Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006856.1 Hibiscus syriacus cultivar Beakdansim tig00017446_pilon, whole genome shotgun sequence
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: 1184065
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 4
Found at i:350 original size:157 final size:158
Alignment explanation
Indices: 14--385 Score: 454
Period size: 157 Copynumber: 2.4 Consensus size: 158
4 ATGGTCTAAC
* *
14 TGTGCACTTGGACA-AAAAGTTTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTGAGTAAA
1 TGTGCACTT-GATAGAAAAGTGTC-ATTATGCCAGTTAGATGAAAGGTTAAATACCTTGAGTAAA
* *
78 AGATTAATAGCCTAGCTGTGCACTTGACATAAAGGTGCAATTATGCCAGTTAGATGATATGTTAA
64 AGATTAATAGCCTAGCTGTGCACTTGACAGAAAGGTGCAATTATGCCAGTTAGATGATAGGTTAA
*
143 ATACTTTGAGTAAAAGATTAATAGCCTAGT
129 ATACTTTGAGTAAAAGATTAATAGCCGAGT
* *
173 TGTGCACTTGATAG-AGAGTGTCATTATGCCAGTTAGATGAAATGTTAAATACCGTTGAGT-AAA
1 TGTGCACTTGATAGAAAAGTGTCATTATGCCAGTTAGATGAAAGGTTAAATACC-TTGAGTAAAA
* * * *
236 TATTAATAGCCTAGCTGTGCACTTGATAGAAAGGTATCAATTATGCGAGTTAGATGA-AGGTTAA
65 GATTAATAGCCTAGCTGTGCACTTGACAGAAAGGT-GCAATTATGCCAGTTAGATGATAGGTTAA
*
300 ATACCTTTGAGT-AAATATTAATAG-CGA-T
129 ATA-CTTTGAGTAAAAGATTAATAGCCGAGT
* * * * * *
328 CTGTGCA-TTTAGTAGAAAAGTGTAAATTATGCAAGTTAGATAAAAGGCTAAATGCCTT
1 -TGTGCACTTGA-TAGAAAAGTGT-CATTATGCCAGTTAGATGAAAGGTTAAATACCTT
386 TCGGTAAACG
Statistics
Matches: 185, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
155 4 0.02
156 11 0.06
157 93 0.50
158 68 0.37
159 9 0.05
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (158 bp):
TGTGCACTTGATAGAAAAGTGTCATTATGCCAGTTAGATGAAAGGTTAAATACCTTGAGTAAAAG
ATTAATAGCCTAGCTGTGCACTTGACAGAAAGGTGCAATTATGCCAGTTAGATGATAGGTTAAAT
ACTTTGAGTAAAAGATTAATAGCCGAGT
Found at i:380 original size:79 final size:81
Alignment explanation
Indices: 13--386 Score: 437
Period size: 79 Copynumber: 4.7 Consensus size: 81
3 AATGGTCTAA
* *
13 CTGTGCACTTGGACA-AAAAGTTTCAATTATGCCAGTTAGATGAAAGGTTAAATACC-TTGAGTA
1 CTGTGCACTT-GATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTA
76 AAAGATTAATAGCCTAG
65 AAAGATTAATAGCCTAG
* * * * *
93 CTGTGCACTTGACATAAAGGTG-CAATTATGCCAGTTAGATGATATGTTAAATA-CTTTGAGTAA
1 CTGTGCACTTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
156 AAGATTAATAGCCTAG
66 AAGATTAATAGCCTAG
* * * *
172 TTGTGCACTTGATAG-AGAGTGTC-ATTATGCCAGTTAGATGAAATGTTAAATACCGTTGAGT-A
1 CTGTGCACTTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
*
234 AATATTAATAGCCTAG
66 AAGATTAATAGCCTAG
* * *
250 CTGTGCACTTGATAGAAAGGTATCAATTATGCGAGTTAGATG-AAGGTTAAATACCTTTGAGT-A
1 CTGTGCACTTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
* * *
313 AATATTAATAG-CGAT
66 AAGATTAATAGCCTAG
* * * * * *
328 CTGTGCA-TTTAGTAGAAAAGTGTAAATTATGCAAGTTAGATAAAAGGCTAAATGCCTTT
1 CTGTGCACTTGA-TAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTT
387 CGGTAAACGA
Statistics
Matches: 257, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
77 3 0.01
78 97 0.38
79 126 0.49
80 31 0.12
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
CTGTGCACTTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
AAGATTAATAGCCTAG
Found at i:2082 original size:162 final size:163
Alignment explanation
Indices: 1886--2211 Score: 487
Period size: 163 Copynumber: 2.0 Consensus size: 163
1876 GAGCTTCATA
* * * *
1886 GCCAAGACCTACTTGGCTCCTTAGCACATCTCCTAGCTACCTTCAGCTGC-CAATTTGGTCACCT
1 GCCAAGACCTACTTGGCTCCTTAGCACATCTCCTAACTACCTTAAGATGCGC-ATTTGGTCACCC
*
1950 TTAGTAACTTAGCTTCA-TTAGTACATCGAGCTAAGTTTAGCTAGC-CTTTAACTCCTCCAGTTA
65 TTAGTAACTTAGCTTCATTTAGTACACCGAGCTAAGTTTAGCTAGCTC-TTAACTCCTCCAGTTA
* *
2013 AGTTAAGCTTCCCATTTTATTCCATGAGTTTCCAT
129 AGATAAGCTTCCCATTGTATTCCATGAGTTTCCAT
* * *
2048 GCCAAGACTTCCTTGGCTCCTTAGCACCTCTCCTAACTACCTTAAGATGCGCATTTGGTCACCCT
1 GCCAAGACCTACTTGGCTCCTTAGCACATCTCCTAACTACCTTAAGATGCGCATTTGGTCACCCT
* * *
2113 TAGTAACTTAGCTTCATTTAGTACACCGAGCTAAGTTTATCTAGTTCTTAACTCCTCCAGTTGAG
66 TAGTAACTTAGCTTCATTTAGTACACCGAGCTAAGTTTAGCTAGCTCTTAACTCCTCCAGTTAAG
*
2178 ATGAGCTTCCCATTGTATTCCATGAGTTTCCAT
131 ATAAGCTTCCCATTGTATTCCATGAGTTTCCAT
2211 G
1 G
2212 GAGATTATGA
Statistics
Matches: 147, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
162 72 0.49
163 74 0.50
164 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (163 bp):
GCCAAGACCTACTTGGCTCCTTAGCACATCTCCTAACTACCTTAAGATGCGCATTTGGTCACCCT
TAGTAACTTAGCTTCATTTAGTACACCGAGCTAAGTTTAGCTAGCTCTTAACTCCTCCAGTTAAG
ATAAGCTTCCCATTGTATTCCATGAGTTTCCAT
Found at i:16744 original size:18 final size:18
Alignment explanation
Indices: 16721--16758 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16711 ACAAGAATGT
16721 AAGGAATAAGAAGTATGC
1 AAGGAATAAGAAGTATGC
16739 AAGGAATAAGAAGTATGC
1 AAGGAATAAGAAGTATGC
16757 AA
1 AA
16759 ACTCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (18 bp):
AAGGAATAAGAAGTATGC
Found at i:22141 original size:56 final size:54
Alignment explanation
Indices: 22067--22172 Score: 142
Period size: 53 Copynumber: 1.9 Consensus size: 54
22057 GCTCATAAGC
22067 TTATTTTTAGCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTATTA
1 TTATTTTTAGCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTATTA
* * * *
22124 TTATTTTT-TCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTAGCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
22173 TGCATGGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 23 0.51
55 2 0.04
56 12 0.27
57 8 0.18
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (54 bp):
TTATTTTTAGCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTATTA
Found at i:30459 original size:22 final size:23
Alignment explanation
Indices: 30433--30487 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
30423 CAGGAAGGGG
*
30433 TATCGGTACCATGGT-AGGGTAA
1 TATCGATACCATGGTAAGGGTAA
30455 TATCGATACCATGGTAAGGG---
1 TATCGATACCATGGTAAGGGTAA
30475 TATCGATACCATG
1 TATCGATACCATG
30488 CAACATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (23 bp):
TATCGATACCATGGTAAGGGTAA
Found at i:30480 original size:20 final size:20
Alignment explanation
Indices: 30413--30487 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
30403 GTCTAAAATT
30413 GGTATCGATA-CA-GG-AAGG
1 GGTATCGATACCATGGTAA-G
*
30431 GGTATCGGTACCATGGT-AG
1 GGTATCGATACCATGGTAAG
30450 GGTAATATCGATACCATGGTAAG
1 GG---TATCGATACCATGGTAAG
30473 GGTATCGATACCATG
1 GGTATCGATACCATG
30488 CAACATCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
18 9 0.19
19 5 0.10
20 16 0.33
22 14 0.29
23 4 0.08
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATGGTAAG
Found at i:30481 original size:94 final size:95
Alignment explanation
Indices: 30356--30577 Score: 304
Period size: 94 Copynumber: 2.4 Consensus size: 95
30346 ATACCGACAA
* * * *
30356 GGTAGTATCGATGCCATGGTAAGGGTATCGATACCAGGTAACATCAAGTCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCAAATATAAAATTGGTATCGA
**
30421 TACAGGAAGGG-GTATCGGTACCATGGTAG
66 TACAGGAAGGGAGTATCGGTACCATAATAG
* *
30450 GGTAATATCGATACCATGGTAAGGGTATCGATACCATGCAACATCAAATATAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCAAATATAAAATTGGTATCGA
* * *
30515 TACCGGAAGGGAGTATCGGTACTATAATAT
66 TACAGGAAGGGAGTATCGGTACCATAATAG
* * *
30545 AGTAGTACCGATACTATGGT-AGGGTATCGATAC
1 GGTAGTATCGATACCATGGTAAGGGTATCGATAC
30578 TACCAAGACA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
94 82 0.73
95 30 0.27
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCAAATATAAAATTGGTATCGA
TACAGGAAGGGAGTATCGGTACCATAATAG
Found at i:31220 original size:135 final size:135
Alignment explanation
Indices: 30978--31411 Score: 679
Period size: 135 Copynumber: 3.2 Consensus size: 135
30968 ACAAAAATAC
* *** * * * *
30978 AATGCATATAGGTGCATTATTGGCATGAAAGGATACCATAGTTGAAATGCATATGGGTGTATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTAT
* *
31043 CAACATAAAAGTATACTATAGTTGAAATACATATGGGTGCATTATCAACATAAAAGTATTCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATTCTATA
31108 GTCAA
131 GTCAA
* *
31113 AATGCATATGGGTGCATTATCAACATAAAAATATACTATAGTTGAAATACATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTAT
* * *
31178 CAACATAAAAGTATGTTATAGTTGAAATGTATATGGGTGCATTATCAACATAAAAGTATTCTACA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATTCTATA
31243 GTCAA
131 GTCAA
* * **
31248 AATGCATATGGGTGCATTATCAATATAAAAGTATATTATAGTTGAAATGCATATGGGCACATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTAT
31313 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATTCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATTCTATA
*
31378 GTCGA
131 GTCAA
*
31383 AATGCATATGGGTGCATTGTCAACATAAA
1 AATGCATATGGGTGCATTATCAACATAAA
31412 TGTAGGCTAT
Statistics
Matches: 272, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 272 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTAT
CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATTCTATA
GTCAA
Found at i:31422 original size:45 final size:45
Alignment explanation
Indices: 30978--31411 Score: 607
Period size: 45 Copynumber: 9.6 Consensus size: 45
30968 ACAAAAATAC
* *** * * *
30978 AATGCATATAGGTGCATTATTGGCATGAAAGGATACCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
*
31023 AATGCATATGGGTGTATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
* * **
31068 AATACATATGGGTGCATTATCAACATAAAAGTATTCTATAGTCAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
*
31113 AATGCATATGGGTGCATTATCAACATAAAAATATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
* **
31158 AATACATATGGGTGCATTATCAACATAAAAGTATGTTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
* * * **
31203 AATGTATATGGGTGCATTATCAACATAAAAGTATTCTACAGTCAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
* *
31248 AATGCATATGGGTGCATTATCAATATAAAAGTATATTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
** *
31293 AATGCATATGGGCACATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
* *
31338 AATGCATATGGGTGCATTATCAACATAAAAGTATTCTATAGTCGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
*
31383 AATGCATATGGGTGCATTGTCAACATAAA
1 AATGCATATGGGTGCATTATCAACATAAA
31412 TGTAGGCTAT
Statistics
Matches: 343, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 343 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
Found at i:32844 original size:10 final size:10
Alignment explanation
Indices: 32827--32867 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
32817 AAATATCATA
32827 ATTATATTTT
1 ATTATATTTT
*
32837 ATTGTATTTT
1 ATTATATTTT
*
32847 TTTATATTTT
1 ATTATATTTT
*
32857 ATTATAATTT
1 ATTATATTTT
32867 A
1 A
32868 AATTGGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTATATTTT
Found at i:32934 original size:13 final size:15
Alignment explanation
Indices: 32910--32942 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
32900 TTATATTATA
32910 TTTGTAAATATT-TT
1 TTTGTAAATATTCTT
32924 TTTGT-AATATTCTT
1 TTTGTAAATATTCTT
32938 TTTGT
1 TTTGT
32943 CAAAACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTGTAAATATTCTT
Found at i:33302 original size:13 final size:14
Alignment explanation
Indices: 33286--33314 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33276 TTTTCTACCA
33286 CACTTTT-AAAAGT
1 CACTTTTCAAAAGT
33299 CACTTTTCAAAAGT
1 CACTTTTCAAAAGT
33313 CA
1 CA
33315 TGCCAAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
CACTTTTCAAAAGT
Found at i:34976 original size:19 final size:21
Alignment explanation
Indices: 34952--35003 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
34942 CGGCCAAGAG
*
34952 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
34971 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
34992 CATGTATTTTCA
1 CATGTATTTTCA
35004 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:36078 original size:181 final size:178
Alignment explanation
Indices: 35808--36281 Score: 488
Period size: 181 Copynumber: 2.6 Consensus size: 178
35798 TAGTGTCAAC
* * * * * * *
35808 TTTTGTAACTAAAAGTTTTAGTAACTATGACAGAAAAAATTGTCACAACAAATAATGAGATTTAG
1 TTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAGATTAAG
* *
35873 ATTTGTTGTGACAAATTTTGTTTGTAATTATATATTTTAATTATAGTGACAAAATGTATAGTCAC
66 -TTT-TTGTGACAAATTATGTTTGTAATTATATATTTTAATTATAGTGACAAAATATATAGTCAC
* * ** **
35938 AAA-TTATTATCTCCA-ATTTTTGGTACCAAAACAAAATCATATAGTGACATG
129 AAAGAT-TTATCTCCATATTTTTGATACC-AAA-AAAATCATATAGCAACAAA
* * *
35989 TTTTGTAACTAT-A-TGCTATAATTATTGTTACAAAAAAAATTATCACAACAAATAATGAGATTC
1 TTTTGTAACTATAAGTG-T-TAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAGATT-
* * ** * * * *
36052 AAGTTTTTAGTAAAAAACAATGTTTGTCATTATATGTTTTAATTATATTGACAAAATATATTGTC
63 AAGTTTTT-GTGACAAATTATGTTTGTAATTATATATTTTAATTATAGTGACAAAATATATAGTC
* * * **
36117 ACAAAGATTTCTCTCCATATTTTTTATGCCAAAAATGTCATATAGCAACAAA
127 ACAAAGATTTATCTCCATATTTTTGATACCAAAAAAATCATATAGCAACAAA
* * *
36169 TTTTGTAACTATAAGTGTTAATAATTATTACAAAAAATATTGTCACAAAAAATAATGATATTAAC
1 TTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAGATTAA-
* * * *
36234 GTTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGA
65 GTTTTTGTGACAAATTATGTTTGTAATTATATATTTTAATTATAGTGA
36282 TAGCATATAT
Statistics
Matches: 236, Mismatches: 48, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
179 34 0.14
180 73 0.31
181 115 0.49
182 14 0.06
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (178 bp):
TTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAGATTAAG
TTTTTGTGACAAATTATGTTTGTAATTATATATTTTAATTATAGTGACAAAATATATAGTCACAA
AGATTTATCTCCATATTTTTGATACCAAAAAAATCATATAGCAACAAA
Found at i:36737 original size:22 final size:22
Alignment explanation
Indices: 36703--36764 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
36693 TGTAGAAAAA
* *
36703 TTTTCATAAAAAAAATT-TA-T
1 TTTTTATAAAAAAAATTCAAGT
36723 TTTTTAATTAAAAAAAGATTCAAGT
1 TTTTT-A-TAAAAAAA-ATTCAAGT
36748 TTTTTATAAAAAAAATT
1 TTTTTATAAAAAAAATT
36765 ATGTTTGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 11 0.31
23 11 0.31
24 2 0.06
25 6 0.17
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (22 bp):
TTTTTATAAAAAAAATTCAAGT
Found at i:37719 original size:17 final size:18
Alignment explanation
Indices: 37697--37736 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
37687 CTCTATTTTA
*
37697 TTTTAAA-GGAAATTGAT
1 TTTTAAAGGGAAACTGAT
*
37714 TTTTAAAGGGAAACTGGT
1 TTTTAAAGGGAAACTGAT
37732 TTTTA
1 TTTTA
37737 GAAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (18 bp):
TTTTAAAGGGAAACTGAT
Found at i:56298 original size:29 final size:29
Alignment explanation
Indices: 56258--56315 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
56248 TTTATTTTGG
*
56258 GAATAAATTGAAATTT-GTTAAAATTTAGA
1 GAATAAATTGAAATTTAATT-AAATTTAGA
*
56287 GAATGAAA-TGAATTTTAATTAAATTTAGA
1 GAAT-AAATTGAAATTTAATTAAATTTAGA
56316 TCCAAATCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (29 bp):
GAATAAATTGAAATTTAATTAAATTTAGA
Found at i:60385 original size:54 final size:54
Alignment explanation
Indices: 60268--60372 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
60258 ATTACATCGA
* * *
60268 AGTGACGAAATGGAAATTCATAGACATATTATGAATTCCATGGATTGCACACAT
1 AGTGACGAAATGGAAATTCACAAACATATTATGAATACCATGGATTGCACACAT
* **
60322 AGTGCCGAAATGGTCATTCACAAACATATTATGAATACCAT-GAGTTGCACA
1 AGTGACGAAATGGAAATTCACAAACATATTATGAATACCATGGA-TTGCACA
60373 TTTAGTGTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (54 bp):
AGTGACGAAATGGAAATTCACAAACATATTATGAATACCATGGATTGCACACAT
Found at i:61251 original size:21 final size:21
Alignment explanation
Indices: 61227--61282 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 21
61217 ACCCACAATT
61227 GTATCAATACTAATTGCATCA
1 GTATCAATACTAATTGCATCA
61248 GTATTATCAATACTAATTGCATCA
1 G---TATCAATACTAATTGCATCA
*
61272 GTATCGATACT
1 GTATCAATACT
61283 GTTCATCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 10 0.32
24 21 0.68
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
GTATCAATACTAATTGCATCA
Found at i:61256 original size:24 final size:24
Alignment explanation
Indices: 61228--61275 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
61218 CCCACAATTG
61228 TATCAATACTAATTGCATCAGTAT
1 TATCAATACTAATTGCATCAGTAT
61252 TATCAATACTAATTGCATCAGTAT
1 TATCAATACTAATTGCATCAGTAT
61276 CGATACTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (24 bp):
TATCAATACTAATTGCATCAGTAT
Found at i:67520 original size:54 final size:54
Alignment explanation
Indices: 67427--67546 Score: 129
Period size: 54 Copynumber: 2.2 Consensus size: 54
67417 ATTCAAGGTA
* ** *
67427 CATGCATTGCAC-CAAAGTGCCGAAATAGAAATTCATAAACTTATTATGAATTC
1 CATGGATTGCACACAAAGTGCCGAAATAGAAATTCATAAACACATTATGAATAC
* ** *
67480 CATGGATTGCACACATAAG-GCCGAAATGGTCATTCTTAAACACATTATGAATAC
1 CATGGATTGCACACA-AAGTGCCGAAATAGAAATTCATAAACACATTATGAATAC
67534 CAT-GAGTTGCACA
1 CATGGA-TTGCACA
67547 TTTAGTGTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 13 0.23
54 40 0.71
55 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (54 bp):
CATGGATTGCACACAAAGTGCCGAAATAGAAATTCATAAACACATTATGAATAC
Found at i:71070 original size:13 final size:14
Alignment explanation
Indices: 71052--71082 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
71042 CAAATGATTC
71052 AAAAGAAAA-AAAT
1 AAAAGAAAATAAAT
71065 AAAAGAAAATAAAT
1 AAAAGAAAATAAAT
71079 AAAA
1 AAAA
71083 AATCTAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (14 bp):
AAAAGAAAATAAAT
Found at i:90616 original size:24 final size:24
Alignment explanation
Indices: 90584--90666 Score: 114
Period size: 24 Copynumber: 3.5 Consensus size: 24
90574 ATCAAAACAT
*
90584 AATCCAGGTAAAGTAT-TAGATCAA
1 AATCCAGGTCAAGTATCT-GATCAA
90608 AATCCAGGTCAAGTATCTGATCAA
1 AATCCAGGTCAAGTATCTGATCAA
* *
90632 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCTGATCAA
*
90656 AATCAAGGTCA
1 AATCCAGGTCA
90667 GATATTATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCTGATCAA
Found at i:93151 original size:17 final size:17
Alignment explanation
Indices: 93109--93151 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
93099 GGTCAACAGT
**
93109 GGTCAACGCCGGTCAAC
1 GGTCAACGGAGGTCAAC
93126 GGTCAACGGAGGTCAAC
1 GGTCAACGGAGGTCAAC
*
93143 GGTTAACGG
1 GGTCAACGG
93152 TCGACCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.14
Consensus pattern (17 bp):
GGTCAACGGAGGTCAAC
Found at i:95381 original size:24 final size:24
Alignment explanation
Indices: 95364--95470 Score: 144
Period size: 24 Copynumber: 4.5 Consensus size: 24
95354 ATCAAAACAT
95364 AATCCAGGTCAAGTATCAGATCCA-
1 AATCCAGGTCAAGTATCAGAT-CAG
* * *
95388 AATCCTGGTTAAGTATCTGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
* *
95412 AATCTAGGTCAAGTATCTGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
95436 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
95460 AATCCAGGTCA
1 AATCCAGGTCA
95471 GGAATTATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 2 0.03
24 72 0.97
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:112328 original size:17 final size:17
Alignment explanation
Indices: 112306--112340 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
112296 TCGGCTATAG
*
112306 GAAATGGTTAAGGTAAA
1 GAAATGGATAAGGTAAA
*
112323 GAAATGGATATGGTAAA
1 GAAATGGATAAGGTAAA
112340 G
1 G
112341 GTAGGATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (17 bp):
GAAATGGATAAGGTAAA
Found at i:112642 original size:18 final size:18
Alignment explanation
Indices: 112602--112636 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
112592 TATAGAAGTC
112602 TTTTTCTTTTCTCTTTTA
1 TTTTTCTTTTCTCTTTTA
112620 TTTTTCTTCTT-TCTTTT
1 TTTTTCTT-TTCTCTTTT
112637 TCTTTTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTCTCTTTTA
Found at i:113435 original size:19 final size:20
Alignment explanation
Indices: 113396--113448 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
113386 AAAACCCCTT
113396 TGAAAATACATGTTTTTTTTAA
1 TGAAAATACATG--TTTTTTAA
113418 TGAAAATACATG-TTTTTAA
1 TGAAAATACATGTTTTTTAA
*
113437 TGAAGATACATG
1 TGAAAATACATG
113449 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 18 0.60
22 12 0.40
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (20 bp):
TGAAAATACATGTTTTTTAA
Found at i:117878 original size:40 final size:40
Alignment explanation
Indices: 117834--117922 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
117824 GATTTGTTGA
*
117834 TGAGTGCTTAAACTTTTCTTTCTTTTCTTTTTCTTATTTT
1 TGAGTGCTTAAACTTTTCTATCTTTTCTTTTTCTTATTTT
* *
117874 TGAGTGCTTCAACTTTTCTATCTTTTCTTTTTCTTCTTTT
1 TGAGTGCTTAAACTTTTCTATCTTTTCTTTTTCTTATTTT
*
117914 TGAATGCTT
1 TGAGTGCTT
117923 TTAATTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.09, T:0.62
Consensus pattern (40 bp):
TGAGTGCTTAAACTTTTCTATCTTTTCTTTTTCTTATTTT
Found at i:117987 original size:11 final size:11
Alignment explanation
Indices: 117971--117996 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
117961 ATTTTGATTT
117971 CTTCACTTGCA
1 CTTCACTTGCA
117982 CTTCACTTGCA
1 CTTCACTTGCA
117993 CTTC
1 CTTC
117997 TTTTTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTCACTTGCA
Found at i:126229 original size:90 final size:89
Alignment explanation
Indices: 126114--126290 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
126104 TAAACCCGAA
* * *
126114 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCAAAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCAAAATATGAT
*
126179 TTGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
**
126204 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCAAAATATGATT
*
126269 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
126291 GTATGTTAGG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 31 0.39
90 49 0.61
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCAAAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:134202 original size:17 final size:17
Alignment explanation
Indices: 134180--134212 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
134170 AGTTAATTTA
*
134180 ATAAATGAACTAGTTTG
1 ATAAATGAAATAGTTTG
134197 ATAAATGAAATAGTTT
1 ATAAATGAAATAGTTT
134213 AATGAACTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.36
Consensus pattern (17 bp):
ATAAATGAAATAGTTTG
Found at i:138170 original size:20 final size:20
Alignment explanation
Indices: 138133--138171 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
138123 TATATTGGGT
* *
138133 TATTGTCTATTGTTTATGGC
1 TATTGTCTATGGTATATGGC
138153 TATTGTCTATGGTATATGG
1 TATTGTCTATGGTATATGG
138172 TTATGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGC
Found at i:138235 original size:45 final size:44
Alignment explanation
Indices: 138172--138279 Score: 198
Period size: 45 Copynumber: 2.4 Consensus size: 44
138162 TGGTATATGG
138172 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
138216 TTATGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGA-TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
138261 TTATGGGATAAATGGTAAG
1 TTAT-GGATAAATGGTAAG
138280 AAATTTTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
44 7 0.11
45 52 0.84
46 3 0.05
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:143452 original size:22 final size:21
Alignment explanation
Indices: 143427--143483 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
143417 GTTCAAAGAC
*
143427 AAAAAGAAGACAAAAATTAGAA
1 AAAAAGAAGACAAAAATT-CAA
*
143449 AAAAAGAAGAAAAGAAATTCAA
1 AAAAAGAAGACAA-AAATTCAA
*
143471 AAAGAGAAG-CAAA
1 AAAAAGAAGACAAA
143484 GCCTAGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 2 0.07
22 22 0.73
23 5 0.17
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (21 bp):
AAAAAGAAGACAAAAATTCAA
Found at i:145869 original size:69 final size:70
Alignment explanation
Indices: 145773--145987 Score: 208
Period size: 69 Copynumber: 3.1 Consensus size: 70
145763 TGGGAGGTTT
* * ** * **
145773 AAAGACGTGACCTTTCAAGAGCCAAGAGGTT-CGACTAATGAAA-AGCAAAGAGTGGTGATTC-T
1 AAAGACGTAACCCTTCAAGAATCAAGAGGTTGCGACTAATGAAAGA-CAAAGAGAGACGATTCTT
145835 CTATCCA
65 C-ATCCA
* * * *
145842 AAAGATGTAACCCTTCAAGAATCAAGA-GTTGTGCCTAATGAAAGACAAAGGGAGACGATTCTTC
1 AAAGACGTAACCCTTCAAGAATCAAGAGGTTGCGACTAATGAAAGACAAAGAGAGACGATTCTTC
145906 ATCCA
66 ATCCA
* * * * *
145911 AATGACGTAACCCTTCAAGAATCAAGA-GTTGTGCCTAATGAAAGACAAATG-GAGGCGATTATT
1 AAAGACGTAACCCTTCAAGAATCAAGAGGTTGCGACTAATGAAAGACAAA-GAGAGACGATTCTT
145974 CATCCA
65 CATCCA
*
145980 AAGGACGT
1 AAAGACGT
145988 GACTTATGAG
Statistics
Matches: 126, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
68 3 0.02
69 119 0.94
70 4 0.03
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (70 bp):
AAAGACGTAACCCTTCAAGAATCAAGAGGTTGCGACTAATGAAAGACAAAGAGAGACGATTCTTC
ATCCA
Found at i:161980 original size:21 final size:20
Alignment explanation
Indices: 161947--161985 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
161937 AAGAACGAAC
161947 GAAAGAAAAGAAAATGAAAT
1 GAAAGAAAAGAAAATGAAAT
*
161967 GAAATAAAGAGAAAATGAA
1 GAAAGAAA-AGAAAATGAA
161986 GATAACTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (20 bp):
GAAAGAAAAGAAAATGAAAT
Found at i:166897 original size:16 final size:16
Alignment explanation
Indices: 166872--166910 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
166862 CCTTAATGAT
* *
166872 CACTCTTGCCGTTTAC
1 CACTCATGCCATTTAC
166888 CACTCATGCCATTTAC
1 CACTCATGCCATTTAC
166904 CACTCAT
1 CACTCAT
166911 ACATTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.38, G:0.08, T:0.33
Consensus pattern (16 bp):
CACTCATGCCATTTAC
Found at i:181012 original size:19 final size:19
Alignment explanation
Indices: 180976--181012 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
180966 ATTTTATCCT
*
180976 TTATTCCTTTATTAATTTA
1 TTATTCCTTTAATAATTTA
*
180995 TTATTCCTTTAATCATTT
1 TTATTCCTTTAATAATTT
181013 CTTTCATTAC
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:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTCCTTTAATAATTTA
Found at i:181224 original size:12 final size:13
Alignment explanation
Indices: 181187--181222 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
181177 GCAACAAAAT
*
181187 AAAATGAAAAAGA
1 AAAAAGAAAAAGA
*
181200 AATAAGAAAAAGA
1 AAAAAGAAAAAGA
181213 AAAAAGAAAA
1 AAAAAGAAAA
181223 GACTCCTACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:186934 original size:20 final size:20
Alignment explanation
Indices: 186911--186949 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
186901 TCAGCTGAAA
*
186911 GAGCTCAACGTTAGCTAATG
1 GAGCTCAACGCTAGCTAATG
186931 GAGCTCAACGCTAGCTAAT
1 GAGCTCAACGCTAGCTAAT
186950 CTCAGCTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
GAGCTCAACGCTAGCTAATG
Found at i:188124 original size:24 final size:23
Alignment explanation
Indices: 188072--188116 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
188062 AAATCCAGAA
188072 AAGAAATTCAAAGCACTCAAAAG
1 AAGAAATTCAAAGCACTCAAAAG
*
188095 AAGAAATTGAAAGCACTCAAAA
1 AAGAAATTCAAAGCACTCAAAA
188117 AGACGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (23 bp):
AAGAAATTCAAAGCACTCAAAAG
Found at i:203765 original size:18 final size:18
Alignment explanation
Indices: 203742--203817 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
203732 TTCATTTTAA
203742 ATTATTATTATTAAAATT
1 ATTATTATTATTAAAATT
**
203760 ATTATTATTATTATTATT
1 ATTATTATTATTAAAATT
* *
203778 ATTATTAATT-GTAATATT
1 ATTATT-ATTATTAAAATT
203796 ATTTATTATTTATTAAATATT
1 A-TTATTA-TTATTAAA-ATT
203817 A
1 A
203818 CAAAGCCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 30 0.64
19 10 0.21
20 3 0.06
21 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
ATTATTATTATTAAAATT
Found at i:203805 original size:3 final size:3
Alignment explanation
Indices: 203742--203784 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
203732 TTCATTTTAA
**
203742 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
203785 ATTGTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:208048 original size:21 final size:21
Alignment explanation
Indices: 208001--208048 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
207991 TTCATACATG
* *
208001 CATTTACATTTTGTATCTGTA
1 CATTTTCATTTTGTATATGTA
*
208022 CATTTTCATTTTGTATATTTA
1 CATTTTCATTTTGTATATGTA
*
208043 CTTTTT
1 CATTTT
208049 ATATCTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.60
Consensus pattern (21 bp):
CATTTTCATTTTGTATATGTA
Found at i:212851 original size:93 final size:93
Alignment explanation
Indices: 212692--213157 Score: 747
Period size: 93 Copynumber: 5.0 Consensus size: 93
212682 AGGAGACCCA
*
212692 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
212757 TCAATGAATTTGGAAGATGAATGTGCTC
66 TCAATGAATTTGGAAGATGAATGTGCTC
*
212785 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
212850 TCAATGAATTTGGAAGATGAATGTGCTC
66 TCAATGAATTTGGAAGATGAATGTGCTC
**
212878 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAATTAA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
*
212943 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCAATGAATTTGGAAGATGAATGTGCTC
* * * *
212971 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAAACCACAAAATCAA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
213036 TCAATGAATTTGGAAGATGAATGTGCTC
66 TCAATGAATTTGGAAGATGAATGTGCTC
* * * *
213064 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAAAACCA
* * ** *
213127 ATCATTGGATTTAAAAGATGAATTTGCTC
65 ATCAATGAATTTGGAAGATGAATGTGCTC
213156 AT
1 AT
213158 GGTAGAAATA
Statistics
Matches: 358, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 37 0.10
93 321 0.90
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAAAACCAA
TCAATGAATTTGGAAGATGAATGTGCTC
Found at i:213264 original size:114 final size:115
Alignment explanation
Indices: 213060--213326 Score: 457
Period size: 114 Copynumber: 2.3 Consensus size: 115
213050 AGATGAATGT
* *
213060 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATATGAACTCCAAAA
*
213124 TCAATCATTGGATTTAAAAGATGAA-TTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
*
213173 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATATGAACTCTAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATATGAACTCCAAAA
*
213238 TCAATCATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
66 TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
* *
213288 ACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
213327 AGTCTGTTCG
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 4 0.03
114 81 0.56
115 60 0.41
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (115 bp):
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATATGAACTCCAAAA
TCAATCATTGGATTTAAAAGATGAATTTTGCTCATAGTAGAAATAAGGAG
Found at i:214593 original size:76 final size:75
Alignment explanation
Indices: 214504--214675 Score: 195
Period size: 76 Copynumber: 2.3 Consensus size: 75
214494 TAACAAGAAA
* * * *
214504 CAAATGTTGGGGCATGCTGAAA-ACCCTTGTCAATCAGAATCAGGAATGTTGATGTATCCTGAAT
1 CAAATATTAGGGCATGCTGAAAGACCCTT-TCAATCAGAATCAAGAATGTTGATGTATCCTGAAC
* *
214568 GTTTATATCAG
65 GCTCATATCAG
* * * **
214579 CAAA-ATGCTAGGGCATACTGAAAGCCCCTTTCAATCAGAATGAAGAATGTTGATGTATTTTGAA
1 CAAATAT--TAGGGCATGCTGAAAGACCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
214643 CGCTCATATCAG
64 CGCTCATATCAG
*
214655 CAAATATTGGGGCATGCTGAA
1 CAAATATTAGGGCATGCTGAA
214676 GGCCCACAAC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
74 1 0.01
75 16 0.20
76 56 0.70
77 7 0.09
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (75 bp):
CAAATATTAGGGCATGCTGAAAGACCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
CTCATATCAG
Found at i:215652 original size:54 final size:54
Alignment explanation
Indices: 215551--215662 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
215541 CAATGATTGA
***
215551 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** * *
215605 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAT
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
215659 GAAC
1 GAAC
215663 CTGCTATTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:216045 original size:22 final size:22
Alignment explanation
Indices: 216016--216070 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
216006 ATCTACACTC
216016 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
* *
216038 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
216060 TTCAAAGATGA
1 TTCAAAGATGA
216071 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:216873 original size:76 final size:76
Alignment explanation
Indices: 216747--217737 Score: 1797
Period size: 76 Copynumber: 13.0 Consensus size: 76
216737 CTATTTCCCA
*
216747 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
216812 AGCCTTAGGGT
66 AGCCTTCGGGT
* *
216823 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
216888 AGCCTTCGGGT
66 AGCCTTCGGGT
216899 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
216964 AGCCTTAGGGT
66 AGCCTTCGGGT
* * *
216975 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
217040 AGCCATCGGGT
66 AGCCTTCGGGT
*
217051 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217116 AGCCTTCGGGT
66 AGCCTTCGGGT
217127 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217192 AGCCTTCGGGT
66 AGCCTTCGGGT
217203 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217268 AGCCTTCGGGT
66 AGCCTTCGGGT
217279 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
217344 AGCCTTAGGGT
66 AGCCTTCGGGT
* *
217355 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217420 AGCCTTCGGGT
66 AGCCTTCGGGT
217431 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217496 AGCCTTCGGGT
66 AGCCTTCGGGT
217507 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
217572 AGCCTTCGGGT
66 AGCCTTCGGGT
217583 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
217648 A-CCCTCAGGGT
66 AGCCTTC-GGGT
* *
217659 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
217724 A-CCCTCAGGGT
66 AGCCTTC-GGGT
217735 CAT
1 CAT
217738 TCATAAGACC
Statistics
Matches: 889, Mismatches: 25, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 4 0.00
76 885 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:217903 original size:3 final size:3
Alignment explanation
Indices: 217895--217975 Score: 99
Period size: 3 Copynumber: 26.3 Consensus size: 3
217885 TTCATTTTAA
**
217895 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
217943 ATT ATT AAT AGT AAT ATT ATTT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT A
217976 AATATTACAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 62 0.91
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:221909 original size:94 final size:95
Alignment explanation
Indices: 221786--222005 Score: 320
Period size: 94 Copynumber: 2.3 Consensus size: 95
221776 TGATTCAATC
** * * *
221786 AGTATCGATACCAACG-AGGTAGTATCGATACCAGGTCACATTGAATCTAAAATGGGTATCGATA
1 AGTATCGATACCATGGTAGGT-GTATCGATACCAGGTAACATCGAATCAAAAATGGGTATCGATA
*
221850 CCGGAAGGGGGTA-CGATACCATAATATAGT
65 CCGGAAGGGGGTATCAATACCATAATATAGT
* *
221880 AGTATCGATACCGTGGTAAGG-GTATCGATACCAGGTAACATCGAATCAAAAATTGGTATCGATA
1 AGTATCGATACCATGGT-AGGTGTATCGATACCAGGTAACATCGAATCAAAAATGGGTATCGATA
*
221944 CCGGAAGGGGGTATCAATACCATAGTATAGT
65 CCGGAAGGGGGTATCAATACCATAATATAGT
221975 AGTATCGATACCATGGTAGGTGTATCGATAC
1 AGTATCGATACCATGGTAGGTGTATCGATAC
222006 TATAGAGCCA
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
94 68 0.61
95 41 0.37
96 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (95 bp):
AGTATCGATACCATGGTAGGTGTATCGATACCAGGTAACATCGAATCAAAAATGGGTATCGATAC
CGGAAGGGGGTATCAATACCATAATATAGT
Found at i:222484 original size:47 final size:47
Alignment explanation
Indices: 222407--222977 Score: 813
Period size: 47 Copynumber: 12.1 Consensus size: 47
222397 AAACTGAATA
* *
222407 CATAACTAAAAATGCATGAAC-GAGTGCATTAAAGCATAAAAGGATGC
1 CATAACTAAAAATGCATGAACGGA-TGCATTAAGGCATGAAAGGATGC
* * * *
222454 CATAACTAAAGATACATGAATGGATTCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
222501 CATAACTAAAAAATGCATGAACGGATTCATTAAGTCATGAAAGGATGC
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
222549 CATAACTAAAAATGCATGAACGGGTGCATTAAGGCATGAAAGGATGT
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
222596 CATAACTAAAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATGC
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
222644 CATAACTAAAAATGCATGAACGGATGCAATAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
222691 CATAACTAAAAAATGCATGAACGGATGCATTCAGGCATGAAAGAATGC
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
222739 CATAACTAAAAATGCATGAATGGATGCATTAAGGCTTGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* ** * *
222786 CTTAACT-AAAATTAATGAACGGATGCATTAAGTCATGAAAAGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * * *
222832 CATAAGTAAAAATGTATGAATGGATGCATTAAGGTATGAAATGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * *
222879 CATAACTAAAAATGCATGAACGGATGCATTAAGGCGTTAAATGATGG
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
222926 CATAACTAAAAATGCATGAACTGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
222973 CATAA
1 CATAA
222978 GTGAAATTAA
Statistics
Matches: 466, Mismatches: 53, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
46 38 0.08
47 295 0.63
48 133 0.29
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (47 bp):
CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:222579 original size:95 final size:94
Alignment explanation
Indices: 222407--222977 Score: 813
Period size: 95 Copynumber: 6.1 Consensus size: 94
222397 AAACTGAATA
* * * *
222407 CATAACTAAAAATGCATGAAC-GAGTGCATTAAAGCATAAAAGGATGCCATAACTAAAGATACAT
1 CATAACTAAAAATGCATGAACGGA-TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAT
* *
222471 GAATGGATTCATTAAGGCATGAAAGGATGC
65 GAACGGATGCATTAAGGCATGAAAGGATGC
* *
222501 CATAACTAAAAAATGCATGAACGGATTCATTAAGTCATGAAAGGATGCCATAACTAAAAATGCAT
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAT
* *
222566 GAACGGGTGCATTAAGGCATGAAAGGATGT
65 GAACGGATGCATTAAGGCATGAAAGGATGC
*
222596 CATAACTAAAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAT
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAT
*
222661 GAACGGATGCAATAAGGCATGAAAGGATGC
65 GAACGGATGCATTAAGGCATGAAAGGATGC
* *
222691 CATAACTAAAAAATGCATGAACGGATGCATTCAGGCATGAAAGAATGCCATAACTAAAAATGCAT
1 CATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAT
* *
222756 GAATGGATGCATTAAGGCTTGAAAGGATGC
65 GAACGGATGCATTAAGGCATGAAAGGATGC
* ** * * * *
222786 CTTAACT-AAAATTAATGAACGGATGCATTAAGTCATGAAAAGATGCCATAAGTAAAAATGTATG
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATG
* * *
222850 AATGGATGCATTAAGGTATGAAATGATGC
66 AACGGATGCATTAAGGCATGAAAGGATGC
* * * *
222879 CATAACTAAAAATGCATGAACGGATGCATTAAGGCGTTAAATGATGGCATAACTAAAAATGCATG
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATG
*
222944 AACTGATGCATTAAGGCATGAAAGGATGC
66 AACGGATGCATTAAGGCATGAAAGGATGC
222973 CATAA
1 CATAA
222978 GTGAAATTAA
Statistics
Matches: 426, Mismatches: 48, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
93 81 0.19
94 85 0.20
95 258 0.61
96 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (94 bp):
CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATG
AACGGATGCATTAAGGCATGAAAGGATGC
Found at i:222682 original size:20 final size:20
Alignment explanation
Indices: 222657--222695 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
222647 AACTAAAAAT
*
222657 GCATGAACGGATGCAATAAG
1 GCATGAAAGGATGCAATAAG
*
222677 GCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCAATAA
222696 CTAAAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (20 bp):
GCATGAAAGGATGCAATAAG
Found at i:227196 original size:64 final size:63
Alignment explanation
Indices: 227128--227306 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
227118 TGGAACACTT
* * * * **
227128 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGATGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* * * *
227192 AGTGCATCGATGCAT-TGCTTGTACATCGATGCATGAAATGCATTCTATGTTTTAATAAAACCCA
1 AGTGCATCGATGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
*
227256 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
227307 CAATTTATTC
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
62 1 0.01
64 92 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:227325 original size:64 final size:64
Alignment explanation
Indices: 227148--227334 Score: 168
Period size: 64 Copynumber: 2.9 Consensus size: 64
227138 TGCACCAAGT
* * * * **
227148 GTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCC--TGAGTGCATCGATGCATTGCT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-CCAATG-GTGCATCGATGCATAGAG
*
227211 T
64 A
* * * *
227212 GTACATCGATGCATGAAATGCATTCTATGTTTTAATAAAACCCAA--GTGCATCGATGCATAGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAT-ATA-CCAATGGTGCATCGATGCATAGAG
227275 A
64 A
* * *
227276 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCAATGGTGCATCGTTGCAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-CCAATGGTGCATCGATGCAT
227335 GGATTGATGC
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
62 4 0.04
63 5 0.05
64 86 0.87
65 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACCAATGGTGCATCGATGCATAGAGA
Found at i:228381 original size:18 final size:19
Alignment explanation
Indices: 228358--228401 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
228348 ATTAGAAGCC
*
228358 GGAGCAGCAGGAGGAG-GA
1 GGAGCAGCAAGAGGAGCGA
*
228376 GGAGCA-CAAGAGGAGCTA
1 GGAGCAGCAAGAGGAGCGA
228394 GGAGCAGC
1 GGAGCAGC
228402 TCGTGAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.34, C:0.16, G:0.48, T:0.02
Consensus pattern (19 bp):
GGAGCAGCAAGAGGAGCGA
Found at i:237205 original size:20 final size:20
Alignment explanation
Indices: 237162--237220 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
237152 TTTGGTGCAG
***
237162 AGGGAATCGATTCCCCCTTT
1 AGGGAATCGATTCCCCCCAC
*
237182 AGGGAATTGATTCCCCCCAC
1 AGGGAATCGATTCCCCCCAC
*
237202 AGGGGAATCGATACCCCCC
1 A-GGGAATCGATTCCCCCC
237221 TAAGGTTCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.20
Consensus pattern (20 bp):
AGGGAATCGATTCCCCCCAC
Found at i:239931 original size:20 final size:20
Alignment explanation
Indices: 239898--239972 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
239888 CTCGGAGGGA
239898 ACCGATTCCCCCCCAGGGGGT
1 ACCGATT-CCCCCCAGGGGGT
** **
239919 ACCGATTCCCCCC-TTGTAT
1 ACCGATTCCCCCCAGGGGGT
**
239938 AACCGATTCCCCATAGGGGGT
1 -ACCGATTCCCCCCAGGGGGT
239959 ACCGATTCCCCCCA
1 ACCGATTCCCCCCA
239973 CGCTCCAAGC
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
19 2 0.05
20 29 0.73
21 9 0.22
ACGTcount: A:0.19, C:0.41, G:0.20, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:245352 original size:64 final size:63
Alignment explanation
Indices: 245284--245462 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
245274 TGAAACACTT
* * * *
245284 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATATCCTA
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* *
245348 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* * * *
245412 AGTGCATCGATACATAGAGAGTGCATCGATGCACGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
245463 CAATTTATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
62 1 0.01
64 95 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:247006 original size:24 final size:24
Alignment explanation
Indices: 246961--247006 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
246951 TCTTCCAAAT
* *
246961 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCAACGTACAC
246985 GATGTATAAAACATCAACGTAC
1 GATGTATAAAACATCAACGTAC
247007 CATATCATGC
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:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (24 bp):
GATGTATAAAACATCAACGTACAC
Found at i:247439 original size:29 final size:30
Alignment explanation
Indices: 247407--247464 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
247397 GAATTGATCC
247407 CCAAATTTT-TAAAAATTACAAAATAGTCG
1 CCAAATTTTCTAAAAATTACAAAATAGTCG
** *
247436 CCAAATTTTCTAAAGCTTATAAAATAGTC
1 CCAAATTTTCTAAAAATTACAAAATAGTC
247465 CTTCATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (30 bp):
CCAAATTTTCTAAAAATTACAAAATAGTCG
Found at i:255222 original size:18 final size:18
Alignment explanation
Indices: 255192--255233 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
255182 TTCGCTCACT
255192 AAAT-AAATCCATTTATG
1 AAATAAAATCCATTTATG
*
255209 AAATAAAATTCATTTATG
1 AAATAAAATCCATTTATG
255227 AAATAAA
1 AAATAAA
255234 CTTTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (18 bp):
AAATAAAATCCATTTATG
Found at i:257711 original size:18 final size:18
Alignment explanation
Indices: 257681--257722 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
257671 TTCGGTCACT
257681 AAAT-AAATCCATTTATG
1 AAATAAAATCCATTTATG
*
257698 AAATAAAATTCATTTATG
1 AAATAAAATCCATTTATG
257716 AAATAAA
1 AAATAAA
257723 CTTTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (18 bp):
AAATAAAATCCATTTATG
Found at i:258188 original size:5 final size:5
Alignment explanation
Indices: 258178--258217 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
258168 CACTTCACAA
* *
258178 TCTTT TATTT TCTTT TCTTT TCTTT TCTTT T-TCT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
258218 TGAGTGCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:258257 original size:22 final size:24
Alignment explanation
Indices: 258207--258258 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
258197 TTCTTTTCTT
*
258207 TTTCTTCTTTTTGAGTGCTTTTAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
258231 TTTCTTC-TTTTGAGTGC-TTCAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
258253 TTTCTT
1 TTTCTT
258259 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:260414 original size:59 final size:58
Alignment explanation
Indices: 260342--260648 Score: 384
Period size: 59 Copynumber: 5.2 Consensus size: 58
260332 ATTAATGTAA
* *
260342 GTATGAATATCCATATGGAGCA-ATGAGTGTGCTAAAATGATAAGGAAATCATATTGAGT
1 GTATGGATTTCCATATGGAGCATAT-A-TGTGCTAAAATGATAAGGAAATCATATTGAGT
*
260401 GTATGAATTTCCATATGGAGCACTATATGTGCTAAAATGATAAGGAAATCATATTGAGT
1 GTATGGATTTCCATATGGAGCA-TATATGTGCTAAAATGATAAGGAAATCATATTGAGT
* *
260460 GTATGGACTTCCATATGGAGCACTATATGTGCTAAAATGATAAGGAAATCATATTGAGC
1 GTATGGATTTCCATATGGAGCA-TATATGTGCTAAAATGATAAGGAAATCATATTGAGT
* * *
260519 GTATGGATTTCTATATGGAGCACTGA-GTGTGCTAAAATGATAAGGAAATCATATTGAAT
1 GTATGGATTTCCATATGGAGCA-T-ATATGTGCTAAAATGATAAGGAAATCATATTGAGT
* * * * * * * * *
260578 ATATGGATTTCCAGATAGTGCATTATATGTGCTAAAATGGTAAGGGAATTATACTAAGT
1 GTATGGATTTCCATATGGAGCA-TATATGTGCTAAAATGATAAGGAAATCATATTGAGT
260637 GTATGGATTTCC
1 GTATGGATTTCC
260649 CGAAAAAGCA
Statistics
Matches: 221, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
58 1 0.00
59 216 0.98
60 2 0.01
61 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (58 bp):
GTATGGATTTCCATATGGAGCATATATGTGCTAAAATGATAAGGAAATCATATTGAGT
Found at i:260659 original size:118 final size:118
Alignment explanation
Indices: 260369--260764 Score: 370
Period size: 118 Copynumber: 3.3 Consensus size: 118
260359 GAGCAATGAG
* * * * * * ***
260369 TGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTATA-TGTGC
1 TGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCAGAAAAAGCACTA-AGTGTGC
* * * * *
260433 TAAAATGATAAGGAAATCATATTGAGTGTATGGACTTCCATATGGAGCACTATA
65 TAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGAGCATTATA
* * * * * * * *** *
260487 TGTGCTAAAATGATAAGGAAATCATATTGAGCGTATGGATTTCTATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCAGAAAAAGCACTAAGTGTGCT
* *
260552 AAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGTGCATTATA
66 AAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGAGCATTATA
* * *
260605 TGTGCTAAAATGGTAAGGGAATTATACTAAGTGTATGGATTTCCCGAAAAAGCACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCAGAAAAAGCACTAAGTGTGCT
* * * * * * *
260670 ACAAGGATAAGGAAATCATAGT-AACAATATGGATTTTCATATAGGGCACTT-CA
66 AAAATGATAAGGAAATCATATTGAA-TATATGGATTTCCATATAGAGCA-TTATA
260723 TGTGCTAAAAATGGTAAAGGG-ATCATACTAA-TGGTATGGATT
1 TGTGCT-AAAATGGT-AAGGGAATCATACTAAGT-GTATGGATT
260765 CTTGAATAGG
Statistics
Matches: 238, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
117 3 0.01
118 202 0.85
119 28 0.12
120 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (118 bp):
TGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCAGAAAAAGCACTAAGTGTGCT
AAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGAGCATTATA
Found at i:260661 original size:177 final size:177
Alignment explanation
Indices: 260354--260689 Score: 458
Period size: 177 Copynumber: 1.9 Consensus size: 177
260344 ATGAATATCC
* * * *
260354 ATATGGAGCAATGAGTGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGAATTTCCATATGG
1 ATATGGAGCAATGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
* * * ***
260419 AGCACTATATGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGGACTTCCATATGGAGCACT
66 AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
* *
260484 ATA-TGTGCTAAAATGATAAGGAAATCATATTGAGCGTATGGATTTCT
131 A-AGGGTGCTAAAAGGATAAGGAAATCATATTGAGCGTATGGATTTCT
* *
260531 ATATGGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
1 ATATGGAGCAATGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
* * * * * * *
260596 TGCATTATATGTGCTAAAATGGTAAGGGAATTATACTAAGTGTATGGATTTCCCGAAAAAGCACT
66 AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
*
260661 AAGGGTGCTACAAGGATAAGGAAATCATA
131 AAGGGTGCTAAAAGGATAAGGAAATCATA
260690 GTAACAATAT
Statistics
Matches: 136, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
176 1 0.01
177 135 0.99
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (177 bp):
ATATGGAGCAATGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
AAGGGTGCTAAAAGGATAAGGAAATCATATTGAGCGTATGGATTTCT
Found at i:260729 original size:177 final size:177
Alignment explanation
Indices: 260354--260732 Score: 435
Period size: 177 Copynumber: 2.1 Consensus size: 177
260344 ATGAATATCC
* * * * * *
260354 ATATGGAGCAATGAGTGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGAATTTCCATATGG
1 ATATGGAGCACTCAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
* * * ***
260419 AGCACTATATGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGGACTTCCATATGGAGCACT
66 AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
* * * * *
260484 ATATGTGCTAAAATGATAAGGAAATCATATTGAGCGTATGGATTTCT
131 ATAGGTGCTAAAAGGATAAGGAAATCATAGTGAACATATGGATTTCT
* *
260531 ATATGGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
1 ATATGGAGCACTCAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
* * * * * * *
260596 TGCATTATATGTGCTAAAATGGTAAGGGAATTATACTAAGTGTATGGATTTCCCGAAAAAGCACT
66 AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
*
260661 A-AGGGTGCTACAAGGATAAGGAAATCATAGT-AACAATATGGATTT-T
131 ATA-GGTGCTAAAAGGATAAGGAAATCATAGTGAAC-ATATGGATTTCT
260707 CATATAGG-GCACTTCA-TGTGCTAAAA
1 -ATAT-GGAGCAC-TCAGTGTGCTAAAA
260733 ATGGTAAAGG
Statistics
Matches: 171, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
176 4 0.02
177 163 0.95
178 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (177 bp):
ATATGGAGCACTCAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGAATTTCCAGATAG
AGCACTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGACTTCCAGAAAAAGCACT
ATAGGTGCTAAAAGGATAAGGAAATCATAGTGAACATATGGATTTCT
Found at i:260764 original size:60 final size:59
Alignment explanation
Indices: 260697--260852 Score: 240
Period size: 60 Copynumber: 2.6 Consensus size: 59
260687 ATAGTAACAA
*
260697 TATGGATTTTCATATAGGGCACTTCATGTGCTAAAAATGGTAAAGGGATCATACTAATGG
1 TATGGATTTTCA-ATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
* *
260757 TATGGATTCTTGAATAGGGCACTTCATGTGCTAAAAATGGTAAATGAATCATACTAATGG
1 TATGGATT-TTCAATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
* *
260817 TATGGATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 TATGGATTTTC-AATAGGGCACTTCATGTGCTAAAA
260853 TGAGAAGGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
59 1 0.01
60 84 0.95
61 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (59 bp):
TATGGATTTTCAATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
Found at i:261169 original size:14 final size:14
Alignment explanation
Indices: 261150--261185 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
261140 AATGGTAAGT
261150 AATCCCTGTAAATA
1 AATCCCTGTAAATA
261164 AATCCCTGTAAATA
1 AATCCCTGTAAATA
261178 AATCCCTG
1 AATCCCTG
261186 CGTAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (14 bp):
AATCCCTGTAAATA
Found at i:261477 original size:44 final size:44
Alignment explanation
Indices: 261414--261719 Score: 522
Period size: 44 Copynumber: 7.0 Consensus size: 44
261404 TTAGTGATGC
* *
261414 AAATTATAGTAAGTATATTGGTAAAATAAGATTACGAGCTTATA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
261458 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
261502 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
261546 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATT
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
261590 AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
261634 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
261678 GAATAATGGTAAGTATATTGGTAAAATAAACTTACGAGCTTA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
261720 GGGATTTAAT
Statistics
Matches: 250, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 250 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:266823 original size:29 final size:29
Alignment explanation
Indices: 266758--266839 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
266748 AACTTGATGA
**
266758 AGCATTTGGAAGACACATACATATTAGTGG
1 AGCATTTGGAAGACACA-ACAGCTTAGTGG
*
266788 AGCATTTTGGAAGACA-AACAGCTTGGTGG
1 AGCA-TTTGGAAGACACAACAGCTTAGTGG
* *
266817 AGCATTTGGGAGACATAACAGCT
1 AGCATTTGGAAGACACAACAGCT
266840 CACAAACATC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.22
29 20 0.43
30 5 0.11
31 11 0.24
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (29 bp):
AGCATTTGGAAGACACAACAGCTTAGTGG
Found at i:284586 original size:15 final size:14
Alignment explanation
Indices: 284545--284587 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
284535 AAATAAGGAT
284545 TGAAAGAAATGGAAA
1 TGAAAGAAAT-GAAA
*
284560 TGATAAGGAATGAAA
1 TGA-AAGAAATGAAA
284575 TGGAAAGAAATGA
1 T-GAAAGAAATGA
284588 TATCAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (14 bp):
TGAAAGAAATGAAA
Found at i:284766 original size:35 final size:35
Alignment explanation
Indices: 284727--284839 Score: 140
Period size: 35 Copynumber: 3.2 Consensus size: 35
284717 GGAATAGTGT
* *
284727 TGATATAGGCGTGAAATGGTGATAGAGGATGGTGA
1 TGATATAGGCGTGAAATGGTGATGGAAGATGGTGA
* *
284762 TGATATAGGTGT-ACAATGGGGATGGAAGATGGTGA
1 TGATATAGGCGTGA-AATGGTGATGGAAGATGGTGA
* *
284797 TGTTATAGGCGTGAAAATGGTGATGGAATATGGTGA
1 TGATATAGGCGTG-AAATGGTGATGGAAGATGGTGA
284833 TGA-ATAG
1 TGATATAG
284840 ATAGTATCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 43 0.65
36 21 0.32
37 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.27
Consensus pattern (35 bp):
TGATATAGGCGTGAAATGGTGATGGAAGATGGTGA
Found at i:288015 original size:17 final size:17
Alignment explanation
Indices: 287993--288025 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
287983 TCGGCTTAAA
287993 AGAAATGGTTAGGGTAT
1 AGAAATGGTTAGGGTAT
*
288010 AGAAATGGTTATGGTA
1 AGAAATGGTTAGGGTA
288026 GGGTAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (17 bp):
AGAAATGGTTAGGGTAT
Found at i:288355 original size:26 final size:26
Alignment explanation
Indices: 288316--288381 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
288306 GTAGGAGTCT
* * *
288316 TTTCTTTTTC-TTTTTGTTTTTCTTC
1 TTTCTTTTGCTTTTTTGCTTATCTTC
*
288341 TTTCTTTTGCTTTTTTGCTTATCTTT
1 TTTCTTTTGCTTTTTTGCTTATCTTC
288367 TTTCTTTTGCTTTTT
1 TTTCTTTTGCTTTTT
288382 GTTACAGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (26 bp):
TTTCTTTTGCTTTTTTGCTTATCTTC
Found at i:288379 original size:13 final size:12
Alignment explanation
Indices: 288315--288381 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 12
288305 TGTAGGAGTC
288315 TTTTCTTTTTCTT
1 TTTTC-TTTTCTT
288328 TTTGT-TTTTCTT
1 TTT-TCTTTTCTT
*
288340 CTTTCTTTTGCTT
1 TTTTCTTTT-CTT
*
288353 TTTTGCTTATCTT
1 TTTT-CTTTTCTT
288366 TTTTCTTTTGCTT
1 TTTTCTTTT-CTT
288379 TTT
1 TTT
288382 GTTACAGAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
11 1 0.02
12 17 0.38
13 22 0.49
14 5 0.11
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:288380 original size:6 final size:6
Alignment explanation
Indices: 288315--288355 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
288305 TGTAGGAGTC
* *
288315 TTTTCT TTTTCT TTTTGT TTTTCT TCTTTCT TTTGCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
288356 TGCTTATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:288852 original size:36 final size:36
Alignment explanation
Indices: 288756--288862 Score: 146
Period size: 35 Copynumber: 3.0 Consensus size: 36
288746 GGAATAGTGC
* *
288756 TGATATAGGCGTG-AAATGGTGATAGAGGATGGTGA
1 TGATATAGGCGTGAAAATGGTGATGGAAGATGGTGA
* * *
288791 TGATATAGGTGT-ACAATGGGGATGGAAGATGGTGA
1 TGATATAGGCGTGAAAATGGTGATGGAAGATGGTGA
*
288826 TGTTATAGGCGTGAAAATGGTGATGGAAGATGGTGA
1 TGATATAGGCGTGAAAATGGTGATGGAAGATGGTGA
288862 T
1 T
288863 AAATAGATAG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 39 0.64
36 22 0.36
ACGTcount: A:0.31, C:0.03, G:0.39, T:0.27
Consensus pattern (36 bp):
TGATATAGGCGTGAAAATGGTGATGGAAGATGGTGA
Found at i:291862 original size:30 final size:28
Alignment explanation
Indices: 291828--291916 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 28
291818 ACAGGTTGGG
291828 ACAACTTGATGAAGCATTTGGAAGACACA
1 ACAACTTGATG-AGCATTTGGAAGACACA
291857 TACAACTT-AGTGGAGCATTTGGGAAGACA-A
1 -ACAACTTGA-T-GAGCATTT-GGAAGACACA
* * *
291887 ACAGCTTGGTTGAGCATTTGGGAGACACA
1 ACAACTT-GATGAGCATTTGGAAGACACA
291916 A
1 A
291917 ACAGCTCACA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
28 7 0.14
29 17 0.34
30 17 0.34
31 9 0.18
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (28 bp):
ACAACTTGATGAGCATTTGGAAGACACA
Found at i:291919 original size:30 final size:30
Alignment explanation
Indices: 291840--291922 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 30
291830 AACTTGATGA
* * *
291840 AGCATTTGGAAGACACATACAACTTAGTGG
1 AGCATTTGGGAGACACAAACAGCTTAGTGG
* * *
291870 AGCATTTGGGA-AGACAAACAGCTTGGTTG
1 AGCATTTGGGAGACACAAACAGCTTAGTGG
291899 AGCATTTGGGAGACACAAACAGCT
1 AGCATTTGGGAGACACAAACAGCT
291923 CACAAAGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 24 0.53
30 21 0.47
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (30 bp):
AGCATTTGGGAGACACAAACAGCTTAGTGG
Found at i:298276 original size:24 final size:21
Alignment explanation
Indices: 298241--298283 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
298231 GGCACATTCT
*
298241 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
298264 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
298284 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:301572 original size:2 final size:2
Alignment explanation
Indices: 301565--301658 Score: 116
Period size: 2 Copynumber: 47.0 Consensus size: 2
301555 GGATCGTATC
* * * * * *
301565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT TT GT GT GT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
301607 GT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
301649 AT AT AT AT AT
1 AT AT AT AT AT
301659 TGAAAATATT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (2 bp):
AT
Found at i:315241 original size:25 final size:25
Alignment explanation
Indices: 315167--315233 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
315157 AGGTTAACTC
*
315167 TTTTATGAGATTTACTGTAATATGA
1 TTTTATGAGATTTACTGCAATATGA
315192 TTTTATGAGATTTACTGCAATATGA
1 TTTTATGAGATTTACTGCAATATGA
315217 TTTTATGAGATTTACTG
1 TTTTATGAGATTTACTG
315234 GACTATGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCAATATGA
Found at i:320688 original size:12 final size:13
Alignment explanation
Indices: 320663--320687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320653 GGGAAAATGA
320663 AAAAAAATATTTT
1 AAAAAAATATTTT
320676 AAAAAAATATTT
1 AAAAAAATATTT
320688 ATATTGGTGT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAAAATATTTT
Found at i:322658 original size:25 final size:25
Alignment explanation
Indices: 322588--322650 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
322578 CAATTCTTTC
* *
322588 ATGAGATTTAATGCAATATGATTTT
1 ATGAGATTTACTACAATATGATTTT
322613 ATGAGATTTACTACAATATGATTTT
1 ATGAGATTTACTACAATATGATTTT
322638 ATGAGATTTACTA
1 ATGAGATTTACTA
322651 GACTATGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATGAGATTTACTACAATATGATTTT
Found at i:329928 original size:17 final size:19
Alignment explanation
Indices: 329891--329929 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
329881 TTACAAAAGG
329891 ATGTACCGATACACTCCCAT
1 ATGTACCGATACAC-CCCAT
329911 ATGTACCGATA-A-CCCAT
1 ATGTACCGATACACCCCAT
329928 AT
1 AT
329930 TTCGAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (19 bp):
ATGTACCGATACACCCCAT
Found at i:338175 original size:24 final size:24
Alignment explanation
Indices: 338148--338196 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
338138 ATTATTATTT
**
338148 AAAA-TTCTTTCATAAAGCATTTTC
1 AAAATTTC-TTCATAAAAAATTTTC
338172 AAAATTTCTTCATAAAAAATTTTC
1 AAAATTTCTTCATAAAAAATTTTC
338196 A
1 A
338197 CCTTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATTTCTTCATAAAAAATTTTC
Found at i:338341 original size:14 final size:15
Alignment explanation
Indices: 338322--338354 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
338312 GGAAAGAAAA
338322 GCAAAATTT-TTGGG
1 GCAAAATTTGTTGGG
338336 GCAAAATTTGTTGGG
1 GCAAAATTTGTTGGG
338351 GCAA
1 GCAA
338355 GAAGAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (15 bp):
GCAAAATTTGTTGGG
Found at i:338503 original size:13 final size:13
Alignment explanation
Indices: 338485--338510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338475 GTCAAATCGA
338485 AGGCACCAAAAAG
1 AGGCACCAAAAAG
338498 AGGCACCAAAAAG
1 AGGCACCAAAAAG
338511 TAGAATGGTT
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:0.23, T:0.00
Consensus pattern (13 bp):
AGGCACCAAAAAG
Found at i:338609 original size:28 final size:29
Alignment explanation
Indices: 338537--338609 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
338527 ACTAAGCACC
338537 AAATAGTACAGGGACTTTACCACCAAGGTT
1 AAATAGTACAGGGACTTTA-CACCAAGGTT
** * *
338567 AAATAGTGTAGGGACTTT-CACTAAGTTT
1 AAATAGTACAGGGACTTTACACCAAGGTT
*
338595 AAATAGTACATGGAC
1 AAATAGTACAGGGAC
338610 CAAGGACATC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 20 0.56
30 16 0.44
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (29 bp):
AAATAGTACAGGGACTTTACACCAAGGTT
Found at i:342773 original size:25 final size:25
Alignment explanation
Indices: 342745--342807 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
342735 TGGAGACTCC
*
342745 AAATTTAAAATTAAACCAAAATCCA
1 AAATTTAAAATTAAACAAAAATCCA
* * * *
342770 AAATTTCAATTTAAATAAAAATCTA
1 AAATTTAAAATTAAACAAAAATCCA
342795 AATATTTTAAAAT
1 AA-A-TTTAAAAT
342808 AAAATCATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 22 0.76
26 1 0.03
27 6 0.21
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTTAAAATTAAACAAAAATCCA
Found at i:342805 original size:21 final size:24
Alignment explanation
Indices: 342779--342829 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
342769 AAAATTTCAA
342779 TTTAAATA-AAAATC-TAAATA-T
1 TTTAAATATAAAATCATAAATATT
*
342800 TTTAAA-ATAAAATCATAATTATT
1 TTTAAATATAAAATCATAAATATT
342823 TTTAAAT
1 TTTAAAT
342830 TAATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 12 0.48
22 5 0.20
23 7 0.28
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATATAAAATCATAAATATT
Found at i:342810 original size:22 final size:22
Alignment explanation
Indices: 342782--342829 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
342772 ATTTCAATTT
342782 AAATAAAAATC-TAAATATTTTA
1 AAAT-AAAATCATAAATATTTTA
* *
342804 AAATAAAATCATAATTATTTTT
1 AAATAAAATCATAAATATTTTA
342826 AAAT
1 AAAT
342830 TAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAAAATCATAAATATTTTA
Found at i:342973 original size:33 final size:33
Alignment explanation
Indices: 342936--343004 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
342926 GCAACACTTA
342936 TTTTCACTGAAGAGACGAGAGAATAGATTATTC
1 TTTTCACTGAAGAGACGAGAGAATAGATTATTC
342969 TTTTCACTGAAGAGACGAGAGAATAGATTATTC
1 TTTTCACTGAAGAGACGAGAGAATAGATTATTC
343002 TTT
1 TTT
343005 GTAAATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (33 bp):
TTTTCACTGAAGAGACGAGAGAATAGATTATTC
Found at i:343884 original size:112 final size:112
Alignment explanation
Indices: 343571--344283 Score: 966
Period size: 112 Copynumber: 6.3 Consensus size: 112
343561 AACTTTCAAC
* ** * * * *
343571 AAAGTATCGATACATGTACAAAAAGTATCGATACTTTCAACATATCCAGTACCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATT
*
343636 TTTTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
343683 AAAGTACCGATACATTTTTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTATCG
1 AAAGTATCGATACA---TTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCG
* * * *
343748 GTTTTTTCATATTGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
63 ATTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
343798 AAAGTA-CTGATACATTTTTATAAAGTAGCGATACTTTCAACATATCCGATAGCTCTTTATCGAT
1 AAAGTATC-GATACATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGAT
** *
343862 TTTGTTGTAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
343910 AAAGTATCGATA-AATTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTTTTTACC-AGT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGA-T
* **
343973 TTTGTCATAATGAAACTGGTTTTGTTATATTTTTACCAATTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
344021 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATT
* * *
344086 TAGTCATAATGAAAATGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* ** * *
344133 AAAGTATCGATACATGTACA-AAATGTATCGATACTTTTAACATATTCGGTAGCTCTTTACCGAT
1 AAAGTATCGATACATTTTTATAAA-GTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGAT
* * *
344197 TTTGTCATTATGAAACTAGTTTTGTCATATTTTTACATGTTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
344245 TATGTATATCGATACATTTTTATAAAGTATCGATACTTT
1 AAAG--TATCGATACATTTTTATAAAGTATCGATACTTT
344284 ATAGGCGTTA
Statistics
Matches: 533, Mismatches: 56, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
110 1 0.00
111 101 0.19
112 299 0.56
113 1 0.00
114 27 0.05
115 104 0.20
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (112 bp):
AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGATT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:344022 original size:223 final size:222
Alignment explanation
Indices: 343571--344283 Score: 943
Period size: 223 Copynumber: 3.2 Consensus size: 222
343561 AACTTTCAAC
* ** * *
343571 AAAGTATCGATACATGTACAAAAAGTATCGATACTTTCAACATATCC-AGTACCTCTTTACCGGT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGA-TAGCTCTTTACCGGT
* *
343635 TTT-TTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTACCGATACATT
65 TTTGTT-ATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATA-A--
* * * *
343699 TTTTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTATCGGTTTTTTCATATTGAA
126 -ATTTTATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTA-CCGTTTTGTCATAATGAA
*
343764 ACTAGTTTTGTCATATTTTTACCTGTTATATTGT
189 ACTAGTTTTGTCATATTTTTACCAGTTATATTGT
* * *
343798 AAAGTA-CTGATACATTTTTATAAAGTAGCGATACTTTCAACATATCCGATAGCTCTTTATCGAT
1 AAAGTATC-GATACATTTTTATAAAGTATCGATACTTTCAACATATCCGATAGCTCTTTACCGGT
*
343862 TTTGTTGTAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATAAATTT
65 TTTGTTATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATAAATTT
* *
343927 TATAAAGTATCGATACTTTCAACATATCCGGTAGCTTTTTACCAGTTTTGTCATAATGAAACTGG
130 TATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACC-GTTTTGTCATAATGAAACTAG
* *
343992 TTTTGTTATATTTTTACCAATTATATTGT
194 TTTTGTCATATTTTTACCAGTTATATTGT
* *
344021 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGATAGCTCTTTACCGGTT
* * * * *
344086 TAGTCATAATGAAAA-TGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCGATACA-TG
66 TTGTTATAAT-AAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATAAATTT
* * * *
344149 TACAAAATGTATCGATACTTTTAACATATTCGGTAGCTCTTTACCGATTTTGTCATTATGAAACT
130 TA-TAAA-GTATCGATACTTTCAACATATCCGGTAGCTCTTTACCG-TTTTGTCATAATGAAACT
344214 AGTTTTGTCATATTTTTA-CATGTTATATTGT
192 AGTTTTGTCATATTTTTACCA-GTTATATTGT
* *
344245 TATGTATATCGATACATTTTTATAAAGTATCGATACTTT
1 AAAG--TATCGATACATTTTTATAAAGTATCGATACTTT
344284 ATAGGCGTTA
Statistics
Matches: 432, Mismatches: 42, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
222 4 0.01
223 202 0.47
224 83 0.19
226 34 0.08
227 106 0.25
228 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (222 bp):
AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCCGATAGCTCTTTACCGGTT
TTGTTATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATAAATTTT
ATAAAGTATCGATACTTTCAACATATCCGGTAGCTCTTTACCGTTTTGTCATAATGAAACTAGTT
TTGTCATATTTTTACCAGTTATATTGT
Found at i:344221 original size:335 final size:338
Alignment explanation
Indices: 343592--344283 Score: 998
Period size: 335 Copynumber: 2.0 Consensus size: 338
343582 ACATGTACAA
* *
343592 AAAGTATCGATACTTTCAACATATCCAGTACCTCTTTACCGGTTTTTTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCCAGTACCTCTTTACCAGTTTTGTCATAATGAAACTGGTTT
** *
343657 TGTCATATTTTTACCTGTTATATTGTAAAGTACCGATACATTTTTTTTATAAAGTATCGATACTT
66 TGTCATATTTTTACCAATTATATTGTAAAGTACCGATACA--TTTTTTATAAAATATCGATACTT
* ** * * *
343722 TCAACATATCCGGTAGCTCTTTATCGGTTTTTTCATATTGAAACTAGTTTTGTCATATTTTTACC
129 TCAACATATCCGGTAGCTCTTTACCGGTTTAGTCATAATGAAAATAGTTTTGTCATATTTTTACA
* **
343787 TGTTATATTGTAAAGTACTGATACATTTTTATAAAGTAGCGATACTTTCAACATATCCGATAGCT
194 TGTTATATTGTAAAGTACTGATACATGTACATAAAGTAGCGATACTTTCAACATATCCGATAGCT
* ** * *
343852 CTTTATCGATTTTGTTGTAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG-TA
259 CTTTACCGATTTTGTCATAATAAAACTAGTTTTGTCATATTTTTACATGTTATATTGTAAAGATA
343916 TCGATA-AATTTTAT
324 TCGATACAATTTTAT
* * *
343930 AAAGTATCGATACTTTCAACATATCCGGTAGCTTTTTACCAGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCCAGTACCTCTTTACCAGTTTTGTCATAATGAAACTGGTTT
* *
343995 TGTTATATTTTTACCAATTATATTGTAAAGTATCGATACA-TTTTTATAAAATATCGATACTTTC
66 TGTCATATTTTTACCAATTATATTGTAAAGTACCGATACATTTTTTATAAAATATCGATACTTTC
*
344059 AACATATCCGGTAGCTCTTTACCGGTTTAGTCATAATGAAAATGGTTTTGTCATATTTTTACATG
131 AACATATCCGGTAGCTCTTTACCGGTTTAGTCATAATGAAAATAGTTTTGTCATATTTTTACATG
* * * *
344124 TTATATTGTAAAGTA-TCGATACATGTACA-AAATGTATCGATACTTTTAACATATTCGGTAGCT
196 TTATATTGTAAAGTACT-GATACATGTACATAAA-GTAGCGATACTTTCAACATATCCGATAGCT
* * * *
344187 CTTTACCGATTTTGTCATTATGAAACTAGTTTTGTCATATTTTTACATGTTATATTGTTATGTAT
259 CTTTACCGATTTTGTCATAATAAAACTAGTTTTGTCATATTTTTACATGTTATATTGTAAAG-AT
*
344252 ATCGATACATTTTTAT
323 ATCGATACAATTTTAT
344268 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
344284 ATAGGCGTTA
Statistics
Matches: 315, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
334 4 0.01
335 184 0.58
337 8 0.03
338 119 0.38
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (338 bp):
AAAGTATCGATACTTTCAACATATCCAGTACCTCTTTACCAGTTTTGTCATAATGAAACTGGTTT
TGTCATATTTTTACCAATTATATTGTAAAGTACCGATACATTTTTTATAAAATATCGATACTTTC
AACATATCCGGTAGCTCTTTACCGGTTTAGTCATAATGAAAATAGTTTTGTCATATTTTTACATG
TTATATTGTAAAGTACTGATACATGTACATAAAGTAGCGATACTTTCAACATATCCGATAGCTCT
TTACCGATTTTGTCATAATAAAACTAGTTTTGTCATATTTTTACATGTTATATTGTAAAGATATC
GATACAATTTTAT
Found at i:344611 original size:74 final size:74
Alignment explanation
Indices: 344365--344610 Score: 363
Period size: 73 Copynumber: 3.4 Consensus size: 74
344355 CAACATATCT
* * * *
344365 GGTAGATAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC
1 GGTAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
344429 AAAAAAACC
66 AAAAAAACC
* * *
344438 GGTAGGTATTTTAATCTAATAAGTAGCG-CAATTTTTTTTACCATTTACATTATTAGCAACCTTA
1 GGTAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
344502 AAAAAAACAC
66 AAAAAAAC-C
* * *
344512 -GTAGGTATTTTAATGTAATAAGTAGTGCCTATTTTTTTTACCGTTTACATTATTAACAACTTTA
1 GGTAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
344576 AAAAAAACC
66 AAAAAAACC
*
344585 GGTAGGTATTTTAATGTAATAGGTAG
1 GGTAGGTATTTTAATGTAATAAGTAG
344611 TTTAAAATTT
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
72 2 0.01
73 88 0.57
74 65 0.42
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (74 bp):
GGTAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
AAAAAAACC
Found at i:344994 original size:135 final size:135
Alignment explanation
Indices: 344748--345044 Score: 452
Period size: 135 Copynumber: 2.2 Consensus size: 135
344738 ATTACGTTAC
* * * * * *
344748 ATAAGCACTACCTAATATGTTATTATAATTGATAATGTTTCTAGTAATTAACCGGTTATATTATT
1 ATAAGCGCTACCTAATATGTTATTATAATTAATAATATTTCCAGTAATTAACCGATTATATTATC
*
344813 CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAATAAATTAAGTAATTAACCTATTTT
66 CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTT
344878 ATTAT
131 ATTAT
* ** *
344883 ATAAGCGCTACCTAATATGTTATTGTGCTTAATAATATTTCCAGTAATTAACCGATTATGTTATC
1 ATAAGCGCTACCTAATATGTTATTATAATTAATAATATTTCCAGTAATTAACCGATTATATTATC
344948 CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTT
66 CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTT
345013 ATTAT
131 ATTAT
* * * *
345018 ATAAACGCTATCTATTACGTTA-TATAA
1 ATAAGCGCTACCTAATATGTTATTATAA
345045 GTACTACCTA
Statistics
Matches: 144, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
134 2 0.01
135 142 0.99
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (135 bp):
ATAAGCGCTACCTAATATGTTATTATAATTAATAATATTTCCAGTAATTAACCGATTATATTATC
CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTT
ATTAT
Found at i:345100 original size:158 final size:158
Alignment explanation
Indices: 344879--345394 Score: 772
Period size: 158 Copynumber: 3.3 Consensus size: 158
344869 ACCTATTTTA
* * * *
344879 TTATATAAGCGCTACCTAATATGTTATTGTGCTTAATAATATTTCCAGTAATTAACCGATTATGT
1 TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACTGGTTATGT
344944 TATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTA
66 TATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTA
345009 TTTTATTATATAAACGCTATCTATTACG
131 TTTTATTATATAAACGCTATCTATTACG
** * *
345037 TTATATAAGTACTACCTAATATGTTATTGTGTTTGATAATGTTTTCAGTAATTAACTGGTTATGT
1 TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACTGGTTATGT
* * *
345102 TATCCTTGGTAACATTTTAGGCGTTTATCTAATATGTTGTAATAACAAATTAAATAATTAACATA
66 TATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTA
* *
345167 TTTTATTATATAAGCGTTATCTATTACG
131 TTTTATTATATAAACGCTATCTATTACG
*
345195 TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCGGTAATTAA-TCGGTTATG
1 TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACT-GGTTATG
*
345259 TTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTATAATAACAAATTAAG----TAACCT
65 TTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCT
* * * *
345320 ATTTTATTATATAATCGCTACCCATTACA
130 ATTTTATTATATAAACGCTATCTATTACG
* * ** *
345349 TTATATAAGCGCTACCTAATATATTATTATATTTGATAATATTTCC
1 TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCC
345395 GGTTAAATGA
Statistics
Matches: 325, Mismatches: 32, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
154 70 0.22
157 1 0.00
158 254 0.78
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (158 bp):
TTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACTGGTTATGT
TATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTA
TTTTATTATATAAACGCTATCTATTACG
Found at i:345220 original size:23 final size:23
Alignment explanation
Indices: 345172--345221 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
345162 ACATATTTTA
* * *
345172 TTATATAAGCGTTATCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
345195 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
345218 TTAT
1 TTAT
345222 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:345374 original size:23 final size:23
Alignment explanation
Indices: 345324--345375 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
345314 TAACCTATTT
* *
345324 TATTATATAATCGCTACCCATTA
1 TATTATATAAGCGCTACCCAATA
* *
345347 CATTATATAAGCGCTACCTAATA
1 TATTATATAAGCGCTACCCAATA
345370 TATTAT
1 TATTAT
345376 TATATTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TATTATATAAGCGCTACCCAATA
Found at i:349862 original size:16 final size:15
Alignment explanation
Indices: 349843--349896 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
349833 ATATATATGT
*
349843 TTTATAGTTTATATA
1 TTTATACTTTATATA
349858 CTTTATACTTTATATA
1 -TTTATACTTTATATA
* *
349874 TTTACACACTTATATA
1 TTTATAC-TTTATATA
349890 TTATATA
1 TT-TATA
349897 TATTCTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 6 0.19
16 23 0.72
17 3 0.09
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTATACTTTATATA
Found at i:349889 original size:2 final size:2
Alignment explanation
Indices: 349884--349946 Score: 57
Period size: 2 Copynumber: 34.0 Consensus size: 2
349874 TTTACACACT
* *
349884 TA TA TA T- TA TA TA TA T- TC T- TA TA TA TG TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
349923 TA T- TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
349947 AGTATAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 6 0.12
2 45 0.87
3 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:349924 original size:60 final size:60
Alignment explanation
Indices: 349782--349937 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
349772 TATACTTATA
* * * * *
349782 TTTTATAGTTTACATGCTTTATACTTCATATATATACACACTTTTATATATATATATATG
1 TTTTATAGTATATATACTTTATACTTTATATATATACACACTTATATATATATATATATG
* *
349842 TTTTATAGTTTATATACTTTATACTTTATATATTTACACACTTATATAT-TATATATAT-
1 TTTTATAGTATATATACTTTATACTTTATATATATACACACTTATATATATATATATATG
349900 TCTTATATATGTATATATAC-TTATA-TTATATATATATA
1 T-TT-TATA-GTATATATACTTTATACTT-TATATATATA
349938 TATATTATAA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.01
59 13 0.15
60 62 0.73
61 9 0.11
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (60 bp):
TTTTATAGTATATATACTTTATACTTTATATATATACACACTTATATATATATATATATG
Found at i:352299 original size:24 final size:24
Alignment explanation
Indices: 352268--352321 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
352258 TTTTCTCTAT
*
352268 TTTGAAATACAATGTTTGATCTGA
1 TTTGAAATACAATGTTTCATCTGA
352292 TTTGAAATACAATGTTTCATCTGA
1 TTTGAAATACAATGTTTCATCTGA
352316 TTTGAA
1 TTTGAA
352322 TACTGTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTGAAATACAATGTTTCATCTGA
Found at i:356093 original size:135 final size:135
Alignment explanation
Indices: 355832--356095 Score: 336
Period size: 135 Copynumber: 2.0 Consensus size: 135
355822 TGATCGACCA
* * * *
355832 TTGACTTTGACCAAAAAGTAAAGTTTTTTGAAAAGTCATATTTTATGTTTTTCGACGTCCTGAGT
1 TTGACATTGACAAAAAAGTAAAATTTTTTGAAAAGTCATATTTTAAGTTTTTCGACGTCCTGAGT
** * * * *
355897 CTGATTCCGAAATTTGTTTTTCCAAATTCAAAACCGAAAGCCTCCAAATTATCAGTCAAACCCGT
66 CTGATTCCGAAATCCGTTTTGCAAAATTCAAAACCGAAAGCCTACAAATTACCAGTCAAACCCGT
355962 TGACT
131 TGACT
* *
355967 TTGACATTGACAAAAAAG-ACAAATTTTTTGAAAAGTTATATTTTAAGTTTTTCGATGTCCTGAG
1 TTGACATTGACAAAAAAGTA-AAATTTTTTGAAAAGTCATATTTTAAGTTTTTCGACGTCCTGAG
* * * *
356031 TCTGATTCC-AAAGTCCGTTTTGCAAAATTCAAACCCGAAAGGCTACGAATTGACCCGT-AAACC
65 TCTGATTCCGAAA-TCCGTTTTGCAAAATTCAAAACCGAAAGCCTACAAATT-ACCAGTCAAACC
356094 CG
128 CG
356096 CAAAATGTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
134 4 0.04
135 102 0.93
136 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (135 bp):
TTGACATTGACAAAAAAGTAAAATTTTTTGAAAAGTCATATTTTAAGTTTTTCGACGTCCTGAGT
CTGATTCCGAAATCCGTTTTGCAAAATTCAAAACCGAAAGCCTACAAATTACCAGTCAAACCCGT
TGACT
Found at i:360090 original size:135 final size:135
Alignment explanation
Indices: 359934--360177 Score: 364
Period size: 135 Copynumber: 1.8 Consensus size: 135
359924 ACCATTGAAT
* ** *
359934 TTGACCAAAAAGTTAAATTTTTTGAAAAGTCATATTTTATGTTTTTCAATGTCCTTG-GTCTGAT
1 TTGACAAAAAAGACAAATTTTTTGAAAAGTCATATTTTAAGTTTTTCAATGTCC-TGAGTCTGAT
* *
359998 TCCGAAGTCCGTTTTTCCAAATTCAAAACCGAAAGCCTCCAAATTATCAGTCAAACCTGTTGACT
65 TCCAAAGTCCGTTTTGCCAAATTCAAAACCGAAAGCCTCCAAATTATCAGTCAAACCTGTTGACT
360063 TTGACA
130 TTGACA
* **
360069 TTGACAAAAAAGACAAATTTTTTGAAAAGTTATATTTTAAGTTTTTCGTTGTCCTGAGTCTGATT
1 TTGACAAAAAAGACAAATTTTTTGAAAAGTCATATTTTAAGTTTTTCAATGTCCTGAGTCTGATT
* * *
360134 CTAAAGTCCGTTTTGCCAAATTCAAAACCGAAAGGCTCCGAATT
66 CCAAAGTCCGTTTTGCCAAATTCAAAACCGAAAGCCTCCAAATT
360178 GACCCGTAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
134 2 0.02
135 94 0.98
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (135 bp):
TTGACAAAAAAGACAAATTTTTTGAAAAGTCATATTTTAAGTTTTTCAATGTCCTGAGTCTGATT
CCAAAGTCCGTTTTGCCAAATTCAAAACCGAAAGCCTCCAAATTATCAGTCAAACCTGTTGACTT
TGACA
Found at i:361939 original size:128 final size:129
Alignment explanation
Indices: 361766--362010 Score: 296
Period size: 129 Copynumber: 1.9 Consensus size: 129
361756 GACTTTAACT
* ** ** *
361766 GTTGACTTTGACCAAAAAGTTAAATTTTTTGAAAAGTCATATTTTA-CGTTTTTGACGTCCTCAG
1 GTTGACTTTGACCAAAAAGTCAAAAGTTTTGAAAAGTCATATTTTATCGTTTTCAACGACCTCAG
* * *
361830 TCCGATTCTGAA-GTCCGTTTTTCCAAATTCAAACCTGAAAGCCTCCAAATTGTCAGTCAAACCC
66 TCCGATTC-CAATGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTGTCAGTCAAACCC
** * * * * *
361894 GTTGACTTTGATTAAAAAGTCAAAAGTTTTGAAAAGTTATTTTTTATGGTTTTCAATGACCTGAG
1 GTTGACTTTGACCAAAAAGTCAAAAGTTTTGAAAAGTCATATTTTATCGTTTTCAACGACCTCAG
* * *
361959 TCTGATTCCAATGTCTGTTTTGCCAAATTCAAACCCGAAAGCCTCCGAATTG
66 TCCGATTCCAATGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTG
362011 ACATATAAAC
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
128 41 0.43
129 55 0.57
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (129 bp):
GTTGACTTTGACCAAAAAGTCAAAAGTTTTGAAAAGTCATATTTTATCGTTTTCAACGACCTCAG
TCCGATTCCAATGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTGTCAGTCAAACCC
Found at i:366088 original size:130 final size:129
Alignment explanation
Indices: 365856--366097 Score: 308
Period size: 130 Copynumber: 1.9 Consensus size: 129
365846 TAACCGTTGA
*
365856 CTTTGACAAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATACTTTTTGACGTCTTGTGTCCGA
1 CTTTGACAAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATACTTTTTGACGTCTTGAGTCCGA
** * *
365921 TTCTGAAGTCCGTTTTTCCAAATTCGAACCCAAAAGCCTCCAAATTGTCAGTCAAACCCATTGG
66 TTCCAAAGTCCGTTTTGCCAAATTCAAACCCAAAAGCCTCCAAATTGTCAGTCAAACCCATTGG
* * * *
365985 CTTTGACAAAAAAATTCAAAATTTTTGAAAAGTTATATTTTAT-GTTTTTCGATGT-TCTGAGTC
1 CTTTGAC-AAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATACTTTTT-GACGTCT-TGAGTC
* * *** *
366048 TGATTCCAAAGTCTGTTTTGCCAAATTCAAACTGGAAAGCCTCCTAATTG
63 CGATTCCAAAGTCCGTTTTGCCAAATTCAAACCCAAAAGCCTCCAAATTG
366098 ACCTGTAAAC
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
129 13 0.14
130 82 0.86
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (129 bp):
CTTTGACAAAAAAGTCAAAATTTTTGAAAAGTCATATTTTATACTTTTTGACGTCTTGAGTCCGA
TTCCAAAGTCCGTTTTGCCAAATTCAAACCCAAAAGCCTCCAAATTGTCAGTCAAACCCATTGG
Found at i:367213 original size:22 final size:22
Alignment explanation
Indices: 367185--367245 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
367175 GTAACAAAGT
367185 AGGTTGAACCCTATTATAAACG
1 AGGTTGAACCCTATTATAAACG
* *
367207 AGGTTGAACCCTATTATGAATG
1 AGGTTGAACCCTATTATAAACG
*
367229 AGGTTGAACCATATTAT
1 AGGTTGAACCCTATTAT
367246 TGGAGGATCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (22 bp):
AGGTTGAACCCTATTATAAACG
Found at i:367313 original size:55 final size:55
Alignment explanation
Indices: 367229--367355 Score: 245
Period size: 55 Copynumber: 2.3 Consensus size: 55
367219 ATTATGAATG
*
367229 AGGTTGAACCATATTATTGGAGGATCCAACCAATAACTATATTGAGTAACAAAGT
1 AGGTTGAACCCTATTATTGGAGGATCCAACCAATAACTATATTGAGTAACAAAGT
367284 AGGTTGAACCCTATTATTGGAGGATCCAACCAATAACTATATTGAGTAACAAAGT
1 AGGTTGAACCCTATTATTGGAGGATCCAACCAATAACTATATTGAGTAACAAAGT
367339 AGGTTGAACCCTATTAT
1 AGGTTGAACCCTATTAT
367356 GAACGAGGTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (55 bp):
AGGTTGAACCCTATTATTGGAGGATCCAACCAATAACTATATTGAGTAACAAAGT
Found at i:380832 original size:59 final size:59
Alignment explanation
Indices: 380769--381623 Score: 1307
Period size: 59 Copynumber: 14.5 Consensus size: 59
380759 ATGGCACTGA
* * * *
380769 GTGTGCAAAAATGTTAAGAAATTCATGCTAAGTGTATCAATTTCCGTATTGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
380828 GTGTGCTAAAATGTTATGAAATTCATACTAAGTGTATCAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * * **
380887 GTGTGCTAAAATGTTATGAAATTCATACTAAGTGTATAAATTTCCTTATTCGATACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* ** * *
380946 GTGTGATAAAATGTTAAGAAATTCATACT-CTTAGTATGAATTTTCGTATTGGGAACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGT-GTATGAATTTCCGTATTGGGCACTTT
* *
381005 GTGTGCTAAAATGTTAAGAAATTCATACTAACTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
381064 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTTTGAATTTCCGCATTGGGTACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
381123 GTGTGCTAAAATGTTAAGAAATTGATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
381182 GTGTGCTAAAATGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
381241 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* ** * * *
381300 GTGTGCTAAAGTGTTAAGAAATTCATTTTACGTGTATGAATTTCCTTATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
381359 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* ** *
381418 GTGCGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTAGTATTGGTCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
381477 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGAACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * * *
381536 GTGTGCTAAAATATTAAGAAATTTATACTAAGTGTATAAATTTCTGTATTGGGTACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
381595 GTGTGCTAAAATGTTAAGAAATGCATACT
1 GTGTGCTAAAATGTTAAGAAATTCATACT
381624 TATAAATTTT
Statistics
Matches: 727, Mismatches: 67, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
58 1 0.00
59 725 1.00
60 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:380974 original size:31 final size:31
Alignment explanation
Indices: 380882--380974 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 31
380872 CGTATTGGGC
* *
380882 ACTTTGTGTGCTAAAATGTTATGAAATTCAT
1 ACTTTGTGTGATAAAATGTTAAGAAATTCAT
** ****
380913 ACTAAGTGT-AT-AAAT-TT-CCTTATTCGAT
1 ACTTTGTGTGATAAAATGTTAAGAAATTC-AT
380941 ACTTTGTGTGATAAAATGTTAAGAAATTCAT
1 ACTTTGTGTGATAAAATGTTAAGAAATTCAT
380972 ACT
1 ACT
380975 CTTAGTATGA
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
27 4 0.09
28 11 0.25
29 6 0.14
30 5 0.11
31 14 0.32
32 4 0.09
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (31 bp):
ACTTTGTGTGATAAAATGTTAAGAAATTCAT
Done.