Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold439
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: 1094049
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 7
Found at i:322748 original size:20 final size:20
Alignment explanation
Indices: 322723--322767 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
322713 TTTTAGCCCA
*
322723 AATGTATCGATACATTCTTC
1 AATGTATCAATACATTCTTC
322743 AATGTATCAATACATTCTTC
1 AATGTATCAATACATTCTTC
322763 AATGT
1 AATGT
322768 TTTCACCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (20 bp):
AATGTATCAATACATTCTTC
Found at i:325551 original size:207 final size:208
Alignment explanation
Indices: 324964--325582 Score: 1008
Period size: 208 Copynumber: 3.0 Consensus size: 208
324954 ATTAGGTTGT
324964 TTCGTTATTTTCTTTTTCGTTTACTAACATGTTTCCTTTCATAGGGACCTTATGCACTT-ATGCT
1 TTCGTTATTTTCTTTTTCGTTTACTAACATGTTTCCTTTCATAGGGACCTTATGCA-TTCATGCT
* * *
325028 TTAAAAAACTATTTTTAAAAATCACAAAATGATAATCTGGTCAATATCTTTCTAGTACTTGACAC
65 TTAAAAAACTATTTTTAAAAATCACAAAATGATAATCTGGTCAATATCTCTCTAGTGCTTGATAC
* * * *
325093 GAAATATTTGATATTTTCCAAACCCAATTCGAAAATCATTTTTATAAAAATCCGTGTGTTGCTCA
130 GAAATATTTGATGTTTTCCAAACCCAATCCGAAAATCATTTTTATAAAAATCCCTGTGTTCCTCA
* * *
325158 CTTCTCTCAATTTG
195 CTTTTCTGAGTTTG
* *
325172 TCCGTTATTTTCTTTTTCGTTTACTAACATGTTTTCTTTCATAGGGACCTTATGCATTCATGCTT
1 TTCGTTATTTTCTTTTTCGTTTACTAACATGTTTCCTTTCATAGGGACCTTATGCATTCATGCTT
* *
325237 TAAAAAACTATTTTTAAAAATCACAAAATGATATTCTGGTCAGTATCTCTCTAGTGCTTGATACG
66 TAAAAAACTATTTTTAAAAATCACAAAATGATAATCTGGTCAATATCTCTCTAGTGCTTGATACG
*
325302 AAATATTTGATGTTTTCCAAACCCAATCCAAAAATCATTTTTATAAAAATCCCTGTGTTCCTCAC
131 AAATATTTGATGTTTTCCAAACCCAATCCGAAAATCATTTTTATAAAAATCCCTGTGTTCCTCAC
325367 TTTTCTGAGTTTG
196 TTTTCTGAGTTTG
* * *
325380 TTCGTTATTTTCTTTTTTGTTTAGTAACATGTTTCCTTTCGTAGGGACCTTATGCATTCATGCTT
1 TTCGTTATTTTCTTTTTCGTTTACTAACATGTTTCCTTTCATAGGGACCTTATGCATTCATGCTT
*
325445 T-AAAAACTATTTTTAAAAATCACAAAATGATAATCTCGTCAATATCTCTCTAGTGCTTGATACG
66 TAAAAAACTATTTTTAAAAATCACAAAATGATAATCTGGTCAATATCTCTCTAGTGCTTGATACG
* * * *
325509 AAATATTTGATGTTTTCCAAACCCAATCCGAAAATTATTTTTATAAAAATTCCTGTATTTCTCAC
131 AAATATTTGATGTTTTCCAAACCCAATCCGAAAATCATTTTTATAAAAATCCCTGTGTTCCTCAC
325574 TTTTCTGAG
196 TTTTCTGAG
325583 GTGCATAGGT
Statistics
Matches: 382, Mismatches: 28, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
207 131 0.34
208 251 0.66
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (208 bp):
TTCGTTATTTTCTTTTTCGTTTACTAACATGTTTCCTTTCATAGGGACCTTATGCATTCATGCTT
TAAAAAACTATTTTTAAAAATCACAAAATGATAATCTGGTCAATATCTCTCTAGTGCTTGATACG
AAATATTTGATGTTTTCCAAACCCAATCCGAAAATCATTTTTATAAAAATCCCTGTGTTCCTCAC
TTTTCTGAGTTTG
Found at i:338865 original size:20 final size:22
Alignment explanation
Indices: 338823--338866 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
338813 GCGATTTTTC
*
338823 AAAAATAGAAAAATTTCAAGAA
1 AAAAATAGAAAAATTACAAGAA
*
338845 AAAAAT-GAAAAA-TACATGAA
1 AAAAATAGAAAAATTACAAGAA
338865 AA
1 AA
338867 TGAATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAATAGAAAAATTACAAGAA
Found at i:338990 original size:165 final size:167
Alignment explanation
Indices: 338819--339122 Score: 461
Period size: 166 Copynumber: 1.8 Consensus size: 167
338809 AAACGCGATT
* *
338819 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATGAAAAA-TACATGAAAATGAATGAAATT-TTGA
1 TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAATTACATGAAAATAAAT-AAATTCTTGA
* * *
338882 AAATTGATTTACTACAAAATAAATAATAATATTTGAT-ATTTTTAAAAATAAAAAACAAAGAAAA
65 AAACTGATTTAATACAAAATAAATAATAATATTTGATGAGTTTTAAAAATAAAAAACAAAGAAAA
338946 ATCTCCCTAAAAAAATTTAAGGAGTAAAAAACTCTGTA
130 ATCTCCCTAAAAAAATTTAAGGAGTAAAAAACTCTGTA
* * **
338984 TTTCAAAAATAAAAAAATTTTAAGAAAAAAATTAAAAATTTTATGAAAATAAATAAATTCTTGAA
1 TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAATTACATGAAAATAAATAAATTCTTGAA
** * *
339049 AACTGATTTAATATTAATTAAATAATAATATTTGATGAGTTTTAAAAATAAAAAACCAAGAAAAA
66 AACTGATTTAATACAAAATAAATAATAATATTTGATGAGTTTTAAAAATAAAAAACAAAGAAAAA
339114 TCTCCCTAA
131 TCTCCCTAA
339123 GAATATTTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
165 40 0.33
166 48 0.39
167 35 0.28
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (167 bp):
TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAATTACATGAAAATAAATAAATTCTTGAA
AACTGATTTAATACAAAATAAATAATAATATTTGATGAGTTTTAAAAATAAAAAACAAAGAAAAA
TCTCCCTAAAAAAATTTAAGGAGTAAAAAACTCTGTA
Found at i:339013 original size:22 final size:22
Alignment explanation
Indices: 338988--339040 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
338978 TCTGTATTTC
338988 AAAAATAAAAAAATTTTAAGAA
1 AAAAATAAAAAAATTTTAAGAA
* *
339010 AAAAAT-TAAAAATTTTATGAA
1 AAAAATAAAAAAATTTTAAGAA
339031 AATAAATAAA
1 AA-AAATAAA
339041 TTCTTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 15 0.58
22 10 0.38
23 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATAAAAAAATTTTAAGAA
Found at i:339146 original size:167 final size:165
Alignment explanation
Indices: 338819--339146 Score: 451
Period size: 167 Copynumber: 2.0 Consensus size: 165
338809 AAACGCGATT
* *
338819 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATGAAAAATACATGAAAATGAATGAAATTTTGAAA
1 TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAATACATGAAAATAAATGAAATTTTGAAA
* * *
338884 ATTGATTTACTACAAAATAAATAATAATATTTGATATTTTTAAAAATAAAAAACAAAGAAAAATC
66 ACTGATTTAATACAAAATAAATAATAATATTTGATAGTTTTAAAAATAAAAAACAAAGAAAAATC
*
338949 TCCCTAAAAAAATTTAAGGAGTAAAAAACTCTGTA
131 TCCCTAAAAAAATTTAAGAAGTAAAAAACTCTGTA
* * **
338984 TTTCAAAAATAAAAAAATTTTAAGAAAAAAATTAAAAATTTTATGAAAATAAAT-AAATTCTTGA
1 TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAA-TACATGAAAATAAATGAAATT-TTGA
** * *
339048 AAACTGATTTAATATTAATTAAATAATAATATTTGATGAGTTTTAAAAATAAAAAACCAAGAAAA
64 AAACTGATTTAATACAAAATAAATAATAATATTTGAT-AGTTTTAAAAATAAAAAACAAAGAAAA
* * ** *
339113 ATCTCCCTAAGAATATTTTTGAAGTAGAAAACTC
128 ATCTCCCTAAAAAAATTTAAGAAGTAAAAAACTC
339147 ATATTTTGGA
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
165 40 0.28
166 48 0.34
167 53 0.38
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (165 bp):
TTTCAAAAATAAAAAAATTTCAAGAAAAAAATGAAAAATACATGAAAATAAATGAAATTTTGAAA
ACTGATTTAATACAAAATAAATAATAATATTTGATAGTTTTAAAAATAAAAAACAAAGAAAAATC
TCCCTAAAAAAATTTAAGAAGTAAAAAACTCTGTA
Found at i:339177 original size:166 final size:166
Alignment explanation
Indices: 338768--339261 Score: 480
Period size: 165 Copynumber: 3.0 Consensus size: 166
338758 TGAATTTAAT
* * ** * * * * * *
338768 AAAACCAAGAGAAATCTCCCCGAAAACATTTACAG-AGTAGAAAACGCGATTTTTCAAAAATAGA
1 AAAACAAAGAAAAATCTCCCTAAAAAAATTTA-AGAAGTAAAAAACTCTATATTTCAAAAATAAA
* * * * * *
338832 AAAATTTCAAGAAAAAAATGAAAAATACATGAAAATGAATGAAATTTTGAAAATTGATTTACTAC
65 AAAATTTGAAGAAAAAAATTAAAAATATATGAAAATAAATGAAATTTTGAAAACTGATTTAATAC
* * *
338897 AAAATAAATAATAATATTTGAT-ATTTTTAAAAATAA
130 TAATTAAATAATAATATTTGATGAGTTTTAAAAATAA
* *
338933 AAAACAAAGAAAAATCTCCCTAAAAAAATTTAAGGAGTAAAAAACTCTGTATTTCAAAAATAAAA
1 AAAACAAAGAAAAATCTCCCTAAAAAAATTTAAGAAGTAAAAAACTCTATATTTCAAAAATAAAA
* *
338998 AAATTTTAAGAAAAAAATTAAAAATTTTATGAAAATAAAT-AAATTCTTGAAAACTGATTTAATA
66 AAATTTGAAGAAAAAAATTAAAAA-TATATGAAAATAAATGAAATT-TTGAAAACTGATTTAATA
*
339062 TTAATTAAATAATAATATTTGATGAGTTTTAAAAATAA
129 CTAATTAAATAATAATATTTGATGAGTTTTAAAAATAA
* * * ** * ** **
339100 AAAACCAAGAAAAATCTCCCTAAGAATATTTTTGAAGTAGAAAACTC-ATATTTTGGAAAA-AGG
1 AAAACAAAGAAAAATCTCCCTAAAAAAATTTAAGAAGTAAAAAACTCTATA-TTTCAAAAATAAA
* * * ** * *
339163 GAACTTTGAAG-AAAAAATTGAAAAA-AGTATCAAAATATGTGAACTTTTGCAAACTGATTTAAT
65 AAAATTTGAAGAAAAAAATT-AAAAATA-TATGAAAATAAATGAAATTTTGAAAACTGATTTAAT
** *
339226 GGTAATTAAATAATAATATTTGATGAAGTTTCAAAA
128 ACTAATTAAATAATAATATTTGATG-AGTTTTAAAA
339262 TTTTAAACCC
Statistics
Matches: 274, Mismatches: 46, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
164 2 0.01
165 135 0.49
166 77 0.28
167 60 0.22
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (166 bp):
AAAACAAAGAAAAATCTCCCTAAAAAAATTTAAGAAGTAAAAAACTCTATATTTCAAAAATAAAA
AAATTTGAAGAAAAAAATTAAAAATATATGAAAATAAATGAAATTTTGAAAACTGATTTAATACT
AATTAAATAATAATATTTGATGAGTTTTAAAAATAA
Found at i:341492 original size:20 final size:20
Alignment explanation
Indices: 341467--341506 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
341457 ATTTGAAGCA
341467 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
341487 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
341507 GAGACAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:341606 original size:19 final size:20
Alignment explanation
Indices: 341562--341612 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
341552 CTGCCAGTTT
* **
341562 CATGTATCGATATAATTGTC
1 CATGTATCGATATAAATGAA
341582 CATGTATCGATA-AAATGAA
1 CATGTATCGATATAAATGAA
341601 CATGTATCGATA
1 CATGTATCGATA
341613 CATTGTATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATATAAATGAA
Found at i:341621 original size:13 final size:13
Alignment explanation
Indices: 341603--341627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341593 AAAATGAACA
341603 TGTATCGATACAT
1 TGTATCGATACAT
341616 TGTATCGATACA
1 TGTATCGATACA
341628 ACGCATAATA
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:342660 original size:13 final size:13
Alignment explanation
Indices: 342642--342667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
342632 CAATTTTTTG
342642 TGTATCGATACAT
1 TGTATCGATACAT
342655 TGTATCGATACAT
1 TGTATCGATACAT
342668 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:345231 original size:20 final size:20
Alignment explanation
Indices: 345206--345282 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
345196 ATAATCCCCC
345206 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
**
345226 TGTATCGATACATTGAATTTCCAAA
1 TGTATCGATACAAAGAA-----AAA
*
345251 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
345271 TGTATCGATACA
1 TGTATCGATACA
345283 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 29 0.63
25 17 0.37
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:347319 original size:15 final size:15
Alignment explanation
Indices: 347299--347329 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
347289 ATTTCGTTTG
*
347299 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
347314 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
347329 G
1 G
347330 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:351388 original size:13 final size:13
Alignment explanation
Indices: 351370--351395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
351360 CAATTTTTTG
351370 TGTATCGATACAT
1 TGTATCGATACAT
351383 TGTATCGATACAT
1 TGTATCGATACAT
351396 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:351410 original size:32 final size:33
Alignment explanation
Indices: 351350--351413 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
351340 TACAAGCCAA
** *
351350 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
351383 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
351414 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:351775 original size:30 final size:30
Alignment explanation
Indices: 351739--351798 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
351729 TTATTCAATC
351739 CTTTGTTATATCAAAACCAAGATCCTAACA
1 CTTTGTTATATCAAAACCAAGATCCTAACA
*
351769 CTTTGTTATATCAAAACCAAGATTCTAACA
1 CTTTGTTATATCAAAACCAAGATCCTAACA
351799 TTCTCCCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (30 bp):
CTTTGTTATATCAAAACCAAGATCCTAACA
Found at i:355083 original size:11 final size:11
Alignment explanation
Indices: 355066--355099 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
355056 TTCTTTTTAA
355066 AAAAAAAACAAC
1 AAAAAAAA-AAC
355078 AAAAAAAAAAC
1 AAAAAAAAAAC
355089 AAAAAAGAAAA
1 AAAAAA-AAAA
355100 AGAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:355083 original size:14 final size:13
Alignment explanation
Indices: 355064--355113 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 13
355054 CATTCTTTTT
355064 AAAAAAAAAACAA
1 AAAAAAAAAACAA
355077 CAAAAAAAAAACAA
1 -AAAAAAAAAACAA
* *
355091 AAAAGAAAAAGAA
1 AAAAAAAAAACAA
355104 AGAAAAAAAA
1 A-AAAAAAAA
355114 GAACTTGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 12 0.38
14 20 0.62
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:355100 original size:19 final size:19
Alignment explanation
Indices: 355064--355116 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
355054 CATTCTTTTT
*
355064 AAAAAAAAAACAACAAAAA-
1 AAAAAAAAAA-AAGAAAAAG
*
355083 AAAAACAAAAAAGAAAAAG
1 AAAAAAAAAAAAGAAAAAG
*
355102 AAAGAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
355117 CTTGCTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAGAAAAAG
Found at i:355105 original size:10 final size:9
Alignment explanation
Indices: 355064--355116 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
355054 CATTCTTTTT
355064 AAAAA-AAA
1 AAAAAGAAA
* *
355072 AACAACAAA
1 AAAAAGAAA
355081 AAAAA-AACA
1 AAAAAGAA-A
355090 AAAAAGAAA
1 AAAAAGAAA
355099 AAGAAAGAAA
1 AA-AAAGAAA
355109 AAAAAGAA
1 AAAAAGAA
355117 CTTGCTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 6 0.15
9 22 0.56
10 11 0.28
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:355116 original size:13 final size:12
Alignment explanation
Indices: 355064--355113 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
355054 CATTCTTTTT
355064 AAAAAAAAAACAA
1 AAAAAAAAAAC-A
355077 CAAAAAAAAAACA
1 -AAAAAAAAAACA
*
355090 AAAAAGAAAAAGA
1 AAAAA-AAAAACA
355103 AAGAAAAAAAA
1 AA-AAAAAAAA
355114 GAACTTGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 5 0.15
13 14 0.42
14 14 0.42
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:356265 original size:55 final size:54
Alignment explanation
Indices: 356181--356426 Score: 269
Period size: 55 Copynumber: 4.4 Consensus size: 54
356171 TTTGCCCTTT
* * * *
356181 AGTCCTTAAAGAGCAGGATGCCTTTTAAAGCCCGCACAAGTTGGTGGTATTTTCC
1 AGTCCTCAAAGAGCAGGACGCC-TTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
356236 AGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACGCCT-TTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
356291 AGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
356346 AGTCCTCAAAGAGCAAGATACTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCA-CTTCC
1 AGTCCTCAAAGAGC-AG-GAC--GC-C--TTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
356406 TAGTCTTCAAAGAGCAGGACG
1 -AGTCCTCAAAGAGCAGGACG
356427 TTCTCTCCTT
Statistics
Matches: 162, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
54 3 0.02
55 109 0.67
56 2 0.01
57 2 0.01
59 3 0.02
60 6 0.04
61 34 0.21
62 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:356425 original size:116 final size:110
Alignment explanation
Indices: 356180--356426 Score: 298
Period size: 110 Copynumber: 2.2 Consensus size: 110
356170 TTTTGCCCTT
* * * *
356180 TAGTCCTT-AAAGAGCAGGATGCCTTTTAAAGCCCGCACAAGTTGGTGGTATTTTCCAGTCCTCA
1 TAGT-CTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
* * *
356244 AAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
65 AAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTAGTGGCACTTCC
* * * *
356290 TAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTTCAGTCCTCAA
1 TAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* * *
356355 AGAGCAAGATACTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCC
66 AGAGC-AG-GAC--GC-C-TCTTAAAGCCCACACAAGTTAGTGGCACTTCC
356406 TAGTCTTCAAAGAGCAGGACG
1 TAGTCTTCAAAGAGCAGGACG
356427 TTCTCTCCTT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
109 2 0.02
110 59 0.52
111 2 0.02
112 2 0.02
114 1 0.01
115 1 0.01
116 47 0.41
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (110 bp):
TAGTCTTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGACGCCTCTTAAAGCCCACACAAGTTAGTGGCACTTCC
Found at i:356488 original size:265 final size:259
Alignment explanation
Indices: 356086--356575 Score: 705
Period size: 265 Copynumber: 1.9 Consensus size: 259
356076 TTCACTTTCC
* * *
356086 CAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGT
1 CAGTCCTCAAAGAGCAAGATGACTTTTCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCCCAGT
* * * ** *
356151 CCTCAAGGATGCTCTCTCCTTTTGCCCTTTAGTCCTTAAAGAGCAGGATGCCTTTTAAAGCCCGC
66 CCTCAAGGAGGCTCTCTCCTTTCGCCCTTTAGTCCTAAAAGAGCAGGACACCTTTTAAAGCCCAC
*
356216 ACAAGTTGGTGGTATTTTCCAGTCCTCAAAGAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGG
131 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGG
* * *
356280 TGGCATTTTCTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTT
195 TGGCAATTCCCAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTT
*
356345 CAGTCCTCAAAGAGCAAGAT-ACTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCCTAG
1 CAGTCCTCAAAGAGCAAGATGACTTT-TCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCCCAG
* * * *
356409 TCTTCAAAGAGCAGGACGTTCTCTCCTTTCGCCCTTTAGTCCTAAAAGTGTAGGACACTTTTTAA
65 TCCTC-AAG-G-AGG-C--TCTCTCCTTTCGCCCTTTAGTCCTAAAAGAGCAGGACACCTTTTAA
*
356474 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACA
124 AGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACA
* *
356539 AGTTGGTGGCAATTCCCAGTCCTCAAAGAGTAGGACG
189 AGTTGGTGGCAATTCCCAGTCCTCAAAAAGCAGGACG
356576 TTCTCTTCTT
Statistics
Matches: 202, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
258 4 0.02
259 59 0.29
260 3 0.01
261 1 0.00
262 2 0.01
263 1 0.00
264 2 0.01
265 130 0.64
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (259 bp):
CAGTCCTCAAAGAGCAAGATGACTTTTCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCCCAGT
CCTCAAGGAGGCTCTCTCCTTTCGCCCTTTAGTCCTAAAAGAGCAGGACACCTTTTAAAGCCCAC
ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGT
GGCAATTCCCAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTT
Found at i:356594 original size:149 final size:150
Alignment explanation
Indices: 356290--356739 Score: 550
Period size: 149 Copynumber: 3.0 Consensus size: 150
356280 TGGCATTTTC
* * * * *
356290 TAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACGCAAGTTGGTGGCATTTTTCAGTCCTCAA
1 TAGTCCTCAAAAAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* * * * *
356355 AGAGCAAGATACTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACTTCCTAGTCTTCAAAGAG
66 AGAGC-AG-GA--TGCTC-TTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
*
356420 CAGGACGTTCTCTCCTTTCGCCCTT
126 CAGGACGTTCTCTTCTTTCGCCCTT
* *
356445 TAGTCCT-AAAAGTGTAGGACACTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1 TAGTCCTCAAAA-AGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
* * *
356509 AAGAGCAGGATGC-CTTTCAAAGCCCACACAAGTTGGTGGCAATTCCCAGTCCTCAAAGAGTAGG
65 AAGAGCAGGATGCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGG
356573 ACGTTCTCTTCTTTCGCCCTT
130 ACGTTCTCTTCTTTCGCCCTT
* * * *
356594 TAGTCCTCAAAAAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGTA-CTTCCCGTCCTCAA
1 TAGTCCTCAAAAAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
*
356658 AGAGCTGGATGCTTTCTCTTTACAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGA
66 AGAGCAGGATG----CTCTTT-CAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGA
* *
356722 GCATGACG-TCTTTTCTTT
125 GCAGGACGTTCTCTTCTTT
356740 TCAAAGCCCA
Statistics
Matches: 258, Mismatches: 28, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
148 22 0.09
149 105 0.41
150 5 0.02
151 2 0.01
152 1 0.00
153 14 0.05
154 49 0.19
155 60 0.23
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (150 bp):
TAGTCCTCAAAAAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGATGCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA
CGTTCTCTTCTTTCGCCCTT
Found at i:356745 original size:61 final size:60
Alignment explanation
Indices: 356616--356803 Score: 238
Period size: 61 Copynumber: 3.1 Consensus size: 60
356606 AGTAGGACGC
* **
356616 CTTTT-AAAGCCCACACAAGTTGGTGGTA-CTTCCCGTCCTCAAAGAGC-TGGATGCTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAT-GATGCTTT-T
* *
356675 CTTTACAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCATGACGTCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCATGATG-CTTTT
* * *
356736 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCATGATGCCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCATGATG-CTTTT
356797 CCTTTTC
1 -CTTTTC
356804 TCCTTTATCC
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
59 4 0.04
60 22 0.19
61 76 0.67
62 11 0.10
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (60 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCATGATGCTTTT
Found at i:356926 original size:42 final size:42
Alignment explanation
Indices: 356811--356938 Score: 118
Period size: 42 Copynumber: 3.0 Consensus size: 42
356801 TTCTCCTTTA
* * * *
356811 TCCTCAAAGAGCAGGACACACTTC-ATTCCCTTCTTTTCCTTTTTG
1 TCCTCAAAGAGCAGGACACATTTCGTTTTCC-TC-TTT-C-TTTGG
* *
356856 TCCTCAAAGAGTAGGACGCACTTT-GTTTTCCTCTTTCTTTGG
1 TCCTCAAAGAGCAGGACACA-TTTCGTTTTCCTCTTTCTTTGG
*
356898 TCCTCAAAGAGCATGACACATTTCGTTTTCCT-TTGTCTTTG
1 TCCTCAAAGAGCAGGACACATTTCGTTTTCCTCTT-TCTTTG
356939 AAAAGCAGGA
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.07
42 35 0.50
43 1 0.01
44 3 0.04
45 20 0.29
46 6 0.09
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.40
Consensus pattern (42 bp):
TCCTCAAAGAGCAGGACACATTTCGTTTTCCTCTTTCTTTGG
Found at i:357010 original size:38 final size:39
Alignment explanation
Indices: 356956--357052 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
356946 GGACATACTC
* * *
356956 TTTTTCACTTTTTCCTCAAGAAGCAGGA-CACTTTCCTT-T
1 TTTTTC-CTTTGTCCTCAAGAAGCAAGACCA-TTTCATTCT
*
356995 TTTTTCCTTTGTCCTCAAGGAGCAAGACCTATTTCATTCT
1 TTTTTCCTTTGTCCTCAAGAAGCAAGACC-ATTTCATTCT
*
357035 CTTTTCCTTTGTCCTCAA
1 TTTTTCCTTTGTCCTCAA
357053 AAAGTGAGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 18 0.36
39 13 0.26
40 19 0.38
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (39 bp):
TTTTTCCTTTGTCCTCAAGAAGCAAGACCATTTCATTCT
Found at i:357675 original size:13 final size:13
Alignment explanation
Indices: 357654--357683 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
357644 ATACATGGTT
*
357654 CATTGTATCGATA
1 CATTATATCGATA
357667 CATTATATCGATA
1 CATTATATCGATA
357680 CATT
1 CATT
357684 TTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:357730 original size:19 final size:20
Alignment explanation
Indices: 357699--357752 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
357689 TTTACCTAGA
*
357699 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
357719 TGTATC-ATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
357738 TGTATCGATACATTG
1 TGTATCGATACATTG
357753 TATCGATGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:357753 original size:13 final size:13
Alignment explanation
Indices: 357735--357764 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
357725 ATACATTGCT
357735 CATTGTATCGATA
1 CATTGTATCGATA
*
357748 CATTGTATCGATG
1 CATTGTATCGATA
357761 CATT
1 CATT
357765 CAGGCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:360179 original size:51 final size:51
Alignment explanation
Indices: 360039--360181 Score: 162
Period size: 50 Copynumber: 2.8 Consensus size: 51
360029 TCCCGGTTCC
* * * *
360039 ATTTCCAAAACGTCAAATTTTCTTAATCGGGGATACTCGAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
* * ** ** *
360090 -TTTCTAAAGCATTGATTTACCACAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
* *
360140 ATTTCCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
360182 CCCGTTATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
50 39 0.55
51 32 0.45
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
Found at i:360203 original size:28 final size:28
Alignment explanation
Indices: 360170--360241 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
360160 TCATAATTGG
**
360170 GGATACTCCAACCCCGTTATTTCATCGA
1 GGATACTCCAACCCCGTTATTTCAGAGA
** *
360198 GGATACTCCAACCCTATTATTTCCGAGA
1 GGATACTCCAACCCCGTTATTTCAGAGA
360226 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
360242 GCTTTATATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCAGAGA
Found at i:360312 original size:28 final size:28
Alignment explanation
Indices: 360273--360346 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
360263 TTTTTTCATA
360273 ATCGAGGG-TACTCCAACCCCGTTATTTC
1 ATCG-GGGATACTCCAACCCCGTTATTTC
**
360301 ATCGGGGATACTCCAATTCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
360329 -TGAGGGGATACTCCAACC
1 AT-CGGGGATACTCCAACC
360347 ATGATTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:360356 original size:108 final size:107
Alignment explanation
Indices: 360119--360396 Score: 328
Period size: 108 Copynumber: 2.6 Consensus size: 107
360109 CCACAATCGG
* * * * *
360119 GGATACTCCAACTC-CGATTTTATTTCCAAAACACCAATTTTTCATAATTGGGGATACTCCAACC
1 GGATACTCCAAC-CACGACTTTATATCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACC
360183 CCGTTATTTCATCGAGGATACTCCAACCCTATTATTTCCGAGA
65 CCGTTATTTCATCGAGGATACTCCAACCCTATTATTTCCGAGA
* * ** *
360226 GGATACTCCAACCCCGGCTTTATATCTAAAAATATTATTTTTTCATAATCGAGGG-TACTCCAAC
1 GGATACTCCAACCACGACTTTATATCT-AAAATACCAATTTTTCATAATCG-GGGATACTCCAAC
* * * * *
360290 CCCGTTATTTCATCGGGGATACTCCAATTCC-GTTATTTCTGAGG
64 CCCGTTATTTCATCGAGGATACTCCAA-CCCTATTATTTCCGAGA
* * * *
360334 GGATACTCCAACCATGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGATACTCCAACCACGACTTTATATCTAAAATACCAATTTTTCATAATCGGGGATACTCCAAC
360397 TCCGATTTTA
Statistics
Matches: 143, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
106 4 0.03
107 49 0.34
108 85 0.59
109 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (107 bp):
GGATACTCCAACCACGACTTTATATCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCC
CGTTATTTCATCGAGGATACTCCAACCCTATTATTTCCGAGA
Found at i:360392 original size:51 final size:50
Alignment explanation
Indices: 360332--360449 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 50
360322 TTATTTCTGA
*
360332 GGGGATACTCCAACCATGATTTTA-TTTCTAAAATACCAATTTT-TCACAATC
1 GGGGATACTCCAACC-CGATTTTATTTTC-AAAATACCAATTTTCT-ACAATC
* *
360383 GGGGATACTCCAACTCCGATTTTATTTTCAAAATACCGATTTTCTATAATC
1 GGGGATACTCCAAC-CCGATTTTATTTTCAAAATACCAATTTTCTACAATC
*
360434 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
360450 TGTTATTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
50 2 0.03
51 52 0.87
52 6 0.10
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTCTACAATC
Found at i:360546 original size:131 final size:130
Alignment explanation
Indices: 360305--360548 Score: 332
Period size: 131 Copynumber: 1.9 Consensus size: 130
360295 TATTTCATCG
* * *
360305 GGGATACTCCAATTCCGTTATTTCTGAGGGGATACTCCAACCATGATTTTATTTCTAAAATACCA
1 GGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACCACGATTTTATTTCTAAAACACCA
* * *
360370 ATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAATACCGATTTTCTATAATCA
66 ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTCCAAAATACCGATTTTCTATAATCA
* *
360435 GGGATACTCCAA-CCCTGTTATTT-TCGAGGGGATACTCCAACCCCGATTTTTATTTCTAGAACA
1 GGGATACTCCAATCCC-GTTATTTCT-GAGGGGATACTCCAACCACGA-TTTTATTTCTAAAACA
* * *
360498 CCAATTTTTCATAATCGGGGATACTCTAGCCCCG-TTGTTATCTCCAAAATA
63 CCAATTTTTCACAATCGGGGATACTCCAACCCCGATT-TTATCTCCAAAATA
360549 TTAAATTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
129 3 0.03
130 40 0.40
131 56 0.57
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (130 bp):
GGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACCACGATTTTATTTCTAAAACACCA
ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTCCAAAATACCGATTTTCTATAATCA
Found at i:362673 original size:13 final size:13
Alignment explanation
Indices: 362655--362684 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
362645 CCGTTTAAAG
362655 CAATGTATCGATA
1 CAATGTATCGATA
362668 CAATGTATCGATA
1 CAATGTATCGATA
362681 CAAT
1 CAAT
362685 ATGCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:362774 original size:29 final size:28
Alignment explanation
Indices: 362732--362821 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
362722 CTGCCAGTTT
362732 CATGTATCGATACAATATCCATGTATCGA
1 CATGTATCGATACAATAT-CATGTATCGA
* *
362761 CATGTATCAATACAATGAACATGTATCGATA
1 CATGTATCGATACAAT-ATCATGTATCG--A
*
362792 CATTGTATCGATACAAGTATAATGTATCGA
1 CA-TGTATCGATACAA-TATCATGTATCGA
362822 TACATCTGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
29 24 0.47
30 2 0.04
31 3 0.06
32 21 0.41
33 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (28 bp):
CATGTATCGATACAATATCATGTATCGA
Found at i:362800 original size:13 final size:13
Alignment explanation
Indices: 362782--362806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362772 ACAATGAACA
362782 TGTATCGATACAT
1 TGTATCGATACAT
362795 TGTATCGATACA
1 TGTATCGATACA
362807 AGTATAATGT
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:362806 original size:32 final size:33
Alignment explanation
Indices: 362734--362826 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 33
362724 GCCAGTTTCA
*
362734 TGTATCGATACAAT-ATCCATGTATCG--ACA-
1 TGTATCGATACAATGATACATGTATCGATACAT
*
362763 TGTATCAATACAATGA-ACATGTATCGATACAT
1 TGTATCGATACAATGATACATGTATCGATACAT
362795 TGTATCGATACAA-GTATA-ATGTATCGATACAT
1 TGTATCGATACAATG-ATACATGTATCGATACAT
362827 CTGGGTGTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
29 22 0.40
30 1 0.02
31 4 0.07
32 27 0.49
33 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGATACATGTATCGATACAT
Found at i:365612 original size:84 final size:84
Alignment explanation
Indices: 365423--365673 Score: 271
Period size: 83 Copynumber: 3.0 Consensus size: 84
365413 AAAATTTTAA
* * * *
365423 TTTTAAGGAAACTCTATCCTT-ACT-ATTCCAAGGGAATACTCTAATCCCAATCTTCAAAAAACT
1 TTTTAGGGAAACTCTA-ACTTCACTCATTCCGAGGG-ATACTCTAATCCCAATCTTTAAAAAACT
* *
365486 TAAACTTTTT-TTCATATAAT
64 CAAACTTTTTCTTCGTATAAT
* * * * * *
365506 CTTTGGGGAAACTCCATCTTCACTCATTCTGAGGGATACTCTAATCCCGATCTTTAAAAAACTCA
1 TTTTAGGGAAACTCTAACTTCACTCATTCCGAGGGATACTCTAATCCCAATCTTTAAAAAACTCA
365571 AACTTTTTCTTCGTATAAT
66 AACTTTTTCTTCGTATAAT
* * * *
365590 TTTTAGGGAAACTCTAACTTCACTC-TTCCGAGGGATACTCTCA-CTCCAAT-ATTCAAAAATTC
1 TTTTAGGGAAACTCTAACTTCACTCATTCCGAGGGATACTCTAATC-CCAATCTTTAAAAAACTC
* *
365652 AAAATTTTTCTTCGTATTAT
65 AAACTTTTTCTTCGTATAAT
365672 TT
1 TT
365674 CATCTTTAGG
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
82 33 0.23
83 70 0.50
84 38 0.27
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.37
Consensus pattern (84 bp):
TTTTAGGGAAACTCTAACTTCACTCATTCCGAGGGATACTCTAATCCCAATCTTTAAAAAACTCA
AACTTTTTCTTCGTATAAT
Found at i:369367 original size:19 final size:20
Alignment explanation
Indices: 369336--369386 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
369326 GAGAGGGCAG
369336 TATTAATACAATTTTTATTT
1 TATTAATACAATTTTTATTT
369356 TATTAA-ACAATTTTTATTT
1 TATTAATACAATTTTTATTT
*
369375 TATCAATACAAT
1 TATTAATACAAT
369387 GTTCAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAATACAATTTTTATTT
Found at i:371527 original size:20 final size:20
Alignment explanation
Indices: 371452--371528 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
371442 AAGTACCTAG
371452 ATGTATCGATACATT-TTTCA
1 ATGTATCGATACATTCTTT-A
* * * *
371472 ATATATCGATA-TTTGTATGA
1 ATGTATCGATACATTCT-TTA
371492 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTTA
371512 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
371529 ATCTTTTTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 41 0.87
21 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTTA
Found at i:383737 original size:20 final size:20
Alignment explanation
Indices: 383712--383761 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
383702 AACTAGATGA
383712 ATCGATACATTATTCAATGT
1 ATCGATACATTATTCAATGT
383732 ATCGATACATTATTCAATGT
1 ATCGATACATTATTCAATGT
383752 ATCGATACAT
1 ATCGATACAT
383762 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (20 bp):
ATCGATACATTATTCAATGT
Found at i:383835 original size:40 final size:39
Alignment explanation
Indices: 383775--383852 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
383765 GGTAAAAAGA
* *
383775 CATAATGTATCGATACATTGAAGAATATATCGTTACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
383814 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
383853 ATGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:383842 original size:20 final size:20
Alignment explanation
Indices: 383778--383852 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
383768 AAAAAGACAT
*
383778 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * * *
383798 AATATATCGTTACATTCATA
1 AATGTATCGATACATTGAAA
* *
383818 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
383838 AATGTATCGATACAT
1 AATGTATCGATACAT
383853 ATGGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:384638 original size:58 final size:57
Alignment explanation
Indices: 384431--386107 Score: 882
Period size: 55 Copynumber: 29.4 Consensus size: 57
384421 CACTAACTTA
* * * * * *
384431 TGTGGGCCTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAAAGTTACCACTGGCT
1 TGTGGG-CTTTAAAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGACT
* *
384493 TGTGGGCTTTAAAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAGAGTTGCTACTGACTT
1 TGTGGGCTTTAAAAGGGTGCCACTGA-CT-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
* * *
384554 GTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTACCACTAACT
1 -TGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
384613 TGTGGGCTTTAAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGTCT
1 TGTGGGCTTTAAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * *
384671 TGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTT-AAAAGGGTGCCATTGACT
1 TGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
384728 TGCGTGGGCTTTGAAAGAGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTAAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
384788 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACT
* * *
384846 CGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * *
384902 TGTTGGCTTTGAAATGGGTTGCCACT---TGTGTGGGCTTTCAAATGGGTTGCCACCGACTT
1 TGTGGGCTTT-AAAAGGG-TGCCACTGACT-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
* * * *
384961 GTGTGGGCTTTGAAATGGGTTGCCA-TCGACTTGTGTGGGCTTT-AAAAGGGTGCCAGTAACT
1 -TGTGGGCTTT-AAAAGGG-TGCCACT-GAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACT
* ** * * * *
385022 TGTGGG-ATTAAAGAGCATGCCAC-GAAGTTGTGGGC-TT-AAAAGGGTGCCACAGAGT
1 TGTGGGCTTTAAA-AGGGTGCCACTG-ACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * *
385077 TGTGGGCTTTGAAAGGGTGCCAC-GAAGTTGTGGACTTT--AAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTG-ACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * * *
385132 TGTGGAC-TTAAAACGATGCCACGGAGTTGTGGGC-TT-AAAATGA-TGCTAC-GAAAT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTG-ACT
* * * * * *
385186 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
385242 TGTGGGCTTTGAAATGGGTTGCCACT---TGTGTGGGCTTTCAAATAG-GTTGCCACCGACTT
1 TGTGGGCTTT-AAAAGGG-TGCCACTGACT-TGTGGGCTTTGAAA-AGAG-TGCCACTGAC-T
* * * * *
385301 GTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT-AAAAGGGTGCCACGGAGT
1 -TGTGGGCTTT-AAAAGGG-TGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * * *
385362 TGTGGACTTT-AAAGGGTCCCACAGAGTTGTGGAC-TT-AAAACGA-TGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTGACT
* * * * * * * *
385416 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGGTACCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * * * * * *
385471 TATGGAC-TTAAAATGATGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * * * *
385526 TGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * * * * * *
385582 TATGGACTTT-AAAGGGTACCACGGAGTTGTGGAC-TT-AAGACGA-TGCTACGGAAT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAA-AAGAGTGCCACTGACT
* * * * * *
385636 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * *
385692 TGTGGGCTTTGAAATGGGTTGCCACT---TGTGTGGGCTTTCAAATGGGATGCCACCGACTT
1 TGTGGGCTTT-AAAAGGG-TGCCACTGACT-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T
* * * * *
385751 GTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT-AAAAGGGTGCCACGGAGT
1 -TGTGGGCTTT-AAAAGGG-TGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * * *
385812 TGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-TT-AAAACGA-TGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GAGTGCCACTGACT
* * * * * *
385866 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGGTGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG-ACT
* * * * * * * * * * *
385921 TGTGGAC-TTAAAACGATGCCACGGAGTTGT-GGATTTTAAATGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * * *
385976 TGTGGACTTTAAAAGGGTGCCA-TGGAGTTGTGGAC-TT-AAAATG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGTGCCACT-GACTTGTGGGCTTTGAAAA-GAGTGCCACTGACT
* * * * * *
386031 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG-ACT
* *
386085 TGTGGACTTTAAAAGGATGCCAC
1 TGTGGGCTTTAAAAGGGTGCCAC
386108 GGAGTTATGG
Statistics
Matches: 1372, Mismatches: 157, Indels: 179
0.80 0.09 0.10
Matches are distributed among these distances:
53 9 0.01
54 214 0.16
55 318 0.23
56 183 0.13
57 105 0.08
58 206 0.15
59 41 0.03
60 156 0.11
61 31 0.02
62 42 0.03
63 31 0.02
64 36 0.03
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:385077 original size:27 final size:28
Alignment explanation
Indices: 384492--386134 Score: 1279
Period size: 28 Copynumber: 57.9 Consensus size: 28
384482 TACCACTGGC
* *
384492 TTGTGGGCTTTAAAAGGGTGCCACTGATT
1 TTGTGGGCTTTAAAAGGGTGCCACGGA-G
* * * *
384521 TGTGTGGGCTTTGAAAAGAGTTGCTACTGACT
1 T-TGTGGGCTTT-AAAAG-GGTGCCACGGA-G
* * *
384553 TGTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 T-TGTGGGCTTT-AAAAGGGTGCCACGGAG
* * ** *
384583 TTGTGGGCTTTGAAAAGAGTACCACTAAC
1 TTGTGGGCTTT-AAAAGGGTGCCACGGAG
* *
384612 TTGTGGGCTTTAAAAGGGGTGCCACTGAC
1 TTGTGGGCTTTAAAA-GGGTGCCACGGAG
* * **
384641 TTGTGGGCTTTGAAAGGGGTGCCACTGTC
1 TTGTGGGCTTT-AAAAGGGTGCCACGGAG
* ** *
384670 TTGTGGGCTTTGAAAAGAGTGCCACTAAC
1 TTGTGGGCTTT-AAAAGGGTGCCACGGAG
* ** *
384699 TTATGGGCTTTAAAAGGGTGCCATTGAC
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
384727 TTGCGTGGGCTTTGAAAGAGGTGCCACTGAC
1 TT--GTGGGCTTTAAAAG-GGTGCCACGGAG
* * *
384758 TTGTGGGCTTTGAAAGGGGTGCCACTGAC
1 TTGTGGGCTTT-AAAAGGGTGCCACGGAG
* ** *
384787 TTGTGGGCTTTGAAAGGGTGCCACTAAC
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
384815 TTGTGGGCTTTGAAAAGAGTTGCCACCGAC
1 TTGTGGGCTTT-AAAAG-GGTGCCACGGAG
* * *
384845 TCGTGGGCTTTAAAAGGGTGCCACTGAC
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
384873 TTGTGGGCTTTGAAAGGGTGCCACTGAT
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * **
384901 TTGTTGGCTTTGAAATGGGTTGCCAC-TTG
1 TTGTGGGCTTT-AAAAGGG-TGCCACGGAG
* * *
384930 -TGTGGGCTTTCAAATGGGTTGCCACCGACT
1 TTGTGGGCTTT-AAAAGGG-TGCCACGGA-G
* *
384960 TGTGTGGGCTTTGAAATGGGTTGCCATC-GACT
1 T-TGTGGGCTTT-AAAAGGG-TGCCA-CGGA-G
* *
384992 TGTGTGGGCTTTAAAAGGGTGCCA-GTAAC
1 T-TGTGGGCTTTAAAAGGGTGCCACG-GAG
* ** *
385021 TTGTGGG-ATTAAAGAGCATGCCACGAAG
1 TTGTGGGCTTTAAA-AGGGTGCCACGGAG
*
385049 TTGTGGGC-TTAAAAGGGTGCCACAGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385076 TTGTGGGCTTTGAAAGGGTGCCACGAAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385104 TTGTGGACTTT-AAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385131 TTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * * * *
385158 TTGTGGGC-TTAAAATGATGCTACGAAA
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385185 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385213 TTGTGGACTTTAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* **
385241 TTGTGGGCTTTGAAATGGGTTGCCAC-TTG
1 TTGTGGGCTTT-AAAAGGG-TGCCACGGAG
* * *
385270 -TGTGGGCTTTCAAATAGGTTGCCACCGACT
1 TTGTGGGCTTT-AAA-AGGGTGCCACGGA-G
* * *
385300 TGTGTGGGCTTTGAAATGGGTTGCCACCGACT
1 T-TGTGGGCTTT-AAAAGGG-TGCCACGGA-G
385332 TGTGTGGGCTTTAAAAGGGTGCCACGGAG
1 T-TGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385361 TTGTGGACTTT-AAAGGGTCCCACAGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385388 TTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385415 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385443 TTGTGGACTTT-AAAGGGTACCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * * *
385470 TTATGGAC-TTAAAATGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385497 TTGTGGACTTTAAAAGGGTGCCACAGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385525 TTGTGGACTTTAAAAGGGTGTCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385553 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385581 TTATGGACTTT-AAAGGGTACCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * * * * *
385608 TTGTGGAC-TTAAGACGATGCTACGGAA
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385635 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385663 TTGTGGACTTTAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* **
385691 TTGTGGGCTTTGAAATGGGTTGCCAC-TTG
1 TTGTGGGCTTT-AAAAGGG-TGCCACGGAG
* * *
385720 -TGTGGGCTTTCAAATGGGATGCCACCGACT
1 TTGTGGGCTTT-AAAAGGG-TGCCACGGA-G
* * *
385750 TGTGTGGGCTTTGAAATGGGTTGCCACCGACT
1 T-TGTGGGCTTT-AAAAGGG-TGCCACGGA-G
385782 TGTGTGGGCTTTAAAAGGGTGCCACGGAG
1 T-TGTGGGCTTTAAAAGGGTGCCACGGAG
*
385811 TTGTGGACTTT-AAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385838 TTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
385865 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385893 TTGTGGACTTT-AAAGGGTGCCACGAAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
385920 TTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
** *
385947 TTGTGGATTTTAAATGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385975 TTGTGGACTTTAAAAGGGTGCCATGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
386003 TTGTGGAC-TTAAAATGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
*
386030 TTGTGGAC-TTAAAAGGGTGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
386057 TTGTGGAC-TTAAAAGGGTGCCACGAAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
386084 TTGTGGACTTTAAAAGGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGTGCCACGGAG
* * *
386112 TTATGGAC-TTAAAAGGATGCCAC
1 TTGTGGGCTTTAAAAGGGTGCCAC
386135 AGAATTATGG
Statistics
Matches: 1388, Mismatches: 175, Indels: 104
0.83 0.10 0.06
Matches are distributed among these distances:
26 12 0.01
27 394 0.28
28 534 0.38
29 170 0.12
30 88 0.06
31 46 0.03
32 143 0.10
33 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.28
Consensus pattern (28 bp):
TTGTGGGCTTTAAAAGGGTGCCACGGAG
Found at i:385152 original size:82 final size:82
Alignment explanation
Indices: 384612--386148 Score: 1146
Period size: 82 Copynumber: 18.1 Consensus size: 82
384602 TACCACTAAC
* * * * * * ** *
384612 TTGTGGGCTTTAAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGTCTTGTGGG
1 TTGTGGAC-TTAAAA-GGGTGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGA
* ** *
384677 CTTTGAAAAGAGTGCCACTAAC
63 CTTT--AAAGGGTGCCACGGAG
* * ** * * * * *
384699 TTATGGGCTTTAAAAGGGTGCCATTGACTTGCGTGGGCTTTGAAAGAGGTGCCACTGACTTGTGG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTT--GTGGACTTTAAAAG-GGTGCCACGGAGTTGTGG
* * *
384764 GCTTTGAAAGGGGTGCCACTGAC
62 ACTTT-AAA-GGGTGCCACGGAG
* * ** * * * * * * *
384787 TTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAG-GGTGCCACGGAGTTGTGGA
* *
384852 CTTTAAAAGGGTGCCACTGAC
63 CTTT-AAAGGGTGCCACGGAG
* * * * * **
384873 TTGTGGGCTTTGAAAGGGTGCCACTGATTTGTTGG-CTTTGAAATGGGTTGCCAC-TTG-TGTGG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTG-TGGACTTT-AAAAGGG-TGCCACGGAGTTGTGG
* * *
384935 GCTTTCAAATGGGTTGCCACCGACT
62 ACTTT-AAA-GGG-TGCCACGGA-G
* * * * * *
384960 TGTGTGGGCTTTGAAATGGGTTGCCATC-GACTTGTGTGGGCTTTAAAAGGGTGCCA-GTAACTT
1 T-TGTGGAC-TT-AAAAGGG-TGCCA-CGGA-GT-TGTGGACTTTAAAAGGGTGCCACG-GAGTT
* *
385023 GTGGGA--TTAAAGAGCATGCCACGAAG
58 GT-GGACTTTAAAG-G-GTGCCACGGAG
* * * * *
385049 TTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAGGGTGCCACGAAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
385114 TAAAGGGTGCCACGGAG
66 TAAAGGGTGCCACGGAG
* * * * * * * *
385131 TTGTGGACTTAAAACGATGCCACGGAGTTGTGGGC-TTAAAATGATGCTACGAAATTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
385195 TAAAAGGGTGCCACGGAG
66 T-AAAGGGTGCCACGGAG
* * * * ** *
385213 TTGTGGACTTTAAAAGGGTGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCAC-TTG-TGTGGG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGG-TGCCACGGAGTTGTGGA
* * *
385276 CTTTCAAATAGGTTGCCACCGACT
63 CTTT--AA-AGGGTGCCACGGA-G
* * * * *
385300 TGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAGTTGT
1 T-TGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGACTTTAAAAGGGTGCCACGGAGTTGT
* *
385365 GGACTTTAAAGGGTCCCACAGAG
60 GGACTTTAAAGGGTGCCACGGAG
* *
385388 TTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
*
385453 TAAAGGGTACCACGGAG
66 TAAAGGGTGCCACGGAG
* * * *
385470 TTATGGACTTAAAATGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
*
385535 TAAAAGGGTGTCACGGAG
66 T-AAAGGGTGCCACGGAG
* *
385553 TTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTT-AAAGGGTACCACGGAGTTGTGGAC-
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
* * * *
385616 TTAAGACGATGCTACGGAA
65 TTAA-AGGGTGCCACGGAG
* * *
385635 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACTGATTTGTGGGCT
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
**
385700 TTGAAATGGGTTGCCAC-TTG
65 TT-AAA-GGG-TGCCACGGAG
* * * * * * * *
385720 -TGTGGGCTTTCAAATGGGATGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TTGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGACTTT-AAAAGGG-TGCCACGGA-GT-
*
385784 TGTGGGCTTTAAAAGGGTGCCACGGAG
57 TGTGGACTTT-AAAGGGTGCCACGGAG
* * *
385811 TTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGATGCCACGGAGTTGTGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
385875 TAAAAGGGTGCCACGGAG
66 T-AAAGGGTGCCACGGAG
* * * * *
385893 TTGTGGACTTTAAAGGGTGCCACGAAGTTGTGGAC-TTAAAACGATGCCACGGAGTTGTGGATTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
385957 TAAATGGGTGCCACGGAG
66 TAAA-GGGTGCCACGGAG
* *
385975 TTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGAC-TTAAAATGGTGCCACGGAGTTGTGGACT
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
*
386039 TAAAAGGGTGCCACGGAG
65 TTAAAGGGTGCCACGGAG
* * *
386057 TTGTGGACTTAAAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAGTTATGGACTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
386122 AAAAGGATGCCACAGAA
66 TAAAGGGTGCCACGGAG
*
386139 TTATGGACTT
1 TTGTGGACTT
386149 TGAAAGAAAA
Statistics
Matches: 1231, Mismatches: 156, Indels: 131
0.81 0.10 0.09
Matches are distributed among these distances:
81 55 0.04
82 410 0.33
83 169 0.14
84 87 0.07
85 35 0.03
86 127 0.10
87 68 0.06
88 105 0.09
89 37 0.03
90 58 0.05
91 31 0.03
92 47 0.04
93 2 0.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.28
Consensus pattern (82 bp):
TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
TAAAGGGTGCCACGGAG
Found at i:385639 original size:450 final size:450
Alignment explanation
Indices: 385038--386153 Score: 1846
Period size: 450 Copynumber: 2.5 Consensus size: 450
385028 ATTAAAGAGC
* * * * *
385038 ATGCCACGAAGTTGTGGGC-TTAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAGGGTGCCACGA
1 ATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGG
* * *
385102 AGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGGC
66 AGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
385166 TTAAAATGATGCTACGAAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
131 TTAAAACGATGCTACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
*
385231 TGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACTTGTGTGGGCTTTCAAATAGGTTGCCACC
196 TGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACTTGTGTGGGCTTTCAAATAGGATGCCACC
385296 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAG
261 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAG
385361 TTGTGGACTTTAAAGGGTCCCACAGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTT
326 TTGTGGACTTTAAAGGGTCCCACAGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTT
* *
385426 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACGGAGTTATGGACTTAAAATG
391 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACGAAGTTATGGACTTAAAACG
*
385486 ATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGTCACGG
1 ATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGG
* * *
385551 AGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTAAAGGGTACCACGGAGTTGTGGAC
66 AGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
*
385616 TTAAGACGATGCTACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
131 TTAAAACGATGCTACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
*
385681 TGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACTTGTGTGGGCTTTCAAATGGGATGCCACC
196 TGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACTTGTGTGGGCTTTCAAATAGGATGCCACC
385746 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAG
261 GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAG
* *
385811 TTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTT
326 TTGTGGACTTTAAAGGGTCCCACAGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTT
* *
385876 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGAAGTTGTGGACTTAAAACG
391 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACGAAGTTATGGACTTAAAACG
* * * *
385936 ATGCCACGGAGTTGTGGATTTTAAATGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATGG
1 ATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGG
*
386001 AGTTGTGGAC-TTAAAATGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 AGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * * *
386065 TTAAAAGGGTGCCAC-GAAGTTGTGGACTTTAAAAGGATGCCACGGAGTTATGGAC-TTAAAAGG
131 TTAAAACGATGCTACGGAA-TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
* * * * *
386128 ATGCCACAGAATTATGGACTTTGAAA
195 GTGCCACTGATTTGTGGGCTTTGAAA
386154 GAAAATGCCA
Statistics
Matches: 622, Mismatches: 43, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
448 49 0.08
449 149 0.24
450 424 0.68
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (450 bp):
ATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGG
AGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
TTAAAACGATGCTACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG
TGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACTTGTGTGGGCTTTCAAATAGGATGCCACC
GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACGGAG
TTGTGGACTTTAAAGGGTCCCACAGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGACTTT
AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACGAAGTTATGGACTTAAAACG
Found at i:386142 original size:27 final size:27
Alignment explanation
Indices: 385039--386148 Score: 1076
Period size: 27 Copynumber: 39.7 Consensus size: 27
385029 TTAAAGAGCA
* *
385039 TGCCACGAAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
385066 TGCCACAGAGTTGTGGGCTTTGAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
385094 TGCCACGAAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
385121 TGCCACGGAGTTGTGGACTTAAAACGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
385148 TGCCACGGAGTTGTGGGCTTAAAATGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
385175 TGCTACGAAATTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
385203 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * *
385231 TGCCACTGATTTGTGGGCTTTGAAATGGG
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGG
** * *
385260 TTGCCAC-TTG-TGTGGGCTTTCAAATAGGT
1 -TGCCACGGAGTTGTGGAC-TT-AAA-AGGG
* * * *
385289 TGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 TGCCACGGA-GT-TGTGGAC-TT-AAAAGGG
* * *
385320 TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
1 -TGCCACGGA-GT-TGTGGAC-TTAAAAGGG
*
385351 TGCCACGGAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
385378 TCCCACAGAGTTGTGGACTTAAAACGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
385405 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
385433 TGCCACGGAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
385460 TACCACGGAGTTATGGACTTAAAATGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
385487 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
385515 TGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
385543 TGTCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
385571 TGCCACGGAGTTATGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
385598 TACCACGGAGTTGTGGACTTAAGACGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
385625 TGCTACGGAATTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
385653 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * *
385681 TGCCACTGATTTGTGGGCTTTGAAATGGG
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGG
** * *
385710 TTGCCAC-TTG-TGTGGGCTTTCAAATGGG
1 -TGCCACGGAGTTGTGGAC-TT-AAAAGGG
* * * *
385738 ATGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACGGA-GT-TGTGGAC-TT-AAAAGGG
* * *
385770 TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
1 -TGCCACGGA-GT-TGTGGAC-TTAAAAGGG
*
385801 TGCCACGGAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
385828 TGCCACGGAGTTGTGGACTTAAAACGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
385855 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
385883 TGCCACGGAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
385910 TGCCACGAAGTTGTGGACTTAAAACGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
385937 TGCCACGGAGTTGTGGATTTTAAATGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
385965 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
385993 TGCCATGGAGTTGTGGACTTAAAATGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
386020 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
386047 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
386074 TGCCACGAAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
386102 TGCCACGGAGTTATGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
386129 TGCCACAGAATTATGGACTT
1 TGCCACGGAGTTGTGGACTT
386149 TGAAAGAAAA
Statistics
Matches: 932, Mismatches: 128, Indels: 46
0.84 0.12 0.04
Matches are distributed among these distances:
27 423 0.45
28 375 0.40
29 16 0.02
30 28 0.03
31 14 0.02
32 76 0.08
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:387504 original size:16 final size:16
Alignment explanation
Indices: 387485--387528 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
387475 TCCCTTTTTA
387485 TTTTGCTTTTGCACTT
1 TTTTGCTTTTGCACTT
* *
387501 TTTTTCTTTT-CATTT
1 TTTTGCTTTTGCACTT
387516 TTTGTGCTTTTGC
1 TTT-TGCTTTTGC
387529 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.11, T:0.68
Consensus pattern (16 bp):
TTTTGCTTTTGCACTT
Found at i:394090 original size:10 final size:11
Alignment explanation
Indices: 394063--394092 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
394053 ACGGAAATAA
394063 AGTTTTTGTTG
1 AGTTTTTGTTG
394074 AGTTTTTGTTG
1 AGTTTTTGTTG
394085 AGTTTTTG
1 AGTTTTTG
394093 GTGTTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (11 bp):
AGTTTTTGTTG
Found at i:394624 original size:20 final size:20
Alignment explanation
Indices: 394577--394651 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
394567 AAAAAGACAT
* * *
394577 AATGTATCGATGCATTGAAG
1 AATGTATCGATACATTCAAA
* *
394597 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
394617 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
394637 AATGTATCGATACAT
1 AATGTATCGATACAT
394652 CTGGGTAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:394634 original size:40 final size:39
Alignment explanation
Indices: 394574--394651 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
394564 GTTAAAAAGA
* *
394574 CATAATGTATCGATGCATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
394613 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
394652 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:395769 original size:20 final size:19
Alignment explanation
Indices: 395741--395814 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
395731 TTTACCTAGA
395741 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
* *
395761 TGCATCGATACATTACTCAT
1 TGTATCGATACATT-TTCAT
* *
395781 TGTATCGATAAATTTTACAA
1 TGTATCGATACATTTT-CAT
395801 TGTATCGATACATT
1 TGTATCGATACATT
395815 CAGGCATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:398285 original size:102 final size:102
Alignment explanation
Indices: 398109--398294 Score: 309
Period size: 102 Copynumber: 1.8 Consensus size: 102
398099 TTTTTCATCT
* * * *
398109 CGGGGATACTCCAATCTCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCAGAGATACTCCAA
1 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
398174 CTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAAC
66 CTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAAC
* *
398211 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAATATCAATTTTTCTTAACCAGGGATACTCCAA
1 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
*
398276 CTCTGATTTTATTTCTAAA
66 CTCCGATTTTATTTCTAAA
398295 ATACCAATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (102 bp):
CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
CTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAAC
Found at i:398296 original size:51 final size:50
Alignment explanation
Indices: 398111--398307 Score: 162
Period size: 51 Copynumber: 3.9 Consensus size: 50
398101 TTTCATCTCG
* *
398111 GGGATACTCCAATCTCGGTTTCATTT-TCAAAACATCAATTTTTCTTAATCA
1 GGGATACTCCAATC-CGATTTCATTTCT-AAAACATCAATTTTTCTTAACCA
* * * * * ** ** *
398162 GAGATACTCCAACTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAACCG
1 GGGATACTCCAA-TCCGATTTCATTTCTAAAACATCAATTTTTCTTAACCA
* * * *
398213 GGGATACTCCAATCCCGGTTTCATCTCCAAAATATCAATTTTTCTTAACCA
1 GGGATACTCCAAT-CCGATTTCATTTCTAAAACATCAATTTTTCTTAACCA
* * * *
398264 GGGATACTCCAACTCTGATTTTATTTCTAAAATACCAATTTTTC
1 GGGATACTCCAA-TCCGATTTCATTTCTAAAACATCAATTTTTC
398308 ACAATTGGGG
Statistics
Matches: 110, Mismatches: 32, Indels: 8
0.73 0.21 0.05
Matches are distributed among these distances:
50 1 0.01
51 105 0.95
52 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (50 bp):
GGGATACTCCAATCCGATTTCATTTCTAAAACATCAATTTTTCTTAACCA
Found at i:398318 original size:102 final size:102
Alignment explanation
Indices: 398109--398331 Score: 286
Period size: 102 Copynumber: 2.2 Consensus size: 102
398099 TTTTTCATCT
* * * *
398109 CGGGGATACTCCAATCTCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCAGAGATACTCCAA
1 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
* * *
398174 CTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAAC
66 CTCCGATTTTATTTCTAAAGACTCAATTTACCACAAC
* *
398211 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAATATCAATTTTTCTTAACCAGGGATACTCCAA
1 CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
* * ** *
398276 CTCTGATTTTATTTCTAAAATAC-CAATTTTTCACAAT
66 CTCCGATTTTATTTCT-AAAGACTCAATTTACCACAAC
* *
398313 TGGGGATACTCCAACCCCG
1 CGGGGATACTCCAATCCCG
398332 TCATTTCATC
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
102 100 0.96
103 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CGGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAACCAGAGATACTCCAA
CTCCGATTTTATTTCTAAAGACTCAATTTACCACAAC
Found at i:398347 original size:28 final size:28
Alignment explanation
Indices: 398314--398387 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
398304 TTTCACAATT
398314 GGGGATACTCCAACCCCGTCATTTCATC-A
1 GGGGATACTCCAACCCCGTCATTT--TCGA
* * *
398343 -GGGATACTCCAATCCTGTTATTTTCGA
1 GGGGATACTCCAACCCCGTCATTTTCGA
398370 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
398388 ATTCTATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 35 0.92
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTCATTTTCGA
Found at i:398447 original size:51 final size:50
Alignment explanation
Indices: 398371--398497 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 50
398361 TATTTTCGAG
* * *
398371 GGGATACTCCAACCCCGATTCTATTTCTAAA-ATACTAATTTTTCACAATC-
1 GGGATACTCCAACCCCGATTATATTTCCAAACAT-C-AATTTCTCACAATCA
*
398421 GGAGATACTCCAACTCCGATTATATTTCCAAAGCATCAATTTCTCACAATCA
1 GG-GATACTCCAACCCCGATTATATTTCCAAA-CATCAATTTCTCACAATCA
*
398473 GGGATATTCCAACCCCG-TTAT-TTTC
1 GGGATACTCCAACCCCGATTATATTTC
398498 GCGGGGATAC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
49 4 0.06
50 6 0.09
51 52 0.78
52 3 0.04
53 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTATATTTCCAAACATCAATTTCTCACAATCA
Found at i:398603 original size:52 final size:51
Alignment explanation
Indices: 398499--398611 Score: 120
Period size: 52 Copynumber: 2.2 Consensus size: 51
398489 GTTATTTTCG
* * *
398499 CGGGGATACTCTAACCCCGACCTCATTTCTAAAGCATCAATTTTTCACAAT
1 CGGGGATACTCCAACCCCGACCTCATTTCTAAAGCACCAATTTTCCACAAT
** * * *
398550 CGGGGATACTCCAACCCCGATTTTTATTTCTAGAA-CACCGATTTTCCATAAT
1 CGGGGATACTCCAACCCCGA-CCTCATTTCTA-AAGCACCAATTTTCCACAAT
*
398602 CGGAGATACT
1 CGGGGATACT
398612 TCAGCCCTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
51 19 0.37
52 30 0.59
53 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (51 bp):
CGGGGATACTCCAACCCCGACCTCATTTCTAAAGCACCAATTTTCCACAAT
Found at i:411036 original size:1 final size:1
Alignment explanation
Indices: 411032--411108 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
411022 CATTCTTTTT
* * * * * * * * * *
411032 AAAAAAAAACAAAACAAAAACAACAGAAAAAAAAAAAAAAACAAAAAACAAAACAAAGAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
411097 AGAAAAAAAAAA
1 AAAAAAAAAAAA
411109 TCTGCTTAAG
Statistics
Matches: 54, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:411102 original size:18 final size:16
Alignment explanation
Indices: 411042--411095 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
411032 AAAAAAAAAC
*
411042 AAAACAAAAACAACAGA
1 AAAAAAAAAACAA-AGA
* *
411059 AAAAAAAAAAAAAACA
1 AAAAAAAAAACAAAGA
*
411075 AAAAACAAAACAAAGA
1 AAAAAAAAAACAAAGA
411091 AAAAA
1 AAAAA
411096 GAGAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAGA
Found at i:411105 original size:12 final size:11
Alignment explanation
Indices: 411032--411108 Score: 84
Period size: 11 Copynumber: 6.8 Consensus size: 11
411022 CATTCTTTTT
411032 AAAAAAAAACA
1 AAAAAAAAACA
*
411043 AAACAAAAACA
1 AAAAAAAAACA
* *
411054 ACAGAAAAA-A
1 AAAAAAAAACA
411064 AAAAAAAAACA
1 AAAAAAAAACA
411075 AAAAACAAAACA
1 AAAAA-AAAACA
*
411087 AAGAAAAAAGAGA
1 AA-AAAAAA-ACA
411100 AAAAAAAAA
1 AAAAAAAAA
411109 TCTGCTTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.14
11 24 0.43
12 17 0.30
13 7 0.12
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:412197 original size:55 final size:55
Alignment explanation
Indices: 412105--412503 Score: 442
Period size: 55 Copynumber: 6.9 Consensus size: 55
412095 GATGCCTTTT
* * * *
412105 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
*
412160 CCTTTCAAAGCCCACACGAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
* * *
412215 CCATTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACG
1 CC-TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
412276 CCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
* * * *
412331 CCTTTCAAAGCCCACACAAGTTGGTGGCAGTTTCCAGTCCTCAAAGAGTAGGATGCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGA--C---A
* ** * *
412391 TCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACA
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
*
412447 CCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAG
1 -----CC-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAG
412504 AATGCACTTT
Statistics
Matches: 295, Mismatches: 28, Indels: 36
0.82 0.08 0.10
Matches are distributed among these distances:
54 2 0.01
55 145 0.49
56 4 0.01
57 1 0.00
59 1 0.00
60 5 0.02
61 132 0.45
62 5 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
Found at i:412229 original size:116 final size:115
Alignment explanation
Indices: 412074--412500 Score: 503
Period size: 116 Copynumber: 3.7 Consensus size: 115
412064 CTTCTTCCAC
** *
412074 TTTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTT
1 TTTTCTAGTCCTCAAAGAGCAGGACACC-TTTCTTTTTAAAGCCCACACAAGTTGGTGGCAGCTT
*
412137 CCTAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCA
65 CC-AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
**
412189 TTTTCTAGTCCTCAAAGAGCAGGACACCATTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTT
1 TTTTCTAGTCCTCAAAGAGCAGGACACC-TTTCTTTTTAAAGCCCACACAAGTTGGTGGCAGCTT
* * *
412254 CCAGTCCTCAAAAAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCA
65 CCAGTCCTCAAAGAGTAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
412305 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTC-----AAAGCCCACACAAGTTGGTGGCAGTTTC
1 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAGCTTC
**
412365 CAGTCCTCAAAGAGTAGGATGCTTTTTCTTTGCAAAGCCCACACAAGTTGGTGGCA
66 CAGTCCTCAAAGAGTAGGA--C---ACCTTT-CAAAGCCCACACAAGTTGGTGGCA
** * * * *
412421 CCTTCCAGTCCTCAAAAAGCAGGACACCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA-CTT
1 TTTTCTAGTCCTCAAAGAGCAGGACACCTTT-CTTTTTAAAGCCCACACAAGTTGGTGGCAGC-T
**
412485 TTTAGTCCTCAAAGAG
64 TCCAGTCCTCAAAGAG
412501 CAGAATGCAC
Statistics
Matches: 273, Mismatches: 22, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
110 44 0.16
112 1 0.00
114 2 0.01
115 11 0.04
116 171 0.63
117 7 0.03
122 37 0.14
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (115 bp):
TTTTCTAGTCCTCAAAGAGCAGGACACCTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAGCTTC
CAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:412253 original size:27 final size:27
Alignment explanation
Indices: 412223--412308 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
412213 CACCATTTCT
412223 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * ** ** *
412250 TTTTCCAGTCCTCA-AAAAGCAGGACGCC
1 TTTTAAAG-CC-CACACAAGTTGGTGGCA
*
412278 TCTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
412305 TTTT
1 TTTT
412309 CTAGTCCTCA
Statistics
Matches: 38, Mismatches: 18, Indels: 6
0.61 0.29 0.10
Matches are distributed among these distances:
26 2 0.05
27 19 0.50
28 15 0.39
29 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:412261 original size:61 final size:59
Alignment explanation
Indices: 412074--412503 Score: 485
Period size: 61 Copynumber: 7.4 Consensus size: 59
412064 CTTCTTCCAC
**
412074 TTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACC-TTT-CTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
412134 -CTTCCTAGTCCTCAAAGAGTAGGACACCTTTC----AAAGCCCACACGAGTTGGTGGCA
1 TTTTCC-AGTCCTCAAAGAGCAGGACACCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
*
412189 TTTTCTAGTCCTCAAAGAGCAGGACACCATTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC-TTTTAAAGCCCACACAAGTTGGTGGCA
* *
412250 TTTTCCAGTCCTCAAAAAGCAGGACGCC--TC--TTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
*
412305 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** * *
412360 GTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACAC-CTTTCTTT-TAAAGCCCACACAAGTTGGTGGCA
** * *
412421 CCTTCCAGTCCTCAAAAAGCAGGACACCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTT-CTTTT-AAAGCCCACACAAGTTGGTGGCA
*
412482 CTTTT-TAGTCCTCAAAGAGCAG
1 -TTTTCCAGTCCTCAAAGAGCAG
412504 AATGCACTTT
Statistics
Matches: 316, Mismatches: 34, Indels: 39
0.81 0.09 0.10
Matches are distributed among these distances:
55 138 0.44
56 11 0.03
57 2 0.01
58 2 0.01
59 3 0.01
60 7 0.02
61 151 0.48
62 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (59 bp):
TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:412372 original size:171 final size:174
Alignment explanation
Indices: 412078--412503 Score: 581
Period size: 171 Copynumber: 2.4 Consensus size: 174
412068 TTCCACTTTT
* ** * *
412078 CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGT
1 CAGTCCTCAAAAAGCAGGACACC--TTCC-TTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGT
* * * *
412143 CCTCAAAGAGTAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCATTTTCTAGTCCTCAAAGAG
63 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAGTTTCCAGTCCTCAAAGAG
** **
412208 CAGGACACCATTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
128 CAGGACACCATTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
*
412255 CAGTCCTCAAAAAGCAGGACGCC-T-C-TTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCT
1 CAGTCCTCAAAAAGCAGGACACCTTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCT
*
412317 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAGTTTCCAGTCCTCAAAGAGTAG
66 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAGTTTCCAGTCCTCAAAGAGCAG
** **
412382 GATGCTTTTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
131 GACACCATTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
*
412426 CAGTCCTCAAAAAGCAGGACACCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAG
1 CAGTCCTCAAAAAGCAGGACACC-TTCC-TTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCTAG
412490 TCCTCAAAGAGCAG
62 TCCTCAAAGAGCAG
412504 AATGCACTTT
Statistics
Matches: 223, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
171 153 0.69
173 2 0.01
174 2 0.01
176 2 0.01
177 60 0.27
178 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (174 bp):
CAGTCCTCAAAAAGCAGGACACCTTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCT
CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAGTTTCCAGTCCTCAAAGAGCAG
GACACCATTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:412693 original size:40 final size:42
Alignment explanation
Indices: 412596--412695 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
412586 GACGTACTGT
* *
412596 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
* * *
412639 TCTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTTC
412679 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
412696 AAAGTGGGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 18 0.36
41 5 0.10
42 23 0.46
43 4 0.08
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
Found at i:413451 original size:13 final size:13
Alignment explanation
Indices: 413433--413458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
413423 CATTATTCAA
413433 TGTATCGATACAT
1 TGTATCGATACAT
413446 TGTATCGATACAT
1 TGTATCGATACAT
413459 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:413526 original size:20 final size:20
Alignment explanation
Indices: 413497--413610 Score: 160
Period size: 20 Copynumber: 5.7 Consensus size: 20
413487 TTTATCCAGA
*
413497 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
413517 TGTATTGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
413537 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
413557 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
413577 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGCT-CAT
413597 TGTATCGATACATT
1 TGTATCGATACATT
413611 CAAGCATTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 85 0.98
21 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:415955 original size:51 final size:51
Alignment explanation
Indices: 415898--416079 Score: 163
Period size: 51 Copynumber: 3.6 Consensus size: 51
415888 ATTTTTCATC
* *
415898 TCGGGGATACTCTAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAATCCCGATTTCATTTTCAAAACATCAATTTTTCTTAA
** * * * * ** **
415949 TCGGGGATACTCCAA-CTATGATTTTA-TTTCTAAAGCCTCGATTTACCGCAA
1 TCGGGGATACTCCAATC-CCGATTTCATTTTC-AAAACATCAATTTTTCTTAA
* * *
416000 CCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAATCCCGATTTCATTTTCAAAACATCAATTTTTCTTAA
* *
416051 TCGAGGATACTCCAA-CTCCGATTTTATTT
1 TCGGGGATACTCCAATC-CCGATTTCATTT
416080 CTAAAATACT
Statistics
Matches: 97, Mismatches: 29, Indels: 10
0.71 0.21 0.07
Matches are distributed among these distances:
50 6 0.06
51 88 0.91
52 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (51 bp):
TCGGGGATACTCCAATCCCGATTTCATTTTCAAAACATCAATTTTTCTTAA
Found at i:416094 original size:51 final size:52
Alignment explanation
Indices: 415935--416275 Score: 193
Period size: 51 Copynumber: 6.6 Consensus size: 52
415925 TTTCAAAACA
* ** **
415935 TCAATTTTTCTTAATCGGGGATACTCCAACTATGATTTTATTTCT-AAAGCC
1 TCAATTTTTCTCAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAATAC
* ** * * * * * *
415986 TCGATTTACCGCAACCGGGGATACTCCAA-TCCCGATTTCATCTCCAAAACA-
1 TCAATTTTTCTCAATCGGGGATACTCCAACT-CCGATTTTATTTCTAAAATAC
* *
416037 TCAATTTTTCTTAATCGAGGATACTCCAACTCCGATTTTATTTCTAAAATAC
1 TCAATTTTTCTCAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAATAC
* * * * * *
416089 T-AATTTTTCACAATTGGGAATACTCCAACCCCG---TCATTTCATCAAGGATAC
1 TCAATTTTTCTCAATCGGGGATACTCCAACTCCGATTTTATTTC-T-AA-AATAC
* * * * *
416140 TCCAATCTCGTTATTTTCGA--GGGGATACTCCAACCCCGGTTCTATTTCTAAAATAC
1 T-CAA--T--TT-TTCTCAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAATAC
* * * **
416196 T-AATTTTTCACAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAGCA-
1 TCAATTTTTCTCAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAATAC
* *
416246 TCAATTTCTCAT-AATTGGGGATACTCCAAC
1 TCAATTTTTC-TCAATCGGGGATACTCCAAC
416276 CCCGTTATTT
Statistics
Matches: 218, Mismatches: 51, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
48 6 0.03
49 5 0.02
50 6 0.03
51 154 0.71
52 6 0.03
53 2 0.01
54 2 0.01
55 1 0.00
56 22 0.10
57 4 0.02
58 5 0.02
59 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (52 bp):
TCAATTTTTCTCAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAATAC
Found at i:416112 original size:102 final size:102
Alignment explanation
Indices: 415898--416275 Score: 325
Period size: 102 Copynumber: 3.7 Consensus size: 102
415888 ATTTTTCATC
* * * * *
415898 TCGGGGATACTCTAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCGGGGATACTCCA
1 TCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCA
** ** * ** *
415963 ACTATGATTTTATTTCT-AAAGCCTCGATTTACCGCAA
66 ACTCCGATTTTATTTCTAAAATACT-AATTTTTCACAA
*
416000 CCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCA
1 TCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCA
416065 ACTCCGATTTTATTTCTAAAATACTAATTTTTCACAA
66 ACTCCGATTTTATTTCTAAAATACTAATTTTTCACAA
* * * **** * * * *
416102 TTGGGAATACTCCAACCCCGTCATTTCATCAAGGATAC-TCCAATCTCGTTATT-TTCGAGGGGA
1 TCGGGGATACTCCAATCCCG--ATTTCATCTCCAAAACAT-CAAT-T-TTTCTTAATCGA--GGA
* * *
416165 TACTCCAACCCCGGTTCTATTTCTAAAATACTAATTTTTCACAA
59 TACTCCAACTCCGATTTTATTTCTAAAATACTAATTTTTCACAA
* * * * * *
416209 TCGGGGATACTCCAA-CTCCGATTGT-ATTTCCAAAGCATCAATTTCTCATAATTGGGGATACTC
1 TCGGGGATACTCCAATC-CCGATT-TCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTC
416272 CAAC
64 CAAC
416276 CCCGTTATTT
Statistics
Matches: 219, Mismatches: 45, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
102 110 0.50
103 8 0.04
104 18 0.08
105 16 0.07
106 7 0.03
107 60 0.27
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (102 bp):
TCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCA
ACTCCGATTTTATTTCTAAAATACTAATTTTTCACAA
Found at i:418727 original size:33 final size:33
Alignment explanation
Indices: 418685--418751 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
418675 CATTAGGCAT
*
418685 AATGTATCGATACAATTAT-TCATGTATCGATAC
1 AATGTATCGATACAA-TATCCCATGTATCGATAC
* *
418718 AATGTATCGATATAATATCCCGTGTATCGATAC
1 AATGTATCGATACAATATCCCATGTATCGATAC
418751 A
1 A
418752 TTTCACTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACAATATCCCATGTATCGATAC
Found at i:425431 original size:32 final size:32
Alignment explanation
Indices: 425390--425462 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
425380 ACAAATAGTA
*
425390 AATGTATCGATACAAAAGTGTTGTATTAATAC
1 AATGTATCGATACAAAAGTGTTGTATCAATAC
* * *
425422 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACAAAAGTGTTGTATCAATAC
425454 AATGTATCG
1 AATGTATCG
425463 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACAAAAGTGTTGTATCAATAC
Found at i:425505 original size:21 final size:21
Alignment explanation
Indices: 425479--425520 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
425469 AGCTACTGCC
425479 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
425500 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
425521 GTATCGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:428107 original size:27 final size:28
Alignment explanation
Indices: 428040--428108 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
428030 TCACAATCGA
* *
428040 GGATACTCCAACCCCGTTATTTTCGTGG
1 GGATACTCCAACCCCATTATTTTCGAGG
428068 GGATACTCCAACCCCATTATTTT-GAGG
1 GGATACTCCAACCCCATTATTTTCGAGG
*
428095 GGATACTCAAACCC
1 GGATACTCCAACCC
428109 TGATTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (28 bp):
GGATACTCCAACCCCATTATTTTCGAGG
Found at i:428221 original size:79 final size:78
Alignment explanation
Indices: 428067--428226 Score: 189
Period size: 79 Copynumber: 2.0 Consensus size: 78
428057 TATTTTCGTG
*
428067 GGGATACTCCAACCCCATTATTTTGAGGGGATACTCAAACCCTGATTTTATTTTCAAAACACCAA
1 GGGATACTCCAACCCCATTATTTTAAGGGGATACTCAAACCCTGATTTTATTTTCAAAACACCAA
* *
428132 TTTGCTATAATTA
66 TTTGCCATAATCA
* * * *
428145 GGGATACTCCAACCCTATTGTTTCTAAGGGGATACTCCAA-CCTCGATTTTA-TTTCTAGAACAC
1 GGGATACTCCAACCCCATTATTT-TAAGGGGATACTCAAACCCT-GATTTTATTTTC-AAAACAC
** *
428208 TGATTTTCCATAATCA
63 CAATTTGCCATAATCA
428224 GGG
1 GGG
428227 GTCTCCAGTC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
78 28 0.41
79 41 0.59
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGATACTCCAACCCCATTATTTTAAGGGGATACTCAAACCCTGATTTTATTTTCAAAACACCAA
TTTGCCATAATCA
Found at i:431700 original size:19 final size:20
Alignment explanation
Indices: 431664--431712 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
431654 CAGTTTCATG
431664 TATCGATACAATTGAGTATA
1 TATCGATACAATTGAGTATA
*
431684 TATCGATACAA-TGAGTATG
1 TATCGATACAATTGAGTATA
*
431703 TGTCGATACA
1 TATCGATACA
431713 TTGTATCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACAATTGAGTATA
Found at i:432968 original size:20 final size:20
Alignment explanation
Indices: 432943--433114 Score: 91
Period size: 20 Copynumber: 8.7 Consensus size: 20
432933 TTGTAATGTA
432943 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
432963 TGTATCGAT--A-----CAT
1 TGTATCGATACATTGTTCAT
*
432976 TGTATCGATACATTGGTTACCAGA
1 TGTATCGATACATT-GTT--CA-T
*
433000 T-TAT-GATACATT-TTGTAT
1 TGTATCGATACATTGTT-CAT
*
433018 T-TAATCGATACATTGCTCA-
1 TGT-ATCGATACATTGTTCAT
*
433037 TGTATCGATACATTATATCGATAT
1 TGTATCGATACATTGT-TC---AT
*
433061 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGTTCAT
* *
433081 TGTATTGATACATT-TTACAA
1 TGTATCGATACATTGTT-CAT
433101 TGTATCGATACATT
1 TGTATCGATACATT
433115 CAGGCATTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
13 12 0.10
15 1 0.01
18 3 0.03
19 16 0.14
20 53 0.45
21 1 0.01
22 8 0.07
23 8 0.07
24 15 0.13
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:432978 original size:13 final size:13
Alignment explanation
Indices: 432960--432990 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
432950 ATACATTGTT
432960 CATTGTATCGATA
1 CATTGTATCGATA
432973 CATTGTATCGATA
1 CATTGTATCGATA
432986 CATTG
1 CATTG
432991 GTTACCAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:433075 original size:13 final size:13
Alignment explanation
Indices: 433037--433075 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
433027 ACATTGCTCA
433037 TGTATCGATACAT
1 TGTATCGATACAT
*
433050 TATATCGAT--AT
1 TGTATCGATACAT
433061 TGTATCGATACAT
1 TGTATCGATACAT
433074 TG
1 TG
433076 CTCATTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:435500 original size:51 final size:51
Alignment explanation
Indices: 435445--435588 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
435435 TCCCGGTTCC
* *
435445 ATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTTCAACACCGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACACCGATTTT
* * * ** * * *
435496 ATTTCTAAAGCATCGATTTACCACAATCGGGGATACTCCAACTCTGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACACCGATTTT
* * *
435547 ATTTTCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
435589 CCTATTATTT
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACACCGATTTT
Found at i:435648 original size:28 final size:28
Alignment explanation
Indices: 435575--435648 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
435565 TTTCATAATT
** **
435575 GGGGATACTCCAACCCTATTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCAGA
*
435603 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
435631 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
435649 GCTTTATATC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:435718 original size:28 final size:27
Alignment explanation
Indices: 435687--435752 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 27
435677 TAATCGGGGG
435687 TACTCCAACCCTGTTATTTCATC-GAGGA
1 TACTCCAACCC-GTTATTTCATCAG-GGA
435715 TACTCCAATCCCGTTATTTCATCAGGGA
1 TACTCCAA-CCCGTTATTTCATCAGGGA
435743 TACTCCAACC
1 TACTCCAACC
435753 TCAATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 2 0.06
28 30 0.83
29 4 0.11
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (27 bp):
TACTCCAACCCGTTATTTCATCAGGGA
Found at i:435762 original size:107 final size:106
Alignment explanation
Indices: 435563--435834 Score: 309
Period size: 107 Copynumber: 2.5 Consensus size: 106
435553 AAAACACCAA
* *
435563 TTTTTCATAATTGGGGATACTCCAACCCTATTATTTCATCGGGGATACTCCAACCCCGTTATTTC
1 TTTTTCATAATCGGGGATACTCCAACCCTATTATTTCATCGAGGATACTCCAACCCCGTTATTTC
** ***
435628 CGAGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTT
66 CGAGGGGATACTCCAACCCCAACTTTAT-TCTAAAAATACCG
* * *
435670 TTTTTCATAATCGGGGGTACTCCAACCCTGTTATTTCATCGAGGATACTCCAATCCCGTTATTTC
1 TTTTTCATAATCGGGGATACTCCAACCCTATTATTTCATCGAGGATACTCCAACCCCGTTATTTC
* * * *
435735 ATC-A-GGGATACTCCAACCTCAATTTTATTTTCAAAATACCG
66 --CGAGGGGATACTCCAACCCCAACTTTATTCTAAAAATACCG
* * *
435776 ATTTTCTATAATCAGGGATACTCCAACCCTATTATTT--TCGAAGGGATACTCCAAGCCCG
1 TTTTTC-ATAATCGGGGATACTCCAACCCTATTATTTCATCG-A-GGATACTCCAACCCCG
435835 ATTTTTATTT
Statistics
Matches: 141, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
105 3 0.02
106 14 0.10
107 122 0.87
108 1 0.01
109 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (106 bp):
TTTTTCATAATCGGGGATACTCCAACCCTATTATTTCATCGAGGATACTCCAACCCCGTTATTTC
CGAGGGGATACTCCAACCCCAACTTTATTCTAAAAATACCG
Found at i:437724 original size:29 final size:29
Alignment explanation
Indices: 437683--437764 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
437673 AAGGTTAGTA
*
437683 TGTAATTTTAAAAAGTTAAGGGGCTAATT
1 TGTAATTTTAAAAAGTTAAGGGGCTAATG
* *
437712 TGTAATTTCAAAAAGTTTAGGGGCTAATG
1 TGTAATTTTAAAAAGTTAAGGGGCTAATG
437741 TGTAATTTTAAGAAAGTTCAAGGG
1 TGTAATTTTAA-AAAGTT-AAGGG
437765 TCAGAGTGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 36 0.78
30 6 0.13
31 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
TGTAATTTTAAAAAGTTAAGGGGCTAATG
Found at i:438650 original size:17 final size:17
Alignment explanation
Indices: 438628--438673 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
438618 GTGATTACAG
438628 AAATCTATAATTCATAA
1 AAATCTATAATTCATAA
* * *
438645 AAATCTACAATTCTTAG
1 AAATCTATAATTCATAA
*
438662 AAATCTGTAATT
1 AAATCTATAATT
438674 GATGCTAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (17 bp):
AAATCTATAATTCATAA
Found at i:443581 original size:30 final size:30
Alignment explanation
Indices: 443517--443571 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
443507 TTTTTTTTAC
* *
443517 AATATATTAAAAATCAACTCTATTAAGCAA
1 AATATATTAAAAATCAAATCTATAAAGCAA
443547 AATATA-TAAAAATCAAAT-TATAAAG
1 AATATATTAAAAATCAAATCTATAAAG
443572 TGAATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 6 0.26
29 11 0.48
30 6 0.26
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (30 bp):
AATATATTAAAAATCAAATCTATAAAGCAA
Found at i:450160 original size:35 final size:34
Alignment explanation
Indices: 450114--450213 Score: 141
Period size: 34 Copynumber: 2.9 Consensus size: 34
450104 CGAAGTGATT
450114 AAGAGGTTCTATCTTAGCCTT-TGAAAAAGATAAGG
1 AAGAGGTTCTATCTTAG-CTTGTG-AAAAGATAAGG
450149 AAGAGGTTCTATCTTAGCTTGTGAAAAGAT-AGG
1 AAGAGGTTCTATCTTAGCTTGTGAAAAGATAAGG
* *
450182 GAGAAAGTTCTATCTTAGCTTGTGAAAAGATA
1 AAG-AGGTTCTATCTTAGCTTGTGAAAAGATA
450214 GAGTTGTAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.08
34 36 0.60
35 19 0.32
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (34 bp):
AAGAGGTTCTATCTTAGCTTGTGAAAAGATAAGG
Found at i:451816 original size:21 final size:20
Alignment explanation
Indices: 451792--451831 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
451782 TAATCTTCTT
*
451792 GAAAAGAAAGTAAATGAATTA
1 GAAAA-AAAATAAATGAATTA
*
451813 GAAAAAAAATTAATGAATT
1 GAAAAAAAATAAATGAATT
451832 GCAAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
GAAAAAAAATAAATGAATTA
Found at i:451852 original size:21 final size:19
Alignment explanation
Indices: 451828--451876 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
451818 AAAATTAATG
451828 AATTGCAAGAAAAAAATAAAA
1 AATTGCAAG--AAAAATAAAA
451849 AATTGACTAAGAAAAATAAAA
1 AATTG-C-AAGAAAAATAAAA
*
451870 ACTTGCA
1 AATTGCA
451877 TGACTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 19 0.76
22 1 0.04
23 3 0.12
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.18
Consensus pattern (19 bp):
AATTGCAAGAAAAATAAAA
Found at i:454033 original size:25 final size:26
Alignment explanation
Indices: 453997--454052 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
453987 GAGAATAGAG
*
453997 GAGAACGTTTATAAAGGGAAAAATT-
1 GAGAACGTTTATAAAAGGAAAAATTA
*
454022 GAGAA-GTGTTATAAAAGGAGAAATTA
1 GAGAACGT-TTATAAAAGGAAAAATTA
454048 GAGAA
1 GAGAA
454053 ATTGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.27, T:0.21
Consensus pattern (26 bp):
GAGAACGTTTATAAAAGGAAAAATTA
Found at i:454771 original size:33 final size:33
Alignment explanation
Indices: 454707--454771 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
454697 CACACCCAGA
*
454707 TGTATCGATACAAATTGCTAATTATCGATACAT
1 TGTATCGATACAAATTGCTAATTATCAATACAT
* *
454740 TGTATTGATACAAATTGCT-TTGTATCAATACA
1 TGTATCGATACAAATTGCTAAT-TATCAATACA
454772 CCATAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAATTATCAATACAT
Found at i:455691 original size:233 final size:232
Alignment explanation
Indices: 455284--455749 Score: 797
Period size: 233 Copynumber: 2.0 Consensus size: 232
455274 TTGACGTAAT
* *
455284 TGAGAAGTTTTATCTTAGCATTTTGAAAAGATAAGGAAAAGATTCTATTTTAGGCTGTGAAAAGA
1 TGAGAAGTTCTATCTTAGCATTTTGAAAAGATAAGGAAAAGATTCTATCTTAGGCTGTGAAAAGA
455349 TAGGATTGTAAGGTTATACCTTAGCCTTAAAGGTAACAATTCGGTTAGTAAATTGTGATAATCAC
66 TAGGATTGTAAGGTTATACCTTAGCCTTAAAGGTAACAATTCGGTTAGTAAATTGTGATAATCAC
* *
455414 TTGGCAAGGAATTTCCAAGAAGAAAGGACATAAGTGTCGAGTTTAAAGACCGAACCTCCATAAAT
131 TTGGCAAGAAATTTCCAAGAAGAAAAGACATAAGTGTCGAGTTTAAAGACCGAACCTCCATAAAT
*
455479 CTCATGTGTAATCTCTCTTACCCTTATTCTCTTTCTTA
196 CTCATGTGTAATCTCTCTTA-CCTTATTCTCTTTATTA
*
455517 TGAGAAGTTCTATCTTAGCCTTTTGAAAAGATAAGGAAAAGATTCTATCTTAGGCTGTGAAAAGA
1 TGAGAAGTTCTATCTTAGCATTTTGAAAAGATAAGGAAAAGATTCTATCTTAGGCTGTGAAAAGA
* * *
455582 TAGGGTTGTAAGGTTATACTTTAGCCTTAAAGGTAACAATTCGGTTAGTGAATTGTGATAATCAC
66 TAGGATTGTAAGGTTATACCTTAGCCTTAAAGGTAACAATTCGGTTAGTAAATTGTGATAATCAC
* * * *
455647 TTGGCAAGAAATTTCCAAGGAGAAAAGACGTAAGTGTCGAGTTTAAAGATCGAACCTCCATCAAT
131 TTGGCAAGAAATTTCCAAGAAGAAAAGACATAAGTGTCGAGTTTAAAGACCGAACCTCCATAAAT
*
455712 CTCGTGTGTAATCTCTCTTACCTTATTCTCTTTATTA
196 CTCATGTGTAATCTCTCTTACCTTATTCTCTTTATTA
455749 T
1 T
455750 TCAATTTATT
Statistics
Matches: 219, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
232 17 0.08
233 202 0.92
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (232 bp):
TGAGAAGTTCTATCTTAGCATTTTGAAAAGATAAGGAAAAGATTCTATCTTAGGCTGTGAAAAGA
TAGGATTGTAAGGTTATACCTTAGCCTTAAAGGTAACAATTCGGTTAGTAAATTGTGATAATCAC
TTGGCAAGAAATTTCCAAGAAGAAAAGACATAAGTGTCGAGTTTAAAGACCGAACCTCCATAAAT
CTCATGTGTAATCTCTCTTACCTTATTCTCTTTATTA
Found at i:456214 original size:2 final size:2
Alignment explanation
Indices: 456207--456257 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
456197 GGATTTGATA
456207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456249 AT AT AT AT A
1 AT AT AT AT A
456258 AACCATCCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:457351 original size:19 final size:19
Alignment explanation
Indices: 457327--457365 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
457317 CCTTGATCAG
457327 TAAAAATATAAATTTTAAT
1 TAAAAATATAAATTTTAAT
457346 TAAAAATATAAATTTTAAT
1 TAAAAATATAAATTTTAAT
457365 T
1 T
457366 TTCTTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATATAAATTTTAAT
Found at i:459469 original size:18 final size:17
Alignment explanation
Indices: 459436--459473 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
459426 AGACAGATAG
459436 TTTAAGTTAGAATTTGTA
1 TTTAAGTTAGAATTTG-A
459454 TTTAA-TTAGAATTTTGA
1 TTTAAGTTAGAA-TTTGA
459471 TTT
1 TTT
459474 TTTAAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (17 bp):
TTTAAGTTAGAATTTGA
Found at i:465724 original size:15 final size:15
Alignment explanation
Indices: 465704--465739 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
465694 AAGTGTGGGG
*
465704 AGAAGTCTATAGGAT
1 AGAAGTATATAGGAT
*
465719 AGAAGTATTTAGGAT
1 AGAAGTATATAGGAT
465734 AGAAGT
1 AGAAGT
465740 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.28
Consensus pattern (15 bp):
AGAAGTATATAGGAT
Found at i:466061 original size:7 final size:7
Alignment explanation
Indices: 466049--466090 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
466039 TTTGCTTTGA
466049 AAAAAAT
1 AAAAAAT
466056 AAAAAA-
1 AAAAAAT
*
466062 ATGAAAAT
1 A-AAAAAT
466070 AAAAAAT
1 AAAAAAT
466077 AAAAAAAT
1 -AAAAAAT
466085 AAAAAA
1 AAAAAA
466091 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 1 0.03
7 21 0.70
8 8 0.27
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:466098 original size:8 final size:8
Alignment explanation
Indices: 466047--466130 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
466037 TATTTGCTTT
466047 GAAAAAAA
1 GAAAAAAA
*
466055 TAAAAAAA
1 GAAAAAAA
466063 TGAAAATAAA
1 -GAAAA-AAA
*
466073 -AAATAAA
1 GAAAAAAA
*
466080 -AAAATAA
1 GAAAAAAA
466087 -AAAAAAA
1 GAAAAAAA
466094 GAAAAAAA
1 GAAAAAAA
* **
466102 GGAAAATT
1 GAAAAAAA
466110 GAAAAAAA
1 GAAAAAAA
466118 -AAATGAAAA
1 GAAA--AAAA
466127 GAAA
1 GAAA
466131 GAAACAATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
7 17 0.29
8 27 0.47
9 8 0.14
10 6 0.10
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
GAAAAAAA
Found at i:466099 original size:39 final size:37
Alignment explanation
Indices: 466048--466134 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 37
466038 ATTTGCTTTG
* *
466048 AAAAAAATAAAAAAATGAAAATAAAAAATAAAAAAATAA
1 AAAAAAAGAAAAAAAGGAAAAT-AAAAA-AAAAAAATAA
** *
466087 AAAAAAAGAAAAAAAGGAAAATTGAAAAAAAAAATGA
1 AAAAAAAGAAAAAAAGGAAAATAAAAAAAAAAAATAA
*
466124 AAAGAAAGAAA
1 AAAAAAAGAAA
466135 CAATTTTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 19 0.45
38 3 0.07
39 20 0.48
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (37 bp):
AAAAAAAGAAAAAAAGGAAAATAAAAAAAAAAAATAA
Found at i:466100 original size:7 final size:8
Alignment explanation
Indices: 466048--466091 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
466038 ATTTGCTTTG
466048 AAAAAAAT
1 AAAAAAAT
466056 AAAAAAAT
1 AAAAAAAT
*
466064 --GAAAAT
1 AAAAAAAT
466070 -AAAAAAT
1 AAAAAAAT
466077 AAAAAAAT
1 AAAAAAAT
466085 AAAAAAA
1 AAAAAAA
466092 AAGAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 5 0.16
8 22 0.69
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:466106 original size:9 final size:9
Alignment explanation
Indices: 466048--466134 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
466038 ATTTGCTTTG
*
466048 AAAAAAATA
1 AAAAAAAGA
*
466057 AAAAAATGA
1 AAAAAAAGA
*
466066 AAATAAAAAA
1 AAA-AAAAGA
*
466076 TAAAAAAATAA
1 -AAAAAAA-GA
466087 AAAAAAAGA
1 AAAAAAAGA
*
466096 AAAAAAGGA
1 AAAAAAAGA
*
466105 AAATTGAAA-A
1 AAA--AAAAGA
*
466115 AAAAAATGA
1 AAAAAAAGA
*
466124 AAAGAAAGA
1 AAAAAAAGA
466133 AA
1 AA
466135 CAATTTTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
8 2 0.03
9 32 0.53
10 19 0.32
11 7 0.12
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:466116 original size:28 final size:31
Alignment explanation
Indices: 466085--466152 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 31
466075 ATAAAAAAAT
*
466085 AAAAAAAAAGAAAA-AAAGGAA-AA-TTGAA
1 AAAAAAAAAGAAAAGAAAGAAACAATTTGAA
*
466113 AAAAAAAATGAAAAGAAAGAAACAATTTTGAA
1 AAAAAAAAAGAAAAGAAAGAAACAA-TTTGAA
466145 AAAAAAAA
1 AAAAAAAA
466153 TTATTTAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 13 0.38
29 6 0.18
30 2 0.06
32 13 0.38
ACGTcount: A:0.76, C:0.01, G:0.12, T:0.10
Consensus pattern (31 bp):
AAAAAAAAAGAAAAGAAAGAAACAATTTGAA
Found at i:466144 original size:32 final size:28
Alignment explanation
Indices: 466085--466153 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 28
466075 ATAAAAAAAT
*
466085 AAAAAAAAA-GAAAAAAAGGAAAATTGA
1 AAAAAAAAATGAAAAAAAGAAAAATTGA
466112 AAAAAAAAATGAAAAGAAAGAAACAATTTTGA
1 AAAAAAAAATGAAAA-AAAGAAA-AA--TTGA
466144 AAAAAAAAAT
1 AAAAAAAAAT
466154 TATTTAAGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 9 0.25
28 5 0.14
29 6 0.17
30 2 0.06
32 14 0.39
ACGTcount: A:0.75, C:0.01, G:0.12, T:0.12
Consensus pattern (28 bp):
AAAAAAAAATGAAAAAAAGAAAAATTGA
Found at i:468841 original size:17 final size:16
Alignment explanation
Indices: 468801--468850 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
468791 ACTATAGGTC
468801 AAATTAAAAA-AGTT-A
1 AAATTAAAAAGA-TTCA
* *
468816 AATTTAAAATGATTCA
1 AAATTAAAAAGATTCA
468832 AAATTAAAAAGATTCA
1 AAATTAAAAAGATTCA
468848 AAA
1 AAA
468851 CCAAATACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (16 bp):
AAATTAAAAAGATTCA
Found at i:480417 original size:22 final size:19
Alignment explanation
Indices: 480387--480435 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
480377 TTAATAGCAT
480387 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
480409 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
480428 TCAGTATT
1 TCA-TATT
480436 TGCTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:486705 original size:13 final size:13
Alignment explanation
Indices: 486687--486712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
486677 ATGCCCGAAA
486687 ATAATAAAAGAAG
1 ATAATAAAAGAAG
486700 ATAATAAAAGAAG
1 ATAATAAAAGAAG
486713 TACATGAAGG
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATAATAAAAGAAG
Found at i:486808 original size:141 final size:141
Alignment explanation
Indices: 486554--486829 Score: 552
Period size: 141 Copynumber: 2.0 Consensus size: 141
486544 TTAGAAGCAC
486554 AGAAGATAATAAAAGAAGTACATGAAGGGATTTGTGGAATCCATGCCAACGGATATAAAATGGCA
1 AGAAGATAATAAAAGAAGTACATGAAGGGATTTGTGGAATCCATGCCAACGGATATAAAATGGCA
486619 AGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGTGATTGCATTAAATATGCCCG
66 AGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGTGATTGCATTAAATATGCCCG
486684 AAAATAATAAA
131 AAAATAATAAA
486695 AGAAGATAATAAAAGAAGTACATGAAGGGATTTGTGGAATCCATGCCAACGGATATAAAATGGCA
1 AGAAGATAATAAAAGAAGTACATGAAGGGATTTGTGGAATCCATGCCAACGGATATAAAATGGCA
486760 AGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGTGATTGCATTAAATATGCCCG
66 AGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGTGATTGCATTAAATATGCCCG
486825 AAAAT
131 AAAAT
486830 GCCACAAATG
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (141 bp):
AGAAGATAATAAAAGAAGTACATGAAGGGATTTGTGGAATCCATGCCAACGGATATAAAATGGCA
AGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGTGATTGCATTAAATATGCCCG
AAAATAATAAA
Found at i:488792 original size:42 final size:42
Alignment explanation
Indices: 488708--489453 Score: 905
Period size: 42 Copynumber: 17.7 Consensus size: 42
488698 CTTTTTTGCT
* *
488708 TTCCCTTAGTCTGCCTGTCGACTTTGA-CCTCGGAGACTTTTT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTC
* * *
488750 TTCCCTTTAGTCTGCCTCTCGGCTTTGACCCTAGAGACTTTTT
1 TTCCC-TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
488793 TTCCCTTAGTCTACCTGTCAGCTTTAACCTTGGAGAC--TGC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
488833 TTCATCTAAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
488877 TACCCTTCAATCTACCTGTCGGCTTCGTCCCTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
488920 TGTCCCTTAGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
488963 TATCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
489006 TACCTTTAGTCTACCAGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
489048 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
489090 TTCCCTTAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTTT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
489132 TATCCCTTAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
489175 TACCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
489217 TTCCCTTAGTCTGCCTGTCGGCTTTGACTCTAGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
489259 TTCCCTCAGTCTGCCTGTC--ATTTAACCTTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
489299 TGTCCCTTAGTCTGCCTGTTGGTTTTGACCC-GAGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTG-GAGACTTTTC
489342 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
489384 ATCCC-TAGTCTGCCTATCGG-TTTCACCCTGGAGATTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
489424 TTTCCCTAAGTCTGCCTGTTGGTTTTGACC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACC
489454 GGGGAGAATA
Statistics
Matches: 605, Mismatches: 82, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
40 39 0.06
41 36 0.06
42 317 0.52
43 201 0.33
44 12 0.02
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.38
Consensus pattern (42 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
Found at i:489089 original size:127 final size:127
Alignment explanation
Indices: 488708--489453 Score: 838
Period size: 127 Copynumber: 5.9 Consensus size: 127
488698 CTTTTTTGCT
* * **
488708 TTCCCTTAGTCTGCCTGTCGACTTTGA-CCTCGGAGACTTTT-TTTCCCTTTAGTCTGCCTCTCG
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTCTAT-CCTTTAGTCTGCCAGTCG
* * * * * * * *
488771 GCTTTGACCCTAGAGACTTTTTTTCCCTTAGTCTACCTGTCAGCTTTAACCTTGGAGAC--TGC
64 GCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
* * * * * * * * *
488833 TTCATCTAAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTCAATCTACCTGTCG
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCCAGTCG
* * * * *
488898 GCTTCGTCCCTGGAGACTTTTCTGTCCCTTAGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTTC
64 GCTTTGACCCTGGAGACTTTTCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
* *
488963 TATCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-CCTTTAGTCTACCAGTCGG
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCCAGTCGG
489027 CTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
65 CTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
* * *
489090 TTCCCTTAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTTTTATCCCTTAGTCTGCCTA-TCGG
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCC-AGTCGG
* *
489154 CTTTGACCCTGGAGACTTTTCTACCCTTAGTCTGCCTGTCGACTTTGACCCT-AGAGACTTTTC
65 CTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTTC
* * * * * *
489217 TTCCCTTAGTCTGCCTGTCGGCTTTGACTCTAGAGACTTTTCT-TCCCTCAGTCTGCCTGTC--A
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCCAGTCGGC
* * * *
489279 TTTAACCTTGGAGACTTTTCTGTCCCTTAGTCTGCCTGTTGGTTTTGACCC-GAGAGACTTTTC
66 TTTGACCCTGGAGACTTTTCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTTC
*
489342 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCC-CTAGTCTGCCTA-TCGG
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCC-AGTCGG
* * * * *
489404 -TTTCACCCTGGAGATTTTTCTTTCCCTAAGTCTGCCTGTTGGTTTTGACC
65 CTTTGACCCTGGAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGACC
489454 GGGGAGAATA
Statistics
Matches: 542, Mismatches: 60, Indels: 38
0.85 0.09 0.06
Matches are distributed among these distances:
124 29 0.05
125 126 0.23
126 59 0.11
127 212 0.39
128 75 0.14
129 34 0.06
130 5 0.01
131 2 0.00
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.38
Consensus pattern (127 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCTTTAGTCTGCCAGTCGGC
TTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
Found at i:489786 original size:12 final size:11
Alignment explanation
Indices: 489748--489794 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
489738 AAAAATTATT
489748 ATTAAACAAAAA
1 ATTAAA-AAAAA
*
489760 A-TAATAAATAA
1 ATTAA-AAAAAA
489771 ATTAAAATAAAA
1 ATTAAAA-AAAA
489783 ATTAAAAAAAA
1 ATTAAAAAAAA
489794 A
1 A
489795 AATCAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (11 bp):
ATTAAAAAAAA
Found at i:489795 original size:12 final size:12
Alignment explanation
Indices: 489748--489795 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
489738 AAAAATTATT
*
489748 ATTAAACAAAAA
1 ATTAAAAAAAAA
* *
489760 A-TAATAAATAA
1 ATTAAAAAAAAA
*
489771 ATTAAAATAAAA
1 ATTAAAAAAAAA
489783 ATTAAAAAAAAA
1 ATTAAAAAAAAA
489795 A
1 A
489796 ATCAAATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (12 bp):
ATTAAAAAAAAA
Found at i:491502 original size:27 final size:27
Alignment explanation
Indices: 491449--491503 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
491439 GATTTTATTG
*
491449 ATTAAGGATTAAAATGCAAACATGAAA
1 ATTAAGGATTAAAATGAAAACATGAAA
* *
491476 ATTAGGGATTAAATTGTAAAACA-GAAA
1 ATTAAGGATTAAAATG-AAAACATGAAA
491503 A
1 A
491504 ATTTTGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (27 bp):
ATTAAGGATTAAAATGAAAACATGAAA
Found at i:496325 original size:14 final size:14
Alignment explanation
Indices: 496301--496345 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
496291 ATTTAATTCG
*
496301 TAATAAAATTAAAT
1 TAATCAAATTAAAT
* *
496315 TACTCAAATTAACT
1 TAATCAAATTAAAT
*
496329 TAATTAAATTAAAT
1 TAATCAAATTAAAT
496343 TAA
1 TAA
496346 ATCTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATCAAATTAAAT
Done.