Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 97 of 205
Found at i:28349225 original size:60 final size:59
Alignment explanation
Indices: 28349110--28349322 Score: 178
Period size: 60 Copynumber: 3.5 Consensus size: 59
28349100 TGGTGGTTTT
* * * * *
28349110 GGTGGTGGTGGAGGCACTGGTGGAGGAGGTGGT-TTAGGTGGG-GGTGCTGGTGGAGGCTTT
1 GGTGGTGGTGGAGG-ACTGGTGGAGGTGGTGGTCTT-GG-GGGTGGTGCGGGAGGAGGATTA
* * *
28349170 GGTGGTGGTGGAGGGCTAGGTGGCGGTGGTGGTCTTGGGGGTGGTGGGGGAGGAGGATTA
1 GGTGGTGGTGGAGGACT-GGTGGAGGTGGTGGTCTTGGGGGTGGTGCGGGAGGAGGATTA
* * * * * * * *
28349230 GGTGGTGGAGGAGGTCTTGGGGGTGGTGGAGGCCTAGGTGGTGGTGCGGGAGGAGGATTA
1 GGTGGTGGTGGAGGAC-TGGTGGAGGTGGTGGTCTTGGGGGTGGTGCGGGAGGAGGATTA
* * * *
28349290 GGTGGTGGAGGTGGTCTTGGTGGAGGTGCTGGT
1 GGTGGTGGTGGAGGAC-TGGTGGAGGTGGTGGT
28349323 GGTGGAGTTG
Statistics
Matches: 126, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
59 5 0.04
60 118 0.94
61 3 0.02
ACGTcount: A:0.10, C:0.06, G:0.59, T:0.25
Consensus pattern (59 bp):
GGTGGTGGTGGAGGACTGGTGGAGGTGGTGGTCTTGGGGGTGGTGCGGGAGGAGGATTA
Found at i:28349294 original size:78 final size:78
Alignment explanation
Indices: 28349212--28349378 Score: 210
Period size: 78 Copynumber: 2.1 Consensus size: 78
28349202 TCTTGGGGGT
* * * * *
28349212 GGTGGGGGAGGAGGAT-TAGGTGGTGGAGGAGGTCTTGGGGGTGGTGGAGGCCTAGGTGGTGGTG
1 GGTGGTGGAGGAGG-TCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTG
28349276 CGGGAGGAGGATTA
65 CGGGAGGAGGATTA
* * * * * * *
28349290 GGTGGTGGAGGTGGTCTTGGTGGAGGTGCTGGTGGTGGAGTTGGTGGAGGCCTGGGTGGTGGTGC
1 GGTGGTGGAGGAGGTCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTGC
28349355 GGGAGGAGGATTA
66 GGGAGGAGGATTA
28349368 GGTGGTGGAGG
1 GGTGGTGGAGG
28349379 TGGTGTTGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
77 1 0.01
78 75 0.99
ACGTcount: A:0.13, C:0.05, G:0.59, T:0.23
Consensus pattern (78 bp):
GGTGGTGGAGGAGGTCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTGC
GGGAGGAGGATTA
Found at i:28349316 original size:24 final size:24
Alignment explanation
Indices: 28349289--28349339 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28349279 GAGGAGGATT
* *
28349289 AGGTGGTGGAGGTGGTCTTGGTGG
1 AGGTGCTGGAGGTGGACTTGGTGG
* *
28349313 AGGTGCTGGTGGTGGAGTTGGTGG
1 AGGTGCTGGAGGTGGACTTGGTGG
28349337 AGG
1 AGG
28349340 CCTGGGTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.04, G:0.59, T:0.27
Consensus pattern (24 bp):
AGGTGCTGGAGGTGGACTTGGTGG
Found at i:28349325 original size:15 final size:15
Alignment explanation
Indices: 28349290--28349329 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
28349280 AGGAGGATTA
*
28349290 GGTGGTGGAGGTGGT
1 GGTGGTGGAGGTGCT
**
28349305 CTTGGTGGAGGTGCT
1 GGTGGTGGAGGTGCT
28349320 GGTGGTGGAG
1 GGTGGTGGAG
28349330 TTGGTGGAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.07, C:0.05, G:0.60, T:0.28
Consensus pattern (15 bp):
GGTGGTGGAGGTGCT
Found at i:28349347 original size:24 final size:24
Alignment explanation
Indices: 28349306--28349351 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28349296 GGAGGTGGTC
*
28349306 TTGGTGGAGGTGCTGGTGGTGGAG
1 TTGGTGGAGGTCCTGGTGGTGGAG
28349330 TTGGTGGAGG-CCTGGGTGGTGG
1 TTGGTGGAGGTCCT-GGTGGTGG
28349352 TGCGGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.07, C:0.07, G:0.59, T:0.28
Consensus pattern (24 bp):
TTGGTGGAGGTCCTGGTGGTGGAG
Found at i:28356407 original size:50 final size:50
Alignment explanation
Indices: 28356347--28356531 Score: 228
Period size: 50 Copynumber: 3.7 Consensus size: 50
28356337 TACTGCTAAT
* * * ** * *
28356347 GCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
** * *
28356397 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
*
28356447 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTA-GTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATAGGTGCCAAC
* *
28356497 GCCATGTCCTAGACATGATCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28356532 TATAATCTCA
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
50 116 0.99
51 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
Found at i:28360316 original size:144 final size:144
Alignment explanation
Indices: 28360056--28360342 Score: 538
Period size: 144 Copynumber: 2.0 Consensus size: 144
28360046 CATCATTTCC
*
28360056 ATACTTTTTCAACAATAACAAACTTAAAAATATATTGAAATCTTGATGTTCTTTCCTTATGCTAT
1 ATACTTTTTCAACAATAACAAACTTAAAAATATATTGAAATCTTGATGTTCTTACCTTATGCTAT
*
28360121 TGATTTCAATCTTTAACTTGATTTTCTCTCTCCTCCAGTTTCTATTTCTTGAATCTAACTTGAAA
66 TGATTTCAATCTTTAACTTGATTTTCTCTCTCCTCCAGCTTCTATTTCTTGAATCTAACTTGAAA
28360186 TTATAGCTCCCCAG
131 TTATAGCTCCCCAG
28360200 ATACTTTTTCAACAATAACAAACTTAAAAATATATTGAAATCTTGATGTTCTTACCTTATGCTAT
1 ATACTTTTTCAACAATAACAAACTTAAAAATATATTGAAATCTTGATGTTCTTACCTTATGCTAT
*
28360265 TGATTTCAATCTTTAACTTGATTTTCTCTCTCCTCCAGCTTCTATTTCTTGAATCTAACTTGACA
66 TGATTTCAATCTTTAACTTGATTTTCTCTCTCCTCCAGCTTCTATTTCTTGAATCTAACTTGAAA
*
28360330 TTCTAGCTCCCCA
131 TTATAGCTCCCCA
28360343 TTGTCTCCTT
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 139 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (144 bp):
ATACTTTTTCAACAATAACAAACTTAAAAATATATTGAAATCTTGATGTTCTTACCTTATGCTAT
TGATTTCAATCTTTAACTTGATTTTCTCTCTCCTCCAGCTTCTATTTCTTGAATCTAACTTGAAA
TTATAGCTCCCCAG
Found at i:28367966 original size:28 final size:28
Alignment explanation
Indices: 28367928--28367999 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
28367918 AAAAATAAAA
* *
28367928 ATTTACTAAAATGT-TATAACTTTTTTTT
1 ATTTACCAAAATATATATAA-TTTTTTTT
28367956 ATTTACCAAAATATATATAATTTTTTTT
1 ATTTACCAAAATATATATAATTTTTTTT
28367984 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
28368000 CAAAAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 36 0.88
29 5 0.12
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTACCAAAATATATATAATTTTTTTT
Found at i:28368137 original size:4 final size:4
Alignment explanation
Indices: 28368128--28368254 Score: 72
Period size: 4 Copynumber: 31.0 Consensus size: 4
28368118 GAAGGAGAGG
* *
28368128 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
28368176 TGGAAA GGAGAA GAGAA -AAA -AAA GAAA GAAA G-AA G-AA G-AA GAAAA
1 --GAAA -GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
28368221 GGAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA
1 -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
28368255 AAAAAGGAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 26
0.76 0.04 0.19
Matches are distributed among these distances:
3 21 0.20
4 52 0.50
5 19 0.18
6 12 0.12
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:28368152 original size:22 final size:22
Alignment explanation
Indices: 28368119--28368285 Score: 94
Period size: 22 Copynumber: 8.0 Consensus size: 22
28368109 GGGGGGGCAG
28368119 AAGGAGAGGGAAAGAAAGAAAGA
1 AAGGAGA-GGAAAGAAAGAAAGA
28368142 AAGGAGAGGAAAGAAAG-AA-A
1 AAGGAGAGGAAAGAAAGAAAGA
28368162 AA-GA-AGGAAAGAAATGGAAAG-
1 AAGGAGAGGAAAGAAA--GAAAGA
* * * *
28368183 GAGAAGAGAAAAAAAAGAAAGA
1 AAGGAGAGGAAAGAAAGAAAGA
* * *
28368205 AAGAAGAAG-AAG-AA-AAGGA
1 AAGGAGAGGAAAGAAAGAAAGA
* *
28368224 AAAGAGAAGAAA-AAAGAAAGA
1 AAGGAGAGGAAAGAAAGAAAGA
*
28368245 AA-GA-AGGAAA-AAA-AAGGA
1 AAGGAGAGGAAAGAAAGAAAGA
28368263 AAGGAGAAGAGAAA-AAA-AAAGA
1 AAGGAG-AG-GAAAGAAAGAAAGA
28368285 A
1 A
28368286 GAAGAAGAGG
Statistics
Matches: 115, Mismatches: 15, Indels: 29
0.72 0.09 0.18
Matches are distributed among these distances:
18 16 0.14
19 23 0.20
20 12 0.10
21 20 0.17
22 29 0.25
23 15 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (22 bp):
AAGGAGAGGAAAGAAAGAAAGA
Found at i:28368153 original size:18 final size:18
Alignment explanation
Indices: 28368132--28368186 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
28368122 GAGAGGGAAA
28368132 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
28368150 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAG-AG
28368168 GAAAGAAATGGAAAGGAGA
1 GAAAGAAA--GAAAGGAGA
28368187 AGAGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 2 0.06
18 22 0.71
20 5 0.16
21 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:28368222 original size:39 final size:38
Alignment explanation
Indices: 28368148--28368316 Score: 144
Period size: 39 Copynumber: 4.6 Consensus size: 38
28368138 AAGAAAGGAG
* * *
28368148 AGGAAAGA-AAGAAAAAGAAGGAAAGAA-ATG--G-AA
1 AGGAAAGAGAAAAAAAAGAAAGAAAGAAGAAGAAGAAA
28368181 AGGAGAAGAGAAAAAAAAGAAAGAAAGAAGAAGAAGAAA
1 AGGA-AAGAGAAAAAAAAGAAAGAAAGAAGAAGAAGAAA
28368220 AGGAAAAGAGAAGAAAAAAGAAAGAAAGAAGGAA-AA-AAA
1 AGG-AAAGAGAA-AAAAAAGAAAGAAAGAA-GAAGAAGAAA
* **
28368259 AGGAAAGGAGAAGAGAAAAAAAAAG-AAGAAGAAG-AGGGA
1 AGGAAA-GAGAA-A-AAAAAGAAAGAAAGAAGAAGAAGAAA
28368298 AGG-AAG-GAAAAAAAAGAAA
1 AGGAAAGAGAAAAAAAAGAAA
28368317 AAAAAGGTAA
Statistics
Matches: 116, Mismatches: 7, Indels: 25
0.78 0.05 0.17
Matches are distributed among these distances:
33 4 0.03
34 12 0.10
35 18 0.16
36 5 0.04
37 1 0.01
38 10 0.09
39 34 0.29
40 29 0.25
41 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.01
Consensus pattern (38 bp):
AGGAAAGAGAAAAAAAAGAAAGAAAGAAGAAGAAGAAA
Found at i:28368231 original size:44 final size:43
Alignment explanation
Indices: 28368151--28368322 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 43
28368141 AAAGGAGAGG
* *
28368151 AAAGAAAGAAA-AAGAAGGAAAGAAATGGAAAGGAGAAGAGAAAAA
1 AAAGAAAGAAAGAAGAA-G-AAGAAAAGGAAAAGAGAA-AGAAAAA
28368196 AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAG-AAG--AAA
1 AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAAGAAAAA
*
28368236 AAAGAAAGAAAGAAGGAA-AA-AAAAGGAAAGGAGAAGAGAAAAA
1 AAAGAAAGAAAGAA-GAAGAAGAAAAGGAAAAGAGAA-AGAAAAA
* *
28368279 AAA-AGAAG-AAGAAGAGGGAAG-GAAGGAAAA-A-AAAGAAAAA
1 AAAGA-AAGAAAGAAGA-AGAAGAAAAGGAAAAGAGAAAGAAAAA
28368319 AAAG
1 AAAG
28368323 GTAATTTTAT
Statistics
Matches: 110, Mismatches: 6, Indels: 26
0.77 0.04 0.18
Matches are distributed among these distances:
39 12 0.11
40 30 0.27
41 9 0.08
42 9 0.08
43 19 0.17
44 14 0.13
45 12 0.11
46 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (43 bp):
AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAAGAAAAA
Found at i:28368258 original size:63 final size:62
Alignment explanation
Indices: 28368133--28368321 Score: 149
Period size: 63 Copynumber: 3.0 Consensus size: 62
28368123 AGAGGGAAAG
* * * *
28368133 AAAGAAAGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAATGGAAAGGAGAAGAGAAAAA
1 AAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAAA-GGAAAGAAGAAGAAAAAAA
*
28368196 AAAGAAAGAAAGAAGAAG-AAGAAAAGGAAAAGAGAA-GAAA-AAA-GAAAGAAAGAAGGAAAAA
1 AAAGAAAGAAAGAAGAAGAAAG-AAA-GAAAA-AGAAGGAAAGAAAGGAAAG-AAGAAGAAAAAA
28368257 A
62 A
* * * * * *
28368258 AAGGAAAGGAGAAG-AGAA-AAAAAAAGAAGAAGAAGAGGGAAGGAAGGAAA-AAAAAGAAAAAA
1 AAAGAAA-GA-AAGAAGAAGAAAGAAAGAAAAAG-A-AGGAAAGAAAGGAAAGAAGAAGAAAAAA
28368320 A
62 A
28368321 A
1 A
28368322 GGTAATTTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
60 2 0.02
61 10 0.10
62 23 0.23
63 45 0.44
64 14 0.14
65 8 0.08
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (62 bp):
AAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAAAGGAAAGAAGAAGAAAAAAA
Found at i:28368322 original size:83 final size:84
Alignment explanation
Indices: 28368151--28368319 Score: 231
Period size: 83 Copynumber: 2.0 Consensus size: 84
28368141 AAAGGAGAGG
* *
28368151 AAAGAAAGAAAAAGAAGGAAAGAAATGGAAAGGAGAAGAGAAAAAAAAGAAAGAAAGAAGAAGAA
1 AAAGAAAG-AAAAGAAGGAAAAAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAAGAAGAAGAA
*
28368216 GAAAAGGAAAAGAGAAGAAA
65 GAAAAGGAAAAAAGAAGAAA
*
28368236 AAAGAAAG-AAAGAAGGAAAAAAAAGGAAAGGAGAAGAGAAAAAAAA-AGAAG-AAGAAGAGGGA
1 AAAGAAAGAAAAGAAGGAAAAAAAAGGAAAGGAGAAGAGAAAAAAAAGA-AAGAAAGAAGA-AGA
*
28368298 AG-GAAGGAAAAAA-AAGAAA
64 AGAAAAGGAAAAAAGAAGAAA
28368317 AAA
1 AAA
28368320 AAGGTAATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
81 9 0.12
82 17 0.22
83 43 0.56
85 8 0.10
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (84 bp):
AAAGAAAGAAAAGAAGGAAAAAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAAGAAGAAGAAG
AAAAGGAAAAAAGAAGAAA
Found at i:28368863 original size:15 final size:15
Alignment explanation
Indices: 28368845--28368875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28368835 ATGTACTGAA
*
28368845 AAAATATAAAATAAT
1 AAAATACAAAATAAT
28368860 AAAATACAAAATAAT
1 AAAATACAAAATAAT
28368875 A
1 A
28368876 TAGGGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATACAAAATAAT
Found at i:28372825 original size:3 final size:3
Alignment explanation
Indices: 28372817--28372845 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28372807 TCTTAATACT
28372817 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
28372846 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:28373141 original size:27 final size:27
Alignment explanation
Indices: 28373085--28373143 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
28373075 CTAATCAATA
****
28373085 TGGCACCATTGGTGCCACCAATGGTTT
1 TGGCACCATTGGTGCCACCAATCCCAT
*
28373112 TGGCACCTTTGGTGCCACCAATCCCAT
1 TGGCACCATTGGTGCCACCAATCCCAT
28373139 TGGCA
1 TGGCA
28373144 TGACCAAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.27
Consensus pattern (27 bp):
TGGCACCATTGGTGCCACCAATCCCAT
Found at i:28373236 original size:27 final size:27
Alignment explanation
Indices: 28373202--28373269 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
28373192 TTTGTTTTTT
28373202 TATATATTTTGGTAAATAAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAATTA
*
28373229 TATATATTTTGGTAAATAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAATTA
28373256 TA-ATATTTTGGTAA
1 TATATATTTTGGTAA
28373270 TTTTTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 12 0.30
27 28 0.70
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (27 bp):
TATATATTTTGGTAAATAAAAAAATTA
Found at i:28373331 original size:3 final size:3
Alignment explanation
Indices: 28373323--28373348 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28373313 GTAACTTATG
28373323 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28373349 TTGTGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28374240 original size:13 final size:13
Alignment explanation
Indices: 28374185--28374245 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
28374175 TTTAAACAAA
*
28374185 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
28374198 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
28374211 ACTTTTCCACAGT
1 ACTTTTCAAAAGC
28374224 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28374237 ACTTTTCAA
1 ACTTTTCAA
28374246 GTAGTTTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28376208 original size:24 final size:24
Alignment explanation
Indices: 28376156--28376209 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
28376146 GTGAGCTAAT
* *
28376156 AATT-TTGGAGGTTATAATTTTAC
1 AATTCTTGGAGGTTAGAATATTAC
* *
28376179 ATTTCTTGGAGGTTAGAATATTAG
1 AATTCTTGGAGGTTAGAATATTAC
28376203 AATTCTT
1 AATTCTT
28376210 TCCACTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (24 bp):
AATTCTTGGAGGTTAGAATATTAC
Found at i:28376984 original size:21 final size:21
Alignment explanation
Indices: 28376958--28376999 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28376948 CCAATTTAAT
28376958 GAAATA-ATTTTTCATAAATAA
1 GAAATACATTTTT-ATAAATAA
28376979 GAAATACATTTTTATAAATAA
1 GAAATACATTTTTATAAATAA
28377000 TTTTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
GAAATACATTTTTATAAATAA
Found at i:28377364 original size:26 final size:28
Alignment explanation
Indices: 28377304--28377370 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
28377294 TTCAAATCAA
* *
28377304 TTTGAGTGTTTGCTTTTTGTTTCTTTTT
1 TTTGAGTGTTTGCTTTTTGTGTCTTTCT
28377332 TTCTGAGTGTTTGCTTTTT-TGT-TTTCT
1 TT-TGAGTGTTTGCTTTTTGTGTCTTTCT
28377359 TTTGAGTGTTTG
1 TTTGAGTGTTTG
28377371 TGAGTTTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 10 0.28
27 6 0.17
28 4 0.11
29 16 0.44
ACGTcount: A:0.04, C:0.07, G:0.21, T:0.67
Consensus pattern (28 bp):
TTTGAGTGTTTGCTTTTTGTGTCTTTCT
Found at i:28379222 original size:62 final size:62
Alignment explanation
Indices: 28379093--28379226 Score: 169
Period size: 62 Copynumber: 2.2 Consensus size: 62
28379083 GGCTTGTGTT
* * * *
28379093 CAGGCCATGTAACTCACTATTTGTGGTACAAAGCCACACGACCAGGGACATAGGCATGTGCC
1 CAGGCCGTGTAACTCACTATTTGTGGTACAAAGCCACACGACCAAGGACACAGGCATGTACC
* * * * **
28379155 CAGGCCGTGTAACTCACTGTTTGTGGTACAAATCCACACGGCCAAGGACACGGGTGTGTACC
1 CAGGCCGTGTAACTCACTATTTGTGGTACAAAGCCACACGACCAAGGACACAGGCATGTACC
*
28379217 TAGGCCGTGT
1 CAGGCCGTGT
28379227 GAGTCATACG
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (62 bp):
CAGGCCGTGTAACTCACTATTTGTGGTACAAAGCCACACGACCAAGGACACAGGCATGTACC
Found at i:28384413 original size:50 final size:50
Alignment explanation
Indices: 28384334--28384576 Score: 328
Period size: 50 Copynumber: 4.9 Consensus size: 50
28384324 CATATAGGTA
* * * *
28384334 AAGAGGACCCATGTCAGGCCATGTTTGGGACATGGCGTTGGCACCAAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAT
*
28384384 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAT
* * * *
28384434 AAGAGGTCCCATGTAAGACCATATCTGGAACAT-GCGTTGGCATCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAT
* * *
28384483 TAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCAAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAT
* * *
28384533 GAGAGGTCTC-TCGTAAGACCATGTATGGGACATGGCGTTGGCAC
1 AAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCGTTGGCAC
28384577 GACATGGCAT
Statistics
Matches: 171, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 45 0.26
50 126 0.74
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAT
Found at i:28384506 original size:99 final size:100
Alignment explanation
Indices: 28384334--28384576 Score: 328
Period size: 99 Copynumber: 2.4 Consensus size: 100
28384324 CATATAGGTA
* * * *
28384334 AAGAGGACCCATGTCAGGCCATGTTTGGGACATGGCGTTGGCACCAAGATAAGAGGTCCCATGTA
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCGTTGGCACCAAGATAAGAGGTCCCATGTA
* * *
28384399 AGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
66 AGACCATGTCTAGGACATGGCATTGGCACCAAGAT
* * * * * *
28384434 AAGAGGTCCCATGTAAGACCATATCTGGAACAT-GCGTTGGCATCGAGATTAGAGGTCCCATGTA
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCGTTGGCACCAAGATAAGAGGTCCCATGTA
28384498 AGACCATGTCTAGGACATGGCATTGGCACCAAGAT
66 AGACCATGTCTAGGACATGGCATTGGCACCAAGAT
* *
28384533 GAGAGGTCTC-TCGTAAGACCATGTATGGGACATGGCGTTGGCAC
1 AAGAGGTCCCAT-GTAAGACCATGTATGGGACATGGCGTTGGCAC
28384577 GACATGGCAT
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
98 1 0.01
99 86 0.70
100 36 0.29
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (100 bp):
AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCGTTGGCACCAAGATAAGAGGTCCCATGTA
AGACCATGTCTAGGACATGGCATTGGCACCAAGAT
Found at i:28399494 original size:49 final size:50
Alignment explanation
Indices: 28399433--28399575 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 50
28399423 CATTTGGGTA
* * *
28399433 AAGAGTTCCCATGTAAGGCCATGTCTGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
28399483 AAGAGGT-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** *
28399532 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGACGTTGGCAC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
28399576 GACATGGCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
49 46 0.54
50 39 0.46
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:28406455 original size:32 final size:32
Alignment explanation
Indices: 28406418--28406483 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
28406408 ATGTACCATC
*
28406418 TATACAGATCATAAGAGCATCAAGTATCTTCT
1 TATACAGACCATAAGAGCATCAAGTATCTTCT
28406450 TATACAGACCATAAGAGCATCAAGTATCTTCT
1 TATACAGACCATAAGAGCATCAAGTATCTTCT
28406482 TA
1 TA
28406484 CGTAGAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (32 bp):
TATACAGACCATAAGAGCATCAAGTATCTTCT
Found at i:28414118 original size:16 final size:16
Alignment explanation
Indices: 28414084--28414126 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28414074 AATTGAAAGG
*
28414084 AATAT-ATATATGTGTA
1 AATATGATA-ATGTGCA
*
28414100 AATGTGATAATGTGCA
1 AATATGATAATGTGCA
28414116 AATATGATAAT
1 AATATGATAAT
28414127 TGGATATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.37
Consensus pattern (16 bp):
AATATGATAATGTGCA
Found at i:28419461 original size:17 final size:17
Alignment explanation
Indices: 28419439--28419471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28419429 CAAAATTGGG
28419439 TGGAAAATCAAGAAAAA
1 TGGAAAATCAAGAAAAA
*
28419456 TGGAAAATTAAGAAAA
1 TGGAAAATCAAGAAAA
28419472 TACCCCTAAA
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:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (17 bp):
TGGAAAATCAAGAAAAA
Found at i:28422712 original size:36 final size:36
Alignment explanation
Indices: 28422660--28422732 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
28422650 TTAGCTGCAC
*
28422660 TTTAAGTTATACAATAATGCTCATTGAGCTATCATA
1 TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
*
28422696 TTTAAGTTCTAAAATAATGCTCATTGAGCTATCATA
1 TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
28422732 T
1 T
28422733 ATTAGATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (36 bp):
TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
Found at i:28429860 original size:17 final size:17
Alignment explanation
Indices: 28429838--28429870 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28429828 CAAAATTGGG
28429838 TGGAAAATCAAGAAAAA
1 TGGAAAATCAAGAAAAA
*
28429855 TGGAAAATTAAGAAAA
1 TGGAAAATCAAGAAAA
28429871 TACCCCTAAA
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:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (17 bp):
TGGAAAATCAAGAAAAA
Found at i:28433111 original size:36 final size:36
Alignment explanation
Indices: 28433059--28433131 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
28433049 TTAGCTGCAC
*
28433059 TTTAAGTTATACAATAATGCTCATTGAGCTATCATA
1 TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
*
28433095 TTTAAGTTCTAAAATAATGCTCATTGAGCTATCATA
1 TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
28433131 T
1 T
28433132 ATTAGATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (36 bp):
TTTAAGTTATAAAATAATGCTCATTGAGCTATCATA
Found at i:28444962 original size:18 final size:18
Alignment explanation
Indices: 28444939--28444974 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28444929 CTAACATCAG
28444939 TAACTGCTAACAACTAAC
1 TAACTGCTAACAACTAAC
*
28444957 TAACTGCTAACAGCTAAC
1 TAACTGCTAACAACTAAC
28444975 CATTACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (18 bp):
TAACTGCTAACAACTAAC
Found at i:28446643 original size:21 final size:22
Alignment explanation
Indices: 28446619--28446670 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
28446609 TCAGGTATTA
28446619 TTCAAATTGTTATGT-GTGTTG
1 TTCAAATTGTTATGTGGTGTTG
* ** *
28446640 TTCAAGTTCCTATTTGGTGTTG
1 TTCAAATTGTTATGTGGTGTTG
28446662 TTC-AATTGT
1 TTCAAATTGT
28446671 AATTTATGTG
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.17, C:0.10, G:0.21, T:0.52
Consensus pattern (22 bp):
TTCAAATTGTTATGTGGTGTTG
Found at i:28451312 original size:20 final size:20
Alignment explanation
Indices: 28451242--28451346 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 20
28451232 TGTAAAAAAA
*
28451242 TTTCGATGCCCCTAATTTGCAC
1 TTTCG-TGCCCCTGA-TTGCAC
* *
28451264 TCTAGTGCCCCTGATTGCAC
1 TTTCGTGCCCCTGATTGCAC
* *
28451284 TTTCATGCCCCTTATTGCAC
1 TTTCGTGCCCCTGATTGCAC
* *
28451304 -TTCGGTGCCCTTGATTGTAC
1 TTTC-GTGCCCCTGATTGCAC
* * *
28451324 TTTCTTGCCACTGTTTGCAC
1 TTTCGTGCCCCTGATTGCAC
28451344 TTT
1 TTT
28451347 GGATCCTCGG
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.05
20 48 0.74
21 11 0.17
22 3 0.05
ACGTcount: A:0.13, C:0.30, G:0.16, T:0.40
Consensus pattern (20 bp):
TTTCGTGCCCCTGATTGCAC
Found at i:28451312 original size:40 final size:41
Alignment explanation
Indices: 28451242--28451345 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 41
28451232 TGTAAAAAAA
*
28451242 TTTCGATGCCCCTAATTTGCAC-TCTAGTGCCCCTGATTGCAC
1 TTTC-ATGCCCCTTA-TTGCACTTCTAGTGCCCCTGATTGCAC
* * *
28451284 TTTCATGCCCCTTATTGCACTTC-GGTGCCCTTGATTGTAC
1 TTTCATGCCCCTTATTGCACTTCTAGTGCCCCTGATTGCAC
* *
28451324 TTTCTTGCCACTGT-TTGCACTT
1 TTTCATGCCCCT-TATTGCACTT
28451346 TGGATCCTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 38 0.70
41 12 0.22
42 4 0.07
ACGTcount: A:0.13, C:0.31, G:0.16, T:0.39
Consensus pattern (41 bp):
TTTCATGCCCCTTATTGCACTTCTAGTGCCCCTGATTGCAC
Found at i:28474521 original size:39 final size:40
Alignment explanation
Indices: 28474478--28474609 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
28474468 AGACTAAGAT
*
28474478 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTC
* *
28474517 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTC
* * *
28474557 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTC
28474597 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28474610 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 36 0.44
40 46 0.56
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTC
Found at i:28474631 original size:79 final size:79
Alignment explanation
Indices: 28474478--28474642 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28474468 AGACTAAGAT
* * **
28474478 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28474543 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28474557 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28474620 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28474636 CCGAAGG
1 CCGAAGG
28474643 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28482163 original size:40 final size:40
Alignment explanation
Indices: 28482065--28482327 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
28482055 TCCTCGTTCA
* * * ** *
28482065 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
28482104 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
28482144 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
28482184 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
28482224 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
28482264 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
28482304 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28482328 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:28489376 original size:40 final size:39
Alignment explanation
Indices: 28489278--28489540 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
28489268 TCCTCGTTCA
* * * *
28489278 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28489317 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28489356 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28489396 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28489436 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28489476 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28489517 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28489541 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28489500 original size:120 final size:119
Alignment explanation
Indices: 28489278--28489540 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
28489268 TCCTCGTTCA
* * *
28489278 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
28489343 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
28489396 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
28489461 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
28489517 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28489541 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:28489549 original size:41 final size:41
Alignment explanation
Indices: 28489472--28489549 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28489462 TTTGTATCTC
* * *
28489472 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28489513 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28489550 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28494059 original size:20 final size:20
Alignment explanation
Indices: 28494021--28494069 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28494011 ATCATGGTCT
*
28494021 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
*
28494040 TCT-CTTACTTGTTTATTTAC
1 T-TGCTTACTTGTTTACTTAC
28494060 TTGCTTACTT
1 TTGCTTACTT
28494070 AAATAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.12, C:0.22, G:0.06, T:0.59
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:28494468 original size:56 final size:51
Alignment explanation
Indices: 28494275--28494468 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 51
28494265 TGATAATAAC
* * ** *
28494275 ATGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGAGTTCTCATA-TCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTCA
* ***
28494325 ATGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCAT-CTCA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTCA
* * * *
28494375 GTGCCAATGCCATGTCCCAGACATGGCCATACGTGGGACCTCTCATAACCTCAATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A-CTC---A
*
28494431 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28494469 TCTCATTCCC
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
50 80 0.68
53 3 0.03
56 34 0.29
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (51 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTCA
Found at i:28494727 original size:21 final size:21
Alignment explanation
Indices: 28494676--28494717 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28494666 TCGGTACAAA
28494676 ATACGATCAAATCTATCAACT
1 ATACGATCAAATCTATCAACT
28494697 ATACGATCAAATCTATCAACT
1 ATACGATCAAATCTATCAACT
28494718 TAGTCCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (21 bp):
ATACGATCAAATCTATCAACT
Found at i:28508492 original size:160 final size:160
Alignment explanation
Indices: 28508228--28508548 Score: 624
Period size: 160 Copynumber: 2.0 Consensus size: 160
28508218 AGTGACATTT
*
28508228 TTCCCAGTTAAGTACTAGATTAGTTTCTTCGTATCTCTGTAATAATTCTGAAGATTACCTAGACA
1 TTCCCAGTTAAGTACTAGATTAGTTTCTTCGTATCTCTGTAATAATTCTCAAGATTACCTAGACA
28508293 CTCTTGTAAAGAGTCTTCATAAAATGAGAAAACATCCATGAATACATCCAAACCTTCTTCCAACA
66 CTCTTGTAAAGAGTCTTCATAAAATGAGAAAACATCCATGAATACATCCAAACCTTCTTCCAACA
*
28508358 TATCAGCAAAAATGGAAGTCATACATTGCA
131 TATCAGCAAAAATGGAAGTCATACATCGCA
28508388 TTCCCAGTTAAGTACTAGATTAGTTTCTTCGTATCTCTGTAATAATTCTCAAGATTACCTAGACA
1 TTCCCAGTTAAGTACTAGATTAGTTTCTTCGTATCTCTGTAATAATTCTCAAGATTACCTAGACA
28508453 CTCTTGTAAAGAGTCTTCATAAAATGAGAAAACATCCATGAATACATCCAAACCTTCTTCCAACA
66 CTCTTGTAAAGAGTCTTCATAAAATGAGAAAACATCCATGAATACATCCAAACCTTCTTCCAACA
28508518 TATCAGCAAAAATGGAAGTCATACATCGCA
131 TATCAGCAAAAATGGAAGTCATACATCGCA
28508548 T
1 T
28508549 AGAGGTTGTT
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (160 bp):
TTCCCAGTTAAGTACTAGATTAGTTTCTTCGTATCTCTGTAATAATTCTCAAGATTACCTAGACA
CTCTTGTAAAGAGTCTTCATAAAATGAGAAAACATCCATGAATACATCCAAACCTTCTTCCAACA
TATCAGCAAAAATGGAAGTCATACATCGCA
Found at i:28516761 original size:23 final size:23
Alignment explanation
Indices: 28516735--28516789 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
28516725 TTCCCTCCCT
28516735 TAGATAGTCTT-GAATGGACTTCC
1 TAGATAGTCTTAG-ATGGACTTCC
28516758 TAGATAGTCTTAGATGGACTTCC
1 TAGATAGTCTTAGATGGACTTCC
*
28516781 CAGATAGTC
1 TAGATAGTC
28516790 CTTGGTAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (23 bp):
TAGATAGTCTTAGATGGACTTCC
Found at i:28516944 original size:28 final size:28
Alignment explanation
Indices: 28516868--28516979 Score: 75
Period size: 28 Copynumber: 4.0 Consensus size: 28
28516858 ACATTCCATG
* * * *
28516868 TAAGATAGTCCTTAGCAGACT-CCTCGCG
1 TAAGACAGTCCTTGGCAGACTCCCT-ACA
* * *
28516896 TAAGACAATCCTTGTCGGACTCCCTACA
1 TAAGACAGTCCTTGGCAGACTCCCTACA
*
28516924 TAAGACAGTCCTTGGCAGACTTCCC-ACT
1 TAAGACAGTCCTTGGCAGAC-TCCCTACA
* ** * *
28516952 TAAGATAGTTTTTGGCGGACTCCGTACA
1 TAAGACAGTCCTTGGCAGACTCCCTACA
28516980 CCACATCACA
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
27 3 0.05
28 54 0.84
29 7 0.11
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (28 bp):
TAAGACAGTCCTTGGCAGACTCCCTACA
Found at i:28522634 original size:31 final size:31
Alignment explanation
Indices: 28522599--28522675 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
28522589 TAACCCCATG
* *
28522599 GAGAAAATCAAGGGAACTACCAACCAGCCTA
1 GAGAAAATCAAGGAAACCACCAACCAGCCTA
* **
28522630 GAGAAAATTAAGGAAACCACTTACCAGCCTA
1 GAGAAAATCAAGGAAACCACCAACCAGCCTA
*
28522661 GAGAAATTCAAGGAA
1 GAGAAAATCAAGGAA
28522676 CCGACGCCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (31 bp):
GAGAAAATCAAGGAAACCACCAACCAGCCTA
Found at i:28527191 original size:38 final size:38
Alignment explanation
Indices: 28527135--28527217 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
28527125 ATTTAACTAT
*
28527135 TCAACCAATATGCAATATAGGCACCTCAAACACATAAA
1 TCAAGCAATATGCAATATAGGCACCTCAAACACATAAA
28527173 TCAAGCAATATGCAATATAGGCACCTCAAACACATAAA
1 TCAAGCAATATGCAATATAGGCACCTCAAACACATAAA
28527211 TCAAGCA
1 TCAAGCA
28527218 TACCTAAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.18
Consensus pattern (38 bp):
TCAAGCAATATGCAATATAGGCACCTCAAACACATAAA
Found at i:28547284 original size:21 final size:21
Alignment explanation
Indices: 28547258--28547308 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
28547248 ATAATTAGGT
*
28547258 TCAAGTGGTATGACCCTCAAG
1 TCAAGTGGTATGACCCTAAAG
*
28547279 TCAAGTGATATGACCCTAAAG
1 TCAAGTGGTATGACCCTAAAG
28547300 TCAAGTGGT
1 TCAAGTGGT
28547309 TTTAGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (21 bp):
TCAAGTGGTATGACCCTAAAG
Found at i:28549730 original size:39 final size:39
Alignment explanation
Indices: 28549687--28549777 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
28549677 ATGGCTCAAA
* *
28549687 TGGCATGTTTTGTGATGGAAGTGTTAGTGGTCATAATTG
1 TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
*
28549726 TGGCATGTTTTGTGATGAAAGTGTTAATTGTCATAATTG
1 TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
28549765 TGGCATGTTTTGT
1 TGGCATGTTTTGT
28549778 TAGAAGTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (39 bp):
TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
Found at i:28550803 original size:15 final size:14
Alignment explanation
Indices: 28550779--28550808 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28550769 TGGATAACCT
28550779 AATTTGACAAATCA
1 AATTTGACAAATCA
28550793 AATTATGACAAATCA
1 AATT-TGACAAATCA
28550808 A
1 A
28550809 CCTCATAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (14 bp):
AATTTGACAAATCA
Found at i:28554335 original size:14 final size:15
Alignment explanation
Indices: 28554309--28554337 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28554299 TTATACAAGG
28554309 TTAAAAATGATTTTT
1 TTAAAAATGATTTTT
28554324 TTAAAAAT-ATTTTT
1 TTAAAAATGATTTTT
28554338 AAATTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAAAAATGATTTTT
Found at i:28560992 original size:41 final size:41
Alignment explanation
Indices: 28560832--28560997 Score: 154
Period size: 41 Copynumber: 4.0 Consensus size: 41
28560822 CGTGCCTCTA
* * * * *
28560832 TTTGTACTTCGATACCCCTAAATTGTAGATACGTG-CCACTG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCA-TG
* * * *
28560873 TTTGTACTTTGGTACCCCTAAATAGCACATACGTGCCCCTA
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
* * * * * *
28560914 TTTATACCTCAGTACCCCTGAATCGCACATGCATGCCCATG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
* * *
28560955 TTTGTACTTCGGCACCCTTGAATAGCACATACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
28560996 TT
1 TT
28560998 AACACTCTGG
Statistics
Matches: 98, Mismatches: 26, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
41 96 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (41 bp):
TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
Found at i:28561245 original size:14 final size:14
Alignment explanation
Indices: 28561226--28561253 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28561216 TGTGGCTATA
28561226 TAGGTTGTTATAGT
1 TAGGTTGTTATAGT
28561240 TAGGTTGTTATAGT
1 TAGGTTGTTATAGT
28561254 ACATTAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TAGGTTGTTATAGT
Found at i:28573479 original size:50 final size:50
Alignment explanation
Indices: 28573422--28573705 Score: 358
Period size: 50 Copynumber: 5.7 Consensus size: 50
28573412 AATATGTGAG
*
28573422 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * *
28573472 CCTTGTAAGACCATGTCTGGGACTTGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
*
28573522 CCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * **
28573572 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * **
28573622 CCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACA-GAAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG-AGAGGTC
* *
28573671 CCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28573706 TGTTATTTTC
Statistics
Matches: 206, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
48 2 0.01
49 37 0.18
50 167 0.81
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:28578830 original size:17 final size:17
Alignment explanation
Indices: 28578801--28578833 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28578791 CTTGATGCGT
28578801 TTTTGAAAAAAAAATAC
1 TTTTGAAAAAAAAATAC
28578818 TTTT-AAAATAAAAATA
1 TTTTGAAAA-AAAAATA
28578834 TTATTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TTTTGAAAAAAAAATAC
Found at i:28579530 original size:18 final size:16
Alignment explanation
Indices: 28579512--28579559 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
28579502 TTTTTATAAT
28579512 TTTTAAGTATTTTACAA
1 TTTTAA-TATTTTACAA
*
28579529 TTTTAATATTTTTGCAA
1 TTTTAATA-TTTTACAA
28579546 CTCTTTAATATTTT
1 -T-TTTAATATTTT
28579560 TTATTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 5 0.19
19 7 0.26
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTTAATATTTTACAA
Found at i:28580785 original size:13 final size:13
Alignment explanation
Indices: 28580767--28580791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28580757 TCTACTTTAT
28580767 TTTGAGATAATTA
1 TTTGAGATAATTA
28580780 TTTGAGATAATT
1 TTTGAGATAATT
28580792 CAAGAAGATA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTGAGATAATTA
Found at i:28583514 original size:32 final size:32
Alignment explanation
Indices: 28583472--28583612 Score: 138
Period size: 32 Copynumber: 4.4 Consensus size: 32
28583462 AATGTGATTA
*
28583472 GCACAAAGCCATCAGTAACAGTGATATGATCG
1 GCACATAGCCATCAGTAACAGTGATATGATCG
* * * *
28583504 GCATATAGCCATCAGTAACGGTAACATGATCG
1 GCACATAGCCATCAGTAACAGTGATATGATCG
* * * ** *
28583536 GTACAAAGCCATTAGTGGCAGTGATATGATCT
1 GCACATAGCCATCAGTAACAGTGATATGATCG
* * * *
28583568 ACACACAGCCATCAGTAACAGTGAAATAATCG
1 GCACATAGCCATCAGTAACAGTGATATGATCG
*
28583600 GCACATAGTCATC
1 GCACATAGCCATC
28583613 GATAACGGGA
Statistics
Matches: 82, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 82 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (32 bp):
GCACATAGCCATCAGTAACAGTGATATGATCG
Found at i:28583600 original size:64 final size:64
Alignment explanation
Indices: 28583474--28583600 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
28583464 TGTGATTAGC
* * * * *
28583474 ACAAAGCCATCAGTAACAGTGATATGATCGGCATATAGCCATCAGTAACGGTAACATGATCGGT
1 ACAAAGCCATCAGTAACAGTGATATGATCGACACACAGCCATCAGTAACAGTAACATAATCGGT
* ** *
28583538 ACAAAGCCATTAGTGGCAGTGATATGATCTACACACAGCCATCAGTAACAGTGAA-ATAATCGG
1 ACAAAGCCATCAGTAACAGTGATATGATCGACACACAGCCATCAGTAACAGT-AACATAATCGG
28583601 CACATAGTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 51 0.96
65 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (64 bp):
ACAAAGCCATCAGTAACAGTGATATGATCGACACACAGCCATCAGTAACAGTAACATAATCGGT
Found at i:28587996 original size:17 final size:17
Alignment explanation
Indices: 28587967--28587999 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28587957 CTTGATGCGT
28587967 TTTTGAAAAAAAAATAC
1 TTTTGAAAAAAAAATAC
28587984 TTTT-AAAATAAAAATA
1 TTTTGAAAA-AAAAATA
28588000 TTATTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TTTTGAAAAAAAAATAC
Found at i:28588696 original size:18 final size:16
Alignment explanation
Indices: 28588678--28588725 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
28588668 TTTTTATAAT
28588678 TTTTAAGTATTTTACAA
1 TTTTAA-TATTTTACAA
*
28588695 TTTTAATATTTTTGCAA
1 TTTTAATA-TTTTACAA
28588712 CTCTTTAATATTTT
1 -T-TTTAATATTTT
28588726 TTATTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 5 0.19
19 7 0.26
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTTAATATTTTACAA
Found at i:28589951 original size:13 final size:13
Alignment explanation
Indices: 28589933--28589957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28589923 TCTACTTTAT
28589933 TTTGAGATAATTA
1 TTTGAGATAATTA
28589946 TTTGAGATAATT
1 TTTGAGATAATT
28589958 CAAGAAGATA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTGAGATAATTA
Found at i:28592680 original size:32 final size:32
Alignment explanation
Indices: 28592637--28592802 Score: 161
Period size: 32 Copynumber: 5.2 Consensus size: 32
28592627 TAATGTGATT
* *
28592637 GGCACAAAGCCATCAGTAGTAGTGATATGGCC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
28592669 GGCACACAGCCATTAGTAACGGTAACATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
*
28592701 GGCACAAAGCCATCAGTAGCAGTGATATGACT
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
28592733 GGCACACAGCCATCAGCAACGGTAACATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* *
28592765 GGCACAAAGCCATTAGTAGCAGTGATATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
28592797 GGCACA
1 GGCACA
28592803 CAGTCATACC
Statistics
Matches: 102, Mismatches: 32, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAGCAGTGATATGACC
Found at i:28592710 original size:64 final size:64
Alignment explanation
Indices: 28592632--28592805 Score: 276
Period size: 64 Copynumber: 2.7 Consensus size: 64
28592622 TACAGTAATG
* * * * *
28592632 TGATTGGCACAAAGCCATCAGTAGTAGTGATATGGCCGGCACACAGCCATTAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
*
28592696 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACTGGCACACAGCCATCAGCAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
* *
28592760 TGATCGGCACAAAGCCATTAGTAGCAGTGATATGATCGGCACACAG
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAG
28592806 TCATACCAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 101 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (64 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
Found at i:28593088 original size:27 final size:27
Alignment explanation
Indices: 28592878--28593183 Score: 243
Period size: 27 Copynumber: 11.5 Consensus size: 27
28592868 GGGAAAAATT
* * *
28592878 AGTCA-TTTACCC-ACCAGGGCATTAC
1 AGTCATTTTACCCTACAAGGGTATTTC
* * * *
28592903 GGTCATTTTACCCTATAGGGGTATTAC
1 AGTCATTTTACCCTACAAGGGTATTTC
* *
28592930 -GATCATTTTACCCTACAAGGGCATTAC
1 AG-TCATTTTACCCTACAAGGGTATTTC
* *
28592957 AGTCATTTTACCCTACAAGGGCATTAC
1 AGTCATTTTACCCTACAAGGGTATTTC
* * * *
28592984 AATCATTTTACCCTATAAGGGCATTAC
1 AGTCATTTTACCCTACAAGGGTATTTC
* * *
28593011 GGTTATTTTATCCTACAAGGGTATTTC
1 AGTCATTTTACCCTACAAGGGTATTTC
* * * **
28593038 AAT-ATTCTACCTTACGGGGGTATTTC
1 AGTCATTTTACCCTACAAGGGTATTTC
*
28593064 AGTCATTTTATCCTACGAA-GGTATTTC
1 AGTCATTTTACCCTAC-AAGGGTATTTC
* * *
28593091 GGT-ATTCTACCCTAC-TGGGTATTTC
1 AGTCATTTTACCCTACAAGGGTATTTC
*
28593116 AGTCATTTTA-CCTATCAATGGTATTTC
1 AGTCATTTTACCCTA-CAAGGGTATTTC
*
28593143 AGTTATTTTA-CCTATCAAGGGTATTTC
1 AGTCATTTTACCCTA-CAAGGGTATTTC
*
28593170 GGTCATTTTACCCT
1 AGTCATTTTACCCT
28593184 TCGGGGTATT
Statistics
Matches: 228, Mismatches: 42, Indels: 19
0.79 0.15 0.07
Matches are distributed among these distances:
25 18 0.08
26 44 0.19
27 162 0.71
28 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (27 bp):
AGTCATTTTACCCTACAAGGGTATTTC
Found at i:28593128 original size:79 final size:79
Alignment explanation
Indices: 28592904--28593195 Score: 202
Period size: 80 Copynumber: 3.7 Consensus size: 79
28592894 GGGCATTACG
* * * * * * * * *
28592904 GTCATTTTACCCTAT-AGGGGTATTACGATCATTTTACCCTACAAGGGCATTACAGTCATTTTAC
1 GTCATTTTA-CCTATCAAGGGTATTTCGGTCATTCTACCCTAC-GGGGTATTTCAAT-ATTCTA-
* *
28592968 CCTA-CAAGGGCATTACA
62 CCTATCAAGGGTATTTCA
* * * * * * *
28592985 ATCATTTTACCCTAT-AAGGGCATTACGGTTATTTTATCCTACAAGGGTATTTCAATATTCTACC
1 GTCATTTTA-CCTATCAAGGGTATTTCGGTCATTCTACCCTAC-GGGGTATTTCAATATTCTACC
**
28593049 T-TACGGGGGTATTTCA
64 TAT-CAAGGGTATTTCA
* * *
28593065 GTCATTTTATCCTA-CGAA-GGTATTTCGGT-ATTCTACCCTACTGGGTATTTCAGTCATTTTAC
1 GTCATTTTA-CCTATC-AAGGGTATTTCGGTCATTCTACCCTACGGGGTATTTCAAT-ATTCTAC
*
28593127 CTATCAATGGTATTTCA
63 CTATCAAGGGTATTTCA
* * *
28593144 GTTATTTTACCTATCAAGGGTATTTCGGTCATTTTACCCTTCGGGGTATTTC
1 GTCATTTTACCTATCAAGGGTATTTCGGTCATTCTACCCTACGGGGTATTTC
28593196 GATCCAGATA
Statistics
Matches: 172, Mismatches: 30, Indels: 19
0.78 0.14 0.09
Matches are distributed among these distances:
78 17 0.10
79 51 0.30
80 55 0.32
81 49 0.28
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (79 bp):
GTCATTTTACCTATCAAGGGTATTTCGGTCATTCTACCCTACGGGGTATTTCAATATTCTACCTA
TCAAGGGTATTTCA
Found at i:28595751 original size:20 final size:18
Alignment explanation
Indices: 28595714--28595761 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
28595704 TTTCACAATT
*
28595714 TCACTTTCACTTTCACTC
1 TCACTCTCACTTTCACTC
28595732 TCACTCTCACTCTGTCACTC
1 TCACTCTCACT-T-TCACTC
* *
28595752 ACACTGTCAC
1 TCACTCTCAC
28595762 GACTCACGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.19, C:0.42, G:0.04, T:0.35
Consensus pattern (18 bp):
TCACTCTCACTTTCACTC
Found at i:28596481 original size:16 final size:16
Alignment explanation
Indices: 28596460--28596493 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28596450 AATTATTGAA
28596460 TATATTGTAATTAATG
1 TATATTGTAATTAATG
28596476 TATATTGTAATTAATG
1 TATATTGTAATTAATG
28596492 TA
1 TA
28596494 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATTGTAATTAATG
Found at i:28599796 original size:24 final size:24
Alignment explanation
Indices: 28599741--28599799 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
28599731 GGTTTAATGC
* *
28599741 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
28599765 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
28599789 AAATGGATATA
1 AAATGGATATA
28599800 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:28599871 original size:17 final size:17
Alignment explanation
Indices: 28599849--28599946 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
28599839 AATTCAAGAC
28599849 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
28599866 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
28599885 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ** *
28599903 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
28599923 TTATGTAATTTTTTTAA
1 TTATGTAATATTTTTAA
28599940 TTATGTA
1 TTATGTA
28599947 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 25 0.43
18 8 0.14
19 7 0.12
20 18 0.31
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:28599889 original size:37 final size:37
Alignment explanation
Indices: 28599840--28599952 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
28599830 TTCTGTGTTA
28599840 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
28599876 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
28599913 ATTCAAATATTTATGTAATTTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
28599950 ATT
1 ATT
28599953 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:28599967 original size:9 final size:9
Alignment explanation
Indices: 28599953--28600087 Score: 153
Period size: 9 Copynumber: 14.3 Consensus size: 9
28599943 TGTAGTGATT
28599953 TAATTCGGG
1 TAATTCGGG
28599962 TAATTCGGG
1 TAATTCGGG
*
28599971 TAATTTGGG
1 TAATTCGGG
*
28599980 TAATTTTTGGG
1 TAA--TTCGGG
28599991 TAATTCGGG
1 TAATTCGGG
*
28600000 TAATTTGGG
1 TAATTCGGG
28600009 TAATTTTCGGG
1 TAA--TTCGGG
28600020 TAATTCGGG
1 TAATTCGGG
28600029 TAATTTTCGGG
1 TAA--TTCGGG
*
28600040 TAATTCAGG
1 TAATTCGGG
*
28600049 TAATTTGGG
1 TAATTCGGG
28600058 TAATTCGGG
1 TAATTCGGG
*
28600067 TAAGTCGGG
1 TAATTCGGG
*
28600076 TAAGTCGGG
1 TAATTCGGG
28600085 TAA
1 TAA
28600088 ATTTTAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
9 85 0.77
11 26 0.23
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:28599993 original size:20 final size:18
Alignment explanation
Indices: 28599953--28600087 Score: 153
Period size: 20 Copynumber: 7.2 Consensus size: 18
28599943 TGTAGTGATT
28599953 TAATTCGGGTAATTCGGG
1 TAATTCGGGTAATTCGGG
* *
28599971 TAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAA--TTCGGG
*
28599991 TAATTCGGGTAATTTGGG
1 TAATTCGGGTAATTCGGG
28600009 TAATTTTCGGGTAATTCGGG
1 TAA--TTCGGGTAATTCGGG
*
28600029 TAATTTTCGGGTAATTCAGG
1 TAA--TTCGGGTAATTCGGG
*
28600049 TAATTTGGGTAATTCGGG
1 TAATTCGGGTAATTCGGG
* *
28600067 TAAGTCGGGTAAGTCGGG
1 TAATTCGGGTAATTCGGG
28600085 TAA
1 TAA
28600088 ATTTTAACCA
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
18 51 0.50
20 52 0.50
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.38
Consensus pattern (18 bp):
TAATTCGGGTAATTCGGG
Found at i:28599993 original size:29 final size:29
Alignment explanation
Indices: 28599956--28600087 Score: 164
Period size: 29 Copynumber: 4.6 Consensus size: 29
28599946 AGTGATTTAA
28599956 TTCGGGTAATTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
*
28599985 TTTGGGTAATTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
28600014 TTCGGGTAATTCGGGTAATTTTCGGGTAA--
1 TTCGGGTAATTCGGGTAA-TTT-GGGTAATT
* * *
28600043 TTCAGGTAATTTGGGTAATTCGGGTAA--
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
* *
28600070 GTCGGGTAAGTCGGGTAA
1 TTCGGGTAATTCGGGTAA
28600088 ATTTTAACCA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
27 20 0.22
28 2 0.02
29 61 0.66
30 3 0.03
31 6 0.07
ACGTcount: A:0.22, C:0.08, G:0.33, T:0.38
Consensus pattern (29 bp):
TTCGGGTAATTCGGGTAATTTGGGTAATT
Found at i:28602863 original size:16 final size:18
Alignment explanation
Indices: 28602842--28602874 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
28602832 TTTGAGATAA
28602842 AAATAAA-A-TTTAAAAT
1 AAATAAATATTTTAAAAT
28602858 AAATAAATATTTTAAAA
1 AAATAAATATTTTAAAA
28602875 CTTAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATATTTTAAAAT
Found at i:28603735 original size:73 final size:72
Alignment explanation
Indices: 28603591--28603736 Score: 179
Period size: 73 Copynumber: 2.0 Consensus size: 72
28603581 TGAAATCAAT
* **
28603591 ATTTTTATCTATAAGTATGATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTGGTA
1 ATTTTTATCTATAAGTATAATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTACTA
28603656 AAATTAA
66 AAATTAA
* * * *
28603663 ATTTCTTATTTATAAGTATAAT-AAATTTTCTTATTAAGTAAATTTATTTATA-CAAATATTTTA
1 ATTT-TTATCTATAAGTATAATAAAAATTT-TTATCAAATAAATTTATTTA-ACCAAATATTTTA
*
28603726 CTAACATTAA
63 CTAAAATTAA
28603736 A
1 A
28603737 ATTATCATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
72 10 0.16
73 52 0.83
74 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (72 bp):
ATTTTTATCTATAAGTATAATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTACTA
AAATTAA
Found at i:28604819 original size:20 final size:20
Alignment explanation
Indices: 28604794--28604831 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28604784 TCCTCTTTCA
28604794 ATCTGTTT-TAATATAATTGG
1 ATCTGTTTGTAAT-TAATTGG
28604814 ATCTGTTTGTAATTAATT
1 ATCTGTTTGTAATTAATT
28604832 TAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
ATCTGTTTGTAATTAATTGG
Found at i:28624254 original size:42 final size:41
Alignment explanation
Indices: 28624145--28624311 Score: 154
Period size: 42 Copynumber: 3.9 Consensus size: 41
28624135 CTTTGATATG
* * * * *
28624145 TGATTTCATGTAAGACCATGTCTGGGACGTTGGAATTGATT
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATA
*
28624186 TGAGAATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
1 T--G-ATTACATGTAAGACCATGTCTGGGACATTGGCATCG-ATA
* * * * *
28624231 TGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATA
* * *
28624272 GTTGATTACATGTAAGACCACGTCTGGAACGTTGGCATCG
1 --TGATTACATGTAAGACCATGTCTGGGACATTGGCATCG
28624312 TACGAGCTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 4 0.04
42 32 0.31
43 32 0.31
44 31 0.30
45 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (41 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATA
Found at i:28641911 original size:27 final size:27
Alignment explanation
Indices: 28641880--28642057 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28641870 TAAATTGTAC
28641880 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28641907 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28641933 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28641961 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28641989 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28642016 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28642043 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28642058 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28641994 original size:82 final size:81
Alignment explanation
Indices: 28641881--28642036 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28641871 AAATTGTACA
* *
28641881 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28641945 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28641962 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28642027 TGCGAGTTGA
65 TGCGAATTGA
28642037 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28642048 original size:82 final size:81
Alignment explanation
Indices: 28641877--28642057 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28641867 GATTAAATTG
* *
28641877 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28641942 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28641958 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28642022 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28642040 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28642058 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28649392 original size:12 final size:12
Alignment explanation
Indices: 28649375--28649401 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28649365 ATTCCGAAGT
28649375 ATATATATATAC
1 ATATATATATAC
28649387 ATATATATATAC
1 ATATATATATAC
28649399 ATA
1 ATA
28649402 AGTATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:28649920 original size:27 final size:27
Alignment explanation
Indices: 28649889--28650066 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28649879 TAAATTGTAC
28649889 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28649916 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28649942 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28649970 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28649998 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28650025 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28650052 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28650067 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28650003 original size:82 final size:81
Alignment explanation
Indices: 28649890--28650045 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28649880 AAATTGTACA
* *
28649890 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28649954 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28649971 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28650036 TGCGAGTTGA
65 TGCGAATTGA
28650046 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28650057 original size:82 final size:81
Alignment explanation
Indices: 28649886--28650066 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28649876 GATTAAATTG
* *
28649886 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28649951 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28649967 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28650031 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28650049 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28650067 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28658592 original size:25 final size:25
Alignment explanation
Indices: 28658555--28658620 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 25
28658545 CCAATTTTCC
28658555 CAACTCGTGTGAGCATTC-GAATT-
1 CAACTCGTGTGAGCATTCTGAATTA
*
28658578 CATAGCTCGTGTGAGCATTCTGATTTA
1 CA-A-CTCGTGTGAGCATTCTGAATTA
28658605 CAACTCGTGTGAGCAT
1 CAACTCGTGTGAGCAT
28658621 ACATGTACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
23 2 0.05
24 1 0.03
25 28 0.74
26 5 0.13
27 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (25 bp):
CAACTCGTGTGAGCATTCTGAATTA
Found at i:28661498 original size:21 final size:20
Alignment explanation
Indices: 28661474--28661512 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28661464 GGACTGAATT
* *
28661474 GAAAACATTCGAAACATTTAA
1 GAAAAAATTC-AAAAATTTAA
28661495 GAAAAAATTCAAAAATTT
1 GAAAAAATTCAAAAATTT
28661513 GAACTACAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
GAAAAAATTCAAAAATTTAA
Found at i:28662778 original size:121 final size:123
Alignment explanation
Indices: 28662547--28662815 Score: 323
Period size: 121 Copynumber: 2.2 Consensus size: 123
28662537 GAGAGTAAAT
* * *
28662547 AGGGGCACTTATGTGCAATTTAAGGGTACCGAAGTTCAAACAAGGGCACGTATGTGCAATTCAGG
1 AGGGGCACGTATGTGCAATTTAGGGGTACCGAAATTCAAACAAGGGCACGTATGTGCAATTCAGG
* ** * * *
28662612 GTTGCTGAAGTTCAAAAAGGGGCACATATGTGTAATTTAAGGGTA-CAAAGTACAAGA-
66 GTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTACAA-AC
* *
28662669 A-GGGCACGTATGTGCAATTTAGGGGTA-CTAAATTACAAACAGGGGCACGTATGTGCAATTCAG
1 AGGGGCACGTATGTGCAATTTAGGGGTACCGAAATT-CAAACAAGGGCACGTATGTGCAATTCAG
* * * *
28662732 AGG-TACCAAAGTTCAAACAGGGGTACGTGTGTGCAATTCAAAGGTACCAAAGTACAAAC
65 -GGTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTACAAAC
* *
28662791 AGGGGCACGTATATGCAATTCAGGG
1 AGGGGCACGTATGTGCAATTTAGGG
28662816 AATAATTAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
120 5 0.04
121 85 0.68
122 14 0.11
123 21 0.17
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (123 bp):
AGGGGCACGTATGTGCAATTTAGGGGTACCGAAATTCAAACAAGGGCACGTATGTGCAATTCAGG
GTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTACAAAC
Found at i:28662811 original size:41 final size:41
Alignment explanation
Indices: 28662547--28662812 Score: 272
Period size: 41 Copynumber: 6.5 Consensus size: 41
28662537 GAGAGTAAAT
* * * *
28662547 AGGGGCACTTATGTGCAATTTAAGGGTACCGAAGTTCAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTACAAAC
* * ** * *
28662588 AAGGGCACGTATGTGCAATTC-AGGGTTGCTGAAGTTCAAAA
1 AGGGGCACGTATGTGCAATTCAAGGG-TACCAAAGTACAAAC
* * *
28662629 AGGGGCACATATGTGTAATTTAAGGGTA-CAAAGTACAAGA-
1 AGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTACAA-AC
* * * *
28662669 A-GGGCACGTATGTGCAATTTAGGGGTACTAAATTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTACAAAC
*
28662709 AGGGGCACGTATGTGCAATTC-AGAGGTACCAAAGTTCAAAC
1 AGGGGCACGTATGTGCAATTCAAG-GGTACCAAAGTACAAAC
* * *
28662750 AGGGGTACGTGTGTGCAATTCAAAGGTACCAAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTACAAAC
*
28662791 AGGGGCACGTATATGCAATTCA
1 AGGGGCACGTATGTGCAATTCA
28662813 GGGAATAATT
Statistics
Matches: 186, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
39 24 0.13
40 22 0.12
41 135 0.73
42 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTACAAAC
Found at i:28668743 original size:29 final size:28
Alignment explanation
Indices: 28668698--28668759 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
28668688 ATAGGGCCAT
* *
28668698 GTGTCACACATGGCTGAGTCACATGCCC
1 GTGTCACACACGACTGAGTCACATGCCC
*
28668726 GTGTCAACACACGACTGAGTCACATGCCT
1 GTGTC-ACACACGACTGAGTCACATGCCC
28668755 GTGTC
1 GTGTC
28668760 TCAGGCAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (28 bp):
GTGTCACACACGACTGAGTCACATGCCC
Found at i:28669856 original size:72 final size:72
Alignment explanation
Indices: 28669739--28669882 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
28669729 GGTCGAGGTA
28669739 ATCTGTGATTTTCGCCTTTCTCCAATTTAGATCCGGTTGAGATTTATCTTGATCATGCAAAGACT
1 ATCTGTGATTTTCGCCTTTCTCCAATTTAGATCCGGTTGAGATTTATCTTGATCATGCAAAGACT
28669804 TGAACTT
66 TGAACTT
* * *
28669811 ATCTGTGATTTTTGCCTTTC-CCTGAA-TTAGATTCGGTTGAGATTTATCTTGATCATGCAAATA
1 ATCTGTGATTTTCGCCTTTCTCC--AATTTAGATCCGGTTGAGATTTATCTTGATCATGCAAAGA
*
28669874 CTTTAACTT
64 CTTGAACTT
28669883 TTTTAAATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
71 2 0.03
72 62 0.94
73 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (72 bp):
ATCTGTGATTTTCGCCTTTCTCCAATTTAGATCCGGTTGAGATTTATCTTGATCATGCAAAGACT
TGAACTT
Found at i:28673235 original size:25 final size:25
Alignment explanation
Indices: 28673172--28673236 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
28673162 TTTTCTTAGT
*
28673172 TTTA-TTTTTATTTCTCATTTTTATC
1 TTTATTTTTTATTT-TCATTTTAATC
* * * * *
28673197 TTTGTCTATAATTTTGATTTTAATC
1 TTTATTTTTTATTTTCATTTTAATC
28673222 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
28673237 AATGTTAGTT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (25 bp):
TTTATTTTTTATTTTCATTTTAATC
Found at i:28673248 original size:19 final size:20
Alignment explanation
Indices: 28673208--28673261 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
28673198 TTGTCTATAA
* *
28673208 TTTTGATTTTAATCTTTA-T
1 TTTTTATTTTAATCGTTATT
28673227 TTTTTATTTTAAT-GTTAGTT
1 TTTTTATTTTAATCGTTA-TT
28673247 TTATTTATTTTAATC
1 TT-TTTATTTTAATC
28673262 AAGGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 3 0.10
21 11 0.38
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTTTATTTTAATCGTTATT
Found at i:28685230 original size:115 final size:115
Alignment explanation
Indices: 28685028--28685375 Score: 626
Period size: 115 Copynumber: 3.0 Consensus size: 115
28685018 AATGCCTTAT
* *
28685028 TGGCATATTGGTTGTG-TGGAATAATGGTATAGTGAATTGGTCATTTCAAGCATGTTTTGGTATG
1 TGGCATATTGATTG-GATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATG
*
28685092 GTTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
65 TTTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
28685143 TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
1 TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
28685208 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
66 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
28685258 TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
1 TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
* * *
28685323 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTCGGTACAGGCTTGAAA
66 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
28685373 TGG
1 TGG
28685376 GTGATGGAAA
Statistics
Matches: 226, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
114 1 0.00
115 225 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (115 bp):
TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
TTTGATGCTTTGAACAAGGGTGCAAATGGCTTATAGGTACATGCTTGAAA
Found at i:28692027 original size:14 final size:14
Alignment explanation
Indices: 28692008--28692044 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
28691998 TTTTCTTTCT
28692008 TTCTTCTCCCTCTC
1 TTCTTCTCCCTCTC
28692022 TTCTTCTCCCTCTC
1 TTCTTCTCCCTCTC
28692036 TTCTTCTCC
1 TTCTTCTCC
28692045 ACTACTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (14 bp):
TTCTTCTCCCTCTC
Found at i:28692784 original size:11 final size:12
Alignment explanation
Indices: 28692768--28692807 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
28692758 TCTTCGTCTG
28692768 CTTCTCCTCC-T
1 CTTCTCCTCCTT
28692779 CTTCTCCTCCTT
1 CTTCTCCTCCTT
* *
28692791 CTTCTTCTTCTT
1 CTTCTCCTCCTT
28692803 CTTCT
1 CTTCT
28692808 TCTTCTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (12 bp):
CTTCTCCTCCTT
Found at i:28692794 original size:3 final size:3
Alignment explanation
Indices: 28692778--28692815 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
28692768 CTTCTCCTCC
* *
28692778 TCT TCT CCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
28692816 ACATAATTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:28692898 original size:21 final size:21
Alignment explanation
Indices: 28692883--28692929 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
28692873 ATGGCTCCGT
28692883 GAAGAGCAACGCTGGCTAAGA
1 GAAGAGCAACGCTGGCTAAGA
*
28692904 GAAGAGCAGCGCTGGCTTAAAGA
1 GAAGAGCAACGCTGGC-T-AAGA
28692927 GAA
1 GAA
28692930 AGAATCGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.38, C:0.17, G:0.34, T:0.11
Consensus pattern (21 bp):
GAAGAGCAACGCTGGCTAAGA
Found at i:28694074 original size:26 final size:26
Alignment explanation
Indices: 28694044--28694093 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
28694034 AACTTGTTTA
28694044 TTGTTCCACTAATATATAATAAAACG
1 TTGTTCCACTAATATATAATAAAACG
28694070 TTGTTCCACTAATATATAATAAAA
1 TTGTTCCACTAATATATAATAAAA
28694094 TTATTATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (26 bp):
TTGTTCCACTAATATATAATAAAACG
Found at i:28694207 original size:6 final size:6
Alignment explanation
Indices: 28694196--28694238 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
28694186 AGATATTATA
28694196 TATATG TATATG TATATG TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG T
28694239 TTATTTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:28696634 original size:25 final size:26
Alignment explanation
Indices: 28696586--28696639 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
28696576 TATTATAGGC
**
28696586 TTTTTATTTATTTATAATTGTATATA
1 TTTTTATAAATTTATAATTGTATATA
*
28696612 TTTTTATAAATTTGTAATT-TATATA
1 TTTTTATAAATTTATAATTGTATATA
28696637 TTT
1 TTT
28696640 AAAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTATAAATTTATAATTGTATATA
Found at i:28700393 original size:144 final size:144
Alignment explanation
Indices: 28700146--28700432 Score: 357
Period size: 144 Copynumber: 2.0 Consensus size: 144
28700136 AAAAAGAGAA
* * *
28700146 AGTTTAGATTTTAAAAATAAAAATATGTTTTCTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTA
1 AGTTTAGATTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAAGTGTAAAATTTTA
*
28700211 AAACAAAGTTTTAATTTTTTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAAATAGT
66 AAACAAAGTTTTAATTCTTTTTCAACTATTTCAAAAT-AAAACTTTGATCTTTAAGAAAAATAGT
*
28700276 -ATTTTTTTAAAGAG
130 GATTTTGTTAAAGAG
** * **
28700290 AGTTTAGATTTTTTTAAATAAAAATCT-ATTT-TTTAGTCATTTTAAAGAAAATGTGTAGATTTT
1 AGTTTAGA-TTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAA-GTGTA-AAATT
* ** ** * *
28700353 TTAAAACAAAGTTTTGA-TCTTTTTCAACTATTTTGAAATAAAGTTTTGATTTTTAAGAAAAGTA
63 TTAAAACAAAGTTTTAATTCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTAAGAAAAATA
28700417 GTGATTTTGTTAAAGA
128 GTGATTTTGTTAAAGA
28700433 AAACTTTTAT
Statistics
Matches: 122, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
143 42 0.34
144 46 0.38
145 34 0.28
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.45
Consensus pattern (144 bp):
AGTTTAGATTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAAGTGTAAAATTTTA
AAACAAAGTTTTAATTCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTAAGAAAAATAGTG
ATTTTGTTAAAGAG
Found at i:28700456 original size:143 final size:143
Alignment explanation
Indices: 28700178--28700456 Score: 323
Period size: 143 Copynumber: 2.0 Consensus size: 143
28700168 ATATGTTTTC
* * *
28700178 TTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTAATTTTTTTTCAACTATTTC
1 TTTAGTCATTTTAAAGAAAAGTGTAAAATTTTAAAACAAAGTTTTAATTCTTTTTCAACTATTTC
* * * **
28700243 AAAATAAAAACTTTGATCTTTAAGAAAAATAGTATTTTTTTAAAGAGAGTTTAGATTTTTTTAAA
66 AAAATAAAAACTTTGATCTTTAAGAAAAATAGTATTTTGTTAAAGAAACTTTAGATTTTTGCAAA
*
28700308 TAAAAATCTATTT
131 AAAAAATCTATTT
** *
28700321 TTTAGTCATTTTAAAGAAAATGTGTAGATTTTTTAAAACAAAGTTTTGA-TCTTTTTCAACTATT
1 TTTAGTCATTTTAAAGAAAA-GTGTA-AAATTTTAAAACAAAGTTTTAATTCTTTTTCAACTATT
** ** * * *
28700385 TTGAAAT-AAAGTTTTGATTTTTAAGAAAAGTAGTGATTTTGTTAAAGAAAACTTT-TA-TTTTG
64 TCAAAATAAAAACTTTGATCTTTAAGAAAAATAGT-ATTTTGTTAAAG-AAACTTTAGATTTTTG
28700447 CAAAAAAAAA
127 CAAAAAAAAA
28700457 AATTCAGCCA
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
143 54 0.48
144 35 0.31
145 24 0.21
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (143 bp):
TTTAGTCATTTTAAAGAAAAGTGTAAAATTTTAAAACAAAGTTTTAATTCTTTTTCAACTATTTC
AAAATAAAAACTTTGATCTTTAAGAAAAATAGTATTTTGTTAAAGAAACTTTAGATTTTTGCAAA
AAAAAATCTATTT
Found at i:28700556 original size:6 final size:6
Alignment explanation
Indices: 28700547--28700585 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28700537 TTGCCAACAT
* *
28700547 AGAAAG AGAAAG AGAAAG AGAAAG AGGAAG AGGAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGA
28700586 TTCTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:28701391 original size:26 final size:26
Alignment explanation
Indices: 28701362--28701427 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
28701352 TTAGTTAAGT
* *
28701362 AGGTGTTATATTTTAACGAAACTATA
1 AGGTGTTACATTTTAACGAAACCATA
* *
28701388 AGGTTTTTACATTTTAATGAAACCATA
1 AGG-TGTTACATTTTAACGAAACCATA
*
28701415 AGGTTTTTACATT
1 AGG-TGTTACATT
28701428 CAGATTTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (26 bp):
AGGTGTTACATTTTAACGAAACCATA
Found at i:28701401 original size:27 final size:27
Alignment explanation
Indices: 28701371--28701427 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
28701361 TAGGTGTTAT
*
28701371 ATTTTAACGAAACTATAAGGTTTTTAC
1 ATTTTAACGAAACCATAAGGTTTTTAC
*
28701398 ATTTTAATGAAACCATAAGGTTTTTAC
1 ATTTTAACGAAACCATAAGGTTTTTAC
28701425 ATT
1 ATT
28701428 CAGATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
ATTTTAACGAAACCATAAGGTTTTTAC
Found at i:28704111 original size:24 final size:23
Alignment explanation
Indices: 28704072--28704117 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
28704062 TTTGGTGCTA
28704072 TTATTTTTCTACTGTTTTTGTTG
1 TTATTTTTCTACTGTTTTTGTTG
*
28704095 TTATTTTTGCTATTGTTTTTGTT
1 TTATTTTT-CTACTGTTTTTGTT
28704118 ATTTGTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.72
Consensus pattern (23 bp):
TTATTTTTCTACTGTTTTTGTTG
Found at i:28705219 original size:9 final size:9
Alignment explanation
Indices: 28705169--28705218 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
28705159 TTTGGTTAAA
28705169 AATTAACCG
1 AATTAACCG
*
28705178 AATTAACTG
1 AATTAACCG
*
28705187 AATTAACCA
1 AATTAACCG
28705196 AATTAACCG
1 AATTAACCG
*
28705205 AATTACCCG
1 AATTAACCG
28705214 AATTA
1 AATTA
28705219 CTCGAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:28705224 original size:9 final size:9
Alignment explanation
Indices: 28705169--28705226 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
28705159 TTTGGTTAAA
*
28705169 AATTAACCG
1 AATTACCCG
* *
28705178 AATTAACTG
1 AATTACCCG
* *
28705187 AATTAACCA
1 AATTACCCG
*
28705196 AATTAACCG
1 AATTACCCG
28705205 AATTACCCG
1 AATTACCCG
*
28705214 AATTACTCG
1 AATTACCCG
28705223 AATT
1 AATT
28705227 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTACCCG
Found at i:28705224 original size:18 final size:19
Alignment explanation
Indices: 28705169--28705226 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
28705159 TTTGGTTAAA
28705169 AATTAACCGAATTAACT-G
1 AATTAACCGAATTAACTCG
*
28705187 AATTAACCAAATTAAC-CG
1 AATTAACCGAATTAACTCG
*
28705205 AATTACCCGAATT-ACTCG
1 AATTAACCGAATTAACTCG
28705223 AATT
1 AATT
28705227 GAATCACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.06
18 33 0.94
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTAACCGAATTAACTCG
Found at i:28705256 original size:17 final size:17
Alignment explanation
Indices: 28705234--28705296 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
28705224 ATTGAATCAC
28705234 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
28705251 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
28705271 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
28705288 TACATAATT
1 TACATAATT
28705297 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:28705271 original size:37 final size:37
Alignment explanation
Indices: 28705225--28705299 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28705215 ATTACTCGAA
*
28705225 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
28705262 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
28705299 T
1 T
28705300 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:28705511 original size:39 final size:38
Alignment explanation
Indices: 28705429--28705543 Score: 203
Period size: 39 Copynumber: 3.0 Consensus size: 38
28705419 CTTAAGAGTT
*
28705429 GACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGGTA
1 GACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTA
28705467 GACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGGTA
1 GACTTTAGTTTTAGTTTTATTGGGTTGG-TAATTGGGTA
28705506 GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGT
1 GACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGGT
28705544 TGGGTTGGAT
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
38 27 0.36
39 45 0.61
40 2 0.03
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (38 bp):
GACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTA
Found at i:28705542 original size:13 final size:13
Alignment explanation
Indices: 28705524--28705548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28705514 TTTTAGTTTT
28705524 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
28705537 ATTGGGTTGGGT
1 ATTGGGTTGGGT
28705549 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:28714624 original size:18 final size:18
Alignment explanation
Indices: 28714601--28714637 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28714591 GCCAAGTGTA
* *
28714601 TATCCTAGCCTTTATATG
1 TATCCTAACCCTTATATG
28714619 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
28714637 T
1 T
28714638 TTTCTTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Done.