Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 124 of 136
Found at i:42205990 original size:9 final size:9
Alignment explanation
Indices: 42205978--42206020 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
42205968 ATTCAATTTT
*
42205978 GTTAATTTG
1 GTTAATTCG
42205987 GTTAATTCG
1 GTTAATTCG
*
42205996 GGTAATTCG
1 GTTAATTCG
42206005 GTTAATTCG
1 GTTAATTCG
*
42206014 ATTAATT
1 GTTAATT
42206021 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:42220448 original size:2 final size:2
Alignment explanation
Indices: 42220441--42220466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42220431 AAATGTACGC
42220441 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42220467 AAAGACAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42221767 original size:31 final size:31
Alignment explanation
Indices: 42221732--42221809 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
42221722 TATATTTCTA
42221732 ATTTATATTTTATACATT-ATTATATTAAATT
1 ATTTATATTTTATAC-TTCATTATATTAAATT
42221763 ATTTAAATATTTTAT--TTCATTATATTAAATT
1 ATTT--ATATTTTATACTTCATTATATTAAATT
*
42221794 ATTT-TATTTAATACTT
1 ATTTATATTTTATACTT
42221810 GAAAATATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
28 7 0.17
30 4 0.10
31 21 0.51
33 9 0.22
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTTATATTTTATACTTCATTATATTAAATT
Found at i:42221881 original size:21 final size:23
Alignment explanation
Indices: 42221843--42221895 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
42221833 ATTTATAAAT
42221843 AATTTA-TTAATATAATTATATA
1 AATTTATTTAATATAATTATATA
*
42221865 AATTTATTTAA-AT-ATTATCTA
1 AATTTATTTAATATAATTATATA
*
42221886 AATTGATTTA
1 AATTTATTTA
42221896 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.57
22 8 0.29
23 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTATTTAATATAATTATATA
Found at i:42223665 original size:31 final size:32
Alignment explanation
Indices: 42223600--42223665 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
42223590 ATATAAAAGT
*
42223600 TAAAAAAAATTATGAATATTTTTAGTTATTATA
1 TAAAAAAAATTATAAATATTTTTA-TTATTATA
*
42223633 TAAAAAATATTA-AAATATTTTT-TTATTAATA
1 TAAAAAAAATTATAAATATTTTTATTATT-ATA
42223664 TA
1 TA
42223666 GCGATAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 5 0.17
32 9 0.30
33 11 0.37
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
TAAAAAAAATTATAAATATTTTTATTATTATA
Found at i:42229079 original size:61 final size:61
Alignment explanation
Indices: 42228984--42229103 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 61
42228974 GTAAATTGTA
*
42228984 AGGATCAAATAATTTAGTTCATTTGCTATCAAC-TTTGTGTTACTAAAAATTTTGTCACTCG
1 AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTG-GTTACTAAAAATTTTGTCACTCG
*
42229045 AGGATCAAATAATTTAGTTCCTCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACT
1 AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACT
42229104 TAACTGAGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 52 0.93
62 4 0.07
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (61 bp):
AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACTCG
Found at i:42248393 original size:17 final size:17
Alignment explanation
Indices: 42248373--42248409 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42248363 TATTTTAATA
*
42248373 AATTTAACATTTATTTT
1 AATTTAACATTTATCTT
*
42248390 AATTTAATATTTATCTT
1 AATTTAACATTTATCTT
42248407 AAT
1 AAT
42248410 AGTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTAACATTTATCTT
Found at i:42248630 original size:25 final size:26
Alignment explanation
Indices: 42248590--42248640 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
42248580 GTTGTAGAGG
42248590 GAAAATTCTATAAAGAAATTATTTTA
1 GAAAATTCTATAAAGAAATTATTTTA
* * *
42248616 GAAAA-TCTCTAAAGATATTTTTTTA
1 GAAAATTCTATAAAGAAATTATTTTA
42248641 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (26 bp):
GAAAATTCTATAAAGAAATTATTTTA
Found at i:42249838 original size:31 final size:32
Alignment explanation
Indices: 42249774--42249838 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
42249764 ATATAATGTA
* *
42249774 ACTTTCGCCCCTTGAACTTGGCAAATAGGTCC
1 ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
* *
42249806 ACTTTGGCCCC-TGAACTTAGCAAGTAGATCC
1 ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
42249837 AC
1 AC
42249839 ATTGTGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (32 bp):
ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
Found at i:42250219 original size:31 final size:31
Alignment explanation
Indices: 42250182--42250243 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
42250172 AGATAATTTT
42250182 AAAGAGTTTTATTA-TGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGT-ATTCAATTACTCTTG
42250213 AAAGAGTTTTATTAGTATTCAATTACTCTTG
1 AAAGAGTTTTATTAGTATTCAATTACTCTTG
42250244 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (31 bp):
AAAGAGTTTTATTAGTATTCAATTACTCTTG
Found at i:42251311 original size:76 final size:76
Alignment explanation
Indices: 42251185--42251356 Score: 328
Period size: 76 Copynumber: 2.3 Consensus size: 76
42251175 AGTGATTAAA
42251185 GTGGACCTGA-TTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAAT
1 GTGGACCT-ACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAAT
42251249 TTAGGGGCTAAT
65 TTAGGGGCTAAT
42251261 GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
1 GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
42251326 TAGGGGCTAAT
66 TAGGGGCTAAT
42251337 GTGGACCTACTTGTCAAGTT
1 GTGGACCTACTTGTCAAGTT
42251357 TAAGGGTTAA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
75 1 0.01
76 94 0.99
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (76 bp):
GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
TAGGGGCTAAT
Found at i:42253077 original size:93 final size:95
Alignment explanation
Indices: 42252944--42253135 Score: 370
Period size: 93 Copynumber: 2.0 Consensus size: 95
42252934 TATTATCAAT
42252944 AAAATTTTGATTAATTCTCATTTTGTTGCCAGAAAGGAAAAGAAAAAAGTGAGACTGAGTGAGAG
1 AAAATTTTGATTAATTCTCATTTTGTTGCCAGAAAGGAAAAGAAAAAAGTGAGACTGAGTGAGAG
42253009 GGAAAAAAAAAAAAAGAGAAAAAAATTATA
66 GGAAAAAAAAAAAAAGAGAAAAAAATTATA
42253039 AAAATTTTGATT-A-TCTCATTTTGTTGCCAGAAAGGAAAAGAAAAAAGTGAGACTGAGTGAGAG
1 AAAATTTTGATTAATTCTCATTTTGTTGCCAGAAAGGAAAAGAAAAAAGTGAGACTGAGTGAGAG
42253102 GGAAAAAAAAAAAAAGAGAAAAAAATTATA
66 GGAAAAAAAAAAAAAGAGAAAAAAATTATA
42253132 AAAA
1 AAAA
42253136 AATAAAGAAA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
93 84 0.87
94 1 0.01
95 12 0.12
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (95 bp):
AAAATTTTGATTAATTCTCATTTTGTTGCCAGAAAGGAAAAGAAAAAAGTGAGACTGAGTGAGAG
GGAAAAAAAAAAAAAGAGAAAAAAATTATA
Found at i:42253830 original size:34 final size:34
Alignment explanation
Indices: 42253789--42253856 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42253779 TAAAGGGCAA
42253789 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
1 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
42253823 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
1 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
42253857 TGTAATGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (34 bp):
AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
Found at i:42260781 original size:17 final size:17
Alignment explanation
Indices: 42260761--42260794 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42260751 ATAGAAGGTT
* *
42260761 AAATTTTAGTTTTAATC
1 AAATTTGAGATTTAATC
42260778 AAATTTGAGATTTAATC
1 AAATTTGAGATTTAATC
42260795 TTTATATTTA
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:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
AAATTTGAGATTTAATC
Found at i:42272835 original size:2 final size:2
Alignment explanation
Indices: 42272828--42272854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42272818 TGAGTGTAAT
42272828 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 T
42272855 GAGTAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42273145 original size:26 final size:26
Alignment explanation
Indices: 42273093--42273146 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
42273083 AGTAATTTCG
*
42273093 TTTTTTTCTTTATGTTCTTTTAACTCT
1 TTTTTTTCTTTATGTTCTATT-ACTCT
*
42273120 TTTTTTCTCTTTATTTTCTATT-CTCT
1 TTTTTT-TCTTTATGTTCTATTACTCT
42273146 T
1 T
42273147 CTGCTTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 13 0.54
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTTTCTTTATGTTCTATTACTCT
Found at i:42273613 original size:29 final size:31
Alignment explanation
Indices: 42273537--42273613 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
42273527 TTAACGGCTC
* *
42273537 AGTGACTAAAATGTTACAGTGCGATAATGTA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
** * *
42273568 AGTGACTAAAACATAACATTTC-A-AATATA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
42273597 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
42273614 CTGAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.53
30 1 0.03
31 17 0.45
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAGTGCGATAATATA
Found at i:42277878 original size:26 final size:26
Alignment explanation
Indices: 42277826--42277879 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
42277816 AGTAATTTCG
*
42277826 TTTTTTTCTTTATGTTCTTTTAACTCT
1 TTTTTTTCTTTATGTTCTATT-ACTCT
*
42277853 TTTTTTCTCTTTATTTTCTATT-CTCT
1 TTTTTT-TCTTTATGTTCTATTACTCT
42277879 T
1 T
42277880 CTGCTTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 13 0.54
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTTTCTTTATGTTCTATTACTCT
Found at i:42278346 original size:29 final size:31
Alignment explanation
Indices: 42278270--42278346 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
42278260 TTAACGGCTC
* *
42278270 AGTGACTAAAATGTTACAGTGCGATAATGTA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
** * *
42278301 AGTGACTAAAACATAACATTTC-A-AATATA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
42278330 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
42278347 CTGAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.53
30 1 0.03
31 17 0.45
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAGTGCGATAATATA
Found at i:42282949 original size:18 final size:18
Alignment explanation
Indices: 42282926--42282966 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42282916 ATTCAAGGCA
42282926 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
42282944 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
42282962 TAATT
1 TAATT
42282967 GAAAACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:42286791 original size:14 final size:14
Alignment explanation
Indices: 42286764--42286840 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 14
42286754 TTAAAATTTA
*
42286764 AAAAATATAAAAATT
1 AAAAATA-ACAAATT
42286779 AAAAATAACAAATT
1 AAAAATAACAAATT
* *
42286793 -AAAGTACACAAACT
1 AAAAATA-ACAAATT
42286807 AAATCAGTATAA-AAATT
1 AAA--A--ATAACAAATT
42286824 AAAAATAACAAATT
1 AAAAATAACAAATT
42286838 AAA
1 AAA
42286841 GTATATAGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
13 9 0.18
14 20 0.40
15 10 0.20
17 8 0.16
18 1 0.02
19 2 0.04
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (14 bp):
AAAAATAACAAATT
Found at i:42294311 original size:17 final size:18
Alignment explanation
Indices: 42294277--42294312 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42294267 TTAGAATTAT
42294277 TATTTAGATTTATTTTAG
1 TATTTAGATTTATTTTAG
*
42294295 TATTTATATTT-TTTTAG
1 TATTTAGATTTATTTTAG
42294312 T
1 T
42294313 TTATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTTAGATTTATTTTAG
Found at i:42294332 original size:27 final size:28
Alignment explanation
Indices: 42294270--42294332 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
42294260 TCGACCCTTA
42294270 GAATTATTATTTAGATTTATTTTAGTATT
1 GAATT-TTATTTAGATTTATTTTAGTATT
* *
42294299 TATATTTT-TTTAG-TTTATTTTTGTACTT
1 GA-ATTTTATTTAGATTTATTTTAGTA-TT
42294327 GAATTT
1 GAATTT
42294333 GACAATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 15 0.52
28 8 0.28
29 3 0.10
30 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (28 bp):
GAATTTTATTTAGATTTATTTTAGTATT
Found at i:42296332 original size:51 final size:51
Alignment explanation
Indices: 42296256--42296355 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
42296246 ATCTGAAAAG
42296256 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
1 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
* * *
42296307 CTCCGATTAGAACTAGGGGAGAGAGATTGGAGAAGTAAGAGATAAGGCA
1 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCA
42296356 GTGGCTAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.33, T:0.15
Consensus pattern (51 bp):
CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
Found at i:42296798 original size:29 final size:29
Alignment explanation
Indices: 42296766--42296825 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
42296756 ATTATGAAAA
*
42296766 ATTGTAGAATAGTAACTTAATCATTTAAG
1 ATTGTAGAATAGTAACTTAACCATTTAAG
*
42296795 ATTGTATAATAGTAACTTAACCATTTAAG
1 ATTGTAGAATAGTAACTTAACCATTTAAG
42296824 AT
1 AT
42296826 AATTGGATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (29 bp):
ATTGTAGAATAGTAACTTAACCATTTAAG
Found at i:42301491 original size:27 final size:27
Alignment explanation
Indices: 42301461--42301524 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
42301451 TTGAAAGCTA
42301461 AATTTTATTTGT-TGAATTTTGTTGTTC
1 AATTTTATTTGTATGAA-TTTGTTGTTC
* *
42301488 AATTTT-TTTTTACTGCATTTGTTGTTC
1 AATTTTATTTGTA-TGAATTTGTTGTTC
42301515 AATTTTATTT
1 AATTTTATTT
42301525 TCAAATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 22 0.69
28 6 0.19
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (27 bp):
AATTTTATTTGTATGAATTTGTTGTTC
Found at i:42302025 original size:17 final size:18
Alignment explanation
Indices: 42302003--42302037 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42301993 GATTGAATCG
*
42302003 AATTTTTAT-TTTTTTAA
1 AATTTTAATATTTTTTAA
42302020 AATTTTAATATTTTTTAA
1 AATTTTAATATTTTTTAA
42302038 TTGAATTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTAATATTTTTTAA
Found at i:42309690 original size:29 final size:29
Alignment explanation
Indices: 42309648--42309706 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42309638 CCGTTACTTT
42309648 TTCTTAACTGGTTAGTAAAATAAGGTTAG
1 TTCTTAACTGGTTAGTAAAATAAGGTTAG
42309677 TTCTTAACTGGTTAGTAAAATAAGGTTAG
1 TTCTTAACTGGTTAGTAAAATAAGGTTAG
42309706 T
1 T
42309707 CAGAAAGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (29 bp):
TTCTTAACTGGTTAGTAAAATAAGGTTAG
Found at i:42311451 original size:21 final size:23
Alignment explanation
Indices: 42311427--42311476 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
42311417 TTTAAAAATT
*
42311427 AAAAAAATCCCA-AAAATT-ATA
1 AAAAAAAGCCCATAAAATTCATA
42311448 AAAAAAAGCCCATAAAATTCATA
1 AAAAAAAGCCCATAAAATTCATA
42311471 AAAAAA
1 AAAAAA
42311477 TAGCAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
22 6 0.23
23 9 0.35
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAAAGCCCATAAAATTCATA
Found at i:42311956 original size:22 final size:22
Alignment explanation
Indices: 42311923--42311968 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
42311913 AATTTAATCC
* *
42311923 TTTACTTTTCTTT-TTTTAAAA
1 TTTAATTTTCTTTCATTTAAAA
42311944 TTTAATTTATCTTTCATTTAAAA
1 TTTAATTT-TCTTTCATTTAAAA
42311967 TT
1 TT
42311969 CAAACCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATTTTCTTTCATTTAAAA
Found at i:42312949 original size:16 final size:17
Alignment explanation
Indices: 42312928--42312959 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42312918 TTTATTTTAA
42312928 TAAAAAT-TAATAAAAG
1 TAAAAATATAATAAAAG
42312944 TAAAAATATAATAAAA
1 TAAAAATATAATAAAA
42312960 TTTAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAAATATAATAAAAG
Found at i:42323714 original size:47 final size:47
Alignment explanation
Indices: 42323645--42323742 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
42323635 AAAGACATGC
* *
42323645 CAATTCATGACAAAATATGATTAATTCTTTTGTTTAAAGGGGAACTG
1 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
42323692 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
1 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
42323739 CAAT
1 CAAT
42323743 GCTTTAGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (47 bp):
CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
Found at i:42326303 original size:324 final size:324
Alignment explanation
Indices: 42325527--42326498 Score: 1786
Period size: 323 Copynumber: 3.0 Consensus size: 324
42325517 TTTTGTATGG
*
42325527 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGATCTAATAAAGTAGT
1 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
* *
42325592 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGGGTTCATACTTACAGGTACAATTATTAAAAAATA
66 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAAAA
* *
42325657 ATAATTACAGATATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
131 ACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
* *
42325722 ATATAAATCACAACAAGTTAAAAATTAAAAGCCTGTAAAAACCATCAA-TTTTTTAAAAAAATTT
196 ATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTTAAAAAAAATT
* *
42325786 AATTACGTTTTTATTCTTTTTTTCATTTAATTTAGTACTTAAACTTTCAATATGCATCAAAAAA
261 AATTACGTTTTTATTCTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
*
42325850 GCTTGTACAATACTGGAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
1 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
42325915 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAAAA
66 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATT-AAAAAAA
42325980 AACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTC
130 AACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTC
*
42326045 GATATAAATCACAATAGGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTTAAAAAAAAT
195 GATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTTAAAAAAAAT
*
42326110 TAATTACGTTTTTATTCTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGTATCAAAAAA
260 TAATTACGTTTTTATTCTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
42326175 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
1 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
*
42326240 TCATTTGATTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATT-AAAAAAA
66 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAAAA
42326304 ACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
131 ACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
*
42326369 ATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAATCATCAATTTTTTTAAAAAAAATT
196 ATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTTAAAAAAAATT
42326434 AATTACGTTTTTATTCTTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
261 AATTACGTTTTTATTC-TTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
42326499 ATCTTTAATT
Statistics
Matches: 629, Mismatches: 17, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
323 270 0.43
324 163 0.26
325 196 0.31
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (324 bp):
GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAAAA
ACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
ATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTTAAAAAAAATT
AATTACGTTTTTATTCTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
Found at i:42326761 original size:20 final size:19
Alignment explanation
Indices: 42326728--42326781 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
42326718 TTATAAAAAT
* *
42326728 TAAAAATCAATAAAATTTAT
1 TAAAAAT-ATTAAAATTTAA
* *
42326748 TCAAAATTATTAAATTTTAA
1 T-AAAAATATTAAAATTTAA
42326768 TAAAAATATTAAAA
1 TAAAAATATTAAAA
42326782 ATTAGAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 11 0.41
20 11 0.41
21 5 0.19
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATATTAAAATTTAA
Found at i:42332014 original size:12 final size:12
Alignment explanation
Indices: 42331997--42332021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42331987 AGTATATATA
42331997 TATTTTAAAATT
1 TATTTTAAAATT
42332009 TATTTTAAAATT
1 TATTTTAAAATT
42332021 T
1 T
42332022 TTAGTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:42340501 original size:2 final size:2
Alignment explanation
Indices: 42340494--42340530 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
42340484 AACAATTATG
*
42340494 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42340531 GTACTCCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:42344804 original size:3 final size:3
Alignment explanation
Indices: 42344796--42344830 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
42344786 GTTCTCTGAG
42344796 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
42344831 TTATTGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42346467 original size:2 final size:2
Alignment explanation
Indices: 42346460--42346485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42346450 CATGTCATCA
42346460 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
42346486 CATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42350056 original size:12 final size:13
Alignment explanation
Indices: 42350041--42350069 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42350031 TAATTTTAGA
42350041 AATAATTT-TTTT
1 AATAATTTATTTT
42350053 AATAATTTATTTT
1 AATAATTTATTTT
42350066 AATA
1 AATA
42350070 CAAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:42357040 original size:21 final size:20
Alignment explanation
Indices: 42357016--42357087 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
42357006 TTTAGTTCTC
* *
42357016 ATGAGCTTCTGTTTAACTCAT
1 ATGAGCTTCCGTTCAACTC-T
* *
42357037 ATGAGTTTCCGTTCAACCCT
1 ATGAGCTTCCGTTCAACTCT
* *
42357057 AATGAGTTTCCGTTCAGCTCT
1 -ATGAGCTTCCGTTCAACTCT
42357078 ATTGAGCTTC
1 A-TGAGCTTC
42357088 TGTTTAACCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (20 bp):
ATGAGCTTCCGTTCAACTCT
Found at i:42359919 original size:2 final size:2
Alignment explanation
Indices: 42359912--42359938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42359902 CCAGATTTGT
42359912 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
42359939 ACTTCCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42364330 original size:35 final size:36
Alignment explanation
Indices: 42364278--42364353 Score: 145
Period size: 35 Copynumber: 2.1 Consensus size: 36
42364268 TAAAATCAAA
42364278 ATTAAATTGTATAAATTATTTAGTTTAAAATAATTG
1 ATTAAATTGTATAAATTATTTAGTTTAAAATAATTG
42364314 ATTAAATTGTAT-AATTATTTAGTTTAAAATAATTG
1 ATTAAATTGTATAAATTATTTAGTTTAAAATAATTG
42364349 ATTAA
1 ATTAA
42364354 TAAATTCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 28 0.70
36 12 0.30
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (36 bp):
ATTAAATTGTATAAATTATTTAGTTTAAAATAATTG
Found at i:42364347 original size:18 final size:18
Alignment explanation
Indices: 42364291--42364347 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
42364281 AAATTGTATA
42364291 AATTATTTAGTTTAAAAT
1 AATTATTTAGTTTAAAAT
* *
42364309 AATTGATTAAATTGT---AT
1 AATT-ATTTAGTT-TAAAAT
42364326 AATTATTTAGTTTAAAAT
1 AATTATTTAGTTTAAAAT
42364344 AATT
1 AATT
42364348 GATTAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 1 0.03
16 6 0.20
17 6 0.20
18 10 0.33
19 6 0.20
20 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (18 bp):
AATTATTTAGTTTAAAAT
Found at i:42369096 original size:33 final size:35
Alignment explanation
Indices: 42369039--42369105 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
42369029 TTTAGCATTT
* *
42369039 AATTAATTTTTAAAAATTTAAAAAAT-ATATAAAAA
1 AATTAATTTTAAAAAAATTAAAAAATCAT-TAAAAA
42369074 AATT-ATTTTAAAAAAATT-AAAAATCATTAAAA
1 AATTAATTTTAAAAAAATTAAAAAATCATTAAAA
42369106 TTATTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 11 0.38
34 14 0.48
35 4 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (35 bp):
AATTAATTTTAAAAAAATTAAAAAATCATTAAAAA
Found at i:42370403 original size:34 final size:33
Alignment explanation
Indices: 42370358--42370448 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 33
42370348 GATTCTTTTT
* *
42370358 AAAAATAATTAAATTAGGTTTTTGGGGTTTTAAA-
1 AAAATTAATTAAATTAGGTTTAT--GGTTTTAAAG
*
42370392 TAAATTAATTAAATTAGAGTTTATGGTTTTAAAG
1 AAAATTAATTAAATTAG-GTTTATGGTTTTAAAG
42370426 AAAATTAATTAAATTATGGTTTA
1 AAAATTAATTAAATTA-GGTTTA
42370449 GTTTTTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
33 9 0.18
34 35 0.70
35 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGTTTATGGTTTTAAAG
Found at i:42370827 original size:126 final size:124
Alignment explanation
Indices: 42370517--42370907 Score: 465
Period size: 126 Copynumber: 3.2 Consensus size: 124
42370507 TTTTGTTTTT
* * * * *
42370517 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTTAGAATACGGTTCTGAAA-AGATAATGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAACAAATAGTGTAAAA
* * *
42370581 GACACTTTAAGTAGGATGCACTGTCAGAAAAATTACTGAAAAAAGCTCCCACGTGAACG--C
65 -ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTG-ACGCTC
* * *
42370641 ----TCTACAGTAGGTCCTGAAAAAATAA-TTTGAGAAGACAGTTCTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGT-AAAA
* * * ** **
42370701 ACGCTTCAAGCAAGATGCACTGTGAGCAAAATTACTGAAAAAAGCTCTTATATAGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGT-GACGCTC
*
42370762 TTTTTCTACAGTAGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGT-AAAA
* *
42370827 ACTCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGT-GACGCTC
*
42370888 TTTTTCTACAATAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
42370908 TTTGGCCTTA
Statistics
Matches: 223, Mismatches: 34, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
118 2 0.01
119 67 0.30
120 28 0.13
121 1 0.00
125 23 0.10
126 102 0.46
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTAAAAA
CACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGACGCTC
Found at i:42374050 original size:25 final size:25
Alignment explanation
Indices: 42373989--42374050 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
42373979 AGAACTAGTA
*
42373989 TTTTATTAAAAATATAAAAATAAAT
1 TTTTATTAAATATATAAAAATAAAT
** *
42374014 TACTATTAAA-ATATTAAAAATAACTT
1 TTTTATTAAATATA-TAAAAATAA-AT
42374040 TTTTATTAAAT
1 TTTTATTAAAT
42374051 GAAACAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.10
25 17 0.59
26 9 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATTAAATATATAAAAATAAAT
Found at i:42374117 original size:90 final size:91
Alignment explanation
Indices: 42373992--42374182 Score: 287
Period size: 93 Copynumber: 2.1 Consensus size: 91
42373982 ACTAGTATTT
*
42373992 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAAC-TT-TTTTATTAAATGAAA
1 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTATTTTATTAAATAAAA
*
42374055 CAATATAAAAACAATTTGTAAAAATA
66 CAATATAAAAACAATTTATAAAAATA
*
42374081 TATTAAAAATATAAAAAATAAATTACTATTAAAATATTAAAAATGACTTTTATTTTATTAAATAA
1 TATTAAAAATAT-AAAAATAAATTACTATTAAAATATTAAAAATAAC-TTTATTTTATTAAATAA
* * * *
42374146 AATAATATAAAATCAGTTTATACAAATA
64 AACAATATAAAAACAATTTATAAAAATA
42374174 TATTAAAAA
1 TATTAAAAA
42374183 AATCAATGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
89 12 0.13
90 33 0.36
92 2 0.02
93 44 0.48
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (91 bp):
TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTATTTTATTAAATAAAA
CAATATAAAAACAATTTATAAAAATA
Found at i:42376290 original size:11 final size:11
Alignment explanation
Indices: 42376264--42376303 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
42376254 ATAGAGCTTT
42376264 GAGAAATTTAGA
1 GAGAAATTT-GA
42376276 GAGAAATTTGA
1 GAGAAATTTGA
*
42376287 GAGAAAATTGA
1 GAGAAATTTGA
42376298 -AGAAAT
1 GAGAAAT
42376304 AATGTGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.23
Consensus pattern (11 bp):
GAGAAATTTGA
Found at i:42382094 original size:49 final size:49
Alignment explanation
Indices: 42382040--42382196 Score: 296
Period size: 49 Copynumber: 3.2 Consensus size: 49
42382030 AGTTATATTA
42382040 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
42382089 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
42382138 ATGTAATAAAATACTAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
42382187 ATGTAATAAA
1 ATGTAATAAA
42382197 GTATCTTACT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 106 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:42383991 original size:20 final size:20
Alignment explanation
Indices: 42383947--42383991 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42383937 TAATTAATTT
42383947 TTAAA-ATTTTAAAAAATAA
1 TTAAATATTTTAAAAAATAA
** *
42383966 AAAAATATTTTAAAAATTAA
1 TTAAATATTTTAAAAAATAA
42383986 TTAAAT
1 TTAAAT
42383992 GTTGACATGT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATATTTTAAAAAATAA
Found at i:42384540 original size:34 final size:34
Alignment explanation
Indices: 42384493--42384563 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
42384483 AAAAAAAAAA
*
42384493 AAAGGGGGAAAACTGAGCAACTAAGGGGGGGGAC
1 AAAGGGGGAAAACTGAGCAACTAAGGGGGGAGAC
* *
42384527 AAAGGGGGTAAACTGAGCAACTAAGGTGGGAGAC
1 AAAGGGGGAAAACTGAGCAACTAAGGGGGGAGAC
42384561 AAA
1 AAA
42384564 TTAAAACTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.39, T:0.08
Consensus pattern (34 bp):
AAAGGGGGAAAACTGAGCAACTAAGGGGGGAGAC
Found at i:42391031 original size:9 final size:9
Alignment explanation
Indices: 42390974--42391038 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
42390964 AGTTACTTAT
42390974 AAATTACTAA
1 AAATTA-TAA
*
42390984 AAATGATAA
1 AAATTATAA
42390993 GAAATTATAA
1 -AAATTATAA
* *
42391003 ACATT-TTA
1 AAATTATAA
42391011 AAATTAATTAA
1 AAATT-A-TAA
42391022 AAATTATAA
1 AAATTATAA
42391031 AAATTATA
1 AAATTATA
42391039 TTAAAGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
9 18 0.40
10 14 0.31
11 7 0.16
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:42392273 original size:38 final size:38
Alignment explanation
Indices: 42392171--42392297 Score: 157
Period size: 38 Copynumber: 3.3 Consensus size: 38
42392161 ATATCATGTA
* **
42392171 AATAGTAGACATGTTTAACATGTATTCAGTTCAACAGT
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
** *
42392209 AGCATTAGACATGCTTAACATGTATTTGGTTCAACA-T
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
*
42392246 CAATAGTAGACATGCTTAACATGTATTTGGTTTAACAGT
1 -AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
* *
42392285 ATTAGTAGGCATG
1 AATAGTAGACATG
42392298 TTGAATATGC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 73 0.97
39 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (38 bp):
AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
Found at i:42396884 original size:32 final size:32
Alignment explanation
Indices: 42396843--42396904 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
42396833 CAAATGATGA
*
42396843 ACCTTGGTATTTCTGCAATTTAGCCAGGTAGT
1 ACCTTGGTATTTCTGCAATTTAACCAGGTAGT
42396875 ACCTTGGTATTTCTGCAATTTAACCAGGTA
1 ACCTTGGTATTTCTGCAATTTAACCAGGTA
42396905 AGTTCATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (32 bp):
ACCTTGGTATTTCTGCAATTTAACCAGGTAGT
Found at i:42402115 original size:13 final size:13
Alignment explanation
Indices: 42402063--42402115 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
42402053 TCTAAACCAA
42402063 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42402076 A-TTTCTTAAAAGC
1 ACTTT-TCAAAAGC
* *
42402089 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
42402102 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
42402115 A
1 A
42402116 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42403663 original size:23 final size:23
Alignment explanation
Indices: 42403637--42403680 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
42403627 ATTTTAGCAC
42403637 ATCAAAGCATTAATGTCTTCCCA
1 ATCAAAGCATTAATGTCTTCCCA
42403660 ATCAAAGCATTAATGTCTTCC
1 ATCAAAGCATTAATGTCTTCC
42403681 TAATTTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (23 bp):
ATCAAAGCATTAATGTCTTCCCA
Found at i:42422977 original size:15 final size:16
Alignment explanation
Indices: 42422946--42422977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42422936 GATATGCATA
42422946 AAAATTTTAAGAAATT
1 AAAATTTTAAGAAATT
42422962 AAAATTTTAA-AAATT
1 AAAATTTTAAGAAATT
42422977 A
1 A
42422978 TTTAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAGAAATT
Found at i:42423244 original size:18 final size:18
Alignment explanation
Indices: 42423212--42423246 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42423202 AACGAATAAA
42423212 ATAACAAATTAAAAATAT
1 ATAACAAATTAAAAATAT
42423230 ATAA-AAATTATAAAATA
1 ATAACAAATTA-AAAATA
42423247 ATTTAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAACAAATTAAAAATAT
Found at i:42429291 original size:15 final size:17
Alignment explanation
Indices: 42429264--42429298 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
42429254 AATTTCAGTA
42429264 ATTATTGTTATTTC-TC
1 ATTATTGTTATTTCTTC
42429280 ATTATT-TTATTTCTTC
1 ATTATTGTTATTTCTTC
42429296 ATT
1 ATT
42429299 TATCTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTGTTATTTCTTC
Found at i:42447476 original size:15 final size:15
Alignment explanation
Indices: 42447452--42447498 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
42447442 ATCTACGTAT
42447452 AATA-AATTATTTAA
1 AATATAATTATTTAA
* *
42447466 AATATATTTATTTCA
1 AATATAATTATTTAA
*
42447481 AATATAATAATTTAA
1 AATATAATTATTTAA
42447496 AAT
1 AAT
42447499 TATGAAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATAATTATTTAA
Found at i:42462796 original size:40 final size:40
Alignment explanation
Indices: 42462655--42462789 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
42462645 GACTTCGAGT
* * *
42462655 CGATGAGACATTGGGTGTCAAATTATTACTTCGAATATATT
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAAT-TATC
* * ** *
42462696 CGATGAGGCACTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
** *
42462733 TAATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
*
42462773 CGATAAGGCACTGGGTG
1 CGATGAGGCACTGGGTG
42462790 CTAAATTGGT
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
37 15 0.21
38 12 0.17
39 2 0.03
40 28 0.39
41 14 0.20
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:42463442 original size:13 final size:13
Alignment explanation
Indices: 42463424--42463448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42463414 TTAAATGATA
42463424 TTTTGATGATATG
1 TTTTGATGATATG
42463437 TTTTGATGATAT
1 TTTTGATGATAT
42463449 AATTGTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
TTTTGATGATATG
Found at i:42466963 original size:117 final size:118
Alignment explanation
Indices: 42466808--42467046 Score: 471
Period size: 117 Copynumber: 2.0 Consensus size: 118
42466798 TAAAAAATGT
42466808 CAAACTTTGGTCCAAAAATAAATATAAAAAGTATATTATTTATATTAATATTAATATTAATATTA
1 CAAACTTTGGTCCAAAAATAAATATAAAAAGTATATTATTTATATTAATATTAATATTAATATTA
42466873 TAAATTTTATAATTAAATTTAAATAAATAAAATAATCCTATTTTTAAATCAGA
66 TAAATTTTATAATTAAATTTAAATAAATAAAATAATCCTATTTTTAAATCAGA
42466926 CAAACTTTGGTCC-AAAATAAATATAAAAAGTATATTATTTATATTAATATTAATATTAATATTA
1 CAAACTTTGGTCCAAAAATAAATATAAAAAGTATATTATTTATATTAATATTAATATTAATATTA
42466990 TAAATTTTATAATTAAATTTAAATAAATAAAATAATCCTATTTTTAAATCAGA
66 TAAATTTTATAATTAAATTTAAATAAATAAAATAATCCTATTTTTAAATCAGA
42467043 CAAA
1 CAAA
42467047 AAAAATTTCA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 108 0.89
118 13 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (118 bp):
CAAACTTTGGTCCAAAAATAAATATAAAAAGTATATTATTTATATTAATATTAATATTAATATTA
TAAATTTTATAATTAAATTTAAATAAATAAAATAATCCTATTTTTAAATCAGA
Found at i:42468069 original size:152 final size:152
Alignment explanation
Indices: 42467686--42468646 Score: 1179
Period size: 152 Copynumber: 6.3 Consensus size: 152
42467676 TTTTTGCCTC
* * * * * *
42467686 TGTTGGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATAATATTTTCTAATTTTTTTATT
1 TGTTCGTATTTTTTTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTATT
* * * *
42467751 TTATATTATTTTAGTACATTATATTTTAAATTTATTAATTTAGTGTGTTTTTTAAATAAA-TTAA
66 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTAA
*
42467815 AAAAATCT-TTATTTCGGCCATT
130 AAAAAACTCTTATTTCGGCCATT
* * * * * *
42467837 TATTTGTATTTTTTTCTCGGCTTTTATTACTTTCAATAAAAATATACTATTTTCTAATTTTCTAA
1 TGTTCGTATTTTTTTCCCGGATTTTATTACTTT-AA-AAAAATATACTATTTTCTAATTTTATTA
* *
42467902 TTTTACATTATTTTAGTACATCAAGTTTGAAATGTATTAATTTA-GTGTTTTTTAAATAAATTTA
64 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTA
*
42467966 AAAAAAACTCTTATTTCAGCCATT
129 AAAAAAACTCTTATTTCGGCCATT
* *
42467990 TGTTCGTATTTTTTTCCCCAGAGTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
1 TGTTCGTATTTTTTT-CCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
* *
42468055 TTTACATTATTTTAGTACATGATGTTTGAAATGTATTAATTTACTGCGTTTTTTAAATAAATTT-
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
* *
42468119 -AAAAAA-TCATTATTTCGTCCCTT
129 AAAAAAACTC-TTATTTCGGCCATT
* * *
42468142 TGTTCGTATTTTTTTCCCCGAATTTTATTACTTT-AAAAAATATAATATTTCCTAATTTTATTAT
1 TGTTCGTATTTTTTT-CCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
*
42468206 TTTACATTATCTTAGTACATTATGTTTGAAATGTATTAATTTACTGTG-TTTTTAAATAAATTTA
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
*
42468270 AAAAAAACTATTATTTCGGTCC-TT
129 AAAAAAACTCTTATTTCGG-CCATT
* * * * *
42468294 TGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAAC-ATTTTATTATTTTAATAT
1 TGTTCGTATTTTTTTCCCGGATTTTATTACTTTAAAAAAATAT-ACTATTTTCTAATTTTATTAT
* * *
42468358 TTTACATTATTTTAGTTCATTATGTTTGAAATGTATTAATTTACTGTATTTTTTAAATAAATTTT
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
* * *
42468423 AAAAAAACCCTTATTTCGGTCTTT
129 AAAAAAACTCTTATTTCGGCCATT
** * *
42468447 TGTTCGTATTTTTTTCCTTGATTTTATTACTTTTAAAAAAA-ATATTATTTTATAATTTTATTAT
1 TGTTCGTATTTTTTTCCCGGATTTTATTAC-TTTAAAAAAATATACTATTTTCTAATTTTATTAT
*
42468511 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTGTTTTTAAATAAACTT
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGT-TTTTTAAATAAA---
** * *
42468576 TTTAAAAAAAAAAACTTATTTTGGCCCTT
125 TTT-AAAAAAAACTCTTATTTCGGCCATT
* * *
42468605 TGTTCATATTTTTTTACCGGACTTTATTACTTTGAATAAAAA
1 TGTTCGTATTTTTTTCCCGGATTTTATTACTTT-AA-AAAAA
42468647 CACACACTAA
Statistics
Matches: 709, Mismatches: 76, Indels: 42
0.86 0.09 0.05
Matches are distributed among these distances:
150 15 0.02
151 136 0.19
152 229 0.32
153 219 0.31
154 53 0.07
157 6 0.01
158 46 0.06
159 5 0.01
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (152 bp):
TGTTCGTATTTTTTTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTATT
TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTAAA
AAAAACTCTTATTTCGGCCATT
Found at i:42468276 original size:305 final size:301
Alignment explanation
Indices: 42467681--42468646 Score: 1211
Period size: 305 Copynumber: 3.1 Consensus size: 301
42467671 TCGTATTTTT
* * * * * *
42467681 GCCTCTGTTGGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATAATATTTTCTAATTTTT
1 GCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTA
* * * * *
42467746 TTATTTTATATTATTTTAGTACATTATATTTTAAATTTATTAATTTAGTGTGTTTTTTAAATAAA
66 TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
* * * * * *
42467811 TTAAAAAAATCTTTATTTCGGCCATTTATTTGTATTTTTTT-CTCGGCTTTTATTACTTTCAATA
131 TTTAAAAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTC-GATTTTATTACTTT--A-A
* * * * *
42467875 AAAATATACTATTTTCTAATTTTCTAATTTTACATTATTTTAGTACATCAAGTTTGAAATGTATT
192 AAAATATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATT
*
42467940 AATTTAGTGT-TTTTTAAATAAATTTAAAAAAAACTCTTATTTCA
257 AATTTAGTGTGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCG
*
42467984 GCCATTTGTTCGTATTTTTTTCCCCAGAGTTTATTACTTTAAAAAAATATACTATTTTCTAATTT
1 GCC-TTTGTTCGTATTTTTTT-CCCAGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTT
* *
42468049 TATTATTTTACATTATTTTAGTACATGATGTTTGAAATGTATTAATTTACTGCGTTTTTTAAATA
64 TATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATA
* *
42468114 AATTTAAAAAATCATTATTTCGTCCCTTTGTTCGTATTTTTTTCCCCGAATTTTATTACTTTAAA
129 AATTTAAAAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTCG-ATTTTATTACTTTAAA
* *
42468179 AAATATAATATTTCCTAATTTTATTATTTTACATTATCTTAGTACATTATGTTTGAAATGTATTA
193 AAATATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
* *
42468244 ATTTACTGTGTTTTTAAATAAATTTAAAAAAAACTATTATTTCG
258 ATTTAGTGTGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCG
* * * * *
42468288 GTCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAAC-ATTTTATTATTT
1 G-CCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTAAAAAAATAT-ACTATTTTCTAATTT
* * *
42468352 TAATATTTTACATTATTTTAGTTCATTATGTTTGAAATGTATTAATTTACTGTATTTTTTAAATA
64 TATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATA
* * * *
42468417 AATTTTAAAAAAACCCTTATTTCGGT-CTTTTGTTCGTATTTTTTTCCTTGATTTTATTACTTTT
129 AA-TTT-AAAAAATCATTATTTC-GTCCATTTGTTCGTATTTTTTTCCTCGATTTTATTAC-TTT
* * *
42468481 AAAAAAAATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTA
190 AAAAAATATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTA
* ** *
42468546 TTCATTTAGTGTGTGTTTTTAAATAAACTTTTTAAAAAAAAAAACTTATTTTG
255 TTAATTTA--GTGTGTTTTTAAATAAA---TTT-AAAAAAAACTCTTATTTCG
* * * *
42468599 GCCCTTTGTTCATATTTTTTTACCGGACTTTATTACTTTGAATAAAAA
1 G-CCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTT-AA-AAAAA
42468647 CACACACTAA
Statistics
Matches: 579, Mismatches: 65, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
303 167 0.29
304 81 0.14
305 241 0.42
306 16 0.03
307 16 0.03
310 3 0.01
311 49 0.08
312 1 0.00
313 5 0.01
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (301 bp):
GCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTA
TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
TTTAAAAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTCGATTTTATTACTTTAAAAAA
TATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
TAGTGTGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCG
Found at i:42482228 original size:11 final size:11
Alignment explanation
Indices: 42482214--42482249 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
42482204 AGCCCGGCCC
42482214 ATATTAAATAT
1 ATATTAAATAT
42482225 ATATTAAATAT
1 ATATTAAATAT
42482236 ATA-T-AATAT
1 ATATTAAATAT
42482245 ATATT
1 ATATT
42482250 TGATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:42484369 original size:20 final size:20
Alignment explanation
Indices: 42484325--42484388 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
42484315 TCTTAGATTT
* *
42484325 TTATGTTTTATATATATTATT
1 TTATGTTATA-ATATATTATA
*
42484346 TTAT-TATATAATATAATATA
1 TTATGT-TATAATATATTATA
*
42484366 TTATGTTATATTATATTATA
1 TTATGTTATAATATATTATA
42484386 TTA
1 TTA
42484389 AATAAACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTATGTTATAATATATTATA
Found at i:42484374 original size:5 final size:5
Alignment explanation
Indices: 42484332--42484388 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
42484322 TTTTTATGTT
* *
42484332 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATG TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
42484381 TTATA TTA
1 TTATA TTA
42484389 AATAAACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 30 0.70
7 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:42485425 original size:21 final size:21
Alignment explanation
Indices: 42485377--42485460 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
42485367 TTTGCCGATA
*
42485377 AGGCACTTTATGTGTCGTTTCTC
1 AGGCACTTTATGTGTCG--TATC
*
42485400 AGGCACTTTATGTGTCGTAGC
1 AGGCACTTTATGTGTCGTATC
* ** *
42485421 AGGCACCTCGTGTGTCGTTTC
1 AGGCACTTTATGTGTCGTATC
*
42485442 AGGAAC-TTATGTGTCGTAT
1 AGGCACTTTATGTGTCGTAT
42485461 ACTGATCAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 10 0.20
21 23 0.46
23 17 0.34
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (21 bp):
AGGCACTTTATGTGTCGTATC
Found at i:42489764 original size:197 final size:198
Alignment explanation
Indices: 42489420--42489814 Score: 783
Period size: 197 Copynumber: 2.0 Consensus size: 198
42489410 AATATAAAAT
42489420 TTAAATACAAATGTAATATATGTATTAAATAACCATATATTATATTTTTACTTAACATATGGCAT
1 TTAAATACAAATGTAATATATGTATTAAATAACCATATATTATATTTTTACTTAACATATGGCAT
42489485 ATTTTTGTATTTTTCTATCAAATTCAAAATTATTGAACATGTTAATAAGGCTTTAATTTAGTTGG
66 ATTTTTGTATTTTTCTATCAAATTCAAAATTATTGAACATGTTAATAAGGCTTTAATTTAGTTGG
42489550 CCATCAAAGTTTGAGACTCACCATGACAATTAGATGTGTGGGTCTTTGAGTTTCATCGTGTATGG
131 CCATCAAAGTTTGAGACTCACCATGACAATTAGATGTGTGGGTCTTTGAGTTTCATCGTGTATGG
42489615 TTG
196 TTG
42489618 TTAAATAC-AATGTAATATATGTATTAAATAACCATATATTATATTTTTACTTAACATATGGCAT
1 TTAAATACAAATGTAATATATGTATTAAATAACCATATATTATATTTTTACTTAACATATGGCAT
42489682 ATTTTTGTATTTTTCTATCAAATTCAAAATTATTGAACATGTTAATAAGGCTTTAATTTAGTTGG
66 ATTTTTGTATTTTTCTATCAAATTCAAAATTATTGAACATGTTAATAAGGCTTTAATTTAGTTGG
42489747 CCATCAAAGTTTGAGACTCACCATGACAATTAGATGTGTGGGTCTTTGAGTTTCATCGTGTATGG
131 CCATCAAAGTTTGAGACTCACCATGACAATTAGATGTGTGGGTCTTTGAGTTTCATCGTGTATGG
42489812 TTG
196 TTG
42489815 CTATATGTAG
Statistics
Matches: 197, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 189 0.96
198 8 0.04
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (198 bp):
TTAAATACAAATGTAATATATGTATTAAATAACCATATATTATATTTTTACTTAACATATGGCAT
ATTTTTGTATTTTTCTATCAAATTCAAAATTATTGAACATGTTAATAAGGCTTTAATTTAGTTGG
CCATCAAAGTTTGAGACTCACCATGACAATTAGATGTGTGGGTCTTTGAGTTTCATCGTGTATGG
TTG
Found at i:42493578 original size:18 final size:18
Alignment explanation
Indices: 42493555--42493599 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42493545 TTTCTTCATA
42493555 TATAAATTCTGGAATTTT
1 TATAAATTCTGGAATTTT
* *
42493573 TATAAATATTTTGAATTTT
1 TATAAAT-TCTGGAATTTT
*
42493592 TAAAAATT
1 TATAAATT
42493600 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TATAAATTCTGGAATTTT
Found at i:42493592 original size:20 final size:20
Alignment explanation
Indices: 42493566--42493612 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
42493556 ATAAATTCTG
42493566 GAATTTTTATAAA-TATTTT
1 GAATTTTTATAAATTATTTT
*
42493585 GAATTTTTAAAAATTATTTT
1 GAATTTTTATAAATTATTTT
42493605 GAATTTTT
1 GAATTTTT
42493613 TTTAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
GAATTTTTATAAATTATTTT
Found at i:42494208 original size:2 final size:2
Alignment explanation
Indices: 42494201--42494243 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42494191 NNNNNNNNNN
42494201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42494243 T
1 T
42494244 GAAAAGGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42497297 original size:14 final size:14
Alignment explanation
Indices: 42497278--42497308 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
42497268 CAGACTAATT
42497278 TAAAATAAATATTA
1 TAAAATAAATATTA
42497292 TAAAATAAATATTA
1 TAAAATAAATATTA
42497306 TAA
1 TAA
42497309 GTTAGAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAAATATTA
Found at i:42500271 original size:22 final size:23
Alignment explanation
Indices: 42500228--42500271 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
42500218 TTAACTTAAA
*
42500228 TTTAATACTTAATTACTTAATTT
1 TTTAATACTTAATTACTAAATTT
*
42500251 TTTAATAC-TACTTACTAAATT
1 TTTAATACTTAATTACTAAATT
42500272 ATTGTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATACTTAATTACTAAATTT
Found at i:42506967 original size:5 final size:5
Alignment explanation
Indices: 42506957--42506981 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42506947 GAGACGAACA
42506957 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
42506982 AAATATTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:42508651 original size:39 final size:38
Alignment explanation
Indices: 42508592--42508668 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 38
42508582 CAATTACTTA
* *
42508592 AATTTTGATTTCAAATTATTTATTTTTGAATGTTATAT
1 AATTTTGATTTCAAAATATTTATTTTTGAATATTATAT
*
42508630 AATTTATGATTTTAAAATATTTATTTTTGAATATTATAT
1 AATTT-TGATTTCAAAATATTTATTTTTGAATATTATAT
42508669 GTTTTAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (38 bp):
AATTTTGATTTCAAAATATTTATTTTTGAATATTATAT
Found at i:42535138 original size:30 final size:32
Alignment explanation
Indices: 42535090--42535154 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
42535080 CTAATCTAAA
* *
42535090 TTTATTATTTAATATTAAA-AATAATA-TTTAT
1 TTTATAATTAAATATTAAATAA-AATATTTTAT
42535121 TTTATAATTAAAT-TTAAATAAAATATTTTAT
1 TTTATAATTAAATATTAAATAAAATATTTTAT
42535152 TTT
1 TTT
42535155 TTATTTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTTATAATTAAATATTAAATAAAATATTTTAT
Found at i:42552262 original size:20 final size:20
Alignment explanation
Indices: 42552226--42552263 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42552216 TATATATAGG
*
42552226 TATGTAAACAAATTATAAAC
1 TATGTAAACAAAATATAAAC
42552246 TATGTATAA-AAAATATAA
1 TATGTA-AACAAAATATAA
42552264 GGGTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TATGTAAACAAAATATAAAC
Found at i:42552341 original size:37 final size:37
Alignment explanation
Indices: 42552295--42552365 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
42552285 AAATATGTAC
*
42552295 GTATCTATGTATATATATATGTATAAATTACAAAAAT
1 GTATCTATGTATATATATATATATAAATTACAAAAAT
* *
42552332 GTATGTATGTATATATGTATATATAAATTACAAA
1 GTATCTATGTATATATATATATATAAATTACAAA
42552366 GTATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (37 bp):
GTATCTATGTATATATATATATATAAATTACAAAAAT
Found at i:42554545 original size:17 final size:17
Alignment explanation
Indices: 42554523--42554558 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42554513 ATGAGATTTC
42554523 TCAATTACAAAAGGACT
1 TCAATTACAAAAGGACT
42554540 TCAATTACAAAAGGACT
1 TCAATTACAAAAGGACT
42554557 TC
1 TC
42554559 GAAGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (17 bp):
TCAATTACAAAAGGACT
Found at i:42555992 original size:25 final size:25
Alignment explanation
Indices: 42555943--42555992 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42555933 CACAAATTGC
**
42555943 AAGTCTGCTTCTAATAGCATGTTTT
1 AAGTCTGCTTCTAATAGCACATTTT
*
42555968 AAGTCTGCTTCTGATAGCACATTTT
1 AAGTCTGCTTCTAATAGCACATTTT
42555993 TGAATCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
AAGTCTGCTTCTAATAGCACATTTT
Found at i:42558448 original size:25 final size:26
Alignment explanation
Indices: 42558420--42558468 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
42558410 ATTTAATATA
42558420 AAAATTATAATA-TATAAAG-AAAAGG
1 AAAA-TATAATATTATAAAGTAAAAGG
*
42558445 AAAATATCATATTATAAAGTAAAA
1 AAAATATAATATTATAAAGTAAAA
42558469 AATAAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAATATAATATTATAAAGTAAAAGG
Found at i:42558819 original size:30 final size:30
Alignment explanation
Indices: 42558783--42558842 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
42558773 TTGTTGCCTA
*
42558783 AGTTTCTTCCATATTCATCTATGGAACATG
1 AGTTTCTTCCATATTCATCTATGAAACATG
*
42558813 AGTTTCTTCCATATTCATGTATGAAACATG
1 AGTTTCTTCCATATTCATCTATGAAACATG
42558843 TTCCTTGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (30 bp):
AGTTTCTTCCATATTCATCTATGAAACATG
Found at i:42564210 original size:17 final size:17
Alignment explanation
Indices: 42564188--42564234 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
42564178 AAAAAGTATT
*
42564188 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
42564205 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
42564222 ATAAATATATTTA
1 TTAAAAATATTTA
42564235 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:42570795 original size:13 final size:13
Alignment explanation
Indices: 42570777--42570801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42570767 GCAGATACAA
42570777 ATATACAGAACAG
1 ATATACAGAACAG
42570790 ATATACAGAACA
1 ATATACAGAACA
42570802 TACCCCCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
ATATACAGAACAG
Found at i:42574533 original size:23 final size:23
Alignment explanation
Indices: 42574507--42574582 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
42574497 GACATTAGAA
42574507 TAAAATTTTATTTATATTATAAT
1 TAAAATTTTATTTATATTATAAT
* *
42574530 TAAAATTTGAATATTAAATTAT-AT
1 TAAAATTT-TAT-TTATATTATAAT
*
42574554 T-AAATTATAGTTT-TATTATAAT
1 TAAAATTTTA-TTTATATTATAAT
*
42574576 TTAAATT
1 TAAAATT
42574583 ATTGAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.12
22 6 0.14
23 19 0.44
24 5 0.12
25 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
TAAAATTTTATTTATATTATAAT
Found at i:42576574 original size:10 final size:10
Alignment explanation
Indices: 42576559--42576583 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42576549 TTGGAGAAGT
42576559 TTTTTTTTTC
1 TTTTTTTTTC
42576569 TTTTTTTTTC
1 TTTTTTTTTC
42576579 TTTTT
1 TTTTT
42576584 GGGGTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:42577044 original size:2 final size:2
Alignment explanation
Indices: 42577039--42577073 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42577029 TTAATCATTT
42577039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42577074 TAATGTGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42585892 original size:23 final size:22
Alignment explanation
Indices: 42585866--42585910 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
42585856 GCCCACTACC
*
42585866 CAAACTTAACCCTAAACCCAAAA
1 CAAACATAACCCT-AACCCAAAA
*
42585889 CAAACATAACCCTAGCCCAAAA
1 CAAACATAACCCTAACCCAAAA
42585911 TTAACCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.51, C:0.36, G:0.02, T:0.11
Consensus pattern (22 bp):
CAAACATAACCCTAACCCAAAA
Found at i:42590480 original size:18 final size:17
Alignment explanation
Indices: 42590437--42590471 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42590427 ATGTGATTTA
42590437 TAAAATTTTAAATATAT
1 TAAAATTTTAAATATAT
42590454 TAAAATTTTAAATATAT
1 TAAAATTTTAAATATAT
42590471 T
1 T
42590472 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTTTAAATATAT
Found at i:42590530 original size:20 final size:20
Alignment explanation
Indices: 42590459--42590543 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
42590449 TATATTAAAA
42590459 TTTTAAATATATTTT-TAATT
1 TTTTAAATA-ATTTTATAATT
* * *
42590479 TTTTTAGTGAATTGTAT-ATGT
1 TTTTAAAT-AATTTTATAAT-T
*
42590500 TTTT--GTAATTTTATAATT
1 TTTTAAATAATTTTATAATT
42590518 TTTTAAATAATTTTAGTAAATT
1 TTTTAAATAATTTTA-T-AATT
42590540 TTTT
1 TTTT
42590544 GTAACTTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
18 12 0.23
19 4 0.08
20 20 0.38
21 8 0.15
22 8 0.15
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTAAATAATTTTATAATT
Found at i:42591143 original size:20 final size:20
Alignment explanation
Indices: 42591108--42591184 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 20
42591098 CTTTATATAT
*
42591108 ATTTTAGAATTTTTTTTGAAA
1 ATTTTATAA-TTTTTTTGAAA
*
42591129 ATTTTATAA-TTTTTTAAAA
1 ATTTTATAATTTTTTTGAAA
* *
42591148 AATATA-AATTTTTTTG-AA
1 ATTTTATAATTTTTTTGAAA
* * *
42591166 TTTTTATAAATATTTTGAA
1 ATTTTATAATTTTTTTGAA
42591185 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
18 7 0.16
19 27 0.63
20 1 0.02
21 8 0.19
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTATAATTTTTTTGAAA
Found at i:42591195 original size:19 final size:21
Alignment explanation
Indices: 42591150--42591209 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
42591140 TTTTAAAAAA
**
42591150 TATAAATTTTTTTGAA-TTTT
1 TATAAATCATTTTGAATTTTT
42591170 TATAAAT-ATTTTGAATTTTT
1 TATAAATCATTTTGAATTTTT
*
42591190 TA-AAATCAATTT-AATTTTT
1 TATAAATCATTTTGAATTTTT
42591209 T
1 T
42591210 TTTGTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (21 bp):
TATAAATCATTTTGAATTTTT
Found at i:42591681 original size:10 final size:10
Alignment explanation
Indices: 42591666--42591712 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
42591656 TTCTCTATAT
42591666 ATTTTTTAGA
1 ATTTTTTAGA
*
42591676 ATTTTTTGAAA
1 ATTTTTT-AGA
*
42591687 ATTTTATA-A
1 ATTTTTTAGA
42591696 ATTTTTT-GA
1 ATTTTTTAGA
42591705 ATTTTTTA
1 ATTTTTTA
42591713 AAATCAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 15 0.48
10 8 0.26
11 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
ATTTTTTAGA
Found at i:42591725 original size:29 final size:30
Alignment explanation
Indices: 42591661--42591731 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
42591651 TAACTTTCTC
* *
42591661 TATATATTTTTTAGAATTTTTTGAAAATTT
1 TATAAATTTTTTAGAATTTTTTGAAAATAT
42591691 TATAAATTTTTT-GAATTTTTT-AAAATCAAT
1 TATAAATTTTTTAGAATTTTTTGAAAAT--AT
42591721 T-TAAATTTTTT
1 TATAAATTTTTT
42591732 TTGTAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.14
29 19 0.51
30 13 0.35
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (30 bp):
TATAAATTTTTTAGAATTTTTTGAAAATAT
Found at i:42595790 original size:20 final size:20
Alignment explanation
Indices: 42595765--42595826 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
42595755 TTTTTGGTTA
*
42595765 AAAATTACCCCAATTACCCG
1 AAAATTACCCAAATTACCCG
*
42595785 AAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCG
42595805 AAAATTACCCAAATTACCCG
1 AAAATTACCCAAATTACCCG
42595825 AA
1 AA
42595827 TTACCTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (20 bp):
AAAATTACCCAAATTACCCG
Found at i:42595836 original size:9 final size:9
Alignment explanation
Indices: 42595767--42595838 Score: 81
Period size: 9 Copynumber: 7.6 Consensus size: 9
42595757 TTTGGTTAAA
*
42595767 AATTACCCC
1 AATTACCCG
42595776 AATTACCCG
1 AATTACCCG
42595785 AAAATTACCCG
1 --AATTACCCG
42595796 AATTACCCG
1 AATTACCCG
*
42595805 AAAATTACCCA
1 --AATTACCCG
42595816 AATTACCCG
1 AATTACCCG
*
42595825 AATTACCTG
1 AATTACCCG
42595834 AATTA
1 AATTA
42595839 AATCACTACA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
9 38 0.69
11 17 0.31
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:42595880 original size:37 final size:37
Alignment explanation
Indices: 42595839--42595951 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
42595829 ACCTGAATTA
* *
42595839 AATCACTACATGATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
42595876 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
42595913 AATCACTACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
42595949 AAT
1 AAT
42595952 TAACACATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 6 0.08
37 66 0.92
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:42595887 original size:20 final size:20
Alignment explanation
Indices: 42595862--42595925 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
42595852 TTAAAAACAT
42595862 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
42595882 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
42595899 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
42595919 TACATAA
1 TACATAA
42595926 TTAAAAACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:42595904 original size:17 final size:17
Alignment explanation
Indices: 42595882--42595942 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
42595872 TTTGAATCAC
42595882 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
42595899 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
42595919 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
42595936 TACATAA
1 TACATAA
42595943 GTCTTGAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 5 0.16
20 8 0.25
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:42598653 original size:8 final size:8
Alignment explanation
Indices: 42598626--42598662 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
42598616 GGGTCTAGGT
42598626 ACTCGGCG
1 ACTCGGCG
*
42598634 ACTCCGGTG
1 ACT-CGGCG
42598643 ACTCGGCG
1 ACTCGGCG
42598651 ACTCGGCG
1 ACTCGGCG
42598659 ACTC
1 ACTC
42598663 CCGATTCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.14, C:0.38, G:0.32, T:0.16
Consensus pattern (8 bp):
ACTCGGCG
Found at i:42605763 original size:21 final size:21
Alignment explanation
Indices: 42605712--42605765 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
42605702 ATTTTTAGTA
*
42605712 AATA-TAATTTTTATATGTGT
1 AATATTAATTTTTATATGAGT
*
42605732 AATATTTATTTTTATATGAGT
1 AATATTAATTTTTATATGAGT
* *
42605753 -GTATTAAATTTTA
1 AATATTAATTTTTA
42605766 GTATTCTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
AATATTAATTTTTATATGAGT
Found at i:42606048 original size:20 final size:20
Alignment explanation
Indices: 42606011--42606048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42606001 TAAATATAAT
*
42606011 TTTTTATATGTGTATATTTA
1 TTTTTATATGAGTATATTTA
*
42606031 TTTTTATATGAGTGTATT
1 TTTTTATATGAGTATATT
42606049 AAATTTTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (20 bp):
TTTTTATATGAGTATATTTA
Found at i:42606055 original size:20 final size:20
Alignment explanation
Indices: 42606012--42606056 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42606002 AAATATAATT
* * *
42606012 TTTTATATGTGTATATTTAT
1 TTTTATATGAGTATATTAAA
*
42606032 TTTTATATGAGTGTATTAAA
1 TTTTATATGAGTATATTAAA
42606052 TTTTA
1 TTTTA
42606057 GTATTCTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (20 bp):
TTTTATATGAGTATATTAAA
Found at i:42606209 original size:291 final size:291
Alignment explanation
Indices: 42605685--42606266 Score: 1148
Period size: 291 Copynumber: 2.0 Consensus size: 291
42605675 TTTTATTTAT
42605685 AAAATCAGAATATCATTATTTTTAGTAAATATAATTTTTATATGTGTAATATTTATTTTTATATG
1 AAAATCAGAATATCATTATTTTTAGTAAATATAATTTTTATATGTGTAATATTTATTTTTATATG
42605750 AGTGTATTAAATTTTAGTATTCTATATTATAGTATGTTCATTTGAAATGATTATTTGAAATATTT
66 AGTGTATTAAATTTTAGTATTCTATATTATAGTATGTTCATTTGAAATGATTATTTGAAATATTT
42605815 CACATATAAAAATATTTGAAATATTGTACCCACAATGTAGATGAAAAAACAACGATATTTGAAAT
131 CACATATAAAAATATTTGAAATATTGTACCCACAATGTAGATGAAAAAACAACGATATTTGAAAT
42605880 AGTTATTTGATTTTATAATATTAAAAATCATCATACCACAATATAGATGGAGAAAATAAATATTT
196 AGTTATTTGATTTTATAATATTAAAAATCATCATACCACAATATAGATGGAGAAAATAAATATTT
42605945 AACATAGAAATATTATATATAAAGAAAAATA
261 AACATAGAAATATTATATATAAAGAAAAATA
42605976 AAAATCAGAATATCATTATTTTTAGTAAATATAATTTTTTATATGTGT-ATATTTATTTTTATAT
1 AAAATCAGAATATCATTATTTTTAGTAAATATAA-TTTTTATATGTGTAATATTTATTTTTATAT
42606040 GAGTGTATTAAATTTTAGTATTCTATATTATAGTATGTTCATTTGAAATGATTATTTGAAATATT
65 GAGTGTATTAAATTTTAGTATTCTATATTATAGTATGTTCATTTGAAATGATTATTTGAAATATT
42606105 TCACATATAAAAATATTTGAAATATTGTACCCACAATGTAGATGAAAAAACAACGATATTTGAAA
130 TCACATATAAAAATATTTGAAATATTGTACCCACAATGTAGATGAAAAAACAACGATATTTGAAA
42606170 TAGTTATTTGATTTTATAATATTAAAAATCATCATACCACAATATAGATGGAGAAAATAAATATT
195 TAGTTATTTGATTTTATAATATTAAAAATCATCATACCACAATATAGATGGAGAAAATAAATATT
42606235 TAACATAGAAATATTATATATAAAGAAAAATA
260 TAACATAGAAATATTATATATAAAGAAAAATA
42606267 TATCAAAAGA
Statistics
Matches: 290, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
291 277 0.96
292 13 0.04
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (291 bp):
AAAATCAGAATATCATTATTTTTAGTAAATATAATTTTTATATGTGTAATATTTATTTTTATATG
AGTGTATTAAATTTTAGTATTCTATATTATAGTATGTTCATTTGAAATGATTATTTGAAATATTT
CACATATAAAAATATTTGAAATATTGTACCCACAATGTAGATGAAAAAACAACGATATTTGAAAT
AGTTATTTGATTTTATAATATTAAAAATCATCATACCACAATATAGATGGAGAAAATAAATATTT
AACATAGAAATATTATATATAAAGAAAAATA
Found at i:42607757 original size:2 final size:2
Alignment explanation
Indices: 42607750--42607809 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
42607740 AAAAGAGGAG
42607750 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
42607792 CT CT CT AT AT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
42607810 ATCCTTCCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42609346 original size:17 final size:17
Alignment explanation
Indices: 42609308--42609358 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
42609298 GGACAAAGAA
*
42609308 AGAAAATTTTGGAACTT
1 AGAAAATTTTGAAACTT
*
42609325 AGAAAATTTTGAAATTT
1 AGAAAATTTTGAAACTT
* * *
42609342 GGAAAACTTGGAAACTT
1 AGAAAATTTTGAAACTT
42609359 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (17 bp):
AGAAAATTTTGAAACTT
Found at i:42610198 original size:27 final size:28
Alignment explanation
Indices: 42610168--42610224 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
42610158 TGAACTTGTC
42610168 AAATAGGGATTAAAT-TGAGAAA-TGTGA
1 AAATAGGGA-TAAATGTGAGAAATTGTGA
* * *
42610195 AAATTGTGATAAATGTGTGAAATTGTGA
1 AAATAGGGATAAATGTGAGAAATTGTGA
42610223 AA
1 AA
42610225 TTTTTGGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.20
27 13 0.52
28 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.30
Consensus pattern (28 bp):
AAATAGGGATAAATGTGAGAAATTGTGA
Found at i:42610210 original size:18 final size:19
Alignment explanation
Indices: 42610187--42610222 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42610177 TTAAATTGAG
42610187 AAATGTG-AAAATTGTGAT
1 AAATGTGTAAAATTGTGAT
*
42610205 AAATGTGTGAAATTGTGA
1 AAATGTGTAAAATTGTGA
42610223 AATTTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (19 bp):
AAATGTGTAAAATTGTGAT
Found at i:42612222 original size:152 final size:152
Alignment explanation
Indices: 42611945--42612273 Score: 498
Period size: 152 Copynumber: 2.2 Consensus size: 152
42611935 CACGGCCTAG
* * *
42611945 CACACGGCTTG-GCACACGAGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTGGCACACGAGCG
1 CACACGGCCTGAG-ACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCG
* *
42612009 TGTAGTCTGGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGGGACACGAC
65 TGTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGAC
**
42612074 CATGTGTCTTAAATTTGAATGCC
130 CATGTGTCCCAAATTTGAATGCC
* *
42612097 TACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGGGCGT
1 CACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCGT
* * *
42612162 GTGGTCTAGTCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGATC
66 GTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGACC
* * *
42612227 GTGTGTCCCCATTTTGAATGCC
131 ATGTGTCCCAAATTTGAATGCC
*
42612249 CACACGGCCTGAGACACAGGCGTGT
1 CACACGGCCTGAGACACGGGCGTGT
42612274 CACATGGCCG
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
152 158 0.99
153 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (152 bp):
CACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCGT
GTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGACC
ATGTGTCCCAAATTTGAATGCC
Found at i:42617507 original size:61 final size:62
Alignment explanation
Indices: 42617427--42617557 Score: 210
Period size: 61 Copynumber: 2.1 Consensus size: 62
42617417 TTGTCCTACT
* * **
42617427 AATTGATTTTCTGTATTATTTCAACGGATTCTTCGCAAGTATTATATATTTATAA-TTTTTA
1 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
*
42617488 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGTAAGTATTATATATACATAATTTTTTA
1 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
42617550 AATTTATT
1 AATTTATT
42617558 CAAAAACAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
61 50 0.78
62 14 0.22
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (62 bp):
AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
Found at i:42623105 original size:6 final size:6
Alignment explanation
Indices: 42623094--42623119 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42623084 TGAACAAATT
42623094 GGCCTA GGCCTA GGCCTA GGCCTA GG
1 GGCCTA GGCCTA GGCCTA GGCCTA GG
42623120 AGTTGTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (6 bp):
GGCCTA
Found at i:42630744 original size:27 final size:27
Alignment explanation
Indices: 42630691--42630745 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
42630681 TTCTTAATTT
*
42630691 AAAATTAAGTAAATTAATCCCTCTTTA
1 AAAATTAAGTAAATTAATCCATCTTTA
* *
42630718 AAAATTAGAGTAATTTAAT-CATTTTTA
1 AAAATTA-AGTAAATTAATCCATCTTTA
42630745 A
1 A
42630746 TTTTAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
AAAATTAAGTAAATTAATCCATCTTTA
Found at i:42631045 original size:100 final size:101
Alignment explanation
Indices: 42630919--42631122 Score: 401
Period size: 100 Copynumber: 2.0 Consensus size: 101
42630909 AATTATGTTT
42630919 AAATAAAATTTTAAGTATTTATTAAAAATTCTCTCTAACTTTTTTTATTATGCTCATTAAAAATG
1 AAATAAAATTTTAAGTATTTATTAAAAATTCTCTCTAACTTTTTTTATTATGCTCATTAAAAATG
42630984 TGGCGAAATATGGTGCAATCCCTTTTAAATAAAATA
66 TGGCGAAATATGGTGCAATCCCTTTTAAATAAAATA
42631020 AAATAAAATTTT-AGTATTTATTAAAAATTCTCTCTAACTTTTTTTATTATGCTCATTAAAAATG
1 AAATAAAATTTTAAGTATTTATTAAAAATTCTCTCTAACTTTTTTTATTATGCTCATTAAAAATG
42631084 TGGCGAAATATGGTGCAATCCCTTTTAAATAAAATA
66 TGGCGAAATATGGTGCAATCCCTTTTAAATAAAATA
42631120 AAA
1 AAA
42631123 AAGAAATTAA
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 91 0.88
101 12 0.12
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (101 bp):
AAATAAAATTTTAAGTATTTATTAAAAATTCTCTCTAACTTTTTTTATTATGCTCATTAAAAATG
TGGCGAAATATGGTGCAATCCCTTTTAAATAAAATA
Found at i:42648568 original size:38 final size:39
Alignment explanation
Indices: 42648516--42648598 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
42648506 ATTTGCCGGC
42648516 TTACTGATTAGGCAC-TTATGTG-CCAACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGTCCAA-TACTGTTACTG
* * *
42648554 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGTCCAATACTGTTACTG
42648593 TTACTG
1 TTACTG
42648599 TTACCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 14 0.35
39 23 0.57
40 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGTCCAATACTGTTACTG
Found at i:42648597 original size:39 final size:39
Alignment explanation
Indices: 42648516--42648642 Score: 125
Period size: 45 Copynumber: 3.1 Consensus size: 39
42648506 ATTTGCCGGC
* * *
42648516 TTACTGATTAGGCAC-TTATGTG-CCAACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAA-TACTGTTACTG
42648554 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
42648593 TTACTG-TTACCGACTCTGTACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATT--CG-----GCACTTTGTGTGTCGAATACTGTTACTG
42648638 TTACT
1 TTACT
42648643 ATTACTATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
38 16 0.21
39 23 0.30
40 5 0.07
45 32 0.42
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:42648616 original size:45 final size:45
Alignment explanation
Indices: 42648543--42648732 Score: 245
Period size: 45 Copynumber: 4.1 Consensus size: 45
42648533 ATGTGCCAAC
*
42648543 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
42648588 TACTGTTACTGTTACCGACTCTGTACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
42648633 TACTGTTACTATTACTATTATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTAC------CGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
42648684 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
42648729 TACT
1 TACT
42648733 ACTACCGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
45 85 0.68
51 40 0.32
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:42648744 original size:96 final size:96
Alignment explanation
Indices: 42648541--42648752 Score: 300
Period size: 96 Copynumber: 2.2 Consensus size: 96
42648531 TTATGTGCCA
* * *
42648541 ACTACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGA
1 ACTACTGTTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGA
* *
42648606 CTCTGTACTTTGTGTGTCGAATACTGTTACT
66 CTCAGCACTTTGTGTGTCGAATACTGTTACT
** *
42648637 GTTACTATTACTATTA-TCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAG
1 ACTACTGTTACTATTACT-GATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAG
* *
42648701 ATTCAGCACTTTGTGTGTTGAATACTGTTACT
65 ACTCAGCACTTTGTGTGTCGAATACTGTTACT
*
42648733 ACTACCGTTACTGATTACTG
1 ACTACTGTTACT-ATTACTG
42648753 TATACTGGTG
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 1 0.01
96 92 0.93
97 5 0.05
98 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (96 bp):
ACTACTGTTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGA
CTCAGCACTTTGTGTGTCGAATACTGTTACT
Done.