Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 21
Found at i:4419115 original size:14 final size:14
Alignment explanation
Indices: 4419086--4419147 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 14
4419076 ACCCACCTTA
4419086 TTTT-TCTTTTCTT
1 TTTTCTCTTTTCTT
4419099 TTTTCTCTTGTTCTT
1 TTTTCTCTT-TTCTT
*
4419114 TTTCTCTTTTTTCCTCT
1 TTT-TCTCTTTT-CT-T
4419131 TTTTCT-TTTTCTT
1 TTTTCTCTTTTCTT
4419144 TTTT
1 TTTT
4419148 ACAATTTAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
13 9 0.21
14 6 0.14
15 14 0.33
16 10 0.23
17 4 0.09
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTCTTTTCTT
Found at i:4419125 original size:23 final size:24
Alignment explanation
Indices: 4419095--4419147 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
4419085 ATTTTTCTTT
4419095 TCTTTTTT-CTCTTGTTCTTTTTC
1 TCTTTTTTCCTCTTGTTCTTTTTC
*
4419118 TCTTTTTTCCTCTTTTTCTTTTTC
1 TCTTTTTTCCTCTTGTTCTTTTTC
4419142 T-TTTTT
1 TCTTTTT
4419148 ACAATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (24 bp):
TCTTTTTTCCTCTTGTTCTTTTTC
Found at i:4419204 original size:16 final size:16
Alignment explanation
Indices: 4419185--4419230 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
4419175 CACCCTAAAA
*
4419185 TTTTTTCTCTTTTTTG
1 TTTTTTCTCTTTTTTC
*
4419201 TTTTTT-TCCTTTTTC
1 TTTTTTCTCTTTTTTC
*
4419216 CTTTTTC-CTTTTTTC
1 TTTTTTCTCTTTTTTC
4419231 AACTTAGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:4419213 original size:7 final size:7
Alignment explanation
Indices: 4419203--4419228 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4419193 CTTTTTTGTT
4419203 TTTTTCC
1 TTTTTCC
4419210 TTTTTCC
1 TTTTTCC
4419217 TTTTTCC
1 TTTTTCC
4419224 TTTTT
1 TTTTT
4419229 TCAACTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:4419213 original size:8 final size:8
Alignment explanation
Indices: 4419185--4419230 Score: 51
Period size: 7 Copynumber: 5.9 Consensus size: 8
4419175 CACCCTAAAA
4419185 TTTTTTCTC
1 TTTTTTC-C
**
4419194 TTTTTTGT
1 TTTTTTCC
4419202 TTTTTTCC
1 TTTTTTCC
4419210 -TTTTTCC
1 TTTTTTCC
4419217 -TTTTTCC
1 TTTTTTCC
4419224 TTTTTTC
1 TTTTTTC
4419231 AACTTAGGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
7 14 0.44
8 12 0.38
9 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:4426711 original size:20 final size:20
Alignment explanation
Indices: 4426686--4426735 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
4426676 CAGACCTATG
4426686 GTATCGATACTGTTAGACCA
1 GTATCGATACTGTTAGACCA
4426706 GTATCGATACTGTTAGACCA
1 GTATCGATACTGTTAGACCA
4426726 GTATCGATAC
1 GTATCGATAC
4426736 CCCTATACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGTTAGACCA
Found at i:4426745 original size:20 final size:20
Alignment explanation
Indices: 4426699--4426745 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4426689 TCGATACTGT
***
4426699 TAGACCAGTATCGATACTGT
1 TAGACCAGTATCGATACCCC
4426719 TAGACCAGTATCGATACCCC
1 TAGACCAGTATCGATACCCC
*
4426739 TATACCA
1 TAGACCA
4426746 AATATCTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
TAGACCAGTATCGATACCCC
Found at i:4430176 original size:31 final size:31
Alignment explanation
Indices: 4430108--4430209 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 31
4430098 ATGGATTTGG
* *
4430108 TTAGGGACCAAAATAAAAATTTT---AAAGT
1 TTAGGGACCAAAGTATAAATTTTGGAAAAGT
* *
4430136 TAAGTGACCAAAGTATAAATTTTGGAAAAGT
1 TTAGGGACCAAAGTATAAATTTTGGAAAAGT
*
4430167 TTAGGGACCAAAGTATAAACTTTGGAAAAGT
1 TTAGGGACCAAAGTATAAATTTTGGAAAAGT
*
4430198 TTAGAGACCAAA
1 TTAGGGACCAAA
4430210 ATGGTAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.30
31 44 0.70
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (31 bp):
TTAGGGACCAAAGTATAAATTTTGGAAAAGT
Found at i:4439520 original size:204 final size:204
Alignment explanation
Indices: 4439168--4439625 Score: 747
Period size: 204 Copynumber: 2.2 Consensus size: 204
4439158 ATTGTTCCGA
* ** * * * * *
4439168 GTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACTGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
*
4439233 AGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCGCCCCTT--CTGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
*
4439298 TGAAATTGACTCTGAATGAAATTTTGTTGACAATCAACCGCCCCTTCGTTGTAAAGTTGAGCTTG
129 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAACCGCCCCTTCGTTGTAAAGTTGAGCTTG
4439363 TGTTGTCTTGG
194 TGTTGTCTTGG
*
4439374 GTCCAATATCCTTCGTTGTAAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
*
4439439 AGTCGCCCCTT-TGCTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
66 AGCCGCCCCTTCTG-TGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
* *
4439503 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGT
130 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAACCGCCCCTTCGTTGTAAAGTTGAGCTTGT
4439568 GTTGTCTTGG
195 GTTGTCTTGG
*
4439578 GTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
4439626 GCCCCTTCTT
Statistics
Matches: 235, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
203 2 0.01
204 167 0.71
206 66 0.28
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (204 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
AGCCGCCCCTTCTGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTTG
AAATTGACTCTGAATGAAATTTTGTTAACAATCAACCGCCCCTTCGTTGTAAAGTTGAGCTTGTG
TTGTCTTGG
Found at i:4439616 original size:100 final size:104
Alignment explanation
Indices: 4439165--4439617 Score: 523
Period size: 100 Copynumber: 4.4 Consensus size: 104
4439155 AGTATTGTTC
* ** * *
4439165 CGAGTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-GAACTG-GAAATTGTTTGTTGACA
* **
4439230 GTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
64 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* **
4439271 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTGACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* * *
4439332 CAACCGCCCCTTCGTTGTAAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * * *
4439371 TGGGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTG-AACT-GGAAATTGTTTGTTGACA
* * *
4439436 GTCAGTCGCCCC-T--TTGCTGAAGTTGAGCTTGTGCTGTAT
64 ATCAGCCGCCCCTTCGTTG-TGAAGTTGAGCTTGTGCTGTCT
* ** *
4439475 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTAACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
*
4439536 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4439575 TGGGTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
4439618 ATTGGGAAGC
Statistics
Matches: 294, Mismatches: 43, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
98 19 0.06
99 2 0.01
100 140 0.48
101 6 0.02
102 6 0.02
103 5 0.02
104 59 0.20
105 5 0.02
106 52 0.18
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:4440722 original size:16 final size:15
Alignment explanation
Indices: 4440693--4440752 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 15
4440683 CTTATTTTTC
4440693 TTTTCTTTTTTCTCT
1 TTTTCTTTTTTCTCT
*
4440708 TGTTCTTTTTCTCTCTT
1 TTTTCTTTTT-TCTC-T
4440725 TTTCTCTTTTTTCCTCT
1 TTT-TCTTTTTT-CTCT
4440742 TTTTCTTTTTT
1 TTTTCTTTTTT
4440753 ACAATTTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.23
16 12 0.31
17 8 0.21
18 10 0.26
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTTCTCT
Found at i:4440726 original size:10 final size:10
Alignment explanation
Indices: 4440711--4440747 Score: 60
Period size: 9 Copynumber: 3.9 Consensus size: 10
4440701 TTTCTCTTGT
4440711 TCTTTTTCTC
1 TCTTTTTCTC
4440721 TCTTTTTCTC
1 TCTTTTTCTC
4440731 T-TTTTTC-C
1 TCTTTTTCTC
4440739 TCTTTTTCT
1 TCTTTTTCT
4440748 TTTTTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 12 0.48
10 11 0.44
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TCTTTTTCTC
Found at i:4440730 original size:8 final size:8
Alignment explanation
Indices: 4440693--4440752 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
4440683 CTTATTTTTC
4440693 TTTTCT-T
1 TTTTCTCT
4440700 TTTTCTCT
1 TTTTCTCT
*
4440708 TGTTCT-T
1 TTTTCTCT
4440715 TTTCTCTCT
1 TTT-TCTCT
4440724 TTTTCTCTT
1 TTTTCTC-T
4440733 TTTTCCTCT
1 TTTT-CTCT
4440742 TTTTCT-T
1 TTTTCTCT
4440749 TTTT
1 TTTT
4440753 ACAATTTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
7 14 0.30
8 15 0.33
9 14 0.30
10 3 0.07
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTCTCT
Found at i:4458351 original size:66 final size:67
Alignment explanation
Indices: 4458242--4458368 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 67
4458232 AAGACTCTGA
* * * **
4458242 CAGGTTCAGTCGCTGCTGGTAATTCCTTGTATAGGTTTTGCACCAACTGGTAATT-CTTATCTGT
1 CAGGTTCAGACGCTACTGGTAAATCCTTGTATAGGTTCAGCACCAACTGGTAATTCCTTATCTGT
4458306 GG
66 GG
4458308 CAGGTTCAGACGCTACTGGTAAATCCTT-TCATAGGTTCAGCACCAACTGGTAATTCCTTAT
1 CAGGTTCAGACGCTACTGGTAAATCCTTGT-ATAGGTTCAGCACCAACTGGTAATTCCTTAT
4458369 GGACCTAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.02
66 48 0.89
67 5 0.09
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (67 bp):
CAGGTTCAGACGCTACTGGTAAATCCTTGTATAGGTTCAGCACCAACTGGTAATTCCTTATCTGT
GG
Found at i:4458550 original size:59 final size:60
Alignment explanation
Indices: 4458476--4458612 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
4458466 TGTCTACATT
* * * *
4458476 GGGTAAGTCCTTATGGGCCTGAGGGCACTCCCCTCAGGTGGGCACCTACG-CTTC-GG-CTA
1 GGGTAAGTCCTTATGGACC-CAAGGCACT-CCCTAAGGTGGGCACCTACGCCTTCGGGCCTA
* ** *
4458535 GGGTAAGACCTTATGGACCCAAGGTTCTCCCTAAGGTTGGCACCTACGCCCTTCGGGCCTA
1 GGGTAAGTCCTTATGGACCCAAGGCACTCCCTAAGGTGGGCACCTACG-CCTTCGGGCCTA
4458596 GGGTAAGTCCTTATGGA
1 GGGTAAGTCCTTATGGA
4458613 TGCAGTTCTG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 18 0.28
58 5 0.08
59 21 0.32
60 2 0.03
61 19 0.29
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.23
Consensus pattern (60 bp):
GGGTAAGTCCTTATGGACCCAAGGCACTCCCTAAGGTGGGCACCTACGCCTTCGGGCCTA
Found at i:4461558 original size:21 final size:21
Alignment explanation
Indices: 4461513--4461558 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4461503 ATTCCATTAA
* *
4461513 TAAAAAATATTTTTTAAATTT
1 TAAAAAATATTTTTTAAAGTG
4461534 TAAAAAATGA-TTTTTAAAGTG
1 TAAAAAAT-ATTTTTTAAAGTG
4461555 TAAA
1 TAAA
4461559 TTGATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAAAAATATTTTTTAAAGTG
Found at i:4462354 original size:12 final size:12
Alignment explanation
Indices: 4462326--4462368 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
4462316 TAATATACAT
*
4462326 ATGAACAATACT
1 ATGAACAATACC
*
4462338 GTGAACAATACC
1 ATGAACAATACC
* *
4462350 ATGAATAGTACC
1 ATGAACAATACC
4462362 ATGAACA
1 ATGAACA
4462369 GTGAAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.21
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:4463189 original size:32 final size:33
Alignment explanation
Indices: 4463085--4463209 Score: 127
Period size: 31 Copynumber: 4.0 Consensus size: 33
4463075 AACCTCGACA
* * *
4463085 ACTGTCCATAGGTC-CTGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCTCAGAAGAACATAGGTAAT
* **
4463116 ACTGTCCATATGTTTC-TTAGAACATAGGT-AT
1 ACTGTCCATATGTCTCAGAAGAACATAGGTAAT
4463147 ACTGTCCATATGTCTCAGAAG-ACATAGGTAAT
1 ACTGTCCATATGTCTCAGAAGAACATAGGTAAT
* * *
4463179 TCTGTCCATATGT-TCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCTCAGAAGAACATAGGTAA
4463210 ACCCTCGACT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.01
31 50 0.64
32 27 0.35
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (33 bp):
ACTGTCCATATGTCTCAGAAGAACATAGGTAAT
Found at i:4463191 original size:63 final size:62
Alignment explanation
Indices: 4463085--4463208 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 62
4463075 AACCTCGACA
* * * *
4463085 ACTGTCCATAGGTCCTGAAGAACCTAGGTAAACTGTCCATATGTTTCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCAGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
4463147 ACTGTCCATATGTCTCAGAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTC-CAGAAGAACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
4463209 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
62 22 0.41
63 32 0.59
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (62 bp):
ACTGTCCATAGGTCCAGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:4467544 original size:32 final size:33
Alignment explanation
Indices: 4467502--4467571 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
4467492 TTAAATCATT
* * * *
4467502 TTTGTAAAGAAGAATTATGTCAAAAATATATTC
1 TTTGTAAAGAAGAATAATATCAAAAAAAAATTC
4467535 TTTG-AAAGAAGAATAATATCAAAAAAAAATTC
1 TTTGTAAAGAAGAATAATATCAAAAAAAAATTC
4467567 TTTGT
1 TTTGT
4467572 GTTTTGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (33 bp):
TTTGTAAAGAAGAATAATATCAAAAAAAAATTC
Found at i:4468681 original size:18 final size:19
Alignment explanation
Indices: 4468658--4468693 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4468648 ATAGGTAAGA
4468658 ATTTTTGTCTTT-GTTTTG
1 ATTTTTGTCTTTAGTTTTG
*
4468676 ATTTTTGTGTTTAGTTTT
1 ATTTTTGTCTTTAGTTTT
4468694 TTAGTAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (19 bp):
ATTTTTGTCTTTAGTTTTG
Found at i:4470807 original size:39 final size:39
Alignment explanation
Indices: 4470742--4470835 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
4470732 CCACTTTTCA
* *
4470742 TAGGCTCCTCGACTTTGTGCTTAGGGTAAGTCCTTACCG
1 TAGGCTCCTCGACTTTATGCTCAGGGTAAGTCCTTACCG
* * *
4470781 TAGGCTCTTCGGCTTTATGCTCAGGGTAAGTCCTTACTG
1 TAGGCTCCTCGACTTTATGCTCAGGGTAAGTCCTTACCG
* * *
4470820 CATGCTCCTCTACTTT
1 TAGGCTCCTCGACTTT
4470836 GTGCACAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.36
Consensus pattern (39 bp):
TAGGCTCCTCGACTTTATGCTCAGGGTAAGTCCTTACCG
Found at i:4477051 original size:23 final size:22
Alignment explanation
Indices: 4477013--4477055 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4477003 CAATTCCTTT
4477013 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
4477035 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
4477056 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:4481214 original size:43 final size:45
Alignment explanation
Indices: 4481139--4481242 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 45
4481129 AGGATTAGAT
* * *
4481139 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAATATTTATTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACATGT-TTAGTTTA
*
4481187 TTATTATTTTATTAGGAATT-A-GAGTTAATACATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACATGTTTAGTTTA
4481230 TTATTATTTTATT
1 TTATTATTTTATT
4481243 CATTAGTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 4 0.08
43 26 0.51
47 1 0.02
48 20 0.39
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACATGTTTAGTTTA
Found at i:4481678 original size:23 final size:22
Alignment explanation
Indices: 4481640--4481682 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4481630 CAATTCCTTT
4481640 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
4481662 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
4481683 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:4485716 original size:17 final size:17
Alignment explanation
Indices: 4485694--4485746 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
4485684 AATTAAGAGT
*
4485694 TAGTTTAATAAATGAAG
1 TAGTTTAATAAATGAAC
* *
4485711 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
4485728 TAGTTTAATTAATAAAC
1 TAGTTTAATAAATGAAC
4485745 TA
1 TA
4485747 ACTTTATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:4493400 original size:6 final size:6
Alignment explanation
Indices: 4493379--4493516 Score: 115
Period size: 6 Copynumber: 22.5 Consensus size: 6
4493369 AAAGATAGGC
* * * * *
4493379 AAAACA AAAA-A AAAAGA AAAAGG AAAAGA AATAGA AATAGA AAAATA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
4493426 TAAAAG- -AAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
4493472 GAAAA-A AAATAAA AAATAGA GAAAAGA AAGAGAGA AGAAAGA AAA
1 -AAAAGA AAA-AGA AAA-AGA -AAAAGA AA-A-AGA A-AAAGA AAA
4493517 TCAATCAAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
4 3 0.03
5 11 0.10
6 67 0.59
7 23 0.20
8 8 0.07
9 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:4493423 original size:52 final size:51
Alignment explanation
Indices: 4493379--4493516 Score: 127
Period size: 52 Copynumber: 2.6 Consensus size: 51
4493369 AAAGATAGGC
* * * *
4493379 AAAACAAAAAAAAAAGAAAAAGGAAAAGAAATAGAAATAGAAAAATATAAAAG
1 AAAA-AAAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAT-AAAG
* *
4493432 AAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAGAAAA-A-AAAT
1 AAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGA-AAAAGATAAAG
* *
4493482 AAAAAATAGAGAAAAGAAAGAGAGAAGAAAGAAAA
1 AAAAAA-AAAAAAAAGAAA-A-AGAA-AAAGAAAA
4493517 TCAATCAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
50 9 0.12
51 9 0.12
52 34 0.47
53 12 0.17
54 8 0.11
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (51 bp):
AAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGATAAAG
Found at i:4493436 original size:46 final size:45
Alignment explanation
Indices: 4493384--4493516 Score: 151
Period size: 46 Copynumber: 2.9 Consensus size: 45
4493374 TAGGCAAAAC
* * * *
4493384 AAAAAAAAAAGAAAAAGGAAAAGAAATAGAAATAGAAAAATATAA
1 AAAAAAAAAAGAAAAAGGAAAAGAAAAAGAAAAAGAAAAAGAGAA
*
4493429 AAGAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAGAA
1 AA-AAAAAAAAGAAAAAGGAAAAGAAAAAGAAAAAGAAAAAGAGAA
* *
4493475 AAAAAATAAA-AAATAGAGAAAAGAAAGAGAGAAGAAAGAAAA
1 AAAAAAAAAAGAAAAAG-GAAAAGAAA-A-AGAA-AAAGAAAA
4493517 TCAATCAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
44 5 0.07
45 17 0.23
46 41 0.55
47 4 0.05
48 8 0.11
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (45 bp):
AAAAAAAAAAGAAAAAGGAAAAGAAAAAGAAAAAGAAAAAGAGAA
Found at i:4493486 original size:18 final size:18
Alignment explanation
Indices: 4493379--4493496 Score: 78
Period size: 20 Copynumber: 6.2 Consensus size: 18
4493369 AAAGATAGGC
*
4493379 AAAACAAAAAAAAA-AGA
1 AAAAAAAAAAAAAAGAGA
** * *
4493396 AAAAGGAAAAGAAATAGA
1 AAAAAAAAAAAAAAGAGA
*
4493414 AATAGAAAAATATAAAAGA-A
1 AA-A-AAAAA-AAAAAAGAGA
*
4493434 AAAAAAGAAAAAGAAAAAGA
1 AAAAAA-AAAAA-AAAGAGA
4493454 AAAAGAAAAAGAAAAAGAGA
1 AAAA-AAAAA-AAAAAGAGA
4493474 AAAAAAATAAAAAATAGAGA
1 AAAAAAA-AAAAAA-AGAGA
4493494 AAA
1 AAA
4493497 GAAAGAGAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 19
0.72 0.10 0.17
Matches are distributed among these distances:
17 11 0.14
18 10 0.13
19 15 0.19
20 34 0.43
21 9 0.11
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAAAAGAGA
Found at i:4493495 original size:40 final size:40
Alignment explanation
Indices: 4493379--4493516 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 40
4493369 AAAGATAGGC
* * * * *
4493379 AAAACAAAAAAAAAAGAAAAAGGAAAAGAAATAGAAATAGA
1 AAAAGAAAAAAGAAA-AAAAAGAAAAAGAAAAAGAAAAAGA
* *
4493420 AAAATATAAAAGAAAAAAAAGAAAAAGAAAAAGAAAAAGA
1 AAAAGAAAAAAGAAAAAAAAGAAAAAGAAAAAGAAAAAGA
* * *
4493460 AAAAGAAAAAGAGAAAAAAAATAAAAA-ATAGAG-AAAAGA
1 AAAAGAAAAA-AGAAAAAAAAGAAAAAGAAAAAGAAAAAGA
*
4493499 AAGAGAGAAGAAAGAAAA
1 AA-A-AGAAAAAAGAAAA
4493517 TCAATCAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
39 8 0.10
40 41 0.50
41 33 0.40
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (40 bp):
AAAAGAAAAAAGAAAAAAAAGAAAAAGAAAAAGAAAAAGA
Found at i:4496899 original size:91 final size:91
Alignment explanation
Indices: 4496791--4497151 Score: 528
Period size: 91 Copynumber: 4.0 Consensus size: 91
4496781 GATAAACCGA
* *
4496791 TCAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
4496856 ATGAAAAGAACTTGTTCAACCTTGGC
66 ATGAAAAGAACTTGTTCAACCTTGGC
* *
4496882 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
4496947 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAAAAGAACTTGTTCAACCTTGGC
* * * * * *
4496973 TCAACACTTCCTGTGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* * *
4497038 AT-AAGAAGGACGTGTTCAACCTTGCC
66 ATGAA-AAGAACTTGTTCAACCTTGGC
* **
4497064 TCAACATTTCC-GATGGAGAGTTCATAATGAGAAGAACCCATCTGACGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
4497128 AATGAGAAGAACTTGTTCAACCTT
65 AATGAAAAGAACTTGTTCAACCTT
4497152 AGCTTGATTC
Statistics
Matches: 243, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 2 0.01
91 240 0.99
92 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAAAAGAACTTGTTCAACCTTGGC
Found at i:4500918 original size:18 final size:18
Alignment explanation
Indices: 4500895--4500935 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
4500885 TCAGTAATTC
4500895 TATTCCCCGGTAATCTTT
1 TATTCCCCGGTAATCTTT
4500913 TATTCCCCGGTAATCTTT
1 TATTCCCCGGTAATCTTT
4500931 TATTC
1 TATTC
4500936 TCATTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.46
Consensus pattern (18 bp):
TATTCCCCGGTAATCTTT
Found at i:4500948 original size:20 final size:20
Alignment explanation
Indices: 4500905--4500969 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
4500895 TATTCCCCGG
* *
4500905 TAATCTTTTATTC-C-CCGG
1 TAATCTTTTATTCTCACTGA
*
4500923 TAATCTTTTATTCTCATTGA
1 TAATCTTTTATTCTCACTGA
4500943 TAATCTTTTATTCTCACTGA
1 TAATCTTTTATTCTCACTGA
4500963 TAATCTT
1 TAATCTT
4500970 ACATTCCGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.32
19 1 0.02
20 27 0.66
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (20 bp):
TAATCTTTTATTCTCACTGA
Found at i:4500975 original size:20 final size:20
Alignment explanation
Indices: 4500932--4500975 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4500922 GTAATCTTTT
* **
4500932 ATTCTCATTGATAATCTTTT
1 ATTCTCACTGATAATCTTAC
4500952 ATTCTCACTGATAATCTTAC
1 ATTCTCACTGATAATCTTAC
4500972 ATTC
1 ATTC
4500976 CGTGAACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTCTCACTGATAATCTTAC
Found at i:4504155 original size:17 final size:17
Alignment explanation
Indices: 4504133--4504223 Score: 76
Period size: 17 Copynumber: 5.3 Consensus size: 17
4504123 TCGAATCAAG
*
4504133 CTCGATTCGAGCTCGAA
1 CTCGATTCAAGCTCGAA
4504150 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
* * * * *
4504167 CTCAAACTCGAA-TTTGAG
1 CTC-GATTC-AAGCTCGAA
* *
4504185 CTCAATTCAAACTCGAA
1 CTCGATTCAAGCTCGAA
*
4504202 CTAGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
4504219 CTCGA
1 CTCGA
4504224 ACTTGAATTT
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
16 2 0.04
17 44 0.77
18 9 0.16
19 2 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:4504165 original size:11 final size:11
Alignment explanation
Indices: 4504073--4504148 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
4504063 AAAATTCAGG
*
4504073 AGCTCGATTGA
1 AGCTCGATTCA
* *
4504084 AGCTCGAGACTCG
1 AGCTC--GATTCA
*
4504097 AGCTCGATTGA
1 AGCTCGATTCA
**
4504108 AGCTCGATTTTG
1 AGCTCGA-TTCA
*
4504120 AGCTCGAATCA
1 AGCTCGATTCA
*
4504131 AGCTCGATTCG
1 AGCTCGATTCA
4504142 AGCTCGA
1 AGCTCGA
4504149 ACTCGATTCA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
11 32 0.65
12 9 0.18
13 8 0.16
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:4504174 original size:23 final size:23
Alignment explanation
Indices: 4504139--4504200 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
4504129 CAAGCTCGAT
* *
4504139 TCGAGCTCGAACTCGATTCAAGC
1 TCGAACTCAAACTCGATTCAAGC
**
4504162 TCGAACTCAAACTCGAATTTGAGC
1 TCGAACTCAAACTCG-ATTCAAGC
*
4504186 TC-AATTCAAACTCGA
1 TCGAACTCAAACTCGA
4504201 ACTAGATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 1 0.03
23 24 0.73
24 8 0.24
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (23 bp):
TCGAACTCAAACTCGATTCAAGC
Found at i:4505767 original size:3 final size:3
Alignment explanation
Indices: 4505759--4505795 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4505749 TCGTGAATTC
4505759 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4505796 GAAAAAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4506575 original size:21 final size:21
Alignment explanation
Indices: 4506549--4506638 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
4506539 ATTCAATCAT
4506549 TATTTAGGGTTTATGATTTAG
1 TATTTAGGGTTTATGATTTAG
4506570 TATTTAGGG-TT-T-A--TAG
1 TATTTAGGGTTTATGATTTAG
* *
4506586 --TTTAGAGTTTATGGTTTAG
1 TATTTAGGGTTTATGATTTAG
* *
4506605 TATTTATGGTTTATAATTTAAG
1 TATTTAGGGTTTATGATTT-AG
4506627 -ATTTAGGGTTTA
1 TATTTAGGGTTTA
4506639 GTATTTATAG
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 4 0.07
18 1 0.02
19 4 0.07
20 2 0.04
21 33 0.61
22 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (21 bp):
TATTTAGGGTTTATGATTTAG
Found at i:4506582 original size:14 final size:14
Alignment explanation
Indices: 4506572--4506666 Score: 61
Period size: 14 Copynumber: 6.8 Consensus size: 14
4506562 TGATTTAGTA
*
4506572 TTTAGGGTTTATAG
1 TTTAGAGTTTATAG
*
4506586 TTTAGAGTTTATGG
1 TTTAGAGTTTATAG
*
4506600 TTTAGTA-TTTATGG
1 TTTAG-AGTTTATAG
* *
4506614 TTTATAATTTA-AG
1 TTTAGAGTTTATAG
*
4506627 ATTTAGGGTTTAGTA-
1 -TTTAGAGTTTA-TAG
* *
4506642 TTTATAGTTTATAT
1 TTTAGAGTTTATAG
*
4506656 TTTAGGGTTTA
1 TTTAGAGTTTA
4506667 GGGTTTTAGG
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
13 4 0.06
14 58 0.91
15 1 0.02
16 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (14 bp):
TTTAGAGTTTATAG
Found at i:4506590 original size:35 final size:35
Alignment explanation
Indices: 4506550--4506672 Score: 156
Period size: 35 Copynumber: 3.5 Consensus size: 35
4506540 TTCAATCATT
* *
4506550 ATTTAGGGTTTATGATTTAGTATTTAGGGTTTATA
1 ATTTAGGGTTTATGGTTTAGTATTTATGGTTTATA
* *
4506585 GTTTAGAGTTTATGGTTTAGTATTTATGGTTTATA
1 ATTTAGGGTTTATGGTTTAGTATTTATGGTTTATA
* * * *
4506620 ATTTAAGATTTAGGGTTTAGTATTTATAGTTTATA
1 ATTTAGGGTTTATGGTTTAGTATTTATGGTTTATA
* *
4506655 TTTTAGGGTTTAGGGTTT
1 ATTTAGGGTTTATGGTTT
4506673 TAGGGTGTGA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.24, C:0.00, G:0.23, T:0.53
Consensus pattern (35 bp):
ATTTAGGGTTTATGGTTTAGTATTTATGGTTTATA
Found at i:4506659 original size:7 final size:7
Alignment explanation
Indices: 4506578--4506659 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
4506568 AGTATTTAGG
4506578 GTTTATA
1 GTTTATA
*
4506585 GTTTAGA
1 GTTTATA
*
4506592 GTTTATG
1 GTTTATA
4506599 GTTTAGTA
1 GTTTA-TA
*
4506607 -TTTATG
1 GTTTATA
4506613 GTTTATA
1 GTTTATA
*
4506620 ATTTA-A
1 GTTTATA
**
4506626 GATTTAGG
1 G-TTTATA
4506634 GTTTAGTA
1 GTTTA-TA
4506642 -TTTATA
1 GTTTATA
4506648 GTTTATA
1 GTTTATA
*
4506655 TTTTA
1 GTTTA
4506660 GGGTTTAGGG
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
6 4 0.07
7 51 0.89
8 2 0.04
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (7 bp):
GTTTATA
Found at i:4506666 original size:21 final size:21
Alignment explanation
Indices: 4506551--4506666 Score: 69
Period size: 21 Copynumber: 5.5 Consensus size: 21
4506541 TCAATCATTA
4506551 TTTAGGGTTTAT-GATTTAGTA-
1 TTTAGGGTTTATAG-TTTA-TAG
*
4506572 TTTAGGGTTTATAGTTTAGAG
1 TTTAGGGTTTATAGTTTATAG
* *
4506593 TTTATGGTTTAGTA-TTTATGG
1 TTTAGGGTTTA-TAGTTTATAG
*** **
4506614 TTTATAATTTA-AGATTTAGGG
1 TTTAGGGTTTATAG-TTTATAG
** *
4506635 TTTAGTATTTATAGTTTATAT
1 TTTAGGGTTTATAGTTTATAG
4506656 TTTAGGGTTTA
1 TTTAGGGTTTA
4506667 GGGTTTTAGG
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 68 0.91
22 5 0.07
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (21 bp):
TTTAGGGTTTATAGTTTATAG
Found at i:4507953 original size:30 final size:27
Alignment explanation
Indices: 4507917--4507998 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 27
4507907 TTTTTTTATC
4507917 TAAGTACCTAAAATATCTTTCTTGTCAAAA
1 TAAGTA-CTAAAATAT-TTT-TTGTCAAAA
*
4507947 TAAGTACTAAAGTTATATTTTTTTATCAAAA
1 TAAGTACTAAA---ATA-TTTTTTGTCAAAA
*
4507978 TAAGTACTTAAATATTTTTTG
1 TAAGTACTAAAATATTTTTTG
4507999 GCCAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
27 6 0.13
28 3 0.07
29 5 0.11
30 6 0.13
31 18 0.40
32 6 0.13
33 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (27 bp):
TAAGTACTAAAATATTTTTTGTCAAAA
Found at i:4510489 original size:31 final size:31
Alignment explanation
Indices: 4510418--4510495 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
4510408 CTTTTAAAAC
** *
4510418 TTGCAATATAATCCCCCAATATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
* *
4510449 TTGCAATATGGTCCCTCAACATTTAGTCCTT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
4510480 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
4510496 GACGTAACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCGT
Found at i:4510799 original size:23 final size:22
Alignment explanation
Indices: 4510749--4510812 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
4510739 TTATAAAATG
* *
4510749 TTAAATTATATAATTATAAATTAG
1 TTAAAATATA-AATT-TAAATTAA
*
4510773 TTAAAAATATAAATTTAATTTAA
1 TT-AAAATATAAATTTAAATTAA
4510796 TTAAAATATAATATTTA
1 TTAAAATATAA-ATTTA
4510813 TAAAACATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 9 0.26
23 13 0.37
24 6 0.17
25 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAAATATAAATTTAAATTAA
Found at i:4512611 original size:12 final size:12
Alignment explanation
Indices: 4512590--4512632 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
4512580 ACCGAAGCCC
*
4512590 AATCAGACCCAA
1 AATCAAACCCAA
4512602 AATCAAACCCAA
1 AATCAAACCCAA
4512614 AACTCAAAAACCCAA
1 AA-TC--AAACCCAA
4512629 AATC
1 AATC
4512633 TAGACTCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 13 0.48
13 2 0.07
14 2 0.07
15 10 0.37
ACGTcount: A:0.56, C:0.33, G:0.02, T:0.09
Consensus pattern (12 bp):
AATCAAACCCAA
Found at i:4515127 original size:18 final size:19
Alignment explanation
Indices: 4515104--4515143 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4515094 AATAAGTCAA
* *
4515104 AATAAATTAATTA-ACTTT
1 AATAAATGAATCATACTTT
4515122 AATAAATGAATCATACTTT
1 AATAAATGAATCATACTTT
4515141 AAT
1 AAT
4515144 TATCGATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (19 bp):
AATAAATGAATCATACTTT
Found at i:4515694 original size:15 final size:15
Alignment explanation
Indices: 4515676--4515729 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
4515666 GAAAGCATAG
4515676 AAAAAAAGAAAGAAA
1 AAAAAAAGAAAGAAA
*
4515691 AAAATAAG-AAGCAAA
1 AAAAAAAGAAAG-AAA
* *
4515706 GAAAAAACAAAGAAA
1 AAAAAAAGAAAGAAA
4515721 AAAAAAAGA
1 AAAAAAAGA
4515730 CAATAAGCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 3 0.10
15 25 0.81
16 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAAAGAAAGAAA
Found at i:4515711 original size:30 final size:31
Alignment explanation
Indices: 4515668--4515729 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
4515658 GATAAAATGA
* * *
4515668 AAGCATAGAAAAAAAGAAAGAAAAAAATAAG
1 AAGCAAAGAAAAAAACAAAGAAAAAAAAAAG
4515699 AAGCAAAG-AAAAAACAAAGAAAAAAAAAAG
1 AAGCAAAGAAAAAAACAAAGAAAAAAAAAAG
4515729 A
1 A
4515730 CAATAAGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (31 bp):
AAGCAAAGAAAAAAACAAAGAAAAAAAAAAG
Found at i:4517096 original size:36 final size:36
Alignment explanation
Indices: 4516998--4517106 Score: 119
Period size: 37 Copynumber: 3.0 Consensus size: 36
4516988 TTTGAGATTG
* * *
4516998 TTTCTCTCGAAACAAAGTGTCGTCTCGCTAGAGACGA
1 TTTCTCTCAAAACAAA-TTTCGTCTCGCTAGAGACAA
* * * *
4517035 TTTTTCTTAAAACCAAATTTTGTCTCGCTTGAGACAA
1 TTTCTCTCAAAA-CAAATTTCGTCTCGCTAGAGACAA
* *
4517072 TTTCTCTCAAAACAAATTTCGTCTCACTGGAGACA
1 TTTCTCTCAAAACAAATTTCGTCTCGCTAGAGACA
4517107 GCTTTTCTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
36 20 0.34
37 35 0.59
38 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTTCGTCTCGCTAGAGACAA
Found at i:4517248 original size:66 final size:65
Alignment explanation
Indices: 4517163--4517347 Score: 192
Period size: 66 Copynumber: 2.7 Consensus size: 65
4517153 AATTGATAAA
* * * *
4517163 ATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTTTTGAGACTGTTTCTCTTGAAGC-A
1 ATCTTTGAG-ATGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAA
4517227 TC
64 TC
* *
4517229 ATCTTTGAGATCGTTTCCCTTGAAACAAATTTTTTTTTTTCTCTCTTAAAACAGTTTCTCTTGAA
1 ATCTTTGAGAT-GTTTCCCTTGAAACAAA-----TTTTGTCTCTCTTGAAACAGTTTCTCTTGAA
4517294 ACAATC
60 ACAATC
* * **
4517300 ATATTTGAGCTTGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAAACA
1 ATCTTTGAG-ATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAAACA
4517348 TCATCTTTGA
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
65 2 0.02
66 43 0.43
70 27 0.27
71 26 0.26
72 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (65 bp):
ATCTTTGAGATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAATC
Found at i:4517390 original size:50 final size:50
Alignment explanation
Indices: 4517285--4517391 Score: 130
Period size: 50 Copynumber: 2.1 Consensus size: 50
4517275 TAAAACAGTT
**
4517285 TCTCTTGAAACAATCATATTTGAGCTTGTTTCCCTTGAAATGAATTTTGTC
1 TCTCTTGAAACAATCATATTTGAGCTTGTTTCCCTTGAAAAAAATTTTG-C
*
4517336 TCTCTTGAAAC-ATCATCTTTGAG-TCTGTTTCCCTTGAAACAAAAATTTTG-
1 TCTCTTGAAACAATCATATTTGAGCT-TGTTTCCCTTG-AA-AAAAATTTTGC
4517386 TCTCTT
1 TCTCTT
4517392 TTGAGACAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
49 1 0.02
50 28 0.56
51 13 0.26
52 8 0.16
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (50 bp):
TCTCTTGAAACAATCATATTTGAGCTTGTTTCCCTTGAAAAAAATTTTGC
Found at i:4517595 original size:40 final size:41
Alignment explanation
Indices: 4517548--4517760 Score: 119
Period size: 40 Copynumber: 4.9 Consensus size: 41
4517538 CATATTATCG
*
4517548 TCCTCATCACGTAGGAACCGTGTCATCC-A-CTGACCATATC
1 TCCTCATCACGTAGGAACCGTGTCATCCTAGATGACCA-ATC
* ** * * *
4517588 TCCTCATCACATAGGAGTCGTGTCACCCTTAGATAACCAACC
1 TCCTCATCACGTAGGAACCGTGTCATCC-TAGATGACCAATC
* *
4517630 TCCTCATCACGTAGGAACTGTGTTATCATCATCCCTAAAGATGACCAAGAC
1 TCCTCATCACGTAGGAACCGTG------TCAT-CCT--AGATGACCAA-TC
* * **
4517681 ATCCTCATCACATAGGAACAGTGTCATCC-A-CCGACCAGATC
1 -TCCTCATCACGTAGGAACCGTGTCATCCTAGATGACCA-ATC
* * *
4517722 TCCTCATCACGTAGGAGCCGTGTCACCCTTAGACGACCA
1 TCCTCATCACGTAGGAACCGTGTCATCC-TAGATGACCA
4517761 GAACTCTTCA
Statistics
Matches: 131, Mismatches: 24, Indels: 33
0.70 0.13 0.18
Matches are distributed among these distances:
40 48 0.37
41 6 0.05
42 24 0.18
43 11 0.08
45 2 0.02
46 4 0.03
48 4 0.03
49 2 0.02
50 9 0.07
51 1 0.01
52 20 0.15
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCTAGATGACCAATC
Found at i:4519755 original size:18 final size:19
Alignment explanation
Indices: 4519732--4519771 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4519722 AATAAGTCAA
* *
4519732 AATAAATTAATTA-ACTTT
1 AATAAATGAATCATACTTT
4519750 AATAAATGAATCATACTTT
1 AATAAATGAATCATACTTT
4519769 AAT
1 AAT
4519772 TATCGATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (19 bp):
AATAAATGAATCATACTTT
Found at i:4525897 original size:33 final size:33
Alignment explanation
Indices: 4525855--4525925 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
4525845 GTCACTGAAC
4525855 TTATTTTTGAAGCTGTTGCAGGCAGTGAAGGTG
1 TTATTTTTGAAGCTGTTGCAGGCAGTGAAGGTG
4525888 TTATTTTTGAAGCTGTTGCAGGCAGTGAAGGTG
1 TTATTTTTGAAGCTGTTGCAGGCAGTGAAGGTG
4525921 TTATT
1 TTATT
4525926 GAAAATGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.39
Consensus pattern (33 bp):
TTATTTTTGAAGCTGTTGCAGGCAGTGAAGGTG
Found at i:4529980 original size:20 final size:20
Alignment explanation
Indices: 4529951--4530009 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
4529941 AAATTCATAA
*
4529951 TTTA-TTTCAGATTCATAGT
1 TTTACTTTCAGATTCATAGC
*
4529970 TTTACTTTCAGATTCATAAC
1 TTTACTTTCAGATTCATAGC
*
4529990 TTTACTTTCAGATTTATAGC
1 TTTACTTTCAGATTCATAGC
4530010 CCAATGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTACTTTCAGATTCATAGC
Found at i:4531814 original size:12 final size:12
Alignment explanation
Indices: 4531797--4531827 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4531787 TCCAAACTTC
4531797 CCAAACTACACA
1 CCAAACTACACA
4531809 CCAAACTACACA
1 CCAAACTACACA
4531821 CCAAACT
1 CCAAACT
4531828 TACCAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.42, G:0.00, T:0.10
Consensus pattern (12 bp):
CCAAACTACACA
Found at i:4531873 original size:19 final size:20
Alignment explanation
Indices: 4531849--4531894 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4531839 CAAAGTGATC
*
4531849 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
4531868 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
4531888 TAATTTC
1 CAATTTC
4531895 CAGCATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:4534270 original size:21 final size:21
Alignment explanation
Indices: 4534246--4534285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4534236 AAAATAATTA
* *
4534246 AATTTATTTATTTTGAAATCT
1 AATTTAATTATTATGAAATCT
4534267 AATTTAATTATTATGAAAT
1 AATTTAATTATTATGAAAT
4534286 TTACATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTAATTATTATGAAATCT
Found at i:4546232 original size:23 final size:23
Alignment explanation
Indices: 4546204--4546257 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
4546194 AAGATTGCAT
*
4546204 CAACATTTTTGCATTCATAATAA
1 CAACATTTTTGCATTCATAAAAA
4546227 CAACATTTTTGCATTCATAAAAA
1 CAACATTTTTGCATTCATAAAAA
*
4546250 CATCATTT
1 CAACATTT
4546258 GCATAATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (23 bp):
CAACATTTTTGCATTCATAAAAA
Found at i:4546939 original size:42 final size:42
Alignment explanation
Indices: 4546875--4546955 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
4546865 ATTGATTTGC
* * *
4546875 AAATCCTTCGGGGCATTAGTAAGTCTTTCGAGCATGATGCTT
1 AAATCCTTCAGGGCATTAGTAAGCCTTTCGAGCAAGATGCTT
*
4546917 AAATCCTTCAGGTCATCT-GTAAGCCTTTCGAGCAAGATG
1 AAATCCTTCAGGGCAT-TAGTAAGCCTTTCGAGCAAGATG
4546956 ATAAGTCCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
AAATCCTTCAGGGCATTAGTAAGCCTTTCGAGCAAGATGCTT
Found at i:4547369 original size:37 final size:36
Alignment explanation
Indices: 4547323--4547443 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 36
4547313 ATCAACGACG
* *
4547323 TCTCGCTTGAGACAATTTCACTCAAAACAACAATTTA
1 TCTCACTTGAGACAATTTCACTTAAAACAA-AATTTA
** ** * **
4547360 TCTCACTTGAGATTATTTTTCTTAAAACAAGATTCG
1 TCTCACTTGAGACAATTTCACTTAAAACAAAATTTA
* * * *
4547396 TCTCACTTGAGGCAATTTCACTTGAAACGAATTTTA
1 TCTCACTTGAGACAATTTCACTTAAAACAAAATTTA
*
4547432 TCTCACCTGAGA
1 TCTCACTTGAGA
4547444 TAGTTCCCCT
Statistics
Matches: 62, Mismatches: 22, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
36 38 0.61
37 24 0.39
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCACTTAAAACAAAATTTA
Found at i:4547505 original size:22 final size:22
Alignment explanation
Indices: 4547480--4547523 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4547470 GCATTCATTT
4547480 AATTTCGTTTCACATTTTTATC
1 AATTTCGTTTCACATTTTTATC
4547502 AATTTCGTTTCACATTTTTATC
1 AATTTCGTTTCACATTTTTATC
4547524 CAGATACTCA
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:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTCGTTTCACATTTTTATC
Found at i:4547803 original size:123 final size:122
Alignment explanation
Indices: 4547657--4548236 Score: 473
Period size: 123 Copynumber: 4.6 Consensus size: 122
4547647 AACATTTAAT
*
4547657 AGAAG-AGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATT
1 AGAAGAAGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
4547721 TGTTCAACCTTTTACTTGACTTTATCACAGAAAGAGATAGACCAGCATCAACATTTCC
66 TGTTCAACCTTTTACTTGA-TTTATCACAGAAAGAGATAGACCAGCATCAACATTTCC
** * *
4547779 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGACAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
** * * * * ** * *
4547844 TGTTCAACC-TTGCCTTGATTTATCGCATATGGAGTTGAATTAACGACACCTCACTTGAGACATC
66 TGTTCAACCTTTTACTTGATTTATCACAGA--AAG-AG-A-T-A-GAC-CAGCA--TCA-ACATT
**
4547908 AAC
120 TCC
* *
4547911 ATTCAATGGAAGAGTTCATAATGAGAATAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGA
1 A--GAA--GAA--GTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGA
* * * * * *** *
4547976 AGAGCATGTTCAACCTTTTGA-TAGATTCTATCA-ATTAAGGAGAT-G----G-ATTGTCATTCC
60 AGAACTTGTTCAACCTTTT-ACTTGATT-TATCACA-GAAAGAGATAGACCAGCATCAACATTTC
4548033 C
122 C
* * * * *
4548034 AGTAGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAATTCGTAATGAGGAGAA
1 AGAAG-A-AGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * * *
4548099 CTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACA-TTCA
64 CTTGTTCAACCTTTTACTTGA-TTTATCACAGAAAGAGATAGACCAGCATCAACATTTCC
* *
4548158 ATGGAAG-AGTTCATAATGAGAAGAACTCGTCCCAAGAGGAAGAAGAAGTTCATAATGAGAATAA
1 A--GAAGAAGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
4548222 CTTGTTCAACCTTTT
64 CTTGTTCAACCTTTT
4548237 GCTACATTCC
Statistics
Matches: 359, Mismatches: 64, Indels: 69
0.73 0.13 0.14
Matches are distributed among these distances:
119 81 0.23
120 4 0.01
121 11 0.03
122 12 0.03
123 137 0.38
124 5 0.01
125 5 0.01
126 5 0.01
127 1 0.00
128 3 0.01
129 3 0.01
131 2 0.01
132 7 0.02
134 2 0.01
135 1 0.00
136 4 0.01
137 1 0.00
138 61 0.17
139 8 0.02
140 6 0.02
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (122 bp):
AGAAGAAGTTCATAATGAGAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
TGTTCAACCTTTTACTTGATTTATCACAGAAAGAGATAGACCAGCATCAACATTTCC
Found at i:4548066 original size:119 final size:118
Alignment explanation
Indices: 4547914--4548303 Score: 460
Period size: 119 Copynumber: 3.2 Consensus size: 118
4547904 CATCAACATT
* *
4547914 CAATGGAAGAGTTCATAATGAGAATAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
1 CAAT-GAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* * * * * *
4547979 GCATGTTCAACCTTTTGATAGATTCTATCA-ATTAAGGAGATGGATTGTCATTCC
65 ACTTGTTCAACCTTTTGCTAGATTCTATCACA-GAAGGAGATGGATCGACATTCC
* * * *
4548033 CAGTAGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAATTCGTAATGAGGAGA
1 CAAT-GAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
4548098 ACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACA-TCAAC
65 ACTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAGATGGATCGACATTC--C
*
4548153 ATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCCAAGAGGAAGAAGAAGTTCATAATGAGA
1 ---CAAT-GAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGAGA
* * * * *
4548218 ATAACTTGTTCAACCTTTTGCTACATTCCATCACAGAAGGAGGTGGATCGACATTCT
62 AGAACTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAGATGGATCGACATTCC
* *
4548275 CAATGGAGAAGTTTATAATGAGAAGAACT
1 CAATGAAG-AGTTCATAATGAGAAGAACT
4548304 TGTTCAACAT
Statistics
Matches: 229, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
118 5 0.02
119 119 0.52
120 2 0.01
123 101 0.44
124 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (118 bp):
CAATGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAGATGGATCGACATTCC
Found at i:4548257 original size:123 final size:123
Alignment explanation
Indices: 4547903--4548259 Score: 465
Period size: 119 Copynumber: 2.9 Consensus size: 123
4547893 CTCACTTGAG
* *
4547903 ACATCAACATTCAATGGAAGAGTTCATAATGAGAATAACTCGTCCGAAGAGGAAGAAGAAGTTCA
1 ACATCAACATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCA
* * * * * **
4547968 TAATGAGAAGAGCATGTTCAACCTTTTGATAGATTCTATCA-ATTAAGGAGATGGATTG
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTCTATCACA-GAAGGAGATAGATCA
* * * *
4548026 TCATTC--C---CAGTAGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAATTC
1 ACA-TCAACATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTC
* * * *
4548086 GTAATGAGGAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCA
65 ATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAGATAGATCA
*
4548145 ACATCAACATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCCAAGAGGAAGAAGAAGTTCA
1 ACATCAACATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCA
* * *
4548210 TAATGAGAATAACTTGTTCAACCTTTTGCTACATTCCATCACAGAAGGAG
66 TAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAG
4548260 GTGGATCGAC
Statistics
Matches: 198, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
118 2 0.01
119 96 0.48
120 2 0.01
122 1 0.01
123 95 0.48
124 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (123 bp):
ACATCAACATTCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTCTATCACAGAAGGAGATAGATCA
Found at i:4548444 original size:3 final size:3
Alignment explanation
Indices: 4548436--4548492 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
4548426 TTTTATCTCG
* * * * * *
4548436 TTA TTA TTA TTA TTA TCA TCA TCA TCA TTA TTA TTA TTA TCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4548484 TTA TTA TTA
1 TTA TTA TTA
4548493 AATAATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:4548488 original size:18 final size:18
Alignment explanation
Indices: 4548444--4548492 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
4548434 CGTTATTATT
* *
4548444 ATTATTATCATCATCATC
1 ATTATTATTATTATCATC
4548462 ATTATTATTATTATCATC
1 ATTATTATTATTATCATC
4548480 ATTATTATTATTA
1 ATTATTATTATTA
4548493 AATAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTATTATTATCATC
Found at i:4552695 original size:23 final size:23
Alignment explanation
Indices: 4552665--4552724 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
4552655 AGAATAATTA
4552665 TGTCTTTGTGGCACATTTATCTC
1 TGTCTTTGTGGCACATTTATCTC
4552688 TGTCTTTGTGGCACATTTATCTC
1 TGTCTTTGTGGCACATTTATCTC
4552711 TGTCTTTGTGGCAC
1 TGTCTTTGTGGCAC
4552725 GTTTTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (23 bp):
TGTCTTTGTGGCACATTTATCTC
Found at i:4553525 original size:197 final size:199
Alignment explanation
Indices: 4553020--4553602 Score: 980
Period size: 197 Copynumber: 2.9 Consensus size: 199
4553010 TTTTCGAATC
*
4553020 TTTTAGTTTGA-TTTTTAACTGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCACG--T
1 TTTTAG-TTGAGTTTTTAACAGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCACGTAT
* *
4553082 TTTTTTAATAGAAGTCGCTAGTATTATTTTAAAGTGAAAATATCCAAAATTACAATAAGAGTTTA
65 TTTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAGTTTA
* * *
4553147 CAACTATCATCATATACTAAATACATGATTTGGACATTTTTTTATAACATTGAAACTAGTCACAC
130 CAACTATTATCATAAACTAAATACATGATTTGAACA-TTTTTTATAACATTGAAACTAGT-ACAC
*
4553212 TTTAATG
193 TTTAATA
* * *
4553219 TTTTAGTTGGGTTTTTAATAGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCATGTATT
1 TTTTAGTTGAGTTTTTAACAGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCACGTATT
4553284 TTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAGTTTAC
66 TTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAGTTTAC
4553349 AACTATTATCATAAACTAAATACATGATTTGAACATTTTTTATAACATTGAAACTAGT-CACTTT
131 AACTATTATCATAAACTAAATACATGATTTGAACATTTTTTATAACATTGAAACTAGTACACTTT
4553413 AATA
196 AATA
4553417 TTTTAGTTGAGTTTTTAACAGAAATGTCCAAATCATGCATT-AAAAAATGTCCAAATCACGTATT
1 TTTTAGTTGAGTTTTTAACAGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCACGTATT
*
4553481 TTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAATTTAC
66 TTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAGTTTAC
4553546 AACTATTATCATAAACTAAATACATGATTT-AGACATTTTCTTATAACATTGAAACTA
131 AACTATTATCATAAACTAAATACATGATTTGA-ACATTTT-TTATAACATTGAAACTA
4553603 ACTACTTTTA
Statistics
Matches: 365, Mismatches: 14, Indels: 11
0.94 0.04 0.03
Matches are distributed among these distances:
196 1 0.00
197 123 0.34
198 68 0.19
199 53 0.15
200 23 0.06
201 97 0.27
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (199 bp):
TTTTAGTTGAGTTTTTAACAGAAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCACGTATT
TTTTTAATAGAAGTCGCTAGTATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAGTTTAC
AACTATTATCATAAACTAAATACATGATTTGAACATTTTTTATAACATTGAAACTAGTACACTTT
AATA
Found at i:4554611 original size:24 final size:24
Alignment explanation
Indices: 4554523--4554611 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
4554513 TTTTTAATAG
*
4554523 AAATGTCCAAATCATACATTAAAAA
1 AAATGTCCAAATCATGCATT-AAAA
*
4554548 AAATGTCCAAATCATTCATTAAAA
1 AAATGTCCAAATCATGCATTAAAA
4554572 AAATGTCCAAATCATGCATTAAAA
1 AAATGTCCAAATCATGCATTAAAA
4554596 AAATGTCCAAATCATG
1 AAATGTCCAAATCATG
4554612 TATTTTTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
24 43 0.69
25 19 0.31
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATGTCCAAATCATGCATTAAAA
Found at i:4554917 original size:197 final size:199
Alignment explanation
Indices: 4554572--4554935 Score: 642
Period size: 197 Copynumber: 1.8 Consensus size: 199
4554562 TTCATTAAAA
*
4554572 AAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCATGTATTTTTTTTAATAGAAGTCGCTAG
1 AAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCAGGTA-TTTTTTTAATAGAAGTCGCTAG
* *
4554637 TATTATTTAAAAATGAAAATATTCAAAATTACAATAAGAGTTTACAACTATTATCATAAACTAAA
65 TATTATTTAAAAATGAAAATATTCAAAATTACAATAAGAATTTACAACTATCATCATAAACTAAA
*
4554702 TACATAATTTGAACATTTT-TTATAACATTGAAACTAGTCACTTTAATATTTTAGTTGGGTTTTT
130 TACATAATTTGAACATTTTCTTATAACATTAAAACTAGTCACTTTAATATTTTAGTTGGGTTTTT
4554766 AACAT
195 AACAT
4554771 AAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCAGGTA-TTTTTTAATAGAAGTCGCTAGT
1 AAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCAGGTATTTTTTTAATAGAAGTCGCTAGT
*
4554835 ATTATTTAAAAGTGAAAATATTCAAAATTACAATAAGAATTTACAACTATCATCATAAACTAAAT
66 ATTATTTAAAAATGAAAATATTCAAAATTACAATAAGAATTTACAACTATCATCATAAACTAAAT
* *
4554900 ACATGATTTGGACATTTTCTTATAACATTAAAACTA
131 ACATAATTTGAACATTTTCTTATAACATTAAAACTA
4554936 ACTACTTTTA
Statistics
Matches: 157, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
197 100 0.64
198 16 0.10
199 41 0.26
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (199 bp):
AAATGTCCAAATCATGCATTAAAAAAATGTCCAAATCAGGTATTTTTTTAATAGAAGTCGCTAGT
ATTATTTAAAAATGAAAATATTCAAAATTACAATAAGAATTTACAACTATCATCATAAACTAAAT
ACATAATTTGAACATTTTCTTATAACATTAAAACTAGTCACTTTAATATTTTAGTTGGGTTTTTA
ACAT
Found at i:4557946 original size:22 final size:22
Alignment explanation
Indices: 4557921--4557987 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
4557911 GATCTGTTAT
*
4557921 AGGTTTAATGCAAGAGTTACAA
1 AGGTTTAATACAAGAGTTACAA
*
4557943 AGGTTTAATACAAGAGTTACAG
1 AGGTTTAATACAAGAGTTACAA
* * *
4557965 AGTTTTATTACATGAGTTACAA
1 AGGTTTAATACAAGAGTTACAA
4557987 A
1 A
4557988 CTGCTGGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (22 bp):
AGGTTTAATACAAGAGTTACAA
Found at i:4564871 original size:21 final size:21
Alignment explanation
Indices: 4564845--4564890 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
4564835 GTAGATGACG
4564845 AATGCCAAGCTGATCATGGAT
1 AATGCCAAGCTGATCATGGAT
4564866 AATGCCAAGCTGATCATGGAT
1 AATGCCAAGCTGATCATGGAT
4564887 AATG
1 AATG
4564891 TCCATGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (21 bp):
AATGCCAAGCTGATCATGGAT
Found at i:4567409 original size:22 final size:21
Alignment explanation
Indices: 4567354--4567421 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
4567344 TTATTGAGTT
* *
4567354 GTTATAG-GTTTAATACAAAA
1 GTTATAGAGTTTAATGCAAGA
* *
4567374 GTTACAAAGCTTTAATGCAAGA
1 GTTATAGAG-TTTAATGCAAGA
* *
4567396 GTTATAGAGTTTTATTGCATGA
1 GTTATAGAG-TTTAATGCAAGA
4567418 GTTA
1 GTTA
4567422 CAAACTGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 5 0.14
21 1 0.03
22 31 0.84
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
GTTATAGAGTTTAATGCAAGA
Found at i:4570706 original size:21 final size:21
Alignment explanation
Indices: 4570651--4570706 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
4570641 ATACCCAATC
*
4570651 TTCGGTATGAATACCAATTCA
1 TTCGGTATGAATACCAACTCA
* *
4570672 -TCTGGTAAGGATACCAACTCA
1 TTC-GGTATGAATACCAACTCA
*
4570693 TTCGGTATGTATAC
1 TTCGGTATGAATAC
4570707 ATGCCCACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (21 bp):
TTCGGTATGAATACCAACTCA
Found at i:4571690 original size:42 final size:42
Alignment explanation
Indices: 4571621--4571721 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
4571611 CAACGATTAT
* * ** *
4571621 TGTGGATATTGTTGATGATTAGGGTGTTGTAGCGAAAGTTAC
1 TGTGGATATTATCGATGATTAAAGTGTTGTAGAGAAAGTTAC
* * *
4571663 TGTGTATATTATCGATGATTAAAGTGTTGTAGAGGAAGTTAT
1 TGTGGATATTATCGATGATTAAAGTGTTGTAGAGAAAGTTAC
*
4571705 TGTGGATATTGTCGATG
1 TGTGGATATTATCGATG
4571722 TTGAGGGTGC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.40
Consensus pattern (42 bp):
TGTGGATATTATCGATGATTAAAGTGTTGTAGAGAAAGTTAC
Found at i:4571924 original size:21 final size:21
Alignment explanation
Indices: 4571899--4571941 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4571889 GTGTGAACAA
* * *
4571899 TCAAATGAGAACAATTTATGG
1 TCAAAAGAGAAAAATATATGG
4571920 TCAAAAGAGAAAAATATATGG
1 TCAAAAGAGAAAAATATATGG
4571941 T
1 T
4571942 GTCAAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (21 bp):
TCAAAAGAGAAAAATATATGG
Found at i:4575075 original size:20 final size:21
Alignment explanation
Indices: 4575039--4575080 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
4575029 ATATTAACAC
4575039 AGAACCGGTAAAGAACC-GGA
1 AGAACCGGTAAAGAACCAGGA
*
4575059 AGAACCGGCTGAA-AACCAGGA
1 AGAACCGG-TAAAGAACCAGGA
4575080 A
1 A
4575081 AATCGGGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.45, C:0.21, G:0.29, T:0.05
Consensus pattern (21 bp):
AGAACCGGTAAAGAACCAGGA
Found at i:4575123 original size:30 final size:30
Alignment explanation
Indices: 4575060--4575116 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4575050 AGAACCGGAA
*
4575060 GAACCGGCTGAAAACCAGGAAAATCGGGGT
1 GAACCGGCTGAAAACCAGGAAAACCGGGGT
4575090 GAACCGGCTGAAAACC-GGCAAAACCGG
1 GAACCGGCTGAAAACCAGG-AAAACCGG
4575117 TTTGAACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.37, C:0.25, G:0.32, T:0.07
Consensus pattern (30 bp):
GAACCGGCTGAAAACCAGGAAAACCGGGGT
Found at i:4575385 original size:24 final size:24
Alignment explanation
Indices: 4575353--4575404 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
4575343 AATTCGATTA
*
4575353 AAGCCTAAAATTTGAGCTCAATTG
1 AAGCATAAAATTTGAGCTCAATTG
4575377 AAGCATAAAATTTGAGCTCAATTG
1 AAGCATAAAATTTGAGCTCAATTG
4575401 AAGC
1 AAGC
4575405 GAAAGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (24 bp):
AAGCATAAAATTTGAGCTCAATTG
Found at i:4577489 original size:20 final size:20
Alignment explanation
Indices: 4577464--4577520 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
4577454 ATAGATCTCC
4577464 AGTCTAAGGATCATACATAT
1 AGTCTAAGGATCATACATAT
4577484 AGTCT-A-GATC-T-C--A-
1 AGTCTAAGGATCATACATAT
4577497 AGTCTAAGGATCATACATAT
1 AGTCTAAGGATCATACATAT
4577517 AGTC
1 AGTC
4577521 ATCACCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
13 5 0.17
14 2 0.07
15 4 0.13
16 2 0.07
17 2 0.07
18 4 0.13
19 2 0.07
20 9 0.30
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
AGTCTAAGGATCATACATAT
Found at i:4577501 original size:33 final size:33
Alignment explanation
Indices: 4577455--4577520 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4577445 TGGGATAACA
*
4577455 TAGATCTCCAGTCTAAGGATCATACATATAGTC
1 TAGATCTCAAGTCTAAGGATCATACATATAGTC
4577488 TAGATCTCAAGTCTAAGGATCATACATATAGTC
1 TAGATCTCAAGTCTAAGGATCATACATATAGTC
4577521 ATCACCATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (33 bp):
TAGATCTCAAGTCTAAGGATCATACATATAGTC
Found at i:4581241 original size:42 final size:42
Alignment explanation
Indices: 4581182--4581338 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
4581172 AGAAACAACG
*
4581182 GTTACTGTGGATGTTGTCGATTATTAGGGTGCTGTAGC-GAGA
1 GTTACTATGGATGTTGTCGATTATTAGGGTGCTGTAGCGGA-A
* * *
4581224 GTTACTATGGATGTTGTCGATTATCAGAGTACTGTAGCGGAA
1 GTTACTATGGATGTTGTCGATTATTAGGGTGCTGTAGCGGAA
* * * * ** *
4581266 GTTACTATAGACGTTGTCAATGATTAGGGTGCTGTAATGGAG
1 GTTACTATGGATGTTGTCGATTATTAGGGTGCTGTAGCGGAA
* * *
4581308 GTTACTGA-AGATGTTTTCAATTATTAGGGTG
1 GTTACT-ATGGATGTTGTCGATTATTAGGGTG
4581339 TTGTTGCAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 93 0.97
43 3 0.03
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (42 bp):
GTTACTATGGATGTTGTCGATTATTAGGGTGCTGTAGCGGAA
Found at i:4583420 original size:42 final size:42
Alignment explanation
Indices: 4583310--4583425 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 42
4583300 GGTTATTGTA
* * * * **
4583310 GATGTTGTT-GATGATTAAGGTGCTCTAGCGAAAGTTATTGTG
1 GATGTT-TTCGATGATCAAGGTGTTGTAGCGGAAGTTACGGTG
* * *
4583352 TATGTTGTCGATGATC-AGAGTATTGTAGCGGAAGTTACGGTG
1 GATGTTTTCGATGATCAAG-GTGTTGTAGCGGAAGTTACGGTG
*
4583394 GATGTTTTCGATGATCAAGGTGTTGTAACGGA
1 GATGTTTTCGATGATCAAGGTGTTGTAGCGGA
4583426 CACTACAACA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 3 0.05
42 53 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (42 bp):
GATGTTTTCGATGATCAAGGTGTTGTAGCGGAAGTTACGGTG
Found at i:4583700 original size:82 final size:82
Alignment explanation
Indices: 4583537--4583705 Score: 198
Period size: 82 Copynumber: 2.1 Consensus size: 82
4583527 AAATGGTAAA
* * * *
4583537 TTTAGCAGTATTTTTATACAAACACCGTAATAGGGTTCATATATAATGGCATTTTTTCAACAAAT
1 TTTAGCAGTATTTGTATAAAAACACCGTAATAGGGTTCATATATAATGACATTTTTACAACAAAT
* *
4583602 GCCGCAATAGAGAGTAC
66 GCCACAACAGAGAGTAC
* * * * * *
4583619 TTTAGCGGTGTTTGTATAAAAATACCTTAATAGGGTTCATATATAGTGACGA-TTTTACAA-TAA
1 TTTAGCAGTATTTGTATAAAAACACCGTAATAGGGTTCATATATAATGAC-ATTTTTACAACAAA
4583682 TGCCACAACAGAGTAGTAC
65 TGCCACAACAGAG-AGTAC
4583701 TTTAG
1 TTTAG
4583706 TGGAGTTTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
81 13 0.18
82 59 0.81
83 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (82 bp):
TTTAGCAGTATTTGTATAAAAACACCGTAATAGGGTTCATATATAATGACATTTTTACAACAAAT
GCCACAACAGAGAGTAC
Found at i:4583814 original size:41 final size:41
Alignment explanation
Indices: 4583769--4583886 Score: 148
Period size: 41 Copynumber: 2.9 Consensus size: 41
4583759 CGTTTTTGAT
*
4583769 CAAACGCCGCAAAATACTCTTACTTTAGTGGCGTTTGTATA
1 CAAACGCCGCAAAAGACTCTTACTTTAGTGGCGTTTGTATA
* ** *
4583810 CAAACGTCGCAAAAGACTCAAACTTTCGTGGCGTTTGTATA
1 CAAACGCCGCAAAAGACTCTTACTTTAGTGGCGTTTGTATA
* * *
4583851 CAAGCGCCGCTACAGACT-TGTACTTTAGTGGCGTTT
1 CAAACGCCGCAAAAGACTCT-TACTTTAGTGGCGTTT
4583887 TTGTTCAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
CAAACGCCGCAAAAGACTCTTACTTTAGTGGCGTTTGTATA
Found at i:4583914 original size:41 final size:40
Alignment explanation
Indices: 4583869--4584024 Score: 125
Period size: 42 Copynumber: 3.7 Consensus size: 40
4583859 GCTACAGACT
*
4583869 TGTACTTTAGTGGCGTTTTTGTTCAAACACCGCAATAGTCA
1 TGTACTTTAGTGGCGTTTTTGTT-AAAAACCGCAATAGTCA
* * *
4583910 TGTACTTTTGTGGCGTTTTT-TTAATAAAAGCTGCAATAATCA
1 TGTACTTTAGTGGCGTTTTTGTT-A-AAAA-CCGCAATAGTCA
* * * * *
4583952 TGTAATTTAGTGGCATTTTTTTGTAATAAATGTCGCAATAGTGA
1 TGTACTTTAGTGGCGTTTTTGT-TAA-AAA--CCGCAATAGTCA
* * *
4583996 TGTACCTTAGTGGCGTTTTTATTATAAAC
1 TGTACTTTAGTGGCGTTTTTGTTAAAAAC
4584025 GTCGTGATTG
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
40 3 0.03
41 22 0.24
42 31 0.34
43 7 0.08
44 28 0.31
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (40 bp):
TGTACTTTAGTGGCGTTTTTGTTAAAAACCGCAATAGTCA
Found at i:4583947 original size:42 final size:43
Alignment explanation
Indices: 4583869--4584023 Score: 149
Period size: 44 Copynumber: 3.7 Consensus size: 43
4583859 GCTACAGACT
* * * *
4583869 TGTACTTTAGTGGCGTTTTTGTTCA-AACA-CCGCAATAGTCA
1 TGTACTTTAGTGGCGTTTTTATTAATAAAAGCTGCAATAGTCA
* *
4583910 TGTACTTTTGTGGCGTTTTT-TTAATAAAAGCTGCAATAATCA
1 TGTACTTTAGTGGCGTTTTTATTAATAAAAGCTGCAATAGTCA
* * * * *
4583952 TGTAATTTAGTGGCATTTTTTTGTAATAAATG-TCGCAATAGTGA
1 TGTACTTTAGTGGCGTTTTTAT-TAATAAAAGCT-GCAATAGTCA
*
4583996 TGTACCTTAGTGGCGTTTTTATT-ATAAA
1 TGTACTTTAGTGGCGTTTTTATTAATAAA
4584024 CGTCGTGATT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
40 3 0.03
41 22 0.23
42 32 0.34
43 3 0.03
44 34 0.36
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (43 bp):
TGTACTTTAGTGGCGTTTTTATTAATAAAAGCTGCAATAGTCA
Found at i:4590400 original size:64 final size:64
Alignment explanation
Indices: 4590332--4590533 Score: 189
Period size: 65 Copynumber: 3.1 Consensus size: 64
4590322 TGCACTAAGA
* * *
4590332 GTGCATCAATGCATCAAGTGCATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCAATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
* * ** *
4590396 GTGCATCGATGAATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCCG-TTCATGGT
1 GTGCATCAATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCAT-CGATGCATGGT
4590459 AT-
63 -TG
* * ** *
4590461 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG-T
4590524 TG
63 TG
4590526 GTGCATCA
1 GTGCATCA
4590534 CTTTGATAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 19
0.76 0.12 0.13
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 41 0.37
65 57 0.51
66 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
Found at i:4590964 original size:2 final size:2
Alignment explanation
Indices: 4590957--4590983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4590947 AATTGATTAA
4590957 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4590984 GCTTAAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4597017 original size:22 final size:21
Alignment explanation
Indices: 4596975--4597014 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4596965 GAGTTTATTT
*
4596975 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4596996 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4597015 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4598390 original size:31 final size:31
Alignment explanation
Indices: 4598352--4598412 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
4598342 GAGTGGTTCG
*
4598352 ACTTTCTCAATCAAAGTCTACGTCCACTACA
1 ACTTTCTCAATCAAAGTCTACGCCCACTACA
4598383 ACTTTCTCAATCAAAGTCTACGCCCACTAC
1 ACTTTCTCAATCAAAGTCTACGCCCACTAC
4598413 CTTAGCTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.28
Consensus pattern (31 bp):
ACTTTCTCAATCAAAGTCTACGCCCACTACA
Found at i:4599092 original size:65 final size:65
Alignment explanation
Indices: 4598959--4599118 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
4598949 TGCACTAAGA
* *
4598959 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCAAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCAACAGTGCATCGATGCATGGCTG
* ** *
4599023 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCAACAGTGCATCGATGCATGGCT
*
4599086 AT
65 -G
*
4599088 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
4599119 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 29 0.34
65 53 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCAACAGTGCATCGATGCATGGCTG
Found at i:4599158 original size:65 final size:62
Alignment explanation
Indices: 4598959--4599168 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 62
4598949 TGCACTAAGA
* ** *
4598959 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCAAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATCTC-AG-GTGCATCGATGCATGG-TT
* *
4599023 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA-GTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-ATAAT-CTCAGGTGCATCGATGCATGGT-
4599087 T
62 T
* *
4599088 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCAATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA--TAATCTCA-GGTGCATCGATGCATGG-T
4599151 T
62 T
* *
4599152 GATGCATTGGTGCATCA
1 G-TGCATCGATGCATCA
4599169 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
62 4 0.03
63 4 0.03
64 48 0.39
65 61 0.50
66 1 0.01
67 4 0.03
68 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATCTCAGGTGCATCGATGCATGGTT
Found at i:4599563 original size:42 final size:42
Alignment explanation
Indices: 4599517--4599658 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 42
4599507 GTTATTATAT
*
4599517 ATGTTGAT-GATGATTAAGATGTTGTAGTGAAAGTTACTGTGG
1 ATGTT-ATCGATGATTAAGATGTTGTAGAGAAAGTTACTGTGG
* **
4599559 ATGTTATCGATGA-TCAGA-GTTCTGTAGAGAAAGTTACTGTAT
1 ATGTTATCGATGATTAAGATG-T-TGTAGAGAAAGTTACTGTGG
* * * * * * *
4599601 ATGCTATCGATGATCAAGGTGTTATAGCGGAAGTTAATGTGG
1 ATGTTATCGATGATTAAGATGTTGTAGAGAAAGTTACTGTGG
*
4599643 ATGTTGTCGATGATTA
1 ATGTTATCGATGATTA
4599659 GGGTGCTGCA
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.01
41 7 0.09
42 66 0.85
43 3 0.04
44 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.28, T:0.36
Consensus pattern (42 bp):
ATGTTATCGATGATTAAGATGTTGTAGAGAAAGTTACTGTGG
Found at i:4599872 original size:21 final size:21
Alignment explanation
Indices: 4599834--4599873 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4599824 GCAATCAAAT
*
4599834 GAGAAAAATTTGTGGTCAATA
1 GAGAAAAATTAGTGGTCAATA
4599855 GAGAAAAATATAGT-GTCAA
1 GAGAAAAAT-TAGTGGTCAA
4599874 ATTTGACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (21 bp):
GAGAAAAATTAGTGGTCAATA
Found at i:4602361 original size:42 final size:41
Alignment explanation
Indices: 4602305--4602448 Score: 141
Period size: 42 Copynumber: 3.5 Consensus size: 41
4602295 ACATTTTTCA
* * * *
4602305 ACAAATGCCACAATAGAGTTATAAATTAGCGACATTTATACC
1 ACAAACGCCGCAATAGA-TTATAAATTAGCGGCGTTTATACC
* * * *
4602347 ACAAACGCTGCAATATATTA-ACATATAGTGGCGTTT-TAGCC
1 ACAAACGCCGCAATAGATTATAAAT-TAGCGGCGTTTATA-CC
*
4602388 A-AAACGCCGCAATAGATCGATAAATTAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGAT-TATAAATTAGCGGCGTTTATACC
*
4602429 ACAAACGCCGTAATAGATTA
1 ACAAACGCCGCAATAGATTA
4602449 CACATATAGT
Statistics
Matches: 81, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
40 19 0.23
41 29 0.36
42 33 0.41
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (41 bp):
ACAAACGCCGCAATAGATTATAAATTAGCGGCGTTTATACC
Found at i:4602466 original size:42 final size:41
Alignment explanation
Indices: 4602339--4602548 Score: 139
Period size: 42 Copynumber: 5.1 Consensus size: 41
4602329 ATTAGCGACA
* *
4602339 TTTATACCACAAACGCTGCAATATATTAACATATAGTGGCG
1 TTTATACCACAAACGCCGCAATAGATTAACATATAGTGGCG
*
4602380 TTT-TAGCCA-AAACGCCGCAATAGATCGATAA-AT-TAGCGGCG
1 TTTATA-CCACAAACGCCGCAATAGAT---TAACATATAGTGGCG
* **
4602421 TTTATACCACAAACGCCGTAATAGATTACACATATAGTGAAG
1 TTTATACCACAAACGCCGCAATAGATTA-ACATATAGTGGCG
* * * * *
4602463 TTTATTCCTA-AAATGCCGCAATAG-TGATAATAAATAGTGGCA
1 TTTATACC-ACAAACGCCGCAATAGAT--TAACATATAGTGGCG
* * * *
4602505 TTTTTA-GACAAACTCCGCAATAGTGTTAATCA-ATAGTGGCG
1 TTTATACCACAAACGCCGCAATAG-ATTAA-CATATAGTGGCG
4602546 TTT
1 TTT
4602549 TTAGAAAAAC
Statistics
Matches: 131, Mismatches: 22, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
39 2 0.02
40 18 0.14
41 48 0.37
42 56 0.43
43 7 0.05
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (41 bp):
TTTATACCACAAACGCCGCAATAGATTAACATATAGTGGCG
Found at i:4602492 original size:82 final size:80
Alignment explanation
Indices: 4602307--4602492 Score: 203
Period size: 82 Copynumber: 2.2 Consensus size: 80
4602297 ATTTTTCAAC
* * * *
4602307 AAATGCCACAATAGAGTTATAAATTAGCGACATTTATACCACAAACGCTGCAATATATTAACATA
1 AAATGCCGCAAT--AGTGATAAATTAGCGACATTTATACCACAAACGCCGCAATAGATTAACATA
**
4602372 TAGTGGCGTTTTAGCCA
64 TAGTGAAGTTTTAGCCA
* * * *
4602389 AAACGCCGCAATAGATCGATAAATTAGCGGCGTTTATACCACAAACGCCGTAATAGATTACACAT
1 AAATGCCGCAATAG-T-GATAAATTAGCGACATTTATACCACAAACGCCGCAATAGATTA-ACAT
*
4602454 ATAGTGAAG-TTTATTCCTA
63 ATAGTGAAGTTTTA-GCC-A
4602473 AAATGCCGCAATAGTGATAA
1 AAATGCCGCAATAGTGATAA
4602493 TAAATAGTGG
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
80 2 0.02
81 1 0.01
82 56 0.64
83 14 0.16
84 14 0.16
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (80 bp):
AAATGCCGCAATAGTGATAAATTAGCGACATTTATACCACAAACGCCGCAATAGATTAACATATA
GTGAAGTTTTAGCCA
Found at i:4602528 original size:41 final size:41
Alignment explanation
Indices: 4602472--4602631 Score: 171
Period size: 41 Copynumber: 3.9 Consensus size: 41
4602462 GTTTATTCCT
* * *
4602472 AAAATGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
* * *
4602513 CAAACTCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
* * *
4602554 AAAACGCCGTAATAGTTTTAATCAATAGTGGCGCTTTTTA-A
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGC-ATTTTTAGA
* ** * *
4602595 TAAACGCCATAATAGTG-TAATCAGTAGTAGCATTTTT
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTT
4602632 TTCTATAAAC
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 5 0.05
40 12 0.12
41 78 0.77
42 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (41 bp):
AAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
Found at i:4611266 original size:21 final size:21
Alignment explanation
Indices: 4611242--4611353 Score: 71
Period size: 21 Copynumber: 5.2 Consensus size: 21
4611232 AGGAAAATGA
*
4611242 AGCAGGGGAAGAAGAGAGAGC
1 AGCAGCGGAAGAAGAGAGAGC
* * **
4611263 AGCAGCAGAAGTAGCCAGAGC
1 AGCAGCGGAAGAAGAGAGAGC
* * * *
4611284 AGCAGTGGAAGCAGAGAAAGA
1 AGCAGCGGAAGAAGAGAGAGC
* * * *
4611305 AGCAGCGGTAGTACAGAGAGA
1 AGCAGCGGAAGAAGAGAGAGC
*
4611326 AGCAGCGGCAACACAGAGAGAAGC
1 AGCAGCGG-AAGA-AGAGAG-AGC
4611350 AGCA
1 AGCA
4611354 TATCAGCAGA
Statistics
Matches: 66, Mismatches: 22, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
21 54 0.82
22 1 0.02
23 5 0.08
24 6 0.09
ACGTcount: A:0.42, C:0.17, G:0.38, T:0.04
Consensus pattern (21 bp):
AGCAGCGGAAGAAGAGAGAGC
Found at i:4611897 original size:43 final size:44
Alignment explanation
Indices: 4611763--4611999 Score: 198
Period size: 43 Copynumber: 5.5 Consensus size: 44
4611753 GCATTTTTAG
* * * * * *
4611763 CAAAAACGCCGCAAAACATCAATACCTACTGCGACGTTTGT-GA
1 CAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTA
* * * * * * *
4611806 GAAAATCACCGCAAAACATCAACACCTACTGCGGCGTTTGT-GA
1 CAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTA
* * *
4611849 GAAAAACGCTGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTA
1 CAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTCTA
* * * * *
4611893 -AAAAATGCCTCTAAATATCAACACCTATTACGGCATTTTTCTA
1 CAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTA
* * *
4611936 -ACAAATGCCGCTAAATATCAACACCTATTGCGGTGTTTGTC-A
1 CAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTA
*
4611978 CACAAACGCCGCTAAATATCAA
1 CAAAAACGCCGCTAAATATCAA
4612000 TACAAAAAAT
Statistics
Matches: 165, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.01
43 161 0.98
44 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (44 bp):
CAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTA
Found at i:4614466 original size:21 final size:20
Alignment explanation
Indices: 4614442--4614492 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
4614432 ATCAAAATCA
*
4614442 TTTTTGAAAATTTCATTTTG
1 TTTTTCAAAATTTCATTTTG
*
4614462 TTTTTCAAAATTTTATTTTG
1 TTTTTCAAAATTTCATTTTG
4614482 TTTTTCAAAAT
1 TTTTTCAAAAT
4614493 CCAATTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (20 bp):
TTTTTCAAAATTTCATTTTG
Found at i:4614499 original size:20 final size:20
Alignment explanation
Indices: 4614456--4614501 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4614446 TGAAAATTTC
***
4614456 ATTTTGTTTTTCAAAATTTT
1 ATTTTGTTTTTCAAAATCCA
4614476 ATTTTGTTTTTCAAAATCCA
1 ATTTTGTTTTTCAAAATCCA
4614496 ATTTTG
1 ATTTTG
4614502 CCTTCAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTTGTTTTTCAAAATCCA
Found at i:4616342 original size:21 final size:21
Alignment explanation
Indices: 4616316--4616368 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
4616306 CCAGAATAGG
4616316 GAGTATCGATACTCTTTTAAT
1 GAGTATCGATACTCTTTTAAT
4616337 GAGTATCGATACTCTTTTAAT
1 GAGTATCGATACTCTTTTAAT
4616358 GAGTATCGATA
1 GAGTATCGATA
4616369 ATTCCTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (21 bp):
GAGTATCGATACTCTTTTAAT
Found at i:4623616 original size:16 final size:16
Alignment explanation
Indices: 4623597--4623628 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4623587 TCATACAATT
4623597 GGAATGCCATAGCATC
1 GGAATGCCATAGCATC
4623613 GGAATGCCATAGCATC
1 GGAATGCCATAGCATC
4623629 ATCAGTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (16 bp):
GGAATGCCATAGCATC
Found at i:4623993 original size:2 final size:2
Alignment explanation
Indices: 4623947--4623976 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4623937 TTTCAAAGAA
4623947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4623977 TAAGTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4624011 original size:20 final size:21
Alignment explanation
Indices: 4623988--4624044 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
4623978 AAGTTATTTG
4623988 TATATAAATTTTATTAAA-AA
1 TATATAAATTTTATTAAATAA
* **
4624008 TATATATAGATTA-TAAATAA
1 TATATAAATTTTATTAAATAA
4624028 TATA-AAATTTATATTAA
1 TATATAAATTT-TATTAA
4624045 GTTATTTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATAAATTTTATTAAATAA
Found at i:4624293 original size:27 final size:30
Alignment explanation
Indices: 4624260--4624316 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
4624250 AATGATTATA
*
4624260 TTAAGTG-TAATAT-AAAA-TAAATAATAG
1 TTAAGTGATAAAATAAAAACTAAATAATAG
4624287 TTAAGTGACTAAAATAAAAACTAAATAATA
1 TTAAGTGA-TAAAATAAAAACTAAATAATA
4624317 ATGGGTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
29 5 0.20
30 4 0.16
31 9 0.36
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.30
Consensus pattern (30 bp):
TTAAGTGATAAAATAAAAACTAAATAATAG
Found at i:4627511 original size:21 final size:21
Alignment explanation
Indices: 4627487--4627529 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4627477 ACAAATGGGC
*
4627487 CTCAAGCTCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4627508 CTCAAGCCCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4627529 C
1 C
4627530 CCAGGACCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.07
Consensus pattern (21 bp):
CTCAAGCCCAAACCAAACCAA
Found at i:4631017 original size:21 final size:21
Alignment explanation
Indices: 4630993--4631035 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4630983 ACAAATGGGC
*
4630993 CTCAAGCTCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4631014 CTCAAGCCCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4631035 C
1 C
4631036 CCAGGACCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.07
Consensus pattern (21 bp):
CTCAAGCCCAAACCAAACCAA
Found at i:4634522 original size:21 final size:21
Alignment explanation
Indices: 4634498--4634540 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4634488 ACAAATGGGC
*
4634498 CTCAAGCTCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4634519 CTCAAGCCCAAACCAAACCAA
1 CTCAAGCCCAAACCAAACCAA
4634540 C
1 C
4634541 CCAGGACCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.07
Consensus pattern (21 bp):
CTCAAGCCCAAACCAAACCAA
Found at i:4637590 original size:23 final size:21
Alignment explanation
Indices: 4637552--4637595 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4637542 GTGTATAGTG
*
4637552 GGGGAATCGGTTCCTGTAGCA
1 GGGGAATCGGTCCCTGTAGCA
4637573 GGGGAATCGGTACCCCTGTAGCA
1 GGGGAATCGGT--CCCTGTAGCA
4637596 TTTTGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGAATCGGTCCCTGTAGCA
Found at i:4638026 original size:45 final size:45
Alignment explanation
Indices: 4637971--4638191 Score: 329
Period size: 46 Copynumber: 4.9 Consensus size: 45
4637961 TGCATATCCC
* * *
4637971 ATATATTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
4638016 ATATACTTACCA-TTATTCCATATGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
4638060 ATATACTTACCATTTATTCCATAAGCGT-GTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGC-TCGTAAGCTTATTTTACCA
* * *
4638105 TTATACTTACCATTTAATCACATAAGCTCGTAAGCTTATTTTACCC
1 ATATACTTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCA
*
4638151 ATATACTTACCATTTAATTACATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTT
4638192 GCATGCGTAC
Statistics
Matches: 160, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
44 41 0.26
45 58 0.36
46 59 0.37
47 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:4641556 original size:25 final size:25
Alignment explanation
Indices: 4641507--4641556 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4641497 ACAAAATTTA
*
4641507 AATTAGTCAAAACTTATAATTTTTT
1 AATTAGTCAAAACTTATAATGTTTT
* *
4641532 AATTAGTCAAAACTTTTTATGTTTT
1 AATTAGTCAAAACTTATAATGTTTT
4641557 TTAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (25 bp):
AATTAGTCAAAACTTATAATGTTTT
Found at i:4642305 original size:51 final size:50
Alignment explanation
Indices: 4642245--4642368 Score: 142
Period size: 51 Copynumber: 2.5 Consensus size: 50
4642235 GAAGTAAAGT
* * * * *
4642245 GCGCCCCCTG-ACCCGCGCTATATGTTGATTTGGCGCCACGTGGGGTATAGC
1 GCGCCCCCTGCA-CCGCGCTATACGCTGATTGGGCGACACGT-GGCTATAGC
**
4642296 GCGCCCCCTGCACCGCGCTATACGCTGATTGGGTTACACGTGGCTATAGC
1 GCGCCCCCTGCACCGCGCTATACGCTGATTGGGCGACACGTGGCTATAGC
* *
4642346 GCGCCCCCTGCTCCGCACTATAC
1 GCGCCCCCTGCACCGCGCTATAC
4642369 CTATTTATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 29 0.46
51 33 0.52
52 1 0.02
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (50 bp):
GCGCCCCCTGCACCGCGCTATACGCTGATTGGGCGACACGTGGCTATAGC
Found at i:4642394 original size:50 final size:51
Alignment explanation
Indices: 4642281--4642398 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 51
4642271 GATTTGGCGC
* *
4642281 CACGTGGGGTATAGCGCGCCCCCTGCACCGCGCTATACGCTGATTGGGTTA
1 CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTGATTGGATTA
* * *
4642332 CACGT-GGCTATAGCGCGCCCCCTGCTCCGCACTATAC-CT-ATT-TATCTGA
1 CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTGATTGGAT-T-A
4642381 CACGTGGGGTATAGCGCG
1 CACGTGGGGTATAGCGCG
4642399 GTACAAGGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
47 1 0.02
48 4 0.07
49 8 0.14
50 40 0.69
51 5 0.09
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (51 bp):
CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTGATTGGATTA
Done.