Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold337
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1638316
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 264207 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:32626 original size:5 final size:5
Alignment explanation
Indices: 32618--32749 Score: 250
Period size: 5 Copynumber: 26.8 Consensus size: 5
32608 CCATACTTGT
32618 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC
32668 CATAC CATAC CATAC CA-AC CATAC CATAC CATAC CATAC CATAC CATAC
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC
32717 CATAC CA-AC CATAC CATAC CATAC CATAC CATA
1 CATAC CATAC CATAC CATAC CATAC CATAC CATA
32750 TAAACTTTCT
Statistics
Matches: 125, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.06
5 117 0.94
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (5 bp):
CATAC
Found at i:43041 original size:22 final size:22
Alignment explanation
Indices: 42993--43044 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
42983 TATCCTAGTT
42993 GACCCAAAGTAAACCCTGACTA
1 GACCCAAAGTAAACCCTGACTA
* * *
43015 AACCCAAAGTAAACCCTGAGTG
1 GACCCAAAGTAAACCCTGACTA
43037 GACCCAAA
1 GACCCAAA
43045 TGTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.31, G:0.15, T:0.12
Consensus pattern (22 bp):
GACCCAAAGTAAACCCTGACTA
Found at i:43092 original size:13 final size:13
Alignment explanation
Indices: 43074--43099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43064 GAGTAAATCC
43074 AAAGTAAACCCGA
1 AAAGTAAACCCGA
43087 AAAGTAAACCCGA
1 AAAGTAAACCCGA
43100 GGTTTAGTTG
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:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAGTAAACCCGA
Found at i:50935 original size:17 final size:18
Alignment explanation
Indices: 50903--50936 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50893 CAACATCATT
50903 AAAATATTGATTATTTTC
1 AAAATATTGATTATTTTC
*
50921 AAAATA-TGTTTATTTT
1 AAAATATTGATTATTTT
50937 ATCTACTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
AAAATATTGATTATTTTC
Found at i:51213 original size:3 final size:3
Alignment explanation
Indices: 51205--51273 Score: 111
Period size: 3 Copynumber: 23.0 Consensus size: 3
51195 CTTTTATGTG
* * *
51205 AGA AGA AGA AGA AGA AGA TGA AGA TGA AGA AGA TGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
51253 AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA
51274 GAGAGAGAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:57777 original size:11 final size:11
Alignment explanation
Indices: 57761--57810 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
57751 CATTCAGTCA
57761 ATTGAAAGGTG
1 ATTGAAAGGTG
57772 ATTGAAAGGTG
1 ATTGAAAGGTG
*
57783 ATTGAAAGGTA
1 ATTGAAAGGTG
*
57794 ACTGAAAGGTG
1 ATTGAAAGGTG
*
57805 ACTGAA
1 ATTGAA
57811 TGGGATAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.24
Consensus pattern (11 bp):
ATTGAAAGGTG
Found at i:64705 original size:3 final size:3
Alignment explanation
Indices: 64684--64729 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
64674 CATTGGTTCA
64684 TTG TTG TTAG TT- TTG -TG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TT-G TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
64728 TT
1 TT
64730 ATGTGTTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.02, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:71377 original size:42 final size:43
Alignment explanation
Indices: 71320--71401 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
71310 CACTGTCATC
* * * *
71320 CCCTGTACATCCCCTGTGTGCCACTGTACAGAGCCCCTGTATA
1 CCCTGTACATACCCTGTGCGCCACTGTACACAACCCCTGTATA
*
71363 CCCTGT-CATACCCTGTGCGCCCCTGTACACAACCCCTGT
1 CCCTGTACATACCCTGTGCGCCACTGTACACAACCCCTGT
71402 GTGCCACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.17, C:0.41, G:0.17, T:0.24
Consensus pattern (43 bp):
CCCTGTACATACCCTGTGCGCCACTGTACACAACCCCTGTATA
Found at i:71461 original size:20 final size:20
Alignment explanation
Indices: 71408--71494 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
71398 CTGTGTGCCA
* *
71408 CTGTAAGCCCCTCTCACCCC
1 CTGTAAGCCCCTGTCATCCC
*
71428 CTGTACGCCCCTGTCATCCC
1 CTGTAAGCCCCTGTCATCCC
*
71448 CTGTAAGCCACTGT-ATGCCC
1 CTGTAAGCCCCTGTCAT-CCC
* *
71468 CTGTGCATGCCCCTGACATCCC
1 CTGT--AAGCCCCTGTCATCCC
71490 CTGTA
1 CTGTA
71495 CGGTGTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 37 0.67
22 14 0.25
23 2 0.04
ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24
Consensus pattern (20 bp):
CTGTAAGCCCCTGTCATCCC
Found at i:72005 original size:2 final size:2
Alignment explanation
Indices: 72000--72062 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
71990 TATAAATCAT
*
72000 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
72042 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
72063 TTATTTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:72806 original size:140 final size:137
Alignment explanation
Indices: 72587--72845 Score: 362
Period size: 140 Copynumber: 1.9 Consensus size: 137
72577 CTGAGAACGT
* * * * *
72587 GTGTGTGTGTATGCAAGTACACGTGTGTCTGTCACCTCATTGTTCTTAAACTCGCTACTGTGCAC
1 GTGTGTGTATATACAAGTACACGTGTGTCTATCACCTCATTGTTCTTAAACTCGCTACCGTGAAC
*
72652 TGCAAATTGTCAAGAAGGGTTGTATACAGTATATAGCTATTATATAATCACTGACCGACCATTCA
66 TGCAAATTGTCAAGAAGGGCTGTATACAG----TAGCTATTATATAATCACTGACCGACCATTCA
72717 GATCTGAGGAA
127 GATCTGAGGAA
* *
72728 GTGTGTGTATATACAAGTACACGTGTGTCTATCATCC-C-TTTTTCCTT-ATCTCGCTACCGTGA
1 GTGTGTGTATATACAAGTACACGTGTGTCTATCA-CCTCATTGTT-CTTAAACTCGCTACCGTGA
*
72790 ACTGCAAATTGTCAAGAAGGGCTGTGTACAGTAGCTATTATATAATCACTGACCGA
64 ACTGCAAATTGTCAAGAAGGGCTGTATACAGTAGCTATTATATAATCACTGACCGA
72846 GTGAAATAAT
Statistics
Matches: 107, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
136 25 0.23
140 45 0.42
141 35 0.33
142 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (137 bp):
GTGTGTGTATATACAAGTACACGTGTGTCTATCACCTCATTGTTCTTAAACTCGCTACCGTGAAC
TGCAAATTGTCAAGAAGGGCTGTATACAGTAGCTATTATATAATCACTGACCGACCATTCAGATC
TGAGGAA
Found at i:73111 original size:2 final size:2
Alignment explanation
Indices: 73104--73138 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73094 ATTAATGCAA
73104 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
73139 GTATAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:73323 original size:2 final size:2
Alignment explanation
Indices: 73316--73356 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
73306 TCAATGCAAA
*
73316 CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
73357 ACATGACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:74352 original size:12 final size:11
Alignment explanation
Indices: 74322--74382 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 11
74312 GTCAAAAGCC
74322 GTACAGGGGAT
1 GTACAGGGGAT
74333 GT-CAGGGGCAT
1 GTACAGGGG-AT
74344 GTACAGGGG-T
1 GTACAGGGGAT
* *
74354 ATAC-GGTGGCT
1 GTACAGG-GGAT
74365 -TACAGGGGAT
1 GTACAGGGGAT
74375 G-ACAGGGG
1 GTACAGGGG
74383 CCTACAGGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
9 2 0.05
10 25 0.60
11 9 0.21
12 6 0.14
ACGTcount: A:0.23, C:0.13, G:0.46, T:0.18
Consensus pattern (11 bp):
GTACAGGGGAT
Found at i:74388 original size:20 final size:20
Alignment explanation
Indices: 74323--74409 Score: 97
Period size: 20 Copynumber: 4.2 Consensus size: 20
74313 TCAAAAGCCG
*
74323 TACAGGGGATGTCAGGGGCAT
1 TACAGGGGATGACAGGGGC-T
74344 GTACAGGGGTAT-AC-GGTGGCT
1 -TACAGGGG-ATGACAGG-GGCT
*
74365 TACAGGGGATGACAGGGGCC
1 TACAGGGGATGACAGGGGCT
*
74385 TACAGGGGGTGACAGGGGCT
1 TACAGGGGATGACAGGGGCT
74405 TACAG
1 TACAG
74410 TGGCACACAG
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.04
20 36 0.63
21 5 0.09
22 12 0.21
23 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.44, T:0.17
Consensus pattern (20 bp):
TACAGGGGATGACAGGGGCT
Found at i:74409 original size:10 final size:10
Alignment explanation
Indices: 74335--74409 Score: 55
Period size: 10 Copynumber: 7.3 Consensus size: 10
74325 CAGGGGATGT
74335 CAGGGGCATGTA
1 CAGGGGC-T-TA
74347 CAGGGG-TATA
1 CAGGGGCT-TA
74357 C-GGTGGCTTA
1 CAGG-GGCTTA
* *
74367 CAGGGGATGA
1 CAGGGGCTTA
*
74377 CAGGGGCCTA
1 CAGGGGCTTA
* *
74387 CAGGGGGTGA
1 CAGGGGCTTA
74397 CAGGGGCTTA
1 CAGGGGCTTA
74407 CAG
1 CAG
74410 TGGCACACAG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 2 0.04
10 38 0.78
11 3 0.06
12 6 0.12
ACGTcount: A:0.23, C:0.17, G:0.44, T:0.16
Consensus pattern (10 bp):
CAGGGGCTTA
Found at i:74484 original size:23 final size:22
Alignment explanation
Indices: 74405--74495 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 22
74395 GACAGGGGCT
*
74405 TACAGTGGCACACAGGGGTTGTG
1 TACAGTGGCACACAGGGG-TATG
* *
74428 TACAGGGGCGCACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
* * * *
74449 -ACAG-AGTATACAGGGGCTCTG
1 TACAGTGGCACACAGGGG-TATG
74470 TACAGTGGCACACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
74491 TACAG
1 TACAG
74496 GGGATGACAG
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 8 0.15
20 4 0.08
21 11 0.21
22 4 0.08
23 25 0.48
ACGTcount: A:0.26, C:0.19, G:0.38, T:0.16
Consensus pattern (22 bp):
TACAGTGGCACACAGGGGTATG
Found at i:74497 original size:11 final size:10
Alignment explanation
Indices: 74481--74540 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
74471 ACAGTGGCAC
74481 ACAGGGGATG
1 ACAGGGGATG
74491 TACAGGGGATG
1 -ACAGGGGATG
**
74502 ACAGTGAAAATG
1 ACAG-G-GGATG
74514 -CAGGGG-TG
1 ACAGGGGATG
*
74522 ACAGGGGAAG
1 ACAGGGGATG
74532 ACAGGGGAT
1 ACAGGGGAT
74541 TTTCATACGG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.05
9 6 0.15
10 14 0.36
11 14 0.36
12 3 0.08
ACGTcount: A:0.33, C:0.10, G:0.45, T:0.12
Consensus pattern (10 bp):
ACAGGGGATG
Found at i:76941 original size:225 final size:224
Alignment explanation
Indices: 76550--76998 Score: 889
Period size: 225 Copynumber: 2.0 Consensus size: 224
76540 CCTCTTGAAA
76550 AAAAATAAAAAAAATGACATTGGCTAATCAAAATGGCATAATGGCCAGAGGTTAAGGTAAACAAA
1 AAAAATAAAAAAAATGACATTGGCTAATCAAAATGGCATAATGGCCAGAGGTTAAGGTAAACAAA
76615 TAGTTCGTAATAATCTTTTATTATGTTTTGTCGTAAAAAGAATTATAAAGAAAGCATATTATCAT
66 TAGTTCGTAATAATCTTTTATTATGTTTTGTCGTAAAAAGAATTATAAAGAAAGCATATTATCAT
76680 ATTTTCTAAAACAAAAATGTTTTGAACATAAAAATAATAAGGTAAAAAGACCTCTTTTGTCGAAA
131 ATTTTCTAAAACAAAAATGTTTTGAACATAAAAATAATAAGGTAAAAAGACCTCTTTTGTCGAAA
76745 ACAATACTTTTCCATCAGTATAACACTAT
196 ACAATACTTTTCCATCAGTATAACACTAT
76774 NAAAAATAAAAAAAATGACATTGGCTAATCAAAATGGCATAATGGCCAGAGGTTAAGGTAAACAA
1 -AAAAATAAAAAAAATGACATTGGCTAATCAAAATGGCATAATGGCCAGAGGTTAAGGTAAACAA
76839 ATAGTTCGTAATAATCTTTTATTATGTTTTGTCGTAAAAAGAATTATAAAGAAAGCATATTATCA
65 ATAGTTCGTAATAATCTTTTATTATGTTTTGTCGTAAAAAGAATTATAAAGAAAGCATATTATCA
76904 TATTTTCTAAAACAAAAATGTTTTGAACATAAAAATAATAAGGTAAAAAGACCTCTTTTGTCGAA
130 TATTTTCTAAAACAAAAATGTTTTGAACATAAAAATAATAAGGTAAAAAGACCTCTTTTGTCGAA
76969 AACAATACTTTTCCATCAGTATAACACTAT
195 AACAATACTTTTCCATCAGTATAACACTAT
76999 TAGTTTTGTC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 224 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (224 bp):
AAAAATAAAAAAAATGACATTGGCTAATCAAAATGGCATAATGGCCAGAGGTTAAGGTAAACAAA
TAGTTCGTAATAATCTTTTATTATGTTTTGTCGTAAAAAGAATTATAAAGAAAGCATATTATCAT
ATTTTCTAAAACAAAAATGTTTTGAACATAAAAATAATAAGGTAAAAAGACCTCTTTTGTCGAAA
ACAATACTTTTCCATCAGTATAACACTAT
Found at i:77083 original size:7 final size:7
Alignment explanation
Indices: 77071--77137 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
77061 GAGAAGGATC
77071 ATTCGAG
1 ATTCGAG
77078 ATTCGAG
1 ATTCGAG
*
77085 ATTCGAA
1 ATTCGAG
*
77092 ATACGAG
1 ATTCGAG
*
77099 ATTCGAA
1 ATTCGAG
*
77106 ATACGAG
1 ATTCGAG
77113 ATTCGAG
1 ATTCGAG
*
77120 ATTCGAA
1 ATTCGAG
77127 ATTCGAG
1 ATTCGAG
77134 ATTC
1 ATTC
77138 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:79264 original size:2 final size:2
Alignment explanation
Indices: 79257--79297 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
79247 GCTAGGTGAT
79257 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
79298 TCGATGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:80075 original size:7 final size:7
Alignment explanation
Indices: 80060--80126 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
80050 TTTAGATATT
80060 GAATCTC
1 GAATCTC
*
80067 GAATTTC
1 GAATCTC
*
80074 GAATATC
1 GAATCTC
80081 GAATCTC
1 GAATCTC
* *
80088 GTATTTC
1 GAATCTC
80095 GAATCTC
1 GAATCTC
* *
80102 GTATTTC
1 GAATCTC
80109 GAATCTC
1 GAATCTC
80116 GAATCTC
1 GAATCTC
80123 GAAT
1 GAAT
80127 GATCCTTCTC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:83603 original size:3 final size:3
Alignment explanation
Indices: 83595--83668 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
83585 NNNNNNNNNN
83595 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
83643 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
83669 AGAGAGAGAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:83824 original size:19 final size:19
Alignment explanation
Indices: 83800--83838 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
83790 ATGTTAAAAT
83800 ACGACATTACGATATGCAC
1 ACGACATTACGATATGCAC
83819 ACGACATTACGATATGCAC
1 ACGACATTACGATATGCAC
83838 A
1 A
83839 TATATGATAA
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:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (19 bp):
ACGACATTACGATATGCAC
Found at i:90666 original size:200 final size:200
Alignment explanation
Indices: 90323--90724 Score: 804
Period size: 200 Copynumber: 2.0 Consensus size: 200
90313 TCCGTGATCC
90323 ATTTGGCATAATTTTGATTAGAATACTGTCTCCGTGGGGCACTGTTTTTTCCAGGCTCCTCGGGT
1 ATTTGGCATAATTTTGATTAGAATACTGTCTCCGTGGGGCACTGTTTTTTCCAGGCTCCTCGGGT
90388 CAAGAGAGTATTTCTAATATTGTATATTACATATATATATTTGATATATGCTGCCATATTGTTTG
66 CAAGAGAGTATTTCTAATATTGTATATTACATATATATATTTGATATATGCTGCCATATTGTTTG
90453 AACGGCGCATGTCGAGTTCAATGTACATGTATGAAATCTATCTGATGTACATGTACTATATATCT
131 AACGGCGCATGTCGAGTTCAATGTACATGTATGAAATCTATCTGATGTACATGTACTATATATCT
90518 GACTG
196 GACTG
90523 ATTTGGCATAATTTTGATTAGAATACTGTCTCCGTGGGGCACTGTTTTTTCCAGGCTCCTCGGGT
1 ATTTGGCATAATTTTGATTAGAATACTGTCTCCGTGGGGCACTGTTTTTTCCAGGCTCCTCGGGT
90588 CAAGAGAGTATTTCTAATATTGTATATTACATATATATATTTGATATATGCTGCCATATTGTTTG
66 CAAGAGAGTATTTCTAATATTGTATATTACATATATATATTTGATATATGCTGCCATATTGTTTG
90653 AACGGCGCATGTCGAGTTCAATGTACATGTATGAAATCTATCTGATGTACATGTACTATATATCT
131 AACGGCGCATGTCGAGTTCAATGTACATGTATGAAATCTATCTGATGTACATGTACTATATATCT
90718 GACTG
196 GACTG
90723 AT
1 AT
90725 ATCTATCTGA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 202 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (200 bp):
ATTTGGCATAATTTTGATTAGAATACTGTCTCCGTGGGGCACTGTTTTTTCCAGGCTCCTCGGGT
CAAGAGAGTATTTCTAATATTGTATATTACATATATATATTTGATATATGCTGCCATATTGTTTG
AACGGCGCATGTCGAGTTCAATGTACATGTATGAAATCTATCTGATGTACATGTACTATATATCT
GACTG
Found at i:105379 original size:13 final size:13
Alignment explanation
Indices: 105361--105385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105351 ACTTTGTCCT
105361 CGATATACTTTCC
1 CGATATACTTTCC
105374 CGATATACTTTC
1 CGATATACTTTC
105386 ACAAGGCGTA
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:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (13 bp):
CGATATACTTTCC
Found at i:106867 original size:15 final size:14
Alignment explanation
Indices: 106835--106871 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
106825 AAATATATGT
*
106835 ATACCATACTTGCC
1 ATACCATACTTACC
106849 ATACCATACCTTACC
1 ATACCATA-CTTACC
106864 ATACCATA
1 ATACCATA
106872 GCATATCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (14 bp):
ATACCATACTTACC
Found at i:117983 original size:34 final size:34
Alignment explanation
Indices: 117938--118160 Score: 338
Period size: 34 Copynumber: 6.6 Consensus size: 34
117928 AAAGTTTATG
* * *
117938 CACATGAAGAGTTGCGTGTACTATTTGTCTGGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
* *
117972 CACATGCAGAGTCGTGTGTACTATTTTTCTTGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
118006 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
*
118040 CACATGCAGAGTCGTGTGTACTATTTGTTTGGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
* * *
118074 CACATACAGAGTCGTGTGTACTATTTTTCTTGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
*
118108 CACATGCAGAGTCATGTGTACTATTTGTCTGGTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
* *
118142 CACTTGCAGAGTCATGTGT
1 CACATGCAGAGTCGTGTGT
118161 GCTACAGTAT
Statistics
Matches: 172, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 172 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (34 bp):
CACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
Found at i:118025 original size:68 final size:68
Alignment explanation
Indices: 117938--118301 Score: 333
Period size: 68 Copynumber: 5.2 Consensus size: 68
117928 AAAGTTTATG
* * * *
117938 CACATGAAGAGTTGCGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTTTCTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTTTCTG
118003 GTT
66 GTT
118006 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTGTT-T
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTT-TTCT
118070 GGTT
65 GGTT
* * * * *
118074 CACATACAGAGTCGTGTGTACTATTTTTCTTGTTCACATGCAGAGTCATGTGTACTATTTGTCTG
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTTTCTG
118139 GTT
66 GTT
* *
118142 CACTTGCAGAGTCATGTGTGCTACAGTATATTTCTGGTTTACTGGTTCACGTGCAGAGTCGTGTG
1 CACATGCAGAGTC--GTGTG-TAC----TA-TT-T-G--T-CTGGTTCACATGCAGAGTCGTGTG
* **
118207 TACTA-ATTT-TAATT
53 TACTATTTTTCTGGTT
* * ** * * * * *
118221 CACATGCAGAGTTGTGTGTATACTAATT-T-TGACTCACGTGCACAGTTGTGTGCAATATTGTTT
1 CACATGCAGAGTCGTGTG--TACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATT-TTT
118284 CTGGTT
63 CTGGTT
118290 CACATGCAGAGT
1 CACATGCAGAGT
118302 AATGTAGACT
Statistics
Matches: 245, Mismatches: 32, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
66 22 0.09
67 1 0.00
68 137 0.56
69 17 0.07
70 5 0.02
71 3 0.01
72 1 0.00
73 1 0.00
74 2 0.01
75 2 0.01
76 2 0.01
77 6 0.02
78 3 0.01
79 14 0.06
80 3 0.01
81 26 0.11
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (68 bp):
CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTTTCTG
GTT
Found at i:118061 original size:102 final size:102
Alignment explanation
Indices: 117938--118160 Score: 374
Period size: 102 Copynumber: 2.2 Consensus size: 102
117928 AAAGTTTATG
* * * *
117938 CACATGAAGAGTTGCGTGTACTATTTGTCTGGTTCACATGCAGAGTCGTGTGTACTATTTTTCTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATACAGAGTCGTGTGTACTATTTTTCTT
*
118003 GTTCACATGCAGAGTCGTGTGTACTATTTGTCTGGTT
66 GTTCACATGCAGAGTCATGTGTACTATTTGTCTGGTT
*
118040 CACATGCAGAGTCGTGTGTACTATTTGTTTGGTTCACATACAGAGTCGTGTGTACTATTTTTCTT
1 CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATACAGAGTCGTGTGTACTATTTTTCTT
118105 GTTCACATGCAGAGTCATGTGTACTATTTGTCTGGTT
66 GTTCACATGCAGAGTCATGTGTACTATTTGTCTGGTT
* *
118142 CACTTGCAGAGTCATGTGT
1 CACATGCAGAGTCGTGTGT
118161 GCTACAGTAT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 113 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (102 bp):
CACATGCAGAGTCGTGTGTACTATTTGTCTGGTTCACATACAGAGTCGTGTGTACTATTTTTCTT
GTTCACATGCAGAGTCATGTGTACTATTTGTCTGGTT
Found at i:118229 original size:32 final size:33
Alignment explanation
Indices: 118187--118250 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
118177 GGTTTACTGG
*
118187 TTCACGTGCAGAGTCGTGTG-TACTAATTTTAA
1 TTCACATGCAGAGTCGTGTGATACTAATTTTAA
*
118219 TTCACATGCAGAGTTGTGTGTATACTAATTTT
1 TTCACATGCAGAGTCGTGTG-ATACTAATTTT
118251 GACTCACGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 18 0.64
34 10 0.36
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (33 bp):
TTCACATGCAGAGTCGTGTGATACTAATTTTAA
Found at i:118250 original size:34 final size:32
Alignment explanation
Indices: 118187--118272 Score: 109
Period size: 34 Copynumber: 2.6 Consensus size: 32
118177 GGTTTACTGG
*
118187 TTCACGTGCAGAGTCGTGTGTACTAATTTTAA
1 TTCACGTGCAGAGTTGTGTGTACTAATTTTAA
* *
118219 TTCACATGCAGAGTTGTGTGTATACTAATTTTGA
1 TTCACGTGCAGAGTTGTGTG--TACTAATTTTAA
* *
118253 CTCACGTGCACAGTTGTGTG
1 TTCACGTGCAGAGTTGTGTG
118273 CAATATTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 18 0.39
34 28 0.61
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (32 bp):
TTCACGTGCAGAGTTGTGTGTACTAATTTTAA
Found at i:118933 original size:10 final size:10
Alignment explanation
Indices: 118917--118977 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
118907 CCGTATGAAA
118917 ATCCCCTGTC
1 ATCCCCTGTC
*
118927 TTCCCCTGTC
1 ATCCCCTGTC
* *
118937 ACCCCCTGTGT
1 ATCCCCTGT-C
* * *
118948 TTTCACTGTC
1 ATCCCCTGTC
118958 ATCCCCTGTAC
1 ATCCCCTGT-C
118969 ATCCCCTGT
1 ATCCCCTGT
118978 GTGCCACTGT
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
10 22 0.59
11 15 0.41
ACGTcount: A:0.10, C:0.44, G:0.11, T:0.34
Consensus pattern (10 bp):
ATCCCCTGTC
Found at i:118986 original size:31 final size:31
Alignment explanation
Indices: 118922--119134 Score: 80
Period size: 32 Copynumber: 6.8 Consensus size: 31
118912 TGAAAATCCC
* **
118922 CTGTCTTCCCCTGTCACCCCCTGTGTTTTCA
1 CTGTCATCCCCTGTCACCCCCTGTGTTGCCA
*
118953 CTGTCATCCCCTGTACATCCCCTGTG-TGCCA
1 CTGTCATCCCCTGT-CACCCCCTGTGTTGCCA
* ** ** *
118984 CTGTACAGAGCCCCTGT-ATACCCTGTCAT-CCC
1 CTGT-C--ATCCCCTGTCACCCCCTGTGTTGCCA
* *
119016 CTGTGC-GCCACTGTACACAACCCCTGTG-TGCCA
1 CTGT-CATCCCCTGT-CAC--CCCCTGTGTTGCCA
* * ** *
119049 CTGTAAGCCCCTGTCACCCCCTGT-ACGCCC
1 CTGTCATCCCCTGTCACCCCCTGTGTTGCCA
* * * * *
119079 CTGTCATCCCCTGTAAGCCACTGT-TTACCC
1 CTGTCATCCCCTGTCACCCCCTGTGTTGCCA
*
119109 CTGTGCATGCCCCTGACACCCCCTGT
1 CTGT-CAT-CCCCTGTCACCCCCTGT
119135 ACGGTCTTTA
Statistics
Matches: 138, Mismatches: 30, Indels: 27
0.71 0.15 0.14
Matches are distributed among these distances:
29 7 0.05
30 36 0.26
31 24 0.17
32 43 0.31
33 20 0.14
34 8 0.06
ACGTcount: A:0.14, C:0.43, G:0.16, T:0.27
Consensus pattern (31 bp):
CTGTCATCCCCTGTCACCCCCTGTGTTGCCA
Found at i:119000 original size:23 final size:22
Alignment explanation
Indices: 118971--119053 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
118961 CCCTGTACAT
*
118971 CCCCTGTGTGCCACTGTACAGAG
1 CCCCTGTGTGCCACTGTACA-AA
* * *
118994 CCCCTGTATACC-CTGT-C-AT
1 CCCCTGTGTGCCACTGTACAAA
*
119013 CCCCTGTGCGCCACTGTACACAA
1 CCCCTGTGTGCCACTGTACA-AA
119036 CCCCTGTGTGCCACTGTA
1 CCCCTGTGTGCCACTGTA
119054 AGCCCCTGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 10 0.21
20 4 0.08
21 2 0.04
22 4 0.08
23 28 0.58
ACGTcount: A:0.17, C:0.40, G:0.19, T:0.24
Consensus pattern (22 bp):
CCCCTGTGTGCCACTGTACAAA
Found at i:119014 original size:42 final size:43
Alignment explanation
Indices: 118961--119042 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
118951 CACTGTCATC
* * *
118961 CCCTGTACATCCCCTGTGTGCCACTGTACAGAGCCCCTGTATA
1 CCCTGTACATCCCCTGTGCGCCACTGTACACAACCCCTGTATA
119004 CCCTGT-CATCCCCTGTGCGCCACTGTACACAACCCCTGT
1 CCCTGTACATCCCCTGTGCGCCACTGTACACAACCCCTGT
119043 GTGCCACTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.17, C:0.41, G:0.17, T:0.24
Consensus pattern (43 bp):
CCCTGTACATCCCCTGTGCGCCACTGTACACAACCCCTGTATA
Found at i:119062 original size:10 final size:10
Alignment explanation
Indices: 119049--119102 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
119039 CTGTGTGCCA
119049 CTGTAAGCCC
1 CTGTAAGCCC
* *
119059 CTGTCACCCC
1 CTGTAAGCCC
*
119069 CTGTACGCCC
1 CTGTAAGCCC
* *
119079 CTGTCATCCC
1 CTGTAAGCCC
*
119089 CTGTAAGCCA
1 CTGTAAGCCC
119099 CTGT
1 CTGT
119103 TTACCCCTGT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (10 bp):
CTGTAAGCCC
Found at i:119072 original size:20 final size:20
Alignment explanation
Indices: 119049--119135 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
119039 CTGTGTGCCA
119049 CTGTAAGCCCCTGTCACCCC
1 CTGTAAGCCCCTGTCACCCC
* *
119069 CTGTACGCCCCTGTCATCCC
1 CTGTAAGCCCCTGTCACCCC
* *
119089 CTGTAAGCCACTGTTTA-CCC
1 CTGTAAGCCCCTG-TCACCCC
* *
119109 CTGTGCATGCCCCTGACACCCC
1 CTGT--AAGCCCCTGTCACCCC
119131 CTGTA
1 CTGTA
119136 CGGTCTTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 37 0.69
21 3 0.06
22 14 0.26
ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24
Consensus pattern (20 bp):
CTGTAAGCCCCTGTCACCCC
Found at i:119395 original size:7 final size:7
Alignment explanation
Indices: 119383--119414 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
119373 GAGAAGGATC
119383 ATTCGAG
1 ATTCGAG
119390 ATTCGAG
1 ATTCGAG
*
119397 ATTCGAA
1 ATTCGAG
119404 ATTCGAG
1 ATTCGAG
119411 ATTC
1 ATTC
119415 AATATCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (7 bp):
ATTCGAG
Found at i:122691 original size:7 final size:7
Alignment explanation
Indices: 122676--122742 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
122666 TTTAGATATT
122676 GAATCTC
1 GAATCTC
*
122683 GAATTTC
1 GAATCTC
122690 GAATCTC
1 GAATCTC
122697 GAATCTC
1 GAATCTC
* *
122704 GTATTTC
1 GAATCTC
122711 GAATCTC
1 GAATCTC
* *
122718 GTATTTC
1 GAATCTC
122725 GAATCTC
1 GAATCTC
122732 GAATCTC
1 GAATCTC
122739 GAAT
1 GAAT
122743 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:122701 original size:21 final size:21
Alignment explanation
Indices: 122676--122742 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
122666 TTTAGATATT
122676 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
122697 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
122718 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
122739 GAAT
1 GAAT
122743 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:123533 original size:2 final size:2
Alignment explanation
Indices: 123526--123571 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
123516 TCGCTGCTGT
123526 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
123568 AG AG
1 AG AG
123572 TTGAATGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:124041 original size:19 final size:19
Alignment explanation
Indices: 124017--124055 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
124007 ATACTATGAT
*
124017 GTCACATTTGTAAATGTGG
1 GTCACAATTGTAAATGTGG
124036 GTCACAATTGTAAATGTGG
1 GTCACAATTGTAAATGTGG
124055 G
1 G
124056 GTGAGCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (19 bp):
GTCACAATTGTAAATGTGG
Found at i:130658 original size:18 final size:18
Alignment explanation
Indices: 130635--130675 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
130625 GTTTATTGGT
*
130635 TGATGTCCGGCGCAAACG
1 TGATGTCCGGCGCAAAAG
130653 TGATGTCCGGCGCAAAAG
1 TGATGTCCGGCGCAAAAG
130671 TGATG
1 TGATG
130676 ATCAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.20
Consensus pattern (18 bp):
TGATGTCCGGCGCAAAAG
Found at i:141758 original size:17 final size:17
Alignment explanation
Indices: 141736--141768 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
141726 CTGGTACTAT
141736 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
141753 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
141769 AATGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:153622 original size:2 final size:2
Alignment explanation
Indices: 153610--153679 Score: 115
Period size: 2 Copynumber: 35.5 Consensus size: 2
153600 GAAGGGGTGC
153610 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
153651 AG AG AG AA AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
153680 TTTTGTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:184592 original size:2 final size:2
Alignment explanation
Indices: 184585--184643 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
184575 AACATAATAT
184585 TC TC TC TC TC TC TC TC TC -C T- TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
184625 TC TC TC TA TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
184644 GCATTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:190174 original size:174 final size:173
Alignment explanation
Indices: 189884--190229 Score: 683
Period size: 174 Copynumber: 2.0 Consensus size: 173
189874 AATTATTCAA
189884 TTAGTTTCATGTCAGGTTCACATGTCCTTAACAATTGCTTCATTGGCATCGGATTATTACATCAT
1 TTAGTTTCATGTCAGGTTCACATGTCCTTAACAATTGCTTCATTGGCATCGGATTATTACATCAT
189949 TGCACTCTATCGATGAAAAGCTGGATGGTGTGAAGCAAATATTGACTTTATGCCCCGATTTAGAT
66 TGCACTCTATCGATGAAAAGCTGGATGGTGTGAAGCAAATATTGACTTTATGCCCCGATTTAGAT
190014 TCTAAATATTGCATTATCCTGACTTCATAAAAATCTATGTANAG
131 TCTAAATATTGCATTATCCTGACTTCATAAAAATCTATGTA-AG
190058 TTAGTTTCATGTCAGGTTCACATGTCCTTAACAATTGCTTCATTGGCATCGGATTATTACATCAT
1 TTAGTTTCATGTCAGGTTCACATGTCCTTAACAATTGCTTCATTGGCATCGGATTATTACATCAT
190123 TGCACTCTATCGATGAAAAGCTGGATGGTGTGAAGCAAATATTGACTTTATGCCCCGATTTAGAT
66 TGCACTCTATCGATGAAAAGCTGGATGGTGTGAAGCAAATATTGACTTTATGCCCCGATTTAGAT
190188 TCTAAATATTGCATTATCCTGACTTCATAAAAATCTATGTAA
131 TCTAAATATTGCATTATCCTGACTTCATAAAAATCTATGTAA
190230 ACAAGATAAA
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 1 0.01
174 171 0.99
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (173 bp):
TTAGTTTCATGTCAGGTTCACATGTCCTTAACAATTGCTTCATTGGCATCGGATTATTACATCAT
TGCACTCTATCGATGAAAAGCTGGATGGTGTGAAGCAAATATTGACTTTATGCCCCGATTTAGAT
TCTAAATATTGCATTATCCTGACTTCATAAAAATCTATGTAAG
Found at i:199908 original size:2 final size:2
Alignment explanation
Indices: 199901--199952 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
199891 GAGTTTTCTT
*
199901 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
199943 GA GA GA GA GA
1 GA GA GA GA GA
199953 TGTACGTGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:201294 original size:2 final size:2
Alignment explanation
Indices: 201287--201316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
201277 ACATTCAAGG
201287 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
201317 TAATATNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:201353 original size:2 final size:2
Alignment explanation
Indices: 201346--201371 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
201336 NNNNNNNNNN
201346 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
201372 CACAGAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:202466 original size:23 final size:23
Alignment explanation
Indices: 202436--202481 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
202426 CATTATTTTA
202436 CGGAGTGACTTTGACTTTAAAAT
1 CGGAGTGACTTTGACTTTAAAAT
202459 CGGAGTGACTTTGACTTTAAAAT
1 CGGAGTGACTTTGACTTTAAAAT
202482 GAAACTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (23 bp):
CGGAGTGACTTTGACTTTAAAAT
Found at i:205774 original size:21 final size:21
Alignment explanation
Indices: 205750--205827 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
205740 ATGGGAGCAG
* **
205750 TGAACCATATCCTCAAATGTC
1 TGAACCGTATCCTCAAATCAC
*
205771 TGAACCGTATCCTAAAATCAC
1 TGAACCGTATCCTCAAATCAC
205792 TGAACCGTATCCTCAAATCAC
1 TGAACCGTATCCTCAAATCAC
* *
205813 AGAACCGTATTCTCA
1 TGAACCGTATCCTCA
205828 TCAGGATTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (21 bp):
TGAACCGTATCCTCAAATCAC
Found at i:205891 original size:3 final size:3
Alignment explanation
Indices: 205839--205876 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
205829 CAGGATTTCA
205839 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
205877 GATTTCACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:215877 original size:12 final size:12
Alignment explanation
Indices: 215860--215884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
215850 CGACAAAACT
215860 TAGAAGTATAGA
1 TAGAAGTATAGA
215872 TAGAAGTATAGA
1 TAGAAGTATAGA
215884 T
1 T
215885 TGTAATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TAGAAGTATAGA
Found at i:218550 original size:42 final size:42
Alignment explanation
Indices: 218503--218596 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
218493 ATTTATATAG
*
218503 TATCGTGCGTGTATACTGTTTTAACGTGCGTTAATCCCATCC
1 TATCGTGCGTGTATACTGTTCTAACGTGCGTTAATCCCATCC
* * * **
218545 TATCGTGCCTGTATACTGTTCTATCGTGCGTTTATCCTGTCC
1 TATCGTGCGTGTATACTGTTCTAACGTGCGTTAATCCCATCC
*
218587 TATAGTGCGT
1 TATCGTGCGT
218597 TAATCCATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.40
Consensus pattern (42 bp):
TATCGTGCGTGTATACTGTTCTAACGTGCGTTAATCCCATCC
Found at i:218551 original size:21 final size:21
Alignment explanation
Indices: 218527--218602 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
218517 ACTGTTTTAA
**
218527 CGTGCGTTAATCCCATCCTAT
1 CGTGCGTTAATCCTGTCCTAT
* * *
218548 CGTGCCTGT-ATACTGTTCTAT
1 CGTGCGT-TAATCCTGTCCTAT
*
218569 CGTGCGTTTATCCTGTCCTAT
1 CGTGCGTTAATCCTGTCCTAT
*
218590 AGTGCGTTAATCC
1 CGTGCGTTAATCC
218603 ATCAGGTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (21 bp):
CGTGCGTTAATCCTGTCCTAT
Found at i:222943 original size:51 final size:51
Alignment explanation
Indices: 222881--223134 Score: 440
Period size: 51 Copynumber: 5.0 Consensus size: 51
222871 TGGGTAACAA
222881 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAG
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAG
* *
222932 CTATATAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATAGATATAG
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCAT--ATATAG
*
222985 GTATAGAGTAGCTTGTGTAGAATCAGTAATATTTATTACAGTCATATATAG
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAG
223036 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATT--AGTCATATATAG
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAG
*
223085 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATTTATA
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATA
223135 TATAGGCCTA
Statistics
Matches: 192, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
49 49 0.26
51 95 0.49
53 48 0.25
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (51 bp):
GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAG
Found at i:223140 original size:104 final size:102
Alignment explanation
Indices: 222881--223134 Score: 440
Period size: 104 Copynumber: 2.5 Consensus size: 102
222871 TGGGTAACAA
* *
222881 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAGCTATATAGTAGCTT
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAGGTATAGAGTAGCTT
222946 GTTTAGAATCAGTAATATTTATTACAGTCATAGATATAG
66 GTTTAGAATCAGTAATATTTATTA-AGTCATA-ATATAG
*
222985 GTATAGAGTAGCTTGTGTAGAATCAGTAATATTTATTACAGTCATATATAGGTATAGAGTAGCTT
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAGGTATAGAGTAGCTT
223050 GTTTAGAATCAGTAATATTTATT-AGTCAT-ATATAG
66 GTTTAGAATCAGTAATATTTATTAAGTCATAATATAG
*
223085 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATTTATA
1 GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATA
223135 TATAGGCCTA
Statistics
Matches: 145, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
100 54 0.37
102 6 0.04
104 85 0.59
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (102 bp):
GTATAGAGTAGCTTGTTTAGAATCAGTAATATTTATTACAGTCATATATAGGTATAGAGTAGCTT
GTTTAGAATCAGTAATATTTATTAAGTCATAATATAG
Found at i:233084 original size:72 final size:72
Alignment explanation
Indices: 232999--233132 Score: 259
Period size: 72 Copynumber: 1.9 Consensus size: 72
232989 ACGCGACGCC
232999 ATTGTTCTTAACGTTCTAAATAGCACGCGACGTTATAGAATGTTCTAGACAGTTCTTAACGTAAT
1 ATTGTTCTTAACGTTCTAAATAGCACGCGACGTTATAGAATGTTCTAGACAGTTCTTAACGTAAT
233064 GTACGTT
66 GTACGTT
*
233071 ATTGTTCTTAACGTTGTAAATAGCACGCGACGTTATAGAATGTTCTAGACAGTTCTTAACGT
1 ATTGTTCTTAACGTTCTAAATAGCACGCGACGTTATAGAATGTTCTAGACAGTTCTTAACGT
233133 TTATTATGTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (72 bp):
ATTGTTCTTAACGTTCTAAATAGCACGCGACGTTATAGAATGTTCTAGACAGTTCTTAACGTAAT
GTACGTT
Found at i:239052 original size:34 final size:34
Alignment explanation
Indices: 239014--239224 Score: 386
Period size: 34 Copynumber: 6.2 Consensus size: 34
239004 AATTCAATGA
*
239014 AGTTGAACTTTATAACTGAGTTAAACTTATCGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
*
239048 AGTTGAACTTTATAACTGAGTTAGACCTATCGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
239082 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
*
239116 AGTTGAACTTTATAACTGAGTTAGACCTATCGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
239150 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
*
239184 AGTTGAACTTTATAACTGAGTTAGACTTATTGTC
1 AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
239218 AGTTGAA
1 AGTTGAA
239225 TATATTTTTG
Statistics
Matches: 171, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 171 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (34 bp):
AGTTGAACTTTATAACTGAGTTAGACTTATCGTC
Found at i:239776 original size:12 final size:12
Alignment explanation
Indices: 239752--239792 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
239742 CTTTCCTCTG
*
239752 CGTCCGTCAGTC
1 CGTCCGTCTGTC
*
239764 CGTCTGTCTGTC
1 CGTCCGTCTGTC
239776 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
239788 TGTCC
1 CGTCC
239793 CACTTCAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.02, C:0.39, G:0.24, T:0.34
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:239782 original size:16 final size:16
Alignment explanation
Indices: 239761--239792 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
239751 GCGTCCGTCA
239761 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
239777 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
239793 CACTTCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (16 bp):
GTCCGTCTGTCTGTCC
Found at i:242964 original size:12 final size:12
Alignment explanation
Indices: 242947--242990 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
242937 CGAATTACAT
242947 AAACAAACGCGC
1 AAACAAACGCGC
242959 AAACAAACGCGC
1 AAACAAACGCGC
**
242971 AAACAATTGCGC
1 AAACAAACGCGC
242983 AAACAAAC
1 AAACAAAC
242991 TGCAATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.52, C:0.30, G:0.14, T:0.05
Consensus pattern (12 bp):
AAACAAACGCGC
Found at i:247189 original size:255 final size:256
Alignment explanation
Indices: 246738--247252 Score: 822
Period size: 255 Copynumber: 2.0 Consensus size: 256
246728 GTATTAGAAG
* *
246738 TTTCCCACCATCTTCTGAGCAGCATCACCCGGTGAGCGTGAAACACTTGCAATTGTAAATGGACC
1 TTTCCCACCATCTTCTGAGCAGCATCACCCGGTGAACCTGAAACACTTGCAATTGTAAATGGACC
* *
246803 TCTTCAGCTCTTATTATCTCGTCTATAAGTCGACTCCTGGGAGTAAACCTTACTCTGTTGATTAT
66 TCTTCAGCTCTTATTATCTCGTCTATAAGTCGACTCATGGGAATAAACCTTACTCTGTTGATTAT
* *
246868 TTTTGCAGGGGGAATTAAGCCAAAGTCTGGAGACTGTAATTATTTCTTCACTCGCCAAATCATTG
131 TTTTGCAGGGGGAATTAAGCCAAAGTCTGGAGACTGTAATAATTTCTGCACTCGCCAAATCATTG
* *
246933 CTTAATTCATTATTACAAAT-AAGTCTAGTTGTGTGCTCCT-ATACGTTCGTATTCAAAGTA
196 CTTAATTCATTAGTACAAATAAAGTCTAGTTGTGTGCTCCTGA-ACGTTCGTATTCAAAGCA
* * * *
246993 TTTCCCACCATCTTCTTAGCGGCATCACCCGTTGAACCT-ATAACACTCT-CCATTGTAAATGGA
1 TTTCCCACCATCTTCTGAGCAGCATCACCCGGTGAACCTGA-AACACT-TGCAATTGTAAATGGA
* * * *
247056 TCTCTTCAGCTCTTATTGTCTCGTCTATAAGTCGACTTATGGGAATTAACCTTACTCTGTTGATT
64 CCTCTTCAGCTCTTATTATCTCGTCTATAAGTCGACTCATGGGAATAAACCTTACTCTGTTGATT
247121 ATTTTTGCAGGGGGAATTAAGCCAAAGTCTGGAGACTGTAATAATTTCTGCACTCGCCAAATCAT
129 ATTTTTGCAGGGGGAATTAAGCCAAAGTCTGGAGACTGTAATAATTTCTGCACTCGCCAAATCAT
*
247186 TGCTTAATTCATTAGTACAAATAAAGTCTAGTTGTGTGCTTCTGAACGTTCGTATTCAAAGCA
194 TGCTTAATTCATTAGTACAAATAAAGTCTAGTTGTGTGCTCCTGAACGTTCGTATTCAAAGCA
247249 TTTC
1 TTTC
247253 TACCTTGTCT
Statistics
Matches: 239, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
254 1 0.00
255 196 0.82
256 41 0.17
257 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (256 bp):
TTTCCCACCATCTTCTGAGCAGCATCACCCGGTGAACCTGAAACACTTGCAATTGTAAATGGACC
TCTTCAGCTCTTATTATCTCGTCTATAAGTCGACTCATGGGAATAAACCTTACTCTGTTGATTAT
TTTTGCAGGGGGAATTAAGCCAAAGTCTGGAGACTGTAATAATTTCTGCACTCGCCAAATCATTG
CTTAATTCATTAGTACAAATAAAGTCTAGTTGTGTGCTCCTGAACGTTCGTATTCAAAGCA
Found at i:270595 original size:13 final size:12
Alignment explanation
Indices: 270538--270598 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
270528 CTTATCAACA
*
270538 GAGAGAGAGAGA
1 GAGAGAGAGAGG
* *
270550 GAGAGAGGGGGG
1 GAGAGAGAGAGG
*
270562 GGGAGAGAGGAGG
1 GAGAGAGA-GAGG
270575 GAGAGAGAGAGG
1 GAGAGAGAGAGG
*
270587 GAAGTGAGAGAG
1 G-AGAGAGAGAG
270599 AAAAAGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.38, C:0.00, G:0.61, T:0.02
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:276170 original size:2 final size:2
Alignment explanation
Indices: 276163--276210 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
276153 TGAATGATAT
276163 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
276205 TC TC TC
1 TC TC TC
276211 CGTTTAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:278796 original size:62 final size:62
Alignment explanation
Indices: 278687--278803 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
278677 ATTTGCATCG
* * * * * *
278687 TTGCACAAGAGGTGTCAAAGCAATATTTATAACTTTTGGTGGGGCGTAAAGATATTATAATA
1 TTGCACAAGAGATGCCAAAGCAATATTTATAAATTTTGATGAGGCGTAAACATATTATAATA
*
278749 TTGCACAAGAGATGCCAAAGCAATATTTA-AAATTTATGATGATGCGTAAACATAT
1 TTGCACAAGAGATGCCAAAGCAATATTTATAAATTT-TGATGAGGCGTAAACATAT
278804 ACATGTATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 5 0.11
62 42 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (62 bp):
TTGCACAAGAGATGCCAAAGCAATATTTATAAATTTTGATGAGGCGTAAACATATTATAATA
Found at i:279897 original size:41 final size:39
Alignment explanation
Indices: 279835--279913 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 39
279825 ACTTTTTTTC
*
279835 GGGGGGGGGGGGGGGGACAAATTTTAAAAATTGAATTGG
1 GGGGGGGGGGGGGGGGACAAATTTGAAAAATTGAATTGG
*
279874 GGGGGGGGGGGGGGGTGATCAAATTTGAAAACTTGAATTG
1 GGGGGGGGGGGGGGG-GA-CAAATTTGAAAAATTGAATTG
279914 CGGAGTGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 15 0.42
40 2 0.06
41 19 0.53
ACGTcount: A:0.27, C:0.04, G:0.48, T:0.22
Consensus pattern (39 bp):
GGGGGGGGGGGGGGGGACAAATTTGAAAAATTGAATTGG
Found at i:280681 original size:2 final size:2
Alignment explanation
Indices: 280676--280720 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
280666 CACTTCGTTT
280676 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
280718 TC T
1 TC T
280721 GGCATTTCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:280844 original size:2 final size:2
Alignment explanation
Indices: 280837--280882 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
280827 ACAGCACCGA
280837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
280879 TC TC
1 TC TC
280883 AGTACGATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:283045 original size:15 final size:16
Alignment explanation
Indices: 283006--283052 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
282996 GTTTTGTTTA
283006 TGTTTGTT--TTTTGTT
1 TGTTTGTTGGTTTT-TT
283021 TGTTTGTTGGTTTTTT
1 TGTTTGTTGGTTTTTT
283037 TGTTT-TTGGTTTTTT
1 TGTTTGTTGGTTTTTT
283052 T
1 T
283053 TAATACATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 19 0.63
16 7 0.23
17 4 0.13
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (16 bp):
TGTTTGTTGGTTTTTT
Found at i:287444 original size:1 final size:1
Alignment explanation
Indices: 287434--287496 Score: 117
Period size: 1 Copynumber: 63.0 Consensus size: 1
287424 GGGAGGGGAA
*
287434 GGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
287497 TGTCCACACA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.02, C:0.00, G:0.98, T:0.00
Consensus pattern (1 bp):
G
Found at i:289051 original size:2 final size:2
Alignment explanation
Indices: 289044--289108 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
289034 TTCCCATGAA
289044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
289086 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
289109 GAACGTTATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:293930 original size:2 final size:2
Alignment explanation
Indices: 293923--293978 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
293913 CTTGAACTTT
293923 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
293965 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
293979 TGCAGACAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:301129 original size:19 final size:20
Alignment explanation
Indices: 301093--301132 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
301083 ATATCGTCAA
301093 TTTTGATAACCATATATTTT
1 TTTTGATAACCATATATTTT
* *
301113 TTTTGGTAA-CATTTATTTT
1 TTTTGATAACCATATATTTT
301132 T
1 T
301133 GAACTCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTGATAACCATATATTTT
Found at i:301211 original size:3 final size:3
Alignment explanation
Indices: 301203--301236 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
301193 TAATGGTAGC
301203 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
301237 TTTAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:302005 original size:23 final size:23
Alignment explanation
Indices: 301974--302024 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
301964 TAATATTTCT
*
301974 CATATCATTGACCAT-CAAATTTG
1 CATACCATTGACC-TCCAAATTTG
301997 CATACCATTGACCTCCAAATTTG
1 CATACCATTGACCTCCAAATTTG
302020 CATAC
1 CATAC
302025 ATGTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.31
Consensus pattern (23 bp):
CATACCATTGACCTCCAAATTTG
Found at i:304769 original size:11 final size:11
Alignment explanation
Indices: 304739--304770 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
304729 TAAAGACGAT
*
304739 CTTTAAGCCAC
1 CTTTAAGCTAC
304750 CTTTAAGCTAC
1 CTTTAAGCTAC
304761 CTTTAAGCTA
1 CTTTAAGCTA
304771 TATGTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:304829 original size:22 final size:22
Alignment explanation
Indices: 304779--304831 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
304769 TATATGTATT
*
304779 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
304801 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
304823 GCTTAAAGA
1 GCTTAAAGA
304832 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:304901 original size:11 final size:11
Alignment explanation
Indices: 304885--304927 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
304875 GTCCAAACTT
304885 CTTTAAGCCAC
1 CTTTAAGCCAC
*
304896 CTTTAAGCTAC
1 CTTTAAGCCAC
304907 CTTTAAGCCAC
1 CTTTAAGCCAC
304918 CTTTAAGCCA
1 CTTTAAGCCA
304928 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:311086 original size:4 final size:4
Alignment explanation
Indices: 311069--311112 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
311059 GTTACGAATG
* *
311069 GACA GACA GGCA GACA GACA GACA GACA GACA GACA AACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
311113 CACATGGGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:311171 original size:2 final size:2
Alignment explanation
Indices: 311164--311220 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
311154 GGTAGACAGC
311164 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
311206 CG AT AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
311221 AATACTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:313308 original size:15 final size:15
Alignment explanation
Indices: 313288--313320 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
313278 CTCCATGATC
313288 CTCTGCTTCTCC-CAT
1 CTCTGCTTC-CCACAT
313303 CTCTGCTTCCCACAT
1 CTCTGCTTCCCACAT
313318 CTC
1 CTC
313321 ATCTTCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.09, C:0.48, G:0.06, T:0.36
Consensus pattern (15 bp):
CTCTGCTTCCCACAT
Found at i:314386 original size:36 final size:36
Alignment explanation
Indices: 314214--314404 Score: 129
Period size: 36 Copynumber: 5.3 Consensus size: 36
314204 TTGTCTGAAT
* * * * *
314214 GCACCTCTTCAGTAGTCACCGTCCCTTCATCTGAAC
1 GCACTTCTTCAGCAGTCACTGTCACTTCATCTAAAC
* * * * * *
314250 ACGCTTATTAAGCAGTCACAGTCTCTTCATC-AGAAC
1 GCACTTCTTCAGCAGTCACTGTCACTTCATCTA-AAC
* *
314286 GCACTT-TGTCAGCAGTCACTGCCCCTTCATC-AGAAC
1 GCACTTCT-TCAGCAGTCACTGTCACTTCATCTA-AAC
* * * * *
314322 GTACTTCTTCAGCAGTTACTAT-ATCTTCACCTCAAC
1 GCACTTCTTCAGCAGTCACTGTCA-CTTCATCTAAAC
*
314358 GCACTTCTTCATCAGTCACTGTCACTTCATCTAAAC
1 GCACTTCTTCAGCAGTCACTGTCACTTCATCTAAAC
* *
314394 GCTCTCCTTCA
1 GCACTTCTTCA
314405 ACTGTCACCA
Statistics
Matches: 119, Mismatches: 30, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
35 1 0.01
36 116 0.97
37 2 0.02
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.30
Consensus pattern (36 bp):
GCACTTCTTCAGCAGTCACTGTCACTTCATCTAAAC
Found at i:314787 original size:11 final size:11
Alignment explanation
Indices: 314771--314811 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
314761 TAAGCAAGTC
*
314771 CTTAAAGGTAG
1 CTTAAAGGTGG
314782 CTTAAAGGTGG
1 CTTAAAGGTGG
*
314793 CCTAAAGGTGG
1 CTTAAAGGTGG
314804 CTTAAAGG
1 CTTAAAGG
314812 ATAAACAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:314837 original size:11 final size:11
Alignment explanation
Indices: 314821--314850 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
314811 GATAAACAAT
314821 CTTTAAGCCAC
1 CTTTAAGCCAC
314832 CTTTAAGCCAC
1 CTTTAAGCCAC
314843 CTTTAAGC
1 CTTTAAGC
314851 TGAGTTTATA
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:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:315105 original size:10 final size:11
Alignment explanation
Indices: 315080--315117 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
315070 TTACGTTCTC
315080 CTTAAAGATAG
1 CTTAAAGATAG
315091 CTTAAAGAT-G
1 CTTAAAGATAG
*
315101 CTTAAAGGTAG
1 CTTAAAGATAG
315112 CTTAAA
1 CTTAAA
315118 TACGATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (11 bp):
CTTAAAGATAG
Found at i:315188 original size:22 final size:22
Alignment explanation
Indices: 315159--315206 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
315149 GTGTTGCTGA
315159 AAAG-TGGCTTAAAGAAAGCGT
1 AAAGATGGCTTAAAGAAAGCGT
**
315180 AAAGATGGCTTAAAGGCAGCGT
1 AAAGATGGCTTAAAGAAAGCGT
315202 AAAGA
1 AAAGA
315207 CTACCTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (22 bp):
AAAGATGGCTTAAAGAAAGCGT
Found at i:315237 original size:10 final size:11
Alignment explanation
Indices: 315209--315238 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
315199 CGTAAAGACT
315209 ACCTTTAAGCC
1 ACCTTTAAGCC
315220 ACCTTTAAGCC
1 ACCTTTAAGCC
315231 A-CTTTAAG
1 ACCTTTAAG
315239 GACAACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (11 bp):
ACCTTTAAGCC
Found at i:315286 original size:11 final size:11
Alignment explanation
Indices: 315270--315323 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
315260 GTCCAAACTT
315270 CTTTAAGCC-C
1 CTTTAAGCCAC
315280 ACTTTAAGCCAC
1 -CTTTAAGCCAC
**
315292 CTTTAAGTTAC
1 CTTTAAGCCAC
*
315303 ATTTAAGCCAC
1 CTTTAAGCCAC
315314 CTTTAAGCCA
1 CTTTAAGCCA
315324 TTAAACTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
11 35 0.97
12 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:315298 original size:22 final size:23
Alignment explanation
Indices: 315270--315322 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
315260 GTCCAAACTT
315270 CTTTAAGCCCAC-TTTAAGCCAC
1 CTTTAAGCCCACATTTAAGCCAC
**
315292 CTTTAAG-TTACATTTAAGCCAC
1 CTTTAAGCCCACATTTAAGCCAC
315314 CTTTAAGCC
1 CTTTAAGCC
315323 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (23 bp):
CTTTAAGCCCACATTTAAGCCAC
Found at i:318035 original size:11 final size:11
Alignment explanation
Indices: 318019--318043 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
318009 AAATCCTTCT
318019 GTTTATCAGAA
1 GTTTATCAGAA
318030 GTTTATCAGAA
1 GTTTATCAGAA
318041 GTT
1 GTT
318044 AAGTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (11 bp):
GTTTATCAGAA
Found at i:318382 original size:36 final size:36
Alignment explanation
Indices: 318335--318443 Score: 218
Period size: 36 Copynumber: 3.0 Consensus size: 36
318325 CCATGTTATA
318335 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
1 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
318371 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
1 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
318407 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
1 TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
318443 T
1 T
318444 TGCCTTTGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (36 bp):
TGACATCTAGCAATGCTTAAGGTGCAACACTCAGTT
Found at i:318899 original size:27 final size:27
Alignment explanation
Indices: 318848--318900 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
318838 TCTTCATGAG
*
318848 CTTACCAAAGCTTACGAATATGCATGT
1 CTTACCAAAGCTTACGAATAGGCATGT
* * *
318875 CTTACCCAAGCTTAGGAGTAGGCATG
1 CTTACCAAAGCTTACGAATAGGCATG
318901 GGTAAGACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
CTTACCAAAGCTTACGAATAGGCATGT
Found at i:321620 original size:2 final size:2
Alignment explanation
Indices: 321613--321662 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
321603 CCCCCTACCC
321613 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
321655 AG AG AG AG
1 AG AG AG AG
321663 CGAGCGAGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:325359 original size:102 final size:102
Alignment explanation
Indices: 325183--325377 Score: 363
Period size: 102 Copynumber: 1.9 Consensus size: 102
325173 GACGCCTATG
*
325183 AAGCGTTGCAATTGCATCCCCTAATGCTTTAAATGCTTGCATTAACAGTTGACAATATCACCCAC
1 AAGCGTTGCAATTGCATCCCCTAATGCTATAAATGCTTGCATTAACAGTTGACAATATCACCCAC
*
325248 TTATGATAAATCGCCGCCTAATGATACAAATATCATT
66 TTAAGATAAATCGCCGCCTAATGATACAAATATCATT
*
325285 AAGCGTTGCAATTGCATCCCCTAATGCTATAAATTCTTGCATTAACAGTTGACAATATCACCCAC
1 AAGCGTTGCAATTGCATCCCCTAATGCTATAAATGCTTGCATTAACAGTTGACAATATCACCCAC
325350 TTAAGATAAATCGCCGCCTAATGATACA
66 TTAAGATAAATCGCCGCCTAATGATACA
325378 TTTTTATCAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (102 bp):
AAGCGTTGCAATTGCATCCCCTAATGCTATAAATGCTTGCATTAACAGTTGACAATATCACCCAC
TTAAGATAAATCGCCGCCTAATGATACAAATATCATT
Found at i:326574 original size:21 final size:22
Alignment explanation
Indices: 326543--326583 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
326533 ATAACAAAAC
326543 ACCCCCACCCCCCCCCCCCACA
1 ACCCCCACCCCCCCCCCCCACA
326565 ACCCCC-CCCCCCCCCCCCA
1 ACCCCCACCCCCCCCCCCCA
326584 AAAAAAANGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (22 bp):
ACCCCCACCCCCCCCCCCCACA
Found at i:330165 original size:166 final size:166
Alignment explanation
Indices: 329891--330195 Score: 452
Period size: 166 Copynumber: 1.8 Consensus size: 166
329881 CTTGGGTGCG
329891 TTAGGGTATCCTTGGAGTTTCCTTGGATATCCATCAGGTTCCCTGGGATTCCTAGAGGTGTATCT
1 TTAGGGTATCCTTGGAGTTTCCTTGGATATCCATCAGGTTCCCTGGGATTCCTAGAGGTGTATCT
* * * * *
329956 GGAATACCAATGAGTCCTCAGGGTTAATAAGAGTTTTAAATTTGTATTATTAGGGTATCCTTGAG
66 GGAATACCAATGAGTCCCCAGGGGTAACAAGAGTTTAAAATTTGTATTATTAGCGTATCCTTGAG
*
330021 GTTCTATGGAGTATCAAGAGTTATGATTCTGTATTA
131 GTTCCATGGAGTATCAAGAGTTATGATTCTGTATTA
* * ** * *
330057 TTAGGGTATTCTTGGAG-TTCCTTGGGATATCCCTGGGGTTCCCTGTGG-TTCTTAGAGGTGTGT
1 TTAGGGTATCCTTGGAGTTTCCTT-GGATATCCATCAGGTTCCCTG-GGATTCCTAGAGGTGTAT
* *
330120 CTGGAATACCAGTGAGTCCCCAGGGGTACCAAGAGTTTAAAATTTGTATTATTAGCGTATCCTTG
64 CTGGAATACCAATGAGTCCCCAGGGGTAACAAGAGTTTAAAATTTGTATTATTAGCGTATCCTTG
330185 AGGTTCCATGG
129 AGGTTCCATGG
330196 GGTTCTATGG
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
165 6 0.05
166 115 0.93
167 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.36
Consensus pattern (166 bp):
TTAGGGTATCCTTGGAGTTTCCTTGGATATCCATCAGGTTCCCTGGGATTCCTAGAGGTGTATCT
GGAATACCAATGAGTCCCCAGGGGTAACAAGAGTTTAAAATTTGTATTATTAGCGTATCCTTGAG
GTTCCATGGAGTATCAAGAGTTATGATTCTGTATTA
Found at i:330367 original size:10 final size:10
Alignment explanation
Indices: 330344--330414 Score: 115
Period size: 10 Copynumber: 6.8 Consensus size: 10
330334 ATTTCTGTTA
330344 TTGGGGTATCC
1 TTGGGGT-TCC
330355 TTGGGGTTCC
1 TTGGGGTTCC
330365 TTGGGGTTTCC
1 TTGGGG-TTCC
330376 TTGGGGTTCC
1 TTGGGGTTCC
330386 TTGGGGTTTCC
1 TTGGGG-TTCC
330397 TTGGGGTTCC
1 TTGGGGTTCC
330407 TTGGGGTT
1 TTGGGGTT
330415 AAAAGACGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
10 31 0.53
11 27 0.47
ACGTcount: A:0.01, C:0.17, G:0.39, T:0.42
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:330370 original size:21 final size:21
Alignment explanation
Indices: 330344--330414 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
330334 ATTTCTGTTA
*
330344 TTGGGGTATCCTTGGGGTTCC
1 TTGGGGTTTCCTTGGGGTTCC
330365 TTGGGGTTTCCTTGGGGTTCC
1 TTGGGGTTTCCTTGGGGTTCC
330386 TTGGGGTTTCCTTGGGGTTCC
1 TTGGGGTTTCCTTGGGGTTCC
330407 TTGGGGTT
1 TTGGGGTT
330415 AAAAGACGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.01, C:0.17, G:0.39, T:0.42
Consensus pattern (21 bp):
TTGGGGTTTCCTTGGGGTTCC
Found at i:333566 original size:22 final size:22
Alignment explanation
Indices: 333541--333604 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 22
333531 TATTTATGTA
333541 ATATCACTATGTTTGTGTAGCT
1 ATATCACTATGTTTGTGTAGCT
* **
333563 ATAT-AGTA--TTCATGTA---
1 ATATCACTATGTTTGTGTAGCT
333579 ATATCACTATGTTTGTGTAGCT
1 ATATCACTATGTTTGTGTAGCT
333601 ATAT
1 ATAT
333605 AGCATTCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
16 4 0.13
17 3 0.10
19 12 0.40
21 3 0.10
22 8 0.27
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (22 bp):
ATATCACTATGTTTGTGTAGCT
Found at i:333578 original size:38 final size:38
Alignment explanation
Indices: 333526--333642 Score: 216
Period size: 38 Copynumber: 3.1 Consensus size: 38
333516 GTTTATGTGG
*
333526 TATAGTATTTATGTAATATCACTATGTTTGTGTAGCTA
1 TATAGTATTCATGTAATATCACTATGTTTGTGTAGCTA
333564 TATAGTATTCATGTAATATCACTATGTTTGTGTAGCTA
1 TATAGTATTCATGTAATATCACTATGTTTGTGTAGCTA
*
333602 TATAGCATTCATGTAATATCACTATGTTTGTGTAGCTA
1 TATAGTATTCATGTAATATCACTATGTTTGTGTAGCTA
333640 TAT
1 TAT
333643 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.45
Consensus pattern (38 bp):
TATAGTATTCATGTAATATCACTATGTTTGTGTAGCTA
Found at i:333635 original size:19 final size:19
Alignment explanation
Indices: 333537--333635 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 19
333527 ATAGTATTTA
333537 TGTAATATCACTATGTTTG
1 TGTAATATCACTATGTTTG
* *
333556 TGTAGCTAT-A-TA-GTATTCA
1 TGTA-ATATCACTATGT-TT-G
333575 TGTAATATCACTATGTTTG
1 TGTAATATCACTATGTTTG
* **
333594 TGTAGCTAT-A-TA-GCATTCA
1 TGTA-ATATCACTATG--TTTG
333613 TGTAATATCACTATGTTTG
1 TGTAATATCACTATGTTTG
333632 TGTA
1 TGTA
333636 GCTATATNNN
Statistics
Matches: 58, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
17 3 0.05
18 12 0.21
19 28 0.48
20 12 0.21
21 3 0.05
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTAATATCACTATGTTTG
Found at i:365731 original size:114 final size:114
Alignment explanation
Indices: 365551--365779 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
365541 ACTTTAAAAA
365551 TAATGCCGAAAATCTTTCTAAATCTGGAGGACGAGCTCTTGGTTCCTTAATATCCAAAATCCACA
1 TAATGCCGAAAATCTTTCTAAATCTGGAGGACGAGCTCTTGGTTCCTTAATATCCAAAATCCACA
365616 GCTTGAAGGACATTGGGTTCACTACGTTTGAAAAATTATTTTATAGCTG
66 GCTTGAAGGACATTGGGTTCACTACGTTTGAAAAATTATTTTATAGCTG
365665 TAATGCCGAAAATCTTTCTAAATCTGGAGGACGAGCTCTTGGTTCCTTAATATCCAAAATCCACA
1 TAATGCCGAAAATCTTTCTAAATCTGGAGGACGAGCTCTTGGTTCCTTAATATCCAAAATCCACA
365730 GCTTGAAGGACATTGGGTTCACTACGTTTGAAAAATTATTTTATAGCTG
66 GCTTGAAGGACATTGGGTTCACTACGTTTGAAAAATTATTTTATAGCTG
365779 T
1 T
365780 GTCGCCCCGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (114 bp):
TAATGCCGAAAATCTTTCTAAATCTGGAGGACGAGCTCTTGGTTCCTTAATATCCAAAATCCACA
GCTTGAAGGACATTGGGTTCACTACGTTTGAAAAATTATTTTATAGCTG
Found at i:372425 original size:20 final size:20
Alignment explanation
Indices: 372343--372432 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
372333 TCAATCCCAG
372343 TCATTTACAGGAATTCCATA
1 TCATTTACAGGAATTCCATA
*
372363 TGATTTACAGGAATTCCATA
1 TCATTTACAGGAATTCCATA
* *
372383 TGATTTACAGGAATTCCAAA
1 TCATTTACAGGAATTCCATA
*
372403 TCATTTACAGGAATTCTATA
1 TCATTTACAGGAATTCCATA
*
372423 TCATCTACAG
1 TCATTTACAG
372433 TAACGTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (20 bp):
TCATTTACAGGAATTCCATA
Found at i:373967 original size:8 final size:8
Alignment explanation
Indices: 373941--374020 Score: 53
Period size: 8 Copynumber: 10.5 Consensus size: 8
373931 ACGTTTGAGT
373941 CGATAGTG
1 CGATAGTG
* *
373949 AGATGGTG
1 CGATAGTG
373957 CGATAGTG
1 CGATAGTG
*
373965 CGAT-G-A
1 CGATAGTG
373971 CGAT-GATG
1 CGATAG-TG
*
373979 CAATAGTG
1 CGATAGTG
*
373987 CGAT-G-A
1 CGATAGTG
*
373993 CGATAATG
1 CGATAGTG
*
374001 CGATGGTG
1 CGATAGTG
374009 CGATAGTG
1 CGATAGTG
374017 CGAT
1 CGAT
374021 GACGATGATG
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
6 9 0.17
7 2 0.04
8 41 0.77
9 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (8 bp):
CGATAGTG
Found at i:373975 original size:22 final size:22
Alignment explanation
Indices: 373950--374012 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
373940 TCGATAGTGA
*
373950 GATGGTGCGATAGTGCGATGAC
1 GATGATGCGATAGTGCGATGAC
*
373972 GATGATGCAATAGTGCGATGAC
1 GATGATGCGATAGTGCGATGAC
* *
373994 GATAATGCGATGGTGCGAT
1 GATGATGCGATAGTGCGAT
374013 AGTGCGATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.24
Consensus pattern (22 bp):
GATGATGCGATAGTGCGATGAC
Found at i:373990 original size:30 final size:30
Alignment explanation
Indices: 373981--374073 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
373971 CGATGATGCA
* *
373981 ATAGTGCGATGACGATAATGCGATGGTGCG
1 ATAGTGCGATGACGATGATGCGATGGCGCG
374011 ATAGTGCGATGACGATGATGCGATGGCGCG
1 ATAGTGCGATGACGATGATGCGATGGCGCG
* * * *
374041 ACAATGCGATGACGATGGTGCGATGGCACG
1 ATAGTGCGATGACGATGATGCGATGGCGCG
374071 ATA
1 ATA
374074 AAGCGATAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.27, C:0.16, G:0.37, T:0.20
Consensus pattern (30 bp):
ATAGTGCGATGACGATGATGCGATGGCGCG
Found at i:374034 original size:8 final size:8
Alignment explanation
Indices: 373950--374163 Score: 61
Period size: 8 Copynumber: 28.5 Consensus size: 8
373940 TCGATAGTGA
*
373950 GATGGTGC
1 GATGATGC
373958 GAT-AGTGC
1 GATGA-TGC
373966 GATGA--C
1 GATGATGC
373972 GATGATGC
1 GATGATGC
*
373980 AAT-AGTGC
1 GATGA-TGC
373988 GATGA--C
1 GATGATGC
*
373994 GATAATGC
1 GATGATGC
*
374002 GATGGTGC
1 GATGATGC
374010 GAT-AGTGC
1 GATGA-TGC
374018 GATGA--C
1 GATGATGC
374024 GATGATGC
1 GATGATGC
**
374032 GATGGCGC
1 GATGATGC
**
374040 GACAATGC
1 GATGATGC
374048 GATGA--C
1 GATGATGC
*
374054 GATGGTGC
1 GATGATGC
***
374062 GATGGCAC
1 GATGATGC
* *
374070 GATAAAGC
1 GATGATGC
374078 GAT-A-GC
1 GATGATGC
374084 GCAATGATGC
1 G--ATGATGC
*
374094 GATGATAC
1 GATGATGC
374102 GAT-A-GC
1 GATGATGC
*
374108 GATAATGC
1 GATGATGC
*
374116 GATGGTGC
1 GATGATGC
374124 GAT-A-GC
1 GATGATGC
* **
374130 AATGACAC
1 GATGATGC
*
374138 GATGTTGC
1 GATGATGC
374146 GAT-A-GC
1 GATGATGC
374152 GATGATGC
1 GATGATGC
374160 GATG
1 GATG
374164 CTCTATCGCG
Statistics
Matches: 148, Mismatches: 34, Indels: 48
0.64 0.15 0.21
Matches are distributed among these distances:
6 38 0.26
7 6 0.04
8 97 0.66
9 4 0.03
10 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (8 bp):
GATGATGC
Found at i:374080 original size:30 final size:30
Alignment explanation
Indices: 373985--374097 Score: 129
Period size: 30 Copynumber: 3.7 Consensus size: 30
373975 GATGCAATAG
* * *
373985 TGCGATGACGATAATGCGATGGTGCGATAG
1 TGCGATGACGATGATGCGATGGCGCGATAA
*
374015 TGCGATGACGATGATGCGATGGCGCGACAA
1 TGCGATGACGATGATGCGATGGCGCGATAA
* *
374045 TGCGATGACGATGGTGCGATGGCACGATAA
1 TGCGATGACGATGATGCGATGGCGCGATAA
*
374075 AGCGAT-AGCGCAATGATGCGATG
1 TGCGATGA-CG--ATGATGCGATG
374098 ATACGATAGC
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
29 1 0.01
30 60 0.85
32 10 0.14
ACGTcount: A:0.27, C:0.17, G:0.36, T:0.19
Consensus pattern (30 bp):
TGCGATGACGATGATGCGATGGCGCGATAA
Found at i:374118 original size:22 final size:22
Alignment explanation
Indices: 374076--374163 Score: 95
Period size: 22 Copynumber: 3.9 Consensus size: 22
374066 GCACGATAAA
374076 GCGATAGCGCAATGATGCGATGAT
1 GCGATAGCG--ATGATGCGATGAT
* * *
374100 ACGATAGCGATAATGCGATGGT
1 GCGATAGCGATGATGCGATGAT
* ** *
374122 GCGATAGCAATGACACGATGTT
1 GCGATAGCGATGATGCGATGAT
374144 GCGATAGCGATGATGCGATG
1 GCGATAGCGATGATGCGATG
374164 CTCTATCGCG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
22 44 0.85
24 8 0.15
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.22
Consensus pattern (22 bp):
GCGATAGCGATGATGCGATGAT
Found at i:375079 original size:22 final size:22
Alignment explanation
Indices: 375047--375134 Score: 113
Period size: 22 Copynumber: 3.9 Consensus size: 22
375037 CGCGATAGAG
*
375047 CATCGCATCATCGCTATCGCAC
1 CATCGCGTCATCGCTATCGCAC
*
375069 CATCGTGTCATCGCTATCGCAC
1 CATCGCGTCATCGCTATCGCAC
* * *
375091 CATCGCGTTATCGCTATCGTAT
1 CATCGCGTCATCGCTATCGCAC
375113 CATCGCGTCATTGCGCTATCGC
1 CATCGCGTCA-T-CGCTATCGC
375135 TTTATCGTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 47 0.84
23 1 0.02
24 8 0.14
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.28
Consensus pattern (22 bp):
CATCGCGTCATCGCTATCGCAC
Found at i:375149 original size:16 final size:16
Alignment explanation
Indices: 375130--375188 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
375120 TCATTGCGCT
*
375130 ATCGCTTTATCGTGCC
1 ATCGCATTATCGTGCC
**
375146 ATCGCACCATCGT--C
1 ATCGCATTATCGTGCC
*
375160 ATCGCATTGTCGTGCC
1 ATCGCATTATCGTGCC
*
375176 ATCGCATCATCGT
1 ATCGCATTATCGT
375189 CATCGCGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.33
16 22 0.67
ACGTcount: A:0.17, C:0.34, G:0.19, T:0.31
Consensus pattern (16 bp):
ATCGCATTATCGTGCC
Found at i:375164 original size:14 final size:14
Alignment explanation
Indices: 375145--375194 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
375135 TTTATCGTGC
*
375145 CATCGCACCATCGT
1 CATCGCATCATCGT
**
375159 CATCGCATTGTCGT
1 CATCGCATCATCGT
375173 GCCATCGCATCATCGT
1 --CATCGCATCATCGT
375189 CATCGC
1 CATCGC
375195 GCTATCGCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.18, C:0.38, G:0.18, T:0.26
Consensus pattern (14 bp):
CATCGCATCATCGT
Found at i:375164 original size:30 final size:30
Alignment explanation
Indices: 375130--375194 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
375120 TCATTGCGCT
*
375130 ATCGCTTTATCGTGCCATCGCACCATCGTC
1 ATCGCATTATCGTGCCATCGCACCATCGTC
* *
375160 ATCGCATTGTCGTGCCATCGCATCATCGTC
1 ATCGCATTATCGTGCCATCGCACCATCGTC
375190 ATCGC
1 ATCGC
375195 GCTATCGCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.17, C:0.35, G:0.18, T:0.29
Consensus pattern (30 bp):
ATCGCATTATCGTGCCATCGCACCATCGTC
Found at i:375203 original size:22 final size:22
Alignment explanation
Indices: 375176--375253 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
375166 TTGTCGTGCC
* *
375176 ATCGCATCATCGTCATCGCGCT
1 ATCGCACCATCGTCATCGCACT
* *
375198 ATCGCACCATCGCCACCGCACT
1 ATCGCACCATCGTCATCGCACT
*
375220 ATCGCATCATCGTCATCGCACT
1 ATCGCACCATCGTCATCGCACT
375242 ATCGCACCATCG
1 ATCGCACCATCG
375254 CACTATCTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (22 bp):
ATCGCACCATCGTCATCGCACT
Found at i:375208 original size:30 final size:30
Alignment explanation
Indices: 375144--375210 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
375134 CTTTATCGTG
* * **
375144 CCATCGCACCATCGTCATCGCATTGTCGTG
1 CCATCGCACCATCGTCATCGCACTATCGCA
* *
375174 CCATCGCATCATCGTCATCGCGCTATCGCA
1 CCATCGCACCATCGTCATCGCACTATCGCA
375204 CCATCGC
1 CCATCGC
375211 CACCGCACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.40, G:0.18, T:0.24
Consensus pattern (30 bp):
CCATCGCACCATCGTCATCGCACTATCGCA
Found at i:377027 original size:65 final size:65
Alignment explanation
Indices: 376951--377146 Score: 392
Period size: 65 Copynumber: 3.0 Consensus size: 65
376941 CCGTTATACA
376951 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
1 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
377016 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
1 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
377081 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
1 TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
377146 T
1 T
377147 CACGGCACAC
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 131 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (65 bp):
TGTTTTTTAAGAATGTAAGGCATTTGCCAGTTATACCACTTTTATGAATTTTAAACCATAAACCC
Found at i:381178 original size:14 final size:14
Alignment explanation
Indices: 381159--381190 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
381149 TTATTATTGC
381159 ACATGTGCTAATAA
1 ACATGTGCTAATAA
*
381173 ACATGTGTTAATAA
1 ACATGTGCTAATAA
381187 ACAT
1 ACAT
381191 TACCCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (14 bp):
ACATGTGCTAATAA
Done.