Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, whole genome shotgun sequence
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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3073255 original size:78 final size:78
Alignment explanation
Indices: 3073122--3073309 Score: 218
Period size: 78 Copynumber: 2.4 Consensus size: 78
3073112 AGCAGGATGT
* * * * *
3073122 TGTAAATAA-AGTTCCATCTAGGAACGAGGGGAGAAGTGTTGGTGTGAATATTACAAACGATCCA
1 TGTAAATAACA-TTCCAGCTGGGAATGAGGGGAGAAGTGTTGGTGTAAATATTACAAAAGATCCA
* * *
3073186 ACATAGGAGATAAA
65 ACACAAGAGAGAAA
* * *
3073200 TGTGAATAACA-TCCTAGCTGGGAATGAGGGGAGAAGTGTTGGTGTAAATTTTACAAAAGCTCCA
1 TGTAAATAACATTCC-AGCTGGGAATGAGGGGAGAAGTGTTGGTGTAAATATTACAAAAGATCCA
* *
3073264 GCACAAGAGAGGAA
65 ACACAAGAGAGAAA
*
3073278 TGTAAATAATATTCCAGCTGGGAATGAGGGGA
1 TGTAAATAACATTCCAGCTGGGAATGAGGGGA
3073310 AGGGTGTTGA
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
77 3 0.03
78 85 0.92
79 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (78 bp):
TGTAAATAACATTCCAGCTGGGAATGAGGGGAGAAGTGTTGGTGTAAATATTACAAAAGATCCAA
CACAAGAGAGAAA
Found at i:3075681 original size:17 final size:17
Alignment explanation
Indices: 3075635--3075682 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3075625 AAATTGTCCT
*
3075635 TATTATATATTTGTATAA
1 TATTATATATTT-TAAAA
* *
3075653 TATTACAAATTTTAAAA
1 TATTATATATTTTAAAA
3075670 TATTATATATTTT
1 TATTATATATTTT
3075683 CTTTAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TATTATATATTTTAAAA
Found at i:3078691 original size:15 final size:15
Alignment explanation
Indices: 3078671--3078701 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3078661 TGATATATCG
3078671 CTGGAGGGGCTTCAA
1 CTGGAGGGGCTTCAA
3078686 CTGGAGGGGCTTCAA
1 CTGGAGGGGCTTCAA
3078701 C
1 C
3078702 GAGAATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.39, T:0.19
Consensus pattern (15 bp):
CTGGAGGGGCTTCAA
Found at i:3080332 original size:18 final size:18
Alignment explanation
Indices: 3080309--3080344 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3080299 TGTATGTTGC
3080309 CTCACTTTTGCCAAATGA
1 CTCACTTTTGCCAAATGA
3080327 CTCACTTTTGCCAAATGA
1 CTCACTTTTGCCAAATGA
3080345 AAATTAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (18 bp):
CTCACTTTTGCCAAATGA
Found at i:3100904 original size:2 final size:2
Alignment explanation
Indices: 3100897--3100924 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3100887 CCATACATGA
3100897 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
3100925 TCATGTAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3101117 original size:37 final size:37
Alignment explanation
Indices: 3101067--3101141 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
3101057 ACAATTATAC
3101067 ATAAAATACGGATGTTTTAAATCCAAATGTTTAAACT
1 ATAAAATACGGATGTTTTAAATCCAAATGTTTAAACT
** *
3101104 ATAAAATACGGATGTTTTAAATCTTAATGTTTGAACT
1 ATAAAATACGGATGTTTTAAATCCAAATGTTTAAACT
3101141 A
1 A
3101142 ATGGACAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (37 bp):
ATAAAATACGGATGTTTTAAATCCAAATGTTTAAACT
Found at i:3104203 original size:26 final size:26
Alignment explanation
Indices: 3104167--3104223 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3104157 CCGACCCGAA
*
3104167 CCGACCCGAATATATGAATTAGAAAT
1 CCGACCCGAATATATGAATTAGAAAC
3104193 CCGACCCGAATATATGAATTAGAAAC
1 CCGACCCGAATATATGAATTAGAAAC
3104219 CCGAC
1 CCGAC
3104224 TCGACCCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (26 bp):
CCGACCCGAATATATGAATTAGAAAC
Found at i:3104229 original size:31 final size:30
Alignment explanation
Indices: 3104160--3104230 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 30
3104150 GTTTCACCCG
3104160 ACCCGAACCGACCCGAATATATGAATTAGAA
1 ACCCG-ACCGACCCGAATATATGAATTAGAA
*
3104191 A----TCCGACCCGAATATATGAATTAGAA
1 ACCCGACCGACCCGAATATATGAATTAGAA
3104217 ACCCGACTCGACCC
1 ACCCGAC-CGACCC
3104231 TACCCTACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
26 25 0.76
30 1 0.03
31 7 0.21
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (30 bp):
ACCCGACCGACCCGAATATATGAATTAGAA
Found at i:3104437 original size:32 final size:32
Alignment explanation
Indices: 3104385--3104472 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 32
3104375 TTTTCACCCT
*
3104385 AAACCCGAACCCGACTCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAA
3104418 AAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
* *
3104450 AAACCTGACCCGAACCAGAATAT
1 AAACCCGACCCG-ACCCGAATAT
3104473 TTTTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 35 0.69
33 16 0.31
ACGTcount: A:0.42, C:0.34, G:0.10, T:0.14
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTAAA
Found at i:3104520 original size:27 final size:26
Alignment explanation
Indices: 3104467--3104524 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
3104457 ACCCGAACCA
3104467 GAATATTTTTAAAAAAATCCGACCCC
1 GAATATTTTTAAAAAAATCCGACCCC
*
3104493 GAATTTTTTTAAAAATAAATCCGA-CCC
1 GAATATTTTT-AAAA-AAATCCGACCCC
3104520 GAATA
1 GAATA
3104525 CCAAAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
27 11 0.39
28 8 0.29
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (26 bp):
GAATATTTTTAAAAAAATCCGACCCC
Found at i:3111849 original size:66 final size:65
Alignment explanation
Indices: 3111740--3111869 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 65
3111730 ACGCATAGTT
* * * * * *
3111740 CACCAGCACCAGGTGATTGGTTCAAGTTGTCTTATATTTATAATTCTCTTTTAGCAATTTGTTGT
1 CACCAGCACCAGATGATTGGCTCAAGTTGTCGTATAGTCATAA-TCCCTTTTAGCAATTTGTTGT
3111805 A
65 A
*
3111806 CACCAGCACCAGATGATTTGCTCAAGTTGTCGTATAGTCATAATCCCTTTTAGCAATTTGTTGT
1 CACCAGCACCAGATGATTGGCTCAAGTTGTCGTATAGTCATAATCCCTTTTAGCAATTTGTTGT
3111870 TTTTGGATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
65 20 0.35
66 37 0.65
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (65 bp):
CACCAGCACCAGATGATTGGCTCAAGTTGTCGTATAGTCATAATCCCTTTTAGCAATTTGTTGTA
Found at i:3122960 original size:15 final size:15
Alignment explanation
Indices: 3122940--3122970 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3122930 CAATCAGATT
*
3122940 CTTCCCTCTTTCCGA
1 CTTCCCTCTTGCCGA
3122955 CTTCCCTCTTGCCGA
1 CTTCCCTCTTGCCGA
3122970 C
1 C
3122971 CTCTGATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.48, G:0.10, T:0.35
Consensus pattern (15 bp):
CTTCCCTCTTGCCGA
Found at i:3128578 original size:9 final size:9
Alignment explanation
Indices: 3128564--3128597 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3128554 TAAGTAAAAT
3128564 ATTAAATAA
1 ATTAAATAA
3128573 ATTAAAT-A
1 ATTAAATAA
*
3128581 CTTAAATAA
1 ATTAAATAA
3128590 ATTAAATA
1 ATTAAATA
3128598 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:3128596 original size:17 final size:17
Alignment explanation
Indices: 3128560--3128598 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3128550 TATATAAGTA
3128560 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
3128576 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
3128593 AAATAC
1 AAATAC
3128599 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:3128611 original size:24 final size:25
Alignment explanation
Indices: 3128576--3128622 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
3128566 TAAATAAATT
*
3128576 AAATACTTAAATA-AATTAAATACA
1 AAATACTTAAATATAATAAAATACA
3128600 AAATA-TTAAAATATAATAAAATA
1 AAATACTT-AAATATAATAAAATA
3128623 TACCTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.50
25 8 0.40
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (25 bp):
AAATACTTAAATATAATAAAATACA
Found at i:3130082 original size:3 final size:3
Alignment explanation
Indices: 3130074--3130121 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
3130064 GCACTAGAAT
*
3130074 TTA TTA TTA TTA TTA TTT TTA TTA TTA TT- TGTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
3130119 TTA
1 TTA
3130122 GTGTTATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.02
3 39 0.95
4 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3130434 original size:18 final size:18
Alignment explanation
Indices: 3130411--3130464 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
3130401 GTTAATTCGA
*
3130411 GATGATGATGATAATAAT
1 GATGATGATAATAATAAT
3130429 GATGATGATAATAATAAT
1 GATGATGATAATAATAAT
* * *
3130447 AATAATAATAATAATAAT
1 GATGATGATAATAATAAT
3130465 AATAATAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (18 bp):
GATGATGATAATAATAAT
Found at i:3130442 original size:3 final size:3
Alignment explanation
Indices: 3130421--3130472 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
3130411 GATGATGATG
* * *
3130421 ATA ATA ATG ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3130469 ATA A
1 ATA A
3130473 ACACATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3130929 original size:21 final size:21
Alignment explanation
Indices: 3130899--3130964 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
3130889 TCATTCAATT
* *
3130899 AAAGGACTTATCCTTTTTATG
1 AAAGGACTTAACCTTTTCATG
*
3130920 AAAGGGCTTAACCTTTTCATG
1 AAAGGACTTAACCTTTTCATG
* * *
3130941 AAATGATTTAATCTTTTCAT-
1 AAAGGACTTAACCTTTTCATG
3130961 AAAG
1 AAAG
3130965 AGGATTTATG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
AAAGGACTTAACCTTTTCATG
Found at i:3133590 original size:25 final size:25
Alignment explanation
Indices: 3133560--3133659 Score: 84
Period size: 25 Copynumber: 4.0 Consensus size: 25
3133550 CTCATATAAA
* *
3133560 TTGCACCGTAGTGCCACGTAGAATT
1 TTGCACCGAAGTGCCACGTAGAAAT
*
3133585 TTGCACCGAAGTGCCGCGTAGAAAT
1 TTGCACCGAAGTGCCACGTAGAAAT
*
3133610 TTGTC-CCGAAG-GACAGCGTAG-AAT
1 TTG-CACCGAAGTGCCA-CGTAGAAAT
*
3133634 TTGTC-CCGAAG-GACCACATAGAAAT
1 TTG-CACCGAAGTG-CCACGTAGAAAT
3133659 T
1 T
3133660 CCTTAAGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
24 21 0.33
25 42 0.66
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
TTGCACCGAAGTGCCACGTAGAAAT
Found at i:3133639 original size:24 final size:25
Alignment explanation
Indices: 3133600--3133647 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
3133590 CCGAAGTGCC
3133600 GCGTAGAAATTTGTCCCGAAGGACA
1 GCGTAGAAATTTGTCCCGAAGGACA
3133625 GCGTAG-AATTTGTCCCGAAGGAC
1 GCGTAGAAATTTGTCCCGAAGGAC
3133648 CACATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (25 bp):
GCGTAGAAATTTGTCCCGAAGGACA
Found at i:3133655 original size:24 final size:24
Alignment explanation
Indices: 3133607--3133656 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3133597 GCCGCGTAGA
*
3133607 AATTTGTCCCGAAGGACAGCGTAG
1 AATTTGTCCCGAAGGACAGCATAG
3133631 AATTTGTCCCGAAGGACCA-CATAG
1 AATTTGTCCCGAAGGA-CAGCATAG
3133655 AA
1 AA
3133657 ATTCCTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACAGCATAG
Found at i:3136296 original size:23 final size:23
Alignment explanation
Indices: 3136266--3136332 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
3136256 ACTCAATTTA
*
3136266 ATTTTGCCAAGACATTTCCATGC
1 ATTTTGCCACGACATTTCCATGC
3136289 ATTTTGCCACGACATTTCCATGC
1 ATTTTGCCACGACATTTCCATGC
3136312 ATTTTGCCACGACATTTCCAT
1 ATTTTGCCACGACATTTCCAT
3136333 TTGCTACCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (23 bp):
ATTTTGCCACGACATTTCCATGC
Found at i:3141218 original size:21 final size:21
Alignment explanation
Indices: 3141194--3141247 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3141184 AATAATTCTC
* *
3141194 TTCATTAAAAGGTTAAGCCAT
1 TTCATCAAAAGGATAAGCCAT
*
3141215 TTCATCAAAAGGATAAGTCAT
1 TTCATCAAAAGGATAAGCCAT
*
3141236 TTCATCGAAAGG
1 TTCATCAAAAGG
3141248 TCTTAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TTCATCAAAAGGATAAGCCAT
Found at i:3143980 original size:2 final size:2
Alignment explanation
Indices: 3143973--3144000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3143963 ATGAACCACA
3143973 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
3144001 GCAAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3145634 original size:2 final size:2
Alignment explanation
Indices: 3145627--3145652 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3145617 ATCTAAGAAG
3145627 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
3145653 GAACTGAGGT
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:3149268 original size:40 final size:42
Alignment explanation
Indices: 3149165--3149271 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 42
3149155 TTTTAATTTT
* *
3149165 ATGTAATAACAATATTAATAAAATAATACTAATAGATGTCAC
1 ATGTTATAAAAATATTAATAAAATAATACTAATAGATGTCAC
**
3149207 ATCATA-AAAAATATTAATAAAATAATACTAACT-GATG-C-C
1 ATGTTATAAAAATATTAATAAAATAATACTAA-TAGATGTCAC
3149246 ATGTTATAAAAATATTAATAAAATAA
1 ATGTTATAAAAATATTAATAAAATAA
3149272 ATTTCAGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
39 5 0.09
40 20 0.35
41 28 0.49
42 4 0.07
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (42 bp):
ATGTTATAAAAATATTAATAAAATAATACTAATAGATGTCAC
Found at i:3151249 original size:20 final size:20
Alignment explanation
Indices: 3151226--3151274 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3151216 TGGGTTTGGG
3151226 TATCGATACTGGATGAACAA
1 TATCGATACTGGATGAACAA
*
3151246 TATCGATACTGGATGAACAT
1 TATCGATACTGGATGAACAA
*
3151266 TATTGATAC
1 TATCGATAC
3151275 CATAAGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACTGGATGAACAA
Found at i:3152316 original size:24 final size:25
Alignment explanation
Indices: 3152276--3152323 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3152266 ATTAAATGTA
3152276 TGATAATGTATG-TTTTTGTATATT
1 TGATAATGTATGATTTTTGTATATT
3152300 TGATATATG-ATGATTTTTGTATAT
1 TGATA-ATGTATGATTTTTGTATAT
3152324 GATAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (25 bp):
TGATAATGTATGATTTTTGTATATT
Found at i:3165730 original size:15 final size:14
Alignment explanation
Indices: 3165710--3165763 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
3165700 GACTAACATG
3165710 AGCTATGTGATAATA
1 AGCTATGTGAT-ATA
3165725 AGCTATGTGATTATA
1 AGCTATGTGA-TATA
* * *
3165740 TGTTTTGTGATATA
1 AGCTATGTGATATA
*
3165754 AGTTATGTGA
1 AGCTATGTGA
3165764 ATTATTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 12 0.36
15 20 0.61
16 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (14 bp):
AGCTATGTGATATA
Found at i:3169260 original size:176 final size:178
Alignment explanation
Indices: 3168966--3169321 Score: 689
Period size: 176 Copynumber: 2.0 Consensus size: 178
3168956 TATATGTGAA
3168966 CATAAGAGATCAAGATATAAGTTATATGGAAATGATCTAAGTGACTATATAAAAGATTGACATGA
1 CATAAGAGATCAAGATATAAGTTATATGGAAATGATCTAAGTGACTATATAAAAGATTGACATGA
3169031 GCTATTTGATAATAAGCTACGTGATTATGTGTTATGTGATATAAGTTATGTGAATTATTATAAAT
66 GCTATTTGATAATAAGCTACGTGATTATGTGTTATGTGATATAAGTTATGTGAATTATTATAAAT
3169096 GATAAAGCCCATAGTATGTGATAT-GAGCTGAGGGTATAATT-GCATG
131 GATAAAGCCCATAGTATGTGATATAGAGCTGAGGGTATAATTGGCATG
3169142 CATAAGAGATCAAGATATAAGTTATATGGAAATGATCTAAGTGACTATATAAAAGATTGACATGA
1 CATAAGAGATCAAGATATAAGTTATATGGAAATGATCTAAGTGACTATATAAAAGATTGACATGA
3169207 GCTATTTGATAATAAGCTACGTGATTATGTGTTATGTGATATAAGTTATGTGAATTATTATAAAT
66 GCTATTTGATAATAAGCTACGTGATTATGTGTTATGTGATATAAGTTATGTGAATTATTATAAAT
3169272 GATAAAGCCCATAGTATGTGATATGAGAGCTGAGGGTATAATTGGCATG
131 GATAAAGCCCATAGTATGTGATAT-AGAGCTGAGGGTATAATTGGCATG
3169321 C
1 C
3169322 CAAGAGTCGA
Statistics
Matches: 177, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
176 154 0.87
178 17 0.10
179 6 0.03
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (178 bp):
CATAAGAGATCAAGATATAAGTTATATGGAAATGATCTAAGTGACTATATAAAAGATTGACATGA
GCTATTTGATAATAAGCTACGTGATTATGTGTTATGTGATATAAGTTATGTGAATTATTATAAAT
GATAAAGCCCATAGTATGTGATATAGAGCTGAGGGTATAATTGGCATG
Found at i:3174887 original size:19 final size:19
Alignment explanation
Indices: 3174863--3174902 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3174853 GTATATAAAA
3174863 TAGAAGTCATGGAAATAAC
1 TAGAAGTCATGGAAATAAC
3174882 TAGAAGTCATGGAAATAAC
1 TAGAAGTCATGGAAATAAC
3174901 TA
1 TA
3174903 TAAAGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (19 bp):
TAGAAGTCATGGAAATAAC
Found at i:3180634 original size:27 final size:27
Alignment explanation
Indices: 3180604--3180746 Score: 286
Period size: 27 Copynumber: 5.3 Consensus size: 27
3180594 CGAATTCTAA
3180604 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
3180631 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
3180658 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
3180685 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
3180712 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
3180739 AAATTTAT
1 AAATTTAT
3180747 TTTTATTATG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATTTATATTATAATTATTAAATTTT
Found at i:3180776 original size:81 final size:81
Alignment explanation
Indices: 3180604--3180777 Score: 251
Period size: 81 Copynumber: 2.1 Consensus size: 81
3180594 CGAATTCTAA
*
3180604 AAATTTATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
1 AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
* *
3180669 ATAATTATTAAATTTT
66 ATAATGATTAAATGTT
* *
3180685 AAATTTATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATTTT
1 AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTA-TAT
* **
3180750 TATTATGATTTTATGTT
65 TATAATGATTAAATGTT
*
3180767 -AGTTGATATTA
1 AAATTGATATTA
3180778 AGAAAAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 70 0.83
82 14 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (81 bp):
AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
ATAATGATTAAATGTT
Found at i:3183115 original size:3 final size:3
Alignment explanation
Indices: 3183107--3183181 Score: 78
Period size: 3 Copynumber: 24.3 Consensus size: 3
3183097 CGTCCCGACT
* * *
3183107 TTA TTA TTA TTT TTA TAA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3183155 TGA GTAA TTAA TTA TTA CTA TTA TTA T
1 TTA -TTA TT-A TTA TTA TTA TTA TTA T
3183182 AAATAAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 54 0.92
4 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3184691 original size:10 final size:10
Alignment explanation
Indices: 3184676--3184706 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3184666 TATCCATGTA
3184676 ATTTTAATTT
1 ATTTTAATTT
3184686 ATTTTAATTT
1 ATTTTAATTT
3184696 ATTTTAATTT
1 ATTTTAATTT
3184706 A
1 A
3184707 GCCCCACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:3185466 original size:131 final size:127
Alignment explanation
Indices: 3185321--3185682 Score: 359
Period size: 131 Copynumber: 2.8 Consensus size: 127
3185311 ATAGATATTG
* * *
3185321 AGAATAGTAATATCTTTTCATTTCATTTGGAGTAATAAATGACTTCTATAAGGCATGAAATGTCA
1 AGAATAGTGATATCTTTTCATTTCA-TTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTCA
* * * * *
3185386 TTTATTCTCGATTAGAAATAATTTGATATTTTCATTCTCTCTCAAATTAATATTGATTTTTACGA
65 TTTATTCTCGATT-GAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTA--A
3185451 T
127 T
* * * ** *
3185452 AGAATAATGATATCTCTTT-ATTTCAATTGGAGCAATAAATGACTGCTTTAAGTTATGAGAGGTC
1 AGAATAGTGATATCT-TTTCATTTC-ATTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTC
* * * * *
3185516 ATTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAT
64 ATTTATTCTCGATT-GAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTAAT
* * ** * *
3185581 ACGGAATAGTGATATCTCTTCAATTCGATCAGAGTAATAAATTA-TTGTTTTAAGGCATGAAAGG
1 A--GAATAGTGATATCTTTTCATTTC-ATTGGAGTAATAAATGACTT-CTTTAAGGCATGAAAGG
* *
3185645 TCATTTATTGTCGATTGAAAATAATTATATATTATCAT
62 TCATTTATTCTCGATTG-AAATAATTAGATATTATCAT
3185683 GTTTCATCTA
Statistics
Matches: 187, Mismatches: 37, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
129 3 0.02
130 4 0.02
131 176 0.94
132 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (127 bp):
AGAATAGTGATATCTTTTCATTTCATTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTCAT
TTATTCTCGATTGAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTAAT
Found at i:3189173 original size:72 final size:72
Alignment explanation
Indices: 3189078--3189226 Score: 228
Period size: 72 Copynumber: 2.1 Consensus size: 72
3189068 GATGATGTAA
* * * * *
3189078 GAGATGGATTAGAGCCTGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACTA-GGGTACATGGA
1 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTAC-AGGGGCACATGCA
3189142 GCAATTAG
65 GCAATTAG
*
3189150 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTTAGAGGATTTTAGATTTACAGGGGCACATGCAG
1 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACAGGGGCACATGCAG
3189215 CAATTAG
66 CAATTAG
3189222 GAGAA
1 GAGAA
3189227 ATAGCTCAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
71 1 0.01
72 69 0.99
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (72 bp):
GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACAGGGGCACATGCAG
CAATTAG
Found at i:3198212 original size:21 final size:21
Alignment explanation
Indices: 3198187--3198265 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
3198177 AACTAGATTT
*
3198187 CCCAGAGGGAACAGATTCCCC
1 CCCAGGGGGAACAGATTCCCC
*
3198208 CCCAGGGGGTATC-GATT---C
1 CCCAGGGGG-AACAGATTCCCC
3198226 CCC---GGGAACAGATTCCCC
1 CCCAGGGGGAACAGATTCCCC
*
3198244 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGAACAGATTCCCC
3198265 C
1 C
3198266 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
14 2 0.04
15 7 0.15
18 8 0.17
21 27 0.59
22 2 0.04
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGAACAGATTCCCC
Found at i:3198234 original size:36 final size:36
Alignment explanation
Indices: 3198193--3198264 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
3198183 ATTTCCCAGA
3198193 GGGAACAGATTCCCCCCCAGGGGGTATC-GATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTA-CAGATTCCCC
3198229 GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
3198265 CTGCATGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
Found at i:3198403 original size:21 final size:21
Alignment explanation
Indices: 3198377--3198416 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3198367 ATTTGAATAT
*
3198377 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3198398 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
3198417 TCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3198480 original size:21 final size:21
Alignment explanation
Indices: 3198447--3198486 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3198437 TGTTTGCAGA
*
3198447 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3198469 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3198487 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3198740 original size:34 final size:32
Alignment explanation
Indices: 3198701--3198770 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3198691 TTTTGTAAAG
* * *
3198701 GGGAAAGGTTTTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3198735 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3198767 GGGA
1 GGGA
3198771 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3199653 original size:19 final size:20
Alignment explanation
Indices: 3199629--3199676 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3199619 AACGATTTTC
*
3199629 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3199648 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3199668 TTTTGAAAA
1 TTTTGAAAA
3199677 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3201239 original size:21 final size:21
Alignment explanation
Indices: 3201213--3201254 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3201203 ATTTGAATAT
*
3201213 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3201234 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3201255 CCTCATTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3201317 original size:21 final size:21
Alignment explanation
Indices: 3201284--3201323 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3201274 TGTTTGCAGA
*
3201284 AAAATCATTCCCAAACGGCTTC
1 AAAATCA-TCCCCAACGGCTTC
3201306 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3201324 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTTC
Found at i:3201578 original size:34 final size:32
Alignment explanation
Indices: 3201539--3201608 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3201529 TTTTGTAAAG
* * *
3201539 GGGAAAGGTTTTAGCTTATCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGGA-AAAA-CTA
*
3201573 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3201605 GGGA
1 GGGA
3201609 GTTGTAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3205442 original size:23 final size:23
Alignment explanation
Indices: 3205416--3205488 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
3205406 GGAATTGATA
3205416 CCCCCCTTGAAGGGGAACCGATT
1 CCCCCCTTGAAGGGGAACCGATT
* * *
3205439 CCCCCTTTGAATGGGAACTGATT
1 CCCCCCTTGAAGGGGAACCGATT
* * * *
3205462 -CCCCCTTGTAGGAGAATCGATA
1 CCCCCCTTGAAGGGGAACCGATT
3205484 CCCCC
1 CCCCC
3205489 TAGGGTTTCT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (23 bp):
CCCCCCTTGAAGGGGAACCGATT
Found at i:3207093 original size:18 final size:18
Alignment explanation
Indices: 3207072--3207112 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3207062 AGAACAGCAC
3207072 GAGGAACAAGCACAAACA
1 GAGGAACAAGCACAAACA
* *
3207090 GAGGAATAAGCACAACCA
1 GAGGAACAAGCACAAACA
3207108 GAGGA
1 GAGGA
3207113 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.20, G:0.27, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACAAACA
Found at i:3209798 original size:10 final size:10
Alignment explanation
Indices: 3209783--3209813 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3209773 CAAATATGAA
3209783 AAAAAGAAAG
1 AAAAAGAAAG
3209793 AAAAAGAAAG
1 AAAAAGAAAG
3209803 AAAAA-AAAG
1 AAAAAGAAAG
3209812 AA
1 AA
3209814 TAAGCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:3211301 original size:134 final size:135
Alignment explanation
Indices: 3211023--3211594 Score: 703
Period size: 134 Copynumber: 4.3 Consensus size: 135
3211013 ATTCAACTCA
* *
3211023 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAACGTCCCCAAATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * * *
3211088 AAAGTGAAACATAT--CTCTCTTTCAAGATTTAATATTCCCTA-AGTAACAGTGGAATAAGTCTG
66 GAAGCGAAACAGATCCCTCTCTTTCAAGATTTAATATTCCCTAGAGTAACAGTAGAACAAGTCTG
*
3211150 CCTCA
131 CCTCG
* *
3211155 ATTCAATTTTCCCT-AAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
** *
3211219 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGGTATTCCCTAG-GTAACAGTAGAAAAAGTCT
65 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTAATATTCCCTAGAGTAACAGTAGAACAAGTCT
3211283 GCCTCG
130 GCCTCG
*
3211289 ATTCAATCTTCCCTG-AGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* * * * * * * *
3211353 A-AAGTGGAATAAATCCCTTTCTTTCAAGAATTAATATTCCCT-GAGTAACAGTGGACCAAGTCT
65 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTAATATTCCCTAGAGTAACAGTAGAACAAGTCT
*
3211416 GCCTTG
130 GCCTCG
** * * *
3211422 ATTCAATCTTCCCTGAAGAACAGTAAAATGAATCAAAGTCCCCAGATTTGATTTTTCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * * * * *
3211487 GAAGCTAAACAGATCCCTCTCTTTCAAGATTTGATCTT-CCTTGAATAACATTAGAACAAGTCTA
66 GAAGCGAAACAGATCCCTCTCTTTCAAGATTTAATATTCCCTAGAGTAACAGTAGAACAAGTCTG
3211551 CCTCG
131 CCTCG
* ** * *
3211556 ATTCCATCTTCTTTGAAGAACATTGGAATGAGTCAACGT
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGT
3211595 TTCTTGATCT
Statistics
Matches: 375, Mismatches: 56, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
131 3 0.01
132 69 0.18
133 113 0.30
134 190 0.51
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (135 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCGAAACAGATCCCTCTCTTTCAAGATTTAATATTCCCTAGAGTAACAGTAGAACAAGTCTG
CCTCG
Found at i:3211499 original size:267 final size:266
Alignment explanation
Indices: 3211023--3211594 Score: 792
Period size: 267 Copynumber: 2.1 Consensus size: 266
3211013 ATTCAACTCA
*
3211023 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAACGTCCCCAAATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAA
* * * *
3211088 AAAGTGAAACATATCTCTCTTTCAAGATTTAATATTCCCTAAGTAACAGTGGAATAAGTCTGCCT
66 AAAGTGAAAAATACCTCTCTTTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCTGCCT
* ** *
3211153 CAATTCAATTTTCCCTAAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCAAG
131 CAATTCAATCTTCCCTAAGTAACAGTAAAATGAATCAAAGTCCCCAGATTTGATTTTCCCTCAAG
* *
3211218 AAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGGTATTCCCTAG-GTAACAGTAGAAAAAGTC
196 AAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATT-CCTAGAATAACAGTAGAAAAAGTC
*
3211282 TGCCTCG
260 TACCTCG
* *
3211289 ATTCAATCTTCCCTG-AGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAG-
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGA
* * * *
3211352 AAAAGTGGAATAAATCCCTTTCTTTCAAGAATTAATATTCCCTGAGTAACAGTGGACCAAGTCTG
65 AAAAGT-GAA-AAATACCTCTCTTTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCTG
** *
3211417 CCTTGATTCAATCTTCCCTGAAG-AACAGTAAAATGAATCAAAGTCCCCAGATTTGATTTTTCCT
128 CCTCAATTCAATCTTCCCT-AAGTAACAGTAAAATGAATCAAAGTCCCCAGATTTGATTTTCCCT
* * * * *
3211481 CAAGAAGAAGCTAAACAGATCCCTCTCTTTCAAGATTTGATCTTCCTTGAATAACATTAGAACAA
192 CAAGAAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCTAGAATAACAGTAGAAAAA
3211546 GTCTACCTCG
257 GTCTACCTCG
* ** * *
3211556 ATTCCATCTTCTTTGAAGAACATTGGAATGAGTCAACGT
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGT
3211595 TTCTTGATCT
Statistics
Matches: 268, Mismatches: 32, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
265 8 0.03
266 64 0.24
267 191 0.71
268 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (266 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTCAAGAA
AAAGTGAAAAATACCTCTCTTTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCTGCCT
CAATTCAATCTTCCCTAAGTAACAGTAAAATGAATCAAAGTCCCCAGATTTGATTTTCCCTCAAG
AAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCTAGAATAACAGTAGAAAAAGTCT
ACCTCG
Found at i:3214124 original size:131 final size:131
Alignment explanation
Indices: 3213890--3214219 Score: 426
Period size: 131 Copynumber: 2.5 Consensus size: 131
3213880 TAAATATATT
* * * * * *
3213890 TTCATTTTGGTTGGAGTTATAAACGACTGCTCTAAGGCATGAGATGTCATTTATTCTCGATTGAA
1 TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGAA
* * * * *
3213955 AATAATTCGATATTATCATTCTCTCTCGAATTAATATTGATTTTTAAGATGGAATAGTGACATCT
66 AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAGTGACATCT
3214020 C
131 C
* * *
3214021 TTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGAATGAGATGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGAA
* * * * * *
3214086 AATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAATACGGAATAGTGATATCT
66 AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAGTGACATCT
3214151 C
131 C
* * * * * *
3214152 TTCATTTCGATCGGAGTAATAAATGATTGTTTTAAGGCATGAAAGGTCATTTATTTTCGATTGAA
1 TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGAA
3214217 AAT
66 AAT
3214220 TTTTATTATT
Statistics
Matches: 170, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
131 170 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (131 bp):
TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGAA
AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAGTGACATCT
C
Found at i:3216187 original size:2 final size:2
Alignment explanation
Indices: 3216182--3216207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3216172 AAAAAACATT
3216182 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3216208 CCTTGTACCA
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):
TA
Found at i:3217817 original size:17 final size:17
Alignment explanation
Indices: 3217791--3217826 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3217781 AAGAAATTAG
*
3217791 GAGTATTTAAAATTTAA
1 GAGTACTTAAAATTTAA
3217808 GAGTACTTAAAATTTAA
1 GAGTACTTAAAATTTAA
3217825 GA
1 GA
3217827 AATTAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (17 bp):
GAGTACTTAAAATTTAA
Found at i:3231365 original size:3 final size:3
Alignment explanation
Indices: 3231357--3231425 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
3231347 TATTTTTCGT
** * * *
3231357 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA -TA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3231404 TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
3231426 AATATATATA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3231434 original size:2 final size:2
Alignment explanation
Indices: 3231427--3231454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3231417 TTATTATTAA
3231427 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
3231455 TACAAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3232081 original size:5 final size:5
Alignment explanation
Indices: 3232073--3232098 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3232063 AAAAGGGGAA
3232073 AAGAG AAGAG AAGAG AAGAG AAGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG A
3232099 GAGCTTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:3232893 original size:12 final size:12
Alignment explanation
Indices: 3232863--3232904 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
3232853 ATCACTTTTA
3232863 TATTTTAATTAT
1 TATTTTAATTAT
*
3232875 GT-CTTTAATTAT
1 -TATTTTAATTAT
3232887 TATTTT-ATTAT
1 TATTTTAATTAT
3232898 TATTTTA
1 TATTTTA
3232905 GTCTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 12 0.48
13 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:3240941 original size:22 final size:22
Alignment explanation
Indices: 3240889--3240964 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
3240879 ATCTACACTC
3240889 TTCAAAGATGATAGATTCTC-T
1 TTCAAAGATGATAGATTCTCTT
3240910 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
3240932 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3240954 TTCAAAGATGA
1 TTCAAAGATGA
3240965 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
21 20 0.38
22 32 0.62
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3241790 original size:165 final size:167
Alignment explanation
Indices: 3241478--3241802 Score: 505
Period size: 165 Copynumber: 2.0 Consensus size: 167
3241468 AAAATGAGCA
*
3241478 TTATCTTCAGATTGGGTCATGTTACCCAATCAACATGTTATTTAAAAAAAACAGAATGAGAAAAC
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTT-AAAAAAACAGAATGAGAAAAC
**
3241543 GATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
65 GATTTTCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
* *
3241608 TCTTAGTTTTTTTACTTAGTAAACTATTTCTAACAGCC
130 TCATAGTTTTCTTACTTAGTAAACTATTTCTAACAGCC
* * ** *
3241646 TTATCTTGAGATTGGGGCATTTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGAAAACG
3241709 A-TTTCTATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATT
66 ATTTTC-ATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATT
3241773 TTCATAG-TTTCTTACTTAGTAAACTATTTC
129 TTCATAGTTTTCTTACTTAGTAAACTATTTC
3241803 CCACATCTGT
Statistics
Matches: 145, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
164 4 0.03
165 58 0.40
166 43 0.30
168 40 0.28
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (167 bp):
TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGAAAACG
ATTTTCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
CATAGTTTTCTTACTTAGTAAACTATTTCTAACAGCC
Found at i:3241932 original size:76 final size:76
Alignment explanation
Indices: 3241806--3242670 Score: 1561
Period size: 76 Copynumber: 11.4 Consensus size: 76
3241796 CTATTTCCCA
3241806 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
3241871 AACCTTAGGGT
66 AGCCTTCGGGT
3241882 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3241947 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3241958 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3242023 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3242034 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3242099 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
3242110 CATCTGTAAGTCCTACAGTGAATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3242175 AGCCTTCGGGT
66 AGCCTTCGGGT
3242186 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3242251 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
3242262 CATCTGTAAGTCCTGCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3242327 AGCCTTTGGGT
66 AGCCTTCGGGT
3242338 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3242403 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3242414 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3242479 AGCCTTAGGGT
66 AGCCTTCGGGT
* *
3242490 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3242555 AGCCTTAGGGT
66 AGCCTTCGGGT
*
3242566 CATCTGTAAGTCCTGCAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3242631 AGCCTTAGGGT
66 AGCCTTCGGGT
* *
3242642 CATCTGTAAGCCCT-TAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
3242671 TTAAGGCCTC
Statistics
Matches: 765, Mismatches: 24, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
75 13 0.02
76 752 0.98
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:3242824 original size:3 final size:3
Alignment explanation
Indices: 3242816--3242881 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
3242806 AATTTTTCGT
** * * *
3242816 TTA TTA TTA TTA AAA TTA TTA TTA TTA TAA ATA TTA TTA TTA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3242863 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
3242882 AATATATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3243533 original size:5 final size:5
Alignment explanation
Indices: 3243523--3243548 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3243513 AAAAGGGGAA
3243523 AAGAG AAGAG AAGAG AAGAG AAGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG A
3243549 GAGCTTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:3250818 original size:23 final size:23
Alignment explanation
Indices: 3250770--3250819 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3250760 TATTTTATTT
** *
3250770 AAATAAATTAAAATTATAAATCA
1 AAATAAAAAAAAATTAAAAATCA
*
3250793 AAATAAAAAAAAATTTAAAAATAA
1 AAATAAAAAAAAA-TTAAAAATCA
3250817 AAA
1 AAA
3250820 ATTGTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATAAAAAAAAATTAAAAATCA
Found at i:3254194 original size:2 final size:2
Alignment explanation
Indices: 3254187--3254223 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3254177 GGATCGGGAC
3254187 TA TA 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 TA TA T
3254224 TCTCATATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3255276 original size:6 final size:6
Alignment explanation
Indices: 3255265--3255293 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3255255 AAATCACAAT
3255265 GGATTA GGATTA GGATTA GGATTA GGATT
1 GGATTA GGATTA GGATTA GGATTA GGATT
3255294 TAGATACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (6 bp):
GGATTA
Found at i:3259331 original size:22 final size:22
Alignment explanation
Indices: 3259301--3259422 Score: 163
Period size: 22 Copynumber: 5.5 Consensus size: 22
3259291 GGCATGTGAA
* *
3259301 ATATATCCCGAAGGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
3259323 ATATGTCCCGAAAGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* * *
3259345 ATATATCCCGAAGGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
3259367 ATATGTCCCGAATGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* *
3259389 ATATGTCCTGAAAGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
3259411 ATATGTCTCGAA
1 ATATGTCCCGAA
3259423 TGACTTATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (22 bp):
ATATGTCCCGAAAGACCTCTGT
Found at i:3259368 original size:44 final size:44
Alignment explanation
Indices: 3259301--3259422 Score: 190
Period size: 44 Copynumber: 2.8 Consensus size: 44
3259291 GGCATGTGAA
*
3259301 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTCTGT
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
*
3259345 ATATATCCCGAAGGACCTATGTATATGTCCCGAATGACCTCTGT
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
* * * *
3259389 ATATGTCCTGAAAGACCTATGTATATGTCTCGAA
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAA
3259423 TGACTTATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
Found at i:3259389 original size:66 final size:66
Alignment explanation
Indices: 3259301--3259433 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
3259291 GGCATGTGAA
*
3259301 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTCTGTATATATCCCGAAGGACCTATG
1 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
3259366 T
66 T
* * * * * * *
3259367 ATATGTCCCGAATGACCTCTGTATATGTCCTGAAAGACCTATGTATATGTCTCGAATGACTTATG
1 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
3259432 T
66 T
3259433 A
1 A
3259434 ACTCTCGACT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (66 bp):
ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
T
Found at i:3262651 original size:54 final size:54
Alignment explanation
Indices: 3262593--3262983 Score: 566
Period size: 54 Copynumber: 7.2 Consensus size: 54
3262583 GATGCACATG
* * * *
3262593 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCCGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* * *
3262647 TAGTGCCTATACGGTTGTTCATCAACTCATGATAAATTCCGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* * * *
3262701 TAGTGCTTGTATGGTTGTTCATCAACTCATGATGAATTTCATGGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGG-TTGCACACA
* * * *
3262756 TAGTACTTGTACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
3262810 TAGTGCATGTACGATTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGG-TTGCACACA
*
3262865 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
3262919 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
3262973 TAATGCCTGTA
1 TAGTGCATGTA
3262984 GTACACATAA
Statistics
Matches: 308, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
54 207 0.67
55 101 0.33
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (54 bp):
TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
Found at i:3262794 original size:109 final size:109
Alignment explanation
Indices: 3262593--3262983 Score: 581
Period size: 109 Copynumber: 3.6 Consensus size: 109
3262583 GATGCACATG
* * * * * * *
3262593 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCCGTGGG-TTGCACACATAGTGCCTAT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
* *
3262657 ACGGTTGTTCATCAACTCATGATAAATTCCGTGGGTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * * * *
3262701 TAGTGCTTGTATGGTTGTTCATCAACTCATGATGAATTTCATGGGTTTGCACACATAGTACTTGT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
*
3262766 ACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
*
3262810 TAGTGCATGTACGATTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
3262875 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * *
3262919 TAGTGCATGTACGGTTATTCATCAACTCATGATGAA-TTCTGTGGG-TTGCACACATAATGCCTG
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTC-GTGGGTTTGCACACATAGTGCATG
3262982 TA
65 TA
3262984 GTACACATAA
Statistics
Matches: 257, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
108 59 0.23
109 198 0.77
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (109 bp):
TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
Found at i:3262913 original size:163 final size:163
Alignment explanation
Indices: 3262602--3262983 Score: 586
Period size: 163 Copynumber: 2.3 Consensus size: 163
3262592 GTAGTGCCTA
* * * *
3262602 TACGGTCGTTCATCAACACATGATGAATTCCGTGGGTTGCACACATAGTGCCTATACGGTTGTTC
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
* *
3262667 ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCTTGTATGGTTGTTCATCAACTCATG
66 ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCATG
* *
3262732 ATGAATTTCATGGGTTTGCACACATAGTACTTG
131 ATGAATTCCATGGGTTTGCACACATAGTACATG
* * *
3262765 TACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACATAGTGCATGTACGATTGTTC
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
* *
3262830 ATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCAT
66 ATCAACTCATGATAAATTCCGTGGG-TTGCACACATAGTGCATGTACGGTTGTTCATCAACTCAT
* *
3262895 GATGAATTCCGT-GGTTTGCACACATAGTGCATG
130 GATGAATTCCATGGGTTTGCACACATAGTACATG
* * *
3262928 TACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAATGCCTGTA
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTA
3262984 GTACACATAA
Statistics
Matches: 197, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
163 150 0.76
164 47 0.24
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (163 bp):
TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCATG
ATGAATTCCATGGGTTTGCACACATAGTACATG
Found at i:3264786 original size:21 final size:21
Alignment explanation
Indices: 3264760--3264862 Score: 125
Period size: 21 Copynumber: 4.9 Consensus size: 21
3264750 ATAAAATTTG
* * **
3264760 TCCCGAAGAACCTCATGCATA
1 TCCCGAAGGACCTCGTATATA
* *
3264781 TCCCGAAAGACCTCGTGTATA
1 TCCCGAAGGACCTCGTATATA
*
3264802 TCCTGAAGGACCTCGTATATA
1 TCCCGAAGGACCTCGTATATA
*
3264823 TCCTGAAGGACCTCGTATATA
1 TCCCGAAGGACCTCGTATATA
*
3264844 TCCCGAAGGACCTCATATA
1 TCCCGAAGGACCTCGTATA
3264863 ACCCTCGACT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (21 bp):
TCCCGAAGGACCTCGTATATA
Found at i:3265591 original size:24 final size:24
Alignment explanation
Indices: 3265559--3265636 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
3265549 CCATGATCGT
3265559 TATCGATACTACTTTACATAGTAG
1 TATCGATACTACTTTACATAGTAG
* **
3265583 TATCGATACT-CCTTGGAT-G-A-
1 TATCGATACTACTTTACATAGTAG
**
3265603 TATCGATACTACTACACATAGTAG
1 TATCGATACTACTTTACATAGTAG
3265627 TATCGATACT
1 TATCGATACT
3265637 CCTTGAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 10 0.24
21 4 0.10
22 2 0.05
23 6 0.14
24 20 0.48
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (24 bp):
TATCGATACTACTTTACATAGTAG
Found at i:3265608 original size:44 final size:44
Alignment explanation
Indices: 3265559--3265656 Score: 153
Period size: 44 Copynumber: 2.2 Consensus size: 44
3265549 CCATGATCGT
**
3265559 TATCGATACTACTTTACATAGTAGTATCGATACTCCTTG-GATGA
1 TATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGA-GA
*
3265603 TATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGAGG
1 TATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGAGA
3265647 TATCGATACT
1 TATCGATACT
3265657 GTTGGGTTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 48 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (44 bp):
TATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGAGA
Found at i:3279533 original size:12 final size:12
Alignment explanation
Indices: 3279516--3279540 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3279506 AATGAATTTT
3279516 AAGATTTTCCAA
1 AAGATTTTCCAA
3279528 AAGATTTTCCAA
1 AAGATTTTCCAA
3279540 A
1 A
3279541 GTATAATCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AAGATTTTCCAA
Found at i:3287207 original size:18 final size:18
Alignment explanation
Indices: 3287186--3287226 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3287176 AGAACAACAC
*
3287186 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
3287204 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
3287222 GAGGA
1 GAGGA
3287227 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.29, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:3293595 original size:18 final size:18
Alignment explanation
Indices: 3293564--3293598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3293554 ACTGAAAATT
* *
3293564 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
3293582 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3293599 TATAATCTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3295294 original size:15 final size:16
Alignment explanation
Indices: 3295269--3295322 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 16
3295259 TCGATACTTG
3295269 CCTTATGGTATCGATAC
1 CCTT-TGGTATCGATAC
3295286 CC-TTGGTATCGAATCTAC
1 CCTTTGGTATCG-A--TAC
3295304 CCTTTAGGTATCGATAC
1 CCTTT-GGTATCGATAC
3295321 CC
1 CC
3295323 CTTGAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 8 0.25
16 2 0.06
17 7 0.22
18 5 0.16
19 3 0.09
20 7 0.22
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (16 bp):
CCTTTGGTATCGATAC
Found at i:3295595 original size:19 final size:20
Alignment explanation
Indices: 3295571--3295608 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3295561 TCATATAACA
3295571 CATCCT-TATCTTCAAATCT
1 CATCCTATATCTTCAAATCT
*
3295590 CATCCTATATCTTGAAATC
1 CATCCTATATCTTCAAATC
3295609 AAGAATCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (20 bp):
CATCCTATATCTTCAAATCT
Found at i:3301535 original size:47 final size:47
Alignment explanation
Indices: 3301466--3301586 Score: 242
Period size: 47 Copynumber: 2.6 Consensus size: 47
3301456 GTAGTTTGAG
3301466 TAGAACATTTAAATAATTAAGTGGTATCTTCCGTTAGATGGTTGGAT
1 TAGAACATTTAAATAATTAAGTGGTATCTTCCGTTAGATGGTTGGAT
3301513 TAGAACATTTAAATAATTAAGTGGTATCTTCCGTTAGATGGTTGGAT
1 TAGAACATTTAAATAATTAAGTGGTATCTTCCGTTAGATGGTTGGAT
3301560 TAGAACATTTAAATAATTAAGTGGTAT
1 TAGAACATTTAAATAATTAAGTGGTAT
3301587 GATTGATAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (47 bp):
TAGAACATTTAAATAATTAAGTGGTATCTTCCGTTAGATGGTTGGAT
Found at i:3306897 original size:35 final size:35
Alignment explanation
Indices: 3306856--3306935 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
3306846 AACACATTCA
* *
3306856 TCAATTATATTTTAAATCC-CAAATTCCAAAACATT
1 TCAATTATATTCTAAA-CCTCAAATTCCAAAACACT
* *
3306891 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTATATTCTAAACCTCAAATTCCAAAACACT
3306926 TCAATTATAT
1 TCAATTATAT
3306936 ACCCAACCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 2 0.05
35 37 0.95
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (35 bp):
TCAATTATATTCTAAACCTCAAATTCCAAAACACT
Found at i:3306949 original size:35 final size:35
Alignment explanation
Indices: 3306873--3306951 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 35
3306863 TATTTTAAAT
* * *
3306873 CCCAAATTCCAAAACATTTCAATTACATTCTAAAC
1 CCCAAATTCCAAAACACTTCAATTACATACCAAAC
* * * *
3306908 CTCAAATTCCAAAATACTTCAATTATATACCCAAC
1 CCCAAATTCCAAAACACTTCAATTACATACCAAAC
3306943 CCCAAATTC
1 CCCAAATTC
3306952 ATAATCCATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (35 bp):
CCCAAATTCCAAAACACTTCAATTACATACCAAAC
Found at i:3309544 original size:11 final size:11
Alignment explanation
Indices: 3309528--3309553 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3309518 ATTATAGTTT
3309528 TAATAAAATTA
1 TAATAAAATTA
3309539 TAATAAAATTA
1 TAATAAAATTA
3309550 TAAT
1 TAAT
3309554 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATTA
Found at i:3309563 original size:28 final size:26
Alignment explanation
Indices: 3309517--3309570 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
3309507 TTTAAAATTT
3309517 AATTATAGTTTTAATAAAATTATAATAA
1 AATTATAGTTTTAATAAAA--ATAATAA
*
3309545 AATTATAATTTTTAA-AAAAATAATAA
1 AATTAT-AGTTTTAATAAAAATAATAA
3309571 TTAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.29
28 10 0.42
29 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AATTATAGTTTTAATAAAAATAATAA
Found at i:3309576 original size:28 final size:28
Alignment explanation
Indices: 3309515--3309585 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
3309505 TGTTTAAAAT
* * *
3309515 TTAATTAT-AGTTTTAATAAAATTATAA
1 TTAATTATAATTTTTAAAAAAATAATAA
*
3309542 TAAAATTATAATTTTTAAAAAAATAATAA
1 T-TAATTATAATTTTTAAAAAAATAATAA
3309571 TTAATT-TAATCTTTT
1 TTAATTATAAT-TTTT
3309586 TAGAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.14
28 14 0.39
29 17 0.47
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TTAATTATAATTTTTAAAAAAATAATAA
Found at i:3309809 original size:29 final size:30
Alignment explanation
Indices: 3309753--3309810 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3309743 AAATTATACA
*
3309753 TTTAGTACCTAAACTATTACTTTATTTCAT
1 TTTAGTACCTAAACTATTAATTTATTTCAT
*
3309783 TTTAGTACCTCAACT-TTCAATTT-TTTCA
1 TTTAGTACCTAAACTATT-AATTTATTTCA
3309811 AAACCATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (30 bp):
TTTAGTACCTAAACTATTAATTTATTTCAT
Found at i:3311344 original size:17 final size:18
Alignment explanation
Indices: 3311312--3311345 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3311302 TAAAATTATA
*
3311312 ATTAATTTTTAATAAATG
1 ATTAATTTTAAATAAATG
3311330 ATTAA-TTTAAATAAAT
1 ATTAATTTTAAATAAAT
3311346 TTTTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTTTAAATAAATG
Found at i:3315512 original size:46 final size:46
Alignment explanation
Indices: 3315460--3315731 Score: 404
Period size: 46 Copynumber: 5.9 Consensus size: 46
3315450 ACCGCTATGT
* ** * *
3315460 ATTTTCATTTGTGGTATCCTTTAATGA-CAATTATGAACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCAT-ACCAATTATGCACTGTTATAC
* * *
3315506 ATTTTCATTTAT-AGCATCCTTTCATATCAATTATGAATTGTTATAC
1 ATTTTCATTTATGA-CATCCTTTCATACCAATTATGCACTGTTATAC
*
3315552 ATTTTCATTTATGACATCATTTCATACCAATTATGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
3315598 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
3315644 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
* * *
3315690 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGTT
1 ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTT
3315732 CTTCATCTAA
Statistics
Matches: 210, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
45 1 0.00
46 208 0.99
47 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGACATCCTTTCATACCAATTATGCACTGTTATAC
Found at i:3316122 original size:53 final size:53
Alignment explanation
Indices: 3315953--3316261 Score: 404
Period size: 55 Copynumber: 5.7 Consensus size: 53
3315943 TACGTTAATA
* * * *
3315953 CATAAACTTGTTATGAATTTCTTAATTTT-CACACAGTGTCCATACAGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCACACAGTGCCCATACGGAAATT
* * *
3316005 CATAAACTTATTATGAATTTCTTAGTTTTGCACATAAAGTGCCTATACAGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCAC--ACAGTGCCCATACGGAAATT
*
3316060 CATAAACTTATTATGAATTTCTTCGTTTTGCACACAGTGCCCATACGGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCACACAGTGCCCATACGGAAATT
* *
3316113 CATAAACTTATTATGAATTTCTTTGTTTTGCACACACATAGTGCCCATACGAAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTG--CACAC--AGTGCCCATACGGAAATT
* * *
3316170 CATAAACTTATAATGAATTTCTTCGTTTTGCACACACAGTGCCCATACGAAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTG--CACACAGTGCCCATACGGAAATT
*
3316225 CATAAACTTATTATGAATTTCTTAATTTTTGCACACA
1 CATAAACTTATTATGAATTTCTT-AGTTTTGCACACA
3316262 CAATACCATT
Statistics
Matches: 233, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
52 27 0.12
53 49 0.21
54 6 0.03
55 94 0.40
56 5 0.02
57 52 0.22
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (53 bp):
CATAAACTTATTATGAATTTCTTAGTTTTGCACACAGTGCCCATACGGAAATT
Found at i:3322051 original size:81 final size:81
Alignment explanation
Indices: 3321896--3322052 Score: 181
Period size: 81 Copynumber: 1.9 Consensus size: 81
3321886 TAAAATTCCT
* ** * *
3321896 TTATTCTCTTACTCAACAGTGTTTAACCCTTTATCTAACTGGCATAATTGACACTTTTCTGCCAA
1 TTATTCTCTTACTCAACAATACTTAACCCTTCATCTAACTGACATAATTGACACTTTTCTGCCAA
*
3321961 TTGCTCAGTTAAACCA
66 TTGCACAGTTAAACCA
* * * * *
3321977 TTATTCTTTTACTCAACAATACTTAATCGTTCATCTATCTGACATAATTGATACATTTT-TGCCA
1 TTATTCTCTTACTCAACAATACTTAACCCTTCATCTAACTGACATAATTGACAC-TTTTCTGCCA
* *
3322041 GTTTCACAGTTA
65 ATTGCACAGTTA
3322053 GGCTTTAAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
81 58 0.94
82 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (81 bp):
TTATTCTCTTACTCAACAATACTTAACCCTTCATCTAACTGACATAATTGACACTTTTCTGCCAA
TTGCACAGTTAAACCA
Found at i:3322081 original size:68 final size:68
Alignment explanation
Indices: 3321997--3322123 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 68
3321987 ACTCAACAAT
* * * * *
3321997 ACTTAATCGTTCATCTATCTGACATAATTGATACATTTTTGCCAGTTTCACAGTTAGGCTTTAAA
1 ACTTAATCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTTCACAGCTAGGCTTTAAA
3322062 GAC
66 GAC
* * *
3322065 ACTTAGTCTTTCATCTAACTGACATAATTGACACATTTCTGTCAATTTCACAGCTAGGC
1 ACTTAATCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTTCACAGCTAGGC
3322124 CATTACATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (68 bp):
ACTTAATCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTTCACAGCTAGGCTTTAAA
GAC
Found at i:3322732 original size:45 final size:45
Alignment explanation
Indices: 3322516--3322770 Score: 298
Period size: 45 Copynumber: 5.7 Consensus size: 45
3322506 CTCTAACATT
* * * * *
3322516 TTTTCTTTTGATAATGCACCAATATTCATTTCAAATATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGTATAC
* * *
3322561 TTTTATGTTGATAATGTACCCATATACATCTCAAC-CATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTC-TAGTATAC
* *
3322606 TTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGTATAC
* *
3322651 TTTTCTGTTGATAATTCACCCATATGCATTTCAACTCTAGTATAC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGTATAC
* * * *
3322696 TTTTTTGTTGATAATGCACCCATATGCATTTCAACTCTGGCAT-C
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGTATAC
* ***
3322740 CTTTCATGCCAATAATGCACCCATATACATT
1 TTTTC-TGTTGATAATGCACCCATATACATT
3322771 ATTCTATTAT
Statistics
Matches: 182, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
44 4 0.02
45 177 0.97
46 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATACATTTCAACTCTAGTATAC
Found at i:3322841 original size:79 final size:79
Alignment explanation
Indices: 3322705--3323017 Score: 464
Period size: 79 Copynumber: 4.0 Consensus size: 79
3322695 CTTTTTTGTT
* * * * ** *
3322705 GATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATACAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
*
3322770 TATTCTATTATGCC
66 TATTCTTTTATGCC
* * *
3322784 GATAATGTACCCATATACATATCAGTTAAGGCATCCTTTCATGCCACTAATGAACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
*
3322849 TATTCTTTTATGTC
66 TATTCTTTTATGCC
* * * * *
3322863 GATAATATACCCATATACATATCAACTAAGGTATCATTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
*
3322928 TATTCTTTTATGCT
66 TATTCTTTTATGCC
3322942 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
3323007 TATTCTTTTAT
66 TATTCTTTTAT
3323018 TCATTAGTTT
Statistics
Matches: 209, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 209 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (79 bp):
GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
TATTCTTTTATGCC
Found at i:3327282 original size:68 final size:68
Alignment explanation
Indices: 3327164--3327290 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 68
3327154 ACTCAACGAT
* ** * *
3327164 ACTTAGTCGTTCATCTATCTGACATAATTGACATTTTTTTGCCAAATTCACAGTTAGGCTTTAAA
1 ACTTAGTCGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATTCACAGCTAGGCTTTAAA
3327229 GAC
66 GAC
* * *
3327232 ACTTAGTCTTTCATCTAACTGACATAATTGACACATTTCTGTCAATTTCACAGCTAGGC
1 ACTTAGTCGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATTCACAGCTAGGC
3327291 CATTACATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (68 bp):
ACTTAGTCGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATTCACAGCTAGGCTTTAAA
GAC
Found at i:3327785 original size:44 final size:44
Alignment explanation
Indices: 3327680--3327845 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 44
3327670 ACCCTAACAT
* *
3327680 CTTTTTTGTTGATAATGCACCCATATACATCTCAGC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCA-CTC-TAGTATA
* *
3327725 CTTTTCTGTTGATAATGTACCCATATACATTTCACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCACTCTAGTATA
** * *
3327769 CTTTTCTGTTGATAATGCAATCATATGCATTCCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTC-ACTCTAGTATA
* *
3327814 CTTTTCTGTTAATAATGCACCCATATGCATTT
1 CTTTTCTGTTGATAATGCACCCATATACATTT
3327846 TAACTTTGGC
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
44 35 0.33
45 70 0.67
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (44 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCACTCTAGTATA
Found at i:3327915 original size:79 final size:79
Alignment explanation
Indices: 3327825--3328136 Score: 435
Period size: 79 Copynumber: 3.9 Consensus size: 79
3327815 TTTTCTGTTA
* * * * ** *
3327825 ATAATGCACCCATATGCATTTTAACTTTGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATT
*
3327890 ATTCTGTTATGCCG
66 ATTCTTTTATGCCG
* * * * *
3327904 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGTCACTAATACACCCACATGTATT
1 ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATT
*
3327969 TTTCTTTTATGCCG
66 ATTCTTTTATGCCG
* * * * *
3327983 ACAATATAACCATATACATATCATCTAAGGCATCCTTTCATGCCACTAATACACCCATATGCATT
1 ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATT
*
3328048 ATTCTTTTATGCTG
66 ATTCTTTTATGCCG
*
3328062 ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATT
3328127 ATTCTTTTAT
66 ATTCTTTTAT
3328137 TCATTAGTTT
Statistics
Matches: 204, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 204 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
ATAATGTACCCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATT
ATTCTTTTATGCCG
Found at i:3328041 original size:45 final size:44
Alignment explanation
Indices: 3327992--3328121 Score: 111
Period size: 45 Copynumber: 3.1 Consensus size: 44
3327982 GACAATATAA
*
3327992 CCATATACATATCATCTAAGGCATCCTTTCATGCCACTAATACAC
1 CCATATACATATCATCTAAGGCATCCTTTCATGCCA-TAATGCAC
* * *
3328037 CCATATGCAT-T-AT-T----C-T--TTT-ATGCTGATAATGTAC
1 CCATATACATATCATCTAAGGCATCCTTTCATGC-CATAATGCAC
*
3328071 CCATATACATATCAACTAAGGCATCCTTTCATGCCAATAATGCAC
1 CCATATACATATCATCTAAGGCATCCTTTCATGCC-ATAATGCAC
3328116 CCATAT
1 CCATAT
3328122 GCATTATTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 26
0.65 0.08 0.27
Matches are distributed among these distances:
34 19 0.30
35 5 0.08
36 1 0.02
37 2 0.03
38 1 0.02
41 1 0.02
42 2 0.03
43 2 0.03
44 4 0.06
45 27 0.42
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (44 bp):
CCATATACATATCATCTAAGGCATCCTTTCATGCCATAATGCAC
Found at i:3328939 original size:21 final size:21
Alignment explanation
Indices: 3328900--3328940 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3328890 TCTACTGAAA
*
3328900 CTCCACCTGTTTTAGAGTATG
1 CTCCACCTGTTTGAGAGTATG
3328921 CTCCACCTGTTGTGA-AGTAT
1 CTCCACCTGTT-TGAGAGTAT
3328941 TACTTGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (21 bp):
CTCCACCTGTTTGAGAGTATG
Found at i:3333261 original size:22 final size:21
Alignment explanation
Indices: 3333222--3333262 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3333212 TTTATTAAGT
**
3333222 TATATATAATATTTTATGTAA
1 TATATATAATATAATATGTAA
3333243 TATATATACATATAATATGT
1 TATATATA-ATATAATATGT
3333263 TGCCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATATAATATAATATGTAA
Found at i:3333343 original size:97 final size:96
Alignment explanation
Indices: 3333240--3333537 Score: 228
Period size: 97 Copynumber: 3.1 Consensus size: 96
3333230 ATATTTTATG
3333240 TAATATATATACATATAATATGTTGCCAATTTTAATTAAGTATTGGACTTAGCATAACGGTTAGA
1 TAATATATATACATATAATATGTTGCCAATTTTAATTAAGTA-TGGACTTAGCATAACGGTTAGA
3333305 ATTAAACCTTTTCTTTCTTTAATTTTCACTAA
65 ATTAAACCTTTTCTTTCTTTAATTTTCACTAA
* * * * *** * *
3333337 TAATATATATTGTCAATTTAAGCTAAGTGATG--AAGTTGGCTT-AGTAT--A-TTA-TATATC-
1 TAATATATA-T-AC-ATATAA--T-A-TGTTGCCAATTTTAATTAAGTATGGACTTAGCATAACG
* * * * * * *
3333394 ATTA-TATT-AA-TTTATTAAGTTATATATATATTTT-A-T-G
59 GTTAGAATTAAACCTT-TT--CTT-TCTTTA-ATTTTCACTAA
3333431 TAATATATATACATATAATATGTTGCCAATTTTAATTAAGTACTGGACTTAGCATAACGGTTAGA
1 TAATATATATACATATAATATGTTGCCAATTTTAATTAAGTA-TGGACTTAGCATAACGGTTAGA
3333496 ATTAAACCTTTTCTTTCTTTAATTTTCACTAA
65 ATTAAACCTTTTCTTTCTTTAATTTTCACTAA
3333528 TAATATATAT
1 TAATATATAT
3333538 TGTCAATCTT
Statistics
Matches: 142, Mismatches: 32, Indels: 54
0.62 0.14 0.24
Matches are distributed among these distances:
87 4 0.03
88 1 0.01
89 7 0.05
90 4 0.03
91 6 0.04
92 3 0.02
93 6 0.04
94 20 0.14
95 15 0.11
96 15 0.11
97 30 0.21
98 6 0.04
99 3 0.02
100 6 0.04
101 4 0.03
102 7 0.05
103 1 0.01
104 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (96 bp):
TAATATATATACATATAATATGTTGCCAATTTTAATTAAGTATGGACTTAGCATAACGGTTAGAA
TTAAACCTTTTCTTTCTTTAATTTTCACTAA
Found at i:3333447 original size:191 final size:194
Alignment explanation
Indices: 3333189--3333574 Score: 742
Period size: 191 Copynumber: 2.0 Consensus size: 194
3333179 TAAGTATATA
3333189 ATATTATATATCATTATATTTAATTTATTAAGTTATATATAATATTTTATGTAATATATATACAT
1 ATATTATATATCATTATATTTAATTTATTAAGTTATATATAATATTTTATGTAATATATATACAT
*
3333254 ATAATATGTTGCCAATTTTAATTAAGTATTGGACTTAGCATAACGGTTAGAATTAAACCTTTTCT
66 ATAATATGTTGCCAATTTTAATTAAGTACTGGACTTAGCATAACGGTTAGAATTAAACCTTTTCT
3333319 TTCTTTAATTTTCACTAATAATATATATTGTCAAT-TTAAGCTAAGTGATGAAGTTGGCTTAGT
131 TTCTTTAATTTTCACTAATAATATATATTGTCAATCTTAAGCTAAGTGATGAAGTTGGCTTAGT
3333382 ATATTATATATCATTATA-TTAATTTATTAAGTTATATAT-ATATTTTATGTAATATATATACAT
1 ATATTATATATCATTATATTTAATTTATTAAGTTATATATAATATTTTATGTAATATATATACAT
3333445 ATAATATGTTGCCAATTTTAATTAAGTACTGGACTTAGCATAACGGTTAGAATTAAACCTTTTCT
66 ATAATATGTTGCCAATTTTAATTAAGTACTGGACTTAGCATAACGGTTAGAATTAAACCTTTTCT
3333510 TTCTTTAATTTTCACTAATAATATATATTGTCAATCTTAAGCTAAGTGATGAAGTTGGCTTAGT
131 TTCTTTAATTTTCACTAATAATATATATTGTCAATCTTAAGCTAAGTGATGAAGTTGGCTTAGT
3333574 A
1 A
3333575 GTTACTAGTT
Statistics
Matches: 191, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
191 123 0.64
192 50 0.26
193 18 0.09
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (194 bp):
ATATTATATATCATTATATTTAATTTATTAAGTTATATATAATATTTTATGTAATATATATACAT
ATAATATGTTGCCAATTTTAATTAAGTACTGGACTTAGCATAACGGTTAGAATTAAACCTTTTCT
TTCTTTAATTTTCACTAATAATATATATTGTCAATCTTAAGCTAAGTGATGAAGTTGGCTTAGT
Found at i:3333872 original size:21 final size:21
Alignment explanation
Indices: 3333842--3333893 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3333832 TTAATATTAT
* *
3333842 TTAAATAATTAAATGATTTGA
1 TTAAAAAATTAAATGAATTGA
* *
3333863 TTAAAAAATTTAATTTAATTGA
1 TTAAAAAA-TTAAATGAATTGA
3333885 TTAAAAAAT
1 TTAAAAAAT
3333894 CACTTTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
TTAAAAAATTAAATGAATTGA
Found at i:3335292 original size:2 final size:2
Alignment explanation
Indices: 3335285--3335332 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
3335275 TGAAACATGA
*
3335285 AT AT AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3335325 AT AT AT AT
1 AT AT AT AT
3335333 TCATGGAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3335956 original size:29 final size:26
Alignment explanation
Indices: 3335897--3335956 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
3335887 ACTTTAATGG
* *
3335897 CAAAATTATATACAATAAAAAACAGG
1 CAAAATTATATACAATAAAAAAAAGA
3335923 CAAAATATATATACAATAAAAAGCAAAGA
1 CAAAAT-TATATACAATAAAAA--AAAGA
3335952 CAAAA
1 CAAAA
3335957 AATAAGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 15 0.52
29 8 0.28
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.17
Consensus pattern (26 bp):
CAAAATTATATACAATAAAAAAAAGA
Found at i:3336136 original size:14 final size:14
Alignment explanation
Indices: 3336119--3336248 Score: 50
Period size: 14 Copynumber: 9.2 Consensus size: 14
3336109 TGCATTAATC
*
3336119 AAAGGACTAAAATT
1 AAAGGAATAAAATT
*** *
3336133 AAAGTTCTGAAAT-
1 AAAGGAATAAAATT
* *
3336146 AAAGGAAAAAAATA
1 AAAGGAATAAAATT
**
3336160 AAAAAAATAAAATT
1 AAAGGAATAAAATT
* *
3336174 AAAGTAATGAAATT
1 AAAGGAATAAAATT
*
3336188 --AGGACTAAAATT
1 AAAGGAATAAAATT
** *
3336200 AAATAAATAAAAACT
1 AAAGGAAT-AAAATT
*
3336215 AAAGGATAGAAAATT
1 AAAGGA-ATAAAATT
*
3336230 AAATGTGCATAAAATT
1 AAA-G-GAATAAAATT
3336246 AAA
1 AAA
3336249 TAACAAAAGT
Statistics
Matches: 81, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
12 9 0.11
13 8 0.10
14 34 0.42
15 17 0.21
16 12 0.15
17 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (14 bp):
AAAGGAATAAAATT
Found at i:3338400 original size:130 final size:131
Alignment explanation
Indices: 3338157--3338515 Score: 427
Period size: 130 Copynumber: 2.7 Consensus size: 131
3338147 CAATATTATC
* * *
3338157 AACATATTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAATTTCAAAATTACAA
1 AACAT-TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCGAAATTATAA
* * * * * * * *
3338222 GTATCGATAC-TTATATGA-CAATATCAATATTTGTACATTTACATCTATTTTCATTATACCTAT
65 GTATCAATACTTTATAT-ATGAGTATCGATACTTGGACATTTACACCTATTTTCATTATACCGAT
3338285 AGA
129 AGA
** ** * * * *
3338288 AATGTTTATCGTGTTTATTGTTAATTTATCTATTACTTGAAAGTAATATGTTT-GAAATTATAAA
1 AACATTTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCGAAATTATAAG
* * * * *
3338352 TATCTATACTTTATATATGAGTTTTGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAG
66 TATCAATACTTTATATATGAGTATCGATACTTGGACATTTACACCTATTTTCATTATACCGATAG
3338417 A
131 A
* * *
3338418 AACATTTACCGTGTACATTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAG
1 AACATTTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCGAAATTATAAG
*
3338483 TATCAATACTTTGTATATGAGTATCGATACTTG
66 TATCAATACTTTATATATGAGTATCGATACTTG
3338516 TTATATACGT
Statistics
Matches: 188, Mismatches: 37, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
129 17 0.09
130 129 0.69
131 42 0.22
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (131 bp):
AACATTTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCGAAATTATAAG
TATCAATACTTTATATATGAGTATCGATACTTGGACATTTACACCTATTTTCATTATACCGATAG
A
Found at i:3339808 original size:22 final size:22
Alignment explanation
Indices: 3339777--3339842 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
3339767 AATTGTTAAC
3339777 AATTA-CCATTTATCTATAGTA
1 AATTATCCATTTATCTATAGTA
* *
3339798 AATTATCCATTTATATTTAGTA
1 AATTATCCATTTATCTATAGTA
3339820 AATTATCCATTTATCTATAGTA
1 AATTATCCATTTATCTATAGTA
3339842 A
1 A
3339843 TTAAATATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 5 0.12
22 35 0.88
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (22 bp):
AATTATCCATTTATCTATAGTA
Found at i:3344294 original size:32 final size:31
Alignment explanation
Indices: 3344222--3344341 Score: 127
Period size: 31 Copynumber: 3.9 Consensus size: 31
3344212 GAGTCGAGGG
* * *
3344222 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCTTTTGAGACATATGGACAAT
*
3344253 TTACCTATGTCTTTTGAGACATATGTACAAT
1 TTACCTATGTCTTTTGAGACATATGGACAAT
* * * *
3344284 ATTACCTATGTCCTTTGGGATATATGGAC-AG
1 -TTACCTATGTCTTTTGAGACATATGGACAAT
*
3344315 TTACCTATGTTCTTTGGA-ACATATGGA
1 TTACCTATG-TCTTTTGAGACATATGGA
3344342 TAGGTCCTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
30 17 0.23
31 33 0.45
32 24 0.32
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (31 bp):
TTACCTATGTCTTTTGAGACATATGGACAAT
Found at i:3344321 original size:30 final size:30
Alignment explanation
Indices: 3344221--3344341 Score: 120
Period size: 32 Copynumber: 3.9 Consensus size: 30
3344211 AGAGTCGAGG
*
3344221 GTTACCTATGT-CTTTCGAGACATATGGATA
1 GTTACCTATGTCCTTT-GAGACATATGGACA
* *
3344251 GTTTACCTATGTCTTTTGAGACATATGTACAA
1 G-TTACCTATGTCCTTTGAGACATATGGAC-A
* * *
3344283 TATTACCTATGTCCTTTGGGATATATGGACA
1 -GTTACCTATGTCCTTTGAGACATATGGACA
*
3344314 GTTACCTATGTTCTTTG-GAACATATGGA
1 GTTACCTATGTCCTTTGAG-ACATATGGA
3344342 TAGGTCCTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
29 1 0.01
30 24 0.32
31 22 0.29
32 28 0.37
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (30 bp):
GTTACCTATGTCCTTTGAGACATATGGACA
Found at i:3344329 original size:63 final size:62
Alignment explanation
Indices: 3344222--3344339 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
3344212 GAGTCGAGGG
* *
3344222 TTACCTATGTCTTTCGAGACATATGGATAGTTTACCTATGTCTTTTGAGACATATGTACAATA
1 TTACCTATGTCTTTCGAGACATATGGACAGTTTACCTATGTCTTTGGA-ACATATGTACAATA
* *
3344285 TTACCTATGTCCTTT-GGGATATATGGACAG-TTACCTATGTTCTTTGGAACATATG
1 TTACCTATGT-CTTTCGAGACATATGGACAGTTTACCTATG-TCTTTGGAACATATG
3344340 GATAGGTCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
62 16 0.33
63 29 0.59
64 4 0.08
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (62 bp):
TTACCTATGTCTTTCGAGACATATGGACAGTTTACCTATGTCTTTGGAACATATGTACAATA
Found at i:3345592 original size:8 final size:8
Alignment explanation
Indices: 3345579--3345603 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3345569 AGATGCGGAT
3345579 TGATGGTG
1 TGATGGTG
3345587 TGATGGTG
1 TGATGGTG
3345595 TGATGGTG
1 TGATGGTG
3345603 T
1 T
3345604 AGCAAATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (8 bp):
TGATGGTG
Found at i:3345711 original size:17 final size:16
Alignment explanation
Indices: 3345689--3345722 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3345679 TAAAAATAGT
3345689 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3345706 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3345722 A
1 A
3345723 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3346239 original size:24 final size:24
Alignment explanation
Indices: 3346195--3346244 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3346185 ATAAAGAACC
*
3346195 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3346219 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
3346243 AA
1 AA
3346245 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3349941 original size:231 final size:243
Alignment explanation
Indices: 3349590--3350066 Score: 852
Period size: 231 Copynumber: 2.0 Consensus size: 243
3349580 GAAAGAGAAA
3349590 AAAAAAAGTTAAAAATTTGGGAGGGAAAAGGGGTGATAGGACGGTTAAGAGAGAAATTAGTGGGT
1 AAAAAAAGTTAAAAATTTGGGAGGGAAAAGGGGTGATAGGACGGTTAAGAGAGAAATTAGTGGGT
3349655 GGGGGTTGTGCGTGTATGGGGAAGGAAAAACTGCCAAAAAGTAATGATGATGATGGGACAAAAAC
66 --GGGTTGTGCGTGTATGGGGAAGGAAAAACTGCCAAAAAGTAATGATGATGATGGGACAAAAAC
3349720 TGTGGAAAGAGAAAAGTAAATGTCAGAAATTAAATTAAAT-AAAAGAAACAAATCAAAAGAATAT
129 TGTGGAAAGAGAAAAGTAAATGTCAGAAATTAAATTAAATAAAAAGAAACAAATCAAAAGAATAT
3349784 CTTTCCAA-TAATGCTTTG-CCTTTCCTCCC-TTGGTAACCGCTCCTTGT
194 CTTTCCAATTAATGCTTTGTCCTTTCCTCCCTTTGGTAACCGCTCCTTGT
3349831 AAAAAAAGTTAAAAATTT-GGAGGGAAAA-GGGTGATAGGACGGTTAAGAGAGAAATTAGTGGGT
1 AAAAAAAGTTAAAAATTTGGGAGGGAAAAGGGGTGATAGGACGGTTAAGAGAGAAATTAGTGGGT
3349894 -GG-T-T-CGTGTAT-GGGAAGG-AAAACTGCCAAAAAGTAATGATGATGATGGGACAAAAACTG
66 GGGTTGTGCGTGTATGGGGAAGGAAAAACTGCCAAAAAGTAATGATGATGATGGGACAAAAACTG
3349953 TGGAAAGAGAAAAGTAAATGTCAGAAATTAAATTAAATAAAAAGAAACAAATCAAAAGAATATCT
131 TGGAAAGAGAAAAGTAAATGTCAGAAATTAAATTAAATAAAAAGAAACAAATCAAAAGAATATCT
3350018 TTCCAATTAATGCTTTGTCCTTTCCTCCCTTTGGTAACCGCTCCTTGT
196 TTCCAATTAATGCTTTGTCCTTTCCTCCCTTTGGTAACCGCTCCTTGT
3350066 A
1 A
3350067 CGGTTTGCAG
Statistics
Matches: 232, Mismatches: 0, Indels: 14
0.94 0.00 0.06
Matches are distributed among these distances:
231 79 0.34
232 39 0.17
233 17 0.07
234 12 0.05
235 20 0.09
236 2 0.01
239 35 0.15
240 10 0.04
241 18 0.08
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (243 bp):
AAAAAAAGTTAAAAATTTGGGAGGGAAAAGGGGTGATAGGACGGTTAAGAGAGAAATTAGTGGGT
GGGTTGTGCGTGTATGGGGAAGGAAAAACTGCCAAAAAGTAATGATGATGATGGGACAAAAACTG
TGGAAAGAGAAAAGTAAATGTCAGAAATTAAATTAAATAAAAAGAAACAAATCAAAAGAATATCT
TTCCAATTAATGCTTTGTCCTTTCCTCCCTTTGGTAACCGCTCCTTGT
Found at i:3356689 original size:24 final size:24
Alignment explanation
Indices: 3356645--3356694 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3356635 ATAAAGAACC
*
3356645 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3356669 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
3356693 AA
1 AA
3356695 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3367383 original size:19 final size:19
Alignment explanation
Indices: 3367359--3367417 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
3367349 CCAAGATCAC
*
3367359 ATAGTGTATTCCCAACGTA
1 ATAGTGCATTCCCAACGTA
*
3367378 ATAGTGCCTTCCCAACGTA
1 ATAGTGCATTCCCAACGTA
3367397 ATAGTGCATTCCCAACGTA
1 ATAGTGCATTCCCAACGTA
3367416 AT
1 AT
3367418 TTTCTCTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (19 bp):
ATAGTGCATTCCCAACGTA
Found at i:3376715 original size:31 final size:32
Alignment explanation
Indices: 3376680--3376749 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
3376670 TATGCTTGTC
3376680 AAAGA-TAGAACAAGTACGAAAAGGGGAAACT
1 AAAGACTAGAACAAGTACGAAAAGGGGAAACT
** *** *
3376711 AAAGACTTTAAGGTGTAGGAAAAGGGGAAACT
1 AAAGACTAGAACAAGTACGAAAAGGGGAAACT
3376743 AAAGACT
1 AAAGACT
3376750 TTAAGGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (32 bp):
AAAGACTAGAACAAGTACGAAAAGGGGAAACT
Found at i:3382845 original size:2 final size:2
Alignment explanation
Indices: 3382838--3382864 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3382828 TTGTTATGAG
3382838 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 T
3382865 TATGTGAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.