Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005483.1 Hibiscus syriacus cultivar Beakdansim tig00012575_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: 106186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2284 original size:20 final size:21
Alignment explanation
Indices: 2250--2310 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
2240 CGTAATTTCA
** *
2250 AACCCTAAATTATAAATC-CT
1 AACCCTAAACCATAAATCAAT
2270 AACCCTAAACCAT-AATACAAT
1 AACCCTAAACCATAAAT-CAAT
2291 AACCTCTAAACCATAAATCA
1 AACC-CTAAACCATAAATCA
2311 TAAATCCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
21 5 0.15
22 11 0.32
23 3 0.09
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTAAACCATAAATCAAT
Found at i:3770 original size:20 final size:21
Alignment explanation
Indices: 3731--3770 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3721 TACTTAAAAT
*
3731 TATTTTATGTAAAATGAATTA
1 TATTTTATGAAAAATGAATTA
*
3752 TATTTTCTGAAAAAT-AATT
1 TATTTTATGAAAAATGAATT
3771 TTCTAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
TATTTTATGAAAAATGAATTA
Found at i:3914 original size:20 final size:20
Alignment explanation
Indices: 3886--3932 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3876 ATAAAATTTG
*
3886 ATTCAATTAATACTAAATCA
1 ATTCGATTAATACTAAATCA
** *
3906 ATTCGATTAATGGTAATTCA
1 ATTCGATTAATACTAAATCA
3926 ATTCGAT
1 ATTCGAT
3933 AGGTGACCGA
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:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (20 bp):
ATTCGATTAATACTAAATCA
Found at i:4004 original size:24 final size:27
Alignment explanation
Indices: 3977--4029 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
3967 TTAATTTTAG
*
3977 TATTTTATCAATA-T-AATAC-TAAAT
1 TATTATATCAATATTAAATACATAAAT
*
4001 TATTATATTAATATTAAATACATAAAT
1 TATTATATCAATATTAAATACATAAAT
4028 TA
1 TA
4030 ATATTACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 1 0.04
26 5 0.21
27 7 0.29
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTATATCAATATTAAATACATAAAT
Found at i:4186 original size:14 final size:15
Alignment explanation
Indices: 4169--4217 Score: 64
Period size: 14 Copynumber: 3.2 Consensus size: 15
4159 AGTACATATT
4169 AATATAATATTA-AA
1 AATATAATATTATAA
4183 AATATAATATTATTAA
1 AATATAATATTA-TAA
*
4199 AATTATAATATAATAA
1 AA-TATAATATTATAA
4215 AAT
1 AAT
4218 TAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 12 0.39
15 1 0.03
16 9 0.29
17 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAATATTATAA
Found at i:4198 original size:17 final size:17
Alignment explanation
Indices: 4176--4234 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
4166 ATTAATATAA
*
4176 TATTAAAAATATAATAT
1 TATTAAAATTATAATAT
4193 TATTAAAATTATAATA-
1 TATTAAAATTATAATAT
*
4209 TAATAAAATTA-AATAT
1 TATTAAAATTATAATAT
*
4225 T-TTAATATTA
1 TATTAAAATTA
4235 ATTTTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.30
16 11 0.30
17 15 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAAATTATAATAT
Found at i:4207 original size:31 final size:31
Alignment explanation
Indices: 4171--4234 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4161 TACATATTAA
*
4171 TATAATAT--TAAAAATATAATATTATTAAAAT
1 TATAATATAATAAAATTA-AATATT-TTAAAAT
*
4202 TATAATATAATAAAATTAAATATTTTAATAT
1 TATAATATAATAAAATTAAATATTTTAAAAT
4233 TA
1 TA
4235 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 16 0.55
32 6 0.21
33 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TATAATATAATAAAATTAAATATTTTAAAAT
Found at i:4271 original size:11 final size:10
Alignment explanation
Indices: 4257--4292 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
4247 TGATGTTTAA
4257 AATATTAAATT
1 AATATTAAA-T
4268 AATATTAAAT
1 AATATTAAAT
4278 AA-ATTAAAT
1 AATATTAAAT
4287 AATATT
1 AATATT
4293 TTTTGAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 6 0.25
11 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATTAAAT
Found at i:4285 original size:9 final size:10
Alignment explanation
Indices: 4164--4292 Score: 62
Period size: 11 Copynumber: 13.5 Consensus size: 10
4154 ATCTGAGTAC
4164 ATATTAATATA
1 ATATTAA-ATA
4175 ATATTAAA-A
1 ATATTAAATA
4184 ATA-T-AATA
1 ATATTAAATA
* *
4192 TTATTAAAATT
1 ATATT-AAATA
*
4203 ATAATATAATA
1 ATATTA-AATA
*
4214 AAATTAAAT-
1 ATATTAAATA
4223 AT-TT---TA
1 ATATTAAATA
* *
4229 ATATTAATTT
1 ATATTAAATA
* *
4239 TTATTAAATG
1 ATATTAAATA
* *
4249 ATGTTTAA-A
1 ATATTAAATA
4258 ATATTAAATTA
1 ATATTAAA-TA
4269 ATATTAAATA
1 ATATTAAATA
4279 A-ATTAAATA
1 ATATTAAATA
4288 ATATT
1 ATATT
4293 TTTTGAGTGC
Statistics
Matches: 87, Mismatches: 18, Indels: 27
0.66 0.14 0.20
Matches are distributed among these distances:
5 1 0.01
6 2 0.02
7 4 0.05
8 6 0.07
9 21 0.24
10 24 0.28
11 29 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (10 bp):
ATATTAAATA
Found at i:4489 original size:30 final size:30
Alignment explanation
Indices: 4441--4501 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4431 ATTATAAAAT
* *
4441 ATTTTTCGTAAAACCAATTACAACTATCAA
1 ATTTTTCGAAAAACCAATTACAAATATCAA
* *
4471 ATTTTTTGAAAAATCAATTACAAATATCAA
1 ATTTTTCGAAAAACCAATTACAAATATCAA
4501 A
1 A
4502 CATTTTCTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (30 bp):
ATTTTTCGAAAAACCAATTACAAATATCAA
Found at i:6936 original size:13 final size:13
Alignment explanation
Indices: 6920--6954 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
6910 CAAGAGATTT
6920 AAACAATCAAATC
1 AAACAATCAAATC
6933 AAACAATCAAATC
1 AAACAATCAAATC
6946 AAAC-ATCAA
1 AAACAATCAA
6955 TAATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (13 bp):
AAACAATCAAATC
Found at i:11584 original size:60 final size:60
Alignment explanation
Indices: 11520--11634 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
11510 AATCCTCAAG
* * * *
11520 CTATGA-CTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTTATTTTCATCCCTAAA
1 CTATGATC-CTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCCCTAAA
* * *
11580 CTATGATCCTCTTTCTAAATTAGCCCCTAAACTTTTAAATATTCTAATTTCATCC
1 CTATGATCCTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCC
11635 TCAAATTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (60 bp):
CTATGATCCTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCCCTAAA
Found at i:11888 original size:60 final size:61
Alignment explanation
Indices: 11824--11953 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 61
11814 AAAGAGGGTC
* * * **
11824 ATAGTTTGA-AGATGAAATT-AAAATGTTCAAAAGTTT-GAGAATTAATTTAGAATGATAGTT
1 ATAGTTTGAGAGATGAAATTGAAAAT-TTAAAAAGTTTAG-GAATCAATTTAAAACAATAGTT
* * *
11884 ATAGTTT-AGGGATGAAATTGAAACTTTAAAAAGTTTAGGGATCAATTTAAAACAATAGTT
1 ATAGTTTGAGAGATGAAATTGAAAATTTAAAAAGTTTAGGAATCAATTTAAAACAATAGTT
11944 ATAGTTTGAG
1 ATAGTTTGAG
11954 GACATATGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
59 1 0.02
60 50 0.86
61 7 0.12
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (61 bp):
ATAGTTTGAGAGATGAAATTGAAAATTTAAAAAGTTTAGGAATCAATTTAAAACAATAGTT
Found at i:12111 original size:2 final size:2
Alignment explanation
Indices: 12104--12140 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12094 ATCAACTGAC
12104 AT AT AT AT AT 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 AT AT AT AT AT A
12141 CACACGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21938 original size:60 final size:60
Alignment explanation
Indices: 21816--21939 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
21806 GGTCCCCCGG
* * ** *
21816 CTATAGGATGTTGCTTTATTAAGCCCTTCGACTATTAAAAATTACAAAATGATCCTCTGA
1 CTATAGAATGTTGCTTTATTAAGCCCTTCGACTATTAAAAATTACAAAATAATAATCCGA
* * * *
21876 CTATAGAATGTTGTTTTATTAAGTCCC-TCGACTGTTCAAAGTTACAAAATAATAATCCGA
1 CTATAGAATGTTGCTTTATTAAG-CCCTTCGACTATTAAAAATTACAAAATAATAATCCGA
21936 CTAT
1 CTAT
21940 TTATTACTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (60 bp):
CTATAGAATGTTGCTTTATTAAGCCCTTCGACTATTAAAAATTACAAAATAATAATCCGA
Found at i:23514 original size:29 final size:29
Alignment explanation
Indices: 23472--23574 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
23462 TATTTTATTA
*
23472 AATTTTTTAATTATTAAAAGTTATAAAAT
1 AATTTTCTAATTATTAAAAGTTATAAAAT
* * ** *
23501 AATTTTCTAGTTA-TAGGATA-TTATTTTATT
1 AATTTTCTAATTATTA--AAAGTTA-TAAAAT
*
23531 AAATTTTTTAATTATTAAAAGTTATAAAAT
1 -AATTTTCTAATTATTAAAAGTTATAAAAT
*
23561 AATTTTCTAGTTAT
1 AATTTTCTAATTAT
23575 AGAGTGTTGT
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 2 0.04
29 26 0.48
30 10 0.19
31 14 0.26
32 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (29 bp):
AATTTTCTAATTATTAAAAGTTATAAAAT
Found at i:23518 original size:60 final size:60
Alignment explanation
Indices: 23451--23576 Score: 252
Period size: 60 Copynumber: 2.1 Consensus size: 60
23441 GTTACTCTGA
23451 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
1 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
23511 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
1 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
23571 TTATAG
1 TTATAG
23577 AGTGTTGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (60 bp):
TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
Found at i:23607 original size:60 final size:60
Alignment explanation
Indices: 23451--23620 Score: 191
Period size: 60 Copynumber: 2.8 Consensus size: 60
23441 GTTACTCTGA
* * * *
23451 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
1 TTATAGGATATTATTTTATTAAAGTCTCTAACTATTAAAAGTTATAAAATAATTTTCTAG
* * * *
23511 TTATAGGATATTATTTTATTAAATTTTTTAATTATTAAAAGTTATAAAATAATTTTCTAG
1 TTATAGGATATTATTTTATTAAAGTCTCTAACTATTAAAAGTTATAAAATAATTTTCTAG
* * * * *
23571 TTATA-GAGTGTTGTTTTGTT-GAGTCTCTAGACTATTAAAAGTTACAAAAT
1 TTATAGGA-TATTATTTTATTAAAGTCTCTA-ACTATTAAAAGTTATAAAAT
23621 GGTCATCCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 7 0.07
60 92 0.93
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.49
Consensus pattern (60 bp):
TTATAGGATATTATTTTATTAAAGTCTCTAACTATTAAAAGTTATAAAATAATTTTCTAG
Found at i:35006 original size:27 final size:27
Alignment explanation
Indices: 34953--35006 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
34943 GAGATTCAAT
*
34953 CGGGAGGAACCGAGGCAGCGGAGTTTG
1 CGGGAGGAACCGAGGAAGCGGAGTTTG
* * * *
34980 CGGGTGGATCCGAGGAAGGGGATTTTG
1 CGGGAGGAACCGAGGAAGCGGAGTTTG
35007 AGAGGTCTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.48, T:0.17
Consensus pattern (27 bp):
CGGGAGGAACCGAGGAAGCGGAGTTTG
Found at i:47210 original size:14 final size:14
Alignment explanation
Indices: 47188--47233 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
47178 CGTTCGTGAA
47188 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
47202 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
*
47216 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
47230 CGTT
1 CGTT
47234 TATGTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:47994 original size:10 final size:10
Alignment explanation
Indices: 47979--48053 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
47969 GGGTCTCCAA
47979 CGTTTATGTT
1 CGTTTATGTT
47989 CGTTTATGTT
1 CGTTTATGTT
47999 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
48010 ATGTTCGTGTT
1 -CGTTTATGTT
48021 CGTTTATGTT
1 CGTTTATGTT
*
48031 CG----TGTC
1 CGTTTATGTT
48037 CGTTTATGTT
1 CGTTTATGTT
48047 CGTTTAT
1 CGTTTAT
48054 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:48010 original size:16 final size:16
Alignment explanation
Indices: 47985--48049 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
47975 CCAACGTTTA
47985 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
48001 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
48017 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
48033 TGTCCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
48049 T
1 T
48050 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.14, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:48140 original size:16 final size:16
Alignment explanation
Indices: 48119--48151 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48109 AAAAAAATTT
48119 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
48135 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
48151 T
1 T
48152 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:48497 original size:136 final size:136
Alignment explanation
Indices: 48237--48629 Score: 612
Period size: 136 Copynumber: 2.9 Consensus size: 136
48227 ATTAATGGAG
* * *
48237 ACGC-AACCGTGTCGAG-TCGTGATG-CTTCGATCGGACTGCGAGATCCTATAATCCTTCACGAA
1 ACGCAAACCGTATCGAGATCGTGATGTC-TCGATCGGACTGCGAGATCCTACAATCCTTCATGAA
* * **
48299 ACGCATATCCTTCATCCAATTAGCAATGACACCAATGCTATGTATGCAACAATTTGAAATTCATT
65 ACGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATT
48364 ACTCAAA
130 ACTCAAA
* *
48371 ATGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCAAGATCCTACAATCCTTCATGAAA
1 ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
**
48436 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGCGTGCAACAATTTGGCATTCATTA
66 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATTA
*
48501 CTCGAA
131 CTCAAA
* *
48507 ACGCAAACCGTATCGAGATCGTGATGTTTCGATCGGACTGCGAGATCCTACAATCCTTCATGCAA
1 ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
* *
48572 TGCATATCCTTCATCCAATTAGCAATGACACTAATGTTACGTATGCAACAATTTGGCA
66 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCA
48630 ACTACAAGAT
Statistics
Matches: 236, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
134 3 0.01
135 11 0.05
136 221 0.94
137 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (136 bp):
ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATTA
CTCAAA
Found at i:51928 original size:2 final size:2
Alignment explanation
Indices: 51921--51956 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
51911 GCCTGGGACA
51921 AT AT AT 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 AT AT AT
51957 CACTTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52636 original size:25 final size:26
Alignment explanation
Indices: 52584--52633 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
52574 AAAGATATTC
52584 AAATAAAGATAAAAAGACATTAAAAT
1 AAATAAAGATAAAAAGACATTAAAAT
*
52610 AAATAAATA-AAAAAGAACATTAAA
1 AAATAAAGATAAAAAG-ACATTAAA
52634 TAAGACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATAAAGATAAAAAGACATTAAAAT
Found at i:54309 original size:2 final size:2
Alignment explanation
Indices: 54302--54326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54292 ATATTCAAGG
54302 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54327 TGTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64839 original size:15 final size:13
Alignment explanation
Indices: 64805--64870 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
64795 TTATTAACGG
64805 TAAAAAA-T-AAA
1 TAAAAAATTAAAA
64816 TAAATAAATTAGAATA
1 TAAA-AAATTA-AA-A
64832 TAAAAAATTATAAA
1 TAAAAAATTA-AAA
*
64846 -ATAAAATTAAACA
1 TAAAAAATTAAA-A
64859 TAAAAAATTAAA
1 TAAAAAATTAAA
64871 CAAATATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.09
12 5 0.11
13 10 0.22
14 11 0.24
15 10 0.22
16 5 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:64875 original size:28 final size:28
Alignment explanation
Indices: 64805--64876 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
64795 TTATTAACGG
*
64805 TAAAAAA-TAAATAAAT-AAATTAGAATA
1 TAAAAAATTAAA-AAATAAAATTAGAACA
*
64832 TAAAAAATTATAAAATAAAATTA-AACA
1 TAAAAAATTAAAAAATAAAATTAGAACA
64859 TAAAAAATTAAACAAATA
1 TAAAAAATTAAA-AAATA
64877 TAATATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 25 0.64
28 14 0.36
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (28 bp):
TAAAAAATTAAAAAATAAAATTAGAACA
Found at i:65163 original size:15 final size:14
Alignment explanation
Indices: 65129--65167 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
65119 AATTGGGAAC
*
65129 TAGGGATTTTGATT
1 TAGGAATTTTGATT
*
65143 TTGGAATTTTAGATT
1 TAGGAATTTT-GATT
65158 TAGGAATTTT
1 TAGGAATTTT
65168 TAGTGATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TAGGAATTTTGATT
Found at i:66576 original size:36 final size:36
Alignment explanation
Indices: 66472--66814 Score: 201
Period size: 38 Copynumber: 9.4 Consensus size: 36
66462 TTTTGACAAA
* * * *
66472 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTT--GAAAA-CATTTT-TAAAATAT
* *
66512 ATATATTATATAGTTTTTGAAAATATTTTTAAAATAT
1 ATATAATATATAG-TTTTGAAAACATTTTTAAAATAT
* *
66549 ATATAATATATAGTTTTGAAAACATTTTGAAAACGTTT
1 ATATAATATATAGTTTTGAAAACATTTTTAAAA--TAT
* * * *
66587 ATATATTATATAGTTTTTAAAACATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTTAAAATAT
* * *
66623 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAAT-T
1 ATATAATATATAGTTTTGAAAACA--TTTT-TAAAATAT
*
66661 ATATAATATATAGTTTTAAAAACATTTTTTGAAAACT-T
1 ATATAATATATAGTTTTGAAAACA-TTTTT-AAAA-TAT
* * *
66699 ATAT-A-ATAT--TTTT-AAAACGTTTTGAAAA-CT
1 ATATAATATATAGTTTTGAAAACATTTTTAAAATAT
* * **
66729 ATGTAATATATAGTTTTG--GA-ATTTTT--TTTA-
1 ATATAATATATAGTTTTGAAAACATTTTTAAAATAT
* *
66759 AGTATAATATATAGTTTTCTAAAACATATTTTTGAAATAT
1 A-TATAATATATAGTTTT-GAAAAC--ATTTTTAAAATAT
*
66799 ATATATTATATAGTTT
1 ATATAATATATAGTTT
66815 ATATCATATT
Statistics
Matches: 243, Mismatches: 35, Indels: 51
0.74 0.11 0.16
Matches are distributed among these distances:
30 5 0.02
31 20 0.08
32 12 0.05
33 6 0.02
34 9 0.04
36 46 0.19
37 33 0.14
38 72 0.30
39 24 0.10
40 12 0.05
41 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAACATTTTTAAAATAT
Found at i:66599 original size:38 final size:36
Alignment explanation
Indices: 66472--66745 Score: 240
Period size: 38 Copynumber: 7.5 Consensus size: 36
66462 TTTTGACAAA
* * *
66472 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTT-A-AAAA-CATTTT-GAAAACTT
* * * *
66512 ATATATTATATAGTTTTTGAAAATATTTTTAAAA-TAT
1 ATATAATATATAG-TTTTAAAAACATTTTGAAAACT-T
*
66549 ATATAATATATAGTTTTGAAAACATTTTGAAAACGTTT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAAC--TT
* * *
66587 ATATATTATATAGTTTTTAAAACATTTTGAAAACAT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAACTT
* *
66623 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAA-TT
1 ATATAATATATAGTTTTAAAAACA--TTTTG-AAAACTT
66661 ATATAATATATAGTTTTAAAAACATTTTTTGAAAACTT
1 ATATAATATATAGTTTTAAAAACA--TTTTGAAAACTT
*
66699 ATAT-A-ATAT--TTTT-AAAACGTTTTGAAAAC-T
1 ATATAATATATAGTTTTAAAAACATTTTGAAAACTT
*
66729 ATGTAATATATAGTTTT
1 ATATAATATATAGTTTT
66746 GGAATTTTTT
Statistics
Matches: 202, Mismatches: 19, Indels: 32
0.80 0.08 0.13
Matches are distributed among these distances:
30 4 0.02
31 11 0.05
32 4 0.02
33 5 0.02
34 8 0.04
36 46 0.23
37 21 0.10
38 80 0.40
39 8 0.04
40 11 0.05
41 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAACTT
Found at i:66637 original size:74 final size:72
Alignment explanation
Indices: 66462--66745 Score: 248
Period size: 74 Copynumber: 3.9 Consensus size: 72
66452 GTAAAAATGT
* *
66462 TTTTGACAAA-ATATA-ATATATAATTTTCAGAAAATGATTTTCGAAAA-TTTATATATTATATA
1 TTTTGA-AAACATATATATATATAGTTTT-A-AAAA-CATTTT-GAAAACTTTATATATTATATA
*
66524 GTTTTTGAAAATA
61 GTTTTT-AAAACA
* * *
66537 TTTTTAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACGTTTATATATTATATAGTT
1 TTTTGAAAACATATAT-ATATATAGTTTTAAAAACATTTTGAAAAC-TTTATATATTATATAGTT
66602 TTTAAAACA
64 TTTAAAACA
* *
66611 TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTGAAA--TTATATAATATATAG
1 TTTTGAAAACATATATA-TATATAGTTTTAAAAACA--TTTTG-AAAACTTTATATATTATATAG
*
66674 TTTTAAAAACA
62 TTTTTAAAACA
* * * *
66685 TTTTTTGAAAAC-T-TATATA-ATA-TTTTTAAAACGTTTTGAAAAC--TATGTAATATATAGTT
1 --TTTTGAAAACATATATATATATAGTTTTAAAAACATTTTGAAAACTTTATATATTATATAGTT
66744 TT
64 TT
66746 GGAATTTTTT
Statistics
Matches: 182, Mismatches: 15, Indels: 31
0.80 0.07 0.14
Matches are distributed among these distances:
68 20 0.11
69 5 0.03
71 9 0.05
72 3 0.02
73 8 0.04
74 72 0.40
75 36 0.20
76 15 0.08
77 14 0.08
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (72 bp):
TTTTGAAAACATATATATATATAGTTTTAAAAACATTTTGAAAACTTTATATATTATATAGTTTT
TAAAACA
Found at i:68135 original size:25 final size:24
Alignment explanation
Indices: 68107--68179 Score: 58
Period size: 26 Copynumber: 2.8 Consensus size: 24
68097 TGATCCTAAG
* *
68107 TTTTATCTTTATTTTTTATTTTACT
1 TTTTAT-TTTATTTTTTATTTAACC
*
68132 TTTTAAATATTT-TTTTTAATTTAACC
1 TTTT--AT-TTTATTTTTTATTTAACC
68158 TTTTATTATTATTTTATTATTT
1 TTTTATT-TTATTTT-TTATTT
68180 CTTTCTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 8 0.21
26 20 0.53
27 5 0.13
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTATTTTATTTTTTATTTAACC
Found at i:71748 original size:2 final size:2
Alignment explanation
Indices: 71743--71767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71733 TTCATATGTG
71743 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
71768 TACACATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73611 original size:17 final size:17
Alignment explanation
Indices: 73589--73623 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
73579 AACAATAGGA
*
73589 TTAACCACACGTTTAAT
1 TTAACCACACGTGTAAT
73606 TTAACCACACGTGTAAT
1 TTAACCACACGTGTAAT
73623 T
1 T
73624 CGCGGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (17 bp):
TTAACCACACGTGTAAT
Found at i:78718 original size:13 final size:13
Alignment explanation
Indices: 78691--78740 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
78681 AATTATAAAC
78691 TTTAAG-TTAGAG
1 TTTAAGTTTAGAG
*
78703 TTTAAGTTTAGGG
1 TTTAAGTTTAGAG
78716 TTTATAGTTTAGAG
1 TTTA-AGTTTAGAG
*
78730 ATTATAGTTTA
1 TTTA-AGTTTA
78741 CGATTTAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 6 0.18
13 9 0.27
14 18 0.55
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TTTAAGTTTAGAG
Found at i:78726 original size:14 final size:14
Alignment explanation
Indices: 78697--78740 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
78687 AAACTTTAAG
78697 TTAGAGTTTA-AGT
1 TTAGAGTTTATAGT
*
78710 TTAGGGTTTATAGT
1 TTAGAGTTTATAGT
*
78724 TTAGAGATTATAGT
1 TTAGAGTTTATAGT
78738 TTA
1 TTA
78741 CGATTTAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTAGAGTTTATAGT
Found at i:78747 original size:21 final size:21
Alignment explanation
Indices: 78723--78767 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
78713 GGGTTTATAG
*
78723 TTTAGAGATTATAGTTTACGA
1 TTTAGAGATTATAATTTACGA
* * *
78744 TTTAGTGTTTATAATTTAGGA
1 TTTAGAGATTATAATTTACGA
78765 TTT
1 TTT
78768 TAAGTTAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (21 bp):
TTTAGAGATTATAATTTACGA
Found at i:84172 original size:2 final size:2
Alignment explanation
Indices: 84165--84232 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
84155 ACTTAAATCG
84165 AT AT AT AT AT AT 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 AT AT AT AT AT AT
84207 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
84233 TCGATAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84315 original size:14 final size:13
Alignment explanation
Indices: 84296--84333 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
84286 AAATATTCAA
84296 AAAAATTAAATATT
1 AAAAATTAAA-ATT
84310 AAAAATT-AAATT
1 AAAAATTAAAATT
84322 AAAATATTAAAA
1 AAAA-ATTAAAA
84334 AAATATCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 5 0.23
14 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:84328 original size:20 final size:17
Alignment explanation
Indices: 84286--84336 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
84276 AAAAGTATTC
*
84286 AAATATTCAAAAAAATT
1 AAATATTAAAAAAAATT
84303 AAATATTAAAAATTAAATT
1 AAATATTAAAAA--AAATT
84322 AAAATATTAAAAAAA
1 -AAATATTAAAAAAA
84337 TATCCATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 5 0.17
20 12 0.40
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATTAAAAAAAATT
Found at i:85745 original size:55 final size:53
Alignment explanation
Indices: 85661--85803 Score: 205
Period size: 55 Copynumber: 2.6 Consensus size: 53
85651 TTGTATGAGA
*
85661 GTGTATCGGTACACTAAGGAGTGTATCGATACGCTCAAAACATCGAATGCCATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATAC-CT-AAAACATCGAATGCCATTT
* * * *
85716 GTGTATCGATACACTGAGGAGTGTATCGATGCACCTAAAACATTGAGTGCTATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGAT--ACCTAAAACATCGAATGCCATTT
85771 GTGTATCGGTACACTGAGGAGTGTATCGATACC
1 GTGTATCGGTACACTGAGGAGTGTATCGATACC
85804 CCCAAGTATG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
53 3 0.04
55 73 0.91
56 2 0.03
57 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (53 bp):
GTGTATCGGTACACTGAGGAGTGTATCGATACCTAAAACATCGAATGCCATTT
Found at i:86379 original size:23 final size:23
Alignment explanation
Indices: 86351--86459 Score: 120
Period size: 23 Copynumber: 4.9 Consensus size: 23
86341 TTCGGGATAA
*
86351 TATGTGACACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
86374 TATGTGGCACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
* *
86397 TATGTGGCACTTTGGTGCAA-TC
1 TATGTGGCACTTCGGTGCAACCC
*
86419 TATGTGGTC-CTTCGG-GACAA--T
1 TATGTGG-CACTTCGGTG-CAACCC
*
86440 TATGTGCCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
86460 ATTACGAGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.21
22 17 0.22
23 42 0.55
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:86457 original size:43 final size:43
Alignment explanation
Indices: 86329--86459 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 43
86319 GAGTCGATGG
* *
86329 TCTATGTGGTTCTTCGGGATAATATGTGACACTTCGGTGCAAC
1 TCTATGTGGTCCTTCGGGACAATATGTGACACTTCGGTGCAAC
* * *
86372 CCTATGTGG-CACTTCGGTG-CAACCCTATGTGGCACTTTGGTGCAA-
1 TCTATGTGGTC-CTTCGG-GACAA---TATGTGACACTTCGGTGCAAC
*
86417 TCTATGTGGTCCTTCGGGACAATTATGTGCCACTTCGGTGCAA
1 TCTATGTGGTCCTTCGGGACAA-TATGTGACACTTCGGTGCAA
86460 ATTACGAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
43 34 0.47
44 2 0.03
45 17 0.24
46 19 0.26
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (43 bp):
TCTATGTGGTCCTTCGGGACAATATGTGACACTTCGGTGCAAC
Found at i:87332 original size:17 final size:17
Alignment explanation
Indices: 87312--87358 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
87302 TTAGTTTTTT
87312 ATATTTAATATTTTTAA
1 ATATTTAATATTTTTAA
* *
87329 ATATTTAAATAATTTTAT
1 ATATTT-AATATTTTTAA
87347 AT-TTATAATATT
1 ATATT-TAATATT
87359 AATATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTAATATTTTTAA
Found at i:87412 original size:22 final size:23
Alignment explanation
Indices: 87369--87429 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
87359 AATATTTTAT
87369 TTTAAAAAAAATAAATCCTTGAAA
1 TTTAAAAAAAATAAAT-CTTGAAA
* **
87393 TTTAAAAAAAATTAAT-TTGACC
1 TTTAAAAAAAATAAATCTTGAAA
*
87415 TTTAAACAAAATAAA
1 TTTAAAAAAAATAAA
87430 AATTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 17 0.53
24 15 0.47
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.31
Consensus pattern (23 bp):
TTTAAAAAAAATAAATCTTGAAA
Found at i:87634 original size:4 final size:4
Alignment explanation
Indices: 87625--87651 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
87615 AATTTACAGC
87625 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
87652 CTCTGCACGT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:98156 original size:2 final size:2
Alignment explanation
Indices: 98149--98207 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
98139 AAGTTTTATC
98149 AT AT AT AT AT AT 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 AT AT AT AT AT AT
98191 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
98208 AAGCACGAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:101540 original size:19 final size:19
Alignment explanation
Indices: 101516--101584 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
101506 AAAAATGTTT
* *
101516 TTTGAATAGTAATTTACTA
1 TTTGAACAGTAAATTACTA
*
101535 TTTGAACAGTAAATTAATA
1 TTTGAACAGTAAATTACTA
* *
101554 TTTGAACAGTAAATCACTG
1 TTTGAACAGTAAATTACTA
101573 TTTGAACAGTAA
1 TTTGAACAGTAA
101585 CCCCGAGGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGAACAGTAAATTACTA
Found at i:101706 original size:20 final size:21
Alignment explanation
Indices: 101670--101710 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
101660 ATTTGAATAT
*
101670 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
101691 TATGAA-GGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
101711 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Done.