Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 24
Found at i:3479677 original size:13 final size:14
Alignment explanation
Indices: 3479659--3479688 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3479649 TTTGACCGGT
3479659 CTGACCCGACC-GA
1 CTGACCCGACCAGA
3479672 CTGACCCGACCAGA
1 CTGACCCGACCAGA
3479686 CTG
1 CTG
3479689 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.10
Consensus pattern (14 bp):
CTGACCCGACCAGA
Found at i:3479700 original size:7 final size:7
Alignment explanation
Indices: 3479688--3479720 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3479678 CGACCAGACT
3479688 GTTGACC
1 GTTGACC
3479695 GTTGACC
1 GTTGACC
3479702 G-TGACC
1 GTTGACC
3479708 GTTGACC
1 GTTGACC
3479715 GTTGAC
1 GTTGAC
3479721 TTCCTTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GTTGACC
Found at i:3479708 original size:13 final size:13
Alignment explanation
Indices: 3479690--3479716 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3479680 ACCAGACTGT
3479690 TGACCGTTGACCG
1 TGACCGTTGACCG
3479703 TGACCGTTGACCG
1 TGACCGTTGACCG
3479716 T
1 T
3479717 TGACTTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:3486842 original size:9 final size:9
Alignment explanation
Indices: 3486828--3486914 Score: 93
Period size: 9 Copynumber: 9.1 Consensus size: 9
3486818 GGCTGGAAAT
3486828 CGGTTTGAC
1 CGGTTTGAC
*
3486837 CGGTTTTCAAC
1 CGG-TTT-GAC
3486848 CGGTTCTGAC
1 CGGTT-TGAC
3486858 CGGTTTGAC
1 CGGTTTGAC
3486867 CGGTTTGAAC
1 CGGTTTG-AC
*
3486877 CAGTTTGAC
1 CGGTTTGAC
*
3486886 CGGTCTGAAC
1 CGGTTTG-AC
3486896 CGGTTTGAC
1 CGGTTTGAC
*
3486905 CGGTCTGAC
1 CGGTTTGAC
3486914 C
1 C
3486915 TGACCCGGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
9 32 0.48
10 28 0.42
11 6 0.09
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:3486870 original size:19 final size:19
Alignment explanation
Indices: 3486828--3486914 Score: 92
Period size: 19 Copynumber: 4.6 Consensus size: 19
3486818 GGCTGGAAAT
*
3486828 CGGTT-TGACCGGTTTTCAAC
1 CGGTTCTGACCGG-TTT-GAC
3486848 CGGTTCTGACCGGTTTGAC
1 CGGTTCTGACCGGTTTGAC
*
3486867 CGGTT-TGAACCAGTTTGAC
1 CGGTTCTG-ACCGGTTTGAC
3486886 CGG-TCTGAACCGGTTTGAC
1 CGGTTCTG-ACCGGTTTGAC
3486905 CGG-TCTGACC
1 CGGTTCTGACC
3486915 TGACCCGGCC
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.10
19 40 0.66
20 8 0.13
21 7 0.11
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (19 bp):
CGGTTCTGACCGGTTTGAC
Found at i:3488833 original size:24 final size:24
Alignment explanation
Indices: 3488800--3488846 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3488790 ATATTGGCAC
3488800 CACCCACTCCCACTGATTCCCACG
1 CACCCACTCCCACTGATTCCCACG
* *
3488824 CACCCGCTCCTACTGATTCCCAC
1 CACCCACTCCCACTGATTCCCAC
3488847 TCAATCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.53, G:0.09, T:0.19
Consensus pattern (24 bp):
CACCCACTCCCACTGATTCCCACG
Found at i:3490128 original size:20 final size:20
Alignment explanation
Indices: 3490103--3490174 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
3490093 AACGCGAATA
*
3490103 GGTAAATCACAATGGTAATT
1 GGTAAATCGCAATGGTAATT
* *
3490123 GGTAAATCGCAACTCG-AATA
1 GGTAAATCGCAA-TGGTAATT
*
3490143 GGTAAATCGCAATGATAATAT
1 GGTAAATCGCAATGGTAAT-T
3490164 -GTAAATCGCAA
1 GGTAAATCGCAA
3490175 CGCAAAAGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 40 0.93
21 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (20 bp):
GGTAAATCGCAATGGTAATT
Found at i:3490133 original size:40 final size:40
Alignment explanation
Indices: 3490089--3490177 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
3490079 GGTTCCAAAT
*
3490089 TCGCAACGCGAATAGGTAAATCACAATGGTAAT-TGGTAAA
1 TCGCAACGCGAATAGGTAAATCACAATGATAATAT-GTAAA
* *
3490129 TCGCAACTCGAATAGGTAAATCGCAATGATAATATGTAAA
1 TCGCAACGCGAATAGGTAAATCACAATGATAATATGTAAA
3490169 TCGCAACGC
1 TCGCAACGC
3490178 AAAAGACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAACGCGAATAGGTAAATCACAATGATAATATGTAAA
Found at i:3490192 original size:20 final size:20
Alignment explanation
Indices: 3490169--3490236 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
3490159 AATATGTAAA
*
3490169 TCGCAACGCAAAAGACAAAT
1 TCGCAACGCAAAAGTCAAAT
3490189 TCGCAACGCAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* *
3490209 TCGCAACGCGAGAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
3490229 TCGCAACG
1 TCGCAACG
3490237 TGAATAGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:3490258 original size:40 final size:39
Alignment explanation
Indices: 3490124--3490260 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 39
3490114 ATGGTAATTG
* ** * * *
3490124 GTAAATCGCAACTCGAATAGGTAAA-TCGCAATGATAATAT
1 GTAAATCGCAACGCGAA-AGACAAATTCGCAACG-CAATAA
*
3490164 GTAAATCGCAACGCAAAAGACAAATTCGCAACGCAA-AA
1 GTAAATCGCAACGCGAAAGACAAATTCGCAACGCAATAA
* * * *
3490202 GTCAAATTCGCAACGCGAGAGTCAAATTCGCAACGTGAATAG
1 GT-AAA-TCGCAACGCGAAAGACAAATTCGCAACG-CAATAA
3490244 GTAAATCGCAACGCGAA
1 GTAAATCGCAACGCGAA
3490261 TTTATGTTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.04
39 10 0.13
40 58 0.73
41 5 0.06
42 3 0.04
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (39 bp):
GTAAATCGCAACGCGAAAGACAAATTCGCAACGCAATAA
Found at i:3490305 original size:19 final size:20
Alignment explanation
Indices: 3490281--3490334 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
3490271 ATAACATAAG
3490281 TTTTCTTTTCGCAACAAG-A
1 TTTTCTTTTCGCAACAAGAA
** *
3490300 TTTTCTAATCGCAACACGAA
1 TTTTCTTTTCGCAACAAGAA
**
3490320 TTTTGATTTCGCAAC
1 TTTTCTTTTCGCAAC
3490335 TCGATTTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTCTTTTCGCAACAAGAA
Found at i:3490331 original size:20 final size:20
Alignment explanation
Indices: 3490308--3490375 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
3490298 GATTTTCTAA
3490308 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* * *
3490328 TCGCAACTCGATTTTTGAAT
1 TCGCAACACGAATTTTGATT
* *
3490348 TCACAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
*
3490368 TTGCAACA
1 TCGCAACA
3490376 GCTTTTATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:3490332 original size:39 final size:40
Alignment explanation
Indices: 3490287--3490375 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
3490277 TAAGTTTTCT
* *
3490287 TTTCGCAACAAGATTTTCT-AA-TCGCAACACGAATTTTGA
1 TTTCGCAACAAGATTTT-TGAATTCACAACACGAATTTTAA
**
3490326 TTTCGCAACTCGATTTTTGAATTCACAACACGAATTTTAA
1 TTTCGCAACAAGATTTTTGAATTCACAACACGAATTTTAA
*
3490366 TTTTGCAACA
1 TTTCGCAACA
3490376 GCTTTTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 17 0.40
40 24 0.57
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (40 bp):
TTTCGCAACAAGATTTTTGAATTCACAACACGAATTTTAA
Found at i:3490551 original size:14 final size:15
Alignment explanation
Indices: 3490532--3490569 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3490522 TCCCCATCTC
3490532 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
3490546 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
3490562 TAATTTTT
1 TAATTTTT
3490570 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:3493363 original size:20 final size:20
Alignment explanation
Indices: 3493340--3493387 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3493330 TTGACTTTCA
*
3493340 CGTTGTGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* **
3493360 CGTTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
3493380 CGTTGCGA
1 CGTTGCGA
3493388 ATTTGTAACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:3495116 original size:7 final size:7
Alignment explanation
Indices: 3495100--3495228 Score: 136
Period size: 7 Copynumber: 18.1 Consensus size: 7
3495090 AGTGTGTGAG
3495100 AAGAAGA
1 AAGAAGA
*
3495107 AAGAATA
1 AAGAAGA
3495114 AAGAAGGA
1 AAGAA-GA
*
3495122 AA-AAGG
1 AAGAAGA
*
3495128 AAGGAGA
1 AAGAAGA
3495135 ATGATGAAGA
1 A--A-GAAGA
*
3495145 AAGAAGG
1 AAGAAGA
*
3495152 AAGAAGT
1 AAGAAGA
*
3495159 AAGAAGG
1 AAGAAGA
3495166 AAGAAGA
1 AAGAAGA
3495173 AAGAAGA
1 AAGAAGA
*
3495180 AAGAAGG
1 AAGAAGA
3495187 AAGAAGA
1 AAGAAGA
3495194 AAGAAGA
1 AAGAAGA
3495201 AAGAAGA
1 AAGAAGA
3495208 AAGAAGA
1 AAGAAGA
*
3495215 AATAAG-
1 AAGAAGA
3495221 AAGAAGA
1 AAGAAGA
3495228 A
1 A
3495229 CCTGCTGCCA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
6 8 0.08
7 84 0.82
8 4 0.04
9 1 0.01
10 5 0.05
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (7 bp):
AAGAAGA
Found at i:3495135 original size:24 final size:24
Alignment explanation
Indices: 3495108--3495216 Score: 66
Period size: 24 Copynumber: 4.6 Consensus size: 24
3495098 AGAAGAAGAA
3495108 AGAATAAAGAAGGAAA-AAGGAAGG
1 AGAATAAAGAA-GAAAGAAGGAAGG
* * *
3495132 AGAATGATGAAGAAAGAAGGAAGA
1 AGAATAAAGAAGAAAGAAGGAAGG
* * * *
3495156 AGTAAGAAGGAAG-AAGAAAGAAGAA
1 AG-AATAAAGAAGAAAGAAGGAAG-G
**
3495181 AGAAGGAAGAAGAAAGAA-GAA--
1 AGAATAAAGAAGAAAGAAGGAAGG
*
3495202 AGAAGAAAGAAGAAA
1 AGAATAAAGAAGAAA
3495217 TAAGAAGAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
21 14 0.20
23 4 0.06
24 38 0.54
25 15 0.21
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (24 bp):
AGAATAAAGAAGAAAGAAGGAAGG
Found at i:3496487 original size:6 final size:6
Alignment explanation
Indices: 3496476--3497171 Score: 1219
Period size: 6 Copynumber: 118.0 Consensus size: 6
3496466 ATTAGTTATA
3496476 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496524 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496572 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496618 TATATG TATATG TATATG TATATG TATATG TATATG TATA-G TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
3496665 TATATG TATAGG TATGTATG TATATG TATATG TATATG TATATG --TATG
1 TATATG TATATG TA--TATG TATATG TATATG TATATG TATATG TATATG
3496713 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496761 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496809 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496857 TATATG --TAT- TATATG TATATG TATATG TATATG TATA-G TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496901 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3496949 TATATG TATATG TATATG TATAATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TAT-ATG TATATG TATATG TATATG TATATG
3496998 --TATG TATATG TATA-G TATATG TATATG TATA-G TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3497042 TATATG TATATG TATATG TATA-G TATATG TATATG TATATG --TATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3497087 T-TATGG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATAT-G TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3497135 TATATG TATATG TATATG TATATG TATATG TAATATG
1 TATATG TATATG TATATG TATATG TATATG T-ATATG
3497172 CATGCATGCA
Statistics
Matches: 667, Mismatches: 2, Indels: 41
0.94 0.00 0.06
Matches are distributed among these distances:
4 19 0.03
5 31 0.05
6 598 0.90
7 14 0.02
8 5 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:3501947 original size:25 final size:25
Alignment explanation
Indices: 3501918--3501998 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
3501908 CCAAATATCT
3501918 TAGGATCATATCAGTAAAATACTTA
1 TAGGATCATATCAGTAAAATACTTA
** * *
3501943 TAGGACTGGC-T-TCTTTCCAAATA-TTT
1 TAGGA-T--CATATCAGT-AAAATACTTA
3501969 TAGGATCATATCAGTAAAATACTTA
1 TAGGATCATATCAGTAAAATACTTA
*
3501994 CAGGA
1 TAGGA
3501999 CTGGTTTCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
23 1 0.03
24 6 0.15
25 15 0.38
26 11 0.28
27 6 0.15
28 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (25 bp):
TAGGATCATATCAGTAAAATACTTA
Found at i:3501951 original size:51 final size:51
Alignment explanation
Indices: 3501873--3502028 Score: 267
Period size: 51 Copynumber: 3.1 Consensus size: 51
3501863 TTAGCTTTTA
*
3501873 CATATCAGTAAAATACTTATAGCACTGGTTTCTTTCCAAATATCTTAGGAT
1 CATATCAGTAAAATACTTATAGGACTGGTTTCTTTCCAAATATCTTAGGAT
* *
3501924 CATATCAGTAAAATACTTATAGGACTGGCTTCTTTCCAAATATTTTAGGAT
1 CATATCAGTAAAATACTTATAGGACTGGTTTCTTTCCAAATATCTTAGGAT
* *
3501975 CATATCAGTAAAATACTTACAGGACTGGTTTCTTTCCAGATATCTTAGGAT
1 CATATCAGTAAAATACTTATAGGACTGGTTTCTTTCCAAATATCTTAGGAT
3502026 CAT
1 CAT
3502029 TTAAACAAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 98 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (51 bp):
CATATCAGTAAAATACTTATAGGACTGGTTTCTTTCCAAATATCTTAGGAT
Found at i:3515071 original size:149 final size:149
Alignment explanation
Indices: 3514801--3515097 Score: 594
Period size: 149 Copynumber: 2.0 Consensus size: 149
3514791 TATGAACATC
3514801 GATTTCACTGGAACCACCATCAGAGCTAGTCAATATACCTTTCCTGAGACGAGAAACAGTTGGCA
1 GATTTCACTGGAACCACCATCAGAGCTAGTCAATATACCTTTCCTGAGACGAGAAACAGTTGGCA
3514866 GTTTCTCAAGTGCAGCCCACATTAAAGCATCTTCATGATCTTCTTCTCGAGAAGACCTTGAATAT
66 GTTTCTCAAGTGCAGCCCACATTAAAGCATCTTCATGATCTTCTTCTCGAGAAGACCTTGAATAT
3514931 GGCTCTACTTCACTGTTTT
131 GGCTCTACTTCACTGTTTT
3514950 GATTTCACTGGAACCACCATCAGAGCTAGTCAATATACCTTTCCTGAGACGAGAAACAGTTGGCA
1 GATTTCACTGGAACCACCATCAGAGCTAGTCAATATACCTTTCCTGAGACGAGAAACAGTTGGCA
3515015 GTTTCTCAAGTGCAGCCCACATTAAAGCATCTTCATGATCTTCTTCTCGAGAAGACCTTGAATAT
66 GTTTCTCAAGTGCAGCCCACATTAAAGCATCTTCATGATCTTCTTCTCGAGAAGACCTTGAATAT
3515080 GGCTCTACTTCACTGTTT
131 GGCTCTACTTCACTGTTT
3515098 CTCCATGCCG
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (149 bp):
GATTTCACTGGAACCACCATCAGAGCTAGTCAATATACCTTTCCTGAGACGAGAAACAGTTGGCA
GTTTCTCAAGTGCAGCCCACATTAAAGCATCTTCATGATCTTCTTCTCGAGAAGACCTTGAATAT
GGCTCTACTTCACTGTTTT
Found at i:3515839 original size:43 final size:43
Alignment explanation
Indices: 3515761--3515946 Score: 196
Period size: 43 Copynumber: 4.4 Consensus size: 43
3515751 TTTTTGGAAC
* * * **
3515761 AAACACCGTTATAAATCTGACCTTTTGCGGGGTTTGTTCCAAA
1 AAACACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCCAAA
* ** *
3515804 CAATGCCGCTATAGATCTGACTTTTTACGACGTTTGTT-CAAA
1 AAACACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCCAAA
* * **
3515846 AAATACCGCTATAGATCTGACTTTTTGCGATGTTTGTTTAAAA
1 AAACACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCCAAA
* * *
3515889 AAACAACGCTATAGAACTGACTTTTTGCGGCGTTTGTTCC-AA
1 AAACACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCCAAA
* *
3515931 AAACGCCGCTAAAGAT
1 AAACACCGCTATAGAT
3515947 ATCAACAAAA
Statistics
Matches: 117, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
42 52 0.44
43 65 0.56
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (43 bp):
AAACACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCCAAA
Found at i:3516585 original size:16 final size:16
Alignment explanation
Indices: 3516555--3516601 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3516545 TAAATTATTT
*
3516555 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
3516572 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
3516588 TTTAAATTGAATTT
1 ATTAAATT-AATTT
3516602 TTCTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:3517885 original size:13 final size:13
Alignment explanation
Indices: 3517867--3517892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3517857 GTCATCGACA
3517867 GTCCATGATTGAT
1 GTCCATGATTGAT
3517880 GTCCATGATTGAT
1 GTCCATGATTGAT
3517893 AACCCTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
GTCCATGATTGAT
Found at i:3518715 original size:64 final size:65
Alignment explanation
Indices: 3518654--3518781 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 65
3518644 GGATGCATTG
*
3518654 ATGCATAAAAT-ACATTCCATGTTTCAAAAAAACCT-GAGTGCATCGATGCATGGTCTTTGCATC
1 ATGCATAAAATCA-ATTCCATGTTTCAAAAAAACATGGAGTGCATCGATGCATGGTCTTTGCATC
3518717 A
65 A
* * * * * *
3518718 ATGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTATGTGCATC
1 ATGCATAAAATCAATTCCATGTTTCAAAAAAACATGGAGTGCATCGATGCATGGTCTTTGCATC
3518782 GGTACACAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
64 28 0.51
65 27 0.49
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (65 bp):
ATGCATAAAATCAATTCCATGTTTCAAAAAAACATGGAGTGCATCGATGCATGGTCTTTGCATCA
Found at i:3520540 original size:39 final size:39
Alignment explanation
Indices: 3520497--3520574 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
3520487 AGAAAAATTC
3520497 ATTGAAAAATCTCGGATTGAGAGGAATATGAC-GATGTTT
1 ATTGAAAAATCTCGGATTGAGAGGAATATG-CTGATGTTT
3520536 ATTGAAAAATCTCGGATTGAGAGGAATATGCTGATGTTT
1 ATTGAAAAATCTCGGATTGAGAGGAATATGCTGATGTTT
3520575 TGCACGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.32
Consensus pattern (39 bp):
ATTGAAAAATCTCGGATTGAGAGGAATATGCTGATGTTT
Found at i:3520732 original size:23 final size:22
Alignment explanation
Indices: 3520706--3520787 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
3520696 TTAAGACATT
3520706 GTGCATCGATGCACATTCAAGAA
1 GTGCATCGATGCACATTCAAG-A
* *
3520729 GTGCATCGGTGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAAGA
* * *
3520751 -TGTATCGATGCACATGCATAGT
1 GTGCATCGATGCACATTCA-AGA
3520773 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
3520788 CTTTATAGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 2 0.04
23 17 0.37
24 13 0.28
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGA
Found at i:3530886 original size:15 final size:16
Alignment explanation
Indices: 3530850--3530888 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3530840 TGAATCATTC
*
3530850 AATCATTCAGCATTTG
1 AATCATTCAGCACTTG
*
3530866 AATCATTCAGCGCTT-
1 AATCATTCAGCACTTG
3530881 AATCATTC
1 AATCATTC
3530889 TGAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (16 bp):
AATCATTCAGCACTTG
Found at i:3531055 original size:15 final size:16
Alignment explanation
Indices: 3531020--3531062 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
3531010 GATGACAAAT
*
3531020 TAATTTATTACACTCC
1 TAATTTATTACACTAC
3531036 TAATTTATTACA-TAC
1 TAATTTATTACACTAC
3531051 TAATTTATTACA
1 TAATTTATTACA
3531063 AATTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTATTACACTAC
Found at i:3531069 original size:15 final size:15
Alignment explanation
Indices: 3531014--3531069 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
3531004 TTATTGGATG
3531014 ACAAATTAATTTATT
1 ACAAATTAATTTATT
*
3531029 AC-ACTCCTAATTTATT
1 ACAAAT--TAATTTATT
* *
3531045 ACATACTAATTTATT
1 ACAAATTAATTTATT
3531060 ACAAATTAAT
1 ACAAATTAAT
3531070 AATATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 2 0.06
15 19 0.59
16 11 0.34
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (15 bp):
ACAAATTAATTTATT
Found at i:3561045 original size:27 final size:27
Alignment explanation
Indices: 3561011--3561063 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3561001 ATAGAGATGA
3561011 TTTGTTACCATTCCTATAAAGATATGG
1 TTTGTTACCATTCCTATAAAGATATGG
*
3561038 TTTGTTACCATTCCTATAGAGATATG
1 TTTGTTACCATTCCTATAAAGATATG
3561064 ATTTTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (27 bp):
TTTGTTACCATTCCTATAAAGATATGG
Found at i:3565395 original size:7 final size:7
Alignment explanation
Indices: 3565378--3565407 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3565368 TCAGAGGATA
3565378 TATGG-T
1 TATGGTT
3565384 TATGGTT
1 TATGGTT
3565391 TATGGTT
1 TATGGTT
3565398 TATGGTT
1 TATGGTT
3565405 TAT
1 TAT
3565408 AATTAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (7 bp):
TATGGTT
Found at i:3569521 original size:3 final size:3
Alignment explanation
Indices: 3569513--3569568 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
3569503 TTTTGTGCTA
*
3569513 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3569561 TAT TAT TA
1 TAT TAT TA
3569569 CAAACCCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3574557 original size:2 final size:2
Alignment explanation
Indices: 3574505--3574543 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3574495 CATATAAGTG
3574505 AT 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 AT A
3574544 ATAATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3577179 original size:55 final size:55
Alignment explanation
Indices: 3577104--3577542 Score: 298
Period size: 55 Copynumber: 8.3 Consensus size: 55
3577094 ATACTTGAAA
* *
3577104 AATCTTCAA-ATAACGGGTCTGCTCCCT-TTACTTTCAAGGAGTATAAGACTCGAAC
1 AATCTTCAACA-AACGGGTCTGCTCCCTATT-CATTCAAGGAGTATAAGACTCGAAT
** * * *
3577159 AATCCTT-GGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAT
1 AAT-CTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAT
* * *
3577214 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAT
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAT
*
3577269 AATCTTCAACAAACGGGTCTGCTCCCTATTCCTTC-AGAGAGTATAAGACTCG---
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAT
* ** * * *
3577321 -ATCTTCAATAAACGTATCCGCTCCCTATTCCTTC-AGAGAGTAT-AGAACTCGAAC
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAG-ACTCGAAT
* * ** * * *
3577375 AATCATCAACGAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATAGGACTC----
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAT
* ** * * *
3577426 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATAGGACTC----
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAT
* ** * * *
3577477 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATAGGACTC----
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAT
3577528 AATCTTCAACAAACG
1 AATCTTCAACAAACG
3577543 AGTTTGCTTC
Statistics
Matches: 346, Mismatches: 27, Indels: 26
0.87 0.07 0.07
Matches are distributed among these distances:
50 2 0.01
51 158 0.46
54 4 0.01
55 175 0.51
56 7 0.02
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (55 bp):
AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAT
Found at i:3577346 original size:51 final size:51
Alignment explanation
Indices: 3577168--3577542 Score: 437
Period size: 51 Copynumber: 7.1 Consensus size: 51
3577158 CAATCCTTGG
* * *
3577168 CAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAATAATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTTCAA
* * *
3577223 CAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTTCAA
* * *
3577278 CAAACGGGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAA
* * *
3577329 TAAACGTATCCGCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCATCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACT----CAATCTTCAA
* * *
3577384 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAA
* * *
3577435 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAA
* * *
3577486 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAA
3577537 CAAACG
1 CAAACG
3577543 AGTTTGCTTC
Statistics
Matches: 294, Mismatches: 20, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.01
51 157 0.53
55 134 0.46
56 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (51 bp):
CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAA
Found at i:3577384 original size:106 final size:106
Alignment explanation
Indices: 3577104--3577542 Score: 491
Period size: 106 Copynumber: 4.1 Consensus size: 106
3577094 ATACTTGAAA
* * *
3577104 AATCTTCAA-ATAACGGGTCTGCTCCCT-TTACTTTCA-AGGAGTATAAGACTCGAACAATCCTT
1 AATCTTCAACA-AACGTGTCCGCTCCCTATT-CCTTCAGA-GAGTATAAGACTCGAACAAT-CTT
** * * *
3577166 -GGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTC
62 CAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
* * * *
3577210 AAATAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTT
1 ----AATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTT
* *
3577275 CAACAAACGGGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
62 CAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
* * * *
3577320 GATCTTCAATAAACGTATCCGCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCATCAA
1 AATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAA
* * *
3577384 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
65 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
* * *
3577426 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAAC
1 AATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
3577487 GAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
66 AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
3577528 AATCTTCAACAAACG
1 AATCTTCAACAAACG
3577543 AGTTTGCTTC
Statistics
Matches: 292, Mismatches: 31, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
102 64 0.22
105 2 0.01
106 132 0.45
107 1 0.00
109 3 0.01
110 87 0.30
111 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (106 bp):
AATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
Found at i:3577577 original size:157 final size:154
Alignment explanation
Indices: 3577168--3577559 Score: 374
Period size: 157 Copynumber: 2.5 Consensus size: 154
3577158 CAATCCTTGG
* * * * * * *
3577168 CAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAATAATCTTCAACAAACGTGT
1 CAAACGTATCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACT---ACAATCATCAACAAACGAGT
* * * * * * *
3577232 CTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACGGGTCTGCTCCCTA
62 CCGCTCACTACTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACGGGTCCGCTCCCTA
*
3577297 TTCCTTCAGAGAGTATAAGACTCGATCTTCAA
123 TTCCTTCAGAGAGTATAAGACTCAATCTTCAA
* * **
3577329 TAAACGTATCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCATCAACGAACTTGTC
1 CAAACGTATCCGCTCCCTATTCCTTCAGAGAGTATAGAACT---ACAATCATCAACAAACGAGTC
* * * **
3577394 CGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCT
63 CGCTCACTACTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGGGTCCGCTCCCTATTCCT
*
3577459 TCAGAGAGTATAGGACTCAATCTTCAA
128 TCAGAGAGTATAAGACTCAATCTTCAA
* * * * * **
3577486 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACAAACGAGTTTGC
1 CAAACGTATCCGCTCCCTATTCCTTCAGAGAGTATAGAACTACAATCATCAACAAACGAGTCCGC
3577550 TTCACTACTC
66 -TCACTACTC
3577560 TTTCGTGAAG
Statistics
Matches: 196, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
153 17 0.09
154 7 0.04
157 90 0.46
161 81 0.41
162 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (154 bp):
CAAACGTATCCGCTCCCTATTCCTTCAGAGAGTATAGAACTACAATCATCAACAAACGAGTCCGC
TCACTACTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCA
GAGAGTATAAGACTCAATCTTCAA
Found at i:3578920 original size:7 final size:7
Alignment explanation
Indices: 3578837--3578986 Score: 54
Period size: 8 Copynumber: 19.9 Consensus size: 7
3578827 ATTTCTCTTT
3578837 TTTTTTC
1 TTTTTTC
3578844 ATTTTTCTC
1 -TTTTT-TC
3578853 TTTTTTC
1 TTTTTTC
* *
3578860 ATTTTCC
1 TTTTTTC
* *
3578867 ATTTTCC
1 TTTTTTC
3578874 ATTTTTTC
1 -TTTTTTC
*
3578882 TTCTTTC
1 TTTTTTC
3578889 TTCTTTTC
1 TT-TTTTC
3578897 GTTTTTTCC
1 -TTTTTT-C
3578906 ATCATTTTTC
1 -T--TTTTTC
3578916 TTTTTTTC
1 -TTTTTTC
**
3578924 TCATTT-
1 TTTTTTC
*
3578930 TTTCTTC
1 TTTTTTC
3578937 -TTTTTC
1 TTTTTTC
*
3578943 TTCTTCTC
1 TT-TTTTC
* *
3578951 ATTTTTA
1 TTTTTTC
3578958 TTATTATT-
1 TT-TT-TTC
3578966 TTTTTTC
1 TTTTTTC
3578973 ATTTTTTC
1 -TTTTTTC
3578981 TTTTTT
1 TTTTTT
3578987 TCTCTTTTAT
Statistics
Matches: 109, Mismatches: 19, Indels: 29
0.69 0.12 0.18
Matches are distributed among these distances:
6 10 0.09
7 39 0.36
8 45 0.41
9 8 0.07
10 2 0.02
11 5 0.05
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTTTC
Found at i:3578920 original size:19 final size:19
Alignment explanation
Indices: 3578892--3578942 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3578882 TTCTTTCTTC
*
3578892 TTTTCGTTTTTTCCATCA-T
1 TTTTCTTTTTTTCC-TCATT
3578911 TTTTCTTTTTTT-CTCATT
1 TTTTCTTTTTTTCCTCATT
3578929 TTTTCTTCTTTTTC
1 TTTTCTT-TTTTTC
3578943 TTCTTCTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 9 0.32
19 16 0.57
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTCTTTTTTTCCTCATT
Found at i:3578967 original size:54 final size:54
Alignment explanation
Indices: 3578867--3579005 Score: 135
Period size: 54 Copynumber: 2.6 Consensus size: 54
3578857 TTCATTTTCC
* *
3578867 ATTTTC-CATTTTTTCTTC--TTTCTTCTTTTCGTTTTTTCCATCATTTTTCTTT
1 ATTTTCTCATTTTTTCTTCTTTTTCTTCTTCTCATTTTTTCCATCATTTTT-TTT
* *
3578919 -TTTTCTCATTTTTTCTTCTTTTTCTTCTTCTCATTTTTAT-TATTATTTTTTTT
1 ATTTTCTCATTTTTTCTTCTTTTTCTTCTTCTCATTTTT-TCCATCATTTTTTTT
* * *
3578972 CATTTTTTCTTTTTTTCTCTTTTATTTCTTCTTC
1 -ATTTTCTCATTTTTTCT-TCTT-TTTCTTCTTC
3579006 AAGCGAAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
51 5 0.07
52 12 0.17
53 3 0.04
54 24 0.33
55 15 0.21
56 3 0.04
57 10 0.14
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.73
Consensus pattern (54 bp):
ATTTTCTCATTTTTTCTTCTTTTTCTTCTTCTCATTTTTTCCATCATTTTTTTT
Found at i:3579001 original size:9 final size:9
Alignment explanation
Indices: 3578910--3579001 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 9
3578900 TTTTCCATCA
3578910 TTTTTCTTT
1 TTTTTCTTT
3578919 TTTTCTCATTT
1 TTTT-TC-TTT
3578930 TTTCTTCTTT
1 TTT-TTCTTT
*
3578940 TTCTTCTTCT
1 TTTTTCTT-T
** *
3578950 CATTT-TTA
1 TTTTTCTTT
* *
3578958 TTATTATTT
1 TTTTTCTTT
*
3578967 TTTTTC-AT
1 TTTTTCTTT
3578975 TTTTTCTTT
1 TTTTTCTTT
3578984 TTTTCTCTTT
1 TTTT-TCTTT
*
3578994 TATTTCTT
1 TTTTTCTT
3579002 CTTCAAGCGA
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
8 9 0.15
9 26 0.42
10 18 0.29
11 8 0.13
12 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3588697 original size:45 final size:47
Alignment explanation
Indices: 3588629--3588717 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
3588619 TGCTTTGTTA
3588629 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
*
3588676 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
3588718 ATTTATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:3600554 original size:23 final size:24
Alignment explanation
Indices: 3600528--3600577 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3600518 AGGGATTTAC
* *
3600528 AGTGGTCTTTCGGGAC-ATTTCAT
1 AGTGGTCCTTCAGGACAATTTCAT
3600551 AGTGGTCCTTCAGGACAAATTTCAT
1 AGTGGTCCTTCAGGAC-AATTTCAT
3600576 AG
1 AG
3600578 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (24 bp):
AGTGGTCCTTCAGGACAATTTCAT
Found at i:3601183 original size:19 final size:19
Alignment explanation
Indices: 3601159--3601206 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3601149 GAATATGCTA
3601159 TGATCAATTTTGGTTATTT
1 TGATCAATTTTGGTTATTT
3601178 TGATCAATTTTGGTTATTT
1 TGATCAATTTTGGTTATTT
*
3601197 TGGTCAATTT
1 TGATCAATTT
3601207 ATATAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.56
Consensus pattern (19 bp):
TGATCAATTTTGGTTATTT
Found at i:3603547 original size:2 final size:2
Alignment explanation
Indices: 3603540--3603580 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3603530 ACGTTATTAC
3603540 AT AT 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 AT AT A
3603581 CTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3609684 original size:24 final size:24
Alignment explanation
Indices: 3609657--3609723 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3609647 AAAGGAATTT
* *
3609657 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTATGCGATCCTTCGGGACAAA
3609681 TTCTATGCGATCCTTCGGGACAAA
1 TTCTATGCGATCCTTCGGGACAAA
*
3609705 TTTCTACGCGA-CACTTCGG
1 -TTCTATGCGATC-CTTCGG
3609724 TGCAAAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCTATGCGATCCTTCGGGACAAA
Found at i:3609729 original size:25 final size:25
Alignment explanation
Indices: 3609707--3609778 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
3609697 GGGACAAATT
3609707 TCTACGCGACACTTCGGTGCAAAAC
1 TCTACGCGACACTTCGGTGCAAAAC
* *
3609732 TCTACGTGGCACTTCGGTGCAAAAC
1 TCTACGCGACACTTCGGTGCAAAAC
*
3609757 TCTATGCGACACTTCGGTGCAA
1 TCTACGCGACACTTCGGTGCAA
3609779 TTTATATGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (25 bp):
TCTACGCGACACTTCGGTGCAAAAC
Found at i:3612968 original size:22 final size:22
Alignment explanation
Indices: 3612926--3612968 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3612916 TTCTGGGCTA
*
3612926 GGGGAATCAGTACCCATTCAAG
1 GGGGAATCAGTACCCACTCAAG
*
3612948 GGGGAATC-GATACCCCCTCAA
1 GGGGAATCAG-TACCCACTCAA
3612969 CCGAACCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGGAATCAGTACCCACTCAAG
Found at i:3614705 original size:25 final size:25
Alignment explanation
Indices: 3614669--3614735 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
3614659 CTATGTGGTT
*
3614669 CTTCGG-GACAAATTTATACGCGGTA
1 CTTCGGTG-CAAATTTATACGCGGCA
** * *
3614694 CTTCGGTGCAAAACTCTATGCGGCA
1 CTTCGGTGCAAATTTATACGCGGCA
3614719 CTTCGGTGC-AATTTATA
1 CTTCGGTGCAAATTTATA
3614736 TGAGCTGTGG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
24 5 0.15
25 27 0.82
26 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (25 bp):
CTTCGGTGCAAATTTATACGCGGCA
Found at i:3619723 original size:29 final size:29
Alignment explanation
Indices: 3619681--3619738 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3619671 CATACCACTT
3619681 GGCTAATTTCCAAGTTAGATCCCCTGAAG
1 GGCTAATTTCCAAGTTAGATCCCCTGAAG
3619710 GGCTAATTTCCAAGTTAGATCCCCTGAAG
1 GGCTAATTTCCAAGTTAGATCCCCTGAAG
3619739 TACATTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (29 bp):
GGCTAATTTCCAAGTTAGATCCCCTGAAG
Found at i:3621745 original size:7 final size:7
Alignment explanation
Indices: 3621728--3621791 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
3621718 CTTAAGTCGA
*
3621728 AAAAAAT
1 AAAAAAC
*
3621735 AAAAATAA
1 AAAAA-AC
*
3621743 AAAAAAT
1 AAAAAAC
3621750 AAAAAAC
1 AAAAAAC
3621757 --AAAAC
1 AAAAAAC
3621762 AAAAAAC
1 AAAAAAC
3621769 AAAACAAAAC
1 --AA-AAAAC
3621779 AAAAAAC
1 AAAAAAC
3621786 AAAAAA
1 AAAAAA
3621792 GAGAAAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.10
7 28 0.58
8 8 0.17
9 2 0.04
10 5 0.10
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (7 bp):
AAAAAAC
Found at i:3621755 original size:17 final size:16
Alignment explanation
Indices: 3621727--3621790 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
3621717 TCTTAAGTCG
* *
3621727 AAAAAAATAAAAATAA
1 AAAAAAAAAAAAACAA
*
3621743 AAAAAATAAAAAACAA
1 AAAAAAAAAAAAACAA
*
3621759 AACAAAAAACAAAACAA
1 AA-AAAAAAAAAAACAA
3621776 AACAAAAAACAAAAA
1 AA-AAAAAA-AAAAA
3621791 AGAGAAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
16 15 0.38
17 21 0.52
18 4 0.10
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:3621760 original size:12 final size:11
Alignment explanation
Indices: 3621727--3621791 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 11
3621717 TCTTAAGTCG
3621727 AAAAAAATAAA-
1 AAAAAAA-AAAC
*
3621738 AATAAAAAAAAT
1 AA-AAAAAAAAC
3621750 AAAAAACAAAAC
1 AAAAAA-AAAAC
3621762 AAAAAACAAAAC
1 AAAAAA-AAAAC
3621774 AAAACAAAAAAC
1 AAAA-AAAAAAC
3621786 AAAAAA
1 AAAAAA
3621792 GAGAAAAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
11 11 0.22
12 36 0.73
13 2 0.04
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:3621799 original size:17 final size:17
Alignment explanation
Indices: 3621752--3621789 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3621742 AAAAAAATAA
3621752 AAAACAAAACAAAAAAC
1 AAAACAAAACAAAAAAC
3621769 AAAACAAAACAAAAAAC
1 AAAACAAAACAAAAAAC
3621786 AAAA
1 AAAA
3621790 AAGAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACAAAACAAAAAAC
Found at i:3621884 original size:13 final size:15
Alignment explanation
Indices: 3621857--3621888 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3621847 GAAAAAATAG
3621857 AAAAAGAACAGAAGA
1 AAAAAGAACAGAAGA
3621872 AAAAAGAA-A-AAGA
1 AAAAAGAACAGAAGA
3621885 AAAA
1 AAAA
3621889 TAAGGTCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAACAGAAGA
Found at i:3625114 original size:3 final size:3
Alignment explanation
Indices: 3625106--3625139 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3625096 TTTAGTCCCT
3625106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3625140 AAGTATTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3625197 original size:17 final size:18
Alignment explanation
Indices: 3625158--3625200 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3625148 GCTCATTTCG
*
3625158 TTTTTTATTATTACTTAC
1 TTTTTTACTATTACTTAC
* *
3625176 CTTTTTACTATTA-TTAT
1 TTTTTTACTATTACTTAC
3625193 TTTTTTAC
1 TTTTTTAC
3625201 CCTACACGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTACTATTACTTAC
Found at i:3625244 original size:12 final size:12
Alignment explanation
Indices: 3625227--3625265 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3625217 TATATATATA
3625227 TATAACTATTAT
1 TATAACTATTAT
**
3625239 TATAACTATTGC
1 TATAACTATTAT
*
3625251 TATCACTATTAT
1 TATAACTATTAT
3625263 TAT
1 TAT
3625266 TATTATTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (12 bp):
TATAACTATTAT
Found at i:3625310 original size:2 final size:2
Alignment explanation
Indices: 3625297--3625395 Score: 189
Period size: 2 Copynumber: 49.5 Consensus size: 2
3625287 TATGGATGTT
*
3625297 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3625339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3625381 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3625396 TAATATTTCT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3627611 original size:3 final size:3
Alignment explanation
Indices: 3627605--3627654 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
3627595 GAAAAAAATA
*
3627605 AAT AAT AAT AAAT AAT AAT AAT AAT GAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
3627652 AAT
1 AAT
3627655 GTATCCTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 38 0.88
4 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3627629 original size:19 final size:19
Alignment explanation
Indices: 3627605--3627653 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3627595 GAAAAAAATA
3627605 AATAATAATAAATAATAAT
1 AATAATAATAAATAATAAT
*
3627624 AATAATGATAAATAATAAT
1 AATAATAATAAATAATAAT
3627643 AATAATAATAA
1 AATAATAATAA
3627654 TGTATCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAATAATAAATAATAAT
Found at i:3627805 original size:36 final size:36
Alignment explanation
Indices: 3627763--3627917 Score: 125
Period size: 36 Copynumber: 4.3 Consensus size: 36
3627753 TTATTTTAAA
*
3627763 ATATTATATAAGTTAAAAAAATGTTTTTAAAATTAT
1 ATATTATATAAGTTAAAAAAATGTTTTAAAAATTAT
* * **
3627799 AAATTATATAATTTTCCAAAAA--TTTTAAAAATCTAT
1 ATATTATATAA-GTTAAAAAAATGTTTTAAAAAT-TAT
* *** * *
3627835 ATACTATATAAGTTTTCAAAATGTGTTAAAAACTAT
1 ATATTATATAAGTTAAAAAAATGTTTTAAAAATTAT
*** * *
3627871 ATATTATATAAGTTTTCAAAATATTTTAAAAACTAT
1 ATATTATATAAGTTAAAAAAATGTTTTAAAAATTAT
*
3627907 ATAATATATAA
1 ATATTATATAA
3627918 ATGTTTTCAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
35 15 0.15
36 68 0.69
37 15 0.15
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (36 bp):
ATATTATATAAGTTAAAAAAATGTTTTAAAAATTAT
Found at i:3627846 original size:72 final size:72
Alignment explanation
Indices: 3627726--3627917 Score: 199
Period size: 72 Copynumber: 2.8 Consensus size: 72
3627716 AAAAATTTCC
3627726 AAAACTAT--ATTATAT-AGTTTTCAAAATTTATTTT--AAA--ATAT--TATATAAGTTAAAAA
1 AAAACTATAAATTATATAAGTTTTCAAAA--TATTTTAAAAACTATATAATATATAAGTTAAAAA
* *
3627782 AATGTTTTT
64 AATGTGTTA
* * ***
3627791 AAAATTATAAATTATATAA-TTTTCCAAAA-ATTTTAAAAATCTATATACTATATAAGTTTTCAA
1 AAAACTATAAATTATATAAGTTTT-CAAAATATTTTAAAAA-CTATATAATATATAAGTTAAAAA
3627854 AATGTGTTA
64 AATGTGTTA
*
3627863 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAA
1 AAAACTATAAATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAA
3627918 ATGTTTTCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
65 12 0.11
67 14 0.13
68 6 0.06
70 4 0.04
72 55 0.52
73 14 0.13
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (72 bp):
AAAACTATAAATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAAGTTAAAAAAA
TGTGTTA
Found at i:3627934 original size:63 final size:63
Alignment explanation
Indices: 3627853--3627977 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
3627843 TAAGTTTTCA
*
3627853 AAATGTGTTAAAAACTATATATTATATA-AGTTTTCAAAATATTTT-AAAAACTATATAATATAT
1 AAATGTGTTAAAAACTATATATTATATATA-TTTTC-AAATATTTTCAAAAACCATATAATATAT
* *
3627916 AAATGTTTTCAAAACTATATATTATATATATTTTCAAATATTTTCAAAAACCATATAATATA
1 AAATGTGTTAAAAACTATATATTATATATATTTTCAAATATTTTCAAAAACCATATAATATA
3627978 CAAACTTTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
62 9 0.16
63 47 0.82
64 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (63 bp):
AAATGTGTTAAAAACTATATATTATATATATTTTCAAATATTTTCAAAAACCATATAATATAT
Found at i:3627941 original size:25 final size:27
Alignment explanation
Indices: 3627889--3627953 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
3627879 TAAGTTTTCA
*
3627889 AAATATTTTAAAAACTATATAATATAT
1 AAATATTTTCAAAACTATATAATATAT
*
3627916 AAATGTTTTCAAAACTATAT-AT-TAT
1 AAATATTTTCAAAACTATATAATATAT
*
3627941 ATATATTTTCAAA
1 AAATATTTTCAAA
3627954 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 14 0.41
26 2 0.06
27 18 0.53
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATATTTTCAAAACTATATAATATAT
Found at i:3627966 original size:36 final size:34
Alignment explanation
Indices: 3627781--3627977 Score: 167
Period size: 36 Copynumber: 5.8 Consensus size: 34
3627771 TAAGTTAAAA
* * * *
3627781 AAATGTTTTTAAAATTATAAATTATATAATTTTCC
1 AAATATTTTAAAAACTATATATTATATAATTTT-C
* *
3627816 AAAAATTTTAAAAATCTATATACTATATAAGTTTTC
1 AAATATTTTAAAAA-CTATATATTATATAA-TTTTC
3627852 AAA-ATGTGTTAAAAACTATATATTATATAAGTTTTC
1 AAATAT-T-TTAAAAACTATATATTATATAA-TTTTC
3627888 AAAATATTTTAAAAACTATATA--ATAT-A---T-
1 -AAATATTTTAAAAACTATATATTATATAATTTTC
* *
3627916 AAATGTTTTCAAAACTATATATTATATATATTTTC
1 AAATATTTTAAAAACTATATATTATATA-ATTTTC
* *
3627951 AAATATTTTCAAAAACCATATAATATA
1 AAATATTTT-AAAAACTATATATTATA
3627978 CAAACTTTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 29
0.76 0.07 0.16
Matches are distributed among these distances:
27 19 0.14
29 5 0.04
31 1 0.01
33 1 0.01
34 5 0.04
35 21 0.16
36 65 0.49
37 15 0.11
38 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (34 bp):
AAATATTTTAAAAACTATATATTATATAATTTTC
Found at i:3627987 original size:36 final size:35
Alignment explanation
Indices: 3627916--3627989 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 35
3627906 TATAATATAT
* * * * * *
3627916 AAATGTTTTCAAAACTATATATTATATATATTTTC
1 AAATATTTTCAAAACCATATAATATACAAACTTTC
3627951 AAATATTTTCAAAAACCATATAATATACAAACTTTC
1 AAATATTTTC-AAAACCATATAATATACAAACTTTC
3627987 AAA
1 AAA
3627990 AATCATTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (35 bp):
AAATATTTTCAAAACCATATAATATACAAACTTTC
Found at i:3628063 original size:2 final size:2
Alignment explanation
Indices: 3628051--3628092 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3628041 ACTATATTAC
*
3628051 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3628093 AAACAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3629099 original size:248 final size:245
Alignment explanation
Indices: 3628677--3629533 Score: 1018
Period size: 248 Copynumber: 3.5 Consensus size: 245
3628667 TGTACCTTGG
* * * * * *
3628677 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTCCTAGCCTTGAGTTATGTT
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAAGCTATGCT
* * ** *
3628742 GTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCT
63 GCAAATGATATGCCCTCG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCT
* *
3628807 CAACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
127 CGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
* *
3628872 GTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGG
192 GTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGA
* * *
3628925 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCT
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAAGCTATGCT
** * ** *
3628990 GTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCTCTTCT
63 GCAAATGATATGCCCTCG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCT
3629055 CGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
127 CGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
* *
3629120 GTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCTCGA
192 GTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGA
* ** * *
3629174 AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACTCTTCTCGACTTAAGCTATGCTGCA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCA
* * * * * * * *
3629239 AATGATGTGTCATTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCT
66 AATGATATGCCCTCGAGCTGAGCGTAATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCT
* * * * * *
3629304 AGACTTAAGTTGTGCTACAAATGATATGTC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT
127 CGACTTAAGCTATGCTGCAAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
* * * * * **
3629367 TGGTGACAGATAACCCTTCTATACTTGAGTTATGCTGTGAATGATATGCCCTCGA
191 TGTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGA
* * ** * *
3629422 AGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCA
* * * *
3629487 AATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
66 AATGATATGCCCTCGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG
3629534 TTGGCAAATA
Statistics
Matches: 548, Mismatches: 55, Indels: 16
0.89 0.09 0.03
Matches are distributed among these distances:
244 4 0.01
245 23 0.04
246 38 0.07
247 1 0.00
248 385 0.70
249 97 0.18
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (245 bp):
AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCA
AATGATATGCCCTCGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGAC
TTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTG
ACAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGA
Found at i:3629193 original size:165 final size:165
Alignment explanation
Indices: 3628877--3629369 Score: 731
Period size: 165 Copynumber: 3.0 Consensus size: 165
3628867 CTTTTGTTGA
* * * * * * *
3628877 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATT-GAGCTGAGCGTAGTCGA
* * * * * * ***
3628941 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTGAATGATATGCCC
65 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCC
3629005 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
130 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
3629041 CAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGCGTAGTCGAA
3629106 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCT
3629171 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
3629206 CAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGCGTAGTCGAA
1 CAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGCGTAGTCGAA
*
3629271 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATG-TCT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCT
* * * * **
3629335 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
3629370 TGACAGATAA
Statistics
Matches: 301, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
164 93 0.31
165 208 0.69
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (165 bp):
CAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCT
CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:3629228 original size:413 final size:413
Alignment explanation
Indices: 3628651--3629539 Score: 1494
Period size: 413 Copynumber: 2.2 Consensus size: 413
3628641 CTTGCTTTGG
* * * * *
3628651 GCTATGTTGTAAATGATGTACC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
1 GCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
* * * * **
3628714 GATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
65 GACAACCCTCCTAGACTTAAGTTATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
* * *
3628779 TCGGGGGTCTTTGGTAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
130 TCGGGGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCATTGAGC
*
3628844 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTGC
195 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTAC
3628909 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
260 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
3628974 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
325 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
3629039 GGCAGATAGCTCTTCTCGACTTAA
390 GGCAGATAGCCCTTCTCGACTTAA
* *
3629063 GCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAG
1 GCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAG
* *
3629128 ACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
66 ACAACCCTCCTAGACTTAAGTTATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
* * *
3629193 CGGGGGTCTTTGGCAGATAACTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCT
131 CGGGGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCATTGAGCT
*
3629258 GAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACA
196 GAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTACA
*
3629323 AATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTA
261 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTA
* *
3629388 TACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTG
326 GACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
3629453 GCAGATAGCCCTTCTCGACTTAA
391 GCAGATAGCCCTTCTCGACTTAA
* *
3629476 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 GCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
3629540 AATAGCCCAT
Statistics
Matches: 444, Mismatches: 31, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
412 45 0.10
413 399 0.90
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (413 bp):
GCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAG
ACAACCCTCCTAGACTTAAGTTATGCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
CGGGGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCATTGAGCT
GAGCGTAGTCGAACTCAAAGGTCTTTTGTTGACAGACAACCCTTCTAGACTTAAGTTGTGCTACA
AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTA
GACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
GCAGATAGCCCTTCTCGACTTAA
Found at i:3633014 original size:18 final size:19
Alignment explanation
Indices: 3632974--3633018 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3632964 AGTTAATGTG
3632974 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
3632993 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
3633011 AATGCAAA
1 AATGCAAA
3633019 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:3633655 original size:17 final size:17
Alignment explanation
Indices: 3633629--3633661 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3633619 TGCAAACGAT
*
3633629 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
3633646 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
3633662 TGAGGTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:3634860 original size:4 final size:4
Alignment explanation
Indices: 3634851--3634885 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
3634841 AAAAGAAAAG
*
3634851 AAAT AAAT AAAT ATA- AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3634886 TATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:3634873 original size:19 final size:19
Alignment explanation
Indices: 3634827--3634882 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
3634817 AAAGTAAATC
* * *
3634827 AAAGAAATAAAAGAAAAAGA
1 AAAGAAAT-AAATAAATATA
3634847 AAAGAAATAAATAAATATA
1 AAAGAAATAAATAAATATA
*
3634866 AAATAAATAAATAAATA
1 AAAGAAATAAATAAATA
3634883 AATTATTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAGAAATAAATAAATATA
Found at i:3634970 original size:20 final size:21
Alignment explanation
Indices: 3634924--3634971 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3634914 TATGAAGTAA
* *
3634924 AAAT-AAACAATGTTAGTACT
1 AAATAAAACAATGTTAATAAT
*
3634944 AATTAAAAC-ATGTTAATAAT
1 AAATAAAACAATGTTAATAAT
3634964 AAATAAAA
1 AAATAAAA
3634972 TAAGACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATAAAACAATGTTAATAAT
Found at i:3636110 original size:10 final size:10
Alignment explanation
Indices: 3636095--3636123 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3636085 AACAAAAAAA
3636095 AATAAATAAT
1 AATAAATAAT
3636105 AATAAATAAT
1 AATAAATAAT
3636115 AAT-AATAAT
1 AATAAATAAT
3636124 GTATCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAAATAAT
Found at i:3636117 original size:13 final size:14
Alignment explanation
Indices: 3636094--3636122 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3636084 AAACAAAAAA
3636094 AAATAAATAATAAT
1 AAATAAATAATAAT
3636108 AAAT-AATAATAAT
1 AAATAAATAATAAT
3636121 AA
1 AA
3636123 TGTATCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:3636247 original size:36 final size:36
Alignment explanation
Indices: 3636207--3636604 Score: 254
Period size: 36 Copynumber: 10.9 Consensus size: 36
3636197 TTTCCAAAAC
3636207 TATATTATAT-AGTTTTCAAAAT-TTATTT----TAA
1 TATATTATATAAGTTTTCAAAATGTT-TTTAAAATAA
* *** *
3636238 AATATTATATAAGTTAAAAAAATGTTTTTTAAAATTA
1 TATATTATATAAGTTTTCAAAATG-TTTTTAAAATAA
* *
3636275 TATATTATATAATTTTTAAAAAATGTTTTTAAAACT-A
1 TATATTATATAAGTTTT-CAAAATGTTTTTAAAA-TAA
* * *
3636312 TATGTTATATAATTTTTCAAAAAAAAATGTTTTTAAAATTA
1 TATATTATATAAGTTTTC-----AAAATGTTTTTAAAATAA
* *
3636353 TATATTATATAATTTTTCAAAA--ATTTTAAAA-AA
1 TATATTATATAAGTTTTCAAAATGTTTTTAAAATAA
* *
3636386 CTATATACTATATAAGTTTTCAAAATGTGTTAAAAACT-A
1 -TATAT--TATATAAGTTTTCAAAATGTTTTTAAAA-TAA
* *
3636425 TATATTATATAAGTTTTCAAAATATTTTAAAAACT-A
1 TATATTATATAAGTTTTCAAAATGTTTTTAAAA-TAA
* * *
3636461 TATAATATATAAATGTTTTCAAAATGTGTTAAAAACT-A
1 TATATTATAT-AA-GTTTTCAAAATGTTTTTAAAA-TAA
* *
3636499 TATATTATATAAGTTTTCAAAATATTTTAAAAACT-A
1 TATATTATATAAGTTTTCAAAATGTTTTTAAAA-TAA
* *
3636535 TATAATATATAAATGTTTTCAAAATGTTTTCAAAACT-A
1 TATATTATAT-AA-GTTTTCAAAATGTTTTTAAAA-TAA
* *
3636573 TATATTATATATA-TTTT-AAAATATTTTCAAAA
1 TATATTATATA-AGTTTTCAAAATGTTTTTAAAA
3636605 ACCATATAAT
Statistics
Matches: 309, Mismatches: 31, Indels: 50
0.79 0.08 0.13
Matches are distributed among these distances:
31 9 0.03
32 9 0.03
33 4 0.01
34 15 0.05
35 14 0.05
36 93 0.30
37 48 0.16
38 82 0.27
39 1 0.00
40 1 0.00
41 33 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATTATATAAGTTTTCAAAATGTTTTTAAAATAA
Found at i:3636334 original size:38 final size:36
Alignment explanation
Indices: 3636256--3636617 Score: 379
Period size: 36 Copynumber: 9.8 Consensus size: 36
3636246 ATAAGTTAAA
* * *
3636256 AAAATGTTTTTTAAAATTATATATTATATAATTTTTAA
1 AAAATG-TTTTAAAAACTATATATTATATAATTTTT-C
* *
3636294 AAAATGTTTTTAAAACTATATGTTATATAATTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
3636330 AAAAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
1 -----AAAATGTTTTAAAAACTATATATTATATAATTTTTC
* * *
3636371 AAAAAT-TTTAAAAAACTATATACTATATAAGTTTTC
1 -AAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
3636407 AAAATGTGTTAAAAACTATATATTATATAAGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
3636443 AAAATATTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATATATTATAT-AAT-TTTTC
* *
3636481 AAAATGTGTTAAAAACTATATATTATATAAGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAATTTTTC
* *
3636517 AAAATATTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATATATTATAT-AAT-TTTTC
*
3636555 AAAATGTTTTCAAAACTATATATTATAT-ATATTTT-
1 AAAATGTTTTAAAAACTATATATTATATAAT-TTTTC
* * *
3636590 AAAATATTTTCAAAAACCATATAATATA
1 AAAATGTTTT-AAAAACTATATATTATA
3636618 CAAACTTTCA
Statistics
Matches: 280, Mismatches: 33, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
35 14 0.05
36 127 0.45
37 39 0.14
38 66 0.24
41 34 0.12
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAATTTTTC
Found at i:3636349 original size:41 final size:41
Alignment explanation
Indices: 3636253--3636375 Score: 191
Period size: 41 Copynumber: 3.1 Consensus size: 41
3636243 TATATAAGTT
3636253 AAAAAAATGTTTTTTAAAATTATATATTATATAATTTTT---
1 AAAAAAATG-TTTTTAAAATTATATATTATATAATTTTTCAA
* *
3636292 -AAAAAATGTTTTTAAAACTATATGTTATATAATTTTTCAA
1 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTCAA
3636332 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTCAA
1 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTCAA
3636373 AAA
1 AAA
3636376 TTTTAAAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
37 27 0.36
38 8 0.11
41 41 0.54
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (41 bp):
AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTCAA
Found at i:3636495 original size:74 final size:73
Alignment explanation
Indices: 3636268--3636617 Score: 431
Period size: 74 Copynumber: 4.7 Consensus size: 73
3636258 AATGTTTTTT
* * * * * **
3636268 AAAATTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATGTTATATAAT-TTTTCAA
1 AAAACTATATATTATATAAGTTTT-CAAAATATTTTAAAAACTATATAATATATAATGTTTTC--
* *
3636332 AAAAAAATGTTTTT
63 ---AAAATGTGTTA
* * *
3636346 AAAATTATATATTATATAATTTTTCAAAA-ATTTTAAAAAACTATATACTATATAA-GTTTTCAA
1 AAAACTATATATTATATAAGTTTTCAAAATATTTT-AAAAACTATATAATATATAATGTTTTCAA
3636409 AATGTGTTA
65 AATGTGTTA
3636418 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAAATGTTTTCAA
1 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATAT-AATGTTTTCAA
3636483 AATGTGTTA
65 AATGTGTTA
3636492 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAAATGTTTTCAA
1 AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATAT-AATGTTTTCAA
* *
3636557 AATGTTTTC
65 AATGTGTTA
*
3636566 AAAACTATATATTATATATA-TTTT-AAAATATTTTCAAAAACCATATAATATA
1 AAAACTATATATTATATA-AGTTTTCAAAATATTTT-AAAAACTATATAATATA
3636618 CAAACTTTCA
Statistics
Matches: 252, Mismatches: 13, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
72 53 0.21
73 17 0.07
74 127 0.50
75 1 0.00
76 4 0.02
77 26 0.10
78 24 0.10
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (73 bp):
AAAACTATATATTATATAAGTTTTCAAAATATTTTAAAAACTATATAATATATAATGTTTTCAAA
ATGTGTTA
Found at i:3636561 original size:11 final size:11
Alignment explanation
Indices: 3636545--3636569 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3636535 TATAATATAT
3636545 AAATGTTTTCA
1 AAATGTTTTCA
3636556 AAATGTTTTCA
1 AAATGTTTTCA
3636567 AAA
1 AAA
3636570 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:3636651 original size:74 final size:72
Alignment explanation
Indices: 3636335--3636658 Score: 291
Period size: 74 Copynumber: 4.4 Consensus size: 72
3636325 TTTTCAAAAA
* * * * *
3636335 AAAATGTTTTTAAAATTATATATTATATA-ATTTTTCAAAA-ATTTTAAAAAACTATATACTATA
1 AAAATATTTTCAAAACTATATATTATATATA-TTTT-AAAATATTTT-AAAAACCATATAATATA
* *
3636398 -TAAGTTTTC
63 CAAAGCTTTC
* * * * *
3636407 AAAATGTGTTAAAAACTATATATTATATA-AGTTTTCAAAATATTTTAAAAACTATATAATATAT
1 AAAATATTTTCAAAACTATATATTATATATA-TTTT-AAAATATTTTAAAAACCATATAATATAC
*
3636471 AAATGTTTTC
64 AAA-GCTTTC
* * * * *
3636481 AAAATGTGTTAAAAACTATATATTATATA-AGTTTTCAAAATATTTTAAAAACTATATAATATAT
1 AAAATATTTTCAAAACTATATATTATATATA-TTTT-AAAATATTTTAAAAACCATATAATATAC
*
3636545 AAATGTTTTC
64 AAA-GCTTTC
*
3636555 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAATATTTTCAAAAACCATATAATATACA
1 AAAATATTTTCAAAACTATATATTATATATATTTTAAAATATTTT-AAAAACCATATAATATACA
3636620 AA-CTTTC
65 AAGCTTTC
*
3636627 AAAAATCATTTTCTGAAAATTATATATTATAT
1 -AAAAT-ATTTTC--AAAACTATATATTATAT
3636659 TTTATCAAAA
Statistics
Matches: 230, Mismatches: 13, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
72 56 0.24
73 22 0.10
74 135 0.59
75 1 0.00
76 16 0.07
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (72 bp):
AAAATATTTTCAAAACTATATATTATATATATTTTAAAATATTTTAAAAACCATATAATATACAA
AGCTTTC
Found at i:3638896 original size:52 final size:53
Alignment explanation
Indices: 3638747--3638926 Score: 186
Period size: 53 Copynumber: 3.4 Consensus size: 53
3638737 TTTTAGGTAC
* * * * * * *
3638747 TAAGATATTGGGAGATGTACCTACTTACA-CAGATATAAGTACGTGTTAACTGT
1 TAAGATATTGAGAGATATACATACTCACACCTG-TATAAGTATGTGTTAATTGT
* * *
3638800 TAAGATATTGAGAGATATACATACTCACGCTTGTATAAGTATGTGTTGATT-T
1 TAAGATATTGAGAGATATACATACTCACACCTGTATAAGTATGTGTTAATTGT
* * *
3638852 CTAAGATATTGAGAGAT-TACATAGTTACACCTGTGTAAGTATGTGTTAATTGT
1 -TAAGATATTGAGAGATATACATACTCACACCTGTATAAGTATGTGTTAATTGT
* *
3638905 AAAGATATTGAGAGATCTACAT
1 TAAGATATTGAGAGATATACAT
3638927 GATTGCTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 44 0.42
53 61 0.58
54 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (53 bp):
TAAGATATTGAGAGATATACATACTCACACCTGTATAAGTATGTGTTAATTGT
Found at i:3644551 original size:13 final size:13
Alignment explanation
Indices: 3644533--3644558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3644523 CATAGTTGAA
3644533 CAGTCTTCATATG
1 CAGTCTTCATATG
3644546 CAGTCTTCATATG
1 CAGTCTTCATATG
3644559 TTCGTCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:3646979 original size:83 final size:83
Alignment explanation
Indices: 3646840--3647004 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 83
3646830 AAGTCAAGAA
3646840 AAAGAAATGAGAGGAATCTATATCAAATACGAATATATCTTACTGCATCGATAAACGAATCACAA
1 AAAGAAATGAGAGGAATCTATATCAAATACGAATATATCTTACTGCATCGATAAACGAATCACAA
*
3646905 CAGATGATCAAACTATTG
66 CAGAGGATCAAACTATTG
*
3646923 AAAGAAATGATAGGAATCTATATCAAATACGAATATATCTTACTGCATCGATAAACGAATCACAA
1 AAAGAAATGAGAGGAATCTATATCAAATACGAATATATCTTACTGCATCGATAAACGAATCACAA
3646988 CAGAGGATCAAACTATT
66 CAGAGGATCAAACTATT
3647005 AGAAGACCAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (83 bp):
AAAGAAATGAGAGGAATCTATATCAAATACGAATATATCTTACTGCATCGATAAACGAATCACAA
CAGAGGATCAAACTATTG
Found at i:3647274 original size:7 final size:7
Alignment explanation
Indices: 3647262--3647308 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
3647252 AAATTATTAA
3647262 AAAAAAT
1 AAAAAAT
3647269 AAAAAAT
1 AAAAAAT
*
3647276 -AAAAAC
1 AAAAAAT
* *
3647282 ACAATAT
1 AAAAAAT
3647289 AAAAAAAT
1 -AAAAAAT
3647297 AAAAAAT
1 AAAAAAT
3647304 AAAAA
1 AAAAA
3647309 CAATAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 5 0.16
7 22 0.69
8 5 0.16
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:3656334 original size:21 final size:19
Alignment explanation
Indices: 3656310--3656353 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3656300 TTACTTTTAA
3656310 ATAAATTTTAACAT-AAAAT
1 ATAAATTTTAA-ATAAAAAT
3656329 ATATAATTTTAAATAAAAAT
1 ATA-AATTTTAAATAAAAAT
3656349 A-AAAT
1 ATAAAT
3656354 AAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.13
19 6 0.26
20 14 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATTTTAAATAAAAAT
Found at i:3657122 original size:21 final size:21
Alignment explanation
Indices: 3657082--3657125 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3657072 GTTATGACTA
* *
3657082 TGATATAATAGTTTACAGTGT
1 TGATATAATAATTCACAGTGT
*
3657103 TGATATAATAATTCATAGTGT
1 TGATATAATAATTCACAGTGT
3657124 TG
1 TG
3657126 GCATAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (21 bp):
TGATATAATAATTCACAGTGT
Found at i:3664689 original size:50 final size:50
Alignment explanation
Indices: 3664619--3664730 Score: 172
Period size: 50 Copynumber: 2.3 Consensus size: 50
3664609 TAGTGCGGAT
* *
3664619 CAGGGGG-GCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCGGGG
* **
3664668 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCGTATAGCGCGGTT
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCGGGG
3664718 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
3664731 TTACTGCTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 7 0.12
50 50 0.88
ACGTcount: A:0.18, C:0.30, G:0.38, T:0.14
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCGGGG
Found at i:3667156 original size:2 final size:2
Alignment explanation
Indices: 3667149--3667216 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
3667139 TTTCTTAATC
3667149 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
3667191 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
3667217 TTGTTAATTG
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:3677120 original size:14 final size:14
Alignment explanation
Indices: 3677103--3677158 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
3677093 GATTGGGTTA
3677103 AACGAACATAACCG
1 AACGAACATAACCG
3677117 AACGAACAT-A---
1 AACGAACATAACCG
*
3677127 AACAAACATAACCG
1 AACGAACATAACCG
3677141 AACGAACATAACCG
1 AACGAACATAACCG
3677155 AACG
1 AACG
3677159 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.27, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:3677134 original size:24 final size:24
Alignment explanation
Indices: 3677101--3677151 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3677091 AAGATTGGGT
*
3677101 TAAACGAACATAACCGAACGAACA
1 TAAACAAACATAACCGAACGAACA
3677125 TAAACAAACATAACCGAACGAACA
1 TAAACAAACATAACCGAACGAACA
3677149 TAA
1 TAA
3677152 CCGAACGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.24, G:0.10, T:0.10
Consensus pattern (24 bp):
TAAACAAACATAACCGAACGAACA
Found at i:3678164 original size:8 final size:8
Alignment explanation
Indices: 3678151--3678175 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3678141 GCTTTTGATT
3678151 GGGGGAGA
1 GGGGGAGA
3678159 GGGGGAGA
1 GGGGGAGA
3678167 GGGGGAGA
1 GGGGGAGA
3678175 G
1 G
3678176 CTTCCCTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (8 bp):
GGGGGAGA
Found at i:3691796 original size:18 final size:18
Alignment explanation
Indices: 3691765--3691799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3691755 AATTTTATGA
* *
3691765 ATATATTTTTATTTTTAT
1 ATATAATTTGATTTTTAT
3691783 ATATAATTTGATTTTTA
1 ATATAATTTGATTTTTA
3691800 GTTTTTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATAATTTGATTTTTAT
Found at i:3694696 original size:12 final size:12
Alignment explanation
Indices: 3694679--3694705 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3694669 AAAGTTATAT
3694679 TTTAACCCATGA
1 TTTAACCCATGA
3694691 TTTAACCCATGA
1 TTTAACCCATGA
3694703 TTT
1 TTT
3694706 TGATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (12 bp):
TTTAACCCATGA
Found at i:3696337 original size:65 final size:65
Alignment explanation
Indices: 3696238--3696360 Score: 246
Period size: 65 Copynumber: 1.9 Consensus size: 65
3696228 TATTCCGCTT
3696238 AACTCAACTCTAGATCGCGTTAAGCACTAAGAATTGGATACTTGTTCGACAAATCAACTCAACTC
1 AACTCAACTCTAGATCGCGTTAAGCACTAAGAATTGGATACTTGTTCGACAAATCAACTCAACTC
3696303 AACTCAACTCTAGATCGCGTTAAGCACTAAGAATTGGATACTTGTTCGACAAATCAAC
1 AACTCAACTCTAGATCGCGTTAAGCACTAAGAATTGGATACTTGTTCGACAAATCAAC
3696361 CACGGAGACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (65 bp):
AACTCAACTCTAGATCGCGTTAAGCACTAAGAATTGGATACTTGTTCGACAAATCAACTCAACTC
Found at i:3716285 original size:37 final size:37
Alignment explanation
Indices: 3716235--3716308 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3716225 ACTGACGGGC
3716235 TAGGAAGAGGAAACCCTCTTCATCCAACTCTTCCAAA
1 TAGGAAGAGGAAACCCTCTTCATCCAACTCTTCCAAA
3716272 TAGGAAGAGGAAACCCTCTTCATCCAACTCTTCCAAA
1 TAGGAAGAGGAAACCCTCTTCATCCAACTCTTCCAAA
3716309 AGTAACAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (37 bp):
TAGGAAGAGGAAACCCTCTTCATCCAACTCTTCCAAA
Found at i:3723079 original size:16 final size:16
Alignment explanation
Indices: 3723027--3723081 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
3723017 AATAAATGAT
*
3723027 AATAAA-AATTAAAAGG
1 AATAAATAA-TAAAAAG
*
3723043 AGATAAATAA-AAAAATA
1 A-ATAAATAATAAAAA-G
3723060 AATAAATAATAAAAAG
1 AATAAATAATAAAAAG
3723076 AATAAA
1 AATAAA
3723082 AAATGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 19 0.59
17 11 0.34
18 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AATAAATAATAAAAAG
Found at i:3724675 original size:12 final size:12
Alignment explanation
Indices: 3724654--3724713 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
3724644 ACTATATAAT
3724654 ATTTTCAAAAAC
1 ATTTTCAAAAAC
*
3724666 ATTTTTAAAAAC
1 ATTTTCAAAAAC
* *
3724678 TATATATT-ATATAC
1 -AT-T-TTCAAAAAC
*
3724692 GTTTTCAAAAAC
1 ATTTTCAAAAAC
3724704 ATTTTCAAAA
1 ATTTTCAAAA
3724714 CTATATATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
11 2 0.05
12 25 0.68
13 3 0.08
14 5 0.14
15 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (12 bp):
ATTTTCAAAAAC
Found at i:3724723 original size:37 final size:36
Alignment explanation
Indices: 3724600--3724844 Score: 247
Period size: 37 Copynumber: 6.8 Consensus size: 36
3724590 TCAAAACGTT
* *
3724600 TTTTCAAAACTATATAATATATA-TTTTAAAAAATTA
1 TTTTCAAAACTATATATTATATAGTTTTCAAAAA-TA
*
3724636 TTTTCAAAAC--TATA-TA-ATA-TTTTCAAAAACA
1 TTTTCAAAACTATATATTATATAGTTTTCAAAAATA
* *
3724667 TTTTTAAAAACTATATATTATATACGTTTTCAAAAACA
1 -TTTTCAAAACTATATATTATATA-GTTTTCAAAAATA
3724705 TTTTCAAAACTATATATTATACGTA-TTTTCAAAAATA
1 TTTTCAAAACTATATATTATA--TAGTTTTCAAAAATA
* *
3724742 TTTTCAAAACTATATATTATATATATATTTTC-AAAATG
1 TTTTCAAAACTATATA-T-TATATA-GTTTTCAAAAATA
*
3724780 TTTTCAAAAACTATATATTATATATGTTTTCAGAAATA
1 TTTTC-AAAACTATATATTATATA-GTTTTCAAAAATA
* *
3724818 TTTTCAAAATTATATAATATAT-GTTTT
1 TTTTCAAAACTATATATTATATAGTTTT
3724845 TAAATCGTAT
Statistics
Matches: 183, Mismatches: 11, Indels: 31
0.81 0.05 0.14
Matches are distributed among these distances:
31 1 0.01
32 21 0.11
33 2 0.01
34 8 0.04
35 7 0.04
36 13 0.07
37 76 0.42
38 33 0.18
39 22 0.12
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATAGTTTTCAAAAATA
Found at i:3724791 original size:76 final size:71
Alignment explanation
Indices: 3724600--3724845 Score: 254
Period size: 76 Copynumber: 3.4 Consensus size: 71
3724590 TCAAAACGTT
**
3724600 TTTTCAAAACTATATA-ATATATATTTTAAAAAATTATTTTCAAAAC--TATA-TA-ATATTTTC
1 TTTTCAAAACTATATATATATATATTTTTCAAAA-TATTTTCAAAACTATATATTATATATTTTC
*
3724660 AAAAACA
65 AAAAATA
* * *
3724667 TTTTTAAAAACTATATAT-TATATACGTTTTCAAAAACATTTTCAAAACTATATATTATACGTAT
1 -TTTTCAAAACTATATATATATATA-TTTTTC-AAAATATTTTCAAAACTATATATTATA--TAT
3724731 TTTCAAAAATA
61 TTTCAAAAATA
*
3724742 TTTTCAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATGT
1 TTTTCAAAACTATATA-TATATATAT-TTTTCAAAATATTTTC-AAAACTATATATTATATA--T
*
3724807 TTTCAGAAATA
61 TTTCAAAAATA
* *
3724818 TTTTCAAAATTATATA-ATATATGTTTTT
1 TTTTCAAAACTATATATATATATATTTTT
3724846 AAATCGTATT
Statistics
Matches: 150, Mismatches: 13, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
68 21 0.14
69 14 0.09
70 4 0.03
71 4 0.03
72 2 0.01
73 5 0.03
74 24 0.16
75 23 0.15
76 53 0.35
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (71 bp):
TTTTCAAAACTATATATATATATATTTTTCAAAATATTTTCAAAACTATATATTATATATTTTCA
AAAATA
Found at i:3724877 original size:85 final size:85
Alignment explanation
Indices: 3724767--3724922 Score: 219
Period size: 85 Copynumber: 1.8 Consensus size: 85
3724757 ATTATATATA
* *
3724767 TATTTTCAAAATGTTTTCAAAAACTATATATTATATATGTTTTC-AGAAATATTTTC-AAAATTA
1 TATTTTCAAAATGTTTTCAAAAACTATAT-GT-TATATGTTTTCGAAAAATATTTTCAAAAATTA
3724830 TATAATATATGTTTTTAAATCG
64 TATAATATATGTTTTTAAATCG
* *
3724852 TATTTTCGAAACTGTTTT-AACAACTATATGTTATATGTTTTCGAAAAATATTTTCAAAAATTAT
1 TATTTTC-AAAATGTTTTCAAAAACTATATGTTATATGTTTTCGAAAAATATTTTCAAAAATTAT
*
3724916 ATTATAT
65 ATAATAT
3724923 TATTATATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
83 11 0.17
84 12 0.19
85 31 0.49
86 9 0.14
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (85 bp):
TATTTTCAAAATGTTTTCAAAAACTATATGTTATATGTTTTCGAAAAATATTTTCAAAAATTATA
TAATATATGTTTTTAAATCG
Found at i:3725642 original size:85 final size:85
Alignment explanation
Indices: 3725505--3725742 Score: 309
Period size: 85 Copynumber: 2.8 Consensus size: 85
3725495 TGTCATCGAG
* * *
3725505 CTGAATGTAATCGAACTTGACAGTTTTTTGTTGACGGATAGCCCTTCTCGCCTTAAACTATGCTG
1 CTGAATGTAATCGAACTCGA-AGATTTTTGTTGACAGATAGCCCTTCTCGCCTTAAACTATGCTG
3725570 TAAATTTAATATGCCCTTGAC
65 TAAATTTAATATGCCCTTGAC
* * * *
3725591 CTGAATAG-AATCGAACTCGAAGGTTTTTGTTGATAGATAGCTCTTCTCGCCTTGATA-TATGCT
1 CTGAAT-GTAATCGAACTCGAAGATTTTTGTTGACAGATAGCCCTTCTCGCCTT-AAACTATGCT
* * * *
3725654 ATAAATTTGATATGGCCTTGAG
64 GTAAATTTAATATGCCCTTGAC
* * *
3725676 CTGAATGTAATCGAACTCGAAGATTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGT
1 CTGAATGTAATCGAACTCGAAGATTTTTGTTGACAGATAGCCCTTCTCGCCTTAAACTATGCTGT
3725741 AA
66 AA
3725743 TAGGCTGAGA
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 109 0.84
86 19 0.15
87 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (85 bp):
CTGAATGTAATCGAACTCGAAGATTTTTGTTGACAGATAGCCCTTCTCGCCTTAAACTATGCTGT
AAATTTAATATGCCCTTGAC
Found at i:3729996 original size:21 final size:23
Alignment explanation
Indices: 3729970--3730030 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 23
3729960 CGTAATTTGC
3729970 ACCGAAGTGCCACATA-ATTGT-T
1 ACCGAAGTGCCACATAGATT-TAT
*
3729992 -CCGAA-TGTCCACATAGGTTTAT
1 ACCGAAGTG-CCACATAGATTTAT
3730014 ACCGAAGTGCCACATAG
1 ACCGAAGTGCCACATAG
3730031 GGTTGCATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
22 3 0.09
23 13 0.39
24 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
ACCGAAGTGCCACATAGATTTAT
Found at i:3730026 original size:23 final size:23
Alignment explanation
Indices: 3729970--3730031 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
3729960 CGTAATTTGC
*
3729970 ACCGAAGTGCCACATA-ATTGTT
1 ACCGAAGTGCCACATAGGTTGTT
3729992 -CCGAA-TGTCCACATAGGTT-TAT
1 ACCGAAGTG-CCACATAGGTTGT-T
3730014 ACCGAAGTGCCACATAGG
1 ACCGAAGTGCCACATAGG
3730032 GTTGCATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 2 0.06
21 13 0.38
22 3 0.09
23 14 0.41
24 2 0.06
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
ACCGAAGTGCCACATAGGTTGTT
Found at i:3730198 original size:14 final size:15
Alignment explanation
Indices: 3730179--3730215 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3730169 GTGTCTCTTA
3730179 TTCACATAGA-TACT
1 TTCACATAGAGTACT
*
3730193 TTCACATAGAGTATT
1 TTCACATAGAGTACT
3730208 TTCACATA
1 TTCACATA
3730216 CACTTGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (15 bp):
TTCACATAGAGTACT
Found at i:3736438 original size:19 final size:19
Alignment explanation
Indices: 3736415--3736462 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3736405 TAAAAATAAT
* *
3736415 AATAAAAAA-ATTAAAAGG
1 AATAAAAAACAATAAAAAG
3736433 AGATAAATAAACAATAAAAAG
1 A-ATAAA-AAACAATAAAAAG
3736454 AATAAAAAA
1 AATAAAAAA
3736463 TGTTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 8 0.32
20 8 0.32
21 8 0.32
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (19 bp):
AATAAAAAACAATAAAAAG
Found at i:3737822 original size:11 final size:10
Alignment explanation
Indices: 3737805--3737868 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
3737795 TTTGGACCCT
3737805 AAAAAAAGAA
1 AAAAAAAGAA
*
3737815 AGAAAAAATAA
1 A-AAAAAAGAA
3737826 AAAAAATA-AA
1 AAAAAA-AGAA
3737836 AAATAAAA-AA
1 AAA-AAAAGAA
*
3737846 ATAAAAGAGAA
1 A-AAAAAAGAA
*
3737857 AAAAAAATAA
1 AAAAAAAGAA
3737867 AA
1 AA
3737869 TGTAATGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 27 0.60
11 18 0.40
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.08
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:3737836 original size:16 final size:16
Alignment explanation
Indices: 3737807--3737868 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
3737797 TGGACCCTAA
*
3737807 AAAAAGAAAGAAAAAAT
1 AAAAA-AAATAAAAAAT
3737824 AAAAAAAATAAAAAAT
1 AAAAAAAATAAAAAAT
3737840 -AAAAAAATAAAAGAGA-
1 AAAAAAAATAAAA-A-AT
3737856 AAAAAAAATAAAA
1 AAAAAAAATAAAA
3737869 TGTAATGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
15 12 0.29
16 11 0.27
17 18 0.44
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.08
Consensus pattern (16 bp):
AAAAAAAATAAAAAAT
Found at i:3737940 original size:41 final size:38
Alignment explanation
Indices: 3737891--3737971 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
3737881 TACATATTAC
3737891 ATATATTTT-AAAAAAGTGTTTTCAAAATCATATATTATAT
1 ATATATTTTGAAAAAA-T-TTTTCAAAAT-ATATATTATAT
* *
3737931 ATATAATTTTGAAAATATTTTTTAAAATATATATTATAT
1 ATAT-ATTTTGAAAAAATTTTTCAAAATATATATTATAT
3737970 AT
1 AT
3737972 TTTTCAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 13 0.35
40 13 0.35
41 6 0.16
42 5 0.14
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (38 bp):
ATATATTTTGAAAAAATTTTTCAAAATATATATTATAT
Found at i:3738024 original size:23 final size:23
Alignment explanation
Indices: 3737998--3738073 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 23
3737988 AATTTTTTTC
*
3737998 TCAAAATTATATAATATATATTT
1 TCAAAACTATATAATATATATTT
3738021 TCAAAACTATAT-A-ATATATTT
1 TCAAAACTATATAATATATATTT
*
3738042 TCAAAAGCTATATATTATATACGTTT
1 TCAAAA-CTATATAATATATA--TTT
3738068 TCAAAA
1 TCAAAA
3738074 ACATTTTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
21 14 0.30
22 7 0.15
23 11 0.24
24 5 0.11
26 9 0.20
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (23 bp):
TCAAAACTATATAATATATATTT
Found at i:3738095 original size:37 final size:36
Alignment explanation
Indices: 3738036--3738197 Score: 139
Period size: 37 Copynumber: 4.7 Consensus size: 36
3738026 ACTATATAAT
3738036 ATATTTTCAAAAGCTATATATTATATACGTTTTCAAAA
1 ATATTTTCAAAA-CTATATATTATATACGTTTTC-AAA
*
3738074 ACATTTTCAAAACTATATA-T-TATACG--------
1 ATATTTTCAAAACTATATATTATATACGTTTTCAAA
**
3738100 -TATTTTCAAAACTATATATTATATATATTTTCAAA
1 ATATTTTCAAAACTATATATTATATACGTTTTCAAA
* *
3738135 ATGTTTTCAAAAACTATATATTATATATGTTTTCAGAA
1 ATATTTTC-AAAACTATATATTATATACGTTTTCA-AA
* * *
3738173 ATATTTTAAAAATTATATAATATAT
1 ATATTTTCAAAACTATATATTATAT
3738198 GTTTTTAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
25 17 0.17
26 1 0.01
27 4 0.04
35 6 0.06
36 7 0.07
37 47 0.47
38 19 0.19
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (36 bp):
ATATTTTCAAAACTATATATTATATACGTTTTCAAA
Found at i:3738104 original size:25 final size:25
Alignment explanation
Indices: 3738076--3738135 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
3738066 TTTCAAAAAC
*
3738076 ATTTTCAAAACTATATATTATACGT
1 ATTTTCAAAACTATATATTATACAT
*
3738101 ATTTTCAAAACTATATATTATATAT
1 ATTTTCAAAACTATATATTATACAT
3738126 ATTTTCAAAA
1 ATTTTCAAAA
3738136 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTTCAAAACTATATATTATACAT
Found at i:3738131 original size:62 final size:60
Alignment explanation
Indices: 3738017--3738162 Score: 199
Period size: 62 Copynumber: 2.4 Consensus size: 60
3738007 TATAATATAT
*
3738017 ATTTTCAAAACTATATA--ATATATTTTCAAAAGCTATATATTATATACGTTTTCAAAAAC
1 ATTTTCAAAACTATATATTATATATTTTCAAAAGCTATATATTATATACATTTTC-AAAAC
* *
3738076 ATTTTCAAAACTATATATTATACGTATTTTCAAAA-CTATATATTATATATATTTTCAAAAT
1 ATTTTCAAAACTATATATTATA--TATTTTCAAAAGCTATATATTATATACATTTTCAAAAC
*
3738137 GTTTTCAAAAACTATATATTATATAT
1 ATTTTC-AAAACTATATATTATATAT
3738163 GTTTTCAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
59 17 0.22
60 3 0.04
61 12 0.15
62 35 0.45
63 11 0.14
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (60 bp):
ATTTTCAAAACTATATATTATATATTTTCAAAAGCTATATATTATATACATTTTCAAAAC
Found at i:3745547 original size:42 final size:41
Alignment explanation
Indices: 3745490--3745600 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 41
3745480 GCTATTTAGC
**
3745490 GGCATTTTTGTTACAAACACCGCTAATAATTAAGTACATAGT-
1 GGCATTTTTCCTACAAACACCGCTAATAATTAAGTA-ATA-TA
* *
3745532 GGCATTTTTCCTACAAACACCGCTAATAATTATGTATTATA
1 GGCATTTTTCCTACAAACACCGCTAATAATTAAGTAATATA
*
3745573 AGCATTTTTCCTCACAAACACCGCTAAT
1 GGCATTTTTCCT-ACAAACACCGCTAAT
3745601 TTTTTACTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.02
41 13 0.21
42 48 0.77
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (41 bp):
GGCATTTTTCCTACAAACACCGCTAATAATTAAGTAATATA
Found at i:3755119 original size:22 final size:23
Alignment explanation
Indices: 3755071--3755116 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3755061 TGATTCCCCT
3755071 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
3755094 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
3755117 GGGCGTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:3755131 original size:22 final size:23
Alignment explanation
Indices: 3755071--3755137 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
3755061 TGATTCCCCT
*
3755071 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGCGAATCGGTTCCCCTTCAA
* *
3755094 AGGGGGAATTGGTTCCCCTTC-A
1 AGGGCGAATCGGTTCCCCTTCAA
* *
3755116 AGGGCGTATCGATTCCCTCTTC
1 AGGGCGAATCGGTTCCC-CTTC
3755138 CCTATAATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 14 0.37
23 24 0.63
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
AGGGCGAATCGGTTCCCCTTCAA
Done.