGATACTCCAACCCCATTATTC-GAGGGGATACTCCAACCCTGTTTTTAAAAATTATC
1 TCATTGGGGATACTCCAACCCCATTATTCTGAGGGGATACTCCAACCCCGTTTTTAAAAATTATC
2284731 AAGATTTAAACCTTAATTTTGCTTAAATTATCA
66 AAGA--TAAACCTTAATTTTGCTTAAATTATCA
* * * * * *
2284764 TCATTGGGGATACTCTATCCCCATTATTCTAAGGGGATACTCTAACCCCGTTTTT-AAACTTGTC
1 TCATTGGGGATACTCCAACCCCATTATTCTGAGGGGATACTCCAACCCCGTTTTTAAAAATTATC
*** *
2284828 AAGATAGTTCTTATTTTTGCTTAAATTATCA
66 AAGATAAACCTTAATTTTGCTTAAATTATCA
* ** * * *
2284859 TCGTCAGGGATACTCCAACCCCATT-TCTCTGAGGAGATACTCCAGCCCCATTTTT
1 TCATTGGGGATACTCCAACCCCATTAT-TCTGAGGGGATACTCCAACCCCGTTTTT
2284914 CAACCAAAAG
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 66 0.52
97 38 0.30
98 22 0.17
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (96 bp):
TCATTGGGGATACTCCAACCCCATTATTCTGAGGGGATACTCCAACCCCGTTTTTAAAAATTATC
AAGATAAACCTTAATTTTGCTTAAATTATCA
Found at i:2287815 original size:80 final size:79
Alignment explanation
Indices: 2287724--2287880 Score: 217
Period size: 80 Copynumber: 2.0 Consensus size: 79
2287714 CCTCATCTCT
* *
2287724 GAGAGGATACTCTAATCCTATTTTTACTTCTAAAACACAAAAATTTT-CATCTCAGGGGATGCTC
1 GAGAGGATACTCTAATCCCACTTTTACTTCTAAAACAC-AAAATTTTACATCT-AGGGGATGCTC
*
2287788 CAACCCTACCATTTTA
64 CAACCCCACCATTTTA
* * ** *
2287804 GAGAGGATACTCTAATCCCACTTTTACTTCTAGAACACCAAATTTTACATCTTTGGGATTCTCCA
1 GAGAGGATACTCTAATCCCACTTTTACTTCTAAAACACAAAATTTTACATCTAGGGGATGCTCCA
2287869 ACCCCACCATTT
66 ACCCCACCATTT
2287881 CTGAGGAGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 28 0.41
80 40 0.59
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (79 bp):
GAGAGGATACTCTAATCCCACTTTTACTTCTAAAACACAAAATTTTACATCTAGGGGATGCTCCA
ACCCCACCATTTTA
Found at i:2289242 original size:154 final size:155
Alignment explanation
Indices: 2288961--2289315 Score: 394
Period size: 154 Copynumber: 2.3 Consensus size: 155
2288951 TACTTAGAGG
* * * * * * * ***
2288961 CATTTTGGTAATTTTTCT-AGAACCGAGTCCTAAGCAATTATCGGGTCATTTTTATGCCAAAAAT
1 CATTTTCGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCATTGGGTTGCTTTTATGCCAAAAAT
** * *
2289025 ATGCTTTGAGGATAAGTTTGTCCTTTTATATCATTTTTGTGTCTTTTAGGGTTACTGAGATACTT
66 ATGCTTTGAGGATAAGTTCATCCTTTTATATCATTTTTGTGTCTTTCAAGGTTACTGAGATACTT
* * *
2289090 TAACATTAAAGGTATACCTTAAAGG-
131 TAACATCAAAAGTATACCCT-AAGGA
* * * * * **
2289115 TATTTTCGTAATTTTT-TTAAAATTGTGTCCTAGGTAATCATTGGGTTGCTTTTATGCTAAAGTT
1 CATTTTCGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCATTGGGTTGCTTTTATGCCAAAAAT
* * *
2289179 ATGCTTTTAGGATAGGTTCATCTTTTTATATCATTTTTGTGTCTTTCAAGGTTA-TCGAGATACT
66 ATGCTTTGAGGATAAGTTCATCCTTTTATATCATTTTTGTGTCTTTCAAGGTTACT-GAGATACT
*
2289243 TTTACATCAAAAGTATACCCTAAGGA
130 TTAACATCAAAAGTATACCCTAAGGA
* *
2289269 CATTTTGGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCTTTGGGT
1 CATTTTCGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCATTGGGT
2289316 ATGGTATTAG
Statistics
Matches: 164, Mismatches: 33, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
153 6 0.04
154 132 0.80
155 26 0.16
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (155 bp):
CATTTTCGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCATTGGGTTGCTTTTATGCCAAAAAT
ATGCTTTGAGGATAAGTTCATCCTTTTATATCATTTTTGTGTCTTTCAAGGTTACTGAGATACTT
TAACATCAAAAGTATACCCTAAGGA
Found at i:2289431 original size:137 final size:137
Alignment explanation
Indices: 2289185--2289438 Score: 339
Period size: 137 Copynumber: 1.9 Consensus size: 137
2289175 AGTTATGCTT
* * * *
2289185 TTAGGATAGGTTCATCTTTTTATATCATTTTTGTGTCTTTCAAGGTTATCGAGATACTTTTACAT
1 TTAGGATAGGTTCATCCTTTTACATAATTTTTGTGTCTTTCAAGGTTATCGAAATACTTTTACAT
* *
2289250 CAAAAGTATACCCTAAGGACATTTTGGTAATTTTTCTCAAAACTGAGTCCTAGGTAATCTTTGGG
66 CAAAAGTATACCCTAAGGACATTTTAGTAAGTTTTCTCAAAACTGAGTCCTAGGTAATCTTTGGG
2289315 TATGGTA
131 TATGGTA
* * *
2289322 TTAGGATAGGTTCATCCTTTTACATAATTTTTGTGTCTTTTAGGGTTATCGAAATA-TTTTCACG
1 TTAGGATAGGTTCATCCTTTTACATAATTTTTGTGTCTTTCAAGGTTATCGAAATACTTTT-ACA
* * ** ** * *
2289386 TCGAAAGTGTACTTTAAGGGTATTTTAGTAAGTTTTCTTAGAACTGAGTCCTA
65 TCAAAAGTATACCCTAAGGACATTTTAGTAAGTTTTCTCAAAACTGAGTCCTA
2289439 AGTAGTCACC
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
136 4 0.04
137 95 0.96
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (137 bp):
TTAGGATAGGTTCATCCTTTTACATAATTTTTGTGTCTTTCAAGGTTATCGAAATACTTTTACAT
CAAAAGTATACCCTAAGGACATTTTAGTAAGTTTTCTCAAAACTGAGTCCTAGGTAATCTTTGGG
TATGGTA
Found at i:2289569 original size:291 final size:290
Alignment explanation
Indices: 2289045--2289576 Score: 646
Period size: 291 Copynumber: 1.8 Consensus size: 290
2289035 GATAAGTTTG
* * * *
2289045 TCCTTTTATATCATTTTTGTGTCTTTTAGGGTTACTGAGATACTTTAACATTAAAGGTATACCTT
1 TCCTTTTACATAATTTTTGTGTCTTTTAGGGTTACTGAAATACTTTAACATGAAAGGTATACCTT
* * * * * ** * *
2289110 AAAGGTATTTTCGTAATTTTTTTAAAATTGTGTCCTAGGTAATCATTGGGTTGCTTTTATGCTAA
66 AAAGGTATTTTAGTAATTTTCTTAAAACTGAGTCCTAAGTAATCACCGGGATGCTTTTATGCCAA
* * * ***
2289175 AGTTATGCTTTTAGGATAGGTTCATCTTTTTATATCATTTTTGTGTCTTTCAAGGTTATCGAGAT
131 AGGTATACATTTAGGATAGGTTCATCTTTTTATATCATTTCCATGTCTTT-AAGGTTATCGAGAT
2289240 ACTTTTACATCAAAAGTATACCCTAAGGACATTTTGGTAATTTTTCTCAAAACTGAGTCCTAGGT
195 ACTTTTACATCAAAAGTATACCCTAAGGACATTTTGGTAATTTTTCTCAAAACTGAGTCCTAGGT
2289305 AATCTTTGGGTATGGTATTAGGATAGGTTCA
260 AATCTTTGGGTATGGTATTAGGATAGGTTCA
* * * * *
2289336 TCCTTTTACATAATTTTTGTGTCTTTTAGGGTTA-TCGAAATATTTTCACGTCGAAA-GTGTACT
1 TCCTTTTACATAATTTTTGTGTCTTTTAGGGTTACT-GAAATACTTTAACAT-GAAAGGTATACC
* * *
2289399 TTAAGGGTATTTTAGTAAGTTTTCTTAGAACTGAGTCCTAAGTAGTCACCGGGATGCTTTTATGC
64 TTAAAGGTATTTTAGTAA-TTTTCTTAAAACTGAGTCCTAAGTAATCACCGGGATGCTTTTATGC
* *
2289464 CAAAGGTGTACATTTAGGATGGGTTCATCTTTTTATAAT-ATTTACCATGTCTTT-AGTGTTA-C
128 CAAAGGTATACATTTAGGATAGGTTCATCTTTTTAT-ATCATTT-CCATGTCTTTAAG-GTTATC
* * *
2289526 -ATGATACTTTTACATCGAAGGTTTACCCTTAAGG-CATTTTGGTAATTTTTC
190 GA-GATACTTTTACATCAAAAGTATACCC-TAAGGACATTTTGGTAATTTTTC
2289577 CTAAAGCAGA
Statistics
Matches: 201, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
290 2 0.01
291 107 0.53
292 83 0.41
293 9 0.04
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (290 bp):
TCCTTTTACATAATTTTTGTGTCTTTTAGGGTTACTGAAATACTTTAACATGAAAGGTATACCTT
AAAGGTATTTTAGTAATTTTCTTAAAACTGAGTCCTAAGTAATCACCGGGATGCTTTTATGCCAA
AGGTATACATTTAGGATAGGTTCATCTTTTTATATCATTTCCATGTCTTTAAGGTTATCGAGATA
CTTTTACATCAAAAGTATACCCTAAGGACATTTTGGTAATTTTTCTCAAAACTGAGTCCTAGGTA
ATCTTTGGGTATGGTATTAGGATAGGTTCA
Found at i:2290138 original size:20 final size:21
Alignment explanation
Indices: 2290099--2290142 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2290089 TTAAGTATAG
2290099 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTTCAAG-ATAAAAATA
2290121 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTTCAAGATAAAAATA
2290141 AT
1 AT
2290143 TCAAAGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:2290372 original size:33 final size:31
Alignment explanation
Indices: 2290330--2290406 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 31
2290320 AAAACTCACT
* *
2290330 TTGTATCGATACAATGTATCAATACATGATGAA
1 TTGTATCGATACAATGTATCAATA-AAG-TAAA
*
2290363 TTGTATCGATATAATGTATCAATAAAGTAAA
1 TTGTATCGATACAATGTATCAATAAAGTAAA
2290394 TTGTATCGATACA
1 TTGTATCGATACA
2290407 TTGAGCCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 15 0.38
32 2 0.05
33 23 0.57
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (31 bp):
TTGTATCGATACAATGTATCAATAAAGTAAA
Found at i:2290922 original size:32 final size:36
Alignment explanation
Indices: 2290841--2290923 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
2290831 GTGATTGAGT
* **
2290841 GGTTCTGTCTTAGCCTTTGAAAAAGATAGGGAGAGA
1 GGTTCTATCTTAGCCCGTGAAAAAGATAGGGAGAGA
*
2290877 GGTTCTATGTTAGCCCGTG-AAAAGATA-GG-GA-A
1 GGTTCTATCTTAGCCCGTGAAAAAGATAGGGAGAGA
*
2290909 GTTTCTATCTTAGCC
1 GGTTCTATCTTAGCC
2290924 TTGAAAGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 14 0.34
33 2 0.05
34 2 0.05
35 8 0.20
36 15 0.37
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (36 bp):
GGTTCTATCTTAGCCCGTGAAAAAGATAGGGAGAGA
Found at i:2292472 original size:21 final size:21
Alignment explanation
Indices: 2292448--2292488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2292438 TAATACTCTT
*
2292448 GAAAAGAAAGTAAATGAGTTG
1 GAAAAGAAAATAAATGAGTTG
*
2292469 GAAAAGAAAATAAGTGAGTT
1 GAAAAGAAAATAAATGAGTT
2292489 ACAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAGTTG
Found at i:2292494 original size:21 final size:20
Alignment explanation
Indices: 2292449--2292510 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2292439 AATACTCTTG
* **
2292449 AAAAGAAAGTAAATGAGTTGG
1 AAAAGAAAAT-AATGAGTTAC
2292470 AAAAGAAAATAAGTGAGTTAC
1 AAAAGAAAATAA-TGAGTTAC
*
2292491 AAAATGAAAATGATGAGTTA
1 AAAA-GAAAATAATGAGTTA
2292511 ACTAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 26 0.74
22 7 0.20
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.21
Consensus pattern (20 bp):
AAAAGAAAATAATGAGTTAC
Found at i:2295594 original size:20 final size:21
Alignment explanation
Indices: 2295555--2295598 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2295545 TTAAGTATAG
2295555 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTTCAAG-ATAAAAATA
2295577 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTTCAAGATAAAAATA
2295597 AT
1 AT
2295599 TCAAAGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:2295817 original size:20 final size:20
Alignment explanation
Indices: 2295792--2295845 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2295782 AAAACTCACT
*
2295792 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATAAA
*
2295812 TTGTATCGATACATGGTAAA
1 TTGTATCGATACATGATAAA
*
2295832 TTGTATCTATACAT
1 TTGTATCGATACAT
2295846 TAGCCCAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATAAA
Found at i:2296289 original size:35 final size:36
Alignment explanation
Indices: 2296223--2296311 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 36
2296213 GTGATTGAGA
2296223 GGTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAAG
1 GGTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAAG
2296259 GGTTCTATCTTAG-CTTGTG-AAAAGATA-GG-G-AG
1 GGTTCTATCTTAGCCTT-TGAAAAAGATAGGGAGAAG
*
2296291 GTTTCTATCTTAGCC-TTGAAA
1 GGTTCTATCTTAGCCTTTGAAA
2296312 GATAGTATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
31 2 0.04
32 17 0.35
33 2 0.04
34 2 0.04
35 11 0.22
36 15 0.31
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (36 bp):
GGTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAAG
Found at i:2296302 original size:32 final size:31
Alignment explanation
Indices: 2296219--2296316 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 31
2296209 CTAAGTGATT
2296219 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGG
1 GAGAGGTTCTATCTTAG-CTTTG-AAAAGATA-G
2296253 GAGAAGGGTTCTATCTTAGCTTGTGAAAAGATAG
1 GAG-A-GGTTCTATCTTAGCTT-TGAAAAGATAG
*
2296287 G-GAGGTTTCTATCTTAGCCTTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCTTTGAAAAGATAG
2296317 TATTGTGAGG
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
30 8 0.14
31 4 0.07
32 14 0.24
33 1 0.02
34 5 0.08
35 12 0.20
36 15 0.25
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (31 bp):
GAGAGGTTCTATCTTAGCTTTGAAAAGATAG
Found at i:2297242 original size:35 final size:38
Alignment explanation
Indices: 2297188--2297258 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 38
2297178 ACCACCCAGT
* *
2297188 CCTAGGAAATAAGAGAATAT-T-AATAATGATATAGCC
1 CCTAGGAAATAAAAAAATATATAAATAATGATATAGCC
2297224 CCTA-GAAATAAAAAAATATATAAAATAATGATATA
1 CCTAGGAAATAAAAAAATATAT-AAATAATGATATA
2297259 TCAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 13 0.43
36 5 0.17
38 12 0.40
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.25
Consensus pattern (38 bp):
CCTAGGAAATAAAAAAATATATAAATAATGATATAGCC
Found at i:2299767 original size:16 final size:16
Alignment explanation
Indices: 2299720--2299769 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2299710 AGTCTTGGTG
*
2299720 TTCGCATTCATATGCA
1 TTCGCACTCATATGCA
* *
2299736 TTCGTAAC-CATGTGCA
1 TTCG-CACTCATATGCA
2299752 TTCGCACTCATATGCA
1 TTCGCACTCATATGCA
2299768 TT
1 TT
2299770 TTTACTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (16 bp):
TTCGCACTCATATGCA
Found at i:2300345 original size:112 final size:113
Alignment explanation
Indices: 2300208--2300445 Score: 325
Period size: 113 Copynumber: 2.1 Consensus size: 113
2300198 ATTTTACAAT
* * * * *
2300208 TTGTATTGATGCAAGAAGTGAATGTATCGATACATGTTTGAAATGTATTGA-TACAGGACCATGT
1 TTGTATCGATACAAAAAGTGAATGTATCGATACATGTCTGAAATGTATCGATTACAGGACCATGT
* * *
2300272 CGAGGCAAATTTCACATTTTGGAAAAAAAATATATCGATACATTTTTA
66 CGAGGCAAATCTCACATTCTGGAAAAAAAATATATCAATACATTTTTA
**
2300320 TTGTATCGATACAAAAAGTGAATGTATCGATACATGTCTGAAATGTATCGATTGTAGGACCATGT
1 TTGTATCGATACAAAAAGTGAATGTATCGATACATGTCTGAAATGTATCGATTACAGGACCATGT
* ** * * *
2300385 TGAGGCAAATCTCGTATTCTGGACAGAAAATGTATCAATACATTTTTA
66 CGAGGCAAATCTCACATTCTGGAAAAAAAATATATCAATACATTTTTA
2300433 TTGTATCGATACA
1 TTGTATCGATACA
2300446 TTCTGGGTTT
Statistics
Matches: 109, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
112 46 0.42
113 63 0.58
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (113 bp):
TTGTATCGATACAAAAAGTGAATGTATCGATACATGTCTGAAATGTATCGATTACAGGACCATGT
CGAGGCAAATCTCACATTCTGGAAAAAAAATATATCAATACATTTTTA
Found at i:2300535 original size:52 final size:51
Alignment explanation
Indices: 2300412--2300600 Score: 231
Period size: 52 Copynumber: 3.7 Consensus size: 51
2300402 TCTGGACAGA
* * * *
2300412 AAATGTATCAATACATTTTTATTGTATCGATACATTCTGGG--TTTGATCC
1 AAATGTATCGATACATTTTCATTGTATCAATACATTCTGGGTTTTTGACCC
2300461 AAATGTATCGATACACTTTTCATTGTATCAATAC-TATCTGGGTTTTTGACCC
1 AAATGTATCGATACA-TTTTCATTGTATCAATACAT-TCTGGGTTTTTGACCC
* * * *
2300513 AAATGTATTGATGCATTATTCATTATATCAATACATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATT-TTCATTGTATCAATACATTCTGGGTTTTTGACCC
* *
2300565 AAATGTATCGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATT-TTCATTGTATCAATACAT
2300601 CCAGTTAAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
49 15 0.12
50 22 0.18
51 2 0.02
52 80 0.67
53 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (51 bp):
AAATGTATCGATACATTTTCATTGTATCAATACATTCTGGGTTTTTGACCC
Found at i:2308697 original size:18 final size:18
Alignment explanation
Indices: 2308682--2308718 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2308672 ATGGTGCACC
2308682 TAGCAATCGAGGTGCAAA
1 TAGCAATCGAGGTGCAAA
2308700 TAGCAATCGAGGTGCAAA
1 TAGCAATCGAGGTGCAAA
2308718 T
1 T
2308719 CAACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (18 bp):
TAGCAATCGAGGTGCAAA
Found at i:2314555 original size:4 final size:4
Alignment explanation
Indices: 2314548--2314576 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2314538 AAAACAAAAA
2314548 AAAT AAAT AAAT AAA- AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2314577 GGGGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:2314563 original size:15 final size:15
Alignment explanation
Indices: 2314545--2314576 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2314535 GGTAAAACAA
2314545 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
2314560 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
2314575 AA
1 AA
2314577 GGGGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:2315908 original size:52 final size:52
Alignment explanation
Indices: 2315815--2316033 Score: 177
Period size: 52 Copynumber: 4.2 Consensus size: 52
2315805 TAAAAATTGC
* * * * * *
2315815 CATCTCTAAGTCCAATGTCGTTAGGCCTTAGATTAGCATGTTGGCACCTTTCT
1 CATCTTTAAGTCCAATGTTGCT-GGCCTTGGATTAGTATGTTGGCAACTTTCT
* * * *
2315868 CATCATTAAGCCCAATGTTGCTGGCCTTGGATTGGTATGTTGGCAATTTTCT
1 CATCTTTAAGTCCAATGTTGCTGGCCTTGGATTAGTATGTTGGCAACTTTCT
* * * * ** * *
2315920 CATCTTTAAGTCTAATGTCAGTTGGCCTTGGATCAGTACATTGGCATCTTTGT
1 CATCTTTAAGTCCAATGT-TGCTGGCCTTGGATTAGTATGTTGGCAACTTTCT
* * * * * * * * *
2315973 CATCTTTAAGTCCAATATTGCTAGCCTTGAATCAGCACGTTGGTATCTTTAT
1 CATCTTTAAGTCCAATGTTGCTGGCCTTGGATTAGTATGTTGGCAACTTTCT
2316025 CATCTTTAA
1 CATCTTTAA
2316034 AATCCAGCTT
Statistics
Matches: 133, Mismatches: 32, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
52 75 0.56
53 58 0.44
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (52 bp):
CATCTTTAAGTCCAATGTTGCTGGCCTTGGATTAGTATGTTGGCAACTTTCT
Found at i:2316015 original size:105 final size:105
Alignment explanation
Indices: 2315815--2316033 Score: 226
Period size: 105 Copynumber: 2.1 Consensus size: 105
2315805 TAAAAATTGC
* * **
2315815 CATCTCTAAGTCCAATGTCGTTAGGCCTTAGATTAGCATGTTGGCACCTTTCTCATCATTAAGCC
1 CATCTTTAAGTCCAATGTCGTTAGGCCTTAGATCAGCACATTGGCACCTTTCTCATCATTAAGCC
* * * ** * * *
2315880 CAATGTTGCTGGCCTTGGATTGGTATGTTGGCAAT-TTTCT
66 CAATATTGCTAGCCTTGAATCAGCACGTTGG-AATCTTTAT
* * * * * * *
2315920 CATCTTTAAGTCTAATGTCAGTT-GGCCTTGGATCAGTACATTGGCATCTTTGTCATCTTTAAGT
1 CATCTTTAAGTCCAATGTC-GTTAGGCCTTAGATCAGCACATTGGCACCTTTCTCATCATTAAGC
*
2315984 CCAATATTGCTAGCCTTGAATCAGCACGTTGGTATCTTTAT
65 CCAATATTGCTAGCCTTGAATCAGCACGTTGGAATCTTTAT
2316025 CATCTTTAA
1 CATCTTTAA
2316034 AATCCAGCTT
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
104 2 0.02
105 87 0.95
106 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (105 bp):
CATCTTTAAGTCCAATGTCGTTAGGCCTTAGATCAGCACATTGGCACCTTTCTCATCATTAAGCC
CAATATTGCTAGCCTTGAATCAGCACGTTGGAATCTTTAT
Found at i:2316814 original size:20 final size:20
Alignment explanation
Indices: 2316789--2316828 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2316779 CAATACAAAT
*
2316789 AGTGAATGTATGGATACATG
1 AGTGAATGTATCGATACATG
2316809 AGTGAATGTATCGATACATG
1 AGTGAATGTATCGATACATG
2316829 TCTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (20 bp):
AGTGAATGTATCGATACATG
Found at i:2319201 original size:50 final size:50
Alignment explanation
Indices: 2319130--2319224 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
2319120 ATTGGGTTAA
2319130 AAACCCAGAATGTATCAATACAAT-AAATAATGTACCGATACATTTAGGTC
1 AAACCCAGAATGTATCAATACAATGAAA-AATGTACCGATACATTTAGGTC
* *
2319180 AAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
1 AAACCCAGAATGTATCAATACAATGAAAAATGTACCGATACATTT
2319225 TCTTTTCAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 39 0.93
51 3 0.07
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (50 bp):
AAACCCAGAATGTATCAATACAATGAAAAATGTACCGATACATTTAGGTC
Found at i:2320074 original size:143 final size:139
Alignment explanation
Indices: 2319917--2320177 Score: 351
Period size: 143 Copynumber: 1.8 Consensus size: 139
2319907 GCTTTTATAA
* * * *
2319917 CTTTAAAAGAAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGGATAAAAGGGGTGCCACTAGCTT
1 CTTTAAAAGAAAAAGACGTAATGCTATTTGAGGACTGAAAAGGATAAAA--GGTGCCAC-AACTT
* * * * *
2319982 GTGTGGGCTTTAAAAAGAAAAAAGTGTCCTACTCTTTGAGAACTGAAAGGGATAAAAAGTGCCAA
63 ATGTAGGCTTTAAAAA-AAAAAAGCGTCCTACTCTTTGAGAACTAAAAGAGATAAAAAGTGCCAA
2320047 CAACTTGCGTAGG
127 CAACTTGCGTAGG
* * * *
2320060 CTTTAAAAGAAAAAGACGTAATGCTATTTGATGACTGAAAGGGATAAAATGTGCCACAATTTATG
1 CTTTAAAAGAAAAAGACGTAATGCTATTTGAGGACTGAAAAGGATAAAAGGTGCCACAACTTATG
* *
2320125 TAGGCTTTAAAAAAGAAAAGCGTCCTACTCTTTGAGGACTAAAAGAGATAAAA
66 TAGGCTTTAAAAAAAAAAAGCGTCCTACTCTTTGAGAACTAAAAGAGATAAAA
2320178 GGGGTACCAC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
139 35 0.34
140 17 0.17
141 7 0.07
143 44 0.43
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.24
Consensus pattern (139 bp):
CTTTAAAAGAAAAAGACGTAATGCTATTTGAGGACTGAAAAGGATAAAAGGTGCCACAACTTATG
TAGGCTTTAAAAAAAAAAAGCGTCCTACTCTTTGAGAACTAAAAGAGATAAAAAGTGCCAACAAC
TTGCGTAGG
Found at i:2320097 original size:70 final size:68
Alignment explanation
Indices: 2319871--2320177 Score: 246
Period size: 69 Copynumber: 4.4 Consensus size: 68
2319861 AAATGAGTCC
* * * * * *
2319871 TGCTCTTTGAGGAC-AAAAGGGAT-AAAAGTGCCACCAGCTTTTATA-ACTTTAAAAGAAAAAGG
1 TGCTCTTTGA-GACTGAAAGGGATAAAAAGTGCCA-CAACTTGTGTAGGCTTTAAAAGAAAAAGA
2319933 CGTCA
64 CGTCA
* * * *
2319938 TGCTCTTTGAGGACTGAAAAGGATAAAAGGGGTGCCACTAGCTTGTGTGGGCTTTAAAAAGAAAA
1 TGCTCTTTGA-GACTGAAAGGGATAAAA--AGTGCCAC-AACTTGTGTAGGCTTT-AAAAGAAAA
* *
2320003 A-AGTGTCC
61 AGA-CGTCA
* *
2320011 TACTCTTTGAGAACTGAAAGGGATAAAAAGTGCCAACAACTTGCGTAGGCTTTAAAAGAAAAAGA
1 TGCTCTTTGAG-ACTGAAAGGGATAAAAAGTGCC-ACAACTTGTGTAGGCTTTAAAAGAAAAAGA
*
2320076 CGTAA
64 CGTCA
* * * * *
2320081 TGCTATTTGATGACTGAAAGGGATAAAATGTGCCACAATTTATGTAGGCTTTAAAAAAGAAAAG-
1 TGCTCTTTGA-GACTGAAAGGGATAAAAAGTGCCACAACTTGTGTAGGCTTTAAAAGA-AAAAGA
*
2320145 CGTCC
64 CGTCA
* * *
2320150 TACTCTTTGAGGACTAAAAGAGATAAAA
1 TGCTCTTTGA-GACTGAAAGGGATAAAA
2320178 GGGGTACCAC
Statistics
Matches: 194, Mismatches: 33, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
67 14 0.07
68 7 0.04
69 49 0.25
70 47 0.24
71 33 0.17
72 7 0.04
73 37 0.19
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (68 bp):
TGCTCTTTGAGACTGAAAGGGATAAAAAGTGCCACAACTTGTGTAGGCTTTAAAAGAAAAAGACG
TCA
Found at i:2320273 original size:68 final size:66
Alignment explanation
Indices: 2320150--2320312 Score: 202
Period size: 65 Copynumber: 2.4 Consensus size: 66
2320140 AAAAGCGTCC
* *
2320150 TACTCTTTGAGGACTAAAAGAGATAAAAGGGGTACCACCAGCTTATGTGGGCTTTGGAAAAAAGA
1 TACTCTTTGAGGACTAAAAAAG-TAAAA-GGGTACCACCAGCTTATGTGGACTTT-G-AAAAA-A
2320215 ATGCCT
61 ATGCCT
* * *
2320221 TACTCTTTGAGGACTAAAAAAGTAAAA-GGTGCCACCAGCTTGTGTGGACTTTGAAAAAAATGTC
1 TACTCTTTGAGGACTAAAAAAGTAAAAGGGTACCACCAGCTTATGTGGACTTTGAAAAAAATGCC
2320285 T
66 T
* * *
2320286 TACTCTTTAAGGACTGAAAAGGTAAAA
1 TACTCTTTGAGGACTAAAAAAGTAAAA
2320313 ATGCCTTCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 30 0.36
66 5 0.06
67 1 0.01
68 22 0.26
70 5 0.06
71 21 0.25
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (66 bp):
TACTCTTTGAGGACTAAAAAAGTAAAAGGGTACCACCAGCTTATGTGGACTTTGAAAAAAATGCC
T
Found at i:2323322 original size:155 final size:155
Alignment explanation
Indices: 2323035--2323332 Score: 526
Period size: 155 Copynumber: 1.9 Consensus size: 155
2323025 ACATGTTCAC
* * *
2323035 CCTCTTTTAATGATTTGGCAATCATATCATCCATGTACACCTCTATTTCCATGTGCATTAGGTCA
1 CCTCCTTTAATGATTTGACAATCATATCATCCATGTACACCTCTATTTCCATGTGCATGAGGTCA
2323100 TGGAACAACATTAGCCCTCTGATAGGTTACCCTAGCATTTTTTAGCCTGAAAGGCATCACCTTGT
66 TGGAACAACATTAGCCCTCTGATAGGTTACCCTAGCATTTTTTAGCCTGAAAGGCATCACCTTGT
2323165 AATAGAAAGTGCCTGAAAGGCATCA
131 AATAGAAAGTGCCTGAAAGGCATCA
*
2323190 CCTCCTTTAATGATTTGACAATCATATCATCCATGTACACCTCTATTTTCATGTGCATGAGGTCA
1 CCTCCTTTAATGATTTGACAATCATATCATCCATGTACACCTCTATTTCCATGTGCATGAGGTCA
* *
2323255 TGGAACAACGTTAGCCCTCTGATAGGTTACCCTAGCATTTTTTAG-CTCGAAAGGCATTACCTTG
66 TGGAACAACATTAGCCCTCTGATAGGTTACCCTAGCATTTTTTAGCCT-GAAAGGCATCACCTTG
2323319 TAATAGAAAGTGCC
130 TAATAGAAAGTGCC
2323333 CCACATGGTT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
154 2 0.01
155 134 0.99
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (155 bp):
CCTCCTTTAATGATTTGACAATCATATCATCCATGTACACCTCTATTTCCATGTGCATGAGGTCA
TGGAACAACATTAGCCCTCTGATAGGTTACCCTAGCATTTTTTAGCCTGAAAGGCATCACCTTGT
AATAGAAAGTGCCTGAAAGGCATCA
Found at i:2332559 original size:81 final size:80
Alignment explanation
Indices: 2332446--2332623 Score: 232
Period size: 80 Copynumber: 2.2 Consensus size: 80
2332436 AAAAGAACCG
* * * * * * *
2332446 GGGTTGGAGTATCCCCTCGAAAATGGTGAGGTTGGAGTATCTCTAAAGATTGACAATTTGATGTT
1 GGGTTGGAGTATCCCCTCCAAAATGGTAAGGTTGGAGTAAC-CCAAAGATGGAAAATTCGATGTT
2332511 TTTAGAAGTAAAAAC-
65 TTTAGAAGTAAAAACA
*
2332526 GAGGTTGGAGTATCCCCTCCAAAATGGTAAGGTTGGAGTAACCCAATGATGGAAAATTCGATGTT
1 G-GGTTGGAGTATCCCCTCCAAAATGGTAAGGTTGGAGTAACCCAAAGATGGAAAATTCGATGTT
* *
2332591 TTTGGAAGTAAAGACA
65 TTTAGAAGTAAAAACA
*
2332607 GGGTTGGAGTATTCCCT
1 GGGTTGGAGTATCCCCT
2332624 TTTATTGTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 47 0.55
81 38 0.45
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (80 bp):
GGGTTGGAGTATCCCCTCCAAAATGGTAAGGTTGGAGTAACCCAAAGATGGAAAATTCGATGTTT
TTAGAAGTAAAAACA
Found at i:2334951 original size:52 final size:50
Alignment explanation
Indices: 2334887--2334999 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 50
2334877 AATAGCTTGC
* * *
2334887 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
1 ATGTATCGATACAATAAAGAATGTATCAATACATTTGGGTC--AAACCCAGA
* *
2334939 ATGTATCGATACAATAAATAATGTATCAATACATTTGGGTCAAACCTAGA
1 ATGTATCGATACAATAAAGAATGTATCAATACATTTGGGTCAAACCCAGA
*
2334989 ATTTATCGATA
1 ATGTATCGATA
2335000 TATTTTCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 18 0.33
52 37 0.67
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACAATAAAGAATGTATCAATACATTTGGGTCAAACCCAGA
Found at i:2336556 original size:23 final size:22
Alignment explanation
Indices: 2336529--2336583 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2336519 AGAAACATAA
2336529 TTTTAATTAT-ATAATATAAATAT
1 TTTTAATTATAATAA-ATAAA-AT
* * *
2336552 TTTTATTTTTAATAAATACAAT
1 TTTTAATTATAATAAATAAAAT
2336574 TTTTAATTAT
1 TTTTAATTAT
2336584 TATTTAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 10 0.38
23 12 0.46
24 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAATTATAATAAATAAAAT
Found at i:2336595 original size:29 final size:29
Alignment explanation
Indices: 2336563--2336754 Score: 144
Period size: 29 Copynumber: 6.5 Consensus size: 29
2336553 TTTATTTTTA
* *
2336563 ATAAATACAATTTTTAATTATTATTTAAC
1 ATAAATATAATTTTTAATTATTATTTAAT
2336592 ATAAA-ATATATTTTTAATT-TATATTTTAAT
1 ATAAATATA-ATTTTTAATTAT-TA-TTTAAT
* * * *
2336622 ATAAATGTAA-TTGTAATAATTCTCTTAAT
1 ATAAATATAATTTTTAATTATTAT-TTAAT
* * * *
2336651 ATAAATATGACTTTTAATTACTATTTAAC
1 ATAAATATAATTTTTAATTATTATTTAAT
2336680 ATAAATATGAATTTATTTATATTTTATTATTTAAT
1 ATAAATAT-AA-TT-TTTA-A--TTATTATTTAAT
*
2336715 ATAACTATAA-TTTTAATT-TT-TTTAAT
1 ATAAATATAATTTTTAATTATTATTTAAT
*
2336741 ATAAATGTAATTTT
1 ATAAATATAATTTT
2336755 AGTAATTTTT
Statistics
Matches: 129, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
26 14 0.11
27 5 0.04
28 6 0.05
29 49 0.38
30 23 0.18
31 7 0.05
32 5 0.04
33 1 0.01
34 2 0.02
35 17 0.13
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (29 bp):
ATAAATATAATTTTTAATTATTATTTAAT
Found at i:2336728 original size:24 final size:25
Alignment explanation
Indices: 2336700--2336755 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
2336690 ATTTATTTAT
*
2336700 ATTTTA-TTATTTAATATAACTATA
1 ATTTTATTTATTTAATATAAATATA
* *
2336724 ATTTTAATTTTTTTAATATAAATGTA
1 ATTTT-ATTTATTTAATATAAATATA
2336750 ATTTTA
1 ATTTTA
2336756 GTAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 2 0.07
26 20 0.74
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATTTATTTAATATAAATATA
Found at i:2336763 original size:26 final size:27
Alignment explanation
Indices: 2336709--2336768 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
2336699 TATTTTATTA
* *
2336709 TTTAATATAACTATAATTTTAAT-TTT
1 TTTAATATAAATATAATTTTAATAATT
* *
2336735 TTTAATATAAATGTAATTTTAGTAATT
1 TTTAATATAAATATAATTTTAATAATT
2336762 TTTAATA
1 TTTAATA
2336769 ATTATTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTAATATAAATATAATTTTAATAATT
Found at i:2336765 original size:99 final size:97
Alignment explanation
Indices: 2336662--2336840 Score: 254
Period size: 97 Copynumber: 1.8 Consensus size: 97
2336652 TAAATATGAC
* * * *
2336662 TTTTAATTACTATTTAACATAAATATGAATTTATTTATATTTTATTATTTAATATAACTAT-AAT
1 TTTTAATAACTATTCAACATAAATAT-AATTT-TTTATACTTT-TTATTTAATATAAATATAAAT
2336726 TTTAATT-TTTTTAATATAAATGTAATTTTAGTAAT
63 TTTAATTATTTTT-ATATAAATGTAATTTTAGTAAT
* *
2336761 TTTTAATAATTATTCAACATAACTATAATTTTTTATACTTTTTATTTAATATAAATATAAATTTT
1 TTTTAATAACTATTCAACATAAATATAATTTTTTATACTTTTTATTTAATATAAATATAAATTTT
2336826 AATTATTTTTATATA
66 AATTATTTTTATATA
2336841 CATATAGACA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
96 16 0.22
97 24 0.33
98 10 0.14
99 22 0.31
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (97 bp):
TTTTAATAACTATTCAACATAAATATAATTTTTTATACTTTTTATTTAATATAAATATAAATTTT
AATTATTTTTATATAAATGTAATTTTAGTAAT
Found at i:2340020 original size:43 final size:43
Alignment explanation
Indices: 2339972--2340057 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2339962 ATCCAATGAA
*
2339972 AATTCAAAGGTCTAGAATCCACATTCTAAATCTAAAAATTGGG
1 AATTCAAAGATCTAGAATCCACATTCTAAATCTAAAAATTGGG
2340015 AATTCAAAGATCTAGAATCCACATTCTAAATCTAAAAATTGGG
1 AATTCAAAGATCTAGAATCCACATTCTAAATCTAAAAATTGGG
2340058 GACATTTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (43 bp):
AATTCAAAGATCTAGAATCCACATTCTAAATCTAAAAATTGGG
Found at i:2343465 original size:72 final size:73
Alignment explanation
Indices: 2343332--2343467 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 73
2343322 GATGAATGTT
* * * **
2343332 ATGAACTTTCAATATTCATGAATCATGTATATACATGAATGTTATTATGTACATTACTGAATTAC
1 ATGAACTTTCAATATTCACGAATCATGAATATACATGAATGGTATTAAATACATTACTGAATTAC
2343397 GTAAATTC
66 GTAAATTC
* *
2343405 ATGAA-TTTGAATATTCACGAA-CTATGAATATACATGAATGGTATTAAATATATT-CATGAATT
1 ATGAACTTTCAATATTCACGAATC-ATGAATATACATGAATGGTATTAAATACATTAC-TGAATT
2343467 A
64 A
2343468 TATATGTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
71 2 0.04
72 47 0.87
73 5 0.09
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (73 bp):
ATGAACTTTCAATATTCACGAATCATGAATATACATGAATGGTATTAAATACATTACTGAATTAC
GTAAATTC
Found at i:2343481 original size:72 final size:72
Alignment explanation
Indices: 2343330--2343487 Score: 158
Period size: 72 Copynumber: 2.2 Consensus size: 72
2343320 TTGATGAATG
* * * * **
2343330 TTATGAACTTTCAATATTCATGAATCATGTATATACATGAATGTTATTATGTACATTACTGAATT
1 TTATGAA-TTTGAATATTCACGAATCATGAATATACATGAATGGTATTAAATACATTACTGAATT
*
2343395 ACGTAAAT
65 ACATAAAT
* *
2343403 TCATGAATTTGAATATTCACGAA-CTATGAATATACATGAATGGTATTAAATATATT-CATGAAT
1 TTATGAATTTGAATATTCACGAATC-ATGAATATACATGAATGGTATTAAATACATTAC-TGAAT
* **
2343466 TATATATGT
64 TACATAAAT
*
2343475 TTATGAATCTGAA
1 TTATGAATTTGAA
2343488 CATTTATCAT
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
71 2 0.03
72 61 0.88
73 6 0.09
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (72 bp):
TTATGAATTTGAATATTCACGAATCATGAATATACATGAATGGTATTAAATACATTACTGAATTA
CATAAAT
Found at i:2349529 original size:20 final size:19
Alignment explanation
Indices: 2349504--2349618 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 19
2349494 ATTTAACTAG
2349504 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAA-A
* *
2349524 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGA-AA
*
2349544 ATGTATCGATACATTAAAA
1 ATGTATCGATACATTGAAA
**
2349563 GATGTATCGATACATCTGGGTA
1 -ATGTATCGATACAT-T-GAAA
*
2349585 ATGTATCGATACATTTTAAA
1 ATGTATCGATACA-TTGAAA
2349605 ATGTATCGATACAT
1 ATGTATCGATACAT
2349619 CTGGTTAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
19 2 0.03
20 60 0.75
21 16 0.20
22 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:2349598 original size:41 final size:41
Alignment explanation
Indices: 2349504--2349622 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 41
2349494 ATTTAACTAG
* *
2349504 ATGTATCGATACATTGAAGAATGTATCGATACAT-T-CATAC
1 ATGTATCGATACATTAAAG-ATGTATCGATACATCTGGATAC
*
2349544 ATGTATCGATACATTAAAAGATGTATCGATACATCTGGGTA-
1 ATGTATCGATACATT-AAAGATGTATCGATACATCTGGATAC
2349585 ATGTATCGATACATTTTAAA-ATGTATCGATACATCTGG
1 ATGTATCGATACA--TTAAAGATGTATCGATACATCTGG
2349623 TTAAAAAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
40 29 0.41
41 35 0.49
42 5 0.07
43 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (41 bp):
ATGTATCGATACATTAAAGATGTATCGATACATCTGGATAC
Found at i:2350508 original size:28 final size:29
Alignment explanation
Indices: 2350386--2350828 Score: 375
Period size: 28 Copynumber: 15.7 Consensus size: 29
2350376 CCACCACTTG
* *
2350386 TGTGGGCTTTAGAGAA-AGTTGCCACCGACTT
1 TGTGGGCTTT-GA-AAGAGATGCCACTGAC-T
* *
2350417 GTGTGGGCTTTAAAAG-GATGCCACTAACT
1 -TGTGGGCTTTGAAAGAGATGCCACTGACT
* * * * *
2350446 TATGTGTTTTGAGA-AG-TGCCTCTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* ** *
2350473 TATGGGCTTT-AAAGAGATGTAATTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
*
2350501 TGTGGGCTTT-AAA-ATGATGCCACTAACT
1 TGTGGGCTTTGAAAGA-GATGCCACTGACT
* *
2350529 CGTGGGCTTTGGAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* *
2350557 TGTGAGCTTTG-AAGAGATGCCACTGAGT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* ** *
2350585 TATTAGCTTTGAAAG-GATGCCATTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * *
2350613 CGTGGGCTTTGAAAAAG-TGCCACAGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * * *
2350641 TATGGGCTATGAAA-AGTTGCCACAGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
*
2350669 TGTGGGCTTTGAAA-AGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGA-GATGCCACTGACT
* * *
2350698 TGTTGGCTTTGAAAG-GATGTCATTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
2350726 TGTGGGCTTT-ATAAG-GATGCCACTGACT
1 TGTGGGCTTTGA-AAGAGATGCCACTGACT
*
2350754 TATGGGCTTTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
2350782 TGTGGGCTTTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
*
2350810 TATGGGCTTTG-AAGAGATG
1 TGTGGGCTTTGAAAGAGATG
2350829 AGCGTTCTAG
Statistics
Matches: 338, Mismatches: 57, Indels: 36
0.78 0.13 0.08
Matches are distributed among these distances:
26 2 0.01
27 29 0.09
28 253 0.75
29 32 0.09
30 11 0.03
31 1 0.00
32 10 0.03
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAGAGATGCCACTGACT
Found at i:2350566 original size:56 final size:57
Alignment explanation
Indices: 2350420--2350822 Score: 435
Period size: 56 Copynumber: 7.2 Consensus size: 57
2350410 CCGACTTGTG
* * * * * * *
2350420 TGGGCTTTAAAAGGATGCCACTAACTTATGTGTTTTGAGAA-G-TGCCTCTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
** * * * **
2350475 TGGGCTTT-AAAGAGATGTAATTGACTTGTGGGCTTT-AAAATGATGCCACTAACTCG
1 TGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
* * * *
2350531 TGGGCTTTGGAAGGATGCCACTGACTTGTGAGCTTTGAAGA-GATGCCACTGAGTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
** * * * *
2350587 TTAGCTTTGAAAGGATGCCATTGACTCGTGGGCTTTGAAAAAG-TGCCACAGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
* * * * * *
2350643 TGGGCTATGAAAAGTTGCCACAGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
* * * *
2350700 TTGGCTTTGAAAGGATGTCATTGACTTGTGGGCTTT-ATAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
2350756 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
2350812 TGGGCTTTGAA
1 TGGGCTTTGAA
2350823 GAGATGAGCG
Statistics
Matches: 284, Mismatches: 56, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
54 7 0.02
55 25 0.09
56 205 0.72
57 47 0.17
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (57 bp):
TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTA
Found at i:2350604 original size:84 final size:84
Alignment explanation
Indices: 2350420--2350828 Score: 421
Period size: 84 Copynumber: 4.9 Consensus size: 84
2350410 CCGACTTGTG
* * ** * * *
2350420 TGGGCTTTAAAAGGATGCCACTAACTTATGTGTTTTGAGAA-G-TGCCTCTGACTTATGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGA-AAGGATGCCACTGACTTATGGGCTTT
* ** * *
2350483 AAAGAGATGTAATTGACTTG
65 GAAGAGATGCCACTGACTTA
* * * * * *
2350503 TGGGCTTTAAAATGATGCCACTAACTCGTGGGCTTTGGAAGGATGCCACTGACTTGTGAGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTG
*
2350568 AAGAGATGCCACTGAGTTA
66 AAGAGATGCCACTGACTTA
** * * * *
2350587 TTAGCTTTGAAAGGATGCCATTGACTCGTGGGCTTTGAAA-AAGTGCCACAGACTTATGGGCTAT
1 TGGGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTATGGGCTTT
* * * *
2350651 GAAAAGTTGCCACAGACTTG
65 GAAGAGATGCCACTGACTTA
* * * * * *
2350671 TGGGCTTTGAAAAGGGTGCCACTGACTTGTTGGCTTTGAAAGGATGTCATTGACTTGTGGGCTTT
1 TGGGCTTTG-AAAGGATGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTT
*
2350736 ATAAG-GATGCCACTGACTTA
65 -GAAGAGATGCCACTGACTTA
*
2350756 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTG
2350821 AAGAGATG
66 AAGAGATG
2350829 AGCGTTCTAG
Statistics
Matches: 264, Mismatches: 55, Indels: 13
0.80 0.17 0.04
Matches are distributed among these distances:
82 2 0.01
83 37 0.14
84 158 0.60
85 64 0.24
86 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (84 bp):
TGGGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTG
AAGAGATGCCACTGACTTA
Found at i:2350753 original size:141 final size:141
Alignment explanation
Indices: 2350433--2350822 Score: 359
Period size: 141 Copynumber: 2.8 Consensus size: 141
2350423 GCTTTAAAAG
* * * * * **
2350433 GATGCCACTAACTTATGTGTTTTGAGAA-G-TGCCTCTGACTTATGGGCTTT-AAAGAGATGTAA
1 GATGCCACTGACTTATGAGCTTTGA-AAGGATGCCACTGACTCATGGGCTTTGAAA-AGATGCCA
** * * * *
2350495 TTGACTTGTGGGCT-TTAAAATGATGCCACTA-ACTCGTGGGCTTTG-GAAGGATGCCACTGACT
64 CAGACTTATGGGCTATGAAAA-GATGCCAC-AGACTTGTGGGCTTTGAAAAGGATGCCACTGACT
2350557 TGTGAGCTTTGAAGA
127 TGTGAGCTTTGAAGA
* * * *
2350572 GATGCCACTGAGTTATTAGCTTTGAAAGGATGCCATTGACTCGTGGGCTTTGAAAA-AGTGCCAC
1 GATGCCACTGACTTATGAGCTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAAGA-TGCCAC
* *
2350636 AGACTTATGGGCTATGAAAAGTTGCCACAGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGT
65 AGACTTATGGGCTATGAAAAGATGCCACAGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG-
2350701 TG-GCTTTGAA-A
129 TGAGCTTTGAAGA
* * * * * *
2350712 GGATGTCATTGACTTGTGGGCTTT-ATAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCA
1 -GATGCCACTGACTTATGAGCTTTGA-AAGGATGCCACTGACTCATGGGCTTTGAAAAGATGCCA
* * * * * *
2350776 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAA
64 CAGACTTATGGGCTATGAAAAGATGCCACAGACTTGTGGGCTTTGAA
2350823 GAGATGAGCG
Statistics
Matches: 204, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
138 2 0.01
139 23 0.11
140 54 0.26
141 122 0.60
142 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (141 bp):
GATGCCACTGACTTATGAGCTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAAGATGCCACA
GACTTATGGGCTATGAAAAGATGCCACAGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTG
AGCTTTGAAGA
Found at i:2352072 original size:1 final size:1
Alignment explanation
Indices: 2352066--2352155 Score: 81
Period size: 1 Copynumber: 90.0 Consensus size: 1
2352056 TCTAGACCCC
* * * * * * * *
2352066 TTTTTTTTTTTTTTTGTCTTTTTTGTGTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2352131 TTTTGTTGTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2352156 GTACGAAAGA
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:2352080 original size:9 final size:9
Alignment explanation
Indices: 2352066--2352157 Score: 134
Period size: 9 Copynumber: 10.0 Consensus size: 9
2352056 TCTAGACCCC
2352066 TTTTTTT-T
1 TTTTTTTGT
2352074 TTTTTTTGT
1 TTTTTTTGT
2352083 CTTTTTTGTGT
1 -TTTTTT-TGT
2352094 TTTTTTTGT
1 TTTTTTTGT
2352103 TTTTTTTGT
1 TTTTTTTGT
2352112 TTTTTTTGT
1 TTTTTTTGT
2352121 TTTTTTTGT
1 TTTTTTTGT
2352130 TTTTTGTTGT
1 TTTTT-TTGT
2352140 TTTTTTCT-T
1 TTTTTT-TGT
2352149 TTTTTTTGT
1 TTTTTTTGT
2352158 ACGAAAGATG
Statistics
Matches: 78, Mismatches: 0, Indels: 11
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.10
9 45 0.58
10 22 0.28
11 3 0.04
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:2352096 original size:27 final size:25
Alignment explanation
Indices: 2352066--2352155 Score: 110
Period size: 25 Copynumber: 3.5 Consensus size: 25
2352056 TCTAGACCCC
2352066 TTTTTTTTTTTTTTTGTCTTTTTTGTG
1 TTTTTTTTTTTTTTTGT-TTTTTT-TG
2352093 TTTTTTTTGTTTTTTTTGTTTTTTTTG
1 -TTTTTTT-TTTTTTTTGTTTTTTTTG
* *
2352120 TTTTTTTTGTTTTTTGTTGTTTTT-
1 TTTTTTTTTTTTTTTGTTTTTTTTG
*
2352144 TTCTTTTTTTTT
1 TTTTTTTTTTTT
2352156 GTACGAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.18
25 15 0.26
26 7 0.12
27 2 0.04
28 13 0.23
29 10 0.18
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTGTTTTTTTTG
Found at i:2361066 original size:16 final size:17
Alignment explanation
Indices: 2361035--2361069 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2361025 CTATTCATAT
*
2361035 ATATTCATAGTTCATGA
1 ATATTCATAATTCATGA
2361052 ATATTCA-AATTCATGA
1 ATATTCATAATTCATGA
2361068 AT
1 AT
2361070 TCATATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
ATATTCATAATTCATGA
Found at i:2365714 original size:28 final size:29
Alignment explanation
Indices: 2365677--2365734 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
2365667 CCTCAAATGC
2365677 CTTTTATTTTCATTTTTCTT-TTATTTCTT
1 CTTTTATTTTC-TTTTTCTTCTTATTTCTT
*
2365706 CTTTT-TTTTCTTTTTTTTCTTATTTCTT
1 CTTTTATTTTCTTTTTCTTCTTATTTCTT
2365734 C
1 C
2365735 CATTTCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 15 0.56
29 5 0.19
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (29 bp):
CTTTTATTTTCTTTTTCTTCTTATTTCTT
Found at i:2365719 original size:38 final size:38
Alignment explanation
Indices: 2365677--2365763 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
2365667 CCTCAAATGC
** *
2365677 CTTTTATTTTCATT-TTTCTTTTATTT-CTTCTTTTTTTT
1 CTTTT-TTTTC-TTATTTCTTCCATTTCCTTCTTTTCTTT
2365715 CTTTTTTTTCTTATTTCTTCCATTTCCTTCTTTTCTTT
1 CTTTTTTTTCTTATTTCTTCCATTTCCTTCTTTTCTTT
*
2365753 CTCTTCTTTTC
1 CT-TTTTTTTC
2365764 CTCTCATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.05
37 15 0.36
38 18 0.43
39 7 0.17
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (38 bp):
CTTTTTTTTCTTATTTCTTCCATTTCCTTCTTTTCTTT
Found at i:2369405 original size:20 final size:20
Alignment explanation
Indices: 2369329--2369407 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
2369319 CAAAACTCAG
* * *
2369329 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTTAAA
*
2369349 AATGTATCGATACAATTGTAAG
1 AATGTATCGATAC-ATT-TAAA
* **
2369371 CATGTATCGATACATTTACT
1 AATGTATCGATACATTTAAA
2369391 AATGTATCGATACATTT
1 AATGTATCGATACATTT
2369408 CCTTGGCAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 31 0.63
21 5 0.10
22 13 0.27
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTTAAA
Found at i:2370304 original size:61 final size:60
Alignment explanation
Indices: 2370147--2370311 Score: 165
Period size: 61 Copynumber: 2.7 Consensus size: 60
2370137 AGATGAGTGC
* * * * * * *
2370147 CAATATGGTGATTCAAGGTCAGCGACATT-GGACTTAAGGATGCGAAGAATGATAAAGGTG
1 CAATATGCTAATTCAAGGTCAGCGATATTAGG-CTTAAAGATGAGAAGAATAAGAAAGGTG
* *
2370207 CTAATATGCTAATTCACA-GTCAACAATA-TAGAGCTTAAAGATGAGAAGAATAAGAAAGGTG
1 C-AATATGCTAATTCA-AGGTCAGCGATATTAG-GCTTAAAGATGAGAAGAATAAGAAAGGTG
* *
2370268 ACAATATGCTAATTCAAGGCCAGGGATATTAGGCTTAAAGATGA
1 -CAATATGCTAATTCAAGGTCAGCGATATTAGGCTTAAAGATGA
2370312 CAAAGGTGCT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
60 3 0.04
61 76 0.89
62 6 0.07
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (60 bp):
CAATATGCTAATTCAAGGTCAGCGATATTAGGCTTAAAGATGAGAAGAATAAGAAAGGTG
Found at i:2370339 original size:52 final size:51
Alignment explanation
Indices: 2370261--2370417 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 51
2370251 GAAGAATAAG
* * ** * *
2370261 AAAGGTGACAATATGCTAATTCAAGGCCAGGGATATTAGG-CTTAA-AGATGAC
1 AAAGGTG-CAATGTGCTGATTCAAGGCCAGCAATATT-GGACTTAAGA-AAGAA
2370313 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAAGAAAGAA
1 AAAGGTGC-AATGTGCTGATTCAAGGCCAGCAATATTGGACTTAAGAAAGAA
* *
2370365 AAAGGTGCCAATGTGCTGATTCAAGGCCAAG-AACATTGTACTTAAGAAAGAA
1 AAAGGTG-CAATGTGCTGATTCAAGGCC-AGCAATATTGGACTTAAGAAAGAA
2370417 A
1 A
2370418 TGGTTTGACA
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
51 3 0.03
52 85 0.92
53 4 0.04
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (51 bp):
AAAGGTGCAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAAGAAAGAA
Found at i:2370521 original size:32 final size:30
Alignment explanation
Indices: 2370477--2370827 Score: 299
Period size: 32 Copynumber: 11.0 Consensus size: 30
2370467 TAGAAGGAGA
2370477 TGCCACTAACTTGTGTGGGCTTTTGAAAAGGT
1 TGCCAC-AACTTGTGTGGGC-TTTGAAAAGGT
* * *
2370509 TTCCACTGACTTGTGTGGGCTTTTGAAGAGGT
1 TGCCAC-AACTTGTGTGGGC-TTTGAAAAGGT
* * *
2370541 TCCCACCAGCTTGTGTGGGCTTTAAAAAGGGT
1 TGCCA-CAACTTGTGTGGGCTTTGAAAA-GGT
2370573 TGCCACTAACTTGTGTGGGCTTTGAAGAA-GT
1 TGCCAC-AACTTGTGTGGGCTTTGAA-AAGGT
* * *
2370604 TGCCACCAGCTTATGTGGGCTTTGAAAAAGT
1 TGCCA-CAACTTGTGTGGGCTTTGAAAAGGT
* *
2370635 TGCCACCAGCTTGTGTGGGCTTTAGAAAGGGT
1 TGCCA-CAACTTGTGTGGGCTTT-GAAAAGGT
* *
2370667 TGCCACCAACTTGTATGGGCTTTGAAGAAGAT
1 TGCCA-CAACTTGTGTGGGCTTTGAA-AAGGT
* * *
2370699 TGCCACGAACTTATGTGGGCCTTAGAAAGGGT
1 TGCCAC-AACTTGTGTGGG-CTTTGAAAAGGT
* * *
2370731 TGCCACCAACTTGTATGGGCTTTAAAGAAGAT
1 TGCCA-CAACTTGTGTGGGCTTTGAA-AAGGT
*
2370763 TGCCACCAACTTGTGTGGGCTTTAAAAAGGGT
1 TGCCA-CAACTTGTGTGGGCTTTGAAAA-GGT
* * *
2370795 TACCACCAACTTGTATAGGCTTTGAAGAAGGT
1 TGCCA-CAACTTGTGTGGGCTTTGAA-AAGGT
2370827 T
1 T
2370828 TCTCCCTGGG
Statistics
Matches: 268, Mismatches: 37, Indels: 28
0.80 0.11 0.08
Matches are distributed among these distances:
30 2 0.01
31 66 0.25
32 188 0.70
33 12 0.04
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (30 bp):
TGCCACAACTTGTGTGGGCTTTGAAAAGGT
Found at i:2370587 original size:64 final size:63
Alignment explanation
Indices: 2370477--2370827 Score: 368
Period size: 64 Copynumber: 5.5 Consensus size: 63
2370467 TAGAAGGAGA
* * * ** *
2370477 TGCCACTAACTTGTGTGGGCTTTTGAAAAGGTTTCCACTGACTTGTGTGGGCTTTTG-AAGAGGT
1 TGCCACCAACTTGTGTGGGC-TTTAAAAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAG-GGT
* * * *
2370541 TCCCACCAGCTTGTGTGGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTT-G-AAGAAGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAA-GGTTGCCACCAACTTGTGTGGGCTTTAGAAAG-GGT
* * *
2370604 TGCCACCAGCTTATGTGGGCTTTGAAAAA-GTTGCCACCAGCTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* * * * * *
2370667 TGCCACCAACTTGTATGGGCTTTGAAGAAGATTGCCACGAACTTATGTGGGCCTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* * *
2370731 TGCCACCAACTTGTATGGGCTTTAAAGAAGATTGCCACCAACTTGTGTGGGCTTTAAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAA-AAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
* * * *
2370795 TACCACCAACTTGTATAGGCTTTGAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAAGGTT
2370828 TCTCCCTGGG
Statistics
Matches: 250, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
62 23 0.09
63 65 0.26
64 160 0.64
65 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (63 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
Found at i:2370790 original size:158 final size:158
Alignment explanation
Indices: 2370477--2370827 Score: 429
Period size: 158 Copynumber: 2.2 Consensus size: 158
2370467 TAGAAGGAGA
* * * ** * *
2370477 TGCCACTAACTTGTGTGGGCTTTTGAAAAGGTTTCCACTGACTTGTGTGGGCTTTTGAAGAGGTT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGGTTGCCACCAACTTGTATGGGCTTTTGAAGAGATT
* * * * * *
2370542 CCCACCAGCTTGTGTGGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTTGAAGAAGTTGC
66 CCCACCAACTTATGTGGGCCTTAAAAAGGGTTGCCACCAACTTGTATGGGCTTTAAAGAAGTTGC
*
2370607 CACCAGCTTATGTGGGCTTTGAAAAAGT
131 CACCAACTTATGTGGGCTTTGAAAAAGT
* *
2370635 TGCCACCAGCTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTATGGGC-TTTGAAGAAGAT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGGTTGCCACCAACTTGTATGGGCTTTTGAAG-AGAT
* * *
2370699 TGCCACGAACTTATGTGGGCCTTAGAAAGGGTTGCCACCAACTTGTATGGGCTTTAAAGAAGATT
65 TCCCACCAACTTATGTGGGCCTTAAAAAGGGTTGCCACCAACTTGTATGGGCTTTAAAGAAG-TT
*
2370764 GCCACCAACTTGTGTGGGCTTT-AAAAAGGGT
129 GCCACCAACTTATGTGGGCTTTGAAAAA--GT
* * *
2370795 TACCACCAACTTGTATAGGCTTT-GAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTAGAA-AAGGTT
2370828 TCTCCCTGGG
Statistics
Matches: 163, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
157 7 0.04
158 105 0.64
159 25 0.15
160 26 0.16
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (158 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAAGGTTGCCACCAACTTGTATGGGCTTTTGAAGAGATT
CCCACCAACTTATGTGGGCCTTAAAAAGGGTTGCCACCAACTTGTATGGGCTTTAAAGAAGTTGC
CACCAACTTATGTGGGCTTTGAAAAAGT
Found at i:2371071 original size:28 final size:28
Alignment explanation
Indices: 2371000--2371071 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
2370990 TATATAGCAA
*
2371000 GTGCCACTGATTA-TGGATTTCAAAAAG
1 GTGCCACTGATTAGTGGACTTCAAAAAG
* * * *
2371027 GTGCAACTAACTT-GTGGACTTCGAAGAG
1 GTGCCACTGA-TTAGTGGACTTCAAAAAG
2371055 GTGCCACTGATTAGTGG
1 GTGCCACTGATTAGTGG
2371072 GCTTTGAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (28 bp):
GTGCCACTGATTAGTGGACTTCAAAAAG
Found at i:2371147 original size:13 final size:13
Alignment explanation
Indices: 2371112--2371164 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2371102 TTTCTTGACG
* *
2371112 AAGTTTCTGACAC
1 AAGTTTTTGACAA
* *
2371125 ATGTTCTTGACAA
1 AAGTTTTTGACAA
2371138 AAGTTTTTGACAA
1 AAGTTTTTGACAA
*
2371151 AAATTTCTTGACAA
1 AAGTTT-TTGACAA
2371165 CAATTTCTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 25 0.78
14 7 0.22
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (13 bp):
AAGTTTTTGACAA
Found at i:2371161 original size:14 final size:14
Alignment explanation
Indices: 2371128--2371175 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
2371118 CTGACACATG
*
2371128 TTCTTGACAAAAGT
1 TTCTTGACAAAAAT
2371142 TT-TTGACAAAAAT
1 TTCTTGACAAAAAT
*
2371155 TTCTTGACAACAAT
1 TTCTTGACAAAAAT
2371169 TTCTTGA
1 TTCTTGA
2371176 TAATGGCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (14 bp):
TTCTTGACAAAAAT
Found at i:2372332 original size:28 final size:28
Alignment explanation
Indices: 2372251--2372332 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2372241 TTTTGGAGAT
*
2372251 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
2372279 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
2372307 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
2372333 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:2372475 original size:51 final size:51
Alignment explanation
Indices: 2372315--2372485 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
2372305 GAAATAACGA
* *
2372315 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2372367 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2372420 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2372471 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2372486 TCAGAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 33 0.34
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2372531 original size:27 final size:28
Alignment explanation
Indices: 2372468--2372543 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2372458 AAAATAAAGT
*
2372468 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2372496 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2372523 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2372544 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2375030 original size:13 final size:13
Alignment explanation
Indices: 2375012--2375037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2375002 ACAAAGATCC
2375012 ATGTATCGATACA
1 ATGTATCGATACA
2375025 ATGTATCGATACA
1 ATGTATCGATACA
2375038 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:2375033 original size:33 final size:33
Alignment explanation
Indices: 2374991--2375057 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2374981 AAAATTTCCA
***
2374991 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2375024 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2375057 A
1 A
2375058 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:2375101 original size:19 final size:18
Alignment explanation
Indices: 2375077--2375144 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2375067 CAGTAGCTAA
2375077 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2375096 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2375111 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2375128 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2375145 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:2375117 original size:13 final size:13
Alignment explanation
Indices: 2375099--2375123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2375089 ACAATACTTA
2375099 TGTATCGATACAT
1 TGTATCGATACAT
2375112 TGTATCGATACA
1 TGTATCGATACA
2375124 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:2375121 original size:32 final size:32
Alignment explanation
Indices: 2375080--2375142 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2375070 TAGCTAATTA
*
2375080 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2375112 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2375143 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:2375224 original size:21 final size:21
Alignment explanation
Indices: 2375200--2375256 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2375190 CATTTGTAGG
2375200 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2375221 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2375242 ATGTATCGATACATT
1 ATGTATCGATACATT
2375257 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2376655 original size:55 final size:55
Alignment explanation
Indices: 2376571--2377908 Score: 2080
Period size: 55 Copynumber: 24.3 Consensus size: 55
2376561 ATAAATTGTA
* * * * *
2376571 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* ** *
2376626 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCCCCTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
2376681 TCCTGCTCTTTGGGGAAT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
2376736 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2376791 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
2376846 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2376901 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2376956 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377011 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2377066 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377121 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
2377176 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2377231 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
2377286 TCCTGCTCGTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377341 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2377396 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377451 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2377506 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377561 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
2377616 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
2377671 TCCTGCTCGTTGAGGACTGGAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377726 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2377781 TCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
2377836 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAACGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2377891 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2377909 AAAAAGCGGA
Statistics
Matches: 1211, Mismatches: 55, Indels: 34
0.93 0.04 0.03
Matches are distributed among these distances:
54 24 0.02
55 1165 0.96
56 22 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:2376866 original size:26 final size:26
Alignment explanation
Indices: 2376837--2376926 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
2376827 GTGTGGGCTT
2376837 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
2376863 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
2376890 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
2376918 TGAAAGGTG
1 TGAAAGGTG
2376927 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 8 0.17
28 9 0.19
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:2376900 original size:29 final size:29
Alignment explanation
Indices: 2376867--2376955 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
2376857 GGGGACTGAA
2376867 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * * * *
2376896 AGGTGTCCTGC-TCTT-TGAGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGGCTTTAAG
2376922 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
2376951 AGGTG
1 AGGTG
2376956 TCCTGCTCGT
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 8 0.19
28 8 0.19
29 13 0.30
30 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:2377198 original size:26 final size:26
Alignment explanation
Indices: 2377169--2377256 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
2377159 GTGGGCTTTA
2377169 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** * *
2377195 AAAGGTG-CCACCAACTTGTGTGGG-CTTT
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
*
2377223 AAGAGGTGTCCTGCTCTTTGAGGACTG
1 AA-AGGTGTCCTGCTCTTTGGGGACTG
2377250 AAAGGTG
1 AAAGGTG
2377257 CCACCAACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.07
26 15 0.33
27 8 0.17
28 9 0.20
29 8 0.17
30 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:2377581 original size:26 final size:26
Alignment explanation
Indices: 2377552--2377641 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
2377542 GTGTGGGCTT
2377552 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
2377578 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
2377605 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
2377633 TGAAAGGTG
1 TGAAAGGTG
2377642 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:2377670 original size:29 final size:29
Alignment explanation
Indices: 2377582--2377670 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
2377572 GAGGACTGAA
2377582 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
2377611 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
2377637 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
2377666 AGGTG
1 AGGTG
2377671 TCCTGCTCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:2378894 original size:1 final size:1
Alignment explanation
Indices: 2378890--2378937 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
2378880 CTTTTCTCTC
* * * * *
2378890 TTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2378938 GAAGAGAAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:2378912 original size:9 final size:9
Alignment explanation
Indices: 2378890--2378938 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
2378880 CTTTTCTCTC
*
2378890 TTTTTCTTT
1 TTTTTGTTT
*
2378899 GTTTTGTTT
1 TTTTTGTTT
2378908 TTTTTGTTT
1 TTTTTGTTT
*
2378917 TTTTT-TTC
1 TTTTTGTTT
2378925 TTTTT-TTT
1 TTTTTGTTT
2378933 TTTTTG
1 TTTTTG
2378939 AAGAGAAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 14 0.41
9 20 0.59
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:2378918 original size:25 final size:25
Alignment explanation
Indices: 2378890--2378938 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2378880 CTTTTCTCTC
*
2378890 TTTTTCTTTGTTTTGTTTTTTTTGT
1 TTTTTCTTTCTTTTGTTTTTTTTGT
* *
2378915 TTTTTTTTTCTTTTTTTTTTTTTG
1 TTTTTCTTTCTTTTGTTTTTTTTG
2378939 AAGAGAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (25 bp):
TTTTTCTTTCTTTTGTTTTTTTTGT
Found at i:2378937 original size:15 final size:15
Alignment explanation
Indices: 2378890--2378937 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
2378880 CTTTTCTCTC
*
2378890 TTTTTCTTTGTTTTG
1 TTTTTCTTTGTTTTT
2378905 TTTTT-TTTGTTTTT
1 TTTTTCTTTGTTTTT
2378919 TTTTTCTTT-TTTTT
1 TTTTTCTTTGTTTTT
2378933 TTTTT
1 TTTTT
2378938 GAAGAGAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 23 0.74
15 8 0.26
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:2444895 original size:19 final size:19
Alignment explanation
Indices: 2444871--2444933 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
2444861 TAGCCAAACT
2444871 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
2444890 TGTATCGAT--AC--A--A
1 TGTATCGATACACAAAGTA
*
2444903 TGTATCGGTACACAAAGTA
1 TGTATCGATACACAAAGTA
2444922 TGTATCGATACA
1 TGTATCGATACA
2444934 ATGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
15 3 0.08
17 3 0.08
19 21 0.58
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAGTA
Found at i:2444907 original size:13 final size:13
Alignment explanation
Indices: 2444889--2444946 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
2444879 TACACAAAGT
2444889 ATGTATCGATACA
1 ATGTATCGATACA
*
2444902 ATGTATCGGTACACAAA
1 ATGTATC-G-ATAC--A
2444919 GTATGTATCGATACA
1 --ATGTATCGATACA
2444934 ATGTATCGATACA
1 ATGTATCGATACA
2444947 CAAAAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
15 4 0.11
17 4 0.11
18 1 0.03
19 7 0.19
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2444915 original size:32 final size:32
Alignment explanation
Indices: 2444871--2444966 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
2444861 TAGCCAAACT
2444871 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
*
2444903 TGTATCGGTACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
**
2444935 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAGTA-TGTATCGATACA
2444967 TTGGCTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 47 0.80
33 12 0.20
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGTATGTATCGATACAA
Found at i:2449033 original size:15 final size:15
Alignment explanation
Indices: 2449013--2449043 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2449003 TAAAAATGTC
*
2449013 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2449028 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2449043 C
1 C
2449044 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:2451142 original size:13 final size:13
Alignment explanation
Indices: 2451124--2451161 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2451114 CATTTTTCTT
2451124 TGTATCGATACAA
1 TGTATCGATACAA
*
2451137 TGTATCGATACAC
1 TGTATCGATACAA
2451150 TGTATCGATACA
1 TGTATCGATACA
2451162 GGAGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2453657 original size:20 final size:19
Alignment explanation
Indices: 2453603--2453657 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
2453593 AAAACCCTTA
*
2453603 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
2453623 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
2453643 AATGTATCGATACAT
1 AAAGTATCGATACAT
2453658 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:2453746 original size:13 final size:13
Alignment explanation
Indices: 2453728--2453753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2453718 TACACAAAGT
2453728 ATGTATCGATACA
1 ATGTATCGATACA
2453741 ATGTATCGATACA
1 ATGTATCGATACA
2453754 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:2453753 original size:32 final size:33
Alignment explanation
Indices: 2453710--2453773 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2453700 TAGCCAAACT
**
2453710 TGTATCCATACACAAAGTA-TGTATCGATACAA
1 TGTATCCATACACAAAAAATTGTATCGATACAA
*
2453742 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCCATACACAAAAAATTGTATCGATACA
2453774 TTGGCTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCCATACACAAAAAATTGTATCGATACAA
Done.