Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:2166659 original size:21 final size:21
Alignment explanation
Indices: 2166609--2166659 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
2166599 TTATTATTAT
*
2166609 GGATTTCAAGTTTGTTGTTAT
1 GGATTTCAAGTTTGTTGTTAC
*
2166630 AGATTTCAAGTTTGTTGTTAC
1 GGATTTCAAGTTTGTTGTTAC
*
2166651 GGATGTCAA
1 GGATTTCAA
2166660 ATTTATTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (21 bp):
GGATTTCAAGTTTGTTGTTAC
Found at i:2166922 original size:43 final size:45
Alignment explanation
Indices: 2166836--2166924 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
2166826 ATACCACTAT
*
2166836 ATGTTATAACATTTAGCGGCTTTTTTTTTGAACAAACGACACAAA
1 ATGTTAGAACATTTAGCGGCTTTTTTTTTGAACAAACGACACAAA
* *
2166881 ATGTTAGAGCATTTAGCGGC-TTTTTTTT-AACAAACGCCACAAA
1 ATGTTAGAACATTTAGCGGCTTTTTTTTTGAACAAACGACACAAA
2166924 A
1 A
2166925 GAAAAGATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 15 0.37
44 8 0.20
45 18 0.44
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (45 bp):
ATGTTAGAACATTTAGCGGCTTTTTTTTTGAACAAACGACACAAA
Found at i:2167911 original size:129 final size:128
Alignment explanation
Indices: 2167681--2167934 Score: 490
Period size: 129 Copynumber: 2.0 Consensus size: 128
2167671 GAAAAAGAAT
2167681 AGAAGGGCATGTTGAAGACGAAGACCTGTGGAAGTTAAGAAAATGCTTAGTTGAAACAATGGCTA
1 AGAAGGGCATGTTGAAGACGAAGACCTGTGGAAGTTAAGAAAATGCTTAGTTGAAACAATGGCTA
2167746 CGGTCTGTAGTGCAATCAGTATTGAGAGAAGACTTTAGGTCTGGGATCTTGGTGAGATCAATGA
66 CGGTCTGTAGTGCAATCAGTATTGAGAGAAGACTTTA-GTCTGGGATCTTGGTGAGATCAATGA
*
2167810 AGAAGGGCATGTTGAAGACGGAGACCTGTGGAAGTTAAGAAAATGCTTAGTTGAAACAATGGCTA
1 AGAAGGGCATGTTGAAGACGAAGACCTGTGGAAGTTAAGAAAATGCTTAGTTGAAACAATGGCTA
2167875 CGGTCTGTAGTGCAATCAGTATTGAGAGAAGACTTTAGTCTGGGATCTTGGTGAGATCAA
66 CGGTCTGTAGTGCAATCAGTATTGAGAGAAGACTTTAGTCTGGGATCTTGGTGAGATCAA
2167935 GATTCAAAGA
Statistics
Matches: 124, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
128 23 0.19
129 101 0.81
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (128 bp):
AGAAGGGCATGTTGAAGACGAAGACCTGTGGAAGTTAAGAAAATGCTTAGTTGAAACAATGGCTA
CGGTCTGTAGTGCAATCAGTATTGAGAGAAGACTTTAGTCTGGGATCTTGGTGAGATCAATGA
Found at i:2170161 original size:27 final size:28
Alignment explanation
Indices: 2170131--2170184 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2170121 CTTTATCTGC
*
2170131 CCAAA-ATTAAGGTGT-TTTTTCTATCTA
1 CCAAAGATT-AGGTGTCTTTTTCCATCTA
*
2170158 CCAAAGATTAGGTTTCTTTTTCCATCT
1 CCAAAGATTAGGTGTCTTTTTCCATCT
2170185 GGCAAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (28 bp):
CCAAAGATTAGGTGTCTTTTTCCATCTA
Found at i:2170925 original size:22 final size:22
Alignment explanation
Indices: 2170900--2170944 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2170890 GGCATGTGAA
** *
2170900 ATATGTCCTGAAGGACCTATGT
1 ATATGTCCCAAAGGACCCATGT
2170922 ATATGTCCCAAAGGACCCATGT
1 ATATGTCCCAAAGGACCCATGT
2170944 A
1 A
2170945 ACCCTCGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (22 bp):
ATATGTCCCAAAGGACCCATGT
Found at i:2171163 original size:7 final size:7
Alignment explanation
Indices: 2171147--2171199 Score: 53
Period size: 6 Copynumber: 8.3 Consensus size: 7
2171137 GTTCACATGA
2171147 ATCATAT
1 ATCATAT
*
2171154 ATCATTT
1 ATCATAT
2171161 ATC-TA-
1 ATCATAT
2171166 ATCATAT
1 ATCATAT
*
2171173 ACCATAT
1 ATCATAT
2171180 AT-ATAT
1 ATCATAT
2171186 AT-ATAT
1 ATCATAT
2171192 AT-ATAT
1 ATCATAT
2171198 AT
1 AT
2171200 ACTTATGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
5 3 0.08
6 21 0.52
7 16 0.40
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (7 bp):
ATCATAT
Found at i:2171183 original size:2 final size:2
Alignment explanation
Indices: 2171176--2171200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2171166 ATCATATACC
2171176 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 A
2171201 CTTATGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2172422 original size:775 final size:775
Alignment explanation
Indices: 2170630--2172987 Score: 3763
Period size: 775 Copynumber: 3.0 Consensus size: 775
2170620 CTTAGTGAGA
*
2170630 CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGCAATCCAATTATGCAAATATAATC
1 CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGTAATCCAATTATGCAAATATAATC
* *
2170695 ATACTCATCATATTATAATTAAGTCATGTCACATATGATTAAGTATATCAATAATAATATGATAG
66 ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTAAGTATAACAATAATAATATGATAG
* * * *
2170760 CATATACTCATTTAAATATTTTTGATATCTTTTATAGGCCCATGTACATTACTGAGAACTTAAGG
131 ---ATACTCATGTAAATATTTTTTATATCTTTTATAGGCCCATGTATATTACTGAGAACATAAGG
* * * * *
2170825 TATGCGAGTACATTGAGGTTGTGCACATATACTGTCACTACAGCTCATATAAAGATCCACTGAGT
193 TATGCGAGTACATTGAGGTTGTGCACATATGCTGTCACCATATCTCGTATAAAGATCCACTGAGT
**
2170890 GGCATGTGAAATATGTCCTGAAGGACCTATGTATATGTCCCAAAGGACCCATGTAACCCTCGACT
258 TTCATGTGAAATATGTCCTGAAGGACC------TA--T-------G------G-AACCCTCGACT
* * *
2170955 CTTAGCATGCCAACTATACCTATGGCTCTCATATCACATAACATGGGCATTATTGTTATACTTCC
301 CTTGGCATGCCAACTATACCTATAGCTCTCATATCACATAACATGGGCATTATTGTTACACTTCC
*
2171020 TATATTCATGTACTCATGTCATATCTCTTATAATCACATATGTCTTTTCTTTTATCATATATCAC
366 TATATTCATGTACTCATGTCATATCTCTTATAATCACATATGTCTTTTCTTCTATCATATATCAC
2171085 ACGTACATATAATCATCAATCTCATATCATATAACATATGTTATTTGAATATGTTCACATGAATC
431 ACGTACATATAATCATCAATCTCATATCATATAACATATGTTATTTGAATATGTTCACATGAATC
* *
2171150 ATATATCATTTATCTAATCATATACCATATATATATATATATATATATATACTTATGCATGCGTT
496 ATATATCATTTATCTAATCATATACC-----CATATATATATATA-A-A-ACTTATGCATGTGTT
*
2171215 TATAATGATCATCATGTATGCATGTTCATAACTATTGGAATATGAATACTAACATAGGAAATAGA
553 TATAATGATCATCATGTATGCATGTTCATAACTATTGGACTATGAATACTAACATAGGAAATAGA
2171280 CTTATCACAAGTCTTATTTCCATTGAATTATACCTATAGTATGCACTCACCTTGGTCTCACTTGA
618 CTTATCACAAGTCTTATTTCCATTGAATTATACCTATAGTATGCACTCACCTTGGTCTCACTTGA
* *
2171345 TCCCAATAACTTCTATAACTTGATTTTTCTTTCTTCATCGATTCTTACTTCTCGGTCATTCCAGA
683 TCCCAATAACTTCTATAACTTGATTTTTCTTTCTTCATCGATTCTAACTTCTTGGTCATTCCAGA
2171410 ACTTGTTTGTGCTCGATATCTACACAAT
748 ACTTGTTTGTGCTCGATATCTACACAAT
*
2171438 CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGTAATCCAATTATGAAAATATAATC
1 CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGTAATCCAATTATGCAAATATAATC
* * *
2171503 ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTCACTATAACAATAACAATATGATAG
66 ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTAAGTATAACAATAATAATATGATAG
*
2171568 ATACTCATGTAAATATTTTTTATATCTTTTATAGGCTCATGTATATTACTGAGAACATAAGGTAT
131 ATACTCATGTAAATATTTTTTATATCTTTTATAGGCCCATGTATATTACTGAGAACATAAGGTAT
* * *
2171633 GCAAGTACATTGAGGTTGTGCACATATGCTATCACCATATCTCGTATAAAGATCCATTGAGTTTC
196 GCGAGTACATTGAGGTTGTGCACATATGCTGTCACCATATCTCGTATAAAGATCCACTGAGTTTC
*
2171698 ATGTGAAATATGTCCCGAAGGACCTATGGAACCCTCGACTCTTGGCATGCCAACTATACCTATAG
261 ATGTGAAATATGTCCTGAAGGACCTATGGAACCCTCGACTCTTGGCATGCCAACTATACCTATAG
*
2171763 CTCTCATATCACATAACATGGGCATTATTGTTACACTGCCTATATTCATGTACTCATGTCATATC
326 CTCTCATATCACATAACATGGGCATTATTGTTACACTTCCTATATTCATGTACTCATGTCATATC
*
2171828 TCTTATAATCACATATGTCTTTTCTTCTATCATATATCACACCTACATATAATCATCAATCTCAT
391 TCTTATAATCACATATGTCTTTTCTTCTATCATATATCACACGTACATATAATCATCAATCTCAT
* *
2171893 ATTATATAACATATGTTATTTGAATATGTTCACATGAATTATATATCATTTATCTAATCATATAC
456 ATCATATAACATATGTTATTTGAATATGTTCACATGAATCATATATCATTTATCTAATCATATAC
2171958 CCATATATATATATAAAACTTATGCATGTGTTTATAATGATCATCATGTATGCATGTTCATAACT
521 CCATATATATATATAAAACTTATGCATGTGTTTATAATGATCATCATGTATGCATGTTCATAACT
2172023 ATTGGACTATGAATACTAACATAGGAAATAGACTTATCACAAGTCTTATTTCCATTGAATTATAC
586 ATTGGACTATGAATACTAACATAGGAAATAGACTTATCACAAGTCTTATTTCCATTGAATTATAC
* *
2172088 CTATAGTATGGACTCACCTTGGTCTCACTTGATACCAATAACTTCTATAACTTGATTTTTCTTTC
651 CTATAGTATGCACTCACCTTGGTCTCACTTGATCCCAATAACTTCTATAACTTGATTTTTCTTTC
* *
2172153 TTCATTGATTCTAACTTCTTGGTCATTCCGGAACTTGTTTGTGCTCGATATCTACACAAT
716 TTCATCGATTCTAACTTCTTGGTCATTCCAGAACTTGTTTGTGCTCGATATCTACACAAT
*
2172213 CATAAACATATAATAATGCATTTCTTATAAATATGAACATGTAATCCAATTATGCAAATATAATC
1 CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGTAATCCAATTATGCAAATATAATC
*
2172278 ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTTAGTATAACAATAATAATATGATAG
66 ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTAAGTATAACAATAATAATATGATAG
2172343 ATACTCATGTAAATATTTTTTATATCTTTTATAGGCCCATGTATATTACTGAGAACATAAGGTAT
131 ATACTCATGTAAATATTTTTTATATCTTTTATAGGCCCATGTATATTACTGAGAACATAAGGTAT
* * *
2172408 GCGAGTAAATTGAGGTTTTGCACATATGTTGTCACCATATCTCGTATAAAGATCCACTGAGTTTC
196 GCGAGTACATTGAGGTTGTGCACATATGCTGTCACCATATCTCGTATAAAGATCCACTGAGTTTC
*
2172473 ATGTGAAATATGTCCTGAAGGACCTATGAAACCCTCGACTCTTGGCATGCCAACTATACCTATAG
261 ATGTGAAATATGTCCTGAAGGACCTATGGAACCCTCGACTCTTGGCATGCCAACTATACCTATAG
*
2172538 CTATCATATCACATAACATGGGCATTATTGTTACACTTCCTATATTCATGTACTCATGTCATATC
326 CTCTCATATCACATAACATGGGCATTATTGTTACACTTCCTATATTCATGTACTCATGTCATATC
* * * *
2172603 TCTTATAATCACATATGTCTTTTCTTCTATCACATAGCACATGTATATATAATCATCAATCTCAT
391 TCTTATAATCACATATGTCTTTTCTTCTATCATATATCACACGTACATATAATCATCAATCTCAT
* * * *
2172668 ATCATATAAAATATGTTATATGAATATGTTAACATGAATCATATATCATTTATCCAATCATATAC
456 ATCATATAACATATGTTATTTGAATATGTTCACATGAATCATATATCATTTATCTAATCATATAC
* * * *
2172733 CC--ATATATATAT--AATTTATGCATCTGTTTATAATGATCATCATGTATACATGTTTATAACT
521 CCATATATATATATAAAACTTATGCATGTGTTTATAATGATCATCATGTATGCATGTTCATAACT
2172794 ATTGGACTATGAATACTAACATAGGAAATAGACTTATCACAAGTCTTATTTCCATTGAATTATAC
586 ATTGGACTATGAATACTAACATAGGAAATAGACTTATCACAAGTCTTATTTCCATTGAATTATAC
* * * * *
2172859 CTATAATATGCACTCACCTTGGCCTCATTTGATCCCAATAACTTATATAACTTGATTTTTATTTC
651 CTATAGTATGCACTCACCTTGGTCTCACTTGATCCCAATAACTTCTATAACTTGATTTTTCTTTC
* * * *
2172924 TTGATCGATTCTAACTT-TTCTGTCGTTCCAGAACTTGCTTGTGCTCGATATCTACACAAT
716 TTCATCGATTCTAACTTCTT-GGTCATTCCAGAACTTGTTTGTGCTCGATATCTACACAAT
2172984 CATA
1 CATA
2172988 CATTCCAAGT
Statistics
Matches: 1465, Mismatches: 84, Indels: 39
0.92 0.05 0.02
Matches are distributed among these distances:
770 2 0.00
771 223 0.15
773 10 0.01
775 725 0.49
776 1 0.00
777 1 0.00
778 13 0.01
783 224 0.15
784 1 0.00
790 1 0.00
797 1 0.00
799 2 0.00
805 138 0.09
808 123 0.08
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (775 bp):
CATAAACATATAATAATGCATTTCTTATAAATCTGAACATGTAATCCAATTATGCAAATATAATC
ATACTCATCATATTATAATTAAGTCATGTCACATATGTTTAAGTATAACAATAATAATATGATAG
ATACTCATGTAAATATTTTTTATATCTTTTATAGGCCCATGTATATTACTGAGAACATAAGGTAT
GCGAGTACATTGAGGTTGTGCACATATGCTGTCACCATATCTCGTATAAAGATCCACTGAGTTTC
ATGTGAAATATGTCCTGAAGGACCTATGGAACCCTCGACTCTTGGCATGCCAACTATACCTATAG
CTCTCATATCACATAACATGGGCATTATTGTTACACTTCCTATATTCATGTACTCATGTCATATC
TCTTATAATCACATATGTCTTTTCTTCTATCATATATCACACGTACATATAATCATCAATCTCAT
ATCATATAACATATGTTATTTGAATATGTTCACATGAATCATATATCATTTATCTAATCATATAC
CCATATATATATATAAAACTTATGCATGTGTTTATAATGATCATCATGTATGCATGTTCATAACT
ATTGGACTATGAATACTAACATAGGAAATAGACTTATCACAAGTCTTATTTCCATTGAATTATAC
CTATAGTATGCACTCACCTTGGTCTCACTTGATCCCAATAACTTCTATAACTTGATTTTTCTTTC
TTCATCGATTCTAACTTCTTGGTCATTCCAGAACTTGTTTGTGCTCGATATCTACACAAT
Found at i:2175586 original size:25 final size:24
Alignment explanation
Indices: 2175546--2175596 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2175536 ATCTAAATGT
2175546 TATTCATATAATTCATC-TTCCTA
1 TATTCATATAATTCATCTTTCCTA
*
2175569 TATTTATATATATATCATCTTTCCTA
1 TATTCATATA-AT-TCATCTTTCCTA
2175595 TA
1 TA
2175597 CTTGTATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 2 0.08
25 5 0.21
26 8 0.33
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTCATATAATTCATCTTTCCTA
Found at i:2182033 original size:25 final size:26
Alignment explanation
Indices: 2182005--2182074 Score: 61
Period size: 28 Copynumber: 2.6 Consensus size: 26
2181995 ACCGAGTACC
2182005 TAAAAATTCAAAGAAAAAT-AATAAA
1 TAAAAATTCAAAGAAAAATAAATAAA
** *
2182030 TAAATAAATTCCCGATAAAAATAAATAAA
1 T-AA-AAATT-CAAAGAAAAATAAATAAA
**
2182059 TAAAAATAAAAAGAAA
1 TAAAAATTCAAAGAAA
2182075 GCAAAGAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.18
27 9 0.27
28 10 0.30
29 7 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (26 bp):
TAAAAATTCAAAGAAAAATAAATAAA
Found at i:2187082 original size:67 final size:67
Alignment explanation
Indices: 2186974--2187133 Score: 295
Period size: 67 Copynumber: 2.4 Consensus size: 67
2186964 CAAAAGGCTC
* *
2186974 AGTTCCAAACAAACTTTGTTGGGTTAGCCACGGGATGGAAGGTCTTGGTGTTTTTTTATCAATTA
1 AGTTCCAAACAAACTTAGTTGGGTTAGCCACGGGATGGAAGGTCTTGGTGTTTTTTTATCAATCA
2187039 AT
66 AT
2187041 AGTTCCAAACAAACTTAGTTGGGTTAGCCACGGGATGGAAGGTCTTGGTGTTTTTTTATCAATCA
1 AGTTCCAAACAAACTTAGTTGGGTTAGCCACGGGATGGAAGGTCTTGGTGTTTTTTTATCAATCA
2187106 AT
66 AT
2187108 AGTTCCAAACAAACTTAGTT-GGTTAG
1 AGTTCCAAACAAACTTAGTTGGGTTAG
2187134 TAGATAGAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
66 6 0.07
67 85 0.93
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (67 bp):
AGTTCCAAACAAACTTAGTTGGGTTAGCCACGGGATGGAAGGTCTTGGTGTTTTTTTATCAATCA
AT
Found at i:2190368 original size:19 final size:19
Alignment explanation
Indices: 2190344--2190395 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2190334 GATCATCTAT
*
2190344 GGTCAAACTCAAT-AGGTCG
1 GGTCAAAGTCAATGA-GTCG
*
2190363 GGTCAAAGTTAATGAGTCG
1 GGTCAAAGTCAATGAGTCG
2190382 GGTCAAAGTCAATG
1 GGTCAAAGTCAATG
2190396 GTTCAGATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (19 bp):
GGTCAAAGTCAATGAGTCG
Found at i:2193018 original size:65 final size:66
Alignment explanation
Indices: 2192937--2193067 Score: 237
Period size: 68 Copynumber: 2.0 Consensus size: 66
2192927 GTCTGATACA
2192937 TAAATATAACACCCACAGACC-GCGAGTGACCTGATCTGATCTGAGGTGTCACATTAGGGCCACA
1 TAAATATAACACCCACAGACCAGCGAGTGACCTGATCTGATCTGAGGTGTCACATTAGGGCCACA
2193001 C
66 C
2193002 TAAATATAACACCCACAGACCGATGCGAGTGACCTGATCTGATCTGAGGTGTCACATTAGGGCCA
1 TAAATATAACACCCACAGACC-A-GCGAGTGACCTGATCTGATCTGAGGTGTCACATTAGGGCCA
2193067 C
64 C
2193068 CAAAGCGACT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
65 21 0.33
68 42 0.67
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (66 bp):
TAAATATAACACCCACAGACCAGCGAGTGACCTGATCTGATCTGAGGTGTCACATTAGGGCCACA
C
Found at i:2196093 original size:20 final size:20
Alignment explanation
Indices: 2196068--2196124 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
2196058 TTAACAGGTC
2196068 GGGTTGACTCTGTTCGGATT
1 GGGTTGACTCTGTTCGGATT
2196088 GGGTTGACTCTGTTCGGATT
1 GGGTTGACTCTGTTCGGATT
*
2196108 AGGTTGACTCTGTTCGG
1 GGGTTGACTCTGTTCGG
2196125 GTTAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.11, C:0.16, G:0.35, T:0.39
Consensus pattern (20 bp):
GGGTTGACTCTGTTCGGATT
Found at i:2198487 original size:207 final size:211
Alignment explanation
Indices: 2198198--2198621 Score: 709
Period size: 210 Copynumber: 2.0 Consensus size: 211
2198188 GCTACTTGTT
2198198 GTCATCCTTCCTTGATTCTGTGTCAAGGTTAACTTCGACGTCGCTTTTTCGCAGGTGCACAAAAC
1 GTCATCCTTCCTTGATTCTGTGTCAAGGTTAACTTCGAC--CG----TTCGCAGGTGCACAAAAC
2198263 AGGTCGTTCAAGTGTATAATAAGGAACAAAGAGGGATAGATAATGGGTGCA-GCAGTCGGATTCA
60 AGGTCGTTCAAGTGTATAATAAGGAACAAAGAGGGATAGATAATGGGTGCATGCAGTCGGATTCA
2198327 GCAAATGGTTA-C-CTCATC-TTTGTGGTGGAGGCCACGACGGCTGTTCATGTGATTACTTTTTC
125 GCAAATGGTTACCTCTCATCTTTTGTGGTGGAGG-CACGACGGCTGTTCATGTGATTACTTTTTC
2198389 TGTAGATCTGGGATTTCGTGAGG
189 TGTAGATCTGGGATTTCGTGAGG
2198412 GTCATCCTTCCCTTGATTCTGTGGTCAAGGTTAACTTCGA-CG-TCGCAGGTGCA-AAAACAGGT
1 GTCATCCTT-CCTTGATTCTGT-GTCAAGGTTAACTTCGACCGTTCGCAGGTGCACAAAACAGGT
2198474 CGTTCAAGTGTATAATAAGGAACAAAGAGGGATAGATAATGGGTGCATGCAGTCGGATTCAGCAA
64 CGTTCAAGTGTATAATAAGGAACAAAGAGGGATAGATAATGGGTGCATGCAGTCGGATTCAGCAA
*
2198539 ATGGTTACCTCTCTTCTTTTGTGGTGGAGGCACGACGGCTGTTCATGTGATTACTTTTTCTGTAG
129 ATGGTTACCTCTCATCTTTTGTGGTGGAGGCACGACGGCTGTTCATGTGATTACTTTTTCTGTAG
2198604 ATCTGGGATTTCGTGAGG
194 ATCTGGGATTTCGTGAGG
2198622 TAATAATAGA
Statistics
Matches: 203, Mismatches: 1, Indels: 16
0.92 0.00 0.07
Matches are distributed among these distances:
207 56 0.28
208 35 0.17
209 1 0.00
210 58 0.29
211 13 0.06
213 2 0.01
214 9 0.04
215 12 0.06
216 17 0.08
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (211 bp):
GTCATCCTTCCTTGATTCTGTGTCAAGGTTAACTTCGACCGTTCGCAGGTGCACAAAACAGGTCG
TTCAAGTGTATAATAAGGAACAAAGAGGGATAGATAATGGGTGCATGCAGTCGGATTCAGCAAAT
GGTTACCTCTCATCTTTTGTGGTGGAGGCACGACGGCTGTTCATGTGATTACTTTTTCTGTAGAT
CTGGGATTTCGTGAGG
Found at i:2205196 original size:54 final size:54
Alignment explanation
Indices: 2205083--2205476 Score: 522
Period size: 54 Copynumber: 7.3 Consensus size: 54
2205073 CTTTGGGGTA
* * * * *
2205083 CACACGTAGTGCCGATACGGTTGTTCATAAAC-CATTATGAATTTCATGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* *
2205136 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* * * *
2205190 CACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAGTTTCGT-GGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* * * * *
2205243 CACAGTTAGTGCTGACACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* * *
2205297 CACACTTAGTGCCGATACGATCGTTCATAAACATATTATTAATTCCATGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* ** *
2205351 CACACTTACTATCGATACGGTCATTCATAAACATATTATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
* * * *
2205405 CACACTTAGTGTCGATGCAGTCGTTCATAAACATATTATGAATTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
*
2205459 CTCACTTAGTGCCGATAC
1 CACACTTAGTGCCGATAC
2205477 TACATATAGT
Statistics
Matches: 300, Mismatches: 39, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
53 77 0.26
54 223 0.74
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTG
Found at i:2205270 original size:107 final size:108
Alignment explanation
Indices: 2205083--2205476 Score: 526
Period size: 107 Copynumber: 3.7 Consensus size: 108
2205073 CTTTGGGGTA
* * *
2205083 CACACGTAGTGCCGATACGGTTGTTCATAAAC-CATTATGAATTTCATGGGTTGCACACTTAGTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG
*
2205147 CCGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
66 CTGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
* * * * *
2205190 CACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAGTTTCGT-GGTTGCACAGTTAGTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG
* * *
2205254 CTGACACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTG
66 CTGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
* * * *
2205297 CACACTTAGTGCCGATACGATCGTTCATAAACATATTATTAATTCCATGGGTTGCACACTTACT-
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG
* *
2205361 ATCGATACGGTCATTCATAAACATATTATGAATTCCGTGGGTTG
66 CT-GATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
* * * * *
2205405 CACACTTAGTGTCGATGCAGTCGTTCATAAACATATTATGAA-TTCTGTGGGTTGCTCACTTAGT
1 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTC-ATGGGTTGCACACTTAGT
*
2205469 GCCGATAC
65 GCTGATAC
2205477 TACATATAGT
Statistics
Matches: 246, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
107 127 0.52
108 119 0.48
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (108 bp):
CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTG
CTGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGTTG
Found at i:2215683 original size:27 final size:26
Alignment explanation
Indices: 2215653--2215706 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2215643 GTCATACCCA
2215653 AAATAAACATAAGCTATGAAATAAAAT
1 AAATAAACATAAGCTATG-AATAAAAT
* * * *
2215680 AAATTAATATAATCTATGTATAAAAT
1 AAATAAACATAAGCTATGAATAAAAT
2215706 A
1 A
2215707 CTATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (26 bp):
AAATAAACATAAGCTATGAATAAAAT
Found at i:2220440 original size:2 final size:2
Alignment explanation
Indices: 2220393--2220425 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2220383 TATTTTTGAA
2220393 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 A
2220426 AGAACCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2224904 original size:23 final size:23
Alignment explanation
Indices: 2224878--2224927 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2224868 TTATTTTATG
2224878 AATTTAATATTA-ATAAAATATTT
1 AATTTAATATTATATAAAATA-TT
* * *
2224901 AATTTTATTTTATTTAAAATATT
1 AATTTAATATTATATAAAATATT
2224924 AATT
1 AATT
2224928 ATTAGAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTAATATTATATAAAATATT
Found at i:2224938 original size:24 final size:21
Alignment explanation
Indices: 2224911--2224967 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
2224901 AATTTTATTT
2224911 TATTTAAAATATTAATTATTAGAA
1 TATTTAAAATA-TAATTATT--AA
*
2224935 TATTTTAAAATATATTTATTAA
1 TA-TTTAAAATATAATTATTAA
*
2224957 TATTTATAATA
1 TATTTAAAATA
2224968 ACATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.27
22 4 0.13
24 9 0.30
25 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTAAAATATAATTATTAA
Found at i:2230393 original size:13 final size:14
Alignment explanation
Indices: 2230375--2230407 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2230365 TAAGATTTTC
2230375 TTTGAAAAT-AAAT
1 TTTGAAAATCAAAT
2230388 TTTG-AAATCAAAT
1 TTTGAAAATCAAAT
2230401 TTTGAAA
1 TTTGAAA
2230408 TTACTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 12 0.67
14 2 0.11
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (14 bp):
TTTGAAAATCAAAT
Found at i:2232762 original size:21 final size:23
Alignment explanation
Indices: 2232698--2232763 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2232688 ATGCATGGCA
2232698 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
2232721 GAGTGCATCGGTGTATC-TTCAA-
1 GAGTGCATCGATGCA-CATTCAAG
*
2232743 GA-TGTATCGATGCACATTCAA
1 GAGTGCATCGATGCACATTCAA
2232764 AGGGATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 2 0.06
23 18 0.50
24 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:2239720 original size:16 final size:18
Alignment explanation
Indices: 2239699--2239737 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2239689 TTTTTCTCTC
2239699 TCTTTTTCT-T-TTCTTT
1 TCTTTTTCTATATTCTTT
*
2239715 TCTTTTTCTATATTTTTT
1 TCTTTTTCTATATTCTTT
2239733 TCTTT
1 TCTTT
2239738 GTTTTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTTTCTATATTCTTT
Found at i:2239721 original size:28 final size:27
Alignment explanation
Indices: 2239689--2239745 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
2239679 ATCTCTCAAT
* *
2239689 TTTTTCTCTCTCTTTTTCTTTTCTTTTC
1 TTTTTCTATATCTTTTTC-TTTCTTTTC
* *
2239717 TTTTTCTATATTTTTTTCTTTGTTTTC
1 TTTTTCTATATCTTTTTCTTTCTTTTC
2239744 TT
1 TT
2239746 ATTTTTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTTCTATATCTTTTTCTTTCTTTTC
Found at i:2239742 original size:11 final size:10
Alignment explanation
Indices: 2239699--2239778 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 10
2239689 TTTTTCTCTC
2239699 TCTTTTTCTTT
1 TCTTTTT-TTT
2239710 TCTTTTCTTTT
1 TCTTTT-TTTT
2239721 TCTATATTTTTT
1 TCT-T-TTTTTT
2239733 TCTTTGTTTTCT
1 TCTTT-TTTT-T
*
2239745 TATTTTTTGGTT
1 TCTTTTTT--TT
*
2239757 TCTTCTATTTT
1 TCTT-TTTTTT
2239768 TCTATTTTTTT
1 TCT-TTTTTTT
2239779 ATTATATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 30 0.54
12 19 0.34
13 6 0.11
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:2242673 original size:45 final size:46
Alignment explanation
Indices: 2242614--2242700 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
2242604 GTTCTTACCA
*
2242614 ATATACATATCATTTA-TCTCATAAGCTCGTAAGCTTATTTTATCC
1 ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTTATCC
* *
2242659 ATATACTTACCATTTATTTTCATAAGCTCGTAAGCTTATTTT
1 ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTT
2242701 CCTGTTTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 14 0.37
46 24 0.63
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (46 bp):
ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTTATCC
Found at i:2248468 original size:16 final size:16
Alignment explanation
Indices: 2248449--2248482 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2248439 AATTAACCAA
2248449 AACCAAAAGCAACTCG
1 AACCAAAAGCAACTCG
* *
2248465 AACCGAATGCAACTCG
1 AACCAAAAGCAACTCG
2248481 AA
1 AA
2248483 TCGTAAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.29, G:0.15, T:0.09
Consensus pattern (16 bp):
AACCAAAAGCAACTCG
Found at i:2250554 original size:47 final size:50
Alignment explanation
Indices: 2250485--2250586 Score: 156
Period size: 47 Copynumber: 2.1 Consensus size: 50
2250475 GGAGTTACTA
*
2250485 TGGTAAGAAGTAACTCCTAATTGTTA-TGT-GC-ATGCATATATGTGCAT
1 TGGTAAGAAGTAACTCCTAATTGTTATTATGGCGATGCATATATGTGCAT
*
2250532 TGGTAAGAAGTGACTCCTAATTGTTATTATGGCGTATGCATATATGTGCAT
1 TGGTAAGAAGTAACTCCTAATTGTTATTATGGCG-ATGCATATATGTGCAT
2250583 TGGT
1 TGGT
2250587 GAGCTTATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
47 25 0.51
48 2 0.04
49 2 0.04
51 20 0.41
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (50 bp):
TGGTAAGAAGTAACTCCTAATTGTTATTATGGCGATGCATATATGTGCAT
Found at i:2252189 original size:12 final size:12
Alignment explanation
Indices: 2252172--2252201 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2252162 GTTTACTGTC
2252172 TGAAACTGAATT
1 TGAAACTGAATT
2252184 TGAAACTGAATT
1 TGAAACTGAATT
2252196 TGAAAC
1 TGAAAC
2252202 AAAAACTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (12 bp):
TGAAACTGAATT
Found at i:2254235 original size:27 final size:27
Alignment explanation
Indices: 2254198--2254315 Score: 173
Period size: 27 Copynumber: 4.3 Consensus size: 27
2254188 ATTTTTCTTA
2254198 TTCTTCTGGCTCATAGCTTTCACTTTC
1 TTCTTCTGGCTCATAGCTTTCACTTTC
*
2254225 TTCTTCTGGCTCATAGCTTTCAGTTTC
1 TTCTTCTGGCTCATAGCTTTCACTTTC
2254252 TTCTTCTGGCTCATAGCTTTCACTTGCTTC
1 TTCTTCTGGCTCATAGCTTTCAC-T--TTC
* * *
2254282 TTCTTTTGGCTCGTAGCTTTCACTTGC
1 TTCTTCTGGCTCATAGCTTTCACTTTC
2254309 TTCTTCT
1 TTCTTCT
2254316 TCAATAATTG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
27 56 0.68
28 1 0.01
29 1 0.01
30 24 0.29
ACGTcount: A:0.09, C:0.28, G:0.14, T:0.49
Consensus pattern (27 bp):
TTCTTCTGGCTCATAGCTTTCACTTTC
Found at i:2254276 original size:54 final size:56
Alignment explanation
Indices: 2254198--2254315 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 56
2254188 ATTTTTCTTA
* *
2254198 TTCTTCTGGCTCATAGCTTTCAC-T-TTCTTCTTCTGGCTCATAGCTTTCAGTTTC
1 TTCTTCTGGCTCATAGCTTTCACTTCTTCTTCTTCTGGCTCATAGCTTTCACTTGC
* *
2254252 TTCTTCTGGCTCATAGCTTTCACTTGCTTCTTCTTTTGGCTCGTAGCTTTCACTTGC
1 TTCTTCTGGCTCATAGCTTTCACTT-CTTCTTCTTCTGGCTCATAGCTTTCACTTGC
2254309 TTCTTCT
1 TTCTTCT
2254316 TCAATAATTG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
54 23 0.40
55 1 0.02
57 33 0.58
ACGTcount: A:0.09, C:0.28, G:0.14, T:0.49
Consensus pattern (56 bp):
TTCTTCTGGCTCATAGCTTTCACTTCTTCTTCTTCTGGCTCATAGCTTTCACTTGC
Found at i:2255491 original size:16 final size:16
Alignment explanation
Indices: 2255470--2255529 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
2255460 GAAATTTAAA
2255470 AATTCAAAATATATTT
1 AATTCAAAATATATTT
*
2255486 AATTCATAAT-TATGTT
1 AATTCAAAATATAT-TT
*
2255502 ATTTC-AAATA-ATTT
1 AATTCAAAATATATTT
*
2255516 AAAT-AAAATATATT
1 AATTCAAAATATATT
2255530 AATATGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
14 9 0.26
15 11 0.31
16 15 0.43
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
AATTCAAAATATATTT
Found at i:2257165 original size:3 final size:3
Alignment explanation
Indices: 2257146--2257213 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
2257136 TTATAATATT
* *
2257146 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
2257193 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
2257214 ATTTAAATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2257175 original size:12 final size:12
Alignment explanation
Indices: 2257138--2257213 Score: 75
Period size: 12 Copynumber: 6.1 Consensus size: 12
2257128 ATTGGGCTTT
2257138 ATAAT-ATT-TA
1 ATAATAATTATA
2257148 ATAAATAATATATA
1 AT-AATAAT-TATA
2257162 ATAATAATTATA
1 ATAATAATTATA
2257174 ATAATAATACTAATA
1 ATAATAAT--T-ATA
*
2257189 ATAATAATTTTA
1 ATAATAATTATA
*
2257201 ATAATAATAATA
1 ATAATAATTATA
2257213 A
1 A
2257214 ATTTAAATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
10 2 0.04
11 3 0.05
12 27 0.48
13 8 0.14
14 5 0.09
15 11 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAATTATA
Found at i:2257501 original size:74 final size:76
Alignment explanation
Indices: 2257346--2257615 Score: 436
Period size: 76 Copynumber: 3.6 Consensus size: 76
2257336 GAAATGTTGA
* * *
2257346 AAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCG
*
2257411 AATGCTTTTTGG
65 AAGGCTTTTTGG
* *
2257423 AAACATCATGCACTGTAGGACTTACAGATGACCCG-AGGGTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2257486 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2257497 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2257562 AGTCTTTTTGG
66 AGGCTTTTTGG
2257573 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
2257616 TTGGAAACAT
Statistics
Matches: 181, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
74 64 0.35
75 11 0.06
76 74 0.41
77 32 0.18
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2257634 original size:47 final size:47
Alignment explanation
Indices: 2257560--2257662 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
2257550 AAAAGCTCCT
*
2257560 GAAGTCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
*
2257607 GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACTC
1 GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
2257654 GAAGGCTTT
1 GAAGGCTTT
2257663 GAAAACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (47 bp):
GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
Found at i:2257634 original size:123 final size:123
Alignment explanation
Indices: 2257481--2257738 Score: 480
Period size: 123 Copynumber: 2.1 Consensus size: 123
2257471 TCAAAAAGCT
*
2257481 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* *
2257546 ATCAAAAAGCTCCTGAAGTCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
2257604 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
2257669 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2257727 CCCGAAGGCTTT
1 CCCGAAGGCTTT
2257739 GAAAACATCA
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 131 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (123 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2257752 original size:199 final size:197
Alignment explanation
Indices: 2257407--2257814 Score: 726
Period size: 199 Copynumber: 2.1 Consensus size: 197
2257397 TCAAAAAGCT
* * *
2257407 CCCGAATGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAGGGTTTGAAACAT
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAGGCTTTGAAACAT
*
2257472 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC
66 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC
* * *
2257537 TTTGAAAACATCAAAAAGCTCCTGAAGTCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
131 TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
2257602 GA
196 GA
*
2257604 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCG-AGGCTTTG-AAAC
2257669 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
64 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
2257734 GCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
129 GCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
2257799 ATGA
194 ATGA
2257803 CCCGAAGGCTTT
1 CCCGAAGGCTTT
2257815 GAAAACATCA
Statistics
Matches: 201, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
197 48 0.24
198 7 0.03
199 146 0.73
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (197 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAGGCTTTGAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC
TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
GA
Found at i:2257936 original size:75 final size:76
Alignment explanation
Indices: 2257604--2257952 Score: 630
Period size: 76 Copynumber: 4.6 Consensus size: 76
2257594 TTACAGATGA
*
2257604 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
2257669 ATCAAAAAGCT
66 ATCAAAAAGCT
2257680 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
2257745 ATCAAAAAACT
66 ATCAAAAAGCT
2257756 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
**
2257821 ATCAAAAATAT
66 ATCAAAAAGCT
*
2257832 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
2257896 ATCAAAAAGCT
66 ATCAAAAAGCT
2257907 CCCGAAGGCTTTTTGGAAACATCATGCACT-ACAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGA-AGGACTTACAGATG
2257953 TGGGAAATAG
Statistics
Matches: 264, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
75 61 0.23
76 203 0.77
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:2258819 original size:22 final size:22
Alignment explanation
Indices: 2258794--2258870 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
2258784 CATAAAGCTT
2258794 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2258816 TCATCTTTAAAAAGAGAATCTT
1 TCATCTTTGAAAAGAGAATCTA
2258838 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2258860 TCATCTTTGAA
1 TCATCTTTGAA
2258871 GAATGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2261437 original size:114 final size:114
Alignment explanation
Indices: 2261237--2261459 Score: 329
Period size: 114 Copynumber: 2.0 Consensus size: 114
2261227 GATCATGCAG
* * * * *
2261237 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * * *
2261302 ACACTTCCAGAATATGTTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
2261351 TTCATCTTTTAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
2261416 ACACTTCCAAAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
2261460 TCACATGGCA
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2263303 original size:20 final size:20
Alignment explanation
Indices: 2263275--2263313 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2263265 GATTCAATTT
2263275 TTTTCTTTT-TTCTTTTTTTG
1 TTTTCTTTTGTT-TTTTTTTG
*
2263295 TTTTGTTTTGTTTTTTTTT
1 TTTTCTTTTGTTTTTTTTT
2263314 CCTTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (20 bp):
TTTTCTTTTGTTTTTTTTTG
Found at i:2270041 original size:14 final size:13
Alignment explanation
Indices: 2270022--2270097 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 13
2270012 ATTGGGCTTT
*
2270022 ATAATATTTAATAA
1 ATAATATATAAT-A
2270036 ATAATATATAATA
1 ATAATATATAATA
*
2270049 ATAAT-TATAATT
1 ATAATATATAATA
2270061 ATAATACTAATAATA
1 ATAATA-T-ATAATA
*
2270076 ATAAT-TTTAATA
1 ATAATATATAATA
2270088 ATAATA-ATAA
1 ATAATATATAA
2270098 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
12 24 0.45
13 7 0.13
14 12 0.23
15 10 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATATATAATA
Found at i:2270049 original size:3 final size:3
Alignment explanation
Indices: 2270030--2270097 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
2270020 TTATAATATT
* * *
2270030 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TTA TAA TAC TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
2270077 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
2270098 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2270086 original size:15 final size:14
Alignment explanation
Indices: 2270022--2270095 Score: 61
Period size: 15 Copynumber: 5.6 Consensus size: 14
2270012 ATTGGGCTTT
2270022 ATAAT-ATTTAAT-
1 ATAATAATTTAATA
*
2270034 A-AATAATAT-ATA
1 ATAATAATTTAATA
2270046 ATAATAA-TT-ATA
1 ATAATAATTTAATA
* *
2270058 ATTATAATACTAATA
1 ATAATAAT-TTAATA
2270073 ATAATAATTTTAATA
1 ATAATAA-TTTAATA
2270088 ATAATAAT
1 ATAATAAT
2270096 AAATTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 5 0.10
12 15 0.31
13 5 0.10
14 2 0.04
15 21 0.43
16 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATAATTTAATA
Found at i:2270102 original size:18 final size:18
Alignment explanation
Indices: 2270068--2270103 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2270058 ATTATAATAC
*
2270068 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
2270086 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
2270104 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:2272830 original size:17 final size:17
Alignment explanation
Indices: 2272808--2272851 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2272798 ATATGCTATT
*
2272808 TATTAATTATATAACCA
1 TATTAATTACATAACCA
* *
2272825 TATTAATCACATAACTA
1 TATTAATTACATAACCA
2272842 TAATTAATTA
1 T-ATTAATTA
2272852 AAGTTTGACC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAATTACATAACCA
Found at i:2283189 original size:15 final size:16
Alignment explanation
Indices: 2283171--2283200 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2283161 TTACAAATAC
2283171 AAAATTTA-ACTTTTG
1 AAAATTTACACTTTTG
2283186 AAAATTTACACTTTT
1 AAAATTTACACTTTT
2283201 ACTCCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAATTTACACTTTTG
Found at i:2283252 original size:29 final size:28
Alignment explanation
Indices: 2283186--2283262 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 28
2283176 TTAACTTTTG
*
2283186 AAAATTTACACTTTTACTCCTTAAAATTT
1 AAAATTTACAC-TTTAGTCCTTAAAATTT
* *
2283215 ACAACTTTACACTTTAGTCCTTAAACTTT
1 A-AAATTTACACTTTAGTCCTTAAAATTT
2283244 CAAAATTTACA-TTCTAGTC
1 -AAAATTTACACTT-TAGTC
2283263 ACCAGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.05
29 29 0.71
30 10 0.24
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAATTTACACTTTAGTCCTTAAAATTT
Found at i:2286008 original size:15 final size:15
Alignment explanation
Indices: 2285990--2286075 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 15
2285980 GGGGTATCAG
2285990 TACCCGGGGTATGGA
1 TACCCGGGGTATGGA
2286005 TACCCTGGAGGGTATAGG-
1 TACCC--G-GGGTAT-GGA
2286023 TACCCGGGGTATGGA
1 TACCCGGGGTATGGA
2286038 TACCCTGGAGGGTATAGG-
1 TACCC--G-GGGTAT-GGA
*
2286056 TACCCGGTGTATGGA
1 TACCCGGGGTATGGA
2286071 TACCC
1 TACCC
2286076 CTGGAGGGTA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
14 4 0.07
15 26 0.43
16 2 0.03
17 2 0.03
18 22 0.37
19 4 0.07
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (15 bp):
TACCCGGGGTATGGA
Found at i:2286026 original size:33 final size:33
Alignment explanation
Indices: 2285981--2286094 Score: 194
Period size: 33 Copynumber: 3.4 Consensus size: 33
2285971 TGCAGCCAGG
2285981 GGGTATCA-GTACCCGGGGTATGGATACCCTGGA
1 GGGTAT-AGGTACCCGGGGTATGGATACCCTGGA
2286014 GGGTATAGGTACCCGGGGTATGGATACCCTGGA
1 GGGTATAGGTACCCGGGGTATGGATACCCTGGA
*
2286047 GGGTATAGGTACCCGGTGTATGGATACCCCTGGA
1 GGGTATAGGTACCCGGGGTATGGATA-CCCTGGA
2286081 GGGTATAGGTACCC
1 GGGTATAGGTACCC
2286095 TCCGAGCAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
32 1 0.01
33 56 0.72
34 21 0.27
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.22
Consensus pattern (33 bp):
GGGTATAGGTACCCGGGGTATGGATACCCTGGA
Found at i:2286160 original size:20 final size:21
Alignment explanation
Indices: 2286118--2286159 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2286108 GAATTTGAGT
2286118 CTTCAGGGGGTATGGATACCC
1 CTTCAGGGGGTATGGATACCC
2286139 CTTCAGGGGGTATCGG-TACCC
1 CTTCAGGGGGTAT-GGATACCC
2286160 TGTAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTCAGGGGGTATGGATACCC
Found at i:2286268 original size:31 final size:31
Alignment explanation
Indices: 2286233--2286291 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2286223 AACTTTGAAT
2286233 AAATTCAATTCAAGTCCAAAAACATTTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTTGC
2286264 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAGTCCAAAAACATTTT
2286292 GCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (31 bp):
AAATTCAATTCAAGTCCAAAAACATTTTTGC
Found at i:2286445 original size:19 final size:18
Alignment explanation
Indices: 2286403--2286459 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 18
2286393 ATGTTTAATG
2286403 AAAAAGATACTAATTGTT
1 AAAAAGATACTAATTGTT
2286421 ACAAAAGGATACTAATTGTT
1 A-AAAA-GATACTAATTGTT
*
2286441 AAAAAGATAACCAATTGTT
1 AAAAAGAT-ACTAATTGTT
2286460 GGAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 4 0.11
19 17 0.49
20 14 0.40
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAAAGATACTAATTGTT
Found at i:2289344 original size:21 final size:20
Alignment explanation
Indices: 2289293--2289333 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2289283 TCGTATATAG
*
2289293 CGTTTGAGATGTTTTGGAGC
1 CGTTGGAGATGTTTTGGAGC
2289313 CGTTGGAGATGTTTTGGAGC
1 CGTTGGAGATGTTTTGGAGC
2289333 C
1 C
2289334 ATTTGGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.37, T:0.37
Consensus pattern (20 bp):
CGTTGGAGATGTTTTGGAGC
Found at i:2289633 original size:30 final size:30
Alignment explanation
Indices: 2289599--2289656 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2289589 AACTTTGAAT
* * *
2289599 AAATTCAATTTAAGTCCAAAAATATTTTGC
1 AAATTCAATTCAAGTCAAAAAACATTTTGC
2289629 AAATTCAATTCAAGTCAAAAAACATTTT
1 AAATTCAATTCAAGTCAAAAAACATTTT
2289657 TCCTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATTCAATTCAAGTCAAAAAACATTTTGC
Found at i:2294907 original size:34 final size:34
Alignment explanation
Indices: 2294864--2294955 Score: 157
Period size: 34 Copynumber: 2.7 Consensus size: 34
2294854 TATACATTAT
*
2294864 ATGATTGCACCAGGAGTGCATATTTATGTATCTG
1 ATGATTGCACCTGGAGTGCATATTTATGTATCTG
*
2294898 ATGATTGCACCTGGAGTGCATATTTATGTATTTG
1 ATGATTGCACCTGGAGTGCATATTTATGTATCTG
*
2294932 ATGATAGCACCTGGAGTGCATATT
1 ATGATTGCACCTGGAGTGCATATT
2294956 GCAGGCACTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (34 bp):
ATGATTGCACCTGGAGTGCATATTTATGTATCTG
Found at i:2295029 original size:18 final size:18
Alignment explanation
Indices: 2295008--2295074 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2294998 TATACATTGG
2295008 GCTATGAATATGAAATGA
1 GCTATGAATATGAAATGA
**
2295026 GCTATGAATCTAAAAAATGA
1 GCTATGAA--TATGAAATGA
* *
2295046 GCTATGACTTTGAAATGA
1 GCTATGAATATGAAATGA
*
2295064 GTTATGAATAT
1 GCTATGAATAT
2295075 AAAAATAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
18 23 0.61
20 15 0.39
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.31
Consensus pattern (18 bp):
GCTATGAATATGAAATGA
Found at i:2303572 original size:19 final size:20
Alignment explanation
Indices: 2303548--2303593 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2303538 CAAAATGACC
*
2303548 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
2303567 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
2303587 AAATTTC
1 CAATTTC
2303594 CAGCATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:2305628 original size:80 final size:81
Alignment explanation
Indices: 2305452--2305755 Score: 395
Period size: 80 Copynumber: 3.8 Consensus size: 81
2305442 ATTTTAAATA
* * *
2305452 AAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAATGTGTCAATTATGCCAA-TTCGATGAAAG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAAGTTAGATGAAAG
*
2305516 GTTAAATGCCTATGAGT
65 GTTAAATGCCTTTGAGT
* * *
2305533 AAAAGCTTAATGGCCTAGCTGTGTATTTGACAGAAAGGTGTCAATTATGC-AGTTAGATGAAAGT
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
2305597 TTAAATGCCTTTGAGT
66 TTAAATGCCTTTGAGT
* * *
2305613 AAAAGATTAATGGCCTAGCTGTGCATTTCATAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
* *
2305678 CT-AATGGCTTTGAGT
66 TTAAATGCCTTTGAGT
* * * *
2305693 TAAAGATTAAAT-GCCTAGCTATGCATTTGGA-AGAAAGGTGTTAATCATGCAAGTTAGA-GAAA
1 AAAAGATT-AATGGCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATTATGCAAGTTAGATGAAA
2305755 G
64 G
2305756 TCTTGAGTTA
Statistics
Matches: 199, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
79 6 0.03
80 130 0.65
81 63 0.32
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (81 bp):
AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
TTAAATGCCTTTGAGT
Found at i:2305657 original size:161 final size:160
Alignment explanation
Indices: 2305452--2305756 Score: 402
Period size: 161 Copynumber: 1.9 Consensus size: 160
2305442 ATTTTAAATA
* * * *
2305452 AAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAATGTGTCAATTATGCCAA-TTCGATGAAAG
1 AAAAGATTAATGGCCTAGCTGTGCATTTCACAAAAAGGTGTCAATAATG-CAAGTTAGATGAAAG
* * * * *
2305516 GTTAAATGCCTATGAGTAAAAGCTT-AATGGCCTAGCTGTGTATTT-GACAGAAAGGTGTCAATT
65 GCT-AATGCCTATGAGTAAAAGATTAAAT-GCCTAGCTATGCATTTGGA-AGAAAGGTGTCAATC
2305579 ATGC-AGTTAGATGAAAGTTTAAATGCCTTTGAGT
127 ATGCAAGTTAGA-GAAAGTTTAAATGCCTTTGAGT
* *
2305613 AAAAGATTAATGGCCTAGCTGTGCATTTCATAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTCACAAAAAGGTGTCAATAATGCAAGTTAGATGAAAGG
* * * *
2305678 CTAATGGCTTTGAGTTAAAGATTAAATGCCTAGCTATGCATTTGGAAGAAAGGTGTTAATCATGC
66 CTAATGCCTATGAGTAAAAGATTAAATGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATCATGC
2305743 AAGTTAGAGAAAGT
131 AAGTTAGAGAAAGT
2305757 CTTGAGTTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
160 57 0.46
161 68 0.54
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (160 bp):
AAAAGATTAATGGCCTAGCTGTGCATTTCACAAAAAGGTGTCAATAATGCAAGTTAGATGAAAGG
CTAATGCCTATGAGTAAAAGATTAAATGCCTAGCTATGCATTTGGAAGAAAGGTGTCAATCATGC
AAGTTAGAGAAAGTTTAAATGCCTTTGAGT
Found at i:2306240 original size:10 final size:10
Alignment explanation
Indices: 2306216--2306271 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
2306206 TGCTTTCTCT
*
2306216 TTGATTCTCTC
1 TTGATTCT-TG
2306227 TTGATTCTTG
1 TTGATTCTTG
*
2306237 TTGATTGTTG
1 TTGATTCTTG
**
2306247 TTTCTTCTTG
1 TTGATTCTTG
*
2306257 TTGATTGTTG
1 TTGATTCTTG
2306267 TTGAT
1 TTGAT
2306272 CAATGGCTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.61
Consensus pattern (10 bp):
TTGATTCTTG
Found at i:2306256 original size:20 final size:20
Alignment explanation
Indices: 2306231--2306268 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2306221 TCTCTCTTGA
2306231 TTCTTGTTGATTGTTGTTTC
1 TTCTTGTTGATTGTTGTTTC
2306251 TTCTTGTTGATTGTTGTT
1 TTCTTGTTGATTGTTGTT
2306269 GATCAATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.08, G:0.21, T:0.66
Consensus pattern (20 bp):
TTCTTGTTGATTGTTGTTTC
Found at i:2306538 original size:64 final size:63
Alignment explanation
Indices: 2306485--2306636 Score: 227
Period size: 64 Copynumber: 2.4 Consensus size: 63
2306475 GTGCACTAAG
*
2306485 AGTGCATCGATGCATAAAATGCATTCAATG-TTTCA-AACAAGCCTGAGTGCATCGATTCATGGT
1 AGTGCATCGATGCATAAAATGCATTCAATGTTTTCATAA-AA-CCTGAGTGCATCGATGCATGGT
* *
2306548 ATGTGCATCGATGTATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 A-GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
*
2306612 AGTGCATCAATGCATAAAATGCATT
1 AGTGCATCGATGCATAAAATGCATT
2306637 TGATATGGTG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
63 23 0.28
64 49 0.60
65 7 0.09
66 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:2308921 original size:18 final size:18
Alignment explanation
Indices: 2308898--2308933 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2308888 TCAAAGACAA
*
2308898 TTTTGAAAAATTGTTTGT
1 TTTTGAAAAATTGATTGT
*
2308916 TTTTGACAAATTGATTGT
1 TTTTGAAAAATTGATTGT
2308934 GAAATCTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (18 bp):
TTTTGAAAAATTGATTGT
Found at i:2309322 original size:45 final size:44
Alignment explanation
Indices: 2309232--2309323 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
2309222 TTGTGCATCA
* *
2309232 ATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGTTTCG
1 ATGCACATTCAAGGAGTGCATCGATGCATCTTCATGATGTATCG
2309276 ATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCAT-AGTGTATCG
1 ATGCACATTC-AAGGAG-TGCATCGATGCATC-TTCATGA-TGTATCG
2309321 ATG
1 ATG
2309324 AATTATGCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
44 13 0.31
45 29 0.69
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (44 bp):
ATGCACATTCAAGGAGTGCATCGATGCATCTTCATGATGTATCG
Found at i:2317591 original size:13 final size:13
Alignment explanation
Indices: 2317573--2317603 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2317563 CAAAGCATGA
2317573 TTCTAGCAATTTC
1 TTCTAGCAATTTC
2317586 TTCTAGCAATTTC
1 TTCTAGCAATTTC
2317599 TTCTA
1 TTCTA
2317604 AAGTTCGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (13 bp):
TTCTAGCAATTTC
Found at i:2319013 original size:22 final size:21
Alignment explanation
Indices: 2318971--2319010 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2318961 ATGATTATTT
*
2318971 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2318992 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2319011 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2320925 original size:18 final size:19
Alignment explanation
Indices: 2320882--2320925 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2320872 AAATATTTCG
*
2320882 ATCGATGCACTAAGAGTGC
1 ATCGATGCACTAAGAATGC
2320901 ATCGATGCA-TAA-AATGC
1 ATCGATGCACTAAGAATGC
2320918 ATTCGATG
1 A-TCGATG
2320926 TTTCAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 9 0.39
19 9 0.39
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (19 bp):
ATCGATGCACTAAGAATGC
Found at i:2320952 original size:64 final size:63
Alignment explanation
Indices: 2320896--2321051 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 63
2320886 ATGCACTAAG
*
2320896 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCGTGAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CATGAGTGCATCGATGCATGGT
2320959 ATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
1 A-GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
* * *
2321023 AATGCATCGAAGCATAAAATACATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
2321052 ATGGTGAGTG
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
63 26 0.30
64 51 0.59
65 7 0.08
66 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
Found at i:2328092 original size:18 final size:18
Alignment explanation
Indices: 2328069--2328105 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2328059 TCAAAAACGA
*
2328069 CGTTTTTTAAAAATTACT
1 CGTTTTTGAAAAATTACT
2328087 CGTTTTTGAAAAATTACT
1 CGTTTTTGAAAAATTACT
2328105 C
1 C
2328106 CCCTTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (18 bp):
CGTTTTTGAAAAATTACT
Found at i:2328418 original size:15 final size:15
Alignment explanation
Indices: 2328392--2328439 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
2328382 TTCAAACATC
*
2328392 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
2328408 CGAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
2328425 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
2328440 ATTAAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.04, T:0.12
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:2334240 original size:20 final size:20
Alignment explanation
Indices: 2334198--2334240 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2334188 TTATTTTAAT
* *
2334198 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
2334218 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
2334238 TTT
1 TTT
2334241 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:2341941 original size:54 final size:54
Alignment explanation
Indices: 2341855--2342298 Score: 600
Period size: 54 Copynumber: 8.1 Consensus size: 54
2341845 GAATGGGCAT
* ** *
2341855 TGTGTGCGTAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTG
1 TGTGTGC--AACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* *
2341911 TTTGTGCAACTTAAGAAATTCATAACAAGTTTATGAATTTTCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * ** *
2341965 TGTGTACAACTTAAGACATTCATAATAAGTTTATAAATTTCCACATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * *
2342019 TGTGTGCAACTTAAGAAATTCATAATGAGTTTATAAATTTTAGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
*
2342073 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * *
2342127 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTTGTATTGACATTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGGCACTA
* *
2342182 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATATTTCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAAT-TTTCGTATTGGCACTA
* * *
2342237 TGTGTGCAACCTAAGAAATTCATAATCAGTTTATGAATTTTTGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
2342291 TGTGTGCA
1 TGTGTGCA
2342299 CCCCATGTAA
Statistics
Matches: 350, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
54 242 0.69
55 102 0.29
56 6 0.02
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (54 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
Found at i:2342311 original size:54 final size:54
Alignment explanation
Indices: 2341868--2342382 Score: 591
Period size: 54 Copynumber: 9.5 Consensus size: 54
2341858 GTGCGTAACT
* ** * * *
2341868 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTGTTTGTGCAACT
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * *
2341922 TAAGAAATTCATAACAAGTTTATGAATTTTCGTATTGGCACTATGTGTACAACT
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * * ** * *
2341976 TAAGACATTCATAATAAGTTTATAAATTTCCACATTGGCACTGTGTGTGCAACT
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * * * *
2342030 TAAGAAATTCATAATGAGTTTATAAATTTTAGTATTGGCACTGTGTGTGCAACT
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
*
2342084 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACC
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * * *
2342138 TAAGAAATTCATAATTAGTTTATGAATTTTTTGTATTGACATTATGTGTGCAACC
1 TAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGGCACTATGTGTGCAACC
*
2342193 TAAGAAATTCATAATTAGTTTATGAATATTTCGTATTGGCACTATGTGTGCAACC
1 TAAGAAATTCATAATAAGTTTATGAAT-TTTCGTATTGGCACTATGTGTGCAACC
* * *
2342248 TAAGAAATTCATAATCAGTTTATGAATTTTTGTATTGGCACTATGTGTGCACCC
1 TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * * * * ** * * * *
2342302 CATGTAATTCATAATGAGTTTGA-GAAATACCGTATCGGAACTAAGCGTGCAACC
1 TAAGAAATTCATAATAAGTTT-ATGAATTTTCGTATTGGCACTATGTGTGCAACC
* * * *
2342356 CATGAAATTCATAATGAGCTTATGAAT
1 TAAGAAATTCATAATAAGTTTATGAAT
2342383 GACCGTATCG
Statistics
Matches: 405, Mismatches: 52, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 301 0.74
55 103 0.25
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (54 bp):
TAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACC
Found at i:2342354 original size:218 final size:217
Alignment explanation
Indices: 2341869--2342382 Score: 586
Period size: 218 Copynumber: 2.4 Consensus size: 217
2341859 TGCGTAACTT
* * ** **** *
2341869 AAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTGTTTGTGCAACTTAAGAAATTCAT
1 AAGAAATTCATAATAAGTTTATGAAATACCGTATGGACACTAAGCGTGCAACCTAAGAAATTCAT
* * * *
2341934 AACAAGTTTATGAA-TTTTCGTATTGGCACTATGTGTACAACTTAAGACATTCATAATAAGTTTA
66 AATAAGTTTATGAATTTTTCGTATTGACACTATGTGTACAACCTAAGAAATTCATAATAAGTTTA
* * *
2341998 TAAATTTCCACATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATAAATTTTAGT
131 TAAATTTCCACATTGGCACTATGTGTGCAACCTAAGAAATTCATAATCAGTTTATAAATTTTAGT
* **
2342063 ATTGGCACTGTGTGTGCAACTT
196 ATTGGCACTATGTGTGCAACCC
* ** * * *
2342085 AAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTAAGAAATTCAT
1 AAGAAATTCATAATAAGTTTATGAAATACCGTATGGACACTAAGCGTGCAACCTAAGAAATTCAT
* * * * *
2342150 AATTAGTTTATGAATTTTTTGTATTGACATTATGTGTGCAACCTAAGAAATTCATAATTAGTTTA
66 AATAAGTTTATGAATTTTTCGTATTGACACTATGTGTACAACCTAAGAAATTCATAATAAGTTTA
** * *
2342215 TGAATATTT-CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATCAGTTTATGAATTTTT
131 T-AA-ATTTCCACATTGGCACTATGTGTGCAACCTAAGAAATTCATAATCAGTTTATAAATTTTA
*
2342279 GTATTGGCACTATGTGTGCACCCC
194 GTATTGGCACTATGTGTGCAACCC
* * * * *
2342303 ATGTAATTCATAATGAGTTTGA-GAAATACCGTATCGGA-ACTAAGCGTGCAACCCATGAAATTC
1 AAGAAATTCATAATAAGTTT-ATGAAATACCGTAT-GGACACTAAGCGTGCAACCTAAGAAATTC
* *
2342366 ATAATGAGCTTATGAAT
64 ATAATAAGTTTATGAAT
2342383 GACCGTATCG
Statistics
Matches: 255, Mismatches: 38, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
216 72 0.28
217 44 0.17
218 132 0.52
219 7 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (217 bp):
AAGAAATTCATAATAAGTTTATGAAATACCGTATGGACACTAAGCGTGCAACCTAAGAAATTCAT
AATAAGTTTATGAATTTTTCGTATTGACACTATGTGTACAACCTAAGAAATTCATAATAAGTTTA
TAAATTTCCACATTGGCACTATGTGTGCAACCTAAGAAATTCATAATCAGTTTATAAATTTTAGT
ATTGGCACTATGTGTGCAACCC
Found at i:2342354 original size:272 final size:270
Alignment explanation
Indices: 2341868--2342406 Score: 648
Period size: 272 Copynumber: 2.0 Consensus size: 270
2341858 GTGCGTAACT
* * *
2341868 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTGTTTGTGCAACTTAAGAAATTCA
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACCTAAGAAATTCA
* *
2341933 TAACAAGTTTATGAATTTTCGTATTGGCACTATGTGTACAACTTAAGACATTCATAATAAGTTTA
66 TAACAAGTTTATGAATTTTCGTATTGGCACTATGTGTACAACCTAAGAAATTCATAATAAGTTTA
* ** * **
2341998 TAAATTTCCACATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATAAATTTTAGT
131 TAAATTTCCACATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTAGAAATTACAGT
* * ** * ** * *** * *
2342063 ATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTAT
196 ATCGGAACTAAGCGTGCAACCCAAGAAATTCATAATAAGCTTATGAATGACCGTATCGACACTAC
2342128 GTGTGCAACC
261 GTGTGCAACC
* ** * *
2342138 TAAGAAATTCATAATTAGTTTATGAATTTTTTGTATTGACATTATGTGTGCAACCTAAGAAATTC
1 TAAGAAATTCATAATAAGTTTATGAA-TTTCCGTATTAACACTATGTGTGCAACCTAAGAAATTC
** * *
2342203 ATAATTAGTTTATGAATATTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATCAGTT
65 ATAACAAGTTTATGAAT-TTTCGTATTGGCACTATGTGTACAACCTAAGAAATTCATAATAAGTT
* **** * * *
2342268 TATGAATTTTTGTATTGGCACTATGTGTGCACCCCATGTAATTCATAATGAGTTTGAGAAA-TAC
129 TATAAATTTCCACATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTT-AGAAATTAC
* * *
2342332 CGTATCGGAACTAAGCGTGCAACCCATGAAATTCATAATGAGCTTATGAATGACCGTATCGACAC
193 AGTATCGGAACTAAGCGTGCAACCCAAGAAATTCATAATAAGCTTATGAATGACCGTATCGACAC
2342397 TACGTGTGCA
258 TACGTGTGCA
2342407 CCCCAAAGAA
Statistics
Matches: 222, Mismatches: 44, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
270 25 0.11
271 46 0.21
272 147 0.66
273 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (270 bp):
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACCTAAGAAATTCA
TAACAAGTTTATGAATTTTCGTATTGGCACTATGTGTACAACCTAAGAAATTCATAATAAGTTTA
TAAATTTCCACATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTAGAAATTACAGT
ATCGGAACTAAGCGTGCAACCCAAGAAATTCATAATAAGCTTATGAATGACCGTATCGACACTAC
GTGTGCAACC
Found at i:2346541 original size:25 final size:25
Alignment explanation
Indices: 2346513--2346562 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2346503 AGTATGAAGA
2346513 GTTGTAAGTGTGGTTACCTTGAATT
1 GTTGTAAGTGTGGTTACCTTGAATT
2346538 GTTGTAAGTGTGGTTACCTTGAATT
1 GTTGTAAGTGTGGTTACCTTGAATT
2346563 CTTTGAGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (25 bp):
GTTGTAAGTGTGGTTACCTTGAATT
Found at i:2358852 original size:34 final size:34
Alignment explanation
Indices: 2358811--2358902 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 34
2358801 TATACATTAT
* *
2358811 ATGATTGCACCAGGAGTGTATATTTATGTATCTG
1 ATGATTGCACCTGGAGTGCATATTTATGTATCTG
* * *
2358845 ATTATTGCACCTGGAGTGCATATTTCTGTTTCTG
1 ATGATTGCACCTGGAGTGCATATTTATGTATCTG
* *
2358879 ATGATAGCACCTGGAGTGCTTATT
1 ATGATTGCACCTGGAGTGCATATT
2358903 GCACGCACTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (34 bp):
ATGATTGCACCTGGAGTGCATATTTATGTATCTG
Found at i:2358973 original size:18 final size:18
Alignment explanation
Indices: 2358955--2359021 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2358945 TATACATTGG
*
2358955 GCTATGAATATGAAATGG
1 GCTATGAATATGAAATGA
**
2358973 GCTATGAATCTAAAAAATGA
1 GCTATGAA--TATGAAATGA
*
2358993 GCTATGAATTTGAAATGA
1 GCTATGAATATGAAATGA
*
2359011 GTTATGAATAT
1 GCTATGAATAT
2359022 AAAAATAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 24 0.62
20 15 0.38
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (18 bp):
GCTATGAATATGAAATGA
Found at i:2367488 original size:19 final size:20
Alignment explanation
Indices: 2367464--2367509 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2367454 CAAAGTGACC
*
2367464 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
2367483 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
2367503 AAATTTC
1 CAATTTC
2367510 CAGCATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:2369644 original size:80 final size:81
Alignment explanation
Indices: 2369400--2369646 Score: 329
Period size: 81 Copynumber: 3.1 Consensus size: 81
2369390 TATGAATGAT
* *
2369400 TGAAAGGTTAAATGCCTATGAG-TAAAGATTAATGGCCTAGCTGTGTATTTGACAGAAAGGTGTC
1 TGAAAGGTTAAATGCCTTTGAGTTAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
*
2369464 AATTATGCCAGTTAGA
66 AATTATGCAAGTTAGA
* * * * *
2369480 TGACAGTTTAAATACCTTTTAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
1 TGAAAGGTTAAATGCCTTTGAGTTAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
* *
2369545 AATCATGAAAGTTAGA
66 AATTATGCAAGTTAGA
* * * * *
2369561 TGAAAGGCTAATTGGCTTTGAGTTAAAGATTAAAT-GCCTAGCTATGCA-TTGGCAGAAAGGTGT
1 TGAAAGGTTAAATGCCTTTGAGTTAAAGATT-AATGGCCTAGCTGTGCATTTGACAGAAAGGTGT
2369624 CAATTATGCAAGTTAGA
65 CAATTATGCAAGTTAGA
2369641 TGAAAG
1 TGAAAG
2369647 TGTTGAGTTA
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 52 0.36
81 88 0.62
82 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (81 bp):
TGAAAGGTTAAATGCCTTTGAGTTAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
AATTATGCAAGTTAGA
Found at i:2370508 original size:63 final size:63
Alignment explanation
Indices: 2370356--2370511 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 63
2370346 GTGCACTAAG
* * ** * *
2370356 AGTGTATCGATGCATAAAATGCATTCAATGTTTCAAACAAGCCTGAGTGCATCGATTCATGGT
1 AGTGCATCAATGCATAAAATGCATTTGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGC
* *
2370419 ATGTGCATCAATGCATAAAATGCATTTGATGTTTTCATAA-AA-CCTTAGTGCATTGATGCATGG
1 A-GTGCATCAATGCATAAAATGCATTTGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGG
2370482 C
63 C
2370483 AGTGCATCAATGCATAAAATGCATTTGAT
1 AGTGCATCAATGCATAAAATGCATTTGAT
2370512 ATGGTGAGTG
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
63 29 0.35
64 44 0.54
65 7 0.09
66 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (63 bp):
AGTGCATCAATGCATAAAATGCATTTGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGC
Found at i:2370541 original size:20 final size:20
Alignment explanation
Indices: 2370516--2370553 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2370506 TTTGATATGG
2370516 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
2370536 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
2370554 CCTTCATAAT
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:2371502 original size:27 final size:27
Alignment explanation
Indices: 2371465--2371519 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2371455 AATCGGTGCC
*
2371465 GGAGGAGGAGGAGCACGA-GAAGAACTA
1 GGAGCAGGAGGAGCAC-ATGAAGAACTA
* *
2371492 GGAGCAGGAGGGGCTCATGAAGAACTA
1 GGAGCAGGAGGAGCACATGAAGAACTA
2371519 G
1 G
2371520 CTCCCGGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.36, C:0.13, G:0.44, T:0.07
Consensus pattern (27 bp):
GGAGCAGGAGGAGCACATGAAGAACTA
Found at i:2373128 original size:21 final size:21
Alignment explanation
Indices: 2373067--2373165 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 21
2373057 CATGGCCTTG
2373067 TGCATCGATGCACATTCA-AGGA
1 TGCATCGATGCACATTCATA--A
2373089 GTGCATC-AGTGCATC-TTCATAA
1 -TGCATCGA-TGCA-CATTCATAA
* *
2373111 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTCATA---A
* *
2373135 TGCATCGATGCACTTTCATAG
1 TGCATCGATGCACATTCATAA
2373156 TGCATCGATG
1 TGCATCGATG
2373166 AATTATGCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.02
21 24 0.39
22 3 0.05
23 14 0.23
24 20 0.32
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACATTCATAA
Found at i:2373154 original size:45 final size:44
Alignment explanation
Indices: 2373067--2373165 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 44
2373057 CATGGCCTTG
2373067 TGCATCGATGCACATTCAAGGAGTGCATCAGTGCATCTTCATAA
1 TGCATCGATGCACATTCAAGGAGTGCATCAGTGCATCTTCATAA
* *
2373111 TGTATCGATGCACATTCAAAGG-GATGCATC-GATGCA-CTTTCATAG
1 TGCATCGATGCACATTC-AAGGAG-TGCATCAG-TGCATC-TTCATAA
2373156 TGCATCGATG
1 TGCATCGATG
2373166 AATTATGCGT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 19 0.40
45 29 0.60
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TGCATCGATGCACATTCAAGGAGTGCATCAGTGCATCTTCATAA
Found at i:2376992 original size:22 final size:21
Alignment explanation
Indices: 2376950--2376989 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2376940 GAGATTATTT
*
2376950 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2376971 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2376990 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2378918 original size:64 final size:63
Alignment explanation
Indices: 2378868--2379023 Score: 226
Period size: 64 Copynumber: 2.5 Consensus size: 63
2378858 GTGCACTAAC
* * *
2378868 AGTGCAGCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGAATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CATGAGTGCATCGATGCATGGT
2378931 ATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
1 A-GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
* *
2378995 AGTGCATCGATGCATAATATACATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
2379024 ATGGTGAGTG
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
63 27 0.32
64 49 0.58
65 7 0.08
66 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
Found at i:2379000 original size:18 final size:18
Alignment explanation
Indices: 2378977--2379044 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
2378967 ATAAAACATG
2378977 AGTGCATCGATGCATGGT
1 AGTGCATCGATGCATGGT
**
2378995 AGTGCATCGATGCATAAT
1 AGTGCATCGATGCATGGT
*
2379013 A-TACATTCGAT--ATGGT
1 AGTGCA-TCGATGCATGGT
2379029 GAGTGCATCGATGCAT
1 -AGTGCATCGATGCAT
2379045 CAATGAGTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.08
17 9 0.23
18 25 0.64
19 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (18 bp):
AGTGCATCGATGCATGGT
Found at i:2379053 original size:20 final size:20
Alignment explanation
Indices: 2379028--2379065 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2379018 TTCGATATGG
2379028 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
2379048 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
2379066 CCTTCATAAT
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:2388147 original size:30 final size:30
Alignment explanation
Indices: 2388077--2388148 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
2388067 AATTTTCTTT
*
2388077 TTCTAAATCAATGATTTTGACTTTTGAAAA
1 TTCTAAATCATTGATTTTGACTTTTGAAAA
2388107 TTCTAAATCATTGATTTTGACTTTTGAAAA
1 TTCTAAATCATTGATTTTGACTTTTGAAAA
2388137 TTCTAAATCATT
1 TTCTAAATCATT
2388149 ATTCAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (30 bp):
TTCTAAATCATTGATTTTGACTTTTGAAAA
Found at i:2388192 original size:21 final size:21
Alignment explanation
Indices: 2388168--2388209 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2388158 TTCATTTTGA
2388168 TTTTCAAAATCAACTT-TTTTC
1 TTTT-AAAATCAACTTATTTTC
2388189 TTTTAAAATCAACTTATTTTC
1 TTTTAAAATCAACTTATTTTC
2388210 AATTTTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAATCAACTTATTTTC
Found at i:2390579 original size:54 final size:54
Alignment explanation
Indices: 2390492--2390881 Score: 537
Period size: 54 Copynumber: 7.2 Consensus size: 54
2390482 CGAATGGGCG
* *
2390492 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
* *
2390546 TTGTTTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
* * *
2390600 CTGTGTGTGCAACTTAAGACATTCATAATAAGTTTATGAATTTCCATATTGGCA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
** * * *
2390654 CTGTGTGTGCAACTTAAGAAATTCATAATGTGTTTATAAATTTTAGTAATGGCA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
* * * *
2390708 CTGTGTGTGTAACGTAAGAAATTCATAATAAGTTTATGAATTTTCATATTTGCA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
* * * *
2390762 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTCGTATTGACA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGGCA
* * * * *
2390817 TTATGTGTGGAACCTAAGAAATTCATAATCAGTTTATGAATTTTCGTATTGGCA
1 CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
*
2390871 CTATGTGTGCA
1 CTGTGTGTGCA
2390882 CCCCATGTAA
Statistics
Matches: 296, Mismatches: 39, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
54 248 0.84
55 48 0.16
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (54 bp):
CTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
Found at i:2390894 original size:54 final size:54
Alignment explanation
Indices: 2390495--2390965 Score: 510
Period size: 54 Copynumber: 8.7 Consensus size: 54
2390485 ATGGGCGCTG
* * * * *
2390495 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACATTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * *
2390549 TTTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * *
2390603 TGTGTGCAACTTAAGACATTCATAATAAGTTTATGAATTTCCATATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* ** * * * *
2390657 TGTGTGCAACTTAAGAAATTCATAATGTGTTTATAAATTTTAGTAATGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * *
2390711 TGTGTGTAACGTAAGAAATTCATAATAAGTTTATGAATTTTCATATTTGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * *
2390765 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTCGTATTGACATTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGGCACTA
* *
2390820 TGTGTGGAACCTAAGAAATTCATAATCAGTTTATGAATTTTCGTATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * * * * ** * **
2390874 TGTGTGCACCCCATGTAATTCATAATGAGTTTGTGAAATACCGTATCGTAACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * * *
2390928 AGTGTGCAACCCATGAAATTCATATTGAGCTTATGAAT
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
2390966 GACTGTATCG
Statistics
Matches: 359, Mismatches: 57, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
54 311 0.87
55 48 0.13
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (54 bp):
TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
Found at i:2390974 original size:54 final size:54
Alignment explanation
Indices: 2390834--2390994 Score: 155
Period size: 54 Copynumber: 3.0 Consensus size: 54
2390824 TGGAACCTAA
* * * ** * * *
2390834 GAAATTCATAATCAGTTTATGAATTTTCGTATTGGCACTATGTGTGCACCCCAT
1 GAAATTCATAATGAGCTTATGAAATACCGTATCGACACTAAGTGTGCACCCCAT
* * * *
2390888 GTAATTCATAATGAGTTTGTGAAATACCGTATCGTA-ACTAAGTGTGCAACCCAT
1 GAAATTCATAATGAGCTTATGAAATACCGTATCG-ACACTAAGTGTGCACCCCAT
* * *
2390942 GAAATTCATATTGAGCTTATG-AATGACTGTATCGACACTACGTGTGCACCCCA
1 GAAATTCATAATGAGCTTATGAAAT-ACCGTATCGACACTAAGTGTGCACCCCA
2390995 AAGAACTTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
53 4 0.05
54 83 0.95
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (54 bp):
GAAATTCATAATGAGCTTATGAAATACCGTATCGACACTAAGTGTGCACCCCAT
Found at i:2390989 original size:217 final size:216
Alignment explanation
Indices: 2390551--2390989 Score: 463
Period size: 217 Copynumber: 2.0 Consensus size: 216
2390541 TGACATTGTT
* * * *
2390551 TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGTGTGTGCAACTTA
1 TGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTA
* * **
2390616 AGACATTCATAATAAGTTTATGAATTTCCATATTGGCACTGTGTGTGCAACTTAAGAAATTCATA
66 AGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACCCAAGAAATTCATA
* ** * ** * ** *
2390681 ATGTGTTTATAAATTTTAGTAATGGCACTGTGTGTGTAACGTAAGAAATTCATAATAAGTTTATG
131 ATGAGTTTATAAATTACAGTAATGGAACTAAGTGTGCAACCCAAGAAATTCATAATAAGCTTATG
** * *
2390746 AATTTTCATATTTGCACTATG
196 AATACTCATATTCGCACTACG
* * *
2390767 TGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTTCGTATTGACATTATGTGTGGAACCT
1 TGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGACACTATGTGTGCAACCT
* * * * * *
2390832 AAGAAATTCATAATCAGTTTATGAATTTTCGTATTGGCACTATGTGTGCACCCCATGTAATTCAT
65 AAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACCCAAGAAATTCAT
* * * * * *
2390897 AATGAGTTTGTGAAA-TACCGT-ATCGTAACTAAGTGTGCAACCCATGAAATTCATATTGAGCTT
130 AATGAGTTTAT-AAATTACAGTAAT-GGAACTAAGTGTGCAACCCAAGAAATTCATAATAAGCTT
*
2390960 ATGAATGACT-GTA-TCGACACTACG
193 ATGAAT-ACTCATATTCG-CACTACG
2390984 TGTGCA
1 TGTGCA
2390990 CCCCAAAGAA
Statistics
Matches: 180, Mismatches: 38, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
216 37 0.21
217 139 0.77
218 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (216 bp):
TGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTA
AGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACCCAAGAAATTCATA
ATGAGTTTATAAATTACAGTAATGGAACTAAGTGTGCAACCCAAGAAATTCATAATAAGCTTATG
AATACTCATATTCGCACTACG
Found at i:2395258 original size:25 final size:25
Alignment explanation
Indices: 2395230--2395279 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2395220 AGTATGAAGA
2395230 GTTGTAAGTGTGGTTACCTTGAATT
1 GTTGTAAGTGTGGTTACCTTGAATT
*
2395255 GTTGTAAGTTTGGTTACCTTGAATT
1 GTTGTAAGTGTGGTTACCTTGAATT
2395280 CTTTGAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.08, G:0.26, T:0.46
Consensus pattern (25 bp):
GTTGTAAGTGTGGTTACCTTGAATT
Found at i:2402697 original size:57 final size:57
Alignment explanation
Indices: 2402606--2402716 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
2402596 TGCTCATGTT
* * *
2402606 ATGATTGCACTTGGAGTGTAGATTATGATCAGTTATAATTGGCACTGTGATGTGTGC
1 ATGATTGCAATTGGAGTGTAGATTATGATAAGTTATAATTGGCACTATGATGTGTGC
2402663 ATGATTGCAATTGGAGTGTAGATTATGATAAGTTATAATTGGCACTATGATGTG
1 ATGATTGCAATTGGAGTGTAGATTATGATAAGTTATAATTGGCACTATGATGTG
2402717 CCTAGTGCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (57 bp):
ATGATTGCAATTGGAGTGTAGATTATGATAAGTTATAATTGGCACTATGATGTGTGC
Found at i:2402704 original size:28 final size:28
Alignment explanation
Indices: 2402616--2402704 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
2402606 ATGATTGCAC
*
2402616 TTGGAGTGTAGATTATGATCAGTTATAA
1 TTGGAGTGTAGATTATGATAAGTTATAA
* * * **
2402644 TTGGCACTGT-GATGTGTGCATGA-TTGCAA
1 TTGG-AGTGTAGAT-TATG-ATAAGTTATAA
2402673 TTGGAGTGTAGATTATGATAAGTTATAA
1 TTGGAGTGTAGATTATGATAAGTTATAA
2402701 TTGG
1 TTGG
2402705 CACTATGATG
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
27 3 0.07
28 22 0.48
29 18 0.39
30 3 0.07
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (28 bp):
TTGGAGTGTAGATTATGATAAGTTATAA
Found at i:2407712 original size:16 final size:16
Alignment explanation
Indices: 2407687--2407723 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2407677 GTTTGGAACC
*
2407687 AAATTTCAAATTTGGT
1 AAATTGCAAATTTGGT
2407703 AAATTGCAAATTTGGT
1 AAATTGCAAATTTGGT
2407719 AAATT
1 AAATT
2407724 ACAAGGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (16 bp):
AAATTGCAAATTTGGT
Found at i:2413176 original size:15 final size:16
Alignment explanation
Indices: 2413153--2413187 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2413143 GTGTTAATAC
*
2413153 TTATTACAAAAAAC-A
1 TTATCACAAAAAACAA
2413168 TTATCACAAAAAACAA
1 TTATCACAAAAAACAA
2413184 TTAT
1 TTAT
2413188 ATTCACGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (16 bp):
TTATCACAAAAAACAA
Found at i:2413744 original size:419 final size:418
Alignment explanation
Indices: 2413051--2413898 Score: 1156
Period size: 419 Copynumber: 2.0 Consensus size: 418
2413041 TATGTTTTAA
*
2413051 ATATAGTAGCAAAATATATTATCAAAAAGATTTCCCTCCATACTTTTTTTTGCGCCAAAAAAGTT
1 ATATAGTAACAAAATATATTATCAAAAAGATTTCCCTCCATAC-TTTTTTTGCGCCAAAAAAGTT
** *
2413116 ATATAGTGGCAAATTTTGTAACTATAAGTGTTAATACTTATTACAAAAAACATTATCACAAAAAA
65 ATATAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTATCACAAAAAA
* * *
2413181 CAATTATATTCACGTTTTTGTGACAATTTATATTTGTAATTATAAATTTTAACTATAGTGATAGC
130 CAATTATATTCACATTTTTGTGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATA-C
* * *
2413246 ATATATTAATTGTCATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGAAAATTTTA
194 ACATATTAATTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGCTATATTGAAAATTTTA
2413311 TAATTATAATTTATAGTTATTGTTATTA-AAAAAATTATCACATCAAATAATAAAATTCAAGTTT
259 TAATTATAATTTATAGTTATTGTTA-TAGAAAAAATTATCACATCAAATAATAAAATTCAAG-TT
* *
2413375 TTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAAGTATAGTATCAAAAC
322 TTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAAGTATACTAT-AAAAA
* * * *
2413440 CATTTCTCCCCATTTTTTAATGTCAAAAATGTT
386 AAATTATCCCCATTTTTTAATGCCAAAAATGTT
* * * *
2413473 ATATAGTAACAAAATATATTGTTATAAAGATTTTCCTCCATA-TTTTTTTG-GACC-AAAAA-TT
1 ATATAGTAACAAAATATATTATCAAAAAGATTTCCCTCCATACTTTTTTTGCG-CCAAAAAAGTT
* * * *
2413534 CATATAGTAATAATTTTTGTAACTATAAGTGTTTATAATTATTACAAAAAACATTGTCACAAAAA
65 -ATATAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTATCACAAAAA
** * * *
2413599 ATGATGT-TATTCACATTTTTGTGAGAAATTATACTTGTAGTTATAAATTTTAATTATAGTGATA
129 ACAAT-TATATTCACATTTTTGTGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATA
* *
2413663 -ACATA-T-ATTGTGATAAATATTTTTCTCCACTTTTTTTTGTTTCAAAAGGCTATATTGATAAG
193 CACATATTAATTGTCATAAATATTTTTCTCCAC--TTTTTTGTTTCAAAA-GCTATATTGA-AAA
* * * *
2413725 TTTTGTAATTATAATTTATATTTATTGTTATAGAAAAAATTATCACATTAGATAATAAAATTCAA
254 TTTTATAATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTCAA
* * *
2413790 GTTTTTTGTAATCAATTATTTTTGTACTTGTATATTTTAATCATTATGAAAAATTATACTATAAA
319 GTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAAGTATACTATAAA
* **
2413855 AAAAATTATCCCTATTTTTTGGTGCCAAAAATGTT
384 AAAAATTATCCCCATTTTTTAATGCCAAAAATGTT
2413890 ATATAGTAA
1 ATATAGTAA
2413899 ATGTTTATTT
Statistics
Matches: 377, Mismatches: 41, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
415 22 0.06
416 1 0.00
417 58 0.15
418 70 0.19
419 178 0.47
420 11 0.03
422 37 0.10
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (418 bp):
ATATAGTAACAAAATATATTATCAAAAAGATTTCCCTCCATACTTTTTTTGCGCCAAAAAAGTTA
TATAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTATCACAAAAAAC
AATTATATTCACATTTTTGTGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATACAC
ATATTAATTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGCTATATTGAAAATTTTATA
ATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTT
GTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAAGTATACTATAAAAAAAATT
ATCCCCATTTTTTAATGCCAAAAATGTT
Found at i:2416478 original size:33 final size:33
Alignment explanation
Indices: 2416390--2416480 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 33
2416380 ACAATACTTT
* * * *
2416390 CTCAAAATAATAACTTTTGACAAAT-TTATTTA
1 CTCAAAATAAAAAATTATGACAAATATTAATTA
* * * * * *
2416422 GTCATAATAACAATTTATAACAAATATTAATTC
1 CTCAAAATAAAAAATTATGACAAATATTAATTA
2416455 CTCAAAATAAAAAATTATGACAAATA
1 CTCAAAATAAAAAATTATGACAAATA
2416481 ATGTTCCTTC
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
32 19 0.42
33 26 0.58
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (33 bp):
CTCAAAATAAAAAATTATGACAAATATTAATTA
Found at i:2416760 original size:197 final size:197
Alignment explanation
Indices: 2416317--2416920 Score: 816
Period size: 198 Copynumber: 3.1 Consensus size: 197
2416307 TAAATCATGC
* *
2416317 ATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTTAAATTTATTTCATCAC
1 ATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTCGTCAC
* * * * * *
2416382 AATACTTTCTCAAAATAATAACTTTTGACAAATTTATTTAGTCATAATAACAATTTATAACAAAT
66 AATATTTTATCAAAATAA-AAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAAT
* ** * * * *
2416447 ATTAATTCCTCAAAATAAAAAATTATGACAAATAATGTTCCTTCACAATAACAAAGTGTAACAAA
130 ATTAATTTCTCATTATAAAAAATTGTGACAAATAATATTCTTTCACAATAACAAATTGTAACAAA
*
2416512 TTT
195 ATT
* ** * *
2416515 ATTTAGTTACAATAACATAGAAAATTTAGTCAAAATAAAATTTTATGTCAAATTTATTTTGTCAC
1 ATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTCGTCAC
* * * *
2416580 AATATTTTATCAAAA-AAAAATTGTAACAAATATATTTAATCAAAATAATAATTTATAAGAAATA
66 AATATTTTATCAAAATAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATA
* *
2416644 TTAATTTCTCATTATAAAAAAATTGCGACAAGTAATATTCTTTCACAATAACAAATTGTAACAAA
131 TTAATTTCTCATTAT-AAAAAATTGTGACAAATAATATTCTTTCACAATAACAAATTGTAACAAA
*
2416709 ATG
195 ATT
* * * * * * *
2416712 ATTTAATCACAATAACACATTAAGTTTTA-TCATAGTAAAAAATTATGTCAAATTTATTTCGTCC
1 ATTTAGTCACAATAACATATTAA-ATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTCGTCA
*
2416776 CAATATTTTATCAAAATGAAAAATTGTGACAAATTTATTTAATCAAAATAACAAATTATAACAAA
65 CAATATTTTATCAAAAT-AAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAA
*
2416841 TATTAATTTCTCATTATAAAAAATTGTGACAAATAATATCCTTTCACAATAACAAATTGTAACAA
129 TATTAATTTCTCATTATAAAAAATTGTGACAAATAATATTCTTTCACAATAACAAATTGTAACAA
*
2416906 ACTT
194 AATT
2416910 ATTTAGTCACA
1 ATTTAGTCACA
2416921 GTAAAAAGTC
Statistics
Matches: 351, Mismatches: 51, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
196 51 0.15
197 109 0.31
198 132 0.38
199 59 0.17
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (197 bp):
ATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTCGTCAC
AATATTTTATCAAAATAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATA
TTAATTTCTCATTATAAAAAATTGTGACAAATAATATTCTTTCACAATAACAAATTGTAACAAAA
TT
Found at i:2416821 original size:32 final size:31
Alignment explanation
Indices: 2416782--2416914 Score: 92
Period size: 33 Copynumber: 4.1 Consensus size: 31
2416772 GTCCCAATAT
2416782 TTTATCAAAATGAAAAATTGTGACAAAT-TTA
1 TTTATCAAAAT-AAAAATTGTGACAAATATTA
* *
2416813 TTTAATCAAAATAACAAATTATAACAAATATTAA
1 TTT-ATCAAAATAA-AAATTGTGACAAATATT-A
* ** *
2416847 TTTCTCATTATAAAAAATTGTGACAAATAATA
1 TTTATCAAAAT-AAAAATTGTGACAAATATTA
* * *
2416879 TCCTT-TCACAATAACAAATTGTAACAAA-CTTA
1 T--TTATCAAAATAA-AAATTGTGACAAATATTA
2416911 TTTA
1 TTTA
2416915 GTCACAGTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
30 2 0.03
31 5 0.06
32 27 0.34
33 38 0.47
34 8 0.10
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (31 bp):
TTTATCAAAATAAAAATTGTGACAAATATTA
Found at i:2416865 original size:100 final size:99
Alignment explanation
Indices: 2416564--2416865 Score: 242
Period size: 100 Copynumber: 3.1 Consensus size: 99
2416554 ATTTTATGTC
* *
2416564 AAATTTATTTTGTCACAATATTTTATCAAAA-AAAAATTGTAACAAATATATTTAATCAAAATAA
1 AAATTTATTTCGTCACAATATTTTATCAAAATAAAAATTGTAACAAATTTATTTAATCAAAATAA
* * *
2416628 TAATTTATAAGAAATATTAATTTCTCATTATAAA
66 CAAATTATAACAAATATTAATTTCTCATTATAAA
* * * * * * *
2416662 AAA---ATTGCGACAAGTAATATTCTT-TCACAATAACAAATTGTAACAAAATGATTTAATCACA
1 AAATTTATTTCGTC-A-CAATATT-TTATCAAAATAA-AAATTGTAACAAATTTATTTAATCAAA
* *** * * *** ***
2416723 ATAACACATTAAGTTTTATCATAGTAA---AAAATTATGTC
62 ATAACAAATT-A-TAACA-AATATTAATTTCTCATTATAAA
* *
2416761 AAATTTATTTCGTCCCAATATTTTATCAAAATGAAAAATTGTGACAAATTTATTTAATCAAAATA
1 AAATTTATTTCGTCACAATATTTTATCAAAAT-AAAAATTGTAACAAATTTATTTAATCAAAATA
2416826 ACAAATTATAACAAATATTAATTTCTCATTATAAA
65 ACAAATTATAACAAATATTAATTTCTCATTATAAA
2416861 AAATT
1 AAATT
2416866 GTGACAAATA
Statistics
Matches: 144, Mismatches: 44, Indels: 30
0.66 0.20 0.14
Matches are distributed among these distances:
95 5 0.03
96 1 0.01
97 17 0.12
98 9 0.06
99 41 0.28
100 55 0.38
101 4 0.03
102 12 0.08
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (99 bp):
AAATTTATTTCGTCACAATATTTTATCAAAATAAAAATTGTAACAAATTTATTTAATCAAAATAA
CAAATTATAACAAATATTAATTTCTCATTATAAA
Found at i:2416873 original size:33 final size:33
Alignment explanation
Indices: 2416779--2416875 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 33
2416769 TTCGTCCCAA
* *
2416779 TATTTTATCAAAATGAAAAATTGTGACAAAT-T
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
* * *
2416811 TATTTAATCAAAATAACAAATTATAACAAATAT
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
* **
2416844 TAATTT-CTCATTATAAAAAATTGTGACAAATA
1 T-ATTTAATCAAAATAAAAAATTGTGACAAATA
2416876 ATATCCTTTC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
32 26 0.50
33 22 0.42
34 4 0.08
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (33 bp):
TATTTAATCAAAATAAAAAATTGTGACAAATAT
Found at i:2421567 original size:6 final size:6
Alignment explanation
Indices: 2421558--2421587 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2421548 AGTAATACCA
2421558 ATAGTG ATAGTG ATAGTG ATAGTG ATAGTG
1 ATAGTG ATAGTG ATAGTG ATAGTG ATAGTG
2421588 GATACTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
ATAGTG
Found at i:2425219 original size:33 final size:33
Alignment explanation
Indices: 2425179--2425245 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
2425169 TTATGATATC
*
2425179 TTTTATTTTAGTTC-TTTACTTTATATTTTTATT
1 TTTTATTTTAG-TCATTTACTTTATATTTTAATT
2425212 TTTTATTTTAGTCATTTACTTTATATTTTAATT
1 TTTTATTTTAGTCATTTACTTTATATTTTAATT
2425245 T
1 T
2425246 ATGTCATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (33 bp):
TTTTATTTTAGTCATTTACTTTATATTTTAATT
Found at i:2425234 original size:25 final size:26
Alignment explanation
Indices: 2425206--2425269 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
2425196 ACTTTATATT
2425206 TTTATTTTTTATTTTA-GTCATTTAC
1 TTTATTTTTTATTTTATGTCATTTAC
* *
2425231 TTTATATTTTAATTTATGTCATTTAC
1 TTTATTTTTTATTTTATGTCATTTAC
*
2425257 TTT-TTATTTATTT
1 TTTATTTTTTATTT
2425270 AATTTCAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 21 0.64
26 12 0.36
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTATTTTTTATTTTATGTCATTTAC
Found at i:2425251 original size:26 final size:25
Alignment explanation
Indices: 2425206--2425265 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
2425196 ACTTTATATT
* *
2425206 TTTATTTTTTATTTTAGTCATTTAC
1 TTTATATTTTAATTTAGTCATTTAC
2425231 TTTATATTTTAATTTATGTCATTTAC
1 TTTATATTTTAATTTA-GTCATTTAC
*
2425257 TTTTTATTT
1 TTTATATTT
2425266 ATTTAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTATATTTTAATTTAGTCATTTAC
Found at i:2425286 original size:14 final size:14
Alignment explanation
Indices: 2425267--2425302 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2425257 TTTTTATTTA
2425267 TTTAATTTCAGTT-C
1 TTTAATTTCA-TTAC
2425281 TTTAATTTCATTAC
1 TTTAATTTCATTAC
2425295 TTTAATTT
1 TTTAATTT
2425303 TCTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTCATTAC
Found at i:2426388 original size:17 final size:16
Alignment explanation
Indices: 2426354--2426394 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
2426344 TATTGCACAA
*
2426354 TTTGCA-TTCTTCTTT
1 TTTGCATTTCTACTTT
2426369 TTTGCATTTCTACATTT
1 TTTGCATTTCTAC-TTT
2426386 TTTGCATTT
1 TTTGCATTT
2426395 TCATGTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 5 0.22
17 12 0.52
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTGCATTTCTACTTT
Found at i:2429023 original size:11 final size:11
Alignment explanation
Indices: 2428999--2429060 Score: 70
Period size: 12 Copynumber: 5.3 Consensus size: 11
2428989 AATAAAAGGG
*
2428999 AAAAGAGATGAA
1 AAAAGAGA-AAA
*
2429011 AAAAGAATAAAA
1 AAAAG-AGAAAA
2429023 AAAAGAGAAAA
1 AAAAGAGAAAA
2429034 AAAAGAGAAAA
1 AAAAGAGAAAA
2429045 AGAAAGAAGAAAA
1 A-AAAG-AGAAAA
2429058 AAA
1 AAA
2429061 TTGAATCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.39
12 18 0.41
13 9 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:2430516 original size:42 final size:42
Alignment explanation
Indices: 2430470--2430599 Score: 106
Period size: 42 Copynumber: 3.1 Consensus size: 42
2430460 GAGGCATCTC
2430470 GAAAGCCCATTTCATACAGAAATAATCCATGTGGGGCATTTT
1 GAAAGCCCATTTCATACAGAAATAATCCATGTGGGGCATTTT
* * * * * * * *
2430512 GAAAGCTCATAT--TA-AG-AAGAAGCAAATGTTGGGACATCTC
1 GAAAGCCCATTTCATACAGAAATAATC-CATG-TGGGGCATTTT
* * * *
2430552 GAAAGCCCATTCCAGACAGAAATGATCCATGTGGGGTATTTT
1 GAAAGCCCATTTCATACAGAAATAATCCATGTGGGGCATTTT
2430594 GAAAGC
1 GAAAGC
2430600 TCACATTAAA
Statistics
Matches: 62, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
38 5 0.08
39 5 0.08
40 19 0.31
42 24 0.39
43 5 0.08
44 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (42 bp):
GAAAGCCCATTTCATACAGAAATAATCCATGTGGGGCATTTT
Found at i:2431132 original size:54 final size:54
Alignment explanation
Indices: 2431050--2431251 Score: 300
Period size: 54 Copynumber: 3.7 Consensus size: 54
2431040 CAATGATTGA
*
2431050 GAACATCTG-GACAGAAGCCAC-GAGAAAGGATAAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGTG-CAGAAGCCACAG-GAAAGGATGAATGTGTTGTCAAATGTTTTAC
* *
2431104 GAACATCAGTGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * *
2431158 GAACATTTGTACAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* *
2431212 GAGCATCTGTGCAGAAACCACAGGAAAGGATGAATGTGTT
1 GAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTT
2431252 ACGAACTAGT
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
54 132 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (54 bp):
GAACATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:2431676 original size:22 final size:21
Alignment explanation
Indices: 2431619--2431677 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
2431609 ATCTACATTC
*
2431619 TTCAAAGATGATAGATTCTCT
1 TTCAAAGATGATAAATTCTCT
2431640 TT-AAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTC-T
* *
2431661 TTCAAATATGAAAAATT
1 TTCAAAGATGATAAATT
2431678 TATTGGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.48
21 5 0.15
22 12 0.36
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
TTCAAAGATGATAAATTCTCT
Found at i:2433104 original size:17 final size:16
Alignment explanation
Indices: 2433073--2433106 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2433063 CACGTGAGGA
2433073 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2433089 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2433106 T
1 T
2433107 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.