Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 137 of 228
Found at i:41047593 original size:59 final size:58
Alignment explanation
Indices: 41047412--41047594 Score: 162
Period size: 64 Copynumber: 3.1 Consensus size: 58
41047402 TATACCATTA
* * *
41047412 TATATTATGATTTTAGTAAATTCATATAAGAATA-TAATATTAAGAATTTCATTAAAT
1 TATATTATGATTTTAGTAAATTTATATAATAATATTAATATTAAGAATTTTATTAAAT
* * * * *
41047469 TATA-TAT--TTTTATTAAATTATATTTAATAATAATT-ATGTTAAATTATATTTTA-TAGCATT
1 TATATTATGATTTTAGTAAATT-TATATAATAAT-ATTAATATT-AA-GA-ATTTTATTA--AAT
*
41047529 ATATATTATGATTTTAGTAAATTTATATCATAATATTTAATATTAAGAATTTTATTAAAT
1 -TATATTATGATTTTAGTAAATTTATATAATAATA-TTAATATTAAGAATTTTATTAAAT
41047589 TATATT
1 TATATT
41047595 TAATAATAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
54 11 0.11
55 8 0.08
56 8 0.08
57 7 0.07
58 3 0.03
59 11 0.11
60 4 0.04
61 10 0.10
62 7 0.07
63 13 0.13
64 15 0.15
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTTAGTAAATTTATATAATAATATTAATATTAAGAATTTTATTAAAT
Found at i:41047693 original size:61 final size:61
Alignment explanation
Indices: 41047628--41047818 Score: 230
Period size: 61 Copynumber: 3.2 Consensus size: 61
41047618 ATTTTATAGT
41047628 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * ** * * * * * *
41047689 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTATATTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TAT-TTAATATTAAGAATTTTATTA-A
41047748 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
41047809 ATTATATATT
1 ATTATATATT
41047819 TTTATTAAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
58 6 0.06
59 33 0.32
60 14 0.14
61 43 0.42
62 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:41047702 original size:120 final size:120
Alignment explanation
Indices: 41047578--41047853 Score: 534
Period size: 120 Copynumber: 2.3 Consensus size: 120
41047568 ATATTAAGAA
41047578 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
41047643 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
* *
41047698 TTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
41047763 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
41047818 TTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAA
41047854 ATATGATTAA
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 153 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
Found at i:41047730 original size:26 final size:25
Alignment explanation
Indices: 41047701--41047754 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
41047691 TATATATTTT
41047701 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAAT-ATTA
* *
41047727 TATTAAATTATATTTTATAGTATTA
1 TATTAAATTATATTTAATAATATTA
41047752 TAT
1 TAT
41047755 ATTATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTAAATTATATTTAATAATATTA
Found at i:41047760 original size:222 final size:220
Alignment explanation
Indices: 41047399--41047815 Score: 744
Period size: 222 Copynumber: 1.9 Consensus size: 220
41047389 TATACAATAT
41047399 TTTTATACCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
1 TTTTATACCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
*
41047464 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATT
66 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCATT
* * *
41047529 ATATATTATGATTTTAGTAAATTTATATCATAATATTTAATATTAAGAATTTTATTAAATTATAT
131 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
41047594 TTAATAATAATTATGTTAAATTACA
196 TTAATAATAATTATGTTAAATTACA
** *
41047619 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
1 TTTTATACCATTATATATTATGATTTTAGTAAATTCATATAAGAATA--TAATATTAAGAATTTC
*
41047684 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTA
64 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCA
41047749 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAT
129 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAT
41047814 AT
194 AT
41047816 ATTTTTATTA
Statistics
Matches: 187, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
220 45 0.24
222 142 0.76
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (220 bp):
TTTTATACCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCATT
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
TTAATAATAATTATGTTAAATTACA
Found at i:41048053 original size:44 final size:44
Alignment explanation
Indices: 41047998--41048085 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
41047988 CCTCCATTCC
*
41047998 ATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCCATTAG
1 ATTCAACCAAACA-ATA-AATTACTATTACACCTCTATTCCATTAG
*
41048042 ATTCAACCAAACAATTAAATTGCTATTACACCTCTATTCCATTA
1 ATTCAACCAAACAA-TAAATTACTATTACACCTCTATTCCATTA
41048086 CGACTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 1 0.03
44 15 0.38
45 23 0.59
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.31
Consensus pattern (44 bp):
ATTCAACCAAACAATAAATTACTATTACACCTCTATTCCATTAG
Found at i:41051137 original size:23 final size:22
Alignment explanation
Indices: 41051109--41051155 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
41051099 AGTGTATGTA
41051109 TTTTT-ATTTTCAAGAATTTAATT
1 TTTTTAATTTT-AA-AATTTAATT
41051132 TTTTTAAATTTTAAAATTTAATT
1 TTTTT-AATTTTAAAATTTAATT
41051155 T
1 T
41051156 CAATTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 15 0.68
24 2 0.09
25 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTAATTTTAAAATTTAATT
Found at i:41052095 original size:16 final size:16
Alignment explanation
Indices: 41052074--41052129 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
41052064 GCAGCAATAT
41052074 TTAAAATATTTCCTTA
1 TTAAAATATTTCCTTA
***
41052090 TTAAAAT-TTTAAAATA
1 TTAAAATATTT-CCTTA
*
41052106 TTTAAAATATTTCCTTC
1 -TTAAAATATTTCCTTA
41052123 TTAAAAT
1 TTAAAAT
41052130 TTTATTGGCT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 3 0.10
16 16 0.53
17 8 0.27
18 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATATTTCCTTA
Found at i:41052101 original size:8 final size:9
Alignment explanation
Indices: 41052069--41052117 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
41052059 CATTTGCAGC
41052069 AATATTTAA
1 AATATTTAA
*
41052078 AATATTT-C
1 AATATTTAA
**
41052086 CTTA-TTAA
1 AATATTTAA
41052094 AAT-TTTAA
1 AATATTTAA
41052102 AATATTTAA
1 AATATTTAA
41052111 AATATTT
1 AATATTT
41052118 CCTTCTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
7 2 0.06
8 10 0.32
9 19 0.61
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (9 bp):
AATATTTAA
Found at i:41052111 original size:33 final size:33
Alignment explanation
Indices: 41052069--41052133 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
41052059 CATTTGCAGC
41052069 AATATTTAAAATATTTCCTTATTAAAATTTTAA
1 AATATTTAAAATATTTCCTTATTAAAATTTTAA
*
41052102 AATATTTAAAATATTTCCTTCTTAAAATTTTA
1 AATATTTAAAATATTTCCTTATTAAAATTTTA
41052134 TTGGCTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (33 bp):
AATATTTAAAATATTTCCTTATTAAAATTTTAA
Found at i:41053713 original size:21 final size:21
Alignment explanation
Indices: 41053682--41053729 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
41053672 AAAAAAAACA
*
41053682 AAAAAATAGCAACAAAACAAT
1 AAAAAACAGCAACAAAACAAT
* *
41053703 AAAAAACAGCAAGAAAACAGT
1 AAAAAACAGCAACAAAACAAT
41053724 AAAAAA
1 AAAAAA
41053730 AGACATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.73, C:0.12, G:0.08, T:0.06
Consensus pattern (21 bp):
AAAAAACAGCAACAAAACAAT
Found at i:41057957 original size:23 final size:23
Alignment explanation
Indices: 41057913--41057958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41057903 AAAATGAGTT
41057913 AATTTTTTAGAAAATTAGAAAAA
1 AATTTTTTAGAAAATTAGAAAAA
* *
41057936 AATTATTTTA-AAATTTATAAAAA
1 AATT-TTTTAGAAAATTAGAAAAA
41057959 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTTTTTAGAAAATTAGAAAAA
Found at i:41062316 original size:33 final size:32
Alignment explanation
Indices: 41062227--41062335 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 32
41062217 AATTAATGAA
*
41062227 ACATAAAATATTTTAAAAACTTAA-AT-ATAAT
1 ACATAAAATA-TTTAAAAATTTAATATAATAAT
* *
41062258 A-ATAAATGATATCTAAAAAATTTAATATAATGAT
1 ACATAAA--ATAT-TTAAAAATTTAATATAATAAT
*
41062292 ACATGAAATATTTAAATAATTTAATATAATAAT
1 ACATAAAATATTTAAA-AATTTAATATAATAAT
41062325 ACATAAAATAT
1 ACATAAAATAT
41062336 AAATTAATCT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
30 5 0.08
31 2 0.03
32 17 0.27
33 31 0.48
34 5 0.08
35 4 0.06
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (32 bp):
ACATAAAATATTTAAAAATTTAATATAATAAT
Found at i:41071158 original size:23 final size:22
Alignment explanation
Indices: 41071106--41071158 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41071096 TCCACGTCTT
*
41071106 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41071128 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41071151 TTTCTTTT
1 TTTCTTTT
41071159 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41071183 original size:27 final size:27
Alignment explanation
Indices: 41071153--41071204 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
41071143 TTCTTCAATT
41071153 TCTTTTTCACTCTCAATCTCTTTTTGC
1 TCTTTTTCACTCTCAATCTCTTTTTGC
* **
41071180 TCTTTTTCATTCTCTTTCTCTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTT
41071205 CCTCACTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.02, T:0.63
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTGC
Found at i:41073554 original size:16 final size:16
Alignment explanation
Indices: 41073519--41073557 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41073509 TAAACTAAGT
*
41073519 AAATAAATAAATAAAG
1 AAATAAATAAATAAAA
41073535 AAATAAATAAA-AATAA
1 AAATAAATAAATAA-AA
41073551 AAATAAA
1 AAATAAA
41073558 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATAAATAAATAAAA
Found at i:41074687 original size:40 final size:40
Alignment explanation
Indices: 41074628--41074839 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
41074618 CATTTGAATG
* *
41074628 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41074668 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * *
41074708 ATACCCGGGTTAAGACTCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
41074748 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41074788 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
41074828 ATATCC-GGCTAA
1 ATATCCGGGCTAA
41074840 ATTCCGAAGA
Statistics
Matches: 138, Mismatches: 32, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
39 8 0.06
40 128 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:41074768 original size:80 final size:79
Alignment explanation
Indices: 41074632--41074848 Score: 301
Period size: 80 Copynumber: 2.7 Consensus size: 79
41074622 TGAATGATAT
* *
41074632 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTG
* *
41074697 TGCGAGTTGCTATAC
65 TGCGAGTTACTAAAC
* *
41074712 CCGGGTTAAGACTCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTG
*
41074777 TGCGAGTTACTAAAT
65 TGCGAGTTACTAAAC
* * * *
41074792 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGA-TCCGAAG
41074849 AAACTTGGGT
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 13 0.11
80 108 0.89
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGT
GCGAGTTACTAAAC
Found at i:41094128 original size:40 final size:40
Alignment explanation
Indices: 41094069--41094280 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
41094059 CATTTGAATG
* *
41094069 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41094109 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
41094149 ATA-CCTGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCC-GGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
41094189 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
41094229 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
41094269 ATATCC-GGCTAA
1 ATATCCGGGCTAA
41094281 ATTCTAAAGA
Statistics
Matches: 147, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
39 12 0.08
40 128 0.87
41 7 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:41094217 original size:80 final size:80
Alignment explanation
Indices: 41094069--41094280 Score: 329
Period size: 80 Copynumber: 2.7 Consensus size: 80
41094059 CATTTGAATG
*
41094069 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
*
41094134 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGAT
*
41094149 ATA-CCTGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGC
1 ATATCC-GGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGC
41094213 ATTTGTGCGAGTTGAT
65 ATTTGTGCGAGTTGAT
* * * * *
41094229 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
41094281 ATTCTAAAGA
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
79 8 0.07
80 111 0.92
81 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGAT
Found at i:41102186 original size:40 final size:40
Alignment explanation
Indices: 41102127--41102335 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
41102117 CATTTGAATG
* *
41102127 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41102167 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
41102207 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41102247 TTATCC-GGCTAAGA-CCGAAGGCATTTGTGCGAGTTA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
41102284 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
41102324 ATATCC-GGCTAA
1 ATATCCGGGCTAA
41102336 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
37 5 0.04
38 27 0.19
39 33 0.24
40 73 0.52
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:41111633 original size:20 final size:21
Alignment explanation
Indices: 41111608--41111649 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41111598 TTCTGGGATC
41111608 ATTTT-GAAACAAAA-TTGAAA
1 ATTTTGGAAA-AAAACTTGAAA
41111628 ATTTTGGAAAAAAACTTGAAA
1 ATTTTGGAAAAAAACTTGAAA
41111649 A
1 A
41111650 CAAGGGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (21 bp):
ATTTTGGAAAAAAACTTGAAA
Found at i:41113401 original size:41 final size:41
Alignment explanation
Indices: 41113344--41113442 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
41113334 ATTTCTATCA
*
41113344 TTTTCGACCTTTTCATTTGATATCCTTTCCGGATAACATCC
1 TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
*
41113385 TTTTCAACCTTTTCATTTGATATCCTTTTCGGATAACATCC
1 TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
*
41113426 TTTTCAACCCTTTCATT
1 TTTTCAACCTTTTCATT
41113443 GATTCAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.46
Consensus pattern (41 bp):
TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
Found at i:41118572 original size:20 final size:20
Alignment explanation
Indices: 41118502--41118572 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
41118492 TTTGTACATC
*
41118502 GGTGCCTCTGTTTGTACTTT
1 GGTGCCTCTGTTTGCACTTT
* * *
41118522 CGTGCCTCT-ATTACACTTT
1 GGTGCCTCTGTTTGCACTTT
* *
41118541 GGTGTCACTGTTTGCACTTT
1 GGTGCCTCTGTTTGCACTTT
*
41118561 GGTGCCTTTGTT
1 GGTGCCTCTGTT
41118573 ACGCATCTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
19 13 0.34
20 25 0.66
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (20 bp):
GGTGCCTCTGTTTGCACTTT
Found at i:41130968 original size:17 final size:17
Alignment explanation
Indices: 41130946--41130981 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41130936 ATGGCTGGAC
41130946 TTCACCTCACATGTAGT
1 TTCACCTCACATGTAGT
41130963 TTCACCTCACATGTAGT
1 TTCACCTCACATGTAGT
41130980 TT
1 TT
41130982 GAATACATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (17 bp):
TTCACCTCACATGTAGT
Found at i:41132258 original size:23 final size:26
Alignment explanation
Indices: 41132228--41132278 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
41132218 CGGTTATTAT
41132228 TATTTTAAAATAT-A-T-AAAATATA
1 TATTTTAAAATATAATTAAAAATATA
41132251 TATTTTAAAATATAATTAAAAATATA
1 TATTTTAAAATATAATTAAAAATATA
41132277 TA
1 TA
41132279 AAAGCCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.52
24 1 0.04
25 1 0.04
26 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TATTTTAAAATATAATTAAAAATATA
Found at i:41132261 original size:14 final size:13
Alignment explanation
Indices: 41132237--41132278 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
41132227 TTATTTTAAA
*
41132237 ATATATAAAATAT
1 ATATTTAAAATAT
41132250 ATATTTTAAAATAT
1 ATA-TTTAAAATAT
*
41132264 A-ATTAAAAATAT
1 ATATTTAAAATAT
41132276 ATA
1 ATA
41132279 AAAGCCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:41137365 original size:18 final size:18
Alignment explanation
Indices: 41137342--41137380 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41137332 AAAGAAAGAC
41137342 AGAAAAAGA-AATCAAAA
1 AGAAAAAGAGAATCAAAA
*
41137359 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATCAAAA
41137377 AGAA
1 AGAA
41137381 CAAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATCAAAA
Found at i:41140932 original size:26 final size:26
Alignment explanation
Indices: 41140896--41140954 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
41140886 TATTTTCTCG
41140896 AAATTTTACCAAGGGCAAAATCATCA
1 AAATTTTACCAAGGGCAAAATCATCA
* *
41140922 AAATTTTACCAGGGGTAAAATCATCA
1 AAATTTTACCAAGGGCAAAATCATCA
41140948 AAATTTT
1 AAATTTT
41140955 GTTGAGGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (26 bp):
AAATTTTACCAAGGGCAAAATCATCA
Found at i:41148765 original size:46 final size:46
Alignment explanation
Indices: 41148694--41148817 Score: 203
Period size: 46 Copynumber: 2.7 Consensus size: 46
41148684 TCTTATAAAA
* *
41148694 ATTCCATCAGTATATATTAACAAAATTATCTTAAAACTCATTTATT
1 ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
* *
41148740 GTTCCATTAGTATATATTAATAAAATTATCTTAAAATTCATTTATT
1 ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
*
41148786 ATTCCATTAGCATATATTAATAAAATTATCTT
1 ATTCCATTAGTATATATTAATAAAATTATCTT
41148818 GGTTTGTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.44
Consensus pattern (46 bp):
ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
Found at i:41148980 original size:24 final size:23
Alignment explanation
Indices: 41148953--41149012 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
41148943 TTATTAACAT
41148953 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
41148977 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
41149000 TGTTCGTGGACAT
1 TGTTCGTGAACAT
41149013 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:41153530 original size:16 final size:16
Alignment explanation
Indices: 41153509--41153540 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41153499 ATTTTGTTGC
*
41153509 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
41153525 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
41153541 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:41153739 original size:46 final size:43
Alignment explanation
Indices: 41153664--41153762 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
41153654 AATAATAACA
* *
41153664 GATACACGGTGGATTCAGTACACAGCAACCACCATTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACAGCAACCACC--TTATAATCAAT
* *
41153710 GATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAAT
41153754 GATACCGGT
1 GATACCGGT
41153763 TCACATAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 13 0.28
46 25 0.53
47 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAAT
Found at i:41153870 original size:51 final size:51
Alignment explanation
Indices: 41153762--41153883 Score: 169
Period size: 51 Copynumber: 2.4 Consensus size: 51
41153752 ATGATACCGG
*
41153762 TTCACATAGTAGCCGT-CACATAGTACTACACATGTGACCATCACTATTCGA
1 TTCACATAGTAGCC-TACACATAGTACTACACACGTGACCATCACTATTCGA
*
41153813 TACACATAGTAGCCTACACATAGTACTACACACGTGACCATCACT-TTC-A
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATTCGA
*
41153862 CTTTCACATAGTGGCCTACACA
1 --TTCACATAGTAGCCTACACA
41153884 CAGTCCATGC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
49 1 0.02
50 4 0.06
51 59 0.92
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (51 bp):
TTCACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATTCGA
Found at i:41155004 original size:23 final size:23
Alignment explanation
Indices: 41154977--41155029 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
41154967 AGTGTTATTG
*
41154977 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
41155000 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41155023 ATCAGTG
1 ATCAGTG
41155030 TGACACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:41159019 original size:26 final size:26
Alignment explanation
Indices: 41158940--41159020 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
41158930 ATGGTCACGT
41158940 GTGTAGTACTATGTGCAGGCTACTAC
1 GTGTAGTACTATGTGCAGGCTACTAC
* *
41158966 GTGTACCGGA--ATGAT--AGG-T-CGTAT
1 GTGTA--GTACTATG-TGCAGGCTAC-TAC
41158990 GTGTAGTACTATGTGCAGGCTACTAC
1 GTGTAGTACTATGTGCAGGCTACTAC
41159016 GTGTA
1 GTGTA
41159021 TCGAATGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 20
0.63 0.06 0.31
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 11 0.27
25 6 0.15
26 16 0.39
27 2 0.05
28 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (26 bp):
GTGTAGTACTATGTGCAGGCTACTAC
Found at i:41159064 original size:51 final size:51
Alignment explanation
Indices: 41158930--41159065 Score: 204
Period size: 50 Copynumber: 2.7 Consensus size: 51
41158920 AGTGAAAGTG
*
41158930 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
** * *
41158981 A-GGTCGTATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
41159030 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
41159066 TGTGAACCAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 6 0.08
50 38 0.50
51 32 0.42
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
Found at i:41159127 original size:45 final size:45
Alignment explanation
Indices: 41159076--41159162 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
41159066 TGTGAACCAA
* *
41159076 ACATCATTGATTAGTAAAGTAGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCACCGG
* * *
41159121 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCAC
1 ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCAC
41159163 TGAGTCTCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCACCGG
Found at i:41163980 original size:50 final size:50
Alignment explanation
Indices: 41163926--41164069 Score: 146
Period size: 49 Copynumber: 2.9 Consensus size: 50
41163916 AGCAATATCA
* * **
41163926 TGATGTCGTGACTTCAACAAGGGAATATTGCAACTATGGAGACAGTAGCT
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
* * * ** * *
41163976 TGATGTTGCGACTT-TAGTAGGGAATGTCACGACTATGGAGACAACAGCT
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
* * * *
41164025 TGATGTCGTAACTTCATCAATGGAATGTCGCAACTATAGAGACAA
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAA
41164070 TTTTCTCAAG
Statistics
Matches: 71, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
49 37 0.52
50 34 0.48
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (50 bp):
TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
Found at i:41165859 original size:28 final size:27
Alignment explanation
Indices: 41165813--41165876 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
41165803 AATCATATGC
41165813 ATGTTATTTGAGTGATTTTCG-TTTGTTA
1 ATGTTATTTGAGTGATTTT-GATTT-TTA
*
41165841 ATGTTATTTGTGT-AGTTTTGATTTTTA
1 ATGTTATTTGAGTGA-TTTTGATTTTTA
*
41165868 ATTTTATTT
1 ATGTTATTT
41165877 TCCCATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (27 bp):
ATGTTATTTGAGTGATTTTGATTTTTA
Found at i:41167782 original size:23 final size:24
Alignment explanation
Indices: 41167752--41167796 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
41167742 TTTAAAAATG
41167752 GTTTAATTA-TT-TTGAGATCCTTA
1 GTTTAATTACTTATTGA-ATCCTTA
41167775 GTTTAATTACTTATTGAATCCT
1 GTTTAATTACTTATTGAATCCT
41167797 CAAGTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (24 bp):
GTTTAATTACTTATTGAATCCTTA
Found at i:41169252 original size:19 final size:19
Alignment explanation
Indices: 41169230--41169266 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41169220 TAAATTATTA
*
41169230 TTTATTTTATAATTAATTT
1 TTTAATTTATAATTAATTT
41169249 TTTAATTTATAATTAATT
1 TTTAATTTATAATTAATT
41169267 ATAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTATAATTAATTT
Found at i:41169275 original size:19 final size:19
Alignment explanation
Indices: 41169235--41169276 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41169225 TATTATTTAT
**
41169235 TTTATAATTAATTTTTTAA
1 TTTATAATTAATTTAATAA
41169254 TTTATAATTAATTATAAT-A
1 TTTATAATTAATT-TAATAA
41169273 TTTA
1 TTTA
41169277 ATTACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATAATTAATTTAATAA
Found at i:41170287 original size:31 final size:31
Alignment explanation
Indices: 41170246--41170304 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
41170236 AAGTTTTTAA
* * *
41170246 ATTTTGAAAAACTCAAAAAATTATAAAAGGT
1 ATTTTCAAAAAATCAAAAAAGTATAAAAGGT
*
41170277 ATTTTCAAAAAATTAAAAAAGTATAAAA
1 ATTTTCAAAAAATCAAAAAAGTATAAAA
41170305 TATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (31 bp):
ATTTTCAAAAAATCAAAAAAGTATAAAAGGT
Found at i:41170295 original size:22 final size:23
Alignment explanation
Indices: 41170258--41170300 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41170248 TTTGAAAAAC
*
41170258 TCAAAAAATTATAAAAGGTATTT
1 TCAAAAAATTATAAAAAGTATTT
41170281 TCAAAAAATTA-AAAAAGTAT
1 TCAAAAAATTATAAAAAGTAT
41170301 AAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (23 bp):
TCAAAAAATTATAAAAAGTATTT
Found at i:41180676 original size:19 final size:18
Alignment explanation
Indices: 41180647--41180683 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41180637 AATTCTTTAA
41180647 TTCTGTAATTTAATATTT
1 TTCTGTAATTTAATATTT
*
41180665 TTCTGATAATTTACTATTT
1 TTCTG-TAATTTAATATTT
41180684 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (18 bp):
TTCTGTAATTTAATATTT
Found at i:41182325 original size:2 final size:2
Alignment explanation
Indices: 41182318--41182346 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41182308 TTTAAAACAT
41182318 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41182347 AGGTTATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41182602 original size:19 final size:19
Alignment explanation
Indices: 41182580--41182625 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
41182570 AAATGTATTT
41182580 ATATATTA-TTATATACATA
1 ATATATTATTTATATA-ATA
41182599 ATATATTATTTATATAATA
1 ATATATTATTTATATAATA
41182618 ATATATTA
1 ATATATTA
41182626 GAGGAGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTATTTATATAATA
Found at i:41183057 original size:22 final size:21
Alignment explanation
Indices: 41183030--41183098 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
41183020 TCGTTTTTAG
41183030 GGGTTTAGGGTATATTAAATTA
1 GGGTTTAGGGT-TATTAAATTA
*
41183052 GGGTTTAAGGTT-TT-AATTA
1 GGGTTTAGGGTTATTAAATTA
*
41183071 GGGTTTAGTGTTTATTAAATTA
1 GGGTTTAG-GGTTATTAAATTA
*
41183093 GCGTTT
1 GGGTTT
41183099 TAGTGTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 12 0.30
20 5 0.12
21 3 0.08
22 20 0.50
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.46
Consensus pattern (21 bp):
GGGTTTAGGGTTATTAAATTA
Found at i:41183077 original size:41 final size:42
Alignment explanation
Indices: 41183030--41183108 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
41183020 TCGTTTTTAG
*
41183030 GGGTTTAGGGTATATTAAATTAGGGTTTAAG-GTTTTAATTA
1 GGGTTTAGGGTATATTAAATTAGCGTTTAAGTGTTTTAATTA
* * *
41183071 GGGTTTAGTGTTTATTAAATTAGCGTTTTAGTGTTTTA
1 GGGTTTAGGGTATATTAAATTAGCGTTTAAGTGTTTTA
41183109 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 27 0.82
42 6 0.18
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (42 bp):
GGGTTTAGGGTATATTAAATTAGCGTTTAAGTGTTTTAATTA
Found at i:41183083 original size:19 final size:19
Alignment explanation
Indices: 41183047--41183108 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
41183037 GGGTATATTA
41183047 AATTAGGGTTTAAG-GTTTT
1 AATTAGGGTTT-AGTGTTTT
41183066 AATTAGGGTTTAGTGTTTATT
1 AATTAGGGTTTAGTG-TT-TT
*
41183087 AAATTAGCGTTTTAGTGTTTT
1 -AATTAG-GGTTTAGTGTTTT
41183108 A
1 A
41183109 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.05
19 12 0.32
20 3 0.08
21 4 0.11
22 8 0.22
23 8 0.22
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.50
Consensus pattern (19 bp):
AATTAGGGTTTAGTGTTTT
Found at i:41183107 original size:42 final size:41
Alignment explanation
Indices: 41183030--41183150 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 41
41183020 TCGTTTTTAG
* * * *
41183030 GGGTTTAGGGTATATTAAATTAGGGTTTAAGGTTTTAATTA
1 GGGTTTAGTGTTTATTAAATTAGCGTTTTAGGTTTTAATTA
*
41183071 GGGTTTAGTGTTTATTAAATTAGCGTTTTAGTGTTTTATTTA
1 GGGTTTAGTGTTTATTAAATTAGCGTTTTAG-GTTTTAATTA
*** *
41183113 ATTTTTAAGTGTTTATT-AATTAGTGTTTTAGAGTTTTA
1 GGGTTT-AGTGTTTATTAAATTAGCGTTTTAG-GTTTTA
41183151 GGAAAAATAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 27 0.40
42 31 0.46
43 10 0.15
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.52
Consensus pattern (41 bp):
GGGTTTAGTGTTTATTAAATTAGCGTTTTAGGTTTTAATTA
Found at i:41183127 original size:19 final size:18
Alignment explanation
Indices: 41183096--41183133 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41183086 TAAATTAGCG
41183096 TTTTAGTGTTTTATTTAAT
1 TTTTAGTGTTTTA-TTAAT
41183115 TTTTAAGTG-TTTATTAAT
1 TTTT-AGTGTTTTATTAAT
41183133 T
1 T
41183134 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTAGTGTTTTATTAAT
Found at i:41183303 original size:30 final size:28
Alignment explanation
Indices: 41183242--41183305 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
41183232 GGGGTTCGAA
* * *
41183242 AAAAATGATTTTGACGAGATGGGTTCTG
1 AAAAATAATTTTGACAAGATGAGTTCTG
41183270 AAAAATAATTTTGACAAGATGAGTTCTG
1 AAAAATAATTTTGACAAGATGAGTTCTG
41183298 AGAAAATA
1 A-AAAATA
41183306 TCCCAGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (28 bp):
AAAAATAATTTTGACAAGATGAGTTCTG
Found at i:41187807 original size:44 final size:43
Alignment explanation
Indices: 41187694--41187810 Score: 103
Period size: 44 Copynumber: 2.7 Consensus size: 43
41187684 AGCTCGTACA
* * *
41187694 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAACATCC
* ** * ** *
41187737 ATGTCTCTGTCTCAGACAG-GACCTTACACGTAAATCTCAA-ATCC
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGT-AATC-AAACATCC
41187781 ATGCCAATGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
41187811 ATAACTCATA
Statistics
Matches: 54, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
43 22 0.41
44 30 0.56
45 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAACATCC
Found at i:41195655 original size:44 final size:43
Alignment explanation
Indices: 41195545--41195659 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 43
41195535 AGCTCATACA
* *
41195545 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCC
* *
41195588 ATGCC-ACTGTCTCAGACAG-GGTCTTACATGTAAATCTCAA-ATCC
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGT-AATC-AAATATCC
41195632 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
41195660 CGATAACTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.03
43 26 0.43
44 29 0.48
45 4 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCC
Found at i:41200947 original size:7 final size:7
Alignment explanation
Indices: 41200935--41200969 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
41200925 TGTCTTTTAA
41200935 ATCACAT
1 ATCACAT
41200942 ATCACAT
1 ATCACAT
41200949 ATCACAT
1 ATCACAT
41200956 ATCACAT
1 ATCACAT
41200963 ATCACAT
1 ATCACAT
41200970 CTCATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCACAT
Found at i:41200961 original size:21 final size:21
Alignment explanation
Indices: 41200935--41200978 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41200925 TGTCTTTTAA
41200935 ATCACATATCACATATCACAT
1 ATCACATATCACATATCACAT
* *
41200956 ATCACATATCACATCTCATAT
1 ATCACATATCACATATCACAT
41200977 AT
1 AT
41200979 ATATTACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
ATCACATATCACATATCACAT
Found at i:41205549 original size:17 final size:18
Alignment explanation
Indices: 41205524--41205569 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
41205514 TATAAGAATA
*
41205524 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
41205541 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
41205559 ATTAAATTATA
1 ATTAAATTATA
41205570 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:41205562 original size:30 final size:30
Alignment explanation
Indices: 41205528--41205686 Score: 77
Period size: 28 Copynumber: 5.2 Consensus size: 30
41205518 AGAATAATTA
41205528 TATTAAGAATTTTATTAAATTATATATTTT
1 TATTAAGAATTTTATTAAATTATATATTTT
* * *
41205558 TATT-A-AATTATATTTAATAATA-ATTATT
1 TATTAAGAATTTTATTAAATTATATATT-TT
*
41205586 T-TT-A-AATTATATT---TTATAGTATTATAT
1 TATTAAGAATTTTATTAAATTATA-TATT-T-T
* *
41205613 ATATTATG-ATTTTAGTAAATTCATATAAGAATATTT
1 -TATTAAGAATTTTATTAAATT-ATAT----AT-TTT
41205649 AATATTAAGAATTTTATTAAATTATATATTTT
1 --TATTAAGAATTTTATTAAATTATATATTTT
41205681 TATTAA
1 TATTAA
41205687 ATTATATTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 38
0.68 0.06 0.26
Matches are distributed among these distances:
24 4 0.04
26 5 0.05
27 16 0.16
28 18 0.18
29 3 0.03
30 16 0.16
32 3 0.03
33 5 0.05
34 3 0.03
36 1 0.01
37 14 0.14
38 13 0.13
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TATTAAGAATTTTATTAAATTATATATTTT
Found at i:41205594 original size:27 final size:27
Alignment explanation
Indices: 41205520--41205599 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
41205510 TTCATATAAG
* * * *
41205520 AATAATTATATTAAGAATTTTATTAAAT
1 AATAATTATTTTTA-AATTATATTTAAT
*
41205548 TATATATT-TTTATTAAATTATATTTAAT
1 AATA-ATTATTT-TTAAATTATATTTAAT
41205576 AATAATTATTTTTAAATTATATTT
1 AATAATTATTTTTAAATTATATTT
41205600 TATAGTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 16 0.37
28 22 0.51
29 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTATTTTTAAATTATATTTAAT
Found at i:41205784 original size:120 final size:120
Alignment explanation
Indices: 41205407--41205833 Score: 793
Period size: 120 Copynumber: 3.5 Consensus size: 120
41205397 AGTTCTATCA
41205407 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
*
41205472 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT
66 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
41205527 -ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTTAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA-TTTTAA
41205591 ATTATATTTTATAGTATTATATATATTATGATTTTAGTAAATTCATATAAGAATATTT
65 ATTATATTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAGAATATTT
41205649 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
*
41205714 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATGTAAGAATATTT
66 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
*
41205769 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
41205834 ATATGAATAA
Statistics
Matches: 300, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
119 57 0.19
120 124 0.41
121 2 0.01
122 60 0.20
123 57 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
Found at i:41206063 original size:16 final size:16
Alignment explanation
Indices: 41206044--41206085 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
41206034 AATTGAATTA
41206044 CTATTAC-GCCTCTATT
1 CTATTACAG-CTCTATT
41206060 CTATTACAGCTCTATT
1 CTATTACAGCTCTATT
*
41206076 CCATTACAGC
1 CTATTACAGC
41206086 GAACCAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (16 bp):
CTATTACAGCTCTATT
Found at i:41233311 original size:39 final size:38
Alignment explanation
Indices: 41233218--41233317 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 38
41233208 AAAATCCTTG
* * *
41233218 TTATAATTATTGTAATTATAATTTATGATCGAATATTA
1 TTATAATTATTGTAATTATAATTTATCATCAAACATTA
* *
41233256 TTATAATTATTGTAATTGTAATTTTTCACTCAAACATTA
1 TTATAATTATTGTAATTATAATTTATCA-TCAAACATTA
41233295 TTATAATTA-TGATAATTATAATT
1 TTATAATTATTG-TAATTATAATT
41233318 ATTATATTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 27 0.50
39 27 0.50
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTATCATCAAACATTA
Found at i:41242848 original size:66 final size:66
Alignment explanation
Indices: 41242737--41242874 Score: 201
Period size: 66 Copynumber: 2.1 Consensus size: 66
41242727 AAAAGACATG
*
41242737 CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTTCAATTTCAATCCAAAT
1 CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTGCAATTTCAATCCAAAT
41242802 T
66 T
* * *
41242803 CCCATTATCCCAA-TAAACCTAATCTTTTTTTAACAGA-TTTCTTAGACTGCAATTTGAATCCAA
1 CCCATTATCCCAACT-AACCTAATCATTATTTAACAGACTTT-TTAGACTGCAATTTCAATCCAA
41242866 ATT
64 ATT
41242869 -CCATTA
1 CCCATTA
41242875 GTTGTGCAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 10 0.15
66 56 0.85
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (66 bp):
CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTGCAATTTCAATCCAAAT
T
Found at i:41253124 original size:7 final size:7
Alignment explanation
Indices: 41253109--41253142 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
41253099 AAAACATAAA
41253109 TTCATTT
1 TTCATTT
*
41253116 TTTATTT
1 TTCATTT
41253123 TTCATTT
1 TTCATTT
41253130 TTCA-TT
1 TTCATTT
41253136 TTCATTT
1 TTCATTT
41253143 GGGAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCATTT
Found at i:41253220 original size:51 final size:49
Alignment explanation
Indices: 41253122--41253225 Score: 113
Period size: 51 Copynumber: 2.1 Consensus size: 49
41253112 ATTTTTTATT
* * *
41253122 TTTCATTTTTCATTTTCATTTGGGAGAAAATCACATTCATTTTCAAATG
1 TTTCATTTCTCATTTTCATTTGGAAGAAAATCACATTCATTTCCAAATG
* *
41253171 ATTTCATTTCTCTATTTTCATTTTGAAGAAAACCTGA-ATT-ATTTCCAAATG
1 -TTTCATTTCTC-ATTTTCATTTGGAAGAAAA--TCACATTCATTTCCAAATG
41253222 TTTC
1 TTTC
41253226 TTATTGTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
50 14 0.30
51 27 0.59
52 3 0.07
53 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (49 bp):
TTTCATTTCTCATTTTCATTTGGAAGAAAATCACATTCATTTCCAAATG
Found at i:41263476 original size:4 final size:5
Alignment explanation
Indices: 41263445--41263483 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
41263435 GATTGAACAG
41263445 AAAACT AAAAT AAAAT AAAAT AAAAT -AAAT AAAAAT AAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
41263484 CAAAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.13
5 19 0.61
6 8 0.26
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41263604 original size:75 final size:75
Alignment explanation
Indices: 41263467--41263663 Score: 252
Period size: 75 Copynumber: 2.6 Consensus size: 75
41263457 AAATAAAATA
* * * ** *
41263467 AAATAAATAAAAATAAACAAAAGAAAGAAAAGGGATTTGATGGCAAAACATAGGTAACGATGATA
1 AAATAAA-AAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAACGATGACA
41263532 ATTAAACAATC
65 ATTAAACAATC
* * * * *
41263543 AAATAAAGAAAATAAACAAAACAAAGAAAAGGGAAGTAATGGCAAAATAGAGACAATGATGACAA
1 AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAACGATGACAA
41263608 TTAAACAATC
66 TTAAACAATC
* * *
41263618 AAATAAACAAAATAAA-AAAACAAAGACAAGGAAATTGATGGCAAAA
1 AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAA
41263664 AAATACGATA
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 26 0.25
75 72 0.69
76 7 0.07
ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15
Consensus pattern (75 bp):
AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAACGATGACAA
TTAAACAATC
Found at i:41275711 original size:6 final size:6
Alignment explanation
Indices: 41275700--41275737 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
41275690 AATTAAATAT
41275700 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AA
1 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AA
41275738 GATTATACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:41276016 original size:31 final size:31
Alignment explanation
Indices: 41275981--41276046 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
41275971 TTATAAGTTG
41275981 GTCATTGAACTATTCAAAAATTTTCATTCAA
1 GTCATTGAACTATTCAAAAATTTTCATTCAA
* * * *
41276012 GTCATTGGACTATTCAAAAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAAATTTTCATTCAA
41276043 GTCA
1 GTCA
41276047 CTGTGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAAATTTTCATTCAA
Found at i:41277382 original size:21 final size:22
Alignment explanation
Indices: 41277356--41277398 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41277346 ATTAGATTAT
41277356 TTTAAATT-TCAAAATGTTTTA
1 TTTAAATTATCAAAATGTTTTA
41277377 TTTAAATTATCAAAATGTTTTA
1 TTTAAATTATCAAAATGTTTTA
41277399 AATTTCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAAATTATCAAAATGTTTTA
Found at i:41279128 original size:5 final size:5
Alignment explanation
Indices: 41279118--41279146 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41279108 GTCTTTTACG
41279118 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
41279147 ATCTTCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:41281732 original size:26 final size:26
Alignment explanation
Indices: 41281677--41281734 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
41281667 TATTAATTGT
**
41281677 TAAAATTGTAAGTTTAAAACTAAGGA
1 TAAAATTGTAAGTTTAAAACTAAAAA
41281703 TAAAATTGTAA-TTATAAAA-TAAAAA
1 TAAAATTGTAAGTT-TAAAACTAAAAA
41281728 CTAAAAT
1 -TAAAAT
41281735 AAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (26 bp):
TAAAATTGTAAGTTTAAAACTAAAAA
Found at i:41282333 original size:25 final size:24
Alignment explanation
Indices: 41282250--41282452 Score: 111
Period size: 23 Copynumber: 8.7 Consensus size: 24
41282240 AATCTACTCT
** * *
41282250 ATTTGGACAGCCCTCATACATC-A
1 ATTTGGACAGCATTTATACACCAA
*
41282273 ATTTGGACAGCATTTATATACCAA
1 ATTTGGACAGCATTTATACACCAA
* *
41282297 A-CTAGACAGCATTT-TCACACCAAA
1 ATTTGGACAGCATTTAT-ACACC-AA
* *
41282321 ATTTGGACAGCATATATACAAC-A
1 ATTTGGACAGCATTTATACACCAA
* ** *
41282344 ATTTGGGCAGCACATATACAACAA
1 ATTTGGACAGCATTTATACACCAA
* *
41282368 A-TT-GAGCAGTATTTTTACACCAA
1 ATTTGGA-CAGCATTTATACACCAA
* *
41282391 AATTGGACAGC-TTATATACAACAA
1 ATTTGGACAGCATT-TATACACCAA
* * *
41282415 A-TTGGGCAGCATATATATACCAA
1 ATTTGGACAGCATTTATACACCAA
41282438 A-TT-GAGCAGCATTTA
1 ATTTGGA-CAGCATTTA
41282453 AGCATAAAAA
Statistics
Matches: 139, Mismatches: 29, Indels: 24
0.72 0.15 0.12
Matches are distributed among these distances:
22 3 0.02
23 97 0.70
24 22 0.16
25 16 0.12
26 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
ATTTGGACAGCATTTATACACCAA
Found at i:41282340 original size:71 final size:70
Alignment explanation
Indices: 41282265--41282521 Score: 266
Period size: 70 Copynumber: 3.7 Consensus size: 70
41282255 GACAGCCCTC
* * * *
41282265 ATACATCAATTTGGACAGCATTTATATACCAAACT-AGACAGCATTTTCACACCAAAATTTGGAC
1 ATACAACAATTTGGGCAGCATATATATACCAAATTGAG-CAGCATTTTCACACCAAAA-TTGGAC
41282329 AGCATAT
64 AGCATAT
* * * * *
41282336 ATACAACAATTTGGGCAGCACATATACAACAAATTGAGCAGTATTTTTACACCAAAATTGGACAG
1 ATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTCACACCAAAATTGGACAG
*
41282401 CTTAT
66 CATAT
* * **
41282406 ATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCA-TTTAAGCATAAAAATTGGACA
1 ATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTCA-CACCAAAATTGGACA
*
41282470 ACATAT
65 GCATAT
* * * * * ** *
41282476 ATGCAACAAATTGAGCAGTATATATACAAGAAATTGGGCAGCATTT
1 ATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTT
41282522 AAGTATCAAA
Statistics
Matches: 156, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
69 4 0.03
70 103 0.66
71 47 0.30
72 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (70 bp):
ATACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTCACACCAAAATTGGACAG
CATAT
Found at i:41282354 original size:23 final size:23
Alignment explanation
Indices: 41282323--41282519 Score: 171
Period size: 23 Copynumber: 8.5 Consensus size: 23
41282313 ACACCAAAAT
* *
41282323 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
*
41282346 TTGGGCAGCACATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
41282369 TTGAGCAGTATTTTTACACCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
41282393 TTGGACAGCTTATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
41282416 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * *
41282439 TTGAGCAGCATTTA-AGCATAAAAA
1 TTGGGCAGCATATATA-CA-ACAAA
* * *
41282463 TTGGACAACATATATGCAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
41282486 TTGAGCAGTATATATACAAGAAA
1 TTGGGCAGCATATATACAACAAA
41282509 TTGGGCAGCAT
1 TTGGGCAGCAT
41282520 TTAAGTATCA
Statistics
Matches: 131, Mismatches: 39, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
22 1 0.01
23 99 0.76
24 31 0.24
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:41282420 original size:70 final size:70
Alignment explanation
Indices: 41282303--41282521 Score: 269
Period size: 70 Copynumber: 3.1 Consensus size: 70
41282293 CCAAACTAGA
* * *
41282303 CAGCATTTTCACACCAAAATTTGGACAGCATATATACAACAATTTGGGCAGCACATATACAACAA
1 CAGCATTTTAACACCAAAA-TTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
41282368 ATTGAG
65 ATTGAG
* * * * *
41282374 CAGTATTTTTACACCAAAATTGGACAGCTTATATACAACAAATTGGGCAGCATATATATACCAAA
1 CAGCATTTTAACACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAAA
41282439 TTGAG
66 TTGAG
** * * * * *
41282444 CAGCA-TTTAAGCATAAAAATTGGACAACATATATGCAACAAATTGAGCAGTATATATACAAGAA
1 CAGCATTTTAA-CACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
*
41282508 ATTGGG
65 ATTGAG
41282514 CAGCATTT
1 CAGCATTT
41282522 AAGTATCAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
69 4 0.03
70 103 0.82
71 19 0.15
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (70 bp):
CAGCATTTTAACACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAAA
TTGAG
Found at i:41282464 original size:47 final size:46
Alignment explanation
Indices: 41282318--41282519 Score: 165
Period size: 47 Copynumber: 4.3 Consensus size: 46
41282308 TTTTCACACC
* * * * *
41282318 AAAATTTGGACAGCATATATACAACAATTTGGGCAGCACATATACA
1 AAAAATTGGGCAGCATATATACAACAAATTGAGCAGCATATATACA
* * * * * * *
41282364 ACAAATTGAGCAGTATTTTTACACCAAAATTG-GACAGCTTATATACA
1 AAAAATTGGGCAGCATATATACAAC-AAATTGAG-CAGCATATATACA
* * * *
41282411 ACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTA-AGCA
1 AAAAATTGGGCAGCATATATACAACAAATTGAGCAGCATATATA-CA
* * * *
41282457 TAAAAATTGGACAACATATATGCAACAAATTGAGCAGTATATATACA
1 -AAAAATTGGGCAGCATATATACAACAAATTGAGCAGCATATATACA
*
41282504 AGAAATTGGGCAGCAT
1 AAAAATTGGGCAGCAT
41282520 TTAAGTATCA
Statistics
Matches: 121, Mismatches: 29, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
45 1 0.01
46 46 0.38
47 73 0.60
48 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (46 bp):
AAAAATTGGGCAGCATATATACAACAAATTGAGCAGCATATATACA
Found at i:41283269 original size:28 final size:28
Alignment explanation
Indices: 41283237--41283390 Score: 245
Period size: 28 Copynumber: 5.5 Consensus size: 28
41283227 TTTAATAAGT
** * *
41283237 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
41283265 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41283293 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41283321 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
41283349 TAGCACACTTAGTACTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41283377 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41283391 TCGAAAGTCA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 116 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:41284737 original size:20 final size:20
Alignment explanation
Indices: 41284712--41284877 Score: 131
Period size: 20 Copynumber: 8.2 Consensus size: 20
41284702 CAATTATTTA
41284712 TGTTTGCACAT-TGATGCCCC
1 TGTTTGCACATCTG-TGCCCC
* **
41284732 TGTTTGCACATC-GATACCTT
1 TGTTTGCACATCTG-TGCCCC
*
41284752 TATTTGCACATCTGTGCCCC
1 TGTTTGCACATCTGTGCCCC
* ** *
41284772 TGTTTGCATATCTGCACCCT
1 TGTTTGCACATCTGTGCCCC
*
41284792 TGTTTGCACATCGGTGCCCC
1 TGTTTGCACATCTGTGCCCC
* *
41284812 TGCTTGCACATCTGTGTCCCT
1 TGTTTGCACATCTGTG-CCCC
* * *
41284833 TTTTTGCAC-TTTGGTGCCCT
1 TGTTTGCACATCT-GTGCCCC
**
41284853 TGACTGCACATCTGTGCCCC
1 TGTTTGCACATCTGTGCCCC
41284873 TGTTT
1 TGTTT
41284878 TACATTAATG
Statistics
Matches: 111, Mismatches: 30, Indels: 10
0.74 0.20 0.07
Matches are distributed among these distances:
20 95 0.86
21 16 0.14
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTTTGCACATCTGTGCCCC
Found at i:41286342 original size:5 final size:5
Alignment explanation
Indices: 41286332--41286358 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41286322 GTTTATTTAG
41286332 TTTGT TTTGT TTTGT TTTGT TTTGT TT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TT
41286359 GCTTGAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTGT
Found at i:41296368 original size:13 final size:13
Alignment explanation
Indices: 41296352--41296383 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41296342 TTTTTGTTTC
41296352 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
41296365 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
41296378 TTTTTT
1 TTTTTT
41296384 ACAAACATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:41299593 original size:20 final size:20
Alignment explanation
Indices: 41299564--41299603 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41299554 TATAACTTTA
41299564 TAAACACAACCCAATAACCC
1 TAAACACAACCCAATAACCC
*
41299584 TAAACCCAACCCAATAACCC
1 TAAACACAACCCAATAACCC
41299604 AAGGTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.42, G:0.00, T:0.10
Consensus pattern (20 bp):
TAAACACAACCCAATAACCC
Found at i:41300211 original size:9 final size:9
Alignment explanation
Indices: 41300197--41300225 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41300187 TTTTTTTTAT
41300197 AATTAAAAA
1 AATTAAAAA
41300206 AATT-AAAA
1 AATTAAAAA
41300214 AATTAAAAA
1 AATTAAAAA
41300223 AAT
1 AAT
41300226 GTGTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTAAAAA
Found at i:41303451 original size:28 final size:28
Alignment explanation
Indices: 41303408--41303464 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41303398 TTTAAAAAGA
41303408 AAGGATATTGAATACTCTACAGCTGATC
1 AAGGATATTGAATACTCTACAGCTGATC
*
41303436 AAGGATATTGAGTACTCTACAGCTGATC
1 AAGGATATTGAATACTCTACAGCTGATC
41303464 A
1 A
41303465 GGTGTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (28 bp):
AAGGATATTGAATACTCTACAGCTGATC
Found at i:41306501 original size:43 final size:42
Alignment explanation
Indices: 41306453--41306615 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 42
41306443 ACGTCGCTAA
* * * *
41306453 CTTTAGCGGCGTTTTTTTCTAAAATGTCGTTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCTC-AAAATGCCGCTAAAGACCAAGAC
* * * *
41306496 CTTTAGGGGTGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCTC-AAAATGCCGCTAAAGACCAAGAC
**
41306539 CTTTAGCGGCGCTTTTCTCACAAATGCCGCTAAAGACCACTAC
1 CTTTAGCGGCGCTTTTCTCA-AAATGCCGCTAAAGACCAAGAC
* * * *
41306582 CTTTAGCGGTGCTTCTCGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCTC-AAAATGCCGCTAAA
41306616 AATATAACCT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.01
43 97 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTCTCAAAATGCCGCTAAAGACCAAGAC
Found at i:41306545 original size:86 final size:86
Alignment explanation
Indices: 41306453--41306615 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
41306443 ACGTCGCTAA
* * * * * *
41306453 CTTTAGCGGCGTTTTTTTCTA-AAATGTCGTTAAAGACCAAGACCTTTAGGGGTGCTTTTCCCAA
1 CTTTAGCGGCGCTTTTCTC-ACAAATGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTCTCCCAA
41306517 AAACGCCGCTAAAGACCAAGAC
65 AAACGCCGCTAAAGACCAAGAC
** *
41306539 CTTTAGCGGCGCTTTTCTCACAAATGCCGCTAAAGACCACTACCTTTAGCGGTGCTTCTCGCAAA
1 CTTTAGCGGCGCTTTTCTCACAAATGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTCTCCCAAA
41306604 AACGCCGCTAAA
66 AACGCCGCTAAA
41306616 AATATAACCT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 1 0.01
86 66 0.99
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTCTCACAAATGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTCTCCCAAA
AACGCCGCTAAAGACCAAGAC
Found at i:41307359 original size:23 final size:23
Alignment explanation
Indices: 41307309--41307360 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
41307299 GTTAGGTGTC
* *
41307309 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
41307332 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
41307355 AGTATG
1 AGTATG
41307361 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:41309234 original size:12 final size:13
Alignment explanation
Indices: 41309212--41309240 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41309202 AAGTTTTATT
41309212 TTTATTTTATTTA
1 TTTATTTTATTTA
41309225 TTTA-TTTATTTA
1 TTTATTTTATTTA
41309237 TTTA
1 TTTA
41309241 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:41311611 original size:18 final size:18
Alignment explanation
Indices: 41311590--41311628 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41311580 GATTGAGAGT
* *
41311590 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
41311608 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
41311626 GAA
1 GAA
41311629 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:41315429 original size:18 final size:18
Alignment explanation
Indices: 41315406--41315444 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41315396 GATTGAGAGT
* *
41315406 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
41315424 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
41315442 GAA
1 GAA
41315445 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:41318106 original size:31 final size:31
Alignment explanation
Indices: 41318065--41318131 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
41318055 TCATTTCTTG
*
41318065 CAACTGATAAATTAGAAGAGATAGAGAATGA
1 CAACTAATAAATTAGAAGAGATAGAGAATGA
*
41318096 CAACTAATAAATTAGAAGAGATAGAGAATGG
1 CAACTAATAAATTAGAAGAGATAGAGAATGA
41318127 CAACT
1 CAACT
41318132 CAACAGAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (31 bp):
CAACTAATAAATTAGAAGAGATAGAGAATGA
Found at i:41319760 original size:26 final size:26
Alignment explanation
Indices: 41319729--41319791 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
41319719 GCTAATTAAT
*
41319729 CTAAACCCTAACCCGACCATGAATCC
1 CTAAACCCTAACACGACCATGAATCC
* *
41319755 CTAAACCCTAACATGACCCTGAATCC
1 CTAAACCCTAACACGACCATGAATCC
*
41319781 CTAACCCCTAA
1 CTAAACCCTAA
41319792 ACATTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.17
Consensus pattern (26 bp):
CTAAACCCTAACACGACCATGAATCC
Found at i:41320675 original size:41 final size:41
Alignment explanation
Indices: 41320618--41320910 Score: 370
Period size: 41 Copynumber: 7.1 Consensus size: 41
41320608 TTTTATTATT
* * * * *
41320618 ATTAGCGTCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
41320659 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
*
41320700 ATTAGCGACGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * *
41320741 ATTAGCGGCGCTTCATCAAAAAATGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCTTC-TCCAAAAACGCCGCTAAAGGCCCGAGC
* * *
41320783 AATAGCGGAGCTTCTACAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * *
41320824 ATTAGCGGCGCTTATCCAAAAACGCTGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
41320865 ATTAGCAGCGCTTCTCCAAAAACACTGCTAAAGGCCCGAGA
1 ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
41320906 ATTAG
1 ATTAG
41320911 TGGTGCTATA
Statistics
Matches: 220, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 184 0.84
42 36 0.16
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:41320842 original size:124 final size:123
Alignment explanation
Indices: 41320646--41320904 Score: 365
Period size: 124 Copynumber: 2.1 Consensus size: 123
41320636 AAAACGTCGT
* * * * *
41320646 TAAAGGCCCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCTCGAGCATTAGCGACGC
1 TAAAGGCCCGAGCAATAGCGGAGCTTCTACAAAAACACCGCTAAAGGCCCGAGCATTAGCGACGC
* * **
41320711 TTCTCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCATCAAAAAATGCCAC
66 TTATCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCAGCGCTTC-TCAAAAAACACCAC
* *
41320770 TAAAGGCCCGAGCAATAGCGGAGCTTCTACAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
1 TAAAGGCCCGAGCAATAGCGGAGCTTCTACAAAAACACCGCTAAAGGCCCGAGCATTAGCGACGC
* * * **
41320835 TTATCCAAAAACGCTGCTAAAGGCTCGAGCATTAGCAGCGCTTCTCCAAAAACACTGC
66 TTATCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCAGCGCTTCTCAAAAAACACCAC
41320893 TAAAGGCCCGAG
1 TAAAGGCCCGAG
41320905 AATTAGTGGT
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
123 21 0.18
124 98 0.82
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (123 bp):
TAAAGGCCCGAGCAATAGCGGAGCTTCTACAAAAACACCGCTAAAGGCCCGAGCATTAGCGACGC
TTATCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCAGCGCTTCTCAAAAAACACCAC
Found at i:41322108 original size:41 final size:41
Alignment explanation
Indices: 41322053--41322249 Score: 283
Period size: 41 Copynumber: 4.8 Consensus size: 41
41322043 GAATGTAATA
* * *
41322053 CAGACGTTACGTCTAGCAGGCTTAATGCCAGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
41322094 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
41322135 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
41322176 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
41322217 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
41322250 TACTGAATCA
Statistics
Matches: 148, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 141 0.95
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:41322157 original size:82 final size:80
Alignment explanation
Indices: 41322053--41322278 Score: 285
Period size: 82 Copynumber: 2.8 Consensus size: 80
41322043 GAATGTAATA
* * *
41322053 CAGACGTTACGTCTAGCAGGCTTAATGCCAGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TAATTCAGACTTTAAGTCTAGCAGGCTTA
41322118 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* *
41322135 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATA-A-TTCAGACTTTAAGTCTAGCAGGCTTA
41322200 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * * *
41322217 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAGCCTAGCAGGC
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG-A-T-AATTCAGACTTTAAGTCTAGCAGGC
41322279 AAATTGCCGG
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
80 2 0.02
81 5 0.04
82 116 0.91
83 1 0.01
84 2 0.02
85 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (80 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATAATTCAGACTTTAAGTCTAGCAGGCTTAAT
GCCGGTGATACATTT
Found at i:41322287 original size:123 final size:123
Alignment explanation
Indices: 41322063--41322289 Score: 295
Period size: 123 Copynumber: 1.8 Consensus size: 123
41322053 CAGACGTTAC
*
41322063 GTCTAGCAGGCTTAATGCCAGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCAGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
* * *
41322128 TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
66 TACATATCAGACTTTAAGCCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
* *
41322186 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGG
1 GTCTAGCAGGCTTAATGCCAGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCTTAA-TGCCGG
*
41322248 TG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGC-AAATTGCCGGT
63 TGATACAT--ATCAGACTTTAAGCCTAGCAGGCTAAA-TGCCGGT
41322290 CAATCTGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
121 3 0.03
122 10 0.11
123 78 0.86
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCAGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
TACATATCAGACTTTAAGCCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
Found at i:41329266 original size:41 final size:41
Alignment explanation
Indices: 41329211--41329407 Score: 283
Period size: 41 Copynumber: 4.8 Consensus size: 41
41329201 GAATGTAATA
* *
41329211 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
41329252 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
*
41329293 TAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
41329334 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
41329375 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
41329408 TACTGAATCA
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 140 0.95
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:41329321 original size:82 final size:80
Alignment explanation
Indices: 41329211--41329436 Score: 285
Period size: 82 Copynumber: 2.8 Consensus size: 80
41329201 GAATGTAATA
* *
41329211 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TAATTCAGACTTTAAGTCTAGCAGGCTTA
41329276 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * *
41329293 TAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATA-A-TTCAGACTTTAAGTCTAGCAGGCTTA
41329358 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * * *
41329375 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAGCCTAGCAGGC
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG-A-T-AATTCAGACTTTAAGTCTAGCAGGC
41329437 AAATTGCCGG
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
80 2 0.02
81 5 0.04
82 115 0.91
83 1 0.01
84 2 0.02
85 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (80 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATAATTCAGACTTTAAGTCTAGCAGGCTTAAT
GCCGGTGATACATTT
Found at i:41329445 original size:123 final size:123
Alignment explanation
Indices: 41329221--41329447 Score: 295
Period size: 123 Copynumber: 1.8 Consensus size: 123
41329211 CAGACGTTAC
*
41329221 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
* * * *
41329286 TACATTTTAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
66 TACATATCAGACTTTAAGCCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
*
41329344 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGG
1 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCTTAA-TGCCGG
*
41329406 TG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGC-AAATTGCCGGT
63 TGATACAT--ATCAGACTTTAAGCCTAGCAGGCTAAA-TGCCGGT
41329448 CAATCTGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
121 3 0.03
122 10 0.11
123 78 0.86
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
TACATATCAGACTTTAAGCCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
Found at i:41330586 original size:39 final size:40
Alignment explanation
Indices: 41330537--41330630 Score: 122
Period size: 39 Copynumber: 2.4 Consensus size: 40
41330527 GGGCTTAGGC
41330537 TTTTT-GCGGCGCTTTTCA-AAAAACGCTGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTTCATAAAAACGCTGCTAATGCTTGA
* *
41330575 TTTTTAGCGGCGTTTTTATAAAAGCGCTGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCATAAAAACGCTGCTAATGCTTGA
* *
41330615 TTTTTAGTGGCATTTT
1 TTTTTAGCGGCGTTTT
41330631 TTGTCCAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 10 0.20
39 24 0.49
40 15 0.31
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCATAAAAACGCTGCTAATGCTTGA
Found at i:41332722 original size:24 final size:23
Alignment explanation
Indices: 41332684--41332738 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 23
41332674 ACAAAGATAG
41332684 TTTTAA-ATAAACTATATCTTTA
1 TTTTAAGATAAACTATATCTTTA
41332706 TTTTAAGATATAACTATATCTTTA
1 TTTTAAGATA-AACTATATCTTTA
41332730 TTTTAAGAT
1 TTTTAAGAT
41332739 TTTACCTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 22 0.71
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTAAGATAAACTATATCTTTA
Found at i:41336242 original size:29 final size:29
Alignment explanation
Indices: 41336200--41336256 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
41336190 TGAAAAGTGA
41336200 CATGCCAATAGGGTTTTGTGCACGCTTGG
1 CATGCCAATAGGGTTTTGTGCACGCTTGG
41336229 CATGCCAATAGGGTTTTGTGCACGCTTG
1 CATGCCAATAGGGTTTTGTGCACGCTTG
41336257 TATGGGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.32
Consensus pattern (29 bp):
CATGCCAATAGGGTTTTGTGCACGCTTGG
Found at i:41337288 original size:36 final size:34
Alignment explanation
Indices: 41337215--41337328 Score: 104
Period size: 34 Copynumber: 3.3 Consensus size: 34
41337205 GAATGTATTT
* * * * *
41337215 ATATATATAATTTTTCAAATACATATGCCAAAAGC
1 ATATATAT-ACTTATCAACTACATATGCCGAATGC
*
41337250 ATATATTTATACTTATCAACTACATGTGCCGAATGC
1 ATATA--TATACTTATCAACTACATATGCCGAATGC
* *
41337286 ATATATATACTTAT-AATCCACATATGTCGAATGC
1 ATATATATACTTATCAA-CTACATATGCCGAATGC
*
41337320 ATACATATA
1 ATATATATA
41337329 TATATACAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.03
34 31 0.47
35 5 0.08
36 25 0.38
37 3 0.05
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (34 bp):
ATATATATACTTATCAACTACATATGCCGAATGC
Found at i:41337778 original size:41 final size:41
Alignment explanation
Indices: 41337497--41337767 Score: 409
Period size: 41 Copynumber: 6.6 Consensus size: 41
41337487 TTTAAACAGA
** * *
41337497 TTCACCGATACTTAGCCTGCTAAGCTTATAACCTGATTCAAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTC-AG
* *
41337539 TT-ACTGGCACTTAGCCTACTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* * * *
41337579 ATCACCGGCAGTTAGCCAGCTAAGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
41337620 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* *
41337661 ATCACCGGCATTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
41337702 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
*
41337743 TTCACCGGCACTTAGCTTGCTAGGC
1 TTCACCGGCACTTAGCCTGCTAGGC
41337768 GCAAAGCCTG
Statistics
Matches: 207, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 2 0.01
41 203 0.98
42 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
Found at i:41338189 original size:23 final size:23
Alignment explanation
Indices: 41338161--41338207 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
41338151 ATAACCATAC
*
41338161 ACATTCGAACCTCACATATACAT
1 ACATTCAAACCTCACATATACAT
41338184 ACATTCAAACCTCACATATACAT
1 ACATTCAAACCTCACATATACAT
41338207 A
1 A
41338208 TATAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.26
Consensus pattern (23 bp):
ACATTCAAACCTCACATATACAT
Found at i:41346763 original size:51 final size:51
Alignment explanation
Indices: 41346569--41346763 Score: 218
Period size: 51 Copynumber: 3.8 Consensus size: 51
41346559 GAAGTTGCTA
* * *
41346569 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAAT
* * ***
41346619 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CTGGAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGATGAAAAT
* * *
41346669 CGATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
* *
41346721 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAATCGG
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
41346764 GTATCATTTA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
49 3 0.03
50 38 0.32
51 76 0.63
52 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
Found at i:41357433 original size:40 final size:40
Alignment explanation
Indices: 41357389--41357615 Score: 384
Period size: 40 Copynumber: 5.7 Consensus size: 40
41357379 GCAAACACAT
* * *
41357389 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41357429 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41357469 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
41357509 TTGCCTTCGGGTCATAGCCCGGA-ATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41357548 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41357588 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
41357616 TCCAATGCTC
Statistics
Matches: 180, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
39 37 0.21
40 143 0.79
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:41357565 original size:119 final size:120
Alignment explanation
Indices: 41357389--41357615 Score: 393
Period size: 119 Copynumber: 1.9 Consensus size: 120
41357379 GCAAACACAT
* *
41357389 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
*
41357454 TATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
41357509 TTGCCTTCGGGTCATAGCCCGGA-ATATCAACTCGCGTAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
*
41357573 TATCAACTCGCGTAATTGCCTTCGGGTCTTAGCCCGGATATAT
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATAT
41357616 TCCAATGCTC
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
119 80 0.79
120 21 0.21
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (120 bp):
TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:41357572 original size:79 final size:80
Alignment explanation
Indices: 41357389--41357615 Score: 384
Period size: 79 Copynumber: 2.9 Consensus size: 80
41357379 GCAAACACAT
* * *
41357389 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
*
41357454 TATCAACTTGCATAA
66 TATCAACTCGCATAA
*
41357469 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGA-A
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
*
41357533 TATCAACTCGCGTAA
66 TATCAACTCGCATAA
*
41357548 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
41357613 TAT
66 TAT
41357616 TCCAATGCTC
Statistics
Matches: 138, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
79 75 0.54
80 63 0.46
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (80 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAA
Found at i:41360428 original size:50 final size:50
Alignment explanation
Indices: 41360310--41360432 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
41360300 ACATTAGGGG
* * * * *
41360310 GATGAG-AC-CCCATGTAAGACCATGTCTGGGACATGGCGTTGGTATCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
* ***
41360358 GATGAGAAGTCCCCCATAAGACCATGTCTGGAACATGGCATGGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
* *
41360408 TATGAGAACTCTCATGTAAGACCAT
1 GATGAGAACTCCCATGTAAGACCAT
41360433 ATCTAGGATA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
48 6 0.10
49 1 0.02
50 51 0.88
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (50 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
Found at i:41371011 original size:42 final size:43
Alignment explanation
Indices: 41370921--41371016 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
41370911 CTAACCATAT
* * * * * *
41370921 ATTTATGGCAGCTTGACTGTAATTACTGGTGGCTTGTCCAGAT
1 ATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGTCCACAG
*
41370964 CTTTCTGGCAGCTTAACTGCAA-AACTGGTGGCTTGTCCACAG
1 ATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGTCCACAG
*
41371006 ATTTCTAGCAG
1 ATTTCTGGCAG
41371017 TATATCTACA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 26 0.59
43 18 0.41
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (43 bp):
ATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGTCCACAG
Found at i:41373121 original size:21 final size:22
Alignment explanation
Indices: 41373096--41373138 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
41373086 AAAAAAATTG
* *
41373096 AATTATTTAATAT-TATTTTTA
1 AATTAGTTAAAATGTATTTTTA
41373117 AATTAGTTAAAATGTATTTTTA
1 AATTAGTTAAAATGTATTTTTA
41373139 TTTTATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
AATTAGTTAAAATGTATTTTTA
Found at i:41373194 original size:20 final size:20
Alignment explanation
Indices: 41373169--41373208 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41373159 ATATAACCAT
41373169 ATAAACACAACCCAATAACC
1 ATAAACACAACCCAATAACC
*
41373189 ATAAACTCAACCCAATAACC
1 ATAAACACAACCCAATAACC
41373209 CAAGGTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (20 bp):
ATAAACACAACCCAATAACC
Found at i:41374011 original size:50 final size:49
Alignment explanation
Indices: 41373950--41374048 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
41373940 AATAAAGTTT
*
41373950 GTCATGTATTATGTAACTCC-TATATTAATTCAGTTTGCATCTTAAATTAA
1 GTCATGCATTATGTAAC-CCATATATTAATTCAGTTTGCATCTT-AATTAA
* * * *
41374000 GTCATGCATTATGTAACCCATTTGTTTATTTAGTTTGCATCTTAATTAA
1 GTCATGCATTATGTAACCCATATATTAATTCAGTTTGCATCTTAATTAA
41374049 ACTATGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 8 0.19
50 35 0.81
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.45
Consensus pattern (49 bp):
GTCATGCATTATGTAACCCATATATTAATTCAGTTTGCATCTTAATTAA
Found at i:41376902 original size:18 final size:18
Alignment explanation
Indices: 41376876--41376924 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
41376866 TTTTAAAAAT
*
41376876 CACAAGAAATAAATCTTA
1 CACAAGAAACAAATCTTA
* *
41376894 CAGAAGAAACAAATCTTG
1 CACAAGAAACAAATCTTA
41376912 CACAAGAAACAAA
1 CACAAGAAACAAA
41376925 CTCCCAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (18 bp):
CACAAGAAACAAATCTTA
Found at i:41381154 original size:13 final size:13
Alignment explanation
Indices: 41381117--41381157 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
41381107 TTTTGCTTTA
41381117 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
41381130 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
41381143 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
41381156 CT
1 CT
41381158 TTGCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:41391982 original size:2 final size:2
Alignment explanation
Indices: 41391977--41392025 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
41391967 TTTTTTATAA
41391977 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41392019 AG AG AG A
1 AG AG AG A
41392026 TCAGTGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.