Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008295.1 Hibiscus syriacus cultivar Beakdansim tig00110962_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: 741301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:538806 original size:23 final size:23
Alignment explanation
Indices: 538780--539137 Score: 160
Period size: 23 Copynumber: 15.6 Consensus size: 23
538770 ATCATTAAAG
538780 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
* *
538803 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATT-AAAGT-AATTATT--A
* * * *
538830 GTAATTATTATTAAA-TCATTA-AA
1 TTAA--ATCATTAAAGTAATTATTA
538853 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTATTA
* * *
538877 TTAAATTATTAAAATTAA--ATCA
1 TTAAATCATT-AAAGTAATTATTA
* * * *
538899 TTAAAGTAATTATTATTAA--ATCA
1 TTAAA-TCATTA-AAGTAATTATTA
*
538922 TTAAA--GTT-AAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
538942 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
* *
538965 TTAAATCATTAAAATTAA--ATCA
1 TTAAATCATT-AAAGTAATTATTA
* * * *
538987 TTAAAGTAATTATTATTAAATCATTAA
1 TTAAA-TCATTA-AAGT-AATTATT-A
539014 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTATTA
* * *
539038 -TAAATTATTAAAATTAA--ATCA
1 TTAAATCATT-AAAGTAATTATTA
* * * *
539059 TTAAAGTAATTATTATTAA--ATCA
1 TTAAA-TCATTA-AAGTAATTATTA
*
539082 TTAAA--GTT-AAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
539102 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
539125 TTAAATCATTAAA
1 TTAAATCATTAAA
539138 ATTAAATCAT
Statistics
Matches: 261, Mismatches: 40, Indels: 68
0.71 0.11 0.18
Matches are distributed among these distances:
18 8 0.03
20 20 0.08
21 3 0.01
22 43 0.16
23 121 0.46
24 23 0.09
25 12 0.05
26 7 0.03
27 11 0.04
28 8 0.03
29 5 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (23 bp):
TTAAATCATTAAAGTAATTATTA
Found at i:538836 original size:9 final size:8
Alignment explanation
Indices: 538673--539200 Score: 63
Period size: 8 Copynumber: 68.9 Consensus size: 8
538663 ATCATTAAAG
538673 TTAAATAA
1 TTAAATAA
*
538681 TT--ATTA
1 TTAAATAA
*
538687 TTAAATCA
1 TTAAATAA
*
538695 TT-AA-AG
1 TTAAATAA
*
538701 TTAAATCA
1 TTAAATAA
538709 TTAAAGTAA
1 TTAAA-TAA
*
538718 TT--ATTA
1 TTAAATAA
*
538724 TTAAATCA
1 TTAAATAA
538732 TT-AA-AA
1 TTAAATAA
*
538738 TTAAATCA
1 TTAAATAA
*
538746 TT-AA-AG
1 TTAAATAA
538752 TTAAATAA
1 TTAAATAA
*
538760 TT--ATTA
1 TTAAATAA
*
538766 TTAAATCA
1 TTAAATAA
*
538774 TT-AA-AG
1 TTAAATAA
*
538780 TTAAATCA
1 TTAAATAA
538788 TTAAAGTAA
1 TTAAA-TAA
*
538797 TT--ATTA
1 TTAAATAA
*
538803 TTAAATCA
1 TTAAATAA
538811 TT-AA-AA
1 TTAAATAA
*
538817 TTAAATCA
1 TTAAATAA
538825 TTAAAGTAA
1 TTAAA-TAA
*
538834 TT--ATTA
1 TTAAATAA
*
538840 TTAAATCA
1 TTAAATAA
*
538848 TT-AA-AG
1 TTAAATAA
*
538854 TTAAATCA
1 TTAAATAA
538862 TTAAAGTAA
1 TTAAA-TAA
*
538871 TT--ATTA
1 TTAAATAA
*
538877 TTAAATTA
1 TTAAATAA
538885 TT-AA-AA
1 TTAAATAA
*
538891 TTAAATCA
1 TTAAATAA
538899 TTAAAGTAA
1 TTAAA-TAA
*
538908 TT--ATTA
1 TTAAATAA
*
538914 TTAAATCA
1 TTAAATAA
538922 TTAAAGTTAA
1 TTAAA--TAA
* *
538932 GTAATTATTA
1 TTAA--ATAA
*
538942 TTAAATCA
1 TTAAATAA
538950 TTAAAGTAA
1 TTAAA-TAA
*
538959 TT--ATTA
1 TTAAATAA
*
538965 TTAAATCA
1 TTAAATAA
538973 TT-AA-AA
1 TTAAATAA
*
538979 TTAAATCA
1 TTAAATAA
538987 TTAAAGTAA
1 TTAAA-TAA
*
538996 TT--ATTA
1 TTAAATAA
*
539002 TTAAATCA
1 TTAAATAA
*
539010 TT--A-AG
1 TTAAATAA
*
539015 TTAAATCA
1 TTAAATAA
539023 TTAAAGTAA
1 TTAAA-TAA
*
539032 TTATTATAAA
1 TTA-AAT-AA
539042 TTATTAA-AA
1 TTA--AATAA
*
539051 TTAAATCA
1 TTAAATAA
539059 TTAAAGTAA
1 TTAAA-TAA
*
539068 TT--ATTA
1 TTAAATAA
*
539074 TTAAATCA
1 TTAAATAA
539082 TTAAAGTTAA
1 TTAAA--TAA
* *
539092 GTAATTATTA
1 TTAA--ATAA
*
539102 TTAAATCA
1 TTAAATAA
539110 TTAAAGTAA
1 TTAAA-TAA
*
539119 TT--ATTA
1 TTAAATAA
*
539125 TTAAATCA
1 TTAAATAA
539133 TT-AA-AA
1 TTAAATAA
*
539139 TTAAATCA
1 TTAAATAA
539147 TTAAAGTAA
1 TTAAA-TAA
*
539156 TT--ATTA
1 TTAAATAA
*
539162 TTAAATCA
1 TTAAATAA
*
539170 TT-AA-AG
1 TTAAATAA
*
539176 TTAAATCA
1 TTAAATAA
539184 TTAAAGTAA
1 TTAAA-TAA
539193 TTGAAATA
1 TT-AAATA
539201 TAATAATACA
Statistics
Matches: 367, Mismatches: 81, Indels: 143
0.62 0.14 0.24
Matches are distributed among these distances:
5 2 0.01
6 76 0.21
7 53 0.14
8 146 0.40
9 57 0.16
10 29 0.08
11 2 0.01
12 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (8 bp):
TTAAATAA
Found at i:539064 original size:72 final size:74
Alignment explanation
Indices: 538570--539194 Score: 604
Period size: 74 Copynumber: 8.5 Consensus size: 74
538560 ATATATTTAA
*
538570 TATTATTATATCATT-AAATATAAATCATTAAAGTCAAGTAATTATTATTAAATCATTAAAGTTA
1 TATTATTAAATCATTAAAAT-TAAATCATT--A---AAGTAATTATTATTAAATCATTAAAGTTA
*
538634 AATCATTAAAGTTAAG
60 AATCATTAAAG-TAAT
* *
538650 TA--ATT--ATTATTAAATCATTAAA--GTTAAA-TAATTATTATTAAATCATTAAAGTTAAATC
1 TATTATTAAATCATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATC
538708 ATTAAAGTAAT
64 ATTAAAGTAAT
538719 TATTATTAAATCATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTAA
1 TATTATTAAATCATTAAAATTAAATCATTAAAG-----TAATTATTATTAAATCATTAAAGTTAA
538784 ATCATTAAAGTAAT
61 ATCATTAAAGTAAT
538798 TATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCAT
538863 TAAAGTAAT
66 TAAAGTAAT
*
538872 TATTATTAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG--------T
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCAT
538929 T-AAGTAAT
66 TAAAGTAAT
* * * **
538937 TATTATTAAATCATT-AAAGTAATTATTATTAAA-TCATTAAAATTAAATCATTAAAG-TAATTA
1 TATTATTAAATCATTAAAATTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAGTTAA--A
* *
538999 TTATTAAA-TCAT
62 TCATTAAAGTAAT
* * * * **
539011 TA--AGTTAAATCATT-AAAGT-AATTATTATAAATTATTAAAATTAAATCATTAAAG-TAATTA
1 TATTA-TTAAATCATTAAAATTAAATCATTA-AAGTAATTATTATTAAATCATTAAAGTTAA--A
* *
539071 TTATTAAA-TCAT
62 TCATTAAAGTAAT
* * * ** *
539083 TA-AAGTTAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
1 TATTA-TTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
539147 TTAAAGTAAT
65 TTAAAGTAAT
*
539157 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAATT
539195 GAAATATAAT
Statistics
Matches: 476, Mismatches: 33, Indels: 78
0.81 0.06 0.13
Matches are distributed among these distances:
64 6 0.01
65 41 0.09
66 10 0.02
69 5 0.01
70 44 0.09
71 13 0.03
72 44 0.09
73 46 0.10
74 160 0.34
75 13 0.03
76 7 0.01
77 2 0.00
78 7 0.01
79 76 0.16
80 2 0.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (74 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCAT
TAAAGTAAT
Found at i:539074 original size:36 final size:37
Alignment explanation
Indices: 538570--538931 Score: 452
Period size: 37 Copynumber: 9.6 Consensus size: 37
538560 ATATATTTAA
*
538570 TATTATTATATCATT-AAATATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAAT-TAAATCATT--A---AAGTAAT
* *
538612 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAG
1 TATTATTAAATCATTAAAATTAAATCATTAAAG-TAAT
* *
538650 TA--ATT--ATTATTAAATCATTAAA--GTTAAA-TAAT
1 TATTATTAAATCATTAAA--ATTAAATCATTAAAGTAAT
*
538682 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
538719 TATTATTAAATCATTAAAATTAAATCATTAAAGTTAAATAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAG-----TAAT
*
538761 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
538798 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
*
538835 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
*
538872 TATTATTAAATTATTAAAATTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
*
538909 TATTATTAAATCATTAAAGTTAA
1 TATTATTAAATCATTAAAATTAA
538932 GTAATTATTA
Statistics
Matches: 286, Mismatches: 18, Indels: 37
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.02
34 21 0.07
36 21 0.07
37 171 0.60
38 5 0.02
40 1 0.00
42 59 0.21
43 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (37 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTAAT
Found at i:539188 original size:51 final size:51
Alignment explanation
Indices: 538617--539151 Score: 411
Period size: 51 Copynumber: 10.3 Consensus size: 51
538607 GTAATTATTA
*
538617 TTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAATTAAATCATT--A---AAGTAATTATTATTAAATCATTAAAG
* ** * * *
538673 TTAAATAATTATTATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTA-
1 TTAAATCATTAAAATTAAATCATTAAAG-TAATTATTATTAAA-TCATTA-AAG
538724 TTAAATCATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAATTAAATCATTAAAG-----TAATTATTATTAAATCATTAAAG
* * * **
538780 TTAAATCATT-AAAGTAATTATTATTAAA-TCATTAAAATTAAATCATTAAAG
1 TTAAATCATTAAAATTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAG
* * * *
538831 -T-AATTATT---ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTA-
1 TTAAATCATTAAAATTAAATCATTAAAG-TAATTATTATTAAA-TCATTA-AAG
*
538877 TTAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* * ** *
538928 TTAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* * *
538979 TTAAATCATT-AAAGTAATTATTATTAAA-TCATTA--AGTTAAATCATTAAAG
1 TTAAATCATTAAAATTAA--ATCATTAAAGTAATTATTA-TTAAATCATTAAAG
*
539029 TAATTATTATAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 -------T-TAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* * ** *
539088 TTAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
539139 TTAAATCATTAAA
1 TTAAATCATTAAA
539152 GTAATTATTA
Statistics
Matches: 384, Mismatches: 56, Indels: 83
0.73 0.11 0.16
Matches are distributed among these distances:
45 15 0.04
46 5 0.01
47 8 0.02
48 7 0.02
49 7 0.02
50 30 0.08
51 186 0.48
52 21 0.05
54 1 0.00
55 10 0.03
56 35 0.09
57 25 0.07
58 13 0.03
59 20 0.05
60 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (51 bp):
TTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:539189 original size:14 final size:14
Alignment explanation
Indices: 538579--539190 Score: 389
Period size: 14 Copynumber: 47.8 Consensus size: 14
538569 ATATTATTAT
538579 ATCATTAAA-TATAA
1 ATCATTAAAGT-TAA
*
538593 ATCATTAAAGTCAA
1 ATCATTAAAGTTAA
* * *
538607 GTAATTATTA-TTAA
1 ATCATTA-AAGTTAA
538621 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
538635 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* * *
538649 GTAATTATTA-TTAA
1 ATCATTA-AAGTTAA
538663 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* *
538677 ATAATTATTA-TTAA
1 ATCATTA-AAGTTAA
538691 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
538705 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538717 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
538728 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
538742 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* *
538756 ATAATTATTA-TTAA
1 ATCATTA-AAGTTAA
538770 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
538784 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538796 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
538807 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
538821 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538833 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
538844 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
538858 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538870 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
* *
538881 ATTATTAAAATTAA
1 ATCATTAAAGTTAA
538895 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538907 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
538918 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* * *
538932 GTAATTATTA-TTAA
1 ATCATTA-AAGTTAA
538946 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538958 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
538969 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
538983 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
538995 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
539006 ATCATT-AAGTTAA
1 ATCATTAAAGTTAA
539019 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
539031 ATTATT--A--TAA
1 ATCATTAAAGTTAA
* *
539041 ATTATTAAAATTAA
1 ATCATTAAAGTTAA
539055 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
539067 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
539078 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* * *
539092 GTAATTATTA-TTAA
1 ATCATTA-AAGTTAA
539106 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
539118 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
539129 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
539143 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
539155 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
539166 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
539180 ATCATTAAAGT
1 ATCATTAAAGT
539191 AATTGAAATA
Statistics
Matches: 468, Mismatches: 62, Indels: 136
0.70 0.09 0.20
Matches are distributed among these distances:
9 1 0.00
10 28 0.06
11 61 0.13
12 68 0.15
13 36 0.08
14 267 0.57
15 7 0.01
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
ATCATTAAAGTTAA
Found at i:540111 original size:51 final size:47
Alignment explanation
Indices: 540052--540159 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 47
540042 CTAATAACAA
*
540052 CAAACTTTTCTTTTATAAAACATGTGCTTGCTTTCGTTTATTGCCAGGGAC
1 CAAACTTTTCTTTTATAAAACATGTAC-T--TTT-GTTTATTGCCAGGGAC
* *
540103 CAAACTTTTCTTTTATAAAACATGTACTTTTGTTTATTGCTAGGGCC
1 CAAACTTTTCTTTTATAAAACATGTACTTTTGTTTATTGCCAGGGAC
540150 CAATACTTTT
1 CAA-ACTTTT
540160 GCAACATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
47 17 0.32
48 9 0.17
50 1 0.02
51 26 0.49
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (47 bp):
CAAACTTTTCTTTTATAAAACATGTACTTTTGTTTATTGCCAGGGAC
Found at i:540348 original size:32 final size:32
Alignment explanation
Indices: 540298--540383 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
540288 ATGATGATGA
540298 TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
* *
540330 TGAATAAGACGCCAAGAACTCCACCCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
*
540362 TGAAGAAGACGCCGAGAGCTCC
1 TGAAGAAGACGCCGAGAACTCC
540384 CATGAACATC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.35, C:0.33, G:0.24, T:0.08
Consensus pattern (32 bp):
TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
Found at i:540434 original size:47 final size:47
Alignment explanation
Indices: 540365--540472 Score: 189
Period size: 47 Copynumber: 2.3 Consensus size: 47
540355 CCAAGGCTGA
540365 AGAAGACGCCGAGAGCTCCCATGAACATCTTTTGAACGAACATATAT
1 AGAAGACGCCGAGAGCTCCCATGAACATCTTTTGAACGAACATATAT
* *
540412 AGAAGACGTCGAGAGCTCCCATGAACATCTTTTGAACTAACATATAT
1 AGAAGACGCCGAGAGCTCCCATGAACATCTTTTGAACGAACATATAT
*
540459 ATAAGACGCCGAGA
1 AGAAGACGCCGAGA
540473 TATCCGATAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (47 bp):
AGAAGACGCCGAGAGCTCCCATGAACATCTTTTGAACGAACATATAT
Found at i:541065 original size:2 final size:2
Alignment explanation
Indices: 541046--541140 Score: 138
Period size: 2 Copynumber: 48.0 Consensus size: 2
541036 TAAATGTATG
* * *
541046 TA TA TA TT TA TG TG 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
*
541088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
541130 CA TA TA T- TA TA
1 TA TA TA TA TA TA
541141 GTTTATTTAG
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 84 0.99
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:543758 original size:23 final size:23
Alignment explanation
Indices: 543708--543758 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
543698 TATTCATGAC
* * * *
543708 TAAACTGGGATTATTTTTTAATA
1 TAAATTGGGATTACTTTTAAAAA
*
543731 GAAATTGGGATTACTTTTAAAAA
1 TAAATTGGGATTACTTTTAAAAA
543754 TAAAT
1 TAAAT
543759 GATTGTGAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (23 bp):
TAAATTGGGATTACTTTTAAAAA
Found at i:548283 original size:24 final size:21
Alignment explanation
Indices: 548224--548283 Score: 52
Period size: 24 Copynumber: 2.8 Consensus size: 21
548214 GGTGTTGTAA
*
548224 ATTAATTAAATATTTATAATT
1 ATTAATTAAATATTAATAATT
*
548245 -TTGATTAAA-ATTTAATTAATATT
1 ATTAATTAAATA-TTAA-T-A-ATT
548268 ATTAATTAAATATTAA
1 ATTAATTAAATATTAA
548284 ATATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
19 1 0.03
20 11 0.37
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.40
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTAATTAAATATTAATAATT
Found at i:557794 original size:24 final size:25
Alignment explanation
Indices: 557766--557813 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
557756 TGAAGTTTGT
557766 GAATGATTT-TATTTGTTTCTATAA
1 GAATGATTTCTATTTGTTTCTATAA
* * *
557790 GAATGTTTTCTGTTTGTTTTTATA
1 GAATGATTTCTATTTGTTTCTATA
557814 CCATGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (25 bp):
GAATGATTTCTATTTGTTTCTATAA
Found at i:558687 original size:17 final size:17
Alignment explanation
Indices: 558665--558697 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
558655 AAATGATAAT
558665 TTTTATAACGTTACACG
1 TTTTATAACGTTACACG
558682 TTTTATAACGTTACAC
1 TTTTATAACGTTACAC
558698 ATCAAGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTTATAACGTTACACG
Found at i:558882 original size:24 final size:23
Alignment explanation
Indices: 558858--558907 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 23
558848 AAACAATTAT
558858 TTTTATTTTTTTAAAT-ATTAATA
1 TTTTA-TTTTTTAAATAATTAATA
558881 --TTATTTTTTAAATAATTAATA
1 TTTTATTTTTTAAATAATTAATA
558902 TCTTTA
1 T-TTTA
558908 AAGAAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.43
21 10 0.43
24 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATTTTTTAAATAATTAATA
Found at i:558889 original size:20 final size:21
Alignment explanation
Indices: 558864--558902 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
558854 TTATTTTTAT
558864 TTTTTTAAAT-ATTAATATTA
1 TTTTTTAAATAATTAATATTA
558884 TTTTTTAAATAATTAATAT
1 TTTTTTAAATAATTAATAT
558903 CTTTAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTAAATAATTAATATTA
Found at i:564294 original size:71 final size:71
Alignment explanation
Indices: 564170--564303 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
564160 GGTAATTCCG
*
564170 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGTTTGCTAGCATGGGGCA
1 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGGCA
564235 ATGCCA
66 ATGCCA
* * * * *
564241 AAATTCTATGAGTGATATCCATCACCATCCTTAAGCAGTGTGAGGGTGCTTGCTAGCATGGGG
1 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGG
564304 TTGTGCAGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (71 bp):
AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGGCA
ATGCCA
Found at i:572606 original size:16 final size:16
Alignment explanation
Indices: 572585--572618 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
572575 ATACTAAATT
* *
572585 TTTAATTTATTTTTAA
1 TTTAATATATATTTAA
572601 TTTAATATATATTTAA
1 TTTAATATATATTTAA
572617 TT
1 TT
572619 CTACCAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATATATATTTAA
Found at i:573519 original size:82 final size:82
Alignment explanation
Indices: 573375--573586 Score: 361
Period size: 82 Copynumber: 2.6 Consensus size: 82
573365 CCAGAACCGC
* * *
573375 GTCCATAGGGCTTACCTTAAGCACACGGCAAAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCC
1 GTCCATAGGGCTTACCCTAAGCACACAGC--AAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCC
*
573440 TGTATCCTTAAGTCCGTAA
64 TGTACCCTTAAGTCCGTAA
*
573459 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACTTAAGGATAGGCTTTGGGGCCTG
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTG
573524 TACCCTTAAGTCCGTAA
66 TACCCTTAAGTCCGTAA
573541 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAA
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAA
573587 TGGAGCATGT
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
82 95 0.78
84 27 0.22
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (82 bp):
GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTG
TACCCTTAAGTCCGTAA
Found at i:577560 original size:21 final size:20
Alignment explanation
Indices: 577518--577555 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
577508 TTGAAAAAAT
577518 ATTTCCATTTCCAATTTTAAC
1 ATTTCCATTTCC-ATTTTAAC
577539 ATTTCCATTTCC-TTTTA
1 ATTTCCATTTCCATTTTA
577556 CAACAATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTCCATTTCCATTTTAAC
Found at i:579333 original size:16 final size:18
Alignment explanation
Indices: 579305--579341 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
579295 AGATTAGAGA
579305 TTTAATTATAATAAT-AT
1 TTTAATTATAATAATAAT
579322 TTTAATTA-AATAATAAT
1 TTTAATTATAATAATAAT
579339 TTT
1 TTT
579342 TAACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATTATAATAATAAT
Found at i:579352 original size:16 final size:19
Alignment explanation
Indices: 579312--579353 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
579302 AGATTTAATT
*
579312 ATAATAATATTTTAATTAA
1 ATAATAATATTTTAATCAA
579331 ATAATAAT-TTTTAA-CAA
1 ATAATAATATTTTAATCAA
579348 A-AATAA
1 ATAATAA
579354 CTCGATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 6 0.27
19 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATATTTTAATCAA
Found at i:583792 original size:21 final size:20
Alignment explanation
Indices: 583750--583787 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
583740 TTGAAAAAAT
583750 ATTTCCATTTCCAATTTTAAC
1 ATTTCCATTTCC-ATTTTAAC
583771 ATTTCCATTTCC-TTTTA
1 ATTTCCATTTCCATTTTA
583788 CAACAATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTCCATTTCCATTTTAAC
Found at i:585916 original size:17 final size:17
Alignment explanation
Indices: 585880--585915 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
585870 AGATTAGAGA
585880 TTTAATTATAATAATAT
1 TTTAATTATAATAATAT
585897 TTTAATTA-AATAATAT
1 TTTAATTATAATAATAT
585913 TTT
1 TTT
585916 TTAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATTATAATAATAT
Found at i:589235 original size:215 final size:216
Alignment explanation
Indices: 588912--589377 Score: 630
Period size: 215 Copynumber: 2.2 Consensus size: 216
588902 GACTAATGAC
*
588912 AAATCACAAATCAAAGTCCAACAATATAAAAAAAATTATTCAAAAACGTAAATCACAAATCCAAA
1 AAATCACAAATCAAAGTCCAACAATAT--AAAAAACTATTCAAAAACGTAAATCACAAATCCAAA
* * * * * * *
588977 TCTAATATGAGGCTCCAAAGAAGGGAGGATCATATACGGAAAATGTAAAAAACCTAATTAAAAAA
64 TCCAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAA
* *
589042 ACCTTGAACAAAATATAGATATGAACACATCTAATTTTATCATAAAATGAACCACAAAAAGAGAT
129 AACTTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGAT
*
589107 TAAACTACTAAAAGACCATCGAG
194 TAAACTACCAAAAGACCATCGAG
* * * ***
589130 AAATCATAAATCAAAGTCCAACAATAT-AAAAACTATTCACAAATGTAAATCATGTATCCAAATC
1 AAATCACAAATCAAAGTCCAACAATATAAAAAACTATTCAAAAACGTAAATCACAAATCCAAATC
* * *
589194 CAATCTAAGGGTCCAAAGAAGGAAGAACCATACAAGGAAAATGTTAAAAACCTAATTAAAAAAAA
66 CAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAAAA
* * * *
589259 CTTGAACAAAATATAGATATGAATATATCTAATTGTATCGTAAAATGAATCACAAAAAGAGATTA
131 CTTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGATTA
* * * *
589324 AGCTACCGAAAGATCATCGAT
196 AACTACCAAAAGACCATCGAG
*
589345 AAATCACAAATCAAAGTCCAGC-ATCATAAAAAA
1 AAATCACAAATCAAAGTCCAACAAT-ATAAAAAA
589378 ATATAACCCC
Statistics
Matches: 216, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
214 2 0.01
215 183 0.85
216 5 0.02
218 26 0.12
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (216 bp):
AAATCACAAATCAAAGTCCAACAATATAAAAAACTATTCAAAAACGTAAATCACAAATCCAAATC
CAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAAAA
CTTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGATTA
AACTACCAAAAGACCATCGAG
Found at i:590052 original size:29 final size:28
Alignment explanation
Indices: 590003--590137 Score: 119
Period size: 29 Copynumber: 4.7 Consensus size: 28
589993 AAATCATGAC
* *
590003 GGGGATATAATCCCATACAGAATTAGAAT
1 GGGGATATAATCCCATGCAGAATAAG-AT
* *
590032 GGGGATATAATCCTATGCAGAATCATGAT
1 GGGGATATAATCCCATGCAGAAT-AAGAT
* * *
590061 GAGGATATAATCCCATGTAGAATAAGGAC
1 GGGGATATAATCCCATGCAGAATAA-GAT
* * *
590090 GTGGATATAATTCCATGCAGAATCAGGAT
1 GGGGATATAATCCCATGCAGAAT-AAGAT
*
590119 GAGGATCA-AATCCCATGCA
1 GGGGAT-ATAATCCCATGCA
590138 AAAACATGAA
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.01
29 82 0.95
30 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (28 bp):
GGGGATATAATCCCATGCAGAATAAGAT
Found at i:590083 original size:58 final size:58
Alignment explanation
Indices: 589987--590137 Score: 180
Period size: 58 Copynumber: 2.6 Consensus size: 58
589977 TAGAGGATCT
* * * * * *
589987 CATGCAAAATCATGACGGGGATATAATCCCATACAGAATTAGAATGGGGATATAA-TC
1 CATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAACGGGGATATAATTC
* * *
590044 CTATGCAGAATCATGATGAGGATATAATCCCATGTAGAATAAGGACGTGGATATAATTC
1 C-ATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAACGGGGATATAATTC
*
590103 CATGCAGAATCAGGATGAGGATCA-AATCCCATGCA
1 CATGCAGAATCATGATGAGGAT-ATAATCCCATGCA
590138 AAAACATGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
57 1 0.01
58 75 0.94
59 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (58 bp):
CATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAACGGGGATATAATTC
Found at i:596962 original size:41 final size:41
Alignment explanation
Indices: 596894--597405 Score: 352
Period size: 41 Copynumber: 12.2 Consensus size: 41
596884 CATTTCTAGC
* * * *
596894 GGCGTTTTTAGAATAAACGCCGCTAAATACTTGTACTTTAAT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGACTTGTACTTTAGT
* * *
596936 GGCGTTTTTATACAAATGCCGCTAAATAC-TGTACTTTAAT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
* *
596976 GGCGTTTTTAGAACAAACGCCGCTATAGA-TTAGTACTTTAGT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGACTT-GTACTTTAGT
** * * * * *
597018 GGATTTTTTTAAACAAACGACGCTATAGACTAGTACTTTCGT
1 GG-CGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
*
597060 GGCATTTTTAT-CAAACGCCGCTAAAGAC-TGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
* * * *
597099 GGCATTTGTATAAAAACGCCGCTAAAGAC-TGTACTATAGACT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAG--T
* * * * ** *** ** *
597141 AGTACTTTATTGGCGTTTGTATAAA-AACGCCGCTAGAGACTGTACTTTTGT
1 -G-GC---GTT----TTTATACAAACGCCG-CTAAAGA-CTTGTACTTTAGT
* * *
597192 GGCGTTTTTATAAAAACGCCGTTAAAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
* * * *
597233 GGCATTTTTATACAAACGTCGCTAAAGACTCGTACTTTTGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
* * *
597274 GGCTTTTTTATACAAACGCCGCTAAAGACTCGTACTTTTGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
* * * * *
597315 GGTGCTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAAT
1 GGCG-TTTTTA-TACAAACGCCGCTAAAGACTTGTACTTTAGT
* * *
597358 GGCGTTTTTATACAAACGCCACTAAAAACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
597399 GGCGTTT
1 GGCGTTT
597406 ATAAAAACAA
Statistics
Matches: 379, Mismatches: 68, Indels: 47
0.77 0.14 0.10
Matches are distributed among these distances:
39 19 0.05
40 61 0.16
41 156 0.41
42 73 0.19
43 40 0.11
44 1 0.00
46 2 0.01
47 3 0.01
49 1 0.00
50 3 0.01
51 12 0.03
53 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGT
Found at i:596977 original size:40 final size:40
Alignment explanation
Indices: 596894--597133 Score: 241
Period size: 40 Copynumber: 5.9 Consensus size: 40
596884 CATTTCTAGC
* * *
596894 GGCGTTTTTAGAATAAACGCCGCTAAATACTTGTACTTTAAT
1 GGCGTTTTTA-AACAAACGCCGCTAAAGAC-TGTACTTTAGT
* * * *
596936 GGCGTTTTTATACAAATGCCGCTAAATACTGTACTTTAAT
1 GGCGTTTTTAAACAAACGCCGCTAAAGACTGTACTTTAGT
* *
596976 GGCGTTTTTAGAACAAACGCCGCTATAGATTAGTACTTTAGT
1 GGCGTTTTTA-AACAAACGCCGCTAAAGACT-GTACTTTAGT
** * * *
597018 GGATTTTTTTAAACAAACGACGCTATAGACTAGTACTTTCGT
1 GG-CGTTTTTAAACAAACGCCGCTAAAGACT-GTACTTTAGT
* *
597060 GGCATTTTT-ATCAAACGCCGCTAAAGACTGTACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAGACTGTACTTTAGT
* *
597099 GGCATTTGTATAA-AAACGCCGCTAAAGACTGTACT
1 GGCGTTTTTA-AACAAACGCCGCTAAAGACTGTACT
597134 ATAGACTAGT
Statistics
Matches: 171, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 17 0.10
40 60 0.35
41 37 0.22
42 51 0.30
43 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTAAACAAACGCCGCTAAAGACTGTACTTTAGT
Found at i:597012 original size:82 final size:82
Alignment explanation
Indices: 596894--597405 Score: 467
Period size: 82 Copynumber: 6.1 Consensus size: 82
596884 CATTTCTAGC
* * * *
596894 GGCGTTTTTAGAATAAACGCCGCTAAATACTTGTACTTTAATGGCGTTTTTATACAAATGCCGCT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGAC-TGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
* *
596959 AAATACT-GTACTTTAAT
65 AAAGACTCGTACTTTAGT
* * ** * *
596976 GGCGTTTTTAGAACAAACGCCGCTATAGATTAGTACTTTAGTGGATTTTTTTAAACAAACGACGC
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGG-CGTTTTTATACAAACGCCGC
* * *
597041 TATAGACTAGTACTTTCGT
64 TAAAGACTCGTACTTTAGT
* * * * *
597060 GGCATTTTT--ATCAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTGTATAAAAACGCCGCTA
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTA
*
597123 AAGACT-GTACTATAGACT
66 AAGACTCGTACTTTAG--T
* * * * * * *
597141 AGTACTTTATTGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGCGTTTTTATAAA
1 -G-GC-GT-TT----TTAG-A-ACAAACGCCGCTAAAGACTGTACTTTAGTGGCGTTTTTATACA
*
597206 AACGCCGTTAAAGACTCGTACTTTAGT
56 AACGCCGCTAAAGACTCGTACTTTAGT
* * * * *
597233 GGCATTTTTA-TACAAACGTCGCTAAAGACTCGTACTTTTGTGGCTTTTTTATACAAACGCCGCT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCGTTTTTATACAAACGCCGCT
*
597297 AAAGACTCGTACTTTTGT
65 AAAGACTCGTACTTTAGT
* * * *
597315 GGTGCTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTTTTTATACAAACGCCAC
1 GGCG-TTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCGTTTTTATACAAACGCCGC
*
597380 TAAAAACTCGTACTTTAGT
64 TAAAGACTCGTACTTTAGT
597399 GGCGTTT
1 GGCGTTT
597406 ATAAAAACAA
Statistics
Matches: 349, Mismatches: 60, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
79 7 0.02
80 21 0.06
81 30 0.09
82 104 0.30
83 31 0.09
84 85 0.24
85 2 0.01
88 2 0.01
89 3 0.01
90 1 0.00
91 1 0.00
92 2 0.01
93 52 0.15
94 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (82 bp):
GGCGTTTTTAGAACAAACGCCGCTAAAGACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTA
AAGACTCGTACTTTAGT
Found at i:597182 original size:93 final size:93
Alignment explanation
Indices: 597040--597309 Score: 271
Period size: 93 Copynumber: 3.0 Consensus size: 93
597030 ACAAACGACG
* * *
597040 CTATAGACTAGTACTTTCGTGGCATTTTTATCAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
1 CTATAGACTAGTACTTTAGTGGCATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
597105 TGTATAAAAACGCCGCTAAAGACT-GTA
66 TGTATAAAAACGCCGCTAAAGACTCGTA
* * * * *
597132 CTATAGACTAGTACTTTATTGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGCGT
1 CTATAGACTAGTACTTTAGTGGCATTTGTAT-AAAACGCCGCTAAAGACTGTACTTTAGTGGCAT
*
597197 TTTTATAAAAACG-C-C----G--T--TA
65 TTGTATAAAAACGCCGCTAAAGACTCGTA
* * * * *
597216 --A-AGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCGTACTTTTGTGGCT
1 CTATAGACTAGTACTTTAGTGGCATTTGTATA-AAACGCCGCTAAAGACT-GTACTTTAGTGGCA
* *
597278 TTTTTATACAAACGCCGCTAAAGACTCGTA
64 TTTGTATAAAAACGCCGCTAAAGACTCGTA
597308 CT
1 CT
597310 TTTGTGGTGC
Statistics
Matches: 146, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
80 1 0.01
81 38 0.26
82 27 0.18
83 1 0.01
84 3 0.02
85 1 0.01
87 1 0.01
88 1 0.01
90 1 0.01
91 1 0.01
92 30 0.21
93 41 0.28
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (93 bp):
CTATAGACTAGTACTTTAGTGGCATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
TGTATAAAAACGCCGCTAAAGACTCGTA
Found at i:597372 original size:125 final size:122
Alignment explanation
Indices: 597131--597413 Score: 365
Period size: 125 Copynumber: 2.3 Consensus size: 122
597121 TAAAGACTGT
* * *
597131 ACTATAGACTAGTACTTTAT-TGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGC
1 ACTAAAGACTCGTACTTT-TGTGGCGTTTGTATAAAAACGCCGCTAAAGACTGTACTTTTGTGGC
* * * *
597195 GTTTTTATAAAAACGCCGTTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGTC
65 GTTTTTAGAAAAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
* * * * *
597253 GCTAAAGACTCGTACTTTTGTGGCTTTTTTATACAAACGCCGCTAAAGACTCGTACTTTTGTGGT
1 ACTAAAGACTCGTACTTTTGTGGCGTTTGTATAAAAACGCCGCTAAAGACT-GTACTTTTGTGGC
* *
597318 GCTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTTTTTATACAAACGCC
65 G-TTTTTAGAA-AAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
* *
597378 ACTAAAAACTCGTACTTTAGTGGCG-TT-TATAAAAAC
1 ACTAAAGACTCGTACTTTTGTGGCGTTTGTATAAAAAC
597414 AAATGCGACA
Statistics
Matches: 138, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
121 1 0.01
122 42 0.30
123 21 0.15
124 10 0.07
125 64 0.46
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (122 bp):
ACTAAAGACTCGTACTTTTGTGGCGTTTGTATAAAAACGCCGCTAAAGACTGTACTTTTGTGGCG
TTTTTAGAAAAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
Found at i:597419 original size:84 final size:82
Alignment explanation
Indices: 597136--597416 Score: 332
Period size: 84 Copynumber: 3.4 Consensus size: 82
597126 ACTGTACTAT
* * * *
597136 AGACTAGTACTTTATTGGCGTTTGTATAA-AAACGCCGCTAGAGACT-GTACTTTTGTGGCGTTT
1 AGACTCGTACTTTAGTGGCGTTT-TAAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTT
* *
597199 TTATAAAAACGCCGTTAA
65 TTATACAAACGCCGCTAA
* * * * *
597217 AGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCGTACTTTTGTGGCTTTTT
1 AGACTCGTACTTTAGTGGCGTTTTAAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTTT
597282 TATACAAACGCCGCTAA
66 TATACAAACGCCGCTAA
* * * * **
597299 AGACTCGTACTTTTGTGGTGCTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTT
1 AGACTCGTACTTTAGT-G-GCGTTTTAAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTT
*
597364 TTTATACAAACGCCACTAA
64 TTTATACAAACGCCGCTAA
*
597383 AAACTCGTACTTTAGTGGCGTTTATAAAAACAAA
1 AGACTCGTACTTTAGTGGCGTTT-T-AAAACAAA
597417 TGCGACAAGT
Statistics
Matches: 168, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.01
81 35 0.21
82 52 0.31
83 3 0.02
84 76 0.45
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (82 bp):
AGACTCGTACTTTAGTGGCGTTTTAAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTTT
TATACAAACGCCGCTAA
Found at i:600887 original size:41 final size:43
Alignment explanation
Indices: 600828--600907 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
600818 TTTTGATATC
* *
600828 GACCTTTTGCGGCGTTTGT-TCCAAAAAGGTCACTATAGGACT
1 GACCTTTTGCGGCGTTTGTATCAAAAAAGGCCACTATAGGACT
*
600870 GACCTTTTG-GGCGTTTGTATCAAAAAATGCCACTATAG
1 GACCTTTTGCGGCGTTTGTATCAAAAAAGGCCACTATAG
600908 ATATAGGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 9 0.26
42 25 0.74
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
GACCTTTTGCGGCGTTTGTATCAAAAAAGGCCACTATAGGACT
Found at i:601668 original size:29 final size:29
Alignment explanation
Indices: 601626--601700 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
601616 TCCGTAGAGG
601626 ATCCCATGCAGAATCAGGACGGA-GATATA
1 ATCCCATGCAGAATCAGGA-GGAGGATATA
* * *
601655 ATCCCATGCAGAATAAGGATGAGGATATT
1 ATCCCATGCAGAATCAGGAGGAGGATATA
* *
601684 ATTCTATGCAGAATCAG
1 ATCCCATGCAGAATCAG
601701 AATGGGAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (29 bp):
ATCCCATGCAGAATCAGGAGGAGGATATA
Found at i:602847 original size:17 final size:17
Alignment explanation
Indices: 602821--602864 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
602811 TTTCTGAGAG
602821 AATTGGAATCTGTCAGT
1 AATTGGAATCTGTCAGT
*
602838 AATTGAAATCTGTCAGT
1 AATTGGAATCTGTCAGT
602855 AATTGGAATC
1 AATTGGAATC
602865 CAATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
AATTGGAATCTGTCAGT
Found at i:603450 original size:199 final size:195
Alignment explanation
Indices: 603234--603595 Score: 582
Period size: 199 Copynumber: 1.8 Consensus size: 195
603224 TTAGAAACCC
*
603234 GACCCGAAATAATAAAAAAATTATTCTTATTCAATAAAAACAATGACTTAATTGGAAAAAAA-AA
1 GACCCGAAATAATAAAAAAATTATTCTTATTCAATAAAAACAACGACTTAATT-GAAAAAAATAA
* * * * *
603298 TATATATAGGGGTATTATTGTAATTATTCCTATATATATAAGGTAAAATTATATATTTTTTGGGT
65 TATATAGAGGGGTATTATTATAATTATTCATAAATATATAAGGTAAAATTATATA-TATTT---T
603363 CGGGCCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATATGAATTAGAAATCCGACCC
126 CGGGCCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATATGAATTAGAAATCCGACCC
603428 GACCT
191 GACCT
* *
603433 GACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGAAAAAAATTAT
1 GACCCGAAATAATAAAAAAATTATTCTTATTCAATAAAAACAACGACTTAATTGAAAAAAATAAT
*
603498 ATATAGAGGGGTATTATTATAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGGT
66 ATATAGAGGGGTATTATTATAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGGC
*
603563 CGGGTATTTTTCACCCTAAACCCGAACTCGACC
131 CGGGTATTTTTCACCCTAAACCCGAACCCGACC
603596 TGACCCGAAT
Statistics
Matches: 152, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
195 37 0.24
198 12 0.08
199 103 0.68
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (195 bp):
GACCCGAAATAATAAAAAAATTATTCTTATTCAATAAAAACAACGACTTAATTGAAAAAAATAAT
ATATAGAGGGGTATTATTATAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGGC
CGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCT
Found at i:604377 original size:13 final size:13
Alignment explanation
Indices: 604361--604386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
604351 AAATTTAAGA
604361 AAAAAACAAAAAC
1 AAAAAACAAAAAC
604374 AAAAAACAAAAAC
1 AAAAAACAAAAAC
604387 GAAGATATGA
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:605920 original size:63 final size:63
Alignment explanation
Indices: 605821--605944 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
605811 TGCACTTCTT
* * *
605821 TAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCACAAG-TGGTGCATCGATGCACCCCC
1 TAAAATAAAAACATCGAATGGCATCAGTGTACCGATGCA-AAGTTAGTGCATCGATGCACCCCC
* * * *
605884 TAAAATACAAACATCGAATGGGATTTA-TGTACCGATGCATAGTTAGTGCATCGATGCACCC
1 TAAAATAAAAACATCGAATGGCA-TCAGTGTACCGATGCAAAGTTAGTGCATCGATGCACCC
605945 GTTAAGGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 48 0.92
64 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (63 bp):
TAAAATAAAAACATCGAATGGCATCAGTGTACCGATGCAAAGTTAGTGCATCGATGCACCCCC
Found at i:606560 original size:18 final size:18
Alignment explanation
Indices: 606499--606571 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
606489 AGGGATTATC
*
606499 AGTGGTCCTTCGTGACAT
1 AGTGGTCCTTCGGGACAT
* * * *
606517 AATCGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
606536 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
606555 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
606572 AATATTCAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 27 0.63
19 4 0.09
20 12 0.28
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:606567 original size:38 final size:38
Alignment explanation
Indices: 606496--606572 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
606486 TTGAGGGATT
* *
606496 ATCAGTGGTCCTTCGTGACATAATCGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAATCGGTCTTCGGAACA
* *
606534 ATCAGTGGTCCTTCGGGACATAGT-GGTCATTCGGGACA
1 ATCAGTGGTCCTTCGGGACATAATCGGTC-TTCGGAACA
606572 A
1 A
606573 ATATTCAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 3 0.09
38 31 0.91
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAATCGGTCTTCGGAACA
Found at i:607016 original size:12 final size:12
Alignment explanation
Indices: 606999--607024 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
606989 TTAAACTAAT
606999 TTTATTAATATA
1 TTTATTAATATA
607011 TTTATTAATATA
1 TTTATTAATATA
607023 TT
1 TT
607025 AAACTAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTAATATA
Found at i:615041 original size:206 final size:207
Alignment explanation
Indices: 614685--615099 Score: 814
Period size: 206 Copynumber: 2.0 Consensus size: 207
614675 CTTTACCTAC
614685 CACAAGAGCCATAAGTATTTACTCACGTTGAAGAAGTTGAATTTGAGGCAGCGTAGATGGGTCAA
1 CACAAGAGCCATAAGTATTTACTCACGTTGAAGAAGTTGAATTTGAGGCA-CGTAGATGGGTCAA
614750 GTTGTTAAAGGATTATGATTGCGTAATCGACTATCACCTATAAAAGTGAATATTGTTATTGATGC
65 GTTGTTAAAGGATTATGATTGCGTAATCGACTATCACCTATAAAAGTGAATATTGTTATTGATGC
614815 TTTGAGCATAAAGTCGATGTCAGAGTTGCAAGCCTTATTTGCACGCTTAAGTTTGTCTAGTGATG
130 TTTGAGCATAAAGTCGATGTCAGAGTTGCAAGCCTTATTTGCACGCTTAAGTTTGTCTAGTGATG
614880 GTGGGTTATTGGT
195 GTGGGTTATTGGT
614893 CACAAGAGCCATAAGTATTTACTCACGTTGAAGAAGTTGAATTTGAGGCA-GTAGATGGGTCAAG
1 CACAAGAGCCATAAGTATTTACTCACGTTGAAGAAGTTGAATTTGAGGCACGTAGATGGGTCAAG
614957 TTGTTAAAGGATTATGATTGCGTAATCGACTATCACCTATAAAAGTGAATATTGTTATTGATGCT
66 TTGTTAAAGGATTATGATTGCGTAATCGACTATCACCTATAAAAGTGAATATTGTTATTGATGCT
615022 TTGAGCATAAAGTCGATGTCAGAGTTGCAAGCCTTATTTGCACGCTTAAGTTTGTCTAGTGATGG
131 TTGAGCATAAAGTCGATGTCAGAGTTGCAAGCCTTATTTGCACGCTTAAGTTTGTCTAGTGATGG
615087 TGGGTTATTGGT
196 TGGGTTATTGGT
615099 C
1 C
615100 GAACTTCATA
Statistics
Matches: 207, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 157 0.76
208 50 0.24
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (207 bp):
CACAAGAGCCATAAGTATTTACTCACGTTGAAGAAGTTGAATTTGAGGCACGTAGATGGGTCAAG
TTGTTAAAGGATTATGATTGCGTAATCGACTATCACCTATAAAAGTGAATATTGTTATTGATGCT
TTGAGCATAAAGTCGATGTCAGAGTTGCAAGCCTTATTTGCACGCTTAAGTTTGTCTAGTGATGG
TGGGTTATTGGT
Found at i:620378 original size:2 final size:2
Alignment explanation
Indices: 620371--620399 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
620361 ATTTATAATT
620371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
620400 CCTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:629854 original size:31 final size:31
Alignment explanation
Indices: 629816--629916 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 31
629806 CAATCATAAC
629816 TTAATTAAATAATAATAAATGTAACTAGATT
1 TTAATTAAATAATAATAAATGTAACTAGATT
** * * *
629847 TTAATTAAATAA-AATTTAT-CAAATA-A-C
1 TTAATTAAATAATAATAAATGTAACTAGATT
*
629874 TTAATCAAATAATAATAAATGTAACTAGATT
1 TTAATTAAATAATAATAAATGTAACTAGATT
629905 TTAATTAAATAA
1 TTAATTAAATAA
629917 AATTTATCAA
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
27 11 0.20
28 6 0.11
29 8 0.15
30 6 0.11
31 23 0.43
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (31 bp):
TTAATTAAATAATAATAAATGTAACTAGATT
Found at i:629884 original size:58 final size:58
Alignment explanation
Indices: 629811--629929 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
629801 CTCAACAATC
*
629811 ATAACTTAATTAAATAATAATAAATGTAACTAGATTTTAATTAAATAAAATTTATCAA
1 ATAACTTAATCAAATAATAATAAATGTAACTAGATTTTAATTAAATAAAATTTATCAA
629869 ATAACTTAATCAAATAATAATAAATGTAACTAGATTTTAATTAAATAAAATTTATCAA
1 ATAACTTAATCAAATAATAATAAATGTAACTAGATTTTAATTAAATAAAATTTATCAA
629927 ATA
1 ATA
629930 TTATATTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (58 bp):
ATAACTTAATCAAATAATAATAAATGTAACTAGATTTTAATTAAATAAAATTTATCAA
Found at i:630491 original size:20 final size:20
Alignment explanation
Indices: 630466--630541 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
630456 ACCGGTTGAA
*
630466 AACCGGTAGAACTGGCTAAG
1 AACCGGTAGAACCGGCTAAG
630486 AACCGGTAGAACCGGCTAAG
1 AACCGGTAGAACCGGCTAAG
* * * * *
630506 AATCAGTAAAATCGGCAAAAG
1 AACCGGTAGAACCGGC-TAAG
*
630527 AACCGGTAAAACCGG
1 AACCGGTAGAACCGG
630542 TGTGAACGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (20 bp):
AACCGGTAGAACCGGCTAAG
Found at i:630760 original size:16 final size:16
Alignment explanation
Indices: 630739--630769 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
630729 TAATATTGAA
630739 ACTCGAACTCAAAAAG
1 ACTCGAACTCAAAAAG
630755 ACTCGAACTCAAAAA
1 ACTCGAACTCAAAAA
630770 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
ACTCGAACTCAAAAAG
Found at i:630943 original size:36 final size:36
Alignment explanation
Indices: 630903--631019 Score: 86
Period size: 36 Copynumber: 3.3 Consensus size: 36
630893 TTAGTTGAGA
630903 TGTTCTTCTATGTTTCTTAGTCATGTGAGATTGTTT
1 TGTTCTTCTATGTTTCTTAGTCATGTGAGATTGTTT
* * * *
630939 TGTTC-TCT-TATTT-TTACTC-T-TTAGACTT-TTGAGA
1 TGTTCTTCTATGTTTCTTAGTCATGTGAGA-TTGTT---T
* *
630973 TGATCTTCTATGTTTCTTAG-CTATGTGGGATTGTTT
1 TGTTCTTCTATGTTTCTTAGTC-ATGTGAGATTGTTT
631009 TGTTCTTCTAT
1 TGTTCTTCTAT
631020 TTTTGCTCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 22
0.64 0.12 0.24
Matches are distributed among these distances:
31 6 0.10
32 3 0.05
33 5 0.08
34 8 0.14
35 6 0.10
36 20 0.34
37 3 0.05
38 3 0.05
39 5 0.08
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.56
Consensus pattern (36 bp):
TGTTCTTCTATGTTTCTTAGTCATGTGAGATTGTTT
Found at i:631010 original size:70 final size:70
Alignment explanation
Indices: 630897--631029 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 70
630887 TAAAAGTTAG
*
630897 TTGAGATGTTCTTCTATGTTTCTTAGTCATGTGAGATTGTTTTGTTC-TCTTATTTTTACTCTTT
1 TTGAGATGATCTTCTATGTTTCTTAGTCATGTGAGATTGTTTTGTTCTTC-TATTTTTACTCTTT
630961 AGACTT
65 AGACTT
* *
630967 TTGAGATGATCTTCTATGTTTCTTAG-CTATGTGGGATTGTTTTGTTCTTCTATTTTTGCTCTT
1 TTGAGATGATCTTCTATGTTTCTTAGTC-ATGTGAGATTGTTTTGTTCTTCTATTTTTACTCTT
631030 CTATGCTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
69 1 0.02
70 55 0.95
71 2 0.03
ACGTcount: A:0.14, C:0.13, G:0.17, T:0.56
Consensus pattern (70 bp):
TTGAGATGATCTTCTATGTTTCTTAGTCATGTGAGATTGTTTTGTTCTTCTATTTTTACTCTTTA
GACTT
Found at i:632313 original size:23 final size:23
Alignment explanation
Indices: 632287--632342 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
632277 CTCTTCTCTC
632287 TTTTTCTTTGATTAGT-TCTTT-GT
1 TTTTTCTTTG-TTA-TATCTTTGGT
*
632310 TTTTTTTTTGTTATACTCTTTGGT
1 TTTTTCTTTGTTATA-TCTTTGGT
632334 TTTTTCTTT
1 TTTTTCTTT
632343 TGGTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 14 0.50
24 10 0.36
ACGTcount: A:0.07, C:0.09, G:0.11, T:0.73
Consensus pattern (23 bp):
TTTTTCTTTGTTATATCTTTGGT
Found at i:632341 original size:12 final size:12
Alignment explanation
Indices: 632287--632362 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
632277 CTCTTCTCTC
*
632287 TTTTTCTTTGAT
1 TTTTTCTTTGGT
**
632299 TAGTTCTTT-GT
1 TTTTTCTTTGGT
*
632310 TTTTT-TTTTGT
1 TTTTTCTTTGGT
**
632321 TATACTCTTTGGT
1 T-TTTTCTTTGGT
632334 TTTTTCTTTTGGT
1 TTTTTC-TTTGGT
*
632347 TTTTTCTTTTGT
1 TTTTTCTTTGGT
632359 TTTT
1 TTTT
632363 CTTCTCTCTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 3 0.06
11 7 0.14
12 21 0.43
13 18 0.37
ACGTcount: A:0.05, C:0.08, G:0.12, T:0.75
Consensus pattern (12 bp):
TTTTTCTTTGGT
Found at i:632354 original size:25 final size:23
Alignment explanation
Indices: 632302--632362 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
632292 CTTTGATTAG
632302 TTCTTTGTTTTTTTTTTGTTATA
1 TTCTTTGTTTTTTTTTTGTTATA
* *
632325 CTCTTTGGTTTTTTCTTTTGGTT-TT
1 TTCTTT-GTTTTTT-TTTT-GTTATA
632350 TTCTTTTGTTTTT
1 TTC-TTTGTTTTT
632363 CTTCTCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.16
24 7 0.23
25 13 0.42
26 6 0.19
ACGTcount: A:0.03, C:0.08, G:0.11, T:0.77
Consensus pattern (23 bp):
TTCTTTGTTTTTTTTTTGTTATA
Found at i:632367 original size:14 final size:13
Alignment explanation
Indices: 632328--632362 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
632318 TGTTATACTC
632328 TTTGGTTTTTTCT
1 TTTGGTTTTTTCT
632341 TTTGGTTTTTTCT
1 TTTGGTTTTTTCT
632354 TTT-GTTTTT
1 TTTGGTTTTT
632363 CTTCTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (13 bp):
TTTGGTTTTTTCT
Found at i:632964 original size:9 final size:9
Alignment explanation
Indices: 632934--632958 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
632924 TTAAGATAGT
632934 TAATAATAC
1 TAATAATAC
632943 TAATAATAC
1 TAATAATAC
632952 TAATAAT
1 TAATAAT
632959 TATAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (9 bp):
TAATAATAC
Found at i:643437 original size:33 final size:33
Alignment explanation
Indices: 643395--643460 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
643385 GGTATTGAGA
643395 TAGACCCATCACAAGAAACGCTACTAACAGCTG
1 TAGACCCATCACAAGAAACGCTACTAACAGCTG
643428 TAGACCCATCACAAGAAACGCTACTAACAGCTG
1 TAGACCCATCACAAGAAACGCTACTAACAGCTG
643461 CTGGTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.15
Consensus pattern (33 bp):
TAGACCCATCACAAGAAACGCTACTAACAGCTG
Found at i:645867 original size:11 final size:12
Alignment explanation
Indices: 645846--645870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
645836 TTTAATAAAA
645846 AAATAATTTTTT
1 AAATAATTTTTT
645858 AAATAATTTTTT
1 AAATAATTTTTT
645870 A
1 A
645871 TCAAAATATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:653657 original size:102 final size:102
Alignment explanation
Indices: 653541--653748 Score: 389
Period size: 102 Copynumber: 2.0 Consensus size: 102
653531 AAAATTTTAG
653541 GATAAACATAAATAATAAAATTAATAATTAATTGAAAAAAATCTGAATTTTAAGATAAACATATG
1 GATAAACATAAATAATAAAATTAATAATTAATTGAAAAAAATCTGAATTTTAAGATAAACATATG
653606 ATCACTTTAAGCAGGGCATACATCTATTATTATCGAA
66 ATCACTTTAAGCAGGGCATACATCTATTATTATCGAA
*
653643 GATAAACATAAATAATAAAATTAATAATTAATTGAAAAAAATCTGAATTTTAAGATAAATATATG
1 GATAAACATAAATAATAAAATTAATAATTAATTGAAAAAAATCTGAATTTTAAGATAAACATATG
* *
653708 ATCACTTTAAGCAGGGCATATATCTATTATTATCGAT
66 ATCACTTTAAGCAGGGCATACATCTATTATTATCGAA
653745 GATA
1 GATA
653749 TAGTTATTGA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.33
Consensus pattern (102 bp):
GATAAACATAAATAATAAAATTAATAATTAATTGAAAAAAATCTGAATTTTAAGATAAACATATG
ATCACTTTAAGCAGGGCATACATCTATTATTATCGAA
Found at i:658676 original size:33 final size:33
Alignment explanation
Indices: 658639--658706 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
658629 TTTTCTAAAG
*
658639 AAAGGAAATATTCGGATAAACTTTTTGAAGAAT
1 AAAGGAAATATTCAGATAAACTTTTTGAAGAAT
*
658672 AAAGGAAATATTCAGATAAACTTTTTGAATAAT
1 AAAGGAAATATTCAGATAAACTTTTTGAAGAAT
658705 AA
1 AA
658707 TAATAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.31
Consensus pattern (33 bp):
AAAGGAAATATTCAGATAAACTTTTTGAAGAAT
Found at i:658919 original size:24 final size:24
Alignment explanation
Indices: 658891--658938 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
658881 AACGCATCTC
*
658891 GTACAATCAAATTAGCAAGAAAAT
1 GTACAATCAAAATAGCAAGAAAAT
*
658915 GTACAATCAAAATGGCAAGAAAAT
1 GTACAATCAAAATAGCAAGAAAAT
658939 CTTGAGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (24 bp):
GTACAATCAAAATAGCAAGAAAAT
Found at i:659972 original size:34 final size:36
Alignment explanation
Indices: 659934--660024 Score: 132
Period size: 34 Copynumber: 2.6 Consensus size: 36
659924 GAAAAAATAA
659934 TTTCAAAGTTTGGTAAATGTTTCTTTG-AAAT-GGT
1 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAATAGGT
* *
659968 TTTCAAAGTTTGATAAATGTTTCTTTGAAAATAGTT
1 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAATAGGT
* *
660004 TTTCAAAATTTGGTAGATGTT
1 TTTCAAAGTTTGGTAAATGTT
660025 GTTGAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 26 0.52
35 4 0.08
36 20 0.40
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.47
Consensus pattern (36 bp):
TTTCAAAGTTTGGTAAATGTTTCTTTGAAAATAGGT
Found at i:661058 original size:179 final size:176
Alignment explanation
Indices: 660680--661044 Score: 558
Period size: 176 Copynumber: 2.0 Consensus size: 176
660670 ATTAAATTTT
*
660680 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAATTATTTAAAACCCAATTAATAAT
1 AAATATT--ATATATTATATATAACATATGGGCTCAACCCAATCATTTAAAACCCAATTAATAAT
*
660745 TGAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATAAATTTTTTATT
64 TGAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATAAAATTTTTATT
* * *
660810 TTATAATTATATTATTTAAATTATTTGTAAACTGTTTTTTTAATTAAA
129 TTATAATTATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
660858 AAATATTATATATTATATATAACATATGGGCT-AAGCCCAAATCATTTAAAACCCAATTAATAAT
1 AAATATTATATATTATATATAACATATGGGCTCAA-CCC-AATCATTTAAAACCCAATTAATAAT
*
660922 T-AAGATTCAATAAC-TTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATTTT
64 TGAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAA-TTA--TAAAATTTT
660985 TATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
125 TATTTTATAA-T-TATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
661038 AAATATT
1 AAATATT
661045 TAATTTTTAT
Statistics
Matches: 173, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
175 30 0.17
176 45 0.26
177 28 0.16
178 7 0.04
179 18 0.10
180 21 0.12
181 24 0.14
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (176 bp):
AAATATTATATATTATATATAACATATGGGCTCAACCCAATCATTTAAAACCCAATTAATAATTG
AAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATAAAATTTTTATTTT
ATAATTATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
Found at i:663236 original size:16 final size:17
Alignment explanation
Indices: 663204--663243 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
663194 ATATGATACG
*
663204 TATATGAATGACATGAT
1 TATATGTATGACATGAT
663221 TATATGTATG-CATGAT
1 TATATGTATGACATGAT
663237 TATATGT
1 TATATGT
663244 GTTAACATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (17 bp):
TATATGTATGACATGAT
Found at i:663754 original size:31 final size:31
Alignment explanation
Indices: 663716--663871 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
663706 AGGGTCGAGG
*
663716 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
663747 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
663778 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
663809 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
663840 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
663871 G
1 G
663872 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:667653 original size:21 final size:21
Alignment explanation
Indices: 667629--667689 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
667619 AACTTTGAAA
667629 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
667650 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
667664 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAAGTTTGGT
667685 AAATG
1 AAATG
667690 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:667735 original size:36 final size:36
Alignment explanation
Indices: 667621--667740 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
667611 TGGTAACCAA
667621 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
667658 CTTTG-AAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
667693 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
667730 -GTTGAAAAATG
1 CTTTGAAAAATG
667741 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:669221 original size:29 final size:28
Alignment explanation
Indices: 669189--669243 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
669179 GATCATCAAA
*
669189 TTATAAATTTAAAAAATATTAAATTTAAT
1 TTATAAATAT-AAAAATATTAAATTTAAT
*
669218 TTATAAATATAAAAATCTTAAATTTA
1 TTATAAATATAAAAATATTAAATTTA
669244 TTCCTACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTATAAATATAAAAATATTAAATTTAAT
Found at i:673300 original size:22 final size:21
Alignment explanation
Indices: 673275--673318 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
673265 GCGTTATTAC
673275 TTTAAAATCCCCAAAGTTAATT
1 TTTAAAA-CCCCAAAGTTAATT
* *
673297 TTTAAAAGCCCTAAGTTAATT
1 TTTAAAACCCCAAAGTTAATT
673318 T
1 T
673319 GTTAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTAAAACCCCAAAGTTAATT
Found at i:673826 original size:17 final size:17
Alignment explanation
Indices: 673804--673854 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
673794 TTATTGAATG
673804 ATAACTTAAACAAATTA
1 ATAACTTAAACAAATTA
* *
673821 ATAACTCAAACTTAATTA
1 ATAACTTAAAC-AAATTA
* *
673839 ATAATTTAAATAAATT
1 ATAACTTAAACAAATT
673855 TTAACATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAACTTAAACAAATTA
Found at i:678021 original size:20 final size:20
Alignment explanation
Indices: 677974--678227 Score: 197
Period size: 20 Copynumber: 12.2 Consensus size: 20
677964 AATGACCAAC
* *
677974 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
677993 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
678013 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* **
678033 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
678054 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
**
678075 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
678096 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
678117 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
678137 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
678158 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
678179 GAAATCGCAACGCGATCTTCCAAG
1 AAAATCGCAACGCGAT-TT---AG
*
678203 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
678223 AAAAT
1 AAAAT
678228 GAGTAAATTC
Statistics
Matches: 186, Mismatches: 36, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
19 18 0.10
20 91 0.49
21 19 0.10
22 40 0.22
23 1 0.01
24 17 0.09
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:678083 original size:42 final size:42
Alignment explanation
Indices: 678031--678218 Score: 185
Period size: 42 Copynumber: 4.4 Consensus size: 42
678021 AACGTTGAAA
* *
678031 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
678073 ATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
678115 AGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGA--TT-C
*
678158 A-AGAATCGCAACGCGA--TT--AAGGAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCAA-G-AATCGCAACGCGA--TT-C
678200 AAGAAAATCGCAACGCGAT
1 -AGAAAATCGCAACGCGAT
678219 TAAGAAAATG
Statistics
Matches: 129, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
39 2 0.02
40 17 0.13
41 1 0.01
42 92 0.71
43 3 0.02
44 14 0.11
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:678123 original size:62 final size:62
Alignment explanation
Indices: 678057--678218 Score: 252
Period size: 62 Copynumber: 2.5 Consensus size: 62
678047 ATCTTCCAAG
* * *
678057 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
*
678119 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGGA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
678181 AATCGCAACGCGATCTTCCAAGAAAATCGCAACGCGAT
1 AATCGCAACGCGA--TT-C-AGAAAATCGCAACGCGAT
678219 TAAGAAAATG
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
62 71 0.77
64 2 0.02
65 1 0.01
66 18 0.20
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (62 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
Found at i:678224 original size:62 final size:60
Alignment explanation
Indices: 677976--678224 Score: 218
Period size: 62 Copynumber: 4.0 Consensus size: 60
677966 TGACCAACAA
** * * * * ****
677976 AATCGCAACGCGA-TATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACG-CGACTTCAAG
*** * *
678036 -ATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAGAAAATCGCAACGCGA-CTT-CAAG
*
678099 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGA-CTT-CAAG
*
678161 AATCGCAACGCGATTAAGGAAATCGCAACGCGATCTTCCAAGAAAATCGCAACGCGA-TT-AAG
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGA--TT-C-AGAAAATCGCAACGCGACTTCAAG
678223 AA
1 AA
678225 AATGAGTAAA
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
59 12 0.08
61 6 0.04
62 101 0.63
63 6 0.04
64 17 0.11
65 1 0.01
66 17 0.11
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (60 bp):
AATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGACTTCAAG
Found at i:678334 original size:6 final size:6
Alignment explanation
Indices: 678323--678349 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
678313 GACACGTATT
678323 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
678350 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:678877 original size:6 final size:6
Alignment explanation
Indices: 678846--678940 Score: 162
Period size: 6 Copynumber: 16.5 Consensus size: 6
678836 TCTCGTCTCG
678846 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
678890 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
678938 GGT
1 GGT
678941 AATACGTGTC
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 20 0.22
6 69 0.78
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:679092 original size:20 final size:20
Alignment explanation
Indices: 679036--679347 Score: 271
Period size: 20 Copynumber: 15.2 Consensus size: 20
679026 GAATTTACTC
*
679036 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
679056 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
679078 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
679098 ATTCT-TGTAATCGCGTTGCG
1 ATTTTCTG-AATCGCGTTGCG
*
679118 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
679138 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
679158 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
679178 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
679200 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
679220 ATTTTCTGAAGATCGCGTTGCG
1 ATTTTCTG-A-ATCGCGTTGCG
* *
679242 ATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
* *
679262 ATTCTT-GGAAGATCGTGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* ** *
679284 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
679304 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
679324 -GTTT-TGATATCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
679343 ATTTT
1 ATTTT
679348 GTTGGTCATT
Statistics
Matches: 238, Mismatches: 32, Indels: 44
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.01
19 20 0.08
20 133 0.56
21 24 0.10
22 59 0.25
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:679303 original size:42 final size:42
Alignment explanation
Indices: 679036--679290 Score: 385
Period size: 42 Copynumber: 6.2 Consensus size: 42
679026 GAATTTACTC
*
679036 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
679078 ATTTTCTGAATCGCGTTGCGATTCTT-GTA-ATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
679118 ATTTTCTAAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
679158 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
679200 ATTTTCTGAATCGCGTTGCGATT-TTCTGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
* * *
679242 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
679284 ATCTTCT
1 ATTTTCT
679291 TTTCAACGTT
Statistics
Matches: 196, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
40 75 0.38
41 6 0.03
42 113 0.58
43 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (42 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
Found at i:682122 original size:3 final size:3
Alignment explanation
Indices: 682116--682159 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
682106 ACAATTTTTT
682116 TTA TTA -TA TTA -TA TTA -TA TTA -TA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
682158 TT
1 TT
682160 TGTAGGCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.22
3 25 0.69
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:682127 original size:5 final size:5
Alignment explanation
Indices: 682117--682158 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
682107 CAATTTTTTT
682117 TATTA TATTA TATTA TATTA TATTA T-TTA TTATTA TTATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA -TATTA -TATTA T
682159 TTGTAGGCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.09
5 23 0.66
6 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:682222 original size:22 final size:22
Alignment explanation
Indices: 682180--682222 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
682170 AATCCAACCA
*
682180 CCCACCATTATCTCACCACTAC
1 CCCACCATTATCTAACCACTAC
682202 CCCACCATTATC-AACCTACTA
1 CCCACCATTATCTAACC-ACTA
682223 AACCACTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (22 bp):
CCCACCATTATCTAACCACTAC
Found at i:682228 original size:22 final size:22
Alignment explanation
Indices: 682181--682228 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
682171 ATCCAACCAC
* **
682181 CCACCATTATCTCACCACTACC
1 CCACCATTATCTAACCACTAAA
682203 CCACCATTATC-AACCTACTAAA
1 CCACCATTATCTAACC-ACTAAA
682225 CCAC
1 CCAC
682229 TACCCACCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (22 bp):
CCACCATTATCTAACCACTAAA
Found at i:684482 original size:10 final size:11
Alignment explanation
Indices: 684468--684500 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
684458 TTTTCATTTA
684468 ATTTTATTTTC
1 ATTTTATTTTC
684479 -TTTTA-TTTC
1 ATTTTATTTTC
684488 ATTTTATTTTC
1 ATTTTATTTTC
684499 AT
1 AT
684501 CATTTGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.20
10 10 0.50
11 6 0.30
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:684491 original size:20 final size:21
Alignment explanation
Indices: 684458--684498 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
684448 CTTACTAACA
684458 TTTTCATTTAATTTTATTTTC
1 TTTTCATTTAATTTTATTTTC
*
684479 TTTT-ATTTCATTTTATTTTC
1 TTTTCATTTAATTTTATTTTC
684499 ATCATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCATTTAATTTTATTTTC
Found at i:686397 original size:19 final size:19
Alignment explanation
Indices: 686370--686435 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
686360 AGATCTAATC
686370 AGAACAAAAAGAAAAAAAAG
1 AGAA-AAAAAGAAAAAAAAG
*
686390 AGAAAAAAAGAAAAAGTAA-
1 AGAAAAAAAGAAAAA-AAAG
* * *
686409 AG-ATAAAATAAAAAAGAG
1 AGAAAAAAAGAAAAAAAAG
686427 AGAAAAAAA
1 AGAAAAAAA
686436 ACAAGACGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 18 0.49
20 6 0.16
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (19 bp):
AGAAAAAAAGAAAAAAAAG
Found at i:686420 original size:11 final size:9
Alignment explanation
Indices: 686370--686436 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
686360 AGATCTAATC
*
686370 AGAACAAAA
1 AGAAAAAAA
686379 AGAAAAAAA
1 AGAAAAAAA
686388 AGAGAAAAAA
1 AGA-AAAAAA
686398 AGAAAAAGTAA
1 AGAAAAA--AA
*
686409 AGATAAAATA
1 AGA-AAAAAA
* *
686419 A-AAAAGAG
1 AGAAAAAAA
686427 AGAAAAAAA
1 AGAAAAAAA
686436 A
1 A
686437 CAAGACGCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.09
9 22 0.48
10 11 0.24
11 5 0.11
12 4 0.09
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:687532 original size:32 final size:32
Alignment explanation
Indices: 687485--687571 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
687475 GAACAATGTG
* *
687485 GGCATCTTTGAAGATTCAACATCAAATGTTGA
1 GGCATCTTTGGAGATTCAACATCAAATATTGA
* * *
687517 GGCAT-TTTCGGAGATTCATCATCGAATATTGG
1 GGCATCTTT-GGAGATTCAACATCAAATATTGA
* *
687549 GGTATCTTTGGGGATTCAACATC
1 GGCATCTTTGGAGATTCAACATC
687572 CATATGTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 3 0.07
32 39 0.87
33 3 0.07
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATATTGA
Found at i:688439 original size:37 final size:35
Alignment explanation
Indices: 688398--688522 Score: 139
Period size: 36 Copynumber: 3.5 Consensus size: 35
688388 GGTCGTATCG
* *
688398 CTTGAGACTAATTTACTCAAAACAAAGTTTTGTCTCT
1 CTTGAGACTAGTTT-CTCGAAACAAA-TTTTGTCTCT
688435 CTTGAGAC-AGTTTCTCTTGAAACAAATTTTGTCTCT
1 CTTGAGACTAGTTTCTC--GAAACAAATTTTGTCTCT
* *
688471 CTTAAGA-TAGTTTCCCTTGAAACAAATTTTGTCTCT
1 CTTGAGACTAGTTT--CTCGAAACAAATTTTGTCTCT
688507 CTTGAGAC-AGTTTCTC
1 CTTGAGACTAGTTTCTC
688523 TTGAAACACC
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
34 2 0.03
35 3 0.04
36 54 0.71
37 15 0.20
38 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
CTTGAGACTAGTTTCTCGAAACAAATTTTGTCTCT
Found at i:688472 original size:21 final size:21
Alignment explanation
Indices: 688447--688511 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
688437 TGAGACAGTT
688447 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* * *
688468 TCTCTT--AAGATA-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
688485 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
688504 TCTCTTGA
1 TCTCTTGA
688512 GACAGTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 6 0.19
18 4 0.12
19 6 0.19
20 1 0.03
21 11 0.34
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:688472 original size:36 final size:36
Alignment explanation
Indices: 688417--688530 Score: 192
Period size: 36 Copynumber: 3.1 Consensus size: 36
688407 AATTTACTCA
688417 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
688454 AAACAAATTTTGTCTCTCTTAAGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
688490 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
688526 AAACA
1 AAACA
688531 CCAATCTTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 64 0.90
37 7 0.10
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:688516 original size:72 final size:65
Alignment explanation
Indices: 688417--688600 Score: 217
Period size: 67 Copynumber: 2.7 Consensus size: 65
688407 AATTTACTCA
*
688417 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AATTTTGTCTCTCTTAAGATAG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAA-----TCT-T-TGAAGAT-G
688481 TTTCCCTTG
57 TTTCCCTTG
* *
688490 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTGAATATGTTTCTCTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-CAATCTTTGAAGATGTTTCCCTT
688555 G
65 G
* *
688556 AAACAAAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACACAA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAA
688601 AAAAAACCTT
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
66 16 0.16
67 40 0.39
68 1 0.01
69 3 0.03
72 34 0.33
73 7 0.07
74 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAATCTTTGAAGATGTTTCCCTTG
Found at i:688885 original size:3 final size:3
Alignment explanation
Indices: 688879--688917 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
688869 ACAAATTTTT
688879 TTA TTA -TA TTA TTA TTTA TTA TTA TTA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TT
688918 TTTTTTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 25 0.76
4 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:688903 original size:13 final size:13
Alignment explanation
Indices: 688879--688917 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
688869 ACAAATTTTT
688879 TTATTATATTATTA
1 TTATT-TATTATTA
688893 TT-TATTATTATTA
1 TTAT-TTATTATTA
688906 TTATTTATTATT
1 TTATTTATTATT
688918 TTTTTTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:688925 original size:16 final size:16
Alignment explanation
Indices: 688878--688917 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
688868 TACAAATTTT
688878 TTTATTA-TATTATTA
1 TTTATTATTATTATTA
688893 TTTATTATTATTATTA
1 TTTATTATTATTATTA
688909 TTTATTATT
1 TTTATTATT
688918 TTTTTTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:688971 original size:22 final size:21
Alignment explanation
Indices: 688942--688985 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
688932 TAATCCAACC
688942 ACCCACCATTATCTCACC-ACT
1 ACCCACCATTATCT-ACCTACT
688963 ACCCTACCATTATCTACCTACT
1 ACCC-ACCATTATCTACCTACT
688985 A
1 A
688986 AGCCACTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCCACCATTATCTACCTACT
Found at i:691934 original size:22 final size:22
Alignment explanation
Indices: 691903--691953 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
691893 CTGAGTGGCA
691903 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
691926 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
691948 TATGAA
1 TATGAA
691954 ACCCTCGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:693427 original size:64 final size:63
Alignment explanation
Indices: 693329--693489 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
693319 TAATGAAGGT
* * *
693329 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
693392 GG
62 GC
*
693394 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
693458 ATGCATCGATGCACTACATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
693490 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:698359 original size:354 final size:354
Alignment explanation
Indices: 697709--698419 Score: 1152
Period size: 354 Copynumber: 2.0 Consensus size: 354
697699 ATAATAGGAG
* * * ** *
697709 TATCAGTTGTGCATCAATCACGAGACTACTCACGAGAATGCTTACGGACCGTACTACTAAGATCA
1 TATCAGTTGTGCATCAATCACGAGACCACTCACAAGAACGCTTACAAACCATACTACTAAGATCA
* * * *
697774 AAGTCGATAGTACCAACACAATAATGTCTCCCCATAGATATTGAGAAATCATCGAATGGGTTAAA
66 AAGTCGACAATACCAACACAATAATGTCTCCCCATAGATACTGAGAAATCATCGAATGAGTTAAA
* *
697839 CGCTTTATGTTCCCGCAACCTTATTTCTTGCTGAGAAGATAATGCATCCACACCAATATTGTATG
131 CGCTTTATGTTCCCGCAACCTCATTTCTTGCTGAGAAGATAATGCATCCACACCAATACTGTATG
* * *
697904 GATTGTACGTTGCACATTGTGATGGTTGTAGATTCATGTCAAATTCCAAGCTAACTACGCAAGAA
196 GATTGTACGTTGCACATTGTGATGGTTGCAGATTCATGTCAAAGTCCAAGCTAACTACGCAAAAA
697969 TACCTTGGCATCAAAGACGATGATGCACCCAAGTCATTGCCCCAACTTTGTGTACTTAATAAGTT
261 TACCTTGGCATCAAAGACGATGATGCACCCAAGTCATTGCCCCAACTTTGTGTACTTAATAAGTT
*
698034 GAAGTCATTACATAAATTAGTTGTTTGAC
326 GAAGTCATTACATAAATTAGTTGTTGGAC
* *
698063 TATCAGTTGTGCATCAATCACGAGACCGCTCACAAGAACGCTTACAAACTATACTACTAAGATCA
1 TATCAGTTGTGCATCAATCACGAGACCACTCACAAGAACGCTTACAAACCATACTACTAAGATCA
* *
698128 AGGTCGACAATACTAACACAATAATGTCTCCCCATAGATACTGAGAAATCATCGAATGAGTTAAA
66 AAGTCGACAATACCAACACAATAATGTCTCCCCATAGATACTGAGAAATCATCGAATGAGTTAAA
* * *
698193 TGCTTTATGTTCCTGCAACCTCATTTCTTGCTGAGAAGATAATGCATCTACACCAATACTGTATG
131 CGCTTTATGTTCCCGCAACCTCATTTCTTGCTGAGAAGATAATGCATCCACACCAATACTGTATG
* *
698258 GATTGTACGTTGCACATTGTGATGGTTGCAGATTCATGTCAAAGTCCATGCTAACTACGTAAAAA
196 GATTGTACGTTGCACATTGTGATGGTTGCAGATTCATGTCAAAGTCCAAGCTAACTACGCAAAAA
* * *
698323 TACCTTGGCATCGAAGACGATGATGCACCTAAGTCATTGCCCCAACTTTGTGTGCTTAATAAGTT
261 TACCTTGGCATCAAAGACGATGATGCACCCAAGTCATTGCCCCAACTTTGTGTACTTAATAAGTT
* *
698388 GAAGTCGTTACGTAAATTAGTTGTTGGAC
326 GAAGTCATTACATAAATTAGTTGTTGGAC
698417 TAT
1 TAT
698420 GAACATTAGG
Statistics
Matches: 327, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
354 327 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (354 bp):
TATCAGTTGTGCATCAATCACGAGACCACTCACAAGAACGCTTACAAACCATACTACTAAGATCA
AAGTCGACAATACCAACACAATAATGTCTCCCCATAGATACTGAGAAATCATCGAATGAGTTAAA
CGCTTTATGTTCCCGCAACCTCATTTCTTGCTGAGAAGATAATGCATCCACACCAATACTGTATG
GATTGTACGTTGCACATTGTGATGGTTGCAGATTCATGTCAAAGTCCAAGCTAACTACGCAAAAA
TACCTTGGCATCAAAGACGATGATGCACCCAAGTCATTGCCCCAACTTTGTGTACTTAATAAGTT
GAAGTCATTACATAAATTAGTTGTTGGAC
Found at i:702427 original size:229 final size:228
Alignment explanation
Indices: 702021--702470 Score: 794
Period size: 229 Copynumber: 2.0 Consensus size: 228
702011 GTAAATTATC
* * *
702021 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTTATTATTATCTTTAG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
*
702086 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
*
702151 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAATT
702216 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
702250 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTTATTATTATATTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTTATTATTATATTTA
*
702314 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAT
65 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAT
* *
702379 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAATAAAT
130 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAT
702444 TGAAACATAAATTACATAACTTTAAAA
195 TGAAACATAAATTACATAACTTTAAAA
702471 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 198 0.94
230 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:702559 original size:20 final size:19
Alignment explanation
Indices: 702536--702581 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
702526 CGATATACCA
702536 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
702556 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
702576 GGTAAA
1 GGTAAA
702582 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:702751 original size:17 final size:19
Alignment explanation
Indices: 702712--702754 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
702702 ATGTAAAAAT
702712 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
702732 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
702749 ATGATA
1 ATGATA
702755 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:705003 original size:21 final size:21
Alignment explanation
Indices: 704976--705040 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
704966 AAGACAATCA
* *
704976 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTCGAG
* *
704997 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
705018 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
705039 AG
1 AG
705041 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:705116 original size:33 final size:33
Alignment explanation
Indices: 705074--705139 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
705064 AAATAGATGG
*
705074 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
705107 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
705140 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:706955 original size:19 final size:19
Alignment explanation
Indices: 706931--706979 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
706921 AATGTAGGGT
706931 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
706950 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
706969 TATTTTTGTAT
1 TAATTTTGTAT
706980 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:708003 original size:200 final size:198
Alignment explanation
Indices: 707098--708263 Score: 2108
Period size: 199 Copynumber: 5.9 Consensus size: 198
707088 CAATATGGCC
* *
707098 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* * * *
707163 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTAAGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
707228 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTTCCAGAATGAA
129 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
707292 TGGAA
194 TGGAA
*
707297 AACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
707362 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
707426 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
707490 GAA
196 GAA
707493 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
707556 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
707621 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
707686 GAA
196 GAA
*
707689 AACAGGGTGCACCCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
707754 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCAGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
707819 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCCAGAATGAA
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT--CCAGAATGAA
707884 TGGAA
194 TGGAA
707889 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
707954 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
708019 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTT-TCCAGAATGAAT
708084 GGAA
195 GGAA
*
708088 AACAGCGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
708153 CAAAAGTATAATGTAATATGTAATTTTTCAATCTGACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
708218 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
708264 CTAATTTAAA
Statistics
Matches: 939, Mismatches: 20, Indels: 16
0.96 0.02 0.02
Matches are distributed among these distances:
194 72 0.08
195 71 0.08
196 165 0.18
197 41 0.04
198 175 0.19
199 222 0.24
200 193 0.21
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:708250 original size:23 final size:23
Alignment explanation
Indices: 708224--708275 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
708214 AGAGAATATG
708224 TATAAATAATGTGTCGACACTAA
1 TATAAATAATGTGTCGACACTAA
* * *
708247 TAT-AGT-TTGTGTCGATACTAA
1 TATAAATAATGTGTCGACACTAA
*
708268 TTTAAATA
1 TATAAATA
708276 TCAAGTGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 4
0.71 0.16 0.13
Matches are distributed among these distances:
21 15 0.68
22 4 0.18
23 3 0.14
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (23 bp):
TATAAATAATGTGTCGACACTAA
Found at i:709749 original size:18 final size:18
Alignment explanation
Indices: 709728--709789 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
709718 AGCGGTCGCA
709728 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
709746 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
709764 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
709782 GAAGATGA
1 GAAGATGA
709790 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:709752 original size:6 final size:6
Alignment explanation
Indices: 709728--709819 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
709718 AGCGGTCGCA
* * * * * *
709728 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
709776 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
709820 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:709763 original size:3 final size:3
Alignment explanation
Indices: 709743--709823 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
709733 TGAAGCTGAC
* * * * * ** *
709743 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
709791 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
709824 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:709782 original size:36 final size:36
Alignment explanation
Indices: 709731--709807 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
709721 GGTCGCAGAA
*
709731 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
709767 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
709803 GATGA
1 GATGA
709808 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:709823 original size:12 final size:12
Alignment explanation
Indices: 709731--709819 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
709721 GGTCGCAGAA
*
709731 GATGAAGCTGAC
1 GATGAAGATGAC
709743 GATGAAGATGAC
1 GATGAAGATGAC
*
709755 GATGATGATGAC
1 GATGAAGATGAC
* *
709767 GATGAAGCTGGC
1 GATGAAGATGAC
*
709779 GATGAAGATGAT
1 GATGAAGATGAC
* * *
709791 GACGATGATGAT
1 GATGAAGATGAC
* *
709803 GATGATGATGAA
1 GATGAAGATGAC
709815 GATGA
1 GATGA
709820 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:709823 original size:18 final size:18
Alignment explanation
Indices: 709728--709819 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
709718 AGCGGTCGCA
*
709728 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
709746 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
709764 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
709782 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
709800 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
709818 GA
1 GA
709820 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:711599 original size:183 final size:182
Alignment explanation
Indices: 711324--712181 Score: 1529
Period size: 183 Copynumber: 4.7 Consensus size: 182
711314 GCAATGCTAT
* *
711324 CGGTATAAATATACCGGTTTTATGCGTGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* * *
711389 GTATCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACA
*
711454 TTTACACATCGGAACCCATAATTATAATGTAATAGATAGTTTTGTAATATAAC
130 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
*
711507 CGGTATAAATATACCGATTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
711572 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAACTGTCGACA
66 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACA
711637 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
711690 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
711755 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACCATTTAAAAAACTGTCGACA
66 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCGACA
711820 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
711873 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
711938 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACA
66 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACA
* *
712003 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
* *
712056 CGGTAT-AATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
712120 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
712182 GTAATTTTAA
Statistics
Matches: 654, Mismatches: 17, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
182 115 0.18
183 535 0.82
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:713260 original size:23 final size:23
Alignment explanation
Indices: 713229--713377 Score: 217
Period size: 23 Copynumber: 6.5 Consensus size: 23
713219 ATAGGTAAAC
*
713229 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
713252 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
713275 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
713298 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
713321 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
713344 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
713367 ATATATTGTAA
1 ATATAATGTAA
713378 AGTATCTATC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:713288 original size:46 final size:46
Alignment explanation
Indices: 713229--713377 Score: 271
Period size: 46 Copynumber: 3.2 Consensus size: 46
713219 ATAGGTAAAC
*
713229 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
713275 ATATAATGTAATAGGTAGTGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
713321 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
713367 ATATATTGTAA
1 ATATAATGTAA
713378 AGTATCTATC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (46 bp):
ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
Found at i:713817 original size:18 final size:18
Alignment explanation
Indices: 713796--713832 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
713786 GTAATTGGAG
713796 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
713814 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
713832 T
1 T
713833 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:713840 original size:24 final size:24
Alignment explanation
Indices: 713788--713834 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
713778 TTTCATATGT
* *
713788 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
713812 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
713835 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:714132 original size:39 final size:39
Alignment explanation
Indices: 714089--714175 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
714079 TCCGATGCTC
*
714089 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* * *
714128 ATCAAAATTCAAATCTCATATGATGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
714167 ATCAAAATC
1 ATCAAAATC
714176 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:714627 original size:23 final size:23
Alignment explanation
Indices: 714596--714668 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
714586 ATAGGTAAAA
*
714596 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
714619 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
714642 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
714665 ATAT
1 ATAT
714669 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:715055 original size:23 final size:23
Alignment explanation
Indices: 715024--715096 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
715014 ATAGGTAAAA
*
715024 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
715047 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
715070 ATATAATGTAATATGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
715093 ATAT
1 ATAT
715097 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:717301 original size:10 final size:10
Alignment explanation
Indices: 717286--717314 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
717276 AGCTGTAATG
717286 TGTGTGTGTC
1 TGTGTGTGTC
717296 TGTGTGTGTC
1 TGTGTGTGTC
717306 TGTGTGTGT
1 TGTGTGTGT
717315 GCGCGCGCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.52
Consensus pattern (10 bp):
TGTGTGTGTC
Done.