Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 90 of 93
Found at i:35746970 original size:45 final size:45
Alignment explanation
Indices: 35746906--35747154 Score: 417
Period size: 45 Copynumber: 5.5 Consensus size: 45
35746896 CACTAATGGG
* * * *
35746906 TTCCATTGATGCAGAAGGCAATAGTGATGGCATGGTCATTGTTGA
1 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
35746951 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
1 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
*
35746996 TTCCACTGATGCAGAAGGCCTTAGTGATGGCATGGCCATTTTTGA
1 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
35747041 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
1 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
*
35747086 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTGTTGA
1 TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
* * *
35747131 TGCCACTGATGGAGAAGACATTAG
1 TTCCACTGATGCAGAAGGCATTAG
35747155 CGATTGCACC
Statistics
Matches: 194, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 194 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (45 bp):
TTCCACTGATGCAGAAGGCATTAGTGATGGCATGGCCATTTTTGA
Found at i:35752401 original size:21 final size:22
Alignment explanation
Indices: 35752375--35752415 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35752365 GACCCATAAA
*
35752375 TTTAATT-TTATTTTTTAAAAT
1 TTTAATTATTAATTTTTAAAAT
35752396 TTTAATTATTAATTTTTAAA
1 TTTAATTATTAATTTTTAAA
35752416 TAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATTATTAATTTTTAAAAT
Found at i:35752407 original size:15 final size:15
Alignment explanation
Indices: 35752378--35752443 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 15
35752368 CCATAAATTT
* *
35752378 AATTTTATTTTTTAA
1 AATTTTAATTATTAA
35752393 AATTTTAATTATT-A
1 AATTTTAATTATTAA
* *
35752407 ATTTTTAA--ATAAA
1 AATTTTAATTATTAA
*
35752420 ATATTTTTATT-TTAA
1 A-ATTTTAATTATTAA
35752435 AATTTTAAT
1 AATTTTAAT
35752444 CAAAATTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
12 2 0.05
13 2 0.05
14 20 0.51
15 15 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTAATTATTAA
Found at i:35752416 original size:21 final size:20
Alignment explanation
Indices: 35752371--35752416 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
35752361 GTGAGACCCA
*
35752371 TAAA-TTTAATTTTATTTTT
1 TAAATTTTAATTTTAATTTT
35752390 TAAAATTTTAATTATTAATTTT
1 T-AAATTTTAATT-TTAATTTT
35752412 TAAAT
1 TAAAT
35752417 AAAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 11 0.48
22 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAAATTTTAATTTTAATTTT
Found at i:35752627 original size:39 final size:39
Alignment explanation
Indices: 35752529--35752627 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 39
35752519 TCTGTTTTCG
35752529 TTAATTTAATAAAATAAAAATATTATTATTATATAATTTTA
1 TTAATTTAA-AAAAT-AAAATATTATTATTATATAATTTTA
**
35752570 TCT--TTTATTAAATTTAAAAT-TTATTATTATATAATTTTA
1 T-TAATTTA--AAAAATAAAATATTATTATTATATAATTTTA
35752609 TTAATTTAAACAAATAAAA
1 TTAATTTAAA-AAATAAAA
35752628 GTCCTGATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
38 3 0.06
39 26 0.54
40 13 0.27
41 4 0.08
42 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (39 bp):
TTAATTTAAAAAATAAAATATTATTATTATATAATTTTA
Found at i:35753434 original size:20 final size:21
Alignment explanation
Indices: 35753395--35753435 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35753385 CAATTAGATA
*
35753395 AATTTTATTGATATTAATAAT
1 AATTTTATTAATATTAATAAT
*
35753416 AATTTTTTTAATA-TAATAAT
1 AATTTTATTAATATTAATAAT
35753436 TTGGATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTTATTAATATTAATAAT
Found at i:35754336 original size:30 final size:30
Alignment explanation
Indices: 35754277--35754339 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
35754267 AACCGTTAGT
* *
35754277 TATAAAAATTTATTTAATTAAAAATAAAAA
1 TATAAAAATTTAATTAATCAAAAATAAAAA
*
35754307 TATAAAAATTTAATTAATC-ATAATAAAAA
1 TATAAAAATTTAATTAATCAAAAATAAAAA
35754336 -ATAA
1 TATAA
35754340 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 4 0.13
29 9 0.30
30 17 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
TATAAAAATTTAATTAATCAAAAATAAAAA
Found at i:35759684 original size:33 final size:33
Alignment explanation
Indices: 35759642--35759716 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
35759632 CTATATATTC
35759642 TCGAGATTAGTAGAATTAAGGCGGCTAATGTAA
1 TCGAGATTAGTAGAATTAAGGCGGCTAATGTAA
35759675 TCGAGATTAGTAGAATTAAGGCGGCTAATGTAA
1 TCGAGATTAGTAGAATTAAGGCGGCTAATGTAA
35759708 TCGAGATTA
1 TCGAGATTA
35759717 TATAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (33 bp):
TCGAGATTAGTAGAATTAAGGCGGCTAATGTAA
Found at i:35772309 original size:18 final size:18
Alignment explanation
Indices: 35772249--35772315 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
35772239 ACAAGTTTAC
*
35772249 TTAATCGTGT-TATCGTGT
1 TTAAACGTGTATA-CGTGT
* *
35772267 TTAAACATGTATATGTGT
1 TTAAACGTGTATACGTGT
35772285 TTAAACGTGTATACGTGT
1 TTAAACGTGTATACGTGT
*
35772303 TTAAACGTATATA
1 TTAAACGTGTATA
35772316 TATGACACGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 40 0.95
19 2 0.05
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (18 bp):
TTAAACGTGTATACGTGT
Found at i:35772973 original size:2 final size:2
Alignment explanation
Indices: 35772966--35772992 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35772956 AAGTAAACAA
35772966 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
35772993 AACAGATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35775340 original size:2 final size:2
Alignment explanation
Indices: 35775335--35775360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35775325 TTTGTTCATT
35775335 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
35775361 AGCCGTCACG
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:35794441 original size:21 final size:21
Alignment explanation
Indices: 35794419--35794457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35794409 TAAGTATGTA
*
35794419 AAAAAAT-ATTTTAAAAAATT
1 AAAAAATGATTTAAAAAAATT
35794439 AAAAAATGATTTAAAAAAA
1 AAAAAATGATTTAAAAAAA
35794458 AAAAGGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAAATGATTTAAAAAAATT
Found at i:35794444 original size:20 final size:20
Alignment explanation
Indices: 35794419--35794456 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35794409 TAAGTATGTA
35794419 AAAAAAT-ATTTTAAAAAATT
1 AAAAAATGA-TTTAAAAAATT
35794439 AAAAAATGATTTAAAAAA
1 AAAAAATGATTTAAAAAA
35794457 AAAAAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAAATGATTTAAAAAATT
Found at i:35795234 original size:2 final size:2
Alignment explanation
Indices: 35795229--35795256 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35795219 TGACACACAC
35795229 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
35795257 TTCCACTCTT
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:35800321 original size:2 final size:2
Alignment explanation
Indices: 35800314--35800358 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
35800304 TGCAAAACTT
*
35800314 GA GA GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35800356 GA G
1 GA G
35800359 CATACACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35801709 original size:3 final size:3
Alignment explanation
Indices: 35801701--35801725 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35801691 CCCCTAGCCT
35801701 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
35801726 GGAGATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35831494 original size:76 final size:76
Alignment explanation
Indices: 35831368--35831519 Score: 243
Period size: 76 Copynumber: 2.0 Consensus size: 76
35831358 GCTGAGAGTT
* * *
35831368 GGAATCTCTTACCTACTCATGGTTGTTGCAAACTTCTCATAGGAAAAGTATAAACAAATGACTAT
1 GGAATCTCTTACCTACTCATGATTGTTGCAAACTTCTCATAGCAAAAGTATAAACAAATGACTAC
35831433 TATAAATTTGC
66 TATAAATTTGC
* *
35831444 GGAATC-CGTTACCTACTCATGATTGTTGCTAACTTCTCATAGCAAAAGTATAAACAAATGGCTA
1 GGAATCTC-TTACCTACTCATGATTGTTGCAAACTTCTCATAGCAAAAGTATAAACAAATGACTA
35831508 CTATAAATTTGC
65 CTATAAATTTGC
35831520 ATTGAGTATC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 1 0.01
76 69 0.99
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (76 bp):
GGAATCTCTTACCTACTCATGATTGTTGCAAACTTCTCATAGCAAAAGTATAAACAAATGACTAC
TATAAATTTGC
Found at i:35840149 original size:27 final size:28
Alignment explanation
Indices: 35840114--35840183 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
35840104 GAATAGATAA
*
35840114 ATATTTTATTAATTATATTAAATT-T-TT
1 ATATATTATTAATTATATT-AATTATATT
35840141 ATATATTATTAA-TATAATTAATTATATT
1 ATATATTATTAATTAT-ATTAATTATATT
35840169 AT-TATTATT-ATTATA
1 ATATATTATTAATTATA
35840184 AAATTAGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 9 0.24
27 25 0.66
28 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATATTATTAATTATATTAATTATATT
Found at i:35840168 original size:21 final size:21
Alignment explanation
Indices: 35840142--35840181 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35840132 TAAATTTTTA
35840142 TATATTATTAATATAATTAAT
1 TATATTATTAATATAATTAAT
* *
35840163 TATATTATTATTATTATTA
1 TATATTATTAATATAATTA
35840182 TAAAATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTATTAATATAATTAAT
Found at i:35842225 original size:24 final size:24
Alignment explanation
Indices: 35842198--35842249 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
35842188 AGTTTCTGAA
*
35842198 TCAGATGAACTCGAGCCCCCAGAT
1 TCAGACGAACTCGAGCCCCCAGAT
* *
35842222 TCAGACGAGCTCGAGCTCCCAGAT
1 TCAGACGAACTCGAGCCCCCAGAT
35842246 TCAG
1 TCAG
35842250 GTTCTGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (24 bp):
TCAGACGAACTCGAGCCCCCAGAT
Found at i:35846382 original size:102 final size:102
Alignment explanation
Indices: 35846212--35846455 Score: 285
Period size: 102 Copynumber: 2.4 Consensus size: 102
35846202 ACGTTTGCCT
* * * ** * * * * * *
35846212 TCTTCCTCATCAGAAGATCCAGAATGCTCTCTCCGCCTATTTTCCTCCTCCTCGTCATGGATTTT
1 TCTTCTTCATCAGAAGATCCAGAATGTTCTCTCCGCCTATCTTCAACATCATCATCACGAATTCT
35846277 TTCTCTTTCTCGCCTTCC-ATCTCTATTGCCAAGCTTG
66 TTCTCTTTCTCG-CTTCCTATCTCTATTGCCAAGCTTG
*
35846314 TCTTCTTCATCAGAAGATCCTGAATGTTCTCTCCGCCTATCCTT-AACATCATCATCACGAATTC
1 TCTTCTTCATCAGAAGATCCAGAATGTTCTCTCCGCCTAT-CTTCAACATCATCATCACGAATTC
* *
35846378 TTTCTCTTTCTCGCTTCCTATCTCTATTGGCACGCTTG
65 TTTCTCTTTCTCGCTTCCTATCTCTATTGCCAAGCTTG
* * ** *
35846416 TCTTCTTCATCAAAAGCTCCAGAGCGTTCTCTCCACCTAT
1 TCTTCTTCATCAGAAGATCCAGAATGTTCTCTCCGCCTAT
35846456 TCTCATCACC
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 5 0.04
102 113 0.94
103 2 0.02
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (102 bp):
TCTTCTTCATCAGAAGATCCAGAATGTTCTCTCCGCCTATCTTCAACATCATCATCACGAATTCT
TTCTCTTTCTCGCTTCCTATCTCTATTGCCAAGCTTG
Found at i:35870844 original size:3 final size:3
Alignment explanation
Indices: 35870836--35870905 Score: 81
Period size: 3 Copynumber: 23.3 Consensus size: 3
35870826 ACCATCGTCT
* * *
35870836 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TGTA TGCA T-A T-G TTA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA T-CA TCA TCA TCA
35870881 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
35870906 GGGCTTGACA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 3 0.05
3 52 0.87
4 5 0.08
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:35882724 original size:21 final size:21
Alignment explanation
Indices: 35882698--35882740 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35882688 ATTTTTATTA
35882698 TTTTATTATTTTTA-ATTAAAT
1 TTTTA-TATTTTTATATTAAAT
*
35882719 TTTTATATTTTTATTTTAAAT
1 TTTTATATTTTTATATTAAAT
35882740 T
1 T
35882741 AAATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATATTTTTATATTAAAT
Found at i:35882750 original size:30 final size:30
Alignment explanation
Indices: 35882647--35882755 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 30
35882637 TTAGGTATAA
* *
35882647 TATT-TTAAA-AATTTTTTAAATTATTTTA-
1 TATTATTAAATAAATTTTTATA-TATTTTAT
* *
35882675 AATTTTTAAATAAATTTTTAT-TATTTTAT
1 TATTATTAAATAAATTTTTATATATTTTAT
* *
35882704 TATTTTTAATTAAATTTTTATAT-TTTTAT
1 TATTATTAAATAAATTTTTATATATTTTAT
35882733 T-TTAAATTAAATAAATTTTTATA
1 TATT--ATTAAATAAATTTTTATA
35882756 ACTAATAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.18
29 31 0.46
30 25 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTATTAAATAAATTTTTATATATTTTAT
Found at i:35882751 original size:29 final size:32
Alignment explanation
Indices: 35882666--35882751 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 32
35882656 AATTTTTTAA
35882666 ATTATTTTAAATTTTTAAATAAATTTTTATTATTTT
1 ATTATTTTAAA---TTAAATAAA-TTTTATTATTTT
*
35882702 ATTATTTTTAATTAAAT---TTTTA-TA-TTT
1 ATTATTTTAAATTAAATAAATTTTATTATTTT
35882729 -TTATTTTAAATTAAATAAATTTT
1 ATTATTTTAAATTAAATAAATTTT
35882752 TATAACTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
26 15 0.33
27 3 0.07
28 2 0.04
29 9 0.20
33 6 0.13
36 10 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
ATTATTTTAAATTAAATAAATTTTATTATTTT
Found at i:35882868 original size:33 final size:33
Alignment explanation
Indices: 35882821--35882885 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
35882811 ACATGATATA
* *
35882821 TTAATATATCATAATCAATTATAATATAACATT
1 TTAACATATCATAATCAATAATAATATAACATT
*
35882854 TTAACATATCATAATCAATAATAATGTAACAT
1 TTAACATATCATAATCAATAATAATATAACAT
35882886 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (33 bp):
TTAACATATCATAATCAATAATAATATAACATT
Found at i:35885335 original size:16 final size:17
Alignment explanation
Indices: 35885314--35885347 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35885304 AGAATAGATT
35885314 CCCCA-CCACACCCCCC
1 CCCCACCCACACCCCCC
*
35885330 CCCCACCCCCACCCCCC
1 CCCCACCCACACCCCCC
35885347 C
1 C
35885348 TTCCCCGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (17 bp):
CCCCACCCACACCCCCC
Found at i:35892031 original size:17 final size:17
Alignment explanation
Indices: 35892005--35892065 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
35891995 AAGTTTTATA
* * *
35892005 TTAATGTAAAATATTTT
1 TTAATTTAAAAAATATT
35892022 TTAATTTAAAAAATATT
1 TTAATTTAAAAAATATT
*
35892039 TTATTTTATAAAAGATATCT
1 TTAATTTA-AAAA-ATAT-T
35892059 TT-ATTTA
1 TTAATTTA
35892066 TAAATTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 21 0.58
18 4 0.11
19 8 0.22
20 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAATTTAAAAAATATT
Found at i:35892050 original size:19 final size:19
Alignment explanation
Indices: 35892028--35892069 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35892018 TTTTTTAATT
35892028 TAAAAAATAT-TTTATTTTA
1 TAAAAAATATCTTTA-TTTA
*
35892047 TAAAAGATATCTTTATTTA
1 TAAAAAATATCTTTATTTA
35892066 TAAA
1 TAAA
35892070 TTCAAAGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TAAAAAATATCTTTATTTA
Found at i:35897268 original size:3 final size:3
Alignment explanation
Indices: 35897260--35897284 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35897250 TGATTATTGG
35897260 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
35897285 AGACTTTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:35898866 original size:2 final size:2
Alignment explanation
Indices: 35898859--35898883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35898849 AAAGAGTTAT
35898859 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
35898884 TGGGAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35899372 original size:2 final size:2
Alignment explanation
Indices: 35899365--35899405 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
35899355 GCTCTTTCTG
* *
35899365 TC TC TC TC TC TC GC TC TC TC TC GC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35899406 AGGTGGAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.05, T:0.46
Consensus pattern (2 bp):
TC
Found at i:35899620 original size:2 final size:2
Alignment explanation
Indices: 35899613--35899650 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
35899603 AGAGCGACTC
*
35899613 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35899651 GGTTTGGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35901928 original size:25 final size:26
Alignment explanation
Indices: 35901896--35901946 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
35901886 AATTTTTATT
35901896 TTTTTAATTAATATTTTATA-AAATA
1 TTTTTAATTAATATTTTATATAAATA
* *
35901921 TTTTTAATTAATTTTTTTTATAAATA
1 TTTTTAATTAATATTTTATATAAATA
35901947 ACTCTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTAATTAATATTTTATATAAATA
Found at i:35901936 original size:12 final size:13
Alignment explanation
Indices: 35901896--35901937 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
35901886 AATTTTTATT
35901896 TTTTTAATTAATA
1 TTTTTAATTAATA
35901909 TTTTATAA--AATA
1 TTTT-TAATTAATA
35901921 TTTTTAATTAAT-
1 TTTTTAATTAATA
35901933 TTTTT
1 TTTTT
35901938 TTATAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 7 0.27
14 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:35933439 original size:12 final size:12
Alignment explanation
Indices: 35933424--35933460 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
35933414 TGCCGGTGTT
*
35933424 GAAGCCGCAGCA
1 GAAGCAGCAGCA
*
35933436 GAAGAAGCAGCA
1 GAAGCAGCAGCA
35933448 GAAGCAGCAGCA
1 GAAGCAGCAGCA
35933460 G
1 G
35933461 TACTAGCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.35, T:0.00
Consensus pattern (12 bp):
GAAGCAGCAGCA
Found at i:35934106 original size:45 final size:45
Alignment explanation
Indices: 35934037--35934181 Score: 236
Period size: 45 Copynumber: 3.2 Consensus size: 45
35934027 GTAGAAGCCG
* * * *
35934037 ATGAACATGCCACGAATAACGATGAACCTGTTGTACTAGCTGCGA
1 ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGCGA
*
35934082 ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGTGA
1 ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGCGA
*
35934127 ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGCGG
1 ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGCGA
35934172 ATGAAGATGC
1 ATGAAGATGC
35934182 TCCAAAAATG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (45 bp):
ATGAAGATGCCCCGAATAAAGATGAACCTGTTGTACTCGCTGCGA
Found at i:35934361 original size:15 final size:12
Alignment explanation
Indices: 35934324--35934354 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35934314 CAGCGGCGAA
35934324 GCGGAAGGTGCT
1 GCGGAAGGTGCT
35934336 GCGGAAGGTGCT
1 GCGGAAGGTGCT
35934348 GCGGAAG
1 GCGGAAG
35934355 AAGGTGCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.16, G:0.52, T:0.13
Consensus pattern (12 bp):
GCGGAAGGTGCT
Found at i:35942556 original size:54 final size:55
Alignment explanation
Indices: 35942443--35942547 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
35942433 TTTTTTCCAT
* *
35942443 TAACACCAGTTTTACTCTGATTATTAACCCTTCCTAAATAGTGCTTTTTCTCAAG
1 TAACACCAATTCTACTCTGATTATTAACCCTTCCTAAATAGTGCTTTTTCTCAAG
* * ** *
35942498 TAACACCAATTCTACTCTGATTGTTTATTCTT-CTAAATGGTGCTTTTTCT
1 TAACACCAATTCTACTCTGATTATTAACCCTTCCTAAATAGTGCTTTTTCT
35942548 TACATAACAG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
54 17 0.40
55 26 0.60
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (55 bp):
TAACACCAATTCTACTCTGATTATTAACCCTTCCTAAATAGTGCTTTTTCTCAAG
Found at i:35949986 original size:2 final size:2
Alignment explanation
Indices: 35949979--35950017 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35949969 ATAACAAAAT
35949979 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35950018 CATACATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35957517 original size:19 final size:18
Alignment explanation
Indices: 35957473--35957517 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
35957463 CTCGGTCGAG
35957473 ATTTAATCAAATAATTGA
1 ATTTAATCAAATAATTGA
* * *
35957491 AATCAATCTAATTAATTGA
1 ATTTAATC-AAATAATTGA
35957510 ATTTAATC
1 ATTTAATC
35957518 GGTCGAGATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTTAATCAAATAATTGA
Found at i:35978259 original size:22 final size:22
Alignment explanation
Indices: 35978229--35978270 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35978219 ACATGGATGC
35978229 TTTTCTTTTCCTTTCTTTTTCT
1 TTTTCTTTTCCTTTCTTTTTCT
* *
35978251 TTTTTTTTTTCTTTCTTTTT
1 TTTTCTTTTCCTTTCTTTTT
35978271 TACTTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTCTTTTCCTTTCTTTTTCT
Found at i:35978261 original size:12 final size:12
Alignment explanation
Indices: 35978244--35978277 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35978234 TTTTCCTTTC
35978244 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
35978256 TTTTTCTTTCTT
1 TTTTTCTTTTTT
*
35978268 TTTTACTTTT
1 TTTTTCTTTT
35978278 GTTTCCCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:35979776 original size:49 final size:48
Alignment explanation
Indices: 35979721--35979819 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 48
35979711 TTTACAAAAC
35979721 TTTTAAAA-TTTTTCTAACATATTTTTATTTTTTAAAAAATTTATAATT
1 TTTTAAAATTTTTTCTAACATATTTTTATTTTTT-AAAAATTTATAATT
* *
35979769 TNTTTAAAATTTTTTTTAACATATTTTTATTTTTTTAAAATTTATAATT
1 T-TTTAAAATTTTTTCTAACATATTTTTATTTTTTAAAAATTTATAATT
35979818 TT
1 TT
35979820 ATCTCAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
48 2 0.04
49 21 0.45
50 24 0.51
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (48 bp):
TTTTAAAATTTTTTCTAACATATTTTTATTTTTTAAAAATTTATAATT
Found at i:35979783 original size:31 final size:31
Alignment explanation
Indices: 35979748--35979811 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
35979738 CATATTTTTA
*
35979748 TTTTTTAAAAAATTTATAATTTNTTTAAAATT
1 TTTTTTAAAAAATTT-TAATTTTTTTAAAATT
* * *
35979780 TTTTTTAACATATTTTTATTTTTTTAAAATT
1 TTTTTTAAAAAATTTTAATTTTTTTAAAATT
35979811 T
1 T
35979812 ATAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTAAAAAATTTTAATTTTTTTAAAATT
Found at i:35984334 original size:60 final size:60
Alignment explanation
Indices: 35984246--35984362 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
35984236 TTGCCATTGA
* *
35984246 GAAGCATATGCTTATGCCAGTATGGTTAGAGCTACCTAGAGCCACCTTTGCTAAGTTGCT
1 GAAGCATATGCTTATGCCAGTATAGTTAGAGCTACCAAGAGCCACCTTTGCTAAGTTGCT
* * *
35984306 GAAGCATATGTTTATGCTAGTATAGTTAGAGCTACCAAGAGTCACCTTTGCTAAGTT
1 GAAGCATATGCTTATGCCAGTATAGTTAGAGCTACCAAGAGCCACCTTTGCTAAGTT
35984363 CAGGAAGTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (60 bp):
GAAGCATATGCTTATGCCAGTATAGTTAGAGCTACCAAGAGCCACCTTTGCTAAGTTGCT
Found at i:35988637 original size:21 final size:21
Alignment explanation
Indices: 35988611--35988657 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
35988601 ACTACCGTCC
35988611 TCCTGCTCCATTCGCCAATAA
1 TCCTGCTCCATTCGCCAATAA
*
35988632 TCCTGCTCCTTTCGCCAATAA
1 TCCTGCTCCATTCGCCAATAA
*
35988653 CCCTG
1 TCCTG
35988658 GTTTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.40, G:0.11, T:0.30
Consensus pattern (21 bp):
TCCTGCTCCATTCGCCAATAA
Found at i:35990356 original size:10 final size:9
Alignment explanation
Indices: 35990341--35990397 Score: 57
Period size: 8 Copynumber: 6.3 Consensus size: 9
35990331 CAGCGGGGGA
35990341 AAGAAAGGAG
1 AAGAAA-GAG
35990351 AAGAAAGAG
1 AAGAAAGAG
35990360 AA-AAA-AG
1 AAGAAAGAG
35990367 AAGAAAGAG
1 AAGAAAGAG
*
35990376 AAAAGAAAAAG
1 --AAGAAAGAG
35990387 AA-AAAGAG
1 AAGAAAGAG
35990395 AAG
1 AAG
35990398 GGGGGAGCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.10
8 13 0.32
9 9 0.22
10 6 0.15
11 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (9 bp):
AAGAAAGAG
Found at i:35990368 original size:16 final size:17
Alignment explanation
Indices: 35990344--35990389 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
35990334 CGGGGGAAAG
*
35990344 AAAGGAGAAGAAAGAGA
1 AAAGAAGAAGAAAGAGA
35990361 AAA-AAGAAGAAAGAGA
1 AAAGAAGAAGAAAGAGA
*
35990377 AAAGAAAAAGAAA
1 AAAGAAGAAGAAA
35990390 AAGAGAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGAAAGAGA
Found at i:35990424 original size:4 final size:4
Alignment explanation
Indices: 35990415--35990490 Score: 81
Period size: 4 Copynumber: 19.2 Consensus size: 4
35990405 CGGCTAGGAG
35990415 AGAA AGAA AGAA AGAA AGTGAA AGAA AG-A AGAA AG-- AGAA AGGAA AGGAA
1 AGAA AGAA AGAA AGAA A--GAA AGAA AGAA AGAA AGAA AGAA A-GAA A-GAA
35990464 AGAA AGAA AGAA A-AA AGAA A-AA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
35990491 AANNNNNNNN
Statistics
Matches: 64, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.03
3 9 0.14
4 40 0.62
5 9 0.14
6 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:35990439 original size:18 final size:17
Alignment explanation
Indices: 35990416--35990483 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 17
35990406 GGCTAGGAGA
35990416 GAAAGAAAGAAAGAAAG
1 GAAAGAAAGAAAGAAAG
35990433 TGAAAGAAAG-AAGAAAG
1 -GAAAGAAAGAAAGAAAG
35990450 AGAAAGGAAAGGAAAGAAA-
1 -GAAA-GAAA-GAAAGAAAG
35990469 GAAAGAAA-AAAGAAA
1 GAAAGAAAGAAAGAAA
35990484 AAAGAAAAAN
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
15 7 0.15
17 15 0.33
18 17 0.37
19 1 0.02
20 6 0.13
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAG
Found at i:35990455 original size:35 final size:35
Alignment explanation
Indices: 35990413--35990483 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 35
35990403 AGCGGCTAGG
*
35990413 AGAGAAA-GAAA-GAAAGAAAGTGAAAGAAAGAAGAA
1 AGAGAAAGGAAAGGAAAGAAA--GAAAGAAAAAAGAA
35990448 AGAGAAAGGAAAGGAAAGAAAGAAAGAAAAAAGAA
1 AGAGAAAGGAAAGGAAAGAAAGAAAGAAAAAAGAA
35990483 A
1 A
35990484 AAAGAAAAAN
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 21 0.64
36 4 0.12
37 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (35 bp):
AGAGAAAGGAAAGGAAAGAAAGAAAGAAAAAAGAA
Found at i:35990464 original size:27 final size:28
Alignment explanation
Indices: 35990416--35990483 Score: 58
Period size: 27 Copynumber: 2.6 Consensus size: 28
35990406 GGCTAGGAGA
* *
35990416 GAAAGAAAGAAAGAAAGTGAAAGAAAGAA
1 GAAAGAAAGAAAGAAAGAGAAAGAAAG-T
35990445 GAAAG--AGAAAGGAAAG-GAAAGAAA--
1 GAAAGAAAGAAA-GAAAGAGAAAGAAAGT
35990469 GAAAGAAA-AAAGAAA
1 GAAAGAAAGAAAGAAA
35990484 AAAGAAAAAN
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
24 9 0.25
25 3 0.08
26 1 0.03
27 13 0.36
28 5 0.14
29 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (28 bp):
GAAAGAAAGAAAGAAAGAGAAAGAAAGT
Found at i:35990487 original size:18 final size:19
Alignment explanation
Indices: 35990415--35990492 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 19
35990405 CGGCTAGGAG
35990415 AGAAAGAAAGAAAGAAAGTGAA
1 AGAAAGAAAGAAAGAAA---AA
*
35990437 AGAAAG-AAGAAAGAGAAA
1 AGAAAGAAAGAAAGAAAAA
*
35990455 GGAAAGGAAAGAAAGAAAGAA
1 AGAAA-GAAAGAAAGAAA-AA
35990476 A-AAAGAAA-AAAGAAAAA
1 AGAAAGAAAGAAAGAAAAA
35990493 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.04
18 13 0.27
19 5 0.10
20 12 0.24
21 11 0.22
22 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (19 bp):
AGAAAGAAAGAAAGAAAAA
Found at i:35990492 original size:8 final size:7
Alignment explanation
Indices: 35990415--35990492 Score: 57
Period size: 7 Copynumber: 10.0 Consensus size: 7
35990405 CGGCTAGGAG
35990415 AGAAAGAA
1 AGAAA-AA
35990423 AGAAAGAA
1 AGAAA-AA
35990431 AGTGAAAGAA
1 A--GAAA-AA
*
35990441 AGAAGAA
1 AGAAAAA
*
35990448 AGAGAAA
1 AGAAAAA
*
35990455 GGAAAGGAA
1 AGAAA--AA
35990464 AGAAAGAA
1 AGAAA-AA
35990472 AGAAAAA
1 AGAAAAA
35990479 AGAAAAA
1 AGAAAAA
35990486 AGAAAAA
1 AGAAAAA
35990493 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
7 26 0.43
8 20 0.33
9 6 0.10
10 8 0.13
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (7 bp):
AGAAAAA
Found at i:35999582 original size:21 final size:22
Alignment explanation
Indices: 35999556--35999598 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
35999546 AGTATTGTGC
*
35999556 TTAAAAAAAA-TAATAAAAAAA
1 TTAAAAAAAATTAAGAAAAAAA
35999577 TTAAAAAAAATTAAGAAAAAAA
1 TTAAAAAAAATTAAGAAAAAAA
35999599 AAACGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (22 bp):
TTAAAAAAAATTAAGAAAAAAA
Found at i:35999585 original size:10 final size:10
Alignment explanation
Indices: 35999556--35999597 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
35999546 AGTATTGTGC
35999556 TTAAAAAAAA
1 TTAAAAAAAA
*
35999566 TAATAAAAAAA
1 TTA-AAAAAAA
35999577 TTAAAAAAAA
1 TTAAAAAAAA
35999587 TTAAGAAAAAA
1 TTAA-AAAAAA
35999598 AAAACGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
TTAAAAAAAA
Found at i:36000723 original size:63 final size:62
Alignment explanation
Indices: 36000508--36000747 Score: 426
Period size: 62 Copynumber: 3.9 Consensus size: 62
36000498 CATTAAAGAA
* * *
36000508 TTAAATCGAACCTGATGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATATTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
36000570 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
* *
36000632 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTGAAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT-TAATTTTGT
36000695 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
36000748 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 111 0.65
63 60 0.35
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (62 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
Found at i:36000740 original size:125 final size:124
Alignment explanation
Indices: 36000508--36000747 Score: 426
Period size: 125 Copynumber: 1.9 Consensus size: 124
36000498 CATTAAAGAA
* *
36000508 TTAAATCGAACCTGATGTGAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTTTAATATTGTTTA
1 TTAAATCGAACCTGATGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTAAATATTGTTTA
36000573 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
66 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
* * *
36000632 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTGAAATTTTGTTT
1 TTAAATCGAACCTGATGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT-AAATATTGTTT
36000697 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
65 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
36000748 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 50 0.45
125 60 0.55
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (124 bp):
TTAAATCGAACCTGATGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTAAATATTGTTTA
AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGT
Found at i:36005029 original size:20 final size:20
Alignment explanation
Indices: 36005004--36005045 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36004994 TGTTCTTCGA
*
36005004 ATTTTTTATATTATAA-ATTT
1 ATTTTTCATATTA-AACATTT
36005024 ATTTTTCATATTAAACATTT
1 ATTTTTCATATTAAACATTT
36005044 AT
1 AT
36005046 ATTGTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTCATATTAAACATTT
Found at i:36009086 original size:40 final size:40
Alignment explanation
Indices: 36009028--36009128 Score: 136
Period size: 38 Copynumber: 2.6 Consensus size: 40
36009018 TCTGGCTCAT
* * *
36009028 GTACATCCCCCCACATCGTGCACATAGTCGGTGCCATTAA
1 GTACATCCCCCCACATCGTGCACATAATCAGTGCCATCAA
* *
36009068 GTGCATCCCCCCACATCGTG--CATAATCAGTGCCATCAT
1 GTACATCCCCCCACATCGTGCACATAATCAGTGCCATCAA
36009106 GTACAT-CCCCCACATCGTGCACA
1 GTACATCCCCCCACATCGTGCACA
36009129 CGGACACTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
37 13 0.25
38 19 0.36
39 2 0.04
40 19 0.36
ACGTcount: A:0.25, C:0.38, G:0.16, T:0.22
Consensus pattern (40 bp):
GTACATCCCCCCACATCGTGCACATAATCAGTGCCATCAA
Found at i:36009125 original size:37 final size:38
Alignment explanation
Indices: 36009024--36009126 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 38
36009014 CACATCTGGC
* *
36009024 TCATGTACATCCCCCCACATCGTGCACATAGTCGGTGCCA
1 TCATGTACATCCCCCCACATCGTG--CATAATCAGTGCCA
* * *
36009064 TTAAGTGCATCCCCCCACATCGTGCATAATCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCATAATCAGTGCCA
36009102 TCATGTACAT-CCCCCACATCGTGCA
1 TCATGTACATCCCCCCACATCGTGCA
36009127 CACGGACACT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 15 0.27
38 19 0.35
40 21 0.38
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (38 bp):
TCATGTACATCCCCCCACATCGTGCATAATCAGTGCCA
Found at i:36009274 original size:109 final size:107
Alignment explanation
Indices: 36009068--36009308 Score: 347
Period size: 109 Copynumber: 2.2 Consensus size: 107
36009058 GTGCCATTAA
*
36009068 GTGCATCCCCCCACATCGTGCATAATCAGTGCCATCATGTACATCCCCCACATCGTGCACACGGA
1 GTGCAT-CCCCCACATCGTGCACAATCAGTGCCATCATGTACATCCCCCACATCGTGCACACGGA
*
36009133 CACTATCCTTATCCATCTCCCACACCGCCATCATCACCAGCAT
65 CACTATCATTATCCATCTCCCACACCGCCATCATCACCAGCAT
* *
36009176 GTGCATCCACCCACATCGTGCACAATCAGTGCCATCGTGTATATCCCCCCACATCGTGCACACGG
1 GTGCATCC-CCCACATCGTGCACAATCAGTGCCATCATGTACAT-CCCCCACATCGTGCACACGG
* * * * *
36009241 TCATTATCATTATCCATCTCCCACACTGTCATCATCACCGGCAT
64 ACACTATCATTATCCATCTCCCACACCGCCATCATCACCAGCAT
* *
36009285 GTGCATTTCCCTACATCGTGCACA
1 GTGCA-TCCCCCACATCGTGCACA
36009309 CACACGGTTA
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
107 2 0.02
108 38 0.32
109 77 0.65
110 2 0.02
ACGTcount: A:0.24, C:0.39, G:0.13, T:0.24
Consensus pattern (107 bp):
GTGCATCCCCCACATCGTGCACAATCAGTGCCATCATGTACATCCCCCACATCGTGCACACGGAC
ACTATCATTATCCATCTCCCACACCGCCATCATCACCAGCAT
Found at i:36009366 original size:2 final size:2
Alignment explanation
Indices: 36009353--36009402 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
36009343 ATCATGCACA
*
36009353 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36009395 AT AT AT AT
1 AT AT AT AT
36009403 CATCATAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36012574 original size:26 final size:26
Alignment explanation
Indices: 36012506--36012575 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
36012496 GTGTAACAAT
*
36012506 AATATTTTTTT-AGCATGGTGTGTAAC
1 AATATTTTTTTCA-CATGGTGTATAAC
**
36012532 AACGTTTTTTTCAACATGGTGTATAAC
1 AATATTTTTTTC-ACATGGTGTATAAC
36012559 AATATTTTTTTCACATG
1 AATATTTTTTTCACATG
36012576 CACTAGAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 14 0.38
27 22 0.59
28 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (26 bp):
AATATTTTTTTCACATGGTGTATAAC
Found at i:36015905 original size:216 final size:216
Alignment explanation
Indices: 36015531--36015953 Score: 792
Period size: 216 Copynumber: 2.0 Consensus size: 216
36015521 TGTTGCTACT
*
36015531 TAAGTTCAACTCAGTTAAATTGAAGCAATTACCAATTTGAGGCGGAATGGGTCCAGTCAATCGAT
1 TAAGTTCAACTCAGTTAAATTGAAGCAATTACCAATTTGAGGCGGAATGGGTCCACTCAATCGAT
*
36015596 TTTGAAAGAGATTCAATGAAACCAGTGCTCTCAAATTTCCAATTTCCTTGGGTATGTGACCTTCT
66 TTTGAAAGAGATCCAATGAAACCAGTGCTCTCAAATTTCCAATTTCCTTGGGTATGTGACCTTCT
*
36015661 AAAAGATTTGACTGGAGGGATAAAGTCAGCAAAGTCTTCAAATCTCCAATTTTTGAAGGGATAGA
131 AAAAGATTTGACTGAAGGGATAAAGTCAGCAAAGTCTTCAAATCTCCAATTTTTGAAGGGATAGA
36015726 ACCAGTGATTCTGTTGTTGCA
196 ACCAGTGATTCTGTTGTTGCA
*
36015747 TAAGTTCAACTCTGTTAAATTGAAGCAATTACCAATTTGAGGCGGAATGGGTCCACTCAATCGAT
1 TAAGTTCAACTCAGTTAAATTGAAGCAATTACCAATTTGAGGCGGAATGGGTCCACTCAATCGAT
*
36015812 TTTGAAAGAGATCCAATGAAGCCAGTGCTCTCAAATTTCCAATTTCCTTGGGTATGTGACCTTCT
66 TTTGAAAGAGATCCAATGAAACCAGTGCTCTCAAATTTCCAATTTCCTTGGGTATGTGACCTTCT
36015877 AAAAGATTTGACTGAAGGGATAAAGTCAGCAAAGTCTTCAAATCTCCAATTTTTGAAGGGATAGA
131 AAAAGATTTGACTGAAGGGATAAAGTCAGCAAAGTCTTCAAATCTCCAATTTTTGAAGGGATAGA
*
36015942 ACCATTGATTCT
196 ACCAGTGATTCT
36015954 ATTGAAGTCA
Statistics
Matches: 201, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
216 201 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (216 bp):
TAAGTTCAACTCAGTTAAATTGAAGCAATTACCAATTTGAGGCGGAATGGGTCCACTCAATCGAT
TTTGAAAGAGATCCAATGAAACCAGTGCTCTCAAATTTCCAATTTCCTTGGGTATGTGACCTTCT
AAAAGATTTGACTGAAGGGATAAAGTCAGCAAAGTCTTCAAATCTCCAATTTTTGAAGGGATAGA
ACCAGTGATTCTGTTGTTGCA
Found at i:36016155 original size:72 final size:72
Alignment explanation
Indices: 36016068--36016874 Score: 961
Period size: 72 Copynumber: 11.2 Consensus size: 72
36016058 ATAATTGAAA
* * * * * *
36016068 TAGAGTGGAAGGAATGGAATCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
**
36016133 ACTCGCC
66 ACTTACC
* * * * *
36016140 TAGAGCGGAAGGAATGAAACCATTAAGAGAGTTA-TAAGATAAA-CCTAAGGTCTCTAAATTGGT
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACT-AGACAAATCC-AGGGTCACTAAATTGGT
36016203 TAACTTACC
64 TAACTTACC
* * *
36016212 TAGAGAGGAAGGAATGGAACCATTAAGAGAGTTACTAGACAAATCTAGGGTCACTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016277 ACTTACC
66 ACTTACC
* ** * * * *
36016284 TAAAGCTAAAGGAATTGAACCACTAAGAGAGTTACGAAACAAATCCAGGGTCACTAAATTAGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016349 ACTTACC
66 ACTTACC
* ** *
36016356 TAAAGCTAAAGGAATGGAACCACTAAGAGAGTTACCAGACAAATCCAGGGTCACTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016421 ACTTACC
66 ACTTACC
* * * * *
36016428 TAAAGCGAAAGGAATGGAATCACTAAGATAGTTACCAGACAAATCCAGGGTCACTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016493 ACTTACC
66 ACTTACC
* * * *
36016500 TAGAGCGGAAGGAATGAAACCACTAAGATAGTTACCAGACAAATCCAAGGTCACTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016565 ACTTACC
66 ACTTACC
* * * * *
36016572 TAGAGCGGAAGGAATGGAACCCCTAAGAGAGTTACGAGACAATTCCAGGGTCACTAAATTAGCTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
36016637 ACTTACC
66 ACTTACC
* ** *
36016644 TAAAGCGGAAGGAATGGAACCACTAAGAGAGTTAAAAGACAAATCCAGGGTCACTAAATTGCTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
** *
36016709 ACGCACT
66 ACTTACC
* * * * * * * **
36016716 TAAAGTGGAACGAATGGAACCACTAAGAAAGTTATTAGACAAATTCAGGTTCTTTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
* *
36016781 ACTCACT
66 ACTTACC
** * * ** *
36016788 TAGAATGGAAGGAATGGAACCACTAAGAGAGTTATTAGACAAATCTAGATTCTCTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
* *
36016853 ACTCACT
66 ACTTACC
*
36016860 TAGAGTGGAAGGAAT
1 TAGAGCGGAAGGAAT
36016875 TGAATCAAAT
Statistics
Matches: 656, Mismatches: 75, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
71 3 0.00
72 651 0.99
73 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (72 bp):
TAGAGCGGAAGGAATGGAACCACTAAGAGAGTTACTAGACAAATCCAGGGTCACTAAATTGGTTA
ACTTACC
Found at i:36028540 original size:18 final size:19
Alignment explanation
Indices: 36028514--36028563 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
36028504 ACACGTTTAC
* *
36028514 TTAATCGTGTTAT-TGTGT
1 TTAAACGTGTTATACGTGT
36028532 TTAAACGTG-TATACGTGT
1 TTAAACGTGTTATACGTGT
36028550 TTAAACGTG-TATAC
1 TTAAACGTGTTATAC
36028564 TTGACACGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.10
18 26 0.90
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (19 bp):
TTAAACGTGTTATACGTGT
Found at i:36028827 original size:9 final size:9
Alignment explanation
Indices: 36028810--36028848 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
36028800 ATATTTTTAA
*
36028810 TTAATCGTG
1 TTAAACGTG
36028819 TTAAACGTG
1 TTAAACGTG
*
36028828 TTAATCGTG
1 TTAAACGTG
36028837 TTAAACGTG
1 TTAAACGTG
36028846 TTA
1 TTA
36028849 TTAATCGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (9 bp):
TTAAACGTG
Found at i:36028833 original size:18 final size:18
Alignment explanation
Indices: 36028810--36028848 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
36028800 ATATTTTTAA
36028810 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACGTG
36028828 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACGTG
36028846 TTA
1 TTA
36028849 TTAATCGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (18 bp):
TTAATCGTGTTAAACGTG
Found at i:36028869 original size:31 final size:31
Alignment explanation
Indices: 36028832--36028901 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
36028822 AACGTGTTAA
* *
36028832 TCGTGTTAAACGTGTTATTAATCGTGT-CGTG
1 TCGTGTTAAACGTG-TATTAAACGTATACGTG
*
36028863 TCGTGTTACACGTGTATTAAACGTATACGTG
1 TCGTGTTAAACGTGTATTAAACGTATACGTG
36028894 TACGTGTT
1 T-CGTGTT
36028902 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 10 0.29
31 18 0.53
32 6 0.18
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (31 bp):
TCGTGTTAAACGTGTATTAAACGTATACGTG
Found at i:36029340 original size:19 final size:18
Alignment explanation
Indices: 36029292--36029340 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
36029282 TTGTTACGGG
* *
36029292 TAAAAAAATATTTTTGAA
1 TAAAATAATATTTTTAAA
*
36029310 TAAAATATTATTTTGTAAA
1 TAAAATAATATTTT-TAAA
*
36029329 TAATATAATATT
1 TAAAATAATATT
36029341 AAAATATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
TAAAATAATATTTTTAAA
Found at i:36030376 original size:13 final size:12
Alignment explanation
Indices: 36030358--36030416 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
36030348 GCTACTGACT
36030358 GAAAAAAAAGAGA
1 GAAAAAAAAGA-A
36030371 GAAAAAAAA-AA
1 GAAAAAAAAGAA
36030382 GAAAAAGAAAGAA
1 GAAAAA-AAAGAA
*
36030395 -AAAAAGTGAAGAA
1 GAAAAA--AAAGAA
36030408 GAAAAAAAA
1 GAAAAAAAA
36030417 ATAAAAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.18
12 11 0.28
13 16 0.41
14 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (12 bp):
GAAAAAAAAGAA
Found at i:36030377 original size:11 final size:11
Alignment explanation
Indices: 36030361--36030398 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
36030351 ACTGACTGAA
*
36030361 AAAAAAGAGAG
1 AAAAAAGAAAG
*
36030372 AAAAAAAAAAG
1 AAAAAAGAAAG
36030383 -AAAAAGAAAG
1 AAAAAAGAAAG
36030393 AAAAAA
1 AAAAAA
36030399 AGTGAAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:36030381 original size:17 final size:17
Alignment explanation
Indices: 36030359--36030417 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
36030349 CTACTGACTG
36030359 AAAAAAAAGAGAGAAAA
1 AAAAAAAAGAGAGAAAA
*
36030376 AAAAAAGAA-AAAG-AAA
1 AAAAAA-AAGAGAGAAAA
* *
36030392 GAAAAAAAGTGAAGAAGAA
1 AAAAAAAAGAG-AGAA-AA
36030411 AAAAAAA
1 AAAAAAA
36030418 TAAAAACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.06
16 8 0.25
17 11 0.34
18 3 0.09
19 8 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAGAGAAAA
Found at i:36030396 original size:20 final size:20
Alignment explanation
Indices: 36030362--36030417 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
36030352 CTGACTGAAA
*
36030362 AAAAAGAGAGAAAAAAAAAAG
1 AAAAAGAAAG-AAAAAAAAAG
**
36030383 AAAAAGAAAGAAAAAAAGTG
1 AAAAAGAAAGAAAAAAAAAG
*
36030403 AAGAAGAAA-AAAAAA
1 AAAAAGAAAGAAAAAA
36030418 TAAAAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.19
20 16 0.52
21 9 0.29
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAGAAAAAAAAAG
Found at i:36031402 original size:57 final size:60
Alignment explanation
Indices: 36031237--36031405 Score: 191
Period size: 60 Copynumber: 2.9 Consensus size: 60
36031227 AAAAAGGGAT
* * * * ** * *
36031237 ACCTGAAACCCCGATTTATATTGGGTGATGTGGATAGTTCCCACGAGTAGGTAAAGGAGG
1 ACCTGAAGCCTCGATTCATAATGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAAGAGG
* * * * *
36031297 ACCTGAAGCCTCGATTTATAATGGGTGGCATTGGTAGTTCTCATGAGTAGGTAAAAGA-G
1 ACCTGAAGCCTCGATTCATAATGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAAGAGG
*
36031356 ACCTGAAGCCTCGATTCAT-CT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 ACCTGAAGCCTCGATTCATAATGGGTGGCGTGGGTAGTTCCCACGAGTAGGT
36031406 GATGATGTCT
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 25 0.27
58 1 0.01
59 19 0.21
60 47 0.51
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (60 bp):
ACCTGAAGCCTCGATTCATAATGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAAGAGG
Found at i:36032690 original size:72 final size:72
Alignment explanation
Indices: 36032594--36032831 Score: 350
Period size: 72 Copynumber: 3.3 Consensus size: 72
36032584 ATAATTGAAA
* * *
36032594 TAGAGTGGAAGGAATGGAATCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTAGTTA
1 TAGAGCGGAAGGAATGGAACCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGTTA
*
36032659 ACTTGCC
66 ACTCGCC
* * *
36032666 TAGAGCGGAAGGAATAGAACCATTAAGAAAGTTATTAGACAAAACCAGGATCTCTAAATTGGTTA
1 TAGAGCGGAAGGAATGGAACCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGTTA
*
36032731 ACTCACC
66 ACTCGCC
* *
36032738 TAAAGCGGAAGGAATGGAACCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGCTA
1 TAGAGCGGAAGGAATGGAACCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGTTA
36032803 ACTCGCC
66 ACTCGCC
*** *
36032810 TAGATTAGAAGGAATTGAACCA
1 TAGAGCGGAAGGAATGGAACCA
36032832 AATAACTTAT
Statistics
Matches: 147, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 147 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (72 bp):
TAGAGCGGAAGGAATGGAACCATTAAGAAAGTTATTAGACAAATCCAGGGTCTCTAAATTGGTTA
ACTCGCC
Found at i:36033560 original size:24 final size:24
Alignment explanation
Indices: 36033529--36033584 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
36033519 AGAGATTCTA
36033529 AAGG-TGTTCCTAGTTTACAAGAC
1 AAGGATGTTCCTAGTTTACAAGAC
36033552 AAGGATGTTCCTAGTTTACAAGAC
1 AAGGATGTTCCTAGTTTACAAGAC
36033576 AAGGATGTT
1 AAGGATGTT
36033585 AAACAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (24 bp):
AAGGATGTTCCTAGTTTACAAGAC
Found at i:36036298 original size:216 final size:216
Alignment explanation
Indices: 36035924--36036574 Score: 1086
Period size: 216 Copynumber: 3.0 Consensus size: 216
36035914 CTCTAAATTG
* * * * *
36035924 TTGTTGCTTAAGTCCAACTCTTCTAGATTGGAGCATTTGCCAATTTGAGGCGGAATGGGTCCACT
1 TTGTTGCTTAAGTCCAACTCTTCTAAATTGAAGCAATTACAAATTTGAGGCGGAATGGGTCCACT
* *
36035989 TAACTCGTTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATTTCCAATTCCCTCAGGTACGA
66 CAACTCGTTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATTTCCAATTTCCTCAGGTACGA
* * *
36036054 GACCTTCTAAAAGATTTGAGTGAAGGAATAAAACACGCAAAGTCTTCAAATCTTCAATTCTTGAA
131 GACCTTCTAAAAGATTTGAGTGAAGGAATAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
36036119 GGGATAGAACCATTGATTCTA
196 GGGATAGAACCATTGATTCTA
*
36036140 TTGTTGCTTAAGTCCAACTCTTCTAAATTGAAGCAATTACGAATTTGAGGCGGAATGGGTCCACT
1 TTGTTGCTTAAGTCCAACTCTTCTAAATTGAAGCAATTACAAATTTGAGGCGGAATGGGTCCACT
* * *
36036205 CAACTCATTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATCTCCAATTTCCTCAGGTAAGA
66 CAACTCGTTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATTTCCAATTTCCTCAGGTACGA
* *
36036270 AACCTTCTAAAAGATTTGAATGAAGGAATAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
131 GACCTTCTAAAAGATTTGAGTGAAGGAATAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
36036335 GGGATAGAACCATTGATTCTA
196 GGGATAGAACCATTGATTCTA
*
36036356 TTGTTGCTTAAGTCCAACTTTTCTAAATTGAAGCAATTACAAATTTGAGGCGGAATGGGTCCACT
1 TTGTTGCTTAAGTCCAACTCTTCTAAATTGAAGCAATTACAAATTTGAGGCGGAATGGGTCCACT
* * * *
36036421 CAACTCGTTTTCATAGAGGTTCAATAAAGTGAGTGCTTTCAAATTTCCAATTTCCTCAGGTACGA
66 CAACTCGTTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATTTCCAATTTCCTCAGGTACGA
* **
36036486 GACCTTCTAAAAAATTTGAGTGAAGGCGTAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
131 GACCTTCTAAAAGATTTGAGTGAAGGAATAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
36036551 GGGATAGAACCATTGATTCTA
196 GGGATAGAACCATTGATTCTA
36036572 TTG
1 TTG
36036575 AAGTCAAGAA
Statistics
Matches: 406, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 406 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (216 bp):
TTGTTGCTTAAGTCCAACTCTTCTAAATTGAAGCAATTACAAATTTGAGGCGGAATGGGTCCACT
CAACTCGTTTTGAGAGAGGTTCAATAAAGTAAGTGCTTCCAAATTTCCAATTTCCTCAGGTACGA
GACCTTCTAAAAGATTTGAGTGAAGGAATAGAACACGCAAAGTCTTCAAATCTCCAATTTTTGAA
GGGATAGAACCATTGATTCTA
Found at i:36036791 original size:72 final size:72
Alignment explanation
Indices: 36036686--36036828 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 72
36036676 TAATGAAAAA
* * * *
36036686 AGAGTAGAAGGAATGGAACCATGAAGTAAGTTATAAGACAAATCCAGGGTCATTAAATTGGTTAA
1 AGAGTAGAAGGAATGAAACCACGAAGCAAGTTATAAGACAAATCCAGGGTCACTAAATTGGTTAA
36036751 CTTGCCT
66 CTTGCCT
* ** * *
36036758 AGAGTGGAAGGAATGAAACCACGAAGCGTGTTATTAGACAAATTCAGGGTCACTAAATTGGTTAA
1 AGAGTAGAAGGAATGAAACCACGAAGCAAGTTATAAGACAAATCCAGGGTCACTAAATTGGTTAA
36036823 CTTGCC
66 CTTGCC
36036829 CAAATTGGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (72 bp):
AGAGTAGAAGGAATGAAACCACGAAGCAAGTTATAAGACAAATCCAGGGTCACTAAATTGGTTAA
CTTGCCT
Found at i:36036933 original size:162 final size:161
Alignment explanation
Indices: 36036666--36037131 Score: 632
Period size: 162 Copynumber: 3.0 Consensus size: 161
36036656 TCGATGGTGA
*
36036666 CCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGAACCATGAAGTAAGTTATAAGACAAATCC
1 CCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGAACCATGAAGTAAGTTATTAGACAAATCC
* *
36036731 AGGGTCATTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGAAACCACGAAGCGTGTTATTAGA
66 AGGGTCACTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGGAACCACGAAGCGTGTTATTAGA
36036796 CAAATTCAGGGTCACTAAATTGGTTAACTTG
131 CAAATTCAGGGTCACTAAATTGGTTAACTTG
*
36036827 CCCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGCACCATGAAGTAAGTTATTAGACAAATC
1 -CCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGAACCATGAAGTAAGTTATTAGACAAATC
* *
36036892 CAGGGTCACTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGGAACCATGAAGCGTGTTATTGG
65 CAGGGTCACTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGGAACCACGAAGCGTGTTATTAG
36036957 ACAAATTCAGGGTCACTAAATTGGTTAACTTG
130 ACAAATTCAGGGTCACTAAATTGGTTAACTTG
*
36036989 CC-----------T------AGAGTGGAAGGAATGGAACCATGAAGCCT-A-TTATTAGACAAAT
1 CCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGAACCATGAAG--TAAGTTATTAGACAAAT
* * *
36037035 CCAGGGTCACTAAATTGGTTAACCTGCCTAGAGTGGAAGGAATGGAACCATC-AAGTGAGTTATT
64 CCAGGGTCACTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGGAACCA-CGAAGCGTGTTATT
* *
36037099 AGACAAA-TCTAGGGTCTCCAAATTGGTTAACTT
128 AGACAAATTC-AGGGTCACTAAATTGGTTAACTT
36037132 ACCTAGAGTA
Statistics
Matches: 285, Mismatches: 15, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
143 2 0.01
144 123 0.43
145 1 0.00
146 1 0.00
150 1 0.00
161 2 0.01
162 155 0.54
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (161 bp):
CCAAATTGGATAATGAAAAAAGAGTAGAAGGAATGGAACCATGAAGTAAGTTATTAGACAAATCC
AGGGTCACTAAATTGGTTAACTTGCCTAGAGTGGAAGGAATGGAACCACGAAGCGTGTTATTAGA
CAAATTCAGGGTCACTAAATTGGTTAACTTG
Found at i:36036953 original size:72 final size:72
Alignment explanation
Indices: 36036848--36037149 Score: 444
Period size: 72 Copynumber: 4.2 Consensus size: 72
36036838 TAATGAAAAA
* * **
36036848 AGAGTAGAAGGAATGGCACCATGAAGTAAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTAA
1 AGAGTGGAAGGAATGGAACCATGAAGCGAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTAA
36036913 CTTGCCT
66 CTTGCCT
* * *
36036920 AGAGTGGAAGGAATGGAACCATGAAGCGTGTTATTGGACAAATTCAGGGTCACTAAATTGGTTAA
1 AGAGTGGAAGGAATGGAACCATGAAGCGAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTAA
36036985 CTTGCCT
66 CTTGCCT
*
36036992 AGAGTGGAAGGAATGGAACCATGAAGCCTA-TTATTAGACAAATCCAGGGTCACTAAATTGGTTA
1 AGAGTGGAAGGAATGGAACCATGAAG-CGAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTA
*
36037056 ACCTGCCT
65 ACTTGCCT
* * * * *
36037064 AGAGTGGAAGGAATGGAACCATCAAGTGAGTTATTAGACAAATCTAGGGTCTCCAAATTGGTTAA
1 AGAGTGGAAGGAATGGAACCATGAAGCGAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTAA
*
36037129 CTTACCT
66 CTTGCCT
*
36037136 AGAGTAGAAGGAAT
1 AGAGTGGAAGGAAT
36037150 TGGACCAAGT
Statistics
Matches: 207, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
71 1 0.00
72 205 0.99
73 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (72 bp):
AGAGTGGAAGGAATGGAACCATGAAGCGAGTTATTAGACAAATCCAGGGTCACTAAATTGGTTAA
CTTGCCT
Found at i:36043310 original size:13 final size:14
Alignment explanation
Indices: 36043286--36043318 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
36043276 TATTTGACAA
36043286 ATAAAAGAAAAAGT
1 ATAAAAGAAAAAGT
*
36043300 A-AAAAGCAAAAGT
1 ATAAAAGAAAAAGT
36043313 ATAAAA
1 ATAAAA
36043319 ATTTTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (14 bp):
ATAAAAGAAAAAGT
Found at i:36045587 original size:101 final size:100
Alignment explanation
Indices: 36045410--36045612 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 100
36045400 CAAGAAACAG
36045410 CCTCTCTCGACATATACTACCTTTCCTTGTAAAGCCAACATTCCTAAACCATCGCAATGCTCCTC
1 CCTCTCTCGACATATACTACCTTTCCTTGTAAAGCCAACATTCCTAAACCATCGCAATGCTCCTC
* *** *
36045475 AGTTTTTTTGCAATATATATTCCCATACTCA-CCC
66 ACTTGGATTGCAATATATATCCCCATACTCATCCC
* * * *
36045509 CCTCTCTCGAATATATACTACCTTTTCCTTGTAAAGCCAACATTCCTGAACCATCGCAATGTTCT
1 CCTCTCTCG-ACATATACTACC-TTTCCTTGTAAAGCCAACATTCCTAAACCATCGCAATGCTCC
*
36045574 TCACTTGGATTGCAGTATATATCCCCATACTCATCCC
64 TCACTTGGATTGCAATATATATCCCCATACTCATCCC
36045611 CC
1 CC
36045613 CTTTCACTCC
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
99 9 0.10
100 11 0.12
101 66 0.73
102 5 0.05
ACGTcount: A:0.26, C:0.33, G:0.08, T:0.33
Consensus pattern (100 bp):
CCTCTCTCGACATATACTACCTTTCCTTGTAAAGCCAACATTCCTAAACCATCGCAATGCTCCTC
ACTTGGATTGCAATATATATCCCCATACTCATCCC
Found at i:36045766 original size:24 final size:24
Alignment explanation
Indices: 36045739--36045797 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
36045729 CCGCCAGGTG
36045739 GTGGCCGTGGCTGTCAACGTGGAC
1 GTGGCCGTGGCTGTCAACGTGGAC
**
36045763 GTGGCCGTGGCTGTGGACGTGGAC
1 GTGGCCGTGGCTGTCAACGTGGAC
36045787 GTGGCCGTGGC
1 GTGGCCGTGGC
36045798 CATGGACATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.08, C:0.24, G:0.47, T:0.20
Consensus pattern (24 bp):
GTGGCCGTGGCTGTCAACGTGGAC
Found at i:36045771 original size:12 final size:12
Alignment explanation
Indices: 36045756--36045796 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
36045746 TGGCTGTCAA
36045756 CGTGGACGTGGC
1 CGTGGACGTGGC
*
36045768 CGTGG-CTGTGGA
1 CGTGGAC-GTGGC
36045780 CGTGGACGTGGC
1 CGTGGACGTGGC
36045792 CGTGG
1 CGTGG
36045797 CCATGGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.07, C:0.22, G:0.51, T:0.20
Consensus pattern (12 bp):
CGTGGACGTGGC
Found at i:36045778 original size:18 final size:18
Alignment explanation
Indices: 36045756--36045796 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
36045746 TGGCTGTCAA
*
36045756 CGTGGACGTGGCCGTGGC
1 CGTGGACGTGGACGTGGC
*
36045774 TGTGGACGTGGACGTGGC
1 CGTGGACGTGGACGTGGC
36045792 CGTGG
1 CGTGG
36045797 CCATGGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.22, G:0.51, T:0.20
Consensus pattern (18 bp):
CGTGGACGTGGACGTGGC
Found at i:36045797 original size:6 final size:6
Alignment explanation
Indices: 36045756--36045798 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
36045746 TGGCTGTCAA
* * * *
36045756 CGTGGA CGTGGC CGTGGC TGTGGA CGTGGA CGTGGC CGTGGC C
1 CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC C
36045799 ATGGACATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.07, C:0.26, G:0.49, T:0.19
Consensus pattern (6 bp):
CGTGGC
Found at i:36045803 original size:18 final size:18
Alignment explanation
Indices: 36045756--36045809 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
36045746 TGGCTGTCAA
* *
36045756 CGTGGACGTGGCCGTGGC
1 CGTGGACATGGACGTGGC
* *
36045774 TGTGGACGTGGACGTGGC
1 CGTGGACATGGACGTGGC
* *
36045792 CGTGGCCATGGACATGGC
1 CGTGGACATGGACGTGGC
36045810 TCGGTGAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (18 bp):
CGTGGACATGGACGTGGC
Found at i:36045803 original size:24 final size:24
Alignment explanation
Indices: 36045755--36045804 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
36045745 GTGGCTGTCA
**
36045755 ACGTGGACGTGGCCGTGGCTGTGG
1 ACGTGGACGTGGCCGTGGCCATGG
36045779 ACGTGGACGTGGCCGTGGCCATGG
1 ACGTGGACGTGGCCGTGGCCATGG
36045803 AC
1 AC
36045805 ATGGCTCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (24 bp):
ACGTGGACGTGGCCGTGGCCATGG
Found at i:36047049 original size:2 final size:2
Alignment explanation
Indices: 36047042--36047076 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36047032 AAAGGAAAAT
*
36047042 TA TA TA TA TA TT 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 T
36047077 TTCTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:36047119 original size:15 final size:14
Alignment explanation
Indices: 36047098--36047130 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
36047088 TTTTTATTTT
*
36047098 TATAAATTTTAAAA
1 TATAAAATTTAAAA
36047112 TATAAAATTTAAAA
1 TATAAAATTTAAAA
36047126 TATAA
1 TATAA
36047131 CATAATATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAAAATTTAAAA
Found at i:36067502 original size:38 final size:38
Alignment explanation
Indices: 36067451--36067531 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
36067441 TACCAGTCAA
*
36067451 TCTTTCGTACAAAAATTTATTGCTTGTTGGTTGTTATT
1 TCTTTCGTACAAAAATTTATTGCTTGTTGGTCGTTATT
* *
36067489 TCTTTGGTACAAAATTTTATTGCTTGTTGGTCGTTATT
1 TCTTTCGTACAAAAATTTATTGCTTGTTGGTCGTTATT
36067527 TCTTT
1 TCTTT
36067532 AACTCCTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (38 bp):
TCTTTCGTACAAAAATTTATTGCTTGTTGGTCGTTATT
Found at i:36091082 original size:15 final size:15
Alignment explanation
Indices: 36091061--36091114 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
36091051 TAGAAATTTT
36091061 CGTTGGAAACAATTC
1 CGTTGGAAACAATTC
* *
36091076 TGTTGGAAGCAATTC
1 CGTTGGAAACAATTC
36091091 CGTTGGAAACAATTC
1 CGTTGGAAACAATTC
36091106 CGTTGGAAA
1 CGTTGGAAA
36091115 ATCGTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (15 bp):
CGTTGGAAACAATTC
Found at i:36093710 original size:18 final size:18
Alignment explanation
Indices: 36093689--36093723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36093679 GTCTTCAAGT
*
36093689 TCATCTTCTTTTTCATCG
1 TCATCTTCATTTTCATCG
36093707 TCATCTTCATTTTCATC
1 TCATCTTCATTTTCATC
36093724 TCTTTCCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.29, G:0.03, T:0.54
Consensus pattern (18 bp):
TCATCTTCATTTTCATCG
Found at i:36093744 original size:30 final size:30
Alignment explanation
Indices: 36093710--36093777 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
36093700 TTCATCGTCA
* *
36093710 TCTTCATTTTCATCTCTTTCCATGTCATCT
1 TCTTCATCTTCATCTCTTTCCATGTCATCG
*
36093740 TCTTCATCTTCATCTCTTTGCATGTCATCG
1 TCTTCATCTTCATCTCTTTCCATGTCATCG
36093770 TCTTCATC
1 TCTTCATC
36093778 CTCAATCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.31, G:0.06, T:0.50
Consensus pattern (30 bp):
TCTTCATCTTCATCTCTTTCCATGTCATCG
Found at i:36101766 original size:18 final size:19
Alignment explanation
Indices: 36101743--36101821 Score: 71
Period size: 18 Copynumber: 4.3 Consensus size: 19
36101733 AAATCGAGAA
36101743 GAGAAA-GAAAGAAGAAAG
1 GAGAAAGGAAAGAAGAAAG
36101761 GAGAAAGG--A-AAGAAAG
1 GAGAAAGGAAAGAAGAAAG
36101777 GAGAAGGAGGGAAAG-AGAAAG
1 GAGAA--A-GGAAAGAAGAAAG
*
36101798 AAGAAAGGAAAGAA-AAAG
1 GAGAAAGGAAAGAAGAAAG
36101816 AGAGAA
1 -GAGAA
36101822 TGAAGATCGG
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
16 12 0.24
17 1 0.02
18 17 0.34
19 9 0.18
21 11 0.22
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGAAAGGAAAGAAGAAAG
Found at i:36101790 original size:15 final size:15
Alignment explanation
Indices: 36101754--36101806 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 15
36101744 AGAAAGAAAG
36101754 AAGAAAGGAGAAAGGA
1 AAGAAAGGAG-AAGGA
36101770 AAGAAAGGAGAAGGA
1 AAGAAAGGAGAAGGA
** *
36101785 GGGAAA-GAGAAAG-
1 AAGAAAGGAGAAGGA
36101798 AAGAAAGGA
1 AAGAAAGGA
36101807 AAGAAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
15 9 0.29
16 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAGAAAGGAGAAGGA
Found at i:36102047 original size:21 final size:21
Alignment explanation
Indices: 36102017--36102064 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
36102007 GCAGCCGACC
* *
36102017 AAGAA-AGAGAGAGGAAAAAA
1 AAGAATAGAGAAAAGAAAAAA
36102037 AAGAATAGAGAAAAGAAAAAA
1 AAGAATAGAGAAAAGAAAAAA
36102058 AA-AATAG
1 AAGAATAG
36102065 TGGGCATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (21 bp):
AAGAATAGAGAAAAGAAAAAA
Found at i:36102137 original size:23 final size:23
Alignment explanation
Indices: 36102108--36102153 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
36102098 CCCATGAGAA
*
36102108 AGGCCCAATAGTAACAAGAAAGG
1 AGGCCCAATAGCAACAAGAAAGG
*
36102131 AGGCCCAATGGCAACAAGAAAGG
1 AGGCCCAATAGCAACAAGAAAGG
36102154 GTAAGCCCAA
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:0.46, C:0.20, G:0.28, T:0.07
Consensus pattern (23 bp):
AGGCCCAATAGCAACAAGAAAGG
Found at i:36102825 original size:59 final size:58
Alignment explanation
Indices: 36102720--36102962 Score: 288
Period size: 58 Copynumber: 4.1 Consensus size: 58
36102710 GAGATATTCT
* * * *
36102720 GAGTAGGTAAAGGGGGACCTGAAGCCTCGATTTATATATGGTGGCGTGGGCAGTTCTCAC
1 GAGTAGGTAAAGGGGGACCTGAAGCCCCGA-TT-TATATGGTGACGTGGGCAATTCCCAC
* * * * * * * *
36102780 GAGTAGGTAAATGGAGACTTGAAGTCCTGATTATATATGGTGGCGTGGGTAATTCTCAC
1 GAGTAGGTAAAGGGGGACCTGAAGCCCCGATT-TATATGGTGACGTGGGCAATTCCCAC
* *
36102839 GAGTAGGTAAAGGGGAACTTGAAGCCCCGATTTATATGGTGACGTGGGCAATTCCCAC
1 GAGTAGGTAAAGGGGGACCTGAAGCCCCGATTTATATGGTGACGTGGGCAATTCCCAC
* * * * *
36102897 GAGTAGGTAAAGGGGGACCTGAAGCCCCAATTCATATGGTGACGTAGGCAGTTCCCAT
1 GAGTAGGTAAAGGGGGACCTGAAGCCCCGATTTATATGGTGACGTGGGCAATTCCCAC
36102955 GAGTAGGT
1 GAGTAGGT
36102963 GATGATATCT
Statistics
Matches: 160, Mismatches: 23, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
58 82 0.51
59 54 0.34
60 24 0.15
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (58 bp):
GAGTAGGTAAAGGGGGACCTGAAGCCCCGATTTATATGGTGACGTGGGCAATTCCCAC
Found at i:36122975 original size:2 final size:2
Alignment explanation
Indices: 36122968--36123005 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
36122958 CATTAAGATA
36122968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36123006 CACAACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36130252 original size:851 final size:852
Alignment explanation
Indices: 36128591--36130294 Score: 3367
Period size: 851 Copynumber: 2.0 Consensus size: 852
36128581 TTGCTAAAGA
36128591 TAATAAATAAATAAATAAATAATCAATACCCTCTAAATTAAGAATAGAAGTACGTACCTCTGATG
1 TAATAAATAAATAAATAAATAATCAATACCCTCTAAATTAAGAATAGAAGTACGTACCTCTGATG
36128656 ATGCAGAGGACAAGGATCAAACCAGAAGAAATAGCTCAAGGTTCAAAGTGCAAAATGAACCCACT
66 ATGCAGAGGACAAGGATCAAACCAGAAGAAATAGCTCAAGGTTCAAAGTGCAAAATGAACCCACT
36128721 TAGTTGCAAGTACAACTGGATCTAGCAAGTCTTGGCGTTTCAGTTTTATACAGCAGAGAGTAATG
131 TAGTTGCAAGTACAACTGGATCTAGCAAGTCTTGGCGTTTCAGTTTTATACAGCAGAGAGTAATG
36128786 AACAAGCTACTTGATTGTTCAGAGTAACTCACCTTTACCAGCAGAATCAATTCCCCACCATCATG
196 AACAAGCTACTTGATTGTTCAGAGTAACTCACCTTTACCAGCAGAATCAATTCCCCACCATCATG
36128851 ATTTGTCTCTTCCTGCTTCACACTTTCACTGACTTGGCAATTTAACCCCGCTTCTTATCTTCTTC
261 ATTTGTCTCTTCCTGCTTCACACTTTCACTGACTTGGCAATTTAACCCCGCTTCTTATCTTCTTC
36128916 CCAACCCAACTAAATGAGGGTGGTACGTAGAGCTGTCCACGGGCCAAGTTACCAGCCCAGTTCGC
326 CCAACCCAACTAAATGAGGGTGGTACGTAGAGCTGTCCACGGGCCAAGTTACCAGCCCAGTTCGC
36128981 AGGCCTCACGTGATTTCAGTCGGGTTTGGATATGATTTTTTAAATTTGGATCCAATTCAGTTCGA
391 AGGCCTCACGTGATTTCAGTCGGGTTTGGATATGATTTTTTAAATTTGGATCCAATTCAGTTCGA
36129046 TTCAAAAATATTATTTTATTATTTAACTTAAATTTAAAAATATATTTTACAATATTAATATAAAA
456 TTCAAAAATATTATTTTATTATTTAACTTAAATTTAAAAATATATTTTACAATATTAATATAAAA
36129111 ATTAATTTTTTTAATATTTAGTAATCAATATAACTTAAATAGATGGATAAGTCTATGTTTTCAAG
521 ATTAATTTTTTTAATATTTAGTAATCAATATAACTTAAATAGATGGATAAGTCTATGTTTTCAAG
36129176 GAGTCTATCGGATCCGATCACCTCTAGCGGTTGATAATTTATATTTTTATTCTTACTTTTAATTG
586 GAGTCTATCGGATCCGATCACCTCTAGCGGTTGATAATTTATATTTTTATTCTTACTTTTAATTG
36129241 TGAAAATTTTTTTATTTATTTTAAAAGATCAAAGATGGGAAAAAATATCTTGATTTTTTTATTTA
651 TGAAAATTTTTTTATTTATTTTAAAAGATCAAAGATGGGAAAAAATATCTTGATTTTTTTATTTA
36129306 TTTTAGTATTTTTTGTAAAACTTTTTTAATTGTCTTAAATTAGACGTTCAATGAAATGAATAATT
716 TTTTAGTATTTTTTGTAAAACTTTTTTAATTGTCTTAAATTAGACGTTCAATGAAATGAATAATT
*
36129371 AATAAGAAAAGTTGTGGCTTTTGAATAAAAAAAATAAGAGTGATATTCGGAAGGTAAAGGAACAA
781 AATAAGAAAAGTTGTGGCTTTTGAATAAAAAAAATAAGAGTGATAGTCGGAAGGTAAAGGAACAA
36129436 AGTCCAT
846 AGTCCAT
36129443 TNAATAAATAAATAAAT-AA-AATCAATACCCTCTAAATTAAGAATAGAAGTACGTACCTCTGAT
1 T-AATAAATAAATAAATAAATAATCAATACCCTCTAAATTAAGAATAGAAGTACGTACCTCTGAT
*
36129506 GATGCAGAGGACGAGGATCAAACCAGAAGAAATAGCTCAAGGTTCAAAGTGCAAAATGAACCCAC
65 GATGCAGAGGACAAGGATCAAACCAGAAGAAATAGCTCAAGGTTCAAAGTGCAAAATGAACCCAC
36129571 TTAGTTGCAAGTACAACTGGATCTAGCAAGTCTTGGCGTTTCAGTTTTATACAGCAGAGAGTAAT
130 TTAGTTGCAAGTACAACTGGATCTAGCAAGTCTTGGCGTTTCAGTTTTATACAGCAGAGAGTAAT
36129636 GAACAAGCTACTTGATTGTTCAGAGTAACTCACCTTTACCAGCAGAATCAATTCCCCACCATCAT
195 GAACAAGCTACTTGATTGTTCAGAGTAACTCACCTTTACCAGCAGAATCAATTCCCCACCATCAT
36129701 GATTTGTCTCTTCCTGCTTCACACTTTCACTGACTTGGCAATTTAACCCCGCTTCTTATCTTCTT
260 GATTTGTCTCTTCCTGCTTCACACTTTCACTGACTTGGCAATTTAACCCCGCTTCTTATCTTCTT
36129766 CCCAACCCAACTAAATGAGGGTGGTACGTAGAGCTGTCCACGGGCCAAGTTACCAGCCCAGTTCG
325 CCCAACCCAACTAAATGAGGGTGGTACGTAGAGCTGTCCACGGGCCAAGTTACCAGCCCAGTTCG
36129831 CAGGCCTCACGTGATTTCAGTCGGGTTTGGATATGATTTTTTAAATTTGGATCCAATTCAGTTCG
390 CAGGCCTCACGTGATTTCAGTCGGGTTTGGATATGATTTTTTAAATTTGGATCCAATTCAGTTCG
36129896 ATTCAAAAATATTATTTTATTATTTAACTTAAATTTAAAAATATATTTTACAATATTAATATAAA
455 ATTCAAAAATATTATTTTATTATTTAACTTAAATTTAAAAATATATTTTACAATATTAATATAAA
36129961 AATTAATTTTTTTAATATTTAGTAATCAATATAACTTAAATAGATGGATAAGTCTATGTTTTCAA
520 AATTAATTTTTTTAATATTTAGTAATCAATATAACTTAAATAGATGGATAAGTCTATGTTTTCAA
36130026 GGAGTCTATCGGATCCGATCACCTCTAGCGGTTGATAATTTATATTTTTATTCTTACTTTTAATT
585 GGAGTCTATCGGATCCGATCACCTCTAGCGGTTGATAATTTATATTTTTATTCTTACTTTTAATT
36130091 GTGAAAATTTTTTTATTTATTTTAAAAGATCAAAGATGGGAAAAAATATCTTGATTTTTTTATTT
650 GTGAAAATTTTTTTATTTATTTTAAAAGATCAAAGATGGGAAAAAATATCTTGATTTTTTTATTT
36130156 ATTTTAGTATTTTTTGTAAAACTTTTTTAATTGTCTTAAATTAGACGTTCAATGAAATGAATAAT
715 ATTTTAGTATTTTTTGTAAAACTTTTTTAATTGTCTTAAATTAGACGTTCAATGAAATGAATAAT
36130221 TAATAAGAAAAGTTGTGGCTTTTGAATAAAAAAAATAAGAGTGATAGTCGGAAGGTAAAGGAACA
780 TAATAAGAAAAGTTGTGGCTTTTGAATAAAAAAAATAAGAGTGATAGTCGGAAGGTAAAGGAACA
36130286 AAGTCCAT
845 AAGTCCAT
36130294 T
1 T
36130295 CAAGAAAAAT
Statistics
Matches: 849, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
851 831 0.98
852 3 0.00
853 15 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (852 bp):
TAATAAATAAATAAATAAATAATCAATACCCTCTAAATTAAGAATAGAAGTACGTACCTCTGATG
ATGCAGAGGACAAGGATCAAACCAGAAGAAATAGCTCAAGGTTCAAAGTGCAAAATGAACCCACT
TAGTTGCAAGTACAACTGGATCTAGCAAGTCTTGGCGTTTCAGTTTTATACAGCAGAGAGTAATG
AACAAGCTACTTGATTGTTCAGAGTAACTCACCTTTACCAGCAGAATCAATTCCCCACCATCATG
ATTTGTCTCTTCCTGCTTCACACTTTCACTGACTTGGCAATTTAACCCCGCTTCTTATCTTCTTC
CCAACCCAACTAAATGAGGGTGGTACGTAGAGCTGTCCACGGGCCAAGTTACCAGCCCAGTTCGC
AGGCCTCACGTGATTTCAGTCGGGTTTGGATATGATTTTTTAAATTTGGATCCAATTCAGTTCGA
TTCAAAAATATTATTTTATTATTTAACTTAAATTTAAAAATATATTTTACAATATTAATATAAAA
ATTAATTTTTTTAATATTTAGTAATCAATATAACTTAAATAGATGGATAAGTCTATGTTTTCAAG
GAGTCTATCGGATCCGATCACCTCTAGCGGTTGATAATTTATATTTTTATTCTTACTTTTAATTG
TGAAAATTTTTTTATTTATTTTAAAAGATCAAAGATGGGAAAAAATATCTTGATTTTTTTATTTA
TTTTAGTATTTTTTGTAAAACTTTTTTAATTGTCTTAAATTAGACGTTCAATGAAATGAATAATT
AATAAGAAAAGTTGTGGCTTTTGAATAAAAAAAATAAGAGTGATAGTCGGAAGGTAAAGGAACAA
AGTCCAT
Found at i:36132407 original size:88 final size:91
Alignment explanation
Indices: 36132206--36132415 Score: 288
Period size: 88 Copynumber: 2.4 Consensus size: 91
36132196 GCCCACCATA
* * *
36132206 TTTCT-TTAAGTCCCATA-TTTCGGTTGCACACGTCTTCGAATTAAGAGTCAACCCTAAATTATT
1 TTTCTATTAAGTCCCA-ACTTTCGATTGCACATGTCTTCGAATTAACAGTCAACCCTAAATTATT
36132269 ATTCTTATTTAGTTTAGATTGCACATC
65 ATTCTTATTTAGTTTAGATTGCACATC
* * *
36132296 TTTCTATTAAGTCCCAACCTTCGATTGCACATGTCCTT-TAATTAACAGTCAATCCTAAATTATT
1 TTTCTATTAAGTCCCAACTTTCGATTGCACATGT-CTTCGAATTAACAGTCAACCCTAAATTATT
*
36132360 A-T-TT-TTTAGTTTAGATTGCACATG
65 ATTCTTATTTAGTTTAGATTGCACATC
*
36132384 TTTCTATTAAATCCCAACTTTCGATTGCACAT
1 TTTCTATTAAGTCCCAACTTTCGATTGCACAT
36132416 CTTCATTGTT
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
88 49 0.45
89 2 0.02
90 7 0.06
91 47 0.44
92 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.41
Consensus pattern (91 bp):
TTTCTATTAAGTCCCAACTTTCGATTGCACATGTCTTCGAATTAACAGTCAACCCTAAATTATTA
TTCTTATTTAGTTTAGATTGCACATC
Found at i:36134522 original size:24 final size:26
Alignment explanation
Indices: 36134480--36134536 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
36134470 TTTAATTTTT
36134480 AAATATACTTTAAACTATT-AATATAA
1 AAATATACTTTAAACTATTCAATA-AA
* *
36134506 AAATATA-TTTTAA-TATTCAATAAT
1 AAATATACTTTAAACTATTCAATAAA
36134530 AAATATA
1 AAATATA
36134537 AAATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.43
25 9 0.32
26 7 0.25
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATACTTTAAACTATTCAATAAA
Found at i:36141176 original size:24 final size:24
Alignment explanation
Indices: 36141138--36141186 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
36141128 TTTTCGTACA
*
36141138 AAAACTAATTGCTTGTTAGCTGTT
1 AAAACTAATTGCTTGTAAGCTGTT
* *
36141162 AAAACTTATTTCTTGTAAGCTGTT
1 AAAACTAATTGCTTGTAAGCTGTT
36141186 A
1 A
36141187 GTTGTCAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (24 bp):
AAAACTAATTGCTTGTAAGCTGTT
Found at i:36148955 original size:24 final size:25
Alignment explanation
Indices: 36148923--36148972 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
36148913 TTTTCGTACA
36148923 AAAACTTATTGCC-TGTTAG-CTGTT
1 AAAACTTATT-CCTTGTTAGCCTGTT
36148947 AAAACTTATTCCTTGTTAGCCTGTT
1 AAAACTTATTCCTTGTTAGCCTGTT
36148972 A
1 A
36148973 GTTGTCAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 2 0.08
24 16 0.67
25 6 0.25
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (25 bp):
AAAACTTATTCCTTGTTAGCCTGTT
Found at i:36149780 original size:15 final size:15
Alignment explanation
Indices: 36149762--36149809 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
36149752 TTTTACGTTC
36149762 AAGTTACTTACATCA
1 AAGTTACTTACATCA
36149777 AAGTTA-TCT-C-TC-
1 AAGTTACT-TACATCA
36149789 AAGTTACTTACATCA
1 AAGTTACTTACATCA
36149804 AAGTTA
1 AAGTTA
36149810 TCTCTAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 4 0.14
15 13 0.46
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (15 bp):
AAGTTACTTACATCA
Found at i:36149790 original size:27 final size:27
Alignment explanation
Indices: 36149760--36149814 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
36149750 AATTTTACGT
36149760 TCAAGTTACTTACATCAAAGTTATCTC
1 TCAAGTTACTTACATCAAAGTTATCTC
36149787 TCAAGTTACTTACATCAAAGTTATCTC
1 TCAAGTTACTTACATCAAAGTTATCTC
36149814 T
1 T
36149815 AATAGCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (27 bp):
TCAAGTTACTTACATCAAAGTTATCTC
Found at i:36156895 original size:31 final size:31
Alignment explanation
Indices: 36156857--36156933 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
36156847 TGCGAAAGCT
* *
36156857 TGCTATATATGCTTAT-ACCATTTACTGTATA
1 TGCTATATATGCTT-TCACCATTCACTCTATA
*
36156888 TGCTATATACGCTTTCACCATTCACTCTATA
1 TGCTATATATGCTTTCACCATTCACTCTATA
*
36156919 TTCTATATATGCTTT
1 TGCTATATATGCTTT
36156934 GATATTCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (31 bp):
TGCTATATATGCTTTCACCATTCACTCTATA
Found at i:36158499 original size:36 final size:36
Alignment explanation
Indices: 36158459--36158558 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
36158449 CGTGTTCAGT
36158459 ACTACTTAATCCGTTAATTACTAACACGTGCTCATA
1 ACTACTTAATCCGTTAATTACTAACACGTGCTCATA
* * * *
36158495 ACTACTTAAT-TGTCAATTATTAACACATGCTCATA
1 ACTACTTAATCCGTTAATTACTAACACGTGCTCATA
* * *
36158530 ACTACTTAATCCTTTAACTACTGACACGT
1 ACTACTTAATCCGTTAATTACTAACACGT
36158559 TTCTCAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 31 0.60
36 21 0.40
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (36 bp):
ACTACTTAATCCGTTAATTACTAACACGTGCTCATA
Found at i:36174793 original size:12 final size:13
Alignment explanation
Indices: 36174778--36174806 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36174768 CTCCCCAAAA
36174778 CCCACCCCCAC-C
1 CCCACCCCCACAC
36174790 CCCACCCCCACAC
1 CCCACCCCCACAC
36174803 CCCA
1 CCCA
36174807 TGCAGTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCACCCCCACAC
Found at i:36189757 original size:28 final size:28
Alignment explanation
Indices: 36189717--36189779 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
36189707 CTCTGTTGGT
36189717 AACAACTTAACGACTTAATGTACCTGGA
1 AACAACTTAACGACTTAATGTACCTGGA
36189745 AACAACTTAACGACTTAATGTACCTGGA
1 AACAACTTAACGACTTAATGTACCTGGA
36189773 AACAACT
1 AACAACT
36189780 CTGCGGAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (28 bp):
AACAACTTAACGACTTAATGTACCTGGA
Found at i:36197203 original size:15 final size:15
Alignment explanation
Indices: 36197184--36197213 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
36197174 TTTAATTTTA
36197184 AAAAATATAAAATAAT
1 AAAAAT-TAAAATAAT
36197200 AAAAATTAAAATAA
1 AAAAATTAAAATAA
36197214 ATCTCATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATTAAAATAAT
Found at i:36199189 original size:14 final size:15
Alignment explanation
Indices: 36199170--36199203 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
36199160 GAACAAATAG
36199170 GTTAATTAA-CAAAA
1 GTTAATTAAGCAAAA
36199184 GTTAATTAAGCAAAA
1 GTTAATTAAGCAAAA
*
36199199 ATTAA
1 GTTAA
36199204 ACGACCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (15 bp):
GTTAATTAAGCAAAA
Found at i:36201615 original size:18 final size:15
Alignment explanation
Indices: 36201580--36201615 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
36201570 GGATGTAAAA
36201580 TAATTAATAATATTT
1 TAATTAATAATATTT
*
36201595 TAATTAATAATA-AT
1 TAATTAATAATATTT
36201609 TAATTAA
1 TAATTAA
36201616 CCATTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTAATAATATTT
Found at i:36216196 original size:21 final size:22
Alignment explanation
Indices: 36216161--36216202 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
36216151 CATGTACACA
36216161 CATGAAACAAATATAAATTATG
1 CATGAAACAAATATAAATTATG
*
36216183 CATG-AACAAGTATAAATTAT
1 CATGAAACAAATATAAATTAT
36216203 AGAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
CATGAAACAAATATAAATTATG
Found at i:36228399 original size:30 final size:30
Alignment explanation
Indices: 36228354--36228410 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
36228344 GGTATTTGTG
36228354 GAGCAAAATAAAGGGTAAGCCTCCAAAATT
1 GAGCAAAATAAAGGGTAAGCCTCCAAAATT
* *
36228384 GAGCACAATACAGGGTAAGCCTCCAAA
1 GAGCAAAATAAAGGGTAAGCCTCCAAA
36228411 TAACTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (30 bp):
GAGCAAAATAAAGGGTAAGCCTCCAAAATT
Found at i:36234280 original size:27 final size:28
Alignment explanation
Indices: 36234215--36234281 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
36234205 GAATCCCTCA
*
36234215 AAATAAA-CTTT-TATTTTTATTTTATT
1 AAATAAATCTTTATATTTTTATTATATT
* *
36234241 -AATCAAGTTTTTATATTTTTA-TATATT
1 AAAT-AAATCTTTATATTTTTATTATATT
36234268 AAATAAATCTTTAT
1 AAATAAATCTTTAT
36234282 TGTTAATGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 16 0.50
28 11 0.34
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (28 bp):
AAATAAATCTTTATATTTTTATTATATT
Done.