Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007594.1 Hibiscus syriacus cultivar Beakdansim tig00021909_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: 124587
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:1128 original size:2 final size:2
Alignment explanation
Indices: 1121--1164 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1111 CTAATGTTGA
1121 AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1161 AT AT
1 AT AT
1165 CACACCCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11100 original size:39 final size:40
Alignment explanation
Indices: 11056--11142 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
11046 TACTCACTTC
*
11056 TGCATATGGTGGACACGACCTTATGTGTA-AGCACTTCGG
1 TGCATATGGTGGACACGACCTTATGTGTATAGCACTTCGA
* *
11095 TGCATATGGTGGGCATGACCTTATGTGTATTAGCACTTCGA
1 TGCATATGGTGGACACGACCTTATGTGTA-TAGCACTTCGA
11136 TGCATAT
1 TGCATAT
11143 TTGACTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 27 0.63
41 16 0.37
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
TGCATATGGTGGACACGACCTTATGTGTATAGCACTTCGA
Found at i:11722 original size:828 final size:819
Alignment explanation
Indices: 10238--11875 Score: 2470
Period size: 828 Copynumber: 2.0 Consensus size: 819
10228 TAGAAAAGTA
* *
10238 ATGGTGGGCACGACCTTATGTGTAAGAACTTCAGTGAATATGGTGGGTATGACCTTATATGTATT
1 ATGGTGGACACGACCTTATGTGTAAGAACTTCAGTGAATATGGTGGGCATGACCTTATATGTATT
* * * * * *
10303 ATCACTTCGGTGCATATTTGACTCGAATACCCATAGTCTTTATAGATTTACGTTTTGGATATGAT
66 AGCACTTCGATGCATATTTGACTCGAATACCCAGAGTCTTCATAAATTTACGTTTAGGATATGAT
* * * *
10368 TTATTGGTTAATAAATGATAAACAGGAAAATAAGCTTACGAGTGACAAGCATATTGGTAAGAAAC
131 TTATTGGTTAATAAATGATAAAAAAGAAAATAAGATTACGAGTGACAAGCATATTGGTAAAAAAC
* * * *
10433 TTTATATCCGGTTATATCATGTTAAATTATGGTAACATGGCTGTAATATAGGTAACATGATCACA
196 TTTATATCCGGTTATATCATGTTAAATCATGGTAACATGGCTGGAATACAGGTAACATGATCAAA
10498 TTGCATTGAATATTATTACTCATTTATATTTATAAGTTGCATTGCTTTGAATATTTATATGATTG
261 TTGCATTGAATATTATTACTCATTTATATTTATAAGTTGCATTGCTTTGAATATTTATATGATTG
* * * * * * *
10563 CCTCACTAAGTGCATACTTAGCTTGGCATCAATCCCCAAGGAAATATTTACAGGTAACAATGATG
326 CCTCACTAAGTACATAATTAGCATGGCATCAATCCCCAAGGAAATA-TAAAAAGTAACAATAATG
* * *
10628 ACATCCTACTGTGTTCTAAAAGTCTTAGCTGACATGCATACAAGAATAAAATGTTTGCAGTTCCT
390 A-A-CCTACTGTGTTCTAAAAGTCTTAGCTGACATGCATACAAGAACAAAATGTCTGCAATTCCT
*
10693 TAATATAGTTAGTATTAAATATAACTAATAGTATGAATAAATATTATGATATTAAACTATGCTTA
453 TAATATAGTTAGTATTAAATATAACTAATAATATGAATAAATATTATGATATTAAACTATGCTTA
10758 GCAAAAATTAATTTGGGTTTTAAATCAAACATGTTAGACAGTCTTATTTTTTTTATGAAAATAGA
518 GCAAAAATTAATTTGGGTTTTAAATCAAACATGTTAGACAGTCTTATTTTTTTTATGAAAATAGA
10823 ACAAAACTGTCTATCACTGCTTGAAACTGGTTTTGAATTAATAACCAACAATATTATATTACGAT
583 ACAAAACTGTCTATCACTGCTTGAAACTGGTTTTGAATTAATAACCAACAATATTATATTACGAT
10888 TTTTCACTGAATAATTATTTTATAAAAAATGTTCAAGTTATAATACTGGTGATGTTTGAATGAAA
648 TTTTCACTGAATAATTATTTTAT-AAAAATGTTCAAGTTATAATACTGGTGATGTTTGAATGAAA
* *
10953 CAAAATTTTACTCAATTCAATTAAAGAAATGTTTTGAATTTCTAATGTGATATTTGTAACTCGTA
712 CAAAATTTTACTCAATTCAATTAAAGAAATGTTTTGAATTTCTAATGTGACATCTGTAACTCGTA
11018 TTGGTTCG-TATATACAGGTTATGGGTGTTACTCACTTCTGCAT
777 TTGGTTCGCT-TATACAGGTTATGGGTGTTACTCACTTCTGCAT
* * * *
11061 ATGGTGGACACGACCTTATGTGTAAGCACTTCGGTGCATATGGTGGGCATGACCTTATGTGTATT
1 ATGGTGGACACGACCTTATGTGTAAGAACTTCAGTGAATATGGTGGGCATGACCTTATATGTATT
* * * *
11126 AGCACTTCGATGCATATTTGACTTGAATACCCAGGGTCTTCATAAATTTACGTTTAGGTTATGGT
66 AGCACTTCGATGCATATTTGACTCGAATACCCAGAGTCTTCATAAATTTACGTTTAGGATATGAT
* *
11191 TTATTGGTTAATAAATGATAAAAAAGAAAATAAGATTACGAGCTTTTGGGATAAATGGTAAGTAT
131 TTATTGGTTAATAAATGATAAAAAAGAAAATAAGATTACGAG----T--G----A---CAAGCAT
* *
11256 ATTGGTAAAAAACTTTATATCCGGTTATATCATGTTAAATCATGGTAACATGGTTGGAATGCAGG
183 ATTGGTAAAAAACTTTATATCCGGTTATATCATGTTAAATCATGGTAACATGGCTGGAATACAGG
11321 TAA-AGTGATCAAATTGCATTGAATATTATTACTCATTTATATTTATAAGTTGCATTGCTTTGAA
248 TAACA-TGATCAAATTGCATTGAATATTATTACTCATTTATATTTATAAGTTGCATTGCTTTGAA
* * * *** * * *
11385 TATTTATATGATTTCCTCACTAAGTATATAATTAGCATGTG-AT-GATTTTCACGTGTAGTA-AA
312 TATTTATATGATTGCCTCACTAAGTACATAATTAGCATG-GCATCAATCCCCAAG-GAAATATAA
* * * * * *
11447 AAAG-AAGAA-AATG-A-GTATTGTGTTCTAAAAGTCTTAGAC-GACATGTATACGAGAACGAAA
375 AAAGTAACAATAATGAACCTACTGTGTTCTAAAAGTCTTAG-CTGACATGCATACAAGAACAAAA
*
11507 TGTCTGCAATTCCTTAATATAGTTAGTATTAAATATAACTAATAATATGAATAAATATTATGATT
439 TGTCTGCAATTCCTTAATATAGTTAGTATTAAATATAACTAATAATATGAATAAATATTATGATA
11572 TTAAACTATGCTTAGCAAAAATTAATTTGGGTTTTTAAATCAAACATGTTAGACAGTCTTA-TTT
504 TTAAACTATGCTTAGCAAAAATTAATTTGGG-TTTTAAATCAAACATGTTAGACAGTCTTATTTT
11636 TTTTATGAAAATAGAACAAAACTGTCTATCACTGCTTGAAACTGGTTTTGAATTAATAACCAACA
568 TTTTATGAAAATAGAACAAAACTGTCTATCACTGCTTGAAACTGGTTTTGAATTAATAACCAACA
11701 ATATTATATTACGATTTTTCACTGAATAATTATTTTATAAAAATGTTCAAGTTATAATACTGGTG
633 ATATTATATTACGATTTTTCACTGAATAATTATTTTATAAAAATGTTCAAGTTATAATACTGGTG
11766 ATGTTTGAATGAAACAAAATTTTACTCAATTCAATTAAAGAAATGTTTTGAATTTCTAATGTGAC
698 ATGTTTGAATGAAACAAAATTTTACTCAATTCAATTAAAGAAATGTTTTGAATTTCTAATGTGAC
*
11831 ATCTGTAACTCGTATTGGTTCGCTTATACGGGTTATGGGTGTTAC
763 ATCTGTAACTCGTATTGGTTCGCTTATACAGGTTATGGGTGTTAC
11876 ATGTTGTGCA
Statistics
Matches: 738, Mismatches: 58, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
823 153 0.21
827 133 0.18
828 237 0.32
829 31 0.04
830 1 0.00
832 3 0.00
833 5 0.01
834 3 0.00
835 6 0.01
836 165 0.22
837 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (819 bp):
ATGGTGGACACGACCTTATGTGTAAGAACTTCAGTGAATATGGTGGGCATGACCTTATATGTATT
AGCACTTCGATGCATATTTGACTCGAATACCCAGAGTCTTCATAAATTTACGTTTAGGATATGAT
TTATTGGTTAATAAATGATAAAAAAGAAAATAAGATTACGAGTGACAAGCATATTGGTAAAAAAC
TTTATATCCGGTTATATCATGTTAAATCATGGTAACATGGCTGGAATACAGGTAACATGATCAAA
TTGCATTGAATATTATTACTCATTTATATTTATAAGTTGCATTGCTTTGAATATTTATATGATTG
CCTCACTAAGTACATAATTAGCATGGCATCAATCCCCAAGGAAATATAAAAAGTAACAATAATGA
ACCTACTGTGTTCTAAAAGTCTTAGCTGACATGCATACAAGAACAAAATGTCTGCAATTCCTTAA
TATAGTTAGTATTAAATATAACTAATAATATGAATAAATATTATGATATTAAACTATGCTTAGCA
AAAATTAATTTGGGTTTTAAATCAAACATGTTAGACAGTCTTATTTTTTTTATGAAAATAGAACA
AAACTGTCTATCACTGCTTGAAACTGGTTTTGAATTAATAACCAACAATATTATATTACGATTTT
TCACTGAATAATTATTTTATAAAAATGTTCAAGTTATAATACTGGTGATGTTTGAATGAAACAAA
ATTTTACTCAATTCAATTAAAGAAATGTTTTGAATTTCTAATGTGACATCTGTAACTCGTATTGG
TTCGCTTATACAGGTTATGGGTGTTACTCACTTCTGCAT
Found at i:11967 original size:2 final size:2
Alignment explanation
Indices: 11960--11988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11950 GGTGTCACAT
11960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11989 TAAAACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12503 original size:20 final size:20
Alignment explanation
Indices: 12478--12886 Score: 118
Period size: 20 Copynumber: 17.7 Consensus size: 20
12468 TTAAATTATG
*
12478 GCATCCTATCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
12498 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
12523 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
12544 GCAT-CATTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
*
12569 GGCATCCTTCCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
12590 GCATTCTTTCACGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
*
12616 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
12637 GCATCATTTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
12663 GTCATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
12684 GCATCCTTTTCATGCATTTTTAGTCAT
1 GCATCC-TTTCATGC---CTTA---AT
12711 AGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
12732 GCATCCTTTCATACATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
*
12758 GACATCCTTTCAAGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* *
12779 GCATCATTTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
* *
12805 GACATTCTTTCATGCATTAAT
1 G-CATCCTTTCATGCCTTAAT
*
12826 GCATCCTTTCATGCATTTTTATTTAT
1 GCATCCTTTCATGC---CTTA---AT
*
12852 GGCATCCTTTCATGTCTTAAT
1 -GCATCCTTTCATGCCTTAAT
12873 GCATCCTTTCATGC
1 GCATCCTTTCATGC
12887 ATTTTTAGTT
Statistics
Matches: 293, Mismatches: 39, Indels: 114
0.66 0.09 0.26
Matches are distributed among these distances:
19 8 0.03
20 94 0.32
21 27 0.09
22 6 0.02
23 15 0.05
24 27 0.09
25 4 0.01
26 31 0.11
27 75 0.26
28 6 0.02
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:12623 original size:47 final size:47
Alignment explanation
Indices: 12473--12898 Score: 658
Period size: 47 Copynumber: 9.1 Consensus size: 47
12463 TACATTTAAA
*
12473 TTATGGCATCCTATCATGCCTTAATGCATCCTTTCATGCA-TTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
12519 TTATGGCATCCTTTCATGCCTTAATGCAT-CATTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * *
12565 TTATGGCATCCTTCCATGCCTTAATGCATTCTTTCACGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* *
12612 TTATGGTATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
12659 TTATGTCATCCTTTCATGCCTTAATGCATCCTTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCC-TTTCATGCATTTTTAG
* * *
12707 TCATAGCATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * *
12754 TTATGACATCCTTTCAAGCCTTAATGCATCATTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * * *
12801 TTATGACATTCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAT
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
12848 TTATGGCATCCTTTCATGTCTTAATGCATCCTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
12895 TTAT
1 TTAT
12899 TGCCTTGCTT
Statistics
Matches: 344, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
45 9 0.03
46 62 0.18
47 229 0.67
48 44 0.13
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
Found at i:12741 original size:142 final size:141
Alignment explanation
Indices: 12473--12898 Score: 667
Period size: 142 Copynumber: 3.0 Consensus size: 141
12463 TACATTTAAA
* * *
12473 TTATGGCATCCTATCATGCCTTAATGCATCCTTTCATGCA-TTTTAGTTATGGCATCCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATG
* * *
12537 CCTTAATGCAT-CATTCATGCATTTTTAGTTATGGCATCCTTCCATGCCTTAATGCATTCTTTCA
66 CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCA
*
12601 CGCATTTTTAG
131 TGCATTTTTAG
* *
12612 TTATGGTATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGTCATCCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATG
* *
12677 CCTTAATGCATCCTTTTCATGCATTTTTAGTCATAGCATCCTTTCATGCCTTAATGCATCCTTTC
66 CCTTAATGCATCC-TTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
*
12742 ATACATTTTTAG
130 ATGCATTTTTAG
* * *
12754 TTATGACATCCTTTCAAGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATTCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATG
* * *
12819 CATTAATGCATCCTTTCATGCATTTTTATTTATGGCATCCTTTCATGTCTTAATGCATCCTTTCA
66 CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCA
12884 TGCATTTTTAG
131 TGCATTTTTAG
12895 TTAT
1 TTAT
12899 TGCCTTGCTT
Statistics
Matches: 262, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
139 37 0.14
140 34 0.13
141 63 0.24
142 128 0.49
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (141 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATG
CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCA
TGCATTTTTAG
Found at i:13247 original size:20 final size:21
Alignment explanation
Indices: 13222--13276 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
13212 ATATTGCCTA
13222 GTATCGATACCCT-TACCATG
1 GTATCGATACCCTATACCATG
* *
13242 GTATCGATACTACTATACTATG
1 GTATCGATAC-CCTATACCATG
13264 GTATCGATACCCT
1 GTATCGATACCCT
13277 CTTACAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 4 0.13
22 16 0.53
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCGATACCCTATACCATG
Found at i:13272 original size:95 final size:96
Alignment explanation
Indices: 13160--13348 Score: 256
Period size: 95 Copynumber: 2.0 Consensus size: 96
13150 ACCCATACTT
* * *
13160 TATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATT-AACTTCGAT-ATTGCCTAG
1 TATACTATGGTACCGATACCCCCTTACAGTATCGATACCAAAATTGAA-TTCAATGATTGCCTAG
* *
13223 TATCGATACCCTTACCATGGTATCGATACTAC
65 TATCAATACCCTTACAATGGTATCGATACTAC
* * * * * *
13255 TATACTATGGTATCGATACCCTCTTACAGTATCGATACCAAAATTGTATTCAATGTTTGCTTGGT
1 TATACTATGGTACCGATACCCCCTTACAGTATCGATACCAAAATTGAATTCAATGATTGCCTAGT
13320 ATCAATACCCTTACAATGGTATCGATACT
66 ATCAATACCCTTACAATGGTATCGATACT
13349 GCCTCAACAA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 46 0.57
96 35 0.43
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (96 bp):
TATACTATGGTACCGATACCCCCTTACAGTATCGATACCAAAATTGAATTCAATGATTGCCTAGT
ATCAATACCCTTACAATGGTATCGATACTAC
Found at i:19581 original size:27 final size:27
Alignment explanation
Indices: 19557--19881 Score: 196
Period size: 27 Copynumber: 13.6 Consensus size: 27
19547 TAATGCATTA
19557 TTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
*
19584 TTTCATGC---CTTA---AT-GCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
19604 TTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
*
19631 TTTCATGC---CTTA---AT-GCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
* *
19651 TTTCATGCATATTTAGATATGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
19678 TTTCATGC----TTA---AT-GCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
19697 TTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
* * *
19724 TTTCAAGC---CTTA---AT-GCATCA
1 TTTCATGCATTTTTAGTTATGGCATCC
* * *
19744 TTTCTTGCATTTTTAGTTATGACATTC
1 TTTCATGCATTTTTAGTTATGGCATCC
* *
19771 TTTCATGC---CTTA---AT-GCATCA
1 TTTCATGCATTTTTAGTTATGGCATCC
*
19791 TTTCATGAATTTTTAGTTATGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
* *
19818 TTTCAAGC---CTTA---AT-GCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
* *
19838 TTTCTTGCATTTTTAGTTAAGGCATCC
1 TTTCATGCATTTTTAGTTATGGCATCC
19865 TTTCATGCATTTTTAGT
1 TTTCATGCATTTTTAGT
19882 CATGCTCTAA
Statistics
Matches: 226, Mismatches: 29, Indels: 86
0.66 0.09 0.25
Matches are distributed among these distances:
19 14 0.06
20 63 0.28
21 10 0.04
23 21 0.09
24 15 0.07
26 11 0.05
27 92 0.41
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (27 bp):
TTTCATGCATTTTTAGTTATGGCATCC
Found at i:19592 original size:47 final size:47
Alignment explanation
Indices: 19480--19872 Score: 594
Period size: 47 Copynumber: 8.4 Consensus size: 47
19470 AATATTTAAA
* *
19480 TTATGGCATCCTATT-ATGCCTTAATGCATCATTCCATGCA-TTATAG
1 TTATGGCATCCT-TTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* *
19526 TTATGACATCCTTTCATGCCTTAATGCATTATTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
*
19573 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* *
19620 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* *
19667 ATATGGCATCCTTTCATG-CTTAATGCATCCTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* *
19713 TTATGGCATCCTTTCAAGCCTTAATGCATCATTTCTTGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* * *
19760 TTATGACATTCTTTCATGCCTTAATGCATCATTTCATGAATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
* * *
19807 TTATGGCATCCTTTCAAGCCTTAATGCATCCTTTCTTGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
*
19854 TTAAGGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGC
19873 ATTTTTAGTC
Statistics
Matches: 317, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
45 2 0.01
46 77 0.24
47 238 0.75
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAG
Found at i:19689 original size:140 final size:140
Alignment explanation
Indices: 19480--19872 Score: 601
Period size: 140 Copynumber: 2.8 Consensus size: 140
19470 AATATTTAAA
* * *
19480 TTATGGCATCCTATT-ATGCCTTAATGCATCATTCCATGCATTATAGTTATGACATCCTTTCATG
1 TTATGGCATCCT-TTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATG
** *
19544 CCTTAATGCATTATTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCA
65 CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCA
19609 TGCATTTTTAG
130 TGCATTTTTAG
* *
19620 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTAGATATGGCATCCTTTCATG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT-TTTAGTTATGGCATCCTTTCATG
* *
19685 -CTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCATTTCT
65 CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCA
19749 TGCATTTTTAG
130 TGCATTTTTAG
* * * *
19760 TTATGACATTCTTTCATGCCTTAATGCATCATTTCATGAATTTTTAGTTATGGCATCCTTTCAAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTTTAGTTATGGCATCCTTTCATG
* *
19825 CCTTAATGCATCCTTTCTTGCATTTTTAGTTAAGGCATCCTTTCATGC
65 CCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGC
19873 ATTTTTAGTC
Statistics
Matches: 230, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
139 2 0.01
140 163 0.71
141 65 0.28
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (140 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTCATGC
CTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCAT
GCATTTTTAG
Found at i:19797 original size:187 final size:186
Alignment explanation
Indices: 19471--19872 Score: 608
Period size: 187 Copynumber: 2.1 Consensus size: 186
19461 ATCCATTTTA
*
19471 ATATTTAAATTATGGCATCCTATT-ATGCCTTAATGCATCATTCCATGCATTATAGTTATGACAT
1 ATATTTAGA-TATGGCATCCT-TTCATG-CTTAATGCATCATTCCATGCATTATAGTTATGACAT
* * *
19535 CCTTTCATGCCTTAATGCATTATTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
63 CCTTTCAAGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGC
* * *
19600 ATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
128 ATCATTTCATGAATTTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCCTTTCATGC
* * * *
19659 ATATTTAGATATGGCATCCTTTCATGCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
1 ATATTTAGATATGGCATCCTTTCATGCTTAATGCATCATTCCATGCA-TTATAGTTATGACATCC
* *
19724 TTTCAAGCCTTAATGCATCATTTCTTGCATTTTTAGTTATGACATTCTTTCATGCCTTAATGCAT
65 TTTCAAGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCAT
*
19789 CATTTCATGAATTTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCCTTTCTTGC
130 CATTTCATGAATTTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCCTTTCATGC
* * *
19846 ATTTTTAGTTAAGGCATCCTTTCATGC
1 ATATTTAGATATGGCATCCTTTCATGC
19873 ATTTTTAGTC
Statistics
Matches: 195, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
186 21 0.11
187 166 0.85
188 8 0.04
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (186 bp):
ATATTTAGATATGGCATCCTTTCATGCTTAATGCATCATTCCATGCATTATAGTTATGACATCCT
TTCAAGCCTTAATGCATCATTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATC
ATTTCATGAATTTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCCTTTCATGC
Found at i:20374 original size:20 final size:21
Alignment explanation
Indices: 20345--20398 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
20335 ATGTTGCCTA
*
20345 GTATCAATACCCT-TA-TCATG
1 GTATCGATACCCTATACT-ATG
*
20365 GTATCGATACTACTATACTATG
1 GTATCGATAC-CCTATACTATG
20387 GTATCGATACCC
1 GTATCGATACCC
20399 CCTTACGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 15 0.54
23 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (21 bp):
GTATCGATACCCTATACTATG
Found at i:20411 original size:95 final size:96
Alignment explanation
Indices: 20274--20469 Score: 263
Period size: 95 Copynumber: 2.1 Consensus size: 96
20264 ACCCTAGTAC
* * *
20274 CGATACTTCTATACTATGGTACCGATACCCCCTTCTAGTATCGATACTAAAATTAGCTTCGATG-
1 CGATACTACTATACTATGGTACCGATACCCCCTTCTAGTATCGATACCAAAATTAGATTCGATGT
20338 TTGCCTAGTATCAATACCCTTATC-ATGGTAT
66 TTGCCTAGTATCAATACCCTTA-CAATGGTAT
* * * *
20369 CGATACTACTATACTATGGTATCGATACCCCCTTAC-GGTATCGATACCAAAATTATATTTGATG
1 CGATACTACTATACTATGGTACCGATACCCCCTT-CTAGTATCGATACCAAAATTAGATTCGATG
* * *
20433 TTTGCTTGGTATCGATACCCTTACAATGGTAT
65 TTTGCCTAGTATCAATACCCTTACAATGGTAT
20465 CGATA
1 CGATA
20470 TTGCCTCAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
95 56 0.64
96 32 0.36
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (96 bp):
CGATACTACTATACTATGGTACCGATACCCCCTTCTAGTATCGATACCAAAATTAGATTCGATGT
TTGCCTAGTATCAATACCCTTACAATGGTAT
Found at i:21690 original size:8 final size:8
Alignment explanation
Indices: 21677--21713 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
21667 TATTAAGGTT
21677 GAAAAGGG
1 GAAAAGGG
21685 GAAAAGGG
1 GAAAAGGG
21693 GAAAAGGG
1 GAAAAGGG
21701 GAAAAGGG
1 GAAAAGGG
21709 GAAAA
1 GAAAA
21714 TGGTAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (8 bp):
GAAAAGGG
Found at i:21728 original size:24 final size:24
Alignment explanation
Indices: 21674--21728 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
21664 ATTTATTAAG
21674 GTTGAAAAGGGGAAAAGGGGAAAA
1 GTTGAAAAGGGGAAAAGGGGAAAA
** * *
21698 GGGGAAAAGGGGAAAATGGTAAAA
1 GTTGAAAAGGGGAAAAGGGGAAAA
21722 GTTGAAA
1 GTTGAAA
21729 CTTGGTTCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (24 bp):
GTTGAAAAGGGGAAAAGGGGAAAA
Found at i:28015 original size:200 final size:199
Alignment explanation
Indices: 27660--29194 Score: 2127
Period size: 200 Copynumber: 7.7 Consensus size: 199
27650 CACATAATAA
* * * * *
27660 GTATCGATCCCAAAAACATCGAAACAAAGAATTATAATATAAAAGGTAAATTTACAATATAACTG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAAC-G
* * *
27725 GTAGATATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTCTTTAAATTTGT
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
* * ** *
27790 GTCGATACGTTTTATCCAGAATCAATATCCAAACGAGGTGTACACAATAAGTGTCGATACATTTA
130 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
27855 AAATT
195 AAATT
* * *
27860 GTATTGATCCCAAAAACATCAAAACAGATAATTATAATGTAATAGGCAAATTTACAATGTAATCG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAA-CG
*
27925 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTATAAATTTGT
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
*
27990 GTCGATACTTTTTGTCCATAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
130 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
28055 AAATT
195 AAATT
* * *
28060 GTATCGATCCCAAAAACATCGAAACCGATAAATATAATGTAATAGGTAACTTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAA-CG
* * * *
28125 GTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCAACACTTTTTAAATTTGC
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
* * * * *
28190 GTCGATA-TATTTTGTCCAGAATGAAT-GCCAAACGGGGTGCACAC-ATAAAGTGTCGATATATT
130 GTCGATACT-TTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAAT-AAGTGTCGATACATT
*
28252 TATTAAA-A
193 TA--AAATT
*
28260 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATATAACTG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAAC-G
* * * *
28325 GTAGATATATACCGGTTTTATGAGAAAATAGGTCTACATAATTTATCGACACTTTTTAAATATGT
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
* *
28390 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACAAGGTGCACGCAATAAGTGTCGATACATTTA
130 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
28455 AAATT
195 AAATT
* * * *
28460 GTATTGATCCCAAAAACATCGAAACAAATAATTATAATATAATAGGTAAATTTACAATATAACTG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAAC-G
* * * * *
28525 GTAGATACATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTCTTTAAATTTGT
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
* ** *
28590 GTCGATACTTTTTGTCTAGAATCAATATCAAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
130 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
28655 AAATT
195 AAATT
* *
28660 GTATCGATCCCAAAAACATCGAAACATATAATTATAATGTAATAGGTAAATTTATAATGTAATCG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAA-CG
* * *
28725 GTATAAATATACCAGTTTTATGAGAAAATAGGTCTACATAATGTATCAACACTTTATAAATTTGT
65 GTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGT
* * *
28790 GTCGATACTTTTTATCCATAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCTATACATTTA
130 GTCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTA
28855 AAATT
195 AAATT
* * * *
28860 GTATCGATCCCAAAAACATCGAAACTGATAAATATAATATAATAGGTAAATTTACAATGTAACAG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACGG
* * *
28925 TATAAATATACCGGTTTTATGAGAGAATAAGTCAACATAATGTATCGACACTTTTTAAATTTGTG
66 TATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTG
* * * *
28990 TTGATACATTTTT-TCCAGAATGAAT-GCCAAAC-AGG-GTGCACACATAAAGTGTCGATACATT
131 TCGATAC-TTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCA-AT-AAGTGTCGATACATT
*
29051 TATTAAA-A
193 TA--AAATT
* * * *
29059 GTATCGATCCCAAAAACATAGAAACCGATAATTACAATGTAATAGGTACATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAA-CG
* * * * *
29124 GTATAAATATATCGGTTTAATTAGAAAA-ACGGTCAACATAATGTATCGAGACTTTTTAAATTTG
65 GTATAAATATACCGGTTTTATGAGAAAATA-GGTCTACATAATGTATCGACACTTTTTAAATTTG
29188 TGTCGAT
129 TGTCGAT
29195 GCCTTTTTAA
Statistics
Matches: 1195, Mismatches: 122, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
196 5 0.00
197 5 0.00
198 25 0.02
199 170 0.14
200 951 0.80
201 37 0.03
202 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACGG
TATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTG
TCGATACTTTTTGTCCAGAATCAATGGCCAAACGAGGTGTACGCAATAAGTGTCGATACATTTAA
AATT
Found at i:28735 original size:20 final size:20
Alignment explanation
Indices: 28686--28735 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28676 CATCGAAACA
28686 TATAATTATAATGTAATAGG
1 TATAATTATAATGTAATAGG
*
28706 TA-AATTTATAATGTAATCGG
1 TATAA-TTATAATGTAATAGG
*
28726 TATAAATATA
1 TATAATTATA
28736 CCAGTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TATAATTATAATGTAATAGG
Found at i:29436 original size:23 final size:23
Alignment explanation
Indices: 29409--29453 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29399 ATTGTACTCT
29409 TTTTTTCCTTAATGTGTTTGTGG
1 TTTTTTCCTTAATGTGTTTGTGG
*
29432 TTTTTTCGTTAATGTGTTTGTG
1 TTTTTTCCTTAATGTGTTTGTG
29454 TTCCAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.22, T:0.62
Consensus pattern (23 bp):
TTTTTTCCTTAATGTGTTTGTGG
Found at i:29543 original size:15 final size:15
Alignment explanation
Indices: 29523--29572 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
29513 GTCTTTCTCA
29523 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
29538 AAGCTCTTCTCAACGAC
1 AAGCTCTTCTCAAC--C
*
29555 AACCTCCTTCTCAACC
1 AAGCT-CTTCTCAACC
29571 AA
1 AA
29573 TCGCTTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 5 0.16
18 9 0.29
ACGTcount: A:0.30, C:0.40, G:0.06, T:0.24
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:29582 original size:18 final size:17
Alignment explanation
Indices: 29527--29583 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
29517 TTCTCAAAGC
29527 TCTTCTCAACCAA-GC-
1 TCTTCTCAACCAACGCT
29542 TCTTCTCAACGACAAC-CT
1 TCTTCTCAAC--CAACGCT
*
29560 CCTTCTCAACCAATCGCT
1 TCTTCTCAACCAA-CGCT
29578 TCTTCT
1 TCTTCT
29584 GATCAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 10 0.29
16 3 0.09
17 5 0.15
18 16 0.47
ACGTcount: A:0.23, C:0.40, G:0.05, T:0.32
Consensus pattern (17 bp):
TCTTCTCAACCAACGCT
Found at i:39272 original size:23 final size:22
Alignment explanation
Indices: 39247--39325 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
39237 CACGGTAGAG
39247 TGCATCGATGCATATTCAAGGA
1 TGCATCGATGCATATTCAAGGA
* * * *
39269 GTGCATCGGTGCATCTT-TATGA
1 -TGCATCGATGCATATTCAAGGA
* * *
39291 TGTATCAATACATATTCAAAGGA
1 TGCATCGATGCATATTC-AAGGA
39314 TGCATCGATGCA
1 TGCATCGATGCA
39326 CTAGATAGTG
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
21 11 0.28
22 3 0.08
23 26 0.65
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATATTCAAGGA
Found at i:41527 original size:20 final size:20
Alignment explanation
Indices: 41502--41539 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41492 TTCCTCTTGA
41502 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
41522 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
41540 TTAACATGTG
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:41635 original size:64 final size:63
Alignment explanation
Indices: 41551--41707 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 63
41541 TAACATGTGT
* * * *
41551 ATCGATGCACTACCCATGCATCGATACACCAATCT-CCTTCGATGTTTTCA-TTTTAAGGGGGTG
1 ATCGATGCACT-CCTATGCATCGATACACCAA-CTGCATTCGATGTGTCCATTTTTAA-GGGGTG
41614 A
63 A
* * * *
41615 ATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATGTGTCCATTTTTAATGGGTGC
1 ATCGATGCACTCC-TATGCATCGATACACCAACTGCATTCGATGTGTCCATTTTTAAGGGGTGA
*
41679 ATCGATGCACTTCCTGTGCATCGATACAC
1 ATCGATGCAC-TCCTATGCATCGATACAC
41708 ACTGAAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 4 0.05
64 66 0.84
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (63 bp):
ATCGATGCACTCCTATGCATCGATACACCAACTGCATTCGATGTGTCCATTTTTAAGGGGTGA
Found at i:48917 original size:6 final size:6
Alignment explanation
Indices: 48877--48916 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
48867 CAAGCGCTCA
* * *
48877 ATGAAG ATGACG ATGAAG ATGAAG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
48917 TCCAAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:50259 original size:24 final size:24
Alignment explanation
Indices: 50232--50283 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
50222 TTTCAAGTTC
50232 ATTTCAAATTT-AATTGGAGTTTGA
1 ATTT-AAATTTCAATTGGAGTTTGA
*
50256 ATTTAAATTTCAATTTGAGTTTGA
1 ATTTAAATTTCAATTGGAGTTTGA
50280 ATTT
1 ATTT
50284 TAATATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (24 bp):
ATTTAAATTTCAATTGGAGTTTGA
Found at i:50294 original size:24 final size:24
Alignment explanation
Indices: 50243--50295 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
50233 TTTCAAATTT
* * *
50243 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
50267 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTAAATATA
50291 AATTT
1 AATTT
50296 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:51737 original size:15 final size:15
Alignment explanation
Indices: 51717--51747 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51707 ATATATCGAC
51717 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
51732 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
51747 A
1 A
51748 AAAAGTGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATAAAGTTTCCAA
Found at i:52424 original size:198 final size:197
Alignment explanation
Indices: 51879--52815 Score: 1177
Period size: 198 Copynumber: 4.7 Consensus size: 197
51869 TTTATTAAAA
* *
51879 GTATCGATCCCTAAAACATCAAAACCGAT-ATTATAATGTAATAGGTAAATTTACAATGTAA-CA
1 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
* *
51942 TGTACAAAATACCGATTTTATGAGAAAAAAGGTATACATAATATATCGACACTTTTAAAATTTGT
66 -GTACAAAATACCG-TTTTATGAGAAAACAGGTATACATAATGTATCGACACTTTTAAAATTTGT
* * * * *
52007 GTCGATACTTTTTGTCCATAATGAATGCCCAAATGAGGTGCACGTAT-AACGTGTCGATATATTT
129 GTCGATACTTTTTGTCCAGAATGAATGCTC-AACGAGGTGCACGCATAAAC-TGTCGATACATTT
**
52071 ATAAAAA
192 A-AAATT
* * * * * * * *
52078 GTATCGATCCCAGAAACAACGAAACCCATAATTATAATGAAATATGTAATTTTTCAATGTAACCG
1 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
* * * * * *
52143 GTATAAATATACCGGTTTAATTAGAAAACAGATCA-ACATAATGTATCGACACTTTTGAAATATG
66 GTACAAA-ATACC-GTTTTATGAGAAAACAGGT-ATACATAATGTATCGACACTTTTAAAATTTG
* *
52207 TGTCAATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAACTGTCGATACAATTA
128 TGTCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAACTGTCGATACATTTA
52272 AAATT
193 AAATT
* * *
52277 GTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTTATAGGTAACTTTACAATGTAACCA
1 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
* * * *
52342 GTACAAAATACCAGTTTTATGAGAAAATAGGTATATATAATGTATCGACACTTTTTACATTTGTG
66 GTACAAAATACC-GTTTTATGAGAAAACAGGTATACATAATGTATCGACACTTTTAAAATTTGTG
* *
52407 TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTTCACGCATAAAGTGTCGATACATTTAAA
130 TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAACTGTCGATACATTTAAA
52472 ATT
195 ATT
* * *
52475 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTGCAATGTAACCG
1 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
* * * * * *
52540 GTA-TAAATACACAGGTTTAATTAGAAAACATGTCA-ACATAATGTATCGACACTTTTGAAATAT
66 GTACAAAATAC-C--GTTTTATGAGAAAACAGGT-ATACATAATGTATCGACACTTTTAAAATTT
* * *
52603 GTGTCGATACGTTTTGTCCAGAATGAATG-ACAACGAGGTGCACGCATAAAGTGTCGATACATTT
127 GTGTCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAACTGTCGATACATTT
*
52667 AAATTT
192 AAAATT
* *
52673 GTATGGATCCCAAAAACATAAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
1 GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
* * * * *
52738 GTAGAAATATATCGATTTTATGAGAGAATAGGTATACATAATGTATTGACACTTTTAAAATTTGT
66 GTACAAA-ATACCG-TTTTATGAGAAAACAGGTATACATAATGTATCGACACTTTTAAAATTTGT
*
52803 GTCGATAATTTTT
129 GTCGATACTTTTT
52816 TTAAATTACG
Statistics
Matches: 637, Mismatches: 87, Indels: 29
0.85 0.12 0.04
Matches are distributed among these distances:
197 9 0.01
198 327 0.51
199 158 0.25
200 64 0.10
201 77 0.12
202 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (197 bp):
GTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCA
GTACAAAATACCGTTTTATGAGAAAACAGGTATACATAATGTATCGACACTTTTAAAATTTGTGT
CGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAACTGTCGATACATTTAAAA
TT
Found at i:52759 original size:397 final size:398
Alignment explanation
Indices: 51872--52815 Score: 1427
Period size: 397 Copynumber: 2.4 Consensus size: 398
51862 TGATACATTT
*
51872 ATTAAAA--GTATCGATCCCTAAAACATCAAAACCGAT-ATTATAATGTAATAGGTAAATTTACA
1 ATTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACA
* *
51934 ATGTAA-CATGTACAAAATACCGATTTTATGAGAAAAAAGGTATACATAATATATCGACACTTTT
66 ATGTAACCA-GTACAAAATA-CGATTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTT
* * * *
51998 AAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCCAAATGAGGTGCACGTATAACGTGTCG
129 AAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCG
* * * *
52063 ATATATTTATAAAAAGTATCGATCCCAGAAACAACGAAACCCATAATTATAATGAAATATGTAAT
194 ATACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGAAATAGGTAAT
* * *
52128 TTTTCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACAGATCAACATAATGTATCGAC
259 TTTGCAATGTAACCGGTATAAATACACAGGTTTAATTAGAAAACAGATCAACATAATGTATCGAC
* *
52193 ACTTTTGAAATATGTGTCAATACTTTTTGTCCAGAATGAATGCTCAACGAGGTGCACGCATAAAC
324 ACTTTTGAAATATGTGTCAATACGTTTTGTCCAGAATGAATGCACAACGAGGTGCACGCATAAAC
52258 TGTCGATACA
389 TGTCGATACA
* *
52268 ATTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTTATAGGTAACTTTACA
1 ATTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACA
* * *
52333 ATGTAACCAGTACAAAATACCAGTTTTATGAGAAAATAGGTATATATAATGTATCGACACTTTTT
66 ATGTAACCAGTACAAAATACGA-TTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTTA
* * *
52398 ACATTTGTGTCGATACTTTTTGTCCAGAATGAATGCTC-AACGAGGTTCACGCATAAAGTGTCGA
130 AAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGA
** * *
52462 TACATTTA-AAATTGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATT
195 TACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGAAATAGGTAATT
52526 TTGCAATGTAACCGGTATAAATACACAGGTTTAATTAGAAAACATG-TCAACATAATGTATCGAC
260 TTGCAATGTAACCGGTATAAATACACAGGTTTAATTAGAAAACA-GATCAACATAATGTATCGAC
* *
52590 ACTTTTGAAATATGTGTCGATACGTTTTGTCCAGAATGAATG-ACAACGAGGTGCACGCATAAAG
324 ACTTTTGAAATATGTGTCAATACGTTTTGTCCAGAATGAATGCACAACGAGGTGCACGCATAAAC
52654 TGTCGATACA
389 TGTCGATACA
* * * * *
52664 TTTAAATTTGTATGGATCCCAAAAACATAAAAACCCATAATTATAATGTAATAGGTAAATTTACA
1 ATTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACA
* * *
52729 ATGTAACCAGTAGAAATATATCGATTTTATGAGAGAATAGGTATACATAATGTATTGACACTTTT
66 ATGTAACCAGTACAAA-ATA-CGATTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTT
*
52794 AAAATTTGTGTCGATAATTTTT
129 AAAATTTGTGTCGATACTTTTT
52816 TTAAATTACG
Statistics
Matches: 495, Mismatches: 45, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
396 110 0.22
397 208 0.42
398 62 0.13
399 113 0.23
400 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (398 bp):
ATTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACA
ATGTAACCAGTACAAAATACGATTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTTAA
AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGAT
ACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGAAATAGGTAATTT
TGCAATGTAACCGGTATAAATACACAGGTTTAATTAGAAAACAGATCAACATAATGTATCGACAC
TTTTGAAATATGTGTCAATACGTTTTGTCCAGAATGAATGCACAACGAGGTGCACGCATAAACTG
TCGATACA
Found at i:57293 original size:148 final size:149
Alignment explanation
Indices: 57024--57310 Score: 490
Period size: 148 Copynumber: 1.9 Consensus size: 149
57014 ACACTTGTGG
*
57024 AATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCAAT
1 AATTTGTGTCAATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCAAT
*
57089 ACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATT
66 ACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATT
57154 TACAATGTAACCGGTATAA
131 TACAATGTAACCGGTATAA
* *
57173 AATTTGTGTCAATA-TATTTTGTCCAGAATGAATG-CCAAACG-GGATGCACGCATAAAGTGTCG
1 AATTTGTGTCAATACT-TATTGTCCAGAATGAATGCCCAAACGAGG-TGCACGCATAAAGTGTCA
*
57235 ATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTACAATGTAATAGGTAAA
64 ATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAA
57300 TTTACAATGTA
129 TTTACAATGTA
57311 CCAGATAGAA
Statistics
Matches: 131, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
147 2 0.02
148 99 0.76
149 30 0.23
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (149 bp):
AATTTGTGTCAATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCAAT
ACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATT
TACAATGTAACCGGTATAA
Found at i:57644 original size:87 final size:87
Alignment explanation
Indices: 57548--57710 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
57538 AAATAGGCCA
*
57548 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
57613 CAAGTTAAATGCCTATTTTATT
66 CAAGTTAAATGCCTATTTTATT
* *
57635 ATATAAGCGCTACCTATTACGTTATATAAGCGGTACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
**
57700 CCGGTTAAATG
66 CAAGTTAAATG
57711 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
CAAGTTAAATGCCTATTTTATT
Found at i:57650 original size:23 final size:23
Alignment explanation
Indices: 57624--57682 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
57614 AAGTTAAATG
*
57624 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
** *
57647 CCTATTACGTTATATAAGCGGTA
1 CCTATTATATTATATAAGCGCTA
*
57670 CCTAATATATTAT
1 CCTATTATATTAT
57683 TGTACTTGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:59262 original size:4 final size:4
Alignment explanation
Indices: 59255--59521 Score: 86
Period size: 4 Copynumber: 66.5 Consensus size: 4
59245 CGCACATACA
* * * * * * *
59255 TGTG TGTG TGCG TGTG TGTG TGTG TGCG CGTG TGTG CGCG TGTG CGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * * * * *
59303 TGTG CGCG TGTG CGCG TGTG CGCG TGTG TGCG TGTG TGCG TGTG TCTG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * * * * *
59351 CGTG TGTG TGTG TGTG CGTG CGTG CGTG CGTG CGTG CGCG CTCT- TAGTG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG -TGTG T-GTG
* * * * * * * *
59400 TGTG TGTG TGTT TGTG TGTG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * * * * * * * * * * *
59448 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* *
59496 TGCG TGTG TGTG CGTG TGTG TGTG TG
1 TGTG TGTG TGTG TGTG TGTG TGTG TG
59522 CGCGCGTGCG
Statistics
Matches: 214, Mismatches: 46, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
3 1 0.00
4 212 0.99
5 1 0.00
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.34
Consensus pattern (4 bp):
TGTG
Found at i:59271 original size:8 final size:8
Alignment explanation
Indices: 59258--59533 Score: 204
Period size: 8 Copynumber: 34.4 Consensus size: 8
59248 ACATACATGT
59258 GTGTGTGC
1 GTGTGTGC
*
59266 GTGTGTGT
1 GTGTGTGC
59274 GTGTGTGCGC
1 GTGTGT--GC
59284 GTGTGTGCGC
1 GTGTGT--GC
*
59294 GTGTGCGC
1 GTGTGTGC
*
59302 GTGTGCGC
1 GTGTGTGC
*
59310 GTGTGCGC
1 GTGTGTGC
*
59318 GTGTGCGC
1 GTGTGTGC
59326 GTGTGTGC
1 GTGTGTGC
59334 GTGTGTGC
1 GTGTGTGC
59342 GTGTGTCTGC
1 GTGTG--TGC
*
59352 GTGTGTGT
1 GTGTGTGC
59360 GTGTGTGC
1 GTGTGTGC
*
59368 GTGCGTGC
1 GTGTGTGC
*
59376 GTGCGTGC
1 GTGTGTGC
* *
59384 GTGCGCGC
1 GTGTGTGC
* *
59392 -TCT-TAGT
1 GTGTGT-GC
*
59399 GTGTGTGT
1 GTGTGTGC
* *
59407 GTGTTTGT
1 GTGTGTGC
59415 GTGTGTGC
1 GTGTGTGC
*
59423 GTGCGTGC
1 GTGTGTGC
*
59431 GTGCGTGC
1 GTGTGTGC
*
59439 GTGCGTGC
1 GTGTGTGC
*
59447 GTGCGTGC
1 GTGTGTGC
*
59455 GTGCGTGC
1 GTGTGTGC
*
59463 GTGCGTGC
1 GTGTGTGC
*
59471 GTGCGTGC
1 GTGTGTGC
*
59479 GTGCGTGC
1 GTGTGTGC
*
59487 GTGCGTGC
1 GTGTGTGC
*
59495 GTGCGT--
1 GTGTGTGC
59501 GTGTGTGC
1 GTGTGTGC
59509 GTGTGT--
1 GTGTGTGC
59515 GTGTGTGC
1 GTGTGTGC
* *
59523 GCGCGTGC
1 GTGTGTGC
59531 GTG
1 GTG
59534 CCTGCGTGCC
Statistics
Matches: 236, Mismatches: 21, Indels: 22
0.85 0.08 0.08
Matches are distributed among these distances:
6 11 0.05
7 2 0.01
8 198 0.84
9 1 0.00
10 24 0.10
ACGTcount: A:0.00, C:0.18, G:0.49, T:0.33
Consensus pattern (8 bp):
GTGTGTGC
Found at i:59534 original size:12 final size:13
Alignment explanation
Indices: 59419--59547 Score: 127
Period size: 12 Copynumber: 10.7 Consensus size: 13
59409 GTTTGTGTGT
59419 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59431 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59443 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59455 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59467 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59479 GTGCGTGCG-TGC
1 GTGCGTGCGCTGC
59491 GTGCGTGCG-T--
1 GTGCGTGCGCTGC
* * *
59501 GTGTGTGCGTGTGT
1 GTGCGTGCG-CTGC
*
59515 GTGTGTGCGC-GC
1 GTGCGTGCGCTGC
59527 GTGCGTGC-CTGC
1 GTGCGTGCGCTGC
*
59539 GTGCCTGCG
1 GTGCGTGCG
59548 TGCTCTTAGT
Statistics
Matches: 106, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
10 8 0.08
11 1 0.01
12 88 0.83
14 9 0.08
ACGTcount: A:0.00, C:0.24, G:0.49, T:0.27
Consensus pattern (13 bp):
GTGCGTGCGCTGC
Found at i:61055 original size:14 final size:15
Alignment explanation
Indices: 61030--61060 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
61020 AACTTTGACC
61030 AAATATTATTTTAAA
1 AAATATTATTTTAAA
61045 AAATA-TATTTTAAA
1 AAATATTATTTTAAA
61059 AA
1 AA
61061 CTTTTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTATTTTAAA
Found at i:62894 original size:21 final size:22
Alignment explanation
Indices: 62864--62910 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
62854 TTTAGTATTA
62864 ATTTTCTATTATTCTTCTCTTT
1 ATTTTCTATTATTCTTCTCTTT
* *
62886 ATTTT-TATTTTTCTTTTCTTT
1 ATTTTCTATTATTCTTCTCTTT
62907 -TTTT
1 ATTTT
62911 GCTTGTACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (22 bp):
ATTTTCTATTATTCTTCTCTTT
Found at i:63046 original size:19 final size:21
Alignment explanation
Indices: 63005--63047 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62995 TTAAAGGGAT
*
63005 GAACTAAAATTCTAATTGGGC
1 GAACTAAAATTCTAATGGGGC
63026 GAACTAAAATTCT-A-GGGGC
1 GAACTAAAATTCTAATGGGGC
63045 GAA
1 GAA
63048 ACAGATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 1 0.05
21 13 0.62
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
GAACTAAAATTCTAATGGGGC
Found at i:67246 original size:2 final size:2
Alignment explanation
Indices: 67234--67277 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
67224 ACCTCTGATC
67234 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67275 AT A
1 AT A
67278 ATTTAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68781 original size:26 final size:27
Alignment explanation
Indices: 68752--68806 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
68742 AGCTTGATAT
68752 TCGGG-TCGGGGTT-TTTTTTTTAAAAA
1 TCGGGATC-GGGTTGTTTTTTTTAAAAA
68778 TCGGGATCGGGTTGGATTTTTTTTAAAAA
1 TCGGGATCGGGTT-G-TTTTTTTTAAAAA
68807 AAATTGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 10 0.40
27 2 0.08
29 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (27 bp):
TCGGGATCGGGTTGTTTTTTTTAAAAA
Found at i:68856 original size:28 final size:28
Alignment explanation
Indices: 68824--68882 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
68814 GTTTGGGTCT
* *
68824 GGTCGGGTTTTTTTAAGTTTGATATTCG
1 GGTCGGATTTTTTTAAGTGTGATATTCG
68852 GGTCGGATTTTTTTAAGTGTGATATTCG
1 GGTCGGATTTTTTTAAGTGTGATATTCG
68880 GGT
1 GGT
68883 TGAGTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.15, C:0.07, G:0.31, T:0.47
Consensus pattern (28 bp):
GGTCGGATTTTTTTAAGTGTGATATTCG
Found at i:77455 original size:17 final size:17
Alignment explanation
Indices: 77433--77472 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
77423 ATGTTTCTCC
77433 GATGAAGTATTCATTCA
1 GATGAAGTATTCATTCA
77450 GATGAAGTATTCATTCA
1 GATGAAGTATTCATTCA
77467 GATGAA
1 GATGAA
77473 ATATCCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (17 bp):
GATGAAGTATTCATTCA
Found at i:82616 original size:22 final size:23
Alignment explanation
Indices: 82568--82616 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
82558 AACAATAATG
**
82568 TATTTTTATTTTTTAGCAGTTTA
1 TATTTTTATTTTTTAAAAGTTTA
*
82591 -ATTTTTA-TTTTTAAAATTTTA
1 TATTTTTATTTTTTAAAAGTTTA
82612 TATTT
1 TATTT
82617 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TATTTTTATTTTTTAAAAGTTTA
Found at i:82722 original size:21 final size:21
Alignment explanation
Indices: 82698--82743 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
82688 ATCAGCCACC
**
82698 ATAAAATATCATGTCAACACA
1 ATAAAATATCACATCAACACA
* *
82719 ATAAAATGTCACATCAACACG
1 ATAAAATATCACATCAACACA
82740 ATAA
1 ATAA
82744 TATTCAACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.22
Consensus pattern (21 bp):
ATAAAATATCACATCAACACA
Found at i:84685 original size:39 final size:37
Alignment explanation
Indices: 84642--84795 Score: 133
Period size: 36 Copynumber: 4.2 Consensus size: 37
84632 TTGTTTTAAC
* *
84642 AAATATATCAATTTAATTATATATAAATTTAAAATATA-A
1 AAATATATCAATTTAA-GA-A-ATAAATATAAAATATATA
*
84681 AAATATATCAA-TTAAGAAATATATATAAAATATATA
1 AAATATATCAATTTAAGAAATAAATATAAAATATATA
* *
84717 AAATATATCAATTT-A-AACTGAAACA-AAAATATATAA
1 AAATATATCAATTTAAGAAAT-AAATATAAAATATAT-A
* * * *
84753 AAATATATCAATTTAA-ACATTAATA-AAAATACAAA
1 AAATATATCAATTTAAGAAATAAATATAAAATATATA
84788 AAATATAT
1 AAATATAT
84796 TTTATAATAT
Statistics
Matches: 98, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
35 35 0.36
36 42 0.43
37 6 0.06
38 4 0.04
39 11 0.11
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (37 bp):
AAATATATCAATTTAAGAAATAAATATAAAATATATA
Found at i:84715 original size:9 final size:9
Alignment explanation
Indices: 84659--84724 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
84649 TCAATTTAAT
84659 TATATATAAA
1 TATATA-AAA
84669 T-T-TAAAA
1 TATATAAAA
84676 TATA-AAAA
1 TATATAAAA
* *
84684 TATATCAAT
1 TATATAAAA
*
84693 TA-AGAAATA
1 TATATAAA-A
84702 TATATAAAA
1 TATATAAAA
84711 TATATAAAA
1 TATATAAAA
84720 TATAT
1 TATAT
84725 CAATTTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
7 4 0.09
8 14 0.31
9 22 0.49
10 5 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
TATATAAAA
Found at i:84766 original size:36 final size:35
Alignment explanation
Indices: 84675--84795 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 35
84665 TAAATTTAAA
* * *
84675 ATATAAAAATATATCAATTAAGAAATATATATAAAAT
1 ATATAAAAATATATCAATTTA-AACTAAATA-AAAAT
*
84712 ATAT-AAAATATATCAATTTAAACTGAAACAAAAAT
1 ATATAAAAATATATCAATTTAAACT-AAATAAAAAT
*
84747 ATATAAAAATATATCAATTTAAACATTAATAAAAAT
1 ATATAAAAATATATCAATTTAAAC-TAAATAAAAAT
*
84783 ACA-AAAAATATAT
1 ATATAAAAATATAT
84796 TTTATAATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
35 22 0.30
36 47 0.64
37 5 0.07
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (35 bp):
ATATAAAAATATATCAATTTAAACTAAATAAAAAT
Found at i:89396 original size:18 final size:16
Alignment explanation
Indices: 89375--89412 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
89365 CAAAGATTAC
89375 AAAAAAAACACAGAGAG
1 AAAAAAAAC-CAGAGAG
*
89392 TAAAAAAACCAGAGAG
1 AAAAAAAACCAGAGAG
89408 AAAAA
1 AAAAA
89413 TAGAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAACCAGAGAG
Found at i:89398 original size:16 final size:15
Alignment explanation
Indices: 89376--89412 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
89366 AAAGATTACA
89376 AAAAAAACACAGAGAG
1 AAAAAAAC-CAGAGAG
89392 TAAAAAAACCAGAGAG
1 -AAAAAAACCAGAGAG
89408 AAAAA
1 AAAAA
89413 TAGAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.70, C:0.11, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAAAAACCAGAGAG
Found at i:90706 original size:14 final size:14
Alignment explanation
Indices: 90687--90731 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
90677 TCATTATACT
90687 TTTATTTTATTTTA
1 TTTATTTTATTTTA
*
90701 TTTATTTTA-TTTC
1 TTTATTTTATTTTA
*
90714 TTTATTATTATTCTA
1 TTTATT-TTATTTTA
90729 TTT
1 TTT
90732 TTACGATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:91322 original size:18 final size:20
Alignment explanation
Indices: 91279--91322 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
91269 AATTTTCAAA
91279 TAAAAATCATAATTGTTTTT
1 TAAAAATCATAATTGTTTTT
* *
91299 TTAAAATTA-AATTG-TTTT
1 TAAAAATCATAATTGTTTTT
91317 TAAAAA
1 TAAAAA
91323 AAAGATGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TAAAAATCATAATTGTTTTT
Found at i:94553 original size:240 final size:240
Alignment explanation
Indices: 94118--94603 Score: 823
Period size: 240 Copynumber: 2.0 Consensus size: 240
94108 TTGCATTTCT
* * **
94118 ATATGCCGCCAGGGCCAAATTCATGCTGCTTGCCGCTTGGGAGAACTGCAGACCGCACGTTGCTT
1 ATATGCTGCCAGGGCCAAATTCATGCCGCTTGCCGCTTGGGAGAACCACAGACCGCACGTTGCTT
* *
94183 TGCTCCTCTCATCCTCCGTTGAGTACGAGCAACATTCCATCTGCAATTACTTGAAATCATATGCA
66 TGCTCCTCTCATCCTCCATCGAGTACGAGCAACATTCCATCTGCAATTACTTGAAATCATATGCA
* ** *
94248 GGTTCAATCTTGGACAGTTTTCTTTTGCGTCAAGTACTTGTCAACATGTTCTGTAACTCGAGACA
131 GGTTCAATCTTGGACAGTTTTCTTTTGCCTCAAGTACTTGTCAACATGTTCTCCAACTAGAGACA
94313 GAAGGCTCTCAGCTGCTCGTTCTTTATCGGGATCACTTTCGTTCG
196 GAAGGCTCTCAGCTGCTCGTTCTTTATCGGGATCACTTTCGTTCG
94358 ATATGCTGCCAGGGCCAAATTCATGCCGCTTGCCGCTTGGGAGAACCACAGACCGCACGTTGCCT
1 ATATGCTGCCAGGGCCAAATTCATGCCGCTTGCCGCTTGGGAGAACCACAGACCGCACGTTG-CT
* * *
94423 TT-CTCCTCTCATCGTCCATCGAGTACGGGCAACATTCCATTTGCAATTACTTGAAATCATATGC
65 TTGCTCCTCTCATCCTCCATCGAGTACGAGCAACATTCCATCTGCAATTACTTGAAATCATATGC
*
94487 AGGTTCAATCTTTGACAGTTTTCTTTTGCCTCAAGTACTTGTCAACATGTTCTCCAACTAGAGAC
130 AGGTTCAATCTTGGACAGTTTTCTTTTGCCTCAAGTACTTGTCAACATGTTCTCCAACTAGAGAC
94552 AGAAGGCTCTCAGCTGCTCGTTCTTTATCGGGATCACTTTCGTTCG
195 AGAAGGCTCTCAGCTGCTCGTTCTTTATCGGGATCACTTTCGTTCG
94598 AT-TGCT
1 ATATGCT
94604 TCCAAATGCA
Statistics
Matches: 231, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
239 4 0.02
240 223 0.97
241 4 0.02
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (240 bp):
ATATGCTGCCAGGGCCAAATTCATGCCGCTTGCCGCTTGGGAGAACCACAGACCGCACGTTGCTT
TGCTCCTCTCATCCTCCATCGAGTACGAGCAACATTCCATCTGCAATTACTTGAAATCATATGCA
GGTTCAATCTTGGACAGTTTTCTTTTGCCTCAAGTACTTGTCAACATGTTCTCCAACTAGAGACA
GAAGGCTCTCAGCTGCTCGTTCTTTATCGGGATCACTTTCGTTCG
Found at i:96266 original size:26 final size:27
Alignment explanation
Indices: 96201--96267 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
96191 AATGGATTTA
96201 TAAAATTTTAAAA-AGATAAAAATAAAT
1 TAAAA-TTTAAAATAGATAAAAATAAAT
* * * *
96228 TAATCATTAAAAATATATAAAAA-AATT
1 TAA-AATTTAAAATAGATAAAAATAAAT
96255 TAAAATTTAAAAT
1 TAAAATTTAAAAT
96268 TTTTAAAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 8 0.25
27 15 0.47
28 9 0.28
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (27 bp):
TAAAATTTAAAATAGATAAAAATAAAT
Found at i:96999 original size:14 final size:12
Alignment explanation
Indices: 96959--96999 Score: 57
Period size: 11 Copynumber: 3.3 Consensus size: 12
96949 GTTTTTTAAA
96959 AAATATTTTTTT
1 AAATATTTTTTT
96971 AAAT-TTTTTTT
1 AAATATTTTTTT
96982 AAATAGATTTTTTT
1 AAAT--ATTTTTTT
96996 AAAT
1 AAAT
97000 TTACCAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.42
12 4 0.15
14 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:100957 original size:470 final size:470
Alignment explanation
Indices: 100077--100980 Score: 1808
Period size: 470 Copynumber: 1.9 Consensus size: 470
100067 TTATTTTTAC
100077 ACTTCTTTCAATGCCAAGATTAAGAAAGATGAGTTATACGATTTGATTTCAATGGAGCTTAAAAA
1 ACTTCTTTCAATGCCAAGATTAAGAAAGATGAGTTATACGATTTGATTTCAATGGAGCTTAAAAA
100142 TCTACAACATGACAATTGTCTTCGTTGCAAGCTAAAGCATATTTCATGTCGACCTTATCAAATGC
66 TCTACAACATGACAATTGTCTTCGTTGCAAGCTAAAGCATATTTCATGTCGACCTTATCAAATGC
100207 AAGCGACCTTCGAAAGATGTTTAAGGCTTACACACGTGTTGGTGGTATGAACATCGAGTTGAATG
131 AAGCGACCTTCGAAAGATGTTTAAGGCTTACACACGTGTTGGTGGTATGAACATCGAGTTGAATG
100272 TAACATTTGAGGAAGAATCACATTCACCAAGTAATACAGTAGTAACTCAGTTATCAAAAGACCAT
196 TAACATTTGAGGAAGAATCACATTCACCAAGTAATACAGTAGTAACTCAGTTATCAAAAGACCAT
100337 GAGGACGAAGAGGCGGTTCTGCTACATTATGCCTGTGAACATTGGGAGAAAGAACTTTAAACAAC
261 GAGGACGAAGAGGCGGTTCTGCTACATTATGCCTGTGAACATTGGGAGAAAGAACTTTAAACAAC
100402 CCGTGTAGTTCATTTTTTATTATGTTTTAAATAAGTATTAAAATCCCTTACCCCATTGCATATGG
326 CCGTGTAGTTCATTTTTTATTATGTTTTAAATAAGTATTAAAATCCCTTACCCCATTGCATATGG
100467 AAATAGGGTTTTGTTGTTGTTGTTGTTTAAATAAGTATTAAAATCTACAACATTAAGAAAGATTA
391 AAATAGGGTTTTGTTGTTGTTGTTGTTTAAATAAGTATTAAAATCTACAACATTAAGAAAGATTA
100532 AGAAAGATGAGTTAT
456 AGAAAGATGAGTTAT
100547 ACTTCTTTCAATGCCAAGATTAAGAAAGATGAGTTATACGATTTGATTTCAATGGAGCTTAAAAA
1 ACTTCTTTCAATGCCAAGATTAAGAAAGATGAGTTATACGATTTGATTTCAATGGAGCTTAAAAA
100612 TCTACAACATGACAATTGTCTTCGTTGCAAGCTAAAGCATATTTCATGTCGACCTTATCAAATGC
66 TCTACAACATGACAATTGTCTTCGTTGCAAGCTAAAGCATATTTCATGTCGACCTTATCAAATGC
100677 AAGCGACCTTCGAAAGATGTTTAAGGCTTACACACGTGTTGGTGGTATGAACATCGAGTTGAATG
131 AAGCGACCTTCGAAAGATGTTTAAGGCTTACACACGTGTTGGTGGTATGAACATCGAGTTGAATG
100742 TAACATTTGAGGAAGAATCACATTCACCAAGTAATACAGTAGTAACTCAGTTATCAAAAGACCAT
196 TAACATTTGAGGAAGAATCACATTCACCAAGTAATACAGTAGTAACTCAGTTATCAAAAGACCAT
100807 GAGGACGAAGAGGCGGTTCTGCTACATTATGCCTGTGAACATTGGGAGAAAGAACTTTAAACAAC
261 GAGGACGAAGAGGCGGTTCTGCTACATTATGCCTGTGAACATTGGGAGAAAGAACTTTAAACAAC
100872 CCGTGTAGTTCATTTTTTATTATGTTTTAAATAAGTATTAAAATCCCTTACCCCATTGCATATGG
326 CCGTGTAGTTCATTTTTTATTATGTTTTAAATAAGTATTAAAATCCCTTACCCCATTGCATATGG
100937 AAATAGGGTTTTGTTGTTGTTGTTGTTTAAATAAGTATTAAAAT
391 AAATAGGGTTTTGTTGTTGTTGTTGTTTAAATAAGTATTAAAAT
100981 AAATTTTAAT
Statistics
Matches: 434, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
470 434 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (470 bp):
ACTTCTTTCAATGCCAAGATTAAGAAAGATGAGTTATACGATTTGATTTCAATGGAGCTTAAAAA
TCTACAACATGACAATTGTCTTCGTTGCAAGCTAAAGCATATTTCATGTCGACCTTATCAAATGC
AAGCGACCTTCGAAAGATGTTTAAGGCTTACACACGTGTTGGTGGTATGAACATCGAGTTGAATG
TAACATTTGAGGAAGAATCACATTCACCAAGTAATACAGTAGTAACTCAGTTATCAAAAGACCAT
GAGGACGAAGAGGCGGTTCTGCTACATTATGCCTGTGAACATTGGGAGAAAGAACTTTAAACAAC
CCGTGTAGTTCATTTTTTATTATGTTTTAAATAAGTATTAAAATCCCTTACCCCATTGCATATGG
AAATAGGGTTTTGTTGTTGTTGTTGTTTAAATAAGTATTAAAATCTACAACATTAAGAAAGATTA
AGAAAGATGAGTTAT
Found at i:105907 original size:17 final size:17
Alignment explanation
Indices: 105871--105914 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
105861 GTGTGTGTTA
* * *
105871 CTCGAACGAGAGTTTTT
1 CTCGAAAGAGAATTTCT
105888 CTCGAAAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
105905 CTC-AAAGAGA
1 CTCGAAAGAGA
105915 GAGAAGGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (17 bp):
CTCGAAAGAGAATTTCT
Found at i:113591 original size:54 final size:54
Alignment explanation
Indices: 113516--113896 Score: 520
Period size: 54 Copynumber: 7.1 Consensus size: 54
113506 ATGCACACAT
* * *
113516 TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGCTGCACACTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
*
113570 TGCCTATACAGTCGTTCATAAACACATTATGAATTT-GTGGGTTGCACACTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
* * * * ** *
113623 TTCCTATATGGTCATTCATAAATACATTATGAATCCCGTGGGTTGCACACTTAT
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
* * *
113677 TGCCTACATGGTCGTTCATAAACACATTATGAATTT-GTGGGTAGCACACTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
* * * *
113730 TGCCTGTACGATCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
* * *
113784 TGCCTTTACGGTCGTTCATAAACACATTATGAATTTCGTGGGTT-TACAGTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
* *
113837 TGCCTATACGGTTGTT--TAAACACATTATGAATTCCGTGGGTTGCACACTTAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
113889 TGCCTATA
1 TGCCTATA
113897 GTACACATAG
Statistics
Matches: 287, Mismatches: 37, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
51 25 0.09
52 15 0.05
53 112 0.39
54 135 0.47
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
TGCCTATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAG
Found at i:113681 original size:107 final size:107
Alignment explanation
Indices: 113516--113896 Score: 543
Period size: 107 Copynumber: 3.6 Consensus size: 107
113506 ATGCACACAT
* * * * *
113516 TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGCTGCACACTTAGTGCCTATACAG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
113581 TCGTTCATAAACACATTATGAATTTGTGGGTTGCACACTTAG
66 TCGTTCATAAACACATTATGAATTTGTGGGTTGCACACTTAG
* * * * * * * *
113623 TTCCTATATGGTCATTCATAAATACATTATGAATCCCGTGGGTTGCACACTTATTGCCTACATGG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
*
113688 TCGTTCATAAACACATTATGAATTTGTGGGTAGCACACTTAG
66 TCGTTCATAAACACATTATGAATTTGTGGGTTGCACACTTAG
* * * *
113730 TGCCTGTACGATCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAGTGCCTTTACGG
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
* *
113795 TCGTTCATAAACACATTATGAATTTCGTGGGTT-TACAGTTAG
66 TCGTTCATAAACACATTATGAATTT-GTGGGTTGCACACTTAG
*
113837 TGCCTATACGGTTGTT--TAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATA
1 TGCCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATA
113897 GTACACATAG
Statistics
Matches: 239, Mismatches: 34, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
105 42 0.18
107 191 0.80
108 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (107 bp):
TGCCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
TCGTTCATAAACACATTATGAATTTGTGGGTTGCACACTTAG
Found at i:120204 original size:52 final size:54
Alignment explanation
Indices: 120143--120409 Score: 323
Period size: 53 Copynumber: 5.1 Consensus size: 54
120133 CATAATACCG
*
120143 ATACAGTC-TTCATAAACATATTATGAATT-CGTGGGTTGCACACTTAGTGCCT
1 ATACAGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * ** **
120195 ATACGGTCTTTCATAAA-ACAATATGAATTATATGGACTGCACACTTAGTGCCT
1 ATACAGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * *
120248 ATATAGTCCTTCATAAACATATTATGAATTGCGTGGGTTGCACACTTAGTGCCT
1 ATACAGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * *
120302 ATA-TGTCGTTCATAAACACATTATGAATTATGTGGGTT-CACACTTAGTGCCT
1 ATACAGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* *
120354 ATACGGTCATTCAT-AACACATTATGAATT-CTGTGAGTTGCACACTTAGTGCCT
1 ATACAGTCATTCATAAACACATTATGAATTAC-GTGGGTTGCACACTTAGTGCCT
120407 ATA
1 ATA
120410 GTACACATAG
Statistics
Matches: 183, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
52 55 0.30
53 96 0.52
54 32 0.17
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (54 bp):
ATACAGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
Found at i:120345 original size:106 final size:106
Alignment explanation
Indices: 120143--120409 Score: 380
Period size: 106 Copynumber: 2.5 Consensus size: 106
120133 CATAATACCG
*
120143 ATACAGT-CTTCATAAACATATTATGAATTCGTGGGTTGCACACTTAGTGCCTATACGGTCTTTC
1 ATACAGTCCTTCATAAACATATTATGAATTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTC
120207 ATAAAACAATATGAATTATATGGACTGCACACTTAGTGCCT
66 ATAAAACAATATGAATTATATGGACTGCACACTTAGTGCCT
* *
120248 ATATAGTCCTTCATAAACATATTATGAATTGCGTGGGTTGCACACTTAGTGCCTATA-TGTCGTT
1 ATACAGTCCTTCATAAACATATTATGAATT-CGTGGGTTGCACACTTAGTGCCTATACGGTCGTT
* * * *
120312 CATAAACACATTATGAATTATGTGG-GTTCACACTTAGTGCCT
65 CATAAA-ACAATATGAATTATATGGACTGCACACTTAGTGCCT
* * * *
120354 ATACGGTCATTCAT-AACACATTATGAATTCTGTGAGTTGCACACTTAGTGCCTATA
1 ATACAGTCCTTCATAAACATATTATGAATTC-GTGGGTTGCACACTTAGTGCCTATA
120410 GTACACATAG
Statistics
Matches: 146, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
104 1 0.01
105 44 0.30
106 59 0.40
107 42 0.29
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (106 bp):
ATACAGTCCTTCATAAACATATTATGAATTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTC
ATAAAACAATATGAATTATATGGACTGCACACTTAGTGCCT
Found at i:120943 original size:20 final size:20
Alignment explanation
Indices: 120918--120968 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
120908 TTTAAACCTA
120918 TAGTGTCGATATTATTCTTT
1 TAGTGTCGATATTATTCTTT
120938 TAGTGTCGATATTATTCTTT
1 TAGTGTCGATATTATTCTTT
*
120958 TAGTATCGATA
1 TAGTGTCGATA
120969 CCCTTACCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.51
Consensus pattern (20 bp):
TAGTGTCGATATTATTCTTT
Found at i:124121 original size:19 final size:19
Alignment explanation
Indices: 124099--124135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
124089 ATATTAAATT
*
124099 AAAAATAAAAAAAAACAAG
1 AAAAACAAAAAAAAACAAG
*
124118 AAAAACAAAGAAAAACAA
1 AAAAACAAAAAAAAACAA
124136 ACAAACAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAACAAAAAAAAACAAG
Done.