Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 75 of 141
Found at i:21469537 original size:173 final size:173
Alignment explanation
Indices: 21469241--21469586 Score: 611
Period size: 173 Copynumber: 2.0 Consensus size: 173
21469231 AAAATTTATG
* *
21469241 ATCCTCCCATTGCATTTTATTTGTTTTGAATTATAGTTTTCATGATGTTTTGTATTTTAAATTTT
1 ATCCTCCCATTGCATTTTATTTGTTTTGAATTATAGTTTTCATCATGTTTTGCATTTTAAATTTT
* *
21469306 TATATCTCCACTCATTGCATTGTATGACCGTTGGTCACACCTTTTTAAGTGGGAGTGAGAAGCTA
66 TATATCTCCACTCATTGCATTGCATGACCGTTGGTCACACCTTTTTAAGTGGGAGTGAGAAACTA
*
21469371 CTCCTTCGTGAGGTTTTCACCTCCGTTCAGGATAGTGGATCGC
131 CTCCTTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGC
* *
21469414 ATCCTCTCATTGCATTTTCTTTGTTTTGAATTATAGTTTTCATCATGTTTTGCATTTTAAATTTT
1 ATCCTCCCATTGCATTTTATTTGTTTTGAATTATAGTTTTCATCATGTTTTGCATTTTAAATTTT
*
21469479 TATATCTCCACTCATTGCATTGCATGACTGTTGGTCACACCTTTTTAAGTGGGAGTGAGAAACTA
66 TATATCTCCACTCATTGCATTGCATGACCGTTGGTCACACCTTTTTAAGTGGGAGTGAGAAACTA
*
21469544 CTCTTTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGC
131 CTCCTTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGC
21469587 TTTCGGGATA
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (173 bp):
ATCCTCCCATTGCATTTTATTTGTTTTGAATTATAGTTTTCATCATGTTTTGCATTTTAAATTTT
TATATCTCCACTCATTGCATTGCATGACCGTTGGTCACACCTTTTTAAGTGGGAGTGAGAAACTA
CTCCTTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGC
Found at i:21470380 original size:19 final size:19
Alignment explanation
Indices: 21470356--21470402 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
21470346 ACGTCTCTTT
*
21470356 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
21470375 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
21470394 TATGCATTA
1 TTTGCATTA
21470403 GGTTTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:21472330 original size:27 final size:27
Alignment explanation
Indices: 21472300--21472355 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
21472290 TCTTTGATTC
*
21472300 TTTTATTCTTTTCGATTTTCTTCCAAA
1 TTTTATTCTTTTAGATTTTCTTCCAAA
21472327 TTTTATTCTTTTAGATTTTCTTCCAAA
1 TTTTATTCTTTTAGATTTTCTTCCAAA
21472354 TT
1 TT
21472356 AATCTTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTATTCTTTTAGATTTTCTTCCAAA
Found at i:21473211 original size:52 final size:48
Alignment explanation
Indices: 21473149--21473266 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 48
21473139 AATTTATTTT
* * *
21473149 AAAAATTAAAATAAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAA-AAAAATTTAAAAAAA--A-TTAAAAAAAAATTTAAAATT-A
*
21473201 AAAAATTAAAAAAAAGTATTTTAAAAAAATTAAAAAAAAATTTAAAATTA
1 AAAAATTAAAAAAAA--ATTTAAAAAAAATTAAAAAAAAATTTAAAATTA
21473251 AAAAATTAAAAAAAAA
1 AAAAATTAAAAAAAAA
21473267 GCATTTTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
48 1 0.02
50 16 0.27
51 21 0.36
52 12 0.20
53 1 0.02
54 8 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (48 bp):
AAAAATTAAAAAAAAATTTAAAAAAAATTAAAAAAAAATTTAAAATTA
Found at i:21473223 original size:41 final size:42
Alignment explanation
Indices: 21473143--21473297 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 42
21473133 ACCAAAAATT
21473143 TATTTTAAAAATTAAAATAAAAATT-AAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAAGTATTTTAAAAA
21473187 TATTTTAAAATT-AAAAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAAGTATTTTAAAAA
* ** * *
21473228 AATTAAAAAAAAATTTAAAATTAAAAAATTAAAAAAAAAGCATTTTAAAAG
1 TATT---TTAAAA-TTAAAA--AA--AATT-AAAAAAAAGTATTTTAAAAA
21473279 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
21473298 TAAATAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 23
0.75 0.07 0.19
Matches are distributed among these distances:
40 7 0.08
41 24 0.26
43 7 0.08
44 10 0.11
45 4 0.04
46 3 0.03
47 6 0.07
48 6 0.07
50 4 0.04
51 21 0.23
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAAGTATTTTAAAAA
Found at i:21474143 original size:1 final size:1
Alignment explanation
Indices: 21474139--21474229 Score: 56
Period size: 1 Copynumber: 91.0 Consensus size: 1
21474129 TAAAAATTGT
* * * * * * * * * * * *
21474139 AAAAAAAAAGAAGAAAAAAAAAGAAGAAAAAAAAAGAGAGAGAAAAAAGAAAAAGAAAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
21474204 AAAAAAAAAAAAAGAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
21474230 GGAGAGGCCA
Statistics
Matches: 62, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (1 bp):
A
Found at i:21474155 original size:10 final size:9
Alignment explanation
Indices: 21474142--21474229 Score: 74
Period size: 9 Copynumber: 9.8 Consensus size: 9
21474132 AAATTGTAAA
21474142 AAAAAAGAAG
1 AAAAAA-AAG
21474152 AAAAAAAAAG
1 -AAAAAAAAG
*
21474162 AAGAAAAA-
1 AAAAAAAAG
* *
21474170 AAAAGAGAG
1 AAAAAAAAG
*
21474179 AGAAAAAAG
1 AAAAAAAAG
21474188 AAAAAGAAAG
1 AAAAA-AAAG
*
21474198 AAAAAGAA-
1 AAAAAAAAG
21474206 AAAAAAAA-
1 AAAAAAAAG
*
21474214 AAAGAAAAG
1 AAAAAAAAG
21474223 AAAAAAA
1 AAAAAAA
21474230 GGAGAGGCCA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
8 19 0.31
9 25 0.40
10 12 0.19
11 6 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:21474155 original size:13 final size:13
Alignment explanation
Indices: 21474139--21474227 Score: 110
Period size: 13 Copynumber: 6.7 Consensus size: 13
21474129 TAAAAATTGT
21474139 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
21474152 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
21474165 AAAAAAAAAGAGAG
1 AAAAAAAAAGA-AG
*
21474179 AGAAAAAAGAAAAAG
1 A-AAAAAA-AAGAAG
*
21474194 AAAGAAAAAGAA-
1 AAAAAAAAAGAAG
21474206 AAAAAAAAA-AAG
1 AAAAAAAAAGAAG
21474218 AAAAGAAAAA
1 AAAA-AAAAA
21474228 AAGGAGAGGC
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
11 2 0.03
12 12 0.18
13 33 0.49
14 8 0.12
15 9 0.13
16 3 0.04
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:21474191 original size:19 final size:17
Alignment explanation
Indices: 21474139--21474229 Score: 83
Period size: 15 Copynumber: 5.8 Consensus size: 17
21474129 TAAAAATTGT
*
21474139 AAAAAAAAAGAAGAAAA-
1 AAAAAGAAAGAA-AAAAG
21474156 AAAAAG-AAGAAAAAA-
1 AAAAAGAAAGAAAAAAG
* *
21474171 AAAGAGAGAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
21474188 AAAAAGAAAG-AAAAAG
1 AAAAAGAAAGAAAAAAG
21474204 -AAAA-AAA-AAAAAAG
1 AAAAAGAAAGAAAAAAG
21474218 -AAAAGAAA-AAAA
1 AAAAAGAAAGAAAA
21474230 GGAGAGGCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
14 13 0.20
15 20 0.31
16 19 0.29
17 13 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:21474202 original size:42 final size:42
Alignment explanation
Indices: 21474139--21474229 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
21474129 TAAAAATTGT
* *
21474139 AAAAAAAAAGAAGAAAAAAAAAG-AAGAAAAAAAAAGAGAGAG
1 AAAAAAAAAGAAGAAAAAAAAAGAAAAAAAAAAAAAGA-AAAG
*
21474181 AAAAAAGAAA-AAGAAAGAAAAAGAAAAAAAAAAAAAGAAAAG
1 AAAAAA-AAAGAAGAAAAAAAAAGAAAAAAAAAAAAAGAAAAG
21474223 AAAAAAA
1 AAAAAAA
21474230 GGAGAGGCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 27 0.61
43 16 0.36
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (42 bp):
AAAAAAAAAGAAGAAAAAAAAAGAAAAAAAAAAAAAGAAAAG
Found at i:21475647 original size:49 final size:48
Alignment explanation
Indices: 21475520--21476153 Score: 302
Period size: 49 Copynumber: 12.8 Consensus size: 48
21475510 ATACCATAGT
* ** * *
21475520 TTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTTCCCAGGCG
1 TTGCAA-TTAAAAGATTGAAGCCACAACGGCGAATCTCGC-TTCCC-GACA
* * * * * * *
21475571 GTGTAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCCTCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCGCTTCC-CGACA
* ** * *
21475621 TTGCAATTAAAAGATTGATGCCACAACGGCGAATCTTACTTTCCCAGGCG
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCGC-TTCCC-GACA
* * * * *
21475671 GTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCTCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCGCTTCC-CGACA
* * ** * *
21475721 TTGCAATTAAAAGATTGAGGCCACAACGGTGAATCTTACTTTACCAGGCA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCGC-TT-CCCGACA
* * * * *
21475771 GTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCGCTT-CCCGACA
* * ** ** *
21475821 TTGCAATTAAAAGATTGAGGCCACAATGGCGAATCTTACTTCTAGGCGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCGCTTCCCGAC-A
*** * * * * * *
21475870 -TGCAGCGGAACAGATTGAAGTCACAACAGCGGATCTAGCTTTCCCGTCA
1 TTGCA-ATTAAAAGATTGAAGCCACAACGGCGAATCTCGC-TTCCCGACA
** * * * ** * *
21475919 TTGCGTTTAAAAAGATTGAAGCTACAATGGTGAATCTTACTTCCAAGAGA
1 TTGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTCGCTTCC-CGACA
*** * * * * *
21475969 -TGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTTGCTTCCCTGACA
1 TTGCA-ATTAAAAGATTGAAGCCACAACGGCGAATCTCGCTTCCC-GACA
* * * ** **
21476018 TTGTAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTCCC-AGG
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCGC-TTCCCGACA
* * * * *
21476066 TGGTGCAGTGGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGTCA
1 T--TGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCGCTT-CCCGACA
* *
21476118 TTACAATTAAACGATTGAAGCCACAACGGCGAATCT
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCT
21476154 TACCTTCCTA
Statistics
Matches: 419, Mismatches: 140, Indels: 50
0.69 0.23 0.08
Matches are distributed among these distances:
48 9 0.02
49 193 0.46
50 105 0.25
51 111 0.26
52 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (48 bp):
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCGCTTCCCGACA
Found at i:21476074 original size:297 final size:299
Alignment explanation
Indices: 21475520--21476195 Score: 925
Period size: 297 Copynumber: 2.3 Consensus size: 299
21475510 ATACCATAGT
* * *
21475520 TTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTTCCCAGGCGGTGTAGTGGAACAG
1 TTGCAA-TTAAAAGATTGAAGCCACAATGGCGAATCTTAC-TTCCTAGGCGATGCAGTGGAACAG
* * *
21475585 ATTGAAGCTACAACGGCAAATCTCGCTTCCTCGACATTGCAATTAAAAGATTGATGCCACAACGG
64 ATTGAAGCTACAACAGCAAATCTAGCTTCCTCGACATTGCAATTAAAAGATTGAAGCCACAACGG
* * * *
21475650 CGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
129 CGAATCTTACTTTCCCAAGAGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
* *
21475715 TCGACATTGCAATTAAAAGATTGAGGCCACAACGGTGAATCTTACTTTACCAGGCAGTGCAGTGG
194 TCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTACCAGGCAGTGCAGTGG
21475780 AACAGATTGAAG-CTACAACGGCGAATCTCGCTTCCCCGACA
259 AACAGATTGAAGTC-ACAACGGCGAATCTCGCTTCCCCGACA
* *
21475821 TTGCAATTAAAAGATTGAGGCCACAATGGCGAATCTTACTT-CTAGGCGATGCAGCGGAACAGAT
1 TTGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCTAGGCGATGCAGTGGAACAGAT
** * ** * *
21475885 TGAAG-TCACAACAGCGGATCTAGCTTTCC-CGTCATTGCGTTTAAAAAGATTGAAGCTACAATG
66 TGAAGCT-ACAACAGCAAATCTAGC-TTCCTCGACATTGCAATT-AAAAGATTGAAGCCACAACG
* * * *
21475948 GTGAATCTTAC-TT-CCAAGAGATGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTTGCTTC
128 GCGAATCTTACTTTCCCAAGAGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTC
* * **
21476011 C-CTGACATTGTAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTCCCAGGTGGTGCAGT
193 CTC-GACATTGCAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTACCAGGCAGTGCAGT
*
21476075 GGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGTCA
257 GGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGACA
* * * *
21476118 TTACAATTAAACGATTGAAGCCACAACGGCGAATCTTACCTTCCTAGGCGATGCAGTGGAATAGA
1 TTGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTA-CTTCCTAGGCGATGCAGTGGAACAGA
21476183 TTGAAGCTACAAC
65 TTGAAGCTACAAC
21476196 GACGAATCTT
Statistics
Matches: 331, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
296 1 0.00
297 174 0.53
298 53 0.16
299 64 0.19
300 33 0.10
301 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (299 bp):
TTGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCTAGGCGATGCAGTGGAACAGAT
TGAAGCTACAACAGCAAATCTAGCTTCCTCGACATTGCAATTAAAAGATTGAAGCCACAACGGCG
AATCTTACTTTCCCAAGAGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCTC
GACATTGCAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTACCAGGCAGTGCAGTGGAA
CAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGACA
Found at i:21476212 original size:100 final size:100
Alignment explanation
Indices: 21475520--21476220 Score: 887
Period size: 100 Copynumber: 7.0 Consensus size: 100
21475510 ATACCATAGT
* * *
21475520 TTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTTCCCAGGCGGTGTAGTGGAACAG
1 TTGCAA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAG
* *
21475585 ATTGAAGCTACAACGGCAAATCTCGCTTCCTCGACA
65 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* *
21475621 TTGCAATTAAAAGATTGATGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAGA
*
21475686 TTGAAGCTACAACGGCGAATCTCGCTTCCTCGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * *
21475721 TTGCAATTAAAAGATTGAGGCCACAACGGTGAATCTTACTTTACCAGGC-AGTGCAGTGGAACAG
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGA-TGCAGTGGAACAG
21475785 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * *
21475821 TTGCAATTAAAAGATTGAGGCCACAATGGCGAATCTTAC-TT-CTAGGCGATGCAGCGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAGA
* * * * *
21475884 TTGAAG-TCACAACAGCGGATCTAGCTTTCCCGTCA
66 TTGAAGCT-ACAACGGCGAATCTCGCTTCCCCGACA
** * * * * * *
21475919 TTGCGTTTAAAAAGATTGAAGCTACAATGGTGAATCTTAC-TT-CCAAGAGATGCAGCGGAACAG
1 TTGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAG
* * * *
21475982 ATTGAAGCTACGACGGTGAATCTTGCTTCCCTGACA
65 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * * *
21476018 TTGTAATTAAAAGATTGAGGCCACAACGGCGAAACTTACTTTCCCAGGTGGTGCAGTGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAGA
*
21476083 TTGAAG-TCACAACGGCGAATCTCGCTTCCCCGTCA
66 TTGAAGCT-ACAACGGCGAATCTCGCTTCCCCGACA
* * * * *
21476118 TTACAATTAAACGATTGAAGCCACAACGGCGAATCTTACCTTCCTAGGCGATGCAGTGGAATAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAGA
* *
21476183 TTGAAGCTACAACGACGAATCTTC-TTTCCCCGACA
66 TTGAAGCTACAACGGCGAATC-TCGCTTCCCCGACA
21476218 TTG
1 TTG
21476221 TAATCTCATT
Statistics
Matches: 525, Mismatches: 65, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
97 1 0.00
98 78 0.15
99 85 0.16
100 352 0.67
101 9 0.02
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (100 bp):
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
Found at i:21476353 original size:172 final size:172
Alignment explanation
Indices: 21476067--21476392 Score: 379
Period size: 172 Copynumber: 1.9 Consensus size: 172
21476057 TTTCCCAGGT
* * ** *
21476067 GGTGCAGTGGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGTCATTACAATTAAACGA
1 GGTGCAGCGGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGACATTACAACCAAAAGA
** * * * *
21476132 TTGAAGCCACAACGGCGAATCTTACCTTCCTAGGCGATGCAGTGGAATAGATTGAAGCTACAACG
66 TTGAAGCCACAACAACGAATCTCACCTTCCTAGGCGATGCAATGGAATAGATTAAAGCCACAACG
21476197 ACGAATCTT-CTTTCCCCGACATTGTAATCTCATTTCCCTAGC
131 ACGAATCTTGCTTT-CCCGACATTGTAATCTCATTTCCCTAGC
* * * * * * * *
21476239 GGTGCAGCGGAATAGATTGAAGTTACGATGGTGAATCTCGTTTCCCCGACATTGCAGCCAAATAG
1 GGTGCAGCGGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGACATTACAACCAAA-AG
* * *
21476304 ATTGAAGCTATAACAACGAATCTCA-CTTCTCT-GGCGATGTAATGGAATAGATTAAAGCCACAA
65 ATTGAAGCCACAACAACGAATCTCACCTTC-CTAGGCGATGCAATGGAATAGATTAAAGCCACAA
* **
21476367 TGGTGAATCTTGCTTTCCCGACATTG
129 CGACGAATCTTGCTTTCCCGACATTG
21476393 CAATTAAAAT
Statistics
Matches: 126, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
172 99 0.79
173 27 0.21
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (172 bp):
GGTGCAGCGGAACAGATTGAAGTCACAACGGCGAATCTCGCTTCCCCGACATTACAACCAAAAGA
TTGAAGCCACAACAACGAATCTCACCTTCCTAGGCGATGCAATGGAATAGATTAAAGCCACAACG
ACGAATCTTGCTTTCCCGACATTGTAATCTCATTTCCCTAGC
Found at i:21478071 original size:3 final size:3
Alignment explanation
Indices: 21478063--21478138 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
21478053 TTATCATCTT
* * * *
21478063 TTA TTA TTA TTA TTG TTT TTA TTA TCT- TTA CTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * * *
21478108 TTA TTG TTA ATA TTA TTG TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21478139 GTTTTTATTT
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 1 0.02
3 54 0.96
4 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:21478086 original size:12 final size:12
Alignment explanation
Indices: 21478066--21478133 Score: 75
Period size: 12 Copynumber: 5.7 Consensus size: 12
21478056 TCATCTTTTA
21478066 TTATTATTATTG
1 TTATTATTATTG
*
21478078 TTTTTATTATCT-
1 TTATTATTAT-TG
* *
21478090 TTACTATTATTA
1 TTATTATTATTG
*
21478102 TTAGTATTATTG
1 TTATTATTATTG
*
21478114 TTAATATTATTG
1 TTATTATTATTG
21478126 TTATTATT
1 TTATTATT
21478134 GTTATGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
11 1 0.02
12 45 0.96
13 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:21478402 original size:19 final size:19
Alignment explanation
Indices: 21478378--21478414 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21478368 ATATATTATT
*
21478378 TTATTTCATTTTTTTAATC
1 TTATTTCATTTTTATAATC
*
21478397 TTATTTTATTTTTATAAT
1 TTATTTCATTTTTATAAT
21478415 TCACATACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTCATTTTTATAATC
Found at i:21478443 original size:18 final size:18
Alignment explanation
Indices: 21478420--21478454 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21478410 ATAATTCACA
* *
21478420 TACGTATATATTTTCTTC
1 TACGTACATATATTCTTC
21478438 TACGTACATATATTCTT
1 TACGTACATATATTCTT
21478455 ATGTTTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (18 bp):
TACGTACATATATTCTTC
Found at i:21485088 original size:45 final size:45
Alignment explanation
Indices: 21484989--21485167 Score: 245
Period size: 45 Copynumber: 4.0 Consensus size: 45
21484979 ATTTGCCGGC
* * * *
21484989 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
*
21485033 ATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTATTGTTACTG
1 -TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
*
21485079 TTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
* **
21485124 TTACAGATTCATCACTTTGTGTGTTC-AATACTGTTACTGTTACT
1 TTACTGATTCGGCACTTTGTGTG-TCGAATACTGTTACTGTTACT
21485168 ACTACCGTTA
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 95 0.78
46 27 0.22
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (45 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
Found at i:21485698 original size:13 final size:15
Alignment explanation
Indices: 21485680--21485711 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21485670 TATATGAAAT
21485680 AATGATT-TT-ATGA
1 AATGATTATTGATGA
21485693 AATGATTATTGATGA
1 AATGATTATTGATGA
21485708 AATG
1 AATG
21485712 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:21487182 original size:26 final size:26
Alignment explanation
Indices: 21487143--21487208 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
21487133 GAGAAAGCAC
*
21487143 TAACGGG-AGCCTCAAAAAGAGCC-TT
1 TAACGGGAAG-CTCAAAAAGAGCCATA
**
21487168 TAATCGGGAAGCTCACGAAGAGCCATA
1 TAA-CGGGAAGCTCAAAAAGAGCCATA
*
21487195 TAACGGGATGCTCA
1 TAACGGGAAGCTCA
21487209 TAAGAGCTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.09
26 25 0.74
27 6 0.18
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.17
Consensus pattern (26 bp):
TAACGGGAAGCTCAAAAAGAGCCATA
Found at i:21491259 original size:24 final size:24
Alignment explanation
Indices: 21491221--21491331 Score: 125
Period size: 24 Copynumber: 4.6 Consensus size: 24
21491211 TCTCAAGCAC
* *
21491221 TATAATGGTAAGCTCATTGAGCCT
1 TATAACGGGAAGCTCATTGAGCCT
* *
21491245 TGTAACTGGAAGCTCATTGAGCCT
1 TATAACGGGAAGCTCATTGAGCCT
* **
21491269 TATAACGGGAAGCTTATCCTG-GCAA
1 TATAACGGGAAGCTCAT--TGAGCCT
21491294 TATAACGGGAAGCTCATTGAGCCT
1 TATAACGGGAAGCTCATTGAGCCT
*
21491318 TGTAACGGGAAGCT
1 TATAACGGGAAGCT
21491332 TATCCGGACA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 49 0.69
25 18 0.25
26 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (24 bp):
TATAACGGGAAGCTCATTGAGCCT
Found at i:21491300 original size:25 final size:25
Alignment explanation
Indices: 21491269--21491356 Score: 101
Period size: 25 Copynumber: 3.6 Consensus size: 25
21491259 CATTGAGCCT
21491269 TATAACGGGAAGCTTATCCTGGCAA
1 TATAACGGGAAGCTTATCCTGGCAA
* **
21491294 TATAACGGGAAGCTCAT--TGAGCCT
1 TATAACGGGAAGCTTATCCTG-GCAA
*
21491318 TGTAACGGGAAGCTTATCC-GGACAA
1 TATAACGGGAAGCTTATCCTGG-CAA
21491343 TATAACGGGAAGCT
1 TATAACGGGAAGCT
21491357 CACAAAGAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.04
24 18 0.35
25 31 0.61
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
TATAACGGGAAGCTTATCCTGGCAA
Found at i:21491310 original size:49 final size:49
Alignment explanation
Indices: 21491247--21491358 Score: 190
Period size: 49 Copynumber: 2.3 Consensus size: 49
21491237 TTGAGCCTTG
*
21491247 TAACTGGAAGCTCATTGAGCCTTATAACGGGAAGCTTATCCTGG-CAATA
1 TAACGGGAAGCTCATTGAGCCTTATAACGGGAAGCTTATCC-GGACAATA
*
21491296 TAACGGGAAGCTCATTGAGCCTTGTAACGGGAAGCTTATCCGGACAATA
1 TAACGGGAAGCTCATTGAGCCTTATAACGGGAAGCTTATCCGGACAATA
21491345 TAACGGGAAGCTCA
1 TAACGGGAAGCTCA
21491359 CAAAGAGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
48 2 0.03
49 58 0.97
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (49 bp):
TAACGGGAAGCTCATTGAGCCTTATAACGGGAAGCTTATCCGGACAATA
Found at i:21503352 original size:12 final size:12
Alignment explanation
Indices: 21503308--21503357 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
21503298 AGGTAAGTAT
21503308 CTGTGATTGTTG
1 CTGTGATTGTTG
*
21503320 CTG-AATT-TTCGG
1 CTGTGATTGTT--G
*
21503332 CTTTGATTGTTG
1 CTGTGATTGTTG
21503344 CTGTGATTGTTG
1 CTGTGATTGTTG
21503356 CT
1 CT
21503358 AAATTTTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
10 2 0.07
11 3 0.10
12 20 0.67
13 3 0.10
14 2 0.07
ACGTcount: A:0.10, C:0.12, G:0.28, T:0.50
Consensus pattern (12 bp):
CTGTGATTGTTG
Found at i:21503599 original size:62 final size:62
Alignment explanation
Indices: 21503517--21503744 Score: 244
Period size: 62 Copynumber: 3.7 Consensus size: 62
21503507 TATTCCCCAA
* * * * *
21503517 AAGACCACATGGCCAAGGACACGGGCGTGTACCCAGACCGTGTAACTCAATGA-TTGTGGTCT
1 AAGACCACACGGCCAGGGACACGAGCGTGTACCCAGGCCGTGTAACTCACT-ATTTGTGGTCT
** * * * * *
21503579 AAGACCGTACGGCCAGGGACACAAGCATGTACCCAGGCCATGTAACTCACTATTTCTAGTCT
1 AAGACCACACGGCCAGGGACACGAGCGTGTACCCAGGCCGTGTAACTCACTATTTGTGGTCT
* *
21503641 AAGACCACACGGCCAGGGACACGAGCGTGTGCTCAGGCCGTGTAACTCACTATTTGTGGTC-
1 AAGACCACACGGCCAGGGACACGAGCGTGTACCCAGGCCGTGTAACTCACTATTTGTGGTCT
* * * * * * *
21503702 AAGACGACATGACTAAGGACACGGGCGTATACCCAGGCCGTGT
1 AAGACCACACGGCCAGGGACACGAGCGTGTACCCAGGCCGTGT
21503745 GAGTTATACG
Statistics
Matches: 135, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
61 35 0.26
62 100 0.74
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (62 bp):
AAGACCACACGGCCAGGGACACGAGCGTGTACCCAGGCCGTGTAACTCACTATTTGTGGTCT
Found at i:21510589 original size:62 final size:62
Alignment explanation
Indices: 21510517--21510747 Score: 230
Period size: 62 Copynumber: 3.7 Consensus size: 62
21510507 TATTAGCGAA
** * * * *
21510517 AAGACCACACGACCAGGGACTTGGGTGTGTACCCAGGCCGTGTAACTTATTGTTTTTGGTCC
1 AAGACCACACGACCAGGGACACGGGCGTGTACCCAGGCCGTGTAACTCACTGTTTGTGGTCC
** * * ** *
21510579 AAGACCACACGGTCAGGGACACGAGCCTGTAAGCAGGCTGTGTAACTCACTGTTTGTGGTCC
1 AAGACCACACGACCAGGGACACGGGCGTGTACCCAGGCCGTGTAACTCACTGTTTGTGGTCC
* * * * * **
21510641 AAGACCACAC-AGCTAGGGACATGGACGTGTGCTCAGGTTGTGTAACTCACTGTTTGTGGTCC
1 AAGACCACACGA-CCAGGGACACGGGCGTGTACCCAGGCCGTGTAACTCACTGTTTGTGGTCC
* * * *
21510703 AATACCACACGACCAAGGACACAGGCGTGTAGCCAGGCCGTGTAA
1 AAGACCACACGACCAGGGACACGGGCGTGTACCCAGGCCGTGTAA
21510748 GTCATACCGG
Statistics
Matches: 132, Mismatches: 35, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
62 131 0.99
63 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (62 bp):
AAGACCACACGACCAGGGACACGGGCGTGTACCCAGGCCGTGTAACTCACTGTTTGTGGTCC
Found at i:21516573 original size:69 final size:69
Alignment explanation
Indices: 21516462--21516755 Score: 392
Period size: 69 Copynumber: 4.3 Consensus size: 69
21516452 ATTCACAAAT
* * * * * * *
21516462 ATTTGGACAGCAGTAAAAACATTTGGACAGCATTGACTTGTACGAAAAATGGACAACATTTAAGC
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACAGCATTTAAGC
21516527 ACTA
66 ACTA
* * * *
21516531 ATTTGGATAGCATTAATAACATTCGGACAGCATAGATTTGTACCAAAAATAGATAGCATTTAAGC
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACAGCATTTAAGC
21516596 ACTA
66 ACTA
* * *
21516600 ATTTGGAAAGCATTAATAACATTCAGACAACATAGATTTGTACAAAAAATGGACAGCATTTAAGC
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACAGCATTTAAGC
21516665 ACTA
66 ACTA
* * * * *
21516669 ATTTGGACAGCATGAATAACATACGGATAGCAT-GAATTTGTATAAAAAATGGATAGCATTTAAG
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAG-ATTTGTACAAAAAATGGACAGCATTTAAG
21516733 CACTA
65 CACTA
*
21516738 ATTTGGACAACATTAATA
1 ATTTGGACAGCATTAATA
21516756 TGCTAAAAAA
Statistics
Matches: 198, Mismatches: 26, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
68 1 0.01
69 197 0.99
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (69 bp):
ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACAGCATTTAAGC
ACTA
Found at i:21516818 original size:34 final size:33
Alignment explanation
Indices: 21516766--21516866 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 33
21516756 TGCTAAAAAA
*
21516766 TGGACAGCATTTATACATGCAAAACAACCACATT
1 TGGACAACATTTA-ACATGCAAAACAACCACATT
*
21516800 TGGACAACATTATAACATGTAAAAACAACCACATT
1 TGGACAACATT-TAACATG-CAAAACAACCACATT
* ** *
21516835 TGGATATTATTTTAATATGCAAAACAACCACA
1 TGGACAACA-TTTAACATGCAAAACAACCACA
21516867 CTTTAATACC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 27 0.47
35 28 0.49
36 2 0.04
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
TGGACAACATTTAACATGCAAAACAACCACATT
Found at i:21517664 original size:43 final size:43
Alignment explanation
Indices: 21517617--21517713 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
21517607 TCCTAGATAT
* * **
21517617 GGTCTTACATGCT-ATCACATCTCGATGCCACTATCCTTGACAG
1 GGTCTTACATG-TAATCACATATCGATGCCAATATCCCAGACAG
* * *
21517660 GGTCTTACATGTAATCTCATATCGATGCCAATGTCCCAGACAT
1 GGTCTTACATGTAATCACATATCGATGCCAATATCCCAGACAG
21517703 GGTCTTACATG
1 GGTCTTACATG
21517714 AAATTATACC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATATCGATGCCAATATCCCAGACAG
Found at i:21527661 original size:21 final size:21
Alignment explanation
Indices: 21527635--21527676 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21527625 GCCTATAACG
21527635 GGTAGCTCCAAAGAGCAATTA
1 GGTAGCTCCAAAGAGCAATTA
*
21527656 GGTAGCTCCGAAGAGCAATTA
1 GGTAGCTCCAAAGAGCAATTA
21527677 ACGGGAAGCA
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:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (21 bp):
GGTAGCTCCAAAGAGCAATTA
Found at i:21532207 original size:242 final size:242
Alignment explanation
Indices: 21531782--21532268 Score: 920
Period size: 242 Copynumber: 2.0 Consensus size: 242
21531772 NNNNNNCTTC
* *
21531782 GTATTTGAATTTTCCAGATCTAAATAAATAAATTTAATCATTAATCTAATACATTTCATGTTCAT
1 GTATTTGAAATTTCCAGATCTAAATAAATAAAATTAATCATTAATCTAATACATTTCATGTTCAT
21531847 GTGTAAGATTCTCTATAATTCCATTATTATTTATAGTGCATTCAAAGCTGTCTCACTGAGTCACA
66 GTGTAAGATTCTCTATAATTCCATTATTATTTATAGTGCATTCAAAGCTGTCTCACTGAGTCACA
21531912 GTAACTAAATTATTTATATCTTGAGCTAAAGAACTCCAAATCAAGATCTGTTAATCTTCCCTGAA
131 GTAACTAAATTATTTATATCTTGAGCTAAAGAACTCCAAATCAAGATCTGTTAATCTTCCCTGAA
*
21531977 ACTAGACTCATATATCTTCTTACCATAAAATTTTCAAAATTTTTGTT
196 ACTAGACTCATATATCTTCTTACCATAAAATTTTCAAAATTTTTGGT
** *
21532024 GTATTTGAAATTTCTGGATTTAAATAAATAAAATTAATCATTAATCTAATACATTTCATGTTCAT
1 GTATTTGAAATTTCCAGATCTAAATAAATAAAATTAATCATTAATCTAATACATTTCATGTTCAT
21532089 GTGTAAGATTCTCTATAATTCCATTATTATTTATAGTGCATTCAAAGCTGTCTCACTGAGTCACA
66 GTGTAAGATTCTCTATAATTCCATTATTATTTATAGTGCATTCAAAGCTGTCTCACTGAGTCACA
21532154 GTAACTAAATTATTTATATCTTGAGCTAAAGAACTCCAAATCAAGATCTGTTAATCTTCCCTGAA
131 GTAACTAAATTATTTATATCTTGAGCTAAAGAACTCCAAATCAAGATCTGTTAATCTTCCCTGAA
21532219 ACTAGACTCATATATCTTCTTACCATAAAATTTTCAAAATTTTTGGT
196 ACTAGACTCATATATCTTCTTACCATAAAATTTTCAAAATTTTTGGT
21532266 GTA
1 GTA
21532269 GCCAATAAGT
Statistics
Matches: 239, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
242 239 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (242 bp):
GTATTTGAAATTTCCAGATCTAAATAAATAAAATTAATCATTAATCTAATACATTTCATGTTCAT
GTGTAAGATTCTCTATAATTCCATTATTATTTATAGTGCATTCAAAGCTGTCTCACTGAGTCACA
GTAACTAAATTATTTATATCTTGAGCTAAAGAACTCCAAATCAAGATCTGTTAATCTTCCCTGAA
ACTAGACTCATATATCTTCTTACCATAAAATTTTCAAAATTTTTGGT
Found at i:21540720 original size:6 final size:6
Alignment explanation
Indices: 21540709--21540749 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
21540699 CTTAAAAAAC
*
21540709 TATAAA TATAAA TATAAA TA-AAA TGTAAA TATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
21540750 AACATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
TATAAA
Found at i:21540737 original size:17 final size:17
Alignment explanation
Indices: 21540712--21540745 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21540702 AAAAAACTAT
21540712 AAATATAAATATAAATA
1 AAATATAAATATAAATA
*
21540729 AAATGTAAATATAAATA
1 AAATATAAATATAAATA
21540746 TAAAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATATAAATATAAATA
Found at i:21549727 original size:44 final size:44
Alignment explanation
Indices: 21549678--21549768 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
21549668 GTAGGTAAAA
*
21549678 TAATATTAAAATAACCTATACTAATTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAAC
*
21549722 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGTAAAC
1 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAAC
21549766 TAA
1 TAA
21549769 AAATAGAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAAC
Found at i:21586071 original size:19 final size:20
Alignment explanation
Indices: 21586047--21586089 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
21586037 GCTAAAATAA
*
21586047 TATCGATACC-AAATAAAAG
1 TATCGATACCTAAAGAAAAG
*
21586066 TATCGATACCTAAAGGAAAG
1 TATCGATACCTAAAGAAAAG
21586086 TATC
1 TATC
21586090 AGTACTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (20 bp):
TATCGATACCTAAAGAAAAG
Found at i:21591464 original size:13 final size:13
Alignment explanation
Indices: 21591446--21591488 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
21591436 AAATTTGAAT
21591446 TATTTAGTGATAA
1 TATTTAGTGATAA
*
21591459 TATTTAG-G--AC
1 TATTTAGTGATAA
21591469 TATTTAGTGATAA
1 TATTTAGTGATAA
21591482 TATTTAG
1 TATTTAG
21591489 GAAAAGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
12 1 0.04
13 15 0.60
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:21591472 original size:23 final size:23
Alignment explanation
Indices: 21591446--21591490 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
21591436 AAATTTGAAT
21591446 TATTTAGTGATAATATTTAGGAC
1 TATTTAGTGATAATATTTAGGAC
21591469 TATTTAGTGATAATATTTAGGA
1 TATTTAGTGATAATATTTAGGA
21591491 AAAGTCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (23 bp):
TATTTAGTGATAATATTTAGGAC
Found at i:21606952 original size:24 final size:24
Alignment explanation
Indices: 21606902--21606954 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
21606892 ATTAGTAAGT
*
21606902 TAAATAAACTATACTAATAAACGC
1 TAAATAAACTATACTAATAAACAC
* * *
21606926 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAACAC
21606950 TAAAT
1 TAAAT
21606955 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAACAC
Found at i:21609246 original size:39 final size:39
Alignment explanation
Indices: 21609192--21609266 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
21609182 GCTTCCTGTT
21609192 CAGTTATAACTGTCAACACTGAAAGGATCTCGCAGGGTG
1 CAGTTATAACTGTCAACACTGAAAGGATCTCGCAGGGTG
21609231 CAGTTATAACTGTCAACACTGAAAGGATCTCGCAGG
1 CAGTTATAACTGTCAACACTGAAAGGATCTCGCAGG
21609267 AAAACACCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (39 bp):
CAGTTATAACTGTCAACACTGAAAGGATCTCGCAGGGTG
Found at i:21617410 original size:23 final size:23
Alignment explanation
Indices: 21617384--21617427 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21617374 TACTAAAACA
*
21617384 TGTAGGTTGTAGATAAACCACCT
1 TGTAGGTCGTAGATAAACCACCT
*
21617407 TGTAGGTCGTGGATAAACCAC
1 TGTAGGTCGTAGATAAACCAC
21617428 TAAATTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (23 bp):
TGTAGGTCGTAGATAAACCACCT
Found at i:21618366 original size:14 final size:11
Alignment explanation
Indices: 21618337--21618378 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
21618327 TCAGTTTCAG
21618337 TGTGGTGGTGA
1 TGTGGTGGTGA
*
21618348 TGTGGTGGTGC
1 TGTGGTGGTGA
*
21618359 TATGGTGGTGA
1 TGTGGTGGTGA
*
21618370 TTTGGTGGT
1 TGTGGTGGT
21618379 TTGGGGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.07, C:0.02, G:0.50, T:0.40
Consensus pattern (11 bp):
TGTGGTGGTGA
Found at i:21620759 original size:54 final size:54
Alignment explanation
Indices: 21620701--21620812 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
21620691 TGACTAAGGC
* * *
21620701 CACACAGCCGTGTCGTAGGCCGTGTGCCAGACCATGTAACTCACTAACTTGATT
1 CACACAGCCGTGTCGCAGACCGTGTGCCAGACCATGTAACTCACTAACTTGATA
* * * **
21620755 CACACGGCTGTGTCGCAGACGGTGTGCCAGACCATGTGGCTCACTAACTTGATA
1 CACACAGCCGTGTCGCAGACCGTGTGCCAGACCATGTAACTCACTAACTTGATA
21620809 CACA
1 CACA
21620813 TGATCATGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (54 bp):
CACACAGCCGTGTCGCAGACCGTGTGCCAGACCATGTAACTCACTAACTTGATA
Found at i:21622599 original size:18 final size:17
Alignment explanation
Indices: 21622576--21622609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21622566 CAAAAATCAC
21622576 TTAACAAAACAAGTTTAT
1 TTAAC-AAACAAGTTTAT
*
21622594 TTAACAACCAAGTTTA
1 TTAACAAACAAGTTTA
21622610 ATAATCTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAACAAACAAGTTTAT
Found at i:21652475 original size:3 final size:3
Alignment explanation
Indices: 21652467--21652524 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
21652457 AAGGAATACT
* * *
21652467 ATA ATA ATA ATA A-C ATA ATT ATA ATTA ATA TTA ATA ATCA CATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A -ATA ATA
21652514 ATA ATA ATA AT
1 ATA ATA ATA AT
21652525 GAGGTAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.82
4 5 0.11
5 2 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:21652509 original size:27 final size:26
Alignment explanation
Indices: 21652471--21652522 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
21652461 AATACTATAA
*
21652471 TAATAATAACATAATTATAATTAATAT
1 TAATAATAACATAATAATAA-TAATAT
*
21652498 TAATAATCACATAATAATAATAATA
1 TAATAATAACATAATAATAATAATA
21652523 ATGAGGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAATAACATAATAATAATAATAT
Found at i:21653591 original size:5 final size:6
Alignment explanation
Indices: 21653571--21653603 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
21653561 TTTTTGAAAT
*
21653571 AAAAGA AAAACA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
21653604 CGCAAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:21655819 original size:18 final size:18
Alignment explanation
Indices: 21655796--21655836 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
21655786 GAGGATCCAC
21655796 CTCCGGCTTCGGCTCCGA
1 CTCCGGCTTCGGCTCCGA
21655814 CTCCGGCTTCGGCTCCGA
1 CTCCGGCTTCGGCTCCGA
*
21655832 GTCCG
1 CTCCG
21655837 AGTCCGGCTT
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:0.05, C:0.44, G:0.29, T:0.22
Consensus pattern (18 bp):
CTCCGGCTTCGGCTCCGA
Found at i:21655844 original size:18 final size:18
Alignment explanation
Indices: 21655796--21655845 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
21655786 GAGGATCCAC
*
21655796 CTCCGGCTTCGGCTCCGA
1 CTCCGGCTCCGGCTCCGA
*
21655814 CTCCGGCTTCGGCTCCGA
1 CTCCGGCTCCGGCTCCGA
*
21655832 GTCCGAG-TCCGGCT
1 CTCCG-GCTCCGGCT
21655846 TCAGCTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.06, C:0.42, G:0.30, T:0.22
Consensus pattern (18 bp):
CTCCGGCTCCGGCTCCGA
Found at i:21655863 original size:24 final size:24
Alignment explanation
Indices: 21655808--21655864 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
21655798 CCGGCTTCGG
* * *
21655808 CTCCGACTCCGGCTTCGGCTCCGA
1 CTCCGAGTCCGGCTTCAGCTCCAA
*
21655832 GTCCGAGTCCGGCTTCAGCTCCAA
1 CTCCGAGTCCGGCTTCAGCTCCAA
*
21655856 CTCTGAGTC
1 CTCCGAGTC
21655865 TGACTTCGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.40, G:0.25, T:0.23
Consensus pattern (24 bp):
CTCCGAGTCCGGCTTCAGCTCCAA
Found at i:21655894 original size:18 final size:18
Alignment explanation
Indices: 21655871--21655905 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21655861 AGTCTGACTT
21655871 CGAGTCCG-GCTCCGGCTC
1 CGAGTCCGAG-TCCGGCTC
21655889 CGAGTCCGAGTCCGGCT
1 CGAGTCCGAGTCCGGCT
21655906 TCAGCTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.09, C:0.40, G:0.34, T:0.17
Consensus pattern (18 bp):
CGAGTCCGAGTCCGGCTC
Found at i:21664584 original size:7 final size:7
Alignment explanation
Indices: 21664568--21664638 Score: 115
Period size: 7 Copynumber: 10.1 Consensus size: 7
21664558 TTAATATGTG
21664568 TTTGATT
1 TTTGATT
*
21664575 TTTTATT
1 TTTGATT
21664582 TTTGATT
1 TTTGATT
21664589 TTTGATT
1 TTTGATT
21664596 TTTGATT
1 TTTGATT
21664603 TTTGATT
1 TTTGATT
21664610 TTTGATT
1 TTTGATT
21664617 TTTGATT
1 TTTGATT
*
21664624 TTTTATT
1 TTTGATT
*
21664631 TTTTATT
1 TTTGATT
21664638 T
1 T
21664639 AAAAATGATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 61 1.00
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (7 bp):
TTTGATT
Found at i:21669332 original size:24 final size:24
Alignment explanation
Indices: 21669300--21669345 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21669290 TGACTACTCT
21669300 CATTAATTCTTCTATAATACCTCC
1 CATTAATTCTTCTATAATACCTCC
* *
21669324 CATTGATTCTTCTGTAATACCT
1 CATTAATTCTTCTATAATACCT
21669346 ATCACTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (24 bp):
CATTAATTCTTCTATAATACCTCC
Found at i:21669356 original size:24 final size:24
Alignment explanation
Indices: 21669303--21669356 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
21669293 CTACTCTCAT
* *
21669303 TAATTCTTCTATAATACCTCCCAT
1 TAATTCTTCTATAATACCTACCAC
* * *
21669327 TGATTCTTCTGTAATACCTATCAC
1 TAATTCTTCTATAATACCTACCAC
21669351 TAATTC
1 TAATTC
21669357 ACTTACACCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (24 bp):
TAATTCTTCTATAATACCTACCAC
Found at i:21670147 original size:28 final size:27
Alignment explanation
Indices: 21670107--21670165 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 27
21670097 TTGAAGGTAG
21670107 CAACAAGGTTTGCAAGCTCAACAAGTCT
1 CAACAAGGTTTGCAAGCTCAACAAG-CT
21670135 CAACAAGGTTTGCAAGCTCAACAAGCT
1 CAACAAGGTTTGCAAGCTCAACAAGCT
21670162 CAAC
1 CAAC
21670166 CAATCACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (27 bp):
CAACAAGGTTTGCAAGCTCAACAAGCT
Found at i:21674171 original size:51 final size:50
Alignment explanation
Indices: 21674068--21674266 Score: 286
Period size: 51 Copynumber: 4.1 Consensus size: 50
21674058 TGAGTACTTC
21674068 TGATCAGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAG
1 TGAT-AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
21674118 TGATACGTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATTAG
1 TGATA-GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
21674169 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC--
1 TGAT-AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
21674218 -G---GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATTTGATCAG
1 TGATAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
21674264 TGA
1 TGA
21674267 CAAGTGATAA
Statistics
Matches: 136, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
44 41 0.30
47 1 0.01
48 1 0.01
49 1 0.01
50 25 0.18
51 66 0.49
52 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (50 bp):
TGATAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:21674184 original size:44 final size:44
Alignment explanation
Indices: 21674124--21674273 Score: 183
Period size: 44 Copynumber: 3.2 Consensus size: 44
21674114 TCAGTGATAC
* * *
21674124 GTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATTAGTGATAA
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATC-------TGATCA
* *
21674175 GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCG
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
*
21674219 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATTTGATCA
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
21674263 GTGACAAGTGA
1 GTGACAAGTGA
21674274 TAAATGTGAT
Statistics
Matches: 93, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
44 56 0.60
51 37 0.40
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (44 bp):
GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
Found at i:21674578 original size:11 final size:13
Alignment explanation
Indices: 21674564--21674596 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
21674554 AATTTCACGA
21674564 AAAAATTTCG-T-
1 AAAAATTTCGTTC
21674575 AAAAATTTCGTTC
1 AAAAATTTCGTTC
21674588 AAAAATTTC
1 AAAAATTTC
21674597 AACGTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 1 0.05
13 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:21675320 original size:30 final size:30
Alignment explanation
Indices: 21675280--21675336 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21675270 AGCTTAGGGA
*
21675280 CAAAAGTGTAAATATTCAAAAGTTTGGGGG
1 CAAAAGTGTAAATATTCAAAAATTTGGGGG
* * *
21675310 CAAAATTGTAATTTTTCAAAAATTTGG
1 CAAAAGTGTAAATATTCAAAAATTTGG
21675337 TTGGAGGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (30 bp):
CAAAAGTGTAAATATTCAAAAATTTGGGGG
Found at i:21675732 original size:33 final size:33
Alignment explanation
Indices: 21675668--21675903 Score: 178
Period size: 33 Copynumber: 6.8 Consensus size: 33
21675658 ATATAAAGGG
*
21675668 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
21675695 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
21675728 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
21675770 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
21675803 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
21675845 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
21675878 GGTTGCTAAGTGTTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
21675904 AACGGATAAC
Statistics
Matches: 169, Mismatches: 15, Indels: 43
0.74 0.07 0.19
Matches are distributed among these distances:
27 22 0.13
31 2 0.01
32 2 0.01
33 60 0.36
34 10 0.06
35 2 0.01
36 4 0.02
37 7 0.04
38 6 0.04
39 4 0.02
40 2 0.01
41 6 0.04
42 42 0.25
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:21675787 original size:42 final size:42
Alignment explanation
Indices: 21675728--21675864 Score: 193
Period size: 42 Copynumber: 3.5 Consensus size: 42
21675718 ATTCATTGGT
21675728 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
* *
21675770 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
21675803 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
21675845 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
21675865 CCGACTCATT
Statistics
Matches: 82, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 41 0.50
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
Found at i:21675814 original size:75 final size:75
Alignment explanation
Indices: 21675691--21675901 Score: 395
Period size: 75 Copynumber: 2.8 Consensus size: 75
21675681 TGATTCCCCC
*
21675691 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
21675756 TTAAATGTGA
66 TTAAATGTGA
21675766 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
21675831 TTAAATGTGA
66 TTAAATGTGA
* *
21675841 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGTTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
21675902 ATAACGGATA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 133 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:21676612 original size:20 final size:20
Alignment explanation
Indices: 21676587--21676626 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21676577 GGGAAAAATT
21676587 TACGGAACATAATTTGGAGC
1 TACGGAACATAATTTGGAGC
*
21676607 TACGGAACTTAATTTGGAGC
1 TACGGAACATAATTTGGAGC
21676627 CATGTAGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
TACGGAACATAATTTGGAGC
Found at i:21676794 original size:27 final size:27
Alignment explanation
Indices: 21676762--21676813 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
21676752 GAATATAAAG
*
21676762 GGGGTTGCTAAGTGTTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
21676789 GGGGTTGCTAAGTGCTGATTCCCCC
1 GGGGTTGCTAAGTGCTGATTCCCCC
21676814 CCTTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.29
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:21681050 original size:43 final size:42
Alignment explanation
Indices: 21680948--21681068 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
21680938 GATTTCGTGG
* * * * *
21680948 AAGACCATGTCTGGGACATCAGCATCGATATGAGATTACGTGT
1 AAGACCATGTCTGGGATAT-GGCATCGATATGTGATAACATGT
*
21680991 AAGACCCTGTCTGGGATAGTGGCATCGATATGTGATAACATGT
1 AAGACCATGTCTGGGATA-TGGCATCGATATGTGATAACATGT
*
21681034 AAGACCATGTCTGGGATATGGCATTG-TATGTGATA
1 AAGACCATGTCTGGGATATGGCATCGATATGTGATA
21681069 TATGTGTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.13
42 7 0.10
43 52 0.75
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (42 bp):
AAGACCATGTCTGGGATATGGCATCGATATGTGATAACATGT
Found at i:21681621 original size:15 final size:15
Alignment explanation
Indices: 21681601--21681637 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
21681591 TTTTGGGAAG
*
21681601 TATGTTTCATGGTTA
1 TATGTTTCATGGCTA
21681616 TATGTTTCATGGCTA
1 TATGTTTCATGGCTA
21681631 TATGTTT
1 TATGTTT
21681638 TGGTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (15 bp):
TATGTTTCATGGCTA
Found at i:21683447 original size:50 final size:50
Alignment explanation
Indices: 21683332--21683485 Score: 227
Period size: 50 Copynumber: 3.1 Consensus size: 50
21683322 GATCATAACA
** *
21683332 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
21683383 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21683433 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
21683483 TGC
1 TGC
21683486 TTGCATTTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 59 0.63
51 34 0.37
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21690432 original size:19 final size:21
Alignment explanation
Indices: 21690408--21690448 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
21690398 ATTTGCCTTC
21690408 TAAAAAT-ATTT-TTTTATTT
1 TAAAAATAATTTATTTTATTT
21690427 TAAAAATAATTTAGTTTTATTT
1 TAAAAATAATTTA-TTTTATTT
21690449 CTTAGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
22 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TAAAAATAATTTATTTTATTT
Found at i:21691110 original size:30 final size:33
Alignment explanation
Indices: 21691074--21691152 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
21691064 ATGTGGAGGG
*
21691074 TTTAA-TTGATTTTTTTG-T-ATTATTTTATGA
1 TTTAATTTAATTTTTTTGTTAATTATTTTATGA
*
21691104 TTTAATTTAATTTTTTTGTTAATTATTTTAGGAAA
1 TTTAATTTAATTTTTTTGTTAATTATTTTATG--A
*
21691139 CTTAATTTAATTTT
1 TTTAATTTAATTTT
21691153 AGATATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.12
31 11 0.27
32 1 0.02
33 10 0.24
35 14 0.34
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (33 bp):
TTTAATTTAATTTTTTTGTTAATTATTTTATGA
Found at i:21691187 original size:10 final size:9
Alignment explanation
Indices: 21691161--21691311 Score: 79
Period size: 10 Copynumber: 15.4 Consensus size: 9
21691151 TTAGATATTA
21691161 TATAAAAAT
1 TATAAAAAT
* *
21691170 TCTCAAAATT
1 TAT-AAAAAT
21691180 TATAAAAAT
1 TATAAAAAT
21691189 TATTAAAATAT
1 TA-TAAAA-AT
* *
21691200 TTTAGAAAT
1 TATAAAAAT
21691209 TATAGAAAAT
1 TATA-AAAAT
21691219 TATATAAGAAT
1 TATA-AA-AAT
* *
21691230 AATTAAAAT
1 TATAAAAAT
*
21691239 GATAAAAAT
1 TATAAAAAT
21691248 TAATAAAAAAAGT
1 T-AT--AAAAA-T
21691261 TATAAAAATT
1 TATAAAAA-T
* *
21691271 TATTAAAAG
1 TATAAAAAT
*
21691280 TATAAAAAGA
1 TATAAAAA-T
*
21691290 TATAAAAAC
1 TATAAAAAT
21691299 TA-AAAAAT
1 TATAAAAAT
21691307 ATATA
1 -TATA
21691312 TAAGAAAATT
Statistics
Matches: 109, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
8 5 0.05
9 35 0.32
10 52 0.48
11 8 0.07
12 7 0.06
13 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (9 bp):
TATAAAAAT
Found at i:21691191 original size:30 final size:28
Alignment explanation
Indices: 21691157--21691256 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 28
21691147 AATTTTAGAT
*
21691157 ATTATATAAAAATTCTCAAAATTTATAAAA
1 ATTATATAAAAATT-TTAAAA-TTATAAAA
21691187 ATTAT-TAAAATATTTTAGAAATTATAGAAA
1 ATTATATAAAA-ATTTTA-AAATTATA-AAA
* * *
21691217 ATTATATAAGAATAATTAAAATGATAAAA
1 ATTATATAAAAAT-TTTAAAATTATAAAA
21691246 ATTA-ATAAAAA
1 ATTATATAAAAA
21691257 AAGTTATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
28 6 0.10
29 19 0.32
30 28 0.47
31 7 0.12
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
ATTATATAAAAATTTTAAAATTATAAAA
Found at i:21691297 original size:19 final size:19
Alignment explanation
Indices: 21691240--21691311 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
21691230 AATTAAAATG
*
21691240 ATAAAAATTAATAAAAAAAGTT
1 ATAAAAA-T-ATATAAAAAG-T
* *
21691262 ATAAAAATTTATTAAAAGT
1 ATAAAAATATATAAAAAGT
* *
21691281 ATAAAAAGATATAAAAACT
1 ATAAAAATATATAAAAAGT
21691300 A-AAAAATATATA
1 ATAAAAATATATA
21691312 TAAGAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 10 0.24
19 17 0.40
20 7 0.17
21 1 0.02
22 7 0.17
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (19 bp):
ATAAAAATATATAAAAAGT
Found at i:21691672 original size:20 final size:18
Alignment explanation
Indices: 21691625--21691671 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
21691615 TTTTAGAAAA
21691625 TTATAAAAAGTATATAAG
1 TTATAAAAAGTATATAAG
21691643 TTATTAAAAAGTAT-TAAATG
1 TTA-TAAAAAGTATAT-AA-G
21691663 TTATAAAAA
1 TTATAAAAA
21691672 AATTAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATAAAAAGTATATAAG
Found at i:21691758 original size:30 final size:30
Alignment explanation
Indices: 21691724--21691794 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
21691714 TATAATCCCT
* ** *
21691724 AAATCAATTAAGCCCTTTTAAAATAATTAA
1 AAATCAATTAAGCCATCATAAAATAATAAA
*
21691754 AAATCAATTAAACCATCATAAAATAATAAA
1 AAATCAATTAAGCCATCATAAAATAATAAA
21691784 AAAT-AATTAAG
1 AAATCAATTAAG
21691795 TCCTCCACGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATCAATTAAGCCATCATAAAATAATAAA
Found at i:21695479 original size:51 final size:51
Alignment explanation
Indices: 21695403--21695504 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
21695393 TCTTGGAAAT
21695403 CAATTGCATAAATAAAAGTGACTTACGATTAAACCTTCACTTAGTGAAAAC
1 CAATTGCATAAATAAAAGTGACTTACGATTAAACCTTCACTTAGTGAAAAC
21695454 CAATTGCATAAATAAAAGTGACTTACGATTAAACCTTCACTTAGTGAAAAC
1 CAATTGCATAAATAAAAGTGACTTACGATTAAACCTTCACTTAGTGAAAAC
21695505 ATGTTAAAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (51 bp):
CAATTGCATAAATAAAAGTGACTTACGATTAAACCTTCACTTAGTGAAAAC
Found at i:21698381 original size:40 final size:40
Alignment explanation
Indices: 21698264--21698382 Score: 93
Period size: 40 Copynumber: 3.0 Consensus size: 40
21698254 TGATGTAAAT
* *
21698264 TTGAGTTATTAGTTAAATAGAATTTTAAGCATCTTAATTA
1 TTGAGTTATTAATTAAATAGAATTTTAGGCATCTTAATTA
* * * * ** *
21698304 -TAACTTAATTATTATTAGAGT-TAATTTT-GTTA-ATTAATTA
1 TTGAGTT-ATTA--ATTA-AATAGAATTTTAGGCATCTTAATTA
21698344 TTGAGTTATTAATTAAATAGAATTTTAGGCATCTTAATT
1 TTGAGTTATTAATTAAATAGAATTTTAGGCATCTTAATT
21698383 GTAACTTAAT
Statistics
Matches: 55, Mismatches: 16, Indels: 16
0.63 0.18 0.18
Matches are distributed among these distances:
37 2 0.04
38 10 0.18
39 6 0.11
40 21 0.38
41 5 0.09
42 9 0.16
43 2 0.04
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (40 bp):
TTGAGTTATTAATTAAATAGAATTTTAGGCATCTTAATTA
Found at i:21698415 original size:80 final size:80
Alignment explanation
Indices: 21698264--21698415 Score: 250
Period size: 80 Copynumber: 1.9 Consensus size: 80
21698254 TGATGTAAAT
*
21698264 TTGAGTTATTAGTTAAATAGAATTTTAAGCATCTTAATTATAACTTAATTATTATTAGAGTTAAT
1 TTGAGTTATTAATTAAATAGAATTTTAAGCATCTTAATTATAACTTAATTATTATTAGAGTTAAT
**
21698329 TTTGTTAATTAATTA
66 CATGTTAATTAATTA
* * *
21698344 TTGAGTTATTAATTAAATAGAATTTTAGGCATCTTAATTGTAACTTAATTATTGTTAGAGTTAAT
1 TTGAGTTATTAATTAAATAGAATTTTAAGCATCTTAATTATAACTTAATTATTATTAGAGTTAAT
21698409 CATGTTA
66 CATGTTA
21698416 GTTATTGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (80 bp):
TTGAGTTATTAATTAAATAGAATTTTAAGCATCTTAATTATAACTTAATTATTATTAGAGTTAAT
CATGTTAATTAATTA
Found at i:21698978 original size:20 final size:21
Alignment explanation
Indices: 21698953--21699008 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
21698943 ATATTAAAAT
21698953 ATTAAAAACAA-AAAAATATC
1 ATTAAAAACAATAAAAATATC
*
21698973 ATTAAAAATAATAAAAATAT-
1 ATTAAAAACAATAAAAATATC
*
21698993 A-TAAAAA-ATTAAAAAT
1 ATTAAAAACAATAAAAAT
21699009 TATGACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 11 0.33
21 8 0.24
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
ATTAAAAACAATAAAAATATC
Found at i:21699397 original size:3 final size:3
Alignment explanation
Indices: 21699389--21699420 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21699379 TATCAAGCGG
21699389 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21699421 AGGACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21701998 original size:17 final size:18
Alignment explanation
Indices: 21701966--21701999 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21701956 ATAAAAACAA
*
21701966 ATAATTTTTGTTTAATTC
1 ATAATTGTTGTTTAATTC
21701984 ATAATTGTT-TTTAATT
1 ATAATTGTTGTTTAATT
21702000 TTTATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (18 bp):
ATAATTGTTGTTTAATTC
Found at i:21709253 original size:15 final size:14
Alignment explanation
Indices: 21709233--21709278 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
21709223 AAGAAATTAG
21709233 TATATTATATTATA
1 TATATTATATTATA
21709247 TTATATTATATTATA
1 -TATATTATATTATA
*
21709262 TATATAATATTAGTA
1 TATATTATATTA-TA
21709277 TA
1 TA
21709279 GTGGTAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TATATTATATTATA
Found at i:21709280 original size:5 final size:5
Alignment explanation
Indices: 21709233--21709273 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
21709223 AAGAAATTAG
*
21709233 TATAT TATAT TATAT TATAT TATAT TATA- TATAT AATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
21709274 GTATAGTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:21717002 original size:48 final size:48
Alignment explanation
Indices: 21716924--21717025 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
21716914 AATATTTACT
** *
21716924 AAATTAAAATTAATATAACATCAAAATTAAAACCCAAAGTTAAAACTTA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAAC-CA
* * ** *
21716973 AAATTAAAAAAAAT-TAACATCACAGTTAAAATTCAAATTTAAAACCA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAACCA
21717020 AAATTA
1 AAATTA
21717026 GCTTAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
47 7 0.16
48 26 0.58
49 12 0.27
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (48 bp):
AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAACCA
Found at i:21729849 original size:294 final size:294
Alignment explanation
Indices: 21729320--21729905 Score: 1100
Period size: 294 Copynumber: 2.0 Consensus size: 294
21729310 ACCACCTATT
** *
21729320 TATACTAGTGGCTTTGAGCCAACTTTCCTAATTTAAAGTTACTATATATAGAAAGTGCATAAAAT
1 TATACTAGTGGCTTTGAGCCAACTTTCCTAATTTAAAGCCACTATACATAGAAAGTGCATAAAAT
21729385 TAGGGAAAAATATTCTCATGATCAAAATAAATCCCTACATAATCTCTTACTAAGTCAATCAGAAA
66 TAGGGAAAAATATTCTCATGATCAAAATAAATCCCTACATAATCTCTTACTAAGTCAATCAGAAA
21729450 ATTTCAGCCAATTACATCTTTTCGAAATTCCATTTCGACCCCCCTTCTTTTGCTTCTTCCTTCAA
131 ATTTCAGCCAATTACATCTTTTCGAAATTCCATTTCGACCCCCCTTCTTTTGCTTCTTCCTTCAA
* *
21729515 TTTAGTCCAATTGTTTTCTTTTTCTTCTATTTAGCCCCAAATTGCACCCCTGTATAAAATTCAAT
196 TCTAGTCCAATTGTTTCCTTTTTCTTCTATTTAGCCCCAAATTGCACCCCTGTATAAAATTCAAT
21729580 ATAAACACGGAAAAATCAGTGGTGCATTCTCAGG
261 ATAAACACGGAAAAATCAGTGGTGCATTCTCAGG
*
21729614 TATACTAGTGGCTTTGAGCCAACTTTTCTAATTTAAAGCCACTATACATAGAAAGTGCATAAAAT
1 TATACTAGTGGCTTTGAGCCAACTTTCCTAATTTAAAGCCACTATACATAGAAAGTGCATAAAAT
21729679 TAGGGAAAAATATTCTCATGATCAAAATAAATCCCTACATAATCTCTTACTAAGTCAATCAGAAA
66 TAGGGAAAAATATTCTCATGATCAAAATAAATCCCTACATAATCTCTTACTAAGTCAATCAGAAA
21729744 ATTTCAGCCAATTACATCTTTTCGAAATTCCATTTCGACCCCCCTTCTTTTGCTTCTTCCTTCAA
131 ATTTCAGCCAATTACATCTTTTCGAAATTCCATTTCGACCCCCCTTCTTTTGCTTCTTCCTTCAA
*
21729809 TCTAGTCCAATTGTTTCCTTTTTCTTCTATTTAGCCCCAAATTGCACCTCTGTATAAAATTCAAT
196 TCTAGTCCAATTGTTTCCTTTTTCTTCTATTTAGCCCCAAATTGCACCCCTGTATAAAATTCAAT
*
21729874 ATAAACATGGAAAAATCAGTGGTGCATTCTCA
261 ATAAACACGGAAAAATCAGTGGTGCATTCTCA
21729906 TAAATTGACC
Statistics
Matches: 284, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 284 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (294 bp):
TATACTAGTGGCTTTGAGCCAACTTTCCTAATTTAAAGCCACTATACATAGAAAGTGCATAAAAT
TAGGGAAAAATATTCTCATGATCAAAATAAATCCCTACATAATCTCTTACTAAGTCAATCAGAAA
ATTTCAGCCAATTACATCTTTTCGAAATTCCATTTCGACCCCCCTTCTTTTGCTTCTTCCTTCAA
TCTAGTCCAATTGTTTCCTTTTTCTTCTATTTAGCCCCAAATTGCACCCCTGTATAAAATTCAAT
ATAAACACGGAAAAATCAGTGGTGCATTCTCAGG
Found at i:21732759 original size:111 final size:111
Alignment explanation
Indices: 21732605--21732823 Score: 271
Period size: 111 Copynumber: 2.0 Consensus size: 111
21732595 ACATAATTCT
* * * * *
21732605 TATTATAAACATAAAAATAGGTTGAGCTTAAGCTTTGGATATTA-ATCTCGCACCCA-ATTTGTA
1 TATTATAAACATAAAAATAAGTTAAGCTTAAACTTTGAATATTAGA-CTCGCA-CCAGATTTATA
*
21732668 TTTTAAACAAGATTAAATTTTTGTTCAAGTCACTTCTCGAGCTTTATA
64 TTTTAAACAAGATTAAATTTTTGTTCAAGTCACTTCTCAAGCTTTATA
* * * *
21732716 TATTATAAACTTAAAAATAAGTTAAGCTTAAACTTTGAATATTAGACTTGTATCAGATTTATATT
1 TATTATAAACATAAAAATAAGTTAAGCTTAAACTTTGAATATTAGACTCGCACCAGATTTATATT
* * * * *
21732781 TTAAACGAGTTTAATTTTTTGTTTAAGTTACTTCTCAAGCTTT
66 TTAAACAAGATTAAATTTTTGTTCAAGTCACTTCTCAAGCTTT
21732824 TTTTTTATGT
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
110 2 0.02
111 88 0.97
112 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (111 bp):
TATTATAAACATAAAAATAAGTTAAGCTTAAACTTTGAATATTAGACTCGCACCAGATTTATATT
TTAAACAAGATTAAATTTTTGTTCAAGTCACTTCTCAAGCTTTATA
Found at i:21733475 original size:7 final size:7
Alignment explanation
Indices: 21733463--21733487 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21733453 AAACAGTAGA
21733463 TTTTGCT
1 TTTTGCT
21733470 TTTTGCT
1 TTTTGCT
21733477 TTTTGCT
1 TTTTGCT
21733484 TTTT
1 TTTT
21733488 ATTCCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGCT
Found at i:21736895 original size:5 final size:5
Alignment explanation
Indices: 21736885--21736909 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21736875 TTCTCATGTC
21736885 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
21736910 TGTCTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:21737355 original size:21 final size:21
Alignment explanation
Indices: 21737316--21737355 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21737306 TTTACTAGTT
* * *
21737316 TCTTTTTTTTTTTACTTTTTA
1 TCTTATTTTTTATAATTTTTA
21737337 TCTTATTTTTTATAATTTT
1 TCTTATTTTTTATAATTTT
21737356 ATTAATAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTTATTTTTTATAATTTTTA
Found at i:21738057 original size:12 final size:12
Alignment explanation
Indices: 21738040--21738065 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21738030 CACCATTTTA
21738040 ATATATATTGCT
1 ATATATATTGCT
21738052 ATATATATTGCT
1 ATATATATTGCT
21738064 AT
1 AT
21738066 TACAAGCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATTGCT
Found at i:21741637 original size:7 final size:7
Alignment explanation
Indices: 21741625--21741650 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21741615 AAACAATTAT
21741625 TATATAA
1 TATATAA
21741632 TATATAA
1 TATATAA
21741639 TATATAA
1 TATATAA
21741646 TATAT
1 TATAT
21741651 GATAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:21744033 original size:52 final size:51
Alignment explanation
Indices: 21743960--21744067 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 51
21743950 TATTTTTTAG
*
21743960 ACTATTTTTAGGGTCTCGTAGACTCGTAATA-AGGGCTGTAAGAGTAAATTTT
1 ACTATTTTTAGGGTATCGTAGACTCGTAATAGA-GG-TGTAAGAGTAAATTTT
21744012 ACTATTTTTAGGGTATCGTAGACTCGTAATAGAGGTGTAAGAGTAAATTTT
1 ACTATTTTTAGGGTATCGTAGACTCGTAATAGAGGTGTAAGAGTAAATTTT
21744063 ACTAT
1 ACTAT
21744068 GAATTGGGGT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 21 0.39
52 32 0.59
53 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (51 bp):
ACTATTTTTAGGGTATCGTAGACTCGTAATAGAGGTGTAAGAGTAAATTTT
Found at i:21745903 original size:27 final size:28
Alignment explanation
Indices: 21745818--21745903 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
21745808 GAATCCTACT
*
21745818 TATAAGATAGTCCTGACGGACTTCCACA
1 TATAAAATAGTCCTGACGGACTTCCACA
* * *
21745846 TATAAAATCGTCTTGATGGACTTCCACA
1 TATAAAATAGTCCTGACGGACTTCCACA
*
21745874 TATAAAATAGTCCTG-CGAACTTCCACA
1 TATAAAATAGTCCTGACGGACTTCCACA
21745901 TAT
1 TAT
21745904 TTTTTCATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
27 13 0.26
28 37 0.74
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (28 bp):
TATAAAATAGTCCTGACGGACTTCCACA
Found at i:21752866 original size:19 final size:18
Alignment explanation
Indices: 21752830--21752870 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
21752820 AGATTAAAGT
*
21752830 TTAATTAATTATGATTAA
1 TTAATTAATTAGGATTAA
*
21752848 GTTAATTAATTAGGTTTAA
1 -TTAATTAATTAGGATTAA
21752867 TTAA
1 TTAA
21752871 AATTAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
TTAATTAATTAGGATTAA
Found at i:21754824 original size:28 final size:28
Alignment explanation
Indices: 21754784--21754839 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
21754774 AAAAACATGT
* *
21754784 TATAAAATTAAAAGAAATATAGAATGGA
1 TATAAAACTAAAAGAAATATAAAATGGA
21754812 TATAAAACTAAAAGAAATATAAAATGGA
1 TATAAAACTAAAAGAAATATAAAATGGA
21754840 CAAAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.23
Consensus pattern (28 bp):
TATAAAACTAAAAGAAATATAAAATGGA
Found at i:21764665 original size:19 final size:20
Alignment explanation
Indices: 21764641--21764689 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
21764631 TGAGTTAGTA
*
21764641 ATTTATTTTATGTATTTTG-
1 ATTTATTTTATGTATATTGT
*
21764660 ATTTA-TTTATTTATATTGT
1 ATTTATTTTATGTATATTGT
21764679 ATTTATTTTAT
1 ATTTATTTTAT
21764690 TTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (20 bp):
ATTTATTTTATGTATATTGT
Found at i:21764670 original size:14 final size:13
Alignment explanation
Indices: 21764642--21764695 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 13
21764632 GAGTTAGTAA
*
21764642 TTTATTTTATGTAT
1 TTTA-TTTATTTAT
21764656 TTTGATTTATTTAT
1 TTT-ATTTATTTAT
21764670 TTATATTGTATTTAT
1 TT-TATT-TATTTAT
21764685 TTTATTT-TTTA
1 TTTATTTATTTA
21764696 ATGTTCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 20 0.56
15 11 0.31
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:21764686 original size:23 final size:25
Alignment explanation
Indices: 21764641--21764699 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
21764631 TGAGTTAGTA
21764641 ATTTATTT-TATGTATTTTGA-TTT
1 ATTTATTTATATGTATTTTGATTTT
21764664 ATTTATTTATATTGTA-TTT-ATTTT
1 ATTTATTTATA-TGTATTTTGATTTT
21764688 ATTT-TTTA-ATGT
1 ATTTATTTATATGT
21764700 TCATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 13 0.39
24 12 0.36
25 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (25 bp):
ATTTATTTATATGTATTTTGATTTT
Found at i:21766835 original size:21 final size:20
Alignment explanation
Indices: 21766782--21766845 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
21766772 CAGTTCAGCA
* *
21766782 CCCCTGATTGCACTCCAATG
1 CCCCTGATTGCACTCTAGTG
21766802 CCCCTGATTGCACTCTAGTG
1 CCCCTGATTGCACTCTAGTG
* *
21766822 CCTCTGATTTGCACTCTTGTG
1 CCCCTGA-TTGCACTCTAGTG
21766843 CCC
1 CCC
21766846 TTGTATGTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.14, C:0.38, G:0.17, T:0.31
Consensus pattern (20 bp):
CCCCTGATTGCACTCTAGTG
Found at i:21771563 original size:29 final size:29
Alignment explanation
Indices: 21771526--21771584 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
21771516 TACTAACAAT
* *
21771526 TTGAGCTAATTAATAACATTATAAAAATA
1 TTGAACTAATTAAGAACATTATAAAAATA
21771555 TTGAACTAATTAAGAACATTATAAAAATA
1 TTGAACTAATTAAGAACATTATAAAAATA
21771584 T
1 T
21771585 AGAGACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (29 bp):
TTGAACTAATTAAGAACATTATAAAAATA
Found at i:21773000 original size:30 final size:30
Alignment explanation
Indices: 21772925--21772987 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
21772915 GTACGAGTAA
* *
21772925 CCTAATATAAACTT-AGCTTGTGTGATCAAT
1 CCTAATATAAA-TTCAGCTTGTGTGAGCAAC
*
21772955 CTTAATATAAATTCAGCTTGTGTGAGCAAC
1 CCTAATATAAATTCAGCTTGTGTGAGCAAC
21772985 CCT
1 CCT
21772988 GATGTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (30 bp):
CCTAATATAAATTCAGCTTGTGTGAGCAAC
Found at i:21774954 original size:45 final size:46
Alignment explanation
Indices: 21774886--21775101 Score: 210
Period size: 45 Copynumber: 4.8 Consensus size: 46
21774876 ACCGTTACAC
* * *
21774886 GGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATTC-
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATATTCT
* * * ** *
21774929 GGTAGAATCATCATATAGCAACCACCTTTATTTTTAATGAT-TTCT
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATATTCT
* * **
21774974 GGTGGAGTCAACACATAGCAGCCACCTTTATTTTCAATGAT-TTCT
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATATTCT
* * * * *
21775019 GATGGAGTCAACACATAGCAACCACCTTTATAATCAATGGTA-CCC
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATATTCT
* *
21775064 GGTGGAATTAGCACATAGCAACCACCTTTATAATCAAT
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAAT
21775102 TATACTCAAT
Statistics
Matches: 144, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
43 4 0.03
44 14 0.10
45 126 0.88
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (46 bp):
GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATATTCT
Found at i:21778318 original size:30 final size:30
Alignment explanation
Indices: 21778262--21778334 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
21778252 AATTTTCAAA
* * *
21778262 AAAAATTAAAAGGTACAATGAGAATTTTC-
1 AAAAATTTAAAGGTACAATAAAAATTTTCT
*
21778291 AAAAATTTAAAGGTTCTAATAAAAATTTTCT
1 AAAAATTTAAAGGTAC-AATAAAAATTTTCT
* *
21778322 GAAAATTTCAAGG
1 AAAAATTTAAAGG
21778335 GAGAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 11 0.31
31 11 0.31
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAAATTTAAAGGTACAATAAAAATTTTCT
Found at i:21784447 original size:7 final size:7
Alignment explanation
Indices: 21784435--21784459 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21784425 TTTGGCAAAA
21784435 ACATAAT
1 ACATAAT
21784442 ACATAAT
1 ACATAAT
21784449 ACATAAT
1 ACATAAT
21784456 ACAT
1 ACAT
21784460 TAAATTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATAAT
Found at i:21792120 original size:9 final size:9
Alignment explanation
Indices: 21792106--21792154 Score: 89
Period size: 9 Copynumber: 5.4 Consensus size: 9
21792096 TTTAGTTAAA
21792106 AATTAACCG
1 AATTAACCG
21792115 AATTAACCG
1 AATTAACCG
*
21792124 AATTACCCG
1 AATTAACCG
21792133 AATTAACCG
1 AATTAACCG
21792142 AATTAACCG
1 AATTAACCG
21792151 AATT
1 AATT
21792155 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:21792205 original size:6 final size:6
Alignment explanation
Indices: 21792194--21792222 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21792184 ACTTTTGGAC
21792194 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
21792223 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:21792246 original size:20 final size:20
Alignment explanation
Indices: 21792194--21792235 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
21792184 ACTTTTGGAC
21792194 TTTAGTTTTAG--TTTTAGT
1 TTTAGTTTTAGAATTTTAGT
*
21792212 TTTAGTTTTAGAATTTTATT
1 TTTAGTTTTAGAATTTTAGT
21792232 TTTA
1 TTTA
21792236 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGAATTTTAGT
Found at i:21792303 original size:18 final size:18
Alignment explanation
Indices: 21792263--21792306 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21792253 AATTTTTATG
*
21792263 ATTGGGTTGGGTTAGGTA
1 ATTGGGTTGGGTTAGATA
21792281 ATTGGGTTGGGTT-GAATA
1 ATTGGGTTGGGTTAG-ATA
*
21792299 CTTGGGTT
1 ATTGGGTT
21792307 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTAGATA
Found at i:21792623 original size:27 final size:27
Alignment explanation
Indices: 21792593--21793003 Score: 416
Period size: 27 Copynumber: 15.2 Consensus size: 27
21792583 AACTTGCGAC
* *
21792593 AAATGATCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * **
21792620 AAATTACTGAAATACCCTCGAAGGACA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
21792647 AAATGACCGAAATAGCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
21792674 AAATGACCAAAATACCCCCTAAGGATA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
21792701 AAATGACCGAAATACCC-CAGAAAGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* *
21792728 AAATAACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** * *
21792755 AAATGAGTGAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
21792782 AAATGATTGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
21792809 AAATAACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
21792836 AAATAACTGAAATACTCGT-GAAGGGTA
1 AAATGACCGAAATAC-CCTCGAAGGGTA
* *
21792863 AAATGACAGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** * **
21792890 AAATGATTGGAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
21792917 AAATGATCGAAATGCCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
21792944 AAATGACCGAAATA-CCTCCGAAGGGTA
1 AAATGACCGAAATACCCT-CGAAGGGTA
* * *
21792971 AAATAACTGAAATACCC-CCATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
21792998 AAATGA
1 AAATGA
21793004 TTTTTATACC
Statistics
Matches: 317, Mismatches: 60, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.02
27 305 0.96
28 5 0.02
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:21792782 original size:108 final size:107
Alignment explanation
Indices: 21792593--21793005 Score: 472
Period size: 108 Copynumber: 3.8 Consensus size: 107
21792583 AACTTGCGAC
* * * * ** *
21792593 AAATGATCGAAATACCCTTGAAGGGTAAAATTACTGAAATACCCTCGAAGGACAAAATGACCGAA
1 AAATGACCGAAATACCC-CGAAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACTGAA
* * *** * *
21792658 ATAGCCTCGAAGGGTAAAATGACCAAAATACCCCCT-AAGGATA
65 ATACCCTCAAAGGGTAAAATGATTGAAATA-CCCTTAAAGGGTA
* * *
21792701 AAATGACCGAAATACCCCAGAAAGGTAAAATAACCAAAATACCCTCGAAGGGTAAAATGAGTGAA
1 AAATGACCGAAATACCCC-GAAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACTGAA
* *
21792766 ATACCCTCAAAAGGTAAAATGATTGAAATACCCTTGAAGGGTA
65 ATACCCTCAAAGGGTAAAATGATTGAAATACCCTTAAAGGGTA
* * * *
21792809 AAATAACCGAAATACCCTCGAAGGGTAAAATAACTGAAATACTCGT-GAAGGGTAAAATGACAGA
1 AAATGACCGAAATACCC-CGAAGGGTAAAATAACCGAAATAC-CCTCGAAGGGTAAAATGACTGA
*
21792873 AATACCCTCAAAGGGTAAAATGATTGGAATACCCTTAAAGGGTA
64 AATACCCTCAAAGGGTAAAATGATTGAAATACCCTTAAAGGGTA
* * * *
21792917 AAATGATCGAAATGCCCCCGAAGGGTAAAATGACCGAAATA-CCTCCGAAGGGTAAAATAACTGA
1 AAATGACCGAAAT-ACCCCGAAGGGTAAAATAACCGAAATACCCT-CGAAGGGTAAAATGACTGA
* *
21792981 AATACCCCCATAGGGTAAAATGATT
64 AATACCCTCAAAGGGTAAAATGATT
21793006 TTTATACCCC
Statistics
Matches: 260, Mismatches: 38, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
106 2 0.01
107 4 0.02
108 248 0.95
109 6 0.02
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (107 bp):
AAATGACCGAAATACCCCGAAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACTGAAA
TACCCTCAAAGGGTAAAATGATTGAAATACCCTTAAAGGGTA
Found at i:21793420 original size:28 final size:28
Alignment explanation
Indices: 21793375--21793477 Score: 154
Period size: 28 Copynumber: 3.7 Consensus size: 28
21793365 ACTGTAATGT
* *
21793375 TACTATATTGGGCTAAGGCCTACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
21793403 TATTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
21793431 TACTGTATTGGGCTAAGGCCCACACT-A
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
21793458 CTACTGAATTGGGCTAAGGC
1 -TACTGTATTGGGCTAAGGC
21793478 ATTCATTATA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
27 1 0.01
28 68 0.99
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGA
Found at i:21795472 original size:23 final size:23
Alignment explanation
Indices: 21795438--21795674 Score: 206
Period size: 23 Copynumber: 10.2 Consensus size: 23
21795428 TGGACAACTC
* * *
21795438 TTATACATCAAATCGGTCAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795461 TTATACACCAAAATTTGACGGCAT
1 TTATACACC-AAATTGGACAGCAT
* * * *
21795485 ATATATACAAAATTGGATAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795508 TTATACACGAAATTGGGCAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795531 ATATATACC-AATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795553 TTATACACGAAATTGGGCAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
21795576 ATATATACCAATTTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795599 TTATGCACCAAAATTTGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
* * *
21795623 ATATATACAAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
21795646 TTACACACCAAAATTTGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
*
21795670 ATATA
1 TTATA
21795675 TATAATTGAT
Statistics
Matches: 164, Mismatches: 46, Indels: 7
0.76 0.21 0.03
Matches are distributed among these distances:
22 18 0.11
23 97 0.59
24 49 0.30
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (23 bp):
TTATACACCAAATTGGACAGCAT
Found at i:21795557 original size:45 final size:47
Alignment explanation
Indices: 21795455--21795676 Score: 306
Period size: 47 Copynumber: 4.8 Consensus size: 47
21795445 TCAAATCGGT
*
21795455 CAGCATTTATACACCAAAATTTGACGGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
* * * * *
21795502 TAGCATTTATACA-CGAAATTGGGCAGCATATATATAC-CAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
* * * * *
21795547 CAGCATTTATACA-CGAAATTGGGCAGCATATATATACCAATTTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
*
21795593 CAGCATTTATGCACCAAAATTTGACAGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
*
21795640 CAGCATTTACACACCAAAATTTGACAGCATATATATA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATA
21795677 TAATTGATCT
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 43 0.28
46 38 0.24
47 75 0.48
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (47 bp):
CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
Found at i:21796320 original size:311 final size:311
Alignment explanation
Indices: 21795754--21796382 Score: 1204
Period size: 311 Copynumber: 2.0 Consensus size: 311
21795744 AATTTCATAT
21795754 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
1 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
*
21795819 TTCAACCTTTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
66 TTCAACCTCTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
21795884 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
131 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
* * *
21795949 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATTTGATTTTTTATACTCGATCT
196 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTCATACTCGATCT
21796014 TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
261 TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
21796065 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
1 ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
*
21796130 TTCAACCTCTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACG
66 TTCAACCTCTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
21796195 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
131 TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
*
21796260 ATATTTTTATAACTCGAATAAATATATACCTGAGCCTTTCTAATCTGAATTTTCATACTCGATCT
196 ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTCATACTCGATCT
21796325 TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
261 TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
21796376 ATCAAAC
1 ATCAAAC
21796383 GTTTCGTACA
Statistics
Matches: 312, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
311 312 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (311 bp):
ATCAAACATATATATATTTGGCATAAATTTTACTTAGGTCGAATACATAAGGAAACATTAGTATA
TTCAACCTCTGCTTCAACACTAACAAAAAGAAACATCATTGGCCGAATATATATATACATTCACA
TATACATACACATAATTCACATTAAAATATGATATTATATCATCAATTCATATATTCGACTTACC
ATATTTTTATAACTCGAATAAATACATACCTGAGCCTTTCTAATCTGAATTTTCATACTCGATCT
TAATTTATTACAGCCCATTGAACCATTCGGAATTAAAAGGATACTCAGAAA
Found at i:21796492 original size:44 final size:43
Alignment explanation
Indices: 21796393--21796507 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 43
21796383 GTTTCGTACA
* * * *
21796393 ATGCCATCGTCCCAAACATGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAAACAGGGTCTTACACGTAATCACAAATCG
21796436 ATGCC-ACTGTCCCAAACAGGGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAAACAGGGTCTTACACGT-AATCACAAATCG
*
21796480 ATGCCAACGTCCCAGAC-GTGGTCTTACA
1 ATGCCAACGTCCCAAACAG-GGTCTTACA
21796508 TGACAACACA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.43
44 33 0.52
45 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAAACAGGGTCTTACACGTAATCACAAATCG
Found at i:21796844 original size:15 final size:15
Alignment explanation
Indices: 21796820--21796849 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21796810 GTTATTGATC
21796820 TAAACACATTCAAAT
1 TAAACACATTCAAAT
*
21796835 TAAACTCATTCAAAT
1 TAAACACATTCAAAT
21796850 GTAATTCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAACACATTCAAAT
Found at i:21801723 original size:33 final size:33
Alignment explanation
Indices: 21801686--21801761 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
21801676 ATTCTGATGA
* * *
21801686 TAAGACCATAACTGGGTTATGGCACTACAAATG
1 TAAGACCATAACAGGGTCATGGCAATACAAATG
* * *
21801719 TAAGACCATGACAGGGTCATGGCAATGCAAGTG
1 TAAGACCATAACAGGGTCATGGCAATACAAATG
21801752 TAAGACCATA
1 TAAGACCATA
21801762 GTTGAACTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (33 bp):
TAAGACCATAACAGGGTCATGGCAATACAAATG
Found at i:21804032 original size:22 final size:20
Alignment explanation
Indices: 21803996--21804054 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
21803986 GGCTCGGTCC
21803996 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
21804018 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
21804039 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
21804055 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:21804073 original size:10 final size:11
Alignment explanation
Indices: 21804036--21804153 Score: 87
Period size: 11 Copynumber: 11.4 Consensus size: 11
21804026 TAAAAATTAA
21804036 AAAAAGTATTTT
1 AAAAA-TATTTT
21804048 AAAAATATTTT
1 AAAAATATTTT
21804059 AAAAATA-TTT
1 AAAAATATTTT
*
21804069 -GAAA-A--TT
1 AAAAATATTTT
*
21804076 AAAAAAATTTT
1 AAAAATATTTT
21804087 AAAAAGTATTTT
1 AAAAA-TATTTT
21804099 AAAAATATTTT
1 AAAAATATTTT
21804110 --AAA-A--TT
1 AAAAATATTTT
* *
21804116 AGAAAATA-ATA
1 A-AAAATATTTT
21804127 AAAAAGTATTTT
1 AAAAA-TATTTT
21804139 AAAAATATTTT
1 AAAAATATTTT
21804150 AAAA
1 AAAA
21804154 TTAAAAAAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 5 0.06
9 10 0.11
10 8 0.09
11 40 0.45
12 21 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:21804079 original size:17 final size:17
Alignment explanation
Indices: 21804057--21804090 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21804047 TAAAAATATT
*
21804057 TTAAAAATATTTGAAAA
1 TTAAAAAAATTTGAAAA
*
21804074 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTGAAAA
21804091 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTGAAAA
Found at i:21804091 original size:51 final size:49
Alignment explanation
Indices: 21804027--21804153 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 49
21804017 AATTTATTTT
** *
21804027 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAATATTTGAAAAT-TAA
1 AAAAATTTTAAAAAGTATTTTAAAAATATTTT--AAA-ATTAGAAAATATAA
21804078 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAGAAAATAATAA
1 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAGAAAAT-ATAA
21804128 AAAAGTATTTTAAAAA-TATTTTAAAA
1 AAAA--ATTTTAAAAAGTATTTTAAAA
21804154 TTAAAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
48 9 0.13
49 3 0.04
50 7 0.10
51 40 0.58
52 10 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (49 bp):
AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAGAAAATATAA
Done.