Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 16 of 147
Found at i:3458114 original size:30 final size:28
Alignment explanation
Indices: 3458008--3458136 Score: 86
Period size: 30 Copynumber: 4.4 Consensus size: 28
3457998 AGTGTATTTA
* *
3458008 TTATTTTATATTTTATATTTATTTTTA-TAA
1 TTATTTTAT-TTTTATCTTTA-TTTTACT-T
* *
3458038 TTATGTTCATTTTTATTTTTTATTTTA--T
1 TTAT-TTTATTTTTA-TCTTTATTTTACTT
3458066 TTATTTTATTCATTTATCTTTATTTTACTT
1 TTATTTTATT--TTTATCTTTATTTTACTT
*
3458096 TTACGTTTTATTTTTATCTTTATCGTTAC-T
1 TTA--TTTTATTTTTATCTTTAT-TTTACTT
*
3458126 TTATCTTATTT
1 TTATTTTATTT
3458137 ATTTTATCAT
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
27 5 0.06
28 21 0.25
29 4 0.05
30 33 0.40
31 13 0.16
32 7 0.08
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (28 bp):
TTATTTTATTTTTATCTTTATTTTACTT
Found at i:3464811 original size:2 final size:2
Alignment explanation
Indices: 3464804--3464852 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
3464794 ACTATGTAAA
* * *
3464804 AT AT AT AT AT AT AT AT AT AT -T TT AT GT A- AA AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3464843 AT AT AT AT AT
1 AT AT AT AT AT
3464853 GCAAATACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3466126 original size:15 final size:15
Alignment explanation
Indices: 3466106--3466134 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3466096 AATGAAATTT
3466106 AAAATAAAATTAATA
1 AAAATAAAATTAATA
3466121 AAAATAAAATTAAT
1 AAAATAAAATTAAT
3466135 TTATTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAATTAATA
Found at i:3468371 original size:11 final size:11
Alignment explanation
Indices: 3468333--3468376 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
3468323 ATTAAATATG
3468333 TAAATATATTT
1 TAAATATATTT
*
3468344 TACATTACTATTTT
1 TA-AATA-TA-TTT
3468358 TAAATATATTT
1 TAAATATATTT
3468369 TAAATATA
1 TAAATATA
3468377 AAATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 13 0.46
12 5 0.18
13 5 0.18
14 5 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAATATATTT
Found at i:3473688 original size:29 final size:29
Alignment explanation
Indices: 3473651--3473710 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
3473641 AGTTAACAGA
* *
3473651 TTTATAGTTTAAACATCACATTAGAA-ATT
1 TTTAAAGTTCAAACATCACATT-GAACATT
*
3473680 TTTAAAGTTCAAATATCACATTGAACATT
1 TTTAAAGTTCAAACATCACATTGAACATT
3473709 TT
1 TT
3473711 ACTATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (29 bp):
TTTAAAGTTCAAACATCACATTGAACATT
Found at i:3483358 original size:15 final size:14
Alignment explanation
Indices: 3483327--3483374 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3483317 TAACAAACTT
*
3483327 AAAATAAAAGAACA
1 AAAATAAAAGAAAA
*
3483341 AAAATAAAAATAAAA
1 AAAAT-AAAAGAAAA
**
3483356 AAAATGGAAGAAAA
1 AAAATAAAAGAAAA
3483370 AAAAT
1 AAAAT
3483375 CAAGCAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.10
Consensus pattern (14 bp):
AAAATAAAAGAAAA
Found at i:3484138 original size:100 final size:99
Alignment explanation
Indices: 3484023--3484213 Score: 266
Period size: 100 Copynumber: 1.9 Consensus size: 99
3484013 TTATAAATTT
* *
3484023 AATTTTTTTT-AAAAAAGATTATTAAACATTT-CAATAGTTTGATAAAATTTAATTTCAAGATTT
1 AATTTTTTTTAAAAAAAG-TCATTAAAC-TTTCCAACAGTTTGATAAAATTTAATTTCAAGATTT
3484086 AAAATT-TTC-AGTAGTTT-AGTAGGATTAATTTTAAAA
64 -AAATTCTTCGA-TAGTTTGA-TAGGATTAATTTTAAAA
*
3484122 AATTATTTTTTAAAAAAAGTCATTAAACTTTCCAACAGTTTGATAAGATTTAATTTCAAGATTTA
1 AATT-TTTTTTAAAAAAAGTCATTAAACTTTCCAACAGTTTGATAAAATTTAATTTCAAGATTTA
3484187 AATTCTTCGATAGTTTGATAGGATTAA
65 AATTCTTCGATAGTTTGATAGGATTAA
3484214 ATAAAAAATG
Statistics
Matches: 83, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
99 12 0.14
100 62 0.75
101 9 0.11
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (99 bp):
AATTTTTTTTAAAAAAAGTCATTAAACTTTCCAACAGTTTGATAAAATTTAATTTCAAGATTTAA
ATTCTTCGATAGTTTGATAGGATTAATTTTAAAA
Found at i:3493884 original size:18 final size:17
Alignment explanation
Indices: 3493858--3493891 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3493848 TATATTTACA
3493858 TATAATTAAAATATAATT
1 TATAATTAAAAT-TAATT
*
3493876 TATATTTAAAATTAAT
1 TATAATTAAAATTAAT
3493892 ATTTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAATTAAAATTAATT
Found at i:3499202 original size:9 final size:9
Alignment explanation
Indices: 3499188--3499222 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
3499178 GTTTATATCT
3499188 GAACGCAAC
1 GAACGCAAC
3499197 GAACGCAAC
1 GAACGCAAC
3499206 GAACGCAAC
1 GAACGCAAC
3499215 GAACGCAA
1 GAACGCAA
3499223 ACGCCGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.31, G:0.23, T:0.00
Consensus pattern (9 bp):
GAACGCAAC
Found at i:3499906 original size:19 final size:19
Alignment explanation
Indices: 3499879--3499922 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3499869 AGATGGTGTT
* *
3499879 GGACACAATCCAAGGCTTC
1 GGACCCAATCCAAGGCCTC
3499898 GGACCCAATCCAAGGCCTC
1 GGACCCAATCCAAGGCCTC
3499917 GGACCC
1 GGACCC
3499923 GTCCATGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.39, G:0.23, T:0.11
Consensus pattern (19 bp):
GGACCCAATCCAAGGCCTC
Found at i:3507435 original size:219 final size:220
Alignment explanation
Indices: 3507076--3507482 Score: 584
Period size: 219 Copynumber: 1.9 Consensus size: 220
3507066 TCTTTTACAG
** *
3507076 TAAAACACCTTCAATATACCATGATGGTTATAGAAGTCATTTATTTAAAAATACGCCTTCAATAT
1 TAAAACACCTTCAATATACCACAATGGTTATAGAAGGCATTTATTTAAAAATAC-CCTTCAATAT
* * * *
3507141 ACCTTTAAACTTAGTAATCCATTATGGAAAGCGTTTGTTAATAACAGATGCTTTCAATATTTTCC
65 ACCTTTAAACTTAATAATCCATTATGGAAAGCATTTGTTAATAACAGACGCCTTCAATATTTTCC
* ***
3507206 CTCTAAAAATTTTAGGCATTATTAAAGGCATCTTTTACTGTAAAATACCTTCAATATACCACGAT
130 CTCAAAAAATTTTAAAAATTATTAAAGGCATCTTTTACTGTAAAATACCTTCAATATACCACGAT
3507271 GGGATTATTAAAGGCATCTTTTATTA
195 GGGATTATTAAAGGCATCTTTTATTA
* * * *
3507297 TAAAACGCCTTCAATATAGCACAATTGTTATAGAAGGCGTTTATTTAAAAAGTA-CCTTCAATAT
1 TAAAACACCTTCAATATACCACAATGGTTATAGAAGGCATTTATTTAAAAA-TACCCTTCAATAT
* * *
3507361 A-CTTTAAACTTAATAATCCATTATTGAAGGCATTTGTTAATAACAGACGCCTTCAATATTTTCT
65 ACCTTTAAACTTAATAATCCATTATGGAAAGCATTTGTTAATAACAGACGCCTTCAATATTTTCC
* * * *
3507425 CTCAAAAAATTTTAAAAATTATTAAAGGCATTTTTTAGTGTAAAATGCCTTTAATATA
130 CTCAAAAAATTTTAAAAATTATTAAAGGCATCTTTTACTGTAAAATACCTTCAATATA
3507483 TCGTCACACA
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
219 106 0.65
220 11 0.07
221 44 0.27
222 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (220 bp):
TAAAACACCTTCAATATACCACAATGGTTATAGAAGGCATTTATTTAAAAATACCCTTCAATATA
CCTTTAAACTTAATAATCCATTATGGAAAGCATTTGTTAATAACAGACGCCTTCAATATTTTCCC
TCAAAAAATTTTAAAAATTATTAAAGGCATCTTTTACTGTAAAATACCTTCAATATACCACGATG
GGATTATTAAAGGCATCTTTTATTA
Found at i:3512611 original size:18 final size:21
Alignment explanation
Indices: 3512571--3512611 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
3512561 ATTTAGTGGC
3512571 GTTTTGATAATAAACACTTGAA
1 GTTTTGATAATAAACAC-TGAA
3512593 GTTTT-ATAA-AAACAC-GAA
1 GTTTTGATAATAAACACTGAA
3512611 G
1 G
3512612 GCTAGCAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.21
20 6 0.32
21 4 0.21
22 5 0.26
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (21 bp):
GTTTTGATAATAAACACTGAA
Found at i:3514943 original size:14 final size:15
Alignment explanation
Indices: 3514924--3514955 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3514914 TTCTAAATTC
3514924 TCTCAAAA-TCTTCT
1 TCTCAAAATTCTTCT
3514938 TCTCAAAATTCTTCT
1 TCTCAAAATTCTTCT
3514953 TCT
1 TCT
3514956 TTACCAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCAAAATTCTTCT
Found at i:3515095 original size:35 final size:35
Alignment explanation
Indices: 3515049--3515120 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3515039 TGATCACTTG
3515049 AATAATAAACATGAATTTGTTTATCTTCTTTAGTA
1 AATAATAAACATGAATTTGTTTATCTTCTTTAGTA
3515084 AATAATAAACATGAATTTGTTTATCTTCTTTAGTA
1 AATAATAAACATGAATTTGTTTATCTTCTTTAGTA
3515119 AA
1 AA
3515121 CTCACCTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (35 bp):
AATAATAAACATGAATTTGTTTATCTTCTTTAGTA
Found at i:3519219 original size:15 final size:16
Alignment explanation
Indices: 3519195--3519238 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3519185 TCAAAAACTG
*
3519195 AAATTCAAAAAAATC-
1 AAATCCAAAAAAATCA
* *
3519210 CAATCTAAAAAAATCA
1 AAATCCAAAAAAATCA
3519226 AAATCCAAAAAAA
1 AAATCCAAAAAAA
3519239 AGACTCGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATCCAAAAAAATCA
Found at i:3520364 original size:17 final size:17
Alignment explanation
Indices: 3520333--3520365 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3520323 ACAAAAGTAA
3520333 TATATAATATATATTTG
1 TATATAATATATATTTG
3520350 TATA-AATATATTATTT
1 TATATAATATA-TATTT
3520366 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATATAATATATATTTG
Found at i:3528295 original size:48 final size:48
Alignment explanation
Indices: 3528239--3528338 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
3528229 TTTGTAAAAG
* *
3528239 ATTTTCGAAAATGGATTTTTAGAA-GTTCTTAAAGGCTTCCGGACATCC
1 ATTTTCGAAAATGCATTTTTAGAATG-TCTTAAAGGCATCCGGACATCC
* * *
3528287 ATTTTCGAAAATTCATTTTTGGAATGTCTTAAAGGCATCTGGACATCC
1 ATTTTCGAAAATGCATTTTTAGAATGTCTTAAAGGCATCCGGACATCC
3528335 ATTT
1 ATTT
3528339 CTGGAAACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (48 bp):
ATTTTCGAAAATGCATTTTTAGAATGTCTTAAAGGCATCCGGACATCC
Found at i:3528872 original size:15 final size:16
Alignment explanation
Indices: 3528852--3528884 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3528842 TAATTTATTT
3528852 TTAATTA-TTTTTCAA
1 TTAATTATTTTTTCAA
3528867 TTAATTATTTTTTCAA
1 TTAATTATTTTTTCAA
3528883 TT
1 TT
3528885 GTAATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTATTTTTTCAA
Found at i:3529677 original size:41 final size:41
Alignment explanation
Indices: 3529598--3529679 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
3529588 TTAAGTATAG
*
3529598 ATTTAAAATATTATTATATTAAAAAAATTATTTAATTTTAA
1 ATTTAAAATATTATTATATTAAAAAAATTATTAAATTTTAA
*
3529639 ATTTAAAATA-TATTTAATATT-ATAAAATT-TTAACATTTTAA
1 ATTTAAAATATTA-TT-ATATTAAAAAAATTATTAA-ATTTTAA
3529680 TAATAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
40 5 0.14
41 26 0.72
42 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (41 bp):
ATTTAAAATATTATTATATTAAAAAAATTATTAAATTTTAA
Found at i:3529804 original size:15 final size:16
Alignment explanation
Indices: 3529784--3529818 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3529774 ACACTTTTTA
3529784 ATTTTTT-AAATTCAT
1 ATTTTTTAAAATTCAT
*
3529799 ATTTTTTAAAATTTAT
1 ATTTTTTAAAATTCAT
3529815 ATTT
1 ATTT
3529819 AAGAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTTTAAAATTCAT
Found at i:3530137 original size:75 final size:76
Alignment explanation
Indices: 3530014--3530166 Score: 281
Period size: 75 Copynumber: 2.0 Consensus size: 76
3530004 ATATTTATAT
* *
3530014 ATAATATGATTTCAAAATCCAATTAGTTATTGTTATTTGTAACAATA-TTTTGATATAACTATTA
1 ATAATATGATTTCAAAATCCAATTAGTTATTGTTATTTGTAACAATATTTTTAATATAAATATTA
3530078 GGTTTAAATCA
66 GGTTTAAATCA
3530089 ATAATATGATTTCAAAATCCAATTAGTTATTGTTATTTGTAACAATATTTTTAATATAAATATTA
1 ATAATATGATTTCAAAATCCAATTAGTTATTGTTATTTGTAACAATATTTTTAATATAAATATTA
3530154 GGTTTAAATCA
66 GGTTTAAATCA
3530165 AT
1 AT
3530167 GTAATCAAGT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 47 0.63
76 28 0.37
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (76 bp):
ATAATATGATTTCAAAATCCAATTAGTTATTGTTATTTGTAACAATATTTTTAATATAAATATTA
GGTTTAAATCA
Found at i:3530878 original size:10 final size:10
Alignment explanation
Indices: 3530863--3530897 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3530853 TGAAAATAAA
3530863 TTTTTAAAAG
1 TTTTTAAAAG
*
3530873 TTTTTAAAGG
1 TTTTTAAAAG
3530883 TTTTTAAAAG
1 TTTTTAAAAG
3530893 CTTTT
1 -TTTT
3530898 CAAATATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (10 bp):
TTTTTAAAAG
Found at i:3536571 original size:2 final size:2
Alignment explanation
Indices: 3536564--3536611 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3536554 CAAGTATTAC
* * * *
3536564 AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3536606 AT AT AT
1 AT AT AT
3536612 GCAGATGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3542039 original size:22 final size:22
Alignment explanation
Indices: 3542012--3542055 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3542002 TAAAAGAGAA
3542012 ATCAAGTTATATCAATAAATAC
1 ATCAAGTTATATCAATAAATAC
3542034 ATCAAGTTATATCAATAAATAC
1 ATCAAGTTATATCAATAAATAC
3542056 TTTAAGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (22 bp):
ATCAAGTTATATCAATAAATAC
Found at i:3543131 original size:23 final size:21
Alignment explanation
Indices: 3543095--3543137 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3543085 AATTTATTTT
3543095 AAAAAATAATTTTTGGATTTAA
1 AAAAAATAATTTTTGG-TTTAA
3543117 AAAAAATAATTTTTTGGTTTA
1 AAAAAATAA-TTTTTGGTTTA
3543138 CGAACAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
AAAAAATAATTTTTGGTTTAA
Found at i:3548654 original size:87 final size:88
Alignment explanation
Indices: 3548547--3548743 Score: 261
Period size: 87 Copynumber: 2.2 Consensus size: 88
3548537 TTCAACAAAC
* * * * * *
3548547 ACTACGTTTTTAATATTAAAAGCGTAATCTTTGTTAAAATTATAAAATTTTGAAAAATAATTTTT
1 ACTACATTTTTAATCTTAAAAACATAATCTTTCTTAAAATTATAAAATTTTGAAAAATAAATTTT
* * *
3548612 TTCACAATATATTTTCAATATAG
66 CTCACAATATATTTTCAATAGAA
* * *
3548635 ACTACA-TTTTAATCTTAAAAACATAGTTTTTCTTGAAATTATAAAATTTTGAAAAATAAATTTT
1 ACTACATTTTTAATCTTAAAAACATAATCTTTCTTAAAATTATAAAATTTTGAAAAATAAATTTT
*
3548699 CTCATAATATATTTTCAATAGAA
66 CTCACAATATATTTTCAATAGAA
*
3548722 ACTATATTTTTAATCTTAAAAA
1 ACTACATTTTTAATCTTAAAAA
3548744 TATATTTTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 74 0.79
88 20 0.21
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (88 bp):
ACTACATTTTTAATCTTAAAAACATAATCTTTCTTAAAATTATAAAATTTTGAAAAATAAATTTT
CTCACAATATATTTTCAATAGAA
Found at i:3548752 original size:87 final size:87
Alignment explanation
Indices: 3548583--3548765 Score: 267
Period size: 87 Copynumber: 2.1 Consensus size: 87
3548573 ATCTTTGTTA
* * * *
3548583 AAATTATAAAATTTTGAAAAATAATTTTTTTCACAATATATTTTCAATATAGACTACATTTTAAT
1 AAATTATAAAATTTTGAAAAATAAATTTTCTCACAATATATTTTCAATAGAAACTACATTTTAAT
3548648 CTTAAAAACATAGTTTTTCTTG
66 CTTAAAAACATAGTTTTTCTTG
* *
3548670 AAATTATAAAATTTTGAAAAATAAATTTTCTCATAATATATTTTCAATAGAAACTATATTTTTAA
1 AAATTATAAAATTTTGAAAAATAAATTTTCTCACAATATATTTTCAATAGAAACTACA-TTTTAA
* * *
3548735 TCTTAAAAATATATTTTTTGTTG
65 TCTTAAAAACATAGTTTTTCTTG
*
3548758 AAACTATA
1 AAATTATA
3548766 CAAAAAATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 52 0.61
88 33 0.39
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (87 bp):
AAATTATAAAATTTTGAAAAATAAATTTTCTCACAATATATTTTCAATAGAAACTACATTTTAAT
CTTAAAAACATAGTTTTTCTTG
Found at i:3548765 original size:18 final size:19
Alignment explanation
Indices: 3548719--3548765 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
3548709 ATTTTCAATA
3548719 GAAACTATATTTTTAATCTT
1 GAAACTATATTTTT-ATCTT
* * *
3548739 AAAAATATATTTTT-TGTT
1 GAAACTATATTTTTATCTT
3548757 GAAACTATA
1 GAAACTATA
3548766 CAAAAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (19 bp):
GAAACTATATTTTTATCTT
Found at i:3553383 original size:113 final size:116
Alignment explanation
Indices: 3553175--3553388 Score: 308
Period size: 113 Copynumber: 1.9 Consensus size: 116
3553165 TTCTCCTAGC
* * *
3553175 TTTACAAATTGTACTGTTAATGTGTTCAAGATAATCCGGTTTCTACAGAGAAAGTGGAAGGTATT
1 TTTACAAATTGTACTGTTAACGTGTTCAAGATAATCCGGATTCTACAGAGAAAGAGGAAGGTATT
3553240 CCTATGGCCTTTCTTTTTGCTCCTTATAAAGTCTCAATATATACACTTGGA
66 CCTATGGCCTTTCTTTTTGCTCCTTATAAAGTCTCAATATATACACTTGGA
** * ** * *
3553291 TTTACAAATTGTACTGTTAACGTGTT-TGGATAATTC-GATTCTATGGAGAAAGAGGAAGTTGTT
1 TTTACAAATTGTACTGTTAACGTGTTCAAGATAATCCGGATTCTACAGAGAAAGAGGAAGGTATT
*
3553354 CC-ATGGCCTTTCTTTTTGCTCCTTGTAAAGTCTCA
66 CCTATGGCCTTTCTTTTTGCTCCTTATAAAGTCTCA
3553389 CTCTGGGACA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
113 32 0.37
114 23 0.26
115 7 0.08
116 25 0.29
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (116 bp):
TTTACAAATTGTACTGTTAACGTGTTCAAGATAATCCGGATTCTACAGAGAAAGAGGAAGGTATT
CCTATGGCCTTTCTTTTTGCTCCTTATAAAGTCTCAATATATACACTTGGA
Found at i:3554989 original size:21 final size:21
Alignment explanation
Indices: 3554963--3555009 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3554953 TTTTTAAATA
*
3554963 TTTATATTTAAAAAAGAACAT
1 TTTATATTAAAAAAAGAACAT
* *
3554984 TTTATATTAAAAAAATAATAT
1 TTTATATTAAAAAAAGAACAT
3555005 TTTAT
1 TTTAT
3555010 TAATTTCGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTATATTAAAAAAAGAACAT
Found at i:3555010 original size:19 final size:20
Alignment explanation
Indices: 3554959--3555012 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
3554949 GATATTTTTA
*
3554959 AATATTTATATTTAAAAAAG
1 AATATTTATATTAAAAAAAG
* *
3554979 AACATTTTATATTAAAAAAAT
1 AATA-TTTATATTAAAAAAAG
3555000 AATATTT-TATTAA
1 AATATTTATATTAA
3555013 TTTCGGGTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 17 0.59
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AATATTTATATTAAAAAAAG
Found at i:3564177 original size:15 final size:15
Alignment explanation
Indices: 3564149--3564217 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
3564139 ATCTCTTTTC
*
3564149 TTTT-TTTTTGTTAT
1 TTTTATTTTTATTAT
3564163 TTTTATTTTTATTA-
1 TTTTATTTTTATTAT
*
3564177 TTTTA-TTTTATATGT
1 TTTTATTTTTAT-TAT
3564192 TTTTACTTTTT-TTAT
1 TTTTA-TTTTTATTAT
3564207 GATTTTATTTT
1 --TTTTATTTT
3564218 AAAAGAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.13
14 10 0.22
15 15 0.33
16 5 0.11
17 9 0.20
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTATTAT
Found at i:3564207 original size:17 final size:16
Alignment explanation
Indices: 3564163--3564217 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 16
3564153 TTTTTGTTAT
3564163 TTTTATTTTTAT-T-A
1 TTTTATTTTTATATGA
*
3564177 TTTTA-TTTTATATGT
1 TTTTATTTTTATATGA
*
3564192 TTTTACTTTTTTTATGA
1 TTTTA-TTTTTATATGA
3564209 TTTTATTTT
1 TTTTATTTT
3564218 AAAAGAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 5 0.15
16 4 0.12
17 13 0.38
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTATATGA
Found at i:3566585 original size:29 final size:30
Alignment explanation
Indices: 3566543--3566603 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
3566533 TAAACACAAG
3566543 ATGAATAAACATGAATAAAAT-ATATATAC
1 ATGAATAAACATGAATAAAATAATATATAC
* * * *
3566572 ATGAATAGATATGACTAACATCAATATATAC
1 ATGAATAAACATGAATAAAAT-AATATATAC
3566603 A
1 A
3566604 AAAATATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (30 bp):
ATGAATAAACATGAATAAAATAATATATAC
Found at i:3567032 original size:9 final size:9
Alignment explanation
Indices: 3567018--3567043 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3567008 TATAAAAAAA
3567018 ATGTTAAAC
1 ATGTTAAAC
3567027 ATGTTAAAC
1 ATGTTAAAC
3567036 ATGTTAAA
1 ATGTTAAA
3567044 TGTACACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (9 bp):
ATGTTAAAC
Found at i:3571616 original size:17 final size:17
Alignment explanation
Indices: 3571573--3571619 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3571563 ATATTAATAT
* *
3571573 ATATTATATTAATAAAA
1 ATATTATATTTATTAAA
*
3571590 ATTTTA-ATTTATTAAA
1 ATATTATATTTATTAAA
3571606 ATATTATATTTATT
1 ATATTATATTTATT
3571620 TATATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATTTATTAAA
Found at i:3571626 original size:17 final size:17
Alignment explanation
Indices: 3571538--3571626 Score: 51
Period size: 17 Copynumber: 5.4 Consensus size: 17
3571528 TATAAAAATA
*
3571538 TATATTTTATTATTTATT
1 TATATATTA-TATTTATT
* *
3571556 TA-ATTTTATA-TTA-A
1 TATATATTATATTTATT
* *
3571570 TATATATTATATTAATA
1 TATATATTATATTTATT
* * *
3571587 AAAATTTTA-ATTTATT
1 TATATATTATATTTATT
* *
3571603 AAAATATTATATTTATT
1 TATATATTATATTTATT
3571620 TATATAT
1 TATATAT
3571627 AAAATTAAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
14 2 0.04
15 10 0.18
16 17 0.30
17 25 0.45
18 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATTATATTTATT
Found at i:3571650 original size:50 final size:49
Alignment explanation
Indices: 3571570--3571667 Score: 108
Period size: 50 Copynumber: 2.0 Consensus size: 49
3571560 TTTATATTAA
* * * * * *
3571570 TATATATTATATTAATAAAAATTTTAATTTATTAAAATATTATATTTATT
1 TATATATAAAATTAAGAAAAATTATAATTTA-AAAAATAATATATTTATT
*
3571620 TATATATAAAATTAAGAAATAATTAT-ATTTAAAAAATAATATTTTTAT
1 TATATATAAAATTAAGAAA-AATTATAATTTAAAAAATAATATATTTAT
3571668 AAATATTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
49 14 0.35
50 21 0.52
51 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (49 bp):
TATATATAAAATTAAGAAAAATTATAATTTAAAAAATAATATATTTATT
Found at i:3575883 original size:6 final size:6
Alignment explanation
Indices: 3575872--3575918 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
3575862 TTTCTATTGA
* *
3575872 TATAAT TATAAT TACAAT TATAAT TATAAT TATAGT TATAAT TATAA
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAA
3575919 AATGACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TATAAT
Found at i:3578791 original size:20 final size:20
Alignment explanation
Indices: 3578759--3578820 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 20
3578749 TTTTTATATA
3578759 TTTATCT-TATTTATCTTTTT
1 TTTATCTGT-TTTATCTTTTT
3578779 TTTATCTGTTTTACTCATTTTT
1 TTTATCTGTTTTA-TC-TTTTT
*
3578801 TATT-TTTGTTTTAT-TTTTT
1 T-TTATCTGTTTTATCTTTTT
3578820 T
1 T
3578821 ATTCATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.16
20 11 0.30
21 4 0.11
22 14 0.38
23 2 0.05
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTATCTGTTTTATCTTTTT
Found at i:3578827 original size:30 final size:28
Alignment explanation
Indices: 3578738--3578837 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
3578728 ACTGGTAGAT
* * *
3578738 TTTTTTATTTATTTTTATATATTTATC-
1 TTTTTTATTTTTTTTTATTTTTTTATCA
* *
3578765 TTATTTATCTTTTTTTTATCTGTTTTACTCA
1 TTTTTTAT-TTTTTTTTAT-TTTTTTA-TCA
3578796 TTTTTTATTTTTGTTTTATTTTTTTATTCA
1 TTTTTTATTTTT-TTTTATTTTTTTA-TCA
**
3578826 TTCATTATTTTT
1 TTTTTTATTTTT
3578838 CTTGTTGATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
27 7 0.12
28 9 0.16
29 4 0.07
30 25 0.43
31 13 0.22
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTTTATTTTTTTTTATTTTTTTATCA
Found at i:3580157 original size:4 final size:4
Alignment explanation
Indices: 3580135--3580186 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
3580125 TTTTACATTA
* * * *
3580135 ATTT GTTT ATTT GTTT ATTT ATTT ATTT GA-TT ATTT ATGT ATTC ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT
3580183 ATTT
1 ATTT
3580187 GTAAATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 1 0.03
4 36 0.95
5 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:3580159 original size:16 final size:16
Alignment explanation
Indices: 3580135--3580177 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3580125 TTTTACATTA
* *
3580135 ATTTGTTTATTTGTTT
1 ATTTATTTATTTGATT
3580151 ATTTATTTATTTGATT
1 ATTTATTTATTTGATT
*
3580167 ATTTATGTATT
1 ATTTATTTATT
3580178 CATTTATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (16 bp):
ATTTATTTATTTGATT
Found at i:3580220 original size:20 final size:21
Alignment explanation
Indices: 3580195--3580233 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3580185 TTGTAAATAT
*
3580195 TTTTTAA-AAATAACAAAGCA
1 TTTTTAACAAATAAAAAAGCA
3580215 TTTTTAACAAATAAAAAAG
1 TTTTTAACAAATAAAAAAG
3580234 AACATTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (21 bp):
TTTTTAACAAATAAAAAAGCA
Found at i:3581768 original size:22 final size:23
Alignment explanation
Indices: 3581736--3581782 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3581726 ATAAAGCATT
*
3581736 ATCATTCATGTAGTACAT-CATC
1 ATCATTCATGTAATACATCCATC
*
3581758 ATCATTTATGTAATACATCCATC
1 ATCATTCATGTAATACATCCATC
3581781 AT
1 AT
3581783 ATCATTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (23 bp):
ATCATTCATGTAATACATCCATC
Found at i:3585674 original size:29 final size:29
Alignment explanation
Indices: 3585623--3585690 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
3585613 ATAAAGTAAA
3585623 AAAAAAAAGAAAAAAAGAAAAAATAAATG
1 AAAAAAAAGAAAAAAAGAAAAAATAAATG
* *
3585652 AAAAATAA-AAAAAAAGAAAAAAATGAATG
1 AAAAAAAAGAAAAAAAG-AAAAAATAAATG
3585681 ATAAAAAAAG
1 A-AAAAAAAG
3585691 GGAAAAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
29 19 0.58
30 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAGAAAAAATAAATG
Found at i:3585695 original size:25 final size:26
Alignment explanation
Indices: 3585626--3585696 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
3585616 AAGTAAAAAA
* *
3585626 AAAAAGAAAAAAAGAAAAAATAAATG
1 AAAAATAAAAAAAGAGAAAATAAATG
*
3585652 AAAAATAAAAAAAAAGAAAA-AAATG
1 AAAAATAAAAAAAGAGAAAATAAATG
** *
3585677 AATGATAAAAAAAGGGAAAA
1 AAAAATAAAAAAAGAGAAAA
3585697 GGAAAAATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 21 0.55
26 17 0.45
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (26 bp):
AAAAATAAAAAAAGAGAAAATAAATG
Found at i:3588993 original size:4 final size:4
Alignment explanation
Indices: 3588984--3589046 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
3588974 TACATTAATC
*
3588984 TATT TATT TA-T T-TT TGTT TATT TATT TATT T-TAT TATT TGA-T TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT T-ATT TATT
* *
3589030 TATG TATT CATT TATT T
1 TATT TATT TATT TATT T
3589047 GTAAATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 6 0.12
4 40 0.83
5 2 0.04
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:3590349 original size:2 final size:2
Alignment explanation
Indices: 3590344--3590392 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
3590334 TTTATATATA
* *
3590344 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3590386 TG TG TG T
1 TG TG TG T
3590393 ATATGAGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.02, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3591460 original size:28 final size:28
Alignment explanation
Indices: 3591396--3591460 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
3591386 TTTGGTTTTT
*
3591396 AAAAAGAAAA-AAAGAAAATAGAGATGG
1 AAAAAGAAAAGGAAGAAAATAGAGATGG
*
3591423 AAAGAGAAAAGGAAGAAAGA-AGAGA-GG
1 AAAAAGAAAAGGAAGAAA-ATAGAGATGG
3591450 AAAAAGTAAAA
1 AAAAAG-AAAA
3591461 ATAGAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 16 0.50
28 15 0.47
29 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (28 bp):
AAAAAGAAAAGGAAGAAAATAGAGATGG
Found at i:3591550 original size:14 final size:14
Alignment explanation
Indices: 3591531--3591564 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3591521 TTTGTTATTT
3591531 TTAATTTTTAATAA
1 TTAATTTTTAATAA
*
3591545 TTAATTTTTATTAA
1 TTAATTTTTAATAA
*
3591559 ATAATT
1 TTAATT
3591565 ATGATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTTTTAATAA
Found at i:3591657 original size:28 final size:30
Alignment explanation
Indices: 3591614--3591671 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
3591604 AGTATCAATA
* * *
3591614 ATTACTTTTTATTAATTAATTATGATTAAT
1 ATTACTTTTTATTAATAAAATATAATTAAT
3591644 ATTA-TTTTTA-TAATAAAATATAATTAAT
1 ATTACTTTTTATTAATAAAATATAATTAAT
3591672 TTAATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
29 6 0.24
30 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTACTTTTTATTAATAAAATATAATTAAT
Found at i:3596404 original size:27 final size:27
Alignment explanation
Indices: 3596374--3596427 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3596364 CACAAAAGTG
3596374 TAATTAGTTAATCCGTTAGTAATAAGC
1 TAATTAGTTAATCCGTTAGTAATAAGC
3596401 TAATTAGTTAATCCGTTAGTAATAAGC
1 TAATTAGTTAATCCGTTAGTAATAAGC
3596428 ATGAAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (27 bp):
TAATTAGTTAATCCGTTAGTAATAAGC
Found at i:3598449 original size:35 final size:35
Alignment explanation
Indices: 3598398--3598470 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3598388 TTTTTTTAGA
* * *
3598398 AAGATAGTTTGTATACGAAACTTGATGTACTTTCG
1 AAGATAATTTGCATACGAAACTTGATGTACTTCCG
*
3598433 AAGATAATTTGCATACGAAATTTGATGTACTTCCG
1 AAGATAATTTGCATACGAAACTTGATGTACTTCCG
3598468 AAG
1 AAG
3598471 TTAAGACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (35 bp):
AAGATAATTTGCATACGAAACTTGATGTACTTCCG
Found at i:3600455 original size:17 final size:17
Alignment explanation
Indices: 3600400--3600458 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 17
3600390 TTATTTAATT
*
3600400 TTATATTTA-T-ATATA
1 TTATATTTATTAAAATA
* * *
3600415 TTATATTAATAAAAATT
1 TTATATTTATTAAAATA
3600432 TTA-ATTTATTAAAATA
1 TTATATTTATTAAAATA
3600448 TTATATTTATT
1 TTATATTTATT
3600459 TATATATAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 8 0.24
16 13 0.38
17 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATTAAAATA
Found at i:3600465 original size:17 final size:17
Alignment explanation
Indices: 3600390--3600465 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 17
3600380 ATCTTATTGC
*
3600390 TTATTT-AATTTTATAT
1 TTATTTAAATATTATAT
*
3600406 TTA--TATATATTATAT
1 TTATTTAAATATTATAT
* ** *
3600421 TAATAAAAATTTTA-AT
1 TTATTTAAATATTATAT
*
3600437 TTATTAAAATATTATAT
1 TTATTTAAATATTATAT
*
3600454 TTATTTATATAT
1 TTATTTAAATAT
3600466 AATTAAGTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
14 1 0.02
15 10 0.22
16 16 0.36
17 18 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTAAATATTATAT
Found at i:3600558 original size:2 final size:2
Alignment explanation
Indices: 3600551--3600589 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3600541 GGATTAAGAT
*
3600551 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3600590 TAGATTGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3606935 original size:18 final size:19
Alignment explanation
Indices: 3606903--3606939 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3606893 TTTGTTGGAT
*
3606903 ATTTTTATTTCAATAATTA
1 ATTTTTATTTAAATAATTA
3606922 ATTTTTA-TTAAATAATTA
1 ATTTTTATTTAAATAATTA
3606940 TGATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTATTTAAATAATTA
Found at i:3606963 original size:25 final size:24
Alignment explanation
Indices: 3606918--3606973 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
3606908 TATTTCAATA
3606918 ATTAATTTTTATTAAATAATTATG
1 ATTAATTTTTATTAAATAATTATG
* * *
3606942 ATTAATTTTATTTTAATTAATTATT
1 ATTAATTTT-TATTAAATAATTATG
3606967 ATTAATT
1 ATTAATT
3606974 AATAATTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTAATTTTTATTAAATAATTATG
Found at i:3606973 original size:14 final size:14
Alignment explanation
Indices: 3606916--3606981 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
3606906 TTTATTTCAA
*
3606916 TAATTAATTTTTAT
1 TAATTAATTATTAT
* *
3606930 TAAATAATTATGAT
1 TAATTAATTATTAT
3606944 TAATT--TTATT-T
1 TAATTAATTATTAT
3606955 TAATTAATTATTAT
1 TAATTAATTATTAT
*
3606969 TAATTAATAATTA
1 TAATTAATTATTA
3606982 GAGAGAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.14
12 4 0.09
13 5 0.12
14 28 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAATTAATTATTAT
Found at i:3607433 original size:20 final size:20
Alignment explanation
Indices: 3607408--3607448 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3607398 GTTTAGATTA
*
3607408 ATTTTTATTGATTTTGAAGT
1 ATTTTTATTGAATTTGAAGT
* *
3607428 ATTTTTTTTTAATTTGAAGT
1 ATTTTTATTGAATTTGAAGT
3607448 A
1 A
3607449 GAGAGTTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (20 bp):
ATTTTTATTGAATTTGAAGT
Found at i:3607937 original size:3 final size:3
Alignment explanation
Indices: 3607929--3607956 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3607919 CATAAAAACT
3607929 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3607957 CATCATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3608030 original size:5 final size:5
Alignment explanation
Indices: 3608020--3608053 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3608010 AAAAAATAAA
*
3608020 AATAT AGTAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
3608054 CTTTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:3609042 original size:2 final size:2
Alignment explanation
Indices: 3609031--3609061 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3609021 AATATCCACT
3609031 TA TA -A 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
3609062 AATAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3609121 original size:14 final size:15
Alignment explanation
Indices: 3609102--3609130 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3609092 CAGTGCACAG
3609102 AAAATTTTTC-TTTT
1 AAAATTTTTCATTTT
3609116 AAAATTTTTCATTTT
1 AAAATTTTTCATTTT
3609131 TCAAATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
AAAATTTTTCATTTT
Found at i:3609293 original size:13 final size:13
Alignment explanation
Indices: 3609267--3609306 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3609257 ATTTCTTTCA
* *
3609267 ATTTTTTAATAAT
1 ATTTTTAAAAAAT
3609280 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
*
3609293 AGTTTTAAAAAAT
1 ATTTTTAAAAAAT
3609306 A
1 A
3609307 AATGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATTTTTAAAAAAT
Found at i:3613187 original size:18 final size:19
Alignment explanation
Indices: 3613160--3613202 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3613150 GATAAATAGT
*
3613160 AAAA-TAAAAAATTTAAAA
1 AAAATTAAAAACTTTAAAA
*
3613178 TAAATTAAAAACTTTAAAA
1 AAAATTAAAAACTTTAAAA
3613197 AAAATT
1 AAAATT
3613203 CGTGGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTAAAAACTTTAAAA
Found at i:3614938 original size:31 final size:31
Alignment explanation
Indices: 3614900--3614962 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3614890 TAGAGTCTTA
* *
3614900 TGAAGAAATTATAAAGTCAATTTGACTTTTG
1 TGAAGAAATTAAAAAATCAATTTGACTTTTG
3614931 TGAAGAAATTAAAAAATCAATTTGACTTTTG
1 TGAAGAAATTAAAAAATCAATTTGACTTTTG
3614962 T
1 T
3614963 TAAATTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (31 bp):
TGAAGAAATTAAAAAATCAATTTGACTTTTG
Found at i:3623835 original size:27 final size:28
Alignment explanation
Indices: 3623805--3623863 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
3623795 TACTAATTCA
3623805 ATTTGATTCATTGATTTTTTAAATT-TT
1 ATTTGATTCATTGATTTTTTAAATTATT
* ** *
3623832 ATTTTATTTTTTTATTTTTTAAATTATT
1 ATTTGATTCATTGATTTTTTAAATTATT
3623860 ATTT
1 ATTT
3623864 TAATATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (28 bp):
ATTTGATTCATTGATTTTTTAAATTATT
Found at i:3626392 original size:2 final size:2
Alignment explanation
Indices: 3626387--3626412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3626377 TGTGTGTGTG
3626387 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
3626413 AGTTCATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3635623 original size:68 final size:68
Alignment explanation
Indices: 3635514--3635682 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 68
3635504 TAATTATTTT
* * * * * * * *
3635514 TTAAAGAATTTCATGTATGGTATCTATATCCTAAGATGGGTTATCTAACTATGAGTTTGCCTAAC
1 TTAAAGTATTTCATATATAGTATCTGTCTCTTAAGATGGGTTATCCAACTATGAGTTTGCATAAC
3635579 TTC
66 TTC
* *
3635582 TTAAAGTATTTCATATATAGTATCTGTCTCTTAAGATGGGTTATCCAATTGTGAGTTTGCATAAC
1 TTAAAGTATTTCATATATAGTATCTGTCTCTTAAGATGGGTTATCCAACTATGAGTTTGCATAAC
*
3635647 TTT
66 TTC
*
3635650 TTAAAGTATTTCATATATA--ATATGTCTCTTAAG
1 TTAAAGTATTTCATATATAGTATCTGTCTCTTAAG
3635683 GTGGTTTTAG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 13 0.15
68 76 0.85
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (68 bp):
TTAAAGTATTTCATATATAGTATCTGTCTCTTAAGATGGGTTATCCAACTATGAGTTTGCATAAC
TTC
Found at i:3638003 original size:9 final size:9
Alignment explanation
Indices: 3637989--3638028 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
3637979 AGTCTTTTAC
3637989 TTATTATTT
1 TTATTATTT
3637998 TTATTA--T
1 TTATTATTT
3638005 TT-TTA-TT
1 TTATTATTT
3638012 TTATTATTT
1 TTATTATTT
3638021 TTATTATT
1 TTATTATT
3638029 AGAATATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.11
7 6 0.21
8 3 0.11
9 16 0.57
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTATTT
Found at i:3638015 original size:14 final size:14
Alignment explanation
Indices: 3637996--3638025 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3637986 TACTTATTAT
3637996 TTTTATTATTTTTA
1 TTTTATTATTTTTA
3638010 TTTTATTATTTTTA
1 TTTTATTATTTTTA
3638024 TT
1 TT
3638026 ATTAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:3638720 original size:120 final size:118
Alignment explanation
Indices: 3638484--3638908 Score: 454
Period size: 120 Copynumber: 3.6 Consensus size: 118
3638474 TTTCTAACAC
* * * * *
3638484 TTTTAGAATATTTTTTTATATAAATATTTTCACTAAAATCACCACTTGTGACTTT-TTTTTATTA
1 TTTTAGAAAATTTCTTTATATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTATTA
* ** * * *
3638548 AT-A-TTTTTTATGCTCACAAAAATTCTAAAATATTTATAACA-TTTTCTGAATA
66 ATAATTTTTTTATACT-TGAAAATTTCTAAAATATTTCTAACACTTTT-AGAATA
* * * *
3638600 TTTTAGAAAATTTCTTTCTGTAAATATTTTTAATAAAATCACCCCTTATGATTTTATTTTTATTA
1 TTTTAGAAAATTTCTTTATATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTATTA
* *
3638665 ATAATTTTTTTTTATACTTGAAAATTTTTAAAATATTTCTAACACTTTTAAAATA
66 ATAA--TTTTTTTATACTTGAAAATTTCTAAAATATTTCTAACACTTTTAGAATA
* * * * * * *
3638720 TTTTAAAAAATTTCTTTTTGTAAATATTTTTAATAAATTCACCACTGGTGATTTTGTTTTTATCA
1 TTTTAGAAAATTTCTTTATATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTATTA
* * *
3638785 ATAATTGTTTTATACTTGAAAATTTCTAAAATATTTCTAATACTTTTAGAATG
66 ATAATTTTTTTATACTTGAAAATTTCTAAAATATTTCTAACACTTTTAGAATA
** * *
3638838 TTTTAGAAAAAAT-TTTATATAAAT-TTTTTAATAACATCATCAC---TGATTTTATTTTTTATT
1 TTTTAGAAAATTTCTTTATATAAATATTTTTAATAAAATCACCACTTGTGATTTTA-TTTTTATT
*
3638898 AATAATATTTT
65 AATAATTTTTT
3638909 ATTTATTTTT
Statistics
Matches: 260, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
113 7 0.03
114 16 0.06
116 62 0.24
117 20 0.08
118 55 0.21
120 86 0.33
121 14 0.05
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.51
Consensus pattern (118 bp):
TTTTAGAAAATTTCTTTATATAAATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTATTA
ATAATTTTTTTATACTTGAAAATTTCTAAAATATTTCTAACACTTTTAGAATA
Found at i:3638926 original size:16 final size:17
Alignment explanation
Indices: 3638907--3638941 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
3638897 TAATAATATT
3638907 TTATTTATTTTT-TTCA
1 TTATTTATTTTTATTCA
3638923 TTATTTATTTTTATTCA
1 TTATTTATTTTTATTCA
3638940 TT
1 TT
3638942 CATTATCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTATTTTTATTCA
Found at i:3640914 original size:15 final size:16
Alignment explanation
Indices: 3640884--3640916 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3640874 GTTTGCTTAC
3640884 TTTAAATGATTTTGGA
1 TTTAAATGATTTTGGA
*
3640900 TTTAATTGA-TTTGGA
1 TTTAAATGATTTTGGA
3640915 TT
1 TT
3640917 AGGGTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTAAATGATTTTGGA
Found at i:3640980 original size:15 final size:15
Alignment explanation
Indices: 3640955--3640991 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3640945 TTTTATAACA
*
3640955 ATTTTGGGTGAATCG
1 ATTTAGGGTGAATCG
*
3640970 GTTTAGGGTGAATCG
1 ATTTAGGGTGAATCG
3640985 ATTTAGG
1 ATTTAGG
3640992 AGTTAGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (15 bp):
ATTTAGGGTGAATCG
Found at i:3641354 original size:4 final size:4
Alignment explanation
Indices: 3641345--3641371 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3641335 AAATTATTGT
3641345 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
3641372 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3641395 original size:16 final size:16
Alignment explanation
Indices: 3641374--3641420 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3641364 ATTAATTATA
3641374 TATATATATATATTTT
1 TATATATATATATTTT
3641390 TATATA-ATGATATTTT
1 TATATATAT-ATATTTT
* *
3641406 TAAATATTTATATTT
1 TATATATATATATTT
3641421 AAAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATATATATATATTTT
Found at i:3641433 original size:20 final size:21
Alignment explanation
Indices: 3641408--3641460 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
3641398 GATATTTTTA
3641408 AATATTTATATTT-AAAAAAT
1 AATATTTATATTTAAAAAAAT
3641428 AATATTTTATATTTAAAAAAAT
1 AATA-TTTATATTTAAAAAAAT
3641450 AATATTT-TATT
1 AATATTTATATT
3641461 AATTTCAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTATATTTAAAAAAAT
Found at i:3641438 original size:21 final size:22
Alignment explanation
Indices: 3641408--3641459 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3641398 GATATTTTTA
3641408 AATA-TTTATATTT-AAAAAAT
1 AATATTTTATATTTAAAAAAAT
3641428 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
3641450 AATATTTTAT
1 AATATTTTAT
3641460 TAATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 17 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:3643536 original size:18 final size:19
Alignment explanation
Indices: 3643515--3643552 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3643505 CTTTTCGTTC
3643515 TTTTT-TTTTGTTTTT-TA
1 TTTTTATTTTGTTTTTATA
3643532 TTTTTATTTTGTTTTTATA
1 TTTTTATTTTGTTTTTATA
3643551 TT
1 TT
3643553 AAATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTGTTTTTATA
Found at i:3648923 original size:21 final size:22
Alignment explanation
Indices: 3648892--3648944 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3648882 TTATATAATT
3648892 ATATATTTATA-TTTAAAAAATA
1 ATAT-TTTATATTTTAAAAAATA
3648914 ATATTTTATATTTTAAAAAATA
1 ATATTTTATATTTTAAAAAATA
3648936 ATATTTTAT
1 ATATTTTAT
3648945 TAACTTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTATATTTTAAAAAATA
Found at i:3651767 original size:29 final size:28
Alignment explanation
Indices: 3651729--3651784 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3651719 AAAATATGAA
*
3651729 AAATATAAAA-TTCAAAAAATTCAAAAAC
1 AAATATAAAAGCT-AAAAAATTCAAAAAC
*
3651757 AAATATGAAAAGCTAAAAAATTGAAAAA
1 AAATAT-AAAAGCTAAAAAATTCAAAAA
3651785 TTAAAACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 17 0.71
30 1 0.04
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (28 bp):
AAATATAAAAGCTAAAAAATTCAAAAAC
Found at i:3651784 original size:37 final size:36
Alignment explanation
Indices: 3651720--3651790 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
3651710 AACAAAGGAA
*
3651720 AAATATGAAAAATATAAAATTCAAAAAATTCAAAAAC
1 AAATATGAAAAATAAAAAATTCAAAAAATT-AAAAAC
* *
3651757 AAATATGAAAAGCTAAAAAATT-GAAAAATTAAAA
1 AAATATGAAAA-ATAAAAAATTCAAAAAATTAAAA
3651791 CATAGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 4 0.13
37 18 0.60
38 8 0.27
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (36 bp):
AAATATGAAAAATAAAAAATTCAAAAAATTAAAAAC
Found at i:3652684 original size:19 final size:19
Alignment explanation
Indices: 3652660--3652701 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3652650 TATTTTTAAA
*
3652660 TTTAGGATTATTTAATTTT
1 TTTAGGATTATTTAAATTT
* *
3652679 TTTAGGTTTGTTTAAATTT
1 TTTAGGATTATTTAAATTT
3652698 TTTA
1 TTTA
3652702 ATTTGCAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (19 bp):
TTTAGGATTATTTAAATTT
Found at i:3656181 original size:34 final size:34
Alignment explanation
Indices: 3656143--3656217 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
3656133 AAATAAGGAG
* *
3656143 GAAAGAGAAAATGAATAAGAAATGTGTAAGATGA
1 GAAAGAGAAAATGAATAAAAAACGTGTAAGATGA
3656177 GAAAGAGAAAATGAATAAAAAACGTGTAAGATGA
1 GAAAGAGAAAATGAATAAAAAACGTGTAAGATGA
3656211 GAAAGAG
1 GAAAGAG
3656218 TTAATAAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.57, C:0.01, G:0.27, T:0.15
Consensus pattern (34 bp):
GAAAGAGAAAATGAATAAAAAACGTGTAAGATGA
Found at i:3662120 original size:18 final size:18
Alignment explanation
Indices: 3662097--3662132 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3662087 TTTTTCTTTT
*
3662097 TTTTTTCTTTCGTTCTAC
1 TTTTTTCTTTCCTTCTAC
*
3662115 TTTTTTTTTTCCTTCTAC
1 TTTTTTCTTTCCTTCTAC
3662133 CTTCTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.22, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTCTTTCCTTCTAC
Found at i:3662139 original size:22 final size:22
Alignment explanation
Indices: 3662090--3662140 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3662080 CACTTTTTTT
* *
3662090 TTCTTTTTTTTTTCTTTCGTTC
1 TTCTTTTTTTTTTCCTTCGTCC
*
3662112 TACTTTTTTTTTTCCTTC-TACC
1 TTCTTTTTTTTTTCCTTCGT-CC
3662134 TTCTTTT
1 TTCTTTT
3662141 CAAGATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (22 bp):
TTCTTTTTTTTTTCCTTCGTCC
Found at i:3664832 original size:16 final size:15
Alignment explanation
Indices: 3664807--3664844 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3664797 GGGGTCTATT
*
3664807 GAAAAAAAAAGGAAA
1 GAAAAAAAAAAGAAA
3664822 GAAATAAAAAAAGAAA
1 GAAA-AAAAAAAGAAA
3664838 -AAAAAAA
1 GAAAAAAA
3664845 GAGCTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 10 0.48
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
GAAAAAAAAAAGAAA
Found at i:3671689 original size:13 final size:13
Alignment explanation
Indices: 3671671--3671695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3671661 TTATTTATAT
3671671 TTTAATTTTTTAA
1 TTTAATTTTTTAA
3671684 TTTAATTTTTTA
1 TTTAATTTTTTA
3671696 TTTTTTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTAATTTTTTAA
Found at i:3672344 original size:16 final size:16
Alignment explanation
Indices: 3672323--3672377 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3672313 ACAAATATTA
3672323 TATTTGCATGATAATT
1 TATTTGCATGATAATT
** * *
3672339 TATTTGGTTAATATTT
1 TATTTGCATGATAATT
*
3672355 TATTTGCATGATTAATA
1 TATTTGCATGA-TAATT
3672372 TATTTG
1 TATTTG
3672378 TGTGATTTAT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.55
Consensus pattern (16 bp):
TATTTGCATGATAATT
Found at i:3672352 original size:32 final size:33
Alignment explanation
Indices: 3672316--3672377 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
3672306 TTACATGACA
*
3672316 AATATTATATTTGCATGA-TAATTTATTTGGTT
1 AATATTATATTTGCATGATTAATATATTTGGTT
*
3672348 AATATTTTATTTGCATGATTAATATATTTG
1 AATATTATATTTGCATGATTAATATATTTG
3672378 TGTGATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.53
Consensus pattern (33 bp):
AATATTATATTTGCATGATTAATATATTTGGTT
Found at i:3672369 original size:20 final size:20
Alignment explanation
Indices: 3672346--3672436 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
3672336 ATTTATTTGG
*
3672346 TTAATATTTTATTTGCATGA
1 TTAATAATTTATTTGCATGA
**
3672366 TTAAT-A--TATTTGTGTGA
1 TTAATAATTTATTTGCATGA
* * *
3672383 TTTATAATATATTTGCATAA
1 TTAATAATTTATTTGCATGA
* *
3672403 CTATTAATTTATTTGCATGA
1 TTAATAATTTATTTGCATGA
3672423 TT-ATCAATTTATTT
1 TTAAT-AATTTATTT
3672437 ATTTGTGTGA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
17 13 0.25
18 1 0.02
19 1 0.02
20 38 0.72
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (20 bp):
TTAATAATTTATTTGCATGA
Found at i:3672491 original size:41 final size:41
Alignment explanation
Indices: 3672446--3672632 Score: 245
Period size: 41 Copynumber: 4.6 Consensus size: 41
3672436 TATTTGTGTG
3672446 ATTGCATGATTATATATTTAATTGCATATTTTATATTGTTA
1 ATTGCATGATTATATATTTAATTGCATATTTTATATTGTTA
* * *
3672487 ATTGCTTAATTATATATTTAGTTGC--ATTTTATATTGTTA
1 ATTGCATGATTATATATTTAATTGCATATTTTATATTGTTA
* * * * *
3672526 ACTGCATCATTATATATTTAGTTGCATGTTTTGTATTGTTA
1 ATTGCATGATTATATATTTAATTGCATATTTTATATTGTTA
* * *
3672567 GTTGCATGATTATATATTTATTTGCATGTTTTATATT-TCTA
1 ATTGCATGATTATATATTTAATTGCATATTTTATATTGT-TA
3672608 ATTGCATGATTATATATTTAATTGC
1 ATTGCATGATTATATATTTAATTGC
3672633 TTATCTATTT
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 36 0.28
40 1 0.01
41 91 0.71
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (41 bp):
ATTGCATGATTATATATTTAATTGCATATTTTATATTGTTA
Found at i:3672532 original size:80 final size:81
Alignment explanation
Indices: 3672448--3672632 Score: 257
Period size: 80 Copynumber: 2.3 Consensus size: 81
3672438 TTTGTGTGAT
*
3672448 TGCATGATTATATATTTAATTGCATATTTTATATTGTTAATTGCTTAATTATATATTTAGTTGCA
1 TGCATGATTATATATTTAATTGCATATTTTATATTGTTAATTGCATAATTATATATTTAGTTGCA
3672513 -TTTTATATTGT-TAAC
66 GTTTTATATT-TCTAAC
* * * * * * *
3672528 TGCATCATTATATATTTAGTTGCATGTTTTGTATTGTTAGTTGCATGATTATATATTTATTTGCA
1 TGCATGATTATATATTTAATTGCATATTTTATATTGTTAATTGCATAATTATATATTTAGTTGCA
*
3672593 TGTTTTATATTTCTAAT
66 -GTTTTATATTTCTAAC
3672610 TGCATGATTATATATTTAATTGC
1 TGCATGATTATATATTTAATTGC
3672633 TTATCTATTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 57 0.63
81 1 0.01
82 33 0.36
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.54
Consensus pattern (81 bp):
TGCATGATTATATATTTAATTGCATATTTTATATTGTTAATTGCATAATTATATATTTAGTTGCA
GTTTTATATTTCTAAC
Found at i:3673744 original size:20 final size:21
Alignment explanation
Indices: 3673716--3673755 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3673706 ATTTTTCTAT
3673716 TTTTCTATTCTGTTTTGTTTG
1 TTTTCTATTCTGTTTTGTTTG
* *
3673737 TTTT-TATTGTTTTTTGTTT
1 TTTTCTATTCTGTTTTGTTT
3673756 ATATATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.78
Consensus pattern (21 bp):
TTTTCTATTCTGTTTTGTTTG
Found at i:3680062 original size:19 final size:18
Alignment explanation
Indices: 3680009--3680062 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
3679999 TTATATTATA
3680009 TTTATATTTAATAGGTA-T
1 TTTATATTTAAT-GGTATT
*
3680027 TTTAAATTTAAAT-GTATT
1 TTTATATTT-AATGGTATT
3680045 TTTATTATTTAATGGTAT
1 TTTA-TATTTAATGGTAT
3680063 AGAAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTATATTTAATGGTATT
Found at i:3682683 original size:23 final size:24
Alignment explanation
Indices: 3682657--3682704 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3682647 AATGCAAGAA
3682657 CAGA-TTTAATTTAAATGCCCTTT
1 CAGATTTTAATTTAAATGCCCTTT
*
3682680 CAGATTTTAGTTTAAATGCCCTTT
1 CAGATTTTAATTTAAATGCCCTTT
3682704 C
1 C
3682705 TAATGATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (24 bp):
CAGATTTTAATTTAAATGCCCTTT
Found at i:3686410 original size:18 final size:17
Alignment explanation
Indices: 3686387--3686434 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3686377 CAACTCTCAC
3686387 TAATATAAAATCTTTTAA
1 TAATATAAAAT-TTTTAA
**
3686405 TAATATTTAATTTTTAA
1 TAATATAAAATTTTTAA
3686422 TAAAATATAAAAT
1 T--AATATAAAAT
3686435 AATTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATATAAAATTTTTAA
Found at i:3686982 original size:20 final size:20
Alignment explanation
Indices: 3686959--3686999 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3686949 ATAATATTTT
* *
3686959 ATAATTTATAAATTTAATAA
1 ATAAATTATAAATATAATAA
*
3686979 ATAAATTATTAATATAATAA
1 ATAAATTATAAATATAATAA
3686999 A
1 A
3687000 ATTCATTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAATTATAAATATAATAA
Found at i:3688694 original size:14 final size:14
Alignment explanation
Indices: 3688677--3688704 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3688667 TAAGATGCAA
3688677 ATGGAAAGAAATAG
1 ATGGAAAGAAATAG
3688691 ATGGAAAGAAATAG
1 ATGGAAAGAAATAG
3688705 TCAAACTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (14 bp):
ATGGAAAGAAATAG
Found at i:3688716 original size:50 final size:50
Alignment explanation
Indices: 3688641--3688740 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3688631 CTAAATGTAA
3688641 ATGGAAAGAAATAGTCAAACTAAGACTAAGATGCAAATGGAAAGAAATAG
1 ATGGAAAGAAATAGTCAAACTAAGACTAAGATGCAAATGGAAAGAAATAG
3688691 ATGGAAAGAAATAGTCAAACTAAGACTAAGATGCAAATGGAAAGAAATAG
1 ATGGAAAGAAATAGTCAAACTAAGACTAAGATGCAAATGGAAAGAAATAG
3688741 TAAAAGGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (50 bp):
ATGGAAAGAAATAGTCAAACTAAGACTAAGATGCAAATGGAAAGAAATAG
Found at i:3694105 original size:39 final size:39
Alignment explanation
Indices: 3694061--3694139 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
3694051 ACACTTCTCA
* *
3694061 AACTCCCTTTCACGTCCAAAACATCTAACCAAATCCTCC
1 AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTCC
*
3694100 AACTCCCTTTCAAGTCTAAAACATCCAACCAAATCCTCC
1 AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTCC
3694139 A
1 A
3694140 GGCCTAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.39, G:0.03, T:0.23
Consensus pattern (39 bp):
AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTCC
Found at i:3707397 original size:6 final size:6
Alignment explanation
Indices: 3707386--3707420 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3707376 ATATACATAA
* *
3707386 ATATAT ATATAT ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
3707421 CCTGAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (6 bp):
ATATAG
Found at i:3707401 original size:12 final size:12
Alignment explanation
Indices: 3707382--3707420 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3707372 AAAAATATAC
*
3707382 ATAAATATATAT
1 ATAAATATAGAT
*
3707394 ATATATATAGAT
1 ATAAATATAGAT
*
3707406 ATAGATATAGAT
1 ATAAATATAGAT
3707418 ATA
1 ATA
3707421 CCTGAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
ATAAATATAGAT
Found at i:3707407 original size:18 final size:18
Alignment explanation
Indices: 3707376--3707420 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3707366 TTGATAAAAA
* *
3707376 ATATACATAAATATATAT
1 ATATATATAAATATAGAT
*
3707394 ATATATATAGATATAGAT
1 ATATATATAAATATAGAT
*
3707412 ATAGATATA
1 ATATATATA
3707421 CCTGAAGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (18 bp):
ATATATATAAATATAGAT
Found at i:3715579 original size:25 final size:25
Alignment explanation
Indices: 3715528--3715583 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
3715518 AAATAGTAAT
* *
3715528 AAAAGTTATTGTAACTATGATTGAA
1 AAAAATTATTGTAACTATGATTAAA
*
3715553 AAAAATTATTGTAGCTACT-ATTAAA
1 AAAAATTATTGTAACTA-TGATTAAA
3715578 AAAAAT
1 AAAAAT
3715584 ATCATAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (25 bp):
AAAAATTATTGTAACTATGATTAAA
Found at i:3719907 original size:21 final size:21
Alignment explanation
Indices: 3719855--3719950 Score: 75
Period size: 21 Copynumber: 4.3 Consensus size: 21
3719845 TTTGAATTAA
*
3719855 TTAAAATTTAAAATAATTCAAAT
1 TTAAAATTT--AATAATTTAAAT
* * * * *
3719878 TTGAAATTTATTGATTTTACT
1 TTAAAATTTAATAATTTAAAT
3719899 TTAAAATTTAATAATTTAAAT
1 TTAAAATTTAATAATTTAAAT
3719920 TTAAAATATGTCAAATAATTTAAAT
1 TTAAAAT-T-T--AATAATTTAAAT
*
3719945 TCAAAA
1 TTAAAA
3719951 AATTTGAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
21 30 0.53
22 1 0.02
23 9 0.16
25 17 0.30
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (21 bp):
TTAAAATTTAATAATTTAAAT
Found at i:3719954 original size:15 final size:15
Alignment explanation
Indices: 3719930--3719974 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3719920 TTAAAATATG
*
3719930 TCAAATAATTTAAAT
1 TCAAAAAATTTAAAT
*
3719945 TCAAAAAATTTGAAT
1 TCAAAAAATTTAAAT
*
3719960 TTAAAATAATTTAAA
1 TCAAAA-AATTTAAA
3719975 CTGAAATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (15 bp):
TCAAAAAATTTAAAT
Found at i:3721749 original size:6 final size:6
Alignment explanation
Indices: 3721734--3721763 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3721724 AGAGCTTATA
3721734 TTTC-T TTTCAT TTTCAT TTTCAT TTTCAT T
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT T
3721764 CTTCTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCAT
Found at i:3727372 original size:39 final size:39
Alignment explanation
Indices: 3727327--3727406 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
3727317 CTCAAACTAT
3727327 TTCCAACAATATTAAATGTATTGCGTAATAAATGCTTAC
1 TTCCAACAATATTAAATGTATTGCGTAATAAATGCTTAC
* *
3727366 TTCCAACAATATTAAATGTATTGTGTATTAAATGCTTAC
1 TTCCAACAATATTAAATGTATTGCGTAATAAATGCTTAC
3727405 TT
1 TT
3727407 GTTTGTCCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (39 bp):
TTCCAACAATATTAAATGTATTGCGTAATAAATGCTTAC
Found at i:3734248 original size:43 final size:44
Alignment explanation
Indices: 3734188--3734310 Score: 212
Period size: 43 Copynumber: 2.8 Consensus size: 44
3734178 GAAAAAGAAA
3734188 AAAAAAAAAAGCTTAATTTCTACATATCCATTATGTCAAAAAAG
1 AAAAAAAAAAGCTTAATTTCTACATATCCATTATGTCAAAAAAG
*
3734232 AAAAAAAAAA-CTTAATTTCTACATATCCATTATGTTAAAAAAG
1 AAAAAAAAAAGCTTAATTTCTACATATCCATTATGTCAAAAAAG
* *
3734275 AAAAAAAAAAGTTTAATTTCTACACATCCATTATGT
1 AAAAAAAAAAGCTTAATTTCTACATATCCATTATGT
3734311 TAAGGTACTA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
43 42 0.56
44 33 0.44
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (44 bp):
AAAAAAAAAAGCTTAATTTCTACATATCCATTATGTCAAAAAAG
Found at i:3735689 original size:21 final size:22
Alignment explanation
Indices: 3735664--3735705 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3735654 TATATATAAC
3735664 TCAAATATTTTGTA-ATAAATA
1 TCAAATATTTTGTACATAAATA
* *
3735685 TCAAATTTTTTTTACATAAAT
1 TCAAATATTTTGTACATAAAT
3735706 TATAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TCAAATATTTTGTACATAAATA
Found at i:3735866 original size:15 final size:16
Alignment explanation
Indices: 3735826--3735867 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3735816 ATGAAAGATC
3735826 ATATGTTTTGTTACATTT
1 ATAT-TTTT-TTACATTT
*
3735844 ATATTTTTTTACTTTT
1 ATATTTTTTTACATTT
3735860 A-ATTTTTT
1 ATATTTTTT
3735868 GTGACTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 4 0.17
18 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (16 bp):
ATATTTTTTTACATTT
Found at i:3737560 original size:45 final size:43
Alignment explanation
Indices: 3737499--3737603 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 43
3737489 AATATATGTG
* * *
3737499 TTATATTAATAA-ATTATTATTTAATACTTTAACTTAATATATTAAT
1 TTATATTAAAAATATTATTATTT-ATA-TATAA-TTAAAATA-TAAT
3737545 TTA-A-TAAAAATATTA-TATTTATATATAATTAAAATATAAT
1 TTATATTAAAAATATTATTATTTATATATAATTAAAATATAAT
*
3737585 TTATATTAAAAATAATATT
1 TTATATTAAAAATATTATT
3737604 TTGTGAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
40 7 0.14
41 8 0.16
42 14 0.27
43 4 0.08
44 10 0.20
45 5 0.10
46 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (43 bp):
TTATATTAAAAATATTATTATTTATATATAATTAAAATATAAT
Found at i:3737573 original size:24 final size:22
Alignment explanation
Indices: 3737545--3737603 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
3737535 ATATATTAAT
3737545 TTAATAAAAATATTATATTTATA
1 TTAATAAAAATATTA-ATTTATA
*
3737568 TATAATTAAAATA-TAATTTATA
1 T-TAATAAAAATATTAATTTATA
3737590 TTAA-AAATAATATT
1 TTAATAAA-AATATT
3737604 TTGTGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 7 0.23
22 9 0.29
23 3 0.10
24 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATAAAAATATTAATTTATA
Found at i:3740465 original size:12 final size:12
Alignment explanation
Indices: 3740448--3740472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3740438 CTTCCATCAC
3740448 CAACAACAGCAG
1 CAACAACAGCAG
3740460 CAACAACAGCAG
1 CAACAACAGCAG
3740472 C
1 C
3740473 TTCAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.36, G:0.16, T:0.00
Consensus pattern (12 bp):
CAACAACAGCAG
Found at i:3744537 original size:4 final size:4
Alignment explanation
Indices: 3744528--3744553 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3744518 CGTTTGGGGA
3744528 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3744554 TTGGTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3745237 original size:24 final size:24
Alignment explanation
Indices: 3745210--3745259 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3745200 GATAATTTAA
3745210 AATATGATATAAAAACATG-ATATG
1 AATATGATATAAAAA-ATGAATATG
*
3745234 AATATGGTATAAAAAATGAATATG
1 AATATGATATAAAAAATGAATATG
3745258 AA
1 AA
3745260 CGTGATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (24 bp):
AATATGATATAAAAAATGAATATG
Done.