Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold256
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: 726231
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 41294 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:192246 original size:8 final size:7
Alignment explanation
Indices: 192233--192278 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
192223 TAACTTATAT
192233 ATAATAAC
1 ATAAT-AC
192241 ATAATA-
1 ATAATAC
*
192247 A-ATTAC
1 ATAATAC
192253 ATAATAC
1 ATAATAC
192260 ATAATAAC
1 ATAAT-AC
192268 ATAATAC
1 ATAATAC
192275 ATAA
1 ATAA
192279 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:192271 original size:15 final size:15
Alignment explanation
Indices: 192233--192278 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
192223 TAACTTATAT
192233 ATAATAACATAAT--
1 ATAATAACATAATAC
*
192246 A-AATTACATAATAC
1 ATAATAACATAATAC
192260 ATAATAACATAATAC
1 ATAATAACATAATAC
192275 ATAA
1 ATAA
192279 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:192300 original size:21 final size:20
Alignment explanation
Indices: 192274--192331 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
192264 TAACATAATA
*
192274 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
*
192295 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
192316 CATAACTTATATATAA
1 CATAACTTATATATAA
192332 TAACTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:192336 original size:14 final size:14
Alignment explanation
Indices: 192317--192344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
192307 AATAACTTCC
192317 ATAACTTATATATA
1 ATAACTTATATATA
192331 ATAACTTATATATA
1 ATAACTTATATATA
192345 TAAGCTTGCA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAACTTATATATA
Found at i:192357 original size:10 final size:9
Alignment explanation
Indices: 192353--192500 Score: 158
Period size: 9 Copynumber: 16.7 Consensus size: 9
192343 TATAAGCTTG
192353 CATAACTTA
1 CATAACTTA
*
192362 CATAAATTA
1 CATAACTTA
*
192371 AATAACTTA
1 CATAACTTA
192380 CATAACTTA
1 CATAACTTA
*
192389 CATAAATTA
1 CATAACTTA
*
192398 CATAAATTA
1 CATAACTTA
*
192407 AATAACTTA
1 CATAACTTA
192416 CATAACTTA
1 CATAACTTA
*
192425 CATAAATTA
1 CATAACTTA
192434 -ATAAACTTA
1 CAT-AACTTA
192443 CATAACTTA
1 CATAACTTA
* *
192452 GATTA--TA
1 CATAACTTA
*
192459 CACAACTTA
1 CATAACTTA
*
192468 CATAAATTA
1 CATAACTTA
*
192477 AATAACTTA
1 CATAACTTA
*
192486 CATAGCTTA
1 CATAACTTA
192495 CATAAC
1 CATAAC
192501 GGGCAAAACA
Statistics
Matches: 113, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 105 0.93
10 2 0.02
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:195123 original size:29 final size:29
Alignment explanation
Indices: 195077--195407 Score: 393
Period size: 29 Copynumber: 11.3 Consensus size: 29
195067 TTTTGATATT
* * *
195077 ATTTGATTAAAAATCCTATCCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
195106 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
195135 ATTTAATTAAAAACCCAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
195164 ATTTAATTAAAAACTCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
195193 ATTTAATTTAAAAACCCTAAACCATAACCTA
1 ATTTAA-TTAAAAACCCT-AACCCTAACCTA
* **
195224 ATTAAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
195253 ATTTTATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
195282 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAACCTA
* *
195312 ATTAAATTAAAAAACCTAA--C---CCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
195336 ATTTAATTAAAAACCCAAACTCTATCCTAATTTA
1 ATTTAATTAAAAACCCTAA--C---CCTAACCTA
195370 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAACCTA
195400 ATTTAATT
1 ATTTAATT
195408 TAATTAAAAA
Statistics
Matches: 261, Mismatches: 27, Indels: 27
0.83 0.09 0.09
Matches are distributed among these distances:
24 20 0.08
27 1 0.00
29 141 0.54
30 61 0.23
31 17 0.07
33 1 0.00
34 18 0.07
35 2 0.01
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAACCTA
Found at i:195322 original size:118 final size:118
Alignment explanation
Indices: 195082--195423 Score: 406
Period size: 118 Copynumber: 2.9 Consensus size: 118
195072 ATATTATTTG
* * * **
195082 ATTAAAAATCCTATCCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
1 ATTAAAAAACCTAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAA
* ** *
195147 ACCCAAACCCTAACCTAATTTAATTAAAAACTCT-AACCCTAACCTAATTTAA
66 ACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAA
* * * *
195199 TTTAAAAACCCTAAACCATAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTTATTAAA
1 ATTAAAAAACCT-AACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTAAA
195264 AACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAA-TTAA
65 AACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAA
** * *
195317 ATTAAAAAACCTAACCCTAATTTAATTAAA--AACCCAAACTCT-ATCCTAATTTAATTTAATTA
1 ATTAAAAAACCTAACCCTAACCTAATTAAATTAA---AAACCCTAACCCTAATTTAATTTAATTA
195379 AAAACCCTAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA
63 AAAACCCT-AA--C---CCTAATTTAATTTAATTAAAAACCCTAA
195424 CCTAATATTA
Statistics
Matches: 194, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
115 2 0.01
117 51 0.26
118 99 0.51
119 13 0.07
120 1 0.01
123 28 0.14
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (118 bp):
ATTAAAAAACCTAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAA
ACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAA
Found at i:195337 original size:88 final size:88
Alignment explanation
Indices: 195077--195453 Score: 440
Period size: 88 Copynumber: 4.2 Consensus size: 88
195067 TTTTGATATT
* * * *
195077 ATTTGATTAAAAATCCTATCCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAA
1 ATTTTATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
* **
195141 TTAAAAACCCAAACCCTAACCTA
66 TTAAAAACCCTAACCCTAATTTA
* * *
195164 ATTTAATTAAAAACTCTAACCCTAACCTAATTTAATTTAAAAACCCTAAACCATAACCTAATTAA
1 ATTTTATTAAAAACCCTAACCCTAACCTAATTTAA-TTAAAAACCCTAAACCCTAACCTAATTAA
195229 ATTAAAAACCCTAACCCTAATTTA
65 ATTAAAAACCCTAACCCTAATTTA
**
195253 ATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
1 ATTTTATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
*
195318 TTAAAAAACCTAACCCTAATTTA
66 TTAAAAACCCTAACCCTAATTTA
** * * **
195341 A--TTAAAAACCCAAACTCT-ATCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATT
1 ATTTTATTAA---AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA-T
195403 TAATTTAATTAAAAACCCTAA-CCTAATATTA
62 T-A---AATTAAAAACCCTAACCCTAAT-TTA
*
195434 TTTTTAATTAAAAACCCTAA
1 ATTTT-ATTAAAAACCCTAA
195454 NNNNNNNNNN
Statistics
Matches: 251, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
86 5 0.02
87 31 0.12
88 104 0.41
89 75 0.30
90 1 0.00
92 6 0.02
93 23 0.09
94 1 0.00
95 2 0.01
96 3 0.01
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (88 bp):
ATTTTATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAA
TTAAAAACCCTAACCCTAATTTA
Found at i:195440 original size:35 final size:34
Alignment explanation
Indices: 195334--195453 Score: 144
Period size: 35 Copynumber: 3.6 Consensus size: 34
195324 AACCTAACCC
*
195334 TAATTTAATTAAAAACCCAAACTCT-ATCCTAATT
1 TAATTTAATTAAAAACCCTAAC-CTAATCCTAATT
195368 TAATTTAATTAAAAACCCTAAACCCTAA-CCTAATT
1 TAATTTAATTAAAAACCCT-AA-CCTAATCCTAATT
* *
195403 TAATTTAATTAAAAACCCTAACCTAAT-ATTA-T
1 TAATTTAATTAAAAACCCTAACCTAATCCTAATT
195435 T--TTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
195454 NNNNNNNNNN
Statistics
Matches: 79, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.23
32 2 0.03
33 7 0.09
34 20 0.25
35 30 0.38
36 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (34 bp):
TAATTTAATTAAAAACCCTAACCTAATCCTAATT
Found at i:195442 original size:30 final size:28
Alignment explanation
Indices: 195077--195453 Score: 299
Period size: 29 Copynumber: 12.7 Consensus size: 28
195067 TTTTGATATT
* * * **
195077 ATTTGATTAAAAATCCTATCCCTAACCTA
1 ATTTAATTAAAAACCCTA-ACCTAATTTA
**
195106 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
* **
195135 ATTTAATTAAAAACCCAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
* **
195164 ATTTAATTAAAAACTCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
**
195193 ATTTAATTTAAAAACCCTAAACCATAACCTA
1 ATTTAA-TTAAAAACCCT-AACC-TAATTTA
*
195224 ATTAAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
*
195253 ATTTTATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
**
195282 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AA-CCTAATTTA
* *
195312 ATTAAATTAAAAAACCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
* * *
195341 A-TTAA-AAACCCAAACTCTATCCTAATTTA
1 ATTTAATTAA---AAACCCTAACCTAATTTA
195370 ATTTAATTAAAAACCCTAAACCCTAACCTAATTTA
1 ATTTAATT---AA----AAACCCTAACCTAATTTA
195405 ATTTAATTAAAAACCCTAACCTAATATTA
1 ATTTAATTAAAAACCCTAACCTAAT-TTA
*
195434 TTTTTAATTAAAAACCCTAA
1 -ATTTAATTAAAAACCCTAA
195454 NNNNNNNNNN
Statistics
Matches: 302, Mismatches: 29, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
27 2 0.01
28 18 0.06
29 160 0.53
30 78 0.26
31 14 0.05
32 2 0.01
34 2 0.01
35 26 0.09
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAATTTA
Found at i:201437 original size:124 final size:125
Alignment explanation
Indices: 201216--201495 Score: 390
Period size: 124 Copynumber: 2.2 Consensus size: 125
201206 CACGAGGGCA
* * * *
201216 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAGCG
* **
201281 AAATCGCGTCCACGGGGTCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGGGGTCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
* *
201341 CGATTTTATACTATTTGTTCAGAAAACGTCAAAAAA-AA-TATTTCTTACATGACCAACTAT-GC
1 CGATTTTATACTATTTGATCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAG-
*
201403 CGAAATGGCGTCCACGAGGG-CACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
64 CGAAATCGCGTCCACG-GGGTCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
*
201465 CGATTTTATACTATTTGACCAGAAACGTCAA
1 CGATTTTATACTATTTGATCAGAAACGTCAA
201496 CTCGAAATAA
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
123 11 0.08
124 92 0.66
125 24 0.17
126 13 0.09
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAGCG
AAATCGCGTCCACGGGGTCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
Found at i:201748 original size:28 final size:27
Alignment explanation
Indices: 201689--201747 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
201679 GATTTTGGGG
*
201689 AAAATGGGCCATTCCGGTAAATAATTAA
1 AAAATGGCCCATTCCGGTAAAT-ATTAA
*
201717 AAAATCGGCCCATTTCGGTAAAT-TTAA
1 AAAAT-GGCCCATTCCGGTAAATATTAA
201744 AAAA
1 AAAA
201748 AGGGCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (27 bp):
AAAATGGCCCATTCCGGTAAATATTAA
Found at i:201783 original size:9 final size:9
Alignment explanation
Indices: 201771--201838 Score: 70
Period size: 9 Copynumber: 7.8 Consensus size: 9
201761 GTGTTTTGCC
201771 CTTACATAA
1 CTTACATAA
201780 CTTACATAA
1 CTTACATAA
* *
201789 ATTAAATAA
1 CTTACATAA
201798 CTTACATAA
1 CTTACATAA
*
201807 CTTACATTA
1 CTTACATAA
201816 --TACATAA
1 CTTACATAA
*
201823 CCTT-CTTAA
1 -CTTACATAA
201832 CTTACAT
1 CTTACAT
201839 TATACACAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 6 0.13
8 3 0.06
9 37 0.79
10 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.37
Consensus pattern (9 bp):
CTTACATAA
Found at i:201865 original size:25 final size:25
Alignment explanation
Indices: 201837--201898 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
201827 CTTAACTTAC
*
201837 ATTATACACAACTCACATAATTAAT
1 ATTATACACAACTCACAGAATTAAT
201862 ATTATACACAACTCACAGAATTAAT
1 ATTATACACAACTCACAGAATTAAT
*
201887 ATTATACCCAAC
1 ATTATACACAAC
201899 CCAATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
ATTATACACAACTCACAGAATTAAT
Found at i:202074 original size:21 final size:21
Alignment explanation
Indices: 202048--202087 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
202038 CTACAACTTA
202048 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
*
202069 AAGCAGAGGCTGCAGCGAG
1 AAGCAGAGGCGGCAGCGAG
202088 AATGCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.47, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:202637 original size:42 final size:41
Alignment explanation
Indices: 202499--202641 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
202489 AATCCCAAAA
* *
202499 TTAGTGGCGTTTTTCGTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTT-TTTAAGCGCCGCTAAAGAACATGATCT
* *
202541 TTGGCGGTGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
* * *
202582 TTAGCCGCGTTTTTTTTAAGTGCCACTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
202623 TTAGCGGCGTTTTTTTTAA
1 TTAGCGGCGTTTTTTTTAA
202642 AAGCGCTGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 80 0.88
42 11 0.12
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
Found at i:210944 original size:20 final size:20
Alignment explanation
Indices: 210905--210950 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
210895 TTTAATAGTA
210905 ATTTAATATTAAAATCATAT
1 ATTTAATATTAAAATCATAT
* * *
210925 ATTTGATATTAAATTTATAT
1 ATTTAATATTAAAATCATAT
210945 -TTTAAT
1 ATTTAAT
210951 TGAATTATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTAATATTAAAATCATAT
Found at i:212228 original size:26 final size:26
Alignment explanation
Indices: 212199--212250 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
212189 AATAAAAGAG
*
212199 TTCAATATCTTGAGTCTATTGACAAT
1 TTCAATATCTTGAGTCCATTGACAAT
212225 TTCAATATCTTGAGTCCATTGACAAT
1 TTCAATATCTTGAGTCCATTGACAAT
212251 AGGGTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (26 bp):
TTCAATATCTTGAGTCCATTGACAAT
Found at i:212489 original size:49 final size:50
Alignment explanation
Indices: 212388--212491 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 50
212378 ATGGTATTGA
*
212388 TTGTGGTTTAAGGTTTACTTAGAAAAGACACATGTATATTATGTAATTCGC
1 TTGTGATTTAAGGTTTACTTAGAAAAGA-ACATGTATATTATGTAATTCGC
*
212439 TTGTGATTTAAGGTTTACTTAGAAAAG-ACATGTATATTATGTAGTTCGC
1 TTGTGATTTAAGGTTTACTTAGAAAAGAACATGTATATTATGTAATTCGC
212488 TTGT
1 TTGT
212492 TACGAACACA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 25 0.49
51 26 0.51
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (50 bp):
TTGTGATTTAAGGTTTACTTAGAAAAGAACATGTATATTATGTAATTCGC
Found at i:224071 original size:22 final size:22
Alignment explanation
Indices: 224041--224083 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
224031 TAATCAGAAT
*
224041 ATTAAAAAAAATAAAAAGATGG
1 ATTAAAAAAAAGAAAAAGATGG
* *
224063 ATTAGAAAAAAGAAGAAGATG
1 ATTAAAAAAAAGAAAAAGATG
224084 TTAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (22 bp):
ATTAAAAAAAAGAAAAAGATGG
Found at i:228431 original size:46 final size:46
Alignment explanation
Indices: 228364--228518 Score: 246
Period size: 46 Copynumber: 3.5 Consensus size: 46
228354 TGATCAGTGA
228364 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
**
228410 CAAGTGACAAAGTGATAAGTGGTAATTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
228456 CAAGTGACAAAGTG-TAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
228500 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
228519 ATCATACTTA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
42 5 0.05
43 11 0.11
44 19 0.19
45 9 0.09
46 58 0.57
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:229496 original size:24 final size:24
Alignment explanation
Indices: 229469--229520 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
229459 GGAGACAAAA
229469 ATGAAG-CCAAGAGTAGAGATGAAG
1 ATGAAGACCAAG-GTAGAGATGAAG
* * *
229493 ATGATGACGACGGTAGAGATGAAG
1 ATGAAGACCAAGGTAGAGATGAAG
229517 ATGA
1 ATGA
229521 GTACAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (24 bp):
ATGAAGACCAAGGTAGAGATGAAG
Found at i:230392 original size:18 final size:18
Alignment explanation
Indices: 230351--230392 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
230341 ACATTGTAAC
*
230351 GCGTTTCAATCTGTACAT
1 GCGTTTCAATCTGTACAG
*
230369 GAGTTTCAATCTGTACAG
1 GCGTTTCAATCTGTACAG
230387 GCGTTT
1 GCGTTT
230393 ACTTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (18 bp):
GCGTTTCAATCTGTACAG
Found at i:238046 original size:26 final size:27
Alignment explanation
Indices: 237992--238048 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
237982 AATTTTAAAA
* *
237992 TATTTTTAAAATACTTTTTTTAATTTT
1 TATTTTTAAAATACATTTTTTAATGTT
**
238019 TATTTTTAAAATA-ATTTTTTGGTGTT
1 TATTTTTAAAATACATTTTTTAATGTT
238045 TATT
1 TATT
238049 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATACATTTTTTAATGTT
Found at i:238147 original size:123 final size:124
Alignment explanation
Indices: 238011--238255 Score: 375
Period size: 124 Copynumber: 2.0 Consensus size: 124
238001 AATACTTTTT
* * * **
238011 TTAATTTTTATTTTTAAAATAATTTTTTGGTGTTTA-TTAAAAAATGGGCCGGGCCGGACTTGGG
1 TTAATTTTAATTTTTAAAATAATTTTTTGGTATTTATTTAAAAAACGGGCCGGGCCGGACCCGGG
* * *
238075 CTTAGGAATTTTTTCCTGGGCCGGGCCTGGACAAAATTTTATGCCCATATTCCGGGCTA
66 CTTAGGAATTTTTTCCCGGGCCGGGCCTGGACAAAATTCTAGGCCCATATTCCGGGCTA
*
238134 TTAATTTTAATTTTTAAAATAATTTTTTGGTATTTATTTAAAAAACGGGCCGGGCCGGGCCCGGG
1 TTAATTTTAATTTTTAAAATAATTTTTTGGTATTTATTTAAAAAACGGGCCGGGCCGGACCCGGG
* * *
238199 CTTATGAATTTTTTCCCGGGCCGGGCCTGGGCAAAATTCTAGGCCCATATTTCGGGC
66 CTTAGGAATTTTTTCCCGGGCCGGGCCTGGACAAAATTCTAGGCCCATATTCCGGGC
238256 CGGGCCGGGC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
123 34 0.31
124 75 0.69
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (124 bp):
TTAATTTTAATTTTTAAAATAATTTTTTGGTATTTATTTAAAAAACGGGCCGGGCCGGACCCGGG
CTTAGGAATTTTTTCCCGGGCCGGGCCTGGACAAAATTCTAGGCCCATATTCCGGGCTA
Found at i:239821 original size:14 final size:14
Alignment explanation
Indices: 239791--239824 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
239781 AAAGTAAGTC
*
239791 ATTTTCCAAAAATT
1 ATTTTCCAAAAACT
*
239805 ATTTTCCAAAAGCT
1 ATTTTCCAAAAACT
239819 ATTTTC
1 ATTTTC
239825 AGTGAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTTTCCAAAAACT
Found at i:248044 original size:19 final size:19
Alignment explanation
Indices: 248020--248058 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
248010 AATAAAAAAA
*
248020 TATTTT-TAATAATATAATT
1 TATTTTGTAA-AAAATAATT
248039 TATTTTGTAAAAAATAATT
1 TATTTTGTAAAAAATAATT
248058 T
1 T
248059 TTATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATTTTGTAAAAAATAATT
Found at i:248059 original size:34 final size:33
Alignment explanation
Indices: 248014--248133 Score: 97
Period size: 33 Copynumber: 3.6 Consensus size: 33
248004 TATAAAAATA
248014 AAAAAAT-ATTTTTAATAATATAATTTATTTTGT
1 AAAAAATAATTTTT-ATAATATAATTTATTTTGT
** *
248047 AAAAAATAATTTTTATAAT-TATATCGCA-ATTG-
1 AAAAAATAATTTTTATAATATA-AT-TTATTTTGT
* *
248079 AAATGATATCTATTTTTA-ATATATAATTTATTTTGT
1 AAA--AAAT-AATTTTTATA-ATATAATTTATTTTGT
248115 AAAAAATAATTTTTATAAT
1 AAAAAATAATTTTTATAAT
248134 TATATCGCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
32 5 0.08
33 26 0.39
34 16 0.24
35 14 0.21
36 5 0.08
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (33 bp):
AAAAAATAATTTTTATAATATAATTTATTTTGT
Found at i:248110 original size:68 final size:69
Alignment explanation
Indices: 248020--248156 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 69
248010 AATAAAAAAA
248020 TATTTTTAATAATATAATTTATTTTGTAAAAAATAATTTTTATAATTATATCGCAATTGAAATGA
1 TATTTTTAATAATATAATTTATTTTGTAAAAAATAATTTTTATAATTATATCGCAATTGAAATGA
248085 TATC
66 TATC
248089 TATTTTTAAT-ATATAATTTATTTTGTAAAAAATAATTTTTATAATTATATCGCAATTGAAATGA
1 TATTTTTAATAATATAATTTATTTTGTAAAAAATAATTTTTATAATTATATCGCAATTGAAATGA
248153 TATC
66 TATC
248157 AATTCAATCA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 58 0.85
69 10 0.15
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (69 bp):
TATTTTTAATAATATAATTTATTTTGTAAAAAATAATTTTTATAATTATATCGCAATTGAAATGA
TATC
Found at i:254529 original size:17 final size:18
Alignment explanation
Indices: 254509--254542 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
254499 CGAAAATGGT
254509 ATAAAA-TTAAAAAAAAC
1 ATAAAAGTTAAAAAAAAC
254526 ATAAAAGTTAAAAAAAA
1 ATAAAAGTTAAAAAAAA
254543 GTTGGGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
ATAAAAGTTAAAAAAAAC
Found at i:254660 original size:10 final size:10
Alignment explanation
Indices: 254647--254761 Score: 87
Period size: 10 Copynumber: 11.5 Consensus size: 10
254637 AGAAGGAGAA
254647 GAAAGAAAAG
1 GAAAGAAAAG
*
254657 GAAAGGAAAG
1 GAAAGAAAAG
254667 GAGAAG-AAAG
1 GA-AAGAAAAG
*
254677 GAAAGGAAAG
1 GAAAGAAAAG
254687 GAGAAG-AAA-
1 GA-AAGAAAAG
*
254696 GAAAAAGAAAG
1 GAAAGA-AAAG
*
254707 GAAAGGAGAA-
1 GAAA-GAAAAG
*
254717 GAAAGGAAAG
1 GAAAGAAAAG
*
254727 GAAAGGAGAA-
1 GAAA-GAAAAG
*
254737 GAAAGAAAAA
1 GAAAGAAAAG
254747 GAAAGAAAAG
1 GAAAGAAAAG
254757 GAAAG
1 GAAAG
254762 GAGAAGAGGG
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.02
9 12 0.14
10 55 0.65
11 15 0.18
12 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:254673 original size:25 final size:25
Alignment explanation
Indices: 254639--254768 Score: 157
Period size: 25 Copynumber: 5.4 Consensus size: 25
254629 GAGAAGAAAG
254639 AAGGAGAAGAAAGAAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
254664 AA-G-G-AG-AAG-AAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
*
254684 AAGGAGAAGAAAGAAAAAGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
*
254709 AAGGAGAAGAAAGGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
* *
254734 GAA-GA-AAGAAAAAGAAAGAAAAGGA
1 -AAGGAGAAGAAAGA-AAAGGAAAGGA
254759 AAGGAGAAGA
1 AAGGAGAAGA
254769 GGGAGGGAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
20 13 0.14
21 4 0.04
22 3 0.03
23 3 0.03
24 12 0.13
25 49 0.54
26 6 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (25 bp):
AAGGAGAAGAAAGAAAAGGAAAGGA
Found at i:254693 original size:45 final size:45
Alignment explanation
Indices: 254639--254758 Score: 222
Period size: 45 Copynumber: 2.7 Consensus size: 45
254629 GAGAAGAAAG
*
254639 AAGGAGAAGAAAGAAAAGGAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
254684 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
*
254729 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGA
254759 AAGGAGAAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (45 bp):
AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
Found at i:254768 original size:20 final size:20
Alignment explanation
Indices: 254626--254751 Score: 143
Period size: 20 Copynumber: 6.2 Consensus size: 20
254616 CATTCGGCTG
254626 AAGGAGAAGAAA-G-AAGGA
1 AAGGAGAAGAAAGGAAAGGA
254644 GAA-GA-AAGAAAAGGAAAGGA
1 -AAGGAGAAG-AAAGGAAAGGA
254664 AAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGGAAAGGA
254684 AAGGAGAAGAAAGAAAAAGAAAGGA
1 AAGGAGAAGAAAG-----GAAAGGA
254709 AAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGGAAAGGA
* *
254729 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGGAAAGGA
254749 AAG
1 AAG
254752 AAAAGGAAAG
Statistics
Matches: 95, Mismatches: 2, Indels: 19
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.03
18 5 0.05
19 5 0.05
20 59 0.62
21 3 0.03
25 20 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGGAAAGGA
Found at i:254902 original size:26 final size:27
Alignment explanation
Indices: 254873--254927 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
254863 ATGTACATTG
*
254873 TATATGTTTTATT-ATTTTATTTAGCA
1 TATATGTTTTATTAAATTTATTTAGCA
*
254899 TATATTTTTTATTAAAATTTATTTAGCA
1 TATATGTTTTATT-AAATTTATTTAGCA
254927 T
1 T
254928 GAAAAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
28 13 0.52
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (27 bp):
TATATGTTTTATTAAATTTATTTAGCA
Found at i:255037 original size:17 final size:17
Alignment explanation
Indices: 255015--255049 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
255005 TTTTTTTACA
*
255015 AAAATAACATTAAAAAT
1 AAAATAACAATAAAAAT
*
255032 AAAATAATAATAAAAAT
1 AAAATAACAATAAAAAT
255049 A
1 A
255050 TGTTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATAACAATAAAAAT
Found at i:255345 original size:129 final size:131
Alignment explanation
Indices: 255190--255455 Score: 428
Period size: 129 Copynumber: 2.0 Consensus size: 131
255180 AAAAACACTC
*
255190 TAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
* * *
255255 TA-TTTTTGAAAGTAATAAAATC-CGAAAAAAATATGAACAAATGGCCAAAATAAGAGTTTTTTA
66 TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
255318 A
131 A
* *
255319 TAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTATAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
* * *
255384 TATTTTTTGAAAGTAATAAAATCTGGGAAAAAATACGAACAAAGGGCCAAAATAAGGGTCTTTTA
66 TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
*
255449 C
131 A
255450 TAAATT
1 TAAATT
255456 TATTTAAAGA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
129 64 0.51
130 20 0.16
131 41 0.33
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (131 bp):
TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
A
Found at i:255352 original size:13 final size:13
Alignment explanation
Indices: 255336--255382 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
255326 ATACATTTCA
255336 AAAATAATGTACT
1 AAAATAATGTACT
255349 AAAATAATGTA-T
1 AAAATAATGTACT
** *
255361 AATAATAAAATACG
1 AA-AATAATGTACT
255375 AAAATAAT
1 AAAATAAT
255383 ATATTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 3 0.11
13 23 0.82
14 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (13 bp):
AAAATAATGTACT
Found at i:255501 original size:153 final size:152
Alignment explanation
Indices: 255319--255866 Score: 893
Period size: 153 Copynumber: 3.6 Consensus size: 152
255309 AGTTTTTTAA
* * * * *
255319 TAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTATAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
* *
255384 TA-TTTT-TTGAAAGTAATAAAATCTGGGAAAAAATACGAACAAAGGGCCAAAATAAGGGTCTTT
66 TATTTTTATTGAAAGTAATAAAAT-TGGGAAAAAATACGAACAAAGGGCCGAAATAAGGAT-TTT
* * *
255447 TACTAAATTTATTTAAAGAACACAG
129 T-TTTAATTTATTTAAAAAACACAG
* * * * *
255472 TAAATTAATAGATTTCAAACACAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
255537 TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTT
66 TATTTTTATTGAAAGTAATAAAATT-GGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTT
255602 TTTAATTTATTTAAAAAACACAG
130 TTTAATTTATTTAAAAAACACAG
*
255625 TAAATTAATACATTTTAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
1 TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
255690 TATTTTTATTGAAAGTAATAAAATTTGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTT
66 TATTTTTATTGAAAGTAATAAAA-TTGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTT
255755 TTTAATTTATTTAAAAAACACAG
130 TTTAATTTATTTAAAAAACACAG
255778 TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
1 TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
255843 TATTTTTATTGAAAGTAATAAAAT
66 TATTTTTATTGAAAGTAATAAAAT
255867 NNNNNNNNNN
Statistics
Matches: 375, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
152 1 0.00
153 314 0.84
154 11 0.03
155 49 0.13
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (152 bp):
TAAATTAATACATTTCAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
TATTTTTATTGAAAGTAATAAAATTGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTT
TTAATTTATTTAAAAAACACAG
Found at i:256213 original size:31 final size:29
Alignment explanation
Indices: 256143--256216 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
256133 GGCTCAAATT
* *
256143 ACATTTTAGTCACTTATGTTTGAGATGTT
1 ACATTTTAGTCACTTATGTTTCAGATGTA
* *
256172 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-GATGTA
256203 ACATTTTAGTCACT
1 ACATTTTAGTCACT
256217 GAGCCATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAGATGTA
Found at i:257094 original size:3 final size:3
Alignment explanation
Indices: 257088--257121 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
257078 CCGGCACCAC
* *
257088 CTT CTT CTT CTT CTT CTT TTT CTT TTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
257122 AGCTAGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
CTT
Found at i:257705 original size:16 final size:16
Alignment explanation
Indices: 257684--257716 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
257674 TTCACATTGC
257684 AAACG-AAAGTGATAGG
1 AAACGAAAAGTGA-AGG
257700 AAACGAAAAGTGAAGG
1 AAACGAAAAGTGAAGG
257716 A
1 A
257717 GAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.06, G:0.30, T:0.09
Consensus pattern (16 bp):
AAACGAAAAGTGAAGG
Found at i:257809 original size:21 final size:20
Alignment explanation
Indices: 257759--257811 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
257749 CAAATGAATA
257759 AAAGAGAGAAAAACGAAAGAG
1 AAAGAGA-AAAAACGAAAGAG
*
257780 ATAGCAGAAAAAACGAAAGAG
1 AAAG-AGAAAAAACGAAAGAG
257801 AGAAGAGAAAA
1 A-AAGAGAAAA
257812 GAGGTTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.02
Consensus pattern (20 bp):
AAAGAGAAAAAACGAAAGAG
Found at i:266210 original size:45 final size:46
Alignment explanation
Indices: 266161--266271 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 46
266151 TGCCATAGTG
*
266161 TCTTTCAATTATGGTCTTACTTAATT-ATGTCATGATGTCAAAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
* * * * * *
266206 TCTTTCAACTATGGTCGTA-TTTATTCTTGTTATGGTGTCATAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
*
266251 TCTTTCAGCTATGGTCTTACT
1 TCTTTCAACTATGGTCTTACT
266272 CATTTTAGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 5 0.09
45 49 0.89
46 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
Found at i:267397 original size:13 final size:13
Alignment explanation
Indices: 267381--267434 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
267371 TTTAAACCAA
*
267381 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
267394 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
267407 ACTTTTTACATAGC
1 ACTTTTCA-AAAGC
267421 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
267434 A
1 A
267435 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:270812 original size:29 final size:30
Alignment explanation
Indices: 270752--270813 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
270742 ACGTACACAT
* *
270752 TTGTACCAAAATCAAAGTTTATGTTTATAA
1 TTGTACCAAAATCAAAGTTAATGTTCATAA
270782 TTGTA-CAAAATCAAAGTTAATGTATCA-AA
1 TTGTACCAAAATCAAAGTTAATGT-TCATAA
270811 TTG
1 TTG
270814 CACATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (30 bp):
TTGTACCAAAATCAAAGTTAATGTTCATAA
Found at i:274376 original size:40 final size:40
Alignment explanation
Indices: 274332--274420 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
274322 CGTTAACACA
274332 TGAACTATTAATTTTTGCTA-ATCTGTTACATATAAATGGT
1 TGAACTATTAATTTTTGCTATATCT-TTACATATAAATGGT
* *
274372 TGAAC-AGTTAATTTTTGCTATTTCTTTACATATAAATTGT
1 TGAACTA-TTAATTTTTGCTATATCTTTACATATAAATGGT
*
274412 TGAATTATT
1 TGAACTATT
274421 GATTAGCGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
39 1 0.02
40 38 0.88
41 4 0.09
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (40 bp):
TGAACTATTAATTTTTGCTATATCTTTACATATAAATGGT
Found at i:292792 original size:109 final size:111
Alignment explanation
Indices: 292672--292891 Score: 309
Period size: 111 Copynumber: 2.0 Consensus size: 111
292662 GTAAATTATT
* * * * * *
292672 TTTTTTTGTGGTGGCTTGCCAATGACCTGCATCACCTTTTTTGTGAGAA-TTTTTTT-TACTTTT
1 TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
*
292735 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTTAAAAAAAA
66 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
* *
292781 TTTTTTGGTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGGAATTTTTTTTATACATTT
1 TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
* * * *
292846 TTCGTGTCAAAAGAAGGTATTAGTATACGGAAAAAGTAAAAAAAAA
66 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
292892 AAATTGTGGT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 42 0.44
110 7 0.07
111 47 0.49
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (111 bp):
TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
Found at i:292912 original size:22 final size:22
Alignment explanation
Indices: 292885--292928 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
292875 GAAAAAGTAA
292885 AAAAAAAAAATTGTGGTGGCCT
1 AAAAAAAAAATTGTGGTGGCCT
292907 AAAAAAAAAATTGTGGTGGCCT
1 AAAAAAAAAATTGTGGTGGCCT
292929 GCCAATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (22 bp):
AAAAAAAAAATTGTGGTGGCCT
Found at i:293012 original size:129 final size:129
Alignment explanation
Indices: 292788--293034 Score: 433
Period size: 129 Copynumber: 1.9 Consensus size: 129
292778 AAATTTTTTG
292788 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGGAATTTTTTTTATACATTTTTCGTGT
1 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGT-GGAATTTTTTTTATACATTTTTCGTGT
*
292853 CAAAAGAAGGTATTAGTATACGGAAAAAGTAAAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAAT
65 CAAAAGAAGGTATTAGTATACGAAAAAAGT-AAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAAT
292918 T
129 T
* *
292919 GTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGT-GAATTTTTTTTTTACATTTTTCGTGTC
1 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGAATTTTTTTTATACATTTTTCGTGTC
*
292983 AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAATTTGTGGTGGCCT
66 AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAAATTGTGGTGGCCT
293035 GCCAATGGTC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
128 22 0.20
129 54 0.48
131 36 0.32
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (129 bp):
GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGAATTTTTTTTATACATTTTTCGTGTC
AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAATT
Found at i:293165 original size:106 final size:105
Alignment explanation
Indices: 292906--293154 Score: 392
Period size: 106 Copynumber: 2.4 Consensus size: 105
292896 TGTGGTGGCC
*
292906 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATTTTTTTTTTAC
1 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATATTTTTTTTAC
* *
292971 ATTTTTCGTGTCAAAAGAAGGTATTAGTATACGAAAAAAG
66 ATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
*
293011 TAAAAAAAAAATTTGTGGTGGCCTGCCAATGGTCGGCACCACCTTTTTTGTGGAA-ATTTTTTTT
1 TAAAAAAAAAA-TTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGT-GAATATTTTTTTT
* * *
293075 ACTTTTTTCGTGTCAATAGCAGGTATCAGTATACAAAAAAAG
64 ACATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
* *
293117 TAAAAAAAAAATTGTGGTGGCTTGGCAATGGCCGGCAC
1 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCAC
293155 AAATTTTTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
105 35 0.27
106 94 0.71
107 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (105 bp):
TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATATTTTTTTTAC
ATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
Found at i:304522 original size:26 final size:26
Alignment explanation
Indices: 304484--304573 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
304474 TGCTCTGGTA
304484 AAAAAACAT-AGGTACTTAATTGGGAC
1 AAAAAAC-TCAGGTACTTAATTGGGAC
** *
304510 AAAAAACTCAGGTACCGAATT-GAAC
1 AAAAAACTCAGGTACTTAATTGGGAC
*
304535 ATTAAAGCCAAATTCAGGTACTTAATTGGGAC
1 ---AAA---AAACTCAGGTACTTAATTGGGAC
304567 AAAAAAC
1 AAAAAAC
304574 AACTCAAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
25 4 0.08
26 20 0.42
28 3 0.06
29 3 0.06
31 15 0.31
32 3 0.06
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.21
Consensus pattern (26 bp):
AAAAAACTCAGGTACTTAATTGGGAC
Found at i:306880 original size:33 final size:33
Alignment explanation
Indices: 306838--306904 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
306828 AAAAGAGAAA
306838 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
1 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
306871 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
1 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
306904 C
1 C
306905 CAACTCCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (33 bp):
CAAAATCACAAAAAAATTTCCTACAATAGGGTG
Found at i:314958 original size:18 final size:19
Alignment explanation
Indices: 314918--314962 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
314908 AAAATCATAA
* *
314918 AAATATTTAAAATTTTAAC
1 AAATTTTTAAAATGTTAAC
*
314937 AAATTTTTAAAA-GTTAAT
1 AAATTTTTAAAATGTTAAC
314955 AAATTTTT
1 AAATTTTT
314963 TAGAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTTTTAAAATGTTAAC
Found at i:316223 original size:41 final size:41
Alignment explanation
Indices: 316166--316246 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
316156 GTTAACTTCT
316166 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
1 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
316207 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGA
1 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGA
316247 TAAAATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (41 bp):
GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
Found at i:321218 original size:13 final size:15
Alignment explanation
Indices: 321189--321220 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
321179 TTGGCTTCCA
321189 TTCTTTTATTGTTTT
1 TTCTTTTATTGTTTT
321204 TTCTTTT-TT-TTTT
1 TTCTTTTATTGTTTT
321217 TTCT
1 TTCT
321221 GGACAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.84
Consensus pattern (15 bp):
TTCTTTTATTGTTTT
Found at i:331807 original size:2 final size:2
Alignment explanation
Indices: 331800--331840 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
331790 ATACTGAAGA
*
331800 AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC 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
331841 TGTATATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:337143 original size:20 final size:20
Alignment explanation
Indices: 337118--337161 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
337108 AAGTACAAAT
*
337118 TATATACATATAGACATACA
1 TATATACATATACACATACA
* *
337138 TATATATATATACATATACA
1 TATATACATATACACATACA
337158 TATA
1 TATA
337162 GGCCTTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (20 bp):
TATATACATATACACATACA
Found at i:337146 original size:18 final size:18
Alignment explanation
Indices: 337119--337153 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
337109 AGTACAAATT
337119 ATATACATATAGACATAC
1 ATATACATATAGACATAC
* *
337137 ATATATATATATACATA
1 ATATACATATAGACATA
337154 TACATATAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATACATATAGACATAC
Found at i:340410 original size:21 final size:21
Alignment explanation
Indices: 340385--340425 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
340375 CAATATCAAG
340385 GGCGACATAATGATCAAACTC
1 GGCGACATAATGATCAAACTC
340406 GGCGACATAATGATCAAACT
1 GGCGACATAATGATCAAACT
340426 GCTGAGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
GGCGACATAATGATCAAACTC
Found at i:354390 original size:56 final size:56
Alignment explanation
Indices: 354278--354390 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
354268 ATCACCTCTA
* ** *
354278 ATTATTACTACACAGAATCATTTAAATGACCTGTTTGTATTCATCATAACTTATTT
1 ATTATTACTACACAAAATCATTTAAATGACCAATTTGTATTCATCATAACTAATTT
*
354334 ATTATTACTACACAAAATCATTTACATGACCAATTTGTATTCATCAT-ACATAATTT
1 ATTATTACTACACAAAATCATTTAAATGACCAATTTGTATTCATCATAAC-TAATTT
354390 A
1 A
354391 CCAATCGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 2 0.04
56 49 0.96
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (56 bp):
ATTATTACTACACAAAATCATTTAAATGACCAATTTGTATTCATCATAACTAATTT
Found at i:355480 original size:76 final size:76
Alignment explanation
Indices: 355354--355502 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
355344 TTTATCACAT
* *
355354 ATTACTTAATAAATACAGTCAATTTATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
355419 ACTTATTCTTC
66 ACTTATTCTTC
355430 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
355495 ACTTATTC
66 ACTTATTC
355503 AACATATAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.46
Consensus pattern (76 bp):
ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
ACTTATTCTTC
Found at i:355539 original size:18 final size:18
Alignment explanation
Indices: 355518--355566 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
355508 ATAAATTTGT
355518 AATTAAATATCATATTAA-
1 AATTAAAT-TCATATTAAC
* *
355536 AATTATATTCATTTTAAC
1 AATTAAATTCATATTAAC
*
355554 AATTAACTTCATA
1 AATTAAATTCATA
355567 ATCAAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATTCATATTAAC
Found at i:360200 original size:15 final size:15
Alignment explanation
Indices: 360175--360209 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
360165 AACTCTATTT
*
360175 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
360189 TAATTAATATTAAGA
1 TAATTAATATTAAGA
360204 TAATTA
1 TAATTA
360210 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:360837 original size:28 final size:28
Alignment explanation
Indices: 360797--360854 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
360787 TTGGCTAGAG
360797 TCAGGTTCCACTAAATCGTAAGTCTAAA
1 TCAGGTTCCACTAAATCGTAAGTCTAAA
*
360825 TCAGGTTCCACTAAATCGTATGTCTAAA
1 TCAGGTTCCACTAAATCGTAAGTCTAAA
360853 TC
1 TC
360855 CTTGGAGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (28 bp):
TCAGGTTCCACTAAATCGTAAGTCTAAA
Found at i:365932 original size:50 final size:50
Alignment explanation
Indices: 365856--366044 Score: 240
Period size: 50 Copynumber: 3.8 Consensus size: 50
365846 TTTCCTGTAC
* * * ** *
365856 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
365906 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
365956 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
366006 TGCCAA---CATGTCCCAGACATGATCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
366045 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
47 31 0.25
50 91 0.75
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:368834 original size:21 final size:22
Alignment explanation
Indices: 368805--368845 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
368795 ACAGCAAGCA
*
368805 ATTTTTTTTCCTTCT-TTTTCG
1 ATTTATTTTCCTTCTCTTTTCG
*
368826 ATTTATTTTCTTTCTCTTTT
1 ATTTATTTTCCTTCTCTTTT
368846 TCGGCCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTATTTTCCTTCTCTTTTCG
Found at i:369784 original size:19 final size:20
Alignment explanation
Indices: 369760--369806 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
369750 TTCCTATACA
*
369760 TATATATGCGCATA-GTTTT
1 TATATATGCACATACGTTTT
*
369779 TATATAATGTACATACGTTTT
1 TATAT-ATGCACATACGTTTT
369800 TATATAT
1 TATATAT
369807 AGTATACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 10 0.42
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
TATATATGCACATACGTTTT
Found at i:369813 original size:19 final size:18
Alignment explanation
Indices: 369791--369830 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
369781 TATAATGTAC
* *
369791 ATACGTTTTTATATATAGT
1 ATACGTTTATACATATA-T
369810 ATACGTTTATACATATAT
1 ATACGTTTATACATATAT
369828 ATA
1 ATA
369831 TAAGTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
ATACGTTTATACATATAT
Found at i:370048 original size:18 final size:18
Alignment explanation
Indices: 370003--370048 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
369993 CACATGCACG
370003 TTTTAAAATACACATGTT
1 TTTTAAAATACACATGTT
* *
370021 TTTCAAAATACACATTTT
1 TTTTAAAATACACATGTT
*
370039 TTTTATAATA
1 TTTTAAAATA
370049 GATATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTAAAATACACATGTT
Found at i:372908 original size:15 final size:15
Alignment explanation
Indices: 372890--372936 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
372880 ATATATTTAT
372890 AAATTAAAATATAAA
1 AAATTAAAATATAAA
* **
372905 AAATTAAATTATACT
1 AAATTAAAATATAAA
372920 AAATTAAAATATAAA
1 AAATTAAAATATAAA
372935 AA
1 AA
372937 TCAAATTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAATATAAA
Found at i:372962 original size:36 final size:36
Alignment explanation
Indices: 372922--373011 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
372912 ATTATACTAA
372922 ATTAAAATATA-AAAATCA-AATTCTAAATTTTAACAT
1 ATTAAAATATACAAAATCATAATT-TAAATTTTAA-AT
* *
372958 ATTAAAA-AAACCAAAATCATAATTTAACTTTTAAAT
1 ATTAAAATATA-CAAAATCATAATTTAAATTTTAAAT
* *
372994 ATTAATATATCCAAAATC
1 ATTAAAATATACAAAATC
373012 GTAAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
35 2 0.04
36 22 0.49
37 17 0.38
38 4 0.09
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (36 bp):
ATTAAAATATACAAAATCATAATTTAAATTTTAAAT
Found at i:373655 original size:26 final size:25
Alignment explanation
Indices: 373593--373659 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
373583 ATTGATATGA
*
373593 TTTATA-ATTTTTTAAGTTATTTTT
1 TTTATATATTTTTTAAATTATTTTT
*
373617 TTTATATA-ATTTTATAATT-TTTATT
1 TTTATATATTTTTTA-AATTATTT-TT
373642 TTTATATATTTTTTAAAT
1 TTTATATATTTTTTAAAT
373660 AATATCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 14 0.39
25 17 0.47
26 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTATATATTTTTTAAATTATTTTT
Found at i:373664 original size:16 final size:16
Alignment explanation
Indices: 373645--373678 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
373635 TTTTATTTTT
373645 ATAT-ATTTTTTAAATA
1 ATATCATTTTTT-AATA
373661 ATATCATTTTTTAATA
1 ATATCATTTTTTAATA
373677 AT
1 AT
373679 TTTAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATCATTTTTTAATA
Found at i:381574 original size:17 final size:17
Alignment explanation
Indices: 381552--381615 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
381542 AATCTTAGAG
381552 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* *
381569 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
*
381588 TTCCAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
381605 TTTTAATTGTA
1 TTCTAATTGTA
381616 GCCCTTGATG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.58
18 2 0.06
19 11 0.31
20 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:381596 original size:36 final size:36
Alignment explanation
Indices: 381544--381614 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
381534 GATTATGTAA
*
381544 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCCAATTGTATACAACTTCTAATTGTG
*
381580 TCTTAGAGTTCCAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCCAATTGTATACAACTTCTAATTGT
381615 AGCCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (36 bp):
TCTTAGAGTTCCAATTGTATACAACTTCTAATTGTG
Found at i:386658 original size:17 final size:17
Alignment explanation
Indices: 386636--386680 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
386626 AATCTTAGAG
386636 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
386653 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAAC
*
386670 TTTTAATTGTA
1 TTCTAATTGTA
386681 GCCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:401018 original size:14 final size:13
Alignment explanation
Indices: 400999--401058 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
400989 TGAATCAAAT
400999 TAAAATATCATATA
1 TAAAAT-TCATATA
*
401013 TAAAATTGCATAAAA
1 TAAAATT-CAT-ATA
401028 TCAAAATTCATATA
1 T-AAAATTCATATA
*
401042 TAACATTGCATAT-
1 TAAAATT-CATATA
401055 TAAA
1 TAAA
401059 CTAAAGTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 9 0.24
14 17 0.45
15 6 0.16
16 6 0.16
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (13 bp):
TAAAATTCATATA
Found at i:401039 original size:29 final size:30
Alignment explanation
Indices: 400980--401053 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
400970 GCTAGTAGTT
* * *
400980 TATAAAATTTGAATCAAATTAAAATATCATA
1 TATAAAA-TTGCATAAAATCAAAATATCATA
401011 TATAAAATTGCATAAAATCAAAAT-TCATA
1 TATAAAATTGCATAAAATCAAAATATCATA
*
401040 TATAACATTGCATA
1 TATAAAATTGCATA
401054 TTAAACTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 18 0.46
30 14 0.36
31 7 0.18
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (30 bp):
TATAAAATTGCATAAAATCAAAATATCATA
Found at i:412955 original size:258 final size:259
Alignment explanation
Indices: 412487--413003 Score: 1027
Period size: 258 Copynumber: 2.0 Consensus size: 259
412477 TATTAAACAC
412487 AAATACAAAATTATATTAATTAATTAATTAATTACTATATTTTATATTTAAATTAATTTATATTC
1 AAATACAAAATTATATTAATTAATTAATTAATTACTATATTTTATATTTAAATTAATTTATATTC
412552 AAGTTATATCCAATTTAATTGGTTCTACCAAGTAAACTAAATGAATTGGTATCTTGTTGATCACA
66 AAGTTATATCCAATTTAATTGGTTCTACCAAGTAAACTAAATGAATTGGTATCTTGTTGATCACA
412617 CCAGTTTGACATCAAGTACGGTTTTTTTGTCAATGCAATTTTTGTATTATATAAGCAGAACTCAA
131 CCAGTTTGACATCAAGTACGGTTTTTTTGTCAATGCAATTTTTGTATTATATAAGCAGAACTCAA
412682 AAGTTGTCATGTGTCTTATTTATTTACTACGTCTTAAAGGGTACATGTCATCCTTTAAGTCTTA
196 AAGTTGTCATGTGTCTTATTTATTTACTACGTCTTAAAGGGTACATGTCATCCTTTAAGTCTTA
412746 AAATACAAAA-TATATTAATTAATTAATTAATTACTATATTTTATATTTAAATTAATTTATATTC
1 AAATACAAAATTATATTAATTAATTAATTAATTACTATATTTTATATTTAAATTAATTTATATTC
412810 AAGTTATATCCAATTTAATTGGTTCTACCAAGTAAACTAAATGAATTGGTATCTTGTTGATCACA
66 AAGTTATATCCAATTTAATTGGTTCTACCAAGTAAACTAAATGAATTGGTATCTTGTTGATCACA
412875 CCAGTTTGACATCAAGTACGGTTTTTTTGTCAATGCAATTTTTGTATTATATAAGCAGAACTCAA
131 CCAGTTTGACATCAAGTACGGTTTTTTTGTCAATGCAATTTTTGTATTATATAAGCAGAACTCAA
412940 AAGTTGTCATGTGTCTTATTTATTTACTACGTCTTAAAGGGTACATGTCATCCTTTAAGTCTTA
196 AAGTTGTCATGTGTCTTATTTATTTACTACGTCTTAAAGGGTACATGTCATCCTTTAAGTCTTA
413004 TTTGTGGAGA
Statistics
Matches: 258, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
258 248 0.96
259 10 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (259 bp):
AAATACAAAATTATATTAATTAATTAATTAATTACTATATTTTATATTTAAATTAATTTATATTC
AAGTTATATCCAATTTAATTGGTTCTACCAAGTAAACTAAATGAATTGGTATCTTGTTGATCACA
CCAGTTTGACATCAAGTACGGTTTTTTTGTCAATGCAATTTTTGTATTATATAAGCAGAACTCAA
AAGTTGTCATGTGTCTTATTTATTTACTACGTCTTAAAGGGTACATGTCATCCTTTAAGTCTTA
Found at i:413464 original size:29 final size:30
Alignment explanation
Indices: 413424--413493 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
413414 TTAAAATTTT
413424 ATGTATAAAATT-ACATAAAATCAAAATCC
1 ATGTATAAAATTAACATAAAATCAAAATCC
* *
413453 ATGTTTAAAATTACACATTAAATCAAAATCC
1 ATGTATAAAATTA-ACATAAAATCAAAATCC
413484 AT-TGATAAAA
1 ATGT-ATAAAA
413494 ATTTATCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 1 0.03
31 23 0.66
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (30 bp):
ATGTATAAAATTAACATAAAATCAAAATCC
Found at i:415717 original size:22 final size:22
Alignment explanation
Indices: 415674--415726 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
415664 ATTTTGATTT
** **
415674 TTTTTAAAAATTTTAACTATAA
1 TTTTTAAAAAAATTAAAAATAA
415696 TTTTTAAAAAAATTAAAAATAA
1 TTTTTAAAAAAATTAAAAATAA
*
415718 -TCTTAAAAA
1 TTTTTAAAAA
415727 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTTAAAAAAATTAAAAATAA
Found at i:416152 original size:8 final size:8
Alignment explanation
Indices: 416139--416167 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
416129 TCAATAAATA
416139 AAATTATT
1 AAATTATT
416147 AAATTATT
1 AAATTATT
416155 AAA-TATT
1 AAATTATT
416162 AAATTA
1 AAATTA
416168 AAATAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:423333 original size:50 final size:50
Alignment explanation
Indices: 423254--423348 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
423244 GCCTTATTCT
* * * *
423254 AATCAATGTCAAATAGAAGGAGAGAAGTTCTATATGGATTCTACTTGTAC
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
*
423304 AATCAATATCAAATAGAAGAAGAGTAGTTCTATACGAATTCTACT
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACT
423349 CGTATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (50 bp):
AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
Found at i:425712 original size:3 final size:3
Alignment explanation
Indices: 425706--425740 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
425696 GCTGGGGTTG
* *
425706 TCT TCT TCT TCT TCT TCT CCT TCT CCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
425741 CTCAGACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:429905 original size:246 final size:247
Alignment explanation
Indices: 429462--429954 Score: 979
Period size: 246 Copynumber: 2.0 Consensus size: 247
429452 TAATTATTTA
429462 TTTATTTTAAATATTATTATTTTTTAAAAGTTTACAACTAAAAATAAAGTTAATCATAATTCAAT
1 TTTATTTTAAATATTATTATTTTTTAAAAGTTTACAACTAAAAATAAAGTTAATCATAATTCAAT
429527 CACAAATATATGTAAAATCAAACAATAATAAACATAAAAAGACTAAGAATCAAAATAATTCGGAC
66 CACAAATATATGTAAAATCAAACAATAATAAACATAAAAAGACTAAGAATCAAAATAATTCGGAC
429592 TAAAATTAACCCTCTAAATTAAAACTTACACATATTAAAATTAAAGACCCACAAATAATATTTAC
131 TAAAATTAACCCTCTAAATTAAAACTTACACATATTAAAATTAAAGACCCACAAATAATATTTAC
429657 ATTTAATGAGACTTGAATTTAGATACTCAAACATCTAAAACCTAGTCTTTGC
196 ATTTAATGAGACTTGAATTTAGATACTCAAACATCTAAAACCTAGTCTTTGC
429709 TTTATTTT-AATATTATTATTTTTTAAAAGTTTACAACTAAAAATAAAGTTAATCATAATTCAAT
1 TTTATTTTAAATATTATTATTTTTTAAAAGTTTACAACTAAAAATAAAGTTAATCATAATTCAAT
429773 CACAAATATATGTAAAATCAAACAATAATAAACATAAAAAGACTAAGAATCAAAATAATTCGGAC
66 CACAAATATATGTAAAATCAAACAATAATAAACATAAAAAGACTAAGAATCAAAATAATTCGGAC
429838 TAAAATTAACCCTCTAAATTAAAACTTACACATATTAAAATTAAAGACCCACAAATAATATTTAC
131 TAAAATTAACCCTCTAAATTAAAACTTACACATATTAAAATTAAAGACCCACAAATAATATTTAC
429903 ATTTAATGAGACTTGAATTTAGATACTCAAACATCTAAAACCTAGTCTTTGC
196 ATTTAATGAGACTTGAATTTAGATACTCAAACATCTAAAACCTAGTCTTTGC
429955 GAATGGTACT
Statistics
Matches: 246, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
246 238 0.97
247 8 0.03
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (247 bp):
TTTATTTTAAATATTATTATTTTTTAAAAGTTTACAACTAAAAATAAAGTTAATCATAATTCAAT
CACAAATATATGTAAAATCAAACAATAATAAACATAAAAAGACTAAGAATCAAAATAATTCGGAC
TAAAATTAACCCTCTAAATTAAAACTTACACATATTAAAATTAAAGACCCACAAATAATATTTAC
ATTTAATGAGACTTGAATTTAGATACTCAAACATCTAAAACCTAGTCTTTGC
Found at i:438915 original size:26 final size:26
Alignment explanation
Indices: 438885--438937 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
438875 AAAAAGAAAG
438885 TTAAAAGACAATTTTATTCTGCTATC
1 TTAAAAGACAATTTTATTCTGCTATC
438911 TTAAAAGACAATTTTATTCTGCTATC
1 TTAAAAGACAATTTTATTCTGCTATC
438937 T
1 T
438938 CTATTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (26 bp):
TTAAAAGACAATTTTATTCTGCTATC
Found at i:446799 original size:48 final size:48
Alignment explanation
Indices: 446679--446835 Score: 199
Period size: 48 Copynumber: 3.2 Consensus size: 48
446669 TTGCACATCG
* * * * *
446679 TCACATATCACACACCGAAGCCATAGCCTAGCTATGGTCTTACACGGAAA
1 TCACATAT--CACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
* *
446729 -CACAAATCACACCGATGTCATATCCCATATATGGTCTTACACGGAAA
1 TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
* * *
446776 TCACATATCACACCGATGTCATATCCTAGATATGATCTTACACAGAAA
1 TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
446824 TCACATATCACA
1 TCACATATCACA
446836 TCACACCAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
47 34 0.36
48 54 0.57
49 6 0.06
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (48 bp):
TCACATATCACACCGATGTCATATCCCAGATATGGTCTTACACGGAAA
Found at i:446874 original size:53 final size:53
Alignment explanation
Indices: 446689--446921 Score: 220
Period size: 53 Copynumber: 4.6 Consensus size: 53
446679 TCACATATCA
* *
446689 CACACCGAAGCCATAGCCTAGCTATGGTCTTACACGGAAA-CAC--A--A-AT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * ** *
446736 CACACCGATGTCATATCCCATATATGGTCTTACACGGAAATCAC--AT---AT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * *
446784 CACACCGATGTCATATCCTAGATATGATCTTACACAGAAATCACATATCACAT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
* * * *
446837 CACACCAATGCCATAGCCCAGCTATGGTCTTATACAG-AAGCACATAGTCACAT
1 CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATA-TCACAT
*
446890 CACACCGATGACATAGCCTAGCTATGGTCTTA
1 CACACCGATGCCATAGCCTAGCTATGGTCTTA
446922 TACGGAAGCA
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
47 34 0.22
48 46 0.29
50 2 0.01
52 8 0.05
53 67 0.43
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.23
Consensus pattern (53 bp):
CACACCGATGCCATAGCCTAGCTATGGTCTTACACAGAAATCACATATCACAT
Found at i:451841 original size:21 final size:21
Alignment explanation
Indices: 451811--451868 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
451801 GCTTCTGTTT
451811 AACCCTTATGGGTTTCCATTC
1 AACCCTTATGGGTTTCCATTC
* * *
451832 AACTCTTATGAGCTTT-CGTTC
1 AACCCTTATG-GGTTTCCATTC
451853 AACCCTTATGGGTTTC
1 AACCCTTATGGGTTTC
451869 TGTTTAGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCATTC
Found at i:451882 original size:42 final size:43
Alignment explanation
Indices: 451761--451895 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 43
451751 TTTCACTAGC
* * * * * *
451761 TTCTGTTTAACTCATATGAGTTTCCGTTTAGCTTTTTTGAGC-
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
* * * *
451803 TTCTGTTTAACCCTTATGGGTTTCCATTCAACTCTTATGAGCT
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
* * *
451846 TTC-GTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGC-
1 TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
451887 TTCTGTTCA
1 TTCTGTTCA
451896 GCCTTCAGGC
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.04
42 70 0.92
43 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (43 bp):
TTCTGTTCAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCT
Found at i:454288 original size:85 final size:85
Alignment explanation
Indices: 454185--454351 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 85
454175 CTCAACATAC
* ** * * *
454185 TTGTGTTGTTGCAGGTATGTCACAAGATCATCTGAAATTGGATTCTGACCTTATCTCTAACATTG
1 TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
*
454250 TCTTATCTATAGTGAAATAT
66 TCTTACCTATAGTGAAATAT
* * **
454270 TTGTGTTGTTACATGTATGTCACAAGATCATCCAAAATTGAACTCTTACATTATCTCTCGCATTG
1 TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
*
454335 TCTTACCTATGGTGAAA
66 TCTTACCTATAGTGAAA
454352 GTGAATCCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (85 bp):
TTGTGTTGTTACAGGTATGTCACAAGATCATCCAAAATTGAACTCTGACATTATCTCTAACATTG
TCTTACCTATAGTGAAATAT
Found at i:458542 original size:10 final size:10
Alignment explanation
Indices: 458527--458558 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
458517 AATTTTATTG
458527 TTTTTATCTC
1 TTTTTATCTC
458537 TTTTTAT-T-
1 TTTTTATCTC
458545 TTTTTATCTC
1 TTTTTATCTC
458555 TTTT
1 TTTT
458559 ATTTTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATCTC
Found at i:458563 original size:16 final size:18
Alignment explanation
Indices: 458519--458563 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
458509 CTTGTTTCAA
458519 TTTTATTGTTTTTATCTCT
1 TTTTATT-TTTTTATCTCT
458538 TTTTATTTTTTTATCTC-
1 TTTTATTTTTTTATCTCT
458555 TTTTATTTT
1 TTTTATTTT
458564 CGTTTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTTATCTCT
Found at i:467867 original size:91 final size:90
Alignment explanation
Indices: 467709--467954 Score: 277
Period size: 91 Copynumber: 2.7 Consensus size: 90
467699 CTTAACAGTG
* * * * *
467709 TAAAAAG-CCCTCAAAGTTTTTCAAGAAAAGCAATTAAGCCCCTGTTTTATTTTTTACACTCAAT
1 TAAAAAGACCCTCAAATTTTTTTAAAAAAAGCAATTAAGCCCCTATTTT-TTTTTTGCACTCAAT
* * *
467773 TGGGTATTTAAACTT-TCAAAATGTAT
65 TGGGTACTTAAA-TTGTCAAAATATAC
*
467799 TAAAAAGACCTTCAAACTTTTTTTAAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTCAAT
1 TAAAAAGACCCTCAAA-TTTTTTTAAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTCAAT
*
467864 TGGGTACTTGAATTGTCAAAATATAC
65 TGGGTACTTAAATTGTCAAAATATAC
* ** *
467890 CAAAAA-AGCCCTC-AATTTTTTT-TTAAAAGCAATTAAGCCCTTACTCTTTTTTTTTGCACTCA
1 TAAAAAGA-CCCTCAAATTTTTTTAAAAAAAGCAATTAAGCCCCTA-T-TTTTTTTTTGCACTCA
467952 ATT
63 ATT
467955 TCCAAAATGC
Statistics
Matches: 135, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
88 18 0.13
89 8 0.06
90 31 0.23
91 49 0.36
92 29 0.21
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (90 bp):
TAAAAAGACCCTCAAATTTTTTTAAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTCAATT
GGGTACTTAAATTGTCAAAATATAC
Found at i:468135 original size:26 final size:26
Alignment explanation
Indices: 468106--468159 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
468096 AATTAAAGTT
*
468106 ATAAAAAGTATTAAATTTTAATAAAA
1 ATAAAAAATATTAAATTTTAATAAAA
* * *
468132 ATAAAAAATATTTATTTTTATTAAAA
1 ATAAAAAATATTAAATTTTAATAAAA
468158 AT
1 AT
468160 TAGAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATAAAAAATATTAAATTTTAATAAAA
Found at i:468166 original size:27 final size:26
Alignment explanation
Indices: 468121--468172 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
468111 AAGTATTAAA
*
468121 TTTTAATAAAAATAAAAAATATTTAT
1 TTTTAATAAAAATAAAAAAAATTTAT
* *
468147 TTTTATTAAAAATTAGAAAAAATTTA
1 TTTTAATAAAAA-TAAAAAAAATTTA
468173 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTTAATAAAAATAAAAAAAATTTAT
Found at i:468497 original size:22 final size:22
Alignment explanation
Indices: 468452--468497 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
468442 TTAAAGGGCA
**
468452 TTTTTATGCATTTTATAATCTT
1 TTTTTATGCATTTTATAAAATT
468474 TTTTTATG-ATTTTTATAAAATT
1 TTTTTATGCA-TTTTATAAAATT
468496 TT
1 TT
468498 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTATGCATTTTATAAAATT
Found at i:468507 original size:21 final size:21
Alignment explanation
Indices: 468483--468522 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
468473 TTTTTTATGA
*
468483 TTTTTATAAAATTTTATAATT
1 TTTTTATAAAATTTAATAATT
* *
468504 TTTTTCTAATATTTAATAA
1 TTTTTATAAAATTTAATAA
468523 AAAATAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTATAAAATTTAATAATT
Found at i:468829 original size:92 final size:89
Alignment explanation
Indices: 468693--468858 Score: 226
Period size: 92 Copynumber: 1.8 Consensus size: 89
468683 ATTGAGTGCA
*
468693 AAAAAAAAAGTAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
1 AAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
**
468758 GTAGTTCAAATACTTAAATGAATG
66 AAAGTTCAAATACTTAAATGAATG
* * * *
468782 AAAAAAAAA-CAGGGGCTTAATTGTTTTATTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGTAT
1 AAAAAAAAAGCAGGGGCTTAA-T-TATT-TTTTTTTG-AAAAGTTTGAGAGCATTTTTGATATAT
468846 TTTGAAAGTTCAA
62 TTTGAAAGTTCAA
468859 GTACCCAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
88 10 0.15
89 10 0.15
90 3 0.05
91 8 0.12
92 35 0.53
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (89 bp):
AAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTG
AAAGTTCAAATACTTAAATGAATG
Found at i:468878 original size:92 final size:89
Alignment explanation
Indices: 468682--468880 Score: 220
Period size: 92 Copynumber: 2.2 Consensus size: 89
468672 TTATTTTGGA
*
468682 AATTGAGTGCAAAAAAAAAAGTAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTT
1 AATTGAGT--AAAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTT
** **
468747 GATATATTTTGGTAGTTCAAATACTT
64 GATATATTTTGAAAGTTCAAATACCC
* * * * *
468773 AAATGAATGAAAAAAAAA-CAGGGGCTTAATTGTTTTATTTTTTTGAAAAAGTTTGAGAGCCTTT
1 AATTGAGTAAAAAAAAAAGCAGGGGCTTAA-T-TATT-TTTTTTTG-AAAAGTTTGAGAGCATTT
* * *
468837 TTTATGTATTTTGAAAGTTCAAGTACCC
62 TTGATATATTTTGAAAGTTCAAATACCC
468865 AATTGAGTAAAAAAAA
1 AATTGAGTAAAAAAAA
468881 GCAGCAACTT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
88 10 0.11
89 10 0.11
90 3 0.03
91 14 0.16
92 51 0.58
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (89 bp):
AATTGAGTAAAAAAAAAAGCAGGGGCTTAATTATTTTTTTTTGAAAAGTTTGAGAGCATTTTTGA
TATATTTTGAAAGTTCAAATACCC
Found at i:468907 original size:92 final size:91
Alignment explanation
Indices: 468719--468914 Score: 214
Period size: 92 Copynumber: 2.1 Consensus size: 91
468709 CTTAATTATT
** **
468719 TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGGTAGTTCAAATACTTAAATGAATGAA
1 TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGAA
***
468784 AAAAAAACAGGGGCTTAATTGTTTTA
66 AAAAAAACAGCAACTTAATTGTTTTA
* * * * * *
468810 TTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGTATTTTGAAAGTTCAAGTACCCAATTGAGT-A
1 TTTTTTTG-AAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGA
* *
468874 AAAAAAAGCAGCAACTTAATTGTCTTTTCT
65 AAAAAAAACAGCAACTTAATTG--TTTT-A
468904 TTTTTTTGAAA
1 TTTTTTTGAAA
468915 TGATGCAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
91 27 0.31
92 44 0.51
93 7 0.08
94 8 0.09
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (91 bp):
TTTTTTTGAAAAGTTTGAGAGCATTTTTGATATATTTTGAAAGTTCAAATACCCAAATGAATGAA
AAAAAAACAGCAACTTAATTGTTTTA
Found at i:470928 original size:12 final size:13
Alignment explanation
Indices: 470909--470946 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
470899 TCGGTCAATA
470909 ATTAGTTTTAATT
1 ATTAGTTTTAATT
* *
470922 ATT-GTTTCATTT
1 ATTAGTTTTAATT
470934 ATTAGTTTTAATT
1 ATTAGTTTTAATT
470947 CTTTTTCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:470964 original size:24 final size:25
Alignment explanation
Indices: 470903--470965 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
470893 TTAAATTCGG
470903 TCAATAATTAGTTTTAATTATTGTT
1 TCAATAATTAGTTTTAATTATTGTT
* * *
470928 TCATTTATTAGTTTTAATTCTT-TT
1 TCAATAATTAGTTTTAATTATTGTT
*
470952 TCAATAATCAGTTT
1 TCAATAATTAGTTT
470966 GTACTTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (25 bp):
TCAATAATTAGTTTTAATTATTGTT
Found at i:479522 original size:3 final size:3
Alignment explanation
Indices: 479509--479568 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
479499 ATTTTCTCCC
* * *
479509 ATT ATTT ATT ATT ATT GTT A-T ATT ATTT ATT ATC ATC ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* *
479555 TTT ATT ATT TTT AT
1 ATT ATT ATT ATT AT
479569 ATTTGTACAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:479553 original size:24 final size:21
Alignment explanation
Indices: 479509--479571 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
479499 ATTTTCTCCC
*
479509 ATTATTTATTATTATTGTTAT
1 ATTATTTATTATTATTATTAT
* *
479530 ATTATTTATTATCATCA-T-T
1 ATTATTTATTATTATTATTAT
*
479549 ATTATTT-TTATTATTTTTAT
1 ATTATTTATTATTATTATTAT
479569 ATT
1 ATT
479572 TGTACATACG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.18
19 9 0.26
20 5 0.15
21 14 0.41
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATTTATTATTATTATTAT
Found at i:479571 original size:8 final size:9
Alignment explanation
Indices: 479509--479572 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
479499 ATTTTCTCCC
479509 ATTATTTATT
1 ATTATTT-TT
479519 ATTATTGTTAT
1 ATTATT-TT-T
479530 ATTATTTATT
1 ATTATTT-TT
* **
479540 ATCATCATT
1 ATTATTTTT
479549 ATTATTTTT
1 ATTATTTTT
479558 ATTATTTTT
1 ATTATTTTT
479567 A-TATTT
1 ATTATTT
479573 GTACATACGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
8 5 0.11
9 18 0.40
10 13 0.29
11 9 0.20
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (9 bp):
ATTATTTTT
Found at i:481941 original size:24 final size:24
Alignment explanation
Indices: 481890--481943 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
481880 AGCTCAGGCA
* * *
481890 AGCCAATAACGGGTAGCTCTGAAG
1 AGCCATTAACGAGAAGCTCTGAAG
* *
481914 AGCCATTAACGAGAAGCTCTGGAT
1 AGCCATTAACGAGAAGCTCTGAAG
481938 AGCCAT
1 AGCCAT
481944 ATATCAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
AGCCATTAACGAGAAGCTCTGAAG
Found at i:482057 original size:26 final size:27
Alignment explanation
Indices: 481969--482058 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 27
481959 AGCAAGTTAT
*
481969 ATCGGGAAGCTC-CGGAGAGCCAT-TA
1 ATCGGGAAGCTCACGAAGAGCCATATA
* * *
481994 ATCAGGAAGCTCACAAAGAGCC-TTTA
1 ATCGGGAAGCTCACGAAGAGCCATATA
* *
482020 ATTGGGTAGCTCACGAAGAGCCATAT-
1 ATCGGGAAGCTCACGAAGAGCCATATA
*
482046 ATCGGGACGCTCA
1 ATCGGGAAGCTCA
482059 TAAGAGCTGT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
25 12 0.24
26 37 0.73
27 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (27 bp):
ATCGGGAAGCTCACGAAGAGCCATATA
Found at i:486510 original size:48 final size:48
Alignment explanation
Indices: 486434--486531 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
486424 CATATGTTCC
*
486434 ACCAGAGAACATTGAGAACATTATTTCTGCTCATGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
486482 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
486530 AC
1 AC
486532 GAAATCCTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (48 bp):
ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
Found at i:492415 original size:12 final size:12
Alignment explanation
Indices: 492398--492430 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
492388 CTCTTGAAAT
492398 ACTTGTGTCCAC
1 ACTTGTGTCCAC
492410 ACTTGTGTCCAC
1 ACTTGTGTCCAC
492422 ACTTGTGTC
1 ACTTGTGTC
492431 TGACACACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.36
Consensus pattern (12 bp):
ACTTGTGTCCAC
Found at i:495423 original size:21 final size:21
Alignment explanation
Indices: 495399--495439 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
495389 ATTATTTGGG
495399 AAAATGTA-AAAAAAATTTAAA
1 AAAAT-TATAAAAAAATTTAAA
*
495420 AAAATTATAAATAAATTTAA
1 AAAATTATAAAAAAATTTAA
495440 TATTTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTATAAAAAAATTTAAA
Found at i:496147 original size:13 final size:13
Alignment explanation
Indices: 496131--496155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
496121 TTATGAAAAA
496131 ATTATTATTATTT
1 ATTATTATTATTT
496144 ATTATTATTATT
1 ATTATTATTATT
496156 AAAATGTGTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:502925 original size:13 final size:13
Alignment explanation
Indices: 502907--502931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502897 AAATAGTAAA
502907 TATATTTAAATTT
1 TATATTTAAATTT
502920 TATATTTAAATT
1 TATATTTAAATT
502932 ATAATAATAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAAATTT
Found at i:505081 original size:41 final size:41
Alignment explanation
Indices: 505013--505213 Score: 271
Period size: 41 Copynumber: 4.9 Consensus size: 41
505003 TGAGTTTTTG
* * * *
505013 GGGCATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTG
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
505054 GGGCCTCTAGCGACGCTTTTT-AGAAAGCGCCGCTAATGCTA
1 GGGCCTTTAGCGACG-TTTTTGAGAAAGCGCCGCTAATGCTC
*
505095 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
505136 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
* *
505177 GGGCCTTTAGC-AGCGTTTTTGAAAAAGTGCCGCTAAT
1 GGGCCTTTAGCGA-CGTTTTTGAGAAAGCGCCGCTAAT
505214 AATAAAAAAA
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 5 0.03
41 134 0.93
42 5 0.03
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (41 bp):
GGGCCTTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTC
Found at i:505161 original size:82 final size:82
Alignment explanation
Indices: 505013--505213 Score: 305
Period size: 82 Copynumber: 2.5 Consensus size: 82
505003 TGAGTTTTTG
* *
505013 GGGCATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGCCTCTAGCGACGCTTTTTAGA
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTTAGA
*
505078 AAGCGCCGCTAATGCTA
66 AAGCGCCACTAATGCTA
* * *
505095 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGCCTTTAGCGGCG-TTTTTGAG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTT-AG
*
505159 AAAGCGCCACTAATGCTC
65 AAAGCGCCACTAATGCTA
* *
505177 GGGCCTTTAGCAGCGTTTTTGAAAAAGTGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
505214 AATAAAAAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 5 0.05
82 103 0.95
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (82 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTCTAGCGACGCTTTTTAGA
AAGCGCCACTAATGCTA
Found at i:507807 original size:2 final size:2
Alignment explanation
Indices: 507800--507825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
507790 AATTTAGCTG
507800 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
507826 TTAGCTTCTT
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):
AT
Found at i:510252 original size:50 final size:51
Alignment explanation
Indices: 510156--510255 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 51
510146 TCAAAATTTT
510156 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
1 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
* *
510207 AAAATTTTCATTTAATCTCTTTAA-ATCTTTAATTATATCAGTTTTAATT
1 AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATT
510256 AGAATAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 25 0.53
51 22 0.47
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (51 bp):
AAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTTAATTG
Found at i:511252 original size:91 final size:91
Alignment explanation
Indices: 511097--511310 Score: 286
Period size: 91 Copynumber: 2.4 Consensus size: 91
511087 TGATACATCG
* * * * * *
511097 ATTGATAGTTCAAGTACCACATTGAACATTTTCCAAGTATAAGTACCACGTTGGGCAATTTATGA
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGACAATTTATGA
* **
511162 AAGTACATGTGTCAAATAAGACACAA
66 AAGTACAGGTACCAAATAAGACACAA
* * *
511188 ATTGATAGTTCAAGTATCACATTGGACATTTTCAAAGTAC-AGATATCACATTAGACATTTTATG
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAG-TACCACATTAGACAATTTATG
*
511252 AAAGTACAGGTACCAAATAATACACAA
65 AAAGTACAGGTACCAAATAAGACACAA
*
511279 ATTAATAGTTCAAGTACCACATTGGACATTTT
1 ATTGATAGTTCAAGTACCACATTGGACATTTT
511311 ATGAAAGTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 2 0.02
91 105 0.98
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (91 bp):
ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTAGACAATTTATGA
AAGTACAGGTACCAAATAAGACACAA
Found at i:514775 original size:12 final size:12
Alignment explanation
Indices: 514758--514789 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
514748 ATATGAATGG
514758 AATAATAATATT
1 AATAATAATATT
514770 AATAATAATATT
1 AATAATAATATT
514782 AATAATAA
1 AATAATAA
514790 CAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAATAATATT
Done.