Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 187 of 292
Found at i:55775249 original size:24 final size:25
Alignment explanation
Indices: 55775217--55775272 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
55775207 TATTAATGAT
* *
55775217 TTTTAAATTG-TTTTATATTATTTA
1 TTTTAAATTGCTTTTATAGTATCTA
55775241 TTTTAAATTGCTTTTATAGTATCTA
1 TTTTAAATTGCTTTTATAGTATCTA
*
55775266 TTCTAAA
1 TTTTAAA
55775273 CCTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (25 bp):
TTTTAAATTGCTTTTATAGTATCTA
Found at i:55775295 original size:2 final size:2
Alignment explanation
Indices: 55775288--55775321 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
55775278 AAATATACAC
*
55775288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55775322 TATGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55789266 original size:24 final size:22
Alignment explanation
Indices: 55789227--55789273 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
55789217 TGCAGTATGG
55789227 AAGGAAAATAAAGAAATGAAAAAA
1 AAGGAAAATAAAGAAA--AAAAAA
* *
55789251 AAGGAAAATGATGAAAAAAAAA
1 AAGGAAAATAAAGAAAAAAAAA
55789273 A
1 A
55789274 GAGTGTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (22 bp):
AAGGAAAATAAAGAAAAAAAAA
Found at i:55790594 original size:29 final size:29
Alignment explanation
Indices: 55790561--55790691 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 29
55790551 GTGACGAGAT
55790561 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
55790590 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
55790619 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
55790648 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
55790677 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
55790692 GAAATCGAGT
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.02
29 79 0.96
30 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:55812275 original size:22 final size:22
Alignment explanation
Indices: 55812247--55812290 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55812237 CTTGAAGTGT
55812247 ACACAACATTTGCCTATTTCAG
1 ACACAACATTTGCCTATTTCAG
55812269 ACACAACATTTGCCTATTTCAG
1 ACACAACATTTGCCTATTTCAG
55812291 TCATTTTTTT
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:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (22 bp):
ACACAACATTTGCCTATTTCAG
Found at i:55813206 original size:14 final size:14
Alignment explanation
Indices: 55813171--55813217 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
55813161 CTGCACAATT
* *
55813171 AATAACATGATTAT
1 AATAACATGAATAA
*
55813185 AATGACATGAATAA
1 AATAACATGAATAA
55813199 AATAACAT-AACTAA
1 AATAACATGAA-TAA
55813213 AATAA
1 AATAA
55813218 TTACATGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 2 0.07
14 26 0.93
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAACATGAATAA
Found at i:55814544 original size:2 final size:2
Alignment explanation
Indices: 55814537--55814567 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55814527 GTTATTAAGA
55814537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55814568 ACTAATCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55818420 original size:20 final size:19
Alignment explanation
Indices: 55818397--55818438 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55818387 AGATTTTATA
55818397 TATTAT-ATTATATAATTGAT
1 TATTATAATTAT-TAATTG-T
55818417 TATTATAATTATTAATTGT
1 TATTATAATTATTAATTGT
55818436 TAT
1 TAT
55818439 GGTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTATAATTATTAATTGT
Found at i:55818560 original size:23 final size:23
Alignment explanation
Indices: 55818534--55818582 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
55818524 GGTGATTAAA
55818534 TTATACAAGTGTAATACATATAT
1 TTATACAAGTGTAATACATATAT
** * *
55818557 TTATACATTTGTAATATATTTAT
1 TTATACAAGTGTAATACATATAT
55818580 TTA
1 TTA
55818583 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (23 bp):
TTATACAAGTGTAATACATATAT
Found at i:55818747 original size:3 final size:3
Alignment explanation
Indices: 55818739--55818777 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55818729 AATAAGATAT
55818739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55818778 AGTTAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55818828 original size:13 final size:13
Alignment explanation
Indices: 55818782--55818833 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
55818772 TTATTAAGTT
55818782 AATAAAATAAA-A
1 AATAAAATAAAGA
*
55818794 TAATAAAAGAAATGA
1 -AATAAAATAAA-GA
55818809 AATAAAATAAAGA
1 AATAAAATAAAGA
* *
55818822 AACAAAACAAAG
1 AATAAAATAAAG
55818834 TAAAGAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:55825912 original size:34 final size:34
Alignment explanation
Indices: 55825874--55825947 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
55825864 AAGCAATAGA
* *
55825874 AAGTAAAAAGGGCCAAAATGACAAATATGTCATT
1 AAGTAAAAAGGGCCAAAATGACAAACATGCCATT
*
55825908 AAGTAAAAAGGGCCAAAATGGCAAACATGCCATT
1 AAGTAAAAAGGGCCAAAATGACAAACATGCCATT
55825942 AAGTAA
1 AAGTAA
55825948 TGGTTGAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.18
Consensus pattern (34 bp):
AAGTAAAAAGGGCCAAAATGACAAACATGCCATT
Found at i:55826025 original size:20 final size:19
Alignment explanation
Indices: 55826002--55826043 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55825992 AGATTATATA
55826002 TATTAT-ATTATATAATTGAT
1 TATTATAATTAT-TAATTG-T
55826022 TATTATAATTATTAATTGT
1 TATTATAATTATTAATTGT
55826041 TAT
1 TAT
55826044 GGTTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTATAATTATTAATTGT
Found at i:55826035 original size:3 final size:3
Alignment explanation
Indices: 55826002--55826120 Score: 95
Period size: 3 Copynumber: 40.7 Consensus size: 3
55825992 AGATTATATA
* * * **
55826002 TAT TA- TAT TA- TAT AAT TGAT TAT TAT AAT TAT TAAT TGT TAT GGT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT
* * * *
55826047 T-T TA- TGT TAT TAT TAG TAT TAA TAT TA- AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55826092 TAT TAT TAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55826121 AAGATAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
2 8 0.09
3 76 0.84
4 6 0.07
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:55826424 original size:13 final size:14
Alignment explanation
Indices: 55826406--55826452 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
55826396 TTATTAAGTT
55826406 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
55826419 AATAAAAGAAATGA
1 AATAAAATAAAAGA
55826433 AATAAAAT-AAAGA
1 AATAAAATAAAAGA
*
55826446 AACAAAA
1 AATAAAA
55826453 CAAAGTAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:55827117 original size:16 final size:16
Alignment explanation
Indices: 55827096--55827136 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
55827086 AGCTTTATAA
55827096 TTAATATGTGTTTAAT
1 TTAATATGTGTTTAAT
55827112 TTAATATGTGTTTAAT
1 TTAATATGTGTTTAAT
55827128 TTAATATGT
1 TTAATATGT
55827137 ATGTGCGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TTAATATGTGTTTAAT
Found at i:55827303 original size:40 final size:40
Alignment explanation
Indices: 55827233--55827314 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
55827223 AATTTATGAG
* *
55827233 TTACTGAATATTGTTTTGAATACCGAATTGAACTGTGAAA
1 TTACTGAATATTGTTATGAATACCGAATTGAACTGTAAAA
* *
55827273 TTACTGAATATTGTTATGTATA-CTATATTGAACTGTAAAA
1 TTACTGAATATTGTTATGAATACCGA-ATTGAACTGTAAAA
55827313 TT
1 TT
55827315 TTTGATGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (40 bp):
TTACTGAATATTGTTATGAATACCGAATTGAACTGTAAAA
Found at i:55827794 original size:2 final size:2
Alignment explanation
Indices: 55827787--55827812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55827777 AATAAGAATG
55827787 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
55827813 TCAAATGGTA
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:55829073 original size:21 final size:20
Alignment explanation
Indices: 55829049--55829089 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55829039 ACAAATATGA
55829049 ATGCAAATAAAAATGAAAAAT
1 ATGCAAATAAAAA-GAAAAAT
* *
55829070 ATGCAATTGAAAAGAAAAAT
1 ATGCAAATAAAAAGAAAAAT
55829090 CAAAAGCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (20 bp):
ATGCAAATAAAAAGAAAAAT
Found at i:55831347 original size:5 final size:5
Alignment explanation
Indices: 55831331--55831378 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
55831321 TAGGAAGATA
*
55831331 TTATT TTGTT TTATT TTATTAT TTATT ATTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTA-T-T TTATT -TTATT TTATT TTATT TTATT
55831379 AATTTAGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 27 0.71
6 7 0.18
7 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:55831370 original size:28 final size:29
Alignment explanation
Indices: 55831329--55831384 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
55831319 AATAGGAAGA
*
55831329 TATTATTTTGTTTTATTTTATT-ATTTAT
1 TATTATTTTATTTTATTTTATTAATTTAT
55831357 TATTATTTTATTTTATTTTATTAATTTA
1 TATTATTTTATTTTATTTTATTAATTTA
55831385 GGTTAGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TATTATTTTATTTTATTTTATTAATTTAT
Found at i:55831377 original size:18 final size:19
Alignment explanation
Indices: 55831329--55831379 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
55831319 AATAGGAAGA
*
55831329 TATTATTTTGTT-TTATTT
1 TATTATTTTATTATTATTT
55831347 TATTA-TTTATTATTATTT
1 TATTATTTTATTATTATTT
55831365 TATTTTATTTTATTA
1 TA--TTATTTTATTA
55831380 ATTTAGGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.18
18 13 0.46
20 3 0.11
21 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTATTTTATTATTATTT
Found at i:55838323 original size:27 final size:26
Alignment explanation
Indices: 55838272--55838376 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 26
55838262 TTAGTTTACT
*
55838272 AAATTACCGAAATACCCT-TAGTTTGTA
1 AAATTA-CGAAATACCCTCGA-TTTGTA
*
55838299 AAAATACTGAAATACCCTCGATTTGTA
1 AAATTAC-GAAATACCCTCGATTTGTA
* * *
55838326 AATTTACCGAAATACCTTCGACTTGTA
1 AAATTA-CGAAATACCCTCGATTTGTA
*
55838353 AAATTACCAAAGTACCCTCGATTT
1 AAATTACGAAA-TACCCTCGATTT
55838377 ACAGAATTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.08
27 57 0.89
28 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACGAAATACCCTCGATTTGTA
Found at i:55838339 original size:54 final size:53
Alignment explanation
Indices: 55838271--55838376 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
55838261 TTTAGTTTAC
* *
55838271 TAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTGAAA-TACCCTCGATTTG
1 TAAATTACCGAAATA-CCTTAGACTTGTAAAAATAC-CAAAGTACCCTCGATTTG
* *
55838324 TAAATTTACCGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCTCGATTT
1 TAAA-TTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTT
55838377 ACAGAATTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 12 0.26
54 34 0.74
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (53 bp):
TAAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTTG
Found at i:55838387 original size:54 final size:53
Alignment explanation
Indices: 55838266--55838388 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 53
55838256 AATACTTTAG
* *
55838266 TTTACTAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGA
1 TTTAC-AAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCGA
** * *
55838320 TTTGTAAATTTACCGAAATA-CCTTCGACTTGTAAAATTAC-CAAAGTACCCTCGA
1 TTTACAAA-TTACCGAAATACCCTTAG-CTTGTAAAAATACTCAAA-TACCCTCGA
55838374 TTTACAGAATTACCG
1 TTTACA-AATTACCG
55838389 TTTTACCCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
53 11 0.19
54 44 0.77
55 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (53 bp):
TTTACAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCGA
Found at i:55838395 original size:27 final size:27
Alignment explanation
Indices: 55838365--55838681 Score: 351
Period size: 27 Copynumber: 11.8 Consensus size: 27
55838355 ATTACCAAAG
*
55838365 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACATAATTACCGTTT
*
55838392 TACCCT-AATTTACATAATTACCGTTT
1 TACCCTCGATTTACATAATTACCGTTT
*
55838418 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACATAATTACCGTTT
* * *
55838445 TACCCTCGACTTATAGAATTACCGTTT
1 TACCCTCGATTTACATAATTACCGTTT
*
55838472 TACCCT-AATTTACATAATTACCGTTT
1 TACCCTCGATTTACATAATTACCGTTT
* *
55838498 TACCC-CTGATTTACATAATTATCATTT
1 TACCCTC-GATTTACATAATTACCGTTT
* * *
55838525 TACCCTCGACTTACAGAATTACTGTTT
1 TACCCTCGATTTACATAATTACCGTTT
*
55838552 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACATAATTACCGTTT
*
55838579 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACATAATTACCGTTT
* * *
55838606 TACCCTCGACTTACAGAATTACTGTTT
1 TACCCTCGATTTACATAATTACCGTTT
* *
55838633 TACCCTCGATTTA-TTGAATTACTGTTT
1 TACCCTCGATTTACAT-AATTACCGTTT
* *
55838660 TACCCTTGATTTACAAAATTAC
1 TACCCTCGATTTACATAATTAC
55838682 TAAAATACCC
Statistics
Matches: 244, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
26 45 0.18
27 196 0.80
28 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACATAATTACCGTTT
Found at i:55838600 original size:81 final size:80
Alignment explanation
Indices: 55838365--55838680 Score: 508
Period size: 81 Copynumber: 3.9 Consensus size: 80
55838355 ATTACCAAAG
*
55838365 TACCCTCGATTTACAGAATTACCGTTTTACCCTAATTTACATAATTACCGTTTTACCCCTGATTT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCTAATTTACATAATTACCGTTTTACCCCTGATTT
55838430 ACATAATTATCGTTT
66 ACATAATTATCGTTT
*
55838445 TACCCTCGACTTATAGAATTACCGTTTTACCCTAATTTACATAATTACCGTTTTACCCCTGATTT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCTAATTTACATAATTACCGTTTTACCCCTGATTT
*
55838510 ACATAATTATCATTT
66 ACATAATTATCGTTT
*
55838525 TACCCTCGACTTACAGAATTACTGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
1 TACCCTCGACTTACAGAATTACCGTTTTA-CCCTAATTTACATAATTACCGTTTTACCCCTGATT
55838590 TACATAATTATCGTTT
65 TACATAATTATCGTTT
* * * * *
55838606 TACCCTCGACTTACAGAATTACTGTTTTACCCTCGATTTA-TTGAATTACTGTTTTACCCTTGAT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCT-AATTTACAT-AATTACCGTTTTACCCCTGAT
*
55838670 TTACAAAATTA
64 TTACATAATTA
55838681 CTAAAATACC
Statistics
Matches: 222, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
80 109 0.49
81 113 0.51
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (80 bp):
TACCCTCGACTTACAGAATTACCGTTTTACCCTAATTTACATAATTACCGTTTTACCCCTGATTT
ACATAATTATCGTTT
Found at i:55838690 original size:27 final size:27
Alignment explanation
Indices: 55838660--55838823 Score: 108
Period size: 27 Copynumber: 6.1 Consensus size: 27
55838650 ATTACTGTTT
55838660 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *** *
55838687 TACCCTTGGTTTGTGAAATTACGAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
** **
55838714 -ACCCTCAATTTGTAAAATTA--AAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *
55838738 TACCC-TAATTTACAAAGTTAC-AGAAA
1 TACCCTTGATTTACAAAATTACTA-AAA
55838764 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACTA-AAA
* * *
55838793 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
55838820 TACC
1 TACC
55838824 TTTGGTTTGT
Statistics
Matches: 109, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
24 15 0.14
25 5 0.05
26 24 0.22
27 39 0.36
28 7 0.06
29 19 0.17
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:55838725 original size:26 final size:24
Alignment explanation
Indices: 55838696--55838748 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
55838686 ATACCCTTGG
*
55838696 TTTGTGAAATTACGAAAA-ACCCTCAA
1 TTTGTAAAATTA--AAAATACCCT-AA
55838722 TTTGTAAAATTAAAAATACCCTAA
1 TTTGTAAAATTAAAAATACCCTAA
55838746 TTT
1 TTT
55838749 ACAAAGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 5 0.20
26 11 0.44
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (24 bp):
TTTGTAAAATTAAAAATACCCTAA
Found at i:55838828 original size:27 final size:27
Alignment explanation
Indices: 55838780--55838831 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
55838770 TGACTTTCTA
55838780 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
55838807 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
55838832 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:55838949 original size:27 final size:27
Alignment explanation
Indices: 55838885--55838949 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
55838875 ACCCCTAAAA
*
55838885 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
55838912 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
55838939 GGTAAAATGAC
1 GGTAAAATGAC
55838950 GAATATGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:55840022 original size:25 final size:25
Alignment explanation
Indices: 55839993--55840040 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55839983 TTATAATATG
* *
55839993 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55840018 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55840041 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55840102 original size:20 final size:20
Alignment explanation
Indices: 55840077--55840142 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
55840067 ATTTTGATAA
*
55840077 ACATGATATGTATGATATGC
1 ACATGATATGCATGATATGC
*
55840097 ACATGACATGCATGATATGC
1 ACATGATATGCATGATATGC
55840117 ACATGATATGCATGATATGC
1 ACATGATATGCATGATATGC
55840137 ACATGA
1 ACATGA
55840143 GATGTTCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
ACATGATATGCATGATATGC
Found at i:55840107 original size:11 final size:11
Alignment explanation
Indices: 55840088--55840142 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
55840078 CATGATATGT
55840088 ATGATATGCAC
1 ATGATATGCAC
*
55840099 ATGACATG--C
1 ATGATATGCAC
55840108 ATGATATGCAC
1 ATGATATGCAC
55840119 ATGATATG--C
1 ATGATATGCAC
55840128 ATGATATGCAC
1 ATGATATGCAC
55840139 ATGA
1 ATGA
55840143 GATGTTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 17 0.45
11 21 0.55
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:55840110 original size:9 final size:9
Alignment explanation
Indices: 55840078--55840137 Score: 66
Period size: 9 Copynumber: 6.2 Consensus size: 9
55840068 TTTTGATAAA
55840078 CATGATATG
1 CATGATATG
*
55840087 TATGATATG
1 CATGATATG
*
55840096 CACATGACATG
1 --CATGATATG
55840107 CATGATATG
1 CATGATATG
55840116 CACATGATATG
1 --CATGATATG
55840127 CATGATATG
1 CATGATATG
55840136 CA
1 CA
55840138 CATGAGATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 27 0.63
11 16 0.37
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (9 bp):
CATGATATG
Found at i:55840224 original size:23 final size:23
Alignment explanation
Indices: 55840194--55840359 Score: 251
Period size: 23 Copynumber: 7.1 Consensus size: 23
55840184 AGGAAGTGCA
55840194 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
55840217 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
55840240 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
55840264 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* * *
55840287 AAAGGGCTTATGCCCCAATGATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
55840311 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
55840334 AAAGGGCTTTTACCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
55840357 AAA
1 AAA
55840360 AGAGGCAAGG
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 88 0.68
24 41 0.32
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:55840285 original size:47 final size:47
Alignment explanation
Indices: 55840194--55840361 Score: 266
Period size: 47 Copynumber: 3.6 Consensus size: 47
55840184 AGGAAGTGCA
*
55840194 AAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
55840240 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
55840287 AAAGGGCTTATGCCCCAATGATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
55840334 AAAGGGCTTTTACCCCAGTTATTAAAAG
1 AAAGGGCTTATGCCCCAGTTATCAAAAG
55840362 AGGCAAGGCC
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 22 0.20
47 90 0.80
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:55840338 original size:70 final size:70
Alignment explanation
Indices: 55840192--55840359 Score: 257
Period size: 70 Copynumber: 2.4 Consensus size: 70
55840182 GGAGGAAGTG
* * * *
55840192 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATGATAAAAGGGCTTACGCCCCA
55840257 GTTAT
66 GTTAT
55840262 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATGATCAAAAGGGCTTACGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATGAT-AAAAGGGCTTACGCCCC
55840327 AGTTAT
65 AGTTAT
* * *
55840333 -TAAAGGGCTTTTACCCCAGTTATTAAA
1 CAAAAGGGCTTATGCCCCAGTTATTAAA
55840360 AGAGGCAAGG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
70 69 0.77
71 21 0.23
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (70 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATGATAAAAGGGCTTACGCCCCA
GTTAT
Found at i:55840564 original size:42 final size:42
Alignment explanation
Indices: 55840501--55840592 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
55840491 TAGTCTCCCC
* **
55840501 AAATGGGTTTGCATACATTCATTGGTATT-TCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTAT-ATGTGATATTG
* *
55840543 AAATGGGCTTGCATTCTTTCATTGACATTATATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
55840585 AAATGGGC
1 AAATGGGC
55840593 CTATGGGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
Found at i:55843162 original size:47 final size:47
Alignment explanation
Indices: 55843090--55843184 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
55843080 TAACAACGTT
* * *
55843090 AAAAAGCGCTTTTTGGGAGGTAACCCAAATTTATTTTCATTTATTTA
1 AAAAAACGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
55843137 AAAAAACGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
1 AAAAAACGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
55843184 A
1 A
55843185 TTTTTAGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (47 bp):
AAAAAACGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
Found at i:55843548 original size:6 final size:6
Alignment explanation
Indices: 55843537--55843564 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55843527 AACTGAGAAA
55843537 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
55843565 TTAAACACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:55846065 original size:4 final size:4
Alignment explanation
Indices: 55846056--55846096 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
55846046 TTTCTTGTGC
*
55846056 ATAA ATAA ATAA ATAA ATAA ATAC ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
55846097 GGTTCAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:55846258 original size:8 final size:8
Alignment explanation
Indices: 55846245--55846270 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
55846235 TTCACCCAAA
55846245 AAAAAAAT
1 AAAAAAAT
55846253 AAAAAAAT
1 AAAAAAAT
55846261 AAAAAAAT
1 AAAAAAAT
55846269 AA
1 AA
55846271 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:55846882 original size:12 final size:13
Alignment explanation
Indices: 55846865--55846893 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55846855 ATTATTTTGT
55846865 TTTATTTTATT-A
1 TTTATTTTATTAA
55846877 TTTATTTTATTAA
1 TTTATTTTATTAA
55846890 TTTA
1 TTTA
55846894 GGTTAGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTATTAA
Found at i:55852354 original size:20 final size:20
Alignment explanation
Indices: 55852322--55852396 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
55852312 ATACGTGGGA
55852322 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
*
55852339 ATATGATATGTACATGATATG
1 -TATGATATGCACATGATATG
55852360 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
55852380 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
55852397 GAATTCATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 8 0.15
20 42 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:55852357 original size:11 final size:11
Alignment explanation
Indices: 55852329--55852381 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
55852319 GGATATGATA
55852329 TACATGAT-TG
1 TACATGATATG
*
55852339 -ATATGATATG
1 TACATGATATG
55852349 TACATGATATG
1 TACATGATATG
55852360 T--ATGATATG
1 TACATGATATG
*
55852369 CACATGATATG
1 TACATGATATG
55852380 TA
1 TA
55852382 TGAAATGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
TACATGATATG
Found at i:55852476 original size:27 final size:26
Alignment explanation
Indices: 55852446--55852544 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
55852436 GAGGAAGTGC
*
55852446 AAAAGGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
55852472 AAAAAGGGCTTATGCCTCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
**
55852499 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
55852525 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
55852545 ATTAAAGAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 10 0.14
26 33 0.48
27 26 0.38
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:55852528 original size:53 final size:51
Alignment explanation
Indices: 55852446--55852544 Score: 144
Period size: 53 Copynumber: 1.9 Consensus size: 51
55852436 GAGGAAGTGC
* ** *
55852446 AAAAGGGCTTATGCCTCAGTTTATTGAAAAAGGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG-AAAAGGGCTT-TGCCCCAGTTTATTG
55852499 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTT
55852545 ATTAAAGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 9 0.21
52 10 0.24
53 23 0.55
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATTG
Found at i:55855360 original size:66 final size:68
Alignment explanation
Indices: 55855284--55855470 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
55855274 TAGTACCACT
*
55855284 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
55855346 CACG
65 CACG
55855350 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
55855415 ATCACG
63 ATCACG
55855421 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
55855471 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:55855395 original size:71 final size:71
Alignment explanation
Indices: 55855307--55855470 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
55855297 CGATTTGTCT
55855307 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
55855372 CTTTCA
66 CTTTCA
55855378 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
55855443 CTTTCA
66 CTTTCA
55855449 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
55855471 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:55855508 original size:71 final size:70
Alignment explanation
Indices: 55855307--55855504 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
55855297 CGATTTGTCT
* * *
55855307 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
55855372 CTTTCA
65 CTTTCA
* * *
55855378 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
55855443 CTTTCA
65 CTTTCA
* *
55855449 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
55855505 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:55862924 original size:66 final size:68
Alignment explanation
Indices: 55862848--55863034 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
55862838 TAGTACCACT
*
55862848 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
55862910 CACG
65 CACG
55862914 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
55862979 ATCACG
63 ATCACG
55862985 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
55863035 ATACATCTCG
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:55862959 original size:71 final size:71
Alignment explanation
Indices: 55862871--55863034 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
55862861 CGATTTGTCT
55862871 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
55862936 CTTTCA
66 CTTTCA
55862942 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
55863007 CTTTCA
66 CTTTCA
55863013 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
55863035 ATACATCTCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:55863072 original size:71 final size:70
Alignment explanation
Indices: 55862871--55863068 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
55862861 CGATTTGTCT
* * * *
55862871 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTATACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
55862936 CTTTCA
65 CTTTCA
* * * *
55862942 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTATACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
55863007 CTTTCA
65 CTTTCA
* *
55863013 CGTAGCTCTCTTGTCTACATGG-ATACAT-C-TCGTATCACGCATTGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTATACATACTTCGAATCACGCA-TGCGACCTAGCTAC
55863069 TACAGTGTCT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
67 10 0.08
68 14 0.12
70 3 0.03
71 93 0.77
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTATACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:55870472 original size:66 final size:66
Alignment explanation
Indices: 55870396--55870582 Score: 250
Period size: 71 Copynumber: 2.7 Consensus size: 66
55870386 TAGTACCACT
*
55870396 CATGCGACCTAGC-CGATTTGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCA
1 CATGCGACCTAGCAC-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCA
55870460 CG
65 CG
*
55870462 CATGCGACCTAGCTACATTTATATTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACA-TT-TA--TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
55870527 ATCACG
61 ATCACG
55870533 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC--T--CGTAGCTCTCTTGTCTACATGG
55870583 GATACATCTC
Statistics
Matches: 108, Mismatches: 3, Indels: 15
0.86 0.02 0.12
Matches are distributed among these distances:
66 13 0.12
67 3 0.03
68 3 0.03
69 3 0.03
70 2 0.02
71 84 0.78
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (66 bp):
CATGCGACCTAGCACATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCAC
G
Found at i:55870507 original size:71 final size:71
Alignment explanation
Indices: 55870419--55870582 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
55870409 CGATTTGTCT
55870419 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
55870484 ATTTCA
66 ATTTCA
55870490 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
*
55870555 CTTTCA
66 ATTTCA
55870561 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
55870583 GATACATCTC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
ATTTCA
Found at i:55870620 original size:71 final size:70
Alignment explanation
Indices: 55870419--55870616 Score: 267
Period size: 71 Copynumber: 2.8 Consensus size: 70
55870409 CGATTTGTCT
* * *
55870419 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
55870484 ATTTCA
65 ATTTCA
* * *
55870490 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
*
55870555 CTTTCA
65 ATTTCA
* *
55870561 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
55870617 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 95 0.79
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATA
TTTCA
Found at i:55878304 original size:20 final size:20
Alignment explanation
Indices: 55878233--55878307 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
55878223 ATACGTGGGA
55878233 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
*
55878250 ATATGATATGCACACGATATG
1 -TATGATATGCACATGATATG
55878271 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
55878291 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
55878308 GAATTCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:55904404 original size:14 final size:14
Alignment explanation
Indices: 55904385--55904414 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55904375 CATCAGTTGA
55904385 GAGTAAAGGAGGCC
1 GAGTAAAGGAGGCC
55904399 GAGTAAAGGAGGCC
1 GAGTAAAGGAGGCC
55904413 GA
1 GA
55904415 TGTCCGTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.43, T:0.07
Consensus pattern (14 bp):
GAGTAAAGGAGGCC
Found at i:55908318 original size:20 final size:20
Alignment explanation
Indices: 55908295--55908332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55908285 CACATCCAAA
*
55908295 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
55908315 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
55908333 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:55916263 original size:20 final size:20
Alignment explanation
Indices: 55916240--55916277 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55916230 CACATCCAAA
*
55916240 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
55916260 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
55916278 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:55921022 original size:13 final size:13
Alignment explanation
Indices: 55921001--55921039 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
55920991 AATATAATTT
*
55921001 TAAACATTAAATA
1 TAAATATTAAATA
55921014 TAAATATTAAATA
1 TAAATATTAAATA
55921027 -AAATA-TAAATA
1 TAAATATTAAATA
55921038 TA
1 TA
55921040 TATTATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:55939571 original size:55 final size:56
Alignment explanation
Indices: 55939427--55939564 Score: 156
Period size: 55 Copynumber: 2.5 Consensus size: 56
55939417 TTTATCAATG
*
55939427 GCCGTGGGCGAACCTGCCAAAACAACACGGGCGTGAGACACGCCCGTGCCTAGAAA
1 GCCGTGGGCGAACCTGCCAAAACAACACGGGCGTGAGACACACCCGTGCCTAGAAA
* * ** ** * *
55939483 -CCTTGGCCGAACCTATCAAATTAACACGGGCGTGCGGCACACCCGTGCC-A-AACA
1 GCCGTGGGCGAACCTGCCAAAACAACACGGGCGTGAGACACACCCGTGCCTAGAA-A
*
55939537 GCCGTGGGCGAACTTGCCAAAACAACAC
1 GCCGTGGGCGAACCTGCCAAAACAACAC
55939565 AAGCGTGGGA
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
53 2 0.03
54 2 0.03
55 60 0.94
ACGTcount: A:0.29, C:0.33, G:0.26, T:0.12
Consensus pattern (56 bp):
GCCGTGGGCGAACCTGCCAAAACAACACGGGCGTGAGACACACCCGTGCCTAGAAA
Found at i:55942704 original size:29 final size:29
Alignment explanation
Indices: 55942662--55942717 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
55942652 TATTTTTTTG
55942662 GAGATTTGAGTTGGAATAATTGCTTAGTC
1 GAGATTTGAGTTGGAATAATTGCTTAGTC
55942691 GAGATTTGAGTTGGAATAATTGCTTAG
1 GAGATTTGAGTTGGAATAATTGCTTAG
55942718 CTATGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (29 bp):
GAGATTTGAGTTGGAATAATTGCTTAGTC
Found at i:55967701 original size:92 final size:92
Alignment explanation
Indices: 55967534--55967759 Score: 258
Period size: 92 Copynumber: 2.5 Consensus size: 92
55967524 AGGCCAAATA
* * *
55967534 AGATAATAGTACGCAGCATAGCTGACGTACGTACAGTACAGTGCAATGCGGTAATCCACTGTACA
1 AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATACA
55967599 GTCATGTTGCAGTTGCACTGCCAGATC
66 GTCATGTTGCAGTTGCACTGCCAGATC
* * ** *
55967626 AGATAATAGTACGTAGCATAGCTAACGTACGTACGGTACAGTGTGATGCGGTAAACCGCTATACC
1 AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATA-C
* *** * * *
55967691 AGTTAT-TTGCAGTCAAACTACCATATT
65 AGTCATGTTGCAGTTGCACTGCCAGATC
* * *
55967718 AGATAA-AGGTACGCAGCAGAGCTGACGTATGTACAGTACAGT
1 AGATAATA-GTACGCAGCATAGCTAACGTACGTACAGTACAGT
55967760 CTTCCTTCTC
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
91 1 0.01
92 105 0.94
93 6 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (92 bp):
AGATAATAGTACGCAGCATAGCTAACGTACGTACAGTACAGTGCAATGCGGTAAACCACTATACA
GTCATGTTGCAGTTGCACTGCCAGATC
Found at i:55971425 original size:2 final size:2
Alignment explanation
Indices: 55971418--55971447 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55971408 AGTACAGAAC
55971418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55971448 GCATACTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55973105 original size:55 final size:53
Alignment explanation
Indices: 55972918--55973169 Score: 210
Period size: 55 Copynumber: 4.8 Consensus size: 53
55972908 CGGGTGCCTT
* * * * * *
55972918 ACCATTGCCATGACTTGTCATGGTCTTACATGGTATCCTT---TTA-AAACTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
* * * *
55972967 ACCATTTCCATGTCTTGAGATGGTCTTACATGGTATCCTTGCCTTATGAACTC
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
* * *
55973020 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTC
* *** * *
55973075 ATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTA-GAAACCTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTC
* * *
55973129 ACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 ACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
55973170 CAACCCTAAT
Statistics
Matches: 167, Mismatches: 26, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
49 36 0.22
52 5 0.03
53 45 0.27
54 8 0.05
55 71 0.43
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
Found at i:55976396 original size:24 final size:21
Alignment explanation
Indices: 55976363--55976428 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
55976353 TATTTTTAAT
55976363 TTTTTAAATAAACATTTTAAAAA
1 TTTTTAAAT-AA-ATTTTAAAAA
55976386 TTTTTAGAATAAATTTTAAAACA
1 TTTTTA-AATAAATTTTAAAA-A
* * *
55976409 TATTT-ATTTAATTTTAAAAA
1 TTTTTAAATAAATTTTAAAAA
55976429 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 9 0.24
23 13 0.34
24 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTTAAATAAATTTTAAAAA
Found at i:55976401 original size:22 final size:23
Alignment explanation
Indices: 55976363--55976406 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
55976353 TATTTTTAAT
55976363 TTTTTAAATAAACATTTTAAAAA
1 TTTTTAAATAAACATTTTAAAAA
55976386 TTTTTAGAAT-AA-ATTTTAAAA
1 TTTTTA-AATAAACATTTTAAAA
55976407 CATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTTAAATAAACATTTTAAAAA
Found at i:55976434 original size:19 final size:21
Alignment explanation
Indices: 55976397--55976436 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55976387 TTTTAGAATA
55976397 AATTTTAAAACATATTTATTT
1 AATTTTAAAACATATTTATTT
55976418 AATTTTAAAA-A-ATTTATTT
1 AATTTTAAAACATATTTATTT
55976437 TTTTGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTAAAACATATTTATTT
Found at i:55978242 original size:18 final size:18
Alignment explanation
Indices: 55978219--55978289 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
55978209 TCATCAATAT
55978219 TAATCAATTATTCAGTAA
1 TAATCAATTATTCAGTAA
* *
55978237 TAATCATTTATTCAATAA
1 TAATCAATTATTCAGTAA
* * *
55978255 CAGTCAATTATTTAGTAA
1 TAATCAATTATTCAGTAA
*
55978273 TAACCAATTATTCAGTA
1 TAATCAATTATTCAGTA
55978290 CCTTTATTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (18 bp):
TAATCAATTATTCAGTAA
Found at i:55979843 original size:40 final size:40
Alignment explanation
Indices: 55979798--55979964 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
55979788 CGGAATATAA
55979798 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
55979838 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
55979878 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55979918 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55979957 CCGGATAT
1 CCGGATAT
55979965 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55987847 original size:40 final size:40
Alignment explanation
Indices: 55987802--55987969 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
55987792 CGGAATATAA
55987802 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
55987842 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
55987882 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
55987922 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55987962 CCGGATAT
1 CCGGATAT
55987970 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55989854 original size:16 final size:15
Alignment explanation
Indices: 55989833--55989863 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
55989823 TCAATTAATC
55989833 AAATATATTCTCAATT
1 AAATATATTC-CAATT
55989849 AAATATATTCCAATT
1 AAATATATTCCAATT
55989864 CACTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATATTCCAATT
Found at i:55991537 original size:6 final size:6
Alignment explanation
Indices: 55991506--55991627 Score: 70
Period size: 6 Copynumber: 19.8 Consensus size: 6
55991496 TATCAAAACT
* * * * * *
55991506 AGAATC AAAATG AGAATC AGAGTC AGAATC AG-GTGAG AGAATT AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * *
55991555 AGAATC AGAATC AGAATT AG-GTGAC AGAATT AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
*
55991604 AGGTAA-C AGAATC AAAATC AGAAT
1 A-G-AATC AGAATC AGAATC AGAAT
55991628 ATGAATGCAA
Statistics
Matches: 86, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
5 4 0.05
6 72 0.84
7 7 0.08
8 3 0.03
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:55991547 original size:37 final size:37
Alignment explanation
Indices: 55991518--55991605 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
55991508 AATCAAAATG
* *
55991518 AGAATCAGAGTCAGAATCAGGTGAGAGAATTAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATTAGAATC
*
55991555 AGAATCAGAATCAGAATTAGGTGACAGAATTAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATTAGAATC
*
55991592 AGAATCAGTATCAG
1 AGAATCAGAATCAG
55991606 GTAACAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATTAGAATC
Found at i:55991584 original size:31 final size:31
Alignment explanation
Indices: 55991549--55991627 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
55991539 TGAGAGAATT
* *
55991549 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
55991580 AGAATTAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
55991611 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
55991628 ATGAATGCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:55991627 original size:37 final size:37
Alignment explanation
Indices: 55991506--55991627 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 37
55991496 TATCAAAACT
* * *
55991506 AGAATCAAAATGAGAATCAGAGTCAGAATCAGGTGAG
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* * *
55991543 AGAATTAGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* *
55991580 AGAAT-----T-AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
55991611 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
55991628 ATGAATGCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
31 27 0.39
32 1 0.01
36 1 0.01
37 41 0.59
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:55991794 original size:27 final size:26
Alignment explanation
Indices: 55991746--55991805 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
55991736 GCGAGGCTGC
*
55991746 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55991773 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
55991799 CAGATAT
1 CAGATAT
55991806 GTAACACCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55992987 original size:28 final size:28
Alignment explanation
Indices: 55992941--55993009 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
55992931 TTTAAAACCC
*
55992941 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
55992968 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
55992996 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
55993010 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:55994661 original size:20 final size:20
Alignment explanation
Indices: 55994638--55994675 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55994628 CACATCCAAA
*
55994638 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
55994658 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
55994676 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:56000973 original size:27 final size:27
Alignment explanation
Indices: 56000943--56001004 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
56000933 TTTAAAACCC
56000943 TAGGGGTATATCGGTAATTTTGCTCTT
1 TAGGGGTATATCGGTAATTTTGCTCTT
*
56000970 TA-GGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGT-ATATCGGTAATTTTGCTCTT
56000997 TAGGGGTA
1 TAGGGGTA
56001005 ATTTCGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.12
27 24 0.75
28 4 0.12
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (27 bp):
TAGGGGTATATCGGTAATTTTGCTCTT
Found at i:56002654 original size:20 final size:20
Alignment explanation
Indices: 56002631--56002668 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56002621 CACATCCAAA
*
56002631 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
56002651 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
56002669 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:56002708 original size:2 final size:2
Alignment explanation
Indices: 56002701--56002744 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
56002691 ATGTTACAAG
56002701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56002743 AT
1 AT
56002745 GGCGAAGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56002823 original size:27 final size:26
Alignment explanation
Indices: 56002775--56002826 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
56002765 GCGAGGCTGC
*
56002775 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
56002801 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
56002827 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56003387 original size:27 final size:27
Alignment explanation
Indices: 56003357--56003464 Score: 96
Period size: 27 Copynumber: 3.9 Consensus size: 27
56003347 GTAAATCTAC
56003357 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
56003384 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
56003410 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* **
56003440 AAATC-AGAGGTATTTTGGTAATTTT
1 AAACCAAG-GGTATTTCAGTAATTTT
56003465 ACAAATTGAG
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
26 3 0.04
27 39 0.57
28 7 0.10
29 18 0.26
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:56003506 original size:54 final size:54
Alignment explanation
Indices: 56003448--56003603 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 54
56003438 GTAAATCAGA
* *
56003448 GGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAAGTTCACAAACCAGT
1 GGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGGTAAGTTCACAAACCAGG
* * * * *
56003502 GGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAAGTTCACAAACCAGG
* * * *
56003556 GGTGTTTTGGTAATTTTACCATAC-AGGGGTATTTCAGTAATTTCACAA
1 GGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTCGGTAAGTTCACAA
56003604 TCGAGGGTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 81 0.93
55 6 0.07
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAAGTTCACAAACCAGG
Found at i:56003568 original size:81 final size:81
Alignment explanation
Indices: 56003420--56003603 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 81
56003410 AGAAAGTCAA
* ** *
56003420 GGGTATTTCTGTAATTTTGTAAATCAGAGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGG
1 GGGTATTTCAGTAATTTTACAAATCAGAGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGG
56003485 TAAGTTCA-CAAACCAG
66 TAAGTTCACCAAA-CAG
* * * * *
56003501 TGGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTGTTTT
1 GGGTATTTCAGTAATTTTACAAATC-AGAGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTC
* * *
56003564 GGTAATTTTACCATACAG
64 GGTAAGTTCACCAAACAG
*
56003582 GGGTATTTCAGTAATTTCACAA
1 GGGTATTTCAGTAATTTTACAA
56003604 TCGAGGGTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 1 0.01
81 80 0.93
82 5 0.06
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCAGAGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGG
TAAGTTCACCAAACAG
Found at i:56003610 original size:27 final size:27
Alignment explanation
Indices: 56003420--56003610 Score: 163
Period size: 27 Copynumber: 7.1 Consensus size: 27
56003410 AGAAAGTCAA
* **
56003420 GGGTATTTCTGTAATTTTGTAAATC-AG
1 GGGTATTTCGGTAATTTTACAAA-CGAG
* * *
56003447 AGGTATTTTGGTAATTTTACAAATTGA-
1 GGGTATTTCGGTAATTTTACAAA-CGAG
* * *
56003474 GGGTATTTCGGTAAGTTCACAAACCAG
1 GGGTATTTCGGTAATTTTACAAACGAG
* *
56003501 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACGAG
* *
56003528 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACGAG
* * *
56003555 GGGTGTTTTGGTAATTTTACCATAC-AG
1 GGGTATTTCGGTAATTTTA-CAAACGAG
* * *
56003582 GGGTATTTCAGTAATTTCACAATCGAG
1 GGGTATTTCGGTAATTTTACAAACGAG
56003609 GG
1 GG
56003611 TAAAATGGTA
Statistics
Matches: 134, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.03
27 125 0.93
28 5 0.04
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAACGAG
Found at i:56003719 original size:81 final size:81
Alignment explanation
Indices: 56003602--56003772 Score: 231
Period size: 81 Copynumber: 2.1 Consensus size: 81
56003592 GTAATTTCAC
* * * *
56003602 AATCGAGGGTAAAATGGTAATTTTGTAAACAGAGGGTAAAATGGTAATTTTGTAAA-CAGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAACAGAGGGTAAAACGATAATTTTGTAAATC-GAGGGT
*
56003666 AAAACGGTAATTCTATA
65 AAAACGGTAATTATATA
*
56003683 AATCGAGGGTAAAATGGTAATTCTATAAATTA-AGGGTAAAACGATAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAA-CAGAGGGTAAAACGATAATTTTGTAAATCGAGGGT
* *
56003747 GAAACGGTAATTATGTA
65 AAAACGGTAATTATATA
56003764 AATCG-GGGT
1 AATCGAGGGT
56003773 GTGACACCCC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.05
81 74 0.93
82 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAACAGAGGGTAAAACGATAATTTTGTAAATCGAGGGTA
AAACGGTAATTATATA
Found at i:56003768 original size:27 final size:27
Alignment explanation
Indices: 56003602--56003772 Score: 195
Period size: 27 Copynumber: 6.4 Consensus size: 27
56003592 GTAATTTCAC
*
56003602 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
56003629 AA-CAGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* *
56003656 AA-CAGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* * *
56003683 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
** *
56003710 AATTAAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
56003737 AATCGAGGGTGAAACGGTAATTATGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
56003764 AATCG-GGGT
1 AATCGAGGGT
56003773 GTGACACCCC
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.04
27 121 0.95
28 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:56006180 original size:46 final size:46
Alignment explanation
Indices: 56005949--56006176 Score: 429
Period size: 46 Copynumber: 5.0 Consensus size: 46
56005939 AGTTAAATAT
56005949 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56005995 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56006041 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
56006087 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56006133 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56006177 AGATGTATAT
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 179 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.32
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56006234 original size:47 final size:47
Alignment explanation
Indices: 56006180--56006290 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56006170 ATGTATGAGA
* * *
56006180 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56006227 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56006274 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56006291 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56008955 original size:40 final size:40
Alignment explanation
Indices: 56008848--56009110 Score: 429
Period size: 40 Copynumber: 6.6 Consensus size: 40
56008838 CTCGACGATG
*
56008848 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
56008888 ATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
56008927 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* **
56008967 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGACGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56009007 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56009047 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56009087 ATCCGGGCTAGGTCCCGAAGAGCA
1 ATCCGGGCTAAGTTCCGAAGAGCA
56009111 ATCATGCTGG
Statistics
Matches: 212, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 38 0.18
40 174 0.82
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
Found at i:56009838 original size:40 final size:40
Alignment explanation
Indices: 56009774--56009874 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
56009764 AATGGTATCT
* ** * *
56009774 GGGCTAAGTCCCGAAGGCTTTTGTGCGAGTTACTA-AATCC
1 GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA-CC
*
56009814 GGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAACC
1 GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACC
*
56009854 GGGCT-ATGTCCCGAAGACAAT
1 GGGCTAAT-TCCCGAAGGCAAT
56009875 CGAGTGAGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 48 0.92
41 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
GGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACC
Found at i:56009890 original size:40 final size:40
Alignment explanation
Indices: 56009812--56009908 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 40
56009802 GTTACTAAAT
* * *
56009812 CCGGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
* * *
56009852 CCGGGCT-ATGTCCCGAAGACAATCGAGTGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGTGAATCACTATAA
* *
56009892 CC-GGTTAAATCCCGAAG
1 CCGGGCTAATTCCCGAAG
56009909 GTACGTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
39 13 0.28
40 34 0.72
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
Found at i:56012628 original size:46 final size:46
Alignment explanation
Indices: 56012577--56012758 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
56012567 AGTTAAATAT
56012577 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56012623 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
56012669 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56012715 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56012759 AGATGTATAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56012816 original size:47 final size:47
Alignment explanation
Indices: 56012762--56012872 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56012752 ATGTATGAGA
* * *
56012762 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56012809 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56012856 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56012873 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56015539 original size:40 final size:40
Alignment explanation
Indices: 56015432--56015694 Score: 429
Period size: 40 Copynumber: 6.6 Consensus size: 40
56015422 CTCGACGATG
*
56015432 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
56015472 ATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
56015511 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* **
56015551 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGACGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56015591 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56015631 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
* *
56015671 ATCCGGGCTAGGTCCCGAAGAGCA
1 ATCCGGGCTAAGTTCCGAAGAGCA
56015695 ATCATGCTGG
Statistics
Matches: 212, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 38 0.18
40 174 0.82
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
Found at i:56016421 original size:40 final size:40
Alignment explanation
Indices: 56016356--56016457 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
56016346 CGAATGGTAT
* ** * *
56016356 CGGGCTAAGTCCCGAAGGCTTTTGTGCGAGTTACTA-AATC
1 CGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA-C
*
56016396 CGGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAAC
1 CGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAAC
*
56016436 CGGGCT-ATGTCCCGAAGACAAT
1 CGGGCTAAT-TCCCGAAGGCAAT
56016458 CGAGTGAGTC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 49 0.92
41 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (40 bp):
CGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAAC
Found at i:56016473 original size:40 final size:40
Alignment explanation
Indices: 56016395--56016491 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 40
56016385 GTTACTAAAT
* * *
56016395 CCGGGCTAATTCCCGAAGGCAATTGTGTGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
* * *
56016435 CCGGGCT-ATGTCCCGAAGACAATCGAGTGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGTGAATCACTATAA
* *
56016475 CC-GGTTAAATCCCGAAG
1 CCGGGCTAATTCCCGAAG
56016492 GTACGTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
39 13 0.28
40 34 0.72
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGTGAATCACTATAA
Found at i:56019207 original size:46 final size:46
Alignment explanation
Indices: 56019156--56019337 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
56019146 AGTTAAATAT
56019156 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
56019202 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
*
56019248 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
* *
56019294 ATATATGTGTGGTAAAGCCAAATGGCTAGTATGAAACATGTATG
1 ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATG
56019338 AGATGTATAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
ATATATGTGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGTG
Found at i:56019395 original size:47 final size:47
Alignment explanation
Indices: 56019341--56019451 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
56019331 ATGTATGAGA
* * *
56019341 TGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTCAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
* *
56019388 TGTATATAAGTGATAAGGCCGAATGGCCAATGCGATGAATATGAAAG
1 TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
*
56019435 TGTATAAATGTGATAAG
1 TGTATATATGTGATAAG
56019452 TCCCGAGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCGAATGGCCAATGCGATGAATATCAAAG
Found at i:56022808 original size:29 final size:28
Alignment explanation
Indices: 56022776--56022875 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 28
56022766 ATATTGAATC
*
56022776 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
56022805 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
56022833 CGCACAC-TAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
56022862 CGCACACTTAGTGC
1 CGCACACTTAGTGC
56022876 CATACCTTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
27 15 0.24
28 11 0.18
29 30 0.48
30 6 0.10
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:56022947 original size:29 final size:29
Alignment explanation
Indices: 56022908--56022994 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
56022898 CAGTGCAGTG
56022908 TATATTTCCAGCATGCACACTTAGTGCCA
1 TATATTTCCAGCATGCACACTTAGTGCCA
*
56022937 TATATTTCCAGCATGTACACTTAGTGCCA
1 TATATTTCCAGCATGCACACTTAGTGCCA
*
56022966 TATATTTTCAGCATGCACACTTAGTGCCA
1 TATATTTCCAGCATGCACACTTAGTGCCA
56022995 ATCTCGTCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (29 bp):
TATATTTCCAGCATGCACACTTAGTGCCA
Found at i:56026844 original size:39 final size:39
Alignment explanation
Indices: 56026792--56026884 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
56026782 GACTTTAAGC
*
56026792 CCGGATATATTTCCAGCACATAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
* *
56026831 CCGGATATGTTTCCAGTACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
56026870 CCGGATATGTTTCCA
1 CCGGATATGTTTCCA
56026885 AGTATCATGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
Found at i:56030299 original size:27 final size:27
Alignment explanation
Indices: 56030261--56030317 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
56030251 TATAAATGAA
56030261 AACTCTTTACCGGATTCAGGCTGCACT
1 AACTCTTTACCGGATTCAGGCTGCACT
56030288 AACTCTTTACCGGATTCAGGCTGCACT
1 AACTCTTTACCGGATTCAGGCTGCACT
56030315 AAC
1 AAC
56030318 ACTGGGGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (27 bp):
AACTCTTTACCGGATTCAGGCTGCACT
Found at i:56034743 original size:39 final size:39
Alignment explanation
Indices: 56034692--56034780 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
56034682 TTTAAGCCCA
*
56034692 GATATATTTCCAGCACATAGCCTGCGGACCTCAAGTCCG
1 GATATGTTTCCAGCACATAGCCTGCGGACCTCAAGTCCG
*
56034731 GATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTCCG
1 GATATGTTTCCAGCACATAGCCTGCGGACCTCAAGTCCG
56034770 GATATGTTTCC
1 GATATGTTTCC
56034781 TAGTATCATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (39 bp):
GATATGTTTCCAGCACATAGCCTGCGGACCTCAAGTCCG
Found at i:56038546 original size:36 final size:37
Alignment explanation
Indices: 56038491--56038560 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
56038481 CTTTCTTTCA
* *
56038491 AACACACCCTTTTACAAAATAAA-AAATCAAAAAATT
1 AACACAACCATTTACAAAATAAACAAATCAAAAAATT
* *
56038527 AACACAACCATTTATAAAATAAACAAATGAAAAA
1 AACACAACCATTTACAAAATAAACAAATCAAAAA
56038561 CTAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 20 0.69
37 9 0.31
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.20
Consensus pattern (37 bp):
AACACAACCATTTACAAAATAAACAAATCAAAAAATT
Found at i:56044033 original size:40 final size:40
Alignment explanation
Indices: 56043967--56044133 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
56043957 AAATTGAATG
* * *
56043967 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
56044006 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
56044046 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
56044086 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
56044126 ATATCCGG
1 ATATCCGG
56044134 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:56052040 original size:40 final size:40
Alignment explanation
Indices: 56051981--56052122 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
56051971 AAATTGAATG
* * *
56051981 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
56052021 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
56052061 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
56052101 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
56052123 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:56052123 original size:40 final size:39
Alignment explanation
Indices: 56052020--56052148 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
56052010 TGCTGGAAAT
* * *
56052020 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
56052060 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
56052100 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
56052140 TATATCCGG
1 TATATCCGG
56052149 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:56056255 original size:96 final size:95
Alignment explanation
Indices: 56056140--56056328 Score: 290
Period size: 96 Copynumber: 2.0 Consensus size: 95
56056130 GTGTCCGAGG
* *
56056140 AAGTCTGTCATCAAAGGGAACGATGGAGCAGACAAGAAGCCCAAGAAA-CTTGGTTCGAGCAAGC
1 AAGTCTGTCATCAAAGGGAACAATGGAGCAGACAAGAAGACCAA-AAAGCTTGGTTCGAGCAAGC
56056204 GAAAAGCCGAAGCCAAGAGGGCAAAGAGGAGT
65 GAAAAG-CGAAGCCAAGAGGGCAAAGAGGAGT
* * *
56056236 AAGTCTGTCATCGAAGGGAACAATGGAGCAGACAAGGAGACCAAAAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCAAAGGGAACAATGGAGCAGACAAGAAGACCAAAAAGCTTGGTTCGAGCAAGCG
* *
56056301 AAAAGCTAAGCGAAGAGGGCAAAGAGGA
66 AAAAGCGAAGCCAAGAGGGCAAAGAGGA
56056329 ACAAAAAGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
95 24 0.28
96 61 0.72
ACGTcount: A:0.40, C:0.17, G:0.32, T:0.11
Consensus pattern (95 bp):
AAGTCTGTCATCAAAGGGAACAATGGAGCAGACAAGAAGACCAAAAAGCTTGGTTCGAGCAAGCG
AAAAGCGAAGCCAAGAGGGCAAAGAGGAGT
Found at i:56068065 original size:43 final size:42
Alignment explanation
Indices: 56068018--56068098 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
56068008 TTATATGGGA
** * *
56068018 TCTCATATCGATGCCAATAGCCTAGCTATGGTCTTACACGAAG
1 TCTCATATCGACACC-ATAGCCCAGATATGGTCTTACACGAAG
*
56068061 TCTCATATCGACACCATATCCCAGATATGGTCTTACAC
1 TCTCATATCGACACCATAGCCCAGATATGGTCTTACAC
56068099 TTAATCTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 20 0.61
43 13 0.39
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (42 bp):
TCTCATATCGACACCATAGCCCAGATATGGTCTTACACGAAG
Found at i:56068107 original size:42 final size:42
Alignment explanation
Indices: 56067989--56068107 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 42
56067979 CATACCAATG
* * * **
56067989 CCATATCCCAGATATGGACTTATA-TGGGATCTCATATCGATG
1 CCATATCCCAGATATGGTCTTACACT-GAATCTCATATCGACA
* * *
56068031 CCAATAGCCTAGCTATGGTCTTACAC-GAAGTCTCATATCGACA
1 CC-ATATCCCAGATATGGTCTTACACTGAA-TCTCATATCGACA
*
56068074 CCATATCCCAGATATGGTCTTACACTTAATCTCA
1 CCATATCCCAGATATGGTCTTACACTGAATCTCA
56068108 ATTAACCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
42 29 0.48
43 32 0.52
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTACACTGAATCTCATATCGACA
Found at i:56070089 original size:6 final size:6
Alignment explanation
Indices: 56070072--56070150 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
56070062 TATCATAACT
* *
56070072 AGAATC AAAATC AGAATC AGAATC AGGTAAT- AGAATC AAAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC
* * *
56070121 AGTATT AGGTAA-C AGAATC AAAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
56070151 GTGAATGCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
5 5 0.09
6 44 0.77
7 4 0.07
8 4 0.07
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:56070107 original size:31 final size:31
Alignment explanation
Indices: 56070071--56070150 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
56070061 TTATCATAAC
56070071 TAGAATCAAAATCAGAATCAGAATCAGGTAA
1 TAGAATCAAAATCAGAATCAGAATCAGGTAA
* *
56070102 TAGAATCAAAATCAGAATCAGTATTAGGTAA
1 TAGAATCAAAATCAGAATCAGAATCAGGTAA
*
56070133 CAGAATCAAAATCAGAAT
1 TAGAATCAAAATCAGAAT
56070151 GTGAATGCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.21
Consensus pattern (31 bp):
TAGAATCAAAATCAGAATCAGAATCAGGTAA
Found at i:56070108 original size:25 final size:27
Alignment explanation
Indices: 56070080--56070147 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 27
56070070 CTAGAATCAA
56070080 AATCAGAATCAGAATCAGGTAATA-G-
1 AATCAGAATCAGAATCAGGTAATAGGT
* *
56070105 AATCAAAATCAGAATCA-GTATTAGGT
1 AATCAGAATCAGAATCAGGTAATAGGT
*
56070131 AA-CAGAATCAAAATCAG
1 AATCAGAATCAGAATCAG
56070148 AATGTGAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 29 0.81
26 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (27 bp):
AATCAGAATCAGAATCAGGTAATAGGT
Found at i:56070610 original size:27 final size:27
Alignment explanation
Indices: 56070553--56070962 Score: 554
Period size: 27 Copynumber: 15.3 Consensus size: 27
56070543 AAGGCAAAAT
* * * *
56070553 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070579 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070606 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
56070633 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
56070660 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
56070687 AGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
56070713 GGTAATTCCACCATACTGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070740 GATAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
56070767 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070794 GGTAATTCTACCCTGCAGGGGTTTTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070821 TGTAATTCTACCCTACTGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
56070848 AGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
56070875 GGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
56070902 GGTAATTCTGCCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
56070929 AATAATTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
56070956 GGTAATT
1 GGTAATT
56070963 ACACAAACTA
Statistics
Matches: 334, Mismatches: 48, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
26 36 0.11
27 298 0.89
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:56071059 original size:27 final size:26
Alignment explanation
Indices: 56070974--56071401 Score: 200
Period size: 27 Copynumber: 15.8 Consensus size: 26
56070964 CACAAACTAG
* **
56070974 GGGTATTTTGGTAATTTTATTGATCGA
1 GGGTA-TTTGGTAATTTTGTAAATCGA
*
56071001 GGGTATTTTGGTAATTTTGTAAA-CAAA
1 GGGTA-TTTGGTAATTTTGTAAATC-GA
* *
56071028 TGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTT-GGTAATTTTGTAAATCGA
** *
56071055 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGT-ATTTGGTAATTTTGTAAATCGA
** * *
56071082 GGGTAAAATGGTAATTCTGTAATTCGA
1 GGGT-ATTTGGTAATTTTGTAAATCGA
** *
56071109 GGGTAAGATGGTAATTCTGTAAATCGA
1 GGGT-ATTTGGTAATTTTGTAAATCGA
** * * *
56071136 GGGTAAAATGGTAATTCTATAAATTGA
1 GGGT-ATTTGGTAATTTTGTAAATCGA
** * *
56071163 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGT-ATTTGGTAATTTTGTAAATCGA
*** *
56071190 GGGTAAAAGGATAATTCTGTAAATCGA
1 GGGTATTTGG-TAATTTTGTAAATCGA
** * *
56071217 GGGTAAAATGGTAATTCTATCT-TA-C-A
1 GGGT-ATTTGGTAATT-T-TGTAAATCGA
* **
56071243 GGAGTATTTTAGTAATTTTACAAATCGA
1 GG-GTA-TTTGGTAATTTTGTAAATCGA
* *
56071271 GGGTATTCTAGTAATTTTGCAAA-CTGA
1 GGGTATT-TGGTAATTTTGTAAATC-GA
**
56071298 GGGTATTTTGGTAATTTTACAAATCGA
1 GGGTA-TTTGGTAATTTTGTAAATCGA
* * *
56071325 GGATATTTGGGTAATTTTATAAATCGG
1 GGGTATTT-GGTAATTTTGTAAATCGA
** *
56071352 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTA-TTTGGTAATTTTGTAAATCGA
* *
56071379 GGGTATTTCAGTAATTTGGTAAA
1 GGGTATTT-GGTAATTTTGTAAA
56071402 CTAAAGTATT
Statistics
Matches: 335, Mismatches: 46, Indels: 40
0.80 0.11 0.10
Matches are distributed among these distances:
25 1 0.00
26 24 0.07
27 290 0.87
28 18 0.05
29 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
GGGTATTTGGTAATTTTGTAAATCGA
Done.