Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007706.1 Hibiscus syriacus cultivar Beakdansim tig00109921_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: 338066
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:10536 original size:26 final size:26
Alignment explanation
Indices: 10500--10551 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10490 TATATAAAAG
10500 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
10526 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
10552 GAACTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TTAAATTTGATTAAATTCGAGTATGT
Found at i:12225 original size:16 final size:15
Alignment explanation
Indices: 12200--12229 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12190 TGAGAGGCTG
12200 AATTAAGCTTAACTA
1 AATTAAGCTTAACTA
12215 AATTGAAGCTTAACT
1 AATT-AAGCTTAACT
12230 GGTTTCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTAAGCTTAACTA
Found at i:18217 original size:16 final size:16
Alignment explanation
Indices: 18196--18227 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18186 TGACTTTGAC
18196 CAAAAAGTCAAATTTT
1 CAAAAAGTCAAATTTT
*
18212 CAAAAAGTCATATTTT
1 CAAAAAGTCAAATTTT
18228 ATGTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (16 bp):
CAAAAAGTCAAATTTT
Found at i:20244 original size:43 final size:43
Alignment explanation
Indices: 20183--20271 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
20173 AATCGGTATC
20183 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
20226 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
20269 TCT
1 TCT
20272 CCTGAACTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (43 bp):
TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
Found at i:24010 original size:24 final size:24
Alignment explanation
Indices: 23956--24010 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
23946 AATGTGCCAT
*
23956 GGATTTACGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
23980 GGATTTTCGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
24004 GGATTTT
1 GGATTTT
24011 GTATGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (24 bp):
GGATTTTCGTAGATGAAACCATCA
Found at i:29066 original size:228 final size:227
Alignment explanation
Indices: 28665--29112 Score: 783
Period size: 228 Copynumber: 2.0 Consensus size: 227
28655 GTAAATTATC
* * *
28665 TATCTTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTAGTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTAGTATTATATTTAGT
*
28730 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
28795 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
28859 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
28892 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTAGTATTATATTTAG
*
28957 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
*
29021 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
29086 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
29113 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
227 38 0.18
228 145 0.69
229 27 0.13
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTAGTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:29200 original size:20 final size:19
Alignment explanation
Indices: 29177--29222 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
29167 CGATATACCA
29177 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
29197 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
29217 GGTAAA
1 GGTAAA
29223 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29367 original size:20 final size:19
Alignment explanation
Indices: 29344--29390 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
29334 CGATATAACA
29344 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
29364 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
29384 GGTAAAA
1 GGTAAAA
29391 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29392 original size:17 final size:18
Alignment explanation
Indices: 29348--29395 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
29338 ATAACAGGTA
29348 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
29367 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
29387 -AAAATGATA
1 AAAAATGATA
29396 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:32142 original size:3 final size:3
Alignment explanation
Indices: 32134--32208 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
32124 TGAAGCTGAC
* * * ** * *
32134 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
32182 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
32209 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:33741 original size:183 final size:183
Alignment explanation
Indices: 33406--33914 Score: 821
Period size: 183 Copynumber: 2.8 Consensus size: 183
33396 CAAAGTTTTC
* * * * * **
33406 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAGAGTTGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * *
33471 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGACAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
33534 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
33590 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
33655 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
33720 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
33773 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCG--A-CATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
33835 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
33900 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
33915 GTGTCGATAC
Statistics
Matches: 306, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
180 84 0.27
181 1 0.00
183 149 0.49
184 69 0.23
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:33844 original size:18 final size:18
Alignment explanation
Indices: 33817--33853 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
33807 AGATTGGAAG
*
33817 AAAAATGTGTCGACATTT
1 AAAAAAGTGTCGACATTT
33835 AAAAAAGTGTCGACATTT
1 AAAAAAGTGTCGACATTT
33853 A
1 A
33854 CACATCGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (18 bp):
AAAAAAGTGTCGACATTT
Found at i:37107 original size:23 final size:23
Alignment explanation
Indices: 37076--37139 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
37066 ATAGGTAAAC
*
37076 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
37099 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
37122 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
37140 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:37146 original size:23 final size:23
Alignment explanation
Indices: 37076--37148 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
37066 ATAGGTAAAC
* **
37076 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
37099 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
37122 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
37145 ATAT
1 ATAT
37149 TTAGTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:37773 original size:21 final size:19
Alignment explanation
Indices: 37727--37774 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
37717 ATAAAAACAA
37727 ACAAACAAAATATTAAAAAT
1 ACAAAC-AAATATTAAAAAT
**
37747 TTAAACAAATATTAATTAAAT
1 ACAAACAAATATTAA--AAAT
37768 ACAAACA
1 ACAAACA
37775 CTTCAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (19 bp):
ACAAACAAATATTAAAAAT
Found at i:38841 original size:24 final size:24
Alignment explanation
Indices: 38814--38859 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
38804 TAAAATTAGA
38814 AATTGAAGGTACATAAATATTTGG
1 AATTGAAGGTACATAAATATTTGG
* *
38838 AATTGAAGTTATATAAATATTT
1 AATTGAAGGTACATAAATATTT
38860 TATAATATTA
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:0.02, G:0.15, T:0.39
Consensus pattern (24 bp):
AATTGAAGGTACATAAATATTTGG
Found at i:57637 original size:22 final size:23
Alignment explanation
Indices: 57593--57637 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
57583 ATATATCAAA
* *
57593 TTTATGGAATCCTTTTTAGGGTT
1 TTTATGGAATCCTTTCTAAGGTT
*
57616 TTTA-GGATTCCTTTCTAAGGTT
1 TTTATGGAATCCTTTCTAAGGTT
57638 AAAGGTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (23 bp):
TTTATGGAATCCTTTCTAAGGTT
Found at i:76070 original size:17 final size:16
Alignment explanation
Indices: 76042--76090 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
76032 TCAAGCAAAA
*
76042 TTTTTATTTTTATTTG
1 TTTTTTTTTTTATTTG
76058 TTTATTTTTTTTAATTTG
1 TTT-TTTTTTTT-ATTTG
*
76076 TTTTTTATTTTATTT
1 TTTTTTTTTTTATTT
76091 TTATTCTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTATTTG
Found at i:80954 original size:25 final size:25
Alignment explanation
Indices: 80919--80978 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
80909 AAACCAAAAA
*
80919 GGGTGGTCCAATAACACATTATAGT
1 GGGTGGACCAATAACACATTATAGT
80944 GGGTGGACCAATAACACATTATAGT
1 GGGTGGACCAATAACACATTATAGT
80969 GGGTGGACCA
1 GGGTGGACCA
80979 TTAAGGTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (25 bp):
GGGTGGACCAATAACACATTATAGT
Found at i:81589 original size:14 final size:15
Alignment explanation
Indices: 81570--81598 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
81560 ACACATGATG
81570 ATAATAAT-ATAAAA
1 ATAATAATAATAAAA
81584 ATAATAATAATAAAA
1 ATAATAATAATAAAA
81599 TTAGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAATAATAAAA
Found at i:82219 original size:31 final size:31
Alignment explanation
Indices: 82175--82241 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
82165 TACAATATAA
* *
82175 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
82206 TCCCTCAACATTTAGTCCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
82237 TCCCT
1 TCCCT
82242 GGTGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCATTTGCAATATGG
Found at i:85762 original size:30 final size:29
Alignment explanation
Indices: 85722--85781 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
85712 TCTAATGAAA
*
85722 ATGATGATTTTGGAACATATAAATAGTCAG
1 ATGATCATTTTGGAA-ATATAAATAGTCAG
* * *
85752 ATGATCATTTTGTAATTTTAAATAGTCAG
1 ATGATCATTTTGGAAATATAAATAGTCAG
85781 A
1 A
85782 GGGCTTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (29 bp):
ATGATCATTTTGGAAATATAAATAGTCAG
Found at i:92260 original size:2 final size:2
Alignment explanation
Indices: 92253--92293 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
92243 GTATACATAG
* *
92253 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AA AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
92294 TACATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.44, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:92274 original size:18 final size:18
Alignment explanation
Indices: 92247--92293 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
92237 TTTATAGTAT
*
92247 ACATAGACACACACACAC
1 ACATACACACACACACAC
92265 ACATACACACACACACAC
1 ACATACACACACACACAC
*
92283 ACAAACACACA
1 ACATACACACA
92294 TACATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.53, C:0.40, G:0.02, T:0.04
Consensus pattern (18 bp):
ACATACACACACACACAC
Found at i:96696 original size:22 final size:21
Alignment explanation
Indices: 96664--96706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
96654 ATTCTTAAAG
* *
96664 TTATAAGATAATTATTAGAATA
1 TTATAAAATAATCATTA-AATA
96686 TTATAAAATAATCATTAAATA
1 TTATAAAATAATCATTAAATA
96707 CATTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
TTATAAAATAATCATTAAATA
Found at i:104526 original size:19 final size:19
Alignment explanation
Indices: 104502--104538 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
104492 CCTCCAAACA
104502 TGTGCAAGGTACCCTTAAC
1 TGTGCAAGGTACCCTTAAC
104521 TGTGCAAGGTACCCTTAA
1 TGTGCAAGGTACCCTTAA
104539 ATGTCCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (19 bp):
TGTGCAAGGTACCCTTAAC
Found at i:105526 original size:12 final size:12
Alignment explanation
Indices: 105509--105533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105499 TGCGATTTTC
105509 CATTTCGCGTTG
1 CATTTCGCGTTG
105521 CATTTCGCGTTG
1 CATTTCGCGTTG
105533 C
1 C
105534 GATAGTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (12 bp):
CATTTCGCGTTG
Found at i:105599 original size:20 final size:20
Alignment explanation
Indices: 105574--105646 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
105564 TAGTCTACAG
105574 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
105594 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
*
105615 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
105635 TCGCGTTGCGAT
1 TCGCGTTGCGAT
105647 AGTCTACAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:105690 original size:41 final size:40
Alignment explanation
Indices: 105556--105674 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 40
105546 TCGCAATTCG
*
105556 CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTC
1 CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTCCATTTC
* *
105596 GCGTTGCGATAGT-TGA-AATTCGCGTTACGATTTTCCATTTC
1 -CGTTGCGATAGTCT-ACAGTT-GCGTTGCGATTTTCCATTTC
105637 GCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 -CGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTCCA
105675 AATTCGTTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.04
41 47 0.69
42 18 0.26
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTCCATTTC
Found at i:105779 original size:6 final size:6
Alignment explanation
Indices: 105768--105793 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
105758 GACACGTATT
105768 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
105794 GGCGGCGGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:106286 original size:6 final size:6
Alignment explanation
Indices: 106265--106331 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
106255 GTCCGTCCCG
106265 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
106311 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
106332 AATGGTAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.16
6 51 0.84
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:106337 original size:6 final size:6
Alignment explanation
Indices: 106328--106382 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
106318 GTCGTGGTCG
106328 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
106376 TGGTAA T
1 TGGTAA T
106383 ACGTGTCTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:106337 original size:12 final size:12
Alignment explanation
Indices: 106275--106373 Score: 72
Period size: 12 Copynumber: 8.2 Consensus size: 12
106265 GGTCGGGTCG
**
106275 GGTCGTGGTCGT
1 GGTCGTGGTAAT
**
106287 GGTCGTGGTCGT
1 GGTCGTGGTAAT
**
106299 GGTCGTGGTCGT
1 GGTCGTGGTAAT
**
106311 GGTCGTGGTCGT
1 GGTCGTGGTAAT
106323 GGTCGTGGTAAT
1 GGTCGTGGTAAT
**
106335 GGTAATGGTAAT
1 GGTCGTGGTAAT
**
106347 GGTAATGGTAAT
1 GGTCGTGGTAAT
**
106359 GGTAATGGTAAT
1 GGTCGTGGTAAT
106371 GGT
1 GGT
106374 AATGGTAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 83 1.00
ACGTcount: A:0.14, C:0.09, G:0.43, T:0.33
Consensus pattern (12 bp):
GGTCGTGGTAAT
Found at i:106520 original size:20 final size:20
Alignment explanation
Indices: 106495--106560 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
106485 TAGACTATCG
106495 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGGAAAATCA
** ** * *
106515 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAA-AATCA
106536 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGGAAAATCA
106556 CAACG
1 CAACG
106561 TGATTTTCAA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCA
Found at i:106533 original size:41 final size:41
Alignment explanation
Indices: 106488--106588 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
106478 ACAACTGTAG
106488 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
*
106529 ACTATCGCAACGCGAAATGGAAAATCACAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
106570 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
106589 CAACGTGAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
Found at i:106592 original size:21 final size:21
Alignment explanation
Indices: 106488--106592 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
106478 ACAACTGTAG
*
106488 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
106509 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
106529 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * * ** *
106550 A-AATCACAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGCA
106570 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
106591 AC
1 AC
106593 GTGAATTTGT
Statistics
Matches: 57, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:106644 original size:20 final size:20
Alignment explanation
Indices: 106621--106726 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
106611 AGATCGCGTT
*
106621 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
106641 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
106661 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
106682 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
106702 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
106723 GCGA
1 GCGA
106727 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:106678 original size:41 final size:41
Alignment explanation
Indices: 106628--106730 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
106618 GTTGCGATTT
*
106628 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
106669 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
106710 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
106731 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:106734 original size:21 final size:21
Alignment explanation
Indices: 106628--106734 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
106618 GTTGCGATTT
106628 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
106649 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
106669 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
106690 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
106710 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
106731 CAAC
1 CAAC
106735 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:106754 original size:142 final size:142
Alignment explanation
Indices: 106488--106759 Score: 456
Period size: 142 Copynumber: 1.9 Consensus size: 142
106478 ACAACTGTAG
* *
106488 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
* * *
106553 TCACAACGTGATTTTCAACTATCGCAACGCGAAATGCAACGTGAATTTGTGATGATGGAGATCGC
66 ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGTGAATTTGCGATGATGGAGATCGC
106618 GTTGCGATTTCA
131 GTTGCGATTTCA
*
106630 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
* *
106695 ACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGAT-AGTGGAGATCG
66 ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGTGAATTTGCGATGA-TGGAGATCG
106759 C
130 C
106760 AATGCGAATT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
141 1 0.01
142 120 0.99
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (142 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGTGAATTTGCGATGATGGAGATCGC
GTTGCGATTTCA
Found at i:115885 original size:31 final size:31
Alignment explanation
Indices: 115825--115884 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
115815 TAGTAACATC
* *
115825 ATCGATAAATGAGAATGAATTTTTAAAAATT
1 ATCGATAAATGAGAATAAATTTATAAAAATT
*
115856 ATCGATAAATTAGAATAAATTTAATAAAA
1 ATCGATAAATGAGAATAAATTT-ATAAAA
115885 TCGATGACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.33
Consensus pattern (31 bp):
ATCGATAAATGAGAATAAATTTATAAAAATT
Found at i:117178 original size:20 final size:20
Alignment explanation
Indices: 117153--117199 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
117143 TTTCCAAATT
*
117153 TCGCAACGCGAATATGTAAA
1 TCGCAACGAGAATATGTAAA
* *
117173 TCGCAAAGATAATATGTAAA
1 TCGCAACGAGAATATGTAAA
117193 TCGCAAC
1 TCGCAAC
117200 ACGGTTTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGAGAATATGTAAA
Found at i:117613 original size:57 final size:57
Alignment explanation
Indices: 117192--117606 Score: 537
Period size: 57 Copynumber: 7.3 Consensus size: 57
117182 TAATATGTAA
* * * ** **
117192 ATCGCAACACGGTTTTCCAAAATCGCAACGCTGATTACCGATGTAGGTAAACAAAACT
1 ATCGCAACACGATTTT-CAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
* * *
117250 ATCACAACACGATTTTCAAATTCGCAACGCTAATTATCGATATAGGTAAACAGTACT
1 ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
*
117307 ATCGCAACGA-GATTTTCAAATTTGCAACGCTAATTACCGACATAGGTAAACAGTACT
1 ATCGCAAC-ACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
* * * * *
117364 ATCGCAACGCGATTTACAAATTCGCAACGTTAAGTACCGACATAGGTAAGCAGTACT
1 ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
* * * *
117421 ATCTCAACGCGATTTTCAAATTCGCAACGCTAATTACCGACATGGGTAAACAGAACT
1 ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
* * * *
117478 ATCGCAACGCGATTTACAAATTCGCAACGCTGATTACCGACATAGGTAAACAATACT
1 ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
** * *
117535 ATCGCAATGCGATTTACAAATTCGCAACGCTAATTACCGACATATGT-AACAGTACT
1 ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
*
117591 ATCACAACACGATTTT
1 ATCGCAACACGATTTT
117607 GGAAATTGTG
Statistics
Matches: 316, Mismatches: 39, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
56 20 0.06
57 281 0.89
58 15 0.05
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (57 bp):
ATCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGACATAGGTAAACAGTACT
Found at i:117625 original size:20 final size:20
Alignment explanation
Indices: 117600--117702 Score: 95
Period size: 20 Copynumber: 5.2 Consensus size: 20
117590 TATCACAACA
*
117600 CGATTTTGGAAATTGTGTTG
1 CGATTTTAGAAATTGTGTTG
* *
117620 CGA-TTTACAAATTCGCGTTG
1 CGATTTTAGAAATT-GTGTTG
* *
117640 CGATTTTTGAAACTGTGTTG
1 CGATTTTAGAAATTGTGTTG
* *
117660 CGA-TTTACAAATTTGCGTTG
1 CGATTTTAGAAA-TTGTGTTG
117680 CGATTTTAG-AATATGTGTTG
1 CGATTTTAGAAAT-TGTGTTG
117700 CGA
1 CGA
117703 AATTAGAGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 15 0.23
20 39 0.60
21 11 0.17
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (20 bp):
CGATTTTAGAAATTGTGTTG
Found at i:117657 original size:40 final size:39
Alignment explanation
Indices: 117600--117702 Score: 152
Period size: 40 Copynumber: 2.6 Consensus size: 39
117590 TATCACAACA
*
117600 CGATTTTGGAAATTGTGTTGCGATTTACAAATTCGCGTTG
1 CGATTTTAGAAA-TGTGTTGCGATTTACAAATTCGCGTTG
* *
117640 CGATTTTTGAAACTGTGTTGCGATTTACAAATTTGCGTTG
1 CGATTTTAGAAA-TGTGTTGCGATTTACAAATTCGCGTTG
117680 CGATTTTAGAATATGTGTTGCGA
1 CGATTTTAGAA-ATGTGTTGCGA
117703 AATTAGAGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (39 bp):
CGATTTTAGAAATGTGTTGCGATTTACAAATTCGCGTTG
Found at i:117708 original size:20 final size:20
Alignment explanation
Indices: 117685--117723 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
117675 CGTTGCGATT
117685 TTAGAATAT-GTGTTGCGAAA
1 TTAGAAT-TCGTGTTGCGAAA
*
117705 TTAGAGTTCGTGTTGCGAA
1 TTAGAATTCGTGTTGCGAA
117724 TTTGTTGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (20 bp):
TTAGAATTCGTGTTGCGAAA
Found at i:118802 original size:20 final size:20
Alignment explanation
Indices: 118777--118822 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
118767 TTAAAAAAGC
118777 TAAAATCCCTTTTTCATATT
1 TAAAATCCCTTTTTCATATT
118797 TAAAATCCCTTTTTCATATT
1 TAAAATCCCTTTTTCATATT
118817 TAAAAT
1 TAAAAT
118823 ACATAACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATCCCTTTTTCATATT
Found at i:119156 original size:18 final size:18
Alignment explanation
Indices: 119114--119168 Score: 85
Period size: 18 Copynumber: 3.0 Consensus size: 18
119104 ATTATATTGT
119114 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAAT-A
119134 AAGATTACCAGGGGAATA
1 AAGATTACCAGGGGAATA
119152 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
119169 GGATTACTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.20
18 11 0.31
19 6 0.17
20 11 0.31
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.18
Consensus pattern (18 bp):
AAGATTACCAGGGGAATA
Found at i:125864 original size:23 final size:23
Alignment explanation
Indices: 125823--125895 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 23
125813 CACACATTTT
* *
125823 TAATAATTTTGATACTTTTTGTAA
1 TAATAATTTTTATAATTTTT-TAA
*
125847 T-ATATTTTTTATAA-TTTTTAA
1 TAATAATTTTTATAATTTTTTAA
*
125868 TAATAATTTTTATAATTTATTTTA
1 TAATAATTTTTATAATTT-TTTAA
125892 TAAT
1 TAAT
125896 TTCCAAAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 12 0.29
24 9 0.22
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (23 bp):
TAATAATTTTTATAATTTTTTAA
Found at i:125882 original size:12 final size:12
Alignment explanation
Indices: 125838--125883 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
125828 ATTTTGATAC
*
125838 TTTTTGTAATATA
1 TTTTTATAATA-A
125851 TTTTT-T-ATAA
1 TTTTTATAATAA
125861 TTTTTAATAATAA
1 TTTTT-ATAATAA
125874 TTTTTATAAT
1 TTTTTATAAT
125884 TTATTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.20
11 3 0.10
12 7 0.23
13 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTTATAATAA
Found at i:127001 original size:25 final size:24
Alignment explanation
Indices: 126952--127017 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
126942 TTTTACCGTA
** *
126952 TATCGTATTA-TAATTTTATAAGT
1 TATCGTATTATTAAAATTAGAAGT
*
126975 TA-CTTATTAATTAATAATTAGAAGT
1 TATCGTATT-ATTAA-AATTAGAAGT
127000 TATCGTATTATTAAAATT
1 TATCGTATTATTAAAATT
127018 TCTTCAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 7 0.21
25 14 0.41
26 5 0.15
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (24 bp):
TATCGTATTATTAAAATTAGAAGT
Found at i:140858 original size:17 final size:17
Alignment explanation
Indices: 140836--140879 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
140826 ATCATTTAAA
140836 ATAAAAAAATCAAAAAT
1 ATAAAAAAATCAAAAAT
140853 ATAAAAAAATCAAAAAT
1 ATAAAAAAATCAAAAAT
140870 ATAAAAAAAT
1 ATAAAAAAAT
140880 ATGAATTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAAAAAAATCAAAAAT
Found at i:140859 original size:9 final size:8
Alignment explanation
Indices: 140833--140880 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
140823 ATCATCATTT
140833 AAAATAAA
1 AAAATAAA
140841 AAAATCAAA
1 AAAAT-AAA
*
140850 AATATAAA
1 AAAATAAA
140858 AAAATCAAA
1 AAAAT-AAA
*
140867 AATATAAA
1 AAAATAAA
140875 AAAATA
1 AAAATA
140881 TGAATTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 20 0.59
9 14 0.41
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:146536 original size:21 final size:21
Alignment explanation
Indices: 146512--146577 Score: 60
Period size: 27 Copynumber: 2.9 Consensus size: 21
146502 AGACCATAAG
146512 AATACTTTCTCCATCCAAATT
1 AATACTTTCTCCATCCAAATT
* *
146533 AATACTTCTACTATCAACGTCAAAATT
1 AATACTT-T-C--TC--CATCCAAATT
146560 AATACTTTCTCCATCCAA
1 AATACTTTCTCCATCCAA
146578 GATACCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
21 12 0.34
22 1 0.03
23 3 0.09
25 3 0.09
26 1 0.03
27 15 0.43
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (21 bp):
AATACTTTCTCCATCCAAATT
Found at i:154817 original size:1 final size:1
Alignment explanation
Indices: 154811--154840 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
154801 AGTTTTGGAT
154811 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
154841 CAAGTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:160096 original size:29 final size:29
Alignment explanation
Indices: 160054--160112 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
160044 TACACAAATG
*
160054 GTCAGCCGACTACA-ATGTGTTGTTTTGTT
1 GTCAGCCGACTACATA-GTATTGTTTTGTT
160083 GTCAGCCGACTACATAGTATTGTTTTGTT
1 GTCAGCCGACTACATAGTATTGTTTTGTT
160112 G
1 G
160113 GATCTCTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (29 bp):
GTCAGCCGACTACATAGTATTGTTTTGTT
Found at i:173838 original size:2 final size:2
Alignment explanation
Indices: 173831--173872 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
173821 TGAAATGATC
173831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173873 GTGTGTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175105 original size:12 final size:12
Alignment explanation
Indices: 175088--175117 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
175078 GCGAGGTGGC
175088 CATACGGGGTGA
1 CATACGGGGTGA
*
175100 CATACGGGTTGA
1 CATACGGGGTGA
175112 CATACG
1 CATACG
175118 AGCCATACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (12 bp):
CATACGGGGTGA
Found at i:175154 original size:35 final size:35
Alignment explanation
Indices: 175112--175199 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
175102 TACGGGTTGA
175112 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
*
175147 CATACGAGCCATACGAACCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
175182 CATACGAGCCATACGAGC
1 CATACGAGCCATACGAGC
175200 GTTCTCCCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.18
Consensus pattern (35 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
Found at i:175222 original size:26 final size:26
Alignment explanation
Indices: 175186--175241 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
175176 CCCATGCATA
175186 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
175212 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
175238 CGAG
1 CGAG
175242 GTGGCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.18
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:175311 original size:29 final size:29
Alignment explanation
Indices: 175272--175409 Score: 190
Period size: 29 Copynumber: 4.8 Consensus size: 29
175262 TGGAATAGAG
*
175272 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-AGGCGACCTTGT
* *
175301 AGGTCGCCATGTGGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCAGGCGACCTTGT
*
175330 AGGTCGCCATGTGGTCCCA-GCGACCTTGT
1 AGGTCGCCATGTAGT-CCAGGCGACCTTGT
*
175359 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCAGGCGACCTTGT
*
175388 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCAGGCG
175410 CCATTCCCAT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
28 2 0.02
29 94 0.94
30 4 0.04
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCAGGCGACCTTGT
Found at i:175428 original size:13 final size:13
Alignment explanation
Indices: 175410--175441 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
175400 AGTCCCGGCG
175410 CCATTCCCATCAT
1 CCATTCCCATCAT
175423 CCATTCCCATCAT
1 CCATTCCCATCAT
175436 CCATTC
1 CCATTC
175442 ACATGCAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.47, G:0.00, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:175602 original size:100 final size:100
Alignment explanation
Indices: 175429--175631 Score: 379
Period size: 100 Copynumber: 2.0 Consensus size: 100
175419 TCATCCATTC
* *
175429 CCATCATCCATTCACATGCAGCCATATATATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCC
1 CCATCATCCATTCACATGCAGCCATATAGATTCCTTCACATGCTCCCCGCTGCATGCTGCATGCC
175494 TACAGCTCCCAATGAAACCATGTGAACCATTTGAG
66 TACAGCTCCCAATGAAACCATGTGAACCATTTGAG
*
175529 CCATCATCCATTCACATGCAGCCATATAGATTCCTTCACATGCTCCTCGCTGCATGCTGCATGCC
1 CCATCATCCATTCACATGCAGCCATATAGATTCCTTCACATGCTCCCCGCTGCATGCTGCATGCC
175594 TACAGCTCCCAATGAAACCATGTGAACCATTTGAG
66 TACAGCTCCCAATGAAACCATGTGAACCATTTGAG
175629 CCA
1 CCA
175632 ATGCATGAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.26
Consensus pattern (100 bp):
CCATCATCCATTCACATGCAGCCATATAGATTCCTTCACATGCTCCCCGCTGCATGCTGCATGCC
TACAGCTCCCAATGAAACCATGTGAACCATTTGAG
Found at i:175738 original size:25 final size:25
Alignment explanation
Indices: 175709--175785 Score: 154
Period size: 25 Copynumber: 3.1 Consensus size: 25
175699 TGTACAATTA
175709 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
175734 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
175759 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
175784 TT
1 TT
175786 ATAAAAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.26
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:175826 original size:23 final size:23
Alignment explanation
Indices: 175798--175843 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
175788 AAAAGAAAGA
*
175798 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGAAGAAGAGATTGCAG
175821 AAGAAAGGAAGAAGAGATTGCAG
1 AAGAAAGGAAGAAGAGATTGCAG
175844 CCGAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.37, T:0.09
Consensus pattern (23 bp):
AAGAAAGGAAGAAGAGATTGCAG
Found at i:175857 original size:25 final size:23
Alignment explanation
Indices: 175798--175858 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
175788 AAAAGAAAGA
**
175798 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
175821 AAGAAAGGAAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
175844 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
175859 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 22 0.67
25 11 0.33
ACGTcount: A:0.52, C:0.07, G:0.34, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:176145 original size:45 final size:45
Alignment explanation
Indices: 176042--176173 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
176032 TACATAAATT
*
176042 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
176084 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
176128 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
176174 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:176374 original size:15 final size:14
Alignment explanation
Indices: 176356--176387 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
176346 AGTTATTAGT
176356 TTATTATATTATAAG
1 TTATTATATTA-AAG
176371 TTATTATATTAAAG
1 TTATTATATTAAAG
176385 TTA
1 TTA
176388 GTGTTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:179170 original size:26 final size:24
Alignment explanation
Indices: 179112--179170 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
179102 CTAATAAACC
*
179112 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
179136 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
179164 TAATAAT
1 TAATAAT
179171 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:179996 original size:28 final size:30
Alignment explanation
Indices: 179956--180018 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
179946 ATTTTTTATA
*
179956 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
179986 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
180014 TAATA
1 TAATA
180019 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:180025 original size:28 final size:28
Alignment explanation
Indices: 179960--180025 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
179950 TTTATATAAT
*
179960 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
179988 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
180016 ATAATTTATA
1 ATAATATATA
180026 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:180028 original size:21 final size:21
Alignment explanation
Indices: 179995--180043 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
179985 CTAATATAAT
179995 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
180016 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
180037 ATTAACT
1 A-TAACT
180044 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:180623 original size:15 final size:15
Alignment explanation
Indices: 180603--180681 Score: 113
Period size: 15 Copynumber: 5.1 Consensus size: 15
180593 CCATCCCCTC
180603 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
180618 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
180633 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
180648 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
180666 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
180681 C
1 C
180682 GTCCCATGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
15 32 0.56
16 12 0.21
17 12 0.21
18 1 0.02
ACGTcount: A:0.18, C:0.54, G:0.08, T:0.20
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:180675 original size:33 final size:33
Alignment explanation
Indices: 180576--180689 Score: 153
Period size: 33 Copynumber: 3.5 Consensus size: 33
180566 GAGGAAGGTT
*
180576 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATG---CATCCCCTCCCCCATGCA
* *
180612 TTCCCAC--CCCATGCATTCCC-ACCCCATGCA
1 TTCCCACGTCCCATGCATCCCCTCCCCCATGCA
180642 TTCCCACGTCCCATGCATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATGCATCCCCTCCCCCATGCA
180675 TTCCCACGTCCCATG
1 TTCCCACGTCCCATG
180690 TTGATTGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
30 16 0.23
31 6 0.09
32 12 0.17
33 24 0.34
34 5 0.07
36 7 0.10
ACGTcount: A:0.18, C:0.53, G:0.09, T:0.21
Consensus pattern (33 bp):
TTCCCACGTCCCATGCATCCCCTCCCCCATGCA
Found at i:182717 original size:6 final size:6
Alignment explanation
Indices: 182706--183422 Score: 1402
Period size: 6 Copynumber: 119.8 Consensus size: 6
182696 TTGGTAGCAT
182706 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
182754 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
182802 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
182850 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
*
182898 ATACAC ATACAC ATACAC ATACAC AT--AC ATACAC ATACAT ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
182944 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
182992 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183040 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
*
183088 ATATAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183136 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183184 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183232 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183280 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183328 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
183376 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
183423 GTTGTCGTGT
Statistics
Matches: 705, Mismatches: 4, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
4 4 0.01
6 701 0.99
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
ATACAC
Found at i:183740 original size:21 final size:21
Alignment explanation
Indices: 183708--183752 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
183698 CAATATTGGT
*
183708 ATTTAATTAATTTAGA-TAAA
1 ATTTAATGAATTTAGATTAAA
*
183728 ATTTCAATGAATTTATATTAAA
1 ATTT-AATGAATTTAGATTAAA
183750 ATT
1 ATT
183753 AATATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTAATGAATTTAGATTAAA
Found at i:185263 original size:22 final size:22
Alignment explanation
Indices: 185235--185279 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
185225 ATTTAAAGGT
185235 CTACATATGGACACTTTTTGGC
1 CTACATATGGACACTTTTTGGC
185257 CTACATATGGACACTTTTTGGC
1 CTACATATGGACACTTTTTGGC
185279 C
1 C
185280 CACACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (22 bp):
CTACATATGGACACTTTTTGGC
Found at i:185567 original size:2 final size:2
Alignment explanation
Indices: 185560--185595 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
185550 ATCGATATTG
185560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185596 CAGTTCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190617 original size:6 final size:6
Alignment explanation
Indices: 190606--190669 Score: 92
Period size: 6 Copynumber: 10.7 Consensus size: 6
190596 CATCTGCCTG
* *
190606 CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA CCCTCA CCCTCA
1 CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA CCCTTA
* *
190654 CCCTCA CCCTCA CCCT
1 CCCTTA CCCTTA CCCT
190670 GTATTTCACA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.27
Consensus pattern (6 bp):
CCCTTA
Found at i:199271 original size:15 final size:15
Alignment explanation
Indices: 199251--199280 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
199241 ATTGTTTTAT
199251 TATTAATCATTTAAA
1 TATTAATCATTTAAA
*
199266 TATTAATTATTTAAA
1 TATTAATCATTTAAA
199281 CACAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATCATTTAAA
Found at i:217417 original size:35 final size:35
Alignment explanation
Indices: 217371--217482 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
217361 AAAACAGTCC
* *
217371 TCAATTTCATTCTAAACCCCAATTTCCAAATTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
217406 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
217441 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
217476 TCAATTT
1 TCAATTT
217483 AAGGTTTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:218650 original size:51 final size:51
Alignment explanation
Indices: 218549--218652 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
218539 TATTTAATTG
** * *
218549 AAGGCGCGTCCCCGGGGATGCGGGTCCCACACGTGGCAGTCGAGCTAGCGA
1 AAGGCGCGTCCCCGGGGATGCGCCTCCCACACGTGGCAGTCCAACTAGCGA
*
218600 AAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGGCA-TCCAACTCAGCGA
1 AAGGCGCGTCCCCGGGGATGCGCCTCCCACACGTGGCAGTCCAACT-AGCGA
218651 AA
1 AA
218653 ACACAGGTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 5 0.11
51 42 0.89
ACGTcount: A:0.20, C:0.34, G:0.34, T:0.12
Consensus pattern (51 bp):
AAGGCGCGTCCCCGGGGATGCGCCTCCCACACGTGGCAGTCCAACTAGCGA
Found at i:219009 original size:2 final size:2
Alignment explanation
Indices: 219002--219032 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
218992 GATTTTAACT
219002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
219033 TAAAATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:220487 original size:20 final size:19
Alignment explanation
Indices: 220464--220505 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
220454 TCGCAACTCA
220464 ATTTCCAAATTCGCGTTGCG
1 ATTTCC-AATTCGCGTTGCG
*
220484 ATTTTCCATTTCGCGTTGCG
1 A-TTTCCAATTCGCGTTGCG
220504 AT
1 AT
220506 AGTCCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 14 0.70
21 5 0.25
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (19 bp):
ATTTCCAATTCGCGTTGCG
Found at i:220511 original size:20 final size:20
Alignment explanation
Indices: 220473--220511 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
220463 AATTTCCAAA
**
220473 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAT
220493 TTCGCGTTGCGATAGTCCA
1 TTCGCGTTGCGATAGTCCA
220512 AAATCGCAAC
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:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCCAT
Found at i:220526 original size:41 final size:42
Alignment explanation
Indices: 220481--220569 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
220471 AATTCGCGTT
* *
220481 GCGATTTTCCAT-TTCG-CGTTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCCATATT-GACATTGCGACAGTCCAAAATCGCAAC
*
220522 GCGA-TTTGCATATTGACATTGCGACAGTCCAAAATCGCAAC
1 GCGATTTTCCATATTGACATTGCGACAGTCCAAAATCGCAAC
220563 GCGATTT
1 GCGATTT
220570 GCAGATTCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 7 0.17
41 33 0.79
42 2 0.05
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (42 bp):
GCGATTTTCCATATTGACATTGCGACAGTCCAAAATCGCAAC
Found at i:221095 original size:41 final size:41
Alignment explanation
Indices: 221036--221181 Score: 150
Period size: 41 Copynumber: 3.8 Consensus size: 41
221026 AGACTTAAGG
*
221036 TTTTGGACTATCGTAATGCGAATCTGAAAATCGCATTGCGA
1 TTTTGGACTATCGCAATGCGAATCTGAAAATCGCATTGCGA
* *
221077 TTTTGGACTATCGCAATGCGAATCTGCAAATCGCAATGC-A
1 TTTTGGACTATCGCAATGCGAATCTGAAAATCGCATTGCGA
* * *
221117 ------A--ATCGCAACGCGAAAT-GGAAAATCGCGTTGCGA
1 TTTTGGACTATCGCAATGCG-AATCTGAAAATCGCATTGCGA
*
221150 TTTTGGACTATCGCAATGTGAATCTGAAAATC
1 TTTTGGACTATCGCAATGCGAATCTGAAAATC
221182 TTCGCAATAC
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
32 21 0.25
33 4 0.05
34 1 0.01
39 1 0.01
40 4 0.05
41 52 0.63
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (41 bp):
TTTTGGACTATCGCAATGCGAATCTGAAAATCGCATTGCGA
Found at i:221112 original size:20 final size:20
Alignment explanation
Indices: 221045--221124 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
221035 GTTTTGGACT
* *
221045 ATCGTAATGCGAATCTGAAA
1 ATCGCAATGCGAATCTGCAA
* * * * *
221065 ATCGCATTGCGATTTTGGACT
1 ATCGCAATGCGAATCTGCA-A
221086 ATCGCAATGCGAATCTGCAA
1 ATCGCAATGCGAATCTGCAA
*
221106 ATCGCAATGCAAATC-GCAA
1 ATCGCAATGCGAATCTGCAA
221125 CGCGAAATGG
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 4 0.09
20 28 0.60
21 15 0.32
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGCAA
Found at i:221173 original size:73 final size:77
Alignment explanation
Indices: 221061--221237 Score: 236
Period size: 73 Copynumber: 2.3 Consensus size: 77
221051 ATGCGAATCT
* *
221061 GAAAATCGCATTGCGATTTTGGACTATCGCAATGCGAATCTGCAAA-TCG-C-AA-TGCAAATCG
1 GAAAATCGCGTTGCGATTTTGGACTATCGCAATGCGAATCTGAAAATTCGACGAACTGCAAATCG
221122 CAACGCGAAATG
66 CAACGCGAAATG
*
221134 GAAAATCGCGTTGCGATTTTGGACTATCGCAATGTGAATCTGAAAATCTTCGCAATACGAATCTG
1 GAAAATCGCGTTGCGATTTTGGACTATCGCAATGCGAATCTGAAAA--TTCG----ACGAA-CTG
221199 CAAATCGCAACGCGAAATG
59 CAAATCGCAACGCGAAATG
221218 GAAAATCGCGTTGCGATTTT
1 GAAAATCGCGTTGCGATTTT
221238 ATCGCCGACT
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
73 43 0.48
76 3 0.03
81 1 0.01
82 2 0.02
84 41 0.46
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (77 bp):
GAAAATCGCGTTGCGATTTTGGACTATCGCAATGCGAATCTGAAAATTCGACGAACTGCAAATCG
CAACGCGAAATG
Found at i:221195 original size:23 final size:23
Alignment explanation
Indices: 221160--221204 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
221150 TTTTGGACTA
**
221160 TCGCAATGTGAATCTGAAAATCT
1 TCGCAATACGAATCTGAAAATCT
*
221183 TCGCAATACGAATCTGCAAATC
1 TCGCAATACGAATCTGAAAATC
221205 GCAACGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
TCGCAATACGAATCTGAAAATCT
Found at i:222017 original size:184 final size:183
Alignment explanation
Indices: 221682--222048 Score: 725
Period size: 184 Copynumber: 2.0 Consensus size: 183
221672 AACACAAGTC
221682 CTTGCCGGAAAACCAGCCGGACTTTTCTACAGCACCGGCGGCCAAGGAAGTGGACAAGACTACCG
1 CTTGCCGGAAAACCAGCCGGACTTTTCTACAGCACCGGCGGCCAAGGAAGTGGACAAGACTACCG
221747 CGTGAGTAAATTGCAAAGTATCAAAATCAGTAACTGTAGTATAATTTGTGATTGTGAACATTTTT
66 CGTGAGTAAATTGCAAAGTATCAAAATCAGTAACTGTAGTATAATTTGTGATTGTGAACATTTTT
221812 GTTTTGGCAGGCTAACTGCAATCACTCAACTTGTTCACCATGGTATGCTTTTT
131 GTTTTGGCAGGCTAACTGCAATCACTCAACTTGTTCACCATGGTATGCTTTTT
221865 CTTGCCGGAAAACCAGCCGGACTTTTCTACAGCACCGGCGGCCAAGGAAGTGGACAAGACTACCG
1 CTTGCCGGAAAACCAGCCGGACTTTTCTACAGCACCGGCGGCCAAGGAAGTGGACAAGACTACCG
221930 CGTGAGTAAATTTGCAAAGTATCAAAATCAGTAACTGTAGTATAATTTGTGATTGTGAACATTTT
66 CGTGAGTAAA-TTGCAAAGTATCAAAATCAGTAACTGTAGTATAATTTGTGATTGTGAACATTTT
221995 TGTTTTGGCAGGCTAACTGCAATCACTCAACTTGTTCACCATGGTATGCTTTTT
130 TGTTTTGGCAGGCTAACTGCAATCACTCAACTTGTTCACCATGGTATGCTTTTT
222049 GTGCCCATCG
Statistics
Matches: 183, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 75 0.41
184 108 0.59
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (183 bp):
CTTGCCGGAAAACCAGCCGGACTTTTCTACAGCACCGGCGGCCAAGGAAGTGGACAAGACTACCG
CGTGAGTAAATTGCAAAGTATCAAAATCAGTAACTGTAGTATAATTTGTGATTGTGAACATTTTT
GTTTTGGCAGGCTAACTGCAATCACTCAACTTGTTCACCATGGTATGCTTTTT
Found at i:223656 original size:28 final size:27
Alignment explanation
Indices: 223605--223666 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
223595 TTATGCATAA
* *
223605 TATATATA-TTTAAAATTATGTTTATTT
1 TATA-ATACTTTAAAATTATATTTAATT
*
223632 TTTAATACTTTACAAATTATATTTAATT
1 TATAATACTTTA-AAATTATATTTAATT
223660 TATAATA
1 TATAATA
223667 TATATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 7 0.24
28 19 0.66
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (27 bp):
TATAATACTTTAAAATTATATTTAATT
Found at i:223692 original size:18 final size:18
Alignment explanation
Indices: 223649--223720 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
223639 CTTTACAAAT
*
223649 TATATTTAATTTATAATA
1 TATATTTAATTTTTAATA
223667 TATATTTAATTTTTAATA
1 TATATTTAATTTTTAATA
*
223685 GTA-GTTTAGTATTTTTAATATA
1 -TATATTTA--ATTTTT-A-ATA
223707 TATATTTAATTTTT
1 TATATTTAATTTTT
223721 TAGTGATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 21 0.47
19 2 0.04
20 12 0.27
21 3 0.07
22 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TATATTTAATTTTTAATA
Found at i:223742 original size:20 final size:18
Alignment explanation
Indices: 223694--223753 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 18
223684 AGTAGTTTAG
*
223694 TATTTTTAATATATATATTT
1 TATTTTTAGTAT-T-TATTT
*
223714 AATTTTTTAGTGATTTAGTTT
1 TA-TTTTTAGT-ATTTA-TTT
223735 TATTTTTAGTATTTATTT
1 TATTTTTAGTATTTATTT
223753 T
1 T
223754 TTGAATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 11 0.32
21 12 0.35
22 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
TATTTTTAGTATTTATTT
Found at i:223748 original size:19 final size:19
Alignment explanation
Indices: 223717--223753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
223707 TATATTTAAT
223717 TTTTTAGTGATTTAGTTTTA
1 TTTTTAGTGATTTA-TTTTA
223737 TTTTTAGT-ATTTATTTT
1 TTTTTAGTGATTTATTTT
223754 TTGAATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTTAGTGATTTATTTTA
Found at i:227694 original size:2 final size:2
Alignment explanation
Indices: 227689--227743 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
227679 TCTCTCTCTG
* * * *
227689 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227731 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
227744 GTATGTGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229111 original size:15 final size:15
Alignment explanation
Indices: 229093--229122 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
229083 TAAACTTATT
229093 AAAAATAAAATTAAA
1 AAAAATAAAATTAAA
*
229108 AAAAATACAATTAAA
1 AAAAATAAAATTAAA
229123 TTTAAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATAAAATTAAA
Found at i:229219 original size:23 final size:23
Alignment explanation
Indices: 229189--229242 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
229179 AAAAAATTAC
* *
229189 TAATTTAGATTGTTATGGTGAAA
1 TAATTTAGAATGTTAAGGTGAAA
229212 TAATTTAGAATGTTAAGGTGAAA
1 TAATTTAGAATGTTAAGGTGAAA
229235 TAATTTAG
1 TAATTTAG
229243 GAATTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (23 bp):
TAATTTAGAATGTTAAGGTGAAA
Found at i:229281 original size:2 final size:2
Alignment explanation
Indices: 229274--229300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
229264 ATATAAAATA
229274 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
229301 AAAGAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229440 original size:22 final size:22
Alignment explanation
Indices: 229415--229481 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
229405 AAAAAATCAT
229415 ATATTTCTATTATAAATATTCA
1 ATATTTCTATTATAAATATTCA
*
229437 ATATTTCTATTATAAATATTCG
1 ATATTTCTATTATAAATATTCA
229459 ATATTTCTATTAT-AATATTCA
1 ATATTTCTATTATAAATATTCA
229480 AT
1 AT
229482 TTTTATGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
21 9 0.21
22 34 0.79
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATTTCTATTATAAATATTCA
Found at i:229596 original size:2 final size:2
Alignment explanation
Indices: 229589--229613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
229579 CAAAATTTTA
229589 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
229614 ATTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:232943 original size:67 final size:68
Alignment explanation
Indices: 232784--232985 Score: 361
Period size: 67 Copynumber: 3.0 Consensus size: 68
232774 TAGGGATTTT
* *
232784 TTTAGGGTAAACTACCTATTTGGTTACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTG
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
232849 TTA
66 TTA
* *
232852 TTTAGGGTAAACTATCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGG-CACTCCATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
232916 TTA
66 TTA
232919 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
232984 TT
66 TT
232986 TTATTTCAAA
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
67 64 0.50
68 63 0.50
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:233109 original size:32 final size:32
Alignment explanation
Indices: 233073--233165 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
233063 ACATGATATT
233073 TTTTTTAATTATGTTTGGATGTTGGACTAACA
1 TTTTTTAATTATGTTTGGATGTTGGACTAACA
233105 TTTTTTAATTATGTTTGGATGTTGGACTAACA
1 TTTTTTAATTATGTTTGGATGTTGGACTAACA
* *
233137 TTTTTTAATTATGTTTGGATATTGAACTA
1 TTTTTTAATTATGTTTGGATGTTGGACTA
233166 TGTAATTCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (32 bp):
TTTTTTAATTATGTTTGGATGTTGGACTAACA
Found at i:233797 original size:13 final size:13
Alignment explanation
Indices: 233779--233810 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
233769 AAAAGTGGAC
233779 AATACATATCGAA
1 AATACATATCGAA
*
233792 AATACATGTCGAA
1 AATACATATCGAA
233805 AATACA
1 AATACA
233811 ATCTAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (13 bp):
AATACATATCGAA
Found at i:237715 original size:2 final size:2
Alignment explanation
Indices: 237708--237768 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
237698 AATTATTGAT
237708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237750 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
237769 TATCCTAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243327 original size:12 final size:12
Alignment explanation
Indices: 243298--243386 Score: 67
Period size: 12 Copynumber: 7.3 Consensus size: 12
243288 AATTATTAAC
243298 ATATTTAA-AAT
1 ATATTTAATAAT
*
243309 ATATTTACTAAT
1 ATATTTAATAAT
*
243321 ATTTTTAATAAT
1 ATATTTAATAAT
*
243333 ATAATATAATAAT
1 AT-ATTTAATAAT
*
243346 ATTATTACAATAAT
1 A-TATT-TAATAAT
* *
243360 ATACTCAAT--T
1 ATATTTAATAAT
243370 ATATTATAATAAT
1 ATATT-TAATAAT
243383 ATAT
1 ATAT
243387 GATACTATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
10 5 0.08
11 10 0.16
12 19 0.31
13 19 0.31
14 8 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:243561 original size:23 final size:21
Alignment explanation
Indices: 243534--243589 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
243524 TAGTCTAATA
243534 ATATTATAAAAATTCCTTAAAAT
1 ATATTATAAAAATT--TTAAAAT
*
243557 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
243580 ATAATATAAA
1 ATATTATAAA
243590 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 3 0.11
25 7 0.25
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:245706 original size:6 final size:6
Alignment explanation
Indices: 245695--245746 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
245685 TTTTTGTTTA
245695 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
245743 TATG
1 TATG
245747 TATGTGTGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (6 bp):
TATGCG
Found at i:248560 original size:20 final size:20
Alignment explanation
Indices: 248522--248560 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
248512 TTTAAGTAAT
* * *
248522 AAAATAATATTTTCGATAAA
1 AAAATAACATTTACAATAAA
248542 AAAATAACATTTACAATAA
1 AAAATAACATTTACAATAA
248561 TATATTTTCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAATAACATTTACAATAAA
Found at i:250134 original size:45 final size:45
Alignment explanation
Indices: 250085--250183 Score: 159
Period size: 43 Copynumber: 2.3 Consensus size: 45
250075 TAGGAATGAT
250085 AATAATAATTTTTCGAATGATCTACGATGATTATAAGACGGTATA
1 AATAATAATTTTTCGAATGATCTACGATGATTATAAGACGGTATA
* *
250130 AAT-A-AATTTTTCGAATGATCTAGGATGATTATAAGACGGTATT
1 AATAATAATTTTTCGAATGATCTACGATGATTATAAGACGGTATA
250173 AA-AATAATTTT
1 AATAATAATTTT
250184 CAATCATTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
43 40 0.80
44 7 0.14
45 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (45 bp):
AATAATAATTTTTCGAATGATCTACGATGATTATAAGACGGTATA
Found at i:251963 original size:2 final size:2
Alignment explanation
Indices: 251914--251945 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
251904 TAACAAAGTA
251914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251946 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258863 original size:21 final size:21
Alignment explanation
Indices: 258839--258887 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
258829 GCGTTGCATT
258839 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
258860 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
258881 TCGCGTT
1 TCGCGTT
258888 ACGGTTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:258949 original size:19 final size:19
Alignment explanation
Indices: 258925--258972 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
258915 TCTACAGTTG
258925 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
258944 TCGTTGCGATTTTCTAAAT
1 TCGTTGCGATTTTCCAAAT
258963 TCGTTGCGAT
1 TCGTTGCGAT
258973 AGTCTATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:258978 original size:19 final size:19
Alignment explanation
Indices: 258904--258978 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
258894 TTCCATTTCG
*
258904 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTA-A-AT-T
** *
258926 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTAAATT
**
258945 CGTTGCGATTTTCTAAATT
1 CGTTGCGATAGTCTAAATT
258964 CGTTGCGATAGTCTA
1 CGTTGCGATAGTCTA
258979 TAGTTGTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 32 0.70
20 1 0.02
21 1 0.02
22 12 0.26
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCTAAATT
Found at i:259843 original size:2 final size:2
Alignment explanation
Indices: 259836--259861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
259826 AAGAGAAAGC
259836 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
259862 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263544 original size:2 final size:2
Alignment explanation
Indices: 263537--263576 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
263527 CTATTTTTAA
263537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263577 GTTTTGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265100 original size:19 final size:19
Alignment explanation
Indices: 265076--265116 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
265066 AAAAACAAAA
*
265076 TTCCCGGTTTTTTCCGGTT
1 TTCCCGGTTTTTTCCGATT
265095 TTCCCGGTTTTTTCCGATT
1 TTCCCGGTTTTTTCCGATT
265114 TTC
1 TTC
265117 AGTCGGTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.27, G:0.17, T:0.54
Consensus pattern (19 bp):
TTCCCGGTTTTTTCCGATT
Found at i:266571 original size:157 final size:157
Alignment explanation
Indices: 266285--266597 Score: 608
Period size: 157 Copynumber: 2.0 Consensus size: 157
266275 ATAAATATGA
266285 GTCGATGAGGAGAATATATATTTAGTGGCGGAGTCAATTTGTGTAATATTTCTACCTTAAATTTC
1 GTCGATGAGGAGAATATATATTTAGTGGCGGAGTCAATTTGTGTAATATTTCTACCTTAAATTTC
266350 GAATTTTCTCTTTACAATTATATGTTTTCTTTTTCTATTATACTTGCTCTGAAATTTTATTTAAG
66 GAATTTTCTCTTTACAATTATATGTTTTCTTTTTCTATTATACTTGCTCTGAAATTTTATTTAAG
*
266415 TGCACCCCACATATAAAATTTATGTGG
131 TACACCCCACATATAAAATTTATGTGG
*
266442 GTCGATGAGGAGAATATATATTTAGTGGCGGAGTCAATTTGTGTAATATTTCTACCTTAAATTTT
1 GTCGATGAGGAGAATATATATTTAGTGGCGGAGTCAATTTGTGTAATATTTCTACCTTAAATTTC
266507 GAATTTTCTCTTTACAATTATATGTTTTCTTTTTCTATTATACTTGCTCTGAAATTTTATTTAAG
66 GAATTTTCTCTTTACAATTATATGTTTTCTTTTTCTATTATACTTGCTCTGAAATTTTATTTAAG
266572 TACACCCCACATATAAAATTTATGTG
131 TACACCCCACATATAAAATTTATGTG
266598 TTGTTAATAT
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.44
Consensus pattern (157 bp):
GTCGATGAGGAGAATATATATTTAGTGGCGGAGTCAATTTGTGTAATATTTCTACCTTAAATTTC
GAATTTTCTCTTTACAATTATATGTTTTCTTTTTCTATTATACTTGCTCTGAAATTTTATTTAAG
TACACCCCACATATAAAATTTATGTGG
Found at i:266861 original size:2 final size:2
Alignment explanation
Indices: 266854--266881 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
266844 CAAATTAATA
266854 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
266882 GTATGTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273225 original size:2 final size:2
Alignment explanation
Indices: 273218--273307 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
273208 TGACAATTTG
273218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
273260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
273302 AT AT AT
1 AT AT AT
273308 GTTACTTTTG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.