Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 40 of 150
Found at i:11018219 original size:93 final size:94
Alignment explanation
Indices: 11018060--11018318 Score: 411
Period size: 93 Copynumber: 2.8 Consensus size: 94
11018050 TTTAAAATGA
*
11018060 TACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACGACATAACTTACTAA
**
11018125 TATATATATTTTA-AAATGATACATAACT
66 TATATATATTGGATAAATGATACATAACT
*
11018153 TACATAACTTATTAATACATAAC-TTATATAATACATAACTTACATAATACGACATAACTTACTA
1 TACATAACTTATTAATACATAACATT-TTTAATACATAACTTACATAATACGACATAACTTACTA
*
11018217 ATATATTTA-TGGATAAATGATACATAACT
65 ATATATATATTGGATAAATGATACATAACT
*
11018246 TACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACGACATAA-TAACATA
1 TACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACGACATAACTTAC-TA
11018310 A-ATATATAT
65 ATATATATAT
11018319 CATATGATAA
Statistics
Matches: 153, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
92 13 0.08
93 138 0.90
94 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.37
Consensus pattern (94 bp):
TACATAACTTATTAATACATAACATTTTTAATACATAACTTACATAATACGACATAACTTACTAA
TATATATATTGGATAAATGATACATAACT
Found at i:11018295 original size:16 final size:15
Alignment explanation
Indices: 11018246--11018287 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
11018236 ATACATAACT
11018246 TACATAACTTATTAA
1 TACATAACTTATTAA
*
11018261 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
11018277 TACATAACTTA
1 TACATAACTTA
11018288 CATAATACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:11023893 original size:21 final size:21
Alignment explanation
Indices: 11023867--11023917 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
11023857 CTACAACTTA
* *
11023867 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
11023888 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
11023909 AAGCTGAGG
1 AAGCAGAGG
11023918 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:11023916 original size:87 final size:87
Alignment explanation
Indices: 11023801--11023998 Score: 283
Period size: 87 Copynumber: 2.3 Consensus size: 87
11023791 ACACAACTTA
* * * *
11023801 AAGCGGAGGCAACATCGAGAGAACCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAAC
11023864 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGGCAGCGAGAG
* * *
11023888 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGTAGCTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
11023953 AAAGCAGATGCGGCAGCGAGAG
66 AAAGCAGATGCGGCAGCGAGAG
* *
11023975 AAGCAGAGGCTGCAGCGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
11023999 TAAAGGCTGC
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 1 0.01
87 95 0.95
88 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.11
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTT
AAAGCAGATGCGGCAGCGAGAG
Found at i:11023978 original size:21 final size:21
Alignment explanation
Indices: 11023954--11024023 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
11023944 CAGTAGCTTA
* * *
11023954 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
11023975 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
11023996 AAGTAAAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
11024017 AAGCAGA
1 AAGCAGA
11024024 ACAGCTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:11024396 original size:43 final size:43
Alignment explanation
Indices: 11024327--11024552 Score: 310
Period size: 43 Copynumber: 5.3 Consensus size: 43
11024317 CTGCCAAAAT
* *
11024327 TAGCGGCGTTTTTTGGCTAAGTGCCGCTAAAGACCATGGTCTA
1 TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTA
* * *
11024370 TAGTGGCGTTTTTTGGGAAAGCGCCGCTAAGGACCATGGTCTA
1 TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTA
* *
11024413 TAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTA
1 TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTA
* * *
11024456 TAGCGACGTTTGTTGGGTAAGCGCCGCTAAATACCATGGTCTA
1 TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTA
* * * *
11024499 TAGCGGCGTTTGTTGGGTAAGCGCCGCTAAAGGTCC-TGATCTT
1 TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAA-GACCATGGTCTA
11024542 TAGCGGCGTTT
1 TAGCGGCGTTT
11024553 ATTATAAAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 162 0.99
44 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTA
Found at i:11025506 original size:27 final size:27
Alignment explanation
Indices: 11025448--11025507 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
11025438 AACATTTAGT
*
11025448 TAATTTTAAAAATTTTAAAATTAAATA
1 TAATTATAAAAATTTTAAAATTAAATA
* *
11025475 AAATTATAAAATATTTTAAATTTAAA-A
1 TAATTATAAAA-ATTTTAAAATTAAATA
11025502 TAATTA
1 TAATTA
11025508 AATGTCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTATAAAAATTTTAAAATTAAATA
Found at i:11029300 original size:17 final size:16
Alignment explanation
Indices: 11029264--11029299 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11029254 ATTTTACATG
*
11029264 AAAATCCTTTCGGGAA
1 AAAATCCTTTAGGGAA
11029280 AAAATCCTTTAGGGAA
1 AAAATCCTTTAGGGAA
11029296 AAAA
1 AAAA
11029300 ACCACTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (16 bp):
AAAATCCTTTAGGGAA
Found at i:11029600 original size:29 final size:29
Alignment explanation
Indices: 11029567--11029625 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
11029557 TCCACCTTGA
* *
11029567 CATGAATTCTCAACGAACAAGTTCTTCAC
1 CATGAACTCTCAACGAACAAGTTCTCCAC
*
11029596 CATGAACTCTCAATGAACAAGTTCTCCAC
1 CATGAACTCTCAACGAACAAGTTCTCCAC
11029625 C
1 C
11029626 TTTTCCATAA
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:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (29 bp):
CATGAACTCTCAACGAACAAGTTCTCCAC
Found at i:11031213 original size:58 final size:59
Alignment explanation
Indices: 11031122--11031243 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 59
11031112 CAGTTTACTA
* * *
11031122 ATGCCTTATCCATTAAGAAGTCCTCTTTTGCTTAATTGTGCCATGTCATTCTCACTCAT
1 ATGCCTTATCCATCAAGAAGTCCTCTTTTGCTTAATTGTGCCATGCCATCCTCACTCAT
* * * * *
11031181 ATGCC-TATCTATCAAGAAGTCCTTTTTTGCTTAATTTTGTCATGCCATCCTCATTCAT
1 ATGCCTTATCCATCAAGAAGTCCTCTTTTGCTTAATTGTGCCATGCCATCCTCACTCAT
11031239 ATGCC
1 ATGCC
11031244 CTAGATGCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 50 0.91
59 5 0.09
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.41
Consensus pattern (59 bp):
ATGCCTTATCCATCAAGAAGTCCTCTTTTGCTTAATTGTGCCATGCCATCCTCACTCAT
Found at i:11037421 original size:20 final size:19
Alignment explanation
Indices: 11037363--11037434 Score: 59
Period size: 20 Copynumber: 4.1 Consensus size: 19
11037353 TCATATATAA
11037363 TATATAAAAAATAAAAAA-
1 TATATAAAAAATAAAAAAT
* *
11037381 TATGT---AAAT-ATAAAT
1 TATATAAAAAATAAAAAAT
11037396 T-T-TAAAAAATAAAAATAT
1 TATATAAAAAATAAAAA-AT
*
11037414 TATATAAAAATTAAAAAAT
1 TATATAAAAAATAAAAAAT
11037433 TA
1 TA
11037435 AAAAAAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 5 0.12
16 4 0.10
17 3 0.07
18 7 0.17
19 5 0.12
20 12 0.29
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (19 bp):
TATATAAAAAATAAAAAAT
Found at i:11037655 original size:26 final size:27
Alignment explanation
Indices: 11037610--11037665 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
11037600 TATATATAAA
* *
11037610 TTTTTAAATTTTTAGAAATTTAGATTT
1 TTTTTAAATGTTTAGAAATTTAGAGTT
*
11037637 TTTTTGAATGTTTAG-AATTTAGAGTT
1 TTTTTAAATGTTTAGAAATTTAGAGTT
11037663 TTT
1 TTT
11037666 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (27 bp):
TTTTTAAATGTTTAGAAATTTAGAGTT
Found at i:11037804 original size:19 final size:19
Alignment explanation
Indices: 11037782--11037821 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11037772 ATTTTTTATT
11037782 TTTTTGAACTT-TTTAAATA
1 TTTTTGAA-TTATTTAAATA
*
11037801 TTTTTGAATTATTTATATA
1 TTTTTGAATTATTTAAATA
11037820 TT
1 TT
11037822 ATATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTGAATTATTTAAATA
Found at i:11038759 original size:2 final size:2
Alignment explanation
Indices: 11038752--11038780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11038742 ACCAAAATAC
11038752 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 A
11038781 GCACCGAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11041148 original size:9 final size:9
Alignment explanation
Indices: 11041134--11041158 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11041124 TGCAAATGCT
11041134 ATAATAACA
1 ATAATAACA
11041143 ATAATAACA
1 ATAATAACA
11041152 ATAATAA
1 ATAATAA
11041159 ATACATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:11042261 original size:23 final size:24
Alignment explanation
Indices: 11042231--11042277 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
11042221 AAATTAAATC
11042231 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
11042254 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
11042278 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:11042289 original size:19 final size:19
Alignment explanation
Indices: 11042254--11042328 Score: 132
Period size: 19 Copynumber: 3.8 Consensus size: 19
11042244 AATCATATCT
11042254 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
11042275 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
11042294 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
11042313 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
11042329 CTCAAAAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 43 0.80
21 11 0.20
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:11042582 original size:45 final size:43
Alignment explanation
Indices: 11042532--11042616 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 43
11042522 GGAGCTAGTG
*
11042532 CTTCAATCTATTCCACTGC-AACTGTAGGGAGATAAGACTTACAAT
1 CTTCAACCTATTCCACTGCTAAC--TAGGGAGATAAGA-TTACAAT
* *
11042577 CTTCAACCTTTTCCACTGCTGACTAGGGAGATAAGATTAC
1 CTTCAACCTATTCCACTGCTAACTAGGGAGATAAGATTAC
11042617 TGACTTCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 4 0.11
44 13 0.36
45 17 0.47
46 2 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
CTTCAACCTATTCCACTGCTAACTAGGGAGATAAGATTACAAT
Found at i:11044457 original size:6 final size:6
Alignment explanation
Indices: 11044446--11044485 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
11044436 ATTTTTTCTA
*
11044446 TTTTTG TTTTTG TTTTTG TCTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
11044486 AATCTGAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:11048281 original size:9 final size:9
Alignment explanation
Indices: 11048267--11048291 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11048257 TGCAAATGCT
11048267 ATAATAACA
1 ATAATAACA
11048276 ATAATAACA
1 ATAATAACA
11048285 ATAATAA
1 ATAATAA
11048292 ATACATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:11049348 original size:19 final size:19
Alignment explanation
Indices: 11049324--11049417 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
11049314 AATCATATCT
11049324 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
11049343 TCTAAGATTGCACATATCATA
1 TCTAAGATT--ACATATCATA
11049364 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
* *
11049383 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
11049402 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
11049418 CTCAAAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:11049763 original size:23 final size:23
Alignment explanation
Indices: 11049736--11049781 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
11049726 TAATTTGTTA
11049736 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
11049759 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
11049782 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:11051438 original size:28 final size:28
Alignment explanation
Indices: 11051398--11051496 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
11051388 AAAAAATTCA
* * *
11051398 TTGGGATAGTAAACATGAGGAAAGTTCG
1 TTGGGACAGTAAACATAAGGAAAGTCCG
*
11051426 TTGGGACAGTAAACATAAGGAAAGTCCA
1 TTGGGACAGTAAACATAAGGAAAGTCCG
* * * * *
11051454 TCGAGACAATAAACACAAGGTAAGTCCG
1 TTGGGACAGTAAACATAAGGAAAGTCCG
*
11051482 TTGGAACAGTAAACA
1 TTGGGACAGTAAACA
11051497 CTGGGTAAGT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.19
Consensus pattern (28 bp):
TTGGGACAGTAAACATAAGGAAAGTCCG
Found at i:11056462 original size:26 final size:26
Alignment explanation
Indices: 11056433--11056487 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
11056423 CCCCTAAATT
*
11056433 TTTTGACGATTTTA-CCCTTGGTAAAA
1 TTTTGACGATTTTATCCC-TGATAAAA
*
11056459 TTTTGATGATTTTATCCCTGATAAAA
1 TTTTGACGATTTTATCCCTGATAAAA
11056485 TTT
1 TTT
11056488 CAAGAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (26 bp):
TTTTGACGATTTTATCCCTGATAAAA
Found at i:11067575 original size:43 final size:43
Alignment explanation
Indices: 11067499--11067653 Score: 174
Period size: 43 Copynumber: 3.7 Consensus size: 43
11067489 CGAGATTACG
*
11067499 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGAATTCA
1 TGTAAGACCATGTCTGGGATATTGGCATCGATATGAGAATTCA
* * * * *
11067541 TGTAAGACTATGTCTGCGATATTGGCATCGATATGTGATTTCG
1 TGTAAGACCATGTCTGGGATATTGGCATCGATATGAGAATTCA
* *
11067584 TGTAAGACCATGGT-TGGGCTATTGGCATCGATACGAG-ATTACA
1 TGTAAGACCAT-GTCTGGGATATTGGCATCGATATGAGAATT-CA
* *
11067627 TGTAAGACCATATATGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGATATTGGCAT
11067654 TGTTACGGTA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
42 27 0.29
43 65 0.69
44 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGATATTGGCATCGATATGAGAATTCA
Found at i:11067648 original size:86 final size:84
Alignment explanation
Indices: 11067492--11067653 Score: 202
Period size: 86 Copynumber: 1.9 Consensus size: 84
11067482 GGGTTACCGA
* * * *
11067492 GATTACGTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATTCATGTAAGACTATGTCTG
1 GATTACGTGTAAGACCATATCTGGGATATGGCATCGATACGAGAATTCATGTAAGACCATATATG
11067557 CGATATTGGCATCGATATGT
66 CGATA-TGGCATCGATATGT
* * *
11067577 GATTTCGTGTAAGACCATGGT-TGGGCTATTGGCATCGATACGAG-ATTACATGTAAGACCATAT
1 GATTACGTGTAAGACCAT-ATCTGGGATA-TGGCATCGATACGAGAATT-CATGTAAGACCATAT
*
11067640 ATGGGATATGGCAT
63 ATGCGATATGGCAT
11067654 TGTTACGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 32 0.48
86 34 0.52
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (84 bp):
GATTACGTGTAAGACCATATCTGGGATATGGCATCGATACGAGAATTCATGTAAGACCATATATG
CGATATGGCATCGATATGT
Found at i:11071100 original size:18 final size:18
Alignment explanation
Indices: 11071054--11071147 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 18
11071044 AGCCATGTAT
11071054 TTATGCGAA-CTCATGTTA
1 TTATGCGAACCT-ATGTTA
* * *
11071072 CTCTACGAACCTATGTTA
1 TTATGCGAACCTATGTTA
*
11071090 TTATGCAAACCCATATTGTATGTTA
1 TTATGCGAA-CC-TA-TG----TTA
*
11071115 TTATGTGAACCTATGTTA
1 TTATGCGAACCTATGTTA
11071133 TTATGCGAACCTATG
1 TTATGCGAACCTATG
11071148 ATTGTATGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
18 34 0.59
19 4 0.07
20 2 0.03
21 2 0.03
22 2 0.03
23 2 0.03
24 2 0.03
25 10 0.17
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATGCGAACCTATGTTA
Found at i:11071127 original size:43 final size:43
Alignment explanation
Indices: 11071078--11071169 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
11071068 GTTACTCTAC
* *
11071078 GAACCTATGTTATTATGCAAACCCAT-ATTGTATGTTATTATGT
1 GAACCTATGTTATTATGCAAACCCATGATTGTATG-AAGTATGT
* *
11071121 GAACCTATGTTATTATGCGAACCTATGATTGTATGAAGTATGT
1 GAACCTATGTTATTATGCAAACCCATGATTGTATGAAGTATGT
11071164 GAACCT
1 GAACCT
11071170 TTATTGATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 36 0.82
44 8 0.18
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (43 bp):
GAACCTATGTTATTATGCAAACCCATGATTGTATGAAGTATGT
Found at i:11085252 original size:2 final size:2
Alignment explanation
Indices: 11085245--11085277 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11085235 NNNNNNNTAT
11085245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11085278 TTCATCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11086564 original size:2 final size:2
Alignment explanation
Indices: 11086557--11086583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11086547 AATCATGCAA
11086557 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11086584 AATTAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11086815 original size:19 final size:20
Alignment explanation
Indices: 11086785--11086834 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
11086775 AAATATAAAT
*
11086785 TAAACT-AATTAAATTAATC
1 TAAACTAAATTAAAGTAATC
11086804 -AAACTAAATT-AAGTAATC
1 TAAACTAAATTAAAGTAATC
*
11086822 TAAAATAAATTAA
1 TAAACTAAATTAA
11086835 TGGAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.46
19 13 0.50
20 1 0.04
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAACTAAATTAAAGTAATC
Found at i:11089279 original size:20 final size:21
Alignment explanation
Indices: 11089235--11089282 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
11089225 TTCATAGCAC
11089235 AATAGAAAAAAACAAAACCAA
1 AATAGAAAAAAACAAAACCAA
*
11089256 AATAGAACAAAAA-AAAA-CAT
1 AATAGAA-AAAAACAAAACCAA
11089276 AATAGAA
1 AATAGAA
11089283 TAGAGCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.75, C:0.10, G:0.06, T:0.08
Consensus pattern (21 bp):
AATAGAAAAAAACAAAACCAA
Found at i:11098760 original size:25 final size:25
Alignment explanation
Indices: 11098707--11098760 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
11098697 TGTAGATCGT
* * *
11098707 TATGCTCTTACGAGCTATAAACTGA
1 TATGCACTTACAAGCTATAAACAGA
11098732 TATGCACTTACAAGCTATAAATCAG-
1 TATGCACTTACAAGCTATAAA-CAGA
11098757 TATG
1 TATG
11098761 ATCTCACGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (25 bp):
TATGCACTTACAAGCTATAAACAGA
Found at i:11106402 original size:25 final size:25
Alignment explanation
Indices: 11106338--11106403 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
11106328 TATAGTTCGA
* *
11106338 TATGCTCTCACAAGCTATAAATCGG
1 TATGCTCTCACGAGCTATAAATCAG
* *
11106363 TATGCTTTTACGAGCTATAAATCAG
1 TATGCTCTCACGAGCTATAAATCAG
*
11106388 TATGCTCTCATGAGCT
1 TATGCTCTCACGAGCT
11106404 GTGGAGTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (25 bp):
TATGCTCTCACGAGCTATAAATCAG
Found at i:11108922 original size:29 final size:29
Alignment explanation
Indices: 11108890--11109042 Score: 191
Period size: 29 Copynumber: 5.3 Consensus size: 29
11108880 TCGGAGTCTC
*
11108890 ACCATAAAGGCATCCTTTTAACAGAGATA
1 ACCACAAAGGCATCCTTTTAACAGAGATA
* *
11108919 ACCACAAAGGCATCCTTTTAACTGAGGTA
1 ACCACAAAGGCATCCTTTTAACAGAGATA
* *
11108948 GCCACAAAGGCATCTTTTTAACAGAGATA
1 ACCACAAAGGCATCCTTTTAACAGAGATA
* * * * *
11108977 GCCACAAAGGTATCCTTTTAATAAAGATCG
1 ACCACAAAGGCATCCTTTTAACAGAGAT-A
11109007 A-CACAAAGGCATCCTTTTAACAGAGATA
1 ACCACAAAGGCATCCTTTTAACAGAGATA
*
11109035 GCCACAAA
1 ACCACAAA
11109043 AGGTAGCCTG
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 104 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (29 bp):
ACCACAAAGGCATCCTTTTAACAGAGATA
Found at i:11108959 original size:58 final size:58
Alignment explanation
Indices: 11108895--11109110 Score: 247
Period size: 58 Copynumber: 3.7 Consensus size: 58
11108885 GTCTCACCAT
* * * *
11108895 AAAGGCATCCTTTTAACAGAGATAACCACAAAGGCATCCTTTTAACT-GAGGTAGCCAC
1 AAAGGCATCCTTTTAACAGAGATAGCCACAAAGGCATCCTTTTAA-TAAAGATAGACAC
* * *
11108953 AAAGGCATCTTTTTAACAGAGATAGCCACAAAGGTATCCTTTTAATAAAGATCGACAC
1 AAAGGCATCCTTTTAACAGAGATAGCCACAAAGGCATCCTTTTAATAAAGATAGACAC
* * * * *
11109011 AAAGGCATCCTTTTAACAGAGATAGCCACAAAAGGTAGCCTGTTAATAAAGATTGTCAC
1 AAAGGCATCCTTTTAACAGAGATAGCCAC-AAAGGCATCCTTTTAATAAAGATAGACAC
* * * * *
11109070 AAAGTCTTCC-TTTAATAGAGATCGCCACAAAGGCTTCCTTT
1 AAAGGCATCCTTTTAACAGAGATAGCCACAAAGGCATCCTTT
11109111 AACATGGATT
Statistics
Matches: 136, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
57 10 0.07
58 93 0.68
59 33 0.24
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (58 bp):
AAAGGCATCCTTTTAACAGAGATAGCCACAAAGGCATCCTTTTAATAAAGATAGACAC
Found at i:11109084 original size:87 final size:88
Alignment explanation
Indices: 11108895--11109133 Score: 231
Period size: 87 Copynumber: 2.8 Consensus size: 88
11108885 GTCTCACCAT
* * * * * *
11108895 AAAGGCATCCTTTTAACAGAGAT-AACCACAAAGGCATCCTTTTAACTGAGGTAGCCAC-AAAGG
1 AAAGGTATCCTTTTAATAAAGATCGA-CACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGG
* * * *
11108958 CATCTTTTTAACAGAGATAGCCAC
65 CAGCCTGTTAACAAAGATAGCCAC
*
11108982 AAAGGTATCCTTTTAATAAAGATCGACACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGGT
1 AAAGGTATCCTTTTAATAAAGATCGACACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGGC
* * *
11109047 AGCCTGTTAATAAAGATTGTCAC
66 AGCCTGTTAACAAAGATAGCCAC
* * * *
11109070 AAA-GTCTTCC-TTTAATAGAGATCGCCACAAAGGCTTCC-TTTAACATG-GATTAGCCAC-AAA
1 AAAGGT-ATCCTTTTAATAAAGATCGACACAAAGGCATCCTTTTAACA-GAGA-TAGCCACAAAA
11109130 GGCA
63 GGCA
11109134 ATTTTTTAGG
Statistics
Matches: 128, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
86 15 0.12
87 85 0.66
88 28 0.22
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (88 bp):
AAAGGTATCCTTTTAATAAAGATCGACACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGGC
AGCCTGTTAACAAAGATAGCCAC
Found at i:11109131 original size:29 final size:28
Alignment explanation
Indices: 11108895--11109132 Score: 176
Period size: 29 Copynumber: 8.2 Consensus size: 28
11108885 GTCTCACCAT
* *
11108895 AAAGGCATCCTTTTAACAGAGATAACCAC
1 AAAGGCTTCC-TTTAACAGAGATAGCCAC
* * *
11108924 AAAGGCATCCTTTTAACTGAGGTAGCCAC
1 AAAGGCTTCC-TTTAACAGAGATAGCCAC
* *
11108953 AAAGGCATCTTTTTAACAGAGATAGCCAC
1 AAAGGCTTC-CTTTAACAGAGATAGCCAC
* * * *
11108982 AAAGG-TATCCTTTTAATAAAGATCGACAC
1 AAAGGCT-TCC-TTTAACAGAGATAGCCAC
*
11109011 AAAGGCATCCTTTTAACAGAGATAGCCAC
1 AAAGGCTTCC-TTTAACAGAGATAGCCAC
* * * * *
11109040 AAAAGG-TAGCCTGTTAATAAAGATTGTCAC
1 -AAAGGCT-TCCT-TTAACAGAGATAGCCAC
* * *
11109070 AAAGTCTTCCTTTAATAGAGATCGCCAC
1 AAAGGCTTCCTTTAACAGAGATAGCCAC
11109098 AAAGGCTTCCTTTAACATG-GATTAGCCAC
1 AAAGGCTTCCTTTAACA-GAGA-TAGCCAC
11109127 AAAGGC
1 AAAGGC
11109133 AATTTTTTAG
Statistics
Matches: 168, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
28 31 0.18
29 116 0.69
30 21 0.12
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGGCTTCCTTTAACAGAGATAGCCAC
Found at i:11115165 original size:14 final size:13
Alignment explanation
Indices: 11115146--11115176 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
11115136 AAATTATATT
11115146 TTAATTAATCTTAA
1 TTAATTAAT-TTAA
11115160 TTAATTAATTTAA
1 TTAATTAATTTAA
11115173 TTAA
1 TTAA
11115177 AACATTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTAATTTAA
Found at i:11119924 original size:14 final size:14
Alignment explanation
Indices: 11119905--11119932 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11119895 CTAAATATGG
11119905 AAAAAATTATCATT
1 AAAAAATTATCATT
11119919 AAAAAATTATCATT
1 AAAAAATTATCATT
11119933 TTGGATCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAAATTATCATT
Found at i:11125267 original size:28 final size:28
Alignment explanation
Indices: 11125222--11125290 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
11125212 CAGAGGGCAT
*
11125222 CAAAGTGCATTAACAGAATAGAACAACAC
1 CAAAGTGC-TTAACAGAACAGAACAACAC
** *
11125251 CGTAGTGCTTATCAGAACAGAACAACAC
1 CAAAGTGCTTAACAGAACAGAACAACAC
11125279 CAAAGTGCTTAA
1 CAAAGTGCTTAA
11125291 ATAAAACAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 27 0.82
29 6 0.18
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (28 bp):
CAAAGTGCTTAACAGAACAGAACAACAC
Found at i:11126169 original size:12 final size:12
Alignment explanation
Indices: 11126154--11126180 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11126144 AAAAATATCT
11126154 ATTAATTTAATA
1 ATTAATTTAATA
11126166 ATTAATTTAATA
1 ATTAATTTAATA
11126178 ATT
1 ATT
11126181 TTGCAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAATTTAATA
Found at i:11153307 original size:12 final size:11
Alignment explanation
Indices: 11153289--11153322 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
11153279 AATTAATTTG
11153289 AAAGAAAACTA
1 AAAGAAAACTA
11153300 ACAAGAAAACCTA
1 A-AAGAAAA-CTA
11153313 AAAGAAAACT
1 AAAGAAAACT
11153323 TAATAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 14 0.67
13 4 0.19
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAGAAAACTA
Found at i:11158235 original size:31 final size:31
Alignment explanation
Indices: 11158197--11158260 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
11158187 CTCAAACTAG
11158197 ATAGAAAAATTAATGTATGTTAACACTGGTT
1 ATAGAAAAATTAATGTATGTTAACACTGGTT
* *
11158228 ATAGAAAAGTTGATGTATGTTAACACTGGTT
1 ATAGAAAAATTAATGTATGTTAACACTGGTT
11158259 AT
1 AT
11158261 GCCACATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (31 bp):
ATAGAAAAATTAATGTATGTTAACACTGGTT
Found at i:11160078 original size:16 final size:16
Alignment explanation
Indices: 11160057--11160088 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11160047 ATAAATTAAT
*
11160057 TAAAATTTAATCATAA
1 TAAAATTTAAACATAA
11160073 TAAAATTTAAACATAA
1 TAAAATTTAAACATAA
11160089 AACACAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATTTAAACATAA
Found at i:11160291 original size:15 final size:16
Alignment explanation
Indices: 11160255--11160293 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
11160245 ATAATAAAAA
11160255 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
11160272 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
11160287 TATAATT
1 TATAATT
11160294 AACTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:11163803 original size:41 final size:41
Alignment explanation
Indices: 11163744--11163825 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
11163734 AACCTAATTG
11163744 GGAAAATAATTCCGTTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCCGTTATTCTAATAAACTACTAAAAGATAA
11163785 GGAAAATAATTCTC-TTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTC-CGTTATTCTAATAAACTACTAAAAGATAA
11163826 AATAAAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 39 0.98
42 1 0.03
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (41 bp):
GGAAAATAATTCCGTTATTCTAATAAACTACTAAAAGATAA
Found at i:11163887 original size:19 final size:19
Alignment explanation
Indices: 11163863--11163903 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
11163853 TGATTTATTC
11163863 TAAGATTTATCTACCCAAA
1 TAAGATTTATCTACCCAAA
*
11163882 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCCAAA
11163901 TAA
1 TAA
11163904 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (19 bp):
TAAGATTTATCTACCCAAA
Found at i:11166680 original size:1 final size:1
Alignment explanation
Indices: 11166674--11166700 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
11166664 GCTCCTACTC
11166674 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
11166701 GCTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11175294 original size:31 final size:31
Alignment explanation
Indices: 11175259--11175322 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
11175249 AAAAATGTAT
** *
11175259 TCAATCTTATTTATCTATTCTCTCAATTCTC
1 TCAATCTTATACATCTATTCTCGCAATTCTC
* *
11175290 TCAATCTTATACATTTATTCTCGCAATTTTC
1 TCAATCTTATACATCTATTCTCGCAATTCTC
11175321 TC
1 TC
11175323 TACTATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.50
Consensus pattern (31 bp):
TCAATCTTATACATCTATTCTCGCAATTCTC
Found at i:11182233 original size:21 final size:21
Alignment explanation
Indices: 11182209--11182261 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
11182199 ACCCACTAGG
*
11182209 GTTAAACAGAAACTCATATGA
1 GTTAAACAGAAACTCACATGA
* * *
11182230 GTT-AAGAGAAGCTCGCATGA
1 GTTAAACAGAAACTCACATGA
*
11182250 GTTAAACGGAAA
1 GTTAAACAGAAA
11182262 GTAAACACGA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (21 bp):
GTTAAACAGAAACTCACATGA
Found at i:11209133 original size:10 final size:9
Alignment explanation
Indices: 11209118--11209156 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
11209108 ATATATTTGT
11209118 TTTATAATTA
1 TTTAT-ATTA
*
11209128 TTTATAATA
1 TTTATATTA
11209137 TTTATATTA
1 TTTATATTA
11209146 TGTTATATTA
1 T-TTATATTA
11209156 T
1 T
11209157 AAACCTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 12 0.46
10 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTATATTA
Found at i:11213012 original size:41 final size:40
Alignment explanation
Indices: 11212903--11213019 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 40
11212893 TAAACCGCCA
* * * * * *
11212903 CTAATGCTCCGCTCTAAAGCGGCGTTTATGGAGAATCACCG
1 CTAATGCTTCGGTCTATAGCGGCGTTTGTGTA-AAACACCG
11212944 CTAATG-TTCCGGTCTATAGCGGCGTTTGTGTAACAACACCG
1 CTAATGCTT-CGGTCTATAGCGGCGTTTGTGTAA-AACACCG
*
11212985 GTAATGCTTCGGTCTATAGCGGCGTTTGTGTAAAA
1 CTAATGCTTCGGTCTATAGCGGCGTTTGTGTAAAA
11213020 ACGCTGCTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.06
41 60 0.91
42 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
CTAATGCTTCGGTCTATAGCGGCGTTTGTGTAAAACACCG
Found at i:11214728 original size:16 final size:16
Alignment explanation
Indices: 11214704--11214734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11214694 ATTTTTCCTC
11214704 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
11214720 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
11214735 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:11221250 original size:87 final size:87
Alignment explanation
Indices: 11221097--11221294 Score: 249
Period size: 87 Copynumber: 2.3 Consensus size: 87
11221087 ACACAACTTA
* * * *
11221097 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTACTGCTACATCTT
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAACAACTACAGCTACATCTT
*
11221162 AAAGCAGATACGGCAGCGAGAG
66 AAAGCAGATACGGCAGCGAAAG
* *
11221184 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAACAACTCCAGCAGTA-A-
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAACAACTACAGC--TACAT
* *
11221246 CTTAAAGTAGATGCGGCAGCGAAAG
63 CTTAAAGCAGATACGGCAGCGAAAG
**
11221271 AAGCAGAGGCTGCAGCGAGAGAAG
1 AAGCAGAGGCAACAGCGAGAGAAG
11221295 TAGATGCTGC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 90 0.93
88 5 0.05
89 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.30, T:0.13
Consensus pattern (87 bp):
AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAACAACTACAGCTACATCTT
AAAGCAGATACGGCAGCGAAAG
Found at i:11221315 original size:21 final size:21
Alignment explanation
Indices: 11221250--11221315 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
11221240 CAGTAACTTA
* *
11221250 AAGTAGATGCGGCAGCGAAAG
1 AAGTAGATGCTGCAGCGAGAG
* *
11221271 AAGCAGAGGCTGCAGCGAGAG
1 AAGTAGATGCTGCAGCGAGAG
* *
11221292 AAGTAGATGCTGCAGTGAGGG
1 AAGTAGATGCTGCAGCGAGAG
11221313 AAG
1 AAG
11221316 CAGAACAGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.41, T:0.11
Consensus pattern (21 bp):
AAGTAGATGCTGCAGCGAGAG
Found at i:11221691 original size:43 final size:43
Alignment explanation
Indices: 11221642--11221978 Score: 389
Period size: 43 Copynumber: 7.8 Consensus size: 43
11221632 GTTTTCCTAA
* *
11221642 AAGCGCCGCTAAAAACCATGAG-CTATAGCGGCGTTTGTTTGTT
1 AAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTTGTTTGAT
* * * *
11221685 AAGCGCCGCTAAAGACCAAGGTCTATAGCGGCGTTTGATAGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTGAT
* * * *
11221728 AAGCGCCGCAAAAGATCATGGTCTATAGCGGCGTTTG-ATGCAA
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTG-AT
* * * *
11221771 AAGCACCACTAAAGACCATGGTCTATAGCGGCGTTT-TATGCAA
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTG-AT
* * *
11221814 AAGCGCCGCTATAGACCATGGTCTATAGCGGCGTTTGATAGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTGAT
*
11221857 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTT-TATAT-AT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGT-T-TGAT
* *
11221900 AAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTT-TATAGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGT-TTGAT
*
11221943 AAGCGCCGCTAAAGTCCATGGTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTT
11221979 ATTATAAAAA
Statistics
Matches: 255, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
42 2 0.01
43 252 0.99
44 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTGAT
Found at i:11221787 original size:86 final size:86
Alignment explanation
Indices: 11221642--11221978 Score: 439
Period size: 86 Copynumber: 3.9 Consensus size: 86
11221632 GTTTTCCTAA
* * * *
11221642 AAGCGCCGCTAAAA-ACCATGAG-CTATAGCGGCGTTTGTTTGTTAAGCGCCGCTAAAGACCAAG
1 AAGCGCCGC-AAAAGACCATG-GTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATG
* *
11221705 GTCTATAGCGGCGTTTGATAGGT
64 GTCTATAGCGGCGTTTTATAGAT
* * * *
11221728 AAGCGCCGCAAAAGATCATGGTCTATAGCGGCGTTTGAT-GCAAAAGCACCACTAAAGACCATGG
1 AAGCGCCGCAAAAGACCATGGTCTATAGCGGCGTTTGATAG-ATAAGCGCCGCTAAAGACCATGG
*
11221792 TCTATAGCGGCGTTTTAT-GCAA
65 TCTATAGCGGCGTTTTATAG-AT
* *
11221814 AAGCGCCGCTATAGACCATGGTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATGGT
1 AAGCGCCGCAAAAGACCATGGTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATGGT
* *
11221879 CTATAGCGGCATTTTATATAT
66 CTATAGCGGCGTTTTATAGAT
* * * *
11221900 AAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTATAGATAAGCGCCGCTAAAGTCCATGGT
1 AAGCGCCGCAAAAGACCATGGTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATGGT
11221965 CTATAGCGGCGTTT
66 CTATAGCGGCGTTT
11221979 ATTATAAAAA
Statistics
Matches: 221, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
85 7 0.03
86 213 0.96
87 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (86 bp):
AAGCGCCGCAAAAGACCATGGTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATGGT
CTATAGCGGCGTTTTATAGAT
Found at i:11221871 original size:129 final size:128
Alignment explanation
Indices: 11221640--11221978 Score: 473
Period size: 129 Copynumber: 2.6 Consensus size: 128
11221630 GCGTTTTCCT
* * * *
11221640 AAAAGCGCCGCTAAAAACCATGAG-CTATAGCGGCGTTTGTTTGTTAAGCGCCGCTAAAGACCAA
1 AAAAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTT-TATGATAAGCGCCGCTAAAGACCAT
* * * *
11221704 GGTCTATAGCGGCGTTTGATAGGTAAGCGCCGCAAAAGATCATGGTCTATAGCGGCGTTTGATGC
64 GGTCTATAGCGGCGTTTGATAGATAAGCGCCGCAAAAGACCATGGTCTATAGCGGCATTTGATAC
* * * *
11221769 AAAAGCACCACTAAAGACCATGGTCTATAGCGGCGTTTTATGCAAAAGCGCCGCTATAGACCATG
1 AAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATG-ATAAGCGCCGCTAAAGACCATG
* * *
11221834 GTCTATAGCGGCGTTTGATAGATAAGCGCCGCTAAAGACCATGGTCTATAGCGGCATTTTATAT
65 GTCTATAGCGGCGTTTGATAGATAAGCGCCGCAAAAGACCATGGTCTATAGCGGCATTTGATAC
* * *
11221898 ATAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTATAGATAAGCGCCGCTAAAGTCCATG
1 AAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTAT-GATAAGCGCCGCTAAAGACCATG
11221963 GTCTATAGCGGCGTTT
65 GTCTATAGCGGCGTTT
11221979 ATTATAAAAA
Statistics
Matches: 185, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
128 4 0.02
129 180 0.97
130 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (128 bp):
AAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGATAAGCGCCGCTAAAGACCATGG
TCTATAGCGGCGTTTGATAGATAAGCGCCGCAAAAGACCATGGTCTATAGCGGCATTTGATAC
Found at i:11230492 original size:14 final size:14
Alignment explanation
Indices: 11230473--11230504 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
11230463 GATTTTTAAA
11230473 TTTTGTCTAATTAT
1 TTTTGTCTAATTAT
*
11230487 TTTTGTTTAATTAT
1 TTTTGTCTAATTAT
11230501 TTTT
1 TTTT
11230505 AATTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTTGTCTAATTAT
Found at i:11235176 original size:37 final size:37
Alignment explanation
Indices: 11235128--11235549 Score: 301
Period size: 37 Copynumber: 11.3 Consensus size: 37
11235118 AAAAAATGAA
* * * *
11235128 TACTGAATATACTGAACGTGCTCAAAAGAACAATGTC
1 TACTGATTATACTGAATGTGCTCAAAAGAGCAATATC
* * *
11235165 TACTGATTATACTGAAAGTTGCTCAAACGAGCGATATC
1 TACTGATTATACTGAATG-TGCTCAAAAGAGCAATATC
* * * ** *
11235203 CACTGATTATACTAAATGGGCTCAAACA-AAAAATGTC
1 TACTGATTATACTGAATGTGCTCAAA-AGAGCAATATC
* * * *
11235240 TACTGATTATATTGAATGTGCTTAAATGAACAATATC
1 TACTGATTATACTGAATGTGCTCAAAAGAGCAATATC
* * * *
11235277 TACTGA-AACTACTGAATGTGCTTAAAATAGTAATATC
1 TACTGATTA-TACTGAATGTGCTCAAAAGAGCAATATC
* * * *
11235314 TACTGATTATATTGAAAGTTGCTCAAACGAGCGATATC
1 TACTGATTATACTGAATG-TGCTCAAAAGAGCAATATC
* * *
11235352 CACTGATTATACTGAATGGGCTCAAATGAGCAATATC
1 TACTGATTATACTGAATGTGCTCAAAAGAGCAATATC
* ** * *
11235389 TACTGAATATACTGAACCTGCTCAAAAGAGCAATGTG
1 TACTGATTATACTGAATGTGCTCAAAAGAGCAATATC
* * * * * **
11235426 TATTGATTATATTGAAAGTTTCTCAAACGAGTGATATC
1 TACTGATTATACTGAATG-TGCTCAAAAGAGCAATATC
* * * *
11235464 CACTGATTATACTAAATGGGCTCAAACA-AGCGATATC
1 TACTGATTATACTGAATGTGCTCAAA-AGAGCAATATC
* * * *
11235501 TACTGATTATACGGAATACATGCTCAAACGAGCATTATC
1 TACTGATTATACTGAAT--GTGCTCAAAAGAGCAATATC
* *
11235540 CAGTGATTAT
1 TACTGATTAT
11235550 GCGAAAGGAG
Statistics
Matches: 293, Mismatches: 81, Indels: 20
0.74 0.21 0.05
Matches are distributed among these distances:
36 1 0.00
37 184 0.63
38 86 0.29
39 22 0.08
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (37 bp):
TACTGATTATACTGAATGTGCTCAAAAGAGCAATATC
Found at i:11235338 original size:112 final size:112
Alignment explanation
Indices: 11235129--11235549 Score: 346
Period size: 112 Copynumber: 3.7 Consensus size: 112
11235119 AAAAATGAAT
* * * * * * ** *
11235129 ACTGAATATACTGAACGTGCTCAAAAGAACAATGTCTACTGATTATACTGAAAGTTGCTCAAACG
1 ACTGATTATACTGAATGGGCTCAAATGAACAATATCTACTGAATATACTG-AACCTGCTCAAAAG
* * * * * *
11235194 AGCGATATCCACTGATTATACT-AAA-TGGGCTCAAACAAAAAATGTCT
65 AGCAATATCTACTGATTATATTGAAAGT-TGCTCAAACAAAAAATATCC
* * * ** * *
11235241 ACTGATTATATTGAATGTGCTTAAATGAACAATATCTACTGAA-ACTACTGAATGTGCTTAAAAT
1 ACTGATTATACTGAATGGGCTCAAATGAACAATATCTACTGAATA-TACTGAACCTGCTCAAAAG
* * ***
11235305 AGTAATATCTACTGATTATATTGAAAGTTGCTCAAACGAGCGATATCC
65 AGCAATATCTACTGATTATATTGAAAGTTGCTCAAACAAAAAATATCC
*
11235353 ACTGATTATACTGAATGGGCTCAAATGAGCAATATCTACTGAATATACTGAACCTGCTCAAAAGA
1 ACTGATTATACTGAATGGGCTCAAATGAACAATATCTACTGAATATACTGAACCTGCTCAAAAGA
* * * * * ***
11235418 GCAATGTGTATTGATTATATTGAAAGTTTCTCAAACGAGTGATATCC
66 GCAATATCTACTGATTATATTGAAAGTTGCTCAAACAAAAAATATCC
* * * * * *
11235465 ACTGATTATACTAAATGGGCTCAAA-CAAGCGATATCTACTGATTATACGGAATACATGCTCAAA
1 ACTGATTATACTGAATGGGCTCAAATGAA-CAATATCTACTGAATATACTG-A-ACCTGCTCAAA
* * * *
11235529 CGAGCATTATCCAGTGATTAT
63 AGAGCAATATCTACTGATTAT
11235550 GCGAAAGGAG
Statistics
Matches: 252, Mismatches: 50, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
111 29 0.12
112 195 0.77
113 3 0.01
114 25 0.10
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (112 bp):
ACTGATTATACTGAATGGGCTCAAATGAACAATATCTACTGAATATACTGAACCTGCTCAAAAGA
GCAATATCTACTGATTATATTGAAAGTTGCTCAAACAAAAAATATCC
Found at i:11235487 original size:149 final size:149
Alignment explanation
Indices: 11235128--11235517 Score: 401
Period size: 149 Copynumber: 2.6 Consensus size: 149
11235118 AAAAAATGAA
* ** * *
11235128 TACTGAATA-TACTGAACGTGCTCAAAAGAACAATGTCTACTGATTATACTGAAAGTTGCTCAAA
1 TACTGAA-ACTACTGAAAGTGCTCAAAAGAGTAATATCCACTGATTATACTGAAAGTTGCTCAAA
* * * * *
11235192 CGAGCGATATCCACTGATTATACTAAATGGGCTCAAACAAAAAATGTCTACTGATTATATTGAAT
65 CGAGCGATATCCACTGATTATACTGAATGGGCTCAAACAAAAAATATCTACTGAATATACTGAAC
* * *
11235257 GTGCTTAAATGAACAATATC
130 CTGCTCAAAAGAACAATATC
* * * * *
11235277 TACTGAAACTACTGAATGTGCTTAAAATAGTAATATCTACTGATTATATTGAAAGTTGCTCAAAC
1 TACTGAAACTACTGAAAGTGCTCAAAAGAGTAATATCCACTGATTATACTGAAAGTTGCTCAAAC
** **
11235342 GAGCGATATCCACTGATTATACTGAATGGGCTCAAATGAGCAATATCTACTGAATATACTGAACC
66 GAGCGATATCCACTGATTATACTGAATGGGCTCAAACAAAAAATATCTACTGAATATACTGAACC
* * *
11235407 TGCTCAAAAGAGCAATGTG
131 TGCTCAAAAGAACAATATC
* * * * * * *
11235426 TATTGATTA-TATTGAAAGTTTCTCAAACGAGTGATATCCACTGATTATACT-AAA-TGGGCTCA
1 TACTGA-AACTACTGAAAG-TGCTCAAAAGAGTAATATCCACTGATTATACTGAAAGT-TGCTCA
* * *
11235488 AACAAGCGATATCTACTGATTATACGGAAT
63 AACGAGCGATATCCACTGATTATACTGAAT
11235518 ACATGCTCAA
Statistics
Matches: 200, Mismatches: 37, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
148 2 0.01
149 172 0.86
150 26 0.13
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (149 bp):
TACTGAAACTACTGAAAGTGCTCAAAAGAGTAATATCCACTGATTATACTGAAAGTTGCTCAAAC
GAGCGATATCCACTGATTATACTGAATGGGCTCAAACAAAAAATATCTACTGAATATACTGAACC
TGCTCAAAAGAACAATATC
Found at i:11238978 original size:17 final size:16
Alignment explanation
Indices: 11238951--11238982 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11238941 CTAGCTTAAG
11238951 TACATTTTATTTTCTT
1 TACATTTTATTTTCTT
11238967 TACATGTTTATTTTCT
1 TACAT-TTTATTTTCT
11238983 GTTTTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (16 bp):
TACATTTTATTTTCTT
Found at i:11241744 original size:22 final size:22
Alignment explanation
Indices: 11241689--11241746 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
11241679 TGTGTACCAG
**
11241689 AAGCTCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
*
11241711 AAGCTCTCATGTTTCACGTACT
1 AAGCTCTCATGTTTAACGTACT
11241733 AAGCTCTCATGTTT
1 AAGCTCTCATGTTT
11241747 GAACAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (22 bp):
AAGCTCTCATGTTTAACGTACT
Found at i:11257209 original size:18 final size:18
Alignment explanation
Indices: 11257188--11257223 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11257178 TGATTATTAG
* *
11257188 ATTTTTATTAAATTATAT
1 ATTTTAATTAAAATATAT
11257206 ATTTTAATTAAAATATAT
1 ATTTTAATTAAAATATAT
11257224 TTAATAATAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATTAAAATATAT
Found at i:11257477 original size:239 final size:238
Alignment explanation
Indices: 11257072--11257604 Score: 886
Period size: 239 Copynumber: 2.2 Consensus size: 238
11257062 TATTTTAAAA
* * *
11257072 TTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTTAAATTATATTTTATA
1 TTTATTAAATTATATATTTTAATT-AAATATATTTAATAATAATTATGTTAAATTATATTTTATA
* * *
11257137 GTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAGATTTTTATTAAATT
65 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAGAATTTTATTAAATT
* *
11257202 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTGTATTTTATAGTATCATATAT
130 ATAGATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATAT
*
11257267 TATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAAT
195 TATGATTTGAGTAAATTAATATAAGAATATTAACTATTAAGAAT
* *
11257311 TTTATTAAATTATATATTTTAATTAGATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
1 TTTATTAAATTATATATTTTAATTAAATATATTTAATAATAATTATGTTAAATTATATTTTATAG
*
11257376 TATCATATATTATGATTTGAGTAAATTCATATAAGATTATTAATTATTAAGAATTTTATTAAATT
66 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATT-AGAATTTTATTAAATT
* *
11257441 ATAGATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATAT
130 ATAGATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATAT
* *
11257506 TATGATTTGAGTAAATTCATATAAGAATATTGACTATTAAGAAT
195 TATGATTTGAGTAAATTAATATAAGAATATTAACTATTAAGAAT
11257550 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TTTATTAAATTATATATTTTAATTA-AATATATTTAATAATAATTATG-TTAAAT
11257605 ATGATTAAAT
Statistics
Matches: 274, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
238 82 0.30
239 165 0.60
240 21 0.08
241 6 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (238 bp):
TTTATTAAATTATATATTTTAATTAAATATATTTAATAATAATTATGTTAAATTATATTTTATAG
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAGAATTTTATTAAATTA
TAGATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATT
ATGATTTGAGTAAATTAATATAAGAATATTAACTATTAAGAAT
Found at i:11257521 original size:120 final size:120
Alignment explanation
Indices: 11257072--11257604 Score: 890
Period size: 119 Copynumber: 4.5 Consensus size: 120
11257062 TATTTTAAAA
* * *
11257072 TTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTTAAATTATATTTTATA
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
* * *
11257137 GTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGATT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
11257191 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTGTATTTTATA
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
*
11257256 GTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
* *
11257311 TTTATTAAATTATATATTTTAATT-AGATATATTTAATAATAATTATGTTAAATTATCTTTTATA
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
*
11257375 GTATCATATATTATGATTTGAGTAAATTCATATAAGATTATTAATTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
* * *
11257430 TTTATTAAATTATAGATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
* *
11257495 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGACTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
11257550 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
11257605 ATGATTAAAT
Statistics
Matches: 388, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
119 220 0.57
120 163 0.42
121 5 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
Found at i:11257582 original size:16 final size:16
Alignment explanation
Indices: 11257561--11257602 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11257551 TTATTAAATT
*
11257561 ATATATTTTAATTATA
1 ATATATTTTAATAATA
11257577 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
11257592 AT-TATGTTTAA
1 ATATAT-TTTAA
11257603 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:11257587 original size:15 final size:15
Alignment explanation
Indices: 11257552--11257593 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11257542 TTAAGAATTT
*
11257552 TATTAAATTAT-ATA
1 TATTTAATTATAATA
11257566 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
11257580 TATTTAATAATAAT
1 TATTTAATTATAAT
11257594 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:11257826 original size:45 final size:44
Alignment explanation
Indices: 11257748--11257835 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
11257738 CCTCTATTCC
11257748 ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAT
1 ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAT
* *
11257792 ATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 ATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
11257836 CGCCTCTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.03
44 15 0.38
45 24 0.60
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (44 bp):
ATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTAT
Found at i:11257837 original size:16 final size:16
Alignment explanation
Indices: 11257816--11257864 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
11257806 TTGATTTGCT
11257816 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
11257832 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
11257848 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
11257864 A
1 A
11257865 ATACAGCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:11266090 original size:19 final size:18
Alignment explanation
Indices: 11266061--11266100 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
11266051 TCTCTCCCCC
11266061 AACTAAAATAAAAAAATA
1 AACTAAAATAAAAAAATA
*
11266079 AACTAGAAATAAAATAATA
1 AACTA-AAATAAAAAAATA
11266098 AAC
1 AAC
11266101 AAAGTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (18 bp):
AACTAAAATAAAAAAATA
Found at i:11266699 original size:35 final size:35
Alignment explanation
Indices: 11266659--11266825 Score: 228
Period size: 35 Copynumber: 4.8 Consensus size: 35
11266649 AAATGTTTAC
* *
11266659 AAGAGCTAGTCCAATCGAAACACGCCAATACTCAT
1 AAGAGCTAGTCCAACCGAAACACGCCAATGCTCAT
* *
11266694 AAGAGCTAGTCCAACC-AAAAACGCCAATGCGCAT
1 AAGAGCTAGTCCAACCGAAACACGCCAATGCTCAT
* * * *
11266728 AAGATCTAGTCCAGCCAAAACAAGCCAATGCTCAT
1 AAGAGCTAGTCCAACCGAAACACGCCAATGCTCAT
* *
11266763 AAGAGCTTGTCCAGCCGAAACACGCCAATGCTCAT
1 AAGAGCTAGTCCAACCGAAACACGCCAATGCTCAT
*
11266798 AAGAGCTAGTCCAACCGAAACATGCCAA
1 AAGAGCTAGTCCAACCGAAACACGCCAA
11266826 ACATAGAGTA
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 29 0.25
35 86 0.75
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (35 bp):
AAGAGCTAGTCCAACCGAAACACGCCAATGCTCAT
Found at i:11267162 original size:9 final size:9
Alignment explanation
Indices: 11267148--11267223 Score: 125
Period size: 9 Copynumber: 8.4 Consensus size: 9
11267138 TTTGGTTAAA
11267148 AATTAACCG
1 AATTAACCG
11267157 AATTAACCG
1 AATTAACCG
11267166 AATTAACCG
1 AATTAACCG
* *
11267175 GATTACCCG
1 AATTAACCG
11267184 AATTAACCG
1 AATTAACCG
*
11267193 AATTATCCG
1 AATTAACCG
11267202 AATTAACCG
1 AATTAACCG
11267211 AATTAACCG
1 AATTAACCG
11267220 AATT
1 AATT
11267224 GAATCACTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 61 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:11267366 original size:18 final size:18
Alignment explanation
Indices: 11267326--11267369 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
11267316 AATTTTTATG
*
11267326 ATTGGGTTGGGTTTGGTA
1 ATTGGGTTGGGTTTGATA
11267344 ATTGGGTTGGG-TTGAATA
1 ATTGGGTTGGGTTTG-ATA
*
11267362 CTTGGGTT
1 ATTGGGTT
11267370 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.14, C:0.02, G:0.41, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTTGATA
Found at i:11276878 original size:17 final size:17
Alignment explanation
Indices: 11276858--11276910 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
11276848 AACTATTAAA
11276858 GAGCTTGCA-ATCTTGGT
1 GAGCTTGCAGAT-TTGGT
* *
11276875 GAGCTTACAGATTTGGG
1 GAGCTTGCAGATTTGGT
* *
11276892 GAGCTCGCATATTTGGT
1 GAGCTTGCAGATTTGGT
11276909 GA
1 GA
11276911 CCTGGCAGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (17 bp):
GAGCTTGCAGATTTGGT
Found at i:11278329 original size:90 final size:90
Alignment explanation
Indices: 11278184--11278350 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
11278174 ATCGTTGGAA
* *
11278184 ATATAGGTGGATGCTATGTGCTGATTCCACCCGATACTAATGAAAATAAAGGTGGTTGATATGTG
1 ATATAGGTGGATGCTATGTGCTGATTCCACCAGATACCAATGAAAATAAAGGTGGTTGATATGTG
*
11278249 TTGATTTCACCGGATACCAATGGTT
66 CTGATTTCACCGGATACCAATGGTT
* * ** *
11278274 ATATAGGTGGTTGCTATGTGCTGACTT-CACCTAG-TACCATTGAGTATACAA-GTGGTTGCTAT
1 ATATAGGTGGATGCTATGTGCTGA-TTCCACC-AGATACCAATGAAAATA-AAGGTGGTTGATAT
11278336 GTGCTGATTTCACCG
63 GTGCTGATTTCACCG
11278351 AGTACTATTG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
90 61 0.92
91 5 0.08
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (90 bp):
ATATAGGTGGATGCTATGTGCTGATTCCACCAGATACCAATGAAAATAAAGGTGGTTGATATGTG
CTGATTTCACCGGATACCAATGGTT
Found at i:11278361 original size:45 final size:44
Alignment explanation
Indices: 11278190--11278355 Score: 158
Period size: 45 Copynumber: 3.7 Consensus size: 44
11278180 GGAAATATAG
* * * **
11278190 GTGGATGCTATGTGCTGATTCCACCCGA-TACTAATGAAAATAAA
1 GTGGTTGCTATGTGCTGATTTCA-CCGAGTACCAATGAGTATAAA
* * *
11278234 GGTGGTTGATATGTGTTGATTTCACCG-GATACCAATG-GTTATATAG
1 -GTGGTTGCTATGTGCTGATTTCACCGAG-TACCAATGAG-TATA-AA
* * *
11278280 GTGGTTGCTATGTGCTGACTTCACCTAGTACCATTGAGTATACAA
1 GTGGTTGCTATGTGCTGATTTCACCGAGTACCAATGAGTATA-AA
11278325 GTGGTTGCTATGTGCTGATTTCACCGAGTAC
1 GTGGTTGCTATGTGCTGATTTCACCGAGTAC
11278356 TATTGACTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
44 3 0.03
45 92 0.94
46 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (44 bp):
GTGGTTGCTATGTGCTGATTTCACCGAGTACCAATGAGTATAAA
Found at i:11283649 original size:17 final size:17
Alignment explanation
Indices: 11283617--11283655 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
11283607 CACTATTGAA
*
11283617 GAGCTCACAGTCTTGGT
1 GAGCTCACAGTCTTGGG
11283634 GAGCTCACAGAT-TTGGG
1 GAGCTCACAG-TCTTGGG
11283651 GAGCT
1 GAGCT
11283656 TGCACATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (17 bp):
GAGCTCACAGTCTTGGG
Found at i:11284061 original size:38 final size:38
Alignment explanation
Indices: 11284010--11284082 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
11284000 TGGTAAACCA
11284010 ATTGCAAAGAAGTAGTTCATGCTTTTCTCGATGCCCCG
1 ATTGCAAAGAAGTAGTTCATGCTTTTCTCGATGCCCCG
11284048 ATTGCAAAGAAGTAGTTCATGCTTTTCTCGATGCC
1 ATTGCAAAGAAGTAGTTCATGCTTTTCTCGATGCC
11284083 TGAGAAGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (38 bp):
ATTGCAAAGAAGTAGTTCATGCTTTTCTCGATGCCCCG
Found at i:11285277 original size:23 final size:23
Alignment explanation
Indices: 11285226--11285269 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11285216 TTCTATCTAC
*
11285226 TATTATATTATATATTATTATAA
1 TATTATAATATATATTATTATAA
11285249 TATTATAATATA-ATTTATTAT
1 TATTATAATATATA-TTATTAT
11285270 TTTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATAATATATATTATTATAA
Found at i:11289491 original size:38 final size:38
Alignment explanation
Indices: 11289449--11289554 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 38
11289439 AACAGAAGAG
* * * *
11289449 CTAAGCCTGCAAGGCACAAAGCCCGAATAACACTGGTA
1 CTAAGCCTGCTAGGCACAAAGCCCAAATAACACCGGCA
* *
11289487 CTAAGTCTGCTAGGCACAAAGCCTAAATAACACCGGCA
1 CTAAGCCTGCTAGGCACAAAGCCCAAATAACACCGGCA
* *
11289525 CTAAGCCTGTTAGGCATAAAGCCCAAATAA
1 CTAAGCCTGCTAGGCACAAAGCCCAAATAA
11289555 TAATATAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (38 bp):
CTAAGCCTGCTAGGCACAAAGCCCAAATAACACCGGCA
Found at i:11300669 original size:20 final size:21
Alignment explanation
Indices: 11300631--11300670 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11300621 AAAACAGGCT
11300631 TTTAGCGGCGCTCTTTTAGCC
1 TTTAGCGGCGCTCTTTTAGCC
11300652 TTTAGCGGCGCT-TTTTAGC
1 TTTAGCGGCGCTCTTTTAGC
11300671 GCCGCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (21 bp):
TTTAGCGGCGCTCTTTTAGCC
Found at i:11300838 original size:42 final size:43
Alignment explanation
Indices: 11300792--11300884 Score: 100
Period size: 44 Copynumber: 2.2 Consensus size: 43
11300782 AGACTAAGAC
*
11300792 CTTTAGTAGCACTTTAGTG-G-AAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCAGC-CTTTAGTGCGAAAGCGCCGCTAAAGATCAGGGT
* * ** *
11300834 CTTTAGCGGCGTTTTTTGCGACAAGCGCCGCTAAAGATTAGGGT
1 CTTTAGCAGCCTTTAGTGCGA-AAGCGCCGCTAAAGATCAGGGT
11300878 CTTTAGC
1 CTTTAGC
11300885 GGCGCTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
41 5 0.12
42 9 0.21
44 28 0.67
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (43 bp):
CTTTAGCAGCCTTTAGTGCGAAAGCGCCGCTAAAGATCAGGGT
Found at i:11300928 original size:43 final size:42
Alignment explanation
Indices: 11300877--11301021 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 42
11300867 AAGATTAGGG
11300877 TCTTTAGCGGCGCTTTTCCCTA-AAACGCCGCAAAAGACCCTGA
1 TCTTTAGCGGCGC-TTTCCC-ACAAACGCCGCAAAAGACCCTGA
* * * * *
11300920 TCTATAGCGGCG-TTTCGACCACAAACGCCACTAAAGAACCTAA
1 TCTTTAGCGGCGCTTTC--CCACAAACGCCGCAAAAGACCCTGA
* *
11300963 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCGAAAGACCATGA
1 TCTTTAGCGGCGCTTT-CCCACAAACGCCGCAAAAGACCCTGA
*
11301006 TCTTTAGGGGCGCTTT
1 TCTTTAGCGGCGCTTT
11301022 TACCAAAAAC
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
41 4 0.05
42 1 0.01
43 76 0.89
44 3 0.04
45 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTTCCCACAAACGCCGCAAAAGACCCTGA
Found at i:11300977 original size:86 final size:86
Alignment explanation
Indices: 11300877--11301041 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 86
11300867 AAGATTAGGG
* *
11300877 TCTTTAGCGGCGCTTTTCCCTA-AAACGCCGCAAAAGACCCTGATCTATAGCGGCG-TTTCGACC
1 TCTTTAGCGGCGC-TTTCCCCACAAACGCCGCAAAAGACCATGATCTATAGCGGCGCTTT-GACC
*
11300940 ACAAACGCCACTAAAGAACCTAA
64 AAAAACGCCACTAAAGAACCTAA
* * * *
11300963 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCGAAAGACCATGATCTTTAGGGGCGCTTTTACCAA
1 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCAAAAGACCATGATCTATAGCGGCGCTTTGACCAA
11301028 AAACGCCACTAAAG
66 AAACGCCACTAAAG
11301042 GCCAACACCT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
85 7 0.10
86 60 0.86
87 3 0.04
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCCCCACAAACGCCGCAAAAGACCATGATCTATAGCGGCGCTTTGACCAA
AAACGCCACTAAAGAACCTAA
Found at i:11301054 original size:86 final size:86
Alignment explanation
Indices: 11300878--11301065 Score: 220
Period size: 86 Copynumber: 2.2 Consensus size: 86
11300868 AGATTAGGGT
* * *
11300878 CTTTAGCGGCGCTTTTCCCTAAAACGCCGCAAAAGACCCTGATCTATAGCGGCGTTTCGACCACA
1 CTTTAGCGGCGCTTTTCCCCAAAACGCCGCAAAAGACCATGATCTATAGCGGCGTTTCGACCAAA
* *
11300943 AACGCCACTAAAGAACCTAAT
66 AACGCCACTAAAGAACCAAAC
* * * *
11300964 CTTTAGCGGCGC-TTTCCCCACAAACGCCGCGAAAGACCATGATCTTTAGGGGCGCTTT-TACCA
1 CTTTAGCGGCGCTTTTCCCCA-AAACGCCGCAAAAGACCATGATCTATAGCGGCG-TTTCGACCA
*
11301027 AAAACGCCACTAAAG-GCCAACAC
64 AAAACGCCACTAAAGAACCAA-AC
* *
11301050 CTTTAGTGGCGTTTTT
1 CTTTAGCGGCGCTTTT
11301066 TTTTGAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
85 10 0.12
86 70 0.81
87 6 0.07
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTCCCCAAAACGCCGCAAAAGACCATGATCTATAGCGGCGTTTCGACCAAA
AACGCCACTAAAGAACCAAAC
Found at i:11301497 original size:21 final size:21
Alignment explanation
Indices: 11301395--11301495 Score: 121
Period size: 21 Copynumber: 4.8 Consensus size: 21
11301385 TTGACGCTGT
11301395 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
**
11301416 TCTGCTTCCCTCGCTTTAGCC
1 TCTGCTTCCCTCGCTGCAGCC
11301437 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
* * * * *
11301458 TGTACTTCTCTCGTTGCCGCC
1 TCTGCTTCCCTCGCTGCAGCC
* *
11301479 TCTGCTTCTCTTGCTGC
1 TCTGCTTCCCTCGCTGC
11301496 CGTATCTGCT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.36
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:11301554 original size:66 final size:66
Alignment explanation
Indices: 11301482--11301623 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 66
11301472 TGCCGCCTCT
* *
11301482 GCTTCTCTTGCTGCCGTATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAACA
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACA
11301545 TCA
64 TCA
* * * *
11301548 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTC
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
11301613 A
66 A
11301614 GCTTCTCTCG
1 GCTTCTCTCG
11301624 ATGTTGCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
A
Found at i:11301639 original size:66 final size:65
Alignment explanation
Indices: 11301503--11301647 Score: 193
Period size: 66 Copynumber: 2.2 Consensus size: 65
11301493 TGCCGTATCT
* *
11301503 GCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGCTGCTGCATC
1 GCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATC
*
11301568 T
65 C
* * * *
11301569 GCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCT
1 GCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTGAACATCAGCTTCTCTCGATGCTGCAT
11301633 CC
64 CC
11301635 GCTTTAAGTTGTG
1 GCTTTAAGTTGTG
11301648 TAATTTGCTC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 2 0.03
66 64 0.91
67 4 0.06
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (65 bp):
GCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCC
Found at i:11304027 original size:33 final size:33
Alignment explanation
Indices: 11303990--11304052 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
11303980 GAAAAATAAT
**
11303990 AATTAAACTATACAACTAAAATATAACCAAAAA
1 AATTAAACTATACAAAAAAAATATAACCAAAAA
11304023 AATTAAACTATACAAAAAAAATATAACCAA
1 AATTAAACTATACAAAAAAAATATAACCAA
11304053 CTTAAAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (33 bp):
AATTAAACTATACAAAAAAAATATAACCAAAAA
Found at i:11304034 original size:20 final size:19
Alignment explanation
Indices: 11304006--11304044 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11303996 ACTATACAAC
*
11304006 TAAAATATAACCAAAAAAAT
1 TAAAATAT-ACAAAAAAAAT
*
11304026 TAAACTATACAAAAAAAAT
1 TAAAATATACAAAAAAAAT
11304045 ATAACCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAATATACAAAAAAAAT
Found at i:11304537 original size:38 final size:38
Alignment explanation
Indices: 11304493--11304582 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
11304483 AATTTGTAAT
11304493 GATAAATGACAGGAAGTTGAAATTATTCAAACAAACCG
1 GATAAATGACAGGAAGTTGAAATTATTCAAACAAACCG
*
11304531 GATAAATGACTGGAAGTTGAAATTATTCAAACAAACCG
1 GATAAATGACAGGAAGTTGAAATTATTCAAACAAACCG
11304569 GATAAATGACAGGA
1 GATAAATGACAGGA
11304583 TTATCTAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (38 bp):
GATAAATGACAGGAAGTTGAAATTATTCAAACAAACCG
Found at i:11305728 original size:22 final size:22
Alignment explanation
Indices: 11305687--11305740 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
11305677 TTGTATTTTC
* *
11305687 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
11305710 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
11305731 -TAAAAGTTTT
1 ATTAAAGTTTT
11305741 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:11305755 original size:21 final size:21
Alignment explanation
Indices: 11305689--11305755 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
11305679 GTATTTTCAT
*
11305689 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
11305711 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
11305731 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
11305752 TAAA
1 TAAA
11305756 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:11305801 original size:21 final size:21
Alignment explanation
Indices: 11305762--11305803 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
11305752 TAAATTTTAG
11305762 TTTTTTATTTCCTTTTTATATA
1 TTTTTTATTT-CTTTTTATATA
11305784 TTTTTTATTT-TTTCTTATAT
1 TTTTTTATTTCTTT-TTATAT
11305804 TTTGGTCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 6 0.32
22 10 0.53
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTCTTTTTATATA
Found at i:11306129 original size:89 final size:89
Alignment explanation
Indices: 11306004--11306253 Score: 446
Period size: 89 Copynumber: 2.8 Consensus size: 89
11305994 CCAAACCCCT
*
11306004 ACCCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
11306069 CCCTAACTCGACCCCAAATCACTA
66 CCCTAACTCGACCCCAAATCACTA
*
11306093 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATTCTAAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
**
11306158 CCCTAACTCGACCCTGAATCACTA
66 CCCTAACTCGACCCCAAATCACTA
* *
11306182 ACCCATAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAATCCTAAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
11306247 CCCTAAC
66 CCCTAAC
11306254 CCTAAATCCC
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 154 1.00
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (89 bp):
ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
CCCTAACTCGACCCCAAATCACTA
Found at i:11306260 original size:20 final size:21
Alignment explanation
Indices: 11306235--11306273 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11306225 ATTAATTAAT
11306235 CTAAAT-CCTAAACCCTAACC
1 CTAAATCCCTAAACCCTAACC
*
11306255 CTAAATCCCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
11306274 ACATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAATCCCTAAACCCTAACC
Found at i:11306318 original size:80 final size:77
Alignment explanation
Indices: 11306006--11306334 Score: 307
Period size: 89 Copynumber: 3.9 Consensus size: 77
11305996 AAACCCCTAC
* * *
11306006 CCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAACCCTAAACC
*
11306071 CTAACTCGACCCCAAATCACTAAC
66 CT-A----A-CCC---T-A--AAT
* **
11306095 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATTCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAACCCTAAACC
11306160 CTAACTCGACCCTGAATCACT
66 CT-A----ACCCT-AA--A-T
*
11306181 AACCCATAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAATCCTAA
1 --CCC-TAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAACCCTAA
11306246 ACCCTAACCCTAAAT
63 ACCCTAACCCTAAAT
* * *
11306261 CCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAACCCTAA
1 CCCTAACCCCTAAACATTATTTAATA-TATA-AA-TTAAAAAACATTAATTAATCTAAACCCTAA
*
11306326 ACTCTAACC
63 ACCCTAACC
11306335 TAACACCGAA
Statistics
Matches: 220, Mismatches: 11, Indels: 27
0.85 0.04 0.10
Matches are distributed among these distances:
77 23 0.10
78 7 0.03
79 2 0.01
80 35 0.16
81 1 0.00
83 3 0.01
84 5 0.02
85 3 0.01
88 7 0.03
89 134 0.61
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.29
Consensus pattern (77 bp):
CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACATTAATTAATCTAAACCCTAAACC
CTAACCCTAAAT
Found at i:11306947 original size:41 final size:41
Alignment explanation
Indices: 11306902--11307166 Score: 419
Period size: 41 Copynumber: 6.5 Consensus size: 41
11306892 GCGCTTCCTC
11306902 AAAAACGCCGCTAAAGGTA-C-GAGCATTAGCGGCGCTTATTA
1 AAAAACGCCGCTAAA-G-ACCTGAGCATTAGCGGCGCTTATTA
*
11306943 AAAAACGCCGCTAAAGACCTGAGCATTCGCGGCGCTTATTA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
*
11306984 AAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTATTA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
* *
11307025 AAAAACGCCGCTAAAGACCTGAGCACTAGCGGCGCTTATTC
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
*
11307066 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTC
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
11307107 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TTCA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT-A
* *
11307148 GAAAATGCCGCTAAAGACC
1 AAAAACGCCGCTAAAGACC
11307167 CTAAAAACTC
Statistics
Matches: 211, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.00
40 4 0.02
41 206 0.98
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
Found at i:11307327 original size:40 final size:40
Alignment explanation
Indices: 11307203--11307337 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
11307193 GGGCTTAGGC
* *
11307203 TTTTT-GCGGCG-CTTTCCAAAAAACGCTGCTAATGCTT-A
1 TTTTTAGCGGCGTTTTTCC-AAAAACGCCGCTAATGCTTGA
* * *
11307241 TTTTTAGCGGCGTTTTT-TAAAAATCGCCGCTAATGATCGA
1 TTTTTAGCGGCGTTTTTCCAAAAA-CGCCGCTAATGCTTGA
** * *
11307281 CCTTTAGCGGCGTTTTTCCAAAAGCGCCGCTACTGCTTGA
1 TTTTTAGCGGCGTTTTTCCAAAAACGCCGCTAATGCTTGA
*
11307321 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
11307338 TGTCCAAACG
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 10 0.13
39 17 0.22
40 46 0.60
41 4 0.05
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCCAAAAACGCCGCTAATGCTTGA
Found at i:11311616 original size:22 final size:22
Alignment explanation
Indices: 11311588--11311659 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
11311578 GTCATGAACC
11311588 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
11311610 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
11311632 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
11311654 CTCATG
1 CTCATG
11311660 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:11339785 original size:48 final size:47
Alignment explanation
Indices: 11339715--11339810 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 47
11339705 TTCAATAGGG
11339715 GATAAATAGTATAAGATCGTAGACAGTAGAAGACCAAGTTTAGCAAT
1 GATAAATAGTATAAGATCGTAGACAGTAGAAGACCAAGTTTAGCAAT
* *
11339762 GATAAATAGTGATAAGAGT-GTAGACAGTGGAAGACCAAGTTTAGTAAT
1 GATAAATAGT-ATAAGA-TCGTAGACAGTAGAAGACCAAGTTTAGCAAT
11339810 G
1 G
11339811 CCTAACATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 10 0.22
48 34 0.76
49 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (47 bp):
GATAAATAGTATAAGATCGTAGACAGTAGAAGACCAAGTTTAGCAAT
Found at i:11341175 original size:39 final size:39
Alignment explanation
Indices: 11341121--11341198 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
11341111 TGTGGTAAAA
* *
11341121 AACACCATGGTGAATGTTGGAAGCTAACTCGAGCTTGTT
1 AACACCAAGGTGAATGTTGGAAACTAACTCGAGCTTGTT
11341160 AACACCAAGGTGAATGTTGGAAACTAACTCGAGCTTGTT
1 AACACCAAGGTGAATGTTGGAAACTAACTCGAGCTTGTT
11341199 TTTGTTGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (39 bp):
AACACCAAGGTGAATGTTGGAAACTAACTCGAGCTTGTT
Found at i:11341279 original size:26 final size:26
Alignment explanation
Indices: 11341250--11341302 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11341240 AAGAATGAGA
11341250 ATGCTACTCTTGTTTCTTCTCAGAGG
1 ATGCTACTCTTGTTTCTTCTCAGAGG
11341276 ATGCTACTCTTGTTTCTTCTCAGAGG
1 ATGCTACTCTTGTTTCTTCTCAGAGG
11341302 A
1 A
11341303 AGGGAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (26 bp):
ATGCTACTCTTGTTTCTTCTCAGAGG
Found at i:11341755 original size:152 final size:153
Alignment explanation
Indices: 11341478--11341779 Score: 570
Period size: 152 Copynumber: 2.0 Consensus size: 153
11341468 ATGTTAATGT
*
11341478 TGAGTTAGTTAAATCGGGAAGTTTAAAAGCCAAGACGTTTAGGGTATCAATAGTTGTGTCAAGTC
1 TGAGTTAGTTAAATCGGGAAGTTTAAAAGCCAAGACGTCTAGGGTATCAATAGTTGTGTCAAGTC
11341543 CTTTGGGGCAGTCTATAATAGTGGATCAAGTGTGTAGGTGATGCCCGTTAGATATACAGAATATA
66 CTTTGGGGCAGTCTATAATAGTGGATCAAGTGTGTAGGTGATGCCCGTTAGATATACAGAATATA
*
11341608 ACATTCCTTGTTGATTTGTTTGC
131 ACATTCCCTGTTGATTTGTTTGC
11341631 TGAGTTAGTTAAATCGGGAAGTTTAAAAGCCAAGACGTCTAGGG-ATCAATAGTTGTGTCAAGTC
1 TGAGTTAGTTAAATCGGGAAGTTTAAAAGCCAAGACGTCTAGGGTATCAATAGTTGTGTCAAGTC
*
11341695 CTTTGGGGCAGTCTATAATAGTGGATCAAGTGTGTGGGTGATGCCCGTTAGATATACAGAATATA
66 CTTTGGGGCAGTCTATAATAGTGGATCAAGTGTGTAGGTGATGCCCGTTAGATATACAGAATATA
11341760 ACATTCCCTGTTGATTTGTT
131 ACATTCCCTGTTGATTTGTT
11341780 AATAATTCCA
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
152 103 0.71
153 43 0.29
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (153 bp):
TGAGTTAGTTAAATCGGGAAGTTTAAAAGCCAAGACGTCTAGGGTATCAATAGTTGTGTCAAGTC
CTTTGGGGCAGTCTATAATAGTGGATCAAGTGTGTAGGTGATGCCCGTTAGATATACAGAATATA
ACATTCCCTGTTGATTTGTTTGC
Found at i:11344028 original size:51 final size:49
Alignment explanation
Indices: 11343898--11344080 Score: 188
Period size: 51 Copynumber: 3.6 Consensus size: 49
11343888 AGTTGCTAGG
* *
11343898 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAT-GATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATAGAT-GA
* * * * *
11343948 TCGCATGTGTAATACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-AT-GA
* * * * * *
11343999 TCACGTGTGCAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGC
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT--AGATGA
11344050 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
11344081 TGTGAACTGG
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
49 4 0.04
50 35 0.32
51 67 0.62
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGATGA
Found at i:11345687 original size:17 final size:17
Alignment explanation
Indices: 11345665--11345707 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
11345655 GAAATTTAGC
11345665 TCAATTAAATGATTTCA
1 TCAATTAAATGATTTCA
11345682 TCAATTAAATGATTTCA
1 TCAATTAAATGATTTCA
11345699 TCAATTAAA
1 TCAATTAAA
11345708 CATTGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (17 bp):
TCAATTAAATGATTTCA
Found at i:11347877 original size:3 final size:3
Alignment explanation
Indices: 11347869--11347919 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
11347859 ATTAAATAGT
*
11347869 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA -AA TAA -ACA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
11347912 TAA -AA TAA
1 TAA TAA TAA
11347920 AGAATAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 7 0.17
3 34 0.83
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:11347975 original size:14 final size:13
Alignment explanation
Indices: 11347956--11347991 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
11347946 CATGCAAATT
11347956 AGAAAAGAAAGAAA
1 AGAAAAGAAAG-AA
11347970 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
*
11347983 CGAAAAGAA
1 AGAAAAGAA
11347992 GGAGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:11350089 original size:54 final size:54
Alignment explanation
Indices: 11350024--11350129 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
11350014 CGTATGACCT
* *
11350024 AAGTCAGTGAGTTACACGGGT-AGAGACACGGGCTGAGACACAACCATGTGTCTC
1 AAGTCAATGAGTTACACGGGTAAG-GACACAGGCTGAGACACAACCATGTGTCTC
* * * *
11350078 AAGTCAATGAGTTACACTGGTAAGGACACAGGCTGGGACACGACCGTGTGTC
1 AAGTCAATGAGTTACACGGGTAAGGACACAGGCTGAGACACAACCATGTGTC
11350130 CCAACTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (54 bp):
AAGTCAATGAGTTACACGGGTAAGGACACAGGCTGAGACACAACCATGTGTCTC
Found at i:11350520 original size:48 final size:48
Alignment explanation
Indices: 11350462--11350555 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
11350452 AAGAAGGGAT
* * * *
11350462 AAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGAC
1 AAATAATGATAAAAGTGTAGACAATGAAAGACCAAGTTTAGCAATGAC
*
11350510 AAATAATGATAAAAGTGTAGACAATGAAAGACCAAGTTTAGTAATG
1 AAATAATGATAAAAGTGTAGACAATGAAAGACCAAGTTTAGCAATG
11350556 CATAGCATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (48 bp):
AAATAATGATAAAAGTGTAGACAATGAAAGACCAAGTTTAGCAATGAC
Found at i:11361634 original size:37 final size:37
Alignment explanation
Indices: 11361584--11361657 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
11361574 AGGGTTTGAT
11361584 AGATTAATTCATATTATTAACGAACAAATTAAGTACC
1 AGATTAATTCATATTATTAACGAACAAATTAAGTACC
11361621 AGATTAATTCATATTATTAACGAACAAATTAAGTACC
1 AGATTAATTCATATTATTAACGAACAAATTAAGTACC
11361658 TAGGTAGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (37 bp):
AGATTAATTCATATTATTAACGAACAAATTAAGTACC
Found at i:11371154 original size:13 final size:13
Alignment explanation
Indices: 11371136--11371163 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11371126 AGGCCTACCT
11371136 AAAAAACAAAACA
1 AAAAAACAAAACA
11371149 AAAAAACAAAACA
1 AAAAAACAAAACA
11371162 AA
1 AA
11371164 TATAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAACA
Found at i:11373870 original size:24 final size:24
Alignment explanation
Indices: 11373842--11373891 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
11373832 TCATCTTCGC
11373842 TATCAATTTATATAAAACATTACA
1 TATCAATTTATATAAAACATTACA
11373866 TATCAATTTATATAAAACATTACA
1 TATCAATTTATATAAAACATTACA
11373890 TA
1 TA
11373892 GACTGATTGG
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:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (24 bp):
TATCAATTTATATAAAACATTACA
Found at i:11376748 original size:9 final size:9
Alignment explanation
Indices: 11376734--11376764 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11376724 GTTAAACGAA
11376734 TCGAGTTAT
1 TCGAGTTAT
*
11376743 TCGAGTTAA
1 TCGAGTTAT
11376752 TCGAGTTAT
1 TCGAGTTAT
11376761 TCGA
1 TCGA
11376765 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:11377103 original size:30 final size:31
Alignment explanation
Indices: 11377055--11377114 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
11377045 AAACCTTTTA
* *
11377055 TTTTCTTCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCTCCAAAACTTTTACTCCCTTCCCAC
* *
11377085 TTTTCCTCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCTCCAAAACTTTTACTCCCTTCCCA
11377115 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTCCTCCAAAACTTTTACTCCCTTCCCAC
Found at i:11377382 original size:9 final size:9
Alignment explanation
Indices: 11377368--11377396 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
11377358 AATTTCACAT
11377368 TTTATATTA
1 TTTATATTA
11377377 TTTATATTA
1 TTTATATTA
11377386 TTTATATTA
1 TTTATATTA
11377395 TT
1 TT
11377397 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:11378901 original size:8 final size:8
Alignment explanation
Indices: 11378874--11378921 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
11378864 TTTTTTGGTT
*
11378874 TTTTTTCA
1 TTTTTTAA
*
11378882 TATTTTAA
1 TTTTTTAA
11378890 -TTTTTAA
1 TTTTTTAA
11378897 TTTTTTAA
1 TTTTTTAA
*
11378905 TTTTCTAA
1 TTTTTTAA
11378913 TATTTTTAA
1 T-TTTTTAA
11378922 AAAAATTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
7 6 0.18
8 21 0.64
9 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTTAA
Done.