Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:3646761 original size:17 final size:17
Alignment explanation
Indices: 3646739--3646788 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
3646729 TTAATATTTT
3646739 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
*
3646756 GTATTTAATGTATTTAA
1 GTATTTAATTTATTTAA
* *
3646773 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
3646789 TTTTTTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:3650257 original size:112 final size:112
Alignment explanation
Indices: 3649877--3650249 Score: 629
Period size: 112 Copynumber: 3.3 Consensus size: 112
3649867 TTTACTATCG
** * * * * *
3649877 GTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATAGATACAT
* *
3649942 TTTTATAAAGTATCGACACTTTCAATATATCCAGTAACACTTTACCT
66 TTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCT
*
3649989 GTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCTGTTATATTGTTATAGATAGATACAT
1 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATAGATACAT
3650054 TTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCT
66 TTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCT
* *
3650101 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTTGTTATATTGTTATCGATAGATACAT
1 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATAGATACAT
*
3650166 TTTTATAAAGTATCGACACTTTCAATATATCTAGTAGCGCTTTACCT
66 TTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCT
3650213 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
1 GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
3650250 ATTGTTATTA
Statistics
Matches: 247, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 247 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (112 bp):
GTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATAGATACAT
TTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCT
Found at i:3656433 original size:21 final size:21
Alignment explanation
Indices: 3656407--3656461 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3656397 GAGTGTGGGT
3656407 GCATCGGTACACTCTCAAGGG
1 GCATCGGTACACTCTCAAGGG
3656428 GCATCGGTACACTCTCAAGGG
1 GCATCGGTACACTCTCAAGGG
*
3656449 GCATCAGTACACT
1 GCATCGGTACACT
3656462 ATGTGTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (21 bp):
GCATCGGTACACTCTCAAGGG
Found at i:3658878 original size:17 final size:18
Alignment explanation
Indices: 3658858--3658891 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3658848 TTTTTATTTC
*
3658858 AAATTTATT-TTTTTGAA
1 AAATTGATTGTTTTTGAA
3658875 AAATTGATTGTTTTTGA
1 AAATTGATTGTTTTTGA
3658892 TGAAATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (18 bp):
AAATTGATTGTTTTTGAA
Found at i:3659297 original size:23 final size:22
Alignment explanation
Indices: 3659260--3659330 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
3659250 TGCAGAGTGT
*
3659260 ATCGATGCACATTCAAGGCATGC
1 ATCGATGCATATTCAAGG-ATGC
*
3659283 ATC-AGTGCATTTTCATA-G-TGC
1 ATCGA-TGCATATTCA-AGGATGC
3659304 ATCGATGCATATTCAAGGAATGC
1 ATCGATGCATATTCAAGG-ATGC
3659327 ATCG
1 ATCG
3659331 GTACACTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
20 1 0.03
21 16 0.41
22 2 0.05
23 19 0.49
24 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (22 bp):
ATCGATGCATATTCAAGGATGC
Found at i:3659327 original size:44 final size:44
Alignment explanation
Indices: 3659255--3659358 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 44
3659245 TACATTGCAG
* * * *
3659255 AGTGTATCGATGCACATTCAAGGCATGCATCAGTGCATTTTCAT
1 AGTGTATCGATGCATATTCAAGGAATGCATCAGTACACTTTCAT
* *
3659299 AGTGCATCGATGCATATTCAAGGAATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCATATTCAAGGAATGCATCAGTACACTTTCAT
*
3659343 AGTGTATCAATGCATA
1 AGTGTATCGATGCATA
3659359 GTGCACAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
AGTGTATCGATGCATATTCAAGGAATGCATCAGTACACTTTCAT
Found at i:3664888 original size:20 final size:21
Alignment explanation
Indices: 3664849--3664888 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3664839 GAAGCTTTAA
* *
3664849 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
3664870 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
3664889 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:3671898 original size:24 final size:24
Alignment explanation
Indices: 3671828--3671899 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
3671818 ACCATGTTTG
**
3671828 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTGCACATAGTA
*
3671852 GTATCGATACTCACTGGAC-----A
1 GTATCGATACT-ACTGCACATAGTA
3671872 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
3671896 GTAT
1 GTAT
3671900 TAGTATTCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 6 0.15
20 12 0.31
24 16 0.41
25 5 0.13
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (24 bp):
GTATCGATACTACTGCACATAGTA
Found at i:3672020 original size:18 final size:17
Alignment explanation
Indices: 3671983--3672016 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3671973 ATACTATCTC
3671983 TTTGTTTTTGACTCCAA
1 TTTGTTTTTGACTCCAA
*
3672000 TTTGTTTTTTACTCCAA
1 TTTGTTTTTGACTCCAA
3672017 ATTTTAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTGTTTTTGACTCCAA
Found at i:3672089 original size:24 final size:22
Alignment explanation
Indices: 3672057--3672129 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 22
3672047 ACCATGTTTG
3672057 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTAC--TACATAGTA
*
3672081 GTATCGATACT-C-AC-TAGACA
1 GTATCGATACTACTACATAG-TA
3672101 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACT--ACATAGTA
3672125 GTATC
1 GTATC
3672130 AGTATTCCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
19 3 0.07
20 14 0.34
21 1 0.02
23 1 0.02
24 19 0.46
25 3 0.07
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (22 bp):
GTATCGATACTACTACATAGTA
Found at i:3672172 original size:229 final size:218
Alignment explanation
Indices: 3671714--3672341 Score: 956
Period size: 229 Copynumber: 2.9 Consensus size: 218
3671704 CTACACAGTA
* * *
3671714 TTGATACCCTTACATATAGTAGTACCGATACCATGGTCATGGTACAGATACTA-C-C----TCTT
1 TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACCGATACTATCTCTTTGTTTT
*
3671773 TGTTTTTTACTCCAAATTTTAACAGAATGCAAAACCGGTACCGATACCATGTTTGGTATCGATAC
66 TGTTTTTTACTCCAAATTTTAACAGAATGCAAAACAGGTACCGATACCATGTTTGGTATCGATAC
* *
3671838 TACTTTACATAGTAGTATCGATACTCACTGGACAGTATCGATACTACTGCACATAGTAGTATTAG
131 TACTTTACATAGTAGTATCGATACTCACTAGACAGTATCGATACTACTGCACATAGTAGTATCAG
3671903 TATTCCTTTAGTAGTATCAATAC
196 TATTCCTTTAGTAGTATCAATAC
3671926 TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACCGATACTATCTCTTTGTTTT
1 TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACCGATACTATCTCTTTG----
*
3671991 TGACTCCAATTTGTTTTTTACTCCAAATTTTAACAGAATGCAAAACGGGTACCGATACCATGTTT
62 T---T----TTTGTTTTTTACTCCAAATTTTAACAGAATGCAAAACAGGTACCGATACCATGTTT
3672056 GGTATCGATACTACTTTACATAGTAGTATCGATACTCACTAGACAGTATCGATACTACTGCACAT
120 GGTATCGATACTACTTTACATAGTAGTATCGATACTCACTAGACAGTATCGATACTACTGCACAT
3672121 AGTAGTATCAGTATTCCTTTAGTAGTATCAATAC
185 AGTAGTATCAGTATTCCTTTAGTAGTATCAATAC
*
3672155 TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACTGATACTATCTCTTTGTTTT
1 TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACCGATACTATCTCTTTGTTTT
* * *
3672220 TG------ACTCCAAATTTTAACAAAATGCAAAACAGGTACCGATACCGTGTTCGGTATCGATAC
66 TGTTTTTTACTCCAAATTTTAACAGAATGCAAAACAGGTACCGATACCATGTTTGGTATCGATAC
* *
3672279 TACTTTACATAGTAGTATCGATACTCACTAGACAATATCAATACTACTGCACATAGTAGTATC
131 TACTTTACATAGTAGTATCGATACTCACTAGACAGTATCGATACTACTGCACATAGTAGTATC
3672342 GATACTCCTA
Statistics
Matches: 386, Mismatches: 13, Indels: 34
0.89 0.03 0.08
Matches are distributed among these distances:
212 165 0.43
213 1 0.00
214 1 0.00
218 4 0.01
222 2 0.01
225 1 0.00
229 212 0.55
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (218 bp):
TTGATACCCTTACATATCGTAGTACCGATACCATGGTCATGGTACCGATACTATCTCTTTGTTTT
TGTTTTTTACTCCAAATTTTAACAGAATGCAAAACAGGTACCGATACCATGTTTGGTATCGATAC
TACTTTACATAGTAGTATCGATACTCACTAGACAGTATCGATACTACTGCACATAGTAGTATCAG
TATTCCTTTAGTAGTATCAATAC
Found at i:3672324 original size:44 final size:43
Alignment explanation
Indices: 3672270--3672352 Score: 130
Period size: 44 Copynumber: 1.9 Consensus size: 43
3672260 CCGTGTTCGG
* **
3672270 TATCGATACTACTTTACATAGTAGTATCGATACTCACTAGACAA
1 TATCAATACTACTGCACATAGTAGTATCGATACTC-CTAGACAA
3672314 TATCAATACTACTGCACATAGTAGTATCGATACTCCTAG
1 TATCAATACTACTGCACATAGTAGTATCGATACTCCTAG
3672353 GGCAGTATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 4 0.11
44 32 0.89
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (43 bp):
TATCAATACTACTGCACATAGTAGTATCGATACTCCTAGACAA
Found at i:3674198 original size:47 final size:47
Alignment explanation
Indices: 3674135--3674229 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
3674125 AAGATTATTC
* *
3674135 ATTTGATGAGTCATTAGAGGAATATTATGAGTTGACCTCGGATTATG
1 ATTTGATAAGTCATTAGAGGAATATTATGAGTTGACCTCGGATGATG
* * *
3674182 ATTTGATAAGTTATTAGAGGAATATTATGAGTTGGCCTTGGATGATG
1 ATTTGATAAGTCATTAGAGGAATATTATGAGTTGACCTCGGATGATG
3674229 A
1 A
3674230 GAAGTTGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (47 bp):
ATTTGATAAGTCATTAGAGGAATATTATGAGTTGACCTCGGATGATG
Found at i:3678185 original size:21 final size:21
Alignment explanation
Indices: 3678140--3678231 Score: 93
Period size: 20 Copynumber: 4.5 Consensus size: 21
3678130 CTCTTGCTAG
* * *
3678140 GTATCGATACTGCTAGCATA-
1 GTATCGATACTACTTGAATAC
3678160 GTATCGATACTACTTGAATGA-
1 GTATCGATACTACTTGAAT-AC
*
3678181 GTATCGATACTA-TT-CATAC
1 GTATCGATACTACTTGAATAC
*
3678200 GTTATCGATACTACTTGAATAG
1 G-TATCGATACTACTTGAATAC
3678222 GTATCGATAC
1 GTATCGATAC
3678232 CCAAGTATCA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 29 0.48
21 24 0.39
22 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
GTATCGATACTACTTGAATAC
Found at i:3678709 original size:18 final size:18
Alignment explanation
Indices: 3678688--3678722 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3678678 AAATTAAAAA
3678688 ATGTGTTTT-ATTTAATTG
1 ATGT-TTTTGATTTAATTG
3678706 ATGTTTTTGATTTAATT
1 ATGTTTTTGATTTAATT
3678723 ACATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
ATGTTTTTGATTTAATTG
Found at i:3688484 original size:21 final size:21
Alignment explanation
Indices: 3688460--3688531 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
3688450 GACATCGATT
3688460 GAAATCATCACCTGAGACGGA
1 GAAATCATCACCTGAGACGGA
* *
3688481 GAAATCATCACCTAAGATGGA
1 GAAATCATCACCTGAGACGGA
3688502 GAAATCATCACCTGAGACGGA
1 GAAATCATCACCTGAGACGGA
3688523 GAAATCATC
1 GAAATCATC
3688532 CTTAAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (21 bp):
GAAATCATCACCTGAGACGGA
Found at i:3716051 original size:19 final size:19
Alignment explanation
Indices: 3716027--3716090 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
3716017 ACAATTTTTT
3716027 TATGAATAGTACCGTACTG
1 TATGAATAGTACCGTACTG
* *
3716046 TATGAATAGTACTGGT-TTG
1 TATGAATAGTAC-CGTACTG
3716065 TATGAATAGTACCGATACTG
1 TATGAATAGTACCG-TACTG
*
3716085 TGTGAA
1 TATGAA
3716091 CAATATCGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 27 0.73
20 9 0.24
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (19 bp):
TATGAATAGTACCGTACTG
Found at i:3716170 original size:21 final size:21
Alignment explanation
Indices: 3716146--3716199 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3716136 ACTGCTACAC
3716146 TAGTATTGATACCATGAACAA
1 TAGTATTGATACCATGAACAA
* * * *
3716167 TAGTATCGATATCGTGAACAG
1 TAGTATTGATACCATGAACAA
3716188 TAGTATTGATAC
1 TAGTATTGATAC
3716200 TATCAAGCCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
TAGTATTGATACCATGAACAA
Found at i:3718893 original size:20 final size:20
Alignment explanation
Indices: 3718848--3718893 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3718838 CATAATTTTT
* *
3718848 TATGAATAGTACCGATATTG
1 TATGAATAGTACCAATACTG
*
3718868 TATGAATAGTATCAATACTG
1 TATGAATAGTACCAATACTG
*
3718888 TGTGAA
1 TATGAA
3718894 CATTAGTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGAATAGTACCAATACTG
Found at i:3718916 original size:21 final size:21
Alignment explanation
Indices: 3718890--3718937 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3718880 CAATACTGTG
*
3718890 TGAACATTAGTATCGATACCA
1 TGAACATTAGTATCAATACCA
3718911 TGAACATTAGTATCAATACCA
1 TGAACATTAGTATCAATACCA
*
3718932 CGAACA
1 TGAACA
3718938 ATACCGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (21 bp):
TGAACATTAGTATCAATACCA
Found at i:3729244 original size:15 final size:15
Alignment explanation
Indices: 3729209--3729237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3729199 GTGCTTCAAC
3729209 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
3729223 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
3729238 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:3734910 original size:23 final size:24
Alignment explanation
Indices: 3734878--3734924 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3734868 AATAAAATTG
3734878 AAAATAAATTCA-AATAAAATAAAA
1 AAAATAAATT-AGAATAAAATAAAA
*
3734902 AAAAT-AATTAGGATAAAATAAAA
1 AAAATAAATTAGAATAAAATAAAA
3734925 TAGAATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.71
24 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAATAAATTAGAATAAAATAAAA
Found at i:3744573 original size:115 final size:115
Alignment explanation
Indices: 3744371--3744589 Score: 291
Period size: 115 Copynumber: 1.9 Consensus size: 115
3744361 TTTTTATCCT
* * * * *
3744371 TCTCTGGACACGTTCTTCTCATTATGAAATCCTCTATTGGAAATGTTAACCCATCTCATTTTGTG
1 TCTCTGGACAAGTTCTTCTCATTATGAAATCCTCCATTGGAAATGTCAACCCATCTCATTATATG
*
3744436 ATGGACGAACCAAGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCC
66 ATGGAAGAACCAAGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCC
* *
3744486 TCTCTGGATAAGTTCTTCT-ACTTATGAACTCCTCCATTGGAAATGTCAATCCACATC-C-TTAT
1 TCTCTGGACAAGTTCTTCTCA-TTATGAAATCCTCCATTGGAAATGTCAA-CC-CATCTCATTAT
* **
3744548 ATTATGGAAGAACCAATTTTGAACAAGTTCTTCTCATTATGA
63 ATGATGGAAGAACCAAGGTTGAACAAGTTCTTCTCATTATGA
3744590 AATCATCTAT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
114 1 0.01
115 82 0.91
116 3 0.03
117 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (115 bp):
TCTCTGGACAAGTTCTTCTCATTATGAAATCCTCCATTGGAAATGTCAACCCATCTCATTATATG
ATGGAAGAACCAAGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCC
Found at i:3744718 original size:190 final size:191
Alignment explanation
Indices: 3744382--3744780 Score: 479
Period size: 190 Copynumber: 2.1 Consensus size: 191
3744372 CTCTGGACAC
* * *
3744382 GTTCTTCTCATTATGAAATCCTCTATTGGAAATGTTAACCCATCTCATTTTGTGATGGACGAACC
1 GTTCTTCTCATTATGAAATCATCTATTGGAAATATTAACCCATCTCATTATGTGATGGACGAA-C
* ** *
3744447 AAGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCCTCTCTGGATAAGTTCTTCTACTTATG
65 AAGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCCTCACCAGACAAGTTCTTCTACTTATG
* **
3744512 AACTCCTCCATTGGAAATGTCAATCCACATCCTTATATT-ATGGA-AGAACCAATTTTGAACAA
130 AACTCCTCCATTGGAAATGTCAATCCACATCCTTAT-TTGATGGATA-AACAAAGGTTGAACAA
* * *
3744574 GTTCTTCTCATTATGAAATCATCTATTGGAAATATTGATCCATCTCCTCTAATG-GAT-GA-GAA
1 GTTCTTCTCATTATGAAATCATCTATTGGAAATATTAACCCATCTCAT-T-ATGTGATGGACGAA
* * *
3744636 -AAGGTTGAACAATTTCTTCTCATTATGAACTTTTTCTCCCTCACCAGACGAGTTCTTCT-CATT
64 CAAGGTTGAACAAGTTCTTCTCATTATG-ACTTATTCTCCCTCACCAGACAAGTTCTTCTAC-TT
* ** * * *
3744699 ATGAATTCCTCCATTGGAAATGTTGATCCACCTCCTTCTTTGATGGATAAGCAAAGGTTGAACAA
127 ATGAACTCCTCCATTGGAAATGTCAATCCACATCCTTATTTGATGGATAAACAAAGGTTGAACAA
*
3744764 GTTTTTCTCATTATGAA
1 GTTCTTCTCATTATGAA
3744781 TTTTTTCTCC
Statistics
Matches: 178, Mismatches: 23, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
189 29 0.16
190 94 0.53
191 4 0.02
192 45 0.25
193 4 0.02
194 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (191 bp):
GTTCTTCTCATTATGAAATCATCTATTGGAAATATTAACCCATCTCATTATGTGATGGACGAACA
AGGTTGAACAAGTTCTTCTCATTATGACTTATTCTCCCTCACCAGACAAGTTCTTCTACTTATGA
ACTCCTCCATTGGAAATGTCAATCCACATCCTTATTTGATGGATAAACAAAGGTTGAACAA
Found at i:3744789 original size:116 final size:113
Alignment explanation
Indices: 3744573--3744841 Score: 371
Period size: 116 Copynumber: 2.4 Consensus size: 113
3744563 ATTTTGAACA
* * * *
3744573 AGTTCTTCTCATTATGAAATCATCTATTGGAAATATTGATCCATCTCCTCTAATGGATGAGAAAA
1 AGTTCTTCTCATTATGAAATCCTCTATTGGAAATGTTGATCCACCTCCTCTAATGGATAAGAAAA
3744638 GGTTGAACAATTTCTTCTCATTATGAACTTTTTCTCCCTCACCAGACG
66 GGTTGAACAATTTCTTCTCATTATGAACTTTTTCTCCCTCACCAGACG
* * * *
3744686 AGTTCTTCTCATTATGAATTCCTCCATTGGAAATGTTGATCCACCTCCTTCTTTGATGGATAAGC
1 AGTTCTTCTCATTATGAAATCCTCTATTGGAAATGTTGATCCACCTCC-TC--TAATGGATAAGA
* *
3744751 AAAGGTTGAACAAGTTT-TTCTCATTATGAATTTTTTCTCCCTCATCAGACG
63 AAAGGTTGAACAA-TTTCTTCTCATTATGAACTTTTTCTCCCTCACCAGACG
* *
3744802 AGTTATTCTCATTATGAACA-CCTCTATTAGAAATGTTGAT
1 AGTTCTTCTCATTATGAA-ATCCTCTATTGGAAATGTTGAT
3744842 TTGTTTTCTC
Statistics
Matches: 137, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
113 43 0.31
114 2 0.01
116 89 0.65
117 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAAATCCTCTATTGGAAATGTTGATCCACCTCCTCTAATGGATAAGAAAA
GGTTGAACAATTTCTTCTCATTATGAACTTTTTCTCCCTCACCAGACG
Found at i:3745355 original size:11 final size:11
Alignment explanation
Indices: 3745341--3745430 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
3745331 TTTAATTTGG
3745341 TTCTTTTTCTT
1 TTCTTTTTCTT
* *
3745352 TTCTTTTCCAT
1 TTCTTTTTCTT
*
3745363 TTATTTCTTCTT
1 TTCTTT-TTCTT
*
3745375 CTTTTTTTCTCATT
1 -TTCTTTT-TC-TT
*
3745389 TTCTCATTT-TT
1 TTCT-TTTTCTT
3745400 TTCTTTTTCTTT
1 TTCTTTTTC-TT
3745412 TTCATTTTTTCTT
1 TTC--TTTTTCTT
3745425 TTCTTT
1 TTCTTT
3745431 ACAATGAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
10 3 0.05
11 23 0.38
12 9 0.15
13 16 0.26
14 10 0.16
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:3745389 original size:21 final size:20
Alignment explanation
Indices: 3745364--3745429 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
3745354 CTTTTCCATT
3745364 TATTTCTTCTTCTTTTTTTC
1 TATTTCTTCTTCTTTTTTTC
3745384 TCA-TT-TTC-TCATTTTTTTC
1 T-ATTTCTTCTTC-TTTTTTTC
* * *
3745403 TTTTTCTTTTTCATTTTTTC
1 TATTTCTTCTTCTTTTTTTC
3745423 T-TTTCTT
1 TATTTCTT
3745430 TACAATGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 13 0.34
21 3 0.08
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTCTTCTTCTTTTTTTC
Found at i:3745417 original size:29 final size:31
Alignment explanation
Indices: 3745341--3745419 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 31
3745331 TTTAATTTGG
3745341 TTCTTTTTC-TTTTC-TTTTCCATTTATTTC
1 TTCTTTTTCTTTTTCATTTTCCATTTATTTC
3745370 TTCTTCTTT-TTTTCTCATTTTCTCA-TT-TTT-
1 TTCTT-TTTCTTTT-TCATTTTC-CATTTATTTC
3745400 TTCTTTTTCTTTTTCATTTT
1 TTCTTTTTCTTTTTCATTTT
3745420 TTCTTTTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
29 15 0.34
30 15 0.34
31 5 0.11
32 7 0.16
33 2 0.05
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (31 bp):
TTCTTTTTCTTTTTCATTTTCCATTTATTTC
Found at i:3751146 original size:37 final size:39
Alignment explanation
Indices: 3751088--3751174 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 39
3751078 ACTAGTATAA
3751088 ATTCATAACTC-TTTTTCAGATTCAAAACTCATTTT-AG
1 ATTCATAACTCATTTTTCAGATTCAAAACTCATTTTCAG
* * ** *
3751125 ATTCATAACTCATTTTT-AGATTTATAACTTGTTTTCAT
1 ATTCATAACTCATTTTTCAGATTCAAAACTCATTTTCAG
3751163 ATTCATAACTCA
1 ATTCATAACTCA
3751175 ATTTCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 25 0.58
38 18 0.42
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (39 bp):
ATTCATAACTCATTTTTCAGATTCAAAACTCATTTTCAG
Found at i:3751179 original size:19 final size:19
Alignment explanation
Indices: 3751088--3751188 Score: 114
Period size: 19 Copynumber: 5.4 Consensus size: 19
3751078 ACTAGTATAA
*
3751088 ATTCATAACTCTTTTTCAG
1 ATTCATAACTCATTTTCAG
*
3751107 ATTCAAAACTCATTTT-AG
1 ATTCATAACTCATTTTCAG
*
3751125 ATTCATAACTCATTTTTAG
1 ATTCATAACTCATTTTCAG
* ** *
3751144 ATTTATAACTTGTTTTCAT
1 ATTCATAACTCATTTTCAG
* *
3751163 ATTCATAACTCAATTTCAA
1 ATTCATAACTCATTTTCAG
3751182 ATTCATA
1 ATTCATA
3751189 GCCCAATGTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
18 17 0.25
19 51 0.75
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.46
Consensus pattern (19 bp):
ATTCATAACTCATTTTCAG
Found at i:3751195 original size:19 final size:19
Alignment explanation
Indices: 3751157--3751195 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3751147 TATAACTTGT
* *
3751157 TTTCATATTCATAACTCAA
1 TTTCAAATTCATAACCCAA
*
3751176 TTTCAAATTCATAGCCCAA
1 TTTCAAATTCATAACCCAA
3751195 T
1 T
3751196 GTATATCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTCAAATTCATAACCCAA
Found at i:3754113 original size:3 final size:3
Alignment explanation
Indices: 3754105--3754139 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3754095 TGTTCATTTA
3754105 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3754140 AAAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3755475 original size:15 final size:15
Alignment explanation
Indices: 3755443--3755476 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3755433 TATTTGTAAT
**
3755443 ATATTATTATTATTA
1 ATATTATTATTACAA
3755458 ATATTATTATTACAA
1 ATATTATTATTACAA
3755473 ATAT
1 ATAT
3755477 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATTATTACAA
Found at i:3756330 original size:28 final size:28
Alignment explanation
Indices: 3756244--3756338 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
3756234 AAATTAAAAA
*
3756244 TTCATATATTTA-ATATATAATTCATTCTT
1 TTCATATATTTATATATAT-ATT-ATTATT
* *
3756273 TTCA-AAATTTTTATATATACTTATTATT
1 TTCATATATTTATATATATA-TTATTATT
*
3756301 TTCATAATATTTATATGTATATTATT-TT
1 TTCAT-ATATTTATATATATATTATTATT
3756329 TT-ATATATTT
1 TTCATATATTT
3756339 TTTATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.11
27 2 0.04
28 19 0.34
29 17 0.30
30 12 0.21
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (28 bp):
TTCATATATTTATATATATATTATTATT
Found at i:3756336 original size:26 final size:30
Alignment explanation
Indices: 3756244--3756338 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 30
3756234 AAATTAAAAA
* *
3756244 TTCAT-ATATTTA-ATATATAATTCATTCTT
1 TTCATAATATTTATATATATACTT-ATTATT
*
3756273 TTCA-AA-ATTTTTATATATACTTATTATT
1 TTCATAATATTTATATATATACTTATTATT
*
3756301 TTCATAATATTTATATGTATA-TTATT-TT
1 TTCATAATATTTATATATATACTTATTATT
3756329 TT-AT-ATATTT
1 TTCATAATATTT
3756339 TTTATTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 6 0.11
27 2 0.04
28 17 0.30
29 21 0.37
30 11 0.19
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (30 bp):
TTCATAATATTTATATATATACTTATTATT
Found at i:3762570 original size:9 final size:9
Alignment explanation
Indices: 3762556--3762587 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3762546 AAATGGCAAT
3762556 CATTCTTTA
1 CATTCTTTA
3762565 CATTCTTTA
1 CATTCTTTA
*
3762574 CATTTTTTA
1 CATTCTTTA
3762583 CATTC
1 CATTC
3762588 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:3766132 original size:16 final size:15
Alignment explanation
Indices: 3766113--3766160 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3766103 AATGAAATAA
3766113 AAAAAGAGAAAAAAAG
1 AAAAAGA-AAAAAAAG
3766129 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
3766144 AAGAAA-ATAAAAAAAG
1 AA-AAAGA-AAAAAAAG
3766160 A
1 A
3766161 GGGTTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:3766138 original size:23 final size:22
Alignment explanation
Indices: 3766098--3766158 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
3766088 TGCTTTTAGA
* *
3766098 AAAAAAATGAAATAAAAAAAGAG
1 AAAAAAA-GAAAAAAAAAAAAAG
3766121 AAAAAAAGAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAA-AAAAAAAAG
* *
3766144 AAGAAAATAAAAAAA
1 AAAAAAAGAAAAAAA
3766159 GAGGGTTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAAAAAAG
Found at i:3766139 original size:25 final size:25
Alignment explanation
Indices: 3766111--3766160 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3766101 AAAATGAAAT
3766111 AAAAAAAG-AGAAAAAAAGAAAAAGA
1 AAAAAAAGAAGAAAAAAA-AAAAAGA
*
3766136 AAAAAAAGAAGAAAATAAAAAAAGA
1 AAAAAAAGAAGAAAAAAAAAAAAGA
3766161 GGGTTAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAAGAAAAAAAAAAAAGA
Found at i:3766537 original size:19 final size:19
Alignment explanation
Indices: 3766489--3766566 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 19
3766479 ATTTATTAAC
3766489 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-T-TG
3766511 AAATTCAATTTATTTTTTG
1 AAATTCAATTTATTTTTTG
* *
3766530 AGATTCAATTTA-TTTTCG
1 AAATTCAATTTATTTTTTG
3766548 AAATTCAATTTATTCTTTT
1 AAATTCAATTTATT-TTTT
3766567 ATTTTGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 17 0.35
19 13 0.27
20 11 0.22
21 2 0.04
22 6 0.12
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.55
Consensus pattern (19 bp):
AAATTCAATTTATTTTTTG
Found at i:3767912 original size:113 final size:112
Alignment explanation
Indices: 3767700--3768149 Score: 679
Period size: 113 Copynumber: 4.0 Consensus size: 112
3767690 TAGCAAAGAT
* *
3767700 TCAAATCCATCAC--AATGGATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAA-AGTTCATAATGAGAAGAACTCATCTGA
3767763 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * * *
3767811 TCAAATCCATCACTTGATGGATCAGCTTTTGCAGAGAAAGTTCAAAATGAGAAGAACTCATATGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGA
3767876 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
3767924 TCAAATCCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGA
* * * ** ** *
3767989 AGAAGGAAGGAGAAATTCATAATGAGAATAATTTGTTCAATTTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * *
3768037 TTGAATTCATCACTCGATGGATCAACTTTTCCAGCAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGA
3768102 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
3768150 ATGACCCTAT
Statistics
Matches: 304, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
111 13 0.04
113 288 0.95
114 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (112 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:3769705 original size:22 final size:22
Alignment explanation
Indices: 3769679--3769738 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
3769669 AAATTATTAA
3769679 TCATTTTTATATAGTTTTAATT
1 TCATTTTTATATAGTTTTAATT
*
3769701 TCATTTATT-T-TAGTTGTTGATT
1 TCATTT-TTATATAGTT-TTAATT
*
3769723 T-AATTTTATAT-GTTTT
1 TCATTTTTATATAGTTTT
3769739 TTTGTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 14 0.44
23 2 0.06
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.65
Consensus pattern (22 bp):
TCATTTTTATATAGTTTTAATT
Found at i:3769754 original size:3 final size:3
Alignment explanation
Indices: 3769748--3769782 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3769738 TTTTGTAATA
* *
3769748 TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3769783 CAAATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3776490 original size:32 final size:32
Alignment explanation
Indices: 3776454--3776542 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
3776444 AATAGTCAAG
*
3776454 GTTGCATTCAGAGAATGCACAACAGAGTCAGT
1 GTTGCATTCAGATAATGCACAACAGAGTCAGT
* * *
3776486 GTTGCATTCAGATAATACATAGA-AGTGTCAGT
1 GTTGCATTCAGATAATGCACA-ACAGAGTCAGT
* *
3776518 GTCGCATTTAGATAATGCACAACAG
1 GTTGCATTCAGATAATGCACAACAG
3776543 TTACAATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (32 bp):
GTTGCATTCAGATAATGCACAACAGAGTCAGT
Found at i:3784197 original size:16 final size:17
Alignment explanation
Indices: 3784173--3784219 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3784163 GGTTTATACT
*
3784173 TGATTTTTTTAT-TAAA
1 TGATGTTTTTATGTAAA
3784189 TGATGTTTTTGATGTAAA
1 TGATGTTTTT-ATGTAAA
*
3784207 -GGTGTTTTTATGT
1 TGATGTTTTTATGT
3784220 CAATTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
17 10 0.37
18 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.57
Consensus pattern (17 bp):
TGATGTTTTTATGTAAA
Found at i:3785078 original size:16 final size:16
Alignment explanation
Indices: 3785036--3785084 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
3785026 GTGCCACGTC
3785036 TATTTTTTTTAAATAAA
1 TATTTTTTTTAAA-AAA
* *
3785053 -ATATTGTTTAAAAAA
1 TATTTTTTTTAAAAAA
3785068 TATTTTTTTTAAAAAA
1 TATTTTTTTTAAAAAA
3785084 T
1 T
3785085 TAGACGTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TATTTTTTTTAAAAAA
Found at i:3788548 original size:59 final size:56
Alignment explanation
Indices: 3788454--3788563 Score: 139
Period size: 59 Copynumber: 1.9 Consensus size: 56
3788444 TTCGAGATAT
* * * * *
3788454 CACTAAAGTATTAGTGCATATGGTGATCATGACCTTATGTGTCATATTCGGGACTG
1 CACTAAAGTATTAGTGCAGATGGTGAGCACGACCTTATATGTCATACTCGGGACTG
*
3788510 CACTAAAGTATAACTAGTGCAGATGGTGGGCACGACCTTATATGTCATACTCGG
1 CACTAAAGTAT---TAGTGCAGATGGTGAGCACGACCTTATATGTCATACTCGG
3788564 ATTAGTACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 11 0.24
59 34 0.76
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (56 bp):
CACTAAAGTATTAGTGCAGATGGTGAGCACGACCTTATATGTCATACTCGGGACTG
Found at i:3796322 original size:20 final size:20
Alignment explanation
Indices: 3796285--3796324 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
3796275 AGTATGTCCA
3796285 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
3796305 GGGGGATATCGATTCCCCCT
1 GGGGG-TATCGATTCCCCCT
3796325 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:3803126 original size:21 final size:21
Alignment explanation
Indices: 3803101--3803140 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3803091 AGTATGTCCA
3803101 GGGGGTATCGATTCCCCCTGG
1 GGGGGTATCGATTCCCCCTGG
3803122 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
3803141 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTGG
Found at i:3803771 original size:15 final size:15
Alignment explanation
Indices: 3803753--3803814 Score: 124
Period size: 15 Copynumber: 4.1 Consensus size: 15
3803743 CGAGGGTACT
3803753 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3803768 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3803783 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3803798 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3803813 GT
1 GT
3803815 CCTACGGGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3803789 original size:30 final size:30
Alignment explanation
Indices: 3803753--3803829 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
3803743 CGAGGGTACT
3803753 GTAGTCCTTCGGGACGTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGACGTAGTCCTTCGGGAC
3803783 GTAGTCCTTCGGGACGTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGACGTAGTCCTTCGGGAC
*
3803813 ---GTCCTACGGGACGTAGT
1 GTAGTCCTTCGGGACGTAGT
3803830 GGTCCTACGG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 16 0.35
30 30 0.65
ACGTcount: A:0.14, C:0.26, G:0.34, T:0.26
Consensus pattern (30 bp):
GTAGTCCTTCGGGACGTAGTCCTTCGGGAC
Found at i:3804941 original size:142 final size:142
Alignment explanation
Indices: 3804685--3804969 Score: 561
Period size: 142 Copynumber: 2.0 Consensus size: 142
3804675 CGATTAATAT
3804685 GTTAATCTGGTTAAACCAGTAATTTCAATTGTTTAGATGATGGAAGAGTAGCAGTACGCTGACAA
1 GTTAATCTGGTTAAACCAGTAATTTCAATTGTTTAGATGATGGAAGAGTAGCAGTACGCTGACAA
*
3804750 TTGGTGGATTTAAGTACAAATAAAAGTTTTTGTTATGAAGGAATCAAAAAGTTTACGATAATCCT
66 TTGGTGGATTTAAGTACAAATAAAAGGTTTTGTTATGAAGGAATCAAAAAGTTTACGATAATCCT
3804815 GAACATACACTG
131 GAACATACACTG
3804827 GTTAATCTGGTTAAACCAGTAATTTCAATTGTTTAGATGATGGAAGAGTAGCAGTACGCTGACAA
1 GTTAATCTGGTTAAACCAGTAATTTCAATTGTTTAGATGATGGAAGAGTAGCAGTACGCTGACAA
3804892 TTGGTGGATTTAAGTACAAATAAAAGGTTTTGTTATGAAGGAATCAAAAAGTTTACGATAATCCT
66 TTGGTGGATTTAAGTACAAATAAAAGGTTTTGTTATGAAGGAATCAAAAAGTTTACGATAATCCT
3804957 GAACATACACTG
131 GAACATACACTG
3804969 G
1 G
3804970 AAAATTACAA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (142 bp):
GTTAATCTGGTTAAACCAGTAATTTCAATTGTTTAGATGATGGAAGAGTAGCAGTACGCTGACAA
TTGGTGGATTTAAGTACAAATAAAAGGTTTTGTTATGAAGGAATCAAAAAGTTTACGATAATCCT
GAACATACACTG
Found at i:3805910 original size:30 final size:30
Alignment explanation
Indices: 3805876--3805932 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3805866 CTAATCCAGT
3805876 AAAGATAAGGAAAGTCAAATGTGTACACAA
1 AAAGATAAGGAAAGTCAAATGTGTACACAA
*
3805906 AAAGATATGGAAAGTCAAATGTGTACA
1 AAAGATAAGGAAAGTCAAATGTGTACA
3805933 TAATGTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (30 bp):
AAAGATAAGGAAAGTCAAATGTGTACACAA
Found at i:3809889 original size:18 final size:17
Alignment explanation
Indices: 3809840--3809891 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 17
3809830 AAGGACTAAA
3809840 ATAAAAGGATAAAA-AT
1 ATAAAAGGATAAAATAT
*
3809856 ATTAAAGGCAATTAAAATAT
1 ATAAAAGG--A-TAAAATAT
3809876 ATAAAAGGACTAAAAT
1 ATAAAAGGA-TAAAAT
3809892 TAAAGTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.24
18 8 0.28
19 5 0.17
20 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.23
Consensus pattern (17 bp):
ATAAAAGGATAAAATAT
Found at i:3809949 original size:14 final size:14
Alignment explanation
Indices: 3809930--3809967 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
3809920 AAATAAATAG
3809930 GAAATTAAA-GTAAT
1 GAAATTAAATG-AAT
3809944 GAAATTAAATGAAT
1 GAAATTAAATGAAT
3809958 GAAATTAAAT
1 GAAATTAAAT
3809968 AAATAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (14 bp):
GAAATTAAATGAAT
Found at i:3818038 original size:22 final size:22
Alignment explanation
Indices: 3818010--3818055 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3818000 ATTGGTTATT
* *
3818010 ATATATATTATTTTTATCATGA
1 ATATATATGATGTTTATCATGA
*
3818032 ATATATATGATGTTTATTATGA
1 ATATATATGATGTTTATCATGA
3818054 AT
1 AT
3818056 GCTATTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
ATATATATGATGTTTATCATGA
Found at i:3823582 original size:22 final size:22
Alignment explanation
Indices: 3823557--3823602 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3823547 ACTGGTTATT
*
3823557 ATATATATGATTTTTATCATGA
1 ATATATATGATGTTTATCATGA
*
3823579 ATATATATGATGTTTATTATGA
1 ATATATATGATGTTTATCATGA
3823601 AT
1 AT
3823603 GTTACTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATATGATGTTTATCATGA
Found at i:3823865 original size:61 final size:60
Alignment explanation
Indices: 3823783--3823896 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
3823773 TGCTAAGCAC
* * *
3823783 AGGTGGAGGCACAACCTTATGTGTCATATCCGGACTAGCACTAGAGTGTAAGCCTATTGT
1 AGGTGGAGGCACAACCTTATGTATCATATCAGGACTAGCACTAGAGCGTAAGCCTATTGT
*
3823843 AGGTGGAGGGCACAACCTTATGTATCATATCAGGATTAGCACTAGAGCGTAAGC
1 AGGTGGA-GGCACAACCTTATGTATCATATCAGGACTAGCACTAGAGCGTAAGC
3823897 TTAGTGCAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 7 0.14
61 42 0.86
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (60 bp):
AGGTGGAGGCACAACCTTATGTATCATATCAGGACTAGCACTAGAGCGTAAGCCTATTGT
Found at i:3825118 original size:20 final size:18
Alignment explanation
Indices: 3825079--3825124 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
3825069 ATGATGTAGA
3825079 AGGGGAAGAAATAAAGAG
1 AGGGGAAGAAATAAAGAG
3825097 AGGGGAAGAAATAAAGAG
1 AGGGGAAGAAATAAAGAG
*
3825115 AGAGGAAGAA
1 AGGGGAAGAA
3825125 GGAAGCACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.04
Consensus pattern (18 bp):
AGGGGAAGAAATAAAGAG
Found at i:3827102 original size:13 final size:13
Alignment explanation
Indices: 3827084--3827109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3827074 TATAAAAATT
3827084 TACAAATATGAAA
1 TACAAATATGAAA
3827097 TACAAATATGAAA
1 TACAAATATGAAA
3827110 ATTAAGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
TACAAATATGAAA
Found at i:3828278 original size:35 final size:36
Alignment explanation
Indices: 3828234--3828325 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
3828224 AAATTTATTA
3828234 TTAAATTTTAATTATTAAATAAATATA-TATAAAAT
1 TTAAATTTTAATTATTAAATAAATATATTATAAAAT
* * * * * *
3828269 TTCAATTTTATTTACTAAA-ATATTTATTTTAAAAT
1 TTAAATTTTAATTATTAAATAAATATATTATAAAAT
* *
3828304 TTAAAATTTAAATATTAAATAA
1 TTAAATTTTAATTATTAAATAA
3828326 CTAAATACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
34 5 0.12
35 37 0.86
36 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (36 bp):
TTAAATTTTAATTATTAAATAAATATATTATAAAAT
Found at i:3830975 original size:31 final size:31
Alignment explanation
Indices: 3830891--3831017 Score: 136
Period size: 31 Copynumber: 4.2 Consensus size: 31
3830881 TTCTTGTAAT
* * *
3830891 ATTTTAAAATTAAGATAAAAATAAAA-AAAT
1 ATTTTTAAATTAAGATAAAAATAAAATATAC
*
3830921 AGTTTTAAATT-A-A-AAAAATAAAATATAC
1 ATTTTTAAATTAAGATAAAAATAAAATATAC
3830949 ATTTTTAAATTAAGATAAAAATAAAATATAC
1 ATTTTTAAATTAAGATAAAAATAAAATATAC
* * * * *
3830980 ATTTTTAAGTTAAAAATAAGAGTAAAATATAT
1 ATTTTTAAATT-AAGATAAAAATAAAATATAC
3831012 ATTTTT
1 ATTTTT
3831018 TGTTAAAATA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.12
28 13 0.16
29 2 0.02
30 10 0.12
31 25 0.30
32 22 0.27
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (31 bp):
ATTTTTAAATTAAGATAAAAATAAAATATAC
Found at i:3831028 original size:30 final size:32
Alignment explanation
Indices: 3830938--3831041 Score: 108
Period size: 31 Copynumber: 3.3 Consensus size: 32
3830928 AATTAAAAAA
* * * *
3830938 ATAAAATATACATTTTTAAATT-AAGATAAAA
1 ATAAAATATATATTTTTAAGTTAAAAATAAAG
*
3830969 ATAAAATATACATTTTTAAGTTAAAAAT-AAG
1 ATAAAATATATATTTTTAAGTTAAAAATAAAG
*
3831000 AGTAAAATATATATTTTT-TGTT-AAAATAAAG
1 A-TAAAATATATATTTTTAAGTTAAAAATAAAG
*
3831031 ATAAATTATAT
1 ATAAAATATAT
3831042 TTGATAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
30 14 0.22
31 31 0.48
32 19 0.30
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (32 bp):
ATAAAATATATATTTTTAAGTTAAAAATAAAG
Found at i:3831084 original size:25 final size:25
Alignment explanation
Indices: 3831051--3831110 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
3831041 TTTGATAATT
* * * * *
3831051 TAAGGTAAAACTAGAATATATTTAG
1 TAAGTTAAAAATACAATATATGTAA
3831076 TAAGTTAAAAATACAATATATGTAA
1 TAAGTTAAAAATACAATATATGTAA
3831101 TAAGTTAAAA
1 TAAGTTAAAA
3831111 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (25 bp):
TAAGTTAAAAATACAATATATGTAA
Found at i:3837523 original size:21 final size:21
Alignment explanation
Indices: 3837498--3837567 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
3837488 TGGAGTATTT
3837498 AATGCTGAAATTTAACTATGG
1 AATGCTGAAATTTAACTATGG
*
3837519 AATGCTGAAATTTAATTATGG
1 AATGCTGAAATTTAACTATGG
* * *
3837540 AATGCTGAATTTTAAGT-TAG
1 AATGCTGAAATTTAACTATGG
3837560 AATGCTGA
1 AATGCTGA
3837568 TTTGAGGATC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 10 0.22
21 35 0.78
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (21 bp):
AATGCTGAAATTTAACTATGG
Found at i:3848287 original size:24 final size:23
Alignment explanation
Indices: 3848259--3848303 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3848249 TATTACTATT
3848259 TGGATCA-ATTTATGGTTGTATTTA
1 TGGATCATATTT-TGGTT-TATTTA
*
3848283 TGGATGATATTTTGGTTTATT
1 TGGATCATATTTTGGTTTATT
3848304 ATAACTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.53
Consensus pattern (23 bp):
TGGATCATATTTTGGTTTATTTA
Found at i:3852488 original size:206 final size:206
Alignment explanation
Indices: 3852134--3852545 Score: 806
Period size: 206 Copynumber: 2.0 Consensus size: 206
3852124 TTTGGAAAGT
3852134 TTGAAGTTATGATTGAATTGTGATTTAGTTTTATATCGATTTAGTATCGATTTTTCTTTATAGAA
1 TTGAAGTTATGATTGAATTGTGATTTAGTTTTATATCGATTTAGTATCGATTTTTCTTTATAGAA
*
3852199 ATTATTTTATCAAAATTAGATTATGTTAGTAGAATACTAACATATGCATTGGATATTTTATTATT
66 ATTATTTTATCAAAATTAGATTATGTTAGTAGAATACTAACATATGCATTGGATATTGTATTATT
*
3852264 TTATGATGATGTTCAGACCATAGTAAACCTAGTGATCTGAGTGGCTCGAAAGGGAAGGAAAAGTA
131 TTATGATGATGTTCAGACCACAGTAAACCTAGTGATCTGAGTGGCTCGAAAGGGAAGGAAAAGTA
3852329 CGAGATTGAAA
196 CGAGATTGAAA
3852340 TTGAAGTTATGATTGAATTGTGATTTAGTTTTATATCGATTTAGTATCGATTTTTCTTTATAGAA
1 TTGAAGTTATGATTGAATTGTGATTTAGTTTTATATCGATTTAGTATCGATTTTTCTTTATAGAA
3852405 ATTATTTTATCAAAATTAGATTATGTTAGTAGAATACTAACATATGCATTGGATATTGTATTATT
66 ATTATTTTATCAAAATTAGATTATGTTAGTAGAATACTAACATATGCATTGGATATTGTATTATT
3852470 TTATGATGATGTTCAGACCACAGTAAACCTAGTGATCTGAGTGGCTCGAAAGGGAAGGAAAAGTA
131 TTATGATGATGTTCAGACCACAGTAAACCTAGTGATCTGAGTGGCTCGAAAGGGAAGGAAAAGTA
3852535 CGAGATTGAAA
196 CGAGATTGAAA
3852546 AAATATAATA
Statistics
Matches: 204, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 204 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (206 bp):
TTGAAGTTATGATTGAATTGTGATTTAGTTTTATATCGATTTAGTATCGATTTTTCTTTATAGAA
ATTATTTTATCAAAATTAGATTATGTTAGTAGAATACTAACATATGCATTGGATATTGTATTATT
TTATGATGATGTTCAGACCACAGTAAACCTAGTGATCTGAGTGGCTCGAAAGGGAAGGAAAAGTA
CGAGATTGAAA
Found at i:3853749 original size:119 final size:120
Alignment explanation
Indices: 3853527--3853765 Score: 432
Period size: 119 Copynumber: 2.0 Consensus size: 120
3853517 CTTATCACTT
3853527 TTATTTTAGTCACTAAAGTTTAAAAACAAAAACCAATACCAAGAAAAAATACGTTGTTTCTCTTC
1 TTATTTTAGTCACTAAAGTTTAAAAACAAAAACCAATACCAAGAAAAAATACGTTGTTTCTCTTC
3853592 AATTGTTTCCCCCCTCCCCTCGTCGATGTTTGGCCTTCTTCTGGTCAATCATGGCG
66 AATTGTTTCCCCCCTCCCCTCGTCGATGTTTGGCC-TCTTCTGGTCAATCATGGCG
3853648 TTATTTTAGTCACTAAAG-TTAAAAAC-AAAACCAATACCAAGAAAAAATACGTTGTTT-TCTTC
1 TTATTTTAGTCACTAAAGTTTAAAAACAAAAACCAATACCAAGAAAAAATACGTTGTTTCTCTTC
*
3853710 AATTGTTTTCCCCCT-CCCTCGTCGATGTTTGGCCTCTTCTGGTCAATCATGGCG
66 AATTGTTTCCCCCCTCCCCTCGTCGATGTTTGGCCTCTTCTGGTCAATCATGGCG
3853764 TT
1 TT
3853766 CAAACCACCC
Statistics
Matches: 117, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
116 22 0.19
117 19 0.16
118 19 0.16
119 31 0.26
120 8 0.07
121 18 0.15
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (120 bp):
TTATTTTAGTCACTAAAGTTTAAAAACAAAAACCAATACCAAGAAAAAATACGTTGTTTCTCTTC
AATTGTTTCCCCCCTCCCCTCGTCGATGTTTGGCCTCTTCTGGTCAATCATGGCG
Found at i:3855879 original size:36 final size:35
Alignment explanation
Indices: 3855828--3855938 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
3855818 TAAGATACTA
3855828 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * * *
3855863 CCTATAACATCACCATCATACATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
3855898 CCTATATCCTTACCATATTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
3855933 CCTATA
1 CCTATA
3855939 TAACCACCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 42 0.68
36 20 0.32
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.31
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:3856292 original size:22 final size:20
Alignment explanation
Indices: 3856267--3856307 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
3856257 TGCTGCAACA
3856267 AAAGCAACAAAAAGAGAAAAAT
1 AAAG-AACAAAAA-AGAAAAAT
*
3856289 AAAGAAGAAAAAAGAAAAA
1 AAAGAACAAAAAAGAAAAA
3856308 GAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAGAACAAAAAAGAAAAAT
Found at i:3858450 original size:55 final size:56
Alignment explanation
Indices: 3858357--3858469 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
3858347 CAATCAATAC
3858357 TCGTTCAGCCATAAAGGGAAAGAAGATTATCCTTACTACTTTAACGCCTAAACAAG
1 TCGTTCAGCCATAAAGGGAAAGAAGATTATCCTTACTACTTTAACGCCTAAACAAG
3858413 TCGTTCAGCCATAAAGGG-AAGAAGATTATCCTTACTACTTTAACGCCTAAACAAG
1 TCGTTCAGCCATAAAGGGAAAGAAGATTATCCTTACTACTTTAACGCCTAAACAAG
3858468 TC
1 TC
3858470 CAGAATGATC
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 39 0.68
56 18 0.32
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (56 bp):
TCGTTCAGCCATAAAGGGAAAGAAGATTATCCTTACTACTTTAACGCCTAAACAAG
Found at i:3860247 original size:36 final size:35
Alignment explanation
Indices: 3860196--3860306 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
3860186 TAAGATACTA
3860196 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
3860231 CCTATAACATCACCATCTTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * * *
3860266 CCTATATCCTTACCATCTTCTATCACTATTTCACT
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
3860301 CCTATA
1 CCTATA
3860307 TAACAACCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 41 0.65
36 22 0.35
ACGTcount: A:0.27, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:3862030 original size:37 final size:37
Alignment explanation
Indices: 3861941--3862044 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3861931 CCTTTTCGTC
3861941 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3861977 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
3862014 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3862045 CCACAAGAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
36 18 0.31
37 40 0.69
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3862785 original size:44 final size:42
Alignment explanation
Indices: 3862737--3862849 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 42
3862727 ATATTTTTTT
3862737 CATTTATTTATTATTATTACTATTTAGTT-TTATTATATTACATA
1 CATTTATTTATT-TTATTA-TATTTAGTTATTATTATATT-CATA
* * * *
3862781 CATTTATATATTTTTATATATATTT-TTTATTATTTTATTTATA
1 CATTTATTTA-TTTTAT-TATATTTAGTTATTATTATATTCATA
3862824 CTATTTATTTATTTTCATTATATTTA
1 C-ATTTATTTATTTT-ATTATATTTA
3862850 TAGTTTCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
43 17 0.29
44 37 0.64
45 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (42 bp):
CATTTATTTATTTTATTATATTTAGTTATTATTATATTCATA
Found at i:3862802 original size:12 final size:11
Alignment explanation
Indices: 3862783--3862835 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
3862773 ATTACATACA
3862783 TTTATATATTT
1 TTTATATATTT
3862794 TTATATATATTT
1 TT-TATATATTT
3862806 TTTAT-TATTTT
1 TTTATATA-TTT
3862817 ATTTATACTATTT
1 -TTTATA-TATTT
3862830 ATTTAT
1 -TTTAT
3862836 TTTCATTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.05
11 8 0.22
12 16 0.43
13 9 0.24
14 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATATATTT
Found at i:3862816 original size:22 final size:21
Alignment explanation
Indices: 3862783--3862848 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
3862773 ATTACATACA
3862783 TTTATATATTTTTATATATATTT
1 TTTAT-TATTTTTAT-TATATTT
* *
3862806 TTTATTA-TTTTATTTATACTA
1 TTTATTATTTTTA-TTATATTT
*
3862827 TTTATTTATTTTCATTATATTT
1 TTTA-TTATTTTTATTATATTT
3862849 ATAGTTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 14 0.40
22 12 0.34
23 9 0.26
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTATTTTTATTATATTT
Found at i:3867171 original size:8 final size:8
Alignment explanation
Indices: 3867160--3867222 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
3867150 CAAAAATGGC
*
3867160 AAAAAACA
1 AAAAAAGA
3867168 AAAAAAG-
1 AAAAAAGA
* *
3867175 AAAGAAGC
1 AAAAAAGA
3867183 AAAAAAGA
1 AAAAAAGA
3867191 AAACAAA-A
1 AAA-AAAGA
3867199 TAAAGAAAGA
1 -AAA-AAAGA
3867209 AAAAAAGA
1 AAAAAAGA
3867217 AAAAAA
1 AAAAAA
3867223 AAGGACAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
7 6 0.13
8 27 0.59
9 12 0.26
10 1 0.02
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:3869174 original size:105 final size:106
Alignment explanation
Indices: 3868797--3870047 Score: 1667
Period size: 105 Copynumber: 12.0 Consensus size: 106
3868787 ATATCGTGCC
* * ** *
3868797 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAA-AAAGCAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-CAACTTCC
* *
3868861 CTAA-TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
65 C-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * **
3868903 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTATCAACAAAC-ACTTCTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3868967 AATTTCATAGCCAATTTCAACTTCACAACGAAGG-TA-TAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3869006 ACTCTAGACAACACAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3869070 AATTTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3869111 ACTCAAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCT-GTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3869175 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3869216 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAA-TAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3869280 AATTTCAGAGCCAATTTCAAATTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
3869321 ACTCCAGACAACG-TAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3869380 ---TTC----CCAATTTC-ACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3869413 ACTCGAGACAACGCAAGTTCAACTTCACGATG-AGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
3869477 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTTG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3869518 ACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGATTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
3869583 GATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3869624 ACTCCGGACAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGGTTGTC-ACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3869687 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3869728 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAA-AAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
3869792 AATTTCAGAGCCAATTTCAAATTCACAGCGAAGTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3869833 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
3869898 AATTTTGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3869939 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTATCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * *
3870003 CGA-TTCAAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3870045 ACT
1 ACT
3870048 TGGAACAATG
Statistics
Matches: 1021, Mismatches: 96, Indels: 56
0.87 0.08 0.05
Matches are distributed among these distances:
92 59 0.06
93 24 0.02
97 4 0.00
100 4 0.00
102 33 0.03
103 57 0.06
104 130 0.13
105 390 0.38
106 317 0.31
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3871463 original size:8 final size:9
Alignment explanation
Indices: 3871444--3871482 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3871434 ATATTATTTT
3871444 TTTATCTATA
1 TTTA-CTATA
3871454 TTTACT-TA
1 TTTACTATA
*
3871462 TTTACTATT
1 TTTACTATA
3871471 TTTACTATA
1 TTTACTATA
3871480 TTT
1 TTT
3871483 TCCTAACGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 8 0.31
9 14 0.54
10 4 0.15
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTACTATA
Found at i:3871463 original size:25 final size:25
Alignment explanation
Indices: 3871408--3871482 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
3871398 TGCGTTATAT
**
3871408 TATATTATTTTCCTAT-TATATATTA
1 TATATTATTTTTTTATCTATAT-TTA
3871433 TATATTATTTTTTTATCTATATTTA
1 TATATTATTTTTTTATCTATATTTA
*
3871458 CT-TATTTACTATTTTTA-CTATATTT
1 -TATA-TTA-TTTTTTTATCTATATTT
3871483 TCCTAACGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 19 0.44
26 17 0.40
27 7 0.16
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
TATATTATTTTTTTATCTATATTTA
Found at i:3871469 original size:17 final size:19
Alignment explanation
Indices: 3871444--3871482 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
3871434 ATATTATTTT
3871444 TTTATCTATATTTACT-TA
1 TTTATCTATATTTACTATA
*
3871462 TTTA-CTATTTTTACTATA
1 TTTATCTATATTTACTATA
3871480 TTT
1 TTT
3871483 TCCTAACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATCTATATTTACTATA
Found at i:3871608 original size:28 final size:27
Alignment explanation
Indices: 3871536--3871610 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 27
3871526 CTATGATTAC
3871536 TATTTTTAGTTAATATTA-TATGTATATT
1 TATTTTTA-TT-ATATTATTATGTATATT
*
3871564 TATTTTTCATATTTATTATTAT-TATATT
1 TATTTTT-AT-TATATTATTATGTATATT
3871592 TAGTATTTTATTATATTAT
1 TA-T-TTTTATTATATTAT
3871611 ACATACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 28 0.70
29 8 0.20
30 4 0.10
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
TATTTTTATTATATTATTATGTATATT
Found at i:3871631 original size:6 final size:6
Alignment explanation
Indices: 3871512--3871667 Score: 61
Period size: 6 Copynumber: 24.8 Consensus size: 6
3871502 TTTACTTCAT
* * * *
3871512 TTTAT- TTTATA TTTCTA TGATTACTA TTTTTA GTTA-A TATTATA TGTATA
1 TTTATA TTTATA TTTATA T--TTA-TA TTTATA TTTATA T-TTATA TTTATA
* *
3871562 TTTATT TTTCATA TTTATTA TTATTATA TTTAGTA TTT-TA -TTATA TTATACA
1 TTTATA TTT-ATA TTTA-TA -T-TTATA TTTA-TA TTTATA TTTATA TT-TATA
** * * * *
3871614 TACATT TTTATA TTTATA TATATA TATATA TTT-TA TTATTTA TTTACTA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TT-TATA TTTA-TA
3871663 TTTAT
1 TTTAT
3871668 TTATTTTCAA
Statistics
Matches: 113, Mismatches: 21, Indels: 33
0.68 0.13 0.20
Matches are distributed among these distances:
4 2 0.02
5 14 0.12
6 55 0.49
7 31 0.27
8 5 0.04
9 6 0.05
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:3871810 original size:23 final size:24
Alignment explanation
Indices: 3871764--3871824 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
3871754 ATATTTTATC
* *
3871764 TTCATTTATTTTATTTTATTCAAT
1 TTCATTTATTTTATTTCATCCAAT
*
3871788 TTCATTT-TTTTGTTTCATCCAA-
1 TTCATTTATTTTATTTCATCCAAT
3871810 TT-ATTTATGTTTATT
1 TTCATTTAT-TTTATT
3871825 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 17 0.55
24 7 0.23
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.66
Consensus pattern (24 bp):
TTCATTTATTTTATTTCATCCAAT
Found at i:3878085 original size:27 final size:28
Alignment explanation
Indices: 3878055--3878109 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
3878045 AGATAGAGAA
3878055 AAATAATGAAGAAGTGGGTG-AGTAGGC
1 AAATAATGAAGAAGTGGGTGAAGTAGGC
3878082 AAATAATGAAGAAGTGGGTGAAGTAGGC
1 AAATAATGAAGAAGTGGGTGAAGTAGGC
3878110 CATTTCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.42, C:0.04, G:0.36, T:0.18
Consensus pattern (28 bp):
AAATAATGAAGAAGTGGGTGAAGTAGGC
Found at i:3885261 original size:43 final size:46
Alignment explanation
Indices: 3885210--3885314 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
3885200 GTAACCATGC
*
3885210 AATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGGAAA
1 AATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGAAA
* * * * *
3885254 AAT-AGCTTACAAGCTTATGGAATTAAATGGTAAGTATTTTGGTAA
1 AATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGAAA
3885299 AATAAGCTTACGAGCT
1 AATAAGCTTACGAGCT
3885315 ATGGATAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
43 16 0.31
44 4 0.08
45 20 0.39
46 11 0.22
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (46 bp):
AATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGAAA
Found at i:3885301 original size:45 final size:45
Alignment explanation
Indices: 3885210--3885329 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 45
3885200 GTAACCATGC
** * *
3885210 AATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAAA
1 AATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGAAA
* *
3885254 AAT-AGCTTACAAGCTTATGGAATTAAATGGTAAGTATTTTGGTAA
1 AATAAGCTTACAAGCTTATGGAA-TAAATGGTAAGTATATTGGAAA
*
3885299 AATAAGCTTACGAGC-TATGG-ATAAATGGTAA
1 AATAAGCTTACAAGCTTATGGAATAAATGGTAA
3885330 AAGATTTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 26 0.39
44 5 0.08
45 25 0.38
46 10 0.15
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGAAA
Found at i:3885413 original size:26 final size:27
Alignment explanation
Indices: 3885380--3885433 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
3885370 AGTAAAATGA
3885380 TTTTATGGAAATTTGA-TTTTTGATAT
1 TTTTATGGAAATTTGATTTTTTGATAT
3885406 TTTTATGGAAATTTGATTTTTTGATAT
1 TTTTATGGAAATTTGATTTTTTGATAT
3885433 T
1 T
3885434 GAAAATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (27 bp):
TTTTATGGAAATTTGATTTTTTGATAT
Found at i:3885781 original size:30 final size:30
Alignment explanation
Indices: 3885747--3885803 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3885737 CTGTAGCAGC
3885747 TACTGTAGCATATCGATGCACTGTTCACGA
1 TACTGTAGCATATCGATGCACTGTTCACGA
* *
3885777 TACTGTAGCGTATCGATGTACTGTTCA
1 TACTGTAGCATATCGATGCACTGTTCA
3885804 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (30 bp):
TACTGTAGCATATCGATGCACTGTTCACGA
Found at i:3888161 original size:21 final size:21
Alignment explanation
Indices: 3888126--3888183 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
3888116 ATATGTATCA
3888126 TTATAATTAGTTATTTATAT-ATG
1 TTAT-ATTA-TTATTTATATGA-G
*
3888149 TTATATTATTATTAATATGAG
1 TTATATTATTATTTATATGAG
*
3888170 TTA-ACTATTATTTA
1 TTATATTATTATTTA
3888184 GCTCTTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 9 0.29
21 13 0.42
22 5 0.16
23 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (21 bp):
TTATATTATTATTTATATGAG
Found at i:3888209 original size:4 final size:4
Alignment explanation
Indices: 3888200--3891316 Score: 5394
Period size: 4 Copynumber: 789.8 Consensus size: 4
3888190 CTATGTGTTT
3888200 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3888248 TATC TA-- TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3888294 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3888342 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3888390 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TACC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3888438 TATC TATC TATC TATC TATC TATC TATC TACC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888486 TATC TACC TATC TATC TATC TACC TATC TACC TATC TATC TACC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * *
3888534 TATC TATC TATC TATC TACC TATC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888582 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888630 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888678 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888726 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888774 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888822 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
3888870 TATC TATC TACC TATC TATC TACC TATC TATC TACC TATC TACC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3888918 TACC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3888966 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3889014 TATC TATC TATCC TATC TATC TAGC TATC TATC TATC TATC TATC TATC
1 TATC TATC TAT-C TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889063 --TC TATC TATC TATC TATC --TC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889107 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889155 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889203 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3889251 TATC TATC TATC TCTC TATC TATC --TC TATC TATC TATC TATC TA--
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889295 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATCC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT-C TATC TATC
3889344 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889392 TATC TATC -ATC TA-C TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889438 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889486 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TA-- TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889532 TATC TATC TATC TATTC TATC TATC TATC TATC TATC TATC --TC TATC
1 TATC TATC TATC TA-TC TATC TATC TATC TATC TATC TATC TATC TATC
3889579 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3889627 TATC TATC TATC TATC TATC --TC TATC TATC TATC TCTC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889673 TA-C TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3889720 TATC TATC TAGC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889768 TATC --TC TATC TATC TATC TATC TATC --TC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889812 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3889860 TATC TATC TATC TATC -ATC TATC TATC TA-- TATC TATC TATC TCTTC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T-ATC
3889906 TATC TATC TATC TATC TATC TATC TATC TATC TA-- TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3889952 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890000 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890048 TATC TATC TATC TATC --TC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890094 TATC TATC TATC TATC TATC TATC TA-C TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890141 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3890189 TATC TCTC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890237 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890285 TATC TA-- TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890331 TATC TA-C TATC TATC ATATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC -TATC TATC TATC TATC TATC TATC TATC TATC
3890379 TATC TATC TATC TATC TATC TATC TATC TATC TATC --TC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890425 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC --TC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3890471 TATC TATC TATC TATC TATC GATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890519 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890567 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890615 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3890663 TA-C TATC TATC TATC TATC TATC ATCTC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC -TATC TATC TATC TATC TATC TATC
3890711 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3890759 TATC TATC TATC TATC TATC GATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890807 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890855 TATC TATC TATC TATC TATC TA-- TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890901 TATC TATC TATC TATC --TC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890947 TATC TATC TATC -ATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3890994 TATC TATC --TC TATC TATC TATC TA-C TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3891039 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3891087 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3891135 TATC TATC TATC TATC TATC TATC TA-C TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* *
3891182 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TCTA
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
3891230 TCTC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
3891278 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
3891317 TAGTTAGATA
Statistics
Matches: 2961, Mismatches: 98, Indels: 108
0.93 0.03 0.03
Matches are distributed among these distances:
2 38 0.01
3 30 0.01
4 2871 0.97
5 22 0.01
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.48
Consensus pattern (4 bp):
TATC
Found at i:3891352 original size:2 final size:2
Alignment explanation
Indices: 3891345--3891389 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3891335 TAGCTATGCT
3891345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3891387 TA T
1 TA T
3891390 GCAATATGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3897924 original size:29 final size:29
Alignment explanation
Indices: 3897884--3897991 Score: 126
Period size: 29 Copynumber: 3.7 Consensus size: 29
3897874 TCTTTTTTTG
* *
3897884 CATGGGATTATATCCCCGTCCTATTTCTA
1 CATGAGATTATATCCCCGTCCTGTTTCTA
**
3897913 CATGAGATTATATCATCGTCCTGTTTCTA
1 CATGAGATTATATCCCCGTCCTGTTTCTA
* * * *
3897942 TATGATATTATATCCTCATCCTGTTTCTA
1 CATGAGATTATATCCCCGTCCTGTTTCTA
* *
3897971 CATGTGATTATATTCCCGTCC
1 CATGAGATTATATCCCCGTCC
3897992 CGATTCTGCT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (29 bp):
CATGAGATTATATCCCCGTCCTGTTTCTA
Found at i:3899365 original size:171 final size:171
Alignment explanation
Indices: 3899080--3899420 Score: 585
Period size: 171 Copynumber: 2.0 Consensus size: 171
3899070 TTAACTTCAG
*
3899080 AGATCTGTTAGGATTTAGCTAGAGGACATTGGTGTTACTATTTCATAGACTATGTTATGTAATGT
1 AGATCTGTTAGGATTTAGCTAGAGGACATTGGTGTTACTATTTCATAGACTATGTTACGTAATGT
* * *
3899145 AACGGAGTACTTTATATGGTTTACTTGGGAATTCACGTATGTTGGGGTGTATTGGATCGACGATA
66 AACAGAGTACTTTAGATGGTTTACTTGGGAATTCACGTATGTTGGGGTGTATTGGATCAACGATA
*
3899210 CCAAGCATCTTCTCGATGATATGAAGTATTCTAAGGATCAT
131 CCAAGCATCTTCTCAATGATATGAAGTATTCTAAGGATCAT
* *
3899251 AGATCTGTTAGGATTTAGCTAGAGGACATTGGTGTTACTATTTCATAGAGTATGTTACGTATTGT
1 AGATCTGTTAGGATTTAGCTAGAGGACATTGGTGTTACTATTTCATAGACTATGTTACGTAATGT
*
3899316 AACAGAGTACTTTAGATGGTTTACTTGGGAATTCACGTCA-GTTGGGGTGTATTGGATCAAGGAT
66 AACAGAGTACTTTAGATGGTTTACTTGGGAATTCACGT-ATGTTGGGGTGTATTGGATCAACGAT
*
3899380 ACCAAGCATCTTCTCAATGATATGAATTATTCTAAGGATCA
130 ACCAAGCATCTTCTCAATGATATGAAGTATTCTAAGGATCA
3899421 GAGACTTCAT
Statistics
Matches: 160, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
171 159 0.99
172 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (171 bp):
AGATCTGTTAGGATTTAGCTAGAGGACATTGGTGTTACTATTTCATAGACTATGTTACGTAATGT
AACAGAGTACTTTAGATGGTTTACTTGGGAATTCACGTATGTTGGGGTGTATTGGATCAACGATA
CCAAGCATCTTCTCAATGATATGAAGTATTCTAAGGATCAT
Found at i:3903937 original size:24 final size:24
Alignment explanation
Indices: 3903905--3903951 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3903895 TTGTGAAAAG
3903905 TTAACATTGATTAAGTGAAATAAA
1 TTAACATTGATTAAGTGAAATAAA
* * *
3903929 TTAATATTGATTACGTGTAATAA
1 TTAACATTGATTAAGTGAAATAA
3903952 TAGTATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (24 bp):
TTAACATTGATTAAGTGAAATAAA
Found at i:3904890 original size:15 final size:16
Alignment explanation
Indices: 3904853--3904890 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3904843 TAAGTCACAA
*
3904853 AATATTTTAAATATAT
1 AATAATTTAAATATAT
*
3904869 AAAAATTTAAAT-TAT
1 AATAATTTAAATATAT
3904884 AATAATT
1 AATAATT
3904891 AGTATAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATTTAAATATAT
Found at i:3910120 original size:22 final size:23
Alignment explanation
Indices: 3910065--3910126 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3910055 CGATTCCTCT
3910065 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
3910088 AGGAGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
3910110 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
3910127 TCTGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:3925416 original size:14 final size:14
Alignment explanation
Indices: 3925397--3925427 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3925387 AGGATTTGGC
3925397 CATGAAGATATATT
1 CATGAAGATATATT
*
3925411 CATGAAGATTTATT
1 CATGAAGATATATT
3925425 CAT
1 CAT
3925428 TTAATTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (14 bp):
CATGAAGATATATT
Found at i:3939659 original size:16 final size:16
Alignment explanation
Indices: 3939638--3939671 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3939628 TAGATATTAT
*
3939638 CTTACTTGTTATCAAC
1 CTTACTGGTTATCAAC
*
3939654 CTTACTGGTTATGAAC
1 CTTACTGGTTATCAAC
3939670 CT
1 CT
3939672 GACATGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (16 bp):
CTTACTGGTTATCAAC
Found at i:3940165 original size:16 final size:16
Alignment explanation
Indices: 3940131--3940165 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3940121 TAAATTGATC
*
3940131 TGATATTTACTTTACT
1 TGATATTTACTTAACT
*
3940147 TGATATTTACTTAAGT
1 TGATATTTACTTAACT
3940163 TGA
1 TGA
3940166 AAGTTACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (16 bp):
TGATATTTACTTAACT
Found at i:3943346 original size:19 final size:19
Alignment explanation
Indices: 3943311--3943348 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3943301 ACACCATCTA
*
3943311 TTTGAATGAAGTTAAAAAT
1 TTTGAATGAAGTGAAAAAT
3943330 TTTGAACTGAA-TGAAAAAT
1 TTTGAA-TGAAGTGAAAAAT
3943349 AGCATGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (19 bp):
TTTGAATGAAGTGAAAAAT
Found at i:3947361 original size:137 final size:137
Alignment explanation
Indices: 3947106--3947642 Score: 624
Period size: 137 Copynumber: 3.9 Consensus size: 137
3947096 TAAATTTGGT
* * *
3947106 GATAACACGGTTCCTACGTGATTAGGAAATCTGGTTATCTAAGGGTGACGCTGCTCCAACGTGAT
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGCTGCTCCTACGTGAT
* * ** *
3947171 GAGGAGATCTGGTCGATGGATTAAATGGTTCCTACGTGAT-ATGGA-AGTATGGCCATCTTTATG
66 GAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGA-GGACAGTCTGGCCATCTTTA-G
3947234 GATAATTGA
129 GATAATTGA
* *
3947243 GATAATACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGC-GACTTCTACGTGA
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGCTG-CTCCTACGTGA
* * *
3947307 TGAGGAGGTTTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGT-TGGCCATCTATAGG
65 TGAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTCTGGCCATCTTTA-G
3947371 GATAATTGA
129 GATAATTGA
** ** * * * * *
3947380 GATAACATAGTTCCTTTGTAATGAGGAAGTTTGGCTATATAAGGGTGAAGCTGCTCCTACGTGAT
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGCTGCTCCTACGTGAT
* * * ** *
3947445 GAGGAGGTATGGTCGGTGGATGACACAGTTCCTATATAATGAGGAC-GTCTGGCCATCTTTAGGA
66 GAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTCTGGCCATCTTTAGGA
*
3947509 TAATGGA
131 TAATTGA
* * * *
3947516 GATAACACGGTTCCAACGTGATTAGGAAGAT-TGGTTATCTAAGGTTGACACTGCTCCTACGTGA
1 GATAACACGGTTCCTACGTGATTAGGAAG-TCTGGCTATCTAAGGGTGACGCTGCTCCTACGTGA
* * *
3947580 TGTGGAGATCTGGTCGGTGGAT--AACATTGTTCCTATGTGATGAAGACA-TCTGGCCATCTTTA
65 TGAGGAGATCTGGTCGGTGGATGAAACA--GTTCCTACGTGATGAGGACAGTCTGGCCATCTTTA
3947642 G
128 G
3947643 AGAAATTTGT
Statistics
Matches: 341, Mismatches: 50, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
134 3 0.01
136 112 0.33
137 221 0.65
138 5 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (137 bp):
GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGCTGCTCCTACGTGAT
GAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTCTGGCCATCTTTAGGA
TAATTGA
Found at i:3947596 original size:273 final size:273
Alignment explanation
Indices: 3947145--3947638 Score: 649
Period size: 273 Copynumber: 1.8 Consensus size: 273
3947135 TCTGGTTATC
* * * ** * *
3947145 TAAGGGTGACGCTGCTCCAACGTGATGAGGAGATCTGGTCGATGGATTAAATGGTTCCTACGTGA
1 TAAGGGTGAAGCTGCTCCAACGTGATGAGGAGATATGGTCGATGGATGAAACAGTTCCTACATAA
* * *
3947210 TATGGAAGTATGGCCATCTTTATGGATAATTGAGATAATACGGTTCCTACGTGATTAGGAAGTCT
66 TATGGAAGTATGGCCATCTTTATGGATAATGGAGATAACACGGTTCCAACGTGATTAGGAAGTCT
* * * *
3947275 GGCTATCTAAGGGTGACGCGACTTCTACGTGATGAGGAGGTTTGGTCGGTGGATGAAACA-GTTC
131 GGCTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGTGGAT--AACATGTTC
*
3947339 CTACGTGATGAGGACAGT-TGGCCATCTATAGGGATAATTGAGATAACATAGTTCCTTTGTAATG
194 CTACGTGATGAAGACA-TCTGGCCATCTATAGGGATAATTGAGATAACATAGTTCCTTTGTAATG
3947403 AGGAAGTTTGGCTATA
258 AGGAAGTTTGGCTATA
* * * * *
3947419 TAAGGGTGAAGCTGCTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACACAGTTCCTATATAA
1 TAAGGGTGAAGCTGCTCCAACGTGATGAGGAGATATGGTCGATGGATGAAACAGTTCCTACATAA
* *
3947484 TGA-GGACGTCTGGCCATCTTTA-GGATAATGGAGATAACACGGTTCCAACGTGATTAGGAAGAT
66 T-ATGGAAGTATGGCCATCTTTATGGATAATGGAGATAACACGGTTCCAACGTGATTAGGAAG-T
* * *
3947547 -TGGTTATCTAAGGTTGACACTG-CTCCTACGTGATGTGGAGATCTGGTCGGTGGATAACATTGT
129 CTGGCTATCTAAGGGTGACAC-GACTCCTACGTGATGAGGAGATCTGGTCGGTGGATAACA-TGT
*
3947610 TCCTATGTGATGAAGACATCTGGCCATCT
192 TCCTACGTGATGAAGACATCTGGCCATCT
3947639 TTAGAGAAAT
Statistics
Matches: 188, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
271 4 0.02
272 1 0.01
273 109 0.58
274 73 0.39
275 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (273 bp):
TAAGGGTGAAGCTGCTCCAACGTGATGAGGAGATATGGTCGATGGATGAAACAGTTCCTACATAA
TATGGAAGTATGGCCATCTTTATGGATAATGGAGATAACACGGTTCCAACGTGATTAGGAAGTCT
GGCTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGTGGATAACATGTTCCT
ACGTGATGAAGACATCTGGCCATCTATAGGGATAATTGAGATAACATAGTTCCTTTGTAATGAGG
AAGTTTGGCTATA
Found at i:3947697 original size:36 final size:34
Alignment explanation
Indices: 3947645--3947765 Score: 110
Period size: 36 Copynumber: 3.6 Consensus size: 34
3947635 ATCTTTAGAG
*
3947645 AAATTTGTTTCCAGAGAAACTGTCTCAAGCAAGAT
1 AAATTTGTTTCAAGAGAAACTGTCTCAAG-AAGAT
**
3947680 ACAATTTGTTTCAAGAGAAA-AATCTC-A-AAGAT
1 A-AATTTGTTTCAAGAGAAACTGTCTCAAGAAGAT
* *
3947712 ---TTATGTTTCAAGAGAAATTGTCTCAAGAGAGACA
1 AAATT-TGTTTCAAGAGAAACTGTCTCAAGA-AGA-T
3947746 AAATTTGTTTCAAGAGAAAC
1 AAATTTGTTTCAAGAGAAAC
3947766 AATCTCAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
28 2 0.03
29 14 0.20
30 4 0.06
31 1 0.01
32 6 0.09
33 3 0.04
34 1 0.01
35 5 0.07
36 31 0.45
37 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (34 bp):
AAATTTGTTTCAAGAGAAACTGTCTCAAGAAGAT
Found at i:3947754 original size:65 final size:67
Alignment explanation
Indices: 3947650--3947786 Score: 199
Period size: 65 Copynumber: 2.1 Consensus size: 67
3947640 TAGAGAAATT
* * *
3947650 TGTTTCCAGAGAAACTGTCTCAAGCAAGATACAATTTGTTTCAAGAGAAA-AATCTCAAA-GATT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGATT
3947713 TA
66 TA
* *
3947715 TGTTTCAAGAGAAATTGTCTCAAG-AGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCA-AGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGAT
3947779 TTA
65 TTA
3947782 TGTTT
1 TGTTT
3947787 TTTTCAAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 44 0.69
66 9 0.14
67 10 0.16
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGATT
TA
Found at i:3947851 original size:101 final size:102
Alignment explanation
Indices: 3947726--3947926 Score: 232
Period size: 102 Copynumber: 2.0 Consensus size: 102
3947716 GTTTCAAGAG
* * * *
3947726 AAATTGTCTCAAGAGAGACAAAATTTG-TTTCAAGAGAAACAATCTCAA-AG-GTTTTATGTTTT
1 AAATTGTCTCAAGAGAGACAAAATTTGTTTTCAA-AGAAACAATATCAAGAGAGATTAAT-TTTG
* *
3947788 TTTCAAGTGAAACAATTTCCAAATTTTCTGCTTTGAGGAA
64 TTTCAAGTAAAACAACTTCCAAATTTT-TGCTTTGAGGAA
* * *
3947828 AAATTGTCTCCAGCA-AGAC-AAATTTGTTTTGAAAGAAACAATATCAAGTGAGATTAATTTTGT
1 AAATTGTCTCAAG-AGAGACAAAATTTGTTTTCAAAGAAACAATATCAAGAGAGATTAATTTTGT
* *
3947891 TTCAAGTAAAACAACTTCGAAATTTTTGTTTTGAGG
65 TTCAAGTAAAACAACTTCCAAATTTTTGCTTTGAGG
3947927 GGAACAGTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
101 29 0.35
102 49 0.58
103 6 0.07
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (102 bp):
AAATTGTCTCAAGAGAGACAAAATTTGTTTTCAAAGAAACAATATCAAGAGAGATTAATTTTGTT
TCAAGTAAAACAACTTCCAAATTTTTGCTTTGAGGAA
Found at i:3950627 original size:14 final size:13
Alignment explanation
Indices: 3950578--3950652 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 13
3950568 TCTTGTCTTC
3950578 TTTTCTTT-CTTT
1 TTTTCTTTGCTTT
3950590 ATTTTCTTT-C-TT
1 -TTTTCTTTGCTTT
*
3950602 GTTT-TTT--TTT
1 TTTTCTTTGCTTT
3950612 TTTTCTTTGCTCTT
1 TTTTCTTTGCT-TT
*
3950626 TTTCCTTTG-TTT
1 TTTTCTTTGCTTT
3950638 TTTTCTCTTGCTTT
1 TTTTCT-TTGCTTT
3950652 T
1 T
3950653 CTCTCTACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.16
11 6 0.12
12 9 0.18
13 14 0.27
14 14 0.27
ACGTcount: A:0.01, C:0.16, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTCTTTGCTTT
Found at i:3951816 original size:72 final size:74
Alignment explanation
Indices: 3951693--3951841 Score: 284
Period size: 72 Copynumber: 2.0 Consensus size: 74
3951683 CTTTAATTGT
3951693 TCAAATCTTGCTTCTATTCTCAATGTGGTGTCACGTGATCAGGACCACTTCCATTAAATTCTCCG
1 TCAAATCTTGCTTCTATTCTCAATGTGGTGTCACGTGATCAGGACCACTTCCATTAAATTCTCCG
3951758 AATTAAACC
66 AATTAAACC
3951767 TCAAATCTTGCTTCTATTCTC-ATGTGGT-TCACGTGATCAGGACCACTTCCATTAAATTCTCCG
1 TCAAATCTTGCTTCTATTCTCAATGTGGTGTCACGTGATCAGGACCACTTCCATTAAATTCTCCG
3951830 AATTAAACC
66 AATTAAACC
3951839 TCA
1 TCA
3951842 TGTTTCACGA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 47 0.63
73 7 0.09
74 21 0.28
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (74 bp):
TCAAATCTTGCTTCTATTCTCAATGTGGTGTCACGTGATCAGGACCACTTCCATTAAATTCTCCG
AATTAAACC
Found at i:3954274 original size:22 final size:23
Alignment explanation
Indices: 3954220--3954274 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3954210 ATTCCTCTAG
3954220 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
*
3954243 GGAGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
*
3954265 GGGGGTATCG
1 GGGGGAATCG
3954275 ATTCTCTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:3985740 original size:3 final size:3
Alignment explanation
Indices: 3985732--3985756 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3985722 AAATAGATAT
3985732 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3985757 ATAAAAAAAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3986293 original size:138 final size:138
Alignment explanation
Indices: 3985958--3986497 Score: 605
Period size: 138 Copynumber: 3.9 Consensus size: 138
3985948 TAAATTTGGT
* * * *
3985958 GATAACACGGTTCCTATGTGATTAGGAAATCTGGTTATCTAAGGGTGACACTGCTCCAACGTGAT
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGAT
* * ** * *
3986023 GAGGAGATCTGGTCGATGGATTAAATGGTTCCTACGTGATGTGGA-AGTATGGCCATCTTTATGG
66 GAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTATGGCCATCTTTAGGG
3986087 ATAATTGA
131 ATAATTGA
* * *
3986095 GATAATACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACGC-GACTTCTACGTGA
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACACTG-CTCCTACGTGA
* * *
3986159 TGAGGAGGTTTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGT-TGGCCATCTATAGG
65 TGAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTATGGCCATCTTTA-G
3986223 GGATAATTGA
129 GGATAATTGA
** ** * * *
3986233 GATAACATAGTTCCTTTGTAATGAGGAAGTCTGGCTATATAAGGGTGA-AGCTGCTCCTACGTGA
1 GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACA-CTGCTCCTACGTGA
* * ** * *
3986297 TGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTATATAATGAGGAC-GTCTGGCCATCTTTAGG
65 TGAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTATGGCCATCTTTAGG
*
3986361 GATAAATGGA
130 GAT-AATTGA
* * *
3986371 GATAACACGGTTCCAACGTGATTAGGAAGAT-TGGTTATCTAAGGTTGACACTGCTCCTACGTGA
1 GATAACACGGTTCCTACGTGATTAGGAAG-TCTGGCTATCTAAGGGTGACACTGCTCCTACGTGA
* * * *
3986435 TGTGGAGATCTGGTCGGTGGAT--AACATTATTCCTATGTGATGAAGG-CA-TCTGGCCATCTTT
65 TGAGGAGATCTGGTCGGTGGATGAAACA--GTTCCTACGTGATG-AGGACAGTATGGCCATCTTT
3986496 AG
127 AG
3986498 AGAAATTTGT
Statistics
Matches: 341, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
136 4 0.01
137 112 0.33
138 219 0.64
139 6 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (138 bp):
GATAACACGGTTCCTACGTGATTAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGAT
GAGGAGATCTGGTCGGTGGATGAAACAGTTCCTACGTGATGAGGACAGTATGGCCATCTTTAGGG
ATAATTGA
Found at i:3986562 original size:36 final size:34
Alignment explanation
Indices: 3986500--3986630 Score: 101
Period size: 36 Copynumber: 3.8 Consensus size: 34
3986490 ATCTTTAGAG
* *
3986500 AAATTTGTTTCCAGAGAAACT-GTCTCAAGCAAGAT
1 AAATTTGTTTCAAGAGAAA-TAATCTCAAG-AAGAT
*
3986535 ACAATTTGTTTCAAGAGAAATAATCTC-A-AAGGT
1 A-AATTTGTTTCAAGAGAAATAATCTCAAGAAGAT
* ** *
3986568 --TTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACA
1 AAATT-TGTTTCAAGAGAAATAATCTCAAGA-AGA-T
*
3986603 AAATTTGTTTCAAGAGAAACAATCTCAA
1 AAATTTGTTTCAAGAGAAATAATCTCAA
3986631 AGGTTTTATG
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
30 2 0.03
31 19 0.25
32 1 0.01
33 5 0.07
34 2 0.03
35 3 0.04
36 41 0.55
37 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (34 bp):
AAATTTGTTTCAAGAGAAATAATCTCAAGAAGAT
Found at i:3986579 original size:31 final size:31
Alignment explanation
Indices: 3986541--3986643 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
3986531 AGATACAATT
3986541 TGTTTCAAGAGAAATAATCTCAAAGGTTTTA
1 TGTTTCAAGAGAAATAATCTCAAAGGTTTTA
** **
3986572 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT-
1 TGTTTCAAGAGAAATAATCTCAA-AG-G----TTTTA
*
3986608 TGTTTCAAGAGAAACAATCTCAAAGGTTTTA
1 TGTTTCAAGAGAAATAATCTCAAAGGTTTTA
3986639 TGTTT
1 TGTTT
3986644 TTTTCAAGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
30 2 0.04
31 26 0.46
32 2 0.04
33 1 0.02
34 1 0.02
35 2 0.04
36 20 0.36
37 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (31 bp):
TGTTTCAAGAGAAATAATCTCAAAGGTTTTA
Found at i:3986613 original size:67 final size:67
Alignment explanation
Indices: 3986505--3986643 Score: 217
Period size: 67 Copynumber: 2.1 Consensus size: 67
3986495 TAGAGAAATT
* * * *
3986505 TGTTTCCAGAGAAACTGTCTCAAGCAAGATACAATTTGTTTCAAGAGAAATAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
3986570 TA
66 TA
*
3986572 TGTTTCAAGAGAAATTGTCTCAAG-AGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCA-AGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
3986636 TTA
65 TTA
3986639 TGTTT
1 TGTTT
3986644 TTTTCAAGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 1 0.02
67 65 0.98
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
TA
Found at i:3989464 original size:4 final size:4
Alignment explanation
Indices: 3989455--3989497 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
3989445 CTTGTCTTCT
* *
3989455 TTTC TTTC TTTC TTTTC TTTC TTTG TTTT TTTC TTT- TTTC TTT
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
3989498 GCTCTTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:3989467 original size:13 final size:13
Alignment explanation
Indices: 3989451--3989490 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
3989441 GCTTCTTGTC
3989451 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
3989464 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
*
3989477 TTGTTTT-TTTCT
1 TTCTTTTCTTTCT
3989489 TT
1 TT
3989491 TTTCTTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:3989511 original size:21 final size:22
Alignment explanation
Indices: 3989463--3989525 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
3989453 CTTTTCTTTC
*
3989463 TTTCTTTTCTTTCTTTG-T-TT
1 TTTCCTTTCTTTCTTTGCTCTT
*
3989483 TTTTCTTT-TTTCTTTGCTCTT
1 TTTCCTTTCTTTCTTTGCTCTT
* *
3989504 TTTCCTTTGTTT-TTTTCTCTT
1 TTTCCTTTCTTTCTTTGCTCTT
3989525 T
1 T
3989526 GCTTTTCCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.22
20 7 0.19
21 18 0.50
22 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTCCTTTCTTTCTTTGCTCTT
Found at i:3989517 original size:33 final size:32
Alignment explanation
Indices: 3989459--3989530 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
3989449 TCTTCTTTTC
* *
3989459 TTTCTTTCTTTTCTTTCTTTGTTTTTTTCTTT
1 TTTCTTTCTTTTCTTCCTTTGTTTTTTTCTCT
3989491 TTTCTTTGCTCTTT-TTCCTTTGTTTTTTTCTCT
1 TTTCTTT-CT-TTTCTTCCTTTGTTTTTTTCTCT
*
3989524 TTGCTTT
1 TTTCTTT
3989531 TCCTCTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 7 0.20
33 25 0.71
34 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (32 bp):
TTTCTTTCTTTTCTTCCTTTGTTTTTTTCTCT
Found at i:3989531 original size:13 final size:12
Alignment explanation
Indices: 3989454--3989531 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 12
3989444 TCTTGTCTTC
3989454 TTTTCTTT-CTTT
1 TTTTCTTTGC-TT
3989466 CTTTTCTTT-CTT
1 -TTTTCTTTGCTT
*
3989478 TGTTT-TTTTCTT
1 T-TTTCTTTGCTT
3989490 TTTTCTTTGCTCT
1 TTTTCTTTGCT-T
*
3989503 TTTTCCTTTGTTTT
1 TTTT-CTTTG-CTT
3989517 TTTCTCTTTGCTT
1 TTT-TCTTTGCTT
3989530 TT
1 TT
3989532 CCTCTACTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
11 7 0.13
12 14 0.25
13 18 0.33
14 14 0.25
15 2 0.04
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTCTTTGCTT
Found at i:3989531 original size:14 final size:14
Alignment explanation
Indices: 3989488--3989531 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3989478 TGTTTTTTTC
3989488 TTTTT-TCTTTGCT
1 TTTTTCTCTTTGCT
*
3989501 CTTTTTC-CTTTGTT
1 -TTTTTCTCTTTGCT
3989515 TTTTTCTCTTTGCT
1 TTTTTCTCTTTGCT
3989529 TTT
1 TTT
3989532 CCTCTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTCTCTTTGCT
Done.