Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2208396 original size:29 final size:29
Alignment explanation
Indices: 2208354--2208459 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
2208344 ATGCAGGAGG
2208354 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
2208383 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
2208412 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
2208441 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
2208460 TGCTGGGAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:2212503 original size:26 final size:25
Alignment explanation
Indices: 2212416--2212505 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
2212406 TACCTATACC
*
2212416 AATGCCAGAAAATGATGCCAAATCT
1 AATGCCAGAAAAGGATGCCAAATCT
* * *
2212441 AATGCCAGAAAAGAATGGCAAATCC
1 AATGCCAGAAAAGGATGCCAAATCT
* ** *
2212466 AACGTTGAAAAAAGGATGCCAAATCT
1 AATG-CCAGAAAAGGATGCCAAATCT
*
2212492 AATGCTAGAAAAGG
1 AATGCCAGAAAAGG
2212506 TACCATTTTC
Statistics
Matches: 49, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
25 31 0.63
26 18 0.37
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (25 bp):
AATGCCAGAAAAGGATGCCAAATCT
Found at i:2213852 original size:44 final size:44
Alignment explanation
Indices: 2213760--2213858 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
2213750 TTCTATTAAT
* * * * *
2213760 AAACGCCACAAAAAGTCAGGTTATTTAGCGGTGTTTGTATACTA
1 AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
* *
2213804 AAACGCCGCTAAAGGTCAGGTTATATAGCGGCGTTT-TAGAATA
1 AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
2213847 CAAACGCCGCAA
1 -AAACGCCGCAA
2213859 CAGGTTCGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 5 0.11
44 41 0.89
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (44 bp):
AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
Found at i:2213878 original size:43 final size:42
Alignment explanation
Indices: 2213760--2213883 Score: 108
Period size: 44 Copynumber: 2.9 Consensus size: 42
2213750 TTCTATTAAT
* * * * * *
2213760 AAACGCCACAAAAAGTCAGGTTATTTAGCGGTGTTTGTATACTA
1 AAACGCCGCTAAAGGTCA-GTTATTTAGCGGCGTTT-TAGAATA
*
2213804 AAACGCCGCTAAAGGTCAGGTTATATAGCGGCGTTTTAGAATA
1 AAACGCCGCTAAAGGTCA-GTTATTTAGCGGCGTTTTAGAATA
*
2213847 CAAACGCCGC-AACAGGTTC-GTTATTTAGCGGCATTTT
1 -AAACGCCGCTAA-AGG-TCAGTTATTTAGCGGCGTTTT
2213884 TTGTCACAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
43 23 0.34
44 43 0.63
45 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCAGTTATTTAGCGGCGTTTTAGAATA
Found at i:2215994 original size:20 final size:20
Alignment explanation
Indices: 2215961--2215999 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2215951 TAGTTTTATA
*
2215961 AAGTTTTCTCTTTTCTTTTC
1 AAGTTTTCTCTTTTATTTTC
2215981 AAGTTTTCAT-TTTTATTTT
1 AAGTTTTC-TCTTTTATTTT
2216000 ATTTTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (20 bp):
AAGTTTTCTCTTTTATTTTC
Found at i:2222345 original size:32 final size:31
Alignment explanation
Indices: 2222309--2222370 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
2222299 TAGTTTTATA
* *
2222309 AAGTTCTC-TCTTTTCTTTTCTTTTCAAGTTTC
1 AAGTTCTCAT-TTTTATTTTATTTT-AAGTTTC
*
2222341 AAGTTTTCATTTTTATTTTATTTTAAGTTT
1 AAGTTCTCATTTTTATTTTATTTTAAGTTT
2222371 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 6 0.23
32 19 0.73
33 1 0.04
ACGTcount: A:0.18, C:0.13, G:0.06, T:0.63
Consensus pattern (31 bp):
AAGTTCTCATTTTTATTTTATTTTAAGTTTC
Found at i:2222548 original size:17 final size:18
Alignment explanation
Indices: 2222515--2222548 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2222505 TCTGCACTTA
2222515 TTTTCAAAATGAAAATTG
1 TTTTCAAAATGAAAATTG
2222533 TTTTCAAAAT-AAAATT
1 TTTTCAAAATGAAAATT
2222549 TTGACTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTTCAAAATGAAAATTG
Found at i:2229708 original size:24 final size:25
Alignment explanation
Indices: 2229632--2229721 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
2229622 CCAGCACCAA
* * * *
2229632 AAAATGATGTCAAATCCAACGCTAG
1 AAAAGGATGCCAAATCCAAAGCCAG
* *
2229657 AAAAAGATGCCAAATCTAAAGCCAG
1 AAAAGGATGCCAAATCCAAAGCCAG
2229682 AAAAGTG-TGCCAAATCCAAAGCC-G
1 AAAAG-GATGCCAAATCCAAAGCCAG
2229706 AAAAGGATGCCAAATC
1 AAAAGGATGCCAAATC
2229722 AAATACCGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
23 1 0.02
24 15 0.27
25 39 0.70
26 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (25 bp):
AAAAGGATGCCAAATCCAAAGCCAG
Found at i:2231609 original size:21 final size:21
Alignment explanation
Indices: 2231580--2231625 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2231570 AATAGATTAT
2231580 ACAAAATTGAGGAATTCATAA
1 ACAAAATTGAGGAATTCATAA
*
2231601 ACAAGATTGAGGAATTCATAA
1 ACAAAATTGAGGAATTCATAA
2231622 ACAA
1 ACAA
2231626 CGAGGCCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (21 bp):
ACAAAATTGAGGAATTCATAA
Found at i:2236211 original size:65 final size:65
Alignment explanation
Indices: 2236089--2236247 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
2236079 TGCACTAACA
* * *
2236089 GTGCAT-GATGCATGAAGTGCATTCGATG-TTTCAAACAAGCACGAGTGCATCGATGCATGGCT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATGG-TA
2236151 T
65 T
2236152 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAAC-CTGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AACAAACAC-GAGTGCATCGATGCATGGT
2236215 AT
64 AT
*
2236217 GTGCATCGATGCATATAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
2236248 CAATTTATTC
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
63 6 0.07
64 22 0.25
65 57 0.66
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATGGTAT
Found at i:2245956 original size:36 final size:36
Alignment explanation
Indices: 2245907--2245978 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
2245897 TACCAAACCC
* *
2245907 GTCCCCGTACCCGTTTAGTATAAATGGTTTTTCCCG
1 GTCCCCGTACCCGTTTAGCATAAACGGTTTTTCCCG
*
2245943 GTCCCCGTCCCCGTTTAGCATAAACGGTTTTTCCCG
1 GTCCCCGTACCCGTTTAGCATAAACGGTTTTTCCCG
2245979 TTCCGTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.33
Consensus pattern (36 bp):
GTCCCCGTACCCGTTTAGCATAAACGGTTTTTCCCG
Found at i:2247648 original size:27 final size:27
Alignment explanation
Indices: 2247596--2247648 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2247586 TTGTTGTTTG
*
2247596 TATATGTTATATAATATTATTCATATA
1 TATATGTTATATAATATTATTAATATA
2247623 TATATGTGTATAT-AT-TTACTTAATAT
1 TATATGT-TATATAATATTA-TTAATAT
2247649 TCTTTGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 15 0.65
28 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (27 bp):
TATATGTTATATAATATTATTAATATA
Found at i:2247846 original size:20 final size:20
Alignment explanation
Indices: 2247805--2247860 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2247795 AAATAACCAA
**
2247805 CAAATTCGCAACAC-GAACTC
1 CAAATTCGCAACACAG-TTTC
*
2247825 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
2247845 CAAATTCGCAACACAG
1 CAAATTCGCAACACAG
2247861 AATTAGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:2247918 original size:20 final size:20
Alignment explanation
Indices: 2247889--2247939 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2247879 GAACAAGGAA
*
2247889 ATTTTT-GCAACGTTAATTT
1 ATTTTTCGCAACGTGAATTT
2247908 ATTTTTCGCAACGTGAATTT
1 ATTTTTCGCAACGTGAATTT
*
2247928 CTTTTTCGCAAC
1 ATTTTTCGCAAC
2247940 TCCAATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTTTCGCAACGTGAATTT
Found at i:2247969 original size:22 final size:21
Alignment explanation
Indices: 2247941--2247981 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2247931 TTTCGCAACT
*
2247941 CCAATTTTGCAACTCGAATTCG
1 CCAATTTCGCAACTC-AATTCG
2247963 CCAATTTCGCAACTCAATT
1 CCAATTTCGCAACTCAATT
2247982 ACCGATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (21 bp):
CCAATTTCGCAACTCAATTCG
Found at i:2248648 original size:20 final size:20
Alignment explanation
Indices: 2248623--2248660 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2248613 CTATATCGGT
*
2248623 AATTCGCGTTGCGAAAATGA
1 AATTCGCGTTGCAAAAATGA
2248643 AATTCGCGTTGCAAAAAT
1 AATTCGCGTTGCAAAAAT
2248661 TTTCATGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
AATTCGCGTTGCAAAAATGA
Found at i:2256621 original size:46 final size:46
Alignment explanation
Indices: 2256568--2256900 Score: 434
Period size: 46 Copynumber: 7.3 Consensus size: 46
2256558 ATTATTCTTT
* * **
2256568 ATTTTCATTTATGACATCCTTTCATGCCAAAAATGCATTGTTATGC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
** *
2256614 ATTTTCATTTATGTTATCCTTTCATGCCGATAATGCACAGTTATGC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
* * *
2256660 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
* * * *
2256706 ATTTTCATTTATGACATCATTTTATGTCAATAATGCACCGTTATGC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
* *
2256752 ATTTTCATTTATGACATCCTTTTATGTCGATAATGCACCGTTATGC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
* * ** *
2256798 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACTATTATAC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
* ** *
2256844 ATTTTCATTTATGGCAT-CTTTCATGTTGATAATGCACCGTTATTC
1 ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
2256889 ATTTTCATTTAT
1 ATTTTCATTTAT
2256901 TCATTCATTT
Statistics
Matches: 255, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
45 34 0.13
46 221 0.87
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (46 bp):
ATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATGC
Found at i:2256788 original size:138 final size:137
Alignment explanation
Indices: 2256568--2256900 Score: 504
Period size: 138 Copynumber: 2.4 Consensus size: 137
2256558 ATTATTCTTT
* * ** **
2256568 ATTTTCATTTATGACATCCTTTCATGCCAAAAATGCATTGTTATGCATTTTCATTTATGTTATCC
1 ATTTTCATTTATGACAT-CTTTCATGTCAATAATGCACCGTTATGCATTTTCATTTATGACATCC
2256633 TTTCATGCCGATAATGCACAGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCAC
65 TTTCATGCCGATAATGCACAGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCAC
*
2256698 CATTATGC
130 CATTATAC
*
2256706 ATTTTCATTTATGACATCATTTTATGTCAATAATGCACCGTTATGCATTTTCATTTATGACATCC
1 ATTTTCATTTATGACATC-TTTCATGTCAATAATGCACCGTTATGCATTTTCATTTATGACATCC
* * *
2256771 TTTTATGTCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCAC
65 TTTCATGCCGATAATGCACAGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCAC
*
2256836 TATTATAC
130 CATTATAC
* ** *
2256844 ATTTTCATTTATGGCATCTTTCATGTTGATAATGCACCGTTATTCATTTTCATTTAT
1 ATTTTCATTTATGACATCTTTCATGTCAATAATGCACCGTTATGCATTTTCATTTAT
2256901 TCATTCATTT
Statistics
Matches: 177, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
137 36 0.20
138 141 0.80
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (137 bp):
ATTTTCATTTATGACATCTTTCATGTCAATAATGCACCGTTATGCATTTTCATTTATGACATCCT
TTCATGCCGATAATGCACAGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACC
ATTATAC
Found at i:2263527 original size:46 final size:46
Alignment explanation
Indices: 2263467--2263669 Score: 352
Period size: 46 Copynumber: 4.4 Consensus size: 46
2263457 AAACCAAATT
* *
2263467 TTTATGGCATCCTTTCATGCCTATAATGCACTGTTATTCATTTTCA
1 TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
*
2263513 TTTATGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCA
1 TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
2263559 TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
1 TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
* *
2263605 TTTATGGCATCCTTTCATGCCGATAATGCACCGCTATGCATTTTCA
1 TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
*
2263651 TTTATGGCATCCTCTCATG
1 TTTATGGCATCCTTTCATG
2263670 TTCATACTCT
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 150 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCA
Found at i:2271284 original size:37 final size:38
Alignment explanation
Indices: 2271213--2271287 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
2271203 TTCCCATGAG
2271213 TCACTTAAAACATTTATTAGAAAAAAAAATAACAACTA
1 TCACTTAAAACATTTATTAGAAAAAAAAATAACAACTA
2271251 TCACTTAAAACATTTATTAG-AAAAAAAATAACAACTA
1 TCACTTAAAACATTTATTAGAAAAAAAAATAACAACTA
2271288 CTATCCAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 17 0.46
38 20 0.54
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (38 bp):
TCACTTAAAACATTTATTAGAAAAAAAAATAACAACTA
Found at i:2273071 original size:18 final size:19
Alignment explanation
Indices: 2273048--2273086 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2273038 TCAAATTATT
2273048 TTTTAA-TATAGTTAATAA
1 TTTTAATTATAGTTAATAA
* *
2273066 TTTTAATTTTATTTAATAA
1 TTTTAATTATAGTTAATAA
2273085 TT
1 TT
2273087 ATATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAATTATAGTTAATAA
Found at i:2273324 original size:18 final size:19
Alignment explanation
Indices: 2273287--2273336 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
2273277 ACATATATGT
2273287 AATTATTAAATAAAATTAA
1 AATTATTAAATAAAATTAA
* *
2273306 AATTATT-AATTATATTAA
1 AATTATTAAATAAAATTAA
* *
2273324 AATAATTTAATAA
1 AATTATTAAATAA
2273337 TTATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATTAAATAAAATTAA
Found at i:2273688 original size:36 final size:38
Alignment explanation
Indices: 2273618--2273694 Score: 131
Period size: 39 Copynumber: 2.1 Consensus size: 38
2273608 TCACCACCTC
2273618 ATTGGATACAAAATAAAATAAATAAAATAATTAAAATTA
1 ATTGGATACAAAATAAAAT-AATAAAATAATTAAAATTA
2273657 ATTGGATACAAAATAAAAT-A-AAAATAATTAAAATTA
1 ATTGGATACAAAATAAAATAATAAAATAATTAAAATTA
2273693 AT
1 AT
2273695 AAAATATCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 18 0.47
37 1 0.03
39 19 0.50
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (38 bp):
ATTGGATACAAAATAAAATAATAAAATAATTAAAATTA
Found at i:2290919 original size:15 final size:15
Alignment explanation
Indices: 2290901--2290930 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2290891 TCTTGCTTTT
2290901 CTTATGAATGCTTCA
1 CTTATGAATGCTTCA
2290916 CTTATGAATGCTTCA
1 CTTATGAATGCTTCA
2290931 TCGTCTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
CTTATGAATGCTTCA
Found at i:2296943 original size:15 final size:15
Alignment explanation
Indices: 2296923--2296963 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2296913 GTTGCAATCA
* *
2296923 ACTAATGGGGTAGCG
1 ACTAATGCGGTAACG
2296938 ACTAATGCGGTAACG
1 ACTAATGCGGTAACG
2296953 ACTAATGCGGT
1 ACTAATGCGGT
2296964 GGTTGCAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (15 bp):
ACTAATGCGGTAACG
Found at i:2306819 original size:90 final size:89
Alignment explanation
Indices: 2306675--2306839 Score: 294
Period size: 90 Copynumber: 1.8 Consensus size: 89
2306665 TTTTATAGCC
2306675 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
1 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
* *
2306740 GAATTTAATAATCCTCTTATATCA
66 AAATTAAATAATCCTCTTATATCA
*
2306764 AAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 AAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
2306829 GAAATTAAATA
65 GAAATTAAATA
2306840 TTCAGGATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 22 0.31
90 50 0.69
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (89 bp):
AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
AAATTAAATAATCCTCTTATATCA
Found at i:2311852 original size:64 final size:66
Alignment explanation
Indices: 2311781--2311920 Score: 169
Period size: 65 Copynumber: 2.2 Consensus size: 66
2311771 CCAAGTGTGC
* * * *
2311781 ATCGATGCATAAAATGCATTCAATG-TTTCA-AAATAGCCTGACTGCATCGATGCATGGA-TGGT
1 ATCGATGCATAAAATACATTCAATGTTTTCATAAA-ACCCCGACTACATCGATGCATGGATTGGT
*
2311843 TA
65 GA
* * *
2311845 ATCGATGCATCAAATACATTCGATGTTTTCATAAAACCCCGAGTACATCGATGCATGGATTGGTG
1 ATCGATGCATAAAATACATTCAATGTTTTCATAAAACCCCGACTACATCGATGCATGGATTGGTG
*
2311910 C
66 A
2311911 ATCGATGCAT
1 ATCGATGCAT
2311921 GGATTGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 22 0.34
65 25 0.39
66 17 0.27
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (66 bp):
ATCGATGCATAAAATACATTCAATGTTTTCATAAAACCCCGACTACATCGATGCATGGATTGGTG
A
Found at i:2311915 original size:20 final size:20
Alignment explanation
Indices: 2311890--2311928 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2311880 ACCCCGAGTA
2311890 CATCGATGCATGGATTGGTG
1 CATCGATGCATGGATTGGTG
2311910 CATCGATGCATGGATTGGT
1 CATCGATGCATGGATTGGT
2311929 AAATCGGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
CATCGATGCATGGATTGGTG
Found at i:2311934 original size:20 final size:20
Alignment explanation
Indices: 2311891--2311940 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2311881 CCCCGAGTAC
**
2311891 ATCGATGCATGGATTGGTGC
1 ATCGATGCATGGATTGGTAA
2311911 ATCGATGCATGGATTGGTAA
1 ATCGATGCATGGATTGGTAA
*
2311931 ATCGGTGCAT
1 ATCGATGCAT
2311941 CACATTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (20 bp):
ATCGATGCATGGATTGGTAA
Found at i:2313797 original size:76 final size:76
Alignment explanation
Indices: 2313561--2313769 Score: 368
Period size: 75 Copynumber: 2.8 Consensus size: 76
2313551 TAATTAAATA
2313561 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
2313626 GGATATTATTT
66 GGATATTATTT
* *
2313637 TTATATTTTATCTTT-TTTTAGGTATTTTAATTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
2313701 GGATATTATTT
66 GGATATTATTT
*
2313712 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
2313770 GGATTTAAGA
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
75 78 0.61
76 49 0.39
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:2314391 original size:17 final size:17
Alignment explanation
Indices: 2314365--2314398 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2314355 CTTTATCCCA
*
2314365 ATTTAGTTATTTTATTT
1 ATTTAGTTATTTAATTT
*
2314382 ATTTATTTATTTAATTT
1 ATTTAGTTATTTAATTT
2314399 TTATTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTAGTTATTTAATTT
Found at i:2314768 original size:83 final size:82
Alignment explanation
Indices: 2314678--2314842 Score: 217
Period size: 83 Copynumber: 2.0 Consensus size: 82
2314668 TGACGCGCAA
* * * *
2314678 TTGTGTGTCATAAATCTATGACATGCATTTATGACGCTT-ATTGCGCGTCATTGAAGCCCCCATC
1 TTGTGTGTCATAAATCTATGACACGCATGTATGA--CTTAATTGCGCGTCATTGAAGCACACATC
*
2314742 A-TAAATGAAGATGACACAT
64 ATTAAA-AAAGATGACACAT
* *
2314761 TTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACATCA
1 TTGTGTGTCATAAATCTATGACACGCATGTATGACTTA-ATTGCGCGTCATTGAAGCACACATCA
2314826 TTAAAAAAGATGACACA
65 TTAAAAAAGATGACACA
2314843 CATTCTTATG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
81 3 0.04
83 65 0.90
84 4 0.06
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (82 bp):
TTGTGTGTCATAAATCTATGACACGCATGTATGACTTAATTGCGCGTCATTGAAGCACACATCAT
TAAAAAAGATGACACAT
Found at i:2323968 original size:60 final size:59
Alignment explanation
Indices: 2323835--2323968 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 59
2323825 GTGTGCAAGA
*
2323835 AAACTTAGTGCAGGTAGTGGACACAACCTTATGTGTCATATCTGGATCCACTAGAGTGT
1 AAACTTAGTGTAGGTAGTGGACACAACCTTATGTGTCATATCTGGATCCACTAGAGTGT
* * * * * *
2323894 AAACCTAGTATAGGTGGTGGGCACGACCTTA-GTGTCATATCTGGATCAGCACTATAGTGT
1 AAACTTAGTGTAGGTAGTGGACACAACCTTATGTGTCATATCTGGATC--CACTAGAGTGT
*
2323954 AAGCTTAGTGTAGGT
1 AAACTTAGTGTAGGT
2323969 TTAGCACTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 16 0.25
59 25 0.40
60 22 0.35
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (59 bp):
AAACTTAGTGTAGGTAGTGGACACAACCTTATGTGTCATATCTGGATCCACTAGAGTGT
Found at i:2335565 original size:18 final size:17
Alignment explanation
Indices: 2335530--2335564 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2335520 AAGGATATCC
*
2335530 TAAAAAATGTTAGATTT
1 TAAAAAATGATAGATTT
2335547 TAAAAAATGATAGATTT
1 TAAAAAATGATAGATTT
2335564 T
1 T
2335565 TCAACTCAAA
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:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (17 bp):
TAAAAAATGATAGATTT
Found at i:2335849 original size:36 final size:36
Alignment explanation
Indices: 2335807--2335897 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
2335797 TGTATTAATG
**
2335807 TCCTTAATGTAATGTATTAAGTTTGTTGTTTTTATC
1 TCCTTAATGTAATGTATTAAGTTCATTGTTTTTATC
* * *
2335843 TTCTTAATGTAATGT-TCATGGTTCATTGTTTTTATC
1 TCCTTAATGTAATGTATTA-AGTTCATTGTTTTTATC
2335879 TCCTTAATGTAATG-ATTAA
1 TCCTTAATGTAATGTATTAA
2335898 TGGTTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (36 bp):
TCCTTAATGTAATGTATTAAGTTCATTGTTTTTATC
Found at i:2338877 original size:23 final size:22
Alignment explanation
Indices: 2338837--2338881 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2338827 TTAAATTTTA
2338837 AAATCTTTATTATCAAACAATG
1 AAATCTTTATTATCAAACAATG
* *
2338859 AAATCATTTTTTATTAAACAATG
1 AAATC-TTTATTATCAAACAATG
2338882 TGGTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATCTTTATTATCAAACAATG
Found at i:2339101 original size:64 final size:64
Alignment explanation
Indices: 2339025--2339181 Score: 232
Period size: 64 Copynumber: 2.5 Consensus size: 64
2339015 TTATTCGATG
*
2339025 TAAAATTAAATATCTCTAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAGAAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAGAAATAT
* **
2339090 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTATAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAGAAATAT
2339154 TAAAATTAGA-ATC-A-AATATAATA-TAAAA
1 TAAAATTA-ATATCTATAATATAATATTAAAA
2339182 TTAAATATAA
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
61 5 0.06
62 9 0.10
63 1 0.01
64 64 0.74
65 8 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAGAAATAT
Found at i:2339129 original size:40 final size:37
Alignment explanation
Indices: 2339046--2339130 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 37
2339036 ATCTCTAATA
*
2339046 TAATATTAAAAAATTAATATTTAATTTATTTAAAAAAG
1 TAATATT-AAAAATTAATATTTAATTAATTTAAAAAAG
* *
2339084 AAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAG
2339124 TAATATT
1 TAATATT
2339131 TAATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 11 0.28
37 1 0.03
38 10 0.26
39 3 0.08
40 14 0.36
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAG
Found at i:2339151 original size:24 final size:27
Alignment explanation
Indices: 2339090--2339155 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 27
2339080 AAAGAAATAT
2339090 TAAAATTAATATCTATAATATAATATTA
1 TAAAATTAATAT-TATAATATAATATTA
* *
2339118 AAAAATTAATATT-TAAT-TTAT-TTA
1 TAAAATTAATATTATAATATAATATTA
2339142 TAAAATTAATATTA
1 TAAAATTAATATTA
2339156 AAATTAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 15 0.44
25 3 0.09
26 4 0.12
27 1 0.03
28 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAATTAATATTATAATATAATATTA
Found at i:2339188 original size:12 final size:12
Alignment explanation
Indices: 2339140--2339193 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
2339130 TTAATTTATT
2339140 TATAAAATT-AA
1 TATAAAATTAAA
*
2339151 TATTAAAATTAGA
1 TA-TAAAATTAAA
*
2339164 -ATCAAA-TATAA
1 TATAAAATTA-AA
2339175 TATAAAATTAAA
1 TATAAAATTAAA
2339187 TATAAAA
1 TATAAAA
2339194 CCTCTTTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 22 0.65
13 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
TATAAAATTAAA
Found at i:2342402 original size:44 final size:44
Alignment explanation
Indices: 2342348--2342440 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
2342338 TATATTTCAT
* *
2342348 GCTATGTGACATGATCTATGAGATTATATGAAAATGTGATATAA
1 GCTATATGACATGATATATGAGATTATATGAAAATGTGATATAA
* * ***
2342392 GCTATATGACATGATATATGTGATTATTTGTCTATGTGATATAA
1 GCTATATGACATGATATATGAGATTATATGAAAATGTGATATAA
2342436 GCTAT
1 GCTAT
2342441 GTGAAATGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (44 bp):
GCTATATGACATGATATATGAGATTATATGAAAATGTGATATAA
Found at i:2342568 original size:23 final size:23
Alignment explanation
Indices: 2342542--2342616 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
2342532 TTCGAGATAA
2342542 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
2342565 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * *
2342588 CTCTATGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
2342611 TTCTAC
1 TTCTAC
2342617 ATGGCACATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.13, C:0.27, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:2347111 original size:12 final size:12
Alignment explanation
Indices: 2347077--2347116 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2347067 TTTCTTCTCT
2347077 TTTTAAGTTTTCA
1 TTTTAAGTTTT-A
*
2347090 TTTTTA-TTTTA
1 TTTTAAGTTTTA
2347101 TTTTAAGTTTTA
1 TTTTAAGTTTTA
2347113 TTTT
1 TTTT
2347117 TTAAAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTAAGTTTTA
Found at i:2353439 original size:12 final size:12
Alignment explanation
Indices: 2353405--2353444 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2353395 TTTCTTTTCT
2353405 TTTTAAGTTTTCA
1 TTTTAAGTTTT-A
*
2353418 TTTTTA-TTTTA
1 TTTTAAGTTTTA
2353429 TTTTAAGTTTTA
1 TTTTAAGTTTTA
2353441 TTTT
1 TTTT
2353445 TTAAAATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTAAGTTTTA
Found at i:2357227 original size:44 final size:44
Alignment explanation
Indices: 2357100--2357239 Score: 181
Period size: 44 Copynumber: 3.2 Consensus size: 44
2357090 TATTTCATGC
* *
2357100 TATGTGACATGTTCTATGTGATTATATGAAAATGTGATATGAGT
1 TATGTGACATGATCTATGTGATTATATGAAAATGTGATATAAGT
* * *
2357144 TATGTGATATTGAACTATGTGATTATATGAAAATTTGATATAAGT
1 TATGTGACA-TGATCTATGTGATTATATGAAAATGTGATATAAGT
* *** *
2357189 TATGTGACATGATCTATGTGATTATTTGTCTATGTGATATAAGC
1 TATGTGACATGATCTATGTGATTATATGAAAATGTGATATAAGT
2357233 TATGTGA
1 TATGTGA
2357240 AATGGTATAA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 43 0.52
45 39 0.48
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (44 bp):
TATGTGACATGATCTATGTGATTATATGAAAATGTGATATAAGT
Found at i:2357237 original size:14 final size:14
Alignment explanation
Indices: 2357179--2357239 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
2357169 TATGAAAATT
*
2357179 TGATATAAGTTATG
1 TGATATAAGCTATG
* * *
2357193 TGACATGATCTATG
1 TGATATAAGCTATG
**
2357207 TGATTATTTGTCTATG
1 TGA-TATAAG-CTATG
2357223 TGATATAAGCTATG
1 TGATATAAGCTATG
2357237 TGA
1 TGA
2357240 AATGGTATAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
14 21 0.60
15 6 0.17
16 8 0.23
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGATATAAGCTATG
Found at i:2357349 original size:23 final size:23
Alignment explanation
Indices: 2357316--2357413 Score: 133
Period size: 23 Copynumber: 4.3 Consensus size: 23
2357306 GAGTCATGGG
*
2357316 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
*
2357339 TTCTACATGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * *
2357362 TTCTATGTGGTCATTCGGGATAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
2357385 TTCTATGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
2357408 TTCTAC
1 TTCTAC
2357414 ATGACAATTC
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:2366743 original size:17 final size:17
Alignment explanation
Indices: 2366713--2366775 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
2366703 GCATGAAACA
**
2366713 ATTAATGAGTTAGTTAG
1 ATTAATGAACTAGTTAG
*
2366730 ATTAATGCACTAGTTTA-
1 ATTAATGAACTAG-TTAG
* *
2366747 ATAAATGAACTAGTTTG
1 ATTAATGAACTAGTTAG
2366764 ATTAATGAACTA
1 ATTAATGAACTA
2366776 ACTTTATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 2 0.05
17 32 0.86
18 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (17 bp):
ATTAATGAACTAGTTAG
Found at i:2366784 original size:17 final size:18
Alignment explanation
Indices: 2366750--2366793 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
2366740 TAGTTTAATA
*
2366750 AATGAACT-AGTTTGATT
1 AATGAACTAACTTTGATT
2366767 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTGATT
2366784 AATGAACTAA
1 AATGAACTAA
2366794 AGGCATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTGATT
Found at i:2366788 original size:34 final size:34
Alignment explanation
Indices: 2366712--2366792 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
2366702 TGCATGAAAC
** * *
2366712 AATTAATGAGTTAGTTAGATTAATGCACTAGTTT
1 AATTAATGAACTAGTTAGATTAATGAACTACTTT
* *
2366746 AATAAATGAACTAGTTTGATTAATGAACTAACTTT
1 AATTAATGAACTAGTTAGATTAATGAACT-ACTTT
2366781 -ATTAATGAACTA
1 AATTAATGAACTA
2366793 AAGGCATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (34 bp):
AATTAATGAACTAGTTAGATTAATGAACTACTTT
Found at i:2367464 original size:17 final size:17
Alignment explanation
Indices: 2367439--2367472 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2367429 AATGAGATAA
*
2367439 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
2367456 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
2367473 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:2368176 original size:24 final size:24
Alignment explanation
Indices: 2368149--2368262 Score: 70
Period size: 25 Copynumber: 4.5 Consensus size: 24
2368139 AAATCCTAAT
2368149 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** ** *
2368173 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
2368198 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
2368225 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
2368249 TAAAATACCTAAAA
1 TAAAATA-CTAAAA
2368263 GAAAGATAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 17
0.66 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 19 0.29
25 23 0.35
26 10 0.15
27 8 0.12
28 2 0.03
ACGTcount: A:0.59, C:0.14, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:2368190 original size:75 final size:76
Alignment explanation
Indices: 2368063--2368278 Score: 319
Period size: 76 Copynumber: 2.9 Consensus size: 76
2368053 TAAAACATCT
* ** * * *
2368063 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAACTAAAACACCTATGACAAAAATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
2368126 AAAGTAATATCC
65 AAAATAATATCC
2368138 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
2368203 AAATAATATCC
66 AAATAATATCC
* * *
2368214 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAGAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
2368279 TGTTTATAAT
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
74 5 0.04
75 50 0.39
76 74 0.57
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.28
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:2368197 original size:44 final size:44
Alignment explanation
Indices: 2368149--2368275 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
2368139 AAATCCTAAT
2368149 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
* *
2368193 TAAAATA-TAAAA---A--T-AA-T---AT-CCTAAAACTTAA-T
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAC-AAAGA
*
2368225 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAGAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
2368269 TAAAATA
1 TAAAATA
2368276 TAATGTTTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 21 0.33
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (44 bp):
TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
Found at i:2408309 original size:22 final size:21
Alignment explanation
Indices: 2408259--2408314 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
2408249 AACAAAAAGT
2408259 GGGTATCGGTACCCTAGTAGG
1 GGGTATCGGTACCCTAGTAGG
2408280 GGGTATCGGTACCCTAGTAGG
1 GGGTATCGGTACCCTAGTAGG
*
2408301 GTGGTATCGATACC
1 G-GGTATCGGTACC
2408315 ATGGTAAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 22 0.67
22 11 0.33
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGTATCGGTACCCTAGTAGG
Found at i:2408909 original size:45 final size:45
Alignment explanation
Indices: 2408842--2409107 Score: 259
Period size: 45 Copynumber: 5.9 Consensus size: 45
2408832 ATAAAAATTA
* * * * *
2408842 AAATGCATACGGGTGCATTATCAGCATGAAATG-ATGCTATAGTTG
1 AAATGTATATGGGTACATTATCAACA-GAAAAGTATGCTATAGTTG
* * * *
2408887 AAATATATATGGGTACTTTATCAACAAAAAAGTATGCAATAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTG
* *
2408932 AAATGTATATGGGTACATTATCAACAGTAAAGTATACTATAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTG
* *
2408977 AAATGTATATGGGTACATTATCAACAGAAAAGTATGTTATTGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTG
* * * **
2409022 AAAT-TCATATGGGTGCATTATCAACATAAAAATATATTAT-GATTG
1 AAATGT-ATATGGGTACATTATCAACAGAAAAGTATGCTATAG-TTG
* * * * * * *
2409067 AAATGTGTATTGGTGCATTATTAACATAAAGGTATGTTATA
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATA
2409108 AGTAATAATG
Statistics
Matches: 187, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
44 6 0.03
45 180 0.96
46 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (45 bp):
AAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTG
Found at i:2409086 original size:135 final size:133
Alignment explanation
Indices: 2408842--2409097 Score: 295
Period size: 135 Copynumber: 1.9 Consensus size: 133
2408832 ATAAAAATTA
* * * *
2408842 AAATGCATACGGGTGCATTATCAGCATGAAATGATGCTATAGTTGAAATATATATGGGTACTTTA
1 AAATGCATACGGGTACATTATCAACATGAAAAGATGCTATAGTTGAAATATATATGGGTACATTA
2408907 TCAACAAAAAAGTATGCAATAGTTGAAATGTATATGGGTACATTATCAACAGTAAAGTATACTAT
66 TCAACAAAAAAGTAT-CAATAGTTGAAATGTATATGGGTACATTATCAACA-TAAAGTATACTAT
2408972 AGTTG
129 AGTTG
* * * * *
2408977 AAATGTATATGGGTACATTATCAACA-GAAAAGTATGTTATTGTTGAAAT-TCATATGGGTGCAT
1 AAATGCATACGGGTACATTATCAACATGAAAAG-ATGCTATAGTTGAAATAT-ATATGGGTACAT
* * * * *
2409040 TATCAACATAAAAA-TAT-ATTATGATTGAAATGTGTATTGGTGCATTATTAACATAAAG
64 TATCAACA-AAAAAGTATCAATA-G-TTGAAATGTATATGGGTACATTATCAACATAAAG
2409098 GTATGTTATA
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
133 3 0.03
134 12 0.12
135 82 0.80
136 5 0.05
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (133 bp):
AAATGCATACGGGTACATTATCAACATGAAAAGATGCTATAGTTGAAATATATATGGGTACATTA
TCAACAAAAAAGTATCAATAGTTGAAATGTATATGGGTACATTATCAACATAAAGTATACTATAG
TTG
Found at i:2415249 original size:23 final size:23
Alignment explanation
Indices: 2415222--2415279 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
2415212 ACTAGAAAGG
2415222 GGGTATCGGTACCCTAGTAGGGT
1 GGGTATCGGTACCCTAGTAGGGT
2415245 GGGTATCGGTACCCTAGTAGGGT
1 GGGTATCGGTACCCTAGTAGGGT
*
2415268 -GGTATCGATACC
1 GGGTATCGGTACC
2415280 ATGGTAAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (23 bp):
GGGTATCGGTACCCTAGTAGGGT
Found at i:2415378 original size:17 final size:16
Alignment explanation
Indices: 2415347--2415380 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2415337 AGGAGTATCG
*
2415347 GTACCATAGTATAGTA
1 GTACCATACTATAGTA
2415363 GTACCGATACTATAGTA
1 GTACC-ATACTATAGTA
2415380 G
1 G
2415381 GGGTATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (16 bp):
GTACCATACTATAGTA
Found at i:2415869 original size:45 final size:45
Alignment explanation
Indices: 2415820--2416115 Score: 362
Period size: 45 Copynumber: 6.6 Consensus size: 45
2415810 CATACGAGTG
* *
2415820 CATTATCAGCATGAAATG-ATGCTATAGTTGAAATGTATATGGGTA
1 CATTATCAACA-GAAAAGTATGCTATAGTTGAAATGTATATGGGTA
*
2415865 CATTATCAACAGAAAAGTATGCAATAGTTGAAATGTATATGGGTA
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* *
2415910 CATTATCAATAGAAAAGTATGCAATAGTTGAAATGTATATGGGTA
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* *
2415955 CATTATCAACAGTAAAGTATACTATAGTTGAAATGTATATGGGTA
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* * * *
2416000 TATTATCAACAGAAAAGTATGTTATTGTTGAAATGCATATGGGTA
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* * ** * * *
2416045 CATTATCAACATAAAAATATATTAT-GACTGAAATGCATATGGGTG
1 CATTATCAACAGAAAAGTATGCTATAG-TTGAAATGTATATGGGTA
* * * *
2416090 CATTATTAACATAAAGGTATGTTATA
1 CATTATCAACAGAAAAGTATGCTATA
2416116 AGTAATAATG
Statistics
Matches: 224, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
44 6 0.03
45 218 0.97
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (45 bp):
CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
Found at i:2417026 original size:13 final size:14
Alignment explanation
Indices: 2417003--2417037 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2416993 TTTAATTTGA
*
2417003 TTATAAAAAATAAT
1 TTATTAAAAATAAT
2417017 TT-TTAAAAATAAT
1 TTATTAAAAATAAT
2417030 TTATTAAA
1 TTATTAAA
2417038 TTTAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATTAAAAATAAT
Found at i:2418674 original size:7 final size:7
Alignment explanation
Indices: 2418662--2418686 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2418652 TAATAATTTT
2418662 ATTTAAA
1 ATTTAAA
2418669 ATTTAAA
1 ATTTAAA
2418676 ATTTAAA
1 ATTTAAA
2418683 ATTT
1 ATTT
2418687 TAATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:2420828 original size:37 final size:37
Alignment explanation
Indices: 2420758--2420847 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 37
2420748 ATTCTCATCA
* *
2420758 AATATAAATTCATAATAATGCATTCATATTTTAATTG
1 AATATAAACTCATAATAATGAATTCATATTTTAATTG
**
2420795 AATATAAACTCATTAATAATGAATTTGTA-TTTAATTG
1 AATATAAACTCA-TAATAATGAATTCATATTTTAATTG
*
2420832 AATATAAATTCA-AATA
1 AATATAAACTCATAATA
2420848 TAATATAGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.09
37 30 0.64
38 13 0.28
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (37 bp):
AATATAAACTCATAATAATGAATTCATATTTTAATTG
Found at i:2421444 original size:2 final size:2
Alignment explanation
Indices: 2421439--2421479 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2421429 ATTTTGAATG
2421439 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
2421480 TTAAAAGTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2421806 original size:23 final size:24
Alignment explanation
Indices: 2421764--2421809 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2421754 AAATATTAAT
2421764 ATTTTAAAATAGATAAAATTATAC
1 ATTTTAAAATAGATAAAATTATAC
* *
2421788 ATTTTATAATA-ATACAATTATA
1 ATTTTAAAATAGATAAAATTATA
2421810 ATTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTTTAAAATAGATAAAATTATAC
Found at i:2422470 original size:37 final size:38
Alignment explanation
Indices: 2422384--2422486 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 38
2422374 ATATTTGTAG
*
2422384 TTAATTAAATAAAAATTTATAAATAATATATTCCTATT
1 TTAATTAAATATAAATTTATAAATAATATATTCCTATT
* ** *
2422422 TGAATCGAATATAAATTTGT-AATAATATATTCAC-ATT
1 TTAATTAAATATAAATTTATAAATAATATATTC-CTATT
* **
2422459 TTAATTTAATATAAATCCATAAATAATA
1 TTAATTAAATATAAATTTATAAATAATA
2422487 GTACATTATC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 29 0.56
38 23 0.44
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (38 bp):
TTAATTAAATATAAATTTATAAATAATATATTCCTATT
Found at i:2425229 original size:29 final size:29
Alignment explanation
Indices: 2425196--2425289 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
2425186 CGTTGACCGA
* * ** *
2425196 TGCTATTCTGGGAATTAATTCGATTTTGG
1 TGCTATTATGGGAATTAATTCAAAATGGG
*
2425225 TGCTATTATTGGAATTAATTCAAAATGGG
1 TGCTATTATGGGAATTAATTCAAAATGGG
* * ** *
2425254 TGCTATTTTGGTAATTAATTTGAAACGGG
1 TGCTATTATGGGAATTAATTCAAAATGGG
2425283 TGCTATT
1 TGCTATT
2425290 TCTCTAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.43
Consensus pattern (29 bp):
TGCTATTATGGGAATTAATTCAAAATGGG
Found at i:2425290 original size:29 final size:28
Alignment explanation
Indices: 2425223--2425290 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
2425213 ATTCGATTTT
*
2425223 GGTGCTATTATTGGAATTAATTCAAAATG
1 GGTGCTATT-TTGGAATTAATTCAAAACG
**
2425252 GGTGCTATTTTGGTAATTAATTTGAAACG
1 GGTGCTATTTTGG-AATTAATTCAAAACG
2425281 GGTGCTATTT
1 GGTGCTATTT
2425291 CTCTAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (28 bp):
GGTGCTATTTTGGAATTAATTCAAAACG
Found at i:2426284 original size:42 final size:41
Alignment explanation
Indices: 2426219--2426453 Score: 252
Period size: 42 Copynumber: 5.7 Consensus size: 41
2426209 TATTATCATA
*
2426219 TCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGG
1 TCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCCCAGG
*
2426261 TCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCAGG
1 TCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCCCAGG
*
2426303 TCCCTTTGCTGTGTGTGAAGGTAAGCCTTACAGTTTCCCAGG
1 TCCCTTTGCTGTGTG-CAAGGTAAGCCTTACAGTTTCCCAGG
*
2426345 TCCCTTTGTTGTGTGCAAGG---G----ACAGTTTCCCAGG
1 TCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCCCAGG
* * * *
2426379 TCCCTTTACTGTGTGCAAGGATAAACCTTAGAGTTTTCCTAGG
1 TCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTCCCAGG
* *
2426422 -CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 TC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
2426454 TAGTGTATAG
Statistics
Matches: 163, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
34 31 0.19
38 1 0.01
41 6 0.04
42 92 0.56
43 22 0.13
44 11 0.07
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (41 bp):
TCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCCCAGG
Found at i:2426375 original size:34 final size:34
Alignment explanation
Indices: 2426332--2426398 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2426322 GGTAAGCCTT
**
2426332 ACAGTTTCCCAGGTCCCTTTGTTGTGTGCAAGGG
1 ACAGTTTCCCAGGTCCCTTTACTGTGTGCAAGGG
2426366 ACAGTTTCCCAGGTCCCTTTACTGTGTGCAAGG
1 ACAGTTTCCCAGGTCCCTTTACTGTGTGCAAGG
2426399 ATAAACCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (34 bp):
ACAGTTTCCCAGGTCCCTTTACTGTGTGCAAGGG
Found at i:2432440 original size:17 final size:18
Alignment explanation
Indices: 2432418--2432458 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2432408 TGACCGGTCA
2432418 CGACCCAACCCGTTGA-C
1 CGACCCAACCCGTTGACC
*
2432435 CGACCCGACCCGTTGACC
1 CGACCCAACCCGTTGACC
2432453 CGACCC
1 CGACCC
2432459 GACCATTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (18 bp):
CGACCCAACCCGTTGACC
Found at i:2432467 original size:17 final size:18
Alignment explanation
Indices: 2432418--2432469 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
2432408 TGACCGGTCA
* *
2432418 CGACCCAACCCGTTGA-C
1 CGACCCGACCCATTGACC
*
2432435 CGACCCGACCCGTTGACC
1 CGACCCGACCCATTGACC
2432453 CGACCCGA-CCATTGACC
1 CGACCCGACCCATTGACC
2432470 GGTGCTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCATTGACC
Found at i:2432531 original size:29 final size:29
Alignment explanation
Indices: 2432499--2432567 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
2432489 GTTCGATTTT
*
2432499 GGTGCTATTATAGG-AATTAATTC-AAAATG
1 GGTGCTATT-T-GGTAATTAATTCGAAAAGG
2432528 GGTGCTACTTTGGTAATTAATTCGAAAAGG
1 GGTGCTA-TTTGGTAATTAATTCGAAAAGG
*
2432558 GGTGTTATTT
1 GGTGCTATTT
2432568 TTGTAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 20 0.57
30 13 0.37
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (29 bp):
GGTGCTATTTGGTAATTAATTCGAAAAGG
Found at i:2433552 original size:42 final size:41
Alignment explanation
Indices: 2433493--2433739 Score: 334
Period size: 42 Copynumber: 5.8 Consensus size: 41
2433483 GAAGTATTAT
2433493 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
2433535 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
2433577 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* *
2433619 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
2433661 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTAC
* *
2433703 CTAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
2433740 TGGTGTATAG
Statistics
Matches: 187, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
41 6 0.03
42 151 0.81
43 18 0.10
44 12 0.06
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:2433636 original size:84 final size:84
Alignment explanation
Indices: 2433493--2433739 Score: 374
Period size: 84 Copynumber: 2.9 Consensus size: 84
2433483 GAAGTATTAT
*
2433493 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGTTGTGTGCAAG
2433558 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
*
2433577 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGTTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGTTGTGTGCAAG
2433642 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* * *
2433661 CAGGTCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTTTCCTAGG-CTCCTCTGCTT-TGTG
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTACC-AGGTC-CCTTTG-TTGTGTG
*
2433723 CACAGGTTAAGCCTTAC
62 CA-AGGGTAAGCCTTAC
2433740 TGGTGTATAG
Statistics
Matches: 151, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
83 4 0.03
84 118 0.78
85 14 0.09
86 15 0.10
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGTTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:2435533 original size:22 final size:23
Alignment explanation
Indices: 2435490--2435533 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
2435480 ATAAAATCAT
* **
2435490 AAATATTATATTTATATTTAATC
1 AAATATTACATTTATAAATAATC
2435513 AAATA-TACATTTATAAATAAT
1 AAATATTACATTTATAAATAAT
2435534 ATATTCCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATTACATTTATAAATAATC
Found at i:2435596 original size:37 final size:36
Alignment explanation
Indices: 2435392--2435597 Score: 189
Period size: 37 Copynumber: 5.5 Consensus size: 36
2435382 TACAATTTTG
* *
2435392 TATTCTAATTGAATAT-AATTTCGTAATAATATATTCG
1 TATT-TAATTGAATATAAATTT-ATAATAATATATTCA
* * *
2435429 TATGTTAATTGAATATAAATTCACAGATAATATATTTA
1 TAT-TTAATTGAATATAAATTTATA-ATAATATATTCA
* * * *
2435467 TATTTAATTGAATATAAAATCATAAATATTATATTTA
1 TATTTAATTGAATATAAATTTAT-AATAATATATTCA
** * *
2435504 TATTTAATCAAATATACATTTATAAATAATATATTCC
1 TATTTAATTGAATATAAATTTAT-AATAATATATTCA
* *
2435541 TATTTCAATCGAATATAAATTTGTAATAATATATTCA
1 TATTT-AATTGAATATAAATTTATAATAATATATTCA
*
2435578 CACTTTAATTGAATATAAAT
1 TA-TTTAATTGAATATAAAT
2435598 CTTTAAATAA
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
37 104 0.74
38 37 0.26
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
TATTTAATTGAATATAAATTTATAATAATATATTCA
Found at i:2438387 original size:16 final size:14
Alignment explanation
Indices: 2438358--2438392 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2438348 CGTTCATTTA
2438358 ATAAATAAACGAAC
1 ATAAATAAACGAAC
2438372 ATAAATGAACACGAAC
1 ATAAAT-AA-ACGAAC
2438388 ATAAA
1 ATAAA
2438393 CGTTGGAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (14 bp):
ATAAATAAACGAAC
Found at i:2439493 original size:10 final size:10
Alignment explanation
Indices: 2439478--2439514 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2439468 AACATAAATG
2439478 AACGAACATA
1 AACGAACATA
2439488 AACGAACATA
1 AACGAACATA
*
2439498 AATGAACATA
1 AACGAACATA
*
2439508 ACCGAAC
1 AACGAAC
2439515 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:2442456 original size:16 final size:16
Alignment explanation
Indices: 2442432--2442462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2442422 TTTCCAGAGT
*
2442432 TTAGTATACTTTTACC
1 TTAGCATACTTTTACC
2442448 TTAGCATACTTTTAC
1 TTAGCATACTTTTAC
2442463 AATTTATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
TTAGCATACTTTTACC
Found at i:2450164 original size:81 final size:81
Alignment explanation
Indices: 2449957--2450428 Score: 746
Period size: 81 Copynumber: 5.8 Consensus size: 81
2449947 TGTTCTAAAA
* * *
2449957 TAAAAGATTAGTGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2450022 GTTAAATACCCTTTGAG
66 GTTAAATA-CTTTTGAG
* * *
2450039 TTAAAGATTATTGGCCTAGTTGTGCATTTGGCTGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2450104 GTTAAATACTTTTGAG
66 GTTAAATACTTTTGAG
* *
2450120 TAAAAGATTAATGGACTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2450185 GTTAAATACTTTTGAG
66 GTTAAATACTTTTGAG
* * * * *
2450201 TAAAAGATTAATGGCCTAGATGTGTATTTGGAAGAAAGGTGTCAAATATGACAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2450266 GTTAAATACTTTTGAG
66 GTTAAATACTTTTGAG
* *
2450282 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2450347 GTTAAATACTTTTGAG
66 GTTAAATACTTTTGAG
* * * * *
2450363 TAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGTCAGTTAAATAAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2450428 G
66 G
2450429 AATGGCCTAG
Statistics
Matches: 359, Mismatches: 31, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
81 291 0.81
82 68 0.19
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACTTTTGAG
Found at i:2450474 original size:56 final size:57
Alignment explanation
Indices: 2450372--2450484 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 57
2450362 GTAAAAGATT
* * *
2450372 AATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGTCAGTTAAATAAAAGG
1 AATGGCCTAGCTATGCATTTGGGAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
* *
2450429 AATGGCCTAGCTATGCATTTGGGA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 AATGGCCTAGCTATGCATTTGGGAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
2450485 TTAAATACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 29 0.57
57 22 0.43
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (57 bp):
AATGGCCTAGCTATGCATTTGGGAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
Found at i:2450559 original size:81 final size:81
Alignment explanation
Indices: 2450429--2450808 Score: 564
Period size: 81 Copynumber: 4.7 Consensus size: 81
2450419 AAATAAAAGG
* *
2450429 AATGGCCTAGCTATGCATTTGGGA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
2450493 CTTTGAGTAAAAGATT
66 CTTTGAGTAAAAGATT
* *
2450509 AATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
*
2450574 CTATGAGTAAAAGATT
66 CTTTGAGTAAAAGATT
* ** * *
2450590 AATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGTAAGTTAAATGAAAGGTTAAATGC
1 AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
*
2450655 CTTTGAGTAAAAAATT
66 CTTTGAGTAAAAGATT
*
2450671 AATGGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
2450736 CTTTGAGTAAAAGATT
66 CTTTGAGTAAAAGATT
* * * * * * ** *
2450752 AATGGCCTACCTGTTCATTTGGCTGGAAGGTTTCAATCATGTAAATTAGATGAAAGG
1 AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
2450809 CTAAGTGTCT
Statistics
Matches: 269, Mismatches: 30, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
80 22 0.08
81 247 0.92
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (81 bp):
AATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
CTTTGAGTAAAAGATT
Found at i:2450565 original size:137 final size:138
Alignment explanation
Indices: 2450291--2450549 Score: 448
Period size: 137 Copynumber: 1.9 Consensus size: 138
2450281 GTAAAAGATT
* *
2450291 AATGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGCTATGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAGATGAAAGGTTAAATAC
* *
2450356 TTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGTCAGTTAA
66 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAA
2450421 ATAAAAGG
131 ATAAAAGG
* *
2450429 AATGGCCTAGCTATGCATTTGGGA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGCTATGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAGATGAAAGGTTAAATAC
*
2450493 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATG
66 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATG
2450550 CTAGTTAGAT
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
137 93 0.82
138 21 0.18
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (138 bp):
AATGGCCTAGCTATGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAGATGAAAGGTTAAATAC
CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAA
ATAAAAGG
Found at i:2450619 original size:218 final size:219
Alignment explanation
Indices: 2450210--2450646 Score: 705
Period size: 218 Copynumber: 2.0 Consensus size: 219
2450200 GTAAAAGATT
* *
2450210 AATGGCCTAGATGTGTATTTGGAAGAAAGGTGTCAAATATGACAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGATATGCATTTGGAAGAAAGGTGTCAAATATGACAGTTAGATGAAAGGTTAAATAC
* * *
2450275 TTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAATTAAGCCAGTTAG
66 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTAAGCCAGTTAG
* * *
2450340 ATGAAAGGTTAAATACTTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGT
131 ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT
*
2450405 CAATTATGTCAGTTAAATAAAAGG
196 CAATTATGTAAGTTAAATAAAAGG
* * * *
2450429 AATGGCCTAGCTATGCATTTGGGA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGCCTAGATATGCATTTGGAAGAAAGGTGTCAAATATGACAGTTAGATGAAAGGTTAAATAC
* * *
2450493 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAG
66 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTAAGCCAGTTAG
*
2450558 ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGT
131 ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT
*
2450623 CAATTATGTAAGTTAAATGAAAGG
196 CAATTATGTAAGTTAAATAAAAGG
2450647 TTAAATGCCT
Statistics
Matches: 200, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
218 180 0.90
219 20 0.10
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (219 bp):
AATGGCCTAGATATGCATTTGGAAGAAAGGTGTCAAATATGACAGTTAGATGAAAGGTTAAATAC
CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTAAGCCAGTTAG
ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT
CAATTATGTAAGTTAAATAAAAGG
Found at i:2450692 original size:299 final size:300
Alignment explanation
Indices: 2450129--2450727 Score: 959
Period size: 299 Copynumber: 2.0 Consensus size: 300
2450119 GTAAAAGATT
*
2450129 AATGGACTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGACTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
* *
2450194 TTTTGAGTAAAAGATTAATGGCCTAGATGTGTATTTGGAAGAAAGGTGTCAAATATGACAGTTAG
66 CTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAAATATGACAGTTAG
* * *
2450259 ATGAAAGGTTAAATACTTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCATAAAGGTGT
131 ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGT
* * * *
2450324 CAATTAAGCCAGTTAGATGAAAGGTTAAATACTTTTGAGTAAAAGATTAATGGCCTAGCTGTGCA
196 CAATTAAGCAAGTTAAATGAAAGGTTAAATACCTTTGAGTAAAAAATTAATGGCCTAGCTGTGCA
* *
2450389 TTTGGTAGAAAGGTGTCAATTATGTCAGTTAAATAAAAGG
261 TTTGGCAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
* *
2450429 AATGGCCTAGCTATGCATTTGGGA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
1 AATGGACTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
* * * *
2450493 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATG-CTAGTTA
66 CTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAAATATGAC-AGTTA
2450557 GATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTG
130 GATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTG
* * *
2450622 TCAATTATGTAAGTTAAATGAAAGGTTAAATGCCTTTGAGTAAAAAATTAATGGCCTAGCTGTGC
195 TCAATTAAGCAAGTTAAATGAAAGGTTAAATACCTTTGAGTAAAAAATTAATGGCCTAGCTGTGC
* * *
2450687 ATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
260 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
2450728 TTAAATACCT
Statistics
Matches: 274, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
298 1 0.00
299 252 0.92
300 21 0.08
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (300 bp):
AATGGACTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAC
CTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAAATATGACAGTTAG
ATGAAAGGTTAAATACCTATGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGT
CAATTAAGCAAGTTAAATGAAAGGTTAAATACCTTTGAGTAAAAAATTAATGGCCTAGCTGTGCA
TTTGGCAGAAAGGTGTCAATTATGCCAGTTAAATAAAAGG
Found at i:2452027 original size:25 final size:25
Alignment explanation
Indices: 2451991--2452042 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2451981 GCATCAAGGG
* *
2451991 TGCGTTATGTTTTAGTAGTTACGAA
1 TGCGTTATGTTTTAGAAGTTACAAA
*
2452016 TGCGTTCA-GTTTTGGAAGTTACAAA
1 TGCGTT-ATGTTTTAGAAGTTACAAA
2452041 TG
1 TG
2452043 TATCTTATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (25 bp):
TGCGTTATGTTTTAGAAGTTACAAA
Found at i:2459513 original size:43 final size:44
Alignment explanation
Indices: 2459428--2459531 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
2459418 ATTTTACTTG
2459428 GCTTAAACCAGCGAAGGGGAGTCATCCAAAGAATCATCCACCTA
1 GCTTAAACCAGCGAAGGGGAGTCATCCAAAGAATCATCCACCTA
* * * * * *
2459472 TCTTAAACCAGTGTAGGGG-GTCATCCAAAGAATCTTTCACCTG
1 GCTTAAACCAGCGAAGGGGAGTCATCCAAAGAATCATCCACCTA
2459515 GCTTAAACTC-GCGAAGG
1 GCTTAAAC-CAGCGAAGG
2459532 AGAATGAGTC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
43 33 0.66
44 17 0.34
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (44 bp):
GCTTAAACCAGCGAAGGGGAGTCATCCAAAGAATCATCCACCTA
Found at i:2466775 original size:90 final size:89
Alignment explanation
Indices: 2466621--2466793 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
2466611 TAACACACCA
* * *
2466621 TTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATATATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATATAT
*
2466686 TTAATTAATTAGAATTTAATAATCC
66 TTAATTAATT-GAAATTAATAATCC
* *
2466711 TTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATATAT
2466776 TTAATTAATTGAAATTAA
66 TTAATTAATTGAAATTAA
2466794 ATATTTGGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATATAT
TTAATTAATTGAAATTAATAATCC
Found at i:2468262 original size:2 final size:2
Alignment explanation
Indices: 2468251--2468355 Score: 76
Period size: 2 Copynumber: 54.0 Consensus size: 2
2468241 TAGTGTAATG
*
2468251 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * * *
2468292 TA AA TA TA TA TA -A TA TA GTT TT TA AA AA TA TA TA -A T- TT TG
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
2468332 TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
2468356 ATTTTTGACA
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
1 5 0.06
2 78 0.92
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2468352 original size:68 final size:70
Alignment explanation
Indices: 2468265--2468399 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 70
2468255 ATATATATAT
*
2468265 ATATATATATATATATATATATAGTTTT-A-AATATATATAATATAGTTTTTAAAAA-TATATAA
1 ATATATATATATATATATATA-AGTTTTGACAACATAT-T-ATATAGTTTTTAAAAAGTATATAA
2468327 TTTTGTAA
63 TTTTGTAA
*
2468335 ATATATATATATATATATATAATTTTTGACAACATATTATATAGTTTTTAAAAATGTATATAATT
1 ATATATATATATATATATATAAGTTTTGACAACATATTATATAGTTTTTAAAAA-GTATATAATT
2468400 GATCATATAG
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
69 21 0.36
70 23 0.39
71 15 0.25
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (70 bp):
ATATATATATATATATATATAAGTTTTGACAACATATTATATAGTTTTTAAAAAGTATATAATTT
TGTAA
Found at i:2468376 original size:30 final size:30
Alignment explanation
Indices: 2468319--2468377 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2468309 GTTTTTAAAA
*
2468319 ATATATAATTTTGTAAATATATATATATAT
1 ATATATAATTTTGTAAACATATATATATAT
2468349 ATATATAATTTT-TGACAACATAT-TATATA
1 ATATATAATTTTGT-A-AACATATATATATA
2468378 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 19 0.73
31 6 0.23
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
ATATATAATTTTGTAAACATATATATATAT
Found at i:2468543 original size:16 final size:15
Alignment explanation
Indices: 2468511--2468558 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2468501 AACATATAGC
*
2468511 ATATAGGATATACTAT
1 ATATAGG-TATATTAT
2468527 ATAATAGGTATATTAT
1 AT-ATAGGTATATTAT
*
2468543 ATATAAGTATTATTAT
1 ATATAGGTA-TATTAT
2468559 TTTAATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (15 bp):
ATATAGGTATATTAT
Found at i:2474143 original size:20 final size:20
Alignment explanation
Indices: 2474118--2474155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2474108 AACCTGAAAT
2474118 TAGTATCAATACCAAAGGGG
1 TAGTATCAATACCAAAGGGG
*
2474138 TAGTATCAATACTAAAGG
1 TAGTATCAATACCAAAGG
2474156 ATCAATATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (20 bp):
TAGTATCAATACCAAAGGGG
Found at i:2498816 original size:16 final size:16
Alignment explanation
Indices: 2498791--2498825 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2498781 AGTTGAGAAA
2498791 ACATACATCAACACAT
1 ACATACATCAACACAT
* *
2498807 ACATATATCAATACAT
1 ACATACATCAACACAT
2498823 ACA
1 ACA
2498826 CACAAGATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
ACATACATCAACACAT
Found at i:2499254 original size:37 final size:36
Alignment explanation
Indices: 2499208--2499312 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 36
2499198 TAGAGATAGT
*
2499208 TTTCT-TAAAAACAAAATTTTTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAAATTTGTCTCGCTTGAGACAA
*
2499243 CTTTCTCTAAAAACAAAATTTGTCTCGCTTGAGATAA
1 -TTTCTCTAAAAACAAAATTTGTCTCGCTTGAGACAA
* *
2499280 TTTCTCTCAAAAA-AAAA-TCGTCTCGCTTAAGAC
1 TTTCTCT-AAAAACAAAATTTGTCTCGCTTGAGAC
2499313 TTTTTTTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
35 13 0.21
36 16 0.26
37 33 0.53
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (36 bp):
TTTCTCTAAAAACAAAATTTGTCTCGCTTGAGACAA
Found at i:2499571 original size:64 final size:66
Alignment explanation
Indices: 2499420--2499578 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 66
2499410 AAAATTGACA
* * * * *
2499420 ATCTTTGAGTCTTTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAATTTTTCTTTAAAAAA
1 ATCTTTGAGT-ATTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTTAAAAAA
2499485 TC
65 TC
* * * * **
2499487 ATCTTTGAGTCA-TTTACCTTGAAACAAAA-TTT-TCTCTCTTGAGACAGCTTCTC-TTGAAGCA
1 ATCTTTGAGT-ATTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTTAAAAAA
2499548 TC
65 TC
2499550 ATCTTTGAGTATGTTTCCCTTGAAACAAA
1 ATCTTTGAGTAT-TTTCCCTTGAAACAAA
2499579 TCCCTAAAGA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 17 0.22
64 32 0.41
65 3 0.04
66 14 0.18
67 11 0.14
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (66 bp):
ATCTTTGAGTATTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTTAAAAAAT
C
Found at i:2499817 original size:131 final size:133
Alignment explanation
Indices: 2499597--2499921 Score: 361
Period size: 131 Copynumber: 2.4 Consensus size: 133
2499587 GATAGTCTAT
* * *
2499597 CATCCTCATCACGTAGGAACTGTGTCATCCACCTACCAAACCTCATCATCACGTAGGAGTCGTGT
1 CATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAACCTCATCATCACGTAGGAGTCATGT
* * * * * *
2499662 CACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACC-TTATTATCATCCCTAAATATGG-CA
66 CAACCTCAGATAACCAGCCATCCTCATCACGTAGGAACCGTTATCACCATCCCTAAAGATGGACA
**
2499725 TGC
131 AAC
* * * *
2499728 CATCCTCATCACGTAGGAACCGTGTCATCCATCGACTAGACCTTC-TCATCACGTAGGAG-CAAT
1 CATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAACC-TCATCATCACGTAGGAGTC-AT
* * * * *
2499791 GTCAACCTCAGATAACCAGTCATCCTCATCGCGTAGGATCCGTGTTATCACCATCCTTGAAGATG
64 GTCAACCTCAGATAACCAGCCATCCTCATCACGTAGGAACC--GTTATCACCATCCCTAAAGATG
2499856 GACAAAC
127 GACAAAC
* * * * *
2499863 CGTCCTCATCACGTAGGAACAGTGTCATCCACTGACCAGATCTCAACATCACGTAGGAG
1 CATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAACCTCATCATCACGTAGGAG
2499922 CCGTGTCACC
Statistics
Matches: 161, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
130 1 0.01
131 87 0.54
132 2 0.01
134 19 0.12
135 52 0.32
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (133 bp):
CATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAACCTCATCATCACGTAGGAGTCATGT
CAACCTCAGATAACCAGCCATCCTCATCACGTAGGAACCGTTATCACCATCCCTAAAGATGGACA
AAC
Found at i:2503566 original size:24 final size:24
Alignment explanation
Indices: 2503549--2503607 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
2503539 ATAATTTTGA
2503549 AAATTTTATTTAAAATAAAAATAT
1 AAATTTTATTTAAAATAAAAATAT
2503573 AAATTTTATTTAAAATAAAAATAT
1 AAATTTTATTTAAAATAAAAATAT
2503597 AAATTTTATTT
1 AAATTTTATTT
2503608 TTAAAAACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTTTATTTAAAATAAAAATAT
Found at i:2510064 original size:39 final size:38
Alignment explanation
Indices: 2510005--2510201 Score: 180
Period size: 39 Copynumber: 5.1 Consensus size: 38
2509995 ATGGTATACC
* * *
2510005 CAGTAAGGACTTACCTTGTGCACAAAGCATAGGAGCCTG
1 CAGTAAGGACTTA-CATGAGCACAAAGCAGAGGAGCCTG
** * * *
2510044 CAGTAAGGTTTTATCATGTGCACAAAGTAGAGGAGCTTG
1 CAGTAAGGACTTA-CATGAGCACAAAGCAGAGGAGCCTG
* * **
2510083 TAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTG
1 CAGTAAGGACTTA-CATGAGCACAAAGCAGAGGAGCCTG
* * *
2510122 TAGTAAGGACTTACACTGAGCACAAAGCCGAGGAGCATG
1 CAGTAAGGACTTACA-TGAGCACAAAGCAGAGGAGCCTG
* *
2510161 CAGTAAGGACTTACCCTGATCACAAAGTC-GAGGAGCCTG
1 CAGTAAGGACTTA-CATGAGCACAAAG-CAGAGGAGCCTG
2510200 CA
1 CA
2510202 AAAAGCGGTA
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 128 0.98
40 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (38 bp):
CAGTAAGGACTTACATGAGCACAAAGCAGAGGAGCCTG
Found at i:2510145 original size:78 final size:78
Alignment explanation
Indices: 2510005--2510201 Score: 252
Period size: 78 Copynumber: 2.5 Consensus size: 78
2509995 ATGGTATACC
* * * ** *
2510005 CAGTAAGGACTTACCTTGTGCACAAAGCATAGGAGCCTGCAGTAAGGTTTTATCATGTGCACAAA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGCAGTAAGGACTTATCATGAGCACAAA
* *
2510070 GTAGAGGAGCTTG
66 GCAGAGGAGCATG
* *
2510083 TAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGTAGTAAGGACTTA-CACTGAGCACAA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGCAGTAAGGACTTATCA-TGAGCACAA
*
2510147 AGCCGAGGAGCATG
65 AGCAGAGGAGCATG
* * *
2510161 CAGTAAGGACTTACCCTGATCACAAAGTCGAGGAGCCTGCA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGCA
2510202 AAAAGCGGTA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 2 0.02
78 100 0.98
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (78 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGCAGTAAGGACTTATCATGAGCACAAA
GCAGAGGAGCATG
Found at i:2512079 original size:14 final size:16
Alignment explanation
Indices: 2512060--2512095 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2512050 ATATTAGACG
2512060 AAAAATAGA-TTTTA-
1 AAAAATAGATTTTTAC
2512074 AAAAAT-GATTTTTAC
1 AAAAATAGATTTTTAC
2512089 AAAAATA
1 AAAAATA
2512096 AATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
AAAAATAGATTTTTAC
Found at i:2512417 original size:37 final size:38
Alignment explanation
Indices: 2512344--2512433 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 38
2512334 TAAAAAATAT
* * *
2512344 TTTATTAAAATAA-AATTCTTATAAATTATGTTAATTA
1 TTTATTAAAATAAGAACTCTTATAAAATATGTAAATTA
2512381 TTTATTAAAATAAGAACT-TTATTAAAATAT-TAAATTA
1 TTTATTAAAATAAGAACTCTTA-TAAAATATGTAAATTA
*
2512418 TAATATT-AAATAAGAA
1 T-TTATTAAAATAAGAA
2512434 TATTATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 32 0.70
38 14 0.30
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (38 bp):
TTTATTAAAATAAGAACTCTTATAAAATATGTAAATTA
Found at i:2512422 original size:13 final size:13
Alignment explanation
Indices: 2512401--2512444 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2512391 TAAGAACTTT
*
2512401 ATTAAAATATTAA
1 ATTATAATATTAA
2512414 ATTATAATATTAA
1 ATTATAATATTAA
* * *
2512427 ATAAGAATATTAT
1 ATTATAATATTAA
2512440 ATTAT
1 ATTAT
2512445 TTTTTGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAATATTAA
Found at i:2512995 original size:17 final size:16
Alignment explanation
Indices: 2512945--2513008 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
2512935 TAGTTACCGG
2512945 TTAAATTATATTT-TA-
1 TTAAATT-TATTTATAT
2512960 TTAATATTT-TTGTAT-T
1 TTAA-ATTTATT-TATAT
*
2512976 TTAAGTTTATTTGATAT
1 TTAAATTTATTT-ATAT
2512993 TTAAATTTATTTATAT
1 TTAAATTTATTTATAT
2513009 AAAAATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 2 0.05
15 10 0.25
16 16 0.40
17 12 0.30
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTAAATTTATTTATAT
Found at i:2515206 original size:25 final size:25
Alignment explanation
Indices: 2515176--2515226 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2515166 AACTTGAAAT
2515176 AAAGCTTGAGGAGTAGAGATTAATA
1 AAAGCTTGAGGAGTAGAGATTAATA
*
2515201 AAAGCTTGAGGAGTGGAGATTAATA
1 AAAGCTTGAGGAGTAGAGATTAATA
2515226 A
1 A
2515227 TCTTACCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (25 bp):
AAAGCTTGAGGAGTAGAGATTAATA
Found at i:2522702 original size:22 final size:22
Alignment explanation
Indices: 2522676--2522732 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
2522666 CTTATTTTCT
2522676 TGTTTATGCTTTACATGTAATG
1 TGTTTATGCTTTACATGTAATG
2522698 TGTTTATGCTTTACATGTAATG
1 TGTTTATGCTTTACATGTAATG
*
2522720 TGTATATGCTTTA
1 TGTTTATGCTTTA
2522733 GACTATGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51
Consensus pattern (22 bp):
TGTTTATGCTTTACATGTAATG
Found at i:2529404 original size:21 final size:21
Alignment explanation
Indices: 2529377--2529426 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2529367 CAAAGGTCAA
2529377 TGATGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
*
2529398 TGGTGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
2529419 TGATGATC
1 TGATGATC
2529427 TTAAAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (21 bp):
TGATGATCATCAAAAGAAAAT
Found at i:2533148 original size:21 final size:21
Alignment explanation
Indices: 2533122--2533161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2533112 CACCCTGTGA
*
2533122 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2533143 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2533162 TGGGATTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2552569 original size:24 final size:24
Alignment explanation
Indices: 2552529--2552587 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2552519 GATTGGTCTT
2552529 AGAGAGATGTAAAATCTTTTATCA
1 AGAGAGATGTAAAATCTTTTATCA
* **
2552553 AGGGAGATGTACCATCTTTTATCA
1 AGAGAGATGTAAAATCTTTTATCA
*
2552577 AGAAAGATGTA
1 AGAGAGATGTA
2552588 TCACATGCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (24 bp):
AGAGAGATGTAAAATCTTTTATCA
Found at i:2566403 original size:2 final size:2
Alignment explanation
Indices: 2566396--2566445 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
2566386 GGAAAGATGG
* *
2566396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT TT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
2566439 AT AT AT A
1 AT AT AT A
2566446 CTTTGTAGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2567199 original size:20 final size:20
Alignment explanation
Indices: 2567174--2567231 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
2567164 TTAAATAACT
*
2567174 GGGGTATCGGTGCCATCCAG
1 GGGGTATCGGTACCATCCAG
2567194 GGGGTATCGGTACCATCCAG
1 GGGGTATCGGTACCATCCAG
2567214 GGGGTATCGGTACCATCC
1 GGGGTATCGGTACCATCC
2567232 GAGCATTCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.17, C:0.26, G:0.36, T:0.21
Consensus pattern (20 bp):
GGGGTATCGGTACCATCCAG
Found at i:2569465 original size:13 final size:13
Alignment explanation
Indices: 2569447--2569485 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2569437 ATGGGCAAAT
*
2569447 TTTGAAAACTATG
1 TTTGAAAACAATG
2569460 TTTGAAAACAATG
1 TTTGAAAACAATG
2569473 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
2569486 ATGTAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:2573842 original size:22 final size:21
Alignment explanation
Indices: 2573801--2573840 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2573791 AAGACTATAT
2573801 TCATTTTTCAATTTTGAAATG
1 TCATTTTTCAATTTTGAAATG
**
2573822 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2573841 ATAAAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATG
Found at i:2575765 original size:20 final size:20
Alignment explanation
Indices: 2575737--2575775 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2575727 TTAAATGACT
2575737 GGGGATATCAG-TACCATCCA
1 GGGGATATC-GTTACCATCCA
*
2575757 GGGGGTATCGTTACCATCC
1 GGGGATATCGTTACCATCC
2575776 GAGCATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (20 bp):
GGGGATATCGTTACCATCCA
Found at i:2579749 original size:4 final size:4
Alignment explanation
Indices: 2579740--2579768 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2579730 ATCGTGTCAG
2579740 TATT TATT TATT TATT TATT TATT T-TT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
2579769 GGTGTTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2579811 original size:23 final size:23
Alignment explanation
Indices: 2579785--2579873 Score: 106
Period size: 23 Copynumber: 3.9 Consensus size: 23
2579775 TGTGCTCGTA
*
2579785 CATTTAAGGTTTGCGAACATGTT
1 CATTTAACGTTTGCGAACATGTT
*
2579808 CATTTAACGTTTACGAACATGTT
1 CATTTAACGTTTGCGAACATGTT
* * * *
2579831 CGTTTAACATTTGGGAATATGTT
1 CATTTAACGTTTGCGAACATGTT
* *
2579854 CATTTAACATTTGCAAACAT
1 CATTTAACGTTTGCGAACAT
2579874 ATTTGTTTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (23 bp):
CATTTAACGTTTGCGAACATGTT
Found at i:2579873 original size:46 final size:46
Alignment explanation
Indices: 2579794--2579883 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
2579784 ACATTTAAGG
* * *
2579794 TTTGCGAACATGTTCATTTAACGTTTACGAACATGTTCGTTTAACA
1 TTTGCGAACATGTTCATTTAACATTTACAAACATATTCGTTTAACA
* * * *
2579840 TTTGGGAATATGTTCATTTAACATTTGCAAACATATTTGTTTAA
1 TTTGCGAACATGTTCATTTAACATTTACAAACATATTCGTTTAA
2579884 TGTTCTGCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (46 bp):
TTTGCGAACATGTTCATTTAACATTTACAAACATATTCGTTTAACA
Found at i:2580099 original size:12 final size:12
Alignment explanation
Indices: 2580084--2580152 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
2580074 AAACTAGTAT
*
2580084 ATAAATGAGTTG
1 ATAAATGAGTTA
* *
2580096 ATAAACGAGTTT
1 ATAAATGAGTTA
* *
2580108 ATAAA-CAATTCA
1 ATAAATGAGTT-A
*
2580120 ATAAATGAGTTT
1 ATAAATGAGTTA
* *
2580132 ACACATGAGTTA
1 ATAAATGAGTTA
2580144 ATAAATGAG
1 ATAAATGAG
2580153 CTTATTCGTG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 3 0.07
12 36 0.86
13 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.30
Consensus pattern (12 bp):
ATAAATGAGTTA
Found at i:2581243 original size:32 final size:32
Alignment explanation
Indices: 2581177--2581243 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2581167 ATGAGTTACG
* * *
2581177 TCATCTAAAATGATAACATAATAAATGTCGTA
1 TCATCAAAAATGATAACATAACAAATGTCATA
* **
2581209 TCATCAAAAATGATAATATAACATGTGTCATA
1 TCATCAAAAATGATAACATAACAAATGTCATA
2581241 TCA
1 TCA
2581244 AAAATTAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (32 bp):
TCATCAAAAATGATAACATAACAAATGTCATA
Done.