Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006674.1 Hibiscus syriacus cultivar Beakdansim tig00016543_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: 97791
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2389 original size:73 final size:75
Alignment explanation
Indices: 2312--2507 Score: 263
Period size: 73 Copynumber: 2.6 Consensus size: 75
2302 CCGTTGTACA
* * *
2312 AGGGGGGAATCGGTACCCCCT-TGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA-A
1 AGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGA
* ** *
2375 TAAACTGTTT
66 CAAACCATTC
* *
2385 A-GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGA
2449 CAAACCATTC
66 CAAACCATTC
*
2459 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCA
2508 ATCTCGAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 17 0.16
73 40 0.37
74 7 0.06
75 21 0.19
77 23 0.21
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGA
CAAACCATTC
Found at i:3636 original size:18 final size:18
Alignment explanation
Indices: 3612--3655 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3602 CTGAGTCAAC
*
3612 TCGTTGACCTTTGATCAGG
1 TCGTTGACCGTTGATC-GG
3631 -CGTTGACCGTTGATCGG
1 TCGTTGACCGTTGATCGG
3648 TCGTTGAC
1 TCGTTGAC
3656 TTTTTTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (18 bp):
TCGTTGACCGTTGATCGG
Found at i:5420 original size:31 final size:31
Alignment explanation
Indices: 5384--5508 Score: 110
Period size: 31 Copynumber: 3.9 Consensus size: 31
5374 AAGACTCTGG
5384 TAGGTTCAGTCCCTACTGGTAATTCCTTGTA
1 TAGGTTCAGTCCCTACTGGTAATTCCTTGTA
* * * * *
5415 TAGGTTCA-ACACTGACTGATAATTCCTATCTT
1 TAGGTTCAGTCCCT-ACTGGTAATTCCT-TGTA
* *
5447 TGGCAGGTTCAGTCGCTGCTGGTAATTCCTTGTA
1 T---AGGTTCAGTCCCTACTGGTAATTCCTTGTA
*
5481 TAGGTTCAG-CACCGACTGGTAATTCCTT
1 TAGGTTCAGTC-CCTACTGGTAATTCCTT
5509 ATGAACCTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
30 4 0.05
31 42 0.58
32 3 0.04
34 3 0.04
35 18 0.25
36 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (31 bp):
TAGGTTCAGTCCCTACTGGTAATTCCTTGTA
Found at i:6864 original size:32 final size:32
Alignment explanation
Indices: 6802--6869 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
6792 CCTTACAAAC
* * * *
6802 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGCTTTTACGGACTAAACTAAAACCTT
*
6834 TCCCTAGCTTTTACGGACTAAGCTAAAACCTT
1 TCCCTAGCTTTTACGGACTAAACTAAAACCTT
6866 TCCC
1 TCCC
6870 CTTTACAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.34
Consensus pattern (32 bp):
TCCCTAGCTTTTACGGACTAAACTAAAACCTT
Found at i:7241 original size:21 final size:21
Alignment explanation
Indices: 7215--7297 Score: 114
Period size: 21 Copynumber: 4.0 Consensus size: 21
7205 ACCGTTAGAC
* *
7215 AGGGGGAACCGGTACCCCCTT
1 AGGGGGAATCGGTACCCCCTG
7236 AGGGGGAATCGGTACCCCCTG
1 AGGGGGAATCGGTACCCCCTG
*
7257 GGGGGGAATCGGTACCCCCTG
1 AGGGGGAATCGGTACCCCCTG
* *
7278 -GAGGGAATCTGTACCCCCTG
1 AGGGGGAATCGGTACCCCCTG
7298 GACAATATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 18 0.32
21 39 0.68
ACGTcount: A:0.18, C:0.30, G:0.36, T:0.16
Consensus pattern (21 bp):
AGGGGGAATCGGTACCCCCTG
Found at i:7284 original size:41 final size:42
Alignment explanation
Indices: 7216--7298 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
7206 CCGTTAGACA
7216 GGGGGAACCGGTACCCCCTTAGGGGGAATCGGTACCCCCTGG
1 GGGGGAACCGGTACCCCCTTAGGGGGAATCGGTACCCCCTGG
* *
7258 GGGGGAATCGGTACCCCC-T-GGAGGGAATCTGTACCCCCTGG
1 GGGGGAACCGGTACCCCCTTAGG-GGGAATCGGTACCCCCTGG
7299 ACAATATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 2 0.05
41 19 0.50
42 17 0.45
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.16
Consensus pattern (42 bp):
GGGGGAACCGGTACCCCCTTAGGGGGAATCGGTACCCCCTGG
Found at i:9648 original size:34 final size:32
Alignment explanation
Indices: 9595--9664 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
9585 CCTTACAAAC
*
9595 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACATT
* * *
9627 TCCCTAGCTTTTATACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACATT
9661 TCCC
1 TCCC
9665 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACATT
Found at i:10047 original size:19 final size:19
Alignment explanation
Indices: 10011--10068 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
10001 TTAGACAGGG
*
10011 GGGAATCGGTACCCCCTGGA
1 GGGAATCTGTA-CCCCTGGA
10031 GGGAATCTGTACCCCTGTG-
1 GGGAATCTGTACCCCTG-GA
*
10050 GGGAATATGTACCCCTGGA
1 GGGAATCTGTACCCCTGGA
10069 CAATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 22 0.65
20 11 0.32
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (19 bp):
GGGAATCTGTACCCCTGGA
Found at i:13050 original size:974 final size:950
Alignment explanation
Indices: 11136--13622 Score: 3043
Period size: 974 Copynumber: 2.6 Consensus size: 950
11126 AATTATACAT
* * *
11136 CCCAAGGCTAACAGTAGCTGAAGCTAGTTAATGTTACATGATGGGAAGTGTTGGATTTTATTTAT
1 CCCAAGGCTGACGGTAGCTGAGGCTAGTTAATGTTACATGATGGGAAGTGTTGGATTTTATTTAT
*
11201 TTTTCCTTGTAGGACATGAAATGTGTTATTCCTTAATAGTTTATGTCCAGCCTACCAAAAACTAA
66 TTTTCCTTGTAGGACATGAAATGTGTTATTCCTTAATAGTTTATGTCCAACCTACCAAAAACTAA
* * * *
11266 TAACTAACATAAAACATAATCATTACTTCATTAGGTTAACCAAATTATACATCATCATCATTTCA
131 TAACTAACATAAAACATAATCATTACTTTATTAGGTTAACCAAATTACACATAATCACCATTTCA
*
11331 TAATTATTTTGCTAATCCACACATTAAAAAAACAAATACAAAACGTACAAAAATCCAAACTTTAA
196 TAATTATATTGCTAATCCACACATTAAAAAAAC--A-A-AAAA-GT-CAAAAATCCAAACTTTAA
*
11396 CCCTTTCTCAATCTTCCACATTCTCACAAAATAAACATTAAGTAATACAAACCCAAAGTTCAATA
255 CTCTTTCTCAATC-TCCACATTCTCACAAAATAAACATTAAGTAATACAAACCCAAAGTTCAAT-
*
11461 CA-TTCTAAATGGCATTAAATAAACCAAAATTTAACCTTTATCCATTTCATTTTCATGGTTTAAG
318 CATTTCTAAATGGCATTAAA-AACCCAAAATTTAACCTTTATCCATTTCATTTTCATGGTTTAAG
* *
11525 TCAGCATTAACAGTTATCAAATTCAATTTCCCTACTTAAGCTACACTCTCCAACTTTTATAAATC
382 TCAGCATTAACAGTTA-CAAATTCAATTTCCCTACTCAAGCTACACTCTTCAACTTTTATAAATC
* * *
11590 CATATTTTTTCTCTTTCTTCTAATAAACTCGTATCGTTGAGGTTGTATTTGTTGTAATATTCCTT
446 CATATTTTTTCTCTTTCTTCTAATAAAC-CCTATTGTTGAGGTTGCATTTGTTGTAATATTCCTT
* * ** * * *
11655 TCATTGTCTCACTTTTCTCGTTTAATTAATGGAAACCTTGCATGAGTTTTTCTTCGACCCTTTCA
510 TCATTGTCTCACTCTTCCCACTTACTGAATGGAAACCTTGCATGAGTTTTTCTTCGACACTTTCA
** * * ** *
11720 ACTTTGGTAGTTCTATCTAAAGTTTTTTGCTTTAGCCAAACTATCATATCAGTTCTTGCCTCTGC
575 ACTTTGACAGTTCCATCTAAACTTTTTTGCCCTAGCCAAACTATCATATCACTTCTTGCCTCTGC
* * * * * * *
11785 TATGGCAACAACTTCATCTTTTGCAAGAGAAAAGGTTATAATCTCTTCCCGTTCCTTTTCTAATG
640 AATGGCAACAACTTCATATCTTGCAAGAGAAAAGGTTATAATATATTCCCGTGCCTTTTCTAACG
* *
11850 CAACCTCAGTAGCAACTTTTTGAGAACTAATCTCATGGAAATTGACGAAAGCTGAAACCAACATA
705 CAACCTCAGCAGCAACTTTTTGAGAACTAATCTCATGGAAATTGACGAAAGCTAAAACCAACATA
* ** * * * *
11915 GTAGTTAATTCGTCTATAGACTCTCTATGTTGCAATTGAAACATTGCATTGGTTAGGAAACGATA
770 GTAGTTAATTCATCTATAGACGATCCATGTTGCAATTAAAACATTACATTGGTAAGGAAACGATA
* * * **
11980 GTATTTTTAAGGAAACAATAGTATAAAAATATAAATTATATTACAGACTTTCAATGACCATTTGT
835 ATATTATTAAGGAAACAATAATATAAAAATATAAATTATATTACAGACTTTCAATGACCAACTGT
* * * *
12045 ATCTCTTGTACAAAGGGGGGTCATAGTCATGCAC-AGGGTGGTCTTGGTCATACATAA
900 AGCTCTTGCACAAAGAGGGGTCATAGTCATGCACTAGGG-GGTC-TAG-C--AC--AA
12102 GGGGGTCTCGGGCAGCCCTAGGCTGACGGTAGCTGAGGCTAGTTAATGTTACATGATGGGAAGTG
1 ------C-C---CA-----AGGCTGACGGTAGCTGAGGCTAGTTAATGTTACATGATGGGAAGTG
* * * * * * *
12167 TTGGATTTTATTTATTTTTCTTTTTTGGACATGAAATGTGTTATTGCTTAATATTTTTTGTTCAA
51 TTGGATTTTATTTATTTTTCCTTGTAGGACATGAAATGTGTTATTCCTTAATAGTTTATGTCCAA
* *
12232 CCTACTAAAAACTAATAACTAATATAAAACATAATCATTACTTTATTAGGTTAACCAAATTACAC
116 CCTACCAAAAACTAATAACTAACATAAAACATAATCATTACTTTATTAGGTTAACCAAATTACAC
* * *
12297 ATAATCACCCTTTTATAATTATATTGCTAATCCACATATTAAAAAAAC-AAAAAGTCAAAAATCC
181 ATAATCACCATTTCATAATTATATTGCTAATCCACACATTAAAAAAACAAAAAAGTCAAAAATCC
* * * *
12361 AAACTTTAACTCTTTCTCAATCATCCACATTCTCACAAAATAAATATTAGGTAATATAAACCCTA
246 AAACTTTAACTCTTTCTCAATC-TCCACATTCTCACAAAATAAACATTAAGTAATACAAACCCAA
* * *
12426 AGTTCAATCATTTCTAAATGGCATTAAAAACCCCAAATTCAACCTTTATCTATTTCATTTTCATG
310 AGTTCAATCATTTCTAAATGGCATTAAAAACCCAAAATTTAACCTTTATCCATTTCATTTTCATG
* * ** *
12491 GTTTAAGTCAGCATTAATAGTTACAAAATTCAATTTCCTTACTCAATATACACTCTTCAACTTCT
375 GTTTAAGTCAGCATTAACAGTTAC-AAATTCAATTTCCCTACTCAAGCTACACTCTTCAACTTTT
* *
12556 ATAAATCCATATTTTTCTCTTTTTCTTCCAATAAACCCTTATTGTTGAGGTTGCATTTGTTGTAA
439 ATAAATCCATATTTTT-TCTCTTTCTTCTAATAAACCC-TATTGTTGAGGTTGCATTTGTTGTAA
12621 TATTCCTTTCATTGTCTCACTCTTCCCACTTACTGAATGGAAACCTTGCATGAGTTTTTCTTCGA
502 TATTCCTTTCATTGTCTCACTCTTCCCACTTACTGAATGGAAACCTTGCATGAGTTTTTCTTCGA
* * **
12686 CACTTTCAA-TCTTGACAGTTCCATC-CAACTTTTCTTGCCCTA-CTCGAACTATTGTATCACCT
567 CACTTTCAACT-TTGACAGTTCCATCTAAACTTTT-TTGCCCTAGC-CAAACTATCATATCA-CT
* ** * * * ***
12748 T-TTGCCTTTGCAATGGCAACAACTTCATATCTTGCAAGATTAATGGTTGTGATATATTTTTGTG
628 TCTTGCCTCTGCAATGGCAACAACTTCATATCTTGCAAGAGAAAAGGTTATAATATATTCCCGTG
* * * *
12812 CCTTTTCTAACGCAATCTCAGCAGTAACTTTTTGAGAATTAATCTCCTGGAAATTGACGAAAGCT
693 CCTTTTCTAACGCAACCTCAGCAGCAACTTTTTGAGAACTAATCTCATGGAAATTGACGAAAGCT
* * * *
12877 AAAACCAATATATTAGTTAATTTATCTATAGACGATCCGTGTTGCAATTAAAACATTACATT-GT
758 AAAACCAACATAGTAGTTAATTCATCTATAGACGATCCATGTTGCAATTAAAACATTACATTGGT
* * * *
12941 GAAGGAAATGATAATATTATTAAGGAAACGATAATATAAAATTATAAATTATATTACGGACTTTC
823 -AAGGAAACGATAATATTATTAAGGAAACAATAATATAAAAATATAAATTATATTACAGACTTTC
* * * ** * *
13006 ACTTATCAACTGTAGCTCTTGCACAGTGAGGGGTCTTGGTCATGCACTAGGGGGTCTAGCACAA
887 AATGACCAACTGTAGCTCTTGCACAAAGAGGGGTCATAGTCATGCACTAGGGGGTCTAGCACAA
* * * * * * * *
13070 CCCAATGTTGATGGTAGCTCAGGTTAGTTAATGTTATATGATGAGAAGAGTTGGATTTTATTTAT
1 CCCAAGGCTGACGGTAGCTGAGGCTAGTTAATGTTACATGATGGGAAGTGTTGGATTTTATTTAT
* *
13135 TTTTCCTTGTAGGACATGAAATGTGTTATTTCTTAATAGTTTATGTCCATCCTACCAAAAACTAA
66 TTTTCCTTGTAGGACATGAAATGTGTTATTCCTTAATAGTTTATGTCCAACCTACCAAAAACTAA
* * *
13200 TAACTAACATAAAACATAATCATTA-TTTCATTAGGTTTACCAAATTACACATTATTACCATTTC
131 TAACTAACATAAAACATAATCATTACTTT-ATTAGGTTAACCAAATTACACATAATCACCATTTC
* *
13264 ATAATTATGTTGCTAATCCACACATTAAAAAAACAAAGAAAG--AAAGA--CAAA----AA-TCT
195 ATAATTATATTGCTAATCCACACATTAAAAAAACAAA-AAAGTCAAAAATCCAAACTTTAACTCT
* *
13320 ATCT---TCT--ACATTCTCACAAAATAAACATTAAGCAATACAAACCCAAAGTTCAATCATTTC
259 TTCTCAATCTCCACATTCTCACAAAATAAACATTAAGTAATACAAACCCAAAGTTCAATCATTTC
* * * * *
13380 CAAGTGGCATTAAAAAACACAAAATTTAAACTTTATCCATTTCATTTTCATGG-TTCA---AG--
324 TAAATGGCATT-AAAAACCCAAAATTTAACCTTTATCCATTTCATTTTCATGGTTTAAGTCAGCA
* *
13439 TTAACAGTTACCAAATTTAACTTCCCTACTCAAGCTACACTCTTCAACTTTTATAAATCCATATT
388 TTAACAGTTA-CAAATTCAATTTCCCTACTCAAGCTACACTCTTCAACTTTTATAAATCCATATT
** *
13504 TTTTCTCTTTCTTCTAATAAACTCCTATTGTTGAGGTTGCATTTACTGTAATGTTCCTTTCATTG
452 TTTTCTCTTTCTTCTAATAAAC-CCTATTGTTGAGGTTGCATTTGTTGTAATATTCCTTTCATTG
* * * * *
13569 TCCCACTCTTCCCCCTTACTGAATGGAAACCTTGTATAAGTTTTTCTTTGACAC
516 TCTCACTCTTCCCACTTACTGAATGGAAACCTTGCATGAGTTTTTCTTCGACAC
13623 CCACTTACCG
Statistics
Matches: 1319, Mismatches: 171, Indels: 88
0.84 0.11 0.06
Matches are distributed among these distances:
934 103 0.08
935 61 0.05
936 1 0.00
937 2 0.00
940 60 0.05
941 36 0.03
942 1 0.00
943 2 0.00
946 6 0.00
947 2 0.00
951 4 0.00
952 3 0.00
953 199 0.15
954 2 0.00
955 4 0.00
958 2 0.00
961 1 0.00
962 1 0.00
968 2 0.00
970 2 0.00
972 3 0.00
973 121 0.09
974 483 0.37
975 8 0.01
976 6 0.00
977 1 0.00
981 203 0.15
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (950 bp):
CCCAAGGCTGACGGTAGCTGAGGCTAGTTAATGTTACATGATGGGAAGTGTTGGATTTTATTTAT
TTTTCCTTGTAGGACATGAAATGTGTTATTCCTTAATAGTTTATGTCCAACCTACCAAAAACTAA
TAACTAACATAAAACATAATCATTACTTTATTAGGTTAACCAAATTACACATAATCACCATTTCA
TAATTATATTGCTAATCCACACATTAAAAAAACAAAAAAGTCAAAAATCCAAACTTTAACTCTTT
CTCAATCTCCACATTCTCACAAAATAAACATTAAGTAATACAAACCCAAAGTTCAATCATTTCTA
AATGGCATTAAAAACCCAAAATTTAACCTTTATCCATTTCATTTTCATGGTTTAAGTCAGCATTA
ACAGTTACAAATTCAATTTCCCTACTCAAGCTACACTCTTCAACTTTTATAAATCCATATTTTTT
CTCTTTCTTCTAATAAACCCTATTGTTGAGGTTGCATTTGTTGTAATATTCCTTTCATTGTCTCA
CTCTTCCCACTTACTGAATGGAAACCTTGCATGAGTTTTTCTTCGACACTTTCAACTTTGACAGT
TCCATCTAAACTTTTTTGCCCTAGCCAAACTATCATATCACTTCTTGCCTCTGCAATGGCAACAA
CTTCATATCTTGCAAGAGAAAAGGTTATAATATATTCCCGTGCCTTTTCTAACGCAACCTCAGCA
GCAACTTTTTGAGAACTAATCTCATGGAAATTGACGAAAGCTAAAACCAACATAGTAGTTAATTC
ATCTATAGACGATCCATGTTGCAATTAAAACATTACATTGGTAAGGAAACGATAATATTATTAAG
GAAACAATAATATAAAAATATAAATTATATTACAGACTTTCAATGACCAACTGTAGCTCTTGCAC
AAAGAGGGGTCATAGTCATGCACTAGGGGGTCTAGCACAA
Found at i:13930 original size:2 final size:2
Alignment explanation
Indices: 13923--13947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13913 AGTATTCTTA
13923 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
13948 AACTAAAATA
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:17391 original size:2 final size:2
Alignment explanation
Indices: 17384--17419 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17374 TGCCAAAGGT
17384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17420 ATGTGTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20556 original size:16 final size:16
Alignment explanation
Indices: 20535--20568 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20525 TTCATGCTAG
20535 CTCTCTTGTTTTGAAA
1 CTCTCTTGTTTTGAAA
20551 CTCTCTTGTTTTGAAA
1 CTCTCTTGTTTTGAAA
20567 CT
1 CT
20569 TGATAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (16 bp):
CTCTCTTGTTTTGAAA
Found at i:22210 original size:15 final size:16
Alignment explanation
Indices: 22186--22222 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
22176 TTTAATTTCT
22186 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
22200 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
22216 TGATTCA
1 T-ATTCA
22223 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:22369 original size:21 final size:21
Alignment explanation
Indices: 22343--22385 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22333 TATTACCTTA
*
22343 AATTGAAGTATTTTATAATTT
1 AATTGAAGTATTTTAGAATTT
22364 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
22385 A
1 A
22386 GGGTTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:22622 original size:29 final size:29
Alignment explanation
Indices: 22570--22627 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
22560 GCAAACGGAA
* *
22570 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
22599 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
22628 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:32195 original size:15 final size:15
Alignment explanation
Indices: 32175--32205 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32165 TCATCTTTCC
32175 GCTTCTTCATAAATG
1 GCTTCTTCATAAATG
32190 GCTTCTTCATAAATG
1 GCTTCTTCATAAATG
32205 G
1 G
32206 ATCTGGCAAA
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:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (15 bp):
GCTTCTTCATAAATG
Found at i:35066 original size:31 final size:32
Alignment explanation
Indices: 35000--35085 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
34990 GTACCCTAGC
* **
35000 ACTAAAATAAAATAAAAAGTTAACAATGGGGT
1 ACTAAAATAAAATAAAAAGTAAACAACCGGGT
* *
35032 ACTAAAATGAAACAAAAAGTAAAC-ACCGGGT
1 ACTAAAATAAAATAAAAAGTAAACAACCGGGT
35063 ACTAAAATAAAATAAAAAGTAAA
1 ACTAAAATAAAATAAAAAGTAAA
35086 TATTATGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 26 0.55
32 21 0.45
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.17
Consensus pattern (32 bp):
ACTAAAATAAAATAAAAAGTAAACAACCGGGT
Found at i:41967 original size:9 final size:9
Alignment explanation
Indices: 41937--41988 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
41927 ATCTGCAAAA
41937 AAATTAAAT
1 AAATTAAAT
*
41946 -AAGTAAA-
1 AAATTAAAT
*
41953 ATATTAAAT
1 AAATTAAAT
41962 AAATTAAAT
1 AAATTAAAT
*
41971 -ACTTAAAT
1 AAATTAAAT
41979 AAATTAAAT
1 AAATTAAAT
41988 A
1 A
41989 TAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:41969 original size:17 final size:16
Alignment explanation
Indices: 41939--41995 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
41929 CTGCAAAAAA
* *
41939 ATTAAATAAGTAAAAT
1 ATTAAATAAATTAAAT
41955 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
41971 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
41988 ATAAAATA
1 ATTAAATA
41996 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:43472 original size:17 final size:17
Alignment explanation
Indices: 43450--43501 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
43440 GACGATGAAG
43450 ATCGGTTTGGCCTTCAC
1 ATCGGTTTGGCCTTCAC
43467 ATCGGTTTGGCCTTCAC
1 ATCGGTTTGGCCTTCAC
43484 ATCGGTTTGGCCTTCAC
1 ATCGGTTTGGCCTTCAC
43501 A
1 A
43502 ATTCACATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.13, C:0.29, G:0.23, T:0.35
Consensus pattern (17 bp):
ATCGGTTTGGCCTTCAC
Found at i:44977 original size:102 final size:102
Alignment explanation
Indices: 44794--45049 Score: 230
Period size: 102 Copynumber: 2.5 Consensus size: 102
44784 GGAAATATCG
* * * * ** * *
44794 CTTCCAGTTCAAGGGGAAGACATTCATCT-GCCAATTTCTTTGACCTGAATATGGAGATGTCCTC
1 CTTCAAGTTCAAGAGGAAGGCATTCAACTAG-CAGCTTCTTCGACCTAAATATGGAGATGTCCTC
* ** *
44858 AACACAACAATCTGTTCAGTACCCATTTGACACGATAT
65 AACACAACAATCAGTTCAAAACCCATATGACACGATAT
* * * * *
44896 CTTCAAGTTCTAGGGGGAGGCATTCAACT-GCGAGCTTCTTCGACCTCAATATGGAGATG-CTTA
1 CTTCAAGTTCAAGAGGAAGGCATTCAACTAGC-AGCTTCTTCGACCTAAATATGGAGATGTCCT-
* * ** * *
44959 CGACACAACATTCAGTTCAAAACCTGTATGACATGATGT
64 CAACACAACAATCAGTTCAAAACCCATATGACACGATAT
* * *
44998 CTTCAAGTTCAAGAGGAATGCATTCAACTATCAGCTTGTTCGACCTAAATAT
1 CTTCAAGTTCAAGAGGAAGGCATTCAACTAGCAGCTTCTTCGACCTAAATAT
45050 CAGCATCACA
Statistics
Matches: 124, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
101 3 0.02
102 120 0.97
103 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (102 bp):
CTTCAAGTTCAAGAGGAAGGCATTCAACTAGCAGCTTCTTCGACCTAAATATGGAGATGTCCTCA
ACACAACAATCAGTTCAAAACCCATATGACACGATAT
Found at i:47074 original size:12 final size:12
Alignment explanation
Indices: 47045--47102 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
47035 TCTATTTGTA
47045 TAATATTTTTAT
1 TAATATTTTTAT
47057 TGAATATTTTTAT
1 T-AATATTTTTAT
47070 TAATATTTTT-T
1 TAATATTTTTAT
*
47081 TGAATATTTGTAT
1 T-AATATTTTTAT
47094 TAATATTTT
1 TAATATTTT
47103 AATATATTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 2 0.05
12 25 0.61
13 14 0.34
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (12 bp):
TAATATTTTTAT
Found at i:47078 original size:24 final size:24
Alignment explanation
Indices: 47037--47103 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
47027 ATATGTGTTC
47037 TATTTGTA-TAATATTTTTATTGAA
1 TATTTGTATTAATA-TTTTATTGAA
* *
47061 TATTTTTATTAATATTTTTTTGAA
1 TATTTGTATTAATATTTTATTGAA
47085 TATTTGTATTAATATTTTA
1 TATTTGTATTAATATTTTA
47104 ATATATTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 33 0.87
25 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTTGTATTAATATTTTATTGAA
Found at i:47224 original size:19 final size:19
Alignment explanation
Indices: 47179--47232 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
47169 ATAAAACATG
*
47179 TATTTAAAATAATT-TTTAA
1 TATTTAAAAT-ATTGTATAA
*
47198 CA-TTAAAATATTGTATAA
1 TATTTAAAATATTGTATAA
*
47216 TATTTAAAATATAGTAT
1 TATTTAAAATATTGTAT
47233 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 12 0.41
19 14 0.48
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TATTTAAAATATTGTATAA
Found at i:47241 original size:19 final size:19
Alignment explanation
Indices: 47199--47243 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
47189 AATTTTTAAC
*
47199 ATTAAAATATTGTATAATA
1 ATTAAAATATAGTATAATA
* **
47218 TTTAAAATATAGTATTTTA
1 ATTAAAATATAGTATAATA
47237 ATTAAAA
1 ATTAAAA
47244 CAAATTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
ATTAAAATATAGTATAATA
Found at i:51804 original size:77 final size:77
Alignment explanation
Indices: 51677--51831 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
51667 ATTAGCTGGC
51677 CCTTATTCTCATATGTAATGGGGTAAGAAAGAAGTAGGATAGTAGATTACCCCCAACGCCAGGTT
1 CCTTATTCTCATATGTAATGGGGTAAGAAAGAAGTAGGATAGTAGATTACCCCCAACGCCAGGTT
51742 AAGAGCAACTTT
66 AAGAGCAACTTT
51754 CCTTATTCTCATATGTAATGGGGTAAGAAAGAAGTAGGATAGTAGATTACCCCCAACGCCAGGTT
1 CCTTATTCTCATATGTAATGGGGTAAGAAAGAAGTAGGATAGTAGATTACCCCCAACGCCAGGTT
51819 AAGAGCAACTTT
66 AAGAGCAACTTT
51831 C
1 C
51832 GTGGGAAACC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (77 bp):
CCTTATTCTCATATGTAATGGGGTAAGAAAGAAGTAGGATAGTAGATTACCCCCAACGCCAGGTT
AAGAGCAACTTT
Found at i:53003 original size:13 final size:13
Alignment explanation
Indices: 52985--53010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52975 AAATGATTTT
52985 TAAAATAATTTGG
1 TAAAATAATTTGG
52998 TAAAATAATTTGG
1 TAAAATAATTTGG
53011 GAGTCGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TAAAATAATTTGG
Found at i:53616 original size:135 final size:135
Alignment explanation
Indices: 53324--53735 Score: 695
Period size: 135 Copynumber: 3.0 Consensus size: 135
53314 AATATGTATA
* * *
53324 AATAAGATATTTATTTATTTAGAAATATCAGAAAAG-GACTTCTAGGTGCTTTAAGACAACTCTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAG-CTTCTAGGTGCCTTAAGACAGCTCTT
*
53388 TTCTTCGATATTAAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAATAAAAATTTATT
65 TTCTTCGATATT-AAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAAAAAAAATTTATT
53453 TTAATAT
129 TTAATAT
53460 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
*
53525 TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAACAAAAATTTATTTT
66 TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAAAAAAAATTTATTTT
53590 AATAT
131 AATAT
*
53595 AATAAGATATTTATTTATTTAAAAATATCAGAAAATAGCTTCTAGGTGCCTTAAGACAGCTCTTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
*
53660 TCTTCGATATTAAAAAAT-AAATAAATAAC-CAAAACATTTTCTTTAAAAATAAAAATAATTTAT
66 TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTC-TTAAAAA-AAAAA-AATTTAT
53723 TTTAATAT
128 TTTAATAT
53731 AATAA
1 AATAA
53736 TAATGAAAAT
Statistics
Matches: 265, Mismatches: 7, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
133 11 0.04
134 18 0.07
135 144 0.54
136 91 0.34
137 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (135 bp):
AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAAAAAAAATTTATTTT
AATAT
Found at i:55196 original size:3 final size:3
Alignment explanation
Indices: 55179--55259 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
55169 TTTGGGCCTG
* * *
55179 TAA TAA -AA TTAA TAA TAAA TAA TAA T-A TTA TAA T-A TGTA TAA TAT
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
**
55224 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55260 AAACAAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.09
3 51 0.80
4 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:55517 original size:76 final size:76
Alignment explanation
Indices: 55414--55898 Score: 837
Period size: 76 Copynumber: 6.4 Consensus size: 76
55404 AGGTCTTAAC
** * *
55414 AACATCATGCACTAAAAGG-CTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AACATCATGCACT-GTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
55478 AGGCTTTTTGAA
65 AGGCTTTTTGGA
* *
55490 AACATCATGCACTGTAGGACTTACAGATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
55555 GGCTTTTTGGA
66 GGCTTTTTGGA
55566 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
55631 GGCTTTTTGGA
66 GGCTTTTTGGA
55642 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
55707 GGCTTTTTGGA
66 GGCTTTTTGGA
* *
55718 AACATCATGCACTGTAGGACTTAAAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
*
55783 GGCTTTTTGAA
66 GGCTTTTTGGA
* *
55794 AACATTATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCAGAA
1 AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
55859 GGCTTTTTGGA
66 GGCTTTTTGGA
*
55870 AACATCATGCACTGCAGGACTTACAGATG
1 AACATCATGCACTGTAGGACTTACAGATG
55899 TGGGAAATAG
Statistics
Matches: 392, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 3 0.01
76 389 0.99
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGA
Found at i:56597 original size:22 final size:22
Alignment explanation
Indices: 56572--56648 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
56562 AATAAAGCTT
56572 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
56594 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
56616 TCATATTT-AAAGAGAGAATCTA
1 TCATCTTTGAAA-AGAGAATCTA
56638 TCATCTTTGAA
1 TCATCTTTGAA
56649 TAATGTAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
21 3 0.06
22 45 0.90
23 2 0.04
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:57939 original size:75 final size:76
Alignment explanation
Indices: 57796--57968 Score: 192
Period size: 75 Copynumber: 2.3 Consensus size: 76
57786 ACAGGATAAT
* * *
57796 ATGGGCTTTCAACATGCCCCAATATTGGCTAATACAAATGTTTAAAAATACCTCAACATTCTTCA
1 ATGGGCTTTCAGCATGCCCCAACATTGGCTAATACAAATGTTTAAAAATACATCAACATTCTTCA
*
57861 TTCTGATTGAA
66 TTCTAATTGAA
* * * * * *
57872 A-GGGTTTTCAGCATGCCCCAACATTTTGCTGATATAAATGTTT-AGAATACATCAATATT-TCT
1 ATGGGCTTTCAGCATGCCCCAACA-TTGGCTAATACAAATGTTTAAAAATACATCAACATTCT-T
*
57934 GATTCTAATTGAA
64 CATTCTAATTGAA
57947 ATGGGCTTTCAGTC-TGCCCCAA
1 ATGGGCTTTCAG-CATGCCCCAA
57969 TATCTGCTTC
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
74 1 0.01
75 45 0.56
76 34 0.42
77 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (76 bp):
ATGGGCTTTCAGCATGCCCCAACATTGGCTAATACAAATGTTTAAAAATACATCAACATTCTTCA
TTCTAATTGAA
Found at i:58845 original size:4 final size:4
Alignment explanation
Indices: 58838--58872 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
58828 TTTTTTCCTT
58838 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
58873 TTTTTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:61506 original size:21 final size:22
Alignment explanation
Indices: 61473--61526 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
61463 TGTAAACATA
*
61473 AAAGTATGAAAAATGAAAATGC
1 AAAGTATGAAAAAGGAAAATGC
* *
61495 AAAG-ATGCAAAAGGCAAATGC
1 AAAGTATGAAAAAGGAAAATGC
*
61516 -ATGTATGAAAA
1 AAAGTATGAAAA
61527 GGTGTTACTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.08
21 20 0.77
22 4 0.15
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (22 bp):
AAAGTATGAAAAAGGAAAATGC
Found at i:69665 original size:21 final size:21
Alignment explanation
Indices: 69629--69710 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
69619 TTTGGTGCAG
*
69629 AGGGAATCGA-TCCCCCCATA
1 AGGGAACCGATTCCCCCCATA
**
69649 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCAT-A
*
69671 AGGGGAACCGATTCCCCCCACA
1 A-GGGAACCGATTCCCCCCATA
* * *
69693 GGGGAATCGATACCCCCC
1 AGGGAACCGATTCCCCCC
69711 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 22 0.44
22 3 0.06
23 16 0.32
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.15
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCATA
Found at i:71678 original size:17 final size:17
Alignment explanation
Indices: 71653--71686 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
71643 TTGAATATTT
*
71653 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
71670 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
71687 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:73598 original size:13 final size:13
Alignment explanation
Indices: 73580--73605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73570 AAATGGTTTT
73580 TAAAATAATTTGG
1 TAAAATAATTTGG
73593 TAAAATAATTTGG
1 TAAAATAATTTGG
73606 GAGTCGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TAAAATAATTTGG
Found at i:74105 original size:135 final size:135
Alignment explanation
Indices: 73927--74337 Score: 693
Period size: 135 Copynumber: 3.0 Consensus size: 135
73917 AATATGTATA
* * *
73927 AATAAGATATTTATTTATTTAGAAATATCAGAAAAG-GACTTCTAGGTGCTTTAAGAAAGCTCTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAG-CTTCTAGGTGCCTTAAGACAGCTCTT
73991 TTCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAATAAAAATTTATTT
65 TTCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAATAAAAATTTATTT
74056 TAATAT
130 TAATAT
*
74062 AATAAGATATTTATTTATTTAAAAATATCAAAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
* *
74127 TATTCGATATTAAAAAATAAAATAAATAACTAAAAACGTTTTCTTAAAAAATAAAAATTTATTTT
66 TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAATAAAAATTTATTTT
74192 AATAT
131 AATAT
74197 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
1 AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
* *
74262 TCTTCGATATTAAAAAAT-AAATAAATAAC-CAAAACATTTTCTTTAAAAATAAAAATAATTTAT
66 TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTC-TTAAAAA-ATAAA-AATTTAT
74325 TTTAATAT
128 TTTAATAT
74333 AATAA
1 AATAA
74338 TAATGAAAAT
Statistics
Matches: 261, Mismatches: 11, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
133 10 0.04
134 18 0.07
135 212 0.81
136 21 0.08
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (135 bp):
AATAAGATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGCTCTTT
TCTTCGATATTAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAATAAAAATTTATTTT
AATAT
Found at i:75795 original size:3 final size:3
Alignment explanation
Indices: 75778--75858 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
75768 TTTGGGCCTG
* *
75778 TAA TAA -AA TTAA TAA TAAA TAA TAA T-A TTA TAA T-A TACA TAA TAT
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* **
75823 TAT TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75859 CAAAAATAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
2 6 0.09
3 51 0.78
4 8 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:80593 original size:90 final size:93
Alignment explanation
Indices: 80332--80581 Score: 299
Period size: 94 Copynumber: 2.7 Consensus size: 93
80322 ACATAAGTTG
* *
80332 AGGTAGGCATCATGGTGCGGCTGAGGGGATACATCTCAGAGCTCACACACCCTTTTATCATACCT
1 AGGTAGGCATCATGGTGCGGCTGAGGGGATACATCTCAGAGCTCACGCACCCTTTTAGCATACCT
* ** *
80397 ATACTACTATGCAACAAACACACAAACTG
66 ATAGTACTATGTGAC-AACACACAAACTA
* * * * * * * *
80426 AGGTAGGCATCATGGTGTGGCTGAGGGGCTATATCTCAAAGCTCACGTACCCCTCTAGCCTACCT
1 AGGTAGGCATCATGGTGCGGCTGAGGGGATACATCTCAGAGCTCACGCACCCTTTTAGCATACCT
*
80491 ATAGTACTATGTGAC-ACACA-AGA-TA
66 ATAGTACTATGTGACAACACACAAACTA
* * * *
80516 AGGTAAGCATCATGGTGCGACTGAGGGGATACATCTCAGAGCTCACGCACCTTTTTAGCTTACCT
1 AGGTAGGCATCATGGTGCGGCTGAGGGGATACATCTCAGAGCTCACGCACCCTTTTAGCATACCT
80581 A
66 A
80582 AGAACTCATG
Statistics
Matches: 130, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
90 56 0.43
91 2 0.02
92 5 0.04
94 67 0.52
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (93 bp):
AGGTAGGCATCATGGTGCGGCTGAGGGGATACATCTCAGAGCTCACGCACCCTTTTAGCATACCT
ATAGTACTATGTGACAACACACAAACTA
Found at i:89331 original size:13 final size:13
Alignment explanation
Indices: 89313--89359 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
89303 AATGATAAAT
89313 AATAAAAAAATAC
1 AATAAAAAAATAC
* *
89326 AATAAAAAAGTCC
1 AATAAAAAAATAC
* *
89339 AATAAACAACTAC
1 AATAAAAAAATAC
89352 AATAAAAA
1 AATAAAAA
89360 GTACTAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.70, C:0.13, G:0.02, T:0.15
Consensus pattern (13 bp):
AATAAAAAAATAC
Found at i:89384 original size:26 final size:26
Alignment explanation
Indices: 89313--89385 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
89303 AATGATAAAT
*
89313 AATAAAAAAATACAATAAAAAAGTCC
1 AATAAACAAATACAATAAAAAAGTCC
* *
89339 AATAAACAACTACAAT-AAAAAGTACT
1 AATAAACAAATACAATAAAAAAGT-CC
* *
89365 AA-ATACAAATATAATAAAAAA
1 AATAAACAAATACAATAAAAAA
89386 ACAAAATCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 17 0.44
26 22 0.56
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.18
Consensus pattern (26 bp):
AATAAACAAATACAATAAAAAAGTCC
Found at i:91596 original size:9 final size:9
Alignment explanation
Indices: 91582--91615 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
91572 TAAGTAAAAT
91582 ATTAAATAA
1 ATTAAATAA
91591 ATTAAAT-A
1 ATTAAATAA
*
91599 CTTAAATAA
1 ATTAAATAA
91608 ATTAAATA
1 ATTAAATA
91616 TAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:91596 original size:17 final size:16
Alignment explanation
Indices: 91578--91622 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
91568 TATATAAGTA
91578 AAATATTAAATAAATT
1 AAATATTAAATAAATT
91594 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
*
91611 AAATATAAAATA
1 AAATATTAAATA
91623 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTAAATAAATT
Done.