Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 57 of 82
Found at i:20602295 original size:16 final size:16
Alignment explanation
Indices: 20602269--20602339 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
20602259 GCATTTTTTA
20602269 AAAAAATAATATAAAAT
1 AAAAAA-AATATAAAAT
*
20602286 -AAAAAAA-AT-AAAG
1 AAAAAAAATATAAAAT
* *
20602299 AAAGAAAATAAAAAAT
1 AAAAAAAATATAAAAT
* *
20602315 ACAAAAAATA-GAAAT
1 AAAAAAAATATAAAAT
20602330 AAACAAAAAT
1 AAA-AAAAAT
20602340 CCCTGATGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
13 3 0.07
14 8 0.19
15 9 0.21
16 22 0.52
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (16 bp):
AAAAAAAATATAAAAT
Found at i:20602306 original size:22 final size:21
Alignment explanation
Indices: 20602281--20602339 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
20602271 AAAATAATAT
20602281 AAAATAAAAAAAATAAAGAAAG
1 AAAATAAAAAAAATAAA-AAAG
* * *
20602303 AAAATAAAAAATACAAAAAAT
1 AAAATAAAAAAAATAAAAAAG
20602324 AGAAATAAACAAAAAT
1 A-AAATAAA-AAAAAT
20602340 CCCTGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 4 0.13
22 22 0.73
23 4 0.13
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAATAAAAAAAATAAAAAAG
Found at i:20614497 original size:25 final size:25
Alignment explanation
Indices: 20614447--20614498 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
20614437 TATATGATAA
*
20614447 TAAATTTTATATATGTTGTTTATAT
1 TAAATTTTATATATGTTGTGTATAT
20614472 TAAATTTTAATATAT-TTGATGT-TAT
1 TAAATTTT-ATATATGTTG-TGTATAT
20614497 TA
1 TA
20614499 TTATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (25 bp):
TAAATTTTATATATGTTGTGTATAT
Found at i:20620145 original size:24 final size:23
Alignment explanation
Indices: 20620087--20620132 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20620077 ATACAATGAC
* *
20620087 CTTATCATAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
20620110 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
20620133 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:20623615 original size:23 final size:23
Alignment explanation
Indices: 20623589--20623634 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20623579 ATACAATAAC
*
20623589 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
20623612 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
20623635 TGTTATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:20625712 original size:2 final size:2
Alignment explanation
Indices: 20625705--20625744 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20625695 TTCCTGCTAC
20625705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20625745 TAATATACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20635853 original size:32 final size:32
Alignment explanation
Indices: 20635808--20635872 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
20635798 AACAAAAACA
*
20635808 AGGTAGGTTCTAATGACAAATTGAAGGATGAC
1 AGGTAGGTCCTAATGACAAATTGAAGGATGAC
*
20635840 AGGTAGGTCCTAATGACATATTGAAGGATGAC
1 AGGTAGGTCCTAATGACAAATTGAAGGATGAC
20635872 A
1 A
20635873 CCAACTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (32 bp):
AGGTAGGTCCTAATGACAAATTGAAGGATGAC
Found at i:20642708 original size:21 final size:22
Alignment explanation
Indices: 20642683--20642746 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
20642673 TATTATAATT
20642683 TAATTAAAAATAAATTTGACAA
1 TAATTAAAAATAAATTTGACAA
** * *
20642705 -AATTACCAATAAATTATTATAA
1 TAATTAAAAATAAATT-TGACAA
20642727 TTTAATTAAAAATAAATTTG
1 --TAATTAAAAATAAATTTG
20642747 CAACATTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
21 13 0.42
22 4 0.13
24 1 0.03
25 13 0.42
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (22 bp):
TAATTAAAAATAAATTTGACAA
Found at i:20642733 original size:25 final size:25
Alignment explanation
Indices: 20642668--20642744 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
20642658 TTTAATTTTT
20642668 TAAATTATTATAATTTAATTAAAAA
1 TAAATTATTATAATTTAATTAAAAA
* * **
20642693 TAAATT-TGACAA---AATTACCAA
1 TAAATTATTATAATTTAATTAAAAA
20642714 TAAATTATTATAATTTAATTAAAAA
1 TAAATTATTATAATTTAATTAAAAA
20642739 TAAATT
1 TAAATT
20642745 TGCAACATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
21 13 0.32
22 4 0.10
24 4 0.10
25 19 0.47
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (25 bp):
TAAATTATTATAATTTAATTAAAAA
Found at i:20643303 original size:15 final size:17
Alignment explanation
Indices: 20643271--20643306 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
20643261 TTCTTCTTTT
20643271 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
20643288 TATTTATA-TA-TTAAC
1 TATTTATATTATTTAAC
20643303 TATT
1 TATT
20643307 ATGTAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:20650538 original size:30 final size:30
Alignment explanation
Indices: 20650504--20650568 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
20650494 AACTAAAGTC
* * *
20650504 TTTATATTTTTATTTTGATTTAAATAAATT
1 TTTATATTTTTATTTTAAGTTAAATAAACT
20650534 TTTATATTTTTATTTTAAGTTAAATAAACT
1 TTTATATTTTTATTTTAAGTTAAATAAACT
20650564 TTTAT
1 TTTAT
20650569 GATTAATGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTATATTTTTATTTTAAGTTAAATAAACT
Found at i:20651009 original size:2 final size:2
Alignment explanation
Indices: 20651002--20651041 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20650992 TACGACAAGG
20651002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20651042 TATTCATTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20659074 original size:28 final size:30
Alignment explanation
Indices: 20659027--20659083 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
20659017 ATTTGACCCA
20659027 AAATAAAAAATATAGAAATTTGA-TTAAATG
1 AAATAAAAAATATAGAAATTT-ATTTAAATG
20659057 AAATAAAAAATA-A-AAATTTATTTAAAT
1 AAATAAAAAATATAGAAATTTATTTAAAT
20659084 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 1 0.04
28 12 0.46
29 1 0.04
30 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATAAAAAATATAGAAATTTATTTAAATG
Found at i:20659453 original size:24 final size:24
Alignment explanation
Indices: 20659416--20659503 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
20659406 GACATATTGA
*
20659416 AAAAATATTATTACATGTCATGTAC
1 AAAAATA-TGTTACATGTCATGTAC
* *
20659441 AAAAATATGTTACATGTCACAGTTAA
1 AAAAATATGTTACATGTCA-TG-TAC
* * *
20659467 AAAAAGT-TGTTACATGCCTTTTAC
1 AAAAA-TATGTTACATGTCATGTAC
*
20659491 AAAAACATGTTAC
1 AAAAATATGTTAC
20659504 TAGTTATATT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
24 24 0.48
25 8 0.16
26 17 0.34
27 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (24 bp):
AAAAATATGTTACATGTCATGTAC
Found at i:20659469 original size:25 final size:24
Alignment explanation
Indices: 20659415--20659470 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
20659405 CGACATATTG
*
20659415 AAAAAATATTATTACATGTCATGT
1 AAAAAATATTATTACATGTCAAGT
*
20659439 ACAAAAATA-TGTTACATGTCACAGTT
1 A-AAAAATATTATTACATGTCA-AG-T
20659465 AAAAAA
1 AAAAAA
20659471 AGTTGTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 12 0.44
25 13 0.48
26 2 0.07
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (24 bp):
AAAAAATATTATTACATGTCAAGT
Found at i:20659538 original size:29 final size:29
Alignment explanation
Indices: 20659506--20659607 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
20659496 CATGTTACTA
20659506 GTTATATTAAAAAAATATTATTATTACAT
1 GTTATATTAAAAAAATATTATTATTACAT
* *
20659535 GTTATATTAAAAAAATATTATTATTATAC
1 GTTATATTAAAAAAATATTATTATTACAT
*** * *
20659564 CCCATATTGAAAAAATATTATTGTTACAT
1 GTTATATTAAAAAAATATTATTATTACAT
*
20659593 GTTATGTTAAAAAAA
1 GTTATATTAAAAAAA
20659608 AATTTTGTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (29 bp):
GTTATATTAAAAAAATATTATTATTACAT
Found at i:20659553 original size:26 final size:26
Alignment explanation
Indices: 20659409--20659557 Score: 78
Period size: 26 Copynumber: 5.8 Consensus size: 26
20659399 TTTACACGAC
* *
20659409 ATATTGAAAAAATATTATTACATGTC
1 ATATTAAAAAAATATTATTACATGTT
* * * *
20659435 AT-GTACAAAAATA-TGTTACATGTC
1 ATATTAAAAAAATATTATTACATGTT
* * * *
20659459 ACAGTTAAAAAAA-GTTGTTACATGCCT
1 ATA-TTAAAAAAATATTATTACATG-TT
* * *
20659486 -T-TTACAAAAACA-TGTTAC-TAGTT
1 ATATTAAAAAAATATTATTACAT-GTT
20659509 ATATTAAAAAAATATTATTATTACATGTT
1 ATATT-AAAAAA-A-TATTATTACATGTT
20659538 ATATTAAAAAAATATTATTA
1 ATATTAAAAAAATATTATTA
20659558 TTATACCCCA
Statistics
Matches: 93, Mismatches: 17, Indels: 26
0.68 0.12 0.19
Matches are distributed among these distances:
23 2 0.02
24 27 0.29
25 10 0.11
26 31 0.33
27 2 0.02
28 7 0.08
29 13 0.14
30 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.38
Consensus pattern (26 bp):
ATATTAAAAAAATATTATTACATGTT
Found at i:20659579 original size:58 final size:57
Alignment explanation
Indices: 20659509--20659620 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
20659499 GTTACTAGTT
*
20659509 ATATTAAAAAAATATTATTATTACATGTTATATTAAAAAAATATTATTATTATACCCC
1 ATATTAAAAAAATATTATTATTACATGTTATATTAAAAAAAAATT-TTATTATACCCC
* * * *
20659567 ATATTGAAAAAATATTATTGTTACATGTTATGTTAAAAAAAAATTTTGTTATAC
1 ATATTAAAAAAATATTATTATTACATGTTATATTAAAAAAAAATTTTATTATAC
20659621 TTTAATGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 8 0.16
58 41 0.84
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (57 bp):
ATATTAAAAAAATATTATTATTACATGTTATATTAAAAAAAAATTTTATTATACCCC
Found at i:20662305 original size:22 final size:23
Alignment explanation
Indices: 20662280--20662338 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
20662270 TGCATCTTTC
20662280 ACTCTATAAGGAAA-TTGAGTCT
1 ACTCTATAAGGAAATTTGAGTCT
* * *
20662302 ACTCTATAAGAAAATTTGGGTTT
1 ACTCTATAAGGAAATTTGAGTCT
20662325 ACTCTATAAGGAAA
1 ACTCTATAAGGAAA
20662339 AAAGAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (23 bp):
ACTCTATAAGGAAATTTGAGTCT
Found at i:20662310 original size:105 final size:106
Alignment explanation
Indices: 20662185--20662422 Score: 329
Period size: 105 Copynumber: 2.3 Consensus size: 106
20662175 AATAATTTCA
* * *
20662185 AAATTTGGGTATACTCTATAAGGAGAA-TGGGTTTACTCTATTAAGGAAAAAAGAAAAATAATTA
1 AAATTTGAGTCTACTCTATAAGGAAAATTGGGTTTACTCTA-TAAGGAAAAAAGAAAAATAATTA
* *
20662249 CAAATTTAGGCAGTTAAGCAATGCATCTTTCACTCTATAAGG
65 CAAATTTAGACAATTAAGCAATGCATCTTTCACTCTATAAGG
20662291 AAA-TTGAGTCTACTCTATAA-GAAAATTTGGGTTTACTCTATAAGGAAAAAAGAAAAATAATTA
1 AAATTTGAGTCTACTCTATAAGGAAAA-TTGGGTTTACTCTATAAGGAAAAAAGAAAAATAATTA
* * * *
20662354 CAAATTTAGACAATTAAGCAATGCATGTTTTACTTTATAGGG
65 CAAATTTAGACAATTAAGCAATGCATCTTTCACTCTATAAGG
* * *
20662396 AAATTTGGGTTTACTGTATAAGGAAAA
1 AAATTTGAGTCTACTCTATAAGGAAAA
20662423 AAAATTTTAA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
104 4 0.03
105 77 0.66
106 30 0.26
107 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (106 bp):
AAATTTGAGTCTACTCTATAAGGAAAATTGGGTTTACTCTATAAGGAAAAAAGAAAAATAATTAC
AAATTTAGACAATTAAGCAATGCATCTTTCACTCTATAAGG
Found at i:20663588 original size:117 final size:122
Alignment explanation
Indices: 20663375--20663621 Score: 297
Period size: 117 Copynumber: 2.1 Consensus size: 122
20663365 CTAAACCCAA
* ** ** * ** *
20663375 GGGATTGTGGGTAATTTATAAATTAGACTTCAATCTTATTTTAGAAAAAAAAATTCAATATGAAT
1 GGGATTGTGGCTAAACTATAAAACAGACTTCAATCCTATACTAGAAAAAAAAATTCAATACGAAT
** * *
20663440 TAATTCCCAATCAAATACCATTAAAATAATTTATAT-AAAAA-AAA-GTTAAAACGT
66 TAATGACCAATCAAATACAATTAAAATAATTTATATAAAAAACAAAGGTTAAAACCT
* *
20663494 GGGATTGTGGCTAAACTATAAAACAGACTTCAATCCTATACTAG-AAAAAAAA-TCAGTCCGAAT
1 GGGATTGTGGCTAAACTATAAAACAGACTTCAATCCTATACTAGAAAAAAAAATTCAATACGAAT
* * *
20663557 TAATGATCAATCAAATATAATTAAAATAATTTATATAAAAAACAAAGGTTCAAACCT
66 TAATGACCAATCAAATACAATTAAAATAATTTATATAAAAAACAAAGGTTAAAACCT
20663614 GGGATTGT
1 GGGATTGT
20663622 ATCTAACTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
117 39 0.36
118 13 0.12
119 39 0.36
120 16 0.15
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (122 bp):
GGGATTGTGGCTAAACTATAAAACAGACTTCAATCCTATACTAGAAAAAAAAATTCAATACGAAT
TAATGACCAATCAAATACAATTAAAATAATTTATATAAAAAACAAAGGTTAAAACCT
Found at i:20663690 original size:120 final size:115
Alignment explanation
Indices: 20663421--20663710 Score: 273
Period size: 120 Copynumber: 2.5 Consensus size: 115
20663411 TATTTTAGAA
** * * *
20663421 AAAAAAATTCAATATGAATTAATTCCCAATCAAATACCATTAAAATAATTTATATAAAAAAAAGT
1 AAAAAAA-TCAATCCGAAATAATGCCCAATCAAATA-AATTAAAATAATTTATATAAAAAAAAGT
* * *
20663486 TAAAACGTGGGATTGTGGCTAAACTATAAAACAGACTTCAATCCTATACTAG
64 TAAAACCTGGGATTGTAGCTAAACTATAAAACAAACTTCAATCCTATACTAG
* * **
20663538 AAAAAAAATCAGTCCGAATTAATGATCAATCAAATATAATTAAAATAATTTATATAAAAAACAAA
1 -AAAAAAATCAATCCGAAATAATGCCCAATCAAATA-AATTAAAATAATTTATAT-AAAAA-AAA
* * * * * *
20663603 GGTTCAAACCTGGGATTGTATCT-AACTTTTACAAATCAAATTTCAATCTTATTCTAG
62 -GTTAAAACCTGGGATTGTAGCTAAAC-TATA-AAA-CAAACTTCAATCCTATACTAG
*
20663660 -AATAAATCAATCC-ACAATAATGCCCAATCAAATAACATT-AAATAATTTATA
1 AAAAAAATCAATCCGA-AATAATGCCCAATCAAATAA-ATTAAAATAATTTATA
20663711 AACAGAGTTA
Statistics
Matches: 142, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
117 39 0.27
118 12 0.08
119 20 0.14
120 51 0.36
121 3 0.02
122 17 0.12
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (115 bp):
AAAAAAATCAATCCGAAATAATGCCCAATCAAATAAATTAAAATAATTTATATAAAAAAAAGTTA
AAACCTGGGATTGTAGCTAAACTATAAAACAAACTTCAATCCTATACTAG
Found at i:20669388 original size:15 final size:15
Alignment explanation
Indices: 20669368--20669422 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
20669358 TTTATAATGC
*
20669368 AATGTGATTGCAGGT
1 AATGTGATTGCAAGT
*
20669383 AATGTGATTGTAAGT
1 AATGTGATTGCAAGT
* **
20669398 AATATGATTGCAAAC
1 AATGTGATTGCAAGT
20669413 AATGTGATTG
1 AATGTGATTG
20669423 TAAGGAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:20669773 original size:55 final size:52
Alignment explanation
Indices: 20669676--20669802 Score: 150
Period size: 55 Copynumber: 2.3 Consensus size: 52
20669666 TTAATATAAT
*
20669676 TTTTTATATTATATATTTTATTTTAATTTCTTTTACCTATATTATATAAATTTTAA
1 TTTTTATATT-T-TATTTTATTTTAATTTCTATTACCTATATTATAT--ATTTTAA
*
20669732 TTTCTTATATTTTATTTTATTTTAATTTCTAATT-CTTATATTATATATTTT-A
1 TTT-TTATATTTTATTTTATTTTAATTTCT-ATTACCTATATTATATATTTTAA
*
20669784 TTTTAATATTTTTATTTTA
1 TTTTTATA-TTTTATTTTA
20669803 ATTATAATAT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
51 4 0.06
52 14 0.22
53 5 0.08
55 29 0.45
56 6 0.09
57 7 0.11
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (52 bp):
TTTTTATATTTTATTTTATTTTAATTTCTATTACCTATATTATATATTTTAA
Found at i:20669796 original size:14 final size:15
Alignment explanation
Indices: 20669774--20669804 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
20669764 TTCTTATATT
20669774 ATATATTTTATTTTA
1 ATATATTTTATTTTA
20669789 ATAT-TTTTATTTTA
1 ATATATTTTATTTTA
20669803 AT
1 AT
20669805 TATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:20669810 original size:20 final size:20
Alignment explanation
Indices: 20669749--20669813 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
20669739 TATTTTATTT
* * *
20669749 TATTTTAATTTCTAATTCTTA
1 TATTTTTATTT-TAATTATAA
* *
20669770 TATTATATATTTT-ATTTTAA
1 TATT-TTTATTTTAATTATAA
20669790 TATTTTTATTTTAATTATAA
1 TATTTTTATTTTAATTATAA
20669810 TATT
1 TATT
20669814 ATAAAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 7 0.19
20 19 0.53
21 5 0.14
22 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTATTTTAATTATAA
Found at i:20669813 original size:33 final size:33
Alignment explanation
Indices: 20669724--20669790 Score: 104
Period size: 31 Copynumber: 2.1 Consensus size: 33
20669714 ATATTATATA
20669724 AATTT-TAATTTCTTATATT-T-TATTTTATTTT
1 AATTTCTAA-TTCTTATATTATATATTTTATTTT
20669755 AATTTCTAATTCTTATATTATATATTTTATTTT
1 AATTTCTAATTCTTATATTATATATTTTATTTT
20669788 AAT
1 AAT
20669791 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 15 0.45
32 4 0.12
33 14 0.42
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (33 bp):
AATTTCTAATTCTTATATTATATATTTTATTTT
Found at i:20672102 original size:27 final size:27
Alignment explanation
Indices: 20672072--20672124 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
20672062 TTTGATTTTG
** * *
20672072 CTTGATGGTTGAAGTGAAATACCCTTA
1 CTTGATGACTGAAGTAAAAGACCCTTA
20672099 CTTGATGACTGAAGTAAAAGACCCTT
1 CTTGATGACTGAAGTAAAAGACCCTT
20672125 CATGGCTGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (27 bp):
CTTGATGACTGAAGTAAAAGACCCTTA
Found at i:20675695 original size:2 final size:2
Alignment explanation
Indices: 20675688--20675716 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20675678 TAAATAATTA
20675688 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
20675717 GTTTGTTTAA
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:20680215 original size:23 final size:22
Alignment explanation
Indices: 20680183--20680228 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
20680173 GCCCTAAACT
*
20680183 CCCCCGATTCCAC-CCTCTCTTTC
1 CCCCCAATTCC-CTCCTCT-TTTC
20680206 CCCCCAATTCCCTCCTCTTTTC
1 CCCCCAATTCCCTCCTCTTTTC
20680228 C
1 C
20680229 TCCCTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.09, C:0.57, G:0.02, T:0.33
Consensus pattern (22 bp):
CCCCCAATTCCCTCCTCTTTTC
Found at i:20685099 original size:19 final size:19
Alignment explanation
Indices: 20685064--20685108 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20685054 ATATTAAAAT
20685064 TTATTA-TATTTGATGTTA
1 TTATTATTATTTGATGTTA
**
20685082 TTATTATTATTTTTTGTTA
1 TTATTATTATTTGATGTTA
*
20685101 TAATTATT
1 TTATTATT
20685109 TTTATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TTATTATTATTTGATGTTA
Found at i:20686531 original size:8 final size:8
Alignment explanation
Indices: 20686518--20686559 Score: 77
Period size: 8 Copynumber: 5.4 Consensus size: 8
20686508 CCCCGTAACT
20686518 CCCACCCC
1 CCCACCCC
20686526 CCCACCCC
1 CCCACCCC
20686534 CCCACCCC
1 CCCACCCC
20686542 CCC-CCCC
1 CCCACCCC
20686549 CCCACCCC
1 CCCACCCC
20686557 CCC
1 CCC
20686560 TGCCAATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.21
8 26 0.79
ACGTcount: A:0.10, C:0.90, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCACCCC
Found at i:20686541 original size:15 final size:16
Alignment explanation
Indices: 20686518--20686559 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
20686508 CCCCGTAACT
20686518 CCCACCCCCCCACCCC
1 CCCACCCCCCCACCCC
20686534 CCCACCCCCCC-CCCC
1 CCCACCCCCCCACCCC
20686549 CCCACCCCCCC
1 CCCACCCCCCC
20686560 TGCCAATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.10, C:0.90, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCACCCCCCCACCCC
Found at i:20686940 original size:4 final size:4
Alignment explanation
Indices: 20686933--20686980 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
20686923 ACAGAATATA
*
20686933 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
20686981 CATTATTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:20687198 original size:154 final size:153
Alignment explanation
Indices: 20686973--20687252 Score: 409
Period size: 154 Copynumber: 1.8 Consensus size: 153
20686963 TGTATGTATA
* *
20686973 TATGTATGCATTATTTTGCTCTTGCTATCTATTTTTATTATAAATTAGAGTCTGTTTCATTTGAC
1 TATGTATGCATTATTTTGATCTTGCCATCTATTTTTATTATAAATTAGAGTCTGTTTCATTTGAC
* ** **
20687038 AGTACACATGCACATGCCAGATTATGTTGCCTTTCAATTCCTTCTCCCCATTCTTCTGAAATTCA
66 AGTACACAGGCACATGCCAGATTATGTTGCCTCCCAATTAATTCTCCCCATTCTTCTGAAATTCA
20687103 GCTCCAGACTTTTTCCATATGTG
131 GCTCCAGACTTTTTCCATATGTG
* *
20687126 TATGTGTGCATTATTTTGATCTTGCCATCT-TTGTTTTTTAATAAATTAGAGTCTGTTTCATTTG
1 TATGTATGCATTATTTTGATCTTGCCATCTATT-TTTATT-ATAAATTAGAGTCTGTTTCATTTG
** ** *
20687190 ACTTTACACAGGCTTATGCCAGATTGTGTTGCCTCCCAATTAATTCTCCCCATTCTTCTGAAA
64 ACAGTACACAGGCACATGCCAGATTATGTTGCCTCCCAATTAATTCTCCCCATTCTTCTGAAA
20687253 ACGACCTAAG
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
152 2 0.02
153 32 0.29
154 77 0.69
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (153 bp):
TATGTATGCATTATTTTGATCTTGCCATCTATTTTTATTATAAATTAGAGTCTGTTTCATTTGAC
AGTACACAGGCACATGCCAGATTATGTTGCCTCCCAATTAATTCTCCCCATTCTTCTGAAATTCA
GCTCCAGACTTTTTCCATATGTG
Found at i:20690587 original size:29 final size:29
Alignment explanation
Indices: 20690545--20690602 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
20690535 TAGGAAGAGT
*
20690545 TTATCAAAATAAAATCTAGGAAGATAGCA
1 TTATCAAAACAAAATCTAGGAAGATAGCA
* * *
20690574 TTATTAAAACAAAATTTTGGAAGATAGCA
1 TTATCAAAACAAAATCTAGGAAGATAGCA
20690603 AAAATATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.28
Consensus pattern (29 bp):
TTATCAAAACAAAATCTAGGAAGATAGCA
Found at i:20701270 original size:35 final size:35
Alignment explanation
Indices: 20701224--20701500 Score: 229
Period size: 35 Copynumber: 7.9 Consensus size: 35
20701214 TCCTTAAGAA
***
20701224 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATCAATTAG
* * *
20701260 GCTCAATAACTTAATTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
20701295 GCCCAACAATTTAATTAAACAATTTTAATCAACTAG
1 GCCCAATAACTTAATTAAATAA-TTTAATCAATTAG
* * * * *
20701331 GCCTAATGACTTAATTAAACAAATTCAATCAATTAA
1 GCCCAATAACTTAATTAAA-TAATTTAATCAATTAG
*** *
20701367 GCCCAATAACTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * *
20701402 GCCCAATGACTTAATTAAACAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
20701437 GCCCAATGA-TTCAATTAAACAATTTAGTTAATTAG
1 GCCCAATAACTT-AATTAAATAATTTAATCAATTAG
* *
20701472 G--C-ACAACTTAATTAAACAATTTTAATCAA
1 GCCCAATAACTTAATTAAATAA-TTTAATCAA
20701501 GTGCTTGAGA
Statistics
Matches: 196, Mismatches: 40, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
32 12 0.06
33 10 0.05
34 2 0.01
35 116 0.59
36 54 0.28
37 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATCAATTAG
Found at i:20701376 original size:107 final size:106
Alignment explanation
Indices: 20701245--20701458 Score: 286
Period size: 107 Copynumber: 2.0 Consensus size: 106
20701235 TTAATTGTTT
* * * *
20701245 AATTTAATCAATTAGGCTCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTCAATCAATTAAGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
*
20701310 TAAACAATTTTAATCAACTAGGCCTAATGACTT-AATTAAACA
66 TAAACAA-TTTAATCAACTAGGCCCAATGA-TTCAATTAAACA
*** * **
20701352 AATTCAATCAATTAAGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTCAATCAATTAAGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
* *
20701417 TAAACAATTTAATTAATTAGGCCCAATGATTCAATTAAACA
66 TAAACAATTTAATCAACTAGGCCCAATGATTCAATTAAACA
20701458 A
1 A
20701459 TTTAGTTAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 2 0.02
106 29 0.31
107 62 0.67
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (106 bp):
AATTCAATCAATTAAGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTAATCAACTAGGCCCAATGATTCAATTAAACA
Found at i:20706545 original size:179 final size:180
Alignment explanation
Indices: 20706306--20706633 Score: 462
Period size: 179 Copynumber: 1.8 Consensus size: 180
20706296 TTAATAGCTT
* ** * *
20706306 AAATCAGCTTGTTTGGCCATGAAAATTTCCAGAACTAATCTTCATTGAACATTTTAATAAAGATA
1 AAATCAGCATGTTTAACCATGAAAATTTCCAGAAATAATCTTCATTGAACATCTTAATAAAGATA
** * *
20706371 ATTTTTTTGAAATTTTTCAGAATTAATTTTCAAGAGTTTCTTGTCAATTAAAACTGAAATTCATG
66 ATTTTCCTGAAATTTTTCAGAATTAATTTTCAAGACTTTCTTGTCAATTAAAACTGAAATTCATA
20706436 CCAAAACAATGAGCTGGACATATTTATATTTGCACCAATTTTCTTACTCG
131 CCAAAACAATGAGCTGGACATATTTATATTTGCACCAATTTTCTTACTCG
* *
20706486 AAATCAGCATGTTTAACCATGATATTTTCCA-AAATAATCCTT-ATTGAACATCTTAATAAAGAT
1 AAATCAGCATGTTTAACCATGAAAATTTCCAGAAATAAT-CTTCATTGAACATCTTAATAAAGAT
* * * * *
20706549 AATTTTCCTGGAATTTTTTAGAATTAATTTTCAAGACTTTTTTGTTAATTAAATCTGAAATTCAT
65 AATTTTCCTGAAATTTTTCAGAATTAATTTTCAAGACTTTCTTGTCAATTAAAACTGAAATTCAT
* * *
20706614 ATCATAACAGTGAGCTGGAC
130 ACCAAAACAATGAGCTGGAC
20706634 TGCTTTCACT
Statistics
Matches: 128, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
179 99 0.77
180 29 0.23
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (180 bp):
AAATCAGCATGTTTAACCATGAAAATTTCCAGAAATAATCTTCATTGAACATCTTAATAAAGATA
ATTTTCCTGAAATTTTTCAGAATTAATTTTCAAGACTTTCTTGTCAATTAAAACTGAAATTCATA
CCAAAACAATGAGCTGGACATATTTATATTTGCACCAATTTTCTTACTCG
Found at i:20707852 original size:71 final size:70
Alignment explanation
Indices: 20707754--20707944 Score: 197
Period size: 71 Copynumber: 2.7 Consensus size: 70
20707744 TTAATTGTTT
* * * *
20707754 AATTTAATCAATTAAGCTCAATAACTTAATTAAA-AATTTTAATTAATTAAACCCAACAATTTAA
1 AATTTAATCAACTAGGCTCAATGACTTAATTAAACAA-TTTAATTAATTAAACCCAACAACTTAA
20707818 TTAAAC
65 TTAAAC
* * ** *
20707824 AATTTTAATCAACTAGGC-CTAATGACTTAATTAAACAAATTCAATCAATTAGGCCCAATAACTT
1 AA-TTTAATCAACTAGGCTC-AATGACTTAATTAAAC-AATTTAATTAATTAAACCCAACAACTT
****
20707888 AATTGTTT
63 AATTAAAC
* *
20707896 AATTTAATTAATTAGGCTCAATGACTTAATTAAACAATTTAATTAATTA
1 AATTTAATCAACTAGGCTCAATGACTTAATTAAACAATTTAATTAATTA
20707945 GGCCCAATGA
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
70 15 0.15
71 56 0.57
72 26 0.26
73 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (70 bp):
AATTTAATCAACTAGGCTCAATGACTTAATTAAACAATTTAATTAATTAAACCCAACAACTTAAT
TAAAC
Found at i:20707854 original size:36 final size:35
Alignment explanation
Indices: 20707754--20708009 Score: 207
Period size: 35 Copynumber: 7.3 Consensus size: 35
20707744 TTAATTGTTT
* * *
20707754 AATTTAATCAATTAAGCTCAATAACTTAATTAAA-
1 AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
* ** ** *
20707788 AATTTTAATTAATTAAACCCAACAATTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATGACTTAATTAAAC
* *
20707824 AATTTTAATCAACTAGGCCTAATGACTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATGACTTAATTAAAC
* * ****
20707860 AAATTCAATCAATTAGGCCCAATAACTTAATTGTTT
1 -AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
* *
20707896 AATTTAATTAATTAGGCTCAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
* *
20707931 AATTTAATTAATTAGGCCCAATGA-TTCAACTAAAC
1 AATTTAATCAATTAGGCCCAATGACTT-AATTAAAC
* * * *
20707966 AATTTAGTTAATTAAGCAC-A--ACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
20707998 AATTTTAATCAA
1 AA-TTTAATCAA
20708010 GTGCTTGAGA
Statistics
Matches: 179, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
32 10 0.06
33 9 0.05
34 5 0.03
35 100 0.56
36 53 0.30
37 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATGACTTAATTAAAC
Found at i:20707902 original size:107 final size:106
Alignment explanation
Indices: 20707754--20708006 Score: 248
Period size: 107 Copynumber: 2.4 Consensus size: 106
20707744 TTAATTGTTT
* * *
20707754 AATTTAATCAATTAAGCTCAATAACTTAATTAAAAATTTTAATTAATTAAACCCAACAATTTAAT
1 AATTCAATCAATTAAGCCCAATAACTTAATTAAAAATTTTAATTAATTAAACCCAACAACTTAAT
* *
20707819 TAAACAATTTTAATCAACTAGGCCTAATGACTT-AATTAAACA
66 TAAACAA-TTTAATCAACTAGGCCCAATGA-TTCAACTAAACA
* *** ** * **
20707861 AATTCAATCAATTAGGCCCAATAACTTAATTGTTTAA-TTTAATTAATTAGGCTCAATGACTTAA
1 AATTCAATCAATTAAGCCCAATAACTTAATT-AAAAATTTTAATTAATTAAACCCAACAACTTAA
* *
20707925 TTAAACAATTTAATTAATTAGGCCCAATGATTCAACTAAAC-
65 TTAAACAATTTAATCAACTAGGCCCAATGATTCAACTAAACA
* * * *
20707966 AATTTAGTTAATTAAG--C-ACAACTTAATTAAACAATTTTAAT
1 AATTCAATCAATTAAGCCCAATAACTTAATTAAA-AATTTTAAT
20708007 CAAGTGCTTG
Statistics
Matches: 118, Mismatches: 24, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
102 12 0.10
103 7 0.06
105 14 0.12
106 26 0.22
107 57 0.48
108 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.36
Consensus pattern (106 bp):
AATTCAATCAATTAAGCCCAATAACTTAATTAAAAATTTTAATTAATTAAACCCAACAACTTAAT
TAAACAATTTAATCAACTAGGCCCAATGATTCAACTAAACA
Found at i:20721687 original size:80 final size:80
Alignment explanation
Indices: 20721553--20721703 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 80
20721543 CAAGGTTATA
* * * * * *
20721553 TTTAAATCTTATGTTTGCCTTTTCTAATTCCGCAGGCATTGATTTGATATAAGTTGCTTATGGTT
1 TTTAAATCTGATGTTTGCCTTTTCTAACTCCGCAGACATTGATTCGATACAAGTTGCCTATGGTT
20721618 GTGATAATCCATATG
66 GTGATAATCCATATG
* * *
20721633 TTTAAATCTGATGTTTGCCTTTTCTAACTCTGCAGACATTGGTTCGATACAAGTTGCCTGTGGTT
1 TTTAAATCTGATGTTTGCCTTTTCTAACTCCGCAGACATTGATTCGATACAAGTTGCCTATGGTT
20721698 GTGATA
66 GTGATA
20721704 GTCTTTAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (80 bp):
TTTAAATCTGATGTTTGCCTTTTCTAACTCCGCAGACATTGATTCGATACAAGTTGCCTATGGTT
GTGATAATCCATATG
Found at i:20730385 original size:12 final size:12
Alignment explanation
Indices: 20730370--20730394 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20730360 TTGATAACAG
20730370 AAATATAAAACT
1 AAATATAAAACT
20730382 AAATATAAAACT
1 AAATATAAAACT
20730394 A
1 A
20730395 TAATTTGTAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAAACT
Found at i:20736355 original size:49 final size:49
Alignment explanation
Indices: 20736302--20736431 Score: 197
Period size: 49 Copynumber: 2.7 Consensus size: 49
20736292 TTACTATTTT
* *
20736302 CTTTACTTGCACACCAAGTAGGTTTATGTTTAATTGGTTATCATAATTA
1 CTTTACTTGCACACCAAGTAGGTTTAGGTTTAATTGGCTATCATAATTA
* * *
20736351 CTTTACTTACACACCAAGTAGGTTTAGGTTTAATTGGCTGTTATAATTA
1 CTTTACTTGCACACCAAGTAGGTTTAGGTTTAATTGGCTATCATAATTA
* *
20736400 CTTTACTCGCACACCAAGTAAGTTTAGGTTTA
1 CTTTACTTGCACACCAAGTAGGTTTAGGTTTA
20736432 GTTAACTATG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (49 bp):
CTTTACTTGCACACCAAGTAGGTTTAGGTTTAATTGGCTATCATAATTA
Found at i:20744568 original size:16 final size:16
Alignment explanation
Indices: 20744544--20744583 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20744534 AAGAAATCAA
*
20744544 TTCAGCTGCAACTTAT
1 TTCACCTGCAACTTAT
20744560 TTCACCTGCAACTTAT
1 TTCACCTGCAACTTAT
20744576 TTCACCTG
1 TTCACCTG
20744584 AAACAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.10, T:0.38
Consensus pattern (16 bp):
TTCACCTGCAACTTAT
Found at i:20749934 original size:42 final size:42
Alignment explanation
Indices: 20749875--20749999 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 42
20749865 TGTTGATGTG
*
20749875 GACCCGACTATGTGCGAGTAAGAGTGCACATAAGCCGTTGTT
1 GACCCGACTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
**
20749917 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
* * * *
20749959 GACCCGACTATATGCGAGT-GGAAGTACGCATAAGCCGTTGC
1 GACCCGACTATGTGCGAGTAAG-AGTGCACATAAGCCGTTGC
20750000 ATATGACATG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
41 2 0.03
42 74 0.97
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
Found at i:20752663 original size:14 final size:15
Alignment explanation
Indices: 20752640--20752668 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20752630 ATGTCTGTTG
20752640 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
20752655 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
20752669 GAGAGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:20752944 original size:17 final size:17
Alignment explanation
Indices: 20752922--20752960 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
20752912 AGTGAGTGCG
20752922 CAGTGGATTGATTTTGT
1 CAGTGGATTGATTTTGT
20752939 CAGTGGATTGATTTTGT
1 CAGTGGATTGATTTTGT
20752956 CAGTG
1 CAGTG
20752961 CAAAACATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.08, G:0.31, T:0.44
Consensus pattern (17 bp):
CAGTGGATTGATTTTGT
Found at i:20754134 original size:22 final size:23
Alignment explanation
Indices: 20754115--20754160 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
20754105 CAATGAAAGA
20754115 ATTGGAATTCAAAGAAGAAAAAATT
1 ATTGGAATTCAAAGAAG-AAAAA-T
20754140 ATTGGAATTCAAAGAAGAAAA
1 ATTGGAATTCAAAGAAGAAAA
20754161 CATTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.22
Consensus pattern (23 bp):
ATTGGAATTCAAAGAAGAAAAAT
Found at i:20754952 original size:27 final size:27
Alignment explanation
Indices: 20754922--20754975 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20754912 TTATTTTATT
**
20754922 TTTATAAA-ATTAAAAATTTATAATTTA
1 TTTA-AAATATTAAAAATAGATAATTTA
*
20754949 TTTAAAATATTAATAATAGATAATTTA
1 TTTAAAATATTAAAAATAGATAATTTA
20754976 AATATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTAAAATATTAAAAATAGATAATTTA
Found at i:20755078 original size:21 final size:20
Alignment explanation
Indices: 20755013--20755078 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 20
20755003 ATTAACATTT
*
20755013 AAATAATTAATATTTTATTTA
1 AAAT-ATTAATATTTTAATTA
* *
20755034 TAATATAAATATTATTATGATTA
1 AAATATTAATATT-TTA--ATTA
20755057 AAATATTAATCATTTTAATTA
1 AAATATTAAT-ATTTTAATTA
20755078 A
1 A
20755079 TTTTTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 8 0.22
21 11 0.31
23 14 0.39
24 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATATTAATATTTTAATTA
Found at i:20755239 original size:202 final size:202
Alignment explanation
Indices: 20755018--20755408 Score: 610
Period size: 202 Copynumber: 1.9 Consensus size: 202
20755008 CATTTAAATA
* *
20755018 ATTAATATTTTATTTATAATATAAATATTATTATGATTAAAATATTAATCATTTTAATTAATTTT
1 ATTAATATTTTATTTATAATATAAATATTATAATGATTAAAATATTAATAATTTTAATT-A-TTT
20755083 TTAAATTTAAAATATTAATTTTT-ATAATATATAATTAAAAACTTAAACAGTTT-ATTATAATAT
64 TTAAATTTAAAATATTAATTTTTAATAATATATAATTAAAAACTTAAAC-GTTTAATTATAATAT
* *
20755146 ATGATTATATATTTTTATTTTA-TTT-TTTAAAAAATATTAATAATTTATAATTTAATTATTAAA
128 ATGATTATATA-TTTTATTTTATTTTGTTTAAAAAATATTAATAATTGATAATTTAAATATTAAA
20755209 AATTTTTAACT
192 AATTTTTAACT
*
20755220 ATTAATATTTTATTTATAATTTAAATATTATAATGATTAAAATATTAATAATTTTAATTATTTTT
1 ATTAATATTTTATTTATAATATAAATATTATAATGATTAAAATATTAATAATTTTAATTATTTTT
*
20755285 AAATTTAAAATATTAATTTTTAATAATATATAATTAAAAACTTAAACTTTTAATTATAATATATG
66 AAATTTAAAATATTAATTTTTAATAATATATAATTAAAAACTTAAACGTTTAATTATAATATATG
* * *** *
20755350 ATTATCTATTTTGTTTTATTTTGTTTTTTACATATTAATAATTGATAATTTAAATATTA
131 ATTATATATTTTATTTTATTTTGTTTAAAAAATATTAATAATTGATAATTTAAATATTA
20755409 TTATGATTAA
Statistics
Matches: 173, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
200 38 0.22
201 49 0.28
202 86 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (202 bp):
ATTAATATTTTATTTATAATATAAATATTATAATGATTAAAATATTAATAATTTTAATTATTTTT
AAATTTAAAATATTAATTTTTAATAATATATAATTAAAAACTTAAACGTTTAATTATAATATATG
ATTATATATTTTATTTTATTTTGTTTAAAAAATATTAATAATTGATAATTTAAATATTAAAAATT
TTTAACT
Found at i:20755266 original size:43 final size:43
Alignment explanation
Indices: 20755188--20755300 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
20755178 AATATTAATA
* * * *
20755188 ATTTATAATTTAATTATTAAAAATTTTTAACTATTAAT-ATTTT
1 ATTTATAATTTAAATATT-AAAATATTAAAATATTAATAATTTT
*
20755231 ATTTATAATTTAAATATTATAATGATTAAAATATTAATAATTTT
1 ATTTATAATTTAAATATTAAAAT-ATTAAAATATTAATAATTTT
* *
20755275 AATTAT-TTTTAAAT-TTAAAATATTAA
1 ATTTATAATTTAAATATTAAAATATTAA
20755301 TTTTTAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 5 0.08
42 10 0.17
43 35 0.58
44 10 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (43 bp):
ATTTATAATTTAAATATTAAAATATTAAAATATTAATAATTTT
Found at i:20755329 original size:29 final size:31
Alignment explanation
Indices: 20755289--20755347 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 31
20755279 ATTTTTAAAT
*
20755289 TTAAAATATT-AATTTTTAATAAT-ATATAA
1 TTAAAATATTAAACTTTTAATAATAATATAA
*
20755318 TTAAAA-ACTTAAACTTTTAATTATAATATA
1 TTAAAATA-TTAAACTTTTAATAATAATATA
20755348 TGATTATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.04
29 8 0.32
30 11 0.44
31 5 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAAAATATTAAACTTTTAATAATAATATAA
Found at i:20756493 original size:235 final size:235
Alignment explanation
Indices: 20756082--20757424 Score: 2470
Period size: 235 Copynumber: 5.7 Consensus size: 235
20756072 TATAAGAGCN
* *
20756082 AGGATATGGGAGGTAATAACATGGGAAGCCTTGGGGGAAGAGTTTAAGAAGGTGAGCTTTGTAGC
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
*
20756147 AGCACCGTTTGTGGTAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
20756212 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
*
20756277 GAAAAGAATGGACGAGGCACTGTTTCCTAAGAAAGAAGGG
196 GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
*
20756317 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGT
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
*
20756382 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTTATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
*
20756447 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAAGACATAAAGAGT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
*
20756512 GAAAAGAATGGACGAGGCGCTGTTTCCAAAGAAAGAAGGG
196 GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
*
20756552 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGGAAGAGTTTAAGAAGGTGAGCTTTGTAGC
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
* *
20756617 AGCACCGTTTGTGGCAGTGGCATTGTCATGGTATTAAGGATTTATTACTCATAGTTTGATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
20756682 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
*
20756747 GAAAAGAATGGACGAGGCGCTGTTTCTTAAGAAAGAAGGG
196 GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
20756787 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
*
20756852 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTTATAAGGATTTATTACTCATAGTTTGATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
*
20756917 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAAGACATAAAGAGT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
*
20756982 GAAAAGAATGGACAAGGCGCTGTTTCCTAAGAAAGAAGGG
196 GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
* * *
20757022 AGTATATGGGAGATAATAACATGGGAAGCCTTGGGGGATGAGTTTAAGAAGGTGAGCTTTGTAGC
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
20757087 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
* * *
20757152 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAAAAGAACATAAAAAGT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
* * *
20757217 GAAAAGAATGGACGAGACGCTGCTTCCAAAGAAAGAAGGG
196 GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
20757257 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
1 AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
20757322 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
66 AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
20757387 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACT
131 TAATAAGGATTTATACTCCTATTTATTTAAAGAACACT
20757425 CTTTCTTTGT
Statistics
Matches: 1070, Mismatches: 38, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
235 1070 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (235 bp):
AGGATATGGGAGATAATAACATGGGAAGCCTTGGGGAAAGAGTTTAAGAAGGTGAGCTTTGTAGC
AGCACCGTTTGTGGCAGTGGCATTGTCACGGTAATAAGGATTTATTACTCATAGTTTGATCCAAC
TAATAAGGATTTATACTCCTATTTATTTAAAGAACACTGCTACTAGCTAGAAGGACATAAAGAGT
GAAAAGAATGGACGAGGCGCTGTTTCCTAAGAAAGAAGGG
Found at i:20760207 original size:26 final size:26
Alignment explanation
Indices: 20760173--20760222 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20760163 TATTTTTTTT
*
20760173 AAATATTAATAATTTATAATTAATTA
1 AAATATTAATAATTAATAATTAATTA
20760199 AAATATTAATAATTAATAATTAAT
1 AAATATTAATAATTAATAATTAAT
20760223 ATATCAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATTAATAATTAATAATTAATTA
Found at i:20760215 original size:7 final size:7
Alignment explanation
Indices: 20760177--20760223 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
20760167 TTTTTTAAAT
20760177 ATTAATA
1 ATTAATA
*
20760184 ATTTATA
1 ATTAATA
20760191 ATTAATTA
1 ATTAA-TA
20760199 A--AAT-
1 ATTAATA
20760203 ATTAATA
1 ATTAATA
20760210 ATTAATA
1 ATTAATA
20760217 ATTAATA
1 ATTAATA
20760224 TATCAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 1 0.03
5 1 0.03
6 5 0.15
7 24 0.71
8 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTAATA
Found at i:20760239 original size:8 final size:8
Alignment explanation
Indices: 20760195--20760241 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
20760185 TTTATAATTA
*
20760195 ATTAAAAT
1 ATTAATAT
20760203 ATTAATA-
1 ATTAATAT
20760210 ATTAATA-
1 ATTAATAT
20760217 ATTAATAT
1 ATTAATAT
*
20760225 ATCAATAT
1 ATTAATAT
*
20760233 TTTAATAT
1 ATTAATAT
20760241 A
1 A
20760242 ATTTAATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
ATTAATAT
Found at i:20760964 original size:22 final size:22
Alignment explanation
Indices: 20760908--20760964 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
20760898 CCACTTAGAG
20760908 AGAGAATAAGAGAGGAAAGAAAA
1 AGAGAA-AAGAGAGGAAAGAAAA
* *
20760931 TGAGAAGAGAGA-GAAAGAAAA
1 AGAGAAAAGAGAGGAAAGAAAA
*
20760952 AGGGAAAATGAGA
1 AGAGAAAA-GAGA
20760965 AAAAAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.50
22 9 0.32
23 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.05
Consensus pattern (22 bp):
AGAGAAAAGAGAGGAAAGAAAA
Found at i:20761580 original size:61 final size:62
Alignment explanation
Indices: 20761485--20761610 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 62
20761475 ATTCGCAAGG
* *
20761485 TTTACAGATCTAGTGTTAATCTATCTTCAGTTCTCAGTTCTCAGTTCTAGTG-TTGTGAAAA
1 TTTACAGATCTAGTATTAATCCATCTTCAGTTCTCAGTTCTCAGTTCTAGTGTTTGTGAAAA
* * **
20761546 TTTACAGATCTCGTATTAATCCATTTTCAGTTCTCAGTTCTTTGTTCTAGTGTTTGTGAAAA
1 TTTACAGATCTAGTATTAATCCATCTTCAGTTCTCAGTTCTCAGTTCTAGTGTTTGTGAAAA
20761608 TTT
1 TTT
20761611 TGGGGAGTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 46 0.79
62 12 0.21
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (62 bp):
TTTACAGATCTAGTATTAATCCATCTTCAGTTCTCAGTTCTCAGTTCTAGTGTTTGTGAAAA
Found at i:20770704 original size:271 final size:268
Alignment explanation
Indices: 20770211--20770718 Score: 692
Period size: 271 Copynumber: 1.9 Consensus size: 268
20770201 GTATTCGTAA
* **
20770211 TTTGGCCTAAATGTTTTAAGCATGCTTAATCCAGCTAAAGGGATGTTAGTTACTTGTTGAATAAT
1 TTTGCCCTAAATGTTTTAAGCATGCTTAATCCAGCTAAAGGGATGTTAGTTACTTACTGAATAAT
* * * * * *
20770276 TAGACTCAGCTTCCTTCAATTTTTTTTCAGGTTGTGATTTGATCAATCACGCGAGAATTTCGAGT
66 TAGACTCACCTTCCTTCAAATTTTTTTCAGGTTGTGATTTGATCAACCACGCAAAAATTTCGAGG
* * * *
20770341 AGTGATATTTAATCTAGTAACATTTAAATTGTCTAGGATTTATTTAAATATTATAAATATCAAAC
131 AGTGATATTTAATCTAGTAACACTTAAATTATCTAGGATTTATTTAAATAATATAAACATCAAAC
20770406 TATCTTAATTAGTATTCAAACTTTTATCTTGACATAATAGCTNAATATTTTGTCTTGGCATTTGT
196 TATCTTAATTAGTATTCAAACTTTTATCTTGACATAATAGCT-AATATTTTGTCTTGGCATTTGT
20770471 AAATGATAT
260 AAATGATAT
* * * * *
20770480 TTTGCCCTAAATGTTTTAAGCATGTTTAATCCGGCTGAAGGGATGTTAGTTACTTACTGAGTAGT
1 TTTGCCCTAAATGTTTTAAGCATGCTTAATCCAGCTAAAGGGATGTTAGTTACTTACTGAATAAT
* * * * *
20770545 TGGACTCACCCCTTCCTTCAAATTTTTTTCGGGTTGTGATTTGGTCAACCACGCAAAAATTTTGG
66 TAGACTCA--CCTTCCTTCAAATTTTTTTCAGGTTGTGATTTGATCAACCACGCAAAAATTTCGA
* * * * * *
20770610 GGAGTGATGTTTAATTTTGTAGCACTTAAATTATCTAGGATTTATTTAAATAATATGAACATCGA
129 GGAGTGATATTTAATCTAGTAACACTTAAATTATCTAGGATTTATTTAAATAATATAAACATCAA
* * * *
20770675 ACTATCTTAATTAGTATTCAGATTTTTATCTTGACTTAGTAGCT
194 ACTATCTTAATTAGTATTCAAACTTTTATCTTGACATAATAGCT
20770719 TTATGGTTTT
Statistics
Matches: 204, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
269 64 0.31
271 140 0.69
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (268 bp):
TTTGCCCTAAATGTTTTAAGCATGCTTAATCCAGCTAAAGGGATGTTAGTTACTTACTGAATAAT
TAGACTCACCTTCCTTCAAATTTTTTTCAGGTTGTGATTTGATCAACCACGCAAAAATTTCGAGG
AGTGATATTTAATCTAGTAACACTTAAATTATCTAGGATTTATTTAAATAATATAAACATCAAAC
TATCTTAATTAGTATTCAAACTTTTATCTTGACATAATAGCTAATATTTTGTCTTGGCATTTGTA
AATGATAT
Found at i:20782050 original size:12 final size:12
Alignment explanation
Indices: 20782028--20782069 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
20782018 AAAAATCATA
20782028 TTTAT-AATTTT
1 TTTATAAATTTT
20782039 TTTATAAATTTT
1 TTTATAAATTTT
*
20782051 TTATATNAATTTT
1 TT-TATAAATTTT
20782064 TTTATA
1 TTTATA
20782070 TTTTTTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 5 0.19
12 11 0.41
13 11 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATAAATTTT
Found at i:20789944 original size:26 final size:26
Alignment explanation
Indices: 20789915--20789964 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20789905 TTTTACAATA
* *
20789915 AAATTTATCAAACA-TTAATTAAAATC
1 AAATTT-TAAAACAGTTAATGAAAATC
20789941 AAATTTTAAAACAGTTAATGAAAA
1 AAATTTTAAAACAGTTAATGAAAA
20789965 GGAGTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (26 bp):
AAATTTTAAAACAGTTAATGAAAATC
Found at i:20805268 original size:17 final size:16
Alignment explanation
Indices: 20805234--20805285 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
20805224 TTTATCTCTA
*
20805234 TAAAATTTTAAAAATTT
1 TAAAATTTT-ATAATTT
20805251 TAACATATTTT-TAATTTT
1 TAA-A-ATTTTATAA-TTT
20805269 TAAAATTTTATAATTT
1 TAAAATTTTATAATTT
20805285 T
1 T
20805286 CTTAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
16 9 0.30
17 9 0.30
18 7 0.23
19 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAATTTTATAATTT
Found at i:20807114 original size:35 final size:35
Alignment explanation
Indices: 20807022--20807166 Score: 130
Period size: 35 Copynumber: 4.1 Consensus size: 35
20807012 TTGTGTGAAG
* * **
20807022 TAGTTATTCTACATGGAGTAGTGCACCACTTATTC
1 TAGTTATTCTACGTGAAGTAGTGCTTCACTTATTC
*** * * *
20807057 TAGTTATTCTGTATGAAATAGTGCTTCA-TATGTTT
1 TAGTTATTCTACGTGAAGTAGTGCTTCACT-TATTC
* *
20807092 TAGTTGTTCTACGTGAAGTAGTGTTTCACTTATTC
1 TAGTTATTCTACGTGAAGTAGTGCTTCACTTATTC
* * * *
20807127 TAGTTATTCTACGTGAAGTAATGTTTCACCTATTT
1 TAGTTATTCTACGTGAAGTAGTGCTTCACTTATTC
20807162 TAGTT
1 TAGTT
20807167 GCTCTCATTA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
34 1 0.01
35 86 0.98
36 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (35 bp):
TAGTTATTCTACGTGAAGTAGTGCTTCACTTATTC
Found at i:20807978 original size:27 final size:27
Alignment explanation
Indices: 20807940--20808004 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
20807930 CAACATGTCT
* *
20807940 GTCATTCCACTTGTGGTATTTCACCAC
1 GTCATTCAACTTGTCGTATTTCACCAC
* *
20807967 GTCATTCAACTTGTCGTGTTTCACCAT
1 GTCATTCAACTTGTCGTATTTCACCAC
20807994 GTCATTCAACT
1 GTCATTCAACT
20808005 CATGTCGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (27 bp):
GTCATTCAACTTGTCGTATTTCACCAC
Found at i:20808067 original size:69 final size:69
Alignment explanation
Indices: 20807990--20808130 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
20807980 TCGTGTTTCA
* * *
20807990 CCATGTCATTCAACTCATGTCGTGTTTTGCCACATTAGTCAACTATGTCATTTTTCACCACATCA
1 CCATGTCATTCAACTCATGTCGTGTTTCGCCACATCAGTCAACTATGTCATGTTTCACCACATCA
20808055 CTTG
66 CTTG
* * * * *
20808059 CCATGTCATTCAACTCATGTCGTGTTTCGTCACGTCATTCAACTATGTCGTGTTTCGCCACATCA
1 CCATGTCATTCAACTCATGTCGTGTTTCGCCACATCAGTCAACTATGTCATGTTTCACCACATCA
20808124 CTTG
66 CTTG
20808128 CCA
1 CCA
20808131 CGTGTTTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.36
Consensus pattern (69 bp):
CCATGTCATTCAACTCATGTCGTGTTTCGCCACATCAGTCAACTATGTCATGTTTCACCACATCA
CTTG
Found at i:20808407 original size:2 final size:2
Alignment explanation
Indices: 20808400--20808427 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20808390 AGATTACCTT
20808400 TA 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 TA
20808428 ACATACACAA
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):
TA
Found at i:20809087 original size:30 final size:30
Alignment explanation
Indices: 20809051--20809120 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
20809041 CATTTGATAC
*
20809051 TTAATAAAATTTGACTTGACCGAGTGAAAA
1 TTAATAAAATTTGACTTGACCAAGTGAAAA
*
20809081 TTAATAAAATTTGGCTTGACCAAGTGAAAA
1 TTAATAAAATTTGACTTGACCAAGTGAAAA
20809111 -TAATAAAATT
1 TTAATAAAATT
20809121 GGAACTATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (30 bp):
TTAATAAAATTTGACTTGACCAAGTGAAAA
Found at i:20809923 original size:16 final size:17
Alignment explanation
Indices: 20809892--20809929 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20809882 CTTTTTCTTT
20809892 CTATTTAGATTATTTAA
1 CTATTTAGATTATTTAA
*
20809909 CTATTTATA-TATTTAA
1 CTATTTAGATTATTTAA
*
20809925 TTATT
1 CTATT
20809930 GCGTGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (17 bp):
CTATTTAGATTATTTAA
Found at i:20816129 original size:50 final size:50
Alignment explanation
Indices: 20816069--20816189 Score: 208
Period size: 50 Copynumber: 2.4 Consensus size: 50
20816059 TTAACATTCA
* *
20816069 GTCGCTAGCTTTATCGCTCATAATTTGGCTGTAATGATAATATGTTATTG
1 GTCGCAAGCTTCATCGCTCATAATTTGGCTGTAATGATAATATGTTATTG
20816119 GTCGCAAGCTTCATCGCTCATAATTTGGCTGTAATGATAATATGTTATTG
1 GTCGCAAGCTTCATCGCTCATAATTTGGCTGTAATGATAATATGTTATTG
20816169 G-CTGCAAGCTTCATCGCTCAT
1 GTC-GCAAGCTTCATCGCTCAT
20816190 CTTTGGCCTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 1 0.01
50 67 0.99
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (50 bp):
GTCGCAAGCTTCATCGCTCATAATTTGGCTGTAATGATAATATGTTATTG
Found at i:20819644 original size:24 final size:23
Alignment explanation
Indices: 20819615--20819682 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
20819605 TAATTTTCAT
20819615 TATTAATATATATAATAAAAATAA
1 TATTAATA-ATATAATAAAAATAA
*
20819639 TATTAACAA-ATGAATAAAAAATAA
1 TATTAATAATAT-AAT-AAAAATAA
* *
20819663 TAATAATAATAAAATAAAAA
1 TATTAATAATATAATAAAAA
20819683 ATAAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.05
23 9 0.24
24 25 0.68
25 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (23 bp):
TATTAATAATATAATAAAAATAA
Found at i:20819683 original size:24 final size:25
Alignment explanation
Indices: 20819651--20819703 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
20819641 TTAACAAATG
*
20819651 AATAAAAAATAATAATAAT-AA-TAA
1 AATAAAAAATAA-AAAAATAAACTAA
20819675 AATAAAAAATAAAAAAATAAACTAA
1 AATAAAAAATAAAAAAATAAACTAA
20819700 AATA
1 AATA
20819704 TATATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
25 7 0.27
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (25 bp):
AATAAAAAATAAAAAAATAAACTAA
Found at i:20819691 original size:33 final size:36
Alignment explanation
Indices: 20819626--20819691 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
20819616 ATTAATATAT
* *
20819626 ATAATAAAAATAATATTAACAAATGAATAAAAAATA
1 ATAATAAAAATAATAATAAAAAATGAATAAAAAATA
*
20819662 ATAATAATAATAA-AATAAAAAAT-AA-AAAAA
1 ATAATAAAAATAATAATAAAAAATGAATAAAAA
20819692 TAAACTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.19
34 2 0.07
35 8 0.30
36 12 0.44
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (36 bp):
ATAATAAAAATAATAATAAAAAATGAATAAAAAATA
Found at i:20819953 original size:2 final size:2
Alignment explanation
Indices: 20819946--20819997 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
20819936 TCAAAGTCAC
20819946 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
20819988 TA TA TA TA TA
1 TA TA TA TA TA
20819998 GAAAGACATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20821130 original size:29 final size:29
Alignment explanation
Indices: 20821098--20821169 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
20821088 CCTGTTCACA
* * *
20821098 TACACCTTCTTCTCTTGTACCTATTCTTG
1 TACAACTTCTTCTCTTGTACCTATCCATG
* *
20821127 TACAACTTACTCCAC-TGTACCTATCCATG
1 TACAACTT-CTTCTCTTGTACCTATCCATG
*
20821156 TACAGCTT-TTCTCT
1 TACAACTTCTTCTCT
20821170 ATCAGCTCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
27 3 0.09
29 26 0.79
30 4 0.12
ACGTcount: A:0.19, C:0.32, G:0.07, T:0.42
Consensus pattern (29 bp):
TACAACTTCTTCTCTTGTACCTATCCATG
Found at i:20823337 original size:2 final size:2
Alignment explanation
Indices: 20823330--20823376 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
20823320 NNNNNNNNNA
*
20823330 AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT AT -T AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
20823371 AA AT AT
1 AT AT AT
20823377 TTAAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20823804 original size:22 final size:23
Alignment explanation
Indices: 20823762--20823804 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20823752 TTGATTACAG
20823762 ATATAAATACATTTATATATTTT
1 ATATAAATACATTTATATATTTT
* *
20823785 ATATAATTAC-TTTCTATATT
1 ATATAAATACATTTATATATT
20823805 GGATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATAAATACATTTATATATTTT
Found at i:20824075 original size:18 final size:19
Alignment explanation
Indices: 20824038--20824075 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
20824028 ATATGTTAGT
**
20824038 AGAAAAGACATTAATTTTA
1 AGAAAAGACATTAAAATTA
20824057 AGAAAA-ACATTAAAATTA
1 AGAAAAGACATTAAAATTA
20824075 A
1 A
20824076 ATAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AGAAAAGACATTAAAATTA
Found at i:20828077 original size:21 final size:21
Alignment explanation
Indices: 20828053--20828106 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
20828043 AGTTTTTACG
20828053 TATTGCGTGACTGACTTTAGA
1 TATTGCGTGACTGACTTTAGA
* * *
20828074 TATTGCGTGATTGACTTTGGG
1 TATTGCGTGACTGACTTTAGA
*
20828095 TATTGCATGACT
1 TATTGCGTGACT
20828107 AATTTTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (21 bp):
TATTGCGTGACTGACTTTAGA
Found at i:20828125 original size:26 final size:26
Alignment explanation
Indices: 20828096--20828331 Score: 212
Period size: 26 Copynumber: 9.6 Consensus size: 26
20828086 GACTTTGGGT
* *
20828096 ATTGCATGACTAATTTTTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
20828122 ATTGCATGACTAGTTTCTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
20828148 ATTACGTGACTA--ATTT--T-AGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
20828169 ATTGCGTGACTAGTTTTTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
20828195 ATTGCGTGACTAGTTTCTGATAAAGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* **
20828221 ATTGTGTGACTA-ACTTTG----GGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
20828242 ATTGCGTGACTAGTTTTTTATAAGGT
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
20828268 ATTGCGTGACTAGCTTCTT-ATAAGGC
1 ATTGCGTGACTAG-TTTTTGATAAGGC
* *
20828294 ATTGCGTGACT--TGTTAG-TAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
20828317 ATTGCATGACTAGTT
1 ATTGCGTGACTAGTT
20828332 AGTAAGGCAT
Statistics
Matches: 169, Mismatches: 27, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
21 28 0.17
22 4 0.02
23 21 0.12
24 2 0.01
25 5 0.03
26 105 0.62
27 4 0.02
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (26 bp):
ATTGCGTGACTAGTTTTTGATAAGGC
Found at i:20828168 original size:21 final size:21
Alignment explanation
Indices: 20828144--20828185 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20828134 GTTTCTGATA
20828144 AGGCATTACGTGACTAATTTT
1 AGGCATTACGTGACTAATTTT
* *
20828165 AGGCATTGCGTGACTAGTTTT
1 AGGCATTACGTGACTAATTTT
20828186 TGATAAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (21 bp):
AGGCATTACGTGACTAATTTT
Found at i:20828173 original size:73 final size:73
Alignment explanation
Indices: 20828096--20828331 Score: 310
Period size: 73 Copynumber: 3.2 Consensus size: 73
20828086 GACTTTGGGT
* * *
20828096 ATTGCATGACTAATTTTTGATAAGGCATTGCATGACTAGTTTCTGATAAGGCATTACGTGACTAA
1 ATTGCATGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAA
20828161 TTTTAGGC
66 TTTTAGGC
* * *
20828169 ATTGCGTGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAAGCATTGTGTGACTAA
1 ATTGCATGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAA
* *
20828234 CTTTGGGC
66 TTTTAGGC
* * * * * **
20828242 ATTGCGTGACTAGTTTTTTATAAGGTATTGCGTGACTAGCTTCTTATAAGGCATTGCGTGACTTG
1 ATTGCATGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAA
*
20828307 TTAGTAAGGC
66 TT--TTAGGC
20828317 ATTGCATGACTAGTT
1 ATTGCATGACTAGTT
20828332 AGTAAGGCAT
Statistics
Matches: 141, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
73 123 0.87
75 18 0.13
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (73 bp):
ATTGCATGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAA
TTTTAGGC
Found at i:20828352 original size:23 final size:23
Alignment explanation
Indices: 20828288--20828348 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
20828278 TAGCTTCTTA
* *
20828288 TAAGGCATTGCGTGACTTGTTAG
1 TAAGGCATTGCATGACTAGTTAG
20828311 TAAGGCATTGCATGACTAGTTAG
1 TAAGGCATTGCATGACTAGTTAG
20828334 TAAGGCATTGC-TGAC
1 TAAGGCATTGCATGAC
20828349 CTAGGCATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (23 bp):
TAAGGCATTGCATGACTAGTTAG
Found at i:20828394 original size:22 final size:22
Alignment explanation
Indices: 20828362--20828418 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
20828352 GGCATTGCTT
* *
20828362 AAAAATCAGTCGCGTAATATCTG
1 AAAAAT-AGTCACGTAATATCTA
* *
20828385 AAAACTAGTCACGTAATGTCTA
1 AAAAATAGTCACGTAATATCTA
20828407 AAAAATAGTCAC
1 AAAAATAGTCAC
20828419 ACAGTGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
AAAAATAGTCACGTAATATCTA
Found at i:20840523 original size:150 final size:149
Alignment explanation
Indices: 20840251--20840537 Score: 387
Period size: 150 Copynumber: 1.9 Consensus size: 149
20840241 TTGCCTTTGG
* * * * *
20840251 AGTGGGAATATGGCTCAATTGAGGGGAACAATTATGAACCATGCATTGTACTCTTTTTTCCTTCT
1 AGTGGCAACATGGCTCAATTGAAGAGAACAATTATGAACCATGCATTGTACTATTTTTTCCTTCT
* ** *
20840316 AACCAATTTTTGTCCCATTGGGTTTTTTTGGCTTAAGGTTTTTAATGAGGCAATACAATGGACAT
66 AACCAATTTTTGTCCCACTGGGTTTTTTCAGCTTAAGGTTTTTAATGAAGCAATACAATGGACAT
20840381 TCAAGGGATAAACCCCAGA
131 TCAAGGGATAAACCCCAGA
*
20840400 AGTGGCAACATGGCTCAATTGAAGAGAAGCAATTATGGACCATGCATTGTACTATTTTTTCCTT-
1 AGTGGCAACATGGCTCAATTGAAGAGAA-CAATTATGAACCATGCATTGTACTATTTTTTCCTTC
** ** * * * *
20840464 TTGCTTGATTTTTGTTCCACTGGGTTTTTTCAGTTTAAGGTTTTTAATGAAGTAGTACAATGGAC
65 TAAC-CAATTTTTGTCCCACTGGGTTTTTTCAGCTTAAGGTTTTTAATGAAGCAATACAATGGAC
20840529 ATTCAAGGG
129 ATTCAAGGG
20840538 GAAGTATTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
149 26 0.22
150 92 0.78
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
AGTGGCAACATGGCTCAATTGAAGAGAACAATTATGAACCATGCATTGTACTATTTTTTCCTTCT
AACCAATTTTTGTCCCACTGGGTTTTTTCAGCTTAAGGTTTTTAATGAAGCAATACAATGGACAT
TCAAGGGATAAACCCCAGA
Found at i:20850913 original size:16 final size:18
Alignment explanation
Indices: 20850869--20850907 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20850859 TAAACAAACA
*
20850869 CTTGTCATTACACACAAG
1 CTTGTCATTGCACACAAG
*
20850887 CTTGTCATTGCACACATG
1 CTTGTCATTGCACACAAG
20850905 CTT
1 CTT
20850908 TATTGCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (18 bp):
CTTGTCATTGCACACAAG
Found at i:20853345 original size:23 final size:21
Alignment explanation
Indices: 20853314--20853370 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
20853304 CCATTTTATT
*
20853314 CATTCTAAATTATTTTAGTATAA
1 CATTTTAAATT-TTTTAG-ATAA
* *
20853337 CATTTTAAAGTTTTTAGATGA
1 CATTTTAAATTTTTTAGATAA
*
20853358 CAGTTTAAATTTT
1 CATTTTAAATTTT
20853371 GGAAATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 14 0.48
22 6 0.21
23 9 0.31
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (21 bp):
CATTTTAAATTTTTTAGATAA
Found at i:20853783 original size:11 final size:10
Alignment explanation
Indices: 20853765--20853816 Score: 61
Period size: 11 Copynumber: 4.9 Consensus size: 10
20853755 ATTACTCAAT
20853765 AAAAATAATA
1 AAAAATAATA
20853775 AACAAATAATA
1 AA-AAATAATA
20853786 AAAAA-AGATA
1 AAAAATA-ATA
20853796 AAAAGATAATA
1 AAAA-ATAATA
20853807 AATAAATAAT
1 AA-AAATAAT
20853817 TCAAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 12 0.32
11 21 0.57
12 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAAATAATA
Found at i:20853796 original size:21 final size:20
Alignment explanation
Indices: 20853762--20853808 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
20853752 AAAATTACTC
*
20853762 AATAAAAATAATAAACAA-AT
1 AATAAAAAAAATAAA-AAGAT
20853782 AATAAAAAAAGATAAAAAGAT
1 AATAAAAAAA-ATAAAAAGAT
20853803 AATAAA
1 AATAAA
20853809 TAAATAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (20 bp):
AATAAAAAAAATAAAAAGAT
Found at i:20862264 original size:27 final size:29
Alignment explanation
Indices: 20862199--20862255 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
20862189 ACACGTGTGG
*
20862199 TGGTGGTGGTGGTGGTGCAAAAGGGTCCCA
1 TGGTGGAGGTGGTGGTGCAAAAGGGT-CCA
*
20862229 TGGGGGAGGTGGTGGTGCAAAAGGGTC
1 TGGTGGAGGTGGTGGTGCAAAAGGGTC
20862256 TTGTGGAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.18, C:0.11, G:0.51, T:0.21
Consensus pattern (29 bp):
TGGTGGAGGTGGTGGTGCAAAAGGGTCCA
Found at i:20884814 original size:2 final size:2
Alignment explanation
Indices: 20884807--20884837 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20884797 AAATAAAAAC
20884807 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20884838 TTATGGGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20884829 original size:15 final size:15
Alignment explanation
Indices: 20884809--20884837 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20884799 ATAAAAACAT
20884809 ATATATATATATATA
1 ATATATATATATATA
20884824 ATATATATATATAT
1 ATATATATATATAT
20884838 TTATGGGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:20905014 original size:17 final size:18
Alignment explanation
Indices: 20904988--20905024 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20904978 CAATCTCAAA
*
20904988 TATTATTTTATCAAG-AT
1 TATTAATTTATCAAGCAT
20905005 TATTAATTTATCAAGCAT
1 TATTAATTTATCAAGCAT
20905023 TA
1 TA
20905025 ATTTATTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (18 bp):
TATTAATTTATCAAGCAT
Found at i:20905090 original size:21 final size:21
Alignment explanation
Indices: 20905064--20905131 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
20905054 ACAAGATAAA
20905064 TGTAATAAAATTACAATTACT
1 TGTAATAAAATTACAATTACT
*
20905085 TGTAATTAAGA--ACTAATTA-T
1 TGTAA-TAAAATTAC-AATTACT
* *
20905105 AGAAATAAAATTACAATTACT
1 TGTAATAAAATTACAATTACT
20905126 TGTAAT
1 TGTAAT
20905132 TAAGAACTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 17 0.47
22 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (21 bp):
TGTAATAAAATTACAATTACT
Found at i:20905112 original size:41 final size:41
Alignment explanation
Indices: 20905067--20905150 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
20905057 AGATAAATGT
20905067 AATAAAATTACAATTACTTGTAATTAAGAACTAATTATAGA
1 AATAAAATTACAATTACTTGTAATTAAGAACTAATTATAGA
20905108 AATAAAATTACAATTACTTGTAATTAAGAACTAATTATAGA
1 AATAAAATTACAATTACTTGTAATTAAGAACTAATTATAGA
20905149 AA
1 AA
20905151 AAACTATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (41 bp):
AATAAAATTACAATTACTTGTAATTAAGAACTAATTATAGA
Found at i:20920797 original size:16 final size:17
Alignment explanation
Indices: 20920766--20920800 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20920756 GGCCTTGCTC
*
20920766 AAACTCTGATTTTTCAT
1 AAACTCTGACTTTTCAT
20920783 AAACTCTG-CTTTTCAT
1 AAACTCTGACTTTTCAT
20920799 AA
1 AA
20920801 TTCGAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (17 bp):
AAACTCTGACTTTTCAT
Found at i:20925470 original size:26 final size:24
Alignment explanation
Indices: 20925439--20925486 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
20925429 TACAATGATT
20925439 TTATTTATATATAATTGATATATTAA
1 TTATTTATATAT-ATT-ATATATTAA
* *
20925465 TTATTTTTGTATATTATATATT
1 TTATTTATATATATTATATATT
20925487 GTCTTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 3 0.15
26 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATTTATATATATTATATATTAA
Found at i:20936724 original size:21 final size:21
Alignment explanation
Indices: 20936700--20936740 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20936690 TAATCTTTCT
*
20936700 TAAGACATTATTGATTTTAAA
1 TAAGACATTATTAATTTTAAA
**
20936721 TAAGATTTTATTAATTTTAA
1 TAAGACATTATTAATTTTAA
20936741 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAGACATTATTAATTTTAAA
Found at i:20937252 original size:15 final size:14
Alignment explanation
Indices: 20937226--20937255 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
20937216 ATTTATAATT
20937226 TTATAATAATTATA
1 TTATAATAATTATA
20937240 TTATAATTAATTATA
1 TTATAA-TAATTATA
20937255 T
1 T
20937256 AAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAATAATTATA
Found at i:20938238 original size:19 final size:19
Alignment explanation
Indices: 20938201--20938256 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
20938191 AGGAAACAAA
20938201 TAATTTTAT-TAATTATTTTT
1 TAATTTTATAT-A-TATTTTT
*
20938221 TACTTTTATATATATTTTT
1 TAATTTTATATATATTTTT
20938240 TAATTTTATATAT-TTTT
1 TAATTTTATATATATTTT
20938257 AATATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 9 0.27
21 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TAATTTTATATATATTTTT
Found at i:20938249 original size:17 final size:19
Alignment explanation
Indices: 20938214--20938256 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
20938204 TTTTATTAAT
*
20938214 TATTTTTTACTTTTATATA
1 TATTTTTTACATTTATATA
20938233 TATTTTTTA-ATTT-TATA
1 TATTTTTTACATTTATATA
20938250 TATTTTT
1 TATTTTT
20938257 AATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTTACATTTATATA
Found at i:20939061 original size:28 final size:29
Alignment explanation
Indices: 20939004--20939063 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
20938994 AATAAAAGTA
* * *
20939004 AAATTATATTAAAATATTATTACGTTATT
1 AAATTATATAAAAATATTAATACATTATT
20939033 AAATTA-ATAAAAATATTAATA-ATTAATT
1 AAATTATATAAAAATATTAATACATT-ATT
20939061 AAA
1 AAA
20939064 AGTTGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 19 0.70
29 6 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
AAATTATATAAAAATATTAATACATTATT
Found at i:20950091 original size:69 final size:69
Alignment explanation
Indices: 20949975--20950121 Score: 177
Period size: 69 Copynumber: 2.1 Consensus size: 69
20949965 TTATGATATT
* * ** * * * * * *
20949975 ACACGTCATGTATAAAAACTTGTGACAAGTTATGGTTAGCGTTTTACATGTCATGTACAAAAACT
1 ACACGTCATGTACAAAAACCTGTGACAAGCCATAGTTAGCATGTTACATGCCATATACAAAAACC
*
20950040 TGTG
66 TATG
*
20950044 ACACGTCATGTACAAAAACCTGTGCCAAGCCATAGTTAGCATGTTACATGCCATATACAAAAACC
1 ACACGTCATGTACAAAAACCTGTGACAAGCCATAGTTAGCATGTTACATGCCATATACAAAAACC
20950109 TATG
66 TATG
*
20950113 ACAAGTCAT
1 ACACGTCAT
20950122 AGTTAACCTG
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (69 bp):
ACACGTCATGTACAAAAACCTGTGACAAGCCATAGTTAGCATGTTACATGCCATATACAAAAACC
TATG
Found at i:20950123 original size:45 final size:45
Alignment explanation
Indices: 20950044--20950166 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 45
20950034 AAAACTTGTG
* * * * *
20950044 ACACGTCATGTACAAAAACCTGTGCCAAGCCATAGTTAGCATGTT
1 ACACGCCATATACAAAAACCTATGACAAGCCATAGTTAACATGTT
* * *
20950089 ACATGCCATATACAAAAACCTATGACAAGTCATAGTTAACCTGTT
1 ACACGCCATATACAAAAACCTATGACAAGCCATAGTTAACATGTT
* * ** *
20950134 ACACGTCATGTACAAAAATATGTGACAAGCCAT
1 ACACGCCATATACAAAAACCTATGACAAGCCAT
20950167 GTACAAAAAC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (45 bp):
ACACGCCATATACAAAAACCTATGACAAGCCATAGTTAACATGTT
Found at i:20950183 original size:24 final size:24
Alignment explanation
Indices: 20950140--20950186 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20950130 TGTTACACGT
* *
20950140 CATGTACAAAAATATGTGACAAGC
1 CATGTACAAAAACATATGACAAGC
*
20950164 CATGTACAAAAACCTATGACAAG
1 CATGTACAAAAACATATGACAAG
20950187 TTATGATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (24 bp):
CATGTACAAAAACATATGACAAGC
Found at i:20950220 original size:69 final size:69
Alignment explanation
Indices: 20950084--20950213 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 69
20950074 CATAGTTAGC
* *
20950084 ATGTTACATGCCATATACAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAA
1 ATGTGACAAGCCATATACAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAA
20950149 AAAT
66 AAAT
* * ***
20950153 ATGTGACAAGCCATGTACAAAAACCTATGACAAGTTAT-GATTAGGTTGTTACACGTCATGT
1 ATGTGACAAGCCATATACAAAAACCTATGACAAGTCATAG-TTAACCTGTTACACGTCATGT
20950214 TGAAAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 52 0.98
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (69 bp):
ATGTGACAAGCCATATACAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAA
AAAT
Found at i:20950220 original size:114 final size:113
Alignment explanation
Indices: 20949973--20950220 Score: 257
Period size: 114 Copynumber: 2.2 Consensus size: 113
20949963 CGTTATGATA
* * * * * * * *
20949973 TTACACGTCATGTATAAAAACTTGTGACAAGTTATGGTTAGCGTTTTACATGTCATGTACAAAAA
1 TTACACGTCATGT-TAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAAAAA
* * * *
20950038 CTTGTGACACGTCATGTACAAAAACCTGTGCCAAGCCATAGTTAGCATG
65 CTTGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAGTTAGCATG
* * * *
20950087 TTACATGCCATATACAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAAAAA
1 TTACACGTCATGT-TAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAAAAA
** **
20950152 -TATGTGACAAGCCATGTACAAAAACCTATGACAAGTTAT-GATTAGGTTG
65 CT-TGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAG-TTAGCATG
20950201 TTACACGTCATGTTGAAAAA
1 TTACACGTCATGTT-AAAAA
20950221 AATATTATTG
Statistics
Matches: 107, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
113 2 0.02
114 105 0.98
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (113 bp):
TTACACGTCATGTTAAAAACCTATGACAAGTCATAGTTAACCTGTTACACGTCATGTACAAAAAC
TTGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAGTTAGCATG
Found at i:20950282 original size:26 final size:25
Alignment explanation
Indices: 20950228--20950302 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
20950218 AAAAATATTA
*
20950228 TTGTTACATGCCATG-TACAAAAAC
1 TTGTTACATGCCATGTTAAAAAAAC
* * *
20950252 ATGTTACATGTCATGGTTAAAAAAAG
1 TTGTTACATGCCAT-GTTAAAAAAAC
*
20950278 TTGTTACATGCCATGTTGAAAAAAC
1 TTGTTACATGCCATGTTAAAAAAAC
20950303 AATATTGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 12 0.29
25 10 0.24
26 19 0.46
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (25 bp):
TTGTTACATGCCATGTTAAAAAAAC
Found at i:20950313 original size:32 final size:29
Alignment explanation
Indices: 20950277--20950348 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
20950267 GTTAAAAAAA
*
20950277 GTTGTTACATGCCATGTTGAAAAAACAATATT
1 GTTGTTACACGCCATGTTG--AAAA-AATATT
**
20950309 GTTGTTACACGTTATGTTGAAAAAATATT
1 GTTGTTACACGCCATGTTGAAAAAATATT
20950338 GTTGTTACACG
1 GTTGTTACACG
20950349 ACATATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.46
30 4 0.11
32 16 0.43
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (29 bp):
GTTGTTACACGCCATGTTGAAAAAATATT
Found at i:20950360 original size:29 final size:29
Alignment explanation
Indices: 20950298--20950361 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
20950288 CCATGTTGAA
** * *
20950298 AAAACAATATTGTTGTTACACGTTATGTTG
1 AAAA-AATATTGTTGTTACACGACATATTC
20950328 AAAAAATATTGTTGTTACACGACATATTC
1 AAAAAATATTGTTGTTACACGACATATTC
20950357 AAAAA
1 AAAAA
20950362 CATTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGACATATTC
Found at i:20955779 original size:29 final size:28
Alignment explanation
Indices: 20955713--20955785 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
20955703 CAAAAAAATT
*
20955713 TAAATAAGTCCTTATCATTTTATTGCAT
1 TAAATAAGTCCTTATCATTTTATTGCAC
*
20955741 TCAATCAAGTCCTTAT-ATTTTATATTG-AGC
1 TAAAT-AAGTCCTTATCA-TTT-TATTGCA-C
20955771 TAAATAAGTCCTTAT
1 TAAATAAGTCCTTAT
20955786 GACAAATGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.13
29 24 0.63
30 9 0.24
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (28 bp):
TAAATAAGTCCTTATCATTTTATTGCAC
Found at i:20957965 original size:16 final size:16
Alignment explanation
Indices: 20957943--20957983 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
20957933 AAAGGTCTGG
20957943 ATTTATTTACTTTTGGT
1 ATTTATTTA-TTTTGGT
20957960 -TTTATTTTATTTTGGT
1 ATTTA-TTTATTTTGGT
20957976 ATTTATTT
1 ATTTATTT
20957984 TTTATTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (16 bp):
ATTTATTTATTTTGGT
Found at i:20957980 original size:17 final size:18
Alignment explanation
Indices: 20957943--20957984 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
20957933 AAAGGTCTGG
20957943 ATTTA-TTTACTTTTGGT
1 ATTTATTTTACTTTTGGT
20957960 -TTTATTTTA-TTTTGGT
1 ATTTATTTTACTTTTGGT
20957976 ATTTATTTT
1 ATTTATTTT
20957985 TTATTCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (18 bp):
ATTTATTTTACTTTTGGT
Found at i:20970558 original size:27 final size:26
Alignment explanation
Indices: 20970528--20970580 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
20970518 AAAGTATTCA
*
20970528 CTATT-TTTGAAATATCTTACTTCAAAC
1 CTATTATTCGAAAT-TCTTACTT-AAAC
*
20970555 CTATTATTCGAAATTGTTACTTAAAC
1 CTATTATTCGAAATTCTTACTTAAAC
20970581 TCCATGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (26 bp):
CTATTATTCGAAATTCTTACTTAAAC
Found at i:20973500 original size:31 final size:31
Alignment explanation
Indices: 20973356--20973516 Score: 121
Period size: 31 Copynumber: 5.2 Consensus size: 31
20973346 ATAAACCAAG
* * * * *
20973356 TCCAAACACCAAAGTAGAAGCAAATATCCAA
1 TCCAAATATCAAAGTTGAAACAAATATCAAA
* * * *
20973387 TCCAAAGT-TTAAGGTTGAAACTAATACCAAA
1 TCCAAA-TATCAAAGTTGAAACAAATATCAAA
* * *
20973418 TCTAAATGTCAGAA-TTGAAACAACTATCAAA
1 TCCAAATATCA-AAGTTGAAACAAATATCAAA
* * * *
20973449 TTCAAACA-CCAAGATCGAAACAAATATCAAA
1 TCCAAATATCAAAG-TTGAAACAAATATCAAA
*
20973480 TCCAAATATTAAAGTTGAAACAAATATCAAA
1 TCCAAATATCAAAGTTGAAACAAATATCAAA
20973511 TCCAAA
1 TCCAAA
20973517 AACTAATGTG
Statistics
Matches: 97, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.02
30 2 0.02
31 89 0.92
32 4 0.04
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (31 bp):
TCCAAATATCAAAGTTGAAACAAATATCAAA
Found at i:20981213 original size:39 final size:38
Alignment explanation
Indices: 20981160--20981241 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 38
20981150 TTTTTTATTG
20981160 ATTT-TTGTAAAGAGAGGTAGAAAAGAGAGAAATCATT
1 ATTTATTGTAAAGAGAGGTAGAAAAGAGAGAAATCATT
*
20981197 ATTTANTTGTAGAGAGAGGTAGAAAAGAGAGAAATCATT
1 ATTTA-TTGTAAAGAGAGGTAGAAAAGAGAGAAATCATT
20981236 ATTTAT
1 ATTTAT
20981242 GTTGAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 4 0.10
38 1 0.02
39 37 0.88
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.29
Consensus pattern (38 bp):
ATTTATTGTAAAGAGAGGTAGAAAAGAGAGAAATCATT
Found at i:20984898 original size:14 final size:14
Alignment explanation
Indices: 20984881--20984910 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20984871 CCACGATGAG
20984881 GAAAGAGAAAGGAT
1 GAAAGAGAAAGGAT
20984895 GAAAGAGAAAGGAT
1 GAAAGAGAAAGGAT
20984909 GA
1 GA
20984911 CGGTAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAAAGAGAAAGGAT
Found at i:20987573 original size:34 final size:34
Alignment explanation
Indices: 20987448--20987609 Score: 120
Period size: 34 Copynumber: 4.9 Consensus size: 34
20987438 ACGCTTGATG
* * * *
20987448 CTAAAGTTTTGGTCTTGACATGTAACATCTGGTA
1 CTAAAGCTTTGGCCTTGGCATGTAACATTTGGTA
* * *
20987482 CTGAAGCTTTGACCTTGGCATGTAAAATTT--T-
1 CTAAAGCTTTGGCCTTGGCATGTAACATTTGGTA
* * * *
20987513 -T-CA-CTTTGGCTTTGGTGCGTGTAACATTTGGTG
1 CTAAAGCTTTGGCCTT-G-GCATGTAACATTTGGTA
* *
20987546 CTCAAGCTTTGGTCTTGGCATGTAACATTTGGTA
1 CTAAAGCTTTGGCCTTGGCATGTAACATTTGGTA
* **
20987580 CTAAAGCTTTGACCTTGGCGCGTAACATTT
1 CTAAAGCTTTGGCCTTGGCATGTAACATTT
20987610 ACCGTTGAAG
Statistics
Matches: 98, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
28 8 0.08
29 2 0.02
30 12 0.12
32 2 0.02
34 64 0.65
35 2 0.02
36 8 0.08
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (34 bp):
CTAAAGCTTTGGCCTTGGCATGTAACATTTGGTA
Done.