Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 135 of 196
Found at i:40184147 original size:6 final size:7
Alignment explanation
Indices: 40184131--40184156 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40184121 TCACAATGTC
40184131 TTTTTGT
1 TTTTTGT
40184138 TTTTTGT
1 TTTTTGT
40184145 TTTTTGT
1 TTTTTGT
40184152 TTTTT
1 TTTTT
40184157 TAATCATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:40184571 original size:18 final size:18
Alignment explanation
Indices: 40184539--40184593 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
40184529 ATTTAATATT
**
40184539 ATAATTTTATTTTTTATA
1 ATAATTTTAAATTTTATA
40184557 ATAATTTTAAATTTTA-A
1 ATAATTTTAAATTTTATA
40184574 ATAATATTTTAATATTTTAT
1 AT-A-ATTTTAA-ATTTTAT
40184594 TAAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.10
18 15 0.48
19 7 0.23
20 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTTAAATTTTATA
Found at i:40184577 original size:20 final size:20
Alignment explanation
Indices: 40184554--40184609 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
40184544 TTTATTTTTT
40184554 ATAATAATTTTAA-ATTTTAA
1 ATAAT-ATTTTAATATTTTAA
40184574 ATAATATTTTAATATTTTATTA
1 ATAATATTTTAATATTTTA--A
*
40184596 AAAATATTTTAATA
1 ATAATATTTTAATA
40184610 ATAAATATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.22
20 11 0.34
22 14 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATATTTTAATATTTTAA
Found at i:40184603 original size:14 final size:15
Alignment explanation
Indices: 40184584--40184617 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40184574 ATAATATTTT
*
40184584 AATATTTTATTAA-A
1 AATATTTTAATAATA
40184598 AATATTTTAATAATA
1 AATATTTTAATAATA
40184613 AATAT
1 AATAT
40184618 GTAGCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:40189436 original size:37 final size:37
Alignment explanation
Indices: 40189395--40189476 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
40189385 AAATATTTAT
* * *
40189395 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
*
40189432 TAATCAATGCTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
40189469 TAATCAAT
1 TAATCAAT
40189477 ACTTAACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (37 bp):
TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
Found at i:40189548 original size:33 final size:33
Alignment explanation
Indices: 40189511--40189586 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
40189501 TTAAAACTTG
*
40189511 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
40189544 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
40189577 AATTATACAT
1 AATTATACAT
40189587 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:40192749 original size:119 final size:119
Alignment explanation
Indices: 40192604--40193585 Score: 1709
Period size: 119 Copynumber: 8.2 Consensus size: 119
40192594 TTTTCAAGTT
*
40192604 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
40192669 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
* *
40192723 ATACATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
40192788 TAATATAAGAACATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
*
40192842 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
40192907 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
*
40192961 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
40193026 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
40193080 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* * *
40193145 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTT-TTTAAATTATATAGTTTAATTAAA
40193201 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* * *
40193266 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTT-TTTAAATTATATAGTTTAATTAAA
40193322 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* * *
40193387 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTT-TTTAAATTATATAGTTTAATTAAA
40193443 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
40193508 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTT-TTAAATTATATAGTTTAATTAAA
40193563 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
40193586 TAAATATGAT
Statistics
Matches: 848, Mismatches: 10, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
118 2 0.00
119 432 0.51
120 68 0.08
121 344 0.41
122 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (119 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
Found at i:40192925 original size:66 final size:62
Alignment explanation
Indices: 40192869--40193539 Score: 247
Period size: 64 Copynumber: 11.1 Consensus size: 62
40192859 TATGTTAATT
40192869 TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
1 TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
* * * * * * * *
40192931 GAATTTTTTA-A--AT--TATA-TA-G-TTTAATTAAAATATATTTAATAATAATT-A-TGTTAA
1 -TATATTTTACAGTATCATATATTATGATTTGAGTAAATTA-ATATAAGAAT-ATTAATTATTAA
40192986 TTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
1 --TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
* * * * * * * *
40193050 GAATTTTTTA-A--AT--TATA-TA-G-TTTAATTAAAATATATTTAATAATAATT-A-TGTTAA
1 -TATATTTTACAGTATCATATATTATGATTTGAGTAAATTA-ATATAAGAAT-ATTAATTATTAA
* *
40193105 TTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATT-ATCCAATTA
1 --TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAAT--TATTA
40193169 A
62 A
* * * * * * * * *
40193170 GA-A-TTT-CATTA-AAT-TA-TAT-ATTTTAATTAAAATATATTTAATAATAATT-A-TGTTAA
1 TATATTTTACAGTATCATATATTATGA-TTTGAGTAAATTA-ATATAAGAAT-ATTAATTATTAA
* *
40193226 TTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATT-ATCCAATTA
1 --TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAAT--TATTA
40193290 A
62 A
* * * * * * * * *
40193291 GA-A-TTT-CATTA-AAT-TA-TAT-ATTTTAATTAAAATATATTTAATAATAATT-A-TGTTAA
1 TATATTTTACAGTATCATATATTATGA-TTTGAGTAAATTA-ATATAAGAAT-ATTAATTATTAA
* *
40193347 TTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATT-ATCCAATTA
1 --TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAAT--TATTA
40193411 A
62 A
* * * * * * * * *
40193412 GA-A-TTT-CATTA-AAT-TA-TAT-ATTTTAATTAAAATATATTTAATAATAATT-A-TGTTAA
1 TATATTTTACAGTATCATATATTATGA-TTTGAGTAAATTA-ATATAAGAAT-ATTAATTATTAA
*
40193468 TTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAA
1 --TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
*
40193532 GA-ATTTTA
1 TATATTTTA
40193540 TTAAATTATA
Statistics
Matches: 441, Mismatches: 96, Indels: 144
0.65 0.14 0.21
Matches are distributed among these distances:
55 30 0.07
56 49 0.11
57 51 0.12
58 41 0.09
59 25 0.06
60 25 0.06
61 35 0.08
62 34 0.08
63 67 0.15
64 69 0.16
65 15 0.03
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (62 bp):
TATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAA
Found at i:40193562 original size:18 final size:17
Alignment explanation
Indices: 40193534--40193568 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40193524 ATTATTAAGA
*
40193534 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40193551 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40193569 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40193798 original size:44 final size:45
Alignment explanation
Indices: 40193733--40193823 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40193723 ACCTCTATTC
* * *
40193733 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
40193777 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
40193822 CA
1 CA
40193824 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:40193838 original size:17 final size:16
Alignment explanation
Indices: 40193804--40193856 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
40193794 GATTAGCTAT
40193804 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40193820 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
40193837 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40193853 TACA
1 TACA
40193857 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40198241 original size:21 final size:21
Alignment explanation
Indices: 40198217--40198259 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
40198207 TACTTTTTTG
40198217 AAGTTAAAA-GTCAAAACCATT
1 AAGTTAAAAGGT-AAAACCATT
40198238 AAGTTAAAAGGTAAAACCATT
1 AAGTTAAAAGGTAAAACCATT
40198259 A
1 A
40198260 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACCATT
Found at i:40198591 original size:16 final size:17
Alignment explanation
Indices: 40198570--40198608 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
40198560 AGTTGAAAAA
40198570 AGATAAAAAAAT-TATT
1 AGATAAAAAAATATATT
*
40198586 AGATAAAATAATATATT
1 AGATAAAAAAATATATT
40198603 A-ATAAA
1 AGATAAA
40198609 GTTATTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AGATAAAAAAATATATT
Found at i:40199751 original size:26 final size:26
Alignment explanation
Indices: 40199721--40199770 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40199711 TGTTATATGA
*
40199721 TTTCTTCGT-TACTTTTGTTTTGTTTT
1 TTTCTTCATCTAC-TTTGTTTTGTTTT
*
40199747 TTTCTTCATCTTCTTTGTTTTGTT
1 TTTCTTCATCTACTTTGTTTTGTT
40199771 CGAATTATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.04, C:0.14, G:0.10, T:0.72
Consensus pattern (26 bp):
TTTCTTCATCTACTTTGTTTTGTTTT
Found at i:40211389 original size:24 final size:25
Alignment explanation
Indices: 40211347--40211395 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
40211337 CGATGGAGGA
*
40211347 CTTTCATATACTTCTTTTT-TTTTT
1 CTTTCATATAATTCTTTTTGTTTTT
40211371 CTTTCATATAATT-TATTTTGTTTTT
1 CTTTCATATAATTCT-TTTTGTTTTT
40211396 ACAAATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 16 0.73
25 5 0.23
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.69
Consensus pattern (25 bp):
CTTTCATATAATTCTTTTTGTTTTT
Found at i:40228709 original size:6 final size:6
Alignment explanation
Indices: 40228698--40228729 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40228688 GGTTATTGGT
40228698 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
40228730 TTGGTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:40228899 original size:94 final size:94
Alignment explanation
Indices: 40228751--40229089 Score: 330
Period size: 94 Copynumber: 3.6 Consensus size: 94
40228741 AAGTTTAAGG
* ** * *
40228751 TTTTAGAGAAAAAAATTAAATAAATAAGAGTTTAGGGTTTTTTAATTAAATTAATTAAAAAAATT
1 TTTTA-AGAAAAAAA-TAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATT
* * * * * *
40228816 CAAAATTGGATTA-GTTTTCGTGTTTATTATT
64 AAAAATTAGATTAGGATTTAGAGTTTAAT-TT
* * * **
40228847 TTTTAAGAAAAAAATAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAATTTTAA
1 TTTTAAGAAAAAAATAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTAA
**
40228912 AAATTAGATTAGGATTTAGAG-TTAAGGGT
66 AAATTAGATTAGGATTTAGAGTTTAA-TTT
* * * *
40228941 TTTTAAG-GAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT-AAAAAATTG
1 TTTTAAGAAAAAAAT-AAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTA
* *
40229004 AAAATCATATTAGGATTTAGAG-TTAAGGGTTT
65 AAAATTAGATTAGGATTTAGAGTTTAA---TTT
* *
40229036 TTTTAA-AAATAAATAAATAAATTAGAGTTAAGGGTTACTTGAGTAAATTAATTA
1 TTTTAAGAAAAAAATAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTA
40229090 TAAATTTATA
Statistics
Matches: 204, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
93 36 0.18
94 135 0.66
95 28 0.14
96 5 0.02
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (94 bp):
TTTTAAGAAAAAAATAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTAA
AAATTAGATTAGGATTTAGAGTTTAATTT
Found at i:40229035 original size:93 final size:91
Alignment explanation
Indices: 40228846--40229161 Score: 361
Period size: 94 Copynumber: 3.4 Consensus size: 91
40228836 TGTTTATTAT
* *
40228846 TTTTTAAGAAAAAAATAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAATTTTA
1 TTTTTAAG-AAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAA-ATTA
*
40228911 AAAATTAGATTAGGATTTAGAGTTAAGGG
64 AAAA-TAAATTAGGATTTAGAGTTAAGGG
* *
40228940 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTGA
1 TTTTTAAGAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTAA
*
40229005 AAATCATATTAGGATTTAGAGTTAAGGG
65 AAAT-AAATTAGGATTTAGAGTTAAGGG
* * * *
40229033 TTTTTTTAA-AAATAAATAAATAAATTAGAGTTAAGGGTTACTTGAGTAAATTAATT-ATAAATT
1 --TTTTTAAGAAA-AAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATT
* * * * *
40229096 TATAATAAATTA-G-TTTAGGGTTTATGG
63 AAAAATAAATTAGGATTTAGAGTTAAGGG
* *
40229123 TTTTTAAGTAAAAACTCAAATAAATTAGGGTTTGGGGTT
1 TTTTTAAG-AAAAAAT-AAATAAATTAGGGTTTAGGGTT
40229162 TACGGTTACT
Statistics
Matches: 194, Mismatches: 20, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
88 7 0.04
89 3 0.02
90 33 0.17
91 1 0.01
92 6 0.03
93 44 0.23
94 89 0.46
95 11 0.06
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (91 bp):
TTTTTAAGAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTAAA
AATAAATTAGGATTTAGAGTTAAGGG
Found at i:40229573 original size:125 final size:126
Alignment explanation
Indices: 40229198--40229620 Score: 672
Period size: 126 Copynumber: 3.4 Consensus size: 126
40229188 TAATTTAAAG
* * * * * *
40229198 AAGCTCCTATGTGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCAAGTAGACATTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
40229263 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
40229324 AAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTACTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
40229389 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAGGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
40229450 AAGCTTCCACGTGGACGCGCTTTTACTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
40229515 CTGAGCAAACAGTGTC-AAAACGCTTTAAGCAGGATGCTTTATCAGCAGAAGTACTGAAAGA
66 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAA-A
* * *
40229576 AA-CTCCCATGTGGACGC-CTTTTTGCTACAGTAACTCCTAAAAAAA
1 AAGCTCCCACGTGGACGCGC-TTTTGCTACAGTAGCTCCTGAAAAAA
40229621 GCTCTCACGT
Statistics
Matches: 275, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
124 1 0.00
125 77 0.28
126 197 0.72
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:40233168 original size:18 final size:18
Alignment explanation
Indices: 40233142--40233184 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40233132 GATTCGAAAA
* *
40233142 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGCT
*
40233160 AGGATACATAAAATGGCT
1 AGGATACATAAAAGGGCT
40233178 AGGATAC
1 AGGATAC
40233185 GCACCTCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40239748 original size:23 final size:23
Alignment explanation
Indices: 40239722--40239765 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40239712 ACGAGATCGG
*
40239722 GGACGTGGCGCGTACGGAGGCAC
1 GGACGTGGCACGTACGGAGGCAC
40239745 GGACGTGGCACGTACGGAGGC
1 GGACGTGGCACGTACGGAGGC
40239766 GTGCGGTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.25, G:0.48, T:0.09
Consensus pattern (23 bp):
GGACGTGGCACGTACGGAGGCAC
Found at i:40239961 original size:12 final size:12
Alignment explanation
Indices: 40239944--40239979 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
40239934 AACTTGGTTA
40239944 TTATTATTATTT
1 TTATTATTATTT
40239956 TTATTATTATTT
1 TTATTATTATTT
40239968 TT-TTATTTATTT
1 TTATTA-TTATTT
40239980 CTGGTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:40239978 original size:15 final size:15
Alignment explanation
Indices: 40239941--40239974 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40239931 AATAACTTGG
40239941 TTATTATTATTATTT
1 TTATTATTATTATTT
40239956 TTATTATTATT-TTT
1 TTATTATTATTATTT
40239970 TTATT
1 TTATT
40239975 TATTTCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:40241620 original size:20 final size:20
Alignment explanation
Indices: 40241596--40241660 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
40241586 GTTTTCCCCA
40241596 AAAGTTCTCCAATTTCCTCT
1 AAAGTTCTCCAATTTCCTCT
* * *
40241616 GAAGTTGCTACCCA---CTTCT
1 AAAGTT-CT-CCAATTTCCTCT
40241635 AAAGTTCTCCAATTTCCTCT
1 AAAGTTCTCCAATTTCCTCT
*
40241655 CAAGTT
1 AAAGTT
40241661 GCTACCCACT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 9 0.27
20 14 0.42
21 2 0.06
22 3 0.09
ACGTcount: A:0.25, C:0.29, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAGTTCTCCAATTTCCTCT
Found at i:40241650 original size:39 final size:39
Alignment explanation
Indices: 40241596--40241674 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
40241586 GTTTTCCCCA
*
40241596 AAAGTTCTCCAATTTCCTCTGAAGTTGCTACCCACTTCT
1 AAAGTTCTCCAATTTCCTCTCAAGTTGCTACCCACTTCT
40241635 AAAGTTCTCCAATTTCCTCTCAAGTTGCTACCCACTTCT
1 AAAGTTCTCCAATTTCCTCTCAAGTTGCTACCCACTTCT
40241674 A
1 A
40241675 TCATTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (39 bp):
AAAGTTCTCCAATTTCCTCTCAAGTTGCTACCCACTTCT
Found at i:40245129 original size:41 final size:41
Alignment explanation
Indices: 40245066--40245165 Score: 139
Period size: 41 Copynumber: 2.4 Consensus size: 41
40245056 GGCTTAGCAC
* * *
40245066 CTAGCAGGCTTATTGCCAGTGAAACAATTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATATGT
*
40245107 CTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATATGT
*
40245148 CTGGCAGGC-TAAGTGCCG
1 CTAGCAGGCTTAA-TGCCG
40245166 ATGTACTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 3 0.06
41 50 0.94
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATATGT
Found at i:40247620 original size:12 final size:12
Alignment explanation
Indices: 40247589--40247622 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40247579 CATCACTTAA
*
40247589 TTTTATAAACGT
1 TTTTATATACGT
*
40247601 TTTTATATATGT
1 TTTTATATACGT
40247613 TTTTATATAC
1 TTTTATATAC
40247623 TATCTTAGCA
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:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (12 bp):
TTTTATATACGT
Found at i:40250285 original size:72 final size:72
Alignment explanation
Indices: 40250167--40250505 Score: 380
Period size: 72 Copynumber: 4.7 Consensus size: 72
40250157 ATTTAATGAC
* * * * * * *
40250167 CGATGGCATGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCAGAATAGAATCTT
1 CGATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCAGCATCGAATCAT
40250232 TCTTTA-
66 TCTTTAT
* * * * * * *
40250238 CTGATGGATTGAGATCGGACATATGTTGCAGATTCTTTAAAGCTTGTGTGAGAAGCATCGAACCA
1 C-GATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCAGCATCGAATCA
40250303 TTCTTTAT
65 TTCTTTAT
* * * * *
40250311 CGATGGCTTGAGATCTGGCATATGTTGC--ATTCTCTGAAGTTTGTGTGAGCATCATGGAATCAT
1 CGATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCAGCATCGAATCAT
40250374 TCTTTAT
66 TCTTTAT
* * *
40250381 CTG-TGGCTTGAGATTCAACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCA
1 C-GATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCAGCATCGAATCA
40250445 TTCTTTAT
65 TTCTTTAT
* * * ** *
40250453 CGGTGGCTTGAGATCCAACACATGTTATGGATTCTCTAAAGCTTGTGTGAGCA
1 CGATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCA
40250506 ACACCCAATA
Statistics
Matches: 226, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
70 57 0.25
71 3 0.01
72 165 0.73
73 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (72 bp):
CGATGGCTTGAGATCCGACATATGTTGCGGATTCTCTAAAGTTTGTGTGAGCAGCATCGAATCAT
TCTTTAT
Found at i:40250427 original size:142 final size:144
Alignment explanation
Indices: 40250167--40250505 Score: 416
Period size: 142 Copynumber: 2.4 Consensus size: 144
40250157 ATTTAATGAC
* *
40250167 CGATGGCATGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCAGAATAGAATCTT
1 CGATGGCTTGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCAGAATAGAATCAT
* *
40250232 TCTTTACTGATGGATTGAGATCGGACATATGTTGCAGATTCTTTAAAGCTTGTGTGAGAAGCATC
66 TCTTTACTGATGGATTGAGATCGAACATATGTTGCAGATTCTCTAAAGCTTGTGTGAGAAGCATC
40250297 GAACCATTCTTTAT
131 GAACCATTCTTTAT
* * * * ** *
40250311 CGATGGCTTGAGATCTGGCATATG-T-TGCATTCTCTGAAGTTTGTGTGAGCATCATGGAATCAT
1 CGATGGCTTGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCAGAATAGAATCAT
* * * * *
40250374 TCTTTATCTG-TGGCTTGAGATTC-AACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCA
66 TCTTTA-CTGATGGATTGAGA-TCGAACATATGTTGCAGATTCTCTAAAGCTTGTGTGAGAAGCA
*
40250437 TCGAATCATTCTTTAT
129 TCGAACCATTCTTTAT
* * * * * * *
40250453 CGGTGGCTTGAGATCCAACACATGTTATGGATTCTCTAAAGCTTGTGTGAGCA
1 CGATGGCTTGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCA
40250506 ACACCCAATA
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
142 115 0.69
143 7 0.04
144 44 0.27
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (144 bp):
CGATGGCTTGAGATCCGACATATGTTGTGAATTCTCTCAAGTTTGTGTGAGCAGAATAGAATCAT
TCTTTACTGATGGATTGAGATCGAACATATGTTGCAGATTCTCTAAAGCTTGTGTGAGAAGCATC
GAACCATTCTTTAT
Found at i:40258736 original size:31 final size:31
Alignment explanation
Indices: 40258679--40258738 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
40258669 AGAGGTGAGA
*
40258679 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
40258710 TGGG-AGGGATTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
40258739 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:40259166 original size:18 final size:18
Alignment explanation
Indices: 40259145--40259179 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40259135 TAATCAACTA
40259145 AATCAATCTAATTCAGTT
1 AATCAATCTAATTCAGTT
*
40259163 AATCAATCTAGTTCAGT
1 AATCAATCTAATTCAGT
40259180 CGGAGATCAG
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:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (18 bp):
AATCAATCTAATTCAGTT
Found at i:40261417 original size:17 final size:16
Alignment explanation
Indices: 40261395--40261427 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
40261385 ACATGAATAC
40261395 TATAAAAATTTATAAAT
1 TATAAAAATTT-TAAAT
40261412 TATAAAAATTTTAAAT
1 TATAAAAATTTTAAAT
40261428 AGATATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAATTTTAAAT
Found at i:40268471 original size:30 final size:30
Alignment explanation
Indices: 40268435--40268497 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40268425 ACTTATTTTA
40268435 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
40268465 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
40268495 TTG
1 TTG
40268498 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:40269690 original size:30 final size:29
Alignment explanation
Indices: 40269618--40269692 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
40269608 TTTATTAGAA
40269618 TTAAAATGTAATTTTATCATTTTAATAAC
1 TTAAAATGTAATTTTATCATTTTAATAAC
** * *
40269647 TT-AAATCAAAATTTTATCAATTTTGGAT-AG
1 TTAAAAT-GTAATTTTATC-ATTTT-AATAAC
40269677 TTAAAATGTAATTTTA
1 TTAAAATGTAATTTTA
40269693 CCATGTACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
28 4 0.11
29 11 0.31
30 15 0.42
31 6 0.17
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (29 bp):
TTAAAATGTAATTTTATCATTTTAATAAC
Found at i:40270899 original size:17 final size:17
Alignment explanation
Indices: 40270863--40270906 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
40270853 TATATCATCT
40270863 TTATTAAA-AAAAATTA
1 TTATTAAATAAAAATTA
40270879 --ATTAAATAAAAATTA
1 TTATTAAATAAAAATTA
40270894 TTATT-AATAAAAA
1 TTATTAAATAAAAA
40270907 ATTTAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.24
15 8 0.32
16 8 0.32
17 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTATTAAATAAAAATTA
Found at i:40270907 original size:17 final size:16
Alignment explanation
Indices: 40270863--40270909 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
40270853 TATATCATCT
40270863 TTATTAAAAAAAATTA
1 TTATTAAAAAAAATTA
40270879 --ATTAAATAAAAATTA
1 TTATTAAA-AAAAATTA
40270894 TTATTAATAAAAAATT
1 TTATTAA-AAAAAATT
40270910 TAAACTCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
17 12 0.44
18 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATTAAAAAAAATTA
Found at i:40273794 original size:24 final size:24
Alignment explanation
Indices: 40273766--40273836 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
40273756 AAGGGTTTAC
40273766 AAGAAGATGAAAGGTTAAAGGTTA
1 AAGAAGATGAAAGGTTAAAGGTTA
** *
40273790 AAGAAGATGAAATTTTGAAGGTTA
1 AAGAAGATGAAAGGTTAAAGGTTA
* * *
40273814 AGGGAGATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTTAAAGGTT
40273837 GAATATCCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (24 bp):
AAGAAGATGAAAGGTTAAAGGTTA
Found at i:40278887 original size:24 final size:24
Alignment explanation
Indices: 40278860--40278911 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40278850 GGGGTTACAA
40278860 GAAA-ATGAAAAATTTAAGGAAGAT
1 GAAAGATGAAAAA-TTAAGGAAGAT
* * *
40278884 GAAAGATGGAAGATTAAGGGAGAT
1 GAAAGATGAAAAATTAAGGAAGAT
40278908 GAAA
1 GAAA
40278912 TGTGAAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (24 bp):
GAAAGATGAAAAATTAAGGAAGAT
Found at i:40288571 original size:3 final size:3
Alignment explanation
Indices: 40288563--40288587 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40288553 GAATATGTCC
40288563 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
40288588 CAGCTTGTAA
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:40292091 original size:31 final size:31
Alignment explanation
Indices: 40292030--40292093 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
40292020 CTTAAGAGCC
* *
40292030 CAGTGACTTAAACAAAAACTTTTGAATAATT
1 CAGTAACTTAAACAAAAACTTTTCAATAATT
**
40292061 CAGTAACTTAAATGAAAAC-TTTCAATTAATT
1 CAGTAACTTAAACAAAAACTTTTCAA-TAATT
40292092 CA
1 CA
40292094 ATGACCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (31 bp):
CAGTAACTTAAACAAAAACTTTTCAATAATT
Found at i:40298975 original size:34 final size:35
Alignment explanation
Indices: 40298915--40298981 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
40298905 CAAACACCAG
*
40298915 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
40298950 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40298982 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40302439 original size:27 final size:27
Alignment explanation
Indices: 40302420--40302473 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
40302410 GTATGGTGGA
40302420 TCAATACCCATCGACGAGTAGGAAAAC
1 TCAATACCCATCGACGAGTAGGAAAAC
*
40302447 TCAATACCCATCGACGAGCAGGAAAAC
1 TCAATACCCATCGACGAGTAGGAAAAC
40302474 ATACTTTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.28, G:0.19, T:0.13
Consensus pattern (27 bp):
TCAATACCCATCGACGAGTAGGAAAAC
Found at i:40303670 original size:13 final size:13
Alignment explanation
Indices: 40303652--40303676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40303642 TCCAGCAACT
40303652 ATGAATTTATTCC
1 ATGAATTTATTCC
40303665 ATGAATTTATTC
1 ATGAATTTATTC
40303677 GATGTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGAATTTATTCC
Found at i:40303883 original size:50 final size:50
Alignment explanation
Indices: 40303776--40304024 Score: 302
Period size: 50 Copynumber: 4.8 Consensus size: 50
40303766 ATCTGGGTAA
* *
40303776 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ACG
* *
40303832 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
*
40303882 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
40303932 AGAGGTCTCC-TATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * *
40303982 AGAACATCCCATGTAAGACCATGTCTGGGGCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40304025 TGTTATTATC
Statistics
Matches: 174, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
50 98 0.56
51 33 0.19
53 3 0.02
55 2 0.01
56 38 0.22
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:40303963 original size:100 final size:103
Alignment explanation
Indices: 40303776--40304025 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 103
40303766 ATCTGGGTAA
*
40303776 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCCTTGAGATCACGAGAGGTCTC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGAT--CGAGAGGTCTC
* * * *
40303841 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
63 ATATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* *
40303882 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GAGAT-GAGAGGTCTCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCTCATA
*
40303944 TAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * *
40303982 AGAACATCCCATGTAAGACCATGTCTGGGGCATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40304026 GTTATTATCA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 47 0.36
101 36 0.28
103 5 0.04
105 2 0.02
106 40 0.31
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCTCATA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:40316586 original size:13 final size:13
Alignment explanation
Indices: 40316566--40316601 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
40316556 TCAAAGTTAT
40316566 CCTAGCCCAAATA
1 CCTAGCCCAAATA
*
40316579 CTTAGCCCAAATA
1 CCTAGCCCAAATA
40316592 CCTAGCCCAA
1 CCTAGCCCAA
40316602 TTGCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (13 bp):
CCTAGCCCAAATA
Found at i:40321691 original size:35 final size:35
Alignment explanation
Indices: 40321645--40321797 Score: 238
Period size: 35 Copynumber: 4.3 Consensus size: 35
40321635 ACTCTCTGTT
40321645 TTGGTGTGTTTC-GATTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGA-TGGACTAGCTCTTATGAGCA
*
40321680 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
40321715 TTGGTGTGTTTC-GAATGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAG-ATGGACTAGCTCTTATGAGCA
*
40321750 TTTGGTGTGTTTCAGATGGACTAGATCTTATGAGCA
1 -TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
40321786 TCTGGTGTGTTT
1 T-TGGTGTGTTT
40321798 AATGGGATTG
Statistics
Matches: 110, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
34 1 0.01
35 64 0.58
36 44 0.40
37 1 0.01
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
Found at i:40323571 original size:28 final size:28
Alignment explanation
Indices: 40323520--40323586 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
40323510 GCGACATGAC
* *
40323520 CAACCATATATCATTCAGGTGGTAGAGC
1 CAACCATATATCATTCAGGCGGTAGAGA
* * *
40323548 CGACCATATATCATTCATGCGGTATAGA
1 CAACCATATATCATTCAGGCGGTAGAGA
40323576 CAACCATATAT
1 CAACCATATAT
40323587 AAAAGCTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (28 bp):
CAACCATATATCATTCAGGCGGTAGAGA
Found at i:40326409 original size:109 final size:108
Alignment explanation
Indices: 40326218--40326526 Score: 464
Period size: 109 Copynumber: 2.9 Consensus size: 108
40326208 CTTCTAATTG
* * *
40326218 AGGCAATATTTAGCGTTTGGAAATTTGAGAAAACATGCTCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGC-CTAAGGTGCTGGGTGTCGATTTTTCT
*
40326283 CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTAAAATA
65 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
*
40326327 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGTCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATG-CCTAAGGTGCTGGGTGTCGATTTTTCT
40326392 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
65 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
* * *
40326436 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATG-CCTAAGGTGCTGGGTGTCGATTTTTCT
* *
40326498 CGTTTAACCAAATTA-CCAAATATCCTCTT
65 CGTTCAACCAAA-TAGCTAAATATCCTCTT
40326527 GAATTTTAAT
Statistics
Matches: 186, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
106 29 0.16
107 2 0.01
108 24 0.13
109 130 0.70
110 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (108 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCTAAGGTGCTGGGTGTCGATTTTTCTC
GTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
Found at i:40330586 original size:21 final size:21
Alignment explanation
Indices: 40330556--40330621 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
40330546 AATCAAAGTC
* *
40330556 AAAATGAAAATGAAAAAATCA
1 AAAATGAAAATAAAAAAAACA
*
40330577 AAAATTAAAATAAAAAAAACA
1 AAAATGAAAATAAAAAAAACA
* *
40330598 AAACA--AAAAGAAAAAAAAGA
1 AAA-ATGAAAATAAAAAAAACA
40330618 AAAA
1 AAAA
40330622 AAATCTAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.41
21 21 0.54
22 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.06, T:0.09
Consensus pattern (21 bp):
AAAATGAAAATAAAAAAAACA
Found at i:40331531 original size:6 final size:6
Alignment explanation
Indices: 40331506--40331564 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
40331496 TGAGTCAAAA
* * *
40331506 AAAATG AGAATG AAAA-- AAAATG AAAAATG AGAATG AAAAATG AAAAAG
1 AAAATG AAAATG AAAATG AAAATG -AAAATG AAAATG -AAAATG AAAATG
40331554 AAAAATG AAAA
1 -AAAATG AAAA
40331565 ATGGAGAGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
4 4 0.10
6 22 0.52
7 16 0.38
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:40331533 original size:7 final size:7
Alignment explanation
Indices: 40331521--40331567 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
40331511 GAGAATGAAA
40331521 AAAAATG
1 AAAAATG
40331528 AAAAATG
1 AAAAATG
*
40331535 -AGAATG
1 AAAAATG
40331541 AAAAATG
1 AAAAATG
40331548 AAAAA-G
1 AAAAATG
40331554 AAAAATG
1 AAAAATG
40331561 AAAAATG
1 AAAAATG
40331568 GAGAGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:40331540 original size:13 final size:13
Alignment explanation
Indices: 40331505--40331561 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
40331495 CTGAGTCAAA
40331505 AAAAATGAGAATG
1 AAAAATGAGAATG
40331518 AAAAA--A-AATG
1 AAAAATGAGAATG
40331528 AAAAATGAGAATG
1 AAAAATGAGAATG
* *
40331541 AAAAATGAAAAAG
1 AAAAATGAGAATG
40331554 AAAAATGA
1 AAAAATGA
40331562 AAAATGGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 9 0.23
11 1 0.03
12 1 0.03
13 28 0.72
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (13 bp):
AAAAATGAGAATG
Found at i:40331544 original size:20 final size:20
Alignment explanation
Indices: 40331505--40331567 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
40331495 CTGAGTCAAA
40331505 AAAAATGAGAATGAAAAAAAATG
1 AAAAATGAGAATG---AAAAATG
40331528 AAAAATGAGAATGAAAAATG
1 AAAAATGAGAATGAAAAATG
*
40331548 AAAAA-GAAAAATGAAAAATG
1 AAAAATG-AGAATGAAAAATG
40331568 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 1 0.03
20 24 0.63
23 13 0.34
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAAATGAGAATGAAAAATG
Found at i:40332960 original size:85 final size:85
Alignment explanation
Indices: 40332854--40333137 Score: 320
Period size: 85 Copynumber: 3.3 Consensus size: 85
40332844 CACACTATCC
*
40332854 TATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAATGATTTTATCTCTCTGAAGTTACAGCA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAATGATCTTATCTCTCTGAAGTTACAGCA
40332919 GAGCAGATCGCATCAGGTCT
66 GAGCAGATCGCATCAGGTCT
* * ** ** *
40332939 TATCTCCCTGAGATTACAGTGGGGCAGACCGAAGA-ATTTCAGATCTTATCTCCCTG-AGATTAC
1 TATCTCCCTGAGATTACAGTGGAGCGGA-TTAAGATAAAT--GATCTTATCTCTCTGAAG-TTAC
* * * * * * *
40333002 AGCGGAGCAAATTGAAGCTAGTAATCC
62 AGCAGAGCAGATCGCATC-AG--GTCT
** * *
40333029 TATCTCTATGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAATGATCTTATCTCTCTGAAGTTACAGCA
40333094 GAGCAGATCGCATCAGGTCT
66 GAGCAGATCGCATCAGGTCT
40333114 TATCTCCCTGAGATTACAGTGGAG
1 TATCTCCCTGAGATTACAGTGGAG
40333138 TAGACCGAAG
Statistics
Matches: 155, Mismatches: 35, Indels: 18
0.75 0.17 0.09
Matches are distributed among these distances:
85 52 0.34
86 6 0.04
87 32 0.21
88 33 0.21
89 5 0.03
90 27 0.17
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (85 bp):
TATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAATGATCTTATCTCTCTGAAGTTACAGCA
GAGCAGATCGCATCAGGTCT
Found at i:40332989 original size:46 final size:45
Alignment explanation
Indices: 40332805--40333441 Score: 304
Period size: 44 Copynumber: 14.6 Consensus size: 45
40332795 AATATTAGAA
* * * * * *
40332805 ATCTTATCTTCTTGAGATTACAGCGGAGCAGATCCAATACA--CACT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGA-ATTCA-G
* * * **
40332850 ATCCTATCTCCCTGAGATTACAGTGGAGCGGAT-TAAG-ATAAATG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATTCA-G
* * ** *
40332894 ATTTTATCTCTCTGA-AGTTACAGCAGAGCAGATC---GCA-TCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAATTCAG
* * *
40332935 GTCTTATCTCCCTGAGATTACAGTGGGGCAGACCGAAGAATTTCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAA-TTCAG
* * * * *
40332981 ATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGT-A-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-AATTCAG
* ** * * **
40333025 ATCCTATCTCTATGAGATTACAGTGGAGCGGAT-TAA-AATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATTCA-G
* ** *
40333069 ATCTTATCTCTCTGA-AGTTACAGCAGAGCAGATC---GCA-TCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAATTCAG
* * *
40333110 GTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAA-TTCAG
* * * * * *
40333156 ATCTTATATCCCTGAGGTTACAGTAGAGCAGATTGAAGCCA--GAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-AATTCAG
* * *
40333200 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG---GCACT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATTCA-G
* * * *
40333243 ATCCTATCTCCCTGA-AGTTACAGCGGAGCAGAT--TA-AA---GG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAATTCAG
* * * *
40333282 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATC---GTA-TCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAATTCAG
* * * *
40333323 GTCTTACCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATT-CAG
* * *
40333369 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGT-A-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGA-ATTCAG
* *
40333413 ATCCTATCTCCCTAAGATTACAGTGGAGC
1 ATCTTATCTCCCTGAGATTACAGTGGAGC
40333442 GGATTAAGGG
Statistics
Matches: 447, Mismatches: 104, Indels: 83
0.71 0.16 0.13
Matches are distributed among these distances:
39 29 0.06
41 81 0.18
42 10 0.02
43 36 0.08
44 148 0.33
45 31 0.07
46 108 0.24
47 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGAATTCAG
Found at i:40333049 original size:90 final size:88
Alignment explanation
Indices: 40332854--40333237 Score: 329
Period size: 87 Copynumber: 4.4 Consensus size: 88
40332844 CACACTATCC
* ** ** * *
40332854 TATCTCCCTGAGATTACAGTGGAGCGGA-TTAAG-A-TAAATGATTTTATCTCTCTGA-AGTTAC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA-GATCTTATCTCCCTGAGA-TTAC
* * * *
40332915 AGCAGAGCAGATCGCATCAG-GTCT
64 AGCAGAGCAGATTGAAGCAGAATCT
*
40332939 TATCTCCCTGAGATTACAGTGGGGCAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
* * *
40333004 CGGAGCAAATTGAAGCTAGTAATCC
66 CAGAGCAGATTGAAGC-AG-AATCT
** * ** ** *
40333029 TATCTCTATGAGATTACAGTGGAGCGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGA-AGTTAC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA-GATCTTATCTCCCTGAGA-TTAC
* * * *
40333090 AGCAGAGCAGATCGCATCAG-GTCT
64 AGCAGAGCAGATTGAAGCAGAATCT
* * *
40333114 TATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATATCCCTGAGGTTACAG
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
*
40333179 TAGAGCAGATTGAAGCCAGAGATCT
66 CAGAGCAGATTGAAG-CAGA-ATCT
* *
40333204 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAG
40333238 GCACTATCCT
Statistics
Matches: 233, Mismatches: 50, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
85 52 0.22
86 5 0.02
87 70 0.30
88 44 0.19
89 2 0.01
90 60 0.26
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
CAGAGCAGATTGAAGCAGAATCT
Found at i:40333097 original size:175 final size:175
Alignment explanation
Indices: 40332850--40333228 Score: 607
Period size: 175 Copynumber: 2.2 Consensus size: 175
40332840 AATACACACT
* * *
40332850 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAATGATTTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
*
40332915 AGCAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGGGCAGACCGAAGAATTTCA
66 AGCAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA
* * *
40332980 GATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTA-
131 GATCTTATATCCCTGAGATTACAGCAGAGCAAATTGAAGCCAG-AG
**
40333025 ATCCTATCTCTATGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
*
40333090 AGCAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCA
66 AGCAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA
* * *
40333155 GATCTTATATCCCTGAGGTTACAGTAGAGCAGATTGAAGCCAGAG
131 GATCTTATATCCCTGAGATTACAGCAGAGCAAATTGAAGCCAGAG
* *
40333200 ATCTTATCTCCCTGAGATTACAGCGGAGC
1 ATCCTATCTCCCTGAGATTACAGTGGAGC
40333229 AGATCGAAGG
Statistics
Matches: 186, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 1 0.01
175 185 0.99
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (175 bp):
ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
AGCAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA
GATCTTATATCCCTGAGATTACAGCAGAGCAAATTGAAGCCAGAG
Found at i:40333263 original size:87 final size:83
Alignment explanation
Indices: 40332898--40333446 Score: 254
Period size: 87 Copynumber: 6.4 Consensus size: 83
40332888 TAAATGATTT
* ** * * * *
40332898 TATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAGG-TCTTATCTCCCTGAGATTACAGTGGG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTG-AACAGGATCTTATCTCCCTGAGATTACAGCGGA
* * *
40332962 GCAGACCGAAGAATTTCAGATCT
65 GCAGATCGAAGCA---C-GATCC
* * * * ** *
40332985 TATCTCCCTG-AGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCTATGAGATTACAGT
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTGAA-C-AG-GATCTTATCTCCCTGAGATTACAGC
* ** ** * *
40333049 GGAGCGGATTAAAATAAAGGATCT
62 GGAGCAGA-TCGAA-GCACGATCC
* ** * * *
40333073 TATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAGG-TCTTATCTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTG-AACAGGATCTTATCTCCCTGAGATTACAGCGGA
* * * *
40333137 GTAGACCGAAGAATTTCAGATCT
65 GCAGATCGAAGCA---C-GATCC
* * *
40333160 TATATCCCTGAGGTTACAGTAGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAA--CAG-GATCTTATCTCCCTGAGATTACAGCG
*
40333225 GAGCAGATCGAAGGCACTATCC
63 GAGCAGATCGAA-GCACGATCC
* * **
40333247 TATCTCCCTGAAGTTACAGCGGAGCAGATT-AA-AGGATCTTATCTCTCTGA-AGTTACAGTAGA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAACAGGATCTTATCTCCCTGAGA-TTACAGCGGA
* * * * *
40333309 GTAGATCGTATCA-GGTCT
65 GCAGATCGAAGCACGATCC
* * ** *
40333327 TACCTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTGAA-CA--G--GATCTTATCTCCCTGAGATTACA
* *
40333391 GCGGAGCAGATCAAAG-ATAGTAATCC
60 GCGGAGCAGATCGAAGCA-CG--ATCC
*
40333417 TATCTCCCT-AAGATTACAGTGGAGCGGATT
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATT
40333447 AAGGGAGCTT
Statistics
Matches: 353, Mismatches: 76, Indels: 63
0.72 0.15 0.13
Matches are distributed among these distances:
79 2 0.01
80 24 0.07
81 5 0.01
82 31 0.09
83 5 0.01
84 2 0.01
85 27 0.08
86 7 0.02
87 117 0.33
88 38 0.11
89 4 0.01
90 85 0.24
91 4 0.01
92 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (83 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTGAACAGGATCTTATCTCCCTGAGATTACAGCGGAG
CAGATCGAAGCACGATCC
Found at i:40333301 original size:39 final size:39
Alignment explanation
Indices: 40333199--40333474 Score: 139
Period size: 39 Copynumber: 6.6 Consensus size: 39
40333189 TGAAGCCAGA
*
40333199 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAG
1 GATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCAAAG
* *
40333238 GCACTATCCTATCTCCCTGAAGTTACAGCGGAGCAGATTAAAG
1 G----ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAG
* ** * *
40333281 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAG
1 GATCTTATCTCCCTGAAGTTACAGCGGAGCAGATC--A-AAG
* * * *
40333323 G-TCTTACCTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTG
1 GATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATC--A-AA--G
40333366 CAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAG
1 --GATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCAAAG
* * * * *
40333407 ATAGTAATCCTATCTCCCT-AAGATTACAGTGGAGCGGATTAAGG
1 ---G--ATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCAAAG
* *
40333451 GAGCTTATCTCTCTGAAGTTACAG
1 GATCTTATCTCCCTGAAGTTACAG
40333475 TAGAGTGGAT
Statistics
Matches: 186, Mismatches: 32, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
39 45 0.24
40 5 0.03
41 30 0.16
42 5 0.03
43 36 0.19
44 35 0.19
45 1 0.01
46 29 0.16
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (39 bp):
GATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAG
Found at i:40333324 original size:213 final size:217
Alignment explanation
Indices: 40332979--40333441 Score: 607
Period size: 213 Copynumber: 2.1 Consensus size: 217
40332969 GAAGAATTTC
* * *
40332979 AGATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCTATGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGCTACTAATCCTATCTCCATGAGATT
* *
40333044 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCA
66 ACAGCGGAGCAGATT---ATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCA
* ** * *
40333109 GGTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATATCCCTGAGGT
128 GGTCTTACCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATATCCCTGAGAT
* ** *
40333174 TACAGTAGAGCAGATTGAAGCCAG-
193 TACAGCAGAGCAGATCAAAGACAGT
* *
40333198 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGC-ACT-ATCCTATCTCCCTGA-AG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAA-GCTACTAATCCTATCTCCATGAGA-
* * *
40333260 TTACAGCGGAGCAGA-T-TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAG
64 TTACAGCGGAGCAGATTATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAG
*
40333323 GTCTTACCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATT
129 GTCTTACCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATATCCCTGAGATT
* *
40333388 ACAGCGGAGCAGATCAAAGATAGT
194 ACAGCAGAGCAGATCAAAGACAGT
* * *
40333412 A-ATCCTATCTCCCTAAGATTACAGTGGAGC
1 AGATCTTATCTCCCTGAGATTACAGCGGAGC
40333442 GGATTAAGGG
Statistics
Matches: 216, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
213 146 0.68
214 1 0.00
217 2 0.01
218 26 0.12
219 39 0.18
220 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (217 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGCTACTAATCCTATCTCCATGAGATT
ACAGCGGAGCAGATTATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAGGT
CTTACCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATATCCCTGAGATTAC
AGCAGAGCAGATCAAAGACAGT
Found at i:40333389 original size:169 final size:170
Alignment explanation
Indices: 40333198--40333525 Score: 500
Period size: 170 Copynumber: 1.9 Consensus size: 170
40333188 TTGAAGCCAG
* *
40333198 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGCACT-ATCCTATCTCCCTGAAG-T
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCT-AAGAT
*
40333261 TACAGCGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTC
65 TACAGCGGAGCAGATTAAAGGAGCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTC
*
40333326 TTACCTCCCTGA-GATTACAGTGGAACAGACCGAAGAATTGC
130 TTACATCCCTGATG-TTACAGTGGAACAGACCGAAGAATTGC
* *
40333367 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCCTAAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTAAGATT
* * * *
40333432 ACAGTGGAGCGGATTAAGGGAGCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTCT
66 ACAGCGGAGCAGATTAAAGGAGCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCT
* **
40333497 TATATCCCTGATGTTGTAGTGGAACAGAC
131 TACATCCCTGATGTTACAGTGGAACAGAC
40333526 TGAAAACGTA
Statistics
Matches: 143, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
169 44 0.31
170 98 0.69
171 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTAAGATT
ACAGCGGAGCAGATTAAAGGAGCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCT
TACATCCCTGATGTTACAGTGGAACAGACCGAAGAATTGC
Found at i:40334245 original size:12 final size:12
Alignment explanation
Indices: 40334228--40334253 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40334218 TACTCTAAGG
40334228 TTTTTTTCTTTT
1 TTTTTTTCTTTT
40334240 TTTTTTTCTTTT
1 TTTTTTTCTTTT
40334252 TT
1 TT
40334254 CATTTCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:40334854 original size:3 final size:3
Alignment explanation
Indices: 40334834--40334871 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
40334824 TAATTAATTA
* *
40334834 ATT AAT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40334872 CATCATTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:40335572 original size:109 final size:109
Alignment explanation
Indices: 40335381--40335689 Score: 491
Period size: 109 Copynumber: 2.9 Consensus size: 109
40335371 TTTCTAATTG
* * * *
40335381 AGGCAATATTTAGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
40335446 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
*
40335490 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGTCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
40335555 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
* * *
40335599 AGGCAATGTTTTGCGTTTGAAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
40335661 CGTTTAACCAAATTA-CCAAATATCCTCTT
66 CGTTCAACCAAA-TAGCTAAATATCCTCTT
40335690 GAATTTTAAT
Statistics
Matches: 188, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
106 29 0.15
107 2 0.01
108 24 0.13
109 133 0.71
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTCTTAAAAATTTTAAAATA
Found at i:40344233 original size:20 final size:19
Alignment explanation
Indices: 40344199--40344248 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
40344189 TAAAAATTCT
*
40344199 AAAATTTATAATTTTTAAA
1 AAAATTTAAAATTTTTAAA
40344218 AAAATTATAAAATTTTTAAA
1 AAAATT-TAAAATTTTTAAA
*
40344238 AAAATCTAAAA
1 AAAATTTAAAA
40344249 GTGACCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTTAAAATTTTTAAA
Found at i:40344671 original size:2 final size:2
Alignment explanation
Indices: 40344664--40344695 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40344654 TGATTTTAGA
40344664 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 A
40344696 AAAGAAGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40346672 original size:20 final size:19
Alignment explanation
Indices: 40346631--40346683 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
40346621 AAAATTTGAC
* *
40346631 AAAATAAATAATACAATGAA
1 AAAATAAATAAAACAA-AAA
*
40346651 AAACTAAATAAAACAAAAA
1 AAAATAAATAAAACAAAAA
*
40346670 AAATTAAATTAAAA
1 AAAATAAA-TAAAA
40346684 AATAAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATAAATAAAACAAAAA
Found at i:40368517 original size:10 final size:9
Alignment explanation
Indices: 40368499--40368532 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
40368489 GTAATTATTC
40368499 TTTTTTCTT
1 TTTTTTCTT
40368508 TTTCTTTCTT
1 TTT-TTTCTT
40368518 TTTTCTTCTT
1 TTTT-TTCTT
40368528 TTTTT
1 TTTTT
40368533 ACATCATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:40373629 original size:127 final size:127
Alignment explanation
Indices: 40373255--40374050 Score: 1441
Period size: 127 Copynumber: 6.3 Consensus size: 127
40373245 GGTGAAACTT
* * *
40373255 CAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAAGAAATCAATTCTATCTCCTTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
40373320 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
40373382 CAGTCTTATCTCCCTGAAGTTGCA-TGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
40373446 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
*
40373508 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCTTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* * * *
40373573 ACAGTGGAGCAGATTAACATCAAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* *
40373635 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATTCTATCTCCTTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
40373700 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
**
40373762 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCATTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
40373827 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
*
40373889 CAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* * *
40373954 GCAATGGAGCGGATTTACATCCAGATCTTATCTTTCTGAGATTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
40374016 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
40374051 TAAAAATAGC
Statistics
Matches: 644, Mismatches: 24, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
126 123 0.19
127 521 0.81
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (127 bp):
CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
Found at i:40375361 original size:3 final size:3
Alignment explanation
Indices: 40375355--40375405 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
40375345 ACTATTATTG
* * *
40375355 TAT TAT TAAT TAT TGT TAT TAT AAT TAT AAT TA- TAT TAT ATAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
40375401 TAT TA
1 TAT TA
40375406 CACCTATAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:40375368 original size:15 final size:15
Alignment explanation
Indices: 40375348--40375382 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40375338 ATTTTTCACT
40375348 ATTATTG-TATTATTA
1 ATTATTGTTATTA-TA
40375363 ATTATTGTTATTATA
1 ATTATTGTTATTATA
40375378 ATTAT
1 ATTAT
40375383 AATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (15 bp):
ATTATTGTTATTATA
Found at i:40375581 original size:9 final size:8
Alignment explanation
Indices: 40375549--40375592 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 8
40375539 GTACACGTAC
*
40375549 ATATATTT
1 ATATTTTT
40375557 ATA-TTTT
1 ATATTTTT
40375564 ATATTTTT
1 ATATTTTT
40375572 ATAGTTTTT
1 ATA-TTTTT
40375581 ATATATTTT
1 ATAT-TTTT
40375590 ATA
1 ATA
40375593 ATCCAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 6 0.19
8 11 0.34
9 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
ATATTTTT
Found at i:40383291 original size:7 final size:7
Alignment explanation
Indices: 40383279--40383306 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
40383269 AAATGGTTGC
40383279 TTGAAAG
1 TTGAAAG
40383286 TTGAAAG
1 TTGAAAG
40383293 TTGAAAG
1 TTGAAAG
40383300 TTGAAAG
1 TTGAAAG
40383307 GTTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
TTGAAAG
Found at i:40386069 original size:207 final size:193
Alignment explanation
Indices: 40385815--40386248 Score: 493
Period size: 191 Copynumber: 2.2 Consensus size: 193
40385805 TATTAAACCG
* *
40385815 CTAATCCAAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTAAATGTTTTTTC
1 CTAATCAAAATGCAATTATATTTATATAATATCATGCTAGACCTTTTA---TT---T-TTCTTT-
* *
40385880 ACATGTTATATACAACCACTTCTTA-AGAAATTTTATGGAATAAATAGGGATAAAATAAGCATGT
58 A-ATCTTATATAC-A-CA--TCTTATAGAAA----ATGGAATAAATAGGGATAAAATAAGCATAT
* *
40385944 AAACTTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAATATTTTTTATTAGAATTATA
114 AAACTTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTA-A
*
40386009 ATTGT-TT-TTATATAA
178 ATT-TATTATTAAATAA
*
40386024 -T-ATCAAAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTCTTTAATCTTTT
1 CTAATCAAAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTCTTTAATCTTAT
* * * * * * *
40386087 TTTCACATGTTATATAAAATGGAATAAATAGGGGTAAAATAGGTATATAAACTTAAATTTAAGGG
66 ATACACATCTTATAGAAAATGGAATAAATAGGGATAAAATAAGCATATAAACTTAAATTTAAGGG
40386152 TCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAATTTATTATTAAATAA
131 TCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAATTTATTATTAAATAA
* *
40386215 CTAATCAAAATGAAATTATTTTTACT-TAATATCA
1 CTAATCAAAATGCAATTATATTTA-TATAATATCA
40386249 ATATATATAT
Statistics
Matches: 202, Mismatches: 17, Indels: 28
0.82 0.07 0.11
Matches are distributed among these distances:
189 1 0.00
190 6 0.03
191 94 0.47
192 1 0.00
193 27 0.13
194 5 0.02
195 4 0.02
196 2 0.01
197 1 0.00
198 7 0.03
199 1 0.00
200 5 0.02
201 1 0.00
204 2 0.01
207 44 0.22
208 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (193 bp):
CTAATCAAAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTCTTTAATCTTAT
ATACACATCTTATAGAAAATGGAATAAATAGGGATAAAATAAGCATATAAACTTAAATTTAAGGG
TCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAATTTATTATTAAATAA
Found at i:40388495 original size:40 final size:40
Alignment explanation
Indices: 40388451--40388574 Score: 141
Period size: 40 Copynumber: 3.1 Consensus size: 40
40388441 AATAATAAAT
*
40388451 ATTTTTTTTATTTTAAAATACTTTTAAAATATTTTTTTTA
1 ATTTTTTTTATTTTAAAATATTTTTAAAATATTTTTTTTA
* * *
40388491 ATTTTAACTTT-TTTT-AAATTTTTTTAAAATA--CTTTTTA
1 ATTTT--TTTTATTTTAAAATATTTTTAAAATATTTTTTTTA
*
40388529 A-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
1 ATTTTTTTTATTTTAAAATATTTTTAAAATA-TTTTTTTTA
40388569 ATTTTT
1 ATTTTT
40388575 ATTTTAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
35 2 0.03
36 4 0.06
37 18 0.26
38 7 0.10
40 26 0.38
41 8 0.12
42 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (40 bp):
ATTTTTTTTATTTTAAAATATTTTTAAAATATTTTTTTTA
Found at i:40388597 original size:25 final size:26
Alignment explanation
Indices: 40388566--40388616 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40388556 ATACTTTTTT
*
40388566 TTAA-TTTTTAT-TTTAATTTTTAAAA
1 TTAATTTTTTATATTT-ATTTTAAAAA
40388591 TTAATTTTTTATATTTATTTTAAAAA
1 TTAATTTTTTATATTTATTTTAAAAA
40388617 CGGGCCGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 16 0.70
27 3 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTAATTTTTTATATTTATTTTAAAAA
Found at i:40390655 original size:3 final size:3
Alignment explanation
Indices: 40390647--40390672 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40390637 TTTCTTTTCT
40390647 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
40390673 TATGTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:40390998 original size:21 final size:21
Alignment explanation
Indices: 40390959--40391004 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
40390949 TTTTTGGACT
40390959 TTTATTAATTTTCTGGTTTA-
1 TTTATTAATTTTCTGGTTTAG
* *
40390979 TTTATTTATTTATTTGGTTTAG
1 TTTATTAATTT-TCTGGTTTAG
40391001 TTTA
1 TTTA
40391005 GTTTGGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (21 bp):
TTTATTAATTTTCTGGTTTAG
Found at i:40391680 original size:20 final size:21
Alignment explanation
Indices: 40391655--40391698 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
40391645 TTAGTGGGAG
40391655 TTAGTGGGGATATGAGTGG-T
1 TTAGTGGGGATATGAGTGGCT
*
40391675 TTAGTGGGGATATGGGTGGCT
1 TTAGTGGGGATATGAGTGGCT
40391696 TTA
1 TTA
40391699 AAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.18, C:0.02, G:0.43, T:0.36
Consensus pattern (21 bp):
TTAGTGGGGATATGAGTGGCT
Found at i:40392258 original size:25 final size:23
Alignment explanation
Indices: 40392234--40392331 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 23
40392224 TATATTAAAT
*
40392234 ATATATATTTTATTTTTAATCAA
1 ATATATATATTATTTTTAATCAA
40392257 ATATATATATTATTTTTAATC-A
1 ATATATATATTATTTTTAATCAA
*
40392279 A-ATATATATTATATTTAATCAA
1 ATATATATATTATTTTTAATCAA
* * *
40392301 ATGTATATA-TA-TTAT-ATTAA
1 ATATATATATTATTTTTAATCAA
40392321 ATATATATATT
1 ATATATATATT
40392332 TAATATGGGC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 12 0.18
21 21 0.32
22 6 0.09
23 26 0.40
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATATATATTATTTTTAATCAA
Found at i:40392337 original size:20 final size:19
Alignment explanation
Indices: 40392259--40392333 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
40392249 TTAATCAAAT
*
40392259 ATATATATTATTTTTAATCAA
1 ATATATA-TATTTAT-ATCAA
40392280 ATATATATTATATT-TAATCAA
1 ATATATA-TAT-TTAT-ATCAA
* *
40392301 ATGTATATATATTATATTAA
1 ATATATATAT-TTATATCAA
40392321 ATATATATATTTA
1 ATATATATATTTA
40392334 ATATGGGCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
19 3 0.06
20 19 0.39
21 25 0.51
22 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (19 bp):
ATATATATATTTATATCAA
Found at i:40392974 original size:6 final size:6
Alignment explanation
Indices: 40392963--40392998 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
40392953 ATAAATTAAT
40392963 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
40392999 CTATTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:40393973 original size:35 final size:35
Alignment explanation
Indices: 40393911--40394034 Score: 169
Period size: 35 Copynumber: 3.5 Consensus size: 35
40393901 TTCTGTTTTG
*
40393911 GTGTGTTTCAGATGGA-TAGCTCTTATGAGCATTA
1 GTGTGTTTCGGATGGATTAGCTCTTATGAGCATTA
* *
40393945 GTGTGTTTTGGATGGATTAGCTCTTATGAACATTA
1 GTGTGTTTCGGATGGATTAGCTCTTATGAGCATTA
* *
40393980 GTGTGTTCCGGATGGATTAGCTCTTATGAGCATCTG
1 GTGTGTTTCGGATGGATTAGCTCTTATGAGCAT-TA
* *
40394016 GTGTGTTTTGGTTGGATTA
1 GTGTGTTTCGGATGGATTA
40394035 TTGATGTACT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 14 0.18
35 47 0.60
36 17 0.22
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.41
Consensus pattern (35 bp):
GTGTGTTTCGGATGGATTAGCTCTTATGAGCATTA
Found at i:40396402 original size:21 final size:22
Alignment explanation
Indices: 40396355--40396410 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
40396345 TGGCCAATTA
* *
40396355 GGCCGTGTGGGCCACACAGGCT
1 GGCCATGTGGGCCACACAGGAT
40396377 GGCCATGTGGGCCACAC-GGAT
1 GGCCATGTGGGCCACACAGGAT
*
40396398 GGCCATGTAGGCC
1 GGCCATGTGGGCC
40396411 CAAAAACTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.16, C:0.30, G:0.39, T:0.14
Consensus pattern (22 bp):
GGCCATGTGGGCCACACAGGAT
Found at i:40398095 original size:11 final size:10
Alignment explanation
Indices: 40398051--40398102 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
40398041 AAACTCTTTT
40398051 AAAATTTT-A
1 AAAATTTTAA
*
40398060 AAAATATTAA
1 AAAATTTTAA
*
40398070 AAAATTATAA
1 AAAATTTTAA
40398080 GAAAATTTTATA
1 -AAAATTTTA-A
40398092 AAAA-TTTAA
1 AAAATTTTAA
40398101 AA
1 AA
40398103 TTTCTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 10 0.28
10 13 0.36
11 12 0.33
12 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:40398238 original size:19 final size:19
Alignment explanation
Indices: 40398206--40398259 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
40398196 TATTTTTATT
*
40398206 TTTTAATAAAAAATTTATAA
1 TTTT-ATAATAAATTTATAA
* * *
40398226 TTTTTTTATAAATTTATGA
1 TTTTATAATAAATTTATAA
40398245 TTTTATAATAAATTT
1 TTTTATAATAAATTT
40398260 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTATAATAAATTTATAA
Found at i:40398985 original size:39 final size:39
Alignment explanation
Indices: 40398921--40399044 Score: 139
Period size: 37 Copynumber: 3.3 Consensus size: 39
40398911 GGTAACCACT
** *
40398921 CAAAACACACCTGAACGCTCAAACGAGCTATATACTATC
1 CAAAACACACCTGATGGCTCGAACGAGCTATATACTATC
*
40398960 CAAAACACACCTGATGGCTCGAACGAGCTATAT--TAAC
1 CAAAACACACCTGATGGCTCGAACGAGCTATATACTATC
* * * * *
40398997 GAAAACACACCTAATGGCTCGAATGAAC--TATACCATC
1 CAAAACACACCTGATGGCTCGAACGAGCTATATACTATC
40399034 CAAAACACACC
1 CAAAACACACC
40399045 AGGGCACTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
35 3 0.04
37 39 0.54
39 30 0.42
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.17
Consensus pattern (39 bp):
CAAAACACACCTGATGGCTCGAACGAGCTATATACTATC
Found at i:40400818 original size:23 final size:20
Alignment explanation
Indices: 40400769--40400806 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40400759 TACCAATTTG
*
40400769 CAAACATTTTAAAATACATT
1 CAAACATTATAAAATACATT
40400789 CAAACATTATAAAATACA
1 CAAACATTATAAAATACA
40400807 CAATTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAACATTATAAAATACATT
Found at i:40405192 original size:27 final size:27
Alignment explanation
Indices: 40405148--40405200 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
40405138 TCATCACCTA
*
40405148 AATTTTTATAATTTC-TTTATGATTTTT
1 AATTTTTATAATTACTTTTA-GATTTTT
40405175 AATTTTT-TAATATACTTTTAGATTTT
1 AATTTTTATAAT-TACTTTTAGATTTT
40405201 ATATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 15 0.65
28 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
AATTTTTATAATTACTTTTAGATTTTT
Found at i:40408900 original size:30 final size:29
Alignment explanation
Indices: 40408866--40408980 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 29
40408856 CCAACACCTA
***
40408866 CACCAGCACTAACACTGGCACCACCTCCGG
1 CACCAGCACT-ACACCAACACCACCTCCGG
*
40408896 CACCAGCACCTGCACCAACACCACCTCCGG
1 CACCAGCA-CTACACCAACACCACCTCCGG
* * ** * *
40408926 CACCAGCACCAGCACCAGCACCTGCACCCG
1 CACCAGCACTA-CACCAACACCACCTCCGG
* *
40408956 CTCCAGCACCTCCACCAACACCACC
1 CACCAGCA-CTACACCAACACCACC
40408981 ACCAGCTCCT
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 1 0.02
30 61 0.94
31 3 0.05
ACGTcount: A:0.27, C:0.53, G:0.13, T:0.07
Consensus pattern (29 bp):
CACCAGCACTACACCAACACCACCTCCGG
Found at i:40408910 original size:6 final size:6
Alignment explanation
Indices: 40408895--40408986 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
40408885 ACCACCTCCG
* * * * *
40408895 GCACCA GCACCT GCACCA ACACCA CCTCCG GCACCA GCACCA GCACCA
1 GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA
* * * * * * *
40408943 GCACCT GCACCC GCTCCA GCACCT CCACCA ACACCA CCACCA GC
1 GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GC
40408987 TCCTACCCCT
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.27, C:0.54, G:0.13, T:0.05
Consensus pattern (6 bp):
GCACCA
Found at i:40408989 original size:30 final size:30
Alignment explanation
Indices: 40408884--40408983 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
40408874 CTAACACTGG
*
40408884 CACCACCTCCGGCACCAGCACCTGCACCAA
1 CACCACCACCGGCACCAGCACCTGCACCAA
* * *
40408914 CACCACCTCCGGCACCAGCACCAGCACCAG
1 CACCACCACCGGCACCAGCACCTGCACCAA
** * * *
40408944 CACCTGCACCCGCTCCAGCACCTCCACCAA
1 CACCACCACCGGCACCAGCACCTGCACCAA
40408974 CACCACCACC
1 CACCACCACC
40408984 AGCTCCTACC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.26, C:0.56, G:0.12, T:0.06
Consensus pattern (30 bp):
CACCACCACCGGCACCAGCACCTGCACCAA
Found at i:40409001 original size:24 final size:24
Alignment explanation
Indices: 40408974--40409024 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
40408964 CCTCCACCAA
* * *
40408974 CACCACCACCAGCTCCTACCCCTC
1 CACCACCACCAGCCCCAACACCTC
* *
40408998 CACCTCCACTAGCCCCAACACCTC
1 CACCACCACCAGCCCCAACACCTC
40409022 CAC
1 CAC
40409025 TTGCTGCAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.61, G:0.04, T:0.12
Consensus pattern (24 bp):
CACCACCACCAGCCCCAACACCTC
Found at i:40409072 original size:24 final size:23
Alignment explanation
Indices: 40409026--40409094 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
40409016 CACCTCCACT
* * *
40409026 TGCTGCAGCACTTCCTCCTGCACC
1 TGCTGCAGCACCTCCACCAGCA-C
*
40409050 TGCTGCAACACCTCCACCAGCAC
1 TGCTGCAGCACCTCCACCAGCAC
* *
40409073 TACCTCCAGCACCTCCACCAGC
1 T-GCTGCAGCACCTCCACCAGC
40409095 TCCTACCCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.20, C:0.49, G:0.13, T:0.17
Consensus pattern (23 bp):
TGCTGCAGCACCTCCACCAGCAC
Found at i:40409194 original size:30 final size:28
Alignment explanation
Indices: 40409160--40409253 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 28
40409150 CCTCCTCCTG
40409160 CACCTCCGCCAACACCACTTCCAGCACCTC
1 CACCTCCGCCAACACCAC-TCCA-CACCTC
* * * * **
40409190 CACCTCCACTAACTCCTACTCCTCCACCAG
1 CACCTCCGCCAACACC-ACTCC-ACACCTC
40409220 CACCTCCGCCAACACCACCTCCTACACCTC
1 CACCTCCGCCAACACCA-CTCC-ACACCTC
40409250 CACC
1 CACC
40409254 ACTACCACCA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.94
31 2 0.04
ACGTcount: A:0.23, C:0.57, G:0.04, T:0.15
Consensus pattern (28 bp):
CACCTCCGCCAACACCACTCCACACCTC
Found at i:40409220 original size:36 final size:36
Alignment explanation
Indices: 40409180--40409254 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
40409170 AACACCACTT
** * *
40409180 CCAGCACCTCCACCTCCACTAACTCCTACTCCTCCA
1 CCAGCACCTCCACCAACACCAACTCCTACACCTCCA
* *
40409216 CCAGCACCTCCGCCAACACCACCTCCTACACCTCCA
1 CCAGCACCTCCACCAACACCAACTCCTACACCTCCA
40409252 CCA
1 CCA
40409255 CTACCACCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.57, G:0.04, T:0.15
Consensus pattern (36 bp):
CCAGCACCTCCACCAACACCAACTCCTACACCTCCA
Found at i:40409226 original size:15 final size:15
Alignment explanation
Indices: 40409208--40409274 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
40409198 CTAACTCCTA
*
40409208 CTCCTCCACCAGCAC
1 CTCCTCCACCACCAC
* *
40409223 CTCCGCCAACACCAC
1 CTCCTCCACCACCAC
* *
40409238 CTCCTACACCTCCAC
1 CTCCTCCACCACCAC
*
40409253 C-ACTACCACCACCAC
1 CTCCT-CCACCACCAC
40409268 CTCCTCC
1 CTCCTCC
40409275 TACACCTCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
14 2 0.05
15 35 0.90
16 2 0.05
ACGTcount: A:0.22, C:0.61, G:0.03, T:0.13
Consensus pattern (15 bp):
CTCCTCCACCACCAC
Found at i:40409253 original size:18 final size:18
Alignment explanation
Indices: 40409190--40409403 Score: 64
Period size: 18 Copynumber: 11.7 Consensus size: 18
40409180 CCAGCACCTC
* *
40409190 CACCTCCACTAACTCCTA
1 CACCTCCACCACCTCCTA
* * * *
40409208 CTCCTCCACCAGCACCTC
1 CACCTCCACCACCTCCTA
* **
40409226 CGCCAACACCACCTCCTA
1 CACCTCCACCACCTCCTA
*
40409244 CACCTCCACCA-CTAC--
1 CACCTCCACCACCTCCTA
* *
40409259 CACCACCACCTCCTCCTA
1 CACCTCCACCACCTCCTA
40409277 CACCTCTACCACCACTAGCTCCTA
1 CA-C-CT-CCACCAC---CTCCTA
* *
40409301 CTCCTCCACCAACC-CCAA
1 CACCTCCACC-ACCTCCTA
* * * *
40409319 CACCACCACCAACACCTG
1 CACCTCCACCACCTCCTA
* * * *
40409337 CACC-CACTCCAGCACCTC
1 CACCTC-CACCACCTCCTA
**
40409355 CACCAACACCACCTCC-A
1 CACCTCCACCACCTCCTA
*
40409372 GCATCTCCACCACC-CCTA
1 -CACCTCCACCACCTCCTA
40409390 GCACCTCCACCACC
1 -CACCTCCACCACC
40409404 CCCAGCTCCA
Statistics
Matches: 142, Mismatches: 39, Indels: 30
0.67 0.18 0.14
Matches are distributed among these distances:
15 9 0.06
16 3 0.02
17 8 0.06
18 96 0.68
19 2 0.01
20 1 0.01
21 11 0.08
22 4 0.03
23 1 0.01
24 7 0.05
ACGTcount: A:0.26, C:0.57, G:0.03, T:0.14
Consensus pattern (18 bp):
CACCTCCACCACCTCCTA
Found at i:40409266 original size:30 final size:30
Alignment explanation
Indices: 40409232--40409402 Score: 95
Period size: 30 Copynumber: 5.8 Consensus size: 30
40409222 CCTCCGCCAA
40409232 CACCACCTCCTACACCTCCACCACTACCAC
1 CACCACCTCCTACACCTCCACCACTACCAC
* *
40409262 CACCACCTCCT---CCTACACCTCTACCAC
1 CACCACCTCCTACACCTCCACCACTACCAC
* * * * *
40409289 CACTAGCTCCTACTCCTCCACCAAC-CCCAA
1 CACCACCTCCTACACCTCCACC-ACTACCAC
* * * *
40409319 CACCACCACCAACACCTGCACCCACT-CCAG
1 CACCACCTCCTACACCTCCA-CCACTACCAC
* * * * * * *
40409349 CACCTCCACCAACACCACCTCCAGC-ATCTC
1 CACCACCTCCTACACCTCCACCA-CTACCAC
40409379 CACCACC-CCTAGCACCTCCACCAC
1 CACCACCTCCTA-CACCTCCACCAC
40409403 CCCCAGCTCC
Statistics
Matches: 106, Mismatches: 26, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
27 23 0.22
29 7 0.07
30 73 0.69
31 3 0.03
ACGTcount: A:0.26, C:0.58, G:0.03, T:0.13
Consensus pattern (30 bp):
CACCACCTCCTACACCTCCACCACTACCAC
Found at i:40409272 original size:60 final size:60
Alignment explanation
Indices: 40409150--40409274 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
40409140 CGTTCCGGCA
* * * * * *
40409150 CCTCCTCCTGCACCTCCGCCAACACCACTTCCAGCACCTCCACCTCCACTAACTCCTACT
1 CCTCCACCAGCACCTCCGCCAACACCACCTCCAGCACCTCCACCACCACCAACACCTACT
* *
40409210 CCTCCACCAGCACCTCCGCCAACACCACCTCCTA-CACCTCCACCACTACCACCACC-ACCT
1 CCTCCACCAGCACCTCCGCCAACACCACCTCC-AGCACCTCCACCACCACCAACACCTA-CT
40409270 CCTCC
1 CCTCC
40409275 TACACCTCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.02
60 53 0.96
61 1 0.02
ACGTcount: A:0.22, C:0.58, G:0.04, T:0.16
Consensus pattern (60 bp):
CCTCCACCAGCACCTCCGCCAACACCACCTCCAGCACCTCCACCACCACCAACACCTACT
Found at i:40409305 original size:33 final size:33
Alignment explanation
Indices: 40409232--40409755 Score: 105
Period size: 33 Copynumber: 16.2 Consensus size: 33
40409222 CCTCCGCCAA
* *
40409232 CACCACCTCCTACACCTCCACCACTACCACCAC
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * * *
40409265 CACCTCCTCCTACACCTCTACCACCACTAGCTC
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* *
40409298 CTA-CTCCTCC-ACCAACC-CCAACACCACCACCAA
1 C-ACCTCCTCCTA-C-ACCTCCACCACCACCACCAC
* * * * *
40409331 CACCTGCACC--CA-CTCCAGCACCTCCACCAA
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * *
40409361 CACCACCTCC-AGCATCTCCACCACC-CCTAGCAC
1 CACCTCCTCCTA-CACCTCCACCACCACC-ACCAC
* * * ** * * *
40409394 CTCCACCACCCCCAGCTCCAACACCACCACCAA
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * * * * * *
40409427 CACTTGCACC--CA-CTCCAGCACCTCCACTAA
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * * *
40409457 CACCACCTCC-AGCACCTCCACCACCACTAGCTC
1 CACCTCCTCCTA-CACCTCCACCACCACCACCAC
*
40409490 CTA-CTCCTCC-ACCAACC-CCACCACCACCACCAA
1 C-ACCTCCTCCTA-C-ACCTCCACCACCACCACCAC
* * * * * *
40409523 TACCTGCACC--CA-CTCCAGCACCTCCTCCTA-
1 CACCTCCTCCTACACCTCCACCACCACCACC-AC
* * * * *
40409553 CACCTCCGCCAACACCACCTCCACCACC-CCTAG
1 CACCTCCTCCTACACCTCCACCACCACCACC-AC
* * *
40409586 CACCTCCACCTCCACCTCCACCTCCACCTCCACCAC
1 CACCTCCTCCTACACCTCCA---CCACCACCACCAC
** **
40409622 CACCAGCTCCTATTCCTCCACCAGCC-CCACCAC
1 CACCTCCTCCTACACCTCCACCA-CCACCACCAC
* * * * * *
40409655 CA---CCACCAATACCTGCA-C-CCA-CTCCAG
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * *
40409682 CACCTCCTCCTACACCTCCGCCAACACCACCTC
1 CACCTCCTCCTACACCTCCACCACCACCACCAC
* * *
40409715 CACCACCT-ATAGCACCTCCACCTCCACCACCAC
1 CACCTCCTCCTA-CACCTCCACCACCACCACCAC
*
40409748 CAGCTCCT
1 CACCTCCT
40409756 ACTCCTCCAC
Statistics
Matches: 352, Mismatches: 103, Indels: 72
0.67 0.20 0.14
Matches are distributed among these distances:
27 8 0.02
29 3 0.01
30 82 0.23
31 6 0.02
32 19 0.05
33 198 0.56
34 12 0.03
36 22 0.06
37 2 0.01
ACGTcount: A:0.25, C:0.58, G:0.04, T:0.13
Consensus pattern (33 bp):
CACCTCCTCCTACACCTCCACCACCACCACCAC
Found at i:40409358 original size:24 final size:24
Alignment explanation
Indices: 40409331--40409478 Score: 64
Period size: 24 Copynumber: 6.2 Consensus size: 24
40409321 CCACCACCAA
40409331 CACCTGCACCCA-CTCCAGCACCTC
1 CACCT-CACCCACCTCCAGCACCTC
* *
40409355 CACC-AACACCACCTCCAGCATCTC
1 CACCTCAC-CCACCTCCAGCACCTC
40409379 CA-C-CA-CC-CCT--AGCACCTC
1 CACCTCACCCACCTCCAGCACCTC
* * * * *
40409397 CACCACCCCCAGCTCCAACACCACCAC
1 CACCTCACCCACCT-C--CAGCACCTC
40409424 CAACACTTGCACCCA-CTCCAGCACCTC
1 C-AC-C-T-CACCCACCTCCAGCACCTC
*
40409451 CA-CTAACACCACCTCCAGCACCTC
1 CACCTCAC-CCACCTCCAGCACCTC
40409475 CACC
1 CACC
40409479 ACCACTAGCT
Statistics
Matches: 93, Mismatches: 13, Indels: 35
0.66 0.09 0.25
Matches are distributed among these distances:
18 9 0.10
19 1 0.01
20 4 0.04
21 4 0.04
22 6 0.06
23 9 0.10
24 32 0.34
25 1 0.01
26 1 0.01
27 15 0.16
28 2 0.02
29 2 0.02
30 2 0.02
31 5 0.05
ACGTcount: A:0.26, C:0.57, G:0.05, T:0.11
Consensus pattern (24 bp):
CACCTCACCCACCTCCAGCACCTC
Found at i:40409415 original size:96 final size:96
Alignment explanation
Indices: 40409058--40409601 Score: 402
Period size: 96 Copynumber: 5.6 Consensus size: 96
40409048 CCTGCTGCAA
* * * * **
40409058 CACCTCCACCAGCACTACCTCCAGCACCTCCACCAGCTCCTA-CCCCTCCACCAGCC-CCAATAC
1 CACCTCCACCAACACCACCTCCAGCACCTCCACCA-CCCCTAGCACCTCCACCA-CCACCAACCC
* * * *
40409121 CACCACCAACACCTACACCCGTTCCGGCACCTC-CTCCTG
64 CAACACCACCACCAACA-CC--T---GCACC-CACTCCAG
* * * * * * * * * * * *
40409160 CACCTCCGCCAACACCACTTCCAGCACCTCCACCTCCACTAACTCCTACTCCTCCACCAGCACCT
1 CACCTCCACCAACACCACCTCCAGCACCTCCACCACCCCTAGCACCTCCACCACCACCAACCCCA
* * * * * * *
40409225 CCGCCAACACCACCTCCT--ACAC-CTCCAC
66 ACACCACCACCAACACCTGCACCCACTCCAG
* * * * * * * *
40409253 CA-CTACCACCACCACCTCCTCCTA-CACCTCTACCACCACTAGCTCCTACTCCTCCACCAACCC
1 CACCT-CCACCAACACCACCTCC-AGCACCTCCACCACCCCTAGCACCTCCACCACCACCAACCC
40409316 CAACACCACCACCAACACCTGCACCCACTCCAG
64 CAACACCACCACCAACACCTGCACCCACTCCAG
* * * *
40409349 CACCTCCACCAACACCACCTCCAGCATCTCCACCACCCCTAGCACCTCCACCACCCCCAGCTCCA
1 CACCTCCACCAACACCACCTCCAGCACCTCCACCACCCCTAGCACCTCCACCACCACCAACCCCA
*
40409414 ACACCACCACCAACACTTGCACCCACTCCAG
66 ACACCACCACCAACACCTGCACCCACTCCAG
* * * * * *
40409445 CACCTCCACTAACACCACCTCCAGCACCTCCACCACCACTAGCTCCTACTCCTCCACCAACCCCA
1 CACCTCCACCAACACCACCTCCAGCACCTCCACCACCCCTAGCACCTCCACCACCACCAACCCCA
* *
40409510 CCACCACCACCAATACCTGCACCCACTCCAG
66 ACACCACCACCAACACCTGCACCCACTCCAG
* * * * * *
40409541 CACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTCCACCTCCACC
1 CACCTCCACCAACACCACC-TC--CAGCACCTCCACCACCCCTAGCACCTCCACCACCACC
40409602 TCCACCTCCA
Statistics
Matches: 356, Mismatches: 74, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
92 2 0.01
93 68 0.19
94 3 0.01
95 4 0.01
96 181 0.51
97 3 0.01
99 33 0.09
101 8 0.02
102 54 0.15
ACGTcount: A:0.25, C:0.57, G:0.05, T:0.13
Consensus pattern (96 bp):
CACCTCCACCAACACCACCTCCAGCACCTCCACCACCCCTAGCACCTCCACCACCACCAACCCCA
ACACCACCACCAACACCTGCACCCACTCCAG
Found at i:40409480 original size:18 final size:18
Alignment explanation
Indices: 40409361--40409481 Score: 75
Period size: 18 Copynumber: 6.4 Consensus size: 18
40409351 CCTCCACCAA
*
40409361 CACCACCTCCAGCATCTC
1 CACCACCTCCAGCACCTC
40409379 CACCACC-CCTAGCACCTC
1 CACCACCTCC-AGCACCTC
* * **
40409397 CACCACCCCCAGCTCCAA
1 CACCACCTCCAGCACCTC
* * * *
40409415 CACCACCACCAACACTTG
1 CACCACCTCCAGCACCTC
40409433 CACC-CACTCCAGCACCTCCAC
1 CACCAC-CTCCAGCACCT---C
40409454 TAACACCACCTCCAGCACCTC
1 ---CACCACCTCCAGCACCTC
40409475 CACCACC
1 CACCACC
40409482 ACTAGCTCCT
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.04
18 57 0.72
19 2 0.03
21 1 0.01
24 15 0.19
25 1 0.01
ACGTcount: A:0.26, C:0.58, G:0.05, T:0.11
Consensus pattern (18 bp):
CACCACCTCCAGCACCTC
Found at i:40409496 original size:54 final size:54
Alignment explanation
Indices: 40409389--40409580 Score: 129
Period size: 54 Copynumber: 3.6 Consensus size: 54
40409379 CACCACCCCT
* * * *
40409389 AGCACCTCCACCACCCCCAGCTCCAACACCACCACCAACACTTGCACCCACTCC
1 AGCACCTCCACCAACACCACCTCCAACACCACCACCAACACTAGCACCCACTCC
* * * * * *
40409443 AGCACCTCCACTAACACCACCTCCAGCACCTCCACCACCACTAGCTCCTACTCC
1 AGCACCTCCACCAACACCACCTCCAACACCACCACCAACACTAGCACCCACTCC
** * * * * ** * * *
40409497 TCCACCAACC-CCACCACCACCACCAATACCTGCACCCACTCCAGCACCTC-CTCC
1 AGCACC-TCCACCAACACCACCTCCAACACCACCACCAACACTAGCACC-CACTCC
* *
40409551 TA-CACCTCCGCCAACACCACCTCCACCACC
1 -AGCACCTCCACCAACACCACCTCCAACACC
40409581 CCTAGCACCT
Statistics
Matches: 103, Mismatches: 31, Indels: 8
0.73 0.22 0.06
Matches are distributed among these distances:
53 2 0.02
54 99 0.96
55 2 0.02
ACGTcount: A:0.27, C:0.57, G:0.05, T:0.11
Consensus pattern (54 bp):
AGCACCTCCACCAACACCACCTCCAACACCACCACCAACACTAGCACCCACTCC
Found at i:40409532 original size:60 final size:60
Alignment explanation
Indices: 40409487--40409626 Score: 137
Period size: 57 Copynumber: 2.4 Consensus size: 60
40409477 CCACCACTAG
* * * *
40409487 CTCCTACTCCTCCACCAACCCCACCACCACCACCAATACCTGCACCCACTCCAGCACCTC
1 CTCCTACACCTCCACCAACACCACCACCACCACCAATACCTGCACCCACACCACCACCTC
* * *
40409547 CTCCTACACCTCCGCCAACACCACCTCCACCACC----CCTAGCACCTC-CACCTCCACCTC
1 CTCCTACACCTCCACCAACACCACCACCACCACCAATACCT-GCACC-CACACCACCACCTC
* * *
40409604 CACCTCCACCTCCACCACCACCA
1 CTCCTACACCTCCACCAACACCA
40409627 GCTCCTATTC
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.04
57 33 0.49
58 1 0.01
60 30 0.45
ACGTcount: A:0.24, C:0.61, G:0.03, T:0.13
Consensus pattern (60 bp):
CTCCTACACCTCCACCAACACCACCACCACCACCAATACCTGCACCCACACCACCACCTC
Found at i:40409594 original size:24 final size:23
Alignment explanation
Indices: 40409567--40409988 Score: 98
Period size: 24 Copynumber: 17.5 Consensus size: 23
40409557 TCCGCCAACA
40409567 CCACCTCCACCACCCCTAGCACCT
1 CCACCTCCACCACCCC-AGCACCT
*
40409591 CCACCT---CCACCTC--CACCT
1 CCACCTCCACCACCCCAGCACCT
*
40409609 CCACCTCCACCACCACCAGCTCCT
1 CCACCTCCACCACC-CCAGCACCT
*** * *
40409633 ATTCCTCCACCAGCCCCACCACCA
1 CCACCTCCACCA-CCCCAGCACCT
*
40409657 CCACCAATACCTGCACCCACTCCAGCACCT
1 CCACC--T--C--CA-CCACCCCAGCACCT
* * * *
40409687 CCTCCTACACCTCCGCCA--A-CA
1 CCACCTCCACCACC-CCAGCACCT
**
40409708 CCACCTCCACCACCTATAGCACCT
1 CCACCTCCACCACC-CCAGCACCT
*
40409732 CCACCTCCACCACCACCAGCTCCT
1 CCACCTCCACCACC-CCAGCACCT
* * * * *
40409756 ACTCCTCCACCGGCCCCAACACCA
1 CCACCTCCACC-ACCCCAGCACCT
*
40409780 CCACCAATACCTGCACCCACTCCAGCACCT
1 CCACC--T--C--CA-CCACCCCAGCACCT
* * * *
40409810 CCTCCTGCACCTCCGCCA--A-CA
1 CCACCTCCACCACC-CCAGCACCT
40409831 CCACCTCCACCACCCCTAGCACCT
1 CCACCTCCACCACCCC-AGCACCT
* *
40409855 CCACCTCCACCACCACCAGCTCTT
1 CCACCTCCACCACC-CCAGCACCT
*** * * *
40409879 ATTCCTCCACCAGCTCCAACACCA
1 CCACCTCCACCA-CCCCAGCACCT
*
40409903 CCACCAATACCGGCACCCACTCCAGCACCT
1 CCACC--T--C--CA-CCACCCCAGCACCT
* * * *
40409933 CCTCCTACACCTCCGCCA--A-CA
1 CCACCTCCACCACC-CCAGCACCT
40409954 CCACCTCCACCACCCCTAGCACCT
1 CCACCTCCACCACCCC-AGCACCT
40409978 CCACCTCCACC
1 CCACCTCCACC
40409989 TCCACCTTCA
Statistics
Matches: 277, Mismatches: 76, Indels: 90
0.63 0.17 0.20
Matches are distributed among these distances:
18 11 0.04
20 4 0.01
21 50 0.18
22 4 0.01
23 12 0.04
24 129 0.47
25 7 0.03
26 3 0.01
28 6 0.02
30 43 0.16
31 8 0.03
ACGTcount: A:0.23, C:0.58, G:0.05, T:0.13
Consensus pattern (23 bp):
CCACCTCCACCACCCCAGCACCT
Found at i:40409595 original size:6 final size:6
Alignment explanation
Indices: 40409567--40409625 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
40409557 TCCGCCAACA
* *
40409567 CCACCT CCACCA CC-CCT AGCACCT CCACCT CCACCT CCACCT CCACCT
1 CCACCT CCACCT CCACCT -CCACCT CCACCT CCACCT CCACCT CCACCT
*
40409615 CCACCA CCACC
1 CCACCT CCACC
40409626 AGCTCCTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 2 0.04
6 41 0.89
7 3 0.07
ACGTcount: A:0.20, C:0.66, G:0.02, T:0.12
Consensus pattern (6 bp):
CCACCT
Found at i:40409643 original size:30 final size:30
Alignment explanation
Indices: 40409469--40409607 Score: 52
Period size: 30 Copynumber: 4.5 Consensus size: 30
40409459 CCACCTCCAG
* *
40409469 CACCTCCACCACCACTAGCTCCTACT-CCTC
1 CACCTCCACCACCACCACCTCCTA-TACCTC
* * * *
40409499 CACCAACC-CCACCACCACCACCAATACCTG
1 CACC-TCCACCACCACCACCTCCTATACCTC
* * * *
40409529 CACC-CACTCCAGCACCTCCTCCTACACCTCCGC
1 CACCTC-CACCACCACCACCTCCTATACCT---C
* * * *
40409562 CAACACCACCTCCACCACC-CCTAGCACCTC
1 CACCTCCACCACCACCACCTCCTA-TACCTC
*
40409592 CACCTCCACCTCCACC
1 CACCTCCACCACCACC
40409608 TCCACCTCCA
Statistics
Matches: 81, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
28 1 0.01
29 2 0.02
30 54 0.67
31 2 0.02
32 4 0.05
33 17 0.21
34 1 0.01
ACGTcount: A:0.24, C:0.60, G:0.04, T:0.13
Consensus pattern (30 bp):
CACCTCCACCACCACCACCTCCTATACCTC
Found at i:40409643 original size:123 final size:123
Alignment explanation
Indices: 40409469--40409994 Score: 586
Period size: 123 Copynumber: 4.1 Consensus size: 123
40409459 CCACCTCCAG
* * * * * *
40409469 CACCTCCACCACCACTAGCTCCTACTCCTCCACCAACCCCACCACCACCACCAATACCTGCACCC
1 CACCTCCACCACCACCAGCTCCTACACCACCACCAGCTCCAACACCACCACCAATACCTGCACCC
40409534 ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
66 ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
* ** * *
40409592 CACCTCCACCTCCACCTCCACCTCCACCACCACCAGCTCCTATTCCTCCACCAGCCCCACCACCA
1 CACCTCCACCACCACCAGCTCCTACACCACCACCAGCTCC-A-------A-CA---CCACCACCA
** *** * * *
40409657 CCACCAATACCTGCAC-CCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCAC
54 ATACCTGCACC--CACTCCA--GCACCTCC---TCCTACACCTCCGCCAACACCACCTCCACCAC
**
40409721 CTATAGCACCTC
112 CCCTAGCACCTC
* * * *
40409733 CACCTCCACCACCACCAGCTCCTACTCCTCCACCGGCCCCAACACCACCACCAATACCTGCACCC
1 CACCTCCACCACCACCAGCTCCTACACCACCACCAGCTCCAACACCACCACCAATACCTGCACCC
*
40409798 ACTCCAGCACCTCCTCCTGCACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
66 ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
* ** * *
40409856 CACCTCCACCACCACCAGCTCTTATTCCTCCACCAGCTCCAACACCACCACCAATACCGGCACCC
1 CACCTCCACCACCACCAGCTCCTACACCACCACCAGCTCCAACACCACCACCAATACCTGCACCC
40409921 ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
66 ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
*
40409979 CACCTCCACCTCCACC
1 CACCTCCACCACCACC
40409995 TTCACCACCA
Statistics
Matches: 335, Mismatches: 48, Indels: 40
0.79 0.11 0.09
Matches are distributed among these distances:
123 203 0.61
124 1 0.00
126 5 0.01
127 3 0.01
128 3 0.01
129 15 0.04
132 4 0.01
133 1 0.00
135 15 0.04
136 3 0.01
137 3 0.01
138 5 0.01
140 1 0.00
141 73 0.22
ACGTcount: A:0.24, C:0.58, G:0.05, T:0.13
Consensus pattern (123 bp):
CACCTCCACCACCACCAGCTCCTACACCACCACCAGCTCCAACACCACCACCAATACCTGCACCC
ACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTC
Found at i:40409763 original size:30 final size:30
Alignment explanation
Indices: 40409729--40409907 Score: 78
Period size: 30 Copynumber: 5.8 Consensus size: 30
40409719 ACCTATAGCA
*
40409729 CCTCCACCTCCACCACCACCAGCTCCTACT
1 CCTCCACCTCCACCACCACCACCTCCTACT
* * * *
40409759 CCTCCACCGGCC-CCAACACCACCACC-AAT
1 CCTCCACC-TCCACCACCACCACCTCCTACT
* * * *
40409788 ACCTGCACC-CACTCCAGCACCTCCTCCTGCACCT
1 -CCTCCACCTC-CACCACCACCACCTCCT--A-CT
* * * * *
40409822 CCGCCAACACCACCTCCACCACC-CCTAGCA
1 CCTCCACCTCCACCACCACCACCTCCTA-CT
* * *
40409852 CCTCCACCTCCACCACCACCAGCTCTTATT
1 CCTCCACCTCCACCACCACCACCTCCTACT
*
40409882 CCTCCACCAGCTCCAACACCACCACC
1 CCTCCA-C--CTCCACCACCACCACC
40409908 AATACCGGCA
Statistics
Matches: 107, Mismatches: 29, Indels: 23
0.67 0.18 0.14
Matches are distributed among these distances:
28 1 0.01
29 3 0.03
30 63 0.59
31 6 0.06
32 3 0.03
33 29 0.27
34 2 0.02
ACGTcount: A:0.23, C:0.58, G:0.06, T:0.13
Consensus pattern (30 bp):
CCTCCACCTCCACCACCACCACCTCCTACT
Found at i:40409766 original size:141 final size:141
Alignment explanation
Indices: 40409443--40409751 Score: 512
Period size: 141 Copynumber: 2.2 Consensus size: 141
40409433 CACCCACTCC
* * *
40409443 AGCACCTCCA-CTAACACCACCTCCAGCACCTCCACCACCACTAGCTCCTACTCCTCCACCAACC
1 AGCACCTCCACCT-CCACCACCACCAGCACCTCCACCACCACCAGCTCCTACTCCTCCACCAACC
40409507 CCACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
65 CCACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
*
40409572 TCCACCACCCCT
130 TCCACCACCCAT
* ** * *
40409584 AGCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCAGCTCCTATTCCTCCACCAGCCC
1 AGCACCTCCACCTCCACCACCACCAGCACCTCCACCACCACCAGCTCCTACTCCTCCACCAACCC
40409649 CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
66 CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
*
40409714 CCACCACCTAT
131 CCACCACCCAT
40409725 AGCACCTCCACCTCCACCACCACCAGC
1 AGCACCTCCACCTCCACCACCACCAGC
40409752 TCCTACTCCT
Statistics
Matches: 154, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
141 152 0.99
142 2 0.01
ACGTcount: A:0.25, C:0.58, G:0.05, T:0.13
Consensus pattern (141 bp):
AGCACCTCCACCTCCACCACCACCAGCACCTCCACCACCACCAGCTCCTACTCCTCCACCAACCC
CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
CCACCACCCAT
Found at i:40409784 original size:141 final size:141
Alignment explanation
Indices: 40409443--40409786 Score: 447
Period size: 141 Copynumber: 2.4 Consensus size: 141
40409433 CACCCACTCC
* * * * * * * * *
40409443 AGCACCTCCA-CTAACACCACCTCCAGCACCTCCACCACCACTAGCTCCTACTCCTCCACCAACC
1 AGCACCTCCACCT-CCACCACCACCACCACCTACACCACCACCAGCCCCAACACCACCACCAACC
40409507 CCACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
65 CCACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
*
40409572 TCCACCACCCCT
130 TCCACCACCCAT
* * * * * ** * *
40409584 AGCACCTCCACCTCCACCTCCACCTCCACCTCCACCACCACCAGCTCCTATTCCTCCACCAGCCC
1 AGCACCTCCACCTCCACCACCACCACCACCTACACCACCACCAGCCCCAACACCACCACCAACCC
40409649 CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
66 CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
*
40409714 CCACCACCTAT
131 CCACCACCCAT
* * * * *
40409725 AGCACCTCCACCTCCACCACCACCAGCTCCTACTCCTCCACCGGCCCCAACACCACCACCAA
1 AGCACCTCCACCTCCACCACCACCACCACCTACACCACCACCAGCCCCAACACCACCACCAA
40409787 TACCTGCACC
Statistics
Matches: 178, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
141 176 0.99
142 2 0.01
ACGTcount: A:0.25, C:0.58, G:0.05, T:0.13
Consensus pattern (141 bp):
AGCACCTCCACCTCCACCACCACCACCACCTACACCACCACCAGCCCCAACACCACCACCAACCC
CACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCT
CCACCACCCAT
Found at i:40409814 original size:12 final size:12
Alignment explanation
Indices: 40409799--40409856 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
40409789 CCTGCACCCA
40409799 CTCCAGCACCTC
1 CTCCAGCACCTC
*
40409811 CTCCTGCACCTC
1 CTCCAGCACCTC
* * *
40409823 CGCCAACACCAC
1 CTCCAGCACCTC
*
40409835 CTCCACCACC-C
1 CTCCAGCACCTC
40409846 CT--AGCACCTC
1 CTCCAGCACCTC
40409856 C
1 C
40409857 ACCTCCACCA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 5 0.14
10 2 0.05
11 3 0.08
12 27 0.73
ACGTcount: A:0.19, C:0.60, G:0.07, T:0.14
Consensus pattern (12 bp):
CTCCAGCACCTC
Found at i:40409982 original size:6 final size:6
Alignment explanation
Indices: 40409954--40410006 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
40409944 TCCGCCAACA
* * * *
40409954 CCACCT CCACCA CC-CCT AGCACCT CCACCT CCACCT CCACCT TCACCA
1 CCACCT CCACCT CCACCT -CCACCT CCACCT CCACCT CCACCT CCACCT
40410002 CCACC
1 CCACC
40410007 AGCTCCTACT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 2 0.05
6 33 0.87
7 3 0.08
ACGTcount: A:0.21, C:0.64, G:0.02, T:0.13
Consensus pattern (6 bp):
CCACCT
Found at i:40409994 original size:18 final size:19
Alignment explanation
Indices: 40409953--40410006 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
40409943 CTCCGCCAAC
40409953 ACCACCTCCACCACC-CCT
1 ACCACCTCCACCACCACCT
* *
40409971 AGCACCTCCACCTCCACCT
1 ACCACCTCCACCACCACCT
*
40409990 -CCACCTTCACCACCACC
1 ACCACCTCCACCACCACC
40410007 AGCTCCTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.22, C:0.63, G:0.02, T:0.13
Consensus pattern (19 bp):
ACCACCTCCACCACCACCT
Found at i:40410001 original size:135 final size:135
Alignment explanation
Indices: 40409850--40410117 Score: 464
Period size: 135 Copynumber: 2.0 Consensus size: 135
40409840 CCACCCCTAG
* * *
40409850 CACCTCCACCTCCACCACCACCAGCTCTTATTCCTCCACCAGCTCCAACACCACCACCAATACCG
1 CACCTCCACCTCCACCACCACCAGCTCCTACTCCTCCACCAGCCCCAACACCACCACCAATACCG
*
40409915 GCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACCTCCACCACCCCTAGCACCTCC
66 GCACCCACTCCAGCACCTCCTCCTACACCTCCGCAAACACCACCTCCACCACCCCTAGCACCTCC
40409980 ACCTC
131 ACCTC
* *
40409985 CACCTCCACCTTCACCACCACCAGCTCCTACTCCTCCACCAGCCCCAACACCACCACCAATACCT
1 CACCTCCACCTCCACCACCACCAGCTCCTACTCCTCCACCAGCCCCAACACCACCACCAATACCG
* *
40410050 GCACCCACTCCAGCACCTCCTCCTGCACCTCCGCAAACACCACCTCCACCACCCTTAGCACCTCC
66 GCACCCACTCCAGCACCTCCTCCTACACCTCCGCAAACACCACCTCCACCACCCCTAGCACCTCC
40410115 ACC
131 ACC
40410118 ACCTCCACCA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 125 1.00
ACGTcount: A:0.24, C:0.57, G:0.05, T:0.14
Consensus pattern (135 bp):
CACCTCCACCTCCACCACCACCAGCTCCTACTCCTCCACCAGCCCCAACACCACCACCAATACCG
GCACCCACTCCAGCACCTCCTCCTACACCTCCGCAAACACCACCTCCACCACCCCTAGCACCTCC
ACCTC
Found at i:40410025 original size:123 final size:120
Alignment explanation
Indices: 40409647--40410129 Score: 533
Period size: 123 Copynumber: 3.8 Consensus size: 120
40409637 CTCCACCAGC
40409647 CCCACCACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCAC
1 CCCA-CACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCAC
** ** * * * *
40409712 CTCCACCACCTATAGCACCTCCACCTCCACCACCACCAGCTCCTACTCCTCCACCGGCC-
65 CTCCACCACCCCTAGCACCTCCACCTCCACCACCACCTTCACC-A--CCACCAGC-TCCA
* *
40409771 CCAACACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTGCACCTCCGCCAACACCACC
1 CCCACACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
* *
40409836 TCCACCACCCCTAGCACCTCCACCTCCACCACCACCAGCTCTTATTCCTCCACCAGCTCCA
66 TCCACCACCCCTAGCACCTCCACCTCCACCACCA-C--CT-TCA--CCACCACCAGCTCCA
*
40409897 ---ACACCACCACCAATACCGGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
1 CCCACACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
*
40409959 TCCACCACCCCTAGCACCTCCACCTCCACCTCCACCTTCACCACCACCAGCTCCTA
66 TCCACCACCCCTAGCACCTCCACCTCCACCACCACCTTCACCACCACCAGCTCC-A
*
40410015 CTCCTCCACCAGCCCCAACACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTGCACCT
1 ------C-CCA----C---ACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCT
* * * *
40410080 CCGCAAACACCACCTCCACCACCCTTAGCACCTCCACCACCTCCACCACC
52 CCGCCAACACCACCTCCACCACCCCTAGCACCTCCACCTCCACCACCACC
40410130 AACTCCTACT
Statistics
Matches: 310, Mismatches: 24, Indels: 39
0.83 0.06 0.10
Matches are distributed among these distances:
117 13 0.04
118 1 0.00
119 2 0.01
120 2 0.01
122 1 0.00
123 185 0.60
124 4 0.01
125 2 0.01
126 7 0.02
128 1 0.00
129 2 0.01
132 1 0.00
135 89 0.29
ACGTcount: A:0.24, C:0.58, G:0.05, T:0.13
Consensus pattern (120 bp):
CCCACACCACCACCAATACCTGCACCCACTCCAGCACCTCCTCCTACACCTCCGCCAACACCACC
TCCACCACCCCTAGCACCTCCACCTCCACCACCACCTTCACCACCACCAGCTCCA
Found at i:40410041 original size:18 final size:18
Alignment explanation
Indices: 40409997--40410043 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40409987 CCTCCACCTT
* *
40409997 CACCACCACCAGCTCCTA
1 CACCACCACCAGCCCCAA
* *
40410015 CTCCTCCACCAGCCCCAA
1 CACCACCACCAGCCCCAA
40410033 CACCACCACCA
1 CACCACCACCA
40410044 ATACCTGCAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.60, G:0.04, T:0.09
Consensus pattern (18 bp):
CACCACCACCAGCCCCAA
Done.