Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold291
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: 746122
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 35978 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:275072 original size:16 final size:16
Alignment explanation
Indices: 275048--275080 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
275038 AACCAATAAA
*
275048 TAATTTTTTATATTTT
1 TAATATTTTATATTTT
275064 TAATATTTTATATTTT
1 TAATATTTTATATTTT
275080 T
1 T
275081 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TAATATTTTATATTTT
Found at i:279872 original size:30 final size:30
Alignment explanation
Indices: 279838--280088 Score: 167
Period size: 30 Copynumber: 8.4 Consensus size: 30
279828 TCATCGACCA
*
279838 ATGAAAAGGGATAGCT-TCGACTATCAAACT
1 ATGAAAAGGGAT-GCTGTCGACCATCAAACT
* * * *
279868 ATGAAAAGGGATAGCT-CCGGCTATCAAATT
1 ATGAAAAGGGAT-GCTGTCGACCATCAAACT
* *
279898 ATGAAAAGGGATGGTGAT-GACCATC-AACA
1 ATGAAAAGGGATGCTG-TCGACCATCAAACT
* * * *
279927 ATGAAAAAGGATGGTGACGACCATCGAACT
1 ATGAAAAGGGATGCTGTCGACCATCAAACT
* * * * *
279957 ATGAAAATGGATAGCT-TCGGCTATCGAATT
1 ATGAAAAGGGAT-GCTGTCGACCATCAAACT
* **
279987 ATGAAAAGGGATGGTGAT-GACCATC-GGCT
1 ATGAAAAGGGATGCTG-TCGACCATCAAACT
* * *
280016 ATGAAAAGGGATGGTGACGACCATCAAAAT
1 ATGAAAAGGGATGCTGTCGACCATCAAACT
* *
280046 ATGGAAAGGGATAGCT-TCGACTATCAAACT
1 ATGAAAAGGGAT-GCTGTCGACCATCAAACT
*
280076 ATGGAAAGGGATG
1 ATGAAAAGGGATG
280089 GTAACAACCA
Statistics
Matches: 177, Mismatches: 34, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
29 53 0.30
30 119 0.67
31 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (30 bp):
ATGAAAAGGGATGCTGTCGACCATCAAACT
Found at i:280101 original size:89 final size:89
Alignment explanation
Indices: 279829--280090 Score: 355
Period size: 89 Copynumber: 2.9 Consensus size: 89
279819 TATCGACGAT
* * * *
279829 CATCGACCAATGAAAAGGGATAGCT-TCGACTATCAAACTATGAAAAGGGATAGCTCCGGCTATC
1 CATCGA-CAATGAAAAGGGAT-GGTGACGACCATCAAACTATGAAAAGGGATAGCTTCGGCTATC
279893 AAATTATGAAAAGGGATGGTGATGAC
64 AAATTATGAAAAGGGATGGTGATGAC
* * * * *
279919 CATCAACAATGAAAAAGGATGGTGACGACCATCGAACTATGAAAATGGATAGCTTCGGCTATCGA
1 CATCGACAATGAAAAGGGATGGTGACGACCATCAAACTATGAAAAGGGATAGCTTCGGCTATCAA
279984 ATTATGAAAAGGGATGGTGATGAC
66 ATTATGAAAAGGGATGGTGATGAC
* * * * *
280008 CATCGGCTATGAAAAGGGATGGTGACGACCATCAAAATATGGAAAGGGATAGCTTCGACTATCAA
1 CATCGACAATGAAAAGGGATGGTGACGACCATCAAACTATGAAAAGGGATAGCTTCGGCTATCAA
* *
280073 ACTATGGAAAGGGATGGT
66 ATTATGAAAAGGGATGGT
280091 AACAACCATC
Statistics
Matches: 150, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
88 2 0.01
89 143 0.95
90 5 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (89 bp):
CATCGACAATGAAAAGGGATGGTGACGACCATCAAACTATGAAAAGGGATAGCTTCGGCTATCAA
ATTATGAAAAGGGATGGTGATGAC
Found at i:285647 original size:2 final size:2
Alignment explanation
Indices: 285640--285667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
285630 CTAAAGCCAC
285640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285668 GTATGTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291437 original size:15 final size:15
Alignment explanation
Indices: 291417--291448 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
291407 CATTTCACTA
*
291417 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
291432 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
291447 TT
1 TT
291449 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:294721 original size:19 final size:21
Alignment explanation
Indices: 294683--294721 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
294673 CCTTTTTTAA
*
294683 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
294704 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
294722 CAGTAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:294925 original size:23 final size:22
Alignment explanation
Indices: 294882--294939 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
294872 AAAGGGTATC
* *
294882 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
294903 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
294926 TACATATCATATCT
1 TACAAATCATATCT
294940 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:294942 original size:19 final size:19
Alignment explanation
Indices: 294895--294965 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 19
294885 AAATTAAATC
*
294895 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
294915 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
294937 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
294958 TCTAAGAT
1 TCTAAGAT
294966 CGCATATCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.20
21 17 0.39
22 7 0.16
23 11 0.25
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:294955 original size:21 final size:21
Alignment explanation
Indices: 294929--294972 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
294919 CTAAGATTAC
*
294929 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATCGCAT
294950 ATATCATATCTAAGATCGCAT
1 ATATCATATCTAAGATCGCAT
294971 AT
1 AT
294973 CCTCGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATCATATCTAAGATCGCAT
Found at i:296181 original size:43 final size:44
Alignment explanation
Indices: 296109--296232 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 44
296099 AAAGCTCATA
* * * *
296109 CAATGCCAA-TGTCCCAGACATGGTATTACATGTAATCACATA-T
1 CAATGCCAACTGTCCCAGACAGGGTCTTACACGTAAACACA-AGT
* *
296152 CGATG-CTACTGTCCCAGACAGGGTCTTACACGTAAACACAAGT
1 CAATGCCAACTGTCCCAGACAGGGTCTTACACGTAAACACAAGT
*
296195 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACA
1 CAATGCCAACTGTCCCAGACAG-GGTCTTACACGTAAACA
296233 AATATCAGAG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 4 0.06
43 61 0.90
44 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (44 bp):
CAATGCCAACTGTCCCAGACAGGGTCTTACACGTAAACACAAGT
Found at i:301186 original size:21 final size:21
Alignment explanation
Indices: 301112--301228 Score: 73
Period size: 21 Copynumber: 5.6 Consensus size: 21
301102 GTTGACCTTT
*
301112 GAATCGAGTT-AAACAAC-AAA
1 GAATCGA-TTCAATCAACAAAA
* *
301132 GAATCGATTCAAACAATAAAAA
1 GAATCGATTCAATCAA-CAAAA
* *
301154 GAATTGAGTCAATCAACAAAA
1 GAATCGATTCAATCAACAAAA
* **
301175 CAATCGATTCAAAT-AAGTAAA
1 GAATCGATTC-AATCAACAAAA
*
301196 GAATCGATTTAAGAT-AACAAAA
1 GAATCGA-TTCA-ATCAACAAAA
301218 -AATCGATTCAA
1 GAATCGATTCAA
301229 AAGAAACAAC
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
19 3 0.04
20 16 0.21
21 29 0.38
22 28 0.37
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.21
Consensus pattern (21 bp):
GAATCGATTCAATCAACAAAA
Found at i:301197 original size:42 final size:43
Alignment explanation
Indices: 301125--301229 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 43
301115 TCGAGTTAAA
* * *
301125 CAACAAAGAATCGATTCAAACAATAAAAAGAATTGA-GTCA-AT
1 CAACAAAAAATCGATTCAAACAAT-AAAAGAATCGATGTAAGAT
* *
301167 CAACAAAACAATCGATTCAAATAAGT-AAAGAATCGATTTAAGAT
1 CAACAAAA-AATCGATTCAAACAA-TAAAAGAATCGATGTAAGAT
301211 -AACAAAAAATCGATTCAAA
1 CAACAAAAAATCGATTCAAA
301230 AGAAACAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
42 28 0.52
43 23 0.43
44 3 0.06
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.20
Consensus pattern (43 bp):
CAACAAAAAATCGATTCAAACAATAAAAGAATCGATGTAAGAT
Found at i:301332 original size:20 final size:20
Alignment explanation
Indices: 301307--301419 Score: 111
Period size: 20 Copynumber: 5.5 Consensus size: 20
301297 GTTGGCCTTT
301307 GAATCGAGTT-AAACAACAAA
1 GAATCGA-TTCAAACAACAAA
* *
301327 GAATCGATTCAAATAATAAA
1 GAATCGATTCAAACAACAAA
*
301347 CAATCGATTCAAACAACAAAAA
1 GAATCGATTCAAACAAC--AAA
* *
301369 GAATCGAGTCAATCAACAAAA
1 GAATCGATTCAAACAAC-AAA
* *
301390 CAATCGATTCAAATAAGCAAA
1 GAATCGATTCAAACAA-CAAA
301411 GAATCGATT
1 GAATCGATT
301420 TAAGACAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.03
20 29 0.38
21 27 0.36
22 18 0.24
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.19
Consensus pattern (20 bp):
GAATCGATTCAAACAACAAA
Found at i:301392 original size:43 final size:43
Alignment explanation
Indices: 301318--301402 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
301308 AATCGAGTTA
* *
301318 AACAACAAAGAATCGATTCAAATAATAAACAATCGATTCAAAC
1 AACAACAAAGAATCGAGTCAAATAAAAAACAATCGATTCAAAC
301361 AACAA-AAAGAATCGAGTC-AATCAACAAAACAATCGATTCAAA
1 AACAACAAAGAATCGAGTCAAAT-AA-AAAACAATCGATTCAAA
301403 TAAGCAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 14 0.37
43 21 0.55
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.16
Consensus pattern (43 bp):
AACAACAAAGAATCGAGTCAAATAAAAAACAATCGATTCAAAC
Found at i:301394 original size:21 final size:22
Alignment explanation
Indices: 301318--301402 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
301308 AATCGAGTTA
*
301318 AACAACAAAGAATCGATTCAAA-
1 AACAA-AAACAATCGATTCAAAC
* *
301340 TA-ATAAACAATCGATTCAAAC
1 AACAAAAACAATCGATTCAAAC
* * *
301361 AACAAAAAGAATCGAGTCAATC
1 AACAAAAACAATCGATTCAAAC
301383 AAC-AAAACAATCGATTCAAA
1 AACAAAAACAATCGATTCAAA
301403 TAAGCAAAGA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
20 15 0.30
21 16 0.32
22 19 0.38
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.16
Consensus pattern (22 bp):
AACAAAAACAATCGATTCAAAC
Found at i:301410 original size:22 final size:21
Alignment explanation
Indices: 301328--301419 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
301318 AACAACAAAG
*
301328 AATCGATTCAAATAA-TAAAC
1 AATCGATTCAAATAACAAAAC
* *
301348 AATCGATTCAAACAACAAAAAG
1 AATCGATTCAAATAAC-AAAAC
*
301370 AATCGAGTC-AATCAACAAAAC
1 AATCGATTCAAAT-AACAAAAC
*
301391 AATCGATTCAAATAAGC-AAAG
1 AATCGATTCAAATAA-CAAAAC
301412 AATCGATT
1 AATCGATT
301420 TAAGACAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
20 14 0.24
21 27 0.46
22 18 0.31
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (21 bp):
AATCGATTCAAATAACAAAAC
Found at i:301412 original size:42 final size:40
Alignment explanation
Indices: 301308--301417 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 40
301298 TTGGCCTTTG
* *
301308 AATCGAGTT-AAACAACAAAGAATCGATTCAAATAATAAAC
1 AATCGA-TTCAAACAACAAAGAATCGAGTCAAATAAAAAAC
301348 AATCGATTCAAACAACAAAAAGAATCGAGTC-AATCAACAAAAC
1 AATCGATTCAAACAAC--AAAGAATCGAGTCAAAT-AA-AAAAC
*
301391 AATCGATTCAAATAAGCAAAGAATCGA
1 AATCGATTCAAACAA-CAAAGAATCGA
301418 TTTAAGACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
39 2 0.03
40 13 0.21
41 3 0.05
42 24 0.39
43 18 0.30
44 1 0.02
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (40 bp):
AATCGATTCAAACAACAAAGAATCGAGTCAAATAAAAAAC
Found at i:302077 original size:3 final size:3
Alignment explanation
Indices: 302069--302093 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
302059 CGTTTCCTTC
302069 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
302094 TAATTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:307990 original size:20 final size:19
Alignment explanation
Indices: 307965--308002 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
307955 GTTAGGATGC
307965 ACTTCGTGTGCCAGATATGT
1 ACTTCGTGTGCCAG-TATGT
307985 ACTTCGTGTGCCAGTATG
1 ACTTCGTGTGCCAGTATG
308003 CGTTGTGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (19 bp):
ACTTCGTGTGCCAGTATGT
Found at i:308499 original size:202 final size:199
Alignment explanation
Indices: 308066--308601 Score: 747
Period size: 201 Copynumber: 2.7 Consensus size: 199
308056 GCCCTACTTC
* * *
308066 GATTTA-TAAGTATTTATAGTTATGAATTATAAGTAAGTGACT-GTTGTGAAATAACAACCCCAA
1 GATTTAGTAAGTTTTTATAGTTATGTATTATAAGCAAGTGA-TAGTTGTGAAATAACAACCCC-A
* *
308129 ATACTTTTTACTAATTATTTTATCATACTTATCAGTCTCTTAA-ATCCTCTTGTTTATAGAGTTA
64 GTACTTTTTACTAATTATTTTCTCATACTTATCAGTCTCTTAAGA--CTCTTGTTTATAGAGTTA
* *
308193 AAAATGTGTAATCAAATAATATTCAAATGTATTAAGTGGAGTATATATTTTTTATTAAATGATAA
127 AAAATGTGTAATCAAATAATAATCAAATGTATTAAGTGGAGTATATATTTTCTATTAAATGATAA
308258 ATAAAAAA
192 ATAAAAAA
* *
308266 GATTTAGTAAGTTTTTATAGTTATGTATTATAAACAAGTGATAGTTGTGAAATAACAACTCCAGG
1 GATTTAGTAAGTTTTTATAGTTATGTATTATAAGCAAGTGATAGTTGTGAAATAACAACCCCA-G
*
308331 TACTTTTTACTAATTATTTTCTCATACTTATCAGTCTCTTAAGACTATTTGTTTATAGAGTTAAA
65 TACTTTTTACTAATTATTTTCTCATACTTATCAGTCTCTTAAGACT-CTTGTTTATAGAGTTAAA
* *
308396 AATGTGTGTATCAAATAATAATCCAATGTATTAAGTGGAGTATATATTTTCTATTAAATGATAAA
129 AATGTGT-AATCAAATAATAATCAAATGTATTAAGTGGAGTATATATTTTCTATTAAATGATAAA
*
308461 TGAAAAA
193 TAAAAAA
* **
308468 GATTTAGTAAGTTTTTATAGTTACGTATTATAAGCAAGTGATAGTTGCAAAATAATAACAACCCC
1 GATTTAGTAAGTTTTTATAGTTATGTATTATAAGCAAGTGATAGTTG--TGA-AATAACAACCCC
* * * * * *
308533 AGT-TTTTTTACTAATTATTTTCTTACACTTATTAGTCTCTTAAGCCTGCCTGTTTATAGAGTTA
63 AGTACTTTTTACTAATTATTTTCTCATACTTATCAGTCTCTTAAGACT-CTTGTTTATAGAGTTA
308597 AAAAT
127 AAAAT
308602 TTTCAACATT
Statistics
Matches: 301, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
200 10 0.03
201 113 0.38
202 105 0.35
203 58 0.19
204 3 0.01
205 12 0.04
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (199 bp):
GATTTAGTAAGTTTTTATAGTTATGTATTATAAGCAAGTGATAGTTGTGAAATAACAACCCCAGT
ACTTTTTACTAATTATTTTCTCATACTTATCAGTCTCTTAAGACTCTTGTTTATAGAGTTAAAAA
TGTGTAATCAAATAATAATCAAATGTATTAAGTGGAGTATATATTTTCTATTAAATGATAAATAA
AAAA
Found at i:309112 original size:17 final size:19
Alignment explanation
Indices: 309069--309122 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
309059 AATATTTTTC
*
309069 CATAAATAATGATTAAAAAT
1 CATAAAAAAT-ATTAAAAAT
309089 CATAAAAAATA-TAAAAAT
1 CATAAAAAATATTAAAAAT
*
309107 TA-AAAAAATATTAAAA
1 CATAAAAAATATTAAAA
309123 CTAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.26
18 13 0.42
19 1 0.03
20 9 0.29
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (19 bp):
CATAAAAAATATTAAAAAT
Found at i:309173 original size:10 final size:9
Alignment explanation
Indices: 309082--309234 Score: 78
Period size: 9 Copynumber: 16.0 Consensus size: 9
309072 AAATAATGAT
*
309082 TAAAAATCA
1 TAAAAATTA
*
309091 TAAAAAATA
1 TAAAAATTA
309100 TAAAAATTA
1 TAAAAATTA
*
309109 -AAAAAATA
1 TAAAAATTA
* *
309117 TTAAAACTAA
1 -TAAAAATTA
*
309127 TATAAATTGA
1 TAAAAATT-A
*
309137 TATAAACTTA
1 TA-AAAATTA
*
309147 TTAAAATTA
1 TAAAAATTA
309156 TAAAAAAAATTA
1 T---AAAAATTA
*
309168 TGAAAACTTA
1 T-AAAAATTA
*
309178 TAAATATTA
1 TAAAAATTA
309187 -AAAAATTA
1 TAAAAATTA
309195 TAAAAAATT-
1 T-AAAAATTA
309204 TATAAAATTAA
1 TA-AAAATT-A
*
309215 TTAAAAAATCA
1 -T-AAAAATTA
309226 TAAAAATTA
1 TAAAAATTA
309235 AATTGGACCG
Statistics
Matches: 108, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
8 15 0.14
9 47 0.44
10 26 0.24
11 5 0.05
12 14 0.13
13 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:309231 original size:21 final size:19
Alignment explanation
Indices: 309187--309235 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
309177 ATAAATATTA
*
309187 AAAAATT-ATAAAAAATTT
1 AAAAATTAATAAAAAATAT
309205 ATAAAATTAATTAAAAAATCAT
1 A-AAAATTAA-TAAAAAAT-AT
309227 AAAAATTAA
1 AAAAATTAA
309236 ATTGGACCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 6 0.23
20 1 0.04
21 16 0.62
22 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTAATAAAAAATAT
Found at i:312871 original size:15 final size:15
Alignment explanation
Indices: 312851--312888 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
312841 TGAAACAGAT
312851 GAATTACAAATAGAC
1 GAATTACAAATAGAC
*
312866 GAATTATAAATAGAC
1 GAATTACAAATAGAC
312881 GAATTACA
1 GAATTACA
312889 TACAACATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.24
Consensus pattern (15 bp):
GAATTACAAATAGAC
Found at i:315985 original size:5 final size:5
Alignment explanation
Indices: 315975--316005 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
315965 TGAGCATTCG
315975 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
316006 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:316638 original size:30 final size:31
Alignment explanation
Indices: 316599--316658 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
316589 GGAGGTGAGA
*
316599 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
316630 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
316659 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:316886 original size:9 final size:9
Alignment explanation
Indices: 316872--316917 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
316862 TATAGTTTGA
316872 TATTCGAAT
1 TATTCGAAT
316881 TATTCGAAT
1 TATTCGAAT
316890 TATTCGAAT
1 TATTCGAAT
*
316899 TATTCGAGT
1 TATTCGAAT
316908 TATTCGAAT
1 TATTCGAAT
316917 T
1 T
316918 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:318955 original size:23 final size:23
Alignment explanation
Indices: 318880--318957 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 23
318870 ATGAACAGGA
* *
318880 AATATTCTCTGGCATGAACAGTAG
1 AATATTCTCTAGCATGAATAGT-G
* *
318904 AA-A-TCTGTGGCA-GAAATAGT-
1 AATATTCTCTAGCATG-AATAGTG
*
318924 AAGATTCTCTAGCATGAATAGTG
1 AATATTCTCTAGCATGAATAGTG
318947 AATATTCTCTA
1 AATATTCTCTA
318958 TAGTTTGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 26 0.59
23 12 0.27
24 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (23 bp):
AATATTCTCTAGCATGAATAGTG
Found at i:319342 original size:18 final size:17
Alignment explanation
Indices: 319294--319343 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
319284 CATATTTCAA
319294 AATTTTAATAATTTATTAG
1 AATTTT-ATAATTT-TTAG
*
319313 AATTTTAT--TTTTTAT
1 AATTTTATAATTTTTAG
319328 AATATTTATAATTTTT
1 AAT-TTTATAATTTTT
319344 TAAAAGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
18 7 0.26
19 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTATAATTTTTAG
Found at i:326132 original size:95 final size:95
Alignment explanation
Indices: 325958--326148 Score: 276
Period size: 95 Copynumber: 2.0 Consensus size: 95
325948 GATTTGTAAT
* * ** **
325958 AACTCGATTTTCAGTGGTGTTGAAAAATATTATTTCAAAACTTCATTTCTGTAAACCGTAAACCA
1 AACTCGATTTTCAGTGGTATTGAAAAATATGATTTCAAAACCCCATTTCCATAAACCGTAAACCA
*
326023 AGTCTGTAAGTATAAAATAGGAATATTTAC
66 AGTCTGTAAATATAAAATAGGAATATTTAC
* * *
326053 AACTCGATTTTTAGTGGTATTGAAAAATATGATTTTAGAACCCCATTTCCATAAACCGTAAACCA
1 AACTCGATTTTCAGTGGTATTGAAAAATATGATTTCAAAACCCCATTTCCATAAACCGTAAACCA
326118 AGT-TCGTAAATATAAAATAGGAATATTTAC
66 AGTCT-GTAAATATAAAATAGGAATATTTAC
326148 A
1 A
326149 GAGTTGATAT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 1 0.01
95 84 0.99
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (95 bp):
AACTCGATTTTCAGTGGTATTGAAAAATATGATTTCAAAACCCCATTTCCATAAACCGTAAACCA
AGTCTGTAAATATAAAATAGGAATATTTAC
Found at i:328230 original size:24 final size:24
Alignment explanation
Indices: 328203--328252 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
328193 TATGTAATGA
328203 TTAGCATAATCTAAACACAATTCT
1 TTAGCATAATCTAAACACAATTCT
328227 TTAGCATAATCTAAACACAATTCT
1 TTAGCATAATCTAAACACAATTCT
328251 TT
1 TT
328253 CTTTTCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAGCATAATCTAAACACAATTCT
Found at i:330901 original size:26 final size:26
Alignment explanation
Indices: 330863--330921 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
330853 TGTTTTCTCG
**
330863 AAATTTTACCAGGGGCAAAATTGTCA
1 AAATTTTACCAGGGGCAAAATCATCA
* *
330889 AAATTTTATCAGGGGTAAAATCATCA
1 AAATTTTACCAGGGGCAAAATCATCA
330915 AAATTTT
1 AAATTTT
330922 GCTGGGGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCATCA
Found at i:337754 original size:13 final size:13
Alignment explanation
Indices: 337736--337760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337726 TAATTAAATC
337736 AATAATATTTATT
1 AATAATATTTATT
337749 AATAATATTTAT
1 AATAATATTTAT
337761 GGACTCGATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATATTTATT
Found at i:344630 original size:13 final size:13
Alignment explanation
Indices: 344612--344636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
344602 CAATCAAATG
344612 CACACAAAATAAA
1 CACACAAAATAAA
344625 CACACAAAATAA
1 CACACAAAATAA
344637 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:347222 original size:26 final size:26
Alignment explanation
Indices: 347192--347244 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
347182 ACCCCAAACA
*
347192 ATATTTTCATTCTCTTTGCCTACATG
1 ATATTTTCATTCTCTTTACCTACATG
347218 ATATTTTCATTCTCTTTACCTACATG
1 ATATTTTCATTCTCTTTACCTACATG
347244 A
1 A
347245 AGTACCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (26 bp):
ATATTTTCATTCTCTTTACCTACATG
Found at i:351933 original size:18 final size:18
Alignment explanation
Indices: 351912--351951 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
351902 GTGTGAGCAT
351912 TACAGATACAGTTACAAA
1 TACAGATACAGTTACAAA
* *
351930 TACAGTTACAGTTACAGA
1 TACAGATACAGTTACAAA
351948 TACA
1 TACA
351952 AGCACACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (18 bp):
TACAGATACAGTTACAAA
Found at i:351945 original size:12 final size:12
Alignment explanation
Indices: 351911--351951 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
351901 CGTGTGAGCA
351911 TTACAGATACAG
1 TTACAGATACAG
*
351923 TTACAAATACAG
1 TTACAGATACAG
*
351935 TTACAGTTACAG
1 TTACAGATACAG
*
351947 ATACA
1 TTACA
351952 AGCACACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (12 bp):
TTACAGATACAG
Found at i:352773 original size:40 final size:40
Alignment explanation
Indices: 352713--352799 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
352703 TTGAAATTGG
*
352713 ATTGATTTAGTGTATGATTTGTGGTACCAAATGATGGCAT
1 ATTGGTTTAGTGTATGATTTGTGGTACCAAATGATGGCAT
*
352753 ATTGGTTTAGTGTATGATTTGTGGTGCCAAATGATGGCAT
1 ATTGGTTTAGTGTATGATTTGTGGTACCAAATGATGGCAT
352793 ATTGGTT
1 ATTGGTT
352800 AGGCACTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (40 bp):
ATTGGTTTAGTGTATGATTTGTGGTACCAAATGATGGCAT
Found at i:355427 original size:16 final size:16
Alignment explanation
Indices: 355390--355430 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
355380 TCAAAAAGTT
* *
355390 TTAATCTAAAAAAATC
1 TTAATCCAAAAAAAAC
*
355406 TAAATCCAAAAAAAAC
1 TTAATCCAAAAAAAAC
355422 TTAATCCAA
1 TTAATCCAA
355431 GCCCACCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (16 bp):
TTAATCCAAAAAAAAC
Found at i:362804 original size:20 final size:20
Alignment explanation
Indices: 362762--362810 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
362752 CACCTGCAAG
*
362762 GAAACAAAACAACAATGAAA
1 GAAACAAAACAACAAAGAAA
* * *
362782 GAAATAAAACAGCAAAGATA
1 GAAACAAAACAACAAAGAAA
*
362802 GAAAGAAAA
1 GAAACAAAA
362811 TCAAAGATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.10, G:0.14, T:0.06
Consensus pattern (20 bp):
GAAACAAAACAACAAAGAAA
Found at i:376212 original size:43 final size:43
Alignment explanation
Indices: 375945--376690 Score: 271
Period size: 44 Copynumber: 17.5 Consensus size: 43
375935 CGGTATCCAG
* * *
375945 TAATCCTATCTC-CTTGAGGTTGCAGTGGAGCGGATTAAAACC-
1 TAATCTTATCTCGC-TGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * ** *
375987 TCAGATCTTATTTCTCTGAAGTTGCAG-AGAGCAGATT-GCATC-
1 T-A-ATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * *
376029 TAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACT--AAGCA
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * **
376070 -AGTCTTATCTTC-CTGAAGTTACAGT-GAGGCAGACTGAAGATTGCA
1 TAATCTTATC-TCGCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-ACCA
* **
376115 -AATCTTATCTCGCTGAAGTTGCAGTGGAGCATATTAACGCCGA
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACC-A
* *
376158 TAATCCTATCTCGCTGAAGTTGCAGTGGA-TAGATTAAAACC-
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * *** *
376199 TCAGATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TCGCATC-
1 T-A-ATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * * * *
376241 TAGTCTTATTTCCCTAAAGTTGCAGTGGAGCAGACT--AAGCA
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * *
376282 -AGTCTTATCCTC-CTGAAGTTGCAGTGAAGCAGATTAAAGCCGA
1 TAATCTTAT-CTCGCTGAAGTTGCAGTGGAGCAGATTAAAACC-A
* * * * *
376325 TAATCCTATCTTGCTGAAGTTACAGTGG-GCGGATTAAAACCT
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * ** *** *
376367 TAGATTTTATCTCTCTGAAGTTGCAG-AAAGCAGA-TCGCATC-
1 TA-ATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * * * *
376408 TAGTCTCATCACCCT-AAGGTTGCAGTGGAGCAGACTAAGCAAGCA
1 TAATCTTATCTCGCTGAA-GTTGCAGTGGAGCAGATTAA--AACCA
* * *
376453 -AGTCTTATCCTC-TTGAAGTTGCAGT-GAGGCAGACTGAAGATGA-CA
1 TAATCTTAT-CTCGCTGAAGTTGCAGTGGA-GCAGA-TTAA-A--ACCA
* * **
376498 -AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCA
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * * *
376540 GTAATCCTATGTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
1 -TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACC-A
* * * * * * *
376585 TGATCTTATCTCTCTGAAGCTGCAG-AGAGCAGA-TCACATCA
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * * * *
376626 -AATCTTATCTCCCTGAAGTCGCAGTGGAACGGATTAAAACCT
1 TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* *
376668 TGGATCTTATCTCTCTGAAGTTG
1 T-AATCTTATCTCGCTGAAGTTG
376691 AAGAGAGCAG
Statistics
Matches: 527, Mismatches: 125, Indels: 102
0.70 0.17 0.14
Matches are distributed among these distances:
39 4 0.01
40 134 0.25
41 35 0.07
42 31 0.06
43 86 0.16
44 173 0.33
45 59 0.11
46 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (43 bp):
TAATCTTATCTCGCTGAAGTTGCAGTGGAGCAGATTAAAACCA
Found at i:376334 original size:167 final size:168
Alignment explanation
Indices: 376112--376535 Score: 537
Period size: 167 Copynumber: 2.5 Consensus size: 168
376102 ACTGAAGATT
* * * *
376112 GCAAATCTTAT-CTCGCTGAAGTTGCAGTGGAGCATATTAACGCCGATAATCCTATCTCGCTGAA
1 GCAAGTCTTATCCTC-CTGAAGTTGCAGTGAAGCAGATTAAAGCCGATAATCCTATCTCGCTGAA
* *
376176 GTTGCAGTGGATAGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATC
65 GTTGCAGTGGACAGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAAAGCAGATCGCATC
* **
376241 TAGTCTTATTTCCCTAAAGTTGCAGTGGAGCAGACT-AA
130 TAGTCTCATCACCCTAAAGTTGCAGTGGAGCAGACTAAA
*
376279 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGATAATCCTATCTTGCTGAAG
1 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGATAATCCTATCTCGCTGAAG
* * * * * *
376344 TTACAGTGGGCGGATTAAAACCTTAGATTTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCT
66 TTGCAGTGGACAGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAAAGCAGATCGCATCT
*
376409 AGTCTCATCACCCTAAGGTTGCAGTGGAGCAGACTAAGCAA
131 AGTCTCATCACCCTAAAGTTGCAGTGGAGCAGACT-A--AA
* * * * ** * * * *
376450 GCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTAAA
1 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGA-TAATCCTATCTCGCTGAA
376515 GTTGCAGTGGAGCAGATTAAA
65 GTTGCAGTGGA-CAGATTAAA
376536 GTCAGTAATC
Statistics
Matches: 219, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
167 144 0.66
168 3 0.01
171 42 0.19
172 22 0.10
173 8 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (168 bp):
GCAAGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGATAATCCTATCTCGCTGAAG
TTGCAGTGGACAGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAAAGCAGATCGCATCT
AGTCTCATCACCCTAAAGTTGCAGTGGAGCAGACTAAA
Found at i:376474 original size:44 final size:45
Alignment explanation
Indices: 376419--376530 Score: 124
Period size: 45 Copynumber: 2.5 Consensus size: 45
376409 AGTCTCATCA
* *
376419 CCCTAAGGTTGCAGTGGAGCAGACT-AAGCAAG-CAAGTCTTATC-
1 CCCTAAAGTTGCAGTGGAGCAGACTGAAG-AAGACAAATCTTATCT
* * *
376462 CTCTTGAAGTTGCAGT-GAGGCAGACTGAAGATGACAAATCTTATCT
1 C-CCTAAAGTTGCAGTGGA-GCAGACTGAAGAAGACAAATCTTATCT
376508 CCCTAAAGTTGCAGTGGAGCAGA
1 CCCTAAAGTTGCAGTGGAGCAGA
376531 TTAAAGTCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
43 3 0.05
44 20 0.36
45 30 0.54
46 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (45 bp):
CCCTAAAGTTGCAGTGGAGCAGACTGAAGAAGACAAATCTTATCT
Found at i:376678 original size:217 final size:215
Alignment explanation
Indices: 376284--376690 Score: 500
Period size: 217 Copynumber: 1.9 Consensus size: 215
376274 ACTAAGCAAG
* * **
376284 TCTTATCCTCCTGAAGTTGCAGTGAAGCAGATTAAAGCCGATAATCCTATCTTGCTGAAGTTACA
1 TCTTATCCTCCTAAAGTTGCAGTGAAGCAGATTAAAGCAGATAATCCTATCTCCCTGAAGTTACA
* * * * *
376349 GTGGGCGGATTAAAACCTTAGATTTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCTAGTCT
66 GTGGGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGCTGCAGAAAGCAGATCACATCAAATCT
* * *
376414 CATCACCCTAAGGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATC-CTCTTGAAGTTGCAGT
131 CATCACCCTAAGGTCGCAGTGGAACAGACTAA-CAACCAAGTCTTATCTCTC-TGAAGTTGCAGT
376478 GAGGCAGACTGAAGATGACAAA
194 GAGGCAGACTGAAGATGACAAA
* * *
376500 TCTTAT-CTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCAG-TAATCCTATGTCCCTGAAGTTG
1 TCTTATCCT-CCTAAAGTTGCAGTGAAGCAGATTAAAG-CAGATAATCCTATCTCCCTGAAGTTA
* *
376563 CAGTGGAGCGGATTAAAACCTTTGATCTTATCTCTCTGAAGCTGCAGAGAGCAGATCACATCAAA
64 CAGTGG-GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGCTGCAGAAAGCAGATCACATCAAA
* * * * **
376628 TCTTATCTCCCTGAA-GTCGCAGTGGAACGGATTAA-AACCTTGGATCTTATCTCTCTGAAGTTG
128 TCTCATCACCCT-AAGGTCGCAGTGGAACAGACTAACAACC-AAG-TCTTATCTCTCTGAAGTTG
376691 AAGAGAGCAG
Statistics
Matches: 161, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
215 5 0.03
216 57 0.35
217 94 0.58
218 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (215 bp):
TCTTATCCTCCTAAAGTTGCAGTGAAGCAGATTAAAGCAGATAATCCTATCTCCCTGAAGTTACA
GTGGGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGCTGCAGAAAGCAGATCACATCAAATCT
CATCACCCTAAGGTCGCAGTGGAACAGACTAACAACCAAGTCTTATCTCTCTGAAGTTGCAGTGA
GGCAGACTGAAGATGACAAA
Found at i:376734 original size:84 final size:84
Alignment explanation
Indices: 376541--376736 Score: 293
Period size: 84 Copynumber: 2.3 Consensus size: 84
376531 TTAAAGTCAG
* * * *
376541 TAATCCTATGTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTTGATCTTATCTCTCTGAAGCT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCTTGGATCTTATCTCTCTGAAGCT
*
376606 GCAGAGAGCAGATCACATC
66 GAAGAGAGCAGATCACATC
* * *
376625 AAATCTTATCTCCCTGAAGTCGCAGTGGAACGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCTTGGATCTTATCTCTCTGAAGCT
*
376690 GAAGAGAGCAGATCGCATC
66 GAAGAGAGCAGATCACATC
* *
376709 TAATCTTATCTCCCTAAAATTGCAGTGG
1 TAATCTTATCTCCCTGAAGTTGCAGTGG
376737 GCCAGACTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 99 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (84 bp):
TAATCTTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCTTGGATCTTATCTCTCTGAAGCT
GAAGAGAGCAGATCACATC
Found at i:377192 original size:20 final size:20
Alignment explanation
Indices: 377150--377198 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
377140 CACTTGCAAG
*
377150 GAAACAAAACAACAAGGAAA
1 GAAACAAAACAACAAAGAAA
* * *
377170 GAAATAAAACAGCAAAGATA
1 GAAACAAAACAACAAAGAAA
*
377190 GAAAGAAAA
1 GAAACAAAA
377199 TCAAAGATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.10, G:0.16, T:0.04
Consensus pattern (20 bp):
GAAACAAAACAACAAAGAAA
Found at i:380551 original size:15 final size:14
Alignment explanation
Indices: 380531--380565 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
380521 AATTGATCGT
380531 GTTAATGGCCGGAGA
1 GTTAATGGCC-GAGA
380546 GTTAATGGCCGAGA
1 GTTAATGGCCGAGA
*
380560 ATTAAT
1 GTTAAT
380566 TCGTCTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (14 bp):
GTTAATGGCCGAGA
Found at i:380564 original size:14 final size:15
Alignment explanation
Indices: 380532--380565 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
380522 ATTGATCGTG
*
380532 TTAATGGCCGGAGAG
1 TTAATGGCCGGAGAA
380547 TTAATGGCC-GAGAA
1 TTAATGGCCGGAGAA
380561 TTAAT
1 TTAAT
380566 TCGTCTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (15 bp):
TTAATGGCCGGAGAA
Found at i:381630 original size:7 final size:7
Alignment explanation
Indices: 381618--381643 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
381608 TAGTCTATTC
381618 GTATTTA
1 GTATTTA
381625 GTATTTA
1 GTATTTA
381632 GTATTTA
1 GTATTTA
381639 GTATT
1 GTATT
381644 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:382297 original size:18 final size:18
Alignment explanation
Indices: 382261--382303 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
382251 TGCCAGGTGC
*
382261 GTATCCTATCTCTTTTAT
1 GTATCCTATCTCTTATAT
382279 GTATCCTAATC-CTTATAT
1 GTATCCT-ATCTCTTATAT
*
382297 GTTTCCT
1 GTATCCT
382304 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.19, C:0.23, G:0.07, T:0.51
Consensus pattern (18 bp):
GTATCCTATCTCTTATAT
Found at i:382590 original size:21 final size:20
Alignment explanation
Indices: 382543--382602 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
382533 CCCAACATCG
* *
382543 GCAACCAAATCCCCTACCTGA
1 GCAACCAAATCCCC-GCCAGA
*
382564 GGAACCAGAATCCCCGCCAGA
1 GCAACCA-AATCCCCGCCAGA
*
382585 GCAACCACAACCCCCGCC
1 GCAACCA-AATCCCCGCC
382603 GAAAGCTGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.32, C:0.47, G:0.15, T:0.07
Consensus pattern (20 bp):
GCAACCAAATCCCCGCCAGA
Found at i:386382 original size:21 final size:20
Alignment explanation
Indices: 386356--386395 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 20
386346 ATAAATATAT
386356 TTTTTTTAATTTTTAAAATAC
1 TTTTTTT-ATTTTTAAAATAC
386377 TTTTTTTATTTTTAAAATA
1 TTTTTTTATTTTTAAAATA
386396 AATTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTATTTTTAAAATAC
Found at i:386401 original size:21 final size:21
Alignment explanation
Indices: 386347--386402 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
386337 CTGAATATAA
*
386347 TAAATATATTTTTTTTAATTTT
1 TAAA-ATAATTTTTTTAATTTT
*
386369 TAAAATACTTTTTTT-ATTTT
1 TAAAATAATTTTTTTAATTTT
*
386389 TAAAATAAATTTTT
1 TAAAATAATTTTTT
386403 GGTGTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAAATAATTTTTTTAATTTT
Found at i:388227 original size:126 final size:126
Alignment explanation
Indices: 387980--388251 Score: 413
Period size: 126 Copynumber: 2.2 Consensus size: 126
387970 GGCCAAATAG
* * ***
387980 GAACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGTGTC
1 GAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATACATC
* * *
388045 CTGCTTGAAGCGTTTTTGACACTATTTTCTCAGAAACATCTTCTCAAAATTATTTTTTC-A
66 CTGCTTAAAGAGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* *
388105 GAAACTACTGTGGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTATTTTTGCTGACAATACAT
1 G-AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATACAT
*
388170 CCTGCTTAAAGAG-TTTTGACACTATTTGCTCAGAAACATCTTCTTAAAATTATTTTTTCAA
65 CCTGCTTAAAGAGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAA
*
388231 GAACTATTGTAGCAAAAGAGC
1 GAACTACTGTAGCAAAAGAGC
388252 TTTCATGTGA
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
125 63 0.48
126 69 0.52
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (126 bp):
GAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATACATC
CTGCTTAAAGAGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAA
Found at i:388458 original size:81 final size:82
Alignment explanation
Indices: 388346--388517 Score: 285
Period size: 81 Copynumber: 2.1 Consensus size: 82
388336 CCTAAACACT
388346 AAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAACCGC-AAACCCTAATT
1 AAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAACC-CTAAACCCTAATT
*
388410 TATTTGATTTTTCCTTAA
65 TATTTAATTTTTCCTTAA
*
388428 AAACCCTAATCT-ATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTT
1 AAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAACCCTAAACCCTAATTT
* *
388492 ATTTAATTTTTTCTTCA
66 ATTTAATTTTTCCTTAA
388509 AAACCCTAA
1 AAACCCTAA
388518 ACACTAAACC
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
80 1 0.01
81 72 0.85
82 12 0.14
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.42
Consensus pattern (82 bp):
AAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAACCCTAAACCCTAATTT
ATTTAATTTTTCCTTAA
Found at i:388526 original size:43 final size:43
Alignment explanation
Indices: 388478--388634 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
388468 TCAAGTAACC
388478 CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAAACA
1 CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAAACA
* * * * * * * *
388521 CTAAACCCTAATCTAATTT-TTTTAAAATTTATAATTAATTTACTCAAGTAACC
1 CTAAACCCTAAT-TTATTTAATTT----TTTCT--TCAA--AACCCTA--AACA
388574 CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAAACA
1 CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAAACA
*
388617 CTAAACCCTAATCTATTT
1 CTAAACCCTAATTTATTT
388635 TTTAAAAATT
Statistics
Matches: 85, Mismatches: 17, Indels: 24
0.67 0.13 0.19
Matches are distributed among these distances:
43 35 0.41
44 5 0.06
45 4 0.05
47 7 0.08
49 7 0.08
51 4 0.05
52 5 0.06
53 18 0.21
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.40
Consensus pattern (43 bp):
CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAAACA
Found at i:388554 original size:96 final size:95
Alignment explanation
Indices: 388428--388721 Score: 468
Period size: 96 Copynumber: 3.1 Consensus size: 95
388418 TTTTCCTTAA
388428 AAACCCTAATCTATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTA
1 AAACCCTAATCTATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTA
388493 TTTAATTTTTTCTTCAAAACCCTAAACACT
66 TTTAATTTTTTCTTCAAAACCCTAAACACT
388523 AAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTT
1 AAACCCTAATCT-ATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTT
388588 ATTTAATTTTTTCTTCAAAACCCTAAACACT
65 ATTTAATTTTTTCTTCAAAACCCTAAACACT
* * * * ** *
388619 AAACCCTAATCTATTTTTTAAAAATTTATAATTAATTTAATTAAGAAACCCTAAACTTTTATTT-
1 AAACCCTAATCTATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTA
*
388683 TTTAATTTTTCCTT-AAAACCCTAAA-ATCT
66 TTTAATTTTTTCTTCAAAACCCTAAACA-CT
388712 AAAACCCTAA
1 -AAACCCTAA
388722 CCCTAATTGT
Statistics
Matches: 188, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 13 0.07
94 22 0.12
95 57 0.30
96 95 0.51
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (95 bp):
AAACCCTAATCTATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTA
TTTAATTTTTTCTTCAAAACCCTAAACACT
Found at i:388582 original size:177 final size:176
Alignment explanation
Indices: 388266--388613 Score: 581
Period size: 177 Copynumber: 2.0 Consensus size: 176
388256 ATGTGAAAGA
* *
388266 TTTTTTAAATTAACAAATAATTTAATTAAGTAAGCCTAAACCCTAATTTATTTAATTTTTTCTTC
1 TTTTTTAAATTAACAAATAATTTAATCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCTTC
388331 AAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAAC
66 AAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAAC
*
388396 CGCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAATCTAT
131 CGCAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAATCTAT
* * * *
388442 TTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCTT
1 TTTTTT-AAATTAACAAATAATTTAATCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCTT
*
388507 CAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAA
65 CAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAA
* *
388572 CC-CTAAACCCTAATTTATTTAATTTTTTCTTCAAAACCCTAA
130 CCGC-AAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAA
388614 ACACTAAACC
Statistics
Matches: 160, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
176 7 0.04
177 153 0.96
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.42
Consensus pattern (176 bp):
TTTTTTAAATTAACAAATAATTTAATCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCTTC
AAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTAAAGTAAC
CGCAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAATCTAT
Found at i:389392 original size:27 final size:27
Alignment explanation
Indices: 389354--389405 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
389344 TGTTTGTAGG
*
389354 TACATGCATGGACAGCATTGAAGATAA
1 TACATGCATGGACAGCAATGAAGATAA
389381 TACATGCATGGACAGCAATGAAGAT
1 TACATGCATGGACAGCAATGAAGAT
389406 GCTTCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAGCAATGAAGATAA
Found at i:389936 original size:23 final size:22
Alignment explanation
Indices: 389899--389948 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
389889 GCCGAATTCA
*
389899 TGAACCATCTTTAATGTTTTAGTG
1 TGAACCATCTTTAAT-TGTT-GTG
*
389923 TGAACCCT-TTTAATTGTTGTG
1 TGAACCATCTTTAATTGTTGTG
389944 TGAAC
1 TGAAC
389949 ACATTAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 6 0.25
24 7 0.29
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (22 bp):
TGAACCATCTTTAATTGTTGTG
Found at i:393992 original size:16 final size:14
Alignment explanation
Indices: 393978--394020 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 14
393968 AACAATTAAT
393978 ACAATTAATAATTA
1 ACAATTAATAATTA
393992 ACAATTAATACAATTA
1 ACAATTAAT--AATTA
394008 ACAATTAATAATT
1 ACAATTAATAATT
394021 TGATAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAATTAATAATTA
Found at i:393998 original size:23 final size:23
Alignment explanation
Indices: 393968--394020 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
393958 ATTTTGTTAC
*
393968 AACAATTAATACAATTAATAATT
1 AACAATTAATACAATTAACAATT
393991 AACAATTAATACAATTAACAATT
1 AACAATTAATACAATTAACAATT
*
394014 AATAATT
1 AACAATT
394021 TGATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (23 bp):
AACAATTAATACAATTAACAATT
Found at i:394045 original size:16 final size:16
Alignment explanation
Indices: 394033--394065 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
394023 ATAATTTTGC
394033 TAACAATTAATTTTAA
1 TAACAATTAATTTTAA
*
394049 TAACAATTAGTTTTAA
1 TAACAATTAATTTTAA
394065 T
1 T
394066 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
TAACAATTAATTTTAA
Found at i:394064 original size:22 final size:23
Alignment explanation
Indices: 394039--394100 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
394029 TTGCTAACAA
* * *
394039 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
394061 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
394084 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
394101 TGAGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:399419 original size:15 final size:15
Alignment explanation
Indices: 399399--399435 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
399389 TTTGAAACTC
*
399399 GTGGTGGTCTTGGAG
1 GTGGTGGTCTTGAAG
399414 GTGGTGGTCTTGAAG
1 GTGGTGGTCTTGAAG
*
399429 GGGGTGG
1 GTGGTGG
399436 GGCACTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.05, G:0.57, T:0.30
Consensus pattern (15 bp):
GTGGTGGTCTTGAAG
Found at i:412812 original size:40 final size:40
Alignment explanation
Indices: 412767--412875 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 40
412757 GTTTGGATAA
*
412767 AAAACGCCGCTAAAGATCGAGCATTAGCGGAACTTTACA-T
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGAACTTTA-AGG
**
412807 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTAAGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGAACTTTAAGG
* *
412847 AAAGCGCCGCTAAAAAT-GAGCATTAGCGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGG
412876 CGTTTTCTGG
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 13 0.21
40 50 0.79
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGAACTTTAAGG
Found at i:413659 original size:43 final size:43
Alignment explanation
Indices: 413598--413925 Score: 337
Period size: 43 Copynumber: 7.7 Consensus size: 43
413588 GTCTATAATA
* *
413598 CTAAAGGTCTTGATCTATAACGGTGTTTGTGGAAAAAGCGCTG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCTG
*
413641 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGCG-AAAAGCGCCG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTG-GAAAAAGCGCTG
* * *
413684 CTAAAGGTCCTGAGCTATAGCGGTGTTTGTGGAAAAAGCGCTG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCTG
*
413727 CTAAAGGTCTTGATCTATAGTGGCGTTTGTGCG-AAAAGCG-TCG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTG-GAAAAAGCGCT-G
* * * * *
413770 CTAAAGGTCCTGAGCTATAGTGGCGTTTGTGGAGAAAGCGCCG
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCTG
* ** * * * **
413813 CTAAAGATCTCAAGCTATAGCAGCGTTTGT-GTAAAAGCGCCA
1 CTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCTG
* *
413855 CTAAAGGTAC-TAATCTATAGCGACGTTTGTGGGAAAAATGC-C-G
1 CTAAAGGT-CTTGATCTATAGCGGCGTTTGT-GGAAAAA-GCGCTG
* *
413898 CTAAAGGTCATGATCCATAGCGGCGTTT
1 CTAAAGGTCTTGATCTATAGCGGCGTTT
413926 ATTTCTAAAA
Statistics
Matches: 240, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
42 36 0.15
43 194 0.81
44 8 0.03
45 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
CTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCTG
Found at i:413743 original size:86 final size:86
Alignment explanation
Indices: 413598--413925 Score: 410
Period size: 86 Copynumber: 3.8 Consensus size: 86
413588 GTCTATAATA
* * * *
413598 CTAAAGGTCTTGATCTATAACGGTGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGCG
1 CTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGCG
413663 GCGTTTGTGCGAAAAGCGCCG
66 GCGTTTGTGCGAAAAGCGCCG
* *
413684 CTAAAGGTCCTGAGCTATAGCGGTGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGTG
1 CTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGCG
*
413749 GCGTTTGTGCGAAAAGCGTCG
66 GCGTTTGTGCGAAAAGCGCCG
* * * * ** * *
413770 CTAAAGGTCCTGAGCTATAGTGGCGTTTGTGGAGAAAGCGCCGCTAAAGATCTCAAGCTATAGCA
1 CTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGCG
* *
413835 GCGTTTGTG-TAAAAGCGCCA
66 GCGTTTGTGCGAAAAGCGCCG
* * * * * *
413855 CTAAAGGTACTAATCTATAGCGACGTTTGTGGGAAAAATGC-C-GCTAAAGGTCATGATCCATAG
1 CTAAAGGTCCTGAGCTATAGCGGCGTTTGT-GGAAAAA-GCGCTGCTAAAGGTCTTGATCTATAG
413918 CGGCGTTT
64 CGGCGTTT
413926 ATTTCTAAAA
Statistics
Matches: 209, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
85 55 0.26
86 152 0.73
87 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (86 bp):
CTAAAGGTCCTGAGCTATAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGCG
GCGTTTGTGCGAAAAGCGCCG
Found at i:413829 original size:129 final size:126
Alignment explanation
Indices: 413597--413925 Score: 378
Period size: 129 Copynumber: 2.6 Consensus size: 126
413587 AGTCTATAAT
* * *
413597 ACTAAAGGTCTTGATCTATAACGGTGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGC
1 ACTAAAGGTCTTGATCTATAGCGGCGTTTGTGG-AAAAGCGC-GCTAAAGGTCATGATCTATAGC
* * * * *
413662 GGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCCTGAGCTATAGCGGTGTTTGTGGAAAAAGCGCT
64 GGCGTTTGTGCGAAAAGCGCCGCTAAAGATCCTAAGCTATAGCAGCGTTTGT-GAAAAAGCGCC
* * * * *
413726 GCTAAAGGTCTTGATCTATAGTGGCGTTTGTGCGAAAAGCGTCGCTAAAGGTCCTGAGCTATAGT
1 ACTAAAGGTCTTGATCTATAGCGGCGTTTGTG-GAAAAGCG-CGCTAAAGGTCATGATCTATAGC
*
413791 GGCGTTTGTG-GAGAAAGCGCCGCTAAAGAT-CTCAAGCTATAGCAGCGTTTGTGTAAAAGCGCC
64 GGCGTTTGTGCGA-AAAGCGCCGCTAAAGATCCT-AAGCTATAGCAGCGTTTGTGAAAAAGCGCC
* * *
413854 ACTAAAGGTAC-TAATCTATAGCGACGTTTGTGGGAAAAATGC-CGCTAAAGGTCATGATCCATA
1 ACTAAAGGT-CTTGATCTATAGCGGCGTTTGT-GG-AAAA-GCGCGCTAAAGGTCATGATCTATA
413917 GCGGCGTTT
62 GCGGCGTTT
413926 ATTTCTAAAA
Statistics
Matches: 171, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
128 65 0.38
129 102 0.60
130 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (126 bp):
ACTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAGCGCGCTAAAGGTCATGATCTATAGCGG
CGTTTGTGCGAAAAGCGCCGCTAAAGATCCTAAGCTATAGCAGCGTTTGTGAAAAAGCGCC
Found at i:414589 original size:31 final size:31
Alignment explanation
Indices: 414551--414615 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
414541 AACAACCTAG
** *
414551 TGACTTAAATAAAAACTTTTGAATAATTCAA
1 TGACTTAAATAAAAACTTTCAAACAATTCAA
*
414582 TGACTTAAATGAAAACTTTCAAACAATTCAA
1 TGACTTAAATAAAAACTTTCAAACAATTCAA
414613 TGA
1 TGA
414616 TAAATTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAACAATTCAA
Found at i:416888 original size:3 final size:3
Alignment explanation
Indices: 416880--416940 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
416870 GTATGTTTAA
* *
416880 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT -AT AA- CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
416926 AAT AA- AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AA
416941 AACAGTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:419171 original size:31 final size:31
Alignment explanation
Indices: 419107--419177 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
419097 AACAATCCAG
** *
419107 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
*
419138 TGACTTAAATAAAAACTTTCAAATAATTTAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
419169 TGAC-TAAAT
1 TGACTTAAAT
419178 TGTAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:424187 original size:75 final size:74
Alignment explanation
Indices: 424081--424274 Score: 223
Period size: 76 Copynumber: 2.6 Consensus size: 74
424071 GATTCGATTT
* * *
424081 GAAGAAAAATATT-ACATTTGTCTCATGTCTCAATTCATAACATTTGCATAGTTTGTTATAGTGA
1 GAAG-AAAATATTGA-ATTTGTGTCGTGTCTCAATTCATAACATTTACATAGTTTGTTATAGTGA
424145 TTCAACTTAAAA
64 TTC-ACTTAAAA
424157 GAAGAAAATATTGAATTTGTGTCGTGTCTCAATTCATAACATATTTTACATAGTTTGTTATAGTG
1 GAAGAAAATATTGAATTTGTGTCGTGTCTCAATTCATAAC--A-TTTACATAGTTTGTTATAGTG
* *
424222 ATTCAGTTTAAA
63 ATTCACTTAAAA
* ** *
424234 GAA-AAAATATTGTATTTACGT-GATGTCTCAATTCTTAACAT
1 GAAGAAAATATTGAATTTGTGTCG-TGTCTCAATTCATAACAT
424275 ATTTTGCATA
Statistics
Matches: 104, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
73 1 0.01
74 1 0.01
75 33 0.32
76 35 0.34
77 10 0.10
78 24 0.23
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (74 bp):
GAAGAAAATATTGAATTTGTGTCGTGTCTCAATTCATAACATTTACATAGTTTGTTATAGTGATT
CACTTAAAA
Found at i:424275 original size:76 final size:79
Alignment explanation
Indices: 424105--424284 Score: 248
Period size: 76 Copynumber: 2.4 Consensus size: 79
424095 CATTTGTCTC
424105 ATGTCTCAATTCATAAC--A-TTTGCATAGTTTGTTATAGTGATTCAACTTAAAAGAAGAAAATA
1 ATGTCTCAATTCATAACATATTTTGCATAGTTTGTTATAGTGATTCAACTTAAAAGAAGAAAATA
**
424167 TTGAATTTGTGTCG
66 TTGAATTTACGTCG
* * *
424181 -TGTCTCAATTCATAACATATTTTACATAGTTTGTTATAGTGATTC-AGTTTAAAGAA-AAAATA
1 ATGTCTCAATTCATAACATATTTTGCATAGTTTGTTATAGTGATTCAACTTAAAAGAAGAAAATA
*
424243 TTGTATTTACGT-G
66 TTGAATTTACGTCG
*
424256 ATGTCTCAATTCTTAACATATTTTGCATA
1 ATGTCTCAATTCATAACATATTTTGCATA
424285 ATTTATCGTA
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
75 17 0.18
76 41 0.45
77 10 0.11
78 24 0.26
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (79 bp):
ATGTCTCAATTCATAACATATTTTGCATAGTTTGTTATAGTGATTCAACTTAAAAGAAGAAAATA
TTGAATTTACGTCG
Found at i:424302 original size:76 final size:76
Alignment explanation
Indices: 424106--424313 Score: 199
Period size: 76 Copynumber: 2.8 Consensus size: 76
424096 ATTTGTCTCA
* * * * * *
424106 TGTCTCAATTCATAAC--A-TTTGCATAGTTTGTTATAGTGATTCAACTTAAAAGAAGAAAATAT
1 TGTCTCAATTCATAACATATTTTACATAATTTATCATAGTAATTCAA-TTTAAAGAA-AAAATAT
**
424168 TGAATTTGTGTCG
64 TGAATTTACGTCG
* * * * *
424181 TGTCTCAATTCATAACATATTTTACATAGTTTGTTATAGTGATTCAGTTTAAAGAAAAAATATTG
1 TGTCTCAATTCATAACATATTTTACATAATTTATCATAGTAATTCAATTTAAAGAAAAAATATTG
*
424246 TATTTACGT-G
66 AATTTACGTCG
* * * *
424256 ATGTCTCAATTCTTAACATATTTTGCATAATTTATCGTAGTAATTCAATTTAGAGAAA
1 -TGTCTCAATTCATAACATATTTTACATAATTTATCATAGTAATTCAATTTAAAGAAA
424314 CTAATGTGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
75 17 0.15
76 63 0.55
77 9 0.08
78 25 0.22
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (76 bp):
TGTCTCAATTCATAACATATTTTACATAATTTATCATAGTAATTCAATTTAAAGAAAAAATATTG
AATTTACGTCG
Found at i:426204 original size:43 final size:43
Alignment explanation
Indices: 426140--426227 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
426130 AGTAGTGAAC
426140 TTAGCATAAAGATGCTCGTTATAAATATGTGATTATATACGAG
1 TTAGCATAAAGATGCTCGTTATAAATATGTGATTATATACGAG
*
426183 TTAGCATAAAGATGCTTGTTATAAATATGTGATTATATACGAG
1 TTAGCATAAAGATGCTCGTTATAAATATGTGATTATATACGAG
426226 TT
1 TT
426228 CATAATTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (43 bp):
TTAGCATAAAGATGCTCGTTATAAATATGTGATTATATACGAG
Found at i:428658 original size:22 final size:21
Alignment explanation
Indices: 428633--428675 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
428623 AATTATGAAC
*
428633 ATGTTAAATTTTAATTAATTTT
1 ATGTCAAATTTTAATT-ATTTT
*
428655 ATGTCAAATTTTGATTATTTT
1 ATGTCAAATTTTAATTATTTT
428676 CGACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
ATGTCAAATTTTAATTATTTT
Found at i:429273 original size:25 final size:25
Alignment explanation
Indices: 429223--429273 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
429213 ACATTTCTCA
* *
429223 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTATTC
*
429248 TCTCTTCATTTCCCT-TCTATTATTC
1 TCTCTTCACTTCCCTCTC-ATTATTC
429273 T
1 T
429274 TCATTCCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTATTC
Found at i:440697 original size:19 final size:19
Alignment explanation
Indices: 440660--440697 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
440650 CATCATCGGT
*
440660 CATAGGTAAAAACTGTGAC
1 CATAGGTAAAAACTCTGAC
440679 CATA-GTAAAAACTACTGAC
1 CATAGGTAAAAACT-CTGAC
440698 GCTAACACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (19 bp):
CATAGGTAAAAACTCTGAC
Found at i:442960 original size:17 final size:19
Alignment explanation
Indices: 442918--442961 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
442908 AATCTAAATT
442918 TATTTTATAATAAGATGAA
1 TATTTTATAATAAGATGAA
*
442937 -GTTTTATAATAA-AT-AA
1 TATTTTATAATAAGATGAA
442953 TATTTTATA
1 TATTTTATA
442962 TAGACTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 9 0.41
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
TATTTTATAATAAGATGAA
Found at i:443132 original size:23 final size:22
Alignment explanation
Indices: 443085--443140 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
443075 AGATTTAAAC
*
443085 AAATATTATATTTATATTATTA
1 AAATATTATATTTATATTATCA
443107 AAATATTCATATTTAATATTA-CA
1 AAATATT-ATATTT-ATATTATCA
*
443130 AAACATT-TATT
1 AAATATTATATT
443141 ACTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 13 0.43
24 6 0.20
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATTATATTTATATTATCA
Found at i:443887 original size:18 final size:18
Alignment explanation
Indices: 443853--443888 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
443843 GTTTCTATTA
*
443853 TTATTTATTTGTGTTTAT
1 TTATTTATTTATGTTTAT
*
443871 TTATTTATTTATTTTTAT
1 TTATTTATTTATGTTTAT
443889 GAATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TTATTTATTTATGTTTAT
Found at i:445194 original size:23 final size:23
Alignment explanation
Indices: 445168--445241 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
445158 TGATTTTTAA
*
445168 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
445191 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
* *
445214 ATTTAGGATTATGTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
445237 ATTTA
1 ATTTA
445242 AGAAAAATCG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:445195 original size:13 final size:13
Alignment explanation
Indices: 445177--445241 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 13
445167 AATTTTGAAT
445177 TATTTAGTGATAA
1 TATTTAGTGATAA
*
445190 TATTTA--GA-AT
1 TATTTAGTGATAA
445200 TATTTAGTGATAA
1 TATTTAGTGATAA
445213 TATTTAG-GAT--
1 TATTTAGTGATAA
*
445223 TATGTAGTGATAA
1 TATTTAGTGATAA
445236 TATTTA
1 TATTTA
445242 AGAAAAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 13 0.31
11 5 0.12
12 5 0.12
13 19 0.45
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:453227 original size:21 final size:21
Alignment explanation
Indices: 453197--453256 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
453187 GGTGGATCGA
* *
453197 CTCTTTTGAGCTTCTGTTCAG
1 CTCTTATGAGCTTTTGTTCAG
453218 CTCTTATGAGCTTTTGTTCAG
1 CTCTTATGAGCTTTTGTTCAG
453239 CTCTTATGAGCTTTTGTT
1 CTCTTATGAGCTTTTGTT
453257 GGTGTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.50
Consensus pattern (21 bp):
CTCTTATGAGCTTTTGTTCAG
Found at i:454137 original size:12 final size:12
Alignment explanation
Indices: 454117--454146 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
454107 TCAGGCAGTT
*
454117 ACACAGCCTAGC
1 ACACGGCCTAGC
454129 ACACGGCCTAGC
1 ACACGGCCTAGC
454141 ACACGG
1 ACACGG
454147 GCGTGCGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:454390 original size:42 final size:42
Alignment explanation
Indices: 454343--454427 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
454333 GAGATACGGG
454343 ACTCAAAATTTAATTCCGTAAATTTTTCCTGAAACTAGACTC
1 ACTCAAAATTTAATTCCGTAAATTTTTCCTGAAACTAGACTC
454385 ACTCAAAATTTAATTCCGTAAATTTTTCCTGAAACTAGACTC
1 ACTCAAAATTTAATTCCGTAAATTTTTCCTGAAACTAGACTC
454427 A
1 A
454428 TATATATTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (42 bp):
ACTCAAAATTTAATTCCGTAAATTTTTCCTGAAACTAGACTC
Found at i:455448 original size:50 final size:50
Alignment explanation
Indices: 455343--455685 Score: 382
Period size: 50 Copynumber: 6.7 Consensus size: 50
455333 ACATGTCAAA
* ** * *
455343 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGGTGCCAAT
* *
455394 GCCATGTCACAGACATGGTCTTA-AGGGGGACCTCTCATCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGGTGCCAAT
* * *
455444 GCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAT
* * ** * *
455494 GCCATGTCCCAAACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGGTGCCAAT
* * * *
455545 GCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGATGCCAAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAT
*
455595 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG-TGCCAAT
* * *
455651 GCCATGTCCCAGACGTGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
455686 TTAGCCAAAT
Statistics
Matches: 247, Mismatches: 36, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
50 134 0.54
51 68 0.28
53 5 0.02
55 1 0.00
56 39 0.16
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAT
Found at i:455538 original size:101 final size:100
Alignment explanation
Indices: 455343--455674 Score: 414
Period size: 101 Copynumber: 3.2 Consensus size: 100
455333 ACATGTCAAA
** ** * * * *
455343 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCACAGAC
1 GCCATGTCCCAGACATGGTCTTACGGGGGA-CCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* *
455408 ATGGTCTTA-AGGGGGACCTCTCATCTCGGTGCCCAT
65 ATGGTCTTACA-TGGGACCTCTCATATCGGTGCCCAT
* *
455444 GCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACA
1 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
**
455509 TGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
66 TGGTCTTACATGGGA-CCTCTCATATCGGTGCCCAT
* *
455545 GCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGATGCCAACGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
*
455610 TGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
66 TGGTCTTACATGGGACCTCTCAT-A--TC--GG-TGCCCAT
*
455651 GCCATGTCCCAGACGTGGTCTTAC
1 GCCATGTCCCAGACATGGTCTTAC
455675 ATGGGATCTC
Statistics
Matches: 201, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
100 46 0.23
101 122 0.61
103 2 0.01
105 2 0.01
106 29 0.14
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (100 bp):
GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
TGGTCTTACATGGGACCTCTCATATCGGTGCCCAT
Found at i:455617 original size:151 final size:154
Alignment explanation
Indices: 455343--455681 Score: 522
Period size: 151 Copynumber: 2.2 Consensus size: 154
455333 ACATGTCAAA
455343 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCACAGAC
1 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCACAGAC
* * * *
455408 ATGGTCTTAAGGGGGACCTCTCATCTCGGTGCCCATGCCATGTCCCAGACATGATCTTACGGGGG
66 ATGGTCTTAAGGGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGACATGATCTTACAGGGG
455473 ACCTCTC-ATCTC-GG-TGCCAAC
131 ACCTCTCAATCTCAGGATGCCAAC
* *
455494 GCCATGTCCCAAACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCACAGAC
* * * *
455559 ATGGTCTTACGGGGGACCTTTCATCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGG
66 ATGGTCTTAAGGGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGACATGATCTTACAGGGG
*
455624 ACCTCTCATGATCTCAAGGATGCCAAT
131 ACCTCTCA--ATCTC-AGGATGCCAAC
*
455651 GCCATGTCCCAGACGTGGTCTTACATGGGAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAT
455682 CTCTTTAGCC
Statistics
Matches: 169, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
151 127 0.75
154 5 0.03
156 2 0.01
157 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (154 bp):
GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCACAGAC
ATGGTCTTAAGGGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGACATGATCTTACAGGGG
ACCTCTCAATCTCAGGATGCCAAC
Found at i:460192 original size:16 final size:16
Alignment explanation
Indices: 460167--460231 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
460157 CGTTTGGTTC
460167 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
460183 GCTATAATGGAATAGA
1 GCTGTAATGGAATAGA
*
460199 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
460215 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
460231 G
1 G
460232 GCATAATAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:460714 original size:193 final size:193
Alignment explanation
Indices: 460385--460764 Score: 724
Period size: 193 Copynumber: 2.0 Consensus size: 193
460375 AGGCAGATTA
460385 TTATTGTTATTAAATTTTAATAAGATTAATAATATAAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTAATAATATAAATAATAAATAATTTAATCATATTTTAAC
* *
460450 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTCTTAGTATTAAATAT
66 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
*
460515 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATCTACTG
131 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAAAATTTAAAATCTACTG
*
460578 TTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAAC
1 TTATTGTTATTAAATTTTAATAAGATTAATAATATAAATAATAAATAATTTAATCATATTTTAAC
460643 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
66 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
460708 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAAAATTTAAAAT
131 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAAAATTTAAAAT
460765 AATAAAATTT
Statistics
Matches: 183, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 183 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (193 bp):
TTATTGTTATTAAATTTTAATAAGATTAATAATATAAATAATAAATAATTTAATCATATTTTAAC
ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAAAATTTAAAATCTACTG
Found at i:460751 original size:61 final size:60
Alignment explanation
Indices: 460479--460752 Score: 144
Period size: 61 Copynumber: 4.3 Consensus size: 60
460469 ATTTAATAAA
* * * *
460479 AATATATAAT-TTGATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATACT-ATAAAATTCTTAATATTAAATATTCTTAT-TAAATTTAATAAAATCAT
* * ** * * *
460540 AATATATAATACTATAAAATATAATTTAAAATCTACTGTTATTGTTATTAAATTTTAATAAGATT
1 AATATATAATACTATAAAAT-T--CTTAATAT-TA--AATATTCTTATTAAA-TTTAATAAAATC
460605 ATT
59 A-T
* * * * ** *
460608 AATATA-AATAATA-AATAATT-TAATCATATTTTAACATAATTATTATTAAATATAATTTAATA
1 AATATATAATACTATAA-AATTCT--T-A-ATATTAA-AT-ATTCTTATTAAATTTAATAAAATC
*
460670 AA
59 AT
* * *
460672 AATATATAAT-TTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATACT-ATAAAATTCTTAATATTAAATATTCTTAT-TAAATTTAATAAAATCAT
460733 AATATATAATACTATAAAAT
1 AATATATAATACTATAAAAT
460753 AAAATTTAAA
Statistics
Matches: 157, Mismatches: 34, Indels: 44
0.67 0.14 0.19
Matches are distributed among these distances:
60 7 0.04
61 47 0.30
62 9 0.06
63 2 0.01
64 13 0.08
65 20 0.13
66 23 0.15
67 29 0.18
68 7 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATACTATAAAATTCTTAATATTAAATATTCTTATTAAATTTAATAAAATCAT
Found at i:460812 original size:20 final size:20
Alignment explanation
Indices: 460765--460803 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
460755 AATTTAAAAT
*
460765 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
460785 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
460804 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:462630 original size:33 final size:32
Alignment explanation
Indices: 462569--462630 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
462559 ATTCCACAAA
* * *
462569 CAAAAAGAACAAAGATAAGCATATTATGCGAG
1 CAAAAAGAACAAAGAAAAGCAAAATATGCGAG
*
462601 CAAAAAGAAAGAAAGAAAAGCAAAATATGC
1 CAAAAAG-AACAAAGAAAAGCAAAATATGC
462631 TATAGCCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 7 0.28
33 18 0.72
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (32 bp):
CAAAAAGAACAAAGAAAAGCAAAATATGCGAG
Found at i:463575 original size:27 final size:27
Alignment explanation
Indices: 463545--463598 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
463535 AGCTTTTGGA
463545 AGGGAATAGAAATCGGGAGGGTAAAAC
1 AGGGAATAGAAATCGGGAGGGTAAAAC
** *
463572 AGGGCTTAGAAATCGGGAGGGTTAAAC
1 AGGGAATAGAAATCGGGAGGGTAAAAC
463599 GGAAAGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.37, T:0.15
Consensus pattern (27 bp):
AGGGAATAGAAATCGGGAGGGTAAAAC
Found at i:466764 original size:50 final size:50
Alignment explanation
Indices: 466620--467068 Score: 515
Period size: 50 Copynumber: 8.8 Consensus size: 50
466610 GATCATAACA
* * * ** *
466620 TGCCAAAGCCATGTCTCAGACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * **
466671 TTCCCATGCCATGTCGCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
466721 TGCC-ACGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * ** *
466771 TGCCCATGCCAT-TAACCAGACATGGTCTTACGGGGGACCTATCATCTCGG
1 TGCCAACGCCATGT-CCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
466821 TGCCAACTCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
466871 TGCCAACGTCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
466921 TGTCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
466971 TGCCAACGCCATGTCCCAGACACGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
467026 ATGCCAATGCCATGTCCCAGGCATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
467069 TTGCCCAAAT
Statistics
Matches: 337, Mismatches: 51, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
49 28 0.08
50 207 0.61
51 57 0.17
53 5 0.01
55 2 0.01
56 38 0.11
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:467188 original size:13 final size:13
Alignment explanation
Indices: 467167--467198 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
467157 GCTTGGATCA
*
467167 TCATCAAATAAAT
1 TCATAAAATAAAT
467180 TCATAAAATAAAT
1 TCATAAAATAAAT
467193 TCATAA
1 TCATAA
467199 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:467445 original size:30 final size:30
Alignment explanation
Indices: 467410--467466 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
467400 CCTCGACTCT
467410 AACTTTGT-CAAAATTATGA-TTTTGCCCCTA
1 AACTTT-TACAAAATTAT-ATTTTTGCCCCTA
*
467440 AACTTTTACATAATTATATTTTTGCCC
1 AACTTTTACAAAATTATATTTTTGCCC
467467 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTATATTTTTGCCCCTA
Found at i:469115 original size:22 final size:22
Alignment explanation
Indices: 469090--469134 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
469080 AATATTATAA
469090 ATTTTTTTATTTACCAAAATAT
1 ATTTTTTTATTTACCAAAATAT
469112 ATTTTTTTATTTACCAAAATAT
1 ATTTTTTTATTTACCAAAATAT
469134 A
1 A
469135 CCAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTTTATTTACCAAAATAT
Found at i:469284 original size:4 final size:4
Alignment explanation
Indices: 469275--469414 Score: 80
Period size: 4 Copynumber: 35.0 Consensus size: 4
469265 GAAGGAGAGG
* * **
469275 GAAA GAAA GAAA GAAA GAAA AAAA GAAA GAAA G-GA GATG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* * *
469322 GAAA AAAA GGAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GGAA
1 GAAA GAAA -GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
*
469367 G-AA GAAGA GGAAA GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAA-A -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
469411 GAAA
1 GAAA
469415 AGGAAAGGAG
Statistics
Matches: 108, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
3 20 0.19
4 62 0.57
5 20 0.19
6 6 0.06
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:469320 original size:39 final size:38
Alignment explanation
Indices: 469266--469349 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
469256 GGGGGACCAG
*
469266 AAGGAGAGGGAAAGAAAGAAAGAAAGAAAAAAAGAAAGA
1 AAGGAGAGGGAAAGAAAGAAAAAAAGAAAAAAA-AAAGA
* * * *
469305 AAGGAGATGGAAAGAAAGAAAAAAAGGAAAGAAAAGGA
1 AAGGAGAGGGAAAGAAAGAAAAAAAGAAAAAAAAAAGA
469343 AAGGAGA
1 AAGGAGA
469350 AGAGAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 11 0.28
39 29 0.73
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGGAGAGGGAAAGAAAGAAAAAAAGAAAAAAAAAAGA
Found at i:469325 original size:35 final size:33
Alignment explanation
Indices: 469279--469432 Score: 107
Period size: 35 Copynumber: 4.3 Consensus size: 33
469269 GAGAGGGAAA
469279 GAAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGATG
1 GAAA-AAAGAAAGAAAAAAAGAAAGAAAGGAGA-G
469314 GAAAGAAAGAAA-AAAAGGAAAGAAAAGGAAAGGAGAAG
1 GAAA-AAAGAAAGAAAA--AAAG-AAA-GAAAGGAG-AG
* * *
469352 AGAAAAAA-AAAGGAAGAAGAAG-AGGAAAGGAGAA
1 -GAAAAAAGAAA-GAA-AAAAAGAAAGAAAGGAGAG
*
469386 GAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
1 GAAAAAAGAAAGAAAAA-AA-GAAAG-AAAGGAGAG
*
469422 GAGAAGAAGAA
1 GA-AAAAAGAA
469433 GAGGGAAGGA
Statistics
Matches: 96, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
32 2 0.02
33 12 0.12
34 9 0.09
35 22 0.23
36 14 0.15
37 13 0.14
38 15 0.16
39 7 0.07
40 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (33 bp):
GAAAAAAGAAAGAAAAAAAGAAAGAAAGGAGAG
Found at i:469341 original size:10 final size:10
Alignment explanation
Indices: 469313--469421 Score: 57
Period size: 10 Copynumber: 10.6 Consensus size: 10
469303 GAAAGGAGAT
469313 GGAAAG-AAA
1 GGAAAGAAAA
469322 -GAAA-AAAA
1 GGAAAGAAAA
469330 GGAAAGAAAA
1 GGAAAGAAAA
469340 GGAAAGGAGAAGA
1 GGAAA-GA-AA-A
* *
469353 GAAAAAAAAA
1 GGAAAGAAAA
*
469363 GGAAGAAGAAGA
1 GG-A-AAGAAAA
*
469375 GGAAAGGAGAA
1 GGAAA-GAAAA
*
469386 -GAAAAAAGAA
1 GGAAAGAA-AA
*
469396 AGAAA-AAGAA
1 GGAAAGAA-AA
469406 GGAAAGAAAA
1 GGAAAGAAAA
469416 GGAAAG
1 GGAAAG
469422 GAGAAGAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
8 7 0.09
9 5 0.06
10 36 0.46
11 15 0.19
12 10 0.13
13 5 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GGAAAGAAAA
Found at i:469385 original size:30 final size:30
Alignment explanation
Indices: 469351--469455 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 30
469341 GAAAGGAGAA
469351 GAGAAAAAAAAAGGAAGAAGAAGAGGAAAG
1 GAGAAAAAAAAAGGAAGAAGAAGAGGAAAG
* * *
469381 GAGAAGAAAAAAGAAAGAAAAAGAAGGAAA-
1 GAGAAAAAAAAAGGAAGAAGAAG-AGGAAAG
** * *
469411 GA-AAAGGAAAGGAGAAGAAGAAGAGGGAAG
1 GAGAAAAAAAAAG-GAAGAAGAAGAGGAAAG
469441 GAAGGAAAAAAAAAG
1 G-A-GAAAAAAAAAG
469456 AAAAAAAAGG
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
29 11 0.20
30 31 0.55
31 7 0.12
33 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (30 bp):
GAGAAAAAAAAAGGAAGAAGAAGAGGAAAG
Found at i:469422 original size:58 final size:55
Alignment explanation
Indices: 469280--469465 Score: 160
Period size: 58 Copynumber: 3.1 Consensus size: 55
469270 AGAGGGAAAG
* * *
469280 AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGATGGAAA-GAAAGAAAAAAAGGAAAGAA
1 AAAGAAGGAAAGAAAAAAAGGAAG-AAGAAGA-GGAAAGGAAAG-AAAAAA-GAAAGAA
*
469338 AAGGAAAGGAGAAGAGAAAAAAAAAGGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAAGAA
1 AAAG-AA-G-GAA-AG--AAAAAAAGGAAGAAGAAGAGGAAAGGA-AAGAAAAAAGAAAGAA
* *
469400 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAGAGGGAAGGAAGGAAAAAA-AAAGAA
1 AAAGAAGGAAAGAAAA--AAA-G-GAAGAAGAAGAGGAAAGGAAAGAAAAAAGAAAGAA
*
469458 AAAAAAGG
1 AAAGAAGG
469466 TAAATTTTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
56 4 0.04
58 21 0.19
59 14 0.13
60 19 0.18
61 5 0.05
62 17 0.16
63 14 0.13
64 14 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (55 bp):
AAAGAAGGAAAGAAAAAAAGGAAGAAGAAGAGGAAAGGAAAGAAAAAAGAAAGAA
Found at i:472682 original size:11 final size:11
Alignment explanation
Indices: 472666--472692 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
472656 TCTATAACTT
472666 AATTTGGATAC
1 AATTTGGATAC
472677 AATTTGGATAC
1 AATTTGGATAC
472688 AATTT
1 AATTT
472693 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:473230 original size:193 final size:194
Alignment explanation
Indices: 472891--473276 Score: 765
Period size: 193 Copynumber: 2.0 Consensus size: 194
472881 CGTCAGATTT
472891 CTCCCTAATGTCCATCTCATTACGGATTCTGCTTGACTGCGGACGACCCCTTGGATTCCTCCGTA
1 CTCCCTAATGTCCATCTCATTACGGATTCTGCTTGACTGCGGACGACCCCTTGGATTCCTCCGTA
472956 GCCCTCTGTCTGGGAGAAGCTCGAAAGTCGTCGGCGGCACCTCCCACGTAGATAGGTCAGGCAGG
66 GCCCTCTGTCTGGGAGAAGCTCGAAAGTCGTCGGCGGCACCTCCCACGTAGATAGGTCAGGCAGG
473021 ACGGGGAACTCATTCTCCCAGACACGCAATGTGCGCTTCAGCGTGTACACATCACCGACATATC
131 ACGGGGAACTCATTCTCCCAGACACGCAATGTGCGCTTCAGCGTGTACACATCACCGACATATC
473085 CTCCCTAAT-TCCATCTCATTACGGATTCTGCTTGACTGCGGACGACCCCTTGGATTCCTCCGTA
1 CTCCCTAATGTCCATCTCATTACGGATTCTGCTTGACTGCGGACGACCCCTTGGATTCCTCCGTA
473149 GCCCTCTGTCTGGGAGAAGCTCGAAAGTCGTCGGCGGCACCTCCCACGTAGATAGGTCAGGCAGG
66 GCCCTCTGTCTGGGAGAAGCTCGAAAGTCGTCGGCGGCACCTCCCACGTAGATAGGTCAGGCAGG
473214 ACGGGGAACTCATTCTCCCAGACACGCAATGTGCGCTTCAGCGTGTACACATCACCGACATAT
131 ACGGGGAACTCATTCTCCCAGACACGCAATGTGCGCTTCAGCGTGTACACATCACCGACATAT
473277 TGTTCAGCAT
Statistics
Matches: 192, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
193 183 0.95
194 9 0.05
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.23
Consensus pattern (194 bp):
CTCCCTAATGTCCATCTCATTACGGATTCTGCTTGACTGCGGACGACCCCTTGGATTCCTCCGTA
GCCCTCTGTCTGGGAGAAGCTCGAAAGTCGTCGGCGGCACCTCCCACGTAGATAGGTCAGGCAGG
ACGGGGAACTCATTCTCCCAGACACGCAATGTGCGCTTCAGCGTGTACACATCACCGACATATC
Found at i:475981 original size:11 final size:11
Alignment explanation
Indices: 475961--476000 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
475951 TAAAAAATAC
475961 CTTCTTTTTCT
1 CTTCTTTTTCT
*
475972 CTTCTCTTTCT
1 CTTCTTTTTCT
475983 C-TCTTTTTCT
1 CTTCTTTTTCT
475993 CTTCTTTT
1 CTTCTTTT
476001 CCGTAGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:475988 original size:21 final size:20
Alignment explanation
Indices: 475963--476001 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
475953 AAAAATACCT
475963 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
475984 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
476002 CGTAGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:476381 original size:44 final size:44
Alignment explanation
Indices: 476326--476411 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
476316 GAGAGTGTAA
* *
476326 GTTTAGGGGCTATACCTTCCTATACCTGGAAGTGTATCTGGGTT
1 GTTTAGGGGCTAGACCTTCCTATACCTGGAAGAGTATCTGGGTT
*
476370 GTTTTGGGGCTAGACCTTCCTATACCTGGAAGAGTATCTGGG
1 GTTTAGGGGCTAGACCTTCCTATACCTGGAAGAGTATCTGGG
476412 CTGCGAAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.34
Consensus pattern (44 bp):
GTTTAGGGGCTAGACCTTCCTATACCTGGAAGAGTATCTGGGTT
Found at i:478836 original size:20 final size:20
Alignment explanation
Indices: 478800--478907 Score: 89
Period size: 20 Copynumber: 5.5 Consensus size: 20
478790 ATACGAAATT
**
478800 AAAATTT-TAATTTAATATC
1 AAAATTTCTAATGCAATATC
*
478819 AAAATCTCTAATGCAATATC
1 AAAATTTCTAATGCAATATC
** **
478839 AATAGGTT-TAATGCAATGCC
1 AA-AATTTCTAATGCAATATC
*
478859 AAAATTTTTAATG-AATA-C
1 AAAATTTCTAATGCAATATC
*
478877 TAATATTTCTAATGCAATATC
1 -AAAATTTCTAATGCAATATC
478898 AAAATTTCTA
1 AAAATTTCTA
478908 GCGAATACCA
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.01
19 23 0.33
20 42 0.61
21 3 0.04
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (20 bp):
AAAATTTCTAATGCAATATC
Found at i:478901 original size:39 final size:40
Alignment explanation
Indices: 478813--478907 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 40
478803 ATTTTAATTT
*
478813 AATATCAAAATCTCTAATGCAATATCAATAGGTTTAATGC
1 AATATCAAAATTTCTAATGCAATATCAATAGGTTTAATGC
** * *
478853 AATGCCAAAATTTTTAATG-AATA-CTAATA-TTTCTAATGC
1 AATATCAAAATTTCTAATGCAATATC-AATAGGTT-TAATGC
478892 AATATCAAAATTTCTA
1 AATATCAAAATTTCTA
478908 GCGAATACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
38 3 0.07
39 27 0.60
40 15 0.33
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (40 bp):
AATATCAAAATTTCTAATGCAATATCAATAGGTTTAATGC
Found at i:479915 original size:20 final size:20
Alignment explanation
Indices: 479841--479927 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
479831 GTTACATATA
* *
479841 TTGGTATTTGGTTTGAAATT
1 TTGGTATTTGATTAGAAATT
* * * *
479861 TTTGTATCTGGTTACAAATT
1 TTGGTATTTGATTAGAAATT
* **
479881 CTGGT-TTCCATTAGAAATT
1 TTGGTATTTGATTAGAAATT
*
479900 TTGTTATTTGATTAGAAATT
1 TTGGTATTTGATTAGAAATT
479920 TTGGTATT
1 TTGGTATT
479928 GTTGGAAAAA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
19 12 0.24
20 38 0.76
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (20 bp):
TTGGTATTTGATTAGAAATT
Found at i:484656 original size:17 final size:17
Alignment explanation
Indices: 484634--484666 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
484624 TTATTTAGTG
484634 TAATTTTATTA-TTTTAT
1 TAATTTT-TTAGTTTTAT
484651 TAATTTTTTAGTTTTA
1 TAATTTTTTAGTTTTA
484667 GGGCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TAATTTTTTAGTTTTAT
Found at i:490124 original size:46 final size:46
Alignment explanation
Indices: 490057--490155 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
490047 AAGCAAAAAG
*
490057 AAAGAAAAATAGGAACACACAGATTTTACGTAAAAACCCTTTCGGT
1 AAAGAAAAATAGGAACACACAGATTTTACGTAAAAAACCTTTCGGT
*
490103 AAAGAAAAATAGGAATACACAGATTTTACGTAAAAAACCTTTCGGT
1 AAAGAAAAATAGGAACACACAGATTTTACGTAAAAAACCTTTCGGT
490149 AAA-AAAA
1 AAAGAAAA
490156 CCACGGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 4 0.08
46 47 0.92
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (46 bp):
AAAGAAAAATAGGAACACACAGATTTTACGTAAAAAACCTTTCGGT
Found at i:490441 original size:15 final size:15
Alignment explanation
Indices: 490421--490474 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
490411 CCACCTTGAC
490421 ACAAATTCTCAACGA
1 ACAAATTCTCAACGA
*
490436 ACAAATTCTTC-AC-C
1 ACAAATTC-TCAACGA
*
490450 ACAAACTCTCAACGA
1 ACAAATTCTCAACGA
*
490465 ACAAGTTCTC
1 ACAAATTCTC
490475 CACCTCTTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.06
14 9 0.29
15 18 0.58
16 2 0.06
ACGTcount: A:0.41, C:0.31, G:0.06, T:0.22
Consensus pattern (15 bp):
ACAAATTCTCAACGA
Found at i:490462 original size:29 final size:29
Alignment explanation
Indices: 490420--490478 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
490410 TCCACCTTGA
* *
490420 CACAAATTCTCAACGAACAAATTCTTCAC
1 CACAAACTCTCAACGAACAAATTCTCCAC
*
490449 CACAAACTCTCAACGAACAAGTTCTCCAC
1 CACAAACTCTCAACGAACAAATTCTCCAC
490478 C
1 C
490479 TCTTCCACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.36, G:0.05, T:0.20
Consensus pattern (29 bp):
CACAAACTCTCAACGAACAAATTCTCCAC
Found at i:491892 original size:19 final size:20
Alignment explanation
Indices: 491855--491893 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
491845 GATTTTTGGG
*
491855 AAAATTAATTTTGATCAAAT
1 AAAATTAATTTTAATCAAAT
491875 AAAATTAA-TTTAATCAAAT
1 AAAATTAATTTTAATCAAAT
491894 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATTAATTTTAATCAAAT
Found at i:500190 original size:11 final size:11
Alignment explanation
Indices: 500174--500212 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
500164 TATATAAATA
500174 TATAAATTAAT
1 TATAAATTAAT
*
500185 TATAAAGTATAT
1 TATAAATTA-AT
500197 TATTAAATTAAT
1 TA-TAAATTAAT
500209 TATA
1 TATA
500213 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Done.